1 /*=========================================================================
3 Module: $RCSfile: bbitkImageSeriesReader.cxx,v $
5 Date: $Date: 2009/05/15 14:57:58 $
6 Version: $Revision: 1.9 $
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);
48 //-----------------------------------------------------------------
49 void ImageSeriesReader::bbUserSetDefaultValues()
51 bbSetInputXSpacing(-1.0);
52 bbSetInputYSpacing(-1.0);
53 bbSetInputZSpacing(-1.0);
56 //-----------------------------------------------------------------
57 void ImageSeriesReader::bbUserInitializeProcessing()
61 //-----------------------------------------------------------------
62 void ImageSeriesReader::bbUserFinalizeProcessing()
68 void ImageSeriesReader::Read()
70 const std::vector<std::string>& filenames = bbGetInputFileNames();
71 if (!filenames.size())
73 typedef Image_uint8_t_2_ptr itype;
74 Image_uint8_t_2::Pointer p = Image_uint8_t_2::New();
75 Image_uint8_t_2::IndexType i;
77 Image_uint8_t_2::SizeType s;
79 Image_uint8_t_2::RegionType r(i,s);
83 bbSetOutputOut(p.GetPointer());
85 //bbtkError("Void vector passed to "<<bbGetFullName());
88 std::string filename = filenames[0];
90 itk::ImageIOBase::Pointer genericReader =
91 itk::ImageIOFactory::CreateImageIO(filename.c_str(),
92 itk::ImageIOFactory::ReadMode);
96 bbtkError(bbGetFullName()<<" : File format unknown (while reading [" << filename << "])");
98 genericReader->SetFileName(filename.c_str());
99 genericReader->ReadImageInformation();
101 // a stack of 2D images will result as a 3D image // JPRx
103 if (filenames.size()>1)
108 bbtk::TypeInfo typ = GetITKImagePtrTypeInfoFromPixelTypeInfoAndDimension(genericReader->GetComponentTypeInfo(), genericReader->GetNumberOfDimensions() + plusUn);
111 BBTK_TEMPLATE_ITK_IMAGE_SWITCH(typ,Read);
119 void ImageSeriesReader::Read()
121 bbtkDebugMessageInc("Core",9,"bbitk::ImageSeriesReader<"
122 <<bbtk::TypeName<T>()
123 <<">::Read()"<<std::endl);
125 typedef T itkImageType;
126 typedef itk::ImageSeriesReader< itkImageType > itkReaderType;
128 typename itkReaderType::Pointer reader = itkReaderType::New();
129 const std::vector<std::string>& filenames = bbGetInputFileNames();
130 reader->SetFileNames(filenames);
131 try { reader->Update(); }
132 catch( std::exception& e )
134 bbtkError("could not read image series : "<<e.what());
138 typename itkImageType::SpacingType spacingJPRx;
140 bool spacingToBeSet = false;
141 if (bbGetInputXSpacing() > 0.)
143 spacingToBeSet = true;
144 spacingJPRx[0]= bbGetInputXSpacing();
146 if (bbGetInputYSpacing() > 0.)
148 spacingToBeSet = true;
149 spacingJPRx[1]= bbGetInputYSpacing();
151 if (bbGetInputZSpacing() > 0.)
153 spacingToBeSet = true;
154 spacingJPRx[2]= bbGetInputZSpacing();
157 reader->GetOutput()->SetSpacing(spacingJPRx);
160 reader->GetOutput()->Register();
161 // if (bbGetOutputOut())
162 bbSetOutputOut ( reader->GetOutput() );
164 bbtkDebugDecTab("Core",9);