From ef3363b7251e5658878aad67118fa491672d48e3 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 2 Feb 2024 15:19:52 +0100
Subject: [PATCH] Some test coverage, those that are failing are because of
issues propagating nested parameters to pydantic models
---
model_server/extensions/chaeo/params.py | 2 +-
model_server/extensions/chaeo/tests/test_zstack.py | 9 ++++-----
model_server/extensions/chaeo/zmask.py | 13 +++++++------
3 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/model_server/extensions/chaeo/params.py b/model_server/extensions/chaeo/params.py
index e9fc2461..9146d435 100644
--- a/model_server/extensions/chaeo/params.py
+++ b/model_server/extensions/chaeo/params.py
@@ -28,7 +28,7 @@ class RoiFilter(BaseModel):
class RoiSetMetaParams(BaseModel):
mask_type: str = 'boxes'
- filters: RoiFilter = {}
+ filters: Union[RoiFilter, None] = None
expand_box_by: List[int] = [128, 0]
diff --git a/model_server/extensions/chaeo/tests/test_zstack.py b/model_server/extensions/chaeo/tests/test_zstack.py
index cc4c0eb0..0287c68b 100644
--- a/model_server/extensions/chaeo/tests/test_zstack.py
+++ b/model_server/extensions/chaeo/tests/test_zstack.py
@@ -5,7 +5,7 @@ import numpy as np
from model_server.conf.testing import output_path
from model_server.extensions.chaeo.conf.testing import multichannel_zstack, pixel_classifier, pipeline_params
-from extensions.chaeo import RoiSetExportParams, RoiSetMetaParams
+from extensions.chaeo.params import RoiSetExportParams, RoiSetMetaParams
from model_server.extensions.chaeo.products import export_patches_from_zstack, export_multichannel_patches_from_zstack, export_patch_masks_from_zstack
from model_server.extensions.chaeo.workflows import infer_object_map_from_zstack
from model_server.extensions.chaeo.zmask import build_zmask_from_object_mask
@@ -42,8 +42,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
zmask, meta, df, interm = build_zmask_from_object_mask(
self.seg_mask,
self.stack_ch_pa,
- mask_type=mask_type,
- **kwargs,
+ params=RoiSetMetaParams(mask_type=mask_type, **kwargs),
)
zmask_acc = InMemoryDataAccessor(zmask)
self.assertTrue(zmask_acc.is_mask())
@@ -75,7 +74,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
zmask, meta, df, interm = build_zmask_from_object_mask(
self.seg_mask,
acc_zstack_slice,
- mask_type='boxes',
+ params=RoiSetMetaParams(mask_type='boxes'),
**kwargs,
)
zmask_acc = InMemoryDataAccessor(zmask)
@@ -119,7 +118,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
zmask, meta, df, interm = build_zmask_from_object_mask(
self.seg_mask,
self.stack_ch_pa,
- mask_type='boxes',
+ params=RoiSetMetaParams(mask_type='boxes')
)
from model_server.extensions.chaeo.zmask import project_stack_from_focal_points
diff --git a/model_server/extensions/chaeo/zmask.py b/model_server/extensions/chaeo/zmask.py
index 30ecabe8..380f7b7d 100644
--- a/model_server/extensions/chaeo/zmask.py
+++ b/model_server/extensions/chaeo/zmask.py
@@ -9,7 +9,7 @@ from sklearn.linear_model import LinearRegression
from model_server.extensions.chaeo.annotators import draw_boxes_on_3d_image
from model_server.extensions.chaeo.products import export_patches_from_zstack, export_multichannel_patches_from_zstack, export_patch_masks_from_zstack, get_patches_from_zmask_meta, get_patch_masks_from_zmask_meta
-from extensions.chaeo import RoiSetMetaParams, RoiSetExportParams
+from extensions.chaeo.params import RoiSetMetaParams, RoiSetExportParams
from model_server.extensions.chaeo.process import mask_largest_object
from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.base.models import InstanceSegmentationModel
@@ -130,16 +130,17 @@ class RoiSet(object):
def build_zmask_from_object_mask(
obmask: GenericImageDataAccessor,
zstack: GenericImageDataAccessor,
- params: RoiSetMetaParams,
+ params: RoiSetMetaParams = RoiSetMetaParams(),
):
"""
Given a 2D mask of objects, build a 3D mask, where each object's z-position is determined by the index of
maximum intensity in z. Return this zmask and a list of each object's meta information.
- :param obmask: GenericImageDataAccessor monochrome 2D inary mask of objects
+ :param obmask: GenericImageDataAccessor monochrome 2D binary mask of objects
:param zstack: GenericImageDataAccessor monochrome zstack of same Y, X dimension as obmask
- :param filters: dictionary of form {attribute: (min, max)}; valid attributes are 'area' and 'solidity'
- :param mask_type: if 'boxes', zmask is True in each object's complete bounding box; otherwise 'contours'
- :param expand_box_by: (xy, z) expands bounding box by (xy, z) pixels except where this hits a boundary
+ :param params: RoiSetMetaParams
+ filters: dictionary of form {attribute: (min, max)}; valid attributes are 'area' and 'solidity'
+ mask_type: if 'boxes', zmask is True in each object's complete bounding box; otherwise 'contours'
+ expand_box_by: (xy, z) expands bounding box by (xy, z) pixels except where this hits a boundary
:return: tuple (zmask, meta)
np.ndarray:
boolean mask of same size as stack
--
GitLab