Source code for tomo.protocols.protocol_ts_base

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
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# * [1] SciLifeLab, Stockholm University
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from pwem.protocols import EMProtocol
from pyworkflow.protocol import STEPS_PARALLEL, STATUS_NEW

from ..objects import TiltSeriesDict, Tomogram
from .protocol_base import ProtTomoBase


[docs]class ProtTsProcess(EMProtocol, ProtTomoBase): """ Base class for Tilt-Series (images or movies) processing protocols. This class should be used by protocols that receive tilt-series as input and produce tilt-series as output. This class will contain some common functionality about the steps execution (also in streaming) and the output generation. """ def __init__(self, **kwargs): EMProtocol.__init__(self, **kwargs) self.stepsExecutionMode = STEPS_PARALLEL # -------------------------- INSERT steps functions --------------------- def _insertAllSteps(self): self._initialize() inputTs = self._getInputTs() self._ciStepId = self._insertFunctionStep('convertInputStep', inputTs.getObjId()) self._insertFunctionStep('createOutputStep', wait=True, prerequisites=[self._ciStepId]) self._coStep = self._steps[-1] # get last step self._tsDict = TiltSeriesDict(inputTs, self._getOutputSet(), newItemsCallback=self._insertNewSteps, doneItemsCallback=self._updateOutput) self._tsDict.update() def _insertNewSteps(self, tsIdList): """ Insert processing steps for newly discovered tilt-series. """ for tsId in tsIdList: tsSteps = [] if self._doInsertTiltImageSteps(): for i, ti in enumerate(self._tsDict.getTiList(tsId)): tiStep = self._insertFunctionStep( 'processTiltImageStep', tsId, ti.getObjId(), *self._getArgs(), prerequisites=[self._ciStepId]) tsSteps.append(tiStep) tsStepId = self._insertFunctionStep('processTiltSeriesStep', tsId, prerequisites=tsSteps) self._coStep.addPrerequisites(tsStepId) self.updateSteps() def _stepsCheck(self): self._tsDict.update() # --------------------------- STEPS functions ----------------------------
[docs] def convertInputStep(self, inputId): """ To be implemented in subclasses. """ pass
[docs] def processTiltImageStep(self, tsId, tiltImageId, *args): """ To be implemented in subclasses. """ pass
[docs] def processTiltSeriesStep(self, tsId): """ To be implemented in subclasses. """ pass
def _updateOutputSet(self, outputSet, tsIdList): """ Update the output set with the finished Tilt-series. Params: :param tsIdList: list of ids of finished tasks. """ for tsId in tsIdList: ts = self._tsDict.getTs(tsId) outputSet.append(ts) for ti in self._tsDict.getTiList(tsId): ts.append(ti) outputSet.update(ts) def _updateOutput(self, tsIdList): """ Update the output set with the finished Tilt-series. Params: :param tsIdList: list of ids of finished tasks. """ # Flag to check the first time we save output self._createOutput = getattr(self, '_createOutput', True) outputSet = self._getOutputSet() if outputSet is None: # Special case just to update the outputSet status # but it only makes sense when there is outputSet if not tsIdList: return outputSet = self._createOutputSet() else: outputSet.enableAppend() self._createOutput = False # Call the sub-class method to update the output self._updateOutputSet(outputSet, tsIdList) outputSet.setStreamState(outputSet.STREAM_OPEN) if self._createOutput: outputSet.updateDim() self._defineOutputs(**{self._getOutputName(): outputSet}) self._defineSourceRelation(self._getInputTsPointer(), outputSet) self._createOutput = False else: outputSet.write() self._store(outputSet) outputSet.close() if self._tsDict.allDone(): self._coStep.setStatus(STATUS_NEW)
[docs] def createOutputStep(self): outputSet = self._getOutputSet() outputSet.setStreamState(outputSet.STREAM_CLOSED) outputSet.write() self._store(outputSet)
# --------------------------- INFO functions ------------------------------ def _validate(self): errors = [] return errors # --------------------------- UTILS functions ------------------------------ def _initialize(self): """ Allow sub-classes to make some initialization before all steps will be inserted in the execution list. """ pass def _getInputTsPointer(self): return None def _getInputTs(self): """ Return the tiltSeries input object. """ return self._getInputTsPointer().get() def _getOutputName(self): """ Return the output name, by default 'outputTiltSeries'. This method can be re-implemented in subclasses that have a different output. (e.g outputTomograms). """ return 'outputTiltSeries' def _getOutputSet(self): return getattr(self, self._getOutputName(), None) def _createOutputSet(self, suffix=''): """ Method to create the output set. By default will a SetOfTiltSeries, but can be re-defined in subclasses. """ outputSet = self._createSetOfTiltSeries(suffix=suffix) outputSet.copyInfo(self._getInputTs()) return outputSet def _getArgs(self): """ Return a list with parameters that will be passed to the process TiltSeries step. It can be redefined by subclasses. """ return [] def _doInsertTiltImageSteps(self): """ Default True, but if return False, the steps for each TiltImage will not be inserted. """ return True
[docs]class ProtTomoReconstruct(ProtTsProcess): """ Base class for Tomogram reconstruction protocols. """ def _doInsertTiltImageSteps(self): # For reconstruction protocols, usually we don't # want one step per each tilt-image return False def _updateOutputSet(self, outputSet, tsIdList): """ Override this method to convert the TiltSeriesM into TiltSeries. """ for tsId in tsIdList: t = Tomogram(location=self._getPath(self._getTomoName(tsId))) outputSet.append(t) def _createOutputSet(self): """ Create the output set of Tomograms. """ outputSet = self._createSetOfTomograms() samplingRate = self._getInputTs().getSamplingRate() if self.bin > 1: samplingRate *= self.bin.get() outputSet.setSamplingRate(samplingRate) return outputSet def _getOutputName(self): return 'outputTomograms' # --------------------------- UTILS functions ---------------------------- def _getInputTsPointer(self): return self.inputTiltSeries def _getTomoName(self, tsId): return '%s_tomo.mrc' % tsId