def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.preProcess...")
self.__edPluginIndexing = self.loadPlugin(self.__strPluginIndexingName , "Indexing")
self.__edPluginIntegration = self.loadPlugin(self.__strPluginIntegrationName, "Integration")
self.__edPluginStrategy = self.loadPlugin(self.__strPluginStrategyName , "Strategy")
if (self.__edPluginIndexing is not None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.preProcess: " + self.__strPluginIndexingName + " Found... setting Data Input")
# create Data Input for indexing
xsDataCollection = self.getDataInput()
xsDataSample = xsDataCollection.getSample()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(xsDataExperimentalCondition)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataIndexingInput.setCrystal(xsDataCrystal)
self.__edPluginIndexing.setDataInput(xsDataIndexingInput)
# Populate characterisation object
self.__xsDataCharacterisation = XSDataCharacterisation()
self.__xsDataCharacterisation.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
def dna_execute_collection3(dna_start,dna_range,dna_number_of_images,dna_exptime,dna_directory,prefix,start_image_number,overlap,dna_res,dna_run_num):
global collect_and_characterize_success,dna_have_strategy_results,dna_have_index_results,picture_taken
global dna_strategy_exptime,dna_strategy_start,dna_strategy_range,dna_strategy_end,dna_strat_dist
global screeningoutputid
dna_filename_list = []
print "number of images " + str(dna_number_of_images) + " overlap = " + str(overlap) + " dna_start " + str(dna_start) + " dna_range " + str(dna_range) + " prefix " + prefix + " start number " + str(start_image_number) + "\n"
collect_and_characterize_success = 0
dna_have_strategy_results = 0
dna_have_index_results = 0
dg2rd = 3.14159265 / 180.0
if (daq_utils.detector_id == "ADSC-Q315"):
det_radius = 157.5
elif (daq_utils.detector_id == "ADSC-Q210"):
det_radius = 105.0
else: #default Q4
det_radius = 94.0
theta_radians = daq_lib.get_field("theta") * dg2rd
wave = daq_lib.get_field("wavelength0")
dx = det_radius/(tan(2.0*(asin(wave/(2.0*dna_res)))-theta_radians))
print "distance = ",dx
#skinner - could move distance and wave and scan axis here, leave wave alone for now
print "skinner about to take reference images."
for i in range(0,int(dna_number_of_images)):
print "skinner prefix7 = " + prefix[0:7] + " startnum + " + str(start_image_number) + "\n"
if (len(prefix)> 8):
if ((prefix[0:7] == "postref") and (start_image_number == 1)):
print "skinner postref bail\n"
time.sleep(float(dna_number_of_images*float(dna_exptime)))
break
#skinner roi - maybe I can measure and use that for dna_start so that first image is face on.
if (daq_lib.need_auto_align_xtal_pic == 1):
daq_lib.measure(1)
# dna_start = daq_lib.var_list[daq_lib.var_list["scan_axis"]] + 75.0
dna_start = daq_lib.get_field("datum_omega")
colstart = float(dna_start) + (i*(abs(overlap)+float(dna_range)))
# colstart = colstart + daq_lib.var_list["datum_omega"]
# daq_lib.move_axis_absolute(daq_lib.var_list["scan_axis"],colstart)
# daq_lib.move_axis_absolute("dist",dx)
dna_prefix = "ref-"+prefix+"_"+str(dna_run_num)
image_number = start_image_number+i
dna_prefix_long = dna_directory+"/"+dna_prefix
filename = daq_lib.create_filename(dna_prefix_long,image_number)
if (daq_lib.need_auto_align_xtal_pic == 1):
daq_lib.need_auto_align_xtal_pic = 0
camera_offset = float(os.environ["CAMERA_OFFSET"])
beamline_lib.mvr("Omega",float(camera_offset))
