def setup(
first_img_path,
soma_diameter,
ball_xy_size,
ball_z_size,
ball_overlap_fraction=0.6,
z_offset=0,
):
plane = tifffile.imread(first_img_path)
plane = plane.T
max_value = get_max_value(plane)
clipping_value = max_value - 2
thrsh_val = max_value - 1
soma_centre_val = max_value
tile_width = soma_diameter * 2
layer_width, layer_height = plane.shape
ball_filter = BallFilter(
layer_width,
layer_height,
ball_xy_size,
ball_z_size,
overlap_fraction=ball_overlap_fraction,
tile_step_width=tile_width,
tile_step_height=tile_width,
threshold_value=thrsh_val,
soma_centre_value=soma_centre_val,
)
start_z = z_offset + int(math.floor(ball_z_size / 2))
cell_detector = CellDetector(layer_width, layer_height, start_z=start_z)
return clipping_value, thrsh_val, ball_filter, cell_detector
def setup_tile_filtering(first_img_path):
plane = tifffile.imread(first_img_path)
plane = plane.T
max_value = get_max_value(plane)
clipping_value = max_value - 2
thrsh_val = max_value - 1
return clipping_value, thrsh_val
def test_get_max_value():
num = random.randint(0, 100)
assert 255 == tools.get_max_value(np.array(num, dtype=np.uint8))
assert 65535 == tools.get_max_value(np.array(num, dtype=np.uint16))