February 2009 - Olena-patches

3378: Fix make::graph and add make::region_adjacency_graph.
by Guillaume Lazzara 16 Feb '09

16 Feb '09

* mln/make/graph.hh: use an adjacency matrix and a neighborhood. * mln/make/region_adjacency_graph.hh: make a graph from a watershed image. * tests/make/Makefile.am, * tests/make/graph.cc, * tests/make/region_adjacency_graph.cc: add new tests. --- milena/ChangeLog | 13 ++ milena/mln/make/graph.hh | 84 ++++++++---- milena/mln/make/region_adjacency_graph.hh | 202 +++++++++++++++++++++++++++ milena/mln/util/graph.hh | 10 ++ milena/tests/make/Makefile.am | 6 +- milena/tests/make/graph.cc | 58 ++++++++ milena/tests/make/region_adjacency_graph.cc | 59 ++++++++ 7 files changed, 403 insertions(+), 29 deletions(-) create mode 100644 milena/mln/make/region_adjacency_graph.hh create mode 100644 milena/tests/make/graph.cc create mode 100644 milena/tests/make/region_adjacency_graph.cc diff --git a/milena/ChangeLog b/milena/ChangeLog index 7797b25..2282bcd 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,16 @@ +2009-02-16 Guillaume Lazzara <z(a)lrde.epita.fr> + + Fix make::graph and add make::region_adjacency_graph. + + * mln/make/graph.hh: use an adjacency matrix and a neighborhood. + + * mln/make/region_adjacency_graph.hh: make a graph from a watershed + image. + + * tests/make/Makefile.am, + * tests/make/graph.cc, + * tests/make/region_adjacency_graph.cc: add new tests. + 2009-02-13 Fabien Freling <fabien.freling(a)lrde.epita.fr> Add unit test for n_max.hh. diff --git a/milena/mln/make/graph.hh b/milena/mln/make/graph.hh index df76416..c9dddb1 100644 --- a/milena/mln/make/graph.hh +++ b/milena/mln/make/graph.hh @@ -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 @@ -34,6 +35,11 @@ /// /// \sa transform::influence_zone_geodesic. +# include <mln/core/concept/image.hh> +# include <mln/core/concept/neighborhood.hh> +# include <mln/core/image/image2d.hh> +# include <mln/core/alias/box2d.hh> +# include <mln/extension/adjust_fill.hh> # include <mln/util/graph.hh> namespace mln @@ -48,8 +54,10 @@ namespace mln /// \param[in] nlabels number of influence zone in \p iz. /// /// \return util::graph Graph based on the adjacency of the influence zones. - template <typename I> - util::graph graph(const Image& iz, mln_value(I) nlabels); + template <typename I, typename N> + util::graph + graph(const Image& iz_, const Neighborhood<N>& nbh, + mln_value(I) nlabels); @@ -59,53 +67,71 @@ namespace mln namespace internal { - template <typename I> + template <typename I, typename N> void - graph_tests(const Image& iz, mln_value(I)) + graph_tests(const Image& iz, const Neighborhood<N>& nbh, + mln_value(I)) { mln_precondition(exact(iz).is_valid()); - + mln_precondition(exact(nbh).is_valid()); (void) iz; + (void) nbh; } } // end of namespace mln::make::internal - namespace impl { namespace generic { - template <typename I> + template <typename I, typename N> util::graph - graph(const Image& iz_, mln_value(I) nlabels) + graph(const Image& iz_, const Neighborhood<N>& nbh_, + mln_value(I) nlabels) { trace::entering("make::impl::generic::graph"); - internal::graph_tests(iz_, nlabels); + internal::graph_tests(iz_, nbh_, nlabels); const I& iz = exact(iz_); + const N& nbh = exact(nbh_); - util::graph g; - g.add_vertices(nlabels.next()); + mln::image2d<bool> adj(mln::box2d(nlabels.next(), nlabels.next())); + data::fill(adj, false); + typedef mln_value(I) L; mln_piter(I) p(iz.domain()); + mln_niter(N) n(nbh, p); for_all(p) { - // Checking 'forward' neighboors and create an edge if necessary. - for (unsigned dim = 0; dim < mln_site_(I)::dim; ++dim) + L l1 = iz(p); + for_all(n) { - mln_site(I) n = p; - ++n[dim]; - - // FIXME: check that calling iz.domain().has() is correct - // and that we don't prefer iz.has(). - if (iz.domain().has(n) && iz(p) != iz(n)) - g.add_edge(iz(p), iz(n)); + if (iz.domain().has(n)) + { + L l2 = iz(n); + if (iz(n) != iz((p))) + { + // l2 is adjacent to l1 + if (l2 < l1) + adj(point2d(l1,l2)) = true; + else + adj(point2d(l2,l1)) = true; + } + } } } + // Construct graph. + util::graph g; + g.add_vertices(nlabels.next()); + for (unsigned i = 0; i < geom::nrows(adj); ++i) + for (unsigned j = 0; j < i; ++j) + if (adj(point2d(i,j))) + g.add_edge(i, j); + trace::exiting("make::impl::generic::graph"); return g; } @@ -119,11 +145,12 @@ namespace mln namespace internal { - template <typename I> + template <typename I, typename N> util::graph - graph_dispatch(const Image& iz, mln_value(I) nlabels) + graph_dispatch(const Image& iz, const Neighborhood<N>& nbh, + mln_value(I) nlabels) { - return make::impl::generic::graph(iz, nlabels); + return make::impl::generic::graph(iz, nbh, nlabels); } } // end of namespace mln::make::internal @@ -132,16 +159,17 @@ namespace mln // Facade - template <typename I> + template <typename I, typename N> inline util::graph - graph(const Image& iz, mln_value(I) nlabels) + graph(const Image& iz, const Neighborhood<N>& nbh, + mln_value(I) nlabels) { trace::entering("make::graph"); - internal::graph_tests(iz, nlabels); + internal::graph_tests(iz, nbh, nlabels); - util::graph g = internal::graph_dispatch(iz, nlabels); + util::graph g = internal::graph_dispatch(iz, nbh, nlabels); trace::exiting("make::graph"); return g; diff --git a/milena/mln/make/region_adjacency_graph.hh b/milena/mln/make/region_adjacency_graph.hh new file mode 100644 index 0000000..695174d --- /dev/null +++ b/milena/mln/make/region_adjacency_graph.hh @@ -0,0 +1,202 @@ +// Copyright (C) 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 +// 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, 51 Franklin Street, Fifth Floor, +// Boston, MA 02111-1307, 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. +// reasons why the executable file might be covered by the GNU General +// Public License. + +#ifndef MLN_MAKE_REGION_ADJACENCY_GRAPH_HH +# define MLN_MAKE_REGION_ADJACENCY_GRAPH_HH + +/// \file mln/make/region_adjacency_graph.hh +/// +/// Create a region_adjacency_graph from a watershed image. +/// +/// \sa morpho::meyer_wst. + +# include <mln/core/concept/image.hh> +# include <mln/core/concept/neighborhood.hh> +# include <mln/core/image/image2d.hh> +# include <mln/core/alias/box2d.hh> +# include <mln/extension/adjust_fill.hh> +# include <mln/util/graph.hh> + +namespace mln +{ + + namespace make + { + + /// Create a region adjacency graph from a watershed image. + /// + /// \param[in] wshd watershed image. + /// \param[in] nbasins number of influence zone in \p wshd. + /// + /// \return util::graph Graph based on the adjacency of the influence zones. + template <typename I, typename N> + util::graph + region_adjacency_graph(const Image& wshd_, + const Neighborhood<N>& nbh, + mln_value(I) nbasins); + + + +# ifndef MLN_INCLUDE_ONLY + + + namespace internal + { + + template <typename I, typename N> + void + region_adjacency_graph_tests(const Image& wshd, + const Neighborhood<N>& nbh, + mln_value(I)) + { + mln_precondition(exact(wshd).is_valid()); + mln_precondition(exact(nbh).is_valid()); + (void) wshd; + (void) nbh; + } + + } // end of namespace mln::make::internal + + + namespace impl + { + + namespace generic + { + + template <typename I, typename N> + util::graph + region_adjacency_graph(const Image& wshd_, + const Neighborhood<N>& nbh_, + mln_value(I) nbasins) + { + trace::entering("make::impl::generic::region_adjacency_graph"); + + internal::region_adjacency_graph_tests(wshd_, nbh_, nbasins); + const I& wshd = exact(wshd_); + const N& nbh = exact(nbh_); + + mln::image2d<bool> adj(mln::box2d(nbasins.next(), nbasins.next())); + data::fill(adj, false); + extension::adjust_fill(wshd, nbh, 0u); + + typedef mln_value(I) L; + L l1, l2; + mln_piter(I) p(wshd.domain()); + mln_niter(N) n(nbh, p); + for_all(p) + { + if (wshd(p) != 0u) + continue; + // p is in the watershed line. + l1 = l2 = 0; + for_all(n) + if (wshd.has(n) && wshd(n) != 0u) + { + if (l1 == 0u) // First label to be stored. + l1 = wshd(n); + else + if (wshd(n) != l1) // Useless: && l2 == 0) + { // Second label to be stored. + mln_invariant(l2 == 0u); + l2 = wshd(n); + break; + } + } + if (l2 == 0u || l1 == 0u) + continue; + if (l2 < l1) + std::swap(l1, l2); + + // adjacency l1 l2 + adj(point2d(l2,l1)) = true; + } + + // Construct graph. + util::graph g; + g.add_vertices(nbasins.next()); + for (unsigned i = 1; i < geom::nrows(adj); ++i) + for (unsigned j = 1; j < i; ++j) + if (adj(point2d(i,j))) + g.add_edge(i, j); + + + trace::exiting("make::impl::generic::region_adjacency_graph"); + return g; + } + + } // end of namespace mln::make::impl::generic + + } // end of namespace mln::make::impl + + + + namespace internal + { + + template <typename I, typename N> + util::graph + region_adjacency_graph_dispatch(const Image& wshd, + const Neighborhood<N>& nbh, + mln_value(I) nbasins) + { + return make::impl::generic::region_adjacency_graph(wshd, nbh, nbasins); + } + + } // end of namespace mln::make::internal + + + + // Facade + + template <typename I, typename N> + inline + util::graph + region_adjacency_graph(const Image& wshd, + const Neighborhood<N>& nbh, + mln_value(I) nbasins) + { + trace::entering("make::region_adjacency_graph"); + + internal::region_adjacency_graph_tests(wshd, nbh, nbasins); + + util::graph g = internal::region_adjacency_graph_dispatch(wshd, nbh, nbasins); + + trace::exiting("make::region_adjacency_graph"); + return g; + } + + +# endif // ! MLN_INCLUDE_ONLY + + + } // end of namespace mln::make + +} // end of namespace mln + + +#endif // ! MLN_MAKE_REGION_ADJACENCY_GRAPH_HH diff --git a/milena/mln/util/graph.hh b/milena/mln/util/graph.hh index 897deb4..f95e1e8 100644 --- a/milena/mln/util/graph.hh +++ b/milena/mln/util/graph.hh @@ -71,8 +71,11 @@ namespace mln vertices_t vertices_; /// The edges. edges_t edges_; + +# ifndef NDEBUG /// An index of the set of edges, for fast-access purpose. edges_set_t edges_set_; +# endif // ! NDEBUG }; } // end of namespace mln::internal @@ -383,8 +386,10 @@ namespace mln unsigned graph::add_edge(unsigned id_v1, unsigned id_v2) { + //FIXME: to be removed! We should not check that, except in without NDEBUG. // Does this edge already exist in the graph? edge_data_t edge(id_v1, id_v2); +# ifndef NDEBUG if (data_->edges_set_.find(edge) != data_->edges_set_.end ()) { // Return the erroneous value. @@ -392,6 +397,7 @@ namespace mln } else { +# endif // ! NDEBUG // Otherwise insert it into the graph. /* FIXME: This is not thread-proof (these two lines should form an atomic section). */ @@ -404,7 +410,11 @@ namespace mln data_->vertices_[edge.second()].push_back(id); return id; + +# ifndef NDEBUG } +# endif // ! NDEBUG + } inline diff --git a/milena/tests/make/Makefile.am b/milena/tests/make/Makefile.am index 913867c..95eb5ea 100644 --- a/milena/tests/make/Makefile.am +++ b/milena/tests/make/Makefile.am @@ -4,18 +4,22 @@ include $(top_srcdir)/milena/tests/tests.mk check_PROGRAMS = \ dual_neighb \ + graph \ h_mat \ image2d \ image3d \ mat \ + region_adjacency_graph \ w_window \ w_window_directional -dual_neighb_SOURCES = dual_neighb.cc +dual_neighb_SOURCES = dual_neighb.c +graph_SOURCES = graph.cc h_mat_SOURCES = h_mat.cc image2d_SOURCES = image2d.cc image3d_SOURCES = image3d.cc mat_SOURCES = mat.cc +region_adjacency_graph_SOURCES = region_adjacency_graph.cc w_window_SOURCES = w_window.cc w_window_directional_SOURCES = w_window_directional.cc diff --git a/milena/tests/make/graph.cc b/milena/tests/make/graph.cc new file mode 100644 index 0000000..bb88706 --- /dev/null +++ b/milena/tests/make/graph.cc @@ -0,0 +1,58 @@ +// Copyright (C) 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 +// 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, 51 Franklin Street, Fifth Floor, +// Boston, MA 02111-1307, 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. + +/// \file tests/make/graph.cc +/// +/// Tests on mln::make::graph. + +#include <mln/make/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/util/graph.hh> +#include <mln/make/graph.hh> +#include <mln/value/label_8.hh> + + +int main() +{ + using namespace mln; + + value::label_8 vals[9] = { 1, 1, 3, + 1, 2, 3, + 1, 0, 4 }; + + image2d<value::label_8> ima = make::image2d(vals); + + util::graph g = make::graph(ima, c4(), 4u); + + mln_assertion(g.e_nmax() == 7u); + mln_assertion(g.v_nmax() == 5u); + mln_assertion(g.v_nmax_nbh_edges(0) == 3); + mln_assertion(g.v_nmax_nbh_edges(1) == 3); + mln_assertion(g.v_nmax_nbh_edges(2) == 3); + mln_assertion(g.v_nmax_nbh_edges(3) == 3); + mln_assertion(g.v_nmax_nbh_edges(4) == 2); +} diff --git a/milena/tests/make/region_adjacency_graph.cc b/milena/tests/make/region_adjacency_graph.cc new file mode 100644 index 0000000..7f8cb12 --- /dev/null +++ b/milena/tests/make/region_adjacency_graph.cc @@ -0,0 +1,59 @@ +// Copyright (C) 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 +// 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, 51 Franklin Street, Fifth Floor, +// Boston, MA 02111-1307, 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. + +/// \file tests/make/graph.cc +/// +/// Tests on mln::make::region_adjacency_graph. + +#include <mln/core/alias/neighb2d.hh> + +#include <mln/util/graph.hh> + +#include <mln/value/label_8.hh> + +#include <mln/make/image2d.hh> +#include <mln/make/region_adjacency_graph.hh> + +int main() +{ + using namespace mln; + + value::label_8 vals[16] = { 1, 0, 3, 3, + 1, 0, 0, 0, + 0, 0, 4, 4, + 2, 2, 0, 4 }; + + image2d<value::label_8> ima = make::image2d(vals); + + util::graph g = make::region_adjacency_graph(ima, c4(), 4u); + + mln_assertion(g.e_nmax() == 4u); + mln_assertion(g.v_nmax() == 5u); + mln_assertion(g.v_nmax_nbh_edges(0) == 0); + for (unsigned i = 1; i < 4; ++i) + mln_assertion(g.v_nmax_nbh_edges(i) == 2); +} -- 1.5.6.5

1 0

ISMM'09 3418: Fix and generate more images for the Applications.
by Roland Levillain 15 Feb '09

15 Feb '09

Hand-made message, because Vcs wouldn't let me send it for obscure diff reasons. Fix and generate more images for the Applications. * article.sty (areaclosing): New operator. Use it... * article.tex: ..here. (section{Applications}): Simplify the chain. Adjust listing, and show actual code. Add more images. Reorganize. * apps/chain.hh: Move the computation of the gradient out of the chain. * apps/image2d.cc: Adjust. * apps/complex.cc: Start to adjust (unfinished work). * apps/chain.lst: New. * apps/lena-g.png: New. * apps/graph.cc, * apps/graph.neato, apps/graph.pdf, * apps/graph-g.nato, apps/graph-g.pdf, * apps/graph-s.neato, apps/graph-s.pdf: New. * pics/graph.cc: Fix a previous patch by adding a missing #include. * apps/new/: New directory. * apps/new/m283.gcl, apps/new/m283.off, apps/new/m283.png * apps/new/m283-c.gcl, apps/new/m283-c.off, apps/new/m283-c.png * apps/new/m283-s.gcl, apps/new/m283-s.off, apps/new/m283-s.png: New. * Makefile (IMAGES): Add apps/lena-g.png. Move old images... (IMAGES_OLD): ...here (new). (article.pdf): Depend on apps/chain.lst. (apps/graph-s.neato): New target. (%-g.gcl, %-c.gcl): New targets. (%-s.off): Disable target. * apps/old/: New directory. * apps/m283.gcl, apps/m283.off, apps/m283.png, * apps/m283-s.off, apps/m283-s.png: Move... * apps/old/m283.gcl, apps/old/m283.off, apps/old/m283.png, * apps/old/m283-s.off, apps/old/m283-s.png: ...here. Index: article.sty =================================================================== --- article.sty (revision 3417) +++ article.sty (revision 3418) @@ -11,6 +11,7 @@ \RequirePackage{amsopn} \DeclareMathOperator{\attrclosing}{attribute-closing} +\DeclareMathOperator{\areaclosing}{area-closing} \DeclareMathOperator{\gradientnorm}{gradient-norm} \DeclareMathOperator{\wst}{wst} Index: article.tex =================================================================== --- article.tex (revision 3417) +++ article.tex (revision 3418) @@ -782,28 +782,24 @@ \section{Applications} \label{sec:applications} -\fixme{Remove the gradient step: $G$ should be our input.} +In this part, we consider a simple, classical image processing chain +(\autoref{fig:chain-diagram}): from an image $I$ (e.g., the magnitude +of a gradient), compute an area closing $C$ using criterion value +$\lambda$; then, perform a \ac{wst} on $C$ to obtain a segmentation +$S$. -In this part, we consider a simple, classical image processing chain: -from an image $I$, produce an image of the magnitude of the gradient -$G$; then compute an attribute closing $C$ using an attribute $\alpha$ -and a criterion value $\lambda$; last, perform a \ac{wst} on $C$ to -obtain a segmentation $S$. - \begin{figure} \centering \begin{tikzpicture} \tikzstyle{im}=[minimum height=0.6cm] \tikzstyle{op}=[rectangle, minimum height=0.6cm] - \node[im] (i) at ( 0.0,2) {$I$}; - \node[op] (closing) at ( 2.0,2) [draw] {$\gradientnorm$}; - \node[im] (c) at ( 4.0,2) {$G$}; - \node[op] (gradient) at ( 6.5,2) [draw] {$\attrclosing$ $(\alpha, \lambda)$}; - \node[im] (g) at ( 9.0,2) {$C$}; + \node[im] (i) at ( 5.0,2) {$I$}; + \node[op] (closing) at ( 7.0,2) [draw] {$\areaclosing$ $(\lambda)$}; + \node[im] (c) at ( 9.0,2) {$C$}; \node[op] (wst) at (10.0,2) [draw] {$\wst$}; \node[im] (s) at (11.0,2) {$S$}; - \foreach \from/\to in {i/closing,closing/c,c/gradient,gradient/g,g/wst,wst/s} + \foreach \from/\to in {i/closing,closing/c,c/wst,wst/s} \draw[->] (\from) -- (\to); \end{tikzpicture} \caption{A generic morphological image processing chain.} @@ -813,7 +809,7 @@ \fixme{More.} % -------------------------------------------------------------------- -\subsubsection{Implementation in Milena} +\subsection{Implementation in Milena} \label{sec:apps-impl} \fixme{Merge this section into the previous one?} @@ -830,63 +826,38 @@ catchments basins (with the special label `0' for watershed sites).}: % -\fixme{Is the remark on \code{mln\_ch\_value} too much? We could use - an abstract type \code{output} for \code{wst} and mask this - detail.}% +\fixme{Is the remark on \code{mln\_ch\_value} too much? If not, + explain \code{mln\_concrete} as well.}% % -%% Actual Milena code is admittedly different. We should converge -%% toward a unique implementation. -\begin{lstlisting}[% +\lstinputlisting[% mathescape, % Identifiers. emph={[1]c,s,ima,nbh,lambda,nbasins},% emphstyle={[1]\color{darkgreen}\bfseries},% % More types. - morekeywords={[2]image}] - // Compute $G$. - image g = gradient(ima, nbh); - // Compute $C$. - image c = attribute_closing<alpha>(g, nbh, lambda); - // Holds the number of basins (to be computed by the Watershed Transform). - unsigned int nbasins; - // Compute $S$. - mln_ch_value(image, unsigned int) s = wst(c, nbh, nbasins); -\end{lstlisting} + morekeywords={[2]I,N,L}]{apps/chain.lst} -\fixme{The \code{gradient} algorithm might be different according to - the application.} -\fixme{Even if this chain is generic, working on edges requires a - slightly different code!} - -\subsubsection{Regular 2-Dimensional Image} -\label{sec:apps-image2d} - -In the classical regular 2-D image, $\Dom$ is a subset of $\Z$ and is -expressed as a 2-D bounding box. Therefore, the notion of -neighborhood does not depend on the site, and neighbors can be -expressed as a set of vectors. For instance a 4-connectivity -neighborhood is the set of 2-D vectors $\{(-1, 0), (0, -1), (0, 1), (1, - 0) \}$. In Milena, such vectors are called \emph{delta-points}, -since they encode a difference between two sites. \fixme{Careful: point - vs. site (?)} - -\fixme{Continue.} - -\subsubsection{Graph-Based Image} -\label{sec:apps-graph} - -\subsubsection{Simplicial Complex-Based Image} -\label{sec:apps-complex} - \begin{figure} \centering \subfigure[Regular 2-Dimensional Image]{ - \includegraphics[width=0.45\textwidth]{apps/lena} + \includegraphics[width=0.30\textwidth]{apps/lena} \label{fig:chain-images:lena} } + % FIXME: Improve dependencies in Makefile. + % * apps/lena-g.pgm (and then apps/lena-g.png) was generated as a + % side effect of apps/image2d with: + % make apps/lena-s.png + \subfigure[Morphological gradient image of + \ref{fig:chain-images:lena}]{ + \includegraphics[width=0.30\textwidth]{apps/lena-g} + \label{fig:chain-images:lena-g} + } + % * apps/lena-s.png (and then apps/lena-s.png) was generated using + % apps/image2d with: + % make apps/lena-s.png \subfigure[Result of the image processing chain on - \ref{fig:chain-images:lena}]{ - \includegraphics[width=0.45\textwidth]{apps/lena-s} + \ref{fig:chain-images:lena-g}]{ + \includegraphics[width=0.30\textwidth]{apps/lena-s} \label{fig:chain-images:lena-s} } @@ -915,23 +886,90 @@ %% \label{fig:chain-images:m272-pinv-curv-s} %% } - \subfigure[FIXME: Caption.]{ - \fbox{\includegraphics[width=0.45\textwidth]{apps/m283}} + \subfigure[Graph-Based Image]{ + \fbox{\includegraphics[width=0.29\textwidth]{apps/graph}} + \label{fig:chain-images:graph} } - \subfigure[FIXME: Caption.]{ - \fbox{\includegraphics[width=0.45\textwidth]{apps/m283-s}} + % FIXME: Improve dependencies in Makefile. + % * apps/graph-g.neato (and then apps/graph-g.pdf) was generated as + % a side effect of apps/graph with: + % make apps/graph-s.neato + \subfigure[Morphological gradient of \ref{fig:chain-images:graph}]{ + \fbox{\includegraphics[width=0.29\textwidth]{apps/graph-g}} + \label{fig:chain-images:graph-g} } + % * apps/graph-s.png (and then apps/graph-s.png) was generated using + % apps/graph with: + % make apps/graph-s.png + \subfigure[Result of the image processing chain on + \ref{fig:chain-images:graph-g}]{ + \fbox{\includegraphics[width=0.29\textwidth]{apps/graph-s}} + \label{fig:chain-images:graph-s} + } + \subfigure[Simplicial Complex-Based Image]{ + \fbox{\includegraphics[width=0.29\textwidth]{apps/new/m283}} + \label{fig:chain-images:new-m283} + } + % FIXME: Turn this into a Make rule (and break the dependency with + % milena/apps/statues). + % * new/m283-c.off was generated with the (Trimesh-based) command: + % milena/apps/statues/mesh-max-curv m283.off new/m283-c.off + \subfigure[Maximum surface curvature computed on + \ref{fig:chain-images:new-m283}]{ + \fbox{\includegraphics[width=0.29\textwidth]{apps/new/m283-c}} + \label{fig:chain-images:new-m283-c} + } + % FIXME: Turn this into a Make rule (and break the dependency with + % milena/apps/statues). + % * new/m283-s.off generated with the command: + % milena/apps/statues/mesh-complex-segm new/m283-c.off 200 new/m283-s.off + \subfigure[Result of the image processing chain on a gradient image + computed on the edges of \ref{fig:chain-images:new-m283-c}]{ + \fbox{\includegraphics[width=0.29\textwidth]{apps/new/m283-s}} + \label{fig:chain-images:new-m283-s} + } + \caption{Results of the image processing chain from \autoref{fig:chain-diagram} applied to various inputs.} \label{fig:chain-images} \end{figure} -\fixme{Careful, \file{apps/m283-s.png} has been generated using - \file{apps/statues/mesh-complex-max-curv-segm.cc} from Milena.} +% FIXME: Remove these subsections' titles? +% -------------------------------------------------------------------- +\subsection{Regular 2-Dimensional Image} +\label{sec:apps-image2d} +In the classical regular 2-D image, $\Dom$ is a subset of $\Z$ and is +expressed as a 2-D bounding box. Therefore, the notion of +neighborhood does not depend on the site, and neighbors can be +expressed as a set of vectors. For instance a 4-connectivity +neighborhood is the set of 2-D vectors $\{(-1, 0), (0, -1), (0, 1), (1, + 0) \}$. In Milena, such vectors are called \emph{delta-points}, +since they encode a difference between two sites. \fixme{Careful: point + vs. site (?)} + +\fixme{Continue.} + +% -------------------------------------------------------------------- +\subsection{Graph-Based Image} +\label{sec:apps-graph} + +% -------------------------------------------------------------------- +\subsection{Simplicial Complex-Based Image} +\label{sec:apps-complex} + +\fixme[inline]{Explain what a max curvature is.} +\fixme[inline]{Explain why the gradient image is not depicted.} + +\cite{alcoverro.08.3dtv} + +% -------------------------------------------------------------------- +\subsection{Other images and possibilities} +\label{sec:apps-other} + \fixme[inline]{Mention other possibilities: color image + gradient as - distance in a color space, etc.} + distance in a color space, gradient on edges etc.} % ==================================================================== @@ -962,8 +1000,6 @@ \cite{duret.00.gcse} (?) % Other libraries. \cite{yoo.04.book} - % Applications. - \cite{alcoverro.08.3dtv} } Index: apps/m283.gcl =================================================================== --- apps/m283.gcl (revision 3417) +++ apps/m283.gcl (revision 3418) @@ -1,10 +0,0 @@ -(load apps/m283.off geometry) -# `g1' is the first loaded (and sole) object. -(bbox-draw g1 no) -# `c0' is the initial camera. -(backcolor c0 1 1 1) -# `g0' is ``the World''. Rotation is expressed in radians around each axis. -(transform g0 g0 focus rotate 0.0 2.3 0.0) -(zoom c0 1.5) -(snapshot c0 apps/m283.ppm) -(quit) Index: apps/m283-s.png =================================================================== Cannot display: file marked as a binary type. svn:mime-type = application/octet-stream Index: apps/m283.png =================================================================== Cannot display: file marked as a binary type. svn:mime-type = application/octet-stream Index: apps/chain.hh =================================================================== --- apps/chain.hh (revision 3417) +++ apps/chain.hh (revision 3418) @@ -1,35 +1,18 @@ -#include <mln/morpho/gradient.hh> -#include <mln/morpho/closing_area.hh> -#include <mln/morpho/meyer_wst.hh> - #ifndef CHAIN_HH # define CHAIN_HH -template <typename I, typename N, typename W, typename L> +#include <mln/morpho/closing_area.hh> +#include <mln/morpho/meyer_wst.hh> + +template <typename I, typename N, typename L> mln_ch_value(I, L) chain(const mln::Image& ima, const mln::Neighborhood<N>& nbh, - const mln::Window<W>& win, unsigned lambda, L& nbasins) + unsigned lambda, L& nbasins) { using namespace mln; - - /* FIXME: Unfortunately, we cannot write - - morpho::gradient(ima, win) - - here, since MM only uses windows (yet?), not neighborhoods. And - we cannot either write - - morpho::gradient(ima, nbh.win()), - - since that window would not contain the center site... - Therefore, this function asks for a window WIN matching the - neighborhood NBH, plus the center site. - - A neighborhood `n' should provide a method `win_p()' returning a - window corresponding to `n' plus the center site. */ - mln_concrete(I) g = morpho::gradient(ima, win); // FIXME: alpha (the criterion) is not changeable here! Change this. - mln_concrete(I) c = morpho::closing_area(g, nbh, lambda); + mln_concrete(I) c = morpho::closing_area(ima, nbh, lambda); + // FIXME: Use morpho::watershed::flooding instead? mln_ch_value(I, L) s = morpho::meyer_wst(c, nbh, nbasins); return s; } Index: apps/chain.lst =================================================================== --- apps/chain.lst (revision 0) +++ apps/chain.lst (revision 3418) @@ -0,0 +1,8 @@ +template <typename I, typename N, typename L> +mln_ch_value(I, L) +chain(const I& ima, const N& nbh, unsigned lambda, L& nbasins) +{ + mln_concrete(I) c = morpho::closing_area(ima, nbh, lambda); // Compute $C$. + mln_ch_value(I, L) s = morpho::wst(c, nbh, nbasins); // Compute $S$. + return s; +} Index: apps/lena-g.png =================================================================== Cannot display: file marked as a binary type. svn:mime-type = application/octet-stream Property changes on: apps/lena-g.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Index: apps/complex.cc =================================================================== --- apps/complex.cc (revision 3417) +++ apps/complex.cc (revision 3418) @@ -47,6 +47,11 @@ down. */ input ima; io::off::load(ima, input_filename); - output s = chain(ima, nbh, win, lambda, nbasins); + + // FIXME: gradient_on_edges is not implemented; extract it from + // apps/statues/mesh-complex-max-curv-segm.cc. + + input g = morpho::gradient_on_edges(ima, win); + output s = chain(ima, nbh, lambda, nbasins); io::off::save(debug::colorize(value::rgb8(), s, nbasins), output_filename); } Index: apps/image2d.cc =================================================================== --- apps/image2d.cc (revision 3417) +++ apps/image2d.cc (revision 3418) @@ -9,7 +9,10 @@ #include <mln/value/int_u8.hh> #include <mln/value/label_8.hh> +#include <mln/morpho/gradient.hh> + #include <mln/io/pgm/load.hh> +#include <mln/io/pgm/save.hh> #include <mln/io/ppm/save.hh> #include <mln/debug/colorize.hh> @@ -43,6 +46,28 @@ // Load, process, save. input ima = io::pgm::load<val>(input_filename); - output s = chain(ima, nbh, win, lambda, nbasins); + // Gradient. + /* FIXME: Unfortunately, we cannot write + + morpho::gradient(ima, win) + + here, since MM only uses windows (yet?), not neighborhoods. And + we cannot either write + + morpho::gradient(ima, nbh.win()), + + since that window would not contain the center site... + Therefore, this function asks for a window WIN matching the + neighborhood NBH, plus the center site. + + A neighborhood `n' should provide a method `win_p()' returning a + window corresponding to `n' plus the center site. */ + input g = morpho::gradient(ima, win); + + // FIXME: get the name as argument. + io::pgm::save(g, "apps/lena-g.pgm"); + + // Chain. + output s = chain(g, nbh, lambda, nbasins); io::ppm::save(debug::colorize(value::rgb8(), s, nbasins), output_filename); } Index: apps/graph.cc =================================================================== --- apps/graph.cc (revision 0) +++ apps/graph.cc (revision 3418) @@ -0,0 +1,495 @@ +// 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 +// 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, 51 Franklin Street, Fifth Floor, +// Boston, MA 02111-1307, 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. + +#include <iostream> +#include <iomanip> + +#include <vector> + +#include <mln/core/image/image2d.hh> +#include <mln/core/routine/duplicate.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/site_set/p_queue_fast.hh> +#include <mln/labeling/blobs.hh> +#include <mln/io/pgm/load.hh> +#include <mln/debug/println.hh> +#include <mln/draw/line.hh> +#include <mln/pw/all.hh> +#include <mln/binarization/threshold.hh> + +#include <mln/value/int_u8.hh> +#include <mln/core/alias/point2d.hh> + +#include <mln/core/site_set/p_faces.hh> +#include <mln/core/image/complex_image.hh> +#include <mln/core/alias/complex_geometry.hh> +#include <mln/core/alias/complex_image.hh> + +// FIXME: Include these elsewhere? (In complex_image.hh?) +#include <mln/core/image/complex_neighborhoods.hh> +#include <mln/core/image/complex_neighborhood_piter.hh> +#include <mln/core/image/complex_windows.hh> + +#include <mln/data/fill.hh> +#include <mln/morpho/gradient.hh> +#include <mln/debug/colorize.hh> + +#include "chain.hh" + + +// FIXME: Copied and adjusted from pics/graph.cc; factor. + +namespace mln +{ + + template <typename I, typename N> + mln_concrete(I) + influence_zones(const I& input, const N& nbh) + { + mln_concrete(I) output = duplicate(input); + + p_queue_fast<mln_site(I)> q; + + { + // Initialization. + mln_piter(I) p(input.domain()); + mln_niter(N) n(nbh, p); + for_all(p) + if (input(p) != 0) + for_all(n) if (input.has(n)) + if (input(n) == 0) + { + q.push(p); + break; + } + } + { + // Body. + mln_site(I) p; + mln_niter(N) n(nbh, p); + while (! q.is_empty()) + { + p = q.pop_front(); + mln_invariant(output(p) != 0); + for_all(n) if (input.has(n)) + if (output(n) == 0) + { + output(n) = output(p); + q.push(n); + } + } + } + + return output; + + } + + + namespace io + { + + namespace neato + { + + /* FIXME: This is just the gray-level version. Handle other value + types as well. */ + void + save(const complex_image<1, discrete_plane_1complex_geometry, + value::int_u8>& ima, + const std::string& filename, + const std::string& bgcolor = "#0000C0", + const std::string& fontcolor = "#0000C0", + bool empty_vertex_label = true) + { + typedef value::int_u8 V; + typedef complex_image<1, discrete_plane_1complex_geometry, V> I; + const unsigned D = 1; + typedef discrete_plane_1complex_geometry G; + + std::ofstream g(filename.c_str()); + g << "graph wst" << std::endl + << "{" << std::endl + << " graph [bgcolor = \"" << bgcolor << "\"]" << std::endl + << " edge [color = \"#FFFFFF\"]" << std::endl + << " node [color = \"#FFFFFF\", height=\"5\", width=\"5\"," + << " fontsize=\"100\", fontcolor = \"" << fontcolor << "\"]" + << std::endl; + + // Vertices. + p_n_faces_fwd_piter<D, G> v(ima.domain(), 0); + typedef complex_higher_neighborhood<D, G> e_nbh_t; + e_nbh_t e_nbh; + for_all(v) + { + V vertex_color = ima(v); + std::ostringstream vertex_color_str; + // FIXME: Only valid for gray-level images. + vertex_color_str << '#' + << std::hex + << std::setfill('0') + << std::setw(2) << vertex_color + << std::setw(2) << vertex_color + << std::setw(2) << vertex_color + << std::dec; + + g << " v" << v.unproxy_().face_id() + << " [pos = \"" + << std::fixed << std::setprecision(1) + << (float)v.to_site().front()[1] << ", " + << -(float)v.to_site().front()[0] + << "\", color = \"" << vertex_color_str.str() + << "\", fillcolor = \"" << vertex_color_str.str() + << "\", pin = \"true\", style=\"filled,setlinewidth(3)\""; + if (empty_vertex_label) + g << ", label = \"\""; + g << "];" + << std::endl; + } + + // Edges. + p_n_faces_fwd_piter<D, G> e(ima.domain(), 1); + typedef complex_lower_neighborhood<D, G> v_nbh_t; + v_nbh_t v_nbh; + mln_niter_(v_nbh_t) adj_v(v_nbh, e); + for_all(e) + { + V edge_color = ima(e); + std::ostringstream edge_color_str; + edge_color_str << '#' + << std::hex + << std::setfill('0') + << std::setw(2) << edge_color + << std::setw(2) << edge_color + << std::setw(2) << edge_color + << std::dec; + + // Adjacent vertices. + adj_v.start(); + topo::face<1> v1 = adj_v.unproxy_().face(); + point2d p1 = adj_v.to_site().front(); + adj_v.next(); + topo::face<1> v2 = adj_v.unproxy_().face(); + point2d p2 = adj_v.to_site().front(); + adj_v.next(); + mln_invariant(!adj_v.is_valid()); + + g << " v" << v1.face_id() << " -- v" << v2.face_id() << " "; + g << "[color = \"" << edge_color_str.str() + << "\", style=\"setlinewidth(10)\"];" << std::endl; + } + + g << "}" << std::endl; + g.close(); + } + + // FIXME: Factor with the previous version. + void + save(const complex_image<1, discrete_plane_1complex_geometry, + value::rgb8>& ima, + const std::string& filename, + const std::string& bgcolor = "#0000C0", + const std::string& fontcolor = "#0000C0", + bool empty_vertex_label = true) + { + typedef value::rgb8 V; + typedef complex_image<1, discrete_plane_1complex_geometry, V> I; + const unsigned D = 1; + typedef discrete_plane_1complex_geometry G; + + std::ofstream g(filename.c_str()); + g << "graph wst" << std::endl + << "{" << std::endl + << " graph [bgcolor = \"" << bgcolor << "\"]" << std::endl + << " edge [color = \"#FFFFFF\"]" << std::endl + << " node [color = \"#FFFFFF\", height=\"5\", width=\"5\"," + << " fontsize=\"100\", fontcolor = \"" << fontcolor << "\"]" + << std::endl; + + // Vertices. + p_n_faces_fwd_piter<D, G> v(ima.domain(), 0); + typedef complex_higher_neighborhood<D, G> e_nbh_t; + e_nbh_t e_nbh; + for_all(v) + { + V vertex_color = ima(v); + std::ostringstream vertex_color_str; + // FIXME: Only valid for gray-level images. + vertex_color_str << '#' + << std::hex + << std::setfill('0') + << std::setw(2) << vertex_color.red() + << std::setw(2) << vertex_color.green() + << std::setw(2) << vertex_color.blue() + << std::dec; + + g << " v" << v.unproxy_().face_id() + << " [pos = \"" + << std::fixed << std::setprecision(1) + << (float)v.to_site().front()[1] << ", " + << -(float)v.to_site().front()[0] + << "\", color = \"" << vertex_color_str.str() + << "\", fillcolor = \"" << vertex_color_str.str() + << "\", pin = \"true\", style=\"filled,setlinewidth(3)\""; + if (empty_vertex_label) + g << ", label = \"\""; + g << "];" + << std::endl; + } + + // Edges. + p_n_faces_fwd_piter<D, G> e(ima.domain(), 1); + typedef complex_lower_neighborhood<D, G> v_nbh_t; + v_nbh_t v_nbh; + mln_niter_(v_nbh_t) adj_v(v_nbh, e); + for_all(e) + { + V edge_color = ima(e); + std::ostringstream edge_color_str; + edge_color_str << '#' + << std::hex + << std::setfill('0') + << std::setw(2) << edge_color.red() + << std::setw(2) << edge_color.green() + << std::setw(2) << edge_color.blue() + << std::dec; + + // Adjacent vertices. + adj_v.start(); + topo::face<1> v1 = adj_v.unproxy_().face(); + point2d p1 = adj_v.to_site().front(); + adj_v.next(); + topo::face<1> v2 = adj_v.unproxy_().face(); + point2d p2 = adj_v.to_site().front(); + adj_v.next(); + mln_invariant(!adj_v.is_valid()); + + g << " v" << v1.face_id() << " -- v" << v2.face_id() << " "; + g << "[color = \"" << edge_color_str.str() + << "\", style=\"setlinewidth(10)\"];" << std::endl; + } + + g << "}" << std::endl; + g.close(); + } + + } // end of namespace mln::io::neato + + } // end of namespace mln::io + +} // end of namespace mln + + +// FIXME: Clean up and move into Milena? +mln::int_u8_1complex_image2d +make_complex_image(const mln::image2d<mln::value::int_u8>& input) +{ + using namespace mln; + using mln::value::int_u8; + + /*----------------------------------------. + | Complex + complex geometry (location). | + `----------------------------------------*/ + + border::thickness = 0; + + unsigned nlabels; + image2d<unsigned> label = + labeling::blobs(mln::binarization::threshold(input, 1), c4(), nlabels); + + std::cout << "n seeds = " << nlabels << std::endl; + { + image2d<int_u8> lab(label.domain()); + data::paste(label, lab); + } + + image2d<unsigned> iz = influence_zones(label, c4()); + { + image2d<int_u8> IZ(iz.domain()); + data::paste(iz, IZ); + } + + + // Make graph/complex. + + std::vector< std::vector<bool> > adj(nlabels + 1); + for (unsigned l = 1; l <= nlabels; ++l) + adj[l].resize(nlabels + 1, false); + + { + box2d::piter p(iz.domain()); + for_all(p) + { + point2d r = p + right, b = p + down; + if (iz.has(r) && iz(p) != iz(r)) + { + if (iz(p) <= iz(r)) + adj[iz(p)][iz(r)] = true; + else + adj[iz(r)][iz(p)] = true; + } + if (iz.has(b) && iz(p) != iz(b)) + { + if (iz(p) <= iz(b)) + adj[iz(p)][iz(b)] = true; + else + adj[iz(b)][iz(p)] = true; + } + } + } + + // end of mk_graph + + + const unsigned D = 1; + + topo::complex<D> c; + + typedef point2d P; + typedef geom::complex_geometry<D, P> G; + G geom; + + // Convenience typedefs. + typedef topo::n_face<0, D> vertex; + typedef topo::n_face<1, D> edge; + + { + + // 0-faces (vertices). + std::vector<vertex> v; + { + box2d::piter p(label.domain()); + for_all(p) + if (label(p) != 0) + { + geom.add_location(p); + v.push_back(c.add_face()); + } + } + + std::cout << "v size = " << v.size() << std::endl; + + // 1-faces (edges). + std::vector<edge> e; + { + for (unsigned l = 1; l <= nlabels; ++l) + for (unsigned ll = l + 1; ll <= nlabels; ++ll) + if (adj[l][ll]) + e.push_back( c.add_face(-v[l-1] + v[ll-1]) ); + } + + std::cout << "e size = " << e.size() << std::endl; + + } + + + /*---------------------. + | Complex-based pset. | + `---------------------*/ + + p_complex<D, G> pc(c, geom); + + /*----------------------. + | Complex-based image. | + `----------------------*/ + + // An image type built on a 1-complex with unsigned values on each + // face (both vertices and edges). + typedef complex_image<D, G, int_u8> output_t; + + // Create and initialize an image based on PC. + output_t output(pc); + + // Color OUTPUT's vertices with INPUT's values. + p_n_faces_fwd_piter<D, G> v(output.domain(), 0); + for_all(v) + output(v) = input(v.to_site().front()); + + // Use a medium gray to color edges. + p_n_faces_fwd_piter<D, G> e(output.domain(), 1); + for_all(e) + output(e) = 128; + + return output; +} + + +// FIXME: Move to Milena? +template <unsigned D, typename G, typename V> +mln::complex_higher_dim_connected_n_face_window_p<D, G> +make_elt_win(const mln::complex_image<D, G, V>& ima) +{ + return mln::complex_higher_dim_connected_n_face_window_p<D, G>(); +} + +// FIXME: Move to Milena? +template <unsigned D, typename G, typename V> +mln::complex_higher_dim_connected_n_face_neighborhood<D, G> +make_elt_nbh(const mln::complex_image<D, G, V>& ima) +{ + return mln::complex_higher_dim_connected_n_face_neighborhood<D, G>(); +} + + +int main(int argc, char* argv[]) +{ + if (argc != 4) + { + std::cerr << "usage: " << argv[0] << " seeds.pgm lambda output.neato" + << std::endl; + std::exit(1); + } + std::string input_filename = argv[1]; + unsigned lambda = atoi(argv[2]); + std::string output_filename = argv[3]; + + using namespace mln; + using mln::value::int_u8; + // Use clearer names. + typedef int_u8_1complex_image2d int_u8_graph_image2d; + + typedef int_u8_graph_image2d input; + typedef value::label_8 label; + typedef mln_ch_value_(input, label) output; + label nbasins; + + // Seeds. + image2d<int_u8> seeds = io::pgm::load<int_u8>(input_filename); + // Input image computed from the graph of influence zones (IZ) of seeds. + typedef int_u8_graph_image2d ima_t; + ima_t ima = make_complex_image(seeds); + io::neato::save(ima, "apps/graph.neato"); + + // Gradient. + input g = morpho::gradient(ima, make_elt_win(ima)); + + // FIXME: get the name as argument. + io::neato::save(g, "apps/graph-g.neato"); + + // Chain. + output s = chain(g, make_elt_nbh(g), lambda, nbasins); + io::neato::save(debug::colorize(value::rgb8(), s, nbasins), output_filename); +} Index: apps/new/m283-c.gcl =================================================================== --- apps/new/m283-c.gcl (revision 0) +++ apps/new/m283-c.gcl (revision 3418) @@ -0,0 +1,10 @@ +(load apps/new/m283-g.off geometry) +# `g1' is the first loaded (and sole) object. +(bbox-draw g1 no) +# `c0' is the initial camera. +(backcolor c0 1 1 1) +# `g0' is ``the World''. Rotation is expressed in radians around each axis. +(transform g0 g0 focus rotate 0.0 2.3 0.0) +(zoom c0 1.5) +(snapshot c0 apps/new/m283-g.ppm) +(quit) Property changes on: apps/new/m283-c.gcl ___________________________________________________________________ Added: svn:mergeinfo Index: apps/new/m283-s.gcl =================================================================== --- apps/new/m283-s.gcl (revision 0) +++ apps/new/m283-s.gcl (revision 3418) @@ -0,0 +1,10 @@ +(load apps/new/m283-s.off geometry) +# `g1' is the first loaded (and sole) object. +(bbox-draw g1 no) +# `c0' is the initial camera. +(backcolor c0 1 1 1) +# `g0' is ``the World''. Rotation is expressed in radians around each axis. +(transform g0 g0 focus rotate 0.0 2.3 0.0) +(zoom c0 1.5) +(snapshot c0 apps/new/m283-s.ppm) +(quit) Index: apps/new/m283.gcl =================================================================== --- apps/new/m283.gcl (revision 0) +++ apps/new/m283.gcl (revision 3418) @@ -0,0 +1,10 @@ +(load apps/new/m283.off geometry) +# `g1' is the first loaded (and sole) object. +(bbox-draw g1 no) +# `c0' is the initial camera. +(backcolor c0 1 1 1) +# `g0' is ``the World''. Rotation is expressed in radians around each axis. +(transform g0 g0 focus rotate 0.0 2.3 0.0) +(zoom c0 1.5) +(snapshot c0 apps/new/m283.ppm) +(quit) Property changes on: apps/new/m283.gcl ___________________________________________________________________ Added: svn:mergeinfo Index: apps/graph-g.neato =================================================================== --- apps/graph-g.neato (revision 0) +++ apps/graph-g.neato (revision 3418) @@ -0,0 +1,67 @@ +graph wst +{ + graph [bgcolor = "#0000C0"] + edge [color = "#FFFFFF"] + node [color = "#FFFFFF", height="5", width="5", fontsize="100", fontcolor = "#0000C0"] + v0 [pos = "44.0, -11.0", color = "#878787", fillcolor = "#878787", pin = "true", style="filled,setlinewidth(3)", label = ""]; + v1 [pos = "26.0, -12.0", color = "#c0c0c0", fillcolor = "#c0c0c0", pin = "true", style="filled,setlinewidth(3)", label = ""]; + v2 [pos = "12.0, -15.0", color = "#9f9f9f", fillcolor = "#9f9f9f", pin = "true", style="filled,setlinewidth(3)", label = ""]; 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+ v4 -- v9 [color = "#808080", style="setlinewidth(10)"]; + v5 -- v7 [color = "#808080", style="setlinewidth(10)"]; + v5 -- v9 [color = "#808080", style="setlinewidth(10)"]; + v5 -- v10 [color = "#808080", style="setlinewidth(10)"]; + v5 -- v11 [color = "#808080", style="setlinewidth(10)"]; + v6 -- v8 [color = "#808080", style="setlinewidth(10)"]; + v6 -- v9 [color = "#808080", style="setlinewidth(10)"]; + v7 -- v10 [color = "#808080", style="setlinewidth(10)"]; + v8 -- v9 [color = "#808080", style="setlinewidth(10)"]; + v8 -- v12 [color = "#808080", style="setlinewidth(10)"]; + v8 -- v16 [color = "#808080", style="setlinewidth(10)"]; + v9 -- v11 [color = "#808080", style="setlinewidth(10)"]; + v9 -- v12 [color = "#808080", style="setlinewidth(10)"]; + v9 -- v15 [color = "#808080", style="setlinewidth(10)"]; + v10 -- v11 [color = "#808080", style="setlinewidth(10)"]; + v10 -- v13 [color = "#808080", style="setlinewidth(10)"]; + v10 -- v14 [color = "#808080", style="setlinewidth(10)"]; + v11 -- v13 [color = "#808080", style="setlinewidth(10)"]; + v11 -- v15 [color = "#808080", style="setlinewidth(10)"]; + v11 -- v17 [color = "#808080", style="setlinewidth(10)"]; + v12 -- v15 [color = "#808080", style="setlinewidth(10)"]; + v12 -- v16 [color = "#808080", style="setlinewidth(10)"]; + v12 -- v18 [color = "#808080", style="setlinewidth(10)"]; + v13 -- v14 [color = "#808080", style="setlinewidth(10)"]; + v13 -- v17 [color = "#808080", style="setlinewidth(10)"]; + v14 -- v17 [color = "#808080", style="setlinewidth(10)"]; + v15 -- v17 [color = "#808080", style="setlinewidth(10)"]; + v15 -- v18 [color = "#808080", style="setlinewidth(10)"]; + v16 -- v18 [color = "#808080", style="setlinewidth(10)"]; +} Index: apps/graph-s.pdf =================================================================== Cannot display: file marked as a binary type. svn:mime-type = application/octet-stream Property changes on: apps/graph-s.pdf ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Index: apps/graph.pdf =================================================================== Cannot display: file marked as a binary type. svn:mime-type = application/octet-stream Property changes on: apps/graph.pdf ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Index: apps/old/m283-s.png =================================================================== Cannot display: file marked as a binary type. svn:mime-type = application/octet-stream Property changes on: apps/old/m283-s.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: svn:mergeinfo Index: apps/old/m283.png =================================================================== Cannot display: file marked as a binary type. svn:mime-type = application/octet-stream Property changes on: apps/old/m283.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: svn:mergeinfo Index: apps/old/m283.gcl =================================================================== --- apps/old/m283.gcl (revision 0) +++ apps/old/m283.gcl (revision 3418) @@ -0,0 +1,10 @@ +(load apps/old/m283.off geometry) +# `g1' is the first loaded (and sole) object. +(bbox-draw g1 no) +# `c0' is the initial camera. +(backcolor c0 1 1 1) +# `g0' is ``the World''. Rotation is expressed in radians around each axis. +(transform g0 g0 focus rotate 0.0 2.3 0.0) +(zoom c0 1.5) +(snapshot c0 apps/old/m283.ppm) +(quit) Property changes on: apps/old/m283.gcl ___________________________________________________________________ Added: svn:mergeinfo Property changes on: apps ___________________________________________________________________ Modified: svn:ignore - *.dSYM image2d complex + *.dSYM image2d graph complex Index: Makefile =================================================================== --- Makefile (revision 3417) +++ Makefile (revision 3418) @@ -20,18 +20,23 @@ CLEANFILES = article.pdf $(BASE).pdf -## apps/m283-s.png is not part of IMAGES since the tool that generated -## it is outside this repository (it is located in Milena's -## apps/statues directory). +## apps/old/m283-s.png is not part of IMAGES since the tools that +## generated it (milena/apps/statues/mesh-complex-max-curv-segm) is +## outside this repository (it is located in Milena's apps/statues +## directory). Note that I do not remember the values of lambda. IMAGES = \ pics/picasso.png pics/picasso-dil.png \ \ pics/graph.neato pics/graph-dil.neato \ pics/graph.png pics/graph-dil.png \ \ + apps/lena.png apps/lena-g.png apps/lena-s.png \ \ - apps/lena.png apps/lena-s.png \ - \ + apps/graph.neato apps/graph.pdf \ + apps/graph-g.neato apps/graph-g.pdf \ + apps/graph-s.neato apps/graph-s.pdf + +IMAGES_OLD = \ apps/m272.png \ apps/m272-max-curv.png \ apps/m272-max-curv-s.off apps/m272-max-curv-s.png \ @@ -51,7 +56,7 @@ article.pdf: article.sty rev.sty # FIXME: Use another extension: these files are not (La)TeX ones. -article.pdf: pics/picasso.lst pics/graph.lst +article.pdf: pics/picasso.lst pics/graph.lst apps/chain.lst ## -------- ## ## Images. ## @@ -98,6 +103,10 @@ # Generate for the 3-D output (*-s.off) a file similar to the one used # to capture the 3-D input (*.off), so that both snapshots show the # same view. +%-g.gcl: %.gcl + sed "s,$*,$*-g,g" $< >$@ +%-c.gcl: %.gcl + sed "s,$*,$*-c,g" $< >$@ %-s.gcl: %.gcl sed "s,$*,$*-s,g" $< >$@ # Likewise for other derived meshes. @@ -123,10 +132,13 @@ apps/image2d: apps/chain.hh # Generate *-s.off from *.off using apps/complex. -%-s.off: %.off apps/complex - apps/complex $< 100 $@ -apps/complex: apps/chain.hh +# FIXME: Disabled. +## %-s.off: %.off apps/complex +## apps/complex $< 100 $@ +## apps/complex: apps/chain.hh +apps/graph-s.neato: pics/seeds.pgm apps/graph + apps/graph $< 2 $@ ## --------- ## ## Install. ## Index: pics/graph.cc =================================================================== --- pics/graph.cc (revision 3417) +++ pics/graph.cc (revision 3418) @@ -45,8 +45,9 @@ #include <mln/core/alias/point2d.hh> #include <mln/core/site_set/p_faces.hh> +#include <mln/core/image/complex_image.hh> #include <mln/core/alias/complex_geometry.hh> -#include <mln/core/image/complex_image.hh> +#include <mln/core/alias/complex_image.hh> // FIXME: Include these elsewhere? (In complex_image.hh?) #include <mln/core/image/complex_neighborhoods.hh> Property changes on: . ___________________________________________________________________ Modified: svn:externals - share -r 3413 https://svn.lrde.epita.fr/svn/lrde-publis/trunk/share + share -r 3417 https://svn.lrde.epita.fr/svn/lrde-publis/trunk/share

