def PyExec(self):
config['default.facility'] = "SNS"
config['default.instrument'] = self._long_inst
self._doIndiv = self.getProperty("DoIndividual").value
self._etBins = self.getProperty(
"EnergyBins").value / MICROEV_TO_MILLIEV
self._qBins = self.getProperty("MomentumTransferBins").value
self._noMonNorm = self.getProperty("NoMonitorNorm").value
self._maskFile = self.getProperty("MaskFile").value
self._groupDetOpt = self.getProperty("GroupDetectors").value
self._normalizeToFirst = self.getProperty("NormalizeToFirst").value
self._normalizeToVanadium = self.getProperty("GroupDetectors").value
self._doNorm = self.getProperty("DivideByVanadium").value
datasearch = config["datasearch.searcharchive"]
if datasearch != "On":
config["datasearch.searcharchive"] = "On"
# Handle masking file override if necessary
self._overrideMask = bool(self._maskFile)
if not self._overrideMask:
config.appendDataSearchDir(DEFAULT_MASK_GROUP_DIR)
self._maskFile = DEFAULT_MASK_FILE
api.LoadMask(Instrument='BASIS',
OutputWorkspace='BASIS_MASK',
InputFile=self._maskFile)
# Work around length issue
_dMask = api.ExtractMask('BASIS_MASK')
self._dMask = _dMask[1]
api.DeleteWorkspace(_dMask[0])
############################
## Process the Vanadium ##
############################
norm_runs = self.getProperty("NormRunNumbers").value
if self._doNorm and bool(norm_runs):
if ";" in norm_runs:
raise SyntaxError("Normalization does not support run groups")
self._doNorm = self.getProperty("NormalizationType").value
self.log().information("Divide by Vanadium with normalization" +
self._doNorm)
# The following steps are common to all types of Vanadium normalization
# norm_runs encompasses a single set, thus _getRuns returns
# a list of only one item
norm_set = self._getRuns(norm_runs, doIndiv=False)[0]
self._normWs = self._sum_and_calibrate(norm_set,
extra_extension="_norm")
# This rebin integrates counts onto a histogram of a single bin
if self._doNorm == "by detectorID":
normRange = self.getProperty("NormWavelengthRange").value
self._normRange = [
normRange[0], normRange[1] - normRange[0], normRange[1]
]
api.Rebin(InputWorkspace=self._normWs,
OutputWorkspace=self._normWs,
Params=self._normRange)
# FindDetectorsOutsideLimits to be substituted by MedianDetectorTest
api.FindDetectorsOutsideLimits(InputWorkspace=self._normWs,
OutputWorkspace="BASIS_NORM_MASK")
# additional reduction steps when normalizing by Q slice
if self._doNorm == "by Q slice":
self._normWs = self._group_and_SofQW(self._normWs,
self._etBins,
isSample=False)
##########################
## Process the sample ##
##########################
self._run_list = self._getRuns(self.getProperty("RunNumbers").value,
doIndiv=self._doIndiv)
for run_set in self._run_list:
self._samWs = self._sum_and_calibrate(run_set)
self._samWsRun = str(run_set[0])
# Mask detectors with insufficient Vanadium signal
if self._doNorm:
api.MaskDetectors(Workspace=self._samWs,
MaskedWorkspace='BASIS_NORM_MASK')
# Divide by Vanadium
if self._doNorm == "by detector ID":
api.Divide(LHSWorkspace=self._samWs,
RHSWorkspace=self._normWs,
OutputWorkspace=self._samWs)
# additional reduction steps
self._samSqwWs = self._group_and_SofQW(self._samWs,
self._etBins,
isSample=True)
# Divide by Vanadium
if self._doNorm == "by Q slice":
api.Integration(InputWorkspace=self._normWs,
OutputWorkspace=self._normWs,
RangeLower=DEFAULT_VANADIUM_ENERGY_RANGE[0],
RangeUpper=DEFAULT_VANADIUM_ENERGY_RANGE[1])
api.Divide(LHSWorkspace=self._samSqwWs,
RHSWorkspace=self._normWs,
OutputWorkspace=self._samSqwWs)
# Clear mask from reduced file. Needed for binary operations
# involving this S(Q,w)
api.ClearMaskFlag(Workspace=self._samSqwWs)
# Scale so that elastic line has Y-values ~ 1
if self._normalizeToFirst:
self._ScaleY(self._samSqwWs)
# Output Dave and Nexus files
extension = "_divided.dat" if self._doNorm else ".dat"
dave_grp_filename = self._makeRunName(self._samWsRun,
False) + extension
api.SaveDaveGrp(Filename=dave_grp_filename,
InputWorkspace=self._samSqwWs,
ToMicroEV=True)
extension = "_divided_sqw.nxs" if self._doNorm else "_sqw.nxs"
processed_filename = self._makeRunName(self._samWsRun,
False) + extension
api.SaveNexus(Filename=processed_filename,
InputWorkspace=self._samSqwWs)
import mantid.simpleapi as mantid
# == Set parameters for calibration ==
filename = 'MAP14919.raw' # Calibration run ( found in \\isis\inst$\NDXMAPS\Instrument\data\cycle_09_5 )
# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'D2_window' # Calibrate D2 window
# Get calibration raw file and integrate it
rawCalibInstWS = mantid.Load(
filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
print("Integrating Workspace")
rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
rangeUpper = 10000 #
CalibInstWS = mantid.Integration(rawCalibInstWS,
RangeLower=rangeLower,
RangeUpper=rangeUpper)
mantid.DeleteWorkspace(rawCalibInstWS)
print(
"Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
)