##### daq_lib.move_axis_relative("omega",camera_offset)
##### daq_lib.take_crystal_picture_with_boxes(daq_lib.html_data_directory_name + "/xtal_align_" + str(daq_lib.sweep_seq_id))
##### daq_lib.move_axis_relative("omega",0-camera_offset)
beamline_lib.mvr("Omega",float(0-camera_offset))
if (daq_lib.need_auto_align_xtal_pic == 2 and daq_lib.has_xtalview):
daq_lib.need_auto_align_xtal_pic = 0
##### daq_lib.take_crystal_picture_with_boxes(daq_lib.html_data_directory_name + "/xtal_postalign_" + str(daq_lib.sweep_seq_id))
postalign_jpg = "xtal_postalign_" + str(daq_lib.sweep_seq_id)
# postalign_jpg_th = "xtal_postalign_th_" + str(daq_lib.sweep_seq_id)
beamline_lib.mva("Omega",float(colstart))
##### daq_lib.move_axis_absolute(daq_lib.get_field("scan_axis"),colstart)
daq_lib.take_image(colstart,dna_range,dna_exptime,filename,daq_lib.get_field("scan_axis"),0,1)
dna_filename_list.append(filename)
##### daq_lib.take_crystal_picture_with_boxes(daq_lib.html_data_directory_name + "/xtal_" + str(daq_lib.sweep_seq_id) + "_" + str(i))
picture_taken = 1
# xml_from_file_list(flux,x_beamsize,y_beamsize,max_exptime_per_dc,aimed_completeness,file_list):
edna_energy_ev = (12.3985/wave) * 1000.0
##### xbeam_size = beamline_lib.get_motor_pos("slitHum")
##### ybeam_size = beamline_lib.get_motor_pos("slitVum")
# if (xbeam_size == 0.0 or ybeam_size == 0.0): #don't know where to get these from yet
if (0):
xbeam_size = .1
ybeam_size = .16
else:
xbeam_size = xbeam_size/1000
ybeam_size = ybeam_size/1000
aimed_completness = daq_lib.get_field('edna_aimed_completeness')
aimed_multiplicity = daq_lib.get_field('edna_aimed_multiplicity')
aimed_resolution = daq_lib.get_field('edna_aimed_resolution')
aimed_ISig = daq_lib.get_field('edna_aimed_ISig')
timeout_check = 0;
while(not os.path.exists(dna_filename_list[len(dna_filename_list)-1])): #this waits for edna images
timeout_check = timeout_check + 1
time.sleep(1.0)
if (timeout_check > 10):
break
print "generating edna input\n"
# edna_input_filename = edna_input_xml.xml_from_file_list(edna_energy_ev,xbeam_size,ybeam_size,1000000,aimed_completness,aimed_ISig,aimed_multiplicity,aimed_resolution,dna_filename_list)
flux = 10000000000 * beamline_lib.get_epics_pv("flux","VAL")
edna_input_filename = daq_lib.data_directory_name + "/adsc1_in.xml"
edna_input_xml_command = "ssh swill \"/h/data/backed-up/pxsys/skinner/edna_header_code/makeAnEDNAXML-bnl.sh 1232 %s %s none %f %f 4000 0.01 0.01 0 xh1223_2_ %f %f %f\" > %s" % (daq_lib.data_directory_name,dna_prefix,3,aimed_ISig,flux,xbeam_size,ybeam_size,edna_input_filename)
print edna_input_xml_command
os.system(edna_input_xml_command)
print "done generating edna input\n"
command_string = "ssh swill \"cd %s; /h/crys/usr-local/fc3/crys_test/john_temp/edna/mxv1/bin/edna-mxv1-characterisation.py --verbose --data %s\"" % (daq_lib.data_directory_name,edna_input_filename)
# command_string = "$EDNA_HOME/mxv1/bin/edna-mxv1-characterisation --data " + edna_input_filename
print command_string
# for i in range (0,len(dna_filename_list)):
# command_string = command_string + " " + dna_filename_list[i]
broadcast_output("\nProcessing with EDNA. Please stand by.\n")
if ( os.path.exists( "edna.log" ) ) :
os.remove( "edna.log" )
if ( os.path.exists( "edna.err" ) ) :
os.remove( "edna.err" )
edna_execution_status = os.system( "%s > edna.log 2> edna.err" % command_string)
fEdnaLogFile = open(daq_lib.get_misc_dir_name() + "/edna.log", "r" )
ednaLogLines = fEdnaLogFile.readlines()
fEdnaLogFile.close()
for outline in ednaLogLines:
# for outline in os.popen(command_string,'r',0).readlines():
####skinner6/11 seg faults? broadcast_output(outline)
if (string.find(outline,"EdnaDir")!= -1):
(param,dirname) = string.split(outline,'=')
strXMLFileName = dirname[0:len(dirname)-1]+"/ControlInterfacev1_2/Characterisation/ControlCharacterisationv1_1_dataOutput.xml"
if (string.find(outline,"characterisation successful!")!= -1):
collect_and_characterize_success = 1
if (not collect_and_characterize_success):
dna_comment = "Indexing Failure"
pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_comment)
return 0
xsDataCharacterisation = XSDataCharacterisation.parseFile( strXMLFileName )
xsDataIndexingResult = xsDataCharacterisation.getIndexingResult()
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution()
xsDataStatisticsIndexing = xsDataIndexingSolutionSelected.getStatistics()
numSpotsFound = xsDataStatisticsIndexing.getSpotsTotal().getValue()
numSpotsUsed = xsDataStatisticsIndexing.getSpotsUsed().getValue()
numSpotsRejected = numSpotsFound-numSpotsUsed
beamShiftX = xsDataStatisticsIndexing.getBeamPositionShiftX().getValue()
beamShiftY = xsDataStatisticsIndexing.getBeamPositionShiftY().getValue()
spotDeviationR = xsDataStatisticsIndexing.getSpotDeviationPositional().getValue()
try:
spotDeviationTheta = xsDataStatisticsIndexing.getSpotDeviationAngular().getValue()
except AttributeError:
spotDeviationTheta = 0.0
diffractionRings = 0 #for now, don't see this in xml except message string
reflections_used = 0 #for now
reflections_used_in_indexing = 0 #for now
rejectedReflections = 0 #for now
xsDataOrientation = xsDataIndexingSolutionSelected.getOrientation()
xsDataMatrixA = xsDataOrientation.getMatrixA()
rawOrientationMatrix_a_x = xsDataMatrixA.getM11()
rawOrientationMatrix_a_y = xsDataMatrixA.getM12()
rawOrientationMatrix_a_z = xsDataMatrixA.getM13()
rawOrientationMatrix_b_x = xsDataMatrixA.getM21()
rawOrientationMatrix_b_y = xsDataMatrixA.getM22()
rawOrientationMatrix_b_z = xsDataMatrixA.getM23()
rawOrientationMatrix_c_x = xsDataMatrixA.getM31()
rawOrientationMatrix_c_y = xsDataMatrixA.getM32()
rawOrientationMatrix_c_z = xsDataMatrixA.getM33()
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataCell = xsDataCrystal.getCell()
unitCell_alpha = xsDataCell.getAngle_alpha().getValue()
unitCell_beta = xsDataCell.getAngle_beta().getValue()
unitCell_gamma = xsDataCell.getAngle_gamma().getValue()
unitCell_a = xsDataCell.getLength_a().getValue()
unitCell_b = xsDataCell.getLength_b().getValue()
unitCell_c = xsDataCell.getLength_c().getValue()
mosaicity = xsDataCrystal.getMosaicity().getValue()
xsSpaceGroup = xsDataCrystal.getSpaceGroup()
spacegroup_name = xsSpaceGroup.getName().getValue()
pointGroup = spacegroup_name #for now
bravaisLattice = pointGroup #for now
statusDescription = "ok" #for now
try:
spacegroup_number = xsSpaceGroup.getITNumber().getValue()
except AttributeError:
spacegroup_number = 0
xsStrategyResult = xsDataCharacterisation.getStrategyResult()
resolutionObtained = -999
if (xsStrategyResult != None):
dna_have_strategy_results = 1
xsCollectionPlan = xsStrategyResult.getCollectionPlan()
xsStrategySummary = xsCollectionPlan[0].getStrategySummary()
resolutionObtained = xsStrategySummary.getRankingResolution().getValue()
xsCollectionStrategy = xsCollectionPlan[0].getCollectionStrategy()
xsSubWedge = xsCollectionStrategy.getSubWedge()
for i in range (0,len(xsSubWedge)):
xsExperimentalCondition = xsSubWedge[i].getExperimentalCondition()
xsGoniostat = xsExperimentalCondition.getGoniostat()
xsDetector = xsExperimentalCondition.getDetector()
