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Code Issues Packages Projects Releases Wiki Activity

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/test/schema.json
+10
View File
@@ -67,6 +67,16 @@
"name": "umap",
"type": "float32",
"dims": ["umap_0", "umap_1"]
},
{
"name": "tsne",
"type": "float32",
"dims": ["tsne_0", "tsne_1"]
},
{
"name": "pca",
"type": "float32",
"dims": ["pca_0", "pca_1"]
}
]
}
server/test/test_anndata_adaptor.py
+17 -3
View File
@@ -34,7 +34,7 @@ Test the anndata adaptor using the pbmc3k data set.
class AdaptorTest(unittest.TestCase):
def setUp(self):
args = {
"embeddings__names": ["umap"],
"embeddings__names": ["umap", "tsne", "pca"],
"presentation__max_categories": 100,
"single_dataset__obs_names": None,
"single_dataset__var_names": None,
@@ -122,9 +122,9 @@ class AdaptorTest(unittest.TestCase):
check_feature("PUT", "/annotations/obs", False)
def test_layout(self):
fbs = self.data.layout_to_fbs_matrix()
fbs = self.data.layout_to_fbs_matrix(fields=None)
layout = decode_fbs.decode_matrix_FBS(fbs)
self.assertEqual(layout["n_cols"], 2)
self.assertEqual(layout["n_cols"], 6)
self.assertEqual(layout["n_rows"], 2638)
X = layout["columns"][0]
@@ -132,6 +132,20 @@ class AdaptorTest(unittest.TestCase):
Y = layout["columns"][1]
self.assertTrue((Y >= 0).all() and (Y <= 1).all())
def test_layout_fields(self):
""" X_pca, X_tsne, X_umap are available """
fbs = self.data.layout_to_fbs_matrix(["pca"])
layout = decode_fbs.decode_matrix_FBS(fbs)
self.assertEqual(layout["n_cols"], 2)
self.assertEqual(layout["n_rows"], 2638)
self.assertCountEqual(layout["col_idx"], ["pca_0", "pca_1"])
fbs = self.data.layout_to_fbs_matrix(["tsne", "pca"])
layout = decode_fbs.decode_matrix_FBS(fbs)
self.assertEqual(layout["n_cols"], 4)
self.assertEqual(layout["n_rows"], 2638)
self.assertCountEqual(layout["col_idx"], ["tsne_0", "tsne_1", "pca_0", "pca_1"])
def test_annotations(self):
fbs = self.data.annotation_to_fbs_matrix("obs")
annotations = decode_fbs.decode_matrix_FBS(fbs)