/*========================================================================= Program: gdcm Module: $RCSfile: gdcmSerieHelper.cxx,v $ Language: C++ Date: $Date: 2005/10/23 15:04:26 $ Version: $Revision: 1.28 $ 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. =========================================================================*/ #include "gdcmSerieHelper.h" #include "gdcmDirList.h" #include "gdcmFile.h" #include "gdcmDictEntry.h" // for TranslateToKey #include "gdcmDebug.h" #include "gdcmUtil.h" #include #include #include #include #include //for sscanf namespace gdcm { //----------------------------------------------------------------------------- //----------------------------------------------------------------------------- // Constructor / Destructor /** * \brief Constructor from a given SerieHelper */ SerieHelper::SerieHelper() { ClearAll(); UserLessThanFunction = 0; DirectOrder = true; } /** * \brief Canonical destructor. */ SerieHelper::~SerieHelper() { ClearAll(); } /** * \brief Preventively, clear everything at constructor time. * ( use it at destructor time.) */ void SerieHelper::ClearAll() { // For all the 'Single SerieUID' Filesets that may already exist FileList *l = GetFirstSingleSerieUIDFileSet(); while (l) { // For all the gdcm::File of a File set for (gdcm::FileList::iterator it = l->begin(); it != l->end(); ++it) { delete *it; // remove each entry } l->clear(); delete l; // remove the container l = GetNextSingleSerieUIDFileSet(); } } //----------------------------------------------------------------------------- //----------------------------------------------------------------------------- // Public /** * \brief add a gdcm::File to the Fileset corresponding to its Serie UID * @param filename Name of the file to deal with */ void SerieHelper::AddFileName(std::string const &filename) { // Create a DICOM file File *header = new File (); header->SetLoadMode(LoadMode); header->SetFileName( filename ); header->Load(); if ( header->IsReadable() ) { int allrules = 1; // First step : the user defined a set of rules for the DICOM file // he is looking for. // Make sure the file corresponds to his set of rules: std::string s; for(SerieExRestrictions::iterator it2 = ExRestrictions.begin(); it2 != ExRestrictions.end(); ++it2) { const ExRule &r = *it2; s = header->GetEntryString( r.group, r.elem ); if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) ) { // Argh ! This rule is unmatched; let's just quit allrules = 0; break; } } if ( allrules ) // all rules are respected: { // Allright! we have a found a DICOM that matches the user expectation. // Let's add it! // 0020 000e UI REL Series Instance UID const std::string &uid = header->GetEntryString(0x0020, 0x000e); // if uid == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND // no need here to do anything special if ( SingleSerieUIDFileSetHT.count(uid) == 0 ) { gdcmDebugMacro(" New Serie UID :[" << uid << "]"); // create a std::list in 'uid' position SingleSerieUIDFileSetHT[uid] = new FileList; } // Current Serie UID and DICOM header seems to match; add the file: SingleSerieUIDFileSetHT[uid]->push_back( header ); } else { // at least one rule was unmatched we need to deallocate the file: delete header; } } else { gdcmWarningMacro("Could not read file: " << filename ); delete header; } } /** * \brief add a gdcm::File to the first (and supposed to be unique) file set * of the gdcm::SerieHelper. * \warning : this method should be used by aware users only! * Passing a gdcm::File* has the same effect than passing a file name! * \todo : decide which one is wrong (the method, or the commentary)! * the following comment doesn't match the method :-( * User is supposed to know the files he want to deal with * and consider them they belong to the same Serie * (even if their Serie UID is different) * user will probabely OrderFileList() this list (actually, ordering * user choosen gdm::File is the sole interest of this method) * Moreover, using vtkGdcmReader::SetCoherentFileList() will avoid * vtkGdcmReader parsing twice the same files. * *no* coherence check is performed, but those specified * by SerieHelper::AddRestriction() * @param header gdcm::File* of the file to deal with */ void SerieHelper::AddGdcmFile(File *header) { int allrules = 1; // First step the user has defined a set of rules for the DICOM // he is looking for. // make sure the file correspond to his set of rules: for(SerieRestrictions::iterator it = Restrictions.begin(); it != Restrictions.end(); ++it) { const Rule &r = *it; const std::string s;// = header->GetEntryValue( r.first ); if ( !Util::DicomStringEqual(s, r.second.c_str()) ) { // Argh ! This rule is unmatch let's just quit allrules = 0; break; } } if ( allrules ) // all rules are respected: { // Allright ! we have a found a DICOM that match the user expectation. // Let's add it ! const std::string &uid = "0"; // Serie UID of the gdcm::File* may be different. // User is supposed to know what he wants if ( SingleSerieUIDFileSetHT.count(uid) == 0 ) { gdcmDebugMacro(" New Serie UID :[" << uid << "]"); // create a std::list in 'uid' position SingleSerieUIDFileSetHT[uid] = new FileList; } // Current Serie UID and DICOM header seems to match; add the file: SingleSerieUIDFileSetHT[uid]->push_back( header ); } // Even if a rule was unmatch we don't deallocate the gdcm::File: } /** * \brief add a rules for restricting a DICOM file to be in the serie we are * trying to find. For example you can select only the DICOM file from a * directory which would have a particular EchoTime==4.0. * This method is a user level, value is not required to be formatted as a DICOM * string * @param group Group number of the target tag. * @param elem Element number of the target tag. * @param value value to be checked to exclude File * @param op operator we want to use to check */ void SerieHelper::AddRestriction(uint16_t group, uint16_t elem, std::string const &value, int op) { ExRule r; r.group = group; r.elem = elem; r.value = value; r.op = op; ExRestrictions.push_back( r ); } #ifndef GDCM_LEGACY_REMOVE void SerieHelper::AddRestriction(TagKey const &key, std::string const &value) { Rule r; r.first = key; r.second = value; Restrictions.push_back( r ); } #endif /** * \brief Sets the root Directory * @param dir Name of the directory to deal with * @param recursive whether we want explore recursively the root Directory */ void SerieHelper::SetDirectory(std::string const &dir, bool recursive) { DirList dirList(dir, recursive); // OS specific DirListType filenames_list = dirList.GetFilenames(); for( DirListType::const_iterator it = filenames_list.begin(); it != filenames_list.end(); ++it) { AddFileName( *it ); } } /** * \brief Sorts the given Fileset * \warning This could be implemented in a 'Strategy Pattern' approach * But as I don't know how to do it, I leave it this way * BTW, this is also a Strategy, I don't know this is * the best approach :) */ void SerieHelper::OrderFileList(FileList *fileSet) { if ( SerieHelper::UserLessThanFunction ) { UserOrdering( fileSet ); return; } else if ( ImagePositionPatientOrdering( fileSet ) ) { return ; } else if ( ImageNumberOrdering(fileSet ) ) { return ; } else { FileNameOrdering(fileSet ); } } /** * \brief Elementary coherence checking of the files with the same Serie UID * Only sizes and pixel type are checked right now ... */ bool SerieHelper::IsCoherent(FileList *fileSet) { if(fileSet->size() == 1) return true; FileList::const_iterator it = fileSet->begin(); int nX = (*it)->GetXSize(); int nY = (*it)->GetYSize(); int pixelSize = (*it)->GetPixelSize(); it ++; for ( ; it != fileSet->end(); ++it) { if ( (*it)->GetXSize() != nX ) return false; if ( (*it)->GetYSize() != nY ) return false; if ( (*it)->GetPixelSize() != pixelSize ) return false; // probabely more is to be checked (?) } return true; } #ifndef GDCM_LEGACY_REMOVE FileList *SerieHelper::GetFirstCoherentFileList() { ItFileSetHt = SingleSerieUIDFileSetHT.begin(); if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() ) return ItFileSetHt->second; return NULL; } FileList *SerieHelper::GetNextCoherentFileList() { gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end()); ++ItFileSetHt; if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() ) return ItFileSetHt->second; return NULL; } FileList *SerieHelper::GetCoherentFileList(std::string SerieUID) { if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 ) return 0; return SingleSerieUIDFileSetHT[SerieUID]; } #endif /** * \brief Get the first Fileset while visiting the SingleSerieUIDFileSetmap * @return The first FileList (SingleSerieUIDFileSet) if found, otherwhise 0 */ FileList *SerieHelper::GetFirstSingleSerieUIDFileSet() { ItFileSetHt = SingleSerieUIDFileSetHT.begin(); if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() ) return ItFileSetHt->second; return NULL; } /** * \brief Get the next Fileset while visiting the SingleSerieUIDFileSetmap * \note : meaningfull only if GetNextSingleSerieUIDFileSet() already called * @return The next FileList (SingleSerieUIDFileSet) if found, otherwhise 0 */ FileList *SerieHelper::GetNextSingleSerieUIDFileSet() { gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end()); ++ItFileSetHt; if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() ) return ItFileSetHt->second; return NULL; } /** * \brief Get the SingleSerieUIDFileSet according to its Serie UID * @param SerieUID SerieUID to retrieve * \return pointer to the FileList (SingleSerieUIDFileSet) if found, otherwhise 0 */ FileList *SerieHelper::GetSingleSerieUIDFileSet(std::string SerieUID) { if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 ) return 0; return SingleSerieUIDFileSetHT[SerieUID]; } /** * \brief Splits a Single SerieUID Fileset according to the Orientations * @param fileSet File Set to be splitted * \return std::map of 'Xcoherent' File sets */ XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) { XCoherentFileSetmap CoherentFileSet; int nb = fileSet->size(); if (nb == 0 ) return CoherentFileSet; float iop[6]; std::ostringstream ossOrient; std::string strOrient; FileList::const_iterator it = fileSet->begin(); it ++; for ( ; it != fileSet->end(); ++it) { // Information is in : // 0020 0037 : Image Orientation (Patient) or // 0020 0035 : Image Orientation (RET) // Let's build again the 'cosines' string, to be sure of it's format (*it)->GetImageOrientationPatient(iop); ossOrient << iop[0]; for (int i = 1; i < 6; i++) { ossOrient << "\\"; ossOrient << iop[i]; } strOrient = ossOrient.str(); if ( CoherentFileSet.count(strOrient) == 0 ) { gdcmDebugMacro(" New Orientation :[" << strOrient << "]"); // create a File set in 'orientation' position CoherentFileSet[strOrient] = new FileList; } // Current Orientation and DICOM header match; add the file: CoherentFileSet[strOrient]->push_back( (*it) ); } return CoherentFileSet; } /** * \brief Splits a Single SerieUID Fileset according to the Positions * @param fileSet File Set to be splitted * \return std::map of 'Xcoherent' File sets */ XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) { XCoherentFileSetmap CoherentFileSet; int nb = fileSet->size(); if (nb == 0 ) return CoherentFileSet; float pos[3]; std::string strImPos; // read on disc std::ostringstream ossPosition; std::string strPosition; // re computed FileList::const_iterator it = fileSet->begin(); it ++; for ( ; it != fileSet->end(); ++it) { // Information is in : // 0020,0032 : Image Position Patient // 0020,0030 : Image Position (RET) strImPos = (*it)->GetEntryString(0x0020,0x0032); if ( strImPos == GDCM_UNFOUND) { gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); strImPos = (*it)->GetEntryString(0x0020,0x0030); // For ACR-NEMA images if ( strImPos == GDCM_UNFOUND ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); // User wants to split on the 'Position' // No 'Position' info found. // We return an empty Htable ! return CoherentFileSet; } } if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", &pos[0], &pos[1], &pos[2]) != 3 ) { gdcmWarningMacro( "Wrong number for Position : [" << strImPos << "]" ); return CoherentFileSet; } // Let's build again the 'position' string, to be sure of it's format ossPosition << pos[0]; for (int i = 1; i < 3; i++) { ossPosition << "\\"; ossPosition << pos[i]; } strPosition = ossPosition.str(); if ( CoherentFileSet.count(strPosition) == 0 ) { gdcmDebugMacro(" New Position :[" << strPosition << "]"); // create a File set in 'position' position CoherentFileSet[strPosition] = new FileList; } // Current Position and DICOM header match; add the file: CoherentFileSet[strPosition]->push_back( (*it) ); } return CoherentFileSet; } /** * \brief Splits a SingleSerieUID File set Coherent according to the * value of a given Tag * @param fileSet File Set to be splitted * @param group group number of the target Element * @param elem element number of the target Element * \return std::map of 'Xcoherent' File sets */ XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, uint16_t group, uint16_t elem) { XCoherentFileSetmap CoherentFileSet; int nb = fileSet->size(); if (nb == 0 ) return CoherentFileSet; std::string strTagValue; // read on disc FileList::const_iterator it = fileSet->begin(); it ++; for ( ; it != fileSet->end(); ++it) { // Information is in : // 0020,0032 : Image Position Patient // 0020,0030 : Image Position (RET) strTagValue = (*it)->GetEntryString(group,elem); if ( CoherentFileSet.count(strTagValue) == 0 ) { gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]"); // create a File set in 'position' position CoherentFileSet[strTagValue] = new FileList; } // Current Tag value and DICOM header match; add the file: CoherentFileSet[strTagValue]->push_back( (*it) ); } return CoherentFileSet; } //----------------------------------------------------------------------------- // Protected //----------------------------------------------------------------------------- // Private /** * \brief sorts the images, according to their Patient Position * We may order, considering : * -# Image Position Patient * -# Image Number * -# File Name * -# More to come :-) * \note : FileList = std::vector * @param fileList Coherent File list (same Serie UID) to sort * @return false only if the header is bugged ! */ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) //based on Jolinda Smith's algorithm { //iop is calculated based on the file file float cosines[6]; float normal[3]; float ipp[3]; float dist; float min = 0, max = 0; bool first = true; int n=0; std::vector distlist; //!\todo rewrite this for loop. for ( FileList::const_iterator it = fileList->begin(); it != fileList->end(); ++it ) { if ( first ) { (*it)->GetImageOrientationPatient( cosines ); // 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]; ipp[0] = (*it)->GetXOrigin(); ipp[1] = (*it)->GetYOrigin(); ipp[2] = (*it)->GetZOrigin(); dist = 0; for ( int i = 0; i < 3; ++i ) { dist += normal[i]*ipp[i]; } distlist.push_back( dist ); max = min = dist; first = false; } else { ipp[0] = (*it)->GetXOrigin(); ipp[1] = (*it)->GetYOrigin(); ipp[2] = (*it)->GetZOrigin(); dist = 0; for ( int i = 0; i < 3; ++i ) { dist += normal[i]*ipp[i]; } distlist.push_back( dist ); min = (min < dist) ? min : dist; max = (max > dist) ? max : dist; } ++n; } // Then I order the slices according to the value "dist". Finally, once // I've read in all the slices, I calculate the z-spacing as the difference // between the "dist" values for the first two slices. FileVector CoherentFileVector(n); // CoherentFileVector.reserve( n ); CoherentFileVector.resize( n ); // gdcmAssertMacro( CoherentFileVector.capacity() >= n ); // 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" ); return false; } float step = (max - min)/(n - 1); int pos; n = 0; //VC++ don't understand what scope is !! it -> it2 for (FileList::const_iterator it2 = fileList->begin(); it2 != fileList->end(); ++it2, ++n) { //2*n sort algo !! //Assumption: all files are present (no one missing) pos = (int)( fabs( (distlist[n]-min)/step) + .5 ); // a Dicom 'Serie' may contain scout views // and images may have differents directions // -> More than one may have the same 'pos' // Sorting has then NO meaning ! if (CoherentFileVector[pos]==NULL) CoherentFileVector[pos] = *it2; else { gdcmWarningMacro( "At least 2 files with same position." << " No PositionPatientOrdering sort performed"); return false; } } fileList->clear(); // doesn't delete list elements, only nodes if (DirectOrder) { //VC++ don't understand what scope is !! it -> it3 for (FileVector::const_iterator it3 = CoherentFileVector.begin(); it3 != CoherentFileVector.end(); ++it3) { fileList->push_back( *it3 ); } } else // user asked for reverse order { FileVector::const_iterator it4; it4 = CoherentFileVector.end(); do { it4--; fileList->push_back( *it4 ); } while (it4 != CoherentFileVector.begin() ); } distlist.clear(); CoherentFileVector.clear(); return true; } bool SerieHelper::ImageNumberLessThan(File *file1, File *file2) { return file1->GetImageNumber() < file2->GetImageNumber(); } bool SerieHelper::ImageNumberGreaterThan(File *file1, File *file2) { return file1->GetImageNumber() > file2->GetImageNumber(); } /** * \brief sorts the images, according to their Image Number * \note Works only on bona fide files (i.e image number is a character string * corresponding to an integer) * within a bona fide serie (i.e image numbers are consecutive) * @param fileList Coherent File list (same Serie UID) to sort * @return false if non bona fide stuff encountered */ bool SerieHelper::ImageNumberOrdering(FileList *fileList) { int min, max, pos; int n = fileList->size(); FileList::const_iterator it = fileList->begin(); min = max = (*it)->GetImageNumber(); for (; it != fileList->end(); ++it, ++n) { pos = (*it)->GetImageNumber(); min = (min < pos) ? min : pos; max = (max > pos) ? max : pos; } // Find out if image numbers are coherent (consecutive) if ( min == max || max == 0 || max >= (n+min) ) { gdcmWarningMacro( " 'Image numbers' not coherent. " << " No ImageNumberOrdering sort performed."); return false; } if (DirectOrder) std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberLessThan ); else std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberGreaterThan ); return true; } bool SerieHelper::FileNameLessThan(File *file1, File *file2) { return file1->GetFileName() < file2->GetFileName(); } bool SerieHelper::FileNameGreaterThan(File *file1, File *file2) { return file1->GetFileName() > file2->GetFileName(); } /** * \brief sorts the images, according to their File Name * @param fileList Coherent File list (same Serie UID) to sort * @return false only if the header is bugged ! */ bool SerieHelper::FileNameOrdering(FileList *fileList) { if (DirectOrder) std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameLessThan); else std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameGreaterThan); return true; } /** * \brief sorts the images, according to user supplied function * @param fileList Coherent File list (same Serie UID) to sort * @return false only if the header is bugged ! */ bool SerieHelper::UserOrdering(FileList *fileList) { std::sort(fileList->begin(), fileList->end(), SerieHelper::UserLessThanFunction); if (!DirectOrder) { std::reverse(fileList->begin(), fileList->end()); } return true; } //----------------------------------------------------------------------------- // Print /** * \brief Canonical printer. */ void SerieHelper::Print(std::ostream &os, std::string const &indent) { // For all the Coherent File lists of the gdcm::Serie SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin(); if ( itl == SingleSerieUIDFileSetHT.end() ) { gdcmWarningMacro( "No SingleSerieUID File set found" ); return; } while (itl != SingleSerieUIDFileSetHT.end()) { os << "Serie UID :[" << itl->first << "]" << std::endl; // For all the files of a SingleSerieUID File set for (FileList::iterator it = (itl->second)->begin(); it != (itl->second)->end(); ++it) { os << indent << " --- " << (*it)->GetFileName() << std::endl; } ++itl; } } //----------------------------------------------------------------------------- } // end namespace gdcm