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;
-    if (!PyArg_ParseTuple(args, "nO", &size, &noise_obj)) {
+    PyObject *noise_obj = NULL;
+    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 parsing of a or b fails we throw an exception in Python
-    if (noise_array) {
+    if (noise_obj) {
+        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