1 /*=========================================================================
3 Module: $RCSfile: bbitkImageSeriesReader.cxx,v $
5 Date: $Date: 2008/11/27 14:55:54 $
6 Version: $Revision: 1.8 $
7 =========================================================================*/
9 /* ---------------------------------------------------------------------
11 * Copyright (c) CREATIS-LRMN (Centre de Recherche en Imagerie Medicale)
12 * Authors : Eduardo Davila, Laurent Guigues, Jean-Pierre Roux
14 * This software is governed by the CeCILL-B license under French law and
15 * abiding by the rules of distribution of free software. You can use,
16 * modify and/ or redistribute the software under the terms of the CeCILL-B
17 * license as circulated by CEA, CNRS and INRIA at the following URL
18 * http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
19 * or in the file LICENSE.txt.
21 * As a counterpart to the access to the source code and rights to copy,
22 * modify and redistribute granted by the license, users are provided only
23 * with a limited warranty and the software's author, the holder of the
24 * economic rights, and the successive licensors have only limited
27 * The fact that you are presently reading this means that you have had
28 * knowledge of the CeCILL-B license and that you accept its terms.
29 * ------------------------------------------------------------------------ */
37 #include "bbitkImageSeriesReader.h"
38 #include "bbitkPackage.h"
39 #include "itkImageSeriesReader.h"
43 BBTK_BLACK_BOX_IMPLEMENTATION(ImageSeriesReader,bbtk::AtomicBlackBox);
45 BBTK_ADD_BLACK_BOX_TO_PACKAGE(itk,ImageSeriesReader);
47 void ImageSeriesReader::bbUserConstructor()
49 bbSetInputXSpacing(-1.);
50 bbSetInputYSpacing(-1.);
51 bbSetInputZSpacing(-1.);
54 void ImageSeriesReader::bbUserCopyConstructor(bbtk::BlackBox::Pointer)
58 void ImageSeriesReader::bbUserDestructor()
62 void ImageSeriesReader::Read()
64 const std::vector<std::string>& filenames = bbGetInputFileNames();
65 if (!filenames.size())
67 typedef Image_uint8_t_2_ptr itype;
68 Image_uint8_t_2::Pointer p = Image_uint8_t_2::New();
69 Image_uint8_t_2::IndexType i;
71 Image_uint8_t_2::SizeType s;
73 Image_uint8_t_2::RegionType r(i,s);
77 bbSetOutputOut(p.GetPointer());
79 //bbtkError("Void vector passed to "<<bbGetFullName());
82 std::string filename = filenames[0];
84 itk::ImageIOBase::Pointer genericReader =
85 itk::ImageIOFactory::CreateImageIO(filename.c_str(),
86 itk::ImageIOFactory::ReadMode);
90 bbtkError(bbGetFullName()<<" : File format unknown (while reading [" << filename << "])");
92 genericReader->SetFileName(filename.c_str());
93 genericReader->ReadImageInformation();
95 // a stack of 2D images will result as a 3D image // JPRx
97 if (filenames.size()>1)
102 bbtk::TypeInfo typ = GetITKImagePtrTypeInfoFromPixelTypeInfoAndDimension(genericReader->GetComponentTypeInfo(), genericReader->GetNumberOfDimensions() + plusUn);
105 BBTK_TEMPLATE_ITK_IMAGE_SWITCH(typ,Read);
113 void ImageSeriesReader::Read()
115 bbtkDebugMessageInc("Core",9,"bbitk::ImageSeriesReader<"
116 <<bbtk::TypeName<T>()
117 <<">::Read()"<<std::endl);
119 typedef T itkImageType;
120 typedef itk::ImageSeriesReader< itkImageType > itkReaderType;
122 typename itkReaderType::Pointer reader = itkReaderType::New();
123 const std::vector<std::string>& filenames = bbGetInputFileNames();
124 reader->SetFileNames(filenames);
125 try { reader->Update(); }
126 catch( std::exception& e )
128 bbtkError("could not read image series : "<<e.what());
132 typename itkImageType::SpacingType spacingJPRx;
134 bool spacingToBeSet = false;
135 if (bbGetInputXSpacing() > 0.)
137 spacingToBeSet = true;
138 spacingJPRx[0]= bbGetInputXSpacing();
140 if (bbGetInputYSpacing() > 0.)
142 spacingToBeSet = true;
143 spacingJPRx[1]= bbGetInputYSpacing();
145 if (bbGetInputZSpacing() > 0.)
147 spacingToBeSet = true;
148 spacingJPRx[2]= bbGetInputZSpacing();
151 reader->GetOutput()->SetSpacing(spacingJPRx);
154 reader->GetOutput()->Register();
155 // if (bbGetOutputOut())
156 bbSetOutputOut ( reader->GetOutput() );
158 bbtkDebugDecTab("Core",9);