Removed warnings

[clitk.git] / common / vvImageReader.txx

diff --git a/common/vvImageReader.txx b/common/vvImageReader.txx
index e3c2bca72d327e25743346b604dac59ba6c11bb0..2d7d5b573f3c9a2985bfef023c21f4a542c53537 100644 (file)
--- a/common/vvImageReader.txx
+++ b/common/vvImageReader.txx
@@ -3,7 +3,7 @@
 
   Authors belong to:
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 #ifndef VVIMAGEREADER_TXX
 #define VVIMAGEREADER_TXX
@@ -23,6 +23,7 @@
 #include <itkImageFileReader.h>
 #include <itkImageSeriesReader.h>
 #include <itkImageToVTKImageFilter.h>
+#include <itkAnalyzeImageIO.h>
 
 #include <vtkTransform.h>
 
@@ -33,7 +34,7 @@
 template<unsigned int VImageDimension>
 void vvImageReader::UpdateWithDim(std::string InputPixelType)
 {
-  if (mType == VECTORFIELD)
+  if (mType == VECTORFIELD || mType == VECTORFIELDWITHTIME)
     UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
   else if (InputPixelType == "short")
     UpdateWithDimAndInputPixelType<short,VImageDimension>();
@@ -66,6 +67,8 @@ void vvImageReader::UpdateWithDim(std::string InputPixelType)
 template<class InputPixelType, unsigned int VImageDimension>
 void vvImageReader::UpdateWithDimAndInputPixelType()
 {
+  itk::AnalyzeImageIO *analyzeImageIO = NULL;
+
   if (mType == MERGEDWITHTIME)   // In this case we can load the images
     // one at the time to avoid excessive
     // memory use
@@ -88,6 +91,7 @@ void vvImageReader::UpdateWithDimAndInputPixelType()
         mLastError = error.str();
         return;
       }
+      analyzeImageIO = dynamic_cast<itk::AnalyzeImageIO*>( reader->GetImageIO() );
     }
   } else if (mType == SLICED) {
     mImage=vvImage::New();
@@ -114,14 +118,17 @@ void vvImageReader::UpdateWithDimAndInputPixelType()
     filter->SetExtractionRegion(extractedRegion);
     filter->SetInput(reader->GetOutput());
     filter->ReleaseDataFlagOn();
+#if ITK_VERSION_MAJOR == 4
+    filter->SetDirectionCollapseToSubmatrix();
+#endif
     try {
       mImage->AddItkImage<SlicedImageType>(filter->GetOutput());
-    }
-    catch ( itk::ExceptionObject & err ) {
+    } catch ( itk::ExceptionObject & err ) {
       std::cerr << "Error while slicing " << mInputFilenames[0].c_str()
                 << "(slice #" << mSlice << ") " << err << std::endl;
       return;
     }
+    analyzeImageIO = dynamic_cast<itk::AnalyzeImageIO*>( reader->GetImageIO() );
   } else {
     if (mInputFilenames.size() > 1) {
       typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
@@ -132,7 +139,12 @@ void vvImageReader::UpdateWithDimAndInputPixelType()
 
       try {
         if (mType == IMAGEWITHTIME)
-          mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
+        {
+          std::cerr << "We should never come here:" << std::endl
+            << "  Calling vvImageReader with multiple images and IMAGEWITHTIME is undefined." << std::endl
+            << "  You are probably looking for MERGEDWITHTIME Type." << std::endl;
+          return;
+        }
         else
           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
       } catch ( itk::ExceptionObject & err ) {
@@ -150,7 +162,7 @@ void vvImageReader::UpdateWithDimAndInputPixelType()
       reader->ReleaseDataFlagOn();
 
       try {
-        if (mType == IMAGEWITHTIME)
+        if (mType == IMAGEWITHTIME || mType == VECTORFIELDWITHTIME)
           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
         else
           mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
@@ -162,6 +174,22 @@ void vvImageReader::UpdateWithDimAndInputPixelType()
         mLastError = error.str();
         return;
       }
+      analyzeImageIO = dynamic_cast<itk::AnalyzeImageIO*>( reader->GetImageIO() );
+    }
+  }
+
+  // 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();
     }
   }
 }