X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmSerieHelper.cxx;h=3761252f910ed4e0294ac29afa763463654249b9;hb=3a0c4256baa5052f854ac46751b93a3e0d0e5f7a;hp=c049e8b45c4807550742db86d83746835c17330b;hpb=04e8ab90af5ff69eb35e51d56177a4d4c487e300;p=gdcm.git diff --git a/src/gdcmSerieHelper.cxx b/src/gdcmSerieHelper.cxx index c049e8b4..3761252f 100644 --- a/src/gdcmSerieHelper.cxx +++ b/src/gdcmSerieHelper.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmSerieHelper.cxx,v $ Language: C++ - Date: $Date: 2005/08/31 16:24:19 $ - Version: $Revision: 1.20 $ + Date: $Date: 2006/01/18 15:25:07 $ + Version: $Revision: 1.42 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -25,7 +25,9 @@ #include #include +#include #include +#include //for sscanf namespace gdcm { @@ -38,23 +40,9 @@ namespace gdcm */ SerieHelper::SerieHelper() { + m_UseSeriesDetails = false; + ClearAll(); 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 (gdcm::FileList::iterator it = l->begin(); - it != l->end(); - ++it) - { - delete *it; // remove entry - } - l->clear(); - delete l; // remove the list - l = GetNextCoherentFileList(); - } DirectOrder = true; } @@ -63,20 +51,29 @@ SerieHelper::SerieHelper() */ SerieHelper::~SerieHelper() { - // For all the Coherent File lists of the gdcm::Serie - FileList *l = GetFirstCoherentFileList(); + ClearAll(); +} + +/** + * \brief Preventively, clear everything at constructor time. + * ( use it at destructor time.) + */ +void SerieHelper::ClearAll() +{ + // For all the 'Single SerieUID' Filesets that may already exist + FileList *l = GetFirstSingleSerieUIDFileSet(); while (l) { - // For all the files of a Coherent File list - for (FileList::iterator it = l->begin(); - it != l->end(); - ++it) + // For all the gdcm::File of a File set + for (gdcm::FileList::iterator it = l->begin(); + it != l->end(); + ++it) { - delete *it; // remove entry + (*it)->Delete(); // remove each entry } l->clear(); - delete l; // remove the list - l = GetNextCoherentFileList(); + delete l; // remove the container + l = GetNextSingleSerieUIDFileSet(); } } @@ -86,13 +83,13 @@ SerieHelper::~SerieHelper() // Public /** - * \brief add a gdcm::File to the list corresponding to its Serie UID + * \brief add a gdcm::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) { // Create a DICOM file - File *header = new File (); + File *header = File::New(); header->SetLoadMode(LoadMode); header->SetFileName( filename ); header->Load(); @@ -100,37 +97,21 @@ void SerieHelper::AddFileName(std::string const &filename) if ( header->IsReadable() ) { int allrules = 1; - // First step the user has defined a set of rules for the DICOM file + // First step : the user defined a set of rules for the DICOM file // he is looking for. - // make sure the file correspond to his set of rules: + // Make sure the file corresponds 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()) ) - { - // 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 ); + s = header->GetEntryString( r.group, r.elem ); if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) ) { - // Argh ! This rule is unmatch let's just quit + // Argh ! This rule is unmatched; let's just quit + allrules = 0; break; } @@ -138,40 +119,44 @@ void SerieHelper::AddFileName(std::string const &filename) if ( allrules ) // all rules are respected: { - // Allright ! we have a found a DICOM that match the user expectation. - // Let's add it ! + // Allright! we have a found a DICOM that matches the user expectation. + // Let's add it! // 0020 000e UI REL Series Instance UID - const std::string &uid = header->GetEntryValue (0x0020, 0x000e); + const std::string &uid = header->GetEntryString(0x0020, 0x000e); // if uid == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND // no need here to do anything special - if ( CoherentFileListHT.count(uid) == 0 ) + + if ( SingleSerieUIDFileSetHT.count(uid) == 0 ) { gdcmDebugMacro(" New Serie UID :[" << uid << "]"); // create a std::list in 'uid' position - CoherentFileListHT[uid] = new FileList; + SingleSerieUIDFileSetHT[uid] = new FileList; } // Current Serie UID and DICOM header seems to match; add the file: - CoherentFileListHT[uid]->push_back( header ); + SingleSerieUIDFileSetHT[uid]->push_back( header ); } else { - // at least one rule was unmatch we need to deallocate the file: - delete header; + // at least one rule was unmatched we need to deallocate the file: + header->Delete(); } } else { gdcmWarningMacro("Could not read file: " << filename ); - delete header; + header->Delete(); } } /** - * \brief add a gdcm::File to the first (and supposed to be unique) list + * \brief add a gdcm::File to the first (and supposed to be unique) file set * of the gdcm::SerieHelper. * \warning : this method should be used by aware users only! + * Passing a gdcm::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 * and consider them they belong to the same Serie * (even if their Serie UID is different) @@ -189,12 +174,12 @@ void SerieHelper::AddGdcmFile(File *header) // 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) + for(SerieRestrictions::iterator it = Restrictions.begin(); + it != Restrictions.end(); + ++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 @@ -211,66 +196,86 @@ void SerieHelper::AddGdcmFile(File *header) // Serie UID of the gdcm::File* may be different. // User is supposed to know what he wants - if ( CoherentFileListHT.count(uid) == 0 ) + if ( SingleSerieUIDFileSetHT.count(uid) == 0 ) { gdcmDebugMacro(" New Serie UID :[" << uid << "]"); // create a std::list in 'uid' position - CoherentFileListHT[uid] = new FileList; + SingleSerieUIDFileSetHT[uid] = new FileList; } // Current Serie UID and DICOM header seems to match; add the file: - CoherentFileListHT[uid]->push_back( header ); + SingleSerieUIDFileSetHT[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 + * \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 */ -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 + * \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 - * @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); + * \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(TagKey const &key, std::string const &value) +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 - * @param recursive whether we want explore recursively the Directory + * @param recursive whether we want explore recursively the root Directory */ void SerieHelper::SetDirectory(std::string const &dir, bool recursive) { @@ -285,30 +290,31 @@ void SerieHelper::SetDirectory(std::string const &dir, bool recursive) } /** - * \brief Sorts the given File List + * \brief Sorts the given Fileset * \warning This could be implemented in a 'Strategy Pattern' approach * But as I don't know how to do it, I leave it this way - * BTW, this is also a Strategy, I don't know this is the best approach :) + * BTW, this is also a Strategy, I don't know this is + * the best approach :) */ -void SerieHelper::OrderFileList(FileList *coherentFileList) +void SerieHelper::OrderFileList(FileList *fileSet) { if ( SerieHelper::UserLessThanFunction ) { - UserOrdering( coherentFileList ); + UserOrdering( fileSet ); return; } - else if ( ImagePositionPatientOrdering( coherentFileList ) ) + else if ( ImagePositionPatientOrdering( fileSet ) ) { return ; } - else if ( ImageNumberOrdering(coherentFileList ) ) + else if ( ImageNumberOrdering(fileSet ) ) { return ; } else { - FileNameOrdering(coherentFileList ); + FileNameOrdering(fileSet ); } } @@ -316,20 +322,20 @@ 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) +bool SerieHelper::IsCoherent(FileList *fileSet) { - if(coherentFileList->size() == 1) + if(fileSet->size() == 1) return true; - FileList::const_iterator it = coherentFileList->begin(); - - int nX = (*it)->GetXSize(); - int nY = (*it)->GetYSize(); - int pixelSize = (*it)->GetPixelSize(); + FileList::const_iterator it = fileSet->begin(); + int nX = (*it)->GetXSize(); + int nY = (*it)->GetYSize(); + int pixelSize = (*it)->GetPixelSize(); + bool signedPixelData = (*it)->IsSignedPixelData(); it ++; for ( ; - it != coherentFileList->end(); + it != fileSet->end(); ++it) { if ( (*it)->GetXSize() != nX ) @@ -338,47 +344,250 @@ bool SerieHelper::IsCoherent(FileList *coherentFileList) 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 + +FileList *SerieHelper::GetFirstCoherentFileList() +{ + ItFileSetHt = SingleSerieUIDFileSetHT.begin(); + if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() ) + return ItFileSetHt->second; + return NULL; +} + + +FileList *SerieHelper::GetNextCoherentFileList() +{ + gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end()); + + ++ItFileSetHt; + if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() ) + return ItFileSetHt->second; + return NULL; +} + + +FileList *SerieHelper::GetCoherentFileList(std::string SerieUID) +{ + if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 ) + return 0; + return SingleSerieUIDFileSetHT[SerieUID]; +} +#endif + + /** - * \brief Get the first List while visiting the CoherentFileListHT - * @return The first FileList if found, otherwhise NULL + * \brief Get the first Fileset while visiting the SingleSerieUIDFileSetmap + * @return The first FileList (SingleSerieUIDFileSet) if found, otherwhise 0 */ -FileList *SerieHelper::GetFirstCoherentFileList() +FileList *SerieHelper::GetFirstSingleSerieUIDFileSet() { - ItListHt = CoherentFileListHT.begin(); - if ( ItListHt != CoherentFileListHT.end() ) - return ItListHt->second; + ItFileSetHt = SingleSerieUIDFileSetHT.begin(); + if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() ) + return ItFileSetHt->second; return NULL; } /** - * \brief Get the next List while visiting the CoherentFileListHT - * \note : meaningfull only if GetFirstCoherentFileList() already called - * @return The next FileList if found, otherwhise NULL + * \brief Get the next Fileset while visiting the SingleSerieUIDFileSetmap + * \note : meaningfull only if GetNextSingleSerieUIDFileSet() already called + * @return The next FileList (SingleSerieUIDFileSet) if found, otherwhise 0 */ -FileList *SerieHelper::GetNextCoherentFileList() +FileList *SerieHelper::GetNextSingleSerieUIDFileSet() { - gdcmAssertMacro (ItListHt != CoherentFileListHT.end()); + gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end()); - ++ItListHt; - if ( ItListHt != CoherentFileListHT.end() ) - return ItListHt->second; + ++ItFileSetHt; + if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() ) + return ItFileSetHt->second; return NULL; } /** - * \brief Get the Coherent Files list according to its Serie UID - * @param SerieUID SerieUID - * \return pointer to the Coherent Files list if found, otherwhise NULL + * \brief Get the SingleSerieUIDFileSet according to its Serie UID + * @param SerieUID SerieUID to retrieve + * \return pointer to the FileList (SingleSerieUIDFileSet) if found, otherwhise 0 */ -FileList *SerieHelper::GetCoherentFileList(std::string SerieUID) +FileList *SerieHelper::GetSingleSerieUIDFileSet(std::string SerieUID) { - if ( CoherentFileListHT.count(SerieUID) == 0 ) + if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 ) return 0; - return CoherentFileListHT[SerieUID]; + return SingleSerieUIDFileSetHT[SerieUID]; +} + +/** + * \brief Splits a Single SerieUID Fileset according to the Orientations + * @param fileSet File Set to be splitted + * \return std::map of 'Xcoherent' File sets + */ + +XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) +{ + XCoherentFileSetmap CoherentFileSet; + + int nb = fileSet->size(); + if (nb == 0 ) + return CoherentFileSet; + float iop[6]; + + std::string strOrient; + std::ostringstream ossOrient; + FileList::const_iterator it = fileSet->begin(); + it ++; + for ( ; + it != fileSet->end(); + ++it) + { + // Information is in : + // 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 + (*it)->GetImageOrientationPatient(iop); + + ossOrient << iop[0]; + for (int i = 1; i < 6; i++) + { + ossOrient << "\\"; + 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 << "]"); + // create a File set in 'orientation' position + CoherentFileSet[strOrient] = new FileList; + } + // 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 + * @param fileSet File Set to be splitted + * \return std::map of 'Xcoherent' File sets + */ + +XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) +{ + XCoherentFileSetmap CoherentFileSet; + + int nb = fileSet->size(); + if (nb == 0 ) + 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) + { + // Information is in : + // 0020,0032 : Image Position Patient + // 0020,0030 : Image Position (RET) + + strImPos = (*it)->GetEntryString(0x0020,0x0032); + if ( strImPos == GDCM_UNFOUND) + { + gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); + strImPos = (*it)->GetEntryString(0x0020,0x0030); // For ACR-NEMA images + if ( strImPos == GDCM_UNFOUND ) + { + gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); + // User wants to split on the 'Position' + // No 'Position' info found. + // We return an empty Htable ! + return CoherentFileSet; + } + } + + if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ", + &pos[0], &pos[1], &pos[2]) != 3 ) + { + gdcmWarningMacro( "Wrong number for Position : [" + << strImPos << "]" ); + return CoherentFileSet; + } + + // Let's build again the 'position' string, to be sure of it's format + + ossPosition << pos[0]; + for (int i = 1; i < 3; i++) + { + ossPosition << "\\"; + ossPosition << pos[i]; + } + strPosition = ossPosition.str(); + ossPosition.str(""); + + if ( CoherentFileSet.count(strPosition) == 0 ) + { + gdcmDebugMacro(" New Position :[" << strPosition << "]"); + // create a File set in 'position' position + CoherentFileSet[strPosition] = new FileList; + } + // Current Position and DICOM header match; add the file: + CoherentFileSet[strPosition]->push_back( (*it) ); + } + return CoherentFileSet; +} + +/** + * \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 + * @param elem element number of the target Element + * \return std::map of 'Xcoherent' File sets + */ + +XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, + uint16_t group, uint16_t elem) +{ + XCoherentFileSetmap CoherentFileSet; + + int nb = fileSet->size(); + if (nb == 0 ) + return CoherentFileSet; + + std::string strTagValue; // read on disc + + FileList::const_iterator it = fileSet->begin(); + it ++; + for ( ; + it != fileSet->end(); + ++it) + { + // Information is in : + // 0020,0032 : Image Position Patient + // 0020,0030 : Image Position (RET) + + strTagValue = (*it)->GetEntryString(group,elem); + + if ( CoherentFileSet.count(strTagValue) == 0 ) + { + gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]"); + // create a File set in 'position' position + CoherentFileSet[strTagValue] = new FileList; + } + // Current Tag value and DICOM header match; add the file: + CoherentFileSet[strTagValue]->push_back( (*it) ); + } + return CoherentFileSet; } //----------------------------------------------------------------------------- @@ -387,12 +596,14 @@ FileList *SerieHelper::GetCoherentFileList(std::string SerieUID) //----------------------------------------------------------------------------- // 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 ! */ @@ -401,15 +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 ) @@ -420,8 +630,8 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) // You only have to do this once for all slices in the volume. Next, // for each slice, calculate the distance along the slice normal - // using the IPP tag ("dist" is initialized to zero before reading - // the first slice) : + // using the IPP ("Image Position Patient") tag. + // ("dist" is initialized to zero before reading the first slice) : normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4]; normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5]; normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3]; @@ -436,7 +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; @@ -453,79 +663,66 @@ 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 ) - { - gdcmWarningMacro( "Looks like all images have the exact same image position." - << "No PositionPatientOrdering sort performed" ); - 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; - } + gdcmWarningMacro("Looks like all images have the exact same image 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; } @@ -539,12 +736,13 @@ 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 + * @param fileList File set (same Serie UID) to sort * @return false if non bona fide stuff encountered */ bool SerieHelper::ImageNumberOrdering(FileList *fileList) @@ -565,13 +763,18 @@ bool SerieHelper::ImageNumberOrdering(FileList *fileList) // Find out if image numbers are coherent (consecutive) if ( min == max || max == 0 || max >= (n+min) ) { - gdcmWarningMacro( " 'Image numbers' not coherent. No ImageNumberOrdering sort performed."); + gdcmWarningMacro( " 'Image numbers' not coherent. " + << " No ImageNumberOrdering sort performed."); return false; } if (DirectOrder) - std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberLessThan ); + Sort(fileList,SerieHelper::ImageNumberLessThan); +// std::sort(fileList->begin(), fileList->end(), +// SerieHelper::ImageNumberLessThan ); else - std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberGreaterThan ); + Sort(fileList,SerieHelper::ImageNumberGreaterThan); +// std::sort(fileList->begin(), fileList->end(), +// SerieHelper::ImageNumberGreaterThan ); return true; } @@ -593,9 +796,13 @@ bool SerieHelper::FileNameGreaterThan(File *file1, File *file2) bool SerieHelper::FileNameOrdering(FileList *fileList) { if (DirectOrder) - std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameLessThan); + Sort(fileList,SerieHelper::FileNameLessThan); +// std::sort(fileList->begin(), fileList->end(), +// SerieHelper::FileNameLessThan); else - std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameGreaterThan); + Sort(fileList,SerieHelper::FileNameGreaterThan); +// std::sort(fileList->begin(), fileList->end(), +// SerieHelper::FileNameGreaterThan); return true; } @@ -607,7 +814,9 @@ bool SerieHelper::FileNameOrdering(FileList *fileList) */ bool SerieHelper::UserOrdering(FileList *fileList) { - std::sort(fileList->begin(), fileList->end(), SerieHelper::UserLessThanFunction); + Sort(fileList,SerieHelper::UserLessThanFunction); +// std::sort(fileList->begin(), fileList->end(), +// SerieHelper::UserLessThanFunction); if (!DirectOrder) { std::reverse(fileList->begin(), fileList->end()); @@ -615,6 +824,184 @@ 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 /** @@ -623,17 +1010,17 @@ 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 - CoherentFileListmap::iterator itl = CoherentFileListHT.begin(); - if ( itl == CoherentFileListHT.end() ) + SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin(); + if ( itl == SingleSerieUIDFileSetHT.end() ) { - gdcmWarningMacro( "No Coherent File list found" ); + gdcmWarningMacro( "No SingleSerieUID File set found" ); return; } - while (itl != CoherentFileListHT.end()) + while (itl != SingleSerieUIDFileSetHT.end()) { os << "Serie UID :[" << itl->first << "]" << std::endl; - // For all the files of a Coherent File list + // For all the files of a SingleSerieUID File set for (FileList::iterator it = (itl->second)->begin(); it != (itl->second)->end(); ++it) @@ -644,5 +1031,15 @@ void SerieHelper::Print(std::ostream &os, std::string const &indent) } } +//----------------------------------------------------------------------------- +// Sort +/** + * \brief Sort FileList. + */ +void SerieHelper::Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) ) +{ + std::sort(fileList->begin(), fileList->end(), pt2Func ); +} + //----------------------------------------------------------------------------- } // end namespace gdcm