X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmSerieHelper.cxx;h=9fef62c65e472e53f3c2c4ab6edf6bebd9c40de2;hb=05c174bd812b9e375823d6a95683cb5036795a02;hp=c049e8b45c4807550742db86d83746835c17330b;hpb=04e8ab90af5ff69eb35e51d56177a4d4c487e300;p=gdcm.git diff --git a/src/gdcmSerieHelper.cxx b/src/gdcmSerieHelper.cxx index c049e8b4..9fef62c6 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: 2005/10/21 07:38:58 $ + Version: $Revision: 1.25 $ 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 +40,8 @@ namespace gdcm */ SerieHelper::SerieHelper() { + 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 +50,29 @@ 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 + delete *it; // remove each entry } l->clear(); - delete l; // remove the list - l = GetNextCoherentFileList(); + delete l; // remove the container + l = GetNextSingleSerieUIDFileSet(); } } @@ -86,7 +82,7 @@ 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) @@ -100,37 +96,20 @@ 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; } @@ -138,26 +117,26 @@ 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: + // at least one rule was unmatched we need to deallocate the file: delete header; } } @@ -169,9 +148,12 @@ void SerieHelper::AddFileName(std::string const &filename) } /** - * \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) @@ -189,9 +171,9 @@ 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 ); @@ -211,14 +193,14 @@ 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: } @@ -270,7 +252,7 @@ void SerieHelper::AddRestriction(TagKey const &key, std::string const &value) /** * \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 +267,31 @@ 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 ); } } @@ -316,12 +299,12 @@ 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(); + FileList::const_iterator it = fileSet->begin(); int nX = (*it)->GetXSize(); int nY = (*it)->GetYSize(); @@ -329,7 +312,7 @@ bool SerieHelper::IsCoherent(FileList *coherentFileList) it ++; for ( ; - it != coherentFileList->end(); + it != fileSet->end(); ++it) { if ( (*it)->GetXSize() != nX ) @@ -342,43 +325,254 @@ bool SerieHelper::IsCoherent(FileList *coherentFileList) } return true; } + +#ifndef GDCM_LEGACY_REMOVE /** - * \brief Get the first List while visiting the CoherentFileListHT + * \brief accessor (DEPRECATED : use GetFirstSingleSerieUIDFileSet ) + * Warning : 'coherent' means here they have the same Serie UID * @return The first FileList if found, otherwhise NULL */ FileList *SerieHelper::GetFirstCoherentFileList() { - 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 + * \brief accessor (DEPRECATED : use GetNextSingleSerieUIDFileSet ) + * Warning : 'coherent' means here they have the same Serie UID + * \note : meaningfull only if GetFirstCoherentFileList() already called * @return The next FileList if found, otherwhise NULL */ FileList *SerieHelper::GetNextCoherentFileList() { - gdcmAssertMacro (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 + * \brief accessor (DEPRECATED : use GetSingleSerieUIDFileSet ) + * Warning : 'coherent' means here they have the same Serie UID * @param SerieUID SerieUID - * \return pointer to the Coherent Files list if found, otherwhise NULL + * \return pointer to the FileList if found, otherwhise NULL */ FileList *SerieHelper::GetCoherentFileList(std::string SerieUID) { - if ( CoherentFileListHT.count(SerieUID) == 0 ) + if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 ) return 0; - return CoherentFileListHT[SerieUID]; + 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 + */ +FileList *SerieHelper::GetSingleSerieUIDFileSet(std::string SerieUID) +{ + if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 ) + return 0; + 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::ostringstream ossOrient; + std::string strOrient; + + 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(); + + 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(); + + 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 SingleSerieUID 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 element) +{ + 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,element); + + 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; } //----------------------------------------------------------------------------- @@ -420,8 +614,8 @@ 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]; @@ -471,11 +665,11 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) // 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" ); + { + 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; @@ -497,7 +691,8 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) CoherentFileVector[pos] = *it2; else { - gdcmWarningMacro( "At least 2 files with same position. No PositionPatientOrdering sort performed"); + gdcmWarningMacro( "At least 2 files with same position." + << " No PositionPatientOrdering sort performed"); return false; } } @@ -539,6 +734,7 @@ 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 @@ -565,13 +761,16 @@ 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 ); + std::sort(fileList->begin(), fileList->end(), + SerieHelper::ImageNumberLessThan ); else - std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberGreaterThan ); + std::sort(fileList->begin(), fileList->end(), + SerieHelper::ImageNumberGreaterThan ); return true; } @@ -593,9 +792,11 @@ bool SerieHelper::FileNameGreaterThan(File *file1, File *file2) bool SerieHelper::FileNameOrdering(FileList *fileList) { if (DirectOrder) - std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameLessThan); + std::sort(fileList->begin(), fileList->end(), + SerieHelper::FileNameLessThan); else - std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameGreaterThan); + std::sort(fileList->begin(), fileList->end(), + SerieHelper::FileNameGreaterThan); return true; } @@ -607,7 +808,8 @@ bool SerieHelper::FileNameOrdering(FileList *fileList) */ bool SerieHelper::UserOrdering(FileList *fileList) { - std::sort(fileList->begin(), fileList->end(), SerieHelper::UserLessThanFunction); + std::sort(fileList->begin(), fileList->end(), + SerieHelper::UserLessThanFunction); if (!DirectOrder) { std::reverse(fileList->begin(), fileList->end()); @@ -623,17 +825,17 @@ 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)