[Olena-patches] last-svn-commit-199-gfe65e41 Start a VTK output for complex-based images.

* mln/io/vtk/save.hh: New. --- milena/ChangeLog | 6 + milena/mln/io/vtk/save.hh | 623 +++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 629 insertions(+), 0 deletions(-) create mode 100644 milena/mln/io/vtk/save.hh diff --git a/milena/ChangeLog b/milena/ChangeLog index f83deda..6523940 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,9 @@ +2010-06-24 Roland Levillain &lt;roland(a)lrde.epita.fr&gt; + + Start a VTK output for complex-based images. + + * mln/io/vtk/save.hh: New. + 2010-08-18 Roland Levillain &lt;roland(a)lrde.epita.fr&gt; * mln/topo/skeleton/breadth_first_thinning.hh: Reindent. diff --git a/milena/mln/io/vtk/save.hh b/milena/mln/io/vtk/save.hh new file mode 100644 index 0000000..10c3f0b --- /dev/null +++ b/milena/mln/io/vtk/save.hh @@ -0,0 +1,623 @@ +// Copyright (C) 2008, 2009, 2010 EPITA Research and Development +// Laboratory (LRDE) +// +// This file is part of Olena. +// +// Olena is free software: you can redistribute it and/or modify it under +// the terms of the GNU General Public License as published by the Free +// Software Foundation, version 2 of the License. +// +// Olena is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with Olena. If not, see <http://www.gnu.org/licenses/>. +// +// As a special exception, you may use this file as part of a free +// software project without restriction. Specifically, if other files +// instantiate templates or use macros or inline functions from this +// file, or you compile this file and link it with other files to produce +// an executable, this file does not by itself cause the resulting +// executable to be covered by the GNU General Public License. This +// exception does not however invalidate any other reasons why the +// executable file might be covered by the GNU General Public License. + +#ifndef MLN_IO_VTK_SAVE_HH +# define MLN_IO_VTK_SAVE_HH + +/// \file +/// Input saving function for VTK files. +/// +/// \see http://www.vtk.org/VTK/img/file-formats.pdf +/// \see http://dunne.uni-hd.de/VisuSimple/documents/vtkfileformat.html + +# include <cstdlib> + +# include <iostream> +# include <fstream> +# include <sstream> + +# include <string> + +# include <mln/core/alias/complex_image.hh> +# include <mln/core/image/complex_neighborhoods.hh> +# include <mln/core/image/complex_neighborhood_piter.hh> + + +namespace mln +{ + + namespace io + { + + namespace vtk + { + + /** \brief Save a (binary) VTK image into a complex image. + + \param[in] ima The image to save. + \param[in] filename The name of the file where to save the image. + + The image is said binary since data represent only the + existence of faces. */ + void save(const bin_2complex_image3df& ima, + const std::string& filename); + + /** \brief Save an 8-bit grey-level VTK image into a complex image. + + \param[in] ima The image to save. + \param[in] filename The name of the file where to save the image. + + Only data is attached to 2-faces is saved; the VTK file + cannot store data attached to faces of other dimensions. */ + void save(const int_u8_2complex_image3df& ima, + const std::string& filename); + + /** \brief Save a floating-point value grey-level VTK image into + a complex image. + + \param[in] ima The image to save. + \param[in] filename The name of the file where to save the image. + + Only data is attached to 2-faces is saved; the VTK file + cannot store data attached to faces of other dimensions. */ + void save(const float_2complex_image3df& ima, + const std::string& filename); + + /** \brief Save a 3x8-bit RGB (color) VTK image into a complex image. + + \param[in] ima The image to save. + \param[in] filename The name of the file where to save the image. + + Only data is attached to 2-faces is saved; the VTK file + cannot store data attached to faces of other dimensions. */ + void save(const rgb8_2complex_image3df& ima, + const std::string& filename); + + + namespace internal + { + + template <typename I, typename E> + struct vtk_saver : public Object<E> + { + /// Type of the image. + typedef I image; + + /// Type of the values. + typedef mln_value(I) value; + + /// Dimension of the built complex. + static const unsigned D = 2; + + /// \brief Constructor, with static checks. + vtk_saver(); + + /// Save an image \a ima into \a filename. + void operator()(const I& ima, const std::string& filename) const; + + protected: + /// Helper factoring the task of writing scalar data + /// associated to faces. + void write_scalar_data(std::ostream& ostr, const image& ima, + const std::string& data_type) const; + }; + + + struct bin_vtk_saver + : public vtk_saver< bin_2complex_image3df, bin_vtk_saver > + { + /// \brief Save face data. + void write_face_data(std::ostream& ostr, const image& ima) const; + }; + + struct int_u8_vtk_saver + : public vtk_saver< int_u8_2complex_image3df, int_u8_vtk_saver > + { + /// \brief Save face data. + void write_face_data(std::ostream& ostr, const image& ima) const; + }; + + + struct float_vtk_saver + : public vtk_saver< float_2complex_image3df, float_vtk_saver > + { + /// \brief Save face data. + void write_face_data(std::ostream& ostr, const image& ima) const; + }; + + + struct rgb8_vtk_saver + : public vtk_saver< rgb8_2complex_image3df, rgb8_vtk_saver > + { + /// \brief Save face data. + void write_face_data(std::ostream& ostr, const image& ima) const; + }; + + } // end of namespace mln::io::vtk::internal + + + +# ifndef MLN_INCLUDE_ONLY + + /*----------. + | Facades. | + `----------*/ + + void + save(const bin_2complex_image3df& ima, const std::string& filename) + { + trace::entering("mln::io::vtk::save"); + internal::bin_vtk_saver()(ima, filename); + trace::exiting("mln::io::vtk::save"); + } + + void + save(const int_u8_2complex_image3df& ima, const std::string& filename) + { + trace::entering("mln::io::vtk::save"); + internal::int_u8_vtk_saver()(ima, filename); + trace::exiting("mln::io::vtk::save"); + } + + void + save(const float_2complex_image3df& ima, const std::string& filename) + { + trace::entering("mln::io::vtk::save"); + internal::float_vtk_saver()(ima, filename); + trace::exiting("mln::io::vtk::save"); + } + + void + save(const rgb8_2complex_image3df& ima, const std::string& filename) + { + trace::entering("mln::io::vtk::save"); + internal::rgb8_vtk_saver()(ima, filename); + trace::exiting("mln::io::vtk::save"); + } + + + /*-------------------------. + | Actual implementations. | + `-------------------------*/ + + // -------- // + // Canvas. // + // -------- // + + namespace internal + { + + template <typename I, typename E> + vtk_saver<I, E>::vtk_saver() + { + // Concept checking. + void (E::*m1)(std::ostream&, const I&) const = + &E::write_face_data; + m1 = 0; + } + + + template <typename I, typename E> + void + vtk_saver<I, E>::operator()(const I& ima, + const std::string& filename) const + { + const std::string me = "mln::io::vtk::save"; + + std::ofstream ostr(filename.c_str()); + if (!ostr) + { + std::cerr << me << ": `" << filename << "' invalid file." + << std::endl; + /* FIXME: Too violent. We should allow the use of + exceptions, at least to have Milena's code behave + correctly in interpreted environments (std::exit() or + std::abort() causes the termination of a Python + interpreter, for instance!). */ + std::exit(1); + } + + /*---------. + | Header. | + `---------*/ + + /* ``The legacy VTK file formats consist of five basic + parts.'' */ + + /* ``1. The first part is the file version and + identifier. This part contains the single line: + + # vtk DataFile Version x.x. + + This line must be exactly as shown with the + exception of the version number x.x, which will vary + with different releases of VTK. (Note: the current + version number is 3.0. Version 1.0 and 2.0 files are + compatible with version 3.0 files.)'' */ + ostr << "# vtk DataFile Version 2.0" << std::endl; + + /* ``2. The second part is the header. The header consists + of a character string terminated by end-of-line + character `\n'. The header is 256 characters + maximum. The header can be used to describe the data + and include any other pertinent information.'' */ + ostr << "Generated by Milena 1.0 http://olena.lrde.epita.fr" + << std::endl; + + /* ``3. The next part is the file format. The file format + describes the type of file, either ASCII or + binary. On this line the single word ASCII or BINARY + must appear.'' */ + ostr << "ASCII" << std::endl; + + /*-------. + | Data. | + `-------*/ + + /* ``4. The fourth part is the dataset structure. The + geometry part describes the geometry and topology of + the dataset. This part begins with a line containing + the keyword DATASET followed by a keyword describing + the type of dataset. Then, depending upon the type + of dataset, other keyword/data combinations define + the actual data.'' + + [...] + + Dataset Format. The Visualization Toolkit supports + five different dataset formats: structured points, + structured grid, rectilinear grid, unstructured + grid, and polygonal data.'' */ + + ostr << "DATASET POLYDATA" << std::endl << std::endl; + + // --------- // + // Complex. // + // --------- // + + typedef mln_geom(I) G; + + /* ``* Polygonal Data + The polygonal dataset consists of arbitrary + combinations of surface graphics primitives + vertices (and polyvertices), lines (and + polylines), polygons (of various types), and + triangle strips. Polygonal data is defined by + the POINTS, VERTICES, LINES, POLYGONS, or + TRIANGLE_STRIPS sections. The POINTS definition + is the same as we saw for structured grid + datasets.'' */ + + // ---------------------------- // + // Geometry (point locations). // + // ---------------------------- // + + ostr << "POINTS " + << ima.domain().cplx().template nfaces_of_static_dim<0>() + << " float" << std::endl; + // Iterate on 0-faces (vertices). + p_n_faces_fwd_piter<D, G> v(ima.domain(), 0); + for_all(v) + { + mln_invariant(v.to_site().size() == 1); + ostr << v.to_site().front()[0] << ' ' + << v.to_site().front()[1] << ' ' + << v.to_site().front()[2] << std::endl; + } + ostr << std::endl; + + /* ``The VERTICES, LINES, POLYGONS, or + TRIANGLE_STRIPS keywords define the polygonal + dataset topology. Each of these keywords + requires two parameters: the number of cells `n' + and the size of the cell list `size'. The cell + list size is the total number of integer values + required to represent the list (i.e., sum of + `numPoints' and connectivity indices over each + cell). None of the keywords VERTICES, LINES, + POLYGONS, or TRIANGLE_STRIPS is required.'' */ + + // ---------- // + // Vertices. // + // ---------- // + + /* We do not use + + ima.domain().cplx().template nfaces_of_static_dim<N>() + + to get the number of N-faces, since the image may be + masked, and exhibit less N-faces than its underlying + complex. Iterating on the N-faces is safer. */ + /* FIXME: Is there anything faster? See what the interface + of the (morphed) image can provide. */ + unsigned nvertices = 0; + for_all(v) + ++nvertices; + + if (nvertices > 0) + { + ostr << "VERTICES " << nvertices << ' ' + /* Each vertex requires two numbers: the cardinal of + its ends (which is always 1) and the indices of the + point among the POINTS section. Hence the total + number of values in the VERTEX section is + nvertices * 2. */ + << nvertices * 2 << std::endl; + + for_all(v) + ostr << "1 " << v.unproxy_().face().face_id() << std::endl; + ostr << std::endl; + } + + // ------- // + // Edges. // + // ------- // + + // Same comment as above about the count of N-faces. + unsigned nedges = 0; + p_n_faces_fwd_piter<D, G> e(ima.domain(), 1); + for_all (e) + ++nedges; + + if (nedges > 0) + { + ostr << "LINES " << nedges << ' ' + /* Each edge requires three numbers: the cardinal of + its ends (which is always 2) and the indices of + these ends among the POINTS section. Hence the + total number of values in the LINES section is + nedges * 3. */ + << nedges * 3 << std::endl; + + // Vertices adjacent to edges. + typedef complex_lower_neighborhood<D, G> adj_vertices_nbh_t; + adj_vertices_nbh_t adj_vertices_nbh; + mln_niter(adj_vertices_nbh_t) adj_v(adj_vertices_nbh, e); + // Iterate on 1-faces (edges). + for_all (e) + { + ostr << "2"; + // Iterate on vertices (0-faces). + for_all (adj_v) + { + // FIXME: Accessing the face id is too complicated. + ostr << " " << adj_v.unproxy_().face().face_id(); + } + ostr << std::endl; + } + ostr << std::endl; + } + + // ---------- // + // Polygons. // + // ---------- // + + // Same comment as above about the count of N-faces. + unsigned npolygons = 0; + p_n_faces_fwd_piter<D, G> p(ima.domain(), 2); + for_all (p) + ++npolygons; + + if (npolygons > 0) + { + // A neighborhood where neighbors are the set of 0-faces + // transitively adjacent to the reference point. + typedef complex_m_face_neighborhood<D, G> nbh_t; + nbh_t nbh; + mln_fwd_niter(nbh_t) u(nbh, p); + /* FIXME: We should be able to pass this value (m) + either at the construction of the neighborhood or at + the construction of the iterator. */ + u.iter().set_m(0); + + /* Compute the number of values (`size') to be passed as + second parameter of the POLYGONS keyword. */ + unsigned polygons_size = 0; + // Iterate on polygons (2-face). + for_all(p) + { + unsigned nvertices = 0; + /* FIXME: There may be a faster way to do this (e.g., + the neighbordhood may provide a method returning + the number of P's neighbors. */ + // Iterate on transitively adjacent vertices (0-face). + for_all(u) + ++nvertices; + // The number of values describing this polygon P is + // the cardinal of its set of vertices (1 value) plus + // the NVERTICES indices of these vertices. + polygons_size += 1 + nvertices; + } + ostr << "POLYGONS " << npolygons << ' ' << polygons_size + << std::endl; + + /* Output polygons (one per line), with their number of + vertices and the indices of these vertices. */ + // Iterate on polygons (2-face). + for_all(p) + { + unsigned nvertices = 0; + std::ostringstream vertices; + // Iterate on transitively adjacent vertices (0-face). + for_all(u) + { + // FIXME: Likewise, this is a bit too long. + vertices << ' ' << u.unproxy_().face().face_id(); + ++nvertices; + } + ostr << nvertices << vertices.str() << std::endl; + } + ostr << std::endl; + } + + /* ``5. The final part describes the dataset attributes. + This part begins with the keywords POINT_DATA or + CELL_DATA,followed by an integer number specifying + the number of points or cells, respectively. (It + doesn't matter whether POINT_DATA or CELL_DATA comes + first.) Other keyword/data combinations then define + the actual dataset attribute values (i.e., scalars, + vectors, tensors, normals, texture coordinates, or + field data).'' */ + + unsigned nfaces = nvertices + nedges + npolygons; + if (nfaces > 0) + { + // We don't use POINT_DATA (to associate values to + // POINTs), since CELL_DATA is used to associate values + // to VERTICES, EDGES and POLYGONS. + ostr << "CELL_DATA " << nfaces << std::endl; + exact(this)->write_face_data(ostr, ima); + } + + ostr.close(); + } + + // ---------------- // + // Specific parts. // + // ---------------- // + + /* ``Dataset Attribute Format. The Visualization Toolkit + supports the following dataset attributes: scalars + (one to four components), vectors, normals, + texture coordinates (1D, 2D, and 3D), 3 x 3 + tensors, and field data. In addition, a lookup + table using the RGBA color specification, + associated with the scalar data, can be defined as + well. Dataset attributes are supported for both + points and cells. + Each type of attribute data has a `dataName' + associated with it. This is a character string + (without embedded whitespace) used to identify a + particular data. The `dataName' is used by the VTK + readers to extract data. As a result, more than + one attribute data of the same type can be + included in a file. For example, two different + scalar fields defined on the dataset points, + pressure and temperature, can be contained in the + same file. (If the appropriate dataName is not + specified in the VTK reader, then the first data + of that type is extracted from the file.) + + * Scalars + Scalar definition includes specification of a + lookup table. The definition of a lookup table + is optional. + + [...] + + SCALARS dataName dataType numComp + LOOKUP_TABLE tableName + s0 + s1 + ... + sn-1'' + + Note: values accepted by Paraview 3.8 for `dataType' are: + "bit", "char", "unsigned_char", "short", "unsigned_short", + "vtkidtype", "int", "unsigned_int", "long", + "unsigned_long", "vtktypeint64", "vtktypeuint64", "float", + "double", "string", "utf8_string" and "variant". */ + + /** \{ */ + template <typename I, typename E> + void + vtk_saver<I, E>::write_scalar_data(std::ostream& ostr, + const image& ima, + const std::string& data_type) const + { + ostr << "SCALARS values " << data_type << std::endl + << "LOOKUP_TABLE default" << std::endl; + // Iterate on all faces, dimension increasing. + mln_fwd_piter(image) p(ima.domain()); + for_all(p) + ostr << ima(p) << std::endl; + } + + + void + bin_vtk_saver::write_face_data(std::ostream& ostr, + const image& ima) const + { + write_scalar_data(ostr, ima, "bit"); + } + + void + int_u8_vtk_saver::write_face_data(std::ostream& ostr, + const image& ima) const + { + write_scalar_data(ostr, ima, "unsigned_char"); + } + + void + float_vtk_saver::write_face_data(std::ostream& ostr, + const image& ima) const + { + write_scalar_data(ostr, ima, "float"); + } + + /* ``The definition of color scalars (i.e., unsigned + char values directly mapped to color) varies + depending upon the number of values (`nValues') + per scalar. If the file format is ASCII, the + color scalars are defined using nValues float + values between (0,1). + + COLOR_SCALARS dataName nValues + c00 c01 ... c0(nValues-1) + c10 c11 ... c1(nValues-1) + ... + c(n-1)0 c(n-1)1 ... c(n-1)(nValues-1)'' */ + + void + rgb8_vtk_saver::write_face_data(std::ostream& ostr, + const image& ima) const + { + ostr << "COLOR_SCALARS values 4" << std::endl; + // Iterate on all faces, dimension increasing. + mln_fwd_piter_(image) p(ima.domain()); + for_all(p) + // RGBA values (with alpha channel always set to 1.0). + ostr << float(ima(p).red()) / mln_max(value::red_t) << ' ' + << float(ima(p).green()) / mln_max(value::green_t) << ' ' + << float(ima(p).blue()) / mln_max(value::blue_t) << ' ' + << 1.f + << std::endl; + } + /** \} */ + + } // end of namespace mln::io::vtk::internal + +# endif // ! MLN_INCLUDE_ONLY + + } // end of namespace mln::io::vtk + + } // end of namespace mln::io + +} // end of namespace mln + + +#endif // ! MLN_IO_VTK_SAVE_HH -- 1.5.6.5