def generateMOSFLMCommands(self):
"""
This method creates a list of MOSFLM integration commands given a valid
XSDataMOSFLMIntegrationingInput as self.getDataInput()
"""
EDPluginMOSFLMv10.generateMOSFLMCommands(self)
self.DEBUG("EDPluginMOSFLMIntegrationv10.generateMOSFLMCommands")
xsDataMOSFLMInputIntegration = self.getDataInput()
if (xsDataMOSFLMInputIntegration is not None):
iImageStart = xsDataMOSFLMInputIntegration.getImageStart().getValue()
iImageEnd = xsDataMOSFLMInputIntegration.getImageEnd().getValue()
fRotationAxisStart = xsDataMOSFLMInputIntegration.getRotationAxisStart().getValue()
fOscillationWidth = xsDataMOSFLMInputIntegration.getOscillationWidth().getValue()
self.addListCommandExecution("HKLOUT process_%d_%d.mtz" %
(iImageStart, iImageEnd))
self.addListCommandExecution("PROCESS %d TO %d START %f ANGLE %f" %
(iImageStart, iImageEnd, fRotationAxisStart, fOscillationWidth))
self.addListCommandExecution("BEST ON")
self.addListCommandExecution("GO")
self.addListCommandExecution("BEST OFF")
# Force name of log file
self.setScriptLogFileName(self.compactPluginName(self.getClassName())+".log")
self.DEBUG("Finished EDPluginMOSFLMIntegrationv10.generateMOSFLMCommands")
def generateMOSFLMCommands(self):
"""
This method creates a list of MOSFLM integration commands given a valid
XSDataMOSFLMIntegrationingInput as self.getDataInput()
"""
EDPluginMOSFLMv10.generateMOSFLMCommands(self)
self.DEBUG("EDPluginMOSFLMIntegrationv10.generateMOSFLMCommands")
xsDataMOSFLMInputIntegration = self.getDataInput()
if (xsDataMOSFLMInputIntegration is not None):
iImageStart = xsDataMOSFLMInputIntegration.getImageStart().getValue()
iImageEnd = xsDataMOSFLMInputIntegration.getImageEnd().getValue()
fRotationAxisStart = xsDataMOSFLMInputIntegration.getRotationAxisStart().getValue()
fOscillationWidth = xsDataMOSFLMInputIntegration.getOscillationWidth().getValue()
self.addListCommandExecution("HKLOUT process_%d_%d.mtz" %
(iImageStart, iImageEnd))
self.addListCommandExecution("PROCESS %d TO %d START %f ANGLE %f" %
(iImageStart, iImageEnd, fRotationAxisStart, fOscillationWidth))
self.addListCommandExecution("BEST ON")
self.addListCommandExecution("GO")
self.addListCommandExecution("BEST OFF")
# Force name of log file
self.setScriptLogFileName(self.compactPluginName(self.getClassName())+".log")
self.DEBUG("Finished EDPluginMOSFLMIntegrationv10.generateMOSFLMCommands")
def generateMOSFLMCommands(self):
"""
This method creates a list of MOSFLM integration commands given a valid
XSDataMOSFLMInputGeneratePrediction as input to the plugin.
"""
EDPluginMOSFLMv10.generateMOSFLMCommands(self)
EDVerbose.DEBUG("EDPluginMOSFLMGeneratePredictionv10.generateMOSFLMCommands")
xsDataMOSFLMInputGeneratePrediction = self.getDataInput()
if (xsDataMOSFLMInputGeneratePrediction is not None):
pyStrTemplate = xsDataMOSFLMInputGeneratePrediction.getTemplate().getValue()
xsDataMOSFLMImage = xsDataMOSFLMInputGeneratePrediction.getImage()
iImageNumber = xsDataMOSFLMImage.getNumber().getValue()
pyStrImageFileName = self.getImageFileNameFromTemplate(pyStrTemplate, iImageNumber)
if (pyStrImageFileName is not None):
self.setPredictionImageFileName(pyStrImageFileName + "_pred.jpg")
fRotationAxisStart = xsDataMOSFLMImage.getRotationAxisStart().getValue()
fRotationAxisEnd = xsDataMOSFLMImage.getRotationAxisEnd().getValue()
self.addListCommandExecution("XGUI ON")
self.addListCommandExecution("IMAGE %d PHI %f TO %f" % (iImageNumber, fRotationAxisStart, fRotationAxisEnd))
self.addListCommandExecution("GO")
self.addListCommandExecution("PREDICT_SPOTS")
self.addListCommandExecution("CREATE_IMAGE PREDICTION ON BINARY TRUE FILENAME %s" % (self.getPredictionImageFileName()))
self.addListCommandExecution("RETURN")
self.addListCommandExecution("EXIT")
self.addListCommandPostExecution("chmod 644 %s" % self.getPredictionImageFileName())
EDVerbose.DEBUG("Finished EDPluginMOSFLMGeneratePredictionv10.generateMOSFLMCommands")
def generateMOSFLMCommands(self):
"""
This method creates a list of MOSFLM indexing commands given a valid
XSDataMOSFLMIndexingingInput as self.getDataInput()
"""
EDPluginMOSFLMv10.generateMOSFLMCommands(self)
EDVerbose.DEBUG("EDPluginMOSFLMIndexingv10.generateMOSFLMCommands")
xsDataMOSFLMIndexingInput = self.getDataInput()
if (xsDataMOSFLMIndexingInput != None):
self.addListCommandExecution("NEWMAT " + self.getNewmatFileName())
xsDataMOSFLMImageList = xsDataMOSFLMIndexingInput.getImage()
for xsDataMOSFLMImage in xsDataMOSFLMImageList:
iImageNumber = xsDataMOSFLMImage.getNumber().getValue()
fRotationAxisStart = xsDataMOSFLMImage.getRotationAxisStart().getValue()
fRotationAxisEnd = xsDataMOSFLMImage.getRotationAxisEnd().getValue()
self.addListCommandExecution("AUTOINDEX DPS REFINE IMAGE " + str(iImageNumber) + " " \
"PHI " + str(fRotationAxisStart) + " " + str(fRotationAxisEnd))
self.addListCommandExecution("GO")
for xsDataImage in xsDataMOSFLMImageList:
self.addListCommandExecution("MOSAIC ESTIMATE %d" % xsDataImage.getNumber().getValue())
self.addListCommandExecution("GO")
# strPrefix = strTemplate.split("#")[0][:-1]
# strGenFileName = strPrefix + ".gen"
# strSptFileName = strPrefix + ".spt"
EDVerbose.DEBUG("Finished EDPluginMOSFLMIndexingv10.generateMOSFLMIndexingCommands")
def generateMOSFLMCommands(self):
"""
This method creates a list of MOSFLM integration commands given a valid
XSDataMOSFLMIntegrationingInput as self.getDataInput()
"""
EDPluginMOSFLMv10.generateMOSFLMCommands(self)
EDVerbose.DEBUG("EDPluginMOSFLMIntegrationv10.generateMOSFLMCommands")
xsDataMOSFLMInputIntegration = self.getDataInput()
if xsDataMOSFLMInputIntegration is not None:
iImageStart = xsDataMOSFLMInputIntegration.getImageStart().getValue()
iImageEnd = xsDataMOSFLMInputIntegration.getImageEnd().getValue()
fRotationAxisStart = xsDataMOSFLMInputIntegration.getRotationAxisStart().getValue()
fOscillationWidth = xsDataMOSFLMInputIntegration.getOscillationWidth().getValue()
self.addListCommandExecution("HKLOUT process_%d_%d.mtz" % (iImageStart, iImageEnd))
self.addListCommandExecution(
"PROCESS %d TO %d START %f ANGLE %f" % (iImageStart, iImageEnd, fRotationAxisStart, fOscillationWidth)
)
self.addListCommandExecution("BEST ON")
self.addListCommandExecution("GO")
self.addListCommandExecution("BEST OFF")
EDVerbose.DEBUG("Finished EDPluginMOSFLMIntegrationv10.generateMOSFLMCommands")
def generateMOSFLMCommands(self):
"""
This method creates a list of MOSFLM integration commands given a valid
XSDataMOSFLMInputGeneratePrediction as input to the plugin.
"""
EDPluginMOSFLMv10.generateMOSFLMCommands(self)
self.DEBUG(
"EDPluginMOSFLMGeneratePredictionv10.generateMOSFLMCommands")
xsDataMOSFLMInputGeneratePrediction = self.getDataInput()
if (xsDataMOSFLMInputGeneratePrediction is not None):
pyStrTemplate = xsDataMOSFLMInputGeneratePrediction.getTemplate(
).getValue()
xsDataMOSFLMImage = xsDataMOSFLMInputGeneratePrediction.getImage()
iImageNumber = xsDataMOSFLMImage.getNumber().getValue()
pyStrImageFileName = self.getImageFileNameFromTemplate(
pyStrTemplate, iImageNumber)
if "master" in xsDataMOSFLMInputGeneratePrediction.template.value:
iImageNumber = 1
if (pyStrImageFileName is not None):
self.setPredictionImageFileName(pyStrImageFileName +
"_pred.jpg")
fRotationAxisStart = xsDataMOSFLMImage.getRotationAxisStart(
).getValue()
fRotationAxisEnd = xsDataMOSFLMImage.getRotationAxisEnd().getValue(
)
self.addListCommandExecution("XGUI ON")
self.addListCommandExecution(
"IMAGE %d PHI %f TO %f" %
(iImageNumber, fRotationAxisStart, fRotationAxisEnd))
self.addListCommandExecution("GO")
self.addListCommandExecution("PREDICT_SPOTS")
self.addListCommandExecution(
"CREATE_IMAGE PREDICTION ON BINARY TRUE FILENAME %s" %
(self.getPredictionImageFileName()))
self.addListCommandExecution("RETURN")
self.addListCommandExecution("EXIT")
self.addListCommandPostExecution("chmod 644 %s" %
self.getPredictionImageFileName())
# Force name of log file
self.setScriptLogFileName(
self.compactPluginName(self.getClassName()) + ".log")
self.DEBUG(
"Finished EDPluginMOSFLMGeneratePredictionv10.generateMOSFLMCommands"
)
def generateMOSFLMCommands(self):
"""
This method creates a list of MOSFLM indexing commands given a valid
XSDataMOSFLMIndexingingInput as self.getDataInput()
"""
EDPluginMOSFLMv10.generateMOSFLMCommands(self)
self.DEBUG("EDPluginMOSFLMIndexingv10.generateMOSFLMCommands")
xsDataMOSFLMIndexingInput = self.getDataInput()
if (xsDataMOSFLMIndexingInput != None):
self.addListCommandExecution("NEWMAT " + self.getNewmatFileName())
xsDataMOSFLMImageList = xsDataMOSFLMIndexingInput.getImage()
for xsDataMOSFLMImage in xsDataMOSFLMImageList:
iImageNumber = xsDataMOSFLMImage.getNumber().getValue()
fRotationAxisStart = xsDataMOSFLMImage.getRotationAxisStart(
).getValue()
fRotationAxisEnd = xsDataMOSFLMImage.getRotationAxisEnd(
).getValue()
self.addListCommandExecution("AUTOINDEX DPS REFINE IMAGE " + str(iImageNumber) + " " \
"PHI " + str(fRotationAxisStart) + " " + str(fRotationAxisEnd))
self.addListCommandExecution("GO")
for xsDataImage in xsDataMOSFLMImageList:
self.addListCommandExecution(
"MOSAIC ESTIMATE %d" % xsDataImage.getNumber().getValue())
self.addListCommandExecution("GO")
# strPrefix = strTemplate.split("#")[0][:-1]
# strGenFileName = strPrefix + ".gen"
# strSptFileName = strPrefix + ".spt"
# Force name of log file
self.setScriptLogFileName(
self.compactPluginName(self.getClassName()) + ".log")
self.DEBUG(
"Finished EDPluginMOSFLMIndexingv10.generateMOSFLMIndexingCommands"
)
