X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmSerieHelper.cxx;h=fc0f2135b7838d77fcb177c1638a773b077998e0;hb=6278320cc85da00d2d56ffbf07806e84966892c3;hp=c8c1cbba86453cc3d502085159704e8562811264;hpb=fc71b6d6df72ee061f0a88e3de407a83511f8ed2;p=gdcm.git diff --git a/src/gdcmSerieHelper.cxx b/src/gdcmSerieHelper.cxx index c8c1cbba..fc0f2135 100644 --- a/src/gdcmSerieHelper.cxx +++ b/src/gdcmSerieHelper.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmSerieHelper.cxx,v $ Language: C++ - Date: $Date: 2006/03/30 16:51:29 $ - Version: $Revision: 1.49 $ + Date: $Date: 2008/05/14 07:48:52 $ + Version: $Revision: 1.69 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -19,7 +19,7 @@ #include "gdcmSerieHelper.h" #include "gdcmDirList.h" #include "gdcmFile.h" -#include "gdcmDictEntry.h" // for TranslateToKey +//#include "gdcmDictEntry.h" // for TranslateToKey : no more ! #include "gdcmDebug.h" #include "gdcmUtil.h" @@ -29,7 +29,7 @@ #include #include //for sscanf -namespace gdcm +namespace GDCM_NAME_SPACE { //----------------------------------------------------------------------------- @@ -43,6 +43,7 @@ SerieHelper::SerieHelper() ClearAll(); UserLessThanFunction = 0; DirectOrder = true; + DropDuplicatePositions = false; } /** @@ -63,8 +64,8 @@ void SerieHelper::ClearAll() FileList *l = GetFirstSingleSerieUIDFileSet(); while (l) { - // For all the gdcm::File of a File set - for (gdcm::FileList::iterator it = l->begin(); + // For all the GDCM_NAME_SPACE::File of a File set + for (GDCM_NAME_SPACE::FileList::iterator it = l->begin(); it != l->end(); ++it) { @@ -84,7 +85,7 @@ void SerieHelper::ClearAll() // Public /** - * \brief add a gdcm::File to the Fileset corresponding to its Serie UID + * \brief add a GDCM_NAME_SPACE::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) @@ -111,10 +112,10 @@ void SerieHelper::AddFileName(std::string const &filename) } /** - * \brief add a gdcm::File to the first (and supposed to be unique) file set - * of the gdcm::SerieHelper. + * \brief add a GDCM_NAME_SPACE::File to the first (and supposed to be unique) file set + * of the GDCM_NAME_SPACE::SerieHelper. * \warning : this method should be used by aware users only! - * Passing a gdcm::File* has the same effect than passing a file name! + * Passing a GDCM_NAME_SPACE::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 @@ -126,7 +127,7 @@ void SerieHelper::AddFileName(std::string const &filename) * 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 + * @param header GDCM_NAME_SPACE::File* of the file to deal with * @return true if file was added, false if file was rejected */ bool SerieHelper::AddFile(File *header) @@ -160,10 +161,10 @@ 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 Serie UID :[" << id << "]"); + gdcmDebugMacro(" New/gdcmSerieHelper.cxx Serie UID :[" << id << "]"); // create a std::list in 'id' position SingleSerieUIDFileSetHT[id] = new FileList; } @@ -209,7 +210,7 @@ void SerieHelper::AddRestriction(TagKey const &key) ExRefine.push_back( r ); } -#ifndef GDCM_LEGACY_REMOVE +//#ifndef GDCM_LEGACY_REMOVE /** * \brief add a rule for restricting a DICOM file to be in the serie we are * trying to find. For example you can select only the DICOM files from a @@ -223,25 +224,26 @@ void SerieHelper::AddRestriction(TagKey const &key) * @deprecated use : AddRestriction(TagKey const &key, * std::string const &value, int op); */ + void SerieHelper::AddRestriction(uint16_t group, uint16_t elem, std::string const &value, int op) { TagKey t(group, elem); AddRestriction(t, value, op); } -#endif + +//#endif /** * \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; @@ -256,6 +258,25 @@ 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 ); + } +} + +/** + * \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(); @@ -274,22 +295,29 @@ void SerieHelper::SetDirectory(std::string const &dir, bool recursive) */ void SerieHelper::OrderFileList(FileList *fileSet) { - + // Only computed during ImagePositionPatientOrdering + // (need to sort the FileList using IPP and IOP !) + ZSpacing = -1.0; + 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 ); } } @@ -327,12 +355,13 @@ bool SerieHelper::IsCoherent(FileList *fileSet) return true; } -#ifndef GDCM_LEGACY_REMOVE +//#ifndef GDCM_LEGACY_REMOVE /** * \brief accessor (DEPRECATED : use GetFirstSingleSerieUIDFileSet ) * Warning : 'coherent' means here they have the same Serie UID * @return The first FileList if found, otherwhise NULL */ + /* FileList *SerieHelper::GetFirstCoherentFileList() { ItFileSetHt = SingleSerieUIDFileSetHT.begin(); @@ -340,13 +369,14 @@ FileList *SerieHelper::GetFirstCoherentFileList() return ItFileSetHt->second; return NULL; } - +*/ /** * \brief accessor (DEPRECATED : use GetNextSingleSerieUIDFileSet ) * Warning : 'coherent' means here they have the same Serie UID * \note : meaningfull only if GetFirstCoherentFileList() already called * @return The next FileList if found, otherwhise NULL */ + /* FileList *SerieHelper::GetNextCoherentFileList() { gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end()); @@ -356,6 +386,7 @@ FileList *SerieHelper::GetNextCoherentFileList() return ItFileSetHt->second; return NULL; } +*/ /** * \brief accessor (DEPRECATED : use GetSingleSerieUIDFileSet ) @@ -363,13 +394,15 @@ FileList *SerieHelper::GetNextCoherentFileList() * @param SerieUID SerieUID * \return pointer to the FileList if found, otherwhise NULL */ + /* FileList *SerieHelper::GetCoherentFileList(std::string SerieUID) { if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 ) return 0; return SingleSerieUIDFileSetHT[SerieUID]; } -#endif +*/ +//#endif /** @@ -422,14 +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) @@ -438,7 +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]; @@ -454,9 +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; } @@ -472,14 +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) @@ -508,7 +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 @@ -539,7 +577,7 @@ XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) * 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 + * @param element element number of the target Element * \return std::map of 'Xcoherent' File sets */ @@ -549,13 +587,15 @@ 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) @@ -568,7 +608,7 @@ 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; } @@ -585,7 +625,7 @@ 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 @@ -611,12 +651,15 @@ 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 ); @@ -655,6 +698,7 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) dist += normal[i]*ipp[i]; } + gdcmDebugMacro("dist : " << dist); distmultimap.insert(std::pair(dist, *it)); max = min = dist; @@ -675,17 +719,20 @@ 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; } @@ -695,23 +742,29 @@ 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 @@ -735,6 +788,19 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) ++it3) { 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; + } } } else // user asked for reverse order @@ -745,6 +811,21 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) { it4--; fileList->push_back( (*it4).second ); + 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() ); } @@ -847,7 +928,7 @@ bool SerieHelper::UserOrdering(FileList *fileList) */ void SerieHelper::Print(std::ostream &os, std::string const &indent) { - // For all the Coherent File lists of the gdcm::Serie + // For all the Coherent File lists of the GDCM_NAME_SPACE::Serie SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin(); if ( itl == SingleSerieUIDFileSetHT.end() ) { @@ -860,8 +941,8 @@ 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; } @@ -879,22 +960,26 @@ 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)); } @@ -906,9 +991,9 @@ 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::File we want to build a Serie Identifier for. + * @param inFile GDCM_NAME_SPACE::File we want to build a Serie Identifier for. * @return the SeriesIdentifier */ std::string SerieHelper::CreateUniqueSeriesIdentifier( File *inFile ) @@ -926,7 +1011,7 @@ std::string SerieHelper::CreateUniqueSeriesIdentifier( File *inFile ) { const ExRule &r = *it2; std::string s = inFile->GetEntryString( r.group, r.elem ); - if( s == gdcm::GDCM_UNFOUND ) + if( s == GDCM_UNFOUND ) { s = ""; } @@ -939,23 +1024,28 @@ 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 { gdcmWarningMacro("Could not parse series info."); - std::string id = gdcm::GDCM_UNFOUND; + std::string id = GDCM_UNFOUND; return id; } } @@ -968,7 +1058,7 @@ 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!) @@ -984,8 +1074,10 @@ 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) { @@ -1000,22 +1092,28 @@ 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; } @@ -1029,5 +1127,14 @@ void SerieHelper::Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *f std::sort(fileList->begin(), fileList->end(), pt2Func ); } +/* +#ifndef GDCM_LEGACY_REMOVE +bool SerieHelper::AddGdcmFile(File* header) +{ + return AddFile(header); +} +#endif +*/ + //----------------------------------------------------------------------------- } // end namespace gdcm