X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmSerieHelper.cxx;h=56aaaabcb1533c75bd01f38caa9016193a715dd0;hb=35ee8ee8af32946514713d271177df8bb2298eb2;hp=5c0919c4baca786a1be5f3e3b8cb8c2ba065e5de;hpb=9b0d1f04cca6a583d85553cab0bef197c2940e61;p=gdcm.git diff --git a/src/gdcmSerieHelper.cxx b/src/gdcmSerieHelper.cxx index 5c0919c4..56aaaabc 100644 --- a/src/gdcmSerieHelper.cxx +++ b/src/gdcmSerieHelper.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmSerieHelper.cxx,v $ Language: C++ - Date: $Date: 2007/10/01 09:28:57 $ - Version: $Revision: 1.62 $ + Date: $Date: 2011/03/29 07:36:00 $ + Version: $Revision: 1.71 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -13,7 +13,7 @@ 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" @@ -43,7 +43,7 @@ SerieHelper::SerieHelper() ClearAll(); UserLessThanFunction = 0; DirectOrder = true; - + DropDuplicatePositions = false; } /** @@ -161,7 +161,7 @@ bool SerieHelper::AddFile(File *header) std::string id = CreateUniqueSeriesIdentifier( header ); // if id == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND // no need here to do anything special - + if ( SingleSerieUIDFileSetHT.count(id) == 0 ) { gdcmDebugMacro(" New/gdcmSerieHelper.cxx Serie UID :[" << id << "]"); @@ -258,11 +258,14 @@ void SerieHelper::AddSeriesDetail(uint16_t group, uint16_t elem, bool convert) 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) { + // std::cout << "-----------------------------filename [" << *it << "]" + // << std::endl; + gdcmDebugMacro("filename [" << *it << "]" ); AddFileName( *it ); } } @@ -578,14 +581,14 @@ XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) * \return std::map of 'Xcoherent' File sets */ -XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, +XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, uint16_t group, uint16_t element) { XCoherentFileSetmap CoherentFileSet; int nb = fileSet->size(); if (nb == 0 ) { - gdcmWarningMacro("Empty FileList passed to SplitOnPosition"); + gdcmWarningMacro("Empty FileList passed to SplitOnTagValue"); return CoherentFileSet; } @@ -602,6 +605,60 @@ XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, // 0020,0030 : Image Position (RET) strTagValue = (*it)->GetEntryString(group,element); + + if ( CoherentFileSet.count(strTagValue) == 0 ) + { + gdcmDebugMacro(" :[" << 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; +} + + +/** + * \brief Splits a 'Single SerieUID' 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 element element number of the target Element + * \return std::map of 'Xcoherent' File sets + */ + +XCoherentFileSetmap SerieHelper::SplitOnTagValueConvertToFloat(FileList *fileSet, + uint16_t group, uint16_t element) +{ + XCoherentFileSetmap CoherentFileSet; + + int nb = fileSet->size(); + if (nb == 0 ) { + gdcmWarningMacro("Empty FileList passed to SplitOnTagValue"); + return CoherentFileSet; + } + + std::string strTagValue; // read on disc + + double dTagValue; + int iTagValue; + char cTagValue[11]; + std::string sTagValue; + + FileList::const_iterator it = fileSet->begin(); + //it ++; + for ( ; + it != fileSet->end(); + ++it) + { + /// \TODO : find a trick to create a string whose value follows lexicographical order + + strTagValue = (*it)->GetEntryString(group,element); + dTagValue = atof( strTagValue.c_str()); + iTagValue = dTagValue; + sprintf(cTagValue, "%010d", iTagValue); + strTagValue = cTagValue; if ( CoherentFileSet.count(strTagValue) == 0 ) { @@ -648,6 +705,8 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) bool first = true; ZSpacing = -1.0; // will be updated if process doesn't fail + gdcmDebugMacro("============================================DropDuplicatePositions : " << DropDuplicatePositions ); + std::multimap distmultimap; // Use a multimap to sort the distances from 0,0,0 for ( FileList::const_iterator @@ -720,6 +779,8 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) } } + gdcmDebugMacro("After parsing vector, nb of elements : " << fileList->size() ); + // Find out if min/max are coherent if ( min == max ) { @@ -735,6 +796,9 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) it2 != distmultimap.end(); ++it2) { + + gdcmDebugMacro("Check if image shares a common position : " << (*it2).second->GetFileName() ); + if (distmultimap.count((*it2).first) != 1) { gdcmWarningMacro("File: [" @@ -780,9 +844,14 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) fileList->push_back( (*it3).second ); if (DropDuplicatePositions) { - /// \todo ImagePositionPatientOrdering wrong duplicates are found ??? - + // 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; } @@ -798,7 +867,16 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) fileList->push_back( (*it4).second ); if (DropDuplicatePositions) // skip all duplicates { - it4 = distmultimap.upper_bound((*it4).first); + // 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; } @@ -1014,7 +1092,7 @@ std::string SerieHelper::CreateUniqueSeriesIdentifier( File *inFile ) } } // deal with Dicom strings trailing '\0' - if(id[s_size-1] == '_') + if(s_size && id[s_size-1] == '_') id.erase(s_size-1, 1); return id; } @@ -1050,6 +1128,8 @@ std::string SerieHelper::CreateUserDefinedFileIdentifier( File *inFile ) { const ExDetail &r = *it2; s = inFile->GetEntryString( r.group, r.elem ); + if (s == "") // avoid troubles when empty string is found + s = "-"; // User is allowed to ask for 'convertion', to allow further ordering // e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK @@ -1066,23 +1146,30 @@ std::string SerieHelper::CreateUserDefinedFileIdentifier( File *inFile ) } } // Eliminate non-alphanum characters, including whitespace. + unsigned int s_size = s.size(); - for(unsigned int i=0; i= '+' && s[i] <= '-') || (s[i] >= 'a' && s[i] <= 'z') || (s[i] >= '0' && s[i] <= '9') || (s[i] >= 'A' && s[i] <= 'Z'))) - { - s.replace(i, 1, "_"); // ImagePositionPatient related stuff will be more human readable + { + s.replace(i, 1, "_"); // ImagePositionPatient related stuff will be more human readable + } } + // deal with Dicom strings trailing '\0' + if(s[s_size-1] == '_') + s.erase(s_size-1, 1); } - // deal with Dicom strings trailing '\0' - if(s[s_size-1] == '_') - s.erase(s_size-1, 1); - id += s.c_str(); id += "%%%"; // make the FileIdentifier Tokenizable }