def _convert_units_wavelength(self, unit, input_ws, output_ws, target):
if unit != 'Wavelength':
# Configure conversion
if unit == 'dSpacing':
emode = 'Elastic'
efixed = 0.0
elif unit == 'DeltaE':
emode = 'Indirect'
from IndirectCommon import getEfixed
efixed = getEfixed(input_ws)
else:
raise ValueError(
'Unit %s in sample workspace is not supported' % unit)
# Do conversion
# Use temporary workspace so we don't modify data
s_api.ConvertUnits(InputWorkspace=input_ws,
OutputWorkspace=output_ws,
Target=target,
EMode=emode,
EFixed=efixed)
else:
# No need to convert
s_api.CloneWorkspace(InputWorkspace=input_ws,
OutputWorkspace=output_ws)
def _get_efixed(self, workspace):
"""
Gets an efixed value form a workspace.
@param workspace Name of workspace to extract from
@return Fixed energy value
"""
from IndirectCommon import getEfixed
try:
# Try to get efixed from the parameters first
efixed = getEfixed(workspace)
except ValueError:
# If that fails then get it by taking from group of all detectors
wsHandle = mtd[workspace]
spectra_list = list(range(0, wsHandle.getNumberHistograms()))
GroupDetectors(InputWorkspace=workspace,
OutputWorkspace=workspace,
SpectraList=spectra_list)
wsHandle = mtd[workspace]
det = wsHandle.getDetector(0)
efixed = wsHandle.getEFixed(det.getID())
return efixed
def _convert_units_wavelength(self, unit, input_ws, output_ws, target):
if unit != 'Wavelength':
# Configure conversion
if unit == 'dSpacing':
emode = 'Elastic'
efixed = 0.0
elif unit == 'DeltaE':
emode = 'Indirect'
from IndirectCommon import getEfixed
efixed = getEfixed(input_ws)
else:
raise ValueError('Unit %s in sample workspace is not supported' % unit)
# Do conversion
# Use temporary workspace so we don't modify data
s_api.ConvertUnits(InputWorkspace=input_ws,
OutputWorkspace=output_ws,
Target=target,
EMode=emode,
EFixed=efixed)
else:
# No need to convert
s_api.CloneWorkspace(InputWorkspace=input_ws,
OutputWorkspace=output_ws)
def _get_efixed(self, workspace):
"""
Gets an efixed value form a workspace.
@param workspace Name of workspace to extract from
@return Fixed energy value
"""
from IndirectCommon import getEfixed
try:
# Try to get efixed from the parameters first
efixed = getEfixed(workspace)
except ValueError:
# If that fails then get it by taking from group of all detectors
wsHandle = mtd[workspace]
spectra_list = list(range(0, wsHandle.getNumberHistograms()))
GroupDetectors(InputWorkspace=workspace,
OutputWorkspace=workspace,
SpectraList=spectra_list)
wsHandle = mtd[workspace]
det = wsHandle.getDetector(0)
efixed = wsHandle.getEFixed(det.getID())
return efixed
def _ascii_3d_import(self):
"""
Import 3D ASCII data (e.g. I(Q, t)).
"""
logger.notice('Loading ASCII data')
from IndirectCommon import getEfixed
from IndirectNeutron import ChangeAngles, InstrParas
# Read file
data = []
x_axis = ('time', 'ns')
v_axis = ('q', 'ang^-1')
with open(self._file_name, 'r') as handle:
for line in handle:
line = line.strip()
# Ignore empty lines
if line == '':
continue
# Data line (if not comment)
elif line.strip()[0] != '#':
line_values = np.array([ast.literal_eval(t.strip()) if 'nan' not in t.lower() else np.nan for t in line.split()])
data.append(line_values)
if x_axis is None or v_axis is None:
raise ValueError('Data is not in expected format for 3D data')
logger.debug('X axis: {0}'.format(x_axis))
logger.debug('V axis: {0}'.format(v_axis))
# Get axis and Y values
data = np.swapaxes(np.array(data), 0, 1)
x_axis_values = data[0,1:]
v_axis_values = data[1:,0]
y_values = np.ravel(data[1:,1:])
# Create the workspace
wks = CreateWorkspace(OutputWorkspace=self._out_ws,
DataX=x_axis_values,
DataY=y_values,
NSpec=v_axis_values.size,
UnitX=x_axis[1],
EnableLogging=False)
# Load the MolDyn instrument
q_max = v_axis_values[-1]
instrument = 'MolDyn'
reflection = '2' if q_max <= 2.0 else '4'
InstrParas(wks.name(), instrument, 'simul', reflection)
# Process angles
efixed = getEfixed(wks.name())
logger.information('Qmax={0}, Efixed={1}'.format(q_max, efixed))
wave = 1.8 * math.sqrt(25.2429 / efixed)
qw = wave * v_axis_values / (4.0 * math.pi)
theta = 2.0 * np.degrees(np.arcsin(qw))
ChangeAngles(wks.name(), instrument, theta)
return wks
def _pre_process_corrections(self):
"""
If the sample is not in wavelength then convert the corrections to
whatever units the sample is in.
"""
unit_id = mtd[self._sample_ws_name].getAxis(0).getUnit().unitID()
logger.information('x-unit is ' + unit_id)
factor_types = ['ass']
if self._use_can:
factor_types.extend(['acc', 'acsc', 'assc'])
for factor_type in factor_types:
input_name = self._get_correction_factor_ws_name(factor_type)
output_name = self._corrections + '_' + factor_type
if unit_id != 'Wavelength':
# Configure conversion
if unit_id == 'dSpacing':
emode = 'Elastic'
efixed = 0.0
elif unit_id == 'DeltaE':
emode = 'Indirect'
from IndirectCommon import getEfixed
efixed = getEfixed(mtd[self._sample_ws_name])
else:
raise ValueError(
'Unit %s in sample workspace is not supported' %
unit_id)
# Do conversion
ConvertUnits(InputWorkspace=input_name,
OutputWorkspace=output_name,
Target=unit_id,
EMode=emode,
EFixed=efixed)
else:
# No need to convert
CloneWorkspace(InputWorkspace=input_name,
OutputWorkspace=output_name)
# Group the temporary factor workspaces (for easy removal later)
GroupWorkspaces(InputWorkspaces=[
self._corrections + '_' + f_type for f_type in factor_types
],
OutputWorkspace=self._corrections)
def RunParas(ascWS, _instr, run, title):
ws = mtd[ascWS]
inst = ws.getInstrument()
AddSampleLog(Workspace=ascWS, LogName="facility", LogType="String", LogText="ILL")
ws.getRun()['run_number'] = run
ws.getRun()['run_title'] = title
efixed = getEfixed(ascWS)
facility = ws.getRun().getLogData('facility').value
logger.information('Facility is ' + facility)
runNo = ws.getRun()['run_number'].value
runTitle = ws.getRun()['run_title'].value.strip()
logger.information('Run : ' + str(runNo) + ' ; Title : ' + runTitle)
an = inst.getStringParameter('analyser')[0]
ref = inst.getStringParameter('reflection')[0]
logger.information('Analyser : ' + an + ref + ' with energy = ' + str(efixed))
return efixed
def RunParas(ascWS, _instr, run, title):
ws = mtd[ascWS]
inst = ws.getInstrument()
AddSampleLog(Workspace=ascWS, LogName="facility", LogType="String", LogText="ILL")
ws.getRun()['run_number'] = run
ws.getRun()['run_title'] = title
efixed = getEfixed(ascWS)
facility = ws.getRun().getLogData('facility').value
logger.information('Facility is ' + facility)
runNo = ws.getRun()['run_number'].value
runTitle = ws.getRun()['run_title'].value.strip()
logger.information('Run : ' + str(runNo) + ' ; Title : ' + runTitle)
an = inst.getStringParameter('analyser')[0]
ref = inst.getStringParameter('reflection')[0]
logger.information('Analyser : ' + an + ref + ' with energy = ' + str(efixed))
return efixed
def _pre_process_corrections(self):
"""
If the sample is not in wavelength then convert the corrections to
whatever units the sample is in.
"""
unit_id = mtd[self._sample_ws_name].getAxis(0).getUnit().unitID()
logger.information("x-unit is " + unit_id)
factor_types = ["ass"]
if self._use_can:
factor_types.extend(["acc", "acsc", "assc"])
for factor_type in factor_types:
input_name = self._get_correction_factor_ws_name(factor_type)
output_name = self._corrections + "_" + factor_type
if unit_id != "Wavelength":
# Configure conversion
if unit_id == "dSpacing":
emode = "Elastic"
efixed = 0.0
elif unit_id == "DeltaE":
emode = "Indirect"
from IndirectCommon import getEfixed
efixed = getEfixed(mtd[self._sample_ws_name])
else:
raise ValueError("Unit %s in sample workspace is not supported" % unit_id)
# Do conversion
ConvertUnits(
InputWorkspace=input_name, OutputWorkspace=output_name, Target=unit_id, EMode=emode, EFixed=efixed
)
else:
# No need to convert
CloneWorkspace(InputWorkspace=input_name, OutputWorkspace=output_name)
# Group the temporary factor workspaces (for easy removal later)
GroupWorkspaces(
InputWorkspaces=[self._corrections + "_" + f_type for f_type in factor_types],
OutputWorkspace=self._corrections,
)
def AbsRunFeeder(inputws, geom, beam, ncan, size, density, sigs, siga, avar,
plotOpt='None'):
'''Handles the feeding of input and plotting of output for the F2PY
absorption correction routine.'''
