optsys 1.0.3

optsys - Integrated toolkit for calculations of optical absorptions from MWAA or BLAnCA data

OPTSYS quick start guide

Installation

In a Linux terminal, create a virtual environment:

python3 -m venv optsys

This will create a virtual environment where you can install the software without affecting any other installation present in the system; to activate the environment:

source optsys/bin/activate

To make the activation automatic on login, you have to modify the terminal configuration file .bashrc. Open it with any text editor (create it if it doesn't exist) and write this line at the bottom: source optsys/bin/activate

Once the environment is activated, you can install the software with the following command:

python3 -m pip install optsys

The environment needs to be activated any time you want to use the toolkit.

Calculating the integrals for MWAA

You need an .xls(x) file for the loaded filters black.xlsx, an .xls(x) file for the blank reference white.xlsx, an .xlsx gain and dark file gd.xlsx (the files can have any name, the names I wrote here are just as an example). You also need to create a folder to store all the output of the calculations, results/. The black, white and gains files have to follow exactly the provided templates.

The command for this step is:

mpre -b black.xlsx -w white.xlsx -g gd.xlsx -o results/ --name analysis_name

The integrals for the black and white filters will be saved in the results/ folder, in a human-readable .csv format and in a machine-readable .json format (which the ABS calculation routine will use as input).

Calculating the integrals for BLAnCA

You need an .xlsx file for the loaded filters black.xlsx, with multiple tabs. Each tab contains the spectra for a filter, and its name corresponds to the filter name. Another file for the blank reference white.xlsx, with only one tab. If in doubt, check the provided templates.

The command for this step is:

bpre -b black.xlsx -w white.xlsx -o results/ --name analysis_name

where results/ is the folder for the output (it does not need to be created in advance, unlike the MWAA case). The integrals for the black and white filters will be saved in the results/ folder, in a human-readable .csv format and in a machine-readable .json format (which the ABS calculation routine will use as input).

ABS minimization

The integral calculation for MWAA and BLAnCA produce an output in the same exact format, so they can be both used for the same minimization procedure. Like previous versions, the configuration for this step is contained in a JSON file, that has to contain all the keywords as the provided template. Generally, the only options that you will need to change are the following:

key	type	explanation
b_integrals	string	The (relative) path to the black integrals file.
w_integrals	string	The (relative) path to the black integrals file.
out_folder	string	The (relative) path to the output folder.
name	string	The analysis name.
tolerance	float	The tolerance for the minimization. The default value of 1e-3 is good enough in most cases.

Start the analysis with

abs config.json

where config.json is the path to the configuration file.