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jlopezalo / PyFMGUI

PyFMGUI is an application for the analysis of force microscopy data capable of analyzing Nanoscope and JPK AFM files.
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Mismatch in the map coordinates of the force curves in JPK force map #9

Open yogi-boi opened 1 year ago

yogi-boi commented 1 year ago

hello Javi,

there is a discrepancy in the map coordinates of a force map from JPk files. The selected force curve in the sample height map(piezo image) and the curve displayed in the analysis window(four plots) are different. I am attaching an image of the PyFM GUI map coordinates and expected coordinates to recreate the expected force map. JPK_force_map_coord_scattered curve index_solution

The error in the current pattern is that code flips the odd columns instead of odd rows of data and to correct this error, the code at line 146 in loadjpkimg.py in the pyfmreader package should be tweaked.

piezoimg_ys = np.zeros((N,N)) for i in range(N): piezoimg_ys[:,i] = piezoimg[:,i] if i%2==1:piezoimg_ys[:,i] = (np.flip(piezoimg[:,i]))

jlopezalo commented 7 months ago

Thanks for noticing this issue I will get to work on it as soon as possible!

Best,

Javier