-#ifndef NKITKXDRIMAGEIO_CXX
-#define NKITKXDRIMAGEIO_CXX
-
/**
- * @file nkitkXDRImageIO.cxx
+ * @file clitkXdrImageIO.cxx
* @author Simon Rit <simon.rit@gmail.com>
* @date Sun Jun 1 22:12:20 2008
*
*
*/
-#include "nkitkXDRImageIO.h"
+#include "clitkXdrImageIO.h"
// std include
#include <iostream>
//defines
#define MAXDIM 5
-#define AVSerror(v) std::cerr << "Error in nkitk::XDRImageIO. Message:" << v << std::endl;
#ifdef _WIN32
#ifdef memicmp
#undef memicmp
20080414 lsp+mgw __sun__ doesn't know <io.h>
*/
-/************************************************************************/
-/* MODULE DOCUMENTATION */
-/************************************************************************/
-/*
- READ_XDR Read XDR file (may be compressed) into field
- name output field handle
- file_expression name of file
- numerical_expression start XDR data in file offset (default 0)
- NOTE: compressed XDR data may not be part of a larger file
-
- READ_XDR_HEADER Get entry from xdr header
- %name Output = string block
- file_expression file name default extension ''
- %string_expression name of element to load
-
- READ_XDR_PREVIEW Read and downsize XDR file (for bitmap)
- name output field handle
- file_expression name of file
- numerical_expression start XDR data in file offset (default 0)
- NOTE: this command is not supported for compressed XDR files
-
- ENUM_XDR_HEADER
- %name Output = string block
- file_expression file name default extension ''
- numerical_expression number of element to find name of
-*/
-/************************************************************************/
-/* INCLUDE FILES */
-/************************************************************************/
-
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <stdlib.h>
#include <ctype.h>
-#if 0
-#ifndef __sun__
-#include <io.h>
-#endif
-#include "mbavs2q.h"
-
-#ifndef QUIRT
-#include <memory.h>
-#include <avs/avs.h>
-#include <avs/field.h>
-#else
-#include "mbfield.h"
-#endif
-#endif
/************************************************************************/
/* DEFINES, ENUMERATED TYPES AND CONSTANTS */
"XDR file reading error",
"Out of memory",
"Decompression failed",
- "Format not handled by nkitkXDRImageIO (RECTILINEAR or IRREGULAR field)"
+ "Format not handled by clitkXdrImageIO (RECTILINEAR or IRREGULAR field)"
};
};
-/************************************************************************/
-/* PROTOTYPES */
-/************************************************************************/
-#if 0
-int Rxdr_compute(AVSfield** ppOut, char* pszFileName, int iOffset);
-
-int RxdrPreview_compute(AVSfield** ppOut, char* pszFileName, int iOffset);
-
-int RxdrHeader_compute(char *pszOut, char *pszFileName, char *pszEntry);
-
-int RxdrEnum_compute(char *pszOut, char *pszFileName, int iEntry);
-
-/******************************************************************************/
-/* AVS/QUIRT INTERFACE */
-/******************************************************************************/
-
-void Rxdr_desc(void)
-{
- int param;
-
- /* Set the module name and type */
- AVSset_module_name("XDR reader", MODULE_DATA);
-
- /* Create output ports for the resulting fields */
- AVScreate_output_port("Output", "field");
-
- /* declare widgets */
- QUIRT_NEXT_PARAMETER_FILE("");
- param = AVSadd_parameter("FileName", "string", "/data/AVS/", NULL, "");
- AVSconnect_widget(param, "browser");
- AVSadd_parameter_prop(param, "height", "integer", 8);
-
- param = AVSadd_parameter("Offset", "integer", 0, 0, INT_UNBOUND);
- AVSconnect_widget(param, "typein_integer");
-
- AVSset_compute_proc(CF Rxdr_compute);
-}
-AVS_TO_QUIRT(READ_XDR, Rxdr_desc);
-
-void RxdrPreview_desc(void)
-{
- int param;
-
- /* Set the module name and type */
- AVSset_module_name("XDR preview reader", MODULE_DATA);
-
- /* Create output ports for the resulting fields */
- AVScreate_output_port("Output", "field");
-
- /* declare widgets */
- QUIRT_NEXT_PARAMETER_FILE("");
- param = AVSadd_parameter("FileName", "string", "/data/AVS/", NULL, "");
- AVSconnect_widget(param, "browser");
- AVSadd_parameter_prop(param, "height", "integer", 8);
-
- param = AVSadd_parameter("Offset", "integer", 0, 0, INT_UNBOUND);
- AVSconnect_widget(param, "typein_integer");
-
- AVSset_compute_proc(CF RxdrPreview_compute);
-}
-AVS_TO_QUIRT(READ_XDR_PREVIEW, RxdrPreview_desc);
-
-void RxdrHeader_desc(void)
-{ /* Set the module name and type */
- AVSset_module_name("Read XDR header", MODULE_DATA);
-
- /* Create output ports for the resulting fields */
- AVSadd_parameter("Output", "string_block", "", NULL, "");
-
- QUIRT_NEXT_PARAMETER_FILE("");
- AVSadd_parameter("FileName", "string", "", NULL, "");
-
- AVSadd_parameter("Entry", "string", "", NULL, "");
-
- AVSset_compute_proc(CF RxdrHeader_compute);
-}
-AVS_TO_QUIRT(READ_XDR_HEADER, RxdrHeader_desc);
-
-void RxdrEnum_desc(void)
-{ /* Set the module name and type */
- AVSset_module_name("Enumerate XDR header", MODULE_DATA);
-
- /* Create output ports for the resulting fields */
- AVSadd_parameter("Output", "string_block", "", NULL, "");
-
- QUIRT_NEXT_PARAMETER_FILE("");
- AVSadd_parameter("FileName", "string", "", NULL, "");
-
- AVSadd_parameter("Entry", "integer", 0, INT_UNBOUND, INT_UNBOUND);
-
- AVSset_compute_proc(CF RxdrEnum_compute);
-}
-AVS_TO_QUIRT(ENUM_XDR_HEADER, RxdrEnum_desc);
-
-#ifndef QUIRT
-AVSinit_modules(void)
-{
- AVSmodule_from_desc( (int_desc_func)Rxdr_desc );
- AVSmodule_from_desc( (int_desc_func)RxdrHeader_desc );
- AVSmodule_from_desc( (int_desc_func)RxdrEnum_desc );
-}
-#endif
-#endif
/************************************************************************/
/* MODULE FUNCTIONS */
/************************************************************************/
return NULL;
}
-/* help routine, enumerates XDR file for names of keyword entrys, returns NULL
- if not found, else returns pointer to start of line upto '='
-*/
-// //Commented out because it does not seem to be needed for vv
-//static char *enum_header(char *file, int iEntry, int offset)
-//{
-// int i, count;
-// static char temp[512];
-// FILE *f;
-// char *p;
-//
-// if ((f = fopen(file, "rt")) == NULL) return NULL;
-// if (offset) fseek(f, offset, SEEK_SET);
-//
-// count = 0;
-//
-// for (i=0; i<200; )
-// {
-// if (fgets(temp, 500, f) == NULL ) break; /* end of file */
-//
-// if (temp[0] == 12 ) break; /* ^L end of header */
-// if (temp[0] != '#') i++; /* The first 200 non comment lines must be read before data is opened. */
-// if ((p = strchr(temp+1, '=')) == NULL) continue; /* no '=' */
-// if (count++ != iEntry) continue; /* no match */
-//
-// *p=0; /* match, end at = */
-//
-// fclose (f);
-// return temp;
-// }
-//
-// fclose(f);
-// return NULL;
-//}
-
-
static int get_nki_compressed_size(FILE *f)
{
NKI_MODE2 Header;
//====================================================================
// Read image information (copied from XDRreader)
-int nkitk::XDRImageIO::ReadImageInformationWithError()
+int clitk::XdrImageIO::ReadImageInformationWithError()
{
int offset=0;
itk::Vector<int,MAXDIM> dim;
- int veclen=1; //, data=AVS_TYPE_BYTE, field=UNIFORM;
-#if 0
- int iNkiCompression = 0;
-#endif
- int total=1/*, datasize=0, iNumRead, HeaderSize*/;
+ int veclen=1;
+ int total=1;
unsigned int coords=0,i,j,ndim,nspace;
char temp[512];
FILE *fstream;
char *c;
-#if 0
- char *buff;
- AVSfield FieldTemplate;
-#endif
+
long swap_test = 0x1000000; /* first byte is 1 when low-endian */
forcenoswap=0;
char *file = const_cast<char *>(m_FileName.c_str());
//====================================================================
// Read image information (copied from XDRreader)
-void nkitk::XDRImageIO::ReadImageInformation() {
+void clitk::XdrImageIO::ReadImageInformation() {
int result = ReadImageInformationWithError();
- if (result) ITKError("nkitk::XDRImageIO::ReadImageInformation",result);
+ if (result) ITKError("clitk::XdrImageIO::ReadImageInformation",result);
}
//====================================================================
-// Read Image Content (copied from XDRreader)
-int nkitk::XDRImageIO::ReadWithError(void * buffer)
+// Read Image Content (copied from Xdr reader)
+int clitk::XdrImageIO::ReadWithError(void * buffer)
{ //AVSINT dim[5];
int /*ndim,*/ nspace/*, veclen=1, data=AVS_TYPE_BYTE, field=UNIFORM*/;
int iNkiCompression = 0;
if (c) HeaderSize = 32768;
else HeaderSize = 2048;
-#if 0
- FIELDdefault(&FieldTemplate);
- FieldTemplate.ndim = ndim;
- FieldTemplate.nspace = nspace;
- FieldTemplate.veclen = veclen;
- FieldTemplate.type = data;
- FieldTemplate.uniform = field;
- FieldTemplate.size = datasize;
-#endif
-
fstream = fopen(file, "rb");
if (fstream == NULL)
return ER_XDR_OPEN;
if (i==iNumRead) return ER_XDR_NOCTRLL;
-#if 0
- if (*output) AVSfield_free(*output);
- *output = (AVSfield *) AVSfield_alloc(&FieldTemplate, dim);
- if (*output == NULL)
- {
- fclose(fstream);
- return ER_OUTOFMEMORY;
- }
-
- total *= datasize * veclen;
- coords *= sizeof(float);
-#endif
total = GetImageSizeInBytes();
//We add casts because the resulting quantity can be negative.
if (!pCompressed)
{
fclose(fstream);
-#if 0
- if (*output) AVSfield_free(*output);
- *output = NULL;
-#endif
return ER_OUTOFMEMORY;
}
if (fread( (void *)pCompressed, 1, iSize, fstream ) != iSize)
{
fclose(fstream);
-#if 0
- if (*output) AVSfield_free(*output);
- *output = NULL;
-#endif
return ER_XDR_READ;
}
if (!nki_private_decompress((short*)buffer, pCompressed, iSize))
{
fclose(fstream);
-#if 0
