This repository was archived by the owner on Feb 5, 2024. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathPapyConvertFile3.c
1521 lines (1214 loc) · 55.6 KB
/
PapyConvertFile3.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
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
/********************************************************************************/
/* */
/* Papyrus 3 library. */
/* This library constitutes a DICOM file system which helps reading and writing */
/* DICOM files and DICOMDIR files. */
/* */
/* Copyright (C) 2004 - Service of Medical Informatics - */
/* University Hospitals of Geneva (HUG), Geneva, Switzerland */
/* */
/* This library is a free software; you can redistribute it and/or modify it */
/* under the terms of the GNU Lesser General Public License as published by the */
/* Free Software Foundation; either version 2.1 of the License, or */
/* (at your option) any later version. */
/* */
/* This library is distributed in the hope that it will be useful, */
/* but WITHOUT ANY WARRANTY; without even the implied warranty of */
/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. */
/* See the GNU Lesser General Public License for more details. */
/* */
/* You should have received a copy of the GNU Lesser General Public License */
/* along with this library; if not, write to */
/* the Free Software Foundation, Inc., */
/* 59 Temple Place, Suite 330, */
/* Boston, MA 02111-1307 USA */
/* */
/* You can contact us for more information at [email protected] */
/* or by writing to Papyrus, */
/* Unite d'Imagerie Numerique / Service d'Informatique Medicale / HUG, */
/* 24, Micheli-du-Crest street, 1211 Geneva 14, Switzerland. */
/* */
/* The University Hopitals of Geneva, hereby disclaims all copyright interest */
/* in the library `Papyrus' (a library for reading and writing DICOM files). */
/* */
/* Geneva, april 2004 */
/* Antoine Geissbuhler, head of the Service of Medical Informatics, */
/* University Hospitals of Geneva, Switzerland */
/* */
/********************************************************************************/
/********************************************************************************/
/* */
/* Project : P A P Y R U S Toolkit */
/* File : PapyConvertFile3.c */
/* Function : contains all the Convertion function */
/* Authors : Marianne Logean */
/* */
/* History : 12.1999 version 1.0 */
/* 04.2001 version 3.7 */
/* 09.2001 version 3.7 on CVS */
/* 11.2001 Modify T1_taille for RGB */
/* */
/********************************************************************************/
/* ------------------------- includes ---------------------------------------*/
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#define CHECK_MEMORY
#define HAVE_BOOLEAN
#include "JPEGLESS.H" /* interface for JPEG lossless */
#include "JPEGLIB.H" /* interface for JPEG lossy */
#ifndef Papyrus3H
#include "Papyrus3.h"
#endif
struct color /* a color is defined by its red, green and blue intensity */
{
int r;
int g;
int b;
};
/********************************************************************************/
/* */
/* ExtractSelection : */
/* return : */
/* */
/********************************************************************************/
PapyUShort *
ExtractSelection(PapyUShort *image_buffer, int image_width,
int depth, int x1, int y1, int x2, int y2)
{
PapyUShort i, j, decal;
PapyULong sel_dim;
sel_dim = (PapyULong)((PapyULong)(x2 - x1) * (y2 - y1));
decal = image_width * y1;
if (depth == 8)
{
PapyUChar *sel_bufferC, *bufferC, *imageChar;
PapyUChar *image = (PapyUChar *) emalloc3 ((PapyULong) sel_dim + 1L);
sel_bufferC = image;
/*bufferC = (PapyUChar *) image_buffer;
bufferC += decal;
for (i = y1; i < y2; i++)
{
bufferC += x1;
for (j = x1; j < x2; j++)
{
*sel_bufferC++ = *bufferC++;
}
bufferC += (image_width - x2);
}*/
imageChar = (PapyUChar *) image_buffer;
for (j = 0; j < (y2 - y1); j++)
{
bufferC = imageChar + ((long)x1 + image_width * (y1 + j));
for (i = 0; i < (x2 - x1); i++)
*sel_bufferC++ = *bufferC++;
}/* endfor */
return ((PapyUShort *) image);
}
else
{
PapyUShort *sel_bufferS, *bufferS;
PapyUShort *image = (PapyUShort *) emalloc3 ((PapyULong) sel_dim * sizeof (PapyUShort) + 1L);
sel_bufferS = image;
/*bufferS = (PapyUShort *) image_buffer;
bufferS += decal;
for (i = y1; i < y2; i++)
{
bufferS += x1;
for (j = x1; j < x2; j++)
{
*sel_bufferS++ = *bufferS++;
}
bufferS += (image_width - x2);
}*/
for (j = 0; j < (y2 - y1); j++)
{
bufferS = image_buffer + ((long)x1 + image_width * (y1 + j));
for (i = 0; i < (x2 - x1); i++)
*sel_bufferS++ = *bufferS++;
}/* endfor */
return ((PapyUShort *) image);
}
} /* endof ExtractSelection */
/********************************************************************************/
/* */
/* GetPapyFileType : */
/* return : the format of the given file */
/* */
/********************************************************************************/
int GetPapyFileType (char *filename, int *imageNb, int *imageNo, enum EModality *modality)
{
/* verify if it is Papyrus3 or dicom file or Papyrus2 */
PapyShort file;
int fileKind;
PapyShort theErr;
int theElemType;
PapyULong theNbVal;
UValue_T *theValP;
SElement *theGroup20P;
if ((file = Papy3FileOpen (filename, (PAPY_FILE) 0, TRUE, 0)) >= 0)
{
*imageNb = (int) Papy3GetNbImages (file);
*modality = (enum EModality) Papy3GetModality (file);
/* if it is a DICOM file: search the dicom image number from the serie */
if (gIsPapyFile [file] == DICOM10 || gIsPapyFile [file] == DICOM_NOT10)
{
/* Image no in Dicom serie */
*imageNo = 0;
Papy3GotoNumber (file, 1, DataSetID);
/* goto group 0x0020 */
if ((theErr = Papy3GotoGroupNb (file, 0x0020)) == 0)
{
/* read group 0x0020 from the file */
if ((theErr = Papy3GroupRead (file, &theGroup20P)) > 0)
{
/* ACQUISITION NUMBER */
theValP = Papy3GetElement (theGroup20P, papAcquisitionNumberGr, &theNbVal, &theElemType);
if (theValP != NULL)
*imageNo = atoi(theValP->a);
/* IMAGE NUMBER */
theValP = Papy3GetElement (theGroup20P, papImageNumberGr, &theNbVal, &theElemType);
if (theValP != NULL)
*imageNo = atoi(theValP->a);
/* free the group 20 */
theErr = Papy3GroupFree (&theGroup20P, TRUE);
}/* read group 0x0020 */
}/* goto group 0x0020 */
}/* if it is a DICOM file */
/* close the file a la Papyrus 3 */
Papy3FileClose (file, TRUE);
fileKind = Papy3GetFileKind (file);
if (fileKind == 1)
return PAPYRUS3;
if (fileKind == 0 || fileKind == 2)
return DICOM10;
else if (fileKind == 3)
return other;
}
else return file;
} /* endof GetPapyFileType */
/********************************************************************************/
/* */
/* TI_taille : resize the original image */
/* return : */
/* */
/********************************************************************************/
unsigned char* TI_taille(unsigned char *ori, int orix, int oriy, int dstx, int dsty,
int depth, int numPlans, long *taille)
{
int n, i, j, k, l, m, linescanned, dstimx, dstimy, diffx, diffy;
float nf;
long oritaille;
unsigned char *tmp;
unsigned char *oriplane;
if (orix > oriy)
nf=(float)((float)orix/dstx);
else
nf=(float)((float)oriy/dsty);
n = (int) nf;
/* use round when divide result is not an integer */
if ((nf - n) > 0) n++;
dstimx = orix/n;
dstimy = oriy/n;
/* bords de l'image a remplir */
diffx = (dstx - dstimx) / 2;
diffy = (dsty - dstimy) / 2;
oritaille = (long)orix * (long)oriy;
*taille = (long)dstx * (long)dsty;
tmp = (unsigned char *) emalloc3 (*taille * (long) numPlans * sizeof(unsigned char));
/*for (i=0;i<dstx;i++)
for(j=0;j<dsty;j++)
tmp[i+j*dstx]=ori[i*n+j*n*orix];
*/
/* image RGB contient trois plans entrelacés: numPlans = 3 */
oriplane = (unsigned char *) ori;
/* top of the image */
for (i = 0, l = 0; l < diffy; l++)
for (j = 0; j < dstx; j++)
for (m = 0; m < numPlans; m++) tmp [i++] = 0;
for (linescanned = 0,j=0, k=0; i<*taille * (long) numPlans; )
{
/* left side */
if (j == 0)
for (j = 0; j < diffx; j++)
for (m = 0; m < numPlans; m++) tmp [i++] = 0;
/* right side */
if (j == dstimx + diffx)
{
for (j = dstimx + diffx; j < dstx; j++)
for (m = 0; m < numPlans; m++) tmp [i++] = 0;
/* eof line : j == dstx */
j = 0;
linescanned += n;
k = linescanned * orix * numPlans;
}
else if (k < oritaille * (long) numPlans)
{
for (m = 0; m < numPlans; m++) tmp[i++] = oriplane[k + m];
k += n * (long) numPlans;
j++;
}
/* bottom of the image */
else for (m = 0; m < numPlans; m++) tmp [i++] = 0;
}
efree3((void**)&ori);
ori = (unsigned char*) emalloc3 (*taille*(long)numPlans*sizeof(unsigned char));
(void) memcpy(ori,tmp,*taille*(long)numPlans*sizeof(unsigned char));
efree3((void**)&tmp);
return(ori);
} /* endof TI_taille */
/********************************************************************************/
/* */
/* Compute8bitsImage : */
/* return : */
/* */
/********************************************************************************/
PapyUChar *Compute8bitsImage (PapyUShort *inPixmap, int inRows, int inColumns,
int inDepth, int inMin, int inMax)
{
long i, size;
PapyUShort *p16b; /* pixels of image */
PapyUChar *newPixmap, *p8b;
/* ======================== NEW ORealImage ================================= */
/* as we do not want to write separate zoom algorithms */
/* for 8 bit and 16 bit images, we just work on 16 bit images */
/* so in case of a 16 bit image, just take the pointer on it */
/* in case of an 8 bit image, create a new 16 bit pixmap */
/* get original color fork min and max */
/*forkMin = fOriginalImage->GetColorManager()->FromCalibratedToRaw (fOriginalImage->GetColorManager()->fMinForkCalib);
forkMax = fOriginalImage->GetColorManager()->FromCalibratedToRaw (fOriginalImage->GetColorManager()->fMaxForkCalib);
*/
/* ============================ 8BITS IMAGE ================================ */
size = inColumns * inRows;
newPixmap = (PapyUChar *) emalloc3 ((PapyULong) size);
p8b = newPixmap;
p16b = inPixmap;
if (inDepth > 8)
{
/* conversion to 8 bit image
convert the 16 bit image into 8 bit image */
unsigned short *tab; /* conversion array */
unsigned short dminmax = inMax - inMin;
int min = inMin;
int max = inMax;
if (min < 0) min = 0;
if (max < 0) max = 0;
tab = (unsigned short *) emalloc3 (65535L * sizeof(unsigned short)); /* conversion array */
for (i=min; i<=max; i++)
tab [i] = (unsigned short) (((long)(i - min)) * 255 / dminmax);
for (i=0; i<min; i++)
tab [i] = 0;
for (i=max; i<65535; i++)
tab [i] = 255;
for (i=0; i<size; i++)
*p8b++ = (unsigned char) tab [*p16b++];
efree3 ( (void **) &tab);
}/* endif */
else
{
/* just copy the pixmap */
for (i=0; i<size; i++)
*p8b++ = (unsigned char) *p16b++;
}/* endelse */
return newPixmap;
} /* endof Compute8bitsImage */
/********************************************************************************/
/* */
/* InitClut : initialize clut */
/* return : */
/* */
/********************************************************************************/
void InitClut (int val, struct color thisClut[])
{
int i;
if (val < 0)
for (i=0; i<256; i++)
{
thisClut[i].r = i;
thisClut[i].g = i;
thisClut[i].b = i;
}/* endfor */
else
for (i=0; i<256; i++)
{
thisClut[i].r = val;
thisClut[i].g = val;
thisClut[i].b = val;
} /* endfor */
}/* endof InitClut */
/********************************************************************************/
/* */
/* Papyrus2Papyrus : convert Papyrus3 file into Papyrus3 format */
/* return : */
/* */
/********************************************************************************/
int Papyrus2Papyrus (char *inPapyrusFilename, char *outPapyrusFilename,
PAPY_FILE aRefNum, int nbImages, int *tabImage)
{
PapyShort fp, fpOrig, nbElemInModule;
int nbImagesOrig, imageNo, *tabIm, moduleCreated;
Item *dataSet;
Module *module;
SElement *gr, *group;
PapyUShort *image, valUS, bitsAllocated, rows, columns, selectedrows, selectedcolumns;
int loop, err;
enum EModality mod;
char myString [256], *myStringPtr;
Data_Set *wrkDS;
UValue_T *val;
int valType, isOpenOrClose;
PapyULong nbVal;
int leftcolumns, toprows, rightcolumns, bottomrows;
enum ETransf_Syntax syntax;
PapyUShort *selectedImage;
/* initialize */
myStringPtr = myString;
tabIm = tabImage;
/* open the original file a la Papyrus 3 */
fpOrig = Papy3FileOpen (inPapyrusFilename, (PAPY_FILE) 0, TRUE, 0);
/* test if the file has been opened correctly */
if (fpOrig < 0) return (int) fpOrig;
nbImagesOrig = (int) Papy3GetNbImages (fpOrig);
mod = (enum EModality) Papy3GetModality (fpOrig);
/* enum EPap_Compression {NONE, JPEG_LOSSLESS, JPEG_LOSSY, RLE}; */
syntax = LITTLE_ENDIAN_EXPL;
#ifdef Mac
isOpenOrClose = FALSE;
#else
isOpenOrClose = TRUE;
aRefNum = (PAPY_FILE)1;
#endif
fp = Papy3FileCreate (outPapyrusFilename, aRefNum,
(PapyUShort) nbImages, syntax, gCompression,
mod, isOpenOrClose, PAPYRUS3, NULL);
if (fp < 0) { PAPY3PRINTERRMSG (); return -1;}
/* get a pointer to the group 2 (File Meta Information) */
gr = Papy3GetGroup2 (fp);
/* fill the necessary elements of this group */
/* SOP instance UID of this data set */
strcpy (myStringPtr, "64.572.218.916");
Papy3PutElement (gr, papMediaStorageSOPInstanceUIDGr, &myStringPtr);
/* who is the creator of this wonderfull file ? */
strcpy (myStringPtr, "PAPYRUS 3.0");
Papy3PutElement (gr, papSourceApplicationEntityTitleGr, &myStringPtr);
/* loop on the images */
for (imageNo = 1; imageNo <= nbImagesOrig, *tabIm == 1; imageNo++, tabIm++)
{
/* creation of the data set object for this image */
dataSet = Papy3CreateDataSet (fp);
/* loop on the modules building a image */
wrkDS = gArrModalities [mod];
nbElemInModule = Papy3GetNbElemInModule (mod);
for (loop = 0; loop < nbElemInModule; loop++)
{
moduleCreated = FALSE;
/* get the module from the original file but it could be blank ... */
module = Papy3GetModule (fpOrig, (short) imageNo, wrkDS->moduleName);
if (module == NULL)
{
/* we have to create the module */
module = Papy3CreateModule (dataSet, wrkDS->moduleName);
moduleCreated = TRUE;
} /* if ...an error occured (bad DICOM file ?) */
/* depending on the module add the modified elements */
switch (wrkDS->moduleName)
{
case Patient :
/* if we dont want to save the patient name (anonymous file) */
/*if (hidePatName == TRUE)
{
err = Papy3ClearElement (module, papPatientsNameP, TRUE);
