This library reads a measurement logbook and associated project/sample information and generates a script for a SAXS instrument. Currently still under development.
python3.12 -m venv .venv
pip install -e .Note that the logbook contains a second sheet with motor positions for sample stages. This is now set up so that you can have an arbitrary number of columns (motors) for a given stage position ID. That should allow for the use of alternative stages such as the GISAXS stage for experiments, which has five motors instead of the normal two cartesian stages we have.
Secondly, the script retrieves project and sample information from the project/sample sheets. These must therefore be present before you run the logbook2mouse script. This is done on purpose to ensure these project/sample sheets are actually used and filled in, as they also allow us to track our experiments better.
The project/sample sheets live in a separate directory structure, whcih must be organized by [year]/[proposalid].xlsx The proposal file name (used as the ProposalID) must start with the four-digit year. In our lab, we use the format [YYYY][nnn].xlsx for these proposal sheets, but in principle you're free to use how you adapt the second part of the filename.
The samples must have the components specified, with an atomic composition and a density estimate (not a range!). Please be careful to ensure the compositions and densities are machine-interpretable, so atomic compositions should be specified like (C2H4)213NaCl(H2O)5 and not (C2H4)n(H2O)x because we don't know what n and x are... Estimates are good enough if you don't know precisely.
The same holds for density esimates. Don't write a range (1.4 - 1.6) or (~1.2), because this cannot be interpreted. Stick to a single representative value when you can. Again, use a reasonable estimate.
python -m logbook2mouse logbook/Logbook_MOUSE.xlsx protocols tests/testdata/projects test_script.py