-
Notifications
You must be signed in to change notification settings - Fork 25
/
minc_file.c
640 lines (585 loc) · 23.4 KB
/
minc_file.c
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
/* ----------------------------- MNI Header -----------------------------------
@NAME : minc_file.c
@DESCRIPTION: Code to do minc file handling.
@METHOD :
@GLOBALS :
@CALLS :
@CREATED : November 26, 1993 (Peter Neelin)
@MODIFIED :
* $Log: minc_file.c,v $
* Revision 6.2 2001-04-09 23:02:50 neelin
* Modified copyright notice, removing permission statement since copying,
* etc. is probably not permitted by our non-disclosure agreement with
* Philips.
*
* Revision 6.1 1999/10/29 17:52:04 neelin
* Fixed Log keyword
*
* Revision 6.0 1997/09/12 13:23:50 neelin
* Release of minc version 0.6
*
* Revision 5.0 1997/08/21 13:24:50 neelin
* Release of minc version 0.5
*
* Revision 4.0 1997/05/07 20:01:07 neelin
* Release of minc version 0.4
*
* Revision 3.0 1995/05/15 19:31:44 neelin
* Release of minc version 0.3
*
* Revision 2.3 1995/02/09 13:51:26 neelin
* Mods for irix 5 lint.
*
* Revision 2.2 1994/11/21 08:08:01 neelin
* Modified code to properly calculate start from centre locations, then
* changed calculation back to old way because it worked.
* Added a ncsetfill(mincid, NC_NOFILL).
*
* Revision 2.1 94/10/20 13:50:15 neelin
* Write out direction cosines to support rotated volumes.
* Store single slices as 1-slice volumes (3D instead of 2D).
* Changed storing of minc history (get args for gyrotominc).
*
* Revision 2.0 94/09/28 10:35:30 neelin
* Release of minc version 0.2
*
* Revision 1.10 94/09/28 10:35:03 neelin
* Pre-release
*
* Revision 1.9 94/05/24 15:09:36 neelin
* Break up multiple echoes or time frames into separate files for 2 echoes
* or 2 frames (put in 1 file for more).
* Changed units of repetition time, echo time, etc to seconds.
* Save echo times in dimension variable when appropriate.
* Changed to file names to end in _mri.mnc.
*
* Revision 1.8 94/03/15 14:25:41 neelin
* Changed image-max/min to use fp_scaled_max/min instead of ext_scale_max/min
* Added acquisition:comments attribute
* Changed reading of configuration file to allow execution of a command on
* the minc file.
*
* Revision 1.7 94/03/14 16:45:28 neelin
* Moved ncendef up a level so that we can catch errors.
*
* Revision 1.6 94/01/18 15:08:57 neelin
* Cast enumerated types to int when they can be negative for gcc on sun.
* (For decrementing loop on Mri_index).
*
* Revision 1.5 94/01/17 15:06:22 neelin
* Added some acquisition parameters (flip angle) and fixed error in writing
* of scanning sequence.
*
* Revision 1.4 94/01/14 11:37:24 neelin
* Fixed handling of multiple reconstructions and image types. Add spiinfo variable with extra info (including window min/max). Changed output
* file name to include reconstruction number and image type number.
*
* Revision 1.3 93/12/14 16:37:18 neelin
* Added MIcomplete attribute to image variable,.
*
* Revision 1.2 93/12/10 15:35:12 neelin
* Improved file name generation from patient name. No buffering on stderr.
* Added spi group list to minc header.
* Optionally read a defaults file to get output minc directory and owner.
*
* Revision 1.1 93/11/30 14:41:43 neelin
* Initial revision
*
@COPYRIGHT :
Copyright 1993 Peter Neelin, McConnell Brain Imaging Centre,
Montreal Neurological Institute, McGill University.
---------------------------------------------------------------------------- */
#include <gcomserver.h>
#include <ctype.h>
/* Global for minc history (sorry, but it was kludged in afterwards) */
char *minc_history = NULL;
/* Define mri dimension names */
static char *mri_dim_names[] = {
NULL, "echo_time", MItime, "phase_number", "chemical_shift", NULL};
/* Macros */
#define STRLEN(s) ((int) strlen(s))
/* ----------------------------- MNI Header -----------------------------------
@NAME : create_minc_file
@INPUT : minc_file - name of file to create. If NULL, a name is
generated internally.
clobber - if TRUE, any existing file will be overwritten.
general_info - information for creating the file.
file_prefix - string providing any directory or prefix
for internally generated filename (if it is a directory,
then it must contain the last "/")
@OUTPUT : output_file_name - returns a pointer to an internal area
containing the file name of the created file if minc_file
is NULL, or simply a pointer to minc_file. If NULL, then
nothing is returned.
@RETURNS : id of image conversion variable (MI_ERROR in case of error).
@DESCRIPTION: Routine to create the minc file.
@METHOD :
@GLOBALS :
CALLS :
@CREATED : November 26, 1993 (Peter Neelin)
@MODIFIED :
---------------------------------------------------------------------------- */
public int create_minc_file(char *minc_file, int clobber,
General_Info *general_info,
char *file_prefix, char **output_file_name)
{
static char temp_name[256];
char patient_name[256];
char *filename;
int minc_clobber;
int mincid, icvid;
Mri_Index imri;
char scan_label[MRI_NDIMS][20];
/* Prefixes for creating file name */
static char *scan_prefix[MRI_NDIMS] =
{"sl", "e", "d", "p", "cs"};
/* Turn off fatal errors */
ncopts = NCOPTS_DEFAULT;
/* Create the file name if needed */
if (minc_file != NULL) {
filename = minc_file;
}
else {
/* Get patient name */
string_to_filename(general_info->patient.name, patient_name,
sizeof(patient_name));
if (STRLEN(patient_name) == 0) {
(void) strcpy(patient_name, "unknown");
}
/* Get strings for echo number, etc. */
for (imri=0; imri < MRI_NDIMS; imri++) {
if ((general_info->size[imri] < general_info->total_size[imri]) &&
(general_info->size[imri] == 1)) {
(void) sprintf(scan_label[imri], "_%s%d", scan_prefix[imri],
general_info->first[imri]+1);
}
else {
(void) strcpy(scan_label[imri], "");
}
}
/* Create file name */
(void) sprintf(temp_name, "%s%s_%s_%s_%02d%02d%s%s%s%s%s_mri.mnc",
file_prefix,
patient_name,
general_info->study.study_id,
general_info->study.acquisition_id,
general_info->rec_num,
general_info->image_type,
scan_label[SLICE],
scan_label[ECHO],
scan_label[TIME],
scan_label[PHASE],
scan_label[CHEM_SHIFT]);
filename = temp_name;
}
/* Set output file name */
if (output_file_name != NULL)
*output_file_name = filename;
/* Set the clobber value */
if (clobber) minc_clobber = NC_CLOBBER;
else minc_clobber = NC_NOCLOBBER;
/* Create the file */
mincid = micreate(filename, minc_clobber);
if (mincid == MI_ERROR) return MI_ERROR;
/* Set up variables */
setup_minc_variables(mincid, general_info);
/* Put the file in data mode */
(void) ncsetfill(mincid, NC_NOFILL);
if (ncendef(mincid) == MI_ERROR) {
return MI_ERROR;
}
/* Create the icv */
icvid = miicv_create();
/* Set the type and range */
(void) miicv_setint(icvid, MI_ICV_TYPE, NC_SHORT);
if (general_info->is_signed)
(void) miicv_setstr(icvid, MI_ICV_SIGN, MI_SIGNED);
else
(void) miicv_setstr(icvid, MI_ICV_SIGN, MI_UNSIGNED);
(void) miicv_setdbl(icvid, MI_ICV_VALID_MIN, general_info->pixel_min);
(void) miicv_setdbl(icvid, MI_ICV_VALID_MAX, general_info->pixel_max);
/* Attach the icv */
(void) miicv_attach(icvid, mincid, ncvarid(mincid, MIimage));
return icvid;
}
/* ----------------------------- MNI Header -----------------------------------
@NAME : setup_minc_variables
@INPUT : mincid
general_info
@OUTPUT : general_info
@RETURNS : (nothing)
@DESCRIPTION: Routine to setup minc variables.
