Program: gdcm
Module: $RCSfile: gdcmSerieHelper.cxx,v $
Language: C++
- Date: $Date: 2005/06/03 16:08:16 $
- Version: $Revision: 1.9 $
+ Date: $Date: 2005/08/30 08:12:40 $
+ Version: $Revision: 1.18 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmSerieHelper.h"
#include "gdcmDirList.h"
#include "gdcmFile.h"
+#include "gdcmDictEntry.h" // for TranslateToKey
#include "gdcmDebug.h"
#include "gdcmUtil.h"
*/
SerieHelper::SerieHelper()
{
- // For all the File lists of the gdcm::Serie
+ 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 (FileList::iterator it = l->begin();
+ for (gdcm::FileList::iterator it = l->begin();
it != l->end();
++it)
{
- delete *it;
+ delete *it; // remove entry
}
l->clear();
- delete l;;
+ delete l; // remove the list
l = GetNextCoherentFileList();
}
+ DirectOrder = true;
}
/**
it != l->end();
++it)
{
- delete *it;
+ delete *it; // remove entry
}
l->clear();
- delete l;
+ delete l; // remove the list
l = GetNextCoherentFileList();
}
}
void SerieHelper::AddFileName(std::string const &filename)
{
// Create a DICOM file
- File *header = new File( filename );
- if( header->IsReadable() )
+ File *header = new File ();
+ header->SetLoadMode(LoadMode);
+ header->SetFileName( filename );
+ header->Load();
+
+ if ( header->IsReadable() )
{
int allrules = 1;
- // First step the user has defined s set of rules for the DICOM he is looking for
+ // 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()))
+ 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 ( allrules ) // all rules are respected:
{
- // Alright ! we have a found a DICOM that match the user expectation.
+ // Allright ! we have a found a DICOM that match the user expectation.
// Let's add it !
// 0020 000e UI REL Series Instance UID
// create a std::list in 'uid' position
CoherentFileListHT[uid] = new FileList;
}
- // Current Serie UID and DICOM header seems to match add the file:
+ // Current Serie UID and DICOM header seems to match; add the file:
CoherentFileListHT[uid]->push_back( header );
}
else
delete header;
}
}
+
+/**
+ * \brief add a gdcm::File to the first (and supposed to be unique) list
+ * of the gdcm::SerieHelper.
+ * \warning : this method should be used by aware users only!
+ * User is supposed to know the files he want to deal with
+ * and consider them they belong to the same Serie
+ * (even if their Serie UID is different)
+ * user will probabely OrderFileList() this list (actually, ordering
+ * user choosen gdm::File is the sole interest of this method)
+ * Moreover, using vtkGdcmReader::SetCoherentFileList() will avoid
+ * vtkGdcmReader parsing twice the same files.
+ * *no* coherence check is performed, but those specified
+ * by SerieHelper::AddRestriction()
+ * @param header gdcm::File* of the file to deal with
+ */
+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)
+ {
+ 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;
+ }
+ }
+ 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 ( 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 );
+ }
+ // Even if a rule was unmatch we don't deallocate the gdcm::File:
+}
+
+/**
+ * \brief add a rules for restricting a DICOM file to be in the serie we are
+ * trying to find. For example you can select only the DICOM file from a
+ * 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
+ */
+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 );
+}
+
+#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
* 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 : AddRestriction(uint16_t group, uint16_t elem,
+ * std::string const &value, int op);
*/
void SerieHelper::AddRestriction(TagKey const &key, std::string const &value)
{
r.second = value;
Restrictions.push_back( r );
}
+#endif
/**
* \brief Sets the root Directory
*/
void SerieHelper::OrderFileList(FileList *coherentFileList)
{
- if( ImagePositionPatientOrdering( coherentFileList ) )
+
+ if ( SerieHelper::UserLessThanFunction )
+ {
+ UserOrdering( coherentFileList );
+ return;
+ }
+ else if ( ImagePositionPatientOrdering( coherentFileList ) )
{
return ;
}
- else if( ImageNumberOrdering(coherentFileList ) )
+ else if ( ImageNumberOrdering(coherentFileList ) )
{
return ;
}
}
}
+/**
+ * \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)
+{
+ if(coherentFileList->size() == 1)
+ return true;
+
+ FileList::const_iterator it = coherentFileList->begin();
+
+ int nX = (*it)->GetXSize();
+ int nY = (*it)->GetYSize();
+ int pixelSize = (*it)->GetPixelSize();
+
+ it ++;
+ for ( ;
+ it != coherentFileList->end();
+ ++it)
+ {
+ if ( (*it)->GetXSize() != nX )
+ return false;
+ if ( (*it)->GetYSize() != nY )
+ return false;
+ if ( (*it)->GetPixelSize() != pixelSize )
+ return false;
+ // probabely more is to be checked (?)
