/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
/**
* @file clitkXdrImageIO.cxx
* @author Simon Rit <simon.rit@gmail.com>
/* DEFINES, ENUMERATED TYPES AND CONSTANTS */
/************************************************************************/
enum {
- OK,
- ER_ILLCOMMFUNCT,
- ER_INARGUMENTS,
- ER_XDR_NDIM,
- ER_XDR_DIM,
- ER_XDR_NSPACE,
- ER_XDR_VECLEN,
- ER_XDR_DATA,
- ER_XDR_FIELD,
- ER_XDR_OPEN,
- ER_XDR_NOCTRLL,
- ER_XDR_READ,
- ER_OUTOFMEMORY,
- ER_DECOMPRESSION,
- ER_NOT_HANDLED
+ OK,
+ ER_ILLCOMMFUNCT,
+ ER_INARGUMENTS,
+ ER_XDR_NDIM,
+ ER_XDR_DIM,
+ ER_XDR_NSPACE,
+ ER_XDR_VECLEN,
+ ER_XDR_DATA,
+ ER_XDR_FIELD,
+ ER_XDR_OPEN,
+ ER_XDR_NOCTRLL,
+ ER_XDR_READ,
+ ER_OUTOFMEMORY,
+ ER_DECOMPRESSION,
+ ER_NOT_HANDLED
};
-typedef struct
-{
- unsigned int iOrgSize;
- unsigned int iMode;
- unsigned int iCompressedSize;
- unsigned int iOrgCRC;
- unsigned int iCompressedCRC; /* Excluding this header */
+typedef struct {
+ unsigned int iOrgSize;
+ unsigned int iMode;
+ unsigned int iCompressedSize;
+ unsigned int iOrgCRC;
+ unsigned int iCompressedCRC; /* Excluding this header */
} NKI_MODE2;
/* GLOBAL VARIABLES */
/************************************************************************/
const char* gl_ErrorMsg[] = {
- "",
- "Command or function not supported in this way.",
- "Error in arguments",
- "XDR file header NDIM error",
- "XDR file header DIMn error",
- "XDR file header NSPACE error",
- "XDR file header VECLEN error",
- "XDR file header DATA(type) error",
- "XDR file header FIELD(coordinate type) error",
- "XDR file could not be opened",
- "XDR file header contains no ^L",
- "XDR file reading error",
- "Out of memory",
- "Decompression failed",
- "Format not handled by clitkXdrImageIO (RECTILINEAR or IRREGULAR field)"
+ "",
+ "Command or function not supported in this way.",
+ "Error in arguments",
+ "XDR file header NDIM error",
+ "XDR file header DIMn error",
+ "XDR file header NSPACE error",
+ "XDR file header VECLEN error",
+ "XDR file header DATA(type) error",
+ "XDR file header FIELD(coordinate type) error",
+ "XDR file could not be opened",
+ "XDR file header contains no ^L",
+ "XDR file reading error",
+ "Out of memory",
+ "Decompression failed",
+ "Format not handled by clitkXdrImageIO (RECTILINEAR or IRREGULAR field)"
};
static const unsigned long CRC32_table[256] = {
- 0x00000000, 0x77073096, 0xee0e612c, 0x990951ba, 0x076dc419, 0x706af48f,
- 0xe963a535, 0x9e6495a3, 0x0edb8832, 0x79dcb8a4, 0xe0d5e91e, 0x97d2d988,
- 0x09b64c2b, 0x7eb17cbd, 0xe7b82d07, 0x90bf1d91, 0x1db71064, 0x6ab020f2,
- 0xf3b97148, 0x84be41de, 0x1adad47d, 0x6ddde4eb, 0xf4d4b551, 0x83d385c7,
- 0x136c9856, 0x646ba8c0, 0xfd62f97a, 0x8a65c9ec, 0x14015c4f, 0x63066cd9,
- 0xfa0f3d63, 0x8d080df5, 0x3b6e20c8, 0x4c69105e, 0xd56041e4, 0xa2677172,
- 0x3c03e4d1, 0x4b04d447, 0xd20d85fd, 0xa50ab56b, 0x35b5a8fa, 0x42b2986c,
- 0xdbbbc9d6, 0xacbcf940, 0x32d86ce3, 0x45df5c75, 0xdcd60dcf, 0xabd13d59,
- 0x26d930ac, 0x51de003a, 0xc8d75180, 0xbfd06116, 0x21b4f4b5, 0x56b3c423,
- 0xcfba9599, 0xb8bda50f, 0x2802b89e, 0x5f058808, 0xc60cd9b2, 0xb10be924,
- 0x2f6f7c87, 0x58684c11, 0xc1611dab, 0xb6662d3d, 0x76dc4190, 0x01db7106,
- 0x98d220bc, 0xefd5102a, 0x71b18589, 0x06b6b51f, 0x9fbfe4a5, 0xe8b8d433,
- 0x7807c9a2, 0x0f00f934, 0x9609a88e, 0xe10e9818, 0x7f6a0dbb, 0x086d3d2d,
- 0x91646c97, 0xe6635c01, 0x6b6b51f4, 0x1c6c6162, 0x856530d8, 0xf262004e,
- 0x6c0695ed, 0x1b01a57b, 0x8208f4c1, 0xf50fc457, 0x65b0d9c6, 0x12b7e950,
- 0x8bbeb8ea, 0xfcb9887c, 0x62dd1ddf, 0x15da2d49, 0x8cd37cf3, 0xfbd44c65,
- 0x4db26158, 0x3ab551ce, 0xa3bc0074, 0xd4bb30e2, 0x4adfa541, 0x3dd895d7,
- 0xa4d1c46d, 0xd3d6f4fb, 0x4369e96a, 0x346ed9fc, 0xad678846, 0xda60b8d0,
- 0x44042d73, 0x33031de5, 0xaa0a4c5f, 0xdd0d7cc9, 0x5005713c, 0x270241aa,
- 0xbe0b1010, 0xc90c2086, 0x5768b525, 0x206f85b3, 0xb966d409, 0xce61e49f,
- 0x5edef90e, 0x29d9c998, 0xb0d09822, 0xc7d7a8b4, 0x59b33d17, 0x2eb40d81,
- 0xb7bd5c3b, 0xc0ba6cad, 0xedb88320, 0x9abfb3b6, 0x03b6e20c, 0x74b1d29a,
- 0xead54739, 0x9dd277af, 0x04db2615, 0x73dc1683, 0xe3630b12, 0x94643b84,
- 0x0d6d6a3e, 0x7a6a5aa8, 0xe40ecf0b, 0x9309ff9d, 0x0a00ae27, 0x7d079eb1,
- 0xf00f9344, 0x8708a3d2, 0x1e01f268, 0x6906c2fe, 0xf762575d, 0x806567cb,
- 0x196c3671, 0x6e6b06e7, 0xfed41b76, 0x89d32be0, 0x10da7a5a, 0x67dd4acc,
- 0xf9b9df6f, 0x8ebeeff9, 0x17b7be43, 0x60b08ed5, 0xd6d6a3e8, 0xa1d1937e,
- 0x38d8c2c4, 0x4fdff252, 0xd1bb67f1, 0xa6bc5767, 0x3fb506dd, 0x48b2364b,
- 0xd80d2bda, 0xaf0a1b4c, 0x36034af6, 0x41047a60, 0xdf60efc3, 0xa867df55,
- 0x316e8eef, 0x4669be79, 0xcb61b38c, 0xbc66831a, 0x256fd2a0, 0x5268e236,
- 0xcc0c7795, 0xbb0b4703, 0x220216b9, 0x5505262f, 0xc5ba3bbe, 0xb2bd0b28,
- 0x2bb45a92, 0x5cb36a04, 0xc2d7ffa7, 0xb5d0cf31, 0x2cd99e8b, 0x5bdeae1d,
- 0x9b64c2b0, 0xec63f226, 0x756aa39c, 0x026d930a, 0x9c0906a9, 0xeb0e363f,
- 0x72076785, 0x05005713, 0x95bf4a82, 0xe2b87a14, 0x7bb12bae, 0x0cb61b38,
- 0x92d28e9b, 0xe5d5be0d, 0x7cdcefb7, 0x0bdbdf21, 0x86d3d2d4, 0xf1d4e242,
- 0x68ddb3f8, 0x1fda836e, 0x81be16cd, 0xf6b9265b, 0x6fb077e1, 0x18b74777,
- 0x88085ae6, 0xff0f6a70, 0x66063bca, 0x11010b5c, 0x8f659eff, 0xf862ae69,
- 0x616bffd3, 0x166ccf45, 0xa00ae278, 0xd70dd2ee, 0x4e048354, 0x3903b3c2,
- 0xa7672661, 0xd06016f7, 0x4969474d, 0x3e6e77db, 0xaed16a4a, 0xd9d65adc,
- 0x40df0b66, 0x37d83bf0, 0xa9bcae53, 0xdebb9ec5, 0x47b2cf7f, 0x30b5ffe9,
