--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: vtkGdcm4DSplitter.cxx,v $
+ Language: C++
+ Date: $Date: 2011/03/29 12:49:27 $
+ Version: $Revision: 1.1 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
+/* Raisons ne pas utiliser itkImageSeriesReader:
+
+On Wed, Feb 16, 2011 at 11:51 AM, Roger Bramon Feixas <rogerbramon@gmail.com>
+ Hi,
+ I'm developing with ITK 3.20 + GDCM 2.0.17 + VTK 5.6 and I've noticed
+ itkImageSeriesReader is ~2x slower than vtkGDCMImageReader (from GDCM2).
+ I compared both codes and I think the difference is the extra copy which
+ itkImageSeriesReader makes from ImageFileReader's output to its own output
+ (ImageSeriesReader::GenerateData() line 393).
+*/
+
+#include "gdcmSerieHelper.h"
+
+#include "vtkGdcmReader.h"
+#include "vtkGdcm4DSplitter.h"
+#include <algorithm>
+#include "gdcmSerieHelper.h" // for ImagePositionPatientOrdering()
+#include <stdlib.h> // for atof
+
+ vtkGdcm4DSplitter::vtkGdcm4DSplitter() :
+ SplitOnPosition(false), SplitOnOrientation(false), SplitOnTag(false),
+ SplitGroup(0), SplitElem(0),
+
+ SortOnPosition(false), SortOnOrientation(false), SortOnTag(false),
+ SortGroup(0), SortElem(0), SortConvertToFloat(false),
+
+ Recursive(false), TypeDir(0),
+ verbose(true)
+ {
+
+ }
+
+ std::vector<vtkImageData*> * vtkGdcm4DSplitter::GetImageDataVector()
+ {
+ if (verbose) std::cout << "TypeDir " << TypeDir << std::endl;
+ if (TypeResult == 2)
+ return ImageDataVector;
+ else
+ if (TypeResult == 1)
+ {
+ std::vector<vtkImageData*> *t = new std::vector<vtkImageData*>;
+ t->push_back( ImageData );
+ return t;
+ }
+ else
+ return (std::vector<vtkImageData*>*) NULL;
+ }
+
+ vtkImageData *vtkGdcm4DSplitter::GetImageData()
+ {
+ if (TypeResult == 1)
+ return ImageData;
+ else
+ if (TypeResult == 1)
+ {
+ return (*ImageDataVector)[0];
+ }
+ else
+ return (vtkImageData*) NULL;
+ }
+
+
+ bool vtkGdcm4DSplitter::setDirName(std::string &dirName)
+ {
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(dirName) )
+ {
+ std::cout << "[" << dirName << "] is NOT a directory" << std::endl;
+ return false;
+ }
+ DirName = dirName;
+ TypeDir=1;
+ return true;
+ }
+
+ bool vtkGdcm4DSplitter::setVectDirName(std::vector<std::string> &vectDirName)
+ {
+ int nbDir = vectDirName.size();
+ for (int iDir=0; iDir<nbDir; iDir++)
+ {
+ if ( ! GDCM_NAME_SPACE::DirList::IsDirectory(vectDirName[iDir]) )
+ {
+ std::cout << "[" << vectDirName[iDir] << "] is NOT a directory" << std::endl;
+ return false;
+ }
+ }
+
+ VectDirName = vectDirName;
+ TypeDir=2;
+ return true;
+ }
+
+ bool vtkGdcm4DSplitter::setVectFileName(std::vector<std::string> &vectFileName)
+ {
+ if ( vectFileName.size() == 0)
+ {
+ std::cout << "[ vectFileName ] : empty list" << std::endl;
+ return false;
+ }
+ VectFileName = vectFileName;
+ TypeDir=3;
+ return true;
+ }
+
+ bool vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
+ {
+ if (verbose) printf ("%04x %04x\n", this->SortGroup,this->SortElem);
+ if (verbose) std :: cout << file1->GetEntryString(SortGroup,SortElem).c_str() << " : "
+ << atof(file1->GetEntryString(SortGroup,SortElem).c_str())
+ << std::endl;
+ return atof(file1->GetEntryString(SortGroup,SortElem).c_str()) < atof(file2->GetEntryString(SortGroup,SortElem).c_str());
+ }
+
+ bool vtkGdcm4DSplitter::CompareOnSortTag(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
+ {
+ return file1->GetEntryString(SortGroup,SortElem) < file2->GetEntryString(SortGroup,SortElem);
+ }
+
+ bool vtkGdcm4DSplitter::Go()
+ {
+ if (!SplitOnPosition && !SplitOnOrientation && !SplitOnTag )
+ {
+ ///\TODO (?) Throw an exception "Choose Splitting mode before!"
+ std::cout << "Choose Splitting mode before!" << std::endl;
+ return false;
+ }
+
+ /// How To :
+ /*
+ entree nom de directory / Vecteur de noms?
