def getDamParOutputFromDNATables(self, _xsDataDnaTables):
xsDataResultBest = XSDataResultBest()
xsTablesCollectionStrategy = EDUtilsTable.getTableListFromTables(_xsDataDnaTables, "dam_par_plan")
iCollectionPlanNumber = 1
for xsTableCollectionStrategy in xsTablesCollectionStrategy:
xsDataBestCollectionPlan = XSDataBestCollectionPlan()
xsDataStrategySummary = XSDataBestStrategySummary()
xsGeneralList = EDUtilsTable.getListsFromTable(xsTableCollectionStrategy, "general")[0]
xsCollectionRunList = EDUtilsTable.getListsFromTable(xsTableCollectionStrategy, "collection_run")
iCollectionRunNumber = 1
for xsCollectionRunItemList in xsCollectionRunList:
xsDataCollectionRun = self.collectionRunItemListToCollectionRun(xsCollectionRunItemList, iCollectionRunNumber)
xsDataBestCollectionPlan.addCollectionRun(xsDataCollectionRun)
iCollectionRunNumber = iCollectionRunNumber + 1
xsDataBestCollectionPlan.setCollectionPlanNumber(XSDataInteger(iCollectionPlanNumber))
xsDataResultBest.addCollectionPlan(xsDataBestCollectionPlan)
iCollectionPlanNumber = iCollectionPlanNumber + 1
xsItemDistance = EDUtilsTable.getItemFromList(xsGeneralList, "distance")
fDistance = float(xsItemDistance.getValueOf_())
xsDataStrategySummary.setDistance(XSDataLength(fDistance))
xsItemResolution = EDUtilsTable.getItemFromList(xsGeneralList, "resolution")
fResolution = float(xsItemResolution.getValueOf_())
xsDataStrategySummary.setResolution(XSDataDouble(fResolution))
xsDataBestCollectionPlan.setStrategySummary(xsDataStrategySummary)
return xsDataResultBest
def getOutputDataFromDNATableFile(self, _strFileName):
xsDataResultBest = XSDataResultBest()
if os.path.exists(_strFileName):
strDnaTablesXML = self.readProcessFile(_strFileName)
# Fix for MXSUP-1751: Error when parsing broken XML
try:
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
except Exception as e:
self.setFailure()
self.error("Parsing of BEST XML file failed: %s" % e)
# Loop through all the tables and fill in the relevant parts of xsDataResultBest
if not self.isFailure():
xsDataStringStrategyOption = self.getDataInput(
).getStrategyOption()
if (xsDataStringStrategyOption is not None):
strStrategyOption = xsDataStringStrategyOption.getValue()
if (strStrategyOption.find("-DamPar") != -1):
xsDataResultBest = self.getDamParOutputFromDNATables(
xsDataDnaTables)
elif (strStrategyOption.find("-Bonly") != -1):
xsDataResultBest = self.getBonlyOutputFromDNATables(
xsDataDnaTables)
else:
xsDataResultBest = self.getDataCollectionOutputDataFromDNATables(
xsDataDnaTables)
else:
xsDataResultBest = self.getDataCollectionOutputDataFromDNATables(
xsDataDnaTables)
return xsDataResultBest
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginBestv1_2.finallyProcess")
strError = self.readProcessErrorLogFile()
if ((strError is not None) and (strError != "")):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginBestv1_2.postProcess', 'EDPluginBestv1_2', strError)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setDataOutput(XSDataResultBest())
self.setFailure()
else:
xsDataResultBest = self.getOutputDataFromDNATableFile(
os.path.join(self.getWorkingDirectory(),
self.getScriptBaseName() + "_dnaTables.xml"))
xsDataFilePathToLog = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
self.getScriptLogFileName())))
xsDataResultBest.setPathToLogFile(xsDataFilePathToLog)
xsDataFilePathToPlotMtv = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
self.getScriptBaseName() + "_plots.mtv")))
xsDataResultBest.setPathToPlotMtvFile(xsDataFilePathToPlotMtv)
self.setDataOutput(xsDataResultBest)
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputBest)
self.setDataOutput(XSDataResultBest())
# This version of the Best plugin requires the latest
# version of Best.
self.addCompatibleVersion("Version 4.1.0 // 02.10.2012")
self.strCONF_BEST_HOME_LABEL = "besthome"
# Default value of strategy complexity
self.strComplexity = "none"
self.strBestHome = None
self.strCommandBestHome = None
self.strCommandBest = None
self.strExposureTime = None
self.strDoseRate = None
self.strDetectorType = None
self.strPathToBestDatFile = None
self.strPathToBestParFile = None
self.listFileBestHKL = []
self.strPathToCorrectLp = None
self.strPathToBkgpixCbf = None
self.strListFileXdsAsciiHkl = None
self.bVersionHigherThan4_0 = False
def getBonlyOutputFromDNATables(self, _xsDataDnaTables):
xsDataResultBest = XSDataResultBest()
xsTablesGeneralInform = EDUtilsTable.getTableListFromTables(_xsDataDnaTables, "general_inform")
xsDataBestCollectionPlan = XSDataBestCollectionPlan()
xsDataCrystalScale = XSDataCrystalScale()
xsCrystalScaleList = EDUtilsTable.getListsFromTable(xsTablesGeneralInform[0], "crystal_scale")[0]
xsItemScal = EDUtilsTable.getItemFromList(xsCrystalScaleList, "scal")
fScal = float(xsItemScal.getValueOf_())
xsDataCrystalScale.setScale(XSDataDouble(fScal))
xsItemBfactor = EDUtilsTable.getItemFromList(xsCrystalScaleList, "B_factor")
fBfactor = float(xsItemBfactor.getValueOf_())
xsDataCrystalScale.setBFactor(XSDataDouble(fBfactor))
xsDataBestCollectionPlan.setCrystalScale(xsDataCrystalScale)
xsDataResultBest.addCollectionPlan(xsDataBestCollectionPlan)
return xsDataResultBest
def getDamParOutputFromDNATables(self, _xsDataDnaTables):
xsDataResultBest = XSDataResultBest()
xsTablesCollectionStrategy = EDUtilsTable.getTableListFromTables(
_xsDataDnaTables, "dam_par_plan")
iCollectionPlanNumber = 1
for xsTableCollectionStrategy in xsTablesCollectionStrategy:
xsDataBestCollectionPlan = XSDataBestCollectionPlan()
xsDataStrategySummary = XSDataBestStrategySummary()
xsGeneralList = EDUtilsTable.getListsFromTable(
xsTableCollectionStrategy, "general")[0]
xsCollectionRunList = EDUtilsTable.getListsFromTable(
xsTableCollectionStrategy, "collection_run")
iCollectionRunNumber = 1
for xsCollectionRunItemList in xsCollectionRunList:
xsDataCollectionRun = self.collectionRunItemListToCollectionRun(
xsCollectionRunItemList, iCollectionRunNumber)
xsDataBestCollectionPlan.addCollectionRun(xsDataCollectionRun)
iCollectionRunNumber = iCollectionRunNumber + 1
xsDataBestCollectionPlan.setCollectionPlanNumber(
XSDataInteger(iCollectionPlanNumber))
xsDataResultBest.addCollectionPlan(xsDataBestCollectionPlan)
iCollectionPlanNumber = iCollectionPlanNumber + 1
xsItemDistance = EDUtilsTable.getItemFromList(
xsGeneralList, "distance")
fDistance = float(xsItemDistance.getValueOf_())
xsDataStrategySummary.setDistance(XSDataLength(fDistance))
xsItemResolution = EDUtilsTable.getItemFromList(
xsGeneralList, "resolution")
fResolution = float(xsItemResolution.getValueOf_())
xsDataStrategySummary.setResolution(XSDataDouble(fResolution))
xsDataBestCollectionPlan.setStrategySummary(xsDataStrategySummary)
return xsDataResultBest
def testGenerateExecutiveSummary(self):
pyStrInputBest = self.readAndParseFile (self.m_edReferenceInputFile)
pyStrResultBest = self.readAndParseFile (self.m_edReferenceResultFile)
from XSDataBestv1_2 import XSDataInputBest
from XSDataBestv1_2 import XSDataResultBest
xsDataInputBest = XSDataInputBest.parseString(pyStrInputBest)
xsDataResultBest = XSDataResultBest.parseString(pyStrResultBest)
edPluginBest = self.createPlugin()
edPluginBest.setDataInput(xsDataInputBest)
edPluginBest.setDataOutput(xsDataResultBest)
edPluginBest.generateExecutiveSummary(edPluginBest)
def testGenerateExecutiveSummary(self):
pyStrInputBest = self.readAndParseFile(self.m_edReferenceInputFile)
pyStrResultBest = self.readAndParseFile(self.m_edReferenceResultFile)
from XSDataBestv1_2 import XSDataInputBest
from XSDataBestv1_2 import XSDataResultBest
xsDataInputBest = XSDataInputBest.parseString(pyStrInputBest)
xsDataResultBest = XSDataResultBest.parseString(pyStrResultBest)
edPluginBest = self.createPlugin()
edPluginBest.setDataInput(xsDataInputBest)
edPluginBest.setDataOutput(xsDataResultBest)
edPluginBest.generateExecutiveSummary(edPluginBest)
def getBonlyOutputFromDNATables(self, _xsDataDnaTables):
xsDataResultBest = XSDataResultBest()
xsTablesGeneralInform = EDUtilsTable.getTableListFromTables(
_xsDataDnaTables, "general_inform")
xsDataBestCollectionPlan = XSDataBestCollectionPlan()
xsDataCrystalScale = XSDataCrystalScale()
xsCrystalScaleList = EDUtilsTable.getListsFromTable(
xsTablesGeneralInform[0], "crystal_scale")[0]
xsItemScal = EDUtilsTable.getItemFromList(xsCrystalScaleList, "scal")
fScal = float(xsItemScal.getValueOf_())
xsDataCrystalScale.setScale(XSDataDouble(fScal))
xsItemBfactor = EDUtilsTable.getItemFromList(xsCrystalScaleList,
"B_factor")
fBfactor = float(xsItemBfactor.getValueOf_())
xsDataCrystalScale.setBFactor(XSDataDouble(fBfactor))
xsDataBestCollectionPlan.setCrystalScale(xsDataCrystalScale)
xsDataResultBest.addCollectionPlan(xsDataBestCollectionPlan)
return xsDataResultBest
def getOutputDataFromDNATableFile(self, _strFileName):
strDnaTablesXML = self.readProcessFile(_strFileName)
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
xsDataResultBest = XSDataResultBest()
# Loop through all the tables and fill in the relevant parts of xsDataResultBest
xsDataStringStrategyOption = self.getDataInput().getStrategyOption()
if (xsDataStringStrategyOption is not None):
strStrategyOption = xsDataStringStrategyOption.getValue()
if (strStrategyOption.find("-DamPar") != -1):
xsDataResultBest = self.getDamParOutputFromDNATables(
xsDataDnaTables)
elif (strStrategyOption.find("-Bonly") != -1):
xsDataResultBest = self.getBonlyOutputFromDNATables(
xsDataDnaTables)
else:
xsDataResultBest = self.getDataCollectionOutputDataFromDNATables(
xsDataDnaTables)
else:
xsDataResultBest = self.getDataCollectionOutputDataFromDNATables(
xsDataDnaTables)
return xsDataResultBest
def getDataCollectionOutputDataFromDNATables(self, _xsDataDnaTables):
xsDataResultBest = XSDataResultBest()
# SubWedges
xsTablesCollectionStrategy = EDUtilsTable.getTableListFromTables(_xsDataDnaTables, "data_collection_strategy")
iCollectionPlanNumber = 1
for xsTableCollectionStrategy in xsTablesCollectionStrategy:
xsDataBestCollectionPlan = XSDataBestCollectionPlan()
xsCollectionRunList = EDUtilsTable.getListsFromTable(xsTableCollectionStrategy, "collection_run")
iCollectionRunNumber = 1
for xsCollectionRunItemList in xsCollectionRunList:
xsDataCollectionRun = self.collectionRunItemListToCollectionRun(xsCollectionRunItemList, iCollectionRunNumber)
xsDataBestCollectionPlan.addCollectionRun(xsDataCollectionRun)
iCollectionRunNumber = iCollectionRunNumber + 1
# Strategy Summary
xsStrategySummaryItemList = EDUtilsTable.getListsFromTable(xsTableCollectionStrategy, "summary")
xsDataStrategySummary = self.strategySummaryItemListToStrategySummary(xsStrategySummaryItemList[0])
# Ranking Resolution
# Not part of strategySummaryItemListToStrategySummary method since it is in the general_form part
xsTableGeneralInform = EDUtilsTable.getTableFromTables(_xsDataDnaTables, "general_inform")
xsRankingResolutionItemList = EDUtilsTable.getListsFromTable(xsTableGeneralInform, "ranking_resolution")
xsItemRankingResolution = EDUtilsTable.getItemFromList(xsRankingResolutionItemList[0], "dmin")
fRankingResolution = float(xsItemRankingResolution.getValueOf_())
xsDataStrategySummary.setRankingResolution(XSDataDouble(fRankingResolution))
xsDataBestCollectionPlan.setStrategySummary(xsDataStrategySummary)
# Satistics
xsTablesStatisticalPrediction = EDUtilsTable.getTableListFromTables(_xsDataDnaTables, "statistical_prediction")
for xsTableStatisticalPrediction in xsTablesStatisticalPrediction:
if(xsTableStatisticalPrediction.getIndex() == xsTableCollectionStrategy.getIndex()):
xsResolutionBinList = EDUtilsTable.getListsFromTable(xsTableStatisticalPrediction, "resolution_bin")
xsDataStatisticalPrediction = XSDataBestStatisticalPrediction()
for xsResolutionBinItemList in xsResolutionBinList:
xsDataResolutionBin = self.resolutionBinItemListToResolutionBin(xsResolutionBinItemList)
xsDataStatisticalPrediction.addResolutionBin(xsDataResolutionBin)
xsDataBestCollectionPlan.setStatisticalPrediction(xsDataStatisticalPrediction)
xsDataBestCollectionPlan.setCollectionPlanNumber(XSDataInteger(iCollectionPlanNumber))
xsDataResultBest.addCollectionPlan(xsDataBestCollectionPlan)
iCollectionPlanNumber = iCollectionPlanNumber + 1
# Fix the order of the collection plans - then low resolution pass should be the first one
listCollectionPlan = xsDataResultBest.getCollectionPlan()
if (len(listCollectionPlan) > 1):
bIsModified = False
for xsDataCollectionPlan in listCollectionPlan:
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary()
strReasoning = xsDataStrategySummary.getResolutionReasoning().getValue()
if ((strReasoning.find("Low-resolution") != -1) and xsDataCollectionPlan.getCollectionPlanNumber().getValue() != 1):
listCollectionPlan.remove(xsDataCollectionPlan)
listCollectionPlan.insert(0, xsDataCollectionPlan)
bIsModified = True
if (bIsModified):
iCollectionPlanNumber = 1
for xsDataCollectionPlan in listCollectionPlan:
xsDataCollectionPlan.setCollectionPlanNumber(XSDataInteger(iCollectionPlanNumber))
iCollectionPlanNumber = iCollectionPlanNumber + 1
return xsDataResultBest
def getDataCollectionOutputDataFromDNATables(self, _xsDataDnaTables):
xsDataResultBest = XSDataResultBest()
# SubWedges
xsTablesCollectionStrategy = EDUtilsTable.getTableListFromTables(
_xsDataDnaTables, "data_collection_strategy")
iCollectionPlanNumber = 1
for xsTableCollectionStrategy in xsTablesCollectionStrategy:
xsDataBestCollectionPlan = XSDataBestCollectionPlan()
xsCollectionRunList = EDUtilsTable.getListsFromTable(
xsTableCollectionStrategy, "collection_run")
iCollectionRunNumber = 1
for xsCollectionRunItemList in xsCollectionRunList:
xsDataCollectionRun = self.collectionRunItemListToCollectionRun(
xsCollectionRunItemList, iCollectionRunNumber)
xsDataBestCollectionPlan.addCollectionRun(xsDataCollectionRun)
iCollectionRunNumber = iCollectionRunNumber + 1
# Strategy Summary
xsStrategySummaryItemList = EDUtilsTable.getListsFromTable(
xsTableCollectionStrategy, "summary")
xsDataStrategySummary = self.strategySummaryItemListToStrategySummary(
xsStrategySummaryItemList[0])
# Ranking Resolution
# Not part of strategySummaryItemListToStrategySummary method since it is in the general_form part
xsTableGeneralInform = EDUtilsTable.getTableFromTables(
_xsDataDnaTables, "general_inform")
xsRankingResolutionItemList = EDUtilsTable.getListsFromTable(
xsTableGeneralInform, "ranking_resolution")
xsItemRankingResolution = EDUtilsTable.getItemFromList(
xsRankingResolutionItemList[0], "dmin")
fRankingResolution = float(xsItemRankingResolution.getValueOf_())
xsDataStrategySummary.setRankingResolution(
XSDataDouble(fRankingResolution))
xsDataBestCollectionPlan.setStrategySummary(xsDataStrategySummary)
# Satistics
xsTablesStatisticalPrediction = EDUtilsTable.getTableListFromTables(
_xsDataDnaTables, "statistical_prediction")
for xsTableStatisticalPrediction in xsTablesStatisticalPrediction:
if (xsTableStatisticalPrediction.getIndex() ==
xsTableCollectionStrategy.getIndex()):
xsResolutionBinList = EDUtilsTable.getListsFromTable(
xsTableStatisticalPrediction, "resolution_bin")
xsDataStatisticalPrediction = XSDataBestStatisticalPrediction(
)
for xsResolutionBinItemList in xsResolutionBinList:
xsDataResolutionBin = self.resolutionBinItemListToResolutionBin(
xsResolutionBinItemList)
xsDataStatisticalPrediction.addResolutionBin(
xsDataResolutionBin)
xsDataBestCollectionPlan.setStatisticalPrediction(
xsDataStatisticalPrediction)
xsDataBestCollectionPlan.setCollectionPlanNumber(
XSDataInteger(iCollectionPlanNumber))
xsDataResultBest.addCollectionPlan(xsDataBestCollectionPlan)
iCollectionPlanNumber = iCollectionPlanNumber + 1
# Fix the order of the collection plans - then low resolution pass should be the first one
listCollectionPlan = xsDataResultBest.getCollectionPlan()
if (len(listCollectionPlan) > 1):
bIsModified = False
for xsDataCollectionPlan in listCollectionPlan:
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary(
)
strReasoning = xsDataStrategySummary.getResolutionReasoning(
).getValue()
if ((strReasoning.find("Low-resolution") != -1)
and xsDataCollectionPlan.getCollectionPlanNumber(
).getValue() != 1):
listCollectionPlan.remove(xsDataCollectionPlan)
listCollectionPlan.insert(0, xsDataCollectionPlan)
bIsModified = True
if (bIsModified):
iCollectionPlanNumber = 1
for xsDataCollectionPlan in listCollectionPlan:
xsDataCollectionPlan.setCollectionPlanNumber(
XSDataInteger(iCollectionPlanNumber))
iCollectionPlanNumber = iCollectionPlanNumber + 1
return xsDataResultBest
