Dev/guess clusters (#355)

- exposing ClusterVector::empty in python
- added member guess_n_clusters

RELEASE.md

@@ -4,6 +4,8 @@
 
 ### API Changes:
 
+- Exposed ``ClusterVector.empty()`` in the Python API.
+- Added ClusterVector.estimate_n_clusters
 - Removed the lmfit dependency and the legacy ``fit_gaus``, ``fit_pol1``,
   ``fit_scurve``, and ``fit_scurve2`` APIs. Use ``Gaussian``, ``Pol1``,
   ``RisingScurve``, or ``FallingScurve`` and call ``model.fit(...)`` (or

include/aare/ClusterFile.hpp

@@ -144,6 +144,19 @@ class ClusterFile {
      */
     size_t chunk_size() const { return m_chunk_size; }
 
+    /**
+     * @brief Estimate the number of clusters in the file from its size
+     *
+     * Frame headers are included in the estimate, so the result may be slightly
+     * larger than the actual number of clusters. The file position is not
+     * changed.
+     *
+     * @throws std::runtime_error if the file is not opened for reading
+     */
+    size_t estimate_n_clusters() const {
+        return std::filesystem::file_size(m_filename) / sizeof(ClusterType);
+    }
+
     /**
      * @brief Set the region of interest to use when reading
      * clusters. If set only clusters within the ROI will be

python/src/bind_ClusterFile.hpp

@@ -47,6 +47,8 @@ void define_ClusterFile(py::module &m, const std::string &typestr) {
              })
         .def("set_roi", &ClusterFile<ClusterType>::set_roi, py::arg("roi"))
         .def("tell", &ClusterFile<ClusterType>::tell)
+        .def("estimate_n_clusters",
+             &ClusterFile<ClusterType>::estimate_n_clusters)
         .def(
             "set_noise_map",
             [](ClusterFile<ClusterType> &self, py::array_t<int32_t> noise_map) {
@@ -82,4 +84,4 @@ void define_ClusterFile(py::module &m, const std::string &typestr) {
         });
 }
 
-#pragma GCC diagnostic pop
+#pragma GCC diagnostic pop

python/src/bind_ClusterVector.hpp

@@ -72,6 +72,7 @@ void define_ClusterVector(py::module &m, const std::string &typestr) {
             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
             )")
         .def_property_readonly("size", &ClusterVector<ClusterType>::size)
+        .def("empty", &ClusterVector<ClusterType>::empty)
         .def("item_size", &ClusterVector<ClusterType>::item_size)
         .def_property_readonly("fmt",
                                [typestr](ClusterVector<ClusterType> &self) {
@@ -169,4 +170,4 @@ void define_3x3_reduction(py::module &m) {
         py::arg("clustervector"));
 }
 
-#pragma GCC diagnostic pop
+#pragma GCC diagnostic pop

python/tests/test_ClusterFile.py

@@ -14,6 +14,8 @@ from conftest import test_data_path
 def test_cluster_file(test_data_path): 
     """Test ClusterFile""" 
     f =  ClusterFile(test_data_path / "clust/single_frame_97_clustrers.clust") 
+    assert f.estimate_n_clusters() == 97
+    assert f.tell() == 0
     cv = f.read_clusters(10) #conversion does not work
 
 
@@ -62,4 +64,4 @@ def test_read_clusters_and_fill_histogram(test_data_path):
         hist_py = pickle.load(f)
         
     #Compare the two histograms
-    assert hist_aare == hist_py
+    assert hist_aare == hist_py

python/tests/test_ClusterVector.py

@@ -16,6 +16,7 @@ def test_create_cluster_vector():
     assert cv.cluster_size_x == 3
     assert cv.cluster_size_y == 3
     assert cv.size == 0
+    assert cv.empty()
 
 
 def test_push_back_on_cluster_vector():
@@ -27,6 +28,7 @@ def test_push_back_on_cluster_vector():
     cluster = _aare.Cluster2x2i(19, 22, np.ones(4, dtype=np.int32))
     cv.push_back(cluster)
     assert cv.size == 1
+    assert not cv.empty()
 
     arr = np.array(cv, copy=False)
     assert arr[0]['x'] == 19
@@ -127,4 +129,4 @@ def test_masking():
     
     assert cv_masked_array[0]["x"] == 1
     assert cv_masked_array[0]["y"] == 2
-    assert (cv_masked_array[0]["data"] == np.ones((3,3),dtype=np.int32)).all()
+    assert (cv_masked_array[0]["data"] == np.ones((3,3),dtype=np.int32)).all()

src/ClusterFile.test.cpp

@@ -17,6 +17,8 @@ TEST_CASE("Read one frame from a cluster file", "[.with-data]") {
     REQUIRE(std::filesystem::exists(fpath));
 
     ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
+    CHECK(f.estimate_n_clusters() == 97);
+    CHECK(f.tell() == 0);
     auto clusters = f.read_frame();
     CHECK(clusters.size() == 97);
     CHECK(clusters.frame_number() == 135);
@@ -250,6 +252,8 @@ TEST_CASE("Read cluster from multiple frame file", "[.with-data]") {
 
     SECTION("Read clusters from both frames") {
         ClusterFile<ClusterType> f(fpath);
+        CHECK(f.estimate_n_clusters() == 8);
+        CHECK(f.tell() == 0);
         auto clusters = f.read_clusters(2);
         REQUIRE(clusters.size() == 2);
         REQUIRE(clusters.frame_number() == 0);