def process(self, _edPlugin=None):
EDPluginExec.process(self, _edPlugin)
self.DEBUG("EDPluginExecSimpleHTMLPagev1_0.process...")
if self.xsDataResultCharacterisation is not None:
# Create the simple characterisation result page
self.page = markupv1_7.page(mode='loose_html')
self.page.init( title="Characterisation Results",
footer="Generated on %s" % time.asctime())
self.page.div( align_="CENTER")
self.page.h1()
if self.xsDataResultCharacterisation is not None:
self.page.strong( "Characterisation Results " )
else:
self.page.strong( "No Characterisation Results! " )
# Link to the EDNA log file
strPathToLogFile = self.findEDNALogFile()
if strPathToLogFile is not None:
self.page.strong("(")
self.strPageEDNALog = os.path.join(self.getWorkingDirectory(), "edna_log.html")
pageEDNALog = markupv1_7.page()
pageEDNALog.h1("EDNA Log")
pageEDNALog.a("Back to previous page", href_=self.strHtmlFileName)
pageEDNALog.pre(cgi.escape(EDUtilsFile.readFile(strPathToLogFile)))
pageEDNALog.a("Back to previous page", href_=self.strHtmlFileName)
EDUtilsFile.writeFile(self.strPageEDNALog, str(pageEDNALog))
self.page.a("EDNA log file", href_="edna_log.html")
self.page.strong(")")
self.page.h1.close()
self.page.div.close()
self.diffractionPlan()
self.strategyResults()
self.graphs()
self.indexingResults()
self.integrationResults()
self.imageQualityIndicatorResults()
def process(self, _edPlugin=None):
EDPluginExec.process(self, _edPlugin)
self.DEBUG("EDPluginExecSimpleHTMLPagev1_0.process...")
if self.xsDataResultCharacterisation is not None:
# Create the simple characterisation result page
self.page = markupv1_7.page(mode='loose_html')
self.page.init( title="Characterisation Results",
footer="Generated on %s" % time.asctime())
self.page.div( align_="CENTER")
self.page.h1()
if self.xsDataResultCharacterisation is not None:
self.page.strong( "Characterisation Results " )
else:
self.page.strong( "No Characterisation Results! " )
# Link to the EDNA log file
strPathToLogFile = self.findEDNALogFile()
if strPathToLogFile is not None:
self.page.strong("(")
self.strPageEDNALog = os.path.join(self.getWorkingDirectory(), "edna_log.html")
pageEDNALog = markupv1_7.page()
pageEDNALog.h1("EDNA Log")
pageEDNALog.a("Back to previous page", href_=self.strHtmlFileName)
pageEDNALog.pre(cgi.escape(EDUtilsFile.readFile(strPathToLogFile)))
pageEDNALog.a("Back to previous page", href_=self.strHtmlFileName)
EDUtilsFile.writeFile(self.strPageEDNALog, str(pageEDNALog))
self.page.a("EDNA log file", href_="edna_log.html")
self.page.strong(")")
self.page.h1.close()
self.page.div.close()
self.diffractionPlan()
self.strategyResults()
self.graphs()
self.indexingResults()
self.integrationResults()
self.imageQualityIndicatorResults()
def integrationResults(self):
# Was the integration successful?
xsDataResultIntegration = self.xsDataResultCharacterisation.getIntegrationResult(
)
if xsDataResultIntegration:
iIntegration = 1
for xsDataIntegrationSubWedgeResult in xsDataResultIntegration.getIntegrationSubWedgeResult(
):
strPathToIntegrationLogFile = xsDataIntegrationSubWedgeResult.getIntegrationLogFile(
).getPath().getValue()
strIntegrationHtmlPageName = "integration_%d_log.html" % iIntegration
strPageIntegrationLog = os.path.join(
self.getWorkingDirectory(), strIntegrationHtmlPageName)
pageIntegrationLog = markupv1_7.page()
pageIntegrationLog.h1("Integration Log No %d" % iIntegration)
pageIntegrationLog.a("Back to previous page",
href_=self.strHtmlFileName)
pageIntegrationLog.pre(
cgi.escape(
EDUtilsFile.readFile(strPathToIntegrationLogFile)))
pageIntegrationLog.a("Back to previous page",
href_=self.strHtmlFileName)
EDUtilsFile.writeFile(strPageIntegrationLog,
str(pageIntegrationLog))
self.page.a("Integration log file %d" % iIntegration,
href=strIntegrationHtmlPageName)
self.page.br()
iIntegration += 1
def createThumbnailRowOfImages(self, _xsDataResultIndexing):
# Thumbnail images of the predictions
xsDataResultPrediction = _xsDataResultIndexing.getPredictionResult()
listPaths = []
self.page.div(align_="left")
self.page.table(class_='imageRow')
self.page.tr(align_="CENTER")
listXSDataReferenceImage = _xsDataResultIndexing.getImage()
for xsDataImagePrediction in xsDataResultPrediction.getPredictionImage(
):
self.page.td()
strPathToPredictionImage = xsDataImagePrediction.getPath(
).getValue()
strFileName = os.path.basename(strPathToPredictionImage)
strReferenceFileName = None
for xsDataReferenceImage in listXSDataReferenceImage:
if xsDataReferenceImage.getNumber().getValue(
) == xsDataImagePrediction.getNumber().getValue():
strReferenceFileName = os.path.basename(
xsDataReferenceImage.getPath().getValue())
if strReferenceFileName is None:
strReferenceFileName = strFileName
strLocalPath = os.path.join(self.getWorkingDirectory(),
strFileName)
shutil.copyfile(strPathToPredictionImage, strLocalPath)
listPaths.append(strLocalPath)
self.page.table(class_='image')
self.page.tr(align_="CENTER")
self.page.td()
strPageReferenceImage = os.path.splitext(strFileName)[0] + ".html"
pageReferenceImage = markupv1_7.page()
pageReferenceImage.init(title=strReferenceFileName,
footer="Generated on %s" % time.asctime())
pageReferenceImage.h1(strReferenceFileName)
pageReferenceImage.a("Back to previous page",
href_=self.strHtmlFileName)
pageReferenceImage.img(src=strFileName, title=strReferenceFileName)
pageReferenceImage.a("Back to previous page",
href_=self.strHtmlFileName)
EDUtilsFile.writeFile(
os.path.join(self.getWorkingDirectory(),
strPageReferenceImage), str(pageReferenceImage))
self.page.a(href=strPageReferenceImage)
self.page.img(src=strFileName,
width=128,
height=128,
title=strFileName)
self.page.a.close()
self.page.td.close()
self.page.tr.close()
self.page.tr(align_="CENTER")
self.page.td(strReferenceFileName, class_="caption")
self.page.td.close()
self.page.tr.close()
self.page.table.close()
self.page.td.close()
self.page.table.close()
self.page.div.close()
def createTableWithIndexResults(self, _xsDataResultIndexing,
_strForcedSpaceGroup):
xsDataSolutionSelected = _xsDataResultIndexing.getSelectedSolution()
xsDataCrystal = xsDataSolutionSelected.getCrystal()
xsDataCell = xsDataCrystal.getCell()
strSpaceGroup = xsDataCrystal.spaceGroup.name.value
if _strForcedSpaceGroup is None:
self.page.h3("Indexing summary: Selected spacegroup: %s" %
strSpaceGroup)
else:
if strSpaceGroup.upper() == _strForcedSpaceGroup.upper():
self.page.h3("Indexing summary: Forced spacegroup: %s" %
strSpaceGroup)
else:
self.page.h3(
"Indexing summary: Selected spacegroup: %s, forced space group: %s"
% strSpaceGroup, _strForcedSpaceGroup)
self.page.table(class_='indexResults', border_="1", cellpadding_="0")
self.page.tr(align_="CENTER", bgcolor_=self.strTableColourTitle1)
self.page.th("Refined unit cell parameters (Å/degrees)",
colspan_="6")
self.page.tr.close()
self.page.tr(align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("a (Å)")
self.page.th("b (Å)")
self.page.th("c (Å)")
self.page.th("alpha (°)")
self.page.th("beta (°)")
self.page.th("gamma (°)")
self.page.tr.close()
self.page.tr(align_="CENTER", bgcolor_=self.strTableColourRows)
self.page.td("%.3f" % xsDataCell.getLength_a().getValue())
self.page.td("%.3f" % xsDataCell.getLength_b().getValue())
self.page.td("%.3f" % xsDataCell.getLength_c().getValue())
self.page.td("%.3f" % xsDataCell.getAngle_alpha().getValue())
self.page.td("%.3f" % xsDataCell.getAngle_beta().getValue())
self.page.td("%.3f" % xsDataCell.getAngle_gamma().getValue())
self.page.td.close()
self.page.tr.close()
self.page.table.close()
if _xsDataResultIndexing.getIndexingLogFile():
strPathToIndexingLogFile = _xsDataResultIndexing.getIndexingLogFile(
).getPath().getValue()
strPageIndexingLog = os.path.join(self.getWorkingDirectory(),
"indexing_log.html")
pageIndexingLog = markupv1_7.page()
pageIndexingLog.h1("Indexing Log")
pageIndexingLog.a("Back to previous page",
href_=self.strHtmlFileName)
pageIndexingLog.pre(
cgi.escape(EDUtilsFile.readFile(strPathToIndexingLogFile)))
pageIndexingLog.a("Back to previous page",
href_=self.strHtmlFileName)
EDUtilsFile.writeFile(strPageIndexingLog, str(pageIndexingLog))
self.page.a("Indexing log file", href="indexing_log.html")
def graphs(self):
self.page.table(class_='bestGraphs', border_="0", cellpadding_="0")
if self.getDataInput().characterisationResult.strategyResult is None:
return
if self.getDataInput(
).characterisationResult.strategyResult.bestGraphFile == []:
return
listXSDataFile = self.getDataInput(
).characterisationResult.strategyResult.bestGraphFile
if listXSDataFile != []:
self.page.tr(align_="CENTER")
iIndex = 1
# If -damPar is used only three plots are available:
if len(listXSDataFile) > 4:
listPlotsToDisplay = [0, 1, 3, 6]
else:
listPlotsToDisplay = range(len(listXSDataFile))
for iIndexPlot in listPlotsToDisplay:
xsDataFile = listXSDataFile[iIndexPlot]
strFileName = os.path.basename(xsDataFile.path.value)
#print strFileName
shutil.copy(
xsDataFile.path.value,
os.path.join(self.getWorkingDirectory(), strFileName))
self.page.td()
strPageGraphFileName = os.path.splitext(
strFileName)[0] + ".html"
strPageGraphPath = os.path.join(self.getWorkingDirectory(),
strPageGraphFileName)
pageGraph = markupv1_7.page()
pageGraph.init(title=strFileName,
footer="Generated on %s" % time.asctime())
pageGraph.h1(strFileName)
pageGraph.a("Back to previous page",
href_=self.strHtmlFileName)
pageGraph.br()
pageGraph.img(src=strFileName, title=strFileName)
pageGraph.a("Back to previous page",
href_=self.strHtmlFileName)
EDUtilsFile.writeFile(strPageGraphPath, str(pageGraph))
self.page.a(href=strPageGraphFileName)
self.page.img(src=strFileName,
width=175,
height=175,
title=strFileName)
self.page.a.close()
self.page.td.close()
iIndex += 1
if iIndex > 4:
iIndex = 1
self.page.tr.close()
self.page.tr(align_="CENTER")
self.page.tr.close()
self.page.table.close()
def createHtmlPage(self):
page = markupv1_7.page(mode='loose_html')
page.init( title="Burn Strategy Results",
footer="Generated on %s" % time.asctime())
page.div( align_="CENTER")
page.h1()
page.strong("Burn Strategy Results")
page.h1.close()
page.img(src=self.strScaleIntensityPlot, title=self.strScaleIntensityPlot)
page.div.close()
strHTML = str(page)
EDUtilsFile.writeFile(os.path.join(self.getWorkingDirectory(), self.strHtmlPath), strHTML)
def createHtmlPage(self):
page = markupv1_7.page(mode='loose_html')
page.init(title="Burn Strategy Results",
footer="Generated on %s" % time.asctime())
page.div(align_="CENTER")
page.h1()
page.strong("Burn Strategy Results")
page.h1.close()
page.img(src=self.strScaleIntensityPlot,
title=self.strScaleIntensityPlot)
page.div.close()
strHTML = str(page)
EDUtilsFile.writeFile(
os.path.join(self.getWorkingDirectory(), self.strHtmlPath),
strHTML)
def createThumbnailRowOfImages(self, _xsDataResultIndexing):
# Thumbnail images of the predictions
xsDataResultPrediction = _xsDataResultIndexing.getPredictionResult()
listPaths = []
self.page.div(align_="left")
self.page.table( class_='imageRow' )
self.page.tr( align_="CENTER" )
listXSDataReferenceImage = _xsDataResultIndexing.getImage()
for xsDataImagePrediction in xsDataResultPrediction.getPredictionImage():
self.page.td()
strPathToPredictionImage = xsDataImagePrediction.getPath().getValue()
strFileName = os.path.basename(strPathToPredictionImage)
strReferenceFileName = None
for xsDataReferenceImage in listXSDataReferenceImage:
if xsDataReferenceImage.getNumber().getValue() == xsDataImagePrediction.getNumber().getValue():
strReferenceFileName = os.path.basename(xsDataReferenceImage.getPath().getValue())
if strReferenceFileName is None:
strReferenceFileName = strFileName
strLocalPath = os.path.join(self.getWorkingDirectory(), strFileName)
if os.path.exists(strPathToPredictionImage):
shutil.copyfile(strPathToPredictionImage, strLocalPath)
listPaths.append(strLocalPath)
self.page.table( class_='image' )
self.page.tr( align_="CENTER" )
self.page.td()
strPageReferenceImage = os.path.splitext(strFileName)[0]+".html"
pageReferenceImage = markupv1_7.page()
pageReferenceImage.init( title=strReferenceFileName,
footer="Generated on %s" % time.asctime())
pageReferenceImage.h1(strReferenceFileName)
pageReferenceImage.a("Back to previous page", href_=self.strHtmlFileName)
pageReferenceImage.img(src=strFileName, title=strReferenceFileName)
pageReferenceImage.a("Back to previous page", href_=self.strHtmlFileName)
EDUtilsFile.writeFile(os.path.join(self.getWorkingDirectory(),strPageReferenceImage), str(pageReferenceImage))
self.page.a( href=strPageReferenceImage)
self.page.img( src=strFileName, width=128, height=128, title=strFileName )
self.page.a.close()
self.page.td.close()
self.page.tr.close()
self.page.tr( align_="CENTER" )
self.page.td( strReferenceFileName, class_="caption")
self.page.td.close()
self.page.tr.close()
self.page.table.close()
self.page.td.close()
self.page.table.close()
self.page.div.close()
def createTableWithIndexResults(self, _xsDataResultIndexing, _strForcedSpaceGroup):
xsDataSolutionSelected = _xsDataResultIndexing.getSelectedSolution()
xsDataCrystal = xsDataSolutionSelected.getCrystal()
xsDataCell = xsDataCrystal.getCell()
strSpaceGroup = xsDataCrystal.spaceGroup.name.value
if _strForcedSpaceGroup is None:
self.page.h3("Indexing summary: Selected spacegroup: %s" % strSpaceGroup)
else:
if strSpaceGroup.upper() == _strForcedSpaceGroup.upper():
self.page.h3("Indexing summary: Forced spacegroup: %s" % strSpaceGroup)
else:
self.page.h3(
"Indexing summary: Selected spacegroup: %s, forced space group: %s" % strSpaceGroup,
_strForcedSpaceGroup,
)
self.page.table(class_="indexResults", border_="1", cellpadding_="0")
self.page.tr(align_="CENTER", bgcolor_=self.strTableColourTitle1)
self.page.th("Refined unit cell parameters (Å/degrees)", colspan_="6")
self.page.tr.close()
self.page.tr(align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("a (Å)")
self.page.th("b (Å)")
self.page.th("c (Å)")
self.page.th("alpha (°)")
self.page.th("beta (°)")
self.page.th("gamma (°)")
self.page.tr.close()
self.page.tr(align_="CENTER", bgcolor_=self.strTableColourRows)
self.page.td("%.3f" % xsDataCell.getLength_a().getValue())
self.page.td("%.3f" % xsDataCell.getLength_b().getValue())
self.page.td("%.3f" % xsDataCell.getLength_c().getValue())
self.page.td("%.3f" % xsDataCell.getAngle_alpha().getValue())
self.page.td("%.3f" % xsDataCell.getAngle_beta().getValue())
self.page.td("%.3f" % xsDataCell.getAngle_gamma().getValue())
self.page.td.close()
self.page.tr.close()
self.page.table.close()
if _xsDataResultIndexing.getIndexingLogFile():
strPathToIndexingLogFile = _xsDataResultIndexing.getIndexingLogFile().getPath().getValue()
strPageIndexingLog = os.path.join(self.getWorkingDirectory(), "indexing_log.html")
pageIndexingLog = markupv1_7.page()
pageIndexingLog.h1("Indexing Log")
pageIndexingLog.a("Back to previous page", href_=self.strHtmlFileName)
pageIndexingLog.pre(cgi.escape(EDUtilsFile.readFile(strPathToIndexingLogFile)))
pageIndexingLog.a("Back to previous page", href_=self.strHtmlFileName)
EDUtilsFile.writeFile(strPageIndexingLog, str(pageIndexingLog))
self.page.a("Indexing log file", href="indexing_log.html")
def integrationResults(self):
# Was the integration successful?
xsDataResultIntegration = self.xsDataResultCharacterisation.getIntegrationResult()
if xsDataResultIntegration:
iIntegration = 1
for xsDataIntegrationSubWedgeResult in xsDataResultIntegration.getIntegrationSubWedgeResult():
strPathToIntegrationLogFile = xsDataIntegrationSubWedgeResult.getIntegrationLogFile().getPath().getValue()
strIntegrationHtmlPageName = "integration_%d_log.html" % iIntegration
strPageIntegrationLog = os.path.join(self.getWorkingDirectory(), strIntegrationHtmlPageName)
pageIntegrationLog = markupv1_7.page()
pageIntegrationLog.h1("Integration Log No %d" % iIntegration)
pageIntegrationLog.a("Back to previous page", href_=self.strHtmlFileName)
pageIntegrationLog.pre(cgi.escape(EDUtilsFile.readFile(strPathToIntegrationLogFile)))
pageIntegrationLog.a("Back to previous page", href_=self.strHtmlFileName)
EDUtilsFile.writeFile(strPageIntegrationLog, str(pageIntegrationLog))
self.page.a("Integration log file %d" % iIntegration, href=strIntegrationHtmlPageName)
self.page.br()
iIntegration += 1
def graphs(self):
self.page.table( class_='bestGraphs', border_="0", cellpadding_="0")
if self.xsDataResultCharacterisation.strategyResult is None:
return
if self.xsDataResultCharacterisation.strategyResult.bestGraphFile == []:
return
listXSDataFile = self.xsDataResultCharacterisation.strategyResult.bestGraphFile
if listXSDataFile != []:
self.page.tr( align_="CENTER" )
iIndex = 1
# If -damPar is used only three plots are available:
if len(listXSDataFile) >= 7:
listPlotsToDisplay = [0, 1, 3, 6]
elif len(listXSDataFile) >= 4:
listPlotsToDisplay = [0, 1, 2, 3]
else:
listPlotsToDisplay = range(len(listXSDataFile))
for iIndexPlot in listPlotsToDisplay:
xsDataFile = listXSDataFile[iIndexPlot]
strFileName = os.path.basename(xsDataFile.path.value)
#print strFileName
shutil.copy(xsDataFile.path.value, os.path.join(self.getWorkingDirectory(), strFileName))
self.page.td()
strPageGraphFileName = os.path.splitext(strFileName)[0]+".html"
strPageGraphPath = os.path.join(self.getWorkingDirectory(), strPageGraphFileName)
pageGraph = markupv1_7.page()
pageGraph.init( title=strFileName,
footer="Generated on %s" % time.asctime())
pageGraph.img(src=strFileName, title=strFileName)
pageGraph.br()
pageGraph.a("Back to previous page", href_=self.strHtmlFileName)
EDUtilsFile.writeFile(strPageGraphPath, str(pageGraph))
self.page.a( href=strPageGraphFileName)
self.page.img( src=strFileName, width=200, height=150, title=strFileName )
self.page.a.close()
self.page.td.close()
iIndex += 1
if iIndex > 4:
iIndex = 1
self.page.tr.close()
self.page.tr( align_="CENTER" )
self.page.tr.close()
self.page.table.close()
def strategyResults(self):
# Was the strategy successful?
xsDataResultStrategy = self.xsDataResultCharacterisation.getStrategyResult()
if xsDataResultStrategy is None:
# Check if indexing and integration results
xsDataResultIntegration = self.xsDataResultCharacterisation.getIntegrationResult()
xsDataResultIndexing = self.xsDataResultCharacterisation.getIndexingResult()
if xsDataResultIndexing is None:
self.page.h2()
self.page.strong("Strategy calculation not performed due to indexing failure, see the " )
self.page.a("EDNA log file", href=self.strPageEDNALog)
self.page.strong(" for more details" )
self.page.h2.close()
elif xsDataResultIntegration is None:
self.page.h2()
self.page.strong("Strategy calculation not performed due to integration failure, see the " )
self.page.a("EDNA log file", href=self.strPageEDNALog)
self.page.strong(" for more details" )
self.page.h2.close()
else:
self.page.h2()
self.page.strong( "Strategy calculation failed, see the " )
self.page.a("EDNA log file", href=self.strPageEDNALog)
self.page.strong(" for more details" )
self.page.h2.close()
else:
# Add link to BEST log file:
if xsDataResultStrategy.getBestLogFile():
strPathToBestLogFile = xsDataResultStrategy.getBestLogFile().getPath().getValue()
strPageBestLog = os.path.join(self.getWorkingDirectory(), "best_log.html")
pageBestLog = markupv1_7.page()
pageBestLog.h1("BEST Log")
pageBestLog.a("Back to previous page", href_=self.strHtmlFileName)
pageBestLog.pre(cgi.escape(EDUtilsFile.readFile(strPathToBestLogFile)))
pageBestLog.a("Back to previous page", href_=self.strHtmlFileName)
EDUtilsFile.writeFile(strPageBestLog, str(pageBestLog))
# Add link to RADDOSE log file:
strPageRaddoseLog = None
if xsDataResultStrategy.getRaddoseLogFile():
strPathToRaddoseLogFile = xsDataResultStrategy.getRaddoseLogFile().getPath().getValue()
strPageRaddoseLog = os.path.join(self.getWorkingDirectory(), "raddose_log.html")
pageRaddoseLog = markupv1_7.page()
pageRaddoseLog.h1("RADDOSE Log")
pageRaddoseLog.a("Back to previous page", href_=self.strHtmlFileName)
pageRaddoseLog.pre(cgi.escape(EDUtilsFile.readFile(strPathToRaddoseLogFile)))
pageRaddoseLog.a("Back to previous page", href_=self.strHtmlFileName)
EDUtilsFile.writeFile(strPageRaddoseLog, str(pageRaddoseLog))
listXSDataCollectionPlan = xsDataResultStrategy.getCollectionPlan()
iNoSubWedges = len(listXSDataCollectionPlan)
self.page.h2()
if iNoSubWedges != 1:
self.page.strong("Multi-wedge collection plan strategy (")
else:
self.page.strong( "Collection plan strategy (" )
if strPageRaddoseLog is not None:
self.page.a("RADDOSE log file", href="raddose_log.html")
self.page.strong(", ")
self.page.a("BEST log file", href="best_log.html")
self.page.strong(")")
self.page.h2.close()
# Check if ranking resolution is higher than the suggested strategy resolution(s)
bHigherResolutionDetected = False
fRankingResolution = None
fResolutionMax = None
fDistanceMin = None
for xsDataCollectionPlan in listXSDataCollectionPlan:
xsDataSummaryStrategy = xsDataCollectionPlan.getStrategySummary()
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy()
if xsDataSummaryStrategy.getRankingResolution():
# Retrieve the resolution...
fResolution = xsDataSummaryStrategy.getResolution().getValue()
# Retrieve the detector distance...
fDistance = xsDataCollectionStrategy.getSubWedge()[0].getExperimentalCondition().getDetector().getDistance().getValue()
if fResolutionMax is None:
fResolutionMax = fResolution
fDistanceMin = fDistance
elif (fResolution < fResolutionMax) and (abs(fResolution-fResolutionMax) > 0.1):
fResolutionMax = fResolution
fDistanceMin = fDistance
fRankingResolution = xsDataSummaryStrategy.getRankingResolution().getValue()
if fRankingResolution != None and fResolutionMax != None:
if fRankingResolution < fResolutionMax:
if not bHigherResolutionDetected:
self.page.font(_color="red", size="+2")
self.page.i()
self.page.h2("Best has detected that the sample can diffract to %.2f Å!" % fRankingResolution)
self.page.i.close()
self.page.font.close()
self.page.font(_color="red", size="+1")
self.page.strong("The current strategy is calculated to %.2f Å." % fResolutionMax)
#self.page.strong("In order to calculate a strategy to %.2f Å set the detector distance to %.2f mm (%.2f Å) and re-launch the EDNA characterisation." % (fRankingResolution,fDistanceMin,fRankingResolution))
self.page.strong("In order to calculate a strategy to %.2f Å move the detector to collect %.2f Å data and re-launch the EDNA characterisation." % (fRankingResolution,fRankingResolution))
self.page.font.close()
bHigherResolutionDetected = True
for xsDataCollectionPlan in listXSDataCollectionPlan:
xsDataSummaryStrategy = xsDataCollectionPlan.getStrategySummary()
fResolutionMax = xsDataSummaryStrategy.getResolution().getValue()
strResolutionReasoning = ""
if xsDataSummaryStrategy.getResolutionReasoning():
strResolutionReasoning = xsDataSummaryStrategy.getResolutionReasoning().getValue()
self.page.table( class_='indexResults', border_="1", cellpadding_="0")
self.page.tr( align_="CENTER" )
self.page.th(strResolutionReasoning, colspan_="9", bgcolor_=self.strTableColourTitle1)
self.page.tr.close()
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Wedge")
self.page.th("Subwedge")
self.page.th("Start (°)")
self.page.th("Width (°)")
self.page.th("No images")
self.page.th("Exp time (s)")
self.page.th("Max res (Å)")
self.page.th("Rel trans (%)")
self.page.th("Distance (mm)")
self.page.tr.close()
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy()
for xsDataSubWegde in xsDataCollectionStrategy.getSubWedge():
xsDataExperimentalCondition = xsDataSubWegde.getExperimentalCondition()
iWedge = xsDataCollectionPlan.getCollectionPlanNumber().getValue()
iRunNumber = xsDataSubWegde.getSubWedgeNumber().getValue()
fRotationAxisStart = xsDataExperimentalCondition.getGoniostat().getRotationAxisStart().getValue()
fRotationAxisEnd = xsDataExperimentalCondition.getGoniostat().getRotationAxisEnd().getValue()
fOscillationWidth = xsDataExperimentalCondition.getGoniostat().getOscillationWidth().getValue()
iNumberOfImages = int((fRotationAxisEnd-fRotationAxisStart)/fOscillationWidth)
fExposureTime = xsDataExperimentalCondition.getBeam().getExposureTime().getValue()
fTransmission = xsDataExperimentalCondition.getBeam().getTransmission().getValue()
fDistance = xsDataExperimentalCondition.getDetector().getDistance().getValue()
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourRows)
self.page.th(iWedge)
self.page.th(iRunNumber)
self.page.th("%.2f" % fRotationAxisStart)
self.page.th("%.2f" % fOscillationWidth)
self.page.th(iNumberOfImages)
self.page.th("%.2f" % fExposureTime)
self.page.th("%.2f" % fResolutionMax)
self.page.th("%.2f" % fTransmission)
self.page.th("%.2f" % fDistance)
self.page.tr.close()
self.page.table.close()
def strategyResults(self):
# Was the strategy successful?
xsDataResultStrategy = self.xsDataResultCharacterisation.getStrategyResult()
if xsDataResultStrategy is None:
# Check if indexing and integration results
xsDataResultIntegration = self.xsDataResultCharacterisation.getIntegrationResult()
xsDataResultIndexing = self.xsDataResultCharacterisation.getIndexingResult()
if xsDataResultIndexing is None:
self.page.font(_color="red", size="+2")
self.page.h2()
self.page.strong("Strategy calculation not performed due to indexing failure, see the " )
self.page.a("EDNA log file", href=self.strPageEDNALog)
self.page.strong(" for more details" )
self.page.h2.close()
self.page.font.close()
elif xsDataResultIntegration is None:
self.page.font(_color="red", size="+2")
self.page.h2()
self.page.strong("Strategy calculation not performed due to integration failure, see the " )
self.page.a("EDNA log file", href=self.strPageEDNALog)
self.page.strong(" for more details" )
self.page.h2.close()
self.page.font.close()
else:
self.page.font(_color="red", size="+2")
self.page.h2()
self.page.strong( "Strategy calculation failed, see the " )
self.page.a("EDNA log file", href=self.strPageEDNALog)
self.page.strong(" for more details" )
self.page.h2.close()
self.page.font.close()
else:
# Add link to BEST log file:
if xsDataResultStrategy.getBestLogFile():
strPathToBestLogFile = xsDataResultStrategy.getBestLogFile().getPath().getValue()
if os.path.exists(strPathToBestLogFile):
strPageBestLog = os.path.join(self.getWorkingDirectory(), "best_log.html")
pageBestLog = markupv1_7.page()
pageBestLog.h1("BEST Log")
pageBestLog.a("Back to previous page", href_=self.strHtmlFileName)
pageBestLog.pre(cgi.escape(EDUtilsFile.readFile(strPathToBestLogFile)))
pageBestLog.a("Back to previous page", href_=self.strHtmlFileName)
EDUtilsFile.writeFile(strPageBestLog, str(pageBestLog))
# Add link to RADDOSE log file:
strPageRaddoseLog = None
if xsDataResultStrategy.getRaddoseLogFile():
strPathToRaddoseLogFile = xsDataResultStrategy.getRaddoseLogFile().getPath().getValue()
strPageRaddoseLog = os.path.join(self.getWorkingDirectory(), "raddose_log.html")
if os.path.exists(strPathToRaddoseLogFile):
pageRaddoseLog = markupv1_7.page()
pageRaddoseLog.h1("RADDOSE Log")
pageRaddoseLog.a("Back to previous page", href_=self.strHtmlFileName)
pageRaddoseLog.pre(cgi.escape(EDUtilsFile.readFile(strPathToRaddoseLogFile)))
pageRaddoseLog.a("Back to previous page", href_=self.strHtmlFileName)
EDUtilsFile.writeFile(strPageRaddoseLog, str(pageRaddoseLog))
listXSDataCollectionPlan = xsDataResultStrategy.getCollectionPlan()
if listXSDataCollectionPlan == []:
self.page.font(_color="red", size="+2")
self.page.h2()
self.page.strong("Strategy calculation failed, see the ")
self.page.a("BEST log file", href="best_log.html")
self.page.strong(" for more details")
if strPageRaddoseLog is not None:
self.page.a(" (RADDOSE log file)", href="raddose_log.html")
self.page.h2.close()
self.page.font.close()
else:
iNoSubWedges = len(listXSDataCollectionPlan)
self.page.h2()
if iNoSubWedges != 1:
self.page.strong("Multi-wedge collection plan strategy (")
else:
self.page.strong( "Collection plan strategy (" )
if strPageRaddoseLog is not None:
self.page.a("RADDOSE log file", href="raddose_log.html")
self.page.strong(", ")
self.page.a("BEST log file", href="best_log.html")
self.page.strong(")")
self.page.h2.close()
# Check if ranking resolution is higher than the suggested strategy resolution(s)
bHigherResolutionDetected = False
fRankingResolution = None
fResolutionMax = None
fDistanceMin = None
for xsDataCollectionPlan in listXSDataCollectionPlan:
xsDataSummaryStrategy = xsDataCollectionPlan.getStrategySummary()
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy()
if xsDataSummaryStrategy.getRankingResolution():
# Retrieve the resolution...
fResolution = xsDataSummaryStrategy.getResolution().getValue()
# Retrieve the detector distance...
fDistance = xsDataCollectionStrategy.getSubWedge()[0].getExperimentalCondition().getDetector().getDistance().getValue()
if fResolutionMax is None:
fResolutionMax = fResolution
fDistanceMin = fDistance
elif (fResolution < fResolutionMax) and (abs(fResolution-fResolutionMax) > 0.1):
fResolutionMax = fResolution
fDistanceMin = fDistance
fRankingResolution = xsDataSummaryStrategy.getRankingResolution().getValue()
if fRankingResolution != None and fResolutionMax != None:
if fRankingResolution < fResolutionMax:
if not bHigherResolutionDetected:
self.page.font(_color="red", size="+2")
self.page.i()
self.page.h2("Best has detected that the sample can diffract to %.2f Å!" % fRankingResolution)
self.page.i.close()
self.page.font.close()
self.page.font(_color="red", size="+1")
self.page.strong("The current strategy is calculated to %.2f Å." % fResolutionMax)
#self.page.strong("In order to calculate a strategy to %.2f Å set the detector distance to %.2f mm (%.2f Å) and re-launch the EDNA characterisation." % (fRankingResolution,fDistanceMin,fRankingResolution))
self.page.strong("In order to calculate a strategy to %.2f Å move the detector to collect %.2f Å data and re-launch the EDNA characterisation." % (fRankingResolution,fRankingResolution))
self.page.font.close()
bHigherResolutionDetected = True
for xsDataCollectionPlan in listXSDataCollectionPlan:
xsDataSummaryStrategy = xsDataCollectionPlan.getStrategySummary()
fResolutionMax = xsDataSummaryStrategy.getResolution().getValue()
strResolutionReasoning = ""
if xsDataSummaryStrategy.getResolutionReasoning():
strResolutionReasoning = xsDataSummaryStrategy.getResolutionReasoning().getValue()
self.page.table( class_='indexResults', border_="1", cellpadding_="0")
self.page.tr( align_="CENTER" )
self.page.th(strResolutionReasoning, colspan_="9", bgcolor_=self.strTableColourTitle1)
self.page.tr.close()
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourTitle2)
self.page.th("Wedge")
self.page.th("Subwedge")
self.page.th("Start (°)")
self.page.th("Width (°)")
self.page.th("No images")
self.page.th("Exp time (s)")
self.page.th("Max res (Å)")
self.page.th("Rel trans (%)")
self.page.th("Distance (mm)")
self.page.tr.close()
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy()
for xsDataSubWegde in xsDataCollectionStrategy.getSubWedge():
xsDataExperimentalCondition = xsDataSubWegde.getExperimentalCondition()
iWedge = xsDataCollectionPlan.getCollectionPlanNumber().getValue()
iRunNumber = xsDataSubWegde.getSubWedgeNumber().getValue()
fRotationAxisStart = xsDataExperimentalCondition.getGoniostat().getRotationAxisStart().getValue()
fRotationAxisEnd = xsDataExperimentalCondition.getGoniostat().getRotationAxisEnd().getValue()
fOscillationWidth = xsDataExperimentalCondition.getGoniostat().getOscillationWidth().getValue()
iNumberOfImages = int((fRotationAxisEnd-fRotationAxisStart)/fOscillationWidth)
fExposureTime = xsDataExperimentalCondition.getBeam().getExposureTime().getValue()
fTransmission = xsDataExperimentalCondition.getBeam().getTransmission().getValue()
fDistance = xsDataExperimentalCondition.getDetector().getDistance().getValue()
self.page.tr( align_="CENTER", bgcolor_=self.strTableColourRows)
self.page.th(iWedge)
self.page.th(iRunNumber)
self.page.th("%.2f" % fRotationAxisStart)
self.page.th("%.2f" % fOscillationWidth)
self.page.th(iNumberOfImages)
self.page.th("%.2f" % fExposureTime)
self.page.th("%.2f" % fResolutionMax)
self.page.th("%.2f" % fTransmission)
self.page.th("%.2f" % fDistance)
self.page.tr.close()
self.page.table.close()
