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/************************************************************************
*
* Copyright (C) 2009-2024 IRCAD France
* Copyright (C) 2012-2020 IHU Strasbourg
*
* This file is part of Sight.
*
* Sight is free software: you can redistribute it and/or modify it under
* the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Sight 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with Sight. If not, see <https://www.gnu.org/licenses/>.
*
***********************************************************************/
// cspell:ignore NOLINTNEXTLINE NOLINT
#include <iostream>
#include <fstream>
#include <vector>
#include <sstream>
#ifdef DEBUG
static std::stringstream spiritDebugStream;
#define BOOST_SPIRIT_DEBUG_OUT spiritDebugStream // NOLINT(cppcoreguidelines-macro-usage): needed by Boost
#define BOOST_SPIRIT_DEBUG // NOLINT(cppcoreguidelines-macro-usage): needed by Boost
#endif
#include <boost/algorithm/string.hpp>
#include <boost/algorithm/string/trim.hpp>
#include <boost/algorithm/string/split.hpp>
#include <boost/algorithm/string/detail/case_conv.hpp>
#include <boost/spirit/include/qi.hpp>
#include <boost/spirit/include/qi_eol.hpp>
#include <boost/phoenix.hpp>
#include <boost/phoenix/core.hpp>
#include <boost/phoenix/operator.hpp>
#include <boost/phoenix/bind.hpp>
#include <boost/phoenix/statement.hpp>
#include <boost/phoenix/stl.hpp>
#include <boost/fusion/include/adapt_struct.hpp>
#include <boost/fusion/container.hpp>
#include <boost/fusion/container/vector/vector.hpp>
#include <boost/fusion/include/vector.hpp>
#include <core/exceptionmacros.hpp>
#include <data/color.hpp>
#include <data/structure_traits_dictionary.hpp>
#include <data/structure_traits.hpp>
#include <data/structure_traits_helper.hpp>
#include <core/runtime/path.hpp>
#include "io/__/reader/dictionary_reader.hpp"
namespace sight::io
{
struct line
{
std::string type;
double red {};
double green {};
double blue {};
double alpha {};
std::string category;
std::string organ_class;
std::string attachment;
std::string native_exp;
std::string native_exp_geo;
std::string anatomic_region;
std::string property_category;
std::string property_type;
};
} // namespace sight::io
BOOST_FUSION_ADAPT_STRUCT(
sight::io::line,
(std::string, type)
(double, red)
(double, green)
(double, blue)
(double, alpha)
(std::string, category)
(std::string, organ_class)
(std::string, attachment)
(std::string, native_exp)
(std::string, native_exp_geo)
(std::string, anatomic_region)
(std::string, property_category)
(std::string, property_type)
)
//------------------------------------------------------------------------------
inline std::string trim(std::string& _s)
{
return boost::algorithm::trim_copy(_s);
}
//------------------------------------------------------------------------------
/// Reformat string in the following way :first letter is uppercase and the rest is lowercase).
std::string reformat_string(std::string& _expr)
{
std::string trim_str = boost::algorithm::trim_copy(_expr);
std::string result = boost::algorithm::to_upper_copy(trim_str.substr(0, 1))
+ boost::algorithm::to_lower_copy(trim_str.substr(1));
return result;
}
//------------------------------------------------------------------------------
/// Return the list of availabe value for the key of the map m.
template<typename map_t>
std::string get_values(const map_t& _m)
{
std::stringstream str;
using const_iterator = typename map_t::const_iterator;
const_iterator iter = _m.begin();
str << "( " << iter->first;
for( ; iter != _m.end() ; ++iter)
{
str << ", " << iter->first;
}
str << ") ";
return str.str();
}
//------------------------------------------------------------------------------
namespace sight::io
{
namespace qi = boost::spirit::qi;
namespace ascii = boost::spirit::ascii;
template<typename Iterator>
struct line_parser : qi::grammar<Iterator,
std::vector<line>()>
{
line_parser() :
line_parser::base_type(lines)
{
using qi::int_;
using qi::lit;
using qi::_1;
using qi::double_;
using qi::blank;
using qi::alnum;
using qi::omit;
using ascii::char_;
using boost::spirit::qi::eol;
using boost::spirit::qi::eoi;
using boost::phoenix::construct;
namespace phx = boost::phoenix;
error.clear();
// NOLINTNEXTLINE(cppcoreguidelines-prefer-member-initializer)
lines = +(line[phx::push_back(qi::_val, qi::_1)] | comment) >> eoi;
comment = *blank >> lit('#') >> *(char_ - eol) >> +qi::eol;
line = trimmed_string >> lit(';')
>> omit[*blank] >> lit('(')
>> dbl >> lit(',')
>> dbl >> lit(',')
>> dbl >> lit(',')
>> dbl
>> lit(')') >> omit[*blank]
>> lit(';')
>> string_set >> lit(';')
>> trimmed_string >> lit(';')
>> trimmed_string >> lit(';')
>> trimmed_string_expr >> lit(';')
>> trimmed_string_expr >> lit(';')
>> trimmed_string >> lit(';')
>> trimmed_string >> lit(';')
>> trimmed_string
>> +qi::eol;
trimmed_string = str[qi::_val = phx::bind(trim, qi::_1)];
str = *((alnum | char_("_"))[qi::_val += qi::_1] | blank[qi::_val += " "]);
trimmed_string_expr = string_expr[qi::_val = phx::bind(trim, qi::_1)];
string_expr = *((alnum | char_("()_,.+-"))[qi::_val += qi::_1] | blank[qi::_val += " "]);
string_set = string_with_comma[qi::_val = phx::bind(trim, qi::_1)];
string_with_comma = *((alnum | char_(",_"))[qi::_val += qi::_1] | blank[qi::_val += " "]);
dbl = omit[*blank] >> double_ >> omit[*blank];
#ifdef BOOST_SPIRIT_DEBUG
BOOST_SPIRIT_DEBUG_NODE(comment);
BOOST_SPIRIT_DEBUG_NODE(trimmed_string);
BOOST_SPIRIT_DEBUG_NODE(trimmed_string_expr);
BOOST_SPIRIT_DEBUG_NODE(string_set);
BOOST_SPIRIT_DEBUG_NODE(dbl);
BOOST_SPIRIT_DEBUG_NODE(line);
BOOST_SPIRIT_DEBUG_NODE(lines);
SIGHT_DEBUG(spiritDebugStream.str());
spiritDebugStream.str(std::string());
#endif
qi::on_error<qi::fail>
(
line
,
phx::ref((std::ostream&) error)
<< phx::val("Error! Expecting ")
<< qi::_4 // what failed?
<< phx::val(" here: \"")
<< phx::construct<std::string>(qi::_3, qi::_2) // iterators to error-pos, end
<< phx::val("\"")
<< std::endl
);
}
qi::rule<Iterator, double()> dbl;
qi::rule<Iterator, std::string()> str;
qi::rule<Iterator, std::string()> string_expr;
qi::rule<Iterator, std::string()> string_with_comma;
qi::rule<Iterator, std::string()> comment;
qi::rule<Iterator, std::string()> trimmed_string_expr;
qi::rule<Iterator, std::string()> trimmed_string;
qi::rule<Iterator, std::string()> string_set;
qi::rule<Iterator, io::line()> line;
qi::rule<Iterator, std::vector<io::line>()> lines;
std::stringstream error;
};
namespace reader
{
//------------------------------------------------------------------------------
std::pair<bool, std::string> parse(std::string& _buf, std::vector<io::line>& _lines)
{
using boost::spirit::ascii::space;
using boost::spirit::ascii::blank;
using boost::spirit::qi::eol;
using boost::spirit::qi::phrase_parse;
using iterator_type = std::string::const_iterator;
using line_parser = io::line_parser<iterator_type>;
iterator_type iter = _buf.begin();
iterator_type end = _buf.end();
line_parser grammar; // Our grammar
bool result = phrase_parse(iter, end, grammar, space - blank - eol, _lines);
bool success = result && (iter == end);
std::string msg = grammar.error.str();
return std::make_pair(success, msg);
}
//------------------------------------------------------------------------------
void dictionary_reader::read()
{
std::filesystem::path path = this->get_file();
SIGHT_INFO("[dictionary_reader::read] dictionary file: " << path.string());
SIGHT_ASSERT("Empty path for dictionary file", !path.empty());
// Reading of the file
std::string buf;
std::ifstream file;
file.open(path.string().c_str(), std::ios::binary);
std::string error_open = "Unable to open " + path.string();
SIGHT_THROW_IF(error_open, !file.is_open());
file.seekg(0, std::ios::end);
const auto length = file.tellg();
file.seekg(0, std::ios::beg);
buf.resize(static_cast<std::size_t>(length));
char* buffer = buf.data();
file.read(buffer, static_cast<std::streamsize>(length));
file.close();
std::vector<io::line> dico_lines;
std::pair<bool, std::string> result = parse(buf, dico_lines);
std::string error = "Unable to parse " + path.string() + " : Bad file format.Error : " + result.second;
SIGHT_THROW_IF(error, !result.first);
// File the dictionary Structure
data::structure_traits_dictionary::sptr struct_dico = get_concrete_object();
for(io::line line : dico_lines)
{
data::structure_traits::sptr new_organ = std::make_shared<data::structure_traits>();
new_organ->set_type(line.type);
std::string class_reformated = reformat_string(
line.organ_class
);
data::structure_traits_helper::class_translator_t::right_const_iterator str_class_iter =
data::structure_traits_helper::CLASSTRANSLATOR.right.find(class_reformated);
std::string available_values = get_values(data::structure_traits_helper::CLASSTRANSLATOR.right);
error =
std::string("Organ class ") + class_reformated + " isn't available. Authorized type are "
+ available_values;
SIGHT_THROW_IF(error, !(str_class_iter != data::structure_traits_helper::CLASSTRANSLATOR.right.end()));
new_organ->set_class(str_class_iter->second);
new_organ->set_color(
std::make_shared<data::color>(
static_cast<float>(line.red) / 255.0F,
static_cast<float>(line.green) / 255.0F,
static_cast<float>(line.blue) / 255.0F,
static_cast<float>(line.alpha) / 100.0F
)
);
std::vector<std::string> categorylist;
boost::algorithm::split(categorylist, line.category, boost::algorithm::is_any_of(","));
data::structure_traits::category_container_t categories;
for(std::string category : categorylist)
{
std::string cat_reformated = reformat_string(
category
);
data::structure_traits_helper::category_translator_t::right_const_iterator str_category_iter =
data::structure_traits_helper::CATEGORYTRANSLATOR.right.find(cat_reformated);
available_values = get_values(
data::structure_traits_helper::CATEGORYTRANSLATOR.right
);
error =
std::string("Category ") + cat_reformated + " isn't available. Authorized type are "
+ available_values;
SIGHT_THROW_IF(
error,
!(str_category_iter != data::structure_traits_helper::CATEGORYTRANSLATOR.right.end())
);
categories.push_back(str_category_iter->second);
}
new_organ->set_categories(categories);
new_organ->set_attachment_type(line.attachment);
new_organ->set_native_exp(line.native_exp);
new_organ->set_native_geometric_exp(line.native_exp_geo);
new_organ->set_anatomic_region(line.anatomic_region);
new_organ->set_property_category(line.property_category);
new_organ->set_property_type(line.property_type);
struct_dico->add_structure(new_organ);
}
}
//------------------------------------------------------------------------------
std::string dictionary_reader::extension() const
{
return ".dic";
}
//------------------------------------------------------------------------------
std::filesystem::path dictionary_reader::get_default_dictionary_path()
{
return core::runtime::get_library_resource_file_path("io/OrganDictionary.dic");
}
//------------------------------------------------------------------------------
} // namespace reader
} // namespace sight::io
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