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load embeddings in parallel (#1352)

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* load embeddings in parallel

* correctly capture unclipped

* test

* another test

* add convenient copy assets target

* cleanup
This commit is contained in:
Bruce Martin
2020-04-07 09:48:07 -07:00
committed by GitHub
parent 3b341a7191
commit bcacb75296
7 changed files with 83 additions and 32 deletions
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server/data_common/data_adaptor.py
+3 -5
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@@ -331,10 +331,9 @@ class DataAdaptor(metaclass=ABCMeta):
normalized_layout = normalized_layout.astype(dtype=np.float32)
return normalized_layout
def layout_to_fbs_matrix(self):
""" same as layout, except returns a flatbuffer """
def layout_to_fbs_matrix(self, fields):
"""
return all embeddings as a flatbuffer, using the cellxgene matrix fbs encoding.
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.
@@ -343,8 +342,7 @@ class DataAdaptor(metaclass=ABCMeta):
* does not support filtering
"""
embeddings = self.get_embedding_names()
embeddings = self.get_embedding_names() if fields is None or len(fields) == 0 else fields
layout_data = []
with ServerTiming.time(f"layout.query"):
for ename in embeddings: