X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vv%2FvvImageReader.cxx;h=0076bf7663767d212d2306b7c52fe8c124fa012b;hb=3d059f81bab4d113bdd5e87bc15a266381ee7182;hp=fde48ce89e5a7e99d462e833b30b5618472dee79;hpb=0b7c9b1e1215634b02cbd38d4e4ba101d6111ba8;p=clitk.git

diff --git a/vv/vvImageReader.cxx b/vv/vvImageReader.cxx
index fde48ce..0076bf7 100644
--- a/vv/vvImageReader.cxx
+++ b/vv/vvImageReader.cxx
@@ -1,7 +1,7 @@
 /*=========================================================================
   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
 
-  Authors belong to: 
+  Authors belong to:
   - University of LYON              http://www.universite-lyon.fr/
   - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
@@ -14,96 +14,170 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
-#ifndef vvImageReader_CXX
-#define vvImageReader_CXX
+  ======================================================================-====*/
+#ifndef VVIMAGEREADER_CXX
+#define VVIMAGEREADER_CXX
+
 #include <QApplication>
 #include <itkImageFileReader.h>
 #include "vvImageReader.h"
 #include "vvImageReader.txx"
+#include "clitkTransformUtilities.h"
 
-
-//====================================================================
+//------------------------------------------------------------------------------
 vvImageReader::vvImageReader()
 {
-    mImage = NULL;
-    mInputFilenames.resize(0);
-    mLastError = "";
-    mType = UNDEFINEDIMAGETYPE;
+  mImage = NULL;
+  mInputFilenames.resize(0);
+  mLastError = "";
+  mType = UNDEFINEDIMAGETYPE;
+  mSlice = 0;
 }
+//------------------------------------------------------------------------------
 
+
+//------------------------------------------------------------------------------
 vvImageReader::~vvImageReader() { }
+//------------------------------------------------------------------------------
+
 
+//------------------------------------------------------------------------------
 void vvImageReader::Update()
 {
-    Update(mType);
+  Update(mType);
 }
+//------------------------------------------------------------------------------
 
+
+//------------------------------------------------------------------------------
 void vvImageReader::Update(LoadedImageType type)
 {
-    itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(mInputFilenames[0].c_str(), itk::ImageIOFactory::ReadMode);
-    if (!reader) {
-        mLastError="Unable to read file.";
-    }
-    else {
-        reader->SetFileName(mInputFilenames[0]);
-        reader->ReadImageInformation();
-        if (mInputFilenames.size() > 1)
-            Update(reader->GetNumberOfDimensions()+1,reader->GetComponentTypeAsString(reader->GetComponentType()),type);
-        else
-            Update(reader->GetNumberOfDimensions(),reader->GetComponentTypeAsString(reader->GetComponentType()),type);
-    }
+  itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(mInputFilenames[0].c_str(), itk::ImageIOFactory::ReadMode);
+  if (!reader) {
+    mLastError="Unable to read file.";
+  } else {
+    reader->SetFileName(mInputFilenames[0]);
+    reader->ReadImageInformation();
+    if (mInputFilenames.size() > 1)
+      Update(reader->GetNumberOfDimensions()+1,reader->GetComponentTypeAsString(reader->GetComponentType()),type);
+    else
+      Update(reader->GetNumberOfDimensions(),reader->GetComponentTypeAsString(reader->GetComponentType()),type);
+  }
 }
+//------------------------------------------------------------------------------
 
-//====================================================================
-void vvImageReader::Update(int dim,std::string inputPixelType, LoadedImageType type) {
-    //CALL_FOR_ALL_DIMS(dim,UpdateWithDim,inputPixelType);
-    mType = type;
-    mDim = dim;
-    mInputPixelType=inputPixelType;
-    this->start(); //Start heavy read operation in a separate thread
-    while (this->isRunning())
-    {
-        qApp->processEvents();
-        this->wait(50);
-    }
+
+//------------------------------------------------------------------------------
+void vvImageReader::Update(int dim,std::string inputPixelType, LoadedImageType type)
+{
+  //CALL_FOR_ALL_DIMS(dim,UpdateWithDim,inputPixelType);
+  mType = type;
+  mDim = dim;
+  mInputPixelType=inputPixelType;
+  this->start(); //Start heavy read operation in a separate thread
+  while (this->isRunning()) {
+    qApp->processEvents();
+    this->wait(50);
+  }
 }
+//------------------------------------------------------------------------------
+
 
+//------------------------------------------------------------------------------
 void vvImageReader::run()
 {
-    switch(mDim)
-    {
-        case 2:
-            UpdateWithDim<2>(mInputPixelType);
-            break;;
-        case 3:
-            UpdateWithDim<3>(mInputPixelType);
-            break;;
-        case 4:
-            UpdateWithDim<4>(mInputPixelType);
-            break;;
-        default:
-            std::cerr << "dimension unknown in Update ! " << std::endl;
-    }
+  switch(mDim)     {
+  case 2:
+    UpdateWithDim<2>(mInputPixelType);
+    break;;
+  case 3:
+    UpdateWithDim<3>(mInputPixelType);
+    break;;
+  case 4:
+    UpdateWithDim<4>(mInputPixelType);
+    break;;
+  default:
+    std::cerr << "dimension unknown in Update ! " << std::endl;
+  }
 }
-//====================================================================
+//------------------------------------------------------------------------------
+
 
-//====================================================================
-/*void vvImageReader::Extract(int dim, std::string inputPixelType, int slice) {
-  CALL_FOR_ALL_DIMS(dim, ExtractWithDim, inputPixelType, slice);
-}*/
-//====================================================================
+//------------------------------------------------------------------------------
 void vvImageReader::SetInputFilename(const std::string & filename)
 {
-    mInputFilenames.resize(0);
-    mInputFilenames.push_back(filename);
+  mInputFilenames.resize(0);
+  mInputFilenames.push_back(filename);
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvImageReader::SetInputFilenames(const std::vector<std::string> & filenames)
+{
+  mInputFilenames = filenames;
 }
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+//Read transformation in NKI format (Xdr, transposed, cm)
+void vvImageReader::ReadNkiImageTransform()
+{
+  bool bRead=false;
+  std::string filename = mInputFilenames[0]+".MACHINEORIENTATION";
+  if(itksys::SystemTools::FileExists(filename.c_str())){
+    typedef itk::ImageFileReader< itk::Image< double, 2 > > MatrixReaderType;
+    MatrixReaderType::Pointer readerTransfo = MatrixReaderType::New();
+    readerTransfo->SetFileName(filename);
+    try {
+      bRead = true;
+      readerTransfo->Update();
+    } catch( itk::ExceptionObject & err ) {
+      bRead=false;
+      std::cerr << "Cannot read " << filename << std::endl
+                << "The error is: " << err << std::endl;
+    }
 
-//====================================================================
-void vvImageReader::SetInputFilenames(const std::vector<std::string> & filenames) {
-    mInputFilenames = filenames;
+    if (bRead) {
+      //Transpose matrix (NKI format)
+      for(int j=0; j<4; j++)
+        for(int i=0; i<4; i++)
+          mImage->GetTransform()->GetMatrix()->SetElement(j,i,readerTransfo->GetOutput()->GetBufferPointer()[4*i+j]);
+
+      //From cm to mm
+      for(int i=0; i<3; i++)
+        mImage->GetTransform()->GetMatrix()->SetElement(i,3,10*mImage->GetTransform()->GetMatrix()->GetElement(i,3));
+
+      mImage->GetTransform()->Inverse();
+    }
+  }
 }
-//====================================================================
+//------------------------------------------------------------------------------
+
 
+//------------------------------------------------------------------------------
+//Read transformation in ASCII format
+void vvImageReader::ReadMatImageTransform()
+{
+  std::string filename(mInputFilenames[0]+".mat");
+  std::ifstream f(filename.c_str());
+  if(f.is_open()) {
+    f.close();
+    
+    itk::Matrix<double, 4, 4> itkMat = clitk::ReadMatrix3D(filename);
+    
+    vtkSmartPointer<vtkTransform> transform = vtkSmartPointer<vtkTransform>::New();
+    transform->Identity();
+    for(int j=0; j<4; j++)
+      for(int i=0; i<4; i++)
+        transform->GetMatrix()->SetElement(j,i,itkMat[j][i]);
+
+    mImage->GetTransform()->PostMultiply();
+    mImage->GetTransform()->Concatenate(transform->GetMatrix());
+    mImage->GetTransform()->Update();
+  }
+}
+//------------------------------------------------------------------------------
 #endif