[Olena-patches] r3536: Fix median threshold and add ImageMagick load support..

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-03-16 Fabien Freling &lt;fabien.freling(a)lrde.epita.fr&gt; Fix median threshold and add ImageMagick load support.. * fabien/igr/Makefile: Update. * fabien/igr/check.sh: Update. * fabien/igr/med.cc: Fix median value. * fabien/magick/Makefile: Update. * fabien/magick/load.hh: Implement Magick support. * fabien/magick/magick.cc: Test file for Magick support. --- igr/Makefile | 2 - igr/check.sh | 7 ++-- igr/med.cc | 26 +++++++++++---- magick/load.hh | 95 ++++++++++++++++++++----------------------------------- magick/magick.cc | 19 +++++++---- 5 files changed, 74 insertions(+), 75 deletions(-) Index: trunk/milena/sandbox/fabien/igr/check.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/check.sh (revision 3535) +++ trunk/milena/sandbox/fabien/igr/check.sh (revision 3536) @@ -12,11 +12,14 @@ echo " for lambda_closing = ${lambda_closing}"; ./clo_vol grad.dump $dim ${lambda_closing} nbasins=`./wst clo_vol.dump $dim` + echo " nbasins = $nbasins" ../bin/dumpl32_to_colorize wst.dump $dim $nbasins results/colorize_${3}_${lambda_closing}.ppm median=`./med wst.dump $dim $input $nbasins` + echo " median = $median" + threshold=$(($median / 2)) ../bin/dumpi12_to_pgm med.dump $dim results/median_${3}_${lambda_closing}.pgm - ./thres med.dump $dim $median - mv bin_result.pbm results/result_${3}_${lambda_closing}.pbm + ./thres med.dump $dim $threshold + mv result.pbm results/result_${3}_${lambda_closing}.pbm #if [ $2 -eq 2 ]; then # if [ ${lambda_closing} -eq 100 ]; then Index: trunk/milena/sandbox/fabien/igr/med.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/med.cc (revision 3535) +++ trunk/milena/sandbox/fabien/igr/med.cc (revision 3536) @@ -20,9 +20,12 @@ #include <mln/core/routine/extend.hh> #include <mln/accu/mean.hh> #include <mln/accu/median_h.hh> -#include <mln/morpho/elementary/dilation.hh> +#include <mln/histo/array.hh> +#include <mln/histo/compute.hh> +#include <mln/labeling/compute.hh> #include <mln/labeling/mean_values.hh> #include <mln/level/compute.hh> +#include <mln/morpho/elementary/dilation.hh> #include <mln/pw/all.hh> #include <mln/util/array.hh> @@ -59,6 +62,8 @@ return 1; } + unsigned median = 0; + if (dim == 2) { image2d<L> labels; @@ -70,18 +75,27 @@ data::fill((labels | (pw::value(labels) == 0u)).rw(), wst_dilate); mln_VAR(wst_mean, labeling::mean_values(dcm, labels, nbasins)); - accu::mean<float> accu_mean; - util::array<float> means = level::compute(accu_mean, wst_mean); - - // FIXME: Take median value of means + histo::array<int_u12> histogram = histo::compute(wst_mean); + int j = 0; + int k = 0; + for (int i = 0; i < histogram.nvalues(); ++i) + { + if (histogram[i]) + histogram[i] = i; + } + image1d<unsigned> ima_histo; + convert::from_to(histogram, ima_histo); + accu::median_h<int_u12> accu_med; + median = level::compute(accu_med, ima_histo | pw::value(ima_histo) != pw::cst(0)); io::dump::save(wst_mean, "med.dump"); - std::cout << median << std::endl; } else { // FIXME } + std::cout << median << std::endl; + return 0; } Index: trunk/milena/sandbox/fabien/igr/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/Makefile (revision 3535) +++ trunk/milena/sandbox/fabien/igr/Makefile (revision 3536) @@ -49,4 +49,4 @@ g++ -I../../../ ${CXXFLAGS} $^ -o thres clean: - rm -rf *.dump *.p?m *.plot *.log *.csv + rm -rf *.dump *.p?m *.plot *.log *.csv *.dSYM Index: trunk/milena/sandbox/fabien/TODO =================================================================== Index: trunk/milena/sandbox/fabien/magick/magick.cc =================================================================== --- trunk/milena/sandbox/fabien/magick/magick.cc (revision 3535) +++ trunk/milena/sandbox/fabien/magick/magick.cc (revision 3536) @@ -1,15 +1,22 @@ #include <mln/core/image/image2d.hh> -#include <mln/value/int_u8.hh> +#include <mln/value/rgb8.hh> #include "load.hh" -int main() +int main(int argc, char* argv[]) { using namespace mln; - using value::int_u8; + using value::rgb8; - image2d<int_u8> lena; + if (argc != 2) + { + std::cout << "Usage: " << argv[0] << " filename.ext" << std::endl; + return 1; + } + + image2d<rgb8> lena; + + io::magick::load(lena, argv[1]); - //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"); + return 0; } Index: trunk/milena/sandbox/fabien/magick/Makefile =================================================================== Index: trunk/milena/sandbox/fabien/magick/load.hh =================================================================== --- trunk/milena/sandbox/fabien/magick/load.hh (revision 3535) +++ trunk/milena/sandbox/fabien/magick/load.hh (revision 3536) @@ -37,6 +37,7 @@ */ # include <mln/core/image/image2d.hh> +# include <mln/value/rgb8.hh> # include <Magick++.h> @@ -59,58 +60,19 @@ void load(Image<I>& ima, const std::string& filename); - /*! Load a magick 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 magick 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::magick::load"); - image2d<V> ima;// = io::pnm::load<V>(MAGICK, filename); - trace::exiting("mln::io::magick::load"); - return ima; - } - - template <typename V> - inline - image3d<V> load(const std::string& filename) - { - trace::entering("mln::io::magick::load"); - image2d<V> ima;// = io::pnm::load<V>(MAGICK, filename); - trace::exiting("mln::io::magick::load"); - return ima; - } - template <typename I> inline - void load(Image<I>& ima, + void load(Image<I>& ima_, const std::string& filename) { trace::entering("mln::io::magick::load"); + I& ima = exact(ima_); + //std::ifstream file(filename.c_str()); //if (! file) //{ @@ -118,24 +80,37 @@ // abort(); //} - Magick::Image file(filename); - //std::cout << "file attribute: " << file.attribute() << std::endl; - std::cout << "width: " << file.columns() << std::endl; - 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; + Magick::Image im_file(filename); + im_file.modifyImage(); + im_file.type(Magick::TrueColorType); + int columns = im_file.columns(); + int rows = im_file.rows(); + /*std::cout << "width: " <<columns << std::endl; + std::cout << "height: " <<rows << std::endl; + std::cout << "depth: " <<im_file.depth() << std::endl; + std::cout << "comment: " <<im_file.comment() << std::endl; + std::cout << "format: " <<im_file.format() << std::endl; + std::cout << "filename: " <<im_file.imageInfo()->filename << std::endl;*/ + + const Magick::PixelPacket *pixel_cache = im_file.getConstPixels(0, 0, columns, rows); + + algebra::vec<mln_site_(I)::dim, unsigned int> vmin; + algebra::vec<mln_site_(I)::dim, unsigned int> vmax; + vmin[0] = 0; + vmin[1] = 0; + vmax[0] = rows - 1; + vmax[1] = columns - 1; + mln_site(I) pmin(vmin); + mln_site(I) pmax(vmax); + mln_concrete(I) result(box<mln_site(I)>(pmin, pmax)); + initialize(ima, result); + mln_piter(I) p(ima.domain()); + for_all(p) + { + const Magick::PixelPacket *pixel = pixel_cache + (int) p.to_site().to_vec()[0] * columns + + (int) p.to_site().to_vec()[1]; + ima(p) = value::rgb8(pixel->red % 256, pixel->green % 256, pixel->blue % 256); // WARNING: Quantum = 16bits but rgb is 8bits + } trace::exiting("mln::io::magick::load"); }