-/*
- 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;
-}