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intra_stack_registration_test.py
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##
# \file intra_stack_registration_test.py
# \brief Class containing unit tests for module IntraStackRegistration
#
# \author Michael Ebner ([email protected])
# \date October 2016
# Import libraries
import SimpleITK as sitk
import itk
import numpy as np
import unittest
import sys
import os
from scipy.ndimage import imread
import pysitk.simple_itk_helper as sitkh
import pysitk.python_helper as ph
# Import modules
import niftymic.base.stack as st
import niftymic.registration.intra_stack_registration as inplanereg
from niftymic.definitions import DIR_TEST
def get_inplane_corrupted_stack(stack,
angle_z,
center_2D,
translation_2D,
scale=1,
intensity_scale=1,
intensity_bias=0,
debug=0,
random=False):
# Convert to 3D:
translation_3D = np.zeros(3)
translation_3D[0:-1] = translation_2D
center_3D = np.zeros(3)
center_3D[0:-1] = center_2D
# Transform to align physical coordinate system with stack-coordinate
# system
affine_centering_sitk = sitk.AffineTransform(3)
affine_centering_sitk.SetMatrix(stack.sitk.GetDirection())
affine_centering_sitk.SetTranslation(stack.sitk.GetOrigin())
# Corrupt first stack towards positive direction
if random:
angle_z_1 = -angle_z*np.random.rand(1)[0]
else:
angle_z_1 = -angle_z
in_plane_motion_sitk = sitk.Euler3DTransform()
in_plane_motion_sitk.SetRotation(0, 0, angle_z_1)
in_plane_motion_sitk.SetCenter(center_3D)
in_plane_motion_sitk.SetTranslation(translation_3D)
motion_sitk = sitkh.get_composite_sitk_affine_transform(
in_plane_motion_sitk, sitk.AffineTransform(
affine_centering_sitk.GetInverse()))
motion_sitk = sitkh.get_composite_sitk_affine_transform(
affine_centering_sitk, motion_sitk)
stack_corrupted_resampled_sitk = sitk.Resample(
stack.sitk, motion_sitk, sitk.sitkLinear)
stack_corrupted_resampled_sitk_mask = sitk.Resample(
stack.sitk_mask, motion_sitk, sitk.sitkLinear)
# Corrupt first stack towards negative direction
if random:
angle_z_2 = -angle_z*np.random.rand(1)[0]
else:
angle_z_2 = -angle_z
in_plane_motion_2_sitk = sitk.Euler3DTransform()
in_plane_motion_2_sitk.SetRotation(0, 0, angle_z_2)
in_plane_motion_2_sitk.SetCenter(center_3D)
in_plane_motion_2_sitk.SetTranslation(-translation_3D)
motion_2_sitk = sitkh.get_composite_sitk_affine_transform(
in_plane_motion_2_sitk, sitk.AffineTransform(
affine_centering_sitk.GetInverse()))
motion_2_sitk = sitkh.get_composite_sitk_affine_transform(
affine_centering_sitk, motion_2_sitk)
stack_corrupted_2_resampled_sitk = sitk.Resample(
stack.sitk, motion_2_sitk, sitk.sitkLinear)
stack_corrupted_2_resampled_sitk_mask = sitk.Resample(
stack.sitk_mask, motion_2_sitk, sitk.sitkLinear)
# Create stack based on those two corrupted stacks
nda = sitk.GetArrayFromImage(stack_corrupted_resampled_sitk)
nda_mask = sitk.GetArrayFromImage(stack_corrupted_resampled_sitk_mask)
nda_neg = sitk.GetArrayFromImage(stack_corrupted_2_resampled_sitk)
nda_neg_mask = sitk.GetArrayFromImage(
stack_corrupted_2_resampled_sitk_mask)
for i in range(0, stack.sitk.GetDepth(), 2):
nda[i, :, :] = nda_neg[i, :, :]
nda_mask[i, :, :] = nda_neg_mask[i, :, :]
stack_corrupted_sitk = sitk.GetImageFromArray(
(nda-intensity_bias)/intensity_scale)
stack_corrupted_sitk_mask = sitk.GetImageFromArray(nda_mask)
stack_corrupted_sitk.CopyInformation(stack.sitk)
stack_corrupted_sitk_mask.CopyInformation(stack.sitk_mask)
# Debug: Show corrupted stacks (before scaling)
if debug:
sitkh.show_sitk_image(
[stack.sitk,
stack_corrupted_resampled_sitk,
stack_corrupted_2_resampled_sitk,
stack_corrupted_sitk],
title=["original",
"corrupted_1",
"corrupted_2",
"corrupted_final_from_1_and_2"])
# Update in-plane scaling
spacing = np.array(stack.sitk.GetSpacing())
spacing[0:-1] /= scale
stack_corrupted_sitk.SetSpacing(spacing)
stack_corrupted_sitk_mask.SetSpacing(spacing)
# Create Stack object
stack_corrupted = st.Stack.from_sitk_image(
stack_corrupted_sitk, "stack_corrupted", stack_corrupted_sitk_mask)
# Debug: Show corrupted stacks (after scaling)
if debug:
stack_corrupted_resampled_sitk = sitk.Resample(
stack_corrupted.sitk, stack.sitk)
sitkh.show_sitk_image(
[stack.sitk,
stack_corrupted_resampled_sitk],
title=["original", "corrupted"])
return stack_corrupted, motion_sitk, motion_2_sitk
class IntraStackRegistrationTest(unittest.TestCase):
# Specify input data
dir_test_data = DIR_TEST
accuracy = 6
def setUp(self):
pass
##
# Test whether the function
# _get_initial_transforms_and_parameters_geometry_moments
# works.
# \date 2016-11-09 23:59:25+0000
#
# \param self The object
#
def test_initial_transform_computation_1(self):
# Create stack of slice with only a dot in the middle
shape_xy = 15
shape_z = 15
# Original stack
nda_3D = np.zeros((shape_z, shape_xy, shape_xy))
nda_3D[:, 0, 0] = 1
stack_sitk = sitk.GetImageFromArray(nda_3D)
stack = st.Stack.from_sitk_image(stack_sitk, "stack")
# Create 'motion corrupted stack', i.e. point moves diagonally with
# step one
nda_3D_corruped = np.zeros_like(nda_3D)
for i in range(0, shape_z):
nda_3D_corruped[i, i, i] = 1
stack_corrupted_sitk = sitk.GetImageFromArray(nda_3D_corruped)
stack_corrupted = st.Stack.from_sitk_image(
stack_corrupted_sitk, "stack_corrupted")
# stack_corrupted.show_slices()
# sitkh.show_stacks([stack, stack_corrupted])
# Ground truth-parameter: zero angle but translation = (1, 1) from one
# slice to the next
parameters = np.ones((shape_z, 3))
parameters[:, 0] = 0
for i in range(0, shape_z):
parameters[i, :] *= i
# 1) Get initial transform in case no reference is given
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted)
inplane_registration.set_transform_initializer_type("moments")
# inplane_registration.set_transform_initializer_type("identity")
inplane_registration._run_registration_pipeline_initialization()
parameters_est = inplane_registration.get_parameters()
nda_diff = parameters - parameters_est
self.assertEqual(np.round(
np.linalg.norm(nda_diff), decimals=self.accuracy), 0)
# 2) Get initial transform in case reference is given
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted, stack)
inplane_registration.set_transform_initializer_type("moments")
# inplane_registration.set_image_transform_reference_fit_term("gradient_magnitude")
# inplane_registration.set_transform_initializer_type("identity")
inplane_registration._run_registration_pipeline_initialization()
inplane_registration._apply_motion_correction()
# stack_corrected = inplane_registration.get_corrected_stack()
# sitkh.show_stacks([stack, stack_corrupted, stack_corrected.get_resampled_stack_from_slices(interpolator="Linear")])
parameters_est = inplane_registration.get_parameters()
nda_diff = parameters - parameters_est
# print(nda_diff)
# print(parameters)
self.assertEqual(np.round(
np.linalg.norm(nda_diff), decimals=self.accuracy), 0)
##
# Test whether the function
# _get_initial_transforms_and_parameters_geometry_moments
# works.
# \date 2016-11-09 23:59:25+0000
#
# \param self The object
#
def test_initial_transform_computation_2(self):
# Create stack of slice with a pyramid in the middle
shape_xy = 250
shape_z = 15
intensity_mask = 10
length = 50
nda_2D = ph.read_image(os.path.join(
DIR_TEST, "2D_Pyramid_Midpoint_" + str(length) + ".png"))
# Original stack
nda_3D = np.zeros((shape_z, shape_xy, shape_xy))
i0 = (shape_xy - length) / 2
for i in range(0, shape_z):
nda_3D[i, i0:-i0, i0:-i0] = nda_2D
stack_sitk = sitk.GetImageFromArray(nda_3D)
stack = st.Stack.from_sitk_image(stack_sitk, "stack")
# Create 'motion corrupted stack', i.e. in-plane translation, and
# associated ground-truth parameters
parameters = np.zeros((shape_z, 3))
parameters[:, 0] = 0
nda_3D_corrupted = np.zeros_like(nda_3D)
nda_3D_corrupted[0, :, :] = nda_3D[0, :, :]
for i in range(1, shape_z):
# Get random translation
[tx, ty] = np.random.randint(0, 50, 2)
# Get image based on corruption
inew = i0 + tx
jnew = i0 + ty
nda_3D_corrupted[i, inew:, jnew:] = \
nda_3D[i, i0:2*i0+length-tx, i0:2*i0+length-ty]
# Get ground-truth parameters
parameters[i, 1] = ty
parameters[i, 2] = tx
stack_corrupted_sitk = sitk.GetImageFromArray(nda_3D_corrupted)
stack_corrupted = st.Stack.from_sitk_image(
stack_corrupted_sitk, "stack_corrupted")
# stack_corrupted.show_slices()
# sitkh.show_stacks([stack, stack_corrupted])
# 1) Get initial transform in case no reference is given
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted)
inplane_registration.set_transform_initializer_type("moments")
# inplane_registration.set_transform_initializer_type("identity")
# inplane_registration.set_transform_initializer_type("geometry")
inplane_registration._run_registration_pipeline_initialization()
# Debug:
# inplane_registration._apply_motion_correction()
# stack_corrected = inplane_registration.get_corrected_stack()
# sitkh.show_stacks(
# [stack,
# stack_corrupted,
# stack_corrected.get_resampled_stack_from_slices(
# interpolator="Linear", filename="stack_corrected")])
parameters_est = inplane_registration.get_parameters()
nda_diff = parameters - parameters_est
self.assertEqual(np.round(
np.linalg.norm(nda_diff), decimals=self.accuracy), 0)
# 2) Get initial transform in case reference is given
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted, stack)
inplane_registration.set_transform_initializer_type("moments")
# inplane_registration.set_transform_initializer_type("identity")
inplane_registration._run_registration_pipeline_initialization()
# Debug:
# inplane_registration._apply_motion_correction()
# stack_corrected = inplane_registration.get_corrected_stack()
# sitkh.show_stacks(
# [stack,
# stack_corrupted,
# stack_corrected.get_resampled_stack_from_slices(
# interpolator="Linear", filename="stack_corrected")])
parameters_est = inplane_registration.get_parameters()
nda_diff = parameters - parameters_est
# print(nda_diff)
# print(parameters)
self.assertEqual(np.round(
np.linalg.norm(nda_diff), decimals=self.accuracy), 0)
##
# Test whether the function
# _get_initial_transforms_and_parameters_geometry_moments
# works.
# \date 2016-11-09 23:59:25+0000
#
# \param self The object
#
def test_initial_transform_computation_3(self):
# Create stack of slice with a pyramid in the middle
shape_xy = 250
shape_z = 15
intensity_mask = 10
length = 50
nda_2D = ph.read_image(os.path.join(
DIR_TEST, "2D_Pyramid_Midpoint_" + str(length) + ".png"))
# Original stack
nda_3D = np.zeros((shape_z, shape_xy, shape_xy))
i0 = (shape_xy - length) / 2
for i in range(0, shape_z):
nda_3D[i, i0:-i0, i0:-i0] = nda_2D
nda_3D_mask = np.array(nda_3D).astype(np.uint8)
nda_3D_mask[np.where(nda_3D_mask <= intensity_mask)] = 0
nda_3D_mask[np.where(nda_3D_mask > intensity_mask)] = 1
# Add additional weight s.t. initialization without mask fails
for i in range(0, shape_z):
nda_3D[i, -i0:, -i0:] = 10
stack_sitk = sitk.GetImageFromArray(nda_3D)
stack_sitk_mask = sitk.GetImageFromArray(nda_3D_mask)
stack = st.Stack.from_sitk_image(stack_sitk, "stack", stack_sitk_mask)
# Create 'motion corrupted stack', i.e. in-plane translation, and
# associated ground-truth parameters
parameters = np.zeros((shape_z, 3))
parameters[:, 0] = 0
nda_3D_corrupted = np.zeros_like(nda_3D)
nda_3D_corrupted[0, :, :] = nda_3D[0, :, :]
nda_3D_corrupted_mask = np.zeros_like(nda_3D_mask)
nda_3D_corrupted_mask[0, :, :] = nda_3D_mask[0, :, :]
for i in range(1, shape_z):
# Get random translation
[tx, ty] = np.random.randint(0, 50, 2)
# Get image based on corruption
inew = i0 + tx
jnew = i0 + ty
nda_3D_corrupted[i, inew:, jnew:] = \
nda_3D[i, i0:2*i0+length-tx, i0:2*i0+length-ty]
nda_3D_corrupted_mask[i, inew:, jnew:] = \
nda_3D_mask[i, i0:2*i0+length-tx, i0:2*i0+length-ty]
# Get ground-truth parameters
parameters[i, 1] = ty
parameters[i, 2] = tx
# nda_3D_corrupted = np.zeros_like(nda_3D)
# nda_3D_corrupted[0, i0:-i0, i0:-i0] = nda_2D
# for i in range(1, shape_z):
# # Get random translation
# [tx, ty] = np.random.randint(0, 50, 2)
# # Get image based on corruption
# inew = i0 + tx
# jnew = i0 + ty
# nda_3D_corrupted[i, inew:inew+length, jnew:jnew+length] = nda_2D
# # Get ground-truth parameters
# parameters[i, 1] = ty
# parameters[i, 2] = tx
stack_corrupted_sitk = sitk.GetImageFromArray(nda_3D_corrupted)
stack_corrupted_sitk_mask = sitk.GetImageFromArray(