- 0xbdbdf21c, 0xcabac28a, 0x53b39330, 0x24b4a3a6, 0xbad03605, 0xcdd70693,
- 0x54de5729, 0x23d967bf, 0xb3667a2e, 0xc4614ab8, 0x5d681b02, 0x2a6f2b94,
- 0xb40bbe37, 0xc30c8ea1, 0x5a05df1b, 0x2d02ef8d
+ 0x00000000, 0x77073096, 0xee0e612c, 0x990951ba, 0x076dc419, 0x706af48f,
+ 0xe963a535, 0x9e6495a3, 0x0edb8832, 0x79dcb8a4, 0xe0d5e91e, 0x97d2d988,
+ 0x09b64c2b, 0x7eb17cbd, 0xe7b82d07, 0x90bf1d91, 0x1db71064, 0x6ab020f2,
+ 0xf3b97148, 0x84be41de, 0x1adad47d, 0x6ddde4eb, 0xf4d4b551, 0x83d385c7,
+ 0x136c9856, 0x646ba8c0, 0xfd62f97a, 0x8a65c9ec, 0x14015c4f, 0x63066cd9,
+ 0xfa0f3d63, 0x8d080df5, 0x3b6e20c8, 0x4c69105e, 0xd56041e4, 0xa2677172,
+ 0x3c03e4d1, 0x4b04d447, 0xd20d85fd, 0xa50ab56b, 0x35b5a8fa, 0x42b2986c,
+ 0xdbbbc9d6, 0xacbcf940, 0x32d86ce3, 0x45df5c75, 0xdcd60dcf, 0xabd13d59,
+ 0x26d930ac, 0x51de003a, 0xc8d75180, 0xbfd06116, 0x21b4f4b5, 0x56b3c423,
+ 0xcfba9599, 0xb8bda50f, 0x2802b89e, 0x5f058808, 0xc60cd9b2, 0xb10be924,
+ 0x2f6f7c87, 0x58684c11, 0xc1611dab, 0xb6662d3d, 0x76dc4190, 0x01db7106,
+ 0x98d220bc, 0xefd5102a, 0x71b18589, 0x06b6b51f, 0x9fbfe4a5, 0xe8b8d433,
+ 0x7807c9a2, 0x0f00f934, 0x9609a88e, 0xe10e9818, 0x7f6a0dbb, 0x086d3d2d,
+ 0x91646c97, 0xe6635c01, 0x6b6b51f4, 0x1c6c6162, 0x856530d8, 0xf262004e,
+ 0x6c0695ed, 0x1b01a57b, 0x8208f4c1, 0xf50fc457, 0x65b0d9c6, 0x12b7e950,
+ 0x8bbeb8ea, 0xfcb9887c, 0x62dd1ddf, 0x15da2d49, 0x8cd37cf3, 0xfbd44c65,
+ 0x4db26158, 0x3ab551ce, 0xa3bc0074, 0xd4bb30e2, 0x4adfa541, 0x3dd895d7,
+ 0xa4d1c46d, 0xd3d6f4fb, 0x4369e96a, 0x346ed9fc, 0xad678846, 0xda60b8d0,
+ 0x44042d73, 0x33031de5, 0xaa0a4c5f, 0xdd0d7cc9, 0x5005713c, 0x270241aa,
+ 0xbe0b1010, 0xc90c2086, 0x5768b525, 0x206f85b3, 0xb966d409, 0xce61e49f,
+ 0x5edef90e, 0x29d9c998, 0xb0d09822, 0xc7d7a8b4, 0x59b33d17, 0x2eb40d81,
+ 0xb7bd5c3b, 0xc0ba6cad, 0xedb88320, 0x9abfb3b6, 0x03b6e20c, 0x74b1d29a,
+ 0xead54739, 0x9dd277af, 0x04db2615, 0x73dc1683, 0xe3630b12, 0x94643b84,
+ 0x0d6d6a3e, 0x7a6a5aa8, 0xe40ecf0b, 0x9309ff9d, 0x0a00ae27, 0x7d079eb1,
+ 0xf00f9344, 0x8708a3d2, 0x1e01f268, 0x6906c2fe, 0xf762575d, 0x806567cb,
+ 0x196c3671, 0x6e6b06e7, 0xfed41b76, 0x89d32be0, 0x10da7a5a, 0x67dd4acc,
+ 0xf9b9df6f, 0x8ebeeff9, 0x17b7be43, 0x60b08ed5, 0xd6d6a3e8, 0xa1d1937e,
+ 0x38d8c2c4, 0x4fdff252, 0xd1bb67f1, 0xa6bc5767, 0x3fb506dd, 0x48b2364b,
+ 0xd80d2bda, 0xaf0a1b4c, 0x36034af6, 0x41047a60, 0xdf60efc3, 0xa867df55,
+ 0x316e8eef, 0x4669be79, 0xcb61b38c, 0xbc66831a, 0x256fd2a0, 0x5268e236,
+ 0xcc0c7795, 0xbb0b4703, 0x220216b9, 0x5505262f, 0xc5ba3bbe, 0xb2bd0b28,
+ 0x2bb45a92, 0x5cb36a04, 0xc2d7ffa7, 0xb5d0cf31, 0x2cd99e8b, 0x5bdeae1d,
+ 0x9b64c2b0, 0xec63f226, 0x756aa39c, 0x026d930a, 0x9c0906a9, 0xeb0e363f,
+ 0x72076785, 0x05005713, 0x95bf4a82, 0xe2b87a14, 0x7bb12bae, 0x0cb61b38,
+ 0x92d28e9b, 0xe5d5be0d, 0x7cdcefb7, 0x0bdbdf21, 0x86d3d2d4, 0xf1d4e242,
+ 0x68ddb3f8, 0x1fda836e, 0x81be16cd, 0xf6b9265b, 0x6fb077e1, 0x18b74777,
+ 0x88085ae6, 0xff0f6a70, 0x66063bca, 0x11010b5c, 0x8f659eff, 0xf862ae69,
+ 0x616bffd3, 0x166ccf45, 0xa00ae278, 0xd70dd2ee, 0x4e048354, 0x3903b3c2,
+ 0xa7672661, 0xd06016f7, 0x4969474d, 0x3e6e77db, 0xaed16a4a, 0xd9d65adc,
+ 0x40df0b66, 0x37d83bf0, 0xa9bcae53, 0xdebb9ec5, 0x47b2cf7f, 0x30b5ffe9,
+ 0xbdbdf21c, 0xcabac28a, 0x53b39330, 0x24b4a3a6, 0xbad03605, 0xcdd70693,
+ 0x54de5729, 0x23d967bf, 0xb3667a2e, 0xc4614ab8, 0x5d681b02, 0x2a6f2b94,
+ 0xb40bbe37, 0xc30c8ea1, 0x5a05df1b, 0x2d02ef8d
};
static char *scan_header(const char *file, const char *name, int offset, int removespaces)
{
- int i, j, iStringLength;
- static char temp[512];
- FILE *f;
- char *p, *q;
-
- if ((f = fopen(file, "rt")) == NULL) return NULL;
- if (offset) fseek(f, offset, SEEK_SET);
-
- for (i=0; i<200; )
- {
- if (fgets(temp, 500, f) == NULL ) break; /* end of file */
-
- if (removespaces)
- {
- temp[500] = 0;
- p = q = temp; /* remove spaces */
- iStringLength = strlen(temp);
- for (j=0; j<iStringLength; j++)
- if (*q!=' ' && *q!=8) *p++ = *q++;
- else q++;
- *p++ = 0;
- }
+ int i, j, iStringLength;
+ static char temp[512];
+ FILE *f;
+ char *p, *q;
+
+ if ((f = fopen(file, "rt")) == NULL) return NULL;
+ if (offset) fseek(f, offset, SEEK_SET);
+
+ for (i=0; i<200; ) {
+ if (fgets(temp, 500, f) == NULL ) break; /* end of file */
+
+ if (removespaces) {
+ temp[500] = 0;
+ p = q = temp; /* remove spaces */
+ iStringLength = strlen(temp);
+ for (j=0; j<iStringLength; j++)
+ if (*q!=' ' && *q!=8) *p++ = *q++;
+ else q++;
+ *p++ = 0;
+ }
- 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 (memicmp(temp, name, p-temp) ) continue; /* no match */
+ 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 (memicmp(temp, name, p-temp) ) continue; /* no match */
- p++; /* match, skip = */
- if (p[strlen(p)-1] == '\n') /* remove \n */
- p[strlen(p)-1] = 0;
+ p++; /* match, skip = */
+ if (p[strlen(p)-1] == '\n') /* remove \n */
+ p[strlen(p)-1] = 0;
- fclose (f);
- return p;
- }
+ fclose (f);
+ return p;
+ }
- fclose(f);
- return NULL;
+ fclose(f);
+ return NULL;
}
static int get_nki_compressed_size(FILE *f)
{
- NKI_MODE2 Header;
- int iMode;
-
- fread((void *)&Header, sizeof(Header), 1 , f);
-
- iMode = Header.iMode;
-
- switch (iMode)
- {
- case 1:
- case 3:
- return 0;
- case 2:
- case 4:
- return Header.iCompressedSize + sizeof(Header);
- default:
- return 0;
- }
+ NKI_MODE2 Header;
+ int iMode;
+
+ fread((void *)&Header, sizeof(Header), 1 , f);
+
+ iMode = Header.iMode;
+
+ switch (iMode) {
+ case 1:
+ case 3:
+ return 0;
+ case 2:
+ case 4:
+ return Header.iCompressedSize + sizeof(Header);
+ default:
+ return 0;
+ }
}
/* decoder for NKI private compressed pixel data
static int nki_private_decompress(short int *dest, signed char *src, int size)
{
- int npixels, retvalue, mode, iMode, val, j;
- NKI_MODE2* pHeader = (NKI_MODE2*)src;
- unsigned long iCRC=0, iCRC2=0;
- //unsigned char* pDestStart = (unsigned char*)dest;
- signed char *save, *end;
-
- retvalue = npixels = pHeader->iOrgSize;
- iMode = pHeader->iMode; // safety: this value is checked in case statement
-
- if (npixels<1) return 0; // safety: check for invalid npixels value
-
- /* Up till now only Mode=1, 2, 3, and 4 are supported */
-
- switch (iMode)
- {
- case 1:
- save = src;
+ int npixels, retvalue, mode, iMode, val, j;
+ NKI_MODE2* pHeader = (NKI_MODE2*)src;
+ unsigned long iCRC=0, iCRC2=0;
+ //unsigned char* pDestStart = (unsigned char*)dest;
+ signed char *save, *end;
+
+ retvalue = npixels = pHeader->iOrgSize;
+ iMode = pHeader->iMode; // safety: this value is checked in case statement
+
+ if (npixels<1) return 0; // safety: check for invalid npixels value
+
+ /* Up till now only Mode=1, 2, 3, and 4 are supported */
+
+ switch (iMode) {
+ case 1:
+ save = src;
+
+ src += 8; // mode 1 only has 8 bytes header: iOrgSize and iMode
+ end = src + size - 3; // for overflow check if we are close to end of input buffer
+
+ *dest = *(short int *)src;
+ src += 2;
+ npixels--;
+
+ do {
+ if (src > end) { // check whether the last few messages fit in input buffer
+ if (src<end+3) val = *src;
+ else val = 0;
+
+ if (val >= -64 && val <= 63) mode = 1; // 7 bit difference
+ else if (val==0x7f) mode = 3; // 16 bit value
+ else if ((val&0xff)==0x80) mode = 2; // run length encoding
+ else mode = 2;
+
+ if (src+mode > end+3)
+ return 0; // safety: overflow input data
+ }
+
+ val = *src;
+
+ if (val >= -64 && val <= 63) { // 7 bit difference
+ dest[1] = dest[0] + val;
+ dest++;
+ src++;
+ } else if (val==0x7f) { // 16 bit value
+ dest[1] = val = ((int)(((unsigned char *)src)[1])<<8) + ((unsigned char*)src)[2];
+ dest++;
+ src+=3;
+ } else if ((val&0xff)==0x80) { // run length encoding
+ mode = ((unsigned char *)src)[1];
+ npixels -= mode-1;
+ if (npixels<=0) return 0; // safety: overflow output data
+ do {
+ dest[1] = dest[0];
+ dest++;
+ } while (--mode);
+ src+=2;
+ } else {
+ signed short diff = ((val^0x40)<<8) + (unsigned char)(src[1]);
+ dest[1] = dest[0] + diff; // 15 bit difference
+ dest++;
+ src+=2;
+ }
+ } while (--npixels);
- src += 8; // mode 1 only has 8 bytes header: iOrgSize and iMode
- end = src + size - 3; // for overflow check if we are close to end of input buffer
+ global_len = src-save;
- *dest = *(short int *)src;
- src += 2;
- npixels--;
+ break;
- do
- {
- if (src > end) // check whether the last few messages fit in input buffer
- {
- if (src<end+3) val = *src;
- else val = 0;
+ case 2:
+ src += sizeof(NKI_MODE2);
+ save = src;
+ end = src + pHeader->iCompressedSize - 3;
- if (val >= -64 && val <= 63) mode = 1; // 7 bit difference
- else if (val==0x7f) mode = 3; // 16 bit value
- else if ((val&0xff)==0x80) mode = 2; // run length encoding
- else mode = 2;
+ if (end > src + size - 3)
+ end = src + size - 3; // may occur if pHeader is corrupted
- if (src+mode > end+3)
- return 0; // safety: overflow input data
- }
+ *dest = val = *(short int *)src;
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
+ src+=2;
- val = *src;
+ npixels--;
- if (val >= -64 && val <= 63) // 7 bit difference
- {
- dest[1] = dest[0] + val;
- dest++;
- src++;
- }
- else if (val==0x7f) // 16 bit value
- {
- dest[1] = val = ((int)(((unsigned char *)src)[1])<<8) + ((unsigned char*)src)[2];
- dest++;
- src+=3;
- }
- else if ((val&0xff)==0x80) // run length encoding
- {
- mode = ((unsigned char *)src)[1];
- npixels -= mode-1;
- if (npixels<=0) return 0; // safety: overflow output data
- do
- {
- dest[1] = dest[0];
- dest++;
- }
- while (--mode);
- src+=2;
- }
- else
- {
- signed short diff = ((val^0x40)<<8) + (unsigned char)(src[1]);
- dest[1] = dest[0] + diff; // 15 bit difference
- dest++;
- src+=2;
- }
- }
- while (--npixels);
+ do {
+ if (src > end) { // check whether the last few messages fit in input buffer
+ if (src<end+3) val = *src;
+ else val = 0;
- global_len = src-save;
+ if (val >= -64 && val <= 63) mode = 1; // 7 bit difference
+ else if (val==0x7f) mode = 3; // 16 bit value
+ else if ((val&0xff)==0x80) mode = 2; // run length encoding
+ else mode = 2;
- break;
+ if (src+mode > end+3)
+ break; // safety: overflow input data
+ }
- case 2:
- src += sizeof(NKI_MODE2);
- save = src;
- end = src + pHeader->iCompressedSize - 3;
+ val = *src;
- if (end > src + size - 3)
- end = src + size - 3; // may occur if pHeader is corrupted
+ if (val >= -64 && val <= 63) { // 7 bits difference
+ dest[1] = val = dest[0] + val;
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
+ dest++;
+ src++;
+ } else if (val==0x7f) { // 16 bit value
+ dest[1] = val = ((int)(((unsigned char *)src)[1])<<8) + ((unsigned char*)src)[2];
- *dest = val = *(short int *)src;
iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
+ dest++;
+ src+=3;
+ } else if ((val&0xff)==0x80) { // run length encoding
+ mode = ((unsigned char *)src)[1];
+ npixels -= mode-1;
