X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=common%2FvvImageReader.cxx;h=0e4c22ba05b468522dace0bf3b08ee2412652d08;hb=bfbffc033e8c2f7a9448dcf8611e5a81b1898559;hp=c795cd9299697c7a34c784c1973541c7012e777d;hpb=2191f760d44987f901445c4105c577df7995b25d;p=clitk.git

diff --git a/common/vvImageReader.cxx b/common/vvImageReader.cxx
index c795cd9..0e4c22b 100644
--- a/common/vvImageReader.cxx
+++ b/common/vvImageReader.cxx
@@ -22,6 +22,7 @@
 #include "vvImageReader.h"
 #include "vvImageReader.txx"
 #include "clitkTransformUtilities.h"
+#include "clitkElastix.h"
 
 //------------------------------------------------------------------------------
 vvImageReader::vvImageReader()
@@ -59,6 +60,8 @@ void vvImageReader::Update(LoadedImageType type)
     reader->ReadImageInformation();
     if (mInputFilenames.size() > 1)
       Update(reader->GetNumberOfDimensions()+1,reader->GetComponentTypeAsString(reader->GetComponentType()),type);
+    else if (reader->GetNumberOfComponents() > 1 && type != VECTORFIELD && type != VECTORFIELDWITHTIME)
+      Update(reader->GetNumberOfDimensions()+1,reader->GetComponentTypeAsString(reader->GetComponentType()),VECTORPIXELIMAGE);
     else
       Update(reader->GetNumberOfDimensions(),reader->GetComponentTypeAsString(reader->GetComponentType()),type);
   }
@@ -77,13 +80,13 @@ void vvImageReader::Update(int dim,std::string inputPixelType, LoadedImageType t
   switch(mDim)     {
   case 2:
     UpdateWithDim<2>(mInputPixelType);
-    break;;
+    break;
   case 3:
     UpdateWithDim<3>(mInputPixelType);
-    break;;
+    break;
   case 4:
     UpdateWithDim<4>(mInputPixelType);
-    break;;
+    break;
   default:
     std::cerr << "dimension unknown in Update ! " << std::endl;
   }
@@ -150,19 +153,48 @@ void vvImageReader::ReadMatImageTransform()
 {
   std::string filename(mInputFilenames[0]);
   std::string ext(itksys::SystemTools::GetFilenameLastExtension(filename));
+
+  // Try a ".mat" extension
   if (ext.length() > 0) {
     size_t pos = filename.rfind(ext);
     filename.replace(pos, ext.length(), ".mat");
   }
   else
     filename += ".mat";
-    
   std::ifstream f(filename.c_str());
+  itk::Matrix<double, 4, 4> itkMat;
+  bool itkMatRead = false;
   if(f.is_open()) {
-    f.close();
+    itkMatRead = true;
 
-    itk::Matrix<double, 4, 4> itkMat = clitk::ReadMatrix3D(filename);
+    itkMat.SetIdentity();
+    try {
+      itkMat = clitk::ReadMatrix3D(filename);
+    }
+    catch (itk::ExceptionObject & err) {
+      itkWarningMacro(<< "Found " << filename
+                      << " but this is not a 4x4 matrix so it is ignored.");
+      itkMatRead = false;
+    }
+  }
+  f.close();
+
+  // Try a ".elx" extension
+  filename = mInputFilenames[0];
+  if (ext.length() > 0) {
+    size_t pos = filename.rfind(ext);
+    filename.replace(pos, ext.length(), ".elx");
+  }
+  else
+    filename += ".elx";
+  f.open(filename.c_str());
+  if(!itkMatRead && f.is_open()) {
+    itkMatRead = true;
+    itkMat = clitk::createMatrixFromElastixFile<3>(filename, true);
+  }
+  f.close();
 
+  if(itkMatRead) {
     vtkSmartPointer<vtkMatrix4x4> matrix = vtkSmartPointer<vtkMatrix4x4>::New();
     matrix->Identity();
     for(int j=0; j<4; j++)
@@ -193,9 +225,21 @@ void vvImageReader::ReadMatImageTransform()
     }
 
     // TODO SR and BP: check on the list of transforms and not the first only
-    mImage->GetTransform()[0]->PostMultiply();
+    mImage->GetTransform()[0]->PreMultiply();
     mImage->GetTransform()[0]->Concatenate(matrix);
     mImage->GetTransform()[0]->Update();
+
+    //for image sequences, apply the transform to each images of the sequence
+    if (mImage->IsTimeSequence())
+    {
+      for (unsigned i = 1 ; i<mImage->GetTransform().size() ; i++)
+      {
+        mImage->GetTransform()[i]->PreMultiply();
+        mImage->GetTransform()[i]->Concatenate(matrix);
+        mImage->GetTransform()[i]->Update();
+      }
+    }
+
   }
 }
 //------------------------------------------------------------------------------