nda_3D_corrupted_mask)
stack_corrupted = st.Stack.from_sitk_image(
stack_corrupted_sitk, "stack_corrupted", stack_corrupted_sitk_mask)
# stack_corrupted.show(1)
# stack_corrupted.show_slices()
# sitkh.show_stacks([stack, stack_corrupted],
# segmentation=stack)
# 1) Get initial transform in case no reference is given
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted,
use_stack_mask=True,
)
inplane_registration.set_transform_initializer_type("moments")
# inplane_registration.set_transform_initializer_type("identity")
# inplane_registration.set_transform_initializer_type("geometry")
inplane_registration._run_registration_pipeline_initialization()
# Debug:
# inplane_registration._apply_motion_correction()
# stack_corrected = inplane_registration.get_corrected_stack()
# sitkh.show_stacks(
# [stack,
# stack_corrupted,
# stack_corrected.get_resampled_stack_from_slices(
# interpolator="Linear", filename="stack_corrected")])
parameters_est = inplane_registration.get_parameters()
nda_diff = parameters - parameters_est
self.assertEqual(np.round(
np.linalg.norm(nda_diff), decimals=self.accuracy), 0)
# 2) Get initial transform in case reference is given
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted, stack)
inplane_registration.set_transform_initializer_type("moments")
# inplane_registration.set_transform_initializer_type("identity")
inplane_registration.use_reference_mask(True)
inplane_registration.use_stack_mask_reference_fit_term(True)
inplane_registration._run_registration_pipeline_initialization()
# Debug:
# inplane_registration._apply_motion_correction()
# stack_corrected = inplane_registration.get_corrected_stack()
# sitkh.show_stacks(
# [stack,
# stack_corrupted,
# stack_corrected.get_resampled_stack_from_slices(
# interpolator="Linear", filename="stack_corrected")])
parameters_est = inplane_registration.get_parameters()
nda_diff = parameters - parameters_est
# print(nda_diff)
# print(parameters)
self.assertEqual(np.round(
np.linalg.norm(nda_diff), decimals=self.accuracy), 0)
##
# Test that initial intensity coefficients are computed
# correctly
# \date 2016-11-10 04:28:06+0000
#
# \param self The object
#
def test_initial_intensity_coefficient_computation(self):
# Create stack
shape_z = 15
nda_2D = imread(self.dir_test_data + "2D_Lena_256.png", flatten=True)
nda_3D = np.tile(nda_2D, (shape_z, 1, 1)).astype('double')
stack_sitk = sitk.GetImageFromArray(nda_3D)
stack = st.Stack.from_sitk_image(stack_sitk, "Lena")
# 1) Create linearly corrupted intensity stack
nda_3D_corruped = np.zeros_like(nda_3D)
for i in range(0, shape_z):
nda_3D_corruped[i, :, :] = nda_3D[i, :, :]/(i+1.)
stack_corrupted_sitk = sitk.GetImageFromArray(nda_3D_corruped)
stack_corrupted = st.Stack.from_sitk_image(
stack_corrupted_sitk, "stack_corrupted")
# stack_corrupted.show_slices()
# sitkh.show_stacks([stack, stack_corrupted])
# Ground truth-parameter: zero angle but translation = (1, 1) from one
# slice to the next
parameters = np.zeros((shape_z, 4))
parameters[:, 0] = 0
for i in range(0, shape_z):
parameters[i, 3:] = 1*(i+1.) # intensity
# Get initial transform in case no reference is given
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted, stack)
# inplane_registration.set_transform_initializer_type("moments")
inplane_registration.set_intensity_correction_type_slice_neighbour_fit(
"linear")
inplane_registration.set_intensity_correction_initializer_type(
"linear")
inplane_registration._run_registration_pipeline_initialization()
parameters_est = inplane_registration.get_parameters()
nda_diff = parameters - parameters_est
self.assertEqual(np.round(
np.linalg.norm(nda_diff), decimals=self.accuracy), 0)
# 2) Create affinely corrupted intensity stack
# HINT: In case of individual slice correction is active!!
nda_3D_corruped = np.zeros_like(nda_3D)
for i in range(0, shape_z):
nda_3D_corruped[i, :, :] = (nda_3D[i, :, :]-10*i)/(i+1.)
