From c45f2910270487388742272ad54c27405a2b1b53 Mon Sep 17 00:00:00 2001
From: Simon Rit <simon.rit@creatis.insa-lyon.fr>
Date: Thu, 31 Oct 2013 16:45:21 +0100
Subject: [PATCH] Option to save VV transform (mhd + .mat) in the new mhd

---
 tools/clitkImageConvert.cxx              |  1 +
 tools/clitkImageConvert.ggo              | 13 +++++++------
 tools/clitkImageConvertGenericFilter.cxx | 21 ++++++++++++++++++++-
 tools/clitkImageConvertGenericFilter.h   |  2 ++
 4 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/tools/clitkImageConvert.cxx b/tools/clitkImageConvert.cxx
index abedc61..3a9beaf 100644
--- a/tools/clitkImageConvert.cxx
+++ b/tools/clitkImageConvert.cxx
@@ -67,6 +67,7 @@ int main(int argc, char * argv[])
   filter->SetInputFilenames(l);
   filter->SetIOVerbose(args_info.verbose_flag);
   filter->SetOutputFilename(output);
+  filter->SetVV(args_info.vv_flag);
   filter->EnableWriteCompression(args_info.compression_flag);
   if (args_info.type_given) filter->SetOutputPixelType(args_info.type_arg);
 
diff --git a/tools/clitkImageConvert.ggo b/tools/clitkImageConvert.ggo
index 837ee03..b6f003c 100644
--- a/tools/clitkImageConvert.ggo
+++ b/tools/clitkImageConvert.ggo
@@ -3,9 +3,10 @@ package "clitkImageConvert"
 version "1.0"
 purpose "Convert an image into another image.\n\tAllow to change the file format and/or the pixel type. \n\tKnown file formats 2D: jpeg png bmp tif mhd hdr vox dcm \n\tKnown file formats 3D: mhd vox hdr dcm\n\tKnown file formats 4D: mhd \n\tKnown images: 2D 3D or 4D, schar, uchar, short, ushort, int, float and double\n\nIf the -o option is not given, the last parameter of the command line is used as output."
 
-option "config"      - "Config file"                     string no
-option "input"       i "Input image filename"            string no
-option "output"      o "Output image filename"           string no
-option "type"        t "Output type (float, ushort ...)" string no
-option "verbose"     v "Verbose"                         flag   off
-option "compression" c "Compress output"                 flag   off
+option "config"      - "Config file"                                                string no
+option "input"       i "Input image filename"                                       string no
+option "output"      o "Output image filename"                                      string no
+option "type"        t "Output type (float, ushort ...)"                            string no
+option "verbose"     v "Verbose"                                                    flag   off
+option "compression" c "Compress output"                                            flag   off
+option "vv"          - "Read image as in vv and save transform in meta information" flag   off
diff --git a/tools/clitkImageConvertGenericFilter.cxx b/tools/clitkImageConvertGenericFilter.cxx
index e8d8efb..2783053 100644
--- a/tools/clitkImageConvertGenericFilter.cxx
+++ b/tools/clitkImageConvertGenericFilter.cxx
@@ -19,6 +19,8 @@
 #define CLITKIMAGECONVERTGENERICFILTER_CXX
 
 #include "clitkImageConvertGenericFilter.h"
+#include "vvImageReader.h"
+#include "vvImageWriter.h"
 
 //--------------------------------------------------------------------
 clitk::ImageConvertGenericFilter::ImageConvertGenericFilter():
@@ -70,7 +72,24 @@ void clitk::ImageConvertGenericFilter::UpdateWithInputImageType()
     }
   }
 
-  if ((m_PixelTypeName == mOutputPixelTypeName) || (mOutputPixelTypeName == "NotSpecified")) {
+  if(mVV) {
+    if (mOutputPixelTypeName != "NotSpecified" || m_WriteCompression) {
+      std::cerr << "--vv is not compatible with --compression and --type options." << std::endl;
+      exit(-1);
+    }
+
+    vvImageReader::Pointer reader = vvImageReader::New();
+    reader->SetInputFilenames(m_InputFilenames);
+    reader->Update(vvImageReader::IMAGE);
+
+    vvImageWriter::Pointer writer = vvImageWriter::New();
+    writer->SetOutputFileName(m_OutputFilenames.front());
+    writer->SetSaveTransform(true);
+    writer->SetInput(reader->GetOutput());
+    writer->Update();
+    return;
+  }
+  else if ((m_PixelTypeName == mOutputPixelTypeName) || (mOutputPixelTypeName == "NotSpecified")) {
     typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
     this->SetNextOutput<InputImageType>(input);
   } else {
diff --git a/tools/clitkImageConvertGenericFilter.h b/tools/clitkImageConvertGenericFilter.h
index 2071714..8ffb360 100644
--- a/tools/clitkImageConvertGenericFilter.h
+++ b/tools/clitkImageConvertGenericFilter.h
@@ -73,6 +73,7 @@ namespace clitk {
     std::string GetInputPixelTypeName() { return m_PixelTypeName; }
     std::string GetOutputPixelTypeName() { return mOutputPixelTypeName; }
     void SetOutputPixelType(std::string p) { mOutputPixelTypeName = p; }
+    void SetVV(bool b) { mVV = b; }
     bool IsWarningOccur() { return mWarningOccur; }
     std::string & GetWarning() { return mWarning; }
     void EnableDisplayWarning(bool b) { mDisplayWarning = b; }
@@ -92,6 +93,7 @@ namespace clitk {
     std::string mWarning;
     bool mWarningOccur;
     bool mDisplayWarning;
+    bool mVV;
 
   private:
     template <class InputImageType, bool isVector>
-- 
2.47.1