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: xmipp3.protocols.protocol_preprocess.protocol_process.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: xmipp3.protocols.protocol_preprocess.protocol_process.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]