pwem.protocols.protocol_particles_picking module

class pwem.protocols.protocol_particles_picking.ProtParticlePicking(**kwargs)[source]

Bases: pwem.protocols.protocol_particles.ProtParticles

OUTPUT_PREFIX = 'outputCoordinates'
createOutputStep()[source]
getCoords()[source]
getCoordsDir()[source]
getCoordsTiltPair()[source]
getInputMicrographs()[source]
getInputMicrographsPointer()[source]
getMethods(output)[source]
getSummary(coordSet)[source]
readSetOfCoordinates(workingDir, coordSet)[source]
registerCoords(coordsDir)[source]

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)[source]

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()[source]
pickMicrographListStep(micNameList, *args)[source]
pickMicrographStep(micName, *args)[source]

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)[source]

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)[source]

Bases: pwem.protocols.protocol_particles_picking.ProtParticlePicking

Protocol to compute the difference between a reference SetOfPartices 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)[source]
getInputMicrographs()[source]