xmipp3.protocols.protocol_preprocess.protocol_mask module

class xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMask(**args)

Bases: object

This class implement the common features for applying a mask with Xmipp either SetOfParticles, Volume or SetOfVolumes objects.

copyMaskFileStep(inputMaskFile, outputMaskFile)

Create a local copy of the mask. We use ImageHandler.convert instead of copyFile because the mask could be inside an stack.

maskStep(args)

class xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMaskParticles(**kwargs)

Bases: ProtMaskParticles, XmippProcessParticles, XmippProtMask, XmippGeometricalMask2D

Applies masks to a set of particle images to isolate specific regions or exclude unwanted background. The mask can be done with a geometry or import an external one. The center can be shift and the pixels outside the mask can be filled with a min avg, max or an specific value. Masking is critical for focusing on structural features and improving alignment and classification.

GEOMETRY_BASECLASS

alias of XmippGeometricalMask2D

MASK_CLASSNAME = 'Mask'

MASK_FILE = 'mask.spi'

class xmipp3.protocols.protocol_preprocess.protocol_mask.XmippProtMaskVolumes(**kwargs)

Bases: ProtMaskVolumes, XmippProcessVolumes, XmippProtMask, XmippGeometricalMask3D

Apply mask to a volume

GEOMETRY_BASECLASS

alias of XmippGeometricalMask3D

MASK_CLASSNAME = 'VolumeMask'

MASK_FILE = 'mask.vol'