# == Create Objects needed for calibration ==
# The positions of the shadows and ends here are an intelligent guess.
# First array gives positions in Metres and second array gives type 1=Gaussian peak 2=edge.
knownPos = [-0.65, -0.22, -0.00, 0.22, 0.65]
funcForm = [2, 1, 1, 1, 2]
# Get fitting parameters
def CalibrateWish(run_per_panel_list):
'''
:param run_per_panel_list: is a list of tuples with the run number and the associated panel
run_per_panel_list = [ (17706, 'panel01'), (17705, 'panel02'), (17701, 'panel03'), (17702, 'panel04'), (17695, 'panel05')]
'''
# == Set parameters for calibration ==
previousDefaultInstrument = mantid.config['default.instrument']
mantid.config['default.instrument'] = "WISH"
# definition of the parameters static for the calibration
lower_tube = numpy.array(
[-0.41, -0.31, -0.21, -0.11, -0.02, 0.09, 0.18, 0.28, 0.39])
upper_tube = numpy.array(lower_tube + 0.003)
funcForm = 9 * [1] # 9 gaussian peaks
margin = 15
low_range = list(range(0, 76))
high_range = list(range(76, 152))
kwargs = {'margin': margin}
# it will copy all the data from the runs to have a single instrument with the calibrated data.
whole_instrument = mantid.LoadRaw(str(run_per_panel_list[0][0]))
whole_instrument = mantid.Integration(whole_instrument)
for (run_number, panel_name) in run_per_panel_list:
panel_name = str(panel_name)
run_number = str(run_number)
# load your data and integrate it
ws = mantid.LoadRaw(run_number, OutputWorkspace=panel_name)
ws = mantid.Integration(ws, 1, 20000, OutputWorkspace=panel_name)
# use the TubeSpec object to be able to copy the data to the whole_instrument
tube_set = TubeSpec(ws)
tube_set.setTubeSpecByString(panel_name)
# update kwargs argument before calling calibrate
kwargs['rangeList'] = low_range # calibrate only the lower tubes
calibrationTable = tube.calibrate(ws, tube_set, lower_tube, funcForm,
**kwargs)
# update kwargs
kwargs[
'calibTable'] = calibrationTable # append calib to calibrationtable
kwargs['rangeList'] = high_range # calibrate only the upper tubes
calibrationTable = tube.calibrate(ws, tube_set, upper_tube, funcForm,
**kwargs)
kwargs['calibTable'] = calibrationTable
mantid.ApplyCalibration(ws, calibrationTable)
# copy data from the current panel to the whole_instrument
for i in range(tube_set.getNumTubes()):
for spec_num in tube_set.getTube(i):
whole_instrument.setY(spec_num, ws.dataY(spec_num))
# calibrate the whole_instrument with the last calibrated panel which has the calibration accumulation
# of all the others
mantid.CopyInstrumentParameters(run_per_panel_list[-1][1],
whole_instrument)
mantid.config['default.instrument'] = previousDefaultInstrument
# Here we run the calibration of WISH panel03
# We base the ideal tube on one tube of this door.
#
from __future__ import absolute_import, division, print_function
import tube
reload(tube) # noqa
from tube_spec import TubeSpec
import tube_calib #from tube_calib import constructIdealTubeFromRealTube
from tube_calib_fit_params import TubeCalibFitParams
import mantid.simpleapi as mantid
filename = 'WISH00017701.raw' # Calibration run ( found in \\isis\inst$\NDXWISH\Instrument\data\cycle_11_1 )
rawCalibInstWS = mantid.Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
CalibInstWS = mantid.Integration( rawCalibInstWS, RangeLower=1, RangeUpper=20000 )
mantid.DeleteWorkspace(rawCalibInstWS)
print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
CalibratedComponent = 'WISH/panel03/tube038'
# Set fitting parameters
eP = [65.0, 113.0, 161.0, 209.0, 257.0, 305.0, 353.0, 401.0, 449.0]
ExpectedHeight = 2000.0 # Expected Height of Gaussian Peaks (initial value of fit parameter)
ExpectedWidth = 32.0 # Expected width of Gaussian peaks in pixels (initial value of fit parameter)
fitPar = TubeCalibFitParams( eP, ExpectedHeight, ExpectedWidth )
fitPar.setAutomatic(True)
print("Created objects needed for calibration.")
func_form = 9*[1]
# Use first tube as ideal tube
def PyExec(self):
config['default.facility'] = 'SNS'
config['default.instrument'] = 'ARCS'
self._runs = self.getProperty('RunNumbers').value
self._vanfile = self.getProperty('Vanadium').value
self._ecruns = self.getProperty('EmptyCanRunNumbers').value
self._ebins_str = self.getProperty('EnergyBins').value
self._qbins_str = self.getProperty('MomentumTransferBins').value
self._snorm = self.getProperty('NormalizeSlices').value
self._clean = self.getProperty('CleanWorkspaces').value
wn_sqes = self.getPropertyValue("OutputWorkspace")
# workspace names
prefix = ''
if self._clean:
prefix = '__'
# Sample files
wn_data = prefix + 'data'
wn_van = prefix + 'vanadium'
wn_reduced = prefix + 'reduced'
wn_ste = prefix + 'S_theta_E'
wn_van_st = prefix + 'vanadium_S_theta'
wn_sten = prefix + 'S_theta_E_normalized'
wn_steni = prefix + 'S_theta_E_normalized_interp'
wn_sqe = prefix + 'S_Q_E'
wn_sqeb = prefix + 'S_Q_E_binned'
wn_sqesn = prefix + wn_sqes + '_norm'
# Empty can files
wn_ec_data = prefix + 'ec_data'
wn_ec_reduced = prefix + 'ec_reduced'
wn_ec_ste = prefix + 'ec_S_theta_E'
datasearch = config["datasearch.searcharchive"]
if datasearch != "On":
config["datasearch.searcharchive"] = "On"
# Load several event files into a sinle workspace. The nominal incident
# energy should be the same to avoid difference in energy resolution
api.Load(Filename=self._runs, OutputWorkspace=wn_data)
# Load the vanadium file, assume to be preprocessed, meaning that
# for every detector all events whithin a particular wide wavelength
# range have been rebinned into a single histogram
api.Load(Filename=self._vanfile, OutputWorkspace=wn_van)
# Load empty can event files, if present
if self._ecruns:
api.Load(Filename=self._ecruns, OutputWorkspace=wn_ec_data)
# Retrieve the mask from the vanadium workspace, and apply it to the data
# (and empty can, if submitted)
api.MaskDetectors(Workspace=wn_data, MaskedWorkspace=wn_van)
if self._ecruns:
api.MaskDetectors(Workspace=wn_ec_data, MaskedWorkspace=wn_van)
# Obtain incident energy as the mean of the nominal Ei values.
# There is one nominal value per events file.
ws_data = api.mtd[wn_data]
Ei = ws_data.getRun()['EnergyRequest'].getStatistics().mean
Ei_std = ws_data.getRun()['EnergyRequest'].getStatistics(
).standard_deviation
# Verify empty can runs were obtained at similar energy
if self._ecruns:
ws_ec_data = api.mtd[wn_ec_data]
ec_Ei = ws_ec_data.getRun()['EnergyRequest'].getStatistics().mean
if abs(Ei - ec_Ei) > Ei_std:
raise RuntimeError(
'Empty can runs were obtained at a significant' +
' different incident energy than the sample runs')
# Obtain energy range
self._ebins = [
float(x)
for x in re.compile(r'\d+[\.\d+]*').findall(self._ebins_str)
]
if len(self._ebins) == 1:
ws_data = api.mtd[wn_data]
Ei = ws_data.getRun()['EnergyRequest'].getStatistics().mean
self._ebins.insert(0, -0.5 * Ei) # prepend
self._ebins.append(0.95 * Ei) # append
# Enforce that the elastic energy (E=0) lies in the middle of the
# central bin with an appropriate small shift in the energy range
Ei_min_reduced = self._ebins[0] / self._ebins[1]
remainder = Ei_min_reduced - int(Ei_min_reduced)
if remainder >= 0.0:
erange_shift = self._ebins[1] * (0.5 - remainder)
else:
erange_shift = self._ebins[1] * (-0.5 - remainder)
self._ebins[0] += erange_shift # shift minimum energy
self._ebins[-1] += erange_shift # shift maximum energy
# Convert to energy transfer. Normalize by proton charge.
# The output workspace is S(detector-id,E)
factor = 0.1 # a fine energy bin
Erange = '{0},{1},{2}'.format(self._ebins[0], factor * self._ebins[1],
self._ebins[2])
api.DgsReduction(SampleInputWorkspace=wn_data,
EnergyTransferRange=Erange,
OutputWorkspace=wn_reduced)
if self._ecruns:
api.DgsReduction(SampleInputWorkspace=wn_ec_data,
EnergyTransferRange=Erange,
IncidentBeamNormalisation='ByCurrent',
OutputWorkspace=wn_ec_reduced)
# Obtain maximum and minimum |Q| values, as well as dQ if none passed
self._qbins = [
float(x)
for x in re.compile(r'\d+[\.\d+]*').findall(self._qbins_str)
]
if len(self._qbins) < 3:
if not self._qbins:
# insert dQ if empty qbins
dE = self._ebins[1]
self._qbins.append(
numpy.sqrt((Ei + dE) / ENERGY_TO_WAVEVECTOR) -
numpy.sqrt(Ei / ENERGY_TO_WAVEVECTOR))
mins, maxs = api.ConvertToMDMinMaxLocal(wn_reduced,
Qdimensions='|Q|',
dEAnalysisMode='Direct')
self._qbins.insert(0, mins[0]) # prepend minimum Q
self._qbins.append(maxs[0]) # append maximum Q
# Clean up the events files. They take a lot of space in memory
api.DeleteWorkspace(wn_data)
if self._ecruns:
api.DeleteWorkspace(wn_ec_data)
# Convert to S(theta,E)
ki = numpy.sqrt(Ei / ENERGY_TO_WAVEVECTOR)
factor = 1. / 5 # a reasonable (heuristic) value
# If dE is the smallest energy transfer considered,
# then dQ/ki is the smallest dtheta (in radians)
dtheta = factor * self._qbins[1] / ki * (180.0 / numpy.pi)
# very small dtheta (<0.15 degrees) prevents interpolation
dtheta = max(0.15, dtheta)
group_file_os_handle, group_file_name = mkstemp(suffix='.xml')
group_file_handle = os.fdopen(group_file_os_handle, 'w')
api.GenerateGroupingPowder(InputWorkspace=wn_reduced,
AngleStep=dtheta,
GroupingFilename=group_file_name)
group_file_handle.close()
api.GroupDetectors(InputWorkspace=wn_reduced,
MapFile=group_file_name,
OutputWorkspace=wn_ste)
if self._ecruns:
api.GroupDetectors(InputWorkspace=wn_ec_reduced,
MapFile=group_file_name,
OutputWorkspace=wn_ec_ste)
# Substract the empty can from the can+sample
api.Minus(LHSWorkspace=wn_ste,
RHSWorkspace=wn_ec_ste,
OutputWorkspace=wn_ste)
# Normalize by the vanadium intensity, but before that we need S(theta)
# for the vanadium. Recall every detector has all energies into a single
# bin, so we get S(theta) instead of S(theta,E)
api.GroupDetectors(InputWorkspace=wn_van,
MapFile=group_file_name,
OutputWorkspace=wn_van_st)
os.remove(group_file_name) # no need for this file
api.Divide(wn_ste, wn_van_st, OutputWorkspace=wn_sten)
api.ClearMaskFlag(Workspace=wn_sten)
max_i_theta = 0.0
min_i_theta = 0.0
# Linear interpolation
# First, find minimum theta index with a non-zero histogram
ws_sten = api.mtd[wn_sten]
for i_theta in range(ws_sten.getNumberHistograms()):
if ws_sten.dataY(i_theta).any():
min_i_theta = i_theta
break
# second, find maximum theta with a non-zero histogram
for i_theta in range(ws_sten.getNumberHistograms() - 1, -1, -1):
if ws_sten.dataY(i_theta).any():
max_i_theta = i_theta
break
# Scan the region [min_i_theta, max_i_theta] and apply interpolation to
# theta angles with no signal whatsoever, S(theta*, E)=0.0 for all energies
api.CloneWorkspace(InputWorkspace=wn_sten, OutputWorkspace=wn_steni)
ws_steni = api.mtd[wn_steni]
i_theta = 1 + min_i_theta
while i_theta < max_i_theta:
if not ws_steni.dataY(i_theta).any():
nonnull_i_theta_start = i_theta - 1 # angle index of non-null histogram
# scan until we find a non-null histogram
while not ws_steni.dataY(i_theta).any():
