X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmSerieHelper.cxx;h=56aaaabcb1533c75bd01f38caa9016193a715dd0;hb=35ee8ee8af32946514713d271177df8bb2298eb2;hp=8d800cea5c626f2eda30e068e3ee2ef406f1bf4c;hpb=5d1e3fd08029804ede29b7392c2f1b7970b3c27f;p=gdcm.git diff --git a/src/gdcmSerieHelper.cxx b/src/gdcmSerieHelper.cxx index 8d800cea..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: 2007/06/08 12:49:37 $ - Version: $Revision: 1.57 $ + 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 << "]"); @@ -236,7 +236,7 @@ void SerieHelper::AddRestriction(uint16_t group, uint16_t elem, /** * \brief add an extra 'SerieDetail' for building a 'Serie Identifier' - * that ensures (hope so) File constistency (Series Instance UID doesn't. + * that ensures (hope so) File consistency (Series Instance UID doesn't) * @param group tag group number we want restrict on a given value * @param elem tag element number we want restrict on a given value * @param convert wether we want 'convertion', to allow further ordering @@ -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 ); } } @@ -298,19 +301,23 @@ void SerieHelper::OrderFileList(FileList *fileSet) if ( SerieHelper::UserLessThanFunction ) { + gdcmDebugMacro("Use UserLessThanFunction"); UserOrdering( fileSet ); return; } else if ( ImagePositionPatientOrdering( fileSet ) ) - { + { + gdcmDebugMacro("ImagePositionPatientOrdering succeeded"); return ; } else if ( ImageNumberOrdering(fileSet ) ) { + gdcmDebugMacro("ImageNumberOrdering succeeded"); return ; } else { + gdcmDebugMacro("Use FileNameOrdering"); FileNameOrdering(fileSet ); } } @@ -448,14 +455,16 @@ XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) XCoherentFileSetmap CoherentFileSet; int nb = fileSet->size(); - if (nb == 0 ) + if (nb == 0 ) { + gdcmWarningMacro("Empty FileList passed to SplitOnOrientation"); return CoherentFileSet; + } + float iop[6]; std::string strOrient; std::ostringstream ossOrient; FileList::const_iterator it = fileSet->begin(); - it ++; for ( ; it != fileSet->end(); ++it) @@ -464,7 +473,7 @@ XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) // 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 + // Let's build again the 'cosines' string, to be sure of its format (*it)->GetImageOrientationPatient(iop); ossOrient << iop[0]; @@ -480,9 +489,11 @@ XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) gdcmDebugMacro(" New Orientation :[" << strOrient << "]"); // create a File set in 'orientation' position CoherentFileSet[strOrient] = new FileList; + gdcmDebugMacro(" CoherentFileSet[strOrient]" << strOrient << "created"); } // Current Orientation and DICOM header match; add the file: CoherentFileSet[strOrient]->push_back( (*it) ); + gdcmDebugMacro(" CoherentFileSet[strOrient]" << "pushed back") } return CoherentFileSet; } @@ -498,14 +509,15 @@ XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) XCoherentFileSetmap CoherentFileSet; int nb = fileSet->size(); - if (nb == 0 ) + if (nb == 0 ) { + gdcmWarningMacro("Empty FileList passed to SplitOnPosition"); 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) @@ -534,7 +546,7 @@ XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) { gdcmWarningMacro( "Wrong number for Position : [" << strImPos << "]" ); - return CoherentFileSet; + return CoherentFileSet; } // Let's build again the 'position' string, to be sure of it's format @@ -569,19 +581,21 @@ 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 ) + if (nb == 0 ) { + gdcmWarningMacro("Empty FileList passed to SplitOnTagValue"); return CoherentFileSet; + } std::string strTagValue; // read on disc FileList::const_iterator it = fileSet->begin(); - it ++; + //it ++; for ( ; it != fileSet->end(); ++it) @@ -591,10 +605,64 @@ 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 ) { - gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]"); + gdcmDebugMacro(" :[" << strTagValue << "]"); // create a File set in 'position' position CoherentFileSet[strTagValue] = new FileList; } @@ -611,7 +679,7 @@ XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, // Private /** * \brief sorts the images, according to their Patient Position. - * As a side effect, it computes the ZSpacing, according to Jolinda Smith' + * As a side effect, it computes the ZSpacing, according to Jolinda Smith's * algorithm. (get it with double GetZSpacing() !) * We may order, considering : * -# Image Position Patient @@ -637,12 +705,15 @@ 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 it = fileList->begin(); it != fileList->end(); ++it ) { + gdcmDebugMacro("deal with " << (*it)->GetFileName() ); if ( first ) { (*it)->GetImageOrientationPatient( cosines ); @@ -681,6 +752,7 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) dist += normal[i]*ipp[i]; } + gdcmDebugMacro("dist : " << dist); distmultimap.insert(std::pair(dist, *it)); max = min = dist; @@ -701,17 +773,19 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) } 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() ); + // 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 PositionPatientOrdering sort performed. " << "No 'ZSpacing' calculated! "); return false; } @@ -722,14 +796,17 @@ 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) { - gdcmErrorMacro("File: [" + gdcmWarningMacro("File: [" << ((*it2).second->GetFileName()) << "] : more than ONE file at distance: '" << (*it2).first - << " (position is not unique!) " - << "No PositionPatientOrdering sort performed. " + << " (position is not unique!) " + << "No PositionPatientOrdering sort performed. " << "No 'ZSpacing' calculated! "); ok = false; @@ -740,8 +817,8 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) if (! DropDuplicatePositions) return false; } - -// Now, we could calculate Z Spacing as the difference + +// 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 @@ -767,7 +844,14 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) fileList->push_back( (*it3).second ); 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; } @@ -783,7 +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; } @@ -902,8 +995,8 @@ void SerieHelper::Print(std::ostream &os, std::string const &indent) // For all the files of a SingleSerieUID File set for (FileList::iterator it = (itl->second)->begin(); - it != (itl->second)->end(); - ++it) + it != (itl->second)->end(); + ++it) { os << indent << " --- " << (*it)->GetFileName() << std::endl; } @@ -935,12 +1028,12 @@ void SerieHelper::CreateDefaultUniqueSeriesIdentifier() // 0028 0010 Rows // If the 2D images in a sequence don't have the same number of rows, - // then it is difficult to reconstruct them into a 3D volume. + // then it is difficult to reconstruct them into a 3D volume. AddRestriction( TagKey(0x0028, 0x0010)); // 0028 0011 Columns // If the 2D images in a sequence don't have the same number of columns, - // then it is difficult to reconstruct them into a 3D volume. + // then it is difficult to reconstruct them into a 3D volume. AddRestriction( TagKey(0x0028, 0x0011)); } @@ -952,7 +1045,7 @@ void SerieHelper::CreateDefaultUniqueSeriesIdentifier() * then additional identifying information is used. * We allow user to add his own critierions, using AddSeriesDetail * (he knows more than we do about his images!) - * ex : in tagging series, the only pertnent tag is + * ex : in tagging series, the only pertinent tag is * 0018|1312 [In-plane Phase Encoding Direction] value : ROW/COLUMN * @param inFile GDCM_NAME_SPACE::File we want to build a Serie Identifier for. * @return the SeriesIdentifier @@ -985,17 +1078,22 @@ std::string SerieHelper::CreateUniqueSeriesIdentifier( File *inFile ) } // Eliminate non-alnum characters, including whitespace... // that may have been introduced by concats. - for(unsigned int i=0; i= '+' && id[i] <= '-') + || (id[i] >= 'a' && id[i] <= 'z') + || (id[i] >= '0' && id[i] <= '9') + || (id[i] >= 'A' && id[i] <= 'Z'))) { - while(i= 'a' && id[i] <= 'z') - || (id[i] >= '0' && id[i] <= '9') - || (id[i] >= 'A' && id[i] <= 'Z'))) - { - id.erase(i, 1); - } + id.replace(i, 1, "_"); // ImagePositionPatient related stuff will be more human readable } + } + // deal with Dicom strings trailing '\0' + if(s_size && id[s_size-1] == '_') + id.erase(s_size-1, 1); return id; } else // Could not open inFile @@ -1014,7 +1112,7 @@ std::string SerieHelper::CreateUniqueSeriesIdentifier( File *inFile ) * -File class? FileHelper class?- * @return FileIdentifier (Tokenizable on '%%%'. Hope it's enough !) */ -std::string SerieHelper::CreateUserDefinedFileIdentifier( File * inFile ) +std::string SerieHelper::CreateUserDefinedFileIdentifier( File *inFile ) { // Deal with all user supplied tags. // (user knows more than we do about his images!) @@ -1030,6 +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 @@ -1046,22 +1146,35 @@ std::string SerieHelper::CreateUserDefinedFileIdentifier( File * inFile ) } } // Eliminate non-alphanum characters, including whitespace. - 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.erase(i, 1); + { + 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); } - id += s.c_str(); id += "%%%"; // make the FileIdentifier Tokenizable } - + id += inFile->GetFileName(); + id += "%%%"; return id; }