def test_temperature_log_is_time_series(self):
outputWorkspaceName = "output_ws"
EditInstrumentGeometry(self._input_ws,
L2="4,8",
Polar="0,15",
Azimuthal="0,0",
DetectorIDs="1,2")
AddTimeSeriesLog(self._input_ws,
'temperature',
'2010-09-14T04:20:12',
Value='0.0')
AddTimeSeriesLog(self._input_ws,
'temperature',
'2010-09-14T04:20:13',
Value='0.0')
AddTimeSeriesLog(self._input_ws,
'temperature',
'2010-09-14T04:20:14',
Value='0.0')
alg_test = run_algorithm("ComputeCalibrationCoefVan",
VanadiumWorkspace=self._input_ws,
EPPTable=self._table,
OutputWorkspace=outputWorkspaceName)
self.assertTrue(alg_test.isExecuted())
wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
self._checkDWF(wsoutput, 0.0)
def __loadCacheFile(self, filename, wkspname):
'''@returns True if a file was loaded'''
if os.path.exists(filename):
self.log().notice('Loading cache from {}'.format(filename))
else:
return False
LoadNexusProcessed(Filename=filename, OutputWorkspace=wkspname)
# TODO LoadNexusProcessed has a bug. When it finds the
# instrument name without xml it reads in from an IDF
# in the instrument directory.
editinstrargs = {}
for name in PROPS_FOR_INSTR:
prop = self.getProperty(name)
if not prop.isDefault:
editinstrargs[name] = prop.value
if editinstrargs:
try:
EditInstrumentGeometry(Workspace=wkspname, **editinstrargs)
except RuntimeError as e:
# treat this as a non-fatal error
self.log().warning(
'Failed to update instrument geometry in cache file: {}'.
format(e))
return True
def test_dwf(self):
outputWorkspaceName = "output_ws"
# change theta to make dwf != 1
EditInstrumentGeometry(self._input_ws,
L2="4,8",
Polar="0,15",
Azimuthal="0,0",
DetectorIDs="1,2")
alg_test = run_algorithm("ComputeCalibrationCoefVan",
VanadiumWorkspace=self._input_ws,
EPPTable=self._table,
OutputWorkspace=outputWorkspaceName)
self.assertTrue(alg_test.isExecuted())
wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
# check dwf calculation
y_sum = sum(self._input_ws.readY(1)[27:75])
mvan = 0.001 * 50.942 / N_A
Bcoef = 4.736767162094296 * 1e+20 * hbar * hbar / (2.0 * mvan * k *
389.0)
dwf = np.exp(-1.0 * Bcoef *
(4.0 * np.pi * np.sin(0.5 * np.radians(15.0)) / 4.0)**2)
self.assertAlmostEqual(y_sum * dwf, wsoutput.readY(1)[0])
DeleteWorkspace(wsoutput)
def test_temperature_from_sample_log(self):
self._input_ws.mutableRun().addProperty('temperature', 0.0, True)
outputWorkspaceName = "output_ws"
EditInstrumentGeometry(self._input_ws, L2="4,8", Polar="0,15",
Azimuthal="0,0", DetectorIDs="1,2")
alg_test = run_algorithm("ComputeCalibrationCoefVan",
VanadiumWorkspace=self._input_ws,
EPPTable=self._table,
OutputWorkspace=outputWorkspaceName)
self.assertTrue(alg_test.isExecuted())
wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
self._checkDWF(wsoutput, 0.0)
DeleteWorkspace(wsoutput)
def test_dwf_using_default_temperature(self):
outputWorkspaceName = "output_ws"
# change theta to make dwf != 1
EditInstrumentGeometry(self._input_ws, L2="4,8", Polar="0,15",
Azimuthal="0,0", DetectorIDs="1,2")
alg_test = run_algorithm("ComputeCalibrationCoefVan",
VanadiumWorkspace=self._input_ws,
EPPTable=self._table,
OutputWorkspace=outputWorkspaceName)
self.assertTrue(alg_test.isExecuted())
wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
self._checkDWF(wsoutput, 293.0)
DeleteWorkspace(wsoutput)
def focus_workspace_list(self, ws_name_list, gsas_ws_name_list, group_ws_name):
""" Do diffraction focus on a list workspaces and also convert them to IDL GSAS
This is the main execution body to be executed in multi-threading environment
:param ws_name_list:
:param gsas_ws_name_list: name for GSAS
:param group_ws_name: name for grouping workspace
:return:
"""
datatypeutility.check_list('Workspace names', ws_name_list)
datatypeutility.check_list('(Output) GSAS workspace name list', gsas_ws_name_list)
if len(ws_name_list) != len(gsas_ws_name_list):
raise RuntimeError('Input workspace names {} have different number than output GSAS workspace names {}'
''.format(ws_name_list, gsas_ws_name_list))
for index in range(len(ws_name_list)):
# set GSAS workspace name same as input workspace name
ws_name = ws_name_list[index]
gsas_ws_name_list[index] = ws_name
gsas_ws_name = ws_name
datatypeutility.check_string_variable('Workspace name', ws_name)
datatypeutility.check_string_variable('Output GSAS workspace name', gsas_ws_name)
# skip empty workspace name that might be returned from FilterEvents
if len(ws_name) == 0:
continue
# focus (simple) it is the same but simplied version in diffraction_focus()
ConvertUnits(InputWorkspace=ws_name, OutputWorkspace=ws_name, Target='dSpacing')
# diffraction focus
DiffractionFocussing(InputWorkspace=ws_name, OutputWorkspace=ws_name,
GroupingWorkspace=group_ws_name)
# convert unit to TOF
ConvertUnits(InputWorkspace=ws_name, OutputWorkspace=ws_name,
Target='TOF', ConvertFromPointData=False)
# edit instrument
try:
EditInstrumentGeometry(Workspace=ws_name,
PrimaryFlightPath=self._focus_instrument_dict['L1'],
SpectrumIDs=self._focus_instrument_dict['SpectrumIDs'],
L2=self._focus_instrument_dict['L2'],
Polar=self._focus_instrument_dict['Polar'],
Azimuthal=self._focus_instrument_dict['Azimuthal'])
except RuntimeError as run_err:
print('[WARNING] Non-critical error from EditInstrumentGeometry for {}: {}'
''.format(ws_name, run_err))
# END-FOR
return
def test_MARI_axis_cylinder(self):
""" Test that default axis for MARI is different"""
ash = Cylinder('Fe', [10, 2])
res = ash.shape
self.assertEqual(res['Height'], 10)
self.assertEqual(res['Radius'], 2)
self.assertTrue(ash._axis_is_default)
test_ws = CreateSampleWorkspace(NumBanks=1, BankPixelWidth=1)
test_ws = ConvertUnits(test_ws, 'DeltaE', Emode='Direct', EFixed=2000)
cor_ws, corrections = ash.correct_absorption(test_ws, is_fast=True)
res = ash.shape
self.assertEqual(res['Axis'], [0., 1., 0])
EditInstrumentGeometry(test_ws, [1], [0], InstrumentName='MARI')
cor_ws, corrections = ash.correct_absorption(test_ws, is_fast=True)
res = ash.shape
self.assertEqual(res['Axis'], [1., 0., 0])
def test_disabled_debye_waller_correction(self):
outputWorkspaceName = "output_ws"
# change theta to make dwf != 1
EditInstrumentGeometry(self._input_ws, L2="4,8", Polar="0,15",
Azimuthal="0,0", DetectorIDs="1,2")
alg_test = run_algorithm("ComputeCalibrationCoefVan",
VanadiumWorkspace=self._input_ws,
EPPTable=self._table,
OutputWorkspace=outputWorkspaceName,
EnableDWF=False)
self.assertTrue(alg_test.isExecuted())
wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
for i in range(wsoutput.getNumberHistograms()):
self.assertEqual(100., wsoutput.readY(i)[0])
self.assertEqual(10., wsoutput.readE(i)[0])
DeleteWorkspace(wsoutput)
def test_temperature_log_name_from_IPF(self):
self._input_ws.mutableRun().addProperty('sample.temperature', 0.0, True)
EditInstrumentGeometry(self._input_ws, L2="4,8", Polar="0,15",
Azimuthal="0,0", DetectorIDs="1,2")
SetInstrumentParameter(
Workspace=self._input_ws,
ParameterName="temperature_log_entry",
ParameterType="String",
Value="sample.temperature")
outputWorkspaceName = "output_ws"
alg_test = run_algorithm("ComputeCalibrationCoefVan",
VanadiumWorkspace=self._input_ws,
EPPTable=self._table,
OutputWorkspace=outputWorkspaceName)
self.assertTrue(alg_test.isExecuted())
wsoutput = AnalysisDataService.retrieve(outputWorkspaceName)
self._checkDWF(wsoutput, 0.)
def create_test_ws():
"""
This creates a workspace with 19 detectors with 2theta from every 5 degress from 0 to 90
"""
wavelength = 1.7982
nspec = 19
ws = CreateWorkspace(DataX=[wavelength - 0.0001, wavelength + 0.0001],
DataY=[0.0] * nspec,
NSpec=nspec,
UnitX="Wavelength",
YUnitLabel="Counts")
EditInstrumentGeometry(ws,
PrimaryFlightPath=5.0,
SpectrumIDs=list(range(1, nspec+1)),
L2=[2.0]*nspec,
Polar=list(range(0, 181, 10)),
Azimuthal=[0.0]*nspec,
DetectorIDs=list(range(1, nspec+1)),
InstrumentName="Instrument")
return ws
def live_reduce(self, input_ws, output_ws):
ws = input_ws
counter_ws = mtd['counter']
index = int(counter_ws.readX(0)[0])
print('index = ', index)
counter_ws.dataX(0)[0] += 1
print('Iteration {0}: Number of events = {1}'.format(index, ws.getNumberEvents()))
curr_ws_name = 'output_{0}'.format(index)
CloneWorkspace(InputWorkspace=input_ws, OutputWorkspace=curr_ws_name)
Rebin(InputWorkspace=input_ws, OutputWorkspace=output_ws, Params='5000., -0.001, 50000.')
AlignAndFocusPowder(InputWorkspace=mtd[curr_ws_name],
OutputWorkspace=curr_ws_name,
CalFileName='/SNS/VULCAN/shared/CALIBRATION/2017_8_11_CAL/VULCAN_calibrate_2017_08_17.h5',
Params='-0.001',
DMin='0.5', DMax='3.5', PreserveEvents=False)
# PrimaryFlightPath=43, SpectrumIDs='0-2', L2='2,2,2', Polar='90,270,145', Azimuthal='0, 0, 0')
print('[SpecialDebug] Interface... EditInstrument on {0}'.format(curr_ws_name))
EditInstrumentGeometry(Workspace=curr_ws_name, PrimaryFlightPath=43.753999999999998,
SpectrumIDs='1,2,3',
L2='2.00944,2.00944,2.00944', Polar='90,270,150')
def PyExec(self):
# Retrieve all relevant notice
in_Runs = self.getProperty("RunNumbers").value
maskWSname = self._getMaskWSname()
# either type of file-based calibration is stored in the same variable
calib = self.getProperty("Calibration").value
if calib == "Calibration File":
cal_File = self.getProperty("CalibrationFilename").value
elif calib == 'DetCal File':
cal_File = self.getProperty('DetCalFilename').value
cal_File = ','.join(cal_File)
else:
cal_File = None
params = self.getProperty("Binning").value
norm = self.getProperty("Normalization").value
if norm == "From Processed Nexus":
norm_File = self.getProperty("NormalizationFilename").value
LoadNexusProcessed(Filename=norm_File, OutputWorkspace='normWS')
normWS = 'normWS'
elif norm == "From Workspace":
normWS = str(self.getProperty("NormalizationWorkspace").value)
else:
normWS = None
group_to_real = {
'Banks': 'Group',
'Modules': 'bank',
'2_4 Grouping': '2_4Grouping'
}
group = self.getProperty('GroupDetectorsBy').value
real_name = group_to_real.get(group, group)
if not mtd.doesExist(group):
if group == '2_4 Grouping':
group = '2_4_Grouping'
CreateGroupingWorkspace(InstrumentName='SNAP',
GroupDetectorsBy=real_name,
OutputWorkspace=group)
Process_Mode = self.getProperty("ProcessingMode").value
prefix = self.getProperty("OptionalPrefix").value
# --------------------------- REDUCE DATA -----------------------------
Tag = 'SNAP'
for r in in_Runs:
self.log().notice("processing run %s" % r)
self.log().information(str(self.get_IPTS_Local(r)))
if self.getProperty("LiveData").value:
Tag = 'Live'
LoadPreNexusLive(Instrument='SNAP', OutputWorkspace='WS')
else:
Load(Filename='SNAP' + str(r), OutputWorkspace='WS')
NormaliseByCurrent(InputWorkspace='WS', OutputWorkspace='WS')
CompressEvents(InputWorkspace='WS', OutputWorkspace='WS')
CropWorkspace(InputWorkspace='WS',
