pwem.protocols.protocol_import.coordinates module

class pwem.protocols.protocol_import.coordinates.ProtImportCoordinates(**kwargs)

Bases: pwem.protocols.protocol_import.base.ProtImportFiles, pwem.protocols.protocol_particles_picking.ProtParticlePicking

Protocol to import a set of coordinates

IMPORT_FROM_AUTO = 0

IMPORT_FROM_DOGPICKER = 4

IMPORT_FROM_EMAN = 3

IMPORT_FROM_RELION = 2

IMPORT_FROM_SCIPION = 5

IMPORT_FROM_XMIPP = 1

correctCoordinatePosition(coord)

createOutputStep(importFrom, *args)

getDefaultBoxSize()

This function is used by the wizard to estimate the box size.

getFormat()

getImportClass()

Return the class in charge of importing the files.

getImportFrom()

getInputMicrographs()

getMatchingMic(coordFile, fileId)

Given a coordinates file check if there is a micrograph that this files matches.

class pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs(**kwargs)

Bases: pwem.protocols.protocol_import.base.ProtImportFiles

Protocol to import a set of tilt pair coordinates

IMPORT_FROM_EMAN = 1

IMPORT_FROM_XMIPP = 0

correctCoordinatePosition(coord)

createOutputStep()

getDefaultBoxSize()

This function is used by the wizard to estimate the box size.

getImportClass()

Return the class in charge of importing the files.

getInputMicrographs()

getMatchingCoord(micU, micT)

Given a pair of mics check if there are coordinates that match.

getSummary(coordSet)

readCoordinates()

registerCoords(coordsDir, store=True, readFromExtra=True)