- if (*output) AVSfield_free(*output);
- *output = NULL;
-#endif
return ER_DECOMPRESSION;
}
if (fread( (void *)buffer, 1, total, fstream ) != total)
{
fclose(fstream);
-#if 0
- if (*output) AVSfield_free(*output);
- *output = NULL;
-#endif
return ER_XDR_READ;
}
}
}
READ_COORDS:
-#if 0
- if (coords) /* expect AVS coordinates ? */
- {
- if (fread( (*output)->points, 1, coords, fstream ) == coords)
- { /* swap data if read-ok and required (xdr is low-endian) */
-
- if (!(*(char *)(&swap_test)) && !forcenoswap)
- {
- c = (char *)(*output)->points;
- for (i=0; i<coords; i+=4)
- {
- j = c[i];
- c[i] = c[i+3];
- c[i+3] = j;
- j = c[i+1];
- c[i+1] = c[i+2];
- c[i+2] = j;
- }
- }
- }
- }
-#endif
fclose(fstream);
return OK;
}
//====================================================================
-// Read image information (copied from XDRreader)
-void nkitk::XDRImageIO::Read(void * buffer) {
+// Read image information (copied from Xdr reader)
+void clitk::XdrImageIO::Read(void * buffer) {
int result = ReadWithError(buffer);
- if (result) ITKError("nkitk::XDRImageIO::Read",result);
-}
-
-#if 0
-static int XDRreader_preview(AVSfield **output, char *file, int offset)
-{
- AVSINT dim[MAXDIM], dim2[MAXDIM], ds[MAXDIM];
- int ndim, nspace, veclen=1, data=AVS_TYPE_BYTE, field=UNIFORM;
- int iNkiCompression = 0;
- int total=1, i, j, k, l, m, coords=0, datasize=0, iNumRead, len, start, sliceax;
- char temp[512];
- FILE *fstream;
- char *c;
- char *buff;
- AVSfield FieldTemplate;
- long swap_test = 0x1000000; /* first byte is 1 when low-endian */
- int forcenoswap=0;
-
- fstream = fopen(file, "rt");
- if (fstream == NULL) return ER_XDR_OPEN;
- fgets(temp, 500, fstream);
- fclose(fstream);
-
- if (memcmp(temp, "# AVS field file (produced by avs_nfwrite.c)", 44)==0) forcenoswap=1;
-
- c = scan_header(file, "ndim", offset, 1);
- if (!c) return ER_XDR_NDIM;
- ndim = atoi(c);
- if (ndim<1 || ndim>MAXDIM) return ER_XDR_NDIM;
- nspace = ndim;
-
- /* defaults for dimensions and downsize */
-
- for (i=0; i<MAXDIM; i++)
- dim[i] = dim2[i] = ds[i] = 1;
-
- for (i=0; i<ndim; i++)
- {
- sprintf(temp, "dim%d", i+1);
- c = scan_header(file, temp, offset, 1);
- if (!c) return ER_XDR_DIM;
- dim[i]=atoi(c);
- if (dim[i]<1 || dim[i]>200000L) return ER_XDR_DIM;
-
- total *= dim[i];
- coords += dim[i];
- }
-
- c = scan_header(file, "nspace", offset, 1);
- if (c) nspace = atoi(c);
- if (nspace<1 || ndim > MAXDIM) return ER_XDR_NSPACE;
-
- c = scan_header(file, "veclen", offset, 1);
- if (c) veclen = atoi(c);
- if (veclen<0 || veclen>100) return ER_XDR_VECLEN;
-
- c = scan_header(file, "data", offset, 1);
-
- if (c)
- {
- if (memicmp(c, "byte", 4) == 0) data=AVS_TYPE_BYTE, datasize=1;
- else if (memicmp(c, "short", 5) == 0) data=AVS_TYPE_SHORT, datasize=2;
- else if (memicmp(c, "int" , 3) == 0) data=AVS_TYPE_INTEGER,datasize=4;
- else if (memicmp(c, "real", 4) == 0) data=AVS_TYPE_REAL, datasize=4;
- else if (memicmp(c, "float", 5) == 0) data=AVS_TYPE_REAL, datasize=4;
- else if (memicmp(c, "double",6) == 0) data=AVS_TYPE_DOUBLE, datasize=8;
-
- else if (memicmp(c, "xdr_byte", 8) == 0) data=AVS_TYPE_BYTE, datasize=1, forcenoswap=0;