+ if (npixels<=0) break; // safety: overflow output data
+ do {
+ dest[1] = val = dest[0];
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
+ dest++;
+ } while (--mode);
src+=2;
+ } else {
+ signed short diff = ((val^0x40)<<8) + ((unsigned char *)src)[1];
+ dest[1] = val = dest[0] + diff; // 15 bit difference
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
+ dest++;
+ src+=2;
+ }
+ } while (--npixels);
+
+ if (iCRC2 != pHeader->iOrgCRC) { // if error in output CRC:
+ src = save; // check input CRC
+ while (src < end) {
+ iCRC = CRC32_table[(unsigned char)iCRC ^ (unsigned char)src[0]] ^ ((iCRC >> 8));
+ src++;
+ }
+
+ if (iCRC != pHeader->iCompressedCRC) {
+ AVSerror("XDR decompression: the file is corrupted");
+ retvalue=0;
+ } else {
+ AVSerror("XDR decompression: internal error");
+ retvalue=0;
+ }
+ }
- npixels--;
-
- do
- {
- if (src > end) // check whether the last few messages fit in input buffer
- {
- if (src<end+3) val = *src;
- else val = 0;
-
- if (val >= -64 && val <= 63) mode = 1; // 7 bit difference
- else if (val==0x7f) mode = 3; // 16 bit value
- else if ((val&0xff)==0x80) mode = 2; // run length encoding
- else mode = 2;
-
- if (src+mode > end+3)
- break; // safety: overflow input data
- }
-
- val = *src;
-
- if (val >= -64 && val <= 63) // 7 bits difference
- {
- dest[1] = val = dest[0] + val;
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
- dest++;
- src++;
- }
- else if (val==0x7f) // 16 bit value
- {
- dest[1] = val = ((int)(((unsigned char *)src)[1])<<8) + ((unsigned char*)src)[2];
-
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
- dest++;
- src+=3;
- }
- else if ((val&0xff)==0x80) // run length encoding
- {
- mode = ((unsigned char *)src)[1];
- npixels -= mode-1;
- if (npixels<=0) break; // safety: overflow output data
- do
- {
- dest[1] = val = dest[0];
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
- dest++;
- }
- while (--mode);
- src+=2;
- }
- else
- {
- signed short diff = ((val^0x40)<<8) + ((unsigned char *)src)[1];
- dest[1] = val = dest[0] + diff; // 15 bit difference
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
- dest++;
- src+=2;
- }
- }
- while (--npixels);
-
- if (iCRC2 != pHeader->iOrgCRC) // if error in output CRC:
- {
- src = save; // check input CRC
- while (src < end)
- {
- iCRC = CRC32_table[(unsigned char)iCRC ^ (unsigned char)src[0]] ^ ((iCRC >> 8));
- src++;
- }
-
- if (iCRC != pHeader->iCompressedCRC)
- {
- AVSerror("XDR decompression: the file is corrupted");
- retvalue=0;
- }
- else
- {
- AVSerror("XDR decompression: internal error");
- retvalue=0;
- }
- }
+ global_len = sizeof(NKI_MODE2) + pHeader->iCompressedSize;
+
+ break;
+
+ case 3:
+ save = src;
+
+ src += 8; // mode 3 only has 8 bytes header: iOrgSize and iMode
+ end = src + size - 3; // for overflow check if we are close to end of input buffer
+
+ *dest = *(short int *)src;
+ src += 2;
+ npixels--;
+
+ do {
+ if (src > end) { // check whether the last few messages fit in input buffer
+ if (src<end+3) val = *src;
+ else val = 0;
+
+ if (val >= -63 && val <= 63) mode = 1; // 7 bit difference
+ else if (val==0x7f) mode = 3; // 16 bit value
+ else if ((val&0xff)==0x80) mode = 2; // run length encoding
+ else if ((val&0xff)==0xC0) mode = 2; // 4 bit encoding
+ else mode = 2;
+
+ if (src+mode > end+3)
+ return 0; // safety: overflow input data
+ }
+
+ val = *src;
+
+ if (val >= -63 && val <= 63) { // 7 bit difference
+ dest[1] = dest[0] + val;
+ dest++;
+ src++;
+ } else if (val==0x7f) { // 16 bit value
+ dest[1] = val = ((int)(((unsigned char *)src)[1])<<8) + ((unsigned char*)src)[2];
+ dest++;
+ src+=3;
+ } else if ((val&0xff)==0x80) { // run length encoding
+ mode = ((unsigned char *)src)[1];
+ npixels -= mode-1;
+ if (npixels<=0) return 0; // safety: overflow output data
+ do {
+ dest[1] = dest[0];
+ dest++;
+ } while (--mode);
+ src+=2;
+ } else if ((val&0xff)==0xC0) { // 4 bit run
+ mode = ((unsigned char *)src)[1];
+ npixels -= mode-1;
+ mode/=2;
+ src+=2;
+ if (npixels<=0) return 0; // safety: overflow output data
+ do {
+ val = *src++;
+ dest[1] = dest[0] + (val>>4);
+ dest++;
+ if (val&8) val |= 0xfffffff0;
+ else val &= 0x0f;
+ dest[1] = dest[0] + val;
+ dest++;
+ } while (--mode);
+ } else {
+ signed short diff = ((val^0x40)<<8) + (unsigned char)(src[1]);
+ dest[1] = dest[0] + diff; // 15 bit difference
+ dest++;
+ src+=2;
+ }
+ } while (--npixels);
- global_len = sizeof(NKI_MODE2) + pHeader->iCompressedSize;
+ global_len = src-save;
- break;
+ break;
- case 3:
- save = src;
+ case 4:
+ src += sizeof(NKI_MODE2);
+ save = src;
+ end = src + pHeader->iCompressedSize - 3;
- src += 8; // mode 3 only has 8 bytes header: iOrgSize and iMode
- end = src + size - 3; // for overflow check if we are close to end of input buffer
+ if (end > src + size - 3)
+ end = src + size - 3; // may occur if pHeader is corrupted
- *dest = *(short int *)src;
- src += 2;
- npixels--;
+ *dest = val = *(short int *)src;
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
+ src += 2;
+ npixels--;
- do
- {
- if (src > end) // check whether the last few messages fit in input buffer
- {
- if (src<end+3) val = *src;
- else val = 0;
+ do {
+ if (src > end) { // check whether the last few messages fit in input buffer
+ if (src<end+3) val = *src;
+ else val = 0;
- if (val >= -63 && val <= 63) mode = 1; // 7 bit difference
- else if (val==0x7f) mode = 3; // 16 bit value
- else if ((val&0xff)==0x80) mode = 2; // run length encoding
- else if ((val&0xff)==0xC0) mode = 2; // 4 bit encoding
- else mode = 2;
+ if (val >= -63 && val <= 63) mode = 1; // 7 bit difference
+ else if (val==0x7f) mode = 3; // 16 bit value
+ else if ((val&0xff)==0x80) mode = 2; // run length encoding
+ else if ((val&0xff)==0xC0) mode = 2; // 4 bit encoding
+ else mode = 2;
- if (src+mode > end+3)
- return 0; // safety: overflow input data
- }
+ if (src+mode > end+3)
+ return 0; // safety: overflow input data
+ }
- val = *src;
+ val = *src;
- if (val >= -63 && val <= 63) // 7 bit difference
- {
- dest[1] = dest[0] + val;
- dest++;
- src++;
- }
- else if (val==0x7f) // 16 bit value
- {
- dest[1] = val = ((int)(((unsigned char *)src)[1])<<8) + ((unsigned char*)src)[2];
- dest++;
- src+=3;
- }
- else if ((val&0xff)==0x80) // run length encoding
- {
- mode = ((unsigned char *)src)[1];
- npixels -= mode-1;
- if (npixels<=0) return 0; // safety: overflow output data
- do
- {
- dest[1] = dest[0];
- dest++;
- }
- while (--mode);
- src+=2;
- }
- else if ((val&0xff)==0xC0) // 4 bit run
- {
- mode = ((unsigned char *)src)[1];
- npixels -= mode-1;
- mode/=2;
- src+=2;
- if (npixels<=0) return 0; // safety: overflow output data
- do
- {
- val = *src++;
- dest[1] = dest[0] + (val>>4);
- dest++;
- if (val&8) val |= 0xfffffff0;
- else val &= 0x0f;
- dest[1] = dest[0] + val;
- dest++;
- }
- while (--mode);
- }
- else
- {
- signed short diff = ((val^0x40)<<8) + (unsigned char)(src[1]);
- dest[1] = dest[0] + diff; // 15 bit difference
- dest++;
- src+=2;
- }
- }
- while (--npixels);
-
- global_len = src-save;
-
- break;
-
- case 4:
- src += sizeof(NKI_MODE2);
- save = src;
- end = src + pHeader->iCompressedSize - 3;
-
- if (end > src + size - 3)
- end = src + size - 3; // may occur if pHeader is corrupted
-
- *dest = val = *(short int *)src;
+ if (val >= -63 && val <= 63) { // 7 bit difference
+ dest[1] = val = dest[0] + val;
iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
- src += 2;
- npixels--;
-
- do
- {
- if (src > end) // check whether the last few messages fit in input buffer
- {
- if (src<end+3) val = *src;
- else val = 0;
-
- if (val >= -63 && val <= 63) mode = 1; // 7 bit difference
- else if (val==0x7f) mode = 3; // 16 bit value
- else if ((val&0xff)==0x80) mode = 2; // run length encoding
- else if ((val&0xff)==0xC0) mode = 2; // 4 bit encoding
- else mode = 2;
-
- if (src+mode > end+3)
- return 0; // safety: overflow input data
- }
-
- val = *src;
-
- if (val >= -63 && val <= 63) // 7 bit difference
- {
- dest[1] = val = dest[0] + val;
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
- dest++;
- src++;
- }
- else if (val==0x7f) // 16 bit value
- {
- dest[1] = val = ((int)(((unsigned char *)src)[1])<<8) + ((unsigned char*)src)[2];
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
- dest++;
- src+=3;
- }
- else if ((val&0xff)==0x80) // run length encoding
- {
- mode = ((unsigned char *)src)[1];
- npixels -= mode-1;
- if (npixels<=0) return 0; // safety: overflow output data
- do
- {
- dest[1] = val = dest[0];
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
- dest++;
- }
- while (--mode);
- src+=2;
- }
- else if ((val&0xff)==0xC0) // 4 bit run
- {
- mode = ((unsigned char *)src)[1];
- npixels -= mode-1;
- mode/=2;
- src+=2;
- if (npixels<=0) return 0; // safety: overflow output data
- do
- {
- val = *src++;
- dest[1] = j = dest[0] + (val>>4);
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)j] ^ ((iCRC2 >> 8));
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(j>>8)] ^ ((iCRC2 >> 8));
- dest++;
- if (val&8) val |= 0xfffffff0;
- else val &= 0x0f;
- dest[1] = j = dest[0] + val;
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)j] ^ ((iCRC2 >> 8));
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(j>>8)] ^ ((iCRC2 >> 8));
- dest++;
- }
- while (--mode);
- }
- else
- {
- signed short diff = ((val^0x40)<<8) + (unsigned char)(src[1]);
- dest[1] = val = dest[0] + diff; // 15 bit difference
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
- iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
- dest++;
- src+=2;
- }
- }
- while (--npixels);
+ dest++;
+ src++;
+ } else if (val==0x7f) { // 16 bit value
+ dest[1] = val = ((int)(((unsigned char *)src)[1])<<8) + ((unsigned char*)src)[2];
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
+ dest++;
+ src+=3;
+ } else if ((val&0xff)==0x80) { // run length encoding
+ mode = ((unsigned char *)src)[1];
+ npixels -= mode-1;
+ if (npixels<=0) return 0; // safety: overflow output data
+ do {
+ dest[1] = val = dest[0];
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
+ dest++;
+ } while (--mode);
+ src+=2;
+ } else if ((val&0xff)==0xC0) { // 4 bit run
+ mode = ((unsigned char *)src)[1];
+ npixels -= mode-1;
+ mode/=2;
+ src+=2;
+ if (npixels<=0) return 0; // safety: overflow output data
+ do {
+ val = *src++;
+ dest[1] = j = dest[0] + (val>>4);
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)j] ^ ((iCRC2 >> 8));
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(j>>8)] ^ ((iCRC2 >> 8));
+ dest++;
+ if (val&8) val |= 0xfffffff0;
+ else val &= 0x0f;
+ dest[1] = j = dest[0] + val;
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)j] ^ ((iCRC2 >> 8));
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(j>>8)] ^ ((iCRC2 >> 8));
+ dest++;
+ } while (--mode);
+ } else {
+ signed short diff = ((val^0x40)<<8) + (unsigned char)(src[1]);
+ dest[1] = val = dest[0] + diff; // 15 bit difference
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)val] ^ ((iCRC2 >> 8));
+ iCRC2 = CRC32_table[(unsigned char)iCRC2 ^ (unsigned char)(val>>8)] ^ ((iCRC2 >> 8));
+ dest++;
+ src+=2;
+ }
+ } while (--npixels);
- if (iCRC2 != pHeader->iOrgCRC) // if error in output CRC:
- retvalue=0;
+ if (iCRC2 != pHeader->iOrgCRC) // if error in output CRC:
+ retvalue=0;
- global_len = sizeof(NKI_MODE2) + pHeader->iCompressedSize;
+ global_len = sizeof(NKI_MODE2) + pHeader->iCompressedSize;
- break;
+ break;
- default:
- AVSerror("XDR decompression: unsupported mode");
- return 0;
- }
+ default:
+ AVSerror("XDR decompression: unsupported mode");
+ return 0;
+ }
- return retvalue;
+ return retvalue;
}
// Read image information (copied from XDRreader)
int clitk::XdrImageIO::ReadImageInformationWithError()
{
- int offset=0;
- itk::Vector<int,MAXDIM> dim;
- int veclen=1;
- int total=1;
- unsigned int coords=0,i,j,ndim,nspace;
- char temp[512];
- FILE *fstream;
- char *c;
-
- long swap_test = 0x1000000; /* first byte is 1 when low-endian */
- forcenoswap=0;
- char *file = const_cast<char *>(m_FileName.c_str());
- AVSType field=UNIFORM;
-
-
- fstream = fopen(file, "rt");
+ int offset=0;
+ itk::Vector<int,MAXDIM> dim;
+ int veclen=1;
+ int total=1;
+ unsigned int coords=0,i,j,ndim,nspace;
+ char temp[512];
+ FILE *fstream;
+ char *c;
+
+ long swap_test = 0x1000000; /* first byte is 1 when low-endian */
+ forcenoswap=0;
+ char *file = const_cast<char *>(m_FileName.c_str());
+ AVSType field=UNIFORM;
+
+
+ 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;
+ SetNumberOfDimensions(ndim);
+
+ nspace = ndim;
+
+ 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) return ER_XDR_DIM;
+
+ total *= dim[i];
+ coords += dim[i];
+ }
+ for (i=0; i<ndim; i++) {
+ SetDimensions(i,dim[i]);
+ SetSpacing(i,1.);
+ SetOrigin(i,0.);
+ }
+
+ c = scan_header(file, "nspace", offset, 1);
+ if (c) nspace = atoi(c);
+ if (nspace<1 || ndim > MAXDIM) return ER_XDR_NSPACE;
+ if (nspace != ndim) return ER_NOT_HANDLED;
+
+ c = scan_header(file, "veclen", offset, 1);
+ if (c) veclen = atoi(c);
+ if (veclen<0 /*|| veclen>1000*/) return ER_XDR_VECLEN;
+ SetNumberOfComponents(veclen);
+ if (veclen==1) SetPixelType(itk::ImageIOBase::SCALAR);
+ else SetPixelType(itk::ImageIOBase::VECTOR);
+
+ c = scan_header(file, "data", offset, 1);
+ if (c) {
+ if (memicmp(c, "byte", 4) == 0 || memicmp(c, "xdr_byte", 8) == 0) SetComponentType(itk::ImageIOBase::CHAR);
+ else if (memicmp(c, "short", 5) == 0 || memicmp(c, "xdr_short", 9) == 0) SetComponentType(itk::ImageIOBase::SHORT);
+ else if (memicmp(c, "int" , 3) == 0 || memicmp(c, "xdr_int" , 7) == 0) SetComponentType(itk::ImageIOBase::INT);
+ else if (memicmp(c, "real", 4) == 0 || memicmp(c, "xdr_real", 8) == 0) SetComponentType(itk::ImageIOBase::FLOAT);
+ else if (memicmp(c, "float", 5) == 0 || memicmp(c, "xdr_float", 9) == 0) SetComponentType(itk::ImageIOBase::FLOAT);
+ else if (memicmp(c, "double",6) == 0 || memicmp(c, "xdr_double",10)== 0) SetComponentType(itk::ImageIOBase::DOUBLE);
+ else return ER_XDR_DATA;
+
+ if (memicmp(c, "xdr_", 4) == 0) forcenoswap=0;
+ }
+
+ //Read coords here
+ 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;
+
+ if (coords) { /* expect AVS coordinates ? */
+ coords *= sizeof(float);
+ fstream = fopen(m_FileName.c_str(), "rb");
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;
- SetNumberOfDimensions(ndim);
-
- nspace = ndim;
-
- 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) return ER_XDR_DIM;
-
- total *= dim[i];
- coords += dim[i];
- }
- for (i=0; i<ndim; i++) {
- SetDimensions(i,dim[i]);
- SetSpacing(i,1.);
- SetOrigin(i,0.);
- }
-
- c = scan_header(file, "nspace", offset, 1);
- if (c) nspace = atoi(c);
- if (nspace<1 || ndim > MAXDIM) return ER_XDR_NSPACE;
- if (nspace != ndim) return ER_NOT_HANDLED;
-
- c = scan_header(file, "veclen", offset, 1);
- if (c) veclen = atoi(c);
- if (veclen<0 /*|| veclen>1000*/) return ER_XDR_VECLEN;
- SetNumberOfComponents(veclen);
- if (veclen==1) SetPixelType(itk::ImageIOBase::SCALAR);
- else SetPixelType(itk::ImageIOBase::VECTOR);
-
- c = scan_header(file, "data", offset, 1);
- if (c)
- {
- if (memicmp(c, "byte", 4) == 0 || memicmp(c, "xdr_byte", 8) == 0) SetComponentType(itk::ImageIOBase::CHAR);
- else if (memicmp(c, "short", 5) == 0 || memicmp(c, "xdr_short", 9) == 0) SetComponentType(itk::ImageIOBase::SHORT);
- else if (memicmp(c, "int" , 3) == 0 || memicmp(c, "xdr_int" , 7) == 0) SetComponentType(itk::ImageIOBase::INT);
- else if (memicmp(c, "real", 4) == 0 || memicmp(c, "xdr_real", 8) == 0) SetComponentType(itk::ImageIOBase::FLOAT);
- else if (memicmp(c, "float", 5) == 0 || memicmp(c, "xdr_float", 9) == 0) SetComponentType(itk::ImageIOBase::FLOAT);
- else if (memicmp(c, "double",6) == 0 || memicmp(c, "xdr_double",10)== 0) SetComponentType(itk::ImageIOBase::DOUBLE);
- else return ER_XDR_DATA;
-
- if (memicmp(c, "xdr_", 4) == 0) forcenoswap=0;
- }
-
- //Read coords here
- 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;
-
- if (coords) /* expect AVS coordinates ? */
- {
- coords *= sizeof(float);
- fstream = fopen(m_FileName.c_str(), "rb");
