Program: gdcm
Module: $RCSfile: vtkGdcm4DSplitter.cxx,v $
Language: C++
- Date: $Date: 2011/03/29 12:51:21 $
- Version: $Revision: 1.2 $
+ Date: $Date: 2011/04/08 00:11:36 $
+ Version: $Revision: 1.8 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
(ImageSeriesReader::GenerateData() line 393).
*/
+
+/* ====================================================================
+vtkGdcm4DSplitter
+
+3D, 2D+T, 3D+T, n*2D+T, 4D images are not always stored the same way :
+ a single 'Dicom Serie',
+ several 'Dicom series' within a single directory
+ several 'Dicom series' within several directories
+A 'Dicom Serie' doesn't mean always the same thing :
+ a given Slice along the time
+ a given Volume at a given time
+Sometimes, an image within a serie is so artefacted than user decides to replace
+it by an other image.
+
+User needs to be aware, *only him* knows want he wants to do.
+vtkGdcm4DSplitter class does the job for hom
+(despite its name, it works on 3D or 2D+T images too)
+
+User will have to specify some points
+
+. Choose input data
+-------------------
+
+- a single directory
+ bool setDirName(std::string &dirName);
+- a list of directories
+ bool setVectDirName(std::vector<std::string> &vectDirName);
+- a list of files
+ bool setVectFileName(std::vector<std::string> &vectFileName);
+
+- Recursive directory exploration
+ void setRecursive(bool recursive);
+
+. Choose 'split' criterion :
+---------------------------
+
+ - ImagePositionPatient
+ void setSplitOnPosition();
+ - ImageOrientationPatient
+ void setSplitOnOrientation();
+ - User choosen tag
+ void setSplitOnTag(unsigned short splitGroup, unsigned short splitElem);
+ void setSplitConvertToFloat(bool conv);
+ - UserDefined Function
+ void setSortOnUserFunction (FoncComp f);
+
+ for 'true' 3D image sets :
+ - if you want to get a single 3D vtkImageData, use SplitOnOrientation -i.e. no split-
+ - if you want to get a vector of 2D vtkImageData, use SplitOnPosition -i.e. one slice in each 'XCoherent filesite'-
+
+ for 'true' 4D multi-orientation image sets (i.e. a stack of axial + sagital + coronal images, at different instants ...)
+ --> this is 5D, right?
+ Nothing done, yet.
+
+
+. Choose 'sort' criterion :
+--------------------------
+
+ - ImagePositionPatient
+ void setSortOnPosition();
+ - ImageOrientationPatient
+ ==> Only in your dreams!
+ ==> or, please, write a IOP sorter ...
+ - UserDefined Function
+ void setSortOnUserFunction (FoncComp f);
+ - File name
+ void setSortOnFileName()
+
+. Execute :
+-----------
+ bool Go();
+
+. Get the result
+----------------
+
+// -a single vtkImageData:
+// vtkImageData *GetImageData();
+- a vector of vtkImageData
+ std::vector<vtkImageData*> *GetImageDataVector();
+
+ ===================================================================== */
+
#include "gdcmSerieHelper.h"
#include "vtkGdcmReader.h"
SortOnPosition(false), SortOnOrientation(false), SortOnTag(false),
SortGroup(0), SortElem(0), SortConvertToFloat(false),
- Recursive(false), TypeDir(0),
- verbose(true)
+ Recursive(false), TypeDir(0),
+ verbose(false)
{
}
std::vector<vtkImageData*> * vtkGdcm4DSplitter::GetImageDataVector()
- {
- if (verbose) std::cout << "TypeDir " << TypeDir << std::endl;
+ {
+/*
+ if (verbose) std::cout << "GetImageDataVector : TypeResult " << TypeResult << std::endl;
if (TypeResult == 2)
return ImageDataVector;
else
}
else
