1 // gdcmHeaderHelper.cxx
2 //-----------------------------------------------------------------------------
3 #include "gdcmHeaderHelper.h"
4 #include "gdcmDirList.h"
11 //-----------------------------------------------------------------------------
13 * \ingroup gdcmHeaderHelper
16 gdcmHeaderHelper::gdcmHeaderHelper() : gdcmHeader( ) {
21 * \ingroup gdcmHeaderHelper
23 * @param InFilename Name of the file to deal with
24 * @param exception_on_error
25 * @param enable_sequences = true to allow the header
26 * to be parsed *inside* the SeQuences,
27 * when they have an actual length
28 * @param ignore_shadow = true if user wants to skip shadow groups
29 * during parsing, to save memory space
31 gdcmHeaderHelper::gdcmHeaderHelper(const char *InFilename,
32 bool exception_on_error,
33 bool enable_sequences,
35 : gdcmHeader( InFilename,
42 //-----------------------------------------------------------------------------
45 //-----------------------------------------------------------------------------
48 * \ingroup gdcmHeaderHelper
49 * \brief Returns the size (in bytes) of a single pixel of data.
50 * @return The size in bytes of a single pixel of data.
53 int gdcmHeaderHelper::GetPixelSize() {
55 // 0028 0100 US IMG Bits Allocated
56 // (in order no to be messed up by old RGB images)
57 if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
60 std::string PixelType = GetPixelType();
61 if (PixelType == "8U" || PixelType == "8S")
63 if (PixelType == "16U" || PixelType == "16S")
65 if (PixelType == "32U" || PixelType == "32S")
67 if (PixelType == "FD") // to help unfortunate users to manage DOUBLE
69 dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
74 * \ingroup gdcmHeaderHelper
75 * \brief Build the Pixel Type of the image.
76 * Possible values are:
77 * - 8U unsigned 8 bit,
79 * - 16U unsigned 16 bit,
80 * - 16S signed 16 bit,
81 * - 32U unsigned 32 bit,
82 * - 32S signed 32 bit,
84 * \warning 12 bit images appear as 16 bit.
85 * 24 bit images appear as 8 bit
86 * 64 bit means 'DOUBLE' images
87 * (no DOUBLE images in kosher DICOM,
88 * but so usefull for people that miss them ;-)
91 std::string gdcmHeaderHelper::GetPixelType() {
92 std::string BitsAlloc;
93 BitsAlloc = GetEntryByNumber(0x0028, 0x0100);
94 if (BitsAlloc == GDCM_UNFOUND) { // Bits Allocated
95 dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
96 BitsAlloc = std::string("16");
98 if (BitsAlloc == "12") // It will be unpacked
99 BitsAlloc = std::string("16");
100 else if (BitsAlloc == "24") // (in order no to be messed up
101 BitsAlloc = std::string("8"); // by old RGB images)
104 Signed = GetEntryByNumber(0x0028, 0x0103);
105 if (Signed == GDCM_UNFOUND) { // "Pixel Representation"
106 dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
107 BitsAlloc = std::string("0");
109 if (BitsAlloc == "64") // to help users that want to deal with DOUBLE
113 Signed = std::string("U");
115 Signed = std::string("S");
117 return( BitsAlloc + Signed);
121 * \ingroup gdcmHeaderHelper
122 * \brief gets the info from 0028,0030 : Pixel Spacing
124 * @return X dimension of a pixel
126 float gdcmHeaderHelper::GetXSpacing() {
127 float xspacing, yspacing;
128 std::string StrSpacing = GetEntryByNumber(0x0028,0x0030);
130 if (StrSpacing == GDCM_UNFOUND) {
131 dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)");
135 if( (nbValues = sscanf( StrSpacing.c_str(), "%f\\%f", &yspacing, &xspacing)) != 2) {
136 if (nbValues==1) // if single value is found, xspacing is defaulted to yspacing
139 if (xspacing == 0.) {
140 dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
141 // seems to be a bug in the header ...