i_theta += 1
nonnull_i_theta_end = i_theta # angle index of non-null histogram
# The range [1+nonnull_i_theta_start, nonnull_i_theta_end]
# contains only null-histograms. Interpolate!
y_start = ws_steni.dataY(nonnull_i_theta_start)
y_end = ws_steni.dataY(nonnull_i_theta_end)
intercept = y_start
slope = (y_end - y_start) / (nonnull_i_theta_end -
nonnull_i_theta_start)
for null_i_theta in range(1 + nonnull_i_theta_start,
nonnull_i_theta_end):
ws_steni.dataY(null_i_theta)[:] = intercept + slope * (
null_i_theta - nonnull_i_theta_start)
i_theta += 1
# Convert S(theta,E) to S(Q,E), then rebin in |Q| and E to MD workspace
api.ConvertToMD(InputWorkspace=wn_steni,
QDimensions='|Q|',
dEAnalysisMode='Direct',
OutputWorkspace=wn_sqe)
Qmin = self._qbins[0]
Qmax = self._qbins[-1]
dQ = self._qbins[1]
Qrange = '|Q|,{0},{1},{2}'.format(Qmin, Qmax, int((Qmax - Qmin) / dQ))
Ei_min = self._ebins[0]
Ei_max = self._ebins[-1]
dE = self._ebins[1]
deltaErange = 'DeltaE,{0},{1},{2}'.format(Ei_min, Ei_max,
int((Ei_max - Ei_min) / dE))
api.BinMD(InputWorkspace=wn_sqe,
AxisAligned=1,
AlignedDim0=Qrange,
AlignedDim1=deltaErange,
OutputWorkspace=wn_sqeb)
# Slice the data by transforming to a Matrix2Dworkspace, with deltaE along the vertical axis
api.ConvertMDHistoToMatrixWorkspace(
InputWorkspace=wn_sqeb,
Normalization='NumEventsNormalization',
OutputWorkspace=wn_sqes)
# Shift the energy axis, since the reported values should be the center
# of the bins, instead of the minimum bin boundary
ws_sqes = api.mtd[wn_sqes]
Eaxis = ws_sqes.getAxis(1)
e_shift = self._ebins[1] / 2.0
for i in range(Eaxis.length()):
Eaxis.setValue(i, Eaxis.getValue(i) + e_shift)
# Normalize each slice
if self._snorm:
api.Integration(InputWorkspace=wn_sqes, OutputWorkspace=wn_sqesn)
api.Divide(LHSWorkspace=wn_sqes,
RHSWorkspace=wn_sqesn,
OutputWorkspace=wn_sqes)
# Clean up workspaces from intermediate steps
if self._clean:
for name in (wn_van, wn_reduced, wn_ste, wn_van_st, wn_sten,
wn_steni, wn_sqe, wn_sqeb, wn_sqesn):
api.DeleteWorkspace(name)
if api.mtd.doesExist('PreprocessedDetectorsWS'):
api.DeleteWorkspace('PreprocessedDetectorsWS')
# Ouput some info
message = '\n****** SOME OUTPUT INFORMATION ***' + \
'\nEnergy bins: ' + ', '.join(['{0:.2f}'.format(x) for x in self._ebins]) + \
'\nQ bins: ' + ', '.join(['{0:.2f}'.format(x) for x in self._qbins]) + \
'\nTheta bins: {0:.2f} {1:.2f} {2:.2f}'.format(min_i_theta * dtheta, dtheta, max_i_theta * dtheta)
logger.notice(message)
self.setProperty("OutputWorkspace", api.mtd[wn_sqes])
def CalibrateMerlin(RunNumber):
# == Set parameters for calibration ==
previousDefaultInstrument = mantid.config['default.instrument']
mantid.config['default.instrument'] = "MERLIN"
filename = str(RunNumber) # Name of calibration run.
rangeLower = 3000 # Integrate counts in each spectra from rangeLower to rangeUpper
rangeUpper = 20000 #
# Set parameters for ideal tube.
Left = 2.0 # Where the left end of tube should be in pixels (target for AP)
Centre = 512.5 # Where the centre of the tube should be in pixels (target for CP)
Right = 1023.0 # Where the right of the tube should be in pixels (target for BP)
ActiveLength = 2.9 # Active length of tube in Metres
# Set initial parameters for peak finding
ExpectedHeight = 1000.0 # Expected Height of Gaussian Peaks (initial value of fit parameter)
ExpectedWidth = 32.0 # Expected width of centre peak in Pixels (initial value of fit parameter)
ExpectedPositions = [
35.0, 512.0, 989.0
] # Expected positions of the edges and peak in pixels (initial values of fit parameters)
# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MERLIN' # Calibrate door 2
# Get calibration raw file and integrate it
print(filename)
rawCalibInstWS = mantid.LoadRaw(filename)
# 'raw' in 'rawCalibInstWS' means unintegrated.
print("Integrating Workspace")
CalibInstWS = mantid.Integration(rawCalibInstWS,
RangeLower=rangeLower,
RangeUpper=rangeUpper)
mantid.DeleteWorkspace(rawCalibInstWS)
print(
"Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
)
# == Create Objects needed for calibration ==
## In the merlin case, the positions are usually given in pixels, instead of being given in
## meters, to convert to meter and put the origin in the center, we have to apply the following
## transformation:
##
## pos = pixel * length/npixels - length/2 = length (pixel/npixels - 1/2)
##
## for merlin: npixels = 1024
knownPos = ActiveLength * (numpy.array([Left, Centre, Right]) / 1024.0 -
0.5)
funcForm = 3 * [1]
# Get fitting parameters
fitPar = TubeCalibFitParams(ExpectedPositions,
ExpectedHeight,
ExpectedWidth,
margin=40)
print("Created objects needed for calibration.")
# == Get the calibration and put results into calibration table ==
# also put peaks into PeakFile
calibrationTable, peakTable = tube.calibrate(CalibInstWS,
CalibratedComponent,
knownPos,
funcForm,
outputPeak=True,
fitPar=fitPar,
plotTube=list(
range(0, 280, 20)))
print(
"Got calibration (new positions of detectors) and put slit peaks into file TubeDemoMerlin01.txt"
)
# == Apply the Calibation ==
mantid.ApplyCalibration(Workspace=CalibInstWS,
CalibrationTable=calibrationTable)
print("Applied calibration")
# == Save workspace ==
# mantid.SaveNexusProcessed(CalibInstWS, 'TubeCalibDemoMerlinResult.nxs', "Result of Running TubeCalibDemoMerlin_Simple.py")
# print("saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMerlinResult.nxs")
# == Reset default instrument ==
mantid.config['default.instrument'] = previousDefaultInstrument
def normalise_workspace(ws_name):
tmp_norm = sapi.Integration(ws_name)
sapi.Divide(LHSWorkspace=ws_name,RHSWorkspace="tmp_norm",OutputWorkspace=ws_name)
safe_delete_ws(tmp_norm)
def generate_plots(run_number, workspace, options=None):
"""
Generate diagnostics plots
"""
n_x = int(
workspace.getInstrument().getNumberParameter("number-of-x-pixels")[0])
n_y = int(
workspace.getInstrument().getNumberParameter("number-of-y-pixels")[0])
# X-TOF plot
tof_min = workspace.getTofMin()
tof_max = workspace.getTofMax()
workspace = api.Rebin(workspace, params="%s, 50, %s" % (tof_min, tof_max))
direct_summed = api.RefRoi(InputWorkspace=workspace,
IntegrateY=True,
NXPixel=n_x,
NYPixel=n_y,
ConvertToQ=False,
YPixelMin=0,
YPixelMax=n_y,
OutputWorkspace="direct_summed")
signal = np.log10(direct_summed.extractY())
tof_axis = direct_summed.extractX()[0] / 1000.0
x_tof_plot = _plot2d(z=signal,
y=np.arange(signal.shape[0]),
x=tof_axis,
x_label="TOF (ms)",
y_label="X pixel",
title="r%s" % run_number)
# X-Y plot
_workspace = api.Integration(workspace)
signal = np.log10(_workspace.extractY())
z = np.reshape(signal, (n_x, n_y))
xy_plot = _plot2d(z=z.T,
x=np.arange(n_x),
y=np.arange(n_y),
title="r%s" % run_number)
# Count per X pixel
integrated = api.Integration(direct_summed)
integrated = api.Transpose(integrated)
signal_y = integrated.readY(0)
signal_x = np.arange(len(signal_y))
peak_pixels = _plot1d(signal_x,
signal_y,
x_label="X pixel",
y_label="Counts",
title="r%s" % run_number)
# TOF distribution
workspace = api.SumSpectra(workspace)
signal_x = workspace.readX(0) / 1000.0
signal_y = workspace.readY(0)
tof_dist = _plot1d(signal_x,
signal_y,
x_range=None,
x_label="TOF (ms)",
y_label="Counts",
title="r%s" % run_number)
return [xy_plot, x_tof_plot, peak_pixels, tof_dist]
def PyExec(self):
self._runs = self.getProperty('RunNumbers').value
self._vanfile = self.getProperty('Vanadium').value
self._ecruns = self.getProperty('EmptyCanRunNumbers').value
self._ebins = (self.getProperty('EnergyBins').value).tolist()
self._qbins = (self.getProperty('MomentumTransferBins').value).tolist()
self._snorm = self.getProperty('NormalizeSlices').value
self._clean = self.getProperty('CleanWorkspaces').value
wn_sqes = self.getPropertyValue("OutputWorkspace")
# workspace names
prefix = ''
if self._clean:
prefix = '__'
# "wn" denotes workspace name
wn_data = prefix + 'data' # Accumulated data events
wn_data_mon = prefix + 'data_monitors' # Accumulated monitors for data
wn_van = prefix + 'vanadium' # White-beam vanadium
wn_van_st = prefix + 'vanadium_S_theta'
wn_reduced = prefix + 'reduced' # data after DGSReduction
wn_ste = prefix + 'S_theta_E' # data after grouping by theta angle
wn_sten = prefix + 'S_theta_E_normalized'
wn_steni = prefix + 'S_theta_E_interp'
wn_sqe = prefix + 'S_Q_E'
wn_sqeb = prefix + 'S_Q_E_binned'
wn_sqesn = prefix + wn_sqes + '_norm'
# Empty can files
wn_ec_data = prefix + 'ec_data' # Accumulated empty can data
wn_ec_data_mon = prefix + 'ec_data_monitors' # Accumulated monitors for empty can
wn_ec_reduced = prefix + 'ec_reduced' # empty can data after DGSReduction
wn_ec_ste = prefix + 'ec_S_theta_E' # empty can data after grouping by theta angle
# Save current configuration
facility = config['default.facility']
instrument = config['default.instrument']
datasearch = config["datasearch.searcharchive"]
# Allows searching for ARCS run numbers
config['default.facility'] = 'SNS'
config['default.instrument'] = 'ARCS'
config["datasearch.searcharchive"] = "On"
try:
# Load the vanadium file, assumed to be preprocessed, meaning that
# for every detector all events within a particular wide wavelength
# range have been rebinned into a single histogram
self._load(self._vanfile, wn_van)
# Check for white-beam vanadium, true if the vertical chopper is absent (vChTrans==2)
if api.mtd[wn_van].run().getProperty('vChTrans').value[0] != 2:
raise ValueError("White-vanadium is required")
# Load several event files into a single workspace. The nominal incident
# energy should be the same to avoid difference in energy resolution
self._load(self._runs, wn_data)
# Load empty can event files, if present
if self._ecruns:
self._load(self._ecruns, wn_ec_data)
finally:
# Recover the default configuration
config['default.facility'] = facility
config['default.instrument'] = instrument
config["datasearch.searcharchive"] = datasearch
# Obtain incident energy as the mean of the nominal Ei values.
# There is one nominal value for each run number.
ws_data = sapi.mtd[wn_data]
Ei = ws_data.getRun()['EnergyRequest'].getStatistics().mean
Ei_std = ws_data.getRun()['EnergyRequest'].getStatistics(
).standard_deviation
# Verify empty can runs were obtained at similar energy
if self._ecruns:
ws_ec_data = sapi.mtd[wn_ec_data]
ec_Ei = ws_ec_data.getRun()['EnergyRequest'].getStatistics().mean
if abs(Ei - ec_Ei) > Ei_std:
raise RuntimeError(
'Empty can runs were obtained at a significant' +
' different incident energy than the sample runs')
# Obtain energy range. If user did not supply a triad
# [Estart, Ewidth, Eend] but only Ewidth, then estimate
# Estart and End from the nominal energies
if len(self._ebins) == 1:
ws_data = sapi.mtd[wn_data]
Ei = ws_data.getRun()['EnergyRequest'].getStatistics().mean
self._ebins.insert(0, -0.5 * Ei) # prepend
self._ebins.append(0.95 * Ei) # append
# Enforce that the elastic energy (E=0) lies in the middle of the
# central bin with an appropriate small shift in the energy range
Ei_min_reduced = self._ebins[0] / self._ebins[1]
remainder = Ei_min_reduced - int(Ei_min_reduced)
if remainder >= 0.0:
erange_shift = self._ebins[1] * (0.5 - remainder)
else:
erange_shift = self._ebins[1] * (-0.5 - remainder)
