From 4aeb9af4e4ba8f56f45f5698ae39458943282ee6 Mon Sep 17 00:00:00 2001
From: Vivien Delmon <vivien.delmon@creatis.insa-lyon.fr>
Date: Fri, 3 Feb 2012 13:22:57 +0100
Subject: [PATCH] Correct bug when opening non 3D vector field

- vvImageReader was opening vector field of nD vectors with the itk 3D
  reader. Now we open the vector field with the appropriate itk reader
  and then convert it to 3D vectors which are the only one supported by
  vv.
---
 common/vvImageReader.h   |  2 +
 common/vvImageReader.txx | 79 +++++++++++++++++++++++++++++++++++++---
 2 files changed, 76 insertions(+), 5 deletions(-)

diff --git a/common/vvImageReader.h b/common/vvImageReader.h
index 2f1de53..dae05e4 100644
--- a/common/vvImageReader.h
+++ b/common/vvImageReader.h
@@ -85,6 +85,8 @@ protected:
   //====================================================================
   template<class InputPixelType, unsigned int VImageDimension>
   void UpdateWithDimAndInputPixelType();
+  template<class InputPixelType, unsigned int VImageDimension>
+  void UpdateWithDimAndInputVectorPixelType();
   ///Input dimension and pixel type
   int mDim;
   std::string mInputPixelType;
diff --git a/common/vvImageReader.txx b/common/vvImageReader.txx
index 2d7d5b5..e15e6d7 100644
--- a/common/vvImageReader.txx
+++ b/common/vvImageReader.txx
@@ -24,6 +24,7 @@
 #include <itkImageSeriesReader.h>
 #include <itkImageToVTKImageFilter.h>
 #include <itkAnalyzeImageIO.h>
+#include <itkVectorCastImageFilter.h>
 
 #include <vtkTransform.h>
 
@@ -35,7 +36,7 @@ template<unsigned int VImageDimension>
 void vvImageReader::UpdateWithDim(std::string InputPixelType)
 {
   if (mType == VECTORFIELD || mType == VECTORFIELDWITHTIME)
-    UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
+    UpdateWithDimAndInputVectorPixelType<itk::Vector<float,VImageDimension>,VImageDimension>();
   else if (InputPixelType == "short")
     UpdateWithDimAndInputPixelType<short,VImageDimension>();
   else if (InputPixelType == "unsigned_short")
@@ -162,10 +163,7 @@ void vvImageReader::UpdateWithDimAndInputPixelType()
       reader->ReleaseDataFlagOn();
 
       try {
-        if (mType == IMAGEWITHTIME || mType == VECTORFIELDWITHTIME)
-          mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
-        else
-          mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
+        mImage = vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(), mType == IMAGEWITHTIME || mType == VECTORFIELDWITHTIME);
       } catch ( itk::ExceptionObject & err ) {
         std::cerr << "Error while reading " << mInputFilenames[0].c_str()
                   << " " << err << std::endl;
@@ -195,6 +193,77 @@ void vvImageReader::UpdateWithDimAndInputPixelType()
 }
 //----------------------------------------------------------------------------
 
+//----------------------------------------------------------------------------
+template<class InputPixelType, unsigned int VImageDimension>
+void vvImageReader::UpdateWithDimAndInputVectorPixelType()
+{
+  itk::AnalyzeImageIO *analyzeImageIO = NULL;
+
+  typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
+  typename InputImageType::Pointer input;
+
+  if (mInputFilenames.size() > 1) {
+    typedef itk::ImageSeriesReader<InputImageType> ReaderType;
+    typename ReaderType::Pointer reader = ReaderType::New();
+    reader->SetFileNames(mInputFilenames);
+    reader->ReleaseDataFlagOn();
+    try {
+      reader->Update();
+      input = reader->GetOutput();
+    } catch ( itk::ExceptionObject & err ) {
+      std::cerr << "Error while reading image series:" << err << std::endl;
+      std::stringstream error;
+      error << err;
+      mLastError = error.str();
+      return;
+    }
+  } else {
+    typedef itk::ImageFileReader<InputImageType> ReaderType;
+    typename ReaderType::Pointer reader = ReaderType::New();
+    reader->SetFileName(mInputFilenames[0]);
+    reader->ReleaseDataFlagOn();
+    try {
+      reader->Update();
+      input = reader->GetOutput();
+    } catch ( itk::ExceptionObject & err ) {
+      std::cerr << "Error while reading " << mInputFilenames[0].c_str()
+        << " " << err << std::endl;
+      std::stringstream error;
+      error << err;
+      mLastError = error.str();
+      return;
+    }
+    analyzeImageIO = dynamic_cast<itk::AnalyzeImageIO*>( reader->GetImageIO() );
+  }
+
+  typedef itk::Image< itk::Vector<float , 3>, VImageDimension > VectorImageType;
+  typedef itk::VectorCastImageFilter<InputImageType, VectorImageType> CasterType;
+  typename VectorImageType::Pointer casted_input;
+  typename CasterType::Pointer caster = CasterType::New();
+  caster->SetInput(input);
+  casted_input = caster->GetOutput();
+
+  mImage = vvImageFromITK<VImageDimension, itk::Vector<float, 3> >(casted_input, mType == IMAGEWITHTIME || mType == VECTORFIELDWITHTIME);
+
+  // For unknown analyze orientations, we set identity
+  if (analyzeImageIO)
+  {
+    const double m[16] = {1.,0.,0.,0.,
+                          0.,0.,1.,0.,
+                          0.,-1.,0.,0.,
+                          0.,0.,0.,1.};
+    int i;
+    for (i = 0; i < 16 && m[i] == mImage->GetTransform()->GetMatrix()->GetElement(i % 4, i / 4); i++)
+      ;
+    if (i == 16)
+    {
+      itkWarningMacro(<< "Analyze image file format detected with unknown orientation. "
+                      << "Forcing identity orientation, use other file format if not ok.");
+      mImage->GetTransform()->Identity();
+    }
+  }
+}
+//----------------------------------------------------------------------------
 
 #endif /* end #define vvImageReader_TXX */
 
-- 
2.45.1