def testGenerateExecutiveSummary(self):
"""
This method tests the generateExecutiveSummary of the Labelit plugin.
It contains no assert call so the contents of the executive summary is not tested.
"""
edPluginLabelitDistlv1_1 = self.createPlugin()
xmlInput1 = self.readAndParseFile(self.__strReferenceInputFile1)
edPluginLabelitDistlv1_1.setDataInput(xmlInput1, "referenceImage")
strImageQualityIndicatorsFile = os.path.join(self.getPluginTestsDataHome(), "XSDataImageQualityIndicators_reference.xml")
strImageQualityIndicatorsXML = self.readAndParseFile(strImageQualityIndicatorsFile)
from XSDataLabelitv1_1 import XSDataImageQualityIndicators
xsDataImageQualityIndicatorsReference = XSDataImageQualityIndicators.parseString(strImageQualityIndicatorsXML)
edPluginLabelitDistlv1_1.setDataOutput(xsDataImageQualityIndicatorsReference, "imageQualityIndicators")
edPluginLabelitDistlv1_1.generateExecutiveSummary(edPluginLabelitDistlv1_1)
def testParseLabelitDistlOutput(self):
"""
This method test the parsing of the Labelit results in the log file.
"""
edPluginLabelitDistlv1_1 = self.createPlugin()
strPathToLabelitLogText = os.path.join(self.getPluginTestsDataHome(), "labelit.distl_v116.log")
strLabelitLogText = self.readAndParseFile(strPathToLabelitLogText)
xsDataImageQualityIndicators = edPluginLabelitDistlv1_1.parseLabelitDistlOutput(strLabelitLogText)
xmlInput1 = self.readAndParseFile(self.__strReferenceInputFile1)
xsDataImage1 = XSDataImage.parseString(xmlInput1)
xsDataImageQualityIndicators.setImage(xsDataImage1)
strLabelitDistlOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataImageQualityIndicators_reference.xml")
strLabelitDistlOutputXML = self.readAndParseFile(strLabelitDistlOutputFile)
from XSDataLabelitv1_1 import XSDataImageQualityIndicators
xsDataImageQualityIndicatorsReference = XSDataImageQualityIndicators.parseString(strLabelitDistlOutputXML)
EDAssert.equal(xsDataImageQualityIndicatorsReference.marshal(), xsDataImageQualityIndicators.marshal())
def testGenerateExecutiveSummary(self):
"""
This method tests the generateExecutiveSummary of the Labelit plugin.
It contains no assert call so the contents of the executive summary is not tested.
"""
edPluginLabelitDistlv1_1 = self.createPlugin()
xmlInput1 = self.readAndParseFile(self.__strReferenceInputFile1)
edPluginLabelitDistlv1_1.setDataInput(xmlInput1, "referenceImage")
strImageQualityIndicatorsFile = os.path.join(
self.getPluginTestsDataHome(),
"XSDataImageQualityIndicators_reference.xml")
strImageQualityIndicatorsXML = self.readAndParseFile(
strImageQualityIndicatorsFile)
from XSDataLabelitv1_1 import XSDataImageQualityIndicators
xsDataImageQualityIndicatorsReference = XSDataImageQualityIndicators.parseString(
strImageQualityIndicatorsXML)
edPluginLabelitDistlv1_1.setDataOutput(
xsDataImageQualityIndicatorsReference, "imageQualityIndicators")
edPluginLabelitDistlv1_1.generateExecutiveSummary(
edPluginLabelitDistlv1_1)
def testParseLabelitDistlOutput(self):
"""
This method test the parsing of the Labelit results in the log file.
"""
edPluginLabelitDistlv1_1 = self.createPlugin()
strPathToLabelitLogText = os.path.join(self.getPluginTestsDataHome(),
"labelit.distl_v116.log")
strLabelitLogText = self.readAndParseFile(strPathToLabelitLogText)
xsDataImageQualityIndicators = edPluginLabelitDistlv1_1.parseLabelitDistlOutput(
strLabelitLogText)
xmlInput1 = self.readAndParseFile(self.__strReferenceInputFile1)
xsDataImage1 = XSDataImage.parseString(xmlInput1)
xsDataImageQualityIndicators.setImage(xsDataImage1)
strLabelitDistlOutputFile = os.path.join(
self.getPluginTestsDataHome(),
"XSDataImageQualityIndicators_reference.xml")
strLabelitDistlOutputXML = self.readAndParseFile(
strLabelitDistlOutputFile)
from XSDataLabelitv1_1 import XSDataImageQualityIndicators
xsDataImageQualityIndicatorsReference = XSDataImageQualityIndicators.parseString(
strLabelitDistlOutputXML)
EDAssert.equal(xsDataImageQualityIndicatorsReference.marshal(),
xsDataImageQualityIndicators.marshal())
def parseLabelitDistlOutput(self, _strLabelitDistlLogText):
EDVerbose.DEBUG("EDPluginDistlSignalStrengthv1_1.parseLabelitDistlOutput")
xsDataImageQualityIndicators = None
if _strLabelitDistlLogText is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
for strLine in _strLabelitDistlLogText.split("\n"):
if strLine.find("Spot Total") != -1:
iSpotTotal = int(strLine.split()[3])
xsDataImageQualityIndicators.setSpotTotal(XSDataInteger(iSpotTotal))
elif strLine.find("In-Resolution Total") != -1:
iInResTotal = int(strLine.split()[3])
xsDataImageQualityIndicators.setInResTotal(XSDataInteger(iInResTotal))
elif strLine.find("Good Bragg Candidates") != -1:
iGoodBraggCandidates = int(strLine.split()[4])
xsDataImageQualityIndicators.setGoodBraggCandidates(XSDataInteger(iGoodBraggCandidates))
elif strLine.find("Ice Rings") != -1:
iIceRings = int(strLine.split()[3])
xsDataImageQualityIndicators.setIceRings(XSDataInteger(iIceRings))
elif strLine.find("Method 1 Resolution") != -1:
fMethod1Res = float(strLine.split()[4])
xsDataImageQualityIndicators.setMethod1Res(XSDataDouble(fMethod1Res))
elif strLine.find("Method 2 Resolution") != -1:
if strLine.split()[4] != "None":
fMethod2Res = float(strLine.split()[4])
xsDataImageQualityIndicators.setMethod2Res(XSDataDouble(fMethod2Res))
elif strLine.find("Maximum unit cell") != -1:
if strLine.split()[4] != "None":
fMaxUnitCell = float(strLine.split()[4])
xsDataImageQualityIndicators.setMaxUnitCell(XSDataDouble(fMaxUnitCell))
elif strLine.find("%Saturation, Top 50 Peaks") != -1:
fPctSaturationTop50Peaks = float(strLine.split()[5])
xsDataImageQualityIndicators.setPctSaturationTop50Peaks(XSDataDouble(fPctSaturationTop50Peaks))
elif strLine.find("In-Resolution Ovrld Spots") != -1:
iInResolutionOvrlSpots = int(strLine.split()[4])
xsDataImageQualityIndicators.setInResolutionOvrlSpots(XSDataInteger(iInResolutionOvrlSpots))
elif strLine.find("Bin population cutoff for method 2 resolution") != -1:
fBinPopCutOffMethod2Res = float(strLine.split()[7][:-1])
xsDataImageQualityIndicators.setBinPopCutOffMethod2Res(XSDataDouble(fBinPopCutOffMethod2Res))
elif strLine.find("Total integrated signal, pixel-ADC units above local background (just the good Bragg candidates)") != -1:
fTotalIntegratedSignal = float(strLine.split()[-1])
xsDataImageQualityIndicators.setTotalIntegratedSignal(XSDataDouble(fTotalIntegratedSignal))
elif strLine.find("Signals range from") != -1:
listStrLine = strLine.split()
fSignalRangeMin = float(listStrLine[3])
fSignalRangeMax = float(listStrLine[5])
fSignalRangeAverage = float(listStrLine[-1])
xsDataImageQualityIndicators.setSignalRangeMin(XSDataDouble(fSignalRangeMin))
xsDataImageQualityIndicators.setSignalRangeMax(XSDataDouble(fSignalRangeMax))
xsDataImageQualityIndicators.setSignalRangeAverage(XSDataDouble(fSignalRangeAverage))
elif strLine.find("Saturations range from") != -1:
listStrLine = strLine.split()
fSaturationRangeMin = float(listStrLine[3][:-1])
fSaturationRangeMax = float(listStrLine[5][:-1])
fSaturationRangeAverage = float(listStrLine[-1][:-1])
xsDataImageQualityIndicators.setSaturationRangeMin(XSDataDouble(fSaturationRangeMin))
xsDataImageQualityIndicators.setSaturationRangeMax(XSDataDouble(fSaturationRangeMax))
xsDataImageQualityIndicators.setSaturationRangeAverage(XSDataDouble(fSaturationRangeAverage))
return xsDataImageQualityIndicators
def parseLabelitDistlOutput(self, _strLabelitDistlLogText):
self.DEBUG(
"EDPluginDistlSignalStrengthThinClientv1_1.parseLabelitDistlOutput"
)
xsDataImageQualityIndicators = None
if _strLabelitDistlLogText is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
for strLine in _strLabelitDistlLogText.split("\n"):
if strLine.find("Spot Total") != -1:
iSpotTotal = int(strLine.split()[-1])
xsDataImageQualityIndicators.setSpotTotal(
XSDataInteger(iSpotTotal))
elif strLine.find("Method-2 Resolution Total") != -1:
iInResTotal = int(strLine.split()[-1])
xsDataImageQualityIndicators.setInResTotal(
XSDataInteger(iInResTotal))
elif strLine.find("Good Bragg Candidates") != -1:
iGoodBraggCandidates = int(strLine.split()[-1])
xsDataImageQualityIndicators.setGoodBraggCandidates(
XSDataInteger(iGoodBraggCandidates))
elif strLine.find("Ice Rings") != -1:
iIceRings = int(strLine.split()[-1])
xsDataImageQualityIndicators.setIceRings(
XSDataInteger(iIceRings))
elif strLine.find("Method 1 Resolution") != -1:
fMethod1Res = float(strLine.split()[-1])
xsDataImageQualityIndicators.setMethod1Res(
XSDataDouble(fMethod1Res))
elif strLine.find("Method 2 Resolution") != -1:
if strLine.split()[4] != "None":
fMethod2Res = float(strLine.split()[-1])
xsDataImageQualityIndicators.setMethod2Res(
XSDataDouble(fMethod2Res))
elif strLine.find("Maximum unit cell") != -1:
if strLine.split()[4] != "None":
fMaxUnitCell = float(strLine.split()[-1])
xsDataImageQualityIndicators.setMaxUnitCell(
XSDataDouble(fMaxUnitCell))
elif strLine.find("Saturation, Top 50 Peaks") != -1:
fPctSaturationTop50Peaks = float(strLine.split()[-2])
xsDataImageQualityIndicators.setPctSaturationTop50Peaks(
XSDataDouble(fPctSaturationTop50Peaks))
elif strLine.find("In-resolution overloaded spots") != -1:
iInResolutionOvrlSpots = int(strLine.split()[-1])
xsDataImageQualityIndicators.setInResolutionOvrlSpots(
XSDataInteger(iInResolutionOvrlSpots))
elif strLine.find(
"Total integrated signal, pixel-ADC units above local background"
) != -1:
fTotalIntegratedSignal = float(strLine.split()[-1])
xsDataImageQualityIndicators.setTotalIntegratedSignal(
XSDataDouble(fTotalIntegratedSignal))
return xsDataImageQualityIndicators
def parseLabelitDistlOutput(self, _strLabelitDistlLogText):
self.DEBUG("EDPluginDistlSignalStrengthv1_1.parseLabelitDistlOutput")
xsDataImageQualityIndicators = None
if _strLabelitDistlLogText is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
for strLine in _strLabelitDistlLogText.split("\n"):
if strLine.find("Spot Total") != -1:
iSpotTotal = int(strLine.split()[3])
xsDataImageQualityIndicators.setSpotTotal(
XSDataInteger(iSpotTotal))
elif strLine.find("In-Resolution Total") != -1:
iInResTotal = int(strLine.split()[3])
xsDataImageQualityIndicators.setInResTotal(
XSDataInteger(iInResTotal))
elif strLine.find("Good Bragg Candidates") != -1:
iGoodBraggCandidates = int(strLine.split()[4])
xsDataImageQualityIndicators.setGoodBraggCandidates(
XSDataInteger(iGoodBraggCandidates))
elif strLine.find("Ice Rings") != -1:
iIceRings = int(strLine.split()[3])
xsDataImageQualityIndicators.setIceRings(
XSDataInteger(iIceRings))
elif strLine.find("Method 1 Resolution") != -1:
fMethod1Res = float(strLine.split()[4])
xsDataImageQualityIndicators.setMethod1Res(
XSDataDouble(fMethod1Res))
elif strLine.find("Method 2 Resolution") != -1:
if strLine.split()[4] != "None":
fMethod2Res = float(strLine.split()[4])
xsDataImageQualityIndicators.setMethod2Res(
XSDataDouble(fMethod2Res))
elif strLine.find("Maximum unit cell") != -1:
if strLine.split()[4] != "None":
fMaxUnitCell = float(strLine.split()[4])
xsDataImageQualityIndicators.setMaxUnitCell(
XSDataDouble(fMaxUnitCell))
elif strLine.find("%Saturation, Top 50 Peaks") != -1:
fPctSaturationTop50Peaks = float(strLine.split()[5])
xsDataImageQualityIndicators.setPctSaturationTop50Peaks(
XSDataDouble(fPctSaturationTop50Peaks))
elif strLine.find("In-Resolution Ovrld Spots") != -1:
iInResolutionOvrlSpots = int(strLine.split()[4])
xsDataImageQualityIndicators.setInResolutionOvrlSpots(
XSDataInteger(iInResolutionOvrlSpots))
elif strLine.find(
"Bin population cutoff for method 2 resolution") != -1:
fBinPopCutOffMethod2Res = float(strLine.split()[7][:-1])
xsDataImageQualityIndicators.setBinPopCutOffMethod2Res(
XSDataDouble(fBinPopCutOffMethod2Res))
elif strLine.find(
"Total integrated signal, pixel-ADC units above local background (just the good Bragg candidates)"
) != -1:
fTotalIntegratedSignal = float(strLine.split()[-1])
xsDataImageQualityIndicators.setTotalIntegratedSignal(
XSDataDouble(fTotalIntegratedSignal))
elif strLine.find("Signals range from") != -1:
listStrLine = strLine.split()
fSignalRangeMin = float(listStrLine[3])
fSignalRangeMax = float(listStrLine[5])
fSignalRangeAverage = float(listStrLine[-1])
xsDataImageQualityIndicators.setSignalRangeMin(
XSDataDouble(fSignalRangeMin))
xsDataImageQualityIndicators.setSignalRangeMax(
XSDataDouble(fSignalRangeMax))
xsDataImageQualityIndicators.setSignalRangeAverage(
XSDataDouble(fSignalRangeAverage))
elif strLine.find("Saturations range from") != -1:
listStrLine = strLine.split()
fSaturationRangeMin = float(listStrLine[3][:-1])
fSaturationRangeMax = float(listStrLine[5][:-1])
fSaturationRangeAverage = float(listStrLine[-1][:-1])
xsDataImageQualityIndicators.setSaturationRangeMin(
XSDataDouble(fSaturationRangeMin))
xsDataImageQualityIndicators.setSaturationRangeMax(
XSDataDouble(fSaturationRangeMax))
xsDataImageQualityIndicators.setSaturationRangeAverage(
XSDataDouble(fSaturationRangeAverage))
return xsDataImageQualityIndicators
def parseLabelitDistlOutput(self, _strLabelitDistlLogText):
EDVerbose.DEBUG("EDPluginLabelitDistlv1_1.parseLabelitDistlOutput")
xsDataImageQualityIndicators = None
if _strLabelitDistlLogText is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
for strLine in _strLabelitDistlLogText.split("\n"):
if strLine.find("Spot Total") != -1:
iSpotTotal = int(strLine.split()[3])
xsDataImageQualityIndicators.setSpotTotal(XSDataInteger(iSpotTotal))
elif strLine.find("In-Resolution Total") != -1:
iInResTotal = int(strLine.split()[3])
xsDataImageQualityIndicators.setInResTotal(XSDataInteger(iInResTotal))
elif strLine.find("Good Bragg Candidates") != -1:
iGoodBraggCandidates = int(strLine.split()[4])
xsDataImageQualityIndicators.setGoodBraggCandidates(XSDataInteger(iGoodBraggCandidates))
elif strLine.find("Ice Rings") != -1:
iIceRings = int(strLine.split()[3])
xsDataImageQualityIndicators.setIceRings(XSDataInteger(iIceRings))
elif strLine.find("Method 1 Resolution") != -1:
fMethod1Res = float(strLine.split()[4])
xsDataImageQualityIndicators.setMethod1Res(XSDataDouble(fMethod1Res))
elif strLine.find("Method 2 Resolution") != -1:
if strLine.split()[4] != "None":
fMethod2Res = float(strLine.split()[4])
xsDataImageQualityIndicators.setMethod2Res(XSDataDouble(fMethod2Res))
elif strLine.find("Maximum unit cell") != -1:
if strLine.split()[4] != "None":
fMaxUnitCell = float(strLine.split()[4])
xsDataImageQualityIndicators.setMaxUnitCell(XSDataDouble(fMaxUnitCell))
elif strLine.find("%Saturation, Top 50 Peaks") != -1:
fPctSaturationTop50Peaks = float(strLine.split()[5])
xsDataImageQualityIndicators.setPctSaturationTop50Peaks(XSDataDouble(fPctSaturationTop50Peaks))
elif strLine.find("In-Resolution Ovrld Spots") != -1:
iInResolutionOvrlSpots = int(strLine.split()[4])
xsDataImageQualityIndicators.setInResolutionOvrlSpots(XSDataInteger(iInResolutionOvrlSpots))
elif strLine.find("Bin population cutoff for method 2 resolution") != -1:
fBinPopCutOffMethod2Res = float(strLine.split()[7][:-1])
xsDataImageQualityIndicators.setBinPopCutOffMethod2Res(XSDataDouble(fBinPopCutOffMethod2Res))
return xsDataImageQualityIndicators
def parseLabelitDistlOutput(self, _strLabelitDistlLogText):
EDVerbose.DEBUG("EDPluginDistlSignalStrengthThinClientv1_1.parseLabelitDistlOutput")
xsDataImageQualityIndicators = None
if _strLabelitDistlLogText is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
for strLine in _strLabelitDistlLogText.split("\n"):
if strLine.find("Spot Total") != -1:
iSpotTotal = int(strLine.split()[-1])
xsDataImageQualityIndicators.setSpotTotal(XSDataInteger(iSpotTotal))
elif strLine.find("Method-2 Resolution Total") != -1:
iInResTotal = int(strLine.split()[-1])
xsDataImageQualityIndicators.setInResTotal(XSDataInteger(iInResTotal))
elif strLine.find("Good Bragg Candidates") != -1:
iGoodBraggCandidates = int(strLine.split()[-1])
xsDataImageQualityIndicators.setGoodBraggCandidates(XSDataInteger(iGoodBraggCandidates))
elif strLine.find("Ice Rings") != -1:
iIceRings = int(strLine.split()[-1])
xsDataImageQualityIndicators.setIceRings(XSDataInteger(iIceRings))
elif strLine.find("Method 1 Resolution") != -1:
fMethod1Res = float(strLine.split()[-1])
xsDataImageQualityIndicators.setMethod1Res(XSDataDouble(fMethod1Res))
elif strLine.find("Method 2 Resolution") != -1:
if strLine.split()[4] != "None":
fMethod2Res = float(strLine.split()[-1])
xsDataImageQualityIndicators.setMethod2Res(XSDataDouble(fMethod2Res))
elif strLine.find("Maximum unit cell") != -1:
if strLine.split()[4] != "None":
fMaxUnitCell = float(strLine.split()[-1])
xsDataImageQualityIndicators.setMaxUnitCell(XSDataDouble(fMaxUnitCell))
elif strLine.find("Saturation, Top 50 Peaks") != -1:
fPctSaturationTop50Peaks = float(strLine.split()[-2])
xsDataImageQualityIndicators.setPctSaturationTop50Peaks(XSDataDouble(fPctSaturationTop50Peaks))
elif strLine.find("In-resolution overloaded spots") != -1:
iInResolutionOvrlSpots = int(strLine.split()[-1])
xsDataImageQualityIndicators.setInResolutionOvrlSpots(XSDataInteger(iInResolutionOvrlSpots))
elif strLine.find("Total integrated signal, pixel-ADC units above local background") != -1:
fTotalIntegratedSignal = float(strLine.split()[-1])
xsDataImageQualityIndicators.setTotalIntegratedSignal(XSDataDouble(fTotalIntegratedSignal))
return xsDataImageQualityIndicators
def parseLabelitDistlOutput(self, _strLabelitDistlLogText):
self.DEBUG("EDPluginLabelitDistlv1_1.parseLabelitDistlOutput")
xsDataImageQualityIndicators = None
if _strLabelitDistlLogText is not None:
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
for strLine in _strLabelitDistlLogText.split("\n"):
if strLine.find("Spot Total") != -1:
iSpotTotal = int(strLine.split()[3])
xsDataImageQualityIndicators.setSpotTotal(XSDataInteger(iSpotTotal))
elif strLine.find("In-Resolution Total") != -1:
iInResTotal = int(strLine.split()[3])
xsDataImageQualityIndicators.setInResTotal(XSDataInteger(iInResTotal))
elif strLine.find("Good Bragg Candidates") != -1:
iGoodBraggCandidates = int(strLine.split()[4])
xsDataImageQualityIndicators.setGoodBraggCandidates(XSDataInteger(iGoodBraggCandidates))
elif strLine.find("Ice Rings") != -1:
iIceRings = int(strLine.split()[3])
xsDataImageQualityIndicators.setIceRings(XSDataInteger(iIceRings))
elif strLine.find("Method 1 Resolution") != -1:
fMethod1Res = float(strLine.split()[4])
xsDataImageQualityIndicators.setMethod1Res(XSDataDouble(fMethod1Res))
elif strLine.find("Method 2 Resolution") != -1:
if strLine.split()[4] != "None":
fMethod2Res = float(strLine.split()[4])
xsDataImageQualityIndicators.setMethod2Res(XSDataDouble(fMethod2Res))
elif strLine.find("Maximum unit cell") != -1:
if strLine.split()[4] != "None":
fMaxUnitCell = float(strLine.split()[4])
xsDataImageQualityIndicators.setMaxUnitCell(XSDataDouble(fMaxUnitCell))
elif strLine.find("%Saturation, Top 50 Peaks") != -1:
fPctSaturationTop50Peaks = float(strLine.split()[5])
xsDataImageQualityIndicators.setPctSaturationTop50Peaks(XSDataDouble(fPctSaturationTop50Peaks))
elif strLine.find("In-Resolution Ovrld Spots") != -1:
iInResolutionOvrlSpots = int(strLine.split()[4])
xsDataImageQualityIndicators.setInResolutionOvrlSpots(XSDataInteger(iInResolutionOvrlSpots))
elif strLine.find("Bin population cutoff for method 2 resolution") != -1:
fBinPopCutOffMethod2Res = float(strLine.split()[7][:-1])
xsDataImageQualityIndicators.setBinPopCutOffMethod2Res(XSDataDouble(fBinPopCutOffMethod2Res))
return xsDataImageQualityIndicators
