fixed size read bug and added tests

src/ClusterReader.c

@@ -61,25 +61,33 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self,
 
     const int ndim = 1;
     Py_ssize_t size = 0;
-    PyObject *noise_obj;
+    PyObject *noise_obj = NULL;
-    if (!PyArg_ParseTuple(args, "nO", &size, &noise_obj)) {
+    PyObject *noise_array = NULL;
+    if (!PyArg_ParseTuple(args, "n|O", &size, &noise_obj)) {
         PyErr_SetString(PyExc_TypeError, "Could not parse args.");
         return NULL;
     }
 
     npy_intp dims[] = {size};
 
-    // Create two numpy arrays from the passed objects, if possible numpy will
+    // If possible numpy will
     // use the underlying buffer, otherwise it will create a copy, for example
     // if data type is different or we pass in a list. The
     // NPY_ARRAY_C_CONTIGUOUS flag ensures that we have contiguous memory.
-    PyObject *noise_array =
+
-        PyArray_FROM_OTF(noise_obj, NPY_DOUBLE, NPY_ARRAY_C_CONTIGUOUS);
+
+
+#ifdef CR_VERBOSE
+    printf("Getting ready to read: %lu clusters. Noise map: %p\n", size,
+           noise_obj);
+#endif
+
+    // If the user passed a noise map we fetch a pointer to that array as well
     int nx = 0, ny = 0;
     double *noise_map = NULL;
-
+    if (noise_obj) {
-    // If parsing of a or b fails we throw an exception in Python
+        noise_array =
-    if (noise_array) {
+            PyArray_FROM_OTF(noise_obj, NPY_DOUBLE, NPY_ARRAY_C_CONTIGUOUS);
 
         int ndim_noise = PyArray_NDIM((PyArrayObject *)(noise_array));
         npy_intp *noise_shape = PyArray_SHAPE((PyArrayObject *)(noise_array));
@@ -126,10 +134,10 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self,
     // Here goes the looping, removing frame numbers etc.
     int n_read = 0;
     if (noise_map)
-        read_clusters_with_cut(self->fp, size, buf, &self->n_left, noise_map,
+        n_read = read_clusters_with_cut(self->fp, size, buf, &self->n_left, noise_map,
                                nx, ny);
     else
-        read_clusters(self->fp, size, buf, &self->n_left);
+        n_read = read_clusters(self->fp, size, buf, &self->n_left);
 
     if (n_read != size) {
         // resize the array to match the number of read photons

tests/test_ClusterReader.py

@@ -85,10 +85,33 @@ def test_read_file_with_37_frames(data_path):
 def test_read_file_with_37_frames_in_chunks(data_path):
     #File shoud contain 37 frames with 5 clusters each
     #Full spec in utils/write_test_data.py
-    fname= (data_path/'37frames_with_5_clusters.clust').as_posix()
+    fname= data_path/'37frames_with_5_clusters.clust'
     r = ClusterFileReader(fname)
     total_clusters = 0
     while (clusters:=r.read(7)).size:
         total_clusters += clusters.size
     assert total_clusters == 185
-    
+    
+
+def test_read_file_with_noise_mask(data_path):
+    #No mask
+    fname= data_path/'noise_test.clust'
+    r = ClusterFileReader(fname)
+    cl = r.read(85) #file contains 70 clusters
+    assert cl.size == 70
+
+    #noise mask with zeros
+    noise_cut = np.zeros((400,400))
+    r = ClusterFileReader(fname)
+    cl = r.read(85, noise_cut)
+    assert cl.size == 70
+
+    #only pixel 80, 133 above noise
+    noise_cut[:] = 100
+
+    #TODO! Agree on orientation of noise mask!
+    # noise_cut[80,133] = 0
+    noise_cut[133,80] = 0
+    r = ClusterFileReader(fname)
+    cl = r.read(85, noise_cut)
+    assert cl.size == 10

utils/write_test_data.py

@@ -40,4 +40,21 @@ with open(path/'37frames_with_5_clusters.clust', 'wb') as f:
             data['data'] = np.arange(j,j+9)
             print(data)
             data.tofile(f)
-        
+        
+#Writing out data to test noise cuts
+header[1] = 7
+
+with open(path/'noise_test.clust', 'wb') as f:
+    for i in range(10):
+        data['x'] = 50
+        data['y'] = 133
+        data['data'][:] = 50
+
+        header.tofile(f)
+        print(header)
+        header[0] += 1
+        
+        for j in range(7):
+            print(data)
+            data.tofile(f)
+            data['x'] += 10