#include <creaImageIOSystem.h>
#include "boost/filesystem.hpp"
-#include <gdcmSerieHelper.h> // JPR
-#include <gdcmFile.h> // JPR
-#include <vtkGdcmReader.h> // JPR
-#include <gdcmDebug.h>
+#if defined(USE_GDCM)
+#include <gdcmGlobal.h>
+#include <gdcmSerieHelper.h>
+#include <vtkGdcmReader.h>
+#endif
+
+#if defined(USE_GDCM2)
+#include <vtkGDCMImageReader.h>
+#endif
-namespace fs = boost::filesystem;
+namespace fs = boost::filesystem;
namespace creaImageIO
{
public:
ImageExtent(const std::string& x, const std::string& y, const std::string& z, const std::string& t)
{
- sscanf(x.c_str(),"%d",&mExtent[0]);
- sscanf(y.c_str(),"%d",&mExtent[1]);
- sscanf(z.c_str(),"%d",&mExtent[2]);
- sscanf(t.c_str(),"%d",&mExtent[3]);
- if(x==""){mExtent[0]=1;}
- if(y==""){mExtent[1]=1;}
- if(z==""){mExtent[2]=1;}
- if(t==""){mExtent[3]=1;}
-
- if (mExtent[3]>1) mDim=4;
- else if (mExtent[2]>1) mDim=3;
- else if (mExtent[1]>1) mDim=2;
- else if (mExtent[0]>1) mDim=1;
- else mDim=0;
+ sscanf(x.c_str(),"%d",&mExtent[0]);
+ sscanf(y.c_str(),"%d",&mExtent[1]);
+ sscanf(z.c_str(),"%d",&mExtent[2]);
+ sscanf(t.c_str(),"%d",&mExtent[3]);
+ if(x==""){mExtent[0]=1;}
+ if(y==""){mExtent[1]=1;}
+ if(z==""){mExtent[2]=1;}
+ if(t==""){mExtent[3]=1;}
+
+ if (mExtent[3]>1) mDim=4;
+ else if (mExtent[2]>1) mDim=3;
+ else if (mExtent[1]>1) mDim=2;
+ else if (mExtent[0]>1) mDim=1;
+ else mDim=0;
}
+
///Clears the extent
void Clear() { mExtent[0] = mExtent[1] = mExtent[2] = mExtent[3] = 1; }
// Anciently started the threads ...
// Threads now automatically start at first image request
//mReader.Start();
+
}
//======================================================================
}
+
//======================================================================
//======================================================================
///Reads Images (Non Threaded)
void GimmickView::ReadImagesNotThreaded(std::vector<vtkImageData*>& s, std::vector<std::string> im, int dimension)
{
-
+ mReader.Stop();
/* remember!
#define GIMMICK_NO_IMAGE_SELECTION 0
// Create the output data
if (im.size()==1)
{
- // Only one image : give it
- vtkImageData* out = vtkImageData::New();
- GimmickDebugMessage(3, "State Check: Full Filename: "
- <<im.front()
- <<std::endl);
+ vtkImageData * out=vtkImageData::New();
out->ShallowCopy(mReader.GetImage(im.front()));
- s.push_back( out );
+ s.push_back(out);
}
- else if (im.size()>1) // Test inutile ? JPR
+ else if (im.size()>1) // Test inutile ? JPR
{
- // Read the FIRST image to get info ... about all the other ones. ?!? // JPR
vtkImageData* first = mReader.GetImage( im.front());
-
if (dimension == 2)
{
// n3D
s.push_back(out);
}
}
- else if (dimension == 3)
+ else
{
- // n*2D to 3D :: --> NON ! Ca va tres bien pour du 2D+T (le ZSpacing, on s'en tape)
- // // ne convient pas pour du n*2D a lire comme un 3D
- // // Il faut un gdcmSerieHelper !
+ // n*2D to 3D
vtkImageData* out = vtkImageData::New();
- out->CopyStructure(first);
+// out->CopyStructure(first);
out->SetScalarType(first->GetScalarType());
+ out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
int ext[6];
- //first->GetExtent(ext); // JPR
+ //first->GetExtent(ext); // JPR
first->GetWholeExtent(ext); // renvoie egalement 0,0 en Z // JPR
- // Normal :
-
-std::cout <<"in GimmickView::ReadImagesNotThreaded GetWholeExtent ext =";
-for (int jjj=0;jjj<6;jjj++)
- std:cout << " [" << jjj << "]=" << ext[jjj];
-std::cout << std::endl;
if(ext[5] == 0)
{
}
out->SetExtent(ext);
- // LG : TODO : Z Spacing ? // Voir + loin // JPR
-
- out->AllocateScalars();
+ // LG : TODO : Z Spacing ?
int dim[3];
first->GetDimensions(dim);
+
+ out->SetDimensions(dim[0], dim[1], im.size() );
+ out->AllocateScalars();
+ out->Update();
+
unsigned long imsize = dim[0] * dim[1];
imsize = imsize * dim[2] ; // deal with multiframes // JPR
+
+
//EED 03-11-2009
- imsize = imsize * first->GetScalarSize();
+ // differents formats char , short, etc...
+ // differents components 1..3 ex. jpg ->RGB 3
+ imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
+
+
+ // Order the file name vector
+
+ double spc[3];
+ first->GetSpacing(spc);
+ spc[2]=OrderTheFileNameVector(im);
+
+ out->SetSpacing(spc);
int slice = 0;
std::vector<std::string>::iterator it;
+
for (it=im.begin(); it!=im.end(); ++it)
{
- vtkImageData* cur = mReader.GetImage( (*it));
- // void* src = cur->GetScalarPointer(0,0,0);
- // void* dst = out->GetScalarPointer(0,0,slice);
+ vtkImageData* cur = mReader.GetImage( (*it) );
memcpy(out->GetScalarPointer(0,0,slice), cur->GetScalarPointer(0,0,0), imsize);
-
slice++;
}
s.push_back(out);
- }
-/**/
- else // ici, on traite le cas *vraiment* n*2D as 3D // JPR
+
+ } // dimension == 3
+
+ } // size >1
+
+}
+ //======================================================================
+
+#if defined(USE_GDCM)
+ double GimmickView::OrderTheFileNameVector(std::vector<std::string> &im)
+{
+ double spacing=1;
+ typedef std::vector<GDCM_NAME_SPACE::File* > FileList;
+ FileList fileVector;
+ //GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New();
+ GDCM_NAME_SPACE::SerieHelper *sh = GDCM_NAME_SPACE::SerieHelper::New();
+ std::vector<std::string> lstAux;
+ std::vector<std::string>::iterator it;
+ for (it=im.begin(); it!=im.end(); ++it)
+ {
+ ///\TODO liberer les GDCM_NAME_SPACE::File a la fin! // JPR
+ GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New();
+ f->SetFileName(*it);
+ f->Load();
+ if (f->IsReadable())
{
- typedef std::vector<GDCM_NAME_SPACE::File* > FileList;
- FileList fileVector;
- //GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New();
- GDCM_NAME_SPACE::SerieHelper *sh = GDCM_NAME_SPACE::SerieHelper::New();
- std::vector<std::string>::iterator it;
- for (it=im.begin(); it!=im.end(); ++it)
- {
- //std::cout << "avant Load ---------" << *it << std::endl;
-
- ///\TODO liberer les GDCM_NAME_SPACE::File a la fin! // JPR
- GDCM_NAME_SPACE::File *f = GDCM_NAME_SPACE::File::New();
-
- f->SetFileName(*it);
- f->Load();
- if (f->IsReadable())
- fileVector.push_back(f);
- else
- std::cout << "File [" << *it << "] not GDCM Readable; Skipped!" << std::endl;
- }
+ fileVector.push_back(f);
+ } else {
+ lstAux.push_back(*it);
+ }
+ } // for
- /*
- for (int i=0; i<fileVector.size();i++)
- {
- std::cout << "avant tri ---------" << fileVector[i]->GetFileName() << std::endl;
- }
- */
- if (!sh->IsCoherent(&fileVector))
- {
- std::cout << "---------fileset is NOT coherent ?!?" << *it << std::endl;
- //return;
- }
- else
+
+ if ((fileVector.size()>1) && (sh->IsCoherent( &fileVector )))
+ {
+ sh->OrderFileList(&fileVector);
+ spacing= sh->GetZSpacing();
+ im.clear();
+ int i;
+ for (i=0; i<fileVector.size(); i++)
{
- sh->OrderFileList(&fileVector);
+ im.push_back( (fileVector[i])->GetFileName() );
}
- /*
- for (int i=0; i<fileVector.size();i++)
+ for (i=0; i<lstAux.size(); i++)
{
- std::cout << "apres tri ---------" << fileVector[i]->GetFileName() << std::endl;
+ im.push_back( lstAux[i] );
}
- */
- vtkGdcmReader *reader = vtkGdcmReader::New();
- reader->SetCoherentFileList(&fileVector);
- reader->Update();
- s.push_back(reader->GetOutput());
- reader->GetOutput()->Print(std::cout);
- }
- /**/
+ }else {
+ std::sort( im.begin(), im.end() );
}
+
+ return spacing;
}
- //======================================================================
+
+
+#endif
+
+#if defined(USE_GDCM2)
+ // TO DO
+ double GimmickView::OrderTheFileNameVector(std::vector<std::string> &im)
+ {
+ return 1;
+ }
+#endif
+//======================================================================
+
void GimmickView::ReadImagesNotThreadedInVector(std::vector<vtkImageData*>& s, std::vector<std::string> im, int dimension)
{
if (dimension == 2)
{
// n3D
- std::vector<std::string>::iterator it;
+ std::vector<std::string>::iterator it;
for (it=im.begin(); it!=im.end(); ++it)
{
- std::cout << "----------------------------------------n3D" << std::endl;
vtkImageData* out = vtkImageData::New();
out->ShallowCopy(mReader.GetImage(*it));
s.push_back(out);
{
// n2D to 3D // NO!
// n *2D + T in a vector :
- std::cout << "---------------------------------------- n *2D + T" << std::endl;
+
std::vector<std::string>::iterator it;
for (it=im.begin(); it!=im.end(); ++it)
{
- std::cout << "---------------------------------------- [" << *it << "]" << std::endl;
- //vtkImageData* out = mReader.GetImage( (*it));
- //s.push_back(out);
- vtkImageData* out = vtkImageData::New();
- out->ShallowCopy(mReader.GetImage(*it));
+ vtkImageData* out = mReader.GetImage( (*it));
s.push_back(out);
}
}
void GimmickView::RequestReading(tree::Node* n,
int prio, int selection_index, boost::shared_ptr<ImagePointerHolder> p)
{
- if(!mReaderStarted)
- {
- mReader.Start();
- mReaderStarted=true;
- }
- ImageEventType t(n,selection_index);
- t.pointerHolder = p;
- mImageEventMap[n->GetAttribute("FullFileName")] = t;
- mReader.Request(this,n->GetAttribute("FullFileName"),prio);
+ if(!mReaderStarted)
+ {
+ mReader.Start();
+ mReaderStarted=true;
+ }
+ ImageEventType t(n,selection_index);
+ t.pointerHolder = p;
+ mImageEventMap[n->GetAttribute("FullFileName")] = t;
+ mReader.Request(this,n->GetAttribute("FullFileName"),prio);
}
//======================================================================
git://git.creatis.insa-lyon.fr / creaImageIO.git / blobdiff