Command-line interface

The nanite command-line interface (CLI) simplifies several functionalities of nanite, making fitting, rating, and the generation of training sets accessible to the user.

nanite-setup-profile

Set up a profile for fitting and rating. The profile is stored in the user’s default configuration directory. Setting up a profile is required prior to running nanite-fit and nanite-rate.

usage: nanite-setup-profile [-h]

nanite-fit

Fit AFM force-distance data. Statistics (.tsv file) and visualizations of the fits (multi-page .tif file) are stored in the results directory.

usage: nanite-fit [-h] data_path out_dir

positional arguments

data_path

input folder containing AFM force-distance data

out_dir

results directory

nanite-rate

Manually rate (the fit to) AFM force-distance data. A graphical user interface allows to rate and comment on each force-distance curve. The fits and the raw data are stored in a rating container that can then be passed to nanite-generate-training-set.

usage: nanite-rate [-h] data_path rating_path

positional arguments

data_path

input folder containing AFM force-distance data

rating_path

path to the output rating container (will be created if it does not already exist)

nanite-generate-training-set

Create a training set for usage in nanite from rating containers (.h5 files manually created with nanite-rate).

usage: nanite-generate-training-set [-h] data_path out_dir

positional arguments

data_path

path to a rating container or a folder containing rating containers

out_dir

directory where the training set will be stored