From 583c415be167c64b1773000ed749ebbada1f1e4f Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 10 Dec 2024 09:33:15 +0100
Subject: [PATCH] Export products no longer throw exceptions when called on
empty RoiSet
---
model_server/base/roiset.py | 15 +++++++++++++--
tests/base/test_roiset.py | 8 ++++++--
2 files changed, 19 insertions(+), 4 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 41edb804..8a1ff62a 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -630,7 +630,9 @@ class RoiSet(object):
def add_df_col(self, name, se: pd.Series) -> None:
self._df[name] = se
- def get_patches_acc(self, channels: list = None, **kwargs) -> PatchStack: # padded, un-annotated 2d patches
+ def get_patches_acc(self, channels: list = None, **kwargs) -> Union[PatchStack, None]: # padded, un-annotated 2d patches
+ if self.count == 0:
+ return None
if channels and len(channels) == 1:
return PatchStack(list(self.get_patches(white_channel=channels[0], **kwargs)))
else:
@@ -857,6 +859,10 @@ class RoiSet(object):
return patches_df.apply(_export_patch, axis=1)
def get_patch_masks(self, pad_to: int = None, expanded: bool = False, make_3d=True) -> pd.DataFrame:
+
+ if self.count == 0:
+ return pd.DataFrame()
+
def _make_patch_mask(roi):
if expanded:
patch = np.zeros((roi.ebb_h, roi.ebb_w, 1, 1), dtype='uint8')
@@ -877,7 +883,9 @@ class RoiSet(object):
dfe['patch_mask'] = dfe.apply(_make_patch_mask, axis=1)
return dfe
- def get_patch_masks_acc(self, **kwargs) -> PatchStack:
+ def get_patch_masks_acc(self, **kwargs) -> Union[PatchStack, None]:
+ if self.count == 0:
+ return None
se_pm = self.get_patch_masks(**kwargs).patch_mask
se_ext = se_pm.apply(lambda x: np.expand_dims(x, 2))
return PatchStack(list(se_ext))
@@ -896,6 +904,9 @@ class RoiSet(object):
**kwargs
) -> pd.Series:
+ if self.count == 0:
+ return pd.Series()
+
# arrange RGB channels if so specified, otherwise copy roiset.raw_acc data
raw = self.acc_raw
if isinstance(rgb_overlay_channels, (list, tuple)) and isinstance(rgb_overlay_weights, (list, tuple)):
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index c134aa9d..943fd6a9 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -871,8 +871,12 @@ class TestEmptyRoiSet(unittest.TestCase):
def test_classify_by(self):
roiset = self.empty_roiset
- res = roiset.classify_by('permissive_model', [0], IntensityThresholdInstanceMaskSegmentationModel(tr=0.0))
- self.assertEqual(1, 0)
+ self.assertFalse('classify_by_permissive_model' in roiset.get_df().columns)
+ self.assertTrue(
+ roiset.classify_by('permissive_model', [0], IntensityThresholdInstanceMaskSegmentationModel(tr=0.0))
+ )
+ self.assertEqual(roiset.count, 0)
+ self.assertTrue('classify_by_permissive_model' in roiset.get_df().columns)
class TestRoiSetObjectDetection(unittest.TestCase):
--
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