def SmhrConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{SmhrOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.SmhrOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{SmhrOptions}
@type options: C{Option}
@param args: The parsed arguments from C{SmhrOptions}
@type args: C{list}
"""
# Call the configuration setter for RefOptions
hlr_ref_options.RefConfiguration(parser, configure, options, args)
# Set the beam divergence calculation flag
if hlr_utils.cli_provide_override(configure, "beamdiv_corr",
"--beamdiv-corr"):
configure.beamdiv_corr = options.beamdiv_corr
# Set the detector spatial resolution
if hlr_utils.cli_provide_override(configure, "det_spat_res",
"--det-spat-res"):
if options.det_spat_res is None:
configure.det_spat_res = options.det_spat_res
else:
# Set this to half its values for the acceptance polygon
# and convert units to meters
configure.det_spat_res = 0.5 * options.det_spat_res * 1.0e-3
# Set the center pixel for the beam divergence calculation
if hlr_utils.cli_provide_override(configure, "center_pix", "--center-pix"):
configure.center_pix = options.center_pix
# Set the number of bins to clean from a cut spectra
if hlr_utils.cli_provide_override(configure, "num_bins_clean",
"--num-bins-clean"):
configure.num_bins_clean = options.num_bins_clean
)
parser.set_defaults(acc_down_time="0.0,0.0,seconds")
parser.add_option("", "--timing", action="store_true", dest="timing", help="Flag to turn on timing of code")
parser.set_defaults(timing=False)
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for SansOptions
hlr_utils.SansConfiguration(parser, configure, options, args)
# Set the accelerator down time
if hlr_utils.cli_provide_override(configure, "acc_down_time", "--acc-down-time"):
configure.acc_down_time = hlr_utils.DrParameterFromString(options.acc_down_time, True)
if configure.lambda_bins is None:
parser.error("Please specify the final wavelength axis!")
# Set timer object if timing option is used
if options.timing:
import sns_timing
timer = sns_timing.DiffTime()
else:
timer = None
# Run the program
run(configure, timer)
parser.set_defaults(wb_norm=False)
parser.add_option("", "--timing", action="store_true", dest="timing",
help="Flag to turn on timing of code")
parser.set_defaults(timing=False)
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for DgsOptions
hlr_utils.DgsConfiguration(parser, configure, options, args)
# Set the high threshold value
if hlr_utils.cli_provide_override(configure, "hi_threshold",
"--hi-threshold"):
configure.hi_threshold = options.hi_threshold
# Set the low threshold value
if hlr_utils.cli_provide_override(configure, "lo_threshold",
"--lo-threshold"):
configure.lo_threshold = options.lo_threshold
# Set the white-beam normalization option
if hlr_utils.cli_provide_override(configure, "wb_norm", "--wb-norm"):
configure.wb_norm = options.wb_norm
# Set timer object if timing option is used
if options.timing:
import sns_timing
timer = sns_timing.DiffTime()
def DgsConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{DgsOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.DgsOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{DgsOptions}
@type options: C{Option}
@param args: The parsed arguments from C{DgsOptions}
@type args: C{list}
"""
# Call the configuration setter for InstOptions
hlr_options.InstConfiguration(parser, configure, options, args, inst="DGS")
# Set the upstream monitor path
if hlr_utils.cli_provide_override(configure, "usmon_path", "--usmon-path"):
configure.usmon_path = hlr_utils.NxPath(options.usmon_path)
# Set the downstream monitor path
if hlr_utils.cli_provide_override(configure, "dsmon_path", "--dsmon-path"):
configure.dsmon_path = hlr_utils.NxPath(options.dsmon_path)
# Set the ROI file
if hlr_utils.cli_provide_override(configure, "roi_file", "--roi-file"):
configure.roi_file = hlr_utils.determine_files(options.roi_file,
one_file=True)
# Set the minimum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_min",
"--tof-cut-min"):
configure.tof_cut_min = options.tof_cut_min
# Set the maximum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_max",
"--tof-cut-max"):
configure.tof_cut_max = options.tof_cut_max
# Set a time-independent background subtraction constant
if hlr_utils.cli_provide_override(configure, "tib_const", "--tib-const"):
configure.tib_const = hlr_utils.DrParameterFromString(\
options.tib_const, True)
# Set the TOF range for the time-independent background determination
if hlr_utils.cli_provide_override(configure, "tib_range", "--tib-range"):
configure.tib_range = options.tib_range
# Stop is both TIB methods are used
if configure.tib_const is not None and configure.tib_range is not None:
parser.error("Please use either --tib-const or --tib-range")
# Set the chopper phase corrections for sample data
if hlr_utils.cli_provide_override(configure, "cwp_data", "--cwp-data"):
if options.cwp_data is not None:
configure.cwp_data = [float(x) \
for x in options.cwp_data.split(',')]
if len(configure.data) != len(configure.cwp_data):
parser.error("Need the same number of chopper phase "\
+"corrections as sample data runs!")
else:
configure.cwp_data = options.cwp_data
# Set the chopper phase corrections for empty can data
if hlr_utils.cli_provide_override(configure, "cwp_ecan", "--cwp-ecan"):
if options.cwp_ecan is not None:
configure.cwp_ecan = [float(x) \
for x in options.cwp_ecan.split(',')]
if len(configure.ecan) != len(configure.cwp_ecan):
parser.error("Need the same number of chopper phase "\
+"corrections as empty can data runs!")
else:
configure.cwp_ecan = options.cwp_ecan
# Set the chopper phase corrections for black can data
if hlr_utils.cli_provide_override(configure, "cwp_bcan", "--cwp-bcan"):
if options.cwp_bcan is not None:
configure.cwp_bcan = [float(x) \
for x in options.cwp_bcan.split(',')]
if len(configure.bcan) != len(configure.cwp_bcan):
parser.error("Need the same number of chopper phase "\
+"corrections as black can data runs!")
else:
configure.cwp_bcan = options.cwp_bcan
# Set the initial energy
if hlr_utils.cli_provide_override(configure, "initial_energy",
"--initial-energy"):
configure.initial_energy = hlr_utils.DrParameterFromString(\
options.initial_energy, True)
# Set the time-zero offset
if hlr_utils.cli_provide_override(configure, "time_zero_offset",
"--time-zero-offset"):
configure.time_zero_offset = hlr_utils.DrParameterFromString(\
options.time_zero_offset, True)
# Set no_mon_norm flag
if hlr_utils.cli_provide_override(configure, "no_mon_norm",
"--no-mon-norm"):
configure.no_mon_norm = options.no_mon_norm
# Set proton charge normalization flag
if hlr_utils.cli_provide_override(configure, "pc_norm",
"--pc-norm"):
configure.pc_norm = options.pc_norm
# Set the proton charge scaling parameter
if hlr_utils.cli_provide_override(configure, "scale_pc", "--scale-pc"):
configure.scale_pc = options.scale_pc
# Set the TOF range for the monitor integration
if hlr_utils.cli_provide_override(configure, "mon_int_range",
"--mon-int-range"):
configure.mon_int_range = options.mon_int_range
# Set the detector efficiency. This can be a tuple (one number for all
# pixels) or a file containing numbers for all pixels.
if hlr_utils.cli_provide_override(configure, "det_eff", "--det-eff"):
try:
configure.det_eff = hlr_utils.DrParameterFromString(\
options.det_eff, True)
except RuntimeError:
configure.det_eff = hlr_utils.determine_files(options.det_eff,
one_file=True)
# Set the transmission coefficient for the sample data background
if hlr_utils.cli_provide_override(configure, "data_trans_coeff",
"--data-trans-coeff"):
configure.data_trans_coeff = hlr_utils.DrParameterFromString(\
options.data_trans_coeff, True)
# Set the transmission coefficient for the normalization background
if hlr_utils.cli_provide_override(configure, "norm_trans_coeff",
"--norm-trans-coeff"):
configure.norm_trans_coeff = hlr_utils.DrParameterFromString(\
options.norm_trans_coeff, True)
# Set the wavelength range for the vanadium normalization integration
if hlr_utils.cli_provide_override(configure, "norm_int_range",
"--norm-int-range"):
configure.norm_int_range = options.norm_int_range
# Set the wavelength bins
if hlr_utils.cli_provide_override(configure, "lambda_bins",
"--lambda-bins"):
configure.lambda_bins = hlr_utils.AxisFromString(options.lambda_bins)
# Set the ability to dump the combined calibrated TOF information
if hlr_utils.cli_provide_override(configure, "dump_ctof_comb",
"--dump-ctof-comb"):
configure.dump_ctof_comb = options.dump_ctof_comb
# Set the ability to dump the combined final wavelength information
if hlr_utils.cli_provide_override(configure, "dump_wave_comb",
"--dump-wave-comb"):
configure.dump_wave_comb = options.dump_wave_comb
# Set the ability to dump the time-independent background information
if hlr_utils.cli_provide_override(configure, "dump_tib", "--dump-tib"):
configure.dump_tib = options.dump_tib
parser.set_defaults(dump_ecell_rtof=False)
parser.add_option("", "--timing", action="store_true", dest="timing",
help="Flag to turn on timing of code")
parser.set_defaults(timing=False)
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for RefRedOptions
hlr_utils.RefConfiguration(parser, configure, options, args)
# Setup the empty cell file list
if hlr_utils.cli_provide_override(configure, "ecell", "--ecell"):
configure.ecell = hlr_utils.determine_files(options.ecell,
configure.inst,
configure.facility)
# If empty cell subtraction is desired, turn off standard background
# subtraction
if configure.ecell is not None:
configure.no_bkg = True
# Setup the substrate transmission coefficients
if hlr_utils.cli_provide_override(configure, "subtrans_coeff",
"--subtrans-coeff"):
configure.subtrans_coeff = options.subtrans_coeff
# Setup the substrate diameter parameter
)
parser.set_defaults(dump_ecell_rtof=False)
parser.add_option("", "--timing", action="store_true", dest="timing", help="Flag to turn on timing of code")
parser.set_defaults(timing=False)
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for RefRedOptions
hlr_utils.RefConfiguration(parser, configure, options, args)
# Setup the empty cell file list
if hlr_utils.cli_provide_override(configure, "ecell", "--ecell"):
configure.ecell = hlr_utils.determine_files(options.ecell, configure.inst, configure.facility)
# If empty cell subtraction is desired, turn off standard background
# subtraction
if configure.ecell is not None:
configure.no_bkg = True
# Setup the substrate transmission coefficients
if hlr_utils.cli_provide_override(configure, "subtrans_coeff", "--subtrans-coeff"):
configure.subtrans_coeff = options.subtrans_coeff
# Setup the substrate diameter parameter
if hlr_utils.cli_provide_override(configure, "substrate_diam", "--substrate-diam"):
configure.substrate_diam = options.substrate_diam
parser.set_defaults(dump_sxl=False)
parser.add_option("-w", "--width", action="store_true", dest="width",
help="Flag to divide the TOF histogram by the bin width")
parser.set_defaults(width=False)
(options, args) = parser.parse_args()
# set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for InstOptions
hlr_utils.InstConfiguration(parser, configure, options, args)
# Set the ROI file
if hlr_utils.cli_provide_override(configure, "roi_file", "--roi-file"):
configure.roi_file = hlr_utils.determine_files(options.roi_file,
one_file=True)
# set the starting ids
if hlr_utils.cli_provide_override(configure, "starting_ids",
"--starting-ids"):
if options.starting_ids is not None:
configure.starting_ids = hlr_utils.create_id_pairs(\
options.starting_ids,\
options.data_paths)
else:
configure.starting_ids = options.starting_ids
# set the ending ids
if hlr_utils.cli_provide_override(configure, "ending_ids", "--ending-ids"):
"--timing",
action="store_true",
dest="timing",
help="Flag to turn on timing of code")
parser.set_defaults(timing=False)
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for SansOptions
hlr_utils.SansConfiguration(parser, configure, options, args)
# Set the background file list
if hlr_utils.cli_provide_override(configure, "back", "--back"):
configure.back = hlr_utils.determine_files(options.back,
configure.inst,
configure.facility)
if configure.lambda_bins is None:
parser.error("Please specify the final wavelength axis!")
# Turn off monitor and detector efficiencies if transmission background is
# present
if configure.back is not None:
if configure.mon_effc:
configure.mon_effc = False
if configure.det_effc:
configure.det_effc = False
def BasicConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{BasicOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.BasicOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{BasicOptions}
@type options: C{Option}
@param args: The parsed arguments from C{BasicOptions}
@type args: C{list}
"""
# Set from a configuration file first
if options.config is not None:
import xml.dom.minidom
conf_doc = xml.dom.minidom.parse(options.config)
configure = hlr_utils.ConfigFromXml(conf_doc, configure)
# Now override options provided on command-line
# Set the verbosity, if present on command-line
if not configure.verbose:
configure.verbose = options.verbose
else:
# Got the verbosity from the config file, but check CLI
if hlr_utils.cli_checker("-v", "-q"):
# Override option
configure.verbose = options.verbose
else:
# No flags present, do nothing
pass
# Define instrument short name first as stuff below depends on it
if hlr_utils.cli_provide_override(configure, "inst", "--inst"):
configure.inst = options.inst
# Define facility short name as stuff below depends on it
if hlr_utils.cli_provide_override(configure, "facility", "--facility"):
configure.facility = options.facility
# Define proposal as stuff below depends on it.
if hlr_utils.cli_provide_override(configure, "proposal", "--proposal"):
configure.proposal = options.proposal
# Get the datafile name and check it
if options.data is not None:
configure.data = hlr_utils.determine_files(options.data,
configure.inst,
configure.facility,
configure.proposal,
stop_on_none=True)
elif len(args) > 0:
configure.data = hlr_utils.determine_files(args, configure.inst,
configure.facility,
configure.proposal,
stop_on_none=True)
elif configure.data:
# We have data from the config file, so everything is OK.
pass
else:
parser.error("Did not specify a datafile")
import os
# Deal with file or directory from output option
if options.output:
filepath = hlr_utils.fix_filename(options.output)
if os.path.exists(filepath):
if os.path.isdir(filepath):
outfile = os.path.basename(configure.data[0])
path = os.path.join(filepath, outfile)
configure.output = hlr_utils.ext_replace(path, "nxs", "txt")
configure.path_replacement = filepath
configure.ext_replacement = "txt"
elif os.path.isfile(filepath):
configure.output = filepath
configure.path_replacement = os.path.dirname(filepath)
configure.ext_replacement = filepath.split('.')[-1]
else:
parser.error("Cannot handle %s in output option" % filepath)
else:
# Assume that this is a file and hope that the directory exists
directory = os.path.dirname(filepath)
if directory != "":
if not os.path.exists(directory):
raise RuntimeError("The directory %s must exist!" \
% directory)
else:
pass
else:
directory = None
configure.output = filepath
configure.path_replacement = directory
configure.ext_replacement = filepath.split('.')[-1]
elif configure.output:
# We have an output file, so no need to do anything else
try:
configure.path_replacement
except AttributeError:
configure.path_replacement = None
# Create the output file name if there isn't one supplied
else:
outfile = os.path.basename(configure.data[0])
path = os.path.join(os.getcwd(), outfile)
configure.output = hlr_utils.ext_replace(path, "nxs", "txt")
configure.path_replacement = None
configure.ext_replacement = "txt"
if configure.verbose and options.output:
print "Using %s as output file" % configure.output
def DgsRedConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{DgsRedOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.DgsRedOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{DgsRedOptions}
@type options: C{Option}
@param args: The parsed arguments from C{DgsRedOptions}
@type args: C{list}
"""
# Call the configuration setter for DgsOptions
hlr_dgs_options.DgsConfiguration(parser, configure, options, args)
# Set the mask file
if hlr_utils.cli_provide_override(configure, "mask_file", "--mask-file"):
configure.mask_file = hlr_utils.determine_files(options.mask_file)
# Set the corner geometry information file
if hlr_utils.cli_provide_override(configure, "corner_geom",
"--corner-geom"):
configure.corner_geom = options.corner_geom
if configure.corner_geom is None:
parser.error("You must provide a corner geometry file via the "\
+"corner-geom option!")
# Set the lambda ratio flag
if hlr_utils.cli_provide_override(configure, "lambda_ratio",
"--lambda-ratio"):
configure.lambda_ratio = options.lambda_ratio
# Set the flag for making the phonon density of states representation
if hlr_utils.cli_provide_override(configure, "pdos_Q", "--pdos-Q"):
configure.pdos_Q = options.pdos_Q
# Set the Debye-Waller constant for the phonon DOS representation
if hlr_utils.cli_provide_override(configure, "debye_waller",
"--debye-waller"):
configure.debye_waller = hlr_utils.DrParameterFromString(\
options.debye_waller)
else:
configure.debye_waller = options.debye_waller
# Set the energy transfer bins
if hlr_utils.cli_provide_override(configure, "E_bins", "--energy-bins"):
configure.E_bins = hlr_utils.AxisFromString(options.E_bins)
if configure.E_bins is None:
parser.error("You must provide energy transfer binning via the "\
+"energy-bins option")
# Set the momentum transfer bins
if hlr_utils.cli_provide_override(configure, "Q_bins", "--mom-trans-bins"):
configure.Q_bins = hlr_utils.AxisFromString(options.Q_bins)
if configure.Q_bins is None:
parser.error("You must provide momentum transfer binning via the "\
+"mom-trans-bins option")
# Set the ability to write SPE and PHX files instead of S(Q, E) dist
if hlr_utils.cli_provide_override(configure, "make_spe", "--make_spe"):
configure.make_spe = options.make_spe
# Set the ability to create the Q vector meshes for each energy slice
if hlr_utils.cli_provide_override(configure, "qmesh", "--qmesh", "-m"):
configure.qmesh = options.qmesh
# Set the ability to write out fixed grid mesh files
if hlr_utils.cli_provide_override(configure, "fixed", "--fixed", "-x"):
configure.fixed = options.fixed
# Set the ability to turn off zero suppression for single crystal data
if hlr_utils.cli_provide_override(configure, "no_zero_supp",
"--no-zero-supp"):
configure.no_zero_supp = options.no_zero_supp
# Set the ability to dump the combined energy transfer information
if hlr_utils.cli_provide_override(configure, "dump_et_comb",
"--dump-et-comb"):
configure.dump_et_comb = options.dump_et_comb
if hlr_utils.cli_provide_override(configure, "split", "--split"):
configure.split = options.split
parser.remove_option("--ncos-polar-bins")
# This one is handled by the loop
parser.remove_option("--ldb-const")
# Block the rescaling as this causes havoc with the looping
parser.remove_option("--rescale-final")
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for AmrOptions
hlr_utils.AmrConfiguration(parser, configure, options, args)
# Set the positive and negative energy transfer axis integration ranges
if hlr_utils.cli_provide_override(configure, "et_int_range",
"--et-int-range"):
configure.et_int_range = hlr_utils.AxisFromString(options.et_int_range)
configure.et_pos_range = (configure.et_int_range.getMinimum(),
configure.et_int_range.getMaximum())
configure.et_neg_range = (-1.0 * configure.et_int_range.getMaximum(),
-1.0 * configure.et_int_range.getMinimum())
# Capture final energy binning
configure.final_E_bins = configure.E_bins
# Reset energy transfer axis to [-E_t_max, E_t_max]
configure.E_bins = hlr_utils.Axis(
-1.0 * configure.et_int_range.getMaximum(),
configure.et_int_range.getMaximum(), configure.et_int_range.getDelta())
)
parser.set_defaults(wb_norm=False)
parser.add_option("", "--timing", action="store_true", dest="timing", help="Flag to turn on timing of code")
parser.set_defaults(timing=False)
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for DgsOptions
hlr_utils.DgsConfiguration(parser, configure, options, args)
# Set the high threshold value
if hlr_utils.cli_provide_override(configure, "hi_threshold", "--hi-threshold"):
configure.hi_threshold = options.hi_threshold
# Set the low threshold value
if hlr_utils.cli_provide_override(configure, "lo_threshold", "--lo-threshold"):
configure.lo_threshold = options.lo_threshold
# Set the white-beam normalization option
if hlr_utils.cli_provide_override(configure, "wb_norm", "--wb-norm"):
configure.wb_norm = options.wb_norm
# Set timer object if timing option is used
if options.timing:
import sns_timing
timer = sns_timing.DiffTime()
def DgsConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{DgsOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.DgsOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{DgsOptions}
@type options: C{Option}
@param args: The parsed arguments from C{DgsOptions}
@type args: C{list}
"""
# Call the configuration setter for InstOptions
hlr_options.InstConfiguration(parser, configure, options, args, inst="DGS")
# Set the upstream monitor path
if hlr_utils.cli_provide_override(configure, "usmon_path", "--usmon-path"):
configure.usmon_path = hlr_utils.NxPath(options.usmon_path)
# Set the downstream monitor path
if hlr_utils.cli_provide_override(configure, "dsmon_path", "--dsmon-path"):
configure.dsmon_path = hlr_utils.NxPath(options.dsmon_path)
# Set the ROI file
if hlr_utils.cli_provide_override(configure, "roi_file", "--roi-file"):
configure.roi_file = hlr_utils.determine_files(options.roi_file, one_file=True)
# Set the minimum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_min", "--tof-cut-min"):
configure.tof_cut_min = options.tof_cut_min
# Set the maximum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_max", "--tof-cut-max"):
configure.tof_cut_max = options.tof_cut_max
# Set a time-independent background subtraction constant
if hlr_utils.cli_provide_override(configure, "tib_const", "--tib-const"):
configure.tib_const = hlr_utils.DrParameterFromString(options.tib_const, True)
# Set the TOF range for the time-independent background determination
if hlr_utils.cli_provide_override(configure, "tib_range", "--tib-range"):
configure.tib_range = options.tib_range
# Stop is both TIB methods are used
if configure.tib_const is not None and configure.tib_range is not None:
parser.error("Please use either --tib-const or --tib-range")
# Set the chopper phase corrections for sample data
if hlr_utils.cli_provide_override(configure, "cwp_data", "--cwp-data"):
if options.cwp_data is not None:
configure.cwp_data = [float(x) for x in options.cwp_data.split(",")]
if len(configure.data) != len(configure.cwp_data):
parser.error("Need the same number of chopper phase " + "corrections as sample data runs!")
else:
configure.cwp_data = options.cwp_data
# Set the chopper phase corrections for empty can data
if hlr_utils.cli_provide_override(configure, "cwp_ecan", "--cwp-ecan"):
if options.cwp_ecan is not None:
configure.cwp_ecan = [float(x) for x in options.cwp_ecan.split(",")]
if len(configure.ecan) != len(configure.cwp_ecan):
parser.error("Need the same number of chopper phase " + "corrections as empty can data runs!")
else:
configure.cwp_ecan = options.cwp_ecan
# Set the chopper phase corrections for black can data
if hlr_utils.cli_provide_override(configure, "cwp_bcan", "--cwp-bcan"):
if options.cwp_bcan is not None:
configure.cwp_bcan = [float(x) for x in options.cwp_bcan.split(",")]
if len(configure.bcan) != len(configure.cwp_bcan):
parser.error("Need the same number of chopper phase " + "corrections as black can data runs!")
else:
configure.cwp_bcan = options.cwp_bcan
# Set the initial energy
if hlr_utils.cli_provide_override(configure, "initial_energy", "--initial-energy"):
configure.initial_energy = hlr_utils.DrParameterFromString(options.initial_energy, True)
# Set the time-zero offset
if hlr_utils.cli_provide_override(configure, "time_zero_offset", "--time-zero-offset"):
configure.time_zero_offset = hlr_utils.DrParameterFromString(options.time_zero_offset, True)
# Set no_mon_norm flag
if hlr_utils.cli_provide_override(configure, "no_mon_norm", "--no-mon-norm"):
configure.no_mon_norm = options.no_mon_norm
# Set proton charge normalization flag
if hlr_utils.cli_provide_override(configure, "pc_norm", "--pc-norm"):
configure.pc_norm = options.pc_norm
# Set the proton charge scaling parameter
if hlr_utils.cli_provide_override(configure, "scale_pc", "--scale-pc"):
configure.scale_pc = options.scale_pc
# Set the TOF range for the monitor integration
if hlr_utils.cli_provide_override(configure, "mon_int_range", "--mon-int-range"):
configure.mon_int_range = options.mon_int_range
# Set the detector efficiency. This can be a tuple (one number for all
# pixels) or a file containing numbers for all pixels.
if hlr_utils.cli_provide_override(configure, "det_eff", "--det-eff"):
try:
configure.det_eff = hlr_utils.DrParameterFromString(options.det_eff, True)
except RuntimeError:
configure.det_eff = hlr_utils.determine_files(options.det_eff, one_file=True)
# Set the transmission coefficient for the sample data background
if hlr_utils.cli_provide_override(configure, "data_trans_coeff", "--data-trans-coeff"):
configure.data_trans_coeff = hlr_utils.DrParameterFromString(options.data_trans_coeff, True)
# Set the transmission coefficient for the normalization background
if hlr_utils.cli_provide_override(configure, "norm_trans_coeff", "--norm-trans-coeff"):
configure.norm_trans_coeff = hlr_utils.DrParameterFromString(options.norm_trans_coeff, True)
# Set the wavelength range for the vanadium normalization integration
if hlr_utils.cli_provide_override(configure, "norm_int_range", "--norm-int-range"):
configure.norm_int_range = options.norm_int_range
# Set the wavelength bins
if hlr_utils.cli_provide_override(configure, "lambda_bins", "--lambda-bins"):
configure.lambda_bins = hlr_utils.AxisFromString(options.lambda_bins)
# Set the ability to dump the combined calibrated TOF information
if hlr_utils.cli_provide_override(configure, "dump_ctof_comb", "--dump-ctof-comb"):
configure.dump_ctof_comb = options.dump_ctof_comb
# Set the ability to dump the combined final wavelength information
if hlr_utils.cli_provide_override(configure, "dump_wave_comb", "--dump-wave-comb"):
configure.dump_wave_comb = options.dump_wave_comb
# Set the ability to dump the time-independent background information
if hlr_utils.cli_provide_override(configure, "dump_tib", "--dump-tib"):
configure.dump_tib = options.dump_tib
def AmrConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{AmrOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.AmrOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{AmrOptions}
@type options: C{Option}
@param args: The parsed arguments from C{AmrOptions}
@type args: C{list}
"""
# Call the configuration setter for IgsOptions
hlr_igs_options.IgsConfiguration(parser, configure, options, args)
# Set the monitor efficiency (tuple)
if hlr_utils.cli_provide_override(configure, "mon_eff", "--mon-eff"):
configure.mon_eff = hlr_utils.DrParameterFromString(options.mon_eff,
True)
# Set the detector efficiency. This can be a tuple (one number for all
# pixels) or a file containing numbers for all pixels.
if hlr_utils.cli_provide_override(configure, "det_eff", "--det-eff"):
try:
configure.det_eff = hlr_utils.DrParameterFromString(\
options.det_eff, True)
except ValueError:
configure.det_eff = hlr_utils.determine_files(options.det_eff,
one_file=True)
# Set the energy transfer bins
if hlr_utils.cli_provide_override(configure, "E_bins", "--energy-bins"):
configure.E_bins = hlr_utils.AxisFromString(options.E_bins)
if configure.E_bins is None:
parser.error("You must provide energy transfer binning via the "\
+"energy-bins option")
# Set the momentum transfer bins
if hlr_utils.cli_provide_override(configure, "Q_bins", "--mom-trans-bins"):
configure.Q_bins = hlr_utils.AxisFromString(options.Q_bins)
# Set the negative cosine polar angle bins
if hlr_utils.cli_provide_override(configure, "ncospol_bins",
"--ncos-polar-bins"):
configure.ncospol_bins = hlr_utils.AxisFromString(options.ncospol_bins)
# Make sure only momentum transfer or negative cosine polar binning is set
if (configure.Q_bins is not None and \
configure.ncospol_bins is not None) or \
(configure.Q_bins is None and configure.ncospol_bins is None):
parser.error("Please specify either --mom-trans-bins or "\
+"--ncos-polar-bins")
# Set the final data rescaling constant
if hlr_utils.cli_provide_override(configure, "rescale_final",
"--rescale-final"):
try:
configure.rescale_final = float(options.rescale_final)
except TypeError:
configure.rescale_final = options.rescale_final
# Set the scaling of the S(Q,E) distribution by the solid angle
# distribution
if hlr_utils.cli_provide_override(configure, "scale_sqe", "--scale-sqe"):
configure.scale_sqe = options.scale_sqe
# Set the lambda-dependent background constant for data
if hlr_utils.cli_provide_override(configure, "ldb_const", "--ldb-const"):
configure.ldb_const = hlr_utils.DrParameterFromString(\
options.ldb_const, True)
# Set the TOF least background channel
if hlr_utils.cli_provide_override(configure, "tof_least_bkg",
"--tof-least-bkg"):
configure.tof_least_bkg = hlr_utils.DrParameterFromString(\
options.tof_least_bkg, True)
# Set the Chopper frequency
if hlr_utils.cli_provide_override(configure, "chopper_freq",
"--chopper-freq"):
configure.chopper_freq = hlr_utils.DrParameterFromString(\
options.chopper_freq, True)
# Set the wavelength center for the Chopper
if hlr_utils.cli_provide_override(configure, "chopper_lambda_cent",
"--chopper-lambda-cent"):
configure.chopper_lambda_cent = hlr_utils.DrParameterFromString(\
options.chopper_lambda_cent, True)
# Set the ability to dump the energy transfer information
if hlr_utils.cli_provide_override(configure, "dump_dslin",
"--dump-dslin"):
configure.dump_dslin = options.dump_dslin
# Set the ability to dump the wavelength information after vanadium norm
if hlr_utils.cli_provide_override(configure, "dump_norm", "--dump-norm"):
configure.dump_norm = options.dump_norm
# Set the ability to dump the energy transfer information
if hlr_utils.cli_provide_override(configure, "dump_energy",
"--dump-energy"):
configure.dump_energy = options.dump_energy
# Set the ability to dump the initial energy information
if hlr_utils.cli_provide_override(configure, "dump_initial_energy",
"--dump-initial-energy"):
configure.dump_initial_energy = options.dump_initial_energy
# Set the ability to dump the pixel contribution information
if hlr_utils.cli_provide_override(configure, "dump_pix_contrib",
"--dump-pix-contrib"):
configure.dump_pix_contrib = options.dump_pix_contrib
if hlr_utils.cli_provide_override(configure, "dump_all", "--dump-all"):
if options.dump_all:
configure.dump_dslin = True
configure.dump_norm = True
configure.dump_energy = True
configure.dump_initial_energy = True
if hlr_utils.cli_provide_override(configure, "split", "--split"):
configure.split = options.split
parser.set_defaults(dump_twod=False)
parser.add_option("", "--timing", action="store_true", dest="timing",
help="Flag to turn on timing of code")
parser.set_defaults(timing=False)
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for RefOptions
hlr_utils.RefConfiguration(parser, configure, options, args)
# Set the lambda perpendicular (lambda_T)
if hlr_utils.cli_provide_override(configure, "lambdap_bins",
"--lambdap-bins"):
configure.lambdap_bins = hlr_utils.AxisFromString(options.lambdap_bins)
# Set mon_norm flag
if hlr_utils.cli_provide_override(configure, "mon_norm", "--mon-norm"):
configure.mon_norm = options.mon_norm
# Set the monitor path
if hlr_utils.cli_provide_override(configure, "mon_path", "--mon-path"):
configure.mon_path = hlr_utils.NxPath(options.mon_path)
# Set the override angle for calculating lambda_T
if hlr_utils.cli_provide_override(configure, "omega", "--omega"):
configure.omega = hlr_utils.DrParameterFromString(options.omega, True)
# Set the ability to dump the R(pid, lambda_T) information
"--timing",
action="store_true",
dest="timing",
help="Flag to turn on timing of code")
parser.set_defaults(timing=False)
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for RefOptions
hlr_utils.RefConfiguration(parser, configure, options, args)
# Set the lambda perpendicular (lambda_T)
if hlr_utils.cli_provide_override(configure, "lambdap_bins",
"--lambdap-bins"):
configure.lambdap_bins = hlr_utils.AxisFromString(options.lambdap_bins)
# Set mon_norm flag
if hlr_utils.cli_provide_override(configure, "mon_norm", "--mon-norm"):
configure.mon_norm = options.mon_norm
# Set the monitor path
if hlr_utils.cli_provide_override(configure, "mon_path", "--mon-path"):
configure.mon_path = hlr_utils.NxPath(options.mon_path)
# Set the override angle for calculating lambda_T
if hlr_utils.cli_provide_override(configure, "omega", "--omega"):
configure.omega = hlr_utils.DrParameterFromString(options.omega, True)
# Set the ability to dump the R(pid, lambda_T) information
def InstConfiguration(parser, configure, options, args, **kwargs):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{InstOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.InstOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{InstOptions}
@type options: C{Option}
@param args: The parsed arguments from C{InstOptions}
@type args: C{list}
@param kwargs: A list of keyword arguments that the function accepts:
@keyword inst: The classification type name of the instrument. Current
names are I{DGS}, I{IGS}, I{PD}, I{REF}, I{SAS}, I{SCD}.
@type inst: C{string}
"""
# Check for keywords
try:
instrument = kwargs["inst"]
except KeyError:
instrument = ""
# Call the configuration setter for BasicOptions
BasicConfiguration(parser, configure, options, args)
# Set the instrument geometry file
if hlr_utils.cli_provide_override(configure, "inst_geom", "--inst-geom"):
configure.inst_geom = hlr_utils.determine_files(options.inst_geom,
one_file=True)
# Set the data paths
if hlr_utils.cli_provide_override(configure, "data_paths", "--data-paths"):
configure.data_paths = hlr_utils.NxPath(options.data_paths)
# Set the normalization file list
if hlr_utils.cli_provide_override(configure, "norm", "--norm"):
configure.norm = hlr_utils.determine_files(options.norm,
configure.inst,
configure.facility,
configure.proposal)
if instrument == "IGS":
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "ecan", "--ecan"):
configure.ecan = hlr_utils.determine_files(options.ecan,
configure.inst,
configure.facility,
configure.proposal)
# Set the background file list
if hlr_utils.cli_provide_override(configure, "back", "--back"):
configure.back = hlr_utils.determine_files(options.back,
configure.inst,
configure.facility,
configure.proposal)
# Set the direct scattering background file list
if hlr_utils.cli_provide_override(configure, "dsback", "--dsback"):
configure.dsback = hlr_utils.determine_files(options.dsback,
configure.inst,
configure.facility,
configure.proposal)
elif instrument == "SAS":
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "ecan", "--ecan"):
configure.ecan = hlr_utils.determine_files(options.ecan,
configure.inst,
configure.facility,
configure.proposal)
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "solv", "--solv"):
configure.solv = hlr_utils.determine_files(options.solv,
configure.inst,
configure.facility,
configure.proposal)
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "open", "--open"):
configure.open = hlr_utils.determine_files(options.open,
configure.inst,
configure.facility,
configure.proposal)
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "dkcur", "--dkcur"):
configure.dkcur = hlr_utils.determine_files(options.dkcur,
configure.inst,
configure.facility,
configure.proposal)
elif instrument == "DGS":
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "ecan", "--ecan"):
configure.ecan = hlr_utils.determine_files(options.ecan,
configure.inst,
configure.facility,
configure.proposal)
# Set the black can file list
if hlr_utils.cli_provide_override(configure, "bcan", "--bcan"):
configure.bcan = hlr_utils.determine_files(options.bcan,
configure.inst,
configure.facility,
configure.proposal)
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "dkcur", "--dkcur"):
configure.dkcur = hlr_utils.determine_files(options.dkcur,
configure.inst,
configure.facility,
configure.proposal)
else:
pass
def RefConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{RefOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.RefOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{RefOptions}
@type options: C{Option}
@param args: The parsed arguments from C{RefOptions}
@type args: C{list}
"""
# Call the configuration setter for InstOptions
hlr_options.InstConfiguration(parser, configure, options, args, inst="REF")
# Set the data instrument geometry file
if hlr_utils.cli_provide_override(configure, "data_inst_geom",
"--data-inst-geom"):
configure.data_inst_geom = hlr_utils.determine_files(\
options.data_inst_geom,
one_file=True)
# Set the normalization instrument geometry file
if hlr_utils.cli_provide_override(configure, "norm_inst_geom",
"--norm-inst-geom"):
configure.norm_inst_geom = hlr_utils.determine_files(\
options.norm_inst_geom,
one_file=True)
# Set the normalization data paths
if hlr_utils.cli_provide_override(configure, "norm_data_paths",
"--norm-data-paths"):
try:
configure.norm_data_paths = hlr_utils.NxPath(\
options.norm_data_paths)
except AttributeError:
configure.norm_data_paths = options.norm_data_paths
# Get the data path for the sample data ROI file
if hlr_utils.cli_provide_override(configure, "data_roi_file",
"--data-roi-file"):
configure.data_roi_file = hlr_utils.determine_files(\
options.data_roi_file,
one_file=True)
# Get the data path for the normalization data ROI file
if hlr_utils.cli_provide_override(configure, "norm_roi_file",
"--norm-roi-file"):
if options.norm_roi_file is not None:
configure.norm_roi_file = hlr_utils.determine_files(\
options.norm_roi_file,
one_file=True)
else:
configure.norm_roi_file = configure.data_roi_file
# Get the data path for the sample data background ROI file
if hlr_utils.cli_provide_override(configure, "dbkg_roi_file",
"--dbkg-roi-file"):
configure.dbkg_roi_file = hlr_utils.determine_files(\
options.dbkg_roi_file,
one_file=True)
# Get the data path for the normalization background ROI file
if hlr_utils.cli_provide_override(configure, "nbkg_roi_file",
"--nbkg-roi-file"):
if options.nbkg_roi_file is not None:
configure.nbkg_roi_file = hlr_utils.determine_files(\
options.nbkg_roi_file,
one_file=True)
else:
configure.nbkg_roi_file = configure.dbkg_roi_file
# Get the polar angle offset
if hlr_utils.cli_provide_override(configure, "angle_offset",
"--angle-offset"):
configure.angle_offset = hlr_utils.DrParameterFromString(\
options.angle_offset, True)
# Set the ability to turn off background estimation and subtraction
if hlr_utils.cli_provide_override(configure, "no_bkg", "--no-bkg"):
configure.no_bkg = options.no_bkg
# Set the ability to turn off normalization background estimation
# and subtraction
if hlr_utils.cli_provide_override(configure, "no_norm_bkg",
"--no-norm-bkg"):
configure.no_norm_bkg = options.no_norm_bkg
# Set the minimum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_min",
"--tof-cut-min"):
configure.tof_cut_min = options.tof_cut_min
# Set the maximum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_max",
"--tof-cut-max"):
configure.tof_cut_max = options.tof_cut_max
# Set the TOF bins to zero out from the data and normalization spectra
if hlr_utils.cli_provide_override(configure, "tof_cuts", "--tof-cuts"):
if options.tof_cuts is not None:
configure.tof_cuts = options.tof_cuts.split(',')
else:
configure.tof_cuts = options.tof_cuts
# Set the momentum transfer bins
if hlr_utils.cli_provide_override(configure, "Q_bins", "--mom-trans-bins"):
configure.Q_bins = hlr_utils.AxisFromString(options.Q_bins)
# Set the no bad data filter flag
if hlr_utils.cli_provide_override(configure, "no_filter", "--no-filter"):
configure.no_filter = options.no_filter
# Set the store delta t over t flag
if hlr_utils.cli_provide_override(configure, "store_dtot", "--store-dtot"):
configure.store_dtot = options.store_dtot
# Set the pixel ID range values for peak exclusion from sample data
if hlr_utils.cli_provide_override(configure, "data_peak_excl",
"--data-peak-excl"):
configure.data_peak_excl = options.data_peak_excl
# Set the pixel ID range values for peak exclusion from normalization data
if hlr_utils.cli_provide_override(configure, "norm_peak_excl",
"--norm-peak-excl"):
configure.norm_peak_excl = options.norm_peak_excl
# Set the integration direction
if hlr_utils.cli_provide_override(configure, "int_dir", "--int-dir"):
configure.int_dir = options.int_dir
# Get the scattering (polar) angle for axis TOF to Q conversion
if hlr_utils.cli_provide_override(configure, "scatt_angle",
"--scatt-angle"):
configure.scatt_angle = hlr_utils.DrParameterFromString(\
options.scatt_angle, True)
# Set the ability to dump the combined specular TOF information
if hlr_utils.cli_provide_override(configure, "dump_specular",
"--dump-specular"):
configure.dump_specular = options.dump_specular
# Set the ability to dump the combined background TOF information
if hlr_utils.cli_provide_override(configure, "dump_bkg", "--dump-bkg"):
configure.dump_bkg = options.dump_bkg
# Set the ability to dump the combined subtracted TOF information
if hlr_utils.cli_provide_override(configure, "dump_sub", "--dump-sub"):
configure.dump_sub = options.dump_sub
# Set the ability to dump the R(TOF) information
if hlr_utils.cli_provide_override(configure, "dump_rtof", "--dump-rtof"):
configure.dump_rtof = options.dump_rtof
# Set the ability to dump the combined R(TOF) information
if hlr_utils.cli_provide_override(configure, "dump_rtof_comb",
"--dump-rtof-comb"):
configure.dump_rtof_comb = options.dump_rtof_comb
# Set the ability to dump the R(Q) information
if hlr_utils.cli_provide_override(configure, "dump_rq", "--dump-rq"):
configure.dump_rq = options.dump_rq
# Set the ability to dump the R(Q) after rebinning information
if hlr_utils.cli_provide_override(configure, "dump_rqr", "--dump-rqr"):
configure.dump_rqr = options.dump_rqr
if hlr_utils.cli_provide_override(configure, "dump_all", "--dump-all"):
if options.dump_all:
configure.dump_specular = True
configure.dump_bkg = True
configure.dump_sub = True
configure.dump_rtof = True
configure.dump_rtof_comb = True
configure.dump_rq = True
configure.dump_rqr = True
def BasicConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{BasicOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.BasicOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{BasicOptions}
@type options: C{Option}
@param args: The parsed arguments from C{BasicOptions}
@type args: C{list}
"""
# Set from a configuration file first
if options.config is not None:
import xml.dom.minidom
conf_doc = xml.dom.minidom.parse(options.config)
configure = hlr_utils.ConfigFromXml(conf_doc, configure)
# Now override options provided on command-line
# Set the verbosity, if present on command-line
if not configure.verbose:
configure.verbose = options.verbose
else:
# Got the verbosity from the config file, but check CLI
if hlr_utils.cli_checker("-v", "-q"):
# Override option
configure.verbose = options.verbose
else:
# No flags present, do nothing
pass
# Define instrument short name first as stuff below depends on it
if hlr_utils.cli_provide_override(configure, "inst", "--inst"):
configure.inst = options.inst
# Define facility short name as stuff below depends on it
if hlr_utils.cli_provide_override(configure, "facility", "--facility"):
configure.facility = options.facility
# Define proposal as stuff below depends on it.
if hlr_utils.cli_provide_override(configure, "proposal", "--proposal"):
configure.proposal = options.proposal
# Get the datafile name and check it
if options.data is not None:
configure.data = hlr_utils.determine_files(options.data,
configure.inst,
configure.facility,
configure.proposal,
stop_on_none=True)
elif len(args) > 0:
configure.data = hlr_utils.determine_files(args,
configure.inst,
configure.facility,
configure.proposal,
stop_on_none=True)
elif configure.data:
# We have data from the config file, so everything is OK.
pass
else:
parser.error("Did not specify a datafile")
import os
# Deal with file or directory from output option
if options.output:
filepath = hlr_utils.fix_filename(options.output)
if os.path.exists(filepath):
if os.path.isdir(filepath):
outfile = os.path.basename(configure.data[0])
path = os.path.join(filepath, outfile)
configure.output = hlr_utils.ext_replace(path, "nxs", "txt")
configure.path_replacement = filepath
configure.ext_replacement = "txt"
elif os.path.isfile(filepath):
configure.output = filepath
configure.path_replacement = os.path.dirname(filepath)
configure.ext_replacement = filepath.split('.')[-1]
else:
parser.error("Cannot handle %s in output option" % filepath)
else:
# Assume that this is a file and hope that the directory exists
directory = os.path.dirname(filepath)
if directory != "":
if not os.path.exists(directory):
raise RuntimeError("The directory %s must exist!" \
% directory)
else:
pass
else:
directory = None
configure.output = filepath
configure.path_replacement = directory
configure.ext_replacement = filepath.split('.')[-1]
elif configure.output:
# We have an output file, so no need to do anything else
try:
configure.path_replacement
except AttributeError:
configure.path_replacement = None
# Create the output file name if there isn't one supplied
else:
outfile = os.path.basename(configure.data[0])
path = os.path.join(os.getcwd(), outfile)
configure.output = hlr_utils.ext_replace(path, "nxs", "txt")
configure.path_replacement = None
configure.ext_replacement = "txt"
if configure.verbose and options.output:
print "Using %s as output file" % configure.output
"--timing",
action="store_true",
dest="timing",
help="Flag to turn on timing of code")
parser.set_defaults(timing=False)
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for SansOptions
hlr_utils.SansConfiguration(parser, configure, options, args)
# Set the accelerator down time
if hlr_utils.cli_provide_override(configure, "acc_down_time",
"--acc-down-time"):
configure.acc_down_time = hlr_utils.DrParameterFromString(\
options.acc_down_time, True)
if configure.lambda_bins is None:
parser.error("Please specify the final wavelength axis!")
# Set timer object if timing option is used
if options.timing:
import sns_timing
timer = sns_timing.DiffTime()
else:
timer = None
# Run the program
run(configure, timer)
def InstConfiguration(parser, configure, options, args, **kwargs):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{InstOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.InstOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{InstOptions}
@type options: C{Option}
@param args: The parsed arguments from C{InstOptions}
@type args: C{list}
@param kwargs: A list of keyword arguments that the function accepts:
@keyword inst: The classification type name of the instrument. Current
names are I{DGS}, I{IGS}, I{PD}, I{REF}, I{SAS}, I{SCD}.
@type inst: C{string}
"""
# Check for keywords
try:
instrument = kwargs["inst"]
except KeyError:
instrument = ""
# Call the configuration setter for BasicOptions
BasicConfiguration(parser, configure, options, args)
# Set the instrument geometry file
if hlr_utils.cli_provide_override(configure, "inst_geom", "--inst-geom"):
configure.inst_geom = hlr_utils.determine_files(options.inst_geom,
one_file=True)
# Set the data paths
if hlr_utils.cli_provide_override(configure, "data_paths", "--data-paths"):
configure.data_paths = hlr_utils.NxPath(options.data_paths)
# Set the normalization file list
if hlr_utils.cli_provide_override(configure, "norm", "--norm"):
configure.norm = hlr_utils.determine_files(options.norm,
configure.inst,
configure.facility,
configure.proposal)
if instrument == "IGS":
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "ecan", "--ecan"):
configure.ecan = hlr_utils.determine_files(options.ecan,
configure.inst,
configure.facility,
configure.proposal)
# Set the background file list
if hlr_utils.cli_provide_override(configure, "back", "--back"):
configure.back = hlr_utils.determine_files(options.back,
configure.inst,
configure.facility,
configure.proposal)
# Set the direct scattering background file list
if hlr_utils.cli_provide_override(configure, "dsback", "--dsback"):
configure.dsback = hlr_utils.determine_files(
options.dsback, configure.inst, configure.facility,
configure.proposal)
elif instrument == "SAS":
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "ecan", "--ecan"):
configure.ecan = hlr_utils.determine_files(options.ecan,
configure.inst,
configure.facility,
configure.proposal)
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "solv", "--solv"):
configure.solv = hlr_utils.determine_files(options.solv,
configure.inst,
configure.facility,
configure.proposal)
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "open", "--open"):
configure.open = hlr_utils.determine_files(options.open,
configure.inst,
configure.facility,
configure.proposal)
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "dkcur", "--dkcur"):
configure.dkcur = hlr_utils.determine_files(
options.dkcur, configure.inst, configure.facility,
configure.proposal)
elif instrument == "DGS":
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "ecan", "--ecan"):
configure.ecan = hlr_utils.determine_files(options.ecan,
configure.inst,
configure.facility,
configure.proposal)
# Set the black can file list
if hlr_utils.cli_provide_override(configure, "bcan", "--bcan"):
configure.bcan = hlr_utils.determine_files(options.bcan,
configure.inst,
configure.facility,
configure.proposal)
# Set the empty can file list
if hlr_utils.cli_provide_override(configure, "dkcur", "--dkcur"):
configure.dkcur = hlr_utils.determine_files(
options.dkcur, configure.inst, configure.facility,
configure.proposal)
else:
pass
+"data.")
parser.add_option("", "--timing", action="store_true", dest="timing",
help="Flag to turn on timing of code")
parser.set_defaults(timing=False)
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for SansOptions
hlr_utils.SansConfiguration(parser, configure, options, args)
# Set the background file list
if hlr_utils.cli_provide_override(configure, "back", "--back"):
configure.back = hlr_utils.determine_files(options.back,
configure.inst,
configure.facility)
if configure.lambda_bins is None:
parser.error("Please specify the final wavelength axis!")
# Turn off monitor and detector efficiencies if transmission background is
# present
if configure.back is not None:
if configure.mon_effc:
configure.mon_effc = False
if configure.det_effc:
configure.det_effc = False
parser.remove_option("--ncos-polar-bins")
# This one is handled by the loop
parser.remove_option("--ldb-const")
# Block the rescaling as this causes havoc with the looping
parser.remove_option("--rescale-final")
(options, args) = parser.parse_args()
# Set up the configuration
configure = hlr_utils.Configure()
# Call the configuration setter for AmrOptions
hlr_utils.AmrConfiguration(parser, configure, options, args)
# Set the positive and negative energy transfer axis integration ranges
if hlr_utils.cli_provide_override(configure, "et_int_range",
"--et-int-range"):
configure.et_int_range = hlr_utils.AxisFromString(options.et_int_range)
configure.et_pos_range = (configure.et_int_range.getMinimum(),
configure.et_int_range.getMaximum())
configure.et_neg_range = (-1.0*configure.et_int_range.getMaximum(),
-1.0*configure.et_int_range.getMinimum())
# Capture final energy binning
configure.final_E_bins = configure.E_bins
# Reset energy transfer axis to [-E_t_max, E_t_max]
configure.E_bins = hlr_utils.Axis(-1.0*configure.et_int_range.getMaximum(),
configure.et_int_range.getMaximum(),
configure.et_int_range.getDelta())
def SansConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{SansOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.SansOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{SansOptions}
@type options: C{Option}
@param args: The parsed arguments from C{SansOptions}
@type args: C{list}
"""
# Call the configuration setter for InstOptions
hlr_utils.InstConfiguration(parser, configure, options, args, inst="SAS")
# Set the beam monitor path
if hlr_utils.cli_provide_override(configure, "bmon_path", "--bmon-path"):
configure.bmon_path = hlr_utils.NxPath(options.bmon_path)
# Set the transmission monitor path
if hlr_utils.cli_provide_override(configure, "tmon_path", "--tmon-path"):
configure.tmon_path = hlr_utils.NxPath(options.tmon_path)
# Set the sample data Transmission spectrum file
if hlr_utils.cli_provide_override(configure, "data_trans", "--data-trans"):
configure.data_trans = hlr_utils.determine_files(options.data_trans,
one_file=True)
# Set the solvent only Transmission spectrum file
if hlr_utils.cli_provide_override(configure, "solv_trans", "--solv-trans"):
configure.solv_trans = hlr_utils.determine_files(options.solv_trans,
one_file=True)
# Set the empty can Transmission spectrum file
if hlr_utils.cli_provide_override(configure, "ecan_trans", "--ecan-trans"):
configure.ecan_trans = hlr_utils.determine_files(options.ecan_trans,
one_file=True)
# Set the beam monitor override file
if hlr_utils.cli_provide_override(configure, "beammon_over",
"--beammon-over"):
configure.beammon_over = hlr_utils.determine_files(\
options.beammon_over,
configure.inst,
configure.facility,
configure.proposal,
stop_on_none=True)
# Set no_bmon_norm flag
if hlr_utils.cli_provide_override(configure, "no_bmon_norm",
"--no-bmon-norm"):
configure.no_bmon_norm = options.no_bmon_norm
# Set mon_effc flag
if hlr_utils.cli_provide_override(configure, "mon_effc", "--mon-effc"):
configure.mon_effc = options.mon_effc
# Set the monitor efficiency constant
if hlr_utils.cli_provide_override(configure, "mon_eff_const",
"--mon-eff-const"):
configure.mon_eff_const = hlr_utils.DrParameterFromString(\
options.mon_eff_const, True)
# Set det_effc flag
if hlr_utils.cli_provide_override(configure, "det_effc", "--det-effc"):
configure.det_effc = options.det_effc
# Set the detector efficiency scaling constant
if hlr_utils.cli_provide_override(configure, "det_eff_scale_const",
"--det-eff-scale-const"):
configure.det_eff_scale_const = hlr_utils.DrParameterFromString(\
options.det_eff_scale_const, True)
# Set the detector efficiency attenuation constant
if hlr_utils.cli_provide_override(configure, "det_eff_atten_const",
"--det-eff-atten-const"):
configure.det_eff_atten_const = hlr_utils.DrParameterFromString(\
options.det_eff_atten_const, True)
# Set the ROI file
if hlr_utils.cli_provide_override(configure, "roi_file", "--roi-file"):
configure.roi_file = hlr_utils.determine_files(options.roi_file,
one_file=True)
# Set the momentum transfer bins
if hlr_utils.cli_provide_override(configure, "Q_bins", "--mom-trans-bins"):
configure.Q_bins = hlr_utils.AxisFromString(options.Q_bins)
# Set the theta bins
if hlr_utils.cli_provide_override(configure, "theta_bins", "--theta-bins"):
configure.theta_bins = hlr_utils.AxisFromString(options.theta_bins)
# Set the radius bins
if hlr_utils.cli_provide_override(configure, "r_bins", "--r-bins"):
configure.r_bins = hlr_utils.AxisFromString(options.r_bins)
# Set the time-zero offset for the detector
if hlr_utils.cli_provide_override(configure, "time_zero_offset_det",
"--time-zero-offset-det"):
configure.time_zero_offset_det = hlr_utils.DrParameterFromString(\
options.time_zero_offset_det, True)
# Set the time-zero offset for the monitor
if hlr_utils.cli_provide_override(configure, "time_zero_offset_mon",
"--time-zero-offset-mon"):
configure.time_zero_offset_mon = hlr_utils.DrParameterFromString(\
options.time_zero_offset_mon, True)
# Set the lambda bins for use with dump-bmnorm-wave
if hlr_utils.cli_provide_override(configure, "lambda_bins",
"--lambda-bins"):
configure.lambda_bins = hlr_utils.AxisFromString(options.lambda_bins)
# Set the low-side lambda cut for cutting wavelength spectra
if hlr_utils.cli_provide_override(configure, "lambda_low_cut",
"--lambda-low-cut"):
try:
configure.lambda_low_cut = float(options.lambda_low_cut)
except TypeError:
configure.lambda_low_cut = options.lambda_low_cut
# Set the high-side lambda cut for cutting wavelength spectra
if hlr_utils.cli_provide_override(configure, "lambda_high_cut",
"--lambda-high-cut"):
try:
configure.lambda_high_cut = float(options.lambda_high_cut)
except TypeError:
configure.lambda_high_cut = options.lambda_high_cut
# Set the coefficients for the wavelength dependent background correction
if hlr_utils.cli_provide_override(configure, "bkg_coeff", "--bkg-coeff"):
try:
configure.bkg_coeff = options.bkg_coeff.split(',')
except AttributeError:
configure.bkg_coeff = options.bkg_coeff
# Set the accelerator down time for sample data
if hlr_utils.cli_provide_override(configure, "data_acc_down_time",
"--data-acc-down-time"):
configure.data_acc_down_time = hlr_utils.DrParameterFromString(\
options.data_acc_down_time, True)
# Set the accelerator down time for sample data
if hlr_utils.cli_provide_override(configure, "solv_acc_down_time",
"--solv-acc-down-time"):
configure.solv_acc_down_time = hlr_utils.DrParameterFromString(\
options.solv_acc_down_time, True)
# Set the accelerator down time for sample ecan
if hlr_utils.cli_provide_override(configure, "ecan_acc_down_time",
"--ecan-acc-down-time"):
configure.ecan_acc_down_time = hlr_utils.DrParameterFromString(\
options.ecan_acc_down_time, True)
# Set the accelerator down time for sample data
if hlr_utils.cli_provide_override(configure, "open_acc_down_time",
"--open-acc-down-time"):
configure.open_acc_down_time = hlr_utils.DrParameterFromString(\
options.open_acc_down_time, True)
# Set the axis dependent background scaling constant
if hlr_utils.cli_provide_override(configure, "bkg_scale", "--bkg-scale"):
try:
configure.bkg_scale = float(options.bkg_scale)
except TypeError:
configure.bkg_scale = options.bkg_scale
# Set the final data rescaling constant
if hlr_utils.cli_provide_override(configure, "rescale_final",
"--rescale-final"):
try:
configure.rescale_final = float(options.rescale_final)
except TypeError:
configure.rescale_final = options.rescale_final
# Set the ability to dump the detector pixel wavelength information
if hlr_utils.cli_provide_override(configure, "dump_wave", "--dump-wave"):
configure.dump_wave = options.dump_wave
# Set the ability to dump the beam monitor wavelength information
if hlr_utils.cli_provide_override(configure, "dump_bmon_wave",
"--dump-bmon-wave"):
configure.dump_bmon_wave = options.dump_bmon_wave
# Set the ability to dump the efficiency corrected beam monitor wavelength
# information
if hlr_utils.cli_provide_override(configure, "dump_bmon_effc",
"--dump-bmon-effc"):
configure.dump_bmon_effc = options.dump_bmon_effc
# Set the ability to dump the rebinned beam monitor wavelength information
if hlr_utils.cli_provide_override(configure, "dump_bmon_rebin",
"--dump-bmon-rebin"):
configure.dump_bmon_rebin = options.dump_bmon_rebin
# Set the ability to dump the wavelength information after beam monitor
# normalization
if hlr_utils.cli_provide_override(configure, "dump_wave_bmnorm",
"--dump-wave-bmnorm"):
configure.dump_wave_bmnorm = options.dump_wave_bmnorm
# Set the ability to dump the fractional counts and fractional area
# separately after rebinning in Q
if hlr_utils.cli_provide_override(configure, "dump_frac_rebin",
"--dump-frac-rebin"):
configure.dump_frac_rebin = options.dump_frac_rebin
# Set the ability to dump a TOF vs radius distribution
if hlr_utils.cli_provide_override(configure, "dump_tof_r", "--dump-tof-r"):
configure.dump_tof_r = options.dump_tof_r
# Set the ability to dump a TOF vs polar angle distribution
if hlr_utils.cli_provide_override(configure, "dump_tof_theta",
"--dump-tof-theta"):
configure.dump_tof_theta = options.dump_tof_theta
# Set the ability to dump a wavelength vs radius distribution
if hlr_utils.cli_provide_override(configure, "dump_wave_r",
"--dump-wave-r"):
configure.dump_wave_r = options.dump_wave_r
# Set the ability to dump a wavelength vs polar angle distribution
if hlr_utils.cli_provide_override(configure, "dump_wave_theta",
"--dump-wave-theta"):
configure.dump_wave_theta = options.dump_wave_theta
# Set the ability to dump a momentum transfer vs radius distribution
if hlr_utils.cli_provide_override(configure, "dump_Q_r", "--dump-Q-r"):
configure.dump_Q_r = options.dump_Q_r
# Set the ability to dump a momentum transfer vs polar angle distribution
if hlr_utils.cli_provide_override(configure, "dump_Q_theta",
"--dump-Q-theta"):
configure.dump_Q_theta = options.dump_Q_theta
if hlr_utils.cli_provide_override(configure, "dump_2d", "--dump-2d"):
if options.dump_2d:
configure.dump_tof_r = True
configure.dump_tof_theta = True
configure.dump_wave_r = True
configure.dump_wave_theta = True
configure.dump_Q_r = True
configure.dump_Q_theta = True
if hlr_utils.cli_provide_override(configure, "dump_all", "--dump-all"):
if options.dump_all:
configure.dump_wave = True
configure.dump_bmon_wave = True
configure.dump_bmon_effc = True
configure.dump_bmon_rebin = True
configure.dump_wave_bmnorm = True
configure.dump_frac_rebin = True
configure.dump_tof_r = True
configure.dump_tof_theta = True
configure.dump_wave_r = True
configure.dump_wave_theta = True
configure.dump_Q_r = True
configure.dump_Q_theta = True
# Do some cross-checks
if configure.dump_tof_r or configure.dump_wave_r or configure.dump_Q_r:
if configure.r_bins is None:
parser.error("Must specify --r-bins option when using 2D "\
+"distribution options --dump-tof-r, "\
+"--dump-wave-r or --dump-Q-r.")
if configure.dump_tof_theta or configure.dump_wave_theta or \
configure.dump_Q_theta:
if configure.theta_bins is None:
parser.error("Must specify --theta-bins option when using 2D "\
+"distribution options --dump-tof-theta, "\
+"--dump-wave-theta or --dump-Q-theta.")
def DgsRedConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{DgsRedOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.DgsRedOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{DgsRedOptions}
@type options: C{Option}
@param args: The parsed arguments from C{DgsRedOptions}
@type args: C{list}
"""
# Call the configuration setter for DgsOptions
hlr_dgs_options.DgsConfiguration(parser, configure, options, args)
# Set the mask file
if hlr_utils.cli_provide_override(configure, "mask_file", "--mask-file"):
configure.mask_file = hlr_utils.determine_files(options.mask_file)
# Set the corner geometry information file
if hlr_utils.cli_provide_override(configure, "corner_geom",
"--corner-geom"):
configure.corner_geom = options.corner_geom
if configure.corner_geom is None:
parser.error("You must provide a corner geometry file via the "\
+"corner-geom option!")
# Set the lambda ratio flag
if hlr_utils.cli_provide_override(configure, "lambda_ratio",
"--lambda-ratio"):
configure.lambda_ratio = options.lambda_ratio
# Set the flag for making the phonon density of states representation
if hlr_utils.cli_provide_override(configure, "pdos_Q", "--pdos-Q"):
configure.pdos_Q = options.pdos_Q
# Set the Debye-Waller constant for the phonon DOS representation
if hlr_utils.cli_provide_override(configure, "debye_waller",
"--debye-waller"):
configure.debye_waller = hlr_utils.DrParameterFromString(\
options.debye_waller)
else:
configure.debye_waller = options.debye_waller
# Set the energy transfer bins
if hlr_utils.cli_provide_override(configure, "E_bins", "--energy-bins"):
configure.E_bins = hlr_utils.AxisFromString(options.E_bins)
if configure.E_bins is None:
parser.error("You must provide energy transfer binning via the "\
+"energy-bins option")
# Set the momentum transfer bins
if hlr_utils.cli_provide_override(configure, "Q_bins", "--mom-trans-bins"):
configure.Q_bins = hlr_utils.AxisFromString(options.Q_bins)
if configure.Q_bins is None:
parser.error("You must provide momentum transfer binning via the "\
+"mom-trans-bins option")
# Set the ability to write SPE and PHX files instead of S(Q, E) dist
if hlr_utils.cli_provide_override(configure, "make_spe", "--make_spe"):
configure.make_spe = options.make_spe
# Set the ability to create the Q vector meshes for each energy slice
if hlr_utils.cli_provide_override(configure, "qmesh", "--qmesh", "-m"):
configure.qmesh = options.qmesh
# Set the ability to write out fixed grid mesh files
if hlr_utils.cli_provide_override(configure, "fixed", "--fixed", "-x"):
configure.fixed = options.fixed
# Set the ability to turn off zero suppression for single crystal data
if hlr_utils.cli_provide_override(configure, "no_zero_supp",
"--no-zero-supp"):
configure.no_zero_supp = options.no_zero_supp
# Set the ability to dump the combined energy transfer information
if hlr_utils.cli_provide_override(configure, "dump_et_comb",
"--dump-et-comb"):
configure.dump_et_comb = options.dump_et_comb
if hlr_utils.cli_provide_override(configure, "split", "--split"):
configure.split = options.split
def IgsConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{IgsOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.IgsOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{IgsOptions}
@type options: C{Option}
@param args: The parsed arguments from C{IgsOptions}
@type args: C{list}
"""
# Call the configuration setter for InstOptions
hlr_options.InstConfiguration(parser, configure, options, args, inst="IGS")
# Set the ROI file
if hlr_utils.cli_provide_override(configure, "roi_file", "--roi-file"):
configure.roi_file = hlr_utils.determine_files(options.roi_file,
one_file=True)
# Set the monitor path
if hlr_utils.cli_provide_override(configure, "mon_path", "--mon-path"):
configure.mon_path = hlr_utils.NxPath(options.mon_path)
# Set the dead time
if hlr_utils.cli_provide_override(configure, "dead_time", "--dead-time"):
configure.dead_time = hlr_utils.DrParameterFromString(\
options.dead_time)
# Set the minimum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_min",
"--tof-cut-min"):
configure.tof_cut_min = options.tof_cut_min
# Set the maximum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_max",
"--tof-cut-max"):
configure.tof_cut_max = options.tof_cut_max
# Set the time-independent background TOFs
if hlr_utils.cli_provide_override(configure, "tib_tofs", "--tib-tofs"):
if options.tib_tofs is not None:
configure.tib_tofs = options.tib_tofs.split(',')
else:
configure.tib_tofs = options.tib_tofs
# Set the time-independent background constant for data
if hlr_utils.cli_provide_override(configure, "tib_data_const",
"--tib-data-const"):
configure.tib_data_const = hlr_utils.DrParameterFromString(\
options.tib_data_const, True)
# Set the time-independent background constant for ecan
if hlr_utils.cli_provide_override(configure, "tib_ecan_const",
"--tib-ecan-const"):
configure.tib_ecan_const = hlr_utils.DrParameterFromString(\
options.tib_ecan_const, True)
# Set the time-independent background constant for back
if hlr_utils.cli_provide_override(configure, "tib_back_const",
"--tib-back-const"):
configure.tib_back_const = hlr_utils.DrParameterFromString(\
options.tib_back_const, True)
# Set the time-independent background constant for norm
if hlr_utils.cli_provide_override(configure, "tib_norm_const",
"--tib-norm-const"):
configure.tib_norm_const = hlr_utils.DrParameterFromString(\
options.tib_norm_const, True)
# Set the time-independent background constant for dsback
if hlr_utils.cli_provide_override(configure, "tib_dsback_const",
"--tib-dsback-const"):
configure.tib_dsback_const = hlr_utils.DrParameterFromString(\
options.tib_dsback_const, True)
# Set the normalization start wavelength
if hlr_utils.cli_provide_override(configure, "norm_start", "--norm_start"):
configure.norm_start = float(options.norm_start)
# Set the normalization end wavelength
if hlr_utils.cli_provide_override(configure, "norm_end", "--norm_end"):
configure.norm_end = float(options.norm_end)
# Set no_mon_norm flag
if hlr_utils.cli_provide_override(configure, "no_mon_norm",
"--no-mon-norm"):
configure.no_mon_norm = options.no_mon_norm
# Set no_mon_effc flag
if hlr_utils.cli_provide_override(configure, "no_mon_effc",
"--no-mon-effc"):
configure.no_mon_effc = options.no_mon_effc
# Set the final wavelength
if hlr_utils.cli_provide_override(configure, "wavelength_final",
"--wavelength-final"):
configure.wavelength_final = hlr_utils.DrParameterFromString(\
options.wavelength_final, True)
# Set the time-zero offset
if hlr_utils.cli_provide_override(configure, "time_zero_offset",
"--time-zero-offset"):
configure.time_zero_offset = hlr_utils.DrParameterFromString(\
options.time_zero_offset, True)
# Set the time-zero slope
if hlr_utils.cli_provide_override(configure, "time_zero_slope",
"--time-zero-slope"):
configure.time_zero_slope = hlr_utils.DrParameterFromString(\
options.time_zero_slope, True)
# Set the lambda bins for use with dump-mnorm-wave
if hlr_utils.cli_provide_override(configure, "lambda_bins",
"--lambda-bins"):
configure.lambda_bins = hlr_utils.AxisFromString(options.lambda_bins)
# Set the ability to dump the time-independent background information
if hlr_utils.cli_provide_override(configure, "dump_tib", "--dump-tib"):
configure.dump_tib = options.dump_tib
# Set the ability to dump the wavelength information
if hlr_utils.cli_provide_override(configure, "dump_wave", "--dump-wave"):
configure.dump_wave = options.dump_wave
# Set the ability to dump the monitor wavelength information
if hlr_utils.cli_provide_override(configure, "dump_mon_wave",
"--dump-mon-wave"):
configure.dump_mon_wave = options.dump_mon_wave
# Set the ability to dump the rebinned monitor wavelength information
if hlr_utils.cli_provide_override(configure, "dump_mon_rebin",
"--dump-mon-rebin"):
configure.dump_mon_rebin = options.dump_mon_rebin
# Set the ability to dump the efficiency corrected monitor wavelength
# information
if hlr_utils.cli_provide_override(configure, "dump_mon_effc",
"--dump-mon-effc"):
configure.dump_mon_effc = options.dump_mon_effc
# Set the ability to dump the wavelength information
if hlr_utils.cli_provide_override(configure, "dump_wave_mnorm",
"--dump-wave-mnorm"):
configure.dump_wave_mnorm = options.dump_wave_mnorm
if hlr_utils.cli_provide_override(configure, "dump_all", "--dump-all"):
if options.dump_all:
configure.dump_tib = True
configure.dump_wave = True
configure.dump_mon_wave = True
configure.dump_mon_wave = True
configure.dump_mon_effc = True
configure.dump_mon_diml = True
configure.dump_mon_rebin = True
configure.dump_wave_mnorm = True
# Set the filter option
if hlr_utils.cli_provide_override(configure, "filter", "--filter",
"--no-filter"):
configure.filter = options.filter
# Set MC option
if hlr_utils.cli_provide_override(configure, "mc", "--mc"):
configure.mc = options.mc
# Set the early background subtraction option
if hlr_utils.cli_provide_override(configure, "hwfix", "--hwfix"):
configure.hwfix = options.hwfix
# Set the constant for scaling the background spectra: sample
if hlr_utils.cli_provide_override(configure, "scale_bs", "--scale-bs"):
configure.scale_bs = hlr_utils.DrParameterFromString(options.scale_bs,
True)
# Set the constant for scaling the background spectra: normalization
if hlr_utils.cli_provide_override(configure, "scale_bn", "--scale-bn"):
configure.scale_bn = hlr_utils.DrParameterFromString(options.scale_bn,
True)
# Set the constant for scaling the background spectra: empty container
# for sample
if hlr_utils.cli_provide_override(configure, "scale_bcs", "--scale-bcs"):
configure.scale_bcs = hlr_utils.DrParameterFromString(\
options.scale_bcs, True)
# Set the constant for scaling the background spectra: empty container
# for normalization
if hlr_utils.cli_provide_override(configure, "scale_bcn", "--scale-bcn"):
configure.scale_bcn = hlr_utils.DrParameterFromString(\
options.scale_bcn, True)
# Set the constant for scaling the empty container spectra: sample
if hlr_utils.cli_provide_override(configure, "scale_cs", "--scale-cs"):
configure.scale_cs = hlr_utils.DrParameterFromString(options.scale_cs,
True)
# Set the constant for scaling the empty container spectra: normalization
if hlr_utils.cli_provide_override(configure, "scale_cn", "--scale-cn"):
configure.scale_cn = hlr_utils.DrParameterFromString(options.scale_cn,
True)
# Set the elastic peak range in TOF
if hlr_utils.cli_provide_override(configure, "tof_elastic",
"--tof-elastic"):
if options.tof_elastic is not None:
configure.tof_elastic = options.tof_elastic.split(',')
else:
configure.tof_elastic = options.tof_elastic
def RefConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{RefOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.RefOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{RefOptions}
@type options: C{Option}
@param args: The parsed arguments from C{RefOptions}
@type args: C{list}
"""
# Call the configuration setter for InstOptions
hlr_options.InstConfiguration(parser, configure, options, args, inst="REF")
# Set the data instrument geometry file
if hlr_utils.cli_provide_override(configure, "data_inst_geom",
"--data-inst-geom"):
configure.data_inst_geom = hlr_utils.determine_files(\
options.data_inst_geom,
one_file=True)
# Set the normalization instrument geometry file
if hlr_utils.cli_provide_override(configure, "norm_inst_geom",
"--norm-inst-geom"):
configure.norm_inst_geom = hlr_utils.determine_files(\
options.norm_inst_geom,
one_file=True)
# Set the normalization data paths
if hlr_utils.cli_provide_override(configure, "norm_data_paths",
"--norm-data-paths"):
try:
configure.norm_data_paths = hlr_utils.NxPath(\
options.norm_data_paths)
except AttributeError:
configure.norm_data_paths = options.norm_data_paths
# Get the data path for the sample data ROI file
if hlr_utils.cli_provide_override(configure, "data_roi_file",
"--data-roi-file"):
configure.data_roi_file = hlr_utils.determine_files(\
options.data_roi_file,
one_file=True)
# Get the data path for the normalization data ROI file
if hlr_utils.cli_provide_override(configure, "norm_roi_file",
