From 644b4e69bda963709abc25b0bdbe7827b6791f75 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 30 Oct 2024 12:14:35 +0100
Subject: [PATCH] Threshold object classifier using PatchStacks passes tests
---
model_server/base/roiset.py | 33 ++++++++++++++++++++-------------
tests/base/test_accessors.py | 1 +
2 files changed, 21 insertions(+), 13 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 23532707..27e32944 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -1190,19 +1190,26 @@ class IntensityThresholdInstanceMaskSegmentationModel(InstanceMaskSegmentationMo
allow_3d: bool = False,
connect_3d: bool = True,
) -> GenericImageDataAccessor:
- labels = get_label_ids(mask)
- df = pd.DataFrame(regionprops_table(
- labels.data_yxz,
- intensity_image=img.get_mono(self.channel).data_yxz,
- properties=('label', 'area', 'intensity_mean', 'bbox')
- ))
- df['intensity_mean'] > self.tr
-
- om = np.zeros(labels.shape, labels.dtype)
- def _label_object_class(la):
- om[labels.data == la] = 1
- df.loc[df['intensity_mean'] > (self.tr * img.dtype_max), 'label'].apply(_label_object_class)
- return InMemoryDataAccessor(om)
+ if isinstance(img, PatchStack): # assume one object per patch
+ df = img.get_object_df(mask)
+ om = np.zeros(mask.shape, 'uint16')
+ def _label_patch_class(la):
+ om[la] = (mask.iat(la).data > 0) * 1
+ df.loc[df['intensity_mean'] > (self.tr * img.dtype_max), 'label'].apply(_label_patch_class)
+ return PatchStack(om)
+ else:
+ labels = get_label_ids(mask)
+ df = pd.DataFrame(regionprops_table(
+ labels.data_yxz,
+ intensity_image=img.get_mono(self.channel).data_yxz,
+ properties=('label', 'area', 'intensity_mean')
+ ))
+
+ om = np.zeros(labels.shape, labels.dtype)
+ def _label_object_class(la):
+ om[labels.data == la] = 1
+ df.loc[df['intensity_mean'] > (self.tr * img.dtype_max), 'label'].apply(_label_object_class)
+ return InMemoryDataAccessor(om)
def label_instance_class(
self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor, **kwargs
diff --git a/tests/base/test_accessors.py b/tests/base/test_accessors.py
index 05663dd7..2c5c052b 100644
--- a/tests/base/test_accessors.py
+++ b/tests/base/test_accessors.py
@@ -302,6 +302,7 @@ class TestPatchStackAccessor(unittest.TestCase):
self.assertEqual(acc.hw, (h, w))
self.assertEqual(acc.get_mono(channel=0).data_yxz.shape, (n, h, w, nz))
self.assertEqual(acc.get_mono(channel=0, mip=True).data_yx.shape, (n, h, w))
+ return acc
def test_object_df(self):
w = 30
--
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