def testGenerateStrategyShortSummary(self):
edPluginStrategy = self.createPlugin()
strReferenceOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataResultStrategy_2_sweep.xml")
strXML = self.readAndParseFile(strReferenceOutputFile)
xsDataStrategyResult = XSDataResultStrategy.parseString(strXML)
edPluginStrategy.generateStrategyShortSummary(xsDataStrategyResult)
for strLine in edPluginStrategy.getDataOutput("strategyShortSummary")[0].getValue().split("\n"):
EDVerbose.unitTest(strLine)
def testGenerateStrategyShortSummary(self):
edPluginStrategy = self.createPlugin()
strReferenceOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataResultStrategy_2_sweep.xml")
strXML = self.readAndParseFile(strReferenceOutputFile)
xsDataStrategyResult = XSDataResultStrategy.parseString(strXML)
edPluginStrategy.generateStrategyShortSummary(xsDataStrategyResult)
for strLine in edPluginStrategy.getDataOutput("strategyShortSummary")[0].getValue().split("\n"):
self.unitTest(strLine)
def mergeStrategyToNewOrientation(_xsDataResultStrategy, _xsDataCollection, _fOmega, _fKappa, _fPhi):
'''
_xsDataResultStrategy: reference strategy results as the template for the new strategy
_xsDataCollection: The data collection that will be merged in
result:
suggestedStrategy(XSDataResultStrategy): the strategy resulted from the merge
'''
# suggestedStrategy = None
# try:
# newpossibleOrientations=XSDataSTACv01.kappa_alignment_response.parseString(_possible_orientation.marshal())
# except:
# newpossibleOrientations=None
#so we will copy the strategy of collecting the reference images inputed to here but at the new orientation
#get the full strategy from the Reference
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataResultStrategy
suggestedStrategy = XSDataResultStrategy.parseString(_xsDataResultStrategy.marshal())
#take only the first CollectionPlan
if len(suggestedStrategy.getCollectionPlan()) > 0:
suggestedStrategy.setCollectionPlan([suggestedStrategy.getCollectionPlan()[0]])
#modify the DC part taking it from the input
suggestedStrategy.getCollectionPlan()[0].setCollectionStrategy(_xsDataCollection)
#and modify the Orientation
# dc = XSDataMXv2.XSDataCollection()
# dc = self.getDataInput("mxv2DataCollection_Reference")[0]
# Orients = _possible_orientation.getPossible_orientation()
# omega = Orients[0].getOmega()
# kappa = Orients[0].getKappa()
# phi = Orients[0].getPhi()
suggestedStrategy = EDHandlerXSDataMXv1v1_0.copyStrategyToNewOrientation(suggestedStrategy, _fOmega, _fKappa, _fPhi, "MERGED")
# for dcplan in suggestedStrategy.getCollectionPlan():
# dcplan.setComment(EDHandlerXSDataMXv1v1_0().replaceElements(dcplan.getComment(), "OMEGA=", omega))
# dcplan.setComment(EDHandlerXSDataMXv1v1_0().replaceElements(dcplan.getComment(), "KAPPA=", kappa))
# dcplan.setComment(EDHandlerXSDataMXv1v1_0().replaceElements(dcplan.getComment(), "PHI=", phi))
#finally take the suggested new orientation out of the list of further possible ones
# if newpossibleOrientations is not None:
# newpossibleOrientations.setPossible_orientation([])
# for i in range(1, Orients.__len__()):
# if (math.fabs(float(Orients[i].getKappa())-float(kappa))<tol and math.fabs(float(Orients[i].getPhi())-float(phi))<tol):
# newpossibleOrientations.addPossible_orientation(Orients[i])
# return [suggestedStrategy,newpossibleOrientations]
return suggestedStrategy
def copyStrategyToNewOrientation(_xsDataResultStrategy, _fOmega, _fKappa, _fPhi, _strategy = "COPIED"):
'''
_xsDataResultStrategy: the strategy results in which the orientation should be changed
omega,kappa,phi: the new orientation
result:
suggestedStrategy(XSDataResultStrategy): the strategy in which the orientation is changed
'''
#we suggest the currently calculated strategy
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataResultStrategy
suggestedStrategy = XSDataResultStrategy.parseString(_xsDataResultStrategy.marshal())
#and we have to add the actual orientation
EDFactoryPluginStatic.loadModule("EDHandlerXSDataCommon")
from EDHandlerXSDataCommon import EDHandlerXSDataCommon
for dcplan in suggestedStrategy.getCollectionPlan():
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "OMEGA=", str(_fOmega)))
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "KAPPA=", str(_fKappa)))
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "PHI=", str(_fPhi)))
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "STRATEGY=", str(_strategy)))
return suggestedStrategy
from EDFactoryPluginStatic import EDFactoryPluginStatic
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataResultStrategy
xsDataResultStrategy = XSDataResultStrategy.parseString(mxv1StrategyResult)
xsDataCollectionPlan = xsDataResultStrategy.getCollectionPlan()[0]
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy()
xsDataSubWedge = xsDataCollectionStrategy.getSubWedge()[0]
xsDataExperimentalCondition = xsDataSubWedge.getExperimentalCondition()
exposureTime = xsDataExperimentalCondition.getBeam().getExposureTime(
).getValue()
detectorDistance = xsDataExperimentalCondition.getDetector().getDistance(
).getValue()
oscillationWidth = xsDataExperimentalCondition.getGoniostat(
).getOscillationWidth().getValue()
rotationAxisStart = xsDataExperimentalCondition.getGoniostat(
).getRotationAxisStart().getValue()
rotationAxisEnd = xsDataExperimentalCondition.getGoniostat(
).getRotationAxisEnd().getValue()
noImages = int((rotationAxisEnd - rotationAxisStart) / oscillationWidth)
runNumberDataCollection = run_number
print "Suggested strategy:"
print "Oscillation start: %.2f" % rotationAxisStart
print "Oscillation width: %.2f" % oscillationWidth
print "No images: %d" % noImages
print "Exposure time: %.2f" % exposureTime
print "Detector distance: %.2f" % detectorDistance
print "Run number: %d " % runNumberDataCollection
from EDFactoryPluginStatic import EDFactoryPluginStatic
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataResultStrategy
xsDataResultStrategy = XSDataResultStrategy.parseString(suggestedStrategy)
for xsDataCollectionPlan in xsDataResultStrategy:
if xsDataCollectionPlan.getCollectionPlanNumber().getValue() == collectionPlanIndex:
break
from EDFactoryPluginStatic import EDFactoryPluginStatic
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataResultStrategy
xsDataResultStrategy = XSDataResultStrategy.parseString(suggestedStrategy)
for xsDataCollectionPlan in xsDataResultStrategy:
if xsDataCollectionPlan.getCollectionPlanNumber().getValue(
) == collectionPlanIndex:
break
from EDFactoryPluginStatic import EDFactoryPluginStatic
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataResultStrategy
xsDataResultStrategy = XSDataResultStrategy.parseString(mxv1StrategyResult)
xsDataCollectionPlan = xsDataResultStrategy.getCollectionPlan()[0]
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy()
xsDataSubWedge = xsDataCollectionStrategy.getSubWedge()[0]
xsDataExperimentalCondition = xsDataSubWedge.getExperimentalCondition()
exposureTime = xsDataExperimentalCondition.getBeam().getExposureTime().getValue()
detectorDistance = xsDataExperimentalCondition.getDetector().getDistance().getValue()
oscillationWidth = xsDataExperimentalCondition.getGoniostat().getOscillationWidth().getValue()
rotationAxisStart = xsDataExperimentalCondition.getGoniostat().getRotationAxisStart().getValue()
rotationAxisEnd = xsDataExperimentalCondition.getGoniostat().getRotationAxisEnd().getValue()
noImages = int( (rotationAxisEnd - rotationAxisStart) / oscillationWidth)
runNumberDataCollection = run_number
print "Suggested strategy:"
print "Oscillation start: %.2f" % rotationAxisStart
print "Oscillation width: %.2f" % oscillationWidth
print "No images: %d" % noImages
print "Exposure time: %.2f" % exposureTime
print "Detector distance: %.2f" % detectorDistance
print "Run number: %d " % runNumberDataCollection
