def functionXMLin(_strFilename):
"""Here we create the XML string to be passed to the EDNA plugin from the input strFilename
This can / should be modified by the final user
@param _strFilename: full path of the input file
@type _strFilename: python string representing the path
@return: string
"""
EDVerbose.screen("Starting processing of image %s" % (_strFilename))
# First check if the filename end with .img or .mccd:
strXML = None
if _strFilename.endswith(".img") or _strFilename.endswith(".mccd") or _strFilename.endswith(".cbf"):
xsDataInputGridScreening = XSDataInputGridScreening()
xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(
XSDataTime(EDParallelExecuteGridScreening.fMaxExposureTime)
)
xsDataInputGridScreening.setDiffractionPlan(xsDataDiffractionPlan)
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(_strFilename))
xsDataInputGridScreening.setImageFile(xsDataFile)
if EDParallelExecuteGridScreening.bOnlyImageQualityIndicators:
xsDataInputGridScreening.setDoOnlyImageQualityIndicators(XSDataBoolean(True))
if EDParallelExecuteGridScreening.bStoreInISPyB:
xsDataInputGridScreening.setStoreImageQualityIndicatorsInISPyB(XSDataBoolean(True))
if EDParallelExecuteGridScreening.bDoOnlyIntegrationWithXMLOutput:
xsDataInputGridScreening.setDoOnlyIntegrationWithXMLOutput(XSDataBoolean(True))
strXML = xsDataInputGridScreening.marshal()
else:
EDVerbose.screen("File name not ending with .img or .mccd - ignored : %s" % _strFilename)
return strXML
def functionXMLin(_strFilename):
"""Here we create the XML string to be passed to the EDNA plugin from the input strFilename
This can / should be modified by the final user
@param _strFilename: full path of the input file
@type _strFilename: python string representing the path
@return: string
"""
EDVerbose.screen("Starting processing of image %s" % (_strFilename))
# First check if the filename end with .img or .mccd:
strXML = None
if (_strFilename.endswith(".img") or _strFilename.endswith(".mccd") or _strFilename.endswith(".cbf")):
xsDataInputGridScreening = XSDataInputGridScreening()
xsDataDiffractionPlan = XSDataDiffractionPlan()
xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(EDParallelExecuteGridScreening.fMaxExposureTime))
xsDataInputGridScreening.setDiffractionPlan(xsDataDiffractionPlan)
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(_strFilename))
xsDataInputGridScreening.setImageFile(xsDataFile)
if EDParallelExecuteGridScreening.bOnlyImageQualityIndicators:
xsDataInputGridScreening.setDoOnlyImageQualityIndicators(XSDataBoolean(True))
if EDParallelExecuteGridScreening.bStoreInISPyB:
xsDataInputGridScreening.setStoreImageQualityIndicatorsInISPyB(XSDataBoolean(True))
if EDParallelExecuteGridScreening.bDoOnlyIntegrationWithXMLOutput:
xsDataInputGridScreening.setDoOnlyIntegrationWithXMLOutput(XSDataBoolean(True))
strXML = xsDataInputGridScreening.marshal()
else:
EDVerbose.screen("File name not ending with .img or .mccd - ignored : %s" % _strFilename)
return strXML
strPathToTempDir = tempfile.mkdtemp(
prefix="edna-image-quality-indicators_")
os.chdir(strPathToTempDir)
EDVerbose.setLogFileName(os.path.join(strPathToTempDir, "edna.log"))
# Popolate input data
EDVerbose.screen("Starting EDNA image quality indicators processing")
EDVerbose.screen("Arguments: %r" % sys.argv)
bVerbose = False
bDebug = False
listPaths = []
for iIndex, strArg in enumerate(sys.argv[1:]):
strarg = strArg.lower()
if strarg == "--verbose":
EDVerbose.setVerboseOn()
elif strarg == "--debug":
EDVerbose.setVerboseDebugOn()
if os.path.exists(strArg):
listPaths.append(os.path.abspath(strArg))
for strPath in listPaths:
xsDataInputGridScreening = XSDataInputGridScreening()
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(strPath))
xsDataInputGridScreening.setImageFile(xsDataFile)
xsDataInputGridScreening.setDoOnlyImageQualityIndicators(
XSDataBoolean(True))
xsDataInputGridScreening.setStoreImageQualityIndicatorsInISPyB(
XSDataBoolean(True))
edPluginGridScreening = EDFactoryPluginStatic.loadPlugin(
"EDPluginControlGridScreeningv1_0")
edPluginGridScreening.setDataInput(xsDataInputGridScreening)
edPluginGridScreening.executeSynchronous()
from XSDataGridScreeningv1_0 import XSDataInputGridScreening
if __name__ == '__main__':
strPathToTempDir = tempfile.mkdtemp(prefix="edna-image-quality-indicators_")
os.chdir(strPathToTempDir)
EDVerbose.setLogFileName(os.path.join(strPathToTempDir, "edna.log"))
# Popolate input data
EDVerbose.screen("Starting EDNA image quality indicators processing")
EDVerbose.screen("Arguments: %r" % sys.argv)
bVerbose = False
bDebug = False
listPaths = []
for iIndex, strArg in enumerate(sys.argv[1:]):
strarg = strArg.lower()
if strarg == "--verbose":
EDVerbose.setVerboseOn()
elif strarg == "--debug":
EDVerbose.setVerboseDebugOn()
if os.path.exists(strArg):
listPaths.append(os.path.abspath(strArg))
for strPath in listPaths:
xsDataInputGridScreening = XSDataInputGridScreening()
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(strPath))
xsDataInputGridScreening.setImageFile(xsDataFile)
xsDataInputGridScreening.setDoOnlyImageQualityIndicators(XSDataBoolean(True))
xsDataInputGridScreening.setStoreImageQualityIndicatorsInISPyB(XSDataBoolean(True))
edPluginGridScreening = EDFactoryPluginStatic.loadPlugin("EDPluginControlGridScreeningv1_0")
edPluginGridScreening.setDataInput(xsDataInputGridScreening)
edPluginGridScreening.executeSynchronous()
