def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("PdAndScConversion")
if len(element_list)>0:
instrument_dom = element_list[0]
self.do_pd_convert = BaseScriptElement.getBoolElement(instrument_dom,
"do_powder_conversion",
default=PdAndScConversionScript.do_pd_convert)
self.pd_q_range_low = BaseScriptElement.getStringElement(instrument_dom,
"pd_q_range/low",
default=PdAndScConversionScript.pd_q_range_low)
self.pd_q_range_width = BaseScriptElement.getStringElement(instrument_dom,
"pd_q_range/width",
default=PdAndScConversionScript.pd_q_range_width)
self.pd_q_range_high = BaseScriptElement.getStringElement(instrument_dom,
"pd_q_range/high",
default=PdAndScConversionScript.pd_q_range_high)
self.save_powder_nxs = BaseScriptElement.getBoolElement(instrument_dom,
"save_powder_nexus",
default=PdAndScConversionScript.save_powder_nxs)
self.save_powder_nxs_file = BaseScriptElement.getStringElement(instrument_dom,
"save_powder_nexus_filename",
default=PdAndScConversionScript.save_powder_nxs_file)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
super(ReductionOptions, self).from_xml(xml_str)
dom = xml.dom.minidom.parseString(xml_str)
# TOF cutoff and correction
element_list = dom.getElementsByTagName("TOFcorr")
if len(element_list)>0:
tof_dom = element_list[0]
self.use_config_cutoff = BaseScriptElement.getBoolElement(tof_dom, "use_config_cutoff",
default = ReductionOptions.use_config_cutoff)
self.correct_for_flight_path = BaseScriptElement.getBoolElement(tof_dom, "perform_flight_path_corr",
default = ReductionOptions.correct_for_flight_path)
self.low_TOF_cut = BaseScriptElement.getFloatElement(tof_dom, "low_tof_cut",
default=ReductionOptions.low_TOF_cut)
self.high_TOF_cut = BaseScriptElement.getFloatElement(tof_dom, "high_tof_cut",
default=ReductionOptions.high_TOF_cut)
# Mask
self.use_config_mask = BaseScriptElement.getBoolElement(dom, "UseConfigMask",
default = ReductionOptions.use_config_mask)
# Resolution
self.compute_resolution = BaseScriptElement.getBoolElement(dom, "ComputeResolution",
default = ReductionOptions.compute_resolution)
self.sample_aperture_diameter = BaseScriptElement.getFloatElement(dom, "SampleApertureDiameter",
default = ReductionOptions.sample_aperture_diameter)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("PdAndScConversion")
if len(element_list) > 0:
instrument_dom = element_list[0]
self.do_pd_convert = BaseScriptElement.getBoolElement(
instrument_dom,
"do_powder_conversion",
default=PdAndScConversionScript.do_pd_convert)
self.pd_q_range_low = BaseScriptElement.getStringElement(
instrument_dom,
"pd_q_range/low",
default=PdAndScConversionScript.pd_q_range_low)
self.pd_q_range_width = BaseScriptElement.getStringElement(
instrument_dom,
"pd_q_range/width",
default=PdAndScConversionScript.pd_q_range_width)
self.pd_q_range_high = BaseScriptElement.getStringElement(
instrument_dom,
"pd_q_range/high",
default=PdAndScConversionScript.pd_q_range_high)
self.save_powder_nxs = BaseScriptElement.getBoolElement(
instrument_dom,
"save_powder_nexus",
default=PdAndScConversionScript.save_powder_nxs)
self.save_powder_nxs_file = BaseScriptElement.getStringElement(
instrument_dom,
"save_powder_nexus_filename",
default=PdAndScConversionScript.save_powder_nxs_file)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("Background")
if len(element_list) > 0:
instrument_dom = element_list[0]
self.sample_thickness = BaseScriptElement.getFloatElement(
instrument_dom,
"sample_thickness",
default=Background.sample_thickness)
self.dark_current_corr = BaseScriptElement.getBoolElement(
instrument_dom,
"dark_current_corr",
default=Background.dark_current_corr)
self.dark_current_file = BaseScriptElement.getStringElement(
instrument_dom, "dark_current_file")
self.background_corr = BaseScriptElement.getBoolElement(
instrument_dom,
"background_corr",
default=Background.background_corr)
self.background_file = BaseScriptElement.getStringElement(
instrument_dom, "background_file")
self.bck_transmission_enabled = BaseScriptElement.getBoolElement(
instrument_dom,
"bck_trans_enabled",
default=Background.bck_transmission_enabled)
self.bck_transmission = BaseScriptElement.getFloatElement(
instrument_dom,
"bck_trans",
default=Background.bck_transmission)
self.bck_transmission_spread = BaseScriptElement.getFloatElement(
instrument_dom,
"bck_trans_spread",
default=Background.bck_transmission_spread)
self.calculate_transmission = BaseScriptElement.getBoolElement(
instrument_dom,
"calculate_trans",
default=Background.calculate_transmission)
self.theta_dependent = BaseScriptElement.getBoolElement(
instrument_dom,
"theta_dependent",
default=Background.theta_dependent)
self.trans_dark_current = BaseScriptElement.getStringElement(
instrument_dom, "trans_dark_current")
for m in [Background.DirectBeam, Background.BeamSpreader]:
method = m()
if method.find(instrument_dom):
method.from_xml(instrument_dom)
self.trans_calculation_method = method
break
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("SampleSetup")
if len(element_list)>0:
instrument_dom = element_list[0]
self.sample_file = BaseScriptElement.getStringElement(instrument_dom,
"sample_input_file",
default=SampleSetupScript.sample_file)
self.output_wsname = BaseScriptElement.getStringElement(instrument_dom,
"output_wsname",
default=SampleSetupScript.output_wsname)
self.detcal_file = BaseScriptElement.getStringElement(instrument_dom,
"detcal_file",
default=SampleSetupScript.detcal_file)
self.relocate_dets = BaseScriptElement.getBoolElement(instrument_dom,
"relocate_dets",
default=SampleSetupScript.relocate_dets)
self.incident_energy_guess = BaseScriptElement.getStringElement(instrument_dom,
"incident_energy_guess",
default=SampleSetupScript.incident_energy_guess)
self.use_ei_guess = BaseScriptElement.getBoolElement(instrument_dom,
"use_ei_guess",
default=SampleSetupScript.use_ei_guess)
self.tzero_guess = BaseScriptElement.getFloatElement(instrument_dom,
"tzero_guess",
default=SampleSetupScript.tzero_guess)
self.monitor1_specid = BaseScriptElement.getIntElement(instrument_dom,
"monitor1_specid",
default=SampleSetupScript.monitor1_specid)
self.monitor2_specid = BaseScriptElement.getIntElement(instrument_dom,
"monitor2_specid",
default=SampleSetupScript.monitor2_specid)
self.et_range_low = BaseScriptElement.getStringElement(instrument_dom,
"et_range/low",
default=SampleSetupScript.et_range_low)
self.et_range_width = BaseScriptElement.getStringElement(instrument_dom,
"et_range/width",
default=SampleSetupScript.et_range_width)
self.et_range_high = BaseScriptElement.getStringElement(instrument_dom,
"et_range/high",
default=SampleSetupScript.et_range_high)
self.et_is_distribution = BaseScriptElement.getBoolElement(instrument_dom,
"sofphie_is_distribution",
default=SampleSetupScript.et_is_distribution)
self.hardmask_file = BaseScriptElement.getStringElement(instrument_dom,
"hardmask_file",
default=SampleSetupScript.hardmask_file)
self.grouping_file = BaseScriptElement.getStringElement(instrument_dom,
"grouping_file",
default=SampleSetupScript.grouping_file)
self.show_workspaces = BaseScriptElement.getBoolElement(instrument_dom,
"show_workspaces",
default=SampleSetupScript.show_workspaces)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("Transmission")
if len(element_list) > 0:
instrument_dom = element_list[0]
self.transmission = BaseScriptElement.getFloatElement(
instrument_dom, "trans", default=SampleData.transmission)
self.transmission_spread = BaseScriptElement.getFloatElement(
instrument_dom,
"trans_spread",
default=SampleData.transmission_spread)
self.calculate_transmission = BaseScriptElement.getBoolElement(
instrument_dom,
"calculate_trans",
default=SampleData.calculate_transmission)
self.theta_dependent = BaseScriptElement.getBoolElement(
instrument_dom,
"theta_dependent",
default=SampleData.theta_dependent)
self.dark_current = BaseScriptElement.getStringElement(
instrument_dom, "dark_current")
for m in self.option_list:
method = m()
if method.find(instrument_dom):
method.from_xml(instrument_dom)
self.calculation_method = method
break
# Data file section
element_list = dom.getElementsByTagName("SampleData")
if len(element_list) > 0:
sample_data_dom = element_list[0]
self.data_files = BaseScriptElement.getStringList(
sample_data_dom, "data_file")
self.sample_thickness = BaseScriptElement.getFloatElement(
sample_data_dom,
"sample_thickness",
default=SampleData.sample_thickness)
self.separate_jobs = BaseScriptElement.getBoolElement(
sample_data_dom,
"separate_jobs",
default=SampleData.separate_jobs)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
# # Get Mantid version
# mtd_version = BaseScriptElement.getMantidBuildVersion(dom)
element_list = dom.getElementsByTagName("Normalization")
if len(element_list)>0:
instrument_dom = element_list[0]
#Peak from/to pixels
self.NormPeakPixels[0] = BaseScriptElement.getStringElement(instrument_dom, "from_peak_pixels")
self.NormPeakPixels[1] = BaseScriptElement.getStringElement(instrument_dom, "to_peak_pixels")
#background flag
self.NormBackgroundFlag = BaseScriptElement.getBoolElement(instrument_dom, "background_flag")
#background from/to pixels
self.NormBackgroundRoi[0] = BaseScriptElement.getStringElement(instrument_dom, "from_back_pixels")
self.NormBackgroundRoi[1] = BaseScriptElement.getStringElement(instrument_dom, "to_back_pixels")
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
# Get Mantid version
mtd_version = BaseScriptElement.getMantidBuildVersion(dom)
# Sensitivity correction
element_list = dom.getElementsByTagName("Sensitivity")
if len(element_list)>0:
instrument_dom = element_list[0]
self.sensitivity_corr = BaseScriptElement.getBoolElement(instrument_dom, "sensitivity_corr",
default = Detector.sensitivity_corr)
self.sensitivity_data = BaseScriptElement.getStringElement(instrument_dom, "sensitivity_data")
self.sensitivity_dark = BaseScriptElement.getStringElement(instrument_dom, "sensitivity_dark")
self.use_sample_dark = BaseScriptElement.getBoolElement(instrument_dom, "use_sample_dark",
default = Detector.use_sample_dark)
self.min_sensitivity = BaseScriptElement.getFloatElement(instrument_dom, "sensitivity_min",
default=Detector.min_sensitivity)
self.max_sensitivity = BaseScriptElement.getFloatElement(instrument_dom, "sensitivity_max",
default=Detector.max_sensitivity)
self.use_sample_beam_center = BaseScriptElement.getBoolElement(instrument_dom, "use_sample_beam_center",
default = Detector.use_sample_beam_center)
beam_center_list = instrument_dom.getElementsByTagName("FloodBeamFinder")
if len(beam_center_list)>0:
beam_finder_dom = beam_center_list[0]
self.flood_x_position = BaseScriptElement.getFloatElement(beam_finder_dom, "x",
default=Detector.flood_x_position)
self.flood_y_position = BaseScriptElement.getFloatElement(beam_finder_dom, "y",
default=Detector.flood_y_position)
self.flood_use_finder = BaseScriptElement.getBoolElement(beam_finder_dom, "use_finder",
default = Detector.flood_use_finder)
self.flood_beam_file = BaseScriptElement.getStringElement(beam_finder_dom, "beam_file")
self.flood_beam_radius = BaseScriptElement.getFloatElement(beam_finder_dom, "beam_radius",
default=Detector.flood_beam_radius)
self.flood_use_direct_beam = BaseScriptElement.getBoolElement(beam_finder_dom, "use_direct_beam",
default = Detector.flood_use_direct_beam)
element_list = dom.getElementsByTagName("BeamFinder")
if len(element_list)>0:
beam_finder_dom = element_list[0]
self.x_position = BaseScriptElement.getFloatElement(beam_finder_dom, "x",
default=Detector.x_position)
self.y_position = BaseScriptElement.getFloatElement(beam_finder_dom, "y",
default=Detector.y_position)
self.use_finder = BaseScriptElement.getBoolElement(beam_finder_dom, "use_finder",
default = Detector.use_finder)
self.beam_file = BaseScriptElement.getStringElement(beam_finder_dom, "beam_file")
self.beam_radius = BaseScriptElement.getFloatElement(beam_finder_dom, "beam_radius",
default=Detector.beam_radius)
self.use_direct_beam = BaseScriptElement.getBoolElement(beam_finder_dom, "use_direct_beam",
default = Detector.use_direct_beam)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("AbsoluteUnits")
if len(element_list)>0:
instrument_dom = element_list[0]
self.find_bad_detectors = BaseScriptElement.getBoolElement(instrument_dom,
"do_absolute_units",
default=AbsoluteUnitsScript.do_absolute_units)
self.absunits_vanadium = BaseScriptElement.getStringElement(instrument_dom,
"absunits_vanadium",
default=AbsoluteUnitsScript.absunits_vanadium)
self.grouping_file = BaseScriptElement.getStringElement(instrument_dom,
"grouping_file",
default=AbsoluteUnitsScript.grouping_file)
self.absunits_detector_vanadium = BaseScriptElement.getStringElement(instrument_dom,
"absunits_detector_vanadium",
default=AbsoluteUnitsScript.absunits_detector_vanadium)
self.incident_energy = BaseScriptElement.getStringElement(instrument_dom,
"incident_energy",
default=AbsoluteUnitsScript.incident_energy)
self.emin = BaseScriptElement.getFloatElement(instrument_dom,
"minimum_energy",
default=AbsoluteUnitsScript.emin)
self.emax = BaseScriptElement.getFloatElement(instrument_dom,
"maximum_energy",
default=AbsoluteUnitsScript.emax)
self.vanadium_mass = BaseScriptElement.getFloatElement(instrument_dom,
"vanadium_mass",
default=AbsoluteUnitsScript.vanadium_mass)
self.sample_mass = BaseScriptElement.getFloatElement(instrument_dom,
"sample_mass",
default=AbsoluteUnitsScript.sample_mass)
self.sample_rmm = BaseScriptElement.getFloatElement(instrument_dom,
"sample_rmm",
default=AbsoluteUnitsScript.sample_rmm)
self.absunits_median_test_out_low = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_out_low",
default=AbsoluteUnitsScript.absunits_median_test_out_low)
self.absunits_median_test_out_high = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_out_high",
default=AbsoluteUnitsScript.absunits_median_test_out_high)# noqa
self.absunits_median_test_low = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_low",
default=AbsoluteUnitsScript.absunits_median_test_low)
self.absunits_median_test_high = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_high",
default=AbsoluteUnitsScript.absunits_median_test_high)
self.absunits_errorbar_criterion = BaseScriptElement.getFloatElement(instrument_dom,
"errorbar_criterion",
default=AbsoluteUnitsScript.absunits_errorbar_criterion)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("AbsoluteUnits")
if len(element_list)>0:
instrument_dom = element_list[0]
self.find_bad_detectors = BaseScriptElement.getBoolElement(instrument_dom,
"do_absolute_units",
default=AbsoluteUnitsScript.do_absolute_units)
self.absunits_vanadium = BaseScriptElement.getStringElement(instrument_dom,
"absunits_vanadium",
default=AbsoluteUnitsScript.absunits_vanadium)
self.grouping_file = BaseScriptElement.getStringElement(instrument_dom,
"grouping_file",
default=AbsoluteUnitsScript.grouping_file)
self.absunits_detector_vanadium = BaseScriptElement.getStringElement(instrument_dom,
"absunits_detector_vanadium",
default=AbsoluteUnitsScript.absunits_detector_vanadium)
self.incident_energy = BaseScriptElement.getStringElement(instrument_dom,
"incident_energy",
default=AbsoluteUnitsScript.incident_energy)
self.emin = BaseScriptElement.getFloatElement(instrument_dom,
"minimum_energy",
default=AbsoluteUnitsScript.emin)
self.emax = BaseScriptElement.getFloatElement(instrument_dom,
"maximum_energy",
default=AbsoluteUnitsScript.emax)
self.vanadium_mass = BaseScriptElement.getFloatElement(instrument_dom,
"vanadium_mass",
default=AbsoluteUnitsScript.vanadium_mass)
self.sample_mass = BaseScriptElement.getFloatElement(instrument_dom,
"sample_mass",
default=AbsoluteUnitsScript.sample_mass)
self.sample_rmm = BaseScriptElement.getFloatElement(instrument_dom,
"sample_rmm",
default=AbsoluteUnitsScript.sample_rmm)
self.absunits_median_test_out_low = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_out_low",
default=AbsoluteUnitsScript.absunits_median_test_out_low)
self.absunits_median_test_out_high = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_out_high",
default=AbsoluteUnitsScript.absunits_median_test_out_high)# noqa
self.absunits_median_test_low = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_low",
default=AbsoluteUnitsScript.absunits_median_test_low)
self.absunits_median_test_high = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_high",
default=AbsoluteUnitsScript.absunits_median_test_high)
self.absunits_errorbar_criterion = BaseScriptElement.getFloatElement(instrument_dom,
"errorbar_criterion",
default=AbsoluteUnitsScript.absunits_errorbar_criterion)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
# Get Mantid version
mtd_version = BaseScriptElement.getMantidBuildVersion(dom)
element_list = dom.getElementsByTagName("Transmission")
if len(element_list)>0:
instrument_dom = element_list[0]
self.transmission = BaseScriptElement.getFloatElement(instrument_dom, "trans",
default=SampleData.transmission)
self.transmission_spread = BaseScriptElement.getFloatElement(instrument_dom, "trans_spread",
default=SampleData.transmission_spread)
self.calculate_transmission = BaseScriptElement.getBoolElement(instrument_dom, "calculate_trans",
default = SampleData.calculate_transmission)
self.theta_dependent = BaseScriptElement.getBoolElement(instrument_dom, "theta_dependent",
default = SampleData.theta_dependent)
self.dark_current = BaseScriptElement.getStringElement(instrument_dom, "dark_current")
for m in self.option_list:
method = m()
if method.find(instrument_dom):
method.from_xml(instrument_dom)
self.calculation_method = method
break
# Data file section - take care of backward compatibility
if mtd_version!=0 and mtd_version<BaseScriptElement.UPDATE_1_CHANGESET_CUTOFF:
element_list = dom.getElementsByTagName("Instrument")
else:
element_list = dom.getElementsByTagName("SampleData")
if len(element_list)>0:
sample_data_dom = element_list[0]
self.data_files = BaseScriptElement.getStringList(sample_data_dom, "data_file")
self.sample_thickness = BaseScriptElement.getFloatElement(sample_data_dom, "sample_thickness",
default=SampleData.sample_thickness)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("Background")
if len(element_list)>0:
instrument_dom = element_list[0]
self.sample_thickness = BaseScriptElement.getFloatElement(instrument_dom, "sample_thickness",
default=Background.sample_thickness)
self.dark_current_corr = BaseScriptElement.getBoolElement(instrument_dom, "dark_current_corr",
default = Background.dark_current_corr)
self.dark_current_file = BaseScriptElement.getStringElement(instrument_dom, "dark_current_file")
self.background_corr = BaseScriptElement.getBoolElement(instrument_dom, "background_corr",
default = Background.background_corr)
self.background_file = BaseScriptElement.getStringElement(instrument_dom, "background_file")
self.bck_transmission_enabled = BaseScriptElement.getBoolElement(instrument_dom, "bck_trans_enabled",
default = Background.bck_transmission_enabled)
self.bck_transmission = BaseScriptElement.getFloatElement(instrument_dom, "bck_trans",
default=Background.bck_transmission)
self.bck_transmission_spread = BaseScriptElement.getFloatElement(instrument_dom, "bck_trans_spread",
default=Background.bck_transmission_spread)
self.calculate_transmission = BaseScriptElement.getBoolElement(instrument_dom, "calculate_trans",
default = Background.calculate_transmission)
self.theta_dependent = BaseScriptElement.getBoolElement(instrument_dom, "theta_dependent",
default = Background.theta_dependent)
self.trans_dark_current = BaseScriptElement.getStringElement(instrument_dom, "trans_dark_current")
for m in [Background.DirectBeam, Background.BeamSpreader]:
method = m()
if method.find(instrument_dom):
method.from_xml(instrument_dom)
self.trans_calculation_method = method
break
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
super(ReductionOptions, self).from_xml(xml_str)
dom = xml.dom.minidom.parseString(xml_str)
instrument_dom = dom.getElementsByTagName("Instrument")[0]
self.detector_offset = BaseScriptElement.getFloatElement(
instrument_dom,
"detector_offset",
default=ReductionOptions.default_detector_offset)
# TOF cutoff and correction
element_list = dom.getElementsByTagName("TOFcorr")
if len(element_list) > 0:
tof_dom = element_list[0]
self.use_config_cutoff = BaseScriptElement.getBoolElement(
tof_dom,
"use_config_cutoff",
default=ReductionOptions.use_config_cutoff)
self.correct_for_flight_path = BaseScriptElement.getBoolElement(
tof_dom,
"perform_flight_path_corr",
default=ReductionOptions.correct_for_flight_path)
self.low_TOF_cut = BaseScriptElement.getFloatElement(
tof_dom, "low_tof_cut", default=ReductionOptions.low_TOF_cut)
self.high_TOF_cut = BaseScriptElement.getFloatElement(
tof_dom, "high_tof_cut", default=ReductionOptions.high_TOF_cut)
# Mask
self.use_config_mask = BaseScriptElement.getBoolElement(
dom, "UseConfigMask", default=ReductionOptions.use_config_mask)
# Resolution
self.compute_resolution = BaseScriptElement.getBoolElement(
dom,
"ComputeResolution",
default=ReductionOptions.compute_resolution)
self.sample_aperture_diameter = BaseScriptElement.getFloatElement(
dom,
"SampleApertureDiameter",
default=ReductionOptions.sample_aperture_diameter)
# TOF correction
self.perform_TOF_correction = BaseScriptElement.getBoolElement(
dom,
"PerformTOFCorrection",
default=ReductionOptions.perform_TOF_correction)
# Normalization option
self.use_beam_monitor = BaseScriptElement.getBoolElement(
dom, "UseBeamMonitor", default=ReductionOptions.use_beam_monitor)
self.beam_monitor_reference = BaseScriptElement.getStringElement(
dom,
"BeamMonitorRef",
default=ReductionOptions.beam_monitor_reference)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
# Sensitivity correction
element_list = dom.getElementsByTagName("Sensitivity")
if len(element_list)>0:
instrument_dom = element_list[0]
self.sensitivity_corr = BaseScriptElement.getBoolElement(instrument_dom, "sensitivity_corr",
default = Detector.sensitivity_corr)
self.sensitivity_data = BaseScriptElement.getStringElement(instrument_dom, "sensitivity_data")
self.sensitivity_dark = BaseScriptElement.getStringElement(instrument_dom, "sensitivity_dark")
self.use_sample_dark = BaseScriptElement.getBoolElement(instrument_dom, "use_sample_dark",
default = Detector.use_sample_dark)
self.min_sensitivity = BaseScriptElement.getFloatElement(instrument_dom, "sensitivity_min",
default=Detector.min_sensitivity)
self.max_sensitivity = BaseScriptElement.getFloatElement(instrument_dom, "sensitivity_max",
default=Detector.max_sensitivity)
self.use_sample_beam_center = BaseScriptElement.getBoolElement(instrument_dom, "use_sample_beam_center",
default = Detector.use_sample_beam_center)
beam_center_list = instrument_dom.getElementsByTagName("FloodBeamFinder")
if len(beam_center_list)>0:
beam_finder_dom = beam_center_list[0]
self.flood_x_position = BaseScriptElement.getFloatElement(beam_finder_dom, "x",
default=Detector.flood_x_position)
self.flood_y_position = BaseScriptElement.getFloatElement(beam_finder_dom, "y",
default=Detector.flood_y_position)
self.flood_use_finder = BaseScriptElement.getBoolElement(beam_finder_dom, "use_finder",
default = Detector.flood_use_finder)
self.flood_beam_file = BaseScriptElement.getStringElement(beam_finder_dom, "beam_file")
self.flood_beam_radius = BaseScriptElement.getFloatElement(beam_finder_dom, "beam_radius",
default=Detector.flood_beam_radius)
self.flood_use_direct_beam = BaseScriptElement.getBoolElement(beam_finder_dom, "use_direct_beam",
default = Detector.flood_use_direct_beam)
element_list = dom.getElementsByTagName("BeamFinder")
if len(element_list)>0:
beam_finder_dom = element_list[0]
self.x_position = BaseScriptElement.getFloatElement(beam_finder_dom, "x",
default=Detector.x_position)
self.y_position = BaseScriptElement.getFloatElement(beam_finder_dom, "y",
default=Detector.y_position)
self.use_finder = BaseScriptElement.getBoolElement(beam_finder_dom, "use_finder",
default = Detector.use_finder)
self.beam_file = BaseScriptElement.getStringElement(beam_finder_dom, "beam_file")
self.beam_radius = BaseScriptElement.getFloatElement(beam_finder_dom, "beam_radius",
default=Detector.beam_radius)
self.use_direct_beam = BaseScriptElement.getBoolElement(beam_finder_dom, "use_direct_beam",
default = Detector.use_direct_beam)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
super(SampleData, self).from_xml(xml_str)
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("Transmission")
if len(element_list)>0:
instrument_dom = element_list[0]
self.combine_transmission_frames = BaseScriptElement.getBoolElement(instrument_dom, "combine_transmission_frames",
default = SampleData.combine_transmission_frames)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
super(Background, self).from_xml(xml_str)
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("Background")
if len(element_list)>0:
instrument_dom = element_list[0]
self.combine_transmission_frames = BaseScriptElement.getBoolElement(instrument_dom, "combine_transmission_frames",
default = Background.combine_transmission_frames)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("DataCorrections")
if len(element_list)>0:
instrument_dom = element_list[0]
self.filter_bad_pulses = BaseScriptElement.getBoolElement(instrument_dom,
"filter_bad_pulses",
default=DataCorrectionsScript.filter_bad_pulses)
self.incident_beam_norm = BaseScriptElement.getStringElement(instrument_dom,
"incident_beam_norm",
default=DataCorrectionsScript.incident_beam_norm)
self.monitor_int_low = BaseScriptElement.getIntElement(instrument_dom,
"monint_range_low",
default=DataCorrectionsScript.monitor_int_low)
self.monitor_int_high = BaseScriptElement.getIntElement(instrument_dom,
"monint_range_high",
default=DataCorrectionsScript.monitor_int_high)
self.tib_subtraction = BaseScriptElement.getBoolElement(instrument_dom,
"timeindepbkg_sub",
default=DataCorrectionsScript.tib_subtraction)
self.tib_tof_start = BaseScriptElement.getIntElement(instrument_dom,
"tib_tof_range_start",
default=DataCorrectionsScript.tib_tof_start)
self.tib_tof_end = BaseScriptElement.getIntElement(instrument_dom,
"tib_tof_range_end",
default=DataCorrectionsScript.tib_tof_end)
self.correct_kikf = BaseScriptElement.getBoolElement(instrument_dom,
"correct_kikf",
default=DataCorrectionsScript.correct_kikf)
self.detector_vanadium = BaseScriptElement.getStringElement(instrument_dom,
"detector_vanadium",
default=DataCorrectionsScript.detector_vanadium)
self.detvan_integration = BaseScriptElement.getBoolElement(instrument_dom,
"use_bounds_detvan",
default=DataCorrectionsScript.detvan_integration)
self.detvan_int_range_low = BaseScriptElement.getStringElement(instrument_dom,
"detvan_range_low",
default=DataCorrectionsScript.detvan_int_range_low)
self.detvan_int_range_high = BaseScriptElement.getStringElement(instrument_dom,
"detvan_range_high",
default=DataCorrectionsScript.detvan_int_range_high)
self.detvan_int_range_units = BaseScriptElement.getStringElement(instrument_dom,
"detvan_range_units",
default=DataCorrectionsScript.detvan_int_range_units)
self.save_proc_detvan = BaseScriptElement.getBoolElement(instrument_dom,
"save_proc_detvan",
default=DataCorrectionsScript.save_proc_detvan)
self.save_proc_detvan_file = BaseScriptElement.getStringElement(instrument_dom,
"save_proc_detvan_filename",
default=DataCorrectionsScript.save_proc_detvan_file)
self.use_proc_detvan = BaseScriptElement.getBoolElement(instrument_dom,
"use_proc_detvan",
default=DataCorrectionsScript.use_proc_detvan)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("DataCorrections")
if len(element_list)>0:
instrument_dom = element_list[0]
self.filter_bad_pulses = BaseScriptElement.getBoolElement(instrument_dom,
"filter_bad_pulses",
default=DataCorrectionsScript.filter_bad_pulses)
self.incident_beam_norm = BaseScriptElement.getStringElement(instrument_dom,
"incident_beam_norm",
default=DataCorrectionsScript.incident_beam_norm)
self.monitor_int_low = BaseScriptElement.getIntElement(instrument_dom,
"monint_range_low",
default=DataCorrectionsScript.monitor_int_low)
self.monitor_int_high = BaseScriptElement.getIntElement(instrument_dom,
"monint_range_high",
default=DataCorrectionsScript.monitor_int_high)
self.tib_subtraction = BaseScriptElement.getBoolElement(instrument_dom,
"timeindepbkg_sub",
default=DataCorrectionsScript.tib_subtraction)
self.tib_tof_start = BaseScriptElement.getIntElement(instrument_dom,
"tib_tof_range_start",
default=DataCorrectionsScript.tib_tof_start)
self.tib_tof_end = BaseScriptElement.getIntElement(instrument_dom,
"tib_tof_range_end",
default=DataCorrectionsScript.tib_tof_end)
self.correct_kikf = BaseScriptElement.getBoolElement(instrument_dom,
"correct_kikf",
default=DataCorrectionsScript.correct_kikf)
self.detector_vanadium = BaseScriptElement.getStringElement(instrument_dom,
"detector_vanadium",
default=DataCorrectionsScript.detector_vanadium)
self.detvan_integration = BaseScriptElement.getBoolElement(instrument_dom,
"use_bounds_detvan",
default=DataCorrectionsScript.detvan_integration)
self.detvan_int_range_low = BaseScriptElement.getStringElement(instrument_dom,
"detvan_range_low",
default=DataCorrectionsScript.detvan_int_range_low)
self.detvan_int_range_high = BaseScriptElement.getStringElement(instrument_dom,
"detvan_range_high",
default=DataCorrectionsScript.detvan_int_range_high)
self.detvan_int_range_units = BaseScriptElement.getStringElement(instrument_dom,
"detvan_range_units",
default=DataCorrectionsScript.detvan_int_range_units)
self.save_proc_detvan = BaseScriptElement.getBoolElement(instrument_dom,
"save_proc_detvan",
default=DataCorrectionsScript.save_proc_detvan)
self.save_proc_detvan_file = BaseScriptElement.getStringElement(instrument_dom,
"save_proc_detvan_filename",
default=DataCorrectionsScript.save_proc_detvan_file)
self.use_proc_detvan = BaseScriptElement.getBoolElement(instrument_dom,
"use_proc_detvan",
default=DataCorrectionsScript.use_proc_detvan)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("Transmission")
if len(element_list)>0:
instrument_dom = element_list[0]
self.transmission = BaseScriptElement.getFloatElement(instrument_dom, "trans",
default=SampleData.transmission)
self.transmission_spread = BaseScriptElement.getFloatElement(instrument_dom, "trans_spread",
default=SampleData.transmission_spread)
self.calculate_transmission = BaseScriptElement.getBoolElement(instrument_dom, "calculate_trans",
default = SampleData.calculate_transmission)
self.theta_dependent = BaseScriptElement.getBoolElement(instrument_dom, "theta_dependent",
default = SampleData.theta_dependent)
self.dark_current = BaseScriptElement.getStringElement(instrument_dom, "dark_current")
for m in self.option_list:
method = m()
if method.find(instrument_dom):
method.from_xml(instrument_dom)
self.calculation_method = method
break
# Data file section
element_list = dom.getElementsByTagName("SampleData")
if len(element_list)>0:
sample_data_dom = element_list[0]
self.data_files = BaseScriptElement.getStringList(sample_data_dom, "data_file")
self.sample_thickness = BaseScriptElement.getFloatElement(sample_data_dom, "sample_thickness",
default=SampleData.sample_thickness)
self.separate_jobs = BaseScriptElement.getBoolElement(sample_data_dom, "separate_jobs",
default = SampleData.separate_jobs)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
super(ReductionOptions, self).from_xml(xml_str)
dom = xml.dom.minidom.parseString(xml_str)
instrument_dom = dom.getElementsByTagName("Instrument")[0]
self.detector_offset = BaseScriptElement.getFloatElement(instrument_dom, "detector_offset",
default=ReductionOptions.default_detector_offset)
# TOF cutoff and correction
element_list = dom.getElementsByTagName("TOFcorr")
if len(element_list)>0:
tof_dom = element_list[0]
self.use_config_cutoff = BaseScriptElement.getBoolElement(tof_dom, "use_config_cutoff",
default = ReductionOptions.use_config_cutoff)
self.correct_for_flight_path = BaseScriptElement.getBoolElement(tof_dom, "perform_flight_path_corr",
default = ReductionOptions.correct_for_flight_path)
self.low_TOF_cut = BaseScriptElement.getFloatElement(tof_dom, "low_tof_cut",
default=ReductionOptions.low_TOF_cut)
self.high_TOF_cut = BaseScriptElement.getFloatElement(tof_dom, "high_tof_cut",
default=ReductionOptions.high_TOF_cut)
# Mask
self.use_config_mask = BaseScriptElement.getBoolElement(dom, "UseConfigMask",
default = ReductionOptions.use_config_mask)
# Resolution
self.compute_resolution = BaseScriptElement.getBoolElement(dom, "ComputeResolution",
default = ReductionOptions.compute_resolution)
self.sample_aperture_diameter = BaseScriptElement.getFloatElement(dom, "SampleApertureDiameter",\
default = ReductionOptions.sample_aperture_diameter)
# TOF correction
self.perform_TOF_correction = BaseScriptElement.getBoolElement(dom, "PerformTOFCorrection",
default = ReductionOptions.perform_TOF_correction)
# Normalization option
self.use_beam_monitor = BaseScriptElement.getBoolElement(dom, "UseBeamMonitor",
default = ReductionOptions.use_beam_monitor)
self.beam_monitor_reference = BaseScriptElement.getStringElement(dom, "BeamMonitorRef",
default = ReductionOptions.beam_monitor_reference)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
# # Get Mantid version
# mtd_version = BaseScriptElement.getMantidBuildVersion(dom)
element_list = dom.getElementsByTagName("Data")
if len(element_list)>0:
instrument_dom = element_list[0]
#Peak selection
self.DataPeakSelectionType = BaseScriptElement.getStringElement(instrument_dom, "peak_selection_type")
#Peak from/to pixels
self.DataPeakPixels[0] = BaseScriptElement.getIntElement(instrument_dom, "from_peak_pixels")
self.DataPeakPixels[1] = BaseScriptElement.getIntElement(instrument_dom, "to_peak_pixels")
#discrete selection string
self.DataBackgroundFlag = BaseScriptElement.getStringElement(instrument_dom, "peak_discrete_selection")
#background flag
self.DataBackgroundFlag = BaseScriptElement.getBoolElement(instrument_dom, "background_flag")
#background from/to pixels
self.DataBackgroundRoi[0] = BaseScriptElement.getStringElement(instrument_dom, "back_roi1_from")
self.DataBackgroundRoi[1] = BaseScriptElement.getStringElement(instrument_dom, "back_roi1_to")
self.DataBackgroundRoi[2] = BaseScriptElement.getStringElement(instrument_dom, "back_roi2_from")
self.DataBackgroundRoi[3] = BaseScriptElement.getStringElement(instrument_dom, "back_roi2_to")
#from TOF and to TOF
self.DataTofRange[0] = BaseScriptElement.getStringElement(instrument_dom, "from_tof_range")
self.DataTofRange[1] = BaseScriptElement.getStringElement(instrument_dom, "to_tof_range")
def get_bol(tag, default):
return BaseScriptElement.getBoolElement(dom, tag, default=default)
def from_xml_element(self, instrument_dom):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
#Peak selection
self.DataPeakSelectionType = BaseScriptElement.getStringElement(
instrument_dom, "peak_selection_type")
#Peak from/to pixels
self.DataPeakPixels = [
BaseScriptElement.getIntElement(instrument_dom,
"from_peak_pixels"),
BaseScriptElement.getIntElement(instrument_dom, "to_peak_pixels")
]
#data metadata
_tthd_value = BaseScriptElement.getStringElement(
instrument_dom, "tthd_value")
if _tthd_value == '':
_tthd_value = 'N/A'
self.tthd_value = _tthd_value
_ths_value = BaseScriptElement.getStringElement(
instrument_dom, "ths_value")
if _ths_value == '':
_ths_value = 'N/A'
self.ths_value = _ths_value
#low resolution range
self.data_x_range_flag = BaseScriptElement.getBoolElement(
instrument_dom, "x_range_flag", default=DataSets.data_x_range_flag)
self.data_x_range = [
BaseScriptElement.getIntElement(instrument_dom, "x_min_pixel"),
BaseScriptElement.getIntElement(instrument_dom, "x_max_pixel")
]
self.norm_x_range_flag = BaseScriptElement.getBoolElement(
instrument_dom,
"norm_x_range_flag",
default=DataSets.norm_x_range_flag)
self.norm_x_range = [
BaseScriptElement.getIntElement(instrument_dom, "norm_x_min"),
BaseScriptElement.getIntElement(instrument_dom, "norm_x_max")
]
#discrete selection string
self.DataPeakDiscreteSelection = BaseScriptElement.getStringElement(
instrument_dom, "peak_discrete_selection")
#background flag
self.DataBackgroundFlag = BaseScriptElement.getBoolElement(
instrument_dom,
"background_flag",
default=DataSets.DataBackgroundFlag)
#background from/to pixels
self.DataBackgroundRoi = [
BaseScriptElement.getIntElement(instrument_dom, "back_roi1_from"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi1_to"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi2_from"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi2_to")
]
#from TOF and to TOF
self.TofRangeFlag = BaseScriptElement.getBoolElement(
instrument_dom, "tof_range_flag", default=DataSets.TofRangeFlag)
self.DataTofRange = [
BaseScriptElement.getFloatElement(instrument_dom,
"from_tof_range"),
BaseScriptElement.getFloatElement(instrument_dom, "to_tof_range")
]
self.data_files = BaseScriptElement.getIntList(instrument_dom,
"data_sets")
#with or without norm
self.NormFlag = BaseScriptElement.getBoolElement(
instrument_dom, "norm_flag", default=DataSets.NormFlag)
#Peak from/to pixels
self.NormPeakPixels = [
BaseScriptElement.getIntElement(instrument_dom,
"norm_from_peak_pixels"),
BaseScriptElement.getIntElement(instrument_dom,
"norm_to_peak_pixels")
]
#background flag
self.NormBackgroundFlag = BaseScriptElement.getBoolElement(
instrument_dom,
"norm_background_flag",
default=DataSets.NormBackgroundFlag)
#background from/to pixels
self.NormBackgroundRoi = [
BaseScriptElement.getIntElement(instrument_dom,
"norm_from_back_pixels"),
BaseScriptElement.getIntElement(instrument_dom,
"norm_to_back_pixels")
]
self.norm_file = BaseScriptElement.getIntElement(
instrument_dom, "norm_dataset")
# Q cut
self.q_min = BaseScriptElement.getFloatElement(instrument_dom,
"q_min",
default=DataSets.q_min)
self.q_step = BaseScriptElement.getFloatElement(
instrument_dom, "q_step", default=DataSets.q_step)
self.auto_q_binning = BaseScriptElement.getBoolElement(
instrument_dom, "auto_q_binning", default=False)
# overlap_lowest_error
self.overlap_lowest_error = BaseScriptElement.getBoolElement(
instrument_dom, "overlap_lowest_error", default=True)
self.overlap_mean_value = BaseScriptElement.getBoolElement(
instrument_dom, "overlap_mean_value", default=False)
# Angle offset
self.angle_offset = BaseScriptElement.getFloatElement(
instrument_dom, "angle_offset", default=DataSets.angle_offset)
self.angle_offset_error = BaseScriptElement.getFloatElement(
instrument_dom,
"angle_offset_error",
default=DataSets.angle_offset_error)
#scaling factor file and options
self.scaling_factor_file = BaseScriptElement.getStringElement(
instrument_dom, "scaling_factor_file")
self.slits_width_flag = BaseScriptElement.getBoolElement(
instrument_dom, "slits_width_flag")
self.scaling_factor_file_flag = BaseScriptElement.getBoolElement(
instrument_dom, "scaling_factor_flag")
# geometry correction switch
self.geometry_correction_switch = BaseScriptElement.getBoolElement(
instrument_dom, "geometry_correction_switch")
#incident medium selected
if BaseScriptElement.getStringList(instrument_dom,
"incident_medium_list") != []:
self.incident_medium_list = BaseScriptElement.getStringList(
instrument_dom, "incident_medium_list")
self.incident_medium_index_selected = BaseScriptElement.getIntElement(
instrument_dom, "incident_medium_index_selected")
else:
self.incident_medium_list = ['H2O']
self.incident_medium_index_selected = 0
#fourth column (precision)
self.fourth_column_flag = BaseScriptElement.getBoolElement(
instrument_dom, "fourth_column_flag")
self.fourth_column_dq0 = BaseScriptElement.getFloatElement(
instrument_dom, "fourth_column_dq0")