self._ebins[0] += erange_shift # shift minimum energy
self._ebins[-1] += erange_shift # shift maximum energy
# Convert to energy transfer. Normalize by proton charge.
# The output workspace is S(detector-id,E)
factor = 0.1 # use a finer energy bin than the one passed (self._ebins[1])
Erange = '{0},{1},{2}'.format(self._ebins[0], factor * self._ebins[1],
self._ebins[2])
Ei_calc, T0 = sapi.GetEiT0atSNS(MonitorWorkspace=wn_data_mon,
IncidentEnergyGuess=Ei)
sapi.MaskDetectors(Workspace=wn_data,
MaskedWorkspace=wn_van) # Use vanadium mask
sapi.DgsReduction(SampleInputWorkspace=wn_data,
SampleInputMonitorWorkspace=wn_data_mon,
IncidentEnergyGuess=Ei_calc,
UseIncidentEnergyGuess=1,
TimeZeroGuess=T0,
EnergyTransferRange=Erange,
IncidentBeamNormalisation='ByCurrent',
OutputWorkspace=wn_reduced)
if self._ecruns:
sapi.MaskDetectors(Workspace=wn_ec_data, MaskedWorkspace=wn_van)
sapi.DgsReduction(SampleInputWorkspace=wn_ec_data,
SampleInputMonitorWorkspace=wn_ec_data_mon,
IncidentEnergyGuess=Ei_calc,
UseIncidentEnergyGuess=1,
TimeZeroGuess=T0,
EnergyTransferRange=Erange,
IncidentBeamNormalisation='ByCurrent',
OutputWorkspace=wn_ec_reduced)
# Obtain maximum and minimum |Q| values, as well as dQ if none passed
if len(self._qbins) < 3:
if not self._qbins:
# insert dQ if empty qbins. The minimal momentum transfer
# is the result on an event where the initial energy was
# Ei and the final energy was Ei+dE.
dE = self._ebins[1]
self._qbins.append(
numpy.sqrt((Ei + dE) / ENERGY_TO_WAVEVECTOR) -
numpy.sqrt(Ei / ENERGY_TO_WAVEVECTOR))
mins, maxs = sapi.ConvertToMDMinMaxLocal(wn_reduced,
Qdimensions='|Q|',
dEAnalysisMode='Direct')
self._qbins.insert(0, mins[0]) # prepend minimum Q
self._qbins.append(maxs[0]) # append maximum Q
# Delete sample and empty can event workspaces to free memory.
if self._clean:
sapi.DeleteWorkspace(wn_data)
if self._ecruns:
sapi.DeleteWorkspace(wn_ec_data)
# Convert to S(theta,E)
ki = numpy.sqrt(Ei / ENERGY_TO_WAVEVECTOR)
# If dE is the smallest energy transfer considered,
# then dQ/ki is the smallest dtheta (in radians)
dtheta = self._qbins[1] / ki * (180.0 / numpy.pi)
# Use a finer dtheta that the nominal smallest value
factor = 1. / 5 # a reasonable (heuristic) value
dtheta *= factor
# Fix: a very small dtheta (<0.15 degrees) prevents correct interpolation
dtheta = max(0.15, dtheta)
# Group detectors according to theta angle for the sample runs
group_file_os_handle, group_file_name = mkstemp(suffix='.xml')
group_file_handle = os.fdopen(group_file_os_handle, 'w')
sapi.GenerateGroupingPowder(InputWorkspace=wn_reduced,
AngleStep=dtheta,
GroupingFilename=group_file_name)
group_file_handle.close()
sapi.GroupDetectors(InputWorkspace=wn_reduced,
MapFile=group_file_name,
OutputWorkspace=wn_ste)
# Group detectors according to theta angle for the emtpy can run
if self._ecruns:
sapi.GroupDetectors(InputWorkspace=wn_ec_reduced,
MapFile=group_file_name,
OutputWorkspace=wn_ec_ste)
# Subtract the empty can from the can+sample
sapi.Minus(LHSWorkspace=wn_ste,
RHSWorkspace=wn_ec_ste,
OutputWorkspace=wn_ste)
# Normalize by the vanadium intensity, but before that we need S(theta)
# for the vanadium. Recall every detector has all energies into a single
# bin, so we get S(theta) instead of S(theta,E)
sapi.GroupDetectors(InputWorkspace=wn_van,
MapFile=group_file_name,
OutputWorkspace=wn_van_st)
# Divide by vanadium. Make sure it is integrated in the energy domain
sapi.Integration(wn_van_st, OutputWorkspace=wn_van_st)
sapi.Divide(wn_ste, wn_van_st, OutputWorkspace=wn_sten)
sapi.ClearMaskFlag(Workspace=wn_sten)
# Temporary file generated by GenerateGroupingPowder to be removed
os.remove(group_file_name) # no need for this file
os.remove(os.path.splitext(group_file_name)[0] + ".par")
max_i_theta = 0.0
min_i_theta = 0.0
# Linear interpolation for those theta values with low intensity
# First, find minimum theta index with a non-zero histogram
ws_sten = sapi.mtd[wn_sten]
for i_theta in range(ws_sten.getNumberHistograms()):
if ws_sten.dataY(i_theta).any():
min_i_theta = i_theta
break
# second, find maximum theta with a non-zero histogram
for i_theta in range(ws_sten.getNumberHistograms() - 1, -1, -1):
if ws_sten.dataY(i_theta).any():
max_i_theta = i_theta
break
# Scan a range of theta angles and apply interpolation to those theta angles
# with considerably low intensity (gaps)
delta_theta = max_i_theta - min_i_theta
gaps = self._findGaps(wn_sten, int(min_i_theta + 0.1 * delta_theta),
int(max_i_theta - 0.1 * delta_theta))
sapi.CloneWorkspace(InputWorkspace=wn_sten, OutputWorkspace=wn_steni)
for gap in gaps:
self._interpolate(wn_steni, gap) # interpolate this gap
# Convert S(theta,E) to S(Q,E), then rebin in |Q| and E to MD workspace
sapi.ConvertToMD(InputWorkspace=wn_steni,
QDimensions='|Q|',
dEAnalysisMode='Direct',
OutputWorkspace=wn_sqe)
Qmin = self._qbins[0]
Qmax = self._qbins[-1]
dQ = self._qbins[1]
Qrange = '|Q|,{0},{1},{2}'.format(Qmin, Qmax, int((Qmax - Qmin) / dQ))
Ei_min = self._ebins[0]
Ei_max = self._ebins[-1]
dE = self._ebins[1]
