xmipp3.protocols.protocol_screen_particles module

class xmipp3.protocols.protocol_screen_particles.XmippProtScreenParticles(**kwargs)[source]

Bases: pwem.protocols.protocol_particles.ProtProcessParticles

Attach different merit values to every particle in order to prune the set. zScore evaluates the similarity of a particles with an average (lower zScore -> high similarity). SSNR evaluates the signal/noise ration in the Fourier space. Variance evaluates the varaince on the micrographs context where the particle was picked.

REJ_MAXZSCORE = 1
REJ_NONE = 0
REJ_PERCENTAGE = 2
REJ_PERCENTAGE_SSNR = 1
REJ_VARGINI = 2
REJ_VARIANCE = 1
SSNR_CHOICES = ['None', 'Percentage']
VAR_CHOICES = ['None', 'Variance', 'Var. and Gini']
ZSCORE_CHOICES = ['None', 'MaxZscore', 'Percentage']
createOutputStep()[source]
sortImagesStep()[source]
xmipp3.protocols.protocol_screen_particles.histThresholding(valuesList, nBins=256, portion=4, takeNegatives=False)[source]

returns the threshold to reject those values above a portionth of the peak. i.e: if portion is 4, the threshold correponds to the 4th of the peak (in the right part).

xmipp3.protocols.protocol_screen_particles.rejectByVariance(inputMdFn, outputMdFn, threshold, mode)[source]

Sets MDL_ENABLED to -1 to those items with a higher value than the threshold