X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmSerieHelper.cxx;h=fc0f2135b7838d77fcb177c1638a773b077998e0;hb=6278320cc85da00d2d56ffbf07806e84966892c3;hp=412d719e82c7aecbd4bb68e27804dd5379c178b8;hpb=98cf38e32be18dc2b7d3d1a13e45f60717b008bc;p=gdcm.git diff --git a/src/gdcmSerieHelper.cxx b/src/gdcmSerieHelper.cxx index 412d719e..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: 2005/12/16 13:48:46 $ - Version: $Revision: 1.40 $ + 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 @@ -19,19 +19,18 @@ #include "gdcmSerieHelper.h" #include "gdcmDirList.h" #include "gdcmFile.h" -#include "gdcmDictEntry.h" // for TranslateToKey +//#include "gdcmDictEntry.h" // for TranslateToKey : no more ! #include "gdcmDebug.h" #include "gdcmUtil.h" #include #include -#include #include +#include #include //for sscanf -namespace gdcm +namespace GDCM_NAME_SPACE { -//----------------------------------------------------------------------------- //----------------------------------------------------------------------------- // Constructor / Destructor @@ -44,6 +43,7 @@ SerieHelper::SerieHelper() ClearAll(); UserLessThanFunction = 0; DirectOrder = true; + DropDuplicatePositions = false; } /** @@ -64,8 +64,8 @@ void SerieHelper::ClearAll() FileList *l = GetFirstSingleSerieUIDFileSet(); while (l) { - // For all the gdcm::File of a File set - for (gdcm::FileList::iterator it = l->begin(); + // For all the GDCM_NAME_SPACE::File of a File set + for (GDCM_NAME_SPACE::FileList::iterator it = l->begin(); it != l->end(); ++it) { @@ -75,6 +75,8 @@ void SerieHelper::ClearAll() delete l; // remove the container l = GetNextSingleSerieUIDFileSet(); } + // Need to clear that too: + SingleSerieUIDFileSetHT.clear(); } //----------------------------------------------------------------------------- @@ -83,7 +85,7 @@ void SerieHelper::ClearAll() // Public /** - * \brief add a gdcm::File to the Fileset 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) @@ -96,48 +98,7 @@ void SerieHelper::AddFileName(std::string const &filename) if ( header->IsReadable() ) { - int allrules = 1; - // First step : the user defined a set of rules for the DICOM file - // he is looking for. - // Make sure the file corresponds 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: - { - // 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->GetEntryString(0x0020, 0x000e); - // if uid == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND - // no need here to do anything special - - - if ( SingleSerieUIDFileSetHT.count(uid) == 0 ) - { - gdcmDebugMacro(" New Serie UID :[" << uid << "]"); - // create a std::list in 'uid' position - SingleSerieUIDFileSetHT[uid] = new FileList; - } - // Current Serie UID and DICOM header seems to match; add the file: - SingleSerieUIDFileSetHT[uid]->push_back( header ); - } - else + if ( !AddFile( header ) ) { // at least one rule was unmatched we need to deallocate the file: header->Delete(); @@ -151,10 +112,10 @@ void SerieHelper::AddFileName(std::string const &filename) } /** - * \brief add a gdcm::File to the first (and supposed to be unique) file set - * of the gdcm::SerieHelper. + * \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::File* has the same effect than passing a file name! + * 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 @@ -166,46 +127,56 @@ void SerieHelper::AddFileName(std::string const &filename) * vtkGdcmReader parsing twice the same files. * *no* coherence check is performed, but those specified * by SerieHelper::AddRestriction() - * @param header gdcm::File* of the file to deal with + * @param header GDCM_NAME_SPACE::File* of the file to deal with + * @return true if file was added, false if file was rejected */ -void SerieHelper::AddGdcmFile(File *header) -{ - int allrules = 1; - // First step the user has defined a set of rules for the DICOM - // he is looking for. - // make sure the file correspond to his set of rules: - for(SerieRestrictions::iterator it = Restrictions.begin(); - it != Restrictions.end(); - ++it) +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) ) { - const Rule &r = *it; - 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 - allrules = 0; - break; - } + // Argh ! This rule is unmatched; let's just quit + allrules = 0; + break; } - if ( allrules ) // all rules are respected: - { - // Allright ! we have a found a DICOM that match the user expectation. - // Let's add it ! + } - const std::string &uid = "0"; - // Serie UID of the gdcm::File* may be different. - // User is supposed to know what he wants + if ( allrules ) // all rules are respected: + { + // 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 ( SingleSerieUIDFileSetHT.count(uid) == 0 ) - { - gdcmDebugMacro(" New Serie UID :[" << uid << "]"); - // create a std::list in 'uid' position - SingleSerieUIDFileSetHT[uid] = new FileList; - } - // Current Serie UID and DICOM header seems to match; add the file: - SingleSerieUIDFileSetHT[uid]->push_back( header ); + if ( SingleSerieUIDFileSetHT.count(id) == 0 ) + { + gdcmDebugMacro(" New/gdcmSerieHelper.cxx Serie UID :[" << id << "]"); + // create a std::list in 'id' position + SingleSerieUIDFileSetHT[id] = new FileList; } - // Even if a rule was unmatch we don't deallocate the gdcm::File: + // Current Serie UID and DICOM header seems to match add the file: + SingleSerieUIDFileSetHT[id]->push_back( header ); + } + else + { + // one rule not matched, tell user: + return false; + } + return true; } /** @@ -214,8 +185,8 @@ void SerieHelper::AddGdcmFile(File *header) * directory which would have a particular EchoTime==4.0. * This method is a user level, value is not required to be formatted as a DICOM * string - * \todo find a trick to allow user if he wants the Rectrictions to be *ored* - * (and not only *anded*) + * \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 @@ -231,43 +202,52 @@ void SerieHelper::AddRestriction(TagKey const &key, 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 file from a + * 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 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 + * @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) { - ExRule r; - r.group = group; - r.elem = elem; - r.value = value; - r.op = op; - ExRestrictions.push_back( r ); + TagKey t(group, elem); + AddRestriction(t, value, op); } +//#endif + /** * \brief add an extra 'SerieDetail' for building a 'Serie Identifier' - * that ensures (hope so) File constistency (Series Instance UID doesn't. + * 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 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) -{ - m_UseSeriesDetails = true; - +void SerieHelper::AddSeriesDetail(uint16_t group, uint16_t elem, bool convert) +{ ExDetail d; - d.group = group; - d.elem = elem; + d.group = group; + d.elem = elem; + d.convert = convert; ExDetails.push_back( d ); } /** @@ -278,6 +258,25 @@ void SerieHelper::AddSeriesDetail(uint16_t group, uint16_t elem) 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(); @@ -296,22 +295,29 @@ void SerieHelper::SetDirectory(std::string const &dir, bool recursive) */ void SerieHelper::OrderFileList(FileList *fileSet) { - + // 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(fileSet ) ) { + gdcmDebugMacro("ImageNumberOrdering succeeded"); return ; } else { + gdcmDebugMacro("Use FileNameOrdering"); FileNameOrdering(fileSet ); } } @@ -344,13 +350,18 @@ bool SerieHelper::IsCoherent(FileList *fileSet) return false; if ( (*it)->IsSignedPixelData() != signedPixelData ) return false; - // probabely more is to be checked (?) + // probabely more is to be checked (?) } return true; } -#ifndef GDCM_LEGACY_REMOVE - +//#ifndef GDCM_LEGACY_REMOVE +/** + * \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() { ItFileSetHt = SingleSerieUIDFileSetHT.begin(); @@ -358,8 +369,14 @@ FileList *SerieHelper::GetFirstCoherentFileList() return ItFileSetHt->second; return 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 + */ + /* FileList *SerieHelper::GetNextCoherentFileList() { gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end()); @@ -369,15 +386,23 @@ FileList *SerieHelper::GetNextCoherentFileList() return ItFileSetHt->second; return NULL; } +*/ - +/** + * \brief accessor (DEPRECATED : use GetSingleSerieUIDFileSet ) + * Warning : 'coherent' means here they have the same Serie UID + * @param SerieUID SerieUID + * \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 +*/ +//#endif /** @@ -430,14 +455,16 @@ XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) XCoherentFileSetmap CoherentFileSet; int nb = fileSet->size(); - if (nb == 0 ) + if (nb == 0 ) { + gdcmWarningMacro("Empty FileList passed to SplitOnOrientation"); return CoherentFileSet; - float iop[6]; + } + float iop[6]; std::string strOrient; - std::ostringstream ossOrient; + std::ostringstream ossOrient; + FileList::const_iterator it = fileSet->begin(); - it ++; for ( ; it != fileSet->end(); ++it) @@ -446,7 +473,7 @@ XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) // 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 + // Let's build again the 'cosines' string, to be sure of its format (*it)->GetImageOrientationPatient(iop); ossOrient << iop[0]; @@ -457,17 +484,17 @@ XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet) } 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; + 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; } @@ -482,14 +509,15 @@ XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) XCoherentFileSetmap CoherentFileSet; int nb = fileSet->size(); - if (nb == 0 ) + 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(); - it ++; for ( ; it != fileSet->end(); ++it) @@ -518,7 +546,7 @@ XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) { gdcmWarningMacro( "Wrong number for Position : [" << strImPos << "]" ); - return CoherentFileSet; + return CoherentFileSet; } // Let's build again the 'position' string, to be sure of it's format @@ -531,7 +559,7 @@ XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) } strPosition = ossPosition.str(); ossPosition.str(""); - + if ( CoherentFileSet.count(strPosition) == 0 ) { gdcmDebugMacro(" New Position :[" << strPosition << "]"); @@ -549,23 +577,25 @@ XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet) * 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 + * @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 elem) + uint16_t group, uint16_t element) { XCoherentFileSetmap CoherentFileSet; int nb = fileSet->size(); - if (nb == 0 ) + if (nb == 0 ) { + gdcmWarningMacro("Empty FileList passed to SplitOnPosition"); return CoherentFileSet; + } std::string strTagValue; // read on disc FileList::const_iterator it = fileSet->begin(); - it ++; + //it ++; for ( ; it != fileSet->end(); ++it) @@ -574,11 +604,11 @@ XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, // 0020,0032 : Image Position Patient // 0020,0030 : Image Position (RET) - strTagValue = (*it)->GetEntryString(group,elem); + strTagValue = (*it)->GetEntryString(group,element); if ( CoherentFileSet.count(strTagValue) == 0 ) { - gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]"); + gdcmDebugMacro(" :[" << strTagValue << "]"); // create a File set in 'position' position CoherentFileSet[strTagValue] = new FileList; } @@ -595,7 +625,8 @@ XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, // Private /** * \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 @@ -608,6 +639,9 @@ XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet, 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]; double normal[3]; @@ -615,17 +649,34 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) double dist; double min = 0, max = 0; bool first = true; + ZSpacing = -1.0; // will be updated if process doesn't fail + 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 ) { + 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 ("Image Position Patient") tag. @@ -633,7 +684,10 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) 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(); @@ -644,6 +698,7 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) dist += normal[i]*ipp[i]; } + gdcmDebugMacro("dist : " << dist); distmultimap.insert(std::pair(dist, *it)); max = min = dist; @@ -651,10 +706,12 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) } 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 ) { @@ -662,51 +719,88 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) } distmultimap.insert(std::pair(dist, *it)); - + gdcmDebugMacro("dist : " << dist); min = (min < dist) ? min : dist; max = (max > dist) ? max : dist; } - } + gdcmDebugMacro("After parsing vector, nb of elements : " << fileList->size() ); + // 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. " + << "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) - { - if (distmultimap.count((*it2).first) != 1) - { - gdcmErrorMacro("File: " - << ((*it2).second->GetFileName()) - << " Distance: " - << (*it2).first - << " position is not unique"); - ok = false; - } - } - if (!ok) - { - return false; - } - + 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("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. + +// 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) + 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 @@ -717,8 +811,23 @@ bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList ) { 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() ); - } + } distmultimap.clear(); @@ -740,7 +849,7 @@ bool SerieHelper::ImageNumberGreaterThan(File *file1, File *file2) * \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 File set (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) @@ -765,12 +874,10 @@ bool SerieHelper::ImageNumberOrdering(FileList *fileList) << " No ImageNumberOrdering sort performed."); return false; } - if (DirectOrder) - std::sort(fileList->begin(), fileList->end(), - SerieHelper::ImageNumberLessThan ); + if (DirectOrder) + Sort(fileList,SerieHelper::ImageNumberLessThan); else - std::sort(fileList->begin(), fileList->end(), - SerieHelper::ImageNumberGreaterThan ); + Sort(fileList,SerieHelper::ImageNumberGreaterThan); return true; } @@ -792,11 +899,9 @@ 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); else - std::sort(fileList->begin(), fileList->end(), - SerieHelper::FileNameGreaterThan); + Sort(fileList,SerieHelper::FileNameGreaterThan); return true; } @@ -808,8 +913,7 @@ bool SerieHelper::FileNameOrdering(FileList *fileList) */ bool SerieHelper::UserOrdering(FileList *fileList) { - std::sort(fileList->begin(), fileList->end(), - SerieHelper::UserLessThanFunction); + Sort(fileList,SerieHelper::UserLessThanFunction); if (!DirectOrder) { std::reverse(fileList->begin(), fileList->end()); @@ -817,152 +921,220 @@ bool SerieHelper::UserOrdering(FileList *fileList) return true; } +//----------------------------------------------------------------------------- +// Print +/** + * \brief Canonical printer. + */ +void SerieHelper::Print(std::ostream &os, std::string const &indent) +{ + // For all the Coherent File lists of the GDCM_NAME_SPACE::Serie + SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin(); + if ( itl == SingleSerieUIDFileSetHT.end() ) + { + gdcmWarningMacro( "No SingleSerieUID File set found" ); + return; + } + while (itl != SingleSerieUIDFileSetHT.end()) + { + os << "Serie UID :[" << itl->first << "]" << std::endl; + + // 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; + } + ++itl; + } +} + +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 Heuritics to *try* to build a Serie Identifier that would ensure + * \brief Heuristics to *try* to build a Serie Identifier that would ensure * all the images are coherent. * - * We allow user to add his own critierions, using AddSerieDetail + * 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 + * ex : in tagging series, the only pertinent tag is * 0018|1312 [In-plane Phase Encoding Direction] value : ROW/COLUMN - * @param inFile gdcm::File we want to build a Serie Identifier for. + * @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); + // 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; iGetEntryString(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 = ""; - } - // 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 = ""; - } + while(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; + } +} - // 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] value : ROW/COLUMN +/** + * \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!) - std::string s; - for(SeriesExDetails::iterator it2 = ExDetails.begin(); - it2 != ExDetails.end(); - ++it2) + 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) { - const ExDetail &r = *it2; - s = inFile->GetEntryString( r.group, r.elem ); - num += s.c_str(); + 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; + } } - - // Append the new info to the SeriesUID - id += "."; - id += num.c_str(); - } - - // Eliminate non-alnum 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'))) + // 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'))) { - id.erase(i, 1); + s.replace(i, 1, "_"); // ImagePositionPatient related stuff will be more human readable } - } - return id; - } - else // Could not open inFile - { - gdcmWarningMacro("Could not parse series info."); - std::string id = gdcm::GDCM_UNFOUND; - return id; - } + } + // 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; } - //----------------------------------------------------------------------------- -// Print +// Sort /** - * \brief Canonical printer. + * \brief Sort FileList. */ -void SerieHelper::Print(std::ostream &os, std::string const &indent) +void SerieHelper::Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) ) { - // For all the Coherent File lists of the gdcm::Serie - SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin(); - if ( itl == SingleSerieUIDFileSetHT.end() ) - { - gdcmWarningMacro( "No SingleSerieUID File set found" ); - return; - } - while (itl != SingleSerieUIDFileSetHT.end()) - { - os << "Serie UID :[" << itl->first << "]" << std::endl; + std::sort(fileList->begin(), fileList->end(), pt2Func ); +} - // 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; - } - ++itl; - } +/* +#ifndef GDCM_LEGACY_REMOVE +bool SerieHelper::AddGdcmFile(File* header) +{ + return AddFile(header); } +#endif +*/ //----------------------------------------------------------------------------- } // end namespace gdcm