X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vv%2FvvImageReader.txx;h=3c5e1545878b27511d100c559db30a1c2f473dbf;hb=b9d8c9a9e84535e8de0b7e2a2f970af1442cd49b;hp=cfa389a7154e5cf803469d6b9da39030536b3949;hpb=b6cfdecc2f880a7015d8f5a73174a0361cfe7924;p=clitk.git

diff --git a/vv/vvImageReader.txx b/vv/vvImageReader.txx
index cfa389a..3c5e154 100644
--- a/vv/vvImageReader.txx
+++ b/vv/vvImageReader.txx
@@ -1,7 +1,7 @@
 /*=========================================================================
   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
 
-  Authors belong to: 
+  Authors belong to:
   - University of LYON              http://www.universite-lyon.fr/
   - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
@@ -22,14 +22,19 @@
 #include <string>
 #include <itkImageFileReader.h>
 #include <itkImageSeriesReader.h>
+#include <itkImageToVTKImageFilter.h>
+
+#include <vtkTransform.h>
+
 #include "clitkCommon.h"
-#include "itkImageToVTKImageFilter.h"
+#include "clitkConfiguration.h"
 #include "vvFromITK.h"
 #include "vvConstants.h"
 
 //----------------------------------------------------------------------------
 template<unsigned int VImageDimension>
-void vvImageReader::UpdateWithDim(std::string InputPixelType) {
+void vvImageReader::UpdateWithDim(std::string InputPixelType)
+{
   if (mType == VECTORFIELD)
     UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
   else if (InputPixelType == "short")
@@ -42,130 +47,125 @@ void vvImageReader::UpdateWithDim(std::string InputPixelType) {
     UpdateWithDimAndInputPixelType<unsigned char,VImageDimension>();
   else if (InputPixelType == "int")
     UpdateWithDimAndInputPixelType<int,VImageDimension>();
+  else if (InputPixelType == "unsigned_int")
+    UpdateWithDimAndInputPixelType<unsigned int,VImageDimension>();
   else if (InputPixelType == "double")
     UpdateWithDimAndInputPixelType<double,VImageDimension>();
   else if (InputPixelType == "float")
     UpdateWithDimAndInputPixelType<float,VImageDimension>();
   else
     std::cerr << "Error, input pixel type : " << InputPixelType << " unknown !" << std::endl;
+
+  if (CLITK_EXPERIMENTAL && mLastError.size()==0) {
+    //ReadNkiImageTransform();
+    ReadMatImageTransform();
+  }
 }
 //----------------------------------------------------------------------------
 
 
 //----------------------------------------------------------------------------
 template<class InputPixelType, unsigned int VImageDimension>
-void vvImageReader::UpdateWithDimAndInputPixelType() {
-
-  //  DD(mType);
-
+void vvImageReader::UpdateWithDimAndInputPixelType()
+{
   if (mType == MERGEDWITHTIME)   // In this case we can load the images
     // one at the time to avoid excessive
     // memory use
-    {
+  {
+    mImage=vvImage::New();
+
+    for (std::vector<std::string>::const_iterator i=mInputFilenames.begin(); i!=mInputFilenames.end(); i++) {
       typedef itk::Image< InputPixelType, VImageDimension-1 > InputImageType;
       typedef itk::ImageFileReader<InputImageType> ReaderType;
       typename ReaderType::Pointer reader = ReaderType::New();
-      typedef itk::ImageToVTKImageFilter <InputImageType> ConnectorType;
-      typename ConnectorType::Pointer connector = ConnectorType::New();
-      connector->SetInput(reader->GetOutput());
-      mImage=vvImage::New();
-      for (std::vector<std::string>::const_iterator i=mInputFilenames.begin();i!=mInputFilenames.end();i++)
-        {
-          std::cout << (*i) << std::endl;
-          reader->SetFileName(*i);
-          try {
-            reader->Update();
-          }
-          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;
-          }
-          try {
-            connector->Update();
-          }
-          catch ( itk::ExceptionObject & err ) {
-            std::cerr << "Error while setting vvImage from ITK (MERGEDWITHTIME)"
-                      << " " << err << std::endl;
-          }
-          vtkImageData *image = vtkImageData::New();
-          image->DeepCopy(connector->GetOutput());
-          mImage->AddImage(image);
-        }
+      reader->ReleaseDataFlagOn();
+      reader->SetFileName(*i);
+      try {
+        mImage->AddItkImage<InputImageType>(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;
+      }
     }
-  else
-    {
-      if (mInputFilenames.size() > 1)
-        {
-          typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
-          typedef itk::ImageSeriesReader<InputImageType> ReaderType;
-          typename ReaderType::Pointer reader = ReaderType::New();
-          for (std::vector<std::string>::const_iterator i=mInputFilenames.begin();i!=mInputFilenames.end();i++)
-            std::cout << (*i) << std::endl;
-          reader->SetFileNames(mInputFilenames);
-          //if (mUseAnObserver) {
-          //reader->AddObserver(itk::ProgressEvent(), mObserver);
-          //}
-          try {
-            reader->Update();
-          }
-          catch ( itk::ExceptionObject & err ) {
-            std::cerr << "Error while reading image series:" << err << std::endl;
-            std::stringstream error;
-            error << err;
-            mLastError = error.str();
-            return;
-          }
-
-          // DD(reader->GetOutput()->GetImageDimension());
-          //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
-          //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
-          //             DD(reader->GetOutput()->GetSpacing()[i]);
-          //           }
-
-          if (mType == IMAGEWITHTIME)
-            mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
-          else
-            mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
-        }
-      else
-        {
-          typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
-          typedef itk::ImageFileReader<InputImageType> ReaderType;
-          typename ReaderType::Pointer reader = ReaderType::New();
-          reader->SetFileName(mInputFilenames[0]);
-          //if (mUseAnObserver) {
-          //reader->AddObserver(itk::ProgressEvent(), mObserver);
-          //}
-          try {
-            reader->Update();
-          }
-          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;
-          }
-
-          // DD(reader->GetOutput()->GetImageDimension());
-          //           DD(reader->GetOutput()->GetNumberOfComponentsPerPixel());
-          //           for(unsigned int i=0; i <reader->GetOutput()->GetImageDimension(); i++) {
-          //             DD(reader->GetOutput()->GetSpacing()[i]);
-          //             DD(reader->GetOutput()->GetOrigin()[i]);
-          //           }
-
-
-          if (mType == IMAGEWITHTIME)
-            mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
-          else
-            mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
-        }
+  } else if (mType == SLICED) {
+    mImage=vvImage::New();
+    typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
+    typedef itk::ImageFileReader<InputImageType> ReaderType;
+    typename ReaderType::Pointer reader = ReaderType::New();
+    reader->SetFileName(mInputFilenames[0]);
+    reader->UpdateOutputInformation();
+
+    typedef itk::Image< InputPixelType, VImageDimension-1 > SlicedImageType;
+    typedef itk::ExtractImageFilter<InputImageType, SlicedImageType> FilterType;
+
+    typename InputImageType::RegionType inputRegion = reader->GetOutput()->GetLargestPossibleRegion();
+    typename InputImageType::SizeType inputSize = inputRegion.GetSize();
+    typename InputImageType::IndexType start = inputRegion.GetIndex();
+    typename InputImageType::SizeType extractedRegionSize = inputSize;
+    typename InputImageType::RegionType extractedRegion;
+    extractedRegionSize[VImageDimension - 1] = 0;
+    extractedRegion.SetSize(extractedRegionSize);
+    start[VImageDimension - 1] = mSlice;
+    extractedRegion.SetIndex(start);
+
+    typename FilterType::Pointer filter = FilterType::New();
+    filter->SetExtractionRegion(extractedRegion);
+    filter->SetInput(reader->GetOutput());
+    filter->ReleaseDataFlagOn();
+    try {
+      mImage->AddItkImage<SlicedImageType>(filter->GetOutput());
+    }
+    catch ( itk::ExceptionObject & err ) {
+      std::cerr << "Error while slicing " << mInputFilenames[0].c_str()
+                << "(slice #" << mSlice << ") " << err << std::endl;
+      return;
+    }
+  } else {
+    if (mInputFilenames.size() > 1) {
+      typedef itk::Image< InputPixelType, VImageDimension > InputImageType;
+      typedef itk::ImageSeriesReader<InputImageType> ReaderType;
+      typename ReaderType::Pointer reader = ReaderType::New();
+      reader->SetFileNames(mInputFilenames);
+      reader->ReleaseDataFlagOn();
+
+      try {
+        if (mType == IMAGEWITHTIME)
+          mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
+        else
+          mImage=vvImageFromITK<VImageDimension,InputPixelType>(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::Image< InputPixelType, VImageDimension > InputImageType;
+      typedef itk::ImageFileReader<InputImageType> ReaderType;
+      typename ReaderType::Pointer reader = ReaderType::New();
+      reader->SetFileName(mInputFilenames[0]);
+      reader->ReleaseDataFlagOn();
+
+      try {
+        if (mType == IMAGEWITHTIME)
+          mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
+        else
+          mImage=vvImageFromITK<VImageDimension,InputPixelType>(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;
+      }
     }
+  }
 }
 //----------------------------------------------------------------------------