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("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): """ 'Public' method to 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("AdvancedSetup") if len(element_list)>0: instrument_dom = element_list[0] self.unwrapref = getFloatElement(instrument_dom, "unwrapref", AdvancedSetupScript.unwrapref) self.lowresref = getFloatElement(instrument_dom, "lowresref", AdvancedSetupScript.lowresref) self.cropwavelengthmin = getFloatElement(instrument_dom, "cropwavelengthmin", AdvancedSetupScript.cropwavelengthmin) self.removepropmppulsewidth = getFloatElement(instrument_dom, "removepromptpulsewidth", AdvancedSetupScript.removepropmppulsewidth) try: self.maxchunksize = BaseScriptElement.getIntElement(instrument_dom, "maxchunksize", default=AdvancedSetupScript.maxchunksize) except ValueError: self.maxchunksize = AdvancedSetupScript.maxchunksize self.filterbadpulses = getFloatElement(instrument_dom, "filterbadpulses", AdvancedSetupScript.filterbadpulses) self.pushdatapositive = BaseScriptElement.getStringElement(instrument_dom, "pushdatapositive", default=AdvancedSetupScript.pushdatapositive) self.stripvanadiumpeaks = getBooleanElement(instrument_dom, "stripvanadiumpeaks", AdvancedSetupScript.stripvanadiumpeaks) self.vanadiumfwhm = getFloatElement(instrument_dom, "vanadiumfwhm", AdvancedSetupScript.vanadiumfwhm) self.vanadiumpeaktol = getFloatElement(instrument_dom, "vanadiumpeaktol", AdvancedSetupScript.vanadiumpeaktol) self.vanadiumsmoothparams = BaseScriptElement.getStringElement(instrument_dom, "vanadiumsmoothparams", default=AdvancedSetupScript.vanadiumsmoothparams) self.extension = BaseScriptElement.getStringElement(instrument_dom, "extension", default=AdvancedSetupScript.extension) self.preserveevents = getBooleanElement(instrument_dom, "preserveevents", default=AdvancedSetupScript.preserveevents) self.outputfileprefix = BaseScriptElement.getStringElement(instrument_dom, "outputfileprefix", default = AdvancedSetupScript.outputfileprefix) self.scaledata = getFloatElement(instrument_dom, "scaledata", AdvancedSetupScript.scaledata) return
def from_xml_element(self, instrument_dom): """ Read in data from XML @param xml_str: text to read the data from """ # incident medium self.incident_medium_list = BaseScriptElement.getStringList( instrument_dom, "incident_medium_list") self.incident_medium_index_selected = BaseScriptElement.getIntElement( instrument_dom, "incident_medium_index_selected") self.tof_min = BaseScriptElement.getFloatElement( instrument_dom, "tof_min") self.tof_max = BaseScriptElement.getFloatElement( instrument_dom, "tof_max") # run number self.data_file = BaseScriptElement.getIntElement( instrument_dom, "data_file") # number of attenuator self.number_attenuator = BaseScriptElement.getIntElement( instrument_dom, "number_attenuator") # peak selection from and to self.peak_selection = [ BaseScriptElement.getIntElement(instrument_dom, "peak_selection_from_pixel"), BaseScriptElement.getIntElement(instrument_dom, "peak_selection_to_pixel") ] # background flag and selection from and to self.back_selection = [ BaseScriptElement.getIntElement(instrument_dom, "back_selection_from_pixel"), BaseScriptElement.getIntElement(instrument_dom, "back_selection_to_pixel") ] # lambda requested self.lambda_requested = BaseScriptElement.getStringElement( instrument_dom, "lambda_requested") # s1h, s2h, s1w, s2w self.s1h = BaseScriptElement.getStringElement(instrument_dom, "s1h") self.s2h = BaseScriptElement.getStringElement(instrument_dom, "s2h") self.s1w = BaseScriptElement.getStringElement(instrument_dom, "s1w") self.s2w = BaseScriptElement.getStringElement(instrument_dom, "s2w") # scaling factor file self.scaling_factor_file = BaseScriptElement.getStringElement( instrument_dom, "scaling_factor_file")
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 from_xml_element(self, instrument_dom): """ Read in data from XML @param xml_str: text to read the data from """ #incident medium self.incident_medium_list = BaseScriptElement.getStringList(instrument_dom, "incident_medium_list") self.incident_medium_index_selected = BaseScriptElement.getIntElement(instrument_dom, "incident_medium_index_selected") self.tof_min = BaseScriptElement.getFloatElement(instrument_dom, "tof_min") self.tof_max = BaseScriptElement.getFloatElement(instrument_dom, "tof_max") #run number self.data_file = BaseScriptElement.getIntElement(instrument_dom, "data_file") #number of attenuator self.number_attenuator = BaseScriptElement.getIntElement(instrument_dom, "number_attenuator") #peak selection from and to self.peak_selection = [BaseScriptElement.getIntElement(instrument_dom, "peak_selection_from_pixel"), BaseScriptElement.getIntElement(instrument_dom, "peak_selection_to_pixel")] #background flag and selection from and to self.back_selection = [BaseScriptElement.getIntElement(instrument_dom, "back_selection_from_pixel"), BaseScriptElement.getIntElement(instrument_dom, "back_selection_to_pixel")] #lambda requested self.lambda_requested = BaseScriptElement.getStringElement(instrument_dom, "lambda_requested") #s1h, s2h, s1w, s2w self.s1h = BaseScriptElement.getStringElement(instrument_dom, "s1h") self.s2h = BaseScriptElement.getStringElement(instrument_dom, "s2h") self.s1w = BaseScriptElement.getStringElement(instrument_dom, "s1w") self.s2w = BaseScriptElement.getStringElement(instrument_dom, "s2w") #scaling factor file self.scaling_factor_file = BaseScriptElement.getStringElement(instrument_dom, "scaling_factor_file")
def from_xml(self, xml_str): """ 'Public' method to 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("RunSetup") if len(element_list)>0: # instrument_dom = element_list[0] # self.runnumbers = BaseScriptElement.getStringElement(instrument_dom,\ "runnumber", default=RunSetupScript.runnumbers) tempbool = BaseScriptElement.getStringElement(instrument_dom,\ "sum", default=str(int(RunSetupScript.dosum))) self.dosum = bool(int(tempbool)) self.calibfilename = BaseScriptElement.getStringElement(instrument_dom,\ "calibrationfile", default=RunSetupScript.calibfilename) self.exp_ini_file_name = BaseScriptElement.getStringElement(instrument_dom,\ 'expinifilename', default=RunSetupScript.exp_ini_file_name) self.charfilename = BaseScriptElement.getStringElement(instrument_dom,\ "characterizationrunsfile", default=RunSetupScript.charfilename) try: self.binning = BaseScriptElement.getFloatElement(instrument_dom,\ "binning", default=RunSetupScript.binning) except ValueError: self.binning = '' try: self.resamplex = BaseScriptElement.getIntElement(instrument_dom,\ "resamplex", default=RunSetupScript.resamplex) except ValueError: self.resamplex = 0 self.doresamplex = BaseScriptElement.getIntElement(instrument_dom,\ "doresamplex", default=RunSetupScript.resamplex) self.doresamplex = bool(self.doresamplex) tempbool = BaseScriptElement.getStringElement(instrument_dom,\ "binindspace", default=str(int(RunSetupScript.binindspace))) self.binindspace = bool(int(tempbool)) self.saveas = BaseScriptElement.getStringElement(instrument_dom,\ "saveas", default=RunSetupScript.saveas) self.outputdir = BaseScriptElement.getStringElement(instrument_dom,\ "outputdirectory", default=RunSetupScript.outputdir) self.finalunits = BaseScriptElement.getStringElement(instrument_dom,\ "finaldataunits", default=RunSetupScript.finalunits) self.bkgdrunnumber = BaseScriptElement.getStringElement(instrument_dom,\ "backgroundnumber", default=RunSetupScript.bkgdrunnumber) tempbool = BaseScriptElement.getStringElement(instrument_dom,\ "disablebackgroundcorrection", default=str(int(RunSetupScript.disablebkgdcorrection))) self.disablebkgdcorrection = bool(int(tempbool)) self.vanrunnumber = BaseScriptElement.getStringElement(instrument_dom,\ "vanadiumnumber", default=RunSetupScript.vanrunnumber) tempbool = BaseScriptElement.getStringElement(instrument_dom,\ "disablevanadiumcorrection", default=str(int(RunSetupScript.disablevancorrection))) self.disablevancorrection = bool(int(tempbool)) self.vanbkgdrunnumber = BaseScriptElement.getStringElement(instrument_dom,\ "vanadiumbackgroundnumber", default=RunSetupScript.vanbkgdrunnumber) tempbool = BaseScriptElement.getStringElement(instrument_dom,\ "disablevanadiumbackgroundcorrection", default=str(int(RunSetupScript.disablevanbkgdcorrection))) self.disablevanbkgdcorrection = bool(int(tempbool)) # tempint = BaseScriptElement.getStringElement(instrument_dom, # try: # self.vannoiserunnumber = int(tempint) # except ValueError: # self.vannoiserunnumber = "" return
def get_int(tag, default): return BaseScriptElement.getIntElement(dom, tag, default=default)
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 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 """ 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) # 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): """ 'Public' method to 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("AdvancedSetup") if len(element_list)>0: instrument_dom = element_list[0] self.unwrapref = getFloatElement(instrument_dom, "unwrapref", AdvancedSetupScript.unwrapref) self.lowresref = getFloatElement(instrument_dom, "lowresref", AdvancedSetupScript.lowresref) self.cropwavelengthmin = getFloatElement(instrument_dom, "cropwavelengthmin", AdvancedSetupScript.cropwavelengthmin) self.cropwavelengthmax = getFloatElement(instrument_dom, 'cropwavelengthmax', AdvancedSetupScript.cropwavelengthmax) self.removepropmppulsewidth = getFloatElement(instrument_dom, "removepromptpulsewidth", AdvancedSetupScript.removepropmppulsewidth) try: self.maxchunksize = BaseScriptElement.getIntElement( instrument_dom, 'maxchunksize', default=AdvancedSetupScript.maxchunksize) except ValueError: self.maxchunksize = AdvancedSetupScript.maxchunksize self.filterbadpulses = getFloatElement(instrument_dom, 'filterbadpulses', AdvancedSetupScript.filterbadpulses) self.bkgdsmoothpars = BaseScriptElement.getStringElement(instrument_dom, "backgroundsmoothparams", default=AdvancedSetupScript.bkgdsmoothpars) self.pushdatapositive = BaseScriptElement.getStringElement(instrument_dom, "pushdatapositive", default=AdvancedSetupScript.pushdatapositive) self.stripvanadiumpeaks = getBooleanElement(instrument_dom, "stripvanadiumpeaks", AdvancedSetupScript.stripvanadiumpeaks) self.vanadiumfwhm = getFloatElement(instrument_dom, "vanadiumfwhm", AdvancedSetupScript.vanadiumfwhm) self.vanadiumpeaktol = getFloatElement(instrument_dom, "vanadiumpeaktol", AdvancedSetupScript.vanadiumpeaktol) self.vanadiumsmoothparams = BaseScriptElement.getStringElement(instrument_dom, "vanadiumsmoothparams", default=AdvancedSetupScript.vanadiumsmoothparams) self.extension = BaseScriptElement.getStringElement(instrument_dom, "extension", default=AdvancedSetupScript.extension) self.preserveevents = getBooleanElement(instrument_dom, "preserveevents", default=AdvancedSetupScript.preserveevents) self.outputfileprefix = BaseScriptElement.getStringElement(instrument_dom, "outputfileprefix", default = AdvancedSetupScript.outputfileprefix) self.scaledata = getFloatElement(instrument_dom, "scaledata", AdvancedSetupScript.scaledata) return
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 """ 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.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) self.savedir = BaseScriptElement.getStringElement( instrument_dom, "savedir", default=SampleSetupScript.savedir)
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(self, xml_str): """ 'Public' method to 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("AdvancedSetup") if len(element_list) > 0: instrument_dom = element_list[0] self.unwrapref = getFloatElement(instrument_dom, "unwrapref", AdvancedSetupScript.unwrapref) self.lowresref = getFloatElement(instrument_dom, "lowresref", AdvancedSetupScript.lowresref) self.cropwavelengthmin = getFloatElement(instrument_dom, "cropwavelengthmin", AdvancedSetupScript.cropwavelengthmin) self.cropwavelengthmax = getFloatElement(instrument_dom, 'cropwavelengthmax', AdvancedSetupScript.cropwavelengthmax) self.removepropmppulsewidth = getFloatElement(instrument_dom, "removepromptpulsewidth", AdvancedSetupScript.removepropmppulsewidth) try: self.maxchunksize = BaseScriptElement.getIntElement( instrument_dom, 'maxchunksize', default=AdvancedSetupScript.maxchunksize) except ValueError: self.maxchunksize = AdvancedSetupScript.maxchunksize self.filterbadpulses = getFloatElement(instrument_dom, 'filterbadpulses', AdvancedSetupScript.filterbadpulses) self.bkgdsmoothpars = BaseScriptElement.getStringElement(instrument_dom, "backgroundsmoothparams", default=AdvancedSetupScript.bkgdsmoothpars) self.pushdatapositive = BaseScriptElement.getStringElement(instrument_dom, "pushdatapositive", default=AdvancedSetupScript.pushdatapositive) self.stripvanadiumpeaks = getBooleanElement(instrument_dom, "stripvanadiumpeaks", AdvancedSetupScript.stripvanadiumpeaks) self.vanadiumfwhm = getFloatElement(instrument_dom, "vanadiumfwhm", AdvancedSetupScript.vanadiumfwhm) self.vanadiumpeaktol = getFloatElement(instrument_dom, "vanadiumpeaktol", AdvancedSetupScript.vanadiumpeaktol) self.vanadiumsmoothparams = BaseScriptElement.getStringElement(instrument_dom, "vanadiumsmoothparams", default=AdvancedSetupScript.vanadiumsmoothparams) self.vanadiumradius = getFloatElement(instrument_dom, "vanadiumradius", AdvancedSetupScript.vanadiumradius) self.extension = BaseScriptElement.getStringElement(instrument_dom, "extension", default=AdvancedSetupScript.extension) self.preserveevents = getBooleanElement(instrument_dom, "preserveevents", default=AdvancedSetupScript.preserveevents) self.outputfileprefix = BaseScriptElement.getStringElement(instrument_dom, "outputfileprefix", default = AdvancedSetupScript.outputfileprefix) self.scaledata = getFloatElement(instrument_dom, "scaledata", AdvancedSetupScript.scaledata) self.sampleformula = BaseScriptElement.getStringElement(instrument_dom, "sampleformula", default=AdvancedSetupScript.sampleformula) self.samplenumberdensity = getFloatElement(instrument_dom, "samplenumberdensity", AdvancedSetupScript.samplenumberdensity) self.measuredmassdensity = getFloatElement(instrument_dom, "measuredmassdensity", AdvancedSetupScript.measuredmassdensity) string_tmp = BaseScriptElement.getStringElement(instrument_dom, "samplegeometry", default=AdvancedSetupScript.samplegeometry) self.samplegeometry = {} if string_tmp: items = string_tmp.replace("{", "").replace("}", "").split(",") keys_tmp = [item.split(":")[0].replace("'", "") for item in items] vals_tmp = [item.split(":")[1].replace("'", "").strip() for item in items] if vals_tmp.count("") == 0: vals_tmp = [float(item) for item in vals_tmp] for count, value in enumerate(keys_tmp): self.samplegeometry[value] = vals_tmp[count] self.containershape = BaseScriptElement.getStringElement(instrument_dom, "containershape", default=AdvancedSetupScript.containershape) self.typeofcorrection = BaseScriptElement.getStringElement(instrument_dom, "typeofcorrection", default=AdvancedSetupScript.typeofcorrection) # Caching options # split it into the three cache dirs # NOTE: there should only be three entries, if not, let it fail early try: self.cache_dir_scan_save, self.cache_dir_scan_1, self.cache_dir_scan_2 = BaseScriptElement.getStringElement( instrument_dom, 'cachedir', default=";;").replace(";", ",").split(",") except ValueError: self.cache_dir_scan_save = '' self.cache_dir_scan_1 = '' self.cache_dir_scan_2 = '' tempbool = BaseScriptElement.getStringElement(instrument_dom, "cleancache", default=str( int(self.__class__.clean_cache))) self.clean_cache = bool(int(tempbool))
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 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): """ 'Public' method to 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("RunSetup") if len(element_list) > 0: # instrument_dom = element_list[0] # self.runnumbers = BaseScriptElement.getStringElement( instrument_dom, "runnumber", default=RunSetupScript.runnumbers) tempbool = BaseScriptElement.getStringElement( instrument_dom, "sum", default=str(int(RunSetupScript.dosum))) self.dosum = bool(int(tempbool)) self.calibfilename = BaseScriptElement.getStringElement( instrument_dom, 'calibrationfile', default=RunSetupScript.calibfilename) self.groupfilename = BaseScriptElement.getStringElement( instrument_dom, 'groupingfile', default=RunSetupScript.groupfilename) self.exp_ini_file_name = BaseScriptElement.getStringElement( instrument_dom, 'expinifilename', default=RunSetupScript.exp_ini_file_name) self.charfilename = BaseScriptElement.getStringElement( instrument_dom, 'characterizationrunsfile', default=RunSetupScript.charfilename) try: self.binning = BaseScriptElement.getFloatElement( instrument_dom, 'binning', default=RunSetupScript.binning) except ValueError: self.binning = '' try: self.resamplex = BaseScriptElement.getIntElement( instrument_dom, 'resamplex', default=RunSetupScript.resamplex) except ValueError: self.resamplex = 0 self.doresamplex = BaseScriptElement.getIntElement( instrument_dom, "doresamplex", default=RunSetupScript.resamplex) self.doresamplex = bool(self.doresamplex) tempbool = BaseScriptElement.getStringElement( instrument_dom, "binindspace", default=str(int(RunSetupScript.binindspace))) self.binindspace = bool(int(tempbool)) self.saveas = BaseScriptElement.getStringElement( instrument_dom, "saveas", default=RunSetupScript.saveas) self.outputdir = BaseScriptElement.getStringElement( instrument_dom, "outputdirectory", default=RunSetupScript.outputdir) self.finalunits = BaseScriptElement.getStringElement( instrument_dom, "finaldataunits", default=RunSetupScript.finalunits) self.bkgdrunnumber = BaseScriptElement.getStringElement( instrument_dom, "backgroundnumber", default=RunSetupScript.bkgdrunnumber) tempbool = BaseScriptElement.getStringElement( instrument_dom, "disablebackgroundcorrection", default=str(int(RunSetupScript.disablebkgdcorrection))) self.disablebkgdcorrection = bool(int(tempbool)) self.vanrunnumber = BaseScriptElement.getStringElement( instrument_dom, "vanadiumnumber", default=RunSetupScript.vanrunnumber) tempbool = BaseScriptElement.getStringElement( instrument_dom, "disablevanadiumcorrection", default=str(int(RunSetupScript.disablevancorrection))) self.disablevancorrection = bool(int(tempbool)) self.vanbkgdrunnumber = BaseScriptElement.getStringElement( instrument_dom, "vanadiumbackgroundnumber", default=RunSetupScript.vanbkgdrunnumber) tempbool = BaseScriptElement.getStringElement( instrument_dom, "disablevanadiumbackgroundcorrection", default=str(int(RunSetupScript.disablevanbkgdcorrection))) self.disablevanbkgdcorrection = bool(int(tempbool)) # tempint = BaseScriptElement.getStringElement(instrument_dom, # try: # self.vannoiserunnumber = int(tempint) # except ValueError: # self.vannoiserunnumber = "" return