add test

[clitk.git] / vv / vvImageReader.cxx

diff --git a/vv/vvImageReader.cxx b/vv/vvImageReader.cxx
index e3e01a3b72076634293edfb0fe473a701116be83..1f33fc72b2abe997ff119adf7f90b156edc7b0e7 100644 (file)
--- a/vv/vvImageReader.cxx
+++ b/vv/vvImageReader.cxx
@@ -22,6 +22,7 @@
 #include <itkImageFileReader.h>
 #include "vvImageReader.h"
 #include "vvImageReader.txx"
+#include "clitkTransformUtilities.h"
 
 //------------------------------------------------------------------------------
 vvImageReader::vvImageReader()
@@ -30,6 +31,7 @@ vvImageReader::vvImageReader()
   mInputFilenames.resize(0);
   mLastError = "";
   mType = UNDEFINEDIMAGETYPE;
+  mSlice = 0;
 }
 //------------------------------------------------------------------------------
 
@@ -122,33 +124,53 @@ void vvImageReader::SetInputFilenames(const std::vector<std::string> & filenames
 //Read transformation in NKI format (Xdr, transposed, cm)
 void vvImageReader::ReadNkiImageTransform()
 {
-  bool bRead=true;
-  typedef itk::ImageFileReader< itk::Image< double, 2 > > MatrixReaderType;
-  MatrixReaderType::Pointer readerTransfo = MatrixReaderType::New();
-  readerTransfo->SetFileName(mInputFilenames[0]+".MACHINEORIENTATION");
-  try {
-    readerTransfo->Update();
-  } catch( itk::ExceptionObject & err ) {
-    bRead=false;
+  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;
+    }
+
+    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();
+      mImage->UpdateReslice();
+    }
   }
+}
+//------------------------------------------------------------------------------
 
-  if (bRead) {
-    double mat[16];
 
-    //Transpose matrix (NKI format)
+//------------------------------------------------------------------------------
+//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);
     for(int j=0; j<4; j++)
       for(int i=0; i<4; i++)
-        mat[4*j+i]=readerTransfo->GetOutput()->GetBufferPointer()[4*i+j];
-
-    //From cm to mm
-    for(int i=0; i<3; i++)
-      mat[4*i+3]*=10;
-
-    //Set Transformation
-    vtkSmartPointer<vtkTransform> pt = vtkSmartPointer<vtkTransform>::New();
-    pt->SetMatrix( mat );
-    pt->Inverse();
-    mImage->SetTransform( pt );
+        mImage->GetTransform()->GetMatrix()->SetElement(j,i,itkMat[j][i]);
+    mImage->UpdateReslice();
   }
 }
 //------------------------------------------------------------------------------