I'm working on processing some FTIR imaging data from an Agilent FTIR microscope with SMAK 3.0.7. The .dmt file loads into SMAK correctly and I see a new Data Channel labeled "FTIR" created along with the correctly processed mozaic tiling in the Display window. When I define the .hdf5 spectrum file (under MCA Spectra->Define MCA File) the x-axis untis are not displayed correctly. My source data should start at 898.67 cm^-1 and end at 3801.01 cm^-1, however it looks like the x-axis has loaded so that the first value is at 466 cm^-1 and the last data point is at 3468 cm^-1 (so the start position is off, as are the bins).
I can see there is an option in MCA Spectra->FTIR Support to load IR Settings, but it's looking for a .json file which I do not have and am unsure the formatting of (and am not sure this will fix the underlying issue).
Is there a recommended way to correct this or set the start value of the energy axis (particularly one that's not an integer, but somethign with several decimal places) as well as my bin size (should be 1.928467 cm-1/bin)?
Thanks!
With the MCA View option set to Specturm I see the FTIR data plotted from 466.0 to 3468.623545 (copy/pasted to clipboard so I could confirm values). You're correct, it looks like the 1.928467 cm-1 spacing is being picked up correctly, but the start value of our spectrum should be 898.665750 cm-1 as far as I can tell. The real test here is where our peaks show up, and they're all shifted by the same amount (even the telltale CO2 peak is shifted too). The Agilent instrument starting range that we specify is 900-3900 cm-1 and appears ~~correct on the instrument itself. When loading our hdf5 files into the data processing package Orange (now named Quasar) it also shows this energy range, with a starting energy of 898.665750 and going up to 3901.289295 cm-1. The data from the Leica instrument at SSRL DOES display the correct energy scale, so this appears to be an Agilent-specific issue. The absolute energy for our Agilent data is off by 432.66575 cm-1 for each data point. Shifting the energy scale I have in SMAK right now by this amount would make 466.0-to-3468.623545 cm-1 into the expected 898.665750-to-3901.289295 cm-1 range. Thanks for any suggestions! ... luckily the Agilent data isn't the most pressing to process at the moment, as we've got lots of Leica data to get through ;)