Alexandria 2.31.0
SDC-CH common library for the Euclid project
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PhotometricBandMappingConfig.cpp
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1/*
2 * Copyright (C) 2012-2022 Euclid Science Ground Segment
3 *
4 * This library is free software; you can redistribute it and/or modify it under
5 * the terms of the GNU Lesser General Public License as published by the Free
6 * Software Foundation; either version 3.0 of the License, or (at your option)
7 * any later version.
8 *
9 * This library is distributed in the hope that it will be useful, but WITHOUT
10 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
11 * FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
12 * details.
13 *
14 * You should have received a copy of the GNU Lesser General Public License
15 * along with this library; if not, write to the Free Software Foundation, Inc.,
16 * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
17 */
18
25#include <algorithm>
26#include <fstream>
27#include <boost/algorithm/string.hpp>
28#include <sstream>
29#include <tuple>
30
34
35namespace po = boost::program_options;
36namespace fs = boost::filesystem;
37
38namespace Euclid {
39namespace Configuration {
40
41static Elements::Logging logger = Elements::Logging::getLogger("PhotometricBandMappingConfig");
42
43static const std::string FILTER_MAPPING_FILE{"filter-mapping-file"};
44static const std::string EXCLUDE_FILTER{"exclude-filter"};
45
47
49 return {
50 {"Input catalog options",
51 {{FILTER_MAPPING_FILE.c_str(), po::value<std::string>()->default_value("filter_mapping.txt"),
52 "The file containing the photometry mapping of the catalog columns"},
53 {EXCLUDE_FILTER.c_str(), po::value<std::vector<std::string>>()->default_value(std::vector<std::string>{}, ""),
54 "A list of filters to ignore"}}}};
55}
56
57static fs::path getMappingFileFromOptions(const Configuration::UserValues& args, const fs::path& base_dir) {
58 fs::path mapping_file{args.at(FILTER_MAPPING_FILE).as<std::string>()};
59 if (mapping_file.is_relative()) {
60 mapping_file = base_dir / mapping_file;
61 }
62 if (!fs::exists(mapping_file)) {
63 throw Elements::Exception() << "Photometry mapping file " << mapping_file << " does not exist";
64 }
65 if (fs::is_directory(mapping_file)) {
66 throw Elements::Exception() << "Photometry mapping file " << mapping_file << " is not a file";
67 }
68 return mapping_file;
69}
70
73parseFile(fs::path filename) {
74 PhotometricBandMappingConfig::MappingMap filter_name_mapping{};
76 PhotometricBandMappingConfig::ConvertFromMagMap convert_from_mag_mapping{};
77 std::ifstream in{filename.string()};
78 std::string line;
79
80 bool header_found = false;
81 int filtr_column_index = 0;
82 int flux_column_index = 1;
83 int error_column_index = 2;
84 int upper_limit_column_index = 3;
85 int convertion_column_index = 4;
86
87 std::vector<std::string> expected_column_name{"Filter", "Flux Column", "Error Column", "Upper Limit/error ratio",
88 "Convert from MAG"};
89
90 while (std::getline(in, line)) {
91 boost::trim(line);
92 if (line[0] == '#') {
93 if (!header_found) {
94 std::string trimmed_line = line.substr(1);
95 boost::trim(trimmed_line);
96 std::vector<int> proposed_column_index{-1, -1, -1, -1, -1};
98 boost::split(strs, trimmed_line, boost::is_any_of(","));
99
100 for (size_t index = 0; index < expected_column_name.size(); ++index) {
101 for (size_t index_string = 0; index_string < strs.size(); ++index_string) {
102 std::string item = strs[index_string];
103 boost::trim(item);
104 if (item == expected_column_name[index]) {
105 proposed_column_index[index] = index_string;
106 }
107 }
108 }
109
110 if (proposed_column_index[0] >= 0 && proposed_column_index[1] >= 0 && proposed_column_index[2] >= 0) {
111 header_found = true;
112 filtr_column_index = proposed_column_index[0];
113 flux_column_index = proposed_column_index[1];
114 error_column_index = proposed_column_index[2];
115 upper_limit_column_index = proposed_column_index[3];
116 convertion_column_index = proposed_column_index[4];
117 }
118 }
119 continue;
120 }
121
123 boost::split(cells, line, boost::is_any_of(" "));
124
125 try {
126 if (int(cells.size()) <= filtr_column_index || int(cells.size()) <= flux_column_index ||
127 int(cells.size()) <= error_column_index) {
128 throw Elements::Exception() << "File with missing values for the mandatory fields";
129 }
130 std::string filter_value = cells[filtr_column_index];
131 boost::trim(filter_value);
132 std::string flux_value = cells[flux_column_index];
133 boost::trim(flux_value);
134 std::string error_value = cells[error_column_index];
135 boost::trim(error_value);
136
137 filter_name_mapping.emplace_back(filter_value, std::make_pair(flux_value, error_value));
138
139 if (upper_limit_column_index > 0 && int(cells.size()) > upper_limit_column_index &&
140 cells[upper_limit_column_index] != "") {
141 float n = std::stof(cells[upper_limit_column_index]);
142 threshold_mapping.emplace_back(filter_value, n);
143 } else {
144 threshold_mapping.emplace_back(filter_value, 3.0);
145 }
146
147 if (convertion_column_index > 0 && int(cells.size()) > convertion_column_index &&
148 cells[convertion_column_index] != "") {
149 bool f = std::stoi(cells[convertion_column_index]);
150 convert_from_mag_mapping.emplace_back(filter_value, f);
151 } else {
152 convert_from_mag_mapping.emplace_back(filter_value, false);
153 }
154 } catch (const std::exception& e) {
155 logger.error() << "Syntax error in " << filename << ": " << line << " => " << e.what();
156 ;
157 throw Elements::Exception() << "Syntax error in " << filename << ": " << line << " => " << e.what();
158 }
159 }
160 return std::make_tuple(filter_name_mapping, threshold_mapping, convert_from_mag_mapping);
161}
162
164
165 // Parse the file with the mapping
167 auto parsed = parseFile(m_mapping_file);
168 auto all_filter_name_mapping = std::get<0>(parsed);
169 auto all_threshold_mapping = std::get<1>(parsed);
170 auto all_convert_mapping = std::get<2>(parsed);
171
172 // Remove the filters which are marked to exclude
173 auto exclude_vector = args.at(EXCLUDE_FILTER).as<std::vector<std::string>>();
174 std::set<std::string> exclude_filters{exclude_vector.begin(), exclude_vector.end()};
175
176 for (auto& pair : all_threshold_mapping) {
177 if (exclude_filters.count(pair.first) == 0) {
179 }
180 }
181
182 for (auto& pair : all_convert_mapping) {
183 if (exclude_filters.count(pair.first) == 0) {
185 }
186 }
187
188 for (auto& pair : all_filter_name_mapping) {
189 if (exclude_filters.count(pair.first) > 0) {
190 exclude_filters.erase(pair.first);
191 } else {
193 }
194 }
195
196 if (!exclude_filters.empty()) {
197 std::stringstream wrong_filters{};
198 for (auto& f : exclude_filters) {
199 wrong_filters << f << " ";
200 }
201 throw Elements::Exception() << "Wrong " << EXCLUDE_FILTER << " option value(s) : " << wrong_filters.str();
202 }
203}
204
205void PhotometricBandMappingConfig::setBaseDir(const boost::filesystem::path& base_dir) {
207 throw Elements::Exception() << "setBaseDir() call to initialized PhotometricBandMappingConfig";
208 }
209 m_base_dir = base_dir;
210}
211
214 throw Elements::Exception() << "getPhotometricBandMapping() call to uninitialized "
215 << "PhotometricBandMappingConfig";
216 }
217 return m_mapping_map;
218}
219
223 throw Elements::Exception() << "getUpperLimitThresholdMapping() call to uninitialized "
224 << "PhotometricBandMappingConfig";
225 }
226 return m_threshold_map;
227}
228
231 throw Elements::Exception() << "getConvertFromMagMapping() call to uninitialized "
232 << "PhotometricBandMappingConfig";
233 }
235}
236
239 throw Elements::Exception() << "getMappingFile() call to uninitialized "
240 << "PhotometricBandMappingConfig";
241 }
242 return m_mapping_file;
243}
244
245} // namespace Configuration
246} // namespace Euclid
T at(T... args)
T begin(T... args)
T c_str(T... args)
void error(const std::string &logMessage)
static Logging getLogger(const std::string &name="")
Superclass of all configuration classes.
State & getCurrentState()
Returns the current state of the configuration.
@ INITIALIZED
The initialize() method has been called.
std::vector< std::pair< std::string, std::pair< std::string, std::string > > > MappingMap
std::vector< std::pair< std::string, bool > > ConvertFromMagMap
const boost::filesystem::path getMappingFile()
Returns the mapping file to be used by other configuration class.
const MappingMap & getPhotometricBandMapping()
Returns the list of the photometric band mapping which will be red from the catalog.
std::map< std::string, OptionDescriptionList > getProgramOptions() override
Returns the program options defined by the PhotometryCatalogConfig.
const UpperLimitThresholdMap & getUpperLimitThresholdMapping()
Returns the mapping of threshold used in the upper limit computation which will be red from the catal...
PhotometricBandMappingConfig(long manager_id)
Constructs a new PhotometricBandMappingConfig object.
void initialize(const UserValues &args) override
It initializes the photometric bands list.
void setBaseDir(const boost::filesystem::path &base_dir)
Sets the directory used when resolving relative paths.
std::vector< std::pair< std::string, float > > UpperLimitThresholdMap
const ConvertFromMagMap & getConvertFromMagMapping()
Returns the mapping of the flag indicating if the photometry has to be computed from a MAG_AB.
T getline(T... args)
T make_pair(T... args)
T make_tuple(T... args)
static Elements::Logging logger
static const std::string EXCLUDE_FILTER
static std::tuple< PhotometricBandMappingConfig::MappingMap, PhotometricBandMappingConfig::UpperLimitThresholdMap, PhotometricBandMappingConfig::ConvertFromMagMap > parseFile(fs::path filename)
static fs::path getMappingFileFromOptions(const Configuration::UserValues &args, const fs::path &base_dir)
static const std::string FILTER_MAPPING_FILE
T push_back(T... args)
T size(T... args)
T stof(T... args)
T stoi(T... args)
T substr(T... args)