Command-Line Arguments

Note

In cases where a behavior can be controlled by both a command line argument, and a configuration file (.json file), the command line argument will ALWAYS take precedence.

run

ASCENT: Automated Simulations to Characterize Electrical Nerve Thresholds

usage: run [-h] [-v] [--version] [-l {runs,samples,sims}]
           {pipeline,tidy_samples,import_n_sims,clean_samples,build_from_input,compare,mock_morphology_generator,install,env_setup,build_dataset}
           ...

Positional Arguments

script

Possible choices: pipeline, tidy_samples, import_n_sims, clean_samples, build_from_input, compare, mock_morphology_generator, install, env_setup, build_dataset

which script to run

Named Arguments

-v, --verbose

verbose printing

Default: False

--version

show program’s version number and exit

-l, --list

Possible choices: runs, samples, sims

List all available indices for the specified option

Sub-commands

pipeline

main ASCENT pipeline

run pipeline [-h] [-i INPUT_NAME]
             [-b {pre_geom_run,post_geom_run,pre_java,post_mesh_distal,pre_mesh_distal,post_material_assign,pre_loop_currents,pre_mesh_proximal,post_mesh_proximal,pre_solve,post_java}]
             [-w WAIT_FOR_LICENSE] [-R RUN_GROUP] [-P {cuff_only,nerve_only}]
             [-E {overwrite,error,selective}] [-e] [-r] [-S] [-c | -C]
             [run_indices ...]

Positional Arguments

run_indices: Space separated indices to run the pipeline over

Named Arguments

-i, --input_name

Sort config files from /input/<input_name>/runs, /samples, /sims, and /models and run these new configs

-b, --break-point

Possible choices: pre_geom_run, post_geom_run, pre_java, post_mesh_distal, pre_mesh_distal, post_material_assign, pre_loop_currents, pre_mesh_proximal, post_mesh_proximal, pre_solve, post_java

Point in pipeline to exit and continue to next run

-w, --wait-for-license

Wait the specified number of hours for a comsol license to become available.

-R, --run-group

Use a list of runs from /config/user/rungroups.json. See /examples/tutorial/rungroups.json for an example. Any additional run indices passed will be appended.

-P, --partial-fem

Possible choices: cuff_only, nerve_only

Only generate the specified geometry.

-E, --export-behavior

Possible choices: overwrite, error, selective

Behavior if n_sim export encounters extant data. Default is selective.

-e, --endo-only-solution

Store basis solutions for endoneurial geometry ONLY

Default: False

-r, --render-deform

Pop-up window will render deformation operations

Default: False

-S, --auto-submit

Automatically submit fibers after each run

Default: False

-c, --comsol-progress

Print COMSOL progress to stdout

Default: False

-C, --comsol-progress-popup

Show COMSOL progress in a pop-up window

Default: False

tidy_samples

Remove specified files from Sample directories

run tidy_samples [-h] [-f FILENAME] [-A] [sample_indices ...]

Positional Arguments

sample_indices: Space separated sample indices to tidy

Named Arguments

-f, --filename

Filename to clear

-A, --all

Run on all samples

Default: False

import_n_sims

Move NEURON outputs into ASCENT directories for analysis

run import_n_sims [-h] [-v] [-f | -D] run_indices [run_indices ...]

Positional Arguments

run_indices: Space separated run indices to import

Named Arguments

-v, --verbose

Print specific files which are missing

Default: False

-f, --force

Import n_sims even if all thresholds are not found

Default: False

-D, --delete-nsims

After importing delete n_sim folder from NSIM_EXPORT_PATH

Default: False

clean_samples

Remove all files except those specified from Sample directories

run clean_samples [-h] [-R] sample_indices [sample_indices ...]

Positional Arguments

sample_indices: Space separated sample indices to clean

Named Arguments

-R, --full-reset

Clear all files except sample.json and model.json

Default: False

build_from_input

Convert all .json files in input/{arg} to valid runs and create a new rungroup

run build_from_input [-h] input_name

Positional Arguments

input_name: Space separated sample names to convert

compare

compare sample directories

run compare [-h] sample_indices sample_indices

Positional Arguments

sample_indices: Space separated sample indices to run the comparison over

mock_morphology_generator

Generate mock morpology for an ASCENT run

run mock_morphology_generator [-h] mock_sample_index

Positional Arguments

mock_sample_index: Mock Sample Index to generate

install

install ASCENT

run install [-h] [--no-conda]

Named Arguments

--no-conda

Skip conda portion of installation

Default: False

env_setup

Set ASCENT environment variables

run env_setup [-h]

build_dataset

Export dataset from ASCENT runs in SPARC format

run build_dataset [-h]
                  dataset_indices [dataset_indices ...] {query,generate} ...

Positional Arguments

dataset_indices

Space separated dataset indices to export

stage

Possible choices: query, generate

build_dataset stage

Sub-commands

query

Use query criteria to build excel output

run build_dataset query [-h]

generate

Generate dataset (keeps files) from excel output

run build_dataset generate [-h] [-f]

Named Arguments

-f, --force

Overwrite existing dataset

Default: False

submit.py

ASCENT: Automated Simulations to Characterize Electrical Nerve Thresholds

usage: submit.py [-h] [-p PARTITION] [-n NUM_CPU] [-m JOB_MEM] [-j NUM_JOBS]
                 [-l] [-A] [-f] [-s] [-S SLURM_PARAMS] [-c] [-L | -C] [-v]
                 [run_indices ...]

Positional Arguments

run_indices: Space separated indices to submit NEURON sims for

Named Arguments

-p, --partition

If submitting on a cluster, overrides slurm_params.json

-n, --num-cpu

For local submission: set number of CPUs to use, overrides run.json

-m, --job-mem

For cluster submission: set amount of RAM per job (in MB), overrides slurm_params.json

-j, --num-jobs

For cluster submission: set number of jobs per array, overrides slurm_params.json

-l, --list-runs

List info for available runs.z If supplying this argument, do not pass any run indices

-A, --all-runs

Submit all runs in the present export folder. If supplying this argument, do not pass any run indices

Default: False

-f, --force-rerun

Rerun fibers even if the outputs already exist

Default: False

-s, --skip-summary

Begin submitting fibers without asking for confirmation

Default: False

-S, --slurm-params

For cluster submission: string for additional slurm parameters (enclose in quotes)

-c, --force-recompile

Force submit.py to recompile NEURON files

Default: False

-L, --local-submit

Set submission context to local, overrides run.json

Default: False

-C, --cluster-submit

Set submission context to cluster, overrides run.json

Default: False

-v, --verbose

Print detailed submission info

Default: False