return (std::vector<vtkImageData*>*) NULL;
+*/
+ return ImageDataVector;
}
vtkImageData *vtkGdcm4DSplitter::GetImageData()
{
+ /*
+ if (verbose) std::cout << "GetImageData : TypeResult " << TypeResult << std::endl;
if (TypeResult == 1)
return ImageData;
else
- if (TypeResult == 1)
+ if (TypeResult == 2)
{
return (*ImageDataVector)[0];
}
else
return (vtkImageData*) NULL;
- }
-
+*/
+ return (*ImageDataVector)[0];
+ }
bool vtkGdcm4DSplitter::setDirName(std::string &dirName)
{
bool vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
{
- if (verbose) printf ("%04x %04x\n", this->SortGroup,this->SortElem);
- if (verbose) std :: cout << file1->GetEntryString(SortGroup,SortElem).c_str() << " : "
+ /* if (verbose) printf ("%04x %04x\n", this->SortGroup,this->SortElem);
+ if (verbose) std :: cout << file1->GetEntryString(SortGroup,SortElem).c_str() << " : "
<< atof(file1->GetEntryString(SortGroup,SortElem).c_str())
<< std::endl;
- return atof(file1->GetEntryString(SortGroup,SortElem).c_str()) < atof(file2->GetEntryString(SortGroup,SortElem).c_str());
+*/
+// return atof(file1->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem).c_str()) < atof(file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem).c_str());
+ return atof(file1->GetEntryString(SortGroup,SortElem).c_str()) < atof(file2->GetEntryString(SortGroup,SortElem).c_str());
}
bool vtkGdcm4DSplitter::CompareOnSortTag(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
{
- return file1->GetEntryString(SortGroup,SortElem) < file2->GetEntryString(SortGroup,SortElem);
+ return file1->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem) < file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem);
}
-
+
+
bool vtkGdcm4DSplitter::Go()
{
if (!SplitOnPosition && !SplitOnOrientation && !SplitOnTag )
TypeResult=2;
ImageDataVector = new std::vector<vtkImageData*>;
- vtkGdcmReader *reader = vtkGdcmReader::New();
+ // vtkGdcmReader *reader = vtkGdcmReader::New(); // move inside the loop, or be clever using vtk!
+
for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
i != xcm.end();
++i)
i != xcm.end();
++i)
{
- if (verbose)
+
+ vtkGdcmReader *reader = vtkGdcmReader::New(); /// \FIXME : unable to delete!
+
+ if (verbose)
std::cout << "==========================================xCoherentName = [" << (*i).first << "]" << std::endl;
- if (SortOnPosition)
- {
+ if (SortOnPosition)
+ {
if (verbose) std::cout << "SortOnPosition" << std::endl;
// (will be IPPSorter, in GDCM2)
s->ImagePositionPatientOrdering((*i).second);
if (verbose) std::cout << "out of SortOnPosition" << std::endl;
- }
+ }
- if (SortOnOrientation)
- {
+ else if (SortOnOrientation)
+ {
if (verbose) std::cout << "SortOnOrientation" << std::endl;
- /// \TODO SortOnOrientation()
- // Within a 'just to see' program,
- // OrderFileList() causes trouble, since some files
- // (eg:MIP views) don't have 'Position', now considered as mandatory
- // --> Activated on user demand.
-
- // Information is in :
- // 0020,0032 : Image Position Patient
- // 0020,0030 : Image Position (RET)
+ /// \TODO SortOnOrientation()
// we still miss an algo to sort an Orientation, given by 6 cosines!
- // Anything like this, in GDCM2?
- std::cout << "SortOnOrientation : not so easy - I(mage)O(rientation)P(atient)Sorter still missing! -" << std::endl;
- // have a look at SerieHelper::SplitOnPosition() to have an idea of the mess!
+ // Anything like this, in GDCM2?
+ std::cout << "SortOnOrientation : not so easy - I(mage)O(rientation)P(atient)Sorter still missing! -" << std::endl;
+ // have a look at SerieHelper::SplitOnOrientation() to have an idea of the mess!
- //Better sort on the file name, right now...
- s->FileNameOrdering((*i).second);
- }
+ //Better sort on the file name, right now...
+ s->FileNameOrdering((*i).second);
+ }
- if (SortOnFileName)
- {
- if (verbose) std::cout << "SortOnFileName" << std::endl;
- if (verbose) std::cout << "taille " << ((*i).second)->size() << std::endl;
- s->FileNameOrdering((*i).second);
- if (verbose) std::cout << "Out of SortOnFileName" << std::endl;
- }
+ else if (SortOnFileName)
+ {
+ if (verbose) std::cout << "SortOnFileName" << std::endl;
+ if (verbose) std::cout << "taille " << ((*i).second)->size() << std::endl;
- if (SortOnTag)
- {
- if (verbose) std::cout << "SortOnTag" << std::endl;
- printf ("--> %04x %04x\n", SortGroup,SortElem);
- if ( SortConvertToFloat )
- s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
- ( &vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat));
- else
- s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
- ( &vtkGdcm4DSplitter::CompareOnSortTag));
+ s->FileNameOrdering((*i).second);
+ if (verbose) std::cout << "Out of SortOnFileName" << std::endl;
+ }
+
+ else if (SortOnTag)
+ {
+ if (verbose) std::cout << "SortOnTag" << std::endl;
+ printf ("--> %04x %04x\n", SortGroup,SortElem);
+ std::cout << "Sorry, troubles not solved yet; use SortOnUserFunction, right now!" << std::endl;
+
+ /* ==> WARNING : This one has troubles; do NOT use it, right now!
+ // a pointer to fonction cannot be casted as a pointer to member function!
+ // Use SortOnUserFunction, instead!
+
+ if ( SortConvertToFloat )
+ s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
+ ( &vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat));
+ else
+ s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
+ ( &vtkGdcm4DSplitter::CompareOnSortTag));
- // Anything like this, in GDCM2?
- s->UserOrdering((*i).second);
- if (verbose) std::cout << "Out of SortOnTag" << std::endl;
- }
+ // Anything like this, in GDCM2?
+ s->UserOrdering((*i).second);
+ */
- reader->SetCoherentFileList((*i).second);
- reader->Update();
- ImageDataVector->push_back(reader->GetOutput() );
+ //if (verbose) std::cout << "Out of SortOnTag" << std::endl;
+ std::cout << "NO ordering performed :-( " << std::endl;
+ }
+
+ else if (SortOnUserFunction)
+ {
+ if (verbose) std::cout << "SortOnUserFunction" << std::endl;
+ s->SetUserLessThanFunction( UserCompareFunction );
+ // Anything like this, in GDCM2?
+ s->UserOrdering((*i).second);
+ if (verbose) std::cout << "Out of SortOnUserFunction" << std::endl;
+ }
- std::cout << std::endl;
+ reader->SetCoherentFileList((*i).second);
+ reader->Update();
+
+ /// \TODO : remove the following
+ if (verbose) {
+ std::cout << "reader->GetOutput() :" << std::endl;
+ reader->GetOutput()->PrintSelf(std::cout, vtkIndent(2));
+ }
+
+ ImageDataVector->push_back(reader->GetOutput() );
+
+ std::vector<vtkImageData*>::iterator it;
+ if (verbose)
+ for(it=ImageDataVector->begin(); it!=ImageDataVector->end(); ++it) {
+ std::cout << "-in vtkGdcm4DSplitter--------------------------" << std::endl;
+ (*it)->PrintSelf(std::cout, vtkIndent(2));
+ }
+ std::cout << std::endl;
}
- reader->Delete();
+ //reader->Delete(); // \TODO : fix
s->Delete();
f->Delete();
delete l;
+
+ return true;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff