1 /*=========================================================================
4 Module: $RCSfile: vtkGdcm4DSplitter.cxx,v $
6 Date: $Date: 2011/04/04 17:01:03 $
7 Version: $Revision: 1.6 $
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
44 User needs to be aware, *only him* knows want he wants to do.
45 vtkGdcm4DSplitter class does the job for hom
46 (despite its name, it works on 3D or 2D+T images too)
48 User will have to specify some points
54 bool setDirName(std::string &dirName);
55 - a list of directories
56 bool setVectDirName(std::vector<std::string> &vectDirName);
58 bool setVectFileName(std::vector<std::string> &vectFileName);
60 - Recursive directory exploration
61 void setRecursive(bool recursive);
63 . Choose 'split' criterion :
64 ---------------------------
66 - ImagePositionPatient
67 void setSplitOnPosition();
68 - ImageOrientationPatient
69 void setSplitOnOrientation();
71 void setSplitOnTag(unsigned short splitGroup, unsigned short splitElem);
72 void setSplitConvertToFloat(bool conv);
73 - UserDefined Function
74 void setSortOnUserFunction (FoncComp f);
76 . Choose 'sort' criterion :
77 --------------------------
79 - ImagePositionPatient
80 void setSortOnPosition();
81 - ImageOrientationPatient
82 ==> Only in your dreams!
83 ==> or, please, write a IOP sorter ...
85 ==> WARNING : This one has troubles; do NOT use it, right now!
86 ==> use setSortOnUserFunction instead
87 void setSortOnTag(unsigned short sortGroup, unsigned short sortElem);
88 void setSortConvertToFloat(bool conv)
89 - UserDefined Function
90 void setSortOnUserFunction (FoncComp f);
92 void setSortOnFileName()
101 -a single vtkImageData:
102 vtkImageData *GetImageData();
103 - a vector of vtkImageData
104 std::vector<vtkImageData*> *GetImageDataVector();
106 ===================================================================== */
108 #include "gdcmSerieHelper.h"
110 #include "vtkGdcmReader.h"
111 #include "vtkGdcm4DSplitter.h"
113 #include "gdcmSerieHelper.h" // for ImagePositionPatientOrdering()
114 #include <stdlib.h> // for atof
116 vtkGdcm4DSplitter::vtkGdcm4DSplitter() :
117 SplitOnPosition(false), SplitOnOrientation(false), SplitOnTag(false),
118 SplitGroup(0), SplitElem(0),
120 SortOnPosition(false), SortOnOrientation(false), SortOnTag(false),
121 SortGroup(0), SortElem(0), SortConvertToFloat(false),
123 Recursive(false), TypeDir(0),
129 std::vector<vtkImageData*> * vtkGdcm4DSplitter::GetImageDataVector()
131 if (verbose) std::cout << "TypeDir " << TypeDir << std::endl;
133 return ImageDataVector;
137 std::vector<vtkImageData*> *t = new std::vector<vtkImageData*>;
138 t->push_back( ImageData );
142 return (std::vector<vtkImageData*>*) NULL;
145 vtkImageData *vtkGdcm4DSplitter::GetImageData()
152 return (*ImageDataVector)[0];
155 return (vtkImageData*) NULL;
158 bool vtkGdcm4DSplitter::setDirName(std::string &dirName)
160 if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirName) )
162 std::cout << "[" << dirName << "] is NOT a directory" << std::endl;
170 bool vtkGdcm4DSplitter::setVectDirName(std::vector<std::string> &vectDirName)
172 int nbDir = vectDirName.size();
173 for (int iDir=0; iDir<nbDir; iDir++)
175 if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(vectDirName[iDir]) )
177 std::cout << "[" << vectDirName[iDir] << "] is NOT a directory" << std::endl;
182 VectDirName = vectDirName;
187 bool vtkGdcm4DSplitter::setVectFileName(std::vector<std::string> &vectFileName)
189 if ( vectFileName.size() == 0)
191 std::cout << "[ vectFileName ] : empty list" << std::endl;
194 VectFileName = vectFileName;
199 bool vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
201 /* if (verbose) printf ("%04x %04x\n", this->SortGroup,this->SortElem);
202 if (verbose) std :: cout << file1->GetEntryString(SortGroup,SortElem).c_str() << " : "
203 << atof(file1->GetEntryString(SortGroup,SortElem).c_str())
206 // return atof(file1->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem).c_str()) < atof(file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem).c_str());
207 return atof(file1->GetEntryString(SortGroup,SortElem).c_str()) < atof(file2->GetEntryString(SortGroup,SortElem).c_str());
210 bool vtkGdcm4DSplitter::CompareOnSortTag(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
212 return file1->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem) < file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem);
216 bool vtkGdcm4DSplitter::Go()
218 if (!SplitOnPosition && !SplitOnOrientation && !SplitOnTag )
220 ///\TODO (?) Throw an exception "Choose Splitting mode before!"
221 std::cout << "Choose Splitting mode before!" << std::endl;
227 entree nom de directory / Vecteur de noms?
229 recuperer la liste des gdcm::File*
230 passer a SerieHelper (pas de check du Serie UID)
233 trier chaque Coherent file set
234 passer chacun a un vtkGcdmReader
235 retourner le (vecteur de) vtkImageData
238 GDCM_NAME_SPACE::SerieHelper *s;
239 s = GDCM_NAME_SPACE::SerieHelper::New();
241 GDCM_NAME_SPACE::File *f;
242 GDCM_NAME_SPACE::DirListType fileNames;
246 ///\TODO (?) Throw an exception "Set input Directory name(s) / file names before!"
247 std::cout << "Set input Directory name(s) / file names before!" << std::endl;
250 else if (TypeDir == 1)
252 GDCM_NAME_SPACE::DirList dirlist(DirName, Recursive); // NO recursive exploration
253 fileNames = dirlist.GetFilenames(); // all the file names
256 else if (TypeDir == 2)
258 int nbDir = VectDirName.size();
259 GDCM_NAME_SPACE::DirListType tmpFileNames;
260 for (int iDir=0; iDir<nbDir; iDir++)
262 GDCM_NAME_SPACE::DirList dirlist(VectDirName[iDir], Recursive);
263 tmpFileNames = dirlist.GetFilenames();
264 // Concat two std::vector
265 //vector1.insert( vector1.end(), vector2.begin(), vector2.end() );
266 fileNames.insert( fileNames.end(), tmpFileNames.begin(), tmpFileNames.end() );
269 else if (TypeDir == 3)
271 fileNames=VectFileName;
274 GDCM_NAME_SPACE::FileList *l = new GDCM_NAME_SPACE::FileList; // (set of gdcm::File)
275 double floatTagvalue;
276 // Loop on all the gdcm-readable files
277 for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin();
278 it != fileNames.end();
281 int maxSize = 0x7fff; // load Elements of any length
282 f = GDCM_NAME_SPACE::File::New();
283 f->SetMaxSizeLoadEntry(maxSize);
284 f->SetFileName( *it );
288 std::cout << " Fail to load [" << *it << "]" << std::endl;
291 GDCM_NAME_SPACE::XCoherentFileSetmap xcm;
293 if (SplitOnOrientation)
295 s->SetDropDuplicatePositions(false);
296 xcm = s->SplitOnOrientation(l);
298 else if (SplitOnPosition)
300 s->SetDropDuplicatePositions(true);
301 xcm = s->SplitOnPosition(l);
305 s->SetDropDuplicatePositions(false);
307 // Crashes if DataElement not found
308 //std:: cout << GDCM_NAME_SPACE::Global::GetDicts()->GetDefaultPubDict()->GetEntry(groupelem[0],groupelem[1])->GetName() << std::endl;
309 if ( ! SplitConvertToFloat )
310 xcm = s->SplitOnTagValue(l, SplitGroup, SplitElem);
313 xcm = s->SplitOnTagValueConvertToFloat(l, SplitGroup, SplitElem);
319 if(verbose) std::cout << "Empty XCoherent File Set after 'split' ?!?" << std::endl;
322 else if (xcm.size() == 1)
327 ImageDataVector = new std::vector<vtkImageData*>;
328 // vtkGdcmReader *reader = vtkGdcmReader::New(); // move inside the loop, or be clever using vtk!
330 for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
335 std::cout << "--- xCoherentName = [" << (*i).first << "]" << std::endl;
337 // XCoherentFileSetmap map < critère de split, FileList (= std::vector de gdcm::File*) >
339 for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
344 vtkGdcmReader *reader = vtkGdcmReader::New(); /// \FIXME : unable to delete!
347 std::cout << "==========================================xCoherentName = [" << (*i).first << "]" << std::endl;
351 if (verbose) std::cout << "SortOnPosition" << std::endl;
352 // (will be IPPSorter, in GDCM2)
353 s->ImagePositionPatientOrdering((*i).second);
354 if (verbose) std::cout << "out of SortOnPosition" << std::endl;
357 else if (SortOnOrientation)
359 if (verbose) std::cout << "SortOnOrientation" << std::endl;
360 /// \TODO SortOnOrientation()
362 // we still miss an algo to sort an Orientation, given by 6 cosines!
363 // Anything like this, in GDCM2?
364 std::cout << "SortOnOrientation : not so easy - I(mage)O(rientation)P(atient)Sorter still missing! -" << std::endl;
365 // have a look at SerieHelper::SplitOnOrientation() to have an idea of the mess!
367 //Better sort on the file name, right now...
368 s->FileNameOrdering((*i).second);
371 else if (SortOnFileName)
373 if (verbose) std::cout << "SortOnFileName" << std::endl;
374 if (verbose) std::cout << "taille " << ((*i).second)->size() << std::endl;
376 s->FileNameOrdering((*i).second);
377 if (verbose) std::cout << "Out of SortOnFileName" << std::endl;
382 if (verbose) std::cout << "SortOnTag" << std::endl;
383 printf ("--> %04x %04x\n", SortGroup,SortElem);
384 std::cout << "Sorry, troubles not solved yet; use SortOnUserFunction, right now!" << std::endl;
386 /* ==> WARNING : This one has troubles; do NOT use it, right now!
387 // a pointer to fonction cannot be casted as a pointer to member function!
388 // Use SortOnUserFunction, instead!
390 if ( SortConvertToFloat )
391 s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
392 ( &vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat));
394 s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
395 ( &vtkGdcm4DSplitter::CompareOnSortTag));
397 // Anything like this, in GDCM2?
398 s->UserOrdering((*i).second);
401 //if (verbose) std::cout << "Out of SortOnTag" << std::endl;
402 std::cout << "NO ordering performed :-( " << std::endl;
405 else if (SortOnUserFunction)
407 if (verbose) std::cout << "SortOnUserFunction" << std::endl;
408 s->SetUserLessThanFunction( UserCompareFunction );
409 // Anything like this, in GDCM2?
410 s->UserOrdering((*i).second);
411 if (verbose) std::cout << "Out of SortOnUserFunction" << std::endl;
414 reader->SetCoherentFileList((*i).second);
417 /// \TODO : remove the following
418 //if (verbose) reader->GetOutput()->PrintSelf(std::cout, vtkIndent(2));
420 ImageDataVector->push_back(reader->GetOutput() );
422 std::cout << std::endl;
425 //reader->Delete(); // \TODO : fix