142 sscanf( StrSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
148 * \ingroup gdcmHeaderHelper
149 * \brief gets the info from 0028,0030 : Pixel Spacing
151 * @return Y dimension of a pixel
153 float gdcmHeaderHelper::GetYSpacing() {
155 std::string StrSpacing = GetEntryByNumber(0x0028,0x0030);
157 if (StrSpacing == GDCM_UNFOUND) {
158 dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)");
161 sscanf( StrSpacing.c_str(), "%f", &yspacing);
166 *\ingroup gdcmHeaderHelper
167 *\brief gets the info from 0018,0088 : Space Between Slices
168 * else from 0018,0050 : Slice Thickness
170 * @return Z dimension of a voxel-to be
172 float gdcmHeaderHelper::GetZSpacing() {
173 // Spacing Between Slices : distance entre le milieu de chaque coupe
174 // Les coupes peuvent etre :
175 // jointives (Spacing between Slices = Slice Thickness)
176 // chevauchantes (Spacing between Slices < Slice Thickness)
177 // disjointes (Spacing between Slices > Slice Thickness)
178 // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
179 // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
180 // Si le Spacing Between Slices est absent,
181 // on suppose que les coupes sont jointives
183 std::string StrSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
185 if (StrSpacingBSlices == GDCM_UNFOUND) {
186 dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices");
187 std::string StrSliceThickness = GetEntryByNumber(0x0018,0x0050);
188 if (StrSliceThickness == GDCM_UNFOUND)
191 // if no 'Spacing Between Slices' is found,
192 // we assume slices join together
193 // (no overlapping, no interslice gap)
194 // if they don't, we're fucked up
195 return atof(StrSliceThickness.c_str());
197 return atof(StrSpacingBSlices.c_str());
202 *\ingroup gdcmHeaderHelper
203 *\brief gets the info from 0028,1052 : Rescale Intercept
204 * @return Rescale Intercept
206 float gdcmHeaderHelper::GetRescaleIntercept() {
208 std::string StrRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept
209 if (StrRescInter != GDCM_UNFOUND) {
210 if( sscanf( StrRescInter.c_str(), "%f", &resInter) != 1) {
211 dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty");
212 // bug in the element 0x0028,0x1052
219 *\ingroup gdcmHeaderHelper
220 *\brief gets the info from 0028,1053 : Rescale Slope
221 * @return Rescale Slope
223 float gdcmHeaderHelper::GetRescaleSlope() {
225 std::string StrRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope
226 if (StrRescSlope != GDCM_UNFOUND) {
227 if( sscanf( StrRescSlope.c_str(), "%f", &resSlope) != 1) {
228 dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty");
229 // bug in the element 0x0028,0x1053
236 * \ingroup gdcmHeaderHelper
237 * \brief This function is intended to user who doesn't want
238 * to have to manage a LUT and expects to get an RBG Pixel image
239 * (or a monochrome one ...)
240 * \warning to be used with GetImagePixels()
241 * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR)
243 int gdcmHeaderHelper::GetNumberOfScalarComponents() {
244 if (GetSamplesPerPixel() ==3)
247 // 0028 0100 US IMG Bits Allocated
248 // (in order no to be messed up by old RGB images)
249 if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
252 std::string PhotometricInterpretation =
253 gdcmHeader::GetEntryByNumber(0x0028,0x0004);
255 if ( ( PhotometricInterpretation == "PALETTE COLOR ") ) {
256 if (HasLUT()) // PALETTE COLOR is NOT enough
262 //beware of trailing space at end of string
263 if (PhotometricInterpretation.find(GDCM_UNFOUND) <
264 PhotometricInterpretation.length() ||
265 PhotometricInterpretation.find("MONOCHROME1") <
266 PhotometricInterpretation.length() ||
267 PhotometricInterpretation.find("MONOCHROME2") <
268 PhotometricInterpretation.length() )
271 // we assume that *all* kinds of YBR are dealt with
276 * \ingroup gdcmHeaderHelper
277 * \brief This function is intended to user that DOESN'T want
278 * to get RGB pixels image when it's stored as a PALETTE COLOR image
279 * - the (vtk) user is supposed to know how deal with LUTs -
280 * \warning to be used with GetImagePixelsRaw()
281 * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
283 int gdcmHeaderHelper::GetNumberOfScalarComponentsRaw() {
285 // 0028 0100 US IMG Bits Allocated
286 // (in order no to be messed up by old RGB images)
287 if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
290 // we assume that *all* kinds of YBR are dealt with
291 return GetSamplesPerPixel();
295 *\ingroup gdcmHeaderHelper
296 *\brief gets the info from 0020,000d : Study Instance UID
297 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
298 * @return Study Instance UID
300 std::string gdcmHeaderHelper::GetStudyUID(){
301 return GetEntryByNumber(0x0020,0x000d); //0020 000d UI REL Study Instance UID
305 *\ingroup gdcmHeaderHelper
306 *\brief gets the info from 0020,000e : Series Instance UID
307 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
308 * @return Series Instance UID
310 std::string gdcmHeaderHelper::GetSeriesUID(){
311 return GetEntryByNumber(0x0020,0x000e); //0020 000e UI REL Series Instance UID
315 *\ingroup gdcmHeaderHelper
316 *\brief gets the info from 0008,0016 : SOP Class UID
317 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
318 * @return SOP Class UID
320 std::string gdcmHeaderHelper::GetClassUID(){
321 return GetEntryByNumber(0x0008,0x0016); //0008 0016 UI ID SOP Class UID
325 *\ingroup gdcmHeaderHelper
326 *\brief gets the info from 0008,0018 : SOP Instance UID
327 *\todo ? : return the ACR-NEMA element value if DICOM one is not found
328 * @return SOP Instance UID
330 std::string gdcmHeaderHelper::GetInstanceUID(){
331 return GetEntryByNumber(0x0008,0x0018); //0008 0018 UI ID SOP Instance UID
334 // -------------- Remember ! ----------------------------------
336 // Image Position Patient (0020,0032):
337 // If not found (ACR_NEMA) we try Image Position (0020,0030)
338 // If not found (ACR-NEMA), we consider Slice Location (0020,1041)
339 // or Location (0020,0050)
340 // as the Z coordinate,
341 // 0. for all the coordinates if nothing is found
343 // TODO : find a way to inform the caller nothing was found
344 // TODO : How to tell the caller a wrong number of values was found?
346 // ---------------------------------------------------------------
350 * \ingroup gdcmHeaderHelper
351 * \brief gets the info from 0020,0032 : Image Position Patient
352 * else from 0020,0030 : Image Position (RET)
354 * @return up-left image corner X position
357 float gdcmHeaderHelper::GetXOrigin() {
358 float xImPos, yImPos, zImPos;
359 std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
361 if (StrImPos == GDCM_UNFOUND) {
362 dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)");
363 StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
364 if (StrImPos == GDCM_UNFOUND) {
365 dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)");
366 // How to tell the caller nothing was found ?
370 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
376 * \ingroup gdcmHeaderHelper
377 * \brief gets the info from 0020,0032 : Image Position Patient
378 * else from 0020,0030 : Image Position (RET)
380 * @return up-left image corner Y position
382 float gdcmHeaderHelper::GetYOrigin() {
383 float xImPos, yImPos, zImPos;
384 std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
386 if (StrImPos == GDCM_UNFOUND) {
387 dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)");
388 StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
389 if (StrImPos == GDCM_UNFOUND) {
390 dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)");
391 // How to tell the caller nothing was found ?
395 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
401 * \ingroup gdcmHeaderHelper
402 * \brief gets the info from 0020,0032 : Image Position Patient
403 * \ else from 0020,0030 : Image Position (RET)
404 * \ else from 0020,1041 : Slice Location
405 * \ else from 0020,0050 : Location
407 * @return up-left image corner Z position
409 float gdcmHeaderHelper::GetZOrigin() {
410 float xImPos, yImPos, zImPos;
411 std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
412 if (StrImPos != GDCM_UNFOUND) {
413 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
414 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)");
415 return 0.; // bug in the element 0x0020,0x0032
420 StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
421 if (StrImPos != GDCM_UNFOUND) {
422 if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
423 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
424 return 0.; // bug in the element 0x0020,0x0032
429 std::string StrSliceLocation = GetEntryByNumber(0x0020,0x1041);// for *very* old ACR-NEMA images
430 if (StrSliceLocation != GDCM_UNFOUND) {
431 if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) {
432 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)");
433 return 0.; // bug in the element 0x0020,0x1041
438 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)");
439 std::string StrLocation = GetEntryByNumber(0x0020,0x0050);
440 if (StrLocation != GDCM_UNFOUND) {
441 if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) {
442 dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)");
443 return 0.; // bug in the element 0x0020,0x0050
448 dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)");
449 return 0.; // Hopeless
453 * \ingroup gdcmHeaderHelper
454 * \brief gets the info from 0020,0013 : Image Number
456 * @return image number
458 int gdcmHeaderHelper::GetImageNumber() {
459 //The function i atoi() takes the address of an area of memory as parameter and converts
460 //the string stored at that location to an integer using the external decimal to internal
461 //binary conversion rules. This may be preferable to sscanf() since atoi() is a much smaller,
462 // simpler and faster function. sscanf() can do all possible conversions whereas atoi() can
463 //only do single decimal integer conversions.
464 std::string StrImNumber = GetEntryByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number
465 if (StrImNumber != GDCM_UNFOUND) {
466 return atoi( StrImNumber.c_str() );
472 * \ingroup gdcmHeaderHelper
473 * \brief gets the info from 0008,0060 : Modality
474 * @return Modality Type
476 ModalityType gdcmHeaderHelper::GetModality(void) {
477 std::string StrModality = GetEntryByNumber(0x0008,0x0060); //0008 0060 CS ID Modality
478 if (StrModality != GDCM_UNFOUND) {
479 if ( StrModality.find("AU") < StrModality.length()) return AU;
480 else if ( StrModality.find("AS") < StrModality.length()) return AS;
481 else if ( StrModality.find("BI") < StrModality.length()) return BI;
482 else if ( StrModality.find("CF") < StrModality.length()) return CF;
483 else if ( StrModality.find("CP") < StrModality.length()) return CP;
484 else if ( StrModality.find("CR") < StrModality.length()) return CR;
485 else if ( StrModality.find("CT") < StrModality.length()) return CT;
486 else if ( StrModality.find("CS") < StrModality.length()) return CS;
487 else if ( StrModality.find("DD") < StrModality.length()) return DD;
488 else if ( StrModality.find("DF") < StrModality.length()) return DF;
489 else if ( StrModality.find("DG") < StrModality.length()) return DG;
490 else if ( StrModality.find("DM") < StrModality.length()) return DM;
491 else if ( StrModality.find("DS") < StrModality.length()) return DS;
492 else if ( StrModality.find("DX") < StrModality.length()) return DX;
493 else if ( StrModality.find("ECG") < StrModality.length()) return ECG;
494 else if ( StrModality.find("EPS") < StrModality.length()) return EPS;
495 else if ( StrModality.find("FA") < StrModality.length()) return FA;
496 else if ( StrModality.find("FS") < StrModality.length()) return FS;
497 else if ( StrModality.find("HC") < StrModality.length()) return HC;
498 else if ( StrModality.find("HD") < StrModality.length()) return HD;
499 else if ( StrModality.find("LP") < StrModality.length()) return LP;
500 else if ( StrModality.find("LS") < StrModality.length()) return LS;
501 else if ( StrModality.find("MA") < StrModality.length()) return MA;
502 else if ( StrModality.find("MR") < StrModality.length()) return MR;
503 else if ( StrModality.find("NM") < StrModality.length()) return NM;
504 else if ( StrModality.find("OT") < StrModality.length()) return OT;
505 else if ( StrModality.find("PT") < StrModality.length()) return PT;
506 else if ( StrModality.find("RF") < StrModality.length()) return RF;
507 else if ( StrModality.find("RG") < StrModality.length()) return RG;
508 else if ( StrModality.find("RTDOSE") < StrModality.length()) return RTDOSE;
509 else if ( StrModality.find("RTIMAGE") < StrModality.length()) return RTIMAGE;
510 else if ( StrModality.find("RTPLAN") < StrModality.length()) return RTPLAN;
511 else if ( StrModality.find("RTSTRUCT")< StrModality.length()) return RTSTRUCT;
512 else if ( StrModality.find("SM") < StrModality.length()) return SM;
513 else if ( StrModality.find("ST") < StrModality.length()) return ST;
514 else if ( StrModality.find("TG") < StrModality.length()) return TG;
515 else if ( StrModality.find("US") < StrModality.length()) return US;
516 else if ( StrModality.find("VF") < StrModality.length()) return VF;
517 else if ( StrModality.find("XA") < StrModality.length()) return XA;
518 else if ( StrModality.find("XC") < StrModality.length()) return XC;
522 //throw error return value ???
523 // specified <> unknow in our database
531 * \ingroup gdcmHeaderHelper
532 * \brief gets the info from 0020,0037 : Image Orientation Patient
533 * @param iop adress of the (6)float aray to receive values
534 * @return cosines of image orientation patient
536 void gdcmHeaderHelper::GetImageOrientationPatient( float* iop ) {
538 //iop is supposed to be float[6]
539 iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0;
541 std::string StrImOriPat = GetEntryByNumber(0x0020,0x0037); // 0020 0037 DS REL Image Orientation (Patient)
542 if (StrImOriPat != GDCM_UNFOUND) {
543 if( sscanf( StrImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
544 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6) {
545 dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0037)");
546 return ; // bug in the element 0x0020,0x0037
553 StrImOriPat = GetEntryByNumber(0x0020,0x0035); //0020 0035 DS REL Image Orientation (RET)
554 if (StrImOriPat != GDCM_UNFOUND) {
555 if( sscanf( StrImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
556 &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6) {
557 dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0035)");
558 return ; // bug in the element 0x0020,0x0035
565 //-----------------------------------------------------------------------------
568 //-----------------------------------------------------------------------------
571 //-----------------------------------------------------------------------------
575 //-----------------------------------------------------------------------------
576 // gdcmSerieHeaderHelper
577 //-----------------------------------------------------------------------------
578 // Constructor / Destructor
579 gdcmSerieHeaderHelper::~gdcmSerieHeaderHelper(){
581 for (std::list<gdcmHeaderHelper*>::iterator it = CoherentGdcmFileList.begin();
582 it != CoherentGdcmFileList.end(); it++)
586 CoherentGdcmFileList.clear();
589 //-----------------------------------------------------------------------------
592 //-----------------------------------------------------------------------------
595 * \ingroup gdcmHeaderHelper
596 * \brief add a gdcmFile to the list based on file name
597 * @param filename Name of the file to deal with
599 void gdcmSerieHeaderHelper::AddFileName(std::string filename) {
600 gdcmHeaderHelper *GdcmFile = new gdcmHeaderHelper( filename.c_str() );
601 this->CoherentGdcmFileList.push_back( GdcmFile );
605 * \ingroup gdcmHeaderHelper
606 * \brief add a gdcmFile to the list
607 * @param file gdcmHeaderHelper to add
609 void gdcmSerieHeaderHelper::AddGdcmFile(gdcmHeaderHelper *file){
610 this->CoherentGdcmFileList.push_back( file );
614 * \ingroup gdcmHeaderHelper
615 * \brief Sets the Directory
616 * @param dir Name of the directory to deal with
618 void gdcmSerieHeaderHelper::SetDirectory(std::string dir){
619 gdcmDirList filenames_list(dir); //OS specific
621 for(gdcmDirList::iterator it = filenames_list.begin();
622 it !=filenames_list.end(); it++)
624 gdcmHeaderHelper *file = new gdcmHeaderHelper( it->c_str() );
625 this->CoherentGdcmFileList.push_back( file );
630 * \ingroup gdcmHeaderHelper
631 * \brief Sorts the File List
632 * \warning This could be implemented in a 'Strategy Pattern' approach
633 * But as I don't know how to do it, I leave it this way
634 * BTW, this is also a Strategy, I don't know this is the best approach :)
636 void gdcmSerieHeaderHelper::OrderGdcmFileList(){
637 if( ImagePositionPatientOrdering() ) {
640 else if( ImageNumberOrdering() ) {
648 * \ingroup gdcmHeaderHelper
649 * \brief Gets the *coherent* File List
650 * @return the *coherent* File List
652 std::list<gdcmHeaderHelper*> &gdcmSerieHeaderHelper::GetGdcmFileList() {
653 return CoherentGdcmFileList;
656 //-----------------------------------------------------------------------------
659 //-----------------------------------------------------------------------------
662 * \ingroup gdcmHeaderHelper
663 * \brief sorts the images, according to their Patient Position
664 * We may order, considering :
666 * -# Image Position Patient
668 * @return false only if the header is bugged !
670 bool gdcmSerieHeaderHelper::ImagePositionPatientOrdering()
671 //based on Jolinda's algorithm
673 //iop is calculated based on the file file
674 float *cosines = new float[6];
681 std::vector<float> distlist;
683 //!\todo rewrite this for loop.
684 for (std::list<gdcmHeaderHelper*>::iterator it = CoherentGdcmFileList.begin();
685 it != CoherentGdcmFileList.end(); it++)
688 (*it)->GetImageOrientationPatient(cosines);
690 //You only have to do this once for all slices in the volume. Next, for
691 //each slice, calculate the distance along the slice normal using the IPP
692 //tag ("dist" is initialized to zero before reading the first slice) :
693 normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
694 normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
695 normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
697 ipp[0] = (*it)->GetXOrigin();
698 ipp[1] = (*it)->GetYOrigin();
699 ipp[2] = (*it)->GetZOrigin();
702 for (int i = 0; i < 3; ++i)
703 dist += normal[i]*ipp[i];
711 distlist.push_back( dist );
717 ipp[0] = (*it)->GetXOrigin();
718 ipp[1] = (*it)->GetYOrigin();
719 ipp[2] = (*it)->GetZOrigin();
722 for (int i = 0; i < 3; ++i)
723 dist += normal[i]*ipp[i];
731 distlist.push_back( dist );
733 min = (min < dist) ? min : dist;
734 max = (max > dist) ? max : dist;
739 //Then I order the slices according to the value "dist". Finally, once
740 //I've read in all the slices, I calculate the z-spacing as the difference
741 //between the "dist" values for the first two slices.
742 std::vector<gdcmHeaderHelper*> CoherentGdcmFileVector(n);
743 //CoherentGdcmFileVector.reserve( n );
744 CoherentGdcmFileVector.resize( n );
745 //assert( CoherentGdcmFileVector.capacity() >= n );
747 float step = (max - min)/(n - 1);
751 //VC++ don't understand what scope is !! it -> it2
752 for (std::list<gdcmHeaderHelper*>::iterator it2 = CoherentGdcmFileList.begin();
753 it2 != CoherentGdcmFileList.end(); it2++, n++)
756 //Assumption: all files are present (no one missing)
757 pos = (int)( fabs( (distlist[n]-min)/step) + .5 );
759 CoherentGdcmFileVector[pos] = *it2;
762 CoherentGdcmFileList.clear(); //this doesn't delete list's element, node only
764 //VC++ don't understand what scope is !! it -> it3
765 for (std::vector<gdcmHeaderHelper*>::iterator it3 = CoherentGdcmFileVector.begin();
766 it3 != CoherentGdcmFileVector.end(); it3++)
768 CoherentGdcmFileList.push_back( *it3 );
772 CoherentGdcmFileVector.clear();
779 * \ingroup gdcmHeaderHelper
780 * \brief sorts the images, according to their Image Number
781 * @return false only if the header is bugged !
784 bool gdcmSerieHeaderHelper::ImageNumberOrdering() {
786 int n = 0;//CoherentGdcmFileList.size() is a O(N) operation !!
787 unsigned char *partition;
789 std::list<gdcmHeaderHelper*>::iterator it = CoherentGdcmFileList.begin();
790 min = max = (*it)->GetImageNumber();
792 for (; it != CoherentGdcmFileList.end(); it++, n++)
794 pos = (*it)->GetImageNumber();
797 min = (min < pos) ? min : pos;
800 //bzeros(partition, n); //Cette fonction est déconseillée, utilisez plutôt memset.
801 partition = new unsigned char[n];
802 memset(partition, 0, n);
804 std::vector<gdcmHeaderHelper*> CoherentGdcmFileVector(n);
806 //VC++ don't understand what scope is !! it -> it2
807 for (std::list<gdcmHeaderHelper*>::iterator it2 = CoherentGdcmFileList.begin();
808 it2 != CoherentGdcmFileList.end(); it2++)
810 pos = (*it2)->GetImageNumber();
811 CoherentGdcmFileVector[pos - min] = *it2;
812 partition[pos - min]++;
815 unsigned char mult = 1;
816 for(int i=0; i<n ; i++)
818 mult *= partition[i];
821 //VC++ don't understand what scope is !! it -> it3
822 CoherentGdcmFileList.clear(); //this doesn't delete list's element, node only
823 for (std::vector<gdcmHeaderHelper*>::iterator it3 = CoherentGdcmFileVector.begin();
824 it3 != CoherentGdcmFileVector.end(); it3++)
826 CoherentGdcmFileList.push_back( *it3 );
828 CoherentGdcmFileVector.clear();
836 * \ingroup gdcmHeaderHelper
837 * \brief sorts the images, according to their File Name
838 * @return false only if the header is bugged !
840 bool gdcmSerieHeaderHelper::FileNameOrdering() {
842 //sort(CoherentGdcmFileList.begin(), CoherentGdcmFileList.end());
846 //-----------------------------------------------------------------------------