def test_callable_data(self):
def fn(*x):
raise ValueError(x)
# 1D test
tiler = Tiler(data_shape=(100, ), tile_shape=(10, ))
for i in range(tiler.n_tiles):
with self.assertRaises(ValueError) as cm:
tiler.get_tile(fn, i)
np.testing.assert_equal(
cm.exception.args[0],
(*tiler.get_tile_bbox_position(i)[0], *tiler.tile_shape))
# 2D test
tiler = Tiler(data_shape=(100, 100), tile_shape=(10, 20))
for i in range(tiler.n_tiles):
with self.assertRaises(ValueError) as cm:
tiler.get_tile(fn, i)
np.testing.assert_equal(
cm.exception.args[0],
(*tiler.get_tile_bbox_position(i)[0], *tiler.tile_shape))
# 3D test
tiler = Tiler(data_shape=(100, 100, 100), tile_shape=(10, 20, 50))
for i in range(tiler.n_tiles):
with self.assertRaises(ValueError) as cm:
tiler.get_tile(fn, i)
np.testing.assert_equal(
cm.exception.args[0],
(*tiler.get_tile_bbox_position(i)[0], *tiler.tile_shape))
# channel dimension test
tiler = Tiler(data_shape=(100, 100, 3),
tile_shape=(10, 20, 3),
channel_dimension=2)
for i in range(tiler.n_tiles):
with self.assertRaises(ValueError) as cm:
tiler.get_tile(fn, i)
np.testing.assert_equal(
cm.exception.args[0],
(*tiler.get_tile_bbox_position(i, with_channel_dim=True)[0],
*tiler.tile_shape))
return img
print('Loading and processing tiles')
imgs = []
for i, img in tqdm(tiler.iterate(reader_func), total=len(tiler)):
imgs.append(preprocess(img))
masks, flows, styles, diams = model.eval(
imgs, diameter=diameter, channels=channels)
# Process shapes
print('Converting masks to shapes')
geoms = []
for tile_idx, mask in tqdm(enumerate(masks), total=len(masks)):
x_offset, y_offset, _ = tiler.get_tile_bbox_position(tile_idx)[0]
for i in range(mask.max()):
m = (mask == i+1).astype(np.uint8)
c, hier = cv2.findContours(m, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
c = max(c, key=cv2.contourArea).squeeze()
c[:, 0] = c[:, 0] + x_offset/downsample
c[:, 1] = c[:, 1] + y_offset/downsample
new_poly = Polygon(c)
# Try to fix invalid geoms
if new_poly.is_valid:
geoms.append(new_poly)
else:
geoms.append(new_poly.buffer(0))
# an auxiliary dictionary to get the original indices
def test_tile_bbox_position(self):
tile_size = 10
tiler = Tiler(data_shape=self.data.shape, tile_shape=(tile_size, ))
tiler2 = Tiler(data_shape=(3, ) + self.data.shape,
tile_shape=(
3,
tile_size,
),
channel_dimension=0)
with self.assertRaises(IndexError):
tiler.get_tile_bbox_position(-1)
with self.assertRaises(IndexError):
tiler.get_tile_bbox_position(len(tiler))
tile_id = 0
np.testing.assert_equal(([0], [10]),
tiler.get_tile_bbox_position(tile_id))
np.testing.assert_equal(([0], [10]),
tiler.get_tile_bbox_position(tile_id, True))
np.testing.assert_equal(([0], [10]),
tiler2.get_tile_bbox_position(tile_id))
np.testing.assert_equal(([0, 0], [3, 10]),
tiler2.get_tile_bbox_position(tile_id, True))
tile_id = len(tiler) - 1
np.testing.assert_equal(([90], [100]),
tiler.get_tile_bbox_position(tile_id))
np.testing.assert_equal(([90], [100]),
tiler.get_tile_bbox_position(tile_id, True))
np.testing.assert_equal(([90], [100]),
tiler2.get_tile_bbox_position(tile_id))
np.testing.assert_equal(([0, 90], [3, 100]),
tiler2.get_tile_bbox_position(tile_id, True))