"--norm-roi-file"):
if options.norm_roi_file is not None:
configure.norm_roi_file = hlr_utils.determine_files(\
options.norm_roi_file,
one_file=True)
else:
configure.norm_roi_file = configure.data_roi_file
# Get the data path for the sample data background ROI file
if hlr_utils.cli_provide_override(configure, "dbkg_roi_file",
"--dbkg-roi-file"):
configure.dbkg_roi_file = hlr_utils.determine_files(\
options.dbkg_roi_file,
one_file=True)
# Get the data path for the normalization background ROI file
if hlr_utils.cli_provide_override(configure, "nbkg_roi_file",
"--nbkg-roi-file"):
if options.nbkg_roi_file is not None:
configure.nbkg_roi_file = hlr_utils.determine_files(\
options.nbkg_roi_file,
one_file=True)
else:
configure.nbkg_roi_file = configure.dbkg_roi_file
# Get the polar angle offset
if hlr_utils.cli_provide_override(configure, "angle_offset",
"--angle-offset"):
configure.angle_offset = hlr_utils.DrParameterFromString(\
options.angle_offset, True)
# Set the ability to turn off background estimation and subtraction
if hlr_utils.cli_provide_override(configure, "no_bkg", "--no-bkg"):
configure.no_bkg = options.no_bkg
# Set the ability to turn off normalization background estimation
# and subtraction
if hlr_utils.cli_provide_override(configure, "no_norm_bkg",
"--no-norm-bkg"):
configure.no_norm_bkg = options.no_norm_bkg
# Set the minimum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_min",
"--tof-cut-min"):
configure.tof_cut_min = options.tof_cut_min
# Set the maximum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_max",
"--tof-cut-max"):
configure.tof_cut_max = options.tof_cut_max
# Set the TOF bins to zero out from the data and normalization spectra
if hlr_utils.cli_provide_override(configure, "tof_cuts", "--tof-cuts"):
if options.tof_cuts is not None:
configure.tof_cuts = options.tof_cuts.split(',')
else:
configure.tof_cuts = options.tof_cuts
# Set the momentum transfer bins
if hlr_utils.cli_provide_override(configure, "Q_bins", "--mom-trans-bins"):
configure.Q_bins = hlr_utils.AxisFromString(options.Q_bins)
# Set the no bad data filter flag
if hlr_utils.cli_provide_override(configure, "no_filter", "--no-filter"):
configure.no_filter = options.no_filter
# Set the store delta t over t flag
if hlr_utils.cli_provide_override(configure, "store_dtot", "--store-dtot"):
configure.store_dtot = options.store_dtot
# Set the pixel ID range values for peak exclusion from sample data
if hlr_utils.cli_provide_override(configure, "data_peak_excl",
"--data-peak-excl"):
configure.data_peak_excl = options.data_peak_excl
# Set the pixel ID range values for peak exclusion from normalization data
if hlr_utils.cli_provide_override(configure, "norm_peak_excl",
"--norm-peak-excl"):
configure.norm_peak_excl = options.norm_peak_excl
# Set the integration direction
if hlr_utils.cli_provide_override(configure, "int_dir", "--int-dir"):
configure.int_dir = options.int_dir
# Get the scattering (polar) angle for axis TOF to Q conversion
if hlr_utils.cli_provide_override(configure, "scatt_angle",
"--scatt-angle"):
configure.scatt_angle = hlr_utils.DrParameterFromString(\
options.scatt_angle, True)
# Set the ability to dump the combined specular TOF information
if hlr_utils.cli_provide_override(configure, "dump_specular",
"--dump-specular"):
configure.dump_specular = options.dump_specular
# Set the ability to dump the combined background TOF information
if hlr_utils.cli_provide_override(configure, "dump_bkg", "--dump-bkg"):
configure.dump_bkg = options.dump_bkg
# Set the ability to dump the combined subtracted TOF information
if hlr_utils.cli_provide_override(configure, "dump_sub", "--dump-sub"):
configure.dump_sub = options.dump_sub
# Set the ability to dump the R(TOF) information
if hlr_utils.cli_provide_override(configure, "dump_rtof", "--dump-rtof"):
configure.dump_rtof = options.dump_rtof
# Set the ability to dump the combined R(TOF) information
if hlr_utils.cli_provide_override(configure, "dump_rtof_comb",
"--dump-rtof-comb"):
configure.dump_rtof_comb = options.dump_rtof_comb
# Set the ability to dump the R(Q) information
if hlr_utils.cli_provide_override(configure, "dump_rq", "--dump-rq"):
configure.dump_rq = options.dump_rq
# Set the ability to dump the R(Q) after rebinning information
if hlr_utils.cli_provide_override(configure, "dump_rqr", "--dump-rqr"):
configure.dump_rqr = options.dump_rqr
if hlr_utils.cli_provide_override(configure, "dump_all", "--dump-all"):
if options.dump_all:
configure.dump_specular = True
configure.dump_bkg = True
configure.dump_sub = True
configure.dump_rtof = True
configure.dump_rtof_comb = True
configure.dump_rq = True
configure.dump_rqr = True
def SansConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{SansOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.SansOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{SansOptions}
@type options: C{Option}
@param args: The parsed arguments from C{SansOptions}
@type args: C{list}
"""
# Call the configuration setter for InstOptions
hlr_utils.InstConfiguration(parser, configure, options, args, inst="SAS")
# Set the beam monitor path
if hlr_utils.cli_provide_override(configure, "bmon_path", "--bmon-path"):
configure.bmon_path = hlr_utils.NxPath(options.bmon_path)
# Set the transmission monitor path
if hlr_utils.cli_provide_override(configure, "tmon_path", "--tmon-path"):
configure.tmon_path = hlr_utils.NxPath(options.tmon_path)
# Set the sample data Transmission spectrum file
if hlr_utils.cli_provide_override(configure, "data_trans", "--data-trans"):
configure.data_trans = hlr_utils.determine_files(options.data_trans,
one_file=True)
# Set the solvent only Transmission spectrum file
if hlr_utils.cli_provide_override(configure, "solv_trans", "--solv-trans"):
configure.solv_trans = hlr_utils.determine_files(options.solv_trans,
one_file=True)
# Set the empty can Transmission spectrum file
if hlr_utils.cli_provide_override(configure, "ecan_trans", "--ecan-trans"):
configure.ecan_trans = hlr_utils.determine_files(options.ecan_trans,
one_file=True)
# Set the beam monitor override file
if hlr_utils.cli_provide_override(configure, "beammon_over",
"--beammon-over"):
configure.beammon_over = hlr_utils.determine_files(\
options.beammon_over,
configure.inst,
configure.facility,
configure.proposal,
stop_on_none=True)
# Set no_bmon_norm flag
if hlr_utils.cli_provide_override(configure, "no_bmon_norm",
"--no-bmon-norm"):
configure.no_bmon_norm = options.no_bmon_norm
# Set mon_effc flag
if hlr_utils.cli_provide_override(configure, "mon_effc", "--mon-effc"):
configure.mon_effc = options.mon_effc
# Set the monitor efficiency constant
if hlr_utils.cli_provide_override(configure, "mon_eff_const",
"--mon-eff-const"):
configure.mon_eff_const = hlr_utils.DrParameterFromString(\
options.mon_eff_const, True)
# Set det_effc flag
if hlr_utils.cli_provide_override(configure, "det_effc", "--det-effc"):
configure.det_effc = options.det_effc
# Set the detector efficiency scaling constant
if hlr_utils.cli_provide_override(configure, "det_eff_scale_const",
"--det-eff-scale-const"):
configure.det_eff_scale_const = hlr_utils.DrParameterFromString(\
options.det_eff_scale_const, True)
# Set the detector efficiency attenuation constant
if hlr_utils.cli_provide_override(configure, "det_eff_atten_const",
"--det-eff-atten-const"):
configure.det_eff_atten_const = hlr_utils.DrParameterFromString(\
options.det_eff_atten_const, True)
# Set the ROI file
if hlr_utils.cli_provide_override(configure, "roi_file", "--roi-file"):
configure.roi_file = hlr_utils.determine_files(options.roi_file,
one_file=True)
# Set the momentum transfer bins
if hlr_utils.cli_provide_override(configure, "Q_bins", "--mom-trans-bins"):
configure.Q_bins = hlr_utils.AxisFromString(options.Q_bins)
# Set the theta bins
if hlr_utils.cli_provide_override(configure, "theta_bins", "--theta-bins"):
configure.theta_bins = hlr_utils.AxisFromString(options.theta_bins)
# Set the radius bins
if hlr_utils.cli_provide_override(configure, "r_bins", "--r-bins"):
configure.r_bins = hlr_utils.AxisFromString(options.r_bins)
# Set the time-zero offset for the detector
if hlr_utils.cli_provide_override(configure, "time_zero_offset_det",
"--time-zero-offset-det"):
configure.time_zero_offset_det = hlr_utils.DrParameterFromString(\
options.time_zero_offset_det, True)
# Set the time-zero offset for the monitor
if hlr_utils.cli_provide_override(configure, "time_zero_offset_mon",
"--time-zero-offset-mon"):
configure.time_zero_offset_mon = hlr_utils.DrParameterFromString(\
options.time_zero_offset_mon, True)
# Set the lambda bins for use with dump-bmnorm-wave
if hlr_utils.cli_provide_override(configure, "lambda_bins",
"--lambda-bins"):
configure.lambda_bins = hlr_utils.AxisFromString(options.lambda_bins)
# Set the low-side lambda cut for cutting wavelength spectra
if hlr_utils.cli_provide_override(configure, "lambda_low_cut",
"--lambda-low-cut"):
try:
configure.lambda_low_cut = float(options.lambda_low_cut)
except TypeError:
configure.lambda_low_cut = options.lambda_low_cut
# Set the high-side lambda cut for cutting wavelength spectra
if hlr_utils.cli_provide_override(configure, "lambda_high_cut",
"--lambda-high-cut"):
try:
configure.lambda_high_cut = float(options.lambda_high_cut)
except TypeError:
configure.lambda_high_cut = options.lambda_high_cut
# Set the coefficients for the wavelength dependent background correction
if hlr_utils.cli_provide_override(configure, "bkg_coeff", "--bkg-coeff"):
try:
configure.bkg_coeff = options.bkg_coeff.split(',')
except AttributeError:
configure.bkg_coeff = options.bkg_coeff
# Set the accelerator down time for sample data
if hlr_utils.cli_provide_override(configure, "data_acc_down_time",
"--data-acc-down-time"):
configure.data_acc_down_time = hlr_utils.DrParameterFromString(\
options.data_acc_down_time, True)
# Set the accelerator down time for sample data
if hlr_utils.cli_provide_override(configure, "solv_acc_down_time",
"--solv-acc-down-time"):
configure.solv_acc_down_time = hlr_utils.DrParameterFromString(\
options.solv_acc_down_time, True)
# Set the accelerator down time for sample ecan
if hlr_utils.cli_provide_override(configure, "ecan_acc_down_time",
"--ecan-acc-down-time"):
configure.ecan_acc_down_time = hlr_utils.DrParameterFromString(\
options.ecan_acc_down_time, True)
# Set the accelerator down time for sample data
if hlr_utils.cli_provide_override(configure, "open_acc_down_time",
"--open-acc-down-time"):
configure.open_acc_down_time = hlr_utils.DrParameterFromString(\
options.open_acc_down_time, True)
# Set the axis dependent background scaling constant
if hlr_utils.cli_provide_override(configure, "bkg_scale", "--bkg-scale"):
try:
configure.bkg_scale = float(options.bkg_scale)
except TypeError:
configure.bkg_scale = options.bkg_scale
# Set the final data rescaling constant
if hlr_utils.cli_provide_override(configure, "rescale_final",
"--rescale-final"):
try:
configure.rescale_final = float(options.rescale_final)
except TypeError:
configure.rescale_final = options.rescale_final
# Set the ability to dump the detector pixel wavelength information
if hlr_utils.cli_provide_override(configure, "dump_wave", "--dump-wave"):
configure.dump_wave = options.dump_wave
# Set the ability to dump the beam monitor wavelength information
if hlr_utils.cli_provide_override(configure, "dump_bmon_wave",
"--dump-bmon-wave"):
configure.dump_bmon_wave = options.dump_bmon_wave
# Set the ability to dump the efficiency corrected beam monitor wavelength
# information
if hlr_utils.cli_provide_override(configure, "dump_bmon_effc",
"--dump-bmon-effc"):
configure.dump_bmon_effc = options.dump_bmon_effc
# Set the ability to dump the rebinned beam monitor wavelength information
if hlr_utils.cli_provide_override(configure, "dump_bmon_rebin",
"--dump-bmon-rebin"):
configure.dump_bmon_rebin = options.dump_bmon_rebin
# Set the ability to dump the wavelength information after beam monitor
# normalization
if hlr_utils.cli_provide_override(configure, "dump_wave_bmnorm",
"--dump-wave-bmnorm"):
configure.dump_wave_bmnorm = options.dump_wave_bmnorm
# Set the ability to dump the fractional counts and fractional area
# separately after rebinning in Q
if hlr_utils.cli_provide_override(configure, "dump_frac_rebin",
"--dump-frac-rebin"):
configure.dump_frac_rebin = options.dump_frac_rebin
# Set the ability to dump a TOF vs radius distribution
if hlr_utils.cli_provide_override(configure, "dump_tof_r", "--dump-tof-r"):
configure.dump_tof_r = options.dump_tof_r
# Set the ability to dump a TOF vs polar angle distribution
if hlr_utils.cli_provide_override(configure, "dump_tof_theta",
"--dump-tof-theta"):
configure.dump_tof_theta = options.dump_tof_theta
# Set the ability to dump a wavelength vs radius distribution
if hlr_utils.cli_provide_override(configure, "dump_wave_r",
"--dump-wave-r"):
configure.dump_wave_r = options.dump_wave_r
# Set the ability to dump a wavelength vs polar angle distribution
if hlr_utils.cli_provide_override(configure, "dump_wave_theta",
"--dump-wave-theta"):
configure.dump_wave_theta = options.dump_wave_theta
# Set the ability to dump a momentum transfer vs radius distribution
if hlr_utils.cli_provide_override(configure, "dump_Q_r",
"--dump-Q-r"):
configure.dump_Q_r = options.dump_Q_r
# Set the ability to dump a momentum transfer vs polar angle distribution
if hlr_utils.cli_provide_override(configure, "dump_Q_theta",
"--dump-Q-theta"):
configure.dump_Q_theta = options.dump_Q_theta
if hlr_utils.cli_provide_override(configure, "dump_2d", "--dump-2d"):
if options.dump_2d:
configure.dump_tof_r = True
configure.dump_tof_theta = True
configure.dump_wave_r = True
configure.dump_wave_theta = True
configure.dump_Q_r = True
configure.dump_Q_theta = True
if hlr_utils.cli_provide_override(configure, "dump_all", "--dump-all"):
if options.dump_all:
configure.dump_wave = True
configure.dump_bmon_wave = True
configure.dump_bmon_effc = True
configure.dump_bmon_rebin = True
configure.dump_wave_bmnorm = True
configure.dump_frac_rebin = True
configure.dump_tof_r = True
configure.dump_tof_theta = True
configure.dump_wave_r = True
configure.dump_wave_theta = True
configure.dump_Q_r = True
configure.dump_Q_theta = True
# Do some cross-checks
if configure.dump_tof_r or configure.dump_wave_r or configure.dump_Q_r:
if configure.r_bins is None:
parser.error("Must specify --r-bins option when using 2D "\
+"distribution options --dump-tof-r, "\
+"--dump-wave-r or --dump-Q-r.")
if configure.dump_tof_theta or configure.dump_wave_theta or \
configure.dump_Q_theta:
if configure.theta_bins is None:
parser.error("Must specify --theta-bins option when using 2D "\
+"distribution options --dump-tof-theta, "\
+"--dump-wave-theta or --dump-Q-theta.")
def IgsConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{IgsOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.IgsOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{IgsOptions}
@type options: C{Option}
@param args: The parsed arguments from C{IgsOptions}
@type args: C{list}
"""
# Call the configuration setter for InstOptions
hlr_options.InstConfiguration(parser, configure, options, args, inst="IGS")
# Set the ROI file
if hlr_utils.cli_provide_override(configure, "roi_file", "--roi-file"):
configure.roi_file = hlr_utils.determine_files(options.roi_file,
one_file=True)
# Set the monitor path
if hlr_utils.cli_provide_override(configure, "mon_path", "--mon-path"):
configure.mon_path = hlr_utils.NxPath(options.mon_path)
# Set the dead time
if hlr_utils.cli_provide_override(configure, "dead_time", "--dead-time"):
configure.dead_time = hlr_utils.DrParameterFromString(\
options.dead_time)
# Set the minimum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_min",
"--tof-cut-min"):
configure.tof_cut_min = options.tof_cut_min
# Set the maximum TOF channel for spectrum cutting
if hlr_utils.cli_provide_override(configure, "tof_cut_max",
"--tof-cut-max"):
configure.tof_cut_max = options.tof_cut_max
# Set the time-independent background TOFs
if hlr_utils.cli_provide_override(configure, "tib_tofs", "--tib-tofs"):
if options.tib_tofs is not None:
configure.tib_tofs = options.tib_tofs.split(',')
else:
configure.tib_tofs = options.tib_tofs
# Set the time-independent background constant for data
if hlr_utils.cli_provide_override(configure, "tib_data_const",
"--tib-data-const"):
configure.tib_data_const = hlr_utils.DrParameterFromString(\
options.tib_data_const, True)
# Set the time-independent background constant for ecan
if hlr_utils.cli_provide_override(configure, "tib_ecan_const",
"--tib-ecan-const"):
configure.tib_ecan_const = hlr_utils.DrParameterFromString(\
options.tib_ecan_const, True)
# Set the time-independent background constant for back
if hlr_utils.cli_provide_override(configure, "tib_back_const",
"--tib-back-const"):
configure.tib_back_const = hlr_utils.DrParameterFromString(\
options.tib_back_const, True)
# Set the time-independent background constant for norm
if hlr_utils.cli_provide_override(configure, "tib_norm_const",
"--tib-norm-const"):
configure.tib_norm_const = hlr_utils.DrParameterFromString(\
options.tib_norm_const, True)
# Set the time-independent background constant for dsback
if hlr_utils.cli_provide_override(configure, "tib_dsback_const",
"--tib-dsback-const"):
configure.tib_dsback_const = hlr_utils.DrParameterFromString(\
options.tib_dsback_const, True)
# Set the normalization start wavelength
if hlr_utils.cli_provide_override(configure, "norm_start", "--norm_start"):
configure.norm_start = float(options.norm_start)
# Set the normalization end wavelength
if hlr_utils.cli_provide_override(configure, "norm_end", "--norm_end"):
configure.norm_end = float(options.norm_end)
# Set no_mon_norm flag
if hlr_utils.cli_provide_override(configure, "no_mon_norm",
"--no-mon-norm"):
configure.no_mon_norm = options.no_mon_norm
# Set no_mon_effc flag
if hlr_utils.cli_provide_override(configure, "no_mon_effc",
"--no-mon-effc"):
configure.no_mon_effc = options.no_mon_effc
# Set the final wavelength
if hlr_utils.cli_provide_override(configure, "wavelength_final",
"--wavelength-final"):
configure.wavelength_final = hlr_utils.DrParameterFromString(\
options.wavelength_final, True)
# Set the time-zero offset
if hlr_utils.cli_provide_override(configure, "time_zero_offset",
"--time-zero-offset"):
configure.time_zero_offset = hlr_utils.DrParameterFromString(\
options.time_zero_offset, True)
# Set the time-zero slope
if hlr_utils.cli_provide_override(configure, "time_zero_slope",
"--time-zero-slope"):
configure.time_zero_slope = hlr_utils.DrParameterFromString(\
options.time_zero_slope, True)
# Set the lambda bins for use with dump-mnorm-wave
if hlr_utils.cli_provide_override(configure, "lambda_bins",
"--lambda-bins"):
configure.lambda_bins = hlr_utils.AxisFromString(options.lambda_bins)
# Set the ability to dump the time-independent background information
if hlr_utils.cli_provide_override(configure, "dump_tib", "--dump-tib"):
configure.dump_tib = options.dump_tib
# Set the ability to dump the wavelength information
if hlr_utils.cli_provide_override(configure, "dump_wave", "--dump-wave"):
configure.dump_wave = options.dump_wave
# Set the ability to dump the monitor wavelength information
if hlr_utils.cli_provide_override(configure, "dump_mon_wave",
"--dump-mon-wave"):
configure.dump_mon_wave = options.dump_mon_wave
# Set the ability to dump the rebinned monitor wavelength information
if hlr_utils.cli_provide_override(configure, "dump_mon_rebin",
"--dump-mon-rebin"):
configure.dump_mon_rebin = options.dump_mon_rebin
# Set the ability to dump the efficiency corrected monitor wavelength
# information
if hlr_utils.cli_provide_override(configure, "dump_mon_effc",
"--dump-mon-effc"):
configure.dump_mon_effc = options.dump_mon_effc
# Set the ability to dump the wavelength information
if hlr_utils.cli_provide_override(configure, "dump_wave_mnorm",
"--dump-wave-mnorm"):
configure.dump_wave_mnorm = options.dump_wave_mnorm
if hlr_utils.cli_provide_override(configure, "dump_all", "--dump-all"):
if options.dump_all:
configure.dump_tib = True
configure.dump_wave = True
configure.dump_mon_wave = True
configure.dump_mon_wave = True
configure.dump_mon_effc = True
configure.dump_mon_diml = True
configure.dump_mon_rebin = True
configure.dump_wave_mnorm = True
# Set the filter option
if hlr_utils.cli_provide_override(configure, "filter", "--filter",
"--no-filter"):
configure.filter = options.filter
# Set MC option
if hlr_utils.cli_provide_override(configure, "mc", "--mc"):
configure.mc = options.mc
# Set the early background subtraction option
if hlr_utils.cli_provide_override(configure, "hwfix", "--hwfix"):
configure.hwfix = options.hwfix
# Set the constant for scaling the background spectra: sample
if hlr_utils.cli_provide_override(configure, "scale_bs", "--scale-bs"):
configure.scale_bs = hlr_utils.DrParameterFromString(
options.scale_bs, True)
# Set the constant for scaling the background spectra: normalization
if hlr_utils.cli_provide_override(configure, "scale_bn", "--scale-bn"):
configure.scale_bn = hlr_utils.DrParameterFromString(
options.scale_bn, True)
# Set the constant for scaling the background spectra: empty container
# for sample
if hlr_utils.cli_provide_override(configure, "scale_bcs", "--scale-bcs"):
configure.scale_bcs = hlr_utils.DrParameterFromString(\
options.scale_bcs, True)
# Set the constant for scaling the background spectra: empty container
# for normalization
if hlr_utils.cli_provide_override(configure, "scale_bcn", "--scale-bcn"):
configure.scale_bcn = hlr_utils.DrParameterFromString(\
options.scale_bcn, True)
# Set the constant for scaling the empty container spectra: sample
if hlr_utils.cli_provide_override(configure, "scale_cs", "--scale-cs"):
configure.scale_cs = hlr_utils.DrParameterFromString(
options.scale_cs, True)
# Set the constant for scaling the empty container spectra: normalization
if hlr_utils.cli_provide_override(configure, "scale_cn", "--scale-cn"):
configure.scale_cn = hlr_utils.DrParameterFromString(
options.scale_cn, True)
# Set the elastic peak range in TOF
if hlr_utils.cli_provide_override(configure, "tof_elastic",
"--tof-elastic"):
if options.tof_elastic is not None:
configure.tof_elastic = options.tof_elastic.split(',')
else:
configure.tof_elastic = options.tof_elastic