deltaErange = 'DeltaE,{0},{1},{2}'.format(Ei_min, Ei_max,
int((Ei_max - Ei_min) / dE))
sapi.BinMD(InputWorkspace=wn_sqe,
AxisAligned=1,
AlignedDim0=Qrange,
AlignedDim1=deltaErange,
OutputWorkspace=wn_sqeb)
# Slice the data by transforming to a Matrix2Dworkspace,
# with deltaE along the vertical axis
sapi.ConvertMDHistoToMatrixWorkspace(
InputWorkspace=wn_sqeb,
Normalization='NumEventsNormalization',
OutputWorkspace=wn_sqes)
# Ensure correct units
sapi.mtd[wn_sqes].getAxis(0).setUnit("MomentumTransfer")
sapi.mtd[wn_sqes].getAxis(1).setUnit("DeltaE")
# Shift the energy axis, since the reported values should be the center
# of the bins, instead of the minimum bin boundary
ws_sqes = sapi.mtd[wn_sqes]
Eaxis = ws_sqes.getAxis(1)
e_shift = self._ebins[1] / 2.0
for i in range(Eaxis.length()):
Eaxis.setValue(i, Eaxis.getValue(i) + e_shift)
# Normalize each slice, if requested
if self._snorm:
sapi.Integration(InputWorkspace=wn_sqes, OutputWorkspace=wn_sqesn)
sapi.Divide(LHSWorkspace=wn_sqes,
RHSWorkspace=wn_sqesn,
OutputWorkspace=wn_sqes)
# Clean up workspaces from intermediate steps
if self._clean:
for name in (wn_van, wn_reduced, wn_ste, wn_van_st, wn_sten,
wn_steni, wn_sqe, wn_sqeb, wn_sqesn,
'PreprocessedDetectorsWS'):
if sapi.mtd.doesExist(name):
sapi.DeleteWorkspace(name)
# Ouput some info as a Notice in the log
ebins = ', '.join(['{0:.2f}'.format(x) for x in self._ebins])
qbins = ', '.join(['{0:.2f}'.format(x) for x in self._qbins])
tbins = '{0:.2f} {1:.2f} {2:.2f}'.format(min_i_theta * dtheta, dtheta,
max_i_theta * dtheta)
message = '\n****** SOME OUTPUT INFORMATION ***' + \
'\nEnergy bins: ' + ebins + \
'\nQ bins: ' + qbins + \
'\nTheta bins: '+tbins
kapi.logger.notice(message)
self.setProperty("OutputWorkspace", sapi.mtd[wn_sqes])
def CalibrateWish(RunNumber, PanelNumber):
'''
:param RunNumber: is the run number of the calibration.
:param PanelNumber: is a string of two-digit number of the panel being calibrated
'''
# == Set parameters for calibration ==
previousDefaultInstrument = mantid.config['default.instrument']
mantid.config['default.instrument'] = "WISH"
filename = str(RunNumber)
CalibratedComponent = 'WISH/panel' + PanelNumber
# Get calibration raw file and integrate it
print("Loading", filename)
rawCalibInstWS = mantid.Load(
filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
CalibInstWS = mantid.Integration(rawCalibInstWS,
RangeLower=1,
RangeUpper=20000)
mantid.DeleteWorkspace(rawCalibInstWS)
print(
"Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
)
# Give y-positions of slit points (gotten for converting first tube's slit point to Y)
# WISH instrument has a particularity. It is composed by a group of upper tubes and lower tubes,
# they are disposed 3 milimiters in difference one among the other
lower_tube = numpy.array(
[-0.41, -0.31, -0.21, -0.11, -0.02, 0.09, 0.18, 0.28, 0.39])
upper_tube = numpy.array(lower_tube + 0.003)
funcForm = 9 * [1] # 9 gaussian peaks
print("Created objects needed for calibration.")
# Get the calibration and put it into the calibration table
# calibrate the lower tubes
calibrationTable, peakTable = tube.calibrate(CalibInstWS,
CalibratedComponent,
lower_tube,
funcForm,
rangeList=list(range(0, 76)),
outputPeak=True)
# calibrate the upper tubes
calibrationTable, peakTable = tube.calibrate(
CalibInstWS,
CalibratedComponent,
upper_tube,
funcForm,
rangeList=list(range(76, 152)),
calibTable=calibrationTable,
# give the calibration table to append data
outputPeak=peakTable # give peak table to append data
)
print("Got calibration (new positions of detectors)")
# Apply the calibration
mantid.ApplyCalibration(Workspace=CalibInstWS,
PositionTable=calibrationTable)
print("Applied calibration")
# == Save workspace ==
# uncomment these lines to save the workspace
# nexusName = "TubeCalibDemoWish"+PanelNumber+"Result.nxs"
# SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoWishResult.nxs',"Result of Running TubeCalibWishMerlin_Simple.py")
# print "saved calibrated workspace (CalibInstWS) into Nexus file",nexusName
# == Reset dafault instrument ==
mantid.config['default.instrument'] = previousDefaultInstrument
def calibrateMerlin(filename):
# == Set parameters for calibration ==
rangeLower = 3000 # Integrate counts in each spectra from rangeLower to rangeUpper
rangeUpper = 20000 #
# Get calibration raw file and integrate it
rawCalibInstWS = mantid.LoadRaw(filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
print("Integrating Workspace")
CalibInstWS = mantid.Integration(rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper)
mantid.DeleteWorkspace(rawCalibInstWS)
print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
# the known positions are given in pixels inside the tubes and transformed to provide the positions
# with the center of the tube as the origin
knownPositions = 2.92713867188 * (numpy.array([27.30074322, 92.5, 294.65178585, 362.37861919,
512.77103043, 663.41425323, 798.3223896, 930.9,
997.08480835]) / 1024 - 0.5)
funcForm = numpy.array([2, 2, 1, 1, 1, 1, 1, 2, 2], numpy.int8)
