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[Backport release 1.15][python/c++] Add C++
SOMACoordinateSpace and…
… use it to push `Scene` metadata down to C++ (#3602) * [python/cpp] Add C++ `SOMACoordinateSpace` and use it to push `Scene` metadata down to C++ (#3580) Create a new class `SOMACoordinateSpace` in C++ and use it to read/write coordinate space metadata. Use this class to write coordinate space metadata for the `SOMAScene` class in C++. This replaces writing the metadata in the Python layer and fixes an issue where the `Scene` metadata was being written in a later timestamp than other core metadata like the SOMA datatype. * std::format -> fmt::format for C++17 on release-1.15 branch * fix merge * re-run lint-fixer after merge --------- Co-authored-by: Julia Dark <[email protected]>
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| /** | ||
| * This file defines classes, structs, and helpers for managing coordinate | ||
| * spaces and coordinate space transformations. | ||
| * @file soma_coordinates.cc | ||
| * | ||
| * @section LICENSE | ||
| * | ||
| * The MIT License | ||
| * | ||
| * @copyright Copyright (c) 2025 TileDB, Inc. | ||
| * | ||
| * Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| * of this software and associated documentation files (the "Software"), to deal | ||
| * in the Software without restriction, including without limitation the rights | ||
| * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| * copies of the Software, and to permit persons to whom the Software is | ||
| * furnished to do so, subject to the following conditions: | ||
| * | ||
| * The above copyright notice and this permission notice shall be included in | ||
| * all copies or substantial portions of the Software. | ||
| * | ||
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| * THE SOFTWARE. | ||
| * | ||
| * @section DESCRIPTION | ||
| * | ||
| * This file defines classes, structs, and helpers for managing coordinate | ||
| * spaces and coordinate space transformations. | ||
| */ | ||
|
|
||
| #include <tiledb/tiledb> | ||
| #include <unordered_set> | ||
| #include "../utils/logger.h" | ||
| #include "nlohmann/json.hpp" | ||
|
|
||
| #include "soma_coordinates.h" | ||
|
|
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| using json = nlohmann::json; | ||
|
|
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| namespace nlohmann { | ||
| template <> | ||
| struct adl_serializer<tiledbsoma::SOMAAxis> { | ||
| static void to_json(json& j, const tiledbsoma::SOMAAxis& axis) { | ||
| // void to_json(json& j, tiledbsoma::SOMAAxis& axis) { | ||
| if (axis.unit.has_value()) { | ||
| j = json{{"name", axis.name}, {"unit", axis.unit.value()}}; | ||
| } else { | ||
| j = json{{"name", axis.name}, {"unit", nullptr}}; | ||
| } | ||
| } | ||
|
|
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| static void from_json(const json& j, tiledbsoma::SOMAAxis& axis) { | ||
| j.at("name").get_to(axis.name); | ||
| auto unit_json = j.at("unit"); | ||
| if (unit_json.is_null()) { | ||
| axis.unit = std::nullopt; | ||
| } else { | ||
| unit_json.get_to(axis.unit); | ||
| } | ||
| } | ||
| }; | ||
| } // namespace nlohmann | ||
|
|
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| namespace tiledbsoma { | ||
|
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| SOMACoordinateSpace::SOMACoordinateSpace() | ||
| : axes_{{"x", std::nullopt}, {"y", std::nullopt}} { | ||
| } | ||
|
|
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| SOMACoordinateSpace::SOMACoordinateSpace(const std::vector<SOMAAxis>& axes) | ||
| : axes_{axes} { | ||
| if (axes_.size() == 0) { | ||
| throw TileDBSOMAError("Coordinate space must have at least one axis."); | ||
| } | ||
| std::unordered_set<std::string> axis_names; | ||
| for (const auto& axis : axes_) { | ||
| axis_names.emplace(axis.name); | ||
| } | ||
| if (axes_.size() != axis_names.size()) { | ||
| throw TileDBSOMAError( | ||
| "The name for coordinate space axes must be unique."); | ||
| } | ||
| } | ||
|
|
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| SOMACoordinateSpace::SOMACoordinateSpace( | ||
| const std::vector<std::string>& axis_names) { | ||
| if (axis_names.size() == 0) { | ||
| throw TileDBSOMAError("Coordinate space must have at least one axis."); | ||
| } | ||
| std::unordered_set<std::string> unique_axis_names( | ||
| axis_names.begin(), axis_names.end()); | ||
| if (axis_names.size() != unique_axis_names.size()) { | ||
| throw TileDBSOMAError( | ||
| "The name for coordinate space axes must be unique."); | ||
| } | ||
| axes_.reserve(axis_names.size()); | ||
| for (const auto& name : axis_names) { | ||
| axes_.push_back({name, std::nullopt}); | ||
| } | ||
| } | ||
|
|
||
| SOMACoordinateSpace::SOMACoordinateSpace( | ||
| const std::vector<std::string>& axis_names, | ||
| const std::vector<std::optional<std::string>>& axis_units) { | ||
| if (axis_names.size() != axis_units.size()) { | ||
| throw TileDBSOMAError( | ||
| "[SOMACoordinateSpace]: Axis names and axis units size mismatch. "); | ||
| } | ||
| auto num_axes = axis_names.size(); | ||
| if (num_axes == 0) { | ||
| throw TileDBSOMAError("Coordinate space must have at least one axis."); | ||
| } | ||
| std::unordered_set<std::string> unique_axis_names( | ||
| axis_names.begin(), axis_names.end()); | ||
| if (axis_names.size() != unique_axis_names.size()) { | ||
| throw TileDBSOMAError( | ||
| "The name for coordinate space axes must be unique."); | ||
| } | ||
| axes_.reserve(num_axes); | ||
| for (size_t index{0}; index < num_axes; ++index) { | ||
| axes_.push_back({axis_names[index], axis_units[index]}); | ||
| } | ||
| } | ||
|
|
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| SOMACoordinateSpace SOMACoordinateSpace::from_metadata( | ||
| tiledb_datatype_t value_type, uint32_t value_num, const void* value) { | ||
| if (value_type != TILEDB_STRING_UTF8 && value_type != TILEDB_STRING_ASCII) { | ||
| throw TileDBSOMAError(fmt::format( | ||
| "[SOMACoordinateSpace]: Unexpected datatype for coordinate space " | ||
| "metadata. Expected {} or {}; got {}", | ||
| tiledb::impl::type_to_str(TILEDB_STRING_UTF8), | ||
| tiledb::impl::type_to_str(TILEDB_STRING_ASCII), | ||
| tiledb::impl::type_to_str(value_type))); | ||
| } | ||
| if (value == nullptr) { | ||
| throw TileDBSOMAError( | ||
| "[SOMACoordinateSpace]: Missing value for coordinate space " | ||
| "metadata."); | ||
| } | ||
| std::string value_str(static_cast<const char*>(value), value_num); | ||
| auto value_json = json::parse(value_str); | ||
| auto axes = value_json.template get<std::vector<SOMAAxis>>(); | ||
|
|
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| return SOMACoordinateSpace(axes); | ||
| } | ||
|
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| std::string SOMACoordinateSpace::to_string() const { | ||
| json serializer(axes_); | ||
| return serializer.dump(-1, ' ', true); | ||
| } | ||
| } // namespace tiledbsoma |
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