RunKerdenSOM

KerDenSOM

2D images KerDenSOM

Select the interesting part of the images using xmipp_xmask; convert to data-format; calculate a 5x5KerDenSOM; convert back to image format; and display the SOM.

xmipp_xmask -img selfile.med.xmp
xmipp_img2data -sel selfile.sel -mname mask.spi -fname selfile.dat
xmipp_kerdensom -din selfile.dat -cout selfileker -xdim 5 -ydim 5 -reg0 500 -reg1 100 -steps 5 -verb 1
xmipp_data2img -sel selfileker.sel -iname selfileker.cod -mname mask.spi
xmipp_show -som selfileker

Rotational Power Spectra KerDenSOM

Calculate the rotational power spectra of a set of images, calculate 5x5KerDenSOM and display the SOM. A improtant previous step is to align the images and to calculate the center of the average image. The coordinates of the center of the average image will be an input to the following step.

xmipp_findcenter -img average.med -x0 50 -y0 50 -low 37 -high 39 -r1 3 -r2 22
Optimal center coordinates: x =    50.125, y =     50.000

This coordinates are inputs for xmipp_makespectra

xmipp_makespectra -sel selfile.sel -out selfile.sim -x0 50.125 -y0 50.00 -low 1 -high 10 -r1 10 -r2 28
xmipp_kerdensom -din selfile.sim -cout selfileker -xdim 5 -ydim 5 -reg0 1000 -reg1 50 -steps 5 -verb 1
xmipp_show -spectsom selfileker -din selfile.sim