--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22
+ generated with the following command:
+ /usr/local/bin/gengetopt --output-dir=/home/tbaudier/vv/vv_static/vv/vv_bin/tools --arg-struct-name=args_info_clitkBinarizeImage --func-name=cmdline_parser_clitkBinarizeImage --file-name=clitkBinarizeImage_ggo --unamed-opts --conf-parser --include-getopt
+
+ The developers of gengetopt consider the fixed text that goes in all
+ gengetopt output files to be in the public domain:
+ we make no copyright claims on it.
+*/
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+
+#include "clitkBinarizeImage_ggo.h"
+
+const char *args_info_clitkBinarizeImage_purpose = "";
+
+const char *args_info_clitkBinarizeImage_usage = "Usage: clitkBinarizeImage [OPTIONS]... [FILES]...";
+
+const char *args_info_clitkBinarizeImage_description = "";
+
+const char *args_info_clitkBinarizeImage_help[] = {
+ " -h, --help Print help and exit",
+ " -V, --version Print version and exit",
+ " --config=STRING Config file",
+ " -v, --verbose Verbose (default=off)",
+ " --imagetypes Display allowed image types (default=off)",
+ " -i, --input=STRING Input image filename",
+ " -o, --output=STRING Output image filename",
+ " -l, --lower=DOUBLE Lower intensity (default=min), fg is greater than this \n value",
+ " -u, --upper=DOUBLE Upper intensity (default=max), fg is lower than this \n value",
+ " --fg=DOUBLE Foreground (FG) or 'inside' value (default=`1')",
+ " --bg=DOUBLE Background (BG) or 'ouside' value (default=`0')",
+ " --mode=STRING Use FG and/or BG values (if FG, the BG is replaced by \n the input image values) (possible values=\"FG\", \n \"BG\", \"both\" default=`both')",
+ 0
+};
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_DOUBLE
+} cmdline_parser_clitkBinarizeImage_arg_type;
+
+static
+void clear_given (struct args_info_clitkBinarizeImage *args_info);
+static
+void clear_args (struct args_info_clitkBinarizeImage *args_info);
+
+static int
+cmdline_parser_clitkBinarizeImage_internal (int argc, char * const *argv, struct args_info_clitkBinarizeImage *args_info,
+ struct cmdline_parser_clitkBinarizeImage_params *params, const char *additional_error);
+
+static int
+cmdline_parser_clitkBinarizeImage_required2 (struct args_info_clitkBinarizeImage *args_info, const char *prog_name, const char *additional_error);
+struct line_list
+{
+ char * string_arg;
+ struct line_list * next;
+};
+
+static struct line_list *cmd_line_list = 0;
+static struct line_list *cmd_line_list_tmp = 0;
+
+static void
+free_cmd_list(void)
+{
+ /* free the list of a previous call */
+ if (cmd_line_list)
+ {
+ while (cmd_line_list) {
+ cmd_line_list_tmp = cmd_line_list;
+ cmd_line_list = cmd_line_list->next;
+ free (cmd_line_list_tmp->string_arg);
+ free (cmd_line_list_tmp);
+ }
+ }
+}
+
+
+char *cmdline_parser_clitkBinarizeImage_mode_values[] = {"FG", "BG", "both", 0} ; /* Possible values for mode. */
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct args_info_clitkBinarizeImage *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->config_given = 0 ;
+ args_info->verbose_given = 0 ;
+ args_info->imagetypes_given = 0 ;
+ args_info->input_given = 0 ;
+ args_info->output_given = 0 ;
+ args_info->lower_given = 0 ;
+ args_info->upper_given = 0 ;
+ args_info->fg_given = 0 ;
+ args_info->bg_given = 0 ;
+ args_info->mode_given = 0 ;
+}
+
+static
+void clear_args (struct args_info_clitkBinarizeImage *args_info)
+{
+ args_info->config_arg = NULL;
+ args_info->config_orig = NULL;
+ args_info->verbose_flag = 0;
+ args_info->imagetypes_flag = 0;
+ args_info->input_arg = NULL;
+ args_info->input_orig = NULL;
+ args_info->output_arg = NULL;
+ args_info->output_orig = NULL;
+ args_info->lower_orig = NULL;
+ args_info->upper_orig = NULL;
+ args_info->fg_arg = 1;
+ args_info->fg_orig = NULL;
+ args_info->bg_arg = 0;
+ args_info->bg_orig = NULL;
+ args_info->mode_arg = gengetopt_strdup ("both");
+ args_info->mode_orig = NULL;
+
+}
+
+static
+void init_args_info(struct args_info_clitkBinarizeImage *args_info)
+{
+
+
+ args_info->help_help = args_info_clitkBinarizeImage_help[0] ;
+ args_info->version_help = args_info_clitkBinarizeImage_help[1] ;
+ args_info->config_help = args_info_clitkBinarizeImage_help[2] ;
+ args_info->verbose_help = args_info_clitkBinarizeImage_help[3] ;
+ args_info->imagetypes_help = args_info_clitkBinarizeImage_help[4] ;
+ args_info->input_help = args_info_clitkBinarizeImage_help[5] ;
+ args_info->output_help = args_info_clitkBinarizeImage_help[6] ;
+ args_info->lower_help = args_info_clitkBinarizeImage_help[7] ;
+ args_info->upper_help = args_info_clitkBinarizeImage_help[8] ;
+ args_info->fg_help = args_info_clitkBinarizeImage_help[9] ;
+ args_info->bg_help = args_info_clitkBinarizeImage_help[10] ;
+ args_info->mode_help = args_info_clitkBinarizeImage_help[11] ;
+
+}
+
+void
+cmdline_parser_clitkBinarizeImage_print_version (void)
+{
+ printf ("%s %s\n", CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE, CMDLINE_PARSER_CLITKBINARIZEIMAGE_VERSION);
+}
+
+static void print_help_common(void) {
+ cmdline_parser_clitkBinarizeImage_print_version ();
+
+ if (strlen(args_info_clitkBinarizeImage_purpose) > 0)
+ printf("\n%s\n", args_info_clitkBinarizeImage_purpose);
+
+ if (strlen(args_info_clitkBinarizeImage_usage) > 0)
+ printf("\n%s\n", args_info_clitkBinarizeImage_usage);
+
+ printf("\n");
+
+ if (strlen(args_info_clitkBinarizeImage_description) > 0)
+ printf("%s\n", args_info_clitkBinarizeImage_description);
+}
+
+void
+cmdline_parser_clitkBinarizeImage_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (args_info_clitkBinarizeImage_help[i])
+ printf("%s\n", args_info_clitkBinarizeImage_help[i++]);
+}
+
+void
+cmdline_parser_clitkBinarizeImage_init (struct args_info_clitkBinarizeImage *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+
+ args_info->inputs = NULL;
+ args_info->inputs_num = 0;
+}
+
+void
+cmdline_parser_clitkBinarizeImage_params_init(struct cmdline_parser_clitkBinarizeImage_params *params)
+{
+ if (params)
+ {
+ params->override = 0;
+ params->initialize = 1;
+ params->check_required = 1;
+ params->check_ambiguity = 0;
+ params->print_errors = 1;
+ }
+}
+
+struct cmdline_parser_clitkBinarizeImage_params *
+cmdline_parser_clitkBinarizeImage_params_create(void)
+{
+ struct cmdline_parser_clitkBinarizeImage_params *params =
+ (struct cmdline_parser_clitkBinarizeImage_params *)malloc(sizeof(struct cmdline_parser_clitkBinarizeImage_params));
+ cmdline_parser_clitkBinarizeImage_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+
+static void
+cmdline_parser_clitkBinarizeImage_release (struct args_info_clitkBinarizeImage *args_info)
+{
+ unsigned int i;
+ free_string_field (&(args_info->config_arg));
+ free_string_field (&(args_info->config_orig));
+ free_string_field (&(args_info->input_arg));
+ free_string_field (&(args_info->input_orig));
+ free_string_field (&(args_info->output_arg));
+ free_string_field (&(args_info->output_orig));
+ free_string_field (&(args_info->lower_orig));
+ free_string_field (&(args_info->upper_orig));
+ free_string_field (&(args_info->fg_orig));
+ free_string_field (&(args_info->bg_orig));
+ free_string_field (&(args_info->mode_arg));
+ free_string_field (&(args_info->mode_orig));
+
+
+ for (i = 0; i < args_info->inputs_num; ++i)
+ free (args_info->inputs [i]);
+
+ if (args_info->inputs_num)
+ free (args_info->inputs);
+
+ clear_given (args_info);
+}
+
+/**
+ * @param val the value to check
+ * @param values the possible values
+ * @return the index of the matched value:
+ * -1 if no value matched,
+ * -2 if more than one value has matched
+ */
+static int
+check_possible_values(const char *val, char *values[])
+{
+ int i, found, last;
+ size_t len;
+
+ if (!val) /* otherwise strlen() crashes below */
+ return -1; /* -1 means no argument for the option */
+
+ found = last = 0;
+
+ for (i = 0, len = strlen(val); values[i]; ++i)
+ {
+ if (strncmp(val, values[i], len) == 0)
+ {
+ ++found;
+ last = i;
+ if (strlen(values[i]) == len)
+ return i; /* exact macth no need to check more */
+ }
+ }
+
+ if (found == 1) /* one match: OK */
+ return last;
+
+ return (found ? -2 : -1); /* return many values or none matched */
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+ int found = -1;
+ if (arg) {
+ if (values) {
+ found = check_possible_values(arg, values);
+ }
+ if (found >= 0)
+ fprintf(outfile, "%s=\"%s\" # %s\n", opt, arg, values[found]);
+ else
+ fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+ } else {
+ fprintf(outfile, "%s\n", opt);
+ }
+}
+
+
+int
+cmdline_parser_clitkBinarizeImage_dump(FILE *outfile, struct args_info_clitkBinarizeImage *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE);
+ return EXIT_FAILURE;
+ }
+
+ if (args_info->help_given)
+ write_into_file(outfile, "help", 0, 0 );
+ if (args_info->version_given)
+ write_into_file(outfile, "version", 0, 0 );
+ if (args_info->config_given)
+ write_into_file(outfile, "config", args_info->config_orig, 0);
+ if (args_info->verbose_given)
+ write_into_file(outfile, "verbose", 0, 0 );
+ if (args_info->imagetypes_given)
+ write_into_file(outfile, "imagetypes", 0, 0 );
+ if (args_info->input_given)
+ write_into_file(outfile, "input", args_info->input_orig, 0);
+ if (args_info->output_given)
+ write_into_file(outfile, "output", args_info->output_orig, 0);
+ if (args_info->lower_given)
+ write_into_file(outfile, "lower", args_info->lower_orig, 0);
+ if (args_info->upper_given)
+ write_into_file(outfile, "upper", args_info->upper_orig, 0);
+ if (args_info->fg_given)
+ write_into_file(outfile, "fg", args_info->fg_orig, 0);
+ if (args_info->bg_given)
+ write_into_file(outfile, "bg", args_info->bg_orig, 0);
+ if (args_info->mode_given)
+ write_into_file(outfile, "mode", args_info->mode_orig, cmdline_parser_clitkBinarizeImage_mode_values);
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+cmdline_parser_clitkBinarizeImage_file_save(const char *filename, struct args_info_clitkBinarizeImage *args_info)
+{
+ FILE *outfile;
+ int i = 0;
+
+ outfile = fopen(filename, "w");
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = cmdline_parser_clitkBinarizeImage_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+cmdline_parser_clitkBinarizeImage_free (struct args_info_clitkBinarizeImage *args_info)
+{
+ cmdline_parser_clitkBinarizeImage_release (args_info);
+}
+
+/** @brief replacement of strdup, which is not standard */
+char *
+gengetopt_strdup (const char *s)
+{
+ char *result = NULL;
+ if (!s)
+ return result;
+
+ result = (char*)malloc(strlen(s) + 1);
+ if (result == (char*)0)
+ return (char*)0;
+ strcpy(result, s);
+ return result;
+}
+
+int
+cmdline_parser_clitkBinarizeImage (int argc, char * const *argv, struct args_info_clitkBinarizeImage *args_info)
+{
+ return cmdline_parser_clitkBinarizeImage2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+cmdline_parser_clitkBinarizeImage_ext (int argc, char * const *argv, struct args_info_clitkBinarizeImage *args_info,
+ struct cmdline_parser_clitkBinarizeImage_params *params)
+{
+ int result;
+ result = cmdline_parser_clitkBinarizeImage_internal (argc, argv, args_info, params, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkBinarizeImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkBinarizeImage2 (int argc, char * const *argv, struct args_info_clitkBinarizeImage *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct cmdline_parser_clitkBinarizeImage_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = cmdline_parser_clitkBinarizeImage_internal (argc, argv, args_info, ¶ms, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkBinarizeImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkBinarizeImage_required (struct args_info_clitkBinarizeImage *args_info, const char *prog_name)
+{
+ int result = EXIT_SUCCESS;
+
+ if (cmdline_parser_clitkBinarizeImage_required2(args_info, prog_name, NULL) > 0)
+ result = EXIT_FAILURE;
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkBinarizeImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkBinarizeImage_required2 (struct args_info_clitkBinarizeImage *args_info, const char *prog_name, const char *additional_error)
+{
+ int error = 0;
+
+ /* checks for required options */
+ if (! args_info->input_given)
+ {
+ fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (! args_info->output_given)
+ {
+ fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+
+ /* checks for dependences among options */
+
+ return error;
+}
+
+/*
+ * Extracted from the glibc source tree, version 2.3.6
+ *
+ * Licensed under the GPL as per the whole glibc source tree.
+ *
+ * This file was modified so that getopt_long can be called
+ * many times without risking previous memory to be spoiled.
+ *
+ * Modified by Andre Noll and Lorenzo Bettini for use in
+ * GNU gengetopt generated files.
+ *
+ */
+
+/*
+ * we must include anything we need since this file is not thought to be
+ * inserted in a file already using getopt.h
+ *
+ * Lorenzo
+ */
+
+struct option
+{
+ const char *name;
+ /* has_arg can't be an enum because some compilers complain about
+ type mismatches in all the code that assumes it is an int. */
+ int has_arg;
+ int *flag;
+ int val;
+};
+
+/* For communication from `getopt' to the caller.
+ When `getopt' finds an option that takes an argument,
+ the argument value is returned here.
+ Also, when `ordering' is RETURN_IN_ORDER,
+ each non-option ARGV-element is returned here. */
+
+static char *optarg;
+
+/* Index in ARGV of the next element to be scanned.
+ This is used for communication to and from the caller
+ and for communication between successive calls to `getopt'.
+
+ On entry to `getopt', zero means this is the first call; initialize.
+
+ When `getopt' returns -1, this is the index of the first of the
+ non-option elements that the caller should itself scan.
+
+ Otherwise, `optind' communicates from one call to the next
+ how much of ARGV has been scanned so far. */
+
+static int optind;
+
+/* Callers store zero here to inhibit the error message `getopt' prints
+ for unrecognized options. */
+
+static int opterr;
+
+/* Set to an option character which was unrecognized. */
+
+static int optopt;
+
+/* This version of `getopt' appears to the caller like standard Unix `getopt'
+ but it behaves differently for the user, since it allows the user
+ to intersperse the options with the other arguments.
+
+ As `getopt' works, it permutes the elements of ARGV so that,
+ when it is done, all the options precede everything else. Thus
+ all application programs are extended to handle flexible argument order.
+*/
+/*
+ If the field `flag' is not NULL, it points to a variable that is set
+ to the value given in the field `val' when the option is found, but
+ left unchanged if the option is not found.
+
+ To have a long-named option do something other than set an `int' to
+ a compiled-in constant, such as set a value from `custom_optarg', set the
+ option's `flag' field to zero and its `val' field to a nonzero
+ value (the equivalent single-letter option character, if there is
+ one). For long options that have a zero `flag' field, `getopt'
+ returns the contents of the `val' field. */
+
+/* Names for the values of the `has_arg' field of `struct option'. */
+#ifndef no_argument
+#define no_argument 0
+#endif
+
+#ifndef required_argument
+#define required_argument 1
+#endif
+
+#ifndef optional_argument
+#define optional_argument 2
+#endif
+
+struct custom_getopt_data {
+ /*
+ * These have exactly the same meaning as the corresponding global variables,
+ * except that they are used for the reentrant versions of getopt.
+ */
+ int custom_optind;
+ int custom_opterr;
+ int custom_optopt;
+ char *custom_optarg;
+
+ /* True if the internal members have been initialized. */
+ int initialized;
+
+ /*
+ * The next char to be scanned in the option-element in which the last option
+ * character we returned was found. This allows us to pick up the scan where
+ * we left off. If this is zero, or a null string, it means resume the scan by
+ * advancing to the next ARGV-element.
+ */
+ char *nextchar;
+
+ /*
+ * Describe the part of ARGV that contains non-options that have been skipped.
+ * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is
+ * the index after the last of them.
+ */
+ int first_nonopt;
+ int last_nonopt;
+};
+
+/*
+ * the variables optarg, optind, opterr and optopt are renamed with
+ * the custom_ prefix so that they don't interfere with getopt ones.
+ *
+ * Moreover they're static so they are visible only from within the
+ * file where this very file will be included.
+ */
+
+/*
+ * For communication from `custom_getopt' to the caller. When `custom_getopt' finds an
+ * option that takes an argument, the argument value is returned here.
+ */
+static char *custom_optarg;
+
+/*
+ * Index in ARGV of the next element to be scanned. This is used for
+ * communication to and from the caller and for communication between
+ * successive calls to `custom_getopt'.
+ *
+ * On entry to `custom_getopt', 1 means this is the first call; initialize.
+ *
+ * When `custom_getopt' returns -1, this is the index of the first of the non-option
+ * elements that the caller should itself scan.
+ *
+ * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV
+ * has been scanned so far.
+ *
+ * 1003.2 says this must be 1 before any call.
+ */
+static int custom_optind = 1;
+
+/*
+ * Callers store zero here to inhibit the error message for unrecognized
+ * options.
+ */
+static int custom_opterr = 1;
+
+/*
+ * Set to an option character which was unrecognized. This must be initialized
+ * on some systems to avoid linking in the system's own getopt implementation.
+ */
+static int custom_optopt = '?';
+
+/*
+ * Exchange two adjacent subsequences of ARGV. One subsequence is elements
+ * [first_nonopt,last_nonopt) which contains all the non-options that have been
+ * skipped so far. The other is elements [last_nonopt,custom_optind), which contains
+ * all the options processed since those non-options were skipped.
+ * `first_nonopt' and `last_nonopt' are relocated so that they describe the new
+ * indices of the non-options in ARGV after they are moved.
+ */
+static void exchange(char **argv, struct custom_getopt_data *d)
+{
+ int bottom = d->first_nonopt;
+ int middle = d->last_nonopt;
+ int top = d->custom_optind;
+ char *tem;
+
+ /*
+ * Exchange the shorter segment with the far end of the longer segment.
+ * That puts the shorter segment into the right place. It leaves the
+ * longer segment in the right place overall, but it consists of two
+ * parts that need to be swapped next.
+ */
+ while (top > middle && middle > bottom) {
+ if (top - middle > middle - bottom) {
+ /* Bottom segment is the short one. */
+ int len = middle - bottom;
+ int i;
+
+ /* Swap it with the top part of the top segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] =
+ argv[top - (middle - bottom) + i];
+ argv[top - (middle - bottom) + i] = tem;
+ }
+ /* Exclude the moved bottom segment from further swapping. */
+ top -= len;
+ } else {
+ /* Top segment is the short one. */
+ int len = top - middle;
+ int i;
+
+ /* Swap it with the bottom part of the bottom segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] = argv[middle + i];
+ argv[middle + i] = tem;
+ }
+ /* Exclude the moved top segment from further swapping. */
+ bottom += len;
+ }
+ }
+ /* Update records for the slots the non-options now occupy. */
+ d->first_nonopt += (d->custom_optind - d->last_nonopt);
+ d->last_nonopt = d->custom_optind;
+}
+
+/* Initialize the internal data when the first call is made. */
+static void custom_getopt_initialize(struct custom_getopt_data *d)
+{
+ /*
+ * Start processing options with ARGV-element 1 (since ARGV-element 0
+ * is the program name); the sequence of previously skipped non-option
+ * ARGV-elements is empty.
+ */
+ d->first_nonopt = d->last_nonopt = d->custom_optind;
+ d->nextchar = NULL;
+ d->initialized = 1;
+}
+
+#define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0')
+
+/* return: zero: continue, nonzero: return given value to user */
+static int shuffle_argv(int argc, char *const *argv,const struct option *longopts,
+ struct custom_getopt_data *d)
+{
+ /*
+ * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been
+ * moved back by the user (who may also have changed the arguments).
+ */
+ if (d->last_nonopt > d->custom_optind)
+ d->last_nonopt = d->custom_optind;
+ if (d->first_nonopt > d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * If we have just processed some options following some
+ * non-options, exchange them so that the options come first.
+ */
+ if (d->first_nonopt != d->last_nonopt &&
+ d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->last_nonopt != d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * Skip any additional non-options and extend the range of
+ * non-options previously skipped.
+ */
+ while (d->custom_optind < argc && NONOPTION_P)
+ d->custom_optind++;
+ d->last_nonopt = d->custom_optind;
+ /*
+ * The special ARGV-element `--' means premature end of options. Skip
+ * it like a null option, then exchange with previous non-options as if
+ * it were an option, then skip everything else like a non-option.
+ */
+ if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) {
+ d->custom_optind++;
+ if (d->first_nonopt != d->last_nonopt
+ && d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->first_nonopt == d->last_nonopt)
+ d->first_nonopt = d->custom_optind;
+ d->last_nonopt = argc;
+ d->custom_optind = argc;
+ }
+ /*
+ * If we have done all the ARGV-elements, stop the scan and back over
+ * any non-options that we skipped and permuted.
+ */
+ if (d->custom_optind == argc) {
+ /*
+ * Set the next-arg-index to point at the non-options that we
+ * previously skipped, so the caller will digest them.
+ */
+ if (d->first_nonopt != d->last_nonopt)
+ d->custom_optind = d->first_nonopt;
+ return -1;
+ }
+ /*
+ * If we have come to a non-option and did not permute it, either stop
+ * the scan or describe it to the caller and pass it by.
+ */
+ if (NONOPTION_P) {
+ d->custom_optarg = argv[d->custom_optind++];
+ return 1;
+ }
+ /*
+ * We have found another option-ARGV-element. Skip the initial
+ * punctuation.
+ */
+ d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-'));
+ return 0;
+}
+
+/*
+ * Check whether the ARGV-element is a long option.
+ *
+ * If there's a long option "fubar" and the ARGV-element is "-fu", consider
+ * that an abbreviation of the long option, just like "--fu", and not "-f" with
+ * arg "u".
+ *
+ * This distinction seems to be the most useful approach.
+ *
+ */
+static int check_long_opt(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char *nameend;
+ const struct option *p;
+ const struct option *pfound = NULL;
+ int exact = 0;
+ int ambig = 0;
+ int indfound = -1;
+ int option_index;
+
+ for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++)
+ /* Do nothing. */ ;
+
+ /* Test all long options for either exact match or abbreviated matches */
+ for (p = longopts, option_index = 0; p->name; p++, option_index++)
+ if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) {
+ if ((unsigned int) (nameend - d->nextchar)
+ == (unsigned int) strlen(p->name)) {
+ /* Exact match found. */
+ pfound = p;
+ indfound = option_index;
+ exact = 1;
+ break;
+ } else if (pfound == NULL) {
+ /* First nonexact match found. */
+ pfound = p;
+ indfound = option_index;
+ } else if (pfound->has_arg != p->has_arg
+ || pfound->flag != p->flag
+ || pfound->val != p->val)
+ /* Second or later nonexact match found. */
+ ambig = 1;
+ }
+ if (ambig && !exact) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' is ambiguous\n",
+ argv[0], argv[d->custom_optind]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+ }
+ if (pfound) {
+ option_index = indfound;
+ d->custom_optind++;
+ if (*nameend) {
+ if (pfound->has_arg != no_argument)
+ d->custom_optarg = nameend + 1;
+ else {
+ if (print_errors) {
+ if (argv[d->custom_optind - 1][1] == '-') {
+ /* --option */
+ fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n",
+ argv[0], pfound->name);
+ } else {
+ /* +option or -option */
+ fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n",
+ argv[0], argv[d->custom_optind - 1][0], pfound->name);
+ }
+
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return '?';
+ }
+ } else if (pfound->has_arg == required_argument) {
+ if (d->custom_optind < argc)
+ d->custom_optarg = argv[d->custom_optind++];
+ else {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' requires an argument\n",
+ argv[0],
+ argv[d->custom_optind - 1]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return optstring[0] == ':' ? ':' : '?';
+ }
+ }
+ d->nextchar += strlen(d->nextchar);
+ if (longind != NULL)
+ *longind = option_index;
+ if (pfound->flag) {
+ *(pfound->flag) = pfound->val;
+ return 0;
+ }
+ return pfound->val;
+ }
+ /*
+ * Can't find it as a long option. If this is not getopt_long_only, or
+ * the option starts with '--' or is not a valid short option, then
+ * it's an error. Otherwise interpret it as a short option.
+ */
+ if (print_errors) {
+ if (argv[d->custom_optind][1] == '-') {
+ /* --option */
+ fprintf(stderr,
+ "%s: unrecognized option `--%s'\n",
+ argv[0], d->nextchar);
+ } else {
+ /* +option or -option */
+ fprintf(stderr,
+ "%s: unrecognized option `%c%s'\n",
+ argv[0], argv[d->custom_optind][0],
+ d->nextchar);
+ }
+ }
+ d->nextchar = (char *) "";
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+}
+
+static int check_short_opt(int argc, char *const *argv, const char *optstring,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char c = *d->nextchar++;
+ char *temp = strchr(optstring, c);
+
+ /* Increment `custom_optind' when we start to process its last character. */
+ if (*d->nextchar == '\0')
+ ++d->custom_optind;
+ if (!temp || c == ':') {
+ if (print_errors)
+ fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
+
+ d->custom_optopt = c;
+ return '?';
+ }
+ if (temp[1] == ':') {
+ if (temp[2] == ':') {
+ /* This is an option that accepts an argument optionally. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ d->custom_optind++;
+ } else
+ d->custom_optarg = NULL;
+ d->nextchar = NULL;
+ } else {
+ /* This is an option that requires an argument. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ /*
+ * If we end this ARGV-element by taking the
+ * rest as an arg, we must advance to the next
+ * element now.
+ */
+ d->custom_optind++;
+ } else if (d->custom_optind == argc) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option requires an argument -- %c\n",
+ argv[0], c);
+ }
+ d->custom_optopt = c;
+ if (optstring[0] == ':')
+ c = ':';
+ else
+ c = '?';
+ } else
+ /*
+ * We already incremented `custom_optind' once;
+ * increment it again when taking next ARGV-elt
+ * as argument.
+ */
+ d->custom_optarg = argv[d->custom_optind++];
+ d->nextchar = NULL;
+ }
+ }
+ return c;
+}
+
+/*
+ * Scan elements of ARGV for option characters given in OPTSTRING.
+ *
+ * If an element of ARGV starts with '-', and is not exactly "-" or "--",
+ * then it is an option element. The characters of this element
+ * (aside from the initial '-') are option characters. If `getopt'
+ * is called repeatedly, it returns successively each of the option characters
+ * from each of the option elements.
+ *
+ * If `getopt' finds another option character, it returns that character,
+ * updating `custom_optind' and `nextchar' so that the next call to `getopt' can
+ * resume the scan with the following option character or ARGV-element.
+ *
+ * If there are no more option characters, `getopt' returns -1.
+ * Then `custom_optind' is the index in ARGV of the first ARGV-element
+ * that is not an option. (The ARGV-elements have been permuted
+ * so that those that are not options now come last.)
+ *
+ * OPTSTRING is a string containing the legitimate option characters.
+ * If an option character is seen that is not listed in OPTSTRING,
+ * return '?' after printing an error message. If you set `custom_opterr' to
+ * zero, the error message is suppressed but we still return '?'.
+ *
+ * If a char in OPTSTRING is followed by a colon, that means it wants an arg,
+ * so the following text in the same ARGV-element, or the text of the following
+ * ARGV-element, is returned in `custom_optarg'. Two colons mean an option that
+ * wants an optional arg; if there is text in the current ARGV-element,
+ * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero.
+ *
+ * If OPTSTRING starts with `-' or `+', it requests different methods of
+ * handling the non-option ARGV-elements.
+ * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
+ *
+ * Long-named options begin with `--' instead of `-'.
+ * Their names may be abbreviated as long as the abbreviation is unique
+ * or is an exact match for some defined option. If they have an
+ * argument, it follows the option name in the same ARGV-element, separated
+ * from the option name by a `=', or else the in next ARGV-element.
+ * When `getopt' finds a long-named option, it returns 0 if that option's
+ * `flag' field is nonzero, the value of the option's `val' field
+ * if the `flag' field is zero.
+ *
+ * The elements of ARGV aren't really const, because we permute them.
+ * But we pretend they're const in the prototype to be compatible
+ * with other systems.
+ *
+ * LONGOPTS is a vector of `struct option' terminated by an
+ * element containing a name which is zero.
+ *
+ * LONGIND returns the index in LONGOPT of the long-named option found.
+ * It is only valid when a long-named option has been found by the most
+ * recent call.
+ *
+ * Return the option character from OPTS just read. Return -1 when there are
+ * no more options. For unrecognized options, or options missing arguments,
+ * `custom_optopt' is set to the option letter, and '?' is returned.
+ *
+ * The OPTS string is a list of characters which are recognized option letters,
+ * optionally followed by colons, specifying that that letter takes an
+ * argument, to be placed in `custom_optarg'.
+ *
+ * If a letter in OPTS is followed by two colons, its argument is optional.
+ * This behavior is specific to the GNU `getopt'.
+ *
+ * The argument `--' causes premature termination of argument scanning,
+ * explicitly telling `getopt' that there are no more options. If OPTS begins
+ * with `--', then non-option arguments are treated as arguments to the option
+ * '\0'. This behavior is specific to the GNU `getopt'.
+ */
+
+static int getopt_internal_r(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ struct custom_getopt_data *d)
+{
+ int ret, print_errors = d->custom_opterr;
+
+ if (optstring[0] == ':')
+ print_errors = 0;
+ if (argc < 1)
+ return -1;
+ d->custom_optarg = NULL;
+
+ /*
+ * This is a big difference with GNU getopt, since optind == 0
+ * means initialization while here 1 means first call.
+ */
+ if (d->custom_optind == 0 || !d->initialized) {
+ if (d->custom_optind == 0)
+ d->custom_optind = 1; /* Don't scan ARGV[0], the program name. */
+ custom_getopt_initialize(d);
+ }
+ if (d->nextchar == NULL || *d->nextchar == '\0') {
+ ret = shuffle_argv(argc, argv, longopts, d);
+ if (ret)
+ return ret;
+ }
+ if (longopts && (argv[d->custom_optind][1] == '-' ))
+ return check_long_opt(argc, argv, optstring, longopts,
+ longind, print_errors, d);
+ return check_short_opt(argc, argv, optstring, print_errors, d);
+}
+
+static int custom_getopt_internal(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind)
+{
+ int result;
+ /* Keep a global copy of all internal members of d */
+ static struct custom_getopt_data d;
+
+ d.custom_optind = custom_optind;
+ d.custom_opterr = custom_opterr;
+ result = getopt_internal_r(argc, argv, optstring, longopts,
+ longind, &d);
+ custom_optind = d.custom_optind;
+ custom_optarg = d.custom_optarg;
+ custom_optopt = d.custom_optopt;
+ return result;
+}
+
+static int custom_getopt_long (int argc, char *const *argv, const char *options,
+ const struct option *long_options, int *opt_index)
+{
+ return custom_getopt_internal(argc, argv, options, long_options,
+ opt_index);
+}
+
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_clitkBinarizeImage_params.check_ambiguity
+ * @param override @see cmdline_parser_clitkBinarizeImage_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+static
+int update_arg(void *field, char **orig_field,
+ unsigned int *field_given, unsigned int *prev_given,
+ char *value, char *possible_values[], const char *default_value,
+ cmdline_parser_clitkBinarizeImage_arg_type arg_type,
+ int check_ambiguity, int override,
+ int no_free, int multiple_option,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *stop_char = 0;
+ const char *val = value;
+ int found;
+ char **string_field;
+
+ stop_char = 0;
+ found = 0;
+
+ if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+ {
+ if (short_opt != '-')
+ fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
+ package_name, long_opt, short_opt,
+ (additional_error ? additional_error : ""));
+ else
+ fprintf (stderr, "%s: `--%s' option given more than once%s\n",
+ package_name, long_opt,
+ (additional_error ? additional_error : ""));
+ return 1; /* failure */
+ }
+
+ if (possible_values && (found = check_possible_values((value ? value : default_value), possible_values)) < 0)
+ {
+ if (short_opt != '-')
+ fprintf (stderr, "%s: %s argument, \"%s\", for option `--%s' (`-%c')%s\n",
+ package_name, (found == -2) ? "ambiguous" : "invalid", value, long_opt, short_opt,
+ (additional_error ? additional_error : ""));
+ else
+ fprintf (stderr, "%s: %s argument, \"%s\", for option `--%s'%s\n",
+ package_name, (found == -2) ? "ambiguous" : "invalid", value, long_opt,
+ (additional_error ? additional_error : ""));
+ return 1; /* failure */
+ }
+
+ if (field_given && *field_given && ! override)
+ return 0;
+ if (prev_given)
+ (*prev_given)++;
+ if (field_given)
+ (*field_given)++;
+ if (possible_values)
+ val = possible_values[found];
+
+ switch(arg_type) {
+ case ARG_FLAG:
+ *((int *)field) = !*((int *)field);
+ break;
+ case ARG_DOUBLE:
+ if (val) *((double *)field) = strtod (val, &stop_char);
+ break;
+ case ARG_STRING:
+ if (val) {
+ string_field = (char **)field;
+ if (!no_free && *string_field)
+ free (*string_field); /* free previous string */
+ *string_field = gengetopt_strdup (val);
+ }
+ break;
+ default:
+ break;
+ };
+
+ /* check numeric conversion */
+ switch(arg_type) {
+ case ARG_DOUBLE:
+ if (val && !(stop_char && *stop_char == '\0')) {
+ fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+ return 1; /* failure */
+ }
+ break;
+ default:
+ ;
+ };
+
+ /* store the original value */
+ switch(arg_type) {
+ case ARG_NO:
+ case ARG_FLAG:
+ break;
+ default:
+ if (value && orig_field) {
+ if (no_free) {
+ *orig_field = value;
+ } else {
+ if (*orig_field)
+ free (*orig_field); /* free previous string */
+ *orig_field = gengetopt_strdup (value);
+ }
+ }
+ };
+
+ return 0; /* OK */
+}
+
+
+int
+cmdline_parser_clitkBinarizeImage_internal (int argc, char * const *argv, struct args_info_clitkBinarizeImage *args_info,
+ struct cmdline_parser_clitkBinarizeImage_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+
+ int error = 0;
+ struct args_info_clitkBinarizeImage local_args_info;
+
+ int override;
+ int initialize;
+ int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+ check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+ cmdline_parser_clitkBinarizeImage_init (args_info);
+
+ cmdline_parser_clitkBinarizeImage_init (&local_args_info);
+
+ optarg = 0;
+ optind = 0;
+ opterr = params->print_errors;
+ optopt = '?';
+
+ while (1)
+ {
+ int option_index = 0;
+
+ static struct option long_options[] = {
+ { "help", 0, NULL, 'h' },
+ { "version", 0, NULL, 'V' },
+ { "config", 1, NULL, 0 },
+ { "verbose", 0, NULL, 'v' },
+ { "imagetypes", 0, NULL, 0 },
+ { "input", 1, NULL, 'i' },
+ { "output", 1, NULL, 'o' },
+ { "lower", 1, NULL, 'l' },
+ { "upper", 1, NULL, 'u' },
+ { "fg", 1, NULL, 0 },
+ { "bg", 1, NULL, 0 },
+ { "mode", 1, NULL, 0 },
+ { NULL, 0, NULL, 0 }
+ };
+
+ custom_optarg = optarg;
+ custom_optind = optind;
+ custom_opterr = opterr;
+ custom_optopt = optopt;
+
+ c = custom_getopt_long (argc, argv, "hVvi:o:l:u:", long_options, &option_index);
+
+ optarg = custom_optarg;
+ optind = custom_optind;
+ opterr = custom_opterr;
+ optopt = custom_optopt;
+
+ if (c == -1) break; /* Exit from `while (1)' loop. */
+
+ switch (c)
+ {
+ case 'h': /* Print help and exit. */
+ cmdline_parser_clitkBinarizeImage_print_help ();
+ cmdline_parser_clitkBinarizeImage_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'V': /* Print version and exit. */
+ cmdline_parser_clitkBinarizeImage_print_version ();
+ cmdline_parser_clitkBinarizeImage_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'v': /* Verbose. */
+
+
+ if (update_arg((void *)&(args_info->verbose_flag), 0, &(args_info->verbose_given),
+ &(local_args_info.verbose_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verbose", 'v',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'i': /* Input image filename. */
+
+
+ if (update_arg( (void *)&(args_info->input_arg),
+ &(args_info->input_orig), &(args_info->input_given),
+ &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "input", 'i',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'o': /* Output image filename. */
+
+
+ if (update_arg( (void *)&(args_info->output_arg),
+ &(args_info->output_orig), &(args_info->output_given),
+ &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "output", 'o',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'l': /* Lower intensity (default=min), fg is greater than this value. */
+
+
+ if (update_arg( (void *)&(args_info->lower_arg),
+ &(args_info->lower_orig), &(args_info->lower_given),
+ &(local_args_info.lower_given), optarg, 0, 0, ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "lower", 'l',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'u': /* Upper intensity (default=max), fg is lower than this value. */
+
+
+ if (update_arg( (void *)&(args_info->upper_arg),
+ &(args_info->upper_orig), &(args_info->upper_given),
+ &(local_args_info.upper_given), optarg, 0, 0, ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "upper", 'u',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ /* Config file. */
+ if (strcmp (long_options[option_index].name, "config") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->config_arg),
+ &(args_info->config_orig), &(args_info->config_given),
+ &(local_args_info.config_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "config", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Display allowed image types. */
+ else if (strcmp (long_options[option_index].name, "imagetypes") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->imagetypes_flag), 0, &(args_info->imagetypes_given),
+ &(local_args_info.imagetypes_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "imagetypes", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Foreground (FG) or 'inside' value. */
+ else if (strcmp (long_options[option_index].name, "fg") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->fg_arg),
+ &(args_info->fg_orig), &(args_info->fg_given),
+ &(local_args_info.fg_given), optarg, 0, "1", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "fg", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Background (BG) or 'ouside' value. */
+ else if (strcmp (long_options[option_index].name, "bg") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->bg_arg),
+ &(args_info->bg_orig), &(args_info->bg_given),
+ &(local_args_info.bg_given), optarg, 0, "0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "bg", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Use FG and/or BG values (if FG, the BG is replaced by the input image values). */
+ else if (strcmp (long_options[option_index].name, "mode") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->mode_arg),
+ &(args_info->mode_orig), &(args_info->mode_given),
+ &(local_args_info.mode_given), optarg, cmdline_parser_clitkBinarizeImage_mode_values, "both", ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "mode", '-',
+ additional_error))
+ goto failure;
+
+ }
+
+ break;
+ case '?': /* Invalid option. */
+ /* `getopt_long' already printed an error message. */
+ goto failure;
+
+ default: /* bug: option not considered. */
+ fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+
+
+ if (check_required)
+ {
+ error += cmdline_parser_clitkBinarizeImage_required2 (args_info, argv[0], additional_error);
+ }
+
+ cmdline_parser_clitkBinarizeImage_release (&local_args_info);
+
+ if ( error )
+ return (EXIT_FAILURE);
+
+ if (optind < argc)
+ {
+ int i = 0 ;
+ int found_prog_name = 0;
+ /* whether program name, i.e., argv[0], is in the remaining args
+ (this may happen with some implementations of getopt,
+ but surely not with the one included by gengetopt) */
+
+
+ args_info->inputs_num = argc - optind - found_prog_name;
+ args_info->inputs =
+ (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+ while (optind < argc)
+ args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
+ }
+
+ return 0;
+
+failure:
+
+ cmdline_parser_clitkBinarizeImage_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
+
+#ifndef CONFIG_FILE_LINE_SIZE
+#define CONFIG_FILE_LINE_SIZE 2048
+#endif
+#define ADDITIONAL_ERROR " in configuration file "
+
+#define CONFIG_FILE_LINE_BUFFER_SIZE (CONFIG_FILE_LINE_SIZE+3)
+/* 3 is for "--" and "=" */
+
+static int
+_cmdline_parser_clitkBinarizeImage_configfile (char * const filename, int *my_argc)
+{
+ FILE* file;
+ char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
+ char linebuf[CONFIG_FILE_LINE_SIZE];
+ int line_num = 0;
+ int result = 0, equal;
+ char *fopt, *farg;
+ char *str_index;
+ size_t len, next_token;
+ char delimiter;
+
+ if ((file = fopen(filename, "r")) == NULL)
+ {
+ fprintf (stderr, "%s: Error opening configuration file '%s'\n",
+ CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
+ {
+ ++line_num;
+ my_argv[0] = '\0';
+ len = strlen(linebuf);
+ if (len > (CONFIG_FILE_LINE_BUFFER_SIZE-1))
+ {
+ fprintf (stderr, "%s:%s:%d: Line too long in configuration file\n",
+ CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+
+ /* find first non-whitespace character in the line */
+ next_token = strspn (linebuf, " \t\r\n");
+ str_index = linebuf + next_token;
+
+ if ( str_index[0] == '\0' || str_index[0] == '#')
+ continue; /* empty line or comment line is skipped */
+
+ fopt = str_index;
+
+ /* truncate fopt at the end of the first non-valid character */
+ next_token = strcspn (fopt, " \t\r\n=");
+
+ if (fopt[next_token] == '\0') /* the line is over */
+ {
+ farg = NULL;
+ equal = 0;
+ goto noarg;
+ }
+
+ /* remember if equal sign is present */
+ equal = (fopt[next_token] == '=');
+ fopt[next_token++] = '\0';
+
+ /* advance pointers to the next token after the end of fopt */
+ next_token += strspn (fopt + next_token, " \t\r\n");
+
+ /* check for the presence of equal sign, and if so, skip it */
+ if ( !equal )
+ if ((equal = (fopt[next_token] == '=')))
+ {
+ next_token++;
+ next_token += strspn (fopt + next_token, " \t\r\n");
+ }
+ str_index += next_token;
+
+ /* find argument */
+ farg = str_index;
+ if ( farg[0] == '\"' || farg[0] == '\'' )
+ { /* quoted argument */
+ str_index = strchr (++farg, str_index[0] ); /* skip opening quote */
+ if (! str_index)
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: unterminated string in configuration file\n",
+ CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+ else
+ { /* read up the remaining part up to a delimiter */
+ next_token = strcspn (farg, " \t\r\n#\'\"");
+ str_index += next_token;
+ }
+
+ /* truncate farg at the delimiter and store it for further check */
+ delimiter = *str_index, *str_index++ = '\0';
+
+ /* everything but comment is illegal at the end of line */
+ if (delimiter != '\0' && delimiter != '#')
+ {
+ str_index += strspn(str_index, " \t\r\n");
+ if (*str_index != '\0' && *str_index != '#')
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: malformed string in configuration file\n",
+ CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+
+ noarg:
+ if (!strcmp(fopt,"include")) {
+ if (farg && *farg) {
+ result = _cmdline_parser_clitkBinarizeImage_configfile(farg, my_argc);
+ } else {
+ fprintf(stderr, "%s:%s:%d: include requires a filename argument.\n",
+ CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE, filename, line_num);
+ }
+ continue;
+ }
+ len = strlen(fopt);
+ strcat (my_argv, len > 1 ? "--" : "-");
+ strcat (my_argv, fopt);
+ if (len > 1 && ((farg && *farg) || equal))
+ strcat (my_argv, "=");
+ if (farg && *farg)
+ strcat (my_argv, farg);
+ ++(*my_argc);
+
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup(my_argv);
+ } /* while */
+
+ if (file)
+ fclose(file);
+ return result;
+}
+
+int
+cmdline_parser_clitkBinarizeImage_configfile (char * const filename,
+ struct args_info_clitkBinarizeImage *args_info,
+ int override, int initialize, int check_required)
+{
+ struct cmdline_parser_clitkBinarizeImage_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ return cmdline_parser_clitkBinarizeImage_config_file (filename, args_info, ¶ms);
+}
+
+int
+cmdline_parser_clitkBinarizeImage_config_file (char * const filename,
+ struct args_info_clitkBinarizeImage *args_info,
+ struct cmdline_parser_clitkBinarizeImage_params *params)
+{
+ int i, result;
+ int my_argc = 1;
+ char **my_argv_arg;
+ char *additional_error;
+
+ /* store the program name */
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup (CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE);
+
+ result = _cmdline_parser_clitkBinarizeImage_configfile(filename, &my_argc);
+
+ if (result != EXIT_FAILURE) {
+ my_argv_arg = (char **) malloc((my_argc+1) * sizeof(char *));
+ cmd_line_list_tmp = cmd_line_list;
+
+ for (i = my_argc - 1; i >= 0; --i) {
+ my_argv_arg[i] = cmd_line_list_tmp->string_arg;
+ cmd_line_list_tmp = cmd_line_list_tmp->next;
+ }
+
+ my_argv_arg[my_argc] = 0;
+
+ additional_error = (char *)malloc(strlen(filename) + strlen(ADDITIONAL_ERROR) + 1);
+ strcpy (additional_error, ADDITIONAL_ERROR);
+ strcat (additional_error, filename);
+ result =
+ cmdline_parser_clitkBinarizeImage_internal (my_argc, my_argv_arg, args_info,
+ params,
+ additional_error);
+
+ free (additional_error);
+ free (my_argv_arg);
+ }
+
+ free_cmd_list();
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkBinarizeImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
--- /dev/null
+/** @file clitkBinarizeImage_ggo.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CLITKBINARIZEIMAGE_GGO_H
+#define CLITKBINARIZEIMAGE_GGO_H
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE
+/** @brief the program name */
+#define CMDLINE_PARSER_CLITKBINARIZEIMAGE_PACKAGE "clitkBinarizeImage"
+#endif
+
+#ifndef CMDLINE_PARSER_CLITKBINARIZEIMAGE_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_CLITKBINARIZEIMAGE_VERSION "1.0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct args_info_clitkBinarizeImage
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ char * config_arg; /**< @brief Config file. */
+ char * config_orig; /**< @brief Config file original value given at command line. */
+ const char *config_help; /**< @brief Config file help description. */
+ int verbose_flag; /**< @brief Verbose (default=off). */
+ const char *verbose_help; /**< @brief Verbose help description. */
+ int imagetypes_flag; /**< @brief Display allowed image types (default=off). */
+ const char *imagetypes_help; /**< @brief Display allowed image types help description. */
+ char * input_arg; /**< @brief Input image filename. */
+ char * input_orig; /**< @brief Input image filename original value given at command line. */
+ const char *input_help; /**< @brief Input image filename help description. */
+ char * output_arg; /**< @brief Output image filename. */
+ char * output_orig; /**< @brief Output image filename original value given at command line. */
+ const char *output_help; /**< @brief Output image filename help description. */
+ double lower_arg; /**< @brief Lower intensity (default=min), fg is greater than this value. */
+ char * lower_orig; /**< @brief Lower intensity (default=min), fg is greater than this value original value given at command line. */
+ const char *lower_help; /**< @brief Lower intensity (default=min), fg is greater than this value help description. */
+ double upper_arg; /**< @brief Upper intensity (default=max), fg is lower than this value. */
+ char * upper_orig; /**< @brief Upper intensity (default=max), fg is lower than this value original value given at command line. */
+ const char *upper_help; /**< @brief Upper intensity (default=max), fg is lower than this value help description. */
+ double fg_arg; /**< @brief Foreground (FG) or 'inside' value (default='1'). */
+ char * fg_orig; /**< @brief Foreground (FG) or 'inside' value original value given at command line. */
+ const char *fg_help; /**< @brief Foreground (FG) or 'inside' value help description. */
+ double bg_arg; /**< @brief Background (BG) or 'ouside' value (default='0'). */
+ char * bg_orig; /**< @brief Background (BG) or 'ouside' value original value given at command line. */
+ const char *bg_help; /**< @brief Background (BG) or 'ouside' value help description. */
+ char * mode_arg; /**< @brief Use FG and/or BG values (if FG, the BG is replaced by the input image values) (default='both'). */
+ char * mode_orig; /**< @brief Use FG and/or BG values (if FG, the BG is replaced by the input image values) original value given at command line. */
+ const char *mode_help; /**< @brief Use FG and/or BG values (if FG, the BG is replaced by the input image values) help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int config_given ; /**< @brief Whether config was given. */
+ unsigned int verbose_given ; /**< @brief Whether verbose was given. */
+ unsigned int imagetypes_given ; /**< @brief Whether imagetypes was given. */
+ unsigned int input_given ; /**< @brief Whether input was given. */
+ unsigned int output_given ; /**< @brief Whether output was given. */
+ unsigned int lower_given ; /**< @brief Whether lower was given. */
+ unsigned int upper_given ; /**< @brief Whether upper was given. */
+ unsigned int fg_given ; /**< @brief Whether fg was given. */
+ unsigned int bg_given ; /**< @brief Whether bg was given. */
+ unsigned int mode_given ; /**< @brief Whether mode was given. */
+
+ char **inputs ; /**< @brief unamed options (options without names) */
+ unsigned inputs_num ; /**< @brief unamed options number */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_clitkBinarizeImage_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure args_info_clitkBinarizeImage (default 1) */
+ int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+ int check_ambiguity; /**< @brief whether to check for options already specified in the option structure args_info_clitkBinarizeImage (default 0) */
+ int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *args_info_clitkBinarizeImage_purpose;
+/** @brief the usage string of the program */
+extern const char *args_info_clitkBinarizeImage_usage;
+/** @brief all the lines making the help output */
+extern const char *args_info_clitkBinarizeImage_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkBinarizeImage (int argc, char * const *argv,
+ struct args_info_clitkBinarizeImage *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkBinarizeImage_ext() instead
+ */
+int cmdline_parser_clitkBinarizeImage2 (int argc, char * const *argv,
+ struct args_info_clitkBinarizeImage *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkBinarizeImage_ext (int argc, char * const *argv,
+ struct args_info_clitkBinarizeImage *args_info,
+ struct cmdline_parser_clitkBinarizeImage_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkBinarizeImage_dump(FILE *outfile,
+ struct args_info_clitkBinarizeImage *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkBinarizeImage_file_save(const char *filename,
+ struct args_info_clitkBinarizeImage *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_clitkBinarizeImage_print_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_clitkBinarizeImage_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_clitkBinarizeImage_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_clitkBinarizeImage_params_init(struct cmdline_parser_clitkBinarizeImage_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_clitkBinarizeImage_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_clitkBinarizeImage_params structure
+ */
+struct cmdline_parser_clitkBinarizeImage_params *cmdline_parser_clitkBinarizeImage_params_create(void);
+
+/**
+ * Initializes the passed args_info_clitkBinarizeImage structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_clitkBinarizeImage_init (struct args_info_clitkBinarizeImage *args_info);
+/**
+ * Deallocates the string fields of the args_info_clitkBinarizeImage structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_clitkBinarizeImage_free (struct args_info_clitkBinarizeImage *args_info);
+
+/**
+ * The config file parser (deprecated version)
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkBinarizeImage_config_file() instead
+ */
+int cmdline_parser_clitkBinarizeImage_configfile (char * const filename,
+ struct args_info_clitkBinarizeImage *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The config file parser
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkBinarizeImage_config_file (char * const filename,
+ struct args_info_clitkBinarizeImage *args_info,
+ struct cmdline_parser_clitkBinarizeImage_params *params);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ * possible errors
+ * @return
+ */
+int cmdline_parser_clitkBinarizeImage_required (struct args_info_clitkBinarizeImage *args_info,
+ const char *prog_name);
+
+extern char *cmdline_parser_clitkBinarizeImage_mode_values[] ; /**< @brief Possible values for mode. */
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CLITKBINARIZEIMAGE_GGO_H */
--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22
+ generated with the following command:
+ /usr/local/bin/gengetopt --output-dir=/home/tbaudier/vv/vv_static/vv/vv_bin/segmentation --arg-struct-name=args_info_clitkConnectedComponentLabeling --func-name=cmdline_parser_clitkConnectedComponentLabeling --file-name=clitkConnectedComponentLabeling_ggo --unamed-opts --conf-parser --include-getopt
+
+ The developers of gengetopt consider the fixed text that goes in all
+ gengetopt output files to be in the public domain:
+ we make no copyright claims on it.
+*/
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+
+#include "clitkConnectedComponentLabeling_ggo.h"
+
+const char *args_info_clitkConnectedComponentLabeling_purpose = "Basic segmentation : connected component labeling ";
+
+const char *args_info_clitkConnectedComponentLabeling_usage = "Usage: clitkConnectedComponentLabeling [OPTIONS]... [FILES]...";
+
+const char *args_info_clitkConnectedComponentLabeling_description = "";
+
+const char *args_info_clitkConnectedComponentLabeling_help[] = {
+ " -h, --help Print help and exit",
+ " -V, --version Print version and exit",
+ " --config=STRING Config file",
+ " -v, --verbose Verbose (default=off)",
+ " --imagetypes Display allowed image types (default=off)",
+ " --verboseOption Display options values (default=off)",
+ "\nI/O:",
+ " -i, --input=STRING Input image filename",
+ " --inputBG=INT Input Background (default=`0')",
+ " -o, --output=STRING Output filename",
+ "\nLabelize:",
+ " --minSize=INT Minimum component size in voxels (default=`100')",
+ " --full Full connecticity (default=off)",
+ 0
+};
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_INT
+} cmdline_parser_clitkConnectedComponentLabeling_arg_type;
+
+static
+void clear_given (struct args_info_clitkConnectedComponentLabeling *args_info);
+static
+void clear_args (struct args_info_clitkConnectedComponentLabeling *args_info);
+
+static int
+cmdline_parser_clitkConnectedComponentLabeling_internal (int argc, char * const *argv, struct args_info_clitkConnectedComponentLabeling *args_info,
+ struct cmdline_parser_clitkConnectedComponentLabeling_params *params, const char *additional_error);
+
+static int
+cmdline_parser_clitkConnectedComponentLabeling_required2 (struct args_info_clitkConnectedComponentLabeling *args_info, const char *prog_name, const char *additional_error);
+struct line_list
+{
+ char * string_arg;
+ struct line_list * next;
+};
+
+static struct line_list *cmd_line_list = 0;
+static struct line_list *cmd_line_list_tmp = 0;
+
+static void
+free_cmd_list(void)
+{
+ /* free the list of a previous call */
+ if (cmd_line_list)
+ {
+ while (cmd_line_list) {
+ cmd_line_list_tmp = cmd_line_list;
+ cmd_line_list = cmd_line_list->next;
+ free (cmd_line_list_tmp->string_arg);
+ free (cmd_line_list_tmp);
+ }
+ }
+}
+
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct args_info_clitkConnectedComponentLabeling *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->config_given = 0 ;
+ args_info->verbose_given = 0 ;
+ args_info->imagetypes_given = 0 ;
+ args_info->verboseOption_given = 0 ;
+ args_info->input_given = 0 ;
+ args_info->inputBG_given = 0 ;
+ args_info->output_given = 0 ;
+ args_info->minSize_given = 0 ;
+ args_info->full_given = 0 ;
+}
+
+static
+void clear_args (struct args_info_clitkConnectedComponentLabeling *args_info)
+{
+ args_info->config_arg = NULL;
+ args_info->config_orig = NULL;
+ args_info->verbose_flag = 0;
+ args_info->imagetypes_flag = 0;
+ args_info->verboseOption_flag = 0;
+ args_info->input_arg = NULL;
+ args_info->input_orig = NULL;
+ args_info->inputBG_arg = 0;
+ args_info->inputBG_orig = NULL;
+ args_info->output_arg = NULL;
+ args_info->output_orig = NULL;
+ args_info->minSize_arg = 100;
+ args_info->minSize_orig = NULL;
+ args_info->full_flag = 0;
+
+}
+
+static
+void init_args_info(struct args_info_clitkConnectedComponentLabeling *args_info)
+{
+
+
+ args_info->help_help = args_info_clitkConnectedComponentLabeling_help[0] ;
+ args_info->version_help = args_info_clitkConnectedComponentLabeling_help[1] ;
+ args_info->config_help = args_info_clitkConnectedComponentLabeling_help[2] ;
+ args_info->verbose_help = args_info_clitkConnectedComponentLabeling_help[3] ;
+ args_info->imagetypes_help = args_info_clitkConnectedComponentLabeling_help[4] ;
+ args_info->verboseOption_help = args_info_clitkConnectedComponentLabeling_help[5] ;
+ args_info->input_help = args_info_clitkConnectedComponentLabeling_help[7] ;
+ args_info->inputBG_help = args_info_clitkConnectedComponentLabeling_help[8] ;
+ args_info->output_help = args_info_clitkConnectedComponentLabeling_help[9] ;
+ args_info->minSize_help = args_info_clitkConnectedComponentLabeling_help[11] ;
+ args_info->full_help = args_info_clitkConnectedComponentLabeling_help[12] ;
+
+}
+
+void
+cmdline_parser_clitkConnectedComponentLabeling_print_version (void)
+{
+ printf ("%s %s\n", CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE, CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_VERSION);
+}
+
+static void print_help_common(void) {
+ cmdline_parser_clitkConnectedComponentLabeling_print_version ();
+
+ if (strlen(args_info_clitkConnectedComponentLabeling_purpose) > 0)
+ printf("\n%s\n", args_info_clitkConnectedComponentLabeling_purpose);
+
+ if (strlen(args_info_clitkConnectedComponentLabeling_usage) > 0)
+ printf("\n%s\n", args_info_clitkConnectedComponentLabeling_usage);
+
+ printf("\n");
+
+ if (strlen(args_info_clitkConnectedComponentLabeling_description) > 0)
+ printf("%s\n", args_info_clitkConnectedComponentLabeling_description);
+}
+
+void
+cmdline_parser_clitkConnectedComponentLabeling_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (args_info_clitkConnectedComponentLabeling_help[i])
+ printf("%s\n", args_info_clitkConnectedComponentLabeling_help[i++]);
+}
+
+void
+cmdline_parser_clitkConnectedComponentLabeling_init (struct args_info_clitkConnectedComponentLabeling *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+
+ args_info->inputs = NULL;
+ args_info->inputs_num = 0;
+}
+
+void
+cmdline_parser_clitkConnectedComponentLabeling_params_init(struct cmdline_parser_clitkConnectedComponentLabeling_params *params)
+{
+ if (params)
+ {
+ params->override = 0;
+ params->initialize = 1;
+ params->check_required = 1;
+ params->check_ambiguity = 0;
+ params->print_errors = 1;
+ }
+}
+
+struct cmdline_parser_clitkConnectedComponentLabeling_params *
+cmdline_parser_clitkConnectedComponentLabeling_params_create(void)
+{
+ struct cmdline_parser_clitkConnectedComponentLabeling_params *params =
+ (struct cmdline_parser_clitkConnectedComponentLabeling_params *)malloc(sizeof(struct cmdline_parser_clitkConnectedComponentLabeling_params));
+ cmdline_parser_clitkConnectedComponentLabeling_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+
+static void
+cmdline_parser_clitkConnectedComponentLabeling_release (struct args_info_clitkConnectedComponentLabeling *args_info)
+{
+ unsigned int i;
+ free_string_field (&(args_info->config_arg));
+ free_string_field (&(args_info->config_orig));
+ free_string_field (&(args_info->input_arg));
+ free_string_field (&(args_info->input_orig));
+ free_string_field (&(args_info->inputBG_orig));
+ free_string_field (&(args_info->output_arg));
+ free_string_field (&(args_info->output_orig));
+ free_string_field (&(args_info->minSize_orig));
+
+
+ for (i = 0; i < args_info->inputs_num; ++i)
+ free (args_info->inputs [i]);
+
+ if (args_info->inputs_num)
+ free (args_info->inputs);
+
+ clear_given (args_info);
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+ if (arg) {
+ fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+ } else {
+ fprintf(outfile, "%s\n", opt);
+ }
+}
+
+
+int
+cmdline_parser_clitkConnectedComponentLabeling_dump(FILE *outfile, struct args_info_clitkConnectedComponentLabeling *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE);
+ return EXIT_FAILURE;
+ }
+
+ if (args_info->help_given)
+ write_into_file(outfile, "help", 0, 0 );
+ if (args_info->version_given)
+ write_into_file(outfile, "version", 0, 0 );
+ if (args_info->config_given)
+ write_into_file(outfile, "config", args_info->config_orig, 0);
+ if (args_info->verbose_given)
+ write_into_file(outfile, "verbose", 0, 0 );
+ if (args_info->imagetypes_given)
+ write_into_file(outfile, "imagetypes", 0, 0 );
+ if (args_info->verboseOption_given)
+ write_into_file(outfile, "verboseOption", 0, 0 );
+ if (args_info->input_given)
+ write_into_file(outfile, "input", args_info->input_orig, 0);
+ if (args_info->inputBG_given)
+ write_into_file(outfile, "inputBG", args_info->inputBG_orig, 0);
+ if (args_info->output_given)
+ write_into_file(outfile, "output", args_info->output_orig, 0);
+ if (args_info->minSize_given)
+ write_into_file(outfile, "minSize", args_info->minSize_orig, 0);
+ if (args_info->full_given)
+ write_into_file(outfile, "full", 0, 0 );
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+cmdline_parser_clitkConnectedComponentLabeling_file_save(const char *filename, struct args_info_clitkConnectedComponentLabeling *args_info)
+{
+ FILE *outfile;
+ int i = 0;
+
+ outfile = fopen(filename, "w");
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = cmdline_parser_clitkConnectedComponentLabeling_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+cmdline_parser_clitkConnectedComponentLabeling_free (struct args_info_clitkConnectedComponentLabeling *args_info)
+{
+ cmdline_parser_clitkConnectedComponentLabeling_release (args_info);
+}
+
+/** @brief replacement of strdup, which is not standard */
+char *
+gengetopt_strdup (const char *s)
+{
+ char *result = NULL;
+ if (!s)
+ return result;
+
+ result = (char*)malloc(strlen(s) + 1);
+ if (result == (char*)0)
+ return (char*)0;
+ strcpy(result, s);
+ return result;
+}
+
+int
+cmdline_parser_clitkConnectedComponentLabeling (int argc, char * const *argv, struct args_info_clitkConnectedComponentLabeling *args_info)
+{
+ return cmdline_parser_clitkConnectedComponentLabeling2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+cmdline_parser_clitkConnectedComponentLabeling_ext (int argc, char * const *argv, struct args_info_clitkConnectedComponentLabeling *args_info,
+ struct cmdline_parser_clitkConnectedComponentLabeling_params *params)
+{
+ int result;
+ result = cmdline_parser_clitkConnectedComponentLabeling_internal (argc, argv, args_info, params, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkConnectedComponentLabeling_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkConnectedComponentLabeling2 (int argc, char * const *argv, struct args_info_clitkConnectedComponentLabeling *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct cmdline_parser_clitkConnectedComponentLabeling_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = cmdline_parser_clitkConnectedComponentLabeling_internal (argc, argv, args_info, ¶ms, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkConnectedComponentLabeling_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkConnectedComponentLabeling_required (struct args_info_clitkConnectedComponentLabeling *args_info, const char *prog_name)
+{
+ int result = EXIT_SUCCESS;
+
+ if (cmdline_parser_clitkConnectedComponentLabeling_required2(args_info, prog_name, NULL) > 0)
+ result = EXIT_FAILURE;
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkConnectedComponentLabeling_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkConnectedComponentLabeling_required2 (struct args_info_clitkConnectedComponentLabeling *args_info, const char *prog_name, const char *additional_error)
+{
+ int error = 0;
+
+ /* checks for required options */
+ if (! args_info->input_given)
+ {
+ fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (! args_info->output_given)
+ {
+ fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+
+ /* checks for dependences among options */
+
+ return error;
+}
+
+/*
+ * Extracted from the glibc source tree, version 2.3.6
+ *
+ * Licensed under the GPL as per the whole glibc source tree.
+ *
+ * This file was modified so that getopt_long can be called
+ * many times without risking previous memory to be spoiled.
+ *
+ * Modified by Andre Noll and Lorenzo Bettini for use in
+ * GNU gengetopt generated files.
+ *
+ */
+
+/*
+ * we must include anything we need since this file is not thought to be
+ * inserted in a file already using getopt.h
+ *
+ * Lorenzo
+ */
+
+struct option
+{
+ const char *name;
+ /* has_arg can't be an enum because some compilers complain about
+ type mismatches in all the code that assumes it is an int. */
+ int has_arg;
+ int *flag;
+ int val;
+};
+
+/* For communication from `getopt' to the caller.
+ When `getopt' finds an option that takes an argument,
+ the argument value is returned here.
+ Also, when `ordering' is RETURN_IN_ORDER,
+ each non-option ARGV-element is returned here. */
+
+static char *optarg;
+
+/* Index in ARGV of the next element to be scanned.
+ This is used for communication to and from the caller
+ and for communication between successive calls to `getopt'.
+
+ On entry to `getopt', zero means this is the first call; initialize.
+
+ When `getopt' returns -1, this is the index of the first of the
+ non-option elements that the caller should itself scan.
+
+ Otherwise, `optind' communicates from one call to the next
+ how much of ARGV has been scanned so far. */
+
+static int optind;
+
+/* Callers store zero here to inhibit the error message `getopt' prints
+ for unrecognized options. */
+
+static int opterr;
+
+/* Set to an option character which was unrecognized. */
+
+static int optopt;
+
+/* This version of `getopt' appears to the caller like standard Unix `getopt'
+ but it behaves differently for the user, since it allows the user
+ to intersperse the options with the other arguments.
+
+ As `getopt' works, it permutes the elements of ARGV so that,
+ when it is done, all the options precede everything else. Thus
+ all application programs are extended to handle flexible argument order.
+*/
+/*
+ If the field `flag' is not NULL, it points to a variable that is set
+ to the value given in the field `val' when the option is found, but
+ left unchanged if the option is not found.
+
+ To have a long-named option do something other than set an `int' to
+ a compiled-in constant, such as set a value from `custom_optarg', set the
+ option's `flag' field to zero and its `val' field to a nonzero
+ value (the equivalent single-letter option character, if there is
+ one). For long options that have a zero `flag' field, `getopt'
+ returns the contents of the `val' field. */
+
+/* Names for the values of the `has_arg' field of `struct option'. */
+#ifndef no_argument
+#define no_argument 0
+#endif
+
+#ifndef required_argument
+#define required_argument 1
+#endif
+
+#ifndef optional_argument
+#define optional_argument 2
+#endif
+
+struct custom_getopt_data {
+ /*
+ * These have exactly the same meaning as the corresponding global variables,
+ * except that they are used for the reentrant versions of getopt.
+ */
+ int custom_optind;
+ int custom_opterr;
+ int custom_optopt;
+ char *custom_optarg;
+
+ /* True if the internal members have been initialized. */
+ int initialized;
+
+ /*
+ * The next char to be scanned in the option-element in which the last option
+ * character we returned was found. This allows us to pick up the scan where
+ * we left off. If this is zero, or a null string, it means resume the scan by
+ * advancing to the next ARGV-element.
+ */
+ char *nextchar;
+
+ /*
+ * Describe the part of ARGV that contains non-options that have been skipped.
+ * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is
+ * the index after the last of them.
+ */
+ int first_nonopt;
+ int last_nonopt;
+};
+
+/*
+ * the variables optarg, optind, opterr and optopt are renamed with
+ * the custom_ prefix so that they don't interfere with getopt ones.
+ *
+ * Moreover they're static so they are visible only from within the
+ * file where this very file will be included.
+ */
+
+/*
+ * For communication from `custom_getopt' to the caller. When `custom_getopt' finds an
+ * option that takes an argument, the argument value is returned here.
+ */
+static char *custom_optarg;
+
+/*
+ * Index in ARGV of the next element to be scanned. This is used for
+ * communication to and from the caller and for communication between
+ * successive calls to `custom_getopt'.
+ *
+ * On entry to `custom_getopt', 1 means this is the first call; initialize.
+ *
+ * When `custom_getopt' returns -1, this is the index of the first of the non-option
+ * elements that the caller should itself scan.
+ *
+ * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV
+ * has been scanned so far.
+ *
+ * 1003.2 says this must be 1 before any call.
+ */
+static int custom_optind = 1;
+
+/*
+ * Callers store zero here to inhibit the error message for unrecognized
+ * options.
+ */
+static int custom_opterr = 1;
+
+/*
+ * Set to an option character which was unrecognized. This must be initialized
+ * on some systems to avoid linking in the system's own getopt implementation.
+ */
+static int custom_optopt = '?';
+
+/*
+ * Exchange two adjacent subsequences of ARGV. One subsequence is elements
+ * [first_nonopt,last_nonopt) which contains all the non-options that have been
+ * skipped so far. The other is elements [last_nonopt,custom_optind), which contains
+ * all the options processed since those non-options were skipped.
+ * `first_nonopt' and `last_nonopt' are relocated so that they describe the new
+ * indices of the non-options in ARGV after they are moved.
+ */
+static void exchange(char **argv, struct custom_getopt_data *d)
+{
+ int bottom = d->first_nonopt;
+ int middle = d->last_nonopt;
+ int top = d->custom_optind;
+ char *tem;
+
+ /*
+ * Exchange the shorter segment with the far end of the longer segment.
+ * That puts the shorter segment into the right place. It leaves the
+ * longer segment in the right place overall, but it consists of two
+ * parts that need to be swapped next.
+ */
+ while (top > middle && middle > bottom) {
+ if (top - middle > middle - bottom) {
+ /* Bottom segment is the short one. */
+ int len = middle - bottom;
+ int i;
+
+ /* Swap it with the top part of the top segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] =
+ argv[top - (middle - bottom) + i];
+ argv[top - (middle - bottom) + i] = tem;
+ }
+ /* Exclude the moved bottom segment from further swapping. */
+ top -= len;
+ } else {
+ /* Top segment is the short one. */
+ int len = top - middle;
+ int i;
+
+ /* Swap it with the bottom part of the bottom segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] = argv[middle + i];
+ argv[middle + i] = tem;
+ }
+ /* Exclude the moved top segment from further swapping. */
+ bottom += len;
+ }
+ }
+ /* Update records for the slots the non-options now occupy. */
+ d->first_nonopt += (d->custom_optind - d->last_nonopt);
+ d->last_nonopt = d->custom_optind;
+}
+
+/* Initialize the internal data when the first call is made. */
+static void custom_getopt_initialize(struct custom_getopt_data *d)
+{
+ /*
+ * Start processing options with ARGV-element 1 (since ARGV-element 0
+ * is the program name); the sequence of previously skipped non-option
+ * ARGV-elements is empty.
+ */
+ d->first_nonopt = d->last_nonopt = d->custom_optind;
+ d->nextchar = NULL;
+ d->initialized = 1;
+}
+
+#define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0')
+
+/* return: zero: continue, nonzero: return given value to user */
+static int shuffle_argv(int argc, char *const *argv,const struct option *longopts,
+ struct custom_getopt_data *d)
+{
+ /*
+ * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been
+ * moved back by the user (who may also have changed the arguments).
+ */
+ if (d->last_nonopt > d->custom_optind)
+ d->last_nonopt = d->custom_optind;
+ if (d->first_nonopt > d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * If we have just processed some options following some
+ * non-options, exchange them so that the options come first.
+ */
+ if (d->first_nonopt != d->last_nonopt &&
+ d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->last_nonopt != d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * Skip any additional non-options and extend the range of
+ * non-options previously skipped.
+ */
+ while (d->custom_optind < argc && NONOPTION_P)
+ d->custom_optind++;
+ d->last_nonopt = d->custom_optind;
+ /*
+ * The special ARGV-element `--' means premature end of options. Skip
+ * it like a null option, then exchange with previous non-options as if
+ * it were an option, then skip everything else like a non-option.
+ */
+ if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) {
+ d->custom_optind++;
+ if (d->first_nonopt != d->last_nonopt
+ && d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->first_nonopt == d->last_nonopt)
+ d->first_nonopt = d->custom_optind;
+ d->last_nonopt = argc;
+ d->custom_optind = argc;
+ }
+ /*
+ * If we have done all the ARGV-elements, stop the scan and back over
+ * any non-options that we skipped and permuted.
+ */
+ if (d->custom_optind == argc) {
+ /*
+ * Set the next-arg-index to point at the non-options that we
+ * previously skipped, so the caller will digest them.
+ */
+ if (d->first_nonopt != d->last_nonopt)
+ d->custom_optind = d->first_nonopt;
+ return -1;
+ }
+ /*
+ * If we have come to a non-option and did not permute it, either stop
+ * the scan or describe it to the caller and pass it by.
+ */
+ if (NONOPTION_P) {
+ d->custom_optarg = argv[d->custom_optind++];
+ return 1;
+ }
+ /*
+ * We have found another option-ARGV-element. Skip the initial
+ * punctuation.
+ */
+ d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-'));
+ return 0;
+}
+
+/*
+ * Check whether the ARGV-element is a long option.
+ *
+ * If there's a long option "fubar" and the ARGV-element is "-fu", consider
+ * that an abbreviation of the long option, just like "--fu", and not "-f" with
+ * arg "u".
+ *
+ * This distinction seems to be the most useful approach.
+ *
+ */
+static int check_long_opt(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char *nameend;
+ const struct option *p;
+ const struct option *pfound = NULL;
+ int exact = 0;
+ int ambig = 0;
+ int indfound = -1;
+ int option_index;
+
+ for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++)
+ /* Do nothing. */ ;
+
+ /* Test all long options for either exact match or abbreviated matches */
+ for (p = longopts, option_index = 0; p->name; p++, option_index++)
+ if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) {
+ if ((unsigned int) (nameend - d->nextchar)
+ == (unsigned int) strlen(p->name)) {
+ /* Exact match found. */
+ pfound = p;
+ indfound = option_index;
+ exact = 1;
+ break;
+ } else if (pfound == NULL) {
+ /* First nonexact match found. */
+ pfound = p;
+ indfound = option_index;
+ } else if (pfound->has_arg != p->has_arg
+ || pfound->flag != p->flag
+ || pfound->val != p->val)
+ /* Second or later nonexact match found. */
+ ambig = 1;
+ }
+ if (ambig && !exact) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' is ambiguous\n",
+ argv[0], argv[d->custom_optind]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+ }
+ if (pfound) {
+ option_index = indfound;
+ d->custom_optind++;
+ if (*nameend) {
+ if (pfound->has_arg != no_argument)
+ d->custom_optarg = nameend + 1;
+ else {
+ if (print_errors) {
+ if (argv[d->custom_optind - 1][1] == '-') {
+ /* --option */
+ fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n",
+ argv[0], pfound->name);
+ } else {
+ /* +option or -option */
+ fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n",
+ argv[0], argv[d->custom_optind - 1][0], pfound->name);
+ }
+
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return '?';
+ }
+ } else if (pfound->has_arg == required_argument) {
+ if (d->custom_optind < argc)
+ d->custom_optarg = argv[d->custom_optind++];
+ else {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' requires an argument\n",
+ argv[0],
+ argv[d->custom_optind - 1]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return optstring[0] == ':' ? ':' : '?';
+ }
+ }
+ d->nextchar += strlen(d->nextchar);
+ if (longind != NULL)
+ *longind = option_index;
+ if (pfound->flag) {
+ *(pfound->flag) = pfound->val;
+ return 0;
+ }
+ return pfound->val;
+ }
+ /*
+ * Can't find it as a long option. If this is not getopt_long_only, or
+ * the option starts with '--' or is not a valid short option, then
+ * it's an error. Otherwise interpret it as a short option.
+ */
+ if (print_errors) {
+ if (argv[d->custom_optind][1] == '-') {
+ /* --option */
+ fprintf(stderr,
+ "%s: unrecognized option `--%s'\n",
+ argv[0], d->nextchar);
+ } else {
+ /* +option or -option */
+ fprintf(stderr,
+ "%s: unrecognized option `%c%s'\n",
+ argv[0], argv[d->custom_optind][0],
+ d->nextchar);
+ }
+ }
+ d->nextchar = (char *) "";
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+}
+
+static int check_short_opt(int argc, char *const *argv, const char *optstring,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char c = *d->nextchar++;
+ char *temp = strchr(optstring, c);
+
+ /* Increment `custom_optind' when we start to process its last character. */
+ if (*d->nextchar == '\0')
+ ++d->custom_optind;
+ if (!temp || c == ':') {
+ if (print_errors)
+ fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
+
+ d->custom_optopt = c;
+ return '?';
+ }
+ if (temp[1] == ':') {
+ if (temp[2] == ':') {
+ /* This is an option that accepts an argument optionally. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ d->custom_optind++;
+ } else
+ d->custom_optarg = NULL;
+ d->nextchar = NULL;
+ } else {
+ /* This is an option that requires an argument. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ /*
+ * If we end this ARGV-element by taking the
+ * rest as an arg, we must advance to the next
+ * element now.
+ */
+ d->custom_optind++;
+ } else if (d->custom_optind == argc) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option requires an argument -- %c\n",
+ argv[0], c);
+ }
+ d->custom_optopt = c;
+ if (optstring[0] == ':')
+ c = ':';
+ else
+ c = '?';
+ } else
+ /*
+ * We already incremented `custom_optind' once;
+ * increment it again when taking next ARGV-elt
+ * as argument.
+ */
+ d->custom_optarg = argv[d->custom_optind++];
+ d->nextchar = NULL;
+ }
+ }
+ return c;
+}
+
+/*
+ * Scan elements of ARGV for option characters given in OPTSTRING.
+ *
+ * If an element of ARGV starts with '-', and is not exactly "-" or "--",
+ * then it is an option element. The characters of this element
+ * (aside from the initial '-') are option characters. If `getopt'
+ * is called repeatedly, it returns successively each of the option characters
+ * from each of the option elements.
+ *
+ * If `getopt' finds another option character, it returns that character,
+ * updating `custom_optind' and `nextchar' so that the next call to `getopt' can
+ * resume the scan with the following option character or ARGV-element.
+ *
+ * If there are no more option characters, `getopt' returns -1.
+ * Then `custom_optind' is the index in ARGV of the first ARGV-element
+ * that is not an option. (The ARGV-elements have been permuted
+ * so that those that are not options now come last.)
+ *
+ * OPTSTRING is a string containing the legitimate option characters.
+ * If an option character is seen that is not listed in OPTSTRING,
+ * return '?' after printing an error message. If you set `custom_opterr' to
+ * zero, the error message is suppressed but we still return '?'.
+ *
+ * If a char in OPTSTRING is followed by a colon, that means it wants an arg,
+ * so the following text in the same ARGV-element, or the text of the following
+ * ARGV-element, is returned in `custom_optarg'. Two colons mean an option that
+ * wants an optional arg; if there is text in the current ARGV-element,
+ * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero.
+ *
+ * If OPTSTRING starts with `-' or `+', it requests different methods of
+ * handling the non-option ARGV-elements.
+ * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
+ *
+ * Long-named options begin with `--' instead of `-'.
+ * Their names may be abbreviated as long as the abbreviation is unique
+ * or is an exact match for some defined option. If they have an
+ * argument, it follows the option name in the same ARGV-element, separated
+ * from the option name by a `=', or else the in next ARGV-element.
+ * When `getopt' finds a long-named option, it returns 0 if that option's
+ * `flag' field is nonzero, the value of the option's `val' field
+ * if the `flag' field is zero.
+ *
+ * The elements of ARGV aren't really const, because we permute them.
+ * But we pretend they're const in the prototype to be compatible
+ * with other systems.
+ *
+ * LONGOPTS is a vector of `struct option' terminated by an
+ * element containing a name which is zero.
+ *
+ * LONGIND returns the index in LONGOPT of the long-named option found.
+ * It is only valid when a long-named option has been found by the most
+ * recent call.
+ *
+ * Return the option character from OPTS just read. Return -1 when there are
+ * no more options. For unrecognized options, or options missing arguments,
+ * `custom_optopt' is set to the option letter, and '?' is returned.
+ *
+ * The OPTS string is a list of characters which are recognized option letters,
+ * optionally followed by colons, specifying that that letter takes an
+ * argument, to be placed in `custom_optarg'.
+ *
+ * If a letter in OPTS is followed by two colons, its argument is optional.
+ * This behavior is specific to the GNU `getopt'.
+ *
+ * The argument `--' causes premature termination of argument scanning,
+ * explicitly telling `getopt' that there are no more options. If OPTS begins
+ * with `--', then non-option arguments are treated as arguments to the option
+ * '\0'. This behavior is specific to the GNU `getopt'.
+ */
+
+static int getopt_internal_r(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ struct custom_getopt_data *d)
+{
+ int ret, print_errors = d->custom_opterr;
+
+ if (optstring[0] == ':')
+ print_errors = 0;
+ if (argc < 1)
+ return -1;
+ d->custom_optarg = NULL;
+
+ /*
+ * This is a big difference with GNU getopt, since optind == 0
+ * means initialization while here 1 means first call.
+ */
+ if (d->custom_optind == 0 || !d->initialized) {
+ if (d->custom_optind == 0)
+ d->custom_optind = 1; /* Don't scan ARGV[0], the program name. */
+ custom_getopt_initialize(d);
+ }
+ if (d->nextchar == NULL || *d->nextchar == '\0') {
+ ret = shuffle_argv(argc, argv, longopts, d);
+ if (ret)
+ return ret;
+ }
+ if (longopts && (argv[d->custom_optind][1] == '-' ))
+ return check_long_opt(argc, argv, optstring, longopts,
+ longind, print_errors, d);
+ return check_short_opt(argc, argv, optstring, print_errors, d);
+}
+
+static int custom_getopt_internal(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind)
+{
+ int result;
+ /* Keep a global copy of all internal members of d */
+ static struct custom_getopt_data d;
+
+ d.custom_optind = custom_optind;
+ d.custom_opterr = custom_opterr;
+ result = getopt_internal_r(argc, argv, optstring, longopts,
+ longind, &d);
+ custom_optind = d.custom_optind;
+ custom_optarg = d.custom_optarg;
+ custom_optopt = d.custom_optopt;
+ return result;
+}
+
+static int custom_getopt_long (int argc, char *const *argv, const char *options,
+ const struct option *long_options, int *opt_index)
+{
+ return custom_getopt_internal(argc, argv, options, long_options,
+ opt_index);
+}
+
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_clitkConnectedComponentLabeling_params.check_ambiguity
+ * @param override @see cmdline_parser_clitkConnectedComponentLabeling_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+static
+int update_arg(void *field, char **orig_field,
+ unsigned int *field_given, unsigned int *prev_given,
+ char *value, char *possible_values[], const char *default_value,
+ cmdline_parser_clitkConnectedComponentLabeling_arg_type arg_type,
+ int check_ambiguity, int override,
+ int no_free, int multiple_option,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *stop_char = 0;
+ const char *val = value;
+ int found;
+ char **string_field;
+
+ stop_char = 0;
+ found = 0;
+
+ if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+ {
+ if (short_opt != '-')
+ fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
+ package_name, long_opt, short_opt,
+ (additional_error ? additional_error : ""));
+ else
+ fprintf (stderr, "%s: `--%s' option given more than once%s\n",
+ package_name, long_opt,
+ (additional_error ? additional_error : ""));
+ return 1; /* failure */
+ }
+
+
+ if (field_given && *field_given && ! override)
+ return 0;
+ if (prev_given)
+ (*prev_given)++;
+ if (field_given)
+ (*field_given)++;
+ if (possible_values)
+ val = possible_values[found];
+
+ switch(arg_type) {
+ case ARG_FLAG:
+ *((int *)field) = !*((int *)field);
+ break;
+ case ARG_INT:
+ if (val) *((int *)field) = strtol (val, &stop_char, 0);
+ break;
+ case ARG_STRING:
+ if (val) {
+ string_field = (char **)field;
+ if (!no_free && *string_field)
+ free (*string_field); /* free previous string */
+ *string_field = gengetopt_strdup (val);
+ }
+ break;
+ default:
+ break;
+ };
+
+ /* check numeric conversion */
+ switch(arg_type) {
+ case ARG_INT:
+ if (val && !(stop_char && *stop_char == '\0')) {
+ fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+ return 1; /* failure */
+ }
+ break;
+ default:
+ ;
+ };
+
+ /* store the original value */
+ switch(arg_type) {
+ case ARG_NO:
+ case ARG_FLAG:
+ break;
+ default:
+ if (value && orig_field) {
+ if (no_free) {
+ *orig_field = value;
+ } else {
+ if (*orig_field)
+ free (*orig_field); /* free previous string */
+ *orig_field = gengetopt_strdup (value);
+ }
+ }
+ };
+
+ return 0; /* OK */
+}
+
+
+int
+cmdline_parser_clitkConnectedComponentLabeling_internal (int argc, char * const *argv, struct args_info_clitkConnectedComponentLabeling *args_info,
+ struct cmdline_parser_clitkConnectedComponentLabeling_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+
+ int error = 0;
+ struct args_info_clitkConnectedComponentLabeling local_args_info;
+
+ int override;
+ int initialize;
+ int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+ check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+ cmdline_parser_clitkConnectedComponentLabeling_init (args_info);
+
+ cmdline_parser_clitkConnectedComponentLabeling_init (&local_args_info);
+
+ optarg = 0;
+ optind = 0;
+ opterr = params->print_errors;
+ optopt = '?';
+
+ while (1)
+ {
+ int option_index = 0;
+
+ static struct option long_options[] = {
+ { "help", 0, NULL, 'h' },
+ { "version", 0, NULL, 'V' },
+ { "config", 1, NULL, 0 },
+ { "verbose", 0, NULL, 'v' },
+ { "imagetypes", 0, NULL, 0 },
+ { "verboseOption", 0, NULL, 0 },
+ { "input", 1, NULL, 'i' },
+ { "inputBG", 1, NULL, 0 },
+ { "output", 1, NULL, 'o' },
+ { "minSize", 1, NULL, 0 },
+ { "full", 0, NULL, 0 },
+ { NULL, 0, NULL, 0 }
+ };
+
+ custom_optarg = optarg;
+ custom_optind = optind;
+ custom_opterr = opterr;
+ custom_optopt = optopt;
+
+ c = custom_getopt_long (argc, argv, "hVvi:o:", long_options, &option_index);
+
+ optarg = custom_optarg;
+ optind = custom_optind;
+ opterr = custom_opterr;
+ optopt = custom_optopt;
+
+ if (c == -1) break; /* Exit from `while (1)' loop. */
+
+ switch (c)
+ {
+ case 'h': /* Print help and exit. */
+ cmdline_parser_clitkConnectedComponentLabeling_print_help ();
+ cmdline_parser_clitkConnectedComponentLabeling_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'V': /* Print version and exit. */
+ cmdline_parser_clitkConnectedComponentLabeling_print_version ();
+ cmdline_parser_clitkConnectedComponentLabeling_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'v': /* Verbose. */
+
+
+ if (update_arg((void *)&(args_info->verbose_flag), 0, &(args_info->verbose_given),
+ &(local_args_info.verbose_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verbose", 'v',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'i': /* Input image filename. */
+
+
+ if (update_arg( (void *)&(args_info->input_arg),
+ &(args_info->input_orig), &(args_info->input_given),
+ &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "input", 'i',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'o': /* Output filename. */
+
+
+ if (update_arg( (void *)&(args_info->output_arg),
+ &(args_info->output_orig), &(args_info->output_given),
+ &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "output", 'o',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ /* Config file. */
+ if (strcmp (long_options[option_index].name, "config") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->config_arg),
+ &(args_info->config_orig), &(args_info->config_given),
+ &(local_args_info.config_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "config", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Display allowed image types. */
+ else if (strcmp (long_options[option_index].name, "imagetypes") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->imagetypes_flag), 0, &(args_info->imagetypes_given),
+ &(local_args_info.imagetypes_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "imagetypes", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Display options values. */
+ else if (strcmp (long_options[option_index].name, "verboseOption") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->verboseOption_flag), 0, &(args_info->verboseOption_given),
+ &(local_args_info.verboseOption_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verboseOption", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Input Background. */
+ else if (strcmp (long_options[option_index].name, "inputBG") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->inputBG_arg),
+ &(args_info->inputBG_orig), &(args_info->inputBG_given),
+ &(local_args_info.inputBG_given), optarg, 0, "0", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "inputBG", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Minimum component size in voxels. */
+ else if (strcmp (long_options[option_index].name, "minSize") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->minSize_arg),
+ &(args_info->minSize_orig), &(args_info->minSize_given),
+ &(local_args_info.minSize_given), optarg, 0, "100", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "minSize", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Full connecticity. */
+ else if (strcmp (long_options[option_index].name, "full") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->full_flag), 0, &(args_info->full_given),
+ &(local_args_info.full_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "full", '-',
+ additional_error))
+ goto failure;
+
+ }
+
+ break;
+ case '?': /* Invalid option. */
+ /* `getopt_long' already printed an error message. */
+ goto failure;
+
+ default: /* bug: option not considered. */
+ fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+
+
+ if (check_required)
+ {
+ error += cmdline_parser_clitkConnectedComponentLabeling_required2 (args_info, argv[0], additional_error);
+ }
+
+ cmdline_parser_clitkConnectedComponentLabeling_release (&local_args_info);
+
+ if ( error )
+ return (EXIT_FAILURE);
+
+ if (optind < argc)
+ {
+ int i = 0 ;
+ int found_prog_name = 0;
+ /* whether program name, i.e., argv[0], is in the remaining args
+ (this may happen with some implementations of getopt,
+ but surely not with the one included by gengetopt) */
+
+
+ args_info->inputs_num = argc - optind - found_prog_name;
+ args_info->inputs =
+ (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+ while (optind < argc)
+ args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
+ }
+
+ return 0;
+
+failure:
+
+ cmdline_parser_clitkConnectedComponentLabeling_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
+
+#ifndef CONFIG_FILE_LINE_SIZE
+#define CONFIG_FILE_LINE_SIZE 2048
+#endif
+#define ADDITIONAL_ERROR " in configuration file "
+
+#define CONFIG_FILE_LINE_BUFFER_SIZE (CONFIG_FILE_LINE_SIZE+3)
+/* 3 is for "--" and "=" */
+
+static int
+_cmdline_parser_clitkConnectedComponentLabeling_configfile (char * const filename, int *my_argc)
+{
+ FILE* file;
+ char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
+ char linebuf[CONFIG_FILE_LINE_SIZE];
+ int line_num = 0;
+ int result = 0, equal;
+ char *fopt, *farg;
+ char *str_index;
+ size_t len, next_token;
+ char delimiter;
+
+ if ((file = fopen(filename, "r")) == NULL)
+ {
+ fprintf (stderr, "%s: Error opening configuration file '%s'\n",
+ CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
+ {
+ ++line_num;
+ my_argv[0] = '\0';
+ len = strlen(linebuf);
+ if (len > (CONFIG_FILE_LINE_BUFFER_SIZE-1))
+ {
+ fprintf (stderr, "%s:%s:%d: Line too long in configuration file\n",
+ CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+
+ /* find first non-whitespace character in the line */
+ next_token = strspn (linebuf, " \t\r\n");
+ str_index = linebuf + next_token;
+
+ if ( str_index[0] == '\0' || str_index[0] == '#')
+ continue; /* empty line or comment line is skipped */
+
+ fopt = str_index;
+
+ /* truncate fopt at the end of the first non-valid character */
+ next_token = strcspn (fopt, " \t\r\n=");
+
+ if (fopt[next_token] == '\0') /* the line is over */
+ {
+ farg = NULL;
+ equal = 0;
+ goto noarg;
+ }
+
+ /* remember if equal sign is present */
+ equal = (fopt[next_token] == '=');
+ fopt[next_token++] = '\0';
+
+ /* advance pointers to the next token after the end of fopt */
+ next_token += strspn (fopt + next_token, " \t\r\n");
+
+ /* check for the presence of equal sign, and if so, skip it */
+ if ( !equal )
+ if ((equal = (fopt[next_token] == '=')))
+ {
+ next_token++;
+ next_token += strspn (fopt + next_token, " \t\r\n");
+ }
+ str_index += next_token;
+
+ /* find argument */
+ farg = str_index;
+ if ( farg[0] == '\"' || farg[0] == '\'' )
+ { /* quoted argument */
+ str_index = strchr (++farg, str_index[0] ); /* skip opening quote */
+ if (! str_index)
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: unterminated string in configuration file\n",
+ CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+ else
+ { /* read up the remaining part up to a delimiter */
+ next_token = strcspn (farg, " \t\r\n#\'\"");
+ str_index += next_token;
+ }
+
+ /* truncate farg at the delimiter and store it for further check */
+ delimiter = *str_index, *str_index++ = '\0';
+
+ /* everything but comment is illegal at the end of line */
+ if (delimiter != '\0' && delimiter != '#')
+ {
+ str_index += strspn(str_index, " \t\r\n");
+ if (*str_index != '\0' && *str_index != '#')
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: malformed string in configuration file\n",
+ CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+
+ noarg:
+ if (!strcmp(fopt,"include")) {
+ if (farg && *farg) {
+ result = _cmdline_parser_clitkConnectedComponentLabeling_configfile(farg, my_argc);
+ } else {
+ fprintf(stderr, "%s:%s:%d: include requires a filename argument.\n",
+ CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE, filename, line_num);
+ }
+ continue;
+ }
+ len = strlen(fopt);
+ strcat (my_argv, len > 1 ? "--" : "-");
+ strcat (my_argv, fopt);
+ if (len > 1 && ((farg && *farg) || equal))
+ strcat (my_argv, "=");
+ if (farg && *farg)
+ strcat (my_argv, farg);
+ ++(*my_argc);
+
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup(my_argv);
+ } /* while */
+
+ if (file)
+ fclose(file);
+ return result;
+}
+
+int
+cmdline_parser_clitkConnectedComponentLabeling_configfile (char * const filename,
+ struct args_info_clitkConnectedComponentLabeling *args_info,
+ int override, int initialize, int check_required)
+{
+ struct cmdline_parser_clitkConnectedComponentLabeling_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ return cmdline_parser_clitkConnectedComponentLabeling_config_file (filename, args_info, ¶ms);
+}
+
+int
+cmdline_parser_clitkConnectedComponentLabeling_config_file (char * const filename,
+ struct args_info_clitkConnectedComponentLabeling *args_info,
+ struct cmdline_parser_clitkConnectedComponentLabeling_params *params)
+{
+ int i, result;
+ int my_argc = 1;
+ char **my_argv_arg;
+ char *additional_error;
+
+ /* store the program name */
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup (CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE);
+
+ result = _cmdline_parser_clitkConnectedComponentLabeling_configfile(filename, &my_argc);
+
+ if (result != EXIT_FAILURE) {
+ my_argv_arg = (char **) malloc((my_argc+1) * sizeof(char *));
+ cmd_line_list_tmp = cmd_line_list;
+
+ for (i = my_argc - 1; i >= 0; --i) {
+ my_argv_arg[i] = cmd_line_list_tmp->string_arg;
+ cmd_line_list_tmp = cmd_line_list_tmp->next;
+ }
+
+ my_argv_arg[my_argc] = 0;
+
+ additional_error = (char *)malloc(strlen(filename) + strlen(ADDITIONAL_ERROR) + 1);
+ strcpy (additional_error, ADDITIONAL_ERROR);
+ strcat (additional_error, filename);
+ result =
+ cmdline_parser_clitkConnectedComponentLabeling_internal (my_argc, my_argv_arg, args_info,
+ params,
+ additional_error);
+
+ free (additional_error);
+ free (my_argv_arg);
+ }
+
+ free_cmd_list();
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkConnectedComponentLabeling_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
--- /dev/null
+/** @file clitkConnectedComponentLabeling_ggo.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CLITKCONNECTEDCOMPONENTLABELING_GGO_H
+#define CLITKCONNECTEDCOMPONENTLABELING_GGO_H
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE
+/** @brief the program name */
+#define CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_PACKAGE "clitkConnectedComponentLabeling"
+#endif
+
+#ifndef CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_CLITKCONNECTEDCOMPONENTLABELING_VERSION "1.0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct args_info_clitkConnectedComponentLabeling
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ char * config_arg; /**< @brief Config file. */
+ char * config_orig; /**< @brief Config file original value given at command line. */
+ const char *config_help; /**< @brief Config file help description. */
+ int verbose_flag; /**< @brief Verbose (default=off). */
+ const char *verbose_help; /**< @brief Verbose help description. */
+ int imagetypes_flag; /**< @brief Display allowed image types (default=off). */
+ const char *imagetypes_help; /**< @brief Display allowed image types help description. */
+ int verboseOption_flag; /**< @brief Display options values (default=off). */
+ const char *verboseOption_help; /**< @brief Display options values help description. */
+ char * input_arg; /**< @brief Input image filename. */
+ char * input_orig; /**< @brief Input image filename original value given at command line. */
+ const char *input_help; /**< @brief Input image filename help description. */
+ int inputBG_arg; /**< @brief Input Background (default='0'). */
+ char * inputBG_orig; /**< @brief Input Background original value given at command line. */
+ const char *inputBG_help; /**< @brief Input Background help description. */
+ char * output_arg; /**< @brief Output filename. */
+ char * output_orig; /**< @brief Output filename original value given at command line. */
+ const char *output_help; /**< @brief Output filename help description. */
+ int minSize_arg; /**< @brief Minimum component size in voxels (default='100'). */
+ char * minSize_orig; /**< @brief Minimum component size in voxels original value given at command line. */
+ const char *minSize_help; /**< @brief Minimum component size in voxels help description. */
+ int full_flag; /**< @brief Full connecticity (default=off). */
+ const char *full_help; /**< @brief Full connecticity help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int config_given ; /**< @brief Whether config was given. */
+ unsigned int verbose_given ; /**< @brief Whether verbose was given. */
+ unsigned int imagetypes_given ; /**< @brief Whether imagetypes was given. */
+ unsigned int verboseOption_given ; /**< @brief Whether verboseOption was given. */
+ unsigned int input_given ; /**< @brief Whether input was given. */
+ unsigned int inputBG_given ; /**< @brief Whether inputBG was given. */
+ unsigned int output_given ; /**< @brief Whether output was given. */
+ unsigned int minSize_given ; /**< @brief Whether minSize was given. */
+ unsigned int full_given ; /**< @brief Whether full was given. */
+
+ char **inputs ; /**< @brief unamed options (options without names) */
+ unsigned inputs_num ; /**< @brief unamed options number */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_clitkConnectedComponentLabeling_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure args_info_clitkConnectedComponentLabeling (default 1) */
+ int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+ int check_ambiguity; /**< @brief whether to check for options already specified in the option structure args_info_clitkConnectedComponentLabeling (default 0) */
+ int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *args_info_clitkConnectedComponentLabeling_purpose;
+/** @brief the usage string of the program */
+extern const char *args_info_clitkConnectedComponentLabeling_usage;
+/** @brief all the lines making the help output */
+extern const char *args_info_clitkConnectedComponentLabeling_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkConnectedComponentLabeling (int argc, char * const *argv,
+ struct args_info_clitkConnectedComponentLabeling *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkConnectedComponentLabeling_ext() instead
+ */
+int cmdline_parser_clitkConnectedComponentLabeling2 (int argc, char * const *argv,
+ struct args_info_clitkConnectedComponentLabeling *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkConnectedComponentLabeling_ext (int argc, char * const *argv,
+ struct args_info_clitkConnectedComponentLabeling *args_info,
+ struct cmdline_parser_clitkConnectedComponentLabeling_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkConnectedComponentLabeling_dump(FILE *outfile,
+ struct args_info_clitkConnectedComponentLabeling *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkConnectedComponentLabeling_file_save(const char *filename,
+ struct args_info_clitkConnectedComponentLabeling *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_clitkConnectedComponentLabeling_print_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_clitkConnectedComponentLabeling_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_clitkConnectedComponentLabeling_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_clitkConnectedComponentLabeling_params_init(struct cmdline_parser_clitkConnectedComponentLabeling_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_clitkConnectedComponentLabeling_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_clitkConnectedComponentLabeling_params structure
+ */
+struct cmdline_parser_clitkConnectedComponentLabeling_params *cmdline_parser_clitkConnectedComponentLabeling_params_create(void);
+
+/**
+ * Initializes the passed args_info_clitkConnectedComponentLabeling structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_clitkConnectedComponentLabeling_init (struct args_info_clitkConnectedComponentLabeling *args_info);
+/**
+ * Deallocates the string fields of the args_info_clitkConnectedComponentLabeling structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_clitkConnectedComponentLabeling_free (struct args_info_clitkConnectedComponentLabeling *args_info);
+
+/**
+ * The config file parser (deprecated version)
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkConnectedComponentLabeling_config_file() instead
+ */
+int cmdline_parser_clitkConnectedComponentLabeling_configfile (char * const filename,
+ struct args_info_clitkConnectedComponentLabeling *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The config file parser
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkConnectedComponentLabeling_config_file (char * const filename,
+ struct args_info_clitkConnectedComponentLabeling *args_info,
+ struct cmdline_parser_clitkConnectedComponentLabeling_params *params);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ * possible errors
+ * @return
+ */
+int cmdline_parser_clitkConnectedComponentLabeling_required (struct args_info_clitkConnectedComponentLabeling *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CLITKCONNECTEDCOMPONENTLABELING_GGO_H */
--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22
+ generated with the following command:
+ /usr/local/bin/gengetopt --output-dir=/home/tbaudier/vv/vv_static/vv/vv_bin/tools --arg-struct-name=args_info_clitkCropImage --func-name=cmdline_parser_clitkCropImage --file-name=clitkCropImage_ggo --unamed-opts --conf-parser --include-getopt
+
+ The developers of gengetopt consider the fixed text that goes in all
+ gengetopt output files to be in the public domain:
+ we make no copyright claims on it.
+*/
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+
+#include "clitkCropImage_ggo.h"
+
+const char *args_info_clitkCropImage_purpose = "Crop an image according to a given extends or AutoCrop with a background value \nor like another image";
+
+const char *args_info_clitkCropImage_usage = "Usage: clitkCropImage [OPTIONS]... [FILES]...";
+
+const char *args_info_clitkCropImage_description = "";
+
+const char *args_info_clitkCropImage_help[] = {
+ " -h, --help Print help and exit",
+ " -V, --version Print version and exit",
+ " --config=STRING Config file",
+ " --imagetypes Display allowed image types (default=off)",
+ " -v, --verbose Verbose (default=off)",
+ " --verboseOption Display options values (default=off)",
+ " --verboseWarningOff Do not display warning (default=off)",
+ "\nI/O:",
+ " -i, --input=STRING Input image filename",
+ " -o, --output=STRING Output image filename",
+ "\nUsed determined crop:",
+ " -b, --boundingBox=INT Bounding box of the crop region (in 3D: \n =x1,x2,y1,y2,z1,z2)",
+ " -l, --lower=INT Size of the lower crop region (multiple values)",
+ " -u, --upper=INT Size of the upper crop region (multiple values)",
+ " --origin Set new origin to zero (default=off)",
+ "\nAutoCrop with BG value:",
+ " --BG=DOUBLE Background value in input. (default=`0')",
+ "\nCrop like another image:",
+ " --like=STRING Crop like this image (must have the same spacing",
+ " --BGLike=DOUBLE Background value in output (if like larger) \n (default=`0')",
+ 0
+};
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_INT
+ , ARG_DOUBLE
+} cmdline_parser_clitkCropImage_arg_type;
+
+static
+void clear_given (struct args_info_clitkCropImage *args_info);
+static
+void clear_args (struct args_info_clitkCropImage *args_info);
+
+static int
+cmdline_parser_clitkCropImage_internal (int argc, char * const *argv, struct args_info_clitkCropImage *args_info,
+ struct cmdline_parser_clitkCropImage_params *params, const char *additional_error);
+
+static int
+cmdline_parser_clitkCropImage_required2 (struct args_info_clitkCropImage *args_info, const char *prog_name, const char *additional_error);
+struct line_list
+{
+ char * string_arg;
+ struct line_list * next;
+};
+
+static struct line_list *cmd_line_list = 0;
+static struct line_list *cmd_line_list_tmp = 0;
+
+static void
+free_cmd_list(void)
+{
+ /* free the list of a previous call */
+ if (cmd_line_list)
+ {
+ while (cmd_line_list) {
+ cmd_line_list_tmp = cmd_line_list;
+ cmd_line_list = cmd_line_list->next;
+ free (cmd_line_list_tmp->string_arg);
+ free (cmd_line_list_tmp);
+ }
+ }
+}
+
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct args_info_clitkCropImage *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->config_given = 0 ;
+ args_info->imagetypes_given = 0 ;
+ args_info->verbose_given = 0 ;
+ args_info->verboseOption_given = 0 ;
+ args_info->verboseWarningOff_given = 0 ;
+ args_info->input_given = 0 ;
+ args_info->output_given = 0 ;
+ args_info->boundingBox_given = 0 ;
+ args_info->lower_given = 0 ;
+ args_info->upper_given = 0 ;
+ args_info->origin_given = 0 ;
+ args_info->BG_given = 0 ;
+ args_info->like_given = 0 ;
+ args_info->BGLike_given = 0 ;
+}
+
+static
+void clear_args (struct args_info_clitkCropImage *args_info)
+{
+ args_info->config_arg = NULL;
+ args_info->config_orig = NULL;
+ args_info->imagetypes_flag = 0;
+ args_info->verbose_flag = 0;
+ args_info->verboseOption_flag = 0;
+ args_info->verboseWarningOff_flag = 0;
+ args_info->input_arg = NULL;
+ args_info->input_orig = NULL;
+ args_info->output_arg = NULL;
+ args_info->output_orig = NULL;
+ args_info->boundingBox_arg = NULL;
+ args_info->boundingBox_orig = NULL;
+ args_info->lower_arg = NULL;
+ args_info->lower_orig = NULL;
+ args_info->upper_arg = NULL;
+ args_info->upper_orig = NULL;
+ args_info->origin_flag = 0;
+ args_info->BG_arg = 0;
+ args_info->BG_orig = NULL;
+ args_info->like_arg = NULL;
+ args_info->like_orig = NULL;
+ args_info->BGLike_arg = 0;
+ args_info->BGLike_orig = NULL;
+
+}
+
+static
+void init_args_info(struct args_info_clitkCropImage *args_info)
+{
+
+
+ args_info->help_help = args_info_clitkCropImage_help[0] ;
+ args_info->version_help = args_info_clitkCropImage_help[1] ;
+ args_info->config_help = args_info_clitkCropImage_help[2] ;
+ args_info->imagetypes_help = args_info_clitkCropImage_help[3] ;
+ args_info->verbose_help = args_info_clitkCropImage_help[4] ;
+ args_info->verboseOption_help = args_info_clitkCropImage_help[5] ;
+ args_info->verboseWarningOff_help = args_info_clitkCropImage_help[6] ;
+ args_info->input_help = args_info_clitkCropImage_help[8] ;
+ args_info->output_help = args_info_clitkCropImage_help[9] ;
+ args_info->boundingBox_help = args_info_clitkCropImage_help[11] ;
+ args_info->boundingBox_min = -1;
+ args_info->boundingBox_max = -1;
+ args_info->lower_help = args_info_clitkCropImage_help[12] ;
+ args_info->lower_min = -1;
+ args_info->lower_max = -1;
+ args_info->upper_help = args_info_clitkCropImage_help[13] ;
+ args_info->upper_min = -1;
+ args_info->upper_max = -1;
+ args_info->origin_help = args_info_clitkCropImage_help[14] ;
+ args_info->BG_help = args_info_clitkCropImage_help[16] ;
+ args_info->like_help = args_info_clitkCropImage_help[18] ;
+ args_info->BGLike_help = args_info_clitkCropImage_help[19] ;
+
+}
+
+void
+cmdline_parser_clitkCropImage_print_version (void)
+{
+ printf ("%s %s\n", CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE, CMDLINE_PARSER_CLITKCROPIMAGE_VERSION);
+}
+
+static void print_help_common(void) {
+ cmdline_parser_clitkCropImage_print_version ();
+
+ if (strlen(args_info_clitkCropImage_purpose) > 0)
+ printf("\n%s\n", args_info_clitkCropImage_purpose);
+
+ if (strlen(args_info_clitkCropImage_usage) > 0)
+ printf("\n%s\n", args_info_clitkCropImage_usage);
+
+ printf("\n");
+
+ if (strlen(args_info_clitkCropImage_description) > 0)
+ printf("%s\n", args_info_clitkCropImage_description);
+}
+
+void
+cmdline_parser_clitkCropImage_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (args_info_clitkCropImage_help[i])
+ printf("%s\n", args_info_clitkCropImage_help[i++]);
+}
+
+void
+cmdline_parser_clitkCropImage_init (struct args_info_clitkCropImage *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+
+ args_info->inputs = NULL;
+ args_info->inputs_num = 0;
+}
+
+void
+cmdline_parser_clitkCropImage_params_init(struct cmdline_parser_clitkCropImage_params *params)
+{
+ if (params)
+ {
+ params->override = 0;
+ params->initialize = 1;
+ params->check_required = 1;
+ params->check_ambiguity = 0;
+ params->print_errors = 1;
+ }
+}
+
+struct cmdline_parser_clitkCropImage_params *
+cmdline_parser_clitkCropImage_params_create(void)
+{
+ struct cmdline_parser_clitkCropImage_params *params =
+ (struct cmdline_parser_clitkCropImage_params *)malloc(sizeof(struct cmdline_parser_clitkCropImage_params));
+ cmdline_parser_clitkCropImage_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+/** @brief generic value variable */
+union generic_value {
+ int int_arg;
+ double double_arg;
+ char *string_arg;
+};
+
+/** @brief holds temporary values for multiple options */
+struct generic_list
+{
+ union generic_value arg;
+ char *orig;
+ struct generic_list *next;
+};
+
+/**
+ * @brief add a node at the head of the list
+ */
+static void add_node(struct generic_list **list) {
+ struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list));
+ new_node->next = *list;
+ *list = new_node;
+ new_node->arg.string_arg = NULL;
+ new_node->orig = NULL;
+}
+
+static void
+free_multiple_field(unsigned int len, void **arg, char ***orig)
+{
+ unsigned int i;
+ if (*arg) {
+ for (i = 0; i < len; ++i)
+ {
+ free_string_field(&((*orig)[i]));
+ }
+
+ free (*arg);
+ *arg = 0;
+ free (*orig);
+ *orig = 0;
+ }
+}
+
+
+static void
+cmdline_parser_clitkCropImage_release (struct args_info_clitkCropImage *args_info)
+{
+ unsigned int i;
+ free_string_field (&(args_info->config_arg));
+ free_string_field (&(args_info->config_orig));
+ free_string_field (&(args_info->input_arg));
+ free_string_field (&(args_info->input_orig));
+ free_string_field (&(args_info->output_arg));
+ free_string_field (&(args_info->output_orig));
+ free_multiple_field (args_info->boundingBox_given, (void **)&(args_info->boundingBox_arg), &(args_info->boundingBox_orig));
+ free_multiple_field (args_info->lower_given, (void **)&(args_info->lower_arg), &(args_info->lower_orig));
+ free_multiple_field (args_info->upper_given, (void **)&(args_info->upper_arg), &(args_info->upper_orig));
+ free_string_field (&(args_info->BG_orig));
+ free_string_field (&(args_info->like_arg));
+ free_string_field (&(args_info->like_orig));
+ free_string_field (&(args_info->BGLike_orig));
+
+
+ for (i = 0; i < args_info->inputs_num; ++i)
+ free (args_info->inputs [i]);
+
+ if (args_info->inputs_num)
+ free (args_info->inputs);
+
+ clear_given (args_info);
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+ if (arg) {
+ fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+ } else {
+ fprintf(outfile, "%s\n", opt);
+ }
+}
+
+static void
+write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, char *values[])
+{
+ int i;
+
+ for (i = 0; i < len; ++i)
+ write_into_file(outfile, opt, (arg ? arg[i] : 0), values);
+}
+
+int
+cmdline_parser_clitkCropImage_dump(FILE *outfile, struct args_info_clitkCropImage *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE);
+ return EXIT_FAILURE;
+ }
+
+ if (args_info->help_given)
+ write_into_file(outfile, "help", 0, 0 );
+ if (args_info->version_given)
+ write_into_file(outfile, "version", 0, 0 );
+ if (args_info->config_given)
+ write_into_file(outfile, "config", args_info->config_orig, 0);
+ if (args_info->imagetypes_given)
+ write_into_file(outfile, "imagetypes", 0, 0 );
+ if (args_info->verbose_given)
+ write_into_file(outfile, "verbose", 0, 0 );
+ if (args_info->verboseOption_given)
+ write_into_file(outfile, "verboseOption", 0, 0 );
+ if (args_info->verboseWarningOff_given)
+ write_into_file(outfile, "verboseWarningOff", 0, 0 );
+ if (args_info->input_given)
+ write_into_file(outfile, "input", args_info->input_orig, 0);
+ if (args_info->output_given)
+ write_into_file(outfile, "output", args_info->output_orig, 0);
+ write_multiple_into_file(outfile, args_info->boundingBox_given, "boundingBox", args_info->boundingBox_orig, 0);
+ write_multiple_into_file(outfile, args_info->lower_given, "lower", args_info->lower_orig, 0);
+ write_multiple_into_file(outfile, args_info->upper_given, "upper", args_info->upper_orig, 0);
+ if (args_info->origin_given)
+ write_into_file(outfile, "origin", 0, 0 );
+ if (args_info->BG_given)
+ write_into_file(outfile, "BG", args_info->BG_orig, 0);
+ if (args_info->like_given)
+ write_into_file(outfile, "like", args_info->like_orig, 0);
+ if (args_info->BGLike_given)
+ write_into_file(outfile, "BGLike", args_info->BGLike_orig, 0);
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+cmdline_parser_clitkCropImage_file_save(const char *filename, struct args_info_clitkCropImage *args_info)
+{
+ FILE *outfile;
+ int i = 0;
+
+ outfile = fopen(filename, "w");
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = cmdline_parser_clitkCropImage_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+cmdline_parser_clitkCropImage_free (struct args_info_clitkCropImage *args_info)
+{
+ cmdline_parser_clitkCropImage_release (args_info);
+}
+
+/** @brief replacement of strdup, which is not standard */
+char *
+gengetopt_strdup (const char *s)
+{
+ char *result = NULL;
+ if (!s)
+ return result;
+
+ result = (char*)malloc(strlen(s) + 1);
+ if (result == (char*)0)
+ return (char*)0;
+ strcpy(result, s);
+ return result;
+}
+
+static char *
+get_multiple_arg_token(const char *arg)
+{
+ char *tok, *ret;
+ size_t len, num_of_escape, i, j;
+
+ if (!arg)
+ return NULL;
+
+ tok = strchr (arg, ',');
+ num_of_escape = 0;
+
+ /* make sure it is not escaped */
+ while (tok)
+ {
+ if (*(tok-1) == '\\')
+ {
+ /* find the next one */
+ tok = strchr (tok+1, ',');
+ ++num_of_escape;
+ }
+ else
+ break;
+ }
+
+ if (tok)
+ len = (size_t)(tok - arg + 1);
+ else
+ len = strlen (arg) + 1;
+
+ len -= num_of_escape;
+
+ ret = (char *) malloc (len);
+
+ i = 0;
+ j = 0;
+ while (arg[i] && (j < len-1))
+ {
+ if (arg[i] == '\\' &&
+ arg[ i + 1 ] &&
+ arg[ i + 1 ] == ',')
+ ++i;
+
+ ret[j++] = arg[i++];
+ }
+
+ ret[len-1] = '\0';
+
+ return ret;
+}
+
+static char *
+get_multiple_arg_token_next(const char *arg)
+{
+ char *tok;
+
+ if (!arg)
+ return NULL;
+
+ tok = strchr (arg, ',');
+
+ /* make sure it is not escaped */
+ while (tok)
+ {
+ if (*(tok-1) == '\\')
+ {
+ /* find the next one */
+ tok = strchr (tok+1, ',');
+ }
+ else
+ break;
+ }
+
+ if (! tok || strlen(tok) == 1)
+ return 0;
+
+ return tok+1;
+}
+
+static int
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc);
+
+int
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc)
+{
+ int error = 0;
+
+ if (option_given && ! (min < 0 && max < 0))
+ {
+ if (min >= 0 && max >= 0)
+ {
+ if (min == max)
+ {
+ /* specific occurrences */
+ if (option_given != min)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be %d\n",
+ prog_name, option_desc, min);
+ error = 1;
+ }
+ }
+ else if (option_given < min
+ || option_given > max)
+ {
+ /* range occurrences */
+ fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n",
+ prog_name, option_desc, min, max);
+ error = 1;
+ }
+ }
+ else if (min >= 0)
+ {
+ /* at least check */
+ if (option_given < min)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be at least %d\n",
+ prog_name, option_desc, min);
+ error = 1;
+ }
+ }
+ else if (max >= 0)
+ {
+ /* at most check */
+ if (option_given > max)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be at most %d\n",
+ prog_name, option_desc, max);
+ error = 1;
+ }
+ }
+ }
+
+ return error;
+}
+int
+cmdline_parser_clitkCropImage (int argc, char * const *argv, struct args_info_clitkCropImage *args_info)
+{
+ return cmdline_parser_clitkCropImage2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+cmdline_parser_clitkCropImage_ext (int argc, char * const *argv, struct args_info_clitkCropImage *args_info,
+ struct cmdline_parser_clitkCropImage_params *params)
+{
+ int result;
+ result = cmdline_parser_clitkCropImage_internal (argc, argv, args_info, params, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkCropImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkCropImage2 (int argc, char * const *argv, struct args_info_clitkCropImage *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct cmdline_parser_clitkCropImage_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = cmdline_parser_clitkCropImage_internal (argc, argv, args_info, ¶ms, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkCropImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkCropImage_required (struct args_info_clitkCropImage *args_info, const char *prog_name)
+{
+ int result = EXIT_SUCCESS;
+
+ if (cmdline_parser_clitkCropImage_required2(args_info, prog_name, NULL) > 0)
+ result = EXIT_FAILURE;
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkCropImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkCropImage_required2 (struct args_info_clitkCropImage *args_info, const char *prog_name, const char *additional_error)
+{
+ int error = 0;
+
+ /* checks for required options */
+ if (! args_info->input_given)
+ {
+ fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (! args_info->output_given)
+ {
+ fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (check_multiple_option_occurrences(prog_name, args_info->boundingBox_given, args_info->boundingBox_min, args_info->boundingBox_max, "'--boundingBox' ('-b')"))
+ error = 1;
+
+ if (check_multiple_option_occurrences(prog_name, args_info->lower_given, args_info->lower_min, args_info->lower_max, "'--lower' ('-l')"))
+ error = 1;
+
+ if (check_multiple_option_occurrences(prog_name, args_info->upper_given, args_info->upper_min, args_info->upper_max, "'--upper' ('-u')"))
+ error = 1;
+
+
+ /* checks for dependences among options */
+
+ return error;
+}
+
+/*
+ * Extracted from the glibc source tree, version 2.3.6
+ *
+ * Licensed under the GPL as per the whole glibc source tree.
+ *
+ * This file was modified so that getopt_long can be called
+ * many times without risking previous memory to be spoiled.
+ *
+ * Modified by Andre Noll and Lorenzo Bettini for use in
+ * GNU gengetopt generated files.
+ *
+ */
+
+/*
+ * we must include anything we need since this file is not thought to be
+ * inserted in a file already using getopt.h
+ *
+ * Lorenzo
+ */
+
+struct option
+{
+ const char *name;
+ /* has_arg can't be an enum because some compilers complain about
+ type mismatches in all the code that assumes it is an int. */
+ int has_arg;
+ int *flag;
+ int val;
+};
+
+/* For communication from `getopt' to the caller.
+ When `getopt' finds an option that takes an argument,
+ the argument value is returned here.
+ Also, when `ordering' is RETURN_IN_ORDER,
+ each non-option ARGV-element is returned here. */
+
+static char *optarg;
+
+/* Index in ARGV of the next element to be scanned.
+ This is used for communication to and from the caller
+ and for communication between successive calls to `getopt'.
+
+ On entry to `getopt', zero means this is the first call; initialize.
+
+ When `getopt' returns -1, this is the index of the first of the
+ non-option elements that the caller should itself scan.
+
+ Otherwise, `optind' communicates from one call to the next
+ how much of ARGV has been scanned so far. */
+
+static int optind;
+
+/* Callers store zero here to inhibit the error message `getopt' prints
+ for unrecognized options. */
+
+static int opterr;
+
+/* Set to an option character which was unrecognized. */
+
+static int optopt;
+
+/* This version of `getopt' appears to the caller like standard Unix `getopt'
+ but it behaves differently for the user, since it allows the user
+ to intersperse the options with the other arguments.
+
+ As `getopt' works, it permutes the elements of ARGV so that,
+ when it is done, all the options precede everything else. Thus
+ all application programs are extended to handle flexible argument order.
+*/
+/*
+ If the field `flag' is not NULL, it points to a variable that is set
+ to the value given in the field `val' when the option is found, but
+ left unchanged if the option is not found.
+
+ To have a long-named option do something other than set an `int' to
+ a compiled-in constant, such as set a value from `custom_optarg', set the
+ option's `flag' field to zero and its `val' field to a nonzero
+ value (the equivalent single-letter option character, if there is
+ one). For long options that have a zero `flag' field, `getopt'
+ returns the contents of the `val' field. */
+
+/* Names for the values of the `has_arg' field of `struct option'. */
+#ifndef no_argument
+#define no_argument 0
+#endif
+
+#ifndef required_argument
+#define required_argument 1
+#endif
+
+#ifndef optional_argument
+#define optional_argument 2
+#endif
+
+struct custom_getopt_data {
+ /*
+ * These have exactly the same meaning as the corresponding global variables,
+ * except that they are used for the reentrant versions of getopt.
+ */
+ int custom_optind;
+ int custom_opterr;
+ int custom_optopt;
+ char *custom_optarg;
+
+ /* True if the internal members have been initialized. */
+ int initialized;
+
+ /*
+ * The next char to be scanned in the option-element in which the last option
+ * character we returned was found. This allows us to pick up the scan where
+ * we left off. If this is zero, or a null string, it means resume the scan by
+ * advancing to the next ARGV-element.
+ */
+ char *nextchar;
+
+ /*
+ * Describe the part of ARGV that contains non-options that have been skipped.
+ * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is
+ * the index after the last of them.
+ */
+ int first_nonopt;
+ int last_nonopt;
+};
+
+/*
+ * the variables optarg, optind, opterr and optopt are renamed with
+ * the custom_ prefix so that they don't interfere with getopt ones.
+ *
+ * Moreover they're static so they are visible only from within the
+ * file where this very file will be included.
+ */
+
+/*
+ * For communication from `custom_getopt' to the caller. When `custom_getopt' finds an
+ * option that takes an argument, the argument value is returned here.
+ */
+static char *custom_optarg;
+
+/*
+ * Index in ARGV of the next element to be scanned. This is used for
+ * communication to and from the caller and for communication between
+ * successive calls to `custom_getopt'.
+ *
+ * On entry to `custom_getopt', 1 means this is the first call; initialize.
+ *
+ * When `custom_getopt' returns -1, this is the index of the first of the non-option
+ * elements that the caller should itself scan.
+ *
+ * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV
+ * has been scanned so far.
+ *
+ * 1003.2 says this must be 1 before any call.
+ */
+static int custom_optind = 1;
+
+/*
+ * Callers store zero here to inhibit the error message for unrecognized
+ * options.
+ */
+static int custom_opterr = 1;
+
+/*
+ * Set to an option character which was unrecognized. This must be initialized
+ * on some systems to avoid linking in the system's own getopt implementation.
+ */
+static int custom_optopt = '?';
+
+/*
+ * Exchange two adjacent subsequences of ARGV. One subsequence is elements
+ * [first_nonopt,last_nonopt) which contains all the non-options that have been
+ * skipped so far. The other is elements [last_nonopt,custom_optind), which contains
+ * all the options processed since those non-options were skipped.
+ * `first_nonopt' and `last_nonopt' are relocated so that they describe the new
+ * indices of the non-options in ARGV after they are moved.
+ */
+static void exchange(char **argv, struct custom_getopt_data *d)
+{
+ int bottom = d->first_nonopt;
+ int middle = d->last_nonopt;
+ int top = d->custom_optind;
+ char *tem;
+
+ /*
+ * Exchange the shorter segment with the far end of the longer segment.
+ * That puts the shorter segment into the right place. It leaves the
+ * longer segment in the right place overall, but it consists of two
+ * parts that need to be swapped next.
+ */
+ while (top > middle && middle > bottom) {
+ if (top - middle > middle - bottom) {
+ /* Bottom segment is the short one. */
+ int len = middle - bottom;
+ int i;
+
+ /* Swap it with the top part of the top segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] =
+ argv[top - (middle - bottom) + i];
+ argv[top - (middle - bottom) + i] = tem;
+ }
+ /* Exclude the moved bottom segment from further swapping. */
+ top -= len;
+ } else {
+ /* Top segment is the short one. */
+ int len = top - middle;
+ int i;
+
+ /* Swap it with the bottom part of the bottom segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] = argv[middle + i];
+ argv[middle + i] = tem;
+ }
+ /* Exclude the moved top segment from further swapping. */
+ bottom += len;
+ }
+ }
+ /* Update records for the slots the non-options now occupy. */
+ d->first_nonopt += (d->custom_optind - d->last_nonopt);
+ d->last_nonopt = d->custom_optind;
+}
+
+/* Initialize the internal data when the first call is made. */
+static void custom_getopt_initialize(struct custom_getopt_data *d)
+{
+ /*
+ * Start processing options with ARGV-element 1 (since ARGV-element 0
+ * is the program name); the sequence of previously skipped non-option
+ * ARGV-elements is empty.
+ */
+ d->first_nonopt = d->last_nonopt = d->custom_optind;
+ d->nextchar = NULL;
+ d->initialized = 1;
+}
+
+#define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0')
+
+/* return: zero: continue, nonzero: return given value to user */
+static int shuffle_argv(int argc, char *const *argv,const struct option *longopts,
+ struct custom_getopt_data *d)
+{
+ /*
+ * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been
+ * moved back by the user (who may also have changed the arguments).
+ */
+ if (d->last_nonopt > d->custom_optind)
+ d->last_nonopt = d->custom_optind;
+ if (d->first_nonopt > d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * If we have just processed some options following some
+ * non-options, exchange them so that the options come first.
+ */
+ if (d->first_nonopt != d->last_nonopt &&
+ d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->last_nonopt != d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * Skip any additional non-options and extend the range of
+ * non-options previously skipped.
+ */
+ while (d->custom_optind < argc && NONOPTION_P)
+ d->custom_optind++;
+ d->last_nonopt = d->custom_optind;
+ /*
+ * The special ARGV-element `--' means premature end of options. Skip
+ * it like a null option, then exchange with previous non-options as if
+ * it were an option, then skip everything else like a non-option.
+ */
+ if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) {
+ d->custom_optind++;
+ if (d->first_nonopt != d->last_nonopt
+ && d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->first_nonopt == d->last_nonopt)
+ d->first_nonopt = d->custom_optind;
+ d->last_nonopt = argc;
+ d->custom_optind = argc;
+ }
+ /*
+ * If we have done all the ARGV-elements, stop the scan and back over
+ * any non-options that we skipped and permuted.
+ */
+ if (d->custom_optind == argc) {
+ /*
+ * Set the next-arg-index to point at the non-options that we
+ * previously skipped, so the caller will digest them.
+ */
+ if (d->first_nonopt != d->last_nonopt)
+ d->custom_optind = d->first_nonopt;
+ return -1;
+ }
+ /*
+ * If we have come to a non-option and did not permute it, either stop
+ * the scan or describe it to the caller and pass it by.
+ */
+ if (NONOPTION_P) {
+ d->custom_optarg = argv[d->custom_optind++];
+ return 1;
+ }
+ /*
+ * We have found another option-ARGV-element. Skip the initial
+ * punctuation.
+ */
+ d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-'));
+ return 0;
+}
+
+/*
+ * Check whether the ARGV-element is a long option.
+ *
+ * If there's a long option "fubar" and the ARGV-element is "-fu", consider
+ * that an abbreviation of the long option, just like "--fu", and not "-f" with
+ * arg "u".
+ *
+ * This distinction seems to be the most useful approach.
+ *
+ */
+static int check_long_opt(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char *nameend;
+ const struct option *p;
+ const struct option *pfound = NULL;
+ int exact = 0;
+ int ambig = 0;
+ int indfound = -1;
+ int option_index;
+
+ for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++)
+ /* Do nothing. */ ;
+
+ /* Test all long options for either exact match or abbreviated matches */
+ for (p = longopts, option_index = 0; p->name; p++, option_index++)
+ if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) {
+ if ((unsigned int) (nameend - d->nextchar)
+ == (unsigned int) strlen(p->name)) {
+ /* Exact match found. */
+ pfound = p;
+ indfound = option_index;
+ exact = 1;
+ break;
+ } else if (pfound == NULL) {
+ /* First nonexact match found. */
+ pfound = p;
+ indfound = option_index;
+ } else if (pfound->has_arg != p->has_arg
+ || pfound->flag != p->flag
+ || pfound->val != p->val)
+ /* Second or later nonexact match found. */
+ ambig = 1;
+ }
+ if (ambig && !exact) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' is ambiguous\n",
+ argv[0], argv[d->custom_optind]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+ }
+ if (pfound) {
+ option_index = indfound;
+ d->custom_optind++;
+ if (*nameend) {
+ if (pfound->has_arg != no_argument)
+ d->custom_optarg = nameend + 1;
+ else {
+ if (print_errors) {
+ if (argv[d->custom_optind - 1][1] == '-') {
+ /* --option */
+ fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n",
+ argv[0], pfound->name);
+ } else {
+ /* +option or -option */
+ fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n",
+ argv[0], argv[d->custom_optind - 1][0], pfound->name);
+ }
+
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return '?';
+ }
+ } else if (pfound->has_arg == required_argument) {
+ if (d->custom_optind < argc)
+ d->custom_optarg = argv[d->custom_optind++];
+ else {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' requires an argument\n",
+ argv[0],
+ argv[d->custom_optind - 1]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return optstring[0] == ':' ? ':' : '?';
+ }
+ }
+ d->nextchar += strlen(d->nextchar);
+ if (longind != NULL)
+ *longind = option_index;
+ if (pfound->flag) {
+ *(pfound->flag) = pfound->val;
+ return 0;
+ }
+ return pfound->val;
+ }
+ /*
+ * Can't find it as a long option. If this is not getopt_long_only, or
+ * the option starts with '--' or is not a valid short option, then
+ * it's an error. Otherwise interpret it as a short option.
