X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmSerieHelper.cxx;h=fc0f2135b7838d77fcb177c1638a773b077998e0;hb=fc4f7706c78baf3f60474c06d871b82db221f37b;hp=f0dcdca3366dad1813b5ed90a56903ad257ceb7a;hpb=95e43356511d138225d8f718f632b3e7a8fcc106;p=gdcm.git diff --git a/src/gdcmSerieHelper.cxx b/src/gdcmSerieHelper.cxx index f0dcdca3..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: 2005/02/05 01:37:09 $ - Version: $Revision: 1.4 $ + 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 @@ -19,13 +19,17 @@ #include "gdcmSerieHelper.h" #include "gdcmDirList.h" #include "gdcmFile.h" +//#include "gdcmDictEntry.h" // for TranslateToKey : no more ! #include "gdcmDebug.h" +#include "gdcmUtil.h" #include #include #include +#include +#include //for sscanf -namespace gdcm +namespace GDCM_NAME_SPACE { //----------------------------------------------------------------------------- @@ -35,21 +39,11 @@ namespace gdcm */ SerieHelper::SerieHelper() { - // For all the File lists of the gdcm::Serie - GdcmFileList *l = GetFirstCoherentFileList(); - while (l) - { - // For all the files of a File list - for (GdcmFileList::iterator it = l->begin(); - it != l->end(); - ++it) - { - delete *it; - } - l->clear(); - delete l;; - l = GetNextCoherentFileList(); - } + m_UseSeriesDetails = false; + ClearAll(); + UserLessThanFunction = 0; + DirectOrder = true; + DropDuplicatePositions = false; } /** @@ -57,21 +51,32 @@ SerieHelper::SerieHelper() */ SerieHelper::~SerieHelper() { - // For all the Coherent File lists of the gdcm::Serie - GdcmFileList *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 (GdcmFileList::iterator it = l->begin(); - it != l->end(); - ++it) + // For all the GDCM_NAME_SPACE::File of a File set + for (GDCM_NAME_SPACE::FileList::iterator it = l->begin(); + it != l->end(); + ++it) { - delete *it; + (*it)->Delete(); // remove each entry } l->clear(); - delete l; - l = GetNextCoherentFileList(); + delete l; // remove the container + l = GetNextSingleSerieUIDFileSet(); } + // Need to clear that too: + SingleSerieUIDFileSetHT.clear(); } //----------------------------------------------------------------------------- @@ -80,44 +85,198 @@ SerieHelper::~SerieHelper() // Public /** - * \brief add a gdcm::File to the list 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) { - //directly use string and not const char*: - File *header = new File( filename ); - if( header->IsReadable() ) + // Create a DICOM file + File *header = File::New(); + header->SetLoadMode(LoadMode); + header->SetFileName( filename ); + header->Load(); + + if ( header->IsReadable() ) + { + if ( !AddFile( header ) ) + { + // at least one rule was unmatched we need to deallocate the file: + header->Delete(); + } + } + else + { + gdcmWarningMacro("Could not read file: " << filename ); + header->Delete(); + } +} + +/** + * \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_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 + * 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_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) +{ + 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: + + std::string s; + for(SerieExRestrictions::iterator it2 = ExRestrictions.begin(); + it2 != ExRestrictions.end(); + ++it2) + { + const ExRule &r = *it2; + s = header->GetEntryString( r.group, r.elem ); + if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) ) + { + // Argh ! This rule is unmatched; let's just quit + allrules = 0; + break; + } + } + + if ( allrules ) // all rules are respected: { - // 0020 000e UI REL Series Instance UID - std::string uid = header->GetEntryValue (0x0020, 0x000e); - // if uid == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND + // Allright! we have a found a DICOM that matches the user expectation. + // Let's add it to the specific 'id' which by default is uid (Serie UID) + // but can be `refined` by user with more paramater (see AddRestriction(g,e)) + + std::string id = CreateUniqueSeriesIdentifier( header ); + // if id == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND // no need here to do anything special - if ( CoherentGdcmFileListHT.count(uid) == 0 ) + if ( SingleSerieUIDFileSetHT.count(id) == 0 ) { - gdcmWarningMacro(" New Serie UID :[" << uid << "]"); - // create a std::list in 'uid' position - CoherentGdcmFileListHT[uid] = new GdcmFileList; + gdcmDebugMacro(" New/gdcmSerieHelper.cxx Serie UID :[" << id << "]"); + // create a std::list in 'id' position + SingleSerieUIDFileSetHT[id] = new FileList; } // Current Serie UID and DICOM header seems to match add the file: - CoherentGdcmFileListHT[uid]->push_back( header ); + SingleSerieUIDFileSetHT[id]->push_back( header ); } else { - gdcmWarningMacro("Could not read file: " << filename ); - delete header; + // one rule not matched, tell user: + return false; } + return true; +} + +/** + * \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 + * \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(TagKey const &key, + std::string const &value, int op) +{ + ExRule r; + r.group = key[0]; + r.elem = key[1]; + r.value = value; + r.op = op; + ExRestrictions.push_back( r ); +} + +void SerieHelper::AddRestriction(TagKey const &key) +{ + ExRule r; + r.group = key[0]; + r.elem = key[1]; + ExRefine.push_back( r ); +} + +//#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 + * 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 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 + * @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 + +/** + * \brief add an extra 'SerieDetail' for building a 'Serie Identifier' + * 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; + 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) { 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(); @@ -128,64 +287,335 @@ 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::OrderGdcmFileList(GdcmFileList *CoherentGdcmFileList) +void SerieHelper::OrderFileList(FileList *fileSet) { - if( ImagePositionPatientOrdering( CoherentGdcmFileList ) ) + // 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(CoherentGdcmFileList ) ) + else if ( ImageNumberOrdering(fileSet ) ) { + gdcmDebugMacro("ImageNumberOrdering succeeded"); return ; } else { - FileNameOrdering(CoherentGdcmFileList ); + gdcmDebugMacro("Use FileNameOrdering"); + FileNameOrdering(fileSet ); + } +} + +/** + * \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 *fileSet) +{ + if(fileSet->size() == 1) + return true; + + 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 != fileSet->end(); + ++it) + { + if ( (*it)->GetXSize() != nX ) + return false; + if ( (*it)->GetYSize() != nY ) + return false; + if ( (*it)->GetPixelSize() != pixelSize ) + return false; + if ( (*it)->IsSignedPixelData() != signedPixelData ) + return false; + // probabely more is to be checked (?) } + return true; } +//#ifndef GDCM_LEGACY_REMOVE /** - * \brief Get the first List while visiting the CoherentFileListHT - * @return The first GdcmFileList if found, otherwhise NULL + * \brief accessor (DEPRECATED : use GetFirstSingleSerieUIDFileSet ) + * Warning : 'coherent' means here they have the same Serie UID + * @return The first FileList if found, otherwhise NULL */ -GdcmFileList *SerieHelper::GetFirstCoherentFileList() + /* +FileList *SerieHelper::GetFirstCoherentFileList() { - ItListHt = CoherentGdcmFileListHT.begin(); - if( ItListHt != CoherentGdcmFileListHT.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 GdcmFileList if found, otherwhise 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 */ -GdcmFileList *SerieHelper::GetNextCoherentFileList() + /* +FileList *SerieHelper::GetNextCoherentFileList() { - gdcmAssertMacro (ItListHt != CoherentGdcmFileListHT.end()); + gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end()); - ++ItListHt; - if ( ItListHt != CoherentGdcmFileListHT.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 + * \brief accessor (DEPRECATED : use GetSingleSerieUIDFileSet ) + * Warning : 'coherent' means here they have the same Serie UID * @param SerieUID SerieUID - * \return pointer to the Coherent Filseslist if found, otherwhise NULL + * \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 + + +/** + * \brief Get the first Fileset while visiting the SingleSerieUIDFileSetmap + * @return The first FileList (SingleSerieUIDFileSet) if found, otherwhise 0 + */ +FileList *SerieHelper::GetFirstSingleSerieUIDFileSet() +{ + ItFileSetHt = SingleSerieUIDFileSetHT.begin(); + if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() ) + return ItFileSetHt->second; + return 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::GetNextSingleSerieUIDFileSet() +{ + gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end()); + + ++ItFileSetHt; + if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() ) + return ItFileSetHt->second; + return 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 */ -GdcmFileList *SerieHelper::GetCoherentFileList(std::string SerieUID) +FileList *SerieHelper::GetSingleSerieUIDFileSet(std::string SerieUID) { - if ( CoherentGdcmFileListHT.count(SerieUID) == 0 ) + if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 ) return 0; - return CoherentGdcmFileListHT[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 ) { + gdcmWarningMacro("Empty FileList passed to SplitOnOrientation"); + return CoherentFileSet; + } + + float iop[6]; + std::string strOrient; + std::ostringstream ossOrient; + + FileList::const_iterator it = fileSet->begin(); + 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 its format + (*it)->GetImageOrientationPatient(iop); + + ossOrient << iop[0]; + for (int i = 1; i < 6; i++) + { + ossOrient << "\\"; + ossOrient << iop[i]; + } + strOrient = ossOrient.str(); + ossOrient.str(""); + if ( CoherentFileSet.count(strOrient) == 0 ) + { + 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; +} + +/** + * \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 ) { + 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(); + 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 element element number of the target Element + * \return std::map of 'Xcoherent' File sets + */ + +XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, + uint16_t group, uint16_t element) +{ + XCoherentFileSetmap CoherentFileSet; + + int nb = fileSet->size(); + if (nb == 0 ) { + gdcmWarningMacro("Empty FileList passed to SplitOnPosition"); + 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,element); + + if ( CoherentFileSet.count(strTagValue) == 0 ) + { + gdcmDebugMacro(" :[" << 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; } //----------------------------------------------------------------------------- @@ -194,44 +624,70 @@ GdcmFileList *SerieHelper::GetCoherentFileList(std::string SerieUID) //----------------------------------------------------------------------------- // Private /** - * \brief sorts the images, according to their Patient Position + * \brief sorts the images, according to their Patient Position. + * 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 * -# Image Number + * -# file name * -# More to come :-) + * \note : FileList = std::vector * @param fileList Coherent File list (same Serie UID) to sort * @return false only if the header is bugged ! */ -bool SerieHelper::ImagePositionPatientOrdering( GdcmFileList *fileList ) -//based on Jolinda's algorithm +bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) +//based on Jolinda Smith's algorithm { +//Tags always use the same coordinate system, where "x" is left +//to right, "y" is posterior to anterior, and "z" is foot to head (RAH). + //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; + ZSpacing = -1.0; // will be updated if process doesn't fail - //!\todo rewrite this for loop. - for ( GdcmFileList::const_iterator + 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 ) { - if( first ) + gdcmDebugMacro("deal with " << (*it)->GetFileName() ); + if ( first ) { (*it)->GetImageOrientationPatient( cosines ); - + + // The "Image Orientation Patient" tag gives the direction cosines + // for the rows and columns for the three axes defined above. + // Typical axial slices will have a value 1/0/0/0/1/0: + // rows increase from left to right, + // columns increase from posterior to anterior. This is your everyday + // "looking up from the bottom of the head with the eyeballs up" image. + + // The "Image Position Patient" tag gives the coordinates of the first + // voxel in the image in the "RAH" coordinate system, relative to some + // origin. + + // First, calculate the slice normal from IOP : + // 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]; - + + // For each slice (here : the first), calculate the distance along + // the slice normal using the IPP tag + ipp[0] = (*it)->GetXOrigin(); ipp[1] = (*it)->GetYOrigin(); ipp[2] = (*it)->GetZOrigin(); @@ -242,85 +698,138 @@ bool SerieHelper::ImagePositionPatientOrdering( GdcmFileList *fileList ) dist += normal[i]*ipp[i]; } - if( dist == 0 ) - { - return false; - } - - distlist.push_back( dist ); + gdcmDebugMacro("dist : " << dist); + distmultimap.insert(std::pair(dist, *it)); max = min = dist; first = false; } else { + // Next, for each slice, calculate the distance along the slice normal + // using the IPP tag ipp[0] = (*it)->GetXOrigin(); ipp[1] = (*it)->GetYOrigin(); ipp[2] = (*it)->GetZOrigin(); - + dist = 0; for ( int i = 0; i < 3; ++i ) { dist += normal[i]*ipp[i]; } - if( dist == 0 ) - { - return false; - } - - distlist.push_back( dist ); - + distmultimap.insert(std::pair(dist, *it)); + gdcmDebugMacro("dist : " << dist); 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. - GdcmFileVector CoherentGdcmFileVector(n); - // CoherentGdcmFileVector.reserve( n ); - CoherentGdcmFileVector.resize( n ); - // gdcmAssertMacro( CoherentGdcmFileVector.capacity() >= n ); - - float step = (max - min)/(n - 1); - int pos; - n = 0; - - //VC++ don't understand what scope is !! it -> it2 - for (GdcmFileList::const_iterator it2 = fileList->begin(); - it2 != fileList->end(); ++it2, ++n) + gdcmDebugMacro("After parsing vector, nb of elements : " << fileList->size() ); + + // Find out if min/max are coherent + if ( min == max ) { - //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 (CoherentGdcmFileVector[pos]==NULL) - CoherentGdcmFileVector[pos] = *it2; - else + gdcmWarningMacro("Looks like all images have the exact same image position. " + << "No PositionPatientOrdering sort performed. " + << "No 'ZSpacing' calculated! "); + 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) + { + + gdcmDebugMacro("Check if image shares a common position : " << (*it2).second->GetFileName() ); + + if (distmultimap.count((*it2).first) != 1) { - gdcmWarningMacro( "2 files same position"); - return false; + gdcmWarningMacro("File: [" + << ((*it2).second->GetFileName()) + << "] : more than ONE file at distance: '" + << (*it2).first + << " (position is not unique!) " + << "No PositionPatientOrdering sort performed. " + << "No 'ZSpacing' calculated! "); + + ok = false; } } + if (!ok) + { + if (! DropDuplicatePositions) + return false; + } + +// Now, we can calculate Z Spacing as the difference +// between the "dist" values for the first two slices. - fileList->clear(); // doesn't delete list elements, only node - - //VC++ don't understand what scope is !! it -> it3 - for (GdcmFileVector::const_iterator it3 = CoherentGdcmFileVector.begin(); - it3 != CoherentGdcmFileVector.end(); ++it3) +// The following (un)-commented out code is let here +// to be re-used by whomsoever is interested... + + std::multimap::iterator it5 = distmultimap.begin(); + double d1 = (*it5).first; + it5++; + double d2 = (*it5).first; + ZSpacing = d1-d2; + if (ZSpacing < 0.0) + ZSpacing = - ZSpacing; + + fileList->clear(); // doesn't delete list elements, only nodes + +// Acording to user requierement, we sort direct order or reverse order. + if (DirectOrder) + { + for (std::multimap::iterator it3 = distmultimap.begin(); + it3 != distmultimap.end(); + ++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 { - fileList->push_back( *it3 ); + std::multimap::const_iterator it4; + it4 = distmultimap.end(); + do + { + 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() ); } - distlist.clear(); - CoherentGdcmFileVector.clear(); + distmultimap.clear(); return true; } @@ -330,20 +839,25 @@ 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 + * @param fileList File set (same Serie UID) to sort + * @return false if non bona fide stuff encountered */ -bool SerieHelper::ImageNumberOrdering(GdcmFileList *fileList) +bool SerieHelper::ImageNumberOrdering(FileList *fileList) { int min, max, pos; int n = fileList->size(); - GdcmFileList::const_iterator it = fileList->begin(); + FileList::const_iterator it = fileList->begin(); min = max = (*it)->GetImageNumber(); for (; it != fileList->end(); ++it, ++n) @@ -354,27 +868,56 @@ bool SerieHelper::ImageNumberOrdering(GdcmFileList *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) + Sort(fileList,SerieHelper::ImageNumberLessThan); + else + Sort(fileList,SerieHelper::ImageNumberGreaterThan); return true; } bool SerieHelper::FileNameLessThan(File *file1, File *file2) { - return file1->GetFileName() < file2->GetFileName(); + 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 * @return false only if the header is bugged ! */ -bool SerieHelper::FileNameOrdering(GdcmFileList *fileList) +bool SerieHelper::FileNameOrdering(FileList *fileList) +{ + if (DirectOrder) + Sort(fileList,SerieHelper::FileNameLessThan); + else + Sort(fileList,SerieHelper::FileNameGreaterThan); + + return true; +} + +/** + * \brief sorts the images, according to user supplied function + * @param fileList Coherent File list (same Serie UID) to sort + * @return false only if the header is bugged ! + */ +bool SerieHelper::UserOrdering(FileList *fileList) { - std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameLessThan); + Sort(fileList,SerieHelper::UserLessThanFunction); + if (!DirectOrder) + { + std::reverse(fileList->begin(), fileList->end()); + } return true; } @@ -383,23 +926,23 @@ bool SerieHelper::FileNameOrdering(GdcmFileList *fileList) /** * \brief Canonical printer. */ -void SerieHelper::Print(std::ostream &os, std::string const & indent) +void SerieHelper::Print(std::ostream &os, std::string const &indent) { - // For all the Coherent File lists of the gdcm::Serie - CoherentFileListmap::iterator itl = CoherentGdcmFileListHT.begin(); - if ( itl == CoherentGdcmFileListHT.end() ) + // For all the Coherent File lists of the GDCM_NAME_SPACE::Serie + SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin(); + if ( itl == SingleSerieUIDFileSetHT.end() ) { - gdcmWarningMacro( "No Coherent File list found" ); + gdcmWarningMacro( "No SingleSerieUID File set found" ); return; } - while (itl != CoherentGdcmFileListHT.end()) + while (itl != SingleSerieUIDFileSetHT.end()) { os << "Serie UID :[" << itl->first << "]" << std::endl; - // For all the files of a Coherent File list - for (GdcmFileList::iterator it = (itl->second)->begin(); - it != (itl->second)->end(); - ++it) + // For all the files of a SingleSerieUID File set + for (FileList::iterator it = (itl->second)->begin(); + it != (itl->second)->end(); + ++it) { os << indent << " --- " << (*it)->GetFileName() << std::endl; } @@ -407,5 +950,191 @@ void SerieHelper::Print(std::ostream &os, std::string const & indent) } } +void SerieHelper::CreateDefaultUniqueSeriesIdentifier() +{ + // 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 + 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. + 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. + AddRestriction( TagKey(0x0028, 0x0011)); +} + +/** + * \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 pertinent tag is + * 0018|1312 [In-plane Phase Encoding Direction] value : ROW/COLUMN + * @param inFile GDCM_NAME_SPACE::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) + { + for(SerieExRestrictions::iterator it2 = ExRefine.begin(); + it2 != ExRefine.end(); + ++it2) + { + const ExRule &r = *it2; + std::string s = inFile->GetEntryString( r.group, r.elem ); + if( s == GDCM_UNFOUND ) + { + s = ""; + } + if( id == uid && !s.empty() ) + { + id += "."; // add separator + } + id += s; + } + } + // Eliminate non-alnum characters, including whitespace... + // that may have been introduced by concats. + unsigned int s_size = id.size(); + 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'))) + { + 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_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 '%%%'. Hope it's enough !) + */ +std::string SerieHelper::CreateUserDefinedFileIdentifier( File *inFile ) +{ + // Deal with all user supplied tags. + // (user knows more than we do about his images!) + + double 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 ); + if (s == "") // avoid troubles when empty string is found + s = "-"; + + // 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) + { + if ( s != GDCM_UNFOUND) // Don't convert unfound fields ! + { + 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. + unsigned int s_size = s.size(); + for(unsigned int i=0; i= '+' && s[i] <= '-') + || (s[i] >= 'a' && s[i] <= 'z') + || (s[i] >= '0' && s[i] <= '9') + || (s[i] >= 'A' && s[i] <= 'Z'))) + { + 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; +} + +//----------------------------------------------------------------------------- +// Sort +/** + * \brief Sort FileList. + */ +void SerieHelper::Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) ) +{ + std::sort(fileList->begin(), fileList->end(), pt2Func ); +} + +/* +#ifndef GDCM_LEGACY_REMOVE +bool SerieHelper::AddGdcmFile(File* header) +{ + return AddFile(header); +} +#endif +*/ + //----------------------------------------------------------------------------- } // end namespace gdcm