February 2009 - Olena-patches

3412: Add new routines to make a 3D image from a list of files.
by Guillaume Lazzara 23 Feb '09

23 Feb '09

* mln/io/pbm/load.hh, * mln/io/pgm/load.hh, * mln/io/ppm/load.hh: load a list of 2D image files and build a 3D image from that. * tests/io/pbm/pbm.cc, * tests/io/pgm/pgm.cc, * tests/io/ppm/ppm.cc: update tests. --- milena/ChangeLog | 13 +++++++ milena/mln/io/pbm/load.hh | 38 ++++++++++++++++++++- milena/mln/io/pgm/load.hh | 67 +++++++++++++++++++++++++++++--------- milena/mln/io/ppm/load.hh | 77 ++++++++++++++++++++++++++++++------------- milena/tests/io/pbm/pbm.cc | 30 +++++++++++++---- milena/tests/io/pgm/pgm.cc | 35 +++++++++++++++++--- milena/tests/io/ppm/ppm.cc | 33 ++++++++++++++++--- 7 files changed, 235 insertions(+), 58 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 4868689..556e3ec 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,18 @@ 2009-02-23 Guillaume Lazzara <z(a)lrde.epita.fr> + Add new routines to make a 3D image from a list of files. + + * mln/io/pbm/load.hh, + * mln/io/pgm/load.hh, + * mln/io/ppm/load.hh: load a list of 2D image files and build a 3D + image from that. + + * tests/io/pbm/pbm.cc, + * tests/io/pgm/pgm.cc, + * tests/io/ppm/ppm.cc: update tests. + +2009-02-23 Guillaume Lazzara <z(a)lrde.epita.fr> + Add more trace::warning in labeling canvas. * mln/canvas/labeling.hh: add new trace::warnings. diff --git a/milena/mln/io/pbm/load.hh b/milena/mln/io/pbm/load.hh index ea9e78c..81ad23d 100644 --- a/milena/mln/io/pbm/load.hh +++ b/milena/mln/io/pbm/load.hh @@ -1,5 +1,5 @@ -// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 EPITA -// Research and Development Laboratory (LRDE) +// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 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 @@ -40,8 +40,11 @@ # include <string> # include <mln/core/image/image2d.hh> +# include <mln/core/image/image3d.hh> # include <mln/io/pnm/load_header.hh> +# include <mln/make/image3d.hh> + namespace mln { @@ -69,6 +72,14 @@ namespace mln /// image2d<bool> load(const std::string& filename); + /// Load ppm images as slices of a 3D Milena image. + /// + /// \param[out] ima A reference to the 3D image which will receive + /// data. + /// \param[in] filenames The list of 2D images to load.. + void load(image3d<bool>& ima, + const util::array<std::string>& filenames); + # ifndef MLN_INCLUDE_ONLY namespace internal @@ -160,6 +171,29 @@ namespace mln ima = load(filename); } + + inline + void load(image3d<bool>& ima, + const util::array<std::string>& filenames) + { + trace::entering("mln::io::pbm::load"); + mln_precondition(!filenames.is_empty()); + + util::array<image2d<bool> > slices; + + for (unsigned i = 0; i < filenames.nelements(); ++i) + { + image2d<bool> tmp; + io::pbm::load(tmp, filenames[i]); + slices.append(tmp); + } + + ima = make::image3d(slices); + + trace::exiting("mln::io::pbm::load"); + } + + # endif // ! MLN_INCLUDE_ONLY } // end of namespace mln::io::pbm diff --git a/milena/mln/io/pgm/load.hh b/milena/mln/io/pgm/load.hh index a82f5b5..c69349c 100644 --- a/milena/mln/io/pgm/load.hh +++ b/milena/mln/io/pgm/load.hh @@ -1,5 +1,5 @@ -// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 EPITA -// Research and Development Laboratory +// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 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 @@ -42,11 +42,13 @@ # include <string> # include <mln/core/image/image2d.hh> +# include <mln/core/image/image3d.hh> # include <mln/value/int_u8.hh> # include <mln/io/pnm/load.hh> +# include <mln/make/image3d.hh> namespace mln { @@ -57,28 +59,38 @@ namespace mln namespace pgm { - /*! Load a pgm image in a Milena image. - * - * \param[out] ima A reference to the image which will receive - * data. - * \param[in] filename The source. - */ + /// Load a pgm image in a Milena image. + /// + /// \param[out] ima A reference to the image which will receive + /// data. + /// \param[in] filename The source. template <typename I> void load(Image& ima, const std::string& filename); - /*! Load a pgm 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. - */ + /// Load a pgm 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 ppm images as slices of a 3D Milena image. + /// + /// \param[out] ima A reference to the 3D image which will receive + /// data. + /// \param[in] filenames The list of 2D images to load.. + /// + template <typename V> + void load(image3d<V>& ima, + const util::array<std::string>& filenames); + + # ifndef MLN_INCLUDE_ONLY template <typename V> @@ -101,6 +113,29 @@ namespace mln trace::exiting("mln::io::pgm::load"); } + + template <typename V> + inline + void load(image3d<V>& ima, + const util::array<std::string>& filenames) + { + trace::entering("mln::io::pgm::load"); + mln_precondition(!filenames.is_empty()); + + util::array<image2d<V> > slices; + + for (unsigned i = 0; i < filenames.nelements(); ++i) + { + image2d<V> tmp; + io::pnm::load<image2d<V> >(PGM, tmp, filenames[i]); + slices.append(tmp); + } + + ima = make::image3d(slices); + + trace::exiting("mln::io::pgm::load"); + } + # endif // ! MLN_INCLUDE_ONLY } // end of namespace mln::io::pgm diff --git a/milena/mln/io/ppm/load.hh b/milena/mln/io/ppm/load.hh index bf9d27b..291eaf8 100644 --- a/milena/mln/io/ppm/load.hh +++ b/milena/mln/io/ppm/load.hh @@ -1,5 +1,5 @@ -// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 EPITA -// Research and Development Laboratory +// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 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 @@ -29,23 +29,23 @@ #ifndef MLN_IO_PPM_LOAD_HH # define MLN_IO_PPM_LOAD_HH -/*! - * \file mln/io/ppm/load.hh - * - * \brief Define a function which loads an image of kind ppm with - * given path. - * - */ +/// \file mln/io/ppm/load.hh +/// +/// Define a function which loads an image of kind ppm with +/// given path. # include <iostream> # include <fstream> # include <string> # include <mln/core/image/image2d.hh> +# include <mln/core/image/image3d.hh> # include <mln/value/rgb8.hh> # include <mln/io/pnm/load.hh> +# include <mln/make/image3d.hh> + namespace mln { @@ -55,27 +55,36 @@ namespace mln namespace ppm { - /*! Load a ppm image in a Milena image. - * - * \param[out] ima A reference to the image which will receive - * data. - * \param[in] filename The source. - */ + /// Load a ppm image in a Milena image. + /// + /// \param[out] ima A reference to the image which will receive + /// data. + /// \param[in] filename The source. template <typename I> void load(Image& ima, const std::string& filename); - /*! Load a ppm 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. - */ + /// Load a ppm 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 ppm images as slices of a 3D Milena image. + /// + /// \param[out] ima A reference to the 3D image which will receive + /// data. + /// \param[in] filenames The list of 2D images to load.. + template <typename V> + void load(image3d<V>& ima, + const util::array<std::string>& filenames); + # ifndef MLN_INCLUDE_ONLY template <typename V> @@ -98,6 +107,28 @@ namespace mln trace::exiting("mln::io::ppm::load"); } + template <typename V> + inline + void load(image3d<V>& ima, + const util::array<std::string>& filenames) + { + trace::entering("mln::io::ppm::load"); + mln_precondition(!filenames.is_empty()); + + util::array<image2d<V> > slices; + + for (unsigned i = 0; i < filenames.nelements(); ++i) + { + image2d<V> tmp; + io::pnm::load<image2d<V> >(PPM, tmp, filenames[i]); + slices.append(tmp); + } + + ima = make::image3d(slices); + + trace::exiting("mln::io::ppm::load"); + } + # endif // ! MLN_INCLUDE_ONLY } // end of namespace mln::io::ppm diff --git a/milena/tests/io/pbm/pbm.cc b/milena/tests/io/pbm/pbm.cc index fc02dda..e54d820 100644 --- a/milena/tests/io/pbm/pbm.cc +++ b/milena/tests/io/pbm/pbm.cc @@ -1,4 +1,5 @@ -// Copyright (C) 2007, 2008 EPITA Research and Development Laboratory (LRDE) +// 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 @@ -25,10 +26,9 @@ // reasons why the executable file might be covered by the GNU General // Public License. -/*! \file tests/io/pbm/pbm.cc - * - * \brief Test on mln::io::pbm::. - */ +/// \file tests/io/pbm/pbm.cc +/// +/// Test on mln::io::pbm::. #include <mln/core/image/image2d.hh> #include <mln/io/pbm/load.hh> @@ -44,10 +44,26 @@ int main() using namespace mln; image2d<bool> pic = io::pbm::load(MLN_IMG_DIR "/picasso.pbm"); - io::pbm::save(pic, "pic.pbm"); - image2d<bool> pic2 = io::pbm::load("pic.pbm"); + io::pbm::save(pic, "out.pbm"); + image2d<bool> pic2 = io::pbm::load("out.pbm"); mln_assertion(pic == pic2); + + + pic2(point2d(0,0)) = true; + io::pbm::save(pic2, "out.pbm"); + + util::array<std::string> files(2); + files[0] = MLN_IMG_DIR "/picasso.pbm"; + files[1] = "out.pbm"; + + image3d<bool> ima3d; + io::pbm::load(ima3d, files); + + mln_assertion(ima3d.nslices() == 2); + mln_assertion(slice(ima3d, 0) == pic); + mln_assertion(slice(ima3d, 1) == pic2); + } diff --git a/milena/tests/io/pgm/pgm.cc b/milena/tests/io/pgm/pgm.cc index 6a6da68..fd22c42 100644 --- a/milena/tests/io/pgm/pgm.cc +++ b/milena/tests/io/pgm/pgm.cc @@ -1,4 +1,5 @@ -// Copyright (C) 2007, 2008 EPITA Research and Development Laboratory (LRDE) +// 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 @@ -25,13 +26,15 @@ // reasons why the executable file might be covered by the GNU General // Public License. -/*! \file tests/io/pgm/pgm.cc - * - * \brief Test on mln::io::pgm::load and mln::io::pgm::save. - */ +/// \file tests/io/pgm/pgm.cc +/// +/// Test on mln::io::pgm::load and mln::io::pgm::save. + #include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> +#include <mln/core/routine/duplicate.hh> #include <mln/value/int_u8.hh> @@ -40,6 +43,8 @@ #include <mln/level/compare.hh> +#include <mln/literal/colors.hh> + #include "tests/data.hh" @@ -65,4 +70,24 @@ int main() io::pgm::load(lena2, "out.pgm"); mln_assertion(lena2 == lena); } + + { + image2d<int_u8> lena = io::pgm::load<int_u8>(MLN_IMG_DIR "/lena.pgm"); + + image2d<int_u8> lena2 = duplicate(lena); + lena2(point2d(0,0)) = 200; + + io::pgm::save(lena2, "out.pgm"); + + util::array<std::string> files(2); + files[0] = MLN_IMG_DIR "/lena.pgm"; + files[1] = "out.pgm"; + + image3d<int_u8> ima3d; + io::pgm::load(ima3d, files); + + mln_assertion(ima3d.nslices() == 2); + mln_assertion(slice(ima3d, 0) == lena); + mln_assertion(slice(ima3d, 1) == lena2); + } } diff --git a/milena/tests/io/ppm/ppm.cc b/milena/tests/io/ppm/ppm.cc index 7dca079..ecc80b4 100644 --- a/milena/tests/io/ppm/ppm.cc +++ b/milena/tests/io/ppm/ppm.cc @@ -1,4 +1,5 @@ -// Copyright (C) 2007, 2008 EPITA Research and Development Laboratory (LRDE) +// 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 @@ -25,12 +26,13 @@ // reasons why the executable file might be covered by the GNU General // Public License. -/*! \file tests/io/ppm/ppm.cc - * - * \brief Test on mln::io::ppm::load and mln::io::ppm::save. - */ +/// \file tests/io/ppm/ppm.cc +/// +/// Test on mln::io::ppm::load and mln::io::ppm::save. + #include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> #include <mln/value/rgb8.hh> #include <mln/io/ppm/load.hh> @@ -38,6 +40,10 @@ #include <mln/level/compare.hh> +#include <mln/util/array.hh> + +#include <mln/literal/colors.hh> + #include "tests/data.hh" @@ -52,4 +58,21 @@ int main() image2d<rgb8> lena2; io::ppm::load(lena2, "out.ppm"); mln_assertion(lena2 == lena); + + + + lena2(point2d(0,0)) = literal::green; + io::ppm::save(lena2, "out.ppm"); + + util::array<std::string> files(2); + files[0] = MLN_IMG_DIR "/lena.ppm"; + files[1] = "out.ppm"; + + image3d<rgb8> ima3d; + io::ppm::load(ima3d, files); + + mln_assertion(ima3d.nslices() == 2); + mln_assertion(slice(ima3d, 0) == lena); + mln_assertion(slice(ima3d, 1) == lena2); } + -- 1.5.6.5

1 0

3410: Update different files.
by Thierry Geraud 23 Feb '09

23 Feb '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Update different files. * theo/exec/superpose.cc: New. * theo/esiee/laurent/presentation/wst2d.cc: Update. * theo/esiee/laurent/presentation/classif.cc: Update. * theo/csi/edwin.cc: Update. csi/edwin.cc | 36 +++++++++++++++++++++++++------ esiee/laurent/presentation/classif.cc | 4 +-- esiee/laurent/presentation/wst2d.cc | 8 ++++++ exec/superpose.cc | 39 ++++++++++++++++++++++++++++++++++ 4 files changed, 78 insertions(+), 9 deletions(-) Index: theo/exec/superpose.cc --- theo/exec/superpose.cc (revision 0) +++ theo/exec/superpose.cc (revision 0) @@ -0,0 +1,39 @@ +#include "filetype.hh" + +#include <mln/core/image/image_if.hh> +#include <mln/data/fill.hh> +#include <mln/pw/all.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input_int_u8.dump input_bool.dump output.dump" << std::endl + << " Superpose." << std::endl; + std::abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc != 4) + usage(argv); + + trace::entering("main"); + + image3d<int_u8> ima; + io::dump::load(ima, argv[1]); + + image3d<bool> msk; + io::dump::load(msk, argv[2]); + + data::fill( (ima | pw::value(msk)).rw(), 255 ); + + io::dump::save(ima, argv[3]); + + trace::exiting("main"); +} Index: theo/esiee/laurent/presentation/wst2d.cc --- theo/esiee/laurent/presentation/wst2d.cc (revision 3409) +++ theo/esiee/laurent/presentation/wst2d.cc (working copy) @@ -5,6 +5,7 @@ # include <mln/io/pgm/load.hh> # include <mln/io/ppm/save.hh> +# include <mln/io/pgm/save.hh> # include <mln/core/var.hh> # include <mln/core/image/image2d.hh> @@ -15,12 +16,15 @@ # include <mln/literal/black.hh> # include <mln/debug/println.hh> +# include <mln/extension/adjust_duplicate.hh> + # include <mln/morpho/closing_area.hh> # include <mln/morpho/gradient.hh> # include <mln/accu/min_max.hh> # include <mln/morpho/meyer_wst.hh> + using namespace mln; using value::int_u8; @@ -32,6 +36,8 @@ const I& input = exact(input_); const N& nbh = exact(nbh_); + extension::adjust_duplicate(input, nbh); + mln_concrete(I) output; initialize(output, input); accu::min_max<mln_value(I)> mm; @@ -92,6 +98,8 @@ { I grad = morpho_gradient(ima, nbh); + io::pgm::save(grad, "temp_grad.pgm"); + I clo; if (lambda > 1) clo = morpho::closing_area(grad, nbh, lambda); Index: theo/esiee/laurent/presentation/classif.cc --- theo/esiee/laurent/presentation/classif.cc (revision 3409) +++ theo/esiee/laurent/presentation/classif.cc (working copy) @@ -358,8 +358,8 @@ `-----------------*/ // Currently, does nothing (lambda = 1). - dist_ima_t closed_dist_ima (dist_ima.domain()); - morpho::closing_height(dist_ima, nbh, atoi(argv[1]), closed_dist_ima); + dist_ima_t closed_dist_ima; // (dist_ima.domain()); + closed_dist_ima = morpho::closing_height(dist_ima, nbh, atoi(argv[1])); /*------. | WST. | Index: theo/csi/edwin.cc --- theo/csi/edwin.cc (revision 3409) +++ theo/csi/edwin.cc (working copy) @@ -28,7 +28,7 @@ void back_propagate(const T& t, A& a) // a value propagates from the representative point to every point - // of the component... + // of the component at the same level (NOT to the branch points!) { mln_fwd_piter(T) p(t.domain()); for_all(p) @@ -41,6 +41,19 @@ template <typename T, typename A> + void + back_propagate_II(const T& t, A& a) + // a value propagates from a representative point to every point + // of the component and the children components (branch). + { + mln_bkd_piter(T) p(t.domain()); + for_all(p) + if (t.is_a_node(p) && a(t.parent(p)) == true) + a(p) = a(t.parent(p)); + } + + + template <typename T, typename A> inline A sample(const T& t, const A& a, bool echo = false) @@ -57,6 +70,7 @@ if (echo) debug::println("aa (before)", aa); + back_propagate_II(t, aa); back_propagate(t, aa); if (echo) debug::println("aa (after)", aa); @@ -71,7 +85,8 @@ void usage(char* argv[]) { - std::cerr << "usage: " << argv[0] << " input.pgm output.pbm" << std::endl; + std::cerr << "usage: " << argv[0] << " input.pgm echo output.pbm" << std::endl; + std::cerr << " echo: 0 (none) or 1 (verbose)" << std::endl; abort(); } @@ -84,11 +99,15 @@ mln_VAR(nbh, c4()); - if (argc != 3) + if (argc != 4) usage(argv); - bool echo = false; - + int echo = std::atoi(argv[2]); + if (echo != 0 && echo != 1) + { + std::cerr << "bad 'echo' value!" << std::endl; + usage(argv); + } typedef image2d<int_u8> I; @@ -96,6 +115,7 @@ io::pgm::load(input, argv[1]); if (echo) debug::println("input", input); +// I f = input; I f = morpho::elementary::gradient(input, nbh); if (echo) debug::println("f", f); @@ -115,8 +135,10 @@ debug::println("a | nodes", a | t.nodes()); } - image2d<bool> b = duplicate((pw::value(a) < pw::cst(10)) | a.domain()); + image2d<bool> b = duplicate((pw::value(a) < pw::cst(21)) | a.domain()); if (echo) debug::println("b", b | t.nodes()); - io::pbm::save(sample(t, b), argv[2]); + io::pbm::save(sample(t, b, + echo), + argv[3]); }

1 0

3409: Add csv2vtk converter.
by Guillaume Lazzara 20 Feb '09

20 Feb '09

* lazzara/csv2vtk/csv2vtk.cc: convert a cloud of points in CSV format to a VTK file. --- milena/sandbox/ChangeLog | 7 +++ milena/sandbox/lazzara/csv2vtk/csv2vtk.cc | 83 +++++++++++++++++++++++++++++ 2 files changed, 90 insertions(+), 0 deletions(-) create mode 100644 milena/sandbox/lazzara/csv2vtk/csv2vtk.cc diff --git a/milena/sandbox/ChangeLog b/milena/sandbox/ChangeLog index 4065f8d..e569149 100644 --- a/milena/sandbox/ChangeLog +++ b/milena/sandbox/ChangeLog @@ -1,5 +1,12 @@ 2009-02-20 Guillaume Lazzara <z(a)lrde.epita.fr> + Add csv2vtk converter. + + * lazzara/csv2vtk/csv2vtk.cc: convert a cloud of points in CSV format + to a VTK file. + +2009-02-20 Guillaume Lazzara <z(a)lrde.epita.fr> + Cleanup sandbox. * lazzara/igr/igr-biggest-comp.cc: new. Variant of igr.cc which diff --git a/milena/sandbox/lazzara/csv2vtk/csv2vtk.cc b/milena/sandbox/lazzara/csv2vtk/csv2vtk.cc new file mode 100644 index 0000000..dc1f686 --- /dev/null +++ b/milena/sandbox/lazzara/csv2vtk/csv2vtk.cc @@ -0,0 +1,83 @@ +// Author: Andrew J. P. Maclean +// Purpose read in a dataset where each line consists of point +// with its position (x,y,z) and (possibly) a scalar. +// Then create and save a vtk polydata array suitable for further rendering. + +#include <iostream> +#include <stdexcept> +#include <string> +#include <fstream> +#include <iomanip> +#include <algorithm> +#include <sstream> +#include <vtkRenderer.h> +#include <vtkRenderWindow.h> +#include <vtkRenderWindowInteractor.h> +#include <vtkPolyDataMapper.h> +#include <vtkActor.h> +#include <vtkXMLPolyDataWriter.h> +#include <vtkXMLPolyDataReader.h> +#include <vtkParticleReader.h> +#include <vtkSmartPointer.h> + + + +int main ( int argc, char* argv[] ) +{ + if ( argc != 3 ) + { + std::cout << "Need input file and output file." << std::endl; + return 1; + } + + std::string ifn = argv[1]; + std::string ofn = argv[2]; + std::cerr << "Input file: " << ifn << std::endl; + std::cerr << "Output file: " << ofn << std::endl; + + if ( ifn == ofn ) + { + std::cerr << "File names cannot be the same." << std::endl; + return 1; + } + + vtkSmartPointer<vtkParticleReader> reader = + vtkSmartPointer<vtkParticleReader>::New(); + + reader->SetFileName(ifn.c_str()); + reader->Update(); + + vtkSmartPointer<vtkXMLPolyDataWriter> writer = + vtkSmartPointer<vtkXMLPolyDataWriter>::New(); + writer->SetInput(reader->GetOutput()); + writer->SetFileName(ofn.c_str()); + writer->Write(); + + // Set up the pipeline. + + vtkSmartPointer<vtkPolyDataMapper> mapper = + vtkSmartPointer<vtkPolyDataMapper>::New(); + + mapper->SetInput(reader->GetOutput()); + + vtkSmartPointer<vtkActor> actor = vtkSmartPointer<vtkActor>::New(); + actor->SetMapper(mapper); + + vtkSmartPointer<vtkRenderer> ren = vtkSmartPointer<vtkRenderer>::New(); + ren->SetBackground(0.2,0.2 ,0.3); + + vtkSmartPointer<vtkRenderWindow> renWin = + vtkSmartPointer<vtkRenderWindow>::New(); + renWin->AddRenderer(ren); + renWin->SetSize(800 ,600); + + vtkSmartPointer<vtkRenderWindowInteractor> iRen = + vtkSmartPointer<vtkRenderWindowInteractor>::New(); + iRen->SetRenderWindow(renWin); + ren->AddViewProp(actor); + ren->Render(); + iRen->Initialize(); + iRen->Start(); +} + + -- 1.5.6.5

1 0

3408: Cleanup sandbox.
by Guillaume Lazzara 20 Feb '09

20 Feb '09

* lazzara/igr/igr-biggest-comp.cc: new. Variant of igr.cc which extract the biggest component before registrating. * lazzara/irm/wst_rag.cc, * lazzara/irm_seg_with_mm_and_rag.mine.cc, * lazzara/igr-cloud.cc, * lazzara/igr.cc, * lazzara/irm/hsl_grad_and_wst.cc, * lazzara/irm/irm_seg_with_mm_and_rag.cc, * lazzara/irm/wst_rag_hsl.cc: Move to... * lazzara/igr/irm/wst_rag.cc, * lazzara/igr/irm_seg_with_mm_and_rag.mine.cc, * lazzara/igr/igr-cloud.cc, * lazzara/igr/igr.cc, * lazzara/igr/irm/hsl_grad_and_wst.cc, * lazzara/igr/irm/irm_seg_with, * lazzara/igr/irm/wst_rag_hsl.cc: ... here. * lazzara/igr/registration_3d.cc: 3D registration. * lazzara/igr/tr_image.cc: quick test on transformed image. --- milena/sandbox/ChangeLog | 27 ++ milena/sandbox/lazzara/igr/igr-biggest-comp.cc | 294 ++++++++++++++++++++ milena/sandbox/lazzara/{ => igr}/igr-cloud.cc | 0 milena/sandbox/lazzara/{ => igr}/igr.cc | 17 +- .../lazzara/{ => igr}/irm/hsl_grad_and_wst.cc | 0 .../{ => igr}/irm/irm_seg_with_mm_and_rag.cc | 0 milena/sandbox/lazzara/{ => igr}/irm/wst_rag.cc | 0 .../sandbox/lazzara/{ => igr}/irm/wst_rag_hsl.cc | 0 .../{ => igr}/irm_seg_with_mm_and_rag.mine.cc | 0 milena/sandbox/lazzara/igr/registration_3d.cc | 48 ++++ milena/sandbox/lazzara/igr/tr_image.cc | 185 ++++++++++++ 11 files changed, 557 insertions(+), 14 deletions(-) create mode 100644 milena/sandbox/lazzara/igr/igr-biggest-comp.cc rename milena/sandbox/lazzara/{ => igr}/igr-cloud.cc (100%) rename milena/sandbox/lazzara/{ => igr}/igr.cc (93%) rename milena/sandbox/lazzara/{ => igr}/irm/hsl_grad_and_wst.cc (100%) rename milena/sandbox/lazzara/{ => igr}/irm/irm_seg_with_mm_and_rag.cc (100%) rename milena/sandbox/lazzara/{ => igr}/irm/wst_rag.cc (100%) rename milena/sandbox/lazzara/{ => igr}/irm/wst_rag_hsl.cc (100%) rename milena/sandbox/lazzara/{ => igr}/irm_seg_with_mm_and_rag.mine.cc (100%) create mode 100644 milena/sandbox/lazzara/igr/registration_3d.cc create mode 100644 milena/sandbox/lazzara/igr/tr_image.cc diff --git a/milena/sandbox/ChangeLog b/milena/sandbox/ChangeLog index e4e1643..4065f8d 100644 --- a/milena/sandbox/ChangeLog +++ b/milena/sandbox/ChangeLog @@ -1,3 +1,30 @@ +2009-02-20 Guillaume Lazzara <z(a)lrde.epita.fr> + + Cleanup sandbox. + + * lazzara/igr/igr-biggest-comp.cc: new. Variant of igr.cc which + extract the biggest component before registrating. + + * lazzara/irm/wst_rag.cc, + * lazzara/irm_seg_with_mm_and_rag.mine.cc, + * lazzara/igr-cloud.cc, + * lazzara/igr.cc, + * lazzara/irm/hsl_grad_and_wst.cc, + * lazzara/irm/irm_seg_with_mm_and_rag.cc, + * lazzara/irm/wst_rag_hsl.cc: Move to... + + * lazzara/igr/irm/wst_rag.cc, + * lazzara/igr/irm_seg_with_mm_and_rag.mine.cc, + * lazzara/igr/igr-cloud.cc, + * lazzara/igr/igr.cc, + * lazzara/igr/irm/hsl_grad_and_wst.cc, + * lazzara/igr/irm/irm_seg_with, + * lazzara/igr/irm/wst_rag_hsl.cc: ... here. + + * lazzara/igr/registration_3d.cc: 3D registration. + + * lazzara/igr/tr_image.cc: quick test on transformed image. + 2009-02-20 Fabien Freling <fabien.freling(a)lrde.epita.fr> Update DICOM support to n dimensions. diff --git a/milena/sandbox/lazzara/igr/igr-biggest-comp.cc b/milena/sandbox/lazzara/igr/igr-biggest-comp.cc new file mode 100644 index 0000000..ecfc7a1 --- /dev/null +++ b/milena/sandbox/lazzara/igr/igr-biggest-comp.cc @@ -0,0 +1,294 @@ +#include <mln/registration/registration.hh> +#include <mln/essential/2d.hh> +#include <mln/core/image/image3d.hh> +#include <mln/binarization/binarization.hh> +#include <mln/labeling/flat_zones.hh> +#include <mln/labeling/background.hh> + +#include <mln/debug/colorize.hh> + + +#include <mln/essential/3d.hh> +#include <mln/core/image/slice_image.hh> +#include <mln/core/image/tr_image.hh> +#include <mln/core/image/interpolated.hh> + +#include <mln/io/cloud/load.hh> +#include <mln/util/timer.hh> +#include <mln/core/concept/function.hh> +#include <mln/trait/ch_value.hh> + +#include <mln/fun/p2b/big_chess.hh> + +#include <mln/fun/x2v/trilinear.hh> + +namespace mln +{ + + struct threshold : mln::Function_p2b<threshold> + { + bool operator()(const mln::value::rgb8& val) const + { + unsigned inty = (val.red() + val.blue() + val.green()); + return inty > 100 && inty < 600; + } + }; + + + namespace registration + { + extern std::string method; + } + + template <typename I> + mln_concrete(I) + fill_holes(const mln::Image& ima) + { + using namespace mln; + + mln_concrete(I) output; + initialize(output, ima); + data::fill(output, true); + + value::label_16 nlabels; + mln_ch_value(I, value::label_16) lbl = labeling::background(ima, c4(), nlabels); + + mln_VAR(lbl_count, labeling::compute(accu::meta::count(), ima, lbl, nlabels)); + + unsigned max_id = 1; + for (unsigned i = 2; i <= nlabels; ++i) + if (lbl_count[max_id] < lbl_count[i]) + max_id = i; + + data::fill((output | pw::value(lbl) == max_id).rw(), false); + + return output; + } + + template <typename I> + mln_concrete(I) + keep_largest_component(const mln::Image& ima) + { + using namespace mln; + + image2d<bool> in_bw_cleaned = fill_holes(ima); + io::pbm::save(in_bw_cleaned, "in_bw_cleaned.pbm"); + + logical::not_inplace(in_bw_cleaned); + image2d<bool> in_bw_cleaned_full = fill_holes(in_bw_cleaned); + io::pbm::save(in_bw_cleaned_full, "in_bw_cleaned_full.pbm"); + + logical::not_inplace(in_bw_cleaned_full); + return in_bw_cleaned_full; + } + + template <typename I> + mln_ch_value(I,bool) + get_main_object_shape(const mln::Image& in) + { + using namespace mln; + + typedef image2d<bool> J; + + value::label_16 nlabels; + mln_ch_value(I, value::label_16) labels = labeling::flat_zones(in, c8(), nlabels); + util::array<unsigned> arr = labeling::compute(accu::meta::count(), + in, labels, nlabels); + + unsigned big_second_count = 0; + unsigned big_second_lbl = 0; + unsigned big_first_count = 0; + unsigned big_first_lbl = 0; + for (unsigned i = 0; i < arr.nelements(); ++i) + { + if (arr[i] > big_second_count) + { + big_second_count = arr[i]; + big_second_lbl = i; + } + if (big_second_count > big_first_count) + { + int swap = big_first_count; + int swap_lbl = big_first_lbl; + big_first_count = big_second_count; + big_first_lbl = big_second_lbl; + big_second_count = swap; + big_second_lbl = swap_lbl; + } + } + + J result; + initialize(result, in); + data::fill(result, false); + data::fill((result | (pw::value(labels) == big_second_lbl)).rw(), true); + + return morpho::elementary::gradient_internal(keep_largest_component(result), c8()); + } + + + namespace debug + { + + template <typename I, typename T> + image3d<value::rgb8> + make_registered_image(Image& P_, Image& X_, const T& transf) + { + I& P = exact(P_); + I& X = exact(X_); + + mln_pset(I) box = geom::bbox(X); + box.enlarge(1, 60); + box.enlarge(2, 60); + + typedef mln_ch_value(I,value::rgb8) result_t; + result_t result(box); + + typedef extension_fun<result_t,pw::cst_<mln_value(result_t)> > result_ext_t; + result_ext_t ext_result(result, pw::cst(value::rgb8(0,0,0))); + + extension_fun<I,pw::cst_<mln_value(I)> > ext_X(X, pw::cst(false)); + data::fill(ext_result, literal::black); + + mln_VAR(ig, (P | pw::value(P) == true)); + mln_piter(ig_t) p(ig.domain()); + for_all(p) + ext_result(transf(p)) = literal::green; + + return ext_result; + } + + template <typename I, typename J> + void + compare_registration(Image& registered_, Image<J>& X_) + { + I& registered = exact(registered_); + J& X = exact(X_); + + typedef mln_ch_value(I,value::rgb8) result_t; + result_t result; + initialize(result, registered); + extension_fun<J,pw::cst_<mln_value(J)> > ext_X(X, pw::cst(false)); + + data::fill(result, literal::black); + data::fill((result | (pw::value(ext_X) == true)).rw(), literal::white); + data::fill((result | (pw::value(registered) != pw::cst(literal::black))).rw(), + literal::cyan); + + io::ppm::save(slice(result,0), "final_registered.ppm"); + } + + + + template <typename I, typename T> + void + compare_registration2(Image& P_, Image& X_, + const T& transf) + { + I& P = exact(P_); + const I& X = exact(X_); + + typedef extension_fun<I,pw::cst_<mln_value(I)> > ext_P_t; + ext_P_t ext_P(P, pw::cst(value::rgb8(literal::black))); + typedef interpolated<ext_P_t, fun::x2v::trilinear> inter_t; + inter_t inter(ext_P); + tr_image<box3d, inter_t, T> trima(X.domain(), inter, transf); + io::ppm::save(slice(trima, 0), "trima.ppm"); + + I tmp = duplicate(X); + fun::p2b::big_chess<box3d> fun(tmp.domain(), 20); + data::paste((trima | fun), tmp); + + io::ppm::save(slice(tmp,0), "registration_filter.ppm"); + } + + } +} + + +int main(int, char* argv[]) +{ + using namespace mln; + using namespace fun::x2x; + using value::rgb8; + using value::int_u8; + using value::label_16; + + //Load image + typedef image2d<rgb8> I; + typedef image2d<bool> J; + typedef image3d<bool> K; + typedef image3d<value::rgb8> L; + +// Load ppm images and apply a threshold. +// I in; +// io::ppm::load(in, argv[1]); +// image2d<bool> in_bw = level::transform(in, threshold()); +// J in_obj = get_main_object_shape(in_bw); +// +// I ref; +// io::ppm::load(ref, argv[2]); +// image2d<bool> ref_bw = level::transform(ref, threshold()); +// J ref_obj = get_main_object_shape(ref_bw); + + + + I in; + io::ppm::load(in, argv[1]); + J in_obj = get_main_object_shape(in); + io::pbm::save(in_obj, "in_obj.pbm"); + + I ref; + io::ppm::load(ref, argv[2]); + J ref_obj = get_main_object_shape(ref); + io::pbm::save(ref_obj, "ref_obj.pbm"); + + I in_orig; + io::ppm::load(in_orig, argv[3]); + + I ref_orig; + io::ppm::load(ref_orig, argv[4]); + + K in_3d = make::image3d(in_obj); + K ref_3d = make::image3d(ref_obj); + std::cout << " igr.cc - in_3d.nsites = " << in_3d.nsites() << std::endl; + std::cout << " igr.cc - ref_3d.nsites = " << ref_3d.nsites() << std::endl; + + typedef p_array<point3d> p_arr_t; + p_arr_t in_3d_ = convert::to<p_arr_t>(in_3d); + p_arr_t ref_3d_ = convert::to<p_arr_t>(ref_3d); + + + /// Add objects shapes in original images. + L in_wborders = make::image3d(in_orig); + data::fill((in_wborders | in_3d_).rw(), literal::green); + io::ppm::save(slice(in_wborders,0), "in_with_borders.ppm"); + + L ref_wborders = make::image3d(ref_orig); + data::fill((ref_wborders | ref_3d_).rw(), literal::green); + io::ppm::save(slice(ref_wborders,0), "ref_with_borders.ppm"); + + // Starting registration. + util::timer t; + t.start(); + typedef rotation<3u,float> rot_t; + typedef translation<3u,float> trans_t; + box3d bbox = geom::bbox(in_3d); + bbox.enlarge(0, in_3d.nslices() / 2); + bbox.enlarge(1, in_3d.nrows() / 2); + bbox.enlarge(2, in_3d.ncols() / 2); + + composed<trans_t,rot_t> qk = registration::registration3(bbox, in_3d_, ref_3d_); + std::cout << "igr.cc - Registration - " << t << "s" << std::endl; + + std::cout << qk.first().mat() << std::endl << std::endl;; + std::cout << qk.first().inv().mat() << std::endl << std::endl;; + std::cout << qk.second().mat() << std::endl; + std::cout << qk.second().inv().mat() << std::endl; + + std::cout << "* Build result image" << std::endl; + image3d<value::rgb8> registered = debug::make_registered_image(in_3d, ref_3d, qk); + debug::compare_registration(registered, ref_3d); + + debug::compare_registration2(in_wborders, ref_wborders, qk); + +} diff --git a/milena/sandbox/lazzara/igr-cloud.cc b/milena/sandbox/lazzara/igr/igr-cloud.cc similarity index 100% rename from milena/sandbox/lazzara/igr-cloud.cc rename to milena/sandbox/lazzara/igr/igr-cloud.cc diff --git a/milena/sandbox/lazzara/igr.cc b/milena/sandbox/lazzara/igr/igr.cc similarity index 93% rename from milena/sandbox/lazzara/igr.cc rename to milena/sandbox/lazzara/igr/igr.cc index 0df1d92..98e1ce4 100644 --- a/milena/sandbox/lazzara/igr.cc +++ b/milena/sandbox/lazzara/igr/igr.cc @@ -202,22 +202,11 @@ namespace mln typedef extension_fun<I,pw::cst_<mln_value(I)> > ext_P_t; ext_P_t ext_P(P, pw::cst(value::rgb8(literal::black))); - tr_image<box3d, ext_P_t, T> trima(P.domain(), ext_P, transf); + typedef interpolated<ext_P_t, fun::x2v::bilinear> inter_t; + inter_t inter(ext_P); + tr_image<box3d, inter_t, T> trima(X.domain(), inter, transf); io::ppm::save(slice(trima, 0), "trima.ppm"); - I reg(X.domain()); - data::fill(reg, literal::black); - mln_piter(I) p(P.domain()); - for_all(p) - if (reg.domain().has(transf(p.to_vec()))) - reg(transf(p.to_vec())) = P(p); - io::ppm::save(slice(reg,0), "registered-2.ppm"); - - I tmp2 = duplicate(X); - fun::p2b::big_chess<box3d> fun2(tmp2.domain(), 20); - data::paste((reg | fun2), tmp2); - io::ppm::save(slice(tmp2,0), "registration_filter-a.ppm"); - I tmp = duplicate(X); fun::p2b::big_chess<box3d> fun(tmp.domain(), 20); data::paste((trima | fun), tmp); diff --git a/milena/sandbox/lazzara/irm/hsl_grad_and_wst.cc b/milena/sandbox/lazzara/igr/irm/hsl_grad_and_wst.cc similarity index 100% rename from milena/sandbox/lazzara/irm/hsl_grad_and_wst.cc rename to milena/sandbox/lazzara/igr/irm/hsl_grad_and_wst.cc diff --git a/milena/sandbox/lazzara/irm/irm_seg_with_mm_and_rag.cc b/milena/sandbox/lazzara/igr/irm/irm_seg_with_mm_and_rag.cc similarity index 100% rename from milena/sandbox/lazzara/irm/irm_seg_with_mm_and_rag.cc rename to milena/sandbox/lazzara/igr/irm/irm_seg_with_mm_and_rag.cc diff --git a/milena/sandbox/lazzara/irm/wst_rag.cc b/milena/sandbox/lazzara/igr/irm/wst_rag.cc similarity index 100% rename from milena/sandbox/lazzara/irm/wst_rag.cc rename to milena/sandbox/lazzara/igr/irm/wst_rag.cc diff --git a/milena/sandbox/lazzara/irm/wst_rag_hsl.cc b/milena/sandbox/lazzara/igr/irm/wst_rag_hsl.cc similarity index 100% rename from milena/sandbox/lazzara/irm/wst_rag_hsl.cc rename to milena/sandbox/lazzara/igr/irm/wst_rag_hsl.cc diff --git a/milena/sandbox/lazzara/irm_seg_with_mm_and_rag.mine.cc b/milena/sandbox/lazzara/igr/irm_seg_with_mm_and_rag.mine.cc similarity index 100% rename from milena/sandbox/lazzara/irm_seg_with_mm_and_rag.mine.cc rename to milena/sandbox/lazzara/igr/irm_seg_with_mm_and_rag.mine.cc diff --git a/milena/sandbox/lazzara/igr/registration_3d.cc b/milena/sandbox/lazzara/igr/registration_3d.cc new file mode 100644 index 0000000..f049d88 --- /dev/null +++ b/milena/sandbox/lazzara/igr/registration_3d.cc @@ -0,0 +1,48 @@ +#include <mln/essential/2d.hh> +#include <mln/essential/3d.hh> +#include <mln/registration/registration.hh> +#include <mln/io/cloud/all.hh> +#include <mln/debug/slices_2d.hh> + +int main(int, char *argv[]) +{ + using namespace mln; + + typedef p_array<point3d> arr_t; + + arr_t in; + io::cloud::load(in, argv[1]); + + arr_t ref; + io::cloud::load(ref, argv[2]); + + // Starting registration. + util::timer t; + t.start(); + + typedef fun::x2x::rotation<3u,float> rot_t; + typedef fun::x2x::translation<3u,float> trans_t; + fun::x2x::composed<trans_t,rot_t> qk = registration::registration3(in, ref); + + std::cout << "igr.cc - Registration - " << t << "s" << std::endl; + + box3d bbox = geom::bbox(ref); + bbox.enlarge(1, 50); + bbox.enlarge(2, 50); + image3d<value::rgb8> ima_in(bbox); + data::fill(ima_in, literal::black); + data::fill((ima_in | in).rw(), literal::green); + + mln_VAR(ext_ima, extended_with(ima_in, pw::cst(value::rgb8(literal::black)))); + mln_VAR(trima, transposed_image(bbox, ext_ima, qk)); + + image3d<value::rgb8> ima_ref(geom::bbox(ref)); + mln_VAR(ext_ima_ref, extended_with(ima_ref, pw::cst(value::rgb8(literal::black)))); + data::fill(ext_ima_ref, literal::black); + data::fill((ext_ima_ref | ref).rw(), literal::white); + data::fill((ext_ima_ref | pw::value(trima) == pw::cst(literal::green)).rw(), literal::green); + +// io::cloud::save(res, "registered.txt"); + + io::ppm::save(debug::slices_2d(ima_ref, 5, 3, literal::black), "registration_3d.ppm"); +} diff --git a/milena/sandbox/lazzara/igr/tr_image.cc b/milena/sandbox/lazzara/igr/tr_image.cc new file mode 100644 index 0000000..d1a8056 --- /dev/null +++ b/milena/sandbox/lazzara/igr/tr_image.cc @@ -0,0 +1,185 @@ +#include <mln/essential/2d.hh> +#include <mln/essential/3d.hh> +#include <mln/fun/x2x/composed.hh> +#include <mln/fun/x2x/rotation.hh> +#include <mln/fun/x2x/translation.hh> +#include <mln/core/image/interpolated.hh> +#include <mln/fun/x2v/trilinear.hh> +#include <mln/fun/x2v/bilinear.hh> +#include <mln/core/image/tr_image.hh> + +#include <mln/io/cloud/save.hh> +#include <mln/debug/slices_2d.hh> + +int main(int, char *argv[]) +{ + using namespace mln; + using namespace fun::x2x; + using value::rgb8; + using value::int_u8; + using value::label_16; + + //Load image + typedef image2d<bool> J; + typedef image3d<rgb8> K; + typedef image2d<rgb8> I; + + I P; + io::ppm::load(P, argv[1]); + K P_3d = make::image3d(P); + + + { + typedef rotation<3u,float> rot_t; + rot_t rot(1.57f, make::vec(0,0, 1)); + typedef translation<3u,float> trans_t; + trans_t trans(make::vec(150, 50, 0)); + typedef composed<trans_t, rot_t> transf_t; + transf_t qk(trans, rot); + +// std::cout << rot.mat() << std::endl; +// + point3d p10_3d(0,1,0); + std::cout << "point " << p10_3d << " == vec " << p10_3d.to_vec() << std::endl; +// point3d p11_3d(0,1,1); +// algebra::vec<4u,float> p10 = make::vec(0,1,0,1); +// algebra::vec<4u,float> p11 = make::vec(0.f,1.f,1.f,1.f); +// algebra::vec<4u,float> p01 = make::vec(0.f,0.f,1.f,1.f); +// algebra::vec<4u,float> p_01 = make::vec(0,0,-1,1); +// +// std::cout << "qk(p10_3d.to_vec) = " << qk(p10_3d.to_vec()) << std::endl; +// std::cout << "rot(p10) = " << (rot.mat() * p10) << std::endl; +// std::cout << "rot(p10) + trans = " << (qk.mat() * p10) << std::endl << std::endl << std::endl; +// +// +// std::cout << "rot.inv()(p10) = " << (rot.inv().mat() * p10) << std::endl; +// std::cout << "rot.inv()(p_01) = " << (rot.inv().mat() * p_01) << std::endl; +// std::cout << "rot.inv()(p01) = " << (rot.inv().mat() * p01) << std::endl; +// std::cout << "qk.inv()(p11_3d) = " << qk.inv()(p11_3d.to_vec()) << std::endl; +// std::cout << "qk.inv().mat() * p11 = " << (qk.inv().mat() * p11) << std::endl; +// std::cout << "rot(p).inv() (p11 + trans.inv) = " << rot.inv().mat() * (trans.inv().mat() * p11) << std::endl; +// std::cout << "trans.inv()(p01) = " << trans.inv().mat() * p01 << std::endl; +// +// std::cout << std::endl << "trans.mat" << std::endl; +// std::cout << trans.mat() << std::endl; +// std::cout << "trans.mat.inv" << std::endl; +// std::cout << trans.inv().mat() << std::endl; +// +// +// std::cout << std::endl << "rot.mat" << std::endl; +// std::cout << rot.mat() << std::endl; +// std::cout << "rot.mat.inv" << std::endl; +// std::cout << rot.inv().mat() << std::endl; +// +// std::cout << "qk.mat" << std::endl; +// std::cout << qk.mat() << std::endl; +// std::cout << "qk.inv().mat()" << std::endl; +// std::cout << qk.inv().mat() << std::endl; + + typedef extension_fun<K,pw::cst_<mln_value_(I)> > ext_P_t; + ext_P_t ext_P(P_3d, pw::cst(value::rgb8(literal::black))); + + typedef interpolated<ext_P_t, fun::x2v::trilinear> inter_t; + inter_t inter(ext_P); + + std::cout << std::endl << "DEBUG TR_IMAGE" << std::endl; + tr_image<box3d, inter_t, transf_t> trima(P_3d.domain(), inter, qk); + + io::ppm::save(slice(trima, 0), "trima_3d2.ppm"); + + } + +// { +// typedef rotation<3u,float> rot_t; +// +// algebra::quat q; +// q[0] = 0 +// q[3] = cos(1.57f / 2); +// rot_t rot(1.57f, make::vec(0, 0, 1)); +// typedef translation<3u,float> trans_t; +// trans_t trans(make::vec(150, 50, 0)); +// typedef composed<trans_t, rot_t> transf_t; +// transf_t qk(trans, rot); +// +// typedef extension_fun<K,pw::cst_<mln_value_(I)> > ext_P_t; +// ext_P_t ext_P(P_3d, pw::cst(value::rgb8(literal::black))); +// +// typedef interpolated<ext_P_t, fun::x2v::trilinear> inter_t; +// inter_t inter(ext_P); +// +// std::cout << std::endl << "DEBUG TR_IMAGE" << std::endl; +// tr_image<box3d, inter_t, transf_t> trima(P_3d.domain(), inter, qk); +// +// io::ppm::save(slice(trima, 0), "trima_3d3.ppm"); +// +// } + + + { + + typedef rotation<2u,float> rot_t; + rot_t rot(1.57f, make::vec(1, 0)); + + typedef translation<2u,float> trans_t; + trans_t trans(make::vec(150, 50)); + typedef composed<trans_t, rot_t> transf_t; + transf_t qk(trans, rot); + + std::cout << rot.mat() << std::endl; + + typedef extension_fun<I,pw::cst_<mln_value_(I)> > ext_P_t; + ext_P_t ext_P(P, pw::cst(value::rgb8(literal::black))); + typedef interpolated<ext_P_t, fun::x2v::bilinear> inter_t; + inter_t inter(ext_P); + tr_image<box2d, inter_t, transf_t> trima(P.domain(), inter, qk); + io::ppm::save(trima, "trima_2d.ppm"); + + } +/* + { + typedef rotation<3u,float> rot_t; + rot_t rot(1.57f, make::vec(0, 0, 1)); + typedef translation<3u,float> trans_t; + trans_t trans(make::vec(160, 60, 0)); + typedef composed<trans_t, rot_t> transf_t; + transf_t qk(trans, rot); + + std::cout << rot.mat() << std::endl; + + typedef extension_fun<K,pw::cst_<mln_value_(I)> > ext_P_t; + ext_P_t ext_P(P_3d, pw::cst(value::rgb8(literal::black))); + typedef interpolated<ext_P_t, fun::x2v::bilinear> inter_t; + inter_t inter(ext_P); + tr_image<box3d, inter_t, transf_t> trima(P_3d.domain(), inter, qk); + io::ppm::save(slice(trima, 0), "trima_3d.ppm"); + + std::cout << std::endl << " points: " << std::endl; + unsigned i = 0; + mln_piter_(box3d) p (P_3d.domain()); + for_all(p) + { + algebra::vec<4,float> tmp; + for (unsigned j = 0; j < 3; ++j) + tmp[j] = p.to_vec()[j]; + tmp[3] = 1; + tmp = (qk.mat() * tmp); + algebra::vec<3,float> res; + for (unsigned j = 0; j < 3; ++j) + res[j] = tmp[j]; + point3d ptmp = res; + std::cout <10) + break; + ++i; + } + } +*/ +// K reg(b); +// data::fill(reg, literal::black); +// mln_piter_(K) p(P_3d.domain()); +// for_all(p) +// if (reg.domain().has(qk(p.to_site().to_vec()))) +// reg(qk(p.to_site().to_vec())) = P_3d(p); +// io::ppm::save(slice(reg,0), "trima_mine.ppm"); + +} -- 1.5.6.5

1 0

3407: Add extended_with routine.
by Guillaume Lazzara 20 Feb '09

20 Feb '09

* mln/core/image/extension_fun.hh, * mln/core/image/extension_ima.hh, * mln/core/image/extension_val.hh: add extended_with routine. --- milena/ChangeLog | 8 ++++++++ milena/mln/core/image/extension_fun.hh | 14 +++++++++++++- milena/mln/core/image/extension_ima.hh | 13 +++++++++++++ milena/mln/core/image/extension_val.hh | 12 ++++++++++++ 4 files changed, 46 insertions(+), 1 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 5c7fdf4..999d18b 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,13 @@ 2009-02-20 Guillaume Lazzara <z(a)lrde.epita.fr> + Add extended_with routine. + + * mln/core/image/extension_fun.hh, + * mln/core/image/extension_ima.hh, + * mln/core/image/extension_val.hh: add extended_with routine. + +2009-02-20 Guillaume Lazzara <z(a)lrde.epita.fr> + Add implicit conversion from algebra::quat to algebra::vec. * mln/algebra/quat.hh: add implicit conversion operator to diff --git a/milena/mln/core/image/extension_fun.hh b/milena/mln/core/image/extension_fun.hh index c140283..0cd09b6 100644 --- a/milena/mln/core/image/extension_fun.hh +++ b/milena/mln/core/image/extension_fun.hh @@ -1,4 +1,5 @@ -// Copyright (C) 2008 EPITA Research and Development Laboratory +// Copyright (C) 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 @@ -266,6 +267,17 @@ namespace mln target = model.extension(); } + template <typename I, typename F> + extension_fun<I,F> + extended_with(Image& ima, const Function_v2v<F>& f) + { + mlc_not_equal(mln_trait_image_ext_domain(I), + trait::image::ext_domain::none)::check(); + mln_precondition(exact(ima).is_valid()); + extension_fun<I,F> tmp(exact(ima), exact(f)); + return tmp; + } + # endif // ! MLN_INCLUDE_ONLY } // end of namespace mln diff --git a/milena/mln/core/image/extension_ima.hh b/milena/mln/core/image/extension_ima.hh index 91055dd..98360b4 100644 --- a/milena/mln/core/image/extension_ima.hh +++ b/milena/mln/core/image/extension_ima.hh @@ -268,6 +268,19 @@ namespace mln target_ = ext_; } + + template <typename I, typename J> + extension_ima<I,J> + extended_with(Image& ima, const Image<J> ext) + { + mlc_not_equal(mln_trait_image_ext_domain(I), + trait::image::ext_domain::none)::check(); + mln_precondition(exact(ima).is_valid()); + mln_precondition(exact(ext).is_valid()); + extension_ima<I,J> tmp(exact(ima), exact(ext)); + return tmp; + } + # endif // ! MLN_INCLUDE_ONLY } // end of namespace mln diff --git a/milena/mln/core/image/extension_val.hh b/milena/mln/core/image/extension_val.hh index 63dbeb7..45f1926 100644 --- a/milena/mln/core/image/extension_val.hh +++ b/milena/mln/core/image/extension_val.hh @@ -268,6 +268,18 @@ namespace mln target = static_cast<V>(model.extension()); } + template <typename I, typename J> + extension_ima<I,J> + extended_with(Image& ima, const Image<J> ext) + { + mlc_not_equal(mln_trait_image_ext_domain(I), + trait::image::ext_domain::none)::check(); + mln_precondition(exact(ima).is_valid()); + mln_precondition(exact(ext).is_valid()); + extension_ima<I,J> tmp(exact(ima), exact(ext)); + return tmp; + } + # endif // ! MLN_INCLUDE_ONLY } // end of namespace mln -- 1.5.6.5

1 0

3406: Add implicit conversion from algebra::quat to algebra::vec.
by Guillaume Lazzara 20 Feb '09

20 Feb '09

* mln/algebra/quat.hh: add implicit conversion operator to algebra::vec. --- milena/ChangeLog | 7 +++++++ milena/mln/algebra/quat.hh | 8 ++++++++ 2 files changed, 15 insertions(+), 0 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 4efb183..5c7fdf4 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,12 @@ 2009-02-20 Guillaume Lazzara <z(a)lrde.epita.fr> + Add implicit conversion from algebra::quat to algebra::vec. + + * mln/algebra/quat.hh: add implicit conversion operator to + algebra::vec. + +2009-02-20 Guillaume Lazzara <z(a)lrde.epita.fr> + Update ICP. * mln/registration/icp.hh: store point indexes instead of points in diff --git a/milena/mln/algebra/quat.hh b/milena/mln/algebra/quat.hh index 33e7d07..85ebcbd 100644 --- a/milena/mln/algebra/quat.hh +++ b/milena/mln/algebra/quat.hh @@ -162,6 +162,8 @@ namespace mln /// Explicit conversion to a 4D algebra::vec. const algebra::vec<4,float>& to_vec() const; + /// Implicit conversion to a 4D algebra::vec. + operator const algebra::vec<4,float>&() const; /// Give the scalar part. float s() const; @@ -340,6 +342,12 @@ namespace mln } inline + quat::operator const algebra::vec<4,float>&() const + { + return this->v_; + } + + inline float quat::s() const { -- 1.5.6.5

1 0

3405: Update ICP.
by Guillaume Lazzara 20 Feb '09

20 Feb '09

* mln/registration/icp.hh: store point indexes instead of points in closest point image. Remove useless to_vec(). * mln/registration/registration.hh: remove useless to_vec(). Pass a domain to the function to be used to compute the closest point image. * mln/transform/internal/closest_point_functor.hh: Store point indexes instead of points. --- milena/ChangeLog | 13 +++ milena/mln/registration/icp.hh | 81 +++++++++++--------- milena/mln/registration/registration.hh | 63 ++++++++-------- .../transform/internal/closest_point_functor.hh | 29 ++++++- 4 files changed, 114 insertions(+), 72 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index ce02eb9..4efb183 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,18 @@ 2009-02-20 Guillaume Lazzara <z(a)lrde.epita.fr> + Update ICP. + + * mln/registration/icp.hh: store point indexes instead of points in + closest point image. Remove useless to_vec(). + + * mln/registration/registration.hh: remove useless to_vec(). Pass a + domain to the function to be used to compute the closest point image. + + * mln/transform/internal/closest_point_functor.hh: Store point indexes + instead of points. + +2009-02-20 Guillaume Lazzara <z(a)lrde.epita.fr> + Reorder data in the vector returned by to_vec(). * mln/core/concept/gdpoint.hh, diff --git a/milena/mln/registration/icp.hh b/milena/mln/registration/icp.hh index de763ea..d484f5c 100644 --- a/milena/mln/registration/icp.hh +++ b/milena/mln/registration/icp.hh @@ -49,28 +49,31 @@ # include <mln/set/compute.hh> //Should be removed when closest_point functors are moved. +# include <mln/core/image/slice_image.hh> +# include <mln/core/image/tr_image.hh> +# include <mln/core/image/extension_fun.hh> + # include <mln/core/alias/neighb3d.hh> + # include <mln/transform/internal/closest_point_functor.hh> # include <mln/canvas/distance_geodesic.hh> # include <mln/pw/all.hh> # include <mln/io/ppm/save.hh> # include <mln/io/pbm/save.hh> + # include <mln/debug/colorize.hh> +# include <mln/debug/histo.hh> + +# include <mln/accu/histo.hh> +# include <mln/accu/sum.hh> + +# include <mln/value/int_u16.hh> # include <mln/literal/black.hh> # include <mln/literal/white.hh> # include <mln/literal/colors.hh> -# include <mln/core/image/slice_image.hh> - -#include <mln/core/image/tr_image.hh> -#include <mln/core/image/extension_fun.hh> - -#include <mln/accu/histo.hh> -#include <mln/accu/sum.hh> -#include <mln/debug/histo.hh> - # include <mln/util/timer.hh> namespace mln @@ -129,7 +132,7 @@ namespace mln class closest_point_with_map { typedef mln_image_from_grid(mln_grid(P), P) I; - typedef mln_ch_value(I, P) cp_ima_t; + typedef mln_ch_value(I, unsigned) cp_ima_t; typedef mln_ch_value(I,value::int_u16) dmap_t; public: @@ -137,6 +140,7 @@ namespace mln closest_point_with_map(const p_array& X) { box3d box = geom::bbox(X); + box.enlarge(0, box.nslis()); box.enlarge(1, box.nrows()); box.enlarge(2, box.ncols()); @@ -144,11 +148,13 @@ namespace mln std::cout << "Map image defined on " << box << std::endl; + X_ = X; init(X, box); } closest_point_with_map(const p_array& X, const box& box) { + X_ = X; init(X, box); } @@ -159,13 +165,14 @@ namespace mln data::fill(model, false); data::fill((model | X).rw(), true); - transform::internal::closest_point_functor<model_t> f; + transform::internal::closest_point_functor<model_t> f(X); + util::timer t; t.start(); dmap_X_ = canvas::distance_geodesic(model, c6(), mln_max(value::int_u16), f); - std::cout << "canvas::distance_geodesic - " << t << "s" << std::endl; + std::cout << "distance_geodesic = " << t << "s" << std::endl; initialize(this->cp_ima_, f.cp_ima); this->cp_ima_ = f.cp_ima; @@ -202,14 +209,18 @@ namespace mln mln_site(I) operator()(const mln_site(I)& p) const { - return cp_ima_(p); + return X_[cp_ima_(p)]; } + // Distance map dmap_t dmap_X_; + + private: + p_array X_; // Closest point image. cp_ima_t cp_ima_; - private: + }; @@ -229,17 +240,18 @@ namespace mln mln_site(I) operator()(const vec3d_f& v) const { - vec3d_f best_x = convert::to<vec3d_f>(X_[0].to_vec()); + vec3d_f best_x = X_[0]; float best_d = norm::l2_distance(v, best_x); mln_piter(X_t) X_i(X_); for_all(X_i) { - float d = norm::l2_distance(v, convert::to<vec3d_f>(X_i)); + vec3d_f X_i_vec = X_i; + float d = norm::l2_distance(v, X_i_vec); if (d < best_d) { best_d = d; - best_x = X_i.to_vec(); + best_x = X_i_vec; } } return best_x; @@ -266,11 +278,11 @@ namespace mln mln_piter(p_array) p(kept); for_all(p) - ext_result(qR.rotate(p.to_vec()) + qT) = literal::green; + ext_result(qR.rotate(p) + qT) = literal::green; mln_piter(p_array) p2(removed); for_all(p2) - ext_result(qR.rotate(p2.to_vec()) + qT) = literal::red; + ext_result(qR.rotate(p2) + qT) = literal::red; io::ppm::save(slice(ext_result,0), "registered-2.ppm"); } @@ -289,7 +301,7 @@ namespace mln mln_piter(p_array) p(P_); for_all(p) { - vec3d_f Pk_i = pair.first.rotate(p.to_vec()) + pair.second; + vec3d_f Pk_i = pair.first.rotate(p) + pair.second; vec3d_f Yk_i = closest_point(Pk_i).to_vec(); // yk_i - pk_i e_k_accu.take(Yk_i - Pk_i); @@ -317,8 +329,8 @@ namespace mln for_all(p) { - vec3d_f Pk_i = pair.first.rotate(p.to_vec()) + pair.second; - vec3d_f Yk_i = closest_point(Pk_i).to_vec(); + vec3d_f Pk_i = pair.first.rotate(p) + pair.second; + vec3d_f Yk_i = closest_point(Pk_i); int d_i = closest_point.dmap_X_(Pk_i); if (d_i >= d_min && d_i <= d_max) @@ -399,7 +411,7 @@ namespace mln for_all(p) { vec3d_f Pk_i = pair.first.rotate(p.to_vec()) + pair.second; - vec3d_f Yk_i = closest_point(Pk_i).to_vec(); + vec3d_f Yk_i = closest_point(Pk_i); int d_i = closest_point.dmap_X_(Pk_i); if (d_i >= d_min && d_i <= d_max) @@ -440,31 +452,27 @@ namespace mln const std::pair<algebra::quat,mln_vec(P)>& pair, const std::string& period, const value::rgb8& c) { -# ifndef NDEBUG data::fill(out, literal::black); data::fill((out | X).rw(), literal::white); -# endif // !NDEBUG mln_piter(p_array) p1(P_); for_all(p1) { - vec3d_f Pk_i = pair.first.rotate(p1.to_vec()) + pair.second; + vec3d_f Pk_i = pair.first.rotate(p1) + pair.second; out(Pk_i) = literal::red; } mln_piter(p_array) p2(P_sub); for_all(p2) { - vec3d_f Pk_i = pair.first.rotate(p2.to_vec()) + pair.second; + vec3d_f Pk_i = pair.first.rotate(p2) + pair.second; out(Pk_i) = c; } -# ifndef NDEBUG std::ostringstream ss; ss << prefix << "_" << r << "_" << period << ".ppm"; io::ppm::save(slice(out,0), ss.str()); -# endif // ! NDEBUG } @@ -483,8 +491,9 @@ namespace mln for_all(p) { // yk_i - pk+1_i - vec3d_f Pk_i = qR_old.rotate(p.to_vec()) + qT_old; - vec3d_f Pk_1_i = qR.rotate(p.to_vec()) + qT; + vec3d_f P_i = p; + vec3d_f Pk_i = qR_old.rotate(P_i) + qT_old; + vec3d_f Pk_1_i = qR.rotate(P_i) + qT; accu.take(closest_point(Pk_i).to_vec() - Pk_1_i); } return accu.to_result(); @@ -508,9 +517,9 @@ namespace mln // FIXME: could we use an accu? for_all(p) { - vec3d_f P_i = p.to_vec(); - vec3d_f Pk_i = qR.rotate(p.to_vec()) + qT; - vec3d_f Yk_i = closest_point(Pk_i).to_vec(); + vec3d_f P_i = p; + vec3d_f Pk_i = qR.rotate(P_i) + qT; + vec3d_f Yk_i = closest_point(Pk_i); Spx += make::mat(P_i - mu_P) * trans(make::mat(Yk_i - mu_Yk)); } Spx /= P_.nsites(); @@ -564,7 +573,7 @@ namespace mln { // yk_i - pk_i vec3d_f Pk_i = qR.rotate(p.to_vec()) + qT; - vec3d_f Yk_i = closest_point(Pk_i).to_vec(); + vec3d_f Yk_i = closest_point(Pk_i); mu_yk.take(Yk_i); e_k_accu.take(Yk_i - Pk_i); } @@ -641,7 +650,7 @@ namespace mln image3d<value::rgb8> tmp_ = duplicate(debug); mln_piter(p_array) p_dbg(P_); for_all(p_dbg) - tmp_(qR_old.rotate(p_dbg.to_vec()) + qT_old) = literal::green; + tmp_(qR_old.rotate(p_dbg) + qT_old) = literal::green; std::ostringstream ss; ss << "tmp_0"; if (k < 10) diff --git a/milena/mln/registration/registration.hh b/milena/mln/registration/registration.hh index 21d6ea5..98c5ae9 100644 --- a/milena/mln/registration/registration.hh +++ b/milena/mln/registration/registration.hh @@ -34,6 +34,7 @@ /// \sa registration::icp # include <mln/core/image/image3d.hh> +# include <mln/core/site_set/box.hh> # include <mln/registration/icp.hh> # include <mln/fun/x2x/all.hh> # include <mln/fun/x2p/closest_point.hh> @@ -56,7 +57,8 @@ namespace mln template <typename P> inline composed< translation<P::dim,float>,rotation<P::dim,float> > - registration1(const p_array& P_, + registration1(const box& domain, + const p_array& P_, const p_array& X); //FIXME: move to registration.hh @@ -70,7 +72,8 @@ namespace mln template <typename P> inline composed< translation<P::dim,float>,rotation<P::dim,float> > - registration2(const p_array& P_, + registration2(const box& domain, + const p_array& P_, const p_array& X); //FIXME: move to registration.hh @@ -83,7 +86,8 @@ namespace mln template <typename P> inline composed< translation<P::dim,float>,rotation<P::dim,float> > - registration3(const p_array& P_, + registration3(const box& domain, + const p_array& P_, const p_array& X); @@ -119,8 +123,9 @@ namespace mln template <typename P> inline composed< translation<P::dim,float>,rotation<P::dim,float> > - registration1(const p_array& P_, - const p_array& X) + registration1(const box& domain, + const p_array& P_, + const p_array& X) { trace::entering("mln::registration::registration1"); @@ -129,7 +134,7 @@ namespace mln t.start(); # endif // ! NDEBUG - registration::closest_point_with_map closest_point(X); + registration::closest_point_with_map closest_point(X, domain); std::pair<algebra::quat,mln_vec(P)> pair = icp(P_, X, closest_point, algebra::quat(1,0,0,0), @@ -153,15 +158,16 @@ namespace mln template <typename P> inline composed< translation<P::dim,float>,rotation<P::dim,float> > - registration2(const p_array& P_, - const p_array& X) + registration2(const box& domain, + const p_array& P_, + const p_array& X) { trace::entering("mln::registration::registration2"); // Used for debug. std::string method = "registration2"; - registration::closest_point_with_map closest_point(X); + registration::closest_point_with_map closest_point(X, domain); # ifndef NDEBUG util::timer t; @@ -175,12 +181,9 @@ namespace mln std::pair<algebra::quat,mln_vec(P)> pair; pair.first = algebra::quat(1,0,0,0); pair.second = literal::zero; - box3d box = geom::bbox(X); - box.enlarge(1, 60); - box.enlarge(2, 60); // Used for debug. - image3d<value::rgb8> out(box); + image3d<value::rgb8> out(domain); p_array removed_set; @@ -219,7 +222,7 @@ namespace mln # ifndef NDEBUG std::cout << "icp = " << t << std::endl; - draw_last_run(box, P_bak, removed_set, X, pair.first, pair.second); + draw_last_run(domain, P_bak, removed_set, X, pair.first, pair.second); # endif typedef rotation<3u,float> rot_t; @@ -237,15 +240,13 @@ namespace mln template <typename P> inline composed< translation<P::dim,float>,rotation<P::dim,float> > - registration3(const p_array& P_, - const p_array& X) + registration3(const box& domain, + const p_array& P_, + const p_array& X) { trace::entering("mln::registration::registration3"); - registration::closest_point_with_map closest_point(X); - std::cout << " pmin and pmax: " << std::endl; - std::cout << closest_point.cp_ima_.domain().pmin() << std::endl; - std::cout << closest_point.cp_ima_.domain().pmax() << std::endl; + registration::closest_point_with_map closest_point(X, domain); // Used for debug. std::string method = "registration3"; @@ -262,12 +263,9 @@ namespace mln std::pair<algebra::quat,mln_vec(P)> pair; pair.first = algebra::quat(1,0,0,0); pair.second = literal::zero; - box3d box = geom::bbox(X); - box.enlarge(1, 60); - box.enlarge(2, 60); // Used for debug. - image3d<value::rgb8> out(box); + image3d<value::rgb8> out(domain); p_array removed_set; @@ -306,7 +304,7 @@ namespace mln # ifndef NDEBUG std::cout << "icp = " << t << std::endl; - draw_last_run(box, P_bak, removed_set, X, pair.first, pair.second); + draw_last_run(domain, P_bak, removed_set, X, pair.first, pair.second); # endif // ! NDEBUG typedef rotation<3u,float> rot_t; @@ -329,7 +327,8 @@ namespace mln template <typename P> inline composed< translation<P::dim,float>,rotation<P::dim,float> > - registration1(const p_array& cloud, + registration1(const box& domain, + const p_array& cloud, const p_array& surface) { trace::entering("registration::registration1"); @@ -337,7 +336,7 @@ namespace mln internal::registration_tests(cloud, surface); composed< translation<P::dim,float>, rotation<P::dim,float> > - qk = impl::registration1(cloud, surface); + qk = impl::registration1(domain, cloud, surface); trace::exiting("registration::registration1"); @@ -348,7 +347,8 @@ namespace mln template <typename P> inline composed< translation<P::dim,float>,rotation<P::dim,float> > - registration2(const p_array& cloud, + registration2(const box& domain, + const p_array& cloud, const p_array& surface) { trace::entering("registration::registration2"); @@ -356,7 +356,7 @@ namespace mln internal::registration_tests(cloud, surface); composed< translation<P::dim,float>, rotation<P::dim,float> > - qk = impl::registration2(cloud, surface); + qk = impl::registration2(domain, cloud, surface); trace::exiting("registration::registration2"); @@ -367,7 +367,8 @@ namespace mln template <typename P> inline composed< translation<P::dim,float>,rotation<P::dim,float> > - registration3(const p_array& cloud, + registration3(const box& domain, + const p_array& cloud, const p_array& surface) { trace::entering("registration::registration3"); @@ -375,7 +376,7 @@ namespace mln internal::registration_tests(cloud, surface); composed< translation<P::dim,float>, rotation<P::dim,float> > - qk = impl::registration3(cloud, surface); + qk = impl::registration3(domain, cloud, surface); trace::exiting("registration::registration3"); diff --git a/milena/mln/transform/internal/closest_point_functor.hh b/milena/mln/transform/internal/closest_point_functor.hh index 99f8391..098c994 100644 --- a/milena/mln/transform/internal/closest_point_functor.hh +++ b/milena/mln/transform/internal/closest_point_functor.hh @@ -50,7 +50,10 @@ namespace mln typedef mln_value(I) V; typedef mln_psite(I) P; - mln_ch_value(I,P) cp_ima; + closest_point_functor(const p_array& pset); + + mln_ch_value(I,unsigned) cp_ima; + const p_array& pset_; void init(const I&); bool inqueue_p_wrt_input_p(const V& input_p); @@ -58,9 +61,13 @@ namespace mln bool inqueue_p_wrt_input_n(const V& input_n); void process(const P&, const P&); - void init_(const I& input) { initialize(cp_ima, input); } + void init_(const I& input) + { + init(input); + } + bool inqueue_p_wrt_input_p_(const V& input_p) { return input_p == true; } - void init_p_(unsigned p) { cp_ima.element(p) = cp_ima.point_at_index(p); } + void init_p_(unsigned) { }//cp_ima.element(p) = pset_(cp_ima.point_at_index(p)); } bool inqueue_p_wrt_input_n_(const V& input_n) { return input_n == false; } void process_(unsigned p, unsigned n) { cp_ima.element(n) = cp_ima.element(p); } }; @@ -70,10 +77,22 @@ namespace mln template <typename I> inline + closest_point_functor::closest_point_functor(const p_array<mln_psite(I)>& pset) + : pset_(pset) + { + } + + template <typename I> + inline void closest_point_functor::init(const I& input) { initialize(cp_ima, input); + data::fill(cp_ima, 0u); + + mln_piter(p_array<mln_psite(I)>) p(pset_); + for_all(p) + cp_ima(p) = p.index(); } template <typename I> @@ -87,9 +106,9 @@ namespace mln template <typename I> inline void - closest_point_functor::init_p(const P& p) + closest_point_functor::init_p(const P&) { - cp_ima(p) = p; +// cp_ima(p) = p; } template <typename I> -- 1.5.6.5

1 0

3404: Reorder data in the vector returned by to_vec().
by Guillaume Lazzara 20 Feb '09

20 Feb '09

* mln/core/concept/gdpoint.hh, * mln/core/concept/gpoint.hh: make to_vec return a new object. * mln/core/dpoint.hh, * mln/core/point.hh: make to_vec return a vector of float with coordinates ordered as a user would expect, (x,y,z...). * mln/fun/x2v/bilinear.hh, * mln/fun/x2v/trilinear.hh: get the coordinates in the proper vector index. * mln/fun/x2x/rotation.hh: normalize the axis. * tests/algebra/h_vec.cc, * tests/core/alias/dpoint3d.cc, * tests/core/alias/point1d.cc: fix tests according these changes. --- milena/ChangeLog | 21 +++++++ milena/mln/core/concept/gdpoint.hh | 2 +- milena/mln/core/concept/gpoint.hh | 2 +- milena/mln/core/dpoint.hh | 34 +++++++++-- milena/mln/core/point.hh | 113 +++++++++++++++++++---------------- milena/mln/fun/x2v/bilinear.hh | 8 +- milena/mln/fun/x2v/trilinear.hh | 6 +- milena/mln/fun/x2x/rotation.hh | 6 +- milena/tests/algebra/h_vec.cc | 14 ++-- milena/tests/core/alias/dpoint3d.cc | 2 +- milena/tests/core/alias/point1d.cc | 12 ++-- 11 files changed, 137 insertions(+), 83 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 401a2a6..ce02eb9 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,26 @@ 2009-02-20 Guillaume Lazzara <z(a)lrde.epita.fr> + Reorder data in the vector returned by to_vec(). + + * mln/core/concept/gdpoint.hh, + * mln/core/concept/gpoint.hh: make to_vec return a new object. + + * mln/core/dpoint.hh, + * mln/core/point.hh: make to_vec return a vector of float with + coordinates ordered as a user would expect, (x,y,z...). + + * mln/fun/x2v/bilinear.hh, + * mln/fun/x2v/trilinear.hh: get the coordinates in the proper vector + index. + + * mln/fun/x2x/rotation.hh: normalize the axis. + + * tests/algebra/h_vec.cc, + * tests/core/alias/dpoint3d.cc, + * tests/core/alias/point1d.cc: fix tests according these changes. + +2009-02-20 Guillaume Lazzara <z(a)lrde.epita.fr> + Revert patch #3397. * mln/algebra/quat.hh, diff --git a/milena/mln/core/concept/gdpoint.hh b/milena/mln/core/concept/gdpoint.hh index 5a5695e..62408e1 100644 --- a/milena/mln/core/concept/gdpoint.hh +++ b/milena/mln/core/concept/gdpoint.hh @@ -166,7 +166,7 @@ namespace mln { typedef mln_grid(E) grid; typedef mln_vec(E) vec; - const vec& (E::*m)() const = & E::to_vec; + vec (E::*m)() const = & E::to_vec; m = 0; } diff --git a/milena/mln/core/concept/gpoint.hh b/milena/mln/core/concept/gpoint.hh index 12f1b38..40a2420 100644 --- a/milena/mln/core/concept/gpoint.hh +++ b/milena/mln/core/concept/gpoint.hh @@ -281,7 +281,7 @@ namespace mln typedef mln_grid(E) grid; typedef mln_delta(E) delta; typedef mln_vec(E) vec; - const vec& (E::*m)() const = & E::to_vec; + vec (E::*m)() const = & E::to_vec; m = 0; } diff --git a/milena/mln/core/dpoint.hh b/milena/mln/core/dpoint.hh index 17245c5..358013c 100644 --- a/milena/mln/core/dpoint.hh +++ b/milena/mln/core/dpoint.hh @@ -125,7 +125,7 @@ namespace mln operator mln::algebra::vec<dpoint<G,C>::dim, Q>() const; /// Explicit conversion. - const vec& to_vec() const; + vec to_vec() const; protected: mln::algebra::vec<G::dim, C> coord_; @@ -161,7 +161,17 @@ namespace mln inline dpoint<G,C>::dpoint(const algebra::vec<dim,C2>& v) { - coord_ = v; + // FIXME: to be improved. + if (dim < 3) + coord_ = v; + else + { + unsigned j = 0; + for (unsigned i = dim - 2; i < dim; ++i) + coord_[i] = v[j++]; + for (unsigned i = 2; i < dim; ++i, ++j) + coord_[i-j] = v[j]; + } } template <typename G, typename C> @@ -249,15 +259,29 @@ namespace mln inline dpoint<G,C>::operator mln::algebra::vec<dpoint<G,C>::dim, Q> () const { - return coord_; + return to_vec(); } template <typename G, typename C> inline - const typename dpoint<G,C>::vec& + typename dpoint<G,C>::vec dpoint<G,C>::to_vec() const { - return coord_; + algebra::vec<G::dim, float> tmp; + + // FIXME: to be improved. + if (dim == 1) + tmp[0] = coord_[0]; + else + { + unsigned j = 0; + for (unsigned i = dim - 2; i < dim; ++i) + tmp[j++] = coord_[i]; + for (unsigned i = 2; i < dim; ++i, ++j) + tmp[j] = coord_[i-j]; + } + + return tmp; } # endif // ! MLN_INCLUDE_ONLY diff --git a/milena/mln/core/point.hh b/milena/mln/core/point.hh index a661fe5..755f50c 100644 --- a/milena/mln/core/point.hh +++ b/milena/mln/core/point.hh @@ -61,22 +61,6 @@ namespace mln /// \} - namespace internal - { - - // Helper point_to_. - - template <typename G, typename C> - struct point_to_ - { - typedef algebra::vec<G::dim, C> metal_vec; - typedef mln::algebra::h_vec<G::dim, C> h_vec; - }; - - } // end of namespace mln::internal - - - /// Generic point class. /// /// Parameters are \c n the dimension of the space and \c C the @@ -108,10 +92,10 @@ namespace mln typedef C coord; /// Algebra vector (vec) associated type. - typedef algebra::vec<G::dim, C> vec; + typedef algebra::vec<G::dim, float> vec; /// Algebra hexagonal vector (hvec) associated type. - typedef algebra::h_vec<G::dim, C> h_vec; + typedef algebra::h_vec<G::dim, float> h_vec; /// Read-only access to the \p i-th coordinate value. /// \param[in] i The coordinate index. @@ -171,23 +155,16 @@ namespace mln /// Shifting by \p the inverse of dp. point<G,C>& operator-=(const delta& dp); - /// Hook to coordinates. - operator typename internal::point_to_<G, C>::metal_vec () const; - /* FIXME: Seems highly non-generic! Moreover, causes - overloading/duplicate errors with the previous operator when - C == float. Disable it for the moment. - + /* FIXME: Seems highly non-generic! This (non documented change, even in ChangeLog) change was introduce by revision 1224, see https://trac.lrde.org/olena/changeset/1224#file2 https://www.lrde.epita.fr/pipermail/olena-patches/2007-October/001592.html */ -#if 0 operator algebra::vec<G::dim, float> () const; -#endif /// Explicit conversion towards mln::algebra::vec. - const vec& to_vec() const; + vec to_vec() const; /// Transform to point in homogene coordinate system. h_vec to_h_vec() const; @@ -214,7 +191,8 @@ namespace mln template <typename G, typename C, typename E> struct subject_point_impl< point<G,C>, E > { - const typename point<G,C>::vec& to_vec() const; + typename point<G,C>::vec to_vec() const; + operator algebra::vec<G::dim, float>() const; private: const E& exact_() const; @@ -281,7 +259,17 @@ namespace mln inline point<G,C>::point(const algebra::vec<dim,C2>& v) { - coord_ = v; + unsigned j = 0; + //FIXME: to be improved. + if (dim < 3) + coord_ = v; + else + { + for (unsigned i = dim - 2; i < dim; ++i) + coord_[i] = v[j++]; + for (unsigned i = 2; i < dim; ++i, ++j) + coord_[i-j] = v[j]; + } } template <typename G, typename C> @@ -406,29 +394,29 @@ namespace mln template <typename G, typename C> inline - point<G,C>::operator typename internal::point_to_<G, C>::metal_vec () const - { - return coord_; // FIXME: Is it OK? - } - - // FIXME: See declaration of this member above. -#if 0 - template <typename G, typename C> - inline point<G,C>::operator algebra::vec<G::dim, float> () const { - algebra::vec<dim, float> tmp; - for (unsigned int i = 0; i < dim; ++i) - tmp[i] = coord_[i]; - return tmp; + return to_vec(); } -#endif template <typename G, typename C> inline - const typename point<G,C>::vec& + typename point<G,C>::vec point<G,C>::to_vec() const { + //FIXME: to be improved. + if (dim > 2) + { + algebra::vec<G::dim, float> tmp; + unsigned j = 0; + for (unsigned i = dim - 2; i < dim; ++i) + tmp[j++] = coord_[i]; + for (unsigned i = 2; i < dim; ++i, ++j) + tmp[j] = coord_[i-j]; + + return tmp; + } + return coord_; } @@ -437,10 +425,23 @@ namespace mln typename point<G,C>::h_vec point<G,C>::to_h_vec() const { - algebra::h_vec<G::dim, C> tmp; - for (unsigned i = 0; i < dim; ++i) - tmp[i] = coord_[i]; - tmp[G::dim] = 1; + algebra::h_vec<G::dim, float> tmp; + + //FIXME: to be improved. + if (dim == 1) + tmp[0] = coord_[0]; + else + { + unsigned j = 0; + for (unsigned i = dim - 2; i < dim; ++i) + tmp[j++] = coord_[i]; + + for (unsigned i = 2; i < dim; ++i, ++j) + tmp[j] = coord_[i-j]; + + tmp[G::dim] = 1; + } + return tmp; } @@ -476,20 +477,27 @@ namespace mln template <typename G, typename C, typename E> inline - const typename point<G,C>::vec& + typename point<G,C>::vec subject_point_impl< point<G,C>, E >::to_vec() const { return exact_().get_subject().to_vec(); } + template <typename G, typename C, typename E> + inline + subject_point_impl< point<G,C>, E >::operator algebra::vec<G::dim, float>() const + { + return exact_().get_subject(); + } + } // end of namespace mln::internal template <typename G, typename C> inline - const algebra::vec<point<G,C>::dim - 1, C>& + algebra::vec<point<G,C>::dim - 1, C> cut_(const point<G,C>& p) { - return *(const algebra::vec<point<G,C>::dim - 1, C>*)(& p.to_vec()); + return *(algebra::vec<point<G,C>::dim - 1, C>*)(& p.to_vec()); } template <typename C> @@ -502,7 +510,8 @@ namespace mln } # endif // ! MLN_INCLUDE_ONLY - + + } // end of namespace mln diff --git a/milena/mln/fun/x2v/bilinear.hh b/milena/mln/fun/x2v/bilinear.hh index e264462..1daefa8 100644 --- a/milena/mln/fun/x2v/bilinear.hh +++ b/milena/mln/fun/x2v/bilinear.hh @@ -79,7 +79,7 @@ namespace mln template <typename I> bilinear::bilinear(const I& ima) : ima(ima) { - //mlc_bool(I::psite::dim == 2)::check(); + mlc_or(mlc_bool(I::psite::dim == 2), mlc_bool(I::psite::dim == 3))::check(); } template <typename I> @@ -141,14 +141,14 @@ namespace mln // | | | // q11----r1----q21 - double x = v[1]; - double y = v[2]; + double x = v[0]; + double y = v[1]; double x1 = std::floor(x); double x2 = std::floor(x) + 1; double y1 = std::floor(y); double y2 = std::floor(y) + 1; - def::coord z = math::round<float>()(v[0]); + def::coord z = math::round<float>()(v[3]); //Following access are supposed valid. vsum q11 = ima(point3d(z, static_cast<unsigned>(x1), static_cast<unsigned>(y1))); diff --git a/milena/mln/fun/x2v/trilinear.hh b/milena/mln/fun/x2v/trilinear.hh index 3015502..2a1d594 100644 --- a/milena/mln/fun/x2v/trilinear.hh +++ b/milena/mln/fun/x2v/trilinear.hh @@ -86,9 +86,9 @@ namespace mln { typedef mln_sum(mln_value(I)) vsum; - double x = v[1]; // row - double y = v[2]; // col - double z = v[0]; // sli + double x = v[0]; // row + double y = v[1]; // col + double z = v[2]; // sli math::round<double> f; unsigned x1 = f(std::floor(x)); diff --git a/milena/mln/fun/x2x/rotation.hh b/milena/mln/fun/x2x/rotation.hh index 9addb50..cbe1dd2 100644 --- a/milena/mln/fun/x2x/rotation.hh +++ b/milena/mln/fun/x2x/rotation.hh @@ -197,10 +197,9 @@ namespace mln inline rotation<n,C>::rotation(const algebra::quat& q) { - mln_precondition(q.is_unit()); - // FIXME: Should also work for 2d. - mln_precondition(n == 3); + mlc_bool(n == 3)::check(); + mln_precondition(q.is_unit()); float w = q.to_vec()[0], @@ -221,6 +220,7 @@ namespace mln axis_[0] = x; axis_[1] = y; axis_[2] = z; + axis_.normalize(); } diff --git a/milena/tests/algebra/h_vec.cc b/milena/tests/algebra/h_vec.cc index e4bffa6..27448e3 100644 --- a/milena/tests/algebra/h_vec.cc +++ b/milena/tests/algebra/h_vec.cc @@ -1,4 +1,5 @@ -// Copyright (C) 2007, 2008 EPITA Research and Development Laboratory +// 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 @@ -25,10 +26,9 @@ // reasons why the executable file might be covered by the GNU General // Public License. -/*! \file tests/algebra/h_vec.cc - * - * \brief Tests on mln::algebra::h_vec. - */ +/// \file tests/algebra/h_vec.cc +/// +/// Tests on mln::algebra::h_vec. #include <mln/algebra/h_vec.hh> #include <mln/core/alias/point3d.hh> @@ -36,11 +36,11 @@ using namespace mln; -void run_in_3d(const algebra::vec<3, def::coord>&) +void run_in_3d(const algebra::vec<3, float>&) { } -void run_in_3d_h(const algebra::h_vec<3, def::coord>&) +void run_in_3d_h(const algebra::h_vec<3, float>&) { } diff --git a/milena/tests/core/alias/dpoint3d.cc b/milena/tests/core/alias/dpoint3d.cc index 20bcbaf..d538f1b 100644 --- a/milena/tests/core/alias/dpoint3d.cc +++ b/milena/tests/core/alias/dpoint3d.cc @@ -49,5 +49,5 @@ int main() mln_assertion(q == p + dp); algebra::vec<3, float> v = dp; - mln_assertion(v[1] == 6); + mln_assertion(v[0] == 6); } diff --git a/milena/tests/core/alias/point1d.cc b/milena/tests/core/alias/point1d.cc index fbe8e72..cbcda23 100644 --- a/milena/tests/core/alias/point1d.cc +++ b/milena/tests/core/alias/point1d.cc @@ -1,4 +1,5 @@ -// Copyright (C) 2007, 2008 EPITA Research and Development Laboratory +// 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 @@ -25,10 +26,9 @@ // reasons why the executable file might be covered by the GNU General // Public License. -/*! \file tests/core/alias/point1d.cc - * - * \brief Tests on mln::point1d. - */ +/// \file tests/core/alias/point1d.cc +/// +/// Tests on mln::point1d. #include <mln/core/alias/point1d.hh> @@ -43,7 +43,7 @@ int main() // assignment p[0] = 4; - algebra::vec<1,def::coord> v = p; + algebra::vec<1,float> v = p; p.ind() += 1; mln_assertion(p.ind() == 5 && p[0] == 5); -- 1.5.6.5

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r3403: Update DICOM support to n dimensions
by Fabien Freling 20 Feb '09

20 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-02-20 Fabien Freling <fabien.freling(a)lrde.epita.fr> Update DICOM support to n dimensions. * fabien/gdcm/gdcm.cc: Update. * fabien/gdcm/load.hh: Update load support for multidimensional DICOM. --- gdcm.cc | 11 ++++++-- load.hh | 80 ++++++++++++++++++---------------------------------------------- 2 files changed, 31 insertions(+), 60 deletions(-) Index: trunk/milena/sandbox/fabien/gdcm/load.hh =================================================================== --- trunk/milena/sandbox/fabien/gdcm/load.hh (revision 3402) +++ trunk/milena/sandbox/fabien/gdcm/load.hh (revision 3403) @@ -39,7 +39,7 @@ # include <mln/core/image/image2d.hh> # include <mln/core/image/image3d.hh> -# include <mln/value/int_u16.hh> +# include <mln/algebra/vec.hh> # include <gdcmReader.h> # include <gdcmImageReader.h> @@ -57,7 +57,7 @@ namespace dicom { - /*! Load a gdcm image in a Milena image. + /*! Load a dicom image in a Milena image. * * \param[out] ima A reference to the image which will receive * data. @@ -67,28 +67,6 @@ void load(Image& ima, const std::string& filename); - /*! Load a gdcm image in a Milena image. To use this routine, you - * should specialize the template whith the value type of the - * image loaded. (ex : load<value::int_u8>("...") ) - * - * \param[in] filename The image source. - * - * \return An image2d which contains loaded data. - */ - template <typename V> - image2d<V> load(const std::string& filename); - - /*! Load a gdcm image in a Milena image. To use this routine, you - * should specialize the template whith the value type of the - * image loaded. (ex : load<value::int_u8>("...") ) - * - * \param[in] filename The image source. - * - * \return An image2d which contains loaded data. - */ - template <typename V> - image3d<V> load(const std::string& filename); - # ifndef MLN_INCLUDE_ONLY template <typename V> @@ -135,52 +113,40 @@ gdcm::Image& image = r.GetImage(); - std::cout << std::endl << "Image information" << std::endl - << "=================" << std::endl; - image.Print(std::cout); - - std::cout << std::endl << "Buffer information" << std::endl - << "=================" << std::endl; - std::cout << "Buffer length: " << image.GetBufferLength() << std::endl; char* dataBuffer = new char[image.GetBufferLength()]; image.GetBuffer(dataBuffer); int ndims = image.GetNumberOfDimensions(); const unsigned int* dims = image.GetDimensions(); - // FIXME: Check ScalarType - if (ndims == 1) - { - - } - if (ndims == 2) - { - //image2d<int_u16> mln_ima(dims[1], dims[0]); - //mln_piter(image2d<int_u16>) p(ima.domain()); - //for_all(p) - //{ - // ima(p) = dataBuffer[(p.col() + p.row() * dims[0]) * 2] * 256 + - // dataBuffer[(p.col() + p.row() * dims[0]) * 2 + 1]; - //} + algebra::vec<mln_site_(I)::dim, unsigned int> vmin; + algebra::vec<mln_site_(I)::dim, unsigned int> vmax; + algebra::vec<mln_site_(I)::dim, unsigned int> vdims; + for (int i = ndims - 1; i >= 0; --i) + { + vmin[i] = 0; + vmax[i] = dims[ndims - i - 1] - 1; + if (i == ndims - 1) + vdims[i] = 1; + else + vdims[i] = dims[ndims - i - 2] * vdims[i + 1]; } - if (ndims == 3) - { - //image3d<int_u16> ima(dims[2], dims[1], dims[0]); - mln_site(I) pmin(0, 0, 0); - mln_site(I) pmax(dims[2] - 1, dims[1] - 1, dims[0] - 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()); + // FIXME: Check ScalarType and HighBit + unsigned int index = 0; for_all(p) { - ima(p) = dataBuffer[(p.col() + p.row() * dims[0] + p.sli() * dims[0] * dims[1]) * 2] * 256 + - dataBuffer[(p.col() + p.row() * dims[0] + p.sli() * dims[0] * dims[1]) * 2 + 1]; - std::cout << (p.col() + p.row() * dims[0] + p.sli() * dims[0] * dims[1]) * 2 << " [" - << "p.col = " << p.col() << "] [" - << "p.row = " << p.row() << "] [" - << "p.sli = " << p.sli() << "]" - << std::endl; + index = 0; + for (int i = 0; i < ndims; ++i) + { + index += p.to_site().to_vec()[i] * vdims[i]; } + ima(p) = dataBuffer[index * 2] * 256 + dataBuffer[index * 2 + 1]; } delete(dataBuffer); Index: trunk/milena/sandbox/fabien/gdcm/gdcm.cc =================================================================== --- trunk/milena/sandbox/fabien/gdcm/gdcm.cc (revision 3402) +++ trunk/milena/sandbox/fabien/gdcm/gdcm.cc (revision 3403) @@ -1,18 +1,23 @@ #include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> #include <mln/value/int_u8.hh> #include <mln/value/int_u16.hh> #include "load.hh" #include <mln/io/dump/save.hh> +#include <mln/io/pgm/save.hh> int main() { using namespace mln; using value::int_u16; - image3d<int_u16> lena; + image2d<int_u16> lena2; + image3d<int_u16> lena3; - io::dicom::load(lena, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0061.dcm"); - io::dump::save(lena, "IM_0061.dump"); + //io::dicom::load(lena3, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0058.dcm"); + io::dicom::load(lena2, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0058.dcm"); + //io::dump::save(lena3, "IM_0058.dump"); + io::pgm::save(lena2, "IM_0058.pgm"); }

1 0

r3402: Update DICOM loader
by Fabien Freling 20 Feb '09

20 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-02-20 Fabien Freling <fabien.freling(a)lrde.epita.fr> Update DICOM loader. * fabien/gdcm/Makefile: Update. * fabien/gdcm/dump2pgm.cc: New tool to convert dump volume to a pgm flat image. * fabien/gdcm/gdcm.cc: Update. * fabien/gdcm/load.hh: Update. --- Makefile | 2 +- dump2pgm.cc | 35 +++++++++++++++++++++++++++++++++++ gdcm.cc | 4 ++-- load.hh | 16 ++++++++++------ 4 files changed, 48 insertions(+), 9 deletions(-) Index: trunk/milena/sandbox/fabien/gdcm/dump2pgm.cc =================================================================== --- trunk/milena/sandbox/fabien/gdcm/dump2pgm.cc (revision 0) +++ trunk/milena/sandbox/fabien/gdcm/dump2pgm.cc (revision 3402) @@ -0,0 +1,35 @@ + +#include <mln/core/image/image2d.hh> +#include <mln/make/image3d.hh> +#include <mln/debug/slices_2d.hh> + +#include <mln/value/int_u16.hh> +#include <mln/io/dump/load.hh> +#include <mln/io/pgm/save.hh> + +#include <mln/literal/colors.hh> + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.dump output.pgm" << std::endl; + abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u16; + + if (argc != 3) + usage(argv); + + image3d<int_u16> vol; + io::dump::load(vol, argv[1]); + + int_u16 bg = 0; + image2d<int_u16> ima = debug::slices_2d(vol, 1.f, bg); + io::pgm::save(ima, argv[2]); +} Index: trunk/milena/sandbox/fabien/gdcm/Makefile =================================================================== --- trunk/milena/sandbox/fabien/gdcm/Makefile (revision 3401) +++ trunk/milena/sandbox/fabien/gdcm/Makefile (revision 3402) @@ -8,5 +8,5 @@ -L/Users/HiSoKa/Downloads/gdcmbin/bin \ -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF -lgdcmexpat -lgdcmjpeg12 -lgdcmjpeg16 -lgdcmjpeg8 -lgdcmopenjpeg -lgdcmuuid -lgdcmzlib \ -framework CoreFoundation \ - -DNDEBUG \ + -DNDEBUG -O1 \ gdcm.cc -o mln_gdcm Index: trunk/milena/sandbox/fabien/gdcm/load.hh =================================================================== --- trunk/milena/sandbox/fabien/gdcm/load.hh (revision 3401) +++ trunk/milena/sandbox/fabien/gdcm/load.hh (revision 3402) @@ -143,10 +143,7 @@ << "=================" << std::endl; std::cout << "Buffer length: " << image.GetBufferLength() << std::endl; char* dataBuffer = new char[image.GetBufferLength()]; - if (image.GetBuffer(dataBuffer)) - std::cout << "GetBuffer success" << std::endl; - else - std::cout << "GetBuffer failure" << std::endl; + image.GetBuffer(dataBuffer); int ndims = image.GetNumberOfDimensions(); const unsigned int* dims = image.GetDimensions(); @@ -170,17 +167,24 @@ { //image3d<int_u16> ima(dims[2], dims[1], dims[0]); mln_site(I) pmin(0, 0, 0); - mln_site(I) pmax(dims[2], dims[1], dims[0]); + mln_site(I) pmax(dims[2] - 1, dims[1] - 1, dims[0] - 1); mln_concrete(I) result(box<mln_site(I)>(pmin, pmax)); initialize(ima, result); - mln_piter(image3d<int_u16>) p(ima.domain()); + mln_piter(I) p(ima.domain()); for_all(p) { ima(p) = dataBuffer[(p.col() + p.row() * dims[0] + p.sli() * dims[0] * dims[1]) * 2] * 256+ dataBuffer[(p.col() + p.row() * dims[0] + p.sli() * dims[0] * dims[1]) * 2 + 1]; + std::cout << (p.col() + p.row() * dims[0] + p.sli() * dims[0] * dims[1]) * 2 << " [" + << "p.col = " << p.col() << "] [" + << "p.row = " << p.row() << "] [" + << "p.sli = " << p.sli() << "]" + << std::endl; } } + delete(dataBuffer); + trace::exiting("mln::io::dicom::load"); } Index: trunk/milena/sandbox/fabien/gdcm/gdcm.cc =================================================================== --- trunk/milena/sandbox/fabien/gdcm/gdcm.cc (revision 3401) +++ trunk/milena/sandbox/fabien/gdcm/gdcm.cc (revision 3402) @@ -13,6 +13,6 @@ image3d<int_u16> lena; - io::dicom::load(lena, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm"); - io::dump::save(lena, "IM_0052.dump"); + io::dicom::load(lena, "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0061.dcm"); + io::dump::save(lena, "IM_0061.dump"); }

1 0