[c++] WKB geometry utilities (#3149)

* Add serialization/deserialization support for geometry entities

* Add default constructors

* Extract geometry utilities into separate namespace
Move template function implementation outside of header files

* lint format

* Bump C++ version

* Replace lambdas with struct overloading operator()

* Revert C++ version bump

* Split write operator declaration

* Add named constants

* Moved geometry out of source directory
Address PR comments

libtiledbsoma/src/CMakeLists.txt

@@ -76,13 +76,55 @@ target_include_directories(TILEDB_SOMA_OBJECTS
   ${pybind11_INCLUDE_DIRS}
 )
 
+# ###########################################################
+# tiledbsoma geometry library target
+# ###########################################################
+
+add_library(TILEDB_SOMA_GEOMETRY_OBJECTS OBJECT
+  ${CMAKE_CURRENT_SOURCE_DIR}/geometry/point.cc
+  ${CMAKE_CURRENT_SOURCE_DIR}/geometry/linestring.cc
+  ${CMAKE_CURRENT_SOURCE_DIR}/geometry/polygon.cc
+  ${CMAKE_CURRENT_SOURCE_DIR}/geometry/multipoint.cc
+  ${CMAKE_CURRENT_SOURCE_DIR}/geometry/multilinestring.cc
+  ${CMAKE_CURRENT_SOURCE_DIR}/geometry/multipolygon.cc
+  ${CMAKE_CURRENT_SOURCE_DIR}/geometry/operators/io/read.cc
+  ${CMAKE_CURRENT_SOURCE_DIR}/geometry/operators/io/write.cc
+)
+
+target_compile_definitions(TILEDB_SOMA_GEOMETRY_OBJECTS
+  PRIVATE
+  -DTILEDB_NO_API_DEPRECATION_WARNINGS
+)
+
+target_compile_options(TILEDB_SOMA_GEOMETRY_OBJECTS
+  PRIVATE
+  ${TILEDBSOMA_COMPILE_OPTIONS}
+  ${TILEDBSOMA_WERROR_OPTION}
+  ${TILEDBSOMA_SANITIZER_OPTIONS}
+)
+
+set_property(TARGET TILEDB_SOMA_GEOMETRY_OBJECTS PROPERTY POSITION_INDEPENDENT_CODE ON)
+target_include_directories(TILEDB_SOMA_GEOMETRY_OBJECTS
+  PRIVATE
+  ${CMAKE_CURRENT_SOURCE_DIR}
+  ${CMAKE_CURRENT_SOURCE_DIR}/vendor
+  ${CMAKE_CURRENT_SOURCE_DIR}/soma
+  ${CMAKE_CURRENT_SOURCE_DIR}/external/khash
+  ${CMAKE_CURRENT_SOURCE_DIR}/external/include
+  ${CMAKE_CURRENT_SOURCE_DIR}/external/include/nanoarrow
+  $<TARGET_PROPERTY:TileDB::tiledb_shared,INTERFACE_INCLUDE_DIRECTORIES>
+  $<TARGET_PROPERTY:spdlog::spdlog,INTERFACE_INCLUDE_DIRECTORIES>
+  ${pybind11_INCLUDE_DIRS}
+)
+
 # ###########################################################
 # tiledbsoma library target
 # ###########################################################
 set(TILEDBSOMA_INSTALL_TARGETS "")
 if(TILEDBSOMA_BUILD_STATIC)
   add_library(tiledbsoma_static STATIC
     $<TARGET_OBJECTS:TILEDB_SOMA_OBJECTS>
+    $<TARGET_OBJECTS:TILEDB_SOMA_GEOMETRY_OBJECTS>
     $<TARGET_OBJECTS:TILEDBSOMA_NANOARROW_OBJECT>
   )
   list(APPEND TILEDBSOMA_INSTALL_TARGETS tiledbsoma_static)
@@ -108,6 +150,7 @@ if(TILEDBSOMA_BUILD_STATIC)
 else()
   add_library(tiledbsoma SHARED
     $<TARGET_OBJECTS:TILEDB_SOMA_OBJECTS>
+    $<TARGET_OBJECTS:TILEDB_SOMA_GEOMETRY_OBJECTS>
     $<TARGET_OBJECTS:TILEDBSOMA_NANOARROW_OBJECT>
   )
   list(APPEND TILEDBSOMA_INSTALL_TARGETS tiledbsoma)
@@ -222,6 +265,9 @@ set(TILEDB_SOMA_EXPORT_HEADER "${TILEDB_SOMA_EXPORT_HEADER}" PARENT_SCOPE)
 target_compile_definitions(TILEDB_SOMA_OBJECTS PRIVATE -DTILEDB_SOMA_OBJECTS_EXPORTS)
 target_include_directories(TILEDB_SOMA_OBJECTS PRIVATE ${TILEDB_SOMA_EXPORT_HEADER_DIR})
 
+target_compile_definitions(TILEDB_SOMA_GEOMETRY_OBJECTS PRIVATE -DTILEDB_SOMA_OBJECTS_EXPORTS)
+target_include_directories(TILEDB_SOMA_GEOMETRY_OBJECTS PRIVATE ${TILEDB_SOMA_EXPORT_HEADER_DIR})
+
 # Add the generated header to the public headers list
 list(APPEND TILEDB_SOMA_PUBLIC_HEADERS
   "${TILEDB_SOMA_EXPORT_HEADER}"

libtiledbsoma/src/geometry/base.h

@@ -0,0 +1,30 @@
+#ifndef TILEDBSOMA_GEOMETRY_BASE_H
+#define TILEDBSOMA_GEOMETRY_BASE_H
+
+#include <math.h>
+#include <memory>
+#include <optional>
+#include <vector>
+
+namespace tiledbsoma::geometry {
+
+struct BasePoint {
+    BasePoint(
+        double_t x,
+        double_t y,
+        std::optional<double_t> z = std::nullopt,
+        std::optional<double_t> m = std::nullopt)
+        : x(x)
+        , y(y)
+        , z(z)
+        , m(m) {
+    }
+
+    double_t x;
+    double_t y;
+    std::optional<double_t> z;
+    std::optional<double_t> m;
+};
+}  // namespace tiledbsoma::geometry
+
+#endif  // TILEDBSOMA_GEOMETRY_BASE_H

libtiledbsoma/src/geometry/geometry.h

@@ -0,0 +1,42 @@
+#ifndef TILEDBSOMA_GEOMETRY_H
+#define TILEDBSOMA_GEOMETRY_H
+
+#include <variant>
+
+#include "linestring.h"
+#include "multilinestring.h"
+#include "multipoint.h"
+#include "multipolygon.h"
+#include "point.h"
+#include "polygon.h"
+
+namespace tiledbsoma::geometry {
+
+enum GeometryType : uint32_t {
+    POINT = 1,
+    LINESTRING = 2,
+    POLYGON = 3,
+    MULTIPOINT = 4,
+    MULTILINESTRING = 5,
+    MULTIPOLYGON = 6,
+    GEOMETRYCOLLECTION = 7
+};
+
+using BinaryBuffer = std::vector<uint8_t>;
+
+struct GeometryCollection;
+using GenericGeometry = std::variant<
+    Point,
+    LineString,
+    Polygon,
+    MultiPoint,
+    MultiLineString,
+    MultiPolygon,
+    GeometryCollection>;
+
+struct GeometryCollection : public std::vector<GenericGeometry> {
+    using std::vector<GenericGeometry>::vector;
+};
+}  // namespace tiledbsoma::geometry
+
+#endif  // TILEDBSOMA_GEOMETRY_H

libtiledbsoma/src/geometry/linestring.cc

@@ -0,0 +1,10 @@
+#include "linestring.h"
+
+namespace tiledbsoma::geometry {
+LineString::LineString(std::vector<BasePoint>&& points)
+    : points(points) {
+}
+
+LineString::~LineString() {
+}
+}  // namespace tiledbsoma::geometry

libtiledbsoma/src/geometry/linestring.h

@@ -0,0 +1,19 @@
+#ifndef TILEDBSOMA_LINESTRING_H
+#define TILEDBSOMA_LINESTRING_H
+
+#include <vector>
+
+#include "base.h"
+
+namespace tiledbsoma::geometry {
+
+class LineString {
+   public:
+    LineString(std::vector<BasePoint>&& points = std::vector<BasePoint>());
+    ~LineString();
+
+    std::vector<BasePoint> points;
+};
+}  // namespace tiledbsoma::geometry
+
+#endif  // TILEDBSOMA_LINESTRING_H

libtiledbsoma/src/geometry/multilinestring.cc

@@ -0,0 +1,10 @@
+#include "multilinestring.h"
+
+namespace tiledbsoma::geometry {
+MultiLineString::MultiLineString(std::vector<LineString>&& linestrings)
+    : linestrings(linestrings) {
+}
+
+MultiLineString::~MultiLineString() {
+}
+}  // namespace tiledbsoma::geometry

libtiledbsoma/src/geometry/multilinestring.h

@@ -0,0 +1,19 @@
+#ifndef TILEDBSOMA_MULTILINESTRING_H
+#define TILEDBSOMA_MULTILINESTRING_H
+
+#include <vector>
+
+#include "linestring.h"
+
+namespace tiledbsoma::geometry {
+class MultiLineString {
+   public:
+    MultiLineString(
+        std::vector<LineString>&& linestring = std::vector<LineString>());
+    ~MultiLineString();
+
+    std::vector<LineString> linestrings;
+};
+}  // namespace tiledbsoma::geometry
+
+#endif  // TILEDBSOMA_MULTILINESTRING_H

libtiledbsoma/src/geometry/multipoint.cc

@@ -0,0 +1,10 @@
+#include "multipoint.h"
+
+namespace tiledbsoma::geometry {
+MultiPoint::MultiPoint(std::vector<Point>&& points)
+    : points(points) {
+}
+
+MultiPoint::~MultiPoint() {
+}
+}  // namespace tiledbsoma::geometry

libtiledbsoma/src/geometry/multipoint.h

@@ -0,0 +1,19 @@
+#ifndef TILEDBSOMA_MULTIPOINT_H
+#define TILEDBSOMA_MULTIPOINT_H
+
+#include <vector>
+
+#include "point.h"
+
+namespace tiledbsoma::geometry {
+class MultiPoint {
+   public:
+    MultiPoint(std::vector<Point>&& points = std::vector<Point>());
+    ~MultiPoint();
+
+    std::vector<Point> points;
+};
+
+}  // namespace tiledbsoma::geometry
+
+#endif  // TILEDBSOMA_MULTIPOINT_H

libtiledbsoma/src/geometry/multipolygon.cc

@@ -0,0 +1,10 @@
+#include "multipolygon.h"
+
+namespace tiledbsoma::geometry {
+MultiPolygon::MultiPolygon(std::vector<Polygon>&& polygons)
+    : polygons(polygons) {
+}
+
+MultiPolygon::~MultiPolygon() {
+}
+}  // namespace tiledbsoma::geometry

libtiledbsoma/src/geometry/multipolygon.h

@@ -0,0 +1,18 @@
+#ifndef TILEDBSOMA_MULTIPOLYGON_H
+#define TILEDBSOMA_MULTIPOLYGON_H
+
+#include <vector>
+
+#include "polygon.h"
+
+namespace tiledbsoma::geometry {
+class MultiPolygon {
+   public:
+    MultiPolygon(std::vector<Polygon>&& polygons = std::vector<Polygon>());
+    ~MultiPolygon();
+
+    std::vector<Polygon> polygons;
+};
+}  // namespace tiledbsoma::geometry
+
+#endif  // TILEDBSOMA_MULTIPOLYGON_H