@METHOD :
@GLOBALS :
CALLS :
@CREATED : November 26, 1993 (Peter Neelin)
@MODIFIED :
---------------------------------------------------------------------------- */
public void setup_minc_variables(int mincid, General_Info *general_info)
{
Mri_Index imri;
Volume_Index ivol;
World_Index iworld;
int ndims;
int dim[MAX_VAR_DIMS];
long dimsize;
char *dimname;
int varid, imgid, spivar;
double valid_range[2];
char name[MAX_NC_NAME];
int index, last;
int regular;
Acr_Group cur_group;
Acr_Element cur_element;
int length;
char *data;
nc_type datatype;
int is_char;
int ich;
/* Define the spatial dimension names */
static char *spatial_dimnames[WORLD_NDIMS] = {MIxspace, MIyspace, MIzspace};
/* Create the dimensions from slowest to fastest */
ndims=0;
/* Create the non-spatial dimensions (from slowest to fastest) */
for (imri=MRI_NDIMS-1; (int) imri > SLICE; imri--) {
dimsize = general_info->size[imri];
if (general_info->size[imri] > 1) {
dimname = mri_dim_names[imri];
dim[ndims] = ncdimdef(mincid, dimname, dimsize);
if (imri == TIME) {
varid = micreate_std_variable(mincid, dimname, NC_DOUBLE, 1,
&dim[ndims]);
(void) miattputstr(mincid, varid, MIunits, "s");
}
else if (imri == ECHO) {
varid = ncvardef(mincid, dimname, NC_DOUBLE, 1, &dim[ndims]);
(void) miattputstr(mincid, varid, MIvartype, MI_DIMENSION);
(void) miattputstr(mincid, varid, MIspacing, MI_IRREGULAR);
(void) miattputstr(mincid, varid, MIunits, "s");
}
general_info->image_index[imri] = ndims;
ndims++;
}
}
/* Next the spatial dimensions */
for (ivol=0; ivol < VOL_NDIMS; ivol++) {
switch (ivol) {
case VSLICE:
dimsize = general_info->size[SLICE];
iworld = general_info->slice_world;
break;
case VROW:
dimsize = general_info->nrows;
iworld = general_info->row_world;
break;
case VCOLUMN:
dimsize = general_info->ncolumns;
iworld = general_info->column_world;
break;
}
dimname = spatial_dimnames[iworld];
dim[ndims] = ncdimdef(mincid, dimname, dimsize);
if (ivol == VSLICE) {
varid = micreate_std_variable(mincid, dimname, NC_DOUBLE,
1, &dim[ndims]);
/* Check for regular slices */
regular = TRUE;
last = general_info->first[SLICE] + general_info->size[SLICE] - 1;
for (index=general_info->first[SLICE]; index < last; index++) {
if (general_info->position[SLICE][index] < 0) {
regular = FALSE;
break;
}
}
if (regular)
(void) miattputstr(mincid, varid, MIspacing, MI_REGULAR);
}
else
varid = micreate_std_variable(mincid, dimname, NC_LONG, 0, NULL);
(void) miattputdbl(mincid, varid, MIstep,
general_info->step[iworld]);
(void) miattputdbl(mincid, varid, MIstart,
general_info->start[iworld]);
(void) miattputstr(mincid, varid, MIspacetype, MI_NATIVE);
(void) ncattput(mincid, varid, MIdirection_cosines,
NC_DOUBLE, WORLD_NDIMS,
general_info->dircos[iworld]);
if (ivol == VSLICE) {
general_info->image_index[SLICE] = ndims;
}
ndims++;
}
/* Set up image variable */
imgid = micreate_std_variable(mincid, MIimage, general_info->datatype,
ndims, dim);
if (general_info->is_signed)
(void) miattputstr(mincid, imgid, MIsigntype, MI_SIGNED);
else
(void) miattputstr(mincid, imgid, MIsigntype, MI_UNSIGNED);
valid_range[0] = general_info->pixel_min;
valid_range[1] = general_info->pixel_max;
(void) ncattput(mincid, imgid, MIvalid_range, NC_DOUBLE, 2, valid_range);
(void) miattputstr(mincid, imgid, MIcomplete, MI_FALSE);
/* Create image max and min variables */
varid = micreate_std_variable(mincid, MIimagemin, NC_DOUBLE, ndims-2, dim);
if (STRLEN(general_info->units) > 0)
(void) miattputstr(mincid, varid, MIunits, general_info->units);
varid = micreate_std_variable(mincid, MIimagemax, NC_DOUBLE, ndims-2, dim);
if (STRLEN(general_info->units) > 0)
(void) miattputstr(mincid, varid, MIunits, general_info->units);
/* Create the patient variable */
varid = micreate_group_variable(mincid, MIpatient);
if (STRLEN(general_info->patient.name) > 0)
(void) miattputstr(mincid, varid, MIfull_name,
general_info->patient.name);
if (STRLEN(general_info->patient.identification) > 0)
(void) miattputstr(mincid, varid, MIidentification,
general_info->patient.identification);
if (STRLEN(general_info->patient.birth_date) > 0)
(void) miattputstr(mincid, varid, MIbirthdate,
general_info->patient.birth_date);
if (STRLEN(general_info->patient.sex) > 0)
(void) miattputstr(mincid, varid, MIsex,
general_info->patient.sex);
if (general_info->patient.weight != -DBL_MAX)
(void) miattputdbl(mincid, varid, MIweight,
general_info->patient.weight);
/* Create the study variable */
varid = micreate_group_variable(mincid, MIstudy);
if (STRLEN(general_info->study.start_time) > 0)
(void) miattputstr(mincid, varid, MIstart_time,
general_info->study.start_time);
if (STRLEN(general_info->study.modality) > 0)
(void) miattputstr(mincid, varid, MImodality,
general_info->study.modality);
if (STRLEN(general_info->study.institution) > 0)
(void) miattputstr(mincid, varid, MIinstitution,
general_info->study.institution);
if (STRLEN(general_info->study.station_id) > 0)
(void) miattputstr(mincid, varid, MIstation_id,
general_info->study.station_id);
if (STRLEN(general_info->study.ref_physician) > 0)
(void) miattputstr(mincid, varid, MIreferring_physician,
general_info->study.ref_physician);
if (STRLEN(general_info->study.procedure) > 0)
(void) miattputstr(mincid, varid, MIprocedure,
general_info->study.procedure);
if (STRLEN(general_info->study.study_id) > 0)
(void) miattputstr(mincid, varid, MIstudy_id,
general_info->study.study_id);
if (STRLEN(general_info->study.acquisition_id) > 0)
(void) miattputstr(mincid, varid, "acquisition_id",
general_info->study.acquisition_id);
/* Create acquisition variable */
varid = micreate_group_variable(mincid, MIacquisition);
if (STRLEN(general_info->acq.scan_seq) > 0)
(void) miattputstr(mincid, varid, MIscanning_sequence,
general_info->acq.scan_seq);
if (general_info->acq.rep_time != -DBL_MAX)
(void) miattputdbl(mincid, varid, MIrepetition_time,
general_info->acq.rep_time);
if ((general_info->acq.echo_time != -DBL_MAX) &&
(general_info->size[ECHO] <= 1))
(void) miattputdbl(mincid, varid, MIecho_time,
general_info->acq.echo_time);
if (general_info->acq.inv_time != -DBL_MAX)
(void) miattputdbl(mincid, varid, MIinversion_time,
general_info->acq.inv_time);
if (general_info->acq.flip_angle != -DBL_MAX)
(void) miattputdbl(mincid, varid, "flip_angle",
general_info->acq.flip_angle);
if (general_info->acq.num_avg != -DBL_MAX)
(void) miattputdbl(mincid, varid, MInum_averages,
general_info->acq.num_avg);
if (general_info->acq.imaging_freq != -DBL_MAX)
(void) miattputdbl(mincid, varid, MIimaging_frequency,
general_info->acq.imaging_freq);
if (STRLEN(general_info->acq.imaged_nucl) > 0)
(void) miattputstr(mincid, varid, MIimaged_nucleus,
