From 46366c5f909dc045d604c7a9bea3e24c670591fa Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 5 Apr 2024 14:17:36 +0200
Subject: [PATCH] Corrected error with overlapping bounding boxes, whereby a
second box would overwrite a first; instead, masks are now just additive;
also catch case when trying to draw contours from a mask that is a single
pixel across
---
model_server/base/process.py | 13 ++++++++++++-
model_server/base/roiset.py | 11 ++++-------
tests/test_process.py | 28 ++++++++++++++++++++++++++--
3 files changed, 42 insertions(+), 10 deletions(-)
diff --git a/model_server/base/process.py b/model_server/base/process.py
index 992c9fb9..94c6cf62 100644
--- a/model_server/base/process.py
+++ b/model_server/base/process.py
@@ -6,7 +6,7 @@ from math import ceil, floor
import numpy as np
import skimage
from skimage.exposure import rescale_intensity
-
+from skimage.measure import find_contours
def is_mask(img):
"""
@@ -117,6 +117,17 @@ def mask_largest_object(
else:
return img
+def get_safe_contours(mask):
+ """
+ Return a list of contour coordinates even if a mask is only one pixel across
+ """
+ if mask.shape[0] == 1 or mask.shape[1] == 1:
+ c0 = mask.shape[0] - 1
+ c1 = mask.shape[1] - 1
+ return [np.array([(0, 0), (c0, c1)])]
+ else:
+ return find_contours(mask)
+
class Error(Exception):
pass
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index bbe3a5f8..f87bb8c8 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -16,7 +16,7 @@ from sklearn.linear_model import LinearRegression
from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.base.models import InstanceSegmentationModel
-from model_server.base.process import pad, rescale, resample_to_8bit, make_rgb
+from model_server.base.process import get_safe_contours, pad, rescale, resample_to_8bit, make_rgb
from model_server.base.annotators import draw_box_on_patch, draw_contours_on_patch, draw_boxes_on_3d_image
from model_server.base.accessors import generate_file_accessor, PatchStack
from model_server.base.process import mask_largest_object
@@ -501,20 +501,17 @@ class RoiSet(object):
if kwargs.get('draw_mask'):
mci = kwargs.get('mask_channel', 0)
- # mask = np.zeros(patch.shape[0:2], dtype=bool)
- # mask[roi.relative_slice[0:2]] = roi.binary_mask
for zi in range(0, patch.shape[3]):
patch[:, :, mci, zi] = np.invert(mask) * patch[:, :, mci, zi]
if kwargs.get('draw_contour'):
mci = kwargs.get('contour_channel', 0)
- # mask = np.zeros(patch.shape[0:2], dtype=bool)
- # mask[roi.relative_slice[0:2]] = roi.binary_mask
for zi in range(0, patch.shape[3]):
+ contours = get_safe_contours(mask)
patch[:, :, mci, zi] = draw_contours_on_patch(
patch[:, :, mci, zi],
- find_contours(mask)
+ contours
)
if pad_to and expanded:
@@ -610,7 +607,7 @@ class RoiSet(object):
try:
ma_acc = generate_file_accessor(where / 'tight_patch_masks' / fname)
bool_mask = ma_acc.data / np.iinfo(ma_acc.data.dtype).max
- id_mask[sl] = r.label * bool_mask
+ id_mask[sl] = id_mask[sl] + r.label * bool_mask
except Exception as e:
raise DeserializeRoiSet(e)
diff --git a/tests/test_process.py b/tests/test_process.py
index 569ac1b7..d2fb33b9 100644
--- a/tests/test_process.py
+++ b/tests/test_process.py
@@ -1,9 +1,10 @@
import unittest
import numpy as np
+from skimage.measure import find_contours
-from model_server.base.process import mask_largest_object
-from model_server.base.process import pad
+from model_server.base.annotators import draw_contours_on_patch
+from model_server.base.process import get_safe_contours, mask_largest_object, pad
class TestProcessingUtilityMethods(unittest.TestCase):
def setUp(self) -> None:
@@ -56,3 +57,26 @@ class TestMaskLargestObject(unittest.TestCase):
self.assertTrue(np.all(np.unique(masked) == [0, 255]))
self.assertTrue(np.all(masked[:, 3:5] == 0))
self.assertTrue(np.all(masked[3:5, :] == 0))
+
+
+class TestSafeContours(unittest.TestCase):
+ def setUp(self) -> None:
+ self.patch = np.ones((10, 20), dtype='uint8')
+ self.mask_ref = np.zeros((10, 20), dtype=bool)
+ self.mask_ref[0:5, 0:10] = True
+ self.mask_test = np.ones((1, 20), dtype=bool)
+
+ def test_contours_on_compliant_mask(self):
+ con = get_safe_contours(self.mask_ref)
+ patch = self.patch.copy()
+ self.assertEqual((patch == 0).sum(), 0)
+ patch = draw_contours_on_patch(patch, con)
+ self.assertEqual((patch == 0).sum(), 14)
+
+ def test_contours_on_noncompliant_mask(self):
+ con = get_safe_contours(self.mask_test)
+ patch = self.patch.copy()
+ self.assertEqual((patch == 0).sum(), 0)
+ patch = draw_contours_on_patch(self.patch, con)
+ self.assertEqual((patch == 0).sum(), 20)
+ self.assertEqual((patch[0, :] == 0).sum(), 20)
\ No newline at end of file
--
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