Program: gdcm
Module: $RCSfile: gdcmSerieHelper.cxx,v $
Language: C++
- Date: $Date: 2007/09/20 12:44:16 $
- Version: $Revision: 1.60 $
+ Date: $Date: 2010/04/09 15:38:18 $
+ Version: $Revision: 1.70 $
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");
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 );
}
}
XCoherentFileSetmap CoherentFileSet;
int nb = fileSet->size();
- if (nb == 0 )
+ 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();
- //it ++;
for ( ;
it != fileSet->end();
++it)
// 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];
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;
}
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)
{
gdcmWarningMacro( "Wrong number for Position : ["
<< strImPos << "]" );
- return CoherentFileSet;
+ return CoherentFileSet;
}
// Let's build again the 'position' string, to be sure of it's format
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
if ( CoherentFileSet.count(strTagValue) == 0 )
{
- gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]");
+ gdcmDebugMacro(" :[" << strTagValue << "]");
// create a File set in 'position' position
CoherentFileSet[strTagValue] = new FileList;
}
// Private
/**
* \brief sorts the images, according to their Patient Position.
- * As a side effect, it computes the ZSpacing, according to Jolinda Smith'
+ * 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
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
it = fileList->begin();
it != fileList->end(); ++it )
{
+ gdcmDebugMacro("deal with " << (*it)->GetFileName() );
if ( first )
{
(*it)->GetImageOrientationPatient( cosines );
dist += normal[i]*ipp[i];
}
+ gdcmDebugMacro("dist : " << dist);
distmultimap.insert(std::pair<const double,File *>(dist, *it));
max = min = dist;
}
distmultimap.insert(std::pair<const double,File *>(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. "
+ << "No PositionPatientOrdering sort performed. "
<< "No 'ZSpacing' calculated! ");
return false;
}
it2 != distmultimap.end();
++it2)
{
+
+ gdcmDebugMacro("Check if image shares a common position : " << (*it2).second->GetFileName() );
+
if (distmultimap.count((*it2).first) != 1)
{
- gdcmErrorMacro("File: ["
+ gdcmWarningMacro("File: ["
<< ((*it2).second->GetFileName())
<< "] : more than ONE file at distance: '"
<< (*it2).first
- << " (position is not unique!) "
- << "No PositionPatientOrdering sort performed. "
+ << " (position is not unique!) "
+ << "No PositionPatientOrdering sort performed. "
<< "No 'ZSpacing' calculated! ");
ok = false;
if (! DropDuplicatePositions)
return false;
}
-
-// Now, we could calculate Z Spacing as the difference
+
+// 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
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;
}
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;
}
// 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;
}
// 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.
+ // 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.
+ // then it is difficult to reconstruct them into a 3D volume.
AddRestriction( TagKey(0x0028, 0x0011));
}
}
// Eliminate non-alnum characters, including whitespace...
// that may have been introduced by concats.
- for(unsigned int i=0; i<id.size(); i++)
+ 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')))
{
- while(i<id.size()
- && !( id[i] == '.'
- || (id[i] >= 'a' && id[i] <= 'z')
- || (id[i] >= '0' && id[i] <= '9')
- || (id[i] >= 'A' && id[i] <= 'Z')))
- {
- id.erase(i, 1);
- }
+ 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
{
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.
- for(unsigned int i=0; i<s.size(); i++)
+
+ unsigned int s_size = s.size();
+ 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.erase(i, 1);
- 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);
}
-
id += s.c_str();
id += "%%%"; // make the FileIdentifier Tokenizable
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff