Skip to content

Commit

Permalink
Remove downsample tests
Browse files Browse the repository at this point in the history
  • Loading branch information
@alanocallaghan
alanocallaghan committed Nov 4, 2024
1 parent 2bc2027 commit 978d841
Show file tree
Hide file tree
Showing 2 changed files with 108 additions and 10 deletions.
4 changes: 2 additions & 2 deletions qubalab/images/labeled_server.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ def _read_block(self, level: int, region: Region2D) -> np.ndarray:
draw_geometry(
image.size,
drawing_context,
self._geometries[i],
shapely.affinity.translate(self._geometries[i], -region.x, -region.y),
1
)
full_image[label, :, :] = np.asarray(image, dtype=self.metadata.dtype)
Expand All @@ -119,7 +119,7 @@ def _read_block(self, level: int, region: Region2D) -> np.ndarray:
draw_geometry(
image.size,
drawing_context,
self._geometries[i],
shapely.affinity.translate(self._geometries[i], -region.x, -region.y),
self._feature_index_to_label[i]
)
return np.expand_dims(np.asarray(image, dtype=self.metadata.dtype), axis=0)
114 changes: 106 additions & 8 deletions tests/images/test_labeled_server.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
large_metadata = ImageMetadata(
"/path/to/img.tiff",
"Image name",
(ImageShape(1000, 500),),
(ImageShape(500, 250),),
PixelCalibration(
PixelLength.create_microns(2.5),
PixelLength.create_microns(2.5)
Expand Down Expand Up @@ -397,21 +397,119 @@ def test_read_polygon_in_single_channel_image_without_label_map_with_downsample(

def test_label_can_hold_many_values():
downsample = 1
max_objects = 500
random.seed(42)
max_objects = 1000
random.seed(1)
def rands():
x = random.randint(0, int(large_metadata.shape.x / downsample))
y = random.randint(0, int(large_metadata.shape.x / downsample))
return (
random.randint(0, int(sample_metadata.shape.x / downsample)),
random.randint(0, int(sample_metadata.shape.y / downsample))
(x, y),
(x + 1, y),
(x + 1, y + 1),
(x, y + 1)
)

coords = [(rands(), rands(), rands(), rands()) for i in range(max_objects)]
coords = list(set(coords))
coords = [rands() for i in range(max_objects)]

n_objects = len(coords)
features = [ImageFeature(geojson.Polygon([coords[i]]), Classification("Some classification")) for i in range(n_objects)]
labeled_server = LabeledImageServer(large_metadata, features, multichannel=False, downsample=downsample)

image = labeled_server.read_region(1, Region2D(0, 0, labeled_server.metadata.width, labeled_server.metadata.height))

assert np.max(image) > 255
assert np.max(image) == max_objects


def test_single_channel_labeled_image_with_region_request():
downsample = 1
features = [ImageFeature(geojson.LineString([(7, 5), (9, 5)]))]
expected_image = np.array(
[[[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 1, 1, 1]]]
)
labeled_server = LabeledImageServer(sample_metadata, features, multichannel=False, downsample=downsample)
region = Region2D(5, 3, labeled_server.metadata.width-5, labeled_server.metadata.height-3)
image = labeled_server.read_region(1, region)

np.testing.assert_array_equal(image, expected_image)

def test_single_channel_labeled_image_with_starting_downsample():
features = [ImageFeature(geojson.LineString([(6, 5), (9, 5)]))]
expected_image = np.array(
[[[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 1, 1]]]
)
labeled_server = LabeledImageServer(sample_metadata, features, multichannel=False, downsample=1)
downsample = 2
region = Region2D(0, 0, labeled_server.metadata.width, labeled_server.metadata.height)
image = labeled_server.read_region(downsample, region)

np.testing.assert_array_equal(image, expected_image)


def test_single_channel_labeled_image_with_request_downsample():
features = [ImageFeature(geojson.LineString([(6, 5), (9, 5)]))]
expected_image = np.array(
[[[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 1, 1]]]
)
downsample = 2
labeled_server = LabeledImageServer(sample_metadata, features, multichannel=False, downsample=downsample)
region = Region2D(0, 0, labeled_server.metadata.width, labeled_server.metadata.height)
image = labeled_server.read_region(1, region)

np.testing.assert_array_equal(image, expected_image)


def test_multi_channel_labeled_image_with_region_request():
downsample = 1
features = [ImageFeature(geojson.LineString([(7, 5), (9, 5)]))]
expected_image = np.array(
[[[False, False, False, False, False],
[False, False, False, False, False],
[False, False, False, False, False]],
[[False, False, False, False, False],
[False, False, False, False, False],
[False, False, True, True, True]]]
)
labeled_server = LabeledImageServer(sample_metadata, features, multichannel=True, downsample=downsample)
region = Region2D(5, 3, labeled_server.metadata.width-5, labeled_server.metadata.height-3)
image = labeled_server.read_region(1, region)
np.testing.assert_array_equal(image, expected_image)

def test_multi_channel_labeled_image_with_starting_downsample():
features = [ImageFeature(geojson.LineString([(6, 5), (9, 5)]))]
expected_image = np.array(
[[[False, False, False, False, False],
[False, False, False, False, False],
[False, False, False, False, False]],
[[False, False, False, False, False],
[False, False, False, False, False],
[False, False, False, True, True]]]
)
downsample = 2
labeled_server = LabeledImageServer(sample_metadata, features, multichannel=True, downsample=downsample)
region = Region2D(0, 0, labeled_server.metadata.width, labeled_server.metadata.height)
image = labeled_server.read_region(1, region)

np.testing.assert_array_equal(image, expected_image)

def test_multi_channel_labeled_image_with_request_downsample():
features = [ImageFeature(geojson.LineString([(6, 5), (9, 5)]))]
expected_image = np.array(
[[[False, False, False, False, False],
[False, False, False, False, False],
[False, False, False, False, False]],
[[False, False, False, False, False],
[False, False, False, False, False],
[False, False, False, True, True]]]
)
labeled_server = LabeledImageServer(sample_metadata, features, multichannel=True, downsample=1)
downsample = 2
region = Region2D(0, 0, labeled_server.metadata.width, labeled_server.metadata.height)
image = labeled_server.read_region(downsample, region)

np.testing.assert_array_equal(image, expected_image)

0 comments on commit 978d841

Please sign in to comment.