Question regarding mass calibration and dealing with iontof image files about pyspm HOT 1 CLOSED

Hi Shohini,
① Some ITA files differs in the content. This is specially true if you use the latest version of iontof. This might the reason why some data are not found by the library. If you can send me the data, then I can see what is wrong. Otherwise it will be tricky for me to guess what is the exact problem.

You can nevertheless do the calibration yourself. You can retrieve the time and intensity and perform the calibration yourself. For this purpose, use the method get_spectrum. You can provide a sf and k0 arguments which are the mass calibration parameters. You can also retrieve the time instead of the mass with time=True. Then look for the times of known peaks, such as H, C, CH, CH₂, CH₃, ... and perform a least square in order to find the exact mass calibrations parameters. You will find more details on the mass calibration on the wiki: https://github.com/scholi/pySPM/wiki/Mass-calibration

② Your error seems to be related to matplotlib. Which version do you have?

import matplotlib
print(matplotlib.__version__)

I use 2.1.0. If you have a lower version, try to upgrade it. WIth pip for ex.:

pip install --upgrade matplotlib

③ Yes you can reconstruct the data. Did you have look at the doc ? : https://nbviewer.jupyter.org/github/scholi/pySPM/blob/master/doc/pySPM%20Documentation.ipynb#SI-image-reconstruction

For that you need the ITM file (not the ITA) and then give the list of peaks with lower, upper mass given as a tuple. You should also pass the mass calibration parameters: sf and k0 as argument.

Let me know if this works.

from pyspm.