Command Line Interface

Top-Level CLI (Module Selection)

master_cli.main()[source]

Parses module selection (simulate or run_tests) and invokes the relevant functions

Arguments

  1. simulate: Used to run the simulator normally. See Simulation CLI below.

  2. run_tests: Used to run the installation and accuracy tests. See Testing CLI below.

Simulation CLI

class src.cli.CLI(subparsers)[source]
Simulation Arguments

  1. n_walkers: Number of spins to populate voxel. Must be an integer greater than zero. It is recommended to use a sufficient number of spins to achieve a spin density of at least 1.0 spin per cubic micrometer.

  2. fiber_fractions: Volume fractions (as a tuple of floats) of each fiber type to populate in simulated voxel. Must be non-negative and sum to less than 1.

  3. fiber_radii: Radii of each desired fiber type (as a tuple of floats) in units of micrometers. Length must match the number of entries in fiber_fractions and value must be non-negative.

  4. thetas: Angles for each fiber bundle to be rotated (w.r.t. the y-axis)

  5. fiber_diffusions: Intrinsic diffusivities (in units of square micrometers per millisecond) of each fiber type. Length must match the number of entries in fiber_fractions and value must be non-negative.

  6. cell_fractions: Volume fractions (as a tuple of floats) of each cell type to populate in simulated voxel. Must be non-negative and sum to less than 1.

  7. cell_radii: Radii of each desired cell type (as a tuple of floats) in units of micrometers. Length must match the number of entries in cell_fractions and be non-negative.

  8. water_diffusivity: Diffusivity of free water (in units of square micrometers per millisecond). Must be non-negative.

  9. voxel_dims: Side length for the simulated isotropic voxel, in units of micrometers. Must be a positive float.

  10. void_dist: Size of edema-like gap to introduce between the fiber bundles.

  11. verbose: yes or no. Select yes to output detailed information to the terminal. Select no to suppress this output.

  12. Delta: Diffusion time (or simulation length) in units of milliseconds.

  13. dt: Size of time step for simulation.

add_subparser_args() → <module 'argparse' from '/home/docs/.asdf/installs/python/3.9.17/lib/python3.9/argparse.py'>[source]

Defines subparsers for each simulation parameter.

Returns:

argparse object containing subparsers for each simulation parameter

Return type:

argparse

run(args)[source]

Run simulation using parsed user inputs

Parameters:

args (dictionary) – User inputs for relevant parameters

validate_args(args)[source]

Validation step for parsed user input arguments

Parameters:

args (dictionary) – Parsed user inputs

Returns:

Parsed and validated arguments

Return type:

dictionary

Testing CLI

class tests.cli.CLI(subparsers)[source]

Command line interface for running the simDRIFT test suite

Arguments

None

add_subparser_args()[source]

Adds subparser for the run_tests command.

Returns:

argparse object containing of subparsers for each input parameter

Return type:

argparse

run(args)[source]

Passes to the test suite file

Parameters:

args (str) – input arguments (Note, run_tests accepts no arguments)

validate_args(args)[source]

Function to validate input arguments for testing

Parameters:

args (str) – input arguments (Note, run_tests accepts no arguments)