xmipp3.protocols.protocol_preprocess.protocol_preprocess module

class xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippPreprocessHelper[source]

Bases: object

Helper class that contains some Protocol utilities methods used by both XmippProtPreprocessParticles and XmippProtPreprocessVolumes.

class xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessParticles(**kwargs)[source]

Bases: XmippProcessParticles

Preprocess a set of particles. You can remove dust, normalize, apply threshold, etc

NORM_NEW = 1

NORM_OLD = 0

NORM_RAMP = 2

centerStep(args, changeInserts)[source]

invertStep(args, changeInserts)[source]

normalizeStep(args, changeInserts)[source]

phaseFlipStep(args, changeInserts)[source]

randomizeStep(args, changeInserts)[source]

removeDustStep(args, changeInserts)[source]

sortImages(outputFn, outputMd)[source]

thresholdStep(args, changeInserts)[source]

class xmipp3.protocols.protocol_preprocess.protocol_preprocess.XmippProtPreprocessVolumes(**kwargs)[source]

Bases: XmippProcessVolumes

Protocol for Xmipp-based preprocess for volumes

AGG_AVERAGE = 0

AGG_SUM = 1

SEG_AMIN = 1

SEG_AUTO = 3

SEG_DALTON = 2

SEG_VOXEL = 0

adjustStep(isFirstStep, changeInserts)[source]

changeHandStep(args, changeInserts)[source]

invertStep(args, changeInserts)[source]

laplacianStep(args, changeInserts)[source]

normalizeStep(args, changeInserts)[source]

projectionStep(changeInserts)[source]

randomizeStep(args, changeInserts)[source]

removeDustStep(args, changeInserts)[source]

rotateIcoStep(args, changeInserts)[source]

segmentStep(args, changeInserts)[source]

symmetrizeStep(args, changeInserts)[source]

thresholdStep(args, changeInserts)[source]