pwem.protocols.protocol_particles module

class pwem.protocols.protocol_particles.ProtExtractParticles(**kwargs)[source]

Bases: ProtParticles

Base class for all extract-particles protocols. This class will take care of the streaming functionality and derived classes should mainly overwrite the ‘_extractMicrograph’ function.

extractMicrographListStep(micKeyList, *args)[source]
extractMicrographStep(micKey, *args)[source]

Step function that will be common for all extraction protocols. It will take an id and will grab the micrograph from a micDict map. The micrograph will be passed as input to the _extractMicrograph function.

readPartsFromMics(micDoneList, outputParts)[source]

This method should be implemented in subclasses to read the particles from a given list of micrographs.

class pwem.protocols.protocol_particles.ProtExtractParticlesOutput(value)[source]

Bases: Enum

Predefined outputs for particle extraction protocols

outputParticles = <class ''>
class pwem.protocols.protocol_particles.ProtExtractParticlesPair(**kwargs)[source]

Bases: ProtParticles

Base class for all extract-particles pairs protocols. Until now, this protocols is not in streaming mode.

class pwem.protocols.protocol_particles.ProtFilterParticles(**kwargs)[source]

Bases: ProtProcessParticles

Base class for filters on particles of type ProtPreprocessParticles.

class pwem.protocols.protocol_particles.ProtMaskParticles(**kwargs)[source]

Bases: ProtProcessParticles

This is the base for the branch of mask, between the ProtPreprocessParticles

class pwem.protocols.protocol_particles.ProtOperateParticles(**args)[source]

Bases: ProtProcessParticles

Base class for operations on particles of type ProtPreprocessParticles.

class pwem.protocols.protocol_particles.ProtParticles(**kwargs)[source]

Bases: EMProtocol

class pwem.protocols.protocol_particles.ProtProcessParticles(**kwargs)[source]

Bases: ProtParticles

This class will serve as a base for all protocol that performs some operation on Particles (i.e. filters, mask, resize, etc) It is mainly defined by an inputParticles and outputParticles.