1 /*=========================================================================
4 Module: $RCSfile: vtkGdcm4DSplitter.cxx,v $
6 Date: $Date: 2011/04/21 09:14:31 $
7 Version: $Revision: 1.14 $
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.html 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 /* Raisons ne pas utiliser itkImageSeriesReader:
21 On Wed, Feb 16, 2011 at 11:51 AM, Roger Bramon Feixas <rogerbramon@gmail.com>
23 I'm developing with ITK 3.20 + GDCM 2.0.17 + VTK 5.6 and I've noticed
24 itkImageSeriesReader is ~2x slower than vtkGDCMImageReader (from GDCM2).
25 I compared both codes and I think the difference is the extra copy which
26 itkImageSeriesReader makes from ImageFileReader's output to its own output
27 (ImageSeriesReader::GenerateData() line 393).
31 /* ====================================================================
34 3D, 2D+T, 3D+T, n*2D+T, 4D images are not always stored the same way :
35 a single 'Dicom Serie',
36 several 'Dicom series' within a single directory
37 several 'Dicom series' within several directories
38 A 'Dicom Serie' doesn't mean always the same thing :
39 a given Slice along the time
40 a given Volume at a given time
41 Sometimes, an image within a serie is so artefacted than user decides to replace it
44 User needs to be aware, *only him* knows want he wants to do.
45 vtkGdcm4DSplitter class does the job for him
46 (despite its name, it works on 3D or 2D+T images too)
48 ==> To (try to) understand how the file store is organised, user is deeply encourage to use something like:
50 PrintFile dirin=Root_Directory_holding_the_images rec > 1.txt
52 open it with any test editor, and/or (Linux users)
53 grep a_supposed_to_be_string_of_interest 1.txt
56 Aware user will have to specify some points :
62 bool setDirName(std::string &dirName);
63 - a list of directories
64 bool setVectDirName(std::vector<std::string> &vectDirName);
66 bool setVectFileName(std::vector<std::string> &vectFileName);
67 - a list of gdcm::File*
68 bool setVectGdcmFile(std::vector<GDCM_NAME_SPACE::File *> &vectGdcmFile);
70 - Recursive directory exploration
71 void setRecursive(bool recursive);
73 . Choose 'split' criterion :
74 ---------------------------
76 - ImagePositionPatient
77 void setSplitOnPosition();
78 - ImageOrientationPatient
79 void setSplitOnOrientation();
81 void setSplitOnTag(unsigned short splitGroup, unsigned short splitElem);
82 void setSplitConvertToFloat(bool conv);
83 - UserDefined Function
84 void setSortOnUserFunction (FoncComp f);
86 for 'true' 3D image sets :
87 - if you want to get a single 3D vtkImageData, use SplitOnOrientation -i.e. no split-
88 - if you want to get a vector of 2D vtkImageData, use SplitOnPosition -i.e. one slice in each 'XCoherent fileset'-
90 for 'true' 4D multi-orientation image sets (i.e. a stack of n axial + m sagital + p coronal images, at different instants ...)
91 --> this is 5D, right?
92 (almost) nothing done, yet :
94 . Use a first time vtkGdcm4DSplitter with setSplitOnOrientation();
95 . Get the VectGdcmFileLists (a std::vector of 'XCoherent fileset')
96 . use vtkGdcm4DSplitter, with as many setVectGdcmFile(std::vector<GDCM_NAME_SPACE::File *> &vectGdcmFile) you need
97 one per element of std::vector<GDCM_NAME_SPACE::File *>
98 think on 'spliting' and 'sorting' it, according to your needs.
100 . Choose 'sort' criterion :
101 --------------------------
103 - ImagePositionPatient
104 void setSortOnPosition();
105 - ImageOrientationPatient
106 ==> Only in your dreams!
107 ==> or, please, write a IOP sorter ...
