def test_model_MD(self):
ws1 = Load("ILL/D22/192068.nxs")
ws2 = Load("ENGINX00228061")
md = CreateMDWorkspace(Dimensions=1,
Extents='-1,1',
Names='A',
Units='U')
md.addExperimentInfo(ws1)
md.addExperimentInfo(ws2)
model = SampleLogsModel(md)
self.assertEqual(model.get_exp(), 0)
self.assertEqual(model.get_name(), 'md')
self.assertEqual(model.getNumExperimentInfo(), 2)
values = model.get_log_display_values("duration")
self.assertEqual(values[0], "duration")
self.assertEqual(values[1], "number")
self.assertEqual(values[2], "120.0")
self.assertEqual(values[3], "Sec")
# Change exp
model.set_exp(1)
self.assertEqual(model.get_exp(), 1)
values = model.get_log_display_values("rb_proposal")
self.assertEqual(values[0], "rb_proposal")
self.assertEqual(values[1], "number")
self.assertEqual(values[2], "1455001")
self.assertEqual(values[3], "")
def runTest(self):
HelperTestingClass.__init__(self)
limits = (-10.0, 10.0, -9.0, 9.0)
ws_nonrotho = CreateMDWorkspace(
Dimensions=3,
Extents=','.join([str(lim) for lim in limits]) + ',-8,8',
Names='A,B,C',
Units='r.l.u.,r.l.u.,r.l.u.',
Frames='HKL,HKL,HKL')
expt_info_nonortho = CreateSampleWorkspace()
ws_nonrotho.addExperimentInfo(expt_info_nonortho)
SetUB(ws_nonrotho, 1, 1, 2, 90, 90, 120)
pres = SliceViewer(ws_nonrotho)
# assert limits of orthog
limits_orthog = pres.view.data_view.get_axes_limits()
self.assertEqual(limits_orthog[0], limits[0:2])
self.assertEqual(limits_orthog[1], limits[2:])
# set nonorthog view and retrieve new limits
pres.nonorthogonal_axes(True)
limits_nonorthog = pres.view.data_view.get_axes_limits()
self.assertAlmostEqual(limits_nonorthog[0][0], -19, delta=1e-5)
self.assertAlmostEqual(limits_nonorthog[0][1], 19, delta=1e-5)
self.assertEqual(limits_nonorthog[1], limits[2:])
pres.view.close()
def test_model_MD(self):
ws1 = LoadEventNexus("CNCS_7860", MetaDataOnly=True)
ws2 = LoadEventNexus("VIS_19351", MetaDataOnly=True)
md = CreateMDWorkspace(Dimensions=1,
Extents='-1,1',
Names='A',
Units='U')
md.addExperimentInfo(ws1)
md.addExperimentInfo(ws2)
model = SampleLogsModel(md)
self.assertEqual(model.get_exp(), 0)
self.assertEqual(model.get_name(), 'md')
self.assertEqual(model.getNumExperimentInfo(), 2)
values = model.get_log_display_values("duration")
self.assertEqual(values[0], "duration")
self.assertEqual(values[1], "number")
self.assertEqual(values[2], 148.0)
self.assertEqual(values[3], "second")
# Change exp
model.set_exp(1)
self.assertEqual(model.get_exp(), 1)
values = model.get_log_display_values("duration")
self.assertEqual(values[0], "duration")
self.assertEqual(values[1], "number")
self.assertEqual(values[2], 4.616606712341309)
self.assertEqual(values[3], "second")
def test_model_MD(self):
ws1 = LoadEventNexus("CNCS_7860", MetaDataOnly=True)
ws2 = LoadEventNexus("VIS_19351", MetaDataOnly=True)
md = CreateMDWorkspace(Dimensions=1, Extents='-1,1', Names='A', Units='U')
md.addExperimentInfo(ws1)
md.addExperimentInfo(ws2)
model = SampleLogsModel(md)
self.assertEqual(model.get_exp(), 0)
self.assertEqual(model.get_name(), 'md')
self.assertEqual(model.getNumExperimentInfo(), 2)
values = model.get_log_display_values("duration")
self.assertEqual(values[0], "duration")
self.assertEqual(values[1], "number")
self.assertEqual(values[2], 148.0)
self.assertEqual(values[3], "second")
# Change exp
model.set_exp(1)
self.assertEqual(model.get_exp(), 1)
values = model.get_log_display_values("duration")
self.assertEqual(values[0], "duration")
self.assertEqual(values[1], "number")
self.assertEqual(values[2], 4.616606712341309)
self.assertEqual(values[3], "second")
def create_hkl_ws():
hkl_ws = CreateMDWorkspace(Dimensions=3,
Extents='-10,10,-9,9,-8,8',
Names='A,B,C',
Units='r.l.u.,r.l.u.,r.l.u.',
Frames='HKL,HKL,HKL',
OutputWorkspace='hkl_ws')
expt_info = CreateSampleWorkspace()
hkl_ws.addExperimentInfo(expt_info)
SetUB(hkl_ws, 1, 1, 1, 90, 90, 90)
return hkl_ws
def runTest(self):
HelperTestingClass.__init__(self)
ws_4D = CreateMDWorkspace(Dimensions=4, Extents=[-1, 1, -1, 1, -1, 1, -1, 1], Names="E,H,K,L",
Frames='General Frame,HKL,HKL,HKL', Units='meV,r.l.u.,r.l.u.,r.l.u.')
expt_info_4D = CreateSampleWorkspace()
ws_4D.addExperimentInfo(expt_info_4D)
SetUB(ws_4D, 1, 1, 2, 90, 90, 120)
pres = SliceViewer(ws_4D)
self._qapp.sendPostedEvents()
non_ortho_action = toolbar_actions(pres, [ToolItemText.NONORTHOGONAL_AXES])[0]
self.assertFalse(non_ortho_action.isEnabled())
pres.view.close()
def setUpClass(cls):
cls.histo_ws = CreateMDHistoWorkspace(
Dimensionality=3,
Extents='-3,3,-10,10,-1,1',
SignalInput=range(100),
ErrorInput=range(100),
NumberOfBins='5,5,4',
Names='Dim1,Dim2,Dim3',
Units='MomentumTransfer,EnergyTransfer,Angstrom',
OutputWorkspace='ws_MD_2d')
cls.histo_ws_positive = CreateMDHistoWorkspace(
Dimensionality=3,
Extents='-3,3,-10,10,-1,1',
SignalInput=range(1, 101),
ErrorInput=range(100),
NumberOfBins='5,5,4',
Names='Dim1,Dim2,Dim3',
Units='MomentumTransfer,EnergyTransfer,Angstrom',
OutputWorkspace='ws_MD_2d_pos')
cls.hkl_ws = CreateMDWorkspace(Dimensions=3,
Extents='-10,10,-9,9,-8,8',
Names='A,B,C',
Units='r.l.u.,r.l.u.,r.l.u.',
Frames='HKL,HKL,HKL',
OutputWorkspace='hkl_ws')
expt_info = CreateSampleWorkspace()
cls.hkl_ws.addExperimentInfo(expt_info)
SetUB('hkl_ws', 1, 1, 1, 90, 90, 90)
def setUpClass(self):
self.ws_MD_3D = CreateMDHistoWorkspace(
Dimensionality=3,
Extents='-3,3,-10,10,-1,1',
SignalInput=range(100),
ErrorInput=range(100),
NumberOfBins='5,5,4',
Names='Dim1,Dim2,Dim3',
Units='MomentumTransfer,EnergyTransfer,Angstrom',
OutputWorkspace='ws_MD_3D')
self.ws_MDE_3D = CreateMDWorkspace(Dimensions='3',