- if (fstream == NULL) return ER_XDR_OPEN;
-
- float *points = (float *)malloc(coords);
- if (points == NULL) return ER_OUTOFMEMORY;
-
- //Seek to coordinates position in file
- if (fseek(fstream,-static_cast<int>(coords),SEEK_END)) return ER_XDR_READ;
- 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;
- }
- }
+ float *points = (float *)malloc(coords);
+ if (points == NULL) return ER_OUTOFMEMORY;
+
+ //Seek to coordinates position in file
+ if (fseek(fstream,-static_cast<int>(coords),SEEK_END)) return ER_XDR_READ;
+ 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;
}
+ }
+ }
- switch (field) {
- case UNIFORM:
- for (i=0; i<GetNumberOfDimensions(); i++) {
- SetSpacing(i,10.*(points[i*2+1]-points[i*2])/(GetDimensions(i)-1));
- SetOrigin(i,10.*points[i*2]);
- }
- break;
- case RECTILINEAR:
- //Rectilinear is reinterpreted as uniform because ITK does not know rectilinear
- //Error if fails
- for (i=0; i<GetNumberOfDimensions(); i++) {
- //Compute mean spacing
- SetSpacing(i,10*(points[GetDimensions(i)-1]-points[0])/(GetDimensions(i)-1));
- SetOrigin(i,10*points[0]);
-
- //Test if rectilinear image is actually uniform (tolerance 0.1 mm)
- for (j=0; j<GetDimensions(i)-1; j++) {
- if (fabs((points[j+1]-points[j])*10-GetSpacing(i))>0.1) {
- free(points);
- fclose(fstream);
- return ER_NOT_HANDLED;
- }
- }
- points += (int)GetDimensions(i);
+ float *p = points;
+ switch (field) {
+ case UNIFORM:
+ for (i=0; i<GetNumberOfDimensions(); i++) {
+ SetSpacing(i,10.*(points[i*2+1]-points[i*2])/(GetDimensions(i)-1));
+ SetOrigin(i,10.*points[i*2]);
+ }
+ break;
+ case RECTILINEAR:
+ //Rectilinear is reinterpreted as uniform because ITK does not know rectilinear
+ //Error if fails
+ for (i=0; i<GetNumberOfDimensions(); i++) {
+ //Compute mean spacing
+ SetSpacing(i,10*(p[GetDimensions(i)-1]-p[0])/(GetDimensions(i)-1));
+ SetOrigin(i,10*p[0]);
+
+ //Test if rectilinear image is actually uniform (tolerance 0.1 mm)
+ if(i<3) { // Only for first 3 dimensions because spacing is barely used in other dims
+ for (j=0; j<GetDimensions(i)-1; j++) {
+ if (fabs((p[j+1]-p[j])*10-GetSpacing(i))>0.1) {
+ free(points);
+ fclose(fstream);
+ return ER_NOT_HANDLED;
}
- for (i=0; i<GetNumberOfDimensions(); i++)
- points -= GetDimensions(i);
- break;
- case IRREGULAR:
- free(points);
- fclose(fstream);
- return ER_NOT_HANDLED;
+ }
}
- free(points);
- fclose(fstream);
+ p += (int)GetDimensions(i);
+ }
+ break;
+ case IRREGULAR:
+ free(points);
+ fclose(fstream);
+ return ER_NOT_HANDLED;
}
- return OK;
+ free(points);
+ fclose(fstream);
+ }
+ return OK;
}
//====================================================================
// Read image information (copied from XDRreader)
-void clitk::XdrImageIO::ReadImageInformation() {
- int result = ReadImageInformationWithError();
- if (result) ITKError("clitk::XdrImageIO::ReadImageInformation",result);
+void clitk::XdrImageIO::ReadImageInformation()
+{
+ int result = ReadImageInformationWithError();
+ if (result) ITKError("clitk::XdrImageIO::ReadImageInformation",result);
}
//====================================================================
// 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;
- int j, coords=0, datasize=0, HeaderSize;
- unsigned int i,iNumRead,total=1;
- 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;
- char *file = const_cast<char *>(m_FileName.c_str());
- int offset=0;
- AVSType field=UNIFORM;
-
- for (i=0; i<GetNumberOfDimensions(); i++) coords += GetDimensions(i);
-
- total = GetImageSizeInPixels();
- nspace = GetNumberOfDimensions();
-
- 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;
+{
+ //AVSINT dim[5];
+ int /*ndim,*/ nspace/*, veclen=1, data=AVS_TYPE_BYTE, field=UNIFORM*/;
+ int iNkiCompression = 0;
+ int j, coords=0, datasize=0, HeaderSize;
+ unsigned int i,iNumRead,total=1;
+ 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;
+ char *file = const_cast<char *>(m_FileName.c_str());
+ int offset=0;
+ // AVSType field=UNIFORM;
+
+ for (i=0; i<GetNumberOfDimensions(); i++) coords += GetDimensions(i);
+
+ total = GetImageSizeInPixels();
+ nspace = GetNumberOfDimensions();
+
+ 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);
+
+ c = scan_header(file, "coord1[0]", offset, 1);
+ if (c) HeaderSize = 32768;
+ else HeaderSize = 2048;
+
+ fstream = fopen(file, "rb");
+ if (fstream == NULL)
+ return ER_XDR_OPEN;
+
+ if (offset) 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;
+ }
+
+ buff = (char*)malloc(HeaderSize);
+ if (buff == NULL) {
+ return ER_OUTOFMEMORY;
+ }
+ memset(buff, 0, HeaderSize);
+ iNumRead = fread(buff, 1, HeaderSize, fstream);
+ if (iNumRead < 1) {
+ free(buff);
+ fclose(fstream);
+ return ER_XDR_READ;
+ }
- c = scan_header(file, "nki_compression", offset, 1);
- if (c) iNkiCompression = atoi(c);
+ for (i=0; i<iNumRead; i++) {
+ if (buff[i] == 12) break;
+ }
- c = scan_header(file, "coord1[0]", offset, 1);
- if (c) HeaderSize = 32768;
- else HeaderSize = 2048;
+ free(buff);
- fstream = fopen(file, "rb");
- if (fstream == NULL)
- return ER_XDR_OPEN;
+ if (i==iNumRead) return ER_XDR_NOCTRLL;
- if (offset) fseek(fstream, offset, SEEK_SET);
+ total = GetImageSizeInBytes();
- while (1)
- {
- if (fgets(temp, 500, fstream) == NULL )
- return ER_XDR_NOCTRLL; /* end of file */
+ //We add casts because the resulting quantity can be negative.
