def run(config, tim=None): """ This method is where the data reduction process gets done. @param config: Object containing the data reduction configuration information. @type config: L{hlr_utils.Configure} @param tim: (OPTIONAL) Object that will allow the method to perform timing evaluations. @type tim: C{sns_time.DiffTime} """ import common_lib import dr_lib import DST if tim is not None: tim.getTime(False) old_time = tim.getOldTime() if config.data is None: raise RuntimeError("Need to pass a data filename to the driver "\ +"script.") # Read in geometry if one is provided if config.inst_geom is not None: if config.verbose: print "Reading in instrument geometry file" inst_geom_dst = DST.getInstance("application/x-NxsGeom", config.inst_geom) else: inst_geom_dst = None config.so_axis = "time_of_flight" try: if type(config.mask_file) == type([]): if len(config.mask_file) > 1: if config.verbose: print "Creating combined mask file" if tim is not None: tim.getTime(False) config.mask_file = hlr_utils.merge_roi_files(\ config.mask_file, config) if tim is not None: tim.getTime(msg="After creating combined mask file") else: config.mask_file = config.mask_file[0] else: # Do nothing since it's already a string pass except TypeError: # No mask files provided, do nothing pass # Steps 1-3: Produce a scaled summed dark current dataset dc_som = dr_lib.scaled_summed_data(config.dkcur, config, dataset_type="dark_current", timer=tim) # Perform Steps 3-6 on black can data if config.bcan is not None: b_som1 = dr_lib.calibrate_dgs_data(config.bcan, config, dc_som, dataset_type="black_can", inst_geom_dst=inst_geom_dst, tib_const=config.tib_const, cwp=config.cwp_bcan, timer=tim) else: b_som1 = None # Perform Steps 3-6 on empty can data if config.ecan is not None: e_som1 = dr_lib.calibrate_dgs_data(config.ecan, config, dc_som, dataset_type="empty_can", inst_geom_dst=inst_geom_dst, tib_const=config.tib_const, cwp=config.cwp_ecan, timer=tim) else: e_som1 = None # Perform Steps 3-6 on sample data d_som1 = dr_lib.calibrate_dgs_data(config.data, config, dc_som, inst_geom_dst=inst_geom_dst, tib_const=config.tib_const, cwp=config.cwp_data, timer=tim) # Perform Steps 7-16 on sample data if config.data_trans_coeff is None: data_trans_coeff = None else: data_trans_coeff = config.data_trans_coeff.toValErrTuple() # Determine if we need to rebin the empty or black can data if config.ecan is not None and e_som1 is not None: ecan_cwp = True else: ecan_cwp = False if config.bcan is not None and b_som1 is not None: bcan_cwp = True else: bcan_cwp = False cwp_used = ecan_cwp or bcan_cwp d_som2 = dr_lib.process_dgs_data(d_som1, config, b_som1, e_som1, data_trans_coeff, cwp_used=cwp_used, timer=tim) del d_som1 del b_som1, e_som1 # Step 18: Normalize sample data by integrated values if config.norm is not None: if config.verbose: print "Reading normalization information" norm_int = dr_lib.add_files(config.norm, Signal_ROI=config.roi_file, Signal_MASK=config.mask_file, dataset_type="normalization", dst_type="text/num-info", Verbose=config.verbose, Timer=tim) # Make the labels and units compatible with a NeXus file based SOM norm_int.setAllAxisLabels(["wavelength"]) norm_int.setAllAxisUnits(["Angstroms"]) norm_int.setYLabel("Intensity") norm_int.setYUnits("Counts/Angstroms") if config.verbose: print "Normalizing data by normalization data" if tim is not None: tim.getTime(False) d_som3 = common_lib.div_ncerr(d_som2, norm_int) if tim is not None: tim.getTime(msg="After normalizing data ") del norm_int else: d_som3 = d_som2 del d_som2 # Step 19: Calculate the initial energy if config.initial_energy is not None: d_som3.attr_list["Initial_Energy"] = config.initial_energy # Steps 20-21: Calculate the energy transfer if config.verbose: print "Calculating energy transfer" if tim is not None: tim.getTime(False) d_som4 = dr_lib.energy_transfer(d_som3, "DGS", "Initial_Energy", lojac=True, scale=config.lambda_ratio) if tim is not None: tim.getTime(msg="After calculating energy transfer ") del d_som3 # Step 22: Rebin energy transfer spectra if config.verbose: print "Rebinning to final energy transfer axis" if tim is not None: tim.getTime(False) d_som5 = common_lib.rebin_axis_1D_frac(d_som4, config.E_bins.toNessiList()) if tim is not None: tim.getTime(msg="After rebinning energy transfer ") del d_som4 if config.dump_et_comb: d_som5_1 = dr_lib.sum_all_spectra(d_som5) hlr_utils.write_file(config.output, "text/Spec", d_som5_1, output_ext="et", data_ext=config.ext_replacement, path_replacement=config.path_replacement, verbose=config.verbose, message="combined energy transfer information") del d_som5_1 # Get the corner geometry information if config.verbose: print "Reading in corner geometry information" if tim is not None: tim.getTime(False) corner_angles = hlr_utils.get_corner_geometry(config.corner_geom) if tim is not None: tim.getTime(msg="After reading in corner geometry information ") if config.make_spe: d_som5.attr_list["corner_geom"] = corner_angles hlr_utils.write_file(config.output, "text/PHX", d_som5, output_ext="phx", data_ext=config.ext_replacement, path_replacement=config.path_replacement, verbose=config.verbose, message="PHX information") hlr_utils.write_file(config.output, "text/PAR", d_som5, output_ext="par", data_ext=config.ext_replacement, path_replacement=config.path_replacement, verbose=config.verbose, message="PAR information") hlr_utils.write_file(config.output, "text/SPE", d_som5, output_ext="spe", data_ext=config.ext_replacement, path_replacement=config.path_replacement, verbose=config.verbose, message="SPE information") # Steps 23-34: Create S(Q, E) distribution if config.verbose: print "Creating S(Q, E)" if tim is not None: tim.getTime(False) d_som5_2 = dr_lib.create_E_vs_Q_dgs(d_som5, config.initial_energy.toValErrTuple(), config.Q_bins.toNessiList(), corner_angles=corner_angles, split=config.split, configure=config, timer=tim) # Writing 2D DAVE file if not config.split: hlr_utils.write_file(config.output, "text/Dave2d", d_som5_2, output_ext="sqe", data_ext=config.ext_replacement, path_replacement=config.path_replacement, verbose=config.verbose, message="S(Q,E)") hlr_utils.write_file(config.output, "application/x-RedNxs", d_som5_2, output_ext="nxs", data_ext=config.ext_replacement, path_replacement=config.path_replacement, verbose=config.verbose, extra_tag="sqe", getsom_kwargs={"entry_name": "sqe"}, message="NeXus S(Q,E)") if tim is not None: tim.getTime(msg="After calculating S(Q,E) spectrum ") del d_som5_2 if config.qmesh: # Steps 23-27,35-36: Create S(Qvec, E) distribution if config.verbose: print "Creating S(Qvec, E)" if tim is not None: tim.getTime(False) dr_lib.create_Qvec_vs_E_dgs(d_som5, config.initial_energy.toValErrTuple(), config, corner_angles=corner_angles, make_fixed=config.fixed, output=config.output, timer=tim) if tim is not None: tim.getTime(msg="After calculating final spectrum ") # Write out RMD file d_som5.attr_list["config"] = config hlr_utils.write_file(config.output, "text/rmd", d_som5, output_ext="rmd", data_ext=config.ext_replacement, path_replacement=config.path_replacement, verbose=config.verbose, message="metadata") if tim is not None: tim.setOldTime(old_time) tim.getTime(msg="Total Running Time")
def run(config, tim=None): """ This method is where the data reduction process gets done. @param config: Object containing the data reduction configuration information. @type config: L{hlr_utils.Configure} @param tim: (OPTIONAL) Object that will allow the method to perform timing evaluations. @type tim: C{sns_time.DiffTime} """ import common_lib import dr_lib import DST if tim is not None: tim.getTime(False) old_time = tim.getOldTime() if config.data is None: raise RuntimeError("Need to pass a data filename to the driver "\ +"script.") # Read in geometry if one is provided if config.inst_geom is not None: if config.verbose: print "Reading in instrument geometry file" inst_geom_dst = DST.getInstance("application/x-NxsGeom", config.inst_geom) else: inst_geom_dst = None # Perform early background subtraction if the hwfix flag is used if config.hwfix: if not config.mc: so_axis = "time_of_flight" else: so_axis = "Time_of_Flight" bkg_som0 = dr_lib.add_files(config.back, Data_Paths=config.data_paths.toPath(), SO_Axis=so_axis, Signal_ROI=config.roi_file, dataset_type="background", Verbose=config.verbose, Timer=tim) bkg_som = dr_lib.fix_bin_contents(bkg_som0) del bkg_som0 else: bkg_som = None # Perform Steps 1-15 on sample data d_som1 = dr_lib.process_igs_data(config.data, config, timer=tim, inst_geom_dst=inst_geom_dst, tib_const=config.tib_data_const, bkg_som=bkg_som) # Perform Steps 1-15 on empty can data if config.ecan is not None: e_som1 = dr_lib.process_igs_data(config.ecan, config, timer=tim, inst_geom_dst=inst_geom_dst, dataset_type="empty_can", tib_const=config.tib_ecan_const, bkg_som=bkg_som) else: e_som1 = None # Perform Steps 1-15 on normalization data if config.norm is not None: n_som1 = dr_lib.process_igs_data(config.norm, config, timer=tim, inst_geom_dst=inst_geom_dst, dataset_type="normalization", tib_const=config.tib_norm_const, bkg_som=bkg_som) else: n_som1 = None # Perform Steps 1-15 on background data if config.back is not None: b_som1 = dr_lib.process_igs_data(config.back, config, timer=tim, inst_geom_dst=inst_geom_dst, dataset_type="background", tib_const=config.tib_back_const, bkg_som=bkg_som) else: b_som1 = None # Perform Step 1-15 on direct scattering background data if config.dsback is not None: ds_som1 = dr_lib.process_igs_data(config.dsback, config, timer=tim, inst_geom_dst=inst_geom_dst, tib_const=config.tib_dsback_const, dataset_type="dsbackground", bkg_som=bkg_som) # Note: time_zero_slope MUST be a tuple if config.time_zero_slope is not None: ds_som1.attr_list["Time_zero_slope"] = \ config.time_zero_slope.toValErrTuple() # Note: time_zero_offset MUST be a tuple if config.time_zero_offset is not None: ds_som1.attr_list["Time_zero_offset"] = \ config.time_zero_offset.toValErrTuple() # Step 16: Linearly interpolate TOF elastic range in direct scattering # background data # First convert TOF elastic range to appropriate pixel initial # wavelengths if config.verbose: print "Determining initial wavelength range for elastic line" if tim is not None: tim.getTime(False) if config.tof_elastic is None: # Units are in microseconds tof_elastic_range = (140300, 141300) else: tof_elastic_range = config.tof_elastic ctof_elastic_low = dr_lib.convert_single_to_list(\ "tof_to_initial_wavelength_igs_lin_time_zero", (tof_elastic_range[0], 0.0), ds_som1) ctof_elastic_high = dr_lib.convert_single_to_list(\ "tof_to_initial_wavelength_igs_lin_time_zero", (tof_elastic_range[1], 0.0), ds_som1) ctof_elastic_range = [(ctof_elastic_low[i][0], ctof_elastic_high[i][0]) for i in xrange(len(ctof_elastic_low))] if tim is not None: tim.getTime(msg="After calculating initial wavelength range for "\ +"elastic line ") del ctof_elastic_low, ctof_elastic_high if config.split: lambda_filter = [(d_som1[i].axis[0].val[0], d_som1[i].axis[0].val[-1]) for i in xrange(len(d_som1))] else: lambda_filter = None # Now interpolate spectra between TOF elastic range (converted to # initial wavelength) if config.verbose: print "Linearly interpolating direct scattering spectra" if tim is not None: tim.getTime(False) ds_som2 = dr_lib.lin_interpolate_spectra(ds_som1, ctof_elastic_range, filter_axis=lambda_filter) if tim is not None: tim.getTime(msg="After linearly interpolating direct scattering "\ +"spectra ") if config.dump_dslin: ds_som2_1 = dr_lib.sum_all_spectra(ds_som2,\ rebin_axis=config.lambda_bins.toNessiList()) hlr_utils.write_file(config.output, "text/Spec", ds_som2_1, output_ext="lin", data_ext=config.ext_replacement, path_replacement=config.path_replacement, verbose=config.verbose, message="dsbackground linear interpolation") del ds_som2_1 del ds_som1 else: ds_som2 = None if inst_geom_dst is not None: inst_geom_dst.release_resource() # Steps 17-18: Subtract background spectrum from sample spectrum if config.dsback is None: back_som = b_som1 bkg_type = "background" else: back_som = ds_som2 bkg_type = "dsbackground" d_som2 = dr_lib.subtract_bkg_from_data(d_som1, back_som, verbose=config.verbose, timer=tim, dataset1="data", dataset2=bkg_type, scale=config.scale_bs) if config.dsback is not None: del ds_som2 # Step 19: Zero region outside TOF elastic for background for empty can if config.dsback is None: bcs_som = b_som1 cs_som = e_som1 else: if config.verbose and b_som1 is not None: print "Zeroing background spectra" if tim is not None and b_som1 is not None: tim.getTime(False) bcs_som = dr_lib.zero_spectra(b_som1, ctof_elastic_range) if tim is not None and b_som1 is not None: tim.getTime(msg="After zeroing background spectra") if config.verbose and e_som1 is not None: print "Zeroing empty can spectra" if tim is not None and e_som1 is not None: tim.getTime(False) cs_som = dr_lib.zero_spectra(e_som1, ctof_elastic_range) if tim is not None and e_som1 is not None: tim.getTime(msg="After zeroing empty can spectra") del ctof_elastic_range # Steps 20-21: Subtract background spectrum from empty can spectrum e_som2 = dr_lib.subtract_bkg_from_data(cs_som, bcs_som, verbose=config.verbose, timer=tim, dataset1="data-empty_can", dataset2="background", scale=config.scale_bcs) # Steps 22-23: Subtract background spectrum from empty can spectrum for # normalization try: config.pre_norm except AttributeError: config.pre_norm = False if not config.pre_norm: e_som3 = dr_lib.subtract_bkg_from_data(e_som1, b_som1, verbose=config.verbose, timer=tim, dataset1="norm-empty_can", dataset2="background", scale=config.scale_bcn) else: e_som3 = None # Steps 24-25: Subtract background spectrum from normalization spectrum if not config.pre_norm: n_som2 = dr_lib.subtract_bkg_from_data(n_som1, b_som1, verbose=config.verbose, timer=tim, dataset1="normalization", dataset2="background", scale=config.scale_bn) else: n_som2 = n_som1 del b_som1, e_som1, bcs_som, cs_som # Steps 26-27: Subtract empty can spectrum from sample spectrum d_som3 = dr_lib.subtract_bkg_from_data(d_som2, e_som2, verbose=config.verbose, timer=tim, dataset1="data", dataset2="empty_can", scale=config.scale_cs) del d_som2, e_som2 # Steps 28-29: Subtract empty can spectrum from normalization spectrum if not config.pre_norm: n_som3 = dr_lib.subtract_bkg_from_data(n_som2, e_som3, verbose=config.verbose, timer=tim, dataset1="normalization", dataset2="empty_can", scale=config.scale_cn) else: n_som3 = n_som2 del n_som2, e_som3 # Step 30-31: Integrate normalization spectra if config.verbose and n_som3 is not None and not config.pre_norm: print "Integrating normalization spectra" if not config.pre_norm: norm_int = dr_lib.integrate_spectra(n_som3, start=config.norm_start, end=config.norm_end, norm=True) else: norm_int = n_som3 del n_som3 # Step 32: Normalize data by integrated values if config.verbose and norm_int is not None: print "Normalizing data by normalization data" if norm_int is not None: d_som4 = common_lib.div_ncerr(d_som3, norm_int) else: d_som4 = d_som3 if norm_int is not None: if tim is not None: tim.getTime(msg="After normalizing data ") del d_som3, norm_int if config.dump_norm: if tim is not None: tim.getTime(False) hlr_utils.write_file(config.output, "text/Spec", d_som4, output_ext="wvn", data_ext=config.ext_replacement, path_replacement=config.path_replacement, verbose=config.verbose, message="wavelength (vanadium norm) information") if tim is not None: tim.getTime(msg="After writing wavelength (vanadium norm) info ") # Steps 33 to end: Creating S(Q,E) if config.Q_bins is not None: if config.verbose: print "Creating 2D spectrum" if tim is not None: tim.getTime(False) d_som5 = dr_lib.create_E_vs_Q_igs(d_som4, config.E_bins.toNessiList(), config.Q_bins.toNessiList(), so_id="Full Detector", y_label="counts", y_units="counts / (ueV * A^-1)", x_labels=["Q transfer", "energy transfer"], x_units=["1/Angstroms","ueV"], split=config.split, Q_filter=False, configure=config) if tim is not None: tim.getTime(msg="After creation of final spectrum ") del d_som4 # Steps 33 to 36: Create S(-cos(polar), E) elif config.ncospol_bins is not None: if config.verbose: print "Convert wavelength to energy transfer" if tim is not None: tim.getTime(False) d_som4a = dr_lib.energy_transfer(d_som4, "IGS", "Wavelength_final", sa_norm=True, scale=True, change_units=True) if tim is not None: tim.getTime(msg="After wavelength to energy transfer conversion ") del d_som4 if config.verbose: print "Creating 2D spectrum" if tim is not None: tim.getTime(False) d_som5 = dr_lib.create_param_vs_Y(d_som4a, "polar", "negcos_param_array", config.ncospol_bins.toNessiList(), rebin_axis=config.E_bins.toNessiList(), y_label="counts", y_units="counts / ueV", x_labels=["-cos(polar)", "Energy Transfer"], x_units=["", "ueV"]) if tim is not None: tim.getTime(msg="After creation of final spectrum ") # If rescaling factor present, rescale the data if config.rescale_final is not None and not config.split: d_som6 = common_lib.mult_ncerr(d_som5, (config.rescale_final, 0.0)) else: d_som6 = d_som5 if tim is None: old_time = None if not __name__ == "amorphous_reduction_sqe": del d_som5 __write_output(d_som6, config, tim, old_time) else: if config.create_output: del d_som5 __write_output(d_som6, config, tim, old_time) else: return d_som6
def run(config, tim=None): """ This method is where the data reduction process gets done. @param config: Object containing the data reduction configuration information. @type config: L{hlr_utils.Configure} @param tim: (OPTIONAL) Object that will allow the method to perform timing evaluations. @type tim: C{sns_time.DiffTime} """ import common_lib import dr_lib import DST if tim is not None: tim.getTime(False) old_time = tim.getOldTime() if config.data is None: raise RuntimeError("Need to pass a data filename to the driver "\ +"script.") # Read in geometry if one is provided if config.inst_geom is not None: if config.verbose: print "Reading in instrument geometry file" inst_geom_dst = DST.getInstance("application/x-NxsGeom", config.inst_geom) else: inst_geom_dst = None # Perform early background subtraction if the hwfix flag is used if config.hwfix: if not config.mc: so_axis = "time_of_flight" else: so_axis = "Time_of_Flight" bkg_som0 = dr_lib.add_files(config.back, Data_Paths=config.data_paths.toPath(), SO_Axis=so_axis, Signal_ROI=config.roi_file, dataset_type="background", Verbose=config.verbose, Timer=tim) bkg_som = dr_lib.fix_bin_contents(bkg_som0) del bkg_som0 else: bkg_som = None # Perform Steps 1-15 on sample data d_som1 = dr_lib.process_igs_data(config.data, config, timer=tim, inst_geom_dst=inst_geom_dst, tib_const=config.tib_data_const, bkg_som=bkg_som) # Perform Steps 1-15 on empty can data if config.ecan is not None: e_som1 = dr_lib.process_igs_data(config.ecan, config, timer=tim, inst_geom_dst=inst_geom_dst, dataset_type="empty_can", tib_const=config.tib_ecan_const, bkg_som=bkg_som) else: e_som1 = None # Perform Steps 1-15 on normalization data if config.norm is not None: n_som1 = dr_lib.process_igs_data(config.norm, config, timer=tim, inst_geom_dst=inst_geom_dst, dataset_type="normalization", tib_const=config.tib_norm_const, bkg_som=bkg_som) else: n_som1 = None # Perform Steps 1-15 on background data if config.back is not None: b_som1 = dr_lib.process_igs_data(config.back, config, timer=tim, inst_geom_dst=inst_geom_dst, dataset_type="background", tib_const=config.tib_back_const, bkg_som=bkg_som) else: b_som1 = None # Perform Step 1-15 on direct scattering background data if config.dsback is not None: ds_som1 = dr_lib.process_igs_data(config.dsback, config, timer=tim, inst_geom_dst=inst_geom_dst, tib_const=config.tib_dsback_const, dataset_type="dsbackground", bkg_som=bkg_som) # Note: time_zero_slope MUST be a tuple if config.time_zero_slope is not None: ds_som1.attr_list["Time_zero_slope"] = \ config.time_zero_slope.toValErrTuple() # Note: time_zero_offset MUST be a tuple if config.time_zero_offset is not None: ds_som1.attr_list["Time_zero_offset"] = \ config.time_zero_offset.toValErrTuple() # Step 16: Linearly interpolate TOF elastic range in direct scattering # background data # First convert TOF elastic range to appropriate pixel initial # wavelengths if config.verbose: print "Determining initial wavelength range for elastic line" if tim is not None: tim.getTime(False) if config.tof_elastic is None: # Units are in microseconds tof_elastic_range = (140300, 141300) else: tof_elastic_range = config.tof_elastic ctof_elastic_low = dr_lib.convert_single_to_list(\ "tof_to_initial_wavelength_igs_lin_time_zero", (tof_elastic_range[0], 0.0), ds_som1) ctof_elastic_high = dr_lib.convert_single_to_list(\ "tof_to_initial_wavelength_igs_lin_time_zero", (tof_elastic_range[1], 0.0), ds_som1) ctof_elastic_range = [(ctof_elastic_low[i][0], ctof_elastic_high[i][0]) for i in xrange(len(ctof_elastic_low))] if tim is not None: tim.getTime(msg="After calculating initial wavelength range for "\ +"elastic line ") del ctof_elastic_low, ctof_elastic_high if config.split: lambda_filter = [(d_som1[i].axis[0].val[0], d_som1[i].axis[0].val[-1]) for i in xrange(len(d_som1))] else: lambda_filter = None # Now interpolate spectra between TOF elastic range (converted to # initial wavelength) if config.verbose: print "Linearly interpolating direct scattering spectra" if tim is not None: tim.getTime(False) ds_som2 = dr_lib.lin_interpolate_spectra(ds_som1, ctof_elastic_range, filter_axis=lambda_filter) if tim is not None: tim.getTime(msg="After linearly interpolating direct scattering "\ +"spectra ") if config.dump_dslin: ds_som2_1 = dr_lib.sum_all_spectra(ds_som2,\ rebin_axis=config.lambda_bins.toNessiList()) hlr_utils.write_file(config.output, "text/Spec", ds_som2_1, output_ext="lin", data_ext=config.ext_replacement, path_replacement=config.path_replacement, verbose=config.verbose, message="dsbackground linear interpolation") del ds_som2_1 del ds_som1 else: ds_som2 = None if inst_geom_dst is not None: inst_geom_dst.release_resource() # Steps 17-18: Subtract background spectrum from sample spectrum if config.dsback is None: back_som = b_som1 bkg_type = "background" else: back_som = ds_som2 bkg_type = "dsbackground" d_som2 = dr_lib.subtract_bkg_from_data(d_som1, back_som, verbose=config.verbose, timer=tim, dataset1="data", dataset2=bkg_type, scale=config.scale_bs) if config.dsback is not None: del ds_som2 # Step 19: Zero region outside TOF elastic for background for empty can if config.dsback is None: bcs_som = b_som1 cs_som = e_som1 else: if config.verbose and b_som1 is not None: print "Zeroing background spectra" if tim is not None and b_som1 is not None: tim.getTime(False) bcs_som = dr_lib.zero_spectra(b_som1, ctof_elastic_range) if tim is not None and b_som1 is not None: tim.getTime(msg="After zeroing background spectra") if config.verbose and e_som1 is not None: print "Zeroing empty can spectra" if tim is not None and e_som1 is not None: tim.getTime(False) cs_som = dr_lib.zero_spectra(e_som1, ctof_elastic_range) if tim is not None and e_som1 is not None: tim.getTime(msg="After zeroing empty can spectra") del ctof_elastic_range # Steps 20-21: Subtract background spectrum from empty can spectrum e_som2 = dr_lib.subtract_bkg_from_data(cs_som, bcs_som, verbose=config.verbose, timer=tim, dataset1="data-empty_can", dataset2="background", scale=config.scale_bcs) # Steps 22-23: Subtract background spectrum from empty can spectrum for # normalization try: config.pre_norm except AttributeError: config.pre_norm = False if not config.pre_norm: e_som3 = dr_lib.subtract_bkg_from_data(e_som1, b_som1, verbose=config.verbose, timer=tim, dataset1="norm-empty_can", dataset2="background", scale=config.scale_bcn) else: e_som3 = None # Steps 24-25: Subtract background spectrum from normalization spectrum if not config.pre_norm: n_som2 = dr_lib.subtract_bkg_from_data(n_som1, b_som1, verbose=config.verbose, timer=tim, dataset1="normalization", dataset2="background", scale=config.scale_bn) else: n_som2 = n_som1 del b_som1, e_som1, bcs_som, cs_som # Steps 26-27: Subtract empty can spectrum from sample spectrum d_som3 = dr_lib.subtract_bkg_from_data(d_som2, e_som2, verbose=config.verbose, timer=tim, dataset1="data", dataset2="empty_can", scale=config.scale_cs) del d_som2, e_som2 # Steps 28-29: Subtract empty can spectrum from normalization spectrum if not config.pre_norm: n_som3 = dr_lib.subtract_bkg_from_data(n_som2, e_som3, verbose=config.verbose, timer=tim, dataset1="normalization", dataset2="empty_can", scale=config.scale_cn) else: n_som3 = n_som2 del n_som2, e_som3 # Step 30-31: Integrate normalization spectra if config.verbose and n_som3 is not None and not config.pre_norm: print "Integrating normalization spectra" if not config.pre_norm: norm_int = dr_lib.integrate_spectra(n_som3, start=config.norm_start, end=config.norm_end, norm=True) else: norm_int = n_som3 del n_som3 # Step 32: Normalize data by integrated values if config.verbose and norm_int is not None: print "Normalizing data by normalization data" if norm_int is not None: d_som4 = common_lib.div_ncerr(d_som3, norm_int) else: d_som4 = d_som3 if norm_int is not None: if tim is not None: tim.getTime(msg="After normalizing data ") del d_som3, norm_int if config.dump_norm: if tim is not None: tim.getTime(False) hlr_utils.write_file(config.output, "text/Spec", d_som4, output_ext="wvn", data_ext=config.ext_replacement, path_replacement=config.path_replacement, verbose=config.verbose, message="wavelength (vanadium norm) information") if tim is not None: tim.getTime(msg="After writing wavelength (vanadium norm) info ") # Steps 33 to end: Creating S(Q,E) if config.Q_bins is not None: if config.verbose: print "Creating 2D spectrum" if tim is not None: tim.getTime(False) d_som5 = dr_lib.create_E_vs_Q_igs( d_som4, config.E_bins.toNessiList(), config.Q_bins.toNessiList(), so_id="Full Detector", y_label="counts", y_units="counts / (ueV * A^-1)", x_labels=["Q transfer", "energy transfer"], x_units=["1/Angstroms", "ueV"], split=config.split, Q_filter=False, configure=config) if tim is not None: tim.getTime(msg="After creation of final spectrum ") del d_som4 # Steps 33 to 36: Create S(-cos(polar), E) elif config.ncospol_bins is not None: if config.verbose: print "Convert wavelength to energy transfer" if tim is not None: tim.getTime(False) d_som4a = dr_lib.energy_transfer(d_som4, "IGS", "Wavelength_final", sa_norm=True, scale=True, change_units=True) if tim is not None: tim.getTime(msg="After wavelength to energy transfer conversion ") del d_som4 if config.verbose: print "Creating 2D spectrum" if tim is not None: tim.getTime(False) d_som5 = dr_lib.create_param_vs_Y( d_som4a, "polar", "negcos_param_array", config.ncospol_bins.toNessiList(), rebin_axis=config.E_bins.toNessiList(), y_label="counts", y_units="counts / ueV", x_labels=["-cos(polar)", "Energy Transfer"], x_units=["", "ueV"]) if tim is not None: tim.getTime(msg="After creation of final spectrum ") # If rescaling factor present, rescale the data if config.rescale_final is not None and not config.split: d_som6 = common_lib.mult_ncerr(d_som5, (config.rescale_final, 0.0)) else: d_som6 = d_som5 if tim is None: old_time = None if not __name__ == "amorphous_reduction_sqe": del d_som5 __write_output(d_som6, config, tim, old_time) else: if config.create_output: del d_som5 __write_output(d_som6, config, tim, old_time) else: return d_som6