X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmSerieHelper.cxx;h=1c18682fc4cced98ed046e8633db7705f434bdb7;hb=02e5b298070faff881e584dd818d85bfc05e92bf;hp=893cc48ec86aa8d80841d3f4865a134e3cd8b4f2;hpb=6cf34d5df01e8ec0572bcef6c6b91be58212ef77;p=gdcm.git diff --git a/src/gdcmSerieHelper.cxx b/src/gdcmSerieHelper.cxx index 893cc48e..1c18682f 100644 --- a/src/gdcmSerieHelper.cxx +++ b/src/gdcmSerieHelper.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmSerieHelper.cxx,v $ Language: C++ - Date: $Date: 2005/06/03 16:08:16 $ - Version: $Revision: 1.9 $ + Date: $Date: 2005/08/30 08:12:40 $ + Version: $Revision: 1.18 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -19,6 +19,7 @@ #include "gdcmSerieHelper.h" #include "gdcmDirList.h" #include "gdcmFile.h" +#include "gdcmDictEntry.h" // for TranslateToKey #include "gdcmDebug.h" #include "gdcmUtil.h" @@ -36,21 +37,24 @@ namespace gdcm */ SerieHelper::SerieHelper() { - // For all the File lists of the gdcm::Serie + UserLessThanFunction = 0; + + // For all the File lists that may already exist within the gdcm::Serie FileList *l = GetFirstCoherentFileList(); while (l) { // For all the files of a File list - for (FileList::iterator it = l->begin(); + for (gdcm::FileList::iterator it = l->begin(); it != l->end(); ++it) { - delete *it; + delete *it; // remove entry } l->clear(); - delete l;; + delete l; // remove the list l = GetNextCoherentFileList(); } + DirectOrder = true; } /** @@ -67,10 +71,10 @@ SerieHelper::~SerieHelper() it != l->end(); ++it) { - delete *it; + delete *it; // remove entry } l->clear(); - delete l; + delete l; // remove the list l = GetNextCoherentFileList(); } } @@ -87,28 +91,53 @@ SerieHelper::~SerieHelper() void SerieHelper::AddFileName(std::string const &filename) { // Create a DICOM file - File *header = new File( filename ); - if( header->IsReadable() ) + File *header = new File (); + header->SetLoadMode(LoadMode); + header->SetFileName( filename ); + header->Load(); + + if ( header->IsReadable() ) { int allrules = 1; - // First step the user has defined s set of rules for the DICOM he is looking for + // First step the user has defined a set of rules for the DICOM file + // he is looking for. // make sure the file correspond to his set of rules: + +/* for(SerieRestrictions::iterator it = Restrictions.begin(); it != Restrictions.end(); ++it) { const Rule &r = *it; + // doesn't compile (no matching function...). const std::string s;// = header->GetEntryValue( r.first ); - if( !Util::DicomStringEqual(s, r.second.c_str())) + if ( !Util::DicomStringEqual(s, r.second.c_str()) ) + { + // Argh ! This rule is unmatch let's just quit + allrules = 0; + break; + } + } +*/ + // Just keep 'new style' for Rules + std::string s; + for(SerieExRestrictions::iterator it2 = ExRestrictions.begin(); + it2 != ExRestrictions.end(); + ++it2) + { + const ExRule &r = *it2; + s = header->GetEntryValue( r.group, r.elem ); + if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) ) { // Argh ! This rule is unmatch let's just quit allrules = 0; break; } } - if( allrules ) // all rules are respected: + + if ( allrules ) // all rules are respected: { - // Alright ! we have a found a DICOM that match the user expectation. + // Allright ! we have a found a DICOM that match the user expectation. // Let's add it ! // 0020 000e UI REL Series Instance UID @@ -122,7 +151,7 @@ void SerieHelper::AddFileName(std::string const &filename) // create a std::list in 'uid' position CoherentFileListHT[uid] = new FileList; } - // Current Serie UID and DICOM header seems to match add the file: + // Current Serie UID and DICOM header seems to match; add the file: CoherentFileListHT[uid]->push_back( header ); } else @@ -137,12 +166,89 @@ void SerieHelper::AddFileName(std::string const &filename) delete header; } } + +/** + * \brief add a gdcm::File to the first (and supposed to be unique) list + * of the gdcm::SerieHelper. + * \warning : this method should be used by aware users only! + * User is supposed to know the files he want to deal with + * and consider them they belong to the same Serie + * (even if their Serie UID is different) + * user will probabely OrderFileList() this list (actually, ordering + * user choosen gdm::File is the sole interest of this method) + * Moreover, using vtkGdcmReader::SetCoherentFileList() will avoid + * 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 + */ +void SerieHelper::AddGdcmFile(File *header) +{ + int allrules = 1; + // First step the user has defined a set of rules for the DICOM + // he is looking for. + // make sure the file correspond to his set of rules: + for(SerieRestrictions::iterator it = Restrictions.begin(); + it != Restrictions.end(); + ++it) + { + const Rule &r = *it; + const std::string s;// = header->GetEntryValue( r.first ); + if ( !Util::DicomStringEqual(s, r.second.c_str()) ) + { + // Argh ! This rule is unmatch let's just quit + allrules = 0; + break; + } + } + if ( allrules ) // all rules are respected: + { + // Allright ! we have a found a DICOM that match the user expectation. + // Let's add it ! + + const std::string &uid = "0"; + // Serie UID of the gdcm::File* may be different. + // User is supposed to know what he wants + + if ( CoherentFileListHT.count(uid) == 0 ) + { + gdcmDebugMacro(" New Serie UID :[" << uid << "]"); + // create a std::list in 'uid' position + CoherentFileListHT[uid] = new FileList; + } + // Current Serie UID and DICOM header seems to match; add the file: + CoherentFileListHT[uid]->push_back( header ); + } + // Even if a rule was unmatch we don't deallocate the gdcm::File: +} + +/** + * \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 + */ +void SerieHelper::AddRestriction(uint16_t group, uint16_t elem, + std::string const &value, int op) +{ + ExRule r; + r.group = group; + r.elem = elem; + 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 + * @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) { @@ -151,6 +257,7 @@ void SerieHelper::AddRestriction(TagKey const &key, std::string const &value) r.second = value; Restrictions.push_back( r ); } +#endif /** * \brief Sets the root Directory @@ -177,11 +284,17 @@ void SerieHelper::SetDirectory(std::string const &dir, bool recursive) */ void SerieHelper::OrderFileList(FileList *coherentFileList) { - if( ImagePositionPatientOrdering( coherentFileList ) ) + + if ( SerieHelper::UserLessThanFunction ) + { + UserOrdering( coherentFileList ); + return; + } + else if ( ImagePositionPatientOrdering( coherentFileList ) ) { return ; } - else if( ImageNumberOrdering(coherentFileList ) ) + else if ( ImageNumberOrdering(coherentFileList ) ) { return ; } @@ -191,6 +304,36 @@ void SerieHelper::OrderFileList(FileList *coherentFileList) } } +/** + * \brief Elementary coherence checking of the files with the same Serie UID + * Only sizes and pixel type are checked right now ... + */ +bool SerieHelper::IsCoherent(FileList *coherentFileList) +{ + if(coherentFileList->size() == 1) + return true; + + FileList::const_iterator it = coherentFileList->begin(); + + int nX = (*it)->GetXSize(); + int nY = (*it)->GetYSize(); + int pixelSize = (*it)->GetPixelSize(); + + it ++; + for ( ; + it != coherentFileList->end(); + ++it) + { + if ( (*it)->GetXSize() != nX ) + return false; + if ( (*it)->GetYSize() != nY ) + return false; + if ( (*it)->GetPixelSize() != pixelSize ) + return false; + // probabely more is to be checked (?) + } + return true; +} /** * \brief Get the first List while visiting the CoherentFileListHT * @return The first FileList if found, otherwhise NULL @@ -198,14 +341,14 @@ void SerieHelper::OrderFileList(FileList *coherentFileList) FileList *SerieHelper::GetFirstCoherentFileList() { ItListHt = CoherentFileListHT.begin(); - if( ItListHt != CoherentFileListHT.end() ) + if ( ItListHt != CoherentFileListHT.end() ) return ItListHt->second; return NULL; } /** * \brief Get the next List while visiting the CoherentFileListHT - * \note : meaningfull only if GetFirstCoherentFileList already called + * \note : meaningfull only if GetFirstCoherentFileList() already called * @return The next FileList if found, otherwhise NULL */ FileList *SerieHelper::GetNextCoherentFileList() @@ -246,7 +389,7 @@ FileList *SerieHelper::GetCoherentFileList(std::string SerieUID) * @return false only if the header is bugged ! */ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) -//based on Jolinda's algorithm +//based on Jolinda Smith's algorithm { //iop is calculated based on the file file float cosines[6]; @@ -263,7 +406,7 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) it = fileList->begin(); it != fileList->end(); ++it ) { - if( first ) + if ( first ) { (*it)->GetImageOrientationPatient( cosines ); @@ -319,9 +462,10 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) // gdcmAssertMacro( CoherentFileVector.capacity() >= n ); // Find out if min/max are coherent - if( min == max ) + if ( min == max ) { - gdcmWarningMacro( "Looks like all images have the exact same image position..."); + gdcmWarningMacro( "Looks like all images have the exact same image position." + << "No PositionPatientOrdering sort performed" ); return false; } @@ -345,19 +489,32 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) CoherentFileVector[pos] = *it2; else { - gdcmWarningMacro( "2 files same position"); + gdcmWarningMacro( "At least 2 files with same position. No PositionPatientOrdering sort performed"); return false; } } - fileList->clear(); // doesn't delete list elements, only node - - //VC++ don't understand what scope is !! it -> it3 - for (FileVector::const_iterator it3 = CoherentFileVector.begin(); - it3 != CoherentFileVector.end(); ++it3) - { - fileList->push_back( *it3 ); + 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) + { + fileList->push_back( *it3 ); + } } + else // user asked for reverse order + { + FileVector::const_iterator it4; + it4 = CoherentFileVector.end(); + do + { + it4--; + fileList->push_back( *it4 ); + } while (it4 != CoherentFileVector.begin() ); + } distlist.clear(); CoherentFileVector.clear(); @@ -370,13 +527,17 @@ bool SerieHelper::ImageNumberLessThan(File *file1, File *file2) return file1->GetImageNumber() < file2->GetImageNumber(); } +bool SerieHelper::ImageNumberGreaterThan(File *file1, File *file2) +{ + return file1->GetImageNumber() > file2->GetImageNumber(); +} /** * \brief sorts the images, according to their Image Number * \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 - * @return false if non nona fide stuff encountered + * @return false if non bona fide stuff encountered */ bool SerieHelper::ImageNumberOrdering(FileList *fileList) { @@ -394,10 +555,15 @@ bool SerieHelper::ImageNumberOrdering(FileList *fileList) } // Find out if image numbers are coherent (consecutive) - if( min == max || max == 0 || max >= (n+min)) + if ( min == max || max == 0 || max >= (n+min) ) + { + gdcmWarningMacro( " 'Image numbers' not coherent. No ImageNumberOrdering sort performed."); return false; - - std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberLessThan ); + } + if (DirectOrder) + std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberLessThan ); + else + std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberGreaterThan ); return true; } @@ -407,6 +573,10 @@ bool SerieHelper::FileNameLessThan(File *file1, File *file2) return file1->GetFileName() < file2->GetFileName(); } +bool SerieHelper::FileNameGreaterThan(File *file1, File *file2) +{ + return file1->GetFileName() > file2->GetFileName(); +} /** * \brief sorts the images, according to their File Name * @param fileList Coherent File list (same Serie UID) to sort @@ -414,10 +584,29 @@ bool SerieHelper::FileNameLessThan(File *file1, File *file2) */ bool SerieHelper::FileNameOrdering(FileList *fileList) { - std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameLessThan); + if (DirectOrder) + std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameLessThan); + else + std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameGreaterThan); + return true; } +/** + * \brief sorts the images, according to user supplied function + * \note Only Direct ordering is allowed + * @param fileList Coherent File list (same Serie UID) to sort + * @return false only if the header is bugged ! + */ +bool SerieHelper::UserOrdering(FileList *fileList) +{ + if (DirectOrder) + std::sort(fileList->begin(), fileList->end(), SerieHelper::UserLessThanFunction); + else + gdcmWarningMacro( " Only Direct ordering allowed " + << "when user function is supplied"); + return true; +} //----------------------------------------------------------------------------- // Print /**