ws = mtd[inputws]
## workdir is default save directory
workdir = mantid.getConfigProperty('defaultsave.directory')
## prefix is instrument short name
prefix = ws.getInstrument().getName()
prefix = ConfigService().facility().instrument(prefix).shortName().lower()
## sam = run number
sam = ws.getRun().getLogData("run_number").value
## efixed can be taken from the instrument parameter file
efixed = getEfixed(inputws)
## Run the routine
workspaces = AbsRun(workdir, prefix, sam, geom, beam, ncan, size, density,
sigs, siga, avar, efixed, inputWS=inputws)
if ( plotOpt == 'None' ):
return
if ( plotOpt == 'Wavelength' or plotOpt == 'Both' ):
graph = plotSpectrum(workspaces, 0)
if ( plotOpt == 'Angle' or plotOpt == 'Both' ):
graph = plotTimeBin(workspaces, 0)
graph.activeLayer().setAxisTitle(Layer.Bottom, 'Angle')
def _get_amplitude_and_fwhm_from_fit(self, workspace):
from IndirectCommon import getEfixed
parameter_values = self._get_fit_parameters_from_fit(workspace, getEfixed(self._temporary_fit_name))
return parameter_values[0], parameter_values[2]
def PyExec(self):
from IndirectCommon import getEfixed
self._setup()
# Set up progress reporting
n_prog_reports = 2
if self._can_ws_name is not None:
n_prog_reports += 1
prog = Progress(self, 0.0, 1.0, n_prog_reports)
efixed = getEfixed(self._sample_ws_name)
sample_wave_ws = '__sam_wave'
ConvertUnits(InputWorkspace=self._sample_ws_name,
OutputWorkspace=sample_wave_ws,
Target='Wavelength',
EMode='Indirect',
EFixed=efixed,
EnableLogging=False)
sample_thickness = self._sample_outer_radius - self._sample_inner_radius
logger.information('Sample thickness: ' + str(sample_thickness))
prog.report('Calculating sample corrections')
if self._sample_density_type == 'Mass Density':
builder = MaterialBuilder()
mat = builder.setFormula(
self._sample_chemical_formula).setMassDensity(
self._sample_density).build()
self._sample_density = mat.numberDensity
SetSampleMaterial(sample_wave_ws,
ChemicalFormula=self._sample_chemical_formula,
SampleNumberDensity=self._sample_density)
AnnularRingAbsorption(
InputWorkspace=sample_wave_ws,
OutputWorkspace=self._ass_ws,
SampleHeight=3.0,
SampleThickness=sample_thickness,
CanInnerRadius=self._can_inner_radius,
CanOuterRadius=self._can_outer_radius,
SampleChemicalFormula=self._sample_chemical_formula,
SampleNumberDensity=self._sample_density,
NumberOfWavelengthPoints=10,
EventsPerPoint=self._events)
group = self._ass_ws
if self._can_ws_name is not None:
can1_wave_ws = '__can1_wave'
can2_wave_ws = '__can2_wave'
ConvertUnits(InputWorkspace=self._can_ws_name,
OutputWorkspace=can1_wave_ws,
Target='Wavelength',
EMode='Indirect',
EFixed=efixed,
EnableLogging=False)
if self._can_scale != 1.0:
logger.information('Scaling container by: ' +
str(self._can_scale))
Scale(InputWorkspace=can1_wave_ws,
OutputWorkspace=can1_wave_ws,
Factor=self._can_scale,
Operation='Multiply')
CloneWorkspace(InputWorkspace=can1_wave_ws,
OutputWorkspace=can2_wave_ws,
EnableLogging=False)
can_thickness_1 = self._sample_inner_radius - self._can_inner_radius
can_thickness_2 = self._can_outer_radius - self._sample_outer_radius
logger.information('Container thickness: %f & %f' %
(can_thickness_1, can_thickness_2))
if self._use_can_corrections:
prog.report('Calculating container corrections')
Divide(LHSWorkspace=sample_wave_ws,
RHSWorkspace=self._ass_ws,
OutputWorkspace=sample_wave_ws)
if self._can_density_type == 'Mass Density':
builder = MaterialBuilder()
mat = builder.setFormula(
self._can_chemical_formula).setMassDensity(
self._can_density).build()
self._can_density = mat.numberDensity
SetSampleMaterial(can1_wave_ws,
ChemicalFormula=self._can_chemical_formula,
SampleNumberDensity=self._can_density)
AnnularRingAbsorption(
InputWorkspace=can1_wave_ws,
OutputWorkspace='__Acc1',
SampleHeight=3.0,
SampleThickness=can_thickness_1,
CanInnerRadius=self._can_inner_radius,
CanOuterRadius=self._sample_outer_radius,
SampleChemicalFormula=self._can_chemical_formula,
SampleNumberDensity=self._can_density,
NumberOfWavelengthPoints=10,
EventsPerPoint=self._events)
SetSampleMaterial(can2_wave_ws,
ChemicalFormula=self._can_chemical_formula,
SampleNumberDensity=self._can_density)
AnnularRingAbsorption(
InputWorkspace=can2_wave_ws,
OutputWorkspace='__Acc2',
SampleHeight=3.0,
SampleThickness=can_thickness_2,
CanInnerRadius=self._sample_inner_radius,
CanOuterRadius=self._can_outer_radius,
SampleChemicalFormula=self._can_chemical_formula,
SampleNumberDensity=self._can_density,
NumberOfWavelengthPoints=10,
EventsPerPoint=self._events)
Multiply(LHSWorkspace='__Acc1',
RHSWorkspace='__Acc2',
OutputWorkspace=self._acc_ws,
EnableLogging=False)
DeleteWorkspace('__Acc1', EnableLogging=False)
DeleteWorkspace('__Acc2', EnableLogging=False)
Divide(LHSWorkspace=can1_wave_ws,
RHSWorkspace=self._acc_ws,
OutputWorkspace=can1_wave_ws)
Minus(LHSWorkspace=sample_wave_ws,
RHSWorkspace=can1_wave_ws,
OutputWorkspace=sample_wave_ws)
group += ',' + self._acc_ws
else:
prog.report('Calculating can scaling')
Minus(LHSWorkspace=sample_wave_ws,
RHSWorkspace=can1_wave_ws,
OutputWorkspace=sample_wave_ws)
Divide(LHSWorkspace=sample_wave_ws,
RHSWorkspace=self._ass_ws,
OutputWorkspace=sample_wave_ws)
DeleteWorkspace(can1_wave_ws, EnableLogging=False)
DeleteWorkspace(can2_wave_ws, EnableLogging=False)
else:
Divide(LHSWorkspace=sample_wave_ws,
RHSWorkspace=self._ass_ws,
OutputWorkspace=sample_wave_ws)
ConvertUnits(InputWorkspace=sample_wave_ws,
OutputWorkspace=self._output_ws,
Target='DeltaE',
EMode='Indirect',
EFixed=efixed,
EnableLogging=False)
DeleteWorkspace(sample_wave_ws, EnableLogging=False)
prog.report('Recording sample logs')
sample_log_workspaces = [self._output_ws, self._ass_ws]
sample_logs = [('sample_shape', 'annulus'),
('sample_filename', self._sample_ws_name),
('sample_inner', self._sample_inner_radius),
('sample_outer', self._sample_outer_radius),
('can_inner', self._can_inner_radius),
('can_outer', self._can_outer_radius)]
if self._can_ws_name is not None:
sample_logs.append(('container_filename', self._can_ws_name))
sample_logs.append(('container_scale', self._can_scale))
if self._use_can_corrections:
sample_log_workspaces.append(self._acc_ws)
sample_logs.append(('container_thickness_1', can_thickness_1))
sample_logs.append(('container_thickness_2', can_thickness_2))
log_names = [item[0] for item in sample_logs]
log_values = [item[1] for item in sample_logs]
for ws_name in sample_log_workspaces:
AddSampleLogMultiple(Workspace=ws_name,
LogNames=log_names,
LogValues=log_values,
EnableLogging=False)
self.setProperty('OutputWorkspace', self._output_ws)
# Output the Ass workspace if it is wanted, delete if not
if self._abs_ws == '':
DeleteWorkspace(self._ass_ws, EnableLogging=False)
if self._can_ws_name is not None and self._use_can_corrections:
DeleteWorkspace(self._acc_ws, EnableLogging=False)
else:
GroupWorkspaces(InputWorkspaces=group,
OutputWorkspace=self._abs_ws,
EnableLogging=False)
self.setProperty('CorrectionsWorkspace', self._abs_ws)
def PyExec(self):
# Check for platform support
if not is_supported_f2py_platform():
unsupported_msg = "This algorithm can only be run on valid platforms." \
+ " please view the algorithm documentation to see" \
+ " what platforms are currently supported"
raise RuntimeError(unsupported_msg)
from IndirectBayes import (CalcErange, GetXYE, ReadNormFile,
ReadWidthFile, QLAddSampleLogs, C2Fw, C2Se,
QuasiPlot)
from IndirectCommon import (CheckXrange, CheckAnalysers, getEfixed,
GetThetaQ, CheckHistZero, CheckHistSame,
IndentifyDataBoundaries)
setup_prog = Progress(self, start=0.0, end=0.3, nreports=5)
self.log().information('BayesQuasi input')
erange = [self._e_min, self._e_max]
nbins = [self._sam_bins, self._res_bins]
setup_prog.report('Converting to binary for Fortran')
#convert true/false to 1/0 for fortran
o_el = 1 if self._elastic else 0
o_w1 = 1 if self._width else 0
o_res = 1 if self._res_norm else 0
#fortran code uses background choices defined using the following numbers
setup_prog.report('Encoding input options')
if self._background == 'Sloping':
o_bgd = 2
elif self._background == 'Flat':
o_bgd = 1
elif self._background == 'Zero':
o_bgd = 0
fitOp = [o_el, o_bgd, o_w1, o_res]
setup_prog.report('Establishing save path')
workdir = config['defaultsave.directory']
if not os.path.isdir(workdir):
workdir = os.getcwd()
logger.information(
'Default Save directory is not set. Defaulting to current working Directory: '
+ workdir)
array_len = 4096 # length of array in Fortran
setup_prog.report('Checking X Range')
CheckXrange(erange, 'Energy')
nbin, nrbin = nbins[0], nbins[1]
logger.information('Sample is ' + self._samWS)
logger.information('Resolution is ' + self._resWS)
# Check for trailing and leading zeros in data
setup_prog.report(
'Checking for leading and trailing zeros in the data')
first_data_point, last_data_point = IndentifyDataBoundaries(
self._samWS)
if first_data_point > self._e_min:
logger.warning(
"Sample workspace contains leading zeros within the energy range."
)
logger.warning("Updating eMin: eMin = " + str(first_data_point))
self._e_min = first_data_point
if last_data_point < self._e_max:
logger.warning(
"Sample workspace contains trailing zeros within the energy range."
)
logger.warning("Updating eMax: eMax = " + str(last_data_point))
self._e_max = last_data_point
# update erange with new values
erange = [self._e_min, self._e_max]
setup_prog.report('Checking Analysers')
CheckAnalysers(self._samWS, self._resWS)
setup_prog.report('Obtaining EFixed, theta and Q')
efix = getEfixed(self._samWS)
theta, Q = GetThetaQ(self._samWS)
nsam, ntc = CheckHistZero(self._samWS)
totalNoSam = nsam
#check if we're performing a sequential fit
if self._loop != True:
nsam = 1
nres = CheckHistZero(self._resWS)[0]
setup_prog.report('Checking Histograms')
if self._program == 'QL':
if nres == 1:
prog = 'QLr' # res file
else:
prog = 'QLd' # data file
CheckHistSame(self._samWS, 'Sample', self._resWS, 'Resolution')
elif self._program == 'QSe':
if nres == 1:
prog = 'QSe' # res file
else:
raise ValueError('Stretched Exp ONLY works with RES file')
logger.information('Version is ' + prog)
logger.information(' Number of spectra = ' + str(nsam))
logger.information(' Erange : ' + str(erange[0]) + ' to ' +
str(erange[1]))
setup_prog.report('Reading files')
Wy, We = ReadWidthFile(self._width, self._wfile, totalNoSam)
dtn, xsc = ReadNormFile(self._res_norm, self._resnormWS, totalNoSam)
setup_prog.report('Establishing output workspace name')
fname = self._samWS[:-4] + '_' + prog
probWS = fname + '_Prob'
fitWS = fname + '_Fit'
wrks = os.path.join(workdir, self._samWS[:-4])
logger.information(' lptfile : ' + wrks + '_' + prog + '.lpt')
lwrk = len(wrks)
wrks.ljust(140, ' ')
wrkr = self._resWS
wrkr.ljust(140, ' ')
setup_prog.report('Initialising probability list')
# initialise probability list
if self._program == 'QL':
prob0 = []
prob1 = []
prob2 = []
xQ = np.array([Q[0]])
for m in range(1, nsam):
xQ = np.append(xQ, Q[m])
xProb = xQ
xProb = np.append(xProb, xQ)
xProb = np.append(xProb, xQ)
eProb = np.zeros(3 * nsam)
group = ''
workflow_prog = Progress(self, start=0.3, end=0.7, nreports=nsam * 3)
for m in range(0, nsam):
logger.information('Group ' + str(m) + ' at angle ' +
str(theta[m]))
nsp = m + 1
nout, bnorm, Xdat, Xv, Yv, Ev = CalcErange(self._samWS, m, erange,
nbin)
Ndat = nout[0]
Imin = nout[1]
Imax = nout[2]
if prog == 'QLd':
mm = m
else:
mm = 0
Nb, Xb, Yb, Eb = GetXYE(self._resWS, mm,
array_len) # get resolution data
numb = [nsam, nsp, ntc, Ndat, nbin, Imin, Imax, Nb, nrbin]
rscl = 1.0
reals = [efix, theta[m], rscl, bnorm]
if prog == 'QLr':
workflow_prog.report(
'Processing Sample number %i as Lorentzian' % nsam)
nd, xout, yout, eout, yfit, yprob = QLr.qlres(
numb, Xv, Yv, Ev, reals, fitOp, Xdat, Xb, Yb, Wy, We, dtn,
xsc, wrks, wrkr, lwrk)
message = ' Log(prob) : ' + str(yprob[0]) + ' ' + str(
yprob[1]) + ' ' + str(yprob[2]) + ' ' + str(yprob[3])
logger.information(message)
if prog == 'QLd':
workflow_prog.report('Processing Sample number %i' % nsam)
nd, xout, yout, eout, yfit, yprob = QLd.qldata(
numb, Xv, Yv, Ev, reals, fitOp, Xdat, Xb, Yb, Eb, Wy, We,
wrks, wrkr, lwrk)
message = ' Log(prob) : ' + str(yprob[0]) + ' ' + str(
yprob[1]) + ' ' + str(yprob[2]) + ' ' + str(yprob[3])
logger.information(message)
if prog == 'QSe':
workflow_prog.report(
'Processing Sample number %i as Stretched Exp' % nsam)
nd,xout,yout,eout,yfit,yprob=Qse.qlstexp(numb,Xv,Yv,Ev,reals,fitOp,\
Xdat,Xb,Yb,Wy,We,dtn,xsc,\
wrks,wrkr,lwrk)
dataX = xout[:nd]
dataX = np.append(dataX, 2 * xout[nd - 1] - xout[nd - 2])
yfit_list = np.split(yfit[:4 * nd], 4)
dataF1 = yfit_list[1]
if self._program == 'QL':
dataF2 = yfit_list[2]
workflow_prog.report('Processing data')
dataG = np.zeros(nd)
datX = dataX
datY = yout[:nd]
datE = eout[:nd]
datX = np.append(datX, dataX)
datY = np.append(datY, dataF1[:nd])
datE = np.append(datE, dataG)
res1 = dataF1[:nd] - yout[:nd]
datX = np.append(datX, dataX)
datY = np.append(datY, res1)
datE = np.append(datE, dataG)
nsp = 3
names = 'data,fit.1,diff.1'
res_plot = [0, 1, 2]
if self._program == 'QL':
workflow_prog.report('Processing Lorentzian result data')
datX = np.append(datX, dataX)
datY = np.append(datY, dataF2[:nd])
datE = np.append(datE, dataG)
res2 = dataF2[:nd] - yout[:nd]
datX = np.append(datX, dataX)
datY = np.append(datY, res2)
datE = np.append(datE, dataG)
nsp += 2
names += ',fit.2,diff.2'
res_plot.append(4)
prob0.append(yprob[0])
prob1.append(yprob[1])
prob2.append(yprob[2])
# create result workspace
fitWS = fname + '_Workspaces'
fout = fname + '_Workspace_' + str(m)
workflow_prog.report('Creating OutputWorkspace')
CreateWorkspace(OutputWorkspace=fout, DataX=datX, DataY=datY, DataE=datE,\
Nspec=nsp, UnitX='DeltaE', VerticalAxisUnit='Text', VerticalAxisValues=names)
# append workspace to list of results
group += fout + ','
comp_prog = Progress(self, start=0.7, end=0.8, nreports=2)
comp_prog.report('Creating Group Workspace')
GroupWorkspaces(InputWorkspaces=group, OutputWorkspace=fitWS)
if self._program == 'QL':
comp_prog.report('Processing Lorentzian probability data')
yPr0 = np.array([prob0[0]])
yPr1 = np.array([prob1[0]])
yPr2 = np.array([prob2[0]])
for m in range(1, nsam):
yPr0 = np.append(yPr0, prob0[m])
yPr1 = np.append(yPr1, prob1[m])
yPr2 = np.append(yPr2, prob2[m])
yProb = yPr0
yProb = np.append(yProb, yPr1)
yProb = np.append(yProb, yPr2)
probWs = CreateWorkspace(OutputWorkspace=probWS, DataX=xProb, DataY=yProb, DataE=eProb,\
Nspec=3, UnitX='MomentumTransfer')
outWS = C2Fw(self._samWS[:-4], fname)
if self._plot != 'None':
QuasiPlot(fname, self._plot, res_plot, self._loop)
if self._program == 'QSe':
comp_prog.report('Runnning C2Se')
outWS = C2Se(fname)
if self._plot != 'None':
QuasiPlot(fname, self._plot, res_plot, self._loop)
log_prog = Progress(self, start=0.8, end=1.0, nreports=8)
#Add some sample logs to the output workspaces
log_prog.report('Copying Logs to outputWorkspace')
CopyLogs(InputWorkspace=self._samWS, OutputWorkspace=outWS)
log_prog.report('Adding Sample logs to Output workspace')
QLAddSampleLogs(outWS, self._resWS, prog, self._background,
self._elastic, erange, (nbin, nrbin), self._resnormWS,
self._wfile)
log_prog.report('Copying logs to fit Workspace')
CopyLogs(InputWorkspace=self._samWS, OutputWorkspace=fitWS)
log_prog.report('Adding sample logs to Fit workspace')
QLAddSampleLogs(fitWS, self._resWS, prog, self._background,
self._elastic, erange, (nbin, nrbin), self._resnormWS,
self._wfile)
log_prog.report('Finialising log copying')
if self._save:
log_prog.report('Saving workspaces')
fit_path = os.path.join(workdir, fitWS + '.nxs')
SaveNexusProcessed(InputWorkspace=fitWS, Filename=fit_path)
out_path = os.path.join(workdir,
outWS + '.nxs') # path name for nxs file
SaveNexusProcessed(InputWorkspace=outWS, Filename=out_path)
logger.information('Output fit file created : ' + fit_path)
logger.information('Output paramter file created : ' + out_path)
self.setProperty('OutputWorkspaceFit', fitWS)
self.setProperty('OutputWorkspaceResult', outWS)
log_prog.report('Setting workspace properties')
if self._program == 'QL':
self.setProperty('OutputWorkspaceProb', probWS)
def PyExec(self):
from IndirectCommon import getEfixed
self._setup()
# Set up progress reporting
n_prog_reports = 2
if self._can_ws_name is not None:
n_prog_reports += 1
prog = Progress(self, 0.0, 1.0, n_prog_reports)
efixed = getEfixed(self._sample_ws)
sample_wave_ws = '__sam_wave'
ConvertUnits(InputWorkspace=self._sample_ws, OutputWorkspace=sample_wave_ws,
Target='Wavelength', EMode='Indirect', EFixed=efixed)
SetSampleMaterial(sample_wave_ws, ChemicalFormula=self._sample_chemical_formula, SampleNumberDensity=self._sample_number_density)
prog.report('Calculating sample corrections')
FlatPlateAbsorption(InputWorkspace=sample_wave_ws,
OutputWorkspace=self._ass_ws,
SampleHeight=self._sample_height,
SampleWidth=self._sample_width,
SampleThickness=self._sample_thickness,
ElementSize=self._element_size,
EMode='Indirect',
EFixed=efixed,
NumberOfWavelengthPoints=10)
plot_data = [self._output_ws, self._sample_ws]
plot_corr = [self._ass_ws]
group = self._ass_ws
if self._can_ws_name is not None:
can_wave_ws = '__can_wave'
ConvertUnits(InputWorkspace=self._can_ws_name, OutputWorkspace=can_wave_ws,
Target='Wavelength', EMode='Indirect', EFixed=efixed)
if self._can_scale != 1.0:
logger.information('Scaling container by: ' + str(self._can_scale))
Scale(InputWorkspace=can_wave_ws, OutputWorkspace=can_wave_ws, Factor=self._can_scale, Operation='Multiply')
if self._use_can_corrections:
prog.report('Calculating container corrections')
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
SetSampleMaterial(can_wave_ws, ChemicalFormula=self._can_chemical_formula, SampleNumberDensity=self._can_number_density)
FlatPlateAbsorption(InputWorkspace=can_wave_ws,
OutputWorkspace=self._acc_ws,
SampleHeight=self._sample_height,
SampleWidth=self._sample_width,
SampleThickness=self._can_front_thickness + self._can_back_thickness,
ElementSize=self._element_size,
EMode='Indirect',
EFixed=efixed,
NumberOfWavelengthPoints=10)
Divide(LHSWorkspace=can_wave_ws, RHSWorkspace=self._acc_ws, OutputWorkspace=can_wave_ws)
Minus(LHSWorkspace=sample_wave_ws, RHSWorkspace=can_wave_ws, OutputWorkspace=sample_wave_ws)
plot_corr.append(self._acc_ws)
group += ',' + self._acc_ws
else:
prog.report('Calculating container scaling')
Minus(LHSWorkspace=sample_wave_ws, RHSWorkspace=can_wave_ws, OutputWorkspace=sample_wave_ws)
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
DeleteWorkspace(can_wave_ws)
plot_data.append(self._can_ws_name)
else:
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
ConvertUnits(InputWorkspace=sample_wave_ws, OutputWorkspace=self._output_ws,
Target='DeltaE', EMode='Indirect', EFixed=efixed)
DeleteWorkspace(sample_wave_ws)
prog.report('Recording samle logs')
sample_log_workspaces = [self._output_ws, self._ass_ws]
sample_logs = [('sample_shape', 'flatplate'),
('sample_filename', self._sample_ws),
('sample_height', self._sample_height),
('sample_width', self._sample_width),
('sample_thickness', self._sample_thickness),
('element_size', self._element_size)]
if self._can_ws_name is not None:
sample_logs.append(('container_filename', self._can_ws_name))
sample_logs.append(('container_scale', self._can_scale))
if self._use_can_corrections:
sample_log_workspaces.append(self._acc_ws)
sample_logs.append(('container_front_thickness', self. _can_front_thickness))
sample_logs.append(('container_back_thickness', self. _can_back_thickness))
log_names = [item[0] for item in sample_logs]
log_values = [item[1] for item in sample_logs]
for ws_name in sample_log_workspaces:
AddSampleLogMultiple(Workspace=ws_name, LogNames=log_names, LogValues=log_values)
self.setProperty('OutputWorkspace', self._output_ws)
# Output the Ass workspace if it is wanted, delete if not
if self._abs_ws == '':
DeleteWorkspace(self._ass_ws)
if self._can_ws_name is not None and self._use_can_corrections:
DeleteWorkspace(self._acc_ws)
else:
GroupWorkspaces(InputWorkspaces=group, OutputWorkspace=self._abs_ws)
self.setProperty('CorrectionsWorkspace', self._abs_ws)
if self._plot:
from IndirectImport import import_mantidplot
mantid_plot = import_mantidplot()
mantid_plot.plotSpectrum(plot_data, 0)
if self._abs_ws != '':
mantid_plot.plotSpectrum(plot_corr, 0)
def PyExec(self):
from IndirectCommon import getEfixed
self._setup()
# Set up progress reporting
n_prog_reports = 2
if self._can_ws_name is not None:
n_prog_reports += 1
prog = Progress(self, 0.0, 1.0, n_prog_reports)
efixed = getEfixed(self._sample_ws)
sample_wave_ws = "__sam_wave"
ConvertUnits(
InputWorkspace=self._sample_ws,
OutputWorkspace=sample_wave_ws,
Target="Wavelength",
EMode="Indirect",
EFixed=efixed,
EnableLogging=False,
)
if self._sample_density_type == "Mass Density":
builder = MaterialBuilder()
mat = builder.setFormula(self._sample_chemical_formula).setMassDensity(self._sample_density).build()
self._sample_density = mat.numberDensity
SetSampleMaterial(
sample_wave_ws, ChemicalFormula=self._sample_chemical_formula, SampleNumberDensity=self._sample_density
)
prog.report("Calculating sample corrections")
FlatPlateAbsorption(
InputWorkspace=sample_wave_ws,
OutputWorkspace=self._ass_ws,
SampleHeight=self._sample_height,
SampleWidth=self._sample_width,
SampleThickness=self._sample_thickness,
ElementSize=self._element_size,
EMode="Indirect",
EFixed=efixed,
NumberOfWavelengthPoints=10,
)
group = self._ass_ws
if self._can_ws_name is not None:
can_wave_ws = "__can_wave"
ConvertUnits(
InputWorkspace=self._can_ws_name,
OutputWorkspace=can_wave_ws,
Target="Wavelength",
EMode="Indirect",
EFixed=efixed,
EnableLogging=False,
)
if self._can_scale != 1.0:
logger.information("Scaling container by: " + str(self._can_scale))
Scale(
InputWorkspace=can_wave_ws,
OutputWorkspace=can_wave_ws,
Factor=self._can_scale,
Operation="Multiply",
)
if self._use_can_corrections:
prog.report("Calculating container corrections")
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
if self._sample_density_type == "Mass Density":
builder = MaterialBuilder()
mat = builder.setFormula(self._can_chemical_formula).setMassDensity(self._can_density).build()
self._can_density = mat.numberDensity
SetSampleMaterial(
can_wave_ws, ChemicalFormula=self._can_chemical_formula, SampleNumberDensity=self._can_density
)
FlatPlateAbsorption(
InputWorkspace=can_wave_ws,
OutputWorkspace=self._acc_ws,
SampleHeight=self._sample_height,
SampleWidth=self._sample_width,
SampleThickness=self._can_front_thickness + self._can_back_thickness,
ElementSize=self._element_size,
EMode="Indirect",
EFixed=efixed,
NumberOfWavelengthPoints=10,
)
Divide(LHSWorkspace=can_wave_ws, RHSWorkspace=self._acc_ws, OutputWorkspace=can_wave_ws)
Minus(LHSWorkspace=sample_wave_ws, RHSWorkspace=can_wave_ws, OutputWorkspace=sample_wave_ws)
group += "," + self._acc_ws
else:
prog.report("Calculating container scaling")
Minus(LHSWorkspace=sample_wave_ws, RHSWorkspace=can_wave_ws, OutputWorkspace=sample_wave_ws)
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
DeleteWorkspace(can_wave_ws, EnableLogging=False)
else:
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
ConvertUnits(
InputWorkspace=sample_wave_ws,
OutputWorkspace=self._output_ws,
Target="DeltaE",
EMode="Indirect",
EFixed=efixed,
EnableLogging=False,
)
DeleteWorkspace(sample_wave_ws, EnableLogging=False)
prog.report("Recording sample logs")
sample_log_workspaces = [self._output_ws, self._ass_ws]
sample_logs = [
("sample_shape", "flatplate"),
("sample_filename", self._sample_ws),
("sample_height", self._sample_height),
("sample_width", self._sample_width),
("sample_thickness", self._sample_thickness),
("element_size", self._element_size),
]
if self._can_ws_name is not None:
sample_logs.append(("container_filename", self._can_ws_name))
sample_logs.append(("container_scale", self._can_scale))
if self._use_can_corrections:
sample_log_workspaces.append(self._acc_ws)
sample_logs.append(("container_front_thickness", self._can_front_thickness))
sample_logs.append(("container_back_thickness", self._can_back_thickness))
log_names = [item[0] for item in sample_logs]
log_values = [item[1] for item in sample_logs]
for ws_name in sample_log_workspaces:
AddSampleLogMultiple(Workspace=ws_name, LogNames=log_names, LogValues=log_values, EnableLogging=False)
self.setProperty("OutputWorkspace", self._output_ws)
# Output the Ass workspace if it is wanted, delete if not
if self._abs_ws == "":
DeleteWorkspace(self._ass_ws, EnableLogging=False)
if self._can_ws_name is not None and self._use_can_corrections:
DeleteWorkspace(self._acc_ws, EnableLogging=False)
else:
GroupWorkspaces(InputWorkspaces=group, OutputWorkspace=self._abs_ws, EnableLogging=False)
self.setProperty("CorrectionsWorkspace", self._abs_ws)
def _ascii_import(self, data, name):
"""
Import ASCII data.
@param data Raw ASCII data
@param name Name of data file
"""
from IndirectCommon import getEfixed
from IndirectNeutron import ChangeAngles, InstrParas
logger.notice('Loading ASCII data: %s' % name)
val = _split_line(data[3])
Q = []
for n in range(1, len(val)):
Q.append(val[n])
nQ = len(Q)
x = []
y = []
for n in range(4, len(data)):
val = _split_line(data[n])
x.append(val[0])
yval = val[1:]
y.append(yval)
nX = len(x)
logger.information('nQ = ' + str(nQ))
logger.information('nT = ' + str(nX))
xT = np.array(x)
eZero = np.zeros(nX)
#Qaxis = ''
for m in range(0, nQ):
logger.information('Q[' + str(m + 1) + '] : ' + str(Q[m]))
S = []
for n in range(0, nX):
S.append(y[n][m])
if m == 0:
#Qaxis += str(Q[m])
xDat = xT
yDat = np.array(S)
eDat = eZero
else:
#Qaxis += ',' + str(Q[m])
xDat = np.append(xDat, xT)
yDat = np.append(yDat, np.array(S))
eDat = np.append(eDat, eZero)
CreateWorkspace(OutputWorkspace=self._out_ws,
DataX=xDat,
DataY=yDat,
DataE=eDat,
Nspec=nQ, UnitX='TOF')
Qmax = Q[nQ - 1]
instr = 'MolDyn'
ana = 'simul'
if Qmax <= 2.0:
refl = '2'
else:
refl = '4'
InstrParas(self._out_ws, instr, ana, refl)
efixed = getEfixed(self._out_ws)# RunParas(self._out_ws, instr, name, name)
logger.information('Qmax = ' + str(Qmax) + ' ; efixed = ' + str(efixed))
pi4 = 4.0 * math.pi
wave = 1.8 * math.sqrt(25.2429 / efixed)
theta = []
for n in range(0, nQ):
qw = wave * Q[n] / pi4
ang = 2.0 * math.degrees(math.asin(qw))
theta.append(ang)
ChangeAngles(self._out_ws, instr, theta)
def _ascii_3d_import(self):
"""
Import 3D ASCII data (e.g. I(Q, t)).
"""
logger.notice('Loading ASCII data')
from IndirectCommon import getEfixed
from IndirectNeutron import ChangeAngles, InstrParas
# Read file
data = []
x_axis = ('time', 'ns')
v_axis = ('q', 'ang^-1')
with open(self._file_name, 'r') as handle:
for line in handle:
line = line.strip()
# Ignore empty lines
if line == '':
continue
# Data line (if not comment)
elif line.strip()[0] != '#':
line_values = np.array([
ast.literal_eval(t.strip())
if 'nan' not in t.lower() else np.nan
for t in line.split()
])
data.append(line_values)
if x_axis is None or v_axis is None:
raise ValueError('Data is not in expected format for 3D data')
logger.debug('X axis: {0}'.format(x_axis))
logger.debug('V axis: {0}'.format(v_axis))
# Get axis and Y values
data = np.swapaxes(np.array(data), 0, 1)
x_axis_values = data[0, 1:]
v_axis_values = data[1:, 0]
y_values = np.ravel(data[1:, 1:])
# Create the workspace
wks = CreateWorkspace(OutputWorkspace=self._out_ws,
DataX=x_axis_values,
DataY=y_values,
NSpec=v_axis_values.size,
UnitX=x_axis[1],
EnableLogging=False)
# Load the MolDyn instrument
q_max = v_axis_values[-1]
instrument = 'MolDyn'
reflection = '2' if q_max <= 2.0 else '4'
InstrParas(wks.name(), instrument, 'simul', reflection)
# Process angles
efixed = getEfixed(wks.name())
logger.information('Qmax={0}, Efixed={1}'.format(q_max, efixed))
wave = 1.8 * math.sqrt(25.2429 / efixed)
qw = wave * v_axis_values / (4.0 * math.pi)
theta = 2.0 * np.degrees(np.arcsin(qw))
ChangeAngles(wks.name(), instrument, theta)
return wks
def PyExec(self):
from IndirectCommon import getEfixed
self._setup()
# Set up progress reporting
n_prog_reports = 2
if self._can_ws_name is not None:
n_prog_reports += 1
prog = Progress(self, 0.0, 1.0, n_prog_reports)
efixed = getEfixed(self._sample_ws)
sample_wave_ws = '__sam_wave'
ConvertUnits(InputWorkspace=self._sample_ws, OutputWorkspace=sample_wave_ws,
Target='Wavelength', EMode='Indirect', EFixed=efixed, EnableLogging = False)
if self._sample_density_type == 'Mass Density':
builder = MaterialBuilder()
mat = builder.setFormula(self._sample_chemical_formula).setMassDensity(self._sample_density).build()
self._sample_density = mat.numberDensity
SetSampleMaterial(sample_wave_ws, ChemicalFormula=self._sample_chemical_formula, SampleNumberDensity=self._sample_density)
prog.report('Calculating sample corrections')
FlatPlateAbsorption(InputWorkspace=sample_wave_ws,
OutputWorkspace=self._ass_ws,
SampleHeight=self._sample_height,
SampleWidth=self._sample_width,
SampleThickness=self._sample_thickness,
ElementSize=self._element_size,
EMode='Indirect',
EFixed=efixed,
NumberOfWavelengthPoints=10)
group = self._ass_ws
if self._can_ws_name is not None:
can_wave_ws = '__can_wave'
ConvertUnits(InputWorkspace=self._can_ws_name, OutputWorkspace=can_wave_ws,
Target='Wavelength', EMode='Indirect', EFixed=efixed, EnableLogging = False)
if self._can_scale != 1.0:
logger.information('Scaling container by: ' + str(self._can_scale))
Scale(InputWorkspace=can_wave_ws, OutputWorkspace=can_wave_ws, Factor=self._can_scale, Operation='Multiply')
if self._use_can_corrections:
prog.report('Calculating container corrections')
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
if self._sample_density_type == 'Mass Density':
builder = MaterialBuilder()
mat = builder.setFormula(self._can_chemical_formula).setMassDensity(self._can_density).build()
self._can_density = mat.numberDensity
SetSampleMaterial(can_wave_ws, ChemicalFormula=self._can_chemical_formula, SampleNumberDensity=self._can_density)
FlatPlateAbsorption(InputWorkspace=can_wave_ws,
OutputWorkspace=self._acc_ws,
SampleHeight=self._sample_height,
SampleWidth=self._sample_width,
SampleThickness=self._can_front_thickness + self._can_back_thickness,
ElementSize=self._element_size,
EMode='Indirect',
EFixed=efixed,
NumberOfWavelengthPoints=10)
Divide(LHSWorkspace=can_wave_ws, RHSWorkspace=self._acc_ws, OutputWorkspace=can_wave_ws)
Minus(LHSWorkspace=sample_wave_ws, RHSWorkspace=can_wave_ws, OutputWorkspace=sample_wave_ws)
group += ',' + self._acc_ws
else:
prog.report('Calculating container scaling')
Minus(LHSWorkspace=sample_wave_ws, RHSWorkspace=can_wave_ws, OutputWorkspace=sample_wave_ws)
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
DeleteWorkspace(can_wave_ws, EnableLogging = False)
else:
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
ConvertUnits(InputWorkspace=sample_wave_ws, OutputWorkspace=self._output_ws,
Target='DeltaE', EMode='Indirect', EFixed=efixed, EnableLogging = False)
DeleteWorkspace(sample_wave_ws, EnableLogging = False)
prog.report('Recording sample logs')
sample_log_workspaces = [self._output_ws, self._ass_ws]
sample_logs = [('sample_shape', 'flatplate'),
('sample_filename', self._sample_ws),
('sample_height', self._sample_height),
('sample_width', self._sample_width),
('sample_thickness', self._sample_thickness),
('element_size', self._element_size)]
if self._can_ws_name is not None:
sample_logs.append(('container_filename', self._can_ws_name))
sample_logs.append(('container_scale', self._can_scale))
if self._use_can_corrections:
sample_log_workspaces.append(self._acc_ws)
sample_logs.append(('container_front_thickness', self. _can_front_thickness))
sample_logs.append(('container_back_thickness', self. _can_back_thickness))
log_names = [item[0] for item in sample_logs]
log_values = [item[1] for item in sample_logs]
for ws_name in sample_log_workspaces:
AddSampleLogMultiple(Workspace=ws_name, LogNames=log_names, LogValues=log_values, EnableLogging = False)
self.setProperty('OutputWorkspace', self._output_ws)
# Output the Ass workspace if it is wanted, delete if not
if self._abs_ws == '':
DeleteWorkspace(self._ass_ws, EnableLogging = False)
if self._can_ws_name is not None and self._use_can_corrections:
DeleteWorkspace(self._acc_ws, EnableLogging = False)
else:
GroupWorkspaces(InputWorkspaces=group, OutputWorkspace=self._abs_ws, EnableLogging = False)
self.setProperty('CorrectionsWorkspace', self._abs_ws)
def _get_e_fixed(self, workspace):
from IndirectCommon import getEfixed
return getEfixed(workspace)
def PyExec(self):
run_f2py_compatibility_test()
from IndirectBayes import (CalcErange, GetXYE)
from IndirectCommon import (CheckXrange, CheckAnalysers, getEfixed, GetThetaQ, CheckHistZero)
setup_prog = Progress(self, start=0.0, end=0.3, nreports = 5)
logger.information('BayesStretch input')
logger.information('Sample is %s' % self._sam_name)
logger.information('Resolution is %s' % self._res_name)
setup_prog.report('Converting to binary for Fortran')
fitOp = self._encode_fit_ops(self._elastic, self._background)
setup_prog.report('Establishing save path')
workdir = self._establish_save_path()
setup_prog.report('Checking X Range')
CheckXrange(self._erange, 'Energy')
setup_prog.report('Checking Analysers')
CheckAnalysers(self._sam_name, self._res_name)
setup_prog.report('Obtaining EFixed, theta and Q')
efix = getEfixed(self._sam_name)
theta, Q = GetThetaQ(self._sam_name)
setup_prog.report('Checking Histograms')
nsam,ntc = CheckHistZero(self._sam_name)
#check if we're performing a sequential fit
if self._loop != True:
nsam = 1
logger.information('Version is Stretch')
logger.information('Number of spectra = %s ' % nsam)
logger.information('Erange : %f to %f ' % (self._erange[0], self._erange[1]))
setup_prog.report('Creating FORTRAN Input')
fname = self._sam_name[:-4] + '_Stretch'
wrks=os.path.join(workdir, self._sam_name[:-4])
logger.information('lptfile : %s_Qst.lpt' % wrks)
lwrk=len(wrks)
wrks.ljust(140, ' ')
wrkr=self._res_name
wrkr.ljust(140, ' ')
eBet0 = np.zeros(self._nbet) # set errors to zero
eSig0 = np.zeros(self._nsig) # set errors to zero
rscl = 1.0
Qaxis = ''
workflow_prog = Progress(self, start=0.3, end=0.7, nreports=nsam*3)
# Empty arrays to hold Sigma and Bet x,y,e values
xSig, ySig, eSig = [],[],[]
xBet, yBet, eBet = [],[],[]
for m in range(nsam):
logger.information('Group %i at angle %f' % (m, theta[m]))
nsp = m + 1
nout, bnorm, Xdat, Xv, Yv, Ev = CalcErange(self._sam_name, m,
self._erange, self._nbins[0])
Ndat = nout[0]
Imin = nout[1]
Imax = nout[2]
# get resolution data (4096 = FORTRAN array length)
Nb, Xb, Yb, _ = GetXYE(self._res_name, 0, 4096)
numb = [nsam, nsp, ntc, Ndat, self._nbins[0], Imin,
Imax, Nb, self._nbins[1], self._nbet, self._nsig]
reals = [efix, theta[m], rscl, bnorm]
workflow_prog.report('Processing spectrum number %i' % m)
xsout, ysout, xbout, ybout, zpout=Que.quest(numb, Xv, Yv, Ev, reals, fitOp,
Xdat, Xb, Yb, wrks, wrkr, lwrk)
dataXs = xsout[:self._nsig] # reduce from fixed FORTRAN array
dataYs = ysout[:self._nsig]
dataXb = xbout[:self._nbet]
dataYb = ybout[:self._nbet]
zpWS = fname + '_Zp' +str(m)
if m > 0:
Qaxis += ','
Qaxis += str(Q[m])
dataXz = []
dataYz = []
dataEz = []
for n in range(self._nsig):
yfit_list = np.split(zpout[:self._nsig*self._nbet], self._nsig)
dataYzp = yfit_list[n]
dataXz = np.append(dataXz, xbout[:self._nbet])
dataYz = np.append(dataYz, dataYzp[:self._nbet])
dataEz = np.append(dataEz, eBet0)
zpWS = fname + '_Zp' + str(m)
self._create_workspace(zpWS, [dataXz, dataYz, dataEz], self._nsig, dataXs, True)
xSig = np.append(xSig,dataXs)
ySig = np.append(ySig,dataYs)
eSig = np.append(eSig,eSig0)
xBet = np.append(xBet,dataXb)
yBet = np.append(yBet,dataYb)
eBet = np.append(eBet,eBet0)
if m == 0:
groupZ = zpWS
else:
groupZ = groupZ +','+ zpWS
#create workspaces for sigma and beta
workflow_prog.report('Creating OutputWorkspace')
self._create_workspace(fname + '_Sigma', [xSig, ySig, eSig], nsam, Qaxis)
self._create_workspace(fname + '_Beta', [xBet, yBet, eBet], nsam, Qaxis)
group = fname + '_Sigma,' + fname + '_Beta'
fit_ws = fname + '_Fit'
s_api.GroupWorkspaces(InputWorkspaces=group,
OutputWorkspace=fit_ws)
contour_ws = fname + '_Contour'
s_api.GroupWorkspaces(InputWorkspaces=groupZ,
OutputWorkspace=contour_ws)
#Add some sample logs to the output workspaces
log_prog = Progress(self, start=0.8, end =1.0, nreports=6)
log_prog.report('Copying Logs to Fit workspace')
copy_log_alg = self.createChildAlgorithm('CopyLogs', enableLogging=False)
copy_log_alg.setProperty('InputWorkspace', self._sam_name)
copy_log_alg.setProperty('OutputWorkspace',fit_ws)
copy_log_alg.execute()
log_prog.report('Adding Sample logs to Fit workspace')
self._add_sample_logs(fit_ws, self._erange, self._nbins[0])
log_prog.report('Copying logs to Contour workspace')
copy_log_alg.setProperty('InputWorkspace',self._sam_name)
copy_log_alg.setProperty('OutputWorkspace',contour_ws)
copy_log_alg.execute()
log_prog.report('Adding sample logs to Contour workspace')
self._add_sample_logs(contour_ws, self._erange, self._nbins[0])
log_prog.report('Finialising log copying')
self.setProperty('OutputWorkspaceFit', fit_ws)
self.setProperty('OutputWorkspaceContour', contour_ws)
log_prog.report('Setting workspace properties')
def _calculate_parameters(self):
"""
Calculates the TransformToIqt parameters and saves in a table workspace.
"""
from IndirectCommon import getEfixed
end_prog = 0.3 if self._calculate_errors else 0.9
workflow_prog = Progress(self, start=0.0, end=end_prog, nreports=8)
workflow_prog.report('Cropping Workspace')
CropWorkspace(InputWorkspace=self._sample,
OutputWorkspace='__TransformToIqt_sample_cropped',
Xmin=self._e_min,
Xmax=self._e_max)
workflow_prog.report('Calculating table properties')
x_data = mtd['__TransformToIqt_sample_cropped'].readX(0)
number_input_points = len(x_data) - 1
num_bins = int(number_input_points / self._number_points_per_bin)
self._e_width = (abs(self._e_min) + abs(self._e_max)) / num_bins
workflow_prog.report('Attempting to Access IPF')
try:
workflow_prog.report('Access IPF')
instrument = mtd[self._sample].getInstrument()
analyserName = instrument.getStringParameter('analyser')[0]
analyser = instrument.getComponentByName(analyserName)
if analyser is not None:
logger.debug(
'Found %s component in instrument %s, will look for resolution there'
% (analyserName, instrument))
resolution = analyser.getNumberParameter('resolution')[0]
else:
logger.debug(
'No %s component found on instrument %s, will look for resolution in top level instrument'
% (analyserName, instrument))
resolution = instrument.getNumberParameter('resolution')[0]
logger.information('Got resolution from IPF: %f' % resolution)
workflow_prog.report('IPF resolution obtained')
except (AttributeError, IndexError):
workflow_prog.report('Resorting to Default')
resolution = getEfixed(self._sample) * 0.01
logger.warning(
'Could not get the resolution from the IPF, using 1% of the E Fixed value for the '
'resolution: {0}'.format(resolution))
resolution_bins = int(round((2 * resolution) / self._e_width))
if resolution_bins < 5:
logger.warning(
'Resolution curve has <5 points. Results may be unreliable.')
workflow_prog.report('Creating Parameter table')
param_table = CreateEmptyTableWorkspace(
OutputWorkspace=self._parameter_table)
workflow_prog.report('Populating Parameter table')
param_table.addColumn('int', 'SampleInputBins')
param_table.addColumn('float', 'BinReductionFactor')
param_table.addColumn('int', 'SampleOutputBins')
param_table.addColumn('float', 'EnergyMin')
param_table.addColumn('float', 'EnergyMax')
param_table.addColumn('float', 'EnergyWidth')
param_table.addColumn('float', 'Resolution')
param_table.addColumn('int', 'ResolutionBins')
param_table.addRow([
number_input_points, self._number_points_per_bin, num_bins,
self._e_min, self._e_max, self._e_width, resolution,
resolution_bins
])
workflow_prog.report('Deleting temp Workspace')
if mtd.doesExist('__TransformToIqt_sample_cropped'):
DeleteWorkspace('__TransformToIqt_sample_cropped')
self.setProperty('ParameterWorkspace', param_table)
def _calculate_parameters(self):
"""
Calculates the TransformToIqt parameters and saves in a table workspace.
"""
from IndirectCommon import getEfixed
end_prog = 0.3 if self._calculate_errors else 0.9
workflow_prog = Progress(self, start=0.0, end=end_prog, nreports=8)
workflow_prog.report('Cropping Workspace')
CropWorkspace(InputWorkspace=self._sample,
OutputWorkspace='__TransformToIqt_sample_cropped',
Xmin=self._e_min,
Xmax=self._e_max)
workflow_prog.report('Calculating table properties')
x_data = mtd['__TransformToIqt_sample_cropped'].readX(0)
number_input_points = len(x_data) - 1
num_bins = int(number_input_points / self._number_points_per_bin)
self._e_width = (abs(self._e_min) + abs(self._e_max)) / num_bins
workflow_prog.report('Attempting to Access IPF')
try:
workflow_prog.report('Access IPF')
instrument = mtd[self._sample].getInstrument()
analyserName = instrument.getStringParameter('analyser')[0]
analyser = instrument.getComponentByName(analyserName)
if analyser is not None:
logger.debug('Found %s component in instrument %s, will look for resolution there'
% (analyserName, instrument))
resolution = analyser.getNumberParameter('resolution')[0]
else:
logger.debug('No %s component found on instrument %s, will look for resolution in top level instrument'
% (analyserName, instrument))
resolution = instrument.getNumberParameter('resolution')[0]
logger.information('Got resolution from IPF: %f' % resolution)
workflow_prog.report('IPF resolution obtained')
except (AttributeError, IndexError):
workflow_prog.report('Resorting to Default')
resolution = getEfixed(self._sample) * 0.01
logger.warning('Could not get the resolution from the IPF, using 1% of the E Fixed value for the '
'resolution: {0}'.format(resolution))
resolution_bins = int(round((2 * resolution) / self._e_width))
if resolution_bins < 5:
logger.warning(
'Resolution curve has <5 points. Results may be unreliable.')
workflow_prog.report('Creating Parameter table')
param_table = CreateEmptyTableWorkspace(
OutputWorkspace=self._parameter_table)
workflow_prog.report('Populating Parameter table')
param_table.addColumn('int', 'SampleInputBins')
param_table.addColumn('float', 'BinReductionFactor')
param_table.addColumn('int', 'SampleOutputBins')
param_table.addColumn('float', 'EnergyMin')
param_table.addColumn('float', 'EnergyMax')
param_table.addColumn('float', 'EnergyWidth')
param_table.addColumn('float', 'Resolution')
param_table.addColumn('int', 'ResolutionBins')
param_table.addRow([number_input_points, self._number_points_per_bin, num_bins,
self._e_min, self._e_max, self._e_width,
resolution, resolution_bins])
workflow_prog.report('Deleting temp Workspace')
if mtd.doesExist('__TransformToIqt_sample_cropped'):
DeleteWorkspace('__TransformToIqt_sample_cropped')
self.setProperty('ParameterWorkspace', param_table)
def PyExec(self):
#from IndirectImport import run_f2py_compatibility_test, is_supported_f2py_platform
run_f2py_compatibility_test()
from IndirectBayes import (CalcErange, GetXYE, ReadNormFile,
ReadWidthFile, QLAddSampleLogs, C2Fw,
C2Se, QuasiPlot)
from IndirectCommon import (CheckXrange, CheckAnalysers, getEfixed, GetThetaQ,
CheckHistZero, CheckHistSame)
setup_prog = Progress(self, start=0.0, end=0.3, nreports = 5)
self.log().information('BayesQuasi input')
erange = [self._e_min, self._e_max]
nbins = [self._sam_bins, self._res_bins]
setup_prog.report('Converting to binary for Fortran')
#convert true/false to 1/0 for fortran
o_el = 1 if self._elastic else 0
o_w1 = 1 if self._width else 0
o_res = 1 if self._res_norm else 0
#fortran code uses background choices defined using the following numbers
setup_prog.report('Encoding input options')
if self._background == 'Sloping':
o_bgd = 2
elif self._background == 'Flat':
o_bgd = 1
elif self._background == 'Zero':
o_bgd = 0
fitOp = [o_el, o_bgd, o_w1, o_res]
setup_prog.report('Establishing save path')
workdir = config['defaultsave.directory']
if not os.path.isdir(workdir):
workdir = os.getcwd()
logger.information('Default Save directory is not set. Defaulting to current working Directory: ' + workdir)
array_len = 4096 # length of array in Fortran
setup_prog.report('Checking X Range')
CheckXrange(erange,'Energy')
nbin,nrbin = nbins[0], nbins[1]
logger.information('Sample is ' + self._samWS)
logger.information('Resolution is ' + self._resWS)
setup_prog.report('Checking Analysers')
CheckAnalysers(self._samWS,self._resWS)
setup_prog.report('Obtaining EFixed, theta and Q')
efix = getEfixed(self._samWS)
theta, Q = GetThetaQ(self._samWS)
nsam,ntc = CheckHistZero(self._samWS)
totalNoSam = nsam
#check if we're performing a sequential fit
if self._loop != True:
nsam = 1
nres = CheckHistZero(self._resWS)[0]
setup_prog.report('Checking Histograms')
if self._program == 'QL':
if nres == 1:
prog = 'QLr' # res file
else:
prog = 'QLd' # data file
CheckHistSame(self._samWS,'Sample',self._resWS,'Resolution')
elif self._program == 'QSe':
if nres == 1:
prog = 'QSe' # res file
else:
raise ValueError('Stretched Exp ONLY works with RES file')
logger.information('Version is ' +prog)
logger.information(' Number of spectra = '+str(nsam))
logger.information(' Erange : '+str(erange[0])+' to '+str(erange[1]))
setup_prog.report('Reading files')
Wy,We = ReadWidthFile(self._width,self._wfile,totalNoSam)
dtn,xsc = ReadNormFile(self._res_norm,self._resnormWS,totalNoSam)
setup_prog.report('Establishing output workspace name')
fname = self._samWS[:-4] + '_'+ prog
probWS = fname + '_Prob'
fitWS = fname + '_Fit'
wrks=os.path.join(workdir, self._samWS[:-4])
logger.information(' lptfile : '+wrks+'_'+prog+'.lpt')
lwrk=len(wrks)
wrks.ljust(140,' ')
wrkr=self._resWS
wrkr.ljust(140,' ')
setup_prog.report('Initialising probability list')
# initialise probability list
if self._program == 'QL':
prob0 = []
prob1 = []
prob2 = []
xQ = np.array([Q[0]])
for m in range(1,nsam):
xQ = np.append(xQ,Q[m])
xProb = xQ
xProb = np.append(xProb,xQ)
xProb = np.append(xProb,xQ)
eProb = np.zeros(3*nsam)
group = ''
workflow_prog = Progress(self, start=0.3, end=0.7, nreports=nsam*3)
for m in range(0,nsam):
logger.information('Group ' +str(m)+ ' at angle '+ str(theta[m]))
nsp = m+1
nout,bnorm,Xdat,Xv,Yv,Ev = CalcErange(self._samWS,m,erange,nbin)
Ndat = nout[0]
Imin = nout[1]
Imax = nout[2]
if prog == 'QLd':
mm = m
else:
mm = 0
Nb,Xb,Yb,Eb = GetXYE(self._resWS,mm,array_len) # get resolution data
numb = [nsam, nsp, ntc, Ndat, nbin, Imin, Imax, Nb, nrbin]
rscl = 1.0
reals = [efix, theta[m], rscl, bnorm]
if prog == 'QLr':
workflow_prog.report('Processing Sample number %i as Lorentzian' % nsam)
nd,xout,yout,eout,yfit,yprob=QLr.qlres(numb,Xv,Yv,Ev,reals,fitOp,
Xdat,Xb,Yb,Wy,We,dtn,xsc,
wrks,wrkr,lwrk)
message = ' Log(prob) : '+str(yprob[0])+' '+str(yprob[1])+' '+str(yprob[2])+' '+str(yprob[3])
logger.information(message)
if prog == 'QLd':
workflow_prog.report('Processing Sample number %i' % nsam)
nd,xout,yout,eout,yfit,yprob=QLd.qldata(numb,Xv,Yv,Ev,reals,fitOp,
Xdat,Xb,Yb,Eb,Wy,We,
wrks,wrkr,lwrk)
message = ' Log(prob) : '+str(yprob[0])+' '+str(yprob[1])+' '+str(yprob[2])+' '+str(yprob[3])
logger.information(message)
if prog == 'QSe':
workflow_prog.report('Processing Sample number %i as Stretched Exp' % nsam)
nd,xout,yout,eout,yfit,yprob=Qse.qlstexp(numb,Xv,Yv,Ev,reals,fitOp,\
Xdat,Xb,Yb,Wy,We,dtn,xsc,\
wrks,wrkr,lwrk)
dataX = xout[:nd]
dataX = np.append(dataX,2*xout[nd-1]-xout[nd-2])
yfit_list = np.split(yfit[:4*nd],4)
dataF1 = yfit_list[1]
if self._program == 'QL':
dataF2 = yfit_list[2]
workflow_prog.report('Processing data')
dataG = np.zeros(nd)
datX = dataX
datY = yout[:nd]
datE = eout[:nd]
datX = np.append(datX,dataX)
datY = np.append(datY,dataF1[:nd])
datE = np.append(datE,dataG)
res1 = dataF1[:nd] - yout[:nd]
datX = np.append(datX,dataX)
datY = np.append(datY,res1)
datE = np.append(datE,dataG)
nsp = 3
names = 'data,fit.1,diff.1'
res_plot = [0, 1, 2]
if self._program == 'QL':
workflow_prog.report('Processing Lorentzian result data')
datX = np.append(datX,dataX)
datY = np.append(datY,dataF2[:nd])
datE = np.append(datE,dataG)
res2 = dataF2[:nd] - yout[:nd]
datX = np.append(datX,dataX)
datY = np.append(datY,res2)
datE = np.append(datE,dataG)
nsp += 2
names += ',fit.2,diff.2'
res_plot.append(4)
prob0.append(yprob[0])
prob1.append(yprob[1])
prob2.append(yprob[2])
# create result workspace
fitWS = fname+'_Workspaces'
fout = fname+'_Workspace_'+ str(m)
workflow_prog.report('Creating OutputWorkspace')
CreateWorkspace(OutputWorkspace=fout, DataX=datX, DataY=datY, DataE=datE,\
Nspec=nsp, UnitX='DeltaE', VerticalAxisUnit='Text', VerticalAxisValues=names)
# append workspace to list of results
group += fout + ','
comp_prog = Progress(self, start=0.7, end=0.8, nreports=2)
comp_prog.report('Creating Group Workspace')
GroupWorkspaces(InputWorkspaces=group,OutputWorkspace=fitWS)
if self._program == 'QL':
comp_prog.report('Processing Lorentzian probability data')
yPr0 = np.array([prob0[0]])
yPr1 = np.array([prob1[0]])
yPr2 = np.array([prob2[0]])
for m in range(1,nsam):
yPr0 = np.append(yPr0,prob0[m])
yPr1 = np.append(yPr1,prob1[m])
yPr2 = np.append(yPr2,prob2[m])
yProb = yPr0
yProb = np.append(yProb,yPr1)
yProb = np.append(yProb,yPr2)
probWs = CreateWorkspace(OutputWorkspace=probWS, DataX=xProb, DataY=yProb, DataE=eProb,\
Nspec=3, UnitX='MomentumTransfer')
outWS = C2Fw(self._samWS[:-4],fname)
if self._plot != 'None':
QuasiPlot(fname,self._plot,res_plot,self._loop)
if self._program == 'QSe':
comp_prog.report('Runnning C2Se')
outWS = C2Se(fname)
if self._plot != 'None':
QuasiPlot(fname,self._plot,res_plot,self._loop)
log_prog = Progress(self, start=0.8, end =1.0, nreports=8)
#Add some sample logs to the output workspaces
log_prog.report('Copying Logs to outputWorkspace')
CopyLogs(InputWorkspace=self._samWS, OutputWorkspace=outWS)
log_prog.report('Adding Sample logs to Output workspace')
QLAddSampleLogs(outWS, self._resWS, prog, self._background, self._elastic, erange,
(nbin, nrbin), self._resnormWS, self._wfile)
log_prog.report('Copying logs to fit Workspace')
CopyLogs(InputWorkspace=self._samWS, OutputWorkspace=fitWS)
log_prog.report('Adding sample logs to Fit workspace')
QLAddSampleLogs(fitWS, self._resWS, prog, self._background, self._elastic, erange,
(nbin, nrbin), self._resnormWS, self._wfile)
log_prog.report('Finialising log copying')
if self._save:
log_prog.report('Saving workspaces')
fit_path = os.path.join(workdir,fitWS+'.nxs')
SaveNexusProcessed(InputWorkspace=fitWS, Filename=fit_path)
out_path = os.path.join(workdir, outWS+'.nxs') # path name for nxs file
SaveNexusProcessed(InputWorkspace=outWS, Filename=out_path)
logger.information('Output fit file created : ' + fit_path)
logger.information('Output paramter file created : ' + out_path)
self.setProperty('OutputWorkspaceFit', fitWS)
self.setProperty('OutputWorkspaceResult', outWS)
log_prog.report('Setting workspace properties')
if self._program == 'QL':
self.setProperty('OutputWorkspaceProb', probWS)
def PyExec(self):
run_f2py_compatibility_test()
from IndirectBayes import (CalcErange, GetXYE)
from IndirectCommon import (CheckXrange, CheckAnalysersOrEFixed,
getEfixed, GetThetaQ, CheckHistZero)
setup_prog = Progress(self, start=0.0, end=0.3, nreports=5)
logger.information('BayesStretch input')
logger.information('Sample is %s' % self._sam_name)
logger.information('Resolution is %s' % self._res_name)
setup_prog.report('Converting to binary for Fortran')
fitOp = self._encode_fit_ops(self._elastic, self._background)
setup_prog.report('Establishing save path')
workdir = self._establish_save_path()
setup_prog.report('Checking X Range')
CheckXrange(self._erange, 'Energy')
setup_prog.report('Checking Analysers')
CheckAnalysersOrEFixed(self._sam_name, self._res_name)
setup_prog.report('Obtaining EFixed, theta and Q')
efix = getEfixed(self._sam_name)
theta, Q = GetThetaQ(self._sam_name)
setup_prog.report('Checking Histograms')
nsam, ntc = CheckHistZero(self._sam_name)
# check if we're performing a sequential fit
if not self._loop:
nsam = 1
logger.information('Version is Stretch')
logger.information('Number of spectra = %s ' % nsam)
logger.information('Erange : %f to %f ' %
(self._erange[0], self._erange[1]))
setup_prog.report('Creating FORTRAN Input')
fname = self._sam_name[:-4] + '_Stretch'
wrks = os.path.join(workdir, self._sam_name[:-4])
logger.information('lptfile : %s_Qst.lpt' % wrks)
lwrk = len(wrks)
wrks.ljust(140, ' ')
wrkr = self._res_name
wrkr.ljust(140, ' ')
eBet0 = np.zeros(self._nbet) # set errors to zero
eSig0 = np.zeros(self._nsig) # set errors to zero
rscl = 1.0
Qaxis = ''
workflow_prog = Progress(self, start=0.3, end=0.7, nreports=nsam * 3)
# Empty arrays to hold Sigma and Bet x,y,e values
xSig, ySig, eSig = [], [], []
xBet, yBet, eBet = [], [], []
for m in range(nsam):
logger.information('Group %i at angle %f' % (m, theta[m]))
nsp = m + 1
nout, bnorm, Xdat, Xv, Yv, Ev = CalcErange(self._sam_name, m,
self._erange,
self._nbins[0])
Ndat = nout[0]
Imin = nout[1]
Imax = nout[2]
# get resolution data (4096 = FORTRAN array length)
Nb, Xb, Yb, _ = GetXYE(self._res_name, 0, 4096)
numb = [
nsam, nsp, ntc, Ndat, self._nbins[0], Imin, Imax, Nb,
self._nbins[1], self._nbet, self._nsig
]
reals = [efix, theta[m], rscl, bnorm]
workflow_prog.report('Processing spectrum number %i' % m)
xsout, ysout, xbout, ybout, zpout = Que.quest(
numb, Xv, Yv, Ev, reals, fitOp, Xdat, Xb, Yb, wrks, wrkr, lwrk)
dataXs = xsout[:self._nsig] # reduce from fixed FORTRAN array
dataYs = ysout[:self._nsig]
dataXb = xbout[:self._nbet]
dataYb = ybout[:self._nbet]
zpWS = fname + '_Zp' + str(m)
if m > 0:
Qaxis += ','
Qaxis += str(Q[m])
dataXz = []
dataYz = []
dataEz = []
for n in range(self._nsig):
yfit_list = np.split(zpout[:self._nsig * self._nbet],
self._nsig)
dataYzp = yfit_list[n]
dataXz = np.append(dataXz, xbout[:self._nbet])
dataYz = np.append(dataYz, dataYzp[:self._nbet])
dataEz = np.append(dataEz, eBet0)
zpWS = fname + '_Zp' + str(m)
self._create_workspace(zpWS, [dataXz, dataYz, dataEz], self._nsig,
dataXs, True)
xSig = np.append(xSig, dataXs)
ySig = np.append(ySig, dataYs)
eSig = np.append(eSig, eSig0)
xBet = np.append(xBet, dataXb)
yBet = np.append(yBet, dataYb)
eBet = np.append(eBet, eBet0)
if m == 0:
groupZ = zpWS
else:
groupZ = groupZ + ',' + zpWS
# create workspaces for sigma and beta
workflow_prog.report('Creating OutputWorkspace')
self._create_workspace(fname + '_Sigma', [xSig, ySig, eSig], nsam,
Qaxis)
self._create_workspace(fname + '_Beta', [xBet, yBet, eBet], nsam,
Qaxis)
group = fname + '_Sigma,' + fname + '_Beta'
fit_ws = fname + '_Fit'
s_api.GroupWorkspaces(InputWorkspaces=group, OutputWorkspace=fit_ws)
contour_ws = fname + '_Contour'
s_api.GroupWorkspaces(InputWorkspaces=groupZ,
OutputWorkspace=contour_ws)
# Add some sample logs to the output workspaces
log_prog = Progress(self, start=0.8, end=1.0, nreports=6)
log_prog.report('Copying Logs to Fit workspace')
copy_log_alg = self.createChildAlgorithm('CopyLogs',
enableLogging=False)
copy_log_alg.setProperty('InputWorkspace', self._sam_name)
copy_log_alg.setProperty('OutputWorkspace', fit_ws)
copy_log_alg.execute()
log_prog.report('Adding Sample logs to Fit workspace')
self._add_sample_logs(fit_ws, self._erange, self._nbins[0])
log_prog.report('Copying logs to Contour workspace')
copy_log_alg.setProperty('InputWorkspace', self._sam_name)
copy_log_alg.setProperty('OutputWorkspace', contour_ws)
copy_log_alg.execute()
log_prog.report('Adding sample logs to Contour workspace')
self._add_sample_logs(contour_ws, self._erange, self._nbins[0])
log_prog.report('Finialising log copying')
# sort x axis
s_api.SortXAxis(InputWorkspace=fit_ws,
OutputWorkspace=fit_ws,
EnableLogging=False)
s_api.SortXAxis(InputWorkspace=contour_ws,
OutputWorkspace=contour_ws,
EnableLogging=False)
self.setProperty('OutputWorkspaceFit', fit_ws)
self.setProperty('OutputWorkspaceContour', contour_ws)
log_prog.report('Setting workspace properties')
def PyExec(self):
from IndirectCommon import getEfixed
self._setup()
# Set up progress reporting
n_prog_reports = 2
if self._can_ws_name is not None:
n_prog_reports += 1
prog = Progress(self, 0.0, 1.0, n_prog_reports)
efixed = getEfixed(self._sample_ws_name)
sample_wave_ws = '__sam_wave'
ConvertUnits(InputWorkspace=self._sample_ws_name, OutputWorkspace=sample_wave_ws,
Target='Wavelength', EMode='Indirect', EFixed=efixed, EnableLogging=False)
sample_thickness = self._sample_outer_radius - self._sample_inner_radius
logger.information('Sample thickness: ' + str(sample_thickness))
prog.report('Calculating sample corrections')
if self._sample_density_type == 'Mass Density':
builder = MaterialBuilder()
mat = builder.setFormula(self._sample_chemical_formula).setMassDensity(self._sample_density).build()
self._sample_density = mat.numberDensity
SetSampleMaterial(sample_wave_ws, ChemicalFormula=self._sample_chemical_formula, SampleNumberDensity=self._sample_density)
AnnularRingAbsorption(InputWorkspace=sample_wave_ws,
OutputWorkspace=self._ass_ws,
SampleHeight=3.0,
SampleThickness=sample_thickness,
CanInnerRadius=self._can_inner_radius,
CanOuterRadius=self._can_outer_radius,
SampleChemicalFormula=self._sample_chemical_formula,
SampleNumberDensity=self._sample_density,
NumberOfWavelengthPoints=10,
EventsPerPoint=self._events)
group = self._ass_ws
if self._can_ws_name is not None:
can1_wave_ws = '__can1_wave'
can2_wave_ws = '__can2_wave'
ConvertUnits(InputWorkspace=self._can_ws_name, OutputWorkspace=can1_wave_ws,
Target='Wavelength', EMode='Indirect', EFixed=efixed, EnableLogging=False)
if self._can_scale != 1.0:
logger.information('Scaling container by: ' + str(self._can_scale))
Scale(InputWorkspace=can1_wave_ws, OutputWorkspace=can1_wave_ws, Factor=self._can_scale, Operation='Multiply')
CloneWorkspace(InputWorkspace=can1_wave_ws, OutputWorkspace=can2_wave_ws, EnableLogging=False)
can_thickness_1 = self._sample_inner_radius - self._can_inner_radius
can_thickness_2 = self._can_outer_radius - self._sample_outer_radius
logger.information('Container thickness: %f & %f' % (can_thickness_1, can_thickness_2))
if self._use_can_corrections:
prog.report('Calculating container corrections')
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
if self._can_density_type == 'Mass Density':
builder = MaterialBuilder()
mat = builder.setFormula(self._can_chemical_formula).setMassDensity(self._can_density).build()
self._can_density = mat.numberDensity
SetSampleMaterial(can1_wave_ws, ChemicalFormula=self._can_chemical_formula,
SampleNumberDensity=self._can_density)
AnnularRingAbsorption(InputWorkspace=can1_wave_ws,
OutputWorkspace='__Acc1',
SampleHeight=3.0,
SampleThickness=can_thickness_1,
CanInnerRadius=self._can_inner_radius,
CanOuterRadius=self._sample_outer_radius,
SampleChemicalFormula=self._can_chemical_formula,
SampleNumberDensity=self._can_density,
NumberOfWavelengthPoints=10,
EventsPerPoint=self._events)
SetSampleMaterial(can2_wave_ws, ChemicalFormula=self._can_chemical_formula, SampleNumberDensity=self._can_density)
AnnularRingAbsorption(InputWorkspace=can2_wave_ws,
OutputWorkspace='__Acc2',
SampleHeight=3.0,
SampleThickness=can_thickness_2,
CanInnerRadius=self._sample_inner_radius,
CanOuterRadius=self._can_outer_radius,
SampleChemicalFormula=self._can_chemical_formula,
SampleNumberDensity=self._can_density,
NumberOfWavelengthPoints=10,
EventsPerPoint=self._events)
Multiply(LHSWorkspace='__Acc1', RHSWorkspace='__Acc2', OutputWorkspace=self._acc_ws, EnableLogging=False)
DeleteWorkspace('__Acc1', EnableLogging=False)
DeleteWorkspace('__Acc2', EnableLogging=False)
Divide(LHSWorkspace=can1_wave_ws, RHSWorkspace=self._acc_ws, OutputWorkspace=can1_wave_ws)
Minus(LHSWorkspace=sample_wave_ws, RHSWorkspace=can1_wave_ws, OutputWorkspace=sample_wave_ws)
group += ',' + self._acc_ws
else:
prog.report('Calculating can scaling')
Minus(LHSWorkspace=sample_wave_ws, RHSWorkspace=can1_wave_ws, OutputWorkspace=sample_wave_ws)
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
DeleteWorkspace(can1_wave_ws, EnableLogging=False)
DeleteWorkspace(can2_wave_ws, EnableLogging=False)
else:
Divide(LHSWorkspace=sample_wave_ws,
RHSWorkspace=self._ass_ws,
OutputWorkspace=sample_wave_ws)
