From a1b567857586b2f2c9ccbc98b97a54709c1cef91 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 23 Sep 2024 09:27:54 +0200
Subject: [PATCH] No errors but seg method comes up with fewer ROIs than bbox
---
model_server/base/accessors.py | 5 +++++
model_server/base/roiset.py | 2 --
tests/base/test_roiset.py | 17 +++++++++--------
3 files changed, 14 insertions(+), 10 deletions(-)
diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index 64a9d683..a9366156 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -440,6 +440,11 @@ class PatchStack(InMemoryDataAccessor):
else:
tifffile.imwrite(fpath, tzcyx, imagej=True)
+ def write(self, fp: Path, mkdir=True):
+ if mkdir:
+ fp.parent.mkdir(parents=True, exist_ok=True)
+ self.export_pyxcz(fp)
+
@property
def shape_dict(self):
return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index c558c549..7a95a947 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -398,8 +398,6 @@ class RoiSet(object):
return RoiSet(acc_raw, df, params)
-
- # TODO: add a generator for the object detection case
@staticmethod
def from_bounding_boxes(
acc_raw: GenericImageDataAccessor,
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index 585ded21..87a1d889 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -640,8 +640,8 @@ class TestRoiSetObjectDetection(unittest.TestCase):
from skimage.measure import label, regionprops, regionprops_table
- mask = self.seg_mask_3d.data_xyz
- labels = label(mask)
+ mask = self.seg_mask_3d
+ labels = label(mask.data_xyz, connectivity=3)
table = pd.DataFrame(
regionprops_table(labels)
).rename(
@@ -654,16 +654,17 @@ class TestRoiSetObjectDetection(unittest.TestCase):
bboxes = table[['y', 'x', 'h', 'w']].to_dict(orient='records')
- roiset = RoiSet.from_bounding_boxes(
- self.stack_ch_pa,
- bboxes,
+ roiset_bbox = RoiSet.from_bounding_boxes(self.stack_ch_pa, bboxes)
- )
+ patches_bbox = roiset_bbox.get_patches_acc()
+ self.assertEqual(len(table), patches_bbox.count)
- patches = roiset.get_patches_acc()
- self.assertEqual(len(table), patches.count)
+ # roiset w/ seg for comparison
+ roiset_seg = RoiSet.from_binary_mask(self.stack_ch_pa, mask)
+ patches_seg = roiset_seg.get_patches_acc()
# TODO: test segments reside in bounding boxes
+ self.assertEqual(roiset_seg.count, roiset_bbox.count)
self.assertTrue(False)
class TestRoiSetPolygons(BaseTestRoiSetMonoProducts, unittest.TestCase):
--
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