# The calibration will follow different steps for sets of tubes
# For the door9, the best points to define the known positions are the 1st edge, 5 peaks, last edge.
points7 = knownPositions[[0, 2, 3, 4, 5, 6, 8]]
points7func = funcForm[[0, 2, 3, 4, 5, 6, 8]]
door9pos = points7
door9func = points7func
CalibratedComponent = 'MERLIN/door9' # door9
# == Get the calibration and put results into calibration table ==
# also put peaks into PeakFile
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, door9pos, door9func,
outputPeak=True,
margin=30,
rangeList=list(range(20))
# because 20, 21, 22, 23 are defective detectors
)
print("Got calibration (new positions of detectors) and put slit peaks into file TubeDemoMerlin01.txt")
analisePeakTable(peakTable, 'door9_tube1_peaks')
# For the door8, the best points to define the known positions are the 1st edge, 5 peaks, last_edge
door8pos = points7
door8func = points7func
CalibratedComponent = 'MERLIN/door8'
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, door8pos,
door8func,
outputPeak=True, # change to peakTable to append to peakTable
calibTable=calibrationTable,
margin=30)
analisePeakTable(peakTable, 'door8_peaks')
# For the doors 7,6,5,4, 2, 1 we may use the 9 points
doorpos = knownPositions
doorfunc = funcForm
CalibratedComponent = ['MERLIN/door%d' % (i) for i in [7, 6, 5, 4, 2, 1]]
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, doorpos,
doorfunc,
outputPeak=True,
calibTable=calibrationTable,
margin=30)
analisePeakTable(peakTable, 'door1to7_peaks')
# The door 3 is a special case, because it is composed by diffent kind of tubes.
# door 3 tubes: 5_8, 5_7, 5_6, 5_5, 5_4, 5_3, 5_2, 5_1, 4_8, 4_7, 4_6, 4_5, 4_4, 4_3, 4_2, 4_1, 3_8, 3_7, 3_6, 3_5, 3_4
# obeys the same rules as the doors 7, 6, 5, 4, 2, 1
# For the tubes 3_3, 3_2, 3_1 -> it is better to skip the central peak
# For the tubes 1_x (smaller tube below), it is better to take the final part of known positions: peak4,peak5,edge6,edge7
# For the tubes 2_x (smaller tube above, it is better to take the first part of known positions: edge1, edge2, peak1,peak2
# NOTE: the smaller tubes they have length = 1.22879882813, but 1024 detectors
# so we have to correct the known positiosn by multiplying by its length and dividing by the longer dimension
from tube_calib_fit_params import TubeCalibFitParams
# calibrating tubes 1_x
CalibratedComponent = ['MERLIN/door3/tube_1_%d' % (i) for i in range(1, 9)]
half_diff_center = (
2.92713867188 - 1.22879882813) / 2
# difference among the expected center position for
# both tubes here a little bit of attempts is necessary.
# The effective center position and length is different for the calibrated tube, that is the reason,
# the calibrated values of the smaller tube does not seems aligned with the others. By, finding the
# 'best' half_diff_center value, the alignment occurs nicely.
half_diff_center = 0.835 #
# the knownpositions were given with the center of the bigger tube as origin, to convert
# to the center of the upper tube as origin is necessary to subtract them with the half_diff_center
doorpos = knownPositions[[5, 6, 7, 8]] - half_diff_center
doorfunc = [1, 1, 2, 2]
# for the smal tubes, automatically searching for the peak position in pixel was not working quite well,
# so we will give the approximate position for these tubes through fitPar argument
fitPar = TubeCalibFitParams([216, 527, 826, 989])
fitPar.setAutomatic(True)
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, doorpos,
doorfunc,
outputPeak=True,
fitPar=fitPar,
calibTable=calibrationTable,
margin=30)
analisePeakTable(peakTable, 'door3_tube1_peaks')
# calibrating tubes 2_x
CalibratedComponent = ['MERLIN/door3/tube_2_%d' % (i) for i in range(1,9)]
# the knownpositions were given with the center of the bigger tube as origin, to convert
# to the center of the lower tube as origin is necessary to sum them with (len_big - len_small)/2
doorpos = knownPositions[[0, 1, 2, 3]] + half_diff_center
doorfunc = [2, 2, 1, 1]
# for the smal tubes, automatically searching for the peak position in pixel was not working quite well,
# so we will give the approximate position for these tubes through fitPar argument
fitPar = TubeCalibFitParams([50, 202, 664, 815])
fitPar.setAutomatic(True)
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, doorpos,
doorfunc,
outputPeak=True,
calibTable=calibrationTable,
fitPar=fitPar,
margin=30)
analisePeakTable(peakTable, 'door3_tube2_peaks')
# calibrating tubes 3_3,3_2,3_1
CalibratedComponent = ['MERLIN/door3/tube_3_%d' % (i) for i in [1, 2, 3]]
doorpos = knownPositions[[0, 1, 2, 3, 5, 6, 7, 8]]
doorfunc = funcForm[[0, 1, 2, 3, 5, 6, 7, 8]]
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, doorpos,
doorfunc,
outputPeak=True,
calibTable=calibrationTable,
margin=30)
analisePeakTable(peakTable, 'door3_123_peaks')
# calibrating others inside door3
# 5_8, 5_7, 5_6, 5_5, 5_4, 5_3, 5_2, 5_1, 4_8, 4_7, 4_6, 4_5, 4_4, 4_3, 4_2, 4_1, 3_8, 3_7, 3_6, 3_5, 3_4
part_3 = ['MERLIN/door3/tube_3_%d' % (i) for i in [4, 5, 6, 7, 8]]
part_4 = ['MERLIN/door3/tube_4_%d' % (i) for i in range(1, 9)]
part_5 = ['MERLIN/door3/tube_5_%d' % (i) for i in range(1, 9)]
CalibratedComponent = part_3 + part_4 + part_5
doorpos = knownPositions
doorfunc = funcForm
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, doorpos,
doorfunc,
outputPeak=True,
calibTable=calibrationTable,
margin=30)
analisePeakTable(peakTable, 'door3_peaks')
# == Apply the Calibation ==
mantid.ApplyCalibration(Workspace=CalibInstWS, CalibrationTable=calibrationTable)
print("Applied calibration")
