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_CRYOSPARC = 6

IMPORT_FROM_DOGPICKER = 4

IMPORT_FROM_EMAN = 3

IMPORT_FROM_RELION = 2

IMPORT_FROM_SCIPION = 5

IMPORT_FROM_XMIPP = 1

OUTPUT_NAME = 'outputCoordinates'

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]