OutputWorkspace='WS',
XMax=50000)
RemovePromptPulse(InputWorkspace='WS',
OutputWorkspace='WS',
Width='1600',
Frequency='60.4')
if maskWSname is not None:
MaskDetectors(Workspace='WS', MaskedWorkspace=maskWSname)
self._alignAndFocus(params, calib, cal_File, group)
normWS = self._generateNormalization('WS_red', norm, normWS)
WS_nor = None
if normWS is not None:
WS_nor = 'WS_nor'
Divide(LHSWorkspace='WS_red',
RHSWorkspace=normWS,
OutputWorkspace='WS_nor')
ReplaceSpecialValues(Inputworkspace='WS_nor',
OutputWorkspace='WS_nor',
NaNValue='0',
NaNError='0',
InfinityValue='0',
InfinityError='0')
new_Tag = Tag
if len(prefix) > 0:
new_Tag += '_' + prefix
# Edit instrument geomety to make final workspace smaller on disk
det_table = PreprocessDetectorsToMD(
Inputworkspace='WS_red', OutputWorkspace='__SNAP_det_table')
polar = np.degrees(det_table.column('TwoTheta'))
azi = np.degrees(det_table.column('Azimuthal'))
EditInstrumentGeometry(Workspace='WS_red',
L2=det_table.column('L2'),
Polar=polar,
Azimuthal=azi)
if WS_nor is not None:
EditInstrumentGeometry(Workspace='WS_nor',
L2=det_table.column('L2'),
Polar=polar,
Azimuthal=azi)
mtd.remove('__SNAP_det_table')
# Save requested formats
basename = '%s_%s_%s' % (new_Tag, r, group)
self._save(r, basename, norm)
# temporary workspace no longer needed
DeleteWorkspace(Workspace='WS')
# rename everything as appropriate and determine output workspace name
RenameWorkspace(Inputworkspace='WS_d',
OutputWorkspace='%s_%s_d' % (new_Tag, r))
RenameWorkspace(Inputworkspace='WS_red',
OutputWorkspace=basename + '_red')
if norm == 'None':
outputWksp = basename + '_red'
else:
outputWksp = basename + '_nor'
RenameWorkspace(Inputworkspace='WS_nor',
OutputWorkspace=basename + '_nor')
if norm == "Extracted from Data":
RenameWorkspace(Inputworkspace='peak_clip_WS',
OutputWorkspace='%s_%s_normalizer' %
(new_Tag, r))
# delte some things in production
if Process_Mode == "Production":
DeleteWorkspace(Workspace='%s_%s_d' %
(new_Tag, r)) # was 'WS_d'
if norm != "None":
DeleteWorkspace(Workspace=basename +
'_red') # was 'WS_red'
if norm == "Extracted from Data":
DeleteWorkspace(Workspace='%s_%s_normalizer' %
(new_Tag, r)) # was 'peak_clip_WS'
propertyName = 'OutputWorkspace_' + str(outputWksp)
self.declareProperty(
WorkspaceProperty(propertyName, outputWksp, Direction.Output))
self.setProperty(propertyName, outputWksp)
def PyExec(self):
filenames = self._getLinearizedFilenames('Filename')
self.filterBadPulses = self.getProperty('FilterBadPulses').value
self.chunkSize = self.getProperty('MaxChunkSize').value
self.absorption = self.getProperty('AbsorptionWorkspace').value
self.charac = self.getProperty('Characterizations').value
finalname = self.getProperty('OutputWorkspace').valueAsStr
self.prog_per_file = 1. / float(
len(filenames)) # for better progress reporting
# these are also passed into the child-algorithms
self.kwargs = self.__getAlignAndFocusArgs()
# outer loop creates chunks to load
for (i, filename) in enumerate(filenames):
# default name is based off of filename
wkspname = os.path.split(filename)[-1].split('.')[0]
self.__determineCharacterizations(
filename, wkspname) # updates instance variable
cachefile = self.__getCacheName(wkspname)
wkspname += '_f%d' % i # add file number to be unique
if cachefile is not None and os.path.exists(cachefile):
LoadNexusProcessed(Filename=cachefile,
OutputWorkspace=wkspname)
# TODO LoadNexusProcessed has a bug. When it finds the
# instrument name without xml it reads in from an IDF
# in the instrument directory.
editinstrargs = {}
for name in PROPS_FOR_INSTR:
prop = self.getProperty(name)
if not prop.isDefault:
editinstrargs[name] = prop.value
if editinstrargs:
EditInstrumentGeometry(Workspace=wkspname, **editinstrargs)
else:
self.__processFile(filename, wkspname,
self.prog_per_file * float(i))
if cachefile is not None:
SaveNexusProcessed(InputWorkspace=wkspname,
Filename=cachefile)
# accumulate runs
if i == 0:
if wkspname != finalname:
RenameWorkspace(InputWorkspace=wkspname,
OutputWorkspace=finalname)
else:
Plus(LHSWorkspace=finalname,
RHSWorkspace=wkspname,
OutputWorkspace=finalname,
ClearRHSWorkspace=self.kwargs['PreserveEvents'])
DeleteWorkspace(Workspace=wkspname)
if self.kwargs['PreserveEvents']:
CompressEvents(InputWorkspace=finalname,
OutputWorkspace=finalname)
# with more than one chunk or file the integrated proton charge is
# generically wrong
mtd[finalname].run().integrateProtonCharge()
# set the output workspace
self.setProperty('OutputWorkspace', mtd[finalname])
def PyExec(self):
in_Runs = self.getProperty("RunNumbers").value
progress = Progress(self, 0., .25, 3)
finalUnits = self.getPropertyValue("FinalUnits")
self.chunkSize = self.getProperty('MaxChunkSize').value
# default arguments for AlignAndFocusPowder
self.alignAndFocusArgs = {'Tmin': 0,
'TMax': 50000,
'RemovePromptPulseWidth': 1600,
'PreserveEvents': False,
'Dspacing': True, # binning parameters in d-space
'Params': self.getProperty("Binning").value,
}
# workspace for loading metadata only to be used in LoadDiffCal and
# CreateGroupingWorkspace
metaWS = None
# either type of file-based calibration is stored in the same variable
calib = self.getProperty("Calibration").value
detcalFile = None
if calib == "Calibration File":
metaWS = self._loadMetaWS(in_Runs[0])
LoadDiffCal(Filename=self.getPropertyValue("CalibrationFilename"),
WorkspaceName='SNAP',
InputWorkspace=metaWS,
MakeGroupingWorkspace=False, MakeMaskWorkspace=False)
self.alignAndFocusArgs['CalibrationWorkspace'] = 'SNAP_cal'
elif calib == 'DetCal File':
detcalFile = ','.join(self.getProperty('DetCalFilename').value)
progress.report('loaded calibration')
norm = self.getProperty("Normalization").value
if norm == "From Processed Nexus":
norm_File = self.getProperty("NormalizationFilename").value
normalizationWS = 'normWS'
LoadNexusProcessed(Filename=norm_File, OutputWorkspace=normalizationWS)
progress.report('loaded normalization')
elif norm == "From Workspace":
normalizationWS = str(self.getProperty("NormalizationWorkspace").value)
progress.report('')
else:
normalizationWS = None
progress.report('')
self.alignAndFocusArgs['GroupingWorkspace'] = self._generateGrouping(in_Runs[0], metaWS, progress)
self.alignAndFocusArgs['MaskWorkspace'] = self._getMaskWSname(in_Runs[0], metaWS) # can be empty string
if metaWS is not None:
DeleteWorkspace(Workspace=metaWS)
Process_Mode = self.getProperty("ProcessingMode").value
prefix = self.getProperty("OptionalPrefix").value
Tag = 'SNAP'
progStart = .25
progDelta = (1.-progStart)/len(in_Runs)
# --------------------------- PROCESS BACKGROUND ----------------------
if not self.getProperty('Background').isDefault:
progDelta = (1. - progStart) / (len(in_Runs) + 1) # redefine to account for background
background = 'SNAP_{}'.format(self.getProperty('Background').value)
self.log().notice("processing run background {}".format(background))
background, unfocussedBkgd = self._alignAndFocus(background,
background+'_bkgd_red',
detCalFilename=detcalFile,
withUnfocussed=(Process_Mode == 'Set-Up'),
progStart=progStart, progDelta=progDelta)
else:
background = None
unfocussedBkgd = ''
# --------------------------- REDUCE DATA -----------------------------
for i, runnumber in enumerate(in_Runs):
self.log().notice("processing run %s" % runnumber)
# put together output names
new_Tag = Tag
if len(prefix) > 0:
new_Tag = prefix + '_' + new_Tag
basename = '%s_%s_%s' % (new_Tag, runnumber, self.alignAndFocusArgs['GroupingWorkspace'])
self.log().warning('{}:{}:{}'.format(i, new_Tag, basename))
redWS, unfocussedWksp = self._alignAndFocus('SNAP_{}'.format(runnumber),
basename + '_red',
detCalFilename=detcalFile,
withUnfocussed=(Process_Mode == 'Set-Up'),
progStart=progStart, progDelta=progDelta*.5)
progStart += .5 * progDelta
# subtract the background if it was supplied
if background:
self.log().information('subtracting {} from {}'.format(background, redWS))
Minus(LHSWorkspace=redWS, RHSWorkspace=background, OutputWorkspace=redWS)
# intentionally don't subtract the unfocussed workspace since it hasn't been normalized by counting time
# the rest takes up .25 percent of the run processing
progress = Progress(self, progStart, progStart+.25*progDelta, 2)
# AlignAndFocusPowder leaves the data in time-of-flight
ConvertUnits(InputWorkspace=redWS, OutputWorkspace=redWS, Target='dSpacing', EMode='Elastic')
# Edit instrument geometry to make final workspace smaller on disk
det_table = PreprocessDetectorsToMD(Inputworkspace=redWS,
OutputWorkspace='__SNAP_det_table')
polar = np.degrees(det_table.column('TwoTheta'))
azi = np.degrees(det_table.column('Azimuthal'))
EditInstrumentGeometry(Workspace=redWS, L2=det_table.column('L2'),
Polar=polar, Azimuthal=azi)
mtd.remove('__SNAP_det_table')
progress.report('simplify geometry')
# AlignAndFocus doesn't necessarily rebin the data correctly
if Process_Mode == "Set-Up":
Rebin(InputWorkspace=unfocussedWksp, Params=self.alignAndFocusArgs['Params'],
Outputworkspace=unfocussedWksp)
if background:
Rebin(InputWorkspace=unfocussedBkgd, Params=self.alignAndFocusArgs['Params'],
Outputworkspace=unfocussedBkgd)
# normalize the data as requested
normalizationWS = self._generateNormalization(redWS, norm, normalizationWS)
normalizedWS = None
if normalizationWS is not None:
normalizedWS = basename + '_nor'
Divide(LHSWorkspace=redWS, RHSWorkspace=normalizationWS,
OutputWorkspace=normalizedWS)
ReplaceSpecialValues(Inputworkspace=normalizedWS,
OutputWorkspace=normalizedWS,
NaNValue='0', NaNError='0',
InfinityValue='0', InfinityError='0')
progress.report('normalized')
else:
progress.report()
# rename everything as appropriate and determine output workspace name
if normalizedWS is None:
outputWksp = redWS
else:
outputWksp = normalizedWS
if norm == "Extracted from Data" and Process_Mode == "Production":
DeleteWorkspace(Workspace=redWS)
DeleteWorkspace(Workspace=normalizationWS)
# Save requested formats - function checks that saving is requested
self._save(runnumber, basename, outputWksp)
# set workspace as an output so it gets history
ConvertUnits(InputWorkspace=str(outputWksp), OutputWorkspace=str(outputWksp), Target=finalUnits,
EMode='Elastic')
self._exportWorkspace('OutputWorkspace_' + str(outputWksp), outputWksp)
# declare some things as extra outputs in set-up
if Process_Mode != "Production":
propprefix = 'OutputWorkspace_{:d}_'.format(i)
propNames = [propprefix + it for it in ['d', 'norm', 'normalizer']]
wkspNames = ['%s_%s_d' % (new_Tag, runnumber),
basename + '_red',
'%s_%s_normalizer' % (new_Tag, runnumber)]
for (propName, wkspName) in zip(propNames, wkspNames):
self._exportWorkspace(propName, wkspName)
if background:
ConvertUnits(InputWorkspace=str(background), OutputWorkspace=str(background), Target=finalUnits,
EMode='Elastic')
prefix = 'OutputWorkspace_{}'.format(len(in_Runs))
propNames = [prefix + it for it in ['', '_d']]
wkspNames = [background, unfocussedBkgd]
for (propName, wkspName) in zip(propNames, wkspNames):
self._exportWorkspace(propName, wkspName)
def PyExec(self):
in_Runs = self.getProperty("RunNumbers").value
maskWSname = self._getMaskWSname()
progress = Progress(self, 0., .25, 3)
# default arguments for AlignAndFocusPowder
alignAndFocusArgs = {
'TMax': 50000,
'RemovePromptPulseWidth': 1600,
'PreserveEvents': False,
'Dspacing': True, # binning parameters in d-space
'Params': self.getProperty("Binning").value
}
# workspace for loading metadata only to be used in LoadDiffCal and
# CreateGroupingWorkspace
metaWS = None
# either type of file-based calibration is stored in the same variable
calib = self.getProperty("Calibration").value
detcalFile = None
if calib == "Calibration File":
metaWS = self._loadMetaWS(in_Runs[0])
LoadDiffCal(Filename=self.getPropertyValue("CalibrationFilename"),
WorkspaceName='SNAP',
InputWorkspace=metaWS,
MakeGroupingWorkspace=False,
MakeMaskWorkspace=False)
alignAndFocusArgs['CalibrationWorkspace'] = 'SNAP_cal'
