June 2009 - Olena-patches

milena r4084: Correct errors in tutorial
by Edwin Carlinet 10 Jun '09

10 Jun '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena ChangeLog: 2009-06-10 Edwin Carlinet <carlinet(a)lrde.epita.fr> Correct errors in tutorial. * tutorial.tex: Correct errors. --- tutorial.tex | 61 +++++++++++++++++++++++++++++++---------------------------- 1 file changed, 33 insertions(+), 28 deletions(-) Index: trunk/milena/doc/tutorial/tutorial.tex =================================================================== --- trunk/milena/doc/tutorial/tutorial.tex (revision 4083) +++ trunk/milena/doc/tutorial/tutorial.tex (revision 4084) @@ -34,6 +34,7 @@ %\usepackage{hevea} + \usepackage{html} \usepackage{graphicx} \usepackage{makeidx} @@ -44,6 +45,10 @@ \usepackage{doxyfuns} \usepackage{milena} +\newcommand{\tofix}[1]{\colortext{red}{(FIXME: #1)}} +%\newcommand{\tofix}[1]{} + + \title{Olena -- Tutorial} \author{LRDE} \date{} @@ -109,29 +114,29 @@ \textit{providers}. \textit{End users} want to apply and assemble algorithms to solve image processing, pattern recognition or computer vision problems, \textit{designers} build new algorithms and \textit{providers} are interested -in developping their own data structures and extend an existing library. +in developing their own data structures and extend an existing library. Whatever the kind of user you are, the key to learning how to use Milena is to become familiar with its palette of objects and the way of combining them. As an \textit{end user}, you may start with this simple tutorial and the Quick -tour (FIXME: ref). They describe and illustrate the key features of the library. +tour \tofix{ref}. They describe and illustrate the key features of the library. \textit{End users} getting familiar with Milena and \textit{designers}, should -take a look at the Quick Reference Guide (FIXME: ref!). +take a look at the Quick Reference Guide \tofix{ref!}. It is a more detailed explanations of the library's features. \textit{end users} and \textit{designers} may be also interested by all the examples provided with the documentation and the tutorial. The source code is -available in \hpath{milena/doc/examples} (FIXME: ref) and is usually pointed +available in \hpath{milena/doc/examples} \tofix{ref} and is usually pointed out and commented by the documentation. Taking a look at the test suite is also a good idea. The tests usually focus on a single functionality and handle several use cases which may overlap your needs. -The test suite is located in \hpath{milena/tests} (FIXME: ref?). +The test suite is located in \hpath{milena/tests} \tofix{ref?}. Still not enough information? More information about all the routines is -available in the User HTML documentation (FIXME:ref). +available in the User HTML documentation \tofix{ref}. It mainly targets \textit{designers} and \textit{providers}. The latter may also be interested by the Developer HTML documentation (not available yet). @@ -223,7 +228,7 @@ (section \ref{tuto1dirstruct}). If you encounter any issues in the installation process or if you have any question, do not forget to join the mailing lists (section \ref{tuto1mailinglists}) -and/or use the other documentations ressources (section ref{tuto1documentation}). +and/or use the other documentations resources (section ref{tuto1documentation}). @@ -265,7 +270,7 @@ (section \ref{tuto1dirstruct}). If you encounter any issues in the installation process or if you have any question, do not forget to join the mailing lists (section -\ref{tuto1mailinglists}) and/or use the other documentations ressources +\ref{tuto1mailinglists}) and/or use the other documentations resources (section \ref{tuto1documentation})). @@ -288,7 +293,7 @@ \textbf{Olena-patches} & patches for the Olena project \\ \end{tabular} -You can subscribe to these mailing lists at the following adress: +You can subscribe to these mailing lists at the following address: \begin{center} \begin{verbatim} @@ -313,7 +318,7 @@ List of \hpath{milena}'s subdirectories: \begin{itemize} -\item \dir{apps} --- A full example of a 3D mesh visualization tool. It +\item \dir{apps} --- A full example of a 3D mesh visualisation tool. It uses milena. \item \dir{doc} --- THE directory you must know. Contains all the @@ -325,7 +330,7 @@ \item \dir{mesh} --- A set of 3D meshes. They can be used with the full example located in \hpath{milena/apps}. -\item \dir{mln} --- The core of the libray. Contains all the library headers. +\item \dir{mln} --- The core of the library. Contains all the library headers. \item \dir{tests} --- The test suite. Is it subdivided in sub directories. The directory hierarchy respects \hpath{milena/mln}'s. @@ -368,7 +373,7 @@ \item \dir{logical} --- Logical operators. \item \dir{make} --- Small routines to construct images, windows, \ldots \item \dir{math} --- Mathematical functions. - \item \dir{metal} --- Metalic macros/structures. Static library helping + \item \dir{metal} --- Metallic macros/structures. Static library helping developing doing static tests. \item \dir{morpho} --- Mathematical morphology. \item \dir{norm} --- Norm computation. @@ -377,7 +382,7 @@ \item \dir{pw} --- Point-wise image related routines. \item \dir{registration} -- Registration related routine. \item \dir{set} --- Set related routines. - \item \dir{subsampling} --- Subsampling related algorithms. + \item \dir{subsampling} --- Sub-sampling related algorithms. \item \dir{tag} --- Tag traits. \item \dir{test} --- Definition of predicates. \item \dir{topo} --- Complex related structures. @@ -444,7 +449,7 @@ %************************** \doxysection{tuto1community}{Community and Support} -Even though Milena is currently developped by the LRDE in EPITA, we are open +Even though Milena is currently developed by the LRDE in EPITA, we are open for new contributors. \begin{itemize} @@ -478,13 +483,13 @@ \begin{itemize} \item Olena's trac\\ \href{https://trac.lrde.org/olena}{https://trac.lrde.org/olena} \\ - Here is the roadmap, the current open tickets/bugs/improvements which + Here is the road-map, the current open tickets/bugs/improvements which are taken in consideration. A source browser is also available. \item Olena's Buildfarm \\ \href{https://buildfarm.lrde.org/buildfarm/oln/}{https://buildfarm.lrde.org/buildfarm/oln/} \\ - The official buildfarm. Every night and after each commit, tests - are compiled and run. The buildfarm can show you whether it is safe + The official build-farm. Every night and after each commit, tests + are compiled and run. The build-farm can show you whether it is safe to update your svn copy of Milena or not\ldots \item Test failures \\ @@ -729,9 +734,9 @@ Currently two tools are available: \\ \begin{tabular}{l l} -area\_flooding.cc & FIXME:description \\ +area\_flooding.cc & \tofix{description} \\ \hline -seed2tiling.cc & FIXME:description \\ +seed2tiling.cc & \tofix{description} \\ \end{tabular} % @@ -757,7 +762,7 @@ $ make check \end{verbatim} -Running the test suite is memory and CPU consumming and will take a while. +Running the test suite is memory and CPU consuming and will take a while. %************************** @@ -809,14 +814,14 @@ So, what would happen if we would like to use it for 3D images, use rgb8 as value or even work on a region of interest? -This implementation would require to be reimplemented and the user would have to +This implementation would require to be re-implemented and the user would have to deal with the various versions of the fill routine. For the developer, it is error prone, redundant and hard to maintain. For the user, it is confusing and forces to always think about what he is manipulating. According to our definition, this algorithm is clearly \B{not} generic. -This is not acceptable and that's why Milena is developped considering -genericity and user/developer friendlyness. +This is not acceptable and that's why Milena is developed considering +genericity and user/developer friendliness. With Milena, the previous example would be written as follow: @@ -861,14 +866,14 @@ instance an image of type \type{image2d} inherits from \type{Image$<$image2d$>$}. So an \type{image2d} is an \type{Image$<$I$>$}. Note that the return type of this function is defined by a macro. -\code{mln\_concrete} is a macro hidding tricky mechanisms (traits) used in Milena. +\code{mln\_concrete} is a macro hiding tricky mechanisms (traits) used in Milena. The important point to remember is that a generic function should not return \type{I} directly but \code{mln\_concrete(I)} instead. \doxycode[3]{tuto3_first_routine} Like any Milena's routine, note that we use \code{trace}. This debugging tool -will be detailled in section \ref{tuto3debughints}. +will be detailed in section \ref{tuto3debughints}. \doxycode[4]{tuto3_first_routine} @@ -876,7 +881,7 @@ be used as such. Indeed, concepts are empty shells only used for dispatching and concept checking, that's the reason why they are parameterized with their exact type. The exact type let us know what is the real type of the object. To get an -objet with the exact type, simply call \code{exact()}. +object with the exact type, simply call \code{exact()}. Of course, it is always a good idea to add few preconditions to help during debug. @@ -1035,7 +1040,7 @@ \doxysubsection{tuto3traces}{Traces} Sometimes, compiling for GDB without optimization flags and with debug -assertions enabled could lead to execution time dramaticaly high. +assertions enabled could lead to execution time dramatically high. If the function parameter values are not necessary for debugging, a good alternative is the trace system provided in Milena. Each time a routine is called, a trace log is written. @@ -1205,7 +1210,7 @@ %==================================== \doxychapter{tuto5}{Load and save images} -After this step you shoud know how to: +After this step you should know how to: \begin{itemize} \item load an image, \item save an image.

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[Olena] #155: Reuse existing script to factor the Makefile machinery in Swilena
by Olena 10 Jun '09

10 Jun '09

#155: Reuse existing script to factor the Makefile machinery in Swilena -------------------------+-------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: enhancement | Status: new Priority: minor | Milestone: Olena 1.0 Component: Swilena | Version: 1.0 Keywords: | -------------------------+-------------------------------------------------- For instance, there are parts to be factored in source:trunk/swilena/python/Makefile.am. See what TC, Olena 0.11 and clspr used. -- Ticket URL: <https://trac.lrde.org/olena/ticket/155> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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Re: [Olena-patches] [Olena] #89: Add three levels of tests
by Olena Trac 10 Jun '09

10 Jun '09

#89: Add three levels of tests --------------------------+------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: enhancement | Status: new Priority: minor | Milestone: Olena 1.1 Component: Milena | Version: 1.0 Resolution: | Keywords: --------------------------+------------------------------------------------- Changes (by levill_r): * milestone: Olena 1.0 => Olena 1.1 -- Ticket URL: <https://trac.lrde.org/olena/ticket/89#comment:2> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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[Olena] #184: Clean the bread-first thinning (skeleton) algorithm
by Olena Trac 10 Jun '09

10 Jun '09

#184: Clean the bread-first thinning (skeleton) algorithm ----------------------+----------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: defect | Status: new Priority: major | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Keywords: | ----------------------+----------------------------------------------------- * Use `image_if` and operator `|` when it is compatible with `complex_image` in source:trunk/milena/apps/statues/mesh_complex_skel.cc. * Likewise in source:trunk/milena/mln/topo/detach.hh. * Use a cell iterator (when available) in the implementation of `mln::make::cell` (source:trunk/milena/mln/make/cell.hh). * Make `mln::topo::is_facet` (source:trunk/milena/mln/topo/is_facet.hh) a method of `mln::complex_psite` (or even of `mln::topo::face`). * Address various `FIXME`s in source:trunk/milena/mln/topo/skeleton/breadth_first_thinning.hh. * Implement the other algorithm (''A1'') from couprie.08.pami to check the simplicity of a cell in source:trunk/milena/mln/topo/is_simple_cell (and factor). -- Ticket URL: <https://trac.lrde.org/olena/ticket/184> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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[PATCH 2/2] Set flags for optional dependencies in tests.
by Roland Levillain 10 Jun '09

10 Jun '09

* tests/tests.mk (GDCM_CPPFLAGS, GDCM_LDFLAGS) (CFITSIO_CPPFLAGS, CFITSIO_LDFLAGS) (MAGICKXX_CPPFLAGS, MAGICKXX_LDFLAGS) (TIFF_CPPFLAGS, TIFF_LDFLAGS): New variables. --- milena/ChangeLog | 11 +++++++++++ milena/tests/tests.mk | 16 ++++++++++++++++ 2 files changed, 27 insertions(+), 0 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index b6992d2..c977f5a 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,14 @@ +2009-06-10 Roland Levillain <roland(a)lrde.epita.fr> + + Set flags for optional dependencies in tests. + + * tests/tests.mk + (GDCM_CPPFLAGS, GDCM_LDFLAGS) + (CFITSIO_CPPFLAGS, CFITSIO_LDFLAGS) + (MAGICKXX_CPPFLAGS, MAGICKXX_LDFLAGS) + (TIFF_CPPFLAGS, TIFF_LDFLAGS): + New variables. + 2009-06-09 Roland Levillain <roland(a)lrde.epita.fr> Aestetic changes and cleanup in documentation and comments. diff --git a/milena/tests/tests.mk b/milena/tests/tests.mk index b10dee4..9ca0803 100644 --- a/milena/tests/tests.mk +++ b/milena/tests/tests.mk @@ -34,5 +34,21 @@ AM_CXXFLAGS = $(TESTS_CXXFLAGS) TESTS_CXXFLAGS_SPEED = @TESTS_CXXFLAGS_SPEED@ TESTS_CXXFLAGS_DEBUG = @TESTS_CXXFLAGS_DEBUG@ + +# Flags for optional dependencies. + +GDCM_CPPFLAGS = @GDCM_CPPFLAGS@ +GDCM_LDFLAGS = @GDCM_LDFLAGS@ + +CFITSIO_CPPFLAGS = @CFITSIO_CPPFLAGS@ +CFITSIO_LDFLAGS = @CFITSIO_LDFLAGS@ + +MAGICKXX_CPPFLAGS = @MAGICKXX_CPPFLAGS@ +MAGICKXX_LDFLAGS = @MAGICKXX_LDFLAGS@ + +TIFF_CPPFLAGS = @TIFF_CPPFLAGS@ +TIFF_LDFLAGS = @TIFF_LDFLAGS@ + + # Inject rules to compile tests (recursively), without running them. include $(top_srcdir)/milena/tests/tests-recursive.mk -- 1.6.2.4

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[PATCH 1/2] Fix Automake macro OLN_WITH_LIB (again).
by Roland Levillain 10 Jun '09

10 Jun '09

* m4/oln-with-lib.m4 (_OLN_WITH_LIB): Set $5_CPPFLAGS instead of $5_CXXFLAGS. --- ChangeLog | 7 +++++++ m4/oln-with-lib.m4 | 4 ++-- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/ChangeLog b/ChangeLog index 5d6c5ef..b9fe2db 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,5 +1,12 @@ 2009-06-10 Roland Levillain <roland(a)lrde.epita.fr> + Fix Automake macro OLN_WITH_LIB (again). + + * m4/oln-with-lib.m4 (_OLN_WITH_LIB): Set $5_CPPFLAGS instead of + $5_CXXFLAGS. + +2009-06-10 Roland Levillain <roland(a)lrde.epita.fr> + Complete the installation of the Make rule `tests' in Olena. * Makefile.am (LOCAL_RECURSIVE_TARGETS): Add tests. diff --git a/m4/oln-with-lib.m4 b/m4/oln-with-lib.m4 index 11bd5d5..1f59714 100644 --- a/m4/oln-with-lib.m4 +++ b/m4/oln-with-lib.m4 @@ -15,7 +15,7 @@ # This macro sets the shell variable oln_have_`SHELL_NAME' to `yes' if # the library is found and if it is working (and to `no' otherwise), # and defines a CPP macro and an Automake conditional both named -# HAVE_`CPP_NAME'. It also sets `CPP_NAME'_CXXFLAGS and +# HAVE_`CPP_NAME'. It also sets `CPP_NAME'_CPPFLAGS and # `CPP_NAME'_LDFLAGS. # # Examples of use: @@ -71,7 +71,7 @@ AC_DEFUN([_OLN_WITH_LIB], LDFLAGS=$oln_save_LDFLAGS TOOLS_LDFLAGS="$TOOLS_LDFLAGS $$5_LDFLAGS" fi - AC_SUBST([$5_CXXFLAGS], [$5_CPPFLAGS]) + AC_SUBST([$5_CPPFLAGS]) AC_SUBST([$5_LDFLAGS]) AM_CONDITIONAL([HAVE_$5], [test x$oln_have_$4 = xyes]) AC_LANG_POP([C++]) -- 1.6.2.4

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[Olena] #200: Add copyright headers to Makefiles
by Olena Trac 10 Jun '09

10 Jun '09

#200: Add copyright headers to Makefiles ----------------------+----------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: task | Status: new Priority: major | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Keywords: | ----------------------+----------------------------------------------------- With the good years, of course! I (Roland) will try to write a script to automate this. -- Ticket URL: <https://trac.lrde.org/olena/ticket/200> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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[Olena] #156: Kill a maximum of warnings in Swilena
by Olena 10 Jun '09

10 Jun '09

#156: Kill a maximum of warnings in Swilena -------------------------+-------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: enhancement | Status: new Priority: minor | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Keywords: | -------------------------+-------------------------------------------------- The Python wrappers have been written quickly, and they lack some information (base classes, etc.), making `swig` emit a lot of warnings. Most of them are harmless, however they clutter the output of the build. Get rid of them. -- Ticket URL: <https://trac.lrde.org/olena/ticket/156> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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Re: [Olena-patches] [Olena] #101: Remove temporary image and ctrl+C
by Olena Trac 10 Jun '09

10 Jun '09

#101: Remove temporary image and ctrl+C ----------------------+----------------------------------------------------- Reporter: duhamel | Owner: Olena Team Type: defect | Status: closed Priority: minor | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Resolution: invalid | Keywords: ----------------------+----------------------------------------------------- Changes (by levill_r): * status: new => closed * resolution: => invalid Comment: `mln::display` is almost empty in [milestone:"Olena 1.0" Olena 1.0], this problem no longer exists. -- Ticket URL: <https://trac.lrde.org/olena/ticket/101#comment:1> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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[Olena] #189: Factor Makefile helpers generators
by Olena Trac 10 Jun '09

10 Jun '09

#189: Factor Makefile helpers generators ---------------------------+------------------------------------------------ Reporter: levill_r | Owner: Olena Team Type: enhancement | Status: new Priority: minor | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Keywords: Make Automake | ---------------------------+------------------------------------------------ Generators * source:trunk/milena/tests/unit_test/build_unit_test.sh and * source:trunk/scribo/tests/unit_test/build_unit_test.sh share most of their code; factor them. Moreover, we should make some effort to factor all generators and move them to a common location (we use `dev/` in Tiger, but `build-aux/` is also acceptable). -- Ticket URL: <https://trac.lrde.org/olena/ticket/189> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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