+ */
+ if (print_errors) {
+ if (argv[d->custom_optind][1] == '-') {
+ /* --option */
+ fprintf(stderr,
+ "%s: unrecognized option `--%s'\n",
+ argv[0], d->nextchar);
+ } else {
+ /* +option or -option */
+ fprintf(stderr,
+ "%s: unrecognized option `%c%s'\n",
+ argv[0], argv[d->custom_optind][0],
+ d->nextchar);
+ }
+ }
+ d->nextchar = (char *) "";
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+}
+
+static int check_short_opt(int argc, char *const *argv, const char *optstring,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char c = *d->nextchar++;
+ char *temp = strchr(optstring, c);
+
+ /* Increment `custom_optind' when we start to process its last character. */
+ if (*d->nextchar == '\0')
+ ++d->custom_optind;
+ if (!temp || c == ':') {
+ if (print_errors)
+ fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
+
+ d->custom_optopt = c;
+ return '?';
+ }
+ if (temp[1] == ':') {
+ if (temp[2] == ':') {
+ /* This is an option that accepts an argument optionally. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ d->custom_optind++;
+ } else
+ d->custom_optarg = NULL;
+ d->nextchar = NULL;
+ } else {
+ /* This is an option that requires an argument. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ /*
+ * If we end this ARGV-element by taking the
+ * rest as an arg, we must advance to the next
+ * element now.
+ */
+ d->custom_optind++;
+ } else if (d->custom_optind == argc) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option requires an argument -- %c\n",
+ argv[0], c);
+ }
+ d->custom_optopt = c;
+ if (optstring[0] == ':')
+ c = ':';
+ else
+ c = '?';
+ } else
+ /*
+ * We already incremented `custom_optind' once;
+ * increment it again when taking next ARGV-elt
+ * as argument.
+ */
+ d->custom_optarg = argv[d->custom_optind++];
+ d->nextchar = NULL;
+ }
+ }
+ return c;
+}
+
+/*
+ * Scan elements of ARGV for option characters given in OPTSTRING.
+ *
+ * If an element of ARGV starts with '-', and is not exactly "-" or "--",
+ * then it is an option element. The characters of this element
+ * (aside from the initial '-') are option characters. If `getopt'
+ * is called repeatedly, it returns successively each of the option characters
+ * from each of the option elements.
+ *
+ * If `getopt' finds another option character, it returns that character,
+ * updating `custom_optind' and `nextchar' so that the next call to `getopt' can
+ * resume the scan with the following option character or ARGV-element.
+ *
+ * If there are no more option characters, `getopt' returns -1.
+ * Then `custom_optind' is the index in ARGV of the first ARGV-element
+ * that is not an option. (The ARGV-elements have been permuted
+ * so that those that are not options now come last.)
+ *
+ * OPTSTRING is a string containing the legitimate option characters.
+ * If an option character is seen that is not listed in OPTSTRING,
+ * return '?' after printing an error message. If you set `custom_opterr' to
+ * zero, the error message is suppressed but we still return '?'.
+ *
+ * If a char in OPTSTRING is followed by a colon, that means it wants an arg,
+ * so the following text in the same ARGV-element, or the text of the following
+ * ARGV-element, is returned in `custom_optarg'. Two colons mean an option that
+ * wants an optional arg; if there is text in the current ARGV-element,
+ * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero.
+ *
+ * If OPTSTRING starts with `-' or `+', it requests different methods of
+ * handling the non-option ARGV-elements.
+ * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
+ *
+ * Long-named options begin with `--' instead of `-'.
+ * Their names may be abbreviated as long as the abbreviation is unique
+ * or is an exact match for some defined option. If they have an
+ * argument, it follows the option name in the same ARGV-element, separated
+ * from the option name by a `=', or else the in next ARGV-element.
+ * When `getopt' finds a long-named option, it returns 0 if that option's
+ * `flag' field is nonzero, the value of the option's `val' field
+ * if the `flag' field is zero.
+ *
+ * The elements of ARGV aren't really const, because we permute them.
+ * But we pretend they're const in the prototype to be compatible
+ * with other systems.
+ *
+ * LONGOPTS is a vector of `struct option' terminated by an
+ * element containing a name which is zero.
+ *
+ * LONGIND returns the index in LONGOPT of the long-named option found.
+ * It is only valid when a long-named option has been found by the most
+ * recent call.
+ *
+ * Return the option character from OPTS just read. Return -1 when there are
+ * no more options. For unrecognized options, or options missing arguments,
+ * `custom_optopt' is set to the option letter, and '?' is returned.
+ *
+ * The OPTS string is a list of characters which are recognized option letters,
+ * optionally followed by colons, specifying that that letter takes an
+ * argument, to be placed in `custom_optarg'.
+ *
+ * If a letter in OPTS is followed by two colons, its argument is optional.
+ * This behavior is specific to the GNU `getopt'.
+ *
+ * The argument `--' causes premature termination of argument scanning,
+ * explicitly telling `getopt' that there are no more options. If OPTS begins
+ * with `--', then non-option arguments are treated as arguments to the option
+ * '\0'. This behavior is specific to the GNU `getopt'.
+ */
+
+static int getopt_internal_r(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ struct custom_getopt_data *d)
+{
+ int ret, print_errors = d->custom_opterr;
+
+ if (optstring[0] == ':')
+ print_errors = 0;
+ if (argc < 1)
+ return -1;
+ d->custom_optarg = NULL;
+
+ /*
+ * This is a big difference with GNU getopt, since optind == 0
+ * means initialization while here 1 means first call.
+ */
+ if (d->custom_optind == 0 || !d->initialized) {
+ if (d->custom_optind == 0)
+ d->custom_optind = 1; /* Don't scan ARGV[0], the program name. */
+ custom_getopt_initialize(d);
+ }
+ if (d->nextchar == NULL || *d->nextchar == '\0') {
+ ret = shuffle_argv(argc, argv, longopts, d);
+ if (ret)
+ return ret;
+ }
+ if (longopts && (argv[d->custom_optind][1] == '-' ))
+ return check_long_opt(argc, argv, optstring, longopts,
+ longind, print_errors, d);
+ return check_short_opt(argc, argv, optstring, print_errors, d);
+}
+
+static int custom_getopt_internal(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind)
+{
+ int result;
+ /* Keep a global copy of all internal members of d */
+ static struct custom_getopt_data d;
+
+ d.custom_optind = custom_optind;
+ d.custom_opterr = custom_opterr;
+ result = getopt_internal_r(argc, argv, optstring, longopts,
+ longind, &d);
+ custom_optind = d.custom_optind;
+ custom_optarg = d.custom_optarg;
+ custom_optopt = d.custom_optopt;
+ return result;
+}
+
+static int custom_getopt_long (int argc, char *const *argv, const char *options,
+ const struct option *long_options, int *opt_index)
+{
+ return custom_getopt_internal(argc, argv, options, long_options,
+ opt_index);
+}
+
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_clitkCropImage_params.check_ambiguity
+ * @param override @see cmdline_parser_clitkCropImage_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+static
+int update_arg(void *field, char **orig_field,
+ unsigned int *field_given, unsigned int *prev_given,
+ char *value, char *possible_values[], const char *default_value,
+ cmdline_parser_clitkCropImage_arg_type arg_type,
+ int check_ambiguity, int override,
+ int no_free, int multiple_option,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *stop_char = 0;
+ const char *val = value;
+ int found;
+ char **string_field;
+
+ stop_char = 0;
+ found = 0;
+
+ if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+ {
+ if (short_opt != '-')
+ fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
+ package_name, long_opt, short_opt,
+ (additional_error ? additional_error : ""));
+ else
+ fprintf (stderr, "%s: `--%s' option given more than once%s\n",
+ package_name, long_opt,
+ (additional_error ? additional_error : ""));
+ return 1; /* failure */
+ }
+
+
+ if (field_given && *field_given && ! override)
+ return 0;
+ if (prev_given)
+ (*prev_given)++;
+ if (field_given)
+ (*field_given)++;
+ if (possible_values)
+ val = possible_values[found];
+
+ switch(arg_type) {
+ case ARG_FLAG:
+ *((int *)field) = !*((int *)field);
+ break;
+ case ARG_INT:
+ if (val) *((int *)field) = strtol (val, &stop_char, 0);
+ break;
+ case ARG_DOUBLE:
+ if (val) *((double *)field) = strtod (val, &stop_char);
+ break;
+ case ARG_STRING:
+ if (val) {
+ string_field = (char **)field;
+ if (!no_free && *string_field)
+ free (*string_field); /* free previous string */
+ *string_field = gengetopt_strdup (val);
+ }
+ break;
+ default:
+ break;
+ };
+
+ /* check numeric conversion */
+ switch(arg_type) {
+ case ARG_INT:
+ case ARG_DOUBLE:
+ if (val && !(stop_char && *stop_char == '\0')) {
+ fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+ return 1; /* failure */
+ }
+ break;
+ default:
+ ;
+ };
+
+ /* store the original value */
+ switch(arg_type) {
+ case ARG_NO:
+ case ARG_FLAG:
+ break;
+ default:
+ if (value && orig_field) {
+ if (no_free) {
+ *orig_field = value;
+ } else {
+ if (*orig_field)
+ free (*orig_field); /* free previous string */
+ *orig_field = gengetopt_strdup (value);
+ }
+ }
+ };
+
+ return 0; /* OK */
+}
+
+/**
+ * @brief store information about a multiple option in a temporary list
+ * @param list where to (temporarily) store multiple options
+ */
+static
+int update_multiple_arg_temp(struct generic_list **list,
+ unsigned int *prev_given, const char *val,
+ char *possible_values[], const char *default_value,
+ cmdline_parser_clitkCropImage_arg_type arg_type,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *multi_token, *multi_next; /* store single arguments */
+
+ if (arg_type == ARG_NO) {
+ (*prev_given)++;
+ return 0; /* OK */
+ }
+
+ multi_token = get_multiple_arg_token(val);
+ multi_next = get_multiple_arg_token_next (val);
+
+ while (1)
+ {
+ add_node (list);
+ if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0,
+ prev_given, multi_token, possible_values, default_value,
+ arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) {
+ if (multi_token) free(multi_token);
+ return 1; /* failure */
+ }
+
+ if (multi_next)
+ {
+ multi_token = get_multiple_arg_token(multi_next);
+ multi_next = get_multiple_arg_token_next (multi_next);
+ }
+ else
+ break;
+ }
+
+ return 0; /* OK */
+}
+
+/**
+ * @brief free the passed list (including possible string argument)
+ */
+static
+void free_list(struct generic_list *list, short string_arg)
+{
+ if (list) {
+ struct generic_list *tmp;
+ while (list)
+ {
+ tmp = list;
+ if (string_arg && list->arg.string_arg)
+ free (list->arg.string_arg);
+ if (list->orig)
+ free (list->orig);
+ list = list->next;
+ free (tmp);
+ }
+ }
+}
+
+/**
+ * @brief updates a multiple option starting from the passed list
+ */
+static
+void update_multiple_arg(void *field, char ***orig_field,
+ unsigned int field_given, unsigned int prev_given, union generic_value *default_value,
+ cmdline_parser_clitkCropImage_arg_type arg_type,
+ struct generic_list *list)
+{
+ int i;
+ struct generic_list *tmp;
+
+ if (prev_given && list) {
+ *orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *));
+
+ switch(arg_type) {
+ case ARG_INT:
+ *((int **)field) = (int *)realloc (*((int **)field), (field_given + prev_given) * sizeof (int)); break;
+ case ARG_DOUBLE:
+ *((double **)field) = (double *)realloc (*((double **)field), (field_given + prev_given) * sizeof (double)); break;
+ case ARG_STRING:
+ *((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break;
+ default:
+ break;
+ };
+
+ for (i = (prev_given - 1); i >= 0; --i)
+ {
+ tmp = list;
+
+ switch(arg_type) {
+ case ARG_INT:
+ (*((int **)field))[i + field_given] = tmp->arg.int_arg; break;
+ case ARG_DOUBLE:
+ (*((double **)field))[i + field_given] = tmp->arg.double_arg; break;
+ case ARG_STRING:
+ (*((char ***)field))[i + field_given] = tmp->arg.string_arg; break;
+ default:
+ break;
+ }
+ (*orig_field) [i + field_given] = list->orig;
+ list = list->next;
+ free (tmp);
+ }
+ } else { /* set the default value */
+ if (default_value && ! field_given) {
+ switch(arg_type) {
+ case ARG_INT:
+ if (! *((int **)field)) {
+ *((int **)field) = (int *)malloc (sizeof (int));
+ (*((int **)field))[0] = default_value->int_arg;
+ }
+ break;
+ case ARG_DOUBLE:
+ if (! *((double **)field)) {
+ *((double **)field) = (double *)malloc (sizeof (double));
+ (*((double **)field))[0] = default_value->double_arg;
+ }
+ break;
+ case ARG_STRING:
+ if (! *((char ***)field)) {
+ *((char ***)field) = (char **)malloc (sizeof (char *));
+ (*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg);
+ }
+ break;
+ default: break;
+ }
+ if (!(*orig_field)) {
+ *orig_field = (char **) malloc (sizeof (char *));
+ (*orig_field)[0] = NULL;
+ }
+ }
+ }
+}
+
+int
+cmdline_parser_clitkCropImage_internal (int argc, char * const *argv, struct args_info_clitkCropImage *args_info,
+ struct cmdline_parser_clitkCropImage_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+
+ struct generic_list * boundingBox_list = NULL;
+ struct generic_list * lower_list = NULL;
+ struct generic_list * upper_list = NULL;
+ int error = 0;
+ struct args_info_clitkCropImage local_args_info;
+
+ int override;
+ int initialize;
+ int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+ check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+ cmdline_parser_clitkCropImage_init (args_info);
+
+ cmdline_parser_clitkCropImage_init (&local_args_info);
+
+ optarg = 0;
+ optind = 0;
+ opterr = params->print_errors;
+ optopt = '?';
+
+ while (1)
+ {
+ int option_index = 0;
+
+ static struct option long_options[] = {
+ { "help", 0, NULL, 'h' },
+ { "version", 0, NULL, 'V' },
+ { "config", 1, NULL, 0 },
+ { "imagetypes", 0, NULL, 0 },
+ { "verbose", 0, NULL, 'v' },
+ { "verboseOption", 0, NULL, 0 },
+ { "verboseWarningOff", 0, NULL, 0 },
+ { "input", 1, NULL, 'i' },
+ { "output", 1, NULL, 'o' },
+ { "boundingBox", 1, NULL, 'b' },
+ { "lower", 1, NULL, 'l' },
+ { "upper", 1, NULL, 'u' },
+ { "origin", 0, NULL, 0 },
+ { "BG", 1, NULL, 0 },
+ { "like", 1, NULL, 0 },
+ { "BGLike", 1, NULL, 0 },
+ { NULL, 0, NULL, 0 }
+ };
+
+ custom_optarg = optarg;
+ custom_optind = optind;
+ custom_opterr = opterr;
+ custom_optopt = optopt;
+
+ c = custom_getopt_long (argc, argv, "hVvi:o:b:l:u:", long_options, &option_index);
+
+ optarg = custom_optarg;
+ optind = custom_optind;
+ opterr = custom_opterr;
+ optopt = custom_optopt;
+
+ if (c == -1) break; /* Exit from `while (1)' loop. */
+
+ switch (c)
+ {
+ case 'h': /* Print help and exit. */
+ cmdline_parser_clitkCropImage_print_help ();
+ cmdline_parser_clitkCropImage_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'V': /* Print version and exit. */
+ cmdline_parser_clitkCropImage_print_version ();
+ cmdline_parser_clitkCropImage_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'v': /* Verbose. */
+
+
+ if (update_arg((void *)&(args_info->verbose_flag), 0, &(args_info->verbose_given),
+ &(local_args_info.verbose_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verbose", 'v',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'i': /* Input image filename. */
+
+
+ if (update_arg( (void *)&(args_info->input_arg),
+ &(args_info->input_orig), &(args_info->input_given),
+ &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "input", 'i',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'o': /* Output image filename. */
+
+
+ if (update_arg( (void *)&(args_info->output_arg),
+ &(args_info->output_orig), &(args_info->output_given),
+ &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "output", 'o',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'b': /* Bounding box of the crop region (in 3D: =x1,x2,y1,y2,z1,z2). */
+
+ if (update_multiple_arg_temp(&boundingBox_list,
+ &(local_args_info.boundingBox_given), optarg, 0, 0, ARG_INT,
+ "boundingBox", 'b',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'l': /* Size of the lower crop region (multiple values). */
+
+ if (update_multiple_arg_temp(&lower_list,
+ &(local_args_info.lower_given), optarg, 0, 0, ARG_INT,
+ "lower", 'l',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'u': /* Size of the upper crop region (multiple values). */
+
+ if (update_multiple_arg_temp(&upper_list,
+ &(local_args_info.upper_given), optarg, 0, 0, ARG_INT,
+ "upper", 'u',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ /* Config file. */
+ if (strcmp (long_options[option_index].name, "config") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->config_arg),
+ &(args_info->config_orig), &(args_info->config_given),
+ &(local_args_info.config_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "config", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Display allowed image types. */
+ else if (strcmp (long_options[option_index].name, "imagetypes") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->imagetypes_flag), 0, &(args_info->imagetypes_given),
+ &(local_args_info.imagetypes_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "imagetypes", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Display options values. */
+ else if (strcmp (long_options[option_index].name, "verboseOption") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->verboseOption_flag), 0, &(args_info->verboseOption_given),
+ &(local_args_info.verboseOption_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verboseOption", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Do not display warning. */
+ else if (strcmp (long_options[option_index].name, "verboseWarningOff") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->verboseWarningOff_flag), 0, &(args_info->verboseWarningOff_given),
+ &(local_args_info.verboseWarningOff_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verboseWarningOff", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Set new origin to zero. */
+ else if (strcmp (long_options[option_index].name, "origin") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->origin_flag), 0, &(args_info->origin_given),
+ &(local_args_info.origin_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "origin", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Background value in input.. */
+ else if (strcmp (long_options[option_index].name, "BG") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->BG_arg),
+ &(args_info->BG_orig), &(args_info->BG_given),
+ &(local_args_info.BG_given), optarg, 0, "0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "BG", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Crop like this image (must have the same spacing. */
+ else if (strcmp (long_options[option_index].name, "like") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->like_arg),
+ &(args_info->like_orig), &(args_info->like_given),
+ &(local_args_info.like_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "like", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Background value in output (if like larger). */
+ else if (strcmp (long_options[option_index].name, "BGLike") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->BGLike_arg),
+ &(args_info->BGLike_orig), &(args_info->BGLike_given),
+ &(local_args_info.BGLike_given), optarg, 0, "0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "BGLike", '-',
+ additional_error))
+ goto failure;
+
+ }
+
+ break;
+ case '?': /* Invalid option. */
+ /* `getopt_long' already printed an error message. */
+ goto failure;
+
+ default: /* bug: option not considered. */
+ fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+
+ update_multiple_arg((void *)&(args_info->boundingBox_arg),
+ &(args_info->boundingBox_orig), args_info->boundingBox_given,
+ local_args_info.boundingBox_given, 0 ,
+ ARG_INT, boundingBox_list);
+ update_multiple_arg((void *)&(args_info->lower_arg),
+ &(args_info->lower_orig), args_info->lower_given,
+ local_args_info.lower_given, 0 ,
+ ARG_INT, lower_list);
+ update_multiple_arg((void *)&(args_info->upper_arg),
+ &(args_info->upper_orig), args_info->upper_given,
+ local_args_info.upper_given, 0 ,
+ ARG_INT, upper_list);
+
+ args_info->boundingBox_given += local_args_info.boundingBox_given;
+ local_args_info.boundingBox_given = 0;
+ args_info->lower_given += local_args_info.lower_given;
+ local_args_info.lower_given = 0;
+ args_info->upper_given += local_args_info.upper_given;
+ local_args_info.upper_given = 0;
+
+ if (check_required)
+ {
+ error += cmdline_parser_clitkCropImage_required2 (args_info, argv[0], additional_error);
+ }
+
+ cmdline_parser_clitkCropImage_release (&local_args_info);
+
+ if ( error )
+ return (EXIT_FAILURE);
+
+ if (optind < argc)
+ {
+ int i = 0 ;
+ int found_prog_name = 0;
+ /* whether program name, i.e., argv[0], is in the remaining args
+ (this may happen with some implementations of getopt,
+ but surely not with the one included by gengetopt) */
+
+
+ args_info->inputs_num = argc - optind - found_prog_name;
+ args_info->inputs =
+ (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+ while (optind < argc)
+ args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
+ }
+
+ return 0;
+
+failure:
+ free_list (boundingBox_list, 0 );
+ free_list (lower_list, 0 );
+ free_list (upper_list, 0 );
+
+ cmdline_parser_clitkCropImage_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
+
+#ifndef CONFIG_FILE_LINE_SIZE
+#define CONFIG_FILE_LINE_SIZE 2048
+#endif
+#define ADDITIONAL_ERROR " in configuration file "
+
+#define CONFIG_FILE_LINE_BUFFER_SIZE (CONFIG_FILE_LINE_SIZE+3)
+/* 3 is for "--" and "=" */
+
+static int
+_cmdline_parser_clitkCropImage_configfile (char * const filename, int *my_argc)
+{
+ FILE* file;
+ char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
+ char linebuf[CONFIG_FILE_LINE_SIZE];
+ int line_num = 0;
+ int result = 0, equal;
+ char *fopt, *farg;
+ char *str_index;
+ size_t len, next_token;
+ char delimiter;
+
+ if ((file = fopen(filename, "r")) == NULL)
+ {
+ fprintf (stderr, "%s: Error opening configuration file '%s'\n",
+ CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
+ {
+ ++line_num;
+ my_argv[0] = '\0';
+ len = strlen(linebuf);
+ if (len > (CONFIG_FILE_LINE_BUFFER_SIZE-1))
+ {
+ fprintf (stderr, "%s:%s:%d: Line too long in configuration file\n",
+ CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+
+ /* find first non-whitespace character in the line */
+ next_token = strspn (linebuf, " \t\r\n");
+ str_index = linebuf + next_token;
+
+ if ( str_index[0] == '\0' || str_index[0] == '#')
+ continue; /* empty line or comment line is skipped */
+
+ fopt = str_index;
+
+ /* truncate fopt at the end of the first non-valid character */
+ next_token = strcspn (fopt, " \t\r\n=");
+
+ if (fopt[next_token] == '\0') /* the line is over */
+ {
+ farg = NULL;
+ equal = 0;
+ goto noarg;
+ }
+
+ /* remember if equal sign is present */
+ equal = (fopt[next_token] == '=');
+ fopt[next_token++] = '\0';
+
+ /* advance pointers to the next token after the end of fopt */
+ next_token += strspn (fopt + next_token, " \t\r\n");
+
+ /* check for the presence of equal sign, and if so, skip it */
+ if ( !equal )
+ if ((equal = (fopt[next_token] == '=')))
+ {
+ next_token++;
+ next_token += strspn (fopt + next_token, " \t\r\n");
+ }
+ str_index += next_token;
+
+ /* find argument */
+ farg = str_index;
+ if ( farg[0] == '\"' || farg[0] == '\'' )
+ { /* quoted argument */
+ str_index = strchr (++farg, str_index[0] ); /* skip opening quote */
+ if (! str_index)
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: unterminated string in configuration file\n",
+ CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+ else
+ { /* read up the remaining part up to a delimiter */
+ next_token = strcspn (farg, " \t\r\n#\'\"");
+ str_index += next_token;
+ }
+
+ /* truncate farg at the delimiter and store it for further check */
+ delimiter = *str_index, *str_index++ = '\0';
+
+ /* everything but comment is illegal at the end of line */
+ if (delimiter != '\0' && delimiter != '#')
+ {
+ str_index += strspn(str_index, " \t\r\n");
+ if (*str_index != '\0' && *str_index != '#')
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: malformed string in configuration file\n",
+ CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+
+ noarg:
+ if (!strcmp(fopt,"include")) {
+ if (farg && *farg) {
+ result = _cmdline_parser_clitkCropImage_configfile(farg, my_argc);
+ } else {
+ fprintf(stderr, "%s:%s:%d: include requires a filename argument.\n",
+ CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE, filename, line_num);
+ }
+ continue;
+ }
+ len = strlen(fopt);
+ strcat (my_argv, len > 1 ? "--" : "-");
+ strcat (my_argv, fopt);
+ if (len > 1 && ((farg && *farg) || equal))
+ strcat (my_argv, "=");
+ if (farg && *farg)
+ strcat (my_argv, farg);
+ ++(*my_argc);
+
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup(my_argv);
+ } /* while */
+
+ if (file)
+ fclose(file);
+ return result;
+}
+
+int
+cmdline_parser_clitkCropImage_configfile (char * const filename,
+ struct args_info_clitkCropImage *args_info,
+ int override, int initialize, int check_required)
+{
+ struct cmdline_parser_clitkCropImage_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ return cmdline_parser_clitkCropImage_config_file (filename, args_info, ¶ms);
+}
+
+int
+cmdline_parser_clitkCropImage_config_file (char * const filename,
+ struct args_info_clitkCropImage *args_info,
+ struct cmdline_parser_clitkCropImage_params *params)
+{
+ int i, result;
+ int my_argc = 1;
+ char **my_argv_arg;
+ char *additional_error;
+
+ /* store the program name */
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup (CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE);
+
+ result = _cmdline_parser_clitkCropImage_configfile(filename, &my_argc);
+
+ if (result != EXIT_FAILURE) {
+ my_argv_arg = (char **) malloc((my_argc+1) * sizeof(char *));
+ cmd_line_list_tmp = cmd_line_list;
+
+ for (i = my_argc - 1; i >= 0; --i) {
+ my_argv_arg[i] = cmd_line_list_tmp->string_arg;
+ cmd_line_list_tmp = cmd_line_list_tmp->next;
+ }
+
+ my_argv_arg[my_argc] = 0;
+
+ additional_error = (char *)malloc(strlen(filename) + strlen(ADDITIONAL_ERROR) + 1);
+ strcpy (additional_error, ADDITIONAL_ERROR);
+ strcat (additional_error, filename);
+ result =
+ cmdline_parser_clitkCropImage_internal (my_argc, my_argv_arg, args_info,
+ params,
+ additional_error);
+
+ free (additional_error);
+ free (my_argv_arg);
+ }
+
+ free_cmd_list();
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkCropImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
--- /dev/null
+/** @file clitkCropImage_ggo.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CLITKCROPIMAGE_GGO_H
+#define CLITKCROPIMAGE_GGO_H
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE
+/** @brief the program name */
+#define CMDLINE_PARSER_CLITKCROPIMAGE_PACKAGE "clitkCropImage"
+#endif
+
+#ifndef CMDLINE_PARSER_CLITKCROPIMAGE_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_CLITKCROPIMAGE_VERSION "1.0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct args_info_clitkCropImage
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ char * config_arg; /**< @brief Config file. */
+ char * config_orig; /**< @brief Config file original value given at command line. */
+ const char *config_help; /**< @brief Config file help description. */
+ int imagetypes_flag; /**< @brief Display allowed image types (default=off). */
+ const char *imagetypes_help; /**< @brief Display allowed image types help description. */
+ int verbose_flag; /**< @brief Verbose (default=off). */
+ const char *verbose_help; /**< @brief Verbose help description. */
+ int verboseOption_flag; /**< @brief Display options values (default=off). */
+ const char *verboseOption_help; /**< @brief Display options values help description. */
+ int verboseWarningOff_flag; /**< @brief Do not display warning (default=off). */
+ const char *verboseWarningOff_help; /**< @brief Do not display warning help description. */
+ char * input_arg; /**< @brief Input image filename. */
+ char * input_orig; /**< @brief Input image filename original value given at command line. */
+ const char *input_help; /**< @brief Input image filename help description. */
+ char * output_arg; /**< @brief Output image filename. */
+ char * output_orig; /**< @brief Output image filename original value given at command line. */
+ const char *output_help; /**< @brief Output image filename help description. */
+ int* boundingBox_arg; /**< @brief Bounding box of the crop region (in 3D: =x1,x2,y1,y2,z1,z2). */
+ char ** boundingBox_orig; /**< @brief Bounding box of the crop region (in 3D: =x1,x2,y1,y2,z1,z2) original value given at command line. */
+ int boundingBox_min; /**< @brief Bounding box of the crop region (in 3D: =x1,x2,y1,y2,z1,z2)'s minimum occurreces */
+ int boundingBox_max; /**< @brief Bounding box of the crop region (in 3D: =x1,x2,y1,y2,z1,z2)'s maximum occurreces */
+ const char *boundingBox_help; /**< @brief Bounding box of the crop region (in 3D: =x1,x2,y1,y2,z1,z2) help description. */
+ int* lower_arg; /**< @brief Size of the lower crop region (multiple values). */
+ char ** lower_orig; /**< @brief Size of the lower crop region (multiple values) original value given at command line. */
+ int lower_min; /**< @brief Size of the lower crop region (multiple values)'s minimum occurreces */
+ int lower_max; /**< @brief Size of the lower crop region (multiple values)'s maximum occurreces */
+ const char *lower_help; /**< @brief Size of the lower crop region (multiple values) help description. */
+ int* upper_arg; /**< @brief Size of the upper crop region (multiple values). */
+ char ** upper_orig; /**< @brief Size of the upper crop region (multiple values) original value given at command line. */
+ int upper_min; /**< @brief Size of the upper crop region (multiple values)'s minimum occurreces */
+ int upper_max; /**< @brief Size of the upper crop region (multiple values)'s maximum occurreces */
+ const char *upper_help; /**< @brief Size of the upper crop region (multiple values) help description. */
+ int origin_flag; /**< @brief Set new origin to zero (default=off). */
+ const char *origin_help; /**< @brief Set new origin to zero help description. */
+ double BG_arg; /**< @brief Background value in input. (default='0'). */
+ char * BG_orig; /**< @brief Background value in input. original value given at command line. */
+ const char *BG_help; /**< @brief Background value in input. help description. */
+ char * like_arg; /**< @brief Crop like this image (must have the same spacing. */
+ char * like_orig; /**< @brief Crop like this image (must have the same spacing original value given at command line. */
+ const char *like_help; /**< @brief Crop like this image (must have the same spacing help description. */
+ double BGLike_arg; /**< @brief Background value in output (if like larger) (default='0'). */
+ char * BGLike_orig; /**< @brief Background value in output (if like larger) original value given at command line. */
+ const char *BGLike_help; /**< @brief Background value in output (if like larger) help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int config_given ; /**< @brief Whether config was given. */
+ unsigned int imagetypes_given ; /**< @brief Whether imagetypes was given. */
+ unsigned int verbose_given ; /**< @brief Whether verbose was given. */
+ unsigned int verboseOption_given ; /**< @brief Whether verboseOption was given. */
+ unsigned int verboseWarningOff_given ; /**< @brief Whether verboseWarningOff was given. */
+ unsigned int input_given ; /**< @brief Whether input was given. */
+ unsigned int output_given ; /**< @brief Whether output was given. */
+ unsigned int boundingBox_given ; /**< @brief Whether boundingBox was given. */
+ unsigned int lower_given ; /**< @brief Whether lower was given. */
+ unsigned int upper_given ; /**< @brief Whether upper was given. */
+ unsigned int origin_given ; /**< @brief Whether origin was given. */
+ unsigned int BG_given ; /**< @brief Whether BG was given. */
+ unsigned int like_given ; /**< @brief Whether like was given. */
+ unsigned int BGLike_given ; /**< @brief Whether BGLike was given. */
+
+ char **inputs ; /**< @brief unamed options (options without names) */
+ unsigned inputs_num ; /**< @brief unamed options number */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_clitkCropImage_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure args_info_clitkCropImage (default 1) */
+ int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+ int check_ambiguity; /**< @brief whether to check for options already specified in the option structure args_info_clitkCropImage (default 0) */
+ int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *args_info_clitkCropImage_purpose;
+/** @brief the usage string of the program */
+extern const char *args_info_clitkCropImage_usage;
+/** @brief all the lines making the help output */
+extern const char *args_info_clitkCropImage_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkCropImage (int argc, char * const *argv,
+ struct args_info_clitkCropImage *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkCropImage_ext() instead
+ */
+int cmdline_parser_clitkCropImage2 (int argc, char * const *argv,
+ struct args_info_clitkCropImage *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkCropImage_ext (int argc, char * const *argv,
+ struct args_info_clitkCropImage *args_info,
+ struct cmdline_parser_clitkCropImage_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkCropImage_dump(FILE *outfile,
+ struct args_info_clitkCropImage *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkCropImage_file_save(const char *filename,
+ struct args_info_clitkCropImage *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_clitkCropImage_print_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_clitkCropImage_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_clitkCropImage_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_clitkCropImage_params_init(struct cmdline_parser_clitkCropImage_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_clitkCropImage_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_clitkCropImage_params structure
+ */
+struct cmdline_parser_clitkCropImage_params *cmdline_parser_clitkCropImage_params_create(void);
+
+/**
+ * Initializes the passed args_info_clitkCropImage structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_clitkCropImage_init (struct args_info_clitkCropImage *args_info);
+/**
+ * Deallocates the string fields of the args_info_clitkCropImage structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_clitkCropImage_free (struct args_info_clitkCropImage *args_info);
+
+/**
+ * The config file parser (deprecated version)
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkCropImage_config_file() instead
+ */
+int cmdline_parser_clitkCropImage_configfile (char * const filename,
+ struct args_info_clitkCropImage *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The config file parser
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkCropImage_config_file (char * const filename,
+ struct args_info_clitkCropImage *args_info,
+ struct cmdline_parser_clitkCropImage_params *params);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ * possible errors
+ * @return
+ */
+int cmdline_parser_clitkCropImage_required (struct args_info_clitkCropImage *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CLITKCROPIMAGE_GGO_H */
--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22
+ generated with the following command:
+ /usr/local/bin/gengetopt --output-dir=/home/tbaudier/vv/vv_static/vv/vv_bin/tools --arg-struct-name=args_info_clitkImageArithm --func-name=cmdline_parser_clitkImageArithm --file-name=clitkImageArithm_ggo --unamed-opts --conf-parser --include-getopt
+
+ The developers of gengetopt consider the fixed text that goes in all
+ gengetopt output files to be in the public domain:
+ we make no copyright claims on it.
+*/
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+
+#include "clitkImageArithm_ggo.h"
+
+const char *args_info_clitkImageArithm_purpose = "Perform an arithmetic operation (+-*/ ...) using two images or using an image \nand a scalar value.";
+
+const char *args_info_clitkImageArithm_usage = "Usage: clitkImageArithm [OPTIONS]... [FILES]...";
+
+const char *args_info_clitkImageArithm_description = "";
+
+const char *args_info_clitkImageArithm_help[] = {
+ " -h, --help Print help and exit",
+ " -V, --version Print version and exit",
+ " --config=STRING Config file",
+ " -v, --verbose Verbose (default=off)",
+ " --imagetypes Display allowed image types (default=off)",
+ " -i, --input1=STRING Input first image filename",
+ " -j, --input2=STRING Input second image filename",
+ " -o, --output=STRING Output image filename",
+ " -s, --scalar=DOUBLE Scalar value",
+ " -t, --operation=INT Type of operation : \n With another image : 0=add*, 1=multiply, \n 2=divide,\n 3=max, 4=min, 5=absdiff, 6=squareddiff, \n 7=difference*, 8=relativ diff\n ; For 'scalar' : 0=add*, 1=multiply*, 2=inverse,\n 3=max, 4=min 5=absval 6=squareval\n 7=log 8=exp 9=sqrt 10=EPID 11=divide* \n 12=normalize (divide by max) 13=-ln(I/IO)**; \n * operations supported with vector fields as \n inputs. \n ** for fluence image, if pixel value == 0, \n consider value=0.5 (default=`0')",
+ " --pixelValue=DOUBLE Default value for NaN/Inf (default=`0.0')",
+ " -f, --setFloatOutput Set output to float pixel type (default=off)",
+ 0
+};
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_INT
+ , ARG_DOUBLE
+} cmdline_parser_clitkImageArithm_arg_type;
+
+static
+void clear_given (struct args_info_clitkImageArithm *args_info);
+static
+void clear_args (struct args_info_clitkImageArithm *args_info);
+
+static int
+cmdline_parser_clitkImageArithm_internal (int argc, char * const *argv, struct args_info_clitkImageArithm *args_info,
+ struct cmdline_parser_clitkImageArithm_params *params, const char *additional_error);
+
+static int
+cmdline_parser_clitkImageArithm_required2 (struct args_info_clitkImageArithm *args_info, const char *prog_name, const char *additional_error);
+struct line_list
+{
+ char * string_arg;
+ struct line_list * next;
+};
+
+static struct line_list *cmd_line_list = 0;
+static struct line_list *cmd_line_list_tmp = 0;
+
+static void
+free_cmd_list(void)
+{
+ /* free the list of a previous call */
+ if (cmd_line_list)
+ {
+ while (cmd_line_list) {
+ cmd_line_list_tmp = cmd_line_list;
+ cmd_line_list = cmd_line_list->next;
+ free (cmd_line_list_tmp->string_arg);
+ free (cmd_line_list_tmp);
+ }
+ }
+}
+
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct args_info_clitkImageArithm *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->config_given = 0 ;
+ args_info->verbose_given = 0 ;
+ args_info->imagetypes_given = 0 ;
+ args_info->input1_given = 0 ;
+ args_info->input2_given = 0 ;
+ args_info->output_given = 0 ;
+ args_info->scalar_given = 0 ;
+ args_info->operation_given = 0 ;
+ args_info->pixelValue_given = 0 ;
+ args_info->setFloatOutput_given = 0 ;
+}
+
+static
+void clear_args (struct args_info_clitkImageArithm *args_info)
+{
+ args_info->config_arg = NULL;
+ args_info->config_orig = NULL;
+ args_info->verbose_flag = 0;
+ args_info->imagetypes_flag = 0;
+ args_info->input1_arg = NULL;
+ args_info->input1_orig = NULL;
+ args_info->input2_arg = NULL;
+ args_info->input2_orig = NULL;
+ args_info->output_arg = NULL;
+ args_info->output_orig = NULL;
+ args_info->scalar_orig = NULL;
+ args_info->operation_arg = 0;
+ args_info->operation_orig = NULL;
+ args_info->pixelValue_arg = 0.0;
+ args_info->pixelValue_orig = NULL;
+ args_info->setFloatOutput_flag = 0;
+
+}
+
+static
+void init_args_info(struct args_info_clitkImageArithm *args_info)
+{
+
+
+ args_info->help_help = args_info_clitkImageArithm_help[0] ;
+ args_info->version_help = args_info_clitkImageArithm_help[1] ;
+ args_info->config_help = args_info_clitkImageArithm_help[2] ;
+ args_info->verbose_help = args_info_clitkImageArithm_help[3] ;
+ args_info->imagetypes_help = args_info_clitkImageArithm_help[4] ;
+ args_info->input1_help = args_info_clitkImageArithm_help[5] ;
+ args_info->input2_help = args_info_clitkImageArithm_help[6] ;
+ args_info->output_help = args_info_clitkImageArithm_help[7] ;
+ args_info->scalar_help = args_info_clitkImageArithm_help[8] ;
+ args_info->operation_help = args_info_clitkImageArithm_help[9] ;
+ args_info->pixelValue_help = args_info_clitkImageArithm_help[10] ;
+ args_info->setFloatOutput_help = args_info_clitkImageArithm_help[11] ;
+
+}
+
+void
+cmdline_parser_clitkImageArithm_print_version (void)
+{
+ printf ("%s %s\n", CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE, CMDLINE_PARSER_CLITKIMAGEARITHM_VERSION);
+}
+
+static void print_help_common(void) {
+ cmdline_parser_clitkImageArithm_print_version ();
+
+ if (strlen(args_info_clitkImageArithm_purpose) > 0)
+ printf("\n%s\n", args_info_clitkImageArithm_purpose);
+
+ if (strlen(args_info_clitkImageArithm_usage) > 0)
+ printf("\n%s\n", args_info_clitkImageArithm_usage);
+
+ printf("\n");
+
+ if (strlen(args_info_clitkImageArithm_description) > 0)
+ printf("%s\n", args_info_clitkImageArithm_description);
+}
+
+void
+cmdline_parser_clitkImageArithm_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (args_info_clitkImageArithm_help[i])
+ printf("%s\n", args_info_clitkImageArithm_help[i++]);
+}
+
+void
+cmdline_parser_clitkImageArithm_init (struct args_info_clitkImageArithm *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+
+ args_info->inputs = NULL;
+ args_info->inputs_num = 0;
+}
+
+void
+cmdline_parser_clitkImageArithm_params_init(struct cmdline_parser_clitkImageArithm_params *params)
+{
+ if (params)
+ {
+ params->override = 0;
+ params->initialize = 1;
+ params->check_required = 1;
+ params->check_ambiguity = 0;
+ params->print_errors = 1;
+ }
+}
+
+struct cmdline_parser_clitkImageArithm_params *
+cmdline_parser_clitkImageArithm_params_create(void)
+{
+ struct cmdline_parser_clitkImageArithm_params *params =
+ (struct cmdline_parser_clitkImageArithm_params *)malloc(sizeof(struct cmdline_parser_clitkImageArithm_params));
+ cmdline_parser_clitkImageArithm_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+
+static void
+cmdline_parser_clitkImageArithm_release (struct args_info_clitkImageArithm *args_info)
+{
+ unsigned int i;
+ free_string_field (&(args_info->config_arg));
+ free_string_field (&(args_info->config_orig));
+ free_string_field (&(args_info->input1_arg));
+ free_string_field (&(args_info->input1_orig));
+ free_string_field (&(args_info->input2_arg));
+ free_string_field (&(args_info->input2_orig));
+ free_string_field (&(args_info->output_arg));
+ free_string_field (&(args_info->output_orig));
+ free_string_field (&(args_info->scalar_orig));
+ free_string_field (&(args_info->operation_orig));
+ free_string_field (&(args_info->pixelValue_orig));
+
+
+ for (i = 0; i < args_info->inputs_num; ++i)
+ free (args_info->inputs [i]);
+
+ if (args_info->inputs_num)
+ free (args_info->inputs);
+
+ clear_given (args_info);
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+ if (arg) {
+ fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+ } else {
+ fprintf(outfile, "%s\n", opt);
+ }
+}
+
+
+int
+cmdline_parser_clitkImageArithm_dump(FILE *outfile, struct args_info_clitkImageArithm *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE);
+ return EXIT_FAILURE;
+ }
+
+ if (args_info->help_given)
+ write_into_file(outfile, "help", 0, 0 );
+ if (args_info->version_given)
+ write_into_file(outfile, "version", 0, 0 );
+ if (args_info->config_given)
+ write_into_file(outfile, "config", args_info->config_orig, 0);
+ if (args_info->verbose_given)
+ write_into_file(outfile, "verbose", 0, 0 );
+ if (args_info->imagetypes_given)
+ write_into_file(outfile, "imagetypes", 0, 0 );
+ if (args_info->input1_given)
+ write_into_file(outfile, "input1", args_info->input1_orig, 0);
+ if (args_info->input2_given)
+ write_into_file(outfile, "input2", args_info->input2_orig, 0);
+ if (args_info->output_given)
+ write_into_file(outfile, "output", args_info->output_orig, 0);
+ if (args_info->scalar_given)
+ write_into_file(outfile, "scalar", args_info->scalar_orig, 0);
+ if (args_info->operation_given)
+ write_into_file(outfile, "operation", args_info->operation_orig, 0);
+ if (args_info->pixelValue_given)
+ write_into_file(outfile, "pixelValue", args_info->pixelValue_orig, 0);
+ if (args_info->setFloatOutput_given)
+ write_into_file(outfile, "setFloatOutput", 0, 0 );
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+cmdline_parser_clitkImageArithm_file_save(const char *filename, struct args_info_clitkImageArithm *args_info)
+{
+ FILE *outfile;
+ int i = 0;
+
+ outfile = fopen(filename, "w");
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = cmdline_parser_clitkImageArithm_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+cmdline_parser_clitkImageArithm_free (struct args_info_clitkImageArithm *args_info)
+{
+ cmdline_parser_clitkImageArithm_release (args_info);
+}
+
+/** @brief replacement of strdup, which is not standard */
+char *
+gengetopt_strdup (const char *s)
+{
+ char *result = NULL;
+ if (!s)
+ return result;
+
+ result = (char*)malloc(strlen(s) + 1);
+ if (result == (char*)0)
+ return (char*)0;
+ strcpy(result, s);
+ return result;
+}
+
+int
+cmdline_parser_clitkImageArithm (int argc, char * const *argv, struct args_info_clitkImageArithm *args_info)
+{
+ return cmdline_parser_clitkImageArithm2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+cmdline_parser_clitkImageArithm_ext (int argc, char * const *argv, struct args_info_clitkImageArithm *args_info,
+ struct cmdline_parser_clitkImageArithm_params *params)
+{
+ int result;
+ result = cmdline_parser_clitkImageArithm_internal (argc, argv, args_info, params, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkImageArithm_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkImageArithm2 (int argc, char * const *argv, struct args_info_clitkImageArithm *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct cmdline_parser_clitkImageArithm_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = cmdline_parser_clitkImageArithm_internal (argc, argv, args_info, ¶ms, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkImageArithm_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkImageArithm_required (struct args_info_clitkImageArithm *args_info, const char *prog_name)
+{
+ int result = EXIT_SUCCESS;
+
+ if (cmdline_parser_clitkImageArithm_required2(args_info, prog_name, NULL) > 0)
+ result = EXIT_FAILURE;
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkImageArithm_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkImageArithm_required2 (struct args_info_clitkImageArithm *args_info, const char *prog_name, const char *additional_error)
+{
+ int error = 0;
+
+ /* checks for required options */
+ if (! args_info->input1_given)
+ {
+ fprintf (stderr, "%s: '--input1' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (! args_info->output_given)
+ {
+ fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+
+ /* checks for dependences among options */
+
+ return error;
+}
+
+/*
+ * Extracted from the glibc source tree, version 2.3.6
+ *
+ * Licensed under the GPL as per the whole glibc source tree.
+ *
+ * This file was modified so that getopt_long can be called
+ * many times without risking previous memory to be spoiled.
+ *
+ * Modified by Andre Noll and Lorenzo Bettini for use in
+ * GNU gengetopt generated files.
+ *
+ */
+
+/*
+ * we must include anything we need since this file is not thought to be
+ * inserted in a file already using getopt.h
+ *
+ * Lorenzo
+ */
+
+struct option
+{
+ const char *name;
+ /* has_arg can't be an enum because some compilers complain about
+ type mismatches in all the code that assumes it is an int. */
+ int has_arg;
+ int *flag;
+ int val;
+};
+
+/* For communication from `getopt' to the caller.
+ When `getopt' finds an option that takes an argument,
+ the argument value is returned here.
+ Also, when `ordering' is RETURN_IN_ORDER,
+ each non-option ARGV-element is returned here. */
+
+static char *optarg;
+
+/* Index in ARGV of the next element to be scanned.
+ This is used for communication to and from the caller
+ and for communication between successive calls to `getopt'.
+
+ On entry to `getopt', zero means this is the first call; initialize.
+
+ When `getopt' returns -1, this is the index of the first of the
+ non-option elements that the caller should itself scan.
+
+ Otherwise, `optind' communicates from one call to the next
+ how much of ARGV has been scanned so far. */
+
+static int optind;
+
+/* Callers store zero here to inhibit the error message `getopt' prints
+ for unrecognized options. */
+
+static int opterr;
+
+/* Set to an option character which was unrecognized. */
+
+static int optopt;
+
+/* This version of `getopt' appears to the caller like standard Unix `getopt'
+ but it behaves differently for the user, since it allows the user
+ to intersperse the options with the other arguments.
+
+ As `getopt' works, it permutes the elements of ARGV so that,
+ when it is done, all the options precede everything else. Thus
+ all application programs are extended to handle flexible argument order.
+*/
+/*
+ If the field `flag' is not NULL, it points to a variable that is set
+ to the value given in the field `val' when the option is found, but
+ left unchanged if the option is not found.
+
+ To have a long-named option do something other than set an `int' to
+ a compiled-in constant, such as set a value from `custom_optarg', set the
+ option's `flag' field to zero and its `val' field to a nonzero
+ value (the equivalent single-letter option character, if there is
+ one). For long options that have a zero `flag' field, `getopt'
+ returns the contents of the `val' field. */
+
+/* Names for the values of the `has_arg' field of `struct option'. */
+#ifndef no_argument
+#define no_argument 0
+#endif
+
+#ifndef required_argument
+#define required_argument 1
+#endif
+
+#ifndef optional_argument
+#define optional_argument 2
+#endif
+
+struct custom_getopt_data {
+ /*
+ * These have exactly the same meaning as the corresponding global variables,
+ * except that they are used for the reentrant versions of getopt.
+ */
+ int custom_optind;
+ int custom_opterr;
+ int custom_optopt;
+ char *custom_optarg;
+
+ /* True if the internal members have been initialized. */
+ int initialized;
+
+ /*
+ * The next char to be scanned in the option-element in which the last option
+ * character we returned was found. This allows us to pick up the scan where
+ * we left off. If this is zero, or a null string, it means resume the scan by
+ * advancing to the next ARGV-element.
+ */
+ char *nextchar;
+
+ /*
+ * Describe the part of ARGV that contains non-options that have been skipped.
+ * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is
+ * the index after the last of them.
+ */
+ int first_nonopt;
+ int last_nonopt;
+};
+
+/*
+ * the variables optarg, optind, opterr and optopt are renamed with
+ * the custom_ prefix so that they don't interfere with getopt ones.
+ *
+ * Moreover they're static so they are visible only from within the
+ * file where this very file will be included.
+ */
+
+/*
+ * For communication from `custom_getopt' to the caller. When `custom_getopt' finds an
+ * option that takes an argument, the argument value is returned here.
+ */
+static char *custom_optarg;
+
+/*
+ * Index in ARGV of the next element to be scanned. This is used for
+ * communication to and from the caller and for communication between
+ * successive calls to `custom_getopt'.
+ *
+ * On entry to `custom_getopt', 1 means this is the first call; initialize.
+ *
+ * When `custom_getopt' returns -1, this is the index of the first of the non-option
+ * elements that the caller should itself scan.
+ *
+ * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV
+ * has been scanned so far.
+ *
+ * 1003.2 says this must be 1 before any call.
+ */
+static int custom_optind = 1;
+
+/*
+ * Callers store zero here to inhibit the error message for unrecognized
+ * options.
+ */
+static int custom_opterr = 1;
+
+/*
+ * Set to an option character which was unrecognized. This must be initialized
+ * on some systems to avoid linking in the system's own getopt implementation.
+ */
+static int custom_optopt = '?';
+
+/*
+ * Exchange two adjacent subsequences of ARGV. One subsequence is elements
+ * [first_nonopt,last_nonopt) which contains all the non-options that have been
+ * skipped so far. The other is elements [last_nonopt,custom_optind), which contains
+ * all the options processed since those non-options were skipped.
+ * `first_nonopt' and `last_nonopt' are relocated so that they describe the new
+ * indices of the non-options in ARGV after they are moved.
+ */
+static void exchange(char **argv, struct custom_getopt_data *d)
+{
+ int bottom = d->first_nonopt;
+ int middle = d->last_nonopt;
+ int top = d->custom_optind;
+ char *tem;
+
+ /*
+ * Exchange the shorter segment with the far end of the longer segment.
+ * That puts the shorter segment into the right place. It leaves the
+ * longer segment in the right place overall, but it consists of two
+ * parts that need to be swapped next.
+ */
+ while (top > middle && middle > bottom) {
+ if (top - middle > middle - bottom) {
+ /* Bottom segment is the short one. */
+ int len = middle - bottom;
+ int i;
+
+ /* Swap it with the top part of the top segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] =
+ argv[top - (middle - bottom) + i];
+ argv[top - (middle - bottom) + i] = tem;
+ }
+ /* Exclude the moved bottom segment from further swapping. */
+ top -= len;
+ } else {
+ /* Top segment is the short one. */
+ int len = top - middle;
+ int i;
+
+ /* Swap it with the bottom part of the bottom segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] = argv[middle + i];
+ argv[middle + i] = tem;
+ }
+ /* Exclude the moved top segment from further swapping. */
+ bottom += len;
+ }
+ }
+ /* Update records for the slots the non-options now occupy. */
+ d->first_nonopt += (d->custom_optind - d->last_nonopt);
+ d->last_nonopt = d->custom_optind;
+}
+
+/* Initialize the internal data when the first call is made. */
+static void custom_getopt_initialize(struct custom_getopt_data *d)
+{
+ /*
+ * Start processing options with ARGV-element 1 (since ARGV-element 0
+ * is the program name); the sequence of previously skipped non-option
+ * ARGV-elements is empty.
+ */
+ d->first_nonopt = d->last_nonopt = d->custom_optind;
+ d->nextchar = NULL;
+ d->initialized = 1;
+}
+
+#define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0')
+
+/* return: zero: continue, nonzero: return given value to user */
+static int shuffle_argv(int argc, char *const *argv,const struct option *longopts,
+ struct custom_getopt_data *d)
+{
+ /*
+ * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been
+ * moved back by the user (who may also have changed the arguments).
+ */
+ if (d->last_nonopt > d->custom_optind)
+ d->last_nonopt = d->custom_optind;
+ if (d->first_nonopt > d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * If we have just processed some options following some
+ * non-options, exchange them so that the options come first.
+ */
+ if (d->first_nonopt != d->last_nonopt &&
+ d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->last_nonopt != d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * Skip any additional non-options and extend the range of
+ * non-options previously skipped.
+ */
+ while (d->custom_optind < argc && NONOPTION_P)
+ d->custom_optind++;
+ d->last_nonopt = d->custom_optind;
+ /*
+ * The special ARGV-element `--' means premature end of options. Skip
+ * it like a null option, then exchange with previous non-options as if
+ * it were an option, then skip everything else like a non-option.
+ */
+ if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) {
+ d->custom_optind++;
+ if (d->first_nonopt != d->last_nonopt
+ && d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->first_nonopt == d->last_nonopt)
+ d->first_nonopt = d->custom_optind;
+ d->last_nonopt = argc;
+ d->custom_optind = argc;
+ }
+ /*
+ * If we have done all the ARGV-elements, stop the scan and back over
+ * any non-options that we skipped and permuted.
+ */
+ if (d->custom_optind == argc) {
+ /*
+ * Set the next-arg-index to point at the non-options that we
+ * previously skipped, so the caller will digest them.
+ */
+ if (d->first_nonopt != d->last_nonopt)
+ d->custom_optind = d->first_nonopt;
+ return -1;
+ }
+ /*
+ * If we have come to a non-option and did not permute it, either stop
+ * the scan or describe it to the caller and pass it by.
+ */
+ if (NONOPTION_P) {
+ d->custom_optarg = argv[d->custom_optind++];
+ return 1;
+ }
+ /*
+ * We have found another option-ARGV-element. Skip the initial
+ * punctuation.
+ */
+ d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-'));
+ return 0;
+}
+
+/*
+ * Check whether the ARGV-element is a long option.
+ *
+ * If there's a long option "fubar" and the ARGV-element is "-fu", consider
+ * that an abbreviation of the long option, just like "--fu", and not "-f" with
+ * arg "u".
+ *
+ * This distinction seems to be the most useful approach.
+ *
+ */
+static int check_long_opt(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char *nameend;
+ const struct option *p;
+ const struct option *pfound = NULL;
+ int exact = 0;
+ int ambig = 0;
+ int indfound = -1;
+ int option_index;
+
+ for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++)
+ /* Do nothing. */ ;
+
+ /* Test all long options for either exact match or abbreviated matches */
+ for (p = longopts, option_index = 0; p->name; p++, option_index++)
+ if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) {
+ if ((unsigned int) (nameend - d->nextchar)
+ == (unsigned int) strlen(p->name)) {
+ /* Exact match found. */
+ pfound = p;
+ indfound = option_index;
+ exact = 1;
+ break;
+ } else if (pfound == NULL) {
+ /* First nonexact match found. */
+ pfound = p;
+ indfound = option_index;
+ } else if (pfound->has_arg != p->has_arg
+ || pfound->flag != p->flag
+ || pfound->val != p->val)
+ /* Second or later nonexact match found. */
+ ambig = 1;
+ }
+ if (ambig && !exact) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' is ambiguous\n",
+ argv[0], argv[d->custom_optind]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+ }
+ if (pfound) {
+ option_index = indfound;
+ d->custom_optind++;
+ if (*nameend) {
+ if (pfound->has_arg != no_argument)
+ d->custom_optarg = nameend + 1;
+ else {
+ if (print_errors) {
+ if (argv[d->custom_optind - 1][1] == '-') {
+ /* --option */
+ fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n",
+ argv[0], pfound->name);
+ } else {
+ /* +option or -option */
+ fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n",
+ argv[0], argv[d->custom_optind - 1][0], pfound->name);
+ }
+
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return '?';
+ }
+ } else if (pfound->has_arg == required_argument) {
+ if (d->custom_optind < argc)
+ d->custom_optarg = argv[d->custom_optind++];
+ else {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' requires an argument\n",
+ argv[0],
+ argv[d->custom_optind - 1]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return optstring[0] == ':' ? ':' : '?';
+ }
+ }
+ d->nextchar += strlen(d->nextchar);
+ if (longind != NULL)
+ *longind = option_index;
+ if (pfound->flag) {
+ *(pfound->flag) = pfound->val;
+ return 0;
+ }
+ return pfound->val;
+ }
+ /*
+ * Can't find it as a long option. If this is not getopt_long_only, or
+ * the option starts with '--' or is not a valid short option, then
+ * it's an error. Otherwise interpret it as a short option.
+ */
+ if (print_errors) {
+ if (argv[d->custom_optind][1] == '-') {
+ /* --option */
+ fprintf(stderr,
+ "%s: unrecognized option `--%s'\n",
+ argv[0], d->nextchar);
+ } else {
+ /* +option or -option */
+ fprintf(stderr,
+ "%s: unrecognized option `%c%s'\n",
+ argv[0], argv[d->custom_optind][0],
+ d->nextchar);
+ }
+ }
+ d->nextchar = (char *) "";
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+}
+
+static int check_short_opt(int argc, char *const *argv, const char *optstring,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char c = *d->nextchar++;
+ char *temp = strchr(optstring, c);
+
+ /* Increment `custom_optind' when we start to process its last character. */
+ if (*d->nextchar == '\0')
+ ++d->custom_optind;
+ if (!temp || c == ':') {
+ if (print_errors)
+ fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
+
+ d->custom_optopt = c;
+ return '?';
+ }
+ if (temp[1] == ':') {
+ if (temp[2] == ':') {
+ /* This is an option that accepts an argument optionally. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ d->custom_optind++;
+ } else
+ d->custom_optarg = NULL;
+ d->nextchar = NULL;
+ } else {
+ /* This is an option that requires an argument. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ /*
+ * If we end this ARGV-element by taking the
+ * rest as an arg, we must advance to the next
+ * element now.
+ */
+ d->custom_optind++;
+ } else if (d->custom_optind == argc) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option requires an argument -- %c\n",
+ argv[0], c);
+ }
+ d->custom_optopt = c;
+ if (optstring[0] == ':')
+ c = ':';
+ else
+ c = '?';
+ } else
+ /*
+ * We already incremented `custom_optind' once;
+ * increment it again when taking next ARGV-elt
+ * as argument.
+ */
+ d->custom_optarg = argv[d->custom_optind++];
+ d->nextchar = NULL;
+ }
+ }
+ return c;
+}
+
+/*
+ * Scan elements of ARGV for option characters given in OPTSTRING.
+ *
+ * If an element of ARGV starts with '-', and is not exactly "-" or "--",
+ * then it is an option element. The characters of this element
+ * (aside from the initial '-') are option characters. If `getopt'
+ * is called repeatedly, it returns successively each of the option characters
+ * from each of the option elements.
+ *
+ * If `getopt' finds another option character, it returns that character,
+ * updating `custom_optind' and `nextchar' so that the next call to `getopt' can
+ * resume the scan with the following option character or ARGV-element.
+ *
+ * If there are no more option characters, `getopt' returns -1.
+ * Then `custom_optind' is the index in ARGV of the first ARGV-element
+ * that is not an option. (The ARGV-elements have been permuted
+ * so that those that are not options now come last.)
+ *
+ * OPTSTRING is a string containing the legitimate option characters.
+ * If an option character is seen that is not listed in OPTSTRING,
+ * return '?' after printing an error message. If you set `custom_opterr' to
+ * zero, the error message is suppressed but we still return '?'.
+ *
+ * If a char in OPTSTRING is followed by a colon, that means it wants an arg,
+ * so the following text in the same ARGV-element, or the text of the following
+ * ARGV-element, is returned in `custom_optarg'. Two colons mean an option that
+ * wants an optional arg; if there is text in the current ARGV-element,
+ * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero.
+ *
+ * If OPTSTRING starts with `-' or `+', it requests different methods of
+ * handling the non-option ARGV-elements.
+ * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
+ *
+ * Long-named options begin with `--' instead of `-'.
+ * Their names may be abbreviated as long as the abbreviation is unique
+ * or is an exact match for some defined option. If they have an
+ * argument, it follows the option name in the same ARGV-element, separated
+ * from the option name by a `=', or else the in next ARGV-element.
+ * When `getopt' finds a long-named option, it returns 0 if that option's
+ * `flag' field is nonzero, the value of the option's `val' field
+ * if the `flag' field is zero.
+ *
+ * The elements of ARGV aren't really const, because we permute them.
+ * But we pretend they're const in the prototype to be compatible
+ * with other systems.
+ *
+ * LONGOPTS is a vector of `struct option' terminated by an
+ * element containing a name which is zero.
+ *
+ * LONGIND returns the index in LONGOPT of the long-named option found.
+ * It is only valid when a long-named option has been found by the most
+ * recent call.
+ *
+ * Return the option character from OPTS just read. Return -1 when there are
+ * no more options. For unrecognized options, or options missing arguments,
+ * `custom_optopt' is set to the option letter, and '?' is returned.
+ *
+ * The OPTS string is a list of characters which are recognized option letters,
+ * optionally followed by colons, specifying that that letter takes an
+ * argument, to be placed in `custom_optarg'.
+ *
+ * If a letter in OPTS is followed by two colons, its argument is optional.
+ * This behavior is specific to the GNU `getopt'.
+ *
+ * The argument `--' causes premature termination of argument scanning,
+ * explicitly telling `getopt' that there are no more options. If OPTS begins
+ * with `--', then non-option arguments are treated as arguments to the option
+ * '\0'. This behavior is specific to the GNU `getopt'.
+ */
+
+static int getopt_internal_r(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ struct custom_getopt_data *d)
+{
+ int ret, print_errors = d->custom_opterr;
+
+ if (optstring[0] == ':')
+ print_errors = 0;
+ if (argc < 1)
+ return -1;
+ d->custom_optarg = NULL;
+
+ /*
+ * This is a big difference with GNU getopt, since optind == 0
+ * means initialization while here 1 means first call.
