Cluster reading, expression templates (#99)

Co-authored-by: froejdh_e <erik.frojdh@psi.ch>

python/src/cluster.hpp

@@ -33,20 +33,20 @@ void define_cluster_finder_bindings(py::module &m) {
                  return clusters;
              });
 
-    py::class_<Cluster>(m, "Cluster", py::buffer_protocol())
+    py::class_<DynamicCluster>(m, "DynamicCluster", py::buffer_protocol())
         .def(py::init<int, int, Dtype>())
-        .def("size", &Cluster::size)
-        .def("begin", &Cluster::begin)
-        .def("end", &Cluster::end)
-        .def_readwrite("x", &Cluster::x)
-        .def_readwrite("y", &Cluster::y)
-        .def_buffer([](Cluster &c) -> py::buffer_info {
+        .def("size", &DynamicCluster::size)
+        .def("begin", &DynamicCluster::begin)
+        .def("end", &DynamicCluster::end)
+        .def_readwrite("x", &DynamicCluster::x)
+        .def_readwrite("y", &DynamicCluster::y)
+        .def_buffer([](DynamicCluster &c) -> py::buffer_info {
             return py::buffer_info(c.data(), c.dt.bytes(), c.dt.format_descr(),
                                    1, {c.size()}, {c.dt.bytes()});
         })
 
-        .def("__repr__", [](const Cluster &a) {
-            return "<Cluster: x: " + std::to_string(a.x) +
+        .def("__repr__", [](const DynamicCluster &a) {
+            return "<DynamicCluster: x: " + std::to_string(a.x) +
                    ", y: " + std::to_string(a.y) + ">";
         });
 }

python/src/cluster_file.hpp

@@ -0,0 +1,50 @@
+#include "aare/ClusterFile.hpp"
+#include "aare/defs.hpp"
+
+
+#include <cstdint>
+#include <filesystem>
+#include <pybind11/iostream.h>
+#include <pybind11/numpy.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+#include <pybind11/stl/filesystem.h>
+#include <string>
+
+namespace py = pybind11;
+using namespace ::aare;
+
+void define_cluster_file_io_bindings(py::module &m) {
+    PYBIND11_NUMPY_DTYPE(Cluster, x, y, data);
+
+    py::class_<ClusterFile>(m, "ClusterFile")
+        .def(py::init<const std::filesystem::path &, size_t>(), py::arg(), py::arg("chunk_size") = 1000)
+        .def("read_clusters",
+             [](ClusterFile &self, size_t n_clusters) {
+                 auto* vec = new std::vector<Cluster>(self.read_clusters(n_clusters));
+                 return return_vector(vec);
+             })
+        .def("read_frame",
+             [](ClusterFile &self) {
+                 int32_t frame_number;
+                 auto* vec = new std::vector<Cluster>(self.read_frame(frame_number));
+                 return py::make_tuple(frame_number, return_vector(vec));
+             })
+        .def("read_cluster_with_cut",
+             [](ClusterFile &self, size_t n_clusters, py::array_t<double> noise_map, int nx, int ny) {
+                 auto view = make_view_2d(noise_map);
+                 auto* vec = new std::vector<Cluster>(self.read_cluster_with_cut(n_clusters, view.data(), nx, ny));
+                 return return_vector(vec);
+             })
+        .def("__enter__", [](ClusterFile &self) { return &self; })
+        .def("__exit__", [](ClusterFile &self, py::args args) { return; })
+        .def("__iter__", [](ClusterFile &self) { return &self; })
+        .def("__next__", [](ClusterFile &self) {
+            auto vec =  new std::vector<Cluster>(self.read_clusters(self.chunk_size()));
+            if(vec->size() == 0) {
+                throw py::stop_iteration();
+            }
+            return return_vector(vec);
+        });
+
+}

python/src/file.hpp

@@ -264,7 +264,7 @@ void define_file_io_bindings(py::module &m) {
 
     //     .def("close", &ClusterFileV2::close);
 
-    // m.def("to_clustV2", [](std::vector<Cluster> &clusters, const int
+    // m.def("to_clustV2", [](std::vector<DynamicCluster> &clusters, const int
     // frame_number) {
     //     std::vector<ClusterV2> clusters_;
     //     for (auto &c : clusters) {

python/src/module.cpp

@@ -6,6 +6,7 @@
 #include "pixel_map.hpp"
 #include "pedestal.hpp"
 #include "cluster.hpp"
+#include "cluster_file.hpp"
 
 //Pybind stuff
 #include <pybind11/pybind11.h>
@@ -22,4 +23,5 @@ PYBIND11_MODULE(_aare, m) {
     define_pedestal_bindings<double>(m, "Pedestal");
     define_pedestal_bindings<float>(m, "Pedestal_float32");
     define_cluster_finder_bindings(m);
+    define_cluster_file_io_bindings(m);
 }