How to shape my data to use this program?
- Open OPUS software. Do all the corrections (Baseline, Atmospheric, Integrations)
If you didn’t write it somewhere, count number of tiles in x and y that you measured (number of columns, number of lines) and also the binning used (64-32-16-8-4 spectra per tile)
** I recommend you to name your files efficiently when you measure, with detector, sample name, number of tiles (nboflines x nbofcolumns), binning (nobin, bin2, bin4, bin8 or bin16) and the number of scans. Ex : FPAmap_LdC01_6x4sq_nobin_64sc.
For MCT map, follow the same format but include step size. Ex : MCTmap_Sample1_42x50_50x50ap_50stp_64sc.
The program analyse your filename, so if you entered the right intel, you will save time!**
- Save the spectra : File -> Save as -> (Don’t change the name of the file or folder, sometimes it crashes) -> Mode (select MATLAB4), -> Save
- Save the integration data. In opus explorer (left panel) clic right on your file and clic on “show report”. A report file will appear in the list. Clic on “TRC” and wait that the data appears. Select the first line, press and hold shift then select the last line. Clic right – copy to clipboard.
Open excel file, write some headers. Then copy the data.
- You should have a excel file starting like this : (please use the same headers, I will try to change that but until now it is mandatory)
If you have only one Integration zone, just copy the same column.
- Put the files in a folder together with the Matlab program. Open matlab and go to that folder. Open the excel file with matlab, import data as column vectors then select the vector on the right panel and save it to a .mat file (as exemple provided with the program)
- Write FPAMaps_GUI on matlab command line : the program is launched.
- Press load button on top left. Select the type of map you want to process (MCT or FPA), then select first the spectra data file, then the integration data. A panel then appears asking for number of tiles and binning/step size. Complete it and press OK.
You can now plot the maps using the popupmenus.
FPAMaps tools :
I already coded some basic tools to be used on your maps.
- Plot parameters : you can set the limit of the colorbar for both graph1 and 2. Auto-scale is also available. You can also chose between a pixel map and a contour map. The number of levels correspond to the number of layers on contour plot.
- Thickness correction : you can use a constant thickness (insert it in µm), or a variable thickness based on overtone map (insert a conversion factor)
- Normalisation : You can divide the map displayed on graph1 by the map displayed on graph2. A new normalised map will then be available. You can insert a normalisation factor (important if you divide by a thickness in micrometre)
- Quantification: When the Normalisation has been done, you can insert an absorbtion coefficient and quantify your map.
- Display spectra : press add button and select spectra with cursor on graph1 or graph2. When finished clic right. Spectra will be displayed on graph 3. Delete allow you to remove spectra. If you set limits, you can restrain the plotting area.
- Save graph: the current graph is replotted on a separate figure and saved.