strcpy (myStringPtr, "Anonymous");
Papy3PutElement (module, papPatientsNameP, &myStringPtr);
err = Papy3ClearElement (module, papOtherPatientNamesP, TRUE);
}*/ /* if ...hide patient name */
break;
case GeneralStudy :
/* build a foo Study Instance UID */
if (module [papStudyInstanceUIDGS].nb_val == 0)
{
strcpy (myStringPtr, "1.2.756.9999.999.99.9");
Papy3PutElement (module, papStudyInstanceUIDGS, &myStringPtr);
} /* if */
break;
case GeneralSeries :
/* build a foo Series Instance UID */
if (module [papSeriesInstanceUIDGS].nb_val == 0)
{
strcpy (myStringPtr, "1.2.756.9999.999.99.9");
Papy3PutElement (module, papSeriesInstanceUIDGS, &myStringPtr);
} /* if */
break;
case FrameOfReference :
if (module [papFrameofReferenceUID].nb_val == 0L)
{
strcpy (myStringPtr, "41.22.333.444.555.666.00.1");
Papy3PutElement (module, papFrameofReferenceUID, &myStringPtr);
} /* if */
break;
case GeneralImage :
if (gCompression == NONE)
strcpy (myStringPtr, "00");
else
strcpy (myStringPtr, "01");
Papy3PutElement (module, papLossyImageCompressionGI, &myStringPtr);
break;
case ImagePixel :
{
Papy3ClearElement (module, papSamplesperPixelIP, TRUE);
valUS = 1;
Papy3PutElement (module, papSamplesperPixelIP, &valUS);
if (module [papPixelRepresentationIP].nb_val == 0)
{
valUS = 0;
Papy3PutElement (module, papPixelRepresentationIP, &valUS);
}
val = Papy3GetElement (module, papRows, &nbVal, &valType);
rows = val->us;
val = Papy3GetElement (module, papColumns, &nbVal, &valType);
columns = val->us;
leftcolumns = (int) (gLeftX*columns);
toprows = (int) (gTopY*rows);
rightcolumns = (int) (gRightX*columns);
bottomrows = (int) (gBottomY*rows);
Papy3ClearElement (module, papRows, TRUE);
selectedrows = (unsigned short) (bottomrows - toprows);
Papy3PutElement (module, papRows, &selectedrows);
Papy3ClearElement (module, papColumns, TRUE);
selectedcolumns = (unsigned short) (rightcolumns - leftcolumns);
Papy3PutElement (module, papColumns, &selectedcolumns);
/* bits allocated and stored */
val = Papy3GetElement (module, papBitsAllocatedIP, &nbVal, &valType);
bitsAllocated = val->us;
/* min and max pixel value in the image */
/* valUS = (PapyUShort) newRealImage->GetMinImage ();
Papy3PutElement (module, papSmallestImagePixelValue, &valUS);
valUS = (PapyUShort) newRealImage->GetMaxImage ();
Papy3PutElement (module, papLargestImagePixelValue, &valUS);
*/
/* PIXEL DATA */
/*image = (PapyUShort *)Papy3GetPixelData (fpOrig, imageNo, module, ImagePixel);*/
Papy3GotoNumber (fpOrig, imageNo, DataSetID);
/* then goto group 0x7FE0 */
Papy3GotoGroupNb (fpOrig, 0x7FE0);
Papy3GroupRead (fpOrig, &group);
/* get the original image because image not present in the module */
/* with Papy3GetModule () */
image = (PapyUShort *)Papy3GetPixelData (fpOrig, imageNo, group, ImagePixel);
selectedImage = ExtractSelection (image, columns, bitsAllocated,
leftcolumns, toprows,
rightcolumns, bottomrows);
efree3 ((void **) &image);
/* put the image */
Papy3PutImage ((PapyShort)fp, module, papPixelData, selectedImage,
(PapyUShort) selectedrows, (PapyUShort) selectedcolumns,
(PapyUShort) bitsAllocated, 0L);
Papy3GotoNumber (fpOrig, imageNo, DataSetID);
}
break;
case CTImage:
{
Papy3ClearElement (module, papReconstructionDiameterCTI, TRUE);
/* if (!strncmp (fMedStudy->GetPixelSizeUnit (), "mm", 2))
{
float pixelSize = fMedStudy->GetPixelSize ();
pixelSize = pixelSize * 100 / fParam->zoomFactor;
sprintf (myStringPtr, "%.5f", (float) (pixelSize * selectedcolumns));
Papy3PutElement (module, papReconstructionDiameterCTI, &myStringPtr);
} */ /* if ...image has been callibrated */
}
break;
case VOILUT :
{
/* compute the WW and WL of the image */
/* int WW = fSaveImage->GetForkMax () - fSaveImage->GetForkMin () + 1;
int WL = (int) ((WW / 2) + fSaveImage->GetForkMin ());
*/
/* clear any previous value */
Papy3ClearElement (module, papWindowCenter, TRUE);
Papy3ClearElement (module, papWindowWidth, TRUE);
/* then put the new one */
/* IntToString (WL, myStringPtr);
Papy3PutElement (module, papWindowCenter, &myStringPtr);
IntToString (WW, myStringPtr);
Papy3PutElement (module, papWindowWidth, &myStringPtr);
*/ }
break;
default :
break;
} /* switch ...add the modified elements */
/* link the read module to the list of modules of the data set to write */
if (!moduleCreated)
Papy3LinkModuleToDS (dataSet, module, wrkDS->moduleName);
wrkDS++;
} /* for ...loop on the modules of the CT images */
/* close the data set and frees the modules */
err = Papy3CloseDataSet (fp, dataSet, TRUE, TRUE);
} /* endfor ...loop on the images */
/* close the original file */
err = (int) Papy3FileClose (fpOrig, TRUE);
/* close the file */
err = Papy3WriteAndCloseFile (fp, TRUE);
if (err < 0) { PAPY3PRINTERRMSG (); return -1;}
} /* endof Papyrus2Papyrus */
/********************************************************************************/
/* */
/* Papyrus2Dicom : convert Papyrus3 file into DICOM format */
/* return : */
/* */
/********************************************************************************/
int Papyrus2Dicom (char *inPapyrusFilename, char *outDicomFilename, PAPY_FILE aRefNum,
int nbImages, int *tabImage)
{
PapyShort fp, fpOrig;
int nbImagesOrig, imageNo, *tabIm;
/* PapyUShort *image, bitsAllocated, rows, columns; */
enum EModality mod;
char myString [256], *myStringPtr;
int isOpenOrClose;
/*int leftcolumns, toprows, rightcolumns, bottomrows; */
enum ETransf_Syntax syntax;
/* PapyUShort *selectedImage; */
PapyShort theErr = 0;
long theFileSize;
PAPY_FILE thePapyFile;
/* initialize */
myStringPtr = myString;
tabIm = tabImage;
/* open the original file a la Papyrus 3 */
fpOrig = Papy3FileOpen (inPapyrusFilename, (PAPY_FILE) 0, TRUE, 0);
/* test if the file has been opened correctly */
if (fpOrig < 0) return (int) fpOrig;
thePapyFile = (PAPY_FILE) Papy3GetFile (fpOrig);
/* get the fileSize */
theErr = Papy3FSeek (thePapyFile, SEEK_END, 0L);
theErr = Papy3FTell (thePapyFile, (PapyLong *) &theFileSize);
theErr = Papy3FSeek (thePapyFile, SEEK_SET, 0L);
nbImagesOrig = (int) Papy3GetNbImages (fpOrig);
mod = (enum EModality) Papy3GetModality (fpOrig);
/* enum EPap_Compression {NONE, JPEG_LOSSLESS, JPEG_LOSSY, RLE}; */
syntax = LITTLE_ENDIAN_EXPL;
#ifdef Mac
isOpenOrClose = FALSE;
#else
isOpenOrClose = TRUE;
aRefNum = (PAPY_FILE) 1;
#endif
SetCompression (Papy3GetCompression (fpOrig));
fp = Papy3FileCreate (outDicomFilename, aRefNum,
(PapyUShort) nbImages, syntax, gCompression,
mod, isOpenOrClose, DICOM10, NULL);
if (fp < 0) { PAPY3PRINTERRMSG (); return -1;}
/* loop on the images */
for (imageNo = 1; imageNo <= nbImagesOrig, *tabIm == 1; imageNo++, tabIm++)
{
PAPY_FILE theFp;
PapyULong theBufSize, theMetaInfoSize;
unsigned char *theBuffP;
void *theVoidP;
/* create the temporary file that will contain the given data set */
if ((theErr = CreateTmpFile3 (fp, &theFp, &theVoidP)) < 0)
RETURN (papFileCreationFailed);
/* if the file is a DICOM one, then put the DICOM header to the temp file */
/* in order to get a real DICOM file part 10 compliant */
theErr = WriteDicomHeader3 (theFp, fp, &theMetaInfoSize);
if (imageNo == nbImagesOrig)
