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diff --git a/doc/rtree.rst b/doc/rtree.rst new file mode 100644 index 0000000..4f691e2 --- /dev/null +++ b/doc/rtree.rst @@ -0,0 +1,727 @@ + +.. highlight:: cpp + +R-tree +====== + +Overview +-------- + +`R-tree <https://en.wikipedia.org/wiki/R-tree>`_ is a tree-based data +structure designed for optimal query performance on multi-dimensional spatial +objects with rectangular bounding shapes. The R-tree implementation included +in this library is a variant of R-tree known as `R*-tree +<https://en.wikipedia.org/wiki/R*_tree>`_ which differs from the original +R-tree in that it may re-insert an object if the insertion of that object +would cause the original target directory to overflow. Such re-insertions +lead to more balanced tree which in turn lead to better query performance, at +the expense of slightly more overhead at insertion time. + +Our implementation of R-tree theoretically supports any number of dimensions +although certain functionalities, especially those related to visualization, +are only supported for 2-dimensional instances. + +R-tree consists of three types of nodes. Value nodes store the values +inserted externally and always sit at the bottom of the tree. Leaf directory +nodes sit directly above the value nodes, and store only value nodes as their +child nodes. The rest are all non-leaf directory nodes which can either store +leaf or non-leaf directory nodes. + + +Quick start +----------- + +Let's go through a very simple example to demonstrate how to use +:cpp:class:`~mdds::rtree`. First, you need to specify a concrete type by +specifying the key type and value type to use:: + + #include <mdds/rtree.hpp> + + #include <string> + #include <iostream> + + // key values are of type double, and we are storing std::string as a + // value for each spatial object. By default, tree becomes 2-dimensional + // object store unless otherwise specified. + using rt_type = mdds::rtree<double, std::string>; + +You'll only need to specify the types of key and value here unless you want to +customize other properties of :cpp:class:`~mdds::rtree` including the number +of dimensions. By default, :cpp:class:`~mdds::rtree` sets the number of +dimensions to 2. + +:: + + rt_type tree; + +Instantiating an rtree instance should be no brainer as it requires no input +parameters. Now, let's insert some data:: + + tree.insert({{0.0, 0.0}, {15.0, 20.0}}, "first rectangle data"); + +This inserts a string value associated with a bounding rectangle of (0, 0) - +(15, 20). Note that in the above code we are passing the bounding rectangle +parameter to rtree's :cpp:func:`~mdds::rtree::insert` method as a nested +initializer list, which implicitly gets converted to +:cpp:class:`~mdds::rtree::extent_type`. You can also use the underlying type +directly as follows:: + + rt_type::extent_type bounds({-2.0, -1.0}, {1.0, 2.0}); + std::cout << "inserting value for " << bounds.to_string() << std::endl; + tree.insert(bounds, "second rectangle data"); + +which inserts a string value associated with a bounding rectangle of (-2, -1) +to (1, 2). You may have noticed that this code also uses extent_type's +:cpp:func:`~mdds::rtree::extent_type::to_string` method which returns a string +representation of the bounding rectangle. This may come in handy when +debugging your code. This method should work as long as the key type used in +your rtree class overloads ``std::ostream``'s ``<<`` operator function. + +Running this code will generate the following output: + +.. code-block:: none + + inserting value for (-2, -1) - (1, 2) + +As :cpp:class:`~mdds::rtree::extent_type` consists of two members called +``start`` and ``end`` both of which are of type +:cpp:class:`~mdds::rtree::point_type`, which in turn contains an array of keys +called ``d`` whose size equals the number of dimensions, you can modify the +extent directly:: + + bounds.start.d[0] = -1.0; // Change the first dimension value of the start rectangle point. + bounds.end.d[1] += 1.0; // Increment the second dimension value of the end rectangle point. + std::cout << "inserting value for " << bounds.to_string() << std::endl; + tree.insert(bounds, "third rectangle data"); + +This code will insert a string value associated with a rectangle of (-1, -1) +to (1, 3), and will generate the following output: + +.. code-block:: none + + inserting value for (-1, -1) - (1, 3) + +So far we have only inserted data associated with rectangle shapes, but +:cpp:class:`~mdds::rtree` also allows data associated with points to co-exist +in the same tree. The following code inserts a string value associated with a +point (5, 6):: + + tree.insert({5.0, 6.0}, "first point data"); + +Like the verfy first rectangle data we've inserted, we are passing the point +data as an initializer list of two elements (for 2-dimensional data storage), +which will implicitly get converted to :cpp:class:`~mdds::rtree::point_type` +before it enters into the call. + +Now that some data have been inserted, it's time to run some queries. Let's +query all objects that overlap with a certain rectangular region either +partially or fully. The following code will do just that:: + + // Search for all objects that overlap with a (4, 4) - (7, 7) rectangle. + auto results = tree.search({{4.0, 4.0}, {7.0, 7.0}}, rt_type::search_type::overlap); + + for (const std::string& v : results) + std::cout << "value: " << v << std::endl; + +In this query, we are specifying the search region to be (4, 4) to (7, 7) +which should overlap with the first rectangle data and the first point data. +Indeed, when you execute this code, you will see the following output: + +.. code-block:: none + + value: first rectangle data + value: first point data + +indicating that the query region does overlap with two of the stored values + +Note that the :cpp:func:`~mdds::rtree::search` method takes exactly two +arguments; the first one specifies the search region while the second two +specifies the type of search to be performed. In the above call we passed +:cpp:type:`~mdds::detail::rtree::search_type`'s ``overlap`` enum value which +picks up all values whose bounding rectangles overlap with the search region +either partially or fully. + +Sometimes, however, you may need to find a value whose bounding rectangle +matches exactly the search region you specify in your query. You can achieve +that by setting the search type to ``match``. + +Here is an example:: + + // Search for all objects whose bounding rectangles are exactly (4, 4) - (7, 7). + auto results = tree.search({{4.0, 4.0}, {7.0, 7.0}}, rt_type::search_type::match); + std::cout << "number of results: " << std::distance(results.begin(), results.end()) << std::endl; + +The search region is identical to that of the previous example, but the search +type is set to ``match`` instead. Then the next line will count the number of +results and print it out. The output you will see is as follows: + +.. code-block:: none + + number of results: 0 + +indicating that the results are empty. That is expected since none of the +objects stored in the tree have an exact bounding rectangle of (4, 4) - (7, +7). When you change the search region to (0, 0) - (15, 20), however, you'll +get one object back. Here is the actual code:: + + // Search for all objects whose bounding rectangles are exactly (0, 0) - (15, 20). + auto results = tree.search({{0.0, 0.0}, {15.0, 20.0}}, rt_type::search_type::match); + std::cout << "number of results: " << std::distance(results.begin(), results.end()) << std::endl; + +which is identical to the previous one except for the search resion. This is +its output: + +.. code-block:: none + + number of results: 1 + +indicating that it has found exactly one object whose bounding rectangle +exactly matches the search region. + +It's worth mentioning that :cpp:class:`~mdds::rtree` supports storage of +multiple objects with identical bounding rectangle. As such, searching with +the search type of ``match`` can return more than one result. + +As you may have noticed in these example codes, the +:cpp:class:`~mdds::rtree::search_results` object does provide +:cpp:func:`~mdds::rtree::search_results::begin` and +:cpp:func:`~mdds::rtree::search_results::end` methods that return standard +iterators which you can plug into various iterator algorithms from the STL. +Dereferencing the iterator will return a reference to the stored value i.e. +this line:: + + std::cout << "value: " << *results.begin() << std::endl; + +which immediately comes after the previous search will output: + +.. code-block:: none + + value: first rectangle data + +In addition to accessing the value that the iterator references, you can also +query from the same iterator object the bounding rectangle associated with the +value as well as its depth in the tree by calling its +:cpp:func:`~mdds::rtree::iterator_base::extent` and +:cpp:func:`~mdds::rtree::iterator_base::depth` methods, respectively, as in +the following code:: + + auto it = results.begin(); + std::cout << "value: " << *it << std::endl; + std::cout << "extent: " << it.extent().to_string() << std::endl; + std::cout << "depth: " << it.depth() << std::endl; + +Running this code will produce the following output: + +.. code-block:: none + + value: first rectangle data + extent: (0, 0) - (15, 20) + depth: 1 + +A depth value represents the distance of the node where the value is stored +from the root node of the tree, and is technically 0-based. However, you will +never see a depth of 0 in the search results since the root node of a R-tree +is always a directory node, and a directory node only stores other child nodes +and never a value (hence never appears in the search results). + + +Removing a value from tree +-------------------------- + +Removing an existing value from the tree first requires you to perform the +search to obtian search results, then from the search results get the iterator +and advance it to the position of the value you wish to remove. Once you have +your iterator set to the right position, pass it to the +:cpp:func:`~mdds::rtree::erase` method to remove that value. + +Note that you can only remove one value at a time, and the iterator becomes +invalid each time you call the :cpp:func:`~mdds::rtree::erase` method to +remove a value. + +Here is a contrived example to demonstrate how erasing a value works:: + + #include <mdds/rtree.hpp> + + #include <string> + #include <iostream> + + int main() + { + using rt_type = mdds::rtree<int, std::string>; + + rt_type tree; + + // Insert multiple values at the same point. + tree.insert({1, 1}, "A"); + tree.insert({1, 1}, "B"); + tree.insert({1, 1}, "C"); + tree.insert({1, 1}, "D"); + tree.insert({1, 1}, "E"); + + // This should return all five values. + auto results = tree.search({1, 1}, rt_type::search_type::match); + + for (const std::string& v : results) + std::cout << v << std::endl; + + // Erase "C". + for (auto it = results.begin(); it != results.end(); ++it) + { + if (*it == "C") + { + tree.erase(it); + break; // This invalidates the iterator. Bail out. + } + } + + std::cout << "'C' has been erased." << std::endl; + + // Now this should only return A, B, D and E. + results = tree.search({1, 1}, rt_type::search_type::match); + + for (const std::string& v : results) + std::cout << v << std::endl; + + return EXIT_SUCCESS; + } + +In this code, we are intentionally putting 5 values to the same 2-dimensional +point (1, 1), then removing one of them based on matching criteria (of being +equal to "C"). + +Compiling and running this code will generate the following output: + +.. code-block:: none + + A + B + C + D + E + 'C' has been erased. + A + B + D + E + +which clearly shows that the 'C' has been successfully erased. + + +Visualize R-tree structure +-------------------------- + +In this section we will illustrate a way to visualize an R-tree structure via +:cpp:func:`~mdds::rtree::export_tree` method, which can be useful when you +need to visually inspect the tree structure to see how well balanced it is (or +not). + +We will be using the following set of 2-dimensional rectangles as the bounding +rectangles for input values. + +.. figure:: _static/images/rtree_bounds_src.png + :align: center + +For input values, we'll simply use linearly increasing series of integer +values, but the values themselves are not the focus of this section, and we'll +not talk much about that. We will also intentionally make the capacity of +directory nodes smaller so that the tree will split more frequently during +insertion even for smaller number of inputs. + +Now, let's take a look at the code:: + + #include <mdds/rtree.hpp> + + #include <iostream> + #include <fstream> + + // Make the node capacity intentionally small. + struct tiny_trait_2d + { + constexpr static size_t dimensions = 2; + constexpr static size_t min_node_size = 2; + constexpr static size_t max_node_size = 5; + constexpr static size_t max_tree_depth = 100; + + constexpr static bool enable_forced_reinsertion = true; + constexpr static size_t reinsertion_size = 2; + }; + + using rt_type = mdds::rtree<int, int, tiny_trait_2d>; + + int main() + { + // 2D rectangle with the top-left position (x, y), width and height. + struct rect + { + int x; + int y; + int w; + int h; + }; + + std::vector<rect> rects = + { + { 3731, 2433, 1356, 937 }, + { 6003, 3172, 1066, 743 }, + { 4119, 6403, 825, 1949 }, + { 10305, 2315, 776, 548 }, + { 13930, 5468, 1742, 626 }, + { 8614, 4107, 2709, 1793 }, + { 14606, 1887, 5368, 1326 }, + { 17990, 5196, 1163, 1911 }, + { 6728, 7881, 3676, 1210 }, + { 14704, 9789, 5271, 1092 }, + { 4071, 10723, 4739, 898 }, + { 11755, 9010, 1357, 2806 }, + { 13978, 4068, 776, 509 }, + { 17507, 3717, 777, 471 }, + { 20358, 6092, 824, 1093 }, + { 6390, 4535, 1066, 1715 }, + { 13978, 7182, 2516, 1365 }, + { 17942, 11580, 2854, 665 }, + { 9919, 10450, 873, 1716 }, + { 5568, 13215, 7446, 509 }, + { 7357, 15277, 3145, 3234 }, + { 3539, 12592, 631, 509 }, + { 4747, 14498, 825, 626 }, + { 4554, 16913, 969, 1443 }, + { 12771, 14693, 2323, 548 }, + { 18714, 8193, 2372, 586 }, + { 22292, 2743, 487, 1638 }, + { 20987, 17535, 1163, 1249 }, + { 19536, 18859, 632, 431 }, + { 19778, 15394, 1356, 626 }, + { 22969, 15394, 631, 2066 }, + }; + + rt_type tree; + + // Insert the rectangle objects into the tree. + int value = 0; + for (const auto& rect : rects) + tree.insert({{rect.x, rect.y}, {rect.x + rect.w, rect.y + rect.h}}, value++); + + // Export the tree structure as a SVG for visualization. + std::string tree_svg = tree.export_tree(rt_type::export_tree_type::extent_as_svg); + std::ofstream fout("bounds.svg"); + fout << tree_svg; + + return EXIT_SUCCESS; + } + +First, we need to talk about how the concrete rtree type is instantiated:: + + // Make the node capacity intentionally small. + struct tiny_trait_2d + { + constexpr static size_t dimensions = 2; + constexpr static size_t min_node_size = 2; + constexpr static size_t max_node_size = 5; + constexpr static size_t max_tree_depth = 100; + + constexpr static bool enable_forced_reinsertion = true; + constexpr static size_t reinsertion_size = 2; + }; + + using rt_type = mdds::rtree<int, int, tiny_trait_2d>; + +The first and second template arguments specify the key and value types to be +both ``int``. This time around, however, we are passing a third template +argument which is a struct containing several static constant values. These +constant values define certain characteristics of your R-tree, and there are +some restrictions you need to be aware of in case you need to use your own +custom trait for your R-tree. Refer to +:cpp:class:`~mdds::detail::rtree::default_rtree_traits`, which is the default +trait used when you don't specify your own, for the descriptions of the +individual constants that your trait struct is expected to have as well as +restrictions that you must be aware of. + +Also be aware that these constants must all be constant expressions with +``constexpr`` specifiers, as some of them are used within ``static_assert`` +declarations, and even those that are currently not used within +``static_assert`` may be used in ``static_assert`` in the future. + +As far as our current example goes, the only part of the custom trait we need +to highlight is that we are setting the directory node size to 2-to-5 instead +of the default size of 40-to-100, to trigger more node splits and make the +tree artificially deeper. + +Let's move on to the next part of the code:: + + // 2D rectangle with the top-left position (x, y), width and height. + struct rect + { + int x; + int y; + int w; + int h; + }; + + std::vector<rect> rects = + { + { 3731, 2433, 1356, 937 }, + { 6003, 3172, 1066, 743 }, + { 4119, 6403, 825, 1949 }, + { 10305, 2315, 776, 548 }, + { 13930, 5468, 1742, 626 }, + { 8614, 4107, 2709, 1793 }, + { 14606, 1887, 5368, 1326 }, + { 17990, 5196, 1163, 1911 }, + { 6728, 7881, 3676, 1210 }, + { 14704, 9789, 5271, 1092 }, + { 4071, 10723, 4739, 898 }, + { 11755, 9010, 1357, 2806 }, + { 13978, 4068, 776, 509 }, + { 17507, 3717, 777, 471 }, + { 20358, 6092, 824, 1093 }, + { 6390, 4535, 1066, 1715 }, + { 13978, 7182, 2516, 1365 }, + { 17942, 11580, 2854, 665 }, + { 9919, 10450, 873, 1716 }, + { 5568, 13215, 7446, 509 }, + { 7357, 15277, 3145, 3234 }, + { 3539, 12592, 631, 509 }, + { 4747, 14498, 825, 626 }, + { 4554, 16913, 969, 1443 }, + { 12771, 14693, 2323, 548 }, + { 18714, 8193, 2372, 586 }, + { 22292, 2743, 487, 1638 }, + { 20987, 17535, 1163, 1249 }, + { 19536, 18859, 632, 431 }, + { 19778, 15394, 1356, 626 }, + { 22969, 15394, 631, 2066 }, + }; + +This ``rects`` variable holds an array of 2-dimensional rectangle data that +represent the positions and sizes of rectangles shown earlier in this section. +This will be used as bounding rectangles for the input values in the next part +of the code:: + + rt_type tree; + + // Insert the rectangle objects into the tree. + int value = 0; + for (const auto& rect : rects) + tree.insert({{rect.x, rect.y}, {rect.x + rect.w, rect.y + rect.h}}, value++); + +Here, the tree is instantiated, and the rectangles are inserted with their +associated values one at a time. Once the tree is populated, the code that +follows will export the structure of the tree as an SVG string, which will +then be saved to a file on disk:: + + // Export the tree structure as a SVG for visualization. + std::string tree_svg = tree.export_tree(rt_type::export_tree_type::extent_as_svg); + std::ofstream fout("bounds.svg"); + fout << tree_svg; + +When you open the exported SVG file named **bounds.svg** in a SVG viewer, +you'll see something similar to this: + +.. figure:: _static/images/rtree_bounds_tree.png + :align: center + +which depicts not only the bounding rectangles of the inserted values +(the red rectangles), but also the bounding rectangles of the directory +nodes as well (the light green rectangles). + + +Bulk-loading data +----------------- + +In this section we will explore on how to bulk-load data into an +:cpp:class:`~mdds::rtree` instance via rtree's own +:cpp:class:`~mdds::rtree::bulk_loader` class. In this example, we'll be using +the same custom trait we've used in the previous section in order to +artificially promote the rate of node splits. The first part of the code:: + + #include <mdds/rtree.hpp> + + #include <iostream> + #include <fstream> + + // Make the node capacity intentionally small. + struct tiny_trait_2d + { + constexpr static size_t dimensions = 2; + constexpr static size_t min_node_size = 2; + constexpr static size_t max_node_size = 5; + constexpr static size_t max_tree_depth = 100; + + constexpr static bool enable_forced_reinsertion = true; + constexpr static size_t reinsertion_size = 2; + }; + + using rt_type = mdds::rtree<int, int, tiny_trait_2d>; + +is pretty much identical to the example in the last section. The next part of +the code defines what bounding rectangles to be inserted. Here, we are using +a different set of rectangles than the previous example to illustrate the +difference between a series of normal insertions and bulk-loading:: + + // 2D rectangle with the top-left position (x, y), width and height. + struct rect + { + int x; + int y; + int w; + int h; + }; + + std::vector<rect> rects = + { + { 3538, 9126, 1908, 1908 }, + { 34272, 52053, 2416, 2543 }, + { 32113, 9761, 2416, 638 }, + { 16493, 16747, 7369, 2289 }, + { 29192, 23732, 3432, 2035 }, + { 35797, 17000, 1781, 892 }, + { 15857, 29319, 2162, 1654 }, + { 5825, 24239, 3559, 8512 }, + { 9127, 46846, 2543, 1019 }, + { 7094, 54338, 5210, 892 }, + { 18779, 39734, 3813, 10417 }, + { 32749, 35923, 2289, 2924 }, + { 26018, 31098, 257, 2797 }, + { 6713, 37066, 2924, 1146 }, + { 19541, 3157, 3305, 1146 }, + { 21953, 10904, 4448, 892 }, + { 15984, 24240, 5210, 1273 }, + { 8237, 15350, 2670, 2797 }, + { 17001, 13826, 4067, 1273 }, + { 30970, 13826, 3940, 765 }, + { 9634, 6587, 1654, 1781 }, + { 38464, 47099, 511, 1400 }, + { 20556, 54085, 1400, 1527 }, + { 37575, 24113, 1019, 765 }, + { 20429, 21064, 1146, 1400 }, + { 31733, 4427, 2543, 638 }, + { 2142, 27161, 1273, 7369 }, + { 3920, 43289, 8131, 1146 }, + { 14714, 34272, 1400, 4956 }, + { 38464, 41258, 1273, 1273 }, + { 35542, 45703, 892, 1273 }, + { 25891, 50783, 1273, 5083 }, + { 35415, 28431, 2924, 1781 }, + { 15476, 7349, 1908, 765 }, + { 12555, 11159, 1654, 2035 }, + { 11158, 21445, 1908, 2416 }, + { 23350, 28049, 3432, 892 }, + { 28684, 15985, 2416, 4321 }, + { 24620, 21953, 1654, 638 }, + { 30208, 30716, 2670, 2162 }, + { 26907, 44179, 2797, 4067 }, + { 21191, 35416, 2162, 1019 }, + { 27668, 38717, 638, 3178 }, + { 3666, 50528, 2035, 1400 }, + { 15349, 48750, 2670, 1654 }, + { 28430, 7221, 2162, 892 }, + { 4808, 3158, 2416, 1273 }, + { 38464, 3666, 1527, 1781 }, + { 2777, 20937, 2289, 1146 }, + { 38209, 9254, 1908, 1781 }, + { 2269, 56497, 2289, 892 }, + }; + +As with the previous example, each line contains the top-left position as well +as the size of a rectangle. We are now going to insert these rectangles in +two different ways. + +First, we insert them via normal :cpp:func:`~mdds::rtree::insert` method:: + + void load_tree() + { + rt_type tree; + + // Insert the rectangle objects into the tree. + int value = 0; + for (const auto& rect : rects) + tree.insert({{rect.x, rect.y}, {rect.x + rect.w, rect.y + rect.h}}, value++); + + // Export the tree structure as a SVG for visualization. + std::string tree_svg = tree.export_tree(rt_type::export_tree_type::extent_as_svg); + std::ofstream fout("bounds2.svg"); + fout << tree_svg; + } + +This code should look familiar since it's nearly identical to the code in the +previous section. After the insertion is done, we export the tree as an SVG +to visualize its structure. + +Next, we insert the same set of rectangles via +:cpp:class:`~mdds::rtree::bulk_loader`:: + + void bulkload_tree() + { + rt_type::bulk_loader loader; + + // Insert the rectangle objects into the tree. + int value = 0; + for (const auto& rect : rects) + loader.insert({{rect.x, rect.y}, {rect.x + rect.w, rect.y + rect.h}}, value++); + + // Start bulk-loading the tree. + rt_type tree = loader.pack(); + + // Export the tree structure as a SVG for visualization. + std::string tree_svg = tree.export_tree(rt_type::export_tree_type::extent_as_svg); + std::ofstream fout("bounds2-bulkload.svg"); + fout << tree_svg; + } + +Inserting via :cpp:class:`~mdds::rtree::bulk_loader` shouldn't be too +different than inserting via rtree's own insert methods. The only +difference is that you instantiate a +:cpp:class:`~mdds::rtree::bulk_loader` instance to insert all your data +to it, then call its :cpp:func:`~mdds::rtree::bulk_loader::pack` method +at the end to construct the final :cpp:class:`~mdds::rtree` instance. + +When the insertion is done and the tree instance created, we are once again +exporting its structure to an SVG file for visualization. + +There are primarily two advantages to using +:cpp:class:`~mdds::rtree::bulk_loader` to load data. First, unlike the +normal insertion, bulk-loading does not trigger re-insertion nor node +splits on the fly. Second, a tree created from bulk loader is typically +well balanced than if you insert the same data through normal insertion. +That is because the bulk loader sorts the data with respect to their +bounding rectangles ahead of time and partition them evenly. The tree +is then built from the bottom-up. You can visually see the effect of +this when comparing the two trees built in our current example. + +The first one is from the tree built via normal insertion: + +.. figure:: _static/images/rtree_bounds2_tree.png + :align: center + +The top part of the picture looks very "busy" indicated by a darker +green area representative of more directory nodes overlaping with each +other. In general, the rectangles look bigger and show higher degree of +overlaps. + +This one, on the other hand, is from the tree built with the same data +set but through bulk-loading: + +.. figure:: _static/images/rtree_bounds2_tree_bulkload.png + :align: center + +The rectangles generally look smaller and show much less overlaps than the +previous picture, which is considered to be a more balanced R-tree structure. + + +API Reference +------------- + +.. doxygenclass:: mdds::rtree + :members: + +.. doxygenstruct:: mdds::detail::rtree::default_rtree_traits + :members: + +.. doxygenstruct:: mdds::detail::rtree::integrity_check_properties + :members: + +.. doxygenenum:: mdds::detail::rtree::export_tree_type + :project: mdds + +.. doxygenenum:: mdds::detail::rtree::search_type + :project: mdds |