From ab36c255369ace09e6c1ac68a91dd32ee69fff76 Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Thu, 23 Jun 2022 15:44:29 +0200
Subject: [PATCH] fix saving tvec
---
align.py | 26 ++++++++++++++------------
1 file changed, 14 insertions(+), 12 deletions(-)
diff --git a/align.py b/align.py
index 7963c3a..ba2272a 100644
--- a/align.py
+++ b/align.py
@@ -65,17 +65,7 @@ def align_multichip(
counts = [o['counts'] for o in out]
tvecs = [o['tvec'] for o in out]
- def prep_tvec(transform_dict):
- transform_dict["tvec"] = List(transform_dict["tvec"])
- return transform_dict
-
- try:
- transform_data = [map(prep_tvec, tvecs)]
- with open(out_path.replace('.zarr', '.transform.json'), 'w') as f:
- json.dump(transform_data, fp=f)
- except Exception as e:
- print('saving transform json failed: ', e.args)
-
+ save_tvecs(tvecs, out_path.replace('.zarr', '.transform.json'))
df = pd.concat(counts, ignore_index=True).sort_values(['[AB]','label'])
df.to_csv(table_path)
@@ -91,7 +81,19 @@ def align_multichip(
)
return out_path
-
+def prep_tvec(transform_dict):
+ t = transform_dict.copy()
+ t["tvec"] = list(t["tvec"])
+ return t
+
+def save_tvecs(tvecs, path):
+ try:
+ transform_data = list(map(prep_tvec, tvecs))
+ with open(path, 'w') as f:
+ json.dump(transform_data, fp=f)
+ except Exception as e:
+ print('saving transform json failed: ', e.args)
+
def align_parallel(args, **kwargs):
return align2D(*args, **kwargs)
--
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