def loadSpicePDData(self, expno, scanno, datafilename):
""" Load SPICE powder diffraction data to MDEventsWorkspaces
"""
# Create base workspace name
try:
basewsname = os.path.basename(datafilename).split(".")[0]
except AttributeError as e:
raise NotImplementedError("Unable to parse data file name due to %s." % (str(e)))
# load SPICE
tablewsname = basewsname + "_RawTable"
infowsname = basewsname + "ExpInfo"
api.LoadSpiceAscii(Filename=datafilename,
OutputWorkspace=tablewsname, RunInfoWorkspace=infowsname)
tablews = AnalysisDataService.retrieve(tablewsname)
infows = AnalysisDataService.retrieve(infowsname)
if tablews is None or infows is None:
raise NotImplementedError('Unable to retrieve either spice table workspace %s or log workspace %s' % (
tablewsname, infowsname))
# Create a reduction manager and add workspaces to it
wsmanager = PDRManager(expno, scanno)
wsmanager.set_raw_workspaces(tablews, infows)
self._myWorkspaceDict[(int(expno), int(scanno))] = wsmanager
return
def parseSpiceData(self, expno, scanno, detefftablews=None):
""" Load SPICE data to MDWorkspaces from raw table workspace
"""
# Get reduction manager
try:
wsmanager = self._myWorkspaceDict[ (int(expno), int(scanno) )]
except KeyError:
raise NotImplementedError("Exp %d Scan %d has not been loaded yet." % (int(expno),int(scanno)))
# Convert to MDWorkspace
tablews = wsmanager.getRawSpiceTable()
infows = wsmanager.getRawInfoMatrixWS()
basewsname = tablews.name().split('_RawTable')[0]
datamdwsname = basewsname + "_DataMD"
monitorwsname = basewsname + "_MonitorMD"
api.ConvertSpiceDataToRealSpace(InputWorkspace=tablews,
RunInfoWorkspace=infows,
OutputWorkspace=datamdwsname,
OutputMonitorWorkspace=monitorwsname,
DetectorEfficiencyTableWorkspace=detefftablews)
datamdws = AnalysisDataService.retrieve(datamdwsname)
monitormdws = AnalysisDataService.retrieve(monitorwsname)
if datamdws is None or monitormdws is None:
raise NotImplementedError("Failed to convert SPICE data to MDEventWorkspaces \
for experiment %d and scan %d." % (expno, scanno))
# Manager:
wsmanager.setupMDWrokspaces(datamdws, monitormdws)
self._myWorkspaceDict[(expno, scanno)] = wsmanager
return True
def make_UB_consistent(self, ws_ref, ws):
# compare U matrix to perform TransformHKL to preserve indexing
U_ref = AnalysisDataService.retrieve(
ws_ref).sample().getOrientedLattice().getU()
U = AnalysisDataService.retrieve(
ws).sample().getOrientedLattice().getU()
# find transform required ( U_ref = U T^-1) - see TransformHKL docs for details
transform = np.linalg.inv(
getSignMaxAbsValInCol(np.linalg.inv(U) @ U_ref))
self.child_TransformHKL(PeaksWorkspace=ws,
HKLTransform=transform,
FindError=False)
def scanEventWorkspaces(self):
"""
"""
wsnames = AnalysisDataService.getObjectNames()
eventwsnames = []
for wsname in wsnames:
wksp = AnalysisDataService.retrieve(wsname)
if wksp.__class__.__name__.count("Event") == 1:
eventwsnames.append(wsname)
# ENDFOR
if len(eventwsnames) > 0:
self.ui.comboBox.clear()
self.ui.comboBox.addItems(eventwsnames)
def _searchTableWorkspaces(self):
""" Search table workspaces and add to 'comboBox_corrWS'
"""
wsnames = AnalysisDataService.getObjectNames()
tablewsnames = []
for wsname in wsnames:
wksp = AnalysisDataService.retrieve(wsname)
if isinstance(wksp, mantid.api.ITableWorkspace):
tablewsnames.append(wsname)
# ENDFOR
self.ui.comboBox_corrWS.clear()
if len(tablewsnames) > 0:
self.ui.comboBox_corrWS.addItems(tablewsnames)
def _searchTableWorkspaces(self):
""" Search table workspaces and add to 'comboBox_corrWS'
"""
wsnames = AnalysisDataService.getObjectNames()
tablewsnames = []
for wsname in wsnames:
wksp = AnalysisDataService.retrieve(wsname)
if isinstance(wksp, mantid.api.ITableWorkspace):
tablewsnames.append(wsname)
# ENDFOR
self.ui.comboBox_corrWS.clear()
if len(tablewsnames) > 0:
self.ui.comboBox_corrWS.addItems(tablewsnames)
def scanEventWorkspaces(self):
"""
"""
wsnames = AnalysisDataService.getObjectNames()
eventwsnames = []
for wsname in wsnames:
wksp = AnalysisDataService.retrieve(wsname)
if wksp.__class__.__name__.count("Event") == 1:
eventwsnames.append(wsname)
# ENDFOR
if len(eventwsnames) > 0:
self.ui.comboBox.clear()
self.ui.comboBox.addItems(eventwsnames)
def test_that_correctly_identifies_normalisation_for_artificial_double_pulse_data(
self):
delta = 0.33
x = np.linspace(0., 15., 100)
x_offset = np.linspace(delta / 2, 15. + delta / 2, 100)
x_offset_neg = np.linspace(-delta / 2, 15. - delta / 2, 100)
testFunction = GausOsc(Frequency=1.5, A=0.22)
y1 = testFunction(x_offset_neg)
y2 = testFunction(x_offset)
N0 = 6.38
y = N0 * (1 + y1 / 2 + y2 / 2)
y_norm = y1 / 2 + y2 / 2
CreateWorkspace(x, y, OutputWorkspace="unnormalised_workspace")
CreateWorkspace(x, y, OutputWorkspace="ws_to_normalise")
CreateWorkspace(x, y_norm, OutputWorkspace="ws_correctly_normalised")
AddSampleLog(Workspace='ws_to_normalise',
LogName="analysis_asymmetry_norm",
LogText="1")
innerFunction = FunctionFactory.createInitialized(
'name=GausOsc,A=0.20,Sigma=0.2,Frequency=1.0,Phi=0')
tf_function = ConvertFitFunctionForMuonTFAsymmetry(
InputFunction=innerFunction, WorkspaceList=['ws_to_normalise'])
CalculateMuonAsymmetry(
MaxIterations=100,
EnableDoublePulse=True,
PulseOffset=delta,
UnNormalizedWorkspaceList='unnormalised_workspace',
ReNormalizedWorkspaceList='ws_to_normalise',
OutputFitWorkspace='DoublePulseFit',
StartX=0,
InputFunction=str(tf_function),
Minimizer='Levenberg-Marquardt')
double_parameter_workspace = AnalysisDataService.retrieve(
'DoublePulseFit_Parameters')
values_column = double_parameter_workspace.column(1)
# Check that the correct normalisation is found.
self.assertAlmostEqual(values_column[0], N0, places=3)
# Check that normalised data is correct
result, message = CompareWorkspaces('ws_to_normalise',
'ws_correctly_normalised',
Tolerance=1e-3)
self.assertTrue(result)
AnalysisDataService.clear()
def output_data(self, x, y, e, data, NSpec, UnitX, norm, outputfn,
metadata):
"""Save reduced data to file"""
createWS_alg = self.createChildAlgorithm("CreateWorkspace",
enableLogging=False)
createWS_alg.setProperty("DataX", x)
createWS_alg.setProperty("DataY", y)
createWS_alg.setProperty("DataE", e)
createWS_alg.setProperty("NSpec", NSpec)
createWS_alg.setProperty("UnitX", UnitX)
createWS_alg.setProperty("YUnitLabel", "Counts")
createWS_alg.setProperty("WorkspaceTitle",
str(metadata['scan_title']) + "_norm_" + norm)
createWS_alg.execute()
outWS = createWS_alg.getProperty("OutputWorkspace").value
AnalysisDataService.addOrReplace(outputfn + "_norm_" + norm, outWS)
self.add_metadata(outWS, metadata, data)
# save reduced workspace to requested format
save_data = self.getProperty("SaveData").value
if save_data:
outputdir = self.getProperty("OutputDirectory").value
outputdir = outputdir if outputdir != "" else f"/HFIR/HB2A/IPTS-{metadata['proposal']}/shared"
_outputfunc = {
'XYE': SaveFocusedXYE,
'GSAS': SaveGSSCW
}[self.getProperty('OutputFormat').value]
_outputext = {
"XYE": 'dat',
"GSAS": 'gss',
}[self.getProperty('OutputFormat').value]
outputbase = os.path.join(outputdir, outputfn)
if norm == "mon":
out_f_name = outputbase
else:
out_f_name = outputbase + "_norm_" + norm
if self.getProperty('OutputFormat').value == "GSAS":
_outputfunc(
InputWorkspace=outWS,
OutputFilename=f"{out_f_name}.{_outputext}",
)
else:
_outputfunc(
InputWorkspace=outWS,
Filename=f"{out_f_name}.{_outputext}",
SplitFiles=False,
)
def _check_region_grouping_ws_exists(grouping_ws_name: str,
inst_ws) -> bool:
"""
Check that the required grouping workspace for this focus exists, and if not present for a North/South bank
focus, retrieve them from the user directories or create them (expected if first focus with loaded calibration)
:param grouping_ws_name: Name of the grouping workspace whose presence in the ADS is being checked
:param inst_ws: Workspace containing the instrument data for use in making a bank grouping workspace
:return: True if the required workspace exists (or has just been loaded/created), False if not
"""
if not Ads.doesExist(grouping_ws_name):
if "North" in grouping_ws_name:
logger.notice(
"NorthBank grouping workspace not present in ADS, loading")
EnggUtils.get_bank_grouping_workspace(1, inst_ws)
return True
elif "South" in grouping_ws_name:
logger.notice(
"SouthBank grouping workspace not present in ADS, loading")
EnggUtils.get_bank_grouping_workspace(2, inst_ws)
return True
else:
logger.warning(
f"Cannot focus as the grouping workspace \"{grouping_ws_name}\" is not present."
