tomo.protocols.protocol_ts_import module

class tomo.protocols.protocol_ts_import.MDoc(fileName, voltage=None, magnification=None, samplingRate=None)

Bases: object

getFileName()

getMagnification()

getSamplingRate()

getTiltsMetadata()

getTsId()

getVoltage()

static normalizeTSId(rawTSId)

Normalizes the name of a TS to prevent sqlite errors, it ends up as a table in a set

read(isImportingTsMovies=True, ignoreFilesValidation=False)

class tomo.protocols.protocol_ts_import.ProtImportTs(**kwargs)

Bases: tomo.protocols.protocol_ts_import.ProtImportTsBase

Protocol to import tilt series.

class tomo.protocols.protocol_ts_import.ProtImportTsBase(**kwargs)

Bases: pwem.protocols.protocol_import.base.ProtImport, tomo.protocols.protocol_base.ProtTomoBase

Base class for Tilt-Series and Tilt-SeriesMovies import protocols.

ANGLES_FROM_FILENAME = 'Filename'

ANGLES_FROM_HEADER = 'Header'

ANGLES_FROM_MDOC = 'Mdoc'

ANGLES_FROM_RANGE = 'Range'

ANGLES_FROM_TLT = 'Tlt'

IMPORT_COPY_FILES = 0

IMPORT_FROM_FILES = 0

IMPORT_LINK_ABS = 1

IMPORT_LINK_REL = 2

MDOC_DATA_SOURCE = False

NOT_MDOC_GUI_COND = 'filesPattern is None or (filesPattern is not None and ".mdoc" not in filesPattern)'

accumDoses = None

acquisitions = None

copyOrLink(source, destination)

Calls the copy or link method chosen by the user in importAction option

fileModified(fileName, fileTimeout)

Check if the fileName modification time is less than a given timeout. Params:

fileName: input filename that will be checked. fileTimeout: timeout

getActions()

This method will allow that the ‘Stop import’ action to appears in the GUI when the user right-click in the protocol import box. It will allow a user to manually stop the streaming.

getMatchingFiles(fileTimeOut=None)

Return an ordered dict with TiltSeries found in the files as key and a list of all tilt images of that series as value.

importStep()

Copy images matching the filename pattern Register other parameters.

isBlacklisted(fileName)

Overwrite in subclasses

isInStreaming()

meanDosesPerFrame = None

sRates = None

stopImport()

Since the actual protocol that is running is in a different process that the one that this method will be invoked from the GUI, we will use a simple mechanism to place an special file to stop the streaming.

streamingHasFinished()

classmethod worksInStreaming()

class tomo.protocols.protocol_ts_import.ProtImportTsMovies(**kwargs)

Bases: tomo.protocols.protocol_ts_import.ProtImportTsBase

Protocol to import tilt series movies.

class tomo.protocols.protocol_ts_import.TiltMetadata(angle=None, angleFile=None, acqOrder=None, accumDose=None)

Bases: object

getAccumDose()

getAcqOrder()

getAngleMovieFile()

getTiltAngle()

setAccumDose(accumDose)

setAcqOorder(order)

setAngleMovieFile(angleMovieFile)

setTiltAngle(tiltAngle)