xsBeam = xsExperimentalCondition.getBeam()
dna_strategy_start = xsGoniostat.getRotationAxisStart().getValue()
dna_strategy_start = dna_strategy_start-(dna_strategy_start%.1)
dna_strategy_range = xsGoniostat.getOscillationWidth().getValue()
dna_strategy_range = dna_strategy_range-(dna_strategy_range%.1)
dna_strategy_end = xsGoniostat.getRotationAxisEnd().getValue()
dna_strategy_end = (dna_strategy_end-(dna_strategy_end%.1)) + dna_strategy_range
dna_strat_dist = xsDetector.getDistance().getValue()
dna_strat_dist = dna_strat_dist-(dna_strat_dist%1)
dna_strategy_exptime = xsBeam.getExposureTime().getValue()
dna_strategy_exptime = dna_strategy_exptime-(dna_strategy_exptime%.1)
program = "edna-1.0" # for now
##### screeningoutputid = pxdb_lib.insert_dna_index_results(daq_lib.sweep_seq_id,daq_lib.get_field("xtal_id"),program,statusDescription,rejectedReflections,resolutionObtained,spotDeviationR,spotDeviationTheta,beamShiftX,beamShiftY,numSpotsFound,numSpotsUsed,numSpotsRejected,mosaicity,diffractionRings,spacegroup_name,pointGroup,bravaisLattice,rawOrientationMatrix_a_x,rawOrientationMatrix_a_y,rawOrientationMatrix_a_z,rawOrientationMatrix_b_x,rawOrientationMatrix_b_y,rawOrientationMatrix_b_z,rawOrientationMatrix_c_x,rawOrientationMatrix_c_y,rawOrientationMatrix_c_z,unitCell_a,unitCell_b,unitCell_c,unitCell_alpha,unitCell_beta,unitCell_gamma)
dna_comment = "spacegroup = " + str(spacegroup_name) + " mosaicity = " + str(mosaicity) + " resolutionHigh = " + str(resolutionObtained) + " cell_a = " + str(unitCell_a) + " cell_b = " + str(unitCell_b) + " cell_c = " + str(unitCell_c) + " cell_alpha = " + str(unitCell_alpha) + " cell_beta = " + str(unitCell_beta) + " cell_gamma = " + str(unitCell_gamma) + " status = " + str(statusDescription)
print "\n\n skinner " + dna_comment + "\n" +str(daq_lib.sweep_seq_id) + "\n"
##### pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_comment)
if (dna_have_strategy_results):
##### pxdb_lib.insert_to_screening_strategy_table(screeningoutputid,dna_strategy_start,dna_strategy_end,dna_strategy_range,dna_strategy_exptime,resolutionObtained,program)
dna_strat_comment = "\ndna Strategy results: Start=" + str(dna_strategy_start) + " End=" + str(dna_strategy_end) + " Width=" + str(dna_strategy_range) + " Time=" + str(dna_strategy_exptime) + " Dist=" + str(dna_strat_dist)
##### pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_strat_comment)
xsStrategyStatistics = xsCollectionPlan[0].getStatistics()
xsStrategyResolutionBins = xsStrategyStatistics.getResolutionBin()
now = time.time()
# edna_isig_plot_filename = dirname[0:len(dirname)-1] + "/edna_isig_res_" + str(now) + ".txt"
edna_isig_plot_filename = dirname[0:len(dirname)-1] + "/edna_isig_res.txt"
isig_plot_file = open(edna_isig_plot_filename,"w")
for i in range (0,len(xsStrategyResolutionBins)-1):
i_over_sigma_bin = xsStrategyResolutionBins[i].getIOverSigma().getValue()
maxResolution_bin = xsStrategyResolutionBins[i].getMaxResolution().getValue()
print str(maxResolution_bin) + " " + str(i_over_sigma_bin)
isig_plot_file.write(str(maxResolution_bin) + " " + str(i_over_sigma_bin)+"\n")
isig_plot_file.close()
comm_s = "isig_res_plot.pl -i " + edna_isig_plot_filename + " -o " + daq_lib.html_data_directory_name + "/edna_isig_res_plot" + str(int(now))
os.system(comm_s)
##### broadcast_output(dna_comment)
if (dna_have_strategy_results):
broadcast_output(dna_strat_comment)
return 1
class EDPluginControlCharacterisationv10(EDPluginControl):
"""
The Plugin that controls the whole characterisation.
"""
def __init__ (self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataCollection)
self.__strPluginIndexingName = "EDPluginControlIndexingv10"
self.__edPluginIndexing = None
self.__strPluginIntegrationName = "EDPluginControlIntegrationv10"
self.__edPluginIntegration = None
self.__strPluginStrategyName = "EDPluginControlStrategyv10"
self.__edPluginStrategy = None
self.__xsDataCharacterisation = None
def checkParameters(self):
"""
Checks the mandatory parameters
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDiffractionPlan(), "diffractionPlan")
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.preProcess...")
self.__edPluginIndexing = self.loadPlugin(self.__strPluginIndexingName , "Indexing")
self.__edPluginIntegration = self.loadPlugin(self.__strPluginIntegrationName, "Integration")
self.__edPluginStrategy = self.loadPlugin(self.__strPluginStrategyName , "Strategy")
if (self.__edPluginIndexing is not None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.preProcess: " + self.__strPluginIndexingName + " Found... setting Data Input")
# create Data Input for indexing
xsDataCollection = self.getDataInput()
xsDataSample = xsDataCollection.getSample()
xsDataSubWedgeList = xsDataCollection.getSubWedge()
xsDataExperimentalCondition = xsDataSubWedgeList[0].getExperimentalCondition()
xsDataIndexingInput = XSDataIndexingInput()
xsDataIndexingInput.setDataCollection(xsDataCollection)
xsDataIndexingInput.setExperimentalCondition(xsDataExperimentalCondition)
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
xsDataStringForcedSpaceGroup = xsDataDiffractionPlan.getForcedSpaceGroup()
if (xsDataStringForcedSpaceGroup is not None):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setName(xsDataStringForcedSpaceGroup)
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataIndexingInput.setCrystal(xsDataCrystal)
self.__edPluginIndexing.setDataInput(xsDataIndexingInput)
# Populate characterisation object
self.__xsDataCharacterisation = XSDataCharacterisation()
self.__xsDataCharacterisation.setDataCollection(XSDataCollection.parseString(xsDataCollection.marshal()))
def process(self, _edObject=None):
EDPluginControl.process(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.process")
self.connectProcess(self.__edPluginIndexing.executeSynchronous)
self.__edPluginIndexing.connectSUCCESS(self.doIndexingToIntegrationTransition)
self.__edPluginIndexing.connectFAILURE(self.doFailureActionIndexing)
self.__edPluginIntegration.connectSUCCESS(self.doIntegrationToStrategyTransition)
self.__edPluginIntegration.connectFAILURE(self.doFailureActionIntegration)
self.__edPluginStrategy.connectFAILURE(self.doFailureActionStrategy)
self.__edPluginStrategy.connectSUCCESS(self.doSuccessActionStrategy)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.postProcess")
if (self.__xsDataCharacterisation is not None):
self.setDataOutput(self.__xsDataCharacterisation)
def doIndexingToIntegrationTransition(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.doIndexingToIntegrationTransition")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv10.doIntegrationToStrategyTransition")
xsDataIndexingResult = self.__edPluginIndexing.getDataOutput()
self.__xsDataCharacterisation.setIndexingResult(xsDataIndexingResult)
xsDataIntegrationInput = XSDataIntegrationInput()
xsDataIntegrationInput.setDataCollection(self.__xsDataCharacterisation.getDataCollection())
xsDataIntegrationInput.setExperimentalConditionRefined(xsDataIndexingResult.getSelectedSolution().getExperimentalConditionRefined())
xsDataIntegrationInput.setSelectedIndexingSolution(xsDataIndexingResult.getSelectedSolution())
self.__edPluginIntegration.setDataInput(xsDataIntegrationInput)
self.__edPluginIntegration.executeSynchronous()
def doIntegrationToStrategyTransition(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.doIntegrationToStrategyTransition")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv10.doIntegrationToStrategyTransition")
xsDataIntegrationOutput = self.__edPluginIntegration.getDataOutput()
self.__xsDataCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
#EDVerbose.DEBUG( self.__xsDataExperimentCharacterisation.marshal() )
xsDataStrategyInput = XSDataStrategyInput()
xsDataSolutionSelected = self.__xsDataCharacterisation.getIndexingResult().getSelectedSolution()
xsDataStrategyInput.setCrystalRefined(xsDataSolutionSelected.getCrystal())
xsDataStrategyInput.setSample(self.__xsDataCharacterisation.getDataCollection().getSample())
xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
xsDataStrategyInput.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
xsDataStrategyInput.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
xsDataStrategyInput.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
xsDataStrategyInput.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