- else if (memicmp(c, "xdr_short", 9) == 0) data=AVS_TYPE_SHORT, datasize=2, forcenoswap=0;
- else if (memicmp(c, "xdr_int" , 7) == 0) data=AVS_TYPE_INTEGER,datasize=4, forcenoswap=0;
- else if (memicmp(c, "xdr_real", 8) == 0) data=AVS_TYPE_REAL, datasize=4, forcenoswap=0;
- else if (memicmp(c, "xdr_float", 9) == 0) data=AVS_TYPE_REAL, datasize=4, forcenoswap=0;
- else if (memicmp(c, "xdr_double",10)== 0) data=AVS_TYPE_DOUBLE, datasize=8, forcenoswap=0;
- else return ER_XDR_DATA;
- }
-
- c = scan_header(file, "field", offset, 1);
- if (c)
- {
- if (memicmp(c, "unifo", 5) == 0) field=UNIFORM, coords=nspace*2;
- else if (memicmp(c, "recti", 5) == 0) field=RECTILINEAR;
- else if (memicmp(c, "irreg", 5) == 0) field=IRREGULAR, coords=total*nspace;
- else return ER_XDR_FIELD;
- }
- else
- coords=0;
-
- c = scan_header(file, "nki_compression", offset, 1);
- if (c) iNkiCompression = atoi(c);
- if (iNkiCompression)
- {
- fclose(fstream);
- return ER_ILLCOMMFUNCT;
- }
-
- FIELDdefault(&FieldTemplate);
- FieldTemplate.ndim = ndim;
- FieldTemplate.nspace = nspace;
- FieldTemplate.veclen = veclen;
- FieldTemplate.type = data;
- FieldTemplate.uniform = field;
- FieldTemplate.size = datasize;
-
- fstream = fopen(file, "rb");
-
- if (fstream == NULL)
- return ER_XDR_OPEN;
-
- buff = (char *)malloc(8192);
- if (buff == NULL)
- {
- return ER_OUTOFMEMORY;
- }
- memset(buff, 0, 8192);
- fseek(fstream, offset, SEEK_SET);
-
- while (1)
- {
- if (fgets(temp, 500, fstream) == NULL )
- return ER_XDR_NOCTRLL; /* end of file */
-
- if (temp[0] == 10) continue;
-
- if (temp[0] == 12)
- {
- fseek(fstream, -2, SEEK_CUR);
- break;
- } /* ^L end of header */
-
- if (temp[0] != '#') break;
- }
- start = ftell(fstream);
-
- iNumRead = fread(buff, 1, 8192, fstream);
- if (iNumRead < 1)
- {
- free(buff);
- fclose(fstream);
- return ER_XDR_READ;
- }
-
- for (i=0; i<iNumRead; i++) {
- if (buff[i] == 12) break;
- }
-
- free(buff);
-
- if (i==iNumRead) return ER_XDR_NOCTRLL;
-
- start += i+2;
-
- /* determine slice axis and downsize slice axis to 3, others to 32 */
-
- sliceax = 2;
-
- if (ndim>=3)
- {
- if (dim[0]==dim[1]) sliceax = 2;
- else sliceax = 1;
- }
-
- total = 1;
-
- for (i=0; i<ndim; i++)
- {
- if (i==sliceax) ds[i] = dim[i] / 3;
- else ds[i] = dim[i] / 32;
- if (ds[i]==0) ds[i]=1;
-
- dim2[i] = dim[i]/ds[i];
- if (dim2[i]==0) dim2[i] = 1;
-
- total *= dim2[i];
- }
-
- if (*output) AVSfield_free(*output);
- *output = (AVSfield *) AVSfield_alloc(&FieldTemplate, dim2);
- if (*output == NULL)
- {
- fclose(fstream);
- return ER_OUTOFMEMORY;
- }
-
- total *= datasize * veclen;
- coords *= sizeof(float);
-
- /* Read and downsize the data */
-
- if (total)
- {
- c = (char *)((*output)->field_data);
-
- buff = (char *)malloc(dim[0] * datasize * veclen);
-
- for (i=0; i<dim2[4]; i++)
- for (j=0; j<dim2[3]; j++)
- for (k=0; k<dim2[2]; k++)
- for (l=0; l<dim2[1]; l++)
- {
- len = i*ds[4];
- len = len * dim[3] + j*ds[3];
- len = len * dim[2] + k*ds[2];
- len = len * dim[1] + l*ds[1];
- len = len * dim[0] * datasize * veclen;
-
- // This is the time-critical statement
- fseek(fstream, start + len, SEEK_SET);
-
- fread(buff, 1, dim[0]*datasize*veclen, fstream);
