1 /*=========================================================================
4 Module: $RCSfile: gdcmHeader.cxx,v $
6 Date: $Date: 2004/06/21 04:18:25 $
7 Version: $Revision: 1.166 $
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)
47 guint32 totalSQlength;
48 guint32 alreadyParsedlength;
52 // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
53 // We may encounter the 'RETired' (0x0028, 0x0200) tag
54 // (Image Location") . This Element contains the number of
55 // the group that contains the pixel data (hence the "Pixel Data"
56 // is found by indirection through the "Image Location").
57 // Inside the group pointed by "Image Location" the searched element
58 // is conventionally the element 0x0010 (when the norm is respected).
59 // When the "Image Location" is absent we default to group 0x7fe0.
61 // This IS the right place for the code
63 std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200);
64 if ( ImageLocation == GDCM_UNFOUND ) { // Image Location
65 GrPixel = 0x7fe0; // default value
67 GrPixel = (guint16) atoi( ImageLocation.c_str() );
69 if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow
70 GrPixel = 0x7fe0; // the supposed processor endianity.
71 // see gdcmData/cr172241.dcm
72 if (GrPixel != 0x7fe0) {
73 // This is a kludge for old dirty Philips imager.
82 * @param exception_on_error whether we want to throw an exception or not
84 gdcmHeader::gdcmHeader(bool exception_on_error) :
85 gdcmDocument(exception_on_error)
91 * \brief Canonical destructor.
93 gdcmHeader::~gdcmHeader (void) {
96 //-----------------------------------------------------------------------------
100 //-----------------------------------------------------------------------------
104 * \brief This predicate, based on hopefully reasonable heuristics,
105 * decides whether or not the current gdcmHeader was properly parsed
106 * and contains the mandatory information for being considered as
107 * a well formed and usable Dicom/Acr File.
108 * @return true when gdcmHeader is the one of a reasonable Dicom/Acr file,
111 bool gdcmHeader::IsReadable(void) {
112 if(!gdcmDocument::IsReadable()) {
115 std::string res = GetEntryByNumber(0x0028, 0x0005);
116 if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
117 return false; // Image Dimensions
118 if ( !GetDocEntryByNumber(0x0028, 0x0100) )
119 return false; // "Bits Allocated"
120 if ( !GetDocEntryByNumber(0x0028, 0x0101) )
121 return false; // "Bits Stored"
122 if ( !GetDocEntryByNumber(0x0028, 0x0102) )
123 return false; // "High Bit"
124 if ( !GetDocEntryByNumber(0x0028, 0x0103) )
125 return false; // "Pixel Representation" i.e. 'Sign'
130 * \brief Retrieve the number of columns of image.
131 * @return The encountered size when found, 0 by default.
132 * 0 means the file is NOT USABLE. The caller will have to check
134 int gdcmHeader::GetXSize(void) {
136 StrSize = GetEntryByNumber(0x0028,0x0011);
137 if (StrSize == GDCM_UNFOUND)
139 return atoi(StrSize.c_str());
143 * \ingroup gdcmHeader
144 * \brief Retrieve the number of lines of image.
145 * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize()
146 * @return The encountered size when found, 1 by default
147 * (The ACR-MEMA file contains a Signal, not an Image).
149 int gdcmHeader::GetYSize(void) {
150 std::string StrSize = GetEntryByNumber(0x0028,0x0010);
151 if (StrSize != GDCM_UNFOUND)
152 return atoi(StrSize.c_str());
156 // The Rows (0028,0010) entry was optional for ACR/NEMA. It might
157 // hence be a signal (1d image). So we default to 1:
162 * \ingroup gdcmHeader
163 * \brief Retrieve the number of planes of volume or the number
164 * of frames of a multiframe.
165 * \warning When present we consider the "Number of Frames" as the third
166 * dimension. When absent we consider the third dimension as
167 * being the ACR-NEMA "Planes" tag content.
168 * @return The encountered size when found, 1 by default (single image).
170 int gdcmHeader::GetZSize(void) {
171 // Both DicomV3 and ACR/Nema consider the "Number of Frames"
172 // as the third dimension.
