Olena-patches February 2010

olena-patches@lrde.epita.fr

6 participants
91 discussions

[Olena] #148: Missing files in the distribution of Olena 0.11

by Olena

#148: Missing files in the distribution of Olena 0.11 ------------------------+--------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: defect | Status: new Priority: trivial | Milestone: Olena 0.11.1 Component: Milena | Version: 0.11 Keywords: EXTRA_DIST | ------------------------+--------------------------------------------------- Reported by Théo, relaunching `bootstrap.sh` from a distributed tarball of Olena 0.11: {{{ este% ./bootstrap.sh sh: Can't open ./cleanup.sh sh: Can't open ./gen_filelists.sh }}} -- Ticket URL: <https://trac.lrde.org/olena/ticket/148> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

14 years, 7 months

[Olena] #217: Nasty bug in mln::data::impl::in memcpy_ with g++ 4.2 on Debian GNU/Linux on IA-32

by Olena Trac

#217: Nasty bug in mln::data::impl::in memcpy_ with g++ 4.2 on Debian GNU/Linux on IA-32 ----------------------+----------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: defect | Status: new Priority: critical | Milestone: Olena 1.1 Component: Milena | Version: 1.0 Keywords: | ----------------------+----------------------------------------------------- Running the following test exhibits this issue: {{{ make -C milena/apps/graph-morpho CXX="ccache g++-4.2" checkTESTS=samples- image2d TESTS_ENVIRONMENT="valgrind" }}} This seems to be a bug (or a weird implementation-defined behavior) in Debian's `g++` 4.2 on IA-32, due to some strict-aliasing rule not respected in Milena's code. I added a `#warning` in `memcpy_.hh` in r4608. But the thing is, `g++` 4.2 is the main compiler in Debian GNU/Linux 5.0, which is used on most GCC-based Olena buildbots, meaning we won't get a successful build on these hosts until we circumvent this bug. That's bad. -- Ticket URL: <https://trac.lrde.org/olena/ticket/217> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

14 years, 7 months

[Olena] #201: Use « olena » instead of « oln » as an identifier

by Olena Trac

#201: Use « olena » instead of « oln » as an identifier ----------------------+----------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: defect | Status: new Priority: major | Milestone: Component: Olena | Version: 1.0 Keywords: | ----------------------+----------------------------------------------------- We should no longer use « `oln` » ; « `olena` » is much more clearer. * The Subversion repository is called `oln`, because `olena` was already used (arg!); we should not do this mistake again: the future Git repository shall be named `olena`. * Likewise, Olena's build farm URL (https://buildfarm.lrde.org/buildfarm/oln/) should be renamed to `olena`. If you find some other places where the project is called `oln` instead of `olena`, please report them here. TIA. -- Ticket URL: <https://trac.lrde.org/olena/ticket/201> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

14 years, 7 months

[Olena] #126: Speed up tests

by Olena

#126: Speed up tests -------------------------+-------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: enhancement | Status: new Priority: major | Milestone: Olena 1.0ß Component: Milena | Version: 1.0 Keywords: | -------------------------+-------------------------------------------------- Some tests take a very long time to execute. Main causes are: * input image(s) are too big [[BR]] => they should be reduced (sometimes, testing on `lena.pgm` is just too costly); * the default, non-optimized compilation settings (`-O0 -ggdb`) produces very inefficient code for certain algorithms [[BR]] => we should locally increase the level of optimization (e.g., `-O1` or `-O2`) for these tests, and '''document''' this in `Makefile.am` (explain why we made changes in `CXXFLAGS` for a given test). We might want to make a list of lengthy tests here before solving this ticket. -- Ticket URL: <https://trac.lrde.org/olena/ticket/126> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image library.

14 years, 7 months

[Olena] #214: Use Automake 1.11's AM_DEFAULT_SOURCE_EXT

by Olena Trac

#214: Use Automake 1.11's AM_DEFAULT_SOURCE_EXT -------------------------+-------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: enhancement | Status: new Priority: minor | Milestone: Component: Milena | Version: 1.0 Keywords: Make | -------------------------+-------------------------------------------------- Quoting the [http://www.mail-archive.com/automake@gnu.org/msg15022.html announce of Automake 1.11]: {{{ - The default source file extension (.c) can be overridden with AM_DEFAULT_SOURCE_EXT now. }}} Which allows us to replace {{{ bin_PROGRAMS = foo bar baz foo_SOURCES = foo.cc bar_SOURCES = bar.cc baz_SOURCES = baz.cc }}} with {{{ bin_PROGRAMS = foo bar baz AM_DEFAULT_SOURCE_EXT = .cc }}} (Of course, « `AM_DEFAULT_SOURCE_EXT = .cc` » should be factored in some `common.mk` file.) This just rocks if you consider the tons of `*_SOURCES` lines in the zillions of `tests/*/Makefile.am` files. On the downward side, this change requires Automake 1.11, which is not even in Debian unstable as of July 24, 2009. We might want to wait a little bit before requiring this version. -- Ticket URL: <https://trac.lrde.org/olena/ticket/214> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

14 years, 7 months

[Olena] #207: Use Automake 1.11

by Olena Trac

#207: Use Automake 1.11 -------------------------+-------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: enhancement | Status: new Priority: major | Milestone: Olena 1.1 Component: Olena | Version: 1.0 Keywords: | -------------------------+-------------------------------------------------- Automake 1.11 provides a better framework for tests: each test can generate a log file, and the test suite is a mere rule generating a summary log, depending on all these logs. The `check` rule is no longer based on a shell `for` loop, and `make` can truly honors its `-j` (parallel instances) option when testing. Of course, one need to be careful with side effects, notably files created by tests, as one test may overwrite the output(s) of another tests. Akim recommends that test `foo` writes its outputs to `foo.dir`. Moreover, this permits many improvements: * One can generate pretty-printed versions of the tests using, e.g., `rst2html` (if the log contains an RST output) on the logs. * One can have a `recheck` rule reruning only the failed tests, since the first line of the log records the outcome of the test (pass or fail). * Also, provided dependencies are well set, this can probably help one write rules to rerun only the needed tests when a change occurred in the source tree (but I don't know yet how to do this). -- Ticket URL: <https://trac.lrde.org/olena/ticket/207> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

14 years, 7 months

[Olena] #129: Reintegrate oln.m4 (full or a part of it) into Olena 1.0

by Olena

#129: Reintegrate oln.m4 (full or a part of it) into Olena 1.0 -----------------------------------+---------------------------------------- Reporter: levill_r | Owner: levill_r Type: enhancement | Status: new Priority: minor | Milestone: Olena 1.0ß Component: Olena | Version: 1.0 Keywords: configure autoconf M4 | -----------------------------------+---------------------------------------- In Olena 0.11, `oln.m4` (which might be renamed to `olena.m4`) provided useful services to both the Olena package (search for libraries, set up flags for tests, etc.) and autoconfiscated packages using Olena, by providing a `--with-oln` (to be renamed to `--with-olena`) flag. We should reintegrate a part of these features, possibly in two M4 macro packages: * one for Olena, * one for Olena-based projects. -- Ticket URL: <https://trac.lrde.org/olena/ticket/129> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image library.

14 years, 8 months

last-svn-commit-25-gd3e640b Extend the histogram visualization tools for new projection concept.

by green

* green/mln/display/project_histo.hh (project2_histo): New functions that keep the max of the histogram or the class associate to it while projecting along a direction. * green/mln/display/project_histo.hh (project3_histo): New functions that keep the color of the class associate to the histogram maximum while projecting along a direction. * green/mln/display/display_histo.hh: New interface functions for project2_histo and project3_histo. --- milena/sandbox/ChangeLog | 13 + milena/sandbox/green/mln/display/display_histo.hh | 50 +++ milena/sandbox/green/mln/display/project_histo.hh | 344 +++++++++++++++++++++ 3 files changed, 407 insertions(+), 0 deletions(-) diff --git a/milena/sandbox/ChangeLog b/milena/sandbox/ChangeLog index f34508b..b9d40cb 100644 --- a/milena/sandbox/ChangeLog +++ b/milena/sandbox/ChangeLog @@ -1,5 +1,18 @@ 2010-01-05 Yann Jacquelet <jacquelet(a)lrde.epita.fr> + Extend the histogram visualization tools for new projection concept. + + * green/mln/display/project_histo.hh (project2_histo): New functions + that keep the max of the histogram or the class associate to it while + projecting along a direction. + * green/mln/display/project_histo.hh (project3_histo): New functions + that keep the color of the class associate to the histogram maximum + while projecting along a direction. + * green/mln/display/display_histo.hh: New interface functions for + project2_histo and project3_histo. + +2010-01-05 Yann Jacquelet <jacquelet(a)lrde.epita.fr> + Build translation table between number of pixels and percentage of pixels in image for the scribo database. diff --git a/milena/sandbox/green/mln/display/display_histo.hh b/milena/sandbox/green/mln/display/display_histo.hh index 1fd5da4..2ba0b61 100644 --- a/milena/sandbox/green/mln/display/display_histo.hh +++ b/milena/sandbox/green/mln/display/display_histo.hh @@ -33,6 +33,8 @@ # include <mln/display/project_histo.hh> # include <mln/fun/v2v/log.hh> # include <mln/value/int_u8.hh> +# include <mln/value/rgb8.hh> +# include <mln/value/label_8.hh> /// \file @@ -55,6 +57,20 @@ namespace mln image2d<value::int_u8> display_histo3d_unsigned(const image3d<unsigned>& histo); + image2d<value::int_u8> + display2_histo3d_unsigned(const image3d<unsigned>& histo); + + image2d<value::label_8> + display2_histo3d_unsigned(const image3d<unsigned>& histo, + const image3d<value::label_8>& label); + + image2d<value::rgb8> + display3_histo3d_unsigned(const image3d<unsigned>& histo); + + image2d<value::rgb8> + display3_histo3d_unsigned(const image3d<unsigned>& histo, + const image3d<value::label_8>& label); + #ifndef MLN_INCLUDE_ONLY /// \brief Allow the visualization of a 3d histogram by projection. @@ -86,6 +102,40 @@ namespace mln return proj_int; } + image2d<value::int_u8> + display2_histo3d_unsigned(const image3d<unsigned>& histo) + { + image2d<value::int_u8> proj = project2_histo<0>(histo); + + return proj; + } + + image2d<value::label_8> + display2_histo3d_unsigned(const image3d<unsigned>& histo, + const image3d<value::label_8>& label) + { + image2d<value::label_8> proj = project2_histo<0>(histo, label); + + return proj; + } + + image2d<value::rgb8> + display3_histo3d_unsigned(const image3d<unsigned>& histo) + { + image2d<value::rgb8> proj = project3_histo<0>(histo); + + return proj; + } + + image2d<value::rgb8> + display3_histo3d_unsigned(const image3d<unsigned>& histo, + const image3d<value::label_8>& label) + { + image2d<value::rgb8> proj = project3_histo<0>(histo, label); + + return proj; + } + #endif // ! MLN_INCLUDE_ONLY diff --git a/milena/sandbox/green/mln/display/project_histo.hh b/milena/sandbox/green/mln/display/project_histo.hh index f0e6858..d842c70 100644 --- a/milena/sandbox/green/mln/display/project_histo.hh +++ b/milena/sandbox/green/mln/display/project_histo.hh @@ -37,6 +37,12 @@ # include <mln/accu/image/take.hh> # include <mln/accu/image/to_result.hh> +# include <mln/opt/at.hh> + +# include <mln/value/int_u8.hh> +# include <mln/value/rgb8.hh> +# include <mln/value/label_8.hh> + /// \file /// /// \brief Allow the visualization of 3d histogram. @@ -54,6 +60,10 @@ namespace mln image2d<mln_result(A)> project_histo(const image3d<V>& histo); + template <typename A, unsigned direction, typename V> + image2d<mln_result(A)> + project2_histo(const image3d<V>& histo); + # ifndef MLN_INCLUDE_ONLY /// \brief Allow the visualization of 3d histogram. @@ -86,6 +96,340 @@ namespace mln return accu::image::to_result(histo_accu); } + template <unsigned direction> + image2d<value::int_u8> + project2_histo(const image3d<unsigned>& histo) + { + image2d<value::int_u8> result; + + if (0 == direction) // blue + { + image2d<value::int_u8> arg_max(histo.ncols(), histo.nslices()); + + for (unsigned j = 0; j < histo.ncols(); ++j) + for (unsigned i = 0; i < histo.nslices(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.nrows(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + opt::at(arg_max,i,j) = pos; + } + + result = arg_max; + } + else if (1 == direction) // red + { + image2d<value::int_u8> arg_max(histo.nrows(), histo.nslices()); + + for (unsigned j = 0; j < histo.nslices(); ++j) + for (unsigned i = 0; i < histo.nrows(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.ncols(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + opt::at(arg_max,i,j) = pos; + } + + result = arg_max; + } + else // 2 == direction // green + { + image2d<value::int_u8> arg_max(histo.nrows(), histo.ncols()); + + for (unsigned j = 0; j < histo.ncols(); ++j) + for (unsigned i = 0; i < histo.nrows(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.nslices(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + opt::at(arg_max,i,j) = pos; + } + + result = arg_max; + } + + return result; + } + + template <unsigned direction> + image2d<value::label_8> + project2_histo(const image3d<unsigned>& histo, + const image3d<value::label_8>& label) + { + image2d<value::label_8> result; + + if (0 == direction) // blue + { + image2d<value::label_8> arg_max(histo.ncols(), histo.nslices()); + + for (unsigned j = 0; j < histo.ncols(); ++j) + for (unsigned i = 0; i < histo.nslices(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.nrows(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + opt::at(arg_max,i,j) = opt::at(label,i,j,pos); + } + + result = arg_max; + } + else if (1 == direction) // red + { + image2d<value::label_8> arg_max(histo.nrows(), histo.nslices()); + + for (unsigned j = 0; j < histo.nslices(); ++j) + for (unsigned i = 0; i < histo.nrows(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.ncols(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + opt::at(arg_max,i,j) = opt::at(label,pos,i,j); + } + + result = arg_max; + } + else // 2 == direction // green + { + image2d<value::label_8> arg_max(histo.nrows(), histo.ncols()); + + for (unsigned j = 0; j < histo.ncols(); ++j) + for (unsigned i = 0; i < histo.nrows(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.nslices(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + opt::at(arg_max,i,j) = opt::at(label,i,pos,j); + } + + result = arg_max; + } + + return result; + } + + + // FIXME ... determine the color of each class. + template <unsigned direction> + image2d<value::rgb8> + project3_histo(const image3d<unsigned>& histo, + const image3d<value::label_8>& label) + { + image2d<value::rgb8> result; + + if (0 == direction) // blue + { + image2d<value::rgb8> arg_max(histo.ncols(), histo.nslices()); + + for (unsigned j = 0; j < histo.ncols(); ++j) + for (unsigned i = 0; i < histo.nslices(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.nrows(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + opt::at(arg_max,i,j) = value::rgb8(i,j,pos); + } + + result = arg_max; + } + else if (1 == direction) // red + { + image2d<value::rgb8> arg_max(histo.nrows(), histo.nslices()); + + for (unsigned j = 0; j < histo.nslices(); ++j) + for (unsigned i = 0; i < histo.nrows(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.ncols(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + opt::at(arg_max,i,j) = value::rgb8(pos,i,j); + } + + result = arg_max; + } + else // 2 == direction // green + { + image2d<value::rgb8> arg_max(histo.nrows(), histo.ncols()); + + for (unsigned j = 0; j < histo.ncols(); ++j) + for (unsigned i = 0; i < histo.nrows(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.nslices(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + // FIXME ... how to fix the n of rgb + opt::at(arg_max,i,j) = value::rgb8(i,pos,j); + } + + result = arg_max; + } + + return result; + } + + template <unsigned direction> + image2d<value::rgb8> + project3_histo(const image3d<unsigned>& histo) + { + image2d<value::rgb8> result; + + if (0 == direction) // blue + { + image2d<value::rgb8> arg_max(histo.ncols(), histo.nslices()); + + for (unsigned j = 0; j < histo.ncols(); ++j) + for (unsigned i = 0; i < histo.nslices(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.nrows(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + opt::at(arg_max,i,j) = value::rgb8(i,j,pos); + } + + result = arg_max; + } + else if (1 == direction) // red + { + image2d<value::rgb8> arg_max(histo.nrows(), histo.nslices()); + + for (unsigned j = 0; j < histo.nslices(); ++j) + for (unsigned i = 0; i < histo.nrows(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.ncols(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + opt::at(arg_max,i,j) = value::rgb8(pos,i,j); + } + + result = arg_max; + } + else // 2 == direction // green + { + image2d<value::rgb8> arg_max(histo.nrows(), histo.ncols()); + + for (unsigned j = 0; j < histo.ncols(); ++j) + for (unsigned i = 0; i < histo.nrows(); ++i) + { + unsigned max = 0; // minimum as possible + signed pos = -1; + + for (unsigned k = 0; k < histo.nslices(); ++k) + { + if (max <= opt::at(histo,i,j,k)) + { + max = opt::at(histo,i,j,k); + pos = k; + } + } + + // FIXME ... how to fix the n of rgb + opt::at(arg_max,i,j) = value::rgb8(i,pos,j); + } + + result = arg_max; + } + + return result; + } + # endif // ! MLN_INCLUDE_ONLY -- 1.5.6.5

14 years, 10 months

last-svn-commit-24-g9028f28 Build translation table between number of pixels and percentage of pixels in image for the scribo database.

by green

* green/demo/labeling/regional_maxima/threshold.txt: New translation table. --- milena/sandbox/ChangeLog | 8 ++++++++ .../demo/labeling/regional_maxima/thresholds.txt | 15 +++++++++++++++ 2 files changed, 23 insertions(+), 0 deletions(-) diff --git a/milena/sandbox/ChangeLog b/milena/sandbox/ChangeLog index cbd9cdc..f34508b 100644 --- a/milena/sandbox/ChangeLog +++ b/milena/sandbox/ChangeLog @@ -1,5 +1,13 @@ 2010-01-05 Yann Jacquelet <jacquelet(a)lrde.epita.fr> + Build translation table between number of pixels and percentage of + pixels in image for the scribo database. + + * green/demo/labeling/regional_maxima/threshold.txt: New translation + table. + +2010-01-05 Yann Jacquelet <jacquelet(a)lrde.epita.fr> + Split the regional maxima binary in small atomic binaries. * green/tools/annotating/histo: New directory. diff --git a/milena/sandbox/green/demo/labeling/regional_maxima/thresholds.txt b/milena/sandbox/green/demo/labeling/regional_maxima/thresholds.txt index ddf5ca7..58f3e6a 100644 --- a/milena/sandbox/green/demo/labeling/regional_maxima/thresholds.txt +++ b/milena/sandbox/green/demo/labeling/regional_maxima/thresholds.txt @@ -5,9 +5,24 @@ image = 1169 x 1567 = 1831823 ----------------------- 0.05 % | 1000.00 1.00 % | 18318.23 + 2.00 % | 36636.46 + 3.00 % | 54954.69 + 4.00 % | 73272.92 5.00 % | 91591.15 + 6.00 % | 109909.38 + 7.00 % | 128227.61 + 8.00 % | 146545.84 + 9.00 % | 164864.07 10.00 % | 183182.30 + 11.00 % | 201500.53 + 12.00 % | 219818.76 + 13.00 % | 238136.99 + 14.00 % | 256455.22 15.00 % | 274773.45 + 16.00 % | 293091.68 + 17.00 % | 311409.91 + 18.00 % | 329728.14 + 19.00 % | 348046.37 20.00 % | 366364.60 25.00 % | 457955.75 30.00 % | 549546.90 -- 1.5.6.5

14 years, 10 months

last-svn-commit-23-g34f317b Split the regional maxima binary in small atomic binaries.

by green

* green/tools/annotating/histo: New directory. * green/tools/annotating/histo/Makefile.am: New Makefile. * green/tools/annotating/histo/histo.cc: New source file. * green/tools/annotating/opening: New directory. * green/tools/annotating/opening/Makefile.am: New Makefile. * green/tools/annotating/opening/opening.cc: New source file. * green/tools/annotating/regmax: New directory. * green/tools/annotating/regmax/Makefile.am: New Makefile. * green/tools/annotating/regmax/regmax.cc: New source file. --- milena/sandbox/ChangeLog | 14 ++ .../annotating/histo}/Makefile.am | 9 +- .../sandbox/green/tools/annotating/histo/histo.cc | 121 ++++++++++++++++++ .../annotating/opening}/Makefile.am | 9 +- .../green/tools/annotating/opening/opening.cc | 79 ++++++++++++ .../annotating/regmax}/Makefile.am | 9 +- .../green/tools/annotating/regmax/regmax.cc | 133 ++++++++++++++++++++ 7 files changed, 359 insertions(+), 15 deletions(-) copy milena/sandbox/green/{exp/annotating/nb_color => tools/annotating/histo}/Makefile.am (96%) create mode 100644 milena/sandbox/green/tools/annotating/histo/histo.cc copy milena/sandbox/green/{exp/annotating/nb_color => tools/annotating/opening}/Makefile.am (96%) create mode 100644 milena/sandbox/green/tools/annotating/opening/opening.cc copy milena/sandbox/green/{exp/annotating/nb_color => tools/annotating/regmax}/Makefile.am (96%) create mode 100644 milena/sandbox/green/tools/annotating/regmax/regmax.cc diff --git a/milena/sandbox/ChangeLog b/milena/sandbox/ChangeLog index 0947048..cbd9cdc 100644 --- a/milena/sandbox/ChangeLog +++ b/milena/sandbox/ChangeLog @@ -1,3 +1,17 @@ +2010-01-05 Yann Jacquelet <jacquelet(a)lrde.epita.fr> + + Split the regional maxima binary in small atomic binaries. + + * green/tools/annotating/histo: New directory. + * green/tools/annotating/histo/Makefile.am: New Makefile. + * green/tools/annotating/histo/histo.cc: New source file. + * green/tools/annotating/opening: New directory. + * green/tools/annotating/opening/Makefile.am: New Makefile. + * green/tools/annotating/opening/opening.cc: New source file. + * green/tools/annotating/regmax: New directory. + * green/tools/annotating/regmax/Makefile.am: New Makefile. + * green/tools/annotating/regmax/regmax.cc: New source file. + 2009-12-23 Yann Jacquelet <jacquelet(a)lrde.epita.fr> Write the opening volume thresholds for the scribo image mp00082c.ppm. diff --git a/milena/sandbox/green/exp/annotating/nb_color/Makefile.am b/milena/sandbox/green/tools/annotating/histo/Makefile.am similarity index 96% copy from milena/sandbox/green/exp/annotating/nb_color/Makefile.am copy to milena/sandbox/green/tools/annotating/histo/Makefile.am index 8e204c6..8cd7511 100644 --- a/milena/sandbox/green/exp/annotating/nb_color/Makefile.am +++ b/milena/sandbox/green/tools/annotating/histo/Makefile.am @@ -6,7 +6,6 @@ # TOOLS # ######### -LOADLIBES= -lboost_filesystem INCLUDES= -I$(HOME)/svn/oln/trunk/milena/sandbox/green #CXXFLAGS= -ggdb -O0 -Wall -W -pedantic -ansi -pipe $(INCLUDES) #CXXFLAGS= -DNDEBUG -O1 -Wall -W -pedantic -ansi -pipe $(INCLUDES) @@ -16,17 +15,17 @@ RM= rm MKDIR= mkdir -p CP= cp -SOURCE_PATTERN= green/exp -BUILD__PATTERN= green/build/exp +SOURCE_PATTERN= green/tools +BUILD__PATTERN= green/build/tools ifeq ($(findstring $(BUILD__PATTERN),$(PWD)), $(BUILD__PATTERN)) # Case where make is done from build directory. SOURCE_DIR= $(subst $(BUILD__PATTERN),$(SOURCE_PATTERN),$(PWD)) -BUILD__DIR= $(PWD)/ +BUILD__DIR= $(PWD) else # Case where make is done from source directory. -SOURCE_DIR= $(PWD)/ +SOURCE_DIR= $(PWD) BUILD__DIR= $(subst $(SOURCE_PATTERN),$(BUILD__PATTERN),$(PWD)) endif diff --git a/milena/sandbox/green/tools/annotating/histo/histo.cc b/milena/sandbox/green/tools/annotating/histo/histo.cc new file mode 100644 index 0000000..ab0b8af --- /dev/null +++ b/milena/sandbox/green/tools/annotating/histo/histo.cc @@ -0,0 +1,121 @@ +// TOOLS ==> Color histogram + +#include <iostream> + +#include <mln/accu/stat/histo3d_rgb.hh> + +#include <mln/core/macros.hh> +#include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> +#include <mln/core/image/dmorph/image_if.hh> + +#include <mln/data/compute.hh> +#include <mln/data/transform.hh> + +#include <mln/display/display_histo.hh> + +#include <mln/fun/v2v/rgb8_to_rgbn.hh> + +#include <mln/io/dump/save.hh> +#include <mln/io/pbm/load.hh> +#include <mln/io/pbm/save.hh> +#include <mln/io/pgm/load.hh> +#include <mln/io/pgm/save.hh> +#include <mln/io/ppm/load.hh> +#include <mln/io/ppm/save.hh> + +#include <mln/opt/at.hh> + +#include <mln/pw/value.hh> + +#include <mln/value/rgb8.hh> +#include <mln/value/rgb.hh> + + +template <unsigned n> +void mk_histo(const std::string& input, + const std::string& output, + const std::string& histo, + const std::string& mask) +{ + typedef mln::value::int_u8 t_int_u8; + typedef mln::value::rgb8 t_rgb8; + typedef mln::value::rgb<n> t_rgbn; + typedef mln::image2d<t_int_u8> t_image2d_int_u8; + typedef mln::image2d<t_rgb8> t_image2d_rgb8; + typedef mln::image2d<t_rgbn> t_image2d_rgbn; + typedef mln::image2d<bool> t_image2d_bool; + typedef mln::image3d<unsigned> t_histo3d; + typedef mln::fun::v2v::rgb8_to_rgbn<n> t_rgb8_to_rgbn; + typedef mln::accu::meta::stat::histo3d_rgb t_histo3d_fun; + + // START OF IMAGE PROCESSING CHAIN + t_image2d_rgb8 i0_input; // input rgb8 + t_image2d_rgbn i1_input; // input rgbn + t_image2d_bool m0_input; // mask input + t_histo3d h1_input; // histo input + t_image2d_int_u8 p1_histo; // histo proj + + mln::io::ppm::load(i0_input, input.c_str()); + i1_input = mln::data::transform(i0_input, t_rgb8_to_rgbn()); + + if (0 < mask.size()) + { + mln::io::pbm::load(m0_input, mask.c_str()); + h1_input = mln::data::compute(t_histo3d_fun(), + (i1_input | mln::pw::value(m0_input)).rw()); + } + else + { + h1_input = mln::data::compute(t_histo3d_fun(), i1_input); + } + // END OF IMAGE PROCESSING CHAIN + + // BEGIN DUMPING + p1_histo = mln::display::display_histo3d_unsigned(h1_input); + mln::io::dump::save(h1_input, histo.c_str()); + mln::io::pgm::save(p1_histo, output.c_str()); + // END DUMPING +} + + +void usage() +{ + std::cout << std::endl; + std::cout << "histo input.ppm q out.ppm histo.dump [msk.pbm]" << std::endl; + std::cout << "where" << std::endl; + std::cout << "input.ppm is the 8 bits color ppm image" << std::endl; + std::cout << "q is the degree of quanification {2,3,4,5,6,7,8}" << std::endl; + std::cout << "out.pgm is the r/g projection of the histogram" << std::endl; + std::cout << "out.dump is the quantified color histogram" << std::endl; + std::cout << "msk.pbm is the mask which select the pixels" << std::endl; + std::cout << std::endl; +} + +int main(int argc, char* args[]) +{ + if (5 == argc || 6 == argc) + { + const std::string input(args[1]); + const char q = args[2][0]; + const std::string output(args[3]); + const std::string histo(args[4]); + const std::string mask(6 == argc? args[5] : ""); + + switch(q) + { + case '2': mk_histo<2>(input, output, histo, mask); break; + case '3': mk_histo<3>(input, output, histo, mask); break; + case '4': mk_histo<4>(input, output, histo, mask); break; + case '5': mk_histo<5>(input, output, histo, mask); break; + case '6': mk_histo<6>(input, output, histo, mask); break; + case '7': mk_histo<7>(input, output, histo, mask); break; + case '8': mk_histo<8>(input, output, histo, mask); break; + default: usage(); break; + } + } + else + usage(); + + return 0; +} diff --git a/milena/sandbox/green/exp/annotating/nb_color/Makefile.am b/milena/sandbox/green/tools/annotating/opening/Makefile.am similarity index 96% copy from milena/sandbox/green/exp/annotating/nb_color/Makefile.am copy to milena/sandbox/green/tools/annotating/opening/Makefile.am index 8e204c6..8cd7511 100644 --- a/milena/sandbox/green/exp/annotating/nb_color/Makefile.am +++ b/milena/sandbox/green/tools/annotating/opening/Makefile.am @@ -6,7 +6,6 @@ # TOOLS # ######### -LOADLIBES= -lboost_filesystem INCLUDES= -I$(HOME)/svn/oln/trunk/milena/sandbox/green #CXXFLAGS= -ggdb -O0 -Wall -W -pedantic -ansi -pipe $(INCLUDES) #CXXFLAGS= -DNDEBUG -O1 -Wall -W -pedantic -ansi -pipe $(INCLUDES) @@ -16,17 +15,17 @@ RM= rm MKDIR= mkdir -p CP= cp -SOURCE_PATTERN= green/exp -BUILD__PATTERN= green/build/exp +SOURCE_PATTERN= green/tools +BUILD__PATTERN= green/build/tools ifeq ($(findstring $(BUILD__PATTERN),$(PWD)), $(BUILD__PATTERN)) # Case where make is done from build directory. SOURCE_DIR= $(subst $(BUILD__PATTERN),$(SOURCE_PATTERN),$(PWD)) -BUILD__DIR= $(PWD)/ +BUILD__DIR= $(PWD) else # Case where make is done from source directory. -SOURCE_DIR= $(PWD)/ +SOURCE_DIR= $(PWD) BUILD__DIR= $(subst $(SOURCE_PATTERN),$(BUILD__PATTERN),$(PWD)) endif diff --git a/milena/sandbox/green/tools/annotating/opening/opening.cc b/milena/sandbox/green/tools/annotating/opening/opening.cc new file mode 100644 index 0000000..3e1dbf2 --- /dev/null +++ b/milena/sandbox/green/tools/annotating/opening/opening.cc @@ -0,0 +1,79 @@ +// TOOLS ==> histogram filtering + +#include <iostream> + +#include <mln/accu/stat/histo3d_rgb.hh> + +#include <mln/core/macros.hh> +#include <mln/core/alias/neighb3d.hh> +#include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> + +#include <mln/data/compute.hh> + +#include <mln/display/display_histo.hh> + +#include <mln/io/dump/load.hh> +#include <mln/io/dump/save.hh> +#include <mln/io/pgm/load.hh> +#include <mln/io/pgm/save.hh> + +#include <mln/morpho/opening/volume.hh> + +#include <mln/value/int_u8.hh> + +void mk_opening(const std::string& input, + const unsigned min_vol, + const std::string& output, + const std::string& opened) +{ + typedef mln::value::int_u8 t_int_u8; + typedef mln::image2d<t_int_u8> t_image2d_int_u8; + typedef mln::image3d<unsigned> t_histo3d; + typedef mln::accu::meta::stat::histo3d_rgb t_histo3d_fun; + + // START OF IMAGE PROCESSING CHAIN + t_histo3d h1_input; // histo input + t_histo3d h2_input; // histo input + t_image2d_int_u8 p1_histo; // histo proj + + mln::io::dump::load(h1_input, input.c_str()); + h2_input = mln::morpho::opening::volume(h1_input, mln::c6(), min_vol); + // END OF IMAGE PROCESSING CHAIN + + // BEGIN DUMPING + p1_histo = mln::display::display_histo3d_unsigned(h2_input); + mln::io::dump::save(h2_input, opened.c_str()); + mln::io::pgm::save(p1_histo, output.c_str()); + // END DUMPING +} + + +void usage() +{ + std::cout << std::endl; + std::cout << "opening input.dump v out.dump out.ppm" << std::endl; + std::cout << "where" << std::endl; + std::cout << "input.dump is the 3d color input histo" << std::endl; + std::cout << "v is the minimum size of each composant" << std::endl; + std::cout << "out.pgm is the r/g proj of the opened histogram" << std::endl; + std::cout << "out.dump is the opened histogram" << std::endl; + std::cout << std::endl; +} + +int main(int argc, char* args[]) +{ + if (5 == argc) + { + const std::string input(args[1]); + const unsigned min_vol = atoi(args[2]); + const std::string output(args[3]); + const std::string opened(args[4]); + + mk_opening(input, min_vol, output, opened); + } + else + usage(); + + return 0; +} diff --git a/milena/sandbox/green/exp/annotating/nb_color/Makefile.am b/milena/sandbox/green/tools/annotating/regmax/Makefile.am similarity index 96% copy from milena/sandbox/green/exp/annotating/nb_color/Makefile.am copy to milena/sandbox/green/tools/annotating/regmax/Makefile.am index 8e204c6..8cd7511 100644 --- a/milena/sandbox/green/exp/annotating/nb_color/Makefile.am +++ b/milena/sandbox/green/tools/annotating/regmax/Makefile.am @@ -6,7 +6,6 @@ # TOOLS # ######### -LOADLIBES= -lboost_filesystem INCLUDES= -I$(HOME)/svn/oln/trunk/milena/sandbox/green #CXXFLAGS= -ggdb -O0 -Wall -W -pedantic -ansi -pipe $(INCLUDES) #CXXFLAGS= -DNDEBUG -O1 -Wall -W -pedantic -ansi -pipe $(INCLUDES) @@ -16,17 +15,17 @@ RM= rm MKDIR= mkdir -p CP= cp -SOURCE_PATTERN= green/exp -BUILD__PATTERN= green/build/exp +SOURCE_PATTERN= green/tools +BUILD__PATTERN= green/build/tools ifeq ($(findstring $(BUILD__PATTERN),$(PWD)), $(BUILD__PATTERN)) # Case where make is done from build directory. SOURCE_DIR= $(subst $(BUILD__PATTERN),$(SOURCE_PATTERN),$(PWD)) -BUILD__DIR= $(PWD)/ +BUILD__DIR= $(PWD) else # Case where make is done from source directory. -SOURCE_DIR= $(PWD)/ +SOURCE_DIR= $(PWD) BUILD__DIR= $(subst $(SOURCE_PATTERN),$(BUILD__PATTERN),$(PWD)) endif diff --git a/milena/sandbox/green/tools/annotating/regmax/regmax.cc b/milena/sandbox/green/tools/annotating/regmax/regmax.cc new file mode 100644 index 0000000..2079bc4 --- /dev/null +++ b/milena/sandbox/green/tools/annotating/regmax/regmax.cc @@ -0,0 +1,133 @@ +// TOOLS ==> regmax on histo + +#include <iostream> + +#include <mln/accu/stat/histo3d_rgb.hh> + +#include <mln/core/macros.hh> +#include <mln/core/alias/neighb3d.hh> +#include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> + +#include <mln/data/compute.hh> + +#include <mln/debug/println.hh> +#include <mln/display/display_histo.hh> + +#include <mln/io/dump/load.hh> +#include <mln/io/dump/save.hh> +#include <mln/io/pgm/load.hh> +#include <mln/io/pgm/save.hh> +#include <mln/io/ppm/save.hh> + +#include <mln/labeling/regional_maxima.hh> + +#include <mln/morpho/opening/volume.hh> + +#include <mln/value/label_8.hh> +#include <mln/value/int_u8.hh> +#include <mln/value/rgb8.hh> + +template <unsigned n> +struct t_labeling_rgbn : mln::Function_v2v< t_labeling_rgbn<n> > +{ + typedef mln::value::rgb<n> t_rgbn; + typedef mln::value::label_8 t_lbl8; + typedef t_rgbn argument; + typedef t_lbl8 result; + typedef mln::image3d<t_lbl8> t_label; + + const t_label& _label; + + t_labeling_rgbn(const t_label& label) : _label(label) {} + + result operator()(const argument& c) const + { + t_lbl8 tmp = mln::opt::at(_label, c.blue(), c.red(), c.green()); + + return tmp; + } +}; + +void mk_regmax(const std::string& input, + const std::string& quant, + const std::string& histo, + const std::string& label, + const std::string& output) +{ + typedef mln::value::label_8 t_lbl8; + typedef mln::value::rgb8 t_rgb8; + typedef mln::value::rgbn t_rgbn; + typedef mln::value::int_u8 t_int_u8; + typedef mln::algebra::vec<3,float> t_v3f; + typedef mln::image2d<t_int_u8> t_image2d_int_u8; + typedef mln::image2d<t_rgb8> t_image2d_rgb8; + typedef mln::image3d<t_lbl8> t_image3d_lbl8; + typedef mln::image2d<t_lbl8> t_image2d_lbl8; + typedef mln::image3d<unsigned> t_histo3d; + typedef mln::accu::meta::stat::histo3d_rgb t_histo3d_fun; + typedef mln::accu::stat::mean<t_v3f,t_v3f,t_v3f> t_mean; + typedef mln::util::array<t_v3f> t_mean_array; + + t_image2d_rgb8 i0_input; // input img + t_image2d_rgbn i1_input; // quant img + t_histo3d h2_input; // opened histo +// t_image2d_int_u8 p2_label; // histo proj + t_image2d_lbl8 p2_label; // histo proj +// t_image2d_rgb8 p2_label; // histo proj + t_image3d_lbl8 l2_histo; // label histo + t_mean_array m2_label; // palette + + t_lbl8 n_lbl; // nb class + + // BEGIN LOADING + mln::io::ppm::load(i0_input, input.c_str()); + mln::io::ppm::load(i1_input, quant.c_str()); + mln::io::dump::load(h2_input, histo.c_str()); + // END LOADING + + // BEGIN IMAGE PROCESSING + l2_histo = mln::labeling::regional_maxima(h2_input, mln::c6(), n_lbl); + // END IMAGE PROCESSING + + // BEGIN SAVING + mln::debug::println(h2_input); + mln::io::dump::save(l2_histo, labeled.c_str()); + + l2_input = mln::data::transform(i1_input, t_labeling_rgbn<n>(l2_histo)); + m2_label = mln::labeling::compute(t_mean(), i0_input, l2_input, n_labels); + p2_label =mln::display::display3_histo3d_unsigned(h2_input,l2_histo,m2_label); + +// mln::io::pgm::save(p2_label, output.c_str()); + mln::io::ppm::save(p2_label, output.c_str()); + std::cout << "Nb classes : " << n_lbl << std::endl; + // END SAVING +} + + +void usage() +{ + std::cout << std::endl; + std::cout << "regmax input.dump out.dump out.ppm" << std::endl; + std::cout << "where" << std::endl; + std::cout << "input.dump is opened histo" << std::endl; + std::cout << "out.pgm is the r/g proj of the opened histogram" << std::endl; + std::cout << "out.dump is the labeled histogram" << std::endl; + std::cout << std::endl; +} + +int main(int argc, char* args[]) +{ + if (4 == argc) + { + const std::string input(args[1]); + const std::string output(args[2]); + const std::string labeled(args[3]); + + mk_regmax(input, output, labeled); + } + else + usage(); + + return 0; +} -- 1.5.6.5

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Olena-patches February 2010