+ */
+ if (d->custom_optind == 0 || !d->initialized) {
+ if (d->custom_optind == 0)
+ d->custom_optind = 1; /* Don't scan ARGV[0], the program name. */
+ custom_getopt_initialize(d);
+ }
+ if (d->nextchar == NULL || *d->nextchar == '\0') {
+ ret = shuffle_argv(argc, argv, longopts, d);
+ if (ret)
+ return ret;
+ }
+ if (longopts && (argv[d->custom_optind][1] == '-' ))
+ return check_long_opt(argc, argv, optstring, longopts,
+ longind, print_errors, d);
+ return check_short_opt(argc, argv, optstring, print_errors, d);
+}
+
+static int custom_getopt_internal(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind)
+{
+ int result;
+ /* Keep a global copy of all internal members of d */
+ static struct custom_getopt_data d;
+
+ d.custom_optind = custom_optind;
+ d.custom_opterr = custom_opterr;
+ result = getopt_internal_r(argc, argv, optstring, longopts,
+ longind, &d);
+ custom_optind = d.custom_optind;
+ custom_optarg = d.custom_optarg;
+ custom_optopt = d.custom_optopt;
+ return result;
+}
+
+static int custom_getopt_long (int argc, char *const *argv, const char *options,
+ const struct option *long_options, int *opt_index)
+{
+ return custom_getopt_internal(argc, argv, options, long_options,
+ opt_index);
+}
+
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_clitkImageArithm_params.check_ambiguity
+ * @param override @see cmdline_parser_clitkImageArithm_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+static
+int update_arg(void *field, char **orig_field,
+ unsigned int *field_given, unsigned int *prev_given,
+ char *value, char *possible_values[], const char *default_value,
+ cmdline_parser_clitkImageArithm_arg_type arg_type,
+ int check_ambiguity, int override,
+ int no_free, int multiple_option,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *stop_char = 0;
+ const char *val = value;
+ int found;
+ char **string_field;
+
+ stop_char = 0;
+ found = 0;
+
+ if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+ {
+ if (short_opt != '-')
+ fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
+ package_name, long_opt, short_opt,
+ (additional_error ? additional_error : ""));
+ else
+ fprintf (stderr, "%s: `--%s' option given more than once%s\n",
+ package_name, long_opt,
+ (additional_error ? additional_error : ""));
+ return 1; /* failure */
+ }
+
+
+ if (field_given && *field_given && ! override)
+ return 0;
+ if (prev_given)
+ (*prev_given)++;
+ if (field_given)
+ (*field_given)++;
+ if (possible_values)
+ val = possible_values[found];
+
+ switch(arg_type) {
+ case ARG_FLAG:
+ *((int *)field) = !*((int *)field);
+ break;
+ case ARG_INT:
+ if (val) *((int *)field) = strtol (val, &stop_char, 0);
+ break;
+ case ARG_DOUBLE:
+ if (val) *((double *)field) = strtod (val, &stop_char);
+ break;
+ case ARG_STRING:
+ if (val) {
+ string_field = (char **)field;
+ if (!no_free && *string_field)
+ free (*string_field); /* free previous string */
+ *string_field = gengetopt_strdup (val);
+ }
+ break;
+ default:
+ break;
+ };
+
+ /* check numeric conversion */
+ switch(arg_type) {
+ case ARG_INT:
+ case ARG_DOUBLE:
+ if (val && !(stop_char && *stop_char == '\0')) {
+ fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+ return 1; /* failure */
+ }
+ break;
+ default:
+ ;
+ };
+
+ /* store the original value */
+ switch(arg_type) {
+ case ARG_NO:
+ case ARG_FLAG:
+ break;
+ default:
+ if (value && orig_field) {
+ if (no_free) {
+ *orig_field = value;
+ } else {
+ if (*orig_field)
+ free (*orig_field); /* free previous string */
+ *orig_field = gengetopt_strdup (value);
+ }
+ }
+ };
+
+ return 0; /* OK */
+}
+
+
+int
+cmdline_parser_clitkImageArithm_internal (int argc, char * const *argv, struct args_info_clitkImageArithm *args_info,
+ struct cmdline_parser_clitkImageArithm_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+
+ int error = 0;
+ struct args_info_clitkImageArithm local_args_info;
+
+ int override;
+ int initialize;
+ int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+ check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+ cmdline_parser_clitkImageArithm_init (args_info);
+
+ cmdline_parser_clitkImageArithm_init (&local_args_info);
+
+ optarg = 0;
+ optind = 0;
+ opterr = params->print_errors;
+ optopt = '?';
+
+ while (1)
+ {
+ int option_index = 0;
+
+ static struct option long_options[] = {
+ { "help", 0, NULL, 'h' },
+ { "version", 0, NULL, 'V' },
+ { "config", 1, NULL, 0 },
+ { "verbose", 0, NULL, 'v' },
+ { "imagetypes", 0, NULL, 0 },
+ { "input1", 1, NULL, 'i' },
+ { "input2", 1, NULL, 'j' },
+ { "output", 1, NULL, 'o' },
+ { "scalar", 1, NULL, 's' },
+ { "operation", 1, NULL, 't' },
+ { "pixelValue", 1, NULL, 0 },
+ { "setFloatOutput", 0, NULL, 'f' },
+ { NULL, 0, NULL, 0 }
+ };
+
+ custom_optarg = optarg;
+ custom_optind = optind;
+ custom_opterr = opterr;
+ custom_optopt = optopt;
+
+ c = custom_getopt_long (argc, argv, "hVvi:j:o:s:t:f", long_options, &option_index);
+
+ optarg = custom_optarg;
+ optind = custom_optind;
+ opterr = custom_opterr;
+ optopt = custom_optopt;
+
+ if (c == -1) break; /* Exit from `while (1)' loop. */
+
+ switch (c)
+ {
+ case 'h': /* Print help and exit. */
+ cmdline_parser_clitkImageArithm_print_help ();
+ cmdline_parser_clitkImageArithm_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'V': /* Print version and exit. */
+ cmdline_parser_clitkImageArithm_print_version ();
+ cmdline_parser_clitkImageArithm_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'v': /* Verbose. */
+
+
+ if (update_arg((void *)&(args_info->verbose_flag), 0, &(args_info->verbose_given),
+ &(local_args_info.verbose_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verbose", 'v',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'i': /* Input first image filename. */
+
+
+ if (update_arg( (void *)&(args_info->input1_arg),
+ &(args_info->input1_orig), &(args_info->input1_given),
+ &(local_args_info.input1_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "input1", 'i',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'j': /* Input second image filename. */
+
+
+ if (update_arg( (void *)&(args_info->input2_arg),
+ &(args_info->input2_orig), &(args_info->input2_given),
+ &(local_args_info.input2_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "input2", 'j',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'o': /* Output image filename. */
+
+
+ if (update_arg( (void *)&(args_info->output_arg),
+ &(args_info->output_orig), &(args_info->output_given),
+ &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "output", 'o',
+ additional_error))
+ goto failure;
+
+ break;
+ case 's': /* Scalar value. */
+
+
+ if (update_arg( (void *)&(args_info->scalar_arg),
+ &(args_info->scalar_orig), &(args_info->scalar_given),
+ &(local_args_info.scalar_given), optarg, 0, 0, ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "scalar", 's',
+ additional_error))
+ goto failure;
+
+ break;
+ case 't': /* Type of operation : \n With another image : 0=add*, 1=multiply, 2=divide,\n 3=max, 4=min, 5=absdiff, 6=squareddiff, 7=difference*, 8=relativ diff\n; For 'scalar' : 0=add*, 1=multiply*, 2=inverse,\n 3=max, 4=min 5=absval 6=squareval\n 7=log 8=exp 9=sqrt 10=EPID 11=divide* 12=normalize (divide by max) 13=-ln(I/IO)**; \n* operations supported with vector fields as inputs. \n** for fluence image, if pixel value == 0, consider value=0.5. */
+
+
+ if (update_arg( (void *)&(args_info->operation_arg),
+ &(args_info->operation_orig), &(args_info->operation_given),
+ &(local_args_info.operation_given), optarg, 0, "0", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "operation", 't',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'f': /* Set output to float pixel type. */
+
+
+ if (update_arg((void *)&(args_info->setFloatOutput_flag), 0, &(args_info->setFloatOutput_given),
+ &(local_args_info.setFloatOutput_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "setFloatOutput", 'f',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ /* Config file. */
+ if (strcmp (long_options[option_index].name, "config") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->config_arg),
+ &(args_info->config_orig), &(args_info->config_given),
+ &(local_args_info.config_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "config", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Display allowed image types. */
+ else if (strcmp (long_options[option_index].name, "imagetypes") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->imagetypes_flag), 0, &(args_info->imagetypes_given),
+ &(local_args_info.imagetypes_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "imagetypes", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Default value for NaN/Inf. */
+ else if (strcmp (long_options[option_index].name, "pixelValue") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->pixelValue_arg),
+ &(args_info->pixelValue_orig), &(args_info->pixelValue_given),
+ &(local_args_info.pixelValue_given), optarg, 0, "0.0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "pixelValue", '-',
+ additional_error))
+ goto failure;
+
+ }
+
+ break;
+ case '?': /* Invalid option. */
+ /* `getopt_long' already printed an error message. */
+ goto failure;
+
+ default: /* bug: option not considered. */
+ fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+
+
+ if (check_required)
+ {
+ error += cmdline_parser_clitkImageArithm_required2 (args_info, argv[0], additional_error);
+ }
+
+ cmdline_parser_clitkImageArithm_release (&local_args_info);
+
+ if ( error )
+ return (EXIT_FAILURE);
+
+ if (optind < argc)
+ {
+ int i = 0 ;
+ int found_prog_name = 0;
+ /* whether program name, i.e., argv[0], is in the remaining args
+ (this may happen with some implementations of getopt,
+ but surely not with the one included by gengetopt) */
+
+
+ args_info->inputs_num = argc - optind - found_prog_name;
+ args_info->inputs =
+ (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+ while (optind < argc)
+ args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
+ }
+
+ return 0;
+
+failure:
+
+ cmdline_parser_clitkImageArithm_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
+
+#ifndef CONFIG_FILE_LINE_SIZE
+#define CONFIG_FILE_LINE_SIZE 2048
+#endif
+#define ADDITIONAL_ERROR " in configuration file "
+
+#define CONFIG_FILE_LINE_BUFFER_SIZE (CONFIG_FILE_LINE_SIZE+3)
+/* 3 is for "--" and "=" */
+
+static int
+_cmdline_parser_clitkImageArithm_configfile (char * const filename, int *my_argc)
+{
+ FILE* file;
+ char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
+ char linebuf[CONFIG_FILE_LINE_SIZE];
+ int line_num = 0;
+ int result = 0, equal;
+ char *fopt, *farg;
+ char *str_index;
+ size_t len, next_token;
+ char delimiter;
+
+ if ((file = fopen(filename, "r")) == NULL)
+ {
+ fprintf (stderr, "%s: Error opening configuration file '%s'\n",
+ CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
+ {
+ ++line_num;
+ my_argv[0] = '\0';
+ len = strlen(linebuf);
+ if (len > (CONFIG_FILE_LINE_BUFFER_SIZE-1))
+ {
+ fprintf (stderr, "%s:%s:%d: Line too long in configuration file\n",
+ CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+
+ /* find first non-whitespace character in the line */
+ next_token = strspn (linebuf, " \t\r\n");
+ str_index = linebuf + next_token;
+
+ if ( str_index[0] == '\0' || str_index[0] == '#')
+ continue; /* empty line or comment line is skipped */
+
+ fopt = str_index;
+
+ /* truncate fopt at the end of the first non-valid character */
+ next_token = strcspn (fopt, " \t\r\n=");
+
+ if (fopt[next_token] == '\0') /* the line is over */
+ {
+ farg = NULL;
+ equal = 0;
+ goto noarg;
+ }
+
+ /* remember if equal sign is present */
+ equal = (fopt[next_token] == '=');
+ fopt[next_token++] = '\0';
+
+ /* advance pointers to the next token after the end of fopt */
+ next_token += strspn (fopt + next_token, " \t\r\n");
+
+ /* check for the presence of equal sign, and if so, skip it */
+ if ( !equal )
+ if ((equal = (fopt[next_token] == '=')))
+ {
+ next_token++;
+ next_token += strspn (fopt + next_token, " \t\r\n");
+ }
+ str_index += next_token;
+
+ /* find argument */
+ farg = str_index;
+ if ( farg[0] == '\"' || farg[0] == '\'' )
+ { /* quoted argument */
+ str_index = strchr (++farg, str_index[0] ); /* skip opening quote */
+ if (! str_index)
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: unterminated string in configuration file\n",
+ CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+ else
+ { /* read up the remaining part up to a delimiter */
+ next_token = strcspn (farg, " \t\r\n#\'\"");
+ str_index += next_token;
+ }
+
+ /* truncate farg at the delimiter and store it for further check */
+ delimiter = *str_index, *str_index++ = '\0';
+
+ /* everything but comment is illegal at the end of line */
+ if (delimiter != '\0' && delimiter != '#')
+ {
+ str_index += strspn(str_index, " \t\r\n");
+ if (*str_index != '\0' && *str_index != '#')
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: malformed string in configuration file\n",
+ CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+
+ noarg:
+ if (!strcmp(fopt,"include")) {
+ if (farg && *farg) {
+ result = _cmdline_parser_clitkImageArithm_configfile(farg, my_argc);
+ } else {
+ fprintf(stderr, "%s:%s:%d: include requires a filename argument.\n",
+ CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE, filename, line_num);
+ }
+ continue;
+ }
+ len = strlen(fopt);
+ strcat (my_argv, len > 1 ? "--" : "-");
+ strcat (my_argv, fopt);
+ if (len > 1 && ((farg && *farg) || equal))
+ strcat (my_argv, "=");
+ if (farg && *farg)
+ strcat (my_argv, farg);
+ ++(*my_argc);
+
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup(my_argv);
+ } /* while */
+
+ if (file)
+ fclose(file);
+ return result;
+}
+
+int
+cmdline_parser_clitkImageArithm_configfile (char * const filename,
+ struct args_info_clitkImageArithm *args_info,
+ int override, int initialize, int check_required)
+{
+ struct cmdline_parser_clitkImageArithm_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ return cmdline_parser_clitkImageArithm_config_file (filename, args_info, ¶ms);
+}
+
+int
+cmdline_parser_clitkImageArithm_config_file (char * const filename,
+ struct args_info_clitkImageArithm *args_info,
+ struct cmdline_parser_clitkImageArithm_params *params)
+{
+ int i, result;
+ int my_argc = 1;
+ char **my_argv_arg;
+ char *additional_error;
+
+ /* store the program name */
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup (CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE);
+
+ result = _cmdline_parser_clitkImageArithm_configfile(filename, &my_argc);
+
+ if (result != EXIT_FAILURE) {
+ my_argv_arg = (char **) malloc((my_argc+1) * sizeof(char *));
+ cmd_line_list_tmp = cmd_line_list;
+
+ for (i = my_argc - 1; i >= 0; --i) {
+ my_argv_arg[i] = cmd_line_list_tmp->string_arg;
+ cmd_line_list_tmp = cmd_line_list_tmp->next;
+ }
+
+ my_argv_arg[my_argc] = 0;
+
+ additional_error = (char *)malloc(strlen(filename) + strlen(ADDITIONAL_ERROR) + 1);
+ strcpy (additional_error, ADDITIONAL_ERROR);
+ strcat (additional_error, filename);
+ result =
+ cmdline_parser_clitkImageArithm_internal (my_argc, my_argv_arg, args_info,
+ params,
+ additional_error);
+
+ free (additional_error);
+ free (my_argv_arg);
+ }
+
+ free_cmd_list();
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkImageArithm_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
--- /dev/null
+/** @file clitkImageArithm_ggo.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CLITKIMAGEARITHM_GGO_H
+#define CLITKIMAGEARITHM_GGO_H
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE
+/** @brief the program name */
+#define CMDLINE_PARSER_CLITKIMAGEARITHM_PACKAGE "clitkImageArithm"
+#endif
+
+#ifndef CMDLINE_PARSER_CLITKIMAGEARITHM_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_CLITKIMAGEARITHM_VERSION "1.0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct args_info_clitkImageArithm
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ char * config_arg; /**< @brief Config file. */
+ char * config_orig; /**< @brief Config file original value given at command line. */
+ const char *config_help; /**< @brief Config file help description. */
+ int verbose_flag; /**< @brief Verbose (default=off). */
+ const char *verbose_help; /**< @brief Verbose help description. */
+ int imagetypes_flag; /**< @brief Display allowed image types (default=off). */
+ const char *imagetypes_help; /**< @brief Display allowed image types help description. */
+ char * input1_arg; /**< @brief Input first image filename. */
+ char * input1_orig; /**< @brief Input first image filename original value given at command line. */
+ const char *input1_help; /**< @brief Input first image filename help description. */
+ char * input2_arg; /**< @brief Input second image filename. */
+ char * input2_orig; /**< @brief Input second image filename original value given at command line. */
+ const char *input2_help; /**< @brief Input second image filename help description. */
+ char * output_arg; /**< @brief Output image filename. */
+ char * output_orig; /**< @brief Output image filename original value given at command line. */
+ const char *output_help; /**< @brief Output image filename help description. */
+ double scalar_arg; /**< @brief Scalar value. */
+ char * scalar_orig; /**< @brief Scalar value original value given at command line. */
+ const char *scalar_help; /**< @brief Scalar value help description. */
+ int operation_arg; /**< @brief Type of operation : \n With another image : 0=add*, 1=multiply, 2=divide,\n 3=max, 4=min, 5=absdiff, 6=squareddiff, 7=difference*, 8=relativ diff\n; For 'scalar' : 0=add*, 1=multiply*, 2=inverse,\n 3=max, 4=min 5=absval 6=squareval\n 7=log 8=exp 9=sqrt 10=EPID 11=divide* 12=normalize (divide by max) 13=-ln(I/IO)**; \n* operations supported with vector fields as inputs. \n** for fluence image, if pixel value == 0, consider value=0.5 (default='0'). */
+ char * operation_orig; /**< @brief Type of operation : \n With another image : 0=add*, 1=multiply, 2=divide,\n 3=max, 4=min, 5=absdiff, 6=squareddiff, 7=difference*, 8=relativ diff\n; For 'scalar' : 0=add*, 1=multiply*, 2=inverse,\n 3=max, 4=min 5=absval 6=squareval\n 7=log 8=exp 9=sqrt 10=EPID 11=divide* 12=normalize (divide by max) 13=-ln(I/IO)**; \n* operations supported with vector fields as inputs. \n** for fluence image, if pixel value == 0, consider value=0.5 original value given at command line. */
+ const char *operation_help; /**< @brief Type of operation : \n With another image : 0=add*, 1=multiply, 2=divide,\n 3=max, 4=min, 5=absdiff, 6=squareddiff, 7=difference*, 8=relativ diff\n; For 'scalar' : 0=add*, 1=multiply*, 2=inverse,\n 3=max, 4=min 5=absval 6=squareval\n 7=log 8=exp 9=sqrt 10=EPID 11=divide* 12=normalize (divide by max) 13=-ln(I/IO)**; \n* operations supported with vector fields as inputs. \n** for fluence image, if pixel value == 0, consider value=0.5 help description. */
+ double pixelValue_arg; /**< @brief Default value for NaN/Inf (default='0.0'). */
+ char * pixelValue_orig; /**< @brief Default value for NaN/Inf original value given at command line. */
+ const char *pixelValue_help; /**< @brief Default value for NaN/Inf help description. */
+ int setFloatOutput_flag; /**< @brief Set output to float pixel type (default=off). */
+ const char *setFloatOutput_help; /**< @brief Set output to float pixel type help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int config_given ; /**< @brief Whether config was given. */
+ unsigned int verbose_given ; /**< @brief Whether verbose was given. */
+ unsigned int imagetypes_given ; /**< @brief Whether imagetypes was given. */
+ unsigned int input1_given ; /**< @brief Whether input1 was given. */
+ unsigned int input2_given ; /**< @brief Whether input2 was given. */
+ unsigned int output_given ; /**< @brief Whether output was given. */
+ unsigned int scalar_given ; /**< @brief Whether scalar was given. */
+ unsigned int operation_given ; /**< @brief Whether operation was given. */
+ unsigned int pixelValue_given ; /**< @brief Whether pixelValue was given. */
+ unsigned int setFloatOutput_given ; /**< @brief Whether setFloatOutput was given. */
+
+ char **inputs ; /**< @brief unamed options (options without names) */
+ unsigned inputs_num ; /**< @brief unamed options number */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_clitkImageArithm_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure args_info_clitkImageArithm (default 1) */
+ int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+ int check_ambiguity; /**< @brief whether to check for options already specified in the option structure args_info_clitkImageArithm (default 0) */
+ int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *args_info_clitkImageArithm_purpose;
+/** @brief the usage string of the program */
+extern const char *args_info_clitkImageArithm_usage;
+/** @brief all the lines making the help output */
+extern const char *args_info_clitkImageArithm_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkImageArithm (int argc, char * const *argv,
+ struct args_info_clitkImageArithm *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkImageArithm_ext() instead
+ */
+int cmdline_parser_clitkImageArithm2 (int argc, char * const *argv,
+ struct args_info_clitkImageArithm *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkImageArithm_ext (int argc, char * const *argv,
+ struct args_info_clitkImageArithm *args_info,
+ struct cmdline_parser_clitkImageArithm_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkImageArithm_dump(FILE *outfile,
+ struct args_info_clitkImageArithm *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkImageArithm_file_save(const char *filename,
+ struct args_info_clitkImageArithm *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_clitkImageArithm_print_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_clitkImageArithm_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_clitkImageArithm_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_clitkImageArithm_params_init(struct cmdline_parser_clitkImageArithm_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_clitkImageArithm_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_clitkImageArithm_params structure
+ */
+struct cmdline_parser_clitkImageArithm_params *cmdline_parser_clitkImageArithm_params_create(void);
+
+/**
+ * Initializes the passed args_info_clitkImageArithm structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_clitkImageArithm_init (struct args_info_clitkImageArithm *args_info);
+/**
+ * Deallocates the string fields of the args_info_clitkImageArithm structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_clitkImageArithm_free (struct args_info_clitkImageArithm *args_info);
+
+/**
+ * The config file parser (deprecated version)
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkImageArithm_config_file() instead
+ */
+int cmdline_parser_clitkImageArithm_configfile (char * const filename,
+ struct args_info_clitkImageArithm *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The config file parser
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkImageArithm_config_file (char * const filename,
+ struct args_info_clitkImageArithm *args_info,
+ struct cmdline_parser_clitkImageArithm_params *params);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ * possible errors
+ * @return
+ */
+int cmdline_parser_clitkImageArithm_required (struct args_info_clitkImageArithm *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CLITKIMAGEARITHM_GGO_H */
--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22
+ generated with the following command:
+ /usr/local/bin/gengetopt --output-dir=/home/tbaudier/vv/vv_static/vv/vv_bin/tools --arg-struct-name=args_info_clitkMIP --func-name=cmdline_parser_clitkMIP --file-name=clitkMIP_ggo --unamed-opts --conf-parser --include-getopt
+
+ The developers of gengetopt consider the fixed text that goes in all
+ gengetopt output files to be in the public domain:
+ we make no copyright claims on it.
+*/
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+
+#include "clitkMIP_ggo.h"
+
+const char *args_info_clitkMIP_purpose = "";
+
+const char *args_info_clitkMIP_usage = "Usage: clitkMIP [OPTIONS]... [FILES]...";
+
+const char *args_info_clitkMIP_description = "";
+
+const char *args_info_clitkMIP_help[] = {
+ " -h, --help Print help and exit",
+ " -V, --version Print version and exit",
+ " --config=STRING Config file",
+ " -v, --verbose Verbose (default=off)",
+ " --imagetypes Display allowed image types (default=off)",
+ " -i, --input=STRING Input image filename",
+ " -o, --output=STRING Output image filename",
+ " -d, --dimension=INT Dimension along which to projetct",
+ 0
+};
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_INT
+} cmdline_parser_clitkMIP_arg_type;
+
+static
+void clear_given (struct args_info_clitkMIP *args_info);
+static
+void clear_args (struct args_info_clitkMIP *args_info);
+
+static int
+cmdline_parser_clitkMIP_internal (int argc, char * const *argv, struct args_info_clitkMIP *args_info,
+ struct cmdline_parser_clitkMIP_params *params, const char *additional_error);
+
+static int
+cmdline_parser_clitkMIP_required2 (struct args_info_clitkMIP *args_info, const char *prog_name, const char *additional_error);
+struct line_list
+{
+ char * string_arg;
+ struct line_list * next;
+};
+
+static struct line_list *cmd_line_list = 0;
+static struct line_list *cmd_line_list_tmp = 0;
+
+static void
+free_cmd_list(void)
+{
+ /* free the list of a previous call */
+ if (cmd_line_list)
+ {
+ while (cmd_line_list) {
+ cmd_line_list_tmp = cmd_line_list;
+ cmd_line_list = cmd_line_list->next;
+ free (cmd_line_list_tmp->string_arg);
+ free (cmd_line_list_tmp);
+ }
+ }
+}
+
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct args_info_clitkMIP *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->config_given = 0 ;
+ args_info->verbose_given = 0 ;
+ args_info->imagetypes_given = 0 ;
+ args_info->input_given = 0 ;
+ args_info->output_given = 0 ;
+ args_info->dimension_given = 0 ;
+}
+
+static
+void clear_args (struct args_info_clitkMIP *args_info)
+{
+ args_info->config_arg = NULL;
+ args_info->config_orig = NULL;
+ args_info->verbose_flag = 0;
+ args_info->imagetypes_flag = 0;
+ args_info->input_arg = NULL;
+ args_info->input_orig = NULL;
+ args_info->output_arg = NULL;
+ args_info->output_orig = NULL;
+ args_info->dimension_orig = NULL;
+
+}
+
+static
+void init_args_info(struct args_info_clitkMIP *args_info)
+{
+
+
+ args_info->help_help = args_info_clitkMIP_help[0] ;
+ args_info->version_help = args_info_clitkMIP_help[1] ;
+ args_info->config_help = args_info_clitkMIP_help[2] ;
+ args_info->verbose_help = args_info_clitkMIP_help[3] ;
+ args_info->imagetypes_help = args_info_clitkMIP_help[4] ;
+ args_info->input_help = args_info_clitkMIP_help[5] ;
+ args_info->output_help = args_info_clitkMIP_help[6] ;
+ args_info->dimension_help = args_info_clitkMIP_help[7] ;
+
+}
+
+void
+cmdline_parser_clitkMIP_print_version (void)
+{
+ printf ("%s %s\n", CMDLINE_PARSER_CLITKMIP_PACKAGE, CMDLINE_PARSER_CLITKMIP_VERSION);
+}
+
+static void print_help_common(void) {
+ cmdline_parser_clitkMIP_print_version ();
+
+ if (strlen(args_info_clitkMIP_purpose) > 0)
+ printf("\n%s\n", args_info_clitkMIP_purpose);
+
+ if (strlen(args_info_clitkMIP_usage) > 0)
+ printf("\n%s\n", args_info_clitkMIP_usage);
+
+ printf("\n");
+
+ if (strlen(args_info_clitkMIP_description) > 0)
+ printf("%s\n", args_info_clitkMIP_description);
+}
+
+void
+cmdline_parser_clitkMIP_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (args_info_clitkMIP_help[i])
+ printf("%s\n", args_info_clitkMIP_help[i++]);
+}
+
+void
+cmdline_parser_clitkMIP_init (struct args_info_clitkMIP *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+
+ args_info->inputs = NULL;
+ args_info->inputs_num = 0;
+}
+
+void
+cmdline_parser_clitkMIP_params_init(struct cmdline_parser_clitkMIP_params *params)
+{
+ if (params)
+ {
+ params->override = 0;
+ params->initialize = 1;
+ params->check_required = 1;
+ params->check_ambiguity = 0;
+ params->print_errors = 1;
+ }
+}
+
+struct cmdline_parser_clitkMIP_params *
+cmdline_parser_clitkMIP_params_create(void)
+{
+ struct cmdline_parser_clitkMIP_params *params =
+ (struct cmdline_parser_clitkMIP_params *)malloc(sizeof(struct cmdline_parser_clitkMIP_params));
+ cmdline_parser_clitkMIP_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+
+static void
+cmdline_parser_clitkMIP_release (struct args_info_clitkMIP *args_info)
+{
+ unsigned int i;
+ free_string_field (&(args_info->config_arg));
+ free_string_field (&(args_info->config_orig));
+ free_string_field (&(args_info->input_arg));
+ free_string_field (&(args_info->input_orig));
+ free_string_field (&(args_info->output_arg));
+ free_string_field (&(args_info->output_orig));
+ free_string_field (&(args_info->dimension_orig));
+
+
+ for (i = 0; i < args_info->inputs_num; ++i)
+ free (args_info->inputs [i]);
+
+ if (args_info->inputs_num)
+ free (args_info->inputs);
+
+ clear_given (args_info);
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+ if (arg) {
+ fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+ } else {
+ fprintf(outfile, "%s\n", opt);
+ }
+}
+
+
+int
+cmdline_parser_clitkMIP_dump(FILE *outfile, struct args_info_clitkMIP *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_CLITKMIP_PACKAGE);
+ return EXIT_FAILURE;
+ }
+
+ if (args_info->help_given)
+ write_into_file(outfile, "help", 0, 0 );
+ if (args_info->version_given)
+ write_into_file(outfile, "version", 0, 0 );
+ if (args_info->config_given)
+ write_into_file(outfile, "config", args_info->config_orig, 0);
+ if (args_info->verbose_given)
+ write_into_file(outfile, "verbose", 0, 0 );
+ if (args_info->imagetypes_given)
+ write_into_file(outfile, "imagetypes", 0, 0 );
+ if (args_info->input_given)
+ write_into_file(outfile, "input", args_info->input_orig, 0);
+ if (args_info->output_given)
+ write_into_file(outfile, "output", args_info->output_orig, 0);
+ if (args_info->dimension_given)
+ write_into_file(outfile, "dimension", args_info->dimension_orig, 0);
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+cmdline_parser_clitkMIP_file_save(const char *filename, struct args_info_clitkMIP *args_info)
+{
+ FILE *outfile;
+ int i = 0;
+
+ outfile = fopen(filename, "w");
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_CLITKMIP_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = cmdline_parser_clitkMIP_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+cmdline_parser_clitkMIP_free (struct args_info_clitkMIP *args_info)
+{
+ cmdline_parser_clitkMIP_release (args_info);
+}
+
+/** @brief replacement of strdup, which is not standard */
+char *
+gengetopt_strdup (const char *s)
+{
+ char *result = NULL;
+ if (!s)
+ return result;
+
+ result = (char*)malloc(strlen(s) + 1);
+ if (result == (char*)0)
+ return (char*)0;
+ strcpy(result, s);
+ return result;
+}
+
+int
+cmdline_parser_clitkMIP (int argc, char * const *argv, struct args_info_clitkMIP *args_info)
+{
+ return cmdline_parser_clitkMIP2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+cmdline_parser_clitkMIP_ext (int argc, char * const *argv, struct args_info_clitkMIP *args_info,
+ struct cmdline_parser_clitkMIP_params *params)
+{
+ int result;
+ result = cmdline_parser_clitkMIP_internal (argc, argv, args_info, params, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkMIP_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkMIP2 (int argc, char * const *argv, struct args_info_clitkMIP *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct cmdline_parser_clitkMIP_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = cmdline_parser_clitkMIP_internal (argc, argv, args_info, ¶ms, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkMIP_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkMIP_required (struct args_info_clitkMIP *args_info, const char *prog_name)
+{
+ int result = EXIT_SUCCESS;
+
+ if (cmdline_parser_clitkMIP_required2(args_info, prog_name, NULL) > 0)
+ result = EXIT_FAILURE;
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkMIP_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkMIP_required2 (struct args_info_clitkMIP *args_info, const char *prog_name, const char *additional_error)
+{
+ int error = 0;
+
+ /* checks for required options */
+ if (! args_info->input_given)
+ {
+ fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (! args_info->output_given)
+ {
+ fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (! args_info->dimension_given)
+ {
+ fprintf (stderr, "%s: '--dimension' ('-d') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+
+ /* checks for dependences among options */
+
+ return error;
+}
+
+/*
+ * Extracted from the glibc source tree, version 2.3.6
+ *
+ * Licensed under the GPL as per the whole glibc source tree.
+ *
+ * This file was modified so that getopt_long can be called
+ * many times without risking previous memory to be spoiled.
+ *
+ * Modified by Andre Noll and Lorenzo Bettini for use in
+ * GNU gengetopt generated files.
+ *
+ */
+
+/*
+ * we must include anything we need since this file is not thought to be
+ * inserted in a file already using getopt.h
+ *
+ * Lorenzo
+ */
+
+struct option
+{
+ const char *name;
+ /* has_arg can't be an enum because some compilers complain about
+ type mismatches in all the code that assumes it is an int. */
+ int has_arg;
+ int *flag;
+ int val;
+};
+
+/* For communication from `getopt' to the caller.
+ When `getopt' finds an option that takes an argument,
+ the argument value is returned here.
+ Also, when `ordering' is RETURN_IN_ORDER,
+ each non-option ARGV-element is returned here. */
+
+static char *optarg;
+
+/* Index in ARGV of the next element to be scanned.
+ This is used for communication to and from the caller
+ and for communication between successive calls to `getopt'.
+
+ On entry to `getopt', zero means this is the first call; initialize.
+
+ When `getopt' returns -1, this is the index of the first of the
+ non-option elements that the caller should itself scan.
+
+ Otherwise, `optind' communicates from one call to the next
+ how much of ARGV has been scanned so far. */
+
+static int optind;
+
+/* Callers store zero here to inhibit the error message `getopt' prints
+ for unrecognized options. */
+
+static int opterr;
+
+/* Set to an option character which was unrecognized. */
+
+static int optopt;
+
+/* This version of `getopt' appears to the caller like standard Unix `getopt'
+ but it behaves differently for the user, since it allows the user
+ to intersperse the options with the other arguments.
+
+ As `getopt' works, it permutes the elements of ARGV so that,
+ when it is done, all the options precede everything else. Thus
+ all application programs are extended to handle flexible argument order.
+*/
+/*
+ If the field `flag' is not NULL, it points to a variable that is set
+ to the value given in the field `val' when the option is found, but
+ left unchanged if the option is not found.
+
+ To have a long-named option do something other than set an `int' to
+ a compiled-in constant, such as set a value from `custom_optarg', set the
+ option's `flag' field to zero and its `val' field to a nonzero
+ value (the equivalent single-letter option character, if there is
+ one). For long options that have a zero `flag' field, `getopt'
+ returns the contents of the `val' field. */
+
+/* Names for the values of the `has_arg' field of `struct option'. */
+#ifndef no_argument
+#define no_argument 0
+#endif
+
+#ifndef required_argument
+#define required_argument 1
+#endif
+
+#ifndef optional_argument
+#define optional_argument 2
+#endif
+
+struct custom_getopt_data {
+ /*
+ * These have exactly the same meaning as the corresponding global variables,
+ * except that they are used for the reentrant versions of getopt.
+ */
+ int custom_optind;
+ int custom_opterr;
+ int custom_optopt;
+ char *custom_optarg;
+
+ /* True if the internal members have been initialized. */
+ int initialized;
+
+ /*
+ * The next char to be scanned in the option-element in which the last option
+ * character we returned was found. This allows us to pick up the scan where
+ * we left off. If this is zero, or a null string, it means resume the scan by
+ * advancing to the next ARGV-element.
+ */
+ char *nextchar;
+
+ /*
+ * Describe the part of ARGV that contains non-options that have been skipped.
+ * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is
+ * the index after the last of them.
+ */
+ int first_nonopt;
+ int last_nonopt;
+};
+
+/*
+ * the variables optarg, optind, opterr and optopt are renamed with
+ * the custom_ prefix so that they don't interfere with getopt ones.
+ *
+ * Moreover they're static so they are visible only from within the
+ * file where this very file will be included.
+ */
+
+/*
+ * For communication from `custom_getopt' to the caller. When `custom_getopt' finds an
+ * option that takes an argument, the argument value is returned here.
+ */
+static char *custom_optarg;
+
+/*
+ * Index in ARGV of the next element to be scanned. This is used for
+ * communication to and from the caller and for communication between
+ * successive calls to `custom_getopt'.
+ *
+ * On entry to `custom_getopt', 1 means this is the first call; initialize.
+ *
+ * When `custom_getopt' returns -1, this is the index of the first of the non-option
+ * elements that the caller should itself scan.
+ *
+ * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV
+ * has been scanned so far.
+ *
+ * 1003.2 says this must be 1 before any call.
+ */
+static int custom_optind = 1;
+
+/*
+ * Callers store zero here to inhibit the error message for unrecognized
+ * options.
+ */
+static int custom_opterr = 1;
+
+/*
+ * Set to an option character which was unrecognized. This must be initialized
+ * on some systems to avoid linking in the system's own getopt implementation.
+ */
+static int custom_optopt = '?';
+
+/*
+ * Exchange two adjacent subsequences of ARGV. One subsequence is elements
+ * [first_nonopt,last_nonopt) which contains all the non-options that have been
+ * skipped so far. The other is elements [last_nonopt,custom_optind), which contains
+ * all the options processed since those non-options were skipped.
+ * `first_nonopt' and `last_nonopt' are relocated so that they describe the new
+ * indices of the non-options in ARGV after they are moved.
+ */
+static void exchange(char **argv, struct custom_getopt_data *d)
+{
+ int bottom = d->first_nonopt;
+ int middle = d->last_nonopt;
+ int top = d->custom_optind;
+ char *tem;
+
+ /*
+ * Exchange the shorter segment with the far end of the longer segment.
+ * That puts the shorter segment into the right place. It leaves the
+ * longer segment in the right place overall, but it consists of two
+ * parts that need to be swapped next.
+ */
+ while (top > middle && middle > bottom) {
+ if (top - middle > middle - bottom) {
+ /* Bottom segment is the short one. */
+ int len = middle - bottom;
+ int i;
+
+ /* Swap it with the top part of the top segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] =
+ argv[top - (middle - bottom) + i];
+ argv[top - (middle - bottom) + i] = tem;
+ }
+ /* Exclude the moved bottom segment from further swapping. */
+ top -= len;
+ } else {
+ /* Top segment is the short one. */
+ int len = top - middle;
+ int i;
+
+ /* Swap it with the bottom part of the bottom segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] = argv[middle + i];
+ argv[middle + i] = tem;
+ }
+ /* Exclude the moved top segment from further swapping. */
+ bottom += len;
+ }
+ }
+ /* Update records for the slots the non-options now occupy. */
+ d->first_nonopt += (d->custom_optind - d->last_nonopt);
+ d->last_nonopt = d->custom_optind;
+}
+
+/* Initialize the internal data when the first call is made. */
+static void custom_getopt_initialize(struct custom_getopt_data *d)
+{
+ /*
+ * Start processing options with ARGV-element 1 (since ARGV-element 0
+ * is the program name); the sequence of previously skipped non-option
+ * ARGV-elements is empty.
+ */
+ d->first_nonopt = d->last_nonopt = d->custom_optind;
+ d->nextchar = NULL;
+ d->initialized = 1;
+}
+
+#define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0')
+
+/* return: zero: continue, nonzero: return given value to user */
+static int shuffle_argv(int argc, char *const *argv,const struct option *longopts,
+ struct custom_getopt_data *d)
+{
+ /*
+ * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been
+ * moved back by the user (who may also have changed the arguments).
+ */
+ if (d->last_nonopt > d->custom_optind)
+ d->last_nonopt = d->custom_optind;
+ if (d->first_nonopt > d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * If we have just processed some options following some
+ * non-options, exchange them so that the options come first.
+ */
+ if (d->first_nonopt != d->last_nonopt &&
+ d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->last_nonopt != d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * Skip any additional non-options and extend the range of
+ * non-options previously skipped.
+ */
+ while (d->custom_optind < argc && NONOPTION_P)
+ d->custom_optind++;
+ d->last_nonopt = d->custom_optind;
+ /*
+ * The special ARGV-element `--' means premature end of options. Skip
+ * it like a null option, then exchange with previous non-options as if
+ * it were an option, then skip everything else like a non-option.
+ */
+ if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) {
+ d->custom_optind++;
+ if (d->first_nonopt != d->last_nonopt
+ && d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->first_nonopt == d->last_nonopt)
+ d->first_nonopt = d->custom_optind;
+ d->last_nonopt = argc;
+ d->custom_optind = argc;
+ }
+ /*
+ * If we have done all the ARGV-elements, stop the scan and back over
+ * any non-options that we skipped and permuted.
+ */
+ if (d->custom_optind == argc) {
+ /*
+ * Set the next-arg-index to point at the non-options that we
+ * previously skipped, so the caller will digest them.
+ */
+ if (d->first_nonopt != d->last_nonopt)
+ d->custom_optind = d->first_nonopt;
+ return -1;
+ }
+ /*
+ * If we have come to a non-option and did not permute it, either stop
+ * the scan or describe it to the caller and pass it by.
+ */
+ if (NONOPTION_P) {
+ d->custom_optarg = argv[d->custom_optind++];
+ return 1;
+ }
+ /*
+ * We have found another option-ARGV-element. Skip the initial
+ * punctuation.
+ */
+ d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-'));
+ return 0;
+}
+
+/*
+ * Check whether the ARGV-element is a long option.
+ *
+ * If there's a long option "fubar" and the ARGV-element is "-fu", consider
+ * that an abbreviation of the long option, just like "--fu", and not "-f" with
+ * arg "u".
+ *
+ * This distinction seems to be the most useful approach.
+ *
+ */
+static int check_long_opt(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char *nameend;
+ const struct option *p;
+ const struct option *pfound = NULL;
+ int exact = 0;
+ int ambig = 0;
+ int indfound = -1;
+ int option_index;
+
+ for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++)
+ /* Do nothing. */ ;
+
+ /* Test all long options for either exact match or abbreviated matches */
+ for (p = longopts, option_index = 0; p->name; p++, option_index++)
+ if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) {
+ if ((unsigned int) (nameend - d->nextchar)
+ == (unsigned int) strlen(p->name)) {
+ /* Exact match found. */
+ pfound = p;
+ indfound = option_index;
+ exact = 1;
+ break;
+ } else if (pfound == NULL) {
+ /* First nonexact match found. */
+ pfound = p;
+ indfound = option_index;
+ } else if (pfound->has_arg != p->has_arg
+ || pfound->flag != p->flag
+ || pfound->val != p->val)
+ /* Second or later nonexact match found. */
+ ambig = 1;
+ }
+ if (ambig && !exact) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' is ambiguous\n",
+ argv[0], argv[d->custom_optind]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+ }
+ if (pfound) {
+ option_index = indfound;
+ d->custom_optind++;
+ if (*nameend) {
+ if (pfound->has_arg != no_argument)
+ d->custom_optarg = nameend + 1;
+ else {
+ if (print_errors) {
+ if (argv[d->custom_optind - 1][1] == '-') {
+ /* --option */
+ fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n",
+ argv[0], pfound->name);
+ } else {
+ /* +option or -option */
+ fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n",
+ argv[0], argv[d->custom_optind - 1][0], pfound->name);
+ }
+
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return '?';
+ }
+ } else if (pfound->has_arg == required_argument) {
+ if (d->custom_optind < argc)
+ d->custom_optarg = argv[d->custom_optind++];
+ else {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' requires an argument\n",
+ argv[0],
+ argv[d->custom_optind - 1]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return optstring[0] == ':' ? ':' : '?';
+ }
+ }
+ d->nextchar += strlen(d->nextchar);
+ if (longind != NULL)
+ *longind = option_index;
+ if (pfound->flag) {
+ *(pfound->flag) = pfound->val;
+ return 0;
+ }
+ return pfound->val;
+ }
+ /*
+ * Can't find it as a long option. If this is not getopt_long_only, or
+ * the option starts with '--' or is not a valid short option, then
+ * it's an error. Otherwise interpret it as a short option.
+ */
+ if (print_errors) {
+ if (argv[d->custom_optind][1] == '-') {
+ /* --option */
+ fprintf(stderr,
+ "%s: unrecognized option `--%s'\n",
+ argv[0], d->nextchar);
+ } else {
+ /* +option or -option */
+ fprintf(stderr,
+ "%s: unrecognized option `%c%s'\n",
+ argv[0], argv[d->custom_optind][0],
+ d->nextchar);
+ }
+ }
+ d->nextchar = (char *) "";
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+}
+
+static int check_short_opt(int argc, char *const *argv, const char *optstring,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char c = *d->nextchar++;
+ char *temp = strchr(optstring, c);
+
+ /* Increment `custom_optind' when we start to process its last character. */
+ if (*d->nextchar == '\0')
+ ++d->custom_optind;
+ if (!temp || c == ':') {
+ if (print_errors)
+ fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
+
+ d->custom_optopt = c;
+ return '?';
+ }
+ if (temp[1] == ':') {
+ if (temp[2] == ':') {
+ /* This is an option that accepts an argument optionally. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ d->custom_optind++;
+ } else
+ d->custom_optarg = NULL;
+ d->nextchar = NULL;
+ } else {
+ /* This is an option that requires an argument. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ /*
+ * If we end this ARGV-element by taking the
+ * rest as an arg, we must advance to the next
+ * element now.
+ */
+ d->custom_optind++;
+ } else if (d->custom_optind == argc) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option requires an argument -- %c\n",
+ argv[0], c);
+ }
+ d->custom_optopt = c;
+ if (optstring[0] == ':')
+ c = ':';
+ else
+ c = '?';
+ } else
+ /*
+ * We already incremented `custom_optind' once;
+ * increment it again when taking next ARGV-elt
+ * as argument.
+ */
+ d->custom_optarg = argv[d->custom_optind++];
+ d->nextchar = NULL;
+ }
+ }
+ return c;
+}
+
+/*
+ * Scan elements of ARGV for option characters given in OPTSTRING.
+ *
+ * If an element of ARGV starts with '-', and is not exactly "-" or "--",
+ * then it is an option element. The characters of this element
+ * (aside from the initial '-') are option characters. If `getopt'
+ * is called repeatedly, it returns successively each of the option characters
+ * from each of the option elements.
+ *
+ * If `getopt' finds another option character, it returns that character,
+ * updating `custom_optind' and `nextchar' so that the next call to `getopt' can
+ * resume the scan with the following option character or ARGV-element.
+ *
+ * If there are no more option characters, `getopt' returns -1.
+ * Then `custom_optind' is the index in ARGV of the first ARGV-element
+ * that is not an option. (The ARGV-elements have been permuted
+ * so that those that are not options now come last.)
+ *
+ * OPTSTRING is a string containing the legitimate option characters.
+ * If an option character is seen that is not listed in OPTSTRING,
+ * return '?' after printing an error message. If you set `custom_opterr' to
+ * zero, the error message is suppressed but we still return '?'.
+ *
+ * If a char in OPTSTRING is followed by a colon, that means it wants an arg,
+ * so the following text in the same ARGV-element, or the text of the following
+ * ARGV-element, is returned in `custom_optarg'. Two colons mean an option that
+ * wants an optional arg; if there is text in the current ARGV-element,
+ * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero.
+ *
+ * If OPTSTRING starts with `-' or `+', it requests different methods of
+ * handling the non-option ARGV-elements.
+ * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
+ *
+ * Long-named options begin with `--' instead of `-'.
+ * Their names may be abbreviated as long as the abbreviation is unique
+ * or is an exact match for some defined option. If they have an
+ * argument, it follows the option name in the same ARGV-element, separated
+ * from the option name by a `=', or else the in next ARGV-element.
+ * When `getopt' finds a long-named option, it returns 0 if that option's
+ * `flag' field is nonzero, the value of the option's `val' field
+ * if the `flag' field is zero.
+ *
+ * The elements of ARGV aren't really const, because we permute them.
+ * But we pretend they're const in the prototype to be compatible
+ * with other systems.
+ *
+ * LONGOPTS is a vector of `struct option' terminated by an
+ * element containing a name which is zero.
+ *
+ * LONGIND returns the index in LONGOPT of the long-named option found.
+ * It is only valid when a long-named option has been found by the most
+ * recent call.
+ *
+ * Return the option character from OPTS just read. Return -1 when there are
+ * no more options. For unrecognized options, or options missing arguments,
+ * `custom_optopt' is set to the option letter, and '?' is returned.
+ *
+ * The OPTS string is a list of characters which are recognized option letters,
+ * optionally followed by colons, specifying that that letter takes an
+ * argument, to be placed in `custom_optarg'.
+ *
+ * If a letter in OPTS is followed by two colons, its argument is optional.
+ * This behavior is specific to the GNU `getopt'.
+ *
+ * The argument `--' causes premature termination of argument scanning,
+ * explicitly telling `getopt' that there are no more options. If OPTS begins
+ * with `--', then non-option arguments are treated as arguments to the option
+ * '\0'. This behavior is specific to the GNU `getopt'.
+ */
+
+static int getopt_internal_r(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ struct custom_getopt_data *d)
+{
+ int ret, print_errors = d->custom_opterr;
+
+ if (optstring[0] == ':')
+ print_errors = 0;
+ if (argc < 1)
+ return -1;
+ d->custom_optarg = NULL;
+
+ /*
+ * This is a big difference with GNU getopt, since optind == 0
+ * means initialization while here 1 means first call.
+ */
+ if (d->custom_optind == 0 || !d->initialized) {
+ if (d->custom_optind == 0)
+ d->custom_optind = 1; /* Don't scan ARGV[0], the program name. */
+ custom_getopt_initialize(d);
+ }
+ if (d->nextchar == NULL || *d->nextchar == '\0') {
+ ret = shuffle_argv(argc, argv, longopts, d);
+ if (ret)
+ return ret;
+ }
+ if (longopts && (argv[d->custom_optind][1] == '-' ))
+ return check_long_opt(argc, argv, optstring, longopts,
+ longind, print_errors, d);
+ return check_short_opt(argc, argv, optstring, print_errors, d);
+}
+
+static int custom_getopt_internal(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind)
+{
+ int result;
+ /* Keep a global copy of all internal members of d */
+ static struct custom_getopt_data d;
+
+ d.custom_optind = custom_optind;
+ d.custom_opterr = custom_opterr;
+ result = getopt_internal_r(argc, argv, optstring, longopts,
+ longind, &d);
+ custom_optind = d.custom_optind;
+ custom_optarg = d.custom_optarg;
+ custom_optopt = d.custom_optopt;
+ return result;
+}
+
+static int custom_getopt_long (int argc, char *const *argv, const char *options,
+ const struct option *long_options, int *opt_index)
+{
+ return custom_getopt_internal(argc, argv, options, long_options,
+ opt_index);
+}
+
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_clitkMIP_params.check_ambiguity
+ * @param override @see cmdline_parser_clitkMIP_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+static
+int update_arg(void *field, char **orig_field,
+ unsigned int *field_given, unsigned int *prev_given,
+ char *value, char *possible_values[], const char *default_value,
+ cmdline_parser_clitkMIP_arg_type arg_type,
+ int check_ambiguity, int override,
+ int no_free, int multiple_option,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *stop_char = 0;
+ const char *val = value;
+ int found;
+ char **string_field;
+
+ stop_char = 0;
+ found = 0;
+
+ if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+ {
+ if (short_opt != '-')
+ fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
+ package_name, long_opt, short_opt,
+ (additional_error ? additional_error : ""));
+ else
+ fprintf (stderr, "%s: `--%s' option given more than once%s\n",
+ package_name, long_opt,
+ (additional_error ? additional_error : ""));
+ return 1; /* failure */
+ }
+
+
+ if (field_given && *field_given && ! override)
+ return 0;
+ if (prev_given)
+ (*prev_given)++;
+ if (field_given)
+ (*field_given)++;
+ if (possible_values)
+ val = possible_values[found];
+
+ switch(arg_type) {
+ case ARG_FLAG:
+ *((int *)field) = !*((int *)field);
+ break;
+ case ARG_INT:
+ if (val) *((int *)field) = strtol (val, &stop_char, 0);
+ break;
+ case ARG_STRING:
+ if (val) {
+ string_field = (char **)field;
+ if (!no_free && *string_field)
+ free (*string_field); /* free previous string */
+ *string_field = gengetopt_strdup (val);
+ }
+ break;
+ default:
+ break;
+ };
+
+ /* check numeric conversion */
+ switch(arg_type) {
+ case ARG_INT:
+ if (val && !(stop_char && *stop_char == '\0')) {
+ fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+ return 1; /* failure */
+ }
+ break;
+ default:
+ ;
+ };
+
+ /* store the original value */
+ switch(arg_type) {
+ case ARG_NO:
+ case ARG_FLAG:
+ break;
+ default:
+ if (value && orig_field) {
+ if (no_free) {
+ *orig_field = value;
+ } else {
+ if (*orig_field)
+ free (*orig_field); /* free previous string */
+ *orig_field = gengetopt_strdup (value);
+ }
+ }
+ };
+
+ return 0; /* OK */
+}
+
+
+int
+cmdline_parser_clitkMIP_internal (int argc, char * const *argv, struct args_info_clitkMIP *args_info,
+ struct cmdline_parser_clitkMIP_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+
+ int error = 0;
+ struct args_info_clitkMIP local_args_info;
+
+ int override;
+ int initialize;
+ int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+ check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+ cmdline_parser_clitkMIP_init (args_info);
+
+ cmdline_parser_clitkMIP_init (&local_args_info);
+
+ optarg = 0;
+ optind = 0;
+ opterr = params->print_errors;
+ optopt = '?';
+
+ while (1)
+ {
+ int option_index = 0;
+
+ static struct option long_options[] = {
+ { "help", 0, NULL, 'h' },
+ { "version", 0, NULL, 'V' },
+ { "config", 1, NULL, 0 },
+ { "verbose", 0, NULL, 'v' },
+ { "imagetypes", 0, NULL, 0 },
+ { "input", 1, NULL, 'i' },
+ { "output", 1, NULL, 'o' },
+ { "dimension", 1, NULL, 'd' },
+ { NULL, 0, NULL, 0 }
+ };
+
+ custom_optarg = optarg;
+ custom_optind = optind;
+ custom_opterr = opterr;
+ custom_optopt = optopt;
+
+ c = custom_getopt_long (argc, argv, "hVvi:o:d:", long_options, &option_index);
+
+ optarg = custom_optarg;
+ optind = custom_optind;
+ opterr = custom_opterr;
+ optopt = custom_optopt;
+
+ if (c == -1) break; /* Exit from `while (1)' loop. */
+
+ switch (c)
+ {
+ case 'h': /* Print help and exit. */
+ cmdline_parser_clitkMIP_print_help ();
+ cmdline_parser_clitkMIP_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'V': /* Print version and exit. */
+ cmdline_parser_clitkMIP_print_version ();
+ cmdline_parser_clitkMIP_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'v': /* Verbose. */
+
+
+ if (update_arg((void *)&(args_info->verbose_flag), 0, &(args_info->verbose_given),
+ &(local_args_info.verbose_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verbose", 'v',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'i': /* Input image filename. */
+
+
+ if (update_arg( (void *)&(args_info->input_arg),
+ &(args_info->input_orig), &(args_info->input_given),
+ &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "input", 'i',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'o': /* Output image filename. */
+
+
+ if (update_arg( (void *)&(args_info->output_arg),
+ &(args_info->output_orig), &(args_info->output_given),
+ &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "output", 'o',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'd': /* Dimension along which to projetct. */
+
+
+ if (update_arg( (void *)&(args_info->dimension_arg),
+ &(args_info->dimension_orig), &(args_info->dimension_given),
+ &(local_args_info.dimension_given), optarg, 0, 0, ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "dimension", 'd',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ /* Config file. */
+ if (strcmp (long_options[option_index].name, "config") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->config_arg),
+ &(args_info->config_orig), &(args_info->config_given),
+ &(local_args_info.config_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "config", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Display allowed image types. */
+ else if (strcmp (long_options[option_index].name, "imagetypes") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->imagetypes_flag), 0, &(args_info->imagetypes_given),
+ &(local_args_info.imagetypes_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "imagetypes", '-',
+ additional_error))
+ goto failure;
+
+ }
+
+ break;
+ case '?': /* Invalid option. */
+ /* `getopt_long' already printed an error message. */
+ goto failure;
+
+ default: /* bug: option not considered. */
+ fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_CLITKMIP_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+
+
+ if (check_required)
+ {
+ error += cmdline_parser_clitkMIP_required2 (args_info, argv[0], additional_error);
+ }
+
+ cmdline_parser_clitkMIP_release (&local_args_info);
+
+ if ( error )
+ return (EXIT_FAILURE);
+
+ if (optind < argc)
+ {
+ int i = 0 ;
+ int found_prog_name = 0;
+ /* whether program name, i.e., argv[0], is in the remaining args
+ (this may happen with some implementations of getopt,
+ but surely not with the one included by gengetopt) */
+
+
+ args_info->inputs_num = argc - optind - found_prog_name;
+ args_info->inputs =
+ (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+ while (optind < argc)
+ args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
+ }
+
+ return 0;
+
+failure:
+
+ cmdline_parser_clitkMIP_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
+
+#ifndef CONFIG_FILE_LINE_SIZE
+#define CONFIG_FILE_LINE_SIZE 2048
+#endif
+#define ADDITIONAL_ERROR " in configuration file "
+
+#define CONFIG_FILE_LINE_BUFFER_SIZE (CONFIG_FILE_LINE_SIZE+3)
+/* 3 is for "--" and "=" */
+
+static int
+_cmdline_parser_clitkMIP_configfile (char * const filename, int *my_argc)
+{
+ FILE* file;
+ char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
+ char linebuf[CONFIG_FILE_LINE_SIZE];
+ int line_num = 0;
+ int result = 0, equal;
+ char *fopt, *farg;
+ char *str_index;
+ size_t len, next_token;
+ char delimiter;
+
+ if ((file = fopen(filename, "r")) == NULL)
+ {
+ fprintf (stderr, "%s: Error opening configuration file '%s'\n",
+ CMDLINE_PARSER_CLITKMIP_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
+ {
+ ++line_num;
+ my_argv[0] = '\0';
+ len = strlen(linebuf);
+ if (len > (CONFIG_FILE_LINE_BUFFER_SIZE-1))
+ {
+ fprintf (stderr, "%s:%s:%d: Line too long in configuration file\n",
+ CMDLINE_PARSER_CLITKMIP_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+
+ /* find first non-whitespace character in the line */
+ next_token = strspn (linebuf, " \t\r\n");
+ str_index = linebuf + next_token;
+
+ if ( str_index[0] == '\0' || str_index[0] == '#')
+ continue; /* empty line or comment line is skipped */
+
+ fopt = str_index;
+
+ /* truncate fopt at the end of the first non-valid character */
+ next_token = strcspn (fopt, " \t\r\n=");
+
+ if (fopt[next_token] == '\0') /* the line is over */
+ {
+ farg = NULL;
+ equal = 0;
+ goto noarg;
+ }
+
+ /* remember if equal sign is present */
+ equal = (fopt[next_token] == '=');
+ fopt[next_token++] = '\0';
+
+ /* advance pointers to the next token after the end of fopt */
+ next_token += strspn (fopt + next_token, " \t\r\n");
+
+ /* check for the presence of equal sign, and if so, skip it */
+ if ( !equal )
+ if ((equal = (fopt[next_token] == '=')))
+ {
+ next_token++;
+ next_token += strspn (fopt + next_token, " \t\r\n");
+ }
+ str_index += next_token;
+
+ /* find argument */
+ farg = str_index;
+ if ( farg[0] == '\"' || farg[0] == '\'' )
+ { /* quoted argument */
+ str_index = strchr (++farg, str_index[0] ); /* skip opening quote */
+ if (! str_index)
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: unterminated string in configuration file\n",
+ CMDLINE_PARSER_CLITKMIP_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+ else
+ { /* read up the remaining part up to a delimiter */
+ next_token = strcspn (farg, " \t\r\n#\'\"");
+ str_index += next_token;
+ }
+
+ /* truncate farg at the delimiter and store it for further check */
+ delimiter = *str_index, *str_index++ = '\0';
+
+ /* everything but comment is illegal at the end of line */
+ if (delimiter != '\0' && delimiter != '#')
+ {
+ str_index += strspn(str_index, " \t\r\n");
+ if (*str_index != '\0' && *str_index != '#')
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: malformed string in configuration file\n",
+ CMDLINE_PARSER_CLITKMIP_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+
+ noarg:
+ if (!strcmp(fopt,"include")) {
+ if (farg && *farg) {
+ result = _cmdline_parser_clitkMIP_configfile(farg, my_argc);
+ } else {
+ fprintf(stderr, "%s:%s:%d: include requires a filename argument.\n",
+ CMDLINE_PARSER_CLITKMIP_PACKAGE, filename, line_num);
+ }
+ continue;
+ }
+ len = strlen(fopt);
+ strcat (my_argv, len > 1 ? "--" : "-");
+ strcat (my_argv, fopt);
+ if (len > 1 && ((farg && *farg) || equal))
+ strcat (my_argv, "=");
+ if (farg && *farg)
+ strcat (my_argv, farg);
+ ++(*my_argc);
+
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup(my_argv);
+ } /* while */
+
+ if (file)
+ fclose(file);
+ return result;
+}
+
+int
+cmdline_parser_clitkMIP_configfile (char * const filename,
+ struct args_info_clitkMIP *args_info,
+ int override, int initialize, int check_required)
+{
+ struct cmdline_parser_clitkMIP_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ return cmdline_parser_clitkMIP_config_file (filename, args_info, ¶ms);
+}
+
+int
+cmdline_parser_clitkMIP_config_file (char * const filename,
+ struct args_info_clitkMIP *args_info,
+ struct cmdline_parser_clitkMIP_params *params)
+{
+ int i, result;
+ int my_argc = 1;
+ char **my_argv_arg;
+ char *additional_error;
+
+ /* store the program name */
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup (CMDLINE_PARSER_CLITKMIP_PACKAGE);
+
+ result = _cmdline_parser_clitkMIP_configfile(filename, &my_argc);
+
+ if (result != EXIT_FAILURE) {
+ my_argv_arg = (char **) malloc((my_argc+1) * sizeof(char *));
+ cmd_line_list_tmp = cmd_line_list;
+
+ for (i = my_argc - 1; i >= 0; --i) {
+ my_argv_arg[i] = cmd_line_list_tmp->string_arg;
+ cmd_line_list_tmp = cmd_line_list_tmp->next;
+ }
+
+ my_argv_arg[my_argc] = 0;
+
+ additional_error = (char *)malloc(strlen(filename) + strlen(ADDITIONAL_ERROR) + 1);
+ strcpy (additional_error, ADDITIONAL_ERROR);
+ strcat (additional_error, filename);
+ result =
+ cmdline_parser_clitkMIP_internal (my_argc, my_argv_arg, args_info,
+ params,
+ additional_error);
+
+ free (additional_error);
+ free (my_argv_arg);
+ }
+
+ free_cmd_list();
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkMIP_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
--- /dev/null
+/** @file clitkMIP_ggo.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CLITKMIP_GGO_H
+#define CLITKMIP_GGO_H
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_CLITKMIP_PACKAGE
+/** @brief the program name */
+#define CMDLINE_PARSER_CLITKMIP_PACKAGE "clitkMIP"
+#endif
+
+#ifndef CMDLINE_PARSER_CLITKMIP_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_CLITKMIP_VERSION "1.0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct args_info_clitkMIP
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ char * config_arg; /**< @brief Config file. */
+ char * config_orig; /**< @brief Config file original value given at command line. */
+ const char *config_help; /**< @brief Config file help description. */
+ int verbose_flag; /**< @brief Verbose (default=off). */
+ const char *verbose_help; /**< @brief Verbose help description. */
+ int imagetypes_flag; /**< @brief Display allowed image types (default=off). */
+ const char *imagetypes_help; /**< @brief Display allowed image types help description. */
+ char * input_arg; /**< @brief Input image filename. */
+ char * input_orig; /**< @brief Input image filename original value given at command line. */
+ const char *input_help; /**< @brief Input image filename help description. */
+ char * output_arg; /**< @brief Output image filename. */
+ char * output_orig; /**< @brief Output image filename original value given at command line. */
+ const char *output_help; /**< @brief Output image filename help description. */
+ int dimension_arg; /**< @brief Dimension along which to projetct. */
+ char * dimension_orig; /**< @brief Dimension along which to projetct original value given at command line. */
+ const char *dimension_help; /**< @brief Dimension along which to projetct help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int config_given ; /**< @brief Whether config was given. */
+ unsigned int verbose_given ; /**< @brief Whether verbose was given. */
+ unsigned int imagetypes_given ; /**< @brief Whether imagetypes was given. */
+ unsigned int input_given ; /**< @brief Whether input was given. */
+ unsigned int output_given ; /**< @brief Whether output was given. */
+ unsigned int dimension_given ; /**< @brief Whether dimension was given. */
+
+ char **inputs ; /**< @brief unamed options (options without names) */
+ unsigned inputs_num ; /**< @brief unamed options number */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_clitkMIP_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure args_info_clitkMIP (default 1) */
+ int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+ int check_ambiguity; /**< @brief whether to check for options already specified in the option structure args_info_clitkMIP (default 0) */
+ int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *args_info_clitkMIP_purpose;
+/** @brief the usage string of the program */
+extern const char *args_info_clitkMIP_usage;
+/** @brief all the lines making the help output */
+extern const char *args_info_clitkMIP_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkMIP (int argc, char * const *argv,
+ struct args_info_clitkMIP *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkMIP_ext() instead
+ */
+int cmdline_parser_clitkMIP2 (int argc, char * const *argv,
+ struct args_info_clitkMIP *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkMIP_ext (int argc, char * const *argv,
+ struct args_info_clitkMIP *args_info,
+ struct cmdline_parser_clitkMIP_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkMIP_dump(FILE *outfile,
+ struct args_info_clitkMIP *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkMIP_file_save(const char *filename,
+ struct args_info_clitkMIP *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_clitkMIP_print_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_clitkMIP_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_clitkMIP_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_clitkMIP_params_init(struct cmdline_parser_clitkMIP_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_clitkMIP_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_clitkMIP_params structure
+ */
+struct cmdline_parser_clitkMIP_params *cmdline_parser_clitkMIP_params_create(void);
+
+/**
+ * Initializes the passed args_info_clitkMIP structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_clitkMIP_init (struct args_info_clitkMIP *args_info);
+/**
+ * Deallocates the string fields of the args_info_clitkMIP structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_clitkMIP_free (struct args_info_clitkMIP *args_info);
+
+/**
+ * The config file parser (deprecated version)
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkMIP_config_file() instead
+ */
+int cmdline_parser_clitkMIP_configfile (char * const filename,
+ struct args_info_clitkMIP *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The config file parser
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkMIP_config_file (char * const filename,
+ struct args_info_clitkMIP *args_info,
+ struct cmdline_parser_clitkMIP_params *params);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ * possible errors
+ * @return
+ */
+int cmdline_parser_clitkMIP_required (struct args_info_clitkMIP *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CLITKMIP_GGO_H */
--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22
+ generated with the following command:
+ /usr/local/bin/gengetopt --output-dir=/home/tbaudier/vv/vv_static/vv/vv_bin/tools --arg-struct-name=args_info_clitkMedianImageFilter --func-name=cmdline_parser_clitkMedianImageFilter --file-name=clitkMedianImageFilter_ggo --unamed-opts --conf-parser --include-getopt
+
+ The developers of gengetopt consider the fixed text that goes in all
+ gengetopt output files to be in the public domain:
+ we make no copyright claims on it.