ConvertUnits(InputWorkspace=sample_wave_ws,
OutputWorkspace=self._output_ws,
Target='DeltaE',
EMode='Indirect',
EFixed=efixed,
EnableLogging=False)
DeleteWorkspace(sample_wave_ws, EnableLogging=False)
prog.report('Recording sample logs')
sample_log_workspaces = [self._output_ws, self._ass_ws]
sample_logs = [('sample_shape', 'annulus'),
('sample_filename', self._sample_ws_name),
('sample_inner', self._sample_inner_radius),
('sample_outer', self._sample_outer_radius),
('can_inner', self._can_inner_radius),
('can_outer', self._can_outer_radius)]
if self._can_ws_name is not None:
sample_logs.append(('container_filename', self._can_ws_name))
sample_logs.append(('container_scale', self._can_scale))
if self._use_can_corrections:
sample_log_workspaces.append(self._acc_ws)
sample_logs.append(('container_thickness_1', can_thickness_1))
sample_logs.append(('container_thickness_2', can_thickness_2))
log_names = [item[0] for item in sample_logs]
log_values = [item[1] for item in sample_logs]
for ws_name in sample_log_workspaces:
AddSampleLogMultiple(Workspace=ws_name, LogNames=log_names, LogValues=log_values, EnableLogging=False)
self.setProperty('OutputWorkspace', self._output_ws)
# Output the Ass workspace if it is wanted, delete if not
if self._abs_ws == '':
DeleteWorkspace(self._ass_ws, EnableLogging=False)
if self._can_ws_name is not None and self._use_can_corrections:
DeleteWorkspace(self._acc_ws, EnableLogging=False)
else:
GroupWorkspaces(InputWorkspaces=group, OutputWorkspace=self._abs_ws, EnableLogging=False)
self.setProperty('CorrectionsWorkspace', self._abs_ws)
def PyExec(self):
run_f2py_compatibility_test()
from IndirectBayes import (CalcErange, GetXYE, C2Fwater)
from IndirectCommon import (CheckXrange, CheckAnalysers, getEfixed, GetThetaQ,
CheckHistZero, CheckHistSame)
erange = [self._e_min, self._e_max]
nbins = [self._sam_bins, self._res_bins]
#convert true/false to 1/0 for fortran
o_el = 1 if self._elastic else 0
o_w1 = 1 if self._width else 0
o_res = 1 if self._res_norm else 0
#fortran code uses background choices defined using the following numbers
if self._background == 'Sloping':
o_bgd = 2
elif self._background == 'Flat':
o_bgd = 1
elif self._background == 'Zero':
o_bgd = 0
fitOp = [o_el, o_bgd, o_w1, o_res]
workdir = config['defaultsave.directory']
if not os.path.isdir(workdir):
workdir = os.getcwd()
logger.information('Default Save directory is not set. Defaulting to current working Directory: ' + workdir)
array_len = 4096 # length of array in Fortran
CheckXrange(erange, 'Energy')
nbin,nrbin = nbins[0], nbins[1]
logger.information('Sample is ' + self._sam_ws)
logger.information('Resolution is ' + self._res_ws)
CheckAnalysersOrEFixed(self._sam_ws, self._res_ws)
efix = getEfixed(self._sam_ws)
theta, Q = GetThetaQ(self._sam_ws)
nsam,ntc = CheckHistZero(self._sam_ws)
totalNoSam = nsam
#check if we're performing a sequential fit
if self._loop != True:
nsam = 1
prog = 'QLw' # res file
logger.information('Program is ' + prog)
logger.information(' Number of spectra = %i' % nsam)
logger.information(' Erange : %f to %f' % (erange[0], erange[1]))
dtn, xsc = self._read_width_file(self._res_norm, self._resnorm_ws, totalNoSam)
Wy, We = self._read_norm_file(self._width,self._wfile,totalNoSam)
fname = self._sam_ws[:-4] + '_'+ prog
fit_ws = fname + '_Fit'
wrks=os.path.join(workdir, self._sam_ws[:-4])
logger.information(' lptfile : ' + wrks + '_' + prog + '.lpt')
lwrk=len(wrks)
wrks.ljust(140, ' ')
wrkr=self._res_ws
wrkr.ljust(140, ' ')
group = ''
workflow_prog = Progress(self, start=0.3, end=0.7, nreports=nsam*3)
for m in range(nsam):
logger.information('Group %i at angle %f' % (m, theta[m]))
nsp = m + 1
nout, bnorm, Xdat, Xv, Yv, Ev = CalcErange(self._sam_ws, m, erange, nbin)
Ndat = nout[0]
Imin = nout[1]
Imax = nout[2]
if prog == 'QLd':
mm = m
else:
mm = 0
Nb, Xb, Yb, Eb = GetXYE(self._res_ws, mm, array_len) # get resolution data
numb = [nsam, nsp, ntc, Ndat, nbin, Imin, Imax, Nb, nrbin]
rscl = 1.0
reals = [efix, theta[m], rscl, bnorm]
workflow_prog.report('Processing spectrum number %i as Water' % m)
nd,xout,yout,eout,yfit,yprob=QLwat.qlwat(numb, Xv, Yv, Ev, reals, fitOp,
Xdat, Xb, Yb, Wy, We, dtn, xsc,
wrks, wrkr, lwrk)
dataX = xout[:nd]
dataX = np.append(dataX, 2*xout[nd - 1] - xout[nd - 2])
yfit_list = np.split(yfit[:4*nd], 4)
dataF1 = yfit_list[1]
workflow_prog.report('Processing data')
dataG = np.zeros(nd)
datX = dataX
datY = yout[:nd]
datE = eout[:nd]
datX = np.append(datX, dataX)
datY = np.append(datY, dataF1[:nd])
datE = np.append(datE, dataG)
res1 = dataF1[:nd] - yout[:nd]
datX = np.append(datX, dataX)
datY = np.append(datY, res1)
datE = np.append(datE, dataG)
nsp = 3
names = 'data, fit.1, diff.1'
res_plot = [0, 1, 2]
# create result workspace
fit_ws = fname + '_Workspaces'
fout = fname + '_Workspace_' + str(m)
workflow_prog.report('Creating OutputWorkspace')
CreateWorkspace(OutputWorkspace=fout,
DataX=datX,
DataY=datY,
DataE=datE,
Nspec=nsp,
UnitX='DeltaE',
VerticalAxisUnit='Text',
VerticalAxisValues=names)
# append workspace to list of results
group += fout + ','
comp_prog = Progress(self, start=0.7, end=0.8, nreports=2)
comp_prog.report('Creating Group Workspace')
GroupWorkspaces(InputWorkspaces=group,
OutputWorkspace=fit_ws)
out_ws = C2Fwater(fname)
#Add some sample logs to the output workspaces
CopyLogs(InputWorkspace=self._sam_ws,
OutputWorkspace=out_ws)
self._add_sample_logs(out_ws, prog, erange, nbins)
CopyLogs(InputWorkspace=self._sam_ws,
OutputWorkspace=fit_ws)
self._add_sample_logs(fit_ws, prog, erange, nbins)
self.setProperty('OutputWorkspaceFit', fit_ws)
self.setProperty('OutputWorkspaceResult', out_ws)
def _get_e_fixed(self, workspace):
from IndirectCommon import getEfixed
return getEfixed(workspace)
def PyExec(self):
from IndirectCommon import getEfixed
self._setup()
# Set up progress reporting
n_prog_reports = 2
if self._can_ws_name is not None:
n_prog_reports += 1
prog = Progress(self, 0.0, 1.0, n_prog_reports)
efixed = getEfixed(self._sample_ws_name)
sample_wave_ws = '__sam_wave'
ConvertUnits(InputWorkspace=self._sample_ws_name, OutputWorkspace=sample_wave_ws,
Target='Wavelength', EMode='Indirect', EFixed=efixed)
SetSampleMaterial(sample_wave_ws, ChemicalFormula=self._sample_chemical_formula, SampleNumberDensity=self._sample_number_density)
prog.report('Calculating sample corrections')
CylinderAbsorption(InputWorkspace=sample_wave_ws,
OutputWorkspace=self._ass_ws,
SampleNumberDensity=self._sample_number_density,
NumberOfWavelengthPoints=10,
CylinderSampleHeight=3.0,
CylinderSampleRadius=self._sample_radius,
NumberOfSlices=1,
NumberOfAnnuli=10)
plot_data = [self._output_ws, self._sample_ws_name]
plot_corr = [self._ass_ws]
group = self._ass_ws
if self._can_ws_name is not None:
can_wave_ws = '__can_wave'
ConvertUnits(InputWorkspace=self._can_ws_name, OutputWorkspace=can_wave_ws,
Target='Wavelength', EMode='Indirect', EFixed=efixed)
if self._can_scale != 1.0:
logger.information('Scaling can by: ' + str(self._can_scale))
Scale(InputWorkspace=can_wave_ws, OutputWorkspace=can_wave_ws, Factor=self._can_scale, Operation='Multiply')
can_thickness = self._can_radius - self._sample_radius
logger.information('Container thickness: ' + str(can_thickness))
if self._use_can_corrections:
# Doing can corrections
prog.report('Calculating container corrections')
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
SetSampleMaterial(can_wave_ws, ChemicalFormula=self._can_chemical_formula, SampleNumberDensity=self._can_number_density)
AnnularRingAbsorption(InputWorkspace=can_wave_ws,
OutputWorkspace=self._acc_ws,
SampleHeight=3.0,
SampleThickness=can_thickness,
CanInnerRadius=0.9*self._sample_radius,
CanOuterRadius=1.1*self._can_radius,
SampleChemicalFormula=self._can_chemical_formula,
SampleNumberDensity=self._can_number_density,
NumberOfWavelengthPoints=10,
EventsPerPoint=self._events)
Divide(LHSWorkspace=can_wave_ws, RHSWorkspace=self._acc_ws, OutputWorkspace=can_wave_ws)
Minus(LHSWorkspace=sample_wave_ws, RHSWorkspace=can_wave_ws, OutputWorkspace=sample_wave_ws)
plot_corr.append(self._acc_ws)
group += ',' + self._acc_ws
else:
# Doing simple can subtraction
prog.report('Calculating container scaling')
Minus(LHSWorkspace=sample_wave_ws, RHSWorkspace=can_wave_ws, OutputWorkspace=sample_wave_ws)
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
DeleteWorkspace(can_wave_ws)
plot_data.append(self._can_ws_name)
else:
Divide(LHSWorkspace=sample_wave_ws, RHSWorkspace=self._ass_ws, OutputWorkspace=sample_wave_ws)
ConvertUnits(InputWorkspace=sample_wave_ws, OutputWorkspace=self._output_ws,
Target='DeltaE', EMode='Indirect', EFixed=efixed)
DeleteWorkspace(sample_wave_ws)
# Record sample logs
prog.report('Recording sample logs')
sample_log_workspaces = [self._output_ws, self._ass_ws]
sample_logs = [('sample_shape', 'cylinder'),
('sample_filename', self._sample_ws_name),
('sample_radius', self._sample_radius)]
if self._can_ws_name is not None:
sample_logs.append(('container_filename', self._can_ws_name))
sample_logs.append(('container_scale', self._can_scale))
if self._use_can_corrections:
sample_log_workspaces.append(self._acc_ws)
sample_logs.append(('container_thickness', can_thickness))
log_names = [item[0] for item in sample_logs]
log_values = [item[1] for item in sample_logs]
for ws_name in sample_log_workspaces:
AddSampleLogMultiple(Workspace=ws_name, LogNames=log_names, LogValues=log_values)
self.setProperty('OutputWorkspace', self._output_ws)
# Output the Abs group workspace if it is wanted, delete if not
if self._abs_ws == '':
DeleteWorkspace(self._ass_ws)
if self._can_ws_name is not None and self._use_can_corrections:
DeleteWorkspace(self._acc_ws)
else:
GroupWorkspaces(InputWorkspaces=group, OutputWorkspace=self._abs_ws)
self.setProperty('CorrectionsWorkspace', self._abs_ws)
if self._plot:
from IndirectImport import import_mantidplot
mantid_plot = import_mantidplot()
mantid_plot.plotSpectrum(plot_data, 0)
if self._abs_ws != '':
mantid_plot.plotSpectrum(plot_corr, 0)