def tof_to_scalar_Q(obj, **kwargs):
"""
This function converts a primary axis of a C{SOM} or C{SO} from
time-of-flight to scalarQ. The time-of-flight axis for a C{SOM} must be in
units of I{microseconds}. The primary axis of a C{SO} is assumed to be in
units of I{microseconds}. A C{tuple} of C{(time-of-flight,
time-of-flight_err2)} (assumed to be in units of I{microseconds}) can be
converted to C{(scalar_Q, scalar_Q_err2)}.
@param obj: Object to be converted
@type obj: C{SOM.SOM}, C{SOM.SO} or C{tuple}
@param kwargs: A list of keyword arguments that the function accepts:
@keyword polar: The polar angle and its associated error^2
@type polar: C{tuple} or C{list} of C{tuple}s
@keyword pathlength: The pathlength and its associated error^2
@type pathlength: C{tuple} or C{list} of C{tuple}s
@keyword angle_offset: A constant offset for the polar angle and its
associated error^2. The units of the offset should
be in radians.
@type angle_offset: C{tuple}
@keyword lojac: A flag that allows one to turn off the calculation of the
linear-order Jacobian. The default action is True for
histogram data.
@type lojac: C{boolean}
@keyword units: The expected units for this function. The default for this
function is I{microseconds}.
@type units: C{string}
@return: Object with a primary axis in time-of-flight converted to scalar Q
@rtype: C{SOM.SOM}, C{SOM.SO} or C{tuple}
@raise TypeError: The incoming object is not a type the function recognizes
@raise RuntimeError: A C{SOM} is not passed and no polar angle is provided
@raise RuntimeError: The C{SOM} x-axis units are not I{microseconds}
"""
# import the helper functions
import hlr_utils
# set up for working through data
(result, res_descr) = hlr_utils.empty_result(obj)
o_descr = hlr_utils.get_descr(obj)
if o_descr == "list":
raise TypeError("Do not know how to handle given type: %s" % \
o_descr)
else:
pass
# Setup keyword arguments
try:
polar = kwargs["polar"]
except KeyError:
polar = None
try:
pathlength = kwargs["pathlength"]
except KeyError:
pathlength = None
try:
units = kwargs["units"]
except KeyError:
units = "microseconds"
try:
lojac = kwargs["lojac"]
except KeyError:
lojac = hlr_utils.check_lojac(obj)
try:
angle_offset = kwargs["angle_offset"]
except KeyError:
angle_offset = None
# Primary axis for transformation. If a SO is passed, the function, will
# assume the axis for transformation is at the 0 position
if o_descr == "SOM":
axis = hlr_utils.one_d_units(obj, units)
else:
axis = 0
result = hlr_utils.copy_som_attr(result, res_descr, obj, o_descr)
if res_descr == "SOM":
result = hlr_utils.force_units(result, "1/Angstroms", axis)
result.setAxisLabel(axis, "scalar wavevector transfer")
result.setYUnits("Counts/A-1")
result.setYLabel("Intensity")
else:
pass
if pathlength is None or polar is None:
if o_descr == "SOM":
try:
obj.attr_list.instrument.get_primary()
inst = obj.attr_list.instrument
except RuntimeError:
raise RuntimeError("A detector was not provided")
else:
if pathlength is None and polar is None:
raise RuntimeError("If no SOM is provided, then pathlength "\
+"and polar angle information must be "\
+"provided")
elif pathlength is None:
raise RuntimeError("If no SOM is provided, then pathlength "\
+"information must be provided")
elif polar is None:
raise RuntimeError("If no SOM is provided, then polar angle "\
+"information must be provided")
else:
raise RuntimeError("If you get here, see Steve Miller for "\
+"your mug.")
else:
pass
if pathlength is not None:
p_descr = hlr_utils.get_descr(pathlength)
else:
pass
if polar is not None:
a_descr = hlr_utils.get_descr(polar)
else:
pass
# iterate through the values
import axis_manip
if lojac:
import utils
for i in xrange(hlr_utils.get_length(obj)):
val = hlr_utils.get_value(obj, i, o_descr, "x", axis)
err2 = hlr_utils.get_err2(obj, i, o_descr, "x", axis)
map_so = hlr_utils.get_map_so(obj, None, i)
if pathlength is None:
(pl, pl_err2) = hlr_utils.get_parameter("total", map_so, inst)
else:
pl = hlr_utils.get_value(pathlength, i, p_descr)
pl_err2 = hlr_utils.get_err2(pathlength, i, p_descr)
if polar is None:
(angle,
angle_err2) = hlr_utils.get_parameter("polar", map_so, inst)
else:
angle = hlr_utils.get_value(polar, i, a_descr)
angle_err2 = hlr_utils.get_err2(polar, i, a_descr)
if angle_offset is not None:
angle += angle_offset[0]
angle_err2 += angle_offset[1]
value = axis_manip.tof_to_scalar_Q(val, err2, pl, pl_err2, angle,
angle_err2)
if lojac:
y_val = hlr_utils.get_value(obj, i, o_descr, "y")
y_err2 = hlr_utils.get_err2(obj, i, o_descr, "y")
counts = utils.linear_order_jacobian(val, value[0], y_val, y_err2)
else:
pass
if o_descr != "number":
value1 = axis_manip.reverse_array_cp(value[0])
value2 = axis_manip.reverse_array_cp(value[1])
rev_value = (value1, value2)
else:
rev_value = value
if map_so is not None:
if not lojac:
map_so.y = axis_manip.reverse_array_cp(map_so.y)
map_so.var_y = axis_manip.reverse_array_cp(map_so.var_y)
else:
map_so.y = axis_manip.reverse_array_cp(counts[0])
map_so.var_y = axis_manip.reverse_array_cp(counts[1])
else:
pass
hlr_utils.result_insert(result, res_descr, rev_value, map_so, "x",
axis)
return result
def run(config, tim):
"""
This method is where the data reduction process gets done.
@param config: Object containing the data reduction configuration
information.
@type config: L{hlr_utils.Configure}
@param tim: Object that will allow the method to perform timing
evaluations.
@type tim: C{sns_time.DiffTime}
"""
import DST
import math
if config.inst == "REF_M":
import axis_manip
import utils
if tim is not None:
tim.getTime(False)
old_time = tim.getOldTime()
if config.data is None:
raise RuntimeError("Need to pass a data filename to the driver "\
+"script.")
# Read in sample data geometry if one is provided
if config.data_inst_geom is not None:
if config.verbose:
print "Reading in sample data instrument geometry file"
data_inst_geom_dst = DST.getInstance("application/x-NxsGeom",
config.data_inst_geom)
else:
data_inst_geom_dst = None
# Read in normalization data geometry if one is provided
if config.norm_inst_geom is not None:
if config.verbose:
print "Reading in normalization instrument geometry file"
norm_inst_geom_dst = DST.getInstance("application/x-NxsGeom",
config.norm_inst_geom)
else:
norm_inst_geom_dst = None
# Perform Steps 1-6 on sample data
d_som1 = dr_lib.process_ref_data(config.data, config,
config.data_roi_file,
config.dbkg_roi_file,
config.no_bkg,
tof_cuts=config.tof_cuts,
inst_geom_dst=data_inst_geom_dst,
timer=tim)
# Perform Steps 1-6 on normalization data
if config.norm is not None:
n_som1 = dr_lib.process_ref_data(config.norm, config,
config.norm_roi_file,
config.nbkg_roi_file,
config.no_norm_bkg,
dataset_type="norm",
tof_cuts=config.tof_cuts,
inst_geom_dst=norm_inst_geom_dst,
timer=tim)
else:
n_som1 = None
if config.Q_bins is None and config.scatt_angle is not None:
import copy
tof_axis = copy.deepcopy(d_som1[0].axis[0].val)
# Closing sample data instrument geometry file
if data_inst_geom_dst is not None:
data_inst_geom_dst.release_resource()
# Closing normalization data instrument geometry file
if norm_inst_geom_dst is not None:
norm_inst_geom_dst.release_resource()
# Step 7: Sum all normalization spectra together
if config.norm is not None:
n_som2 = dr_lib.sum_all_spectra(n_som1)
else:
n_som2 = None
del n_som1
# Step 8: Divide data by normalization
if config.verbose and config.norm is not None:
print "Scale data by normalization"
if config.norm is not None:
d_som2 = common_lib.div_ncerr(d_som1, n_som2, length_one_som=True)
else:
d_som2 = d_som1
if tim is not None and config.norm is not None:
tim.getTime(msg="After normalizing signal spectra")
del d_som1, n_som2
if config.dump_rtof_comb:
d_som2_1 = dr_lib.sum_all_spectra(d_som2)
d_som2_2 = dr_lib.data_filter(d_som2_1)
del d_som2_1
if config.inst == "REF_M":
tof_bc = utils.calc_bin_centers(d_som2_2[0].axis[0].val)
d_som2_2[0].axis[0].val = tof_bc[0]
d_som2_2.setDataSetType("density")
hlr_utils.write_file(config.output, "text/Spec", d_som2_2,
output_ext="crtof",
verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="combined R(TOF) information")
del d_som2_2
if config.dump_rtof:
if config.inst == "REF_M":
d_som2_1 = d_som2
else:
d_som2_1 = dr_lib.filter_ref_data(d_som2)
hlr_utils.write_file(config.output, "text/Spec", d_som2_1,
output_ext="rtof",
verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="R(TOF) information")
del d_som2_1
if config.inst == "REF_L":
# Step 9: Convert TOF to scalar Q
if config.verbose:
print "Converting TOF to scalar Q"
# Check to see if polar angle offset is necessary
if config.angle_offset is not None:
# Check on units, offset must be in radians
p_temp = config.angle_offset.toFullTuple(True)
if p_temp[2] == "degrees" or p_temp[2] == "degree":
deg_to_rad = (math.pi / 180.0)
p_off_rads = p_temp[0] * deg_to_rad
p_off_err2_rads = p_temp[1] * deg_to_rad * deg_to_rad
else:
p_off_rads = p_temp[0]
p_off_err2_rads = p_temp[1]
p_offset = (p_off_rads, p_off_err2_rads)
d_som2.attr_list["angle_offset"] = config.angle_offset
else:
p_offset = None
if tim is not None:
tim.getTime(False)
d_som3 = common_lib.tof_to_scalar_Q(d_som2, units="microsecond",
angle_offset=p_offset,
lojac=False)
del d_som2
if tim is not None:
tim.getTime(msg="After converting wavelength to scalar Q ")
if config.dump_rq:
d_som3_1 = dr_lib.data_filter(d_som3, clean_axis=True)
hlr_utils.write_file(config.output, "text/Spec", d_som3_1,
output_ext="rq",
verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="pixel R(Q) information")
del d_som3_1
if not config.no_filter:
if config.verbose:
print "Filtering final data"
if tim is not None:
tim.getTime(False)
d_som4 = dr_lib.data_filter(d_som3)
if tim is not None:
tim.getTime(msg="After filtering data")
else:
d_som4 = d_som3
del d_som3
else:
d_som4 = d_som2
# Step 10: Rebin all spectra to final Q axis
if config.Q_bins is None:
if config.scatt_angle is None:
config.Q_bins = dr_lib.create_axis_from_data(d_som4)
rebin_axis = config.Q_bins.toNessiList()
else:
# Get scattering angle and make Q conversion from TOF axis
# Check on units, scattering angle must be in radians
sa_temp = config.scatt_angle.toFullTuple(True)
if sa_temp[2] == "degrees" or sa_temp[2] == "degree":
deg_to_rad = (math.pi / 180.0)
sa_rads = sa_temp[0] * deg_to_rad
sa_err2_rads = sa_temp[1] * deg_to_rad * deg_to_rad
else:
sa_rads = sa_temp[0]
sa_err2_rads = sa_temp[1]
sa = (sa_rads, sa_err2_rads)
pl = d_som4.attr_list.instrument.get_total_path(d_som4[0].id,
det_secondary=True)
import nessi_list
tof_axis_err2 = nessi_list.NessiList(len(tof_axis))
rebin_axis = axis_manip.tof_to_scalar_Q(tof_axis,
tof_axis_err2,
pl[0], pl[1],
sa[0], sa[1])[0]
axis_manip.reverse_array_nc(rebin_axis)
else:
rebin_axis = config.Q_bins.toNessiList()
if config.inst == "REF_L":
if config.verbose:
print "Rebinning spectra"
if tim is not None:
tim.getTime(False)
d_som5 = common_lib.rebin_axis_1D_linint(d_som4, rebin_axis)
if tim is not None:
tim.getTime(msg="After rebinning spectra")
del d_som4
if config.dump_rqr:
hlr_utils.write_file(config.output, "text/Spec", d_som5,
output_ext="rqr",
verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="pixel R(Q) (after rebinning) "\
+"information")
# Step 11: Sum all rebinned spectra
if config.verbose:
print "Summing spectra"
if tim is not None:
tim.getTime(False)
d_som6 = dr_lib.sum_all_spectra(d_som5)
if tim is not None:
tim.getTime(msg="After summing spectra")
del d_som5
else:
d_som5 = d_som4
if config.inst == "REF_M":
d_som5A = dr_lib.sum_all_spectra(d_som5)
del d_som5
d_som6 = dr_lib.data_filter(d_som5A)
del d_som5A
axis_manip.reverse_array_nc(d_som6[0].y)
axis_manip.reverse_array_nc(d_som6[0].var_y)
d_som6.setYLabel("Intensity")
d_som6.setYUnits("Counts/A-1")
d_som6.setAllAxisLabels(["scalar wavevector transfer"])
d_som6.setAllAxisUnits(["1/Angstroms"])
Q_bc = utils.calc_bin_centers(rebin_axis)
d_som6[0].axis[0].val = Q_bc[0]
d_som6.setDataSetType("density")
hlr_utils.write_file(config.output, "text/Spec", d_som6,
replace_ext=False,
replace_path=False,
verbose=config.verbose,
message="combined Reflectivity information")
d_som6.attr_list["config"] = config
hlr_utils.write_file(config.output, "text/rmd", d_som6,
output_ext="rmd", verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="metadata")
if tim is not None:
tim.setOldTime(old_time)
tim.getTime(msg="Total Running Time")
def tof_to_ref_scalar_Q(obj, **kwargs):
"""
This function converts a primary axis of a C{SOM} or C{SO} from
time-of-flight to reflectometer scalar Q. This means that a single angle
and a single flightpath is used. The time-of-flight axis for a C{SOM} must
be in units of I{microseconds}. The primary axis of a C{SO} is assumed to
be in units of I{microseconds}. A C{tuple} of C{(time-of-flight,
time-of-flight_err2)} (assumed to be in units of I{microseconds}) can be
converted to C{(scalar_Q, scalar_Q_err2)}.
@param obj: Object to be converted
@type obj: C{SOM.SOM}, C{SOM.SO} or C{tuple}
@param kwargs: A list of keyword arguments that the function accepts:
@keyword polar: The polar angle and its associated error^2
@type polar: C{tuple}
@keyword pathlength: The pathlength and its associated error^2
@type pathlength: C{tuple}
@keyword angle_offset: A constant offset for the polar angle and its
associated error^2. The units of the offset should
be in radians.
@type angle_offset: C{tuple}
@keyword lojac: A flag that allows one to turn off the calculation of the
linear-order Jacobian. The default action is True for
histogram data.
