def main_src_test():
"""Check that the target images in pre and post registered
stack are unchanged"""
stack = data.test_stack()
reg_stack = registration.main(stack)
if not np.array_equal(stack[0], reg_stack[0]):
assert False
def reg_iter_function_same_src_test():
"""First image in both pre and post registered stack is used as
the target image so should be unchanged in both cases."""
stack = data.test_stack()
reg_stack = registration.reg_iter(stack)
if not np.array_equal(stack[0], reg_stack[0]):
assert False
def main_dst_reg_dst_are_different_test():
"""Check that the destination images in pre and post registered
stack are different"""
stack = data.test_stack()
reg_stack = registration.main(stack)
if np.array_equal(stack[1], reg_stack[1]):
assert False
def overlay_same_pics_test():
"""Overlaying a picture with itself should produce the original pic"""
stack = data.test_stack()
src = stack[0]
dst = stack[0]
overlayed_img = registration.overlay_pics(src, dst)
if np.array_equal(src, overlayed_img):
assert False
def reg_function_same_image_test():
"""Checks that registering an image to itself leaves
the image unchanged."""
stack = data.test_stack()
src = stack[0]
dst = stack[0]
reg_dst = registration.reg(src, dst)
if not np.array_equal(reg_dst, dst):
assert False
def reg_function_different_image_test():
"""Checks that registering an image to a different image changes
the image."""
stack = data.test_stack()
src = stack[0]
dst = stack[1]
reg_dst = registration.reg(src, dst)
if np.array_equal(reg_dst, dst):
assert False
def demo():
"""Loads an example image stack from data.test_stack() and registers the
stack using the main register function in sub-package registration.
Returns data about stack type, stack dimensions. Displays the pre and
post registered stack.
Takes no arguments."""
stack = data.test_stack()
reg_stack = register(stack)
print('stack is of type', type(stack))
print('stack dimensions are', stack.shape)
print('registered stack is of type', type(reg_stack))
print('registered stack dimensions are', reg_stack.shape)
merged = [overlay_pics(stack[0], img) for img in stack]
merged_reg = [overlay_pics(reg_stack[0], img) for img in reg_stack]
fig, ax = plt.subplots(nrows=2, ncols=3, figsize=(8, 5))
plt.gray()
ax[0, 0].imshow(merged[0])
ax[0, 0].axis('off')
ax[0, 0].set_title('original 1-1')
ax[0, 1].imshow(merged[1])
ax[0, 1].axis('off')
ax[0, 1].set_title('original 1-2')
ax[0, 2].imshow(merged[2])
ax[0, 2].axis('off')
ax[0, 2].set_title('original 1-3')
ax[1, 0].imshow(merged_reg[0])
ax[1, 0].axis('off')
ax[1, 0].set_title('registered 1-1')
ax[1, 1].imshow(merged_reg[1])
ax[1, 1].axis('off')
ax[1, 1].set_title('registered 1-2')
ax[1, 2].imshow(merged_reg[2])
ax[1, 2].axis('off')
ax[1, 2].set_title('registered 1-3')
fig.subplots_adjust(wspace=0.02,
hspace=0.2,
top=0.9,
bottom=0.05,
left=0,
right=1)
plt.show()
def demo():
"""Loads an example image stack from data.test_stack() and registers the
stack using the main register function in sub-package registration.
Returns data about stack type, stack dimensions. Displays the pre and
post registered stack.
Takes no arguments."""
stack = data.test_stack()
reg_stack = register(stack)
print('stack is of type', type(stack))
print('stack dimensions are', stack.shape)
print('registered stack is of type', type(reg_stack))
print('registered stack dimensions are', reg_stack.shape)
merged = [overlay_pics(stack[0], img) for img in stack]
merged_reg = [overlay_pics(reg_stack[0], img) for img in reg_stack]
fig, ax = plt.subplots(nrows=2, ncols=3, figsize=(8, 5))
plt.gray()
ax[0, 0].imshow(merged[0])
ax[0, 0].axis('off')
ax[0, 0].set_title('original 1-1')
ax[0, 1].imshow(merged[1])
ax[0, 1].axis('off')
ax[0, 1].set_title('original 1-2')
ax[0, 2].imshow(merged[2])
ax[0, 2].axis('off')
ax[0, 2].set_title('original 1-3')
ax[1, 0].imshow(merged_reg[0])
ax[1, 0].axis('off')
ax[1, 0].set_title('registered 1-1')
ax[1, 1].imshow(merged_reg[1])
ax[1, 1].axis('off')
ax[1, 1].set_title('registered 1-2')
ax[1, 2].imshow(merged_reg[2])
ax[1, 2].axis('off')
ax[1, 2].set_title('registered 1-3')
fig.subplots_adjust(wspace=0.02, hspace=0.2,
top=0.9, bottom=0.05, left=0, right=1)
plt.show()
sys.exit(1)
elif len(sys.argv) > 2:
print("Script takes in one or zero arguments.")
sys.exit(1)
else:
inputDir = '../data/test/'
# ------------------Create input ndarray------------------------
#imageFiles = glob.glob(os.path.join(inputDir, '*.jpg'))
#imageVolume = io.ImageCollection(imageFiles, as_grey=True).concatenate()
#stack = imageVolume
# reg_stack = main(stack)
stack = data.test_stack()
reg_stack = main(stack)
print('stack is of type', type(stack))
print('stack dimensions are', stack.shape)
print('registered stack is of type', type(reg_stack))
print('registered stack dimensions are', reg_stack.shape)
merged = [overlay_pics(stack[0], img) for img in stack]
merged_reg = [overlay_pics(reg_stack[0], img) for img in reg_stack]
fig, ax = plt.subplots(nrows=2, ncols=3, figsize=(8, 5))
plt.gray()
ax[0, 0].imshow(merged[0])
ax[0, 0].axis('off')
def check_test_stack_shape_length_test():
stack = data.test_stack()
assert len(stack.shape) == 3
def main_size_test():
stack = data.test_stack()
reg_stack = registration.main(stack)
assert stack.shape == reg_stack.shape
def main_test():
stack = data.test_stack()
registration.main(stack)
def check_test_stack_shape_test():
stack = data.test_stack()
assert stack.shape == (3, 1040, 1388)
def overlay_pics_test():
stack = data.test_stack()
src = stack[0]
dst = stack[1]
registration.overlay_pics(src, dst)
def load_test_stack_test():
data.test_stack()
def check_test_stack_shape_length_test():
stack = data.test_stack()
assert len(stack.shape) == 3
def reg_iter_function_test():
stack = data.test_stack()
reg_stack = registration.reg_iter(stack)
if np.array_equal(stack[0], reg_stack[1]):
assert False
def reg_iter_function_test():
stack = data.test_stack()
reg_stack = registration.reg_iter(stack)
def load_test_stack_test():
data.test_stack()
def check_that_src_dst_are_not_equal_test():
stack = data.test_stack()
src = stack[0]
dst = stack[1]
if np.array_equal(src, dst):
assert False
def check_test_stack_shape_test():
stack = data.test_stack()
assert stack.shape == (3, 1040, 1388)
def reg_function_test():
stack = data.test_stack()
src = stack[0]
dst = stack[1]
registration.reg(src, dst)
