def run(self, inData):
listImagePath = inData["imagePath"]
prefix = UtilsImage.getPrefix(listImagePath[0])
listSubWedge = self.getListSubWedge(inData)
diffractionPlan = inData.get("diffractionPlan", {})
sample = inData.get("sample", {})
# Check if flux is present
flux = None
absorbedDoseRate = None
experimentalCondition = inData.get("experimentalCondition", None)
if experimentalCondition is not None:
beam = experimentalCondition.get("beam", None)
if beam is not None:
flux = beam.get("flux", None)
# if not "size" in beam:
# beam["size"] = listSubWedge[0]["experimentalCondition"]["beam"]["size"]
beam["exposureTime"] = listSubWedge[0][
"experimentalCondition"]["beam"]["exposureTime"]
beam["wavelength"] = listSubWedge[0]["experimentalCondition"][
"beam"]["wavelength"]
# Convert images to CBF
firstImage = listSubWedge[0]["image"][0]["path"]
import os
import pprint
listH5ToCBF = []
suffix = os.path.splitext(firstImage)[1]
if suffix == ".h5":
for subWedge in listSubWedge:
imageList = subWedge["image"]
for image in imageList:
imagePath = image["path"]
hdf5ImageNumber = UtilsImage.getImageNumber(imagePath)
inDataH5ToCBF = {
"hdf5File": imagePath,
"hdf5ImageNumber": hdf5ImageNumber,
"imageNumber": 1,
"forcedOutputDirectory":
str(self.getWorkingDirectory()),
"forcedOutputImageNumber": hdf5ImageNumber,
}
h5ToCBF = H5ToCBFTask(inData=inDataH5ToCBF)
h5ToCBF.start()
listH5ToCBF.append((image, h5ToCBF))
# Join CBF creation
for image, h5ToCBF in listH5ToCBF:
h5ToCBF.join()
image["path"] = h5ToCBF.outData["outputCBFFile"]
pprint.pprint(listSubWedge)
# Start indexing
outDataIndexing, outDataGB, listSubWedge = self.indexing(
prefix, listSubWedge, self.getWorkingDirectory())
if outDataIndexing is not None and outDataGB is not None:
listXdsAsciiHkl, correctLp, bkgpixCbf = self.integration(
prefix, listSubWedge, outDataIndexing, outDataGB)
if listXdsAsciiHkl is not None:
# Check if Raddose should be run
estimateRadiationDamage = self.checkEstimateRadiationDamage(
inData, flux)
if estimateRadiationDamage:
# Check if forced space group
forcedSpaceGroup = None
numOperators = None
cell = None
if ("diffractionPlan" in inData and "forcedSpaceGroup"
in inData["diffractionPlan"]):
forcedSpaceGroup = inData["diffractionPlan"][
"forcedSpaceGroup"]
if forcedSpaceGroup is not None:
if forcedSpaceGroup != "":
forcedSpaceGroup = forcedSpaceGroup.replace(
" ", "")
numOperators = UtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
forcedSpaceGroup)
else:
forcedSpaceGroup = None
if forcedSpaceGroup is None:
# Get indexing space group IT number
if "resultIndexing" in outDataIndexing:
resultIndexing = outDataIndexing["resultIndexing"]
cell = resultIndexing["cell"]
if "spaceGroupNumber" in resultIndexing:
spaceGroupNumber = resultIndexing[
"spaceGroupNumber"]
numOperators = UtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
spaceGroupNumber)
if numOperators is None:
raise RuntimeError(
"Error when trying to determine number of symmetry operators!"
)
chemicalComposition = self.getDefaultChemicalComposition(
cell, numOperators)
numberOfImages = self.getNumberOfImages(listSubWedge)
sample = inData["sample"]
inDataRaddose = {
"experimentalCondition": experimentalCondition,
"chemicalComposition": chemicalComposition,
"sample": sample,
"cell": cell,
"numberOfImages": numberOfImages,
"numOperators": numOperators,
}
# import pprint
# pprint.pprint(inDataRaddose)
raddose = Raddose(inData=inDataRaddose,
workingDirectorySuffix=prefix)
raddose.execute()
if raddose.isSuccess():
absorbedDoseRate = raddose.outData["absorbedDoseRate"]
inDataBest = {
"diffractionPlan": diffractionPlan,
"sample": sample,
"subWedge": listSubWedge,
"xdsAsciiHkl": listXdsAsciiHkl,
"bkgpixCbf": bkgpixCbf,
"correctLp": correctLp,
"crystalAbsorbedDoseRate": absorbedDoseRate,
}
bestTask = Best(inData=inDataBest,
workingDirectorySuffix=prefix)
bestTask.execute()
def run(self, inData):
outData = {}
listImagePath = inData["imagePath"]
prefix = UtilsImage.getPrefix(listImagePath[0])
listSubWedge = self.getListSubWedge(inData)
diffractionPlan = inData.get("diffractionPlan", {})
sample = inData.get("sample", {})
# Check if flux is present
flux = None
absorbedDoseRate = None
experimentalCondition = inData.get("experimentalCondition", None)
if experimentalCondition is not None:
beam = experimentalCondition.get("beam", None)
if beam is not None:
flux = beam.get("flux", None)
# if not "size" in beam:
# beam["size"] = listSubWedge[0]["experimentalCondition"]["beam"]["size"]
beam["exposureTime"] = listSubWedge[0]["experimentalCondition"]["beam"]["exposureTime"]
beam["wavelength"] = listSubWedge[0]["experimentalCondition"]["beam"]["wavelength"]
# Start indexing
outDataIndexing, outDataGB = self.indexing(prefix, listSubWedge)
if outDataIndexing is not None and outDataGB is not None:
listXdsAsciiHkl, correctLp, bkgpixCbf = self.integration(
prefix, listSubWedge, outDataIndexing, outDataGB)
if listXdsAsciiHkl is not None:
# Check if Raddose should be run
estimateRadiationDamage = self.checkEstimateRadiationDamage(inData, flux)
if estimateRadiationDamage:
# Check if forced space group
forcedSpaceGroup = None
numOperators = None
cell = None
if "diffractionPlan" in inData and "forcedSpaceGroup" in inData["diffractionPlan"]:
forcedSpaceGroup = inData["diffractionPlan"]["forcedSpaceGroup"]
if forcedSpaceGroup is not None:
if forcedSpaceGroup != "":
forcedSpaceGroup = forcedSpaceGroup.replace(" ", "")
numOperators = UtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(forcedSpaceGroup)
else:
forcedSpaceGroup = None
if forcedSpaceGroup is None:
# Get indexing space group IT number
if "resultIndexing" in outDataIndexing:
resultIndexing = outDataIndexing["resultIndexing"]
cell = resultIndexing["cell"]
if "spaceGroupNumber" in resultIndexing:
spaceGroupNumber = resultIndexing["spaceGroupNumber"]
numOperators = UtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(spaceGroupNumber)
if numOperators is None:
raise RuntimeError("Error when trying to determine number of symmetry operators!")
chemicalComposition = self.getDefaultChemicalComposition(cell, numOperators)
numberOfImages = self.getNumberOfImages(listSubWedge)
sample = inData["sample"]
inDataRaddose = {
"experimentalCondition": experimentalCondition,
"chemicalComposition": chemicalComposition,
"sample": sample,
"cell": cell,
"numberOfImages": numberOfImages,
"numOperators": numOperators
}
# import pprint
# pprint.pprint(inDataRaddose)
raddose = Raddose(
inData=inDataRaddose,
workingDirectorySuffix=prefix)
raddose.execute()
if raddose.isSuccess():
absorbedDoseRate = raddose.outData["absorbedDoseRate"]
inDataBest = {
"diffractionPlan": diffractionPlan,
"sample": sample,
"subWedge": listSubWedge,
"xdsAsciiHkl": listXdsAsciiHkl,
"bkgpixCbf": bkgpixCbf,
"correctLp": correctLp,
"crystalAbsorbedDoseRate": absorbedDoseRate
}
bestTask = Best(
inData=inDataBest,
workingDirectorySuffix=prefix
)
bestTask.execute()