Doxygen Source Code Documentation
ge4_header.c File Reference
#include <stdio.h>#include <stdlib.h>#include <string.h>#include "ge4_header.h"Go to the source code of this file.
Functions | |
| unsigned long | THD_filesize (char *pathname) |
| int | swap_2 (void *ptr) |
| int | swap_4 (void *ptr) |
| int | swap_2_multi (void *ptr, int num_shorts) |
| int | ge4_read_header (ge4_header *H, char *filename, int get_image) |
| int | ge4_validate_header (ge4_header *h) |
| int | ge4_swap_all_bytes (ge4_header *h) |
| int | idisp_ge4_study_header (char *info, ge4_study_t *st) |
| int | idisp_ge4_image_header (char *info, ge4_image_t *im) |
| int | idisp_ge4_series_header (char *info, ge4_series_t *s) |
Variables | |
| char * | g_ge4_sl_im_modes [] |
| char * | g_ge4_sl_pulse_seqs [] |
| char * | g_ge4_sl_orient [] = { "supine", "prone", "Lt", "Rt" } |
Function Documentation
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Validate and read header data from a GEMS 4.x formatted file.
Definition at line 77 of file ge4_header.c. References ge4_study_t::age, ge4_series_t::center, ge4_study_t::date, ge4_image_t::echo_num, ge4_image_t::flip_angle, ge4_image_t::fNEX, ge4_series_t::fov, free, GE4_HEADER_LENGTH, GE4_IMAGE_SIZE, GE4_IMAGE_TITLE, GE4_L_IM_NUM, GE4_L_IM_TITLE, GE4_L_SER_PL_DESC, GE4_L_SER_SER_NUM, GE4_L_SER_TITLE, GE4_L_STDY_AGE, GE4_L_STDY_DATE, GE4_L_STDY_NUM, GE4_L_STDY_PAT_ID, GE4_L_STDY_PAT_NAME, GE4_L_STDY_TIME, GE4_L_STDY_TITLE, GE4_OFF_IMG_ECHO_NUM, GE4_OFF_IMG_FLIP_ANGLE, GE4_OFF_IMG_IM_LOCN, GE4_OFF_IMG_IM_NUM, GE4_OFF_IMG_IM_SPACING, GE4_OFF_IMG_IM_THICK, GE4_OFF_IMG_NEX_INT, GE4_OFF_IMG_NEX_REAL, GE4_OFF_IMG_NUM_ECHOS, GE4_OFF_IMG_TABLE_POSN, GE4_OFF_IMG_TE, GE4_OFF_IMG_TI, GE4_OFF_IMG_TITLE, GE4_OFF_IMG_TR, GE4_OFF_SER_CENTER, GE4_OFF_SER_FOV, GE4_OFF_SER_IM_MAT, GE4_OFF_SER_IM_MODE, GE4_OFF_SER_ORIENT, GE4_OFF_SER_PLANE_DESC, GE4_OFF_SER_PLANE_TYPE, GE4_OFF_SER_PULSE_SEQ, GE4_OFF_SER_SCAN_MAT_X, GE4_OFF_SER_SCAN_MAT_Y, GE4_OFF_SER_SERIES_NUM, GE4_OFF_SER_TITLE, GE4_OFF_STDY_AGE, GE4_OFF_STDY_DATE, GE4_OFF_STDY_NUM, GE4_OFF_STDY_PAT_ID, GE4_OFF_STDY_PAT_NAME, GE4_OFF_STDY_SEX, GE4_OFF_STDY_TIME, GE4_OFF_STDY_TITLE, GE4_SERIES_TITLE, GE4_STUDY_TITLE, ge4_validate_header(), ge4_header::im_bytes, ge4_header::im_h, ge4_image_t::im_loc, ge4_series_t::im_mat, ge4_series_t::im_mode, ge4_image_t::im_num, ge4_image_t::im_spacing, ge4_image_t::im_thickness, ge4_header::image, ge4_image_t::iNEX, malloc, ge4_study_t::num, ge4_image_t::num_echoes, ge4_series_t::orient, ge4_study_t::pat_id, ge4_study_t::pat_name, ge4_series_t::plane_desc, ge4_series_t::plane_type, ge4_series_t::pulse_seq, ge4_series_t::scan_mat_x, ge4_series_t::scan_mat_y, ge4_header::ser_h, ge4_series_t::series_num, ge4_study_t::sex, ge4_header::std_h, ge4_header::swap, swap_2_multi(), ge4_image_t::table_posn, ge4_image_t::te, THD_filesize(), ge4_image_t::ti, ge4_study_t::time, ge4_study_t::title, ge4_series_t::title, ge4_image_t::title, and ge4_image_t::tr. Referenced by mri_read_ge4(), and process_ge4().
