frame reading for cluster file

docs/CMakeLists.txt

@@ -10,31 +10,35 @@ configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
 set(SPHINX_SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 set(SPHINX_BUILD ${CMAKE_CURRENT_BINARY_DIR})
 
-set(SPHINX_SOURCE_FILES
-  src/index.rst
-  src/Installation.rst
-  src/Requirements.rst
-  src/NDArray.rst
-  src/NDView.rst
-  src/File.rst
-  src/Frame.rst
-  src/Dtype.rst
-  src/ClusterFinder.rst
-  src/Pedestal.rst
-  src/RawFile.rst
-  src/RawSubFile.rst
-  src/RawMasterFile.rst
-  src/VarClusterFinder.rst
-  src/pyVarClusterFinder.rst
-  src/pyFile.rst
-  src/pyCtbRawFile.rst
-  src/pyRawFile.rst
-  src/pyRawMasterFile.rst
-)
+
+file(GLOB SPHINX_SOURCE_FILES CONFIGURE_DEPENDS "src/*.rst")
+# set(SPHINX_SOURCE_FILES
+#   src/index.rst
+#   src/Installation.rst
+#   src/Requirements.rst
+#   src/NDArray.rst
+#   src/NDView.rst
+#   src/File.rst
+#   src/Frame.rst
+#   src/Dtype.rst
+#   src/ClusterFinder.rst
+#   src/ClusterFile.rst
+#   src/Pedestal.rst
+#   src/RawFile.rst
+#   src/RawSubFile.rst
+#   src/RawMasterFile.rst
+#   src/VarClusterFinder.rst
+#   src/pyVarClusterFinder.rst
+#   src/pyFile.rst
+#   src/pyCtbRawFile.rst
+#   src/pyRawFile.rst
+#   src/pyRawMasterFile.rst
+# )
 
 foreach(filename ${SPHINX_SOURCE_FILES})
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${filename} 
-              "${SPHINX_BUILD}/${filename}")
+    get_filename_component(fname ${filename} NAME)
+    message(STATUS "Copying ${filename} to ${SPHINX_BUILD}/src/${fname}")
+    configure_file(${filename} "${SPHINX_BUILD}/src/${fname}")  
 endforeach(filename ${SPHINX_SOURCE_FILES})
 
 configure_file(

docs/src/ClusterFile.rst

@@ -0,0 +1,7 @@
+ClusterFile
+=============
+
+.. doxygenclass:: aare::ClusterFile
+   :members:
+   :undoc-members:
+   :private-members:

docs/src/index.rst

@@ -20,21 +20,12 @@ AARE
     
     pyFile
     pyCtbRawFile
+    pyClusterFile
     pyRawFile
     pyRawMasterFile
     pyVarClusterFinder
 
 
-.. toctree::
-    :caption: Python API
-    :maxdepth: 1
-    
-    pyFile
-    pyCtbRawFile
-    pyRawMasterFile
-    pyVarClusterFinder
-
-
 .. toctree::
     :caption: C++ API
     :maxdepth: 1
@@ -45,6 +36,7 @@ AARE
     File
     Dtype
     ClusterFinder
+    ClusterFile
     Pedestal
     RawFile
     RawSubFile

docs/src/pyClusterFile.rst

@@ -0,0 +1,11 @@
+
+ClusterFile
+============
+
+.. py:currentmodule:: aare
+
+.. autoclass:: ClusterFile
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:

include/aare/ClusterFile.hpp

@@ -38,6 +38,8 @@ struct ClusterAnalysis {
     double etay;
 };
 
+
+
 class ClusterFile {
     FILE *fp{};
     uint32_t m_num_left{};
@@ -46,6 +48,7 @@ class ClusterFile {
   public:
     ClusterFile(const std::filesystem::path &fname, size_t chunk_size = 1000);
     std::vector<Cluster> read_clusters(size_t n_clusters);
+    std::vector<Cluster> read_frame(int32_t &out_fnum);
     std::vector<Cluster>
     read_cluster_with_cut(size_t n_clusters, double *noise_map, int nx, int ny);
 

python/examples/play.py

@@ -6,8 +6,10 @@ from aare import ClusterFile
 
 base = Path('~/data/aare_test_data/clusters').expanduser()
 
-# f = ClusterFile(base / 'beam_En700eV_-40deg_300V_10us_d0_f0_100.clust')
-f = ClusterFile(base / 'single_frame_97_clustrers.clust')
-
+f = ClusterFile(base / 'beam_En700eV_-40deg_300V_10us_d0_f0_100.clust')
+# f = ClusterFile(base / 'single_frame_97_clustrers.clust')
 
 
+for i in range(10):
+    fn, cl = f.read_frame()
+    print(fn, cl.size)

python/src/cluster_file.hpp

@@ -24,6 +24,12 @@ void define_cluster_file_io_bindings(py::module &m) {
                  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);

src/ClusterFile.cpp

@@ -13,14 +13,9 @@ std::vector<Cluster> ClusterFile::read_clusters(size_t n_clusters) {
     std::vector<Cluster> clusters(n_clusters);
 
     int32_t iframe = 0; // frame number needs to be 4 bytes!
-
     size_t nph_read = 0;
-
-    //     uint32_t nn = *n_left;
     uint32_t nn = m_num_left;
-    //     uint32_t nph = *n_left; // number of clusters in frame needs to be 4
-    //     bytes!
-    uint32_t nph = m_num_left;
+    uint32_t nph = m_num_left; // number of clusters in frame needs to be 4
 
     auto buf = reinterpret_cast<Cluster *>(clusters.data());
     // if there are photons left from previous frame read them first
@@ -61,6 +56,28 @@ std::vector<Cluster> ClusterFile::read_clusters(size_t n_clusters) {
     return clusters;
 }
 
+std::vector<Cluster> ClusterFile::read_frame(int32_t &out_fnum) {
+    if (m_num_left) {
+        throw std::runtime_error("There are still photons left in the last frame");
+    }
+
+    if (fread(&out_fnum, sizeof(out_fnum), 1, fp) != 1) {
+        throw std::runtime_error("Could not read frame number");
+    }
+
+    int n_clusters;
+    if (fread(&n_clusters, sizeof(n_clusters), 1, fp) != 1) {
+        throw std::runtime_error("Could not read number of clusters");
+    }
+    std::vector<Cluster> clusters(n_clusters);
+
+    if (fread(clusters.data(), sizeof(Cluster), n_clusters, fp) != n_clusters) {
+        throw std::runtime_error("Could not read clusters");
+    }
+    return clusters;
+
+}
+
 std::vector<Cluster> ClusterFile::read_cluster_with_cut(size_t n_clusters,
                                                         double *noise_map,
                                                         int nx, int ny) {