X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vv%2FvvImageReader.txx;h=af11299b9e4497f0a715636ae864b866745992ce;hb=71e5a41c04015e6fc1df20d68b01d6f10588a717;hp=a22c5b73f46ee9495f77c941c5d07b1ce1834d2c;hpb=0b7c9b1e1215634b02cbd38d4e4ba101d6111ba8;p=clitk.git

diff --git a/vv/vvImageReader.txx b/vv/vvImageReader.txx
index a22c5b7..af11299 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
@@ -14,140 +14,162 @@
 
   - 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
-#include<string>
+  ======================================================================-====*/
 
+#ifndef VVIMAGEREADER_TXX
+#define VVIMAGEREADER_TXX
+
+#include <string>
 #include <itkImageFileReader.h>
 #include <itkImageSeriesReader.h>
+#include <itkImageToVTKImageFilter.h>
+
+#include <vtkTransform.h>
 
 #include "clitkCommon.h"
-#include "itkImageToVTKImageFilter.h"
 #include "vvFromITK.h"
 #include "vvConstants.h"
 
+//----------------------------------------------------------------------------
 template<unsigned int VImageDimension>
 void vvImageReader::UpdateWithDim(std::string InputPixelType)
 {
-    if (mType == VECTORFIELD)
-        UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
-    else if (InputPixelType == "short")
-        UpdateWithDimAndInputPixelType<short,VImageDimension>();
-    else if (InputPixelType == "unsigned_short")
-        UpdateWithDimAndInputPixelType<unsigned short,VImageDimension>();
-    else if (InputPixelType == "char")
-        UpdateWithDimAndInputPixelType<char,VImageDimension>();
-    else if (InputPixelType == "unsigned_char")
-        UpdateWithDimAndInputPixelType<unsigned char,VImageDimension>();
-    else if (InputPixelType == "int")
-        UpdateWithDimAndInputPixelType<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 (mType == VECTORFIELD)
+    UpdateWithDimAndInputPixelType<itk::Vector<float,3>,VImageDimension>();
+  else if (InputPixelType == "short")
+    UpdateWithDimAndInputPixelType<short,VImageDimension>();
+  else if (InputPixelType == "unsigned_short")
+    UpdateWithDimAndInputPixelType<unsigned short,VImageDimension>();
+  else if (InputPixelType == "char")
+    UpdateWithDimAndInputPixelType<char,VImageDimension>();
+  else if (InputPixelType == "unsigned_char")
+    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()
 {
-    if (mType == MERGEDWITHTIME)   // In this case we can load the images
-                                   // one at the time to avoid excessive
-                                   // memory use
-    {
-        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);
-        }
+
+  //  DD(mType);
+
+  if (mType == MERGEDWITHTIME)   // In this case we can load the images
+    // one at the time to avoid excessive
+    // memory use
+  {
+    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->ShallowCopy(connector->GetOutput());
+      mImage->AddImage(image);
     }
-    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;
-            }
-            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;
-            }
-            if (mType == IMAGEWITHTIME)
-                mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput(),true);
-            else
-                mImage=vvImageFromITK<VImageDimension,InputPixelType>(reader->GetOutput());
-        }
+  } 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());
     }
+  }
 }
-//====================================================================
+//----------------------------------------------------------------------------
 
 
 #endif /* end #define vvImageReader_TXX */