def runTest(self):
# Load raw data (bank 1)
wsMD = LoadMD(
"WISH38237_MD.nxs") # default so doesn't get overwrite van
# For each mod vec, predict and integrate peaks and combine
qs = [(0.15, 0, 0.3), (-0.15, 0, 0.3)]
all_pks = CreatePeaksWorkspace(InstrumentWorkspace=wsMD,
NumberOfPeaks=0,
OutputWorkspace="all_pks")
LoadIsawUB(InputWorkspace=all_pks,
Filename='Wish_Diffuse_Scattering_ISAW_UB.mat')
# PredictPeaks
parent = PredictPeaks(InputWorkspace=all_pks,
WavelengthMin=0.8,
WavelengthMax=9.3,
MinDSpacing=0.5,
ReflectionCondition="Primitive")
self._pfps = []
self._saved_files = []
for iq, q in enumerate(qs):
wsname = f'pfp_{iq}'
PredictFractionalPeaks(Peaks=parent,
IncludeAllPeaksInRange=True,
Hmin=0,
Hmax=0,
Kmin=1,
Kmax=1,
Lmin=0,
Lmax=1,
ReflectionCondition='Primitive',
MaxOrder=1,
ModVector1=",".join([str(qi) for qi in q]),
FracPeaks=wsname)
FilterPeaks(InputWorkspace=wsname,
OutputWorkspace=wsname,
FilterVariable='Wavelength',
FilterValue=9.3,
Operator='<') # should get rid of one peak in q1 table
FilterPeaks(InputWorkspace=wsname,
OutputWorkspace=wsname,
FilterVariable='Wavelength',
FilterValue=0.8,
Operator='>')
IntegratePeaksMD(InputWorkspace=wsMD,
PeakRadius='0.1',
BackgroundInnerRadius='0.1',
BackgroundOuterRadius='0.15',
PeaksWorkspace=wsname,
OutputWorkspace=wsname,
IntegrateIfOnEdge=False,
UseOnePercentBackgroundCorrection=False)
all_pks = CombinePeaksWorkspaces(LHSWorkspace=all_pks,
RHSWorkspace=wsname)
self._pfps.append(ADS.retrieve(wsname))
self._filepath = os.path.join(config['defaultsave.directory'],
'WISH_IntegratedSatellite.int')
SaveReflections(InputWorkspace=all_pks,
Filename=self._filepath,
Format='Jana')
self._all_pks = all_pks
def SCDCalibratePanels2DiagnosticsPlot(
peaksWorkspace: Union[PeaksWorkspace, str],
banknames: Union[str, List[str]] = None,
config: Dict[str, str] = {
"prefix": "fig",
"type": "png",
"saveto": ".",
"mode": "modern",
},
showPlots: bool = True,
) -> None:
"""
Generate diagnostic plots from SCDCalibratePanels2
@param peaksWorkspace: peaks workspace with calibrated instrument applied
@param banknames: bank(s) for diagnostics
@param config: plot configuration dictionary
type: ["png", "pdf", "jpeg"]
mode: ["modern", "legacy"]
@param showPlots: open diagnostics plots after generating them.
@returs: None
"""
# parse input
pws = mtd[peaksWorkspace] if isinstance(peaksWorkspace,
str) else peaksWorkspace
logging.info(f"Start diagnostics with {peaksWorkspace.name()}.")
# process all banks if banknames is None
if banknames is None:
banknames = set(
[pws.row(i)["BankName"] for i in range(pws.getNumberPeaks())])
elif isinstance(banknames, str):
banknames = [me.strip() for me in banknames.split(",")]
else:
pass
# one bank at a time
for bn in banknames:
logging.info(f"--processing bank: {bn}")
pws_filtered = FilterPeaks(
InputWorkspace=pws,
FilterVariable='h^2+k^2+l^2',
FilterValue=0,
Operator='>',
BankName=bn,
)
# generate the plot
figname = f"{config['prefix']}_{bn}.{config['type']}"
SCDCalibratePanels2DiagnosticsPlotBank(
filteredPeaksWS=pws_filtered,
figname=figname,
savedir=config["saveto"],
showPlots=showPlots,
mode=config["mode"],
)
# close backend handle
if not showPlots:
plt.close("all")
def runTest(self):
ws = LoadRaw(Filename='WISH00038237.raw', OutputWorkspace='38237')
ws = ConvertUnits(ws, 'dSpacing', OutputWorkspace='38237')
UB = np.array([[-0.00601763, 0.07397297, 0.05865706],
[ 0.05373321, 0.050198, -0.05651455],
[-0.07822144, 0.0295911, -0.04489172]])
SetUB(ws, UB=UB)
self._peaks = PredictPeaks(ws, WavelengthMin=0.1, WavelengthMax=100,
OutputWorkspace='peaks')
# We specifically want to check peak -5 -1 -7 exists, so filter for it
self._filtered = FilterPeaks(self._peaks, "h^2+k^2+l^2", 75, '=',
OutputWorkspace='filtered')
SaveIsawPeaks(self._peaks, Filename='WISHSXReductionPeaksTest.peaks')
def runTest(self):
ws = LoadRaw(Filename='WISH00038237.raw', OutputWorkspace='38237')
ws = ConvertUnits(ws, 'dSpacing', OutputWorkspace='38237')
UB = np.array([[-0.00601763, 0.07397297, 0.05865706],
[ 0.05373321, 0.050198, -0.05651455],
[-0.07822144, 0.0295911, -0.04489172]])
SetUB(ws, UB=UB)
self._peaks = PredictPeaks(ws, WavelengthMin=0.1, WavelengthMax=100,
OutputWorkspace='peaks')
# We specifically want to check peak -5 -1 -7 exists, so filter for it
self._filtered = FilterPeaks(self._peaks, "h^2+k^2+l^2", 75, '=',
OutputWorkspace='filtered')
SaveIsawPeaks(self._peaks, Filename='WISHSXReductionPeaksTest.peaks')
class WISHSingleCrystalPeakPredictionTest(MantidSystemTest):
"""
At the time of writing WISH users rely quite heavily on the PredictPeaks
algorithm. As WISH has tubes rather than rectangular detectors sometimes
peaks fall between the gaps in the tubes.
Here we check that PredictPeaks works on a real WISH dataset & UB. This also
includes an example of a peak whose center is predicted to fall between two
tubes.
"""
def requiredFiles(self):
return ["WISHPredictedSingleCrystalPeaks.nxs"]
def cleanup(self):
ADS.clear()
try:
os.remove(self._peaks_file)
except:
pass
def runTest(self):
ws = LoadEmptyInstrument(InstrumentName='WISH')
UB = np.array([[-0.00601763, 0.07397297, 0.05865706],
[0.05373321, 0.050198, -0.05651455],
[-0.07822144, 0.0295911, -0.04489172]])
SetUB(ws, UB=UB)
self._peaks = PredictPeaks(ws,
WavelengthMin=0.1,
WavelengthMax=100,
OutputWorkspace='peaks')
# We specifically want to check peak -5 -1 -7 exists, so filter for it
self._filtered = FilterPeaks(self._peaks,
"h^2+k^2+l^2",
75,
'=',
OutputWorkspace='filtered')
SaveIsawPeaks(self._peaks, Filename='WISHSXReductionPeaksTest.peaks')
def validate(self):
self.assertEqual(self._peaks.rowCount(), 527)
self.assertEqual(self._filtered.rowCount(), 7)