00078 {
00079 ge4_image_t * ih;
00080 ge4_series_t * sh;
00081 ge4_study_t * st;
00082 FILE * fp;
00083 int file_len;
00084 int rres = 0; /* read result */
00085
00086 if ( filename == NULL || H == NULL )
00087 {
00088 fprintf( stderr, "** rg4h : bad params: %p, %p\n", filename, H );
00089 return -1;
00090 }
00091
00092 file_len = THD_filesize( filename );
00093
00094 /* file size must be fixed at 145408 bytes (142 KB) */
00095 if ( file_len != (GE4_HEADER_LENGTH + GE4_IMAGE_SIZE) )
00096 return 1;
00097
00098 /* clear structure */
00099 memset( H, 0, sizeof(ge4_header) );
00100
00101 if ( (fp = fopen( filename, "r" )) == NULL )
00102 {
00103 fprintf( stderr, "ge4_read_header: failed to open '%s' for reading\n",
00104 filename);
00105 return -1;
00106 }
00107
00108 /* quickly scan and validate titles */
00109
00110 sh = &H->ser_h; /* set helper pointer */
00111 ih = &H->im_h; /* set helper pointer */
00112 st = &H->std_h; /* set helper pointer */
00113
00114 fseek( fp, GE4_OFF_STDY_TITLE, SEEK_SET );
00115 rres |= (1 - fread( st->title, GE4_L_STDY_TITLE, 1, fp ));
00116
00117 fseek( fp, GE4_OFF_SER_TITLE, SEEK_SET );
00118 rres |= (1 - fread( sh->title, GE4_L_SER_TITLE, 1, fp ));
00119
00120 fseek( fp, GE4_OFF_IMG_TITLE, SEEK_SET );
00121 rres |= (1 - fread( ih->title, GE4_L_IM_TITLE, 1, fp ));
00122
00123 /* if read failure or bad title fields, we're outta' here */
00124 if ( rres ||
00125 strncmp( st->title, GE4_STUDY_TITLE, GE4_L_STDY_TITLE ) ||
00126 strncmp( sh->title, GE4_SERIES_TITLE, GE4_L_SER_TITLE ) ||
00127 strncmp( ih->title, GE4_IMAGE_TITLE, GE4_L_IM_TITLE )
00128 )
00129 return 1;
00130
00131
00132 /* study header fields */
00133
00134 fseek( fp, GE4_OFF_STDY_NUM, SEEK_SET );
00135 rres |= (1 - fread( st->num, GE4_L_STDY_NUM, 1, fp ));
00136
00137 fseek( fp, GE4_OFF_STDY_DATE, SEEK_SET );
00138 rres |= (1 - fread( st->date, GE4_L_STDY_DATE, 1, fp ));
00139
00140 fseek( fp, GE4_OFF_STDY_TIME, SEEK_SET );
00141 rres |= (1 - fread( st->time, GE4_L_STDY_TIME, 1, fp ));
00142
00143 fseek( fp, GE4_OFF_STDY_PAT_NAME, SEEK_SET );
00144 rres |= (1 - fread( st->pat_name, GE4_L_STDY_PAT_NAME, 1, fp ));
00145
00146 fseek( fp, GE4_OFF_STDY_PAT_ID, SEEK_SET );
00147 rres |= (1 - fread( st->pat_id, GE4_L_STDY_PAT_ID, 1, fp ));
00148
00149 fseek( fp, GE4_OFF_STDY_AGE, SEEK_SET );
00150 rres |= (1 - fread( st->age, GE4_L_STDY_AGE, 1, fp ));
00151
00152 fseek( fp, GE4_OFF_STDY_SEX, SEEK_SET );
00153 rres |= (1 - fread( &st->sex, 1, 1, fp ));
00154
00155 /* series header fields */
00156
00157 fseek( fp, GE4_OFF_SER_SERIES_NUM, SEEK_SET );
00158 rres |= (1 - fread( sh->series_num, GE4_L_SER_SER_NUM, 1, fp ));
00159
00160 fseek( fp, GE4_OFF_SER_PLANE_TYPE, SEEK_SET );
00161 rres |= (1 - fread( &sh->plane_type, sizeof(sh->plane_type), 1, fp ));
00162
00163 fseek( fp, GE4_OFF_SER_PLANE_DESC, SEEK_SET );
00164 rres |= (1 - fread( sh->plane_desc, GE4_L_SER_PL_DESC, 1, fp ));
00165
00166 fseek( fp, GE4_OFF_SER_IM_MODE, SEEK_SET );
00167 rres |= (1 - fread( &sh->im_mode, sizeof(sh->im_mode), 1, fp ));
00168
00169 fseek( fp, GE4_OFF_SER_PULSE_SEQ, SEEK_SET );
00170 rres |= (1 - fread( &sh->pulse_seq, sizeof(sh->pulse_seq), 1, fp ));
00171
00172 fseek( fp, GE4_OFF_SER_FOV, SEEK_SET );
00173 rres |= (1 - fread( &sh->fov, sizeof(sh->fov), 1, fp ));
00174
00175 fseek( fp, GE4_OFF_SER_CENTER, SEEK_SET );
00176 rres |= (1 - fread( sh->center, sizeof(sh->center), 1, fp ));
00177
00178 fseek( fp, GE4_OFF_SER_ORIENT, SEEK_SET );
00179 rres |= (1 - fread( &sh->orient, sizeof(sh->orient), 1, fp ));
00180
00181 fseek( fp, GE4_OFF_SER_SCAN_MAT_X, SEEK_SET );
00182 rres |= (1 - fread( &sh->scan_mat_x, sizeof(sh->scan_mat_x), 1, fp ));
00183
00184 fseek( fp, GE4_OFF_SER_SCAN_MAT_Y, SEEK_SET );
00185 rres |= (1 - fread( &sh->scan_mat_y, sizeof(sh->scan_mat_y), 1, fp ));
00186
00187 fseek( fp, GE4_OFF_SER_IM_MAT, SEEK_SET );
00188 rres |= (1 - fread( &sh->im_mat, sizeof(sh->im_mat), 1, fp ));
00189
00190
00191 /* image header fields */
00192
00193 fseek( fp, GE4_OFF_IMG_IM_NUM, SEEK_SET );
00194 rres |= (1 - fread( ih->im_num, GE4_L_IM_NUM, 1, fp ));
00195
00196 fseek( fp, GE4_OFF_IMG_IM_LOCN, SEEK_SET );
00197 rres |= (1 - fread( &ih->im_loc, sizeof(ih->im_loc), 1, fp ));
00198
00199 fseek( fp, GE4_OFF_IMG_TABLE_POSN, SEEK_SET );
00200 rres |= (1 - fread( &ih->table_posn, sizeof(ih->table_posn), 1, fp ));
00201
00202 fseek( fp, GE4_OFF_IMG_IM_THICK, SEEK_SET );
00203 rres |= (1 - fread( &ih->im_thickness, sizeof(ih->im_thickness), 1, fp ));
00204
00205 fseek( fp, GE4_OFF_IMG_IM_SPACING, SEEK_SET );
00206 rres |= (1 - fread( &ih->im_spacing, sizeof(ih->im_spacing), 1, fp ));
00207
00208 fseek( fp, GE4_OFF_IMG_TR, SEEK_SET );
00209 rres |= (1 - fread( &ih->tr, sizeof(ih->tr), 1, fp ));
00210
00211 fseek( fp, GE4_OFF_IMG_TE, SEEK_SET );
00212 rres |= (1 - fread( &ih->te, sizeof(ih->te), 1, fp ));
00213
00214 fseek( fp, GE4_OFF_IMG_TI, SEEK_SET );
00215 rres |= (1 - fread( &ih->ti, sizeof(ih->ti), 1, fp ));
00216
00217 fseek( fp, GE4_OFF_IMG_NUM_ECHOS, SEEK_SET );
00218 rres |= (1 - fread( &ih->num_echoes, sizeof(ih->num_echoes), 1, fp ));
00219
00220 fseek( fp, GE4_OFF_IMG_ECHO_NUM, SEEK_SET );
00221 rres |= (1 - fread( &ih->echo_num, sizeof(ih->echo_num), 1, fp ));
00222
00223 fseek( fp, GE4_OFF_IMG_NEX_INT, SEEK_SET );
00224 rres |= (1 - fread( &ih->iNEX, sizeof(ih->iNEX), 1, fp ));
00225
00226 fseek( fp, GE4_OFF_IMG_NEX_REAL, SEEK_SET );
00227 rres |= (1 - fread( &ih->fNEX, sizeof(ih->fNEX), 1, fp ));
00228
00229 fseek( fp, GE4_OFF_IMG_FLIP_ANGLE, SEEK_SET );
00230 rres |= (1 - fread( &ih->flip_angle, sizeof(ih->flip_angle), 1, fp ));
00231
00232 if ( rres )
00233 {
00234 fprintf( stderr, "** failed to read ge4 header for '%s'\n", filename );
00235 return -1;
00236 }
00237
00238 if ( ge4_validate_header( H ) )
00239 return 1;
00240
00241 if ( get_image )
00242 {
00243 if ( (H->image = (short *)malloc( GE4_IMAGE_SIZE )) == NULL )
00244 {
00245 fprintf( stderr, "** failed to allocate %d bytes for image\n",
00246 GE4_IMAGE_SIZE );
00247 return -1;
00248 }
00249
00250 fseek( fp, GE4_HEADER_LENGTH, SEEK_SET );
00251 rres = fread( H->image, GE4_IMAGE_SIZE, 1, fp );
00252
00253 if ( rres != 1 )
00254 {
00255 fprintf( stderr, "** failed to read ge4 image for file '%s'\n",
00256 filename );
00257 free( H->image );
00258 return -1;
00259 }
00260
00261 H->im_bytes = GE4_IMAGE_SIZE; /* note it for "outsiders" */
00262
00263 if ( H->swap )
00264 swap_2_multi( H->image, GE4_IMAGE_SIZE/2 );
00265 }
00266
00267 return 0;
00268 }
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Definition at line 285 of file ge4_header.c. References ge4_swap_all_bytes(), ge4_header::im_h, ge4_series_t::im_mode, ge4_series_t::plane_type, ge4_series_t::pulse_seq, and ge4_header::ser_h. Referenced by ge4_read_header().
