/*========================================================================= Program: gdcm Module: $RCSfile: vtkGdcm4DSplitter.cxx,v $ Language: C++ Date: $Date: 2011/04/11 11:28:31 $ Version: $Revision: 1.9 $ 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 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). */ /* ==================================================================== vtkGdcm4DSplitter 3D, 2D+T, 3D+T, n*2D+T, 4D images are not always stored the same way : a single 'Dicom Serie', several 'Dicom series' within a single directory several 'Dicom series' within several directories A 'Dicom Serie' doesn't mean always the same thing : a given Slice along the time a given Volume at a given time Sometimes, an image within a serie is so artefacted than user decides to replace it by an other image. User needs to be aware, *only him* knows want he wants to do. vtkGdcm4DSplitter class does the job for hom (despite its name, it works on 3D or 2D+T images too) User will have to specify some points . Choose input data ------------------- - a single directory bool setDirName(std::string &dirName); - a list of directories bool setVectDirName(std::vector &vectDirName); - a list of files bool setVectFileName(std::vector &vectFileName); - Recursive directory exploration void setRecursive(bool recursive); . Choose 'split' criterion : --------------------------- - ImagePositionPatient void setSplitOnPosition(); - ImageOrientationPatient void setSplitOnOrientation(); - User choosen tag void setSplitOnTag(unsigned short splitGroup, unsigned short splitElem); void setSplitConvertToFloat(bool conv); - UserDefined Function void setSortOnUserFunction (FoncComp f); for 'true' 3D image sets : - if you want to get a single 3D vtkImageData, use SplitOnOrientation -i.e. no split- - if you want to get a vector of 2D vtkImageData, use SplitOnPosition -i.e. one slice in each 'XCoherent filesite'- for 'true' 4D multi-orientation image sets (i.e. a stack of axial + sagital + coronal images, at different instants ...) --> this is 5D, right? Nothing done, yet. . Choose 'sort' criterion : -------------------------- - ImagePositionPatient void setSortOnPosition(); - ImageOrientationPatient ==> Only in your dreams! ==> or, please, write a IOP sorter ... - UserDefined Function void setSortOnUserFunction (FoncComp f); - File name void setSortOnFileName() . Execute : ----------- bool Go(); . Get the result ---------------- // -a single vtkImageData: // vtkImageData *GetImageData(); - a vector of vtkImageData std::vector *GetImageDataVector(); ===================================================================== */ #include "gdcmSerieHelper.h" #include "vtkGdcmReader.h" #include "vtkGdcm4DSplitter.h" #include #include "gdcmSerieHelper.h" // for ImagePositionPatientOrdering() #include // 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(false) { } std::vector * vtkGdcm4DSplitter::GetImageDataVector() { /* if (verbose) std::cout << "GetImageDataVector : TypeResult " << TypeResult << std::endl; if (TypeResult == 2) return ImageDataVector; else if (TypeResult == 1) { std::vector *t = new std::vector; t->push_back( ImageData ); return t; } else return (std::vector*) NULL; */ return ImageDataVector; } vtkImageData *vtkGdcm4DSplitter::GetImageData() { /* if (verbose) std::cout << "GetImageData : TypeResult " << TypeResult << std::endl; if (TypeResult == 1) return ImageData; else if (TypeResult == 2) { return (*ImageDataVector)[0]; } else return (vtkImageData*) NULL; */ return (*ImageDataVector)[0]; } 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 &vectDirName) { int nbDir = vectDirName.size(); for (int iDir=0; iDir &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(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem).c_str()) < atof(file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem).c_str()); 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(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem) < file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::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; iDirSetMaxSizeLoadEntry(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); // reorg the std::map xcm according to position // JPR // the key of xcm follows lexicographical order // (that may be different than the 'distance' order) // we have to reorganize it! reorgXCoherentFileSetmap(xcm); } 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; // vtkGdcmReader *reader = vtkGdcmReader::New(); // move inside the loop, or be clever using vtk! 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) { vtkGdcmReader *reader = vtkGdcmReader::New(); /// \FIXME : unable to delete! 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; } else if (SortOnOrientation) { if (verbose) std::cout << "SortOnOrientation" << std::endl; /// \TODO SortOnOrientation() // 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::SplitOnOrientation() to have an idea of the mess! //Better sort on the file name, right now... s->FileNameOrdering((*i).second); } else 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; } else if (SortOnTag) { if (verbose) std::cout << "SortOnTag" << std::endl; printf ("--> %04x %04x\n", SortGroup,SortElem); std::cout << "Sorry, troubles not solved yet; use SortOnUserFunction, right now!" << std::endl; /* ==> WARNING : This one has troubles; do NOT use it, right now! // a pointer to fonction cannot be casted as a pointer to member function! // Use SortOnUserFunction, instead! if ( SortConvertToFloat ) s->SetUserLessThanFunction( reinterpret_cast ( &vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat)); else s->SetUserLessThanFunction( reinterpret_cast ( &vtkGdcm4DSplitter::CompareOnSortTag)); // Anything like this, in GDCM2? s->UserOrdering((*i).second); */ //if (verbose) std::cout << "Out of SortOnTag" << std::endl; std::cout << "NO ordering performed :-( " << std::endl; } else if (SortOnUserFunction) { if (verbose) std::cout << "SortOnUserFunction" << std::endl; s->SetUserLessThanFunction( UserCompareFunction ); // Anything like this, in GDCM2? s->UserOrdering((*i).second); if (verbose) std::cout << "Out of SortOnUserFunction" << std::endl; } reader->SetCoherentFileList((*i).second); reader->Update(); /// \TODO : remove the following if (verbose) { std::cout << "reader->GetOutput() :" << std::endl; reader->GetOutput()->PrintSelf(std::cout, vtkIndent(2)); } ImageDataVector->push_back(reader->GetOutput() ); std::vector::iterator it; if (verbose) for(it=ImageDataVector->begin(); it!=ImageDataVector->end(); ++it) { std::cout << "-in vtkGdcm4DSplitter--------------------------" << std::endl; (*it)->PrintSelf(std::cout, vtkIndent(2)); } std::cout << std::endl; } //reader->Delete(); // \TODO : fix s->Delete(); f->Delete(); delete l; return true; } void vtkGdcm4DSplitter::reorgXCoherentFileSetmap(GDCM_NAME_SPACE::XCoherentFileSetmap &xcm) { ELEM e; std::vector vectElem; /* typedef struct { std::string strIPP; double dist; GDCM_NAME_SPACE::File *file; } ELEM; */ bool Debug=true; for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin(); i != xcm.end(); ++i) { if (verbose) std::cout << "--- xCoherentName = [" << (*i).first << "]" << std::endl; e.strIPP = (*i).first; e.file = *(((*i).second)->begin()); // all the gdcm::File of a given xcm item *have* the same IPP; first one is enough e.dist=0.0; vectElem.push_back(e); } sortVectElem(&vectElem); // now, create the final std::map ! // final_xcm // xcm = final_xcm; // check what we need to free ! int dist; char c_dist[100]; std::string str_dist; int lgr=vectElem.size(); GDCM_NAME_SPACE::XCoherentFileSetmap final_xcm; for (int i2=0; i2 *fileList) { //based on Jolinda Smith's algorithm //Tags always use the same coordinate system, where "x" is left //to right, "y" is posterior to anterior, and "z" is foot to head (RAH). //iop is calculated based on the file file float cosines[6]; double normal[3]; double ipp[3]; double dist; double min = 0, max = 0; bool first = true; double ZSpacing; // useless here! // JPR bool DirectOrder = true; // remove it! ZSpacing = -1.0; // will be updated if process doesn't fail //std::multimap distmultimap; // JPR std::multimap distmultimap; // JPR // Use a multimap to sort the distances from 0,0,0 //for ( FileList::const_iterator // JPR for ( std::vector::iterator // JPR it = fileList->begin(); it != fileList->end(); ++it ) { //gdcmDebugMacro("deal with " << (*it)->file->GetFileName() ); if ( first ) { (*it).file->GetImageOrientationPatient( cosines ); // The "Image Orientation Patient" tag gives the direction cosines // for the rows and columns for the three axes defined above. // Typical axial slices will have a value 1/0/0/0/1/0: // rows increase from left to right, // columns increase from posterior to anterior. This is your everyday // "looking up from the bottom of the head with the eyeballs up" image. // The "Image Position Patient" tag gives the coordinates of the first // voxel in the image in the "RAH" coordinate system, relative to some // origin. // First, calculate the slice normal from IOP : // You only have to do this once for all slices in the volume. Next, // for each slice, calculate the distance along the slice normal // using the IPP ("Image Position Patient") tag. // ("dist" is initialized to zero before reading the first slice) : normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4]; normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5]; normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3]; // For each slice (here : the first), calculate the distance along // the slice normal using the IPP tag ipp[0] = (*it).file->GetXOrigin(); ipp[1] = (*it).file->GetYOrigin(); ipp[2] = (*it).file->GetZOrigin(); dist = 0; for ( int i = 0; i < 3; ++i ) { dist += normal[i]*ipp[i]; } //gdcmDebugMacro("dist : " << dist); distmultimap.insert(std::pair(dist, *it)); max = min = dist; first = false; } else { // Next, for each slice, calculate the distance along the slice normal // using the IPP tag ipp[0] = (*it).file->GetXOrigin(); ipp[1] = (*it).file->GetYOrigin(); ipp[2] = (*it).file->GetZOrigin(); dist = 0; for ( int i = 0; i < 3; ++i ) { dist += normal[i]*ipp[i]; } (*it).dist = dist; // JPR distmultimap.insert(std::pair(dist, *it)); //gdcmDebugMacro("dist : " << dist); min = (min < dist) ? min : dist; max = (max > dist) ? max : dist; } } // gdcmDebugMacro("After parsing vector, nb of elements : " << fileList->size() ); /*Useless here. // JPR // Find out if min/max are coherent if ( min == max ) { gdcmWarningMacro("Looks like all images have the exact same image position. " << "No PositionPatientOrdering sort performed. " << "No 'ZSpacing' calculated! "); return false; } */ /* Useless here, 'split' already done. // JPR // Check to see if image shares a common position bool ok = true; for (std::multimap::iterator it2 = distmultimap.begin(); it2 != distmultimap.end(); ++it2) { gdcmDebugMacro("Check if image shares a common position : " << ((*it2).second).file->GetFileName() ); if (distmultimap.count((*it2).first) != 1) { gdcmWarningMacro("File: [" << ((*it2).second->GetFileName()) << "] : more than ONE file at distance: '" << (*it2).first << " (position is not unique!) " << "No PositionPatientOrdering sort performed. " << "No 'ZSpacing' calculated! "); ok = false; } } if (!ok) { if (! DropDuplicatePositions) return false; } */ // Now, we can calculate Z Spacing as the difference // between the "dist" values for the first two slices. // The following (un)-commented out code is let here // to be re-used by whomsoever is interested... std::multimap::iterator it5 = distmultimap.begin(); double d1 = (*it5).first; it5++; double d2 = (*it5).first; ZSpacing = d1-d2; if (ZSpacing < 0.0) ZSpacing = - ZSpacing; fileList->clear(); // doesn't delete list elements, only nodes // Acording to user requierement, we sort direct order or reverse order. if (DirectOrder) { for (std::multimap::iterator it3 = distmultimap.begin(); it3 != distmultimap.end(); ++it3) { fileList->push_back( (*it3).second ); /* useless here! // JPR if (DropDuplicatePositions) { // ImagePositionPatientOrdering wrong duplicates are found ??? // --> fixed. See comment it3 = distmultimap.upper_bound((*it3).first); // skip all duplicates // the upper_bound function increments the iterator to the next non-duplicate entry // The for loop iteration also increments the iterator, which causes the code to skip every other image // --> decrement the iterator after the upper_bound function call it3--; if (it3 == distmultimap.end() ) // if last image, stop iterate break; } */ } } else // user asked for reverse order { std::multimap::const_iterator it4; it4 = distmultimap.end(); do { it4--; fileList->push_back( (*it4).second ); /* useless here // JPR if (DropDuplicatePositions) // skip all duplicates { // lower_bound finds the next element that is // less than or *equal to* the current value! //it4 = distmultimap.lower_bound((*it4).first); // David Feng's fix std::multimap::const_iterator itPrev = it4; while (itPrev->first == it4->first) --itPrev; it4 = itPrev; if (it4 == distmultimap.begin() ) // if first image, stop iterate break; } */ } while (it4 != distmultimap.begin() ); } distmultimap.clear(); return true; }