pwem.protocols.protocol_batch module

class pwem.protocols.protocol_batch.BatchProtocol(**kwargs)

Bases: EMProtocol

Base class to all protocols that are launched through other GUIs (such as showj) and that are called “batch” protocols. They should not be executed from normal “form” of other protocols.

class pwem.protocols.protocol_batch.ProtCreateFSC(**kwargs)

Bases: BatchProtocol

createOutputStep()

setInputFscList(fscList)

setInputObj(obj)

class pwem.protocols.protocol_batch.ProtCreateMask(**kwargs)

Bases: BatchProtocol

createMaskStep()

class pwem.protocols.protocol_batch.ProtUserSubSet(**args)

Bases: BatchProtocol

Create subsets from the GUI. This protocol will be executed mainly from the ShowJ gui or the new metadata viewer. For ShowJ: The enabled/disabled changes will be stored in a temporary sqlite For the Metadata viewer: the original sqlite is passed and a path of a txt file with the ids selected.

Example of a ShowJ socket message:

run protocol ProtUserSubSet inputObject=380 sqliteFile=’Runs/000335_ProtImodTSNormalization/tiltseries_state.sqlite’,’’ outputClassName=SetOfTiltSeries other=’’ label=’create subset’

run protocol is received by ProjectTCPRequestHandler.handle()

createSetObject()

Moves the sqlite with the enable/disable status to its own path to keep it and names it subset.sqlite

createSetStep()

getDefaultSummary()

usingShowJ()