def annotation_to_fbs_matrix(self, axis, fields=None, labels=None):
with ServerTiming.time(f"annotations.{axis}.query"):
A = self.open_array(str(axis))
# may raise if fields contains unknown key
cxg_fields, anno_fields, return_fields, index_field = self._annotations_field_split(axis, fields, A, labels)
if cxg_fields is None:
data = A[:]
elif cxg_fields:
data = A.query(attrs=cxg_fields)[:]
else:
data = {}
df = pd.DataFrame.from_dict(data)
if axis == Axis.OBS and labels is not None and not labels.empty:
if anno_fields is None:
assert index_field
df = df.join(labels, index_field)
elif anno_fields:
assert index_field
df = df.join(labels[anno_fields], index_field)
if return_fields:
df = df[return_fields]
with ServerTiming.time(f"annotations.{axis}.encode"):
fbs = encode_matrix_fbs(df, col_idx=df.columns)
return fbs
def create_matrix(self, dataset_name, num_cat, max_labels):
with self.elapsed_timer() as elapsed:
annon_dict = self.create_annotations_dict_multi_process(
dataset_name, num_cat, max_labels)
dict_size = sum(
sys.getsizeof(value)
for value in annon_dict.values()) / 1024**2
self.test_notes[dataset_name][f"num_categories_{num_cat}"][
f"max_label_{max_labels}"]["annotation_dict"] = {
"creation_time": str(elapsed()),
"size": f"{dict_size} mb",
}
df = pd.DataFrame(annon_dict)
df_size = sys.getsizeof(df) / 1024**2
self.test_notes[dataset_name][f"num_categories_{num_cat}"][
f"max_label_{max_labels}"]["data_frame"] = {
"creation_time": str(elapsed()),
"size": f"{df_size} mb",
}
try:
matrix = encode_matrix_fbs(matrix=df,
row_idx=None,
col_idx=df.columns)
matrix_size = sys.getsizeof(matrix) / 1024**2
self.test_notes[dataset_name][f"num_categories_{num_cat}"][
f"max_label_{max_labels}"]["fbs_matrix"] = {
"creation_time": str(elapsed()),
"size": f"{matrix_size} mb",
}
return matrix
except Exception as e:
print(f"Issue creating fbs matrix: {e}, for {dataset_name}")
return []
def layout_to_fbs_matrix(self, fields):
"""
return specified embeddings as a flatbuffer, using the cellxgene matrix fbs encoding.
* returns only first two dimensions, with name {ename}_0 and {ename}_1,
where {ename} is the embedding name.
* client assumes each will be individually centered & scaled (isotropically)
to a [0, 1] range.
* does not support filtering
"""
embeddings = self.get_embedding_names() if fields is None or len(fields) == 0 else fields
layout_data = []
with ServerTiming.time("layout.query"):
for ename in embeddings:
embedding = self.get_embedding_array(ename, 2)
normalized_layout = DataAdaptor.normalize_embedding(embedding)
layout_data.append(pd.DataFrame(normalized_layout, columns=[f"{ename}_0", f"{ename}_1"]))
with ServerTiming.time("layout.encode"):
if layout_data:
df = pd.concat(layout_data, axis=1, copy=False)
else:
df = pd.DataFrame()
fbs = encode_matrix_fbs(df, col_idx=df.columns, row_idx=None)
return fbs
def data_frame_to_fbs_matrix(self, filter, axis):
"""
Retrieves data 'X' and returns in a flatbuffer Matrix.
:param filter: filter: dictionary with filter params
:param axis: string obs or var
:return: flatbuffer Matrix
Caveats:
* currently only supports access on VAR axis
* currently only supports filtering on VAR axis
"""
if axis != Axis.VAR:
raise ValueError("Only VAR dimension access is supported")
try:
obs_selector, var_selector = self._filter_to_mask(filter)
except (KeyError, IndexError, TypeError, AttributeError):
raise FilterError("Error parsing filter")
if obs_selector is not None:
raise FilterError("filtering on obs unsupported")
num_columns = self.get_shape()[1] if var_selector is None else np.count_nonzero(var_selector)
if self.server_config.exceeds_limit("column_request_max", num_columns):
raise ExceedsLimitError("Requested dataframe columns exceed column request limit")
X = self.get_X_array(obs_selector, var_selector)
col_idx = np.nonzero([] if var_selector is None else var_selector)[0]
return encode_matrix_fbs(X, col_idx=col_idx, row_idx=None)
def compute_embedding(self, method, obsFilter):
if Axis.VAR in obsFilter:
raise FilterError(
"Observation filters may not contain variable conditions")
if method != "umap":
raise NotImplementedError(
f"re-embedding method {method} is not available.")
try:
shape = self.get_shape()
obs_mask = self._axis_filter_to_mask(Axis.OBS, obsFilter["obs"],
shape[0])
except (KeyError, IndexError):
raise FilterError("Error parsing filter")
with ServerTiming.time("layout.compute"):
X_umap = scanpy_umap(self.data, obs_mask)
normalized_layout = DataAdaptor.normalize_embedding(X_umap)
# Server picks reemedding name, which must not collide with any other
# embedding name generated by this backed.
name = f"reembed:{method}_{datetime.now().isoformat(timespec='milliseconds')}"
dims = [f"{name}_0", f"{name}_1"]
df = pd.DataFrame(normalized_layout, columns=dims)
fbs = encode_matrix_fbs(df, col_idx=df.columns, row_idx=None)
schema = {"name": name, "type": "float32", "dims": dims}
return (schema, fbs)
def test_encode_DataFrame(self):
df = pd.DataFrame(
data={
"a": np.zeros((10,), dtype=np.float32),
"b": np.ones((10,), dtype=np.int64),
"c": np.array([i for i in range(0, 10)], dtype=np.uint16),
"d": pd.Series(["x", "y", "z", "x", "y", "z", "a", "x", "y", "z"], dtype="category"),
}
)
expected_types = ((np.ndarray, np.float32), (np.ndarray, np.int32), (np.ndarray, np.uint32), (list, None))
fbs = encode_matrix_fbs(matrix=df, row_idx=None, col_idx=df.columns)
self.fbs_checks(fbs, (10, 4), expected_types, ["a", "b", "c", "d"])
def annotation_to_fbs_matrix(self, axis, fields=None, labels=None):
if axis == Axis.OBS:
if labels is not None and not labels.empty:
df = self.data.obs.join(labels, self.parameters.get("obs_names"))
else:
df = self.data.obs
else:
df = self.data.var
if fields is not None and len(fields) > 0:
df = df[fields]
return encode_matrix_fbs(df, col_idx=df.columns)
def test_encode_boundary(self):
""" test various boundary checks """
# row indexing is unsupported
with self.assertRaises(ValueError):
encode_matrix_fbs(matrix=pd.DataFrame(), row_idx=[])
# matrix must be 2D
with self.assertRaises(ValueError):
encode_matrix_fbs(matrix=np.zeros((3, 2, 1)))
with self.assertRaises(ValueError):
encode_matrix_fbs(matrix=np.ones((10,)))
def test_roundtrip(self):
dfSrc = pd.DataFrame(
data={
"a": np.zeros((10,), dtype=np.float32),
"b": np.ones((10,), dtype=np.int64),
"c": np.array([i for i in range(0, 10)], dtype=np.uint16),
"d": pd.Series(["x", "y", "z", "x", "y", "z", "a", "x", "y", "z"], dtype="category"),
}
)
dfDst = decode_matrix_fbs(encode_matrix_fbs(matrix=dfSrc, col_idx=dfSrc.columns))
self.assertEqual(dfSrc.shape, dfDst.shape)
self.assertEqual(set(dfSrc.columns), set(dfDst.columns))
for c in dfSrc.columns:
self.assertTrue(c in dfDst.columns)
if isinstance(dfSrc[c], pd.Series):
self.assertTrue(np.all(dfSrc[c] == dfDst[c]))
else:
self.assertEqual(dfSrc[c], dfDst[c])
def convert(mat, cols):
return decode_matrix_fbs(encode_matrix_fbs(
mat, col_idx=cols)).to_numpy()
def convert_to_fbs(annotation_dict):
df = pd.DataFrame(annotation_dict)
return encode_matrix_fbs(matrix=df, row_idx=None, col_idx=df.columns)
def make_fbs(data):
df = pd.DataFrame(data)
return encode_matrix_fbs(matrix=df, row_idx=None, col_idx=df.columns)
def test_encode_sparse(self):
csc = sparse.csc_matrix(np.array([[0, 1, 2], [3, 0, 4]]))
expected_types = ((np.ndarray, np.int32), (np.ndarray, np.int32), (np.ndarray, np.int32))
fbs = encode_matrix_fbs(matrix=csc, row_idx=None, col_idx=None)
self.fbs_checks(fbs, (2, 3), expected_types, None)
def test_encode_ndarray(self):
arr = np.zeros((3, 2), dtype=np.float32)
expected_types = ((np.ndarray, np.float32), (np.ndarray, np.float32), (np.ndarray, np.float32))
fbs = encode_matrix_fbs(matrix=arr, row_idx=None, col_idx=None)
self.fbs_checks(fbs, (3, 2), expected_types, None)
