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cgal/Stream_support/include/CGAL/IO/VTK.h

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// Copyright (c) 2018-2020 GeometryFactory Sarl (France).
// All rights reserved.
//
// Licensees holding a valid commercial license may use this file in
// accordance with the commercial license agreement provided with the software.
//
// This file is part of CGAL (www.cgal.org)
//
// $URL$
// $Id$
// SPDX-License-Identifier: LGPL-3.0-or-later OR LicenseRef-Commercial
//
// Author(s) : Maxime Gimeno
#ifndef CGAL_IO_VTK_H
#define CGAL_IO_VTK_H
#include <CGAL/IO/VTK/VTK_reader.h>
#include <CGAL/IO/VTK/VTK_writer.h>
#include <CGAL/Named_function_parameters.h>
#include <CGAL/boost/graph/named_params_helper.h>
#include <CGAL/Cartesian_converter.h>
#include <CGAL/Simple_cartesian.h>
#include <boost/range.hpp>
#ifdef CGAL_USE_VTK
#include <vtkSmartPointer.h>
#include <vtkCommand.h>
#include <vtkCell.h>
#include <vtkXMLPolyDataReader.h>
#include <vtkDataSetReader.h>
#include <vtkPointSet.h>
#include <vtkPolyData.h>
#include <vtkUnstructuredGrid.h>
#endif
#if defined(CGAL_USE_VTK) || defined(DOXYGEN_RUNNING)
namespace CGAL {
namespace IO {
namespace internal {
//append the content of poly_data to a soup.
template <typename PointRange, typename PolygonRange, typename NamedParameters>
bool vtkPointSet_to_polygon_soup(vtkPointSet* poly_data,
PointRange& points,
PolygonRange& polygons,
const NamedParameters&)
{
vtkIdType nb_points = poly_data->GetNumberOfPoints();
vtkIdType nb_cells = poly_data->GetNumberOfCells();
polygons.reserve(nb_cells);
std::size_t initial_number_of_pts = points.size();
// extract points
points.reserve(initial_number_of_pts+nb_points);
for(vtkIdType i=0; i<nb_points; ++i)
{
double coords[3];
poly_data->GetPoint(i, coords);
points.emplace_back(coords[0], coords[1], coords[2]);
}
// extract cells
for(vtkIdType i=0; i<nb_cells; ++i)
{
int cell_type = poly_data->GetCellType(i);
if(cell_type != 5
&& cell_type != 7
&& cell_type != 9) // only supported cells are triangles, quads and polygons
continue;
vtkCell* cell_ptr = poly_data->GetCell(i);
vtkIdType nb_vertices = cell_ptr->GetNumberOfPoints();
if(nb_vertices < 3)
return false;
std::vector<std::size_t> ids(nb_vertices);
for(vtkIdType k=0; k<nb_vertices; ++k)
{
vtkIdType id = cell_ptr->GetPointId(k);
ids[k] = id+initial_number_of_pts;
}
polygons.push_back(ids);
}
return true;
}
} // namespace internal
////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////
// Read
template <typename PointRange, typename PolygonRange, typename NamedParameters>
bool read_VTP(const std::string& fname,
PointRange& points,
PolygonRange& polygons,
const NamedParameters& np)
{
std::ifstream test(fname);
if(!test.good())
{
std::cerr<<"File doesn't exist."<<std::endl;
return false;
}
vtkSmartPointer<vtkPointSet> data;
vtkSmartPointer<internal::ErrorObserverVtk> obs =
vtkSmartPointer<internal::ErrorObserverVtk>::New();
data = vtkPolyData::SafeDownCast(internal::read_vtk_file<vtkXMLPolyDataReader>(fname, obs)->GetOutput());
if (obs->GetError())
return false;
return internal::vtkPointSet_to_polygon_soup(data, points, polygons, np);
}
/*!
* \ingroup PkgStreamSupportIoFuncsVTK
*
* \brief reads the content of the input file into `points` and `polygons`, using the \ref IOStreamVTK.
*
* \attention The polygon soup is not cleared, and the data from the file are appended.
*
* \tparam PointRange a model of the concepts `RandomAccessContainer` and `BackInsertionSequence`
* whose `value_type` is the point type
* \tparam PolygonRange a model of the concepts `SequenceContainer` and `BackInsertionSequence`
* whose `value_type` is itself a model of the concept `SequenceContainer`
* and `BackInsertionSequence` whose `value_type` is an unsigned integer type
* convertible to `std::size_t`
*
* \param fname the path to the input file
* \param points points of the soup of polygons
* \param polygons a range of polygons. Each element in it describes a polygon
* using the indices of the points in `points`.
*
* \returns `true` if the reading was successful, `false` otherwise.
*/
template <typename PointRange, typename PolygonRange>
bool read_VTP(const std::string& fname, PointRange& points, PolygonRange& polygons)
{
return read_VTP(fname, points, polygons, parameters::default_values());
}
template <typename PointRange, typename PolygonRange, typename NamedParameters>
bool read_VTK(const std::string& fname,
PointRange& points,
PolygonRange& polygons,
const NamedParameters& np)
{
std::ifstream test(fname);
if(!test.good())
{
std::cerr<<"File doesn't exist."<<std::endl;
return false;
}
vtkSmartPointer<vtkPointSet> data;
vtkSmartPointer<internal::ErrorObserverVtk> obs =
vtkSmartPointer<internal::ErrorObserverVtk>::New();
vtkSmartPointer<vtkDataSetReader> reader =
CGAL::IO::internal::read_vtk_file<vtkDataSetReader>(fname,obs);
data = vtkPolyData::SafeDownCast(reader->GetOutput());
if (!data)
data = vtkUnstructuredGrid::SafeDownCast(reader->GetOutput());
if (obs->GetError())
return false;
return internal::vtkPointSet_to_polygon_soup(data, points, polygons, np);
}
/*!
* \ingroup PkgStreamSupportIoFuncsVTK
*
* \brief reads the content of the input file into `points` and `polygons`, using the legacy file format of the \ref IOStreamVTK.
*
* \attention The polygon soup is not cleared, and the data from the file are appended.
*
* \tparam PointRange a model of the concepts `RandomAccessContainer` and `BackInsertionSequence`
* whose `value_type` is the point type
* \tparam PolygonRange a model of the concepts `SequenceContainer` and `BackInsertionSequence`
* whose `value_type` is itself a model of the concept `SequenceContainer`
* and `BackInsertionSequence` whose `value_type` is an unsigned integer type
* convertible to `std::size_t`
*
* \param fname the path to the input file
* \param points points of the soup of polygons
* \param polygons a range of polygons. Each element in it describes a polygon
* using the indices of the points in `points`.
*
* \returns `true` if the reading was successful, `false` otherwise.
*/
template <typename PointRange, typename PolygonRange>
bool read_VTK(const std::string& fname, PointRange& points, PolygonRange& polygons)
{
return read_VTK(fname, points, polygons, parameters::default_values());
}
////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////
// Write
namespace internal {
// writes the polys appended data at the end of the .vtp file
template <typename PolygonRange>
void write_soup_polys(std::ostream& os,
const PolygonRange& polygons,
const std::vector<std::size_t>& offsets,
const std::vector<unsigned char>& cell_type)
{
std::vector<std::size_t> connectivity_table;
std::size_t off = 0;
std::vector<std::size_t> cumul_offsets(offsets);
for(size_t i = 0; i < polygons.size(); ++i)
{
const auto& poly = polygons[i];
off+=offsets[i];
cumul_offsets[i]=off;
for(const std::size_t& i : poly)
connectivity_table.push_back(i);
}
write_vector<std::size_t>(os, connectivity_table);
write_vector<std::size_t>(os, cumul_offsets);
write_vector<unsigned char>(os, cell_type);
}
template <typename PointRange>
void write_soup_points_tag(std::ostream& os,
const PointRange& points,
bool binary,
std::size_t& offset)
{
typedef typename boost::range_value<PointRange>::type Point;
typedef typename CGAL::Kernel_traits<Point>::Kernel Gt;
typedef typename Gt::FT FT;
std::string format = binary ? "appended" : "ascii";
std::string type = (std::is_same_v<CGAL::cpp20::remove_cvref_t<FT>, float>) ? "Float32" : "Float64";
std::size_t sizeof_FT = (std::is_same_v<CGAL::cpp20::remove_cvref_t<FT>, float>) ? 4 : 8;
os << " <Points>\n"
<< " <DataArray type =\"" << type << "\" NumberOfComponents=\"3\" format=\""
<< format;
if(binary)
{
os << "\" offset=\"" << offset << "\"/>\n";
offset += 3 * points.size() * sizeof_FT + sizeof(std::size_t);
// 3 coords per points + length of the encoded data (size_t)
}
else
{
typedef Simple_cartesian<double> SC;
Cartesian_converter<Gt,SC> conv;
os << "\">\n";
for(const Point& p : points)
os << conv(p) << " ";
os << " </DataArray>\n";
}
os << " </Points>\n";
}
template <typename PolygonRange>
void write_soup_polys_tag(std::ostream& os,
const PolygonRange& polygons,
bool binary,
std::size_t& offset,
std::vector<std::size_t>& size_map,
std::vector<unsigned char>& cell_type)
{
std::string formatattribute = binary ? " format=\"appended\"" : " format=\"ascii\"";
std::string typeattribute;
switch(sizeof(std::size_t))
{
case 8: typeattribute = " type=\"UInt64\""; break;
case 4: typeattribute = " type=\"UInt32\""; break;
default: CGAL_error_msg("Unknown size of std::size_t");
}
// Write connectivity table
os << " <Polys>\n"
<< " <DataArray Name=\"connectivity\""
<< formatattribute << typeattribute;
//fill a vector of sizes
size_map.resize(polygons.size());
cell_type.resize(polygons.size());
std::size_t total_size=0;
for(std::size_t i = 0; i < polygons.size(); ++i)
{
size_map[i] = polygons[i].size();
CGAL_assertion(size_map[i]>=3);
total_size +=size_map[i];
}
// if binary output, just write the xml tag
if(binary)
{
os << " offset=\"" << offset << "\"/>\n";
offset += (total_size + 1) * sizeof(std::size_t);
// n indices (size_t) per triangle + length of the encoded data (size_t)
}
else
{
os << ">\n";
for(const auto& poly : polygons)
{
for(const std::size_t& id : poly)
os << id << " ";
}
os << " </DataArray>\n";
}
// Write offsets
os << " <DataArray Name=\"offsets\""
<< formatattribute << typeattribute;
if(binary) { // if binary output, just write the xml tag
os << " offset=\"" << offset << "\"/>\n";
offset += (polygons.size() + 1) * sizeof(std::size_t);
// 1 offset (size_t) per triangle + length of the encoded data (size_t)
}
else
{
os << ">\n";
std::size_t polys_offset = 0;
for(std::size_t i = 0; i < polygons.size(); ++i)
{
polys_offset += size_map[i];
os << polys_offset << " ";
}
os << " </DataArray>\n";
}
// Write cell type (triangle == 5)
os << " <DataArray Name=\"types\""
<< formatattribute << " type=\"UInt8\"";
if(binary)
{
os << " offset=\"" << offset << "\"/>\n";
offset += polygons.size() + sizeof(std::size_t);
// 1 unsigned char per cell + length of the encoded data (size_t)
}
else
{
os << ">\n";
for(std::size_t i = 0; i< polygons.size(); ++i)
{
switch(size_map[i]){
case 3:
cell_type[i]=5;
os << "5 ";//triangle
break;
case 4:
cell_type[i]=7;
os << "7 ";//quad
break;
default:
cell_type[i]=9;
os << "9 ";//polygon
break;
}
}
os << " </DataArray>\n";
}
os << " </Polys>\n";
}
// writes the points appended data at the end of the .vtp file
template <typename PointRange>
void write_soup_polys_points(std::ostream& os,
const PointRange& points)
{
typedef typename boost::range_value<PointRange>::type Point;
typedef typename CGAL::Kernel_traits<Point>::Kernel Gt;
typedef typename Gt::FT FT;
if(std::is_same_v<CGAL::cpp20::remove_cvref_t<FT>, float> ||
std::is_same_v<CGAL::cpp20::remove_cvref_t<FT>, double>){
std::vector<FT> coordinates;
for(const Point& p : points)
{
coordinates.push_back(p.x());
coordinates.push_back(p.y());
coordinates.push_back(p.z());
}
write_vector<FT>(os, coordinates);
}else{
std::vector<double> coordinates;
for(const Point& p : points)
{
coordinates.push_back(CGAL::to_double(p.x()));
coordinates.push_back(CGAL::to_double(p.y()));
coordinates.push_back(CGAL::to_double(p.z()));
}
write_vector<double>(os, coordinates);
}
}
} // namespace internal
/*!
* \ingroup PkgStreamSupportIoFuncsVTK
*
* \brief writes the content of `points` and `polygons` in `out`, using the \ref IOStreamVTK.
*
* \tparam PointRange a model of the concept `RandomAccessContainer` whose `value_type` is the point type
* \tparam PolygonRange a model of the concept `SequenceContainer`
* whose `value_type` is itself a model of the concept `SequenceContainer`
* whose `value_type` is an unsigned integer type convertible to `std::size_t`
* \tparam NamedParameters a sequence of \ref bgl_namedparameters "Named Parameters"
*
* \param os the output stream
* \param points points of the soup of polygons
* \param polygons a range of polygons. Each element in it describes a polygon
* using the indices of the points in `points`.
* \param np optional sequence of \ref bgl_namedparameters "Named Parameters" among the ones listed below
*
* \cgalNamedParamsBegin
* \cgalParamNBegin{use_binary_mode}
* \cgalParamDescription{indicates whether data should be written in binary (`true`) or in \ascii (`false`)}
* \cgalParamType{Boolean}
* \cgalParamDefault{`true`}
* \cgalParamNEnd
*
* \cgalParamNBegin{stream_precision}
* \cgalParamDescription{a parameter used to set the precision (i.e. how many digits are generated) of the output stream}
* \cgalParamType{int}
* \cgalParamDefault{the precision of the stream `os`}
* \cgalParamNEnd
* \cgalNamedParamsEnd
*
* \return `true` if the writing was successful, `false` otherwise.
*/
template <typename PointRange,
typename PolygonRange,
typename CGAL_NP_TEMPLATE_PARAMETERS>
bool write_VTP(std::ostream& os,
const PointRange& points,
const PolygonRange& polygons,
const CGAL_NP_CLASS& np = parameters::default_values())
{
using parameters::get_parameter;
using parameters::choose_parameter;
if(!os.good())
return false;
set_stream_precision_from_NP(os, np);
os << "<?xml version=\"1.0\"?>\n"
<< "<VTKFile type=\"PolyData\" version=\"0.1\"";
#ifdef CGAL_LITTLE_ENDIAN
os << " byte_order=\"LittleEndian\"";
#else // CGAL_BIG_ENDIAN
os << " byte_order=\"BigEndian\"";
#endif
switch(sizeof(std::size_t))
{
case 4: os << " header_type=\"UInt32\""; break;
case 8: os << " header_type=\"UInt64\""; break;
default: CGAL_error_msg("Unknown size of std::size_t");
}
os << ">\n"
<< " <PolyData>" << "\n";
os << " <Piece NumberOfPoints=\"" << points.size()
<< "\" NumberOfPolys=\"" << polygons.size() << "\">\n";
std::size_t offset = 0;
const bool binary = choose_parameter(get_parameter(np, internal_np::use_binary_mode), true);
std::vector<std::size_t> size_map;
std::vector<unsigned char> cell_type;
internal::write_soup_points_tag(os, points, binary, offset);
internal::write_soup_polys_tag(os, polygons, binary, offset, size_map, cell_type);
os << " </Piece>\n"
<< " </PolyData>\n";
if(binary)
{
os << "<AppendedData encoding=\"raw\">\n_";
internal::write_soup_polys_points(os, points);
internal::write_soup_polys(os, polygons,size_map, cell_type);
}
os << "</VTKFile>" << std::endl;
return true;
}
/*!
* \ingroup PkgStreamSupportIoFuncsVTK
*
* \brief writes the content of `points` and `polygons` in a file named `fname`, using the \ref IOStreamVTK.
*
* \tparam PointRange a model of the concept `RandomAccessContainer` whose `valuetype` is the point type
* \tparam PolygonRange a model of the concept `SequenceContainer`
* whose `value_type` is itself a model of the concept `SequenceContainer`
* whose `value_type` is an unsigned integer type convertible to `std::size_t`
* \tparam NamedParameters a sequence of \ref bgl_namedparameters "Named Parameters"
*
* \param fname the path to the output file
* \param points points of the soup of polygons
* \param polygons a range of polygons. Each element in it describes a polygon
* using the indices of the points in `points`.
* \param np optional sequence of \ref bgl_namedparameters "Named Parameters" among the ones listed below
*
* \cgalNamedParamsBegin
* \cgalParamNBegin{use_binary_mode}
* \cgalParamDescription{indicates whether data should be written in binary (`true`) or in \ascii (`false`)}
* \cgalParamType{Boolean}
* \cgalParamDefault{`true`}
* \cgalParamNEnd
*
* \cgalParamNBegin{stream_precision}
* \cgalParamDescription{a parameter used to set the precision (i.e. how many digits are generated) of the output stream}
* \cgalParamType{int}
* \cgalParamDefault{`6`}
* \cgalParamNEnd
* \cgalNamedParamsEnd
*
* \return `true` if the writing was successful, `false` otherwise.
*/
template <typename PointRange, typename PolygonRange, typename CGAL_NP_TEMPLATE_PARAMETERS>
bool write_VTP(const std::string& fname,
const PointRange& points,
const PolygonRange& polygons,
const CGAL_NP_CLASS& np = parameters::default_values())
{
const bool binary = CGAL::parameters::choose_parameter(CGAL::parameters::get_parameter(np, internal_np::use_binary_mode), true);
if(binary)
{
std::ofstream os(fname, std::ios::binary);
CGAL::IO::set_mode(os, CGAL::IO::BINARY);
return write_VTP(os, points, polygons, np);
}
else
{
std::ofstream os(fname);
CGAL::IO::set_mode(os, CGAL::IO::ASCII);
return write_VTP(os, points, polygons, np);
}
}
} // namespace IO
} // namespace CGAL
#endif // defined(CGAL_USE_VTK) || defined(DOXYGEN_RUNNING)
#endif // CGAL_IO_VTK_H
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