X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmSerieHelper.cxx;h=7c8bf536fc8599ed2ef3f4a3d8c492931323a73f;hb=17daf7e7caceddf44e73864ee8d366613a1f0c82;hp=47b2b57c7543109f331b92cd5cf53caf7de92c4e;hpb=c4a199d505f107da14e4901ec765a2bf1395cfa7;p=gdcm.git diff --git a/src/gdcmSerieHelper.cxx b/src/gdcmSerieHelper.cxx index 47b2b57c..7c8bf536 100644 --- a/src/gdcmSerieHelper.cxx +++ b/src/gdcmSerieHelper.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmSerieHelper.cxx,v $ Language: C++ - Date: $Date: 2005/10/21 08:49:36 $ - Version: $Revision: 1.26 $ + Date: $Date: 2005/11/28 17:23:37 $ + Version: $Revision: 1.38 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -40,6 +40,7 @@ namespace gdcm */ SerieHelper::SerieHelper() { + m_UseSeriesDetails = false; ClearAll(); UserLessThanFunction = 0; DirectOrder = true; @@ -54,8 +55,8 @@ SerieHelper::~SerieHelper() } /** - * \brief - Preventively, clear everything at constructor time. - * - use it at destructor time. + * \brief Preventively, clear everything at constructor time. + * ( use it at destructor time.) */ void SerieHelper::ClearAll() { @@ -68,7 +69,7 @@ void SerieHelper::ClearAll() it != l->end(); ++it) { - delete *it; // remove each entry + (*it)->Delete(); // remove each entry } l->clear(); delete l; // remove the container @@ -88,7 +89,7 @@ void SerieHelper::ClearAll() void SerieHelper::AddFileName(std::string const &filename) { // Create a DICOM file - File *header = new File (); + File *header = File::New(); header->SetLoadMode(LoadMode); header->SetFileName( filename ); header->Load(); @@ -110,6 +111,7 @@ void SerieHelper::AddFileName(std::string const &filename) if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) ) { // Argh ! This rule is unmatched; let's just quit + allrules = 0; break; } @@ -125,6 +127,7 @@ void SerieHelper::AddFileName(std::string const &filename) // 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 << "]"); @@ -137,13 +140,13 @@ void SerieHelper::AddFileName(std::string const &filename) else { // at least one rule was unmatched we need to deallocate the file: - delete header; + header->Delete(); } } else { gdcmWarningMacro("Could not read file: " << filename ); - delete header; + header->Delete(); } } @@ -176,7 +179,7 @@ void SerieHelper::AddGdcmFile(File *header) ++it) { const Rule &r = *it; - const std::string s;// = header->GetEntryValue( r.first ); + const std::string s;// = header->GetEntryString( r.first ); if ( !Util::DicomStringEqual(s, r.second.c_str()) ) { // Argh ! This rule is unmatch let's just quit @@ -211,44 +214,21 @@ void SerieHelper::AddGdcmFile(File *header) * 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 key Target tag we want restrict on a given value * @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, +void SerieHelper::AddRestriction(TagKey const &key, std::string const &value, int op) { ExRule r; - r.group = group; - r.elem = elem; + r.group = key[0]; + r.elem = key[1]; r.value = value; r.op = op; ExRestrictions.push_back( r ); } -#ifndef GDCM_LEGACY_REMOVE -/** - * \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 - * @deprecated use : AddRestriction(uint16_t group, uint16_t elem, - * std::string const &value, int op); - */ -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 @@ -306,10 +286,10 @@ bool SerieHelper::IsCoherent(FileList *fileSet) FileList::const_iterator it = fileSet->begin(); - int nX = (*it)->GetXSize(); - int nY = (*it)->GetYSize(); - int pixelSize = (*it)->GetPixelSize(); - + int nX = (*it)->GetXSize(); + int nY = (*it)->GetYSize(); + int pixelSize = (*it)->GetPixelSize(); + bool signedPixelData = (*it)->IsSignedPixelData(); it ++; for ( ; it != fileSet->end(); @@ -321,17 +301,15 @@ bool SerieHelper::IsCoherent(FileList *fileSet) return false; if ( (*it)->GetPixelSize() != pixelSize ) return false; - // probabely more is to be checked (?) + if ( (*it)->IsSignedPixelData() != signedPixelData ) + return false; + // probabely more is to be checked (?) } return true; } #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(); @@ -340,12 +318,7 @@ FileList *SerieHelper::GetFirstCoherentFileList() 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()); @@ -356,12 +329,7 @@ FileList *SerieHelper::GetNextCoherentFileList() return NULL; } -/* * - * \brief accessor (DEPRECATED : use GetSingleSerieUIDFileSet ) - * Warning : 'coherent' means here they have the same Serie UID - * @param SerieUID SerieUID - * \return pointer to the FileList if found, otherwhise NULL - */ + FileList *SerieHelper::GetCoherentFileList(std::string SerieUID) { if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 ) @@ -424,9 +392,9 @@ XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) if (nb == 0 ) return CoherentFileSet; float iop[6]; - std::ostringstream ossOrient; + std::string strOrient; - + std::ostringstream ossOrient; FileList::const_iterator it = fileSet->begin(); it ++; for ( ; @@ -439,6 +407,7 @@ XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) // 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++) { @@ -446,7 +415,9 @@ XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) ossOrient << iop[i]; } strOrient = ossOrient.str(); - + ossOrient.str(""); + // FIXME : is it a 'cleaner' way to initialize an ostringstream? + if ( CoherentFileSet.count(strOrient) == 0 ) { gdcmDebugMacro(" New Orientation :[" << strOrient << "]"); @@ -455,12 +426,12 @@ XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) } // 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 + * \brief Splits a 'Single SerieUID' Fileset according to the Positions * @param fileSet File Set to be splitted * \return std::map of 'Xcoherent' File sets */ @@ -518,7 +489,8 @@ XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) ossPosition << pos[i]; } strPosition = ossPosition.str(); - + ossPosition.str(""); + if ( CoherentFileSet.count(strPosition) == 0 ) { gdcmDebugMacro(" New Position :[" << strPosition << "]"); @@ -532,7 +504,7 @@ XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) } /** - * \brief Splits a SingleSerieUID File set Coherent according to the + * \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 @@ -581,12 +553,14 @@ XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, //----------------------------------------------------------------------------- // Private /** - * \brief sorts the images, according to their Patient Position + * \brief sorts the images, according to their Patient Position. + * * We may order, considering : * -# Image Position Patient * -# Image Number + * -# file name * -# More to come :-) - * WARNING : FileList = std::vector + * \note : FileList = std::vector * @param fileList Coherent File list (same Serie UID) to sort * @return false only if the header is bugged ! */ @@ -595,15 +569,14 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) { //iop is calculated based on the file file float cosines[6]; - float normal[3]; - float ipp[3]; - float dist; - float min = 0, max = 0; + double normal[3]; + double ipp[3]; + double dist; + double min = 0, max = 0; bool first = true; - int n=0; - std::vector distlist; - //!\todo rewrite this for loop. + 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 ) @@ -630,7 +603,7 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) dist += normal[i]*ipp[i]; } - distlist.push_back( dist ); + distmultimap.insert(std::pair(dist, *it)); max = min = dist; first = false; @@ -647,21 +620,13 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) dist += normal[i]*ipp[i]; } - distlist.push_back( dist ); + distmultimap.insert(std::pair(dist, *it)); 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 ) @@ -671,56 +636,50 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) 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; - } - } - + // Check to see if image shares a common position + bool ok = true; + for (std::multimap::iterator it2 = distmultimap.begin(); + it2 != distmultimap.end(); + ++it2) + { + if (distmultimap.count((*it2).first) != 1) + { + gdcmErrorMacro("File: " + << ((*it2).second->GetFileName()) + << " Distance: " + << (*it2).first + << " position is not unique"); + ok = false; + } + } + if (!ok) + { + 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) + for (std::multimap::iterator it3 = distmultimap.begin(); + it3 != distmultimap.end(); + ++it3) { - fileList->push_back( *it3 ); + fileList->push_back( (*it3).second ); } } else // user asked for reverse order { - FileVector::const_iterator it4; - it4 = CoherentFileVector.end(); + std::multimap::const_iterator it4; + it4 = distmultimap.end(); do { it4--; - fileList->push_back( *it4 ); - } while (it4 != CoherentFileVector.begin() ); + fileList->push_back( (*it4).second ); + } while (it4 != distmultimap.begin() ); } - distlist.clear(); - CoherentFileVector.clear(); + distmultimap.clear(); return true; } @@ -740,7 +699,7 @@ bool SerieHelper::ImageNumberGreaterThan(File *file1, File *file2) * \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 + * @param fileList File set (same Serie UID) to sort * @return false if non bona fide stuff encountered */ bool SerieHelper::ImageNumberOrdering(FileList *fileList) @@ -817,6 +776,97 @@ bool SerieHelper::UserOrdering(FileList *fileList) return true; } +std::string SerieHelper::CreateUniqueSeriesIdentifier( File * inFile ) +{ + if( inFile->IsReadable() ) + { + // 0020 000e UI REL Series Instance UID + std::string uid = inFile->GetEntryString (0x0020, 0x000e); + std::string id = uid.c_str(); + if(m_UseSeriesDetails) + { + // If the user requests, additional information can be appended + // to the SeriesUID to further differentiate volumes in the DICOM + // objects being processed. + + // 0020 0011 Series Number + // A scout scan prior to a CT volume scan can share the same + // SeriesUID, but they will sometimes have a different Series Number + std::string sNum = inFile->GetEntryString(0x0020, 0x0011); + if( sNum == gdcm::GDCM_UNFOUND ) + { + sNum = ""; + } + // 0018 0024 Sequence Name + // For T1-map and phase-contrast MRA, the different flip angles and + // directions are only distinguished by the Sequence Name + std::string sName = inFile->GetEntryString(0x0018, 0x0024); + if( sName == gdcm::GDCM_UNFOUND ) + { + sName = ""; + } + // 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. + std::string sThick = inFile->GetEntryString (0x0018, 0x0050); + if( sThick == gdcm::GDCM_UNFOUND ) + { + sThick = ""; + } + // 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. + std::string sRows = inFile->GetEntryString (0x0028, 0x0010); + if( sRows == gdcm::GDCM_UNFOUND ) + { + sRows = ""; + } + // 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. + std::string sColumns = inFile->GetEntryString (0x0028, 0x0011); + if( sColumns == gdcm::GDCM_UNFOUND ) + { + sColumns = ""; + } + + // Concat the new info + std::string num = sNum.c_str(); + num += sName.c_str(); + num += sThick.c_str(); + num += sRows.c_str(); + num += sColumns.c_str(); + + // Append the new info to the SeriesUID + id += "."; + id += num.c_str(); + } + + // Eliminate non-alnum characters, including whitespace... + // that may have been introduced by concats. + for(unsigned int i=0; i= 'a' && id[i] <= 'z') + || (id[i] >= '0' && id[i] <= '9') + || (id[i] >= 'A' && id[i] <= 'Z'))) + { + id.erase(i, 1); + } + } + return id; + } + else // Could not open inFile + { + gdcmWarningMacro("Could not parse series info."); + std::string id = gdcm::GDCM_UNFOUND; + return id; + } +} + + //----------------------------------------------------------------------------- // Print /**