+ recursif oui/non
+ recuperer la liste des gdcm::File*
+ passer a SerieHelper (pas de check du Serie UID)
+ set critere de split
+
+ trier chaque Coherent file set
+ passer chacun a un vtkGcdmReader
+ retourner le (vecteur de) vtkImageData
+ */
+
+ GDCM_NAME_SPACE::SerieHelper *s;
+ s = GDCM_NAME_SPACE::SerieHelper::New();
+
+ GDCM_NAME_SPACE::File *f;
+ GDCM_NAME_SPACE::DirListType fileNames;
+
+ if (TypeDir == 0 )
+ {
+ ///\TODO (?) Throw an exception "Set input Directory name(s) / file names before!"
+ std::cout << "Set input Directory name(s) / file names before!" << std::endl;
+ return false;
+ }
+ else if (TypeDir == 1)
+ {
+ GDCM_NAME_SPACE::DirList dirlist(DirName, Recursive); // NO recursive exploration
+ fileNames = dirlist.GetFilenames(); // all the file names
+ }
+
+ else if (TypeDir == 2)
+ {
+ int nbDir = VectDirName.size();
+ GDCM_NAME_SPACE::DirListType tmpFileNames;
+ for (int iDir=0; iDir<nbDir; iDir++)
+ {
+ GDCM_NAME_SPACE::DirList dirlist(VectDirName[iDir], Recursive);
+ tmpFileNames = dirlist.GetFilenames();
+ // Concat two std::vector
+ //vector1.insert( vector1.end(), vector2.begin(), vector2.end() );
+ fileNames.insert( fileNames.end(), tmpFileNames.begin(), tmpFileNames.end() );
+ }
+ }
+ else if (TypeDir == 3)
+ {
+ fileNames=VectFileName;
+ }
+
+ GDCM_NAME_SPACE::FileList *l = new GDCM_NAME_SPACE::FileList; // (set of gdcm::File)
+ double floatTagvalue;
+ // Loop on all the gdcm-readable files
+ for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin();
+ it != fileNames.end();
+ ++it)
+ {
+ int maxSize = 0x7fff; // load Elements of any length
+ f = GDCM_NAME_SPACE::File::New();
+ f->SetMaxSizeLoadEntry(maxSize);
+ f->SetFileName( *it );
+ if (f->Load())
+ l->push_back(f);
+ else
+ std::cout << " Fail to load [" << *it << "]" << std::endl;
+ }
+
+ GDCM_NAME_SPACE::XCoherentFileSetmap xcm;
+
+ if (SplitOnOrientation)
+ {
+ s->SetDropDuplicatePositions(false);
+ xcm = s->SplitOnOrientation(l);
+ }
+ else if (SplitOnPosition)
+ {
+ s->SetDropDuplicatePositions(true);
+ xcm = s->SplitOnPosition(l);
+ }
+ else if (SplitOnTag)
+ {
+ s->SetDropDuplicatePositions(false);
+
+ // Crashes if DataElement not found
+ //std:: cout << GDCM_NAME_SPACE::Global::GetDicts()->GetDefaultPubDict()->GetEntry(groupelem[0],groupelem[1])->GetName() << std::endl;
+ if ( ! SplitConvertToFloat )
+ xcm = s->SplitOnTagValue(l, SplitGroup, SplitElem);
+ else
+ {
+ xcm = s->SplitOnTagValueConvertToFloat(l, SplitGroup, SplitElem);
+ }
+ }
+
+ if (xcm.size() == 0)
+ {
+ if(verbose) std::cout << "Empty XCoherent File Set after 'split' ?!?" << std::endl;
+ return false;
+ }
+ else if (xcm.size() == 1)
+ TypeResult=1;
+ else
+ TypeResult=2;
+
+ ImageDataVector = new std::vector<vtkImageData*>;
+ vtkGdcmReader *reader = vtkGdcmReader::New();
+ for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
+ i != xcm.end();
+ ++i)
+ {
+ if (verbose)
+ std::cout << "--- xCoherentName = [" << (*i).first << "]" << std::endl;
+ }
+ // XCoherentFileSetmap map < critère de split, FileList (= std::vector de gdcm::File*) >
+
+ for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
+ i != xcm.end();
+ ++i)
+ {
+ if (verbose)
+ std::cout << "==========================================xCoherentName = [" << (*i).first << "]" << std::endl;
+
+ if (SortOnPosition)
+ {
+ if (verbose) std::cout << "SortOnPosition" << std::endl;
+ // (will be IPPSorter, in GDCM2)
+ s->ImagePositionPatientOrdering((*i).second);
+ if (verbose) std::cout << "out of SortOnPosition" << std::endl
+ }
+
+ if (SortOnOrientation)
+ {
+ if (verbose) std::cout << "SortOnOrientation" << std::endl;
+ /// \TODO SortOnOrientation()
+ // Within a 'just to see' program,
+ // OrderFileList() causes trouble, since some files
+ // (eg:MIP views) don't have 'Position', now considered as mandatory
+ // --> Activated on user demand.
+
+ // Information is in :
+ // 0020,0032 : Image Position Patient
+ // 0020,0030 : Image Position (RET)
+
+ // we still miss an algo to sort an Orientation, given by 6 cosines!
+ // Anything like this, in GDCM2?
+ std::cout << "SortOnOrientation : not so easy - I(mage)O(rientation)P(atient)Sorter still missing! -" << std::endl;
+ // have a look at SerieHelper::SplitOnPosition() to have an idea of the mess!
+
+ //Better sort on the file name, right now...
+ s->FileNameOrdering((*i).second);
+ }
+
+ if (SortOnFileName)
+ {
+ if (verbose) std::cout << "SortOnFileName" << std::endl;
+ if (verbose) std::cout << "taille " << ((*i).second)->size() << std::endl;
+ s->FileNameOrdering((*i).second);
+ if (verbose) std::cout << "Out of SortOnFileName" << std::endl;
+ }
+
+ if (SortOnTag)
+ {
+ if (verbose) std::cout << "SortOnTag" << std::endl;
+ printf ("--> %04x %04x\n", SortGroup,SortElem);
+ if ( SortConvertToFloat )
+ s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
+ ( &vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat));
+ else
+ s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
+ ( &vtkGdcm4DSplitter::CompareOnSortTag));
+
+ // Anything like this, in GDCM2?
+ s->UserOrdering((*i).second);
+ if (verbose) std::cout << "Out of SortOnTag" << std::endl;
+ }
+
+ reader->SetCoherentFileList((*i).second);
+ reader->Update();
+ ImageDataVector->push_back(reader->GetOutput() );
+
+ std::cout << std::endl;
+ }
+
+ reader->Delete();
+ s->Delete();
+ f->Delete();
+ delete l;
+ }
+
--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: vtkGdcm4DSplitter.h,v $
+ Language: C++
+ Date: $Date: 2011/03/29 12:49:27 $
+ Version: $Revision: 1.1 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
+#ifndef _VTKGDCM4DSPLITTER_H_
+#define _VTKGDCM4DSPLITTER_H_
+
+#include <vector>
+#include <vtkImageData.h>
+#include "gdcmDirList.h"
+
+//namespace GDCM_NAME_SPACE
+//{
+ class vtkGdcm4DSplitter {
+ public:
+
+ vtkGdcm4DSplitter();
+ ~vtkGdcm4DSplitter(){};
+ bool setDirName(std::string &dirName);
+ bool setVectDirName(std::vector<std::string> &vectDirName);
+ bool setVectFileName(std::vector<std::string> &vectFileName);
+
+ inline void setSplitOnPosition() {SplitOnPosition=true; SplitOnOrientation=false; SplitOnTag=false;}
+ inline void setSplitOnOrientation(){SplitOnPosition=false; SplitOnOrientation=true; SplitOnTag=false;}
+ inline void setSplitOnTag(unsigned short int splitGroup, unsigned short int splitElem)
+ {SplitOnPosition=false; SplitOnOrientation=false; SplitOnTag=true;
+ SplitGroup=splitGroup; SplitElem=splitElem;}
+ inline void setSplitConvertToFloat(bool conv) {SplitConvertToFloat=conv;}
+
+ inline void setSortOnPosition() {SortOnPosition=true; SortOnOrientation=false; SortOnTag=false; SortOnFileName=false;}
+ // SortOnOrientation : not yet made
+ //inline void setSortOnOrientation(){SortOnPosition=false; SortOnOrientation=true; SortOnTag=false; SortOnFileName=false;}
+ inline void setSortOnTag(unsigned short int sortGroup, unsigned short int sortElem)
+ {SortOnPosition=false; SortOnOrientation=false; SortOnTag=true; SortOnFileName=false;
+ SortGroup=sortGroup; SortElem=sortElem;}
+ inline void setSortConvertToFloat(bool conv) {SortConvertToFloat=conv;}
+
+ inline void setSortOnFileName() {SortOnPosition=false; SortOnOrientation=false; SortOnTag=false; SortOnFileName=true;}
+ inline void setRecursive(bool recursive) { Recursive=recursive;}
+
+ std::vector<vtkImageData*> *GetImageDataVector();
+ vtkImageData *GetImageData();
+
+ bool Go();
+
+ protected:
+ private:
+ bool CompareOnSortTag (GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2);
+ bool CompareOnSortTagConvertToFloat(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2);
+
+ // Data
+ // ----
+ public:
+ protected:
+ private:
+ std::string DirName;
+ std::vector<std::string> VectDirName;
+ std::vector<std::string> VectFileName;
+
+ bool SplitOnPosition;
+ bool SplitOnOrientation;
+ bool SplitOnTag;
+
+ unsigned short int SplitGroup;
+ unsigned short int SplitElem;
+ bool SplitConvertToFloat;
+
+ bool SortOnPosition;
+ bool SortOnOrientation;
+ bool SortOnTag;
+ bool SortOnFileName;
+
+ unsigned short int SortGroup;
+ unsigned short int SortElem;
+ bool SortConvertToFloat;
+
+ bool Recursive;
+ int TypeDir;
+ int TypeResult;
+ bool verbose;
+ std::vector<vtkImageData*> *ImageDataVector;
+ vtkImageData *ImageData;
+ };
+
+//} // end namespace gdcm
+
+//-----------------------------------------------------------------------------
+#endif
projects / gdcm.git / commitdiff