CoSSSmallTricks

COSS Small Tricks

This a list of commonly used tiny image processing steps that are not always obvious with a single command

----++ Generate an empty image with a template image of the desired size

Sol: Multiply the template by 0

xmipp_operate -i1 template.xmp -mult 0 -o empty.xmp

----++ Count the number of pixels below/above a certain threshold

Sol: Use the counting capability of xmipp_mask

xmipp_mask -i image.xmp -count_above 0.5

----++ Estimate the minimum value, maximum value, average, and standard deviation of a set of files

Sol: Use xmipp_infogeo

For a set of images/volumes:

xmipp_infogeo selfile.sel -stats

For a single image/volume

xmipp_infogeo image.xmp -stats

Note that xmipp_infogeo can also evaluate statistics inside a mask

----++ Generate a mask

Sol: Use xmipp_mask

xmipp_mask -i template.xmp -create_mask maskCreated.xmp -mask circular -30

-- Main.CoSS - 05 Feb 2007