def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlH5ToCBFv1_0.process")
imageNumber = self.dataInput.imageNumber.value
if self.dataInput.hdf5ImageNumber is None:
hdf5ImageNumber = imageNumber
else:
hdf5ImageNumber = self.dataInput.hdf5ImageNumber.value
if self.dataInput.ispybDataCollection is None:
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection(
)
xsDataImage = XSDataImage(self.dataInput.hdf5File.path)
xsDataInputRetrieveDataCollection.image = xsDataImage
self.edPluginISPyBRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
self.edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = self.edPluginISPyBRetrieveDataCollection.dataOutput
dataCollection = xsDataResultRetrieveDataCollection.dataCollection
else:
dataCollection = self.dataInput.ispybDataCollection
if dataCollection is not None:
if dataCollection.overlap is None:
overlap = 0.0
else:
overlap = dataCollection.overlap
axisStart = dataCollection.axisStart
oscillationRange = dataCollection.axisRange
axisStartNew = axisStart - (overlap +
oscillationRange) * (imageNumber - 1)
dataCollection.axisStart = axisStartNew
xsDataISPyBDataCollection = XSDataISPyBDataCollection.parseString(
dataCollection.marshal())
else:
xsDataISPyBDataCollection = None
xsDataInputH5ToCBF = XSDataInputH5ToCBF()
xsDataInputH5ToCBF.hdf5File = self.dataInput.hdf5File
xsDataInputH5ToCBF.imageNumber = self.dataInput.imageNumber
xsDataInputH5ToCBF.hdf5ImageNumber = XSDataInteger(hdf5ImageNumber)
xsDataInputH5ToCBF.dataCollection = xsDataISPyBDataCollection
xsDataInputH5ToCBF.forcedOutputDirectory = self.dataInput.forcedOutputDirectory
self.edPluginEDPluginH5ToCBF.dataInput = xsDataInputH5ToCBF
self.edPluginEDPluginH5ToCBF.executeSynchronous()
if self.edPluginEDPluginH5ToCBF.dataOutput is not None:
self.dataOutput.outputCBFFile = self.edPluginEDPluginH5ToCBF.dataOutput.outputCBFFile
if dataCollection is not None:
self.dataOutput.ispybDataCollection = XSDataISPyBDataCollection.parseString(
dataCollection.marshal())
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlH5ToCBFv1_0.process")
imageNumber = self.dataInput.imageNumber.value
if self.dataInput.hdf5ImageNumber is None:
hdf5ImageNumber = imageNumber
else:
hdf5ImageNumber = self.dataInput.hdf5ImageNumber.value
if self.dataInput.ispybDataCollection is None:
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataImage = XSDataImage(self.dataInput.hdf5File.path)
xsDataInputRetrieveDataCollection.image = xsDataImage
self.edPluginISPyBRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
self.edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = self.edPluginISPyBRetrieveDataCollection.dataOutput
dataCollection = xsDataResultRetrieveDataCollection.dataCollection
else:
dataCollection = self.dataInput.ispybDataCollection
if dataCollection is not None:
if dataCollection.overlap is None:
overlap = 0.0
else:
overlap = dataCollection.overlap
axisStart = dataCollection.axisStart
oscillationRange = dataCollection.axisRange
axisStartNew = axisStart - (overlap + oscillationRange) * (imageNumber - 1)
dataCollection.axisStart = axisStartNew
xsDataISPyBDataCollection = XSDataISPyBDataCollection.parseString(dataCollection.marshal())
else:
xsDataISPyBDataCollection = None
xsDataInputH5ToCBF = XSDataInputH5ToCBF()
xsDataInputH5ToCBF.hdf5File = self.dataInput.hdf5File
xsDataInputH5ToCBF.imageNumber = self.dataInput.imageNumber
xsDataInputH5ToCBF.hdf5ImageNumber = XSDataInteger(hdf5ImageNumber)
xsDataInputH5ToCBF.dataCollection = xsDataISPyBDataCollection
xsDataInputH5ToCBF.forcedOutputDirectory = self.dataInput.forcedOutputDirectory
self.edPluginEDPluginH5ToCBF.dataInput = xsDataInputH5ToCBF
self.edPluginEDPluginH5ToCBF.executeSynchronous()
if self.edPluginEDPluginH5ToCBF.dataOutput is not None:
self.dataOutput.outputCBFFile = self.edPluginEDPluginH5ToCBF.dataOutput.outputCBFFile
if dataCollection is not None:
self.dataOutput.ispybDataCollection = XSDataISPyBDataCollection.parseString(dataCollection.marshal())
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginControlDozorv1_0.postProcess")
# Write a file to be used with ISPyB or GNUPLOT only if data collection id in input
dataCollectionId = None
if self.dataInput.dataCollectionId is None and len(self.dataInput.image) > 0:
# Only try to obtain data collection id if at the ESRF and path starts with "/data"
if EDUtilsPath.isESRF() and self.dataInput.image[0].path.value.startswith("/data"):
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
xsDataInputRetrieveDataCollection.image = XSDataImage(self.dataInput.image[0].path)
edPluginISPyBRetrieveDataCollection = self.loadPlugin("EDPluginISPyBRetrieveDataCollectionv1_4")
edPluginISPyBRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
edPluginISPyBRetrieveDataCollection.executeSynchronous()
xsDataResultRetrieveDataCollection = edPluginISPyBRetrieveDataCollection.dataOutput
if xsDataResultRetrieveDataCollection is not None:
dataCollection = xsDataResultRetrieveDataCollection.dataCollection
if dataCollection is not None:
dataCollectionId = dataCollection.dataCollectionId
elif self.dataInput.dataCollectionId is not None:
dataCollectionId = self.dataInput.dataCollectionId.value
if dataCollectionId is not None:
minImageNumber = None
maxImageNumber = None
minAngle = None
maxAngle = None
minDozorValue = None
maxDozorValue = None
minResolution = None
maxResolution = None
dozorPlotFileName = "dozor_{0}.png".format(dataCollectionId)
dozorCsvFileName = "dozor_{0}.csv".format(dataCollectionId)
with open(os.path.join(self.getWorkingDirectory(), dozorCsvFileName), "w") as gnuplotFile:
gnuplotFile.write("# Data directory: {0}\n".format(self.directory))
gnuplotFile.write("# File template: {0}\n".format(self.template.replace("%04d", "####")))
gnuplotFile.write("# {0:>9s}{1:>16s}{2:>16s}{3:>16s}{4:>16s}{5:>16s}\n".format("'Image no'",
"'Angle'",
"'No of spots'",
"'Main score (*10)'",
"'Spot score'",
"'Visible res.'",
))
for imageDozor in self.dataOutput.imageDozor:
gnuplotFile.write("{0:10d},{1:15.3f},{2:15d},{3:15.3f},{4:15.3f},{5:15.3f}\n".format(imageDozor.number.value,
imageDozor.angle.value,
imageDozor.spotsNumOf.value,
10 * imageDozor.mainScore.value,
imageDozor.spotScore.value,
imageDozor.visibleResolution.value,
))
if minImageNumber is None or minImageNumber > imageDozor.number.value:
minImageNumber = imageDozor.number.value
minAngle = imageDozor.angle.value
if maxImageNumber is None or maxImageNumber < imageDozor.number.value:
maxImageNumber = imageDozor.number.value
maxAngle = imageDozor.angle.value
if minDozorValue is None or minDozorValue > imageDozor.mainScore.value:
minDozorValue = imageDozor.spotScore.value
if maxDozorValue is None or maxDozorValue < imageDozor.mainScore.value:
maxDozorValue = imageDozor.spotScore.value
# Min resolution: the higher the value the lower the resolution
if minResolution is None or minResolution < imageDozor.visibleResolution.value:
# Disregard resolution worse than 10.0
if imageDozor.visibleResolution.value < 10.0:
minResolution = imageDozor.visibleResolution.value
# Max resolution: the lower the number the better the resolution
if maxResolution is None or maxResolution > imageDozor.visibleResolution.value:
maxResolution = imageDozor.visibleResolution.value
xtics = ""
if minImageNumber is not None and minImageNumber == maxImageNumber:
minAngle -= 1.0
maxAngle += 1.0
noImages = maxImageNumber - minImageNumber + 1
if noImages <= 4:
minImageNumber -= 0.1
maxImageNumber += 0.1
deltaAngle = maxAngle - minAngle
minAngle -= deltaAngle * 0.1 / noImages
maxAngle += deltaAngle * 0.1 / noImages
xtics = "1"
if maxResolution is None or maxResolution > 0.8:
maxResolution = 0.8
else:
maxResolution = int(maxResolution * 10.0) / 10.0
if minResolution is None or minResolution < 4.5:
minResolution = 4.5
else:
minResolution = int(minResolution * 10.0) / 10.0 + 1
if maxDozorValue < 0.001 and minDozorValue < 0.001:
yscale = "set yrange [-0.5:0.5]\n set ytics 1"
else:
yscale = "set autoscale y"
gnuplotFile.close()
gnuplotScript = \
"""#
set terminal png
set output '{dozorPlotFileName}'
set title '{title}'
set grid x2 y2
set xlabel 'Image number'
set x2label 'Angle (degrees)'
set y2label 'Resolution (A)'
set ylabel 'Number of spots / Dozor score (*10)'
set xtics {xtics} nomirror
set x2tics
set ytics nomirror
set y2tics
set xrange [{minImageNumber}:{maxImageNumber}]
set x2range [{minAngle}:{maxAngle}]
{yscale}
set y2range [{minResolution}:{maxResolution}]
set key below
plot '{dozorCsvFileName}' using 1:3 title 'Number of spots' axes x1y1 with points linetype rgb 'goldenrod' pointtype 7 pointsize 1.5, \
'{dozorCsvFileName}' using 1:4 title 'Dozor score' axes x1y1 with points linetype 3 pointtype 7 pointsize 1.5, \
'{dozorCsvFileName}' using 1:6 title 'Visible resolution' axes x1y2 with points linetype 1 pointtype 7 pointsize 1.5
""".format(title=self.template.replace("%04d", "####"),
dozorPlotFileName=dozorPlotFileName,
dozorCsvFileName=dozorCsvFileName,
minImageNumber=minImageNumber,
maxImageNumber=maxImageNumber,
minAngle=minAngle,
maxAngle=maxAngle,
minResolution=minResolution,
maxResolution=maxResolution,
xtics=xtics,
yscale=yscale,
)
pathGnuplotScript = os.path.join(self.getWorkingDirectory(), "gnuplot.sh")
data_file = open(pathGnuplotScript, "w")
data_file.write(gnuplotScript)
data_file.close()
oldCwd = os.getcwd()
os.chdir(self.getWorkingDirectory())
os.system("{0} {1}".format(self.gnuplot, pathGnuplotScript))
os.chdir(oldCwd)
self.dataOutput.dozorPlot = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), dozorPlotFileName)))
if self.dataInput.processDirectory is not None:
processDirectory = self.dataInput.processDirectory.path.value
else:
processDirectory = os.path.join(self.directory.replace("RAW_DATA", "PROCESSED_DATA"), "DozorPlot")
resultsDirectory = os.path.join(processDirectory, "results")
dozorPlotResultPath = os.path.join(resultsDirectory, dozorPlotFileName)
dozorCsvResultPath = os.path.join(resultsDirectory, dozorCsvFileName)
try:
if not os.path.exists(resultsDirectory):
os.makedirs(resultsDirectory, 0o755)
shutil.copy(os.path.join(self.getWorkingDirectory(), dozorPlotFileName), dozorPlotResultPath)
shutil.copy(os.path.join(self.getWorkingDirectory(), dozorCsvFileName), dozorCsvResultPath)
except:
self.warning("Couldn't copy files to results directory: {0}".format(resultsDirectory))
try:
# Create paths on pyarch
dozorPlotPyarchPath = EDHandlerESRFPyarchv1_0.createPyarchFilePath(dozorPlotResultPath)
dozorCsvPyarchPath = EDHandlerESRFPyarchv1_0.createPyarchFilePath(dozorCsvResultPath)
if not os.path.exists(os.path.dirname(dozorPlotPyarchPath)):
os.makedirs(os.path.dirname(dozorPlotPyarchPath), 0o755)
shutil.copy(dozorPlotResultPath, dozorPlotPyarchPath)
shutil.copy(dozorCsvResultPath, dozorCsvPyarchPath)
# Upload to data collection
xsDataInputISPyBSetImageQualityIndicatorsPlot = XSDataInputISPyBSetImageQualityIndicatorsPlot()
xsDataInputISPyBSetImageQualityIndicatorsPlot.dataCollectionId = XSDataInteger(dataCollectionId)
xsDataInputISPyBSetImageQualityIndicatorsPlot.imageQualityIndicatorsPlotPath = XSDataString(dozorPlotPyarchPath)
xsDataInputISPyBSetImageQualityIndicatorsPlot.imageQualityIndicatorsCSVPath = XSDataString(dozorCsvPyarchPath)
EDPluginISPyBSetImageQualityIndicatorsPlot = self.loadPlugin("EDPluginISPyBSetImageQualityIndicatorsPlotv1_4")
EDPluginISPyBSetImageQualityIndicatorsPlot.dataInput = xsDataInputISPyBSetImageQualityIndicatorsPlot
EDPluginISPyBSetImageQualityIndicatorsPlot.executeSynchronous()
except:
self.warning("Couldn't copy files to pyarch: {0}".format(dozorPlotPyarchPath))
self.sendMessageToMXCuBE("Processing finished", "info")
self.setStatusToMXCuBE("Success")
