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