elif calib == 'DetCal File':
detcalFile = ','.join(self.getProperty('DetCalFilename').value)
progress.report('loaded calibration')
norm = self.getProperty("Normalization").value
if norm == "From Processed Nexus":
norm_File = self.getProperty("NormalizationFilename").value
normalizationWS = 'normWS'
LoadNexusProcessed(Filename=norm_File,
OutputWorkspace=normalizationWS)
progress.report('loaded normalization')
elif norm == "From Workspace":
normalizationWS = str(
self.getProperty("NormalizationWorkspace").value)
progress.report('')
else:
normalizationWS = None
progress.report('')
group = self._generateGrouping(in_Runs[0], metaWS, progress)
if metaWS is not None:
DeleteWorkspace(Workspace=metaWS)
Process_Mode = self.getProperty("ProcessingMode").value
prefix = self.getProperty("OptionalPrefix").value
# --------------------------- REDUCE DATA -----------------------------
Tag = 'SNAP'
if self.getProperty("LiveData").value:
Tag = 'Live'
progStart = .25
progDelta = (1. - progStart) / len(in_Runs)
for i, runnumber in enumerate(in_Runs):
self.log().notice("processing run %s" % runnumber)
self.log().information(str(self.get_IPTS_Local(runnumber)))
# put together output names
new_Tag = Tag
if len(prefix) > 0:
new_Tag += '_' + prefix
basename = '%s_%s_%s' % (new_Tag, runnumber, group)
if self.getProperty("LiveData").value:
raise RuntimeError('Live data is not currently supported')
else:
Load(Filename='SNAP' + str(runnumber),
OutputWorkspace=basename + '_red',
startProgress=progStart,
endProgress=progStart + .25 * progDelta)
progStart += .25 * progDelta
redWS = basename + '_red'
# overwrite geometry with detcal files
if calib == 'DetCal File':
LoadIsawDetCal(InputWorkspace=redWS, Filename=detcalFile)
# create unfocussed data if in set-up mode
if Process_Mode == "Set-Up":
unfocussedWksp = '{}_{}_d'.format(new_Tag, runnumber)
else:
unfocussedWksp = ''
AlignAndFocusPowder(
InputWorkspace=redWS,
OutputWorkspace=redWS,
MaskWorkspace=maskWSname, # can be empty string
GroupingWorkspace=group,
UnfocussedWorkspace=unfocussedWksp, # can be empty string
startProgress=progStart,
endProgress=progStart + .5 * progDelta,
**alignAndFocusArgs)
progStart += .5 * progDelta
# the rest takes up .25 percent of the run processing
progress = Progress(self, progStart, progStart + .25 * progDelta,
2)
# AlignAndFocusPowder leaves the data in time-of-flight
ConvertUnits(InputWorkspace=redWS,
OutputWorkspace=redWS,
Target='dSpacing',
EMode='Elastic')
# Edit instrument geometry to make final workspace smaller on disk
det_table = PreprocessDetectorsToMD(
Inputworkspace=redWS, OutputWorkspace='__SNAP_det_table')
polar = np.degrees(det_table.column('TwoTheta'))
azi = np.degrees(det_table.column('Azimuthal'))
EditInstrumentGeometry(Workspace=redWS,
L2=det_table.column('L2'),
Polar=polar,
Azimuthal=azi)
mtd.remove('__SNAP_det_table')
progress.report('simplify geometry')
# AlignAndFocus doesn't necessarily rebin the data correctly
if Process_Mode == "Set-Up":
Rebin(InputWorkspace=unfocussedWksp,
Params=alignAndFocusArgs['Params'],
Outputworkspace=unfocussedWksp)
NormaliseByCurrent(InputWorkspace=redWS, OutputWorkspace=redWS)
# normalize the data as requested
normalizationWS = self._generateNormalization(
redWS, norm, normalizationWS)
normalizedWS = None
if normalizationWS is not None:
normalizedWS = basename + '_nor'
Divide(LHSWorkspace=redWS,
RHSWorkspace=normalizationWS,
OutputWorkspace=normalizedWS)
ReplaceSpecialValues(Inputworkspace=normalizedWS,
OutputWorkspace=normalizedWS,
NaNValue='0',
NaNError='0',
InfinityValue='0',
InfinityError='0')
progress.report('normalized')
else:
progress.report()
# rename everything as appropriate and determine output workspace name
if normalizedWS is None:
outputWksp = redWS
else:
outputWksp = normalizedWS
if norm == "Extracted from Data" and Process_Mode == "Production":
DeleteWorkspace(Workspace=redWS)
DeleteWorkspace(Workspace=normalizationWS)
# Save requested formats
saveDir = self.getPropertyValue("OutputDirectory").strip()
if len(saveDir) <= 0:
self.log().notice('Using default save location')
saveDir = os.path.join(self.get_IPTS_Local(runnumber),
'shared', 'data')
self._save(saveDir, basename, outputWksp)
# set workspace as an output so it gets history
propertyName = 'OutputWorkspace_' + str(outputWksp)
self.declareProperty(
WorkspaceProperty(propertyName, outputWksp, Direction.Output))
self.setProperty(propertyName, outputWksp)
# declare some things as extra outputs in set-up
if Process_Mode != "Production":
prefix = 'OuputWorkspace_{:d}_'.format(i)
propNames = [prefix + it for it in ['d', 'norm', 'normalizer']]
wkspNames = [
'%s_%s_d' % (new_Tag, runnumber), basename + '_red',
'%s_%s_normalizer' % (new_Tag, runnumber)
]
for (propName, wkspName) in zip(propNames, wkspNames):
if mtd.doesExist(wkspName):
self.declareProperty(
WorkspaceProperty(propName, wkspName,
Direction.Output))
self.setProperty(propName, wkspName)
def PyExec(self):
filenames = self._getLinearizedFilenames('Filename')
self.filterBadPulses = self.getProperty('FilterBadPulses').value
self.chunkSize = self.getProperty('MaxChunkSize').value
self.absorption = self.getProperty('AbsorptionWorkspace').value
self.charac = self.getProperty('Characterizations').value
finalname = self.getPropertyValue('OutputWorkspace')
useCaching = len(self.getProperty('CacheDir').value) > 0
# accumulate the unfocused workspace if it was requested
# empty string means it is not used
unfocusname = self.getPropertyValue('UnfocussedWorkspace')
unfocusname_file = ''
if len(unfocusname) > 0:
unfocusname_file = '__{}_partial'.format(unfocusname)
if useCaching:
# unfocus check only matters if caching is requested
if unfocusname != '':
self.log().warning(
'CacheDir is specified with "UnfocussedWorkspace" - reading cache files disabled'
)
else:
self.log().warning(
'CacheDir is not specified - functionality disabled')
self.prog_per_file = 1. / float(
len(filenames)) # for better progress reporting
# these are also passed into the child-algorithms
self.kwargs = self.__getAlignAndFocusArgs()
# outer loop creates chunks to load
for (i, filename) in enumerate(filenames):
# default name is based off of filename
wkspname = os.path.split(filename)[-1].split('.')[0]
if useCaching:
self.__determineCharacterizations(
filename, wkspname, True) # updates instance variable
cachefile = self.__getCacheName(wkspname)
else:
cachefile = None
wkspname += '_f%d' % i # add file number to be unique
# if the unfocussed data is requested, don't read it from disk
# because of the extra complication of the unfocussed workspace
if useCaching and os.path.exists(cachefile) and unfocusname == '':
LoadNexusProcessed(Filename=cachefile,
OutputWorkspace=wkspname)
# TODO LoadNexusProcessed has a bug. When it finds the
# instrument name without xml it reads in from an IDF
# in the instrument directory.
editinstrargs = {}
for name in PROPS_FOR_INSTR:
prop = self.getProperty(name)
if not prop.isDefault:
editinstrargs[name] = prop.value
if editinstrargs:
EditInstrumentGeometry(Workspace=wkspname, **editinstrargs)
else:
self.__processFile(filename, wkspname, unfocusname_file,
self.prog_per_file * float(i),
not useCaching)
# write out the cachefile for the main reduced data independent of whether
# the unfocussed workspace was requested
if useCaching:
SaveNexusProcessed(InputWorkspace=wkspname,
Filename=cachefile)
# accumulate runs
if i == 0:
if wkspname != finalname:
RenameWorkspace(InputWorkspace=wkspname,
OutputWorkspace=finalname)
if unfocusname != '':
RenameWorkspace(InputWorkspace=unfocusname_file,
OutputWorkspace=unfocusname)
else:
Plus(LHSWorkspace=finalname,
RHSWorkspace=wkspname,
OutputWorkspace=finalname,
ClearRHSWorkspace=self.kwargs['PreserveEvents'])
DeleteWorkspace(Workspace=wkspname)
if unfocusname != '':
Plus(LHSWorkspace=unfocusname,
RHSWorkspace=unfocusname_file,
OutputWorkspace=unfocusname,
ClearRHSWorkspace=self.kwargs['PreserveEvents'])
DeleteWorkspace(Workspace=unfocusname_file)
if self.kwargs['PreserveEvents']:
CompressEvents(InputWorkspace=finalname,
OutputWorkspace=finalname)
# not compressing unfocussed workspace because it is in d-spacing
# and is likely to be from a different part of the instrument
# with more than one chunk or file the integrated proton charge is
# generically wrong
mtd[finalname].run().integrateProtonCharge()
# set the output workspace
self.setProperty('OutputWorkspace', mtd[finalname])
if unfocusname != '':
self.setProperty('UnfocussedWorkspace', mtd[unfocusname])
