def testRepresentativePoint(self):
image = np.zeros([300, 200], dtype=np.uint8)
image = draw_square_by_corner(image, 50, (150, 50), color=255)
slices = mask_to_objects_2d(image)
y, x = representative_point(slices[0].polygon, image, label=255)
self.assertEqual(image[y, x], 255)
def testTwoPoints(self):
mask = np.array([[0, 0, 0, 0], [0, 1, 1, 0], [0, 0, 0, 0]],
dtype=np.uint8)
polygon = Polygon([(1, 1), (1, 2), (3, 2), (3, 1), (1, 1)])
slices = mask_to_objects_2d(mask)
self.assertEqual(len(slices), 1)
self.assertTrue(slices[0].polygon.equals(polygon))
def testOffset(self):
image = np.zeros([300, 200], dtype=np.uint8)
image = draw_square_by_corner(image, 100, (150, 50), color=255)
slices = mask_to_objects_2d(image, offset=(320, 255))
self.assertEqual(len(slices), 1)
self.assertEqual(slices[0].label, 255)
self.assertTrue(slices[0].polygon.equals(box(305, 470, 406, 571)),
msg="Polygon is equal")
def testExportOneSquare(self):
image = np.zeros([300, 200], dtype=np.uint8)
image = draw_square_by_corner(image, 100, (150, 50), color=255)
slices = mask_to_objects_2d(image)
self.assertEqual(len(slices), 1)
self.assertEqual(slices[0].label, 255)
self.assertTrue(slices[0].polygon.equals(box(50, 150, 151, 251)),
msg="Polygon is equal")
def extract_tiled_annotations(in_tiles, out_path, nj, label_merging=False):
"""
in_images: iterable
List of BiaflowsTile
out_path: str
Path of output tiles
nj: BiaflowsJob
A BIAflows job object
label_merging: bool
True for merging only polygons having the same label. False for merging based on geometry only
"""
# regroup tiles by original images
grouped_tiles = defaultdict(list)
for in_tile in in_tiles:
grouped_tiles[in_tile.in_image.original_filename].append(in_tile)
default_tile_builder = DefaultTileBuilder()
annotations = AnnotationCollection()
for tiles in grouped_tiles.values():
# recreate the topology
in_image = tiles[0].in_image
topology = BiaflowsSldcImage(in_image, is_2d=True).tile_topology(
default_tile_builder,
max_width=nj.flags["tile_width"],
max_height=nj.flags["tile_height"],
overlap=nj.flags["tile_overlap"])
# extract polygons for each tile
ids, polygons, labels = list(), list(), list()
label = -1
for tile in tiles:
out_tile_path = os.path.join(out_path, tile.filename)
slices = mask_to_objects_2d(imread(out_tile_path),
offset=tile.tile.abs_offset[::-1])
ids.append(tile.tile.identifier)
polygons.append([s.polygon for s in slices])
labels.append([s.label for s in slices])
# save label for use after merging
if len(slices) > 0:
label = slices[0]
# merge
merged = SemanticMerger(tolerance=1).merge(
ids, polygons, topology, labels=labels if label_merging else None)
if label_merging:
merged = merged[0]
annotations.extend([
create_annotation_from_slice(
_slice=AnnotationSlice(p, label),
id_image=in_image.object.id,
image_height=in_image.object.height,
id_project=nj.project.id,
) for p in merged
])
return annotations
def testAdjacentWithoutSeperation(self):
image = np.zeros([300, 200], dtype=np.uint8)
image = draw_square_by_corner(image, 50, (150, 50), color=255)
image = draw_square_by_corner(image, 50, (150, 101), color=127)
slices = mask_to_objects_2d(image)
# sort by bounding box top left corner
slices = sorted(slices, key=lambda s: s.polygon.bounds[:2])
self.assertEqual(len(slices), 2)
self.assertEqual(slices[0].label, 255)
self.assertEqual(slices[1].label, 127)
def skeleton_mask_to_objects_2d(mask, background=0, offset=None):
"""Process a 2d skeleton mask
Parameters
----------
mask: ndqrrqy
background: int
offset: tuple
"""
dilated = morphology.dilation(mask, selem=morphology.selem.disk(2))
return mask_to_objects_2d(dilated, background=background, offset=offset)
def testOtherPixels(self):
mask = np.array(
[[0, 0, 0, 0, 0, 0], [0, 1, 1, 0, 1, 1], [0, 0, 1, 0, 1, 0],
[0, 0, 0, 1, 0, 0], [0, 0, 0, 0, 0, 0]],
dtype=np.uint8)
p1 = Polygon([(1, 1), (1, 2), (2, 2), (2, 3), (3, 3), (3, 1), (1, 1)])
p2 = Polygon([(4, 1), (4, 3), (5, 3), (5, 2), (6, 2), (6, 1), (4, 1)])
p3 = Polygon([(3, 3), (3, 4), (4, 4), (4, 3), (3, 3)])
slices = mask_to_objects_2d(mask)
self.assertEqual(len(slices), 3)
self.assertTrue(slices[0].polygon.equals(p1))
self.assertTrue(slices[1].polygon.equals(p2))
self.assertTrue(slices[2].polygon.equals(p3))
def testSmallObject(self):
image = np.zeros([100, 100], dtype=np.uint8)
image = draw_poly(image,
Polygon([(15, 77), (15, 78), (16, 78), (15, 77)]),
color=127)
image = draw_poly(image, box(1, 1, 2, 2), color=255)
slices = mask_to_objects_2d(image)
# sort by bounding box top left corner
slices = sorted(slices, key=lambda s: s.polygon.bounds[:2])
self.assertEqual(len(slices), 2)
self.assertEqual(slices[0].label, 255)
self.assertEqual(slices[1].label, 127)
def testSeveralObjects(self):
image = np.zeros([300, 200], dtype=np.uint8)
image = draw_square_by_corner(image, 50, (150, 50), color=255)
image = draw_square_by_corner(image, 50, (205, 105), color=127)
slices = mask_to_objects_2d(image)
# sort by bounding box top left corner
slices = sorted(slices, key=lambda s: s.polygon.bounds[:2])
self.assertEqual(len(slices), 2)
self.assertEqual(slices[0].label, 255)
self.assertTrue(slices[0].polygon.equals(box(50, 150, 101, 201)),
msg="Polygon is equal")
self.assertEqual(slices[1].label, 127)
self.assertTrue(slices[1].polygon.equals(box(105, 205, 156, 256)),
msg="Polygon is equal")