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improve type handling for non-string annotation data (#465)

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* improve type handling for non-string annotation data

* improve clarity of code
This commit is contained in:
Bruce Martin
2018-11-26 10:32:29 -08:00
committed by Charlotte Weaver
parent 2b5094665f
commit 138d30909a
8 changed files with 273 additions and 159 deletions
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server/app/scanpy_engine/scanpy_engine.py
+24 -6
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@@ -65,6 +65,22 @@ class ScanpyEngine(CXGDriver):
else:
raise KeyError(f"Annotation name {name}, specified in --{ax_name}_name does not exist.")
@staticmethod
def _can_cast_to_float32(ann):
if ann.dtype.kind == "f" and np.can_cast(ann.dtype, np.float32):
return True
return False
@staticmethod
def _can_cast_to_int32(ann):
if ann.dtype.kind in ["i", "u"]:
if np.can_cast(ann.dtype, np.int32):
return True
ii32 = np.iinfo(np.int32)
if ann.min() >= ii32.min and ann.max() <= ii32.max:
return True
return False
def _create_schema(self):
self.schema = {
"dataframe": {
@@ -81,16 +97,18 @@ class ScanpyEngine(CXGDriver):
curr_axis = getattr(self.data, str(ax))
for ann in curr_axis:
ann_schema = {"name": ann}
data_kind = curr_axis[ann].dtype.kind
if data_kind == "f":
dtype = curr_axis[ann].dtype
data_kind = dtype.kind
if self._can_cast_to_float32(curr_axis[ann]):
ann_schema["type"] = "float32"
elif data_kind in ["i", "u"]:
elif self._can_cast_to_int32(curr_axis[ann]):
ann_schema["type"] = "int32"
elif data_kind == "?":
elif dtype == np.bool_:
ann_schema["type"] = "boolean"
elif data_kind == "O" and curr_axis[ann].dtype == "object":
elif data_kind == "O" and dtype == "object":
ann_schema["type"] = "string"
elif data_kind == "O" and curr_axis[ann].dtype == "category":
elif data_kind == "O" and dtype == "category":
ann_schema["type"] = "categorical"
ann_schema["categories"] = curr_axis[ann].dtype.categories.tolist()
else: