Usage
After starting the software, you will be greeted by the main window:
The interface is divided into three panes:
- Left pane: files with experimental spectra for analysis and spectrometer settings
- Middle pane: Graph view showing both experimental spectra as well as analysis from the analysis modules
- Right pane: The different analysis modules, each in a separate tab
You can resize and hide the left and right pane as indicated in the screenshot or by using the 'View' menu.
You can use the "Open files" and "Open folder" buttons to load files or simply use drag and drop for both files and folders:
load_files.mp4
All subfolders are also added to the list and can be explored in the list as shown in the video. For files that contain multiple spectra, these will show up below the main file after clicking on them the first time.
Individual files can be removed again from the list using a right-click context menu on the file. All files can be cleared out using the "Clear button" below the file list.
The spectra of selected files will be shown in the graph view in the middle pane. Multiple spectra can be shown simultaneously by using crtl + left click. Alternativley, the behavior can be changed to only plot spectra that are enabled using the small checkbox left to the file name. The dropdown menu below the file list allows you to change between these "plot selected" and "plot checked" modes.
For files that already contain acquired background data (like Avantes files), this background is subtracted by default. An option will be shown at the bottom to disable the background subtraction. This menu is hidden if no background data is found within the file.
Alternatively, the background data from a separate file can be used. This file can be selected by using the "Open" button at the bottom of the tab or from the file list above, using right-clicking on the file to open the context menu and selecting "Use as background". If the selected background file has a different size (different amount of pixels) than the main data file, background subtraction will silently fail.
The software currently supports the following file types:
- Avantes .txt: Supports optional background subtraction and multiple measurements.
- Andor .asc
- Ocean Optics txt
- Other Text/ascii/csv: Automatic determination of headers, delimiters and decimal symbol. Please open an issue with an example if your text file fails to load.
- Avantes .RAW8 (but not .RWD8 or .STR8)
- Andor .sif
- Princeton Instruments .SPE
The settings tab in the left pane contains spectrometer settings. Here, you can apply an intensity calibration to account for the wavelength dependency of the detector sensitivity. To this end, you need to place a calibration file into the correct folder, which you can open by pressing the "Open folder" button. Please make sure that the file is a text file that contains only two columns, with the wavelength in nm and the sensitivity of the spectrometer in arbitrary units, representing the photon count per second. The file must use a point as the decimal delimiter and tab as the delimiter between the two columns. You can place multiple files in the folder and select between them using the combo box.
For line broadening and fitting of molecular bands, instrumental broadening is very important. You can use a Pseudo Voigt profile with a shape parameter between 0 (Gaussian shape) and 1 (Lorentzian shape) and a custom width. The profile is defined in the code as:
def psd_voigt_function(x, xc, w, mu):
return (1 * ( mu * (2/np.pi) * (w / (4*(x-xc)**2 + w**2)) +
(1 - mu) * (np.sqrt(4*np.log(2)) / (np.sqrt(np.pi) * w)) *
np.exp(-(4*np.log(2)/w**2)*(x-xc)**2) ))The graph view in the middle pane shows data from files selected in the left pane and results from the analysis modules in the right pane. The graph view uses PyQtGraph and, therefore, has a lot of options for graph manipulation and presentation. Most options are accessed via a right-click context menu. The default navigation behavior is as follows:
- Mouse left click + drag: Move the graph
- Mouse right click + drag right/left: X zoom in/out
- Mouse right click + drag up/down: Y zoom in/out
- Mouse wheel: Zoom in and out This behavior needs some getting used to but then works extremely well when using a mouse. For laptops without a mouse, you can change the behavior via the right-click context menu -> Mouse mode -> 1 button. Then, a click + drag creates a box for zooming onto the selected part of the graph.
In both cases, the default zoom level can be restored by pressing the "A" button at the bottom left of the graph view or via the right-click context menu (View All).
You can copy an image of whatever you are viewing in the graph view to clipboard by pressing the corresponding button below the graph. This creates a figure that can be pasted into programs like MS Paint or PowerPoint to quickly share some results with co-workers. The created graph uses the zoom settings of the graph view, so make sure to adjust it before pushing the button.
For presentations or publications, you will want to plot the data yourself in a separate program. To this end, you can export the graph data using the "File" menu in the main menu bar (at the top of the window). Using File -> Export -> Plot data will export all data currently shown in the graph view to a text file at a chosen location. The zoom level of the graph view is disregarded; everything is exported.
The spectrum analysis is sorted into modules, shown as tabs in the right pane of the window. Current modules are:
Information on how to use the modules can be found on their respective pages.