108 - UserDefined Function
109 void setSortOnUserFunction (FoncComp f);
111 void setSortOnFileName()
113 - Choose 'flip' option
114 ----------------------
115 VTK reader 'flop upside down' the images to display them correctly ?!?
116 When a 'math guy' gets the image, the first thing he does is flipping it again.
117 Avoid loosing CPU time using :
118 void SetFlipY(bool); // Wrong = no flip
127 // -a single vtkImageData:
128 // vtkImageData *GetImageData();
129 - a vector of vtkImageData
130 std::vector<vtkImageData*> *GetImageDataVector();
132 ===================================================================== */
134 #include "vtkGdcmReader.h"
135 #include "vtkGdcm4DSplitter.h"
137 #include "gdcmSerieHelper.h" // for ImagePositionPatientOrdering()
138 #include <stdlib.h> // for atof
140 // Constructor / Destructor
142 * \brief Constructor from a given vtkGdcm4DSplitter
144 vtkGdcm4DSplitter::vtkGdcm4DSplitter() :
145 SplitOnPosition(false), SplitOnOrientation(false), SplitOnTag(false),
146 SplitGroup(0), SplitElem(0), SplitConvertToFloat(false), SplitOnly(false),
148 SortOnPosition(false), SortOnOrientation(false), /* SortOnTag(false),*/ SortOnFileName(false), SortOnUserFunction(false),
149 /*SortGroup(0), SortElem(0), SortConvertToFloat(false),*/
151 Recursive(false),FlipY(true), TypeDir(0),
158 * \brief Canonical destructor.
160 vtkGdcm4DSplitter::~vtkGdcm4DSplitter()
162 /// \TODO : delete everything that must be!
165 // Locate Data to process
166 // ======================
168 * \brief sets the directories exploration mode
169 * @param recursive whether we want explore recursively the root Directory
171 void vtkGdcm4DSplitter::setRecursive(bool recursive)
177 * \brief Sets the root Directory to get the images from
178 * @param dirName name of the directory to deal with
180 bool vtkGdcm4DSplitter::setDirName(std::string &dirName)
182 if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirName) )
184 std::cout << "[" << dirName << "] is NOT a directory" << std::endl;
193 * \brief Sets a list of Directories to get the images from
194 * @param vectDirName vector of directory names to deal with
196 bool vtkGdcm4DSplitter::setVectDirName(std::vector<std::string> &vectDirName)
198 int nbDir = vectDirName.size();
199 for (int iDir=0; iDir<nbDir; iDir++)
201 if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(vectDirName[iDir]) )
203 std::cout << "[" << vectDirName[iDir] << "] is NOT a directory" << std::endl;
208 VectDirName = vectDirName;
214 * \brief Sets a list of files names to read
215 * @param vectFileName vector of file names to deal with
217 bool vtkGdcm4DSplitter::setVectFileName(std::vector<std::string> &vectFileName)
219 if ( vectFileName.size() == 0)
221 std::cout << "[ vectFileName ] : empty list" << std::endl;
224 VectFileName = vectFileName;
230 * \brief Sets an already filled std::vector of gdcm::File *
231 * @param vectGdcmFileName std::vector of gdcm::File *
234 bool vtkGdcm4DSplitter::setVectGdcmFile(GDCM_NAME_SPACE::FileList *vectGdcmFile)
236 if ( vectGdcmFile->size() == 0)
238 std::cout << "[ vectGdcmFile ] : empty list" << std::endl;
242 VectGdcmFile = vectGdcmFile;
251 * \brief asks for splitting Filesets according to the Position
253 void vtkGdcm4DSplitter::setSplitOnPosition()
255 SplitOnPosition=true;
256 SplitOnOrientation=false;
261 * \brief asks for splitting Filesets according to the Orientation
263 void vtkGdcm4DSplitter::setSplitOnOrientation()
265 SplitOnPosition=false;
266 SplitOnOrientation=true;
271 * \brief asks for splitting Filesets according to the value of a given Tag
272 * @param group group number of the target Element
273 * @param element element number of the target Element
275 void vtkGdcm4DSplitter::setSplitOnTag(unsigned short int splitGroup, unsigned short int splitElem)
277 SplitOnPosition=false;
278 SplitOnOrientation=false;
280 SplitGroup=splitGroup;
285 * \brief asks for converting to 'float' the tag values used as a splitting criteria (lexicographic order may not be suitable)
287 void vtkGdcm4DSplitter::setSplitConvertToFloat(bool conv) {SplitConvertToFloat=conv;}
290 * \brief asks for splitting Filesets according to what was asked for (no sorting, no reading data)
292 void vtkGdcm4DSplitter::setSplitOnly(bool s)
302 * \brief asks for IPP sorting each XCoherent gdcm::FILE set
304 void vtkGdcm4DSplitter::setSortOnPosition()
307 SortOnOrientation=false;
309 SortOnFileName=false;
310 SortOnUserFunction=false;
314 // use setSortOnUserFunction, instead!
