X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=packages%2Fitk%2Fsrc%2FbbitkImageSeriesReader.cxx;h=a39bb5f59d91440e6ac4b2f2a7fb22bbd7273f80;hb=cfad95b6e08e6e53846ffcda7fbc5932065f2c47;hp=36432d54e3b847b2ca1c39e6b350c8e7b3eaed31;hpb=4ad5b5ee44357ad873bc8c43230defb6d0a79879;p=bbtk.git

diff --git a/packages/itk/src/bbitkImageSeriesReader.cxx b/packages/itk/src/bbitkImageSeriesReader.cxx
index 36432d5..a39bb5f 100644
--- a/packages/itk/src/bbitkImageSeriesReader.cxx
+++ b/packages/itk/src/bbitkImageSeriesReader.cxx
@@ -1,20 +1,40 @@
+/*
+ # ---------------------------------------------------------------------
+ #
+ # 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: 2008/04/18 12:59:50 $
-  Version:   $Revision: 1.3 $
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/bbtk/License.html for details.
-                                                                                
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notices for more information.
-                                                                                
+  Date:      $Date: 2012/11/16 08:50:39 $
+  Version:   $Revision: 1.12 $
 =========================================================================*/
+
+
+
 /**
  *  \file 
  *  \brief 
@@ -31,72 +51,140 @@ 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()) 
       {
-  	bbtkError("Void vector passed to "<<bbGetFullName());
+	typedef	Image_uint8_t_2_ptr itype;
+	Image_uint8_t_2::Pointer p = Image_uint8_t_2::New();
+	Image_uint8_t_2::IndexType i;
+	i.Fill(0);
+	Image_uint8_t_2::SizeType s;
+	s.Fill(1);
+	Image_uint8_t_2::RegionType r(i,s);
+	p->SetRegions(r);
+	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);
+    					 
     if (!genericReader)
       {
-	bbtkError(bbGetFullName()<<" : File format unknown (while reading \"" << filename << "\")");
+	bbtkError(bbGetFullName()<<" : File format unknown (while reading [" << filename << "])");
       }
     genericReader->SetFileName(filename.c_str());
-    genericReader->ReadImageInformation();  
+    genericReader->ReadImageInformation();
     
-    bbtk::TypeInfo typ = GetITKImagePtrTypeInfoFromPixelTypeInfoAndDimension(genericReader->GetComponentTypeInfo(), genericReader->GetNumberOfDimensions());
+    // a stack of 2D images will result as a 3D image // JPRx
+    int plusUn;
+    if (filenames.size()>1)
+       plusUn = 1;
+    else
+       plusUn = 0;
     
+    bbtk::TypeInfo typ = GetITKImagePtrTypeInfoFromPixelTypeInfoAndDimension(genericReader->GetComponentTypeInfo(), genericReader->GetNumberOfDimensions() + plusUn);
+      
     BBTK_TEMPLATE_ITK_IMAGE_SWITCH(typ,Read);
-  
+    
   }
 
-
-
   /** 
       Template Processing 
   */
   template<class T>
   void ImageSeriesReader::Read()
   {
+std::cout << "--------------------------------------------------- ImageSeriesReader::Read()" << std::endl;
     bbtkDebugMessageInc("Core",9,"bbitk::ImageSeriesReader<"
 			<<bbtk::TypeName<T>()
 			<<">::Read()"<<std::endl);
 
-
-
     typedef T itkImageType;
     typedef itk::ImageSeriesReader< itkImageType > itkReaderType;
 
     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() );
 
     bbtkDebugDecTab("Core",9);
   }
 
-
-
-
-
-
 }
 // eo namespace bbtk