pwem.protocols.protocol_import.coordinates module

class pwem.protocols.protocol_import.coordinates.ProtImportCoordinates(**kwargs)[source]

Bases: ProtImportFiles, 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)[source]
createOutputStep(importFrom, *args)[source]
getDefaultBoxSize()[source]

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

getFormat()[source]
getImportClass()[source]

Return the class in charge of importing the files.

getImportFrom()[source]
getInputMicrographs()[source]
getMatchingMic(coordFile, fileId)[source]

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

class pwem.protocols.protocol_import.coordinates.ProtImportCoordinatesPairs(**kwargs)[source]

Bases: ProtImportFiles

Protocol to import a set of tilt pair coordinates

IMPORT_FROM_EMAN = 1
IMPORT_FROM_XMIPP = 0
correctCoordinatePosition(coord)[source]
createOutputStep()[source]
getDefaultBoxSize()[source]

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

getImportClass()[source]

Return the class in charge of importing the files.

getInputMicrographs()[source]
getMatchingCoord(micU, micT)[source]

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

getSummary(coordSet)[source]
readCoordinates()[source]
registerCoords(coordsDir, store=True, readFromExtra=True)[source]