Alexandria 2.25.0
SDC-CH common library for the Euclid project
FitsSerialize.icpp
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1/*
2 * Copyright (C) 2012-2021 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
19/*
20 * @file FitsSerialize.icpp
21 * @author nikoapos
22 */
23
24#include "GridConstructionHelper.h"
25#include "GridContainer/GridContainer.h"
26#include "Table/FitsWriter.h"
27#include "Table/Table.h"
28#include "XYDataset/QualifiedName.h"
29#include <CCfits/CCfits>
30#include <boost/filesystem.hpp>
31#include <type_traits>
32#include <valarray>
33
34namespace Euclid {
35namespace GridContainer {
36
37template <typename T>
38struct FitsBpixTraits {
39 static_assert(!std::is_same<T, T>::value, "FITS arrays of type T are not supported");
40};
41
42template <>
43struct FitsBpixTraits<std::int8_t> {
44 static constexpr int BPIX = BYTE_IMG;
45};
46
47template <>
48struct FitsBpixTraits<std::int16_t> {
49 static constexpr int BPIX = SHORT_IMG;
50};
51
52template <>
53struct FitsBpixTraits<std::int32_t> {
54 static constexpr int BPIX = LONG_IMG;
55};
56
57template <>
58struct FitsBpixTraits<std::int64_t> {
59 static constexpr int BPIX = LONGLONG_IMG;
60};
61
62template <>
63struct FitsBpixTraits<float> {
64 static constexpr int BPIX = FLOAT_IMG;
65};
66
67template <>
68struct FitsBpixTraits<double> {
69 static constexpr int BPIX = DOUBLE_IMG;
70};
71
72template <typename T>
73struct GridAxisValueFitsHelper {
74 using FitsType = T;
75 static FitsType axisToFits(const T& value) {
76 return value;
77 }
78 static T FitsToAxis(const FitsType& value) {
79 return value;
80 }
81};
82
83template <>
84struct GridAxisValueFitsHelper<XYDataset::QualifiedName> {
85 using FitsType = std::string;
86 static FitsType axisToFits(const XYDataset::QualifiedName& value) {
87 return value.qualifiedName();
88 }
89 static XYDataset::QualifiedName FitsToAxis(const FitsType& value) {
90 return value;
91 }
92};
93
94template <typename... AxesTypes>
95struct GridAxesToFitsHelper {
96
97 template <int I>
98 static void addGridAxesToFitsFile(const boost::filesystem::path& filename, const std::string& array_hdu_name,
99 const std::tuple<GridAxis<AxesTypes>...>& axes_tuple, const TemplateLoopCounter<I>&) {
100 addGridAxesToFitsFile(filename, array_hdu_name, axes_tuple, TemplateLoopCounter<I - 1>{});
101
102 auto& axis = std::get<I - 1>(axes_tuple);
103 using AxisType = typename std::remove_reference<decltype(axis)>::type::data_type;
104 using FitsType = typename GridAxisValueFitsHelper<AxisType>::FitsType;
105
106 std::vector<Table::ColumnInfo::info_type> info_list{Table::ColumnInfo::info_type{"Index", typeid(int32_t)},
107 Table::ColumnInfo::info_type{"Value", typeid(FitsType)}};
108 std::shared_ptr<Table::ColumnInfo> column_info{new Table::ColumnInfo{std::move(info_list)}};
109
110 std::vector<Table::Row> row_list{};
111 for (size_t i = 0; i < axis.size(); ++i) {
112 auto fits_value = GridAxisValueFitsHelper<AxisType>::axisToFits(axis[i]);
113 row_list.push_back(Table::Row{{(int)i, fits_value}, column_info});
114 }
115 Table::Table table{row_list};
116
117 Table::FitsWriter{filename.string(), false}
118 .setFormat(Table::FitsWriter::Format::BINARY)
119 .setHduName(axis.name() + "_" + array_hdu_name)
120 .addData(table);
121 }
122
123 static void addGridAxesToFitsFile(const boost::filesystem::path&, const std::string&, const std::tuple<GridAxis<AxesTypes>...>&,
124 const TemplateLoopCounter<0>&) {}
125};
126
127template <typename GridCellManager, typename... AxesTypes>
128void gridFitsExport(const boost::filesystem::path& filename, const std::string& hdu_name,
129 const GridContainer<GridCellManager, AxesTypes...>& grid) {
130 auto& axes = grid.getAxesTuple();
131
132 // Create the first HDU with the array. We do that in a scope so the file is
133 // created and the data are flushed into it before we continue.
134 {
135 CCfits::FITS fits(filename.string(), CCfits::Write);
136
137 auto ext_ax_size_t =
138 GridConstructionHelper<AxesTypes...>::createAxesSizesVector(axes, TemplateLoopCounter<sizeof...(AxesTypes)>{});
139 std::vector<long> ext_ax{ext_ax_size_t.begin(), ext_ax_size_t.end()};
140
141 using cell_type = typename GridCellManagerTraits<GridCellManager>::data_type;
142 auto bpix = FitsBpixTraits<cell_type>::BPIX;
143 fits.addImage(hdu_name, bpix, ext_ax);
144 std::valarray<cell_type> data(grid.size());
145 int i = 0;
146 for (auto value : grid) {
147 data[i] = value;
148 ++i;
149 }
150 fits.currentExtension().write(1, grid.size(), data);
151 }
152
153 GridAxesToFitsHelper<AxesTypes...>::addGridAxesToFitsFile(filename, hdu_name, axes, TemplateLoopCounter<sizeof...(AxesTypes)>{});
154}
155
156template <typename GridType>
157class GridAxisFitsReader {
158
159 template <int I>
160 using AxisType = typename std::remove_reference<decltype(std::declval<GridType>().template getAxis<I>())>::type;
161
162 template <int I, typename = void>
163 struct AxesTupleType {
164 using previous = typename AxesTupleType<I - 1>::type;
165 using type = decltype(std::tuple_cat(std::declval<previous>(), std::declval<std::tuple<AxisType<I>>>()));
166 };
167
168 template <int I>
169 struct AxesTupleType<I, typename std::enable_if<I == -1>::type> {
170 using type = std::tuple<>;
171 };
172
173 template <int I>
174 using GridAxisType = typename std::remove_reference<decltype(std::declval<GridType>().template getAxis<I>())>::type;
175
176 template <int I>
177 static GridAxisType<I> readAxis(const std::string& grid_name, CCfits::ExtHDU& hdu) {
178 using KnotType = typename GridAxisType<I>::data_type;
179 using FitsType = typename GridAxisValueFitsHelper<KnotType>::FitsType;
180
181 auto axis_name = hdu.name().substr(0, hdu.name().size() - grid_name.size() - 1);
182 std::vector<FitsType> data{};
183 try {
184 auto& column = hdu.column("Value");
185 column.read(data, 1, column.rows());
186 } catch (CCfits::FitsException e) {
187 throw Elements::Exception() << e.message();
188 }
189 std::vector<KnotType> knots{};
190 for (std::size_t i = 0; i < data.size(); ++i) {
191 knots.emplace_back(GridAxisValueFitsHelper<KnotType>::FitsToAxis(data[i]));
192 }
193 return {std::move(axis_name), std::move(knots)};
194 }
195
196 template <int I>
197 static typename AxesTupleType<I>::type readAxesTuple(CCfits::FITS& fits, const std::string& grid_name, int hdu_index,
198 const TemplateLoopCounter<I>&) {
199 auto axis = readAxis<I>(grid_name, fits.extension(hdu_index));
200 auto previous = readAxesTuple(fits, grid_name, hdu_index - 1, TemplateLoopCounter<I - 1>{});
201 return std::tuple_cat(std::move(previous), std::tuple<decltype(axis)>{std::move(axis)});
202 }
203
204 static std::tuple<> readAxesTuple(CCfits::FITS&, const std::string&, int, const TemplateLoopCounter<-1>&) {
205 return {};
206 }
207
208public:
209 static typename AxesTupleType<GridType::axisNumber() - 1>::type readAllAxes(CCfits::FITS& fits, int hdu_index) {
210 auto name = fits.extension(hdu_index).name();
211 return readAxesTuple(fits, name, hdu_index + GridType::axisNumber(), TemplateLoopCounter<GridType::axisNumber() - 1>{});
212 }
213};
214
215template <typename GridType>
216GridType gridFitsImport(const boost::filesystem::path& filename, int hdu_index) {
217 CCfits::FITS fits(filename.string(), CCfits::Read);
218
219 auto axes = GridAxisFitsReader<GridType>::readAllAxes(fits, hdu_index);
220
221 GridType grid{std::move(axes)};
222
223 std::valarray<typename GridType::cell_type> data{};
224 fits.extension(hdu_index).read(data);
225
226 int i = 0;
227 for (auto iter = grid.begin(); iter != grid.end(); ++iter, ++i) {
228 *iter = data[i];
229 }
230
231 return grid;
232}
233
234} // end of namespace GridContainer
235} // end of namespace Euclid