From c3e3ff61c697b32900577420a7008111d3148eb0 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 20 Dec 2023 15:30:53 +0100
Subject: [PATCH] Test covers instance segmentation base class
---
model_server/models.py | 23 +++++++++++++++++++++--
tests/test_model.py | 29 ++++++++++++++++++-----------
2 files changed, 39 insertions(+), 13 deletions(-)
diff --git a/model_server/models.py b/model_server/models.py
index f0864147..06bef01c 100644
--- a/model_server/models.py
+++ b/model_server/models.py
@@ -90,8 +90,7 @@ class InstanceSegmentationModel(ImageToImageModel):
raise InvalidInputImageError('Expect input image and mask to be the same shape')
-
-class DummySegmentationModel(SemanticSegmentationModel):
+class DummySemanticSegmentationModel(SemanticSegmentationModel):
model_id = 'dummy_make_white_square'
@@ -111,6 +110,26 @@ class DummySegmentationModel(SemanticSegmentationModel):
mask, _ = self.infer(img)
return mask
+class DummyInstanceSegmentationModel(InstanceSegmentationModel):
+
+ model_id = 'dummy_pass_input_mask'
+
+ def load(self):
+ return True
+
+ def infer(
+ self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor
+ ) -> (GenericImageDataAccessor, dict):
+ return mask
+
+ def label_instance_class(
+ self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor, **kwargs
+ ) -> GenericImageDataAccessor:
+ """
+ Returns a trivial segmentation, i.e. the input mask
+ """
+ super(DummyInstanceSegmentationModel, self).label_instance_class(img, mask, **kwargs)
+ return self.infer(img, mask)
class Error(Exception):
pass
diff --git a/tests/test_model.py b/tests/test_model.py
index 0d5f98ae..8730c666 100644
--- a/tests/test_model.py
+++ b/tests/test_model.py
@@ -1,49 +1,56 @@
import unittest
from conf.testing import czifile
from model_server.accessors import CziImageFileAccessor
-from model_server.models import DummySegmentationModel, CouldNotLoadModelError
+from model_server.models import DummySemanticSegmentationModel, DummyInstanceSegmentationModel, CouldNotLoadModelError
class TestCziImageFileAccess(unittest.TestCase):
def setUp(self) -> None:
self.cf = CziImageFileAccessor(czifile['path'])
def test_instantiate_model(self):
- model = DummySegmentationModel(params=None)
+ model = DummySemanticSegmentationModel(params=None)
self.assertTrue(model.loaded)
def test_instantiate_model_with_nondefault_kwarg(self):
- model = DummySegmentationModel(autoload=False)
+ model = DummySemanticSegmentationModel(autoload=False)
self.assertFalse(model.autoload, 'Could not override autoload flag in subclass of Model.')
def test_raise_error_if_cannot_load_model(self):
- class UnloadableDummyImageToImageModel(DummySegmentationModel):
+ class UnloadableDummyImageToImageModel(DummySemanticSegmentationModel):
def load(self):
return False
with self.assertRaises(CouldNotLoadModelError):
mi = UnloadableDummyImageToImageModel()
- def test_czifile_is_correct_shape(self):
- model = DummySegmentationModel()
- img, _ = model.infer(self.cf)
+ def test_dummy_pixel_segmentation(self):
+ model = DummySemanticSegmentationModel()
+ img = self.cf.get_one_channel_data(0)
+ mask = model.label_pixel_class(img)
w = czifile['w']
h = czifile['h']
self.assertEqual(
- img.shape,
+ mask.shape,
(h, w, 1, 1),
'Inferred image is not the expected shape'
)
self.assertEqual(
- img.data[int(w/2), int(h/2)],
+ mask.data[int(w/2), int(h/2)],
255,
'Middle pixel is not white as expected'
)
self.assertEqual(
- img.data[0, 0],
+ mask.data[0, 0],
0,
'First pixel is not black as expected'
- )
\ No newline at end of file
+ )
+ return img, mask
+
+ def test_dummy_instance_segmentation(self):
+ img, mask = self.test_dummy_pixel_segmentation()
+ model = DummyInstanceSegmentationModel()
+ obmap = model.label_instance_class(img, mask)
--
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