315 // void setSortOnTag(unsigned short int sortGroup, unsigned short int sortElem)
317 // SortOnPosition=false;
318 // SortOnOrientation=false;
320 // SortOnFileName=false;
321 // SortOnUserFunction=false;
322 // SortGroup=sortGroup; SortElem=sortElem;
327 * \brief sets a user supplied function (comparison)
328 * @param f comparison function
330 void vtkGdcm4DSplitter::setSortOnUserFunction (FoncComp f)
332 UserCompareFunction=f;
333 SortOnPosition=false;
334 SortOnOrientation=false;
336 SortOnFileName=false;
337 SortOnUserFunction=true;
340 // void setSortConvertToFloat(bool conv)
342 // SortConvertToFloat=conv;
346 * \brief asks for sorting each XCoherent gdcm::FILE set, according to the File names
348 void vtkGdcm4DSplitter::setSortOnFileName()
350 SortOnPosition=false;
351 SortOnOrientation=false;
354 SortOnUserFunction=false;
358 * \brief returns a std::vector of gdcm::FileList* (gdcm::FileList : actually, a std::vector of gdcm::File*)
360 std::vector<GDCM_NAME_SPACE::FileList *> *vtkGdcm4DSplitter::GetVectGdcmFileLists()
363 return &VectGdcmFileLists;
365 GDCM_NAME_SPACE::XCoherentFileSetmap::iterator it;
366 for ( it = xcm.begin();
370 VectGdcmFileLists.push_back((*it).second);
372 return &VectGdcmFileLists;
376 * \brief returns a std::vector of [2D/3D, depending on what was passed] vtkImageData*
378 std::vector<vtkImageData*> * vtkGdcm4DSplitter::GetImageDataVector()
382 return ImageDataVector;
386 * \brief when user _knows_ only _one_ vtkImageData* is returned he may be interested in not getting a vector...
388 vtkImageData *vtkGdcm4DSplitter::GetImageData()
392 return (*ImageDataVector)[0];
396 // bool vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
398 // return atof(file1->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem).c_str()) < atof(file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem).c_str());
399 // return atof(file1->GetEntryString(SortGroup,SortElem).c_str()) < atof(file2->GetEntryString(SortGroup,SortElem).c_str());
402 // bool vtkGdcm4DSplitter::CompareOnSortTag(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
404 // return file1->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem) < file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem);
408 bool vtkGdcm4DSplitter::Go()
412 entree nom de directory / Vecteur de noms?
414 recuperer la liste des gdcm::File*
415 passer a SerieHelper (pas de check du Serie UID)
418 trier chaque Coherent file set
419 passer chacun a un vtkGcdmReader
420 retourner le (vecteur de) vtkImageData
423 if (!SplitOnPosition && !SplitOnOrientation && !SplitOnTag)
425 ///\TODO (?) Throw an exception "Choose Splitting mode before!"
