1 /*=========================================================================
4 Module: $RCSfile: gdcmHeader.cxx,v $
6 Date: $Date: 2004/06/28 09:30:58 $
7 Version: $Revision: 1.170 $
9 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
10 l'Image). All rights reserved. See Doc/License.txt or
11 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details.
13 This software is distributed WITHOUT ANY WARRANTY; without even
14 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 PURPOSE. See the above copyright notices for more information.
17 =========================================================================*/
19 #include "gdcmHeader.h"
20 #include "gdcmGlobal.h"
22 #include "gdcmDebug.h"
24 #include "gdcmValEntry.h"
28 //-----------------------------------------------------------------------------
29 // Constructor / Destructor
32 * @param InFilename name of the file whose header we want to analyze
33 * @param exception_on_error whether we want to throw an exception or not
34 * @param enable_sequences = true to allow the header
35 * to be parsed *inside* the SeQuences, when they have an actual length
36 * @param ignore_shadow = true if user wants to skip shadow groups
37 * during parsing, to save memory space
39 gdcmHeader::gdcmHeader(std::string const & filename,
40 bool exception_on_error,
41 bool enable_sequences,
43 gdcmDocument(filename,exception_on_error,enable_sequences,ignore_shadow)
45 // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
46 // We may encounter the 'RETired' (0x0028, 0x0200) tag
47 // (Image Location") . This Element contains the number of
48 // the group that contains the pixel data (hence the "Pixel Data"
49 // is found by indirection through the "Image Location").
50 // Inside the group pointed by "Image Location" the searched element
51 // is conventionally the element 0x0010 (when the norm is respected).
52 // When the "Image Location" is absent we default to group 0x7fe0.
54 // This IS the right place for the code
56 std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
57 if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
58 GrPixel = 0x7fe0; // default value
60 GrPixel = (guint16) atoi( ImageLocation.c_str() );
62 if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow
63 GrPixel = 0x7fe0; // the supposed processor endianity.
64 // see gdcmData/cr172241.dcm
65 if (GrPixel != 0x7fe0) {
66 // This is a kludge for old dirty Philips imager.
75 * @param exception_on_error whether we want to throw an exception or not
77 gdcmHeader::gdcmHeader(bool exception_on_error) :
78 gdcmDocument(exception_on_error)
84 * \brief Canonical destructor.
86 gdcmHeader::~gdcmHeader () {
89 //-----------------------------------------------------------------------------
93 //-----------------------------------------------------------------------------
97 * \brief This predicate, based on hopefully reasonable heuristics,
98 * decides whether or not the current gdcmHeader was properly parsed
99 * and contains the mandatory information for being considered as
100 * a well formed and usable Dicom/Acr File.
101 * @return true when gdcmHeader is the one of a reasonable Dicom/Acr file,
104 bool gdcmHeader::IsReadable() {
105 if(!gdcmDocument::IsReadable()) {
106 //std::cout << "doc non Readable " << std::endl; //JPR
109 std::string res = GetEntryByNumber(0x0028, 0x0005);
110 if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
111 return false; // Image Dimensions
112 if ( !GetDocEntryByNumber(0x0028, 0x0100) )
113 return false; // "Bits Allocated"
114 if ( !GetDocEntryByNumber(0x0028, 0x0101) )
115 return false; // "Bits Stored"
116 if ( !GetDocEntryByNumber(0x0028, 0x0102) )
117 return false; // "High Bit"
118 if ( !GetDocEntryByNumber(0x0028, 0x0103) )
119 return false; // "Pixel Representation" i.e. 'Sign'
124 * \brief Retrieve the number of columns of image.
125 * @return The encountered size when found, 0 by default.
126 * 0 means the file is NOT USABLE. The caller will have to check
128 int gdcmHeader::GetXSize() {
130 StrSize = GetEntryByNumber(0x0028,0x0011);
131 if (StrSize == GDCM_UNFOUND)
133 return atoi(StrSize.c_str());
137 * \ingroup gdcmHeader
138 * \brief Retrieve the number of lines of image.
139 * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize()
140 * @return The encountered size when found, 1 by default
141 * (The ACR-NEMA file contains a Signal, not an Image).
143 int gdcmHeader::GetYSize() {
144 std::string StrSize = GetEntryByNumber(0x0028,0x0010);
145 if (StrSize != GDCM_UNFOUND)
146 return atoi(StrSize.c_str());
150 // The Rows (0028,0010) entry was optional for ACR/NEMA. It might
151 // hence be a signal (1d image). So we default to 1:
156 * \ingroup gdcmHeader
157 * \brief Retrieve the number of planes of volume or the number
158 * of frames of a multiframe.
159 * \warning When present we consider the "Number of Frames" as the third
160 * dimension. When absent we consider the third dimension as
161 * being the ACR-NEMA "Planes" tag content.
162 * @return The encountered size when found, 1 by default (single image).
164 int gdcmHeader::GetZSize() {
165 // Both DicomV3 and ACR/Nema consider the "Number of Frames"
166 // as the third dimension.
167 std::string StrSize = GetEntryByNumber(0x0028,0x0008);
168 if (StrSize != GDCM_UNFOUND)
169 return atoi(StrSize.c_str());
171 // We then consider the "Planes" entry as the third dimension
172 StrSize = GetEntryByNumber(0x0028,0x0012);
173 if (StrSize != GDCM_UNFOUND)
174 return atoi(StrSize.c_str());
179 * \ingroup gdcmHeader
180 * \brief gets the info from 0028,0030 : Pixel Spacing
182 * @return X dimension of a pixel
184 float gdcmHeader::GetXSpacing() {
185 float xspacing, yspacing;
186 std::string StrSpacing = GetEntryByNumber(0x0028,0x0030);
188 if (StrSpacing == GDCM_UNFOUND) {
189 dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)");
193 if( (nbValues = sscanf( StrSpacing.c_str(), "%f\\%f", &yspacing, &xspacing)) != 2) {
194 if (nbValues==1) // if single value is found, xspacing is defaulted to yspacing
197 if (xspacing == 0.) {
198 dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
199 // seems to be a bug in the header ...
200 sscanf( StrSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
206 * \ingroup gdcmHeader
207 * \brief gets the info from 0028,0030 : Pixel Spacing
209 * @return Y dimension of a pixel
211 float gdcmHeader::GetYSpacing() {
213 std::string StrSpacing = GetEntryByNumber(0x0028,0x0030);
215 if (StrSpacing == GDCM_UNFOUND) {
216 dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)");
219 sscanf( StrSpacing.c_str(), "%f", &yspacing);
225 *\brief gets the info from 0018,0088 : Space Between Slices
226 * else from 0018,0050 : Slice Thickness
228 * @return Z dimension of a voxel-to be
230 float gdcmHeader::GetZSpacing() {
231 // Spacing Between Slices : distance entre le milieu de chaque coupe
232 // Les coupes peuvent etre :
233 // jointives (Spacing between Slices = Slice Thickness)
234 // chevauchantes (Spacing between Slices < Slice Thickness)
235 // disjointes (Spacing between Slices > Slice Thickness)
236 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
237 // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
238 // Si le Spacing Between Slices est absent,
239 // on suppose que les coupes sont jointives
241 std::string StrSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
243 if (StrSpacingBSlices == GDCM_UNFOUND) {
244 dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices");
245 std::string StrSliceThickness = GetEntryByNumber(0x0018,0x0050);
246 if (StrSliceThickness == GDCM_UNFOUND)
249 // if no 'Spacing Between Slices' is found,
250 // we assume slices join together
251 // (no overlapping, no interslice gap)
252 // if they don't, we're fucked up
253 return atof(StrSliceThickness.c_str());
255 return atof(StrSpacingBSlices.c_str());
261 *\brief gets the info from 0028,1052 : Rescale Intercept
262 * @return Rescale Intercept
264 float gdcmHeader::GetRescaleIntercept() {
266 std::string StrRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept
267 if (StrRescInter != GDCM_UNFOUND) {
268 if( sscanf( StrRescInter.c_str(), "%f", &resInter) != 1) {
269 dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty");
270 // bug in the element 0x0028,0x1052
278 *\brief gets the info from 0028,1053 : Rescale Slope
279 * @return Rescale Slope
281 float gdcmHeader::GetRescaleSlope() {
283 std::string StrRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope
284 if (StrRescSlope != GDCM_UNFOUND) {
285 if( sscanf( StrRescSlope.c_str(), "%f", &resSlope) != 1) {
286 dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty");
287 // bug in the element 0x0028,0x1053
294 * \ingroup gdcmHeader
295 * \brief This function is intended to user who doesn't want
296 * to have to manage a LUT and expects to get an RBG Pixel image
297 * (or a monochrome one ...)
