Program: gdcm
Module: $RCSfile: gdcmSerieHelper.cxx,v $
Language: C++
- Date: $Date: 2005/07/21 05:00:15 $
- Version: $Revision: 1.14 $
+ Date: $Date: 2011/03/29 07:36:00 $
+ Version: $Revision: 1.71 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
-
+
=========================================================================*/
#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 <math.h>
#include <vector>
#include <algorithm>
+#include <map>
+#include <stdio.h> //for sscanf
-namespace gdcm
+namespace GDCM_NAME_SPACE
{
//-----------------------------------------------------------------------------
*/
SerieHelper::SerieHelper()
{
- // For all the File lists of 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;
- }
- l->clear();
- delete l;;
- l = GetNextCoherentFileList();
- }
+ m_UseSeriesDetails = false;
+ ClearAll();
+ UserLessThanFunction = 0;
+ DirectOrder = true;
+ DropDuplicatePositions = false;
}
/**
*/
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_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();
}
//-----------------------------------------------------------------------------
// 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)
{
// Create a DICOM file
- File *header = new File ();
+ File *header = File::New();
header->SetLoadMode(LoadMode);
header->SetFileName( filename );
header->Load();
if ( header->IsReadable() )
{
- int allrules = 1;
- // First step the user has defined a set of rules for the DICOM file
- // he is looking for.
- // make sure the file correspond to his set of rules:
-
-/*
- for(SerieRestrictions::iterator it = Restrictions.begin();
- it != Restrictions.end();
- ++it)
- {
- const Rule &r = *it;
- // doesn't compile (no matching function...).
- const std::string s;// = header->GetEntryValue( r.first );
- if ( !Util::DicomStringEqual(s, r.second.c_str()) )
- {
- // Argh ! This rule is unmatch let's just quit
- allrules = 0;
- break;
- }
- }
-*/
- // Just keep 'new style' for Rules
- std::string s;
- for(SerieExRestrictions::iterator it2 = ExRestrictions.begin();
- it2 != ExRestrictions.end();
- ++it2)
- {
- const ExRule &r = *it2;
- s = header->GetEntryValue( r.group, r.elem );
- if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) )
- {
- // Argh ! This rule is unmatch let's just quit
- allrules = 0;
- break;
- }
- }
-
- if ( allrules ) // all rules are respected:
+ if ( !AddFile( header ) )
{
- // Allright ! we have a found a DICOM that match the user expectation.
- // Let's add it !
-
- // 0020 000e UI REL Series Instance UID
- const std::string &uid = header->GetEntryValue (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 )
- {
- gdcmDebugMacro(" New Serie UID :[" << uid << "]");
- // create a std::list in 'uid' position
- CoherentFileListHT[uid] = new FileList;
- }
- // Current Serie UID and DICOM header seems to match; add the file:
- CoherentFileListHT[uid]->push_back( header );
- }
- else
- {
- // at least one rule was unmatch we need to deallocate the file:
- delete header;
+ // at least one rule was unmatched we need to deallocate the file:
+ header->Delete();
}
}
else
{
gdcmWarningMacro("Could not read file: " << filename );
- delete header;
+ header->Delete();
}
}
/**
- * \brief add a gdcm::File to the first (and supposed to be unique) list
- * 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_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)
* 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->GetEntryValue( 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 ( CoherentFileListHT.count(uid) == 0 )
- {
- gdcmDebugMacro(" New Serie UID :[" << uid << "]");
- // create a std::list in 'uid' position
- CoherentFileListHT[uid] = new FileList;
- }
- // Current Serie UID and DICOM header seems to match; add the file:
- CoherentFileListHT[uid]->push_back( header );
+ 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;
}
-
/**
- * \brief add a rules for restricting a DICOM file to be in the serie we are
- * trying to find. For example you can select only the DICOM file from a
+ * \brief add a rule for restricting a DICOM file to be in the serie we are
+ * trying to find. For example you can select only the DICOM files from a
* directory which would have a particular EchoTime==4.0.
* This method is a user level, value is not required to be formatted as a DICOM
* string
+ * \todo find a trick to allow user to say if he wants the Rectrictions
+ * to be *ored* (and not only *anded*)
+ * @param key Target tag we want restrict on a given value
+ * @param value value to be checked to exclude File
+ * @param op operator we want to use to check
*/
-void SerieHelper::AddRestriction(uint16_t group, uint16_t elem,
+void SerieHelper::AddRestriction(TagKey const &key,
std::string const &value, int op)
{
ExRule r;
- r.group = group;
- r.elem = elem;
+ r.group = key[0];
+ r.elem = key[1];
r.value = value;
r.op = op;
ExRestrictions.push_back( r );
}
-#ifndef GDCM_LEGACY_REMOVE
+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 rules for restricting a DICOM file to be in the serie we are
- * trying to find. For example you can select only the DICOM file from a
+ * \brief add a rule for restricting a DICOM file to be in the serie we are
+ * trying to find. For example you can select only the DICOM files from a
* directory which would have a particular EchoTime==4.0.
* This method is a user level, value is not required to be formatted as a DICOM
* string
- * @deprecated use :
+ * @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(TagKey const &key, std::string const &value)
+
+void SerieHelper::AddRestriction(uint16_t group, uint16_t elem,
+ std::string const &value, int op)
{
- Rule r;
- r.first = key;
- r.second = value;
- Restrictions.push_back( r );
+ TagKey t(group, elem);
+ AddRestriction(t, value, op);
}
-#endif
+//#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();
}
/**
- * \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 ( ImagePositionPatientOrdering( coherentFileList ) )
+ // 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(coherentFileList ) )
+ else if ( ImageNumberOrdering(fileSet ) )
{
+ gdcmDebugMacro("ImageNumberOrdering succeeded");
return ;
}
else
{
- FileNameOrdering(coherentFileList );
+ 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
+ * \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 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 CoherentFileListHT[SerieUID];
+ return SingleSerieUIDFileSetHT[SerieUID];
+}
+
+/**
+ * \brief Splits a Single SerieUID Fileset according to the Orientations
+ * @param fileSet File Set to be splitted
+ * \return std::map of 'Xcoherent' File sets
+ */
+
+XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet)
+{
+ XCoherentFileSetmap CoherentFileSet;
+
+ int nb = fileSet->size();
+ if (nb == 0 ) {
+ 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 SplitOnTagValue");
+ 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;
+}
+
+
+/**
+ * \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::SplitOnTagValueConvertToFloat(FileList *fileSet,
+ uint16_t group, uint16_t element)
+{
+ XCoherentFileSetmap CoherentFileSet;
+
+ int nb = fileSet->size();
+ if (nb == 0 ) {
+ gdcmWarningMacro("Empty FileList passed to SplitOnTagValue");
+ return CoherentFileSet;
+ }
+
+ std::string strTagValue; // read on disc
+
+ double dTagValue;
+ int iTagValue;
+ char cTagValue[11];
+ std::string sTagValue;
+
+ FileList::const_iterator it = fileSet->begin();
+ //it ++;
+ for ( ;
+ it != fileSet->end();
+ ++it)
+ {
+ /// \TODO : find a trick to create a string whose value follows lexicographical order
+
+ strTagValue = (*it)->GetEntryString(group,element);
+ dTagValue = atof( strTagValue.c_str());
+ iTagValue = dTagValue;
+ sprintf(cTagValue, "%010d", iTagValue);
+ strTagValue = cTagValue;
+
+ 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;
}
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// 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 :-)
- * WARNING : FileList = std::vector<File* >
+ * \note : FileList = std::vector<File* >
* @param fileList Coherent File list (same Serie UID) to sort
* @return false only if the header is bugged !
*/
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<float> distlist;
+ ZSpacing = -1.0; // will be updated if process doesn't fail
- //!\todo rewrite this for loop.
+ gdcmDebugMacro("============================================DropDuplicatePositions : " << DropDuplicatePositions );
+
+ std::multimap<double,File *> 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 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();
dist += normal[i]*ipp[i];
}
- distlist.push_back( dist );
+ gdcmDebugMacro("dist : " << dist);
+ distmultimap.insert(std::pair<const double,File *>(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];
}
- distlist.push_back( dist );
-
+ distmultimap.insert(std::pair<const double,File *>(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.
- FileVector CoherentFileVector(n);
- // CoherentFileVector.reserve( n );
- CoherentFileVector.resize( n );
- // gdcmAssertMacro( CoherentFileVector.capacity() >= n );
+ 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;
- }
+ }
- float step = (max - min)/(n - 1);
- int pos;
- n = 0;
-
- //VC++ don't understand what scope is !! it -> it2
- for (FileList::const_iterator it2 = fileList->begin();
- it2 != fileList->end(); ++it2, ++n)
+ // Check to see if image shares a common position
+ bool ok = true;
+ for (std::multimap<double, File *>::iterator it2 = distmultimap.begin();
+ it2 != distmultimap.end();
+ ++it2)
{
- //2*n sort algo !!
- //Assumption: all files are present (no one missing)
- pos = (int)( fabs( (distlist[n]-min)/step) + .5 );
-
- // a Dicom 'Serie' may contain scout views
- // and images may have differents directions
- // -> More than one may have the same 'pos'
- // Sorting has then NO meaning !
- if (CoherentFileVector[pos]==NULL)
- CoherentFileVector[pos] = *it2;
- else
+
+ gdcmDebugMacro("Check if image shares a common position : " << (*it2).second->GetFileName() );
+
+ if (distmultimap.count((*it2).first) != 1)
{
- gdcmWarningMacro( "At least 2 files with same position. No PositionPatientOrdering sort performed");
- 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.
+
+// The following (un)-commented out code is let here
+// to be re-used by whomsoever is interested...
+
+ std::multimap<double, File *>::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
-
- //VC++ don't understand what scope is !! it -> it3
- for (FileVector::const_iterator it3 = CoherentFileVector.begin();
- it3 != CoherentFileVector.end(); ++it3)
+
+// Acording to user requierement, we sort direct order or reverse order.
+ if (DirectOrder)
+ {
+ for (std::multimap<double, File *>::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<double, File *>::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<double, File *>::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();
- CoherentFileVector.clear();
+ distmultimap.clear();
return true;
}
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
+ * @param fileList File set (same Serie UID) to sort
* @return false if non bona fide stuff encountered
*/
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;
}
- 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
*/
bool SerieHelper::FileNameOrdering(FileList *fileList)
{
- std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameLessThan);
+ 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)
+{
+ Sort(fileList,SerieHelper::UserLessThanFunction);
+ if (!DirectOrder)
+ {
+ std::reverse(fileList->begin(), fileList->end());
+ }
return true;
}
*/
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() )
+ // 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 != 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)
+ it != (itl->second)->end();
+ ++it)
{
os << indent << " --- " << (*it)->GetFileName() << std::endl;
}
}
}
+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<s_size; i++)
+ {
+ while(i<s_size
+ && !( id[i] == '.' || id[i] == '%' || id[i] == '_'
+ || (id[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();
+ if(s_size == 0)
+ { // to avoid further troubles when wild anonymization was performed
+ s = "a";
+ }
+ else
+ {
+ for(unsigned int i=0; i<s_size; i++)
+ {
+ while(i<s_size
+ && !( s[i] == '.' || s[i] == '%' || s[i] == '_'
+ || (s[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
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff