Index

_

__init__() (objects.cell method) (objects.fiber method) (objects.spin method) _add_noise() (in module save) _caclulate_volumes() (in module diffusion) _diffusion_context_manager() (in module diffusion) _diffusion_in_cell() (in module walk_in_cell) _diffusion_in_fiber() (in module walk_in_fiber) _diffusion_in_water() (in module walk_in_water) _find_spin_locations() (in module spin_init_positions) _find_spin_locations_kernel() (in module spin_init_positions) _generate_signals_and_trajectories() (in module save) _get_bundle() (objects.fiber method) _get_bundle_index() (objects.spin method) _get_cell_index() (objects.spin method) _get_center() (objects.cell method) (objects.fiber method) _get_diffusivity() (objects.cell method) (objects.fiber method) _get_direction() (objects.fiber method) _get_fiber_index() (objects.spin method)

_get_position_t1m() (objects.spin method) _get_position_t2p() (objects.spin method) _get_radius() (objects.cell method) (objects.fiber method) _get_water_index() (objects.spin method) _place_cells() (in module set_voxel_configuration) _place_fiber_grid() (in module set_voxel_configuration) _place_spins() (in module set_voxel_configuration) _save_data() (in module save) _set_cell_index() (objects.spin method) _set_center() (objects.cell method) _set_diffusivity() (objects.cell method) _set_fiber_bundle() (objects.spin method) _set_fiber_index() (objects.spin method) _set_num_cells() (in module set_voxel_configuration) _set_num_fibers() (in module set_voxel_configuration) _set_position_t2p() (objects.spin method) _set_radius() (objects.cell method) _set_water_index() (objects.spin method) _signal() (in module save) _simulate_diffusion() (in module diffusion)

A

add_subparser_args() (src.cli.CLI method) (tests.cli.CLI method)

affine_transformation() (in module linalg)

B

buffer (simulation.Parameters property)

bvals (simulation.Parameters property) bvecs (simulation.Parameters property)

C

cell (class in objects) cell_fractions (simulation.Parameters property) cell_radii (simulation.Parameters property)

cfg_path (simulation.Parameters property) CLI (class in src.cli) (class in tests.cli) custom_diff_scheme_flag (simulation.Parameters property)

D

Delta (simulation.Parameters property) diff_scheme (simulation.Parameters property) diffusion module

dL2() (in module linalg) dmri_sim_wrapper() (in module simulation) dmri_simulation (class in simulation) dt (simulation.Parameters property)

F

fiber (class in objects) fiber_configuration (simulation.Parameters property)

fiber_diffusions (simulation.Parameters property) fiber_fractions (simulation.Parameters property) fiber_radii (simulation.Parameters property)

L

linalg module

M

main() (in module master_cli) module diffusion linalg save set_voxel_configuration spin_init_positions

N

n_walkers (simulation.Parameters property)

O

output_directory (simulation.Parameters property)

P

Parameters (class in simulation)

R

run() (in module simulation) (simulation.dmri_simulation method) (src.cli.CLI method) (tests.cli.CLI method)

Ry() (in module linalg)

S

save module set_voxel_configuration module

spin (class in objects) spin_init_positions module

T

thetas (simulation.Parameters property)

V

validate_args() (src.cli.CLI method) (tests.cli.CLI method)

verbose (simulation.Parameters property) void_distance (simulation.Parameters property) voxel_dimensions (simulation.Parameters property)

W

water_diffusivity (simulation.Parameters property)