298 * \warning to be used with GetImagePixels()
299 * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR)
301 int gdcmHeader::GetNumberOfScalarComponents() {
302 if (GetSamplesPerPixel() ==3)
305 // 0028 0100 US IMG Bits Allocated
306 // (in order no to be messed up by old RGB images)
307 if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
310 std::string PhotometricInterpretation =
311 gdcmHeader::GetEntryByNumber(0x0028,0x0004);
313 if ( ( PhotometricInterpretation == "PALETTE COLOR ") ) {
314 if (HasLUT()) // PALETTE COLOR is NOT enough
320 //beware of trailing space at end of string
321 if (PhotometricInterpretation.find(GDCM_UNFOUND) <
322 PhotometricInterpretation.length() ||
323 PhotometricInterpretation.find("MONOCHROME1") <
324 PhotometricInterpretation.length() ||
325 PhotometricInterpretation.find("MONOCHROME2") <
326 PhotometricInterpretation.length() )
329 // we assume that *all* kinds of YBR are dealt with
334 * \ingroup gdcmHeader
335 * \brief This function is intended to user that DOESN'T want
336 * to get RGB pixels image when it's stored as a PALETTE COLOR image
337 * - the (vtk) user is supposed to know how deal with LUTs -
338 * \warning to be used with GetImagePixelsRaw()
339 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
341 int gdcmHeader::GetNumberOfScalarComponentsRaw() {
343 // 0028 0100 US IMG Bits Allocated
344 // (in order no to be messed up by old RGB images)
345 if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
348 // we assume that *all* kinds of YBR are dealt with
349 return GetSamplesPerPixel();
354 *\brief gets the info from 0020,000d : Study Instance UID
355 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
356 * @return Study Instance UID
358 //std::string gdcmHeader::GetStudyUID(){
359 // return GetEntryByNumber(0x0020,0x000d); //0020 000d UI REL Study Instance UID
364 *\brief gets the info from 0020,000e : Series Instance UID
365 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
366 * @return Series Instance UID
368 //std::string gdcmHeader::GetSeriesUID(){
369 // return GetEntryByNumber(0x0020,0x000e); //0020 000e UI REL Series Instance UID
374 *\brief gets the info from 0008,0016 : SOP Class UID
375 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
376 * @return SOP Class UID
378 //std::string gdcmHeader::GetClassUID(){
379 // return GetEntryByNumber(0x0008,0x0016); //0008 0016 UI ID SOP Class UID
383 *\brief gets the info from 0008,0018 : SOP Instance UID
384 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
385 * @return SOP Instance UID
387 //std::string gdcmHeader::GetInstanceUID(){
388 // return GetEntryByNumber(0x0008,0x0018); //0008 0018 UI ID SOP Instance UID
391 // -------------- Remember ! ----------------------------------
393 // Image Position Patient (0020,0032):
394 // If not found (ACR_NEMA) we try Image Position (0020,0030)
395 // If not found (ACR-NEMA), we consider Slice Location (0020,1041)
396 // or Location (0020,0050)
397 // as the Z coordinate,
398 // 0. for all the coordinates if nothing is found
400 // \todo find a way to inform the caller nothing was found
401 // \todo How to tell the caller a wrong number of values was found?
403 // ---------------------------------------------------------------
407 * \brief gets the info from 0020,0032 : Image Position Patient
408 * else from 0020,0030 : Image Position (RET)
410 * @return up-left image corner X position
413 float gdcmHeader::GetXOrigin() {
414 float xImPos, yImPos, zImPos;
415 std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
417 if (StrImPos == GDCM_UNFOUND) {
418 dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)");
419 StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
420 if (StrImPos == GDCM_UNFOUND) {
421 dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)");
422 /// \todo How to tell the caller nothing was found ?
426 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
432 * \brief gets the info from 0020,0032 : Image Position Patient
433 * else from 0020,0030 : Image Position (RET)
435 * @return up-left image corner Y position
437 float gdcmHeader::GetYOrigin() {
438 float xImPos, yImPos, zImPos;
439 std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
441 if (StrImPos == GDCM_UNFOUND) {
442 dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)");
443 StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
444 if (StrImPos == GDCM_UNFOUND) {
445 dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)");
446 /// \todo How to tell the caller nothing was found ?