- for (m=0; m<dim2[0]; m++)
- {
- memcpy(c, buff+m*datasize*veclen*ds[0], datasize*veclen);
- c += datasize*veclen;
- };
- };
-
- free (buff);
- }
-
- /* swap data if required (xdr is low-endian) */
-
- if (!(*(char *)(&swap_test)) && !forcenoswap)
- {
- if (datasize==2)
- {
- c = (char *)(*output)->field_data;
- for (i=0; i<total; i+=2)
- {
- j = c[i];
- c[i] = c[i+1];
- c[i+1] = j;
- }
- }
- else if (datasize==4)
- {
- c = (char *)(*output)->field_data;
- for (i=0; i<total; i+=4)
- {
- j = c[i];
- c[i] = c[i+3];
- c[i+3] = j;
- j = c[i+1];
- c[i+1] = c[i+2];
- c[i+2] = j;
- }
- }
- else if (datasize==8)
- {
- c = (char *)(*output)->field_data;
- for (i=0; i<total; i+=8)
- {
- j = c[i];
- c[i] = c[i+7];
- c[i+7] = j;
- j = c[i+1];
- c[i+1] = c[i+6];
- c[i+6] = j;
- j = c[i+2];
- c[i+2] = c[i+5];
- c[i+5] = j;
- j = c[i+3];
- c[i+3] = c[i+4];
- c[i+4] = j;
- }
- }
- }
-
-
- /*
- if (coords)
- { if (read( fHandle,(*output)->points, coords ) == coords)
- { if (!(*(char *)(&swap_test)) && !forcenoswap)
- { c = (char *)(*output)->points;
- for (i=0; i<coords; i+=4)
- { j = c[i]; c[i] = c[i+3]; c[i+3] = j;
- j = c[i+1]; c[i+1] = c[i+2]; c[i+2] = j;
- }
- }
- }
- }
- */
-
- fclose(fstream);
- return OK;
+ if (result) ITKError("clitk::XdrImageIO::Read",result);
}
-int Rxdr_compute(AVSfield** ppOut, char* pszFileName, int iOffset)
-{
- int rc;
- char szMsg[64];
-
- rc = XDRreader(ppOut, pszFileName, iOffset);
- if (rc == OK)
- rc = AVS_OK;
- else
- {
- strcpy(szMsg, "Avs_rxdr: ");
- strcat(szMsg, gl_ErrorMsg[rc]);
- AVSerror(szMsg);
- rc = AVS_ERROR;
- }
- return rc;
-}
-
-int RxdrPreview_compute(AVSfield** ppOut, char* pszFileName, int iOffset)
-{
- int rc;
- char szMsg[64];
-
- rc = XDRreader_preview(ppOut, pszFileName, iOffset);
- if (rc == OK)
- rc = AVS_OK;
- else
- {
- strcpy(szMsg, "Avs_rxdr: ");
- strcat(szMsg, gl_ErrorMsg[rc]);
- AVSerror(szMsg);
- rc = AVS_ERROR;
- }
- return rc;
-}
-
-int RxdrHeader_compute(char *pszOut, char *pszFileName, char *pszEntry)
-{
- char *cc;
-
- cc = scan_header(pszFileName, pszEntry, 0, 0);
- if (cc) strcpy(pszOut, cc);
- else *pszOut = 0;
-
- return AVS_OK;
-}
-
-int RxdrEnum_compute(char *pszOut, char *pszFileName, int iEntry)
-{
- char *cc;
-
- cc = enum_header(pszFileName, iEntry, 0);
- if (cc) strcpy(pszOut, cc);
- else *pszOut = 0;
-
- return AVS_OK;
-}
-#endif
-
//====================================================================
// Read Image Information
-bool nkitk::XDRImageIO::CanReadFile(const char* FileNameToRead)
+bool clitk::XdrImageIO::CanReadFile(const char* FileNameToRead)
{
char temp[512];
FILE *fstream;
fstream = fopen(FileNameToRead, "rt");
if (fstream == NULL)
+ {
+ AVSerror("Couldn't open file " << FileNameToRead);
return false;
+ }
fgets(temp, 500, fstream);
fclose(fstream);
return false;
} ////
-void nkitk::XDRImageIO::ITKError(std::string funcName, int msgID) {
+void clitk::XdrImageIO::ITKError(std::string funcName, int msgID) {
itkExceptionMacro(<< "Error in " << funcName << ". Message: " << gl_ErrorMsg[msgID]);
}
-#endif /* end #define NKITKXDRIMAGEIO_CXX */
-
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff