def getFluxAndBeamSizeFromISPyB(self, _xsDataFirstImage,
_xsDataExperimentalCondition):
"""
This method retrieves the flux and beamsize from ISPyB
"""
xsDataExperimentalCondition = None
if (_xsDataExperimentalCondition is not None):
bFoundValidFlux = False
xsDataExperimentalCondition = _xsDataExperimentalCondition.copy()
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection(
)
xsDataInputRetrieveDataCollection.setImage(
XSDataImage(_xsDataFirstImage.getPath()))
self.edPluginISPyBRetrieveDataCollection.setDataInput(
xsDataInputRetrieveDataCollection)
self.edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = self.edPluginISPyBRetrieveDataCollection.getDataOutput(
)
if xsDataResultRetrieveDataCollection is not None:
xsDataISPyBDataCollection = xsDataResultRetrieveDataCollection.getDataCollection(
)
if xsDataISPyBDataCollection is not None:
fFlux = xsDataISPyBDataCollection.getFlux()
if fFlux is not None:
self.screen(
"ISPyB reports flux to be: %g photons/sec" % fFlux)
if fFlux > self.fFluxThreshold:
xsDataExperimentalCondition.getBeam().setFlux(
XSDataFlux(fFlux))
bFoundValidFlux = True
fBeamSizeAtSampleX = xsDataISPyBDataCollection.beamSizeAtSampleX
fBeamSizeAtSampleY = xsDataISPyBDataCollection.beamSizeAtSampleY
if fBeamSizeAtSampleX is not None and fBeamSizeAtSampleY is not None:
self.screen("ISPyB reports beamsize X to be: %.3f mm" %
fBeamSizeAtSampleX)
self.screen("ISPyB reports beamsize Y to be: %.3f mm" %
fBeamSizeAtSampleY)
xsDataSize = XSDataSize()
xsDataSize.x = XSDataLength(fBeamSizeAtSampleX)
xsDataSize.y = XSDataLength(fBeamSizeAtSampleY)
xsDataExperimentalCondition.getBeam().setSize(
xsDataSize)
if not bFoundValidFlux:
self.screen(
"No valid flux could be retrieved from ISPyB! Trying to obtain flux from input data."
)
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataBeamFlux = xsDataBeam.getFlux()
if xsDataBeamFlux is not None:
fFluxMXCuBE = xsDataBeamFlux.getValue()
self.screen("MXCuBE reports flux to be: %g photons/sec" %
fFluxMXCuBE)
if fFluxMXCuBE < self.fFluxThreshold:
self.screen("MXCuBE flux invalid!")
return xsDataExperimentalCondition
def getFluxAndBeamSizeFromISPyB(self, _xsDataFirstImage, _xsDataExperimentalCondition):
"""
This method retrieves the flux and beamsize from ISPyB
"""
xsDataExperimentalCondition = None
if _xsDataExperimentalCondition is not None:
bFoundValidFlux = False
xsDataExperimentalCondition = _xsDataExperimentalCondition.copy()
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.setImage(XSDataImage(_xsDataFirstImage.getPath()))
self.edPluginISPyBRetrieveDataCollection.setDataInput(xsDataInputRetrieveDataCollection)
self.edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = self.edPluginISPyBRetrieveDataCollection.getDataOutput()
if xsDataResultRetrieveDataCollection is not None:
xsDataISPyBDataCollection = xsDataResultRetrieveDataCollection.getDataCollection()
if xsDataISPyBDataCollection is not None:
fFlux = xsDataISPyBDataCollection.getFlux_end()
if fFlux is not None:
self.screen("ISPyB reports flux to be: %g photons/sec" % fFlux)
if fFlux > self.fFluxThreshold:
xsDataExperimentalCondition.getBeam().setFlux(XSDataFlux(fFlux))
bFoundValidFlux = True
fBeamSizeAtSampleX = xsDataISPyBDataCollection.beamSizeAtSampleX
fBeamSizeAtSampleY = xsDataISPyBDataCollection.beamSizeAtSampleY
if fBeamSizeAtSampleX is not None and fBeamSizeAtSampleY is not None:
self.screen("ISPyB reports beamsize X to be: %.3f mm" % fBeamSizeAtSampleX)
self.screen("ISPyB reports beamsize Y to be: %.3f mm" % fBeamSizeAtSampleY)
xsDataSize = XSDataSize()
xsDataSize.x = XSDataLength(fBeamSizeAtSampleX)
xsDataSize.y = XSDataLength(fBeamSizeAtSampleY)
xsDataExperimentalCondition.getBeam().setSize(xsDataSize)
# Get transmission if it's not already there
if xsDataExperimentalCondition.beam.transmission is None:
fTransmission = xsDataISPyBDataCollection.transmission
xsDataExperimentalCondition.beam.transmission = XSDataDouble(fTransmission)
if not bFoundValidFlux:
self.screen("No valid flux could be retrieved from ISPyB! Trying to obtain flux from input data.")
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataBeamFlux = xsDataBeam.getFlux()
if xsDataBeamFlux is not None:
fFluxMXCuBE = xsDataBeamFlux.getValue()
self.screen("MXCuBE reports flux to be: %g photons/sec" % fFluxMXCuBE)
if fFluxMXCuBE < self.fFluxThreshold:
self.screen("MXCuBE flux lower than threshold flux %g photons/s!" % self.fFluxThreshold)
self.screen("Forcing flux to 0.0 photons/s")
xsDataExperimentalCondition.getBeam().setFlux(XSDataFlux(0.0))
else:
# Force missing flux to 0.0
self.screen("No flux neither in ISPyB nor in mxCuBE, forcing flux to 0.0 photon/s")
xsDataExperimentalCondition.getBeam().setFlux(XSDataFlux(0.0))
return xsDataExperimentalCondition
def getFluxAndBeamSizeFromISPyB(self, _xsDataFirstImage, _xsDataExperimentalCondition):
"""
This method retrieves the flux and beamsize from ISPyB
"""
xsDataExperimentalCondition = None
if (_xsDataExperimentalCondition is not None):
bFoundValidFlux = False
xsDataExperimentalCondition = _xsDataExperimentalCondition.copy()
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.setImage(XSDataImage(_xsDataFirstImage.getPath()))
self.edPluginISPyBRetrieveDataCollection.setDataInput(xsDataInputRetrieveDataCollection)
self.edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = self.edPluginISPyBRetrieveDataCollection.getDataOutput()
if xsDataResultRetrieveDataCollection is not None:
xsDataISPyBDataCollection = xsDataResultRetrieveDataCollection.getDataCollection()
if xsDataISPyBDataCollection is not None:
fFlux = xsDataISPyBDataCollection.getFlux_end()
if fFlux is not None:
self.screen("ISPyB reports flux to be: %g photons/sec" % fFlux)
if fFlux > self.fFluxThreshold:
xsDataExperimentalCondition.getBeam().setFlux(XSDataFlux(fFlux))
bFoundValidFlux = True
fBeamSizeAtSampleX = xsDataISPyBDataCollection.beamSizeAtSampleX
fBeamSizeAtSampleY = xsDataISPyBDataCollection.beamSizeAtSampleY
if fBeamSizeAtSampleX is not None and fBeamSizeAtSampleY is not None:
self.screen("ISPyB reports beamsize X to be: %.3f mm" % fBeamSizeAtSampleX)
self.screen("ISPyB reports beamsize Y to be: %.3f mm" % fBeamSizeAtSampleY)
xsDataSize = XSDataSize()
xsDataSize.x = XSDataLength(fBeamSizeAtSampleX)
xsDataSize.y = XSDataLength(fBeamSizeAtSampleY)
xsDataExperimentalCondition.getBeam().setSize(xsDataSize)
# Get transmission if it's not already there
if xsDataExperimentalCondition.beam.transmission is None:
fTransmission = xsDataISPyBDataCollection.transmission
xsDataExperimentalCondition.beam.transmission = XSDataDouble(fTransmission)
if not bFoundValidFlux:
self.screen("No valid flux could be retrieved from ISPyB! Trying to obtain flux from input data.")
