#include <creaImageIOSystem.h>
#include "boost/filesystem.hpp"
+#include <gdcmSerieHelper.h> // JPR
+#include <gdcmFile.h> // JPR
+#include <vtkGdcmReader.h> // JPR
+#include <gdcmDebug.h>
+
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();
-
}
//======================================================================
mReaderStarted=false;
}
//======================================================================
-
+
//======================================================================
/// Finalize
void GimmickView::Finalize()
/// Create a tree view with a given name
void GimmickView::CreateSingleTreeView(std::string &i_name)
{
- this->CreateTreeView(mGimmick->GetTreeHandlerMap()[i_name]);
+ this->CreateTreeView(mGimmick->GetTreeHandlerMap()[i_name]);
}
-
//======================================================================
//======================================================================
GimmickError("INTERNAL ERROR : GimmickView::UpdateTreeView : '"
<<t<<"' is not in TreeViewMap");
}
- i->second->UpdateLevel(l);
+ i->second->UpdateLevel(l);
}
+
//======================================================================
/// Clears the status and begins a new selection process
void GimmickView::ResetExtent()
valid=true;
}
-
//======================================================================
-
+
//======================================================================
bool ImageExtent::IsCompatible(const ImageExtent& ie)
{
}
//======================================================================
-
+
//======================================================================
void ImageExtent::Add(const ImageExtent& ie)
{
else
{
boost::shared_ptr<ImageExtent> ie=boost::shared_ptr<ImageExtent>(new ImageExtent((*sel).GetAttribute("D0028_0010"),
- (*sel).GetAttribute("D0028_0011"),
- (*sel).GetAttribute("D0028_0012"),
- ""));
+ (*sel).GetAttribute("D0028_0011"),
+ (*sel).GetAttribute("D0028_0012"),
+ ""));
if(mImageExtent==0)
{
mImageExtent=ie;
{
std::stringstream out;
out << mImageExtent->GetDimension() << "D image " << mImageExtent->Get(0) << "x"<< mImageExtent->Get(1) << "x"<< mImageExtent->Get(2) <<" selected";
- mMessage = out.str();
+ mMessage = out.str();
mImageExtent->SetDimension(2);
valid=true;
}
}
else
{
- mImageExtent->Add(*ie);
- std::stringstream out;
- out << mImageExtent->GetDimension() << "D image " << mImageExtent->Get(0) << "x"<< mImageExtent->Get(1) << "x"<< mImageExtent->Get(2) <<" selected";
- mMessage = out.str();
+ mImageExtent->Add(*ie);
+ std::stringstream out;
+ out << mImageExtent->GetDimension() << "D image " << mImageExtent->Get(0) << "x"<< mImageExtent->Get(1) << "x"<< mImageExtent->Get(2) <<" selected";
+ mMessage = out.str();
}
}
else
///Reads Images (Non Threaded)
void GimmickView::ReadImagesNotThreaded(std::vector<vtkImageData*>& s, std::vector<std::string> im, int dimension)
{
+
+/* remember!
+
+#define GIMMICK_NO_IMAGE_SELECTION 0
+#define GIMMICK_2D_IMAGE_SELECTION 2
+#define GIMMICK_3D_IMAGE_SELECTION 3
+#define GIMMICK_4D_IMAGE_SELECTION 4
+
+#define NATIVE 0
+#define _2D 2
+#define _3D 3
+
+*/
// 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);
- out->ShallowCopy(mReader.GetImage(im.front()));
- s.push_back( out );
- }
- else if (im.size()>1) // Test inutile ? JPR
{
+ // O0.
+ }
+ 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)
- {
+
+ if (dimension == 2)
+ {
// n3D
std::vector<std::string>::iterator it;
for (it=im.begin(); it!=im.end(); ++it)
s.push_back(out);
}
}
- else
+ else if (dimension == 3)
{
- // n2D to 3D
+ // 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 !
vtkImageData* out = vtkImageData::New();
out->CopyStructure(first);
out->SetScalarType(first->GetScalarType());
+ out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
int ext[6];
- first->GetExtent(ext);
+ //first->GetExtent(ext); // JPR
+ first->GetWholeExtent(ext); // renvoie egalement 0,0 en Z // JPR
+ // Normal :
+
if(ext[5] == 0)
{
ext[5] = im.size()-1;
ext[5] = ext[5] * im.size()-1; // to deal with multiframes - JPR
}
out->SetExtent(ext);
- // LG : TODO : Z Spacing ?
- out->AllocateScalars();
-
- //first->Print(std::cout);
- // out->Print(std::cout);
+ // LG : TODO : Z Spacing ? // Voir + loin // JPR
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
+ imsize = imsize * dim[2] ; // deal with multiframes // JPR
+
+
+//EED 03-11-2009
+ // differents formats char , short, etc...
+ // differents components 1..3 ex. jpg ->RGB 3
+ imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
- /*
- ( (unsigned long)first->GetScalarPointer(0,1,0)
- - (unsigned long)first->GetScalarPointer(0,0,0))
- *dim[1];*/
+ // Order the file name vector
+
+ double spc[3];
+ out->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);
- memcpy(out->GetScalarPointer(0,0,slice),cur->GetScalarPointer(0,0,0),imsize*first->GetScalarSize());
-
- slice++;
+ vtkImageData* cur = mReader.GetImage( (*it) );
+ memcpy(out->GetScalarPointer(0,0,slice), cur->GetScalarPointer(0,0,0), imsize);
+ slice++;
}
s.push_back(out);
+
+ } // dimension == 3
+
+ } // size >1
+
+}
+ //======================================================================
+
+
+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())
+ {
+ fileVector.push_back(f);
+ } else {
+ lstAux.push_back(*it);
}
+ } // for
+
+
+ if ((fileVector.size()>1) && (sh->IsCoherent( &fileVector )))
+ {
+ sh->OrderFileList(&fileVector);
+ spacing= sh->GetZSpacing();
+ im.clear();
+ int i;
+ for (i=0; i<fileVector.size(); i++)
+ {
+ im.push_back( (fileVector[i])->GetFileName() );
+ }
+ for (i=0; i<lstAux.size(); i++)
+ {
+ im.push_back( lstAux[i] );
+ }
+ }else {
+ std::sort( im.begin(), im.end() );
}
+
+ return spacing;
}
- //======================================================================
+
+
+//======================================================================
+
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)
{
- vtkImageData* out = mReader.GetImage( (*it));
+ std::cout << "---------------------------------------- [" << *it << "]" << std::endl;
+ //vtkImageData* out = mReader.GetImage( (*it));
+ //s.push_back(out);
+ vtkImageData* out = vtkImageData::New();
+ out->ShallowCopy(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