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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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Defining regions of interest (ROI) #20

Closed andrealucero closed 3 years ago

andrealucero commented 3 years ago

Hi! I've been reading (and running) the "Introduction to pySPM a python library for ToF-SIMS data analysis" tutorial. When it comes to defining a ROI, the example you provide is by thresholding the SI data. I was wondering if there are other options to define a ROI, for example: drawing a rectangle in the SI intensity image (and then obtain the spectrum from the area inside the rectangle). Thanks again!

scholi commented 3 years ago

did you try the help file? help(pySPM.ITM.get_raw_spectrum) You should get: ROI: Region Of Interest. It can be: 1) None: All pixels are used 2) A list of images. The pixels will be added to the spectrum i if the value of the i-th image is True for that pixel 3) An image with integer value. The current pixels will be added to the i-th spectrum if the value of ROI at that pixel is i.

Then you can create a ROI with a one values in a rectangular portion.

andrealucero commented 3 years ago

I used pySPM.utils.plotMask with a mask I created with the rectangle to have a proper image of the roi and then used pySPM.ITM.get_raw_spectrum (with the same mask). Looks like it works :)