00286 {
00287 ge4_series_t * s;
00288 ge4_image_t * im;
00289
00290 if ( h == NULL )
00291 return -1;
00292
00293 s = &h->ser_h;
00294 im = &h->im_h;
00295
00296 /* note that titles have already been validated */
00297
00298 if ( (s->plane_type < 0) || (s->plane_type > 4) ||
00299 (s->im_mode < 0) || (s->im_mode > 4) ||
00300 (s->pulse_seq < 0) || (s->pulse_seq > 25) )
00301 {
00302 ge4_swap_all_bytes( h );
00303 }
00304
00305 /* if these are still off, we are hosed... */
00306 if ( (s->plane_type < 0) || (s->plane_type > 4) ||
00307 (s->im_mode < 0) || (s->im_mode > 4) ||
00308 (s->pulse_seq < 0) || (s->pulse_seq > 25) )
00309 {
00310 return -1;
00311 }
00312
00313 return 0;
00314 }
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Definition at line 406 of file ge4_header.c. References ge4_image_t::echo_num, ge4_image_t::flip_angle, ge4_image_t::fNEX, ge4_image_t::im_loc, ge4_image_t::im_num, ge4_image_t::im_spacing, ge4_image_t::im_thickness, ge4_image_t::iNEX, ge4_image_t::num_echoes, ge4_image_t::table_posn, ge4_image_t::te, ge4_image_t::ti, ge4_image_t::title, and ge4_image_t::tr. Referenced by process_ge4().
00407 {
00408 if ( info )
00409 fputs( info, stdout );
00410
00411 if ( im == NULL )
00412 {
00413 printf( "r_idisp_ge4_image_t: im == NULL" );
00414 return -1;
00415 }
00416
00417 printf( " ge4_image_t at %p :\n"
00418 " title = %s\n"
00419 " im_num = %s\n"
00420 " im_loc = %.3f\n"
00421 " table_posn = %.3f\n"
00422 " im_thickness = %.3f\n"
00423 " im_spacing = %.3f\n"
00424 " tr (in ms) = %.3f\n"
00425 " te (in ms) = %.3f\n"
00426 " ti (in ms) = %.3f\n"
00427 " num_echoes = %d\n"
00428 " echo_num = %d\n"
00429 " iNEX = %d\n"
00430 " fNEX = %.3f\n"
00431 " flip_angle = %d\n",
00432 im, im->title, im->im_num, im->im_loc, im->table_posn,
00433 im->im_thickness, im->im_spacing, im->tr, im->te, im->ti,
00434 im->num_echoes, im->echo_num, im->iNEX, im->fNEX, im->flip_angle
00435 );
00436
00437 return 0;
00438 }
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Definition at line 445 of file ge4_header.c. References ge4_series_t::center, ge4_series_t::fov, g_ge4_sl_im_modes, g_ge4_sl_orient, g_ge4_sl_pulse_seqs, GE4M_IND2STR, ge4_series_t::im_mat, ge4_series_t::im_mode, ge4_series_t::orient, ge4_series_t::plane_desc, ge4_series_t::plane_type, ge4_series_t::pulse_seq, ge4_series_t::scan_mat_x, ge4_series_t::scan_mat_y, ge4_series_t::series_num, and ge4_series_t::title. Referenced by process_ge4().
00446 {
00447 if ( info )
00448 fputs( info, stdout );
00449
00450 if ( s == NULL )
00451 {
00452 printf( "r_idisp_ge4_series_t: s == NULL" );
00453 return -1;
00454 }
00455
00456 printf( " ge4_series_t at %p :\n"
00457 " title = %s\n"
00458 " series_num = %s\n"
00459 " plane_type, plane_desc = %d, %s\n"
00460 " image_mode = %d (%s)\n"
00461 " pulse_seq = %d (%s)\n"
00462 " FOV (in mm) = %.3f\n"
00463 " center[0], c[1], c[2] = %.3f, %.3f, %.3f\n"
00464 " orient = %d (%s)\n"
00465 " scan_mat_x, scan_mat_y = %d, %d\n"
00466 " im_mat = %d\n",
00467 s, s->title, s->series_num, s->plane_type, s->plane_desc,
00468 s->im_mode, GE4M_IND2STR(s->im_mode, g_ge4_sl_im_modes),
00469 s->pulse_seq, GE4M_IND2STR(s->pulse_seq, g_ge4_sl_pulse_seqs),
00470 s->fov, s->center[0], s->center[1], s->center[2],
00471 s->orient, GE4M_IND2STR(s->orient,g_ge4_sl_orient),
00472 s->scan_mat_x, s->scan_mat_y, s->im_mat
00473 );
00474
00475 return 0;
00476 }
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Definition at line 374 of file ge4_header.c. References ge4_study_t::age, ge4_study_t::date, ge4_study_t::num, ge4_study_t::pat_id, ge4_study_t::pat_name, ge4_study_t::sex, ge4_study_t::time, and ge4_study_t::title. Referenced by process_ge4().
00375 {
00376 if ( info )
00377 fputs( info, stdout );
00378
00379 if ( st == NULL )
00380 {
00381 printf( "r_idisp_ge4_study_t: st == NULL" );
00382 return -1;
00383 }
00384
00385 printf( " ge4_study_t at %p :\n"
00386 " title = %s\n"
00387 " num = %s\n"
00388 " date = %s\n"
00389 " time = %s\n"
00390 " pat_name = %s\n"
00391 " pat_id = %s\n"
00392 " age = %s\n"
00393 " sex = %c\n",
00394 st, st->title, st->num, st->date, st->time,
00395 st->pat_name, st->pat_id, st->age, st->sex
00396 );
00397
00398 return 0;
00399 }
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Swap the 2 bytes pointed to by ppp: ab -> ba. Definition at line 526 of file ge4_header.c.
00527 {
00528 unsigned char * addr = ptr;
00529
00530 addr[0] ^= addr[1]; addr[1] ^= addr[0]; addr[0] ^= addr[1];
00531
00532 return 0;
00533 }
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Definition at line 483 of file ge4_header.c. Referenced by ge4_read_header().
00484 {
00485 unsigned char * cp0, * cp1;
00486 unsigned char tmpc;
00487 int index;
00488
00489 if ( ptr == NULL ) return -1;
00490
00491 cp0 = (unsigned char *)ptr;
00492 cp1 = cp0 + 1;
00493
00494 for ( index = 0; index < num_shorts; index++ )
00495 {
00496 tmpc = *cp0;
00497 *cp0 = *cp1;
00498 *cp1 = tmpc;
00499
00500 cp0 += 2;
00501 cp1 += 2;
00502 }
00503
00504 return 0;
00505 }
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Swap the 4 bytes pointed to by ppp: abcd -> dcba. Definition at line 512 of file ge4_header.c.
00513 {
00514 unsigned char * addr = ptr;
00515
00516 addr[0] ^= addr[3]; addr[3] ^= addr[0]; addr[0] ^= addr[3];
00517 addr[1] ^= addr[2]; addr[2] ^= addr[1]; addr[1] ^= addr[2];
00518
00519 return 0;
00520 }
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Return the file length (0 if file not found). Definition at line 499 of file Ifile.c.
00500 {
00501 static struct stat buf ; int ii ;
00502
00503 if( pathname == NULL ) return -1 ;
00504 ii = stat( pathname , &buf ) ; if( ii != 0 ) return -1 ;
00505 return buf.st_size ;
00506 }
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Variable Documentation
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Initial value:
{ "2D single", "2D multiple", "3D volume", "cine",
"spectroscopy" }Definition at line 52 of file ge4_header.c. Referenced by idisp_ge4_series_header(). |
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Definition at line 61 of file ge4_header.c. Referenced by idisp_ge4_series_header(). |
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Initial value:
{ "memp", "ir", "ps", "rm", "rmge", "gre", "vemp",
"mpgr", "mpgrv", "mpirs", "mpiri", "3d/gre",
"cine/gre", "spgr", "sspf", "cin/spgr", "3d/spgr",
"fse", "fve", "fspr", "fgr", "fmpspgr", "fmpgr",
"fmpir", "probe.s", "probe.p" }Definition at line 55 of file ge4_header.c. Referenced by idisp_ge4_series_header(). |