@type lojac: C{boolean}
@keyword units: The expected units for this function. The default for this
function is I{microseconds}.
@type units: C{string}
@keyword configure: This is the object containing the driver configuration.
This will signal the function to write out the counts
and fractional area to files.
@type configure: C{Configure}
@return: Object with a primary axis in time-of-flight converted to
reflectometer scalar Q
@rtype: C{SOM.SOM}, C{SOM.SO} or C{tuple}
@raise TypeError: The incoming object is not a type the function recognizes
@raise RuntimeError: A C{SOM} is not passed and no polar angle is provided
@raise RuntimeError: The C{SOM} x-axis units are not I{microseconds}
"""
# import the helper functions
import hlr_utils
# set up for working through data
(result, res_descr) = hlr_utils.empty_result(obj)
o_descr = hlr_utils.get_descr(obj)
if o_descr == "list":
raise TypeError("Do not know how to handle given type: %s" % \
o_descr)
else:
pass
# Setup keyword arguments
polar = kwargs.get("polar")
pathlength = kwargs.get("pathlength")
units = kwargs.get("units", "microseconds")
lojac = kwargs.get("lojac", hlr_utils.check_lojac(obj))
angle_offset = kwargs.get("angle_offset")
config = kwargs.get("configure")
if config is None:
beamdiv_corr = False
else:
beamdiv_corr = config.beamdiv_corr
# Primary axis for transformation. If a SO is passed, the function, will
# assume the axis for transformation is at the 0 position
if o_descr == "SOM":
axis = hlr_utils.one_d_units(obj, units)
else:
axis = 0
result = hlr_utils.copy_som_attr(result, res_descr, obj, o_descr)
if res_descr == "SOM":
result = hlr_utils.force_units(result, "1/Angstroms", axis)
result.setAxisLabel(axis, "scalar wavevector transfer")
result.setYUnits("Counts/A-1")
result.setYLabel("Intensity")
else:
pass
if pathlength is None or polar is None:
if o_descr == "SOM":
try:
obj.attr_list.instrument.get_primary()
inst = obj.attr_list.instrument
except RuntimeError:
raise RuntimeError("A detector was not provided")
else:
if pathlength is None and polar is None:
raise RuntimeError("If no SOM is provided, then pathlength "\
+"and polar angle information must be "\
+"provided")
elif pathlength is None:
raise RuntimeError("If no SOM is provided, then pathlength "\
+"information must be provided")
elif polar is None:
raise RuntimeError("If no SOM is provided, then polar angle "\
+"information must be provided")
else:
raise RuntimeError("If you get here, see Steve Miller for "\
+"your mug.")
else:
pass
if pathlength is None:
(pl,
pl_err2) = obj.attr_list.instrument.get_total_path(obj[0].id,
det_secondary=True)
else:
(pl, pl_err2) = pathlength
if polar is None:
angle = hlr_utils.get_special(obj.attr_list["data-theta"], obj[0])[0]
angle_err2 = 0.0
else:
(angle, angle_err2) = polar
if angle_offset is not None:
angle += angle_offset[0]
angle_err2 += angle_offset[1]
# Need to multiply angle by 2.0 in order to make it be Theta to
# underlying conversion function
angle *= 2.0
angle_err2 *= 4.0
# iterate through the values
import axis_manip
if lojac:
import utils
if beamdiv_corr:
import dr_lib
for i in xrange(hlr_utils.get_length(obj)):
skip_pixel = False
val = hlr_utils.get_value(obj, i, o_descr, "x", axis)
err2 = hlr_utils.get_err2(obj, i, o_descr, "x", axis)
map_so = hlr_utils.get_map_so(obj, None, i)
if beamdiv_corr:
dangle = dr_lib.ref_beamdiv_correct(obj.attr_list, map_so.id,
config.det_spat_res,
config.center_pix)
# We subtract due to the inversion of the z coordinates from the
# mirror reflection of the beam at the sample.
if dangle is not None:
pangle = angle - (2.0 * dangle)
else:
pangle = angle
skip_pixel = True
else:
pangle = angle
value = axis_manip.tof_to_scalar_Q(val, err2, pl, pl_err2, pangle,
angle_err2)
if lojac:
y_val = hlr_utils.get_value(obj, i, o_descr, "y")
y_err2 = hlr_utils.get_err2(obj, i, o_descr, "y")
counts = utils.linear_order_jacobian(val, value[0], y_val, y_err2)
else:
pass
if o_descr != "number":
value1 = axis_manip.reverse_array_cp(value[0])
value2 = axis_manip.reverse_array_cp(value[1])
rev_value = (value1, value2)
else:
rev_value = value
if map_so is not None:
if not lojac:
map_so.y = axis_manip.reverse_array_cp(map_so.y)
map_so.var_y = axis_manip.reverse_array_cp(map_so.var_y)
else:
map_so.y = axis_manip.reverse_array_cp(counts[0])
map_so.var_y = axis_manip.reverse_array_cp(counts[1])
else:
pass
if not skip_pixel:
hlr_utils.result_insert(result, res_descr, rev_value, map_so, "x",
axis)
return result
def run(config, tim):
"""
This method is where the data reduction process gets done.
@param config: Object containing the data reduction configuration
information.
@type config: L{hlr_utils.Configure}
@param tim: Object that will allow the method to perform timing
evaluations.
@type tim: C{sns_time.DiffTime}
"""
import DST
import math
if config.inst == "REF_M":
import axis_manip
import utils
if tim is not None:
tim.getTime(False)
old_time = tim.getOldTime()
if config.data is None:
raise RuntimeError("Need to pass a data filename to the driver " + "script.")
# Read in sample data geometry if one is provided
if config.data_inst_geom is not None:
if config.verbose:
print "Reading in sample data instrument geometry file"
data_inst_geom_dst = DST.getInstance("application/x-NxsGeom", config.data_inst_geom)
else:
data_inst_geom_dst = None
# Read in normalization data geometry if one is provided
if config.norm_inst_geom is not None:
if config.verbose:
print "Reading in normalization instrument geometry file"
norm_inst_geom_dst = DST.getInstance("application/x-NxsGeom", config.norm_inst_geom)
else:
norm_inst_geom_dst = None
# Perform Steps 1-6 on sample data
d_som1 = dr_lib.process_ref_data(
config.data,
config,
config.data_roi_file,
config.dbkg_roi_file,
config.no_bkg,
tof_cuts=config.tof_cuts,
inst_geom_dst=data_inst_geom_dst,
timer=tim,
)
# Perform Steps 1-6 on normalization data
if config.norm is not None:
n_som1 = dr_lib.process_ref_data(
config.norm,
config,
config.norm_roi_file,
config.nbkg_roi_file,
config.no_norm_bkg,
dataset_type="norm",
tof_cuts=config.tof_cuts,
inst_geom_dst=norm_inst_geom_dst,
timer=tim,
)
else:
n_som1 = None
if config.Q_bins is None and config.scatt_angle is not None:
import copy
tof_axis = copy.deepcopy(d_som1[0].axis[0].val)
# Closing sample data instrument geometry file
if data_inst_geom_dst is not None:
data_inst_geom_dst.release_resource()
# Closing normalization data instrument geometry file
if norm_inst_geom_dst is not None:
norm_inst_geom_dst.release_resource()
# Step 7: Sum all normalization spectra together
if config.norm is not None:
n_som2 = dr_lib.sum_all_spectra(n_som1)
else:
n_som2 = None
del n_som1
# Step 8: Divide data by normalization
if config.verbose and config.norm is not None:
print "Scale data by normalization"
if config.norm is not None:
d_som2 = common_lib.div_ncerr(d_som1, n_som2, length_one_som=True)
else:
d_som2 = d_som1
if tim is not None and config.norm is not None:
tim.getTime(msg="After normalizing signal spectra")
del d_som1, n_som2
if config.dump_rtof_comb:
d_som2_1 = dr_lib.sum_all_spectra(d_som2)
d_som2_2 = dr_lib.data_filter(d_som2_1)
del d_som2_1
if config.inst == "REF_M":
tof_bc = utils.calc_bin_centers(d_som2_2[0].axis[0].val)
d_som2_2[0].axis[0].val = tof_bc[0]
d_som2_2.setDataSetType("density")
hlr_utils.write_file(
config.output,
"text/Spec",
d_som2_2,
output_ext="crtof",
verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="combined R(TOF) information",
)
del d_som2_2
if config.dump_rtof:
if config.inst == "REF_M":
d_som2_1 = d_som2
else:
d_som2_1 = dr_lib.filter_ref_data(d_som2)
hlr_utils.write_file(
config.output,
"text/Spec",
d_som2_1,
output_ext="rtof",
verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="R(TOF) information",
)
del d_som2_1
if config.inst == "REF_L":
# Step 9: Convert TOF to scalar Q
if config.verbose:
print "Converting TOF to scalar Q"
# Check to see if polar angle offset is necessary
if config.angle_offset is not None:
# Check on units, offset must be in radians
p_temp = config.angle_offset.toFullTuple(True)
if p_temp[2] == "degrees" or p_temp[2] == "degree":
deg_to_rad = math.pi / 180.0
p_off_rads = p_temp[0] * deg_to_rad
p_off_err2_rads = p_temp[1] * deg_to_rad * deg_to_rad
else:
p_off_rads = p_temp[0]
p_off_err2_rads = p_temp[1]
p_offset = (p_off_rads, p_off_err2_rads)
d_som2.attr_list["angle_offset"] = config.angle_offset
else:
p_offset = None
if tim is not None:
tim.getTime(False)
d_som3 = common_lib.tof_to_scalar_Q(d_som2, units="microsecond", angle_offset=p_offset, lojac=False)
del d_som2
if tim is not None:
tim.getTime(msg="After converting wavelength to scalar Q ")
if config.dump_rq:
d_som3_1 = dr_lib.data_filter(d_som3, clean_axis=True)
hlr_utils.write_file(
config.output,
"text/Spec",
d_som3_1,
output_ext="rq",
verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="pixel R(Q) information",
)
del d_som3_1
