From 34a01200831d9622bfa101c2a60520a2c45fbbec Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 21 Dec 2023 15:03:23 +0100
Subject: [PATCH] Filters propagate from parameters dict
---
extensions/chaeo/params.py | 2 +-
extensions/chaeo/tests/test_zstack.py | 6 +++++-
extensions/chaeo/zmask.py | 5 +++--
3 files changed, 9 insertions(+), 4 deletions(-)
diff --git a/extensions/chaeo/params.py b/extensions/chaeo/params.py
index 0ba956fb..a1f6aa8c 100644
--- a/extensions/chaeo/params.py
+++ b/extensions/chaeo/params.py
@@ -28,7 +28,7 @@ class RoiFilter(BaseModel):
class RoiSetMetaParams(BaseModel):
mask_type: str = 'boxes'
- filters: RoiFilter = None
+ filters: RoiFilter = {}
expand_box_by: List[int] = [128, 0]
diff --git a/extensions/chaeo/tests/test_zstack.py b/extensions/chaeo/tests/test_zstack.py
index 7778370a..1779286b 100644
--- a/extensions/chaeo/tests/test_zstack.py
+++ b/extensions/chaeo/tests/test_zstack.py
@@ -211,7 +211,9 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
roi_params = RoiSetMetaParams(**{
'mask_type': 'boxes',
- 'filters': {},
+ 'filters': {
+ 'area': {'min': 1e3, 'max': 1e8}
+ },
'expand_box_by': [128, 2]
})
@@ -232,6 +234,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
'annotated_zstacks': {},
'object_classes': True
})
+
infer_object_map_from_zstack(
multichannel_zstack['path'],
output_path / 'roiset' / 'workflow',
@@ -241,5 +244,6 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
segmentation_channel=pp['segmentation_channel'],
patches_channel=pp['patches_channel'],
export_params=export_params,
+ roi_params=roi_params,
)
diff --git a/extensions/chaeo/zmask.py b/extensions/chaeo/zmask.py
index 1441e9ae..053f1d44 100644
--- a/extensions/chaeo/zmask.py
+++ b/extensions/chaeo/zmask.py
@@ -174,9 +174,10 @@ def build_zmask_from_object_mask(
lamap = label(obmask.data[:, :, 0, 0]).astype('uint16')
query_str = 'label > 0' # always true
if filters is not None:
- for k in filters.keys():
+ for k, val in filters.dict(exclude_unset=True).items():
assert k in ('area', 'solidity')
- vmin, vmax = filters[k]
+ vmin = val['min']
+ vmax = val['max']
assert vmin >= 0
query_str = query_str + f' & {k} > {vmin} & {k} < {vmax}'
--
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