def main():
args = surfcut_parser().parse_args()
image_path = args.image_path
print(image_path)
data = tifffile.imread(image_path)
print(data.shape)
view(data)
def main():
start_time = datetime.now()
args = surfcut_parser().parse_args()
image_path = args.image_path
print("Loading data")
data = tifffile.imread(image_path)
print("Converting to 8 bit")
data = data.astype(np.uint8)
print("Smoothing")
filtered = np.copy(data)
for idx, plane in enumerate(filtered):
filtered[idx] = filters.gaussian_filter(plane, args.gauss_sigma)
print("Thresholding")
binary = filtered > args.threshold
del filtered
print("Detecting edges")
binary = edge_detect(binary)
print("Shifting binary object down")
shift_mag = int(args.shift + (args.depth / 2))
down_shift = binary[0:-shift_mag]
padding = np.zeros((shift_mag, binary.shape[1], binary.shape[2]))
down_shift = np.append(padding, down_shift, axis=0)
print("Shifting binary object up")
shift_mag = int(args.shift - (args.depth / 2))
up_shift = binary[0:-shift_mag]
padding = np.zeros((shift_mag, binary.shape[1], binary.shape[2]))
up_shift = np.append(padding, up_shift, axis=0)
del binary
print("Generating mask")
mask = up_shift - down_shift
del up_shift
del down_shift
mask = mask > 0
print("Masking data")
masked = data * mask
print("Projecting data")
projection = np.max(masked, axis=0)
print(f"Finished. Total time taken: {format(datetime.now() - start_time)}")
if not args.no_viewer:
print("Opening viewer")
view(data, masked, projection)
def straight(data, mask):
args = surfcut_parser().parse_args()
imarray_real = numpy.array(data)
imarray = numpy.array(mask)
imdim = imarray.shape
zthick = args.depth
straightened = numpy.empty((zthick, imdim[1], imdim[2]))
for i in range(1, imdim[1], 5):
for j in range(1, imdim[2], 5):
index = list(zip(*numpy.where(imarray[:, i, j] == True)))
if index:
index_first = index[0][0]
if (index_first + args.depth + args.shift) < imdim[0]:
straightened[0:zthick, (i - 2):(i + 3),
(j - 2):(j + 3)] = imarray_real[(
index_first +
args.shift):(index_first + args.shift +
args.depth), (i - 2):(i + 3),
(j - 2):(j +
3), ]
return straightened