Program: gdcm
Module: $RCSfile: gdcmSerieHelper.cxx,v $
Language: C++
- Date: $Date: 2006/05/30 08:10:19 $
- Version: $Revision: 1.53 $
+ Date: $Date: 2011/03/31 21:45:11 $
+ Version: $Revision: 1.72 $
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 <map>
#include <stdio.h> //for sscanf
-namespace gdcm
+namespace GDCM_NAME_SPACE
{
//-----------------------------------------------------------------------------
ClearAll();
UserLessThanFunction = 0;
DirectOrder = true;
+ DropDuplicatePositions = false;
}
/**
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)
{
// 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)
}
/**
- * \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
* 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
*/
bool SerieHelper::AddFile(File *header)
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 << "]");
/**
* \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 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;
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();
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
* \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 )
+ if (nb == 0 ) {
+ gdcmWarningMacro("Empty FileList passed to SplitOnTagValue");
return CoherentFileSet;
+ }
std::string strTagValue; // read on disc
FileList::const_iterator it = fileSet->begin();
- it ++;
+ //it ++;
for ( ;
it != fileSet->end();
++it)
// 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 )
{
- 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" );
+ gdcmWarningMacro("Looks like all images have the exact same image position. "
+ << "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())
- << " Distance: "
+ << "] : more than ONE file at distance: '"
<< (*it2).first
- << " position is not unique");
+ << " (position is not unique!) "
+ << "No PositionPatientOrdering sort performed. "
+ << "No 'ZSpacing' calculated! ");
ok = false;
}
}
if (!ok)
{
- return 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
++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
{
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() );
}
*/
void SerieHelper::Print(std::ostream &os, std::string const &indent)
{
- // For all the Coherent File lists of the gdcm::Serie
+ // For all the Coherent File lists of the GDCM_NAME_SPACE::Serie
SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
if ( itl == SingleSerieUIDFileSetHT.end() )
{
// 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;
}
// 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.
+ // 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));
}
* 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 )
{
const ExRule &r = *it2;
std::string s = inFile->GetEntryString( r.group, r.elem );
- if( s == gdcm::GDCM_UNFOUND )
+ if( s == GDCM_UNFOUND )
{
s = "";
}
}
// 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
{
gdcmWarningMacro("Could not parse series info.");
- std::string id = gdcm::GDCM_UNFOUND;
+ std::string id = GDCM_UNFOUND;
return id;
}
}
* -File class? FileHelper class?-
* @return FileIdentifier (Tokenizable on '%%%'. Hope it's enough !)
*/
-std::string SerieHelper::CreateUserDefinedFileIdentifier( File * inFile )
+std::string SerieHelper::CreateUserDefinedFileIdentifier( File *inFile )
{
// Deal with all user supplied tags.
// (user knows more than we do about his images!)
{
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 'convertion', to allow further ordering
+ // 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)
{
}
}
// 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()
- && !( s[i] == '.' || s[i] == '%'
- || (s[i] >= 'a' && s[i] <= 'z')
- || (s[i] >= '0' && s[i] <= '9')
- || (s[i] >= 'A' && s[i] <= 'Z')))
+ for(unsigned int i=0; i<s_size; i++)
{
- s.erase(i, 1);
+ 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;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff