def get_default_characterisation_parameters(self):
"""
:returns: A CharacterisationsParameters object with default parameters.
"""
input_fname = self.data_analysis_hwobj.edna_default_file
hwr_dir = HardwareRepository().getHardwareRepositoryPath()
with open(os.path.join(hwr_dir, input_fname), 'r') as f:
edna_default_input = ''.join(f.readlines())
edna_input = XSDataInputMXCuBE.parseString(edna_default_input)
diff_plan = edna_input.getDiffractionPlan()
#edna_beam = edna_input.getExperimentalCondition().getBeam()
edna_sample = edna_input.getSample()
char_params = queue_model_objects.CharacterisationParameters()
char_params.experiment_type = queue_model_enumerables.EXPERIMENT_TYPE.OSC
# Optimisation parameters
char_params.use_aimed_resolution = False
char_params.aimed_resolution = diff_plan.getAimedResolution().getValue(
)
char_params.use_aimed_multiplicity = False
#char_params.aimed_multiplicity = diff_plan.getAimedMultiplicity().getValue()
char_params.aimed_i_sigma = diff_plan.getAimedIOverSigmaAtHighestResolution(
).getValue()
char_params.aimed_completness = diff_plan.getAimedCompleteness(
).getValue()
char_params.strategy_complexity = 0
char_params.induce_burn = False
char_params.use_permitted_rotation = False
char_params.permitted_phi_start = 0.0
char_params.permitted_phi_end = 360
char_params.low_res_pass_strat = False
# Crystal
char_params.max_crystal_vdim = edna_sample.getSize().getY().getValue()
char_params.min_crystal_vdim = edna_sample.getSize().getZ().getValue()
char_params.max_crystal_vphi = 90
char_params.min_crystal_vphi = 0.0
char_params.space_group = ""
# Characterisation type
char_params.use_min_dose = True
char_params.use_min_time = False
char_params.min_dose = 30.0
char_params.min_time = 0.0
char_params.account_rad_damage = True
char_params.auto_res = True
char_params.opt_sad = False
char_params.sad_res = 0.5
char_params.determine_rad_params = False
char_params.burn_osc_start = 0.0
char_params.burn_osc_interval = 3
# Radiation damage model
char_params.rad_suscept = edna_sample.getSusceptibility().getValue()
char_params.beta = 1
char_params.gamma = 0.06
return char_params
def get_default_characterisation_parameters(self):
"""
:returns: A CharacterisationsParameters object with default parameters.
"""
input_fname = self.data_analysis_hwobj.edna_default_file
hwr_dir = HardwareRepository().getHardwareRepositoryPath()
with open(os.path.join(hwr_dir, input_fname), 'r') as f:
edna_default_input = ''.join(f.readlines())
edna_input = XSDataInputMXCuBE.parseString(edna_default_input)
diff_plan = edna_input.getDiffractionPlan()
#edna_beam = edna_input.getExperimentalCondition().getBeam()
edna_sample = edna_input.getSample()
char_params = queue_model_objects.CharacterisationParameters()
char_params.experiment_type = queue_model_enumerables.EXPERIMENT_TYPE.OSC
# Optimisation parameters
char_params.use_aimed_resolution = False
char_params.aimed_resolution = diff_plan.getAimedResolution().getValue()
char_params.use_aimed_multiplicity = False
#char_params.aimed_multiplicity = diff_plan.getAimedMultiplicity().getValue()
char_params.aimed_i_sigma = diff_plan.getAimedIOverSigmaAtHighestResolution().getValue()
char_params.aimed_completness = diff_plan.getAimedCompleteness().getValue()
char_params.strategy_complexity = 0
char_params.induce_burn = False
char_params.use_permitted_rotation = False
char_params.permitted_phi_start = 0.0
char_params.permitted_phi_end = 360
char_params.low_res_pass_strat = False
# Crystal
char_params.max_crystal_vdim = edna_sample.getSize().getY().getValue()
char_params.min_crystal_vdim = edna_sample.getSize().getZ().getValue()
char_params.max_crystal_vphi = 90
char_params.min_crystal_vphi = 0.0
char_params.space_group = ""
# Characterisation type
char_params.use_min_dose = True
char_params.use_min_time = False
char_params.min_dose = 30.0
char_params.min_time = 0.0
char_params.account_rad_damage = True
char_params.auto_res = True
char_params.opt_sad = False
char_params.sad_res = 0.5
char_params.determine_rad_params = False
char_params.burn_osc_start = 0.0
char_params.burn_osc_interval = 3
# Radiation damage model
char_params.rad_suscept = edna_sample.getSusceptibility().getValue()
char_params.beta = 1
char_params.gamma = 0.06
return char_params
def from_params(self, data_collection, char_params):
edna_input = XSDataInputMXCuBE.parseString(self.edna_default_input)
if data_collection.id:
edna_input.setDataCollectionId(XSDataInteger(data_collection.id))
#Beam object
beam = edna_input.getExperimentalCondition().getBeam()
try:
transmission = self.collect_obj.get_transmission()
beam.setTransmission(XSDataDouble(transmission))
except AttributeError:
pass
try:
wavelength = self.collect_obj.get_wavelength()
beam.setWavelength(XSDataWavelength(wavelength))
except AttributeError:
pass
try:
beam.setFlux(XSDataFlux(self.collect_obj.get_measured_intensity()))
except AttributeError:
pass
try:
beamsize = self.get_beam_size()
if not None in beamsize:
beam.setSize(
XSDataSize(x=XSDataLength(float(beamsize[0])),
y=XSDataLength(float(beamsize[1]))))
except AttributeError:
pass
#Optimization parameters
diff_plan = edna_input.getDiffractionPlan()
aimed_i_sigma = XSDataDouble(char_params.aimed_i_sigma)
aimed_completness = XSDataDouble(char_params.aimed_completness)
aimed_multiplicity = XSDataDouble(char_params.aimed_multiplicity)
aimed_resolution = XSDataDouble(char_params.aimed_resolution)
complexity = char_params.strategy_complexity
complexity = XSDataString(qme.STRATEGY_COMPLEXITY[complexity])
permitted_phi_start = XSDataAngle(char_params.permitted_phi_start)
_range = char_params.permitted_phi_end - char_params.permitted_phi_start
rotation_range = XSDataAngle(_range)
diff_plan.setAimedIOverSigmaAtHighestResolution(aimed_i_sigma)
diff_plan.setAimedCompleteness(aimed_completness)
if char_params.use_aimed_multiplicity:
diff_plan.setAimedMultiplicity(aimed_multiplicity)
if char_params.use_aimed_resolution:
diff_plan.setAimedResolution(aimed_resolution)
diff_plan.setComplexity(complexity)
if char_params.use_permitted_rotation:
diff_plan.setUserDefinedRotationStart(permitted_phi_start)
diff_plan.setUserDefinedRotationRange(rotation_range)
#Vertical crystal dimension
sample = edna_input.getSample()
sample.getSize().setY(XSDataLength(char_params.max_crystal_vdim))
sample.getSize().setZ(XSDataLength(char_params.min_crystal_vdim))
#Radiation damage model
sample.setSusceptibility(XSDataDouble(char_params.rad_suscept))
sample.setChemicalComposition(None)
sample.setRadiationDamageModelBeta(XSDataDouble(char_params.beta /
1e6))
sample.setRadiationDamageModelGamma(
XSDataDouble(char_params.gamma / 1e6))
diff_plan.setForcedSpaceGroup(XSDataString(char_params.space_group))
# Characterisation type - Routine DC
if char_params.use_min_dose:
pass
if char_params.use_min_time:
time = XSDataTime(char_params.min_time)
diff_plan.setMaxExposureTimePerDataCollection(time)
# Account for radiation damage
if char_params.induce_burn:
diff_plan.setStrategyOption(XSDataString("-DamPar"))
else:
diff_plan.setStrategyOption(None)
# Characterisation type - SAD
if char_params.opt_sad:
diff_plan.setAnomalousData(XSDataBoolean(True))
else:
diff_plan.setAnomalousData(XSDataBoolean(False))
#Data set
data_set = XSDataMXCuBEDataSet()
acquisition_parameters = data_collection.acquisitions[
0].acquisition_parameters
path_template = data_collection.acquisitions[0].path_template
path_str = os.path.join(path_template.directory,
path_template.get_image_file_name())
for img_num in range(int(acquisition_parameters.num_images)):
image_file = XSDataFile()
path = XSDataString()
path.setValue(path_str % (img_num + 1))
image_file.setPath(path)
data_set.addImageFile(image_file)
edna_input.addDataSet(data_set)
edna_input.process_directory = path_template.process_directory
return edna_input
def from_params(self, data_collection, char_params):
edna_input = XSDataInputMXCuBE.parseString(EDNA_DEFAULT_INPUT)
if data_collection.id:
edna_input.setDataCollectionId(XSDataInteger(data_collection.id))
#Beam object
beam = edna_input.getExperimentalCondition().getBeam()
try:
beam.setTransmission(XSDataDouble(self.collect_obj.get_transmission()))
except AttributeError:
pass
try:
beam.setWavelength(XSDataWavelength(self.collect_obj.get_wavelength()))
except AttributeError:
pass
try:
beam.setFlux(XSDataFlux(self.collect_obj.get_measured_intensity()))
except AttributeError:
pass
try:
beamsize = self.get_beam_size()
if not None in beamsize:
beam.setSize(XSDataSize(x=XSDataLength(float(beamsize[0])),
y=XSDataLength(float(beamsize[1]))))
except AttributeError:
pass
#Optimization parameters
diff_plan = edna_input.getDiffractionPlan()
diff_plan.setAimedIOverSigmaAtHighestResolution(\
XSDataDouble(char_params.aimed_i_sigma))
diff_plan.setAimedCompleteness(XSDataDouble(char_params.\
aimed_completness))
if char_params.use_aimed_multiplicity:
diff_plan.setAimedMultiplicity(XSDataDouble(char_params.\
aimed_multiplicity))
if char_params.use_aimed_resolution:
diff_plan.setAimedResolution(XSDataDouble(char_params.aimed_resolution))
diff_plan.setComplexity(XSDataString(\
queue_model_enumerables.STRATEGY_COMPLEXITY[char_params.strategy_complexity]))
if char_params.use_permitted_rotation:
diff_plan.setUserDefinedRotationStart(XSDataAngle(char_params.\
permitted_phi_start))
diff_plan.setUserDefinedRotationRange(XSDataAngle(char_params.permitted_phi_end -\
char_params.permitted_phi_start))
#Vertical crystal dimension
sample = edna_input.getSample()
sample.getSize().setY(XSDataLength(char_params.max_crystal_vdim))
sample.getSize().setZ(XSDataLength(char_params.min_crystal_vdim))
#Radiation damage model
sample.setSusceptibility(XSDataDouble(char_params.rad_suscept))
sample.setChemicalComposition(None)
sample.setRadiationDamageModelBeta(XSDataDouble(char_params.beta/1e6))
sample.setRadiationDamageModelGamma(XSDataDouble(char_params.gamma/1e6))
diff_plan.setForcedSpaceGroup(XSDataString(char_params.\
space_group))
# Characterisation type - Routine DC
if char_params.use_min_dose:
pass
if char_params.use_min_time:
diff_plan.setMaxExposureTimePerDataCollection(XSDataTime(char_params.\
min_time))
# Account for radiation damage
if char_params.induce_burn:
diff_plan.setStrategyOption(XSDataString("-DamPar")) # What is -DamPar ?
