SYMBOL INDEX (839 symbols across 84 files) FILE: niftymic/application/correct_bias_field.py function main (line 23) | def main(): FILE: niftymic/application/correct_intensities.py function main (line 24) | def main(): FILE: niftymic/application/multiply.py function main (line 18) | def main(): FILE: niftymic/application/nifti2dicom.py function main (line 70) | def main(): FILE: niftymic/application/propagate_mask.py function main (line 26) | def main(): FILE: niftymic/application/reconstruct_volume.py function main (line 37) | def main(): FILE: niftymic/application/reconstruct_volume_from_slices.py function main (line 32) | def main(): FILE: niftymic/application/register_image.py function main (line 27) | def main(): FILE: niftymic/application/rsfmri_estimate_motion.py function main (line 33) | def main(): FILE: niftymic/application/rsfmri_reconstruct_volume_from_slices.py function main (line 33) | def main(): FILE: niftymic/application/run_reconstruction_parameter_study.py function main (line 24) | def main(): FILE: niftymic/application/run_reconstruction_pipeline.py function main (line 31) | def main(): FILE: niftymic/application/segment_fetal_brains.py function main (line 23) | def main(): FILE: niftymic/application/show_slice_coverage.py function main (line 21) | def main(): FILE: niftymic/base/data_reader.py class DataReader (line 34) | class DataReader(object): method read_data (line 38) | def read_data(self): method get_data (line 42) | def get_data(self): class ImageHeaderReader (line 46) | class ImageHeaderReader(DataReader): method __init__ (line 48) | def __init__(self, path_to_image): method read_data (line 52) | def read_data(self): method get_data (line 55) | def get_data(self): method get_niftymic_version (line 58) | def get_niftymic_version(self): class ImageDataReader (line 81) | class ImageDataReader(DataReader): method __init__ (line 84) | def __init__(self): method get_data (line 96) | def get_data(self): class ImageDirectoryReader (line 109) | class ImageDirectoryReader(ImageDataReader): method __init__ (line 126) | def __init__(self, method read_data (line 141) | def read_data(self): class MultipleImagesReader (line 198) | class MultipleImagesReader(ImageDataReader): method __init__ (line 219) | def __init__(self, method read_data (line 251) | def read_data(self): method _check_input (line 289) | def _check_input(self): method _get_path_to_potential_mask (line 307) | def _get_path_to_potential_mask(self, file_path): class ImageSlicesDirectoryReader (line 358) | class ImageSlicesDirectoryReader(ImageDataReader): method __init__ (line 373) | def __init__(self, method read_data (line 387) | def read_data(self): method get_slice_transforms_sitk (line 453) | def get_slice_transforms_sitk(self): class MultiComponentImageReader (line 461) | class MultiComponentImageReader(ImageDataReader): method __init__ (line 463) | def __init__(self, method read_data (line 479) | def read_data(self): class TransformationDataReader (line 527) | class TransformationDataReader(DataReader): method __init__ (line 530) | def __init__(self): method get_data (line 540) | def get_data(self): method _get_sitk_transform_from_filepath (line 543) | def _get_sitk_transform_from_filepath(self, path_to_sitk_transform): class SliceTransformationDirectoryReader (line 567) | class SliceTransformationDirectoryReader(TransformationDataReader): method __init__ (line 569) | def __init__(self, directory, suffix_slice="_slice"): method read_data (line 574) | def read_data(self): class TransformationDirectoryReader (line 603) | class TransformationDirectoryReader(TransformationDataReader): method __init__ (line 605) | def __init__(self, directory): method read_data (line 621) | def read_data(self, extension="tfm"): class MultipleTransformationsReader (line 640) | class MultipleTransformationsReader(TransformationDataReader): method __init__ (line 642) | def __init__(self, file_paths): method read_data (line 654) | def read_data(self): FILE: niftymic/base/data_writer.py class DataWriter (line 21) | class DataWriter(object): method _get_header_update (line 37) | def _get_header_update(description=None): method write_image (line 51) | def write_image( method write_mask (line 72) | def write_mask( class StacksWriter (line 93) | class StacksWriter(object): method __init__ (line 96) | def __init__(self, stacks): method set_stacks (line 99) | def set_stacks(self, stacks): method write_data (line 103) | def write_data(self): class MultipleStacksWriter (line 107) | class MultipleStacksWriter(StacksWriter): method __init__ (line 109) | def __init__(self, method set_directory (line 125) | def set_directory(self, directory): method write_data (line 128) | def write_data(self): class MultiComponentImageWriter (line 137) | class MultiComponentImageWriter(StacksWriter): method __init__ (line 139) | def __init__(self, method set_filename (line 155) | def set_filename(self, filename): method write_data (line 158) | def write_data(self): FILE: niftymic/base/exceptions.py class InputFilesNotValid (line 14) | class InputFilesNotValid(Exception): method __init__ (line 22) | def __init__(self, directory): method __str__ (line 25) | def __str__(self): class ObjectNotCreated (line 36) | class ObjectNotCreated(Exception): method __init__ (line 45) | def __init__(self, function_call): method __str__ (line 48) | def __str__(self): class FileNotExistent (line 57) | class FileNotExistent(Exception): method __init__ (line 66) | def __init__(self, missing_file): method __str__ (line 69) | def __str__(self): class DirectoryNotExistent (line 78) | class DirectoryNotExistent(Exception): method __init__ (line 87) | def __init__(self, missing_directory): method __str__ (line 90) | def __str__(self): class FilenameAmbiguous (line 100) | class FilenameAmbiguous(Exception): method __init__ (line 109) | def __init__(self, ambiguous_filename): method __str__ (line 112) | def __str__(self): class IOError (line 120) | class IOError(Exception): method __init__ (line 129) | def __init__(self, error): method __str__ (line 132) | def __str__(self): FILE: niftymic/base/psf.py class PSF (line 16) | class PSF: method get_covariance_matrix_in_reconstruction_space (line 31) | def get_covariance_matrix_in_reconstruction_space( method get_covariance_matrix_in_reconstruction_space_sitk (line 57) | def get_covariance_matrix_in_reconstruction_space_sitk( method get_predefined_covariance_matrix_in_reconstruction_space (line 91) | def get_predefined_covariance_matrix_in_reconstruction_space( method get_gaussian_psf_covariance_matrix_from_spacing (line 120) | def get_gaussian_psf_covariance_matrix_from_spacing(spacing): method _get_relative_rotation_matrix (line 144) | def _get_relative_rotation_matrix(slice_direction_sitk, FILE: niftymic/base/slice.py class Slice (line 24) | class Slice: method from_sitk_image (line 32) | def from_sitk_image(cls, method from_filename (line 112) | def from_filename(cls, method from_slice (line 176) | def from_slice(cls, slice_to_copy): method update_motion_correction (line 222) | def update_motion_correction(self, affine_transform_sitk): method get_filename (line 257) | def get_filename(self): method set_filename (line 260) | def set_filename(self, filename): method get_slice_number (line 265) | def get_slice_number(self): method get_slice_thickness (line 268) | def get_slice_thickness(self): method get_inplane_resolution (line 271) | def get_inplane_resolution(self): method get_directory (line 276) | def get_directory(self): method get_affine_transform (line 282) | def get_affine_transform(self): method get_motion_correction_transform (line 293) | def get_motion_correction_transform(self): method get_registration_history (line 300) | def get_registration_history(self): method set_registration_history (line 305) | def set_registration_history(self, registration_history): method show (line 314) | def show(self, show_segmentation=0, label=None, viewer=VIEWER, verbose... method write (line 336) | def write(self, method _update_affine_transform (line 398) | def _update_affine_transform(self, affine_transform_sitk): method _generate_identity_mask (line 464) | def _generate_identity_mask(self): FILE: niftymic/base/stack.py class Stack (line 30) | class Stack: method __init__ (line 32) | def __init__(self): method from_filename (line 49) | def from_filename(cls, method from_slice_filenames (line 170) | def from_slice_filenames(cls, method from_sitk_image (line 285) | def from_sitk_image(cls, method from_stack (line 361) | def from_stack(cls, stack_to_copy, filename=None): method get_slices (line 418) | def get_slices(self): method get_slice (line 433) | def get_slice(self, index): method get_slice_thickness (line 443) | def get_slice_thickness(self): method get_inplane_resolution (line 446) | def get_inplane_resolution(self): method get_deleted_slice_numbers (line 459) | def get_deleted_slice_numbers(self): method set_slice (line 470) | def set_slice(self, slice, index): method delete_slice (line 492) | def delete_slice(self, slice): method get_deleted_slice_numbers (line 504) | def get_deleted_slice_numbers(self): method get_directory (line 510) | def get_directory(self): method set_filename (line 513) | def set_filename(self, filename): method get_filename (line 523) | def get_filename(self): method get_registration_history (line 530) | def get_registration_history(self): method set_registration_history (line 535) | def set_registration_history(self, registration_history): method get_number_of_slices (line 544) | def get_number_of_slices(self): method is_unity_mask (line 547) | def is_unity_mask(self): method show (line 552) | def show(self, show_segmentation=0, label=None, viewer=VIEWER, verbose... method show_slices (line 569) | def show_slices(self): method write (line 579) | def write(self, method update_motion_correction (line 669) | def update_motion_correction(self, affine_transform_sitk): method update_motion_correction_of_slices (line 697) | def update_motion_correction_of_slices(self, affine_transforms_sitk): method _update_affine_transform (line 708) | def _update_affine_transform(self, affine_transform_sitk): method get_resampled_stack_from_slices (line 756) | def get_resampled_stack_from_slices(self, resampling_grid=None, interp... method get_resampled_stack (line 875) | def get_resampled_stack(self, resampling_grid=None, spacing=None, inte... method get_stack_multiplied_with_mask (line 949) | def get_stack_multiplied_with_mask(self, filename=None, mask_sitk=None): method get_isotropically_resampled_stack_from_slices (line 972) | def get_isotropically_resampled_stack_from_slices(self, resolution=Non... method get_isotropically_resampled_stack (line 1048) | def get_isotropically_resampled_stack(self, resolution=None, interpola... method get_increased_stack (line 1106) | def get_increased_stack(self, extra_slices_z=0): method get_cropped_stack_based_on_mask (line 1150) | def get_cropped_stack_based_on_mask(self, boundary_i=0, boundary_j=0, ... method _get_rectangular_masked_region (line 1199) | def _get_rectangular_masked_region(self, mask_sitk): method _crop_image_to_region (line 1247) | def _crop_image_to_region(self, image_sitk, range_x, range_y, range_z): method _extract_slices (line 1259) | def _extract_slices(self, slice_thickness, slice_numbers=None): method _generate_identity_mask (line 1285) | def _generate_identity_mask(self): FILE: niftymic/reconstruction/admm_solver.py class ADMMSolver (line 26) | class ADMMSolver(Solver): method __init__ (line 53) | def __init__(self, method set_rho (line 100) | def set_rho(self, rho): method get_rho (line 105) | def get_rho(self): method set_iterations (line 114) | def set_iterations(self, iterations): method get_iterations (line 119) | def get_iterations(self): method get_setting_specific_filename (line 132) | def get_setting_specific_filename(self, prefix="SRR_"): method get_solver (line 151) | def get_solver(self): method _run (line 201) | def _run(self): method _print_info_text (line 219) | def _print_info_text(self): FILE: niftymic/reconstruction/linear_operators.py class LinearOperators (line 26) | class LinearOperators(object): method __init__ (line 44) | def __init__(self, method A_itk (line 111) | def A_itk(self, reconstruction_itk, slice_itk, slice_spacing): method A (line 150) | def A(self, reconstruction, stack_slice, interpolator_mask="Linear"): method A_adj_itk (line 219) | def A_adj_itk(self, slice_itk, reconstruction_itk, slice_spacing): method M_itk (line 249) | def M_itk(self, image_itk, image_itk_mask): method _get_covariance_full_3d (line 261) | def _get_covariance_full_3d( method _get_covariance_only_in_plane (line 280) | def _get_covariance_only_in_plane( method _get_covariance_predefined (line 303) | def _get_covariance_predefined( FILE: niftymic/reconstruction/primal_dual_solver.py class PrimalDualSolver (line 34) | class PrimalDualSolver(Solver): method __init__ (line 36) | def __init__(self, method get_setting_specific_filename (line 86) | def get_setting_specific_filename(self, prefix="SRR_"): method get_solver (line 111) | def get_solver(self): method _run (line 173) | def _run(self, verbose=0): method _print_info_text (line 191) | def _print_info_text(self): FILE: niftymic/reconstruction/scattered_data_approximation.py class ScatteredDataApproximation (line 26) | class ScatteredDataApproximation: method __init__ (line 45) | def __init__(self, method set_sigma (line 90) | def set_sigma(self, sigma): method set_stacks (line 93) | def set_stacks(self, stacks): method set_sigma_array (line 107) | def set_sigma_array(self, sigma_array): method get_sigma_array (line 116) | def get_sigma_array(self): method set_approach (line 122) | def set_approach(self, sda_approach): method get_approach (line 131) | def get_approach(self): method get_reconstruction (line 136) | def get_reconstruction(self): method get_setting_specific_filename (line 139) | def get_setting_specific_filename(self, prefix="SDA_"): method get_computational_time (line 161) | def get_computational_time(self): method run (line 166) | def run(self): method generate_mask_from_stack_mask_unions (line 191) | def generate_mask_from_stack_mask_unions(self, method generate_mask_from_stack_mask_intersections (line 246) | def generate_mask_from_stack_mask_intersections(self, method _get_image_slice (line 294) | def _get_image_slice(slice): method _get_masked_image_slice (line 298) | def _get_masked_image_slice(slice): method _get_mask_slice (line 304) | def _get_mask_slice(slice): method _run_discrete_shepard_reconstruction (line 311) | def _run_discrete_shepard_reconstruction(self): method _run_discrete_shepard_based_on_Deriche_reconstruction (line 439) | def _run_discrete_shepard_based_on_Deriche_reconstruction(self): FILE: niftymic/reconstruction/solver.py class Solver (line 31) | class Solver(object): method __init__ (line 63) | def __init__(self, method set_stacks (line 148) | def set_stacks(self, stacks): method set_use_masks (line 168) | def set_use_masks(self, use_masks): method set_reconstruction (line 171) | def set_reconstruction(self, reconstruction): method set_alpha (line 191) | def set_alpha(self, alpha): method get_alpha (line 196) | def get_alpha(self): method set_iter_max (line 208) | def set_iter_max(self, iter_max): method get_iter_max (line 213) | def get_iter_max(self): method set_minimizer (line 223) | def set_minimizer(self, minimizer): method get_minimizer (line 226) | def get_minimizer(self): method set_data_loss (line 236) | def set_data_loss(self, data_loss): method set_huber_gamma (line 241) | def set_huber_gamma(self, huber_gamma): method get_huber_gamma (line 244) | def get_huber_gamma(self): method set_verbose (line 247) | def set_verbose(self, verbose): method get_verbose (line 250) | def get_verbose(self): method run (line 253) | def run(self): method get_reconstruction (line 260) | def get_reconstruction(self): method get_alpha_cut (line 265) | def get_alpha_cut(self): method get_computational_time (line 270) | def get_computational_time(self): method get_A (line 281) | def get_A(self): method get_A_adj (line 292) | def get_A_adj(self): method get_b (line 303) | def get_b(self): method get_x0 (line 315) | def get_x0(self): method get_x_scale (line 318) | def get_x_scale(self): method get_setting_specific_filename (line 332) | def get_setting_specific_filename(self, prefix=""): method _run (line 336) | def _run(self): method get_solver (line 340) | def get_solver(self): method get_predefined_covariance (line 351) | def get_predefined_covariance(self): method _get_M_y (line 366) | def _get_M_y(self): method _Mk_Ak (line 414) | def _Mk_Ak(self, reconstruction_itk, slice_k): method _Ak_adj_Mk (line 445) | def _Ak_adj_Mk(self, slice_itk, slice_k): method _MA (line 480) | def _MA(self, reconstruction_nda_vec): method _A_adj_M (line 530) | def _A_adj_M(self, stacked_slices_nda_vec): method _get_itk_image_from_array_vec (line 580) | def _get_itk_image_from_array_vec(self, nda_vec, image_itk_ref): FILE: niftymic/reconstruction/tikhonov_solver.py class TikhonovSolver (line 59) | class TikhonovSolver(Solver): method __init__ (line 93) | def __init__(self, method set_regularization_type (line 141) | def set_regularization_type(self, reg_type): method get_regularization_type (line 146) | def get_regularization_type(self): method get_setting_specific_filename (line 159) | def get_setting_specific_filename(self, prefix="SRR_"): method get_solver (line 180) | def get_solver(self): method _run (line 237) | def _run(self): method _print_info_text (line 255) | def _print_info_text(self): class TemporalTikhonovSolver (line 288) | class TemporalTikhonovSolver(object): method __init__ (line 290) | def __init__(self, method get_computational_time (line 344) | def get_computational_time(self): method get_reconstructions (line 347) | def get_reconstructions(self): method run (line 350) | def run(self): method _A_fw (line 429) | def _A_fw(self, x, sqrt_alpha, sqrt_beta): method _A_bw (line 463) | def _A_bw(self, b, sqrt_alpha, sqrt_beta): method _get_reconstructions (line 504) | def _get_reconstructions(self, x): method _print_info_text (line 521) | def _print_info_text(self): method get_setting_specific_filename (line 555) | def get_setting_specific_filename(self, prefix="SRR_"): FILE: niftymic/registration/flirt.py class FLIRT (line 27) | class FLIRT(AffineRegistrationMethod): method __init__ (line 29) | def __init__(self, method set_options (line 60) | def set_options(self, options): method get_options (line 71) | def get_options(self): method _run (line 74) | def _run(self): method _get_warped_moving_sitk (line 106) | def _get_warped_moving_sitk(self): FILE: niftymic/registration/intra_stack_registration.py class IntraStackRegistration (line 26) | class IntraStackRegistration(StackRegistrationBase): method __init__ (line 126) | def __init__(self, method set_transform_type (line 277) | def set_transform_type(self, transform_type): method get_transform_type (line 284) | def get_transform_type(self): method set_intensity_correction_type_slice_neighbour_fit (line 294) | def set_intensity_correction_type_slice_neighbour_fit(self, intensity_... method get_intensity_correction_type_slice_neighbour_fit (line 303) | def get_intensity_correction_type_slice_neighbour_fit(self): method set_intensity_correction_type_reference_fit (line 313) | def set_intensity_correction_type_reference_fit(self, intensity_correc... method get_intensity_correction_type_reference_fit (line 323) | def get_intensity_correction_type_reference_fit(self): method set_intensity_correction_initializer_type (line 336) | def set_intensity_correction_initializer_type(self, intensity_correcti... method get_intensity_correction_initializer_type (line 346) | def get_intensity_correction_initializer_type(self): method set_prior_scale (line 356) | def set_prior_scale(self, prior_scale): method set_prior_intensity_coefficients (line 360) | def set_prior_intensity_coefficients(self, coefficients): method set_image_transform_reference_fit_term (line 377) | def set_image_transform_reference_fit_term(self, image_transform_refer... method use_stack_mask_reference_fit_term (line 386) | def use_stack_mask_reference_fit_term(self, flag): method use_stack_mask_neighbour_fit_term (line 389) | def use_stack_mask_neighbour_fit_term(self, flag): method get_final_cost (line 392) | def get_final_cost(self): method print_statistics (line 397) | def print_statistics(self): method get_setting_specific_filename (line 418) | def get_setting_specific_filename(self, prefix="_"): method _print_info_text_least_squares (line 452) | def _print_info_text_least_squares(self): method _print_info_text_minimize (line 460) | def _print_info_text_minimize(self): method _print_into_text_common (line 468) | def _print_into_text_common(self): method _run_registration_pipeline_initialization (line 501) | def _run_registration_pipeline_initialization(self): method _get_residual_call (line 672) | def _get_residual_call(self): method _get_jacobian_residual_call (line 784) | def _get_jacobian_residual_call(self): method _get_residual_reference_fit (line 897) | def _get_residual_reference_fit(self, method _get_jacobian_residual_reference_fit (line 970) | def _get_jacobian_residual_reference_fit(self, method _get_residual_slice_neighbours_fit (line 1081) | def _get_residual_slice_neighbours_fit(self, parameters_vec): method _get_jacobian_residual_slice_neighbours_fit (line 1175) | def _get_jacobian_residual_slice_neighbours_fit(self, parameters_vec): method _get_jacobian_slice_in_slice_neighbours_fit (line 1247) | def _get_jacobian_slice_in_slice_neighbours_fit(self, method _get_gradient_with_respect_to_transform_parameters (line 1303) | def _get_gradient_with_respect_to_transform_parameters(self, method _get_gradient_image_nda_from_sitk_image (line 1323) | def _get_gradient_image_nda_from_sitk_image(self, slice_sitk): method _get_residual_scale (line 1381) | def _get_residual_scale(self, parameters_vec): method _get_jacobian_residual_scale (line 1390) | def _get_jacobian_residual_scale(self, parameters_vec): method _get_residual_intensity_coefficients_None (line 1410) | def _get_residual_intensity_coefficients_None(self, parameters_vec): method _get_jacobian_residual_intensity_coefficients_None (line 1413) | def _get_jacobian_residual_intensity_coefficients_None(self, method _get_residual_intensity_coefficients_linear (line 1417) | def _get_residual_intensity_coefficients_linear(self, parameters_vec): method _get_jacobian_residual_intensity_coefficients_linear (line 1427) | def _get_jacobian_residual_intensity_coefficients_linear(self, method _get_residual_intensity_coefficients_affine (line 1439) | def _get_residual_intensity_coefficients_affine(self, parameters_vec): method _get_jacobian_residual_intensity_coefficients_affine (line 1449) | def _get_jacobian_residual_intensity_coefficients_affine(self, method _apply_image_transform_identity (line 1471) | def _apply_image_transform_identity(self, slice_2D_sitk): method _apply_image_transform_dx (line 1474) | def _apply_image_transform_dx(self, slice_2D_sitk): method _apply_image_transform_dy (line 1480) | def _apply_image_transform_dy(self, slice_2D_sitk): method _apply_image_transform_gradient_magnitude (line 1486) | def _apply_image_transform_gradient_magnitude(self, slice_2D_sitk): method _get_dx_image_sitk (line 1494) | def _get_dx_image_sitk(self, image_sitk): method _get_dy_image_sitk (line 1500) | def _get_dy_image_sitk(self, image_sitk): method _compute_statistics_residuals_ell2 (line 1514) | def _compute_statistics_residuals_ell2(self): method _get_initial_transforms_and_parameters_identity (line 1548) | def _get_initial_transforms_and_parameters_identity(self): method _get_initial_transforms_and_parameters_geometry_moments (line 1571) | def _get_initial_transforms_and_parameters_geometry_moments(self): method _get_initial_intensity_correction_parameters_None (line 1704) | def _get_initial_intensity_correction_parameters_None(self): method _get_initial_intensity_correction_parameters_linear (line 1717) | def _get_initial_intensity_correction_parameters_linear(self): method _get_initial_intensity_correction_parameters_affine (line 1745) | def _get_initial_intensity_correction_parameters_affine(self): method _apply_intensity_correction_None (line 1775) | def _apply_intensity_correction_None(self, method _apply_intensity_correction_linear (line 1780) | def _apply_intensity_correction_linear(self, method _apply_intensity_correction_affine (line 1785) | def _apply_intensity_correction_affine(self, method _add_gradient_with_respect_to_intensity_correction_parameters_None (line 1803) | def _add_gradient_with_respect_to_intensity_correction_parameters_None( method _add_gradient_with_respect_to_intensity_correction_parameters_linear (line 1809) | def _add_gradient_with_respect_to_intensity_correction_parameters_linear( method _add_gradient_with_respect_to_intensity_correction_parameters_affine (line 1822) | def _add_gradient_with_respect_to_intensity_correction_parameters_affine( method _get_projected_2D_slices_of_stack (line 1850) | def _get_projected_2D_slices_of_stack(self, method _get_TPP_transform (line 1969) | def _get_TPP_transform(self, slice_sitk): method _new_rigid_transform_sitk (line 1984) | def _new_rigid_transform_sitk(self): method _new_rigid_transform_itk (line 1987) | def _new_rigid_transform_itk(self): method _new_similarity_transform_sitk (line 1990) | def _new_similarity_transform_sitk(self): method _new_similarity_transform_itk (line 1993) | def _new_similarity_transform_itk(self): method _new_affine_transform_sitk (line 1996) | def _new_affine_transform_sitk(self): method _new_affine_transform_itk (line 1999) | def _new_affine_transform_itk(self): method _apply_motion_correction (line 2011) | def _apply_motion_correction(self): method _apply_rigid_motion_correction_and_compute_slice_transforms (line 2023) | def _apply_rigid_motion_correction_and_compute_slice_transforms(self): method _apply_similarity_motion_correction_and_compute_slice_transforms (line 2074) | def _apply_similarity_motion_correction_and_compute_slice_transforms(s... method _apply_affine_motion_correction_and_compute_slice_transforms (line 2165) | def _apply_affine_motion_correction_and_compute_slice_transforms(self): method _get_3D_from_2D_rigid_transform_sitk (line 2219) | def _get_3D_from_2D_rigid_transform_sitk(self, rigid_transform_2D_sitk): method _get_3D_from_2D_affine_transform_sitk (line 2253) | def _get_3D_from_2D_affine_transform_sitk(self, affine_transform_2D_si... FILE: niftymic/registration/niftyreg.py class RegAladin (line 26) | class RegAladin(AffineRegistrationMethod): method __init__ (line 28) | def __init__(self, method set_options (line 59) | def set_options(self, options): method get_options (line 70) | def get_options(self): method _run (line 73) | def _run(self): method _get_warped_moving_sitk (line 112) | def _get_warped_moving_sitk(self): class RegF3D (line 116) | class RegF3D(RegistrationMethod): method __init__ (line 118) | def __init__(self, method set_options (line 143) | def set_options(self, options): method get_options (line 154) | def get_options(self): method _run (line 157) | def _run(self): method get_warped_moving (line 193) | def get_warped_moving(self): FILE: niftymic/registration/registration_method.py class RegistrationMethod (line 24) | class RegistrationMethod(object): method __init__ (line 39) | def __init__(self, method set_fixed (line 62) | def set_fixed(self, fixed): method get_fixed (line 73) | def get_fixed(self): method set_moving (line 84) | def set_moving(self, moving): method get_moving (line 95) | def get_moving(self): method use_fixed_mask (line 105) | def use_fixed_mask(self, use_fixed_mask): method use_moving_mask (line 115) | def use_moving_mask(self, use_moving_mask): method use_verbose (line 125) | def use_verbose(self, use_verbose): method get_computational_time (line 136) | def get_computational_time(self): method get_registration_transform_sitk (line 147) | def get_registration_transform_sitk(self): method run (line 156) | def run(self): method _run (line 179) | def _run(self): method get_warped_moving (line 192) | def get_warped_moving(self): class AffineRegistrationMethod (line 200) | class AffineRegistrationMethod(RegistrationMethod): method __init__ (line 215) | def __init__(self, method set_registration_type (line 240) | def set_registration_type(self, registration_type): method get_registration_type (line 254) | def get_registration_type(self): method get_warped_moving (line 266) | def get_warped_moving(self): method get_transformed_fixed (line 304) | def get_transformed_fixed(self): method _get_warped_moving_sitk (line 310) | def _get_warped_moving_sitk(self): FILE: niftymic/registration/simple_itk_registration.py class SimpleItkRegistration (line 33) | class SimpleItkRegistration(AffineRegistrationMethod): method __init__ (line 35) | def __init__( method use_multiresolution_framework (line 99) | def use_multiresolution_framework(self, flag): method use_oriented_psf (line 106) | def use_oriented_psf(self, flag): method set_initializer_type (line 111) | def set_initializer_type(self, initializer_type): method get_initializer_type (line 119) | def get_initializer_type(self): method set_interpolator (line 124) | def set_interpolator(self, interpolator_type): method get_interpolator (line 129) | def get_interpolator(self): method set_metric (line 132) | def set_metric(self, metric): method set_metric_params (line 135) | def set_metric_params(self, metric_params): method set_optimizer (line 138) | def set_optimizer(self, optimizer): method set_optimizer_params (line 141) | def set_optimizer_params(self, optimizer_params): method set_scales_estimator (line 146) | def set_scales_estimator(self, scales_estimator): method _run (line 153) | def _run(self): method _get_warped_moving_sitk (line 223) | def _get_warped_moving_sitk(self): FILE: niftymic/registration/stack_registration_base.py class StackRegistrationBase (line 38) | class StackRegistrationBase(object): method __init__ (line 82) | def __init__(self, method set_stack (line 158) | def set_stack(self, stack): method get_stack (line 162) | def get_stack(self): method set_reference (line 172) | def set_reference(self, reference): method get_reference (line 175) | def get_reference(self): method use_stack_mask (line 186) | def use_stack_mask(self, flag): method use_reference_mask (line 197) | def use_reference_mask(self, flag): method use_verbose (line 207) | def use_verbose(self, flag): method use_parameter_normalization (line 217) | def use_parameter_normalization(self, flag): method set_transform_initializer_type (line 232) | def set_transform_initializer_type(self, transform_initializer_type): method get_transform_initializer_type (line 239) | def get_transform_initializer_type(self): method set_interpolator (line 249) | def set_interpolator(self, interpolator): method get_interpolator (line 253) | def get_interpolator(self): method set_alpha_neighbour (line 263) | def set_alpha_neighbour(self, alpha_neighbour): method get_alpha_neighbour (line 266) | def get_alpha_neighbour(self): method set_alpha_reference (line 277) | def set_alpha_reference(self, alpha_reference): method get_alpha_reference (line 280) | def get_alpha_reference(self): method set_alpha_parameter (line 292) | def set_alpha_parameter(self, alpha_parameter): method get_alpha_parameter (line 295) | def get_alpha_parameter(self): method set_optimizer (line 298) | def set_optimizer(self, optimizer): method get_optimizer (line 301) | def get_optimizer(self): method set_optimizer_iter_max (line 316) | def set_optimizer_iter_max(self, optimizer_iter_max): method get_optimizer_iter_max (line 319) | def get_optimizer_iter_max(self): method set_optimizer_loss (line 332) | def set_optimizer_loss(self, optimizer_loss): method get_optimizer_loss (line 339) | def get_optimizer_loss(self): method set_optimizer_method (line 351) | def set_optimizer_method(self, optimizer_method): method get_optimizer_method (line 358) | def get_optimizer_method(self): method get_parameters (line 369) | def get_parameters(self): method get_corrected_stack (line 380) | def get_corrected_stack(self): method get_slice_transforms_sitk (line 404) | def get_slice_transforms_sitk(self): method print_statistics (line 413) | def print_statistics(self): method run (line 428) | def run(self): method _run_optimizer_least_squares (line 538) | def _run_optimizer_least_squares(self, fun, jac, x0, method, loss, ite... method _run_optimizer_minimize (line 554) | def _run_optimizer_minimize(self, fun, jac, x0, method, loss, iter_max... method _print_info_text_least_squares (line 576) | def _print_info_text_least_squares(self): method _print_info_text_minimize (line 580) | def _print_info_text_minimize(self): method _run_registration_pipeline_initialization (line 592) | def _run_registration_pipeline_initialization(self): method _get_residual_call (line 605) | def _get_residual_call(self): method _get_initial_transforms_and_parameters_identity (line 617) | def _get_initial_transforms_and_parameters_identity(self): method _get_initial_transforms_and_parameters_geometry_moments (line 631) | def _get_initial_transforms_and_parameters_geometry_moments(self): method _apply_motion_correction (line 643) | def _apply_motion_correction(self): FILE: niftymic/registration/transform_initializer.py class TransformInitializer (line 29) | class TransformInitializer(object): method __init__ (line 31) | def __init__(self, method get_transform_sitk (line 50) | def get_transform_sitk(self): method run (line 53) | def run(self, debug=False): method get_pca_from_mask (line 95) | def get_pca_from_mask(mask_sitk, robust=False): method _get_best_transform (line 123) | def _get_best_transform(self, transformations, debug=False): method _run_registrations (line 179) | def _run_registrations(self, transformations): FILE: niftymic/registration/wrap_itk_registration.py class WrapItkRegistration (line 33) | class WrapItkRegistration(SimpleItkRegistration): method __init__ (line 35) | def __init__( method _run (line 92) | def _run(self): FILE: niftymic/utilities/binary_mask_from_mask_srr_estimator.py class BinaryMaskFromMaskSRREstimator (line 25) | class BinaryMaskFromMaskSRREstimator(object): method __init__ (line 27) | def __init__(self, method get_mask_sitk (line 47) | def get_mask_sitk(self): method run (line 50) | def run(self): FILE: niftymic/utilities/brain_stripping.py class BrainStripping (line 29) | class BrainStripping(object): method __init__ (line 44) | def __init__(self, method from_filename (line 81) | def from_filename(cls, method from_sitk_image (line 115) | def from_sitk_image(cls, method from_stack (line 146) | def from_stack(cls, method set_input_image_sitk (line 171) | def set_input_image_sitk(self, sitk_image): method compute_brain_image (line 181) | def compute_brain_image(self, compute_brain_image): method compute_brain_mask (line 191) | def compute_brain_mask(self, compute_brain_mask): method compute_skull_image (line 201) | def compute_skull_image(self, compute_skull_image): method set_bet_options (line 211) | def set_bet_options(self, bet_options): method get_input_image_sitk (line 222) | def get_input_image_sitk(self): method get_brain_masked_stack (line 238) | def get_brain_masked_stack(self, filename="Unknown", extract_slices=Fa... method get_brain_image_sitk (line 262) | def get_brain_image_sitk(self): method get_brain_mask_sitk (line 277) | def get_brain_mask_sitk(self, dilate_radius=0): method get_skull_mask_sitk (line 311) | def get_skull_mask_sitk(self, method get_mask_around_skull (line 358) | def get_mask_around_skull(self, method run (line 414) | def run(self): method _run_bet_for_brain_stripping (line 424) | def _run_bet_for_brain_stripping(self, debug=0): FILE: niftymic/utilities/data_preprocessing.py class DataPreprocessing (line 21) | class DataPreprocessing: method __init__ (line 44) | def __init__(self, method use_N4BiasFieldCorrector (line 79) | def use_N4BiasFieldCorrector(self, flag): method run (line 88) | def run(self): method get_preprocessed_stacks (line 177) | def get_preprocessed_stacks(self): method get_computational_time (line 182) | def get_computational_time(self): method write_preprocessed_data (line 187) | def write_preprocessed_data(self, dir_output): FILE: niftymic/utilities/input_arparser.py class InputArgparser (line 38) | class InputArgparser(object): method __init__ (line 40) | def __init__(self, method get_parser (line 77) | def get_parser(self): method parse_args (line 80) | def parse_args(self): method print_arguments (line 88) | def print_arguments(self, args, title="Configuration:"): method log_config (line 117) | def log_config(self, method add_filename (line 172) | def add_filename( method add_filename_mask (line 182) | def add_filename_mask( method add_dir_input (line 192) | def add_dir_input( method add_dir_input_mc (line 202) | def add_dir_input_mc( method add_subfolder_motion_correction (line 213) | def add_subfolder_motion_correction( method add_subfolder_comparison (line 224) | def add_subfolder_comparison( method add_dir_inputs (line 235) | def add_dir_inputs( method add_filenames (line 246) | def add_filenames( method add_filenames_masks (line 256) | def add_filenames_masks( method add_label (line 266) | def add_label( method add_fixed (line 276) | def add_fixed( method add_fixed_mask (line 286) | def add_fixed_mask( method add_moving (line 296) | def add_moving( method add_moving_mask (line 307) | def add_moving_mask( method add_metric (line 317) | def add_metric( method add_metric_radius (line 327) | def add_metric_radius( method add_labels (line 337) | def add_labels( method add_image_selection (line 347) | def add_image_selection( method add_reference (line 358) | def add_reference( method add_reference_mask (line 368) | def add_reference_mask( method add_output (line 378) | def add_output( method add_dir_output (line 388) | def add_dir_output( method add_suffix_mask (line 398) | def add_suffix_mask( method add_use_masks_srr (line 412) | def add_use_masks_srr( method add_outlier_rejection (line 423) | def add_outlier_rejection( method add_boundary_stacks (line 434) | def add_boundary_stacks( method add_prefix_output (line 447) | def add_prefix_output( method add_target_stack_index (line 457) | def add_target_stack_index( method add_target_stack (line 468) | def add_target_stack( method add_reconstruction (line 479) | def add_reconstruction( method add_reconstruction_space (line 490) | def add_reconstruction_space( method add_gestational_age (line 501) | def add_gestational_age( method add_search_angle (line 512) | def add_search_angle( method add_multiresolution (line 521) | def add_multiresolution( method add_shrink_factors (line 530) | def add_shrink_factors( method add_smoothing_sigmas (line 540) | def add_smoothing_sigmas( method add_two_step_cycles (line 550) | def add_two_step_cycles( method add_sigma (line 561) | def add_sigma( method add_minimizer (line 571) | def add_minimizer( method add_alpha (line 584) | def add_alpha( method add_alpha_first (line 595) | def add_alpha_first( method add_threshold (line 605) | def add_threshold( method add_threshold_first (line 615) | def add_threshold_first( method add_s2v_smoothing (line 625) | def add_s2v_smoothing( method add_interleave (line 634) | def add_interleave( method add_iter_max (line 643) | def add_iter_max( method add_iter_max_first (line 652) | def add_iter_max_first( method add_rho (line 662) | def add_rho( method add_iterations (line 672) | def add_iterations( method add_tv_solver (line 681) | def add_tv_solver( method add_data_loss (line 690) | def add_data_loss( method add_data_loss_scale (line 701) | def add_data_loss_scale( method add_pd_alg_type (line 714) | def add_pd_alg_type( method add_dilation_radius (line 726) | def add_dilation_radius( method add_extra_frame_target (line 737) | def add_extra_frame_target( method add_bias_field_correction (line 747) | def add_bias_field_correction( method add_intensity_correction (line 757) | def add_intensity_correction( method add_isotropic_resolution (line 767) | def add_isotropic_resolution( method add_log_config (line 778) | def add_log_config( method add_write_motion_correction (line 787) | def add_write_motion_correction( method add_provide_comparison (line 799) | def add_provide_comparison( method add_verbose (line 816) | def add_verbose( method add_option (line 825) | def add_option( method add_argument (line 836) | def add_argument( method add_psf_aware (line 843) | def add_psf_aware( method add_stack_recon_range (line 852) | def add_stack_recon_range( method add_alphas (line 861) | def add_alphas( method add_data_losses (line 872) | def add_data_losses( method add_data_loss_scales (line 882) | def add_data_loss_scales( method add_study_name (line 893) | def add_study_name( method add_measures (line 903) | def add_measures( method add_reconstruction_type (line 916) | def add_reconstruction_type( method add_interpolator (line 927) | def add_interpolator( method add_slice_thicknesses (line 937) | def add_slice_thicknesses( method add_viewer (line 950) | def add_viewer( method add_v2v_method (line 961) | def add_v2v_method( method _parse_config_file (line 985) | def _parse_config_file(self): method _add_argument (line 1033) | def _add_argument(self, allvars): FILE: niftymic/utilities/intensity_correction.py class IntensityCorrection (line 28) | class IntensityCorrection(object): method __init__ (line 51) | def __init__(self, method set_stack (line 102) | def set_stack(self, stack): method set_reference (line 112) | def set_reference(self, reference): method set_additional_stack (line 124) | def set_additional_stack(self, additional_stack): method use_verbose (line 134) | def use_verbose(self, verbose): method use_reference_mask (line 137) | def use_reference_mask(self, use_reference_mask): method use_stack_mask (line 140) | def use_stack_mask(self, use_stack_mask): method use_individual_slice_correction (line 150) | def use_individual_slice_correction(self, flag): method get_intensity_corrected_stack (line 161) | def get_intensity_corrected_stack(self): method get_intensity_corrected_additional_stack (line 166) | def get_intensity_corrected_additional_stack(self): method get_intensity_correction_coefficients (line 179) | def get_intensity_correction_coefficients(self): method run_lower_percentile_capping_of_stack (line 189) | def run_lower_percentile_capping_of_stack(self, percentile=10): method run_linear_intensity_correction (line 226) | def run_linear_intensity_correction(self): method run_affine_intensity_correction (line 239) | def run_affine_intensity_correction(self): method _run_intensity_correction (line 251) | def _run_intensity_correction(self, correction_model): method _apply_affine_intensity_correction (line 324) | def _apply_affine_intensity_correction(self, nda, nda_reference, nda_m... method _apply_linear_intensity_correction (line 365) | def _apply_linear_intensity_correction(self, nda, nda_reference, nda_m... method _get_data_arrays_prior_to_intensity_correction (line 399) | def _get_data_arrays_prior_to_intensity_correction(self): method _create_stack_from_corrected_intensity_array (line 447) | def _create_stack_from_corrected_intensity_array(self, nda, stack): FILE: niftymic/utilities/joint_image_mask_builder.py class JointImageMaskBuilder (line 16) | class JointImageMaskBuilder(object): method __init__ (line 18) | def __init__(self, method run (line 33) | def run(self): method get_stack (line 67) | def get_stack(self): FILE: niftymic/utilities/motion_updater.py class MotionUpdater (line 38) | class MotionUpdater(object): method __init__ (line 57) | def __init__( method run (line 76) | def run(self, older_than_v3=False): method get_data (line 231) | def get_data(self): method _check_against_json_true (line 250) | def _check_against_json_true(self, stack_name, slice_number): method _check_against_json_false (line 272) | def _check_against_json_false(self, stack_name, slice_number): FILE: niftymic/utilities/n4_bias_field_correction.py class N4BiasFieldCorrection (line 27) | class N4BiasFieldCorrection(object): method __init__ (line 29) | def __init__(self, method set_stack (line 50) | def set_stack(self, stack): method get_bias_field_corrected_stack (line 53) | def get_bias_field_corrected_stack(self): method get_computational_time (line 56) | def get_computational_time(self): method run_bias_field_correction (line 59) | def run_bias_field_correction(self): FILE: niftymic/utilities/outlier_rejector.py class OutlierRejector (line 24) | class OutlierRejector(object): method __init__ (line 26) | def __init__(self, method get_stacks (line 44) | def get_stacks(self): method run (line 47) | def run(self): FILE: niftymic/utilities/parameter_normalization.py class ParameterNormalization (line 25) | class ParameterNormalization(object): method __init__ (line 36) | def __init__(self, parameters_array): method get_normalization_coefficients (line 59) | def get_normalization_coefficients(self): method compute_normalization_coefficients (line 70) | def compute_normalization_coefficients(self): method normalize_parameters (line 98) | def normalize_parameters(self, parameters): method denormalize_parameters (line 119) | def denormalize_parameters(self, parameters): FILE: niftymic/utilities/segmentation_propagation.py class SegmentationPropagation (line 27) | class SegmentationPropagation(object): method __init__ (line 30) | def __init__(self, method set_stack (line 55) | def set_stack(self, stack): method get_stack (line 58) | def get_stack(self): method set_template (line 61) | def set_template(self, template): method get_template (line 64) | def get_template(self): method set_dilation_radius (line 67) | def set_dilation_radius(self, dilation_radius): method get_dilation_radius (line 70) | def get_dilation_radius(self): method set_dilation_kernel (line 73) | def set_dilation_kernel(self, dilation_kernel): method get_dilation_kernel (line 79) | def get_dilation_kernel(self): method get_segmented_stack (line 82) | def get_segmented_stack(self): method get_registration_transform_sitk (line 94) | def get_registration_transform_sitk(self): method run_segmentation_propagation (line 97) | def run_segmentation_propagation(self): FILE: niftymic/utilities/siena.py class Siena (line 26) | class Siena(object): method __init__ (line 28) | def __init__(self, method run (line 41) | def run(self): method print_statistics (line 63) | def print_statistics(self): method _extract_percentage_brain_volume_change (line 74) | def _extract_percentage_brain_volume_change(self): method get_percentage_brain_volume_change (line 83) | def get_percentage_brain_volume_change(self): FILE: niftymic/utilities/stack_mask_morphological_operations.py class StackMaskMorphologicalOperations (line 25) | class StackMaskMorphologicalOperations(object): method __init__ (line 37) | def __init__(self, dilation_radius, dilation_kernel, use_dilation_in_p... method from_sitk_mask (line 44) | def from_sitk_mask(cls, mask_sitk=None, dilation_radius=0, dilation_ke... method from_stack (line 55) | def from_stack(cls, stack=None, dilation_radius=0, dilation_kernel="Ba... method set_mask_sitk (line 65) | def set_mask_sitk(self, mask_sitk): method get_mask_sitk (line 68) | def get_mask_sitk(self): method get_stack (line 71) | def get_stack(self): method set_dilation_radius (line 74) | def set_dilation_radius(self, dilation_radius): method get_dilation_radius (line 77) | def get_dilation_radius(self): method set_dilation_kernel (line 80) | def set_dilation_kernel(self, dilation_kernel): method get_dilation_kernel (line 86) | def get_dilation_kernel(self): method get_processed_mask_sitk (line 89) | def get_processed_mask_sitk(self): method get_processed_stack (line 92) | def get_processed_stack(self): method get_computational_time (line 98) | def get_computational_time(self): method run_dilation (line 101) | def run_dilation(self): FILE: niftymic/utilities/target_stack_estimator.py class TargetStackEstimator (line 25) | class TargetStackEstimator(object): method __init__ (line 27) | def __init__(self): method get_target_stack_index (line 43) | def get_target_stack_index(self): method get_computational_time (line 46) | def get_computational_time(self): method _compute_volume (line 50) | def _compute_volume(file_path): method _compute_singular_values (line 61) | def _compute_singular_values(stack): method _compute_motion_score_kainz2015 (line 85) | def _compute_motion_score_kainz2015( method _compute_motion_score_github (line 123) | def _compute_motion_score_github(sing_values, threshold=0.99): method from_volume (line 157) | def from_volume(cls, file_paths_masks): method from_motion_score (line 197) | def from_motion_score(cls, file_paths, file_paths_masks): FILE: niftymic/utilities/template_stack_estimator.py class TemplateStackEstimator (line 26) | class TemplateStackEstimator(object): method __init__ (line 28) | def __init__(self): method get_path_to_template (line 40) | def get_path_to_template(self): method get_estimated_gw (line 43) | def get_estimated_gw(self): method from_mask (line 54) | def from_mask(cls, file_path_mask): method get_largest_connected_region_mask (line 123) | def get_largest_connected_region_mask(mask_nda): FILE: niftymic/utilities/toolkit_executor.py class ToolkitExecuter (line 21) | class ToolkitExecuter(object): method __init__ (line 23) | def __init__(self, paths_to_images, paths_to_masks, dir_output): method get_function_call_irtk (line 45) | def get_function_call_irtk( method write_function_call_to_file (line 117) | def write_function_call_to_file(function_call, path_to_file): method _exe_to_fetch_slice_thickness (line 133) | def _exe_to_fetch_slice_thickness(self, paths_to_images): method _exe_dilate_masks (line 158) | def _exe_dilate_masks(self, kernel, paths_to_masks, label=1): FILE: niftymic/utilities/volumetric_reconstruction_pipeline.py class Pipeline (line 35) | class Pipeline(object): method __init__ (line 38) | def __init__(self, stacks, verbose, viewer): method set_stacks (line 45) | def set_stacks(self, stacks): method get_stacks (line 48) | def get_stacks(self): method set_verbose (line 51) | def set_verbose(self, verbose): method get_verbose (line 54) | def get_verbose(self): method get_computational_time (line 57) | def get_computational_time(self): method run (line 60) | def run(self): method _run (line 73) | def _run(self): class RegistrationPipeline (line 81) | class RegistrationPipeline(Pipeline): method __init__ (line 95) | def __init__(self, verbose, stacks, reference, registration_method, vi... method set_reference (line 102) | def set_reference(self, reference): method get_reference (line 105) | def get_reference(self): class VolumeToVolumeRegistration (line 113) | class VolumeToVolumeRegistration(RegistrationPipeline): method __init__ (line 125) | def __init__(self, method _run (line 143) | def _run(self): class SliceToVolumeRegistration (line 181) | class SliceToVolumeRegistration(RegistrationPipeline): method __init__ (line 196) | def __init__(self, method set_print_prefix (line 216) | def set_print_prefix(self, print_prefix): method _run (line 219) | def _run(self): class SliceSetToVolumeRegistration (line 261) | class SliceSetToVolumeRegistration(RegistrationPipeline): method __init__ (line 276) | def __init__(self, method _run (line 297) | def _run(self, debug=1): method _get_stack_subgroup (line 354) | def _get_stack_subgroup(self, indices): class ReconstructionRegistrationPipeline (line 411) | class ReconstructionRegistrationPipeline(RegistrationPipeline): method __init__ (line 430) | def __init__(self, method get_iterative_reconstructions (line 458) | def get_iterative_reconstructions(self): method get_computational_time_reconstruction (line 461) | def get_computational_time_reconstruction(self): method get_computational_time_registration (line 464) | def get_computational_time_registration(self): class TwoStepSliceToVolumeRegistrationReconstruction (line 473) | class TwoStepSliceToVolumeRegistrationReconstruction( method __init__ (line 499) | def __init__(self, method _run (line 546) | def _run(self): class HieararchicalSliceSetRegistration (line 657) | class HieararchicalSliceSetRegistration(RegistrationPipeline): method __init__ (line 672) | def __init__(self, method _run (line 693) | def _run(self, debug=0): method _recursive_split (line 744) | def _recursive_split(self, indices, indices_split, N_min): class MultiComponentReconstruction (line 768) | class MultiComponentReconstruction(Pipeline): method __init__ (line 781) | def __init__(self, method set_reconstruction_method (line 795) | def set_reconstruction_method(self, reconstruction_method): method get_reconstruction_method (line 798) | def get_reconstruction_method(self): method set_suffix (line 801) | def set_suffix(self, suffix): method get_suffix (line 804) | def get_suffix(self): method get_reconstructions (line 807) | def get_reconstructions(self): method _run (line 810) | def _run(self): FILE: niftymic/validation/evaluate_image_similarity.py function main (line 27) | def main(): FILE: niftymic/validation/evaluate_simulated_stack_similarity.py function main (line 25) | def main(): FILE: niftymic/validation/evaluate_slice_residual_similarity.py function main (line 25) | def main(): FILE: niftymic/validation/export_side_by_side_simulated_vs_original_slice_comparison.py function export_comparison_to_file (line 38) | def export_comparison_to_file(nda_original, function _export_image_side_by_side (line 74) | def _export_image_side_by_side( function _resize_image (line 122) | def _resize_image(path_to_file, resize): function _export_pdf_from_side_by_side_images (line 140) | def _export_pdf_from_side_by_side_images(directory, path_to_file, extens... function main (line 154) | def main(): FILE: niftymic/validation/image_similarity_evaluator.py class ImageSimilarityEvaluator (line 29) | class ImageSimilarityEvaluator(object): method __init__ (line 43) | def __init__( method set_stacks (line 69) | def set_stacks(self, stacks): method set_reference (line 79) | def set_reference(self, reference): method get_similarities (line 90) | def get_similarities(self): method get_measures (line 93) | def get_measures(self): method compute_similarities (line 105) | def compute_similarities(self): method write_similarities (line 154) | def write_similarities(self, directory): method read_similarities (line 193) | def read_similarities(self, directory): method _get_filename_paths (line 226) | def _get_filename_paths(self, directory): FILE: niftymic/validation/motion_evaluator.py class MotionEvaluator (line 29) | class MotionEvaluator(object): method __init__ (line 31) | def __init__(self, transforms_sitk): method run (line 56) | def run(self): method display (line 76) | def display(self, title=None, dir_output=None): method show (line 115) | def show(self, title=None, dir_output=None): method _get_scaled_params (line 168) | def _get_scaled_params(self, transform_params): method _replace_string (line 172) | def _replace_string(self, string): FILE: niftymic/validation/motion_simulator.py class MotionSimulator (line 18) | class MotionSimulator(object): method __init__ (line 21) | def __init__(self, dimension, verbose): method simulate_motion (line 27) | def simulate_motion(self): method get_transforms_sitk (line 30) | def get_transforms_sitk(self): method write_transforms_sitk (line 39) | def write_transforms_sitk(self, class RigidMotionSimulator (line 51) | class RigidMotionSimulator(MotionSimulator): method __init__ (line 54) | def __init__(self, dimension, verbose): class RandomRigidMotionSimulator (line 59) | class RandomRigidMotionSimulator(RigidMotionSimulator): method __init__ (line 61) | def __init__(self, method simulate_motion (line 71) | def simulate_motion(self, seed=None, simulations=1): FILE: niftymic/validation/residual_evaluator.py class ResidualEvaluator (line 34) | class ResidualEvaluator(object): method __init__ (line 49) | def __init__( method _get_original_number_of_slices (line 71) | def _get_original_number_of_slices(stack): method set_stacks (line 91) | def set_stacks(self, stacks): method set_reference (line 101) | def set_reference(self, reference): method get_measures (line 104) | def get_measures(self): method get_slice_similarities (line 121) | def get_slice_similarities(self): method get_slice_projections (line 135) | def get_slice_projections(self): method compute_slice_projections (line 147) | def compute_slice_projections(self): method evaluate_slice_similarities (line 182) | def evaluate_slice_similarities(self): method write_slice_similarities (line 255) | def write_slice_similarities(self, directory): method read_slice_similarities (line 283) | def read_slice_similarities(self, directory, ext="txt"): method show_slice_similarities (line 332) | def show_slice_similarities( FILE: niftymic/validation/show_evaluated_simulated_stack_similarity.py function main (line 31) | def main(): FILE: niftymic/validation/simulate_stacks_from_reconstruction.py function main (line 35) | def main(): FILE: niftymic/validation/slice_acquisition.py class SliceAcqusition (line 27) | class SliceAcqusition(object): method __init__ (line 30) | def __init__(self, method run (line 43) | def run(self): method _run (line 47) | def _run(self): method _get_interpolator (line 50) | def _get_interpolator(self, stack_slice): method get_output (line 70) | def get_output(self): class StaticSliceAcquisition (line 74) | class StaticSliceAcquisition(SliceAcqusition): method __init__ (line 76) | def __init__(self, method set_stack_slice (line 89) | def set_stack_slice(self, stack_slice): method _run (line 92) | def _run(self): FILE: niftymic/validation/slice_coverage.py class SliceCoverage (line 17) | class SliceCoverage(object): method __init__ (line 19) | def __init__(self, stacks, reconstruction_sitk): method get_coverage_sitk (line 34) | def get_coverage_sitk(self): method run (line 45) | def run(self): method _add_slice_contribution (line 72) | def _add_slice_contribution(slice, coverage_sitk): FILE: niftymic/validation/write_random_motion_transforms.py function main (line 15) | def main(): FILE: setup.py function install_requires (line 31) | def install_requires(fname="requirements.txt"): FILE: tests/brain_stripping_test.py class BrainStrippingTest (line 19) | class BrainStrippingTest(unittest.TestCase): method setUp (line 26) | def setUp(self): method test_01_input_output (line 32) | def test_01_input_output(self): method test_02_brain_mask (line 59) | def test_02_brain_mask(self): FILE: tests/case_study_fetal_brain_test.py class CaseStudyFetalBrainTest (line 21) | class CaseStudyFetalBrainTest(unittest.TestCase): method setUp (line 23) | def setUp(self): method test_reconstruct_volume (line 34) | def test_reconstruct_volume(self): method test_reconstruct_volume_from_slices (line 105) | def test_reconstruct_volume_from_slices(self): method test_register_image (line 140) | def test_register_image(self): FILE: tests/case_study_rsfmri_test.py class CaseStudyRestingStateFMRITest (line 24) | class CaseStudyRestingStateFMRITest(unittest.TestCase): method setUp (line 26) | def setUp(self): method test_estimate_motion (line 34) | def test_estimate_motion(self): method test_reconstruct_volume_from_slices (line 89) | def test_reconstruct_volume_from_slices(self): method test_reconstruct_volume_from_slices_temporal_reg (line 125) | def test_reconstruct_volume_from_slices_temporal_reg(self): FILE: tests/data_reader_test.py class DataReaderTest (line 21) | class DataReaderTest(unittest.TestCase): method setUp (line 23) | def setUp(self): method test_read_transformations (line 40) | def test_read_transformations(self): FILE: tests/image_similarity_evaluator_test.py class ImageSimilarityEvaluatorTest (line 23) | class ImageSimilarityEvaluatorTest(unittest.TestCase): method setUp (line 25) | def setUp(self): method test_compute_write_read_similarities (line 28) | def test_compute_write_read_similarities(self): method test_results_not_created (line 61) | def test_results_not_created(self): FILE: tests/installation_test.py class InstallationTest (line 20) | class InstallationTest(unittest.TestCase): method setUp (line 22) | def setUp(self): method test_fsl (line 36) | def test_fsl(self): method test_niftyreg (line 51) | def test_niftyreg(self): method test_itk_niftymic (line 67) | def test_itk_niftymic(self): FILE: tests/installation_test_fetal_brain_seg.py class InstallationTest (line 18) | class InstallationTest(unittest.TestCase): method setUp (line 20) | def setUp(self): method test_fetal_brain_seg (line 30) | def test_fetal_brain_seg(self): FILE: tests/installation_test_monaifbs.py class InstallationTestMonaiFbs (line 18) | class InstallationTestMonaiFbs(unittest.TestCase): method setUp (line 20) | def setUp(self): method test_fetal_brain_seg (line 30) | def test_fetal_brain_seg(self): FILE: tests/intensity_correction_test.py class IntensityCorrectionTest (line 21) | class IntensityCorrectionTest(unittest.TestCase): method setUp (line 29) | def setUp(self): method test_linear_intensity_correction (line 32) | def test_linear_intensity_correction(self): method test_affine_intensity_correction (line 79) | def test_affine_intensity_correction(self): FILE: tests/intra_stack_registration_test.py function get_inplane_corrupted_stack (line 28) | def get_inplane_corrupted_stack(stack, class IntraStackRegistrationTest (line 140) | class IntraStackRegistrationTest(unittest.TestCase): method setUp (line 147) | def setUp(self): method test_initial_transform_computation_1 (line 158) | def test_initial_transform_computation_1(self): method test_initial_transform_computation_2 (line 226) | def test_initial_transform_computation_2(self): method test_initial_transform_computation_3 (line 329) | def test_initial_transform_computation_3(self): method test_initial_intensity_coefficient_computation (line 466) | def test_initial_intensity_coefficient_computation(self): method test_inplane_rigid_alignment_to_neighbour (line 550) | def test_inplane_rigid_alignment_to_neighbour(self): method test_inplane_rigid_alignment_to_reference (line 640) | def test_inplane_rigid_alignment_to_reference(self): method test_inplane_rigid_alignment_to_reference_with_intensity_correction_linear (line 712) | def test_inplane_rigid_alignment_to_reference_with_intensity_correctio... method test_inplane_rigid_alignment_to_reference_with_intensity_correction_affine (line 794) | def test_inplane_rigid_alignment_to_reference_with_intensity_correctio... method test_inplane_similarity_alignment_to_reference (line 866) | def test_inplane_similarity_alignment_to_reference(self): method test_inplane_rigid_alignment_to_reference_multimodal (line 969) | def test_inplane_rigid_alignment_to_reference_multimodal(self): method test_inplane_uniform_scale_similarity_alignment_to_reference (line 1061) | def test_inplane_uniform_scale_similarity_alignment_to_reference(self): FILE: tests/linear_image_quality_transfer_test.py class LinearImageQualityTransferTest (line 20) | class LinearImageQualityTransferTest(unittest.TestCase): method setUp (line 27) | def setUp(self): method test_kernel_2D_as_kernel_3D (line 36) | def test_kernel_2D_as_kernel_3D(self): FILE: tests/linear_operators_test.py class LinearOperatorsTest (line 26) | class LinearOperatorsTest(unittest.TestCase): method setUp (line 28) | def setUp(self): method test_forward_operator_stack (line 48) | def test_forward_operator_stack(self): method test_simulate_stacks_from_slices (line 94) | def test_simulate_stacks_from_slices(self): FILE: tests/niftyreg_test.py class NiftyRegTest (line 24) | class NiftyRegTest(unittest.TestCase): method setUp (line 31) | def setUp(self): method test_affine_transform_reg_aladin (line 34) | def test_affine_transform_reg_aladin(self): FILE: tests/parameter_normalization_test.py class ParameterNormalizationTest (line 26) | class ParameterNormalizationTest(unittest.TestCase): method setUp (line 33) | def setUp(self): method test_parameter_normalization (line 36) | def test_parameter_normalization(self): FILE: tests/registration_test.py class RegistrationTest (line 32) | class RegistrationTest(unittest.TestCase): method setUp (line 39) | def setUp(self): method test_translation_registration_of_slices (line 252) | def test_translation_registration_of_slices(self): FILE: tests/residual_evaluator_test.py class ResidualEvaluatorTest (line 23) | class ResidualEvaluatorTest(unittest.TestCase): method setUp (line 25) | def setUp(self): method test_compute_write_read_slice_similarities (line 29) | def test_compute_write_read_slice_similarities(self): method test_slice_projections_not_created (line 62) | def test_slice_projections_not_created(self): FILE: tests/segmentation_propagation_test.py class SegmentationPropagationTest (line 23) | class SegmentationPropagationTest(unittest.TestCase): method setUp (line 30) | def setUp(self): method test_registration (line 33) | def test_registration(self): FILE: tests/simulator_slice_acquisition_test.py class SimulatorSliceAcqusitionTest (line 29) | class SimulatorSliceAcqusitionTest(unittest.TestCase): method setUp (line 36) | def setUp(self): method test_conversion_image_direction (line 39) | def test_conversion_image_direction(self): method test_run_simulation_view (line 84) | def test_run_simulation_view(self): method test_ground_truth_affine_transforms_no_motion (line 179) | def test_ground_truth_affine_transforms_no_motion(self): method test_ground_truth_affine_transforms_with_motion_NearestNeighbor (line 226) | def test_ground_truth_affine_transforms_with_motion_NearestNeighbor(se... method test_ground_truth_affine_transforms_with_motion_OrientedGaussian (line 274) | def test_ground_truth_affine_transforms_with_motion_OrientedGaussian(s... FILE: tests/stack_test.py class StackTest (line 22) | class StackTest(unittest.TestCase): method setUp (line 30) | def setUp(self): method test_get_resampled_stack_from_slices (line 33) | def test_get_resampled_stack_from_slices(self): method test_io_image_not_existent (line 60) | def test_io_image_not_existent(self): method test_io_image_and_mask_1 (line 74) | def test_io_image_and_mask_1(self): method test_io_image_and_mask_2 (line 88) | def test_io_image_and_mask_2(self): method test_io_image_and_mask_3 (line 101) | def test_io_image_and_mask_3(self): method test_io_image_and_mask_4 (line 114) | def test_io_image_and_mask_4(self): method test_update_write_transform (line 127) | def test_update_write_transform(self):