Extents='-3,3,-4,4,-5,5',
Names='h,k,l',
Units='rlu,rlu,rlu',
SplitInto='4',
OutputWorkspace='ws_MDE_3D')
FakeMDEventData('ws_MDE_3D',
PeakParams='100000,0,0,0,0.1',
RandomSeed='63759',
RandomizeSignal='1')
FakeMDEventData('ws_MDE_3D',
PeakParams='40000,1,0,0,0.1',
RandomSeed='63759',
RandomizeSignal='1')
self.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')
def runTest(self):
HelperTestingClass.__init__(self)
ws_non_ortho = CreateMDWorkspace(Dimensions='3', Extents='-6,6,-4,4,-0.5,0.5',
Names='H,K,L', Units='r.l.u.,r.l.u.,r.l.u.',
Frames='HKL,HKL,HKL',
SplitInto='2', SplitThreshold='50')
expt_info_nonortho = CreateSampleWorkspace()
ws_non_ortho.addExperimentInfo(expt_info_nonortho)
SetUB(ws_non_ortho, 1, 1, 2, 90, 90, 120)
pres = SliceViewer(ws_non_ortho)
ClearUB(ws_non_ortho)
self._qapp.sendPostedEvents()
self.assert_no_toplevel_widgets()
self.assertEqual(pres.ads_observer, None)
def setUpClass(cls):
"""
Create fake workspaces, 3D and 2D
"""
# 3D
DeltaPDF3DTest_MDE = CreateMDWorkspace(Dimensions='3', Extents='-3.1,3.1,-3.1,3.1,-3.1,3.1', Names='[H,0,0],[0,K,0],[0,0,L]',
Units='rlu,rlu,rlu', SplitInto='4',Frames='HKL,HKL,HKL')
# Add Bragg peaks
for h in range(-3,4):
for k in range(-3,4):
for l in range(-3,4):
FakeMDEventData(DeltaPDF3DTest_MDE, PeakParams='100,'+str(h)+','+str(k)+','+str(l)+',0.1', RandomSeed='1337')
# Add addiontal peaks on [0.5,0.5,0.5] type positions
# This would correspond to negative substitutional correlations
for h in np.arange(-2.5,3):
for k in np.arange(-2.5,3):
for l in np.arange(-2.5,3):
FakeMDEventData(DeltaPDF3DTest_MDE, PeakParams='20,'+str(h)+','+str(k)+','+str(l)+',0.1', RandomSeed='13337')
BinMD(InputWorkspace='DeltaPDF3DTest_MDE', AlignedDim0='[H,0,0],-3.05,3.05,61', AlignedDim1='[0,K,0],-3.05,3.05,61',
AlignedDim2='[0,0,L],-3.05,3.05,61', OutputWorkspace='DeltaPDF3DTest_MDH')
# 2D
DeltaPDF3DTest_MDE_2 = CreateMDWorkspace(Dimensions='3', Extents='-3.1,3.1,-3.1,3.1,-0.1,0.1', Names='[H,0,0],[0,K,0],[0,0,L]',
Units='rlu,rlu,rlu', SplitInto='4',Frames='HKL,HKL,HKL')
# Add Bragg peaks
for h in range(-3,4):
for k in range(-3,4):
FakeMDEventData(DeltaPDF3DTest_MDE_2, PeakParams='100,'+str(h)+','+str(k)+',0,0.01', RandomSeed='1337')
# Add addiontal peaks on [0.5,0.5,0.5] type positions
# This would correspond to negative substitutional correlations
for h in np.arange(-2.5,3):
for k in np.arange(-2.5,3):
FakeMDEventData(DeltaPDF3DTest_MDE_2, PeakParams='20,'+str(h)+','+str(k)+',0,0.1', RandomSeed='13337')
BinMD(InputWorkspace='DeltaPDF3DTest_MDE_2', AlignedDim0='[H,0,0],-3.05,3.05,61', AlignedDim1='[0,K,0],-3.05,3.05,61',
AlignedDim2='[0,0,L],-0.1,0.1,1', OutputWorkspace='DeltaPDF3DTest_MDH_2')
def test_mdhisto_workspace_q(self):
from mantid.simpleapi import (CreateMDWorkspace, FakeMDEventData,
BinMD)
md_event = CreateMDWorkspace(Dimensions=3,
Extents=[-10, 10, -10, 10, -10, 10],
Names='Q_x,Q_y,Q_z',
Units='U,U,U',
Frames='QLab,QLab,QLab',
StoreInADS=False)
FakeMDEventData(InputWorkspace=md_event,
PeakParams=[100000, 0, 0, 0, 1],
StoreInADS=False) # Add Peak
md_histo = BinMD(InputWorkspace=md_event,
AlignedDim0='Q_y,-10,10,3',
AlignedDim1='Q_x,-10,10,4',
AlignedDim2='Q_z,-10,10,5',
StoreInADS=False)
histo_data_array = mantidcompat.convert_MDHistoWorkspace_to_data_array(
md_histo)
self.assertEqual(histo_data_array.coords[sc.Dim.Qx].values.shape,
(4, ))
self.assertEqual(histo_data_array.coords[sc.Dim.Qy].values.shape,
(3, ))
self.assertEqual(histo_data_array.coords[sc.Dim.Qz].values.shape,
(5, ))
self.assertEqual(histo_data_array.coords[sc.Dim.Qx].unit,
sc.units.dimensionless / sc.units.angstrom)
self.assertEqual(histo_data_array.coords[sc.Dim.Qy].unit,
sc.units.dimensionless / sc.units.angstrom)
self.assertEqual(histo_data_array.coords[sc.Dim.Qz].unit,
sc.units.dimensionless / sc.units.angstrom)
self.assertEquals(histo_data_array.values.shape, (3, 4, 5))
# Sum over 2 dimensions to simplify finding max.
max_1d = sc.sum(sc.sum(histo_data_array, dim=sc.Dim.Qy),
dim=sc.Dim.Qx).values
max_index = np.argmax(max_1d)
# Check position of max 'peak'
self.assertEqual(np.floor(len(max_1d) / 2), max_index)
# All events in central 'peak'
self.assertEqual(100000, max_1d[max_index])
self.assertTrue('nevents' in histo_data_array.attrs)
def runTest(self):
HelperTestingClass.__init__(self)
def scale_ws(ws):
ws = ws * 100
ws = CreateMDWorkspace(Dimensions='3',
EventType='MDEvent',
Extents='-10,10,-5,5,-1,1',
Names='Q_lab_x,Q_lab_y,Q_lab_z',
Units='1\\A,1\\A,1\\A')
FakeMDEventData(ws, UniformParams="1000000")
pres = SliceViewer(ws)
self._assertNoErrorInADSHandlerFromSeparateThread(partial(scale_ws, ws))
self._qapp.sendPostedEvents()
self.assertTrue(pres.view in self.find_widgets_of_type(str(type(pres.view))))
self.assertNotEqual(pres.ads_observer, None)
pres.view.close()
def test_view_updates_on_replace_when_model_properties_dont_change_mdeventws(
self):
def scale_ws(ws):
ws = ws * 100
ws = CreateMDWorkspace(Dimensions='3',
EventType='MDEvent',
Extents='-10,10,-5,5,-1,1',
Names='Q_lab_x,Q_lab_y,Q_lab_z',
Units='1\\A,1\\A,1\\A')
FakeMDEventData(ws, UniformParams="1000000")
pres = SliceViewer(ws)
self._assertNoErrorInADSHandlerFromSeparateThread(partial(
scale_ws, ws))
QApplication.sendPostedEvents()
self.assertTrue(
pres.view in self.find_widgets_of_type(str(type(pres.view))))
self.assertNotEqual(pres.ads_observer, None)
pres.view.close()
def test_mdhisto_workspace_many_dims(self):
from mantid.simpleapi import (CreateMDWorkspace, FakeMDEventData,
BinMD)
md_event = CreateMDWorkspace(
Dimensions=4,
