[Olena-patches] last-svn-commit-7-g1875111 Add a routine to read DICOM files header.

* mln/io/dicom/all.hh: Include a new file. * mln/io/dicom/get_header.hh: New. * mln/io/dicom/load.hh: Add more doc. --- milena/ChangeLog | 10 +++ milena/mln/io/dicom/all.hh | 4 +- .../mln/io/{cloud/save.hh => dicom/get_header.hh} | 83 ++++++++++---------- milena/mln/io/dicom/load.hh | 17 +++- 4 files changed, 66 insertions(+), 48 deletions(-) copy milena/mln/io/{cloud/save.hh => dicom/get_header.hh} (54%) diff --git a/milena/ChangeLog b/milena/ChangeLog index b0cc268..05234c0 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,15 @@ 2010-02-16 Guillaume Lazzara &lt;z(a)lrde.epita.fr&gt; + Add a routine to read DICOM files header. + + * mln/io/dicom/all.hh: Include a new file. + + * mln/io/dicom/get_header.hh: New. + + * mln/io/dicom/load.hh: Add more doc. + +2010-02-16 Guillaume Lazzara &lt;z(a)lrde.epita.fr&gt; + Add A new routine to draw plain boxes. * mln/draw/all.hh: Include new file. diff --git a/milena/mln/io/dicom/all.hh b/milena/mln/io/dicom/all.hh index c6d9256..1aa3d8c 100644 --- a/milena/mln/io/dicom/all.hh +++ b/milena/mln/io/dicom/all.hh @@ -1,4 +1,5 @@ -// Copyright (C) 2009 EPITA Research and Development Laboratory (LRDE) +// Copyright (C) 2009, 2010 EPITA Research and Development Laboratory +// (LRDE) // // This file is part of Olena. // @@ -41,6 +42,7 @@ namespace mln } +# include <mln/io/dicom/get_header.hh> # include <mln/io/dicom/load.hh> #endif // ! MLN_IO_DICOM_ALL_HH diff --git a/milena/mln/io/cloud/save.hh b/milena/mln/io/dicom/get_header.hh similarity index 54% copy from milena/mln/io/cloud/save.hh copy to milena/mln/io/dicom/get_header.hh index 7d0ef7b..6d85850 100644 --- a/milena/mln/io/cloud/save.hh +++ b/milena/mln/io/dicom/get_header.hh @@ -1,4 +1,4 @@ -// Copyright (C) 2009 EPITA Research and Development Laboratory (LRDE) +// Copyright (C) 2010 EPITA Research and Development Laboratory (LRDE) // // This file is part of Olena. // @@ -23,18 +23,21 @@ // exception does not however invalidate any other reasons why the // executable file might be covered by the GNU General Public License. -#ifndef MLN_IO_CLOUD_SAVE_HH -# define MLN_IO_CLOUD_SAVE_HH +#ifndef MLN_IO_DICOM_GET_HEADER_HH +# define MLN_IO_DICOM_GET_HEADER_HH /// \file /// -/// Save an image as a cloud of points. +/// Load a DICOM file header. # include <iostream> # include <fstream> # include <mln/core/concept/image.hh> -# include <mln/core/site_set/p_array.hh> +# include <mln/core/routine/initialize.hh> +# include <mln/core/box_runstart_piter.hh> +# include <mln/core/pixel.hh> +# include <mln/data/memcpy_.hh> namespace mln { @@ -42,67 +45,63 @@ namespace mln namespace io { - namespace cloud + namespace dicom { - /// Load a cloud of points - /// - /// \param[in] arr the cloud of points to save. - /// \param[in] filename the destination. - template <typename P> - void save(const p_array<P>& arr, const std::string& filename); - + /// Store dicom file header. + struct dicom_header + { + // The number of dimensions. + unsigned dim; -# ifndef MLN_INCLUDE_ONLY + // The size in each dimension. + util::array<unsigned> size; + }; - namespace internal - { - template <typename P> - inline - void save_data(const p_array<P>& arr, std::ofstream& file) - { - mln_piter(p_array<P>) p(arr); - for_all(p) - { - std::ostringstream sline; - algebra::vec<P::dim,float> v = p.to_site().to_vec(); - sline << v[0]; - for (unsigned i = 1; i < P::dim; ++i) - sline << ' ' << v[i]; - sline << std::endl; - file << sline.str(); - } - } + /// Retrieve header in a dicom file. + dicom_header get_header(const std::string& filename); - } // end of namespace mln::io::cloud::internal +# ifndef MLN_INCLUDE_ONLY - template <typename P> - void save(const p_array<P>& arr, const std::string& filename) + dicom_header get_header(const std::string& filename) { - trace::entering("mln::io::cloud::save"); + trace::entering("mln::io::dicom::get_header"); + + dicom_header header; - std::ofstream file(filename.c_str()); - if (! file) + gdcm::ImageReader r; + r.SetFileName(filename.c_str()); + if (!r.Read()) { std::cerr << "error: cannot open file '" << filename << "'!"; abort(); } - internal::save_data(arr, file); + gdcm::Image& image = r.GetImage(); + + header.dim = image.GetNumberOfDimensions(); + const unsigned int* dims = image.GetDimensions(); - trace::exiting("mln::io::cloud::save"); + for (unsigned i = 2; i < header.dim; ++i) + header.size.append(dims[i]); // sli, ... + for (unsigned i = 0; i < 2; ++i) + header.size.append(dims[i]); // row, col + + trace::exiting("mln::io::dicom::get_header"); + return header; } # endif // ! MLN_INCLUDE_ONLY - } // end of namespace mln::io::cloud + } // end of namespace mln::io::dicom } // end of namespace mln::io } // end of namespace mln -#endif // ! MLN_IO_CLOUD_SAVE_HH +#endif // ! MLN_IO_DICOM_GET_HEADER_HH + diff --git a/milena/mln/io/dicom/load.hh b/milena/mln/io/dicom/load.hh index 360c87f..f250a16 100644 --- a/milena/mln/io/dicom/load.hh +++ b/milena/mln/io/dicom/load.hh @@ -50,11 +50,18 @@ namespace mln namespace dicom { - /// Load a DICOM file in a Milena image. - /// - /// \param[out] ima A reference to the image which will receive - /// data. - /// \param[in] filename The source. + /*! Load a DICOM file in a Milena image. + + \param[out] ima A reference to the image which will receive + data. + \param[in] filename The source. + + + Common compilation flags to link to gdcm if this file is used: + + -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF -lgdcmexpat -lgdcmjpeg12 -lgdcmjpeg16 -lgdcmjpeg8 -lgdcmopenjpeg -lgdcmuuid -lgdcmzlib + + */ template <typename I> void load(Image<I>& ima, const std::string& filename); -- 1.5.6.5