/* compute DataSet size for this image */
theBufSize = theFileSize - *(gRefImagePointer [fpOrig] + imageNo - 1);
else
/* compute DataSet size for this image */
theBufSize = *(gRefImagePointer [fpOrig] + imageNo) -
*(gRefImagePointer [fpOrig] + imageNo - 1);
/* alloc the buffer that will contain the ready to write group */
theBuffP = (unsigned char *) emalloc3 ((PapyULong) theBufSize);
/* position the file pointer to the begining of the data set */
theErr = Papy3GotoNumber (fpOrig, imageNo, DataSetID);
theErr = (PapyShort) Papy3FRead (gPapyFile [fpOrig], &theBufSize, 1L, theBuffP);
/* write the buffer to the temporary file */
if ((theErr = WriteGroup3 (theFp, theBuffP, theBufSize)) < 0)
RETURN (theErr);
/* frees the allocated buffer */
efree3 ((void **) &theBuffP);
/* close the file */
Papy3FClose (&theFp);
} /* loop on the images */
} /* endof Papyrus2Dicom */
/********************************************************************************/
/* */
/* ReadDicomFile : */
/* return : */
/* */
/********************************************************************************/
int ReadDicomFile (char *inDicomFilename, PapyShort inPapyrusFilePointer)
{
enum EModality mod;
PapyShort dicomFilePointer;
Data_Set *wrkDS;
Module *module;
Item *dataSet;
int nbImagesOrig, noImage;
int moduleCreated, loop, err = 0;
PapyUShort *image, bitsAllocated, rows, columns, samplesPerPixel;
UValue_T *val;
int valType;
PapyULong nbVal;
SElement *group;
/* open the original file a la Papyrus 3 */
dicomFilePointer = Papy3FileOpen (inDicomFilename, (PAPY_FILE) 0, TRUE, 0);
/* test if the file has been opened correctly */
if (dicomFilePointer < 0) return (int) dicomFilePointer;
mod = (enum EModality) Papy3GetModality (dicomFilePointer);
/* same MODALITY */
if (mod != gFileModality [inPapyrusFilePointer]) return (-1);
/* is it a multi-frame dicom file */
nbImagesOrig = (int) Papy3GetNbImages (dicomFilePointer);
for (noImage = 1; noImage <= nbImagesOrig; noImage++)
{
/* goto the image */
Papy3GotoNumber (dicomFilePointer, noImage, DataSetID);
/* creation of the data set object for this image */
dataSet = Papy3CreateDataSet (inPapyrusFilePointer);
/* loop on the modules */
wrkDS = gArrModalities [mod];
for (loop = 0; loop < gArrModuleNb [mod]; loop++)
{
moduleCreated = FALSE;
/* get the module from the original file but it could be blank ... */
module = Papy3GetModule (dicomFilePointer, (short) noImage, wrkDS->moduleName);
/*if (module == NULL)
{
/* we have to create the module */
/* module = Papy3CreateModule (dataSet, wrkDS->moduleName);
moduleCreated = TRUE;
} /* if ...an error occured (bad DICOM file ?) */
/* depending on the module add the modified elements */
switch (wrkDS->moduleName)
{
case ImagePixel :
{
val = Papy3GetElement (module, papRows, &nbVal, &valType);
rows = val->us;
val = Papy3GetElement (module, papColumns, &nbVal, &valType);
columns = val->us;
/*
leftcolumns = (int) (leftX*columns);
toprows = (int) (topY*rows);
rightcolumns = (int) (rightX*columns);
bottomrows = (int) (bottomY*rows);
Papy3ClearElement (module, papRows, TRUE);
selectedrows = (unsigned short) (bottomrows - toprows);
Papy3PutElement (module, papRows, &selectedrows);
Papy3ClearElement (module, papColumns, TRUE);
selectedcolumns = (unsigned short) (rightcolumns - leftcolumns);
Papy3PutElement (module, papColumns, &selectedcolumns);
*/
/* bits allocated and stored */
val = Papy3GetElement (module, papBitsAllocatedIP, &nbVal, &valType);
bitsAllocated = val->us;
/* samples per pixel */
val = Papy3GetElement (module, papSamplesperPixelIP, &nbVal, &valType);
samplesPerPixel = val->us;
/* min and max pixel value in the image */
/*
valUS = (PapyUShort) newRealImage->GetMinImage ();
Papy3PutElement (module, papSmallestImagePixelValue, &valUS);
valUS = (PapyUShort) newRealImage->GetMaxImage ();
Papy3PutElement (module, papLargestImagePixelValue, &valUS);
*/
/* PIXEL DATA */
/*image = (PapyUHShort *)Papy3GetPixelData (fpOrig, imageNb, module, ImagePixel);*/
Papy3GotoNumber (dicomFilePointer, noImage, DataSetID);
/* then goto group 0x7FE0 */
Papy3GotoGroupNb (dicomFilePointer, 0x7FE0);
Papy3GroupRead (dicomFilePointer, &group);
/* get the original image because image not present in the module */
/* with Papy3GetModule () */
image = (PapyUShort *)Papy3GetPixelData (dicomFilePointer, noImage, group, ImagePixel);
/*selectedImage = ExtractSelection (image, columns, bitsAllocated,
leftcolumns, toprows,
rightcolumns, bottomrows);
efree3 ((void **) &image);
/* put the image */
/*Papy3PutImage ((PapyShort)inPapyrusFilePointer, module, papPixelData, selectedImage,
(PapyUShort) selectedrows, (PapyUShort) selectedcolumns,
(PapyUShort) bitsAllocated, 0L);*/
Papy3PutImage ((PapyShort)inPapyrusFilePointer, module, papPixelData, image,
(PapyUShort) rows, (PapyUShort) columns,
(PapyUShort) (bitsAllocated * samplesPerPixel), 0L);
Papy3GotoNumber (dicomFilePointer, noImage, DataSetID);
}
break;
default :
break;
} /* switch ...add the modified elements */
/* link the read module to the list of modules of the data set to write */
/*if (!moduleCreated)*/
if (module != NULL)
Papy3LinkModuleToDS (dataSet, module, wrkDS->moduleName);
wrkDS++;
} /* for ...loop on the modules of the image */
/* close the data set and frees the modules */
err = Papy3CloseDataSet (inPapyrusFilePointer, dataSet, TRUE, FALSE);
} /* endfor ...loop on the images */
/* close the original file */
err = (int) Papy3FileClose (dicomFilePointer, TRUE);
} /* endof ReadDicomFile */
/********************************************************************************/
/* */
/* Dicom2Papyrus : convert DICOM serie into a single papyrus file */
/* return : */
/* */
/********************************************************************************/
int Dicom2Papyrus (char *outPapyrusFilename, int inNbDicomImages, char **inDicomFilename,
int inIsSerie, enum EModality modality)
{
int i, isOpenOrClose, err = 0;
PAPY_FILE aRefNum;
PapyShort papyrusFilePointer;
char *dicomPath;
enum ETransf_Syntax syntax;
SElement *gr;
char myString [256], *myStringPtr;
int nbImages, imageNo;
/* initialize */
myStringPtr = myString;
if (inNbDicomImages == 1)
GetPapyFileType (inDicomFilename[1], &nbImages, &imageNo, &modality);
else nbImages = inNbDicomImages;
/* enum EPap_Compression {NONE, JPEG_LOSSLESS, JPEG_LOSSY, RLE}; */
syntax = LITTLE_ENDIAN_EXPL;
isOpenOrClose = TRUE;
aRefNum = (PAPY_FILE)1;
papyrusFilePointer = Papy3FileCreate (outPapyrusFilename, aRefNum,
(PapyUShort) nbImages, syntax, gCompression,
modality, isOpenOrClose, PAPYRUS3, NULL);
/*if (papyrusFilePointer < 0) { PAPY3PRINTERRMSG (); return -1;}*/
if (papyrusFilePointer < 0) { PAPY3PRINTERRMSG (); return (int)papyrusFilePointer;}
/* get a pointer to the group 2 (File Meta Information) */
gr = Papy3GetGroup2 (papyrusFilePointer);
/* fill the necessary elements of this group */
/* SOP instance UID of this data set */
strcpy (myStringPtr, "64.572.218.916");
Papy3PutElement (gr, papMediaStorageSOPInstanceUIDGr, &myStringPtr);
/* who is the creator of this wonderfull file ? */