Program: gdcm
Module: $RCSfile: vtkGdcm4DSplitter.cxx,v $
Language: C++
- Date: $Date: 2011/04/15 15:14:40 $
- Version: $Revision: 1.11 $
+ Date: $Date: 2011/09/20 16:09:05 $
+ Version: $Revision: 1.15 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
VTK reader 'flop upside down' the images to display them correctly ?!?
When a 'math guy' gets the image, the first thing he does is flipping it again.
Avoid loosing CPU time using :
- bool SetFlipY(bool); // Wrong = no flip
+ void SetFlipY(bool); // Wrong = no flip
. Execute :
-----------
*/
vtkGdcm4DSplitter::vtkGdcm4DSplitter() :
SplitOnPosition(false), SplitOnOrientation(false), SplitOnTag(false),
- SplitGroup(0), SplitElem(0), SplitConvertToFloat(false),
+ SplitGroup(0), SplitElem(0), SplitConvertToFloat(false), SplitOnly(false),
- SortOnPosition(false), SortOnOrientation(false), SortOnTag(false), SortOnFileName(false), SortOnUserFunction(false),
- SortGroup(0), SortElem(0), SortConvertToFloat(false),
+ SortOnPosition(false), SortOnOrientation(false), /* SortOnTag(false),*/ SortOnFileName(false), SortOnUserFunction(false),
+ /*SortGroup(0), SortElem(0), SortConvertToFloat(false),*/
- Recursive(false), TypeDir(0),
+ Recursive(false),FlipY(true), TypeDir(0),
verbose(false)
{
*/
vtkGdcm4DSplitter::~vtkGdcm4DSplitter()
{
- /// \TODO : delete everything that must be!
+ /// \TODO : delete everything that must be!
+
+ GDCM_NAME_SPACE::XCoherentFileSetmap::iterator it;
+ std::vector<GDCM_NAME_SPACE::File*>::iterator it2;
+
+ for ( it = xcm.begin(); // for each std::vector<gdcm::File*>
+ it != xcm.end();
+ ++it)
+ {
+ for ( it2 = (*it).second->begin(); // for each gdcm::File*
+ it2 != (*it).second->end();
+ ++it2)
+ {
+ (*it2)->Delete(); // delete gdcm::File
+ }
+ delete (*it).second; // delete the now empty std::vector<gdcm::File*>
+ }
+
+ // VectGdcmFileLists is a vector of pointers on elements of xcm : nothing to do!
+
}
// Locate Data to process
}
/**
- * \brief Sets a list of files read
+ * \brief Sets a list of files names to read
* @param vectFileName vector of file names to deal with
*/
bool vtkGdcm4DSplitter::setVectFileName(std::vector<std::string> &vectFileName)
}
/**
- * \brief Sets a vector of gdcm::File *
- * @param vectGdcmFileName vector of gdcm::File *
+ * \brief Sets an already filled std::vector of gdcm::File *
+ * @param vectGdcmFileName std::vector of gdcm::File *
*/
bool vtkGdcm4DSplitter::setVectGdcmFile(GDCM_NAME_SPACE::FileList *vectGdcmFile)
}
- // Split
- // =====
+ // Split criterion
+ // ===============
+ //
/**
* \brief asks for splitting Filesets according to the Position
- */
-
+ */
void vtkGdcm4DSplitter::setSplitOnPosition()
{
SplitOnPosition=true;
SplitOnOrientation=false;
SplitOnTag=false;
}
+
/**
* \brief asks for splitting Filesets according to the Orientation
- */
+ */
void vtkGdcm4DSplitter::setSplitOnOrientation()
{
SplitOnPosition=false;
SplitOnOrientation=true;
SplitOnTag=false;
}
+
/**
* \brief asks for splitting Filesets according to the value of a given Tag
* @param group group number of the target Element
SplitGroup=splitGroup;
SplitElem=splitElem;
}
+
/**
* \brief asks for converting to 'float' the tag values used as a splitting criteria (lexicographic order may not be suitable)
*/
{
SplitOnly = s;
}
- // Sort
- // ====
-
+
+ // Sort criterion
+ // ==============
+ //
+
+/**
+ * \brief asks for IPP sorting each XCoherent gdcm::FILE set
+ */
void vtkGdcm4DSplitter::setSortOnPosition()
{
SortOnPosition=true;
SortOnOrientation=false;
- SortOnTag=false;
+ //SortOnTag=false;
SortOnFileName=false;
SortOnUserFunction=false;
SortOnPosition=true;
}
- // use setSortOnUserFunction, instead!
- // void setSortOnTag(unsigned short int sortGroup, unsigned short int sortElem)
- // {
- // SortOnPosition=false;
- // SortOnOrientation=false;
- // SortOnTag=true;
- // SortOnFileName=false;
- // SortOnUserFunction=false;
- // SortGroup=sortGroup; SortElem=sortElem;
- // }
+ // use setSortOnUserFunction, instead!
+ // void setSortOnTag(unsigned short int sortGroup, unsigned short int sortElem)
+ // {
+ // SortOnPosition=false;
+ // SortOnOrientation=false;
+ // SortOnTag=true;
+ // SortOnFileName=false;
+ // SortOnUserFunction=false;
+ // SortGroup=sortGroup; SortElem=sortElem;
+ // }
/**
UserCompareFunction=f;
SortOnPosition=false;
SortOnOrientation=false;
- SortOnTag=false;
+ //SortOnTag=false;
SortOnFileName=false;
SortOnUserFunction=true;
- }
-
+ }
// void setSortConvertToFloat(bool conv)
// {
// }
/**
- * \brief asks for sorting the images, according to their File Name
+ * \brief asks for sorting each XCoherent gdcm::FILE set, according to the File names
*/
void vtkGdcm4DSplitter::setSortOnFileName()
{
SortOnPosition=false;
SortOnOrientation=false;
- SortOnTag=false;
+ //SortOnTag=false;
SortOnFileName=true;
SortOnUserFunction=false;
}
-
- std::vector<vtkImageData*> * vtkGdcm4DSplitter::GetImageDataVector()
- {
- if (SplitOnly)
- return NULL;
-
- return ImageDataVector;
- }
-
+/**
+ * \brief returns a std::vector of gdcm::FileList* (gdcm::FileList : actually, a std::vector of gdcm::File*)
+ */
std::vector<GDCM_NAME_SPACE::FileList *> *vtkGdcm4DSplitter::GetVectGdcmFileLists()
{
if (SplitOnly)
- return NULL;
+ return &VectGdcmFileLists;
GDCM_NAME_SPACE::XCoherentFileSetmap::iterator it;
for ( it = xcm.begin();
}
return &VectGdcmFileLists;
}
-
+/**
+ * \brief returns a std::vector of [2D/3D, depending on what was passed] vtkImageData*
+ */
+ std::vector<vtkImageData*> * vtkGdcm4DSplitter::GetImageDataVector()
+ {
+ if (SplitOnly)
+ return NULL;
+ return ImageDataVector;
+ }
+
+/**
+ * \brief when user _knows_ only _one_ vtkImageData* is returned he may be interested in not getting a vector...
+ */
vtkImageData *vtkGdcm4DSplitter::GetImageData()
{
if (SplitOnly)
return NULL;
- return (*ImageDataVector)[0];
+ return (*ImageDataVector)[0];
}
- 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() << " : "
- << atof(file1->GetEntryString(SortGroup,SortElem).c_str())
- << std::endl;
-*/
+// bool vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
+// {
// 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());
- }
+// 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(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem) < file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem);
- }
+// bool vtkGdcm4DSplitter::CompareOnSortTag(GDCM_NAME_SPACE::File *file1, GDCM_NAME_SPACE::File *file2)
+// {
+// return file1->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem) < file2->GetEntryString(vtkGdcm4DSplitter::SortGroup,vtkGdcm4DSplitter::SortElem);
+// }
bool vtkGdcm4DSplitter::Go()
{
- if (!SplitOnPosition && !SplitOnOrientation && !SplitOnTag)
- {
- ///\TODO (?) Throw an exception "Choose Splitting mode before!"
- std::cout << "Choose Splitting mode before!" << std::endl;
- return false;
- }
-
/// How To :
/*
entree nom de directory / Vecteur de noms?
trier chaque Coherent file set
passer chacun a un vtkGcdmReader
retourner le (vecteur de) vtkImageData
- */
-
- GDCM_NAME_SPACE::SerieHelper *s;
- s = GDCM_NAME_SPACE::SerieHelper::New();
+ */
- GDCM_NAME_SPACE::File *f;
- GDCM_NAME_SPACE::DirListType fileNames;
-
- //
- // Fill fileNames with the user supplied file names (in any)
- // --------------------------------------
- //
- if (TypeDir == 0 )
- {
- ///\TODO (?) Throw an exception "Set input Directory name(s) / file names before!"
- std::cout << "Set input Directory name(s) / file names before!" << std::endl;
- return false;
- }
- else if (TypeDir == 1)
- {
- GDCM_NAME_SPACE::DirList dirlist(DirName, Recursive); // NO recursive exploration
- fileNames = dirlist.GetFilenames(); // all the file names
- }
-
- else if (TypeDir == 2)
+ if (!SplitOnPosition && !SplitOnOrientation && !SplitOnTag)
{
- int nbDir = VectDirName.size();
- GDCM_NAME_SPACE::DirListType tmpFileNames;
- for (int iDir=0; iDir<nbDir; iDir++)
- {
- GDCM_NAME_SPACE::DirList dirlist(VectDirName[iDir], Recursive);
- tmpFileNames = dirlist.GetFilenames();
- // Concat two std::vector
- //vector1.insert( vector1.end(), vector2.begin(), vector2.end() );
- fileNames.insert( fileNames.end(), tmpFileNames.begin(), tmpFileNames.end() );
- }
+ ///\TODO (?) Throw an exception "Choose Splitting mode before!"
+ std::cout << "Choose Splitting mode before!" << std::endl;
+ return false;
}
- else if (TypeDir == 3)
- {
- fileNames=VectFileName;
- }
- //
- // Fill l with the gdcm::File* corresponding to the files
- // --------------------------------------
- //
-
- GDCM_NAME_SPACE::FileList *l = new GDCM_NAME_SPACE::FileList; // (set of gdcm::File)
-
- if (TypeDir == 4)
- {
- // User passed a vector of gdcm::File*
- l = VectGdcmFile;
- }
- else
- {
- double floatTagvalue;
- // Loop on all the gdcm-readable files
- for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin();
- it != fileNames.end();
- ++it)
- {
- int maxSize = 0x7fff; // load Elements of any length
- f = GDCM_NAME_SPACE::File::New();
- f->SetMaxSizeLoadEntry(maxSize);
- f->SetFileName( *it );
- if (f->Load())
- l->push_back(f);
- else
- std::cout << " Fail to load [" << *it << "]" << std::endl;
- }
- }
+ GDCM_NAME_SPACE::FileList *l;
+ GDCM_NAME_SPACE::SerieHelper *s;
+ s = GDCM_NAME_SPACE::SerieHelper::New();
+//
+// Load the gdcm::File* set, according to user's requierements
+// ------------------------------------------------------------
+//
+ l = getGdcmFileList();
+std::cout << l->size() << " gdcm::File read" << std::endl;
//
// Split the gdcm::File* set, according to user's requierements
// ------------------------------------------------------------
xcm = s->SplitOnTagValue(l, SplitGroup, SplitElem);
else
{
- xcm = s->SplitOnTagValueConvertToFloat(l, SplitGroup, SplitElem);
+ xcm = s->SplitOnTagValueConvertToFloat(l, SplitGroup, SplitElem);
}
- }
-
+ }
+
if (xcm.size() == 0)
{
- if(verbose) std::cout << "Empty XCoherent File Set after 'split' ?!?" << std::endl;
+ if(verbose)
+ std::cout << "Empty XCoherent File Set after 'split' ?!?" << std::endl;
return false;
}
-/*
- else if (xcm.size() == 1)
- TypeResult=1;
else
- TypeResult=2;
-*/
+ {
+ std::cout << xcm.size() << " XCoherent entries found" << std::endl;
+ }
+
+ // put here, to avoid segfault when unaware user sets SplitOnly to true, and the asks for ImageDataVector
+ ImageDataVector = new std::vector<vtkImageData*>;
+ std::cout <<"SplitOnly " << SplitOnly << std::endl;
if(SplitOnly)
return true;
//
//
// ------------------------------------------------------------
//
- ImageDataVector = new std::vector<vtkImageData*>;
+// ImageDataVector = new std::vector<vtkImageData*>;
+
/// \TODO move inside the loop, or be clever using vtk!
- // vtkGdcmReader *reader = vtkGdcmReader::New(); // move inside the loop, or be clever using vtk!
-
- // XCoherentFileSetmap map < critère de split, FileList (= std::vector de gdcm::File*) >
+ vtkGdcmReader *reader = vtkGdcmReader::New(); // move inside the loop, or be clever using vtk!
+
+ // XCoherentFileSetmap map < critère de split, FileList (= std::vector de gdcm::File*) >
for (GDCM_NAME_SPACE::XCoherentFileSetmap::iterator i = xcm.begin();
- i != xcm.end();
- ++i)
+ i != xcm.end();
+ ++i)
{
- vtkGdcmReader *reader = vtkGdcmReader::New(); /// \TODO FIXME : unable to delete!
+ //vtkGdcmReader *reader = vtkGdcmReader::New(); /// \TODO FIXME : unable to delete!
reader->SetFlipY(FlipY);
// better user SetFileLowerLeft()
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;
+// 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));
+ // s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
+ // ( &vtkGdcm4DSplitter::CompareOnSortTagConvertToFloat));
// else
// s->SetUserLessThanFunction( reinterpret_cast<bool (*)(gdcm13::File*, gdcm13::File*)>
- ( &vtkGdcm4DSplitter::CompareOnSortTag));
+ ( &vtkGdcm4DSplitter::CompareOnSortTag));
// Anything like this, in GDCM2?
// s->UserOrdering((*i).second);
*/
- //if (verbose) std::cout << "Out of SortOnTag" << std::endl;
- std::cout << "NO ordering performed :-( " << std::endl;
- }
+// //if (verbose) std::cout << "Out of SortOnTag" << std::endl;
+// std::cout << "NO ordering performed :-( " << std::endl;
+// }
else if (SortOnUserFunction)
{
/// \TODO : remove the following
if (verbose) {
- std::cout << "reader->GetOutput() :" << std::endl;
- reader->GetOutput()->PrintSelf(std::cout, vtkIndent(2));
+ // 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)
+ //if (verbose) // JPR
+
for(it=ImageDataVector->begin(); it!=ImageDataVector->end(); ++it) {
- std::cout << "-in vtkGdcm4DSplitter--------------------------" << std::endl;
- (*it)->PrintSelf(std::cout, vtkIndent(2));
+ // std::cout << "-in vtkGdcm4DSplitter --------------------------" << std::endl;
+ // (*it)->PrintSelf(std::cout, vtkIndent(2));
}
- std::cout << std::endl;
+ //std::cout << std::endl;
}
- //reader->Delete(); // \TODO : fix
+ reader->Delete(); // \TODO : fix
s->Delete();
- f->Delete();
+ // f->Delete();
delete l;
return true;
}
+/**
+ * \brief Load the gdcm::File* set, according to user's requierements
+ * returns a std::vector of gdcm::File* (gdcm::FileList : actually, a std::vector of gdcm::File*)
+ */
+
+
+GDCM_NAME_SPACE::FileList *vtkGdcm4DSplitter::getGdcmFileList()
+{
+
+ GDCM_NAME_SPACE::File *f;
+ GDCM_NAME_SPACE::DirListType fileNames;
+
+ //
+ // Fill fileNames with the user supplied file names (in any)
+ // ------------------------------------------------
+ //
+ if (TypeDir == 0 ) // Nothing was set as input...
+ {
+ ///\TODO (?) Throw an exception "Set input Directory name(s) / file names before!"
+ std::cout << "Set input Directory name(s) / file names before!" << std::endl;
+ return false;
+ }
+ else if (TypeDir == 1) // A root directory name was set as input
+ {
+ GDCM_NAME_SPACE::DirList dirlist(DirName, Recursive); // NO recursive exploration
+ fileNames = dirlist.GetFilenames(); // all the file names
+ }
+
+ else if (TypeDir == 2) // a std::vector of directory names was set as input
+ {
+ int nbDir = VectDirName.size();
+ GDCM_NAME_SPACE::DirListType tmpFileNames;
+ for (int iDir=0; iDir<nbDir; iDir++)
+ {
+ GDCM_NAME_SPACE::DirList dirlist(VectDirName[iDir], Recursive);
+ tmpFileNames = dirlist.GetFilenames();
+ // Concat two std::vector
+ //vector1.insert( vector1.end(), vector2.begin(), vector2.end() );
+ fileNames.insert( fileNames.end(), tmpFileNames.begin(), tmpFileNames.end() );
+ }
+ }
+ else if (TypeDir == 3) // a list of files names was set as input
+ {
+ fileNames=VectFileName;
+ }
+
+ //
+ // Fill l with the gdcm::File* corresponding to the files
+ // --------------------------------------
+ //
+
+ GDCM_NAME_SPACE::FileList *l = new GDCM_NAME_SPACE::FileList; // (set of gdcm::File*)
+
+ if (TypeDir == 4) // an already existing std::vector of gdcm::File* was set as input
+ {
+ l = VectGdcmFile;
+ }
+ else
+ {
+ double floatTagvalue;
+ // Loop on all the gdcm-readable files
+ for (GDCM_NAME_SPACE::DirListType::iterator it = fileNames.begin();
+ it != fileNames.end();
+ ++it)
+ {
+ int maxSize = 0x7fff; // load Elements of any length
+ /// \TODO ? gdcm::File are never free'd
+ f = GDCM_NAME_SPACE::File::New();
+ f->SetMaxSizeLoadEntry(maxSize);
+ f->SetFileName( *it );
+ if (f->Load())
+ l->push_back(f);
+ else
+ std::cout << " Fail to load [" << *it << "]" << std::endl;
+ }
+ }
+ return l;
+}
+
+
+
void vtkGdcm4DSplitter::reorgXCoherentFileSetmap(GDCM_NAME_SPACE::XCoherentFileSetmap &xcm)
{
/*
ELEM e;
std::vector<ELEM> vectElem;
-/* remenber :
+/* just to remember :
typedef struct
{
std::string strIPP;
bool vtkGdcm4DSplitter::sortVectElem(std::vector<ELEM> *fileList)
{
//based on Jolinda Smith's algorithm
+//
// NOTE : if you need to use Jolinda Smith's algorithm, get the one inside gdcm::SerieHelper
// this one is a light version.
//to right, "y" is posterior to anterior, and "z" is foot to head (RAH).
//iop is calculated based on the file file
- float cosines[6];
+ float cosines[6];
double normal[3];
double ipp[3];
double dist;
double min = 0, max = 0;
- bool first = true;
+ bool first = true;
//double ZSpacing; // useless here! // JPR
bool DirectOrder = true; // remove it!
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff