From 017e52cebd3d95de9846e869f574efeaf27d79a3 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 4 Apr 2024 10:27:49 +0200
Subject: [PATCH] Serialize after running other exports, as patch path is
embedded in dataframe; write this with subdirectory
---
model_server/base/roiset.py | 8 ++++----
tests/test_roiset.py | 8 ++++----
2 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 697f22a3..59ed23b3 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -537,9 +537,6 @@ class RoiSet(object):
if not self.count:
return
- # export dataframe and patch masks
- record = self.serialize(where, prefix=prefix)
-
for k in params.dict().keys():
subdir = where / k
pr = prefix
@@ -561,7 +558,7 @@ class RoiSet(object):
df_exp = self.export_patches(
subdir, white_channel=channel, prefix=pr, make_3d=False, **kp
)
- self._df = self._df.join(df_exp.patch_path)
+ self._df = self._df.join(df_exp.patch_path.apply(lambda x: str(Path('patches_2d') / x)))
self._df['patch_id'] = self._df.apply(lambda _: uuid4(), axis=1)
record[k] = [str(Path(k) / fn) for fn in df_exp.patch_path]
if k == 'annotated_zstacks':
@@ -572,6 +569,9 @@ class RoiSet(object):
write_accessor_data_to_file(fp, acc)
record[f'{k}_{kc}'] = str(fp)
+ # export dataframe and patch masks
+ record = {**record, **self.serialize(where, prefix=prefix)}
+
return record
def serialize(self, where: Path, prefix='') -> dict:
diff --git a/tests/test_roiset.py b/tests/test_roiset.py
index da9b43db..1d2b972b 100644
--- a/tests/test_roiset.py
+++ b/tests/test_roiset.py
@@ -395,10 +395,10 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
# test on paths in CSV
test_df = pd.read_csv(where / res['dataframe'])
- for c in test_df.columns:
- if '_path' in c:
- for f in test_df[c]:
- self.assertTrue((where / f).exists(), where / f)
+ for c in ['tight_patch_masks_path', 'patch_path']:
+ self.assertTrue(c in test_df.columns)
+ for f in test_df[c]:
+ self.assertTrue((where / f).exists(), where / f)
--
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