173 std::string StrSize = GetEntryByNumber(0x0028,0x0008);
174 if (StrSize != GDCM_UNFOUND)
175 return atoi(StrSize.c_str());
177 // We then consider the "Planes" entry as the third dimension
178 StrSize = GetEntryByNumber(0x0028,0x0012);
179 if (StrSize != GDCM_UNFOUND)
180 return atoi(StrSize.c_str());
185 * \ingroup gdcmHeader
186 * \brief gets the info from 0028,0030 : Pixel Spacing
188 * @return X dimension of a pixel
190 float gdcmHeader::GetXSpacing() {
191 float xspacing, yspacing;
192 std::string StrSpacing = GetEntryByNumber(0x0028,0x0030);
194 if (StrSpacing == GDCM_UNFOUND) {
195 dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)");
199 if( (nbValues = sscanf( StrSpacing.c_str(), "%f\\%f", &yspacing, &xspacing)) != 2) {
200 if (nbValues==1) // if single value is found, xspacing is defaulted to yspacing
203 if (xspacing == 0.) {
204 dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
205 // seems to be a bug in the header ...
206 sscanf( StrSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
212 * \ingroup gdcmHeader
213 * \brief gets the info from 0028,0030 : Pixel Spacing
215 * @return Y dimension of a pixel
217 float gdcmHeader::GetYSpacing() {
219 std::string StrSpacing = GetEntryByNumber(0x0028,0x0030);
221 if (StrSpacing == GDCM_UNFOUND) {
222 dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)");
225 sscanf( StrSpacing.c_str(), "%f", &yspacing);
231 *\brief gets the info from 0018,0088 : Space Between Slices
232 * else from 0018,0050 : Slice Thickness
234 * @return Z dimension of a voxel-to be
236 float gdcmHeader::GetZSpacing() {
237 // Spacing Between Slices : distance entre le milieu de chaque coupe
238 // Les coupes peuvent etre :
239 // jointives (Spacing between Slices = Slice Thickness)
240 // chevauchantes (Spacing between Slices < Slice Thickness)
241 // disjointes (Spacing between Slices > Slice Thickness)
242 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
243 // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
244 // Si le Spacing Between Slices est absent,
245 // on suppose que les coupes sont jointives
247 std::string StrSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
249 if (StrSpacingBSlices == GDCM_UNFOUND) {
250 dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices");
251 std::string StrSliceThickness = GetEntryByNumber(0x0018,0x0050);
252 if (StrSliceThickness == GDCM_UNFOUND)
255 // if no 'Spacing Between Slices' is found,
256 // we assume slices join together
257 // (no overlapping, no interslice gap)
258 // if they don't, we're fucked up
259 return atof(StrSliceThickness.c_str());
261 return atof(StrSpacingBSlices.c_str());
267 *\brief gets the info from 0028,1052 : Rescale Intercept
268 * @return Rescale Intercept
270 float gdcmHeader::GetRescaleIntercept() {
272 std::string StrRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept
273 if (StrRescInter != GDCM_UNFOUND) {
274 if( sscanf( StrRescInter.c_str(), "%f", &resInter) != 1) {
275 dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty");
276 // bug in the element 0x0028,0x1052
284 *\brief gets the info from 0028,1053 : Rescale Slope
285 * @return Rescale Slope
287 float gdcmHeader::GetRescaleSlope() {
289 std::string StrRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope
290 if (StrRescSlope != GDCM_UNFOUND) {
291 if( sscanf( StrRescSlope.c_str(), "%f", &resSlope) != 1) {
292 dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty");
293 // bug in the element 0x0028,0x1053
300 * \ingroup gdcmHeader
301 * \brief This function is intended to user who doesn't want
302 * to have to manage a LUT and expects to get an RBG Pixel image
303 * (or a monochrome one ...)
304 * \warning to be used with GetImagePixels()
305 * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR)
307 int gdcmHeader::GetNumberOfScalarComponents() {
308 if (GetSamplesPerPixel() ==3)
311 // 0028 0100 US IMG Bits Allocated
312 // (in order no to be messed up by old RGB images)
313 if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
316 std::string PhotometricInterpretation =
317 gdcmHeader::GetEntryByNumber(0x0028,0x0004);
319 if ( ( PhotometricInterpretation == "PALETTE COLOR ") ) {
320 if (HasLUT()) // PALETTE COLOR is NOT enough
326 //beware of trailing space at end of string
327 if (PhotometricInterpretation.find(GDCM_UNFOUND) <
328 PhotometricInterpretation.length() ||
329 PhotometricInterpretation.find("MONOCHROME1") <
330 PhotometricInterpretation.length() ||
331 PhotometricInterpretation.find("MONOCHROME2") <
332 PhotometricInterpretation.length() )
335 // we assume that *all* kinds of YBR are dealt with
340 * \ingroup gdcmHeader
341 * \brief This function is intended to user that DOESN'T want
342 * to get RGB pixels image when it's stored as a PALETTE COLOR image
343 * - the (vtk) user is supposed to know how deal with LUTs -
344 * \warning to be used with GetImagePixelsRaw()
345 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
347 int gdcmHeader::GetNumberOfScalarComponentsRaw() {
349 // 0028 0100 US IMG Bits Allocated
350 // (in order no to be messed up by old RGB images)
351 if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
354 // we assume that *all* kinds of YBR are dealt with
355 return GetSamplesPerPixel();
360 *\brief gets the info from 0020,000d : Study Instance UID
361 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
362 * @return Study Instance UID
364 //std::string gdcmHeader::GetStudyUID(){
365 // return GetEntryByNumber(0x0020,0x000d); //0020 000d UI REL Study Instance UID
370 *\brief gets the info from 0020,000e : Series Instance UID
371 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
372 * @return Series Instance UID
374 //std::string gdcmHeader::GetSeriesUID(){
375 // return GetEntryByNumber(0x0020,0x000e); //0020 000e UI REL Series Instance UID
380 *\brief gets the info from 0008,0016 : SOP Class UID
381 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
382 * @return SOP Class UID
384 //std::string gdcmHeader::GetClassUID(){
385 // return GetEntryByNumber(0x0008,0x0016); //0008 0016 UI ID SOP Class UID
389 *\brief gets the info from 0008,0018 : SOP Instance UID
390 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
391 * @return SOP Instance UID
393 //std::string gdcmHeader::GetInstanceUID(){
394 // return GetEntryByNumber(0x0008,0x0018); //0008 0018 UI ID SOP Instance UID
397 // -------------- Remember ! ----------------------------------
399 // Image Position Patient (0020,0032):
400 // If not found (ACR_NEMA) we try Image Position (0020,0030)
401 // If not found (ACR-NEMA), we consider Slice Location (0020,1041)
402 // or Location (0020,0050)
403 // as the Z coordinate,
404 // 0. for all the coordinates if nothing is found
406 // \todo find a way to inform the caller nothing was found
407 // \todo How to tell the caller a wrong number of values was found?
409 // ---------------------------------------------------------------
413 * \brief gets the info from 0020,0032 : Image Position Patient
414 * else from 0020,0030 : Image Position (RET)
416 * @return up-left image corner X position
419 float gdcmHeader::GetXOrigin() {
420 float xImPos, yImPos, zImPos;
421 std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
423 if (StrImPos == GDCM_UNFOUND) {
424 dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)");
425 StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
426 if (StrImPos == GDCM_UNFOUND) {
427 dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)");
428 /// \todo How to tell the caller nothing was found ?
432 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
438 * \brief gets the info from 0020,0032 : Image Position Patient
439 * else from 0020,0030 : Image Position (RET)
441 * @return up-left image corner Y position
443 float gdcmHeader::GetYOrigin() {
444 float xImPos, yImPos, zImPos;
445 std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
447 if (StrImPos == GDCM_UNFOUND) {
448 dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)");
449 StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
450 if (StrImPos == GDCM_UNFOUND) {
451 dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)");
452 /// \todo How to tell the caller nothing was found ?
456 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
462 * \brief gets the info from 0020,0032 : Image Position Patient
463 * \ else from 0020,0030 : Image Position (RET)
464 * \ else from 0020,1041 : Slice Location
465 * \ else from 0020,0050 : Location
467 * @return up-left image corner Z position
469 float gdcmHeader::GetZOrigin() {
470 float xImPos, yImPos, zImPos;
471 std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
472 if (StrImPos != GDCM_UNFOUND) {
473 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
474 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)");
475 return 0.; // bug in the element 0x0020,0x0032
480 StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
481 if (StrImPos != GDCM_UNFOUND) {
482 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
483 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
484 return 0.; // bug in the element 0x0020,0x0032
489 std::string StrSliceLocation = GetEntryByNumber(0x0020,0x1041);// for *very* old ACR-NEMA images
490 if (StrSliceLocation != GDCM_UNFOUND) {
491 if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) {
492 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)");
493 return 0.; // bug in the element 0x0020,0x1041
498 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)");
499 std::string StrLocation = GetEntryByNumber(0x0020,0x0050);
500 if (StrLocation != GDCM_UNFOUND) {
501 if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) {
502 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)");
503 return 0.; // bug in the element 0x0020,0x0050
508 dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)");
509 return 0.; // Hopeless
513 * \brief gets the info from 0020,0013 : Image Number
515 * @return image number
517 int gdcmHeader::GetImageNumber() {
518 // The function i atoi() takes the address of an area of memory as
519 // parameter and converts the string stored at that location to an integer
520 // using the external decimal to internal binary conversion rules. This may
521 // be preferable to sscanf() since atoi() is a much smaller, simpler and
522 // faster function. sscanf() can do all possible conversions whereas
523 // atoi() can only do single decimal integer conversions.
524 std::string StrImNumber = GetEntryByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number
525 if (StrImNumber != GDCM_UNFOUND) {
526 return atoi( StrImNumber.c_str() );
532 * \brief gets the info from 0008,0060 : Modality
533 * @return Modality Type
535 ModalityType gdcmHeader::GetModality(void) {
536 // 0008 0060 CS ID Modality
537 std::string StrModality = GetEntryByNumber(0x0008,0x0060);
538 if (StrModality != GDCM_UNFOUND) {
539 if ( StrModality.find("AU") < StrModality.length()) return AU;
540 else if ( StrModality.find("AS") < StrModality.length()) return AS;
541 else if ( StrModality.find("BI") < StrModality.length()) return BI;
542 else if ( StrModality.find("CF") < StrModality.length()) return CF;
543 else if ( StrModality.find("CP") < StrModality.length()) return CP;
544 else if ( StrModality.find("CR") < StrModality.length()) return CR;
545 else if ( StrModality.find("CT") < StrModality.length()) return CT;
546 else if ( StrModality.find("CS") < StrModality.length()) return CS;
547 else if ( StrModality.find("DD") < StrModality.length()) return DD;
548 else if ( StrModality.find("DF") < StrModality.length()) return DF;
549 else if ( StrModality.find("DG") < StrModality.length()) return DG;
550 else if ( StrModality.find("DM") < StrModality.length()) return DM;
551 else if ( StrModality.find("DS") < StrModality.length()) return DS;
552 else if ( StrModality.find("DX") < StrModality.length()) return DX;
553 else if ( StrModality.find("ECG") < StrModality.length()) return ECG;
554 else if ( StrModality.find("EPS") < StrModality.length()) return EPS;
555 else if ( StrModality.find("FA") < StrModality.length()) return FA;
556 else if ( StrModality.find("FS") < StrModality.length()) return FS;
557 else if ( StrModality.find("HC") < StrModality.length()) return HC;
558 else if ( StrModality.find("HD") < StrModality.length()) return HD;
559 else if ( StrModality.find("LP") < StrModality.length()) return LP;
560 else if ( StrModality.find("LS") < StrModality.length()) return LS;
561 else if ( StrModality.find("MA") < StrModality.length()) return MA;
562 else if ( StrModality.find("MR") < StrModality.length()) return MR;
563 else if ( StrModality.find("NM") < StrModality.length()) return NM;
564 else if ( StrModality.find("OT") < StrModality.length()) return OT;
565 else if ( StrModality.find("PT") < StrModality.length()) return PT;
566 else if ( StrModality.find("RF") < StrModality.length()) return RF;
567 else if ( StrModality.find("RG") < StrModality.length()) return RG;
568 else if ( StrModality.find("RTDOSE") < StrModality.length()) return RTDOSE;
569 else if ( StrModality.find("RTIMAGE") < StrModality.length()) return RTIMAGE;
570 else if ( StrModality.find("RTPLAN") < StrModality.length()) return RTPLAN;
571 else if ( StrModality.find("RTSTRUCT")< StrModality.length()) return RTSTRUCT;
572 else if ( StrModality.find("SM") < StrModality.length()) return SM;
573 else if ( StrModality.find("ST") < StrModality.length()) return ST;
574 else if ( StrModality.find("TG") < StrModality.length()) return TG;
575 else if ( StrModality.find("US") < StrModality.length()) return US;
576 else if ( StrModality.find("VF") < StrModality.length()) return VF;
577 else if ( StrModality.find("XA") < StrModality.length()) return XA;
578 else if ( StrModality.find("XC") < StrModality.length()) return XC;
582 /// \todo throw error return value ???
583 /// specified <> unknow in our database
591 * \ingroup gdcmHeader
592 * \brief Retrieve the number of Bits Stored (actually used)
593 * (as opposite to number of Bits Allocated)
594 * @return The encountered number of Bits Stored, 0 by default.
595 * 0 means the file is NOT USABLE. The caller has to check it !
597 int gdcmHeader::GetBitsStored() {
598 std::string StrSize = GetEntryByNumber(0x0028,0x0101);
599 if (StrSize == GDCM_UNFOUND)
600 return 0; // It's supposed to be mandatory
601 // the caller will have to check
602 return atoi(StrSize.c_str());
606 * \ingroup gdcmHeader
607 * \brief Retrieve the number of Bits Allocated
608 * (8, 12 -compacted ACR-NEMA files, 16, ...)
609 * @return The encountered number of Bits Allocated, 0 by default.
610 * 0 means the file is NOT USABLE. The caller has to check it !
612 int gdcmHeader::GetBitsAllocated(void) {
613 std::string StrSize = GetEntryByNumber(0x0028,0x0100);
614 if (StrSize == GDCM_UNFOUND)
615 return 0; // It's supposed to be mandatory
616 // the caller will have to check
617 return atoi(StrSize.c_str());
621 * \ingroup gdcmHeader
622 * \brief Retrieve the number of Samples Per Pixel
623 * (1 : gray level, 3 : RGB -1 or 3 Planes-)
624 * @return The encountered number of Samples Per Pixel, 1 by default.
625 * (Gray level Pixels)
627 int gdcmHeader::GetSamplesPerPixel(void) {
628 std::string StrSize = GetEntryByNumber(0x0028,0x0002);
629 if (StrSize == GDCM_UNFOUND)
630 return 1; // Well, it's supposed to be mandatory ...
631 // but sometimes it's missing : *we* assume Gray pixels
632 return atoi(StrSize.c_str());
636 * \ingroup gdcmHeader
637 * \brief Retrieve the Planar Configuration for RGB images
638 * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
639 * @return The encountered Planar Configuration, 0 by default.
641 int gdcmHeader::GetPlanarConfiguration(void) {
642 std::string StrSize = GetEntryByNumber(0x0028,0x0006);
643 if (StrSize == GDCM_UNFOUND)
645 return atoi(StrSize.c_str());
649 * \ingroup gdcmHeader
650 * \brief Return the size (in bytes) of a single pixel of data.
651 * @return The size in bytes of a single pixel of data; 0 by default
652 * 0 means the file is NOT USABLE; the caller will have to check
654 int gdcmHeader::GetPixelSize() {
655 // 0028 0100 US IMG Bits Allocated
656 // (in order no to be messed up by old RGB images)
657 // if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
660 std::string PixelType = GetPixelType();
661 if (PixelType == "8U" || PixelType == "8S")
663 if (PixelType == "16U" || PixelType == "16S")
665 if (PixelType == "32U" || PixelType == "32S")
667 if (PixelType == "FD")
669 dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
674 * \ingroup gdcmHeader
675 * \brief Build the Pixel Type of the image.
676 * Possible values are:
677 * - 8U unsigned 8 bit,
679 * - 16U unsigned 16 bit,
680 * - 16S signed 16 bit,
681 * - 32U unsigned 32 bit,
682 * - 32S signed 32 bit,
683 * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
684 * \warning 12 bit images appear as 16 bit.
685 * 24 bit images appear as 8 bit
686 * @return 0S if nothing found. NOT USABLE file. The caller has to check
688 std::string gdcmHeader::GetPixelType() {
689 std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated
690 if (BitsAlloc == GDCM_UNFOUND) {
691 dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
692 BitsAlloc = std::string("16");
694 if (BitsAlloc == "64") // )
696 if (BitsAlloc == "12") // It will be unpacked
697 BitsAlloc = std::string("16");
698 else if (BitsAlloc == "24") // (in order no to be messed up
699 BitsAlloc = std::string("8"); // by old RGB images)
701 std::string Signed = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation"
702 if (Signed == GDCM_UNFOUND) {
703 dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
704 BitsAlloc = std::string("0");
707 Signed = std::string("U");
709 Signed = std::string("S");
711 return( BitsAlloc + Signed);
716 * \ingroup gdcmHeader
717 * \brief Recover the offset (from the beginning of the file)
718 * of *image* pixels (not *icone image* pixels, if any !)
719 * @return Pixel Offset
721 size_t gdcmHeader::GetPixelOffset(void) {
723 gdcmDocEntry* PixelElement = GetDocEntryByNumber(GrPixel,NumPixel);
726 return PixelElement->GetOffset();
729 std::cout << "Big trouble : Pixel Element ("
730 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
736 // TODO : unify those two (previous one and next one)
738 * \ingroup gdcmHeader
739 * \brief Recover the pixel area length (in Bytes)
740 * @return Pixel Element Length, as stored in the header
741 * (NOT the memory space necessary to hold the Pixels
742 * -in case of embeded compressed image-)
743 * 0 : NOT USABLE file. The caller has to check.
745 size_t gdcmHeader::GetPixelAreaLength(void) {
747 gdcmDocEntry* PixelElement = GetDocEntryByNumber(GrPixel,NumPixel);
750 return PixelElement->GetLength();
753 std::cout << "Big trouble : Pixel Element ("
754 << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
762 * \ingroup gdcmHeader
763 * \brief tells us if LUT are used
764 * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
765 * are NOT considered as LUT, since nobody knows
766 * how to deal with them
767 * Please warn me if you know sbdy that *does* know ... jprx
768 * @return true if LUT Descriptors and LUT Tables were found
770 bool gdcmHeader::HasLUT() {
772 // Check the presence of the LUT Descriptors, and LUT Tables
774 if ( !GetDocEntryByNumber(0x0028,0x1101) )
776 // LutDescriptorGreen
777 if ( !GetDocEntryByNumber(0x0028,0x1102) )
780 if ( !GetDocEntryByNumber(0x0028,0x1103) )
782 // Red Palette Color Lookup Table Data
783 if ( !GetDocEntryByNumber(0x0028,0x1201) )
785 // Green Palette Color Lookup Table Data
786 if ( !GetDocEntryByNumber(0x0028,0x1202) )
788 // Blue Palette Color Lookup Table Data
789 if ( !GetDocEntryByNumber(0x0028,0x1203) )
791 // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
792 // NOT taken into account, but we don't know how to use it ...
797 * \ingroup gdcmHeader
798 * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
800 * @return Lookup Table number of Bits , 0 by default
801 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
802 * @ return bit number of each LUT item
804 int gdcmHeader::GetLUTNbits(void) {
805 std::vector<std::string> tokens;
809 //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue
810 // Consistency already checked in GetLUTLength
811 std::string LutDescription = GetEntryByNumber(0x0028,0x1101);
812 if (LutDescription == GDCM_UNFOUND)
814 tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
815 Tokenize (LutDescription, tokens, "\\");
816 //LutLength=atoi(tokens[0].c_str());
817 //LutDepth=atoi(tokens[1].c_str());
818 LutNbits=atoi(tokens[2].c_str());
824 * \ingroup gdcmHeader
825 * \brief builts Red/Green/Blue/Alpha LUT from Header
826 * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
827 * and (0028,1101),(0028,1102),(0028,1102)
828 * - xxx Palette Color Lookup Table Descriptor - are found
829 * and (0028,1201),(0028,1202),(0028,1202)
830 * - xxx Palette Color Lookup Table Data - are found
831 * \warning does NOT deal with :
832 * 0028 1100 Gray Lookup Table Descriptor (Retired)
833 * 0028 1221 Segmented Red Palette Color Lookup Table Data
834 * 0028 1222 Segmented Green Palette Color Lookup Table Data
835 * 0028 1223 Segmented Blue Palette Color Lookup Table Data
836 * no known Dicom reader deals with them :-(
837 * @return a RGBA Lookup Table
839 unsigned char * gdcmHeader::GetLUTRGBA(void) {
841 // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables
843 // if Photometric Interpretation # PALETTE COLOR, no LUT to be done
844 if (GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR ") {
847 int lengthR, debR, nbitsR;
848 int lengthG, debG, nbitsG;
849 int lengthB, debB, nbitsB;
851 // Get info from Lut Descriptors
852 // (the 3 LUT descriptors may be different)
853 std::string LutDescriptionR = GetEntryByNumber(0x0028,0x1101);
854 if (LutDescriptionR == GDCM_UNFOUND)
856 std::string LutDescriptionG = GetEntryByNumber(0x0028,0x1102);
857 if (LutDescriptionG == GDCM_UNFOUND)
859 std::string LutDescriptionB = GetEntryByNumber(0x0028,0x1103);
860 if (LutDescriptionB == GDCM_UNFOUND)
863 std::vector<std::string> tokens;
865 tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
866 Tokenize (LutDescriptionR, tokens, "\\");
867 lengthR=atoi(tokens[0].c_str()); // Red LUT length in Bytes
868 debR =atoi(tokens[1].c_str()); // subscript of the first Lut Value
869 nbitsR =atoi(tokens[2].c_str()); // Lut item size (in Bits)
872 tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
873 Tokenize (LutDescriptionG, tokens, "\\");
874 lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes
875 debG =atoi(tokens[1].c_str()); // subscript of the first Lut Value
876 nbitsG =atoi(tokens[2].c_str()); // Lut item size (in Bits)
879 tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
880 Tokenize (LutDescriptionB, tokens, "\\");
881 lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes
882 debB =atoi(tokens[1].c_str()); // subscript of the first Lut Value
883 nbitsB =atoi(tokens[2].c_str()); // Lut item size (in Bits)
886 // Load LUTs into memory, (as they were stored on disk)
887 unsigned char *lutR = (unsigned char *)
888 GetEntryVoidAreaByNumber(0x0028,0x1201);
889 unsigned char *lutG = (unsigned char *)
890 GetEntryVoidAreaByNumber(0x0028,0x1202);
891 unsigned char *lutB = (unsigned char *)
892 GetEntryVoidAreaByNumber(0x0028,0x1203);
894 if (!lutR || !lutG || !lutB ) {
897 // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT
899 unsigned char *LUTRGBA = new unsigned char[1024]; // 256 * 4 (R, G, B, Alpha)
903 memset(LUTRGBA, 0, 1024);
906 std::string str_nb = GetEntryByNumber(0x0028,0x0100);
907 if (str_nb == GDCM_UNFOUND ) {
910 nb = atoi(str_nb.c_str() );
914 if (nbitsR==16 && nb==8) // when LUT item size is different than pixel size
915 mult=2; // high byte must be = low byte
916 else // See PS 3.3-2003 C.11.1.1.2 p 619
919 // if we get a black image, let's just remove the '+1'
920 // from 'i*mult+1' and check again
921 // if it works, we shall have to check the 3 Palettes
922 // to see which byte is ==0 (first one, or second one)
924 // We give up the checking to avoid some (useless ?)overhead
925 // (optimistic asumption)
930 for(i=0;i<lengthR;i++) {
935 for(i=0;i<lengthG;i++) {
940 for(i=0;i<lengthB;i++) {
946 *a = 1; // Alpha component
950 //How to free the now useless LUTs?
951 //free(LutR); free(LutB); free(LutG); // Seg Fault when used
956 * \brief Accesses the info from 0002,0010 : Transfert Syntax and gdcmTS
958 * @return The full Transfert Syntax Name (as opposed to Transfert Syntax UID)
960 std::string gdcmHeader::GetTransfertSyntaxName(void) {
961 // use the gdcmTS (TS : Transfert Syntax)
962 std::string TransfertSyntax = GetEntryByNumber(0x0002,0x0010);
963 if (TransfertSyntax == GDCM_UNFOUND) {
964 dbg.Verbose(0, "gdcmHeader::GetTransfertSyntaxName:"
965 " unfound Transfert Syntax (0002,0010)");
966 return "Uncompressed ACR-NEMA";
968 // we do it only when we need it
969 gdcmTS * ts = gdcmGlobal::GetTS();
970 std::string tsName=ts->GetValue(TransfertSyntax);
971 //delete ts; /// \todo Seg Fault when deleted ?!
976 * \brief Sets the Pixel Area size in the Header
977 * --> not-for-rats function
978 * @param ImageDataSize new Pixel Area Size
979 * warning : nothing else is checked
981 void gdcmHeader::SetImageDataSize(size_t ImageDataSize) {
982 std::string content1;
985 sprintf(car,"%d",ImageDataSize);
987 gdcmDocEntry *a = GetDocEntryByNumber(GrPixel, NumPixel);
988 a->SetLength(ImageDataSize);
991 sprintf(car,"%d",ImageDataSize);
993 SetEntryByNumber(content1, GrPixel, NumPixel);
996 //-----------------------------------------------------------------------------
1000 * \brief anonymize a Header (removes Patient's personal info)
1001 * (read the code to see which ones ...)
1003 bool gdcmHeader::AnonymizeHeader() {
1005 gdcmDocEntry *patientNameHE = GetDocEntryByNumber (0x0010, 0x0010);
1007 ReplaceIfExistByNumber (" ",0x0010, 0x2154); // Telephone
1008 ReplaceIfExistByNumber (" ",0x0010, 0x1040); // Adress
1009 ReplaceIfExistByNumber (" ",0x0010, 0x0020); // Patient ID
1011 if (patientNameHE) {
1012 std::string studyInstanceUID = GetEntryByNumber (0x0020, 0x000d);
1013 if (studyInstanceUID !=GDCM_UNFOUND)
1014 ReplaceOrCreateByNumber(studyInstanceUID, 0x0010, 0x0010);
1016 ReplaceOrCreateByNumber(std::string("anonymised"), 0x0010, 0x0010);
1020 // (if any) remove or replace all the stuff that contains a Date
1022 //0008 0012 DA ID Instance Creation Date
1023 //0008 0020 DA ID Study Date
1024 //0008 0021 DA ID Series Date
1025 //0008 0022 DA ID Acquisition Date
1026 //0008 0023 DA ID Content Date
1027 //0008 0024 DA ID Overlay Date
1028 //0008 0025 DA ID Curve Date
1029 //0008 002a DT ID Acquisition Datetime
1030 //0018 9074 DT ACQ Frame Acquisition Datetime
1031 //0018 9151 DT ACQ Frame Reference Datetime
1032 //0018 a002 DT ACQ Contribution Date Time
1033 //0020 3403 SH REL Modified Image Date (RET)
1034 //0032 0032 DA SDY Study Verified Date
1035 //0032 0034 DA SDY Study Read Date
1036 //0032 1000 DA SDY Scheduled Study Start Date
1037 //0032 1010 DA SDY Scheduled Study Stop Date
1038 //0032 1040 DA SDY Study Arrival Date
1039 //0032 1050 DA SDY Study Completion Date
1040 //0038 001a DA VIS Scheduled Admission Date
1041 //0038 001c DA VIS Scheduled Discharge Date
1042 //0038 0020 DA VIS Admitting Date
1043 //0038 0030 DA VIS Discharge Date
1044 //0040 0002 DA PRC Scheduled Procedure Step Start Date
1045 //0040 0004 DA PRC Scheduled Procedure Step End Date
1046 //0040 0244 DA PRC Performed Procedure Step Start Date
1047 //0040 0250 DA PRC Performed Procedure Step End Date
1048 //0040 2004 DA PRC Issue Date of Imaging Service Request
1049 //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
1050 //0040 4011 DT PRC Expected Completion Date and Time
1051 //0040 a030 DT PRC Verification Date Time
1052 //0040 a032 DT PRC Observation Date Time
1053 //0040 a120 DT PRC DateTime
1054 //0040 a121 DA PRC Date
1055 //0040 a13a DT PRC Referenced Datetime
1056 //0070 0082 DA ??? Presentation Creation Date
1057 //0100 0420 DT ??? SOP Autorization Date and Time
1058 //0400 0105 DT ??? Digital Signature DateTime
1059 //2100 0040 DA PJ Creation Date
1060 //3006 0008 DA SSET Structure Set Date
1061 //3008 0024 DA ??? Treatment Control Point Date
1062 //3008 0054 DA ??? First Treatment Date
1063 //3008 0056 DA ??? Most Recent Treatment Date
1064 //3008 0162 DA ??? Safe Position Exit Date
1065 //3008 0166 DA ??? Safe Position Return Date
1066 //3008 0250 DA ??? Treatment Date
1067 //300a 0006 DA RT RT Plan Date
1068 //300a 022c DA RT Air Kerma Rate Reference Date
1069 //300e 0004 DA RT Review Date
1074 * \brief gets the info from 0020,0037 : Image Orientation Patient
1075 * @param iop adress of the (6)float aray to receive values
1076 * @return cosines of image orientation patient
1078 void gdcmHeader::GetImageOrientationPatient( float* iop ) {
1080 //iop is supposed to be float[6]
1081 iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0;
1083 // 0020 0037 DS REL Image Orientation (Patient)
1084 std::string StrImOriPat = GetEntryByNumber(0x0020,0x0037);
1085 if (StrImOriPat != GDCM_UNFOUND) {
1086 if( sscanf( StrImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
1087 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6) {
1088 dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0037)");
1089 return ; // bug in the element 0x0020,0x0037
1096 // 0020 0035 DS REL Image Orientation (RET)
1097 StrImOriPat = GetEntryByNumber(0x0020,0x0035);
1098 if (StrImOriPat != GDCM_UNFOUND) {
1099 if( sscanf( StrImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
1100 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6) {
1101 dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0035)");
1102 return ; // bug in the element 0x0020,0x0035
1109 //-----------------------------------------------------------------------------
1112 //-----------------------------------------------------------------------------