self.fourth_column_dq_over_q = BaseScriptElement.getFloatElement(
instrument_dom, "fourth_column_dq_over_q")
# Primary fraction
self.clocking_from = BaseScriptElement.getIntElement(instrument_dom,
"clocking_from",
default=None)
self.clocking_to = BaseScriptElement.getIntElement(instrument_dom,
"clocking_to",
default=None)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("SampleSetup")
if len(element_list) > 0:
instrument_dom = element_list[0]
self.sample_file = BaseScriptElement.getStringElement(instrument_dom,
"sample_input_file",
default=SampleSetupScript.sample_file)
self.live_button = BaseScriptElement.getBoolElement(instrument_dom,
"live_button",
default=SampleSetupScript.live_button)
self.output_wsname = BaseScriptElement.getStringElement(instrument_dom,
"output_wsname",
default=SampleSetupScript.output_wsname)
self.detcal_file = BaseScriptElement.getStringElement(instrument_dom,
"detcal_file",
default=SampleSetupScript.detcal_file)
self.relocate_dets = BaseScriptElement.getBoolElement(instrument_dom,
"relocate_dets",
default=SampleSetupScript.relocate_dets)
self.incident_energy_guess = BaseScriptElement.getStringElement(instrument_dom,
"incident_energy_guess",
default=SampleSetupScript.incident_energy_guess)
self.use_ei_guess = BaseScriptElement.getBoolElement(instrument_dom,
"use_ei_guess",
default=SampleSetupScript.use_ei_guess)
self.tzero_guess = BaseScriptElement.getFloatElement(instrument_dom,
"tzero_guess",
default=SampleSetupScript.tzero_guess)
self.monitor1_specid = BaseScriptElement.getStringElement(instrument_dom,
"monitor1_specid",
default=SampleSetupScript.monitor1_specid)
self.monitor2_specid = BaseScriptElement.getStringElement(instrument_dom,
"monitor2_specid",
default=SampleSetupScript.monitor2_specid)
self.et_range_low = BaseScriptElement.getStringElement(instrument_dom,
"et_range/low",
default=SampleSetupScript.et_range_low)
self.et_range_width = BaseScriptElement.getStringElement(instrument_dom,
"et_range/width",
default=SampleSetupScript.et_range_width)
self.et_range_high = BaseScriptElement.getStringElement(instrument_dom,
"et_range/high",
default=SampleSetupScript.et_range_high)
self.et_is_distribution = BaseScriptElement.getBoolElement(instrument_dom,
"sofphie_is_distribution",
default=SampleSetupScript.et_is_distribution)
self.hardmask_file = BaseScriptElement.getStringElement(instrument_dom,
"hardmask_file",
default=SampleSetupScript.hardmask_file)
self.grouping_file = BaseScriptElement.getStringElement(instrument_dom,
"grouping_file",
default=SampleSetupScript.grouping_file)
self.show_workspaces = BaseScriptElement.getBoolElement(instrument_dom,
"show_workspaces",
default=SampleSetupScript.show_workspaces)
self.savedir = BaseScriptElement.getStringElement(instrument_dom,
"savedir",
default=SampleSetupScript.savedir)
def from_xml_element(self, instrument_dom):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
# Peak from/to pixels
self.DataPeakPixels = [BaseScriptElement.getIntElement(instrument_dom, "from_peak_pixels"),
BaseScriptElement.getIntElement(instrument_dom, "to_peak_pixels")]
# low resolution range
self.data_x_range_flag = BaseScriptElement.getBoolElement(instrument_dom, "x_range_flag",
default=DataSets.data_x_range_flag)
self.data_x_range = [BaseScriptElement.getIntElement(instrument_dom, "x_min_pixel"),
BaseScriptElement.getIntElement(instrument_dom, "x_max_pixel")]
self.norm_x_range_flag = BaseScriptElement.getBoolElement(instrument_dom, "norm_x_range_flag",
default=DataSets.norm_x_range_flag)
self.norm_x_range = [BaseScriptElement.getIntElement(instrument_dom, "norm_x_min"),
BaseScriptElement.getIntElement(instrument_dom, "norm_x_max")]
# discrete selection string
self.DataPeakDiscreteSelection = BaseScriptElement.getStringElement(instrument_dom, "peak_discrete_selection")
# background flag
self.DataBackgroundFlag = BaseScriptElement.getBoolElement(instrument_dom,
"background_flag",
default=DataSets.DataBackgroundFlag)
# background from/to pixels
self.DataBackgroundRoi = [BaseScriptElement.getIntElement(instrument_dom, "back_roi1_from"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi1_to"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi2_from"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi2_to")]
# from TOF and to TOF
# self.crop_TOF_range = BaseScriptElement.getBoolElement(instrument_dom, "crop_tof",
# default=DataSets.crop_TOF_range)
self.DataTofRange = [BaseScriptElement.getFloatElement(instrument_dom, "from_tof_range"),
BaseScriptElement.getFloatElement(instrument_dom, "to_tof_range")]
self.TOFstep = BaseScriptElement.getFloatElement(instrument_dom, "tof_step",
default=DataSets.TOFstep)
self.data_files = BaseScriptElement.getStringList(instrument_dom, "data_sets")
# with or without norm
self.NormFlag = BaseScriptElement.getBoolElement(instrument_dom, "norm_flag",
default=DataSets.NormFlag)
# Peak from/to pixels
self.NormPeakPixels = [BaseScriptElement.getIntElement(instrument_dom, "norm_from_peak_pixels"),
BaseScriptElement.getIntElement(instrument_dom, "norm_to_peak_pixels")]
# background flag
self.NormBackgroundFlag = BaseScriptElement.getBoolElement(instrument_dom,
"norm_background_flag",
default=DataSets.NormBackgroundFlag)
# background from/to pixels
self.NormBackgroundRoi = [BaseScriptElement.getIntElement(instrument_dom, "norm_from_back_pixels"),
BaseScriptElement.getIntElement(instrument_dom, "norm_to_back_pixels")]
self.norm_file = BaseScriptElement.getStringElement(instrument_dom, "norm_dataset")
# Q cut
self.q_min = BaseScriptElement.getFloatElement(instrument_dom, "q_min", default=DataSets.q_min)
self.q_step = BaseScriptElement.getFloatElement(instrument_dom, "q_step", default=DataSets.q_step)
self.q_bins = BaseScriptElement.getIntElement(instrument_dom, "q_bins", default=DataSets.q_bins)
self.q_log = BaseScriptElement.getBoolElement(instrument_dom, "q_log", default=DataSets.q_log)
# scattering angle
self.theta = BaseScriptElement.getFloatElement(instrument_dom, "theta", default=DataSets.theta)
# self.use_center_pixel = BaseScriptElement.getBoolElement(instrument_dom,
# "use_center_pixel",
# default=DataSets.use_center_pixel)
# Sample log overwrites
self.set_detector_angle = BaseScriptElement.getBoolElement(instrument_dom,
"set_detector_angle",
default=DataSets.set_detector_angle)
self.detector_angle = BaseScriptElement.getFloatElement(instrument_dom,
"detector_angle",
default=DataSets.detector_angle)
self.set_detector_angle_offset = BaseScriptElement.getBoolElement(instrument_dom,
"set_detector_angle_offset",
default=DataSets.set_detector_angle_offset)
self.detector_angle_offset = BaseScriptElement.getFloatElement(instrument_dom,
"detector_angle_offset",
default=DataSets.detector_angle_offset)
self.set_direct_pixel = BaseScriptElement.getBoolElement(instrument_dom,
"set_direct_pixel",
default=DataSets.set_direct_pixel)
self.direct_pixel = BaseScriptElement.getFloatElement(instrument_dom,
"direct_pixel",
default=DataSets.direct_pixel)
self.output_dir = BaseScriptElement.getStringElement(instrument_dom,
"output_dir",
default=DataSets.output_dir)
def from_xml_element(self, instrument_dom):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
# Peak from/to pixels
self.DataPeakPixels = [
BaseScriptElement.getIntElement(instrument_dom, "from_peak_pixels"),
BaseScriptElement.getIntElement(instrument_dom, "to_peak_pixels"),
]
# low resolution range
self.data_x_range_flag = BaseScriptElement.getBoolElement(
instrument_dom, "x_range_flag", default=DataSets.data_x_range_flag
)
self.data_x_range = [
BaseScriptElement.getIntElement(instrument_dom, "x_min_pixel"),
BaseScriptElement.getIntElement(instrument_dom, "x_max_pixel"),
]
self.norm_x_range_flag = BaseScriptElement.getBoolElement(
instrument_dom, "norm_x_range_flag", default=DataSets.norm_x_range_flag
)
self.norm_x_range = [
BaseScriptElement.getIntElement(instrument_dom, "norm_x_min"),
BaseScriptElement.getIntElement(instrument_dom, "norm_x_max"),
]
# discrete selection string
self.DataPeakDiscreteSelection = BaseScriptElement.getStringElement(instrument_dom, "peak_discrete_selection")
# background flag
self.DataBackgroundFlag = BaseScriptElement.getBoolElement(
instrument_dom, "background_flag", default=DataSets.DataBackgroundFlag
)
# background from/to pixels
self.DataBackgroundRoi = [
BaseScriptElement.getIntElement(instrument_dom, "back_roi1_from"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi1_to"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi2_from"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi2_to"),
]
# from TOF and to TOF
# self.crop_TOF_range = BaseScriptElement.getBoolElement(instrument_dom, "crop_tof",
# default=DataSets.crop_TOF_range)
self.DataTofRange = [
BaseScriptElement.getFloatElement(instrument_dom, "from_tof_range"),
BaseScriptElement.getFloatElement(instrument_dom, "to_tof_range"),
]
self.TOFstep = BaseScriptElement.getFloatElement(instrument_dom, "tof_step", default=DataSets.TOFstep)
self.data_files = BaseScriptElement.getStringList(instrument_dom, "data_sets")
# with or without norm
self.NormFlag = BaseScriptElement.getBoolElement(instrument_dom, "norm_flag", default=DataSets.NormFlag)
# Peak from/to pixels
self.NormPeakPixels = [
BaseScriptElement.getIntElement(instrument_dom, "norm_from_peak_pixels"),
BaseScriptElement.getIntElement(instrument_dom, "norm_to_peak_pixels"),
]
# background flag
self.NormBackgroundFlag = BaseScriptElement.getBoolElement(
instrument_dom, "norm_background_flag", default=DataSets.NormBackgroundFlag
)
# background from/to pixels
self.NormBackgroundRoi = [
BaseScriptElement.getIntElement(instrument_dom, "norm_from_back_pixels"),
BaseScriptElement.getIntElement(instrument_dom, "norm_to_back_pixels"),
]
self.norm_file = BaseScriptElement.getStringElement(instrument_dom, "norm_dataset")
# Q cut
self.q_min = BaseScriptElement.getFloatElement(instrument_dom, "q_min", default=DataSets.q_min)
self.q_step = BaseScriptElement.getFloatElement(instrument_dom, "q_step", default=DataSets.q_step)
self.q_bins = BaseScriptElement.getIntElement(instrument_dom, "q_bins", default=DataSets.q_bins)
self.q_log = BaseScriptElement.getBoolElement(instrument_dom, "q_log", default=DataSets.q_log)
# scattering angle
self.theta = BaseScriptElement.getFloatElement(instrument_dom, "theta", default=DataSets.theta)
# self.use_center_pixel = BaseScriptElement.getBoolElement(instrument_dom,
# "use_center_pixel",
# default=DataSets.use_center_pixel)
# Sample log overwrites
self.set_detector_angle = BaseScriptElement.getBoolElement(
instrument_dom, "set_detector_angle", default=DataSets.set_detector_angle
)
self.detector_angle = BaseScriptElement.getFloatElement(
instrument_dom, "detector_angle", default=DataSets.detector_angle
)
self.set_detector_angle_offset = BaseScriptElement.getBoolElement(
instrument_dom, "set_detector_angle_offset", default=DataSets.set_detector_angle_offset
)
self.detector_angle_offset = BaseScriptElement.getFloatElement(
instrument_dom, "detector_angle_offset", default=DataSets.detector_angle_offset
)
self.set_direct_pixel = BaseScriptElement.getBoolElement(
instrument_dom, "set_direct_pixel", default=DataSets.set_direct_pixel
)
self.direct_pixel = BaseScriptElement.getFloatElement(
instrument_dom, "direct_pixel", default=DataSets.direct_pixel
)
self.output_dir = BaseScriptElement.getStringElement(instrument_dom, "output_dir", default=DataSets.output_dir)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
instrument_dom = dom.getElementsByTagName("Instrument")[0]
self.nx_pixels = BaseScriptElement.getIntElement(
instrument_dom, "nx_pixels", default=ReductionOptions.nx_pixels)
self.ny_pixels = BaseScriptElement.getIntElement(
instrument_dom, "ny_pixels", default=ReductionOptions.ny_pixels)
self.instrument_name = BaseScriptElement.getStringElement(
instrument_dom, "name")
self.pixel_size = BaseScriptElement.getFloatElement(
instrument_dom, "pixel_size", default=ReductionOptions.pixel_size)
self.sample_detector_distance = BaseScriptElement.getFloatElement(
instrument_dom,
"sample_det_dist",
default=ReductionOptions.sample_detector_distance)
self.detector_offset = BaseScriptElement.getFloatElement(
instrument_dom,
"detector_offset",
default=ReductionOptions.detector_offset)
self.wavelength = BaseScriptElement.getFloatElement(
instrument_dom, "wavelength", default=ReductionOptions.wavelength)
self.wavelength_spread = BaseScriptElement.getFloatElement(
instrument_dom,
"wavelength_spread",
default=ReductionOptions.wavelength_spread)
self.solid_angle_corr = BaseScriptElement.getBoolElement(
instrument_dom,
"solid_angle_corr",
default=ReductionOptions.solid_angle_corr)
# Output directory
self.use_data_directory = BaseScriptElement.getBoolElement(
instrument_dom,
"UseDataDirectory",
default=ReductionOptions.use_data_directory)
self.output_directory = BaseScriptElement.getStringElement(
instrument_dom,
"OutputDirectory",
default=ReductionOptions.output_directory)
# Dark current
self.dark_current_corr = BaseScriptElement.getBoolElement(
instrument_dom,
"dark_current_corr",
default=ReductionOptions.dark_current_corr)
self.dark_current_data = BaseScriptElement.getStringElement(
instrument_dom, "dark_current_data")
self.n_q_bins = BaseScriptElement.getIntElement(
instrument_dom, "n_q_bins", default=ReductionOptions.n_q_bins)
self.n_sub_pix = BaseScriptElement.getIntElement(
instrument_dom, "n_sub_pix", default=ReductionOptions.n_sub_pix)
self.log_binning = BaseScriptElement.getBoolElement(
instrument_dom,
"log_binning",
default=ReductionOptions.log_binning)
self.align_log_with_decades = BaseScriptElement.getBoolElement(
instrument_dom,
"align_log_with_decades",
default=ReductionOptions.align_log_with_decades)
self.error_weighting = BaseScriptElement.getBoolElement(
instrument_dom,
"error_weighting",
default=ReductionOptions.error_weighting)
self.n_wedges = BaseScriptElement.getIntElement(
instrument_dom, "n_wedges", default=ReductionOptions.n_wedges)
self.wedge_angle = BaseScriptElement.getFloatElement(
instrument_dom,
"wedge_angle",
default=ReductionOptions.wedge_angle)
self.wedge_offset = BaseScriptElement.getFloatElement(
instrument_dom,
"wedge_offset",
default=ReductionOptions.wedge_offset)
self.normalization = BaseScriptElement.getIntElement(
instrument_dom,
"normalization",
default=ReductionOptions.normalization)
# Mask
element_list = dom.getElementsByTagName("Mask")
if len(element_list) > 0:
mask_dom = element_list[0]
self.top = BaseScriptElement.getIntElement(
mask_dom, "mask_top", default=ReductionOptions.top)
self.bottom = BaseScriptElement.getIntElement(
mask_dom, "mask_bottom", default=ReductionOptions.bottom)
self.right = BaseScriptElement.getIntElement(
mask_dom, "mask_right", default=ReductionOptions.right)
self.left = BaseScriptElement.getIntElement(
mask_dom, "mask_left", default=ReductionOptions.left)
self.masked_side = BaseScriptElement.getStringElement(
mask_dom, "mask_side", default=ReductionOptions.masked_side)
self.shapes = []
shapes_dom_list = mask_dom.getElementsByTagName("Shapes")
if len(shapes_dom_list) > 0:
shapes_dom = shapes_dom_list[0]
for item in shapes_dom.getElementsByTagName("rect"):
x_min = float(item.getAttribute("x_min"))
x_max = float(item.getAttribute("x_max"))
y_min = float(item.getAttribute("y_min"))
y_max = float(item.getAttribute("y_max"))
self.shapes.append(
ReductionOptions.RectangleMask(x_min, x_max, y_min,
y_max))
self.detector_ids = BaseScriptElement.getIntList(mask_dom,
"DetectorIDs",
default=[])
self.mask_file = BaseScriptElement.getStringElement(
mask_dom, "mask_file")
self.use_mask_file = BaseScriptElement.getBoolElement(
mask_dom,
"use_mask_file",
default=ReductionOptions.use_mask_file)
# Absolute scaling
element_list = dom.getElementsByTagName("AbsScale")
if len(element_list) > 0:
scale_dom = element_list[0]
self.manual_beam_diam = BaseScriptElement.getBoolElement(
scale_dom,
"manual_beam_diam",
default=ReductionOptions.manual_beam_diam)
self.scaling_factor = BaseScriptElement.getFloatElement(
scale_dom,
"scaling_factor",
default=ReductionOptions.scaling_factor)
self.calculate_scale = BaseScriptElement.getBoolElement(
scale_dom,
"calculate_scale",
default=ReductionOptions.calculate_scale)
self.scaling_direct_file = BaseScriptElement.getStringElement(
scale_dom, "scaling_direct_file")
self.scaling_att_trans = BaseScriptElement.getFloatElement(
scale_dom,
"scaling_att_trans",
default=ReductionOptions.scaling_att_trans)
self.scaling_beam_diam = BaseScriptElement.getFloatElement(
scale_dom,
"scaling_beam_diam",
default=ReductionOptions.scaling_beam_diam)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
# Get Mantid version
mtd_version = BaseScriptElement.getMantidBuildVersion(dom)
instrument_dom = dom.getElementsByTagName("Instrument")[0]
self.nx_pixels = BaseScriptElement.getIntElement(instrument_dom, "nx_pixels",
default=ReductionOptions.nx_pixels)
self.ny_pixels = BaseScriptElement.getIntElement(instrument_dom, "ny_pixels",
default=ReductionOptions.ny_pixels)
self.instrument_name = BaseScriptElement.getStringElement(instrument_dom, "name")
self.pixel_size = BaseScriptElement.getFloatElement(instrument_dom, "pixel_size",
default=ReductionOptions.pixel_size)
self.sample_detector_distance = BaseScriptElement.getFloatElement(instrument_dom, "sample_det_dist",
default=ReductionOptions.sample_detector_distance)
self.detector_offset = BaseScriptElement.getFloatElement(instrument_dom, "detector_offset",
default=ReductionOptions.detector_offset)
self.wavelength = BaseScriptElement.getFloatElement(instrument_dom, "wavelength",
default=ReductionOptions.wavelength)
self.wavelength_spread = BaseScriptElement.getFloatElement(instrument_dom, "wavelength_spread",
default=ReductionOptions.wavelength_spread)
self.solid_angle_corr = BaseScriptElement.getBoolElement(instrument_dom, "solid_angle_corr",
default = ReductionOptions.solid_angle_corr)
# Output directory
self.use_data_directory = BaseScriptElement.getBoolElement(instrument_dom, "UseDataDirectory",
default = ReductionOptions.use_data_directory)
self.output_directory = BaseScriptElement.getStringElement(instrument_dom, "OutputDirectory",
default = ReductionOptions.output_directory)
# Dark current - take care of backward compatibility
if mtd_version!=0 and mtd_version<BaseScriptElement.UPDATE_1_CHANGESET_CUTOFF:
bck_entries = dom.getElementsByTagName("Background")
if len(bck_entries)>0:
self.dark_current_corr = BaseScriptElement.getBoolElement(bck_entries[0], "dark_current_corr",
default = ReductionOptions.dark_current_corr)
self.dark_current_data = BaseScriptElement.getStringElement(bck_entries[0], "dark_current_file")
else:
self.dark_current_corr = BaseScriptElement.getBoolElement(instrument_dom, "dark_current_corr",
default = ReductionOptions.dark_current_corr)
self.dark_current_data = BaseScriptElement.getStringElement(instrument_dom, "dark_current_data")
self.n_q_bins = BaseScriptElement.getIntElement(instrument_dom, "n_q_bins",
default=ReductionOptions.n_q_bins)
self.n_sub_pix = BaseScriptElement.getIntElement(instrument_dom, "n_sub_pix",
default=ReductionOptions.n_sub_pix)
self.log_binning = BaseScriptElement.getBoolElement(instrument_dom, "log_binning",
default = ReductionOptions.log_binning)
self.normalization = BaseScriptElement.getIntElement(instrument_dom, "normalization",
default=ReductionOptions.normalization)
# Mask - take care of backward compatibility
if mtd_version!=0 and mtd_version<BaseScriptElement.UPDATE_1_CHANGESET_CUTOFF:
self.top = BaseScriptElement.getIntElement(instrument_dom, "mask_top", default=ReductionOptions.top)
self.bottom = BaseScriptElement.getIntElement(instrument_dom, "mask_bottom", default=ReductionOptions.bottom)
self.right = BaseScriptElement.getIntElement(instrument_dom, "mask_right", default=ReductionOptions.right)
self.left = BaseScriptElement.getIntElement(instrument_dom, "mask_left", default=ReductionOptions.left)
else:
element_list = dom.getElementsByTagName("Mask")
if len(element_list)>0:
mask_dom = element_list[0]
self.top = BaseScriptElement.getIntElement(mask_dom, "mask_top", default=ReductionOptions.top)
self.bottom = BaseScriptElement.getIntElement(mask_dom, "mask_bottom", default=ReductionOptions.bottom)
self.right = BaseScriptElement.getIntElement(mask_dom, "mask_right", default=ReductionOptions.right)
self.left = BaseScriptElement.getIntElement(mask_dom, "mask_left", default=ReductionOptions.left)
self.shapes = []
shapes_dom_list = mask_dom.getElementsByTagName("Shapes")
if len(shapes_dom_list)>0:
shapes_dom = shapes_dom_list[0]
for item in shapes_dom.getElementsByTagName("rect"):
x_min = float(item.getAttribute("x_min"))
x_max = float(item.getAttribute("x_max"))
y_min = float(item.getAttribute("y_min"))
y_max = float(item.getAttribute("y_max"))
self.shapes.append(ReductionOptions.RectangleMask(x_min, x_max, y_min, y_max))
self.detector_ids = BaseScriptElement.getIntList(mask_dom, "DetectorIDs", default=[])
self.mask_file = BaseScriptElement.getStringElement(mask_dom, "mask_file")
self.use_mask_file = BaseScriptElement.getBoolElement(mask_dom, "use_mask_file",
default = ReductionOptions.use_mask_file)
# Absolute scaling
element_list = dom.getElementsByTagName("AbsScale")
if len(element_list)>0:
scale_dom = element_list[0]
self.manual_beam_diam = BaseScriptElement.getBoolElement(scale_dom, "manual_beam_diam",
default = ReductionOptions.manual_beam_diam)
self.scaling_factor = BaseScriptElement.getFloatElement(scale_dom, "scaling_factor",
default=ReductionOptions.scaling_factor)
self.calculate_scale = BaseScriptElement.getBoolElement(scale_dom, "calculate_scale",
default = ReductionOptions.calculate_scale)
self.scaling_direct_file = BaseScriptElement.getStringElement(scale_dom, "scaling_direct_file")
self.scaling_att_trans = BaseScriptElement.getFloatElement(scale_dom, "scaling_att_trans",
default=ReductionOptions.scaling_att_trans)
self.scaling_beam_diam = BaseScriptElement.getFloatElement(scale_dom, "scaling_beam_diam",
default=ReductionOptions.scaling_beam_diam)
def get_bol(tag, default):
return BaseScriptElement.getBoolElement(dom,
tag,
default=default)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("DiagnoseDetectors")
if len(element_list) > 0:
instrument_dom = element_list[0]
self.high_counts = BaseScriptElement.getFloatElement(
instrument_dom,
"high_counts",
default=DiagnoseDetectorsScript.high_counts)
self.low_counts = BaseScriptElement.getFloatElement(
instrument_dom,
"low_counts",
default=DiagnoseDetectorsScript.low_counts)
self.median_test_out_low = BaseScriptElement.getFloatElement(
instrument_dom,
"median_test_out_low",
default=DiagnoseDetectorsScript.median_test_out_low)
self.median_test_out_high = BaseScriptElement.getFloatElement(
instrument_dom,
"median_test_out_high",
default=DiagnoseDetectorsScript.median_test_out_high)
self.median_test_low = BaseScriptElement.getFloatElement(
instrument_dom,
"median_test_low",
default=DiagnoseDetectorsScript.median_test_low)
self.median_test_high = BaseScriptElement.getFloatElement(
instrument_dom,
"median_test_high",
default=DiagnoseDetectorsScript.median_test_high)
self.errorbar_criterion = BaseScriptElement.getFloatElement(
instrument_dom,
"errorbar_criterion",
default=DiagnoseDetectorsScript.errorbar_criterion)
self.det_van2 = BaseScriptElement.getStringElement(
instrument_dom,
"det_van2",
default=DiagnoseDetectorsScript.det_van2)
self.detvan_ratio_var = BaseScriptElement.getFloatElement(
instrument_dom,
"detvan_ratio_var",
default=DiagnoseDetectorsScript.detvan_ratio_var)
self.background_check = BaseScriptElement.getBoolElement(
instrument_dom,
"background_check",
default=DiagnoseDetectorsScript.background_check)
self.sambkg_median_test_low = BaseScriptElement.getFloatElement(
instrument_dom,
"sambkg_median_test_low",
default=DiagnoseDetectorsScript.sambkg_median_test_low)
self.sambkg_median_test_high = BaseScriptElement.getFloatElement(
instrument_dom,
"sambkg_median_test_high",
default=DiagnoseDetectorsScript.sambkg_median_test_high)
self.sambkg_errorbar_criterion = BaseScriptElement.getFloatElement(
instrument_dom,
"sambkg_errorbar_criterion",
default=DiagnoseDetectorsScript.sambkg_errorbar_criterion)
self.tof_start = BaseScriptElement.getIntElement(
instrument_dom,
"background_tof_start",
default=DiagnoseDetectorsScript.tof_start)
self.tof_end = BaseScriptElement.getIntElement(
instrument_dom,
"background_tof_end",
default=DiagnoseDetectorsScript.tof_end)
self.reject_zero_bkg = BaseScriptElement.getBoolElement(
instrument_dom,
"reject_zero_bkg",
default=DiagnoseDetectorsScript.reject_zero_bkg)
self.psd_bleed = BaseScriptElement.getBoolElement(
instrument_dom,
"psd_bleed",
default=DiagnoseDetectorsScript.psd_bleed)
self.max_framerate = BaseScriptElement.getStringElement(
instrument_dom,
"max_framerate",
default=DiagnoseDetectorsScript.max_framerate)
self.ignored_pixels = BaseScriptElement.getStringElement(
instrument_dom,
"ignored_pixels",
default=DiagnoseDetectorsScript.ignored_pixels)
def from_xml_element(self, instrument_dom):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
#Peak selection
self.DataPeakSelectionType = BaseScriptElement.getStringElement(instrument_dom, "peak_selection_type")
#Peak from/to pixels
self.DataPeakPixels = [BaseScriptElement.getIntElement(instrument_dom, "from_peak_pixels"),
BaseScriptElement.getIntElement(instrument_dom, "to_peak_pixels")]
#data metadata
_tthd_value = BaseScriptElement.getStringElement(instrument_dom, "tthd_value")
if (_tthd_value == ''):
_tthd_value = 'N/A'
self.tthd_value = _tthd_value
_ths_value = BaseScriptElement.getStringElement(instrument_dom, "ths_value")
if (_ths_value == ''):
_ths_value = 'N/A'
self.ths_value = _ths_value
#low resolution range
self.data_x_range_flag = BaseScriptElement.getBoolElement(instrument_dom, "x_range_flag",
default=DataSets.data_x_range_flag)
self.data_x_range = [BaseScriptElement.getIntElement(instrument_dom, "x_min_pixel"),
BaseScriptElement.getIntElement(instrument_dom, "x_max_pixel")]
self.norm_x_range_flag = BaseScriptElement.getBoolElement(instrument_dom, "norm_x_range_flag",
default=DataSets.norm_x_range_flag)
self.norm_x_range = [BaseScriptElement.getIntElement(instrument_dom, "norm_x_min"),
BaseScriptElement.getIntElement(instrument_dom, "norm_x_max")]
#discrete selection string
self.DataPeakDiscreteSelection = BaseScriptElement.getStringElement(instrument_dom, "peak_discrete_selection")
#background flag
self.DataBackgroundFlag = BaseScriptElement.getBoolElement(instrument_dom,
"background_flag",
default=DataSets.DataBackgroundFlag)
#background from/to pixels
self.DataBackgroundRoi = [BaseScriptElement.getIntElement(instrument_dom, "back_roi1_from"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi1_to"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi2_from"),
BaseScriptElement.getIntElement(instrument_dom, "back_roi2_to")]
#from TOF and to TOF
self.TofRangeFlag = BaseScriptElement.getBoolElement(instrument_dom, "tof_range_flag",
default=DataSets.TofRangeFlag)
self.DataTofRange = [BaseScriptElement.getFloatElement(instrument_dom, "from_tof_range"),
BaseScriptElement.getFloatElement(instrument_dom, "to_tof_range")]
self.data_files = BaseScriptElement.getIntList(instrument_dom, "data_sets")
#with or without norm
self.NormFlag = BaseScriptElement.getBoolElement(instrument_dom, "norm_flag",
default=DataSets.NormFlag)
#Peak from/to pixels
self.NormPeakPixels = [BaseScriptElement.getIntElement(instrument_dom, "norm_from_peak_pixels"),
BaseScriptElement.getIntElement(instrument_dom, "norm_to_peak_pixels")]
#background flag
self.NormBackgroundFlag = BaseScriptElement.getBoolElement(instrument_dom,
"norm_background_flag",
default=DataSets.NormBackgroundFlag)
#background from/to pixels
self.NormBackgroundRoi = [BaseScriptElement.getIntElement(instrument_dom, "norm_from_back_pixels"),
BaseScriptElement.getIntElement(instrument_dom, "norm_to_back_pixels")]
self.norm_file = BaseScriptElement.getIntElement(instrument_dom, "norm_dataset")
# Q cut
self.q_min = BaseScriptElement.getFloatElement(instrument_dom, "q_min", default=DataSets.q_min)
self.q_step = BaseScriptElement.getFloatElement(instrument_dom, "q_step", default=DataSets.q_step)
self.auto_q_binning = BaseScriptElement.getBoolElement(instrument_dom, "auto_q_binning", default=False)
# Angle offset
self.angle_offset = BaseScriptElement.getFloatElement(instrument_dom, "angle_offset", default=DataSets.angle_offset)
self.angle_offset_error = BaseScriptElement.getFloatElement(instrument_dom, "angle_offset_error", default=DataSets.angle_offset_error)
#scaling factor file and options
self.scaling_factor_file = BaseScriptElement.getStringElement(instrument_dom, "scaling_factor_file")
self.slits_width_flag = BaseScriptElement.getBoolElement(instrument_dom, "slits_width_flag")
self.scaling_factor_file_flag = BaseScriptElement.getBoolElement(instrument_dom, "scaling_factor_flag")
#incident medium selected
if BaseScriptElement.getStringList(instrument_dom, "incident_medium_list") != []:
self.incident_medium_list = BaseScriptElement.getStringList(instrument_dom, "incident_medium_list")
self.incident_medium_index_selected = BaseScriptElement.getIntElement(instrument_dom, "incident_medium_index_selected")
else:
self.incident_medium_list = ['H2O']
self.incident_medium_index_selected = 0
#fourth column (precision)
self.fourth_column_flag = BaseScriptElement.getBoolElement(instrument_dom, "fourth_column_flag")
self.fourth_column_dq0 = BaseScriptElement.getFloatElement(instrument_dom, "fourth_column_dq0")
self.fourth_column_dq_over_q = BaseScriptElement.getFloatElement(instrument_dom, "fourth_column_dq_over_q")
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
instrument_dom = dom.getElementsByTagName("Instrument")[0]
self.nx_pixels = BaseScriptElement.getIntElement(instrument_dom, "nx_pixels",
default=ReductionOptions.nx_pixels)
self.ny_pixels = BaseScriptElement.getIntElement(instrument_dom, "ny_pixels",
default=ReductionOptions.ny_pixels)
self.instrument_name = BaseScriptElement.getStringElement(
instrument_dom, "name")
self.pixel_size = BaseScriptElement.getFloatElement(instrument_dom, "pixel_size",
default=ReductionOptions.pixel_size)
self.sample_detector_distance = BaseScriptElement.getFloatElement(instrument_dom, "sample_det_dist",
default=ReductionOptions.sample_detector_distance)
self.detector_offset = BaseScriptElement.getFloatElement(instrument_dom, "detector_offset",
default=ReductionOptions.detector_offset)
self.wavelength = BaseScriptElement.getFloatElement(instrument_dom, "wavelength",
default=ReductionOptions.wavelength)
self.wavelength_spread = BaseScriptElement.getFloatElement(instrument_dom, "wavelength_spread",
default=ReductionOptions.wavelength_spread)
self.solid_angle_corr = BaseScriptElement.getBoolElement(instrument_dom, "solid_angle_corr",
default=ReductionOptions.solid_angle_corr)
# Output directory
self.use_data_directory = BaseScriptElement.getBoolElement(instrument_dom, "UseDataDirectory",
default=ReductionOptions.use_data_directory)
self.output_directory = BaseScriptElement.getStringElement(instrument_dom, "OutputDirectory",
default=ReductionOptions.output_directory)
# Dark current
self.dark_current_corr = BaseScriptElement.getBoolElement(instrument_dom, "dark_current_corr",
default=ReductionOptions.dark_current_corr)
self.dark_current_data = BaseScriptElement.getStringElement(
instrument_dom, "dark_current_data")
self.n_q_bins = BaseScriptElement.getIntElement(instrument_dom, "n_q_bins",
default=ReductionOptions.n_q_bins)
self.n_sub_pix = BaseScriptElement.getIntElement(instrument_dom, "n_sub_pix",
default=ReductionOptions.n_sub_pix)
self.log_binning = BaseScriptElement.getBoolElement(instrument_dom, "log_binning",
default=ReductionOptions.log_binning)
self.align_log_with_decades = BaseScriptElement.getBoolElement(instrument_dom, "align_log_with_decades",
default=ReductionOptions.align_log_with_decades)
self.error_weighting = BaseScriptElement.getBoolElement(instrument_dom, "error_weighting",
default=ReductionOptions.error_weighting)
self.n_wedges = BaseScriptElement.getIntElement(instrument_dom, "n_wedges",
default=ReductionOptions.n_wedges)
self.wedge_angle = BaseScriptElement.getFloatElement(instrument_dom, "wedge_angle",
default=ReductionOptions.wedge_angle)
self.wedge_offset = BaseScriptElement.getFloatElement(instrument_dom, "wedge_offset",
default=ReductionOptions.wedge_offset)
self.normalization = BaseScriptElement.getIntElement(instrument_dom, "normalization",
default=ReductionOptions.normalization)
# Mask
element_list = dom.getElementsByTagName("Mask")
if len(element_list) > 0:
mask_dom = element_list[0]
self.top = BaseScriptElement.getIntElement(
mask_dom, "mask_top", default=ReductionOptions.top)
self.bottom = BaseScriptElement.getIntElement(
mask_dom, "mask_bottom", default=ReductionOptions.bottom)
self.right = BaseScriptElement.getIntElement(
mask_dom, "mask_right", default=ReductionOptions.right)
self.left = BaseScriptElement.getIntElement(
mask_dom, "mask_left", default=ReductionOptions.left)
self.masked_side = BaseScriptElement.getStringElement(
mask_dom, "mask_side", default=ReductionOptions.masked_side)
self.shapes = []
shapes_dom_list = mask_dom.getElementsByTagName("Shapes")
if len(shapes_dom_list) > 0:
shapes_dom = shapes_dom_list[0]
for item in shapes_dom.getElementsByTagName("rect"):
x_min = float(item.getAttribute("x_min"))
x_max = float(item.getAttribute("x_max"))
y_min = float(item.getAttribute("y_min"))
y_max = float(item.getAttribute("y_max"))
self.shapes.append(ReductionOptions.RectangleMask(
x_min, x_max, y_min, y_max))
self.detector_ids = BaseScriptElement.getIntList(
mask_dom, "DetectorIDs", default=[])
self.mask_file = BaseScriptElement.getStringElement(
mask_dom, "mask_file")
self.use_mask_file = BaseScriptElement.getBoolElement(mask_dom, "use_mask_file",
default=ReductionOptions.use_mask_file)
# Absolute scaling
element_list = dom.getElementsByTagName("AbsScale")
if len(element_list) > 0:
scale_dom = element_list[0]
self.manual_beam_diam = BaseScriptElement.getBoolElement(scale_dom, "manual_beam_diam",
default=ReductionOptions.manual_beam_diam)
self.scaling_factor = BaseScriptElement.getFloatElement(scale_dom, "scaling_factor",
default=ReductionOptions.scaling_factor)
self.calculate_scale = BaseScriptElement.getBoolElement(scale_dom, "calculate_scale",
default=ReductionOptions.calculate_scale)
self.scaling_direct_file = BaseScriptElement.getStringElement(
scale_dom, "scaling_direct_file")
self.scaling_att_trans = BaseScriptElement.getFloatElement(scale_dom, "scaling_att_trans",
default=ReductionOptions.scaling_att_trans)
self.scaling_beam_diam = BaseScriptElement.getFloatElement(scale_dom, "scaling_beam_diam",
default=ReductionOptions.scaling_beam_diam)
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
# # Get Mantid version
# mtd_version = BaseScriptElement.getMantidBuildVersion(dom)
element_list = dom.getElementsByTagName("Advanced")
if len(element_list)>0:
instrument_dom = element_list[0]
#general
self.FilteringDataFlag = BaseScriptElement.getBoolElement(instrument_dom, "filtering_data_flag")
self.DtOverTFlag = BaseScriptElement.getBoolElement(instrument_dom, "dt_over_t_flag")
self.AutoCleanupFlag = BaseScriptElement.getBoolElement(instrument_dom, "auto_cleanup_flag")
self.PercentageQToRemove = BaseScriptElement.getStringElement(instrument_dom, "percentage_q_to_remove")
self.OverwriteDataGeometryFlag = BaseScriptElement.getBoolElement(instrument_dom, "overwrite_data_geometry")
self.DataGeometryFileName = BaseScriptElement.getStringElement(instrument_dom, "data_geometry_file_name")
self.OverwriteNormGeometryFlag = BaseScriptElement.getBoolElement(instrument_dom, "overwrite_norm_geometry")
self.DataCombinedBckFlag = BaseScriptElement.getBoolElement(instrument_dom, "data_combined_bck_flag")
self.DataCombinedSpecularFlag = BaseScriptElement.getBoolElement(instrument_dom, "data_combined_specular_flag")
self.DataCombinedSubtractedFlag = BaseScriptElement.getBoolElement(instrument_dom, "data_combined_subtracted_flag")
self.NormCombinedBckFlag = BaseScriptElement.getBoolElement(instrument_dom, "norm_combined_bck_flag")
self.NormCombinedSpecularFlag = BaseScriptElement.getBoolElement(instrument_dom, "norm_combined_specular_flag")
self.NormCombinedSubtractedFlag = BaseScriptElement.getBoolElement(instrument_dom, "norm_combined_subtracted_flag")
self.RvsTOFFlag = BaseScriptElement.getBoolElement(instrument_dom, "r_vs_tof_flag")
self.RvsTOFCombinedFlag = BaseScriptElement.getBoolElement(instrument_dom, "r_vs_tof_combined_flag")
self.RvsQFlag = BaseScriptElement.getBoolElement(instrument_dom, "r_vs_q_flag")
self.RvsQRebinningFlag = BaseScriptElement.getBoolElement(instrument_dom, "r_vs_q_rebinning_flag")
def from_xml(self, xml_str):
"""
Read in data from XML
@param xml_str: text to read the data from
"""
dom = xml.dom.minidom.parseString(xml_str)
element_list = dom.getElementsByTagName("DiagnoseDetectors")
if len(element_list)>0:
instrument_dom = element_list[0]
self.high_counts = BaseScriptElement.getFloatElement(instrument_dom,
"high_counts",
default=DiagnoseDetectorsScript.high_counts)
self.low_counts = BaseScriptElement.getFloatElement(instrument_dom,
"low_counts",
default=DiagnoseDetectorsScript.low_counts)
self.median_test_out_low = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_out_low",
default=DiagnoseDetectorsScript.median_test_out_low)
self.median_test_out_high = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_out_high",
default=DiagnoseDetectorsScript.median_test_out_high)
self.median_test_low = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_low",
default=DiagnoseDetectorsScript.median_test_low)
self.median_test_high = BaseScriptElement.getFloatElement(instrument_dom,
"median_test_high",
default=DiagnoseDetectorsScript.median_test_high)
self.errorbar_criterion = BaseScriptElement.getFloatElement(instrument_dom,
"errorbar_criterion",
default=DiagnoseDetectorsScript.errorbar_criterion)
self.det_van2 = BaseScriptElement.getStringElement(instrument_dom,
"det_van2",
default=DiagnoseDetectorsScript.det_van2)
self.detvan_ratio_var = BaseScriptElement.getFloatElement(instrument_dom,
"detvan_ratio_var",
default=DiagnoseDetectorsScript.detvan_ratio_var)
self.background_check = BaseScriptElement.getBoolElement(instrument_dom,
"background_check",
default=DiagnoseDetectorsScript.background_check)
self.sambkg_median_test_low = BaseScriptElement.getFloatElement(instrument_dom,
"sambkg_median_test_low",
default=DiagnoseDetectorsScript.sambkg_median_test_low)
self.sambkg_median_test_high = BaseScriptElement.getFloatElement(instrument_dom,
"sambkg_median_test_high",
default=DiagnoseDetectorsScript.sambkg_median_test_high)
self.sambkg_errorbar_criterion = BaseScriptElement.getFloatElement(instrument_dom,
"sambkg_errorbar_criterion",
default=DiagnoseDetectorsScript.sambkg_errorbar_criterion)
self.tof_start = BaseScriptElement.getIntElement(instrument_dom,\
"background_tof_start",\
default=DiagnoseDetectorsScript.tof_start)
self.tof_end = BaseScriptElement.getIntElement(instrument_dom,
"background_tof_end",
default=DiagnoseDetectorsScript.tof_end)
self.reject_zero_bkg = BaseScriptElement.getBoolElement(instrument_dom,
"reject_zero_bkg",
default=DiagnoseDetectorsScript.reject_zero_bkg)
self.psd_bleed = BaseScriptElement.getBoolElement(instrument_dom,
"psd_bleed",
default=DiagnoseDetectorsScript.psd_bleed)
self.max_framerate = BaseScriptElement.getStringElement(instrument_dom,
"max_framerate",
default=DiagnoseDetectorsScript.max_framerate)
self.ignored_pixels = BaseScriptElement.getStringElement(instrument_dom,
"ignored_pixels",
default=DiagnoseDetectorsScript.ignored_pixels)
