def createHtmlPage(self, strImagePrefix, xsDataResultDimple, strResultsDirectory, strHtmlPath, strProposal, strSessionDate, strBeamline):
"""Create an HTML page with the results"""
if not os.path.exists(strHtmlPath):
os.makedirs(strHtmlPath, 0o755)
strSample = "_".join(strImagePrefix.split("_")[0:-1])
strHtmlFileName = "ep_%s_index.html" % strImagePrefix
strPath = os.path.join(strHtmlPath, strHtmlFileName)
page = markupv1_10.page(mode='loose_html')
# Title and footer
page.init(title="Dimple Results",
footer="Generated on %s" % time.asctime())
page.div(align_="LEFT")
page.h1()
page.strong("Dimple Results for sample {0} from proposal {1}".format(strSample, strProposal))
page.h1.close()
page.h3("Session date: {0}-{1}-{2}".format(strSessionDate[0:4], strSessionDate[4:6], strSessionDate[6:]))
page.h3("Beamline: {0}".format(strBeamline))
page.h3("Dimple output files can be found in :")
page.strong(strResultsDirectory)
page.div.close()
# Results of REFMAC 5
page.h3("Final results of Recmac 5:")
page.pre(self.extractFinalResultsFromRefmac5RestrLog(xsDataResultDimple.refmac5restrLog.path.value))
# Results of findblobs
page.h3("Findblobs log:")
page.pre(open(xsDataResultDimple.findBlobsLog.path.value).read())
# Blobs
page.br()
listImageHTML = []
for xsDataFileBlob in xsDataResultDimple.blob:
# Copy blob file to html directory
strBlobName = os.path.basename(xsDataFileBlob.path.value).split(".")[0]
strBlobImage = "ep_%s_%s_dimple.png" % (strImagePrefix, strBlobName)
strTargetPath = os.path.join(strHtmlPath, strBlobImage)
shutil.copyfile(xsDataFileBlob.path.value, strTargetPath)
strPageBlobPath = os.path.join(strHtmlPath, "ep_%s_%s_dimple.html" % (strImagePrefix, strBlobName))
pageBlob = markupv1_10.page()
pageBlob.init(title=strBlobName,
footer="Generated on %s" % time.asctime())
pageBlob.h1(strBlobName)
pageBlob.div(align_="LEFT")
pageBlob.img(src=strBlobImage, title=strBlobName)
pageBlob.div.close()
pageBlob.br()
pageBlob.div(align_="LEFT")
pageBlob.a("Back to previous page", href_=os.path.basename(strPath))
pageBlob.div.close()
EDUtilsFile.writeFile(strPageBlobPath, str(pageBlob))
listImageHTML.append(strPageBlobPath)
page.a(href=os.path.basename(strPageBlobPath))
page.img(src=strBlobImage, width=200, height=200, title=strBlobName)
page.a.close()
if strBlobName == "blob1v3":
page.br()
page.br()
# FInalise html page
strHTML = str(page)
EDUtilsFile.writeFile(strPath, strHTML)
listHTML = [strPath] + listImageHTML
return listHTML
def integrationResults(self):
# Was the integration successful?
xsDataResultIntegration = self.xsDataResultCharacterisation.getIntegrationResult(
)
if xsDataResultIntegration:
iIntegration = 1
for xsDataIntegrationSubWedgeResult in xsDataResultIntegration.getIntegrationSubWedgeResult(
):
if xsDataIntegrationSubWedgeResult.getIntegrationLogFile(
) is not None:
strPathToIntegrationLogFile = xsDataIntegrationSubWedgeResult.getIntegrationLogFile(
).getPath().getValue()
strIntegrationHtmlPageName = "integration_%d_log.html" % iIntegration
strPageIntegrationLog = os.path.join(
self.getWorkingDirectory(), strIntegrationHtmlPageName)
pageIntegrationLog = markupv1_10.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 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,
align_="LEFT")
else:
if strSpaceGroup.upper() == _strForcedSpaceGroup.upper():
self.page.h3("Indexing summary: Forced spacegroup: %s" %
strSpaceGroup,
align_="LEFT")
else:
self.page.h3(
"Indexing summary: Selected spacegroup: %s, forced space group: %s"
% (strSpaceGroup, _strForcedSpaceGroup),
align_="LEFT")
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_10.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 process(self, _edPlugin=None):
EDPluginExec.process(self, _edPlugin)
self.DEBUG("EDPluginExecSimpleHTMLPagev2_0.process...")
if self.xsDataResultCharacterisation is not None:
# Create the simple characterisation result page
self.page = markupv1_10.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_10.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.dataCollectionInfo()
self.diffractionPlan()
self.strategyResults()
self.graphs()
self.stacResults()
self.indexingResults()
self.integrationResults()
self.imageQualityIndicatorResults()
def __renderImage(self, page, item, pathToHtmlDir):
imageName = item["title"].replace(" ", "_")
pathToImage = os.path.join(pathToHtmlDir,
"{0}.{1}".format(imageName, item["suffix"]))
if os.path.exists(pathToImage):
fd, pathToImage = tempfile.mkstemp(suffix="." + item["suffix"],
prefix=imageName + "_",
dir=pathToHtmlDir)
os.close(fd)
open(pathToImage, "wb").write(base64.b64decode(item["value"]))
os.chmod(pathToImage, 0o644)
if "thumbnailValue" in item:
thumbnailImageName = imageName + "_thumbnail"
pathToThumbnailImage = os.path.join(
pathToHtmlDir, "{0}.{1}".format(thumbnailImageName,
item["suffix"]))
if os.path.exists(pathToThumbnailImage):
fd, pathToThumbnailImage = tempfile.mkstemp(
suffix="." + item["suffix"],
prefix=thumbnailImageName + "_",
dir=pathToHtmlDir)
os.close(fd)
open(pathToThumbnailImage,
"wb").write(base64.b64decode(item["thumbnailValue"]))
os.chmod(pathToThumbnailImage, 0o644)
pageReferenceImage = markupv1_10.page(mode='loose_html')
pageReferenceImage.init(title=imageName,
footer="Generated on %s" % time.asctime())
pageReferenceImage.h1(imageName)
pageReferenceImage.br()
pageReferenceImage.img(src=os.path.basename(pathToImage),
title=imageName,
width=item["xsize"],
height=item["ysize"])
pageReferenceImage.br()
pathPageReferenceImage = os.path.join(pathToHtmlDir,
"{0}.html".format(imageName))
filePage = open(pathPageReferenceImage, "w")
filePage.write(str(pageReferenceImage))
filePage.close()
page.a(href=os.path.basename(pathPageReferenceImage))
page.img(src=os.path.basename(pathToThumbnailImage),
title=imageName,
width=item["thumbnailXsize"],
height=item["thumbnailYsize"])
page.a.close()
else:
page.img(src=os.path.basename(pathToImage),
title=item["title"],
width=item["xsize"],
height=item["ysize"])
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_10.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 process(self, _edPlugin=None):
EDPluginExec.process(self, _edPlugin)
self.DEBUG("EDPluginExecSimpleHTMLPagev2_0.process...")
if self.xsDataResultCharacterisation is not None:
# Create the simple characterisation result page
self.page = markupv1_10.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_10.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.dataCollectionInfo()
self.diffractionPlan()
self.strategyResults()
self.graphs()
self.stacResults()
self.indexingResults()
self.integrationResults()
self.imageQualityIndicatorResults()
def createHtmlPage(self):
plotImage = Image.open(os.path.join(self.getWorkingDirectory(), self.strScaleIntensityPlot))
plotImageWidth, plotImageHeight = plotImage.size # (width,height) tuple
page = markupv1_10.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,
height=plotImageHeight, width=plotImageWidth)
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_10.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, align_="LEFT")
else:
if strSpaceGroup.upper() == _strForcedSpaceGroup.upper():
self.page.h3("Indexing summary: Forced spacegroup: %s" % strSpaceGroup, align_="LEFT")
else:
self.page.h3("Indexing summary: Selected spacegroup: %s, forced space group: %s" % (strSpaceGroup, _strForcedSpaceGroup), align_="LEFT")
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_10.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():
if xsDataIntegrationSubWedgeResult.getIntegrationLogFile() is not None:
strPathToIntegrationLogFile = xsDataIntegrationSubWedgeResult.getIntegrationLogFile().getPath().getValue()
strIntegrationHtmlPageName = "integration_%d_log.html" % iIntegration
strPageIntegrationLog = os.path.join(self.getWorkingDirectory(), strIntegrationHtmlPageName)
pageIntegrationLog = markupv1_10.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_10.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 __renderImage(self, page, item, pathToHtmlDir):
imageName = item["title"].replace(" ", "_")
pathToImage = os.path.join(pathToHtmlDir, "{0}.{1}".format(imageName, item["suffix"]))
if os.path.exists(pathToImage):
fd, pathToImage = tempfile.mkstemp(suffix="." + item["suffix"],
prefix=imageName + "_",
dir=pathToHtmlDir)
os.close(fd)
open(pathToImage, "w").write(base64.b64decode(item["value"]))
os.chmod(pathToImage, 0o644)
if "thumbnailValue" in item:
thumbnailImageName = imageName + "_thumbnail"
pathToThumbnailImage = os.path.join(pathToHtmlDir, "{0}.{1}".format(thumbnailImageName, item["suffix"]))
if os.path.exists(pathToThumbnailImage):
fd, pathToThumbnailImage = tempfile.mkstemp(suffix="." + item["suffix"],
prefix=thumbnailImageName + "_",
dir=pathToHtmlDir)
os.close(fd)
open(pathToThumbnailImage, "w").write(base64.b64decode(item["thumbnailValue"]))
os.chmod(pathToThumbnailImage, 0o644)
pageReferenceImage = markupv1_10.page(mode='loose_html')
pageReferenceImage.init(title=imageName, footer="Generated on %s" % time.asctime())
pageReferenceImage.h1(imageName)
pageReferenceImage.br()
pageReferenceImage.img(src=os.path.basename(pathToImage),
title=imageName,
width=item["xsize"], height=item["ysize"])
pageReferenceImage.br()
pathPageReferenceImage = os.path.join(pathToHtmlDir, "{0}.html".format(imageName))
filePage = open(pathPageReferenceImage, "w")
filePage.write(str(pageReferenceImage))
filePage.close()
page.a(href=os.path.basename(pathPageReferenceImage))
page.img(src=os.path.basename(pathToThumbnailImage),
title=imageName, width=item["thumbnailXsize"], height=item["thumbnailYsize"])
page.a.close()
else:
page.img(src=os.path.basename(pathToImage),
title=item["title"],
width=item["xsize"],
height=item["ysize"])
def renderHtml(self, pathToHtmlDir, nameOfIndexFile="index.html"):
page = markupv1_10.page(mode='loose_html')
page.init(title=self.dictReport["title"],
footer="Generated on %s" % time.asctime())
page.div(align_="LEFT")
page.h1()
page.strong(self.dictReport["title"])
page.h1.close()
page.div.close()
for item in self.dictReport["items"]:
if "value" in item:
itemValue = item["value"]
if "title" in item:
itemTitle = self.escapeCharacters(item["title"])
if item["type"] == "info":
page.p(itemValue)
if item["type"] == "warning":
page.font(_color="red", size="+1")
page.p()
page.strong(itemValue)
page.p.close()
page.font.close()
elif item["type"] == "image":
self.__renderImage(page, item, pathToHtmlDir)
page.br()
page.p(itemTitle)
elif item["type"] == "images":
page.table()
page.tr(align_="CENTER")
for item in item["items"]:
itemTitle = self.escapeCharacters(item["title"])
page.td()
page.table()
page.tr()
page.td()
self.__renderImage(page, item, pathToHtmlDir)
page.td.close()
page.tr.close()
page.tr(align_="CENTER")
page.td(itemTitle)
page.tr.close()
page.table.close()
page.td.close()
page.tr.close()
page.table.close()
page.br()
elif item["type"] == "table":
titleBgColour = "#99c2ff"
columnTitleBgColour = "#ffffff"
dataBgColour = "#e6f0ff"
page.table(
border_="1",
cellpadding_="2",
width="100%",
style_=
"border: 1px solid black; border-collapse: collapse; margin: 0px; font-size: 12px"
)
page.tr(align_="LEFT")
# page.strong(itemTitle)
page.th(
itemTitle,
bgcolor_=titleBgColour,
align_="LEFT",
style_=
"border: 1px solid black; border-collapse: collapse; padding: 5px;",
colspan_=str(len(item["columns"])))
page.tr.close()
if "orientation" in item and item["orientation"] == "vertical":
for index1 in range(len(item["columns"])):
itemColumn = self.escapeCharacters(
item["columns"][index1])
page.tr(align_="LEFT")
page.th(
itemColumn,
bgcolor_=columnTitleBgColour,
align_="LEFT",
style_=
"border: 1px solid black; border-collapse: collapse; padding: 5px;"
)
for index2 in range(len(item["data"])):
itemData = self.escapeCharacters(
str(item["data"][index2][index1]))
page.th(itemData,
bgcolor_=dataBgColour,
style_="padding: 5px;")
page.tr.close()
else:
page.tr(
align_="LEFT",
bgcolor_=columnTitleBgColour,
style_=
"border: 1px solid black; border-collapse: collapse; padding: 5px;"
)
for column in item["columns"]:
itemColumn = self.escapeCharacters(column)
page.th(
itemColumn,
style_=
"border: 1px solid black; border-collapse: collapse; padding: 5px;"
)
page.tr.close()
for listRow in item["data"]:
page.tr(
align_="LEFT",
bgcolor_=dataBgColour,
style_="border-collapse: collapse; padding: 5px;")
for cell in listRow:
itemCell = self.escapeCharacters(str(cell))
page.th(
itemCell,
style_=
"border: 1px solid black; border-collapse: collapse; padding: 5px;"
)
page.tr.close()
page.table.close()
page.br()
elif item["type"] == "logFile":
pathToLogHtml = os.path.join(pathToHtmlDir,
itemTitle + ".html")
if os.path.exists(pathToLogHtml):
fd, pathToLogHtml = tempfile.mkstemp(
suffix=".html",
prefix=itemTitle.replace(" ", "_") + "_",
dir=pathToHtmlDir)
os.close(fd)
pageLogHtml = markupv1_10.page()
pageLogHtml.h1(itemTitle)
# pageLogHtml.pre(html.escape(item["logText"]))
open(pathToLogHtml, "w").write(str(pageLogHtml))
os.chmod(pathToLogHtml, 0o644)
page.p()
page.a(item["linkText"], href_=os.path.basename(pathToLogHtml))
page.p.close()
html = str(page)
pagePath = os.path.join(pathToHtmlDir, nameOfIndexFile)
filePage = open(pagePath, "w")
filePage.write(html)
filePage.close()
return pagePath
def renderHtml(self, pathToHtmlDir, nameOfIndexFile="index.html"):
page = markupv1_10.page(mode='loose_html')
page.init(title=self.dictReport["title"],
footer="Generated on %s" % time.asctime())
page.div(align_="LEFT")
page.h1()
page.strong(self.dictReport["title"])
page.h1.close()
page.div.close()
for item in self.dictReport["items"]:
if item["type"] == "info":
page.p(item["value"])
if item["type"] == "warning":
page.font(_color="red", size="+1")
page.p()
page.strong(item["value"])
page.p.close()
page.font.close()
elif item["type"] == "image":
self.__renderImage(page, item, pathToHtmlDir)
page.br()
page.p(item["title"])
elif item["type"] == "images":
page.table()
page.tr(align_="CENTER")
for item in item["items"]:
page.td()
page.table()
page.tr()
page.td()
self.__renderImage(page, item, pathToHtmlDir)
page.td.close()
page.tr.close()
page.tr(align_="CENTER")
page.td(item["title"])
page.tr.close()
page.table.close()
page.td.close()
page.tr.close()
page.table.close()
page.br()
elif item["type"] == "table":
page.h3()
page.strong(item["title"])
page.h3.close()
page.table(border_="1", cellpadding_="2")
if "orientation" in item and item["orientation"] == "vertical":
for index1 in range(len(item["columns"])):
page.tr(align_="CENTER")
page.th(item["columns"][index1].replace("\n", "<br>"),
bgcolor_="#F0F0FF",
align_="LEFT")
for index2 in range(len(item["data"])):
page.th(str(item["data"][index2][index1]).replace(
"\n", "<br>"),
bgcolor_="#FFFFA0")
page.tr.close()
else:
page.tr(align_="CENTER", bgcolor_="#F0F0FF")
for column in item["columns"]:
page.th(column.replace("\n", "<br>"))
page.tr.close()
for listRow in item["data"]:
page.tr(align_="CENTER", bgcolor_="#FFFFA0")
for cell in listRow:
page.th(str(cell).replace("\n", "<br>"))
page.tr.close()
page.table.close()
elif item["type"] == "logFile":
fd, pathToLogHtml = tempfile.mkstemp(
suffix=".html",
prefix=item["title"].replace(" ", "_") + "_",
dir=pathToHtmlDir)
os.close(fd)
pageLogHtml = markupv1_10.page()
pageLogHtml.h1(item["title"])
pageLogHtml.pre(cgi.escape(item["logText"]))
open(pathToLogHtml, "w").write(str(pageLogHtml))
os.chmod(pathToLogHtml, 0o644)
page.p()
page.a(item["linkText"], href_=os.path.basename(pathToLogHtml))
page.p.close()
html = str(page)
pagePath = os.path.join(pathToHtmlDir, nameOfIndexFile)
filePage = open(pagePath, "w")
filePage.write(html)
filePage.close()
return pagePath
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_10.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 renderHtml(self, pathToHtmlDir, nameOfIndexFile="index.html"):
page = markupv1_10.page(mode='loose_html')
page.init(title=self.dictReport["title"],
footer="Generated on %s" % time.asctime())
page.div(align_="LEFT")
page.h1()
page.strong(self.dictReport["title"])
page.h1.close()
page.div.close()
for item in self.dictReport["items"]:
if "value" in item:
itemValue = self.escapeCharacters(item["value"])
if "title" in item:
itemTitle = self.escapeCharacters(item["title"])
if item["type"] == "info":
page.p(itemValue)
if item["type"] == "warning":
page.font(_color="red", size="+1")
page.p()
page.strong(itemValue)
page.p.close()
page.font.close()
elif item["type"] == "image":
self.__renderImage(page, item, pathToHtmlDir)
page.br()
page.p(itemTitle)
elif item["type"] == "images":
page.table()
page.tr(align_="CENTER")
for item in item["items"]:
itemTitle = self.escapeCharacters(item["title"])
page.td()
page.table()
page.tr()
page.td()
self.__renderImage(page, item, pathToHtmlDir)
page.td.close()
page.tr.close()
page.tr(align_="CENTER")
page.td(itemTitle)
page.tr.close()
page.table.close()
page.td.close()
page.tr.close()
page.table.close()
page.br()
elif item["type"] == "table":
titleBgColour = "#99c2ff"
columnTitleBgColour = "#ffffff"
dataBgColour = "#e6f0ff"
page.table(border_="1",
cellpadding_="2",
width="100%",
style_="border: 1px solid black; border-collapse: collapse; margin: 0px; font-size: 12px")
page.tr(align_="LEFT")
# page.strong(itemTitle)
page.th(itemTitle, bgcolor_=titleBgColour, align_="LEFT", style_="border: 1px solid black; border-collapse: collapse; padding: 5px;", colspan_=str(len(item["columns"])))
page.tr.close()
if "orientation" in item and item["orientation"] == "vertical":
for index1 in range(len(item["columns"])):
itemColumn = self.escapeCharacters(item["columns"][index1])
page.tr(align_="LEFT")
page.th(itemColumn, bgcolor_=columnTitleBgColour, align_="LEFT", style_="border: 1px solid black; border-collapse: collapse; padding: 5px;")
for index2 in range(len(item["data"])):
itemData = self.escapeCharacters(str(item["data"][index2][index1]))
page.th(itemData, bgcolor_=dataBgColour, style_="padding: 5px;")
page.tr.close()
else:
page.tr(align_="LEFT", bgcolor_=columnTitleBgColour, style_="border: 1px solid black; border-collapse: collapse; padding: 5px;")
for column in item["columns"]:
itemColumn = self.escapeCharacters(column)
page.th(itemColumn, style_="border: 1px solid black; border-collapse: collapse; padding: 5px;")
page.tr.close()
for listRow in item["data"]:
page.tr(align_="LEFT", bgcolor_=dataBgColour, style_="border-collapse: collapse; padding: 5px;")
for cell in listRow:
itemCell = self.escapeCharacters(str(cell))
page.th(itemCell, style_="border: 1px solid black; border-collapse: collapse; padding: 5px;")
page.tr.close()
page.table.close()
page.br()
elif item["type"] == "logFile":
pathToLogHtml = os.path.join(pathToHtmlDir, itemTitle + ".html")
if os.path.exists(pathToLogHtml):
fd, pathToLogHtml = tempfile.mkstemp(suffix=".html",
prefix=itemTitle.replace(" ", "_") + "_",
dir=pathToHtmlDir)
os.close(fd)
pageLogHtml = markupv1_10.page()
pageLogHtml.h1(itemTitle)
pageLogHtml.pre(cgi.escape(item["logText"]))
open(pathToLogHtml, "w").write(str(pageLogHtml))
os.chmod(pathToLogHtml, 0o644)
page.p()
page.a(item["linkText"], href_=os.path.basename(pathToLogHtml))
page.p.close()
html = str(page)
pagePath = os.path.join(pathToHtmlDir, nameOfIndexFile)
filePage = open(pagePath, "w")
filePage.write(html)
filePage.close()
return pagePath
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_10.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_10.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()
def renderHtml(self, pathToHtmlDir, nameOfIndexFile="index.html"):
page = markupv1_10.page(mode='loose_html')
page.init(title=self.dictReport["title"],
footer="Generated on %s" % time.asctime())
page.div(align_="LEFT")
page.h1()
page.strong(self.dictReport["title"])
page.h1.close()
page.div.close()
for item in self.dictReport["items"]:
if item["type"] == "info":
page.p(item["value"])
if item["type"] == "warning":
page.font(_color="red", size="+1")
page.p()
page.strong(item["value"])
page.p.close()
page.font.close()
elif item["type"] == "image":
self.__renderImage(page, item, pathToHtmlDir)
page.br()
page.p(item["title"])
elif item["type"] == "images":
page.table()
page.tr(align_="CENTER")
for item in item["items"]:
page.td()
page.table()
page.tr()
page.td()
self.__renderImage(page, item, pathToHtmlDir)
page.td.close()
page.tr.close()
page.tr(align_="CENTER")
page.td(item["title"])
page.tr.close()
page.table.close()
page.td.close()
page.tr.close()
page.table.close()
page.br()
elif item["type"] == "table":
page.h3()
page.strong(item["title"])
page.h3.close()
page.table(border_="1",
cellpadding_="2")
if "orientation" in item and item["orientation"] == "vertical":
for index1 in range(len(item["columns"])):
page.tr(align_="CENTER")
page.th(item["columns"][index1].replace("\n", "<br>"), bgcolor_="#F0F0FF", align_="LEFT")
for index2 in range(len(item["data"])):
page.th(str(item["data"][index2][index1]).replace("\n", "<br>"), bgcolor_="#FFFFA0")
page.tr.close()
else:
page.tr(align_="CENTER", bgcolor_="#F0F0FF")
for column in item["columns"]:
page.th(column.replace("\n", "<br>"))
page.tr.close()
for listRow in item["data"]:
page.tr(align_="CENTER", bgcolor_="#FFFFA0")
for cell in listRow:
page.th(str(cell).replace("\n", "<br>"))
page.tr.close()
page.table.close()
elif item["type"] == "logFile":
pathToLogHtml = tempfile.mkstemp(suffix=".html",
prefix=item["title"].replace(" ", "_") + "_",
dir=pathToHtmlDir)[1]
pageLogHtml = markupv1_10.page()
pageLogHtml.h1(item["title"])
pageLogHtml.pre(cgi.escape(item["logText"]))
open(pathToLogHtml, "w").write(str(pageLogHtml))
os.chmod(pathToLogHtml, 0o644)
page.p()
page.a(item["linkText"], href_=os.path.basename(pathToLogHtml))
page.p.close()
html = str(page)
pagePath = os.path.join(pathToHtmlDir, nameOfIndexFile)
filePage = open(pagePath, "w")
filePage.write(html)
filePage.close()
return pagePath
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_10.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_10.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()