1 0

3377: Finalize ICIP 2009 code.
by Thierry Geraud 13 Feb '09

13 Feb '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Finalize ICIP 2009 code. * theo/publis/icip2009/compute_a.cc (a_data): New. (compute_a): Rename as... (compute_data): ...this. Update. (compute_filter): New. (main): Update. compute_a.cc | 376 +++++++++++++++++++++++++++++++++++++++++------------------ 1 file changed, 264 insertions(+), 112 deletions(-) Index: theo/publis/icip2009/compute_a.cc --- theo/publis/icip2009/compute_a.cc (revision 3376) +++ theo/publis/icip2009/compute_a.cc (working copy) @@ -34,7 +34,9 @@ #include <mln/core/alias/neighb2d.hh> #include <mln/value/int_u8.hh> #include <mln/io/pgm/load.hh> +#include <mln/io/pgm/save.hh> #include <mln/debug/println.hh> +#include <mln/core/routine/duplicate.hh> #include <mln/core/site_set/p_array.hh> #include <mln/level/sort_psites.hh> @@ -44,6 +46,8 @@ #include <mln/morpho/tree/data.hh> #include <mln/morpho/tree/compute_attribute_image.hh> +#include <mln/morpho/watershed/flooding.hh> +#include <mln/morpho/elementary/gradient.hh> #include <mln/labeling/regional_minima.hh> #include <mln/accu/count.hh> @@ -93,13 +97,36 @@ } - //------------------------------- compute_a + + //------------------------------- data + + + + template <typename I, typename A> + struct a_data + { + typedef mln_site(I) P; + typedef p_array S; + + unsigned n_regmins; + S s; + + mln_ch_value(I, mln_result(A)) a; + mln_ch_value(I, unsigned) nchildren; + mln_ch_value(I, P) par; + mln_ch_value(I, bool) flag; + }; + + + + + //------------------------------- compute_data template <typename I, typename N, typename A> - mln_ch_value(I, mln_result(A)) - compute_a(const I& f, const N& nbh, A, unsigned& n_regmins, + a_data<I,A> + compute_data(const I& f, const N& nbh, A, unsigned& n_regmins, bool echo = false) { typedef mln_site(I) P; @@ -192,22 +219,15 @@ - // Output is the attribute image. - mln_ch_value(I, mln_result(A)) a; + // Outputing. + + mln_ch_value(I, mln_result(A)) a; // Attribute image. initialize(a, f); data::paste(attr, a); - - // Back-propagate flags to non-representant component sites. - { - mln_bkd_piter(S) p(s); // Reverse. - for_all(p) - if (f(par(p)) == f(p) && flag(par(p)) != flag(p)) - flag(p) = flag(par(p)); - if (echo) - debug::println("flag", flag); - } - + mln_ch_value(I, unsigned) nchildren; // Number of children. + initialize(nchildren, f); + data::fill(nchildren, 0); unsigned n_sites = 0, @@ -215,24 +235,80 @@ n_nodes = 0; - // Tree canonization + // Finalization. { mln_bkd_piter(S) p(s); // Reverse. for_all(p) { - P q = par(p); - if (f(par(q)) == f(q)) - par(p) = par(q); - ++n_sites; - if (par(p) == p) - ++n_roots; - if (par(p) == p || f(par(p)) != f(p)) - ++n_nodes; + + // Tree canonization + P par_p = par(p); + if (f(par(par_p)) == f(par_p) && par(p) != par(par_p)) + { + par(p) = par(par_p); + par_p = par(p); + } + + ++n_sites; // Counting. + + if (f(par_p) == f(p)) + { + if (par_p == p) + { + ++n_roots; // Counting. + ++n_nodes; // Counting. + } + else + { + a(p) = a(par_p); // Attribute image. + flag(p) = flag(par_p); // Flag (regional minima image). + } + } + else + { + ++nchildren(par_p); // Nchildren. + ++n_nodes; // Counting. + } + + +// // Counting. +// ++n_sites; +// if (par_p == p) +// ++n_roots; +// if (par_p == p || f(par_p) != f(p)) +// ++n_nodes; + +// // Attributes. +// if (f(par_p) == f(p)) +// a(p) = a(par_p); + +// // Flag (regional minima image). +// if (f(par_p) == f(p) && flag(par_p) != flag(p)) +// flag(p) = flag(par_p); + +// // Nchildren. +// if (f(par_p) != f(p)) +// ++nchildren(par_p); + } - // Test. + } + + + + + std::cout << "%age nodes = " + << (float(n_nodes) / n_sites * 100.f) << std::endl + << std::endl; + + /* + + // Tests. + { + + // Tree canonization { - mln_piter(S) p(s); + mln_bkd_piter(S) p(s); // Reverse. for_all(p) { P q = par(p); @@ -244,31 +320,61 @@ mln_invariant(f(par(q)) != f(q)); } } - } - - std::cout << "%age nodes = " - << (float(n_nodes) / n_sites * 100.f) << std::endl - << std::endl; + // Nchildren and Attributes. + { + typedef morpho::tree::data<I,S> T; + S s_ = reverse(s); + T t(f, s_, nbh); + typedef typename T::function C; + mln_ch_value(C, unsigned) nc_ref; + initialize(nc_ref, t.f()); + data::fill(nc_ref, 0); + mln_fwd_piter(T) p(t.domain()); + for_all(p) + if (t.is_a_non_root_node(p)) { - // The attr image is not correct on flat zones since there is - // no back-propagation of the attribute value of the component - // root. For instance with f="v v v" we get attr="1 2 3" - // instead of "3 3 3". So a finalization is required. + mln_invariant(t.is_a_node(t.parent(p))); + ++nc_ref(t.parent(p)); + } + mln_invariant((nchildren | t.domain()) == nc_ref); - mln_bkd_piter(S) p(s); // Reverse. + accu::count< util::pix > fixme_; + mln_ch_value(I, mln_result(A)) a_ref; + a_ref = morpho::tree::compute_attribute_image(fixme_, t); + mln_assertion(a == a_ref); + } + + // Nregmins. + { + unsigned n_ref; + mln_ch_value(I, unsigned) ref; + ref = labeling::regional_minima(f, nbh, n_ref); + // debug::println("ref", ref); + + mln_assertion(n_regmins == n_ref); + mln_assertion(((pw::value(ref) != 0) | ref.domain()) == flag); + } + { + unsigned n = 0; + mln_fwd_piter(S) p(s); for_all(p) - if (f(par(p)) == f(p)) - a(p) = a(par(p)); + if (f(par(p)) != f(p) && flag(p)) + ++n; + mln_assertion(n == n_regmins); } - // Display tree. + } // end of Tests. + + if (echo) { + // Display tree, attributes, flags, and nchildren. + mln_ch_value(I, char) tree; initialize(tree, f); data::fill(tree, ' '); @@ -282,82 +388,128 @@ else tree(p) = '.'; debug::println(tree); + + debug::println("a", a); + debug::println("flag", flag); + debug::println("nchildren", nchildren); } +*/ + a_data<I,A> dta; + dta.s = s; + dta.a = a; + dta.nchildren = nchildren; + dta.par = par; + dta.flag = flag; + dta.n_regmins = n_regmins; - { - mln_ch_value(I, unsigned) nchildren; - initialize(nchildren, f); - data::fill(nchildren, 0); + return dta; - mln_fwd_piter(S) p(s); - for_all(p) - if (f(par(p)) != f(p)) - { - // Since the tree is canonized, par(p) is a node - // (a component representative): - P q = par(p); - mln_invariant(par(q) == q || f(par(q)) != f(q)); - ++nchildren(par(p)); - } + } // compute_data - if (echo) - debug::println("nchildren", nchildren); - // Test. - { - typedef morpho::tree::data<I,S> T; - S s_ = reverse(s); - T t(f, s_, nbh); - typedef typename T::function C; - mln_ch_value(C, unsigned) ref; - initialize(ref, t.f()); - data::fill(ref, 0); - mln_fwd_piter(T) p(t.domain()); - for_all(p) - if (t.is_a_non_root_node(p)) + + + //------------------------------- compute_filter + + + + template <typename I, typename A> + mln_concrete(I) + compute_filter(const I& f, const a_data<I,A>& dta, + unsigned n_objects, + mln_result(A)& lambda, + bool echo = false) { - mln_invariant(t.is_a_node(t.parent(p))); - ++ref(t.parent(p)); - } + typedef mln_site(I) P; + typedef p_array S; - mln_invariant((nchildren | t.domain()) == ref); - } + const S& s = dta.s; + mln_ch_value(I, mln_result(A)) a = dta.a; + mln_ch_value(I, unsigned) nchildren = dta.nchildren; + mln_ch_value(I, P) par = dta.par; + unsigned n_regmins = dta.n_regmins; + + if (n_objects >= n_regmins) + { + std::cout << "warning: number of expected objects is greater than number of regmins!" << std::endl; + std::cout << "aborting..." << std::endl; + return duplicate(f); } + unsigned + count = dta.n_regmins, + less = 0; + + // NOW attributes are sorted increasingly! + S s_a = level::sort_psites_increasing(a); - // Tests. - { + + mln_fwd_piter(S) p(s_a); + for_all(p) // with increasing attribute. { - unsigned n_ref; - mln_ch_value(I, unsigned) ref; - ref = labeling::regional_minima(f, nbh, n_ref); - // debug::println("ref", ref); + if (! (par(p) == p || f(par(p)) != f(p))) // Not a node. + continue; - mln_assertion(n_regmins == n_ref); - mln_assertion(((pw::value(ref) != 0) | ref.domain()) == flag); + if (a(p) < lambda && par(p) != p) + { + mln_assertion(nchildren(par(p)) > 0); + --nchildren(par(p)); + if (nchildren(par(p)) != 0) + { + if (count <= n_objects) + { + ++less; // minus 1 object wrt the expected number! } + --count; + if (count == n_objects) { - unsigned n = 0; - mln_fwd_piter(S) p(s); + lambda = a(p) + 1; + std::cout << "lambda = " << lambda << std::endl + << std::endl; + } + } + } + } + + if (less != 0) + std::cerr << "WARNING: less objects (" << less << ") than expected..." << std::endl + << std::endl; + + if (echo) + debug::println("nchildren =", nchildren); + + + // Filtering. + mln_concrete(I) g; + initialize(g, f); + + { + mln_bkd_piter(S) p(s); // Reverse. for_all(p) - if (f(par(p)) != f(p) && flag(p)) - ++n; - mln_assertion(n == n_regmins); + { + if ((par(p) == p || f(par(p)) != f(p)) // p is a node. + && + a(p) >= lambda) // Keep it. + g(p) = f(p); + else + g(p) = g(par(p)); // Propagate => filtering. } - } // end of Tests. - return a; + if (echo) + debug::println("g =", g); + } - } // compute + return g; + } // compute_filter } // mln @@ -367,7 +519,7 @@ void usage(char* argv[]) { - std::cerr << "usage: " << argv[0] << " input.pgm echo" << std::endl; + std::cerr << "usage: " << argv[0] << " input.pgm n_objects filtered.pgm echo" << std::endl; std::abort(); } @@ -378,10 +530,14 @@ using namespace mln; using value::int_u8; - if (argc != 3) + if (argc != 5) + usage(argv); + + int n_objects = std::atoi(argv[2]); + if (n_objects < 0) usage(argv); - int echo = std::atoi(argv[2]); + int echo = std::atoi(argv[4]); if (echo != 0 && echo != 1) usage(argv); @@ -390,37 +546,33 @@ typedef image2d<int_u8> I; - I f; - io::pgm::load(f, argv[1]); + I input; + io::pgm::load(input, argv[1]); if (echo) - debug::println("f", f); + debug::println("input", input); - accu::count<point2d> area; - unsigned n_regmins; - image2d<unsigned> a = compute_a(f, nbh, area, n_regmins, echo); + I f = morpho::elementary::gradient(input, nbh); if (echo) - debug::println("a", a); + debug::println("f (gradient)", f); + typedef accu::count<point2d> A; + typedef mln_result_(A) L; + A area; + unsigned n_regmins; - { - // Test of 'a'. - typedef p_array<point2d> S; - S s = level::sort_psites_decreasing(f); - morpho::tree::data<I,S> t(f, s, nbh); - accu::count< util::pix > area; - image2d<unsigned> a_ref = morpho::tree::compute_attribute_image(area, t); - // debug::println("a_ref", a_ref); - mln_assertion(a == a_ref); - } - + a_data<I,A> dta = compute_data(f, nbh, area, n_regmins, echo); + L lambda; + I g = compute_filter(f, dta, n_objects, lambda, echo); + io::pgm::save(g, argv[3]); -// unsigned n_wanted = 10; -// I g = filtering(f, a, nbh, n_regmins, n_wanted); + unsigned n_basins; + morpho::watershed::flooding(g, nbh, n_basins); + std::cout << "n basins = " << n_basins << std::endl; }

1 0

3376: Update ICIP 2009 code.
by Thierry Geraud 13 Feb '09

13 Feb '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Update ICIP 2009 code. * theo/publis, * theo/publis/icip2009: New directories. * theo/tufa_2008/regmin_count.cc: Move... * theo/publis/icip2009/regmin_count.cc: ...here. * theo/tufa_2008/compute_a.cc: Move... * theo/publis/icip2009/compute_a.cc: ...here. Update. compute_a.cc | 366 ++++++++++++++++++++++++++++++----------------------------- 1 file changed, 190 insertions(+), 176 deletions(-) Index: theo/publis/icip2009/compute_a.cc --- theo/publis/icip2009/compute_a.cc (revision 0) +++ theo/publis/icip2009/compute_a.cc (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 @@ -25,7 +26,7 @@ // reasons why the executable file might be covered by the GNU General // Public License. -/// \file sandbox/geraud/tufa/compute_a.cc +/// \file sandbox/theo/publis/icip2009/compute_a.cc #include <mln/core/image/image2d.hh> #include <mln/core/image/image_if.hh> @@ -47,6 +48,7 @@ #include <mln/accu/count.hh> #include <mln/opt/at.hh> +#include <mln/set/card.hh> @@ -80,6 +82,16 @@ } + template <typename P> + p_array reverse(const p_array& arr) + { + p_array out; + mln_bkd_piter(p_array) p(arr); + for_all(p) + out.insert(p); + return out; + } + //------------------------------- compute_a @@ -87,14 +99,16 @@ template <typename I, typename N, typename A> mln_ch_value(I, mln_result(A)) - compute_a(const I& f, const N& nbh, A, unsigned& n_regmins) + compute_a(const I& f, const N& nbh, A, unsigned& n_regmins, + bool echo = false) { - typedef p_array<mln_psite(I)> S; + typedef mln_site(I) P; + typedef p_array S; S s = level::sort_psites_increasing(f); // s maps increasing attributes. - mln_ch_value(I, mln_site(I)) par; - mln_ch_value(I, mln_site(I)) zpar; + mln_ch_value(I, P) par; + mln_ch_value(I, P) zpar; mln_ch_value(I, bool) deja_vu, flag; mln_ch_value(I, A) attr; @@ -122,7 +136,7 @@ // First Pass. { - mln_site(I) r; + P r; mln_fwd_piter(S) p(s); mln_niter(N) n(nbh, p); for_all(p) @@ -138,230 +152,211 @@ r = find_root__(zpar, n); if (r != p) { - // Fully compressed union. - zpar(r) = p; - attr(p).take(attr(r)); + par(r) = p; // Min-tree computation. + zpar(r) = p; // Fully compressed union. + + attr(p).take(attr(r)); // Attribute computation. if (f(r) == f(p)) { - // Weak-Union; only for flat zones. - par(r) = p; - + // Flat zones. if (flag(p) == false && flag(r) == false) { // Two non-reg-min components merge (same flat // zone) so we had an extra invalidation. ++n_regmins; } + else flag(p) = flag(p) && flag(r); --n_regmins; // So we get the number of flat zones // minus the non-reg-min flat zones. } else { - mln_invariant(f(r) < f(p)); + mln_invariant(f(r) < f(p)); // Increasing browsing. if (flag(p) == true) + { --n_regmins; // Invalidation. flag(p) = false; } } } + } deja_vu(p) = true; } + } // end of First Pass. std::cout << "n reg min = " << n_regmins << std::endl; - { - unsigned n = 0; - mln_fwd_piter(S) p(s); - for_all(p) - if (par(p) == p && flag(p)) - ++n; - mln_assertion(n == n_regmins); - } - - - // The attr image is not correct on flat zones since there is - // no back-propagation of the attribute value of the component - // root. For instance with f="v v v" we get attr="1 2 3" - // instead of "3 3 3". So a finalization is required. + // Output is the attribute image. mln_ch_value(I, mln_result(A)) a; initialize(a, f); data::paste(attr, a); - // Finalization. + + // Back-propagate flags to non-representant component sites. { mln_bkd_piter(S) p(s); // Reverse. - - unsigned n_non_compressed_par = 0; for_all(p) - { - a(p) = a(par(p)); - if (par(par(p)) != par(p)) - ++ n_non_compressed_par; - } - std::cout << "n_non_compressed_par = " << n_non_compressed_par << std::endl; + if (f(par(p)) == f(p) && flag(par(p)) != flag(p)) + flag(p) = flag(par(p)); + if (echo) + debug::println("flag", flag); } - // TODO: compress at least the reg minima! + unsigned + n_sites = 0, + n_roots = 0, + n_nodes = 0; + + // Tree canonization { - image2d<unsigned> regmin; - initialize(regmin, f); - { - unsigned i_regmin = 0; - mln_bkd_piter(S) p(s); + mln_bkd_piter(S) p(s); // Reverse. for_all(p) { + P q = par(p); + if (f(par(q)) == f(q)) + par(p) = par(q); + ++n_sites; if (par(p) == p) + ++n_roots; + if (par(p) == p || f(par(p)) != f(p)) + ++n_nodes; + } + + // Test. { - if (flag(p)) - regmin(p) = ++i_regmin; - else - regmin(p) = 0; + mln_piter(S) p(s); + for_all(p) + { + P q = par(p); + if (q == p || par(q) == q) // Either p or par(p) is root. + continue; + if (f(q) == f(p)) + // p and par(p) within a flat zone + // so q=par(p) is the representant + mln_invariant(f(par(q)) != f(q)); } - else - regmin(p) = regmin(par(p)); } } - debug::println("f", f); - debug::println("flag", flag); - // We can see that some point are at true for components that - // are not reg min; flag is a candidate to be compressed... + std::cout << "%age nodes = " + << (float(n_nodes) / n_sites * 100.f) << std::endl + << std::endl; + - debug::println("regmin", regmin); + { + // The attr image is not correct on flat zones since there is + // no back-propagation of the attribute value of the component + // root. For instance with f="v v v" we get attr="1 2 3" + // instead of "3 3 3". So a finalization is required. + mln_bkd_piter(S) p(s); // Reverse. + for_all(p) + if (f(par(p)) == f(p)) + a(p) = a(par(p)); + } - // TODO: - // On veut tester ici dans quel ordre on voit les - // reg min lorsque a croit. Pour tous les points d'un reg min, - // est-ce que le root est vu en premier ? + // Display tree. + if (echo) + { + mln_ch_value(I, char) tree; + initialize(tree, f); + data::fill(tree, ' '); + mln_piter(I) p(f.domain()); + for_all(p) + if (par(p) == p) // Root. + tree(p) = '@'; + else + if (f(par(p)) != f(p)) // Representative. + tree(p) = 'o'; + else + tree(p) = '.'; + debug::println(tree); + } - image2d<bool> seen; - initialize(seen, f); - data::fill(seen, false); + { + mln_ch_value(I, unsigned) nchildren; + initialize(nchildren, f); + data::fill(nchildren, 0); - s = level::sort_psites_increasing(a); - mln_bkd_piter(S) p(s); + mln_fwd_piter(S) p(s); for_all(p) + if (f(par(p)) != f(p)) { - if (regmin(p) == 0) - continue; - // p is in a regional minimum. - if (par(p) != p) // A non-root point. - { - mln_assertion(regmin(par(p)) != 0); // Root in a regional minimum. - mln_assertion(regmin(par(p)) == regmin(p)); // and the same as p. - mln_assertion(seen(par(p))); - } - seen(p) = true; + // Since the tree is canonized, par(p) is a node + // (a component representative): + P q = par(p); + mln_invariant(par(q) == q || f(par(q)) != f(q)); + ++nchildren(par(p)); } - debug::println(seen); -// if (flag(p)) -// std::cout << a(p) << ' ' < T; + S s_ = reverse(s); + T t(f, s_, nbh); + + typedef typename T::function C; + mln_ch_value(C, unsigned) ref; + initialize(ref, t.f()); + data::fill(ref, 0); + + mln_fwd_piter(T) p(t.domain()); + for_all(p) + if (t.is_a_non_root_node(p)) + { + mln_invariant(t.is_a_node(t.parent(p))); + ++ref(t.parent(p)); } - return a; + mln_invariant((nchildren | t.domain()) == ref); + } } - //------------------------------- filtering + // Tests. + { + { + unsigned n_ref; + mln_ch_value(I, unsigned) ref; + ref = labeling::regional_minima(f, nbh, n_ref); + // debug::println("ref", ref); + + mln_assertion(n_regmins == n_ref); + mln_assertion(((pw::value(ref) != 0) | ref.domain()) == flag); + } + { + unsigned n = 0; + mln_fwd_piter(S) p(s); + for_all(p) + if (f(par(p)) != f(p) && flag(p)) + ++n; + mln_assertion(n == n_regmins); + } + } // end of Tests. -// template <typename I, typename A, typename N> -// mln_concrete(I) filtering(const I& f, const A& a, const N& nbh, -// unsigned n_regmins, unsigned n_wanted) -// { -// typedef p_array<mln_psite(I)> S; -// S s = level::sort_psites_increasing(a); - -// // s maps increasing attributes. - -// mln_concrete(I) out; -// initialize(out, f); - -// mln_ch_value(I, mln_site(I)) par; -// mln_ch_value(I, bool) deja_vu, flag; - -// // Initialization. -// { -// initialize(par, f); -// mln_piter(A) p(par.domain()); -// for_all(p) -// par(p) = p; -// initialize(deja_vu, f); -// data::fill(deja_vu, false); - -// // flag -// initialize(flag, f); -// data::fill(flag, true); -// } - - -// int counter = 0; -// // We are trying to count the number of merges of regional minima... - - -// // First Pass. -// { -// mln_site(I) r; -// mln_fwd_piter(S) p(s); -// mln_niter(N) n(nbh, p); -// for_all(p) -// { -// for_all(n) -// if (a.domain().has(n) && deja_vu(n)) -// { -// r = find_root__(par, n); -// if (r != p) -// if (a(r) == a(p)) -// { -// par(r) = p; // Union. -// if (flag(r) == true && flag(p) == true) -// --counter; -// flag(p) = flag(p) && flag(r); -// } -// else // a(r) != a(p) -// { -// if (flag(r) == true && flag(p) == true) -// ++counter; -// mln_invariant(a(p) > a(r)); -// flag(p) = false; -// } -// } -// deja_vu(p) = true; -// } -// std::cout << counter << std::endl; -// } - -// // // Second Pass. -// // { -// // mln_bkd_piter(S) p(s); -// // for_all(p) -// // if (par(p) == p) -// // out(p) = f(p); -// // else -// // out(p) = out(par(p)); -// // } -// return out; -// } + return a; + } // compute @@ -370,43 +365,62 @@ -int main(int, char* argv[]) +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.pgm echo" << std::endl; + std::abort(); +} + + + +int main(int argc, char* argv[]) { using namespace mln; using value::int_u8; + if (argc != 3) + usage(argv); + + int echo = std::atoi(argv[2]); + if (echo != 0 && echo != 1) + usage(argv); + + + neighb2d nbh = c4(); + + typedef image2d<int_u8> I; I f; io::pgm::load(f, argv[1]); - // debug::println(f); + if (echo) + debug::println("f", f); accu::count<point2d> area; unsigned n_regmins; - image2d<unsigned> a = compute_a(f, c4(), area, n_regmins); - // debug::println(a); -// { -// // Test of 'n_regmins'. -// unsigned ref; -// labeling::regional_minima(f, c4(), ref); -// mln_assertion(n_regmins == ref); -// } - -// { -// // Test of 'a'. -// typedef p_array<point2d> S; -// S s = level::sort_psites_decreasing(f); -// morpho::tree::data<I,S> t(f, s, c4()); -// accu::count< util::pix > area; -// image2d<unsigned> ref = morpho::tree::compute_attribute_image(area, t); -// mln_assertion(a == ref); -// } + image2d<unsigned> a = compute_a(f, nbh, area, n_regmins, echo); + if (echo) + debug::println("a", a); + + + + + { + // Test of 'a'. + typedef p_array<point2d> S; + S s = level::sort_psites_decreasing(f); + morpho::tree::data<I,S> t(f, s, nbh); + accu::count< util::pix > area; + image2d<unsigned> a_ref = morpho::tree::compute_attribute_image(area, t); + // debug::println("a_ref", a_ref); + mln_assertion(a == a_ref); + } // unsigned n_wanted = 10; -// I g = filtering(f, a, c4(), n_regmins, n_wanted); +// I g = filtering(f, a, nbh, n_regmins, n_wanted); } Property changes on: theo/publis/icip2009/compute_a.cc ___________________________________________________________________ Added: svn:mergeinfo Property changes on: theo/publis/icip2009/regmin_count.cc ___________________________________________________________________ Added: svn:mergeinfo

1 0

r3375: Create a sandbox for DICOM support..
by Fabien Freling 13 Feb '09

13 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-02-13 Fabien Freling <fabien.freling(a)lrde.epita.fr> Create a sandbox for DICOM support.. * fabien/dicom/load.hh: Load implementation. * fabien/dicom/save.hh: Save implementation. * fabien/igr/igr.cc: Minor fixes. --- dicom/load.hh | 547 +++++++++++++++++++++++++++ dicom/save.hh | 1171 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ igr/igr.cc | 2 3 files changed, 1719 insertions(+), 1 deletion(-) Index: trunk/milena/sandbox/fabien/igr/igr.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/igr.cc (revision 3374) +++ trunk/milena/sandbox/fabien/igr/igr.cc (revision 3375) @@ -41,7 +41,7 @@ #include <mln/io/cloud/all.hh> #include <mln/io/dump/all.hh> -#include <mln/core/alias/neighb2d.hh> +#include <mln/core/alias/neigyyhb2d.hh> #include <mln/core/alias/neighb3d.hh> #include <mln/labeling/flat_zones.hh> #include <mln/labeling/background.hh> Index: trunk/milena/sandbox/fabien/dicom/save.hh =================================================================== --- trunk/milena/sandbox/fabien/dicom/save.hh (revision 0) +++ trunk/milena/sandbox/fabien/dicom/save.hh (revision 3375) @@ -0,0 +1,1171 @@ +/* + * + * Copyright (C) 1994-2005, OFFIS + * + * This software and supporting documentation were developed by + * + * Kuratorium OFFIS e.V. + * Healthcare Information and Communication Systems + * Escherweg 2 + * D-26121 Oldenburg, Germany + * + * THIS SOFTWARE IS MADE AVAILABLE, AS IS, AND OFFIS MAKES NO WARRANTY + * REGARDING THE SOFTWARE, ITS PERFORMANCE, ITS MERCHANTABILITY OR + * FITNESS FOR ANY PARTICULAR USE, FREEDOM FROM ANY COMPUTER DISEASES OR + * ITS CONFORMITY TO ANY SPECIFICATION. THE ENTIRE RISK AS TO QUALITY AND + * PERFORMANCE OF THE SOFTWARE IS WITH THE USER. + * + * Module: dcmdata + * + * Author: Andreas Barth + * + * Purpose: create a Dicom FileFormat or DataSet from an ASCII-dump + * + * Last Update: $Author: onken $ + * Update Date: $Date: 2005/12/16 09:07:03 $ + * CVS/RCS Revision: $Revision: 1.51 $ + * Status: $State: Exp $ + * + * CVS/RCS Log at end of file + * + */ + +/* + * Input File Description: + * The input file be an output of dcmdump. One element (Tag, VR, value) must + * be written into one line separated by arbitrary spaces or tab characters. + * A # begins a comment that ends at the line end. Empty lines are allowed. + * This parts of a line have the following syntax: + * Tag: (gggg,eeee) + * with gggg and eeee are 4 character hexadecimal values representing + * group- and element-tag. Spaces and Tabs can be anywhere in a Tag + * specification + * VR: Value Representation must be written as 2 characters as in Part 6 + * of the DICOM 3.0 standard. No Spaces or Tabs are allowed between the + * two characters. If the VR can determined from the Tag, this part of + * a line is optional. + * Value: There are several rules for writing values: + * 1. US, SS, SL, UL, FD, FL are written as + * decimal strings that can be read by scanf. + * 2. AT is written as (gggg,eeee) with additional spaces stripped off + * automatically and gggg and eeee being decimal strings that + * can be read by scanf. + * 3. OB, OW values are written as byte or word hexadecimal values + * separated by '\' character. Alternatively, OB or OW values can + * be read from a separate file by writing the filename prefixed + * by a '=' character (e.g. =largepixeldata.dat). The contents of + * the file will be read as is. OW data is expected to be little + * endian ordered and will be swapped if necessary. No checks will + * be made to ensure that the amount of data is reasonable in terms + * of other attributes such as Rows or Columns. + * 4. UI is written as =Name in data dictionary or as + * unique identifer string (see 6.) , e.g. [1.2.840.....] + * 5. Strings without () <> [] spaces, tabs and # can be + * written directly + * 6. Other strings with must be surrounded by [ ]. No + * bracket structure is passed. The value ends at the last ] in + * the line. Anything after the ] is interpreted as comment. + * 7. ( < are interpreted special and may not be used when writing + * an input file by hand as beginning characters of a string. + * Multiple Value are separated by \ + * The sequence of lines must not be ordered but they can. + * References in DICOM Directories are not supported. + * Semantic errors are not detected. + * + * Examples: + * (0008,0020) DA [19921012] # 8, 1 StudyDate + * (0008,0016) UI =MRImageStorage # 26, 1 SOPClassUID + * (0002,0012) UI [1.2.276.0.7230010.100.1.1] + * (0020,0032) DS [0.0\0.0] # 8, 2 ImagePositionPatient + * (0028,0009) AT (3004,000c) # 4, 1 FrameIncrementPointer + * (0028,0010) US 256 # 4, 1 Rows + * (0002,0001) OB 01\00 + * + */ + +#include "dcmtk/config/osconfig.h" + +#define INCLUDE_CSTDLIB +#define INCLUDE_CSTDIO +#define INCLUDE_CCTYPE +#include "dcmtk/ofstd/ofstdinc.h" + +#ifdef HAVE_SYS_TYPES_H +#include <sys/types.h> +#endif +#ifdef HAVE_SYS_STAT_H +#include <sys/stat.h> +#endif +#ifdef HAVE_STAT_H +#include <stat.h> +#endif +#ifdef HAVE_GUSI_H +#include <GUSI.h> +#endif + +#include "dcmtk/ofstd/ofstream.h" +#include "dcmtk/dcmdata/dctk.h" +#include "dcmtk/dcmdata/dcdebug.h" +#include "dcmtk/dcmdata/cmdlnarg.h" +#include "dcmtk/ofstd/ofconapp.h" +#include "dcmtk/ofstd/ofstd.h" +#include "dcmtk/dcmdata/dcuid.h" /* for dcmtk version name */ + +#ifdef WITH_ZLIB +#include <zlib.h> /* for zlibVersion() */ +#endif + +#define OFFIS_CONSOLE_APPLICATION "dump2dcm" + +static char rcsid[] = "$dcmtk: " OFFIS_CONSOLE_APPLICATION " v" + OFFIS_DCMTK_VERSION " " OFFIS_DCMTK_RELEASEDATE " $"; + +#define SHORTCOL 3 +#define LONGCOL 21 + +// Maximum Line Size + +const unsigned int DCM_DumpMaxLineSize = 4096; + + +// Field definition separators + +#define DCM_DumpCommentChar '#' +#define DCM_DumpTagDelim ')' +#define DCM_DumpOpenString '[' +#define DCM_DumpCloseString ']' +#define DCM_DumpOpenDescription '(' +#define DCM_DumpOpenFile '<' +#define DCM_DumpCloseFile '>' + +static void +stripWhitespace(char* s) +{ + char* p; + + if (s == NULL) return; + + p = s; + while (*s != '\0') { + if (isspace(*s) == OFFalse) { + *p++ = *s; + } + s++; + } + *p = '\0'; +} + +static char* +stripTrailingWhitespace(char* s) +{ + int i, n; + if (s == NULL) return s; + + n = strlen(s); + for (i = n - 1; i >= 0 && isspace(s[i]); i--) + s[i] = '\0'; + return s; +} + + +static char * +stripPrecedingWhitespace(char * s) +{ + char * p; + if (s == NULL) return s; + + for(p = s; *p && isspace(*p); p++) + ; + + return p; +} + +static OFBool +onlyWhitespace(const char* s) +{ + int len = strlen(s); + int charsFound = OFFalse; + + for (int i=0; (!charsFound) && (i<len); i++) { + charsFound = !isspace(s[i]); + } + return (!charsFound)?(OFTrue):(OFFalse); +} + +static char* +getLine(char* line, int maxLineLen, FILE* f, const unsigned long lineNumber) +{ + char* s; + + s = fgets(line, maxLineLen, f); + + // if line is too long, throw rest of it away + if (s && strlen(s) == size_t(maxLineLen-1) && s[maxLineLen-2] != '\n') + { + int c = fgetc(f); + while(c != '\n' && c != EOF) + c = fgetc(f); + CERR << "line " << lineNumber << " too long." << endl; + } + + /* strip any trailing white space */ + stripTrailingWhitespace(s); + + return s; +} + +static OFBool +isaCommentLine(const char* s) +{ + OFBool isComment = OFFalse; /* assumption */ + int len = strlen(s); + int i = 0; + for (i=0; i<len && isspace(s[i]); i++) /*loop*/; + isComment = (s[i] == DCM_DumpCommentChar); + return isComment; +} + +static OFBool +parseTag(char* & s, DcmTagKey& key) +{ + OFBool ok = OFTrue; + char * p; + unsigned int g, e; + + // find tag begin + p = strchr(s, DCM_DumpTagDelim); + if (p) + { + // string all white spaces and read tag + int len = p-s+1; + p = new char[len+1]; + OFStandard::strlcpy(p, s, len+1); + stripWhitespace(p); + s += len; + + if (sscanf(p, "(%x,%x)", &g, &e) == 2) { + key.set(g, e); + } else { + ok = OFFalse; + } + delete[] p; + } + else ok = OFFalse; + + return ok; +} + + +static OFBool +parseVR(char * & s, DcmEVR & vr) +{ + OFBool ok = OFTrue; + + s = stripPrecedingWhitespace(s); + + // Are there two upper characters? + if (isupper(*s) && isupper(*(s+1))) + { + char c_vr[3]; + OFStandard::strlcpy(c_vr, s, 3); + // Convert to VR + DcmVR dcmVR(c_vr); + vr = dcmVR.getEVR(); + s+=2; + } + else if ((*s == 'p')&&(*(s+1) == 'i')) + { + vr = EVR_pixelItem; + s+=2; + } + else if (((*s == 'o')&&(*(s+1) == 'x')) || ((*s == 'x')&&(*(s+1) == 's')) || + (*s == 'n')&&(*(s+1) == 'a') || ((*s == 'u')&&(*(s+1) == 'p'))) + { + // swallow internal VRs + vr = EVR_UNKNOWN; + s+=2; + } + else ok = OFFalse; + + return ok; +} + + +static int +searchLastClose(char *s, char closeChar) +{ + // search last close bracket in a line + // no bracket structure will be considered + + char * found = NULL; + char * p = s; + + while(p && *p) + { + p = strchr(p, closeChar); + if (p) + { + found = p; + p++; + } + } + + if (found) + return (found - s) + 1; + else + return 0; +} + + +static int +searchCommentOrEol(char *s) +{ + char * comment = strchr(s, DCM_DumpCommentChar); + if (comment) + return comment - s; + else if (s) + return strlen(s); + else + return 0; +} + + +static char* +convertNewlineCharacters(char* s) +{ + // convert the string "\n" into the \r\n combination required by DICOM + if (s == NULL || s[0] == '\0') return s; + int len = strlen(s); + int i = 0; + for (i=0; i<(len-1); i++) { + if (s[i] == '\\' && s[i+1] == 'n') { + s[i] = '\r'; + s[i+1] = '\n'; + i++; + } + } + + return s; +} + +static OFBool +parseValue(char * & s, char * & value, const DcmEVR & vr) +{ + OFBool ok = OFTrue; + int len; + value = NULL; + + s = stripPrecedingWhitespace(s); + + switch (*s) + { + case DCM_DumpOpenString: + len = searchLastClose(s, DCM_DumpCloseString); + if (len == 0) + ok = OFFalse; + else if (len > 2) + { + value = new char[len-1]; + OFStandard::strlcpy(value, s+1, len-1); + value = convertNewlineCharacters(value); + } + else + value = NULL; + break; + + case DCM_DumpOpenDescription: + /* need to distinguish vr=AT from description field */ + /* NB: if the vr is unknown this workaround will not succeed */ + if (vr == EVR_AT) + { + len = searchLastClose(s, DCM_DumpTagDelim); + if (len >= 11) // (gggg,eeee) allow non-significant spaces + { + char *pv = s; + DcmTagKey tag; + if (parseTag(pv, tag)) // check for valid tag format + { + value = new char[len+1]; + OFStandard::strlcpy(value, s, len+1); + stripWhitespace(value); + } else + ok = OFFalse; // skip description + } + else + ok = OFFalse; // skip description + } + break; + + case DCM_DumpOpenFile: + ok = OFFalse; // currently not supported + break; + + case DCM_DumpCommentChar: + break; + + default: + len = searchCommentOrEol(s); + if (len) + { + value = new char[len+1]; + OFStandard::strlcpy(value, s, len+1); + stripTrailingWhitespace(value); + } + break; + } + return ok; +} + + +static unsigned long +fileSize(const char *fname) +{ + struct stat s; + unsigned long nbytes = 0; + + if (stat(fname, &s) == 0) { + nbytes = s.st_size; + } + return nbytes; +} + +static OFCondition +putFileContentsIntoElement(DcmElement* elem, const char* filename) +{ + FILE* f = NULL; + OFCondition ec = EC_Normal; + + if ((f = fopen(filename, "rb")) == NULL) { + CERR << "ERROR: cannot open binary data file: " << filename << endl; + return EC_InvalidTag; + } + + unsigned long len = fileSize(filename); + unsigned long buflen = len; + if (buflen & 1) buflen++; /* if odd then make even (DICOM required even length values) */ + + Uint8* buf = new Uint8[buflen]; + if (buf == NULL) { + CERR << "ERROR: out of memory reading binary data file: " << filename << endl; + ec = EC_MemoryExhausted; + } else if (fread(buf, 1, OFstatic_cast(size_t, len), f) != len) { + CERR << "ERROR: error reading binary data file: " << filename << ": "; + perror(NULL); + ec = EC_CorruptedData; + } else { + /* assign buffer to attribute */ + DcmEVR evr = elem->getVR(); + if (evr == EVR_OB) { + /* put 8 bit OB data into the attribute */ + ec = elem->putUint8Array(buf, buflen); + } else if (evr == EVR_OW) { + /* put 16 bit OW data into the attribute */ + swapIfNecessary(gLocalByteOrder, EBO_LittleEndian, buf, buflen, sizeof(Uint16)); + ec = elem->putUint16Array(OFreinterpret_cast(Uint16 *, buf), buflen / 2); + } else if (evr == EVR_pixelItem) { + /* pixel item not yet supported */ + } + } + + fclose(f); + delete[] buf; + return ec; +} + +static OFCondition +insertIntoSet(DcmStack & stack, DcmTagKey tagkey, DcmEVR vr, char * value) +{ + // insert new Element into dataset or metaheader + + OFCondition l_error = EC_Normal; + OFCondition newElementError = EC_Normal; + + if (stack.empty()) + l_error = EC_CorruptedData; + + if (l_error == EC_Normal) + { + DcmElement * newElement = NULL; + DcmObject * topOfStack = stack.top(); + + // convert tagkey to tag including VR + DcmTag tag(tagkey); + DcmVR dcmvr(vr); + + const DcmEVR tagvr = tag.getEVR(); + if (tagvr != vr && vr != EVR_UNKNOWN && tagvr != EVR_UNKNOWN && + (tagkey != DCM_LUTData || (vr != EVR_US && vr != EVR_SS && vr != EVR_OW)) && + (tagvr != EVR_xs || (vr != EVR_US && vr != EVR_SS)) && + (tagvr != EVR_ox || (vr != EVR_OB && vr != EVR_OW)) && + (tagvr != EVR_na || vr != EVR_pixelItem)) + { + CERR << "Warning: Tag " << tag << " with wrong VR " + << dcmvr.getVRName() << " found, correct is " + << tag.getVR().getVRName() << endl; + } + + if (vr != EVR_UNKNOWN) + tag.setVR(dcmvr); + + // create new element + newElementError = newDicomElement(newElement, tag); + + if (newElementError == EC_Normal) + { + // tag describes an Element + if (!newElement) + // Tag was ambiguous + l_error = EC_InvalidVR; + else + { + // fill value + if (value) + { + if (value[0] == '=' && (tag.getEVR() == EVR_OB || tag.getEVR() == EVR_OW)) + { + /* + * Special case handling for OB or OW data. + * Allow a value beginning with a '=' character to represent + * a file containing data to be used as the attribute value. + * A '=' character is not a normal value since OB and OW values + * must be written as multivalued hexidecimal (e.g. "00\ff\0d\8f"); + */ + l_error = putFileContentsIntoElement(newElement, value+1); + } + else if (tag.getEVR() == EVR_pixelItem) + { + /* pixel items not yet supported */ + l_error = EC_InvalidTag; + } else { + l_error = newElement->putString(value); + } + } + + // insert element into hierarchy + if (l_error == EC_Normal) + { + switch(topOfStack->ident()) + { + case EVR_item: + case EVR_dirRecord: + case EVR_dataset: + case EVR_metainfo: + { + DcmItem *item = OFstatic_cast(DcmItem *, topOfStack); + item -> insert(newElement); + if (newElement->ident() == EVR_SQ || newElement->ident() == EVR_pixelSQ) + stack.push(newElement); + } + break; + default: + l_error = EC_InvalidTag; + break; + } + } + } + } + else if (newElementError == EC_SequEnd) + { + // pop stack if stack object was a sequence + if (topOfStack->ident() == EVR_SQ || topOfStack->ident() == EVR_pixelSQ) + stack.pop(); + else + l_error = EC_InvalidTag; + } + else if (newElementError == EC_ItemEnd) + { + // pop stack if stack object was an item + switch (topOfStack->ident()) + { + case EVR_item: + case EVR_dirRecord: + case EVR_dataset: + case EVR_metainfo: + stack.pop(); + break; + + default: + l_error = EC_InvalidTag; + break; + } + } + else if (newElementError == EC_InvalidTag) + { + if (tag.getXTag() == DCM_Item) + { + DcmItem * item = NULL; + if (topOfStack->getTag().getXTag() == DCM_DirectoryRecordSequence) + { + // an Item must be pushed to the stack + item = new DcmDirectoryRecord(tag, 0); + OFstatic_cast(DcmSequenceOfItems *, topOfStack) -> insert(item); + stack.push(item); + } + else if (topOfStack->ident() == EVR_SQ) + { + // an item must be pushed to the stack + item = new DcmItem(tag); + OFstatic_cast(DcmSequenceOfItems *, topOfStack) -> insert(item); + stack.push(item); + } + else + l_error = EC_InvalidTag; + } + else + l_error = EC_InvalidTag; + } + else + { + l_error = EC_InvalidTag; + } + } + + return l_error; +} + +static OFBool +readDumpFile(DcmMetaInfo * metaheader, DcmDataset * dataset, + FILE * infile, const char * ifname, const OFBool stopOnErrors, + const unsigned long maxLineLength) +{ + char * lineBuf = new char[maxLineLength]; + int lineNumber = 0; + OFBool errorOnThisLine = OFFalse; + char * parse = NULL; + char * value = NULL; + DcmEVR vr = EVR_UNKNOWN; + int errorsEncountered = 0; + DcmTagKey tagkey; + DcmStack metaheaderStack; + DcmStack datasetStack; + + if (metaheader) + metaheaderStack.push(metaheader); + + datasetStack.push(dataset); + + while(getLine(lineBuf, int(maxLineLength), infile, lineNumber+1)) + { + lineNumber++; + + // ignore empty lines and comment lines + if (onlyWhitespace(lineBuf)) + continue; + if (isaCommentLine(lineBuf)) + continue; + + errorOnThisLine = OFFalse; + + parse = &lineBuf[0]; + + // parse tag an the line + if (!parseTag(parse, tagkey)) + { + CERR << OFFIS_CONSOLE_APPLICATION ": "<< ifname << ": " + << "no Tag found (line " << lineNumber << ")"<< endl; + errorOnThisLine = OFTrue; + } + + // parse optional VR + if (!errorOnThisLine && !parseVR(parse, vr)) + vr = EVR_UNKNOWN; + + // parse optional value + if (!errorOnThisLine && !parseValue(parse, value, vr)) + { + CERR << OFFIS_CONSOLE_APPLICATION ": "<< ifname << ": " + << "incorrect value specification (line " << lineNumber << ")"<< endl; + errorOnThisLine = OFTrue; + } + + + // insert new element that consists of tag, VR, and value + if (!errorOnThisLine) + { + OFCondition l_error = EC_Normal; + if (tagkey.getGroup() == 2) + { + if (metaheader) + l_error = insertIntoSet(metaheaderStack, tagkey, vr, value); + } + else + l_error = insertIntoSet(datasetStack, tagkey, vr, value); + + if (value) + { + delete[] value; + value = NULL; + } + if (l_error != EC_Normal) + { + errorOnThisLine = OFTrue; + CERR << OFFIS_CONSOLE_APPLICATION ": " << ifname << ": Error in creating Element: " + << l_error.text() << " (line " << lineNumber << ")"<< endl; + } + + } + + if (errorOnThisLine) + errorsEncountered++; + } + + + // test blocking structure + if (metaheader && metaheaderStack.card() != 1) + { + CERR << OFFIS_CONSOLE_APPLICATION ": " << ifname << ": Block Error in metaheader" << endl; + errorsEncountered++; + } + + if (datasetStack.card() != 1) + { + CERR << OFFIS_CONSOLE_APPLICATION ": " << ifname << ": Block Error in dataset" << endl; + errorsEncountered++; + } + + delete[] lineBuf; + + if (errorsEncountered) + { + CERR << errorsEncountered << " Errors found in " << ifname << endl; + return !stopOnErrors; + } + else + return OFTrue; +} + +// ******************************************** + +int main(int argc, char *argv[]) +{ +#ifdef HAVE_GUSI_H + GUSISetup(GUSIwithSIOUXSockets); + GUSISetup(GUSIwithInternetSockets); +#endif + + SetDebugLevel(( 0 )); + + OFConsoleApplication app(OFFIS_CONSOLE_APPLICATION , "Convert ASCII dump to DICOM file", rcsid); + OFCommandLine cmd; + + cmd.setOptionColumns(LONGCOL, SHORTCOL); + cmd.setParamColumn(LONGCOL + SHORTCOL + 4); + + cmd.addParam("dumpfile-in", "dump input filename"); + cmd.addParam("dcmfile-out", "DICOM output filename"); + + cmd.addGroup("general options:", LONGCOL, SHORTCOL + 2); + cmd.addOption("--help", "-h", "print this help text and exit"); + cmd.addOption("--version", "print version information and exit", OFTrue /* exclusive */); + cmd.addOption("--verbose", "-v", "verbose mode, print processing details"); + cmd.addOption("--debug", "-d", "debug mode, print debug information"); + + cmd.addGroup("input options:", LONGCOL, SHORTCOL + 2); + cmd.addOption("--line", "+l", 1, "[m]ax-length: integer", + "maximum line length m (default 4096)"); + + cmd.addGroup("output options:"); + cmd.addSubGroup("output file format:"); + cmd.addOption("--write-file", "+F", "write file format (default)"); + cmd.addOption("--write-dataset", "-F", "write data set without file meta information"); + cmd.addSubGroup("output transfer syntax:"); + cmd.addOption("--write-xfer-little", "+te", "write with explicit VR little endian (default)"); + cmd.addOption("--write-xfer-big", "+tb", "write with explicit VR big endian TS"); + cmd.addOption("--write-xfer-implicit", "+ti", "write with implicit VR little endian TS"); + cmd.addSubGroup("error handling:"); + cmd.addOption("--stop-on-error", "-E", "do not write if dump is damaged (default)"); + cmd.addOption("--ignore-errors", "+E", "attempt to write even if dump is damaged"); + cmd.addSubGroup("post-1993 value representations:"); + cmd.addOption("--enable-new-vr", "+u", "enable support for new VRs (UN/UT) (default)"); + cmd.addOption("--disable-new-vr", "-u", "disable support for new VRs, convert to OB"); + cmd.addSubGroup("group length encoding:"); + cmd.addOption("--group-length-recalc", "+g=", "recalculate group lengths if present (default)"); + cmd.addOption("--group-length-create", "+g", "always write with group length elements"); + cmd.addOption("--group-length-remove", "-g", "always write without group length elements"); + cmd.addSubGroup("length encoding in sequences and items:"); + cmd.addOption("--length-explicit", "+e", "write with explicit lengths (default)"); + cmd.addOption("--length-undefined", "-e", "write with undefined lengths"); + cmd.addSubGroup("data set trailing padding (not with --write-dataset):"); + cmd.addOption("--padding-retain", "-p=", "do not change padding\n(default if not --write-dataset)"); + cmd.addOption("--padding-off", "-p", "no padding (implicit if --write-dataset)"); + cmd.addOption("--padding-create", "+p", 2, "[f]ile-pad [i]tem-pad: integer", + "align file on multiple of f bytes\nand items on multiple of i bytes"); + + int opt_debugMode = 0; + const char* ifname = NULL; + const char* ofname = NULL; + E_TransferSyntax oxfer = EXS_LittleEndianExplicit; + E_EncodingType oenctype = EET_ExplicitLength; + E_GrpLenEncoding oglenc = EGL_recalcGL; + E_PaddingEncoding opadenc = EPD_withoutPadding; + OFCmdUnsignedInt opt_filepad = 0; + OFCmdUnsignedInt opt_itempad = 0; + OFCmdUnsignedInt opt_linelength = DCM_DumpMaxLineSize; + OFBool verbosemode = OFFalse; + OFBool stopOnErrors = OFTrue; + OFBool createFileFormat = OFTrue; + + /* evaluate command line */ + prepareCmdLineArgs(argc, argv, OFFIS_CONSOLE_APPLICATION); + if (app.parseCommandLine(cmd, argc, argv, OFCommandLine::ExpandWildcards)) + { + /* check exclusive options first */ + + if (cmd.getParamCount() == 0) + { + if (cmd.findOption("--version")) + { + app.printHeader(OFTrue /*print host identifier*/); // uses ofConsole.lockCerr() + CERR << endl << "External libraries used:"; +#ifdef WITH_ZLIB + CERR << endl << "- ZLIB, Version " << zlibVersion() << endl; +#else + CERR << " none" << endl; +#endif + return 0; + } + } + + /* command line parameters */ + + cmd.getParam(1, ifname); + cmd.getParam(2, ofname); + + if (cmd.findOption("--verbose")) verbosemode = OFTrue; + if (cmd.findOption("--debug")) opt_debugMode = 5; + + if (cmd.findOption("--line")) + { + app.checkValue(cmd.getValueAndCheckMin(opt_linelength, 80)); + } + + cmd.beginOptionBlock(); + if (cmd.findOption("--write-file")) createFileFormat = OFTrue; + if (cmd.findOption("--write-dataset")) createFileFormat = OFFalse; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--write-xfer-little")) oxfer = EXS_LittleEndianExplicit; + if (cmd.findOption("--write-xfer-big")) oxfer = EXS_BigEndianExplicit; + if (cmd.findOption("--write-xfer-implicit")) oxfer = EXS_LittleEndianImplicit; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--stop-on-error")) stopOnErrors = OFTrue; + if (cmd.findOption("--ignore-errors")) stopOnErrors = OFFalse; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--enable-new-vr")) + { + dcmEnableUnknownVRGeneration.set(OFTrue); + dcmEnableUnlimitedTextVRGeneration.set(OFTrue); + } + if (cmd.findOption("--disable-new-vr")) + { + dcmEnableUnknownVRGeneration.set(OFFalse); + dcmEnableUnlimitedTextVRGeneration.set(OFFalse); + } + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--group-length-recalc")) oglenc = EGL_recalcGL; + if (cmd.findOption("--group-length-create")) oglenc = EGL_withGL; + if (cmd.findOption("--group-length-remove")) oglenc = EGL_withoutGL; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--length-explicit")) oenctype = EET_ExplicitLength; + if (cmd.findOption("--length-undefined")) oenctype = EET_UndefinedLength; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--padding-retain")) + { + if (!createFileFormat) app.printError("--padding-retain not allowed with --write-dataset"); + opadenc = EPD_noChange; + } + if (cmd.findOption("--padding-off")) opadenc = EPD_withoutPadding; + if (cmd.findOption("--padding-create")) + { + if (!createFileFormat) app.printError("--padding-create not allowed with --write-dataset"); + app.checkValue(cmd.getValueAndCheckMin(opt_filepad, 0)); + app.checkValue(cmd.getValueAndCheckMin(opt_itempad, 0)); + opadenc = EPD_withPadding; + } + cmd.endOptionBlock(); + + } + + DcmFileFormat fileformat; + DcmMetaInfo * metaheader = fileformat.getMetaInfo(); + DcmDataset * dataset = fileformat.getDataset(); + + SetDebugLevel((opt_debugMode)); + + /* make sure data dictionary is loaded */ + if (!dcmDataDict.isDictionaryLoaded()) { + CERR << "Warning: no data dictionary loaded, " + << "check environment variable: " + << DCM_DICT_ENVIRONMENT_VARIABLE << endl; + } + + if (verbosemode) + COUT << "reading dump file: " << ifname << endl; + + // open input dump file + if ((ifname == NULL) || (strlen(ifname) == 0)) + { + CERR << "invalid input filename: <empty string>" << endl; + return 1; + } + FILE * dumpfile = fopen(ifname, "r"); + if (!dumpfile) + { + CERR << "input file does not exist: " << ifname << endl; + return 1; + } + + // read dump file into metaheader and dataset + if (readDumpFile(metaheader, dataset, dumpfile, ifname, stopOnErrors, + OFstatic_cast(unsigned long, opt_linelength))) + { + // write into file format or dataset + if (verbosemode) + COUT << "writing DICOM file" << endl; + + OFCondition l_error = fileformat.saveFile(ofname, oxfer, oenctype, oglenc, opadenc, + OFstatic_cast(Uint32, opt_filepad), OFstatic_cast(Uint32, opt_itempad), !createFileFormat); + + if (l_error == EC_Normal) + COUT << "dump successfully converted." << endl; + else + { + CERR << "Error: " << l_error.text() + << ": writing file: " << ofname << endl; + return 1; + } + } + + return 0; +} + +//******************************* + +/* +** CVS/RCS Log: +** $Log: dump2dcm.cc,v $ +** Revision 1.51 2005/12/16 09:07:03 onken +** - Added variable initialization to avoid compiler warning +** +** Revision 1.50 2005/12/08 15:40:50 meichel +** Changed include path schema for all DCMTK header files +** +** Revision 1.49 2004/07/13 09:43:10 meichel +** Fixed memory leak occuring when raw data is read from file. +** +** Revision 1.48 2004/03/05 09:59:00 joergr +** Avoid wrong warning for LUTData (0028,3006) having a VR of US or SS. +** Added initial "hooks" for (compressed) pixel items. +** Added "ignore errors" option (similar to dcmdump). +** +** Revision 1.47 2004/01/16 10:53:16 joergr +** Adapted type casts to new-style typecast operators defined in ofcast.h. +** Removed acknowledgements with e-mail addresses from CVS log. +** +** Revision 1.46 2003/11/05 16:15:27 meichel +** Removed useless "--write-xfer-same" command line option +** +** Revision 1.45 2002/12/05 13:59:29 joergr +** Fixed typo. +** +** Revision 1.44 2002/11/27 12:07:18 meichel +** Adapted module dcmdata to use of new header file ofstdinc.h +** +** Revision 1.43 2002/11/26 08:43:02 meichel +** Replaced all includes for "zlib.h" with <zlib.h> +** to avoid inclusion of zlib.h in the makefile dependencies. +** +** Revision 1.42 2002/09/23 17:52:04 joergr +** Prepared code for future support of 'config.guess' host identifiers. +** +** Revision 1.41 2002/09/23 13:50:42 joergr +** Added new command line option "--version" which prints the name and version +** number of external libraries used. +** +** Revision 1.40 2002/08/21 10:14:16 meichel +** Adapted code to new loadFile and saveFile methods, thus removing direct +** use of the DICOM stream classes. +** +** Revision 1.39 2002/04/16 13:38:55 joergr +** Added configurable support for C++ ANSI standard includes (e.g. streams). +** +** Revision 1.38 2001/12/11 14:00:39 joergr +** Fixed bug in 'dump2dcm' parser causing AT attribute values to be ignored. +** +** Revision 1.37 2001/11/09 15:50:53 joergr +** Renamed some of the getValue/getParam methods to avoid ambiguities reported +** by certain compilers. +** +** Revision 1.36 2001/09/25 17:21:01 meichel +** Adapted dcmdata to class OFCondition +** +** Revision 1.35 2001/06/01 15:48:30 meichel +** Updated copyright header +** +** Revision 1.34 2000/04/14 15:42:54 meichel +** Global VR generation flags are now derived from OFGlobal and, thus, +** safe for use in multi-thread applications. +** +** Revision 1.33 2000/03/08 16:26:06 meichel +** Updated copyright header. +** +** Revision 1.32 2000/03/06 18:09:38 joergr +** Avoid empty statement in the body of if-statements (MSVC6 reports warnings). +** +** Revision 1.31 2000/03/03 14:05:16 meichel +** Implemented library support for redirecting error messages into memory +** instead of printing them to stdout/stderr for GUI applications. +** +** Revision 1.30 2000/02/29 11:48:51 meichel +** Removed support for VS value representation. This was proposed in CP 101 +** but never became part of the standard. +** +** Revision 1.29 2000/02/23 15:11:36 meichel +** Corrected macro for Borland C++ Builder 4 workaround. +** +** Revision 1.28 2000/02/10 16:02:51 joergr +** Enhanced handling of PixelData/Item element. Externally stored raw data is +** now always imported as little endian and swapped if necessary. This change +** reflects the new 'export' feature of dcmdump. +** +** Revision 1.27 2000/02/01 10:11:58 meichel +** Avoiding to include <stdlib.h> as extern "C" on Borland C++ Builder 4, +** workaround for bug in compiler header files. +** +** Revision 1.26 1999/05/03 14:13:40 joergr +** Minor code purifications to keep Sun CC 2.0.1 quiet. +** +** Revision 1.25 1999/04/27 17:50:53 joergr +** Adapted console applications to new OFCommandLine and OFConsoleApplication +** functionality. +** +** Revision 1.24 1999/04/27 12:23:27 meichel +** Prevented dcmdata applications from opening a file with empty filename, +** leads to application crash on Win32. +** +** Revision 1.23 1999/03/31 09:24:23 meichel +** Updated copyright header in module dcmdata +** +** Revision 1.22 1999/03/29 10:14:15 meichel +** Adapted command line options of dcmdata applications to new scheme. +** +** Revision 1.21 1999/03/22 16:16:01 meichel +** dump2dcm now allows to include the contents of binary files +** as OB/OW values while converting a dump to a DICOM file. +** +** Revision 1.20 1999/01/07 14:13:12 meichel +** Corrected bug in dump2dcm that prevented the correct processing of +** dumps created with dcmdump if they contained the "internal" VR markers +** "xs" (US or SS) or "ox" (OB or OW). +** +** Revision 1.19 1998/01/27 10:51:27 meichel +** Removed some unused variables, meaningless const modifiers +** and unreached statements. +** +** Revision 1.18 1998/01/14 14:41:15 hewett +** Modified existing -u command line option to also disable generation +** of UT and VS (previously just disabled generation of UN). +** +** Revision 1.17 1997/08/05 07:34:54 andreas +** Corrected Error handling of SQ in dump2dcm +** +** Revision 1.16 1997/07/21 07:59:02 andreas +** - Deleted support for DcmPixelItems and DcmPixelSequences in dump2dcm +** ToDo: New support should be added in the future compatible to +** the new DcmPixel class. +** - Replace all boolean types (BOOLEAN, CTNBOOLEAN, DICOM_BOOL, BOOL) +** with one unique boolean type OFBool. +** +** Revision 1.15 1997/07/03 15:09:40 andreas +** - removed debugging functions Bdebug() and Edebug() since +** they write a static array and are not very useful at all. +** Cdebug and Vdebug are merged since they have the same semantics. +** The debugging functions in dcmdata changed their interfaces +** (see dcmdata/include/dcdebug.h) +** +** Revision 1.14 1997/05/30 06:44:57 andreas +** - fixed scanf format problem leading to warnings on 64 bit machines. +** +** Revision 1.13 1997/05/29 15:52:52 meichel +** Added constant for dcmtk release date in dcuid.h. +** All dcmtk applications now contain a version string +** which is displayed with the command line options ("usage" message) +** and which can be queried in the binary with the "ident" command. +** +** Revision 1.12 1997/05/22 13:26:25 hewett +** Modified the test for presence of a data dictionary to use the +** method DcmDataDictionary::isDictionaryLoaded(). +** +** Revision 1.11 1997/05/20 07:57:12 andreas +** - Removed obsolete applications file2ds and ds2file. The functionality of these +** applications is now peformed by dcmconv. Unified calling parameters +** are implemented in dump2dcm, dcmdump and dcmconv. +** +** Revision 1.10 1997/05/16 08:31:06 andreas +** - Revised handling of GroupLength elements and support of +** DataSetTrailingPadding elements. The enumeratio E_GrpLenEncoding +** got additional enumeration values (for a description see dctypes.h). +** addGroupLength and removeGroupLength methods are replaced by +** computeGroupLengthAndPadding. To support Padding, the parameters of +** element and sequence write functions changed. +** +** Revision 1.9 1997/04/18 08:06:56 andreas +** - Minor corrections: correct some warnings of the SUN-C++ Compiler +** concerning the assignments of wrong types and inline compiler +** errors +** - The put/get-methods for all VRs did not conform to the C++-Standard +** draft. Some Compilers (e.g. SUN-C++ Compiler, Metroworks +** CodeWarrier, etc.) create many warnings concerning the hiding of +** overloaded get methods in all derived classes of DcmElement. +** So the interface of all value representation classes in the +** library are changed rapidly, e.g. +** OFCondition get(Uint16 & value, const unsigned long pos); +** becomes +** OFCondition getUint16(Uint16 & value, const unsigned long pos); +** All (retired) "returntype get(...)" methods are deleted. +** For more information see dcmdata/include/dcelem.h +** +** Revision 1.8 1997/03/27 15:47:25 hewett +** Added command line switche to allow generation of UN to be +** disabled (it is enabled by default). +** +** Revision 1.7 1996/09/24 16:13:51 hewett +** Added preliminary support for the Macintosh environment (GUSI library). +** +** Revision 1.6 1996/05/02 17:00:23 hewett +** Corrected program name in usage description. +** +** Revision 1.5 1996/05/02 15:55:11 hewett +** Stopped whitespace being stripped from inside value strings when +** no [] delimiter present. Now only leading and trailing whitespace +** is stripped. +** +** Revision 1.4 1996/04/27 12:13:01 hewett +** Corrected bug in last bug-fix. A tag value [some text] was being +** parsed as an empty string. Now both [] and [some text] appear to +** work as intended. +** +** Revision 1.3 1996/03/22 12:38:44 andreas +** Correct some mistakes: handling [] as empty string (no value field) +** handling =Name correct if Name is not correct +** +** Revision 1.2 1996/03/12 15:11:39 hewett +** Added call to prepareCmdLineArgs to enable command line arguments +** in environments which do not provide them. +** +** Revision 1.1 1996/01/29 13:36:38 andreas +** dump2dcm added convert ASCII descriptions into DICOM files +** +** +*/ Index: trunk/milena/sandbox/fabien/dicom/load.hh =================================================================== --- trunk/milena/sandbox/fabien/dicom/load.hh (revision 0) +++ trunk/milena/sandbox/fabien/dicom/load.hh (revision 3375) @@ -0,0 +1,547 @@ +/* + * + * Copyright (C) 1994-2005, OFFIS + * + * This software and supporting documentation were developed by + * + * Kuratorium OFFIS e.V. + * Healthcare Information and Communication Systems + * Escherweg 2 + * D-26121 Oldenburg, Germany + * + * THIS SOFTWARE IS MADE AVAILABLE, AS IS, AND OFFIS MAKES NO WARRANTY + * REGARDING THE SOFTWARE, ITS PERFORMANCE, ITS MERCHANTABILITY OR + * FITNESS FOR ANY PARTICULAR USE, FREEDOM FROM ANY COMPUTER DISEASES OR + * ITS CONFORMITY TO ANY SPECIFICATION. THE ENTIRE RISK AS TO QUALITY AND + * PERFORMANCE OF THE SOFTWARE IS WITH THE USER. + * + * Module: dcmdata + * + * Author: Gerd Ehlers + * + * Purpose: List the contents of a dicom file + * + * Last Update: $Author: meichel $ + * Update Date: $Date: 2005/12/08 15:40:46 $ + * CVS/RCS Revision: $Revision: 1.55 $ + * Status: $State: Exp $ + * + * CVS/RCS Log at end of file + * + */ + +#include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */ +#include "dcmtk/ofstd/ofstream.h" +#include "dcmtk/dcmdata/dctk.h" +#include "dcmtk/dcmdata/dcdebug.h" +#include "dcmtk/dcmdata/cmdlnarg.h" +#include "dcmtk/ofstd/ofconapp.h" +#include "dcmtk/dcmdata/dcuid.h" /* for dcmtk version name */ +#include "dcmtk/dcmdata/dcistrmz.h" /* for dcmZlibExpectRFC1950Encoding */ + +#define INCLUDE_CSTDLIB +#define INCLUDE_CSTRING +#include "dcmtk/ofstd/ofstdinc.h" + +#ifdef WITH_ZLIB +#include <zlib.h> /* for zlibVersion() */ +#endif + +#define OFFIS_CONSOLE_APPLICATION "dcmdump" + +static char rcsid[] = "$dcmtk: " OFFIS_CONSOLE_APPLICATION " v" + OFFIS_DCMTK_VERSION " " OFFIS_DCMTK_RELEASEDATE " $"; + +#ifdef HAVE_GUSI_H + /* needed for Macintosh */ +#include <GUSI.h> +#include <SIOUX.h> +#endif + +static int dumpFile(ostream & out, + const char *ifname, + const E_FileReadMode readMode, + const E_TransferSyntax xfer, + const size_t printFlags, + const OFBool loadIntoMemory, + const OFBool stopOnErrors, + const OFBool writePixelData, + const char *pixelDirectory); + +// ******************************************** + +static OFBool printAllInstances = OFTrue; +static OFBool prependSequenceHierarchy = OFFalse; +static int printTagCount = 0; +static const int MAX_PRINT_TAG_NAMES = 1024; +static const char* printTagNames[MAX_PRINT_TAG_NAMES]; +static const DcmTagKey* printTagKeys[MAX_PRINT_TAG_NAMES]; +static OFCmdUnsignedInt maxReadLength = 4096; // default is 4 KB + +static OFBool addPrintTagName(const char* tagName) +{ + if (printTagCount >= MAX_PRINT_TAG_NAMES) { + CERR << "error: too many print Tag options (max: " << MAX_PRINT_TAG_NAMES << ")" << endl; + return OFFalse; + } + + unsigned int group = 0xffff; + unsigned int elem = 0xffff; + if (sscanf( tagName, "%x,%x", &group, &elem ) != 2 ) + { + /* it is a name */ + const DcmDataDictionary& globalDataDict = dcmDataDict.rdlock(); + const DcmDictEntry *dicent = globalDataDict.findEntry(tagName); + if( dicent == NULL ) { + CERR << "error: unrecognised tag name: '" << tagName << "'" << endl; + dcmDataDict.unlock(); + return OFFalse; + } else { + /* note for later */ + printTagKeys[printTagCount] = new DcmTagKey(dicent->getKey()); + } + dcmDataDict.unlock(); + } else { + /* tag name has format xxxx,xxxx */ + /* do not lookup in dictionary, tag could be private */ + printTagKeys[printTagCount] = NULL; + } + + printTagNames[printTagCount] = strcpy(OFstatic_cast(char*, malloc(strlen(tagName)+1)), tagName); + printTagCount++; + return OFTrue; +} + +#define SHORTCOL 3 +#define LONGCOL 20 + +int main(int argc, char *argv[]) +{ + int opt_debugMode = 0; + OFBool loadIntoMemory = OFTrue; + size_t printFlags = DCMTypes::PF_shortenLongTagValues /*| DCMTypes::PF_showTreeStructure*/; + OFBool printFilename = OFFalse; + OFBool writePixelData = OFFalse; + E_FileReadMode readMode = ERM_autoDetect; + E_TransferSyntax xfer = EXS_Unknown; + OFBool stopOnErrors = OFTrue; + const char *current = NULL; + const char *pixelDirectory = NULL; + + +#ifdef HAVE_GUSI_H + /* needed for Macintosh */ + /* set options for the Metrowerks CodeWarrior SIOUX console */ + SIOUXSettings.autocloseonquit = OFFalse; + SIOUXSettings.asktosaveonclose = OFFalse; + SIOUXSettings.showstatusline = OFTrue; + SIOUXSettings.setupmenus = OFTrue; + /* set options for the GUSI sockets library */ + GUSISetup(GUSIwithSIOUXSockets); + GUSISetup(GUSIwithInternetSockets); +#endif + + SetDebugLevel(( 0 )); + + OFConsoleApplication app(OFFIS_CONSOLE_APPLICATION, "Dump DICOM file and data set", rcsid); + OFCommandLine cmd; + cmd.setOptionColumns(LONGCOL, SHORTCOL); + cmd.setParamColumn(LONGCOL + SHORTCOL + 4); + + cmd.addParam("dcmfile-in", "DICOM input filename to be dumped", OFCmdParam::PM_MultiMandatory); + + cmd.addGroup("general options:", LONGCOL, SHORTCOL + 2); + cmd.addOption("--help", "-h", "print this help text and exit"); + cmd.addOption("--version", "print version information and exit", OFTrue /* exclusive */); +#ifdef USE_EXPERIMENTAL_QUIET_MODE + cmd.addOption("--quiet", "-q", "quiet mode, print no warnings and errors"); +#endif + cmd.addOption("--debug", "-d", "debug mode, print debug information"); + + cmd.addGroup("input options:"); + cmd.addSubGroup("input file format:"); + cmd.addOption("--read-file", "+f", "read file format or data set (default)"); + cmd.addOption("--read-file-only", "+fo", "read file format only"); + cmd.addOption("--read-dataset", "-f", "read data set without file meta information"); + cmd.addSubGroup("input transfer syntax:"); + cmd.addOption("--read-xfer-auto", "-t=", "use TS recognition (default)"); + cmd.addOption("--read-xfer-detect", "-td", "ignore TS specified in the file meta header"); + cmd.addOption("--read-xfer-little", "-te", "read with explicit VR little endian TS"); + cmd.addOption("--read-xfer-big", "-tb", "read with explicit VR big endian TS"); + cmd.addOption("--read-xfer-implicit", "-ti", "read with implicit VR little endian TS"); + cmd.addSubGroup("parsing of odd-length attributes:"); + cmd.addOption("--accept-odd-length", "+ao", "accept odd length attributes (default)"); + cmd.addOption("--assume-even-length", "+ae", "assume real length is one byte larger"); + cmd.addSubGroup("handling of undefined length UN elements:"); + cmd.addOption("--enable-cp246", "+ui", "read undefined len UN as implicit VR (default)"); + cmd.addOption("--disable-cp246", "-ui", "read undefined len UN as explicit VR"); + cmd.addSubGroup("handling of defined length UN elements:"); + cmd.addOption("--retain-un", "-uc", "retain elements as UN (default)"); + cmd.addOption("--convert-un", "+uc", "convert to real VR if known"); + cmd.addSubGroup("automatic data correction:"); + cmd.addOption("--enable-correction", "+dc", "enable automatic data correction (default)"); + cmd.addOption("--disable-correction", "-dc", "disable automatic data correction"); +#ifdef WITH_ZLIB + cmd.addSubGroup("bitstream format of deflated input:"); + cmd.addOption("--bitstream-deflated", "+bd", "expect deflated bitstream (default)"); + cmd.addOption("--bitstream-zlib", "+bz", "expect deflated zlib bitstream"); +#endif + + cmd.addGroup("output options:"); + cmd.addSubGroup("printing:"); + cmd.addOption("--load-all", "+M", "load very long tag values (default)"); + cmd.addOption("--load-short", "-M", "do not load very long values (e.g. pixel data)"); + cmd.addOption("--max-read-length", "+R", 1, "[k]bytes: integer [4..4194302] (default: 4)", + "set threshold for long values to k kbytes"); + cmd.addOption("--print-all", "+L", "print long tag values completely"); + cmd.addOption("--print-short", "-L", "print long tag values shortened (default)"); + cmd.addOption("--print-filename", "+F", "print header with filename for each input file"); + + cmd.addSubGroup("error handling:"); + cmd.addOption("--stop-on-error", "-E", "do not print if file is damaged (default)"); + cmd.addOption("--ignore-errors", "+E", "attempt to print even if file is damaged"); + + cmd.addSubGroup("searching:"); + cmd.addOption("--search", "+P", 1, "[t]ag: \"xxxx,xxxx\" or a data dictionary name", + "print the value of tag t\nthis option can be specified multiple times\n(default: the complete file is printed)"); + + cmd.addOption("--search-all", "+s", "print all instances of searched tags (default)"); + cmd.addOption("--search-first", "-s", "only print first instance of searched tags"); + + cmd.addOption("--prepend", "+p", "prepend sequence hierarchy to printed tag,\ndenoted by: (xxxx,xxxx).(xxxx,xxxx).*\n(only with --search-all or --search-first)"); + cmd.addOption("--no-prepend", "-p", "do not prepend hierarchy to tag (default)"); + + cmd.addSubGroup("writing:"); + cmd.addOption("--write-pixel", "+W", 1, "[d]irectory : string", + "write pixel data to a .raw file stored in d\n(little endian, filename created automatically)"); + + /* evaluate command line */ + prepareCmdLineArgs(argc, argv, OFFIS_CONSOLE_APPLICATION); + if (app.parseCommandLine(cmd, argc, argv, OFCommandLine::ExpandWildcards)) + { + /* check exclusive options first */ + + if (cmd.getParamCount() == 0) + { + if (cmd.findOption("--version")) + { + app.printHeader(OFTrue /*print host identifier*/); // uses ofConsole.lockCerr() + CERR << endl << "External libraries used:"; +#ifdef WITH_ZLIB + CERR << endl << "- ZLIB, Version " << zlibVersion() << endl; +#else + CERR << " none" << endl; +#endif + return 0; + } + } + + /* options */ + +#ifdef USE_EXPERIMENTAL_QUIET_MODE + if (cmd.findOption("--quiet")) + { + // tbd: disable ofConsole output! + app.setQuietMode(); + } +#endif + if (cmd.findOption("--debug")) opt_debugMode = 5; + + cmd.beginOptionBlock(); + if (cmd.findOption("--read-file")) readMode = ERM_autoDetect; + if (cmd.findOption("--read-file-only")) readMode = ERM_fileOnly; + if (cmd.findOption("--read-dataset")) readMode = ERM_dataset; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--read-xfer-auto")) + xfer = EXS_Unknown; + if (cmd.findOption("--read-xfer-detect")) + dcmAutoDetectDatasetXfer.set(OFTrue); + if (cmd.findOption("--read-xfer-little")) + { + app.checkDependence("--read-xfer-little", "--read-dataset", readMode == ERM_dataset); + xfer = EXS_LittleEndianExplicit; + } + if (cmd.findOption("--read-xfer-big")) + { + app.checkDependence("--read-xfer-big", "--read-dataset", readMode == ERM_dataset); + xfer = EXS_BigEndianExplicit; + } + if (cmd.findOption("--read-xfer-implicit")) + { + app.checkDependence("--read-xfer-implicit", "--read-dataset", readMode == ERM_dataset); + xfer = EXS_LittleEndianImplicit; + } + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--accept-odd-length")) + { + dcmAcceptOddAttributeLength.set(OFTrue); + } + if (cmd.findOption("--assume-even-length")) + { + dcmAcceptOddAttributeLength.set(OFFalse); + } + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--enable-cp246")) + { + dcmEnableCP246Support.set(OFTrue); + } + if (cmd.findOption("--disable-cp246")) + { + dcmEnableCP246Support.set(OFFalse); + } + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--retain-un")) + { + dcmEnableUnknownVRConversion.set(OFFalse); + } + if (cmd.findOption("--convert-un")) + { + dcmEnableUnknownVRConversion.set(OFTrue); + } + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--enable-correction")) + { + dcmEnableAutomaticInputDataCorrection.set(OFTrue); + } + if (cmd.findOption("--disable-correction")) + { + dcmEnableAutomaticInputDataCorrection.set(OFFalse); + } + cmd.endOptionBlock(); + +#ifdef WITH_ZLIB + cmd.beginOptionBlock(); + if (cmd.findOption("--bitstream-deflated")) + { + dcmZlibExpectRFC1950Encoding.set(OFFalse); + } + if (cmd.findOption("--bitstream-zlib")) + { + dcmZlibExpectRFC1950Encoding.set(OFTrue); + } + cmd.endOptionBlock(); +#endif + + if (cmd.findOption("--max-read-length")) + { + app.checkValue(cmd.getValueAndCheckMinMax(maxReadLength, 4, 4194302)); + maxReadLength *= 1024; // convert kbytes to bytes + } + cmd.beginOptionBlock(); + if (cmd.findOption("--load-all")) loadIntoMemory = OFTrue; + if (cmd.findOption("--load-short")) loadIntoMemory = OFFalse; + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--print-all")) printFlags &= ~DCMTypes::PF_shortenLongTagValues; + if (cmd.findOption("--print-short")) printFlags |= DCMTypes::PF_shortenLongTagValues; + cmd.endOptionBlock(); + + if (cmd.findOption("--print-filename")) + printFilename = OFTrue; + + cmd.beginOptionBlock(); + if (cmd.findOption("--stop-on-error")) stopOnErrors = OFTrue; + if (cmd.findOption("--ignore-errors")) stopOnErrors = OFFalse; + cmd.endOptionBlock(); + + if (cmd.findOption("--search", 0, OFCommandLine::FOM_First)) + { + do + { + app.checkValue(cmd.getValue(current)); + if (!addPrintTagName(current)) return 1; + } while (cmd.findOption("--search", 0, OFCommandLine::FOM_Next)); + } + + cmd.beginOptionBlock(); + if (cmd.findOption("--search-all")) + { + app.checkDependence("--search-all", "--search", printTagCount>0); + printAllInstances = OFTrue; + } + if (cmd.findOption("--search-first")) + { + app.checkDependence("--search-first", "--search", printTagCount>0); + printAllInstances = OFFalse; + } + cmd.endOptionBlock(); + + cmd.beginOptionBlock(); + if (cmd.findOption("--prepend")) + { + app.checkDependence("--prepend", "--search", printTagCount>0); + prependSequenceHierarchy = OFTrue; + } + if (cmd.findOption("--no-prepend")) + { + app.checkDependence("--no-prepend", "--search", printTagCount>0); + prependSequenceHierarchy = OFFalse; + } + cmd.endOptionBlock(); + + if (cmd.findOption("--write-pixel")) + { + app.checkValue(cmd.getValue(pixelDirectory)); + writePixelData = OFTrue; + } + } + + SetDebugLevel((opt_debugMode)); + + /* make sure data dictionary is loaded */ + if (!dcmDataDict.isDictionaryLoaded()) + { + CERR << "Warning: no data dictionary loaded, " + << "check environment variable: " + << DCM_DICT_ENVIRONMENT_VARIABLE; + } + + int errorCount = 0; + int count = cmd.getParamCount(); + for (int i=1; i<=count; i++) + { + cmd.getParam(i, current); + if (printFilename) + { + /* a newline separates two consecutive "dumps" */ + if (i > 1) + COUT << endl; + /* print header with filename */ + COUT << "# " << OFFIS_CONSOLE_APPLICATION << " (" << i << "/" << count << "): " << current << endl; + } + errorCount += dumpFile(COUT, current, readMode, xfer, printFlags, loadIntoMemory, stopOnErrors, + writePixelData, pixelDirectory); + } + + return errorCount; +} + +static void printResult(ostream& out, DcmStack& stack, size_t printFlags) +{ + unsigned long n = stack.card(); + if (n == 0) { + return; + } + + if (prependSequenceHierarchy) { + /* print the path leading up to the top stack elem */ + for (unsigned long i=n-1; i>=1; i--) { + DcmObject *dobj = stack.elem(i); + /* do not print if a DCM_Item as this is not + * very helpful to distinguish instances. + */ + if (dobj != NULL && dobj->getTag().getXTag() != DCM_Item) { + char buf[512]; + sprintf(buf, "(%x,%x).", + OFstatic_cast(unsigned, dobj->getGTag()), + OFstatic_cast(unsigned, dobj->getETag())); + out << buf; + } + } + } + + /* print the tag and its value */ + DcmObject *dobj = stack.top(); + dobj->print(out, printFlags); +} + +static int dumpFile(ostream & out, + const char *ifname, + const E_FileReadMode readMode, + const E_TransferSyntax xfer, + const size_t printFlags, + const OFBool loadIntoMemory, + const OFBool stopOnErrors, + const OFBool writePixelData, + const char *pixelDirectory) +{ + int result = 0; + + if ((ifname == NULL) || (strlen(ifname) == 0)) + { + CERR << OFFIS_CONSOLE_APPLICATION << ": invalid filename: <empty string>" << endl; + return 1; + } + + DcmFileFormat dfile; + DcmObject *dset = &dfile; + + if (readMode == ERM_dataset) dset = dfile.getDataset(); + + // Load file + + OFCondition cond = dfile.loadFile(ifname, xfer, EGL_noChange, maxReadLength, readMode); + + // Read error + + if (! cond.good()) + { + CERR << OFFIS_CONSOLE_APPLICATION << ": error: " << dfile.error().text() + << ": reading file: "<< ifname << endl; + + result = 1; + if (stopOnErrors) return result; + } + + if (loadIntoMemory) dfile.loadAllDataIntoMemory(); + + if (printTagCount == 0) + { + if (writePixelData) + { + OFString str = ifname; + OFString rname = pixelDirectory; + if ((rname.length() > 0) && (rname[rname.length() - 1] != PATH_SEPARATOR)) + rname += PATH_SEPARATOR; + size_t pos = str.find_last_of(PATH_SEPARATOR); + if (pos == OFString_npos) + rname += str; + else + rname += str.substr(pos + 1); + size_t counter = 0; + dset->print(out, printFlags, 0 /*level*/, rname.c_str(), &counter); + } else + dset->print(out, printFlags); + } else { + /* only print specified tags */ + for (int i=0; i<printTagCount; i++) + { + unsigned int group = 0xffff; + unsigned int elem = 0xffff; + DcmTagKey searchKey; + const char* tagName = printTagNames[i]; + if (printTagKeys[i]) searchKey = *printTagKeys[i]; + else if (sscanf( tagName, "%x,%x", &group, &elem ) == 2 ) searchKey.set(group, elem); + else { + CERR << "Internal ERROR in File " << __FILE__ << ", Line " + << __LINE__ << endl + << "-- Named tag inconsistency" << endl; + abort(); + } + + DcmStack stack; + if (dset->search(searchKey, stack, ESM_fromHere, OFTrue) == EC_Normal) + { + printResult(out, stack, printFlags); + if (printAllInstances) + { + while (dset->search(searchKey, stack, ESM_afterStackTop, OFTrue) == EC_Normal) + printResult(out, stack, printFlags); + } + } + } + } + + return result; +}

1 0

milena r3374: Add unit test for n_max.hh
by Fabien Freling 13 Feb '09

13 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena ChangeLog: 2009-02-13 Fabien Freling <fabien.freling(a)lrde.epita.fr> Add unit test for n_max.hh. * mln/labeling/all.hh: Update for n_max.hh * tests/labeling/Makefile.am: Update for n_max.cc * tests/labeling/n_max.cc: Unit test for n_max(). --- mln/labeling/all.hh | 1 tests/labeling/Makefile.am | 2 + tests/labeling/n_max.cc | 70 +++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 73 insertions(+) Index: trunk/milena/tests/labeling/n_max.cc =================================================================== --- trunk/milena/tests/labeling/n_max.cc (revision 0) +++ trunk/milena/tests/labeling/n_max.cc (revision 3374) @@ -0,0 +1,70 @@ +// Copyright (C) 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 +// 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, 51 Franklin Street, Fifth Floor, +// Boston, MA 02111-1307, 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. + +/// \file tests/labeling/n_max.cc +/// +/// Test on mln::labeling::n_max. + +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/value/int_u8.hh> +#include <mln/value/label_16.hh> + +#include <mln/labeling/flat_zones.hh> +#include <mln/labeling/compute.hh> +#include <mln/labeling/n_max.hh> + +#include <mln/fun/v2b/threshold.hh> +#include <mln/level/transform.hh> + +#include <mln/accu/count.hh> + +#include <mln/io/pgm/all.hh> + +#include "tests/data.hh" + + +int main() +{ + using namespace mln; + using value::int_u8; + using value::label_16; + + image2d<int_u8> lena = io::pgm::load<int_u8>(MLN_IMG_DIR "/lena.pgm"); + + image2d<bool> threshold = level::transform(lena, fun::v2b::threshold<int_u8>(100)); + label_16 nlabels; + image2d<label_16> labels = labeling::flat_zones(threshold, c4(), nlabels); + accu::count<int_u8> a_; + + util::array<unsigned> a = labeling::compute(a_, threshold, labels, nlabels); + util::array<label_16> arr_big = labeling::n_max<label_16>(a, 3); + + mln_assertion(arr_big[1] == 4); + mln_assertion(arr_big[2] == 6); + mln_assertion(arr_big[3] == 323); +} Index: trunk/milena/tests/labeling/Makefile.am =================================================================== --- trunk/milena/tests/labeling/Makefile.am (revision 3373) +++ trunk/milena/tests/labeling/Makefile.am (revision 3374) @@ -10,6 +10,7 @@ flat_zones \ foreground \ level \ + n_max \ regional_maxima \ regional_minima \ relabel @@ -21,6 +22,7 @@ flat_zones_SOURCES = flat_zones.cc foreground_SOURCES = foreground.cc level_SOURCES = level.cc +n_max_SOURCES = n_max.cc regional_maxima_SOURCES = regional_maxima.cc regional_minima_SOURCES = regional_minima.cc relabel_SOURCES = relabel.cc Index: trunk/milena/mln/labeling/all.hh =================================================================== --- trunk/milena/mln/labeling/all.hh (revision 3373) +++ trunk/milena/mln/labeling/all.hh (revision 3374) @@ -60,6 +60,7 @@ # include <mln/labeling/flat_zones.hh> # include <mln/labeling/foreground.hh> # include <mln/labeling/level.hh> +# include <mln/labeling/n_max.hh> # include <mln/labeling/regional_maxima.hh> # include <mln/labeling/regional_minima.hh>

1 0

3373: Fix labeling fill holes and add a 3D ball window.
by Thierry Geraud 13 Feb '09

13 Feb '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Fix labeling fill holes and add a 3D ball window. * mln/labeling/fill_holes.hh: Fix. * mln/labeling/all.hh: Update. * tests/labeling/fill_holes.cc: New. * tests/labeling/Makefile.am: Update. * mln/win/ball3d.hh: New. * mln/win/all.hh: Update. mln/labeling/all.hh | 4 ++- mln/labeling/fill_holes.hh | 14 +++++----- mln/win/all.hh | 11 ++++---- mln/win/ball3d.hh | 41 ++++++++++++++++---------------- tests/labeling/Makefile.am | 2 + tests/labeling/fill_holes.cc | 55 +++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 94 insertions(+), 33 deletions(-) Index: mln/win/ball3d.hh --- mln/win/ball3d.hh (revision 3368) +++ mln/win/ball3d.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 @@ -26,39 +26,39 @@ // reasons why the executable file might be covered by the GNU General // Public License. -#ifndef MLN_WIN_DISK2D_HH -# define MLN_WIN_DISK2D_HH +#ifndef MLN_WIN_BALL3D_HH +# define MLN_WIN_BALL3D_HH -/// \file mln/win/disk2d.hh +/// \file mln/win/ball3d.hh /// -/// Definition of the mln::win::disk2d window. +/// Definition of the mln::win::ball3d window. # include <mln/core/internal/classical_window_base.hh> -# include <mln/core/alias/dpoint2d.hh> +# include <mln/core/alias/dpoint3d.hh> namespace mln { - mln_internal_add_classical_window_trait(disk2d); + mln_internal_add_classical_window_trait(ball3d); namespace win { - /*! \brief Disk window defined on the 2D square grid. + /*! \brief Ball (sphere) window defined on the 3D square grid. * - * A disk2d is centered and symmetric. + * A ball3d is centered and symmetric. * */ - struct disk2d : public internal::classical_window_base< dpoint2d, disk2d > + struct ball3d : public internal::classical_window_base< dpoint3d, ball3d > { /*! \brief Constructor. * * \param[in] length Length, thus diameter. * */ - disk2d(unsigned length); + ball3d(unsigned length); /*! \brief Give the disk diameter. */ @@ -80,7 +80,7 @@ # ifndef MLN_INCLUDE_ONLY inline - disk2d::disk2d(unsigned length) + ball3d::ball3d(unsigned length) : length_(length) { mln_precondition(length % 2 == 1); @@ -90,26 +90,27 @@ r2 = static_cast<def::coord>(r * r); for (def::coord a = minus_r; a <= r; ++a) for (def::coord b = minus_r; b <= r; ++b) - if (a * a + b * b <= r2) - insert(dpoint2d(a, b)); + for (def::coord c = minus_r; c <= r; ++c) + if (a * a + b * b + c * c <= r2) + insert(dpoint3d(a, b, c)); } inline - unsigned disk2d::length() const + unsigned ball3d::length() const { return length_; } inline - unsigned disk2d::delta_() const + unsigned ball3d::delta_() const { return length_ / 2; } inline - void disk2d::print_(std::ostream& ostr) const + void ball3d::print_(std::ostream& ostr) const { - ostr << "[disk2d: length=" << length_ << ']'; + ostr << "[ball3d: length=" << length_ << ']'; } # endif // ! MLN_INCLUDE_ONLY @@ -120,4 +121,4 @@ -#endif // ! MLN_WIN_DISK2D_HH +#endif // ! MLN_WIN_BALL3D_HH Property changes on: mln/win/ball3d.hh ___________________________________________________________________ Added: svn:mergeinfo Index: mln/win/all.hh --- mln/win/all.hh (revision 3372) +++ mln/win/all.hh (working copy) @@ -1,4 +1,5 @@ -// Copyright (C) 2007, 2008 EPITA Research and Development Laboratory +// Copyright (C) 2007, 2008 EPITA, 2009 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 @@ -28,10 +29,9 @@ #ifndef MLN_WIN_ALL_HH # define MLN_WIN_ALL_HH -/*! \file mln/win/all.hh - * - * \brief File that includes all win-related routines. - */ +/// \file mln/win/all.hh +/// +/// File that includes all win-related routines. namespace mln @@ -46,6 +46,7 @@ // Types. # include <mln/win/backdiag2d.hh> +# include <mln/win/ball3d.hh> # include <mln/win/cube3d.hh> # include <mln/win/cuboid3d.hh> # include <mln/win/diag2d.hh> Index: mln/labeling/all.hh --- mln/labeling/all.hh (revision 3372) +++ mln/labeling/all.hh (working copy) @@ -1,4 +1,5 @@ -// Copyright (C) 2007, 2008 EPITA Research and Development Laboratory +// 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 @@ -55,6 +56,7 @@ # include <mln/labeling/background.hh> # include <mln/labeling/blobs.hh> # include <mln/labeling/compute.hh> +# include <mln/labeling/fill_holes.hh> # include <mln/labeling/flat_zones.hh> # include <mln/labeling/foreground.hh> # include <mln/labeling/level.hh> Index: mln/labeling/fill_holes.hh --- mln/labeling/fill_holes.hh (revision 3372) +++ mln/labeling/fill_holes.hh (working copy) @@ -36,10 +36,9 @@ # include <mln/labeling/background.hh> # include <mln/labeling/compute.hh> +# include <mln/core/image/image_if.hh> # include <mln/accu/count.hh> -# include <mln/value/int_u8.hh> - namespace mln { @@ -81,19 +80,20 @@ mln_precondition(exact(input).is_valid()); mln_precondition(exact(nbh).is_valid()); - using value::int_u8; - mln_ch_value(I, bool) output; initialize(output, input); data::fill(output, false); - accu::count<int_u8> a_; mln_ch_value(I, L) lbls = labeling::background(input, nbh, nlabels); + + accu::count<mln_value(I)> a_; util::array<unsigned> arr = labeling::compute(a_, input, lbls, nlabels); + int bg_count = 0; int bg_lbl = 0; - for (int i = 0; i < arr.nelements(); ++i) + // We start at 1 to ignore the object. + for (int i = 1; i < arr.nelements(); ++i) { if (arr[i] > bg_count) { @@ -102,7 +102,7 @@ } } - data::fill((output | pw::value(lbls) != bg_lbl).rw(), true); + data::fill((output | (pw::value(lbls) != bg_lbl)).rw(), true); trace::exiting("labeling::fill_holes"); return output; Index: tests/labeling/fill_holes.cc --- tests/labeling/fill_holes.cc (revision 0) +++ tests/labeling/fill_holes.cc (revision 0) @@ -0,0 +1,55 @@ +// Copyright (C) 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 +// 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, 51 Franklin Street, Fifth Floor, +// Boston, MA 02111-1307, 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. + +/// \file tests/labeling/fill_holes.cc +/// +/// Test on mln::labeling::fill_holes. + +#include <mln/core/image/image2d.hh> +#include <mln/io/pbm/load.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/labeling/fill_holes.hh> +#include <mln/value/label_8.hh> + +#include <mln/debug/println.hh> +#include <mln/io/pbm/save.hh> + +#include "tests/data.hh" + + +int main() +{ + using namespace mln; + + image2d<bool> pic = io::pbm::load(MLN_IMG_DIR "/picasso.pbm"); + debug::println(pic); + value::label_8 n; + image2d<bool> out = labeling::fill_holes(pic, c4(), n); + debug::println(out); + io::pbm::save(out, "out.pbm"); +// mln_assertion(n == 33); +} Index: tests/labeling/Makefile.am --- tests/labeling/Makefile.am (revision 3372) +++ tests/labeling/Makefile.am (working copy) @@ -6,6 +6,7 @@ background \ blobs \ compute \ + fill_holes \ flat_zones \ foreground \ level \ @@ -16,6 +17,7 @@ background_SOURCES = background.cc blobs_SOURCES = blobs.cc compute_SOURCES = compute.cc +fill_holes_SOURCES = fill_holes.cc flat_zones_SOURCES = flat_zones.cc foreground_SOURCES = foreground.cc level_SOURCES = level.cc

1 0

3372: Add source for command executables.
by Thierry Geraud 13 Feb '09

13 Feb '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Add source for command executables. * theo/igr/dump2pgm.cc: Move and rename as... * theo/exec/dump2pnm.cc: ...this. Update to also handle pbm and ppm. * theo/igr/pgms2dump.cc: Move and rename as... * theo/exec/pnms2dump.cc: ...this. Update to also handle pbm and ppm. * theo/exec/clean_holes.cc: New. * theo/exec/threshold_low.cc: New. * theo/exec/dump2cloud.cc: New. * theo/exec/closing_area.cc: New. * theo/exec/closing_isotropic.cc: New. clean_holes.cc | 66 +++++++++++++++++++++++++++++++++++++++++++ closing_area.cc | 60 +++++++++++++++++++++++++++++++++++++++ closing_isotropic.cc | 71 +++++++++++++++++++++++++++++++++++++++++++++++ dump2cloud.cc | 34 ++++++++++++++++++++++ dump2pnm.cc | 77 +++++++++++++++++++++++++++++++++++++++++++++------ pnms2dump.cc | 71 +++++++++++++++++++++++++++++++++++++++++++---- threshold_low.cc | 69 +++++++++++++++++++++++++++++++++++++++++++++ 7 files changed, 433 insertions(+), 15 deletions(-) Index: theo/exec/clean_holes.cc --- theo/exec/clean_holes.cc (revision 0) +++ theo/exec/clean_holes.cc (revision 0) @@ -0,0 +1,66 @@ +#include "filetype.hh" + +#include <mln/value/label_16.hh> +#include <mln/labeling/fill_holes.hh> +#include <mln/logical/not.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.xxx output.xxx" << std::endl + << " Clean holes." << std::endl + << " xxx is pbm (2D) or dump (3D)." << std::endl; + std::abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc != 3) + usage(argv); + + trace::entering("main"); + + std::string filename = argv[1]; + + switch (get_filetype(argv[1])) + { + case filetype::pbm: + { + image2d<bool> ima, out; + io::pbm::load(ima, argv[1]); + value::label_16 n; + out = labeling::fill_holes(ima, c4(), n); + out = labeling::fill_holes(logical::not_(out), c4(), n); + io::pbm::save(out, argv[2]); + } + break; + + case filetype::dump: + { + image3d<bool> ima, out; + io::dump::load(ima, argv[1]); + value::label_16 n; + out = labeling::fill_holes(ima, c6(), n); + out = labeling::fill_holes(logical::not_(out), c6(), n); + io::dump::save(out, argv[2]); + } + break; + + case filetype::unknown: + std::cerr << "unknown filename extension!" << std::endl; + usage(argv); + break; + + default: + std::cerr << "file type not handled!" << std::endl; + usage(argv); + } + + trace::exiting("main"); +} Index: theo/exec/threshold_low.cc --- theo/exec/threshold_low.cc (revision 0) +++ theo/exec/threshold_low.cc (revision 0) @@ -0,0 +1,69 @@ +#include "filetype.hh" + +#include <mln/core/routine/duplicate.hh> +#include <mln/pw/all.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.xxx low output.xxx" << std::endl + << " Low threshold." << std::endl + << " xxx is pbm (2D) or dump (3D)." << std::endl; + std::abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc != 4) + usage(argv); + + + trace::entering("main"); + + std::string filename = argv[1]; + + int low = std::atoi(argv[2]); + if (low < 0 || low > 255) + { + std::cerr << "bad threshold!" << std::endl; + usage(argv); + } + + + + switch (get_filetype(argv[1])) + { + case filetype::pgm: + { + image2d<int_u8> ima; + io::pgm::load(ima, argv[1]); + io::pbm::save(duplicate((pw::value(ima) < pw::cst(low)) | ima.domain()), argv[3]); + } + break; + + case filetype::dump: + { + image3d<int_u8> ima; + io::dump::load(ima, argv[1]); + io::dump::save(duplicate((pw::value(ima) < pw::cst(low)) | ima.domain()), argv[3]); + } + break; + + case filetype::unknown: + std::cerr << "unknown filename extension!" << std::endl; + usage(argv); + break; + + default: + std::cerr << "file type not handled!" << std::endl; + usage(argv); + } + + trace::exiting("main"); +} Index: theo/exec/dump2cloud.cc --- theo/exec/dump2cloud.cc (revision 0) +++ theo/exec/dump2cloud.cc (revision 0) @@ -0,0 +1,34 @@ +#include "filetype.hh" + +#include <mln/io/cloud/save.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.dump output.txt" << std::endl + << " Dump (binary, 3D) to cloud." << std::endl; + std::abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + + if (argc != 3) + usage(argv); + + trace::entering("main"); + + std::string filename = argv[1]; + + image3d<bool> vol; + io::dump::load(vol, argv[1]); + p_array<point3d> arr; + convert::from_to(vol, arr); + io::cloud::save(arr, argv[2]); + + trace::exiting("main"); +} Index: theo/exec/dump2pnm.cc --- theo/exec/dump2pnm.cc (revision 3368) +++ theo/exec/dump2pnm.cc (working copy) @@ -1,17 +1,15 @@ +#include "filetype.hh" -#include <mln/core/image/image2d.hh> -#include <mln/make/image3d.hh> +#include <mln/literal/black.hh> #include <mln/debug/slices_2d.hh> -#include <mln/value/int_u8.hh> -#include <mln/io/dump/load.hh> -#include <mln/io/pgm/save.hh> - void usage(char* argv[]) { - std::cerr << "usage: " << argv[0] << " input.dump output.pgm" << std::endl; + std::cerr << "usage: " << argv[0] << " input.dump output.pnm" << std::endl; + std::cerr << " It works with binary (pbm), gray-level (int_u8), and color (rgb8) images." << std::endl; + std::cerr << " Sample use: binary input.dump -> output.pbm" << std::endl; abort(); } @@ -20,15 +18,76 @@ int main(int argc, char* argv[]) { using namespace mln; - using value::int_u8; if (argc != 3) usage(argv); - image3d<int_u8> vol; + trace::entering("main"); + + std::string filename = argv[2]; + + switch (get_filetype(argv[2])) + { + case filetype::pbm: + { + image3d<bool> vol; io::dump::load(vol, argv[1]); + bool bg = false; + image2d<bool> ima = debug::slices_2d(vol, 1.f, bg); + io::pbm::save(ima, argv[2]); + } + break; + case filetype::pgm: + { + using value::int_u8; + image3d<int_u8> vol; + io::dump::load(vol, argv[1]); int_u8 bg = 0; image2d<int_u8> ima = debug::slices_2d(vol, 1.f, bg); io::pgm::save(ima, argv[2]); } + break; + + case filetype::ppm: + { + using value::rgb8; + image3d<rgb8> vol; + io::dump::load(vol, argv[1]); + rgb8 bg = literal::black; + image2d<rgb8> ima = debug::slices_2d(vol, 1.f, bg); + io::ppm::save(ima, argv[2]); + } + break; + + case filetype::dump: + { + std::cerr << "Output shall not be a dump file!" << std::endl; + usage(argv); + } + break; + + case filetype::unknown: + std::cerr << "unknown filename extension!" << std::endl; + usage(argv); + break; + + default: + std::cerr << "file type not handled!" << std::endl; + usage(argv); + } + + trace::exiting("main"); + + + + +// using namespace mln; +// using value::int_u8; + +// if (argc != 3) +// usage(argv); + +// std::string filename = argv[2]; + +} Property changes on: theo/exec/dump2pnm.cc ___________________________________________________________________ Added: svn:mergeinfo Index: theo/exec/pnms2dump.cc --- theo/exec/pnms2dump.cc (revision 3368) +++ theo/exec/pnms2dump.cc (working copy) @@ -1,16 +1,14 @@ +#include "filetype.hh" -#include <mln/core/image/image2d.hh> #include <mln/make/image3d.hh> -#include <mln/value/int_u8.hh> -#include <mln/io/pgm/load.hh> -#include <mln/io/dump/save.hh> void usage(char* argv[]) { - std::cerr << "usage: " << argv[0] << " output.dump input1.pgm .. inputn.pgm" << std::endl; + std::cerr << "usage: " << argv[0] << " output.dump input1.xxx .. inputn.xxx" << std::endl; + std::cerr << " It works with binary (pbm), gray-level (int_u8), and color (rgb8) images." << std::endl; abort(); } @@ -20,12 +18,35 @@ { using namespace mln; using value::int_u8; - typedef image2d<int_u8> I; if (argc < 3) usage(argv); + trace::entering("main"); + + std::string filename = argv[2]; + switch (get_filetype(argv[2])) + { + case filetype::pbm: + { + typedef image2d<bool> I; + util::array arr; + for (int i = 2; i < argc; ++i) + { + I ima; + io::pbm::load(ima, argv[i]); + arr.append(ima); + } + image3d<bool> vol = make::image3d(arr); + io::dump::save(vol, argv[1]); + } + break; + + case filetype::pgm: + { + using value::int_u8; + typedef image2d<int_u8> I; util::array arr; for (int i = 2; i < argc; ++i) { @@ -36,3 +57,41 @@ image3d<int_u8> vol = make::image3d(arr); io::dump::save(vol, argv[1]); } + break; + + case filetype::ppm: + { + using value::rgb8; + typedef image2d<rgb8> I; + util::array arr; + for (int i = 2; i < argc; ++i) + { + I ima; + io::ppm::load(ima, argv[i]); + arr.append(ima); + } + image3d<rgb8> vol = make::image3d(arr); + io::dump::save(vol, argv[1]); + } + break; + + case filetype::dump: + { + std::cerr << "Output shall not be a dump file!" << std::endl; + usage(argv); + } + break; + + case filetype::unknown: + std::cerr << "unknown filename extension!" << std::endl; + usage(argv); + break; + + default: + std::cerr << "file type not handled!" << std::endl; + usage(argv); + } + + trace::exiting("main"); + +} Property changes on: theo/exec/pnms2dump.cc ___________________________________________________________________ Added: svn:mergeinfo Index: theo/exec/closing_area.cc --- theo/exec/closing_area.cc (revision 0) +++ theo/exec/closing_area.cc (revision 0) @@ -0,0 +1,60 @@ +#include "filetype.hh" +#include <mln/morpho/closing_area.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.xxx lambda output.xxx" << std::endl + << " Area closing." << std::endl + << " xxx in { pgm, dump }" << std::endl; + std::abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc != 4) + usage(argv); + + trace::entering("main"); + + std::string filename = argv[1]; + unsigned lambda = atoi(argv[2]); + + switch (get_filetype(argv[1])) + { + case filetype::pgm: + { + image2d<int_u8> ima, clo; + io::pgm::load(ima, argv[1]); + clo = morpho::closing_area(ima, c4(), lambda); + io::pgm::save(clo, argv[3]); + } + break; + + case filetype::dump: + { + image3d<int_u8> ima, clo; + io::dump::load(ima, argv[1]); + clo = morpho::closing_area(ima, c6(), lambda); + io::dump::save(clo, argv[3]); + } + break; + + case filetype::unknown: + std::cerr << "unknown filename extension!" << std::endl; + usage(argv); + break; + + default: + std::cerr << "file type not handled!" << std::endl; + usage(argv); + } + + trace::exiting("main"); +} Index: theo/exec/closing_isotropic.cc --- theo/exec/closing_isotropic.cc (revision 0) +++ theo/exec/closing_isotropic.cc (revision 0) @@ -0,0 +1,71 @@ +#include "filetype.hh" + +#include <mln/morpho/closing.hh> +#include <mln/win/disk2d.hh> +#include <mln/win/ball3d.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.xxx r output.xxx" << std::endl + << " Closing with an isotropic structuring element." << std::endl + << " xxx is pbm (2D) or dump (3D)." << std::endl; + std::abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + + if (argc != 4) + usage(argv); + + trace::entering("main"); + + int r = std::atoi(argv[2]); + if (r < 0) + { + std::cerr << "bad radius!" << std::endl; + usage(argv); + } + + + std::string filename = argv[1]; + + switch (get_filetype(argv[1])) + { + case filetype::pbm: + { + image2d<bool> ima, out; + io::pbm::load(ima, argv[1]); + out = morpho::closing(ima, win::disk2d(2 * r + 1)); + io::pbm::save(out, argv[3]); + } + break; + + case filetype::dump: + { + image3d<bool> ima, out; + io::dump::load(ima, argv[1]); + out = morpho::closing(ima, win::ball3d(2 * r + 1)); + io::dump::save(out, argv[3]); + } + break; + + case filetype::unknown: + std::cerr << "unknown filename extension!" << std::endl; + usage(argv); + break; + + default: + std::cerr << "file type not handled!" << std::endl; + usage(argv); + } + + + + trace::exiting("main"); +}

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milena r3371: Add n_max() function to compute n maxima in an array
by Fabien Freling 13 Feb '09

13 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena ChangeLog: 2009-02-13 Fabien Freling <fabien.freling(a)lrde.epita.fr> Add n_max() function to compute n maxima in an array. * mln/labeling/n_max.hh: Implement the n_max() function. --- n_max.hh | 90 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 90 insertions(+) Index: trunk/milena/mln/labeling/n_max.hh =================================================================== --- trunk/milena/mln/labeling/n_max.hh (revision 0) +++ trunk/milena/mln/labeling/n_max.hh (revision 3371) @@ -0,0 +1,90 @@ +// Copyright (C) 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 +// 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, 51 Franklin Street, Fifth Floor, +// Boston, MA 02111-1307, 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_LABELING_N_MAX_HH +# define MLN_LABELING_N_MAX_HH + +# include <mln/core/concept/image.hh> +# include <mln/util/array.hh> + +/// \file mln/labeling/mean_values.hh +/// +/// Construct from a count accumulator of a labeled image an array with +/// the ordered n biggest labels +/// +/// \return an array starting at index 1 + + +namespace mln +{ + + namespace labeling + { + + template <typename L, typename V> + util::array<L> + n_max(const util::array<V>& in_arr, unsigned n); + + +# ifndef MLN_INCLUDE_ONLY + + template <typename L, typename V> + util::array<L> + n_max(const util::array<V>& in_arr, unsigned n) + { + trace::entering("mln::labeling::n_max"); + + util::array<L> output(n + 1, 0); + + int swap = 0; + for (unsigned i = 0; i < in_arr.nelements(); ++i) + { + if (in_arr[i] > in_arr[output[n]]) + { + output[n] = i; + } + int j = n - 1; + while (j > 0 && in_arr[output[j]] < in_arr[output[j + 1]]) + { + swap = output[j]; + output[j] = output[j + 1]; + output[j + 1] = swap; + --j; + } + } + + trace::exiting("mln::labeling::n_max"); + return output; + } + +# endif // !MLN_INCLUDE_ONLY + + } // end of namespace mln::labeling + +} // end of namespace mln + +#endif // ! MLN_LABELING_N_MAX_HH

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r3370: Call the n_max() function..
by Fabien Freling 13 Feb '09

13 Feb '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-02-13 Fabien Freling <fabien.freling(a)lrde.epita.fr> Call the n_max() function.. * fabien/igr/igr.cc: Call the n_max() function instead of doing the computation. --- igr.cc | 61 ++++--------------------------------------------------------- 1 file changed, 4 insertions(+), 57 deletions(-) Index: trunk/milena/sandbox/fabien/igr/igr.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/igr.cc (revision 3369) +++ trunk/milena/sandbox/fabien/igr/igr.cc (revision 3370) @@ -53,6 +53,7 @@ #include <mln/labeling/blobs.hh> #include <mln/labeling/compute.hh> #include <mln/labeling/fill_holes.hh> +#include <mln/labeling/n_max.hh> #include <mln/level/compare.hh> #include <mln/level/transform.hh> @@ -119,67 +120,13 @@ initialize(big_second, input); data::fill(big_second, false); -// mln_ch_value(I, bool) in_bool; -// initialize(in_bool, input); -// data::fill(in_bool, false); - - unsigned big_third_count = 0; - unsigned big_third_lbl = 0; - unsigned big_second_count = 0; - unsigned big_second_lbl = 0; - unsigned big_first_count = 0; - unsigned big_first_lbl = 0; - for (int i = 0; i < a.nelements(); ++i) - { - if (a[i] > big_third_count) - { - big_third_count = a[i]; - big_third_lbl = i; - } - if (big_third_count > big_second_count) - { - int swap = big_second_count; - int swap_lbl = big_second_lbl; - big_second_count = big_third_count; - big_second_lbl = big_third_lbl; - big_third_count = swap; - big_third_lbl = swap_lbl; - } - if (big_second_count > big_first_count) - { - int swap = big_first_count; - int swap_lbl = big_first_lbl; - big_first_count = big_second_count; - big_first_lbl = big_second_lbl; - big_second_count = swap; - big_second_lbl = swap_lbl; - } - } - data::fill((big_second | (pw::value(labels) == big_second_lbl)).rw(), true); - mln_VAR(big_third, threshold | pw::value(labels) == big_third_lbl); -// data::fill((in_bool | (pw::value(labels) == big_second_lbl || pw::value(labels) == big_third_lbl)).rw(), true); + util::array<L> arr_big = labeling::n_max<L>(a, 3); + data::fill((big_second | (pw::value(labels) == arr_big[2])).rw(), true); + mln_VAR(big_third, threshold | pw::value(labels) == arr_big[3]); // Fill holes. big_second = labeling::fill_holes(big_second, nbh, nlabels); -// box<mln_site(I)> h_box = geom::bbox((in_bool | pw::value(labels) == big_second_lbl).domain()); - //h_box.enlarge(1); - - //mln_ch_value(I, L) h_lbls = labeling::background(big_second /*in_bool | h_box*/, nbh, nlabels); - //util::array<unsigned> arr_holes = labeling::compute(a_, big_second /*in_bool | h_box*/, h_lbls, nlabels); - //int bg_count = 0; - //int bg_lbl = 0; - //for (int i = 0; i < arr_holes.nelements(); ++i) - //{ - // if (arr_holes[i] > bg_count) - // { - // bg_count = a[i]; - // bg_lbl = i; - // } - //} - //data::fill((/*(*/big_second /*in_bool | h_box).rw()*/ | pw::value(h_lbls) != bg_lbl).rw(), true); - - /*return level::transform(h_lbls, L_to_int_u8<label_16>());*/ // Gradient.

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