Command Line Interface

diameter-synthesis

Cli to learn and generate diameters of neurons.

diameter-synthesis [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

plot_diff

Plot original and new neurons as well as their differences.

diameter-synthesis plot_diff [OPTIONS]

Options

--orig-path <orig_path>

Required Path to original cells

--diam-path <diam_path>

Required Path to diametrized cells

-o, --out-dir <out_dir>

Required Directory to output the analysis results

-n, --ncells <ncells>

Max number of cells to plot

-e, --ext <ext>

Figures extension

run_analysis

Produce figures for validation/analysis.

diameter-synthesis run_analysis [OPTIONS]

Options

--orig-path <orig_path>

Required Path to original cells

--diam-path <diam_path>

Required Path to diametrized cells

--mtypes-file <mtypes_file>

Path to mtypes file

-o, --out-dir <out_dir>

Required Directory to output the analysis results

--cumulative

Cumulative distribution plots

--individual

Output a plot for each neuron

--violin

Violin distribution plots

-e, --ext <ext>

Figures extension

run_diameters

Build new diameters from config file and diameter model.

diameter-synthesis run_diameters [OPTIONS] CONFIG_FILE MODELS_PARAMS_FILE

Arguments

CONFIG_FILE

Required argument

MODELS_PARAMS_FILE

Required argument

run_models

Run the model extraction from config file.

diameter-synthesis run_models [OPTIONS] CONFIG_FILE

Options

--plot
--ext <ext>

Arguments

CONFIG_FILE

Required argument