xsDataStrategyInput.setDiffractionPlan(self.__xsDataCharacterisation.getDataCollection().getDiffractionPlan())
#print xsDataStrategyInput.marshal()
self.__edPluginStrategy.setDataInput(xsDataStrategyInput)
self.__edPluginStrategy.executeSynchronous()
def doFailureActionIndexing(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.doFailureActionIndexing")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlCharacterisationv10.doFailureActionIndexing")
def doFailureActionIntegration(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.doFailureActionIntegration")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlCharacterisationv10.doFailureActionIntegration")
def doFailureActionStrategy(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.doFailureActionStrategy")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlCharacterisationv10.doFailureActionStrategy")
def doSuccessActionStrategy(self, _edPlugin):
"""
retrieve the potential warning messages
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.doSuccessActionStrategy")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv10.doSuccessActionStrategy")
xsDataStrategyResult = self.__edPluginStrategy.getDataOutput()
self.__xsDataCharacterisation.setStrategyResult(xsDataStrategyResult)
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlCharacterisationv01.configure")
pluginConfiguration = self.getConfiguration()
if(pluginConfiguration == None):
strWarningMessage = EDMessage.WARNING_NO_PLUGIN_CONFIGURATION_ITEM_FOUND_02 % ('EDPluginControlCharacterisationv01.configure', self.getPluginName())
EDVerbose.DEBUG(strWarningMessage)
else:
strSymopHome = EDConfiguration.getStringParamValue(pluginConfiguration, "KAPPA")
if(strSymopHome == None or strSymopHome != "ON"):
self.__strPluginStrategyName = "EDPluginControlStrategyv10"
else:
self.__strPluginStrategyName = "EDPluginControlKappaStrategyv10"
strSymopHome = EDConfiguration.getStringParamValue(pluginConfiguration, "POINTLESS")
if(strSymopHome == None or strSymopHome != "ON"):
self.__strPluginIntegrationName = "EDPluginControlIntegrationv10"
else:
self.__strPluginIntegrationName = "EDPluginControlIntegrationPointlessv10"
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
EDVerbose.DEBUG("EDPluginControlCharacterisationv10.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of characterisation:")
self.addErrorWarningMessagesToExecutiveSummary("Characterisation failure! Error messages: ")
self.addExecutiveSummarySeparator()
xsDataCollection = self.getDataInput()
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
self.addExecutiveSummaryLine("Diffraction plan:")
if (xsDataDiffractionPlan.getComplexity() is not None):
self.addExecutiveSummaryLine("BEST complexity : %s" % xsDataDiffractionPlan.getComplexity().getValue())
if (xsDataDiffractionPlan.getAimedCompleteness() is not None):
self.addExecutiveSummaryLine("Aimed completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getAimedCompleteness().getValue()))
if (xsDataDiffractionPlan.getRequiredCompleteness() is not None):
self.addExecutiveSummaryLine("Required completeness : %6.1f [%%]" % (100.0 * xsDataDiffractionPlan.getRequiredCompleteness().getValue()))
if (xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution() is not None):
self.addExecutiveSummaryLine("Aimed I/sigma at highest resolution : %6.1f" % xsDataDiffractionPlan.getAimedIOverSigmaAtHighestResolution().getValue())
if (xsDataDiffractionPlan.getAimedResolution() is not None):
self.addExecutiveSummaryLine("Aimed resolution : %6.1f [A]" % xsDataDiffractionPlan.getAimedResolution().getValue())
if (xsDataDiffractionPlan.getRequiredResolution() is not None):
self.addExecutiveSummaryLine("Required resolution : %6.1f [A]" % xsDataDiffractionPlan.getRequiredResolution().getValue())
if (xsDataDiffractionPlan.getAimedMultiplicity() is not None):
self.addExecutiveSummaryLine("Aimed multiplicity : %6.1f" % xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if (xsDataDiffractionPlan.getRequiredMultiplicity() is not None):
self.addExecutiveSummaryLine("Required multiplicity : %6.1f" % xsDataDiffractionPlan.getRequiredMultiplicity().getValue())
if (xsDataDiffractionPlan.getForcedSpaceGroup() is not None):
self.addExecutiveSummaryLine("Forced space group : %6s" % xsDataDiffractionPlan.getForcedSpaceGroup().getValue())
if (xsDataDiffractionPlan.getMaxExposureTimePerDataCollection() is not None):
self.addExecutiveSummaryLine("Max exposure time per data collection : %6.1f [s]" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue())
self.addExecutiveSummarySeparator()
if (self.__edPluginIndexing is not None):
self.appendExecutiveSummary(self.__edPluginIndexing, "Indexing : ")
if (self.__edPluginIntegration is not None):
self.appendExecutiveSummary(self.__edPluginIntegration, "Integration : ")
if (self.__edPluginStrategy is not None):
self.appendExecutiveSummary(self.__edPluginStrategy, "Strategy : ")
