Spectropy is a simple tool to view, compare and match Raman and infrared spectra of minerals.
On MacOS, Spectropy is available via Homebrew. Please install it as described on their website. Usually, you should just need to open the Terminal App and paste the following command:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Once done, install Spectropy using the following commands:
brew tap simonecnt/3dz2
brew install spectropy
Spectropy will be available in you Application folder.
The first time you will try to open it, you will get a warning, like this:
Click "Done", then open the MacOS System Settings from the Apple menu on the top right, go to the Privacy & Security tab, and when you read "Spectropy.app was blocked to protect your Mac." click "Open Anyway". After that, it Spectropy should open properly.
To upgrade Spectropy to a new version, open a Terminal and type:
brew upgrade
And to uninstall Spectropy:
brew uninstall spectropy
Spectropy is a python application using tkinter for the graphical user interface. You need first to install these via your Linux distribution package manager (apt, pacman, ...). The details depend on your operating system. To verify that tkinter is available run this command in the Terminal:
python3 -m tkinter
You should see a little window opening with the tkinter version. If instead you get any error, it means something went wrong somewhere...
At this point you should have python and tkinter installed. you can now install Spectropy via pip:
pip3 install --user --upgrade https://github.com/SimoneCnt/spectropy/archive/refs/heads/main.zip
This command should install all needed dependences, and you should be able to run Spectropy from the Terminal via:
python3 -m spectropy
No idea, I've never tested this.
Figure: Main Spectropy window at first use.
Upon opening Spectropy for the first time, you probably want to load a Raman spectra you measured or received. For this, just click on the "Open New Spectrum" button and navigate to the file you want to open. Spectropy currently support Raman spectra in a few formats: spc, LRD 1.1, the format used by the RRUFF project and a plain text format. Spectropy tries to automatically detect the format, but it may fail. If that happens, or if your spectra is in a not supported format, please sent it to me, and I'll see what I can do.
Once loaded you can change a few settings:
- Label: change the text in the legend.
- Color: change the color!
- Min and Max: limit the range of Raman shifts in the plot.
- Shift: shift vertically the whole graph.
- Filter: increase/decrease the number of peaks detected.
- Baseline: compute and eventually remove a baseline correction; try to play with the L and P parameters to see what it "looks best".
- Calibrate: m,q are two parameters to shift horizontally and scale the graph; this is useful in case your Raman spectrometer is not calibrated and a simple linear regression may fix the issue (m is the slope, q the intercept of such linear regression). Click apply to see its effect.
- Match: match the spectra with a database of reference spectra (see below).
- Save: save a text file with the new spectra; useful when removing the baseline and calibrating it.
- Remove: delete the current spectra.
Figure: Spectropy window after loading a first spectrum.
You can load multiple spectra at the same time, for comparisons. If you are loading a lot of spectra you can save the current setup with the "Save config" button. The "Load config" will reopen it as it was left. The "Update graph" should be useless, as the graph should be updated every time your change any parameter. In case you don't see some setting being applied, try the "Update graph" button. The buttons "RefLib Setup" and "RefLib View" allow you to load and view the reference library, see description below.
Raman spectroscopy is close to useless without a reliable database of reference spectra. The RRUFF project provides, free for everyone, such reference database for minerals.
With the "RefLib Setup" button you can download and setup a copy of the RRUFF database for use in Spectropy. First, you need to download it, so click on the "Get new version" button. It will take a while, and, once done, it should show the text "Last downloded:" with the current date. The RRUFF project regularly update their database, so you may want to download a new fresh copy from time to time (no idea how often, maybe every few months?).
Figure: Setup of the Reference Library.
With a copy of the RRUFF database you can now create a matching library to be used to match your spectra with. You can select how many different spectra of the same mineral you want (a couple should be enough, increase if you want), and the preferred wavelength of the laser to use. Raman spectra can differ with the used laser, so using as reference spectra obtained with the same laser could help. If no spectra with your preferred laser are found, the closest ones are selected instead. Then click the "Generate new matching library" button. It will take again a little while, and, after that, it should show a text saying: "Library available with max_spectra=x and preferred_laser=xxx".
You are now ready to go! Close to window and click the "RefLib View" button. This will open a new window where you can select a mineral, then a laser wavelength, and then a RRUFF ID. By clicking the RRUFF ID, that spectra will be loaded in the main window. The number in square brackets is the "quality" of the spectra as listed by RRUFF: 3 is high quality, 0 is low quality. This library view will show all spectra available, not only the ones selected in the generation of the matching library.
Figure: View of the Reference Library once loaded.
Once you have loaded a reference matching library you can click on the "Match" button of your spectra and this will run 3 different matching algorithms. The best matching spectra will be listed in a new window, and you can open any of them by just clicking on them.
This overall interface need to be improved... todo!