def main():
np.random.seed(1000)
if len(sys.argv) < 3:
print('register_example.py: Too few parameters. Give the path to two gray-scale image files.')
print('Example: python2 register_example.py reference_image floating_image')
return False
ref_im_path = sys.argv[1]
flo_im_path = sys.argv[2]
ref_im = scipy.misc.imread(ref_im_path, 'L')
flo_im = scipy.misc.imread(flo_im_path, 'L')
# Save copies of original images
ref_im_orig = ref_im.copy()
flo_im_orig = flo_im.copy()
ref_im = filters.normalize(ref_im, 0.0, None)
flo_im = filters.normalize(flo_im, 0.0, None)
diag = 0.5 * (transforms.image_diagonal(ref_im, spacing) + transforms.image_diagonal(flo_im, spacing))
weights1 = np.ones(ref_im.shape)
mask1 = np.ones(ref_im.shape, 'bool')
weights2 = np.ones(flo_im.shape)
mask2 = np.ones(flo_im.shape, 'bool')
# Initialize registration framework for 2d images
reg = Register(2)
reg.set_report_freq(param_report_freq)
reg.set_alpha_levels(alpha_levels)
reg.set_reference_image(ref_im)
reg.set_reference_mask(mask1)
reg.set_reference_weights(weights1)
reg.set_floating_image(flo_im)
reg.set_floating_mask(mask2)
reg.set_floating_weights(weights2)
# Setup the Gaussian pyramid resolution levels
reg.add_pyramid_level(4, 5.0)
reg.add_pyramid_level(2, 3.0)
reg.add_pyramid_level(1, 0.0)
# Learning-rate / Step lengths [[start1, end1], [start2, end2] ...] (for each pyramid level)
step_lengths = np.array([[1.0 ,1.0], [1.0, 0.5], [0.5, 0.1]])
# Create the transform and add it to the registration framework (switch between affine/rigid transforms by commenting/uncommenting)
# Affine
reg.add_initial_transform(AffineTransform(2), np.array([1.0/diag, 1.0/diag, 1.0/diag, 1.0/diag, 1.0, 1.0]))
# Rigid 2D
#reg.add_initial_transform(Rigid2DTransform(2), np.array([1.0/diag, 1.0, 1.0]))
# Set the parameters
reg.set_iterations(param_iterations)
reg.set_gradient_magnitude_threshold(0.001)
reg.set_sampling_fraction(param_sampling_fraction)
reg.set_step_lengths(step_lengths)
# Create output directory
directory = os.path.dirname('./test_images/output/')
if not os.path.exists(directory):
os.makedirs(directory)
# Start the pre-processing
reg.initialize('./test_images/output/')
# Control the formatting of numpy
np.set_printoptions(suppress=True, linewidth=200)
# Start the registration
reg.run()
(transform, value) = reg.get_output(0)
### Warp final image
c = transforms.make_image_centered_transform(transform, ref_im, flo_im, spacing, spacing)
# Print out transformation parameters
print('Transformation parameters: %s.' % str(transform.get_params()))
# Create the output image
ref_im_warped = np.zeros(ref_im.shape)
# Transform the floating image into the reference image space by applying transformation 'c'
c.warp(In = flo_im_orig, Out = ref_im_warped, in_spacing=spacing, out_spacing=spacing, mode='spline', bg_value = 0.0)
# Save the registered image
scipy.misc.imsave('./test_images/output/registered.png', ref_im_warped)
# Compute the absolute difference image between the reference and registered images
D1 = np.abs(ref_im_orig-ref_im_warped)
err = np.sum(D1)
print("Err: %f" % err)
scipy.misc.imsave('./test_images/output/diff.png', D1)
return True
def main():
np.random.seed(1000)
if len(sys.argv) < 3:
print(
f'{sys.argv[0]}: Too few parameters. Give the path to two gray-scale image files.'
)
print(f'Example: python {sys.argv[0]} reference_image floating_image')
return False
ref_im_path = sys.argv[1]
flo_im_path = sys.argv[2]
ref_im = Image.open(ref_im_path).convert('L')
flo_im = Image.open(flo_im_path).convert('L')
ref_im = np.asarray(ref_im) / 255.
flo_im = np.asarray(flo_im) / 255.
# Make copies of original images
ref_im_orig = ref_im.copy()
flo_im_orig = flo_im.copy()
# Preprocess images
ref_im = filters.normalize(ref_im, 0.0, None)
flo_im = filters.normalize(flo_im, 0.0, None)
weights1 = np.ones(ref_im.shape)
mask1 = np.ones(ref_im.shape, 'bool')
weights2 = np.ones(flo_im.shape)
mask2 = np.ones(flo_im.shape, 'bool')
# Initialize registration framework for 2d images
reg = Register(2)
reg.set_image_data(ref_im, flo_im, mask1, mask2, weights1, weights2)
# Choose a registration model
reg.set_model('alphaAMD', alpha_levels=alpha_levels, \
symmetric_measure=symmetric_measure, \
squared_measure=squared_measure)
# Setup the Gaussian pyramid resolution levels
reg.add_pyramid_level(4, 5.0)
reg.add_pyramid_level(2, 3.0)
reg.add_pyramid_level(1, 0.0)
# Choose an optimizer and set optimizer-specific parameters
# For GD and adam, learning-rate / Step lengths given by [[start1, end1], [start2, end2] ...] (for each pyramid level)
reg.set_optimizer('adam', \
gradient_magnitude_threshold=0.01, \
iterations=param_iterations
)
# reg.set_optimizer('gd', \
# step_length=np.array([1., 0.5, 0.25]), \
# end_step_length=np.array([0.4, 0.2, 0.01]), \
# gradient_magnitude_threshold=0.01, \
# iterations=param_iterations
# )
# reg.set_optimizer('scipy', \
# iterations=param_iterations, \
# epsilon=0.001 \
# )
# Scale all transform parameters to approximately the same order of magnitude, based on sizes of images
diag = 0.5 * (transforms.image_diagonal(ref_im, spacing) +
transforms.image_diagonal(flo_im, spacing))
# Create the initial transform and add it to the registration framework
# (switch between affine/rigid transforms by commenting/uncommenting)
# # Affine
# initial_transform = transforms.AffineTransform(2)
# param_scaling = np.array([1.0/diag, 1.0/diag, 1.0/diag, 1.0/diag, 1.0, 1.0])
# reg.add_initial_transform(initial_transform, param_scaling=param_scaling)
# # Rigid 2D
# initial_transform = transforms.Rigid2DTransform()
# param_scaling = np.array([1.0/diag, 1.0, 1.0])
# reg.add_initial_transform(initial_transform, param_scaling=param_scaling)
# Composite scale + rigid
param_scaling = np.array([1.0 / diag, 1.0 / diag, 1.0, 1.0])
initial_transform = transforms.CompositeTransform(2, [transforms.ScalingTransform(2, uniform=True), \
transforms.Rigid2DTransform()])
reg.add_initial_transform(initial_transform, param_scaling=param_scaling)
# Set up other registration framework parameters
reg.set_report_freq(param_report_freq)
reg.set_sampling_fraction(param_sampling_fraction)
# Create output directory
directory = os.path.dirname(outdir)
if not os.path.exists(directory):
os.makedirs(directory)
# Start the pre-processing
reg.initialize(outdir)
# Control the formatting of numpy
np.set_printoptions(suppress=True, linewidth=200)
# Start the registration
reg.run()
(transform, value) = reg.get_output(0)
### Warp final image
c = transforms.make_image_centered_transform(transform, ref_im, flo_im,
spacing, spacing)
# Print out transformation parameters and status
print('Starting from %s, optimizer terminated with message: %s'%(str(initial_transform.get_params()), \
reg.get_output_messages()[0]))
print('Final transformation parameters: %s.' % str(transform.get_params()))
# Create the output image
ref_im_warped = np.zeros(ref_im.shape)
mask = np.ones(flo_im_orig.shape, dtype='bool')
warped_mask = np.zeros(ref_im.shape, dtype='bool')
# Transform the floating image into the reference image space by applying transformation 'c'
c.warp(In=flo_im_orig,
Out=ref_im_warped,
in_spacing=spacing,
out_spacing=spacing,
mode='spline',
bg_value=0.0)
c.warp(In=mask,
Out=warped_mask,
in_spacing=spacing,
out_spacing=spacing,
mode='spline',
bg_value=0.0)
# Save the registered image
Image.fromarray(ref_im_warped).convert('RGB').save(outdir +
'registered.png')
# Compute the absolute difference image between the reference and registered images
D1 = np.abs(ref_im_orig - ref_im_warped)
err = np.mean(D1[warped_mask])
print("Err: %f" % err)
Image.fromarray(D1).convert('RGB').save(outdir + 'diff.png')
return True
