detectors/python_cluster_reader
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Merge branch 'memory-leak' into 'main'

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Memory leak

Closes #3

See merge request sls_detectors_software/python_cluster_reader!3
This commit is contained in:
froejdh_e 2024-05-07 14:06:39 +02:00
commit a6eec65f7a
2 changed files with 38 additions and 33 deletions
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67
src/ClusterReader.c
View File

@ -74,10 +74,12 @@ static void ClusterFileReader_dealloc(ClusterFileReader *self) {
static PyObject *ClusterFileReader_read(ClusterFileReader *self,
PyObject *args) {
const int ndim = 1;
Py_ssize_t size = 0;
PyObject *noise_obj = NULL;
PyObject *noise_array = NULL;
//refcount of the python object is not increased when parsing with O
if (!PyArg_ParseTuple(args, "|nO", &size, &noise_obj)) {
PyErr_SetString(PyExc_TypeError, "Could not parse args.");
return NULL;
@ -101,44 +103,43 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self,
// If the user passed a noise map we fetch a pointer to that array as well
int nx = 0, ny = 0;
PyObject *noise_array = NULL;
double *noise_map = NULL;
if (noise_obj) {
noise_array =
PyArray_FROM_OTF(noise_obj, NPY_DOUBLE, NPY_ARRAY_C_CONTIGUOUS);
//The user could have passes Py_None to indicate no noise map
//in that case we do nothing.
if (noise_obj == Py_None){
printf("Got Py_None as noise map, doing nothing\n");
}else{
//Check that we really got a numpy array and not any kind of PyObject
if(!PyArray_CheckExact(noise_obj)){
PyErr_SetString(PyExc_TypeError, "Noise map has to be a numpy array (or None).");
//TODO! Cleanup?
return NULL;
}
int ndim_noise = PyArray_NDIM((PyArrayObject *)(noise_array));
npy_intp *noise_shape = PyArray_SHAPE((PyArrayObject *)(noise_array));
noise_array =
PyArray_FROM_OTF(noise_obj, NPY_DOUBLE, NPY_ARRAY_IN_ARRAY | NPY_ARRAY_ENSUREARRAY);
int ndim_noise = PyArray_NDIM((PyArrayObject *)(noise_array));
npy_intp *noise_shape = PyArray_SHAPE((PyArrayObject *)(noise_array));
// For the C++ function call we need pointers (or another C++ type/data
// structure)
noise_map = (double *)(PyArray_DATA((PyArrayObject *)(noise_array)));
/* for (int i=0; i< ndim_noise; i++) { */
/* printf("Dimension %d size %d pointer \n",i,noise_shape[i],
* noise_map); */
/* } */
if (ndim_noise == 2) {
nx = noise_shape[0];
ny = noise_shape[1];
// printf("Noise map found size %d %d %d\n",nx,ny,noise_map);
} else {
nx = 0;
if (ndim_noise == 1)
// For the C++ function call we need pointers (or another C++ type/data
// structure)
if (ndim_noise == 2) {
nx = noise_shape[0];
ny = 0;
noise_map = NULL;
// printf("NO Noise map found %d %d %d
//%d\n",ndim_noise,nx,ny,noise_map);
ny = noise_shape[1];
noise_map = (double *)(PyArray_DATA((PyArrayObject *)(noise_array)));
} else {
PyErr_SetString(PyExc_TypeError, "Noise map has to be 2D.");
//TODO! Cleanup?
return NULL;
}
}
}
// Create an uninitialized numpy array
const int ndim = 1;
PyObject *clusters = PyArray_SimpleNewFromDescr(ndim, dims, cluster_dt());
// Fill with zeros
@ -172,6 +173,10 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self,
PyArray_Resize((PyArrayObject *)clusters, &new_shape, 1, NPY_ANYORDER);
}
//refcount of noise_obj was not increased
//XDECREF also works if noise_array is NULL
Py_XDECREF(noise_array);
return clusters;
}

4
tests/test_ClusterReader.py
View File

@ -92,7 +92,7 @@ def test_read_file_with_37_frames_in_chunks(data_path):
total_clusters += clusters.size
assert total_clusters == 185
@pytest.mark.skip(reason="Need to check how the selection is made")
def test_read_file_with_noise_mask(data_path):
#No mask
fname= data_path/'noise_test.clust'
@ -114,7 +114,7 @@ def test_read_file_with_noise_mask(data_path):
noise_cut[133,80] = 0
r = ClusterFileReader(fname)
cl = r.read(85, noise_cut)
assert cl.size == 10
assert cl.size == 1
def test_chunk_config(data_path):
fname= data_path/'noise_test.clust'