def query_extract_region(fixed_image: sitk.Image, moving_image: sitk.Image,
transform: sitk.Transform,
registration_method: sitk.ImageRegistrationMethod):
do_extract = util.query_yes_no(
'Do you wish to extract a sub-region to register based on? [y/n] >> ')
if do_extract:
itkplt.plot_overlay(fixed_image, moving_image, transform=transform)
size = util.query_int('Enter the region size >> ')
origin = []
for dim in range(len(fixed_image.GetSpacing())):
origin_in_dim = util.query_float(
'Enter the origin in dimension {0} >> '.format(dim))
origin.append(origin_in_dim)
origin = np.array(origin)
fixed_region = extract_region(fixed_image, size, origin)
moving_region = extract_region(moving_image, size * 1.1,
origin - 0.05 * size, transform)
query_registration_sampling_change(registration_method)
return fixed_region, moving_region, do_extract
else:
return fixed_image, moving_image, do_extract
def query_rotation_change(fixed_image: sitk.Image, moving_image: sitk.Image,
initial_transform: sitk.Transform):
"""Ask if the user wants a new 2D ITK origin based on image overlay"""
itkplt.plot_overlay(fixed_image, moving_image, initial_transform)
change_rotation = util.query_yes_no(
'Do you want to change the rotation? [y/n] >> ')
if change_rotation:
while True:
rotation = util.query_float('Enter new rotation (degrees): ')
tran.set_transform_rotation(initial_transform, rotation)
itkplt.plot_overlay(fixed_image, moving_image, initial_transform,
rotation)
# bug: The image does not show up till after the question
if util.query_yes_no('Is this rotation good? [y/n] >> '): break
def query_good_registration(transform: sitk.Transform, metric, stop):
print('\nFinal metric value: {0}'.format(metric))
print('\n{0}'.format(stop))
transform_params = transform.GetParameters()
matrix = np.array([transform_params[0:2], transform_params[2:4]])
translation = np.array(transform_params[4:6])
print('\nTransform Matrix: \n{0}'.format(matrix))
print('\nTransform Translation: \n{0}'.format(translation))
return util.query_yes_no('Is this registration good? [y/n] >>> ')
def _check_for_output(self):
output_path = Path(
self.fuse_args['output_file_directory'].replace('[', '').replace(
']', ''), self.output_name)
if output_path.is_file():
if self.overwrite_tif is not None:
return not self.overwrite_tif
else:
return util.query_yes_no(
'{} already exists. Skip image fusion? >> '.format(
output_path))
else:
return False
def query_translation_change(fixed_image: sitk.Image, moving_image: sitk.Image,
transform: sitk.Transform):
"""Ask if the user wants a new 2D ITK translation based on image overlay"""
change_origin = util.query_yes_no(
'Do you want to change the initial translation? [y/n] >> ')
translation = tran.get_translation(transform)
if change_origin:
while True:
print('Current physical shift: ' + str(-1 * np.array(translation)))
new_translation = []
for dim in range(len(translation)):
new_dim_translation = -1 * util.query_float(
'Enter the new shift in dimension {0} >> '.format(
str(dim)))
new_translation.append(new_dim_translation)
tran.set_translation(transform, new_translation)
itkplt.plot_overlay(fixed_image, moving_image, transform)
# bug: The image does not show up till after the question
if util.query_yes_no('Is this translation good? [y/n] >>> '): break
def _check_for_xml(self):
"""
Check for the dataset.xml file and ask if the user wants to skip reading/resaving the .mat files.
:return: boolean whether to skip dataset definition or not.
"""
if self.intermediate_save_dir is not None:
xml_path = Path(self.intermediate_save_dir, 'dataset.xml')
if xml_path.is_file():
if self.overwrite_dataset is None:
return util.query_yes_no(
'XML file already exists. Skip reading .mat files? >> '
)
else:
return not self.overwrite_dataset
else:
return False
def query_registration_sampling_change(
registration_method: sitk.ImageRegistrationMethod):
"""
Ask the user if they want to change the registration sampling rate, and to what if they do.
:param registration_method: The registration method being used in the registration algorithm
:return:
"""
do_change = util.query_yes_no(
'Do you wish to change the registration sampling rate (default 0.01)? [y/n] >> '
)
if do_change:
while True:
new_rate = util.query_float('Please enter a rate >0 and <= 1 >> ')
if new_rate > 0 and new_rate <= 1:
break
print('{0} is an invalid rate'.format(new_rate))
registration_method.SetMetricSamplingPercentage(new_rate)
def setup_image(path_image: Path,
unit_workspace: str = 'microns',
write_changes: bool = True,
dimensions: int = 2):
"""
Read in an itk image and ensure that its spacing is in the right units/has been set in the first place
:param path_image: path to the image file
:param unit_workspace: unit that the workspace is working in
:param write_changes: Whether to save new metadata
:dimensions: Number of spatial dimensions for the image type
:return:
"""
image = sitk.ReadImage(str(path_image))
metadata = read_metadata(path_image)
if metadata is None:
print('{0} has no metadata.'.format(str(path_image.name)))
image.SetMetaData('Unit', unit_workspace)
current_spacing = image.GetSpacing()
change_spacing = util.query_yes_no(
'Change the spacing? Current spacing is {0} [y/n] >> '.format(
current_spacing))
if change_spacing:
spacing = _query_spacing(unit_workspace, dimensions)
image.SetSpacing(spacing)
if write_changes:
write_image(image, path_image)
else:
for key in metadata:
image.SetMetaData(key, metadata[key])
if len(image.GetSpacing()) > dimensions:
# todo: nd to rgb
image = three_d_to_rgb(image)
return image
def test_bad_input_then_yes(self, monkeypatch, user_input_fixture):
user_inputs = user_input_fixture(['5', 'y', 'test'])
assert util.query_yes_no(user_inputs) is True
def test_yes_no_inputs(self, input, expected, monkeypatch):
monkeypatch.setattr('builtins.input', lambda x: input)
assert util.query_yes_no('') is expected