Change serie number to serie UID

[clitk.git] / common / vvImageReader.cxx

diff --git a/common/vvImageReader.cxx b/common/vvImageReader.cxx
index f4f1a907214912b61b4bbe295a1c2652c6359c8e..a2fc4e964ab8edeeef1e57cb0f6a4b742c371d44 100644 (file)
--- a/common/vvImageReader.cxx
+++ b/common/vvImageReader.cxx
@@ -19,9 +19,11 @@
 #define VVIMAGEREADER_CXX
 
 #include <itkImageFileReader.h>
+#include "gdcmImageHelper.h"
 #include "vvImageReader.h"
 #include "vvImageReader.txx"
 #include "clitkTransformUtilities.h"
+#include "clitkElastix.h"
 
 //------------------------------------------------------------------------------
 vvImageReader::vvImageReader()
@@ -31,6 +33,7 @@ vvImageReader::vvImageReader()
   mLastError = "";
   mType = UNDEFINEDIMAGETYPE;
   mSlice = 0;
+  mPatientCoordinateSystem = false;
 }
 //------------------------------------------------------------------------------
 
@@ -48,6 +51,14 @@ void vvImageReader::Update()
 //------------------------------------------------------------------------------
 
 
+//------------------------------------------------------------------------------
+void vvImageReader::SetPatientCoordinateSystem(bool patientCoordinateSystem)
+{
+  mPatientCoordinateSystem = patientCoordinateSystem;
+}
+//------------------------------------------------------------------------------
+
+
 //------------------------------------------------------------------------------
 void vvImageReader::Update(LoadedImageType type)
 {
@@ -56,9 +67,12 @@ void vvImageReader::Update(LoadedImageType type)
     mLastError="Unable to read file.";
   } else {
     reader->SetFileName(mInputFilenames[0]);
+    gdcm::ImageHelper::SetForcePixelSpacing(true);
     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);
   }
@@ -150,19 +164,48 @@ 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;
+
+    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();
 
-    itk::Matrix<double, 4, 4> itkMat = clitk::ReadMatrix3D(filename);
+  // 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++)
@@ -200,12 +243,12 @@ void vvImageReader::ReadMatImageTransform()
     //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();
-        }
+      for (unsigned i = 1 ; i<mImage->GetTransform().size() ; i++)
+      {
+        mImage->GetTransform()[i]->PreMultiply();
+        mImage->GetTransform()[i]->Concatenate(matrix);
+        mImage->GetTransform()[i]->Update();
+      }
     }
 
   }