def mask_bank(bank_name: str, tubes_fit_success: np.ndarray, output_table: str) -> Optional[TableWorkspace]:
r"""
Creates a single-column `TableWorkspace` object containing the detector ID's of the
unsuccessfully fitted tubes
If all tubes were fit successfully, no `TableWorkspace` is created, and `None` is returned.
:param bank_name: a string of the form 'bankI' where 'I' is a bank number
:param tubes_fit_success: array of boolean containing a True/False entry for each tube, indicating wether
the tube was successfully calibrated.
:param output_table: name of the output TableWorkspace containing one column for detector ID from tubes
not successfully calibrated.
:raise AssertionError: the string bank_name does not follow the pattern 'bankI' where 'I' in an integer
:return: name of the mask TableWorkspace. Returns `None` if no TableWorkspace is created.
"""
assert re.match(r'^bank\d+$', bank_name), 'The bank name must be of the form "bankI" where "I" in an integer'
if False not in tubes_fit_success:
return None # al tubes were fit successfully
bank_number = bank_name[4:] # drop 'bank' from bank_name
tube_numbers = 1 + np.where(tubes_fit_success == False)[0] # noqa E712 unsuccessfully fitted tube numbers
tube_numbers = ','.join([str(n) for n in tube_numbers]) # failing tubes as a string
detector_ids = MaskBTP(Instrument='CORELLI', Bank=bank_number, Tube=tube_numbers)
table = CreateEmptyTableWorkspace(OutputWorkspace=output_table)
table.addColumn('long64', 'Detector ID')
[table.addRow([detector_id]) for detector_id in detector_ids.tolist()]
if AnalysisDataService.doesExist('CORELLIMaskBTP'):
DeleteWorkspaces(['CORELLIMaskBTP'])
return mtd[output_table]
def setUp(self):
config['default.facility'] = 'ILL'
config['default.instrument'] = 'D22'
config['logging.loggers.root.level'] = 'Warning'
config.appendDataSearchSubDir('ILL/D22/')
MaskBTP(Instrument='D22', Pixel='0-12,245-255')
MaskBTP(Workspace='D22MaskBTP', Tube='54-75', Pixel='108-150')
RenameWorkspace(InputWorkspace='D22MaskBTP', OutputWorkspace='D22_mask_central')
def setUp(self):
config['default.facility'] = 'ILL'
config['default.instrument'] = 'D11'
config['logging.loggers.root.level'] = 'Warning'
config.appendDataSearchSubDir('ILL/D11/')
# prepare mask for instrument edges first:
MaskBTP(Instrument='D11', Tube='1-3,253-256')
RenameWorkspace(InputWorkspace='D11MaskBTP', OutputWorkspace='mask_vertical')
MaskBTP(Instrument='D11', Pixel='1-3,253-256')
Plus(LHSWorkspace='mask_vertical', RHSWorkspace='D11MaskBTP', OutputWorkspace='edge_masks')
# the edges mask can be used as a default mask for all distances and wavelengths
MaskBTP(Instrument='D11', Tube='116-139', Pixel='90-116')
RenameWorkspace(InputWorkspace='D11MaskBTP', OutputWorkspace='mask_39m_10A')
MaskBTP(Instrument='D11', Tube='115-140', Pixel='115-140')
RenameWorkspace(InputWorkspace='D11MaskBTP', OutputWorkspace='mask_8m_4_6A')
MaskBTP(Instrument='D11', Tube='105-145', Pixel='105-145')
RenameWorkspace(InputWorkspace='D11MaskBTP', OutputWorkspace='mask_1m_4_6A')
def PyExec(self):
filename = self.getProperty("Filename").value
wavelength = self.getProperty("wavelength").value
outWS = self.getPropertyValue("OutputWorkspace")
LoadEventNexus(Filename=filename,
OutputWorkspace=outWS,
LoadMonitors=True)
Integration(InputWorkspace=outWS, OutputWorkspace=outWS)
if self.getProperty("ApplyMask").value:
MaskBTP(outWS, Bank='8', Tube='449-480')
MaskBTP(outWS, Pixel='1,2,511,512')
mtd[outWS].getAxis(0).setUnit("Wavelength")
w = [wavelength - 0.001, wavelength + 0.001]
for idx in range(mtd[outWS].getNumberHistograms()):
mtd[outWS].setX(idx, w)
SetGoniometer(outWS, Axis0="HB2C:Mot:s1,0,1,0,1")
AddSampleLog(outWS,
LogName="gd_prtn_chrg",
LogType='Number',
NumberType='Double',
LogText=str(mtd[outWS + '_monitors'].getNumberEvents()))
DeleteWorkspace(outWS + '_monitors')
AddSampleLog(outWS,
LogName="Wavelength",
LogType='Number',
NumberType='Double',
LogText=str(wavelength))
AddSampleLog(outWS,
LogName="Ei",
LogType='Number',
NumberType='Double',
LogText=str(
UnitConversion.run('Wavelength', 'Energy', wavelength,
0, 0, 0, Elastic, 0)))
self.setProperty('OutputWorkspace', outWS)
def setUp(self):
config['default.facility'] = 'ILL'
config['default.instrument'] = 'D11'
config['logging.loggers.root.level'] = 'Warning'
config.appendDataSearchSubDir('ILL/D11/')
# prepare mask for instrument edges first:
MaskBTP(Instrument='D11', Tube='0-6,250-256')
RenameWorkspace(InputWorkspace='D11MaskBTP',
OutputWorkspace='mask_vertical')
MaskBTP(Instrument='D11', Pixel='0-6,250-256')
Plus(LHSWorkspace='mask_vertical',
RHSWorkspace='D11MaskBTP',
OutputWorkspace='edge_masks')
# the edges mask can be used as a default mask for all distances and wavelengths
MaskBTP(Instrument='D11', Tube='114-142,', Pixel='114-142')
RenameWorkspace(InputWorkspace='D11MaskBTP',
OutputWorkspace='mask_8m_4_6A_center')
MaskBTP(Instrument='D11', Tube='3-14', Pixel='240-256')
Plus(LHSWorkspace='D11MaskBTP',
RHSWorkspace='mask_8m_4_6A_center',
OutputWorkspace='mask_8m_4_6A')
MaskBTP(Instrument='D11', Tube='103-147', Pixel='103-147')
RenameWorkspace(InputWorkspace='D11MaskBTP',
OutputWorkspace='mask_1m_4_6A_center')
MaskBTP(Instrument='D11', Tube='3-14', Pixel='240-256')
Plus(LHSWorkspace='D11MaskBTP',
RHSWorkspace='mask_1m_4_6A_center',
OutputWorkspace='mask_1m_4_6A')
def PyExec(self):
runs = self.getProperty("Filename").value
if not runs:
ipts = self.getProperty("IPTS").value
runs = [
'/HFIR/HB2C/IPTS-{}/nexus/HB2C_{}.nxs.h5'.format(ipts, run)
for run in self.getProperty("RunNumbers").value
]
wavelength = self.getProperty("wavelength").value
outWS = self.getPropertyValue("OutputWorkspace")
group_names = []
grouping = self.getProperty("Grouping").value
if grouping == 'None':
grouping = 1
else:
grouping = 2 if grouping == '2x2' else 4
for i, run in enumerate(runs):
data = np.zeros((512 * 480 * 8), dtype=np.int64)
with h5py.File(run, 'r') as f:
monitor_count = f['/entry/monitor1/total_counts'].value[0]
run_number = f['/entry/run_number'].value[0]
for b in range(8):
data += np.bincount(f['/entry/bank' + str(b + 1) +
'_events/event_id'].value,
minlength=512 * 480 * 8)
data = data.reshape((480 * 8, 512))
if grouping == 2:
data = data[::2, ::2] + data[
1::2, ::2] + data[::2, 1::2] + data[1::2, 1::2]
elif grouping == 4:
data = (data[::4, ::4] + data[1::4, ::4] + data[2::4, ::4] +
data[3::4, ::4] + data[::4, 1::4] + data[1::4, 1::4] +
data[2::4, 1::4] + data[3::4, 1::4] + data[::4, 2::4] +
data[1::4, 2::4] + data[2::4, 2::4] +
data[3::4, 2::4] + data[::4, 3::4] + data[1::4, 3::4] +
data[2::4, 3::4] + data[3::4, 3::4])
CreateWorkspace(DataX=[wavelength - 0.001, wavelength + 0.001],
DataY=data,
DataE=np.sqrt(data),
UnitX='Wavelength',
YUnitLabel='Counts',
NSpec=1966080 // grouping**2,
OutputWorkspace='__tmp_load',
EnableLogging=False)
LoadNexusLogs('__tmp_load', Filename=run, EnableLogging=False)
AddSampleLog('__tmp_load',
LogName="monitor_count",
LogType='Number',
NumberType='Double',
LogText=str(monitor_count),
EnableLogging=False)
AddSampleLog('__tmp_load',
LogName="gd_prtn_chrg",
LogType='Number',
NumberType='Double',
LogText=str(monitor_count),
EnableLogging=False)
AddSampleLog('__tmp_load',
LogName="Wavelength",
LogType='Number',
NumberType='Double',
LogText=str(wavelength),
EnableLogging=False)
AddSampleLog('__tmp_load',
LogName="Ei",
LogType='Number',
NumberType='Double',
LogText=str(
UnitConversion.run('Wavelength', 'Energy',
wavelength, 0, 0, 0, Elastic,
0)),
EnableLogging=False)
AddSampleLog('__tmp_load',
LogName="run_number",
LogText=run_number,
EnableLogging=False)
if grouping > 1: # Fix detector IDs per spectrum before loading instrument
__tmp_load = mtd['__tmp_load']
for n in range(__tmp_load.getNumberHistograms()):
s = __tmp_load.getSpectrum(n)
for i in range(grouping):
for j in range(grouping):
s.addDetectorID(
int(n * grouping % 512 + n //
(512 / grouping) * 512 * grouping + j +
i * 512))
LoadInstrument('__tmp_load',
InstrumentName='WAND',
RewriteSpectraMap=False,
EnableLogging=False)
else:
LoadInstrument('__tmp_load',
InstrumentName='WAND',
RewriteSpectraMap=True,
EnableLogging=False)
SetGoniometer('__tmp_load',
Axis0="HB2C:Mot:s1,0,1,0,1",
EnableLogging=False)
if self.getProperty("ApplyMask").value:
MaskBTP('__tmp_load', Pixel='1,2,511,512', EnableLogging=False)
if mtd['__tmp_load'].getRunNumber(
) > 26600: # They changed pixel mapping and bank name order here
MaskBTP('__tmp_load',
Bank='1',
Tube='479-480',
EnableLogging=False)
MaskBTP('__tmp_load',
Bank='8',
Tube='1-2',
EnableLogging=False)
else:
MaskBTP('__tmp_load',
Bank='8',
Tube='475-480',
EnableLogging=False)
if len(runs) == 1:
RenameWorkspace('__tmp_load', outWS, EnableLogging=False)
else:
outName = outWS + "_" + str(mtd['__tmp_load'].getRunNumber())
group_names.append(outName)
RenameWorkspace('__tmp_load', outName, EnableLogging=False)
if len(runs) > 1:
GroupWorkspaces(group_names,
OutputWorkspace=outWS,
EnableLogging=False)
self.setProperty('OutputWorkspace', outWS)
def runTest(self):
# Load Empty Instrument
ws = LoadEmptyInstrument(InstrumentName='WISH', OutputWorkspace='WISH')
axis = ws.getAxis(0)
axis.setUnit("TOF") # need this to add peak to table
# CreatePeaksWorkspace with peaks in specific detectors
peaks = CreatePeaksWorkspace(InstrumentWorkspace=ws,
NumberOfPeaks=0,
OutputWorkspace='peaks')
AddPeak(PeaksWorkspace=peaks,
RunWorkspace=ws,
TOF=20000,
DetectorID=1707204,
Height=521,
BinCount=0) # pixel in first tube in panel 1
AddPeak(PeaksWorkspace=peaks,
RunWorkspace=ws,
TOF=20000,
DetectorID=1400510,
Height=1,
BinCount=0) # pixel at top of a central tube in panel 1
AddPeak(PeaksWorkspace=peaks,
RunWorkspace=ws,
TOF=20000,
DetectorID=1408202,
Height=598,
BinCount=0) # pixel in middle of bank 1 (not near edge)
AddPeak(PeaksWorkspace=peaks,
RunWorkspace=ws,
TOF=20000,
DetectorID=1100173,
Height=640,
BinCount=0) # pixel in last tube of panel 1 (next to panel 2)
# create dummy MD workspace for integration (don't need data as checking peak shape)
MD = CreateMDWorkspace(Dimensions='3',
Extents='-1,1,-1,1,-1,1',
Names='Q_lab_x,Q_lab_y,Q_lab_z',
Units='U,U,U',
Frames='QLab,QLab,QLab',
SplitInto='2',
SplitThreshold='50')
# Integrate peaks masking all pixels at tube end (built into IntegratePeaksMD)
self._peaks_pixels = IntegratePeaksMD(InputWorkspace=MD,
PeakRadius='0.02',
PeaksWorkspace=peaks,
IntegrateIfOnEdge=False,
OutputWorkspace='peaks_pixels',
MaskEdgeTubes=False)
# Apply masking to specific tubes next to beam in/out (subset of all edge tubes) and integrate again
MaskBTP(Workspace='peaks', Bank='5-6', Tube='152')
MaskBTP(Workspace='peaks', Bank='1,10', Tube='1')
self._peaks_pixels_beamTubes = IntegratePeaksMD(
InputWorkspace='MD',
PeakRadius='0.02',
PeaksWorkspace=peaks,
IntegrateIfOnEdge=False,
OutputWorkspace='peaks_pixels_beamTubes',
MaskEdgeTubes=False)
# Integrate masking all edge tubes
self._peaks_pixels_edgeTubes = IntegratePeaksMD(
InputWorkspace='MD',
PeakRadius='0.02',
PeaksWorkspace='peaks',
IntegrateIfOnEdge=False,
OutputWorkspace='peaks_pixels_edgeTubes',
MaskEdgeTubes=True)
corelli = LoadEmptyInstrument(InstrumentName='CORELLI')
corelli = CalculateDIFC(corelli)
difc0 = corelli.extractY().flatten()
ApplyCalibration('corelli', 'CalibTable')
corelli = CalculateDIFC(corelli)
difc = corelli.extractY().flatten()
plt.plot(difc / difc0)
plt.show()
LoadDiffCal(
Filename='../cal_Si_C60/cal_Si2_47327-47334_TubeCal_sum16_mask_lt_2.cal',
InstrumentName='CORELLI',
WorkspaceName='si')
MaskBTP(Workspace='si_mask', Pixel="1-16,241-256")
LoadDiffCal(
Filename='../cal_Si_C60/cal_C60_2_47367-47382_TubeCal_sum16_mask_lt_2.h5',
InstrumentName='CORELLI',
WorkspaceName='c60')
MaskBTP(Workspace='c60_mask', Pixel="1-16,241-256")
si = mtd['si_cal']
c60 = mtd['c60_cal']
si_mask = mtd['si_mask']
c60_mask = mtd['c60_mask']
plt.plot(corelli.extractY())
plt.plot(si.column(0), si.column(1))
plt.plot(c60.column(0), c60.column(1))
row.append(leftbound)
row.append(rightbound)
fitwinws.addRow(row)
for run in range(first, last + 1):
LoadEventNexus(Filename='CORELLI_' + str(run), OutputWorkspace='data')
if tube_cal:
ApplyCalibration('data', 'CalibTable')
SetInstrumentParameter(Workspace="data",
ParameterName="t0_formula",
Value="(23.5 * exp(-incidentEnergy/205.8))")
ModeratorTzero(InputWorkspace="data",
OutputWorkspace="data",
EMode="Elastic")
MaskBTP(Workspace='data', Pixel="1-16,241-256")
ConvertUnits(InputWorkspace='data',
OutputWorkspace='data',
Target='dSpacing')
Rebin(InputWorkspace='data',
OutputWorkspace='data',
Params='0.5,-0.004,10')
SumNeighbours(InputWorkspace="data",
OutputWorkspace="data",
SumX=1,
SumY=SumY)
GetDetOffsetsMultiPeaks(InputWorkspace='data',
DReference=FinalDReference,
FitwindowTableWorkspace='fitwinws',
PeakFunction="Gaussian",
BackgroundType="Linear",
from mantid.simpleapi import LoadEmptyInstrument, MaskBTP, SaveMask
LoadEmptyInstrument(InstrumentName='CORELLI', OutputWorkspace='CORELLI')
# Missing banks
MaskBTP('CORELLI', Bank='1-6,29,30,62,63-68,91')
# End of tubes
MaskBTP('CORELLI', Pixel='1-15,242-256')
# Beam center
MaskBTP('CORELLI', Bank='58', Tube='13-16', Pixel='80-130')
MaskBTP('CORELLI', Bank='59', Tube='1-4', Pixel='80-130')
SaveMask('CORELLI', 'corelli_mask.xml')