-/*=========================================================================
-
+/*=========================================================================
Program: bbtk
Module: $RCSfile: bbitkImageSeriesReader.cxx,v $
Language: C++
- Date: $Date: 2008/06/26 07:55:12 $
- Version: $Revision: 1.5 $
-
- 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: 2009/06/24 08:08:57 $
+ Version: $Revision: 1.10 $
=========================================================================*/
+
+/* ---------------------------------------------------------------------
+
+* 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
* \brief
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())
{
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<class T>
void ImageSeriesReader::Read()
{
+std::cout << "--------------------------------------------------- ImageSeriesReader::Read()" << std::endl;
bbtkDebugMessageInc("Core",9,"bbitk::ImageSeriesReader<"
<<bbtk::TypeName<T>()
<<">::Read()"<<std::endl);
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< 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
git://git.creatis.insa-lyon.fr / bbtk.git / blobdiff