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 test_generate_plot_command_returns_correct_string_for_sample_log(self):
kwargs = copy(LINE2D_KWARGS)
kwargs["drawstyle"] = 'steps-post'
kwargs.update({
"LogName": "my_log",
"ExperimentInfo": 0,
"Filtered": True
})
# add a log
AddTimeSeriesLog(self.test_ws,
Name="my_log",
Time="2010-01-01T00:00:00",
Value=100)
AddTimeSeriesLog(self.test_ws,
Name="my_log",
Time="2010-01-01T00:30:00",
Value=15)
AddTimeSeriesLog(self.test_ws,
Name="my_log",
Time="2010-01-01T00:50:00",
Value=100.2)
line = self.ax.plot(self.test_ws, **kwargs)[0]
output = generate_plot_command(line)
expected_command = ("plot({}, {})".format(
self.test_ws.name(), convert_args_to_string(None, kwargs)))
self.assertEqual(expected_command, output)
def setUpClass(cls):
cls.g1da = config['graph1d.autodistribution']
config['graph1d.autodistribution'] = 'On'
cls.ws2d_histo = CreateWorkspace(DataX=[10, 20, 30, 10, 20, 30],
DataY=[2, 3, 4, 5],
DataE=[1, 2, 3, 4],
NSpec=2,
Distribution=True,
YUnitLabel="Counts per $\\AA$",
UnitX='Wavelength',
VerticalAxisUnit='DeltaE',
VerticalAxisValues=[4, 6, 8],
OutputWorkspace='ws2d_histo')
cls.ws2d_histo_non_dist = CreateWorkspace(DataX=[10, 20, 30, 10, 20, 30],
DataY=[2, 3, 4, 5],
DataE=[1, 2, 3, 4],
NSpec=2,
Distribution=False,
YUnitLabel='Counts',
UnitX='Wavelength',
OutputWorkspace='ws2d_histo_non_dist')
cls.ws2d_histo_rag = CreateWorkspace(DataX=[1, 2, 3, 4, 5, 2, 4, 6, 8, 10],
DataY=[2] * 8,
NSpec=2,
VerticalAxisUnit='DeltaE',
VerticalAxisValues=[5, 7, 9],
OutputWorkspace='ws2d_histo_rag')
cls.ws_MD_2d = CreateMDHistoWorkspace(Dimensionality=3,
Extents='-3,3,-10,10,-1,1',
SignalInput=range(25),
ErrorInput=range(25),
NumberOfEvents=10 * np.ones(25),
NumberOfBins='5,5,1',
Names='Dim1,Dim2,Dim3',
Units='MomentumTransfer,EnergyTransfer,Angstrom',
OutputWorkspace='ws_MD_2d')
cls.ws_MD_1d = CreateMDHistoWorkspace(Dimensionality=3,
Extents='-3,3,-10,10,-1,1',
SignalInput=range(5),
ErrorInput=range(5),
NumberOfEvents=10 * np.ones(5),
NumberOfBins='1,5,1',
Names='Dim1,Dim2,Dim3',
Units='MomentumTransfer,EnergyTransfer,Angstrom',
OutputWorkspace='ws_MD_1d')
cls.ws2d_point_uneven = CreateWorkspace(DataX=[10, 20, 30],
DataY=[1, 2, 3],
NSpec=1,
OutputWorkspace='ws2d_point_uneven')
wp = CreateWorkspace(DataX=[15, 25, 35, 45], DataY=[1, 2, 3, 4], NSpec=1)
ConjoinWorkspaces(cls.ws2d_point_uneven, wp, CheckOverlapping=False)
cls.ws2d_point_uneven = mantid.mtd['ws2d_point_uneven']
cls.ws2d_histo_uneven = CreateWorkspace(DataX=[10, 20, 30, 40],
DataY=[1, 2, 3],
NSpec=1,
OutputWorkspace='ws2d_histo_uneven')
