[Olena-patches] r3394: Experiment DICOM support with GDCM

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-02-19 Fabien Freling &lt;fabien.freling(a)lrde.epita.fr&gt; Experiment DICOM support with GDCM. * fabien/gdcm/Makefile: Specific Makefile to test. * fabien/gdcm/gdcm.cc: New test file. * fabien/gdcm/load.hh: Implement GDCM DICOM support. * fabien/magick/Makefile: Update. * fabien/magick/load.hh: Update ImageMagick DICOM support. * fabien/magick/magick.cc: Update. --- gdcm/Makefile | 12 +++ gdcm/gdcm.cc | 18 +++++ gdcm/load.hh | 196 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ magick/load.hh | 10 ++ magick/magick.cc | 3 5 files changed, 238 insertions(+), 1 deletion(-) Index: trunk/milena/sandbox/fabien/gdcm/Makefile =================================================================== --- trunk/milena/sandbox/fabien/gdcm/Makefile (revision 0) +++ trunk/milena/sandbox/fabien/gdcm/Makefile (revision 3394) @@ -0,0 +1,12 @@ +all: gdcm.cc + g++ -I../../../ \ + -I/Users/HiSoKa/Downloads/gdcm-2.0.10/Source/Common/ \ + -I/Users/HiSoKa/Downloads/gdcmbin/Source/Common/ \ + -I/Users/HiSoKa/Downloads/gdcm-2.0.10/Source/DataDictionary/ \ + -I/Users/HiSoKa/Downloads/gdcm-2.0.10/Source/MediaStorageAndFileFormat/ \ + -I/Users/HiSoKa/Downloads/gdcm-2.0.10/Source/DataStructureAndEncodingDefinition/ \ + -L/Users/HiSoKa/Downloads/gdcmbin/bin \ + -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF -lgdcmexpat -lgdcmjpeg12 -lgdcmjpeg16 -lgdcmjpeg8 -lgdcmopenjpeg -lgdcmuuid -lgdcmzlib \ + -framework CoreFoundation \ + -DNDEBUG \ + gdcm.cc -o mln_gdcm Index: trunk/milena/sandbox/fabien/gdcm/load.hh =================================================================== --- trunk/milena/sandbox/fabien/gdcm/load.hh (revision 0) +++ trunk/milena/sandbox/fabien/gdcm/load.hh (revision 3394) @@ -0,0 +1,196 @@ +// Copyright (C) 2009 EPITA Research and Development Laboratory +// +// This file is part of the Olena Library. This library is free +// software; you can redistribute it and/or modify it under the terms +// of the GNU General Public License version 2 as published by the +// Free Software Foundation. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this library; see the file COPYING. If not, write to +// the Free Software Foundation, 51 Franklin Street, Fifth Floor, +// Boston, MA 02111-1307, USA. +// +// As a special exception, you may use this file as part of a free +// software library without restriction. Specifically, if other files +// instantiate templates or use macros or inline functions from this +// file, or you compile this file and link it with other files to +// produce an executable, this file does not by itself cause the +// resulting executable to be covered by the GNU General Public +// License. This exception does not however invalidate any other +// reasons why the executable file might be covered by the GNU General +// Public License. + +#ifndef MLN_IO_DICOM_LOAD_HH +# define MLN_IO_DICOM_LOAD_HH + +/*! + * \file mln/io/magick/load.hh + * + * \brief Define a function which loads an image of kind magick with + * given path. + * + */ + +# include <mln/core/image/image2d.hh> +# include <mln/core/image/image3d.hh> + +# include <mln/value/int_u16.hh> + +# include <gdcmReader.h> +# include <gdcmImageReader.h> +# include <gdcmWriter.h> +# include <gdcmDataSet.h> +# include <gdcmAttribute.h> + + +namespace mln +{ + + namespace io + { + + namespace dicom + { + + /*! Load a gdcm image in a Milena image. + * + * \param[out] ima A reference to the image which will receive + * data. + * \param[in] filename The source. + */ + template <typename I> + void load(Image<I>& ima, + const std::string& filename); + + /*! Load a gdcm image in a Milena image. To use this routine, you + * should specialize the template whith the value type of the + * image loaded. (ex : load<value::int_u8>("...") ) + * + * \param[in] filename The image source. + * + * \return An image2d which contains loaded data. + */ + template <typename V> + image2d<V> load(const std::string& filename); + + /*! Load a gdcm image in a Milena image. To use this routine, you + * should specialize the template whith the value type of the + * image loaded. (ex : load<value::int_u8>("...") ) + * + * \param[in] filename The image source. + * + * \return An image2d which contains loaded data. + */ + template <typename V> + image3d<V> load(const std::string& filename); + +# ifndef MLN_INCLUDE_ONLY + + template <typename V> + inline + image2d<V> load(const std::string& filename) + { + trace::entering("mln::io::gdcm::load"); + image2d<V> ima;// = io::pnm::load<V>(MAGICK, filename); + trace::exiting("mln::io::gdcm::load"); + return ima; + } + + template <typename V> + inline + image3d<V> load(const std::string& filename) + { + trace::entering("mln::io::gdcm::load"); + image2d<V> ima;// = io::pnm::load<V>(MAGICK, filename); + trace::exiting("mln::io::gdcm::load"); + return ima; + } + + + template <typename I> + inline + void load(Image<I>& ima_, + const std::string& filename) + { + trace::entering("mln::io::gdcm::load"); + + using value::int_u16; + I& ima = exact(ima_); + + gdcm::ImageReader r; + r.SetFileName(filename.c_str()); + if (!r.Read()) + { + std::cerr << "error: cannot open file '" << filename << "'!"; + abort(); + } + + gdcm::File &file = r.GetFile(); + gdcm::DataSet& ds = file.GetDataSet(); + + gdcm::Image& image = r.GetImage(); + + std::cout << std::endl << "Image information" << std::endl + << "=================" << std::endl; + image.Print(std::cout); + + std::cout << std::endl << "Buffer information" << std::endl + << "=================" << std::endl; + std::cout << "Buffer length: " << image.GetBufferLength() << std::endl; + char* dataBuffer = new char[image.GetBufferLength()]; + if (image.GetBuffer(dataBuffer)) + std::cout << "GetBuffer success" << std::endl; + else + std::cout << "GetBuffer failure" << std::endl; + + int ndims = image.GetNumberOfDimensions(); + const unsigned int* dims = image.GetDimensions(); + + // FIXME: Check ScalarType + if (ndims == 1) + { + + } + if (ndims == 2) + { + //image2d<int_u16> mln_ima(dims[1], dims[0]); + //mln_piter(image2d<int_u16>) p(ima.domain()); + //for_all(p) + //{ + // ima(p) = dataBuffer[(p.col() + p.row() * dims[0]) * 2] * 256 + + // dataBuffer[(p.col() + p.row() * dims[0]) * 2 + 1]; + //} + } + if (ndims == 3) + { + //image3d<int_u16> ima(dims[2], dims[1], dims[0]); + mln_site(I) pmin(0, 0, 0); + mln_site(I) pmax(dims[2], dims[1], dims[0]); + mln_concrete(I) result(box<mln_site(I)>(pmin, pmax)); + initialize(ima, result); + mln_piter(image3d<int_u16>) p(ima.domain()); + for_all(p) + { + ima(p) = dataBuffer[(p.col() + p.row() * dims[0] + p.sli() * dims[0] * dims[1]) * 2] * 256+ + dataBuffer[(p.col() + p.row() * dims[0] + p.sli() * dims[0] * dims[1]) * 2 + 1]; + } + } + + trace::exiting("mln::io::dicom::load"); + } + +# endif // ! MLN_INCLUDE_ONLY + + } // end of namespace mln::io::dicom + + } // end of namespace mln::io + +} // end of namespace mln + + +#endif // ! MLN_IO_DICOM_LOAD_HH Index: trunk/milena/sandbox/fabien/gdcm/gdcm.cc =================================================================== --- trunk/milena/sandbox/fabien/gdcm/gdcm.cc (revision 0) +++ trunk/milena/sandbox/fabien/gdcm/gdcm.cc (revision 3394) @@ -0,0 +1,18 @@ +#include <mln/core/image/image2d.hh> +#include <mln/value/int_u8.hh> +#include <mln/value/int_u16.hh> + +#include "load.hh" + +#include <mln/io/dump/save.hh> + +int main() +{ + using namespace mln; + using value::int_u16; + + image3d<int_u16> lena; + + io::dicom::load(lena, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm"); + io::dump::save(lena, "IM_0052.dump"); +} Index: trunk/milena/sandbox/fabien/magick/magick.cc =================================================================== --- trunk/milena/sandbox/fabien/magick/magick.cc (revision 3393) +++ trunk/milena/sandbox/fabien/magick/magick.cc (revision 3394) @@ -10,5 +10,6 @@ image2d<int_u8> lena; - io::magick::load(lena, "/Users/HiSoKa/Work/LRDE/Olena/resources/CardiacCT/178562160.dcm"); + //io::magick::load(lena, "/Users/HiSoKa/Work/LRDE/Olena/resources/CardiacCT/178562160.dcm"); + io::magick::load(lena, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm"); } Index: trunk/milena/sandbox/fabien/magick/Makefile =================================================================== Index: trunk/milena/sandbox/fabien/magick/load.hh =================================================================== --- trunk/milena/sandbox/fabien/magick/load.hh (revision 3393) +++ trunk/milena/sandbox/fabien/magick/load.hh (revision 3394) @@ -124,8 +124,18 @@ std::cout << "height: " << file.rows() << std::endl; std::cout << "x resolution: " << file.xResolution() << std::endl; std::cout << "y resolution: " << file.yResolution() << std::endl; + std::cout << "depth: " << file.depth() << std::endl; + //std::cout << "packets: " << file.packets() << std::endl; + //std::cout << "packet size: " << file.packetSize() << std::endl; std::cout << "comment: " << file.comment() << std::endl; std::cout << "format: " << file.format() << std::endl; + std::cout << "number of scenes: " << file.imageInfo()->number_scenes << std::endl; + std::cout << "scene: " << file.imageInfo()->scene << std::endl; + std::cout << "filename: " << file.imageInfo()->filename << std::endl; + + //Magick::Pixels::Pixels pixels(file); + //std::cout << "sizeof PixelPacket: " << sizeof (pixel_cache) << std::endl; + //std::cout << "sizeof *PixelPacket: " << sizeof (*pixel_cache) << std::endl; trace::exiting("mln::io::magick::load"); }