else:
diff_plan.setStrategyOption(None)
# Characterisation type - SAD
if queue_model_enumerables.EXPERIMENT_TYPE[char_params.experiment_type] is \
queue_model_enumerables.EXPERIMENT_TYPE.SAD:
diff_plan.setAnomalousData(XSDataBoolean(True))
else:
diff_plan.setAnomalousData(XSDataBoolean(False))
#Data set
data_set = XSDataMXCuBEDataSet()
acquisition_parameters = data_collection.acquisitions[0].acquisition_parameters
path_str = os.path.join(data_collection.acquisitions[0].path_template.directory,
data_collection.acquisitions[0].path_template.get_image_file_name())
for img_num in range(int(acquisition_parameters.num_images)):
image_file = XSDataFile()
path = XSDataString()
path.setValue(path_str % (img_num + 1))
image_file.setPath(path)
data_set.addImageFile(image_file)
edna_input.addDataSet(data_set)
edna_input.process_directory = data_collection.acquisitions[0].path_template.process_directory
return edna_input
def get_default_characterisation_parameters(self):
"""
Returns:
(queue_model_objects.CharacterisationsParameters) object with default
parameters.
"""
edna_input = XSDataInputMXCuBE.parseString(self.edna_default_input)
diff_plan = edna_input.getDiffractionPlan()
edna_sample = edna_input.getSample()
char_params = qmo.CharacterisationParameters()
char_params.experiment_type = qme.EXPERIMENT_TYPE.OSC
# Optimisation parameters
char_params.use_aimed_resolution = False
try:
char_params.aimed_resolution = diff_plan.getAimedResolution().getValue()
except Exception:
char_params.aimed_resolution = None
char_params.use_aimed_multiplicity = False
try:
char_params.aimed_i_sigma = (
diff_plan.getAimedIOverSigmaAtHighestResolution().getValue()
)
char_params.aimed_completness = diff_plan.getAimedCompleteness().getValue()
except Exception:
char_params.aimed_i_sigma = None
char_params.aimed_completness = None
char_params.strategy_complexity = 0
char_params.induce_burn = False
char_params.use_permitted_rotation = False
char_params.permitted_phi_start = 0.0
char_params.permitted_phi_end = 360
char_params.low_res_pass_strat = False
# Crystal
char_params.max_crystal_vdim = edna_sample.getSize().getY().getValue()
char_params.min_crystal_vdim = edna_sample.getSize().getZ().getValue()
char_params.max_crystal_vphi = 90
char_params.min_crystal_vphi = 0.0
char_params.space_group = ""
# Characterisation type
char_params.use_min_dose = True
char_params.use_min_time = False
char_params.min_dose = 30.0
char_params.min_time = 0.0
char_params.account_rad_damage = True
char_params.auto_res = True
char_params.opt_sad = False
char_params.sad_res = 0.5
char_params.determine_rad_params = False
char_params.burn_osc_start = 0.0
char_params.burn_osc_interval = 3
# Radiation damage model
char_params.rad_suscept = edna_sample.getSusceptibility().getValue()
char_params.beta = 1
char_params.gamma = 0.06
return char_params
def initialiseEDNAdefaults(self):
self.ednaInput = XSDataInputMXCuBE.parseFile(self.ednaDefaultsInputFile)
self.ednaDefaultInput = copy.deepcopy(self.ednaInput)
def from_params(self, data_collection, char_params):
edna_input = XSDataInputMXCuBE.parseString(self.edna_default_input)
if data_collection.id:
edna_input.setDataCollectionId(XSDataInteger(data_collection.id))
# Beam object
beam = edna_input.getExperimentalCondition().getBeam()
try:
transmission = self.collect_obj.get_transmission()
beam.setTransmission(XSDataDouble(transmission))
except AttributeError:
import traceback
logging.getLogger("HWR").debug("DataAnalysis. transmission not saved ")
logging.getLogger("HWR").debug(traceback.format_exc())
try:
wavelength = self.collect_obj.get_wavelength()
beam.setWavelength(XSDataWavelength(wavelength))
except AttributeError:
pass
try:
beam.setFlux(XSDataFlux(self.collect_obj.get_measured_intensity()))
except AttributeError:
pass
try:
min_exp_time = self.collect_obj.detector_hwobj.get_exposure_time_limits()[0]
beam.setMinExposureTimePerImage(XSDataTime(min_exp_time))
except AttributeError:
pass
try:
beamsize = self.get_beam_size()
if None not in beamsize:
beam.setSize(
XSDataSize(
x=XSDataLength(float(beamsize[0])),
y=XSDataLength(float(beamsize[1])),
)
)
except AttributeError:
pass
# Optimization parameters
diff_plan = edna_input.getDiffractionPlan()
aimed_i_sigma = XSDataDouble(char_params.aimed_i_sigma)
aimed_completness = XSDataDouble(char_params.aimed_completness)
aimed_multiplicity = XSDataDouble(char_params.aimed_multiplicity)
aimed_resolution = XSDataDouble(char_params.aimed_resolution)
complexity = char_params.strategy_complexity
complexity = XSDataString(qme.STRATEGY_COMPLEXITY[complexity])
permitted_phi_start = XSDataAngle(char_params.permitted_phi_start)
_range = char_params.permitted_phi_end - char_params.permitted_phi_start
rotation_range = XSDataAngle(_range)
if char_params.aimed_i_sigma:
diff_plan.setAimedIOverSigmaAtHighestResolution(aimed_i_sigma)
if char_params.aimed_completness:
diff_plan.setAimedCompleteness(aimed_completness)
if char_params.use_aimed_multiplicity:
diff_plan.setAimedMultiplicity(aimed_multiplicity)
if char_params.use_aimed_resolution:
diff_plan.setAimedResolution(aimed_resolution)
diff_plan.setComplexity(complexity)
if char_params.use_permitted_rotation:
diff_plan.setUserDefinedRotationStart(permitted_phi_start)
diff_plan.setUserDefinedRotationRange(rotation_range)
# Vertical crystal dimension
sample = edna_input.getSample()
sample.getSize().setY(XSDataLength(char_params.max_crystal_vdim))
sample.getSize().setZ(XSDataLength(char_params.min_crystal_vdim))
# Radiation damage model
sample.setSusceptibility(XSDataDouble(char_params.rad_suscept))
sample.setChemicalComposition(None)
sample.setRadiationDamageModelBeta(XSDataDouble(char_params.beta / 1e6))
sample.setRadiationDamageModelGamma(XSDataDouble(char_params.gamma / 1e6))
diff_plan.setForcedSpaceGroup(XSDataString(char_params.space_group))
# Characterisation type - Routine DC
if char_params.use_min_dose:
pass
if char_params.use_min_time:
time = XSDataTime(char_params.min_time)
diff_plan.setMaxExposureTimePerDataCollection(time)
# Account for radiation damage
if char_params.induce_burn:
self.modify_strategy_option(diff_plan, "-DamPar")
# Characterisation type - SAD
if char_params.opt_sad:
if char_params.auto_res:
diff_plan.setAnomalousData(XSDataBoolean(True))
else:
diff_plan.setAnomalousData(XSDataBoolean(False))
self.modify_strategy_option(diff_plan, "-SAD yes")
diff_plan.setAimedResolution(XSDataDouble(char_params.sad_res))
else:
diff_plan.setAnomalousData(XSDataBoolean(False))
# Data set
data_set = XSDataMXCuBEDataSet()
acquisition_parameters = data_collection.acquisitions[0].acquisition_parameters
path_template = data_collection.acquisitions[0].path_template
path_str = os.path.join(
path_template.directory, path_template.get_image_file_name()
)
for img_num in range(int(acquisition_parameters.num_images)):
image_file = XSDataFile()
path = XSDataString()
path.setValue(path_str % (img_num + 1))
image_file.setPath(path)
data_set.addImageFile(image_file)
edna_input.addDataSet(data_set)
edna_input.process_directory = path_template.process_directory
return edna_input
