March 2009 - Olena-patches

[Olena] #143: Reorganize milena/mln/core/
by Olena 18 May '09

18 May '09

#143: Reorganize milena/mln/core/ ----------------------+----------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: task | Status: new Priority: minor | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Keywords: | ----------------------+----------------------------------------------------- (This ticket is just a proposal. We might close it even if no change occur in `milena/mln/core`.) There are many things in source:trunk/milena/mln/core/, that could be reorganized and/or split in several directories/subdirectories: * basic/classic images and entites (`mln::image2d`, etc.) * graph-based images and entities (`mln::graph_image`, etc.) * non classic images and associated tools (`mln::rle_image`, etc.) * morphers (`mln::cast_image`, etc.) * internal/core mechanisms (`initialize.hh` etc.) * general tools (`contract.hh`, `inplace.hh`, etc.) * concepts (though they are located in their own directory, `mln/core/concept/`) * implementation/factoring classes (thought most of them are in `mln/core/internal/`) * other entities, that should be moved elsewhere (`mln::h_vec`, etc.) * and so on. To my (Roland) mind, we should: 1. Identify the different kind of files present in `core/`. 2. Assign one (maybe two) kinds to each file of this directory. 3. Determine a new file layout, and perform the moves. -- Ticket URL: <https://trac.lrde.org/olena/ticket/143> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

2 3

[Olena] #167: Write iterators on complexes
by Olena 18 May '09

18 May '09

#167: Write iterators on complexes ----------------------+----------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: task | Status: new Priority: major | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Keywords: | ----------------------+----------------------------------------------------- Most of this task is described in [source:branches/cleanup-2008/milena/tests/topo/complex.cc tests/topo/complex.cc] (r2411) : {{{ /*------------------------------. | Iterators on adjacent faces. | `------------------------------*/ /* FIXME: Write and exercise more iterators (see milena/tests/core/complex_image.cc) and ticket #162 (https://trac.lrde.org/olena/ticket/162) */ /* Iterate on the the set of (n-1)-faces adjacent to AF. Note: this can be solved with iterators where the dimension can be either static or dynamic. Let's start with a dynamic one, as it would allow us to write something like this: mln_fwd_citer_(topo::complex<D>) f(c); mln_fwd_lower_nciter(topo::complex<D>) n(c); for_all(c) for_all(n) // ... (Note: we might want to get rid of the name `citer', and use `fiter' everywhere.). A static version might be useful (and more efficient) too. Likewise, our iterators on n-faces (both faces_piter and complex_faces_piter) use a static `n'. We should also have n-faces iterators where n could be dynamic. But first, we need to clarify (existing) names. ----------------------------------------------------------------- Current name New name Definition ----------------------------------------------------------------- complex<D> (n/a) General complex face<N, D> face_data<N, D> Face data face_handle<N, D> n_face<N, D> (Static) n-face handle faces_set<N, D> n_faces_set<N, D> Set of face handles any_face_handle<D> face<D> Dynamic face handle complex_fwd_iter_<D>(c) face_fwd_iter<D>(c) | Iterators on all complex_bkd_iter_<D>(c) face_bkd_iter<D>(c) | faces of c complex_iter_base_<F, E> complex_iter_base<F, E> | Factoring base | class. ----------------------------------------------------------------- (Note: get rid of trailing underscores, even for entities in mln::internal::.) Next, write these: ----------------------------------------------------------------- Name Definition ----------------------------------------------------------------- n_faces_fwd_iter<D>(c) | Iterators on n-faces, n_faces_bkd_iter<D>(c) | n being dynamic adj_lower_faces_fwd_iter<D>(c, f) | Iterators on the adjacent adj_lower_faces_bkd_iter<D>(c, f) | (lower) (n-1)-faces of the | n-face f of the complex c, | n being dynamic adj_higher_faces_fwd_iter<D>(c, f) | Iterators on the adjacent adj_higher_faces_bkd_iter<D>(c, f) | (higher) (n+1)-faces of the | n-face f of the complex c, | n being dynamic adj_lower_dim_connected_n_faces_fwd_iter<D>(c, f) adj_lower_dim_connected_n_faces_bkd_iter<D>(c, f) (FIXME: These names are admittedly too long.) | Iterators on the the set of | n-faces sharing an adjacent | (n-1)-face with f, n being | dynamic adj_higher_dim_connected_n_faces_fwd_iter<D>(c, f) adj_higher_dim_connected_n_faces_bkd_iter<D>(c, f) (FIXME: These names are admittedly too long.) | Iterators on the the set of | n-faces sharing an adjacent | (n+1)-face with f, n being | dynamic cell_fwd_iter<D>(c, f) | Iterators on the set of the cell_bkd_iter<D>(c, f) | faces in the « cell » | including p, i.e. the set of | all m-faces adjacent to p, | where m is in [0, n-1]; | this set is name « f-hat » cell_boundary_fwd_iter<D>(c, f) | Likewise, but excluding p; cell_boundary_bkd_iter<D>(c, f) | this set is named « p-hat* » ----------------------------------------------------------------- We could also have generic iterators based on predicated, and even use them to provide first (non efficient) implementations of the iterators from the previous list. ----------------------------------------------------------------- Name Definition ----------------------------------------------------------------- generic_face_fwd_iter<D>(c, pred) | Generic face iterators on c generic_face_bkd_iter<D>(c, pred) | using predicate pred to | define the iterated subset. ----------------------------------------------------------------- I'm unsure about the following existing iterators; should we keep them? What are they good for, except testing our code? ----------------------------------------------------------------- Current name Definition ----------------------------------------------------------------- complex_faces_fwd_iter_<N, D> Iterators on N-faces, N being complex_faces_fwd_iter_<N, D> static, acting as proxies of face_handle<N, D>'s. faces_fwd_iter_<N, D> Iterators on N-faces, N being faces_fwd_iter_<N, D> static, acting as proxies of any_face_handle<N, D>'s. ----------------------------------------------------------------- */ }}} (This should be turned into actual documentation, BTW.) See also #162 for applications of these iterators in windows/neighborhoods and images. -- Ticket URL: <https://trac.lrde.org/olena/ticket/167> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

2 6

[Olena] #161: Implement more complex psite iterators
by Olena 18 May '09

18 May '09

#161: Implement more complex psite iterators ----------------------+----------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: task | Status: new Priority: major | Milestone: Component: Milena | Version: 1.0 Keywords: | ----------------------+----------------------------------------------------- As of r2148, we only have a single piter couple on complex : `mln::p_complex_fwd_piter_` and `mln::p_complex_bkd_piter_` (source:trunk/milena/mln/core/p_complex_piter.hh:2148). Comments (FIXMEs) at the end of source:trunk/milena/tests/core/complex_image.cc:2148 suggest to add these additional iterators: * iterators on ''n''-faces with ''n'' fixed in [0, ''d''] (using `mln::p_faces` and `mln::faces_psite`?) * iterators on ''n''-faces with ''n'' in a subset of [0, ''d'']; * etc. -- Ticket URL: <https://trac.lrde.org/olena/ticket/161> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

2 3

[Olena] #140: Add points having floating-point coordinates
by Olena 18 May '09

18 May '09

#140: Add points having floating-point coordinates ----------------------+----------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: task | Status: new Priority: major | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Keywords: | ----------------------+----------------------------------------------------- Name regular instances `point1df`, `point2df` and `point3df`. (N.B.: Aroune will need them so as to build the 3-d surface graph from a set of triangles.) -- Ticket URL: <https://trac.lrde.org/olena/ticket/140> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

2 1

[Olena] #182: Repair Swilena
by Olena 15 May '09

15 May '09

#182: Repair Swilena ----------------------+----------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: defect | Status: new Priority: minor | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Keywords: | ----------------------+----------------------------------------------------- [source:trunk/swilena Swilena] is broken since the end of Summer 2008 (before the merging back of [source:branches/cleanup-2008 cleanup-2008/] into [source:trunk/ trunk/]). Have it compile and pass the tests again. -- Ticket URL: <https://trac.lrde.org/olena/ticket/182> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

2 2

[Olena] #162: Implement windows, neighborhoods, and corresponding iterators for complex-based images
by Olena 14 May '09

14 May '09

#162: Implement windows, neighborhoods, and corresponding iterators for complex- based images ----------------------+----------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: task | Status: new Priority: major | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Keywords: | ----------------------+----------------------------------------------------- For a given (fixed) dimension ''n'' and a psite ''p'' on a ''n''-face, implement windows/neighborhoods (and corresponding iterators) returning * the set of (''n''-1)-faces adjacent to ''p'' (using ``mln::p_faces`` and ``mln::faces_psite``?); * the set of (''n''+1)-faces adjacent to ''p'' (using ``mln::p_faces`` and ``mln::faces_psite``?); * the set of ''n''-faces sharing a (''n''-1)-face with ''p''; * the set of ''n''-faces sharing a (''n''-1)-face or (''n''-2)-face (by transitivity) with ''p'' (is it useful?); * the set of the faces in the ``cell'' including ''p'' (named ``''p''-hat'' in couprie.08.pami), i.e., the set of all ''m''-faces adjacent to ''p'', where ''m'' is in [0, ''n''-1].[[BR]] In that definition, ''p'' is said adjacent to an ''m''-face ''q'' if there is a sequence (''m,,1,,'', ''m,,2,,'', ..., ''m,,k,,'') of faces so that * ''m,,1,,'' is an (''n''-1)-face adjacent to ''p'' ; * ''m,,2,,'' is an (''n''-2)-face adjacent to ''m,,1,,'' ; * ... (and so on) * ''m,,k,,'' is an (''m''+1)-face adjacent to ''q''. * what else? As in #139, we might want to factor things using implementation classes: * ``mln::internal::complex_vicinity`` * ``mln::internal::complex_vicinity_piter`` We might even be able to factor them with graph-based ones. -- Ticket URL: <https://trac.lrde.org/olena/ticket/162> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

2 11

[Olena] #130: Don not pass neighborhoods as argument to algorithms
by Olena 14 May '09

14 May '09

#130: Don not pass neighborhoods as argument to algorithms ----------------------+----------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: defect | Status: new Priority: major | Milestone: Olena 1.0ß Component: Milena | Version: 1.0 Keywords: | ----------------------+----------------------------------------------------- Neighborhoods shall be bound to images: they are a property of them. Hence an algorithm (at least a facade) shall not accept an image along with an ''external'' neighborhood. Most of the time, these algorithms are based on windows improperly called neighborhoods. Here is the list of files to revamp, as of revision 1663: * source:trunk/labeling/level.spe.hh * source:trunk/labeling/regional_maxima.hh * source:trunk/labeling/regional_minima.hh * source:trunk/make/voronoi.hh * source:trunk/milena/mln/geom/labeling/blobs.hh * source:trunk/milena/mln/geom/seeds2tiling_roundness.hh * source:trunk/milena/mln/labeling/background.hh * source:trunk/milena/mln/labeling/flat_zones.hh * source:trunk/milena/mln/labeling/foreground.hh * source:trunk/milena/mln/labeling/level.hh * source:trunk/morpho/Rd.hh * source:trunk/morpho/dilation.hh * source:trunk/morpho/opening_area.hh * source:trunk/morpho/opening_attribute.hh -- Ticket URL: <https://trac.lrde.org/olena/ticket/130> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image library.

2 11

[Olena] #159: Distribute SWIG wrappers
by Olena 14 May '09

14 May '09

#159: Distribute SWIG wrappers -------------------------+-------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: enhancement | Status: new Priority: minor | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Keywords: | -------------------------+-------------------------------------------------- According to Alexandre Hamez, files generated by `swig` (e.g., `*.py` and `*-wrap.cc`) are portable. We should distribute them, as * it would save users wanting to use Swilena some time; * it would free them to have SWIG to compile Swilena. To do: * distribute these files (remove `nodist_` prefixes); * ensure they're available at distribution time (use `dist-hook` in `Makefile.am`); * add generated files to `MAINTAINERCLEANFILES`; * adjust `configure.ac`? (see what Alexandre uses). -- Ticket URL: <https://trac.lrde.org/olena/ticket/159> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

2 2

r3597: Update spatial smoothing
by Fabien Freling 31 Mar '09

31 Mar '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-03-31 Fabien Freling <fabien.freling(a)lrde.epita.fr> Update spatial smoothing. * fabien/igr/Makefile: Update. * fabien/igr/space_smooth/linear.cc: Fix spatial smoothing. * fabien/igr/space_smooth/median.cc: Implement spatial smoothing. * fabien/igr/space_smooth/morpho.cc: Draft. * fabien/igr/time_smooth/linear.cc: Small fix. --- Makefile | 5 +- space_smooth/linear.cc | 8 +-- space_smooth/median.cc | 111 +++++++++++++++++++++++++++++++------------------ space_smooth/morpho.cc | 12 +---- time_smooth/linear.cc | 2 5 files changed, 83 insertions(+), 55 deletions(-) Index: trunk/milena/sandbox/fabien/igr/space_smooth/median.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/median.cc (revision 3596) +++ trunk/milena/sandbox/fabien/igr/space_smooth/median.cc (revision 3597) @@ -11,6 +11,7 @@ #include <mln/io/plot/save.hh> #include <mln/accu/median_h.hh> +#include <mln/core/alias/window2d.hh> #include <mln/util/array.hh> @@ -33,15 +34,11 @@ /////////////////// image3d<int_u12> input; io::dicom::load(input, argv[1]); - image2d<util::array<int_u12> > ima_arr(input.nrows(), input.ncols()); + util::array<image2d<int_u12> > arr_ima; for (int i = 0; i < input.nslices(); ++i) { image2d<int_u12> tmp_slice = duplicate(slice(input, i)); - mln_piter_(image2d<int_u12>) p(tmp_slice.domain()); - for_all(p) - { - ima_arr(p).append(tmp_slice(p)); - } + arr_ima.append(tmp_slice); } //////////// @@ -49,41 +46,52 @@ // Median // // // //////////// - image2d<util::array<int_u12> > ima_median3; - image2d<util::array<int_u12> > ima_median5; - initialize(ima_median3, ima_arr); - initialize(ima_median5, ima_arr); - mln_piter_(image2d<int_u12>) p(ima_median3.domain()); - accu::median_h<int_u12> accu_med; + window2d win_c12p; + win_c12p + .insert(-1, -1) + .insert( 0, -1) + .insert(+1, -1) + .insert(-1, 0) + .insert( 0, 0) + .insert(+1, 0) + .insert(-1, +1) + .insert( 0, +1) + .insert(+1, +1) + .insert(+2, +2) + .insert(-2, -2) + .insert(+2, -2) + .insert(-2, +2); + window2d win_c4 = win_c4p(); + util::array<image2d<int_u12> > ima_median3; + util::array<image2d<int_u12> > ima_median5; + accu::median_h<int_u12> accu_med3; + accu::median_h<int_u12> accu_med5; + image2d<int_u12> tmp; + initialize(tmp, arr_ima[0]); + mln_piter_(image2d<int_u12>) p(arr_ima[0].domain()); + mln_qiter_(window2d) q3(win_c4, p); + mln_qiter_(window2d) q5(win_c12p, p); + for (unsigned i = 0; i < arr_ima.nelements(); ++i) + { for_all(p) { // Median 3 - ima_median3(p).append(ima_arr(p)[0]); - for (unsigned i = 1; i < ima_arr(p).nelements() - 1; ++i) - { - accu_med.init(); - accu_med.take(ima_arr(p)[i - 1]); - accu_med.take(ima_arr(p)[i]); - accu_med.take(ima_arr(p)[i + 1]); - ima_median3(p).append(accu_med.to_result()); + accu_med3.init(); + for_all(q3) if (arr_ima[i].domain().has(q3)) + accu_med3.take(arr_ima[i](q3)); + tmp(p) = accu_med3.to_result(); } - ima_median3(p).append(ima_arr(p)[ima_arr(p).nelements() - 1]); + ima_median3.append(duplicate(tmp)); + for_all(p) + { // Median 5 - ima_median5(p).append(ima_arr(p)[0]); - ima_median5(p).append(ima_arr(p)[1]); - for (unsigned i = 2; i < ima_arr(p).nelements() - 2; ++i) - { - accu_med.init(); - accu_med.take(ima_arr(p)[i - 2]); - accu_med.take(ima_arr(p)[i - 1]); - accu_med.take(ima_arr(p)[i]); - accu_med.take(ima_arr(p)[i + 1]); - accu_med.take(ima_arr(p)[i + 2]); - ima_median5(p).append(accu_med.to_result()); + accu_med5.init(); + for_all(q5) if (arr_ima[i].domain().has(q5)) + accu_med5.take(arr_ima[i](q5)); + tmp(p) = accu_med5.to_result(); } - ima_median5(p).append(ima_arr(p)[ima_arr(p).nelements() - 2]); - ima_median5(p).append(ima_arr(p)[ima_arr(p).nelements() - 1]); + ima_median5.append(duplicate(tmp)); } ///////////// @@ -91,12 +99,35 @@ // Outputs // // // ///////////// - io::plot::save(ima_median3(point2d(160, 120)), "median3_tumeur.plot"); - io::plot::save(ima_median3(point2d(34, 94)), "median3_air.plot"); - io::plot::save(ima_median3(point2d(122, 115)), "median3_poumon.plot"); - io::plot::save(ima_median5(point2d(160, 120)), "median5_tumeur.plot"); - io::plot::save(ima_median5(point2d(34, 94)), "median5_air.plot"); - io::plot::save(ima_median5(point2d(122, 115)), "median5_poumon.plot"); + util::array<int_u12> arr_tumeur3; + util::array<int_u12> arr_tumeur5; + for (unsigned i = 0; i < ima_median3.nelements(); ++i) + { + arr_tumeur3.append(ima_median3[i](point2d(160, 120))); + arr_tumeur5.append(ima_median5[i](point2d(160, 120))); + } + io::plot::save(arr_tumeur3, "median3_tumeur.plot"); + io::plot::save(arr_tumeur5, "median5_tumeur.plot"); + + util::array<int_u12> arr_air3; + util::array<int_u12> arr_air5; + for (unsigned i = 0; i < ima_median3.nelements(); ++i) + { + arr_air3.append(ima_median3[i](point2d(34, 94))); + arr_air5.append(ima_median5[i](point2d(34, 94))); + } + io::plot::save(arr_air3, "median3_air.plot"); + io::plot::save(arr_air5, "median5_air.plot"); + + util::array<int_u12> arr_poumon3; + util::array<int_u12> arr_poumon5; + for (unsigned i = 0; i < ima_median3.nelements(); ++i) + { + arr_poumon3.append(ima_median3[i](point2d(122, 115))); + arr_poumon5.append(ima_median5[i](point2d(122, 115))); + } + io::plot::save(arr_poumon3, "median3_poumon.plot"); + io::plot::save(arr_poumon5, "median5_poumon.plot"); return 0; } Index: trunk/milena/sandbox/fabien/igr/space_smooth/morpho.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/morpho.cc (revision 3596) +++ trunk/milena/sandbox/fabien/igr/space_smooth/morpho.cc (revision 3597) @@ -48,15 +48,11 @@ /////////////////// image3d<int_u12> input; io::dicom::load(input, argv[1]); - image2d<util::array<int_u12> > ima_arr(input.nrows(), input.ncols()); + util::array<image2d<int_u12> > arr_ima; for (int i = 0; i < input.nslices(); ++i) { image2d<int_u12> tmp_slice = duplicate(slice(input, i)); - mln_piter_(image2d<int_u12>) p(tmp_slice.domain()); - for_all(p) - { - ima_arr(p).append(tmp_slice(p)); - } + arr_ima.append(tmp_slice); } //////////// @@ -64,10 +60,8 @@ // Morpho // // // //////////// - image2d<image1d<int_u12> > ima_morpho; - initialize(ima_morpho, ima_arr); + util::array<image2d<int_u12> > ima_morpho; mln_piter_(image2d<int_u12>) p(ima_morpho.domain()); - accu::median_h<int_u12> accu_med; for_all(p) { image1d<int_u12> tmp_ima; Index: trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc (revision 3596) +++ trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc (revision 3597) @@ -48,12 +48,12 @@ // Linear convolution // // // //////////////////////// - float ws[] = { 0, 1/8, 0, - 1/8, 1/2, 1/8, - 0, 1/8, 0 }; + float ws[] = { 0, 1/8.f, 0, + 1/8.f, 1/2.f, 1/8.f, + 0, 1/8.f, 0 }; util::array<image2d<float> > ima_linear; - for (unsigned i = 1; i < arr_ima.nelements(); ++i) + for (unsigned i = 0; i < arr_ima.nelements(); ++i) ima_linear.append(linear::convolve(arr_ima[i], make::w_window2d(ws))); ///////////// Index: trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc (revision 3596) +++ trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc (revision 3597) @@ -52,7 +52,7 @@ image2d<util::array<int_u12> > ima_linear; initialize(ima_linear, ima_arr); mln_piter_(image2d<int_u12>) p(ima_linear.domain()); - accu::median<int_u12> accu_med; + accu::median_h<int_u12> accu_med; for_all(p) { ima_linear(p).append(ima_arr(p)[0]); Index: trunk/milena/sandbox/fabien/igr/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/Makefile (revision 3596) +++ trunk/milena/sandbox/fabien/igr/Makefile (revision 3597) @@ -47,6 +47,9 @@ time_max: time_max.cc ${CXX} -I../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} -lm $^ -o time_max +first_slice_dicom: first_slice_dicom.cc + ${CXX} -I../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} -lm $^ -o first_slice_dicom + clean: rm -rf *.dump *.p?m *.plot *.log *.csv *.dSYM - rm seg2d seg3d wsd2d wsd3d nbasins_finder grad clo_vol wst graph med thres matlab time_max + rm seg2d seg3d wsd2d wsd3d nbasins_finder grad clo_vol wst graph med thres matlab time_max first_slice_dicom

1 0

3596: Several bug fixes.
by Thierry Geraud 30 Mar '09

30 Mar '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Several bug fixes. * mln/histo/array.hh: Layout. * mln/core/image/image1d.hh (from_to_): Remove border setting to 0. Add some hints of future code. (todo): New. * mln/core/alias/point1d.hh: Upgrade doc style. (row, row_t): Fix naming as... (ind, ind_t): ...those. * mln/linear/gaussian_directional_2d.hh: New. * mln/linear/gaussian_1d.hh: New. Both files have been copied from my sandbox. * mln/linear/all.hh: Update. * mln/accu/center.hh (to_result): Make it work when invalid. (todo): New. * mln/value/label.hh (prev): New. * mln/canvas/morpho/attribute_filter.hh (lambda): Use macro for this arg type. (attribute_filter_dispatch): Fix missing border adjustment for the fastest version. (attribute_filter_fastest): New precondition. Fix missing border initialization so that it is neutral. * tests/morpho/closing/volume.cc: Force no border to test that the border is correctly adapted to nbh. * mln/labeling/compute.hh: Move code intro trace. mln/accu/center.hh | 18 ++--- mln/canvas/morpho/attribute_filter.hh | 42 ++++++++----- mln/core/alias/point1d.hh | 48 +++++++------- mln/core/image/image1d.hh | 12 +++ mln/histo/array.hh | 1 mln/labeling/compute.hh | 15 +++- mln/linear/all.hh | 11 ++- mln/linear/gaussian_1d.hh | 109 ++++++++++++++++++++++++++++++++++ mln/linear/gaussian_directional_2d.hh | 98 ++++++++++++++++++++++++------ mln/value/label.hh | 11 +++ tests/morpho/closing/volume.cc | 5 + 11 files changed, 291 insertions(+), 79 deletions(-) Index: mln/histo/array.hh --- mln/histo/array.hh (revision 3595) +++ mln/histo/array.hh (working copy) @@ -81,6 +81,7 @@ + # ifndef MLN_INCLUDE_ONLY template <typename T> Index: mln/core/image/image1d.hh --- mln/core/image/image1d.hh (revision 3595) +++ mln/core/image/image1d.hh (working copy) @@ -32,6 +32,8 @@ /// \file mln/core/image/image1d.hh /// /// Definition of the basic mln::image1d class. +/// +/// \todo Rewrite from_to(histo, image1d) after Etienne's work. # include <mln/core/internal/fixme.hh> # include <mln/core/internal/image_primary.hh> @@ -576,7 +578,13 @@ void from_to_(const histo::array<V>& from, image1d<T>& to) { - to.init_(make::box1d(from.nvalues()), 0); + // FIXME: The code should looks like: + +// box1d b(point1d(mln_min(V)), point1d(mln_max(V))); +// ima.init_(b, 0); +// for_all(v) +// from_to(h(v), ima.at_( index_of(v) )); + to.init_(make::box1d(from.nvalues())); for (unsigned i = 0; i < from.nvalues(); ++i) from_to(from[i], to(point1d(i))); } @@ -587,7 +595,7 @@ void from_to_(const util::array<V>& from, image1d<T>& to) { - to.init_(make::box1d(from.nelements()), 0); + to.init_(make::box1d(from.nelements())); for (unsigned i = 0; i < from.nelements(); ++i) from_to(from[i], to(point1d(i))); } Index: mln/core/alias/point1d.hh --- mln/core/alias/point1d.hh (revision 3595) +++ mln/core/alias/point1d.hh (working copy) @@ -1,5 +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 @@ -29,25 +29,26 @@ #ifndef MLN_CORE_ALIAS_POINT1D_HH # define MLN_CORE_ALIAS_POINT1D_HH -/*! \file mln/core/alias/point1d.hh - * - * \brief Definition of the mln::point1d alias and of its construction - * routine. - */ +/// \file mln/core/alias/point1d.hh +/// +/// Definition of the mln::point1d alias and of its construction +/// routine. # include <mln/core/point.hh> // For site_const_impl and site_mutable_impl. # include <mln/core/concept/site_proxy.hh> # include <mln/core/internal/force_exact.hh> + namespace mln { - /*! \brief Type alias for a point defined on the 1D square grid with - * integer coordinates. - */ + /// Type alias for a point defined on the 1D square grid with + /// integer coordinates. + // typedef point<grid::tick, def::coord> point1d; + namespace internal { @@ -59,8 +60,8 @@ typedef C coord; enum { dim = 1 }; - typedef const C& row_t; - const C& row() const; + typedef const C& ind_t; + const C& ind() const; const C& operator[](unsigned i) const; const C& last_coord() const; @@ -79,8 +80,8 @@ typedef subject_impl< const point<grid::tick, C>, E > super_; E& exact_(); public: - using super_::row; - C& row(); + using super_::ind; + C& ind(); using super_::operator[]; C& operator[](unsigned i); }; @@ -94,9 +95,9 @@ template <typename C, typename E> inline const C& - subject_impl< const point<grid::tick, C>, E >::row() const + subject_impl< const point<grid::tick, C>, E >::ind() const { - return exact_().get_subject().row(); + return exact_().get_subject().ind(); } template <typename C, typename E> @@ -104,8 +105,9 @@ const C& subject_impl< const point<grid::tick, C>, E >::operator[](unsigned i) const { - mln_precondition(i < 1); - return exact_().get_subject()[i]; + mln_precondition(i == 0); + (void)i; + return exact_().get_subject()[0]; } template <typename C, typename E> @@ -121,9 +123,9 @@ template <typename C, typename E> inline C& - subject_impl< point<grid::tick, C>, E >::row() + subject_impl< point<grid::tick, C>, E >::ind() { - return exact_().get_subject().row(); + return exact_().get_subject().ind(); } template <typename C, typename E> @@ -131,15 +133,15 @@ C& subject_impl< point<grid::tick, C>, E >::operator[](unsigned i) { - mln_precondition(i < 2); - return exact_().get_subject()[i]; + mln_precondition(i == 0); + (void)i; + return exact_().get_subject()[0]; } # endif // ! MLN_INCLUDE_ONLY } // end of namespace mln::internal - } // end of namespace mln Index: mln/linear/all.hh --- mln/linear/all.hh (revision 3595) +++ mln/linear/all.hh (working copy) @@ -1,5 +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 @@ -50,8 +50,7 @@ { /// Namespace of local linear routines implementation details. - namespace impl - {} + namespace impl {} } } @@ -62,7 +61,11 @@ # include <mln/linear/convolve.hh> # include <mln/linear/convolve_2x1d.hh> # include <mln/linear/convolve_directional.hh> + # include <mln/linear/gaussian.hh> +# include <mln/linear/gaussian_directional_2d.hh> +# include <mln/linear/gaussian_1d.hh> + # include <mln/linear/lap.hh> # include <mln/linear/log.hh> //# include <mln/linear/sobel.hh> Index: mln/linear/gaussian_directional_2d.hh --- mln/linear/gaussian_directional_2d.hh (revision 3588) +++ mln/linear/gaussian_directional_2d.hh (working copy) @@ -1,3 +1,38 @@ +// Copyright (C) 2009 EPITA Research and Laboratory (LRDE) +// +// This file is part of the Olena Library. This library is free +// software; you can redistribute it and/or modify it under the terms +// of the GNU General Public License version 2 as published by the +// Free Software Foundation. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this library; see the file COPYING. If not, write to +// the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, +// Boston, MA 02110-1301, USA. +// +// As a special exception, you may use this file as part of a free +// software library without restriction. Specifically, if other files +// instantiate templates or use macros or inline functions from this +// file, or you compile this file and link it with other files to +// produce an executable, this file does not by itself cause the +// resulting executable to be covered by the GNU General Public +// License. This exception does not however invalidate any other +// reasons why the executable file might be covered by the GNU General +// Public License. + +#ifndef MLN_LINEAR_GAUSSIAN_DIRECTIONAL_2D_HH +# define MLN_LINEAR_GAUSSIAN_DIRECTIONAL_2D_HH + +/// \file mln/linear/gaussian_directional_2d.hh +/// +/// Directional Gaussian filter for 2D images. +/// +/// \todo This is experimental code to be merged with regular code... #include <mln/core/image/image2d.hh> #include <mln/extension/adjust_fill.hh> @@ -11,6 +46,17 @@ namespace linear { + + template <typename I> + mln_concrete(I) + gaussian_directional_2d(const Image<I>& input, + unsigned dir, double sigma, + const mln_value(I)& bdr); + + + +# ifndef MLN_INCLUDE_ONLY + namespace my { @@ -20,14 +66,14 @@ DericheGaussianFirstDerivative, DericheGaussianSecondDerivative }; - std::vector<MLN_FLOAT> n, d, nm, dm; - MLN_FLOAT sumA, sumC; + std::vector<double> n, d, nm, dm; + double sumA, sumC; - recursivefilter_coef_(MLN_FLOAT a0, MLN_FLOAT a1, - MLN_FLOAT b0, MLN_FLOAT b1, - MLN_FLOAT c0, MLN_FLOAT c1, - MLN_FLOAT w0, MLN_FLOAT w1, - MLN_FLOAT s, FilterType filter_type) + recursivefilter_coef_(double a0, double a1, + double b0, double b1, + double c0, double c1, + double w0, double w1, + double s, FilterType filter_type) { n.reserve(5); d.reserve(5); @@ -39,10 +85,10 @@ w0 /= s; w1 /= s; - MLN_FLOAT sin0 = sin(w0); - MLN_FLOAT sin1 = sin(w1); - MLN_FLOAT cos0 = cos(w0); - MLN_FLOAT cos1 = cos(w1); + double sin0 = sin(w0); + double sin1 = sin(w1); + double cos0 = cos(w0); + double cos1 = cos(w1); switch (filter_type) { @@ -81,7 +127,7 @@ case DericheGaussianSecondDerivative : { - MLN_FLOAT aux; + double aux; aux = 12.0 * cos0 * exp( 3.0 * b0 ) - 3.0 * exp( 2.0 * b0 ) + 8.0 * cos0 * cos0 * cos0 * exp( 3.0 * b0 ) - 12.0 * cos0 * cos0 * @@ -197,15 +243,15 @@ template <typename I, typename C> inline void - recursivefilter_directional_2d_generic(I& ima, + recursivefilter_directional_generic(I& ima, const C& c, const mln_psite(I)& start, const mln_psite(I)& finish, int len, const mln_deduce(I, psite, delta)& d) { - std::vector<MLN_FLOAT> tmp1(len); - std::vector<MLN_FLOAT> tmp2(len); + std::vector<double> tmp1(len); + std::vector<double> tmp2(len); tmp1[0] = c.n[0]*ima(start); @@ -292,7 +338,7 @@ template <typename I, typename C> inline void - recursivefilter_directional_2d_fastest(I& ima, + recursivefilter_directional_fastest(I& ima, const C& c, const mln_psite(I)& start, const mln_psite(I)& finish, @@ -303,8 +349,8 @@ // extension::adjust_fill(ima, 5 * int(151 + .50001) + 1, bdr); // extension::fill(ima, bdr); - std::vector<MLN_FLOAT> tmp1(len); - std::vector<MLN_FLOAT> tmp2(len); + std::vector<double> tmp1(len); + std::vector<double> tmp2(len); unsigned delta_offset = ima.delta_index(d); unsigned @@ -418,9 +464,14 @@ inline mln_concrete(I) gaussian_directional_2d(const Image<I>& input_, - unsigned dir, MLN_FLOAT sigma, + unsigned dir, double sigma, const mln_value(I)& bdr) { + trace::entering("linear::gaussian_directional_2d"); + + typedef mln_site(I) P; + mlc_bool(P::dim == 2)::check(); + const I& input = exact(input_); mln_precondition(dir == 0 || dir == 1); @@ -447,7 +498,7 @@ if (dir == 0) { for (int j = 0; j < ncols; ++j) - recursivefilter_directional_2d_fastest(output, coef, + recursivefilter_directional_fastest(output, coef, point2d(- b, j), point2d(nrows - 1 + b, j), nrows + 2 * b, @@ -458,7 +509,7 @@ if (dir == 1) { for (int i = 0; i < nrows; ++i) - recursivefilter_directional_2d_fastest(output, coef, + recursivefilter_directional_fastest(output, coef, point2d(i, - b), point2d(i, ncols - 1 + b), ncols + 2 * b, @@ -466,10 +517,15 @@ bdr); } + trace::exiting("linear::gaussian_directional_2d"); return output; } +# endif // ! MLN_INCLUDE_ONLY } // end of namespace mln::linear } // end of namespace mln + + +#endif // ! MLN_LINEAR_GAUSSIAN_DIRECTIONAL_2D_HH Property changes on: mln/linear/gaussian_directional_2d.hh ___________________________________________________________________ Added: svn:mergeinfo Index: mln/linear/gaussian_1d.hh --- mln/linear/gaussian_1d.hh (revision 0) +++ mln/linear/gaussian_1d.hh (revision 0) @@ -0,0 +1,109 @@ +// Copyright (C) 2009 EPITA Research and Laboratory (LRDE) +// +// This file is part of the Olena Library. This library is free +// software; you can redistribute it and/or modify it under the terms +// of the GNU General Public License version 2 as published by the +// Free Software Foundation. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this library; see the file COPYING. If not, write to +// the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, +// Boston, MA 02110-1301, USA. +// +// As a special exception, you may use this file as part of a free +// software library without restriction. Specifically, if other files +// instantiate templates or use macros or inline functions from this +// file, or you compile this file and link it with other files to +// produce an executable, this file does not by itself cause the +// resulting executable to be covered by the GNU General Public +// License. This exception does not however invalidate any other +// reasons why the executable file might be covered by the GNU General +// Public License. + +#ifndef MLN_LINEAR_GAUSSIAN_1D_HH +# define MLN_LINEAR_GAUSSIAN_1D_HH + +/// \file mln/linear/gaussian_1d.hh +/// +/// Gaussian filter for fastest 1D images. +/// +/// \todo This is experimental code to be merged with regular code... + +#include <mln/core/image/image1d.hh> +#include <mln/linear/gaussian_directional_2d.hh> + + + +namespace mln +{ + + namespace linear + { + + + template <typename I> + mln_concrete(I) + gaussian_1d(const Image<I>& input, + double sigma, + const mln_value(I)& bdr); + + + +# ifndef MLN_INCLUDE_ONLY + + template <typename I> + inline + mln_concrete(I) + gaussian_1d(const Image<I>& input_, + double sigma, + const mln_value(I)& bdr) + { + trace::entering("linear::gaussian_1d"); + + typedef mln_site(I) P; + mlc_bool(P::dim == 1)::check(); + + const I& input = exact(input_); + mln_precondition(input.is_valid()); + + my::recursivefilter_coef_ coef(1.68f, 3.735f, + 1.783f, 1.723f, + -0.6803f, -0.2598f, + 0.6318f, 1.997f, + sigma, + my::recursivefilter_coef_::DericheGaussian); + + extension::adjust_fill(input, 5 * int(sigma + .50001) + 1, bdr); + mln_concrete(I) output = duplicate(input); + + if (sigma < 0.006) + return output; + + int + ninds = geom::ninds(input), + b = input.border(); + + recursivefilter_directional_fastest(output, coef, + point1d(- b), + point1d(ninds - 1 + b), + ninds + 2 * b, + dpoint1d(1), + bdr); + + trace::exiting("linear::gaussian_1d"); + return output; + } + +# endif // ! MLN_INCLUDE_ONLY + + } // end of namespace mln::linear + +} // end of namespace mln + + +#endif // ! MLN_LINEAR_GAUSSIAN_1D_HH Index: mln/accu/center.hh --- mln/accu/center.hh (revision 3595) +++ mln/accu/center.hh (working copy) @@ -1,4 +1,5 @@ -// Copyright (C) 2008, 2009 EPITA Research and Development Laboratory (LRDE) +// 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 @@ -31,7 +32,8 @@ /// \file mln/accu/center.hh /// /// Define an accumulator that computes the mass center of a site set. - +/// +/// \todo Fix to_result() value when invalid... # include <mln/accu/internal/base.hh> # include <mln/accu/bbox.hh> @@ -66,7 +68,6 @@ /// Get the value of the accumulator. V to_result() const; - operator V() const; operator P() const; /// Check whether this accu is able to return a result. @@ -136,19 +137,14 @@ V center<P,V>::to_result() const { - mln_precondition(is_valid()); + // mln_precondition(is_valid()); + if (! is_valid()) + return V(); return center_ / nsites_; } template <typename P, typename V> inline - center<P,V>::operator V() const - { - return to_result(); - } - - template <typename P, typename V> - inline center<P,V>::operator P() const { return P(to_result()); Index: mln/value/label.hh --- mln/value/label.hh (revision 3595) +++ mln/value/label.hh (working copy) @@ -155,6 +155,9 @@ /// Return the next value. label<n> next() const; + /// Return the previous value. + label<n> prev() const; + }; @@ -279,6 +282,14 @@ template <unsigned n> inline + label<n> + label<n>::prev() const + { + return label<n>(this->v_ - 1); + } + + template <unsigned n> + inline std::ostream& operator<<(std::ostream& ostr, const label<n>& i) { return ostr << debug::format(i.to_equiv()); Index: mln/canvas/morpho/attribute_filter.hh --- mln/canvas/morpho/attribute_filter.hh (revision 3595) +++ mln/canvas/morpho/attribute_filter.hh (working copy) @@ -1,5 +1,5 @@ -// Copyright (C) 2007, 2008, 2009 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 @@ -39,14 +39,15 @@ # include <mln/core/concept/accumulator.hh> # include <mln/level/sort_offsets.hh> - # include <mln/trait/accumulators.hh> - # include <mln/util/pix.hh> +# include <mln/border/get.hh> # include <mln/data/fill.hh> +# include <mln/extension/adjust_fill.hh> # include <mln/level/sort_psites.hh> + namespace mln { @@ -56,16 +57,20 @@ namespace morpho { - // Facade Fwd Declaration + // FIXME: Doc! + template <typename I, typename N, typename A> mln_concrete(I) attribute_filter(const Image<I>& input, const Neighborhood<N>& nbh, - const Accumulator<A>& a, const typename A::result& lambda, + const Accumulator<A>& a, const mln_result(A)& lambda, bool increasing); + + # ifndef MLN_INCLUDE_ONLY - namespace impl { + namespace impl + { template <typename A, typename I> void take_as_init_fastest (trait::accumulator::when_pix::use_none, A& accu, @@ -128,8 +133,9 @@ } - namespace generic { + namespace generic + { //////////////////////// /// Generic version. /// @@ -153,7 +159,7 @@ const Neighborhood<N>& nbh_, const Site_Set<S>& s_, const Accumulator<A>& a_, - const typename A::result& lambda) + const mln_result(A)& lambda) { trace::entering("canvas::morpho::impl::generic::attribute_filter"); // FIXME: Test?! @@ -278,7 +284,7 @@ const Neighborhood<N>& nbh_, const util::array<unsigned>& s, const Accumulator<A>& a_, - const typename A::result& lambda) + const mln_result(A)& lambda) { trace::entering("canvas::morpho::impl::attribute_filter_fastest"); // FIXME: Tests? @@ -287,6 +293,10 @@ const N& nbh = exact(nbh_); (void)a_; + // The border adaptation is performed in the calling scope since + // we want offsets of 's' to match the image structure / dimensions. + mln_precondition(border::get(input) >= nbh.delta()); + mln_concrete(I) output; initialize(output, input); @@ -303,6 +313,8 @@ { initialize(deja_vu, input); data::fill(deja_vu, false); + extension::fill(deja_vu, true); // So the border is neutral. + initialize(activity, input); data::fill(activity, true); initialize(parent, input); @@ -387,7 +399,7 @@ const Image<I>& input, const Neighborhood<N>& nbh, const Accumulator<A>& a, - const typename A::result& lambda, + const mln_result(A)& lambda, bool increasing) { p_array<mln_psite(I)> s = increasing ? @@ -405,9 +417,11 @@ const Image<I>& input, const Neighborhood<N>& nbh, const Accumulator<A>& a, - const typename A::result& lambda, + const mln_result(A)& lambda, bool increasing) { + extension::adjust(input, nbh); + util::array<unsigned> s = increasing ? level::sort_offsets_increasing(input) : @@ -424,7 +438,7 @@ attribute_filter_dispatch(const Image<I>& input, const Neighborhood<N>& nbh, const Accumulator<A>& a, - const typename A::result& lambda, + const mln_result(A)& lambda, bool increasing) { enum { @@ -451,7 +465,7 @@ attribute_filter(const Image<I>& input, const Neighborhood<N>& nbh, const Accumulator<A>& a, - const typename A::result& lambda, + const mln_result(A)& lambda, bool increasing) { return internal::attribute_filter_dispatch(input, nbh, a, lambda, increasing); Index: mln/labeling/compute.hh --- mln/labeling/compute.hh (revision 3595) +++ mln/labeling/compute.hh (working copy) @@ -1,4 +1,5 @@ -// Copyright (C) 2008 EPITA Research and Development Laboratory (LRDE) +// 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 @@ -39,7 +40,7 @@ # include <mln/core/concept/accumulator.hh> # include <mln/core/concept/meta_accumulator.hh> # include <mln/util/array.hh> -# include <mln/convert/to.hh> +# include <mln/convert/from_to.hh> namespace mln @@ -180,8 +181,11 @@ for_all(p) accus[label(p)].take(p); + util::array<mln_result(A)> res; + convert::from_to(accus, res); + trace::exiting("labeling::impl::generic::compute"); - return convert::to< util::array<mln_result(A)> >(accus); + return res; } @@ -206,8 +210,11 @@ for_all(p) accus[label(p)].take(input(p)); + util::array<mln_result(A)> res; + convert::from_to(accus, res); + trace::exiting("labeling::impl::generic::compute"); - return convert::to< util::array<mln_result(A)> >(accus); + return res; } } // end of namespace mln::labeling::impl::generic Index: tests/morpho/closing/volume.cc --- tests/morpho/closing/volume.cc (revision 3595) +++ tests/morpho/closing/volume.cc (working copy) @@ -40,6 +40,8 @@ #include <mln/morpho/closing/volume.hh> #include <mln/morpho/attribute/volume.hh> +#include <mln/border/resize.hh> + #include "tests/data.hh" @@ -51,6 +53,9 @@ typedef image2d<int_u8> I; I lena; io::pgm::load(lena, MLN_IMG_DIR "/tiny.pgm"); + + border::resize(lena, 0); + io::pgm::save(morpho::closing::volume(lena, c4(), 10000), "ref.pgm");

1 0