From 426b5b79d7309ac763298344c8c87630e71aca7a Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 3 May 2024 16:21:58 +0200
Subject: [PATCH] Added static constructor for making RoiSets from segmentation
masks
---
model_server/base/roiset.py | 19 +++++++++++++++++++
tests/test_roiset.py | 21 ++++++++-------------
2 files changed, 27 insertions(+), 13 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index f3c0c947..d289284f 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -152,6 +152,25 @@ class RoiSet(object):
"""Expose ROI meta information via the Pandas.DataFrame API"""
return self._df.itertuples(name='Roi')
+ @staticmethod
+ def from_segmentation(
+ acc_raw: GenericImageDataAccessor,
+ acc_seg: GenericImageDataAccessor,
+ allow_3d=False,
+ connect_3d=True,
+ params: RoiSetMetaParams = RoiSetMetaParams()
+ ):
+ """
+ Create a RoiSet from a binary segmentation mask (either 2D or 3D)
+ :param acc_raw: accessor to a generally a multichannel z-stack
+ :param acc_seg: accessor of a binary segmentation mask (mono) of either two or three dimensions
+ :param allow_3d: return a 3D map if True; return a 2D map of the mask's maximum intensity project if False
+ :param connect_3d: objects can span multiple z-positions if True; objects are unique to a single z if False
+ :param params: optional arguments that influence the definition and representation of ROIs
+ :return: object identities map
+ """
+ return RoiSet(acc_raw, _get_label_ids(acc_seg, allow_3d=allow_3d, connect_3d=connect_3d), params)
+
@staticmethod
def make_df(acc_raw, acc_obj_ids, expand_box_by) -> pd.DataFrame:
"""
diff --git a/tests/test_roiset.py b/tests/test_roiset.py
index 47856888..c1d773c6 100644
--- a/tests/test_roiset.py
+++ b/tests/test_roiset.py
@@ -10,7 +10,7 @@ import pandas as pd
from model_server.conf.testing import output_path, roiset_test_data
from model_server.base.roiset import RoiSetExportParams, RoiSetMetaParams
-from model_server.base.roiset import _get_label_ids, RoiSet
+from model_server.base.roiset import RoiSet
from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file, PatchStack
from model_server.base.models import DummyInstanceSegmentationModel
@@ -26,10 +26,9 @@ class BaseTestRoiSetMonoProducts(object):
class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
def _make_roi_set(self, mask_type='boxes', **kwargs):
- id_map = _get_label_ids(self.seg_mask)
- roiset = RoiSet(
+ roiset = RoiSet.from_segmentation(
self.stack_ch_pa,
- id_map,
+ self.seg_mask,
params=RoiSetMetaParams(
mask_type=mask_type,
filters=kwargs.get('filters', {'area': {'min': 1e3, 'max': 1e4}}),
@@ -67,9 +66,8 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
def test_roiset_from_non_zstacks(self, **kwargs):
acc_zstack_slice = InMemoryDataAccessor(self.stack_ch_pa.data[:, :, :, 0])
self.assertEqual(acc_zstack_slice.nz, 1)
- id_map = _get_label_ids(self.seg_mask)
- roiset = RoiSet(acc_zstack_slice, id_map, params=RoiSetMetaParams(mask_type='boxes'))
+ roiset = RoiSet.from_segmentation(acc_zstack_slice, self.seg_mask, params=RoiSetMetaParams(mask_type='boxes'))
zmask = roiset.get_zmask()
zmask_acc = InMemoryDataAccessor(zmask)
@@ -158,9 +156,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
self.assertEqual(result.shape, roiset.acc_raw.shape)
def test_flatten_image(self):
- id_map = _get_label_ids(self.seg_mask)
-
- roiset = RoiSet(self.stack_ch_pa, id_map, params=RoiSetMetaParams(mask_type='boxes'))
+ roiset = RoiSet.from_segmentation(self.stack_ch_pa, self.seg_mask, params=RoiSetMetaParams(mask_type='boxes'))
df = roiset.get_df()
from model_server.base.roiset import project_stack_from_focal_points
@@ -270,10 +266,9 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
def setUp(self) -> None:
super().setUp()
- id_map = _get_label_ids(self.seg_mask)
- self.roiset = RoiSet(
+ self.roiset = RoiSet.from_segmentation(
self.stack,
- id_map,
+ self.seg_mask,
params=RoiSetMetaParams(
expand_box_by=(128, 2),
mask_type='boxes',
@@ -492,7 +487,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
print('res')
-
+from model_server.base.roiset import _get_label_ids
class TestRoiSetSerialization(unittest.TestCase):
def setUp(self) -> None:
--
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