X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmSerieHelper.cxx;h=164023edab87c904f38b428e9a473265ff8b8bbd;hb=6ea13c737fda10fabd9923ab62837c5148176df1;hp=23e60112f8a1c034b658593be36d4c05d34d7194;hpb=e2b53c6ca71e08414aaab01dac851c36a6530903;p=gdcm.git diff --git a/src/gdcmSerieHelper.cxx b/src/gdcmSerieHelper.cxx index 23e60112..164023ed 100644 --- a/src/gdcmSerieHelper.cxx +++ b/src/gdcmSerieHelper.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmSerieHelper.cxx,v $ Language: C++ - Date: $Date: 2005/11/08 16:31:21 $ - Version: $Revision: 1.34 $ + Date: $Date: 2005/12/21 14:48:09 $ + Version: $Revision: 1.41 $ 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; @@ -178,7 +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 @@ -208,13 +209,14 @@ void SerieHelper::AddGdcmFile(File *header) } /** - * \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 + * \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 * 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. + * \todo find a trick to allow user to say if he wants the Rectrictions + * to be *ored* (and not only *anded*) + * @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 */ @@ -229,16 +231,47 @@ void SerieHelper::AddRestriction(TagKey const &key, ExRestrictions.push_back( r ); } -#ifndef GDCM_LEGACY_REMOVE -void SerieHelper::AddRestriction(TagKey const &key, std::string const &value) +/** + * \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 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 + * \todo find a trick to allow user if he wants the Rectrictions to be *ored* + * (and not only *anded*) + * @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 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, + std::string const &value, int op) { - Rule r; - r.first = key; - r.second = value; - Restrictions.push_back( r ); + ExRule r; + r.group = group; + r.elem = elem; + r.value = value; + r.op = op; + ExRestrictions.push_back( r ); } -#endif +/** + * \brief add an extra 'SerieDetail' for building a 'Serie Identifier' + * that ensures (hope so) File constistency (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; + d.convert = convert; + ExDetails.push_back( d ); +} /** * \brief Sets the root Directory * @param dir Name of the directory to deal with @@ -563,11 +596,12 @@ 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 + * -# file name * -# More to come :-) * \note : FileList = std::vector * @param fileList Coherent File list (same Serie UID) to sort @@ -578,15 +612,14 @@ 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 ) @@ -613,7 +646,7 @@ 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; @@ -630,21 +663,13 @@ 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 ) @@ -654,56 +679,50 @@ 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; } @@ -792,7 +811,7 @@ bool SerieHelper::FileNameOrdering(FileList *fileList) bool SerieHelper::UserOrdering(FileList *fileList) { std::sort(fileList->begin(), fileList->end(), - SerieHelper::UserLessThanFunction); + SerieHelper::UserLessThanFunction); if (!DirectOrder) { std::reverse(fileList->begin(), fileList->end()); @@ -800,6 +819,184 @@ bool SerieHelper::UserOrdering(FileList *fileList) return true; } +/** + * \brief Heuristics to *try* to build a Serie Identifier that would ensure + * all the images are coherent. + * + * By default, uses the SeriesUID. If UseSeriesDetails(true) has been called, + * 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 + * 0018|1312 [In-plane Phase Encoding Direction] value : ROW/COLUMN + * @param inFile gdcm::File we want to build a Serie Identifier for. + * @return the SeriesIdentifier + */ +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 = ""; + } + + // You can think on checking Image Orientation (0020,0037), as well. + + + // 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(); + + // Add a loop, here, to deal with any extra user supplied tag. + // We allow user to add his own critierions + // (he knows more than we do about his images!) + // ex : in tagging series, the only pertinent tag is + // 0018|1312 [In-plane Phase Encoding Direction] values : ROW/COLUMN + + std::string s; + for(SeriesExDetails::iterator it2 = ExDetails.begin(); + it2 != ExDetails.end(); + ++it2) + { + const ExDetail &r = *it2; + s = inFile->GetEntryString( r.group, r.elem ); + num += s.c_str(); + } + + // Append the new info to the SeriesUID + id += "."; + id += num.c_str(); + } + + // Eliminate non-alphanum 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; + } +} + +/** + * \brief Allow user to build is own File Identifier (to be able to sort + * temporal series just as he wants) + * Criterions will be set with AddSeriesDetail. + * (Maybe the method should be moved elsewhere + * -File class? FileHelper class?- + * @return FileIdentifier (Tokenizable on '_') + */ +std::string SerieHelper::CreateUserDefinedFileIdentifier( File * inFile ) +{ + // Deal with all user supplied tags. + // (user knows more than we do about his images!) + + float converted; + std::string id; + std::string s; + char charConverted[17]; + + for(SeriesExDetails::iterator it2 = ExDetails.begin(); + it2 != ExDetails.end(); + ++it2) + { + const ExDetail &r = *it2; + s = inFile->GetEntryString( r.group, r.elem ); + + // User is allowed to ask 'convertion', to allow further ordering + // e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK + if (it2->convert) + { + converted = atof(s.c_str()); + // probabely something much more complicated is possible, + // using C++ features + /// \todo check the behaviour when there are >0 and <0 numbers + sprintf(charConverted, "%016.6f",converted); + s = charConverted; + } + // 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'))) + { + s.erase(i, 1); + } + } + + id += s.c_str(); + id += "_"; // make the FileIdentifier Tokenizable + } + + return id; +} //----------------------------------------------------------------------------- // Print /**