)
return False
return True
def getVectorProcessVanToPlot(self, exp, scan, tempdata=False):
""" Get vec x and y for the processed vanadium spectrum
"""
# get on hold of processed vanadium data workspace
wsmanager = self.getWorkspace(exp, scan, raiseexception=True)
if tempdata is True:
procVanWs = wsmanager.getProcessedVanadiumWSTemp()
else:
procVanWs = wsmanager.getProcessedVanadiumWS()
#procVanWs = wsmanager._processedVanWS
if procVanWs is None:
raise NotImplementedError(
"Exp %d Scan %d does not have processed vanadium workspace." %
(exp, scan))
# convert to point data if necessary
if len(procVanWs.readX(0)) != len(procVanWs.readY(0)):
wsname = procVanWs.name() + "_pd"
api.ConvertToPointData(InputWorkspace=procVanWs,
OutputWorkspace=wsname)
outws = AnalysisDataService.retrieve(wsname)
else:
outws = procVanWs
# get vectors
return outws.readX(0), outws.readY(0)
def PyExec(self):
ws_list = self.getProperty('InputWorkspaces').value
x_min = self.getProperty('XMin').value
x_max = self.getProperty('XMax').value
scale_bool = self.getProperty('CalculateScale').value
offset_bool = self.getProperty('CalculateOffset').value
flattened_list = self.unwrap_groups(ws_list)
largest_range_spectrum, rebin_param = self.get_common_bin_range_and_largest_spectra(flattened_list)
CloneWorkspace(InputWorkspace=flattened_list[0], OutputWorkspace='ws_conjoined')
Rebin(InputWorkspace='ws_conjoined', OutputWorkspace='ws_conjoined', Params=rebin_param)
for ws in flattened_list[1:]:
temp = CloneWorkspace(InputWorkspace=ws)
temp = Rebin(InputWorkspace=temp, Params=rebin_param)
ConjoinWorkspaces(InputWorkspace1='ws_conjoined',
InputWorkspace2=temp,
CheckOverlapping=False)
ws_conjoined = AnalysisDataService.retrieve('ws_conjoined')
ref_spec = ws_conjoined.getSpectrum(largest_range_spectrum).getSpectrumNo()
ws_conjoined, offset, scale, chisq = MatchSpectra(InputWorkspace=ws_conjoined,
ReferenceSpectrum=ref_spec,
CalculateScale=scale_bool,
CalculateOffset=offset_bool)
x_min, x_max, bin_width = self.fit_x_lims_to_match_histogram_bins(ws_conjoined, x_min, x_max)
ws_conjoined = CropWorkspaceRagged(InputWorkspace=ws_conjoined, XMin=x_min, XMax=x_max)
ws_conjoined = Rebin(InputWorkspace=ws_conjoined, Params=[min(x_min), bin_width, max(x_max)])
merged_ws = SumSpectra(InputWorkspace=ws_conjoined, WeightedSum=True, MultiplyBySpectra=False, StoreInADS=False)
DeleteWorkspace(ws_conjoined)
self.setProperty('OutputWorkspace', merged_ws)
def load_full_instrument_calibration():
if ADS.doesExist("full_inst_calib"):
full_calib = ADS.retrieve("full_inst_calib")
else:
full_calib_path = get_setting(
output_settings.INTERFACES_SETTINGS_GROUP,
output_settings.ENGINEERING_PREFIX, "full_calibration")
try:
full_calib = Load(full_calib_path,
OutputWorkspace="full_inst_calib")
except ValueError:
logger.error(
"Error loading Full instrument calibration - this is set in the interface settings."
)
return
return full_calib
def getVectorProcessVanToPlot(self, exp, scan, tempdata=False):
""" Get vec x and y for the processed vanadium spectrum
"""
# get on hold of processed vanadium data workspace
wsmanager = self.getWorkspace(exp, scan, raiseexception=True)
if tempdata is True:
procVanWs = wsmanager.getProcessedVanadiumWSTemp()
else:
procVanWs = wsmanager.getProcessedVanadiumWS()
#procVanWs = wsmanager._processedVanWS
if procVanWs is None:
raise NotImplementedError("Exp %d Scan %d does not have processed vanadium workspace." % (exp, scan))
# convert to point data if necessary
if len(procVanWs.readX(0)) != len(procVanWs.readY(0)):
wsname = procVanWs.name() + "_pd"
api.ConvertToPointData(InputWorkspace=procVanWs, OutputWorkspace=wsname)
outws = AnalysisDataService.retrieve(wsname)
else:
outws = procVanWs
# get vectors
return outws.readX(0), outws.readY(0)
def generate_tof_fit_dictionary(cal_name=None) -> dict:
"""
Generate a dictionary of data to plot showing the results of the calibration
:param cal_name: Name of the region of interest of the calibration
:return: dict, keys: x = expected peaks (dSpacing), y = fitted peaks (TOF), e = y error data,
y2 = calculated peaks (TOF), r = residuals (y - y2)
"""
if not cal_name:
generate_tof_fit_dictionary("bank_1")
generate_tof_fit_dictionary("bank_2")
if cal_name[-1:] == '1': # bank_1
diag_ws_name = "diag_bank_1"
elif cal_name[-1:] == '2':
diag_ws_name = "diag_bank_2"
else:
diag_ws_name = "diag_" + cal_name
fitparam_ws_name = diag_ws_name + "_fitparam"
fitted_ws_name = diag_ws_name + "_fitted"
fiterror_ws_name = diag_ws_name + "_fiterror"
fitparam_ws = ADS.retrieve(fitparam_ws_name)
fitted_ws = ADS.retrieve(fitted_ws_name)
fiterror_ws = ADS.retrieve(fiterror_ws_name)
expected_dspacing_peaks = default_ceria_expected_peaks(final=True)
expected_d_peaks_x = []
fitted_tof_peaks_y = []
tof_peaks_error_e = []
calculated_tof_peaks_y2 = []
residuals = []
for irow in range(0, fitparam_ws.rowCount()):
expected_d_peaks_x.append(expected_dspacing_peaks[-(irow + 1)])
fitted_tof_peaks_y.append(fitparam_ws.cell(irow, 5))
tof_peaks_error_e.append(fiterror_ws.cell(irow, 5))
calculated_tof_peaks_y2.append(
convert_single_value_dSpacing_to_TOF(expected_d_peaks_x[irow],
fitted_ws))
residuals.append(fitted_tof_peaks_y[irow] -
calculated_tof_peaks_y2[irow])
return {
'x': expected_d_peaks_x,
'y': fitted_tof_peaks_y,
'e': tof_peaks_error_e,
'y2': calculated_tof_peaks_y2,
'r': residuals
}
def PyExec(self):
# setup progress bar
prog_reporter = Progress(self, start=0.0, end=1.0, nreports=3)
# Get input
ws_list = self.getProperty("PeakWorkspaces").value
a = self.getProperty('a').value
b = self.getProperty('b').value
c = self.getProperty('c').value
alpha = self.getProperty('alpha').value
beta = self.getProperty('beta').value
gamma = self.getProperty('gamma').value
self.tol = self.getProperty('Tolerance').value
# Find initial UB and use to index peaks in all runs
prog_reporter.report(1, "Find initial UB for peak indexing")
self.find_initial_indexing(
a, b, c, alpha, beta, gamma,
ws_list) # removes runs from ws_list if can't index
# optimize the lattice parameters across runs (i.e. B matrix)
prog_reporter.report(2, "Optimize B")
def fobj(x):
return self.calcResiduals(x, ws_list)
alatt0 = [a, b, c, alpha, beta, gamma]
try:
alatt, cov, info, msg, ier = leastsq(fobj,
x0=alatt0,
full_output=True)
# eval the fobj at optimal solution to set UB (leastsq iteration stops at a next sub-optimal solution)
fobj(alatt)
except ValueError:
logger.error(
"CalculateUMatrix failed - check initial lattice parameters and tolerance provided."
)
return
success = ier in [
1, 2, 3, 4
] and cov is not None # cov is None when matrix is singular
if success:
# calculate errors
dof = sum(
[self.child_IndexPeaks(ws, RoundHKLs=True)
for ws in ws_list]) - len(alatt0)
err = np.sqrt(abs(np.diag(cov)) * (info['fvec']**2).sum() / dof)
for wsname in ws_list:
ws = AnalysisDataService.retrieve(wsname)
ws.sample().getOrientedLattice().setError(*err)
logger.notice(
f"Lattice parameters successfully refined for workspaces: {ws_list}\n"
f"Lattice Parameters: {np.array2string(alatt, precision=6)}\n"
f"Parameter Errors : {np.array2string(err, precision=6)}")
else:
logger.warning(
f"Error in optimization of lattice parameters: {msg}")
# complete progress
prog_reporter.report(3, "Done")
def _get_region_calib_ws(region: str): # -> Workspace
"""
Retrieve region calibration workspace from the ADS
:param region: String describing region of interest
:return: Region calibration workspace
"""
ws_name = REGION_CALIB_WS_PREFIX + region
return Ads.retrieve(ws_name)
def reduceSpicePDData(self, exp, scan, unit, xmin, xmax, binsize, wavelength=None, excludeddetlist=None,scalefactor=None):
""" Reduce SPICE powder diffraction data.
Return - Boolean as reduction is successful or not
"""
# Default
if excludeddetlist is None:
excludeddetlist = None
# Get reduction manager
try:
wsmanager = self._myWorkspaceDict[(int(exp), int(scan))]
except KeyError:
raise NotImplementedError("SPICE data for Exp %d Scan %d has not been loaded." % (
int(exp), int(scan)))
datamdws = wsmanager.datamdws
monitormdws = wsmanager.monitormdws
# binning from MD to single spectrum ws
# set up binning parameters
if xmin is None or xmax is None:
binpar = "%.7f" % (binsize)
else:
binpar = "%.7f, %.7f, %.7f" % (xmin, binsize, xmax)
# scale-factor
if scalefactor is None:
scalefactor = 1.
else:
scalefactor = float(scalefactor)
basewsname = datamdws.name().split("_DataMD")[0]
outwsname = basewsname + "_Reduced"
print "[DB]", numpy.array(excludeddetlist)
api.ConvertCWPDMDToSpectra(InputWorkspace=datamdws,
InputMonitorWorkspace=monitormdws,
OutputWorkspace=outwsname,
BinningParams=binpar,
UnitOutput = unit,
NeutronWaveLength=wavelength,
ExcludedDetectorIDs=numpy.array(excludeddetlist),
ScaleFactor=scalefactor)
print "[DB] Reduction is finished. Data is in workspace %s. " % (outwsname)
# Set up class variable for min/max and
outws = AnalysisDataService.retrieve(outwsname)
if outws is None:
raise NotImplementedError("Failed to bin the MDEventWorkspaces to MatrixWorkspace.")
# Manager:
wsmanager = PDRManager(exp, scan)
wsmanager.setup(datamdws, monitormdws, outws, unit, binsize)
wsmanager.setWavelength(wavelength)
self._myWorkspaceDict[(exp, scan)] = wsmanager
return True
def fetch_correction_workspaces(vanadium_path: str, instrument: str):
# -> Workspace2D, Workspace2D
"""
Fetch workspaces from the ADS or create new ones.
:param vanadium_path: The path to the requested vanadium run raw data.
:param instrument: The instrument the data came from.
"""
van_run_no = path_handling.get_run_number_from_path(
vanadium_path, instrument)
if not check_workspaces_exist(van_run_no):
van_integration_ws, van_processed_inst_ws = create_vanadium_corrections(
vanadium_path, instrument)
else:
van_integration_ws = Ads.retrieve(
str(van_run_no) + '_' + INTEGRATED_WORKSPACE_NAME)
van_processed_inst_ws = Ads.retrieve(
str(van_run_no) + '_' + PROCESSED_WORKSPACE_NAME)
return van_integration_ws, van_processed_inst_ws
def _locate_global_xlimit(self):
"""Find the global bin from all spectrum"""
input_workspaces = self.getProperty("InputWorkspace").value
mask = self.getProperty("MaskWorkspace").value
maks_angle = self.getProperty("MaskAngle").value
target = self.getProperty("Target").value
e_fixed = self.getProperty("EFixed").value
# NOTE:
# Due to range difference among incoming spectra, a common bin para is needed
# such that all data can be binned exactly the same way.
_xMin, _xMax = 1e16, -1e16
# BEGIN_FOR: located_global_xMin&xMax
for n, _wsn in enumerate(input_workspaces):
_ws = AnalysisDataService.retrieve(_wsn)
_mskn = f"__mask_{n}"
self.temp_workspace_list.append(_mskn)
ExtractMask(_ws, OutputWorkspace=_mskn, EnableLogging=False)
if maks_angle != Property.EMPTY_DBL:
MaskAngle(
Workspace=_mskn,
MinAngle=maks_angle,
Angle="Phi",
EnableLogging=False,
)
if mask is not None:
BinaryOperateMasks(
InputWorkspace1=_mskn,
InputWorkspace2=mask,
OperationType="OR",
OutputWorkspace=_mskn,
EnableLogging=False,
)
_ws_tmp = ExtractUnmaskedSpectra(
InputWorkspace=_ws, MaskWorkspace=_mskn, EnableLogging=False
)
if isinstance(mtd["_ws_tmp"], IEventWorkspace):
_ws_tmp = Integration(InputWorkspace=_ws_tmp, EnableLogging=False)
_ws_tmp = ConvertSpectrumAxis(
InputWorkspace=_ws_tmp,
Target=target,
EFixed=e_fixed,
EnableLogging=False,
)
_ws_tmp = Transpose(
InputWorkspace=_ws_tmp, OutputWorkspace=f"__ws_{n}", EnableLogging=False
)
_xMin = min(_xMin, _ws_tmp.readX(0).min())
_xMax = max(_xMax, _ws_tmp.readX(0).max())
# END_FOR: located_global_xMin&xMax
return _xMin, _xMax
def test_MatchAndMergeWorkspaces_accepts_a_list_of_workspaces(self):
x_min = np.array([2, 5, 10])
x_max = np.array([10, 20, 30])
ws_group = AnalysisDataService.retrieve('ws_group')
ws_list = [ws_group[0], ws_group[1], ws_group[2]]
ws_merged = MatchAndMergeWorkspaces(InputWorkspaces=ws_list, XMin=x_min, XMax=x_max)
self.assertIsInstance(ws_merged, MatrixWorkspace)
self.assertEqual(ws_merged.getNumberHistograms(), 1)
self.assertAlmostEqual(min(ws_merged.dataX(0)), 2, places=0)
self.assertAlmostEqual(max(ws_merged.dataX(0)), 30, places=0)
def unwrap_groups(inputs):
output = []
for name_in_list in inputs:
ws_in_list = AnalysisDataService.retrieve(name_in_list)
if isinstance(ws_in_list, Workspace2D):
output.append(ws_in_list)
if isinstance(ws_in_list, WorkspaceGroup):
for ws_in_group in ws_in_list:
output.append(ws_in_group)
return output
def plot_cut_ws(self, wsname):
if len(self.figure.axes[0].tracked_workspaces) == 0:
self.figure.axes[0].errorbar(ADS.retrieve(wsname),
wkspIndex=None,
marker='o',
capsize=2,
color='k',
markersize=3)
self._format_cut_figure()
self.figure.canvas.draw()
def _calculate_vanadium_correction(vanadium_path):
"""
Runs the vanadium correction algorithm.
:param vanadium_path: The path to the vanadium data.
:return: The integrated workspace and the curves generated by the algorithm.
"""
try:
Load(Filename=vanadium_path, OutputWorkspace=VANADIUM_INPUT_WORKSPACE_NAME)
except Exception as e:
logger.error("Error when loading vanadium sample data. "
"Could not run Load algorithm with vanadium run number: " +
str(vanadium_path) + ". Error description: " + str(e))
raise RuntimeError
EnggVanadiumCorrections(VanadiumWorkspace=VANADIUM_INPUT_WORKSPACE_NAME,
OutIntegrationWorkspace=INTEGRATED_WORKSPACE_NAME,
OutCurvesWorkspace=CURVES_WORKSPACE_NAME)
Ads.remove(VANADIUM_INPUT_WORKSPACE_NAME)
integrated_workspace = Ads.Instance().retrieve(INTEGRATED_WORKSPACE_NAME)
curves_workspace = Ads.Instance().retrieve(CURVES_WORKSPACE_NAME)
return integrated_workspace, curves_workspace
def _expand_groups(self):
"""expand workspace groups"""
workspaces = self.getProperty("InputWorkspace").value
input_workspaces = []
for wsname in workspaces:
wks = AnalysisDataService.retrieve(wsname)
if isinstance(wks, WorkspaceGroup):
input_workspaces.extend(wks.getNames())
else:
input_workspaces.append(wsname)
return input_workspaces
def testNoBackgroundNoiseDefaults(self):
self.__setupTestWS()
self.__createRandPeaksWS(self.peak_amplitude)
basews = AnalysisDataService.retrieve("Baseline")
peakws = AnalysisDataService.retrieve("PeakData")
clippedws = ClipPeaks(peakws,
LLSCorrection=True,
IncreasingWindow=False,
SmoothingRange=10,
WindowSize=10,
OutputWorkspace="clipout")
# Validate by subtracting peak clip results with baseline function
np.testing.assert_allclose(clippedws.extractY(),
basews.extractY(),
rtol=self.tolerance)
DeleteWorkspaces(WorkspaceList=["Baseline", "PeakData", "clipout"])
def __createRandPeaksWS(self, amplitude=1.0):
"""
Creates a test WS with random peaks added to the baseline function
"""
# Create a new generator, get a permutation of indices used to add peaks to the data.
np.random.seed(self.rand_seed)
peaklist = np.random.randint(self.peak_border_lim,
self.resolution - self.peak_border_lim,
self.npeaks)
self.assertTrue(AnalysisDataService.doesExist("Baseline"))
basews = AnalysisDataService.retrieve("Baseline")
x = basews.extractX()
y = basews.extractY()
# Add a simple peak to the indices chosen by the random permutation
for i in peaklist:
y[0][i] = y[0][i] + amplitude * np.abs(np.sin(x[0][i]))
CreateWorkspace(DataX=x, DataY=y, OutputWorkspace="PeakData")
def get_bank_grouping_workspace(bank: int, sample_raw): # -> GroupingWorkspace
"""
Retrieve the grouping workspace for the North/South bank from the user directories, or create a new one from the
sample workspace instrument data if not found
:param bank: integer denoting the bank, 1 or 2 for North/South respectively
:param sample_raw: Workspace containing the instrument data that can be used to create a new grouping workspace
:return: The loaded or created grouping workspace
"""
if bank == 1:
try:
if ADS.doesExist("NorthBank_grouping"):
return ADS.retrieve("NorthBank_grouping")
grp_ws = mantid.LoadDetectorsGroupingFile(
InputFile="ENGINX_North_grouping.xml",
OutputWorkspace="NorthBank_grouping")
return grp_ws
except ValueError:
logger.notice(
"NorthBank grouping file not found in user directories - creating one"
)
bank_name = "NorthBank"
elif bank == 2:
try:
if ADS.doesExist("SouthBank_grouping"):
return ADS.retrieve("SouthBank_grouping")
grp_ws = mantid.LoadDetectorsGroupingFile(
InputFile="ENGINX_South_grouping.xml",
OutputWorkspace="SouthBank_grouping")
return grp_ws
except ValueError:
logger.notice(
"SouthBank grouping file not found in user directories - creating one"
)
bank_name = "SouthBank"
else:
raise ValueError("Invalid bank number given")
ws_name = bank_name + "_grouping"
grp_ws, _, _ = mantid.CreateGroupingWorkspace(InputWorkspace=sample_raw,
GroupNames=bank_name,
OutputWorkspace=ws_name)
return grp_ws
def _plot_focused_workspaces(focused_workspaces):
fig = plt.figure()
gs = gridspec.GridSpec(1, len(focused_workspaces))
plots = [
fig.add_subplot(gs[i], projection="mantid")
for i in range(len(focused_workspaces))
]
for ax, ws_name in zip(plots, focused_workspaces):
ax.plot(Ads.retrieve(ws_name), wkspIndex=0)
ax.set_title(ws_name)
fig.show()
def test_that_plotting_ws_without_giving_spec_num_sets_correct_spec_num_after_spectra_removed(
self):
CreateWorkspace(DataX=[10, 20, 30],
DataY=[10, 20, 30],
DataE=[1, 1, 1],
NSpec=3,
OutputWorkspace="ws-with-3-spec")
RemoveSpectra("ws-with-3-spec", [0, 1], OutputWorkspace='out_ws')
out_ws = ADS.retrieve('out_ws')
self.ax.plot(out_ws)
ws_artist = self.ax.tracked_workspaces['out_ws'][0]
self.assertEqual(3, ws_artist.spec_num)
def get_detector_ids_for_bank(bank):
"""
Find the detector IDs for an instrument bank. Note this is at this point specific to
the ENGINX instrument.
@param bank :: name/number as a string.
@returns list of detector IDs corresponding to the specified Engg bank number
"""
import os
grouping_file_path = os.path.join(mantid.config.getInstrumentDirectory(),
'Grouping', 'ENGINX_Grouping.xml')
alg = AlgorithmManager.create('LoadDetectorsGroupingFile')
alg.initialize()
alg.setLogging(False)
alg.setProperty('InputFile', grouping_file_path)
group_name = '__EnginXGrouping'
alg.setProperty('OutputWorkspace', group_name)
alg.execute()
# LoadDetectorsGroupingFile produces a 'Grouping' workspace.
# PropertyWithValue<GroupingWorkspace> not working (GitHub issue 13437)
# => cannot run as child and get outputworkspace property properly
if not ADS.doesExist(group_name):
raise RuntimeError(
'LoadDetectorsGroupingFile did not run correctly. Could not '
'find its output workspace: ' + group_name)
grouping = mtd[group_name]
detector_ids = set()
# less then zero indicates both banks, from line 98
bank_int = int(bank)
if bank_int < 0:
# both banks, north and south
bank_int = [1, 2]
else:
# make into list so that the `if in` check works
bank_int = [bank_int]
for i in range(grouping.getNumberHistograms()):
if grouping.readY(i)[0] in bank_int:
detector_ids.add(grouping.getDetector(i).getID())
mantid.DeleteWorkspace(grouping)
if len(detector_ids) == 0:
raise ValueError('Could not find any detector for this bank: ' + bank +
'. This looks like an unknown bank')
return detector_ids
def test_fit_cubic_spline_via_mantid_produces_fit_with_same_range_as_binning_for_calc(
self):
binning_for_calc = "0.2,0.1,3.0"
binning_for_fit = "0.2,0.1,4.0"
alg_test = run_algorithm("FitIncidentSpectrum",
InputWorkspace=self.incident_wksp,
OutputWorkspace="fit_wksp",
BinningForCalc=binning_for_calc,
BinningForFit=binning_for_fit,
FitSpectrumWith="CubicSplineViaMantid")
self.assertTrue(alg_test.isExecuted())
fit_wksp = AnalysisDataService.retrieve("fit_wksp")
self.assertEqual(fit_wksp.readX(0).all(), np.arange(0.2, 3, 0.1).all())
def _check_region_calib_ws_exists(region: str) -> bool:
"""
Check that the required workspace for use in focussing the provided region of interest exist in the ADS
:param region: String describing region of interest
:return: True if present, False if not
"""
region_ws_name = REGION_CALIB_WS_PREFIX + region
present = Ads.doesExist(region_ws_name)
if not present:
logger.warning(
f"Cannot focus as the region calibration workspace \"{region_ws_name}\" is not "
f"present.")
return present
def use_existWS(self):
""" Set up workspace to an existing one
"""
wsname = str(self.ui.comboBox.currentText())
try:
dataws = AnalysisDataService.retrieve(wsname)
self._importDataWorkspace(dataws)
except KeyError:
pass
# Reset GUI
self._resetGUI(resetfilerun=True)
def test_MatchAndMergeWorkspaces_accepts_a_mixture_of_ws_size(self):
x_min = np.array([2, 5, 10, 15, 20])
x_max = np.array([10, 20, 30, 40, 45])
ws_group = AnalysisDataService.retrieve('ws_group')
ConjoinWorkspaces(InputWorkspace1=ws_group[3],
InputWorkspace2=ws_group[4],
CheckOverlapping=False)
ws_list = [ws_group[0], ws_group[1], ws_group[2], ws_group[3]]
ws_merged = MatchAndMergeWorkspaces(InputWorkspaces=ws_list, XMin=x_min, XMax=x_max)
self.assertIsInstance(ws_merged, MatrixWorkspace)
self.assertEqual(ws_merged.getNumberHistograms(), 1)
self.assertAlmostEqual(min(ws_merged.dataX(0)), 2, places=0)
self.assertAlmostEqual(max(ws_merged.dataX(0)), 45, places=0)
def use_existWS(self):
""" Set up workspace to an existing one
"""
wsname = str(self.ui.comboBox.currentText())
try:
dataws = AnalysisDataService.retrieve(wsname)
self._importDataWorkspace(dataws)
except KeyError:
pass
# Reset GUI
self._resetGUI(resetfilerun=True)
def create_vanadium_corrections(vanadium_path: str,
instrument: str): # -> Workspace, Workspace
"""
Runs the vanadium correction algorithm.
:param vanadium_path: The path to the vanadium data.
:return: The integrated workspace and the processed instrument workspace generated.
"""
try:
run_no = path_handling.get_run_number_from_path(
vanadium_path, instrument)
van_ws = Load(Filename=vanadium_path,
OutputWorkspace=str(run_no) + '_' +
VANADIUM_INPUT_WORKSPACE_NAME)
except Exception as e:
logger.error(
"Error when loading vanadium sample data. "
"Could not run Load algorithm with vanadium run number: " +
str(vanadium_path) + ". Error description: " + str(e))
raise RuntimeError
# get full instrument calibration for instrument processing calculation
if Ads.doesExist("full_inst_calib"):
full_calib_ws = Ads.retrieve("full_inst_calib")
else:
full_calib_path = get_setting(
output_settings.INTERFACES_SETTINGS_GROUP,
output_settings.ENGINEERING_PREFIX, "full_calibration")
try:
full_calib_ws = Load(full_calib_path,
OutputWorkspace="full_inst_calib")
except ValueError:
logger.error(
"Error loading Full instrument calibration - this is set in the interface settings."
)
return
integral_ws = _calculate_vanadium_integral(van_ws, run_no)
processed_ws = _calculate_vanadium_processed_instrument(
van_ws, full_calib_ws, integral_ws, run_no)
return integral_ws, processed_ws
def getMergedVector(self, mkey):
""" Get vector X and Y from merged scans
"""
if self._myMergedWSDict.has_key(mkey) is True:
wksp = self._myMergedWSDict[mkey]
# convert to point data if necessary
if len(wksp.readX(0)) != len(wksp.readY(0)):
wsname = wksp.name() + "_pd"
api.ConvertToPointData(InputWorkspace=wksp, OutputWorkspace=wsname)
wksp = AnalysisDataService.retrieve(wsname)
vecx = wksp.readX(0)
vecy = wksp.readY(0)
else:
raise NotImplementedError("No merged workspace for key = %s." % (str(mkey)))
return (vecx, vecy)
def getVectorToPlot(self, exp, scan):
""" Get vec x and vec y of the reduced workspace to plot
"""
# get on hold of reduced workspace
wsmanager = self.getWorkspace(exp, scan, raiseexception=True)
reducedws = wsmanager.reducedws
if reducedws is None:
raise NotImplementedError("Exp %d Scan %d does not have reduced workspace." % (exp, scan))
# convert to point data if necessary
if len(reducedws.readX(0)) != len(reducedws.readY(0)):
wsname = reducedws.name() + "_pd"
api.ConvertToPointData(InputWorkspace=reducedws, OutputWorkspace=wsname)
outws = AnalysisDataService.retrieve(wsname)
else:
outws = reducedws
# get vectors
return outws.readX(0), outws.readY(0)
def _plotTimeCounts(self, wksp):
""" Plot time/counts
"""
import datetime
# Rebin events by pulse time
try:
# Get run start and run stop
if wksp.getRun().hasProperty("run_start"):
runstart = wksp.getRun().getProperty("run_start").value
else:
runstart = wksp.getRun().getProperty("proton_charge").times[0]
runstop = wksp.getRun().getProperty("proton_charge").times[-1]
runstart = str(runstart).split(".")[0].strip()
runstop = str(runstop).split(".")[0].strip()
t0 = datetime.datetime.strptime(runstart, "%Y-%m-%dT%H:%M:%S")
tf = datetime.datetime.strptime(runstop, "%Y-%m-%dT%H:%M:%S")
# Calcualte
dt = tf-t0
timeduration = dt.days*3600*24 + dt.seconds
timeres = float(timeduration)/MAXTIMEBINSIZE
if timeres < 1.0:
timeres = 1.0
sumwsname = "_Summed_%s"%(str(wksp))
if AnalysisDataService.doesExist(sumwsname) is False:
sumws = api.SumSpectra(InputWorkspace=wksp, OutputWorkspace=sumwsname)
sumws = api.RebinByPulseTimes(InputWorkspace=sumws, OutputWorkspace = sumwsname,
Params="%f"%(timeres))
sumws = api.ConvertToPointData(InputWorkspace=sumws, OutputWorkspace=sumwsname)
else:
sumws = AnalysisDataService.retrieve(sumwsname)
except RuntimeError as e:
return str(e)
vecx = sumws.readX(0)
vecy = sumws.readY(0)
xmin = min(vecx)
xmax = max(vecx)
ymin = min(vecy)
ymax = max(vecy)
# Reset graph
self.ui.mainplot.set_xlim(xmin, xmax)
self.ui.mainplot.set_ylim(ymin, ymax)
self.ui.mainplot.set_xlabel('Time (seconds)', fontsize=13)
self.ui.mainplot.set_ylabel('Counts', fontsize=13)
# Set up main line
setp(self.mainline, xdata=vecx, ydata=vecy)
# Reset slide
newslidery = [min(vecy), max(vecy)]
newleftx = xmin + (xmax-xmin)*self._leftSlideValue*0.01
setp(self.leftslideline, xdata=[newleftx, newleftx], ydata=newslidery)
newrightx = xmin + (xmax-xmin)*self._rightSlideValue*0.01
setp(self.rightslideline, xdata=[newrightx, newrightx], ydata=newslidery)
self.ui.graphicsView.draw()
return
def mergeReduceSpiceData(self, expno, scannolist, unit, xmin, xmax, binsize):
""" Merge and reduce SPICE data files
Arguements:
- expscanfilelist: list of 3 tuples: expnumber, scannumber and file name
"""
# Collect data MD workspaces and monitor MD workspaces
datamdwslist = []
monitormdwslist = []
self._lastWkspToMerge = []
print "[Checkpoint 0] Scans = ", str(scannolist)
for scanno in sorted(scannolist):
try:
wsmanager = self.getWorkspace(expno, scanno, True)
datamdwslist.append(wsmanager.datamdws)
monitormdwslist.append(wsmanager.monitormdws)
self._lastWkspToMerge.append(wsmanager)
except KeyError as ne:
print '[Error] Unable to retrieve MDWorkspaces for Exp %d Scan %d due to %s.' % (
expno, scanno, str(ne))
scannolist.remove(scanno)
# ENDFOR
print "[Checkpoing 1] Scans = ", str(scannolist)
# Merge and binning
if len(datamdwslist) > 1:
mg_datamdws = datamdwslist[0] + datamdwslist[1]
mg_monitormdws = monitormdwslist[0] + monitormdwslist[1]
else:
mg_datamdws = datamdwslist[0]
mg_monitormdws = monitormdwslist[0]
for iw in xrange(2, len(datamdwslist)):
mg_datamdws += datamdwslist[iw]
mg_monitormdws += monitormdwslist[iw]
# Set up binning parameters
if xmin is None or xmax is None:
binpar = "%.7f" % (binsize)
else:
binpar = "%.7f, %.7f, %.7f" % (xmin, binsize, xmax)
# set up output workspace's name
scannolist = sorted(scannolist)
outwsname = "Merged_Exp%d_Scan%s_%s" % (expno, scannolist[0], scannolist[-1])
# Merge
wavelength = self.getWavelength(expno, scannolist[0])
api.ConvertCWPDMDToSpectra(InputWorkspace=mg_datamdws,
InputMonitorWorkspace=mg_monitormdws,
OutputWorkspace=outwsname,
BinningParams=binpar,
UnitOutput=unit,
NeutronWaveLength=wavelength)
moutws = AnalysisDataService.retrieve(outwsname)
if moutws is None:
raise NotImplementedError("Merge failed.")
key = (expno, str(scannolist))
self._myMergedWSDict[key] = moutws
return key