stack_corrupted_sitk = sitk.GetImageFromArray(nda_3D_corruped)
stack_corrupted = st.Stack.from_sitk_image(
stack_corrupted_sitk, "stack_corrupted")
# stack_corrupted.show_slices()
# sitkh.show_stacks([stack, stack_corrupted])
# Ground truth-parameter: zero angle but translation = (1, 1) from one
# slice to the next
parameters = np.zeros((shape_z, 5))
parameters[:, 0] = 0
for i in range(0, shape_z):
parameters[i, 3:] = (i+1, 10*i) # intensity
# Get initial transform in case no reference is given
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted, stack)
# inplane_registration.set_transform_initializer_type("moments")
inplane_registration.set_intensity_correction_type_slice_neighbour_fit(
"affine")
inplane_registration.set_intensity_correction_initializer_type(
"affine")
inplane_registration._run_registration_pipeline_initialization()
parameters_est = inplane_registration.get_parameters()
nda_diff = parameters - parameters_est
self.assertEqual(np.round(
np.linalg.norm(nda_diff), decimals=self.accuracy), 0)
##
# Verify that in-plane rigid registration works
# \date 2016-11-02 21:56:19+0000
#
# Verify that in-plane rigid registration works, i.e. test
# 1) registration parameters are close to ground truth (up to zero dp)
# 2) affine transformations for each slice correctly describes the
# registration
#
# \param self The object
#
def test_inplane_rigid_alignment_to_neighbour(self):
filename_stack = "fetal_brain_0"
# filename_recon = "FetalBrain_reconstruction_3stacks_myAlg"
# stack_sitk = sitk.ReadImage(self.dir_test_data + filename_stack + ".nii.gz")
# recon_sitk = sitk.ReadImage(self.dir_test_data + filename_recon + ".nii.gz")
# recon_resampled_sitk = sitk.Resample(recon_sitk, stack_sitk)
# stack = st.Stack.from_sitk_image(recon_resampled_sitk, "original")
stack = st.Stack.from_filename(
os.path.join(self.dir_test_data, filename_stack + ".nii.gz"),
os.path.join(self.dir_test_data, filename_stack + "_mask.nii.gz")
)
nda = sitk.GetArrayFromImage(stack.sitk)
nda_mask = sitk.GetArrayFromImage(stack.sitk_mask)
i = 5
nda_slice = np.array(nda[i, :, :])
nda_mask_slice = np.array(nda_mask[i, :, :])
for i in range(0, nda.shape[0]):
nda[i, :, :] = nda_slice
nda_mask[i, :, :] = nda_mask_slice
stack_sitk = sitk.GetImageFromArray(nda)
stack_sitk_mask = sitk.GetImageFromArray(nda_mask)
stack_sitk.CopyInformation(stack.sitk)
stack_sitk_mask.CopyInformation(stack.sitk_mask)
stack = st.Stack.from_sitk_image(
stack_sitk, stack.get_filename(), stack_sitk_mask)
# Create in-plane motion corruption
angle_z = 0.1
center_2D = (0, 0)
translation_2D = np.array([1, -2])
# Get corrupted stack and corresponding motions
stack_corrupted, motion_sitk, motion_2_sitk = get_inplane_corrupted_stack(
stack, angle_z, center_2D, translation_2D, random=True)
# stack.show(1)
# stack_corrupted.show(1)
# Perform in-plane rigid registration
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted, stack)
# inplane_registration = inplanereg.IntraStackRegistration(stack_corrupted)
inplane_registration.set_transform_initializer_type("moments")
inplane_registration.set_optimizer_iter_max(20)
inplane_registration.set_alpha_neighbour(1)
inplane_registration.set_alpha_reference(2)
# inplane_registration.use_parameter_normalization(True)
inplane_registration.use_stack_mask(1)
inplane_registration.use_reference_mask(0)
# inplane_registration.set_optimizer_loss("linear") # linear, soft_l1,
# huber
inplane_registration.set_optimizer_method("trf") # trf, lm, dogbox
# inplane_registration._run_registration_pipeline_initialization()
# inplane_registration._apply_motion_correction()
inplane_registration.use_verbose(True)
inplane_registration.run()
inplane_registration.print_statistics()
stack_registered = inplane_registration.get_corrected_stack()
parameters = inplane_registration.get_parameters()
sitkh.show_stacks([stack, stack_corrupted, stack_registered.get_resampled_stack_from_slices(
interpolator="Linear")])
# self.assertEqual(np.round(
# np.linalg.norm(nda_diff)
# , decimals = self.accuracy), 0)
# 2) Test slice transforms
slice_transforms_sitk = inplane_registration.get_slice_transforms_sitk()
stack_tmp = st.Stack.from_stack(stack_corrupted)
stack_tmp.update_motion_correction_of_slices(slice_transforms_sitk)
stack_diff_sitk = stack_tmp.get_resampled_stack_from_slices(
resampling_grid=stack.sitk).sitk - stack_registered.get_resampled_stack_from_slices(resampling_grid=stack.sitk).sitk
stack_diff_nda = sitk.GetArrayFromImage(stack_diff_sitk)
self.assertEqual(np.round(
np.linalg.norm(stack_diff_nda), decimals=8), 0)
def test_inplane_rigid_alignment_to_reference(self):
filename_stack = "fetal_brain_0"
# filename_recon = "FetalBrain_reconstruction_3stacks_myAlg"
# stack_sitk = sitk.ReadImage(self.dir_test_data + filename_stack + ".nii.gz")
# recon_sitk = sitk.ReadImage(self.dir_test_data + filename_recon + ".nii.gz")
# recon_resampled_sitk = sitk.Resample(recon_sitk, stack_sitk)
# stack = st.Stack.from_sitk_image(recon_resampled_sitk, "original")
stack = st.Stack.from_filename(
os.path.join(self.dir_test_data, filename_stack + ".nii.gz"),
os.path.join(self.dir_test_data, filename_stack + "_mask.nii.gz")
)
# Create in-plane motion corruption
angle_z = 0.1
center_2D = (0, 0)
translation_2D = np.array([1, -2])
# Get corrupted stack and corresponding motions
stack_corrupted, motion_sitk, motion_2_sitk = get_inplane_corrupted_stack(
stack, angle_z, center_2D, translation_2D)
# stack.show(1)
# stack_corrupted.show(1)
# Perform in-plane rigid registration
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted, stack)
# inplane_registration = inplanereg.IntraStackRegistration(stack_corrupted)
inplane_registration.set_transform_initializer_type("moments")
inplane_registration.set_optimizer_iter_max(10)
inplane_registration.set_alpha_neighbour(0)
inplane_registration.set_alpha_parameter(0)
inplane_registration.use_stack_mask(1)
inplane_registration.use_reference_mask(0)
inplane_registration.set_optimizer_loss("linear")
# inplane_registration.set_optimizer_method("trf")
# inplane_registration._run_registration_pipeline_initialization()
# inplane_registration._apply_motion_correction()
# inplane_registration.use_verbose(True)
inplane_registration.run()
inplane_registration.print_statistics()
stack_registered = inplane_registration.get_corrected_stack()
parameters = inplane_registration.get_parameters()
sitkh.show_stacks([stack, stack_corrupted, stack_registered.get_resampled_stack_from_slices(
interpolator="Linear", resampling_grid=stack.sitk)])
print(parameters)
# self.assertEqual(np.round(
# np.linalg.norm(nda_diff)
# , decimals = self.accuracy), 0)
# 2) Test slice transforms
slice_transforms_sitk = inplane_registration.get_slice_transforms_sitk()
stack_tmp = st.Stack.from_stack(stack_corrupted)
stack_tmp.update_motion_correction_of_slices(slice_transforms_sitk)
stack_diff_sitk = stack_tmp.get_resampled_stack_from_slices(
resampling_grid=stack.sitk).sitk - stack_registered.get_resampled_stack_from_slices(resampling_grid=stack.sitk).sitk
stack_diff_nda = sitk.GetArrayFromImage(stack_diff_sitk)
self.assertEqual(np.round(
np.linalg.norm(stack_diff_nda), decimals=8), 0)
def test_inplane_rigid_alignment_to_reference_with_intensity_correction_linear(self):
filename_stack = "fetal_brain_0"
filename_recon = "FetalBrain_reconstruction_3stacks_myAlg"
stack_sitk = sitk.ReadImage(
self.dir_test_data + filename_stack + ".nii.gz")
recon_sitk = sitk.ReadImage(
self.dir_test_data + filename_recon + ".nii.gz")
recon_resampled_sitk = sitk.Resample(recon_sitk, stack_sitk)
stack = st.Stack.from_sitk_image(recon_resampled_sitk, "original")
# Create in-plane motion corruption
angle_z = 0.05
center_2D = (0, 0)
translation_2D = np.array([1, -2])
intensity_scale = 10
intensity_bias = 0
# Get corrupted stack and corresponding motions
stack_corrupted, motion_sitk, motion_2_sitk = get_inplane_corrupted_stack(
stack, angle_z, center_2D, translation_2D, intensity_scale=intensity_scale, intensity_bias=intensity_bias)
# Perform in-plane rigid registration
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted, stack)
# inplane_registration = inplanereg.IntraStackRegistration(stack_corrupted)
inplane_registration.set_transform_initializer_type("moments")
inplane_registration.set_transform_type("rigid")
inplane_registration.set_intensity_correction_initializer_type(
"linear")
inplane_registration.set_intensity_correction_type_slice_neighbour_fit(
"linear")
inplane_registration.set_intensity_correction_type_reference_fit(
"linear")
inplane_registration.set_optimizer_loss(
"linear") # linear, soft_l1, huber
inplane_registration.use_parameter_normalization(True)
inplane_registration.use_verbose(True)
inplane_registration.set_alpha_reference(1)
inplane_registration.set_alpha_neighbour(0)
inplane_registration.set_alpha_parameter(0)
inplane_registration.set_optimizer_iter_max(30)
inplane_registration.use_verbose(True)
inplane_registration.run()
inplane_registration.print_statistics()
stack_registered = inplane_registration.get_corrected_stack()
parameters = inplane_registration.get_parameters()
sitkh.show_stacks([stack, stack_corrupted, stack_registered.get_resampled_stack_from_slices(
resampling_grid=None, interpolator="Linear")])
print("Final parameters:")
print(parameters)
self.assertEqual(np.round(
np.linalg.norm(parameters[:, -1] - intensity_scale), decimals=0), 0)
# 2) Test slice transforms
slice_transforms_sitk = inplane_registration.get_slice_transforms_sitk()
stack_tmp = st.Stack.from_stack(stack_corrupted)
stack_tmp.update_motion_correction_of_slices(slice_transforms_sitk)
stack_diff_sitk = stack_tmp.get_resampled_stack_from_slices(
resampling_grid=stack.sitk).sitk - stack_registered.get_resampled_stack_from_slices(resampling_grid=stack.sitk).sitk
stack_diff_nda = sitk.GetArrayFromImage(stack_diff_sitk)
self.assertEqual(np.round(
np.linalg.norm(stack_diff_nda), decimals=8), 0)
##
# \bug There is some issue with slice based and uniform intensity correction.
# Unit test needs to be fixed at some point
# \date 2017-07-12 12:40:01+0100
#
# \param self The object
#
def test_inplane_rigid_alignment_to_reference_with_intensity_correction_affine(self):
filename_stack = "fetal_brain_0"
filename_recon = "FetalBrain_reconstruction_3stacks_myAlg"
stack_sitk = sitk.ReadImage(
self.dir_test_data + filename_stack + ".nii.gz")
recon_sitk = sitk.ReadImage(
self.dir_test_data + filename_recon + ".nii.gz")
recon_resampled_sitk = sitk.Resample(recon_sitk, stack_sitk)
stack = st.Stack.from_sitk_image(recon_resampled_sitk, "original")
# Create in-plane motion corruption
angle_z = 0.01
center_2D = (0, 0)
translation_2D = np.array([1, 0])
intensity_scale = 5
intensity_bias = 5
# Get corrupted stack and corresponding motions
stack_corrupted, motion_sitk, motion_2_sitk = get_inplane_corrupted_stack(
stack, angle_z, center_2D, translation_2D, intensity_scale=intensity_scale, intensity_bias=intensity_bias)
# Perform in-plane rigid registration
inplane_registration = inplanereg.IntraStackRegistration(
stack_corrupted, stack)
# inplane_registration = inplanereg.IntraStackRegistration(stack_corrupted)
inplane_registration.set_transform_type("rigid")
inplane_registration.set_transform_initializer_type("identity")
inplane_registration.set_optimizer_loss("linear")
inplane_registration.set_intensity_correction_initializer_type(
"affine")
inplane_registration.set_intensity_correction_type_slice_neighbour_fit(
"affine")
inplane_registration.use_parameter_normalization(True)
inplane_registration.use_verbose(True)
inplane_registration.use_stack_mask(True)
inplane_registration.set_prior_intensity_coefficients(
(intensity_scale-0.4, intensity_bias+0.7))
inplane_registration.set_alpha_reference(1)
inplane_registration.set_alpha_neighbour(1)
inplane_registration.set_alpha_parameter(1e3)
inplane_registration.set_optimizer_iter_max(15)
inplane_registration.use_verbose(True)
inplane_registration.run()
inplane_registration.print_statistics()
stack_registered = inplane_registration.get_corrected_stack()
parameters = inplane_registration.get_parameters()
sitkh.show_stacks([stack, stack_corrupted, stack_registered.get_resampled_stack_from_slices(
resampling_grid=None, interpolator="Linear")])
self.assertEqual(np.round(
np.linalg.norm(parameters[:, -2:] - np.array([intensity_scale, intensity_bias])), decimals=0), 0)
# 2) Test slice transforms
slice_transforms_sitk = inplane_registration.get_slice_transforms_sitk()
stack_tmp = st.Stack.from_stack(stack_corrupted)
stack_tmp.update_motion_correction_of_slices(slice_transforms_sitk)
stack_diff_sitk = stack_tmp.get_resampled_stack_from_slices(
resampling_grid=stack.sitk).sitk - stack_registered.get_resampled_stack_from_slices(resampling_grid=stack.sitk).sitk
stack_diff_nda = sitk.GetArrayFromImage(stack_diff_sitk)
self.assertEqual(np.round(
np.linalg.norm(stack_diff_nda), decimals=8), 0)
def test_inplane_similarity_alignment_to_reference(self):
filename_stack = "fetal_brain_0"
# filename_stack = "3D_SheppLoganPhantom_64"
stack = st.Stack.from_filename(
os.path.join(self.dir_test_data, filename_stack + ".nii.gz"),
os.path.join(self.dir_test_data, filename_stack + "_mask.nii.gz")
)
# stack.show(1)
nda = sitk.GetArrayFromImage(stack.sitk)
nda_mask = sitk.GetArrayFromImage(stack.sitk_mask)
i = 5
nda_slice = np.array(nda[i, :, :])
nda_mask_slice = np.array(nda_mask[i, :, :])
for i in range(0, nda.shape[0]):
nda[i, :, :] = nda_slice
nda_mask[i, :, :] = nda_mask_slice
stack_sitk = sitk.GetImageFromArray(nda)
stack_sitk_mask = sitk.GetImageFromArray(nda_mask)
stack_sitk.CopyInformation(stack.sitk)
stack_sitk_mask.CopyInformation(stack.sitk_mask)
stack = st.Stack.from_sitk_image(
stack_sitk, stack.get_filename(), stack_sitk_mask)
# Create in-plane motion corruption
scale = 1.2
angle_z = 0.05
center_2D = (0, 0)
# translation_2D = np.array([0,0])
translation_2D = np.array([1, -1])
intensity_scale = 10
intensity_bias = 50
# Get corrupted stack and corresponding motions
stack_corrupted, motion_sitk, motion_2_sitk = get_inplane_corrupted_stack(
stack, angle_z, center_2D, translation_2D, scale=scale, intensity_scale=intensity_scale, intensity_bias=intensity_bias, debug=0)
# stack_corrupted.show(1)
# stack.show(1)
# Perform in-plane rigid registrations
inplane_registration = inplanereg.IntraStackRegistration(
stack=stack_corrupted, reference=stack)
# inplane_registration = inplanereg.IntraStackRegistration(stack_corrupted)
inplane_registration.set_transform_initializer_type("geometry")
# inplane_registration.set_transform_initializer_type("identity")
inplane_registration.set_intensity_correction_initializer_type(
"affine")
inplane_registration.set_transform_type("similarity")
inplane_registration.set_interpolator("Linear")
inplane_registration.set_optimizer_loss("linear")
# inplane_registration.use_reference_mask(True)
inplane_registration.use_stack_mask(True)
inplane_registration.use_parameter_normalization(True)
inplane_registration.set_prior_scale(1/scale)
inplane_registration.set_prior_intensity_coefficients(
(intensity_scale, intensity_bias))
inplane_registration.set_intensity_correction_type_slice_neighbour_fit(
"affine")
inplane_registration.set_intensity_correction_type_reference_fit(
"affine")
inplane_registration.use_verbose(True)
inplane_registration.set_alpha_reference(1)
inplane_registration.set_alpha_neighbour(0)
inplane_registration.set_alpha_parameter(1e10)
inplane_registration.set_optimizer_iter_max(20)
inplane_registration.use_verbose(True)
inplane_registration.run()
inplane_registration.print_statistics()
# inplane_registration._run_registration_pipeline_initialization()
# inplane_registration._apply_motion_correction()
stack_registered = inplane_registration.get_corrected_stack()
parameters = inplane_registration.get_parameters()
sitkh.show_sitk_image([stack.sitk, stack_corrupted.get_resampled_stack_from_slices(interpolator="Linear", resampling_grid=stack.sitk).sitk,
stack_registered.get_resampled_stack_from_slices(interpolator="Linear", resampling_grid=stack.sitk).sitk], label=["original", "corrupted", "recovered"])
# self.assertEqual(np.round(
# np.linalg.norm(nda_diff)
# , decimals = self.accuracy), 0)
# 2) Test slice transforms
slice_transforms_sitk = inplane_registration.get_slice_transforms_sitk()
stack_tmp = st.Stack.from_stack(stack_corrupted)
stack_tmp.update_motion_correction_of_slices(slice_transforms_sitk)
stack_diff_sitk = stack_tmp.get_resampled_stack_from_slices(
resampling_grid=stack.sitk).sitk - stack_registered.get_resampled_stack_from_slices(resampling_grid=stack.sitk).sitk
stack_diff_nda = sitk.GetArrayFromImage(stack_diff_sitk)
self.assertEqual(np.round(
np.linalg.norm(stack_diff_nda), decimals=8), 0)
def test_inplane_rigid_alignment_to_reference_multimodal(self):
filename_stack = "fetal_brain_0"
filename_recon = "FetalBrain_reconstruction_3stacks_myAlg"
stack_tmp = st.Stack.from_filename(
os.path.join(self.dir_test_data, filename_stack + ".nii.gz"),
os.path.join(self.dir_test_data, filename_stack + "_mask.nii.gz")
)
recon = st.Stack.from_filename(
os.path.join(self.dir_test_data, filename_recon)
)
recon_sitk = recon.get_resampled_stack_from_slices(
resampling_grid=stack_tmp.sitk, interpolator="Linear").sitk
stack = st.Stack.from_sitk_image(
recon_sitk, "original", stack_tmp.sitk_mask)
# recon_resampled_sitk = sitk.Resample(recon_sitk, stack_sitk)
# stack = st.Stack.from_sitk_image(recon_resampled_sitk, "original")
# Create in-plane motion corruption
scale = 1.05
angle_z = 0.05
center_2D = (0, 0)
translation_2D = np.array([1, -2])
intensity_scale = 1
intensity_bias = 0