def process_sas_data(datalist, conf, **kwargs):
"""
This function combines Steps 1 through 9 of the data reduction process for
Small-Angle Scattering section 2.5.1 as specified by the documents at
U{http://neutrons.ornl.gov/asg/projects/SCL/reqspec/DR_Lib_RS.doc}. The
function takes a list of file names, a L{hlr_utils.Configure} object and
processes the data accordingly. This function should really only be used in
the context of I{sas_reduction}.
@param datalist: A list containing the filenames of the data to be
processed.
@type datalist: C{list} of C{string}s
@param conf: Object that contains the current setup of the driver.
@type conf: L{hlr_utils.Configure}
@param kwargs: A list of keyword arguments that the function accepts:
@keyword inst_geom_dst: File object that contains instrument geometry
information.
@type inst_geom_dst: C{DST.GeomDST}
@keyword dataset_type: The practical name of the dataset being processed.
The default value is I{data}.
@type dataset_type: C{string}
@keyword trans_data: Alternate data for the transmission spectrum. This is
used in the absence of transmission monitors.
@type trans_data: C{string}
@keyword transmission: A flag that signals the function to stop after
doing the conversion from TOF to wavelength. The
default is I{False}.
@type transmission: C{boolean}
@keyword bkg_subtract: A list of coefficients that help determine the
wavelength dependent background subtraction.
@type bkg_subtract: C{list}
@keyword get_background: A flag that signals the function to convert the
main data to wavelength and exit before
normalizing to the beam monitor.
@type get_background: C{boolean}
@keyword acc_down_time: The information for the accelerator downtime.
@type acc_down_time: C{tuple}
@keyword bkg_scale: The scaling used for the axis dependent background
parameters.
@type bkg_scale: C{float}
@keyword timer: Timing object so the function can perform timing estimates.
@type timer: C{sns_timer.DiffTime}
@return: Object that has undergone all requested processing steps
@rtype: C{SOM.SOM}
"""
import common_lib
import dr_lib
import hlr_utils
# Check keywords
try:
dataset_type = kwargs["dataset_type"]
except KeyError:
dataset_type = "data"
try:
i_geom_dst = kwargs["inst_geom_dst"]
except KeyError:
i_geom_dst = None
try:
t = kwargs["timer"]
except KeyError:
t = None
try:
transmission = kwargs["transmission"]
except KeyError:
transmission = False
try:
bkg_subtract = kwargs["bkg_subtract"]
except KeyError:
bkg_subtract = None
try:
trans_data = kwargs["trans_data"]
except KeyError:
trans_data = None
try:
get_background = kwargs["get_background"]
except KeyError:
get_background = False
acc_down_time = kwargs.get("acc_down_time")
bkg_scale = kwargs.get("bkg_scale")
# Add so_axis to Configure object
conf.so_axis = "time_of_flight"
# Step 0: Open appropriate data files
# Data
if conf.verbose:
print "Reading %s file" % dataset_type
# The [0] is to get the data SOM and ignore the None background SOM
dp_som = dr_lib.add_files(datalist, Data_Paths=conf.data_paths.toPath(),
SO_Axis=conf.so_axis, Signal_ROI=conf.roi_file,
dataset_type=dataset_type,
Verbose=conf.verbose, Timer=t)
if t is not None:
t.getTime(msg="After reading %s " % dataset_type)
dp_som1 = dr_lib.fix_bin_contents(dp_som)
del dp_som
if conf.inst_geom is not None:
i_geom_dst.setGeometry(conf.data_paths.toPath(), dp_som1)
if conf.dump_tof_r:
dp_som1_1 = dr_lib.create_param_vs_Y(dp_som1, "radius", "param_array",
conf.r_bins.toNessiList(),
y_label="counts",
y_units="counts / (usec * m)",
x_labels=["Radius", "TOF"],
x_units=["m", "usec"])
hlr_utils.write_file(conf.output, "text/Dave2d", dp_som1_1,
output_ext="tvr",
extra_tag=dataset_type,
verbose=conf.verbose,
data_ext=conf.ext_replacement,
path_replacement=conf.path_replacement,
message="TOF vs radius information")
del dp_som1_1
if conf.dump_tof_theta:
dp_som1_1 = dr_lib.create_param_vs_Y(dp_som1, "polar", "param_array",
conf.theta_bins.toNessiList(),
y_label="counts",
y_units="counts / (usec * rads)",
x_labels=["Polar Angle", "TOF"],
x_units=["rads", "usec"])
hlr_utils.write_file(conf.output, "text/Dave2d", dp_som1_1,
output_ext="tvt",
extra_tag=dataset_type,
verbose=conf.verbose,
data_ext=conf.ext_replacement,
path_replacement=conf.path_replacement,
message="TOF vs polar angle information")
del dp_som1_1
# Beam monitor
if not get_background:
if conf.beammon_over is None:
if conf.verbose:
print "Reading in beam monitor data from %s file" \
% dataset_type
# The [0] is to get the data SOM and ignore the None
# background SOM
dbm_som0 = dr_lib.add_files(datalist,
Data_Paths=conf.bmon_path.toPath(),
SO_Axis=conf.so_axis,
dataset_type=dataset_type,
Verbose=conf.verbose,
Timer=t)
if t is not None:
t.getTime(msg="After reading beam monitor data ")
if conf.inst_geom is not None:
i_geom_dst.setGeometry(conf.bmon_path.toPath(), dbm_som0)
else:
if conf.verbose:
print "Reading in vanadium data"
dbm_som0 = dr_lib.add_files(datalist,
Data_Paths=conf.data_paths.toPath(),
Signal_ROI=conf.roi_file,
SO_Axis=conf.so_axis,
dataset_type=dataset_type,
Verbose=conf.verbose,
Timer=t)
if t is not None:
t.getTime(msg="After reading vanadium data ")
if conf.inst_geom is not None:
i_geom_dst.setGeometry(conf.data_paths.toPath(), dbm_som0)
dbm_som1 = dr_lib.fix_bin_contents(dbm_som0)
del dbm_som0
else:
dbm_som1 = None
# Transmission monitor
if trans_data is None:
if conf.verbose:
print "Reading in transmission monitor data from %s file" \
% dataset_type
try:
dtm_som0 = dr_lib.add_files(datalist,
Data_Paths=conf.tmon_path.toPath(),
SO_Axis=conf.so_axis,
dataset_type=dataset_type,
Verbose=conf.verbose,
Timer=t)
if t is not None:
t.getTime(msg="After reading transmission monitor data ")
if conf.inst_geom is not None:
i_geom_dst.setGeometry(conf.tmon_path.toPath(), dtm_som0)
dtm_som1 = dr_lib.fix_bin_contents(dtm_som0)
del dtm_som0
# Transmission monitor cannot be found
except KeyError:
if conf.verbose:
print "Transmission monitor not found"
dtm_som1 = None
else:
dtm_som1 = None
# Note: time_zero_offset_det MUST be a tuple
if conf.time_zero_offset_det is not None:
dp_som1.attr_list["Time_zero_offset_det"] = \
conf.time_zero_offset_det.toValErrTuple()
# Note: time_zero_offset_mon MUST be a tuple
if conf.time_zero_offset_mon is not None and not get_background and \
conf.beammon_over is None:
dbm_som1.attr_list["Time_zero_offset_mon"] = \
conf.time_zero_offset_mon.toValErrTuple()
if conf.beammon_over is not None:
dbm_som1.attr_list["Time_zero_offset_det"] = \
conf.time_zero_offset_det.toValErrTuple()
if trans_data is None and dtm_som1 is not None:
dtm_som1.attr_list["Time_zero_offset_mon"] = \
conf.time_zero_offset_mon.toValErrTuple()
# Step 1: Convert TOF to wavelength for data and monitor
if conf.verbose:
print "Converting TOF to wavelength"
if t is not None:
t.getTime(False)
if not get_background:
# Convert beam monitor
if conf.beammon_over is None:
dbm_som2 = common_lib.tof_to_wavelength_lin_time_zero(
dbm_som1,
units="microsecond",
time_zero_offset=conf.time_zero_offset_mon.toValErrTuple())
else:
dbm_som2 = common_lib.tof_to_wavelength_lin_time_zero(
dbm_som1,
units="microsecond",
time_zero_offset=conf.time_zero_offset_det.toValErrTuple(),
inst_param="total")
else:
dbm_som2 = None
# Convert detector pixels
dp_som2 = common_lib.tof_to_wavelength_lin_time_zero(
dp_som1,
units="microsecond",
time_zero_offset=conf.time_zero_offset_det.toValErrTuple(),
inst_param="total")
if get_background:
return dp_som2
if dtm_som1 is not None:
# Convert transmission monitor
dtm_som2 = common_lib.tof_to_wavelength_lin_time_zero(
dtm_som1,
units="microsecond",
time_zero_offset=conf.time_zero_offset_mon.toValErrTuple())
else:
dtm_som2 = dtm_som1
if t is not None:
t.getTime(msg="After converting TOF to wavelength ")
del dp_som1, dbm_som1, dtm_som1
if conf.verbose and (conf.lambda_low_cut is not None or \
conf.lambda_high_cut is not None):
print "Cutting data spectra"
if t is not None:
t.getTime(False)
dp_som3 = dr_lib.cut_spectra(dp_som2, conf.lambda_low_cut,
conf.lambda_high_cut)
if t is not None:
t.getTime(msg="After cutting data spectra ")
del dp_som2
if conf.beammon_over is not None:
dbm_som2 = dr_lib.cut_spectra(dbm_som2, conf.lambda_low_cut,
conf.lambda_high_cut)
if conf.dump_wave:
hlr_utils.write_file(conf.output, "text/Spec", dp_som3,
output_ext="pxl",
extra_tag=dataset_type,
verbose=conf.verbose,
data_ext=conf.ext_replacement,
path_replacement=conf.path_replacement,
message="pixel wavelength information")
if conf.dump_bmon_wave:
if conf.beammon_over is None:
hlr_utils.write_file(conf.output, "text/Spec", dbm_som2,
output_ext="bmxl",
extra_tag=dataset_type,
verbose=conf.verbose,
data_ext=conf.ext_replacement,
path_replacement=conf.path_replacement,
message="beam monitor wavelength information")
else:
dbm_som2_1 = dr_lib.sum_by_rebin_frac(dbm_som2,
conf.lambda_bins.toNessiList())
hlr_utils.write_file(conf.output, "text/Spec", dbm_som2_1,
output_ext="bmxl",
extra_tag=dataset_type,
verbose=conf.verbose,
data_ext=conf.ext_replacement,
path_replacement=conf.path_replacement,
message="beam monitor override wavelength "\
+"information")
del dbm_som2_1
# Step 2: Subtract wavelength dependent background if necessary
if conf.verbose and bkg_subtract is not None:
print "Subtracting wavelength dependent background"
if bkg_subtract is not None:
if t is not None:
t.getTime(False)
duration = dp_som3.attr_list["%s-duration" % dataset_type]
scale = duration.getValue() - acc_down_time[0]
dp_som4 = dr_lib.subtract_axis_dep_bkg(dp_som3, bkg_subtract,
old_scale=bkg_scale,
new_scale=scale)
if t is not None:
t.getTime(msg="After subtracting wavelength dependent background ")
else:
dp_som4 = dp_som3
del dp_som3
# Step 3: Efficiency correct beam monitor
if conf.verbose and conf.mon_effc:
print "Efficiency correct beam monitor data"
if t is not None:
t.getTime(False)
if conf.mon_effc:
dbm_som3 = dr_lib.feff_correct_mon(dbm_som2, inst_name=conf.inst,
eff_const=conf.mon_eff_const)
else:
dbm_som3 = dbm_som2
if t is not None and conf.mon_effc:
t.getTime(msg="After efficiency correcting beam monitor ")
if conf.dump_bmon_effc and conf.mon_effc:
hlr_utils.write_file(conf.output, "text/Spec", dbm_som3,
output_ext="bmel",
extra_tag=dataset_type,
verbose=conf.verbose,
data_ext=conf.ext_replacement,
path_replacement=conf.path_replacement,
message="beam monitor wavelength information "\
+"(efficiency)")
del dbm_som2
# Step 4: Efficiency correct transmission monitor
if dtm_som2 is not None:
if conf.verbose and conf.mon_effc:
print "Efficiency correct transmission monitor data"
if t is not None:
t.getTime(False)
if conf.mon_effc:
dtm_som3 = dr_lib.feff_correct_mon(dtm_som2)
else:
dtm_som3 = dtm_som2
else:
dtm_som3 = dtm_som2
if t is not None and conf.mon_effc and dtm_som2 is not None:
t.getTime(msg="After efficiency correcting beam monitor ")
# Step 5: Efficiency correct detector pixels
if conf.det_effc:
if conf.verbose:
print "Calculating detector efficiency"
if t is not None:
t.getTime(False)
det_eff = dr_lib.create_det_eff(dp_som4, inst_name=conf.inst,
eff_scale_const=conf.det_eff_scale_const,
eff_atten_const=conf.det_eff_atten_const)
if t is not None:
t.getTime(msg="After calculating detector efficiency")
if conf.verbose:
print "Applying detector efficiency"
if t is not None:
t.getTime(False)
dp_som5 = common_lib.div_ncerr(dp_som4, det_eff)
if t is not None:
t.getTime(msg="After spplying detector efficiency")
else:
dp_som5 = dp_som4
del dp_som4
# Step 6: Rebin beam monitor axis onto detector pixel axis
if conf.beammon_over is None:
if not conf.no_bmon_norm:
if conf.verbose:
print "Rebin beam monitor axis to detector pixel axis"
if t is not None:
t.getTime(False)
dbm_som4 = dr_lib.rebin_monitor(dbm_som3, dp_som5, rtype="frac")
if t is not None:
t.getTime(msg="After rebinning beam monitor ")
else:
dbm_som4 = dbm_som3
else:
dbm_som4 = dbm_som3
del dbm_som3
if conf.dump_bmon_rebin:
hlr_utils.write_file(conf.output, "text/Spec", dbm_som4,
output_ext="bmrl",
extra_tag=dataset_type,
verbose=conf.verbose,
data_ext=conf.ext_replacement,
path_replacement=conf.path_replacement,
message="beam monitor wavelength information "\
+"(rebinned)")
# Step 7: Normalize data by beam monitor
if not conf.no_bmon_norm:
if conf.verbose:
print "Normalizing data by beam monitor"
if t is not None:
t.getTime(False)
dp_som6 = common_lib.div_ncerr(dp_som5, dbm_som4)
if t is not None:
t.getTime(msg="After normalizing data by beam monitor ")
else:
dp_som6 = dp_som5
del dp_som5
if transmission:
return dp_som6
if conf.dump_wave_bmnorm:
dp_som6_1 = dr_lib.sum_by_rebin_frac(dp_som6,
conf.lambda_bins.toNessiList())
write_message = "combined pixel wavelength information"
write_message += " (beam monitor normalized)"
hlr_utils.write_file(conf.output, "text/Spec", dp_som6_1,
output_ext="pbml",
extra_tag=dataset_type,
verbose=conf.verbose,
data_ext=conf.ext_replacement,
path_replacement=conf.path_replacement,
message=write_message)
del dp_som6_1
if conf.dump_wave_r:
dp_som6_1 = dr_lib.create_param_vs_Y(dp_som6, "radius", "param_array",
conf.r_bins.toNessiList(),
rebin_axis=conf.lambda_bins.toNessiList(),
y_label="counts",
y_units="counts / (Angstrom * m)",
x_labels=["Radius", "Wavelength"],
x_units=["m", "Angstrom"])
hlr_utils.write_file(conf.output, "text/Dave2d", dp_som6_1,
output_ext="lvr",
extra_tag=dataset_type,
verbose=conf.verbose,
data_ext=conf.ext_replacement,
path_replacement=conf.path_replacement,
message="wavelength vs radius information")
del dp_som6_1
if conf.dump_wave_theta:
dp_som6_1 = dr_lib.create_param_vs_Y(dp_som6, "polar", "param_array",
conf.theta_bins.toNessiList(),
rebin_axis=conf.lambda_bins.toNessiList(),
y_label="counts",
y_units="counts / (Angstrom * rads)",
x_labels=["Polar Angle", "Wavelength"],
x_units=["rads", "Angstrom"])
hlr_utils.write_file(conf.output, "text/Dave2d", dp_som6_1,
output_ext="lvt",
extra_tag=dataset_type,
verbose=conf.verbose,
data_ext=conf.ext_replacement,
path_replacement=conf.path_replacement,
message="wavelength vs polar angle information")
del dp_som6_1
# Step 8: Rebin transmission monitor axis onto detector pixel axis
if trans_data is not None:
print "Reading in transmission monitor data from file"
dtm_som3 = dr_lib.add_files([trans_data],
dataset_type=dataset_type,
dst_type="text/Spec",
Verbose=conf.verbose,
Timer=t)
if conf.verbose and dtm_som3 is not None:
print "Rebin transmission monitor axis to detector pixel axis"
if t is not None:
t.getTime(False)
dtm_som4 = dr_lib.rebin_monitor(dtm_som3, dp_som6, rtype="frac")
if t is not None and dtm_som3 is not None:
t.getTime(msg="After rebinning transmission monitor ")
del dtm_som3
# Step 9: Normalize data by transmission monitor
if conf.verbose and dtm_som4 is not None:
print "Normalizing data by transmission monitor"
if t is not None:
t.getTime(False)
if dtm_som4 is not None:
# The transmission spectra derived from sas_tranmission does not have
# the same y information by convention as sample data or a
# tranmission monitor. Therefore, we'll fake it by setting the
# y information from the sample data into the transmission
if trans_data is not None:
dtm_som4.setYLabel(dp_som6.getYLabel())
dtm_som4.setYUnits(dp_som6.getYUnits())
dp_som7 = common_lib.div_ncerr(dp_som6, dtm_som4)
else:
dp_som7 = dp_som6
if t is not None and dtm_som4 is not None:
t.getTime(msg="After normalizing data by transmission monitor ")
del dp_som6
# Step 10: Convert wavelength to Q for data
if conf.verbose:
print "Converting data from wavelength to scalar Q"
if t is not None:
t.getTime(False)
dp_som8 = common_lib.wavelength_to_scalar_Q(dp_som7)
if t is not None:
t.getTime(msg="After converting wavelength to scalar Q ")
del dp_som7
if conf.facility == "LENS":
# Step 11: Apply SAS correction factor to data
if conf.verbose:
print "Applying geometrical correction"
if t is not None:
t.getTime(False)
dp_som9 = dr_lib.apply_sas_correct(dp_som8)
if t is not None:
t.getTime(msg="After applying geometrical correction ")
return dp_som9
else:
return dp_som8
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 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 Steps 1-11 on sample data
d_som1 = dr_lib.process_sas_data(config.data, config, timer=tim,
inst_geom_dst=inst_geom_dst,
bkg_subtract=config.bkg_coeff,
acc_down_time=config.data_acc_down_time.toValErrTuple(),
bkg_scale=config.bkg_scale,
trans_data=config.data_trans)
# Perform Steps 1-11 on buffer/solvent only data
if config.solv is not None:
s_som1 = dr_lib.process_sas_data(config.solv, config, timer=tim,
inst_geom_dst=inst_geom_dst,
dataset_type="solvent",
bkg_subtract=config.bkg_coeff,
acc_down_time=config.solv_acc_down_time.toValErrTuple(),
bkg_scale=config.bkg_scale,
trans_data=config.solv_trans)
else:
s_som1 = None
# Step 12: Subtract buffer/solvent only spectrum from sample spectrum
d_som2 = dr_lib.subtract_bkg_from_data(d_som1, s_som1,
verbose=config.verbose,
timer=tim,
dataset1="data",
dataset2="solvent")
del s_som1, d_som1
# Perform Steps 1-11 on empty-can data
if config.ecan is not None:
e_som1 = dr_lib.process_sas_data(config.ecan, config, timer=tim,
inst_geom_dst=inst_geom_dst,
dataset_type="empty_can",
bkg_subtract=config.bkg_coeff,
acc_down_time=config.ecan_acc_down_time.toValErrTuple(),
bkg_scale=config.bkg_scale,
trans_data=config.ecan_trans)
else:
e_som1 = None
# Step 13: Subtract empty-can spectrum from sample spectrum
d_som3 = dr_lib.subtract_bkg_from_data(d_som2, e_som1,
verbose=config.verbose,
timer=tim,
dataset1="data",
dataset2="empty_can")
del e_som1, d_som2
# Perform Steps 1-11 on open beam data
if config.open is not None:
o_som1 = dr_lib.process_sas_data(config.open, config, timer=tim,
inst_geom_dst=inst_geom_dst,
dataset_type="open_beam",
bkg_subtract=config.bkg_coeff,
acc_down_time=config.open_acc_down_time.toValErrTuple(),
bkg_scale=config.bkg_scale)
else:
o_som1 = None
# Step 14: Subtract open beam spectrum from sample spectrum
d_som4 = dr_lib.subtract_bkg_from_data(d_som3, o_som1,
verbose=config.verbose,
timer=tim,
dataset1="data",
dataset2="open_beam")
del o_som1, d_som3
# Perform Steps 1-11 on dark current data
if config.dkcur is not None:
dc_som1 = dr_lib.process_sas_data(config.open, config, timer=tim,
inst_geom_dst=inst_geom_dst,
dataset_type="dark_current",
bkg_subtract=config.bkg_coeff)
else:
dc_som1 = None
# Step 15: Subtract dark current spectrum from sample spectrum
d_som5 = dr_lib.subtract_bkg_from_data(d_som4, dc_som1,
verbose=config.verbose,
timer=tim,
dataset1="data",
dataset2="dark_current")
del dc_som1, d_som4
# Create 2D distributions is necessary
if config.dump_Q_r:
d_som5_1 = dr_lib.create_param_vs_Y(d_som5, "radius", "param_array",
config.r_bins.toNessiList(),
rebin_axis=config.Q_bins.toNessiList(),
binnorm=True,
y_label="S",
y_units="Counts / A^-1 m",
x_labels=["Radius", "Q"],
x_units=["m", "1/Angstroms"])
hlr_utils.write_file(config.output, "text/Dave2d", d_som5_1,
output_ext="qvr", verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="S(r, Q) information")
del d_som5_1
if config.dump_Q_theta:
d_som5_1 = dr_lib.create_param_vs_Y(d_som5, "polar", "param_array",
config.theta_bins.toNessiList(),
rebin_axis=config.Q_bins.toNessiList(),
binnorm=True,
y_label="S",
y_units="Counts / A^-1 rads",
x_labels=["Polar Angle", "Q"],
x_units=["rads", "1/Angstroms"])
hlr_utils.write_file(config.output, "text/Dave2d", d_som5_1,
output_ext="qvt", verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="S(theta, Q) information")
del d_som5_1
# Steps 16 and 17: Rebin and sum all spectra
if config.verbose:
print "Rebinning and summing for final spectrum"
if tim is not None:
tim.getTime(False)
if config.dump_frac_rebin:
set_conf = config
else:
set_conf = None
d_som6 = dr_lib.sum_by_rebin_frac(d_som5, config.Q_bins.toNessiList(),
configure=set_conf)
if tim is not None:
tim.getTime(msg="After rebinning and summing for spectrum")
del d_som5
if config.facility == "LENS":
# Step 18: Scale final spectrum by Q bin centers
if config.verbose:
print "Scaling final spectrum by Q centers"
if tim is not None:
tim.getTime(False)
d_som7 = dr_lib.fix_bin_contents(d_som6, scale=True, width=True,
units="1/Angstroms")
if tim is not None:
tim.getTime(msg="After scaling final spectrum")
else:
d_som7 = d_som6
del d_som6
# If rescaling factor present, rescale the data
if config.rescale_final is not None:
import common_lib
d_som8 = common_lib.mult_ncerr(d_som7, (config.rescale_final, 0.0))
else:
d_som8 = d_som7
del d_som7
hlr_utils.write_file(config.output, "text/Spec", d_som8,
verbose=config.verbose,
replace_path=False,
replace_ext=False,
message="combined S(Q) information")
# Create 1D canSAS file
hlr_utils.write_file(config.output, "text/canSAS", d_som8,
verbose=config.verbose,
output_ext="xml",
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="combined S(Q) information")
d_som8.attr_list["config"] = config
hlr_utils.write_file(config.output, "text/rmd", d_som8,
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
