diff --git a/extensions/chaeo/params.py b/extensions/chaeo/params.py index 0ba956fba3446c84955c1ac829c2dc3561a9ff29..a1f6aa8c8304f4616442582a1a8cf696cd36449d 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 7778370add1a2421480cfa9f5c460d6e1f63a5d7..1779286bec10887b91ef1d174ce34ba29a6dbb07 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 1441e9ae278a845616e3d68b34677a8f83a71e72..053f1d442e250aff7ca88dadbbce5cb3351965cf 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}'