X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=packages%2Fitk%2Fsrc%2FbbitkImageSeriesReader.cxx;h=a39bb5f59d91440e6ac4b2f2a7fb22bbd7273f80;hb=724236f8156e84f206c497b755135fbdd2ccb889;hp=1a18bcbb97138b1024ac4780cf6da16f7581165d;hpb=a273de250e863c9dec9b9cc426d8b079665d5895;p=bbtk.git

diff --git a/packages/itk/src/bbitkImageSeriesReader.cxx b/packages/itk/src/bbitkImageSeriesReader.cxx
index 1a18bcb..a39bb5f 100644
--- a/packages/itk/src/bbitkImageSeriesReader.cxx
+++ b/packages/itk/src/bbitkImageSeriesReader.cxx
@@ -1,32 +1,39 @@
-/*=========================================================================                                                                               
+/*
+ # ---------------------------------------------------------------------
+ #
+ # Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image
+ #                        pour la SantÈ)
+ # Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton
+ # Previous Authors : Laurent Guigues, Jean-Pierre Roux
+ # CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil
+ #
+ #  This software is governed by the CeCILL-B license under French law and
+ #  abiding by the rules of distribution of free software. You can  use,
+ #  modify and/ or redistribute the software under the terms of the CeCILL-B
+ #  license as circulated by CEA, CNRS and INRIA at the following URL
+ #  http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ #  or in the file LICENSE.txt.
+ #
+ #  As a counterpart to the access to the source code and  rights to copy,
+ #  modify and redistribute granted by the license, users are provided only
+ #  with a limited warranty  and the software's author,  the holder of the
+ #  economic rights,  and the successive licensors  have only  limited
+ #  liability.
+ #
+ #  The fact that you are presently reading this means that you have had
+ #  knowledge of the CeCILL-B license and that you accept its terms.
+ # ------------------------------------------------------------------------ */
+
+
+/*=========================================================================
   Program:   bbtk
   Module:    $RCSfile: bbitkImageSeriesReader.cxx,v $
   Language:  C++
-  Date:      $Date: 2008/11/26 10:13:32 $
-  Version:   $Revision: 1.7 $
+  Date:      $Date: 2012/11/16 08:50:39 $
+  Version:   $Revision: 1.12 $
 =========================================================================*/
 
-/* ---------------------------------------------------------------------
-
-* Copyright (c) CREATIS-LRMN (Centre de Recherche en Imagerie Medicale)
-* Authors : Eduardo Davila, Laurent Guigues, Jean-Pierre Roux
-*
-*  This software is governed by the CeCILL-B license under French law and 
-*  abiding by the rules of distribution of free software. You can  use, 
-*  modify and/ or redistribute the software under the terms of the CeCILL-B 
-*  license as circulated by CEA, CNRS and INRIA at the following URL 
-*  http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 
-*  or in the file LICENSE.txt.
-*
-*  As a counterpart to the access to the source code and  rights to copy,
-*  modify and redistribute granted by the license, users are provided only
-*  with a limited warranty  and the software's author,  the holder of the
-*  economic rights,  and the successive licensors  have only  limited
-*  liability. 
-*
-*  The fact that you are presently reading this means that you have had
-*  knowledge of the CeCILL-B license and that you accept its terms.
-* ------------------------------------------------------------------------ */                                                                         
+
 
 /**
  *  \file 
@@ -44,8 +51,30 @@ namespace bbitk
   
   BBTK_ADD_BLACK_BOX_TO_PACKAGE(itk,ImageSeriesReader);
 
+    
+	//-----------------------------------------------------------------	
+	void ImageSeriesReader::bbUserSetDefaultValues()
+	{
+		bbSetInputXSpacing(-1.0);
+		bbSetInputYSpacing(-1.0);
+		bbSetInputZSpacing(-1.0);		
+	}
+	
+	//-----------------------------------------------------------------	
+	void ImageSeriesReader::bbUserInitializeProcessing()
+	{
+	}
+	
+	//-----------------------------------------------------------------	
+	void ImageSeriesReader::bbUserFinalizeProcessing()
+	{
+	}	
+	
+	
+	
   void ImageSeriesReader::Read()
   {
+std::cout << "--------------------------------------------------- ImageSeriesReader::Read( NO template)" << std::endl;
     const std::vector<std::string>& filenames = bbGetInputFileNames();
     if (!filenames.size()) 
       {
@@ -60,12 +89,16 @@ namespace bbitk
 	p->Allocate();
 	p->Register();
 	bbSetOutputOut(p.GetPointer());
+std::cout << "--------------------------------------------------- ImageSeriesReader::Read( NO image found)" << std::endl;
 	return;
   	//bbtkError("Void vector passed to "<<bbGetFullName());
       }
 
     std::string filename = filenames[0];
-    
+    std::cout << "--------------------------------------------------- size " << filenames.size() << std::endl;
+std::cout << "--------------------------------------------------- filenames[0] : " << filenames[0]<< std::endl; 
+std::cout << "--------------------------------------------------- filename.c_str : " << filename.c_str()<< std::endl; 
+   
     itk::ImageIOBase::Pointer genericReader = 
       itk::ImageIOFactory::CreateImageIO(filename.c_str(), 
 					 itk::ImageIOFactory::ReadMode);
@@ -77,6 +110,7 @@ namespace bbitk
     genericReader->SetFileName(filename.c_str());
     genericReader->ReadImageInformation();
     
+    // a stack of 2D images will result as a 3D image // JPRx
     int plusUn;
     if (filenames.size()>1)
        plusUn = 1;
@@ -95,6 +129,7 @@ namespace bbitk
   template<class T>
   void ImageSeriesReader::Read()
   {
+std::cout << "--------------------------------------------------- ImageSeriesReader::Read()" << std::endl;
     bbtkDebugMessageInc("Core",9,"bbitk::ImageSeriesReader<"
 			<<bbtk::TypeName<T>()
 			<<">::Read()"<<std::endl);
@@ -104,13 +139,45 @@ namespace bbitk
 
     typename itkReaderType::Pointer reader = itkReaderType::New();
     const std::vector<std::string>& filenames = bbGetInputFileNames();
-    reader->SetFileNames(filenames);
+    
+std::cout << "--------------------------------------------------- size " << filenames.size() << std::endl;
+	for (int i = 0; i< (int)(filenames.size()); i++)
+	std::cout << "-- [" <<filenames[i] << "]" << std::endl;
+	
+    reader->SetFileNames(filenames);    
+
     try { reader->Update(); }
     catch( std::exception& e ) 
       {
 	bbtkError("could not read image series : "<<e.what());
       }
 
+    // JPRx     
+    typename itkImageType::SpacingType spacingJPRx;
+        
+    bool spacingToBeSet = false;
+    if (bbGetInputXSpacing() > 0.)
+    {
+       spacingToBeSet = true;
+       spacingJPRx[0]= bbGetInputXSpacing();
+    }
+
+    if (bbGetInputYSpacing() > 0.)
+    {
+       spacingToBeSet = true;
+       spacingJPRx[1]= bbGetInputYSpacing();
+    }
+
+    if (bbGetInputZSpacing() > 0.)
+    {
+       spacingToBeSet = true;
+       spacingJPRx[2]= bbGetInputZSpacing();
+    }
+
+    if (spacingToBeSet)
+       reader->GetOutput()->SetSpacing(spacingJPRx);   
+    // JPRx 
+
     reader->GetOutput()->Register();
     //    if (bbGetOutputOut()) 
     bbSetOutputOut ( reader->GetOutput() );
@@ -118,7 +185,6 @@ namespace bbitk
     bbtkDebugDecTab("Core",9);
   }
 
-
 }
 // eo namespace bbtk