+ //There is no risk of looping because i and iNumRead are about the size of the header
+ fseek(fstream, static_cast<int>(i)+2-static_cast<int>(iNumRead), SEEK_CUR);
- if (temp[0] == 10) continue;
+ if (total && iNkiCompression) {
+ long iCurPos;
+ unsigned long iSize;
+ signed char* pCompressed;
- if (temp[0] == 12)
- {
- fseek(fstream, -2, SEEK_CUR);
- break;
- } /* ^L end of header */
+ /* Read or guess the size of the compressed data */
+ iCurPos = ftell(fstream);
+ iSize = get_nki_compressed_size(fstream);
- if (temp[0] != '#') break;
- }
+ if (iSize==0) {
+ fseek(fstream, 0, SEEK_END);
+ iSize = ftell(fstream);
+ iSize = iSize - iCurPos - coords;
- buff = (char*)malloc(HeaderSize);
- if (buff == NULL)
- {
- return ER_OUTOFMEMORY;
- }
- memset(buff, 0, HeaderSize);
- iNumRead = fread(buff, 1, HeaderSize, fstream);
- if (iNumRead < 1)
- {
- free(buff);
- fclose(fstream);
- return ER_XDR_READ;
+ // Get compressed size from header if possible; else use uncompressed size as safe estimate
+ if (iSize>total && offset) iSize=total+8;
}
- for (i=0; i<iNumRead; i++) {
- if (buff[i] == 12) break;
- }
-
- free(buff);
-
- if (i==iNumRead) return ER_XDR_NOCTRLL;
-
- total = GetImageSizeInBytes();
-
- //We add casts because the resulting quantity can be negative.
- //There is no risk of looping because i and iNumRead are about the size of the header
- fseek(fstream, static_cast<int>(i)+2-static_cast<int>(iNumRead), SEEK_CUR);
-
- if (total && iNkiCompression)
- {
- long iCurPos;
- unsigned long iSize;
- signed char* pCompressed;
-
- /* Read or guess the size of the compressed data */
- iCurPos = ftell(fstream);
- iSize = get_nki_compressed_size(fstream);
+ fseek(fstream, iCurPos, SEEK_SET);
- if (iSize==0)
- {
- fseek(fstream, 0, SEEK_END);
- iSize = ftell(fstream);
- iSize = iSize - iCurPos - coords;
-
- // Get compressed size from header if possible; else use uncompressed size as safe estimate
- if (iSize>total && offset) iSize=total+8;
- }
-
- fseek(fstream, iCurPos, SEEK_SET);
-
- /* Allocate space for the compressed pixels */
- pCompressed = (signed char*)malloc(iSize);
- if (!pCompressed)
- {
- fclose(fstream);
- return ER_OUTOFMEMORY;
- }
+ /* Allocate space for the compressed pixels */
+ pCompressed = (signed char*)malloc(iSize);
+ if (!pCompressed) {
+ fclose(fstream);
+ return ER_OUTOFMEMORY;
+ }
- /* Read the compressed pixels */
- if (fread( (void *)pCompressed, 1, iSize, fstream ) != iSize)
- {
- fclose(fstream);
- return ER_XDR_READ;
- }
+ /* Read the compressed pixels */
+ if (fread( (void *)pCompressed, 1, iSize, fstream ) != iSize) {
+ fclose(fstream);
+ return ER_XDR_READ;
+ }
- if (!nki_private_decompress((short*)buffer, pCompressed, iSize))
- {
- fclose(fstream);
- return ER_DECOMPRESSION;
- }
+ if (!nki_private_decompress((short*)buffer, pCompressed, iSize)) {
+ fclose(fstream);
+ return ER_DECOMPRESSION;
+ }
- // if (offset)
- fseek(fstream, iCurPos + global_len, SEEK_SET);
+ // if (offset)
+ fseek(fstream, iCurPos + global_len, SEEK_SET);
- free(pCompressed);
- goto READ_COORDS;
- }
+ free(pCompressed);
+ goto READ_COORDS;
+ }
- if (total)
- {
- if (fread( (void *)buffer, 1, total, fstream ) != total)
- {
- fclose(fstream);
- return ER_XDR_READ;
- }
+ if (total) {
+ if (fread( (void *)buffer, 1, total, fstream ) != total) {
+ fclose(fstream);
+ return ER_XDR_READ;
}
-
- /* swap data if required (xdr is low-endian) */
-
- datasize = GetComponentSize();
- if (!(*(char *)(&swap_test)) && !forcenoswap)
- {
- if (datasize==2)
- {
- c = (char *)buffer;
- 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 *)buffer;
- 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 *)buffer;
- 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;
- }
- }
+ }
+
+ /* swap data if required (xdr is low-endian) */
+
+ datasize = GetComponentSize();
+ if (!(*(char *)(&swap_test)) && !forcenoswap) {
+ if (datasize==2) {
+ c = (char *)buffer;
+ 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 *)buffer;
+ 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 *)buffer;
+ 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;
+ }
}
+ }
READ_COORDS:
- fclose(fstream);
- return OK;
+ fclose(fstream);
+ return OK;
}
//====================================================================
// Read image information (copied from Xdr reader)
-void clitk::XdrImageIO::Read(void * buffer) {
- int result = ReadWithError(buffer);
- if (result) ITKError("clitk::XdrImageIO::Read",result);
+void clitk::XdrImageIO::Read(void * buffer)
+{
+ int result = ReadWithError(buffer);
+ if (result) ITKError("clitk::XdrImageIO::Read",result);
}
//====================================================================
// Read Image Information
bool clitk::XdrImageIO::CanReadFile(const char* FileNameToRead)
{
- char temp[512];
- FILE *fstream;
+ char temp[512];
+ FILE *fstream;
- fstream = fopen(FileNameToRead, "rt");
- if (fstream == NULL)
+ fstream = fopen(FileNameToRead, "rt");
+ if (fstream == NULL)
// {
// AVSerror("Couldn't open file " << FileNameToRead);
- return false;
+ return false;
// }
- fgets(temp, 500, fstream);
- fclose(fstream);
+ fgets(temp, 500, fstream);
+ fclose(fstream);
- if (memcmp(temp, "# AVS", 5)==0)
- return true;
- else
- return false;
+ if (memcmp(temp, "# AVS", 5)==0)
+ return true;
+ else
+ return false;
} ////
-void clitk::XdrImageIO::ITKError(std::string funcName, int msgID) {
- itkExceptionMacro(<< "Error in " << funcName << ". Message: " << gl_ErrorMsg[msgID]);
+void clitk::XdrImageIO::ITKError(std::string funcName, int msgID)
+{
+ itkExceptionMacro(<< "Error in " << funcName << ". Message: " << gl_ErrorMsg[msgID]);
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff