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Merge branch 'main' into testing/cuda_cf_api
Three files conflicted: - ClusterFinderMT::collect(): both sides rewrote it. Keep this branch's version (f4bbbc9), which reads the stop flags before sweeping, over main's (afce91b), which still samples queue emptiness mid-condition. The staged splice had also lost a brace, swallowing popFront(). - python/aare/ClusterFinder.py: restore the CUDA API deleted by the resolution (_cuda_available, _CUDA_ALGORITHMS, ClusterFinderCUDA, find_cluster_views_batched_iter, ClusterFinderCUDAGraph), and main's min_pedestal_samples forwarding, dropped as an adjacent hunk. - bind_ClusterVector.hpp: keep py::module_local() (133cedf) alongside main's new docstrings; without it _aare and _aare_cuda cannot both register Cluster/ClusterVector under pybind11 3. Does not build on its own: ClusterFinderFrozen and the CUDA drivers still call Pedestal APIs main removed. Fixed in the follow-up.
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@@ -29,37 +29,73 @@ void define_ClusterVector(py::module &m, const std::string &typestr) {
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py::class_<ClusterVector<
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Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType>, void>>(
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m, class_name.c_str(), py::buffer_protocol(),
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py::module_local())
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m, class_name.c_str(), R"doc(
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A contiguous, move-only container of fixed-size clusters.
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.def(py::init()) // TODO change!!!
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The class supports the Python buffer protocol, so ``numpy.array`` can
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either copy its data or create a zero-copy view. A zero-copy view is
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valid only while the ClusterVector's underlying allocation and size
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remain unchanged.
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)doc",
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py::buffer_protocol(), py::module_local())
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.def(py::init(), R"doc(
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Create an empty ClusterVector with frame number 0 and space reserved
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for at least 1024 clusters.
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)doc")
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.def(
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"__call__",
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[](ClusterVector<ClusterType> &self, py::array_t<bool> mask) {
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[](ClusterVector<ClusterType> &self,
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py::array_t<bool, py::array::c_style> mask) {
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return self(make_view_1d(mask));
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},
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py::arg("mask"), R"(
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Create a copy of the clustervector and apply a boolean mask to the ClusterVector.
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py::arg("mask").noconvert(), R"doc(
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Return a filtered copy of this ClusterVector.
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Parameters
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----------
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mask : numpy.ndarray
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One-dimensional, writable, C-contiguous array with dtype
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``numpy.bool_`` and one element per cluster.
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mask : 1d boolean numpy array
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Mask to apply to the ClusterVector. Must be the same length as the number of clusters in the ClusterVector.
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Returns
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-------
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ClusterVector
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Selected clusters in their original order. The frame number is
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preserved.
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)doc")
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)")
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.def(
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"push_back",
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[](ClusterVector<ClusterType> &self, const ClusterType &cluster) {
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self.push_back(cluster);
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},
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py::arg("cluster"), R"doc(
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Append one cluster.
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.def("push_back",
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[](ClusterVector<ClusterType> &self, const ClusterType &cluster) {
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self.push_back(cluster);
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})
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Notes
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-----
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Do not call this method while a zero-copy NumPy view of the
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ClusterVector exists. Reallocation invalidates the view, while an
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append without reallocation leaves its shape unchanged.
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)doc")
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.def("sum",
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[](ClusterVector<ClusterType> &self) {
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auto *vec = new std::vector<Type>(self.sum());
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return return_vector(vec);
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})
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.def(
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"sum",
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[](ClusterVector<ClusterType> &self) {
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auto *vec = new std::vector<Type>(self.sum());
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return return_vector(vec);
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},
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R"doc(
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Return the sum of all pixels in each cluster.
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Returns
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-------
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numpy.ndarray
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One value per cluster, in container order and with the cluster
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pixel dtype.
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)doc")
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.def(
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"sum_2x2",
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[](ClusterVector<ClusterType> &self) {
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@@ -68,24 +104,45 @@ void define_ClusterVector(py::module &m, const std::string &typestr) {
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return return_vector(vec);
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},
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R"(calculates sum of 2x2 subcluster with highest energy and index relative to cluster center 0: top_left, 1: top_right, 2: bottom_left, 3: bottom_right
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)")
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.def_property_readonly("size", &ClusterVector<ClusterType>::size)
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.def("empty", &ClusterVector<ClusterType>::empty)
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.def("item_size", &ClusterVector<ClusterType>::item_size)
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.def_property_readonly("fmt",
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[typestr](ClusterVector<ClusterType> &self) {
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return fmt_format<ClusterType>;
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})
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R"doc(
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Return the highest-sum center-adjacent 2x2 subcluster for each
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cluster.
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Returns
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-------
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numpy.ndarray
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Structured array with ``sum`` and ``index`` fields. Indices are
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0 for top-left, 1 for top-right, 2 for bottom-left, and 3 for
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bottom-right, relative to the cluster center.
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)doc")
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.def_property_readonly("size", &ClusterVector<ClusterType>::size,
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"Number of stored clusters.")
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.def("empty", &ClusterVector<ClusterType>::empty,
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"Return True when no clusters are stored.")
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.def("item_size", &ClusterVector<ClusterType>::item_size,
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"Return the size in bytes of one stored cluster, including "
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"padding.")
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.def_property_readonly(
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"fmt",
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[typestr](ClusterVector<ClusterType> &self) {
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return fmt_format<ClusterType>;
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},
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"PEP 3118 format string for one stored cluster.")
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.def_property_readonly("cluster_size_x",
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&ClusterVector<ClusterType>::cluster_size_x)
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&ClusterVector<ClusterType>::cluster_size_x,
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"Cluster size in the x dimension.")
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.def_property_readonly("cluster_size_y",
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&ClusterVector<ClusterType>::cluster_size_y)
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&ClusterVector<ClusterType>::cluster_size_y,
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"Cluster size in the y dimension.")
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.def_property_readonly("capacity",
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&ClusterVector<ClusterType>::capacity)
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&ClusterVector<ClusterType>::capacity,
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"Number of clusters that fit without "
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"reallocation.")
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.def_property("frame_number", &ClusterVector<ClusterType>::frame_number,
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&ClusterVector<ClusterType>::set_frame_number)
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&ClusterVector<ClusterType>::set_frame_number,
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"Signed 32-bit frame number; 0 can indicate clusters "
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"from multiple frames.")
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.def_buffer(
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[typestr](ClusterVector<ClusterType> &self) -> py::buffer_info {
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return py::buffer_info(
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@@ -99,31 +156,38 @@ void define_ClusterVector(py::module &m, const std::string &typestr) {
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});
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// Free functions using ClusterVector
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m.def("hitmap",
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[](std::array<size_t, 2> image_size, ClusterVector<ClusterType> &cv) {
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// Create a numpy array to hold the hitmap
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// The shape of the array is (image_size[0], image_size[1])
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// note that the python array is passed as [row, col] which
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// is the opposite of the clusters [x,y]
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py::array_t<int32_t> hitmap(image_size);
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auto r = hitmap.mutable_unchecked<2>();
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m.def(
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"hitmap",
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[](std::array<size_t, 2> image_size, ClusterVector<ClusterType> &cv) {
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// Create a numpy array to hold the hitmap
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// The shape of the array is (image_size[0], image_size[1])
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// note that the python array is passed as [row, col] which
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// is the opposite of the clusters [x,y]
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py::array_t<int32_t> hitmap(image_size);
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auto r = hitmap.mutable_unchecked<2>();
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// Initialize hitmap to 0
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for (py::ssize_t i = 0; i < r.shape(0); i++)
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for (py::ssize_t j = 0; j < r.shape(1); j++)
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r(i, j) = 0;
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// Initialize hitmap to 0
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for (py::ssize_t i = 0; i < r.shape(0); i++)
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for (py::ssize_t j = 0; j < r.shape(1); j++)
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r(i, j) = 0;
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// Loop over the clusters and increment the hitmap
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// Skip out of bound clusters
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for (const auto &cluster : cv) {
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auto x = cluster.x;
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auto y = cluster.y;
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if (x < image_size[1] && y < image_size[0])
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r(cluster.y, cluster.x) += 1;
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}
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// Loop over the clusters and increment the hitmap
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// Skip out of bound clusters
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for (const auto &cluster : cv) {
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auto x = cluster.x;
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auto y = cluster.y;
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if (x < image_size[1] && y < image_size[0])
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r(cluster.y, cluster.x) += 1;
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}
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return hitmap;
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});
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return hitmap;
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},
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py::arg("image_size"), py::arg("clusters"), R"doc(
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Count cluster centers into an ``int32`` image whose shape is given by
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``image_size`` as ``(rows, columns)``. Element ``[y, x]`` contains the
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number of cluster centers at that coordinate. Out-of-bounds centers are
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ignored.
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)doc");
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}
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template <typename Type, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
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@@ -136,15 +200,12 @@ void define_2x2_reduction(py::module &m) {
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return new ClusterVector<Cluster<Type, 2, 2, CoordType>>(
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reduce_to_2x2(cv));
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},
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R"(
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Reduce cluster to 2x2 subcluster by taking the 2x2 subcluster with
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the highest photon energy.
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Parameters
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cv : ClusterVector (clusters are filled in row-major ordering starting at the top left. Thus for a max subcluster in the top left corner the photon hit is at the fourth position.)
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)",
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R"doc(
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Reduce every cluster to its highest-sum center-adjacent 2x2 block.
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Returns a new ClusterVector; cluster order, coordinates, and frame
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number are preserved. Input pixel data is interpreted in row-major
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order.
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)doc",
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py::arg("clustervector"));
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}
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@@ -159,13 +220,13 @@ void define_3x3_reduction(py::module &m) {
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return new ClusterVector<Cluster<Type, 3, 3, CoordType>>(
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reduce_to_3x3(cv));
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},
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R"(
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Reduce cluster to 3x3 subcluster
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Parameters
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cv : ClusterVector
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)",
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R"doc(
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Reduce every cluster to the 3x3 block around its center index.
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Both input dimensions must be at least 3, and at least one must be
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greater than 3.
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Returns a new ClusterVector; cluster order, coordinates, and frame
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number are preserved.
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)doc",
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py::arg("clustervector"));
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}
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