Program: gdcm
Module: $RCSfile: gdcmSerieHelper.cxx,v $
Language: C++
- Date: $Date: 2007/10/01 09:28:57 $
- Version: $Revision: 1.62 $
+ Date: $Date: 2011/04/04 17:33:58 $
+ Version: $Revision: 1.73 $
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"
ClearAll();
UserLessThanFunction = 0;
DirectOrder = true;
-
+ DropDuplicatePositions = false;
}
/**
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(id) == 0 )
{
gdcmDebugMacro(" New/gdcmSerieHelper.cxx Serie UID :[" << id << "]");
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 );
}
}
if ( SerieHelper::UserLessThanFunction )
{
- gdcmDebugMacro("Use UserLessThanFunction");
+ gdcmDebugMacro("Use UserLessThanFunction");
UserOrdering( fileSet );
return;
}
* \return std::map of 'Xcoherent' File sets
*/
-XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet,
+XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet,
uint16_t group, uint16_t element)
{
XCoherentFileSetmap CoherentFileSet;
int nb = fileSet->size();
if (nb == 0 ) {
- gdcmWarningMacro("Empty FileList passed to SplitOnPosition");
+ gdcmWarningMacro("Empty FileList passed to SplitOnTagValue");
return CoherentFileSet;
}
// 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*10000.;
+ sprintf(cTagValue, "%010d", iTagValue);
+ strTagValue = cTagValue;
if ( CoherentFileSet.count(strTagValue) == 0 )
{
bool first = true;
ZSpacing = -1.0; // will be updated if process doesn't fail
+ gdcmDebugMacro("============================================DropDuplicatePositions : " << DropDuplicatePositions );
+
std::multimap<double,File *> distmultimap;
// Use a multimap to sort the distances from 0,0,0
for ( FileList::const_iterator
}
}
+ gdcmDebugMacro("After parsing vector, nb of elements : " << fileList->size() );
+
// Find out if min/max are coherent
if ( min == max )
{
it2 != distmultimap.end();
++it2)
{
+
+ gdcmDebugMacro("Check if image shares a common position : " << (*it2).second->GetFileName() );
+
if (distmultimap.count((*it2).first) != 1)
{
gdcmWarningMacro("File: ["
fileList->push_back( (*it3).second );
if (DropDuplicatePositions)
{
- /// \todo ImagePositionPatientOrdering wrong duplicates are found ???
-
+ // 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;
}
fileList->push_back( (*it4).second );
if (DropDuplicatePositions) // skip all duplicates
{
- it4 = distmultimap.upper_bound((*it4).first);
+ // 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;
}
}
}
// deal with Dicom strings trailing '\0'
- if(id[s_size-1] == '_')
+ if(s_size && id[s_size-1] == '_')
id.erase(s_size-1, 1);
return id;
}
{
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
}
// Eliminate non-alphanum characters, including whitespace.
unsigned int s_size = s.size();
- for(unsigned int i=0; i<s_size; i++)
+ if(s_size == 0)
+ { // to avoid further troubles when wild anonymization was performed
+ s = "a";
+ }
+ else
{
- while(i<s_size
+ 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
+ {
+ 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);
}
- // 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
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff