pwem.protocols.protocol_particles_picking module

class pwem.protocols.protocol_particles_picking.ProtParticlePicking(**kwargs)

Bases: pwem.protocols.protocol_particles.ProtParticles

OUTPUT_PREFIX = 'outputCoordinates'

createOutputStep()

getCoords()

getCoordsDir()

getCoordsTiltPair()

getInputMicrographs()

getInputMicrographsPointer()

getMethods(output)

getSummary(coordSet)

readSetOfCoordinates(workingDir, coordSet)

registerCoords(coordsDir)

This method is usually inherited by all Pickers and it is used from the Java picking GUI to register a new SetOfCoordinates when the user click on +Particles button.

class pwem.protocols.protocol_particles_picking.ProtParticlePickingAuto(**kwargs)

Bases: pwem.protocols.protocol_particles_picking.ProtParticlePicking

A derived class from ProtParticlePicking to differentiate those picking protocols that works in automatic way, i.e., that are not interactive and are also good candidates to be run in streaming.

createOutputStep()

pickMicrographListStep(micNameList, *args)

pickMicrographStep(micName, *args)

Step function that will be common for all picking protocols. It will take care of re-building the micrograph object from the micDict argument and perform any conversion if needed. Then, the function _pickMicrograph will be called, that should be implemented by each picking protocol.

readCoordsFromMics(outputDir, micDoneList, outputCoords)

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

class pwem.protocols.protocol_particles_picking.ProtPickingDifference(**kwargs)

Bases: pwem.protocols.protocol_particles_picking.ProtParticlePicking

Protocol to compute the difference between a reference SetOfParticles and a another set (usually a negative reference).

The output will be a SetOfCoordinates with the particles in the reference input that are not close to coordinates in the negative input.

createOutputStep(inputId, negId, radius)

getInputMicrographs()