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scholi / pySPM

Python library to handle Scanning Probe Microscopy Images. Can read nanoscan .xml data, Bruker AFM images, Nanonis SXM files as well as iontof images(ITA, ITM and ITS).
Apache License 2.0
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Calibration of ITM files #12

Closed sbrtn closed 4 years ago

sbrtn commented 4 years ago

Hello,

Thanks for your previous assistance with my questions. I have been using your "reconstruct" function for making SI images from saved ITM (uncalibrated) files from the IonTof instrument. I was wondering if there is anyway to calibrate the raw ITM file. Otherwise, I currently have to compare the calibrated ITA file (calibrated with your spectragui) and the uncalibrated ITM file and try to spot the ion of interest. I was also wondering if you have any advice on making the reconstruct function compile faster. Currently, reconstructing 14 scans of a 512x512 image takes around 5+ minutes.

Thanks so much, Shohini

scholi commented 4 years ago

Hi Shohini, Yes reconstruction is slow, as slow as with the iontof software. This is because the reconstruction need to perform a lot of reading from the HDD and how its fileformat works. You can probably increase its speed by using a SSD drive and by adding a caching system of the ITM class.

Now I'm not sure to understand what you mean in your question. You can retrieve the raw spectrum and apply a mass calibration by using ITM.get_raw_spectrum(sf=sf, k0=k0) and you can do a reconstruction using the same mass calibration using also the sf and k0 argument. There is already one example in the help file. Is this what you meant?