xmipp3.protocols.protocol_screen_particles module

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

Bases: ProtProcessParticles

Protocol to attach different merit values to every particle metadata for subsequent pruning the set. There are different merit values to be calculated:

zScore evaluates the similarity of a particles with an average (lower zScore -> higher 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