+*/
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+
+#include "clitkMedianImageFilter_ggo.h"
+
+const char *args_info_clitkMedianImageFilter_purpose = "";
+
+const char *args_info_clitkMedianImageFilter_usage = "Usage: clitkMedianImageFilter [OPTIONS]... [FILES]...";
+
+const char *args_info_clitkMedianImageFilter_description = "";
+
+const char *args_info_clitkMedianImageFilter_help[] = {
+ " -h, --help Print help and exit",
+ " -V, --version Print version and exit",
+ " --config=STRING Config file",
+ " -v, --verbose Verbose (default=off)",
+ " -i, --input=STRING Input image filename",
+ " -o, --output=STRING Output image filename",
+ " -r, --radius=INT Radius in each Direction (default=`1')",
+ 0
+};
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_INT
+} cmdline_parser_clitkMedianImageFilter_arg_type;
+
+static
+void clear_given (struct args_info_clitkMedianImageFilter *args_info);
+static
+void clear_args (struct args_info_clitkMedianImageFilter *args_info);
+
+static int
+cmdline_parser_clitkMedianImageFilter_internal (int argc, char * const *argv, struct args_info_clitkMedianImageFilter *args_info,
+ struct cmdline_parser_clitkMedianImageFilter_params *params, const char *additional_error);
+
+static int
+cmdline_parser_clitkMedianImageFilter_required2 (struct args_info_clitkMedianImageFilter *args_info, const char *prog_name, const char *additional_error);
+struct line_list
+{
+ char * string_arg;
+ struct line_list * next;
+};
+
+static struct line_list *cmd_line_list = 0;
+static struct line_list *cmd_line_list_tmp = 0;
+
+static void
+free_cmd_list(void)
+{
+ /* free the list of a previous call */
+ if (cmd_line_list)
+ {
+ while (cmd_line_list) {
+ cmd_line_list_tmp = cmd_line_list;
+ cmd_line_list = cmd_line_list->next;
+ free (cmd_line_list_tmp->string_arg);
+ free (cmd_line_list_tmp);
+ }
+ }
+}
+
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct args_info_clitkMedianImageFilter *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->config_given = 0 ;
+ args_info->verbose_given = 0 ;
+ args_info->input_given = 0 ;
+ args_info->output_given = 0 ;
+ args_info->radius_given = 0 ;
+}
+
+static
+void clear_args (struct args_info_clitkMedianImageFilter *args_info)
+{
+ args_info->config_arg = NULL;
+ args_info->config_orig = NULL;
+ args_info->verbose_flag = 0;
+ args_info->input_arg = NULL;
+ args_info->input_orig = NULL;
+ args_info->output_arg = NULL;
+ args_info->output_orig = NULL;
+ args_info->radius_arg = NULL;
+ args_info->radius_orig = NULL;
+
+}
+
+static
+void init_args_info(struct args_info_clitkMedianImageFilter *args_info)
+{
+
+
+ args_info->help_help = args_info_clitkMedianImageFilter_help[0] ;
+ args_info->version_help = args_info_clitkMedianImageFilter_help[1] ;
+ args_info->config_help = args_info_clitkMedianImageFilter_help[2] ;
+ args_info->verbose_help = args_info_clitkMedianImageFilter_help[3] ;
+ args_info->input_help = args_info_clitkMedianImageFilter_help[4] ;
+ args_info->output_help = args_info_clitkMedianImageFilter_help[5] ;
+ args_info->radius_help = args_info_clitkMedianImageFilter_help[6] ;
+ args_info->radius_min = -1;
+ args_info->radius_max = -1;
+
+}
+
+void
+cmdline_parser_clitkMedianImageFilter_print_version (void)
+{
+ printf ("%s %s\n", CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE, CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_VERSION);
+}
+
+static void print_help_common(void) {
+ cmdline_parser_clitkMedianImageFilter_print_version ();
+
+ if (strlen(args_info_clitkMedianImageFilter_purpose) > 0)
+ printf("\n%s\n", args_info_clitkMedianImageFilter_purpose);
+
+ if (strlen(args_info_clitkMedianImageFilter_usage) > 0)
+ printf("\n%s\n", args_info_clitkMedianImageFilter_usage);
+
+ printf("\n");
+
+ if (strlen(args_info_clitkMedianImageFilter_description) > 0)
+ printf("%s\n", args_info_clitkMedianImageFilter_description);
+}
+
+void
+cmdline_parser_clitkMedianImageFilter_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (args_info_clitkMedianImageFilter_help[i])
+ printf("%s\n", args_info_clitkMedianImageFilter_help[i++]);
+}
+
+void
+cmdline_parser_clitkMedianImageFilter_init (struct args_info_clitkMedianImageFilter *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+
+ args_info->inputs = NULL;
+ args_info->inputs_num = 0;
+}
+
+void
+cmdline_parser_clitkMedianImageFilter_params_init(struct cmdline_parser_clitkMedianImageFilter_params *params)
+{
+ if (params)
+ {
+ params->override = 0;
+ params->initialize = 1;
+ params->check_required = 1;
+ params->check_ambiguity = 0;
+ params->print_errors = 1;
+ }
+}
+
+struct cmdline_parser_clitkMedianImageFilter_params *
+cmdline_parser_clitkMedianImageFilter_params_create(void)
+{
+ struct cmdline_parser_clitkMedianImageFilter_params *params =
+ (struct cmdline_parser_clitkMedianImageFilter_params *)malloc(sizeof(struct cmdline_parser_clitkMedianImageFilter_params));
+ cmdline_parser_clitkMedianImageFilter_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+/** @brief generic value variable */
+union generic_value {
+ int int_arg;
+ char *string_arg;
+};
+
+/** @brief holds temporary values for multiple options */
+struct generic_list
+{
+ union generic_value arg;
+ char *orig;
+ struct generic_list *next;
+};
+
+/**
+ * @brief add a node at the head of the list
+ */
+static void add_node(struct generic_list **list) {
+ struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list));
+ new_node->next = *list;
+ *list = new_node;
+ new_node->arg.string_arg = NULL;
+ new_node->orig = NULL;
+}
+
+static void
+free_multiple_field(unsigned int len, void **arg, char ***orig)
+{
+ unsigned int i;
+ if (*arg) {
+ for (i = 0; i < len; ++i)
+ {
+ free_string_field(&((*orig)[i]));
+ }
+
+ free (*arg);
+ *arg = 0;
+ free (*orig);
+ *orig = 0;
+ }
+}
+
+
+static void
+cmdline_parser_clitkMedianImageFilter_release (struct args_info_clitkMedianImageFilter *args_info)
+{
+ unsigned int i;
+ free_string_field (&(args_info->config_arg));
+ free_string_field (&(args_info->config_orig));
+ free_string_field (&(args_info->input_arg));
+ free_string_field (&(args_info->input_orig));
+ free_string_field (&(args_info->output_arg));
+ free_string_field (&(args_info->output_orig));
+ free_multiple_field (args_info->radius_given, (void **)&(args_info->radius_arg), &(args_info->radius_orig));
+
+
+ for (i = 0; i < args_info->inputs_num; ++i)
+ free (args_info->inputs [i]);
+
+ if (args_info->inputs_num)
+ free (args_info->inputs);
+
+ clear_given (args_info);
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+ if (arg) {
+ fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+ } else {
+ fprintf(outfile, "%s\n", opt);
+ }
+}
+
+static void
+write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, char *values[])
+{
+ int i;
+
+ for (i = 0; i < len; ++i)
+ write_into_file(outfile, opt, (arg ? arg[i] : 0), values);
+}
+
+int
+cmdline_parser_clitkMedianImageFilter_dump(FILE *outfile, struct args_info_clitkMedianImageFilter *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE);
+ return EXIT_FAILURE;
+ }
+
+ if (args_info->help_given)
+ write_into_file(outfile, "help", 0, 0 );
+ if (args_info->version_given)
+ write_into_file(outfile, "version", 0, 0 );
+ if (args_info->config_given)
+ write_into_file(outfile, "config", args_info->config_orig, 0);
+ if (args_info->verbose_given)
+ write_into_file(outfile, "verbose", 0, 0 );
+ if (args_info->input_given)
+ write_into_file(outfile, "input", args_info->input_orig, 0);
+ if (args_info->output_given)
+ write_into_file(outfile, "output", args_info->output_orig, 0);
+ write_multiple_into_file(outfile, args_info->radius_given, "radius", args_info->radius_orig, 0);
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+cmdline_parser_clitkMedianImageFilter_file_save(const char *filename, struct args_info_clitkMedianImageFilter *args_info)
+{
+ FILE *outfile;
+ int i = 0;
+
+ outfile = fopen(filename, "w");
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = cmdline_parser_clitkMedianImageFilter_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+cmdline_parser_clitkMedianImageFilter_free (struct args_info_clitkMedianImageFilter *args_info)
+{
+ cmdline_parser_clitkMedianImageFilter_release (args_info);
+}
+
+/** @brief replacement of strdup, which is not standard */
+char *
+gengetopt_strdup (const char *s)
+{
+ char *result = NULL;
+ if (!s)
+ return result;
+
+ result = (char*)malloc(strlen(s) + 1);
+ if (result == (char*)0)
+ return (char*)0;
+ strcpy(result, s);
+ return result;
+}
+
+static char *
+get_multiple_arg_token(const char *arg)
+{
+ char *tok, *ret;
+ size_t len, num_of_escape, i, j;
+
+ if (!arg)
+ return NULL;
+
+ tok = strchr (arg, ',');
+ num_of_escape = 0;
+
+ /* make sure it is not escaped */
+ while (tok)
+ {
+ if (*(tok-1) == '\\')
+ {
+ /* find the next one */
+ tok = strchr (tok+1, ',');
+ ++num_of_escape;
+ }
+ else
+ break;
+ }
+
+ if (tok)
+ len = (size_t)(tok - arg + 1);
+ else
+ len = strlen (arg) + 1;
+
+ len -= num_of_escape;
+
+ ret = (char *) malloc (len);
+
+ i = 0;
+ j = 0;
+ while (arg[i] && (j < len-1))
+ {
+ if (arg[i] == '\\' &&
+ arg[ i + 1 ] &&
+ arg[ i + 1 ] == ',')
+ ++i;
+
+ ret[j++] = arg[i++];
+ }
+
+ ret[len-1] = '\0';
+
+ return ret;
+}
+
+static char *
+get_multiple_arg_token_next(const char *arg)
+{
+ char *tok;
+
+ if (!arg)
+ return NULL;
+
+ tok = strchr (arg, ',');
+
+ /* make sure it is not escaped */
+ while (tok)
+ {
+ if (*(tok-1) == '\\')
+ {
+ /* find the next one */
+ tok = strchr (tok+1, ',');
+ }
+ else
+ break;
+ }
+
+ if (! tok || strlen(tok) == 1)
+ return 0;
+
+ return tok+1;
+}
+
+static int
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc);
+
+int
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc)
+{
+ int error = 0;
+
+ if (option_given && ! (min < 0 && max < 0))
+ {
+ if (min >= 0 && max >= 0)
+ {
+ if (min == max)
+ {
+ /* specific occurrences */
+ if (option_given != min)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be %d\n",
+ prog_name, option_desc, min);
+ error = 1;
+ }
+ }
+ else if (option_given < min
+ || option_given > max)
+ {
+ /* range occurrences */
+ fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n",
+ prog_name, option_desc, min, max);
+ error = 1;
+ }
+ }
+ else if (min >= 0)
+ {
+ /* at least check */
+ if (option_given < min)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be at least %d\n",
+ prog_name, option_desc, min);
+ error = 1;
+ }
+ }
+ else if (max >= 0)
+ {
+ /* at most check */
+ if (option_given > max)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be at most %d\n",
+ prog_name, option_desc, max);
+ error = 1;
+ }
+ }
+ }
+
+ return error;
+}
+int
+cmdline_parser_clitkMedianImageFilter (int argc, char * const *argv, struct args_info_clitkMedianImageFilter *args_info)
+{
+ return cmdline_parser_clitkMedianImageFilter2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+cmdline_parser_clitkMedianImageFilter_ext (int argc, char * const *argv, struct args_info_clitkMedianImageFilter *args_info,
+ struct cmdline_parser_clitkMedianImageFilter_params *params)
+{
+ int result;
+ result = cmdline_parser_clitkMedianImageFilter_internal (argc, argv, args_info, params, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkMedianImageFilter_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkMedianImageFilter2 (int argc, char * const *argv, struct args_info_clitkMedianImageFilter *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct cmdline_parser_clitkMedianImageFilter_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = cmdline_parser_clitkMedianImageFilter_internal (argc, argv, args_info, ¶ms, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkMedianImageFilter_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkMedianImageFilter_required (struct args_info_clitkMedianImageFilter *args_info, const char *prog_name)
+{
+ int result = EXIT_SUCCESS;
+
+ if (cmdline_parser_clitkMedianImageFilter_required2(args_info, prog_name, NULL) > 0)
+ result = EXIT_FAILURE;
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkMedianImageFilter_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkMedianImageFilter_required2 (struct args_info_clitkMedianImageFilter *args_info, const char *prog_name, const char *additional_error)
+{
+ int error = 0;
+
+ /* checks for required options */
+ if (! args_info->input_given)
+ {
+ fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (! args_info->output_given)
+ {
+ fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (check_multiple_option_occurrences(prog_name, args_info->radius_given, args_info->radius_min, args_info->radius_max, "'--radius' ('-r')"))
+ error = 1;
+
+
+ /* checks for dependences among options */
+
+ return error;
+}
+
+/*
+ * Extracted from the glibc source tree, version 2.3.6
+ *
+ * Licensed under the GPL as per the whole glibc source tree.
+ *
+ * This file was modified so that getopt_long can be called
+ * many times without risking previous memory to be spoiled.
+ *
+ * Modified by Andre Noll and Lorenzo Bettini for use in
+ * GNU gengetopt generated files.
+ *
+ */
+
+/*
+ * we must include anything we need since this file is not thought to be
+ * inserted in a file already using getopt.h
+ *
+ * Lorenzo
+ */
+
+struct option
+{
+ const char *name;
+ /* has_arg can't be an enum because some compilers complain about
+ type mismatches in all the code that assumes it is an int. */
+ int has_arg;
+ int *flag;
+ int val;
+};
+
+/* For communication from `getopt' to the caller.
+ When `getopt' finds an option that takes an argument,
+ the argument value is returned here.
+ Also, when `ordering' is RETURN_IN_ORDER,
+ each non-option ARGV-element is returned here. */
+
+static char *optarg;
+
+/* Index in ARGV of the next element to be scanned.
+ This is used for communication to and from the caller
+ and for communication between successive calls to `getopt'.
+
+ On entry to `getopt', zero means this is the first call; initialize.
+
+ When `getopt' returns -1, this is the index of the first of the
+ non-option elements that the caller should itself scan.
+
+ Otherwise, `optind' communicates from one call to the next
+ how much of ARGV has been scanned so far. */
+
+static int optind;
+
+/* Callers store zero here to inhibit the error message `getopt' prints
+ for unrecognized options. */
+
+static int opterr;
+
+/* Set to an option character which was unrecognized. */
+
+static int optopt;
+
+/* This version of `getopt' appears to the caller like standard Unix `getopt'
+ but it behaves differently for the user, since it allows the user
+ to intersperse the options with the other arguments.
+
+ As `getopt' works, it permutes the elements of ARGV so that,
+ when it is done, all the options precede everything else. Thus
+ all application programs are extended to handle flexible argument order.
+*/
+/*
+ If the field `flag' is not NULL, it points to a variable that is set
+ to the value given in the field `val' when the option is found, but
+ left unchanged if the option is not found.
+
+ To have a long-named option do something other than set an `int' to
+ a compiled-in constant, such as set a value from `custom_optarg', set the
+ option's `flag' field to zero and its `val' field to a nonzero
+ value (the equivalent single-letter option character, if there is
+ one). For long options that have a zero `flag' field, `getopt'
+ returns the contents of the `val' field. */
+
+/* Names for the values of the `has_arg' field of `struct option'. */
+#ifndef no_argument
+#define no_argument 0
+#endif
+
+#ifndef required_argument
+#define required_argument 1
+#endif
+
+#ifndef optional_argument
+#define optional_argument 2
+#endif
+
+struct custom_getopt_data {
+ /*
+ * These have exactly the same meaning as the corresponding global variables,
+ * except that they are used for the reentrant versions of getopt.
+ */
+ int custom_optind;
+ int custom_opterr;
+ int custom_optopt;
+ char *custom_optarg;
+
+ /* True if the internal members have been initialized. */
+ int initialized;
+
+ /*
+ * The next char to be scanned in the option-element in which the last option
+ * character we returned was found. This allows us to pick up the scan where
+ * we left off. If this is zero, or a null string, it means resume the scan by
+ * advancing to the next ARGV-element.
+ */
+ char *nextchar;
+
+ /*
+ * Describe the part of ARGV that contains non-options that have been skipped.
+ * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is
+ * the index after the last of them.
+ */
+ int first_nonopt;
+ int last_nonopt;
+};
+
+/*
+ * the variables optarg, optind, opterr and optopt are renamed with
+ * the custom_ prefix so that they don't interfere with getopt ones.
+ *
+ * Moreover they're static so they are visible only from within the
+ * file where this very file will be included.
+ */
+
+/*
+ * For communication from `custom_getopt' to the caller. When `custom_getopt' finds an
+ * option that takes an argument, the argument value is returned here.
+ */
+static char *custom_optarg;
+
+/*
+ * Index in ARGV of the next element to be scanned. This is used for
+ * communication to and from the caller and for communication between
+ * successive calls to `custom_getopt'.
+ *
+ * On entry to `custom_getopt', 1 means this is the first call; initialize.
+ *
+ * When `custom_getopt' returns -1, this is the index of the first of the non-option
+ * elements that the caller should itself scan.
+ *
+ * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV
+ * has been scanned so far.
+ *
+ * 1003.2 says this must be 1 before any call.
+ */
+static int custom_optind = 1;
+
+/*
+ * Callers store zero here to inhibit the error message for unrecognized
+ * options.
+ */
+static int custom_opterr = 1;
+
+/*
+ * Set to an option character which was unrecognized. This must be initialized
+ * on some systems to avoid linking in the system's own getopt implementation.
+ */
+static int custom_optopt = '?';
+
+/*
+ * Exchange two adjacent subsequences of ARGV. One subsequence is elements
+ * [first_nonopt,last_nonopt) which contains all the non-options that have been
+ * skipped so far. The other is elements [last_nonopt,custom_optind), which contains
+ * all the options processed since those non-options were skipped.
+ * `first_nonopt' and `last_nonopt' are relocated so that they describe the new
+ * indices of the non-options in ARGV after they are moved.
+ */
+static void exchange(char **argv, struct custom_getopt_data *d)
+{
+ int bottom = d->first_nonopt;
+ int middle = d->last_nonopt;
+ int top = d->custom_optind;
+ char *tem;
+
+ /*
+ * Exchange the shorter segment with the far end of the longer segment.
+ * That puts the shorter segment into the right place. It leaves the
+ * longer segment in the right place overall, but it consists of two
+ * parts that need to be swapped next.
+ */
+ while (top > middle && middle > bottom) {
+ if (top - middle > middle - bottom) {
+ /* Bottom segment is the short one. */
+ int len = middle - bottom;
+ int i;
+
+ /* Swap it with the top part of the top segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] =
+ argv[top - (middle - bottom) + i];
+ argv[top - (middle - bottom) + i] = tem;
+ }
+ /* Exclude the moved bottom segment from further swapping. */
+ top -= len;
+ } else {
+ /* Top segment is the short one. */
+ int len = top - middle;
+ int i;
+
+ /* Swap it with the bottom part of the bottom segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] = argv[middle + i];
+ argv[middle + i] = tem;
+ }
+ /* Exclude the moved top segment from further swapping. */
+ bottom += len;
+ }
+ }
+ /* Update records for the slots the non-options now occupy. */
+ d->first_nonopt += (d->custom_optind - d->last_nonopt);
+ d->last_nonopt = d->custom_optind;
+}
+
+/* Initialize the internal data when the first call is made. */
+static void custom_getopt_initialize(struct custom_getopt_data *d)
+{
+ /*
+ * Start processing options with ARGV-element 1 (since ARGV-element 0
+ * is the program name); the sequence of previously skipped non-option
+ * ARGV-elements is empty.
+ */
+ d->first_nonopt = d->last_nonopt = d->custom_optind;
+ d->nextchar = NULL;
+ d->initialized = 1;
+}
+
+#define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0')
+
+/* return: zero: continue, nonzero: return given value to user */
+static int shuffle_argv(int argc, char *const *argv,const struct option *longopts,
+ struct custom_getopt_data *d)
+{
+ /*
+ * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been
+ * moved back by the user (who may also have changed the arguments).
+ */
+ if (d->last_nonopt > d->custom_optind)
+ d->last_nonopt = d->custom_optind;
+ if (d->first_nonopt > d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * If we have just processed some options following some
+ * non-options, exchange them so that the options come first.
+ */
+ if (d->first_nonopt != d->last_nonopt &&
+ d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->last_nonopt != d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * Skip any additional non-options and extend the range of
+ * non-options previously skipped.
+ */
+ while (d->custom_optind < argc && NONOPTION_P)
+ d->custom_optind++;
+ d->last_nonopt = d->custom_optind;
+ /*
+ * The special ARGV-element `--' means premature end of options. Skip
+ * it like a null option, then exchange with previous non-options as if
+ * it were an option, then skip everything else like a non-option.
+ */
+ if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) {
+ d->custom_optind++;
+ if (d->first_nonopt != d->last_nonopt
+ && d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->first_nonopt == d->last_nonopt)
+ d->first_nonopt = d->custom_optind;
+ d->last_nonopt = argc;
+ d->custom_optind = argc;
+ }
+ /*
+ * If we have done all the ARGV-elements, stop the scan and back over
+ * any non-options that we skipped and permuted.
+ */
+ if (d->custom_optind == argc) {
+ /*
+ * Set the next-arg-index to point at the non-options that we
+ * previously skipped, so the caller will digest them.
+ */
+ if (d->first_nonopt != d->last_nonopt)
+ d->custom_optind = d->first_nonopt;
+ return -1;
+ }
+ /*
+ * If we have come to a non-option and did not permute it, either stop
+ * the scan or describe it to the caller and pass it by.
+ */
+ if (NONOPTION_P) {
+ d->custom_optarg = argv[d->custom_optind++];
+ return 1;
+ }
+ /*
+ * We have found another option-ARGV-element. Skip the initial
+ * punctuation.
+ */
+ d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-'));
+ return 0;
+}
+
+/*
+ * Check whether the ARGV-element is a long option.
+ *
+ * If there's a long option "fubar" and the ARGV-element is "-fu", consider
+ * that an abbreviation of the long option, just like "--fu", and not "-f" with
+ * arg "u".
+ *
+ * This distinction seems to be the most useful approach.
+ *
+ */
+static int check_long_opt(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char *nameend;
+ const struct option *p;
+ const struct option *pfound = NULL;
+ int exact = 0;
+ int ambig = 0;
+ int indfound = -1;
+ int option_index;
+
+ for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++)
+ /* Do nothing. */ ;
+
+ /* Test all long options for either exact match or abbreviated matches */
+ for (p = longopts, option_index = 0; p->name; p++, option_index++)
+ if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) {
+ if ((unsigned int) (nameend - d->nextchar)
+ == (unsigned int) strlen(p->name)) {
+ /* Exact match found. */
+ pfound = p;
+ indfound = option_index;
+ exact = 1;
+ break;
+ } else if (pfound == NULL) {
+ /* First nonexact match found. */
+ pfound = p;
+ indfound = option_index;
+ } else if (pfound->has_arg != p->has_arg
+ || pfound->flag != p->flag
+ || pfound->val != p->val)
+ /* Second or later nonexact match found. */
+ ambig = 1;
+ }
+ if (ambig && !exact) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' is ambiguous\n",
+ argv[0], argv[d->custom_optind]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+ }
+ if (pfound) {
+ option_index = indfound;
+ d->custom_optind++;
+ if (*nameend) {
+ if (pfound->has_arg != no_argument)
+ d->custom_optarg = nameend + 1;
+ else {
+ if (print_errors) {
+ if (argv[d->custom_optind - 1][1] == '-') {
+ /* --option */
+ fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n",
+ argv[0], pfound->name);
+ } else {
+ /* +option or -option */
+ fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n",
+ argv[0], argv[d->custom_optind - 1][0], pfound->name);
+ }
+
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return '?';
+ }
+ } else if (pfound->has_arg == required_argument) {
+ if (d->custom_optind < argc)
+ d->custom_optarg = argv[d->custom_optind++];
+ else {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' requires an argument\n",
+ argv[0],
+ argv[d->custom_optind - 1]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return optstring[0] == ':' ? ':' : '?';
+ }
+ }
+ d->nextchar += strlen(d->nextchar);
+ if (longind != NULL)
+ *longind = option_index;
+ if (pfound->flag) {
+ *(pfound->flag) = pfound->val;
+ return 0;
+ }
+ return pfound->val;
+ }
+ /*
+ * Can't find it as a long option. If this is not getopt_long_only, or
+ * the option starts with '--' or is not a valid short option, then
+ * it's an error. Otherwise interpret it as a short option.
+ */
+ if (print_errors) {
+ if (argv[d->custom_optind][1] == '-') {
+ /* --option */
+ fprintf(stderr,
+ "%s: unrecognized option `--%s'\n",
+ argv[0], d->nextchar);
+ } else {
+ /* +option or -option */
+ fprintf(stderr,
+ "%s: unrecognized option `%c%s'\n",
+ argv[0], argv[d->custom_optind][0],
+ d->nextchar);
+ }
+ }
+ d->nextchar = (char *) "";
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+}
+
+static int check_short_opt(int argc, char *const *argv, const char *optstring,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char c = *d->nextchar++;
+ char *temp = strchr(optstring, c);
+
+ /* Increment `custom_optind' when we start to process its last character. */
+ if (*d->nextchar == '\0')
+ ++d->custom_optind;
+ if (!temp || c == ':') {
+ if (print_errors)
+ fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
+
+ d->custom_optopt = c;
+ return '?';
+ }
+ if (temp[1] == ':') {
+ if (temp[2] == ':') {
+ /* This is an option that accepts an argument optionally. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ d->custom_optind++;
+ } else
+ d->custom_optarg = NULL;
+ d->nextchar = NULL;
+ } else {
+ /* This is an option that requires an argument. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ /*
+ * If we end this ARGV-element by taking the
+ * rest as an arg, we must advance to the next
+ * element now.
+ */
+ d->custom_optind++;
+ } else if (d->custom_optind == argc) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option requires an argument -- %c\n",
+ argv[0], c);
+ }
+ d->custom_optopt = c;
+ if (optstring[0] == ':')
+ c = ':';
+ else
+ c = '?';
+ } else
+ /*
+ * We already incremented `custom_optind' once;
+ * increment it again when taking next ARGV-elt
+ * as argument.
+ */
+ d->custom_optarg = argv[d->custom_optind++];
+ d->nextchar = NULL;
+ }
+ }
+ return c;
+}
+
+/*
+ * Scan elements of ARGV for option characters given in OPTSTRING.
+ *
+ * If an element of ARGV starts with '-', and is not exactly "-" or "--",
+ * then it is an option element. The characters of this element
+ * (aside from the initial '-') are option characters. If `getopt'
+ * is called repeatedly, it returns successively each of the option characters
+ * from each of the option elements.
+ *
+ * If `getopt' finds another option character, it returns that character,
+ * updating `custom_optind' and `nextchar' so that the next call to `getopt' can
+ * resume the scan with the following option character or ARGV-element.
+ *
+ * If there are no more option characters, `getopt' returns -1.
+ * Then `custom_optind' is the index in ARGV of the first ARGV-element
+ * that is not an option. (The ARGV-elements have been permuted
+ * so that those that are not options now come last.)
+ *
+ * OPTSTRING is a string containing the legitimate option characters.
+ * If an option character is seen that is not listed in OPTSTRING,
+ * return '?' after printing an error message. If you set `custom_opterr' to
+ * zero, the error message is suppressed but we still return '?'.
+ *
+ * If a char in OPTSTRING is followed by a colon, that means it wants an arg,
+ * so the following text in the same ARGV-element, or the text of the following
+ * ARGV-element, is returned in `custom_optarg'. Two colons mean an option that
+ * wants an optional arg; if there is text in the current ARGV-element,
+ * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero.
+ *
+ * If OPTSTRING starts with `-' or `+', it requests different methods of
+ * handling the non-option ARGV-elements.
+ * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
+ *
+ * Long-named options begin with `--' instead of `-'.
+ * Their names may be abbreviated as long as the abbreviation is unique
+ * or is an exact match for some defined option. If they have an
+ * argument, it follows the option name in the same ARGV-element, separated
+ * from the option name by a `=', or else the in next ARGV-element.
+ * When `getopt' finds a long-named option, it returns 0 if that option's
+ * `flag' field is nonzero, the value of the option's `val' field
+ * if the `flag' field is zero.
+ *
+ * The elements of ARGV aren't really const, because we permute them.
+ * But we pretend they're const in the prototype to be compatible
+ * with other systems.
+ *
+ * LONGOPTS is a vector of `struct option' terminated by an
+ * element containing a name which is zero.
+ *
+ * LONGIND returns the index in LONGOPT of the long-named option found.
+ * It is only valid when a long-named option has been found by the most
+ * recent call.
+ *
+ * Return the option character from OPTS just read. Return -1 when there are
+ * no more options. For unrecognized options, or options missing arguments,
+ * `custom_optopt' is set to the option letter, and '?' is returned.
+ *
+ * The OPTS string is a list of characters which are recognized option letters,
+ * optionally followed by colons, specifying that that letter takes an
+ * argument, to be placed in `custom_optarg'.
+ *
+ * If a letter in OPTS is followed by two colons, its argument is optional.
+ * This behavior is specific to the GNU `getopt'.
+ *
+ * The argument `--' causes premature termination of argument scanning,
+ * explicitly telling `getopt' that there are no more options. If OPTS begins
+ * with `--', then non-option arguments are treated as arguments to the option
+ * '\0'. This behavior is specific to the GNU `getopt'.
+ */
+
+static int getopt_internal_r(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ struct custom_getopt_data *d)
+{
+ int ret, print_errors = d->custom_opterr;
+
+ if (optstring[0] == ':')
+ print_errors = 0;
+ if (argc < 1)
+ return -1;
+ d->custom_optarg = NULL;
+
+ /*
+ * This is a big difference with GNU getopt, since optind == 0
+ * means initialization while here 1 means first call.
+ */
+ if (d->custom_optind == 0 || !d->initialized) {
+ if (d->custom_optind == 0)
+ d->custom_optind = 1; /* Don't scan ARGV[0], the program name. */
+ custom_getopt_initialize(d);
+ }
+ if (d->nextchar == NULL || *d->nextchar == '\0') {
+ ret = shuffle_argv(argc, argv, longopts, d);
+ if (ret)
+ return ret;
+ }
+ if (longopts && (argv[d->custom_optind][1] == '-' ))
+ return check_long_opt(argc, argv, optstring, longopts,
+ longind, print_errors, d);
+ return check_short_opt(argc, argv, optstring, print_errors, d);
+}
+
+static int custom_getopt_internal(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind)
+{
+ int result;
+ /* Keep a global copy of all internal members of d */
+ static struct custom_getopt_data d;
+
+ d.custom_optind = custom_optind;
+ d.custom_opterr = custom_opterr;
+ result = getopt_internal_r(argc, argv, optstring, longopts,
+ longind, &d);
+ custom_optind = d.custom_optind;
+ custom_optarg = d.custom_optarg;
+ custom_optopt = d.custom_optopt;
+ return result;
+}
+
+static int custom_getopt_long (int argc, char *const *argv, const char *options,
+ const struct option *long_options, int *opt_index)
+{
+ return custom_getopt_internal(argc, argv, options, long_options,
+ opt_index);
+}
+
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_clitkMedianImageFilter_params.check_ambiguity
+ * @param override @see cmdline_parser_clitkMedianImageFilter_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+static
+int update_arg(void *field, char **orig_field,
+ unsigned int *field_given, unsigned int *prev_given,
+ char *value, char *possible_values[], const char *default_value,
+ cmdline_parser_clitkMedianImageFilter_arg_type arg_type,
+ int check_ambiguity, int override,
+ int no_free, int multiple_option,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *stop_char = 0;
+ const char *val = value;
+ int found;
+ char **string_field;
+
+ stop_char = 0;
+ found = 0;
+
+ if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+ {
+ if (short_opt != '-')
+ fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
+ package_name, long_opt, short_opt,
+ (additional_error ? additional_error : ""));
+ else
+ fprintf (stderr, "%s: `--%s' option given more than once%s\n",
+ package_name, long_opt,
+ (additional_error ? additional_error : ""));
+ return 1; /* failure */
+ }
+
+
+ if (field_given && *field_given && ! override)
+ return 0;
+ if (prev_given)
+ (*prev_given)++;
+ if (field_given)
+ (*field_given)++;
+ if (possible_values)
+ val = possible_values[found];
+
+ switch(arg_type) {
+ case ARG_FLAG:
+ *((int *)field) = !*((int *)field);
+ break;
+ case ARG_INT:
+ if (val) *((int *)field) = strtol (val, &stop_char, 0);
+ break;
+ case ARG_STRING:
+ if (val) {
+ string_field = (char **)field;
+ if (!no_free && *string_field)
+ free (*string_field); /* free previous string */
+ *string_field = gengetopt_strdup (val);
+ }
+ break;
+ default:
+ break;
+ };
+
+ /* check numeric conversion */
+ switch(arg_type) {
+ case ARG_INT:
+ if (val && !(stop_char && *stop_char == '\0')) {
+ fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+ return 1; /* failure */
+ }
+ break;
+ default:
+ ;
+ };
+
+ /* store the original value */
+ switch(arg_type) {
+ case ARG_NO:
+ case ARG_FLAG:
+ break;
+ default:
+ if (value && orig_field) {
+ if (no_free) {
+ *orig_field = value;
+ } else {
+ if (*orig_field)
+ free (*orig_field); /* free previous string */
+ *orig_field = gengetopt_strdup (value);
+ }
+ }
+ };
+
+ return 0; /* OK */
+}
+
+/**
+ * @brief store information about a multiple option in a temporary list
+ * @param list where to (temporarily) store multiple options
+ */
+static
+int update_multiple_arg_temp(struct generic_list **list,
+ unsigned int *prev_given, const char *val,
+ char *possible_values[], const char *default_value,
+ cmdline_parser_clitkMedianImageFilter_arg_type arg_type,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *multi_token, *multi_next; /* store single arguments */
+
+ if (arg_type == ARG_NO) {
+ (*prev_given)++;
+ return 0; /* OK */
+ }
+
+ multi_token = get_multiple_arg_token(val);
+ multi_next = get_multiple_arg_token_next (val);
+
+ while (1)
+ {
+ add_node (list);
+ if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0,
+ prev_given, multi_token, possible_values, default_value,
+ arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) {
+ if (multi_token) free(multi_token);
+ return 1; /* failure */
+ }
+
+ if (multi_next)
+ {
+ multi_token = get_multiple_arg_token(multi_next);
+ multi_next = get_multiple_arg_token_next (multi_next);
+ }
+ else
+ break;
+ }
+
+ return 0; /* OK */
+}
+
+/**
+ * @brief free the passed list (including possible string argument)
+ */
+static
+void free_list(struct generic_list *list, short string_arg)
+{
+ if (list) {
+ struct generic_list *tmp;
+ while (list)
+ {
+ tmp = list;
+ if (string_arg && list->arg.string_arg)
+ free (list->arg.string_arg);
+ if (list->orig)
+ free (list->orig);
+ list = list->next;
+ free (tmp);
+ }
+ }
+}
+
+/**
+ * @brief updates a multiple option starting from the passed list
+ */
+static
+void update_multiple_arg(void *field, char ***orig_field,
+ unsigned int field_given, unsigned int prev_given, union generic_value *default_value,
+ cmdline_parser_clitkMedianImageFilter_arg_type arg_type,
+ struct generic_list *list)
+{
+ int i;
+ struct generic_list *tmp;
+
+ if (prev_given && list) {
+ *orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *));
+
+ switch(arg_type) {
+ case ARG_INT:
+ *((int **)field) = (int *)realloc (*((int **)field), (field_given + prev_given) * sizeof (int)); break;
+ case ARG_STRING:
+ *((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break;
+ default:
+ break;
+ };
+
+ for (i = (prev_given - 1); i >= 0; --i)
+ {
+ tmp = list;
+
+ switch(arg_type) {
+ case ARG_INT:
+ (*((int **)field))[i + field_given] = tmp->arg.int_arg; break;
+ case ARG_STRING:
+ (*((char ***)field))[i + field_given] = tmp->arg.string_arg; break;
+ default:
+ break;
+ }
+ (*orig_field) [i + field_given] = list->orig;
+ list = list->next;
+ free (tmp);
+ }
+ } else { /* set the default value */
+ if (default_value && ! field_given) {
+ switch(arg_type) {
+ case ARG_INT:
+ if (! *((int **)field)) {
+ *((int **)field) = (int *)malloc (sizeof (int));
+ (*((int **)field))[0] = default_value->int_arg;
+ }
+ break;
+ case ARG_STRING:
+ if (! *((char ***)field)) {
+ *((char ***)field) = (char **)malloc (sizeof (char *));
+ (*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg);
+ }
+ break;
+ default: break;
+ }
+ if (!(*orig_field)) {
+ *orig_field = (char **) malloc (sizeof (char *));
+ (*orig_field)[0] = NULL;
+ }
+ }
+ }
+}
+
+int
+cmdline_parser_clitkMedianImageFilter_internal (int argc, char * const *argv, struct args_info_clitkMedianImageFilter *args_info,
+ struct cmdline_parser_clitkMedianImageFilter_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+ union generic_value multiple_default_value;
+
+ struct generic_list * radius_list = NULL;
+ int error = 0;
+ struct args_info_clitkMedianImageFilter local_args_info;
+
+ int override;
+ int initialize;
+ int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+ check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+ cmdline_parser_clitkMedianImageFilter_init (args_info);
+
+ cmdline_parser_clitkMedianImageFilter_init (&local_args_info);
+
+ optarg = 0;
+ optind = 0;
+ opterr = params->print_errors;
+ optopt = '?';
+
+ while (1)
+ {
+ int option_index = 0;
+
+ static struct option long_options[] = {
+ { "help", 0, NULL, 'h' },
+ { "version", 0, NULL, 'V' },
+ { "config", 1, NULL, 0 },
+ { "verbose", 0, NULL, 'v' },
+ { "input", 1, NULL, 'i' },
+ { "output", 1, NULL, 'o' },
+ { "radius", 1, NULL, 'r' },
+ { NULL, 0, NULL, 0 }
+ };
+
+ custom_optarg = optarg;
+ custom_optind = optind;
+ custom_opterr = opterr;
+ custom_optopt = optopt;
+
+ c = custom_getopt_long (argc, argv, "hVvi:o:r:", long_options, &option_index);
+
+ optarg = custom_optarg;
+ optind = custom_optind;
+ opterr = custom_opterr;
+ optopt = custom_optopt;
+
+ if (c == -1) break; /* Exit from `while (1)' loop. */
+
+ switch (c)
+ {
+ case 'h': /* Print help and exit. */
+ cmdline_parser_clitkMedianImageFilter_print_help ();
+ cmdline_parser_clitkMedianImageFilter_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'V': /* Print version and exit. */
+ cmdline_parser_clitkMedianImageFilter_print_version ();
+ cmdline_parser_clitkMedianImageFilter_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'v': /* Verbose. */
+
+
+ if (update_arg((void *)&(args_info->verbose_flag), 0, &(args_info->verbose_given),
+ &(local_args_info.verbose_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verbose", 'v',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'i': /* Input image filename. */
+
+
+ if (update_arg( (void *)&(args_info->input_arg),
+ &(args_info->input_orig), &(args_info->input_given),
+ &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "input", 'i',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'o': /* Output image filename. */
+
+
+ if (update_arg( (void *)&(args_info->output_arg),
+ &(args_info->output_orig), &(args_info->output_given),
+ &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "output", 'o',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'r': /* Radius in each Direction. */
+
+ if (update_multiple_arg_temp(&radius_list,
+ &(local_args_info.radius_given), optarg, 0, "1", ARG_INT,
+ "radius", 'r',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ /* Config file. */
+ if (strcmp (long_options[option_index].name, "config") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->config_arg),
+ &(args_info->config_orig), &(args_info->config_given),
+ &(local_args_info.config_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "config", '-',
+ additional_error))
+ goto failure;
+
+ }
+
+ break;
+ case '?': /* Invalid option. */
+ /* `getopt_long' already printed an error message. */
+ goto failure;
+
+ default: /* bug: option not considered. */
+ fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+
+ multiple_default_value.int_arg = 1;
+ update_multiple_arg((void *)&(args_info->radius_arg),
+ &(args_info->radius_orig), args_info->radius_given,
+ local_args_info.radius_given, &multiple_default_value ,
+ ARG_INT, radius_list);
+
+ args_info->radius_given += local_args_info.radius_given;
+ local_args_info.radius_given = 0;
+
+ if (check_required)
+ {
+ error += cmdline_parser_clitkMedianImageFilter_required2 (args_info, argv[0], additional_error);
+ }
+
+ cmdline_parser_clitkMedianImageFilter_release (&local_args_info);
+
+ if ( error )
+ return (EXIT_FAILURE);
+
+ if (optind < argc)
+ {
+ int i = 0 ;
+ int found_prog_name = 0;
+ /* whether program name, i.e., argv[0], is in the remaining args
+ (this may happen with some implementations of getopt,
+ but surely not with the one included by gengetopt) */
+
+
+ args_info->inputs_num = argc - optind - found_prog_name;
+ args_info->inputs =
+ (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+ while (optind < argc)
+ args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
+ }
+
+ return 0;
+
+failure:
+ free_list (radius_list, 0 );
+
+ cmdline_parser_clitkMedianImageFilter_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
+
+#ifndef CONFIG_FILE_LINE_SIZE
+#define CONFIG_FILE_LINE_SIZE 2048
+#endif
+#define ADDITIONAL_ERROR " in configuration file "
+
+#define CONFIG_FILE_LINE_BUFFER_SIZE (CONFIG_FILE_LINE_SIZE+3)
+/* 3 is for "--" and "=" */
+
+static int
+_cmdline_parser_clitkMedianImageFilter_configfile (char * const filename, int *my_argc)
+{
+ FILE* file;
+ char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
+ char linebuf[CONFIG_FILE_LINE_SIZE];
+ int line_num = 0;
+ int result = 0, equal;
+ char *fopt, *farg;
+ char *str_index;
+ size_t len, next_token;
+ char delimiter;
+
+ if ((file = fopen(filename, "r")) == NULL)
+ {
+ fprintf (stderr, "%s: Error opening configuration file '%s'\n",
+ CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
+ {
+ ++line_num;
+ my_argv[0] = '\0';
+ len = strlen(linebuf);
+ if (len > (CONFIG_FILE_LINE_BUFFER_SIZE-1))
+ {
+ fprintf (stderr, "%s:%s:%d: Line too long in configuration file\n",
+ CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+
+ /* find first non-whitespace character in the line */
+ next_token = strspn (linebuf, " \t\r\n");
+ str_index = linebuf + next_token;
+
+ if ( str_index[0] == '\0' || str_index[0] == '#')
+ continue; /* empty line or comment line is skipped */
+
+ fopt = str_index;
+
+ /* truncate fopt at the end of the first non-valid character */
+ next_token = strcspn (fopt, " \t\r\n=");
+
+ if (fopt[next_token] == '\0') /* the line is over */
+ {
+ farg = NULL;
+ equal = 0;
+ goto noarg;
+ }
+
+ /* remember if equal sign is present */
+ equal = (fopt[next_token] == '=');
+ fopt[next_token++] = '\0';
+
+ /* advance pointers to the next token after the end of fopt */
+ next_token += strspn (fopt + next_token, " \t\r\n");
+
+ /* check for the presence of equal sign, and if so, skip it */
+ if ( !equal )
+ if ((equal = (fopt[next_token] == '=')))
+ {
+ next_token++;
+ next_token += strspn (fopt + next_token, " \t\r\n");
+ }
+ str_index += next_token;
+
+ /* find argument */
+ farg = str_index;
+ if ( farg[0] == '\"' || farg[0] == '\'' )
+ { /* quoted argument */
+ str_index = strchr (++farg, str_index[0] ); /* skip opening quote */
+ if (! str_index)
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: unterminated string in configuration file\n",
+ CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+ else
+ { /* read up the remaining part up to a delimiter */
+ next_token = strcspn (farg, " \t\r\n#\'\"");
+ str_index += next_token;
+ }
+
+ /* truncate farg at the delimiter and store it for further check */
+ delimiter = *str_index, *str_index++ = '\0';
+
+ /* everything but comment is illegal at the end of line */
+ if (delimiter != '\0' && delimiter != '#')
+ {
+ str_index += strspn(str_index, " \t\r\n");
+ if (*str_index != '\0' && *str_index != '#')
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: malformed string in configuration file\n",
+ CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+
+ noarg:
+ if (!strcmp(fopt,"include")) {
+ if (farg && *farg) {
+ result = _cmdline_parser_clitkMedianImageFilter_configfile(farg, my_argc);
+ } else {
+ fprintf(stderr, "%s:%s:%d: include requires a filename argument.\n",
+ CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE, filename, line_num);
+ }
+ continue;
+ }
+ len = strlen(fopt);
+ strcat (my_argv, len > 1 ? "--" : "-");
+ strcat (my_argv, fopt);
+ if (len > 1 && ((farg && *farg) || equal))
+ strcat (my_argv, "=");
+ if (farg && *farg)
+ strcat (my_argv, farg);
+ ++(*my_argc);
+
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup(my_argv);
+ } /* while */
+
+ if (file)
+ fclose(file);
+ return result;
+}
+
+int
+cmdline_parser_clitkMedianImageFilter_configfile (char * const filename,
+ struct args_info_clitkMedianImageFilter *args_info,
+ int override, int initialize, int check_required)
+{
+ struct cmdline_parser_clitkMedianImageFilter_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ return cmdline_parser_clitkMedianImageFilter_config_file (filename, args_info, ¶ms);
+}
+
+int
+cmdline_parser_clitkMedianImageFilter_config_file (char * const filename,
+ struct args_info_clitkMedianImageFilter *args_info,
+ struct cmdline_parser_clitkMedianImageFilter_params *params)
+{
+ int i, result;
+ int my_argc = 1;
+ char **my_argv_arg;
+ char *additional_error;
+
+ /* store the program name */
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup (CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE);
+
+ result = _cmdline_parser_clitkMedianImageFilter_configfile(filename, &my_argc);
+
+ if (result != EXIT_FAILURE) {
+ my_argv_arg = (char **) malloc((my_argc+1) * sizeof(char *));
+ cmd_line_list_tmp = cmd_line_list;
+
+ for (i = my_argc - 1; i >= 0; --i) {
+ my_argv_arg[i] = cmd_line_list_tmp->string_arg;
+ cmd_line_list_tmp = cmd_line_list_tmp->next;
+ }
+
+ my_argv_arg[my_argc] = 0;
+
+ additional_error = (char *)malloc(strlen(filename) + strlen(ADDITIONAL_ERROR) + 1);
+ strcpy (additional_error, ADDITIONAL_ERROR);
+ strcat (additional_error, filename);
+ result =
+ cmdline_parser_clitkMedianImageFilter_internal (my_argc, my_argv_arg, args_info,
+ params,
+ additional_error);
+
+ free (additional_error);
+ free (my_argv_arg);
+ }
+
+ free_cmd_list();
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkMedianImageFilter_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
--- /dev/null
+/** @file clitkMedianImageFilter_ggo.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CLITKMEDIANIMAGEFILTER_GGO_H
+#define CLITKMEDIANIMAGEFILTER_GGO_H
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE
+/** @brief the program name */
+#define CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_PACKAGE "clitkMedianImageFilter"
+#endif
+
+#ifndef CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_CLITKMEDIANIMAGEFILTER_VERSION "1.0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct args_info_clitkMedianImageFilter
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ char * config_arg; /**< @brief Config file. */
+ char * config_orig; /**< @brief Config file original value given at command line. */
+ const char *config_help; /**< @brief Config file help description. */
+ int verbose_flag; /**< @brief Verbose (default=off). */
+ const char *verbose_help; /**< @brief Verbose help description. */
+ char * input_arg; /**< @brief Input image filename. */
+ char * input_orig; /**< @brief Input image filename original value given at command line. */
+ const char *input_help; /**< @brief Input image filename help description. */
+ char * output_arg; /**< @brief Output image filename. */
+ char * output_orig; /**< @brief Output image filename original value given at command line. */
+ const char *output_help; /**< @brief Output image filename help description. */
+ int* radius_arg; /**< @brief Radius in each Direction (default='1'). */
+ char ** radius_orig; /**< @brief Radius in each Direction original value given at command line. */
+ int radius_min; /**< @brief Radius in each Direction's minimum occurreces */
+ int radius_max; /**< @brief Radius in each Direction's maximum occurreces */
+ const char *radius_help; /**< @brief Radius in each Direction help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int config_given ; /**< @brief Whether config was given. */
+ unsigned int verbose_given ; /**< @brief Whether verbose was given. */
+ unsigned int input_given ; /**< @brief Whether input was given. */
+ unsigned int output_given ; /**< @brief Whether output was given. */
+ unsigned int radius_given ; /**< @brief Whether radius was given. */
+
+ char **inputs ; /**< @brief unamed options (options without names) */
+ unsigned inputs_num ; /**< @brief unamed options number */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_clitkMedianImageFilter_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure args_info_clitkMedianImageFilter (default 1) */
+ int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+ int check_ambiguity; /**< @brief whether to check for options already specified in the option structure args_info_clitkMedianImageFilter (default 0) */
+ int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *args_info_clitkMedianImageFilter_purpose;
+/** @brief the usage string of the program */
+extern const char *args_info_clitkMedianImageFilter_usage;
+/** @brief all the lines making the help output */
+extern const char *args_info_clitkMedianImageFilter_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkMedianImageFilter (int argc, char * const *argv,
+ struct args_info_clitkMedianImageFilter *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkMedianImageFilter_ext() instead
+ */
+int cmdline_parser_clitkMedianImageFilter2 (int argc, char * const *argv,
+ struct args_info_clitkMedianImageFilter *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkMedianImageFilter_ext (int argc, char * const *argv,
+ struct args_info_clitkMedianImageFilter *args_info,
+ struct cmdline_parser_clitkMedianImageFilter_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkMedianImageFilter_dump(FILE *outfile,
+ struct args_info_clitkMedianImageFilter *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkMedianImageFilter_file_save(const char *filename,
+ struct args_info_clitkMedianImageFilter *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_clitkMedianImageFilter_print_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_clitkMedianImageFilter_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_clitkMedianImageFilter_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_clitkMedianImageFilter_params_init(struct cmdline_parser_clitkMedianImageFilter_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_clitkMedianImageFilter_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_clitkMedianImageFilter_params structure
+ */
+struct cmdline_parser_clitkMedianImageFilter_params *cmdline_parser_clitkMedianImageFilter_params_create(void);
+
+/**
+ * Initializes the passed args_info_clitkMedianImageFilter structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_clitkMedianImageFilter_init (struct args_info_clitkMedianImageFilter *args_info);
+/**
+ * Deallocates the string fields of the args_info_clitkMedianImageFilter structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_clitkMedianImageFilter_free (struct args_info_clitkMedianImageFilter *args_info);
+
+/**
+ * The config file parser (deprecated version)
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkMedianImageFilter_config_file() instead
+ */
+int cmdline_parser_clitkMedianImageFilter_configfile (char * const filename,
+ struct args_info_clitkMedianImageFilter *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The config file parser
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkMedianImageFilter_config_file (char * const filename,
+ struct args_info_clitkMedianImageFilter *args_info,
+ struct cmdline_parser_clitkMedianImageFilter_params *params);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ * possible errors
+ * @return
+ */
+int cmdline_parser_clitkMedianImageFilter_required (struct args_info_clitkMedianImageFilter *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CLITKMEDIANIMAGEFILTER_GGO_H */
--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22
+ generated with the following command:
+ /usr/local/bin/gengetopt --output-dir=/home/tbaudier/vv/vv_static/vv/vv_bin/tools --arg-struct-name=args_info_clitkProfileImage --func-name=cmdline_parser_clitkProfileImage --file-name=clitkProfileImage_ggo --unamed-opts --conf-parser --include-getopt
+
+ The developers of gengetopt consider the fixed text that goes in all
+ gengetopt output files to be in the public domain:
+ we make no copyright claims on it.
+*/
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+
+#include "clitkProfileImage_ggo.h"
+
+const char *args_info_clitkProfileImage_purpose = "Save the profile between 2 points of the input image in the output text file";
+
+const char *args_info_clitkProfileImage_usage = "Usage: clitkProfileImage [OPTIONS]... [FILES]...";
+
+const char *args_info_clitkProfileImage_description = "";
+
+const char *args_info_clitkProfileImage_help[] = {
+ " -h, --help Print help and exit",
+ " -V, --version Print version and exit",
+ " --config=STRING Config file",
+ " -v, --verbose Verbose (default=off)",
+ " --imagetypes Display allowed image types (default=off)",
+ " -i, --input=STRING Input image filename",
+ " -o, --output=STRING Output texte filename",
+ " -f, --point1=DOUBLE First point (mm)",
+ " -s, --point2=DOUBLE Second point (mm)",
+ 0
+};
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_DOUBLE
+} cmdline_parser_clitkProfileImage_arg_type;
+
+static
+void clear_given (struct args_info_clitkProfileImage *args_info);
+static
+void clear_args (struct args_info_clitkProfileImage *args_info);
+
+static int
+cmdline_parser_clitkProfileImage_internal (int argc, char * const *argv, struct args_info_clitkProfileImage *args_info,
+ struct cmdline_parser_clitkProfileImage_params *params, const char *additional_error);
+
+static int
+cmdline_parser_clitkProfileImage_required2 (struct args_info_clitkProfileImage *args_info, const char *prog_name, const char *additional_error);
+struct line_list
+{
+ char * string_arg;
+ struct line_list * next;
+};
+
+static struct line_list *cmd_line_list = 0;
+static struct line_list *cmd_line_list_tmp = 0;
+
+static void
+free_cmd_list(void)
+{
+ /* free the list of a previous call */
+ if (cmd_line_list)
+ {
+ while (cmd_line_list) {
+ cmd_line_list_tmp = cmd_line_list;
+ cmd_line_list = cmd_line_list->next;
+ free (cmd_line_list_tmp->string_arg);
+ free (cmd_line_list_tmp);
+ }
+ }
+}
+
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct args_info_clitkProfileImage *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->config_given = 0 ;
+ args_info->verbose_given = 0 ;
+ args_info->imagetypes_given = 0 ;
+ args_info->input_given = 0 ;
+ args_info->output_given = 0 ;
+ args_info->point1_given = 0 ;
+ args_info->point2_given = 0 ;
+}
+
+static
+void clear_args (struct args_info_clitkProfileImage *args_info)
+{
+ args_info->config_arg = NULL;
+ args_info->config_orig = NULL;
+ args_info->verbose_flag = 0;
+ args_info->imagetypes_flag = 0;
+ args_info->input_arg = NULL;
+ args_info->input_orig = NULL;
+ args_info->output_arg = NULL;
+ args_info->output_orig = NULL;
+ args_info->point1_arg = NULL;
+ args_info->point1_orig = NULL;
+ args_info->point2_arg = NULL;
+ args_info->point2_orig = NULL;
+
+}
+
+static
+void init_args_info(struct args_info_clitkProfileImage *args_info)
+{
+
+
+ args_info->help_help = args_info_clitkProfileImage_help[0] ;
+ args_info->version_help = args_info_clitkProfileImage_help[1] ;
+ args_info->config_help = args_info_clitkProfileImage_help[2] ;
+ args_info->verbose_help = args_info_clitkProfileImage_help[3] ;
+ args_info->imagetypes_help = args_info_clitkProfileImage_help[4] ;
+ args_info->input_help = args_info_clitkProfileImage_help[5] ;
+ args_info->output_help = args_info_clitkProfileImage_help[6] ;
+ args_info->point1_help = args_info_clitkProfileImage_help[7] ;
+ args_info->point1_min = -1;
+ args_info->point1_max = 4;
+ args_info->point2_help = args_info_clitkProfileImage_help[8] ;
+ args_info->point2_min = -1;
+ args_info->point2_max = 4;
+
+}
+
+void
+cmdline_parser_clitkProfileImage_print_version (void)
+{
+ printf ("%s %s\n", CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE, CMDLINE_PARSER_CLITKPROFILEIMAGE_VERSION);
+}
+
+static void print_help_common(void) {
+ cmdline_parser_clitkProfileImage_print_version ();
+
+ if (strlen(args_info_clitkProfileImage_purpose) > 0)
+ printf("\n%s\n", args_info_clitkProfileImage_purpose);
+
+ if (strlen(args_info_clitkProfileImage_usage) > 0)
+ printf("\n%s\n", args_info_clitkProfileImage_usage);
+
+ printf("\n");
+
+ if (strlen(args_info_clitkProfileImage_description) > 0)
+ printf("%s\n", args_info_clitkProfileImage_description);
+}
+
+void
+cmdline_parser_clitkProfileImage_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (args_info_clitkProfileImage_help[i])
+ printf("%s\n", args_info_clitkProfileImage_help[i++]);
+}
+
+void
+cmdline_parser_clitkProfileImage_init (struct args_info_clitkProfileImage *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+
+ args_info->inputs = NULL;
+ args_info->inputs_num = 0;
+}
+
+void
+cmdline_parser_clitkProfileImage_params_init(struct cmdline_parser_clitkProfileImage_params *params)
+{
+ if (params)
+ {
+ params->override = 0;
+ params->initialize = 1;
+ params->check_required = 1;
+ params->check_ambiguity = 0;
+ params->print_errors = 1;
+ }
+}
+
+struct cmdline_parser_clitkProfileImage_params *
+cmdline_parser_clitkProfileImage_params_create(void)
+{
+ struct cmdline_parser_clitkProfileImage_params *params =
+ (struct cmdline_parser_clitkProfileImage_params *)malloc(sizeof(struct cmdline_parser_clitkProfileImage_params));
+ cmdline_parser_clitkProfileImage_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+/** @brief generic value variable */
+union generic_value {
+ double double_arg;
+ char *string_arg;
+};
+
+/** @brief holds temporary values for multiple options */
+struct generic_list
+{
+ union generic_value arg;
+ char *orig;
+ struct generic_list *next;
+};
+
+/**
+ * @brief add a node at the head of the list
+ */
+static void add_node(struct generic_list **list) {
+ struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list));
+ new_node->next = *list;
+ *list = new_node;
+ new_node->arg.string_arg = NULL;
+ new_node->orig = NULL;
+}
+
+static void
+free_multiple_field(unsigned int len, void **arg, char ***orig)
+{
+ unsigned int i;
+ if (*arg) {
+ for (i = 0; i < len; ++i)
+ {
+ free_string_field(&((*orig)[i]));
+ }
+
+ free (*arg);
+ *arg = 0;
+ free (*orig);
+ *orig = 0;
+ }
+}
+
+
+static void
+cmdline_parser_clitkProfileImage_release (struct args_info_clitkProfileImage *args_info)
+{
+ unsigned int i;
+ free_string_field (&(args_info->config_arg));
+ free_string_field (&(args_info->config_orig));
+ free_string_field (&(args_info->input_arg));
+ free_string_field (&(args_info->input_orig));
+ free_string_field (&(args_info->output_arg));
+ free_string_field (&(args_info->output_orig));
+ free_multiple_field (args_info->point1_given, (void **)&(args_info->point1_arg), &(args_info->point1_orig));
+ free_multiple_field (args_info->point2_given, (void **)&(args_info->point2_arg), &(args_info->point2_orig));
+
+
+ for (i = 0; i < args_info->inputs_num; ++i)
+ free (args_info->inputs [i]);
+
+ if (args_info->inputs_num)
+ free (args_info->inputs);
+
+ clear_given (args_info);
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+ if (arg) {
+ fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+ } else {
+ fprintf(outfile, "%s\n", opt);
+ }
+}
+
+static void
+write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, char *values[])
+{
+ int i;
+
+ for (i = 0; i < len; ++i)
+ write_into_file(outfile, opt, (arg ? arg[i] : 0), values);
+}
+
+int
+cmdline_parser_clitkProfileImage_dump(FILE *outfile, struct args_info_clitkProfileImage *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE);
+ return EXIT_FAILURE;
+ }
+
+ if (args_info->help_given)
+ write_into_file(outfile, "help", 0, 0 );
+ if (args_info->version_given)
+ write_into_file(outfile, "version", 0, 0 );
+ if (args_info->config_given)
+ write_into_file(outfile, "config", args_info->config_orig, 0);
+ if (args_info->verbose_given)
+ write_into_file(outfile, "verbose", 0, 0 );
+ if (args_info->imagetypes_given)
+ write_into_file(outfile, "imagetypes", 0, 0 );
+ if (args_info->input_given)
+ write_into_file(outfile, "input", args_info->input_orig, 0);
+ if (args_info->output_given)
+ write_into_file(outfile, "output", args_info->output_orig, 0);
+ write_multiple_into_file(outfile, args_info->point1_given, "point1", args_info->point1_orig, 0);
+ write_multiple_into_file(outfile, args_info->point2_given, "point2", args_info->point2_orig, 0);
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+cmdline_parser_clitkProfileImage_file_save(const char *filename, struct args_info_clitkProfileImage *args_info)
+{
+ FILE *outfile;
+ int i = 0;
+
+ outfile = fopen(filename, "w");
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = cmdline_parser_clitkProfileImage_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+cmdline_parser_clitkProfileImage_free (struct args_info_clitkProfileImage *args_info)
+{
+ cmdline_parser_clitkProfileImage_release (args_info);
+}
+
+/** @brief replacement of strdup, which is not standard */
+char *
+gengetopt_strdup (const char *s)
+{
+ char *result = NULL;
+ if (!s)
+ return result;
+
+ result = (char*)malloc(strlen(s) + 1);
+ if (result == (char*)0)
+ return (char*)0;
+ strcpy(result, s);
+ return result;
+}
+
+static char *
+get_multiple_arg_token(const char *arg)
+{
+ char *tok, *ret;
+ size_t len, num_of_escape, i, j;
+
+ if (!arg)
+ return NULL;
+
+ tok = strchr (arg, ',');
+ num_of_escape = 0;
+
+ /* make sure it is not escaped */
+ while (tok)
+ {
+ if (*(tok-1) == '\\')
+ {
+ /* find the next one */
+ tok = strchr (tok+1, ',');
+ ++num_of_escape;
+ }
+ else
+ break;
+ }
+
+ if (tok)
+ len = (size_t)(tok - arg + 1);
+ else
+ len = strlen (arg) + 1;
+
+ len -= num_of_escape;
+
+ ret = (char *) malloc (len);
+
+ i = 0;
+ j = 0;
+ while (arg[i] && (j < len-1))
+ {
+ if (arg[i] == '\\' &&
+ arg[ i + 1 ] &&
+ arg[ i + 1 ] == ',')
+ ++i;
+
+ ret[j++] = arg[i++];
+ }
+
+ ret[len-1] = '\0';
+
+ return ret;
+}
+
+static char *
+get_multiple_arg_token_next(const char *arg)
+{
+ char *tok;
+
+ if (!arg)
+ return NULL;
+
+ tok = strchr (arg, ',');
+
+ /* make sure it is not escaped */
+ while (tok)
+ {
+ if (*(tok-1) == '\\')
+ {
+ /* find the next one */
+ tok = strchr (tok+1, ',');
+ }
+ else
+ break;
+ }
+
+ if (! tok || strlen(tok) == 1)
+ return 0;
+
+ return tok+1;
+}
+
+static int
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc);
+
+int
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc)
+{
+ int error = 0;
+
+ if (option_given && ! (min < 0 && max < 0))
+ {
+ if (min >= 0 && max >= 0)
+ {
+ if (min == max)
+ {
+ /* specific occurrences */
+ if (option_given != min)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be %d\n",
+ prog_name, option_desc, min);
+ error = 1;
+ }
+ }
+ else if (option_given < min
+ || option_given > max)
+ {
+ /* range occurrences */
+ fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n",
+ prog_name, option_desc, min, max);
+ error = 1;
+ }
+ }
+ else if (min >= 0)
+ {
+ /* at least check */
+ if (option_given < min)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be at least %d\n",
+ prog_name, option_desc, min);
+ error = 1;
+ }
+ }
+ else if (max >= 0)
+ {
+ /* at most check */
+ if (option_given > max)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be at most %d\n",
+ prog_name, option_desc, max);
+ error = 1;
+ }
+ }
+ }
+
+ return error;
+}
+int
+cmdline_parser_clitkProfileImage (int argc, char * const *argv, struct args_info_clitkProfileImage *args_info)
+{
+ return cmdline_parser_clitkProfileImage2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+cmdline_parser_clitkProfileImage_ext (int argc, char * const *argv, struct args_info_clitkProfileImage *args_info,
+ struct cmdline_parser_clitkProfileImage_params *params)
+{
+ int result;
+ result = cmdline_parser_clitkProfileImage_internal (argc, argv, args_info, params, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkProfileImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkProfileImage2 (int argc, char * const *argv, struct args_info_clitkProfileImage *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct cmdline_parser_clitkProfileImage_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = cmdline_parser_clitkProfileImage_internal (argc, argv, args_info, ¶ms, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkProfileImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkProfileImage_required (struct args_info_clitkProfileImage *args_info, const char *prog_name)
+{
+ int result = EXIT_SUCCESS;
+
+ if (cmdline_parser_clitkProfileImage_required2(args_info, prog_name, NULL) > 0)
+ result = EXIT_FAILURE;
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkProfileImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkProfileImage_required2 (struct args_info_clitkProfileImage *args_info, const char *prog_name, const char *additional_error)
+{
+ int error = 0;
+
+ /* checks for required options */
+ if (! args_info->input_given)
+ {
+ fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (! args_info->output_given)
+ {
+ fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (! args_info->point1_given)
+ {
+ fprintf (stderr, "%s: '--point1' ('-f') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (check_multiple_option_occurrences(prog_name, args_info->point1_given, args_info->point1_min, args_info->point1_max, "'--point1' ('-f')"))
+ error = 1;
+
+ if (! args_info->point2_given)
+ {
+ fprintf (stderr, "%s: '--point2' ('-s') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (check_multiple_option_occurrences(prog_name, args_info->point2_given, args_info->point2_min, args_info->point2_max, "'--point2' ('-s')"))
+ error = 1;
+
+
+ /* checks for dependences among options */
+
+ return error;
+}
+
+/*
+ * Extracted from the glibc source tree, version 2.3.6
+ *
+ * Licensed under the GPL as per the whole glibc source tree.