450 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
456 * \brief gets the info from 0020,0032 : Image Position Patient
457 * \ else from 0020,0030 : Image Position (RET)
458 * \ else from 0020,1041 : Slice Location
459 * \ else from 0020,0050 : Location
461 * @return up-left image corner Z position
463 float gdcmHeader::GetZOrigin() {
464 float xImPos, yImPos, zImPos;
465 std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
466 if (StrImPos != GDCM_UNFOUND) {
467 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
468 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)");
469 return 0.; // bug in the element 0x0020,0x0032
474 StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
475 if (StrImPos != GDCM_UNFOUND) {
476 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
477 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
478 return 0.; // bug in the element 0x0020,0x0032
483 std::string StrSliceLocation = GetEntryByNumber(0x0020,0x1041);// for *very* old ACR-NEMA images
484 if (StrSliceLocation != GDCM_UNFOUND) {
485 if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) {
486 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)");
487 return 0.; // bug in the element 0x0020,0x1041
492 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)");
493 std::string StrLocation = GetEntryByNumber(0x0020,0x0050);
494 if (StrLocation != GDCM_UNFOUND) {
495 if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) {
496 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)");
497 return 0.; // bug in the element 0x0020,0x0050
502 dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)");
503 return 0.; // Hopeless
507 * \brief gets the info from 0020,0013 : Image Number
509 * @return image number
511 int gdcmHeader::GetImageNumber() {
512 // The function i atoi() takes the address of an area of memory as
513 // parameter and converts the string stored at that location to an integer
514 // using the external decimal to internal binary conversion rules. This may
515 // be preferable to sscanf() since atoi() is a much smaller, simpler and
516 // faster function. sscanf() can do all possible conversions whereas
517 // atoi() can only do single decimal integer conversions.
518 std::string StrImNumber = GetEntryByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number
519 if (StrImNumber != GDCM_UNFOUND) {
520 return atoi( StrImNumber.c_str() );
526 * \brief gets the info from 0008,0060 : Modality
527 * @return Modality Type
529 ModalityType gdcmHeader::GetModality() {
530 // 0008 0060 CS ID Modality
531 std::string StrModality = GetEntryByNumber(0x0008,0x0060);
532 if (StrModality != GDCM_UNFOUND) {
533 if ( StrModality.find("AU") < StrModality.length()) return AU;
534 else if ( StrModality.find("AS") < StrModality.length()) return AS;
535 else if ( StrModality.find("BI") < StrModality.length()) return BI;
536 else if ( StrModality.find("CF") < StrModality.length()) return CF;
537 else if ( StrModality.find("CP") < StrModality.length()) return CP;
538 else if ( StrModality.find("CR") < StrModality.length()) return CR;
539 else if ( StrModality.find("CT") < StrModality.length()) return CT;
540 else if ( StrModality.find("CS") < StrModality.length()) return CS;
541 else if ( StrModality.find("DD") < StrModality.length()) return DD;
542 else if ( StrModality.find("DF") < StrModality.length()) return DF;
543 else if ( StrModality.find("DG") < StrModality.length()) return DG;
544 else if ( StrModality.find("DM") < StrModality.length()) return DM;
545 else if ( StrModality.find("DS") < StrModality.length()) return DS;
546 else if ( StrModality.find("DX") < StrModality.length()) return DX;
547 else if ( StrModality.find("ECG") < StrModality.length()) return ECG;
548 else if ( StrModality.find("EPS") < StrModality.length()) return EPS;
549 else if ( StrModality.find("FA") < StrModality.length()) return FA;
550 else if ( StrModality.find("FS") < StrModality.length()) return FS;
551 else if ( StrModality.find("HC") < StrModality.length()) return HC;
552 else if ( StrModality.find("HD") < StrModality.length()) return HD;
553 else if ( StrModality.find("LP") < StrModality.length()) return LP;
554 else if ( StrModality.find("LS") < StrModality.length()) return LS;
555 else if ( StrModality.find("MA") < StrModality.length()) return MA;
556 else if ( StrModality.find("MR") < StrModality.length()) return MR;
557 else if ( StrModality.find("NM") < StrModality.length()) return NM;
558 else if ( StrModality.find("OT") < StrModality.length()) return OT;
559 else if ( StrModality.find("PT") < StrModality.length()) return PT;
560 else if ( StrModality.find("RF") < StrModality.length()) return RF;
561 else if ( StrModality.find("RG") < StrModality.length()) return RG;
562 else if ( StrModality.find("RTDOSE") < StrModality.length()) return RTDOSE;
563 else if ( StrModality.find("RTIMAGE") < StrModality.length()) return RTIMAGE;
564 else if ( StrModality.find("RTPLAN") < StrModality.length()) return RTPLAN;
565 else if ( StrModality.find("RTSTRUCT")< StrModality.length()) return RTSTRUCT;
566 else if ( StrModality.find("SM") < StrModality.length()) return SM;
567 else if ( StrModality.find("ST") < StrModality.length()) return ST;
568 else if ( StrModality.find("TG") < StrModality.length()) return TG;
569 else if ( StrModality.find("US") < StrModality.length()) return US;
570 else if ( StrModality.find("VF") < StrModality.length()) return VF;
571 else if ( StrModality.find("XA") < StrModality.length()) return XA;
572 else if ( StrModality.find("XC") < StrModality.length()) return XC;
576 /// \todo throw error return value ???
577 /// specified <> unknow in our database
585 * \ingroup gdcmHeader
586 * \brief Retrieve the number of Bits Stored (actually used)
587 * (as opposite to number of Bits Allocated)
588 * @return The encountered number of Bits Stored, 0 by default.
589 * 0 means the file is NOT USABLE. The caller has to check it !
591 int gdcmHeader::GetBitsStored() {
592 std::string StrSize = GetEntryByNumber(0x0028,0x0101);
593 if (StrSize == GDCM_UNFOUND)
594 return 0; // It's supposed to be mandatory
595 // the caller will have to check
596 return atoi(StrSize.c_str());
600 * \ingroup gdcmHeader
601 * \brief Retrieve the number of Bits Allocated
602 * (8, 12 -compacted ACR-NEMA files, 16, ...)
603 * @return The encountered number of Bits Allocated, 0 by default.
604 * 0 means the file is NOT USABLE. The caller has to check it !
606 int gdcmHeader::GetBitsAllocated() {
607 std::string StrSize = GetEntryByNumber(0x0028,0x0100);
608 if (StrSize == GDCM_UNFOUND)
609 return 0; // It's supposed to be mandatory
610 // the caller will have to check
611 return atoi(StrSize.c_str());
615 * \ingroup gdcmHeader
616 * \brief Retrieve the number of Samples Per Pixel
617 * (1 : gray level, 3 : RGB -1 or 3 Planes-)
618 * @return The encountered number of Samples Per Pixel, 1 by default.
619 * (Gray level Pixels)
621 int gdcmHeader::GetSamplesPerPixel() {
622 std::string StrSize = GetEntryByNumber(0x0028,0x0002);
623 if (StrSize == GDCM_UNFOUND)
624 return 1; // Well, it's supposed to be mandatory ...
625 // but sometimes it's missing : *we* assume Gray pixels
626 return atoi(StrSize.c_str());
630 * \ingroup gdcmHeader
631 * \brief Retrieve the Planar Configuration for RGB images
632 * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
633 * @return The encountered Planar Configuration, 0 by default.
635 int gdcmHeader::GetPlanarConfiguration() {
636 std::string StrSize = GetEntryByNumber(0x0028,0x0006);
637 if (StrSize == GDCM_UNFOUND)
639 return atoi(StrSize.c_str());
643 * \ingroup gdcmHeader
644 * \brief Return the size (in bytes) of a single pixel of data.
645 * @return The size in bytes of a single pixel of data; 0 by default
646 * 0 means the file is NOT USABLE; the caller will have to check
648 int gdcmHeader::GetPixelSize() {
649 // 0028 0100 US IMG Bits Allocated
650 // (in order no to be messed up by old RGB images)
651 // if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
654 std::string PixelType = GetPixelType();
655 if (PixelType == "8U" || PixelType == "8S")
657 if (PixelType == "16U" || PixelType == "16S")
659 if (PixelType == "32U" || PixelType == "32S")
661 if (PixelType == "FD")
663 dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
668 * \ingroup gdcmHeader
669 * \brief Build the Pixel Type of the image.
670 * Possible values are:
671 * - 8U unsigned 8 bit,
673 * - 16U unsigned 16 bit,
674 * - 16S signed 16 bit,
675 * - 32U unsigned 32 bit,
676 * - 32S signed 32 bit,
677 * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
678 * \warning 12 bit images appear as 16 bit.
679 * 24 bit images appear as 8 bit
680 * @return 0S if nothing found. NOT USABLE file. The caller has to check
682 std::string gdcmHeader::GetPixelType() {
683 std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
684 if (BitsAlloc == GDCM_UNFOUND) {
685 dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
686 BitsAlloc = std::string("16");
688 if (BitsAlloc == "64") // )
690 if (BitsAlloc == "12") // It will be unpacked
691 BitsAlloc = std::string("16");
692 else if (BitsAlloc == "24") // (in order no to be messed up
693 BitsAlloc = std::string("8"); // by old RGB images)
695 std::string Signed = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation"
696 if (Signed == GDCM_UNFOUND) {
697 dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
698 BitsAlloc = std::string("0");
701 Signed = std::string("U");
703 Signed = std::string("S");
705 return( BitsAlloc + Signed);
710 * \ingroup gdcmHeader
711 * \brief Recover the offset (from the beginning of the file)
712 * of *image* pixels (not *icone image* pixels, if any !)
713 * @return Pixel Offset
715 size_t gdcmHeader::GetPixelOffset() {
717 gdcmDocEntry* PixelElement = GetDocEntryByNumber(GrPixel,NumPixel);
720 return PixelElement->GetOffset();
723 std::cout << "Big trouble : Pixel Element ("
724 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
730 // TODO : unify those two (previous one and next one)
732 * \ingroup gdcmHeader
733 * \brief Recover the pixel area length (in Bytes)
734 * @return Pixel Element Length, as stored in the header
735 * (NOT the memory space necessary to hold the Pixels
736 * -in case of embeded compressed image-)
737 * 0 : NOT USABLE file. The caller has to check.
739 size_t gdcmHeader::GetPixelAreaLength() {
741 gdcmDocEntry* PixelElement = GetDocEntryByNumber(GrPixel,NumPixel);
744 return PixelElement->GetLength();
747 std::cout << "Big trouble : Pixel Element ("
748 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
756 * \ingroup gdcmHeader
757 * \brief tells us if LUT are used
758 * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
759 * are NOT considered as LUT, since nobody knows
760 * how to deal with them
761 * Please warn me if you know sbdy that *does* know ... jprx
762 * @return true if LUT Descriptors and LUT Tables were found
764 bool gdcmHeader::HasLUT() {
766 // Check the presence of the LUT Descriptors, and LUT Tables
768 if ( !GetDocEntryByNumber(0x0028,0x1101) )
770 // LutDescriptorGreen
771 if ( !GetDocEntryByNumber(0x0028,0x1102) )
774 if ( !GetDocEntryByNumber(0x0028,0x1103) )
776 // Red Palette Color Lookup Table Data
777 if ( !GetDocEntryByNumber(0x0028,0x1201) )
779 // Green Palette Color Lookup Table Data
780 if ( !GetDocEntryByNumber(0x0028,0x1202) )
782 // Blue Palette Color Lookup Table Data
783 if ( !GetDocEntryByNumber(0x0028,0x1203) )
785 // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
786 // NOT taken into account, but we don't know how to use it ...
791 * \ingroup gdcmHeader
792 * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
794 * @return Lookup Table number of Bits , 0 by default
795 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
796 * @ return bit number of each LUT item
798 int gdcmHeader::GetLUTNbits() {
799 std::vector<std::string> tokens;
803 //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue
804 // Consistency already checked in GetLUTLength
805 std::string LutDescription = GetEntryByNumber(0x0028,0x1101);
806 if (LutDescription == GDCM_UNFOUND)
808 tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
809 Tokenize (LutDescription, tokens, "\\");
810 //LutLength=atoi(tokens[0].c_str());
811 //LutDepth=atoi(tokens[1].c_str());
812 LutNbits=atoi(tokens[2].c_str());
818 * \ingroup gdcmHeader
819 * \brief builts Red/Green/Blue/Alpha LUT from Header
820 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
821 * and (0028,1101),(0028,1102),(0028,1102)
822 * - xxx Palette Color Lookup Table Descriptor - are found
823 * and (0028,1201),(0028,1202),(0028,1202)
824 * - xxx Palette Color Lookup Table Data - are found
825 * \warning does NOT deal with :
826 * 0028 1100 Gray Lookup Table Descriptor (Retired)
827 * 0028 1221 Segmented Red Palette Color Lookup Table Data
828 * 0028 1222 Segmented Green Palette Color Lookup Table Data
829 * 0028 1223 Segmented Blue Palette Color Lookup Table Data
830 * no known Dicom reader deals with them :-(
831 * @return a RGBA Lookup Table
833 unsigned char * gdcmHeader::GetLUTRGBA() {
835 // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
837 // if Photometric Interpretation # PALETTE COLOR, no LUT to be done
838 if (GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR ") {
841 int lengthR, debR, nbitsR;
842 int lengthG, debG, nbitsG;
843 int lengthB, debB, nbitsB;
845 // Get info from Lut Descriptors
846 // (the 3 LUT descriptors may be different)
847 std::string LutDescriptionR = GetEntryByNumber(0x0028,0x1101);
848 if (LutDescriptionR == GDCM_UNFOUND)
850 std::string LutDescriptionG = GetEntryByNumber(0x0028,0x1102);
851 if (LutDescriptionG == GDCM_UNFOUND)
853 std::string LutDescriptionB = GetEntryByNumber(0x0028,0x1103);
854 if (LutDescriptionB == GDCM_UNFOUND)
857 std::vector<std::string> tokens;
859 tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
860 Tokenize (LutDescriptionR, tokens, "\\");
861 lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes
862 debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value
863 nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits)
866 tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
867 Tokenize (LutDescriptionG, tokens, "\\");
868 lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes
869 debG =atoi(tokens[1].c_str()); // subscript of the first Lut Value
870 nbitsG =atoi(tokens[2].c_str()); // Lut item size (in Bits)
873 tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
874 Tokenize (LutDescriptionB, tokens, "\\");
875 lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes
876 debB =atoi(tokens[1].c_str()); // subscript of the first Lut Value
877 nbitsB =atoi(tokens[2].c_str()); // Lut item size (in Bits)
880 // Load LUTs into memory, (as they were stored on disk)
881 unsigned char *lutR = (unsigned char *)
882 GetEntryVoidAreaByNumber(0x0028,0x1201);
883 unsigned char *lutG = (unsigned char *)
884 GetEntryVoidAreaByNumber(0x0028,0x1202);
885 unsigned char *lutB = (unsigned char *)
886 GetEntryVoidAreaByNumber(0x0028,0x1203);
888 if (!lutR || !lutG || !lutB ) {
891 // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
893 unsigned char *LUTRGBA = new unsigned char[1024]; // 256 * 4 (R, G, B, Alpha)
897 memset(LUTRGBA, 0, 1024);
900 std::string str_nb = GetEntryByNumber(0x0028,0x0100);
901 if (str_nb == GDCM_UNFOUND ) {
904 nb = atoi(str_nb.c_str() );
908 if (nbitsR==16 && nb==8) // when LUT item size is different than pixel size
909 mult=2; // high byte must be = low byte
910 else // See PS 3.3-2003 C.11.1.1.2 p 619
913 // if we get a black image, let's just remove the '+1'
914 // from 'i*mult+1' and check again
915 // if it works, we shall have to check the 3 Palettes
916 // to see which byte is ==0 (first one, or second one)
918 // We give up the checking to avoid some (useless ?)overhead
919 // (optimistic asumption)
924 for(i=0;i<lengthR;i++) {
929 for(i=0;i<lengthG;i++) {
934 for(i=0;i<lengthB;i++) {
940 *a = 1; // Alpha component
944 //How to free the now useless LUTs?
945 //free(LutR); free(LutB); free(LutG); // Seg Fault when used
950 * \brief Accesses the info from 0002,0010 : Transfert Syntax and gdcmTS
952 * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID)
954 std::string gdcmHeader::GetTransfertSyntaxName() {
955 // use the gdcmTS (TS : Transfert Syntax)
956 std::string TransfertSyntax = GetEntryByNumber(0x0002,0x0010);
957 if (TransfertSyntax == GDCM_UNFOUND) {
958 dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName:"
959 " unfound Transfert Syntax (0002,0010)");
960 return "Uncompressed ACR-NEMA";
962 // we do it only when we need it
963 gdcmTS * ts = gdcmGlobal::GetTS();
964 std::string tsName=ts->GetValue(TransfertSyntax);
965 //delete ts; /// \todo Seg Fault when deleted ?!
970 * \brief Sets the Pixel Area size in the Header
971 * --> not-for-rats function
972 * @param ImageDataSize new Pixel Area Size
973 * warning : nothing else is checked
975 void gdcmHeader::SetImageDataSize(size_t ImageDataSize) {
976 std::string content1;
979 sprintf(car,"%d",ImageDataSize);
981 gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel);
982 a->SetLength(ImageDataSize);
985 sprintf(car,"%d",ImageDataSize);
987 SetEntryByNumber(content1, GrPixel, NumPixel);
990 //-----------------------------------------------------------------------------
994 * \brief anonymize a Header (removes Patient's personal info)
995 * (read the code to see which ones ...)
997 bool gdcmHeader::AnonymizeHeader() {
999 gdcmDocEntry *patientNameHE = GetDocEntryByNumber (0x0010, 0x0010);
1001 ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone
1002 ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress
1003 ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID
1005 if (patientNameHE) {
1006 std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d);
1007 if (studyInstanceUID !=GDCM_UNFOUND)
1008 ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010);
1010 ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010);
1014 // (if any) remove or replace all the stuff that contains a Date
1016 //0008 0012 DA ID Instance Creation Date
1017 //0008 0020 DA ID Study Date
1018 //0008 0021 DA ID Series Date
1019 //0008 0022 DA ID Acquisition Date
1020 //0008 0023 DA ID Content Date
1021 //0008 0024 DA ID Overlay Date
1022 //0008 0025 DA ID Curve Date
1023 //0008 002a DT ID Acquisition Datetime
1024 //0018 9074 DT ACQ Frame Acquisition Datetime
1025 //0018 9151 DT ACQ Frame Reference Datetime
1026 //0018 a002 DT ACQ Contribution Date Time
1027 //0020 3403 SH REL Modified Image Date (RET)
1028 //0032 0032 DA SDY Study Verified Date
1029 //0032 0034 DA SDY Study Read Date
1030 //0032 1000 DA SDY Scheduled Study Start Date
1031 //0032 1010 DA SDY Scheduled Study Stop Date
1032 //0032 1040 DA SDY Study Arrival Date
1033 //0032 1050 DA SDY Study Completion Date
1034 //0038 001a DA VIS Scheduled Admission Date
1035 //0038 001c DA VIS Scheduled Discharge Date
1036 //0038 0020 DA VIS Admitting Date
1037 //0038 0030 DA VIS Discharge Date
1038 //0040 0002 DA PRC Scheduled Procedure Step Start Date
1039 //0040 0004 DA PRC Scheduled Procedure Step End Date
1040 //0040 0244 DA PRC Performed Procedure Step Start Date
1041 //0040 0250 DA PRC Performed Procedure Step End Date
1042 //0040 2004 DA PRC Issue Date of Imaging Service Request
1043 //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
1044 //0040 4011 DT PRC Expected Completion Date and Time
1045 //0040 a030 DT PRC Verification Date Time
1046 //0040 a032 DT PRC Observation Date Time
1047 //0040 a120 DT PRC DateTime
1048 //0040 a121 DA PRC Date
1049 //0040 a13a DT PRC Referenced Datetime
1050 //0070 0082 DA ??? Presentation Creation Date
1051 //0100 0420 DT ??? SOP Autorization Date and Time
1052 //0400 0105 DT ??? Digital Signature DateTime
1053 //2100 0040 DA PJ Creation Date
1054 //3006 0008 DA SSET Structure Set Date
1055 //3008 0024 DA ??? Treatment Control Point Date
1056 //3008 0054 DA ??? First Treatment Date
1057 //3008 0056 DA ??? Most Recent Treatment Date
1058 //3008 0162 DA ??? Safe Position Exit Date
1059 //3008 0166 DA ??? Safe Position Return Date
1060 //3008 0250 DA ??? Treatment Date
1061 //300a 0006 DA RT RT Plan Date
1062 //300a 022c DA RT Air Kerma Rate Reference Date
1063 //300e 0004 DA RT Review Date
1068 * \brief gets the info from 0020,0037 : Image Orientation Patient
1069 * @param iop adress of the (6)float aray to receive values
1070 * @return cosines of image orientation patient
1072 void gdcmHeader::GetImageOrientationPatient( float* iop ) {
1074 //iop is supposed to be float[6]
1075 iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0;
1077 // 0020 0037 DS REL Image Orientation (Patient)
1078 std::string StrImOriPat = GetEntryByNumber(0x0020,0x0037);
1079 if (StrImOriPat != GDCM_UNFOUND) {
1080 if( sscanf( StrImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
1081 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6) {
1082 dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0037)");
1083 return ; // bug in the element 0x0020,0x0037
1090 // 0020 0035 DS REL Image Orientation (RET)
1091 StrImOriPat = GetEntryByNumber(0x0020,0x0035);
1092 if (StrImOriPat != GDCM_UNFOUND) {
1093 if( sscanf( StrImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
1094 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6) {
1095 dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0035)");
1096 return ; // bug in the element 0x0020,0x0035
1103 //-----------------------------------------------------------------------------
1106 //-----------------------------------------------------------------------------