general_info->acq.imaged_nucl);
if (STRLEN(general_info->acq.comments) > 0)
(void) miattputstr(mincid, varid, MIcomments,
general_info->acq.comments);
/* Create the spi info variable */
varid = ncvardef(mincid, "spiinfo", NC_LONG, 0, NULL);
(void) miattputstr(mincid, varid, MIvartype, MI_GROUP);
(void) miattputstr(mincid, varid, MIvarid, "MNI SPI information variable");
(void) miadd_child(mincid, ncvarid(mincid, MIrootvariable), varid);
(void) miattputint(mincid, varid, "rec_num", general_info->rec_num);
if (STRLEN(general_info->image_type_string) > 0)
(void) miattputstr(mincid, varid, "image_type",
general_info->image_type_string);
(void) miattputdbl(mincid, varid, "window_min", general_info->window_min);
(void) miattputdbl(mincid, varid, "window_max", general_info->window_max);
/* Put group info in header */
cur_group = general_info->group_list;
spivar = ncvardef(mincid, SPI_ROOT_VAR, NC_LONG, 0, NULL);
(void) miattputstr(mincid, spivar, MIvartype, MI_GROUP);
(void) miattputstr(mincid, spivar, MIvarid, "MNI SPI variable");
(void) miadd_child(mincid, ncvarid(mincid, MIrootvariable), spivar);
while (cur_group != NULL) {
/* Create variable for group */
(void) sprintf(name, "spi_0x%04x", acr_get_group_group(cur_group));
varid = ncvardef(mincid, name, NC_LONG, 0, NULL);
(void) miattputstr(mincid, varid, MIvartype, MI_GROUP);
(void) miattputstr(mincid, varid, MIvarid, "MNI SPI variable");
(void) miadd_child(mincid, spivar, varid);
/* Loop through elements of group */
cur_element = acr_get_group_element_list(cur_group);
while (cur_element != NULL) {
(void) sprintf(name, "el_0x%04x",
acr_get_element_element(cur_element));
is_char = TRUE;
length = acr_get_element_length(cur_element);
data = acr_get_element_data(cur_element);
for (ich=0; ich < length; ich++) {
if (!isprint((int) data[ich])) {
is_char = FALSE;
break;
}
}
if (is_char)
datatype = NC_CHAR;
else
datatype = NC_BYTE;
ncattput(mincid, varid, name, datatype, length, data);
cur_element = acr_get_element_next(cur_element);
}
cur_group = acr_get_group_next(cur_group);
}
/* Create the history attribute */
if (minc_history != NULL) {
(void) miattputstr(mincid, NC_GLOBAL, MIhistory, minc_history);
}
return;
}
/* ----------------------------- MNI Header -----------------------------------
@NAME : save_minc_image
@INPUT : icvid
general_info
file_info
image
@OUTPUT : (none)
@RETURNS : (nothing)
@DESCRIPTION: Routine to save the image in the minc file
@METHOD :
@GLOBALS :
CALLS :
@CREATED : November 26, 1993 (Peter Neelin)
@MODIFIED :
---------------------------------------------------------------------------- */
public void save_minc_image(int icvid, General_Info *general_info,
File_Info *file_info, Image_Data *image)
{
int mincid, imgid;
long start[MAX_VAR_DIMS], count[MAX_VAR_DIMS];
int index;
int idim;
Mri_Index imri;
char *dimname;
unsigned short pvalue, pmax, pmin;
double dvalue, maximum, minimum, scale, offset;
long ipix, imagepix;
/* Get the minc file id */
(void) miicv_inqint(icvid, MI_ICV_CDFID, &mincid);
(void) miicv_inqint(icvid, MI_ICV_VARID, &imgid);
/* Create start and count variables */
idim = 0;
for (imri=MRI_NDIMS-1; (int) imri >= 0; imri--) {
if (general_info->image_index[imri] >= 0) {
index = general_info->image_index[imri];
start[index] = ((general_info->position[imri] != NULL) ?