+ *
+ * This file was modified so that getopt_long can be called
+ * many times without risking previous memory to be spoiled.
+ *
+ * Modified by Andre Noll and Lorenzo Bettini for use in
+ * GNU gengetopt generated files.
+ *
+ */
+
+/*
+ * we must include anything we need since this file is not thought to be
+ * inserted in a file already using getopt.h
+ *
+ * Lorenzo
+ */
+
+struct option
+{
+ const char *name;
+ /* has_arg can't be an enum because some compilers complain about
+ type mismatches in all the code that assumes it is an int. */
+ int has_arg;
+ int *flag;
+ int val;
+};
+
+/* For communication from `getopt' to the caller.
+ When `getopt' finds an option that takes an argument,
+ the argument value is returned here.
+ Also, when `ordering' is RETURN_IN_ORDER,
+ each non-option ARGV-element is returned here. */
+
+static char *optarg;
+
+/* Index in ARGV of the next element to be scanned.
+ This is used for communication to and from the caller
+ and for communication between successive calls to `getopt'.
+
+ On entry to `getopt', zero means this is the first call; initialize.
+
+ When `getopt' returns -1, this is the index of the first of the
+ non-option elements that the caller should itself scan.
+
+ Otherwise, `optind' communicates from one call to the next
+ how much of ARGV has been scanned so far. */
+
+static int optind;
+
+/* Callers store zero here to inhibit the error message `getopt' prints
+ for unrecognized options. */
+
+static int opterr;
+
+/* Set to an option character which was unrecognized. */
+
+static int optopt;
+
+/* This version of `getopt' appears to the caller like standard Unix `getopt'
+ but it behaves differently for the user, since it allows the user
+ to intersperse the options with the other arguments.
+
+ As `getopt' works, it permutes the elements of ARGV so that,
+ when it is done, all the options precede everything else. Thus
+ all application programs are extended to handle flexible argument order.
+*/
+/*
+ If the field `flag' is not NULL, it points to a variable that is set
+ to the value given in the field `val' when the option is found, but
+ left unchanged if the option is not found.
+
+ To have a long-named option do something other than set an `int' to
+ a compiled-in constant, such as set a value from `custom_optarg', set the
+ option's `flag' field to zero and its `val' field to a nonzero
+ value (the equivalent single-letter option character, if there is
+ one). For long options that have a zero `flag' field, `getopt'
+ returns the contents of the `val' field. */
+
+/* Names for the values of the `has_arg' field of `struct option'. */
+#ifndef no_argument
+#define no_argument 0
+#endif
+
+#ifndef required_argument
+#define required_argument 1
+#endif
+
+#ifndef optional_argument
+#define optional_argument 2
+#endif
+
+struct custom_getopt_data {
+ /*
+ * These have exactly the same meaning as the corresponding global variables,
+ * except that they are used for the reentrant versions of getopt.
+ */
+ int custom_optind;
+ int custom_opterr;
+ int custom_optopt;
+ char *custom_optarg;
+
+ /* True if the internal members have been initialized. */
+ int initialized;
+
+ /*
+ * The next char to be scanned in the option-element in which the last option
+ * character we returned was found. This allows us to pick up the scan where
+ * we left off. If this is zero, or a null string, it means resume the scan by
+ * advancing to the next ARGV-element.
+ */
+ char *nextchar;
+
+ /*
+ * Describe the part of ARGV that contains non-options that have been skipped.
+ * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is
+ * the index after the last of them.
+ */
+ int first_nonopt;
+ int last_nonopt;
+};
+
+/*
+ * the variables optarg, optind, opterr and optopt are renamed with
+ * the custom_ prefix so that they don't interfere with getopt ones.
+ *
+ * Moreover they're static so they are visible only from within the
+ * file where this very file will be included.
+ */
+
+/*
+ * For communication from `custom_getopt' to the caller. When `custom_getopt' finds an
+ * option that takes an argument, the argument value is returned here.
+ */
+static char *custom_optarg;
+
+/*
+ * Index in ARGV of the next element to be scanned. This is used for
+ * communication to and from the caller and for communication between
+ * successive calls to `custom_getopt'.
+ *
+ * On entry to `custom_getopt', 1 means this is the first call; initialize.
+ *
+ * When `custom_getopt' returns -1, this is the index of the first of the non-option
+ * elements that the caller should itself scan.
+ *
+ * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV
+ * has been scanned so far.
+ *
+ * 1003.2 says this must be 1 before any call.
+ */
+static int custom_optind = 1;
+
+/*
+ * Callers store zero here to inhibit the error message for unrecognized
+ * options.
+ */
+static int custom_opterr = 1;
+
+/*
+ * Set to an option character which was unrecognized. This must be initialized
+ * on some systems to avoid linking in the system's own getopt implementation.
+ */
+static int custom_optopt = '?';
+
+/*
+ * Exchange two adjacent subsequences of ARGV. One subsequence is elements
+ * [first_nonopt,last_nonopt) which contains all the non-options that have been
+ * skipped so far. The other is elements [last_nonopt,custom_optind), which contains
+ * all the options processed since those non-options were skipped.
+ * `first_nonopt' and `last_nonopt' are relocated so that they describe the new
+ * indices of the non-options in ARGV after they are moved.
+ */
+static void exchange(char **argv, struct custom_getopt_data *d)
+{
+ int bottom = d->first_nonopt;
+ int middle = d->last_nonopt;
+ int top = d->custom_optind;
+ char *tem;
+
+ /*
+ * Exchange the shorter segment with the far end of the longer segment.
+ * That puts the shorter segment into the right place. It leaves the
+ * longer segment in the right place overall, but it consists of two
+ * parts that need to be swapped next.
+ */
+ while (top > middle && middle > bottom) {
+ if (top - middle > middle - bottom) {
+ /* Bottom segment is the short one. */
+ int len = middle - bottom;
+ int i;
+
+ /* Swap it with the top part of the top segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] =
+ argv[top - (middle - bottom) + i];
+ argv[top - (middle - bottom) + i] = tem;
+ }
+ /* Exclude the moved bottom segment from further swapping. */
+ top -= len;
+ } else {
+ /* Top segment is the short one. */
+ int len = top - middle;
+ int i;
+
+ /* Swap it with the bottom part of the bottom segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] = argv[middle + i];
+ argv[middle + i] = tem;
+ }
+ /* Exclude the moved top segment from further swapping. */
+ bottom += len;
+ }
+ }
+ /* Update records for the slots the non-options now occupy. */
+ d->first_nonopt += (d->custom_optind - d->last_nonopt);
+ d->last_nonopt = d->custom_optind;
+}
+
+/* Initialize the internal data when the first call is made. */
+static void custom_getopt_initialize(struct custom_getopt_data *d)
+{
+ /*
+ * Start processing options with ARGV-element 1 (since ARGV-element 0
+ * is the program name); the sequence of previously skipped non-option
+ * ARGV-elements is empty.
+ */
+ d->first_nonopt = d->last_nonopt = d->custom_optind;
+ d->nextchar = NULL;
+ d->initialized = 1;
+}
+
+#define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0')
+
+/* return: zero: continue, nonzero: return given value to user */
+static int shuffle_argv(int argc, char *const *argv,const struct option *longopts,
+ struct custom_getopt_data *d)
+{
+ /*
+ * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been
+ * moved back by the user (who may also have changed the arguments).
+ */
+ if (d->last_nonopt > d->custom_optind)
+ d->last_nonopt = d->custom_optind;
+ if (d->first_nonopt > d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * If we have just processed some options following some
+ * non-options, exchange them so that the options come first.
+ */
+ if (d->first_nonopt != d->last_nonopt &&
+ d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->last_nonopt != d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * Skip any additional non-options and extend the range of
+ * non-options previously skipped.
+ */
+ while (d->custom_optind < argc && NONOPTION_P)
+ d->custom_optind++;
+ d->last_nonopt = d->custom_optind;
+ /*
+ * The special ARGV-element `--' means premature end of options. Skip
+ * it like a null option, then exchange with previous non-options as if
+ * it were an option, then skip everything else like a non-option.
+ */
+ if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) {
+ d->custom_optind++;
+ if (d->first_nonopt != d->last_nonopt
+ && d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->first_nonopt == d->last_nonopt)
+ d->first_nonopt = d->custom_optind;
+ d->last_nonopt = argc;
+ d->custom_optind = argc;
+ }
+ /*
+ * If we have done all the ARGV-elements, stop the scan and back over
+ * any non-options that we skipped and permuted.
+ */
+ if (d->custom_optind == argc) {
+ /*
+ * Set the next-arg-index to point at the non-options that we
+ * previously skipped, so the caller will digest them.
+ */
+ if (d->first_nonopt != d->last_nonopt)
+ d->custom_optind = d->first_nonopt;
+ return -1;
+ }
+ /*
+ * If we have come to a non-option and did not permute it, either stop
+ * the scan or describe it to the caller and pass it by.
+ */
+ if (NONOPTION_P) {
+ d->custom_optarg = argv[d->custom_optind++];
+ return 1;
+ }
+ /*
+ * We have found another option-ARGV-element. Skip the initial
+ * punctuation.
+ */
+ d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-'));
+ return 0;
+}
+
+/*
+ * Check whether the ARGV-element is a long option.
+ *
+ * If there's a long option "fubar" and the ARGV-element is "-fu", consider
+ * that an abbreviation of the long option, just like "--fu", and not "-f" with
+ * arg "u".
+ *
+ * This distinction seems to be the most useful approach.
+ *
+ */
+static int check_long_opt(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char *nameend;
+ const struct option *p;
+ const struct option *pfound = NULL;
+ int exact = 0;
+ int ambig = 0;
+ int indfound = -1;
+ int option_index;
+
+ for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++)
+ /* Do nothing. */ ;
+
+ /* Test all long options for either exact match or abbreviated matches */
+ for (p = longopts, option_index = 0; p->name; p++, option_index++)
+ if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) {
+ if ((unsigned int) (nameend - d->nextchar)
+ == (unsigned int) strlen(p->name)) {
+ /* Exact match found. */
+ pfound = p;
+ indfound = option_index;
+ exact = 1;
+ break;
+ } else if (pfound == NULL) {
+ /* First nonexact match found. */
+ pfound = p;
+ indfound = option_index;
+ } else if (pfound->has_arg != p->has_arg
+ || pfound->flag != p->flag
+ || pfound->val != p->val)
+ /* Second or later nonexact match found. */
+ ambig = 1;
+ }
+ if (ambig && !exact) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' is ambiguous\n",
+ argv[0], argv[d->custom_optind]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+ }
+ if (pfound) {
+ option_index = indfound;
+ d->custom_optind++;
+ if (*nameend) {
+ if (pfound->has_arg != no_argument)
+ d->custom_optarg = nameend + 1;
+ else {
+ if (print_errors) {
+ if (argv[d->custom_optind - 1][1] == '-') {
+ /* --option */
+ fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n",
+ argv[0], pfound->name);
+ } else {
+ /* +option or -option */
+ fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n",
+ argv[0], argv[d->custom_optind - 1][0], pfound->name);
+ }
+
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return '?';
+ }
+ } else if (pfound->has_arg == required_argument) {
+ if (d->custom_optind < argc)
+ d->custom_optarg = argv[d->custom_optind++];
+ else {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' requires an argument\n",
+ argv[0],
+ argv[d->custom_optind - 1]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return optstring[0] == ':' ? ':' : '?';
+ }
+ }
+ d->nextchar += strlen(d->nextchar);
+ if (longind != NULL)
+ *longind = option_index;
+ if (pfound->flag) {
+ *(pfound->flag) = pfound->val;
+ return 0;
+ }
+ return pfound->val;
+ }
+ /*
+ * Can't find it as a long option. If this is not getopt_long_only, or
+ * the option starts with '--' or is not a valid short option, then
+ * it's an error. Otherwise interpret it as a short option.
+ */
+ if (print_errors) {
+ if (argv[d->custom_optind][1] == '-') {
+ /* --option */
+ fprintf(stderr,
+ "%s: unrecognized option `--%s'\n",
+ argv[0], d->nextchar);
+ } else {
+ /* +option or -option */
+ fprintf(stderr,
+ "%s: unrecognized option `%c%s'\n",
+ argv[0], argv[d->custom_optind][0],
+ d->nextchar);
+ }
+ }
+ d->nextchar = (char *) "";
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+}
+
+static int check_short_opt(int argc, char *const *argv, const char *optstring,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char c = *d->nextchar++;
+ char *temp = strchr(optstring, c);
+
+ /* Increment `custom_optind' when we start to process its last character. */
+ if (*d->nextchar == '\0')
+ ++d->custom_optind;
+ if (!temp || c == ':') {
+ if (print_errors)
+ fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
+
+ d->custom_optopt = c;
+ return '?';
+ }
+ if (temp[1] == ':') {
+ if (temp[2] == ':') {
+ /* This is an option that accepts an argument optionally. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ d->custom_optind++;
+ } else
+ d->custom_optarg = NULL;
+ d->nextchar = NULL;
+ } else {
+ /* This is an option that requires an argument. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ /*
+ * If we end this ARGV-element by taking the
+ * rest as an arg, we must advance to the next
+ * element now.
+ */
+ d->custom_optind++;
+ } else if (d->custom_optind == argc) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option requires an argument -- %c\n",
+ argv[0], c);
+ }
+ d->custom_optopt = c;
+ if (optstring[0] == ':')
+ c = ':';
+ else
+ c = '?';
+ } else
+ /*
+ * We already incremented `custom_optind' once;
+ * increment it again when taking next ARGV-elt
+ * as argument.
+ */
+ d->custom_optarg = argv[d->custom_optind++];
+ d->nextchar = NULL;
+ }
+ }
+ return c;
+}
+
+/*
+ * Scan elements of ARGV for option characters given in OPTSTRING.
+ *
+ * If an element of ARGV starts with '-', and is not exactly "-" or "--",
+ * then it is an option element. The characters of this element
+ * (aside from the initial '-') are option characters. If `getopt'
+ * is called repeatedly, it returns successively each of the option characters
+ * from each of the option elements.
+ *
+ * If `getopt' finds another option character, it returns that character,
+ * updating `custom_optind' and `nextchar' so that the next call to `getopt' can
+ * resume the scan with the following option character or ARGV-element.
+ *
+ * If there are no more option characters, `getopt' returns -1.
+ * Then `custom_optind' is the index in ARGV of the first ARGV-element
+ * that is not an option. (The ARGV-elements have been permuted
+ * so that those that are not options now come last.)
+ *
+ * OPTSTRING is a string containing the legitimate option characters.
+ * If an option character is seen that is not listed in OPTSTRING,
+ * return '?' after printing an error message. If you set `custom_opterr' to
+ * zero, the error message is suppressed but we still return '?'.
+ *
+ * If a char in OPTSTRING is followed by a colon, that means it wants an arg,
+ * so the following text in the same ARGV-element, or the text of the following
+ * ARGV-element, is returned in `custom_optarg'. Two colons mean an option that
+ * wants an optional arg; if there is text in the current ARGV-element,
+ * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero.
+ *
+ * If OPTSTRING starts with `-' or `+', it requests different methods of
+ * handling the non-option ARGV-elements.
+ * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
+ *
+ * Long-named options begin with `--' instead of `-'.
+ * Their names may be abbreviated as long as the abbreviation is unique
+ * or is an exact match for some defined option. If they have an
+ * argument, it follows the option name in the same ARGV-element, separated
+ * from the option name by a `=', or else the in next ARGV-element.
+ * When `getopt' finds a long-named option, it returns 0 if that option's
+ * `flag' field is nonzero, the value of the option's `val' field
+ * if the `flag' field is zero.
+ *
+ * The elements of ARGV aren't really const, because we permute them.
+ * But we pretend they're const in the prototype to be compatible
+ * with other systems.
+ *
+ * LONGOPTS is a vector of `struct option' terminated by an
+ * element containing a name which is zero.
+ *
+ * LONGIND returns the index in LONGOPT of the long-named option found.
+ * It is only valid when a long-named option has been found by the most
+ * recent call.
+ *
+ * Return the option character from OPTS just read. Return -1 when there are
+ * no more options. For unrecognized options, or options missing arguments,
+ * `custom_optopt' is set to the option letter, and '?' is returned.
+ *
+ * The OPTS string is a list of characters which are recognized option letters,
+ * optionally followed by colons, specifying that that letter takes an
+ * argument, to be placed in `custom_optarg'.
+ *
+ * If a letter in OPTS is followed by two colons, its argument is optional.
+ * This behavior is specific to the GNU `getopt'.
+ *
+ * The argument `--' causes premature termination of argument scanning,
+ * explicitly telling `getopt' that there are no more options. If OPTS begins
+ * with `--', then non-option arguments are treated as arguments to the option
+ * '\0'. This behavior is specific to the GNU `getopt'.
+ */
+
+static int getopt_internal_r(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ struct custom_getopt_data *d)
+{
+ int ret, print_errors = d->custom_opterr;
+
+ if (optstring[0] == ':')
+ print_errors = 0;
+ if (argc < 1)
+ return -1;
+ d->custom_optarg = NULL;
+
+ /*
+ * This is a big difference with GNU getopt, since optind == 0
+ * means initialization while here 1 means first call.
+ */
+ if (d->custom_optind == 0 || !d->initialized) {
+ if (d->custom_optind == 0)
+ d->custom_optind = 1; /* Don't scan ARGV[0], the program name. */
+ custom_getopt_initialize(d);
+ }
+ if (d->nextchar == NULL || *d->nextchar == '\0') {
+ ret = shuffle_argv(argc, argv, longopts, d);
+ if (ret)
+ return ret;
+ }
+ if (longopts && (argv[d->custom_optind][1] == '-' ))
+ return check_long_opt(argc, argv, optstring, longopts,
+ longind, print_errors, d);
+ return check_short_opt(argc, argv, optstring, print_errors, d);
+}
+
+static int custom_getopt_internal(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind)
+{
+ int result;
+ /* Keep a global copy of all internal members of d */
+ static struct custom_getopt_data d;
+
+ d.custom_optind = custom_optind;
+ d.custom_opterr = custom_opterr;
+ result = getopt_internal_r(argc, argv, optstring, longopts,
+ longind, &d);
+ custom_optind = d.custom_optind;
+ custom_optarg = d.custom_optarg;
+ custom_optopt = d.custom_optopt;
+ return result;
+}
+
+static int custom_getopt_long (int argc, char *const *argv, const char *options,
+ const struct option *long_options, int *opt_index)
+{
+ return custom_getopt_internal(argc, argv, options, long_options,
+ opt_index);
+}
+
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_clitkProfileImage_params.check_ambiguity
+ * @param override @see cmdline_parser_clitkProfileImage_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+static
+int update_arg(void *field, char **orig_field,
+ unsigned int *field_given, unsigned int *prev_given,
+ char *value, char *possible_values[], const char *default_value,
+ cmdline_parser_clitkProfileImage_arg_type arg_type,
+ int check_ambiguity, int override,
+ int no_free, int multiple_option,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *stop_char = 0;
+ const char *val = value;
+ int found;
+ char **string_field;
+
+ stop_char = 0;
+ found = 0;
+
+ if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+ {
+ if (short_opt != '-')
+ fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
+ package_name, long_opt, short_opt,
+ (additional_error ? additional_error : ""));
+ else
+ fprintf (stderr, "%s: `--%s' option given more than once%s\n",
+ package_name, long_opt,
+ (additional_error ? additional_error : ""));
+ return 1; /* failure */
+ }
+
+
+ if (field_given && *field_given && ! override)
+ return 0;
+ if (prev_given)
+ (*prev_given)++;
+ if (field_given)
+ (*field_given)++;
+ if (possible_values)
+ val = possible_values[found];
+
+ switch(arg_type) {
+ case ARG_FLAG:
+ *((int *)field) = !*((int *)field);
+ break;
+ case ARG_DOUBLE:
+ if (val) *((double *)field) = strtod (val, &stop_char);
+ break;
+ case ARG_STRING:
+ if (val) {
+ string_field = (char **)field;
+ if (!no_free && *string_field)
+ free (*string_field); /* free previous string */
+ *string_field = gengetopt_strdup (val);
+ }
+ break;
+ default:
+ break;
+ };
+
+ /* check numeric conversion */
+ switch(arg_type) {
+ case ARG_DOUBLE:
+ if (val && !(stop_char && *stop_char == '\0')) {
+ fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+ return 1; /* failure */
+ }
+ break;
+ default:
+ ;
+ };
+
+ /* store the original value */
+ switch(arg_type) {
+ case ARG_NO:
+ case ARG_FLAG:
+ break;
+ default:
+ if (value && orig_field) {
+ if (no_free) {
+ *orig_field = value;
+ } else {
+ if (*orig_field)
+ free (*orig_field); /* free previous string */
+ *orig_field = gengetopt_strdup (value);
+ }
+ }
+ };
+
+ return 0; /* OK */
+}
+
+/**
+ * @brief store information about a multiple option in a temporary list
+ * @param list where to (temporarily) store multiple options
+ */
+static
+int update_multiple_arg_temp(struct generic_list **list,
+ unsigned int *prev_given, const char *val,
+ char *possible_values[], const char *default_value,
+ cmdline_parser_clitkProfileImage_arg_type arg_type,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *multi_token, *multi_next; /* store single arguments */
+
+ if (arg_type == ARG_NO) {
+ (*prev_given)++;
+ return 0; /* OK */
+ }
+
+ multi_token = get_multiple_arg_token(val);
+ multi_next = get_multiple_arg_token_next (val);
+
+ while (1)
+ {
+ add_node (list);
+ if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0,
+ prev_given, multi_token, possible_values, default_value,
+ arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) {
+ if (multi_token) free(multi_token);
+ return 1; /* failure */
+ }
+
+ if (multi_next)
+ {
+ multi_token = get_multiple_arg_token(multi_next);
+ multi_next = get_multiple_arg_token_next (multi_next);
+ }
+ else
+ break;
+ }
+
+ return 0; /* OK */
+}
+
+/**
+ * @brief free the passed list (including possible string argument)
+ */
+static
+void free_list(struct generic_list *list, short string_arg)
+{
+ if (list) {
+ struct generic_list *tmp;
+ while (list)
+ {
+ tmp = list;
+ if (string_arg && list->arg.string_arg)
+ free (list->arg.string_arg);
+ if (list->orig)
+ free (list->orig);
+ list = list->next;
+ free (tmp);
+ }
+ }
+}
+
+/**
+ * @brief updates a multiple option starting from the passed list
+ */
+static
+void update_multiple_arg(void *field, char ***orig_field,
+ unsigned int field_given, unsigned int prev_given, union generic_value *default_value,
+ cmdline_parser_clitkProfileImage_arg_type arg_type,
+ struct generic_list *list)
+{
+ int i;
+ struct generic_list *tmp;
+
+ if (prev_given && list) {
+ *orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *));
+
+ switch(arg_type) {
+ case ARG_DOUBLE:
+ *((double **)field) = (double *)realloc (*((double **)field), (field_given + prev_given) * sizeof (double)); break;
+ case ARG_STRING:
+ *((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break;
+ default:
+ break;
+ };
+
+ for (i = (prev_given - 1); i >= 0; --i)
+ {
+ tmp = list;
+
+ switch(arg_type) {
+ case ARG_DOUBLE:
+ (*((double **)field))[i + field_given] = tmp->arg.double_arg; break;
+ case ARG_STRING:
+ (*((char ***)field))[i + field_given] = tmp->arg.string_arg; break;
+ default:
+ break;
+ }
+ (*orig_field) [i + field_given] = list->orig;
+ list = list->next;
+ free (tmp);
+ }
+ } else { /* set the default value */
+ if (default_value && ! field_given) {
+ switch(arg_type) {
+ case ARG_DOUBLE:
+ if (! *((double **)field)) {
+ *((double **)field) = (double *)malloc (sizeof (double));
+ (*((double **)field))[0] = default_value->double_arg;
+ }
+ break;
+ case ARG_STRING:
+ if (! *((char ***)field)) {
+ *((char ***)field) = (char **)malloc (sizeof (char *));
+ (*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg);
+ }
+ break;
+ default: break;
+ }
+ if (!(*orig_field)) {
+ *orig_field = (char **) malloc (sizeof (char *));
+ (*orig_field)[0] = NULL;
+ }
+ }
+ }
+}
+
+int
+cmdline_parser_clitkProfileImage_internal (int argc, char * const *argv, struct args_info_clitkProfileImage *args_info,
+ struct cmdline_parser_clitkProfileImage_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+
+ struct generic_list * point1_list = NULL;
+ struct generic_list * point2_list = NULL;
+ int error = 0;
+ struct args_info_clitkProfileImage local_args_info;
+
+ int override;
+ int initialize;
+ int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+ check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+ cmdline_parser_clitkProfileImage_init (args_info);
+
+ cmdline_parser_clitkProfileImage_init (&local_args_info);
+
+ optarg = 0;
+ optind = 0;
+ opterr = params->print_errors;
+ optopt = '?';
+
+ while (1)
+ {
+ int option_index = 0;
+
+ static struct option long_options[] = {
+ { "help", 0, NULL, 'h' },
+ { "version", 0, NULL, 'V' },
+ { "config", 1, NULL, 0 },
+ { "verbose", 0, NULL, 'v' },
+ { "imagetypes", 0, NULL, 0 },
+ { "input", 1, NULL, 'i' },
+ { "output", 1, NULL, 'o' },
+ { "point1", 1, NULL, 'f' },
+ { "point2", 1, NULL, 's' },
+ { NULL, 0, NULL, 0 }
+ };
+
+ custom_optarg = optarg;
+ custom_optind = optind;
+ custom_opterr = opterr;
+ custom_optopt = optopt;
+
+ c = custom_getopt_long (argc, argv, "hVvi:o:f:s:", long_options, &option_index);
+
+ optarg = custom_optarg;
+ optind = custom_optind;
+ opterr = custom_opterr;
+ optopt = custom_optopt;
+
+ if (c == -1) break; /* Exit from `while (1)' loop. */
+
+ switch (c)
+ {
+ case 'h': /* Print help and exit. */
+ cmdline_parser_clitkProfileImage_print_help ();
+ cmdline_parser_clitkProfileImage_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'V': /* Print version and exit. */
+ cmdline_parser_clitkProfileImage_print_version ();
+ cmdline_parser_clitkProfileImage_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'v': /* Verbose. */
+
+
+ if (update_arg((void *)&(args_info->verbose_flag), 0, &(args_info->verbose_given),
+ &(local_args_info.verbose_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verbose", 'v',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'i': /* Input image filename. */
+
+
+ if (update_arg( (void *)&(args_info->input_arg),
+ &(args_info->input_orig), &(args_info->input_given),
+ &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "input", 'i',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'o': /* Output texte filename. */
+
+
+ if (update_arg( (void *)&(args_info->output_arg),
+ &(args_info->output_orig), &(args_info->output_given),
+ &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "output", 'o',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'f': /* First point (mm). */
+
+ if (update_multiple_arg_temp(&point1_list,
+ &(local_args_info.point1_given), optarg, 0, 0, ARG_DOUBLE,
+ "point1", 'f',
+ additional_error))
+ goto failure;
+
+ break;
+ case 's': /* Second point (mm). */
+
+ if (update_multiple_arg_temp(&point2_list,
+ &(local_args_info.point2_given), optarg, 0, 0, ARG_DOUBLE,
+ "point2", 's',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ /* Config file. */
+ if (strcmp (long_options[option_index].name, "config") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->config_arg),
+ &(args_info->config_orig), &(args_info->config_given),
+ &(local_args_info.config_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "config", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Display allowed image types. */
+ else if (strcmp (long_options[option_index].name, "imagetypes") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->imagetypes_flag), 0, &(args_info->imagetypes_given),
+ &(local_args_info.imagetypes_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "imagetypes", '-',
+ additional_error))
+ goto failure;
+
+ }
+
+ break;
+ case '?': /* Invalid option. */
+ /* `getopt_long' already printed an error message. */
+ goto failure;
+
+ default: /* bug: option not considered. */
+ fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+
+ update_multiple_arg((void *)&(args_info->point1_arg),
+ &(args_info->point1_orig), args_info->point1_given,
+ local_args_info.point1_given, 0 ,
+ ARG_DOUBLE, point1_list);
+ update_multiple_arg((void *)&(args_info->point2_arg),
+ &(args_info->point2_orig), args_info->point2_given,
+ local_args_info.point2_given, 0 ,
+ ARG_DOUBLE, point2_list);
+
+ args_info->point1_given += local_args_info.point1_given;
+ local_args_info.point1_given = 0;
+ args_info->point2_given += local_args_info.point2_given;
+ local_args_info.point2_given = 0;
+
+ if (check_required)
+ {
+ error += cmdline_parser_clitkProfileImage_required2 (args_info, argv[0], additional_error);
+ }
+
+ cmdline_parser_clitkProfileImage_release (&local_args_info);
+
+ if ( error )
+ return (EXIT_FAILURE);
+
+ if (optind < argc)
+ {
+ int i = 0 ;
+ int found_prog_name = 0;
+ /* whether program name, i.e., argv[0], is in the remaining args
+ (this may happen with some implementations of getopt,
+ but surely not with the one included by gengetopt) */
+
+
+ args_info->inputs_num = argc - optind - found_prog_name;
+ args_info->inputs =
+ (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+ while (optind < argc)
+ args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
+ }
+
+ return 0;
+
+failure:
+ free_list (point1_list, 0 );
+ free_list (point2_list, 0 );
+
+ cmdline_parser_clitkProfileImage_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
+
+#ifndef CONFIG_FILE_LINE_SIZE
+#define CONFIG_FILE_LINE_SIZE 2048
+#endif
+#define ADDITIONAL_ERROR " in configuration file "
+
+#define CONFIG_FILE_LINE_BUFFER_SIZE (CONFIG_FILE_LINE_SIZE+3)
+/* 3 is for "--" and "=" */
+
+static int
+_cmdline_parser_clitkProfileImage_configfile (char * const filename, int *my_argc)
+{
+ FILE* file;
+ char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
+ char linebuf[CONFIG_FILE_LINE_SIZE];
+ int line_num = 0;
+ int result = 0, equal;
+ char *fopt, *farg;
+ char *str_index;
+ size_t len, next_token;
+ char delimiter;
+
+ if ((file = fopen(filename, "r")) == NULL)
+ {
+ fprintf (stderr, "%s: Error opening configuration file '%s'\n",
+ CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
+ {
+ ++line_num;
+ my_argv[0] = '\0';
+ len = strlen(linebuf);
+ if (len > (CONFIG_FILE_LINE_BUFFER_SIZE-1))
+ {
+ fprintf (stderr, "%s:%s:%d: Line too long in configuration file\n",
+ CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+
+ /* find first non-whitespace character in the line */
+ next_token = strspn (linebuf, " \t\r\n");
+ str_index = linebuf + next_token;
+
+ if ( str_index[0] == '\0' || str_index[0] == '#')
+ continue; /* empty line or comment line is skipped */
+
+ fopt = str_index;
+
+ /* truncate fopt at the end of the first non-valid character */
+ next_token = strcspn (fopt, " \t\r\n=");
+
+ if (fopt[next_token] == '\0') /* the line is over */
+ {
+ farg = NULL;
+ equal = 0;
+ goto noarg;
+ }
+
+ /* remember if equal sign is present */
+ equal = (fopt[next_token] == '=');
+ fopt[next_token++] = '\0';
+
+ /* advance pointers to the next token after the end of fopt */
+ next_token += strspn (fopt + next_token, " \t\r\n");
+
+ /* check for the presence of equal sign, and if so, skip it */
+ if ( !equal )
+ if ((equal = (fopt[next_token] == '=')))
+ {
+ next_token++;
+ next_token += strspn (fopt + next_token, " \t\r\n");
+ }
+ str_index += next_token;
+
+ /* find argument */
+ farg = str_index;
+ if ( farg[0] == '\"' || farg[0] == '\'' )
+ { /* quoted argument */
+ str_index = strchr (++farg, str_index[0] ); /* skip opening quote */
+ if (! str_index)
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: unterminated string in configuration file\n",
+ CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+ else
+ { /* read up the remaining part up to a delimiter */
+ next_token = strcspn (farg, " \t\r\n#\'\"");
+ str_index += next_token;
+ }
+
+ /* truncate farg at the delimiter and store it for further check */
+ delimiter = *str_index, *str_index++ = '\0';
+
+ /* everything but comment is illegal at the end of line */
+ if (delimiter != '\0' && delimiter != '#')
+ {
+ str_index += strspn(str_index, " \t\r\n");
+ if (*str_index != '\0' && *str_index != '#')
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: malformed string in configuration file\n",
+ CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+
+ noarg:
+ if (!strcmp(fopt,"include")) {
+ if (farg && *farg) {
+ result = _cmdline_parser_clitkProfileImage_configfile(farg, my_argc);
+ } else {
+ fprintf(stderr, "%s:%s:%d: include requires a filename argument.\n",
+ CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE, filename, line_num);
+ }
+ continue;
+ }
+ len = strlen(fopt);
+ strcat (my_argv, len > 1 ? "--" : "-");
+ strcat (my_argv, fopt);
+ if (len > 1 && ((farg && *farg) || equal))
+ strcat (my_argv, "=");
+ if (farg && *farg)
+ strcat (my_argv, farg);
+ ++(*my_argc);
+
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup(my_argv);
+ } /* while */
+
+ if (file)
+ fclose(file);
+ return result;
+}
+
+int
+cmdline_parser_clitkProfileImage_configfile (char * const filename,
+ struct args_info_clitkProfileImage *args_info,
+ int override, int initialize, int check_required)
+{
+ struct cmdline_parser_clitkProfileImage_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ return cmdline_parser_clitkProfileImage_config_file (filename, args_info, ¶ms);
+}
+
+int
+cmdline_parser_clitkProfileImage_config_file (char * const filename,
+ struct args_info_clitkProfileImage *args_info,
+ struct cmdline_parser_clitkProfileImage_params *params)
+{
+ int i, result;
+ int my_argc = 1;
+ char **my_argv_arg;
+ char *additional_error;
+
+ /* store the program name */
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup (CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE);
+
+ result = _cmdline_parser_clitkProfileImage_configfile(filename, &my_argc);
+
+ if (result != EXIT_FAILURE) {
+ my_argv_arg = (char **) malloc((my_argc+1) * sizeof(char *));
+ cmd_line_list_tmp = cmd_line_list;
+
+ for (i = my_argc - 1; i >= 0; --i) {
+ my_argv_arg[i] = cmd_line_list_tmp->string_arg;
+ cmd_line_list_tmp = cmd_line_list_tmp->next;
+ }
+
+ my_argv_arg[my_argc] = 0;
+
+ additional_error = (char *)malloc(strlen(filename) + strlen(ADDITIONAL_ERROR) + 1);
+ strcpy (additional_error, ADDITIONAL_ERROR);
+ strcat (additional_error, filename);
+ result =
+ cmdline_parser_clitkProfileImage_internal (my_argc, my_argv_arg, args_info,
+ params,
+ additional_error);
+
+ free (additional_error);
+ free (my_argv_arg);
+ }
+
+ free_cmd_list();
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkProfileImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
--- /dev/null
+/** @file clitkProfileImage_ggo.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CLITKPROFILEIMAGE_GGO_H
+#define CLITKPROFILEIMAGE_GGO_H
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE
+/** @brief the program name */
+#define CMDLINE_PARSER_CLITKPROFILEIMAGE_PACKAGE "clitkProfileImage"
+#endif
+
+#ifndef CMDLINE_PARSER_CLITKPROFILEIMAGE_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_CLITKPROFILEIMAGE_VERSION "1.0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct args_info_clitkProfileImage
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ char * config_arg; /**< @brief Config file. */
+ char * config_orig; /**< @brief Config file original value given at command line. */
+ const char *config_help; /**< @brief Config file help description. */
+ int verbose_flag; /**< @brief Verbose (default=off). */
+ const char *verbose_help; /**< @brief Verbose help description. */
+ int imagetypes_flag; /**< @brief Display allowed image types (default=off). */
+ const char *imagetypes_help; /**< @brief Display allowed image types help description. */
+ char * input_arg; /**< @brief Input image filename. */
+ char * input_orig; /**< @brief Input image filename original value given at command line. */
+ const char *input_help; /**< @brief Input image filename help description. */
+ char * output_arg; /**< @brief Output texte filename. */
+ char * output_orig; /**< @brief Output texte filename original value given at command line. */
+ const char *output_help; /**< @brief Output texte filename help description. */
+ double* point1_arg; /**< @brief First point (mm). */
+ char ** point1_orig; /**< @brief First point (mm) original value given at command line. */
+ int point1_min; /**< @brief First point (mm)'s minimum occurreces */
+ int point1_max; /**< @brief First point (mm)'s maximum occurreces */
+ const char *point1_help; /**< @brief First point (mm) help description. */
+ double* point2_arg; /**< @brief Second point (mm). */
+ char ** point2_orig; /**< @brief Second point (mm) original value given at command line. */
+ int point2_min; /**< @brief Second point (mm)'s minimum occurreces */
+ int point2_max; /**< @brief Second point (mm)'s maximum occurreces */
+ const char *point2_help; /**< @brief Second point (mm) help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int config_given ; /**< @brief Whether config was given. */
+ unsigned int verbose_given ; /**< @brief Whether verbose was given. */
+ unsigned int imagetypes_given ; /**< @brief Whether imagetypes was given. */
+ unsigned int input_given ; /**< @brief Whether input was given. */
+ unsigned int output_given ; /**< @brief Whether output was given. */
+ unsigned int point1_given ; /**< @brief Whether point1 was given. */
+ unsigned int point2_given ; /**< @brief Whether point2 was given. */
+
+ char **inputs ; /**< @brief unamed options (options without names) */
+ unsigned inputs_num ; /**< @brief unamed options number */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_clitkProfileImage_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure args_info_clitkProfileImage (default 1) */
+ int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+ int check_ambiguity; /**< @brief whether to check for options already specified in the option structure args_info_clitkProfileImage (default 0) */
+ int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *args_info_clitkProfileImage_purpose;
+/** @brief the usage string of the program */
+extern const char *args_info_clitkProfileImage_usage;
+/** @brief all the lines making the help output */
+extern const char *args_info_clitkProfileImage_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkProfileImage (int argc, char * const *argv,
+ struct args_info_clitkProfileImage *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkProfileImage_ext() instead
+ */
+int cmdline_parser_clitkProfileImage2 (int argc, char * const *argv,
+ struct args_info_clitkProfileImage *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkProfileImage_ext (int argc, char * const *argv,
+ struct args_info_clitkProfileImage *args_info,
+ struct cmdline_parser_clitkProfileImage_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkProfileImage_dump(FILE *outfile,
+ struct args_info_clitkProfileImage *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkProfileImage_file_save(const char *filename,
+ struct args_info_clitkProfileImage *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_clitkProfileImage_print_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_clitkProfileImage_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_clitkProfileImage_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_clitkProfileImage_params_init(struct cmdline_parser_clitkProfileImage_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_clitkProfileImage_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_clitkProfileImage_params structure
+ */
+struct cmdline_parser_clitkProfileImage_params *cmdline_parser_clitkProfileImage_params_create(void);
+
+/**
+ * Initializes the passed args_info_clitkProfileImage structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_clitkProfileImage_init (struct args_info_clitkProfileImage *args_info);
+/**
+ * Deallocates the string fields of the args_info_clitkProfileImage structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_clitkProfileImage_free (struct args_info_clitkProfileImage *args_info);
+
+/**
+ * The config file parser (deprecated version)
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkProfileImage_config_file() instead
+ */
+int cmdline_parser_clitkProfileImage_configfile (char * const filename,
+ struct args_info_clitkProfileImage *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The config file parser
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkProfileImage_config_file (char * const filename,
+ struct args_info_clitkProfileImage *args_info,
+ struct cmdline_parser_clitkProfileImage_params *params);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ * possible errors
+ * @return
+ */
+int cmdline_parser_clitkProfileImage_required (struct args_info_clitkProfileImage *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CLITKPROFILEIMAGE_GGO_H */
--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22
+ generated with the following command:
+ /usr/local/bin/gengetopt --output-dir=/home/tbaudier/vv/vv_static/vv/vv_bin/segmentation --arg-struct-name=args_info_clitkRegionGrowing --func-name=cmdline_parser_clitkRegionGrowing --file-name=clitkRegionGrowing_ggo --unamed-opts --conf-parser --include-getopt
+
+ The developers of gengetopt consider the fixed text that goes in all
+ gengetopt output files to be in the public domain:
+ we make no copyright claims on it.
+*/
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+
+#include "clitkRegionGrowing_ggo.h"
+
+const char *args_info_clitkRegionGrowing_purpose = "Region growing from a seed point using various types of conditions to control \nthe growing";
+
+const char *args_info_clitkRegionGrowing_usage = "Usage: clitkRegionGrowing [OPTIONS]... [FILES]...";
+
+const char *args_info_clitkRegionGrowing_description = "";
+
+const char *args_info_clitkRegionGrowing_help[] = {
+ " -h, --help Print help and exit",
+ " -V, --version Print version and exit",
+ " --config=STRING Config file",
+ " -v, --verbose Verbose (default=off)",
+ "\nI/O:",
+ " -i, --input=STRING Input image filename",
+ " -o, --output=STRING Output image filename",
+ "\nParameters:",
+ " -t, --type=INT Region growing filter type: 0=threshold , \n 1=neighborhood-threshold , 2=confidence , 3= \n locally-adaptive-threshold, 4= \n explosion-controlled-threshold (default=`0')",
+ " -l, --lower=DOUBLE 1,2,3,4: Lower threshold value (default=`310')",
+ " -u, --upper=DOUBLE 1,2,3,4: Upper threshold value (default=`4000')",
+ " --maxUpper=DOUBLE 4: Maximum upper threshold value (default=`2000')",
+ " --minLower=DOUBLE 4: Minimum lower threshold value (default=`-1000')",
+ " --step=DOUBLE 4: Threshold step size (default=`64.0')",
+ " --minStep=DOUBLE 4: Minimum threshold step size (default=`1')",
+ " --adaptLower 3,4: (locally) adapt lower thresholding \n (default=off)",
+ " --adaptUpper 3,4: (locally) adapt upper thresholding \n (default=off)",
+ " -m, --multiplier=DOUBLE 2-4: (2-3) accept if within mean+-mutiplier*SD, (4) \n explosion if size increases multiplier times \n (default=`2.0')",
+ " -s, --seed=INT Seed index postion (in voxels) (default=`0')",
+ " --seedRadius=INT Radius used for seed dilatation(in voxel) \n (default=`0')",
+ " -p, --pad=DOUBLE The replace padding value (default=`1.0')",
+ " -r, --radius=INT 1-3: The radius of the neighborhood (default=`1')",
+ " --maxSD=DOUBLE 3: Limit to SD",
+ " --full 4: use full connectivity (not implemented yet) \n (default=off)",
+ " --iter=INT 2: Iterations (default=`5')",
+ 0
+};
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_INT
+ , ARG_DOUBLE
+} cmdline_parser_clitkRegionGrowing_arg_type;
+
+static
+void clear_given (struct args_info_clitkRegionGrowing *args_info);
+static
+void clear_args (struct args_info_clitkRegionGrowing *args_info);
+
+static int
+cmdline_parser_clitkRegionGrowing_internal (int argc, char * const *argv, struct args_info_clitkRegionGrowing *args_info,
+ struct cmdline_parser_clitkRegionGrowing_params *params, const char *additional_error);
+
+static int
+cmdline_parser_clitkRegionGrowing_required2 (struct args_info_clitkRegionGrowing *args_info, const char *prog_name, const char *additional_error);
+struct line_list
+{
+ char * string_arg;
+ struct line_list * next;
+};
+
+static struct line_list *cmd_line_list = 0;
+static struct line_list *cmd_line_list_tmp = 0;
+
+static void
+free_cmd_list(void)
+{
+ /* free the list of a previous call */
+ if (cmd_line_list)
+ {
+ while (cmd_line_list) {
+ cmd_line_list_tmp = cmd_line_list;
+ cmd_line_list = cmd_line_list->next;
+ free (cmd_line_list_tmp->string_arg);
+ free (cmd_line_list_tmp);
+ }
+ }
+}
+
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct args_info_clitkRegionGrowing *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->config_given = 0 ;
+ args_info->verbose_given = 0 ;
+ args_info->input_given = 0 ;
+ args_info->output_given = 0 ;
+ args_info->type_given = 0 ;
+ args_info->lower_given = 0 ;
+ args_info->upper_given = 0 ;
+ args_info->maxUpper_given = 0 ;
+ args_info->minLower_given = 0 ;
+ args_info->step_given = 0 ;
+ args_info->minStep_given = 0 ;
+ args_info->adaptLower_given = 0 ;
+ args_info->adaptUpper_given = 0 ;
+ args_info->multiplier_given = 0 ;
+ args_info->seed_given = 0 ;
+ args_info->seedRadius_given = 0 ;
+ args_info->pad_given = 0 ;
+ args_info->radius_given = 0 ;
+ args_info->maxSD_given = 0 ;
+ args_info->full_given = 0 ;
+ args_info->iter_given = 0 ;
+}
+
+static
+void clear_args (struct args_info_clitkRegionGrowing *args_info)
+{
+ args_info->config_arg = NULL;
+ args_info->config_orig = NULL;
+ args_info->verbose_flag = 0;
+ args_info->input_arg = NULL;
+ args_info->input_orig = NULL;
+ args_info->output_arg = NULL;
+ args_info->output_orig = NULL;
+ args_info->type_arg = 0;
+ args_info->type_orig = NULL;
+ args_info->lower_arg = 310;
+ args_info->lower_orig = NULL;
+ args_info->upper_arg = 4000;
+ args_info->upper_orig = NULL;
+ args_info->maxUpper_arg = 2000;
+ args_info->maxUpper_orig = NULL;
+ args_info->minLower_arg = -1000;
+ args_info->minLower_orig = NULL;
+ args_info->step_arg = 64.0;
+ args_info->step_orig = NULL;
+ args_info->minStep_arg = 1;
+ args_info->minStep_orig = NULL;
+ args_info->adaptLower_flag = 0;
+ args_info->adaptUpper_flag = 0;
+ args_info->multiplier_arg = 2.0;
+ args_info->multiplier_orig = NULL;
+ args_info->seed_arg = NULL;
+ args_info->seed_orig = NULL;
+ args_info->seedRadius_arg = NULL;
+ args_info->seedRadius_orig = NULL;
+ args_info->pad_arg = 1.0;
+ args_info->pad_orig = NULL;
+ args_info->radius_arg = NULL;
+ args_info->radius_orig = NULL;
+ args_info->maxSD_orig = NULL;
+ args_info->full_flag = 0;
+ args_info->iter_arg = 5;
+ args_info->iter_orig = NULL;
+
+}
+
+static
+void init_args_info(struct args_info_clitkRegionGrowing *args_info)
+{
+
+
+ args_info->help_help = args_info_clitkRegionGrowing_help[0] ;
+ args_info->version_help = args_info_clitkRegionGrowing_help[1] ;
+ args_info->config_help = args_info_clitkRegionGrowing_help[2] ;
+ args_info->verbose_help = args_info_clitkRegionGrowing_help[3] ;
+ args_info->input_help = args_info_clitkRegionGrowing_help[5] ;
+ args_info->output_help = args_info_clitkRegionGrowing_help[6] ;
+ args_info->type_help = args_info_clitkRegionGrowing_help[8] ;
+ args_info->lower_help = args_info_clitkRegionGrowing_help[9] ;
+ args_info->upper_help = args_info_clitkRegionGrowing_help[10] ;
+ args_info->maxUpper_help = args_info_clitkRegionGrowing_help[11] ;
+ args_info->minLower_help = args_info_clitkRegionGrowing_help[12] ;
+ args_info->step_help = args_info_clitkRegionGrowing_help[13] ;
+ args_info->minStep_help = args_info_clitkRegionGrowing_help[14] ;
+ args_info->adaptLower_help = args_info_clitkRegionGrowing_help[15] ;
+ args_info->adaptUpper_help = args_info_clitkRegionGrowing_help[16] ;
+ args_info->multiplier_help = args_info_clitkRegionGrowing_help[17] ;
+ args_info->seed_help = args_info_clitkRegionGrowing_help[18] ;
+ args_info->seed_min = -1;
+ args_info->seed_max = -1;
+ args_info->seedRadius_help = args_info_clitkRegionGrowing_help[19] ;
+ args_info->seedRadius_min = -1;
+ args_info->seedRadius_max = -1;
+ args_info->pad_help = args_info_clitkRegionGrowing_help[20] ;
+ args_info->radius_help = args_info_clitkRegionGrowing_help[21] ;
+ args_info->radius_min = -1;
+ args_info->radius_max = -1;
+ args_info->maxSD_help = args_info_clitkRegionGrowing_help[22] ;
+ args_info->full_help = args_info_clitkRegionGrowing_help[23] ;
+ args_info->iter_help = args_info_clitkRegionGrowing_help[24] ;
+
+}
+
+void
+cmdline_parser_clitkRegionGrowing_print_version (void)
+{
+ printf ("%s %s\n", CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE, CMDLINE_PARSER_CLITKREGIONGROWING_VERSION);
+}
+
+static void print_help_common(void) {
+ cmdline_parser_clitkRegionGrowing_print_version ();
+
+ if (strlen(args_info_clitkRegionGrowing_purpose) > 0)
+ printf("\n%s\n", args_info_clitkRegionGrowing_purpose);
+
+ if (strlen(args_info_clitkRegionGrowing_usage) > 0)
+ printf("\n%s\n", args_info_clitkRegionGrowing_usage);
+
+ printf("\n");
+
+ if (strlen(args_info_clitkRegionGrowing_description) > 0)
+ printf("%s\n", args_info_clitkRegionGrowing_description);
+}
+
+void
+cmdline_parser_clitkRegionGrowing_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (args_info_clitkRegionGrowing_help[i])
+ printf("%s\n", args_info_clitkRegionGrowing_help[i++]);
+}
+
+void
+cmdline_parser_clitkRegionGrowing_init (struct args_info_clitkRegionGrowing *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+
+ args_info->inputs = NULL;
+ args_info->inputs_num = 0;
+}
+
+void
+cmdline_parser_clitkRegionGrowing_params_init(struct cmdline_parser_clitkRegionGrowing_params *params)
+{
+ if (params)
+ {
+ params->override = 0;
+ params->initialize = 1;
+ params->check_required = 1;
+ params->check_ambiguity = 0;
+ params->print_errors = 1;
+ }
+}
+
+struct cmdline_parser_clitkRegionGrowing_params *
+cmdline_parser_clitkRegionGrowing_params_create(void)
+{
+ struct cmdline_parser_clitkRegionGrowing_params *params =
+ (struct cmdline_parser_clitkRegionGrowing_params *)malloc(sizeof(struct cmdline_parser_clitkRegionGrowing_params));
+ cmdline_parser_clitkRegionGrowing_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+/** @brief generic value variable */
+union generic_value {
+ int int_arg;
+ double double_arg;
+ char *string_arg;
+};
+
+/** @brief holds temporary values for multiple options */
+struct generic_list
+{
+ union generic_value arg;
+ char *orig;
+ struct generic_list *next;
+};
+
+/**
+ * @brief add a node at the head of the list
+ */
+static void add_node(struct generic_list **list) {
+ struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list));
+ new_node->next = *list;
+ *list = new_node;
+ new_node->arg.string_arg = NULL;
+ new_node->orig = NULL;
+}
+
+static void
+free_multiple_field(unsigned int len, void **arg, char ***orig)
+{
+ unsigned int i;
+ if (*arg) {
+ for (i = 0; i < len; ++i)
+ {
+ free_string_field(&((*orig)[i]));
+ }
+
+ free (*arg);
+ *arg = 0;
+ free (*orig);
+ *orig = 0;
+ }
+}
+
+
+static void
+cmdline_parser_clitkRegionGrowing_release (struct args_info_clitkRegionGrowing *args_info)
+{
+ unsigned int i;
+ free_string_field (&(args_info->config_arg));
+ free_string_field (&(args_info->config_orig));
+ free_string_field (&(args_info->input_arg));
+ free_string_field (&(args_info->input_orig));
+ free_string_field (&(args_info->output_arg));
+ free_string_field (&(args_info->output_orig));
+ free_string_field (&(args_info->type_orig));
+ free_string_field (&(args_info->lower_orig));
+ free_string_field (&(args_info->upper_orig));
+ free_string_field (&(args_info->maxUpper_orig));
+ free_string_field (&(args_info->minLower_orig));
+ free_string_field (&(args_info->step_orig));
+ free_string_field (&(args_info->minStep_orig));
+ free_string_field (&(args_info->multiplier_orig));
+ free_multiple_field (args_info->seed_given, (void **)&(args_info->seed_arg), &(args_info->seed_orig));
+ free_multiple_field (args_info->seedRadius_given, (void **)&(args_info->seedRadius_arg), &(args_info->seedRadius_orig));
+ free_string_field (&(args_info->pad_orig));
+ free_multiple_field (args_info->radius_given, (void **)&(args_info->radius_arg), &(args_info->radius_orig));
+ free_string_field (&(args_info->maxSD_orig));
+ free_string_field (&(args_info->iter_orig));
+
+
+ for (i = 0; i < args_info->inputs_num; ++i)
+ free (args_info->inputs [i]);
+
+ if (args_info->inputs_num)
+ free (args_info->inputs);
+
+ clear_given (args_info);
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+ if (arg) {
+ fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+ } else {
+ fprintf(outfile, "%s\n", opt);
+ }
+}
+
+static void
+write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, char *values[])
+{
+ int i;
+
+ for (i = 0; i < len; ++i)
+ write_into_file(outfile, opt, (arg ? arg[i] : 0), values);
+}
+
+int
+cmdline_parser_clitkRegionGrowing_dump(FILE *outfile, struct args_info_clitkRegionGrowing *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE);
+ return EXIT_FAILURE;
+ }
+
+ if (args_info->help_given)
+ write_into_file(outfile, "help", 0, 0 );
+ if (args_info->version_given)
+ write_into_file(outfile, "version", 0, 0 );
+ if (args_info->config_given)
+ write_into_file(outfile, "config", args_info->config_orig, 0);
+ if (args_info->verbose_given)
+ write_into_file(outfile, "verbose", 0, 0 );
+ if (args_info->input_given)
+ write_into_file(outfile, "input", args_info->input_orig, 0);
+ if (args_info->output_given)
+ write_into_file(outfile, "output", args_info->output_orig, 0);
+ if (args_info->type_given)
+ write_into_file(outfile, "type", args_info->type_orig, 0);
+ if (args_info->lower_given)
+ write_into_file(outfile, "lower", args_info->lower_orig, 0);
+ if (args_info->upper_given)
+ write_into_file(outfile, "upper", args_info->upper_orig, 0);
+ if (args_info->maxUpper_given)
+ write_into_file(outfile, "maxUpper", args_info->maxUpper_orig, 0);
+ if (args_info->minLower_given)
+ write_into_file(outfile, "minLower", args_info->minLower_orig, 0);
+ if (args_info->step_given)
+ write_into_file(outfile, "step", args_info->step_orig, 0);
+ if (args_info->minStep_given)
+ write_into_file(outfile, "minStep", args_info->minStep_orig, 0);
+ if (args_info->adaptLower_given)
+ write_into_file(outfile, "adaptLower", 0, 0 );
+ if (args_info->adaptUpper_given)
+ write_into_file(outfile, "adaptUpper", 0, 0 );
+ if (args_info->multiplier_given)
+ write_into_file(outfile, "multiplier", args_info->multiplier_orig, 0);
+ write_multiple_into_file(outfile, args_info->seed_given, "seed", args_info->seed_orig, 0);
+ write_multiple_into_file(outfile, args_info->seedRadius_given, "seedRadius", args_info->seedRadius_orig, 0);
+ if (args_info->pad_given)
+ write_into_file(outfile, "pad", args_info->pad_orig, 0);
+ write_multiple_into_file(outfile, args_info->radius_given, "radius", args_info->radius_orig, 0);
+ if (args_info->maxSD_given)
+ write_into_file(outfile, "maxSD", args_info->maxSD_orig, 0);
+ if (args_info->full_given)
+ write_into_file(outfile, "full", 0, 0 );
+ if (args_info->iter_given)
+ write_into_file(outfile, "iter", args_info->iter_orig, 0);
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+cmdline_parser_clitkRegionGrowing_file_save(const char *filename, struct args_info_clitkRegionGrowing *args_info)
+{
+ FILE *outfile;
+ int i = 0;
+
+ outfile = fopen(filename, "w");
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = cmdline_parser_clitkRegionGrowing_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+cmdline_parser_clitkRegionGrowing_free (struct args_info_clitkRegionGrowing *args_info)
+{
+ cmdline_parser_clitkRegionGrowing_release (args_info);
+}
+
+/** @brief replacement of strdup, which is not standard */
+char *
+gengetopt_strdup (const char *s)
+{
+ char *result = NULL;
+ if (!s)
+ return result;
+
+ result = (char*)malloc(strlen(s) + 1);
+ if (result == (char*)0)
+ return (char*)0;
+ strcpy(result, s);
+ return result;
+}
+
+static char *
+get_multiple_arg_token(const char *arg)
+{
+ char *tok, *ret;
+ size_t len, num_of_escape, i, j;
+
+ if (!arg)
+ return NULL;
+
+ tok = strchr (arg, ',');
+ num_of_escape = 0;
+
+ /* make sure it is not escaped */
+ while (tok)
+ {
+ if (*(tok-1) == '\\')
+ {
+ /* find the next one */
+ tok = strchr (tok+1, ',');
+ ++num_of_escape;
+ }
+ else
+ break;
+ }
+
+ if (tok)
+ len = (size_t)(tok - arg + 1);
+ else
+ len = strlen (arg) + 1;
+
+ len -= num_of_escape;
+
+ ret = (char *) malloc (len);
+
+ i = 0;
+ j = 0;
+ while (arg[i] && (j < len-1))
+ {
+ if (arg[i] == '\\' &&
+ arg[ i + 1 ] &&
+ arg[ i + 1 ] == ',')
+ ++i;
+
+ ret[j++] = arg[i++];
+ }
+
+ ret[len-1] = '\0';
+
+ return ret;
+}
+
+static char *
+get_multiple_arg_token_next(const char *arg)
+{
+ char *tok;
+
+ if (!arg)
+ return NULL;
+
+ tok = strchr (arg, ',');
+
+ /* make sure it is not escaped */
+ while (tok)
+ {
+ if (*(tok-1) == '\\')
+ {
+ /* find the next one */
+ tok = strchr (tok+1, ',');
+ }
+ else
+ break;
+ }
+
+ if (! tok || strlen(tok) == 1)
+ return 0;
+
+ return tok+1;
+}
+
+static int
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc);
+
+int
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc)
+{
+ int error = 0;
+
+ if (option_given && ! (min < 0 && max < 0))
+ {
+ if (min >= 0 && max >= 0)
+ {
+ if (min == max)
+ {
+ /* specific occurrences */
+ if (option_given != min)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be %d\n",
+ prog_name, option_desc, min);
+ error = 1;
+ }
+ }
+ else if (option_given < min
+ || option_given > max)
+ {
+ /* range occurrences */
+ fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n",
+ prog_name, option_desc, min, max);
+ error = 1;
+ }
+ }
+ else if (min >= 0)
+ {
+ /* at least check */
+ if (option_given < min)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be at least %d\n",
+ prog_name, option_desc, min);
+ error = 1;
+ }
+ }
+ else if (max >= 0)
+ {
+ /* at most check */
+ if (option_given > max)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be at most %d\n",
+ prog_name, option_desc, max);
+ error = 1;
+ }
+ }
+ }
+
+ return error;
+}
+int
+cmdline_parser_clitkRegionGrowing (int argc, char * const *argv, struct args_info_clitkRegionGrowing *args_info)
+{
+ return cmdline_parser_clitkRegionGrowing2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+cmdline_parser_clitkRegionGrowing_ext (int argc, char * const *argv, struct args_info_clitkRegionGrowing *args_info,
+ struct cmdline_parser_clitkRegionGrowing_params *params)
+{
+ int result;
+ result = cmdline_parser_clitkRegionGrowing_internal (argc, argv, args_info, params, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkRegionGrowing_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkRegionGrowing2 (int argc, char * const *argv, struct args_info_clitkRegionGrowing *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct cmdline_parser_clitkRegionGrowing_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = cmdline_parser_clitkRegionGrowing_internal (argc, argv, args_info, ¶ms, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkRegionGrowing_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkRegionGrowing_required (struct args_info_clitkRegionGrowing *args_info, const char *prog_name)
+{
+ int result = EXIT_SUCCESS;
+
+ if (cmdline_parser_clitkRegionGrowing_required2(args_info, prog_name, NULL) > 0)
+ result = EXIT_FAILURE;
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkRegionGrowing_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkRegionGrowing_required2 (struct args_info_clitkRegionGrowing *args_info, const char *prog_name, const char *additional_error)
+{
+ int error = 0;
+
+ /* checks for required options */
+ if (! args_info->input_given)
+ {
+ fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (! args_info->output_given)
+ {
+ fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (check_multiple_option_occurrences(prog_name, args_info->seed_given, args_info->seed_min, args_info->seed_max, "'--seed' ('-s')"))
+ error = 1;
+
+ if (check_multiple_option_occurrences(prog_name, args_info->seedRadius_given, args_info->seedRadius_min, args_info->seedRadius_max, "'--seedRadius'"))
+ error = 1;
+
+ if (check_multiple_option_occurrences(prog_name, args_info->radius_given, args_info->radius_min, args_info->radius_max, "'--radius' ('-r')"))
+ error = 1;
+
+
+ /* checks for dependences among options */
+
+ return error;
+}
+
+/*
+ * Extracted from the glibc source tree, version 2.3.6
+ *
+ * Licensed under the GPL as per the whole glibc source tree.
+ *
+ * This file was modified so that getopt_long can be called
+ * many times without risking previous memory to be spoiled.
+ *
+ * Modified by Andre Noll and Lorenzo Bettini for use in
+ * GNU gengetopt generated files.
+ *
+ */
+
+/*
+ * we must include anything we need since this file is not thought to be
+ * inserted in a file already using getopt.h
+ *
+ * Lorenzo
+ */
+
+struct option
+{
+ const char *name;
+ /* has_arg can't be an enum because some compilers complain about
+ type mismatches in all the code that assumes it is an int. */
+ int has_arg;
+ int *flag;
+ int val;
+};
+
+/* For communication from `getopt' to the caller.
+ When `getopt' finds an option that takes an argument,
+ the argument value is returned here.
+ Also, when `ordering' is RETURN_IN_ORDER,
+ each non-option ARGV-element is returned here. */
+
+static char *optarg;
+
+/* Index in ARGV of the next element to be scanned.
+ This is used for communication to and from the caller
+ and for communication between successive calls to `getopt'.
+
+ On entry to `getopt', zero means this is the first call; initialize.
+
+ When `getopt' returns -1, this is the index of the first of the
+ non-option elements that the caller should itself scan.
+
+ Otherwise, `optind' communicates from one call to the next
+ how much of ARGV has been scanned so far. */
+
+static int optind;
+
+/* Callers store zero here to inhibit the error message `getopt' prints
+ for unrecognized options. */
+
+static int opterr;
+
+/* Set to an option character which was unrecognized. */
+
+static int optopt;
+
+/* This version of `getopt' appears to the caller like standard Unix `getopt'
+ but it behaves differently for the user, since it allows the user
+ to intersperse the options with the other arguments.
+
+ As `getopt' works, it permutes the elements of ARGV so that,
+ when it is done, all the options precede everything else. Thus
+ all application programs are extended to handle flexible argument order.
+*/
+/*
+ If the field `flag' is not NULL, it points to a variable that is set
+ to the value given in the field `val' when the option is found, but
+ left unchanged if the option is not found.
+
+ To have a long-named option do something other than set an `int' to
+ a compiled-in constant, such as set a value from `custom_optarg', set the
+ option's `flag' field to zero and its `val' field to a nonzero
+ value (the equivalent single-letter option character, if there is
+ one). For long options that have a zero `flag' field, `getopt'
+ returns the contents of the `val' field. */
+
+/* Names for the values of the `has_arg' field of `struct option'. */
+#ifndef no_argument
+#define no_argument 0
+#endif
+
+#ifndef required_argument
+#define required_argument 1
+#endif
+
+#ifndef optional_argument
+#define optional_argument 2
+#endif
+
+struct custom_getopt_data {
+ /*
+ * These have exactly the same meaning as the corresponding global variables,
+ * except that they are used for the reentrant versions of getopt.
+ */
+ int custom_optind;
+ int custom_opterr;
+ int custom_optopt;
+ char *custom_optarg;
+
+ /* True if the internal members have been initialized. */
+ int initialized;
+
+ /*
+ * The next char to be scanned in the option-element in which the last option
+ * character we returned was found. This allows us to pick up the scan where
+ * we left off. If this is zero, or a null string, it means resume the scan by
+ * advancing to the next ARGV-element.
+ */
+ char *nextchar;
+
+ /*
+ * Describe the part of ARGV that contains non-options that have been skipped.
+ * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is
+ * the index after the last of them.
+ */
+ int first_nonopt;
+ int last_nonopt;
+};
+
+/*
+ * the variables optarg, optind, opterr and optopt are renamed with
+ * the custom_ prefix so that they don't interfere with getopt ones.
+ *
+ * Moreover they're static so they are visible only from within the
+ * file where this very file will be included.
+ */
+
+/*
+ * For communication from `custom_getopt' to the caller. When `custom_getopt' finds an
+ * option that takes an argument, the argument value is returned here.
+ */
+static char *custom_optarg;
+
+/*
+ * Index in ARGV of the next element to be scanned. This is used for
+ * communication to and from the caller and for communication between
+ * successive calls to `custom_getopt'.
+ *
+ * On entry to `custom_getopt', 1 means this is the first call; initialize.
+ *
+ * When `custom_getopt' returns -1, this is the index of the first of the non-option
+ * elements that the caller should itself scan.
+ *
+ * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV
+ * has been scanned so far.
+ *
+ * 1003.2 says this must be 1 before any call.
+ */
+static int custom_optind = 1;
+
+/*
+ * Callers store zero here to inhibit the error message for unrecognized
+ * options.
+ */
+static int custom_opterr = 1;
+
+/*
+ * Set to an option character which was unrecognized. This must be initialized
+ * on some systems to avoid linking in the system's own getopt implementation.
+ */
+static int custom_optopt = '?';
+
+/*
+ * Exchange two adjacent subsequences of ARGV. One subsequence is elements
+ * [first_nonopt,last_nonopt) which contains all the non-options that have been
+ * skipped so far. The other is elements [last_nonopt,custom_optind), which contains
+ * all the options processed since those non-options were skipped.
+ * `first_nonopt' and `last_nonopt' are relocated so that they describe the new
+ * indices of the non-options in ARGV after they are moved.
+ */
+static void exchange(char **argv, struct custom_getopt_data *d)
+{
+ int bottom = d->first_nonopt;
+ int middle = d->last_nonopt;
+ int top = d->custom_optind;
+ char *tem;
+
+ /*
+ * Exchange the shorter segment with the far end of the longer segment.
+ * That puts the shorter segment into the right place. It leaves the
+ * longer segment in the right place overall, but it consists of two
+ * parts that need to be swapped next.
+ */
+ while (top > middle && middle > bottom) {
+ if (top - middle > middle - bottom) {
+ /* Bottom segment is the short one. */
+ int len = middle - bottom;
+ int i;
+
+ /* Swap it with the top part of the top segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] =
+ argv[top - (middle - bottom) + i];
+ argv[top - (middle - bottom) + i] = tem;
+ }
+ /* Exclude the moved bottom segment from further swapping. */
+ top -= len;
+ } else {
+ /* Top segment is the short one. */
+ int len = top - middle;
+ int i;
+
+ /* Swap it with the bottom part of the bottom segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] = argv[middle + i];
+ argv[middle + i] = tem;
+ }
+ /* Exclude the moved top segment from further swapping. */
+ bottom += len;
+ }
+ }
+ /* Update records for the slots the non-options now occupy. */
+ d->first_nonopt += (d->custom_optind - d->last_nonopt);
+ d->last_nonopt = d->custom_optind;
+}
+
+/* Initialize the internal data when the first call is made. */
+static void custom_getopt_initialize(struct custom_getopt_data *d)
+{
+ /*
+ * Start processing options with ARGV-element 1 (since ARGV-element 0
+ * is the program name); the sequence of previously skipped non-option
+ * ARGV-elements is empty.
+ */
+ d->first_nonopt = d->last_nonopt = d->custom_optind;
+ d->nextchar = NULL;
+ d->initialized = 1;
+}
+
+#define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0')
+
+/* return: zero: continue, nonzero: return given value to user */
+static int shuffle_argv(int argc, char *const *argv,const struct option *longopts,
+ struct custom_getopt_data *d)
+{
+ /*
+ * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been
+ * moved back by the user (who may also have changed the arguments).
+ */
+ if (d->last_nonopt > d->custom_optind)
+ d->last_nonopt = d->custom_optind;
+ if (d->first_nonopt > d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * If we have just processed some options following some
+ * non-options, exchange them so that the options come first.
+ */
+ if (d->first_nonopt != d->last_nonopt &&
+ d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->last_nonopt != d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * Skip any additional non-options and extend the range of
+ * non-options previously skipped.
+ */
+ while (d->custom_optind < argc && NONOPTION_P)
+ d->custom_optind++;
+ d->last_nonopt = d->custom_optind;
+ /*
+ * The special ARGV-element `--' means premature end of options. Skip
+ * it like a null option, then exchange with previous non-options as if
+ * it were an option, then skip everything else like a non-option.
+ */
+ if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) {
+ d->custom_optind++;
+ if (d->first_nonopt != d->last_nonopt
+ && d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->first_nonopt == d->last_nonopt)
+ d->first_nonopt = d->custom_optind;
+ d->last_nonopt = argc;
+ d->custom_optind = argc;
+ }
+ /*
+ * If we have done all the ARGV-elements, stop the scan and back over
+ * any non-options that we skipped and permuted.
+ */
+ if (d->custom_optind == argc) {
+ /*
+ * Set the next-arg-index to point at the non-options that we
+ * previously skipped, so the caller will digest them.
+ */
+ if (d->first_nonopt != d->last_nonopt)
+ d->custom_optind = d->first_nonopt;
+ return -1;
+ }
+ /*
+ * If we have come to a non-option and did not permute it, either stop
+ * the scan or describe it to the caller and pass it by.
+ */
+ if (NONOPTION_P) {
+ d->custom_optarg = argv[d->custom_optind++];
+ return 1;
+ }
+ /*
+ * We have found another option-ARGV-element. Skip the initial
+ * punctuation.
+ */
+ d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-'));
+ return 0;
+}
+
+/*
+ * Check whether the ARGV-element is a long option.
+ *
+ * If there's a long option "fubar" and the ARGV-element is "-fu", consider
+ * that an abbreviation of the long option, just like "--fu", and not "-f" with
+ * arg "u".
+ *
+ * This distinction seems to be the most useful approach.
+ *
+ */
+static int check_long_opt(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char *nameend;
+ const struct option *p;
+ const struct option *pfound = NULL;
+ int exact = 0;
+ int ambig = 0;
+ int indfound = -1;
+ int option_index;
+
+ for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++)
+ /* Do nothing. */ ;
+
+ /* Test all long options for either exact match or abbreviated matches */
+ for (p = longopts, option_index = 0; p->name; p++, option_index++)
+ if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) {
+ if ((unsigned int) (nameend - d->nextchar)
+ == (unsigned int) strlen(p->name)) {
+ /* Exact match found. */
+ pfound = p;
+ indfound = option_index;
+ exact = 1;
+ break;
+ } else if (pfound == NULL) {
+ /* First nonexact match found. */
+ pfound = p;
+ indfound = option_index;
+ } else if (pfound->has_arg != p->has_arg
+ || pfound->flag != p->flag
+ || pfound->val != p->val)
+ /* Second or later nonexact match found. */
+ ambig = 1;
+ }
+ if (ambig && !exact) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' is ambiguous\n",
+ argv[0], argv[d->custom_optind]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+ }
+ if (pfound) {
+ option_index = indfound;
+ d->custom_optind++;
+ if (*nameend) {
+ if (pfound->has_arg != no_argument)
+ d->custom_optarg = nameend + 1;
+ else {
+ if (print_errors) {
+ if (argv[d->custom_optind - 1][1] == '-') {
+ /* --option */
+ fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n",
+ argv[0], pfound->name);
+ } else {
+ /* +option or -option */
+ fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n",
+ argv[0], argv[d->custom_optind - 1][0], pfound->name);
+ }
+
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return '?';
+ }
+ } else if (pfound->has_arg == required_argument) {
+ if (d->custom_optind < argc)
+ d->custom_optarg = argv[d->custom_optind++];
+ else {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' requires an argument\n",
+ argv[0],
+ argv[d->custom_optind - 1]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return optstring[0] == ':' ? ':' : '?';
+ }
+ }
+ d->nextchar += strlen(d->nextchar);
+ if (longind != NULL)
+ *longind = option_index;
+ if (pfound->flag) {
+ *(pfound->flag) = pfound->val;
+ return 0;
+ }
+ return pfound->val;
+ }
+ /*
+ * Can't find it as a long option. If this is not getopt_long_only, or
+ * the option starts with '--' or is not a valid short option, then
+ * it's an error. Otherwise interpret it as a short option.
+ */
+ if (print_errors) {
+ if (argv[d->custom_optind][1] == '-') {
+ /* --option */
+ fprintf(stderr,
+ "%s: unrecognized option `--%s'\n",
+ argv[0], d->nextchar);
+ } else {
+ /* +option or -option */
+ fprintf(stderr,
+ "%s: unrecognized option `%c%s'\n",
+ argv[0], argv[d->custom_optind][0],
+ d->nextchar);
+ }
+ }
+ d->nextchar = (char *) "";
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+}
+
+static int check_short_opt(int argc, char *const *argv, const char *optstring,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char c = *d->nextchar++;
+ char *temp = strchr(optstring, c);
+
+ /* Increment `custom_optind' when we start to process its last character. */
+ if (*d->nextchar == '\0')
+ ++d->custom_optind;
+ if (!temp || c == ':') {
+ if (print_errors)
+ fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
+
+ d->custom_optopt = c;
+ return '?';
+ }
+ if (temp[1] == ':') {
+ if (temp[2] == ':') {
+ /* This is an option that accepts an argument optionally. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ d->custom_optind++;
+ } else
+ d->custom_optarg = NULL;
+ d->nextchar = NULL;
+ } else {
+ /* This is an option that requires an argument. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ /*
+ * If we end this ARGV-element by taking the
+ * rest as an arg, we must advance to the next
+ * element now.
+ */
+ d->custom_optind++;
+ } else if (d->custom_optind == argc) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option requires an argument -- %c\n",
+ argv[0], c);
+ }
+ d->custom_optopt = c;
+ if (optstring[0] == ':')
+ c = ':';
+ else
+ c = '?';
+ } else
+ /*
+ * We already incremented `custom_optind' once;
+ * increment it again when taking next ARGV-elt
+ * as argument.
+ */
+ d->custom_optarg = argv[d->custom_optind++];
+ d->nextchar = NULL;
+ }
+ }
+ return c;
+}
+
+/*
+ * Scan elements of ARGV for option characters given in OPTSTRING.
+ *
+ * If an element of ARGV starts with '-', and is not exactly "-" or "--",
+ * then it is an option element. The characters of this element
+ * (aside from the initial '-') are option characters. If `getopt'
+ * is called repeatedly, it returns successively each of the option characters
+ * from each of the option elements.
+ *
+ * If `getopt' finds another option character, it returns that character,
+ * updating `custom_optind' and `nextchar' so that the next call to `getopt' can
+ * resume the scan with the following option character or ARGV-element.
+ *
+ * If there are no more option characters, `getopt' returns -1.
+ * Then `custom_optind' is the index in ARGV of the first ARGV-element
+ * that is not an option. (The ARGV-elements have been permuted
+ * so that those that are not options now come last.)
+ *
+ * OPTSTRING is a string containing the legitimate option characters.
+ * If an option character is seen that is not listed in OPTSTRING,
+ * return '?' after printing an error message. If you set `custom_opterr' to
+ * zero, the error message is suppressed but we still return '?'.
+ *
+ * If a char in OPTSTRING is followed by a colon, that means it wants an arg,
+ * so the following text in the same ARGV-element, or the text of the following
+ * ARGV-element, is returned in `custom_optarg'. Two colons mean an option that
+ * wants an optional arg; if there is text in the current ARGV-element,
+ * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero.
+ *
+ * If OPTSTRING starts with `-' or `+', it requests different methods of
+ * handling the non-option ARGV-elements.
+ * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
+ *
+ * Long-named options begin with `--' instead of `-'.
+ * Their names may be abbreviated as long as the abbreviation is unique
+ * or is an exact match for some defined option. If they have an
+ * argument, it follows the option name in the same ARGV-element, separated
+ * from the option name by a `=', or else the in next ARGV-element.
+ * When `getopt' finds a long-named option, it returns 0 if that option's
+ * `flag' field is nonzero, the value of the option's `val' field
+ * if the `flag' field is zero.
+ *
+ * The elements of ARGV aren't really const, because we permute them.
+ * But we pretend they're const in the prototype to be compatible
+ * with other systems.
+ *
+ * LONGOPTS is a vector of `struct option' terminated by an
+ * element containing a name which is zero.
+ *
+ * LONGIND returns the index in LONGOPT of the long-named option found.
+ * It is only valid when a long-named option has been found by the most
+ * recent call.
+ *
+ * Return the option character from OPTS just read. Return -1 when there are
+ * no more options. For unrecognized options, or options missing arguments,
+ * `custom_optopt' is set to the option letter, and '?' is returned.
+ *
+ * The OPTS string is a list of characters which are recognized option letters,
+ * optionally followed by colons, specifying that that letter takes an
+ * argument, to be placed in `custom_optarg'.
+ *
+ * If a letter in OPTS is followed by two colons, its argument is optional.
+ * This behavior is specific to the GNU `getopt'.
+ *
+ * The argument `--' causes premature termination of argument scanning,
+ * explicitly telling `getopt' that there are no more options. If OPTS begins
+ * with `--', then non-option arguments are treated as arguments to the option
+ * '\0'. This behavior is specific to the GNU `getopt'.
+ */
+
+static int getopt_internal_r(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ struct custom_getopt_data *d)
+{
+ int ret, print_errors = d->custom_opterr;
+
+ if (optstring[0] == ':')
+ print_errors = 0;
+ if (argc < 1)
+ return -1;
+ d->custom_optarg = NULL;
+
+ /*
+ * This is a big difference with GNU getopt, since optind == 0
+ * means initialization while here 1 means first call.
+ */
+ if (d->custom_optind == 0 || !d->initialized) {
+ if (d->custom_optind == 0)
+ d->custom_optind = 1; /* Don't scan ARGV[0], the program name. */
+ custom_getopt_initialize(d);
+ }
+ if (d->nextchar == NULL || *d->nextchar == '\0') {
+ ret = shuffle_argv(argc, argv, longopts, d);
+ if (ret)
+ return ret;
+ }
+ if (longopts && (argv[d->custom_optind][1] == '-' ))
+ return check_long_opt(argc, argv, optstring, longopts,
+ longind, print_errors, d);
+ return check_short_opt(argc, argv, optstring, print_errors, d);
+}
+
+static int custom_getopt_internal(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind)
+{
+ int result;
+ /* Keep a global copy of all internal members of d */
+ static struct custom_getopt_data d;
+
+ d.custom_optind = custom_optind;
+ d.custom_opterr = custom_opterr;
+ result = getopt_internal_r(argc, argv, optstring, longopts,
+ longind, &d);
+ custom_optind = d.custom_optind;
+ custom_optarg = d.custom_optarg;
+ custom_optopt = d.custom_optopt;
+ return result;
+}
+
+static int custom_getopt_long (int argc, char *const *argv, const char *options,
+ const struct option *long_options, int *opt_index)
+{
+ return custom_getopt_internal(argc, argv, options, long_options,
+ opt_index);
+}
+
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_clitkRegionGrowing_params.check_ambiguity
+ * @param override @see cmdline_parser_clitkRegionGrowing_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+static
+int update_arg(void *field, char **orig_field,
+ unsigned int *field_given, unsigned int *prev_given,
+ char *value, char *possible_values[], const char *default_value,
+ cmdline_parser_clitkRegionGrowing_arg_type arg_type,
+ int check_ambiguity, int override,
+ int no_free, int multiple_option,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *stop_char = 0;
+ const char *val = value;
+ int found;
+ char **string_field;
+
+ stop_char = 0;
+ found = 0;
+
+ if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+ {
+ if (short_opt != '-')
+ fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
+ package_name, long_opt, short_opt,
+ (additional_error ? additional_error : ""));
+ else
+ fprintf (stderr, "%s: `--%s' option given more than once%s\n",
+ package_name, long_opt,
+ (additional_error ? additional_error : ""));
+ return 1; /* failure */
+ }
+
+
+ if (field_given && *field_given && ! override)
+ return 0;
+ if (prev_given)
+ (*prev_given)++;
+ if (field_given)
+ (*field_given)++;
+ if (possible_values)
+ val = possible_values[found];
+
+ switch(arg_type) {
+ case ARG_FLAG:
+ *((int *)field) = !*((int *)field);
+ break;
+ case ARG_INT:
+ if (val) *((int *)field) = strtol (val, &stop_char, 0);
+ break;
+ case ARG_DOUBLE:
+ if (val) *((double *)field) = strtod (val, &stop_char);
+ break;
+ case ARG_STRING:
+ if (val) {
+ string_field = (char **)field;
+ if (!no_free && *string_field)
+ free (*string_field); /* free previous string */
+ *string_field = gengetopt_strdup (val);
+ }
+ break;
+ default:
+ break;
+ };
+
+ /* check numeric conversion */
+ switch(arg_type) {
+ case ARG_INT:
+ case ARG_DOUBLE:
+ if (val && !(stop_char && *stop_char == '\0')) {
+ fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+ return 1; /* failure */
+ }
+ break;
+ default:
+ ;
+ };
+
+ /* store the original value */
+ switch(arg_type) {
+ case ARG_NO:
+ case ARG_FLAG:
+ break;
+ default:
+ if (value && orig_field) {
+ if (no_free) {
+ *orig_field = value;
+ } else {
+ if (*orig_field)
+ free (*orig_field); /* free previous string */
+ *orig_field = gengetopt_strdup (value);
+ }
+ }
+ };
+
+ return 0; /* OK */
+}
+
+/**
+ * @brief store information about a multiple option in a temporary list
+ * @param list where to (temporarily) store multiple options
+ */
+static
+int update_multiple_arg_temp(struct generic_list **list,
+ unsigned int *prev_given, const char *val,
+ char *possible_values[], const char *default_value,
+ cmdline_parser_clitkRegionGrowing_arg_type arg_type,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *multi_token, *multi_next; /* store single arguments */
+
+ if (arg_type == ARG_NO) {
+ (*prev_given)++;
+ return 0; /* OK */
+ }
+
+ multi_token = get_multiple_arg_token(val);
+ multi_next = get_multiple_arg_token_next (val);
+
+ while (1)
+ {
+ add_node (list);
+ if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0,
+ prev_given, multi_token, possible_values, default_value,
+ arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) {
+ if (multi_token) free(multi_token);
+ return 1; /* failure */
+ }
+
+ if (multi_next)
+ {
+ multi_token = get_multiple_arg_token(multi_next);
+ multi_next = get_multiple_arg_token_next (multi_next);
+ }
+ else
+ break;
+ }
+
+ return 0; /* OK */
+}
+
+/**
+ * @brief free the passed list (including possible string argument)
+ */
+static
+void free_list(struct generic_list *list, short string_arg)
+{
+ if (list) {
+ struct generic_list *tmp;
+ while (list)
+ {
+ tmp = list;
+ if (string_arg && list->arg.string_arg)
+ free (list->arg.string_arg);
+ if (list->orig)
+ free (list->orig);
+ list = list->next;
+ free (tmp);
+ }
+ }
+}
+
+/**
+ * @brief updates a multiple option starting from the passed list
+ */
+static
+void update_multiple_arg(void *field, char ***orig_field,
+ unsigned int field_given, unsigned int prev_given, union generic_value *default_value,
+ cmdline_parser_clitkRegionGrowing_arg_type arg_type,
+ struct generic_list *list)
+{
+ int i;
+ struct generic_list *tmp;
+
+ if (prev_given && list) {
+ *orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *));
+
+ switch(arg_type) {
+ case ARG_INT:
+ *((int **)field) = (int *)realloc (*((int **)field), (field_given + prev_given) * sizeof (int)); break;
+ case ARG_DOUBLE:
+ *((double **)field) = (double *)realloc (*((double **)field), (field_given + prev_given) * sizeof (double)); break;
+ case ARG_STRING:
+ *((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break;
+ default:
+ break;
+ };
+
+ for (i = (prev_given - 1); i >= 0; --i)
+ {
+ tmp = list;
+
+ switch(arg_type) {
+ case ARG_INT:
+ (*((int **)field))[i + field_given] = tmp->arg.int_arg; break;
+ case ARG_DOUBLE:
+ (*((double **)field))[i + field_given] = tmp->arg.double_arg; break;
+ case ARG_STRING:
+ (*((char ***)field))[i + field_given] = tmp->arg.string_arg; break;
+ default:
+ break;
+ }
+ (*orig_field) [i + field_given] = list->orig;
+ list = list->next;
+ free (tmp);
+ }
+ } else { /* set the default value */
+ if (default_value && ! field_given) {
+ switch(arg_type) {
+ case ARG_INT:
+ if (! *((int **)field)) {
+ *((int **)field) = (int *)malloc (sizeof (int));
+ (*((int **)field))[0] = default_value->int_arg;
+ }
+ break;
+ case ARG_DOUBLE:
+ if (! *((double **)field)) {
+ *((double **)field) = (double *)malloc (sizeof (double));
+ (*((double **)field))[0] = default_value->double_arg;
+ }
+ break;
+ case ARG_STRING:
+ if (! *((char ***)field)) {
+ *((char ***)field) = (char **)malloc (sizeof (char *));
+ (*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg);
+ }
+ break;
+ default: break;
+ }
+ if (!(*orig_field)) {
+ *orig_field = (char **) malloc (sizeof (char *));
+ (*orig_field)[0] = NULL;
+ }
+ }
+ }
+}
+
+int
+cmdline_parser_clitkRegionGrowing_internal (int argc, char * const *argv, struct args_info_clitkRegionGrowing *args_info,
+ struct cmdline_parser_clitkRegionGrowing_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+ union generic_value multiple_default_value;
+
+ struct generic_list * seed_list = NULL;
+ struct generic_list * seedRadius_list = NULL;
+ struct generic_list * radius_list = NULL;
+ int error = 0;
+ struct args_info_clitkRegionGrowing local_args_info;
+
+ int override;
+ int initialize;
+ int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+ check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+ cmdline_parser_clitkRegionGrowing_init (args_info);
+
+ cmdline_parser_clitkRegionGrowing_init (&local_args_info);
+
+ optarg = 0;
+ optind = 0;
+ opterr = params->print_errors;
+ optopt = '?';
+
+ while (1)
+ {
+ int option_index = 0;
+
+ static struct option long_options[] = {
+ { "help", 0, NULL, 'h' },
+ { "version", 0, NULL, 'V' },
+ { "config", 1, NULL, 0 },
+ { "verbose", 0, NULL, 'v' },
+ { "input", 1, NULL, 'i' },
+ { "output", 1, NULL, 'o' },
+ { "type", 1, NULL, 't' },
+ { "lower", 1, NULL, 'l' },
+ { "upper", 1, NULL, 'u' },
+ { "maxUpper", 1, NULL, 0 },
+ { "minLower", 1, NULL, 0 },
+ { "step", 1, NULL, 0 },
+ { "minStep", 1, NULL, 0 },
+ { "adaptLower", 0, NULL, 0 },
+ { "adaptUpper", 0, NULL, 0 },
+ { "multiplier", 1, NULL, 'm' },
+ { "seed", 1, NULL, 's' },
+ { "seedRadius", 1, NULL, 0 },
+ { "pad", 1, NULL, 'p' },
+ { "radius", 1, NULL, 'r' },
+ { "maxSD", 1, NULL, 0 },
+ { "full", 0, NULL, 0 },
+ { "iter", 1, NULL, 0 },
+ { NULL, 0, NULL, 0 }
+ };
+
+ custom_optarg = optarg;
+ custom_optind = optind;
+ custom_opterr = opterr;
+ custom_optopt = optopt;
+
+ c = custom_getopt_long (argc, argv, "hVvi:o:t:l:u:m:s:p:r:", long_options, &option_index);
+
+ optarg = custom_optarg;
+ optind = custom_optind;
+ opterr = custom_opterr;
+ optopt = custom_optopt;
+
+ if (c == -1) break; /* Exit from `while (1)' loop. */
+
+ switch (c)
+ {
+ case 'h': /* Print help and exit. */
+ cmdline_parser_clitkRegionGrowing_print_help ();
+ cmdline_parser_clitkRegionGrowing_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'V': /* Print version and exit. */
+ cmdline_parser_clitkRegionGrowing_print_version ();
+ cmdline_parser_clitkRegionGrowing_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'v': /* Verbose. */
+
+
+ if (update_arg((void *)&(args_info->verbose_flag), 0, &(args_info->verbose_given),
+ &(local_args_info.verbose_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verbose", 'v',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'i': /* Input image filename. */
+
+
+ if (update_arg( (void *)&(args_info->input_arg),
+ &(args_info->input_orig), &(args_info->input_given),
+ &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "input", 'i',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'o': /* Output image filename. */
+
+
+ if (update_arg( (void *)&(args_info->output_arg),
+ &(args_info->output_orig), &(args_info->output_given),
+ &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "output", 'o',
+ additional_error))
+ goto failure;
+
+ break;
+ case 't': /* Region growing filter type: 0=threshold , 1=neighborhood-threshold , 2=confidence , 3= locally-adaptive-threshold, 4= explosion-controlled-threshold. */
+
+
+ if (update_arg( (void *)&(args_info->type_arg),
+ &(args_info->type_orig), &(args_info->type_given),
+ &(local_args_info.type_given), optarg, 0, "0", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "type", 't',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'l': /* 1,2,3,4: Lower threshold value. */
+
+
+ if (update_arg( (void *)&(args_info->lower_arg),
+ &(args_info->lower_orig), &(args_info->lower_given),
+ &(local_args_info.lower_given), optarg, 0, "310", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "lower", 'l',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'u': /* 1,2,3,4: Upper threshold value. */
+
+
+ if (update_arg( (void *)&(args_info->upper_arg),
+ &(args_info->upper_orig), &(args_info->upper_given),
+ &(local_args_info.upper_given), optarg, 0, "4000", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "upper", 'u',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'm': /* 2-4: (2-3) accept if within mean+-mutiplier*SD, (4) explosion if size increases multiplier times. */
+
+
+ if (update_arg( (void *)&(args_info->multiplier_arg),
+ &(args_info->multiplier_orig), &(args_info->multiplier_given),
+ &(local_args_info.multiplier_given), optarg, 0, "2.0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "multiplier", 'm',
+ additional_error))
+ goto failure;
+
+ break;
+ case 's': /* Seed index postion (in voxels). */
+
+ if (update_multiple_arg_temp(&seed_list,
+ &(local_args_info.seed_given), optarg, 0, "0", ARG_INT,
+ "seed", 's',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'p': /* The replace padding value. */
+
+
+ if (update_arg( (void *)&(args_info->pad_arg),
+ &(args_info->pad_orig), &(args_info->pad_given),
+ &(local_args_info.pad_given), optarg, 0, "1.0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "pad", 'p',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'r': /* 1-3: The radius of the neighborhood. */
+
+ if (update_multiple_arg_temp(&radius_list,
+ &(local_args_info.radius_given), optarg, 0, "1", ARG_INT,
+ "radius", 'r',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ /* Config file. */
+ if (strcmp (long_options[option_index].name, "config") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->config_arg),
+ &(args_info->config_orig), &(args_info->config_given),
+ &(local_args_info.config_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "config", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* 4: Maximum upper threshold value. */
+ else if (strcmp (long_options[option_index].name, "maxUpper") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->maxUpper_arg),
+ &(args_info->maxUpper_orig), &(args_info->maxUpper_given),
+ &(local_args_info.maxUpper_given), optarg, 0, "2000", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "maxUpper", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* 4: Minimum lower threshold value. */
+ else if (strcmp (long_options[option_index].name, "minLower") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->minLower_arg),
+ &(args_info->minLower_orig), &(args_info->minLower_given),
+ &(local_args_info.minLower_given), optarg, 0, "-1000", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "minLower", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* 4: Threshold step size. */
+ else if (strcmp (long_options[option_index].name, "step") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->step_arg),
+ &(args_info->step_orig), &(args_info->step_given),
+ &(local_args_info.step_given), optarg, 0, "64.0", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "step", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* 4: Minimum threshold step size. */
+ else if (strcmp (long_options[option_index].name, "minStep") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->minStep_arg),
+ &(args_info->minStep_orig), &(args_info->minStep_given),
+ &(local_args_info.minStep_given), optarg, 0, "1", ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "minStep", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* 3,4: (locally) adapt lower thresholding. */
+ else if (strcmp (long_options[option_index].name, "adaptLower") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->adaptLower_flag), 0, &(args_info->adaptLower_given),
+ &(local_args_info.adaptLower_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "adaptLower", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* 3,4: (locally) adapt upper thresholding. */
+ else if (strcmp (long_options[option_index].name, "adaptUpper") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->adaptUpper_flag), 0, &(args_info->adaptUpper_given),
+ &(local_args_info.adaptUpper_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "adaptUpper", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Radius used for seed dilatation(in voxel). */
+ else if (strcmp (long_options[option_index].name, "seedRadius") == 0)
+ {
+
+ if (update_multiple_arg_temp(&seedRadius_list,
+ &(local_args_info.seedRadius_given), optarg, 0, "0", ARG_INT,
+ "seedRadius", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* 3: Limit to SD. */
+ else if (strcmp (long_options[option_index].name, "maxSD") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->maxSD_arg),
+ &(args_info->maxSD_orig), &(args_info->maxSD_given),
+ &(local_args_info.maxSD_given), optarg, 0, 0, ARG_DOUBLE,
+ check_ambiguity, override, 0, 0,
+ "maxSD", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* 4: use full connectivity (not implemented yet). */
+ else if (strcmp (long_options[option_index].name, "full") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->full_flag), 0, &(args_info->full_given),
+ &(local_args_info.full_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "full", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* 2: Iterations. */
+ else if (strcmp (long_options[option_index].name, "iter") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->iter_arg),
+ &(args_info->iter_orig), &(args_info->iter_given),
+ &(local_args_info.iter_given), optarg, 0, "5", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "iter", '-',
+ additional_error))
+ goto failure;
+
+ }
+
+ break;
+ case '?': /* Invalid option. */
+ /* `getopt_long' already printed an error message. */
+ goto failure;
+
+ default: /* bug: option not considered. */
+ fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+
+ update_multiple_arg((void *)&(args_info->seed_arg),
+ &(args_info->seed_orig), args_info->seed_given,
+ local_args_info.seed_given, 0 ,
+ ARG_INT, seed_list);
+ update_multiple_arg((void *)&(args_info->seedRadius_arg),
+ &(args_info->seedRadius_orig), args_info->seedRadius_given,
+ local_args_info.seedRadius_given, 0 ,
+ ARG_INT, seedRadius_list);
+ multiple_default_value.int_arg = 1;
+ update_multiple_arg((void *)&(args_info->radius_arg),
+ &(args_info->radius_orig), args_info->radius_given,
+ local_args_info.radius_given, &multiple_default_value ,
+ ARG_INT, radius_list);
+
+ args_info->seed_given += local_args_info.seed_given;
+ local_args_info.seed_given = 0;
+ args_info->seedRadius_given += local_args_info.seedRadius_given;
+ local_args_info.seedRadius_given = 0;
+ args_info->radius_given += local_args_info.radius_given;
+ local_args_info.radius_given = 0;
+
+ if (check_required)
+ {
+ error += cmdline_parser_clitkRegionGrowing_required2 (args_info, argv[0], additional_error);
+ }
+
+ cmdline_parser_clitkRegionGrowing_release (&local_args_info);
+
+ if ( error )
+ return (EXIT_FAILURE);
+
+ if (optind < argc)
+ {
+ int i = 0 ;
+ int found_prog_name = 0;
+ /* whether program name, i.e., argv[0], is in the remaining args
+ (this may happen with some implementations of getopt,
+ but surely not with the one included by gengetopt) */
+
+
+ args_info->inputs_num = argc - optind - found_prog_name;
+ args_info->inputs =
+ (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+ while (optind < argc)
+ args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
+ }
+
+ return 0;
+
+failure:
+ free_list (seed_list, 0 );
+ free_list (seedRadius_list, 0 );
+ free_list (radius_list, 0 );
+
+ cmdline_parser_clitkRegionGrowing_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
+
+#ifndef CONFIG_FILE_LINE_SIZE
+#define CONFIG_FILE_LINE_SIZE 2048
+#endif
+#define ADDITIONAL_ERROR " in configuration file "
+
+#define CONFIG_FILE_LINE_BUFFER_SIZE (CONFIG_FILE_LINE_SIZE+3)
+/* 3 is for "--" and "=" */
+
+static int
+_cmdline_parser_clitkRegionGrowing_configfile (char * const filename, int *my_argc)
+{
+ FILE* file;
+ char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
+ char linebuf[CONFIG_FILE_LINE_SIZE];
+ int line_num = 0;
+ int result = 0, equal;
+ char *fopt, *farg;
+ char *str_index;
+ size_t len, next_token;
+ char delimiter;
+
+ if ((file = fopen(filename, "r")) == NULL)
+ {
+ fprintf (stderr, "%s: Error opening configuration file '%s'\n",
+ CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
+ {
+ ++line_num;
+ my_argv[0] = '\0';
+ len = strlen(linebuf);
+ if (len > (CONFIG_FILE_LINE_BUFFER_SIZE-1))
+ {
+ fprintf (stderr, "%s:%s:%d: Line too long in configuration file\n",
+ CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+
+ /* find first non-whitespace character in the line */
+ next_token = strspn (linebuf, " \t\r\n");
+ str_index = linebuf + next_token;
+
+ if ( str_index[0] == '\0' || str_index[0] == '#')
+ continue; /* empty line or comment line is skipped */
+
+ fopt = str_index;
+
+ /* truncate fopt at the end of the first non-valid character */
+ next_token = strcspn (fopt, " \t\r\n=");
+
+ if (fopt[next_token] == '\0') /* the line is over */
+ {
+ farg = NULL;
+ equal = 0;
+ goto noarg;
+ }
+
+ /* remember if equal sign is present */
+ equal = (fopt[next_token] == '=');
+ fopt[next_token++] = '\0';
+
+ /* advance pointers to the next token after the end of fopt */
+ next_token += strspn (fopt + next_token, " \t\r\n");
+
+ /* check for the presence of equal sign, and if so, skip it */
+ if ( !equal )
+ if ((equal = (fopt[next_token] == '=')))
+ {
+ next_token++;
+ next_token += strspn (fopt + next_token, " \t\r\n");
+ }
+ str_index += next_token;
+
+ /* find argument */
+ farg = str_index;
+ if ( farg[0] == '\"' || farg[0] == '\'' )
+ { /* quoted argument */
+ str_index = strchr (++farg, str_index[0] ); /* skip opening quote */
+ if (! str_index)
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: unterminated string in configuration file\n",
+ CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+ else
+ { /* read up the remaining part up to a delimiter */
+ next_token = strcspn (farg, " \t\r\n#\'\"");
+ str_index += next_token;
+ }
+
+ /* truncate farg at the delimiter and store it for further check */
+ delimiter = *str_index, *str_index++ = '\0';
+
+ /* everything but comment is illegal at the end of line */
+ if (delimiter != '\0' && delimiter != '#')
+ {
+ str_index += strspn(str_index, " \t\r\n");
+ if (*str_index != '\0' && *str_index != '#')
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: malformed string in configuration file\n",
+ CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+
+ noarg:
+ if (!strcmp(fopt,"include")) {
+ if (farg && *farg) {
+ result = _cmdline_parser_clitkRegionGrowing_configfile(farg, my_argc);
+ } else {
+ fprintf(stderr, "%s:%s:%d: include requires a filename argument.\n",
+ CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE, filename, line_num);
+ }
+ continue;
+ }
+ len = strlen(fopt);
+ strcat (my_argv, len > 1 ? "--" : "-");
+ strcat (my_argv, fopt);
+ if (len > 1 && ((farg && *farg) || equal))
+ strcat (my_argv, "=");
+ if (farg && *farg)
+ strcat (my_argv, farg);
+ ++(*my_argc);
+
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup(my_argv);
+ } /* while */
+
+ if (file)
+ fclose(file);
+ return result;
+}
+
+int
+cmdline_parser_clitkRegionGrowing_configfile (char * const filename,
+ struct args_info_clitkRegionGrowing *args_info,
+ int override, int initialize, int check_required)
+{
+ struct cmdline_parser_clitkRegionGrowing_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ return cmdline_parser_clitkRegionGrowing_config_file (filename, args_info, ¶ms);
+}
+
+int
+cmdline_parser_clitkRegionGrowing_config_file (char * const filename,
+ struct args_info_clitkRegionGrowing *args_info,
+ struct cmdline_parser_clitkRegionGrowing_params *params)
+{
+ int i, result;
+ int my_argc = 1;
+ char **my_argv_arg;
+ char *additional_error;
+
+ /* store the program name */
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup (CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE);
+
+ result = _cmdline_parser_clitkRegionGrowing_configfile(filename, &my_argc);
+
+ if (result != EXIT_FAILURE) {
+ my_argv_arg = (char **) malloc((my_argc+1) * sizeof(char *));
+ cmd_line_list_tmp = cmd_line_list;
+
+ for (i = my_argc - 1; i >= 0; --i) {
+ my_argv_arg[i] = cmd_line_list_tmp->string_arg;
+ cmd_line_list_tmp = cmd_line_list_tmp->next;
+ }
+
+ my_argv_arg[my_argc] = 0;
+
+ additional_error = (char *)malloc(strlen(filename) + strlen(ADDITIONAL_ERROR) + 1);
+ strcpy (additional_error, ADDITIONAL_ERROR);
+ strcat (additional_error, filename);
+ result =
+ cmdline_parser_clitkRegionGrowing_internal (my_argc, my_argv_arg, args_info,
+ params,
+ additional_error);
+
+ free (additional_error);
+ free (my_argv_arg);
+ }
+
+ free_cmd_list();
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkRegionGrowing_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
--- /dev/null
+/** @file clitkRegionGrowing_ggo.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CLITKREGIONGROWING_GGO_H
+#define CLITKREGIONGROWING_GGO_H
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE
+/** @brief the program name */
+#define CMDLINE_PARSER_CLITKREGIONGROWING_PACKAGE "clitkRegionGrowing"
+#endif
+
+#ifndef CMDLINE_PARSER_CLITKREGIONGROWING_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_CLITKREGIONGROWING_VERSION "1.0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct args_info_clitkRegionGrowing
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ char * config_arg; /**< @brief Config file. */
+ char * config_orig; /**< @brief Config file original value given at command line. */
+ const char *config_help; /**< @brief Config file help description. */
+ int verbose_flag; /**< @brief Verbose (default=off). */
+ const char *verbose_help; /**< @brief Verbose help description. */
+ char * input_arg; /**< @brief Input image filename. */
+ char * input_orig; /**< @brief Input image filename original value given at command line. */
+ const char *input_help; /**< @brief Input image filename help description. */
+ char * output_arg; /**< @brief Output image filename. */
+ char * output_orig; /**< @brief Output image filename original value given at command line. */
+ const char *output_help; /**< @brief Output image filename help description. */
+ int type_arg; /**< @brief Region growing filter type: 0=threshold , 1=neighborhood-threshold , 2=confidence , 3= locally-adaptive-threshold, 4= explosion-controlled-threshold (default='0'). */
+ char * type_orig; /**< @brief Region growing filter type: 0=threshold , 1=neighborhood-threshold , 2=confidence , 3= locally-adaptive-threshold, 4= explosion-controlled-threshold original value given at command line. */
+ const char *type_help; /**< @brief Region growing filter type: 0=threshold , 1=neighborhood-threshold , 2=confidence , 3= locally-adaptive-threshold, 4= explosion-controlled-threshold help description. */
+ double lower_arg; /**< @brief 1,2,3,4: Lower threshold value (default='310'). */
+ char * lower_orig; /**< @brief 1,2,3,4: Lower threshold value original value given at command line. */
+ const char *lower_help; /**< @brief 1,2,3,4: Lower threshold value help description. */
+ double upper_arg; /**< @brief 1,2,3,4: Upper threshold value (default='4000'). */
+ char * upper_orig; /**< @brief 1,2,3,4: Upper threshold value original value given at command line. */
+ const char *upper_help; /**< @brief 1,2,3,4: Upper threshold value help description. */
+ double maxUpper_arg; /**< @brief 4: Maximum upper threshold value (default='2000'). */
+ char * maxUpper_orig; /**< @brief 4: Maximum upper threshold value original value given at command line. */
+ const char *maxUpper_help; /**< @brief 4: Maximum upper threshold value help description. */
+ double minLower_arg; /**< @brief 4: Minimum lower threshold value (default='-1000'). */
+ char * minLower_orig; /**< @brief 4: Minimum lower threshold value original value given at command line. */
+ const char *minLower_help; /**< @brief 4: Minimum lower threshold value help description. */
+ double step_arg; /**< @brief 4: Threshold step size (default='64.0'). */
+ char * step_orig; /**< @brief 4: Threshold step size original value given at command line. */
+ const char *step_help; /**< @brief 4: Threshold step size help description. */
+ double minStep_arg; /**< @brief 4: Minimum threshold step size (default='1'). */
+ char * minStep_orig; /**< @brief 4: Minimum threshold step size original value given at command line. */
+ const char *minStep_help; /**< @brief 4: Minimum threshold step size help description. */
+ int adaptLower_flag; /**< @brief 3,4: (locally) adapt lower thresholding (default=off). */
+ const char *adaptLower_help; /**< @brief 3,4: (locally) adapt lower thresholding help description. */
+ int adaptUpper_flag; /**< @brief 3,4: (locally) adapt upper thresholding (default=off). */
+ const char *adaptUpper_help; /**< @brief 3,4: (locally) adapt upper thresholding help description. */
+ double multiplier_arg; /**< @brief 2-4: (2-3) accept if within mean+-mutiplier*SD, (4) explosion if size increases multiplier times (default='2.0'). */
+ char * multiplier_orig; /**< @brief 2-4: (2-3) accept if within mean+-mutiplier*SD, (4) explosion if size increases multiplier times original value given at command line. */
+ const char *multiplier_help; /**< @brief 2-4: (2-3) accept if within mean+-mutiplier*SD, (4) explosion if size increases multiplier times help description. */
+ int* seed_arg; /**< @brief Seed index postion (in voxels) (default='0'). */
+ char ** seed_orig; /**< @brief Seed index postion (in voxels) original value given at command line. */
+ int seed_min; /**< @brief Seed index postion (in voxels)'s minimum occurreces */
+ int seed_max; /**< @brief Seed index postion (in voxels)'s maximum occurreces */
+ const char *seed_help; /**< @brief Seed index postion (in voxels) help description. */
+ int* seedRadius_arg; /**< @brief Radius used for seed dilatation(in voxel) (default='0'). */
+ char ** seedRadius_orig; /**< @brief Radius used for seed dilatation(in voxel) original value given at command line. */
+ int seedRadius_min; /**< @brief Radius used for seed dilatation(in voxel)'s minimum occurreces */
+ int seedRadius_max; /**< @brief Radius used for seed dilatation(in voxel)'s maximum occurreces */
+ const char *seedRadius_help; /**< @brief Radius used for seed dilatation(in voxel) help description. */
+ double pad_arg; /**< @brief The replace padding value (default='1.0'). */
+ char * pad_orig; /**< @brief The replace padding value original value given at command line. */
+ const char *pad_help; /**< @brief The replace padding value help description. */
+ int* radius_arg; /**< @brief 1-3: The radius of the neighborhood (default='1'). */
+ char ** radius_orig; /**< @brief 1-3: The radius of the neighborhood original value given at command line. */
+ int radius_min; /**< @brief 1-3: The radius of the neighborhood's minimum occurreces */
+ int radius_max; /**< @brief 1-3: The radius of the neighborhood's maximum occurreces */
+ const char *radius_help; /**< @brief 1-3: The radius of the neighborhood help description. */
+ double maxSD_arg; /**< @brief 3: Limit to SD. */
+ char * maxSD_orig; /**< @brief 3: Limit to SD original value given at command line. */
+ const char *maxSD_help; /**< @brief 3: Limit to SD help description. */
+ int full_flag; /**< @brief 4: use full connectivity (not implemented yet) (default=off). */
+ const char *full_help; /**< @brief 4: use full connectivity (not implemented yet) help description. */
+ int iter_arg; /**< @brief 2: Iterations (default='5'). */
+ char * iter_orig; /**< @brief 2: Iterations original value given at command line. */
+ const char *iter_help; /**< @brief 2: Iterations help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int config_given ; /**< @brief Whether config was given. */
+ unsigned int verbose_given ; /**< @brief Whether verbose was given. */
+ unsigned int input_given ; /**< @brief Whether input was given. */
+ unsigned int output_given ; /**< @brief Whether output was given. */
+ unsigned int type_given ; /**< @brief Whether type was given. */
+ unsigned int lower_given ; /**< @brief Whether lower was given. */
+ unsigned int upper_given ; /**< @brief Whether upper was given. */
+ unsigned int maxUpper_given ; /**< @brief Whether maxUpper was given. */
+ unsigned int minLower_given ; /**< @brief Whether minLower was given. */
+ unsigned int step_given ; /**< @brief Whether step was given. */
+ unsigned int minStep_given ; /**< @brief Whether minStep was given. */
+ unsigned int adaptLower_given ; /**< @brief Whether adaptLower was given. */
+ unsigned int adaptUpper_given ; /**< @brief Whether adaptUpper was given. */
+ unsigned int multiplier_given ; /**< @brief Whether multiplier was given. */
+ unsigned int seed_given ; /**< @brief Whether seed was given. */
+ unsigned int seedRadius_given ; /**< @brief Whether seedRadius was given. */
+ unsigned int pad_given ; /**< @brief Whether pad was given. */
+ unsigned int radius_given ; /**< @brief Whether radius was given. */
+ unsigned int maxSD_given ; /**< @brief Whether maxSD was given. */
+ unsigned int full_given ; /**< @brief Whether full was given. */
+ unsigned int iter_given ; /**< @brief Whether iter was given. */
+
+ char **inputs ; /**< @brief unamed options (options without names) */
+ unsigned inputs_num ; /**< @brief unamed options number */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_clitkRegionGrowing_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure args_info_clitkRegionGrowing (default 1) */
+ int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+ int check_ambiguity; /**< @brief whether to check for options already specified in the option structure args_info_clitkRegionGrowing (default 0) */
+ int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *args_info_clitkRegionGrowing_purpose;
+/** @brief the usage string of the program */
+extern const char *args_info_clitkRegionGrowing_usage;
+/** @brief all the lines making the help output */
+extern const char *args_info_clitkRegionGrowing_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkRegionGrowing (int argc, char * const *argv,
+ struct args_info_clitkRegionGrowing *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkRegionGrowing_ext() instead
+ */
+int cmdline_parser_clitkRegionGrowing2 (int argc, char * const *argv,
+ struct args_info_clitkRegionGrowing *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkRegionGrowing_ext (int argc, char * const *argv,
+ struct args_info_clitkRegionGrowing *args_info,
+ struct cmdline_parser_clitkRegionGrowing_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkRegionGrowing_dump(FILE *outfile,
+ struct args_info_clitkRegionGrowing *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkRegionGrowing_file_save(const char *filename,
+ struct args_info_clitkRegionGrowing *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_clitkRegionGrowing_print_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_clitkRegionGrowing_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_clitkRegionGrowing_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_clitkRegionGrowing_params_init(struct cmdline_parser_clitkRegionGrowing_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_clitkRegionGrowing_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_clitkRegionGrowing_params structure
+ */
+struct cmdline_parser_clitkRegionGrowing_params *cmdline_parser_clitkRegionGrowing_params_create(void);
+
+/**
+ * Initializes the passed args_info_clitkRegionGrowing structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_clitkRegionGrowing_init (struct args_info_clitkRegionGrowing *args_info);
+/**
+ * Deallocates the string fields of the args_info_clitkRegionGrowing structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_clitkRegionGrowing_free (struct args_info_clitkRegionGrowing *args_info);
+
+/**
+ * The config file parser (deprecated version)
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkRegionGrowing_config_file() instead
+ */
+int cmdline_parser_clitkRegionGrowing_configfile (char * const filename,
+ struct args_info_clitkRegionGrowing *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The config file parser
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkRegionGrowing_config_file (char * const filename,
+ struct args_info_clitkRegionGrowing *args_info,
+ struct cmdline_parser_clitkRegionGrowing_params *params);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ * possible errors
+ * @return
+ */
+int cmdline_parser_clitkRegionGrowing_required (struct args_info_clitkRegionGrowing *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CLITKREGIONGROWING_GGO_H */
--- /dev/null
+/*
+ File autogenerated by gengetopt version 2.22
+ generated with the following command:
+ /usr/local/bin/gengetopt --output-dir=/home/tbaudier/vv/vv_static/vv/vv_bin/tools --arg-struct-name=args_info_clitkResampleImage --func-name=cmdline_parser_clitkResampleImage --file-name=clitkResampleImage_ggo --unamed-opts --conf-parser --include-getopt
+
+ The developers of gengetopt consider the fixed text that goes in all
+ gengetopt output files to be in the public domain:
+ we make no copyright claims on it.
+*/
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+
+#include "clitkResampleImage_ggo.h"
+
+const char *args_info_clitkResampleImage_purpose = "Resample an image. You can specify the interpolation, you can apply a Gaussian \nfilter before (automated if downsample).";
+
+const char *args_info_clitkResampleImage_usage = "Usage: clitkResampleImage [OPTIONS]... [FILES]...";
+
+const char *args_info_clitkResampleImage_description = "";
+
+const char *args_info_clitkResampleImage_help[] = {
+ " -h, --help Print help and exit",
+ " -V, --version Print version and exit",
+ "\nCommon:",
+ " --config=STRING Config file",
+ " -v, --verbose Verbose (default=off)",
+ " --imagetypes Verbose: allowed image types (default=off)",
+ " --thread=INT Nb of thread to use (default=max)",
+ "\nInput & Output options:",
+ " -i, --input=STRING Input image filename",
+ " -o, --output=STRING Output image filename",
+ " -l, --like=STRING Resample like this image",
+ " --size=INT Number of pixels of each coordonate (default=`0')",
+ " --spacing=FLOAT Spacing in mm between pixels (default=`-1.0')",
+ " -d, --default=FLOAT Default pixel value (default=`0.0')",
+ " -t, --time Last Dimension Is Time -> do not resample it (auto on \n for 4D) (default=off)",
+ "\nInterpolation:",
+ " --interp=STRING Interpolation type: {nn, linear, bspline, blut} \n (default=`nn')",
+ " -b, --order=INT BSpline ordre (range 0-5) (default=`3')",
+ " -s, --sampling=INT BLUT sampling value (default=`30')",
+ "\nGaussian filtering:",
+ " -g, --gauss=FLOAT Apply Gaussian before (sigma in mm) (default=`0.0')",
+ " -a, --autogauss Apply Gaussian with auto sigma when downsample \n (default=off)",
+ 0
+};
+
+typedef enum {ARG_NO
+ , ARG_FLAG
+ , ARG_STRING
+ , ARG_INT
+ , ARG_FLOAT
+} cmdline_parser_clitkResampleImage_arg_type;
+
+static
+void clear_given (struct args_info_clitkResampleImage *args_info);
+static
+void clear_args (struct args_info_clitkResampleImage *args_info);
+
+static int
+cmdline_parser_clitkResampleImage_internal (int argc, char * const *argv, struct args_info_clitkResampleImage *args_info,
+ struct cmdline_parser_clitkResampleImage_params *params, const char *additional_error);
+
+static int
+cmdline_parser_clitkResampleImage_required2 (struct args_info_clitkResampleImage *args_info, const char *prog_name, const char *additional_error);
+struct line_list
+{
+ char * string_arg;
+ struct line_list * next;
+};
+
+static struct line_list *cmd_line_list = 0;
+static struct line_list *cmd_line_list_tmp = 0;
+
+static void
+free_cmd_list(void)
+{
+ /* free the list of a previous call */
+ if (cmd_line_list)
+ {
+ while (cmd_line_list) {
+ cmd_line_list_tmp = cmd_line_list;
+ cmd_line_list = cmd_line_list->next;
+ free (cmd_line_list_tmp->string_arg);
+ free (cmd_line_list_tmp);
+ }
+ }
+}
+
+
+static char *
+gengetopt_strdup (const char *s);
+
+static
+void clear_given (struct args_info_clitkResampleImage *args_info)
+{
+ args_info->help_given = 0 ;
+ args_info->version_given = 0 ;
+ args_info->config_given = 0 ;
+ args_info->verbose_given = 0 ;
+ args_info->imagetypes_given = 0 ;
+ args_info->thread_given = 0 ;
+ args_info->input_given = 0 ;
+ args_info->output_given = 0 ;
+ args_info->like_given = 0 ;
+ args_info->size_given = 0 ;
+ args_info->spacing_given = 0 ;
+ args_info->default_given = 0 ;
+ args_info->time_given = 0 ;
+ args_info->interp_given = 0 ;
+ args_info->order_given = 0 ;
+ args_info->sampling_given = 0 ;
+ args_info->gauss_given = 0 ;
+ args_info->autogauss_given = 0 ;
+}
+
+static
+void clear_args (struct args_info_clitkResampleImage *args_info)
+{
+ args_info->config_arg = NULL;
+ args_info->config_orig = NULL;
+ args_info->verbose_flag = 0;
+ args_info->imagetypes_flag = 0;
+ args_info->thread_orig = NULL;
+ args_info->input_arg = NULL;
+ args_info->input_orig = NULL;
+ args_info->output_arg = NULL;
+ args_info->output_orig = NULL;
+ args_info->like_arg = NULL;
+ args_info->like_orig = NULL;
+ args_info->size_arg = NULL;
+ args_info->size_orig = NULL;
+ args_info->spacing_arg = NULL;
+ args_info->spacing_orig = NULL;
+ args_info->default_arg = 0.0;
+ args_info->default_orig = NULL;
+ args_info->time_flag = 0;
+ args_info->interp_arg = gengetopt_strdup ("nn");
+ args_info->interp_orig = NULL;
+ args_info->order_arg = 3;
+ args_info->order_orig = NULL;
+ args_info->sampling_arg = 30;
+ args_info->sampling_orig = NULL;
+ args_info->gauss_arg = NULL;
+ args_info->gauss_orig = NULL;
+ args_info->autogauss_flag = 0;
+
+}
+
+static
+void init_args_info(struct args_info_clitkResampleImage *args_info)
+{
+
+
+ args_info->help_help = args_info_clitkResampleImage_help[0] ;
+ args_info->version_help = args_info_clitkResampleImage_help[1] ;
+ args_info->config_help = args_info_clitkResampleImage_help[3] ;
+ args_info->verbose_help = args_info_clitkResampleImage_help[4] ;
+ args_info->imagetypes_help = args_info_clitkResampleImage_help[5] ;
+ args_info->thread_help = args_info_clitkResampleImage_help[6] ;
+ args_info->input_help = args_info_clitkResampleImage_help[8] ;
+ args_info->output_help = args_info_clitkResampleImage_help[9] ;
+ args_info->like_help = args_info_clitkResampleImage_help[10] ;
+ args_info->size_help = args_info_clitkResampleImage_help[11] ;
+ args_info->size_min = -1;
+ args_info->size_max = -1;
+ args_info->spacing_help = args_info_clitkResampleImage_help[12] ;
+ args_info->spacing_min = -1;
+ args_info->spacing_max = -1;
+ args_info->default_help = args_info_clitkResampleImage_help[13] ;
+ args_info->time_help = args_info_clitkResampleImage_help[14] ;
+ args_info->interp_help = args_info_clitkResampleImage_help[16] ;
+ args_info->order_help = args_info_clitkResampleImage_help[17] ;
+ args_info->sampling_help = args_info_clitkResampleImage_help[18] ;
+ args_info->gauss_help = args_info_clitkResampleImage_help[20] ;
+ args_info->gauss_min = -1;
+ args_info->gauss_max = -1;
+ args_info->autogauss_help = args_info_clitkResampleImage_help[21] ;
+
+}
+
+void
+cmdline_parser_clitkResampleImage_print_version (void)
+{
+ printf ("%s %s\n", CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE, CMDLINE_PARSER_CLITKRESAMPLEIMAGE_VERSION);
+}
+
+static void print_help_common(void) {
+ cmdline_parser_clitkResampleImage_print_version ();
+
+ if (strlen(args_info_clitkResampleImage_purpose) > 0)
+ printf("\n%s\n", args_info_clitkResampleImage_purpose);
+
+ if (strlen(args_info_clitkResampleImage_usage) > 0)
+ printf("\n%s\n", args_info_clitkResampleImage_usage);
+
+ printf("\n");
+
+ if (strlen(args_info_clitkResampleImage_description) > 0)
+ printf("%s\n", args_info_clitkResampleImage_description);
+}
+
+void
+cmdline_parser_clitkResampleImage_print_help (void)
+{
+ int i = 0;
+ print_help_common();
+ while (args_info_clitkResampleImage_help[i])
+ printf("%s\n", args_info_clitkResampleImage_help[i++]);
+}
+
+void
+cmdline_parser_clitkResampleImage_init (struct args_info_clitkResampleImage *args_info)
+{
+ clear_given (args_info);
+ clear_args (args_info);
+ init_args_info (args_info);
+
+ args_info->inputs = NULL;
+ args_info->inputs_num = 0;
+}
+
+void
+cmdline_parser_clitkResampleImage_params_init(struct cmdline_parser_clitkResampleImage_params *params)
+{
+ if (params)
+ {
+ params->override = 0;
+ params->initialize = 1;
+ params->check_required = 1;
+ params->check_ambiguity = 0;
+ params->print_errors = 1;
+ }
+}
+
+struct cmdline_parser_clitkResampleImage_params *
+cmdline_parser_clitkResampleImage_params_create(void)
+{
+ struct cmdline_parser_clitkResampleImage_params *params =
+ (struct cmdline_parser_clitkResampleImage_params *)malloc(sizeof(struct cmdline_parser_clitkResampleImage_params));
+ cmdline_parser_clitkResampleImage_params_init(params);
+ return params;
+}
+
+static void
+free_string_field (char **s)
+{
+ if (*s)
+ {
+ free (*s);
+ *s = 0;
+ }
+}
+
+/** @brief generic value variable */
+union generic_value {
+ int int_arg;
+ float float_arg;
+ char *string_arg;
+};
+
+/** @brief holds temporary values for multiple options */
+struct generic_list
+{
+ union generic_value arg;
+ char *orig;
+ struct generic_list *next;
+};
+
+/**
+ * @brief add a node at the head of the list
+ */
+static void add_node(struct generic_list **list) {
+ struct generic_list *new_node = (struct generic_list *) malloc (sizeof (struct generic_list));
+ new_node->next = *list;
+ *list = new_node;
+ new_node->arg.string_arg = NULL;
+ new_node->orig = NULL;
+}
+
+static void
+free_multiple_field(unsigned int len, void **arg, char ***orig)
+{
+ unsigned int i;
+ if (*arg) {
+ for (i = 0; i < len; ++i)
+ {
+ free_string_field(&((*orig)[i]));
+ }
+
+ free (*arg);
+ *arg = 0;
+ free (*orig);
+ *orig = 0;
+ }
+}
+
+
+static void
+cmdline_parser_clitkResampleImage_release (struct args_info_clitkResampleImage *args_info)
+{
+ unsigned int i;
+ free_string_field (&(args_info->config_arg));
+ free_string_field (&(args_info->config_orig));
+ free_string_field (&(args_info->thread_orig));
+ free_string_field (&(args_info->input_arg));
+ free_string_field (&(args_info->input_orig));
+ free_string_field (&(args_info->output_arg));
+ free_string_field (&(args_info->output_orig));
+ free_string_field (&(args_info->like_arg));
+ free_string_field (&(args_info->like_orig));
+ free_multiple_field (args_info->size_given, (void **)&(args_info->size_arg), &(args_info->size_orig));
+ free_multiple_field (args_info->spacing_given, (void **)&(args_info->spacing_arg), &(args_info->spacing_orig));
+ free_string_field (&(args_info->default_orig));
+ free_string_field (&(args_info->interp_arg));
+ free_string_field (&(args_info->interp_orig));
+ free_string_field (&(args_info->order_orig));
+ free_string_field (&(args_info->sampling_orig));
+ free_multiple_field (args_info->gauss_given, (void **)&(args_info->gauss_arg), &(args_info->gauss_orig));
+
+
+ for (i = 0; i < args_info->inputs_num; ++i)
+ free (args_info->inputs [i]);
+
+ if (args_info->inputs_num)
+ free (args_info->inputs);
+
+ clear_given (args_info);
+}
+
+
+static void
+write_into_file(FILE *outfile, const char *opt, const char *arg, char *values[])
+{
+ if (arg) {
+ fprintf(outfile, "%s=\"%s\"\n", opt, arg);
+ } else {
+ fprintf(outfile, "%s\n", opt);
+ }
+}
+
+static void
+write_multiple_into_file(FILE *outfile, int len, const char *opt, char **arg, char *values[])
+{
+ int i;
+
+ for (i = 0; i < len; ++i)
+ write_into_file(outfile, opt, (arg ? arg[i] : 0), values);
+}
+
+int
+cmdline_parser_clitkResampleImage_dump(FILE *outfile, struct args_info_clitkResampleImage *args_info)
+{
+ int i = 0;
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE);
+ return EXIT_FAILURE;
+ }
+
+ if (args_info->help_given)
+ write_into_file(outfile, "help", 0, 0 );
+ if (args_info->version_given)
+ write_into_file(outfile, "version", 0, 0 );
+ if (args_info->config_given)
+ write_into_file(outfile, "config", args_info->config_orig, 0);
+ if (args_info->verbose_given)
+ write_into_file(outfile, "verbose", 0, 0 );
+ if (args_info->imagetypes_given)
+ write_into_file(outfile, "imagetypes", 0, 0 );
+ if (args_info->thread_given)
+ write_into_file(outfile, "thread", args_info->thread_orig, 0);
+ if (args_info->input_given)
+ write_into_file(outfile, "input", args_info->input_orig, 0);
+ if (args_info->output_given)
+ write_into_file(outfile, "output", args_info->output_orig, 0);
+ if (args_info->like_given)
+ write_into_file(outfile, "like", args_info->like_orig, 0);
+ write_multiple_into_file(outfile, args_info->size_given, "size", args_info->size_orig, 0);
+ write_multiple_into_file(outfile, args_info->spacing_given, "spacing", args_info->spacing_orig, 0);
+ if (args_info->default_given)
+ write_into_file(outfile, "default", args_info->default_orig, 0);
+ if (args_info->time_given)
+ write_into_file(outfile, "time", 0, 0 );
+ if (args_info->interp_given)
+ write_into_file(outfile, "interp", args_info->interp_orig, 0);
+ if (args_info->order_given)
+ write_into_file(outfile, "order", args_info->order_orig, 0);
+ if (args_info->sampling_given)
+ write_into_file(outfile, "sampling", args_info->sampling_orig, 0);
+ write_multiple_into_file(outfile, args_info->gauss_given, "gauss", args_info->gauss_orig, 0);
+ if (args_info->autogauss_given)
+ write_into_file(outfile, "autogauss", 0, 0 );
+
+
+ i = EXIT_SUCCESS;
+ return i;
+}
+
+int
+cmdline_parser_clitkResampleImage_file_save(const char *filename, struct args_info_clitkResampleImage *args_info)
+{
+ FILE *outfile;
+ int i = 0;
+
+ outfile = fopen(filename, "w");
+
+ if (!outfile)
+ {
+ fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ i = cmdline_parser_clitkResampleImage_dump(outfile, args_info);
+ fclose (outfile);
+
+ return i;
+}
+
+void
+cmdline_parser_clitkResampleImage_free (struct args_info_clitkResampleImage *args_info)
+{
+ cmdline_parser_clitkResampleImage_release (args_info);
+}
+
+/** @brief replacement of strdup, which is not standard */
+char *
+gengetopt_strdup (const char *s)
+{
+ char *result = NULL;
+ if (!s)
+ return result;
+
+ result = (char*)malloc(strlen(s) + 1);
+ if (result == (char*)0)
+ return (char*)0;
+ strcpy(result, s);
+ return result;
+}
+
+static char *
+get_multiple_arg_token(const char *arg)
+{
+ char *tok, *ret;
+ size_t len, num_of_escape, i, j;
+
+ if (!arg)
+ return NULL;
+
+ tok = strchr (arg, ',');
+ num_of_escape = 0;
+
+ /* make sure it is not escaped */
+ while (tok)
+ {
+ if (*(tok-1) == '\\')
+ {
+ /* find the next one */
+ tok = strchr (tok+1, ',');
+ ++num_of_escape;
+ }
+ else
+ break;
+ }
+
+ if (tok)
+ len = (size_t)(tok - arg + 1);
+ else
+ len = strlen (arg) + 1;
+
+ len -= num_of_escape;
+
+ ret = (char *) malloc (len);
+
+ i = 0;
+ j = 0;
+ while (arg[i] && (j < len-1))
+ {
+ if (arg[i] == '\\' &&
+ arg[ i + 1 ] &&
+ arg[ i + 1 ] == ',')
+ ++i;
+
+ ret[j++] = arg[i++];
+ }
+
+ ret[len-1] = '\0';
+
+ return ret;
+}
+
+static char *
+get_multiple_arg_token_next(const char *arg)
+{
+ char *tok;
+
+ if (!arg)
+ return NULL;
+
+ tok = strchr (arg, ',');
+
+ /* make sure it is not escaped */
+ while (tok)
+ {
+ if (*(tok-1) == '\\')
+ {
+ /* find the next one */
+ tok = strchr (tok+1, ',');
+ }
+ else
+ break;
+ }
+
+ if (! tok || strlen(tok) == 1)
+ return 0;
+
+ return tok+1;
+}
+
+static int
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc);
+
+int
+check_multiple_option_occurrences(const char *prog_name, unsigned int option_given, int min, int max, const char *option_desc)
+{
+ int error = 0;
+
+ if (option_given && ! (min < 0 && max < 0))
+ {
+ if (min >= 0 && max >= 0)
+ {
+ if (min == max)
+ {
+ /* specific occurrences */
+ if (option_given != min)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be %d\n",
+ prog_name, option_desc, min);
+ error = 1;
+ }
+ }
+ else if (option_given < min
+ || option_given > max)
+ {
+ /* range occurrences */
+ fprintf (stderr, "%s: %s option occurrences must be between %d and %d\n",
+ prog_name, option_desc, min, max);
+ error = 1;
+ }
+ }
+ else if (min >= 0)
+ {
+ /* at least check */
+ if (option_given < min)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be at least %d\n",
+ prog_name, option_desc, min);
+ error = 1;
+ }
+ }
+ else if (max >= 0)
+ {
+ /* at most check */
+ if (option_given > max)
+ {
+ fprintf (stderr, "%s: %s option occurrences must be at most %d\n",
+ prog_name, option_desc, max);
+ error = 1;
+ }
+ }
+ }
+
+ return error;
+}
+int
+cmdline_parser_clitkResampleImage (int argc, char * const *argv, struct args_info_clitkResampleImage *args_info)
+{
+ return cmdline_parser_clitkResampleImage2 (argc, argv, args_info, 0, 1, 1);
+}
+
+int
+cmdline_parser_clitkResampleImage_ext (int argc, char * const *argv, struct args_info_clitkResampleImage *args_info,
+ struct cmdline_parser_clitkResampleImage_params *params)
+{
+ int result;
+ result = cmdline_parser_clitkResampleImage_internal (argc, argv, args_info, params, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkResampleImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkResampleImage2 (int argc, char * const *argv, struct args_info_clitkResampleImage *args_info, int override, int initialize, int check_required)
+{
+ int result;
+ struct cmdline_parser_clitkResampleImage_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ result = cmdline_parser_clitkResampleImage_internal (argc, argv, args_info, ¶ms, NULL);
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkResampleImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkResampleImage_required (struct args_info_clitkResampleImage *args_info, const char *prog_name)
+{
+ int result = EXIT_SUCCESS;
+
+ if (cmdline_parser_clitkResampleImage_required2(args_info, prog_name, NULL) > 0)
+ result = EXIT_FAILURE;
+
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkResampleImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
+
+int
+cmdline_parser_clitkResampleImage_required2 (struct args_info_clitkResampleImage *args_info, const char *prog_name, const char *additional_error)
+{
+ int error = 0;
+
+ /* checks for required options */
+ if (! args_info->input_given)
+ {
+ fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (! args_info->output_given)
+ {
+ fprintf (stderr, "%s: '--output' ('-o') option required%s\n", prog_name, (additional_error ? additional_error : ""));
+ error = 1;
+ }
+
+ if (check_multiple_option_occurrences(prog_name, args_info->size_given, args_info->size_min, args_info->size_max, "'--size'"))
+ error = 1;
+
+ if (check_multiple_option_occurrences(prog_name, args_info->spacing_given, args_info->spacing_min, args_info->spacing_max, "'--spacing'"))
+ error = 1;
+
+ if (check_multiple_option_occurrences(prog_name, args_info->gauss_given, args_info->gauss_min, args_info->gauss_max, "'--gauss' ('-g')"))
+ error = 1;
+
+
+ /* checks for dependences among options */
+
+ return error;
+}
+
+/*
+ * Extracted from the glibc source tree, version 2.3.6
+ *
+ * Licensed under the GPL as per the whole glibc source tree.
+ *
+ * This file was modified so that getopt_long can be called
+ * many times without risking previous memory to be spoiled.
+ *
+ * Modified by Andre Noll and Lorenzo Bettini for use in
+ * GNU gengetopt generated files.
+ *
+ */
+
+/*
+ * we must include anything we need since this file is not thought to be
+ * inserted in a file already using getopt.h
+ *
+ * Lorenzo
+ */
+
+struct option
+{
+ const char *name;
+ /* has_arg can't be an enum because some compilers complain about
+ type mismatches in all the code that assumes it is an int. */
+ int has_arg;
+ int *flag;
+ int val;
+};
+
+/* For communication from `getopt' to the caller.
+ When `getopt' finds an option that takes an argument,
+ the argument value is returned here.
+ Also, when `ordering' is RETURN_IN_ORDER,
+ each non-option ARGV-element is returned here. */
+
+static char *optarg;
+
+/* Index in ARGV of the next element to be scanned.
+ This is used for communication to and from the caller
+ and for communication between successive calls to `getopt'.
+
+ On entry to `getopt', zero means this is the first call; initialize.
+
+ When `getopt' returns -1, this is the index of the first of the
+ non-option elements that the caller should itself scan.
+
+ Otherwise, `optind' communicates from one call to the next
+ how much of ARGV has been scanned so far. */
+
+static int optind;
+
+/* Callers store zero here to inhibit the error message `getopt' prints
+ for unrecognized options. */
+
+static int opterr;
+
+/* Set to an option character which was unrecognized. */
+
+static int optopt;
+
+/* This version of `getopt' appears to the caller like standard Unix `getopt'
+ but it behaves differently for the user, since it allows the user
+ to intersperse the options with the other arguments.
+
+ As `getopt' works, it permutes the elements of ARGV so that,
+ when it is done, all the options precede everything else. Thus
+ all application programs are extended to handle flexible argument order.
+*/
+/*
+ If the field `flag' is not NULL, it points to a variable that is set
+ to the value given in the field `val' when the option is found, but
+ left unchanged if the option is not found.
+
+ To have a long-named option do something other than set an `int' to
+ a compiled-in constant, such as set a value from `custom_optarg', set the
+ option's `flag' field to zero and its `val' field to a nonzero
+ value (the equivalent single-letter option character, if there is
+ one). For long options that have a zero `flag' field, `getopt'
+ returns the contents of the `val' field. */
+
+/* Names for the values of the `has_arg' field of `struct option'. */
+#ifndef no_argument
+#define no_argument 0
+#endif
+
+#ifndef required_argument
+#define required_argument 1
+#endif
+
+#ifndef optional_argument
+#define optional_argument 2
+#endif
+
+struct custom_getopt_data {
+ /*
+ * These have exactly the same meaning as the corresponding global variables,
+ * except that they are used for the reentrant versions of getopt.
+ */
+ int custom_optind;
+ int custom_opterr;
+ int custom_optopt;
+ char *custom_optarg;
+
+ /* True if the internal members have been initialized. */
+ int initialized;
+
+ /*
+ * The next char to be scanned in the option-element in which the last option
+ * character we returned was found. This allows us to pick up the scan where
+ * we left off. If this is zero, or a null string, it means resume the scan by
+ * advancing to the next ARGV-element.
+ */
+ char *nextchar;
+
+ /*
+ * Describe the part of ARGV that contains non-options that have been skipped.
+ * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is
+ * the index after the last of them.
+ */
+ int first_nonopt;
+ int last_nonopt;
+};
+
+/*
+ * the variables optarg, optind, opterr and optopt are renamed with
+ * the custom_ prefix so that they don't interfere with getopt ones.
+ *
+ * Moreover they're static so they are visible only from within the
+ * file where this very file will be included.
+ */
+
+/*
+ * For communication from `custom_getopt' to the caller. When `custom_getopt' finds an
+ * option that takes an argument, the argument value is returned here.
+ */
+static char *custom_optarg;
+
+/*
+ * Index in ARGV of the next element to be scanned. This is used for
+ * communication to and from the caller and for communication between
+ * successive calls to `custom_getopt'.
+ *
+ * On entry to `custom_getopt', 1 means this is the first call; initialize.
+ *
+ * When `custom_getopt' returns -1, this is the index of the first of the non-option
+ * elements that the caller should itself scan.
+ *
+ * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV
+ * has been scanned so far.
+ *
+ * 1003.2 says this must be 1 before any call.
+ */
+static int custom_optind = 1;
+
+/*
+ * Callers store zero here to inhibit the error message for unrecognized
+ * options.
+ */
+static int custom_opterr = 1;
+
+/*
+ * Set to an option character which was unrecognized. This must be initialized
+ * on some systems to avoid linking in the system's own getopt implementation.
+ */
+static int custom_optopt = '?';
+
+/*
+ * Exchange two adjacent subsequences of ARGV. One subsequence is elements
+ * [first_nonopt,last_nonopt) which contains all the non-options that have been
+ * skipped so far. The other is elements [last_nonopt,custom_optind), which contains
+ * all the options processed since those non-options were skipped.
+ * `first_nonopt' and `last_nonopt' are relocated so that they describe the new
+ * indices of the non-options in ARGV after they are moved.
+ */
+static void exchange(char **argv, struct custom_getopt_data *d)
+{
+ int bottom = d->first_nonopt;
+ int middle = d->last_nonopt;
+ int top = d->custom_optind;
+ char *tem;
+
+ /*
+ * Exchange the shorter segment with the far end of the longer segment.
+ * That puts the shorter segment into the right place. It leaves the
+ * longer segment in the right place overall, but it consists of two
+ * parts that need to be swapped next.
+ */
+ while (top > middle && middle > bottom) {
+ if (top - middle > middle - bottom) {
+ /* Bottom segment is the short one. */
+ int len = middle - bottom;
+ int i;
+
+ /* Swap it with the top part of the top segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] =
+ argv[top - (middle - bottom) + i];
+ argv[top - (middle - bottom) + i] = tem;
+ }
+ /* Exclude the moved bottom segment from further swapping. */
+ top -= len;
+ } else {
+ /* Top segment is the short one. */
+ int len = top - middle;
+ int i;
+
+ /* Swap it with the bottom part of the bottom segment. */
+ for (i = 0; i < len; i++) {
+ tem = argv[bottom + i];
+ argv[bottom + i] = argv[middle + i];
+ argv[middle + i] = tem;
+ }
+ /* Exclude the moved top segment from further swapping. */
+ bottom += len;
+ }
+ }
+ /* Update records for the slots the non-options now occupy. */
+ d->first_nonopt += (d->custom_optind - d->last_nonopt);
+ d->last_nonopt = d->custom_optind;
+}
+
+/* Initialize the internal data when the first call is made. */
+static void custom_getopt_initialize(struct custom_getopt_data *d)
+{
+ /*
+ * Start processing options with ARGV-element 1 (since ARGV-element 0
+ * is the program name); the sequence of previously skipped non-option
+ * ARGV-elements is empty.
+ */
+ d->first_nonopt = d->last_nonopt = d->custom_optind;
+ d->nextchar = NULL;
+ d->initialized = 1;
+}
+
+#define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0')
+
+/* return: zero: continue, nonzero: return given value to user */
+static int shuffle_argv(int argc, char *const *argv,const struct option *longopts,
+ struct custom_getopt_data *d)
+{
+ /*
+ * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been
+ * moved back by the user (who may also have changed the arguments).
+ */
+ if (d->last_nonopt > d->custom_optind)
+ d->last_nonopt = d->custom_optind;
+ if (d->first_nonopt > d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * If we have just processed some options following some
+ * non-options, exchange them so that the options come first.
+ */
+ if (d->first_nonopt != d->last_nonopt &&
+ d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->last_nonopt != d->custom_optind)
+ d->first_nonopt = d->custom_optind;
+ /*
+ * Skip any additional non-options and extend the range of
+ * non-options previously skipped.
+ */
+ while (d->custom_optind < argc && NONOPTION_P)
+ d->custom_optind++;
+ d->last_nonopt = d->custom_optind;
+ /*
+ * The special ARGV-element `--' means premature end of options. Skip
+ * it like a null option, then exchange with previous non-options as if
+ * it were an option, then skip everything else like a non-option.
+ */
+ if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) {
+ d->custom_optind++;
+ if (d->first_nonopt != d->last_nonopt
+ && d->last_nonopt != d->custom_optind)
+ exchange((char **) argv, d);
+ else if (d->first_nonopt == d->last_nonopt)
+ d->first_nonopt = d->custom_optind;
+ d->last_nonopt = argc;
+ d->custom_optind = argc;
+ }
+ /*
+ * If we have done all the ARGV-elements, stop the scan and back over
+ * any non-options that we skipped and permuted.
+ */
+ if (d->custom_optind == argc) {
+ /*
+ * Set the next-arg-index to point at the non-options that we
+ * previously skipped, so the caller will digest them.
+ */
+ if (d->first_nonopt != d->last_nonopt)
+ d->custom_optind = d->first_nonopt;
+ return -1;
+ }
+ /*
+ * If we have come to a non-option and did not permute it, either stop
+ * the scan or describe it to the caller and pass it by.
+ */
+ if (NONOPTION_P) {
+ d->custom_optarg = argv[d->custom_optind++];
+ return 1;
+ }
+ /*
+ * We have found another option-ARGV-element. Skip the initial
+ * punctuation.
+ */
+ d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-'));
+ return 0;
+}
+
+/*
+ * Check whether the ARGV-element is a long option.
+ *
+ * If there's a long option "fubar" and the ARGV-element is "-fu", consider
+ * that an abbreviation of the long option, just like "--fu", and not "-f" with
+ * arg "u".
+ *
+ * This distinction seems to be the most useful approach.
+ *
+ */
+static int check_long_opt(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char *nameend;
+ const struct option *p;
+ const struct option *pfound = NULL;
+ int exact = 0;
+ int ambig = 0;
+ int indfound = -1;
+ int option_index;
+
+ for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++)
+ /* Do nothing. */ ;
+
+ /* Test all long options for either exact match or abbreviated matches */
+ for (p = longopts, option_index = 0; p->name; p++, option_index++)
+ if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) {
+ if ((unsigned int) (nameend - d->nextchar)
+ == (unsigned int) strlen(p->name)) {
+ /* Exact match found. */
+ pfound = p;
+ indfound = option_index;
+ exact = 1;
+ break;
+ } else if (pfound == NULL) {
+ /* First nonexact match found. */
+ pfound = p;
+ indfound = option_index;
+ } else if (pfound->has_arg != p->has_arg
+ || pfound->flag != p->flag
+ || pfound->val != p->val)
+ /* Second or later nonexact match found. */
+ ambig = 1;
+ }
+ if (ambig && !exact) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' is ambiguous\n",
+ argv[0], argv[d->custom_optind]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+ }
+ if (pfound) {
+ option_index = indfound;
+ d->custom_optind++;
+ if (*nameend) {
+ if (pfound->has_arg != no_argument)
+ d->custom_optarg = nameend + 1;
+ else {
+ if (print_errors) {
+ if (argv[d->custom_optind - 1][1] == '-') {
+ /* --option */
+ fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n",
+ argv[0], pfound->name);
+ } else {
+ /* +option or -option */
+ fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n",
+ argv[0], argv[d->custom_optind - 1][0], pfound->name);
+ }
+
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return '?';
+ }
+ } else if (pfound->has_arg == required_argument) {
+ if (d->custom_optind < argc)
+ d->custom_optarg = argv[d->custom_optind++];
+ else {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option `%s' requires an argument\n",
+ argv[0],
+ argv[d->custom_optind - 1]);
+ }
+ d->nextchar += strlen(d->nextchar);
+ d->custom_optopt = pfound->val;
+ return optstring[0] == ':' ? ':' : '?';
+ }
+ }
+ d->nextchar += strlen(d->nextchar);
+ if (longind != NULL)
+ *longind = option_index;
+ if (pfound->flag) {
+ *(pfound->flag) = pfound->val;
+ return 0;
+ }
+ return pfound->val;
+ }
+ /*
+ * Can't find it as a long option. If this is not getopt_long_only, or
+ * the option starts with '--' or is not a valid short option, then
+ * it's an error. Otherwise interpret it as a short option.
+ */
+ if (print_errors) {
+ if (argv[d->custom_optind][1] == '-') {
+ /* --option */
+ fprintf(stderr,
+ "%s: unrecognized option `--%s'\n",
+ argv[0], d->nextchar);
+ } else {
+ /* +option or -option */
+ fprintf(stderr,
+ "%s: unrecognized option `%c%s'\n",
+ argv[0], argv[d->custom_optind][0],
+ d->nextchar);
+ }
+ }
+ d->nextchar = (char *) "";
+ d->custom_optind++;
+ d->custom_optopt = 0;
+ return '?';
+}
+
+static int check_short_opt(int argc, char *const *argv, const char *optstring,
+ int print_errors, struct custom_getopt_data *d)
+{
+ char c = *d->nextchar++;
+ char *temp = strchr(optstring, c);
+
+ /* Increment `custom_optind' when we start to process its last character. */
+ if (*d->nextchar == '\0')
+ ++d->custom_optind;
+ if (!temp || c == ':') {
+ if (print_errors)
+ fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
+
+ d->custom_optopt = c;
+ return '?';
+ }
+ if (temp[1] == ':') {
+ if (temp[2] == ':') {
+ /* This is an option that accepts an argument optionally. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ d->custom_optind++;
+ } else
+ d->custom_optarg = NULL;
+ d->nextchar = NULL;
+ } else {
+ /* This is an option that requires an argument. */
+ if (*d->nextchar != '\0') {
+ d->custom_optarg = d->nextchar;
+ /*
+ * If we end this ARGV-element by taking the
+ * rest as an arg, we must advance to the next
+ * element now.
+ */
+ d->custom_optind++;
+ } else if (d->custom_optind == argc) {
+ if (print_errors) {
+ fprintf(stderr,
+ "%s: option requires an argument -- %c\n",
+ argv[0], c);
+ }
+ d->custom_optopt = c;
+ if (optstring[0] == ':')
+ c = ':';
+ else
+ c = '?';
+ } else
+ /*
+ * We already incremented `custom_optind' once;
+ * increment it again when taking next ARGV-elt
+ * as argument.
+ */
+ d->custom_optarg = argv[d->custom_optind++];
+ d->nextchar = NULL;
+ }
+ }
+ return c;
+}
+
+/*
+ * Scan elements of ARGV for option characters given in OPTSTRING.
+ *
+ * If an element of ARGV starts with '-', and is not exactly "-" or "--",
+ * then it is an option element. The characters of this element
+ * (aside from the initial '-') are option characters. If `getopt'
+ * is called repeatedly, it returns successively each of the option characters
+ * from each of the option elements.
+ *
+ * If `getopt' finds another option character, it returns that character,
+ * updating `custom_optind' and `nextchar' so that the next call to `getopt' can
+ * resume the scan with the following option character or ARGV-element.
+ *
+ * If there are no more option characters, `getopt' returns -1.
+ * Then `custom_optind' is the index in ARGV of the first ARGV-element
+ * that is not an option. (The ARGV-elements have been permuted
+ * so that those that are not options now come last.)
+ *
+ * OPTSTRING is a string containing the legitimate option characters.
+ * If an option character is seen that is not listed in OPTSTRING,
+ * return '?' after printing an error message. If you set `custom_opterr' to
+ * zero, the error message is suppressed but we still return '?'.
+ *
+ * If a char in OPTSTRING is followed by a colon, that means it wants an arg,
+ * so the following text in the same ARGV-element, or the text of the following
+ * ARGV-element, is returned in `custom_optarg'. Two colons mean an option that
+ * wants an optional arg; if there is text in the current ARGV-element,
+ * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero.
+ *
+ * If OPTSTRING starts with `-' or `+', it requests different methods of
+ * handling the non-option ARGV-elements.
+ * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
+ *
+ * Long-named options begin with `--' instead of `-'.
+ * Their names may be abbreviated as long as the abbreviation is unique
+ * or is an exact match for some defined option. If they have an
+ * argument, it follows the option name in the same ARGV-element, separated
+ * from the option name by a `=', or else the in next ARGV-element.
+ * When `getopt' finds a long-named option, it returns 0 if that option's
+ * `flag' field is nonzero, the value of the option's `val' field
+ * if the `flag' field is zero.
+ *
+ * The elements of ARGV aren't really const, because we permute them.
+ * But we pretend they're const in the prototype to be compatible
+ * with other systems.
+ *
+ * LONGOPTS is a vector of `struct option' terminated by an
+ * element containing a name which is zero.
+ *
+ * LONGIND returns the index in LONGOPT of the long-named option found.
+ * It is only valid when a long-named option has been found by the most
+ * recent call.
+ *
+ * Return the option character from OPTS just read. Return -1 when there are
+ * no more options. For unrecognized options, or options missing arguments,
+ * `custom_optopt' is set to the option letter, and '?' is returned.
+ *
+ * The OPTS string is a list of characters which are recognized option letters,
+ * optionally followed by colons, specifying that that letter takes an
+ * argument, to be placed in `custom_optarg'.
+ *
+ * If a letter in OPTS is followed by two colons, its argument is optional.
+ * This behavior is specific to the GNU `getopt'.
+ *
+ * The argument `--' causes premature termination of argument scanning,
+ * explicitly telling `getopt' that there are no more options. If OPTS begins
+ * with `--', then non-option arguments are treated as arguments to the option
+ * '\0'. This behavior is specific to the GNU `getopt'.
+ */
+
+static int getopt_internal_r(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind,
+ struct custom_getopt_data *d)
+{
+ int ret, print_errors = d->custom_opterr;
+
+ if (optstring[0] == ':')
+ print_errors = 0;
+ if (argc < 1)
+ return -1;
+ d->custom_optarg = NULL;
+
+ /*
+ * This is a big difference with GNU getopt, since optind == 0
+ * means initialization while here 1 means first call.
+ */
+ if (d->custom_optind == 0 || !d->initialized) {
+ if (d->custom_optind == 0)
+ d->custom_optind = 1; /* Don't scan ARGV[0], the program name. */
+ custom_getopt_initialize(d);
+ }
+ if (d->nextchar == NULL || *d->nextchar == '\0') {
+ ret = shuffle_argv(argc, argv, longopts, d);
+ if (ret)
+ return ret;
+ }
+ if (longopts && (argv[d->custom_optind][1] == '-' ))
+ return check_long_opt(argc, argv, optstring, longopts,
+ longind, print_errors, d);
+ return check_short_opt(argc, argv, optstring, print_errors, d);
+}
+
+static int custom_getopt_internal(int argc, char *const *argv, const char *optstring,
+ const struct option *longopts, int *longind)
+{
+ int result;
+ /* Keep a global copy of all internal members of d */
+ static struct custom_getopt_data d;
+
+ d.custom_optind = custom_optind;
+ d.custom_opterr = custom_opterr;
+ result = getopt_internal_r(argc, argv, optstring, longopts,
+ longind, &d);
+ custom_optind = d.custom_optind;
+ custom_optarg = d.custom_optarg;
+ custom_optopt = d.custom_optopt;
+ return result;
+}
+
+static int custom_getopt_long (int argc, char *const *argv, const char *options,
+ const struct option *long_options, int *opt_index)
+{
+ return custom_getopt_internal(argc, argv, options, long_options,
+ opt_index);
+}
+
+
+static char *package_name = 0;
+
+/**
+ * @brief updates an option
+ * @param field the generic pointer to the field to update
+ * @param orig_field the pointer to the orig field
+ * @param field_given the pointer to the number of occurrence of this option
+ * @param prev_given the pointer to the number of occurrence already seen
+ * @param value the argument for this option (if null no arg was specified)
+ * @param possible_values the possible values for this option (if specified)
+ * @param default_value the default value (in case the option only accepts fixed values)
+ * @param arg_type the type of this option
+ * @param check_ambiguity @see cmdline_parser_clitkResampleImage_params.check_ambiguity
+ * @param override @see cmdline_parser_clitkResampleImage_params.override
+ * @param no_free whether to free a possible previous value
+ * @param multiple_option whether this is a multiple option
+ * @param long_opt the corresponding long option
+ * @param short_opt the corresponding short option (or '-' if none)
+ * @param additional_error possible further error specification
+ */
+static
+int update_arg(void *field, char **orig_field,
+ unsigned int *field_given, unsigned int *prev_given,
+ char *value, char *possible_values[], const char *default_value,
+ cmdline_parser_clitkResampleImage_arg_type arg_type,
+ int check_ambiguity, int override,
+ int no_free, int multiple_option,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *stop_char = 0;
+ const char *val = value;
+ int found;
+ char **string_field;
+
+ stop_char = 0;
+ found = 0;
+
+ if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
+ {
+ if (short_opt != '-')
+ fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
+ package_name, long_opt, short_opt,
+ (additional_error ? additional_error : ""));
+ else
+ fprintf (stderr, "%s: `--%s' option given more than once%s\n",
+ package_name, long_opt,
+ (additional_error ? additional_error : ""));
+ return 1; /* failure */
+ }
+
+
+ if (field_given && *field_given && ! override)
+ return 0;
+ if (prev_given)
+ (*prev_given)++;
+ if (field_given)
+ (*field_given)++;
+ if (possible_values)
+ val = possible_values[found];
+
+ switch(arg_type) {
+ case ARG_FLAG:
+ *((int *)field) = !*((int *)field);
+ break;
+ case ARG_INT:
+ if (val) *((int *)field) = strtol (val, &stop_char, 0);
+ break;
+ case ARG_FLOAT:
+ if (val) *((float *)field) = (float)strtod (val, &stop_char);
+ break;
+ case ARG_STRING:
+ if (val) {
+ string_field = (char **)field;
+ if (!no_free && *string_field)
+ free (*string_field); /* free previous string */
+ *string_field = gengetopt_strdup (val);
+ }
+ break;
+ default:
+ break;
+ };
+
+ /* check numeric conversion */
+ switch(arg_type) {
+ case ARG_INT:
+ case ARG_FLOAT:
+ if (val && !(stop_char && *stop_char == '\0')) {
+ fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
+ return 1; /* failure */
+ }
+ break;
+ default:
+ ;
+ };
+
+ /* store the original value */
+ switch(arg_type) {
+ case ARG_NO:
+ case ARG_FLAG:
+ break;
+ default:
+ if (value && orig_field) {
+ if (no_free) {
+ *orig_field = value;
+ } else {
+ if (*orig_field)
+ free (*orig_field); /* free previous string */
+ *orig_field = gengetopt_strdup (value);
+ }
+ }
+ };
+
+ return 0; /* OK */
+}
+
+/**
+ * @brief store information about a multiple option in a temporary list
+ * @param list where to (temporarily) store multiple options
+ */
+static
+int update_multiple_arg_temp(struct generic_list **list,
+ unsigned int *prev_given, const char *val,
+ char *possible_values[], const char *default_value,
+ cmdline_parser_clitkResampleImage_arg_type arg_type,
+ const char *long_opt, char short_opt,
+ const char *additional_error)
+{
+ char *multi_token, *multi_next; /* store single arguments */
+
+ if (arg_type == ARG_NO) {
+ (*prev_given)++;
+ return 0; /* OK */
+ }
+
+ multi_token = get_multiple_arg_token(val);
+ multi_next = get_multiple_arg_token_next (val);
+
+ while (1)
+ {
+ add_node (list);
+ if (update_arg((void *)&((*list)->arg), &((*list)->orig), 0,
+ prev_given, multi_token, possible_values, default_value,
+ arg_type, 0, 1, 1, 1, long_opt, short_opt, additional_error)) {
+ if (multi_token) free(multi_token);
+ return 1; /* failure */
+ }
+
+ if (multi_next)
+ {
+ multi_token = get_multiple_arg_token(multi_next);
+ multi_next = get_multiple_arg_token_next (multi_next);
+ }
+ else
+ break;
+ }
+
+ return 0; /* OK */
+}
+
+/**
+ * @brief free the passed list (including possible string argument)
+ */
+static
+void free_list(struct generic_list *list, short string_arg)
+{
+ if (list) {
+ struct generic_list *tmp;
+ while (list)
+ {
+ tmp = list;
+ if (string_arg && list->arg.string_arg)
+ free (list->arg.string_arg);
+ if (list->orig)
+ free (list->orig);
+ list = list->next;
+ free (tmp);
+ }
+ }
+}
+
+/**
+ * @brief updates a multiple option starting from the passed list
+ */
+static
+void update_multiple_arg(void *field, char ***orig_field,
+ unsigned int field_given, unsigned int prev_given, union generic_value *default_value,
+ cmdline_parser_clitkResampleImage_arg_type arg_type,
+ struct generic_list *list)
+{
+ int i;
+ struct generic_list *tmp;
+
+ if (prev_given && list) {
+ *orig_field = (char **) realloc (*orig_field, (field_given + prev_given) * sizeof (char *));
+
+ switch(arg_type) {
+ case ARG_INT:
+ *((int **)field) = (int *)realloc (*((int **)field), (field_given + prev_given) * sizeof (int)); break;
+ case ARG_FLOAT:
+ *((float **)field) = (float *)realloc (*((float **)field), (field_given + prev_given) * sizeof (float)); break;
+ case ARG_STRING:
+ *((char ***)field) = (char **)realloc (*((char ***)field), (field_given + prev_given) * sizeof (char *)); break;
+ default:
+ break;
+ };
+
+ for (i = (prev_given - 1); i >= 0; --i)
+ {
+ tmp = list;
+
+ switch(arg_type) {
+ case ARG_INT:
+ (*((int **)field))[i + field_given] = tmp->arg.int_arg; break;
+ case ARG_FLOAT:
+ (*((float **)field))[i + field_given] = tmp->arg.float_arg; break;
+ case ARG_STRING:
+ (*((char ***)field))[i + field_given] = tmp->arg.string_arg; break;
+ default:
+ break;
+ }
+ (*orig_field) [i + field_given] = list->orig;
+ list = list->next;
+ free (tmp);
+ }
+ } else { /* set the default value */
+ if (default_value && ! field_given) {
+ switch(arg_type) {
+ case ARG_INT:
+ if (! *((int **)field)) {
+ *((int **)field) = (int *)malloc (sizeof (int));
+ (*((int **)field))[0] = default_value->int_arg;
+ }
+ break;
+ case ARG_FLOAT:
+ if (! *((float **)field)) {
+ *((float **)field) = (float *)malloc (sizeof (float));
+ (*((float **)field))[0] = default_value->float_arg;
+ }
+ break;
+ case ARG_STRING:
+ if (! *((char ***)field)) {
+ *((char ***)field) = (char **)malloc (sizeof (char *));
+ (*((char ***)field))[0] = gengetopt_strdup(default_value->string_arg);
+ }
+ break;
+ default: break;
+ }
+ if (!(*orig_field)) {
+ *orig_field = (char **) malloc (sizeof (char *));
+ (*orig_field)[0] = NULL;
+ }
+ }
+ }
+}
+
+int
+cmdline_parser_clitkResampleImage_internal (int argc, char * const *argv, struct args_info_clitkResampleImage *args_info,
+ struct cmdline_parser_clitkResampleImage_params *params, const char *additional_error)
+{
+ int c; /* Character of the parsed option. */
+ union generic_value multiple_default_value;
+
+ struct generic_list * size_list = NULL;
+ struct generic_list * spacing_list = NULL;
+ struct generic_list * gauss_list = NULL;
+ int error = 0;
+ struct args_info_clitkResampleImage local_args_info;
+
+ int override;
+ int initialize;
+ int check_required;
+ int check_ambiguity;
+
+ package_name = argv[0];
+
+ override = params->override;
+ initialize = params->initialize;
+ check_required = params->check_required;
+ check_ambiguity = params->check_ambiguity;
+
+ if (initialize)
+ cmdline_parser_clitkResampleImage_init (args_info);
+
+ cmdline_parser_clitkResampleImage_init (&local_args_info);
+
+ optarg = 0;
+ optind = 0;
+ opterr = params->print_errors;
+ optopt = '?';
+
+ while (1)
+ {
+ int option_index = 0;
+
+ static struct option long_options[] = {
+ { "help", 0, NULL, 'h' },
+ { "version", 0, NULL, 'V' },
+ { "config", 1, NULL, 0 },
+ { "verbose", 0, NULL, 'v' },
+ { "imagetypes", 0, NULL, 0 },
+ { "thread", 1, NULL, 0 },
+ { "input", 1, NULL, 'i' },
+ { "output", 1, NULL, 'o' },
+ { "like", 1, NULL, 'l' },
+ { "size", 1, NULL, 0 },
+ { "spacing", 1, NULL, 0 },
+ { "default", 1, NULL, 'd' },
+ { "time", 0, NULL, 't' },
+ { "interp", 1, NULL, 0 },
+ { "order", 1, NULL, 'b' },
+ { "sampling", 1, NULL, 's' },
+ { "gauss", 1, NULL, 'g' },
+ { "autogauss", 0, NULL, 'a' },
+ { NULL, 0, NULL, 0 }
+ };
+
+ custom_optarg = optarg;
+ custom_optind = optind;
+ custom_opterr = opterr;
+ custom_optopt = optopt;
+
+ c = custom_getopt_long (argc, argv, "hVvi:o:l:d:tb:s:g:a", long_options, &option_index);
+
+ optarg = custom_optarg;
+ optind = custom_optind;
+ opterr = custom_opterr;
+ optopt = custom_optopt;
+
+ if (c == -1) break; /* Exit from `while (1)' loop. */
+
+ switch (c)
+ {
+ case 'h': /* Print help and exit. */
+ cmdline_parser_clitkResampleImage_print_help ();
+ cmdline_parser_clitkResampleImage_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'V': /* Print version and exit. */
+ cmdline_parser_clitkResampleImage_print_version ();
+ cmdline_parser_clitkResampleImage_free (&local_args_info);
+ exit (EXIT_SUCCESS);
+
+ case 'v': /* Verbose. */
+
+
+ if (update_arg((void *)&(args_info->verbose_flag), 0, &(args_info->verbose_given),
+ &(local_args_info.verbose_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "verbose", 'v',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'i': /* Input image filename. */
+
+
+ if (update_arg( (void *)&(args_info->input_arg),
+ &(args_info->input_orig), &(args_info->input_given),
+ &(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "input", 'i',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'o': /* Output image filename. */
+
+
+ if (update_arg( (void *)&(args_info->output_arg),
+ &(args_info->output_orig), &(args_info->output_given),
+ &(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "output", 'o',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'l': /* Resample like this image. */
+
+
+ if (update_arg( (void *)&(args_info->like_arg),
+ &(args_info->like_orig), &(args_info->like_given),
+ &(local_args_info.like_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "like", 'l',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'd': /* Default pixel value. */
+
+
+ if (update_arg( (void *)&(args_info->default_arg),
+ &(args_info->default_orig), &(args_info->default_given),
+ &(local_args_info.default_given), optarg, 0, "0.0", ARG_FLOAT,
+ check_ambiguity, override, 0, 0,
+ "default", 'd',
+ additional_error))
+ goto failure;
+
+ break;
+ case 't': /* Last Dimension Is Time -> do not resample it (auto on for 4D). */
+
+
+ if (update_arg((void *)&(args_info->time_flag), 0, &(args_info->time_given),
+ &(local_args_info.time_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "time", 't',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'b': /* BSpline ordre (range 0-5). */
+
+
+ if (update_arg( (void *)&(args_info->order_arg),
+ &(args_info->order_orig), &(args_info->order_given),
+ &(local_args_info.order_given), optarg, 0, "3", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "order", 'b',
+ additional_error))
+ goto failure;
+
+ break;
+ case 's': /* BLUT sampling value. */
+
+
+ if (update_arg( (void *)&(args_info->sampling_arg),
+ &(args_info->sampling_orig), &(args_info->sampling_given),
+ &(local_args_info.sampling_given), optarg, 0, "30", ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "sampling", 's',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'g': /* Apply Gaussian before (sigma in mm). */
+
+ if (update_multiple_arg_temp(&gauss_list,
+ &(local_args_info.gauss_given), optarg, 0, "0.0", ARG_FLOAT,
+ "gauss", 'g',
+ additional_error))
+ goto failure;
+
+ break;
+ case 'a': /* Apply Gaussian with auto sigma when downsample. */
+
+
+ if (update_arg((void *)&(args_info->autogauss_flag), 0, &(args_info->autogauss_given),
+ &(local_args_info.autogauss_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "autogauss", 'a',
+ additional_error))
+ goto failure;
+
+ break;
+
+ case 0: /* Long option with no short option */
+ /* Config file. */
+ if (strcmp (long_options[option_index].name, "config") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->config_arg),
+ &(args_info->config_orig), &(args_info->config_given),
+ &(local_args_info.config_given), optarg, 0, 0, ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "config", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Verbose: allowed image types. */
+ else if (strcmp (long_options[option_index].name, "imagetypes") == 0)
+ {
+
+
+ if (update_arg((void *)&(args_info->imagetypes_flag), 0, &(args_info->imagetypes_given),
+ &(local_args_info.imagetypes_given), optarg, 0, 0, ARG_FLAG,
+ check_ambiguity, override, 1, 0, "imagetypes", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Nb of thread to use (default=max). */
+ else if (strcmp (long_options[option_index].name, "thread") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->thread_arg),
+ &(args_info->thread_orig), &(args_info->thread_given),
+ &(local_args_info.thread_given), optarg, 0, 0, ARG_INT,
+ check_ambiguity, override, 0, 0,
+ "thread", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Number of pixels of each coordonate. */
+ else if (strcmp (long_options[option_index].name, "size") == 0)
+ {
+
+ if (update_multiple_arg_temp(&size_list,
+ &(local_args_info.size_given), optarg, 0, "0", ARG_INT,
+ "size", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Spacing in mm between pixels. */
+ else if (strcmp (long_options[option_index].name, "spacing") == 0)
+ {
+
+ if (update_multiple_arg_temp(&spacing_list,
+ &(local_args_info.spacing_given), optarg, 0, "-1.0", ARG_FLOAT,
+ "spacing", '-',
+ additional_error))
+ goto failure;
+
+ }
+ /* Interpolation type: {nn, linear, bspline, blut}. */
+ else if (strcmp (long_options[option_index].name, "interp") == 0)
+ {
+
+
+ if (update_arg( (void *)&(args_info->interp_arg),
+ &(args_info->interp_orig), &(args_info->interp_given),
+ &(local_args_info.interp_given), optarg, 0, "nn", ARG_STRING,
+ check_ambiguity, override, 0, 0,
+ "interp", '-',
+ additional_error))
+ goto failure;
+
+ }
+
+ break;
+ case '?': /* Invalid option. */
+ /* `getopt_long' already printed an error message. */
+ goto failure;
+
+ default: /* bug: option not considered. */
+ fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE, c, (additional_error ? additional_error : ""));
+ abort ();
+ } /* switch */
+ } /* while */
+
+
+ update_multiple_arg((void *)&(args_info->size_arg),
+ &(args_info->size_orig), args_info->size_given,
+ local_args_info.size_given, 0 ,
+ ARG_INT, size_list);
+ multiple_default_value.float_arg = -1.0;
+ update_multiple_arg((void *)&(args_info->spacing_arg),
+ &(args_info->spacing_orig), args_info->spacing_given,
+ local_args_info.spacing_given, &multiple_default_value ,
+ ARG_FLOAT, spacing_list);
+ multiple_default_value.float_arg = 0.0;
+ update_multiple_arg((void *)&(args_info->gauss_arg),
+ &(args_info->gauss_orig), args_info->gauss_given,
+ local_args_info.gauss_given, &multiple_default_value ,
+ ARG_FLOAT, gauss_list);
+
+ args_info->size_given += local_args_info.size_given;
+ local_args_info.size_given = 0;
+ args_info->spacing_given += local_args_info.spacing_given;
+ local_args_info.spacing_given = 0;
+ args_info->gauss_given += local_args_info.gauss_given;
+ local_args_info.gauss_given = 0;
+
+ if (check_required)
+ {
+ error += cmdline_parser_clitkResampleImage_required2 (args_info, argv[0], additional_error);
+ }
+
+ cmdline_parser_clitkResampleImage_release (&local_args_info);
+
+ if ( error )
+ return (EXIT_FAILURE);
+
+ if (optind < argc)
+ {
+ int i = 0 ;
+ int found_prog_name = 0;
+ /* whether program name, i.e., argv[0], is in the remaining args
+ (this may happen with some implementations of getopt,
+ but surely not with the one included by gengetopt) */
+
+
+ args_info->inputs_num = argc - optind - found_prog_name;
+ args_info->inputs =
+ (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+ while (optind < argc)
+ args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
+ }
+
+ return 0;
+
+failure:
+ free_list (size_list, 0 );
+ free_list (spacing_list, 0 );
+ free_list (gauss_list, 0 );
+
+ cmdline_parser_clitkResampleImage_release (&local_args_info);
+ return (EXIT_FAILURE);
+}
+
+#ifndef CONFIG_FILE_LINE_SIZE
+#define CONFIG_FILE_LINE_SIZE 2048
+#endif
+#define ADDITIONAL_ERROR " in configuration file "
+
+#define CONFIG_FILE_LINE_BUFFER_SIZE (CONFIG_FILE_LINE_SIZE+3)
+/* 3 is for "--" and "=" */
+
+static int
+_cmdline_parser_clitkResampleImage_configfile (char * const filename, int *my_argc)
+{
+ FILE* file;
+ char my_argv[CONFIG_FILE_LINE_BUFFER_SIZE+1];
+ char linebuf[CONFIG_FILE_LINE_SIZE];
+ int line_num = 0;
+ int result = 0, equal;
+ char *fopt, *farg;
+ char *str_index;
+ size_t len, next_token;
+ char delimiter;
+
+ if ((file = fopen(filename, "r")) == NULL)
+ {
+ fprintf (stderr, "%s: Error opening configuration file '%s'\n",
+ CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE, filename);
+ return EXIT_FAILURE;
+ }
+
+ while ((fgets(linebuf, CONFIG_FILE_LINE_SIZE, file)) != NULL)
+ {
+ ++line_num;
+ my_argv[0] = '\0';
+ len = strlen(linebuf);
+ if (len > (CONFIG_FILE_LINE_BUFFER_SIZE-1))
+ {
+ fprintf (stderr, "%s:%s:%d: Line too long in configuration file\n",
+ CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+
+ /* find first non-whitespace character in the line */
+ next_token = strspn (linebuf, " \t\r\n");
+ str_index = linebuf + next_token;
+
+ if ( str_index[0] == '\0' || str_index[0] == '#')
+ continue; /* empty line or comment line is skipped */
+
+ fopt = str_index;
+
+ /* truncate fopt at the end of the first non-valid character */
+ next_token = strcspn (fopt, " \t\r\n=");
+
+ if (fopt[next_token] == '\0') /* the line is over */
+ {
+ farg = NULL;
+ equal = 0;
+ goto noarg;
+ }
+
+ /* remember if equal sign is present */
+ equal = (fopt[next_token] == '=');
+ fopt[next_token++] = '\0';
+
+ /* advance pointers to the next token after the end of fopt */
+ next_token += strspn (fopt + next_token, " \t\r\n");
+
+ /* check for the presence of equal sign, and if so, skip it */
+ if ( !equal )
+ if ((equal = (fopt[next_token] == '=')))
+ {
+ next_token++;
+ next_token += strspn (fopt + next_token, " \t\r\n");
+ }
+ str_index += next_token;
+
+ /* find argument */
+ farg = str_index;
+ if ( farg[0] == '\"' || farg[0] == '\'' )
+ { /* quoted argument */
+ str_index = strchr (++farg, str_index[0] ); /* skip opening quote */
+ if (! str_index)
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: unterminated string in configuration file\n",
+ CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+ else
+ { /* read up the remaining part up to a delimiter */
+ next_token = strcspn (farg, " \t\r\n#\'\"");
+ str_index += next_token;
+ }
+
+ /* truncate farg at the delimiter and store it for further check */
+ delimiter = *str_index, *str_index++ = '\0';
+
+ /* everything but comment is illegal at the end of line */
+ if (delimiter != '\0' && delimiter != '#')
+ {
+ str_index += strspn(str_index, " \t\r\n");
+ if (*str_index != '\0' && *str_index != '#')
+ {
+ fprintf
+ (stderr,
+ "%s:%s:%d: malformed string in configuration file\n",
+ CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE, filename, line_num);
+ result = EXIT_FAILURE;
+ break;
+ }
+ }
+
+ noarg:
+ if (!strcmp(fopt,"include")) {
+ if (farg && *farg) {
+ result = _cmdline_parser_clitkResampleImage_configfile(farg, my_argc);
+ } else {
+ fprintf(stderr, "%s:%s:%d: include requires a filename argument.\n",
+ CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE, filename, line_num);
+ }
+ continue;
+ }
+ len = strlen(fopt);
+ strcat (my_argv, len > 1 ? "--" : "-");
+ strcat (my_argv, fopt);
+ if (len > 1 && ((farg && *farg) || equal))
+ strcat (my_argv, "=");
+ if (farg && *farg)
+ strcat (my_argv, farg);
+ ++(*my_argc);
+
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup(my_argv);
+ } /* while */
+
+ if (file)
+ fclose(file);
+ return result;
+}
+
+int
+cmdline_parser_clitkResampleImage_configfile (char * const filename,
+ struct args_info_clitkResampleImage *args_info,
+ int override, int initialize, int check_required)
+{
+ struct cmdline_parser_clitkResampleImage_params params;
+
+ params.override = override;
+ params.initialize = initialize;
+ params.check_required = check_required;
+ params.check_ambiguity = 0;
+ params.print_errors = 1;
+
+ return cmdline_parser_clitkResampleImage_config_file (filename, args_info, ¶ms);
+}
+
+int
+cmdline_parser_clitkResampleImage_config_file (char * const filename,
+ struct args_info_clitkResampleImage *args_info,
+ struct cmdline_parser_clitkResampleImage_params *params)
+{
+ int i, result;
+ int my_argc = 1;
+ char **my_argv_arg;
+ char *additional_error;
+
+ /* store the program name */
+ cmd_line_list_tmp = (struct line_list *) malloc (sizeof (struct line_list));
+ cmd_line_list_tmp->next = cmd_line_list;
+ cmd_line_list = cmd_line_list_tmp;
+ cmd_line_list->string_arg = gengetopt_strdup (CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE);
+
+ result = _cmdline_parser_clitkResampleImage_configfile(filename, &my_argc);
+
+ if (result != EXIT_FAILURE) {
+ my_argv_arg = (char **) malloc((my_argc+1) * sizeof(char *));
+ cmd_line_list_tmp = cmd_line_list;
+
+ for (i = my_argc - 1; i >= 0; --i) {
+ my_argv_arg[i] = cmd_line_list_tmp->string_arg;
+ cmd_line_list_tmp = cmd_line_list_tmp->next;
+ }
+
+ my_argv_arg[my_argc] = 0;
+
+ additional_error = (char *)malloc(strlen(filename) + strlen(ADDITIONAL_ERROR) + 1);
+ strcpy (additional_error, ADDITIONAL_ERROR);
+ strcat (additional_error, filename);
+ result =
+ cmdline_parser_clitkResampleImage_internal (my_argc, my_argv_arg, args_info,
+ params,
+ additional_error);
+
+ free (additional_error);
+ free (my_argv_arg);
+ }
+
+ free_cmd_list();
+ if (result == EXIT_FAILURE)
+ {
+ cmdline_parser_clitkResampleImage_free (args_info);
+ exit (EXIT_FAILURE);
+ }
+
+ return result;
+}
--- /dev/null
+/** @file clitkResampleImage_ggo.h
+ * @brief The header file for the command line option parser
+ * generated by GNU Gengetopt version 2.22
+ * http://www.gnu.org/software/gengetopt.
+ * DO NOT modify this file, since it can be overwritten
+ * @author GNU Gengetopt by Lorenzo Bettini */
+
+#ifndef CLITKRESAMPLEIMAGE_GGO_H
+#define CLITKRESAMPLEIMAGE_GGO_H
+
+/* If we use autoconf. */
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h> /* for FILE */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE
+/** @brief the program name */
+#define CMDLINE_PARSER_CLITKRESAMPLEIMAGE_PACKAGE "clitkResampleImage"
+#endif
+
+#ifndef CMDLINE_PARSER_CLITKRESAMPLEIMAGE_VERSION
+/** @brief the program version */
+#define CMDLINE_PARSER_CLITKRESAMPLEIMAGE_VERSION "2.0"
+#endif
+
+/** @brief Where the command line options are stored */
+struct args_info_clitkResampleImage
+{
+ const char *help_help; /**< @brief Print help and exit help description. */
+ const char *version_help; /**< @brief Print version and exit help description. */
+ char * config_arg; /**< @brief Config file. */
+ char * config_orig; /**< @brief Config file original value given at command line. */
+ const char *config_help; /**< @brief Config file help description. */
+ int verbose_flag; /**< @brief Verbose (default=off). */
+ const char *verbose_help; /**< @brief Verbose help description. */
+ int imagetypes_flag; /**< @brief Verbose: allowed image types (default=off). */
+ const char *imagetypes_help; /**< @brief Verbose: allowed image types help description. */
+ int thread_arg; /**< @brief Nb of thread to use (default=max). */
+ char * thread_orig; /**< @brief Nb of thread to use (default=max) original value given at command line. */
+ const char *thread_help; /**< @brief Nb of thread to use (default=max) help description. */
+ char * input_arg; /**< @brief Input image filename. */
+ char * input_orig; /**< @brief Input image filename original value given at command line. */
+ const char *input_help; /**< @brief Input image filename help description. */
+ char * output_arg; /**< @brief Output image filename. */
+ char * output_orig; /**< @brief Output image filename original value given at command line. */
+ const char *output_help; /**< @brief Output image filename help description. */
+ char * like_arg; /**< @brief Resample like this image. */
+ char * like_orig; /**< @brief Resample like this image original value given at command line. */
+ const char *like_help; /**< @brief Resample like this image help description. */
+ int* size_arg; /**< @brief Number of pixels of each coordonate (default='0'). */
+ char ** size_orig; /**< @brief Number of pixels of each coordonate original value given at command line. */
+ int size_min; /**< @brief Number of pixels of each coordonate's minimum occurreces */
+ int size_max; /**< @brief Number of pixels of each coordonate's maximum occurreces */
+ const char *size_help; /**< @brief Number of pixels of each coordonate help description. */
+ float* spacing_arg; /**< @brief Spacing in mm between pixels (default='-1.0'). */
+ char ** spacing_orig; /**< @brief Spacing in mm between pixels original value given at command line. */
+ int spacing_min; /**< @brief Spacing in mm between pixels's minimum occurreces */
+ int spacing_max; /**< @brief Spacing in mm between pixels's maximum occurreces */
+ const char *spacing_help; /**< @brief Spacing in mm between pixels help description. */
+ float default_arg; /**< @brief Default pixel value (default='0.0'). */
+ char * default_orig; /**< @brief Default pixel value original value given at command line. */
+ const char *default_help; /**< @brief Default pixel value help description. */
+ int time_flag; /**< @brief Last Dimension Is Time -> do not resample it (auto on for 4D) (default=off). */
+ const char *time_help; /**< @brief Last Dimension Is Time -> do not resample it (auto on for 4D) help description. */
+ char * interp_arg; /**< @brief Interpolation type: {nn, linear, bspline, blut} (default='nn'). */
+ char * interp_orig; /**< @brief Interpolation type: {nn, linear, bspline, blut} original value given at command line. */
+ const char *interp_help; /**< @brief Interpolation type: {nn, linear, bspline, blut} help description. */
+ int order_arg; /**< @brief BSpline ordre (range 0-5) (default='3'). */
+ char * order_orig; /**< @brief BSpline ordre (range 0-5) original value given at command line. */
+ const char *order_help; /**< @brief BSpline ordre (range 0-5) help description. */
+ int sampling_arg; /**< @brief BLUT sampling value (default='30'). */
+ char * sampling_orig; /**< @brief BLUT sampling value original value given at command line. */
+ const char *sampling_help; /**< @brief BLUT sampling value help description. */
+ float* gauss_arg; /**< @brief Apply Gaussian before (sigma in mm) (default='0.0'). */
+ char ** gauss_orig; /**< @brief Apply Gaussian before (sigma in mm) original value given at command line. */
+ int gauss_min; /**< @brief Apply Gaussian before (sigma in mm)'s minimum occurreces */
+ int gauss_max; /**< @brief Apply Gaussian before (sigma in mm)'s maximum occurreces */
+ const char *gauss_help; /**< @brief Apply Gaussian before (sigma in mm) help description. */
+ int autogauss_flag; /**< @brief Apply Gaussian with auto sigma when downsample (default=off). */
+ const char *autogauss_help; /**< @brief Apply Gaussian with auto sigma when downsample help description. */
+
+ unsigned int help_given ; /**< @brief Whether help was given. */
+ unsigned int version_given ; /**< @brief Whether version was given. */
+ unsigned int config_given ; /**< @brief Whether config was given. */
+ unsigned int verbose_given ; /**< @brief Whether verbose was given. */
+ unsigned int imagetypes_given ; /**< @brief Whether imagetypes was given. */
+ unsigned int thread_given ; /**< @brief Whether thread was given. */
+ unsigned int input_given ; /**< @brief Whether input was given. */
+ unsigned int output_given ; /**< @brief Whether output was given. */
+ unsigned int like_given ; /**< @brief Whether like was given. */
+ unsigned int size_given ; /**< @brief Whether size was given. */
+ unsigned int spacing_given ; /**< @brief Whether spacing was given. */
+ unsigned int default_given ; /**< @brief Whether default was given. */
+ unsigned int time_given ; /**< @brief Whether time was given. */
+ unsigned int interp_given ; /**< @brief Whether interp was given. */
+ unsigned int order_given ; /**< @brief Whether order was given. */
+ unsigned int sampling_given ; /**< @brief Whether sampling was given. */
+ unsigned int gauss_given ; /**< @brief Whether gauss was given. */
+ unsigned int autogauss_given ; /**< @brief Whether autogauss was given. */
+
+ char **inputs ; /**< @brief unamed options (options without names) */
+ unsigned inputs_num ; /**< @brief unamed options number */
+} ;
+
+/** @brief The additional parameters to pass to parser functions */
+struct cmdline_parser_clitkResampleImage_params
+{
+ int override; /**< @brief whether to override possibly already present options (default 0) */
+ int initialize; /**< @brief whether to initialize the option structure args_info_clitkResampleImage (default 1) */
+ int check_required; /**< @brief whether to check that all required options were provided (default 1) */
+ int check_ambiguity; /**< @brief whether to check for options already specified in the option structure args_info_clitkResampleImage (default 0) */
+ int print_errors; /**< @brief whether getopt_long should print an error message for a bad option (default 1) */
+} ;
+
+/** @brief the purpose string of the program */
+extern const char *args_info_clitkResampleImage_purpose;
+/** @brief the usage string of the program */
+extern const char *args_info_clitkResampleImage_usage;
+/** @brief all the lines making the help output */
+extern const char *args_info_clitkResampleImage_help[];
+
+/**
+ * The command line parser
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkResampleImage (int argc, char * const *argv,
+ struct args_info_clitkResampleImage *args_info);
+
+/**
+ * The command line parser (version with additional parameters - deprecated)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkResampleImage_ext() instead
+ */
+int cmdline_parser_clitkResampleImage2 (int argc, char * const *argv,
+ struct args_info_clitkResampleImage *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The command line parser (version with additional parameters)
+ * @param argc the number of command line options
+ * @param argv the command line options
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkResampleImage_ext (int argc, char * const *argv,
+ struct args_info_clitkResampleImage *args_info,
+ struct cmdline_parser_clitkResampleImage_params *params);
+
+/**
+ * Save the contents of the option struct into an already open FILE stream.
+ * @param outfile the stream where to dump options
+ * @param args_info the option struct to dump
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkResampleImage_dump(FILE *outfile,
+ struct args_info_clitkResampleImage *args_info);
+
+/**
+ * Save the contents of the option struct into a (text) file.
+ * This file can be read by the config file parser (if generated by gengetopt)
+ * @param filename the file where to save
+ * @param args_info the option struct to save
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkResampleImage_file_save(const char *filename,
+ struct args_info_clitkResampleImage *args_info);
+
+/**
+ * Print the help
+ */
+void cmdline_parser_clitkResampleImage_print_help(void);
+/**
+ * Print the version
+ */
+void cmdline_parser_clitkResampleImage_print_version(void);
+
+/**
+ * Initializes all the fields a cmdline_parser_clitkResampleImage_params structure
+ * to their default values
+ * @param params the structure to initialize
+ */
+void cmdline_parser_clitkResampleImage_params_init(struct cmdline_parser_clitkResampleImage_params *params);
+
+/**
+ * Allocates dynamically a cmdline_parser_clitkResampleImage_params structure and initializes
+ * all its fields to their default values
+ * @return the created and initialized cmdline_parser_clitkResampleImage_params structure
+ */
+struct cmdline_parser_clitkResampleImage_params *cmdline_parser_clitkResampleImage_params_create(void);
+
+/**
+ * Initializes the passed args_info_clitkResampleImage structure's fields
+ * (also set default values for options that have a default)
+ * @param args_info the structure to initialize
+ */
+void cmdline_parser_clitkResampleImage_init (struct args_info_clitkResampleImage *args_info);
+/**
+ * Deallocates the string fields of the args_info_clitkResampleImage structure
+ * (but does not deallocate the structure itself)
+ * @param args_info the structure to deallocate
+ */
+void cmdline_parser_clitkResampleImage_free (struct args_info_clitkResampleImage *args_info);
+
+/**
+ * The config file parser (deprecated version)
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param override whether to override possibly already present options
+ * @param initialize whether to initialize the option structure my_args_info
+ * @param check_required whether to check that all required options were provided
+ * @return 0 if everything went fine, NON 0 if an error took place
+ * @deprecated use cmdline_parser_clitkResampleImage_config_file() instead
+ */
+int cmdline_parser_clitkResampleImage_configfile (char * const filename,
+ struct args_info_clitkResampleImage *args_info,
+ int override, int initialize, int check_required);
+
+/**
+ * The config file parser
+ * @param filename the name of the config file
+ * @param args_info the structure where option information will be stored
+ * @param params additional parameters for the parser
+ * @return 0 if everything went fine, NON 0 if an error took place
+ */
+int cmdline_parser_clitkResampleImage_config_file (char * const filename,
+ struct args_info_clitkResampleImage *args_info,
+ struct cmdline_parser_clitkResampleImage_params *params);
+
+/**
+ * Checks that all the required options were specified
+ * @param args_info the structure to check
+ * @param prog_name the name of the program that will be used to print
+ * possible errors
+ * @return
+ */
+int cmdline_parser_clitkResampleImage_required (struct args_info_clitkResampleImage *args_info,
+ const char *prog_name);
+
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+#endif /* CLITKRESAMPLEIMAGE_GGO_H */
--- /dev/null
+#include "vvToolMedianFilter.h"
+extern const vvToolCreator<vvToolMedianFilter> *dummyvvToolMedianFilter;
+const vvToolCreator<vvToolMedianFilter> *dummyvvToolMedianFilter2 = dummyvvToolMedianFilter;
+
+#include "vvToolRigidReg.h"
+extern const vvToolCreator<vvToolRigidReg> *dummyvvToolRigidReg;
+const vvToolCreator<vvToolRigidReg> *dummyvvToolRigidReg2 = dummyvvToolRigidReg;
+
+#include "vvToolCropImage.h"
+extern const vvToolCreator<vvToolCropImage> *dummyvvToolCropImage;
+const vvToolCreator<vvToolCropImage> *dummyvvToolCropImage2 = dummyvvToolCropImage;
+
+#include "vvToolBinarize.h"
+extern const vvToolCreator<vvToolBinarize> *dummyvvToolBinarize;
+const vvToolCreator<vvToolBinarize> *dummyvvToolBinarize2 = dummyvvToolBinarize;
+
+#include "vvToolImageArithm.h"
+extern const vvToolCreator<vvToolImageArithm> *dummyvvToolImageArithm;
+const vvToolCreator<vvToolImageArithm> *dummyvvToolImageArithm2 = dummyvvToolImageArithm;
+
+#include "vvToolResample.h"
+extern const vvToolCreator<vvToolResample> *dummyvvToolResample;
+const vvToolCreator<vvToolResample> *dummyvvToolResample2 = dummyvvToolResample;
+
+#include "vvToolMIP.h"
+extern const vvToolCreator<vvToolMIP> *dummyvvToolMIP;
+const vvToolCreator<vvToolMIP> *dummyvvToolMIP2 = dummyvvToolMIP;
+
+#include "vvToolConvert.h"
+extern const vvToolCreator<vvToolConvert> *dummyvvToolConvert;
+const vvToolCreator<vvToolConvert> *dummyvvToolConvert2 = dummyvvToolConvert;
+
+#include "vvToolROIManager.h"
+extern const vvToolCreator<vvToolROIManager> *dummyvvToolROIManager;
+const vvToolCreator<vvToolROIManager> *dummyvvToolROIManager2 = dummyvvToolROIManager;
+
+#include "vvToolSegmentation.h"
+extern const vvToolCreator<vvToolSegmentation> *dummyvvToolSegmentation;
+const vvToolCreator<vvToolSegmentation> *dummyvvToolSegmentation2 = dummyvvToolSegmentation;
+
+#include "vvToolProfile.h"
+extern const vvToolCreator<vvToolProfile> *dummyvvToolProfile;
+const vvToolCreator<vvToolProfile> *dummyvvToolProfile2 = dummyvvToolProfile;
+
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff