Olena-patches November 2011

olena-patches@lrde.epita.fr

5 participants
178 discussions

by Guillaume Lazzara

--- Makefile.am | 11 ++++++++--- doc/Makefile.am | 25 +++++++++++++++---------- 2 files changed, 23 insertions(+), 13 deletions(-) diff --git a/Makefile.am b/Makefile.am index 677a9c3..ef6090a 100644 --- a/Makefile.am +++ b/Makefile.am @@ -1,5 +1,5 @@ -# Copyright (C) 2006, 2007, 2008, 2009, 2010 EPITA Research and Development -# Laboratory (LRDE). +# Copyright (C) 2006, 2007, 2008, 2009, 2010, 2011 EPITA Research and +# Development Laboratory (LRDE). # # This file is part of Olena. # @@ -17,7 +17,7 @@ ACLOCAL_AMFLAGS = -I m4 -SUBDIRS = build-aux doc external milena +SUBDIRS = build-aux external milena if ENABLE_SWILENA SUBDIRS += swilena @@ -27,6 +27,11 @@ if ENABLE_SCRIBO SUBDIRS += scribo endif ENABLE_SCRIBO +# We rely on Automake to ensure that the documentions are generated in +# the right order. Here, we make sure that the general documentation +# will be generated after milena's and scribo'd documentation. +SUBDIRS += doc + # Target shortcuts delegating the actual action to milena/Makefile. LOCAL_RECURSIVE_TARGETS = pretty-check tests $(LOCAL_RECURSIVE_TARGETS): diff --git a/doc/Makefile.am b/doc/Makefile.am index 099b497..8a45e4e 100644 --- a/doc/Makefile.am +++ b/doc/Makefile.am @@ -35,9 +35,6 @@ TEXI2DVI_FLAGS += \ -I $(srcdir) -I $(srcdir)/outputs -I $(srcdir)/outputs/split \ -I $(srcdir)/img -I $(srcdir)/examples/split -# Additional files for LaTeX compilations. -DOC_PACKAGES = doxyfuns.sty milena.sty - # ----------------------- # # User Reference Manual. # @@ -55,27 +52,38 @@ DOXYFILE_USER = Doxyfile_user # Images -REFMAN_IMAGES = $(srcdir)/images/olena_layers.png -EXTRA_DIST = $(REFMAN_IMAGES) +REFMAN_IMAGES = \ + $(srcdir)/images/olena_layers.png \ + $(srcdir)/images/logo.jpg + +EXTRA_DIST = \ + $(REFMAN_IMAGES) \ + $(srcdir)/images/olena_layers.svg # Documentation content REFMAN_deps = $(srcdir)/footer.html \ $(srcdir)/header.html \ $(srcdir)/doxygen.css \ $(srcdir)/mainpage.dox \ + $(srcdir)/about.dox \ $(srcdir)/DoxygenLayout.xml \ $(srcdir)/modules_list.dox \ $(srcdir)/olena.bib \ + $(srcdir)/lrde.bib \ + $(srcdir)/doc.bib \ $(srcdir)/contributors.dox \ $(srcdir)/bibliography.dox \ $(srcdir)/license.dox \ $(srcdir)/license_commercial.dox \ $(srcdir)/online_resources.dox \ $(srcdir)/get_sources.dox \ + $(srcdir)/subdoc_footer.html \ contributors.html \ lrde_olena.html \ $(REFMAN_IMAGES) + + # Sed is used to generate Doxyfile from Doxyfile.in instead of # configure, because the former is way faster than the latter. # @@ -142,13 +150,13 @@ contributors.html: $(top_srcdir)/AUTHORS ## Bibliography. ## ## -------------- ## -# Warning: also generate lrde_olena.cite +# Warning: also generates lrde_olena.cite lrde_olena.bib: bib2bib -s plain -oc lrde_olena.cite -ob lrde_olena.bib -c \ 'project = "Image" or project = "Olena"' \ -s year -r $(srcdir)/lrde.bib -# Warning: also generate lrde_olena_bib.html +# Warning: also generates lrde_olena_bib.html lrde_olena.html: lrde_olena.bib bibtex2html -s plain -nokeywords -citefile lrde_olena.cite \ -noabstract -nofooter -labelname -nodoc -linebreak -nf urllrde PDF lrde_olena.bib @@ -163,11 +171,8 @@ MAINTAINERCLEANFILES += lrde_olena.cite \ ## Cleaning. ## ## ---------- ## -MAINTAINERCLEANFILES += $(dist_pdf_DATA) - maintainer-clean-local: -rm -rf $(USER_REFMAN).tmp $(srcdir)/$(USER_REFMAN) - -rm -rf $(DEVEL_REFMAN).tmp $(srcdir)/$(DEVEL_REFMAN) -for d in $(DATA_html_dirs); do \ rm -rf $$d.tmp $(srcdir)/$$d; \ done -- 1.7.2.5

13 years

olena-2.0-27-gd821327 Move logo

by Guillaume Lazzara

--- doc/Doxyfile.in | 2 +- doc/{ => images}/logo.jpg | Bin 7477 -> 7477 bytes milena/doc/Doxyfile.in | 2 +- scribo/doc/Doxyfile.in | 2 +- 4 files changed, 3 insertions(+), 3 deletions(-) rename doc/{ => images}/logo.jpg (100%) diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in index 777a6ac..51b712a 100644 --- a/doc/Doxyfile.in +++ b/doc/Doxyfile.in @@ -22,7 +22,7 @@ PROJECT_NAME = "Olena" PROJECT_NUMBER = "@PACKAGE_VERSION@" PROJECT_BRIEF = "An Image Processing Platform" -PROJECT_LOGO = @top_srcdir@/doc/logo.jpg +PROJECT_LOGO = @top_srcdir@/doc/images/logo.jpg OUTPUT_DIRECTORY = @builddir@/user-refman.tmp CREATE_SUBDIRS = NO OUTPUT_LANGUAGE = English diff --git a/doc/logo.jpg b/doc/images/logo.jpg similarity index 100% rename from doc/logo.jpg rename to doc/images/logo.jpg diff --git a/milena/doc/Doxyfile.in b/milena/doc/Doxyfile.in index 5cbaaef..b695b77 100644 --- a/milena/doc/Doxyfile.in +++ b/milena/doc/Doxyfile.in @@ -23,7 +23,7 @@ PROJECT_NAME = "Milena" PROJECT_NUMBER = "@PACKAGE_VERSION@" PROJECT_BRIEF = "An Image Processing Platform" -PROJECT_LOGO = @top_srcdir@/doc/logo.jpg +PROJECT_LOGO = @top_srcdir@/doc/images/logo.jpg OUTPUT_DIRECTORY = @builddir@/user-refman.tmp CREATE_SUBDIRS = YES OUTPUT_LANGUAGE = English diff --git a/scribo/doc/Doxyfile.in b/scribo/doc/Doxyfile.in index 4207145..1986828 100644 --- a/scribo/doc/Doxyfile.in +++ b/scribo/doc/Doxyfile.in @@ -22,7 +22,7 @@ PROJECT_NAME = "Scribo" PROJECT_NUMBER = "User documentation @PACKAGE_VERSION@" PROJECT_BRIEF = "An Image Processing Platform" -PROJECT_LOGO = @top_srcdir@/doc/logo.jpg +PROJECT_LOGO = @top_srcdir@/doc/images/logo.jpg OUTPUT_DIRECTORY = @builddir@/user-refman.tmp CREATE_SUBDIRS = YES OUTPUT_LANGUAGE = English -- 1.7.2.5

13 years

[Olena] #247: mln_min() of a floating type is not the effective minimum of the range value

by Olena Trac

#247: mln_min() of a floating type is not the effective minimum of the range value -----------------------------------------------------+---------------------- Reporter: David Coeurjolly and Julien Marquegnies | Owner: Olena Team Type: defect | Status: new Priority: critical | Milestone: Component: Milena | Version: 2.0 Keywords: | -----------------------------------------------------+---------------------- According to David Coeurjolly {{{ int main() { mln::accu::stat::max<double> mm; mm.init(); mm.take(-0.02); mm.take(-0.92); mm.take(-0.03); std::cout<<" max= "<<mm.to_result()<<std::endl; } }}} In many situations (w/o init, w/o 'to_result() method in the ostream), I always get a wrong value (2.22-308, which seems to be min_val for positive double). Julien Marquegnies confirmed that mln_min(double) or mln_min(float) returns DBL_MIN instead of -DBL_MAX. According to the meaning of mln_min/max which are supposed to give the lower and upper bounds of the range values, returning -DBL_MAX '''should''' fix the issue. -- Ticket URL: <https://trac.lrde.org/olena/ticket/247> Olena <http://olena.lrde.epita.fr> Olena, a software platform dedicated to image processing.

13 years

olena-2.0-44-gae6f6e5 mln/io/dicom/load.hh: Update comments.

by Guillaume Lazzara

--- milena/ChangeLog | 4 ++++ milena/mln/io/dicom/load.hh | 2 +- 2 files changed, 5 insertions(+), 1 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index ecf9a42..cd7886f 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,7 @@ +2011-11-25 Guillaume Lazzara <z(a)lrde.epita.fr> + + * mln/io/dicom/load.hh: Update comments. + 2011-11-24 Guillaume Lazzara <z(a)lrde.epita.fr> Improve io::dump tests with floating values. diff --git a/milena/mln/io/dicom/load.hh b/milena/mln/io/dicom/load.hh index 7369c0f..ece9b9d 100644 --- a/milena/mln/io/dicom/load.hh +++ b/milena/mln/io/dicom/load.hh @@ -60,7 +60,7 @@ namespace mln Common compilation flags to link to gdcm if this file is used: - -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF -lgdcmexpat -lgdcmjpeg12 -lgdcmjpeg16 -lgdcmjpeg8 -lgdcmopenjpeg -lgdcmuuid -lgdcmzlib + -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF -lgdcmjpeg12 -lgdcmjpeg16 -lgdcmjpeg8 */ template <typename I> -- 1.7.2.5

13 years, 1 month

branch next updated: olena-2.0-18-g6c73505

by git＠lrde.epita.fr

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "Olena, a generic and efficient image processing platform". The branch next has been updated via 6c73505ca244e78dfc6557fe69387381d2e81916 (commit) from 861239963254a72f51b25bfd8323a12ff4a58b82 (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- 6c73505 Update lrde-scmstats.sh. ----------------------------------------------------------------------- Summary of changes: ChangeLog | 8 ++++++++ lrde-scmstats.sh | 21 ++++++++++++--------- 2 files changed, 20 insertions(+), 9 deletions(-) hooks/post-receive -- Olena, a generic and efficient image processing platform

13 years, 1 month

olena-2.0-18-g6c73505 Update lrde-scmstats.sh.

by Roland Levillain

* lrde-scmstats.sh: Look more like lrde-upload.sh. Ensure generated data is readable from the Web. Anonymize some names as requested by some contributors. --- ChangeLog | 8 ++++++++ lrde-scmstats.sh | 21 ++++++++++++--------- 2 files changed, 20 insertions(+), 9 deletions(-) diff --git a/ChangeLog b/ChangeLog index 75e4788..31ebcf6 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,11 @@ +2011-11-25 Roland Levillain <roland(a)lrde.epita.fr> + + Update lrde-scmstats.sh. + + * lrde-scmstats.sh: Look more like lrde-upload.sh. + Ensure generated data is readable from the Web. + Anonymize some names as requested by some contributors. + 2011-11-24 Guillaume Lazzara <z(a)lrde.epita.fr> * distrib/macports/Portfile.in: Fix maintainers field. diff --git a/lrde-scmstats.sh b/lrde-scmstats.sh index 859f100..f1f0073 100755 --- a/lrde-scmstats.sh +++ b/lrde-scmstats.sh @@ -17,7 +17,7 @@ # along with Olena. If not, see <http://www.gnu.org/licenses/>. -# This file is run by the LRDE autobuilder before compilation. +# This file is run by the LRDE autobuilder before the build. # It is not meant to be distributed with Olena. set -ex @@ -25,19 +25,22 @@ set -ex # Buildbot will tell us the name of the branch being compiled using $1. branch=$1 -# We might want to filter stats for specific branches. -# Currently gitstats does not allow that. +# Filter stats for specific branches. case "$branch" in -# # Consider these branches only. + # Consider these branches only. master|next|swilena|mesh-segm-skel|stable/scribo|unstable/scribo) ;; -# # Don't upload other branches. + # Don't compute statistics for other branches. *) exit ;; esac -DEST=/lrde/dload/olena/stats/ +subdir=$branch +DEST=/lrde/dload/olena/stats/$subdir -# option '-c commit_end=$branch' is not needed since buildbot and git -# only checkout the current branch as 'master'. -gitstats . $DEST/$branch +# Compute statistics. +gitstats . $DEST +# Anonymize some names. +find "$DEST" -name "*.html" -exec sed -i 's/J.r.me Darbon/JD/g' {} \; +# Expose uploaded files. +chmod -R a+rX $DEST -- 1.7.2.5

13 years, 1 month

branch apps-morphers updated: olena-2.0-15-gbd2670f

by git＠lrde.epita.fr

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "Olena, a generic and efficient image processing platform". The branch apps-morphers has been updated discards 1c0192b12c825aa99845049dec9f41b4a63585d7 (commit) discards d10d4508a41f5d5709cdfe65a03c5298226d7dac (commit) discards 8d55a9e8af616eaf0dd3521699fb264ef4500d1d (commit) via bd2670fbf582fc5c238507bdb3d9543d5bcb0577 (commit) via 849c13701f8eb2e08d838979c7b3539332cf099a (commit) via dcad6adc4a6b9469f79c055f1c2a5138c74e6f29 (commit) This update added new revisions after undoing existing revisions. That is to say, the old revision is not a strict subset of the new revision. This situation occurs when you --force push a change and generate a repository containing something like this: * -- * -- B -- O -- O -- O (1c0192b12c825aa99845049dec9f41b4a63585d7) \ N -- N -- N (bd2670fbf582fc5c238507bdb3d9543d5bcb0577) When this happens we assume that you've already had alert emails for all of the O revisions, and so we here report only the revisions in the N branch from the common base, B. Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- bd2670f New morpher example: recording a watershed transform. 849c137 Work around decorated_image's lack of properties, for the recorder. dcad6ad Fix the initialization of mln::decorated_image. ----------------------------------------------------------------------- Summary of changes: hooks/post-receive -- Olena, a generic and efficient image processing platform

13 years, 1 month

branch apps-morphers updated: olena-2.0-15-g1c0192b

by git＠lrde.epita.fr

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "Olena, a generic and efficient image processing platform". The branch apps-morphers has been updated via 1c0192b12c825aa99845049dec9f41b4a63585d7 (commit) via d10d4508a41f5d5709cdfe65a03c5298226d7dac (commit) via 8d55a9e8af616eaf0dd3521699fb264ef4500d1d (commit) from 21c2800d395c87adb3e456adb3a2f1ece83fe0fd (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- 1c0192b New morpher example: recording a watershed transform. d10d450 Work around decorated_image's lack of properties, for the recorder. 8d55a9e * mln/tag/init.hh (tag::data_t): New tag type. (tag::data): New tag. * mln/core/image/imorph/decorated_image.hh (init_(tag::data_t, D&, const decorated_image<I,D>&)) (init_(tag::data_t, D&, const decorated_image<I,D2>&)) (init_(tag::image_t, decorated_image<I,D>&, const J&)): New functions. ----------------------------------------------------------------------- Summary of changes: milena/ChangeLog | 37 ++++++++ milena/apps/morphers/Makefile.am | 3 + milena/apps/morphers/mask+channel.cc | 7 +- milena/apps/morphers/mask+recorder.cc | 6 +- milena/apps/morphers/recorder-wst.cc | 106 +++++++++++++++++++++++ milena/apps/morphers/recorder.cc | 5 +- milena/apps/morphers/recorder.hh | 77 +++++++++++++++-- milena/mln/core/image/imorph/decorated_image.hh | 26 ++++++ milena/mln/tag/init.hh | 3 + 9 files changed, 250 insertions(+), 20 deletions(-) create mode 100644 milena/apps/morphers/recorder-wst.cc hooks/post-receive -- Olena, a generic and efficient image processing platform

13 years, 1 month

olena-2.0-15-gbd2670f New morpher example: recording a watershed transform.

by Roland Levillain

* apps/morphers/recorder-wst.cc: New. * apps/morphers/Makefile.am (noinst_PROGRAMS): Add recorder-wst. (recorder_wst_SOURCES): New. (MOSTLYCLEANFILES): lena-wst??????.ppm. --- milena/ChangeLog | 9 +++ milena/apps/morphers/Makefile.am | 3 + milena/apps/morphers/recorder-wst.cc | 106 ++++++++++++++++++++++++++++++++++ 3 files changed, 118 insertions(+), 0 deletions(-) create mode 100644 milena/apps/morphers/recorder-wst.cc diff --git a/milena/ChangeLog b/milena/ChangeLog index 4b904dc..2b98497 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,14 @@ 2011-11-24 Roland Levillain <roland(a)lrde.epita.fr> + New morpher example: recording a watershed transform. + + * apps/morphers/recorder-wst.cc: New. + * apps/morphers/Makefile.am (noinst_PROGRAMS): Add recorder-wst. + (recorder_wst_SOURCES): New. + (MOSTLYCLEANFILES): lena-wst??????.ppm. + +2011-11-24 Roland Levillain <roland(a)lrde.epita.fr> + Work around decorated_image's lack of properties, for the recorder. * apps/morphers/recorder.hh diff --git a/milena/apps/morphers/Makefile.am b/milena/apps/morphers/Makefile.am index d448c1d..a3b9a41 100644 --- a/milena/apps/morphers/Makefile.am +++ b/milena/apps/morphers/Makefile.am @@ -25,15 +25,18 @@ AM_CXXFLAGS = $(APPS_CXXFLAGS) noinst_PROGRAMS = \ mask+channel \ recorder \ + recorder-wst \ mask+recorder mask_channel_SOURCES = mask+channel.cc recorder_SOURCES = recorder.cc recorder.hh +recorder_wst_SOURCES = recorder-wst.cc recorder.hh mask_recorder_SOURCES = mask+recorder.cc recorder.hh MOSTLYCLEANFILES = \ lena-mask-channel.ppm \ lena-fill??????.ppm \ + lena-wst??????.ppm \ lena-roi-fill??????.ppm # FIXME: Also produce movies (see comments in recorder.cc and diff --git a/milena/apps/morphers/recorder-wst.cc b/milena/apps/morphers/recorder-wst.cc new file mode 100644 index 0000000..e4aade5 --- /dev/null +++ b/milena/apps/morphers/recorder-wst.cc @@ -0,0 +1,106 @@ +// Copyright (C) 2011 EPITA Research and Development Laboratory (LRDE) +// +// This file is part of Olena. +// +// Olena is free software: you can redistribute it and/or modify it under +// the terms of the GNU General Public License as published by the Free +// Software Foundation, version 2 of the License. +// +// Olena 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 Olena. If not, see <http://www.gnu.org/licenses/>. +// +// As a special exception, you may use this file as part of a free +// software project 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. + +/// \file +/// \brief Exercise a morpher recording every change in the morphed +/// image with the watershed transform. +/// +/// To produce an AVI movie from the `lena-wst*.ppm' files, use: +/// +/// for f in lena-wst*ppm; convert $f -scale 2500% $(basename $f .ppm).png +/// mencoder "mf://lena-wst*.png" -o lena-wst.avi -ovc lavc -lavcopts vcodec=mjpeg +/// +/// The output `lena-wst.avi' can be embedded in a PDF file. */ + +#include <string> + +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> + +#include <mln/value/int_u8.hh> +#include <mln/value/label_8.hh> +#include <mln/value/rgb8.hh> +#include <mln/literal/colors.hh> + +#include <mln/morpho/gradient.hh> +#include <mln/morpho/closing/area.hh> +#include <mln/morpho/watershed/flooding.hh> + +#include <mln/test/predicate.hh> +#include <mln/pw/value.hh> + +#include <mln/labeling/colorize.hh> + +#include <mln/io/pgm/load.hh> +#include <mln/io/ppm/save.hh> + +#include "apps/morphers/recorder.hh" + +#include "apps/data.hh" + + +int main() +{ + using namespace mln; + using mln::value::int_u8; + using mln::value::label_8; + + typedef image2d<int_u8> I; + I lena = io::pgm::load<int_u8>(MLN_IMG_DIR "/tiny.pgm"); + + // Gradient. + I grad = morpho::gradient(lena, win_c4p()); + // Simplification of the gradient. + unsigned lambda = 5; + I closed_grad = morpho::closing::area(grad, c4(), lambda); + // Attach recorder to closed gradient. + decorated_image< I, recorder<I> > closed_grad_rec = record(closed_grad); + + // Watershed transform. + typedef label_8 L; + L nbasins; + typedef mln_ch_value_(I, L) J; + decorated_image< J, recorder<J> > wst_rec = + morpho::watershed::flooding(closed_grad_rec, c4(), nbasins); + std::cout << nbasins << std::endl; + + // Dump recorded frames. + /* FIXME: Hand-made (it partly duplicates ppm::save() for + decorated_image's). We should be able to process sequences of + images. */ + for (size_t i = 0; i < wst_rec.decoration().sequence.size(); ++i) + { + J frame = wst_rec.decoration().sequence[i]; + + // Skip ``empty'' frames. + if (test::predicate(frame.domain(), pw::value(frame) == 0)) + continue; + + std::stringstream s; + s << std::setfill ('0') << std::setw (6) << i; + io::ppm::save(labeling::colorize(value::rgb8(), frame, nbasins), + std::string("lena-wst") + s.str() + ".ppm"); + } +} -- 1.7.2.5

13 years, 1 month

olena-2.0-15-g1c0192b New morpher example: recording a watershed transform.

by Roland Levillain

13 years, 1 month

← Newer
1
...
6
7
8
9
10
11
12
...
18
Older →

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Olena-patches November 2011