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
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
