- Olena-patches

r3689: inim: Fix configure
by Warren Seine 20 Apr '09

20 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-20 Warren Seine <soow(a)lrde.epita.fr> inim: Fix configure. * boxes/Makefile: Fix bad include. * boxes/configure: Add test. --- Makefile | 2 +- configure | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) Index: trunk/milena/sandbox/inim/2010/boxes/configure =================================================================== --- trunk/milena/sandbox/inim/2010/boxes/configure (revision 3688) +++ trunk/milena/sandbox/inim/2010/boxes/configure (revision 3689) @@ -10,6 +10,11 @@ fi done +if [ x$MLN_DIR == x ]; then + echo "MLN_DIR not set" > /dev/stderr + exit 1 +fi + rm -f Makefile.rules touch Makefile.rules Index: trunk/milena/sandbox/inim/2010/boxes/Makefile =================================================================== --- trunk/milena/sandbox/inim/2010/boxes/Makefile (revision 3688) +++ trunk/milena/sandbox/inim/2010/boxes/Makefile (revision 3689) @@ -1,4 +1,4 @@ -include makefile.rules +include Makefile.rules TARGET=boxes boxes_SRC=boxes.cc -- :: Warren Seine // SooW :: :: warren.seine @ gmail.com :: :: EPITA CSI 2010 ::

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r3688: Process line: WST from color image using tree component. (BUG)
by Edwin Carlinet 19 Apr '09

19 Apr '09

ChangeLog: 2009-04-19 Edwin Carlinet <carlinet(a)lrde.epita.fr> Process line: WST from color image using tree component. (BUG). * edwin/rush/exo2/wst_from_tree.cc: Process line. * edwin/tree/components.hh: Fix bug related to research of n components method. --- rush/exo2/Makefile | 7 - rush/exo2/wst_from_tree.cc | 235 +++++++++++++++++++++++++++++++++++++++++++++ tree/components.hh | 12 +- 3 files changed, 247 insertions(+), 7 deletions(-) Index: trunk/milena/sandbox/edwin/tree/components.hh =================================================================== --- trunk/milena/sandbox/edwin/tree/components.hh (revision 3687) +++ trunk/milena/sandbox/edwin/tree/components.hh (revision 3688) @@ -222,7 +222,7 @@ p_array< mln_psite(A) > components; mln_ch_value(A, bool) activity; p_array< mln_psite(A) > max_arr = tree.nodes(); - unsigned arr_pos = 0; //position in max_array + unsigned arr_pos; //position in max_array unsigned n = 0; unsigned* nb_leaves = uses_leaves ? new unsigned(0) : 0; @@ -237,11 +237,13 @@ p = max_arr[arr_pos]; if (a(p) == 0) break; + //std::cout << p << " " << a(p) << std::endl; components.insert(p); morpho::tree::propagate_node_to_descendants(p, tree, activity, false, nb_leaves); morpho::tree::propagate_node_to_ancestors(p, tree, activity, false); activity(p) = false; - mln_assertion(nb_leaves == 0 || *nb_leaves <= n); + n++; + mln_assertion(nb_leaves == 0 || *nb_leaves < mln_max(unsigned)); } while (pred(p, n, nb_leaves)); @@ -281,8 +283,10 @@ mln_precondition(tree.f().domain() == a.domain()); mln_precondition(a.is_valid()); - p_array< mln_psite(A) > components = - internal::get_components(tree, a, internal::pred_n_components(n), false); + p_array< mln_psite(A) > components; + + if (n > 0) + components = internal::get_components(tree, a, internal::pred_n_components(n), false); trace::exiting("mln::morpho::tree::get_components"); return components; Index: trunk/milena/sandbox/edwin/rush/exo2/wst_from_tree.cc =================================================================== --- trunk/milena/sandbox/edwin/rush/exo2/wst_from_tree.cc (revision 0) +++ trunk/milena/sandbox/edwin/rush/exo2/wst_from_tree.cc (revision 3688) @@ -0,0 +1,235 @@ +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development Laboratory +// (LRDE) +// +// 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. + +/* core */ +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> + +#include <mln/value/int_u8.hh> +#include <mln/value/int_u16.hh> +#include <mln/value/rgb8.hh> +#include <mln/value/label_16.hh> + +/* io */ +#include <mln/io/ppm/load.hh> +#include <mln/io/ppm/save.hh> + +/* Gradient */ +#include "color_internal_gradient.hh" + +/* Labeling */ +#include <mln/level/convert.hh> +#include "color_labeling_mean.hh" + +/* WST */ +#include <mln/morpho/watershed/all.hh> +#include <mln/morpho/elementary/dilation.hh> + +/* Tree computation */ +#include <mln/level/sort_psites.hh> +#include <mln/morpho/tree/data.hh> +#include "../../tree/propagate.hh" +#include "../../tree/components.hh" + +#include <mln/morpho/tree/compute_attribute_image.hh> +#include <mln/morpho/attribute/sharpness.hh> + +/* pw */ +#include <mln/core/concept/function.hh> +#include <mln/fun/p2v/ternary.hh> +#include <mln/pw/all.hh> + +//std +#include <iostream> +#include <string> + +#include <mln/level/stretch.hh> +#include <mln/io/pgm/save.hh> + +namespace mln +{ + // Sharpness Attribute -> Height Attribute + template <typename P2V> + struct height_wrapper_ : Function_p2v< height_wrapper_<P2V> > + { + typedef unsigned result; + + height_wrapper_(const Function_p2v<P2V>& f) : + f_ (exact(f)) + { + mlc_is_a(mln_result(P2V), Accumulator)::check(); + } + + template <typename P> + unsigned operator() (const P& p) const + { + return f_(p).height(); + } + + private: + const P2V& f_; + }; + + // meta + template <typename P2V> + inline + height_wrapper_<P2V> + height_wrapper(const Function_p2v<P2V>& f) + { + return height_wrapper_<P2V>(f); + } +} + + + + + +void usage(char** argv) +{ + std::cout << "Usage: " << argv[0] << " input.ppm height [-o1 | -o2 | -o3]" + << std::endl + << "-o1\tSuperpose WS on input image (out: superpose.ppm)" << std::endl + << "-o2\tCount number of basins" << std::endl + << "-o3\tReplace basin by its mean color on the input (out: mean.ppm)" + << std::endl; + abort(); +} + + +int main(int argc, char** argv) +{ + using namespace mln; + using value::int_u8; + using value::int_u16; + using value::rgb8; + + if (argc < 3) + usage(argv); + + int output_ = 0; + int lambda_h = std::atoi(argv[2]); + + if (argc == 4) + if (std::string(argv[3]) == "-o1") + output_ = 1; + else if (std::string(argv[3]) == "-o2") + output_ = 2; + else if (std::string(argv[3]) == "-o3") + output_ = 3; + else + usage(argv); + + + + // Load color image. + typedef image2d<rgb8> I_; + + I_ input_; + io::ppm::load(input_, argv[1]); + + /***************************/ + /* Preprocessing (gradient)*/ + /***************************/ + typedef image2d<int_u8> I; + + I input = color_internal_gradient(input_); + + /***************************/ + /* Component tree creation */ + /***************************/ + typedef p_array<point2d> S; + typedef morpho::tree::data<I,S> tree_t; + + S s = level::sort_psites_decreasing(input); + tree_t t(input, s, c4()); + + + /******************************/ + /* Compute Attribute On Image */ + /******************************/ + typedef mln_ch_value_(I, double) A; + A a; + { + typedef morpho::attribute::sharpness sharp_t; + typedef mln_ch_value_(I, sharp_t) B; + + // Attribute Pruning + B a_img; + a = morpho::tree::compute_attribute_image(sharp_t (), t, &a_img); + + // Component filtering + a = duplicate((fun::p2v::ternary(height_wrapper(pw::value(a_img)) > pw::cst(lambda_h), + pw::value(a), + pw::cst(0.0))) | a.domain()); + } + + /************************************************/ + /* Retrieve Components (Maximising the criteria)*/ + /************************************************/ + A component_img; + { + p_array< mln_psite_(A) > obj_array; + I output = level::stretch(int_u8(), a); //adapt to 0-255 + io::pgm::save(output, "components.pgm"); + + obj_array = morpho::tree::get_components(t, a); + std::cout << obj_array.nsites() << std::endl; + + component_img = morpho::tree::propagate_components(a, t, obj_array, 1); + + // debug + //I output = level::stretch(int_u8(), component_img); //adapt to 0-255 + //io::pgm::save(output, "components.pgm"); + + } + + + /************************************************/ + /* WATERSHED */ + /************************************************/ + typedef image2d<int_u16> WST; + int_u16 n_basins = 0; + WST wst = morpho::watershed::flooding(component_img, c4(), n_basins); + + if (!output_ || output_ == 1) + { + I_ out = morpho::watershed::superpose(input_, wst); + io::ppm::save(out, "superpose.pgm"); + } + if (!output_ || output_ == 2) + std::cout << "Number of basins: " << n_basins << std::endl; + + if (!output_ || output_ == 3) + { + typedef image2d<value::label_16> L; + L lab = level::convert(value::label_16(), + morpho::elementary::dilation(wst, c8())); + I_ out = color_labeling_mean(input_, lab, n_basins); + io::ppm::save(out, "mean.pgm"); + } +} Index: trunk/milena/sandbox/edwin/rush/exo2/Makefile =================================================================== --- trunk/milena/sandbox/edwin/rush/exo2/Makefile (revision 3687) +++ trunk/milena/sandbox/edwin/rush/exo2/Makefile (revision 3688) @@ -13,8 +13,10 @@ SRC= OUT_IMG=superpose.pgm mean.pgm gradient.pgm closing.pgm +BIN=wst_from_closing wst_from_tree -all: wst_from_closing + +all: $(BIN) %: %.cc $(CXX) $(CXXFLAGS) $< -o $@ @@ -22,8 +24,7 @@ clean: rm -f $(OUT_IMG) - rm -f wst_from_closing - + rm -f $(BIN) %.o: %.cc $(CXX) $(CXXFLAGS) -c $< \ No newline at end of file

1 0

r3687: Process line: watershed from color image after height closing
by Edwin Carlinet 19 Apr '09

19 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-19 Edwin Carlinet <carlinet(a)lrde.epita.fr> Process line: watershed from color image after height closing. * edwin/rush/*, * edwin/rush/leaves: New directory for leaves export routines. Move rush/* to rush/leaves.* * edwin/rush/exo2: New. * edwin/rush/exo2/color_internal_gradient.hh: Routine that computes internal gradient from color image. * edwin/rush/exo2/color_labeling_mean.hh: Routine that replaces a basin label by its mean color. * edwin/rush/exo2/wst_from_closing.cc: Process line. --- exo2/Makefile | 29 +++++++ exo2/color_internal_gradient.hh | 149 ++++++++++++++++++++++++++++++++++++++++ exo2/color_labeling_mean.hh | 70 ++++++++++++++++++ exo2/configure | 21 +++++ exo2/wst_from_closing.cc | 127 ++++++++++++++++++++++++++++++++++ leaves/Makefile | 35 +++++++++ leaves/chain.sh | 34 +++++++++ leaves/configure | 21 +++++ leaves/export_leaves.hh | 115 ++++++++++++++++++++++++++++++ leaves/get_leaves.cc | 65 +++++++++++++++++ leaves/splot.sh | 10 ++ leaves/test/Makefile | 41 +++++++++++ leaves/test/configure | 21 +++++ leaves/test/export.cc | 63 ++++++++++++++++ 14 files changed, 801 insertions(+) Index: trunk/milena/sandbox/edwin/rush/configure (deleted) =================================================================== Index: trunk/milena/sandbox/edwin/rush/get_leaves.cc (deleted) =================================================================== Index: trunk/milena/sandbox/edwin/rush/splot.sh (deleted) =================================================================== Index: trunk/milena/sandbox/edwin/rush/chain.sh (deleted) =================================================================== Index: trunk/milena/sandbox/edwin/rush/Makefile (deleted) =================================================================== Index: trunk/milena/sandbox/edwin/rush/export_leaves.hh (deleted) =================================================================== Index: trunk/milena/sandbox/edwin/rush/leaves/test/configure =================================================================== --- trunk/milena/sandbox/edwin/rush/leaves/test/configure (revision 0) +++ trunk/milena/sandbox/edwin/rush/leaves/test/configure (revision 3687) @@ -0,0 +1,21 @@ +#! /bin/bash + +for arg in "$@"; do + if [ "$arg" == "--debug" ]; then + debug=1; + elif [ "$arg" == "--release" ]; then + release=1; + elif [ "${arg#--mln_dir=}" ]; then + MLN_DIR=${arg#--mln_dir=} + fi +done + +rm -f makefile.rules +touch makefile.rules +if [ "$debug" ]; then + echo 'DEBUG = 1' >> makefile.rules +fi +if [ "$release" ]; then + echo 'RELEASE = 1' >> makefile.rules +fi +echo "MLN_DIR = $MLN_DIR" >> makefile.rules \ No newline at end of file Property changes on: trunk/milena/sandbox/edwin/rush/leaves/test/configure ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/edwin/rush/leaves/test/export.cc =================================================================== --- trunk/milena/sandbox/edwin/rush/leaves/test/export.cc (revision 0) +++ trunk/milena/sandbox/edwin/rush/leaves/test/export.cc (revision 3687) @@ -0,0 +1,63 @@ +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development Laboratory +// (LRDE) +// +// 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. + +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/site_set/p_array.hh> + +#include <mln/level/sort_psites.hh> + +#include <mln/morpho/tree/data.hh> +#include "../export_leaves.hh" + +#include <mln/io/pbm/save.hh> + + +int main() +{ + using namespace mln; + + typedef image2d<int> I; + typedef p_array<point2d> S; + typedef morpho::tree::data<I,S> tree_t; + + int vals[] = {3, 3, 4, + 3, 5, 4, + 4, 4, 4 }; + + I ima = make::image2d(vals); + S s = level::sort_psites_decreasing(ima); + tree_t t(ima, s, c4()); + + export_leaves_to_file(t, ima); + + typedef mln_ch_value_(I, bool) B; + B b_img = export_leaves_to_img(t, ima); + + io::pbm::save(b_img, "leaves.pbm"); +} Index: trunk/milena/sandbox/edwin/rush/leaves/test/Makefile =================================================================== --- trunk/milena/sandbox/edwin/rush/leaves/test/Makefile (revision 0) +++ trunk/milena/sandbox/edwin/rush/leaves/test/Makefile (revision 3687) @@ -0,0 +1,41 @@ +include makefile.rules +TARGET=export +#sharp_SRC=sharp.cc +#sharp_OBJS=${sharp_SRC:.cc=.o} + +export_SRC=export.cc +export_OBJS=${export_SRC:.cc=.o} + +OLENADIR=$(MLN_DIR)/.. +MILENADIR=$(MLN_DIR) + +CXXFLAGS=-I$(MILENADIR) -I./ -W -Wall + + +CXXFLAGS += $(if $(DEBUG), -g -ggdb, -DNDEBUG\ + $(if $(RELEASE), -O3, -O1)) + +CXX=g++ +LD=g++ +LDFLAGS= + +all: $(TARGET) + + +$(TARGET): $($(TARGET)_OBJS) $($(TARGET)_SRC) + $(LD) $(LDFLAGS) -o $@ $($(TARGET)_OBJS) + +%.o: %.cc + $(CXX) $(CXXFLAGS) -c $< + +%.o: %.hh + $(CXX) $(CXXFLAGS) -c $< + +depend: + makedepend -- $(CXXFLAGS) -- -v $($(TARGET)_SRC) + +clean: + rm -f *.o $(TARGET) + #rm -f *.pbm + #find -name "*.pgm" \! -regex ".*/affiche2?.pgm" -delete +# DO NOT DELETE \ No newline at end of file Index: trunk/milena/sandbox/edwin/rush/leaves/configure =================================================================== --- trunk/milena/sandbox/edwin/rush/leaves/configure (revision 0) +++ trunk/milena/sandbox/edwin/rush/leaves/configure (revision 3687) @@ -0,0 +1,21 @@ +#! /bin/bash + +for arg in "$@"; do + if [ "$arg" == "--debug" ]; then + debug=1; + elif [ "$arg" == "--release" ]; then + release=1; + elif [ "${arg#--mln_dir=}" ]; then + MLN_DIR=${arg#--mln_dir=} + fi +done + +rm -f makefile.rules +touch makefile.rules +if [ "$debug" ]; then + echo 'DEBUG = 1' >> makefile.rules +fi +if [ "$release" ]; then + echo 'RELEASE = 1' >> makefile.rules +fi +echo "MLN_DIR = $MLN_DIR" >> makefile.rules \ No newline at end of file Property changes on: trunk/milena/sandbox/edwin/rush/leaves/configure ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/edwin/rush/leaves/get_leaves.cc =================================================================== --- trunk/milena/sandbox/edwin/rush/leaves/get_leaves.cc (revision 0) +++ trunk/milena/sandbox/edwin/rush/leaves/get_leaves.cc (revision 3687) @@ -0,0 +1,65 @@ +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/site_set/p_array.hh> + +#include <mln/level/sort_psites.hh> + +#include <mln/morpho/tree/data.hh> +#include <mln/morpho/tree/compute_attribute_image.hh> +#include "export_leaves.hh" + +#include <mln/morpho/attribute/sharpness.hh> + +#include <mln/io/pbm/save.hh> +#include <mln/io/pgm/load.hh> + +#include <mln/value/int_u8.hh> + +#include <iostream> + + + +void usage(char** argv) +{ + std::cout << "Retrieve leaves of the component tree using sharpness" + << " attribute. It returns a binary image of leaves and creates" + << " txt file that contains nodes of the branch that the leaf belongs to." + << std::endl; + std::cout << "Usage: " << argv[0] << " input.pgm" << std::endl; + abort(); +} + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc == 0) + usage(argv); + + + // Load a pgm img (Gray level Or Gradient Image) + typedef image2d<int_u8> I; + I input; + io::pgm::load(input, argv[1]); + + // Tree Creation + typedef p_array<point2d> S; + typedef morpho::tree::data<I,S> tree_t; + S s = level::sort_psites_decreasing(input); + tree_t t(input, s, c4()); + + // Attribute pruning. + typedef morpho::attribute::sharpness sharp_t; + typedef mln_ch_value_(I, double) A; + + A a = morpho::tree::compute_attribute_image(sharp_t (), t); + + + //Export Leaves + typedef mln_ch_value_(I, bool) B; + B b_img = export_leaves_to_img(t, a); + io::pbm::save(b_img, "leaves.pbm"); + export_leaves_to_file(t, a); +} Index: trunk/milena/sandbox/edwin/rush/leaves/splot.sh =================================================================== --- trunk/milena/sandbox/edwin/rush/leaves/splot.sh (revision 0) +++ trunk/milena/sandbox/edwin/rush/leaves/splot.sh (revision 3687) @@ -0,0 +1,10 @@ +#! /bin/bash +FILE=gplot.batch + +echo "set terminal png" > "$FILE" +for f in *.txt; do + echo 'set output "'$f'.png"' >> "$FILE" + echo 'plot "'$f'"' >> "$FILE" +done; + +gnuplot "$FILE" \ No newline at end of file Property changes on: trunk/milena/sandbox/edwin/rush/leaves/splot.sh ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/edwin/rush/leaves/chain.sh =================================================================== --- trunk/milena/sandbox/edwin/rush/leaves/chain.sh (revision 0) +++ trunk/milena/sandbox/edwin/rush/leaves/chain.sh (revision 3687) @@ -0,0 +1,34 @@ +#! /bin/bash + +function usage() +{ +echo "./chain.sh input.ppm (--graylevel | --gradient)" +exit 2 +} + +if [ $# -ne 2 ]; then + usage +fi + +if [ "$2" = "--gradient" ]; then + gradient=1 +elif [ "$2" = "--graylevel" ]; then + graylevel=1 +else + usage +fi + +make leaves +if [ "x$gradient" = "x1" ]; then + make all + name="gradient.pgm" + ./gradient "$1" "$name" +else + name="$1" + name="${name%.ppm}.pgm" + convert +compress -depth 8 -colorspace Gray "$1" "$name" +fi +./leaves "$name" +rm -Rf "$1".dir +mkdir "$1".dir +mv *.txt "leaves.pbm" "$name" "$1".dir \ No newline at end of file Property changes on: trunk/milena/sandbox/edwin/rush/leaves/chain.sh ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/edwin/rush/leaves/Makefile =================================================================== --- trunk/milena/sandbox/edwin/rush/leaves/Makefile (revision 0) +++ trunk/milena/sandbox/edwin/rush/leaves/Makefile (revision 3687) @@ -0,0 +1,35 @@ +include makefile.rules + + +OLENADIR=$(MLN_DIR)/.. +MILENADIR=$(MLN_DIR) + +CXXFLAGS = -I$(MILENADIR) -I./ -W -Wall +CXXFLAGS += $(if $(DEBUG), -g -ggdb, -DNDEBUG\ + $(if $(RELEASE), -O3, -O1)) +CXX=g++ +LD=g++ +LDFLAGS= +SRC= + + +GRADIENT_SRC = $(MLN_DIR)/sandbox/theo/exec/color_internal_gradient.cc +LEAVES_SRC = get_leaves.cc + + +all: leaves gradient + + +leaves: $(LEAVES_SRC) + $(CXX) $(CXXFLAGS) $< -o leaves + +gradient: $(GRADIENT_SRC) + $(CXX) $(CXXFLAGS) $< -o gradient + + +clean: + rm -f leaves gradient + + +%.o: %.cc + $(CXX) $(CXXFLAGS) -c $< \ No newline at end of file Index: trunk/milena/sandbox/edwin/rush/leaves/export_leaves.hh =================================================================== --- trunk/milena/sandbox/edwin/rush/leaves/export_leaves.hh (revision 0) +++ trunk/milena/sandbox/edwin/rush/leaves/export_leaves.hh (revision 3687) @@ -0,0 +1,115 @@ +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development Laboratory +// (LRDE) +// +// 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 EXPORT_LEAVES_HH_ +# define EXPORT_LEAVES_HH_ + +# include <mln/core/concept/image.hh> + +# include <mln/morpho/tree/data.hh> +# include "../../tree/propagate.hh" + + +# include <mln/data/fill.hh> + +# include <fstream> +# include <sstream> + +namespace mln { + + template <typename T, typename A> + inline + void + export_leaves_to_file(const T& tree, const Image<A>& attr_image); + + template <typename T, typename A> + inline + mln_ch_value(A, bool) + export_leaves_to_img(const T& tree, const Image<A>& attr_image); + + +# ifndef MLN_INCLUDE_ONLY + + template <typename T, typename A> + inline + void + export_leaves_to_file(const T& tree, const Image<A>& attr_image) + { + mln_precondition(tree.f().domain() == attr_image.domain()); + + const A& a = exact(attr_image); + mln_leaf_piter(T) leaf(tree); + + for_all(leaf) + { + std::stringstream fn; + for (int i = 0; i < leaf.dim; i++) + fn << "[" << leaf[i] << "]"; + fn << ".txt"; + + std::ofstream out(fn.str().c_str()); + mln_psite(T) n = leaf; + int i = 0; + while (!tree.is_root(n)) + { + out << i++ << " " << a(n) << std::endl; + n = tree.parent(n); + } + out < + inline + mln_ch_value(A, bool) + export_leaves_to_img(const T& tree, const Image<A>& attr_image) + { + mln_precondition(tree.f().domain() == attr_image.domain()); + + typedef mln_ch_value(A, bool) I; + const A& a = exact(attr_image); + + I output; + initialize(output, a); + data::fill(output, false); + + mln_leaf_piter(T) l(tree); + for_all(l) + output(l) = true; + + morpho::tree::propagate_representant(tree, output); + return output; + } + + + +# endif /* !MLN_INCLUDE_ONLY */ + +} // end of namespace mln + +#endif /* !EXPORT_LEAVES_HH_ */ Index: trunk/milena/sandbox/edwin/rush/exo2/configure =================================================================== --- trunk/milena/sandbox/edwin/rush/exo2/configure (revision 0) +++ trunk/milena/sandbox/edwin/rush/exo2/configure (revision 3687) @@ -0,0 +1,21 @@ +#! /bin/bash + +for arg in "$@"; do + if [ "$arg" == "--debug" ]; then + debug=1; + elif [ "$arg" == "--release" ]; then + release=1; + elif [ "${arg#--mln_dir=}" ]; then + MLN_DIR=${arg#--mln_dir=} + fi +done + +rm -f makefile.rules +touch makefile.rules +if [ "$debug" ]; then + echo 'DEBUG = 1' >> makefile.rules +fi +if [ "$release" ]; then + echo 'RELEASE = 1' >> makefile.rules +fi +echo "MLN_DIR = $MLN_DIR" >> makefile.rules \ No newline at end of file Property changes on: trunk/milena/sandbox/edwin/rush/exo2/configure ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/edwin/rush/exo2/wst_from_closing.cc =================================================================== --- trunk/milena/sandbox/edwin/rush/exo2/wst_from_closing.cc (revision 0) +++ trunk/milena/sandbox/edwin/rush/exo2/wst_from_closing.cc (revision 3687) @@ -0,0 +1,127 @@ +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development Laboratory +// (LRDE) +// +// 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. + +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> + +#include <mln/value/int_u8.hh> +#include <mln/value/int_u16.hh> +#include <mln/value/rgb8.hh> +#include <mln/value/label_16.hh> +#include <mln/level/convert.hh> + +#include <mln/io/ppm/load.hh> +#include <mln/io/ppm/save.hh> +#include <mln/io/pgm/save.hh> + +#include "color_internal_gradient.hh" +#include "color_labeling_mean.hh" +#include <mln/morpho/closing/height.hh> +#include <mln/morpho/watershed/all.hh> +#include <mln/morpho/elementary/dilation.hh> + + +#include <iostream> +#include <string> + + +void usage(char** argv) +{ + std::cout << "Usage: " << argv[0] << " input.ppm height [-o1 | -o2 | -o3]" + << std::endl + << "-o1\tSuperpose WS on input image (out: superpose.ppm)" << std::endl + << "-o2\tCount number of basins" << std::endl + << "-o3\tReplace basin by its mean color on the input (out: mean.ppm)" + << std::endl; + abort(); +} + + + +int main(int argc, char** argv) +{ + using namespace mln; + using value::int_u8; + using value::int_u16; + using value::rgb8; + + if (argc < 3) + usage(argv); + + int output_ = 0; + int lambda_h = std::atoi(argv[2]); + + if (argc == 4) + if (std::string(argv[3]) == "-o1") + output_ = 1; + else if (std::string(argv[3]) == "-o2") + output_ = 2; + else if (std::string(argv[3]) == "-o3") + output_ = 3; + else + usage(argv); + + + + // Load color image. + typedef image2d<rgb8> I_; + I_ input_; + io::ppm::load(input_, argv[1]); + + // Gradient. + typedef image2d<int_u8> I; + I input = color_internal_gradient(input_); + + // Closing + std::cout << lambda_h << std::endl; + input = morpho::closing::height(input, c4(), lambda_h); + + // Watershed + typedef image2d<int_u16> WST; + int_u16 n_basins = 0; + WST wst = morpho::watershed::flooding(input, c4(), n_basins); + + if (!output_ || output_ == 1) + { + I_ out = morpho::watershed::superpose(input_, wst); + io::ppm::save(out, "superpose.pgm"); + } + + if (!output_ || output_ == 2) + std::cout << "Number of basins: " << n_basins << std::endl; + + if (!output_ || output_ == 3) + { + typedef image2d<value::label_16> L; + L lab = level::convert(value::label_16(), + morpho::elementary::dilation(wst, c8())); + I_ out = color_labeling_mean(input_, lab, n_basins); + io::ppm::save(out, "mean.pgm"); + } + +} Index: trunk/milena/sandbox/edwin/rush/exo2/color_internal_gradient.hh =================================================================== --- trunk/milena/sandbox/edwin/rush/exo2/color_internal_gradient.hh (revision 0) +++ trunk/milena/sandbox/edwin/rush/exo2/color_internal_gradient.hh (revision 3687) @@ -0,0 +1,149 @@ +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development Laboratory +// (LRDE) +// +// 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 COLOR_INTERNAL_GRADIENT_HH_ +# define COLOR_INTERNAL_GRADIENT_HH_ + +#include <mln/core/alias/neighb2d.hh> +#include <mln/morpho/elementary/gradient_internal.hh> +#include <mln/math/diff_abs.hh> + +#include <mln/accu/image/init.hh> +#include <mln/accu/image/take.hh> +#include <mln/accu/image/to_result.hh> + +#include <mln/accu/max.hh> + +namespace mln +{ + + value::int_u8 + dist(const value::rgb8& c1, + const value::rgb8& c2) + { + unsigned d = 0; + d += math::diff_abs(c1.red(), c2.red()); + d += math::diff_abs(c1.green(), c2.green()); + d += math::diff_abs(c1.blue(), c2.blue()); + if (d > 255) + d = 255; + return d; + } + + template <typename N> + image2d<value::int_u8> + color_gradient(const image2d<value::rgb8>& input, + const N& nbh) + { + using value::int_u8; + image2d<int_u8> output(input.domain()); + + mln_piter(box2d) p(input.domain()); + mln_niter(N) n(nbh, p); + for_all(p) + { + int_u8 d = 0u; + for_all(n) if (input.domain().has(n)) + { + int_u8 d_ = dist(input(p), input(n)); + if (d_ > d) + d = d_; + } + output(p) = d; + } + + return output; + } + + + + template <typename I> + image2d<value::int_u8> + get_red(const I& input) + { + typedef image2d<value::int_u8> J; + J output(input.domain()); + + mln_pixter(const I) p_in(input); + mln_pixter(J) p_out(output); + for_all_2(p_in, p_out) + p_out.val() = p_in.val().red(); + return output; + } + + template <typename I> + image2d<value::int_u8> + get_green(const I& input) + { + typedef image2d<value::int_u8> J; + J output(input.domain()); + + mln_pixter(const I) p_in(input); + mln_pixter(J) p_out(output); + for_all_2(p_in, p_out) + p_out.val() = p_in.val().green(); + return output; + } + + template <typename I> + image2d<value::int_u8> + get_blue(const I& input) + { + typedef image2d<value::int_u8> J; + J output(input.domain()); + + mln_pixter(const I) p_in(input); + mln_pixter(J) p_out(output); + for_all_2(p_in, p_out) + p_out.val() = p_in.val().blue(); + return output; + } + + image2d<value::int_u8> + color_internal_gradient(const image2d<value::rgb8>& input) + { + typedef accu::max< value::int_u8 > A; + image2d<A> grad(input.domain()); + + using morpho::elementary::gradient_internal; + + accu::image::init(grad); + + accu::image::take(grad, + gradient_internal(get_red(input), c4())); + accu::image::take(grad, + gradient_internal(get_green(input), c4())); + accu::image::take(grad, + gradient_internal(get_blue(input), c4())); + + return accu::image::to_result(grad); + } + +} // mln + +#endif /* !COLOR_INTERNAL_GRADIENT_HH_ */ Index: trunk/milena/sandbox/edwin/rush/exo2/color_labeling_mean.hh =================================================================== --- trunk/milena/sandbox/edwin/rush/exo2/color_labeling_mean.hh (revision 0) +++ trunk/milena/sandbox/edwin/rush/exo2/color_labeling_mean.hh (revision 3687) @@ -0,0 +1,70 @@ +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development Laboratory +// (LRDE) +// +// 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 COLOR_LABELING_MEAN_HH_ +# define COLOR_LABELING_MEAN_HH_ + +# include <mln/core/image/image2d.hh> + +# include <mln/labeling/compute.hh> +# include <mln/accu/mean.hh> +# include <mln/level/transform.hh> + +# include <mln/value/label_8.hh> +# include <mln/value/int_u16.hh> + +namespace mln { + + template <typename L> + image2d< value::rgb8 > + color_labeling_mean(const image2d< value::rgb8>& input, + const Image<L>& label, + unsigned nlabels) + { + using value::rgb8; + typedef algebra::vec<3,float> V; + + accu::mean<value::rgb8> m_; + util::array<V> m = labeling::compute(m_, input, exact(label), nlabels); + + util::array<rgb8> c(unsigned(nlabels) + 1); + + c[0] = rgb8(0,0,0); + for (unsigned l = 1; l <= nlabels; ++l) + { + c[l].red() = m[l][0]; + c[l].green() = m[l][1]; + c[l].blue() = m[l][2]; + } + + return level::transform(label, c); + } + +} // mln + +#endif /* !COLOR_LABELING_MEAN_HH_ */ Index: trunk/milena/sandbox/edwin/rush/exo2/Makefile =================================================================== --- trunk/milena/sandbox/edwin/rush/exo2/Makefile (revision 0) +++ trunk/milena/sandbox/edwin/rush/exo2/Makefile (revision 3687) @@ -0,0 +1,29 @@ +include makefile.rules + + +OLENADIR=$(MLN_DIR)/.. +MILENADIR=$(MLN_DIR) + +CXXFLAGS = -I$(MILENADIR) -I./ -W -Wall +CXXFLAGS += $(if $(DEBUG), -g -ggdb, -DNDEBUG\ + $(if $(RELEASE), -O3, -O1)) +CXX=g++ +LD=g++ +LDFLAGS= +SRC= + +OUT_IMG=superpose.pgm mean.pgm gradient.pgm closing.pgm + +all: wst_from_closing + +%: %.cc + $(CXX) $(CXXFLAGS) $< -o $@ + + +clean: + rm -f $(OUT_IMG) + rm -f wst_from_closing + + +%.o: %.cc + $(CXX) $(CXXFLAGS) -c $< \ No newline at end of file

1 0

r3686: Routines to export leaves toward several representation
by Edwin Carlinet 18 Apr '09

18 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-19 Edwin Carlinet <carlinet(a)lrde.epita.fr> Routines to export leaves toward several representation. * edwin/rush/Makefile: New. * edwin/rush/chain.sh: Script that handles process. * edwin/rush/configure: New. * edwin/rush/export_leaves.hh: Leaves exportation methods. * edwin/rush/get_leaves.cc: Process file that import pgm image, creates tree, applies an attribute and export the leaves. * edwin/rush/splot.sh: New file to autogenerate gnuplot graphics. * edwin/rush/test/Makefile: New. * edwin/rush/test/configure: New. * edwin/rush/test/export.cc: Test file for routines. * edwin/rush/test: New test folder. * edwin/rush: New. * edwin/tree/propagate.hh: Add missing include. --- rush/Makefile | 35 +++++++++++++++ rush/chain.sh | 34 ++++++++++++++ rush/configure | 21 +++++++++ rush/export_leaves.hh | 115 ++++++++++++++++++++++++++++++++++++++++++++++++++ rush/get_leaves.cc | 65 ++++++++++++++++++++++++++++ rush/splot.sh | 10 ++++ rush/test/Makefile | 41 +++++++++++++++++ rush/test/configure | 21 +++++++++ rush/test/export.cc | 63 +++++++++++++++++++++++++++ tree/propagate.hh | 1 10 files changed, 406 insertions(+) Index: trunk/milena/sandbox/edwin/tree/propagate.hh =================================================================== --- trunk/milena/sandbox/edwin/tree/propagate.hh (revision 3685) +++ trunk/milena/sandbox/edwin/tree/propagate.hh (revision 3686) @@ -33,6 +33,7 @@ /// Functions to propagate a node value in the tree. #include <mln/morpho/tree/data.hh> +# include "propagate_node.hh" namespace mln { namespace morpho { Index: trunk/milena/sandbox/edwin/rush/test/configure =================================================================== --- trunk/milena/sandbox/edwin/rush/test/configure (revision 0) +++ trunk/milena/sandbox/edwin/rush/test/configure (revision 3686) @@ -0,0 +1,21 @@ +#! /bin/bash + +for arg in "$@"; do + if [ "$arg" == "--debug" ]; then + debug=1; + elif [ "$arg" == "--release" ]; then + release=1; + elif [ "${arg#--mln_dir=}" ]; then + MLN_DIR=${arg#--mln_dir=} + fi +done + +rm -f makefile.rules +touch makefile.rules +if [ "$debug" ]; then + echo 'DEBUG = 1' >> makefile.rules +fi +if [ "$release" ]; then + echo 'RELEASE = 1' >> makefile.rules +fi +echo "MLN_DIR = $MLN_DIR" >> makefile.rules \ No newline at end of file Property changes on: trunk/milena/sandbox/edwin/rush/test/configure ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/edwin/rush/test/export.cc =================================================================== --- trunk/milena/sandbox/edwin/rush/test/export.cc (revision 0) +++ trunk/milena/sandbox/edwin/rush/test/export.cc (revision 3686) @@ -0,0 +1,63 @@ +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development Laboratory +// (LRDE) +// +// 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. + +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/site_set/p_array.hh> + +#include <mln/level/sort_psites.hh> + +#include <mln/morpho/tree/data.hh> +#include "../export_leaves.hh" + +#include <mln/io/pbm/save.hh> + + +int main() +{ + using namespace mln; + + typedef image2d<int> I; + typedef p_array<point2d> S; + typedef morpho::tree::data<I,S> tree_t; + + int vals[] = {3, 3, 4, + 3, 5, 4, + 4, 4, 4 }; + + I ima = make::image2d(vals); + S s = level::sort_psites_decreasing(ima); + tree_t t(ima, s, c4()); + + export_leaves_to_file(t, ima); + + typedef mln_ch_value_(I, bool) B; + B b_img = export_leaves_to_img(t, ima); + + io::pbm::save(b_img, "leaves.pbm"); +} Index: trunk/milena/sandbox/edwin/rush/test/Makefile =================================================================== --- trunk/milena/sandbox/edwin/rush/test/Makefile (revision 0) +++ trunk/milena/sandbox/edwin/rush/test/Makefile (revision 3686) @@ -0,0 +1,41 @@ +include makefile.rules +TARGET=export +#sharp_SRC=sharp.cc +#sharp_OBJS=${sharp_SRC:.cc=.o} + +export_SRC=export.cc +export_OBJS=${export_SRC:.cc=.o} + +OLENADIR=$(MLN_DIR)/.. +MILENADIR=$(MLN_DIR) + +CXXFLAGS=-I$(MILENADIR) -I./ -W -Wall + + +CXXFLAGS += $(if $(DEBUG), -g -ggdb, -DNDEBUG\ + $(if $(RELEASE), -O3, -O1)) + +CXX=g++ +LD=g++ +LDFLAGS= + +all: $(TARGET) + + +$(TARGET): $($(TARGET)_OBJS) $($(TARGET)_SRC) + $(LD) $(LDFLAGS) -o $@ $($(TARGET)_OBJS) + +%.o: %.cc + $(CXX) $(CXXFLAGS) -c $< + +%.o: %.hh + $(CXX) $(CXXFLAGS) -c $< + +depend: + makedepend -- $(CXXFLAGS) -- -v $($(TARGET)_SRC) + +clean: + rm -f *.o $(TARGET) + #rm -f *.pbm + #find -name "*.pgm" \! -regex ".*/affiche2?.pgm" -delete +# DO NOT DELETE \ No newline at end of file Index: trunk/milena/sandbox/edwin/rush/configure =================================================================== --- trunk/milena/sandbox/edwin/rush/configure (revision 0) +++ trunk/milena/sandbox/edwin/rush/configure (revision 3686) @@ -0,0 +1,21 @@ +#! /bin/bash + +for arg in "$@"; do + if [ "$arg" == "--debug" ]; then + debug=1; + elif [ "$arg" == "--release" ]; then + release=1; + elif [ "${arg#--mln_dir=}" ]; then + MLN_DIR=${arg#--mln_dir=} + fi +done + +rm -f makefile.rules +touch makefile.rules +if [ "$debug" ]; then + echo 'DEBUG = 1' >> makefile.rules +fi +if [ "$release" ]; then + echo 'RELEASE = 1' >> makefile.rules +fi +echo "MLN_DIR = $MLN_DIR" >> makefile.rules \ No newline at end of file Property changes on: trunk/milena/sandbox/edwin/rush/configure ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/edwin/rush/get_leaves.cc =================================================================== --- trunk/milena/sandbox/edwin/rush/get_leaves.cc (revision 0) +++ trunk/milena/sandbox/edwin/rush/get_leaves.cc (revision 3686) @@ -0,0 +1,65 @@ +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/site_set/p_array.hh> + +#include <mln/level/sort_psites.hh> + +#include <mln/morpho/tree/data.hh> +#include <mln/morpho/tree/compute_attribute_image.hh> +#include "export_leaves.hh" + +#include <mln/morpho/attribute/sharpness.hh> + +#include <mln/io/pbm/save.hh> +#include <mln/io/pgm/load.hh> + +#include <mln/value/int_u8.hh> + +#include <iostream> + + + +void usage(char** argv) +{ + std::cout << "Retrieve leaves of the component tree using sharpness" + << " attribute. It returns a binary image of leaves and creates" + << " txt file that contains nodes of the branch that the leaf belongs to." + << std::endl; + std::cout << "Usage: " << argv[0] << " input.pgm" << std::endl; + abort(); +} + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc == 0) + usage(argv); + + + // Load a pgm img (Gray level Or Gradient Image) + typedef image2d<int_u8> I; + I input; + io::pgm::load(input, argv[1]); + + // Tree Creation + typedef p_array<point2d> S; + typedef morpho::tree::data<I,S> tree_t; + S s = level::sort_psites_decreasing(input); + tree_t t(input, s, c4()); + + // Attribute pruning. + typedef morpho::attribute::sharpness sharp_t; + typedef mln_ch_value_(I, double) A; + + A a = morpho::tree::compute_attribute_image(sharp_t (), t); + + + //Export Leaves + typedef mln_ch_value_(I, bool) B; + B b_img = export_leaves_to_img(t, a); + io::pbm::save(b_img, "leaves.pbm"); + export_leaves_to_file(t, a); +} Index: trunk/milena/sandbox/edwin/rush/splot.sh =================================================================== --- trunk/milena/sandbox/edwin/rush/splot.sh (revision 0) +++ trunk/milena/sandbox/edwin/rush/splot.sh (revision 3686) @@ -0,0 +1,10 @@ +#! /bin/bash +FILE=gplot.batch + +echo "set terminal png" > "$FILE" +for f in *.txt; do + echo 'set output "'$f'.png"' >> "$FILE" + echo 'plot "'$f'"' >> "$FILE" +done; + +gnuplot "$FILE" \ No newline at end of file Property changes on: trunk/milena/sandbox/edwin/rush/splot.sh ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/edwin/rush/chain.sh =================================================================== --- trunk/milena/sandbox/edwin/rush/chain.sh (revision 0) +++ trunk/milena/sandbox/edwin/rush/chain.sh (revision 3686) @@ -0,0 +1,34 @@ +#! /bin/bash + +function usage() +{ +echo "./chain.sh input.ppm (--graylevel | --gradient)" +exit 2 +} + +if [ $# -ne 2 ]; then + usage +fi + +if [ "$2" = "--gradient" ]; then + gradient=1 +elif [ "$2" = "--graylevel" ]; then + graylevel=1 +else + usage +fi + +make leaves +if [ "x$gradient" = "x1" ]; then + make all + name="gradient.pgm" + ./gradient "$1" "$name" +else + name="$1" + name="${name%.ppm}.pgm" + convert +compress -depth 8 -colorspace Gray "$1" "$name" +fi +./leaves "$name" +rm -Rf "$1".dir +mkdir "$1".dir +mv *.txt "leaves.pbm" "$name" "$1".dir \ No newline at end of file Property changes on: trunk/milena/sandbox/edwin/rush/chain.sh ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/edwin/rush/Makefile =================================================================== --- trunk/milena/sandbox/edwin/rush/Makefile (revision 0) +++ trunk/milena/sandbox/edwin/rush/Makefile (revision 3686) @@ -0,0 +1,35 @@ +include makefile.rules + + +OLENADIR=$(MLN_DIR)/.. +MILENADIR=$(MLN_DIR) + +CXXFLAGS = -I$(MILENADIR) -I./ -W -Wall +CXXFLAGS += $(if $(DEBUG), -g -ggdb, -DNDEBUG\ + $(if $(RELEASE), -O3, -O1)) +CXX=g++ +LD=g++ +LDFLAGS= +SRC= + + +GRADIENT_SRC = $(MLN_DIR)/sandbox/theo/exec/color_internal_gradient.cc +LEAVES_SRC = get_leaves.cc + + +all: leaves gradient + + +leaves: $(LEAVES_SRC) + $(CXX) $(CXXFLAGS) $< -o leaves + +gradient: $(GRADIENT_SRC) + $(CXX) $(CXXFLAGS) $< -o gradient + + +clean: + rm -f leaves gradient + + +%.o: %.cc + $(CXX) $(CXXFLAGS) -c $< \ No newline at end of file Index: trunk/milena/sandbox/edwin/rush/export_leaves.hh =================================================================== --- trunk/milena/sandbox/edwin/rush/export_leaves.hh (revision 0) +++ trunk/milena/sandbox/edwin/rush/export_leaves.hh (revision 3686) @@ -0,0 +1,115 @@ +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development Laboratory +// (LRDE) +// +// 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 EXPORT_LEAVES_HH_ +# define EXPORT_LEAVES_HH_ + +# include <mln/core/concept/image.hh> + +# include <mln/morpho/tree/data.hh> +# include "../tree/propagate.hh" + + +# include <mln/data/fill.hh> + +# include <fstream> +# include <sstream> + +namespace mln { + + template <typename T, typename A> + inline + void + export_leaves_to_file(const T& tree, const Image<A>& attr_image); + + template <typename T, typename A> + inline + mln_ch_value(A, bool) + export_leaves_to_img(const T& tree, const Image<A>& attr_image); + + +# ifndef MLN_INCLUDE_ONLY + + template <typename T, typename A> + inline + void + export_leaves_to_file(const T& tree, const Image<A>& attr_image) + { + mln_precondition(tree.f().domain() == attr_image.domain()); + + const A& a = exact(attr_image); + mln_leaf_piter(T) leaf(tree); + + for_all(leaf) + { + std::stringstream fn; + for (int i = 0; i < leaf.dim; i++) + fn << "[" << leaf[i] << "]"; + fn << ".txt"; + + std::ofstream out(fn.str().c_str()); + mln_psite(T) n = leaf; + int i = 0; + while (!tree.is_root(n)) + { + out << i++ << " " << a(n) << std::endl; + n = tree.parent(n); + } + out < + inline + mln_ch_value(A, bool) + export_leaves_to_img(const T& tree, const Image<A>& attr_image) + { + mln_precondition(tree.f().domain() == attr_image.domain()); + + typedef mln_ch_value(A, bool) I; + const A& a = exact(attr_image); + + I output; + initialize(output, a); + data::fill(output, false); + + mln_leaf_piter(T) l(tree); + for_all(l) + output(l) = true; + + morpho::tree::propagate_representant(tree, output); + return output; + } + + + +# endif /* !MLN_INCLUDE_ONLY */ + +} // end of namespace mln + +#endif /* !EXPORT_LEAVES_HH_ */

1 0

3685: Update src of 'color labeling mean'.
by Thierry Geraud 17 Apr '09

17 Apr '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Update src of 'color labeling mean'. * theo/exec/color_labeling_mean.cc: Update. color_labeling_mean.cc | 36 +++++++++++++++++++++++++++--------- 1 file changed, 27 insertions(+), 9 deletions(-) Index: theo/exec/color_labeling_mean.cc --- theo/exec/color_labeling_mean.cc (revision 3684) +++ theo/exec/color_labeling_mean.cc (working copy) @@ -6,6 +6,8 @@ #include <mln/level/transform.hh> #include <mln/value/label_8.hh> +#include <mln/value/int_u16.hh> +#include <mln/level/convert.hh> #include <mln/io/pgm/load.hh> #include <mln/io/ppm/load.hh> @@ -13,32 +15,48 @@ +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.ppm label.pgm output.pgm" << std::endl + << " Replace every label by its mean color value." << std::endl; + std::abort(); +} int main(int argc, char* argv[]) { using namespace mln; using value::int_u8; + using value::int_u16; using value::label_8; using value::rgb8; + if (argc != 4) + usage(argv); + + + image2d<rgb8> ima; + io::ppm::load(ima, argv[1]); + + image2d<int_u8> lab; - io::pgm::load(lab, argv[1]); + io::pgm::load(lab, argv[2]); - int_u8 min, nlabels; - estim::min_max(lab, min, nlabels); + image2d<int_u16> lab_ = level::convert(int_u16(), lab); - std::cout << min << ' ' << nlabels << std::endl; + int_u16 min, nlabels; + estim::min_max(lab_, min, nlabels); - image2d<rgb8> ima; - io::ppm::load(ima, argv[2]); + std::cout << "n labels = " << nlabels << std::endl; accu::mean<rgb8> m_; typedef algebra::vec<3,float> V; - util::array<V> m = labeling::compute(m_, ima, lab, nlabels); + util::array<V> m = labeling::compute(m_, ima, lab_, nlabels); + + util::array<rgb8> c(unsigned(nlabels) + 1); - util::array<rgb8> c(nlabels + 1); - for (unsigned l = 0; l <= nlabels; ++l) + c[0] = rgb8(0,0,0); + for (unsigned l = 1; l <= nlabels; ++l) { c[l].red() = m[l][0]; c[l].green() = m[l][1];

1 0

Re: [Olena-patches] [Olena] #3: Migrate Olena 0.11 (and previous revisions) from PRCS to Git (was: Migrate Olena 0.11 (and previous revisions) from PRCS to Subversion)
by Olena Trac 17 Apr '09

17 Apr '09

#3: Migrate Olena 0.11 (and previous revisions) from PRCS to Git --------------------------+------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: enhancement | Status: reopened Priority: blocker | Milestone: Olena 0.11.1 Component: other | Version: 0.11 Resolution: | Keywords: prcs subversion svn git --------------------------+------------------------------------------------- Changes (by levill_r): * keywords: prcs subversion svn => prcs subversion svn git * status: closed => reopened * resolution: wontfix => Old description: > '''No further development should be done on the 0.11 branch until this > task is either fixed or removed.''' > > This task is an open discussion. I haven't much tried to convert the > PRCS Olena repository to a Subversion one, and I think it '''is''' really > feasible, though not trivial. If you're interested in this migration, > please ask me (Roland) first before making actual changes to the PRCS or > the SVN repository. New description: Use `prcs2git` (http://takaki-web.media-as.org/my_works/prcs2git) to convert the old PRCS revisions of Olena to Git. I (Roland) made an attempt and successfully converted the whole repository (minus two bogus revisions, namely 10.138 and 10.139) by using it. However there is room for improvement: * ignoring revisions is not possible (there should be an option taking an ignore pattern as argument) * information about author and committer (name, e-mail, date) is not propagated; * log title (short messages) are filled with PRCS metadata (ugly!) ; we should retrieve the title from somewhere (PRCS, the !ChangeLog(s) or even the mailing list); * log messages are meaningless. Branches, however, have been well translated. '''Remember that no further development should be done on the 0.11 branch until this task is either fixed or removed.''' -- Comment: s/Subversion/Git/. -- Ticket URL: <https://trac.lrde.org/olena/ticket/3#comment:8> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

1 0

milena r3684: Remove check save + modification in compute attribute method
by Edwin Carlinet 17 Apr '09

17 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena ChangeLog: 2009-04-17 Edwin Carlinet <carlinet(a)lrde.epita.fr> Remove check save + modification in compute attribute method. * mln/io/pgm/save.hh: Remove static check unit_8 while saving pgm. * mln/morpho/tree/compute_attribute_image.hh: Add extra argument where the accumulator image will be store. --- io/pgm/save.hh | 3 - morpho/tree/compute_attribute_image.hh | 57 ++++++++++++++++++++++----------- 2 files changed, 38 insertions(+), 22 deletions(-) Index: trunk/milena/mln/morpho/tree/compute_attribute_image.hh =================================================================== --- trunk/milena/mln/morpho/tree/compute_attribute_image.hh (revision 3683) +++ trunk/milena/mln/morpho/tree/compute_attribute_image.hh (revision 3684) @@ -35,6 +35,7 @@ /// /// \todo Specialize for low quant (and try fastest). +# include <mln/core/routine/duplicate.hh> # include <mln/core/concept/image.hh> # include <mln/morpho/tree/data.hh> # include <mln/trait/accumulators.hh> @@ -42,7 +43,6 @@ # include <mln/data/fill.hh> - namespace mln { @@ -52,25 +52,38 @@ namespace tree { - /// Compute a tree with a parent relationship between sites. - /// - /// Warning: \p s translates the ordering related to the - /// "natural" childhood relationship. The parenthood is thus - /// inverted w.r.t. to \p s. - /// - /// It is very convenient since all processing upon the parent - /// tree are performed following \p s (in the default "forward" - /// way). - /// - /// FIXME: Put it more clearly... - /// - /// The parent result image verifies: \n - /// - p is root iff parent(p) == p \n - /// - p is a node iff either p is root or f(parent(p)) != f(p). - + /** + ** Compute an attribute image using tree with a parent + ** relationship between sites. In the attribute image, the + ** resulting value at a node is the 'sum' of its sub-components + ** value + the attribute value at this node. + ** + ** Warning: \p s translates the ordering related to the + ** "natural" childhood relationship. The parenthood is thus + ** inverted w.r.t. to \p s. + ** + ** It is very convenient since all processing upon the parent + ** tree are performed following \p s (in the default "forward" + ** way). + ** + ** FIXME: Put it more clearly... + ** + ** The parent result image verifies: \n + ** - p is root iff parent(p) == p \n + ** - p is a node iff either p is root or f(parent(p)) != f(p). + ** + ** @param[in] a Attribute. + ** @param[in] t Component tree. + ** @param[out] accu_image Optional argument used to store image + ** of attribute accumulator. + ** + ** @return The attribute image. + */ template <typename A, typename T> mln_ch_value(typename T::function, mln_result(A)) - compute_attribute_image(const Accumulator<A>& a, const T& t); + compute_attribute_image(const Accumulator<A>& a, + const T& t, + mln_ch_value(typename T::function, A)* accu_image = 0); @@ -121,7 +134,9 @@ template <typename A, typename T> inline mln_ch_value(typename T::function, mln_result(A)) - compute_attribute_image(const Accumulator<A>& a_, const T& t) + compute_attribute_image(const Accumulator<A>& a_, + const T& t, + mln_ch_value(typename T::function, A)* accu_image = 0) { trace::entering("morpho::tree::compute_attribute_image"); @@ -161,6 +176,10 @@ } } + // Store accumulator image. + if (accu_image) + *accu_image = duplicate(acc); + typedef typename T::function I; mln_ch_value(I, mln_result(A)) output; initialize(output, acc); Index: trunk/milena/mln/io/pgm/save.hh =================================================================== --- trunk/milena/mln/io/pgm/save.hh (revision 3683) +++ trunk/milena/mln/io/pgm/save.hh (revision 3684) @@ -82,9 +82,6 @@ // FIXME: Is it exhaustive? mlc_is_not_a(mln_value(I), value::Vectorial)::check(); mlc_converts_to(mln_value(I),unsigned)::check(); - /// Make sure this is a low quantification value type - /// (mln_card returns 0 if it is not) - metal::bool_<mln_card(mln_value(I)) != 0>::check(); trace::entering("mln::io::pgm::save"); io::pnm::save(PGM, exact(ima), filename);

1 0

r3683: Add labeling output and add doc
by Edwin Carlinet 17 Apr '09

17 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-17 Edwin Carlinet <carlinet(a)lrde.epita.fr> Add labeling output and add doc. * edwin/tree/components.hh, * edwin/tree/propagate.hh, * edwin/tree/propagate_node.hh: Clean and add documentation. * edwin/tree/sharp.cc: Add labeling and benchmark. --- components.hh | 43 +++++++++++++++++++++++++++++-- propagate.hh | 25 +++++++++++++++++- propagate_node.hh | 4 +- sharp.cc | 74 +++++++++++++++++++++++++++--------------------------- 4 files changed, 103 insertions(+), 43 deletions(-) Index: trunk/milena/sandbox/edwin/tree/propagate.hh =================================================================== --- trunk/milena/sandbox/edwin/tree/propagate.hh (revision 3682) +++ trunk/milena/sandbox/edwin/tree/propagate.hh (revision 3683) @@ -71,7 +71,7 @@ */ template <typename A, typename T> inline - A set_value_to_components(const Image<A>& attr_image, + A propagate_components(const Image<A>& attr_image, const T& tree, const p_array< mln_psite(A) >& component_list, const mln_value(A)& null) @@ -91,6 +91,29 @@ return out; } + + template <typename T, typename V> + inline + mln_ch_value(typename T::function, V) + set_value_to_components(const T& tree, + const p_array< mln_psite(T) >& component_list, + const V& value, + const V& null) + { + mln_ch_value(typename T::function, V) out; + initialize(out, tree.f()); + data::fill(out, null); + + mln_piter(p_array< mln_psite(T) >) p(component_list); + for_all(p) + { + out(p) = value; + morpho::tree::propagate_node_to_descendants(p, tree, out); + } + morpho::tree::propagate_representant(tree, out); + return out; + } + } // end of namespace mln::morpho::tree } // end of namespace mln::morpho } // end of namespace mln Index: trunk/milena/sandbox/edwin/tree/sharp.cc =================================================================== --- trunk/milena/sandbox/edwin/tree/sharp.cc (revision 3682) +++ trunk/milena/sandbox/edwin/tree/sharp.cc (revision 3683) @@ -30,10 +30,15 @@ #include <mln/pw/all.hh> /* level */ -#include <mln/level/stretch.hh> +//#include <mln/level/stretch.hh> + +/* label */ +#include <mln/labeling/blobs.hh> +#include <mln/value/label_16.hh> /* trace */ #include <mln/trace/quiet.hh> +#include <mln/util/timer.hh> /* std */ #include <string> @@ -49,12 +54,14 @@ abort(); } -void dsp(const std::string& str) +void dsp(const std::string& str, mln::util::timer& timer) { + std::cout << "in " << timer.read() << std::endl; std::cout << std::endl << "*********************" << std::endl << "** " << str << std::endl << "*********************" << std::endl; + timer.restart(); } namespace mln @@ -170,6 +177,7 @@ unsigned card = 0; unsigned height = 0; double sharpness = 0; + util::timer timer; if (argc < 2) usage(argv); @@ -195,9 +203,8 @@ /********************/ /* Load & Pre-treat */ /********************/ - if (mydebug) - dsp("Load & Pre-treat"); + dsp("Load & Pre-treat", timer); typedef image2d<int_u8> I; I input; @@ -208,7 +215,7 @@ /***************************/ if (mydebug) - dsp("Component tree creation"); + dsp("Component tree creation", timer); typedef p_array< mln_site_(I) > S; typedef morpho::tree::data<I,S> tree_t; @@ -221,7 +228,7 @@ /* Compute Attribute On Image */ /******************************/ if (mydebug) - dsp("Image sharp attribute"); + dsp("Image sharp attribute", timer); // TODO: l'attribut devrait favoriser les composantes plus larges // dans son calcul. Ainsi au lieu de faire un sharpness, on aurait @@ -251,7 +258,7 @@ if (card) { if (mydebug) - dsp("Image card attribute"); + dsp("Image card attribute", timer); a = duplicate((fun::p2v::ternary(card_wrapper(pw::value(a_img)) > pw::cst(card), pw::value(a), @@ -261,7 +268,7 @@ if (height) { if (mydebug) - dsp("Image height attribute"); + dsp("Image height attribute", timer); a = duplicate((fun::p2v::ternary(height_wrapper(pw::value(a_img)) > pw::cst(height), pw::value(a), pw::cst(0.0))) | a.domain()); @@ -271,7 +278,6 @@ /* Retrieve Components (Maximising the criteria) */ /************************************************/ - accumulator::arg_max<A> argmax(a); p_array< mln_psite_(A) > obj_array; // Array of object components. if (mydebug) { @@ -283,7 +289,7 @@ s << "components whose treshold > " << sharpness; else s << "components util leaves are glutted"; - dsp(s.str()); + dsp(s.str(), timer); } if (nb_components) { @@ -297,48 +303,42 @@ /* Print them */ - if (mydebug) { - dsp("Image Filtered Components"); - mln_fwd_piter_(p_array< mln_psite_(I) >) c(obj_array); - for_all(c) - std::cout << c; - } +// if (mydebug) { +// mln_fwd_piter_(p_array< mln_psite_(I) >) c(obj_array); +// for_all(c) +// std::cout << c; +// } /***********************************/ /* Use components in output image */ /***********************************/ if (mydebug) { - dsp("Create mask and propagate"); + dsp("Propagate components and stretch", timer); } // Note: now we must propagate the representant value to the other components sites. - A pre_output = morpho::tree::set_value_to_components(a, tree, obj_array, 0); - I output = level::stretch(int_u8(), pre_output); //adapt to 0-255 - io::pgm::save(output, "components.pgm"); + + //a = morpho::tree::propagate_components(a, tree, obj_array, 0); + //I output = level::stretch(int_u8(), a); //adapt to 0-255 + //io::pgm::save(output, "components.pgm"); /* EXTRA */ -// typedef mln_ch_value_(I, bool) M; -// M mask; -// initialize(mask, a); -// data::fill(mask, false); + // labeling + typedef mln_ch_value_(I, bool) M; + typedef mln_ch_value_(I, value::label<16>) L; + + M mask = morpho::tree::set_value_to_components(tree, obj_array, true, false); + value::label<16> nlabel; + L label = labeling::blobs(mask, c4(), nlabel); + io::pgm::save(label, "label.pgm"); -// mln_fwd_piter_(p_array< mln_psite_(I) >) c(obj_array); -// for_all(c) -// { -// mask(c) = true; -// propagate_node_to_descendants(c, tree, mask); -// } + if (mydebug) { + dsp("Finish", timer); + } - // mask now contains all nodes related to objects - - // /* Labeling */ -// typedef mln_ch_value_(I, value::label<8>) L; -// value::label<8> nlabel; -// L label = labeling::blobs(mask, c4(), nlabel); -// io::ppm::save(debug::colorize(value::rgb8(), label, nlabel), "label.pgm"); // /* Now store output image */ Index: trunk/milena/sandbox/edwin/tree/components.hh =================================================================== --- trunk/milena/sandbox/edwin/tree/components.hh (revision 3682) +++ trunk/milena/sandbox/edwin/tree/components.hh (revision 3683) @@ -26,8 +26,8 @@ // reasons why the executable file might be covered by the GNU General // Public License. -#ifndef COMPONENTS_HH_ -# define COMPONENTS_HH_ +#ifndef MLN_MORPHO_TREE_COMPONENTS_HH_ +# define MLN_MORPHO_TREE_COMPONENTS_HH_ # include <mln/core/concept/image.hh> # include <mln/core/concept/function.hh> @@ -40,19 +40,56 @@ # include <mln/trace/exiting.hh> +/** +** \file mln/morpho/tree/components.hh +** +** Routines that offers different way of retrieving tree components. +** Tree components are nodes maximising the attribute. +*/ + namespace mln { namespace morpho { namespace tree { + /** + ** Retrieve components from the tree until all leaves belong to + ** components. + ** + ** @param tree Component tree. + ** @param attr_image Attribute image. + ** + ** @return Array of components. + */ template <typename T, typename A> p_array< mln_psite(A) > get_components(const T& tree, const Image<A>& attr_image); + /** + ** Retrieve the \p n most important components from the tree. n + ** should be lesser than the maximum number of components. If + ** not, the functions stops when there's no more components. + ** + ** @param tree Component tree. + ** @param attr_image Attribute image. + ** @param n Number of components to get. + ** + ** @return Array of components. + */ template <typename T, typename A> p_array< mln_psite(A) > get_components(const T& tree, const Image<A>& attr_image, unsigned n); + /** + ** Retrieve the most important components that check + ** predicate \p pred. + ** + ** @param tree Component tree. + ** @param attr_image Attribute image. + ** @param pred Predicate that components must check. + ** + ** @return Array of components. + */ template <typename T, typename A, typename P2B> p_array< mln_psite(A) > get_components(const T& tree, const Image<A>& attr_image, const Function_p2b<P2B>& pred); @@ -275,4 +312,4 @@ # endif /* !MLN_INCLUDE_ONLY */ -#endif /* !COMPONENTS_HH_ */ +#endif /* !MLN_MORPHO_TREE_COMPONENTS_HH_ */ Index: trunk/milena/sandbox/edwin/tree/propagate_node.hh =================================================================== --- trunk/milena/sandbox/edwin/tree/propagate_node.hh (revision 3682) +++ trunk/milena/sandbox/edwin/tree/propagate_node.hh (revision 3683) @@ -29,9 +29,9 @@ #ifndef MLN_MORPHO_TREE_PROPAGATE_NODE_HH_ # define MLN_MORPHO_TREE_PROPAGATE_NODE_HH_ +# include <mln/core/concept/image.hh> +# include <mln/core/macros.hh> #include <mln/morpho/tree/data.hh> -#include <mln/core/site_set/p_array.hh> -#include <stack> /// \file mln/morpho/tree/propagate_node.hh ///

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Re: [Olena-patches] 3681: Update tutorial - Write "Getting started with Milena".
by Alexandre Duret-Lutz 17 Apr '09

17 Apr '09

>>> "z" == Guillaume Lazzara <z(a)lrde.epita.fr> writes: [...] z> --- a/milena/doc/examples/Makefile.am z> +++ b/milena/doc/examples/Makefile.am [...] z> +colorize_SOURCES = tuto3/colorize.cc z> +println_SOURCES = tuto3/println.cc z> +trace_SOURCES = tuto3/trace.cc [...] z> --- a/milena/doc/examples/examples.mk z> +++ b/milena/doc/examples/examples.mk [...] z> +examples/tuto3 \ z> +examples/tuto3/fill_non_generic.cc.raw \ z> +examples/tuto3/colorize.cc \ z> +examples/tuto3/println.cc \ z> +examples/tuto3/trace.cc \ z> +examples/tuto3/first_routine.cc \ Il sert à quoi cet horrible fichier examples.mk ? Si c'est ce que je crois (une définition de EXTRA_DIST), c'est monstrueusement evil ! 1) Les *.cc qui sont listés dans _SOURCES sont déjà distribués. 2) Les répertoires qui sont listés dans EXTRA_DIST (e.g. tuto3) sont recursivement distribués. 3) Au total trace.cc/colorize.cc/println.cc sont donc distribués 3 fois. Ça veut dire que make dist va copier les fichier trois fois les écrasant à chaque fois (perte de temps). Et vous aurez peut-être droit certains bugs de distcheck qui peuvent survenir lorsqu'un fichier et distribué à la fois implicitement (parce qu'il fait partie d'un répertoire EXTRA_DISTé) et explicitement. -- Alexandre Duret-Lutz

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r3682: Add normalization, broken
by Fabien Freling 17 Apr '09

17 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-17 Fabien Freling <fabien.freling(a)lrde.epita.fr> Add normalization, broken. * fabien/igr/Makefile: Update with norm target. * fabien/igr/all_labels2gif.sh: Update. * fabien/igr/fun_labels.cc: Update. * fabien/igr/fun_labels.sh: Update. * fabien/igr/norm.cc: Normalize plot. * fabien/igr/time_max.cc: Update. --- Makefile | 3 + all_labels2gif.sh | 10 ++--- fun_labels.cc | 8 ++-- fun_labels.sh | 11 +++-- norm.cc | 102 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ time_max.cc | 4 ++ 6 files changed, 123 insertions(+), 15 deletions(-) Index: trunk/milena/sandbox/fabien/igr/time_max.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/time_max.cc (revision 3681) +++ trunk/milena/sandbox/fabien/igr/time_max.cc (revision 3682) @@ -73,22 +73,26 @@ unsigned dim3 = arr_ima.nelements(); + ///////////// // // // Lissage // // // ///////////// + util::array<image2d<double> > arr_smooth; arr_smooth.append(arr_ima[0] * 1.0); for (unsigned k = 1; k < dim3 - 1; ++k) arr_smooth.append(arr_ima[k] * 0.5 + arr_ima[k - 1] * 0.25 + arr_ima[k + 1] * 0.25); arr_smooth.append(arr_ima[dim3 - 1] * 1.0); + /////////////////////////////////// // // // Calcul image max et temps max // // // /////////////////////////////////// + image2d<float> ima_c; initialize(ima_c, arr_smooth[0]); data::fill(ima_c, 0.0); Index: trunk/milena/sandbox/fabien/igr/fun_labels.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/fun_labels.cc (revision 3681) +++ trunk/milena/sandbox/fabien/igr/fun_labels.cc (revision 3682) @@ -52,7 +52,7 @@ template <typename I, typename L, typename V> inline -void plot_label(I ima, L ima_labels, V lbl) +void plot_label(Image& ima, Image<L>& ima_labels, V lbl) { mln_VAR(vol_label, ima | pw::value(ima_labels) == pw::cst(lbl)); util::array<float> arr; @@ -92,7 +92,7 @@ template <typename I, typename L> inline -void plot_all_labels(I ima, L ima_labels, unsigned nlabels) +void plot_all_labels(Image& ima, Image<L>& ima_labels, unsigned nlabels) { util::array<util::array<float> > arrays(nlabels); accu::mean<int_u12> accu_mean; @@ -145,7 +145,7 @@ template <typename I, typename L> inline -void plot_point(I ima, L ima_labels, point2d point, const char* desc) +void plot_point(Image& ima, Image<L>& ima_labels, point2d point, const char* desc) { util::array<float> arr; label_16 prev_lbl; @@ -213,7 +213,7 @@ point2d p_poumon(122, 115); image3d<L> ima_labels; io::dump::load(ima_labels, argv[1]); - image3d<int_u12> ima; + image3d<float> ima; io::dump::load(ima, argv[2]); mln_VAR(dilate, morpho::elementary::dilation(extend(ima_labels | (pw::value(ima_labels) == 0u), ima_labels), c6())); data::fill((ima_labels | (pw::value(ima_labels) == 0u)).rw(), dilate); Index: trunk/milena/sandbox/fabien/igr/norm.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/norm.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/norm.cc (revision 3682) @@ -0,0 +1,102 @@ +#include <iostream> +#include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> +#include <mln/core/image/slice_image.hh> + +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/alias/window2d.hh> +#include <mln/core/alias/neighb3d.hh> +#include <mln/core/alias/window3d.hh> + +#include <mln/io/dump/all.hh> + +#include <mln/value/int_u12.hh> + +#include <mln/accu/image/all.hh> +#include <mln/accu/mean.hh> +#include <mln/arith/all.hh> +#include <mln/data/paste.hh> + +// DEBUG +/*#include <mln/accu/min.hh> +#include <mln/accu/max.hh> +#include <mln/level/compute.hh>*/ + +using namespace mln; +using value::int_u12; + + + +template <typename I> +inline +image2d<float> mean_slices(Image& ima, int first, int last) +{ + image2d<accu::mean<float> > result; + + initialize(result, slice(ima, first)); + + accu::image::init(result); + for (int i = first; i <= last; ++i) + accu::image::take(result, slice(ima, i)); + + return accu::image::to_result(result); +} + +template <typename I> +inline +image3d<float> normalize(Image& ima, int first, int last) +{ + + int min_sli = geom::bbox(ima).pmin().sli(); + int max_sli = geom::bbox(ima).pmax().sli(); + + mln_precondition(first >= min_sli && first <= max_sli); + mln_precondition(last >= min_sli && last <= max_sli); + + image3d<float> ima_f; + initialize(ima_f, ima); + data::fill(ima_f, ima); + + image2d<float> ima_ini = mean_slices(ima_f, first, last); + + image3d<float> ima_result; + initialize(ima_result, ima_f); + + for (int i = min_sli; i <= max_sli; ++i) + data::paste((slice(ima_f, i) - ima_ini), slice(ima_result, i).rw()); + + // DEBUG + /*accu::min<float> accu_min; + accu::max<float> accu_max; + float min = level::compute(accu_min, ima_ini); + float max = level::compute(accu_max, ima_ini); + std::cout << "min = " << min << std::endl; + std::cout << "max = " << max << std::endl;*/ + + return ima_result; +} + + +/////////////////// +// // +// Main Function // +// // +/////////////////// + + +int main(int argc, char *argv[]) +{ + if (argc != 3) + { + std::cout << "Usage: " << argv[0] << " ima.dump output.dump" + << std::endl; + return 1; + } + + image3d<int_u12> ima; + io::dump::load(ima, argv[1]); + image3d<float> norm = normalize(ima, 1, 8); + io::dump::save(norm, argv[2]); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/Makefile (revision 3681) +++ trunk/milena/sandbox/fabien/igr/Makefile (revision 3682) @@ -54,6 +54,9 @@ label2gif: label2gif.cc ${CXX} -I../../../ ${DICOM} ${CXXFLAGS} $^ -o label2gif +norm: norm.cc + ${CXX} -I../../../ ${CXXFLAGS} $^ -o norm + clean: rm -rf *.dump *.p?m *.plot *.log *.csv *.dSYM rm seg2d seg3d wsd2d wsd3d nbasins_finder grad clo_vol wst graph med thres matlab time_max first_slice_dicom Index: trunk/milena/sandbox/fabien/igr/fun_labels.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/fun_labels.sh (revision 3681) +++ trunk/milena/sandbox/fabien/igr/fun_labels.sh (revision 3682) @@ -51,7 +51,7 @@ ./crop $input 0 50 90 149 230 170 crop.dump ./grad crop.dump $dim - for lambda_closing in 5000; do + for lambda_closing in 10000; do echo " for lambda_closing = ${lambda_closing}"; ./clo_vol grad.dump $dim ${lambda_closing} nbasins=`./wst clo_vol.dump $dim` @@ -61,13 +61,14 @@ #../bin/dumpi12_to_png mean_slices.dump $dim mean_slices_${3}_${lambda_closing}.png #../bin/dumpi12_to_pgm mean_slices.dump $dim mean_slices_${3}_${lambda_closing}.pgm - ./fun_labels wst.dump crop.dump $nbasins + ./norm crop.dump norm.dump + ./fun_labels wst.dump norm.dump $nbasins rename_label_plots ${lambda_closing} - ./all_labels2gif.sh ima.dump labels.dump $nbasins ${lambda_closing} +#./all_labels2gif.sh crop.dump labels.dump $nbasins ${lambda_closing} - mv *.gif results/plots/ - mv *.plot results/plots/ +#mv *.gif results/ +#mv *.plot results/plots/ #reconstruct_plot tumeur ${lambda_closing} #create_anim tumeur ${lambda_closing} Index: trunk/milena/sandbox/fabien/igr/all_labels2gif.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/all_labels2gif.sh (revision 3681) +++ trunk/milena/sandbox/fabien/igr/all_labels2gif.sh (revision 3682) @@ -8,13 +8,12 @@ for i in debug_label_${4}_*.pgm; do j=${i:r}.png convert $i $j -#rm $i + rm $i sips -r 90 $j -o $j > /dev/null 2> /dev/null sips -f horizontal $j -o $j > /dev/null 2> /dev/null done - echo $4 $5 - convert -delay 10 -loop 0 debug_label_${4}_*.png debug_label_${4}_${5}.gif -#rm debug_label_${4}_*.png + convert -delay 10 -loop 0 debug_label_${4}_*.png debug_${5}_label_${4}.gif + rm debug_label_${4}_*.png } create_all_labels () @@ -31,5 +30,4 @@ echo "./all_labels2gif.sh ima ima_labels nlabels closing" } -#create_all_labels $1 $2 $3 $4 -create_label_anim $1 $2 $3 0 $4 +create_all_labels $1 $2 $3 $4

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