general_info->position[imri][file_info->index[imri]] :
0);
count[index] = 1;
idim++;
}
}
start[idim] = 0;
start[idim+1] = 0;
count[idim] = general_info->nrows;
count[idim+1] = general_info->ncolumns;
/* Write out slice position */
switch (general_info->slice_world) {
case XCOORD: dimname = MIxspace; break;
case YCOORD: dimname = MIyspace; break;
case ZCOORD: dimname = MIzspace; break;
default: dimname = MIzspace;
}
(void) mivarput1(mincid, ncvarid(mincid, dimname),
&start[general_info->image_index[SLICE]],
NC_DOUBLE, NULL, &file_info->slice_position);
/* Write out time of slice, if needed */
if (general_info->size[TIME] > 1) {
(void) mivarput1(mincid, ncvarid(mincid, mri_dim_names[TIME]),
&start[general_info->image_index[TIME]],
NC_DOUBLE, NULL, &file_info->dyn_begin_time);
}
/* Write out echo time of slice, if needed */
if (general_info->size[ECHO] > 1) {
(void) mivarput1(mincid, ncvarid(mincid, mri_dim_names[ECHO]),
&start[general_info->image_index[ECHO]],
NC_DOUBLE, NULL, &file_info->echo_time);
}
/* Search image for max and min */
imagepix = general_info->nrows * general_info->ncolumns;
pmax = 0;
pmin = USHRT_MAX;
for (ipix=0; ipix < imagepix; ipix++) {
pvalue = image->data[ipix];
if (pvalue > pmax) pmax = pvalue;
if (pvalue < pmin) pmin = pvalue;
}
/* Re-scale the images */
if (pmax > pmin)
scale = (general_info->pixel_max - general_info->pixel_min) /
((double) pmax - (double) pmin);
else
scale = 0.0;
offset = general_info->pixel_min - scale * (double) pmin;
for (ipix=0; ipix < imagepix; ipix++) {
dvalue = image->data[ipix];
image->data[ipix] = dvalue * scale + offset;
}
/* Calculate new intensity max and min */
if (general_info->pixel_max > general_info->pixel_min)
scale = (file_info->slice_max - file_info->slice_min) /
(general_info->pixel_max - general_info->pixel_min);
else
scale = 0.0;
offset = file_info->slice_min - scale * general_info->pixel_min;
minimum = (double) pmin * scale + offset;
maximum = (double) pmax * scale + offset;
/* Write out the max and min values */
(void) mivarput1(mincid, ncvarid(mincid, MIimagemin), start, NC_DOUBLE,
NULL, &minimum);
(void) mivarput1(mincid, ncvarid(mincid, MIimagemax), start, NC_DOUBLE,
NULL, &maximum);
/* Write out the image */
(void) miicv_put(icvid, start, count, image->data);
return;
}
/* ----------------------------- MNI Header -----------------------------------
@NAME : close_minc_file
@INPUT : icvid - value returned by create_minc_file
@OUTPUT : (none)
@RETURNS : (nothing)
@DESCRIPTION: Routine to close the minc file.
@METHOD :
@GLOBALS :
CALLS :
@CREATED : November 30, 1993 (Peter Neelin)
@MODIFIED :
---------------------------------------------------------------------------- */
public void close_minc_file(int icvid)
{
int mincid;
/* Get the minc file id */
(void) miicv_inqint(icvid, MI_ICV_CDFID, &mincid);
/* Write out the complete attribute */
(void) miattputstr(mincid, ncvarid(mincid, MIimage), MIcomplete, MI_TRUE);
/* Close the file */
(void) miclose(mincid);
(void) miicv_free(icvid);
return;
}