Extents=[-10, 10, -10, 10, -10, 10, -10, 10],
Names='deltae,y,z,T',
Units='U,U,U,U',
StoreInADS=False)
FakeMDEventData(InputWorkspace=md_event,
PeakParams=[100000, 0, 0, 0, 0, 1],
StoreInADS=False) # Add Peak
md_histo = BinMD(InputWorkspace=md_event,
AlignedDim0='deltae,-10,10,3',
AlignedDim1='y,-10,10,4',
AlignedDim2='z,-10,10,5',
AlignedDim3='T,-10,10,7',
StoreInADS=False)
histo_data_array = scn.mantid.convert_MDHistoWorkspace_to_data_array(
md_histo)
self.assertEqual(4, len(histo_data_array.dims))
def _setup_test(self) -> None:
self._workspace_type = "MDWorkspace"
CreateMDWorkspace(Dimensions="3", EventType="MDEvent", Extents='-10,10,-5,5,-1,1',
Names="Q_lab_x,Q_lab_y,Q_lab_z", Units="1\\A,1\\A,1\\A", OutputWorkspace="ws")
def test_Q_Sample(self):
md = CreateMDWorkspace(Dimensions=3,
Extents='0,10,0,10,0,10',
Names='x,y,z',
Units='r.l.u.,r.l.u.,r.l.u.',
Frames='QSample,QSample,QSample')
pw_name = 'peaks_add_delete_test'
CreatePeaksWorkspace(OutputType='LeanElasticPeak',
NUmberOfPeaks=0,
OutputWorkspace=pw_name)
self.assertEqual(mtd[pw_name].getNumberPeaks(), 0)
sliceViewer = SliceViewer(md)
# select z=3.0 slice
sliceViewer.view.dimensions.set_slicepoint((None, None, 3.0))
event = Mock(inaxes=True, xdata=1.0, ydata=2.0)
sliceViewer.canvas_clicked(event)
# nothing should happen since peaksviewer isn't active
self.assertEqual(mtd[pw_name].getNumberPeaks(), 0)
# overlay_peaks_workspaces
sliceViewer._create_peaks_presenter_if_necessary(
).overlay_peaksworkspaces([pw_name])
sliceViewer.canvas_clicked(event)
# nothing should happen since add/remove peak action not selected
self.assertEqual(mtd[pw_name].getNumberPeaks(), 0)
# click the "Add Peaks" button
sliceViewer.view.peaks_view.peak_actions_view.ui.add_peaks_button.click(
)
sliceViewer.canvas_clicked(event) # should add a peak at (1, 2, 3)
# peak should now be added
self.assertEqual(mtd[pw_name].getNumberPeaks(), 1)
peak = mtd[pw_name].getPeak(0)
q_sample = peak.getQSampleFrame()
self.assertAlmostEqual(q_sample[0], 1.0, delta=1e-10)
self.assertAlmostEqual(q_sample[1], 2.0, delta=1e-10)
self.assertAlmostEqual(q_sample[2], 3.0, delta=1e-10)
self.assertEqual(peak.getH(), 0)
self.assertEqual(peak.getK(), 0)
self.assertEqual(peak.getL(), 0)
# change to x-z slice, y=4, check that the transform is working
sliceViewer.view.dimensions.dims[2].y_clicked()
sliceViewer.view.dimensions.set_slicepoint((None, 4.0, None))
sliceViewer.canvas_clicked(event) # should add a peak at (1, 4, 2)
self.assertEqual(mtd[pw_name].getNumberPeaks(), 2)
peak = mtd[pw_name].getPeak(1)
q_sample = peak.getQSampleFrame()
self.assertAlmostEqual(q_sample[0], 1.0, delta=1e-10)
self.assertAlmostEqual(q_sample[1], 4.0, delta=1e-10)
self.assertAlmostEqual(q_sample[2], 2.0, delta=1e-10)
self.assertEqual(peak.getH(), 0)
self.assertEqual(peak.getK(), 0)
self.assertEqual(peak.getL(), 0)
# click the "Remove Peaks" button
sliceViewer.view.peaks_view.peak_actions_view.ui.remove_peaks_button.click(
)
sliceViewer.view.dimensions.set_slicepoint((None, 0.0, None))
event = Mock(inaxes=True, xdata=1.0, ydata=1.0)
sliceViewer.canvas_clicked(
event) # should remove the peak closest to (1, 0, 1)
self.assertEqual(mtd[pw_name].getNumberPeaks(), 1)
# should be left with the seconds peak that was added
peak = mtd[pw_name].getPeak(0)
q_sample = peak.getQSampleFrame()
self.assertAlmostEqual(q_sample[0], 1.0, delta=1e-10)
self.assertAlmostEqual(q_sample[1], 4.0, delta=1e-10)
self.assertAlmostEqual(q_sample[2], 2.0, delta=1e-10)
self.assertEqual(peak.getH(), 0)
self.assertEqual(peak.getK(), 0)
self.assertEqual(peak.getL(), 0)
# remove another peaks, should be none remaining
sliceViewer.canvas_clicked(
event) # should remove the peak closest to (1, 0, 1)
self.assertEqual(mtd[pw_name].getNumberPeaks(), 0)
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 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)
def test_add_experiment_info(self):
ws1 = CreateSampleWorkspace()
md = CreateMDWorkspace(Dimensions=1, Extents='-1,1', Names='A', Units='U')
md.addExperimentInfo(ws1)
with h5py.File(filename, 'r') as f_in:
bc = np.zeros((pixels), dtype=np.int64)
for b in range(8):
bc += np.bincount(f_in['/entry/bank' + str(b + 1) +
'_events/event_id'].value,
minlength=pixels)
bc = bc.reshape((-1, 512)).T
data_array[n] = bc
phi_array[n] = f_in[
'entry/DASlogs/HB2C:Mot:s1.RBV/average_value'].value[0]
t1 = time.time()
print(t1 - t0)
print(data_array.shape)
mdws = CreateMDWorkspace(Dimensions=3,
Extents='-10,10,-10,10,-10,10',
Names='A,B,C',
Units='U,U,U')
t2 = time.time()
binned_ws = BinMD(InputWorkspace=mdws,
AlignedDim0='A,0,10,1801',
AlignedDim1='B,-10,10,512',
AlignedDim2='C,-10,10,3840')
t3 = time.time()
binned_ws.setSignalArray(data_array)
t4 = time.time()
print(t2 - t1)
print(t3 - t2)
print(t4 - t3)
def test_HKL(self):
md = CreateMDWorkspace(Dimensions=3,
Extents='0,10,0,10,0,10',
Names='H,K,L',
Units='r.l.u.,r.l.u.,r.l.u.',
Frames='HKL,HKL,HKL')
pw_name = 'peaks_add_delete_test'
CreatePeaksWorkspace(OutputType='LeanElasticPeak',
NUmberOfPeaks=0,
OutputWorkspace=pw_name)
SetUB(pw_name, 2 * np.pi, 2 * np.pi, 4 * np.pi, u='0,0,1', v='1,0,0')
self.assertEqual(mtd[pw_name].getNumberPeaks(), 0)
sliceViewer = SliceViewer(md)
# select z=3.0 slice
sliceViewer.view.dimensions.set_slicepoint((None, None, 3.0))
# overlay_peaks_workspaces
sliceViewer._create_peaks_presenter_if_necessary(
).overlay_peaksworkspaces([pw_name])
# click the "Add Peaks" button
sliceViewer.view.peaks_view.peak_actions_view.ui.add_peaks_button.click(
)
# click on 3 different points on the canvas
sliceViewer.canvas_clicked(
Mock(inaxes=True, xdata=1.0,
ydata=2.0)) # should add a peak at HKL=(1, 2, 3)
sliceViewer.canvas_clicked(
Mock(inaxes=True, xdata=2.0,
ydata=2.0)) # should add a peak at HKL=(2, 2, 3)
sliceViewer.canvas_clicked(
Mock(inaxes=True, xdata=1.5,
ydata=1.5)) # should add a peak at HKL=(1.5, 1.5, 3)
# peaks should be added
self.assertEqual(mtd[pw_name].getNumberPeaks(), 3)
# (1, 2, 3)
peak = mtd[pw_name].getPeak(0)
q_sample = peak.getQSampleFrame()
self.assertAlmostEqual(q_sample[0], 1.0, delta=1e-10)
self.assertAlmostEqual(q_sample[1], 2.0, delta=1e-10)
self.assertAlmostEqual(q_sample[2], 1.5, delta=1e-10)
self.assertAlmostEqual(peak.getH(), 1, delta=1e-10)
self.assertAlmostEqual(peak.getK(), 2, delta=1e-10)
self.assertAlmostEqual(peak.getL(), 3, delta=1e-10)
# (2, 2, 3)
peak = mtd[pw_name].getPeak(1)
q_sample = peak.getQSampleFrame()
self.assertAlmostEqual(q_sample[0], 2.0, delta=1e-10)
self.assertAlmostEqual(q_sample[1], 2.0, delta=1e-10)
self.assertAlmostEqual(q_sample[2], 1.5, delta=1e-10)
self.assertAlmostEqual(peak.getH(), 2, delta=1e-10)
self.assertAlmostEqual(peak.getK(), 2, delta=1e-10)
self.assertAlmostEqual(peak.getL(), 3, delta=1e-10)
# (1.5, 1.5, 3)
peak = mtd[pw_name].getPeak(2)
q_sample = peak.getQSampleFrame()
self.assertAlmostEqual(q_sample[0], 1.5, delta=1e-10)
self.assertAlmostEqual(q_sample[1], 1.5, delta=1e-10)
self.assertAlmostEqual(q_sample[2], 1.5, delta=1e-10)
self.assertAlmostEqual(peak.getH(), 1.5, delta=1e-10)
self.assertAlmostEqual(peak.getK(), 1.5, delta=1e-10)
self.assertAlmostEqual(peak.getL(), 3, delta=1e-10)
# click the "Remove Peaks" button
sliceViewer.view.peaks_view.peak_actions_view.ui.remove_peaks_button.click(
)
sliceViewer.canvas_clicked(Mock(
inaxes=True, xdata=2.0,
ydata=1.9)) # should remove the peak closest to HKL=(2, 1.9, 3)
self.assertEqual(mtd[pw_name].getNumberPeaks(), 2)
# should have deleted the (2, 2, 3) peak, leaving (1, 2, 3) and (1.5, 1.5, 3)
# (1, 2, 3)
peak = mtd[pw_name].getPeak(0)
q_sample = peak.getQSampleFrame()
self.assertAlmostEqual(q_sample[0], 1.0, delta=1e-10)
self.assertAlmostEqual(q_sample[1], 2.0, delta=1e-10)
self.assertAlmostEqual(q_sample[2], 1.5, delta=1e-10)
self.assertAlmostEqual(peak.getH(), 1, delta=1e-10)
self.assertAlmostEqual(peak.getK(), 2, delta=1e-10)
self.assertAlmostEqual(peak.getL(), 3, delta=1e-10)
# (1.5, 1.5, 3)
peak = mtd[pw_name].getPeak(1)
q_sample = peak.getQSampleFrame()
self.assertAlmostEqual(q_sample[0], 1.5, delta=1e-10)
self.assertAlmostEqual(q_sample[1], 1.5, delta=1e-10)
self.assertAlmostEqual(q_sample[2], 1.5, delta=1e-10)
self.assertAlmostEqual(peak.getH(), 1.5, delta=1e-10)
self.assertAlmostEqual(peak.getK(), 1.5, delta=1e-10)
self.assertAlmostEqual(peak.getL(), 3, delta=1e-10)