426 std::cout << "Choose Splitting mode before!" << std::endl;
430 GDCM_NAME_SPACE::FileList *l;
432 GDCM_NAME_SPACE::SerieHelper *s;
433 s = GDCM_NAME_SPACE::SerieHelper::New();
436 // Load the gdcm::File* set, according to user's requierements
437 // ------------------------------------------------------------
439 l = getGdcmFileList();
440 std::cout << l->size() << " gdcm::File read" << std::endl;
442 // Split the gdcm::File* set, according to user's requierements
443 // ------------------------------------------------------------
445 if (SplitOnOrientation)
447 s->SetDropDuplicatePositions(false);
448 xcm = s->SplitOnOrientation(l);
450 else if (SplitOnPosition)
452 s->SetDropDuplicatePositions(true);
453 xcm = s->SplitOnPosition(l);
455 // the key of xcm follows lexicographical order
456 // (that may be different than the 'distance' order)
457 // we have to reorganize it!
459 reorgXCoherentFileSetmap(xcm);
463 s->SetDropDuplicatePositions(false);
465 // Crashes if DataElement not found
466 //std:: cout << GDCM_NAME_SPACE::Global::GetDicts()->GetDefaultPubDict()->GetEntry(groupelem[0],groupelem[1])->GetName() << std::endl;
467 if ( ! SplitConvertToFloat )
468 xcm = s->SplitOnTagValue(l, SplitGroup, SplitElem);
471 xcm = s->SplitOnTagValueConvertToFloat(l, SplitGroup, SplitElem);
478 std::cout << "Empty XCoherent File Set after 'split' ?!?" << std::endl;
483 std::cout << xcm.size() << " XCoherent entries found" << std::endl;
486 // put here, to avoid segfault when unaware user sets SplitOnly to true, and the asks for ImageDataVector
487 ImageDataVector = new std::vector<vtkImageData*>;
489 std::cout <<"SplitOnly " << SplitOnly << std::endl;
494 // ------------------------------------------------------------
496 // ImageDataVector = new std::vector<vtkImageData*>;
498 /// \TODO move inside the loop, or be clever using vtk!
499 // vtkGdcmReader *reader = vtkGdcmReader::New(); // move inside the loop, or be clever using vtk!
501 // XCoherentFileSetmap map < critère de split, FileList (= std::vector de gdcm::File*) >
503 for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
507 vtkGdcmReader *reader = vtkGdcmReader::New(); /// \TODO FIXME : unable to delete!
509 reader->SetFlipY(FlipY);
510 // better user SetFileLowerLeft()
511 /// \TODO : modify vtkGdcmReader !
513 std::cout << " --- xCoherentName = [" << (*i).first << "]" << std::endl;
517 if (verbose) std::cout << "SortOnPosition" << std::endl;
518 // (will be IPPSorter, in GDCM2)
519 s->ImagePositionPatientOrdering((*i).second);
520 if (verbose) std::cout << "out of SortOnPosition" << std::endl;
523 else if (SortOnOrientation)
525 if (verbose) std::cout << "SortOnOrientation" << std::endl;
526 /// \TODO (?) SortOnOrientation()
528 // we still miss an algo to sort an Orientation, given by 6 cosines!
529 // Anything like this, in GDCM2?
530 std::cout << "SortOnOrientation : not so easy - I(mage)O(rientation)P(atient)Sorter still missing! -" << std::endl;
531 // have a look at SerieHelper::SplitOnOrientation() to have an idea of the mess!
533 //Better sort on the file name, right now...
534 s->FileNameOrdering((*i).second);
537 else if (SortOnFileName)
539 if (verbose) std::cout << "SortOnFileName" << std::endl;
540 if (verbose) std::cout << "taille " << ((*i).second)->size() << std::endl;
542 s->FileNameOrdering((*i).second);
543 if (verbose) std::cout << "Out of SortOnFileName" << std::endl;
546 // else if (SortOnTag)
548 // if (verbose) std::cout << "SortOnTag" << std::endl;
549 // printf ("--> %04x %04x\n", SortGroup,SortElem);
550 // std::cout << "Sorry, troubles not solved yet; use SortOnUserFunction, right now!" << std::endl;
552 /* ==> WARNING : This one has troubles; do NOT use it, right now!
553 // a pointer to fonction cannot be casted as a pointer to member function!
554 // Use SortOnUserFunction, instead!
556 // if ( SortConvertToFloat )
557 // s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
558 // ( &vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat));
560 // s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
561 ( &vtkGdcm4DSplitter::CompareOnSortTag));
563 // Anything like this, in GDCM2?
564 // s->UserOrdering((*i).second);
567 // //if (verbose) std::cout << "Out of SortOnTag" << std::endl;
568 // std::cout << "NO ordering performed :-( " << std::endl;
571 else if (SortOnUserFunction)
573 if (verbose) std::cout << "SortOnUserFunction" << std::endl;
574 s->SetUserLessThanFunction( UserCompareFunction );
575 // Anything like this, in GDCM2?
576 s->UserOrdering((*i).second);
577 if (verbose) std::cout << "Out of SortOnUserFunction" << std::endl;
580 reader->SetCoherentFileList((*i).second);
583 /// \TODO : remove the following
585 // std::cout << "reader->GetOutput() :" << std::endl;
586 // reader->GetOutput()->PrintSelf(std::cout, vtkIndent(2));
589 ImageDataVector->push_back(reader->GetOutput() );
591 std::vector<vtkImageData*>::iterator it;
592 //if (verbose) // JPR
594 for(it=ImageDataVector->begin(); it!=ImageDataVector->end(); ++it) {
595 // std::cout << "-in vtkGdcm4DSplitter --------------------------" << std::endl;
596 // (*it)->PrintSelf(std::cout, vtkIndent(2));
598 //std::cout << std::endl;
601 //reader->Delete(); // \TODO : fix
611 * \brief Load the gdcm::File* set, according to user's requierements
612 * returns a std::vector of gdcm::File* (gdcm::FileList : actually, a std::vector of gdcm::File*)
616 GDCM_NAME_SPACE::FileList *vtkGdcm4DSplitter::getGdcmFileList()
619 GDCM_NAME_SPACE::File *f;
620 GDCM_NAME_SPACE::DirListType fileNames;
623 // Fill fileNames with the user supplied file names (in any)
624 // ------------------------------------------------
626 if (TypeDir == 0 ) // Nothing was set as input...
628 ///\TODO (?) Throw an exception "Set input Directory name(s) / file names before!"
629 std::cout << "Set input Directory name(s) / file names before!" << std::endl;
632 else if (TypeDir == 1) // A root directory name was set as input
634 GDCM_NAME_SPACE::DirList dirlist(DirName, Recursive); // NO recursive exploration
635 fileNames = dirlist.GetFilenames(); // all the file names
638 else if (TypeDir == 2) // a std::vector of directory names was set as input
640 int nbDir = VectDirName.size();
641 GDCM_NAME_SPACE::DirListType tmpFileNames;
642 for (int iDir=0; iDir<nbDir; iDir++)
644 GDCM_NAME_SPACE::DirList dirlist(VectDirName[iDir], Recursive);
645 tmpFileNames = dirlist.GetFilenames();
646 // Concat two std::vector
647 //vector1.insert( vector1.end(), vector2.begin(), vector2.end() );
648 fileNames.insert( fileNames.end(), tmpFileNames.begin(), tmpFileNames.end() );
651 else if (TypeDir == 3) // a list of files names was set as input
653 fileNames=VectFileName;
657 // Fill l with the gdcm::File* corresponding to the files
658 // --------------------------------------
661 GDCM_NAME_SPACE::FileList *l = new GDCM_NAME_SPACE::FileList; // (set of gdcm::File*)
663 if (TypeDir == 4) // an already existing std::vector of gdcm::File* was set as input
669 double floatTagvalue;
670 // Loop on all the gdcm-readable files
671 for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin();
672 it != fileNames.end();
675 int maxSize = 0x7fff; // load Elements of any length
676 f = GDCM_NAME_SPACE::File::New();
677 f->SetMaxSizeLoadEntry(maxSize);
678 f->SetFileName( *it );
682 std::cout << " Fail to load [" << *it << "]" << std::endl;
690 void vtkGdcm4DSplitter::reorgXCoherentFileSetmap(GDCM_NAME_SPACE::XCoherentFileSetmap &xcm)
693 the key of the 'XCoherentFileSetmap', is a std::string, used as if it was found in the Dicom header
694 Normaly(?), it's suitable for almost everything ...
695 ... but the 'Image Position Patient'.
696 We need to order the 'XCoherentFileSetmap' (NOT the content of each XCoherentFileSet!) according to the IPP,
697 using Jolinda Smith's algorithm.
698 (we use a subset of the one defined in gdcm::SerieHelper)
703 std::vector<ELEM> vectElem;
705 /* just to remember :
710 GDCM_NAME_SPACE::File *file;
716 for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
721 std::cout << "--- xCoherentName = [" << (*i).first << "]" << std::endl;
723 e.strIPP = (*i).first;
724 e.file = *(((*i).second)->begin()); // all the gdcm::File of a given xcm item *have* the same IPP; first one is enough
726 vectElem.push_back(e);
728 sortVectElem(&vectElem);
730 // now, create the final std::map !
731 // final_xcm<to_str(e.dist , xcm[e.strIPP]>
733 // check what we need to free !
737 std::string str_dist;
738 int lgr=vectElem.size();
739 GDCM_NAME_SPACE::XCoherentFileSetmap final_xcm;
740 for (int i2=0; i2<lgr; i2++)
742 dist = (vectElem[i2].dist*1000);
743 sprintf(c_dist,"%010d",dist);
746 std::cout << "dist " << vectElem[i2].dist
747 << " str_dist " << str_dist
748 << " IPP " << vectElem[i2].strIPP
752 final_xcm[str_dist] = xcm[vectElem[i2].strIPP];
755 /// \TODO : check what needs to be cleared // JPR
762 bool vtkGdcm4DSplitter::sortVectElem(std::vector<ELEM> *fileList)
764 //based on Jolinda Smith's algorithm
766 // NOTE : if you need to use Jolinda Smith's algorithm, get the one inside gdcm::SerieHelper
767 // this one is a light version.
769 //Tags always use the same coordinate system, where "x" is left
770 //to right, "y" is posterior to anterior, and "z" is foot to head (RAH).
772 //iop is calculated based on the file file
777 double min = 0, max = 0;
780 //double ZSpacing; // useless here! // JPR
781 bool DirectOrder = true; // remove it!
783 // ZSpacing = -1.0; // will be updated if process doesn't fail
785 //std::multimap<double,File *> distmultimap; // JPR
786 std::multimap<double,ELEM> distmultimap; // JPR
788 // Use a multimap to sort the distances from 0,0,0
789 //for ( FileList::const_iterator // JPR
790 for ( std::vector<ELEM>::iterator // JPR
791 it = fileList->begin();
792 it != fileList->end(); ++it )
794 //gdcmDebugMacro("deal with " << (*it)->file->GetFileName() );
797 (*it).file->GetImageOrientationPatient( cosines );
799 // The "Image Orientation Patient" tag gives the direction cosines
800 // for the rows and columns for the three axes defined above.
801 // Typical axial slices will have a value 1/0/0/0/1/0:
802 // rows increase from left to right,
803 // columns increase from posterior to anterior. This is your everyday
804 // "looking up from the bottom of the head with the eyeballs up" image.
806 // The "Image Position Patient" tag gives the coordinates of the first
807 // voxel in the image in the "RAH" coordinate system, relative to some
810 // First, calculate the slice normal from IOP :
812 // You only have to do this once for all slices in the volume. Next,
813 // for each slice, calculate the distance along the slice normal
814 // using the IPP ("Image Position Patient") tag.
815 // ("dist" is initialized to zero before reading the first slice) :
817 normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
818 normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
819 normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
821 // For each slice (here : the first), calculate the distance along
822 // the slice normal using the IPP tag
824 ipp[0] = (*it).file->GetXOrigin();
825 ipp[1] = (*it).file->GetYOrigin();
826 ipp[2] = (*it).file->GetZOrigin();
829 for ( int i = 0; i < 3; ++i )
831 dist += normal[i]*ipp[i];
834 //gdcmDebugMacro("dist : " << dist);
835 distmultimap.insert(std::pair<const double,ELEM>(dist, *it));
842 // Next, for each slice, calculate the distance along the slice normal
844 ipp[0] = (*it).file->GetXOrigin();
845 ipp[1] = (*it).file->GetYOrigin();
846 ipp[2] = (*it).file->GetZOrigin();
849 for ( int i = 0; i < 3; ++i )
851 dist += normal[i]*ipp[i];
854 (*it).dist = dist; // JPR
856 distmultimap.insert(std::pair<const double,ELEM>(dist, *it));
857 //gdcmDebugMacro("dist : " << dist);
858 min = (min < dist) ? min : dist;
859 max = (max > dist) ? max : dist;
863 // gdcmDebugMacro("After parsing vector, nb of elements : " << fileList->size() );
865 /*Useless here. // JPR
867 // Find out if min/max are coherent
870 gdcmWarningMacro("Looks like all images have the exact same image position. "
871 << "No PositionPatientOrdering sort performed. "
872 << "No 'ZSpacing' calculated! ");
877 /* Useless here, 'split' already done. // JPR
879 // Check to see if image shares a common position
881 for (std::multimap<double, File *>::iterator it2 = distmultimap.begin();
882 it2 != distmultimap.end();
886 gdcmDebugMacro("Check if image shares a common position : " << ((*it2).second).file->GetFileName() );
888 if (distmultimap.count((*it2).first) != 1)
890 gdcmWarningMacro("File: ["
891 << ((*it2).second->GetFileName())
892 << "] : more than ONE file at distance: '"
894 << " (position is not unique!) "
895 << "No PositionPatientOrdering sort performed. "
896 << "No 'ZSpacing' calculated! ");
903 if (! DropDuplicatePositions)
909 // Now, we can calculate Z Spacing as the difference
910 // between the "dist" values for the first two slices.
912 // The following (un)-commented out code is let here
913 // to be re-used by whomsoever is interested...
915 //std::multimap<double, ELEM>::iterator it5 = distmultimap.begin();
916 //double d1 = (*it5).first;
918 //double d2 = (*it5).first;
920 //if (ZSpacing < 0.0)
921 // ZSpacing = - ZSpacing;
923 fileList->clear(); // doesn't delete list elements, only nodes
925 // Acording to user requierement, we sort direct order or reverse order.
928 for (std::multimap<double, ELEM>::iterator it3 = distmultimap.begin();
929 it3 != distmultimap.end();
932 fileList->push_back( (*it3).second );
934 /* useless here! // JPR
936 if (DropDuplicatePositions)
938 // ImagePositionPatientOrdering wrong duplicates are found ???
939 // --> fixed. See comment
941 it3 = distmultimap.upper_bound((*it3).first); // skip all duplicates
942 // the upper_bound function increments the iterator to the next non-duplicate entry
943 // The for loop iteration also increments the iterator, which causes the code to skip every other image
944 // --> decrement the iterator after the upper_bound function call
946 if (it3 == distmultimap.end() ) // if last image, stop iterate
952 else // user asked for reverse order
954 std::multimap<double, ELEM>::const_iterator it4;
955 it4 = distmultimap.end();
959 fileList->push_back( (*it4).second );
961 /* useless here // JPR
963 if (DropDuplicatePositions) // skip all duplicates
965 // lower_bound finds the next element that is
966 // less than or *equal to* the current value!
967 //it4 = distmultimap.lower_bound((*it4).first);
970 std::multimap<double, ELEM>::const_iterator itPrev = it4;
971 while (itPrev->first == it4->first)
975 if (it4 == distmultimap.begin() ) // if first image, stop iterate
979 } while (it4 != distmultimap.begin() );
982 distmultimap.clear();