X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmSerieHelper.cxx;h=eb6dd6a0c02c8844d76a7fd1ce03b15272017add;hb=224876ca6cbe71952f2a1d66d9853eca7745d3a0;hp=accac6161b547689383dd4bffcb10b56a12b758a;hpb=57faf3646d5227613b7a3407876c6f5e3bf11eb9;p=gdcm.git diff --git a/src/gdcmSerieHelper.cxx b/src/gdcmSerieHelper.cxx index accac616..eb6dd6a0 100644 --- a/src/gdcmSerieHelper.cxx +++ b/src/gdcmSerieHelper.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmSerieHelper.cxx,v $ Language: C++ - Date: $Date: 2007/05/23 15:30:29 $ - Version: $Revision: 1.55 $ + Date: $Date: 2007/10/30 14:51:00 $ + Version: $Revision: 1.64 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -43,6 +43,7 @@ SerieHelper::SerieHelper() ClearAll(); UserLessThanFunction = 0; DirectOrder = true; + DropDuplicatePositions = false; } /** @@ -235,15 +236,14 @@ 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 * e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK */ void SerieHelper::AddSeriesDetail(uint16_t group, uint16_t elem, bool convert) -{ - +{ ExDetail d; d.group = group; d.elem = elem; @@ -267,6 +267,22 @@ void SerieHelper::SetDirectory(std::string const &dir, bool recursive) } } +/** + * \brief Sets the DicomDirSerie + * @param se DicomDirSerie to deal with + */ +void SerieHelper::SetDicomDirSerie(DicomDirSerie *se) +{ + DirList dirList(se); + + 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 @@ -282,19 +298,23 @@ 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 ); } } @@ -432,14 +452,16 @@ 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) @@ -448,7 +470,7 @@ 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]; @@ -464,9 +486,11 @@ 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; } @@ -482,14 +506,15 @@ 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) @@ -518,7 +543,7 @@ 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 @@ -559,13 +584,15 @@ XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, XCoherentFileSetmap CoherentFileSet; int nb = fileSet->size(); - if (nb == 0 ) + if (nb == 0 ) { + gdcmWarningMacro("Empty FileList passed to SplitOnPosition"); return CoherentFileSet; + } std::string strTagValue; // read on disc FileList::const_iterator it = fileSet->begin(); - it ++; + //it ++; for ( ; it != fileSet->end(); ++it) @@ -578,7 +605,7 @@ XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, if ( CoherentFileSet.count(strTagValue) == 0 ) { - gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]"); + gdcmDebugMacro(" :[" << strTagValue << "]"); // create a File set in 'position' position CoherentFileSet[strTagValue] = new FileList; } @@ -595,7 +622,7 @@ 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 @@ -621,12 +648,15 @@ 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 ); @@ -665,6 +695,7 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) dist += normal[i]*ipp[i]; } + gdcmDebugMacro("dist : " << dist); distmultimap.insert(std::pair(dist, *it)); max = min = dist; @@ -685,17 +716,20 @@ 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" ); + gdcmWarningMacro("Looks like all images have the exact same image position. " + << "No PositionPatientOrdering sort performed. " + << "No 'ZSpacing' calculated! "); return false; } @@ -705,23 +739,29 @@ 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()) - << " Distance: " + << "] : more than ONE file at distance: '" << (*it2).first - << " position is not unique"); + << " (position is not unique!) " + << "No PositionPatientOrdering sort performed. " + << "No 'ZSpacing' calculated! "); ok = false; } } if (!ok) { - return false; + 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 @@ -745,6 +785,14 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) ++it3) { fileList->push_back( (*it3).second ); + if (DropDuplicatePositions) + { + /// \todo ImagePositionPatientOrdering wrong duplicates are found ??? + + it3 = distmultimap.upper_bound((*it3).first); // skip all duplicates + if (it3 == distmultimap.end() ) // if last image, stop iterate + break; + } } } else // user asked for reverse order @@ -755,6 +803,12 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) { it4--; fileList->push_back( (*it4).second ); + if (DropDuplicatePositions) // skip all duplicates + { + it4 = distmultimap.upper_bound((*it4).first); + if (it4 == distmultimap.begin() ) // if first image, stop iterate + break; + } } while (it4 != distmultimap.begin() ); } @@ -870,8 +924,8 @@ 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; } @@ -889,22 +943,26 @@ void SerieHelper::CreateDefaultUniqueSeriesIdentifier() // A scout scan prior to a CT volume scan can share the same // SeriesUID, but they will sometimes have a different Series Number AddRestriction( TagKey(0x0020, 0x0011) ); + // 0018 0024 Sequence Name // For T1-map and phase-contrast MRA, the different flip angles and // directions are only distinguished by the Sequence Name AddRestriction( TagKey(0x0018, 0x0024) ); + // 0018 0050 Slice Thickness // On some CT systems, scout scans and subsequence volume scans will // have the same SeriesUID and Series Number - YET the slice // thickness will differ from the scout slice and the volume slices. AddRestriction( TagKey(0x0018, 0x0050)); + // 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)); } @@ -916,7 +974,7 @@ 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 @@ -949,17 +1007,22 @@ 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(id[s_size-1] == '_') + id.erase(s_size-1, 1); return id; } else // Could not open inFile @@ -978,7 +1041,7 @@ 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!) @@ -994,8 +1057,10 @@ 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 'convertion', to allow further ordering + // User is allowed to ask for 'convertion', to allow further ordering // e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK if (it2->convert) { @@ -1010,22 +1075,28 @@ std::string SerieHelper::CreateUserDefinedFileIdentifier( File * inFile ) } } // Eliminate non-alphanum characters, including whitespace. - for(unsigned int i=0; i= 'a' && s[i] <= 'z') - || (s[i] >= '0' && s[i] <= '9') - || (s[i] >= 'A' && s[i] <= 'Z'))) + while(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; }