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
config.so_axis = "time_of_flight"
# 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 normalization data
n_som1 = dr_lib.calibrate_dgs_data(config.data, config, dc_som,
dataset_type="normalization",
inst_geom_dst=inst_geom_dst,
tib_const=config.tib_const,
cwp=config.cwp_data,
timer=tim)
# Perform Steps 7-16 on normalization data
if config.norm_trans_coeff is None:
norm_trans_coeff = None
else:
norm_trans_coeff = config.norm_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
n_som2 = dr_lib.process_dgs_data(n_som1, config, b_som1, e_som1,
norm_trans_coeff,
dataset_type="normalization",
cwp_used=cwp_used,
timer=tim)
del n_som1, b_som1, e_som1
# Step 17: Integrate normalization spectra
if config.verbose:
print "Integrating normalization spectra"
if tim is not None:
tim.getTime(False)
if config.norm_int_range is None:
start_val = float("inf")
end_val = float("inf")
else:
if not config.wb_norm:
# Translate energy transfer to final energy
ef_start = config.initial_energy.getValue() - \
config.norm_int_range[0]
ef_end = config.initial_energy.getValue() - \
config.norm_int_range[1]
# Convert final energy to final wavelength
start_val = common_lib.energy_to_wavelength((ef_start, 0.0))[0]
end_val = common_lib.energy_to_wavelength((ef_end, 0.0))[0]
else:
start_val = config.norm_int_range[0]
end_val = config.norm_int_range[1]
n_som3 = dr_lib.integrate_spectra(n_som2, start=start_val,
end=end_val, width=True)
del n_som2
if tim is not None:
tim.getTime(msg="After integrating normalization spectra ")
file_comment = "Normalization Integration range: %0.3fA, %0.3fA" \
% (start_val, end_val)
hlr_utils.write_file(config.output, "text/num-info", n_som3,
output_ext="norm",
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
verbose=config.verbose,
message="normalization values",
comments=[file_comment],
tag="Integral", units="counts")
if tim is not None:
tim.getTime(False)
if config.verbose:
print "Making mask file"
# Make mask file from threshold
dr_lib.filter_normalization(n_som3, config.lo_threshold,
config.hi_threshold, config)
if tim is not None:
tim.getTime(msg="After making mask file ")
# Write out RMD file
n_som3.attr_list["config"] = config
hlr_utils.write_file(config.output, "text/rmd", n_som3,
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"
# 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 normalization data
n_som1 = dr_lib.calibrate_dgs_data(
config.data,
config,
dc_som,
dataset_type="normalization",
inst_geom_dst=inst_geom_dst,
tib_const=config.tib_const,
cwp=config.cwp_data,
timer=tim,
)
# Perform Steps 7-16 on normalization data
if config.norm_trans_coeff is None:
norm_trans_coeff = None
else:
norm_trans_coeff = config.norm_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
n_som2 = dr_lib.process_dgs_data(
n_som1, config, b_som1, e_som1, norm_trans_coeff, dataset_type="normalization", cwp_used=cwp_used, timer=tim
)
del n_som1, b_som1, e_som1
# Step 17: Integrate normalization spectra
if config.verbose:
print "Integrating normalization spectra"
if tim is not None:
tim.getTime(False)
if config.norm_int_range is None:
start_val = float("inf")
end_val = float("inf")
else:
if not config.wb_norm:
# Translate energy transfer to final energy
ef_start = config.initial_energy.getValue() - config.norm_int_range[0]
ef_end = config.initial_energy.getValue() - config.norm_int_range[1]
# Convert final energy to final wavelength
start_val = common_lib.energy_to_wavelength((ef_start, 0.0))[0]
end_val = common_lib.energy_to_wavelength((ef_end, 0.0))[0]
else:
start_val = config.norm_int_range[0]
end_val = config.norm_int_range[1]
n_som3 = dr_lib.integrate_spectra(n_som2, start=start_val, end=end_val, width=True)
del n_som2
if tim is not None:
tim.getTime(msg="After integrating normalization spectra ")
file_comment = "Normalization Integration range: %0.3fA, %0.3fA" % (start_val, end_val)
hlr_utils.write_file(
config.output,
"text/num-info",
n_som3,
output_ext="norm",
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
verbose=config.verbose,
message="normalization values",
comments=[file_comment],
tag="Integral",
units="counts",
)
if tim is not None:
tim.getTime(False)
if config.verbose:
print "Making mask file"
# Make mask file from threshold
dr_lib.filter_normalization(n_som3, config.lo_threshold, config.hi_threshold, config)
if tim is not None:
tim.getTime(msg="After making mask file ")
# Write out RMD file
n_som3.attr_list["config"] = config
hlr_utils.write_file(
config.output,
"text/rmd",
n_som3,
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")