mirror of https://github.com/CGAL/cgal
Add support for SEP images to the Io_image_plugin
This commit is contained in:
Maxime Gimeno
parent
502dfc29c1
commit
b01999b634
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@ -0,0 +1,421 @@
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// Copyright (c) 2016 GeometryFactory
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// All rights reserved.
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//
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// This file is part of CGAL (www.cgal.org); you can redistribute it and/or
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// modify it under the terms of the GNU Lesser General Public License as
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// published by the Free Software Foundation; either version 3 of the License,
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// or (at your option) any later version.
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//
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// Licensees holding a valid commercial license may use this file in
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// accordance with the commercial license agreement provided with the software.
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//
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// This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
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// WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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//
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// $URL$
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// $Id$
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//
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//
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// Author(s) : Laurent Rineau
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#ifndef CGAL_READ_SEP_IMAGE_DATA_H
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#define CGAL_READ_SEP_IMAGE_DATA_H
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#include <string>
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#include <fstream>
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#include <iostream>
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#include <algorithm>
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#include <limits>
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#include <boost/filesystem/path.hpp>
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#include <boost/filesystem/operations.hpp>
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#ifndef BOOST_FILESYSTEM_VERSION
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// That macro was not defined in previous releases of Boost.
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# define BOOST_FILESYSTEM_VERSION 2
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#endif
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#include <boost/spirit/include/qi.hpp>
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#include <boost/spirit/include/phoenix_core.hpp>
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#include <boost/spirit/include/phoenix_operator.hpp>
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#include <boost/spirit/include/phoenix_stl.hpp>
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#include <CGAL/ImageIO.h>
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#include <CGAL/Image_3.h>
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namespace read_file {
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namespace qi = boost::spirit::qi;
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namespace ascii = boost::spirit::ascii;
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template <typename Iterator>
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bool parse_comment_or_empty(Iterator first, Iterator last) {
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using qi::phrase_parse;
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using ascii::space;
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using qi::char_;
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using qi::string;
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using qi::eoi;
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bool r = phrase_parse(
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first, /*< start iterator >*/
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last, /*< end iterator >*/
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string("#") >> *(char_)|eoi, /*< the parser >*/
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space /*< the skip-parser >*/
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);
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if (first != last) // fail if we did not get a full match
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return false;
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return r;
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}
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template <typename Iterator, typename Parser, typename Value>
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bool parse_assignement(Iterator first, Iterator last,
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Parser parser,
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std::string& parameter_name, Value& value)
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{
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using qi::phrase_parse;
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using ascii::space;
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using qi::char_;
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using boost::spirit::qi::_1;
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using boost::phoenix::ref;
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using boost::phoenix::push_back;
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bool r = phrase_parse(first, /*< start iterator >*/
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last, /*< end iterator >*/
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*(char_ - '=')[push_back( boost::phoenix::ref(parameter_name), _1)]
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>> '='
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>> parser[ boost::phoenix::ref(value) = _1], /*< the parser >*/
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space /*< the skip-parser >*/
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);
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if (first != last) // fail if we did not get a full match
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return false;
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return r;
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}
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template <typename Iterator>
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bool parse_string_assignement(Iterator first, Iterator last,
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std::string& parameter_name,
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std::string& value)
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{
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using qi::phrase_parse;
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using ascii::space;
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using qi::char_;
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using boost::spirit::qi::_1;
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using boost::phoenix::ref;
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using boost::phoenix::push_back;
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bool r = phrase_parse(first, /*< start iterator >*/
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last, /*< end iterator >*/
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*(char_ - '=')[push_back( boost::phoenix::ref(parameter_name), _1)]
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>> '='
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>> *char_[push_back( boost::phoenix::ref(value), _1)],
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/*< the parser >*/
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space /*< the skip-parser >*/
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);
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if (first != last) // fail if we did not get a full match
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return false;
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return r;
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}
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} // end namespace read_file
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template <typename T>
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class Sep_reader
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{
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protected:
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std::string _fileName;
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boost::array<std::size_t, 3> _n;
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boost::array<double, 3> _d;
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boost::array<double, 3> _o;
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T* _data;
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_image* _im;
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CGAL::Image_3* _cgal_image;
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bool valid;
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std::string err_msg;
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std::map<std::string, int> int_dict;
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std::map<std::string, double> double_dict;
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std::map<std::string, std::string> string_dict;
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int dimension;
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const T special_value;
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bool parseHeader(std::string fileName) {
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using boost::spirit::qi::int_;
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using boost::spirit::qi::double_;
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std::ifstream input(fileName.c_str());
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if(!input) {
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std::cerr << "Error: cannot open the header file \""
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<< fileName << "\"!\n";
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return false;
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}
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std::string line;
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while(std::getline(input, line)) {
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if(read_file::parse_comment_or_empty(line.begin(), line.end())) continue;
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std::string parameter;
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int i;
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if(read_file::parse_assignement(line.begin(), line.end(),
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int_,
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parameter,
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i))
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{
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int_dict[parameter] = i;
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continue;
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}
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parameter.clear();
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double d;
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if(read_file::parse_assignement(line.begin(), line.end(),
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double_,
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parameter,
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d))
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{
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// std::cerr << parameter << "=" << d << std::endl;
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double_dict[parameter] = d;
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continue;
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}
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parameter.clear();
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std::string s;
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if(read_file::parse_string_assignement(line.begin(), line.end(),
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parameter,
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s))
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{
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// std::cerr << parameter << "=" << s << std::endl;
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string_dict[parameter] = s;
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continue;
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}
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return false;
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}
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return true;
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}
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double& o(int i) { return _o[i-1]; }
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double& d(int i) { return _d[i-1]; }
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std::size_t& n(int i) { return _n[i-1]; }
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public:
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const double& o(int i) const { return _o[i-1]; }
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const double& d(int i) const { return _d[i-1]; }
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const std::size_t& n(int i) const { return _n[i-1]; }
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bool is_valid() const { return valid; }
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std::string error_msg() const { return err_msg; }
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Sep_reader(std::string fileName,
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const T special_value = std::numeric_limits<T>::infinity())
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: _fileName(fileName), _im(0), _cgal_image(0),
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valid(false), err_msg()
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, dimension(0), special_value(special_value)
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{
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if(!parseHeader(fileName)) {
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err_msg = "Invalid header file \"";
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err_msg += fileName;
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err_msg += "\"";
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return;
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}
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n(1) = int_dict["n1"];
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n(2) = int_dict["n2"];
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n(3) = int_dict["n3"];
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if(n(3)==0) {
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n(3) = 1;
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dimension = 2;
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}
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else {
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dimension = 3;
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}
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d(1) = double_dict["d1"];
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d(2) = double_dict["d2"];
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d(3) = double_dict["d3"];
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o(1) = double_dict["o1"];
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o(2) = double_dict["o2"];
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o(3) = double_dict["o3"];
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std::cout << "Header file: " << fileName << std::endl;
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std::cout << "Parameters:\n";
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std::cout << "dimension = " << dimension << "\n";
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for(int i = 1; i <= 3 ; ++i) {
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std::cout << "d" << i << " = " << d(i) << "\n";
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std::cout << "n" << i << " = " << n(i) << "\n";
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std::cout << "o" << i << " = " << o(i) << "\n";
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}
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std::cout << "in = " << string_dict["in"] << std::endl;
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boost::filesystem::path headerFile(fileName);
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boost::filesystem::path dataFile(string_dict["in"]);
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#if BOOST_FILESYSTEM_VERSION == 2
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dataFile = boost::filesystem::complete(dataFile,
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boost::filesystem::complete(headerFile.parent_path()));
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#else
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dataFile = boost::filesystem::absolute(dataFile,
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boost::filesystem::absolute(headerFile.parent_path()));
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#endif
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if(!load_data(dataFile.string())) {
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return;
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err_msg = "Invalid data file \"";
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err_msg += dataFile.string();
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err_msg += "\"";
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}
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std::cout << "min = " << (min)() << std::endl;
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std::cout << "special value = " << special_value << std::endl;
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valid = true;
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}
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~Sep_reader()
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{
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if(_cgal_image != 0) delete _cgal_image;
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std::cerr << "Sep_reader destroyed\n";
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}
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CGAL::Image_3* cgal_image() { return _cgal_image; }
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const CGAL::Image_3* cgal_image() const { return _cgal_image; }
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const T& raw_value(std::size_t i, std::size_t j, std::size_t k = 0) const {
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const T* result = &_data[i + n(1) * ( j + n(2)*k )];
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// if(*result <= special_value) result = &raw_value(i, j, k + 1);
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return *result;
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}
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T interpolation(const double& x, const double& y) const
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{
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const double lx = (x - o(1)) / d(1);
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const double ly = (y - o(2)) / d(2);
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const std::size_t i1 = convert2index<1>(x);
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const std::size_t j1 = convert2index<2>(y);
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std::size_t i2 = i1 + 1;
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std::size_t j2 = j1 + 1;
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if(i2 == n(1)) i2 = n(1) - 1;
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if(j2 == n(2)) j2 = n(2) - 1;
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const double di2 = i2 - lx;
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const double di1 = lx - i1;
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const double dj2 = j2 - ly;
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const double dj1 = ly - j1;
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const double v11 = raw_value(i1, j1);
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const double v12 = raw_value(i1, j2);
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const double v22 = raw_value(i2, j2);
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const double v21 = raw_value(i2, j1);
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return
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(v11 * di2 + v12 * di1) * dj2 +
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(v11 * di2 + v12 * di1) * dj1;
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}
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const T& operator()(const double& x, const double& y) const
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{
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const std::size_t i = convert2index<1>(x);
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const std::size_t j = convert2index<2>(y);
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return raw_value(i, j, 0);
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}
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const T& operator()(const double& x, const double& y, const double& z) const
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{
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const std::size_t i = convert2index<1>(x);
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const std::size_t j = convert2index<2>(y);
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const std::size_t k = convert2index<3>(z);
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return raw_value(i, j, k);
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}
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template <int dim>
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std::size_t convert2index(const double& x) const {
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const double k = (x - o(dim)) / d(dim);
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if (k < 0) return 0;
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else if (k >= n(dim)) return n(dim) - 1;
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else return static_cast<std::size_t>(k);
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}
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template <int dim>
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double index2coord(const std::size_t& i) const {
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return o(dim) + d(dim) * i;
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}
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T min BOOST_PREVENT_MACRO_SUBSTITUTION() const {
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return *std::min_element(_data, _data + n(1) * n(2) * n(3));
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}
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T max BOOST_PREVENT_MACRO_SUBSTITUTION() const {
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return *std::max_element(_data, _data + n(1) * n(2) * n(3));
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}
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protected :
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bool load_data(std::string dataFilename)
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{
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if(_im) delete _im;
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_im = new _image;
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_im->xdim = static_cast<unsigned int>(n(1));
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_im->ydim = static_cast<unsigned int>(n(2));
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_im->zdim = static_cast<unsigned int>(n(3));
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_im->vdim = 1;
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// spacing
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_im->vx = d(1);
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_im->vy = d(2);
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_im->vz = d(3);
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if(_im->vz == 0.f) _im->vz=1.f;
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// image offset
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_im->tx = static_cast<float>(o(1));
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_im->ty = static_cast<float>(o(2));
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_im->tz = static_cast<float>(o(3));
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// image center
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_im->cx = _im->cy = _im->cz = 0;
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// image rotation
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_im->rx = _im->ry = _im->rz = 0.0;
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_im->fd = NULL;
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_im->openMode = OM_CLOSE;
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if(string_dict["data_format"] == "native_float" ||
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string_dict["data_format"] == "\"native_float\"")
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{
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std::cerr << "little endian\n";
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_im->endianness = END_LITTLE;
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} else {
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std::cerr << "big endian\n";
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_im->endianness = END_BIG;
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}
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_im->dataMode = DM_BINARY;
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// no user string
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_im->user = NULL;
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_im->nuser = 0;
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// word type (unsigned byte)
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_im->wdim = sizeof(T);
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_im->wordKind = WK_FLOAT;
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_im->vectMode = VM_SCALAR;
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_im->sign = SGN_SIGNED;
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_im->imageFormat = NULL;
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::_openReadImage(_im, dataFilename.c_str());
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if(!_im->fd) return false;
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// Compute number of element
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const std::size_t size = n(1) * n(2) * n(3);
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// Allocate array
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_data = new T[size];
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_im->data = (void*)_data;
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// // Read file
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if(_readImageData(_im) < 0) return false;
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// char* buffer = reinterpret_cast<char*>(_data);
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// in.read (buffer, size * sizeof(T));
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ImageIO_close(_im);
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_cgal_image = new CGAL::Image_3(_im);
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return true;
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}
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};
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#endif // CGAL_READ_SEP_IMAGE_DATA_H
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@ -117,7 +117,7 @@ endif()
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if(CGAL_Qt5_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND)
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set(Boost_USE_MULTITHREADED ON)
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find_package(Boost COMPONENTS thread system)
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find_package(Boost COMPONENTS thread system filesystem)
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include_directories ( ${QGLVIEWER_INCLUDE_DIR} )
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qt5_wrap_ui( MainWindowUI_files MainWindow.ui)
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@ -13,6 +13,7 @@
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#include <CGAL/Image_3.h>
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#include <CGAL/ImageIO.h>
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#include <CGAL/read_sep_image_data.h>
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#include <CGAL/Three/Polyhedron_demo_plugin_helper.h>
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#include <CGAL/Three/Polyhedron_demo_plugin_interface.h>
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#include <CGAL/Three/Scene_interface.h>
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@ -49,6 +50,7 @@
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#include "Raw_image_dialog.h"
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#include <CGAL/Three/Polyhedron_demo_io_plugin_interface.h>
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#include <fstream>
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#include <cstdlib>
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#ifdef CGAL_USE_VTK
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#include <CGAL/read_vtk_image_data.h>
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@ -798,7 +800,9 @@ private Q_SLOTS:
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QString Io_image_plugin::nameFilters() const {
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return QString("Inrimage files (*.inr *.inr.gz) ;; Analyze files (*.hdr *.img *img.gz)");
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return QString("Inrimage files (*.inr *.inr.gz) ;; "
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"Analyze files (*.hdr *.img *img.gz) ;; "
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"Stanford Exploration Project files (*.H *.HH)");
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}
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@ -828,8 +832,8 @@ CGAL::Three::Scene_item*
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Io_image_plugin::load(QFileInfo fileinfo) {
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QApplication::restoreOverrideCursor();
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Image* image = new Image;
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QApplication::restoreOverrideCursor();
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if(!image->read(fileinfo.filePath().toUtf8()))
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if(fileinfo.suffix() != "H" && fileinfo.suffix() != "HH" &&
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!image->read(fileinfo.filePath().toUtf8()))
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{
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QMessageBox qmb(QMessageBox::NoIcon,
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||||
"Raw Dialog",
|
||||
|
|
@ -915,6 +919,13 @@ Io_image_plugin::load(QFileInfo fileinfo) {
|
|||
return NULL;
|
||||
}
|
||||
}
|
||||
//read a sep file
|
||||
else if(fileinfo.suffix() == "H" || fileinfo.suffix() == "HH")
|
||||
{
|
||||
Sep_reader<float> reader(fileinfo.filePath().toUtf8().data());
|
||||
*image = *reader.cgal_image();
|
||||
is_gray = true;
|
||||
}
|
||||
// Get display precision
|
||||
QDialog dialog;
|
||||
ui.setupUi(&dialog);
|
||||
|
|
|
|||
Loading…
Reference in New Issue