if not config.no_filter:
if config.verbose:
print "Filtering final data"
if tim is not None:
tim.getTime(False)
d_som4 = dr_lib.data_filter(d_som3)
if tim is not None:
tim.getTime(msg="After filtering data")
else:
d_som4 = d_som3
del d_som3
else:
d_som4 = d_som2
# Step 10: Rebin all spectra to final Q axis
if config.Q_bins is None:
if config.scatt_angle is None:
config.Q_bins = dr_lib.create_axis_from_data(d_som4)
rebin_axis = config.Q_bins.toNessiList()
else:
# Get scattering angle and make Q conversion from TOF axis
# Check on units, scattering angle must be in radians
sa_temp = config.scatt_angle.toFullTuple(True)
if sa_temp[2] == "degrees" or sa_temp[2] == "degree":
deg_to_rad = math.pi / 180.0
sa_rads = sa_temp[0] * deg_to_rad
sa_err2_rads = sa_temp[1] * deg_to_rad * deg_to_rad
else:
sa_rads = sa_temp[0]
sa_err2_rads = sa_temp[1]
sa = (sa_rads, sa_err2_rads)
pl = d_som4.attr_list.instrument.get_total_path(d_som4[0].id, det_secondary=True)
import nessi_list
tof_axis_err2 = nessi_list.NessiList(len(tof_axis))
rebin_axis = axis_manip.tof_to_scalar_Q(tof_axis, tof_axis_err2, pl[0], pl[1], sa[0], sa[1])[0]
axis_manip.reverse_array_nc(rebin_axis)
else:
rebin_axis = config.Q_bins.toNessiList()
if config.inst == "REF_L":
if config.verbose:
print "Rebinning spectra"
if tim is not None:
tim.getTime(False)
d_som5 = common_lib.rebin_axis_1D_linint(d_som4, rebin_axis)
if tim is not None:
tim.getTime(msg="After rebinning spectra")
del d_som4
if config.dump_rqr:
hlr_utils.write_file(
config.output,
"text/Spec",
d_som5,
output_ext="rqr",
verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="pixel R(Q) (after rebinning) " + "information",
)
# Step 11: Sum all rebinned spectra
if config.verbose:
print "Summing spectra"
if tim is not None:
tim.getTime(False)
d_som6 = dr_lib.sum_all_spectra(d_som5)
if tim is not None:
tim.getTime(msg="After summing spectra")
del d_som5
else:
d_som5 = d_som4
if config.inst == "REF_M":
d_som5A = dr_lib.sum_all_spectra(d_som5)
del d_som5
d_som6 = dr_lib.data_filter(d_som5A)
del d_som5A
axis_manip.reverse_array_nc(d_som6[0].y)
axis_manip.reverse_array_nc(d_som6[0].var_y)
d_som6.setYLabel("Intensity")
d_som6.setYUnits("Counts/A-1")
d_som6.setAllAxisLabels(["scalar wavevector transfer"])
d_som6.setAllAxisUnits(["1/Angstroms"])
Q_bc = utils.calc_bin_centers(rebin_axis)
d_som6[0].axis[0].val = Q_bc[0]
d_som6.setDataSetType("density")
hlr_utils.write_file(
config.output,
"text/Spec",
d_som6,
replace_ext=False,
replace_path=False,
verbose=config.verbose,
message="combined Reflectivity information",
)
d_som6.attr_list["config"] = config
hlr_utils.write_file(
config.output,
"text/rmd",
d_som6,
output_ext="rmd",
verbose=config.verbose,
data_ext=config.ext_replacement,
path_replacement=config.path_replacement,
message="metadata",
)
if tim is not None:
tim.setOldTime(old_time)
tim.getTime(msg="Total Running Time")
def tof_to_ref_scalar_Q(obj, **kwargs):
"""
This function converts a primary axis of a C{SOM} or C{SO} from
time-of-flight to reflectometer scalar Q. This means that a single angle
and a single flightpath is used. The time-of-flight axis for a C{SOM} must
be in units of I{microseconds}. The primary axis of a C{SO} is assumed to
be in units of I{microseconds}. A C{tuple} of C{(time-of-flight,
time-of-flight_err2)} (assumed to be in units of I{microseconds}) can be
converted to C{(scalar_Q, scalar_Q_err2)}.
@param obj: Object to be converted
@type obj: C{SOM.SOM}, C{SOM.SO} or C{tuple}
@param kwargs: A list of keyword arguments that the function accepts:
@keyword polar: The polar angle and its associated error^2
@type polar: C{tuple}
@keyword pathlength: The pathlength and its associated error^2
@type pathlength: C{tuple}
@keyword angle_offset: A constant offset for the polar angle and its
associated error^2. The units of the offset should
be in radians.
@type angle_offset: C{tuple}
@keyword lojac: A flag that allows one to turn off the calculation of the
linear-order Jacobian. The default action is True for
histogram data.
@type lojac: C{boolean}
@keyword units: The expected units for this function. The default for this
function is I{microseconds}.
@type units: C{string}
@keyword configure: This is the object containing the driver configuration.
This will signal the function to write out the counts
and fractional area to files.
@type configure: C{Configure}
@return: Object with a primary axis in time-of-flight converted to
reflectometer scalar Q
@rtype: C{SOM.SOM}, C{SOM.SO} or C{tuple}
@raise TypeError: The incoming object is not a type the function recognizes
@raise RuntimeError: A C{SOM} is not passed and no polar angle is provided
@raise RuntimeError: The C{SOM} x-axis units are not I{microseconds}
"""
# import the helper functions
import hlr_utils
# set up for working through data
(result, res_descr) = hlr_utils.empty_result(obj)
o_descr = hlr_utils.get_descr(obj)
if o_descr == "list":
raise TypeError("Do not know how to handle given type: %s" % \
o_descr)
else:
pass
# Setup keyword arguments
polar = kwargs.get("polar")
pathlength = kwargs.get("pathlength")
units = kwargs.get("units", "microseconds")
lojac = kwargs.get("lojac", hlr_utils.check_lojac(obj))
angle_offset = kwargs.get("angle_offset")
config = kwargs.get("configure")
if config is None:
beamdiv_corr = False
else:
beamdiv_corr = config.beamdiv_corr
# Primary axis for transformation. If a SO is passed, the function, will
# assume the axis for transformation is at the 0 position
if o_descr == "SOM":
axis = hlr_utils.one_d_units(obj, units)
else:
axis = 0
result = hlr_utils.copy_som_attr(result, res_descr, obj, o_descr)
if res_descr == "SOM":
result = hlr_utils.force_units(result, "1/Angstroms", axis)
result.setAxisLabel(axis, "scalar wavevector transfer")
result.setYUnits("Counts/A-1")
result.setYLabel("Intensity")
else:
pass
if pathlength is None or polar is None:
if o_descr == "SOM":
try:
obj.attr_list.instrument.get_primary()
inst = obj.attr_list.instrument
except RuntimeError:
raise RuntimeError("A detector was not provided")
else:
if pathlength is None and polar is None:
raise RuntimeError("If no SOM is provided, then pathlength "\
+"and polar angle information must be "\
+"provided")
elif pathlength is None:
raise RuntimeError("If no SOM is provided, then pathlength "\
+"information must be provided")
elif polar is None:
raise RuntimeError("If no SOM is provided, then polar angle "\
+"information must be provided")
else:
raise RuntimeError("If you get here, see Steve Miller for "\
+"your mug.")
else:
pass
if pathlength is None:
(pl, pl_err2) = obj.attr_list.instrument.get_total_path(obj[0].id,
det_secondary=True)
else:
(pl, pl_err2) = pathlength
if polar is None:
angle = hlr_utils.get_special(obj.attr_list["data-theta"], obj[0])[0]
angle_err2 = 0.0
else:
(angle, angle_err2) = polar
if angle_offset is not None:
angle += angle_offset[0]
angle_err2 += angle_offset[1]
# Need to multiply angle by 2.0 in order to make it be Theta to
# underlying conversion function
angle *= 2.0
angle_err2 *= 4.0
# iterate through the values
import axis_manip
if lojac:
import utils
if beamdiv_corr:
import dr_lib
for i in xrange(hlr_utils.get_length(obj)):
skip_pixel = False
val = hlr_utils.get_value(obj, i, o_descr, "x", axis)
err2 = hlr_utils.get_err2(obj, i, o_descr, "x", axis)
map_so = hlr_utils.get_map_so(obj, None, i)
if beamdiv_corr:
dangle = dr_lib.ref_beamdiv_correct(obj.attr_list, map_so.id,
config.det_spat_res,
config.center_pix)
# We subtract due to the inversion of the z coordinates from the
# mirror reflection of the beam at the sample.
if dangle is not None:
pangle = angle - (2.0 * dangle)
else:
pangle = angle
skip_pixel = True
else:
pangle = angle
value = axis_manip.tof_to_scalar_Q(val, err2, pl, pl_err2, pangle,
angle_err2)
if lojac:
y_val = hlr_utils.get_value(obj, i, o_descr, "y")
y_err2 = hlr_utils.get_err2(obj, i, o_descr, "y")
counts = utils.linear_order_jacobian(val, value[0],
y_val, y_err2)
else:
pass
if o_descr != "number":
value1 = axis_manip.reverse_array_cp(value[0])
value2 = axis_manip.reverse_array_cp(value[1])
rev_value = (value1, value2)
else:
rev_value = value
if map_so is not None:
if not lojac:
map_so.y = axis_manip.reverse_array_cp(map_so.y)
map_so.var_y = axis_manip.reverse_array_cp(map_so.var_y)
else:
map_so.y = axis_manip.reverse_array_cp(counts[0])
map_so.var_y = axis_manip.reverse_array_cp(counts[1])
else:
pass
if not skip_pixel:
hlr_utils.result_insert(result, res_descr, rev_value, map_so, "x",
axis)
return result
def tof_to_scalar_Q(obj, **kwargs):
"""
This function converts a primary axis of a C{SOM} or C{SO} from
time-of-flight to scalarQ. The time-of-flight axis for a C{SOM} must be in
units of I{microseconds}. The primary axis of a C{SO} is assumed to be in
units of I{microseconds}. A C{tuple} of C{(time-of-flight,
time-of-flight_err2)} (assumed to be in units of I{microseconds}) can be
converted to C{(scalar_Q, scalar_Q_err2)}.
@param obj: Object to be converted
@type obj: C{SOM.SOM}, C{SOM.SO} or C{tuple}
@param kwargs: A list of keyword arguments that the function accepts:
@keyword polar: The polar angle and its associated error^2
@type polar: C{tuple} or C{list} of C{tuple}s
@keyword pathlength: The pathlength and its associated error^2
@type pathlength: C{tuple} or C{list} of C{tuple}s
@keyword angle_offset: A constant offset for the polar angle and its
associated error^2. The units of the offset should
be in radians.
@type angle_offset: C{tuple}
@keyword lojac: A flag that allows one to turn off the calculation of the
linear-order Jacobian. The default action is True for
histogram data.
@type lojac: C{boolean}
@keyword units: The expected units for this function. The default for this
function is I{microseconds}.
@type units: C{string}
@return: Object with a primary axis in time-of-flight converted to scalar Q
@rtype: C{SOM.SOM}, C{SOM.SO} or C{tuple}
@raise TypeError: The incoming object is not a type the function recognizes
@raise RuntimeError: A C{SOM} is not passed and no polar angle is provided
@raise RuntimeError: The C{SOM} x-axis units are not I{microseconds}
"""
# import the helper functions
import hlr_utils
# set up for working through data
(result, res_descr) = hlr_utils.empty_result(obj)
o_descr = hlr_utils.get_descr(obj)
if o_descr == "list":
raise TypeError("Do not know how to handle given type: %s" % \
o_descr)
else:
pass
# Setup keyword arguments
try:
polar = kwargs["polar"]
except KeyError:
polar = None
try:
pathlength = kwargs["pathlength"]
except KeyError:
pathlength = None
try:
units = kwargs["units"]
except KeyError:
units = "microseconds"
try:
lojac = kwargs["lojac"]
except KeyError:
lojac = hlr_utils.check_lojac(obj)
try:
angle_offset = kwargs["angle_offset"]
except KeyError:
angle_offset = None
# Primary axis for transformation. If a SO is passed, the function, will
# assume the axis for transformation is at the 0 position
if o_descr == "SOM":
axis = hlr_utils.one_d_units(obj, units)
else:
axis = 0
result = hlr_utils.copy_som_attr(result, res_descr, obj, o_descr)
if res_descr == "SOM":
result = hlr_utils.force_units(result, "1/Angstroms", axis)
result.setAxisLabel(axis, "scalar wavevector transfer")
result.setYUnits("Counts/A-1")
result.setYLabel("Intensity")
else:
pass
if pathlength is None or polar is None:
if o_descr == "SOM":
try:
obj.attr_list.instrument.get_primary()
inst = obj.attr_list.instrument
except RuntimeError:
raise RuntimeError("A detector was not provided")
else:
if pathlength is None and polar is None:
raise RuntimeError("If no SOM is provided, then pathlength "\
+"and polar angle information must be "\
+"provided")
elif pathlength is None:
raise RuntimeError("If no SOM is provided, then pathlength "\
+"information must be provided")
elif polar is None:
raise RuntimeError("If no SOM is provided, then polar angle "\
+"information must be provided")
else:
raise RuntimeError("If you get here, see Steve Miller for "\
+"your mug.")
else:
pass
if pathlength is not None:
p_descr = hlr_utils.get_descr(pathlength)
else:
pass
if polar is not None:
a_descr = hlr_utils.get_descr(polar)
else:
pass
# iterate through the values
import axis_manip
if lojac:
import utils
for i in xrange(hlr_utils.get_length(obj)):
val = hlr_utils.get_value(obj, i, o_descr, "x", axis)
err2 = hlr_utils.get_err2(obj, i, o_descr, "x", axis)
map_so = hlr_utils.get_map_so(obj, None, i)
if pathlength is None:
(pl, pl_err2) = hlr_utils.get_parameter("total", map_so, inst)
else:
pl = hlr_utils.get_value(pathlength, i, p_descr)
pl_err2 = hlr_utils.get_err2(pathlength, i, p_descr)
if polar is None:
(angle, angle_err2) = hlr_utils.get_parameter("polar", map_so,
inst)
else:
angle = hlr_utils.get_value(polar, i, a_descr)
angle_err2 = hlr_utils.get_err2(polar, i, a_descr)
if angle_offset is not None:
angle += angle_offset[0]
angle_err2 += angle_offset[1]
value = axis_manip.tof_to_scalar_Q(val, err2, pl, pl_err2, angle,
angle_err2)
if lojac:
y_val = hlr_utils.get_value(obj, i, o_descr, "y")
y_err2 = hlr_utils.get_err2(obj, i, o_descr, "y")
counts = utils.linear_order_jacobian(val, value[0],
y_val, y_err2)
else:
pass
if o_descr != "number":
value1 = axis_manip.reverse_array_cp(value[0])
value2 = axis_manip.reverse_array_cp(value[1])
rev_value = (value1, value2)
else:
rev_value = value
if map_so is not None:
if not lojac:
map_so.y = axis_manip.reverse_array_cp(map_so.y)
map_so.var_y = axis_manip.reverse_array_cp(map_so.var_y)
else:
map_so.y = axis_manip.reverse_array_cp(counts[0])
map_so.var_y = axis_manip.reverse_array_cp(counts[1])
else:
pass
hlr_utils.result_insert(result, res_descr, rev_value, map_so, "x",
axis)
return result