+ }
+ return true;
+}
/**
* \brief Get the first List while visiting the CoherentFileListHT
* @return The first FileList if found, otherwhise NULL
FileList *SerieHelper::GetFirstCoherentFileList()
{
ItListHt = CoherentFileListHT.begin();
- if( ItListHt != CoherentFileListHT.end() )
+ if ( ItListHt != CoherentFileListHT.end() )
return ItListHt->second;
return NULL;
}
/**
* \brief Get the next List while visiting the CoherentFileListHT
- * \note : meaningfull only if GetFirstCoherentFileList already called
+ * \note : meaningfull only if GetFirstCoherentFileList() already called
* @return The next FileList if found, otherwhise NULL
*/
FileList *SerieHelper::GetNextCoherentFileList()
* @return false only if the header is bugged !
*/
bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList )
-//based on Jolinda's algorithm
+//based on Jolinda Smith's algorithm
{
//iop is calculated based on the file file
float cosines[6];
it = fileList->begin();
it != fileList->end(); ++it )
{
- if( first )
+ if ( first )
{
(*it)->GetImageOrientationPatient( cosines );
// gdcmAssertMacro( CoherentFileVector.capacity() >= n );
// Find out if min/max are coherent
- if( min == max )
+ if ( min == max )
{
- gdcmWarningMacro( "Looks like all images have the exact same image position...");
+ gdcmWarningMacro( "Looks like all images have the exact same image position."
+ << "No PositionPatientOrdering sort performed" );
return false;
}
CoherentFileVector[pos] = *it2;
else
{
- gdcmWarningMacro( "2 files same position");
+ gdcmWarningMacro( "At least 2 files with same position. No PositionPatientOrdering sort performed");
return false;
}
}
- fileList->clear(); // doesn't delete list elements, only node
-
- //VC++ don't understand what scope is !! it -> it3
- for (FileVector::const_iterator it3 = CoherentFileVector.begin();
- it3 != CoherentFileVector.end(); ++it3)
- {
- fileList->push_back( *it3 );
+ fileList->clear(); // doesn't delete list elements, only nodes
+
+ if (DirectOrder)
+ {
+ //VC++ don't understand what scope is !! it -> it3
+ for (FileVector::const_iterator it3 = CoherentFileVector.begin();
+ it3 != CoherentFileVector.end(); ++it3)
+ {
+ fileList->push_back( *it3 );
+ }
}
+ else // user asked for reverse order
+ {
+ FileVector::const_iterator it4;
+ it4 = CoherentFileVector.end();
+ do
+ {
+ it4--;
+ fileList->push_back( *it4 );
+ } while (it4 != CoherentFileVector.begin() );
+ }
distlist.clear();
CoherentFileVector.clear();
return file1->GetImageNumber() < file2->GetImageNumber();
}
+bool SerieHelper::ImageNumberGreaterThan(File *file1, File *file2)
+{
+ return file1->GetImageNumber() > file2->GetImageNumber();
+}
/**
* \brief sorts the images, according to their Image Number
* \note Works only on bona fide files (i.e image number is a character string
* corresponding to an integer)
* within a bona fide serie (i.e image numbers are consecutive)
* @param fileList Coherent File list (same Serie UID) to sort
- * @return false if non nona fide stuff encountered
+ * @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))
+ if ( min == max || max == 0 || max >= (n+min) )
+ {
+ gdcmWarningMacro( " 'Image numbers' not coherent. No ImageNumberOrdering sort performed.");
return false;
-
- std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberLessThan );
+ }
+ if (DirectOrder)
+ std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberLessThan );
+ else
+ std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberGreaterThan );
return true;
}
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)
+ std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameLessThan);
+ else
+ std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameGreaterThan);
+
return true;
}
+/**
+ * \brief sorts the images, according to user supplied function
+ * \note Only Direct ordering is allowed
+ * @param fileList Coherent File list (same Serie UID) to sort
+ * @return false only if the header is bugged !
+ */
+bool SerieHelper::UserOrdering(FileList *fileList)
+{
+ if (DirectOrder)
+ std::sort(fileList->begin(), fileList->end(), SerieHelper::UserLessThanFunction);
+ else
+ gdcmWarningMacro( " Only Direct ordering allowed "
+ << "when user function is supplied");
+ return true;
+}
//-----------------------------------------------------------------------------
// Print
/**
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff