[Olena-patches] 3220: Add segmentation scheme for volumes.

https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox Index: ChangeLog from Thierry Geraud &lt;thierry.geraud(a)lrde.epita.fr&gt; Add segmentation scheme for volumes. * theo/igr: New directory. * theo/igr/pgms2pgm.cc: New. * theo/igr/raw2pgm.cc: New. * theo/igr/pgms2raw.cc: New. * theo/igr/irm_anat_segm.cc: New. * theo/igr/irm_anat_segm__2D_ONLY.cc: New. irm_anat_segm.cc | 60 ++++++++++++++++++++++++++++++++++++++++++++++ irm_anat_segm__2D_ONLY.cc | 59 +++++++++++++++++++++++++++++++++++++++++++++ pgms2pgm.cc | 41 +++++++++++++++++++++++++++++++ pgms2raw.cc | 38 +++++++++++++++++++++++++++++ raw2pgm.cc | 34 ++++++++++++++++++++++++++ 5 files changed, 232 insertions(+) Index: theo/igr/pgms2pgm.cc --- theo/igr/pgms2pgm.cc (revision 0) +++ theo/igr/pgms2pgm.cc (revision 0) @@ -0,0 +1,41 @@ +#include <mln/core/image/image2d.hh> +#include <mln/make/image3d.hh> +#include <mln/debug/slices_2d.hh> + +#include <mln/value/int_u8.hh> +#include <mln/io/pgm/load.hh> +#include <mln/io/pgm/save.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " output.pgm input1.pgm .. inputn.pgm" << std::endl; + abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + typedef image2d<int_u8> I; + + if (argc < 3) + usage(argv); + + + util::array<I> arr; + for (int i = 2; i < argc; ++i) + { + I ima; + io::pgm::load(ima, argv[i]); + arr.append(ima); + } + image3d<int_u8> vol = make::image3d(arr); + + int_u8 bg = 0; + I out = debug::slices_2d(vol, 1.f, bg); + io::pgm::save(out, argv[1]); +} Index: theo/igr/raw2pgm.cc --- theo/igr/raw2pgm.cc (revision 0) +++ theo/igr/raw2pgm.cc (revision 0) @@ -0,0 +1,34 @@ + +#include <mln/core/image/image2d.hh> +#include <mln/make/image3d.hh> +#include <mln/debug/slices_2d.hh> + +#include <mln/value/int_u8.hh> +#include <mln/io/raw/load.hh> +#include <mln/io/pgm/save.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.raw output.pgm" << std::endl; + abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc != 3) + usage(argv); + + image3d<int_u8> vol; + io::raw::load(vol, argv[1]); + + int_u8 bg = 0; + image2d<int_u8> ima = debug::slices_2d(vol, 1.f, bg); + io::pgm::save(ima, argv[2]); +} Index: theo/igr/pgms2raw.cc --- theo/igr/pgms2raw.cc (revision 0) +++ theo/igr/pgms2raw.cc (revision 0) @@ -0,0 +1,38 @@ + +#include <mln/core/image/image2d.hh> +#include <mln/make/image3d.hh> + +#include <mln/value/int_u8.hh> +#include <mln/io/pgm/load.hh> +#include <mln/io/raw/save.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " output.raw input1.pgm .. inputn.pgm" << std::endl; + abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + typedef image2d<int_u8> I; + + if (argc < 3) + usage(argv); + + + util::array<I> arr; + for (int i = 2; i < argc; ++i) + { + I ima; + io::pgm::load(ima, argv[i]); + arr.append(ima); + } + image3d<int_u8> vol = make::image3d(arr); + io::raw::save(vol, argv[1]); +} Index: theo/igr/irm_anat_segm.cc --- theo/igr/irm_anat_segm.cc (revision 0) +++ theo/igr/irm_anat_segm.cc (revision 0) @@ -0,0 +1,60 @@ + +#include <mln/core/image/image3d.hh> +#include <mln/core/alias/neighb3d.hh> + +#include <mln/value/int_u8.hh> +#include <mln/io/raw/load.hh> +#include <mln/io/raw/save.hh> + +#include <mln/morpho/elementary/gradient.hh> +#include <mln/morpho/closing_volume.hh> +#include <mln/morpho/meyer_wst.hh> + +#include <mln/accu/mean.hh> +#include <mln/labeling/compute.hh> +#include <mln/fun/i2v/array.hh> +#include <mln/level/transform.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.raw output.raw" << std::endl; + abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc != 3) + usage(argv); + + trace::quiet = false; + + image3d<int_u8> vol, grad, clo; + io::raw::load(vol, argv[1]); + + grad = morpho::elementary::gradient(vol, c6()); + clo = morpho::closing_volume(grad, c6(), 666); + + typedef value::label_16 L; + L n_basins; + image3d<L> wst = morpho::meyer_wst(clo, c6(), n_basins); + + std::cout << n_basins << std::endl; + + accu::mean<int_u8, float, int_u8> a_; + util::array<int_u8> a = labeling::compute(a_, vol, wst, n_basins); + std::cout << a << std::endl; + a[0] = 0; + + fun::i2v::array<int_u8> f; + convert::from_to(a, f); + image3d<int_u8> out = level::transform(wst, f); + + io::raw::save(out, argv[2]); +} Index: theo/igr/irm_anat_segm__2D_ONLY.cc --- theo/igr/irm_anat_segm__2D_ONLY.cc (revision 0) +++ theo/igr/irm_anat_segm__2D_ONLY.cc (revision 0) @@ -0,0 +1,59 @@ +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> + +#include <mln/value/int_u8.hh> +#include <mln/io/pgm/load.hh> +#include <mln/io/pgm/save.hh> + +#include <mln/morpho/elementary/gradient.hh> +#include <mln/morpho/closing_volume.hh> +#include <mln/morpho/meyer_wst.hh> + +#include <mln/accu/mean.hh> +#include <mln/labeling/compute.hh> +#include <mln/fun/i2v/array.hh> +#include <mln/level/transform.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.pgm output.pgm" << std::endl; + abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc != 3) + usage(argv); + + trace::quiet = false; + + image2d<int_u8> vol, grad, clo; + io::pgm::load(vol, argv[1]); + + grad = morpho::elementary::gradient(vol, c4()); + clo = morpho::closing_volume(grad, c4(), 666); + + typedef value::label_16 L; + L n_basins; + image2d<L> wst = morpho::meyer_wst(clo, c4(), n_basins); + + std::cout << n_basins << std::endl; + + accu::mean<int_u8, float, int_u8> a_; + util::array<int_u8> a = labeling::compute(a_, vol, wst, n_basins); + std::cout << a << std::endl; + a[0] = 0; + + fun::i2v::array<int_u8> f; + convert::from_to(a, f); + image2d<int_u8> out = level::transform(wst, f); + + io::pgm::save(out, argv[2]); +}