From 97d6b156174ae2e48682987843a3c1d2078c55ae Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 20 Sep 2024 09:56:06 +0200
Subject: [PATCH] Preparing to make binary mask optional in case of object
detection result
---
model_server/base/roiset.py | 36 ++++++++++++++++++++++++------------
tests/base/test_roiset.py | 16 ++++++++++------
2 files changed, 34 insertions(+), 18 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index f529da22..f624460f 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -216,12 +216,13 @@ def make_df_from_object_ids(acc_raw, acc_obj_ids, expand_box_by) -> pd.DataFrame
:param acc_raw: accessor to raw image data
:param acc_obj_ids: accessor to map of object IDs
:param expand_box_by: number of pixels to expand bounding box in all directions (without exceeding image boundary)
- # :param deproject: assign object's z-position based on argmax of raw data if True
+
:return: pd.DataFrame
"""
# build dataframe of objects, assign z index to each object
# TODO: don't assume that channel 0 is the basis of z-argmax
+ # TODO: :param deproject: assign object's z-position based on argmax of raw data if True
if acc_obj_ids.nz == 1: # deproject objects' z-coordinates from argmax of raw image
df = pd.DataFrame(regionprops_table(
acc_obj_ids.data_xy,
@@ -246,6 +247,7 @@ def make_df_from_object_ids(acc_raw, acc_obj_ids, expand_box_by) -> pd.DataFrame
cropped = acc.get_mono(0, mip=True).crop_hw((r.y0, r.x0, (r.y1 - r.y0), (r.x1 - r.x0))).data_xy
return cropped
+
df['binary_mask'] = df.apply(
_make_binary_mask,
axis=1,
@@ -314,6 +316,7 @@ def safe_add(a, g, b):
).astype(a.dtype)
def make_object_ids_from_df(df: pd.DataFrame, sd: dict) -> InMemoryDataAccessor:
+ # TODO: generate rectangular masks if running without segmentation
id_mask = np.zeros((sd['Y'], sd['X'], 1, sd['Z']), dtype='uint16')
if 'binary_mask' not in df.columns:
raise MissingSegmentationError('RoiSet dataframe does not contain segmentation')
@@ -405,17 +408,20 @@ class RoiSet(object):
params.get('expand_box_by', 0)
)
- def _make_binary_mask(r):
- # TODO: make square mask array
- # acc = InMemoryDataAccessor(acc_obj_ids.data == r.label)
- # cropped = acc.get_mono(0, mip=True).crop_hw((r.y0, r.x0, (r.y1 - r.y0), (r.x1 - r.x0))).data_xy
- return cropped
-
- df['binary_mask'] = df.apply(
- _make_binary_mask,
- axis=1,
- result_type='reduce',
- )
+ # TODO: don't even make binary_mask column in obj det case
+
+ # def _make_binary_mask(r):
+ # # acc = InMemoryDataAccessor(acc_obj_ids.data == r.label)
+ # # cropped = acc.get_mono(0, mip=True).crop_hw((r.y0, r.x0, (r.y1 - r.y0), (r.x1 - r.x0))).data_xy
+ # return cropped
+ #
+ #
+ #
+ # df['binary_mask'] = df.apply(
+ # _make_binary_mask,
+ # axis=1,
+ # result_type='reduce',
+ # )
return RoiSet(acc_raw, df, params)
@@ -639,7 +645,10 @@ class RoiSet(object):
return InMemoryDataAccessor(om)
def export_dataframe(self, csv_path: Path) -> str:
+ # TODO: move this inside of .serialize()
csv_path.parent.mkdir(parents=True, exist_ok=True)
+
+ # TODO: suppress errors or check if binary_mask doesn't exist
self._df.drop(['expanded_slice', 'slice', 'relative_slice', 'binary_mask'], axis=1).to_csv(csv_path, index=False)
return csv_path.name
@@ -961,6 +970,9 @@ class RoiSet(object):
return self._df.apply(_poly_from_mask, axis=1)
+ @property
+ def contains_segmentation(self):
+ return 'binary_mask' in self._df.columns
@property
def acc_obj_ids(self):
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index 6794dac2..afc75f35 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -623,6 +623,9 @@ class TestRoiSetSerialization(unittest.TestCase):
t_acc = generate_file_accessor(pt)
self.assertTrue(np.all(r_acc.data == t_acc.data))
+ self.assertTrue(ref_roiset.contains_segmentation)
+ self.assertTrue(ref_roiset.contains_segmentation)
+
def test_create_roiset_from_bounding_boxes(self):
from skimage.measure import label, regionprops, regionprops_table
@@ -640,15 +643,16 @@ class TestRoiSetSerialization(unittest.TestCase):
table['h'] = table['y1'] - table['y0']
- # bbox =
- self.assertTrue(False)
- # RoiSet.from_bounding_boxes(
- # self.stack_ch_pa,
- #
- # )
+ roiset = RoiSet.from_bounding_boxes(
+ self.stack_ch_pa,
+
+ )
# test segments reside in bounding boxes
+ self.assertFalse(roiset.contains_segmentation)
+ self.assertTrue(False)
+
class TestRoiSetPolygons(BaseTestRoiSetMonoProducts, unittest.TestCase):
def test_compute_polygons(self):
--
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