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataBeamFlux = xsDataBeam.getFlux()
if xsDataBeamFlux is not None:
fFluxMXCuBE = xsDataBeamFlux.getValue()
self.screen("MXCuBE reports flux to be: %g photons/sec" % fFluxMXCuBE)
if fFluxMXCuBE < self.fFluxThreshold:
self.screen("MXCuBE flux lower than threshold flux %g photons/s!" % self.fFluxThreshold)
self.screen("Forcing flux to 0.0 photons/s")
xsDataExperimentalCondition.getBeam().setFlux(XSDataFlux(0.0))
else:
# Force missing flux to 0.0
self.screen("No flux neither in ISPyB nor in mxCuBE, forcing flux to 0.0 photon/s")
xsDataExperimentalCondition.getBeam().setFlux(XSDataFlux(0.0))
return xsDataExperimentalCondition
def getFluxAndBeamSizeFromISPyB(self, _xsDataFirstImage, _xsDataExperimentalCondition):
"""
This method retrieves the flux and beamsize from ISPyB
"""
xsDataExperimentalCondition = None
if (_xsDataExperimentalCondition is not None):
bFoundValidFlux = False
xsDataExperimentalCondition = _xsDataExperimentalCondition.copy()
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.setImage(XSDataImage(_xsDataFirstImage.getPath()))
self.edPluginISPyBRetrieveDataCollection.setDataInput(xsDataInputRetrieveDataCollection)
self.edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = self.edPluginISPyBRetrieveDataCollection.getDataOutput()
if xsDataResultRetrieveDataCollection is not None:
xsDataISPyBDataCollection = xsDataResultRetrieveDataCollection.getDataCollection()
if xsDataISPyBDataCollection is not None:
fFlux = xsDataISPyBDataCollection.getFlux()
if fFlux is not None:
self.screen("ISPyB reports flux to be: %g photons/sec" % fFlux)
if fFlux > self.fFluxThreshold:
xsDataExperimentalCondition.getBeam().setFlux(XSDataFlux(fFlux))
bFoundValidFlux = True
fBeamSizeAtSampleX = xsDataISPyBDataCollection.beamSizeAtSampleX
fBeamSizeAtSampleY = xsDataISPyBDataCollection.beamSizeAtSampleY
if fBeamSizeAtSampleX is not None and fBeamSizeAtSampleY is not None:
self.screen("ISPyB reports beamsize X to be: %.3f mm" % fBeamSizeAtSampleX)
self.screen("ISPyB reports beamsize Y to be: %.3f mm" % fBeamSizeAtSampleY)
xsDataSize = XSDataSize()
xsDataSize.x = XSDataLength(fBeamSizeAtSampleX)
xsDataSize.y = XSDataLength(fBeamSizeAtSampleY)
xsDataExperimentalCondition.getBeam().setSize(xsDataSize)
if not bFoundValidFlux:
self.screen("No valid flux could be retrieved from ISPyB! Trying to obtain flux from input data.")
xsDataBeam = xsDataExperimentalCondition.getBeam()
xsDataBeamFlux = xsDataBeam.getFlux()
if xsDataBeamFlux is not None:
fFluxMXCuBE = xsDataBeamFlux.getValue()
self.screen("MXCuBE reports flux to be: %g photons/sec" % fFluxMXCuBE)
if fFluxMXCuBE < self.fFluxThreshold:
self.screen("MXCuBE flux invalid!")
return xsDataExperimentalCondition
def getFluxFromISPyB(self, _xsDataFirstImage, _xsDataExperimentalCondition):
"""
This method retrieves the flux from ISPyB
"""
xsDataExperimentalCondition = None
if (_xsDataExperimentalCondition is not None):
xsDataExperimentalCondition = _xsDataExperimentalCondition.copy()
bFoundValidFlux = False
xsDataBeam = xsDataExperimentalCondition.getBeam()
if xsDataBeam is None:
xsDataBeam = XSDataBeam()
xsDataExperimentalCondition.setBeam(xsDataBeam)
xsDataBeamFlux = xsDataBeam.getFlux()
if xsDataBeamFlux is not None:
fFluxMXCuBE = xsDataBeamFlux.getValue()
self.screen("MXCuBE reports flux to be: %g photons/sec" % fFluxMXCuBE)
if fFluxMXCuBE > self.fFluxThreshold:
bFoundValidFlux = True
else:
self.screen("MXCuBE flux invalid! Trying to obtain flux from ISPyB.")
if not bFoundValidFlux:
# Here we try to retrieve the flux from ISPyB
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.setImage(XSDataImage(_xsDataFirstImage.getPath()))
self.edPluginISPyBRetrieveDataCollection.setDataInput(xsDataInputRetrieveDataCollection)
self.edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = self.edPluginISPyBRetrieveDataCollection.getDataOutput()
if xsDataResultRetrieveDataCollection is not None:
xsDataISPyBDataCollection = xsDataResultRetrieveDataCollection.getDataCollection()
if xsDataISPyBDataCollection is not None:
fFlux = xsDataISPyBDataCollection.getFlux()
if fFlux is not None:
self.screen("ISPyB reports flux to be: %g photons/sec" % fFlux)
xsDataExperimentalCondition.getBeam().setFlux(XSDataFlux(fFlux))
bFoundValidFlux = True
if not bFoundValidFlux:
self.screen("No valid flux could be retrieved from ISPyB!")
return xsDataExperimentalCondition