AddTimeSeriesLog(cls.ws2d_histo, Name="my_log", Time="2010-01-01T00:00:00", Value=100)
AddTimeSeriesLog(cls.ws2d_histo, Name="my_log", Time="2010-01-01T00:30:00", Value=15)
AddTimeSeriesLog(cls.ws2d_histo, Name="my_log", Time="2010-01-01T00:50:00", Value=100.2)
def test_create_results_table_with_logs_selected(self):
workspace = CreateWorkspace([0, 1, 2, 3, 4, 5], [0, 1, 2, 3, 4, 5])
workspace.mutableRun().addProperty(
"run_start", "1970-01-01T00:00:01 to 1970-01-01T00:00:01", True)
AddTimeSeriesLog(workspace,
Name="sample_temp",
Time="2010-01-01T00:00:00",
Value=100)
AddTimeSeriesLog(workspace,
Name="sample_temp",
Time="2010-01-01T00:30:00",
Value=65)
AddTimeSeriesLog(workspace,
Name="sample_temp",
Time="2010-01-01T00:50:00",
Value=100.2)
workspace.mutableRun().addProperty("sample_magn_field", 2, True)
_, model = create_test_model(
('ws1', ), 'func1', self.parameters,
[StaticWorkspaceWrapper('ws1', workspace)], self.logs)
selected_results = [('ws1', 0)]
table = model.create_results_table(self.log_names, selected_results)
# workspace_name => no error col as its a string
# sample_temp => time series and will have non-zero error
# sample_magn_field => just a number
expected_cols = [
'workspace_name', 'run_start', 'run_start_seconds', 'sample_temp',
'sample_tempError', 'sample_magn_field', 'sample_magn_fieldError',
'f0.Height', 'f0.HeightError', 'f0.PeakCentre',
'f0.PeakCentreError', 'f0.Sigma', 'f0.SigmaError', 'f1.Height',
'f1.HeightError', 'f1.PeakCentre', 'f1.PeakCentreError',
'f1.Sigma', 'f1.SigmaError', 'Cost function value'
]
expected_types = (TableColumnType.NoType, TableColumnType.X,
TableColumnType.X, TableColumnType.X,
TableColumnType.XErr, TableColumnType.X,
TableColumnType.XErr, TableColumnType.Y,
TableColumnType.YErr, TableColumnType.Y,
TableColumnType.YErr, TableColumnType.Y,
TableColumnType.YErr, TableColumnType.Y,
TableColumnType.YErr, TableColumnType.Y,
TableColumnType.YErr, TableColumnType.Y,
TableColumnType.YErr, TableColumnType.Y)
avg_log_values = "1970-01-01T00:00:01 to 1970-01-01T00:00:01", 1, 86., 2.0
expected_content = [
('ws1_Parameters', avg_log_values[0], avg_log_values[1],
avg_log_values[2], 17.146, avg_log_values[3], 0.,
self.f0_height[0], self.f0_height[1], self.f0_centre[0],
self.f0_centre[1], self.f0_sigma[0], self.f0_sigma[1],
self.f1_height[0], self.f1_height[1], self.f1_centre[0],
self.f1_centre[1], self.f1_sigma[0], self.f1_sigma[1],
self.cost_function[0])
]
self._assert_table_matches_expected(zip(expected_cols, expected_types),
expected_content, table,
model.results_table_name())
def provide_workspace_with_proton_charge(output_name, is_event=True):
ws_type = "Event" if is_event else "Histogram"
# AddTimeSeriesLog forces us to store in ADS
dummy_ws = CreateSampleWorkspace(NumBanks=1, BankPixelWidth=2,
WorkspaceType=ws_type, OutputWorkspace=output_name)
# Provide a proton charge
time = DateAndTime("2010-01-01T00:10:00")
value = 1.0
for index in range(0, 10):
time += 1000000000
AddTimeSeriesLog(Workspace=dummy_ws, Name="proton_charge", Type="double",
Time=str(time), Value=value)
return dummy_ws
def _create_event_workspace(self,
run_number,
prefix='',
includeMonitors=True):
name = prefix + str(run_number)
CreateSampleWorkspace(WorkspaceType='Event',
NumBanks=1,
NumMonitors=3,
BankPixelWidth=2,
XMin=200,
OutputWorkspace=name)
if includeMonitors:
CropWorkspace(InputWorkspace=name,
StartWorkspaceIndex=0,
EndWorkspaceIndex=2,
OutputWorkspace=name + '_monitors')
Rebin(InputWorkspace=name + '_monitors',
Params='0,200,20000',
OutputWorkspace=name + '_monitors',
PreserveEvents=False)
CropWorkspace(InputWorkspace=name,
StartWorkspaceIndex=3,
EndWorkspaceIndex=4,
OutputWorkspace=name)
AddSampleLog(Workspace=name,
LogName='run_number',
LogText=str(run_number))
AddTimeSeriesLog(Workspace=name,
Name="proton_charge",
Time="2010-01-01T00:00:00",
Value=100)
AddTimeSeriesLog(Workspace=name,
Name="proton_charge",
Time="2010-01-01T00:10:00",
Value=100)
AddTimeSeriesLog(Workspace=name,
Name="proton_charge",
Time="2010-01-01T00:20:00",
Value=80)
AddTimeSeriesLog(Workspace=name,
Name="proton_charge",
Time="2010-01-01T00:30:00",
Value=80)
AddTimeSeriesLog(Workspace=name,
Name="proton_charge",
Time="2010-01-01T00:40:00",
Value=15)
AddTimeSeriesLog(Workspace=name,
Name="proton_charge",
Time="2010-01-01T00:50:00",
Value=100)
def runTest(self):
# Na Mn Cl3
# R -3 H (148)
# 6.592 6.592 18.585177 90 90 120
# UB/wavelength from /HFIR/HB3A/IPTS-25470/shared/autoreduce/HB3A_exp0769_scan0040.nxs
ub = np.array([[1.20297e-01, 1.70416e-01, 1.43000e-04],
[8.16000e-04, -8.16000e-04, 5.38040e-02],
[1.27324e-01, -4.05110e-02, -4.81000e-04]])
wavelength = 1.553
# create fake MDEventWorkspace, similar to what is expected from exp769 after loading with HB3AAdjustSampleNorm
MD_Q_sample = CreateMDWorkspace(
Dimensions='3',
Extents='-5,5,-5,5,-5,5',
Names='Q_sample_x,Q_sample_y,Q_sample_z',
Units='rlu,rlu,rlu',
Frames='QSample,QSample,QSample')
inst = LoadEmptyInstrument(InstrumentName='HB3A')
AddTimeSeriesLog(inst, 'omega', '2010-01-01T00:00:00', 0.)
AddTimeSeriesLog(inst, 'phi', '2010-01-01T00:00:00', 0.)
AddTimeSeriesLog(inst, 'chi', '2010-01-01T00:00:00', 0.)
MD_Q_sample.addExperimentInfo(inst)
SetUB(MD_Q_sample, UB=ub)
ol = OrientedLattice()
ol.setUB(ub)
sg = SpaceGroupFactory.createSpaceGroup("R -3")
hkl = []
sat_hkl = []
for h in range(0, 6):
for k in range(0, 6):
for l in range(0, 11):
if sg.isAllowedReflection([h, k, l]):
if h == k == l == 0:
continue
q = V3D(h, k, l)
q_sample = ol.qFromHKL(q)
if not np.any(np.array(q_sample) > 5):
hkl.append(q)
FakeMDEventData(
MD_Q_sample,
PeakParams='1000,{},{},{},0.05'.format(
*q_sample))
# satellite peaks at 0,0,+1.5
q = V3D(h, k, l + 1.5)
q_sample = ol.qFromHKL(q)
if not np.any(np.array(q_sample) > 5):
sat_hkl.append(q)
FakeMDEventData(
MD_Q_sample,
PeakParams='100,{},{},{},0.02'.format(
*q_sample))
# satellite peaks at 0,0,-1.5
q = V3D(h, k, l - 1.5)
q_sample = ol.qFromHKL(q)
if not np.any(np.array(q_sample) > 5):
sat_hkl.append(q)
FakeMDEventData(
MD_Q_sample,
PeakParams='100,{},{},{},0.02'.format(
*q_sample))
# Check that this fake workpsace gives us the expected UB
peaks = FindPeaksMD(MD_Q_sample,
PeakDistanceThreshold=1,
OutputType='LeanElasticPeak')
FindUBUsingFFT(peaks, MinD=5, MaxD=20)
ShowPossibleCells(peaks)
SelectCellOfType(peaks,
CellType='Rhombohedral',
Centering='R',
Apply=True)
OptimizeLatticeForCellType(peaks, CellType='Hexagonal', Apply=True)
found_ol = peaks.sample().getOrientedLattice()
self.assertAlmostEqual(found_ol.a(), 6.592, places=2)
self.assertAlmostEqual(found_ol.b(), 6.592, places=2)
self.assertAlmostEqual(found_ol.c(), 18.585177, places=2)
self.assertAlmostEqual(found_ol.alpha(), 90)
self.assertAlmostEqual(found_ol.beta(), 90)
self.assertAlmostEqual(found_ol.gamma(), 120)
# nuclear peaks
predict = HB3APredictPeaks(
MD_Q_sample,
Wavelength=wavelength,
ReflectionCondition='Rhombohedrally centred, obverse',
SatellitePeaks=True,
IncludeIntegerHKL=True)
predict = HB3AIntegratePeaks(MD_Q_sample, predict, 0.25)
self.assertEqual(predict.getNumberPeaks(), 66)
# check that the found peaks are expected
for n in range(predict.getNumberPeaks()):
HKL = predict.getPeak(n).getHKL()
self.assertTrue(HKL in hkl, msg=f"Peak {n} with HKL={HKL}")
# magnetic peaks
satellites = HB3APredictPeaks(
MD_Q_sample,
Wavelength=wavelength,
ReflectionCondition='Rhombohedrally centred, obverse',
SatellitePeaks=True,
ModVector1='0,0,1.5',
MaxOrder=1,
IncludeIntegerHKL=False)
satellites = HB3AIntegratePeaks(MD_Q_sample, satellites, 0.1)
self.assertEqual(satellites.getNumberPeaks(), 80)
# check that the found peaks are expected
for n in range(satellites.getNumberPeaks()):
HKL = satellites.getPeak(n).getHKL()
self.assertTrue(HKL in sat_hkl, msg=f"Peak {n} with HKL={HKL}")
def setUpClass(cls):
cls.g1da = config['graph1d.autodistribution']
config['graph1d.autodistribution'] = 'On'
cls.ws2d_non_distribution = CreateWorkspace(
DataX=[10, 20, 30, 10, 20, 30],
DataY=[2, 3, 4, 5],
DataE=[1, 2, 3, 4],
NSpec=2,
Distribution=False,
UnitX='Wavelength',
YUnitLabel='Counts per microAmp.hour',
VerticalAxisUnit='DeltaE',
VerticalAxisValues=[4, 6, 8],
OutputWorkspace='ws2d_non_distribution')
cls.ws2d_distribution = CreateWorkspace(
DataX=[10, 20, 30, 10, 20, 30],
DataY=[2, 3, 4, 5, 6],
DataE=[1, 2, 3, 4, 6],
NSpec=1,
Distribution=True,
UnitX='Wavelength',
YUnitLabel='Counts per microAmp.hour',
OutputWorkspace='ws2d_distribution')
cls.ws2d_histo = CreateWorkspace(DataX=[10, 20, 30, 10, 20, 30],
DataY=[2, 3, 4, 5],
DataE=[1, 2, 3, 4],
NSpec=2,
Distribution=True,
UnitX='Wavelength',
VerticalAxisUnit='DeltaE',
VerticalAxisValues=[4, 6, 8],
OutputWorkspace='ws2d_histo')
cls.ws2d_point = CreateWorkspace(
DataX=[1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4],
DataY=[2] * 12,
NSpec=3,
OutputWorkspace='ws2d_point')
cls.ws1d_point = CreateWorkspace(DataX=[1, 2],
DataY=[1, 2],
NSpec=1,
Distribution=False,
OutputWorkspace='ws1d_point')
cls.ws2d_histo_rag = CreateWorkspace(
DataX=[1, 2, 3, 4, 5, 2, 4, 6, 8, 10],
DataY=[2] * 8,
NSpec=2,
VerticalAxisUnit='DeltaE',
VerticalAxisValues=[5, 7, 9],
OutputWorkspace='ws2d_histo_rag')
cls.ws2d_point_rag = CreateWorkspace(DataX=[1, 2, 3, 4, 2, 4, 6, 8],
DataY=[2] * 8,
NSpec=2,
OutputWorkspace='ws2d_point_rag')
cls.ws_MD_2d = CreateMDHistoWorkspace(
Dimensionality=3,
Extents='-3,3,-10,10,-1,1',
SignalInput=range(25),
ErrorInput=range(25),
NumberOfEvents=10 * np.ones(25),
NumberOfBins='5,5,1',
Names='Dim1,Dim2,Dim3',
Units='MomentumTransfer,EnergyTransfer,Angstrom',
OutputWorkspace='ws_MD_2d')
cls.ws_MD_1d = CreateMDHistoWorkspace(
Dimensionality=3,
Extents='-3,3,-10,10,-1,1',
SignalInput=range(5),
ErrorInput=range(5),
NumberOfEvents=10 * np.ones(5),
NumberOfBins='1,5,1',
Names='Dim1,Dim2,Dim3',
Units='MomentumTransfer,EnergyTransfer,Angstrom',
OutputWorkspace='ws_MD_1d')
cls.ws2d_point_uneven = CreateWorkspace(
DataX=[10, 20, 30],
DataY=[1, 2, 3],
NSpec=1,
OutputWorkspace='ws2d_point_uneven')
cls.ws2d_high_counting_detector = CreateWorkspace(
DataX=[1, 2, 3, 4] * 1000,
DataY=[2] * 4 * 12 + [200] * 4 + [2] * 987 * 4,
NSpec=1000,
OutputWorkspace='ws2d_high_counting_detector')
wp = CreateWorkspace(DataX=[15, 25, 35, 45],
DataY=[1, 2, 3, 4],
NSpec=1)
ConjoinWorkspaces(cls.ws2d_point_uneven, wp, CheckOverlapping=False)
cls.ws2d_point_uneven = mantid.mtd['ws2d_point_uneven']
cls.ws2d_histo_uneven = CreateWorkspace(
DataX=[10, 20, 30, 40],
DataY=[1, 2, 3],
NSpec=1,
OutputWorkspace='ws2d_histo_uneven')
wp = CreateWorkspace(DataX=[15, 25, 35, 45, 55],
DataY=[1, 2, 3, 4],
NSpec=1)
ConjoinWorkspaces(cls.ws2d_histo_uneven, wp, CheckOverlapping=False)
cls.ws2d_histo_uneven = mantid.mtd['ws2d_histo_uneven']
newYAxis = mantid.api.NumericAxis.create(3)
newYAxis.setValue(0, 10)
newYAxis.setValue(1, 15)
newYAxis.setValue(2, 25)
cls.ws2d_histo_uneven.replaceAxis(1, newYAxis)
AddTimeSeriesLog(cls.ws2d_histo,
Name="my_log",
Time="2010-01-01T00:00:00",
Value=100)
AddTimeSeriesLog(cls.ws2d_histo,
Name="my_log",
Time="2010-01-01T00:30:00",
Value=15)
AddTimeSeriesLog(cls.ws2d_histo,
Name="my_log",
Time="2010-01-01T00:50:00",
Value=100.2)