# The peak at [-5 -1 -7] is known to fall between the gaps of WISH's tubes
# Specifically check this one is predicted to exist because past bugs have
# been found in the ray tracing.
BasicPeak = namedtuple('Peak', ('DetID', 'BankName', 'h', 'k', 'l'))
expected = BasicPeak(DetID=9202086,
BankName='WISHpanel09',
h=-5.0,
k=-1.0,
l=-7.0)
expected_peak_found = False
peak_count = self._filtered.rowCount()
for i in range(
peak_count
): # iterate of the table representation of the PeaksWorkspace
peak_row = self._filtered.row(i)
peak = BasicPeak(**{k: peak_row[k] for k in BasicPeak._fields})
if peak == expected:
expected_peak_found = True
break
self.assertTrue(
expected_peak_found,
msg="Peak at {} expected but it was not found".format(expected))
self._peaks_file = os.path.join(config['defaultsave.directory'],
'WISHSXReductionPeaksTest.peaks')
self.assertTrue(os.path.isfile(self._peaks_file))
return self._peaks.name(), "WISHPredictedSingleCrystalPeaks.nxs"
def PyExec(self):
# create peaks workspace to store linked peaks
linked_peaks = CreatePeaksWorkspace(
InstrumentWorkspace=self._workspace,
NumberOfPeaks=0,
StoreInADS=False)
# create peaks table to store linked predicted peaks
linked_peaks_predicted = CreatePeaksWorkspace(
InstrumentWorkspace=self._workspace,
NumberOfPeaks=0,
StoreInADS=False)
for m in range(0, self._iterations):
if m == 0:
predictor = self._predicted_peaks
if m > 0:
predictor = linked_peaks_predicted
qtol_var = self._qtol * self._qdecrement**m
num_peaks_var = self._num_peaks + self._peak_increment * m
# add q_lab and dpsacing values of found peaks to a list
qlabs_observed = np.array(self._observed_peaks.column("QLab"))
dspacings_observed = np.array(
self._observed_peaks.column("DSpacing"))
# sort the predicted peaks from largest to smallest dspacing
qlabs_predicted = np.array(predictor.column("QLab"))
dspacings_predicted = np.array(predictor.column("DSpacing"))
# get the indexing list that sorts dspacing from largest to
# smallest
hkls = np.array([[p.getH(), p.getK(), p.getL()]
for p in predictor])
idx = dspacings_predicted.argsort()[::-1]
HKL_predicted = hkls[idx, :]
# sort q, d and h, k, l by this indexing
qlabs_predicted = qlabs_predicted[idx]
dspacings_predicted = dspacings_predicted[idx]
q_ordered = qlabs_predicted[:num_peaks_var]
d_ordered = dspacings_predicted[:num_peaks_var]
HKL_ordered = HKL_predicted[:num_peaks_var]
# loop through the ordered find peaks, compare q and d to each
# predicted peak if the q and d values of a found peak match a
# predicted peak within tolerance, the found peak inherits
# the HKL of the predicted peak
for i in range(len(qlabs_observed)):
qx_obs, qy_obs, qz_obs = qlabs_observed[i]
q_obs = V3D(qx_obs, qy_obs, qz_obs)
p_obs = linked_peaks.createPeak(q_obs)
d_obs = dspacings_observed[i]
for j in range(len(q_ordered)):
qx_pred, qy_pred, qz_pred = q_ordered[j]
d_pred = d_ordered[j]
if (qx_pred - qtol_var <= qx_obs <= qx_pred + qtol_var and
qy_pred - qtol_var <= qy_obs <= qy_pred + qtol_var
and
qz_pred - qtol_var <= qz_obs <= qz_pred + qtol_var
and d_pred - self._dtol <= d_obs <=
d_pred + self._dtol):
h, k, l = HKL_ordered[j]
p_obs.setHKL(h, k, l)
linked_peaks.addPeak(p_obs)
# Clean up peaks where H == K == L == 0
linked_peaks = FilterPeaks(linked_peaks,
FilterVariable="h^2+k^2+l^2",
Operator="!=",
FilterValue="0")
# force UB on linked_peaks using known lattice parameters
CalculateUMatrix(PeaksWorkspace=linked_peaks,
a=self._a,
b=self._b,
c=self._c,
alpha=self._alpha,
beta=self._beta,
gamma=self._gamma,
StoreInADS=False)
# new linked predicted peaks
linked_peaks_predicted = PredictPeaks(
InputWorkspace=linked_peaks,
WavelengthMin=self._wavelength_min,
WavelengthMax=self._wavelength_max,
MinDSpacing=self._min_dspacing,
MaxDSpacing=self._max_dspacing,
ReflectionCondition=self._reflection_condition,
StoreInADS=False)
# clean up
self.setProperty("LinkedPeaks", linked_peaks)
self.setProperty("LinkedPredictedPeaks", linked_peaks_predicted)
if mtd.doesExist("linked_peaks"):
DeleteWorkspace(linked_peaks)
if mtd.doesExist("linked_peaks_predicted"):
DeleteWorkspace(linked_peaks_predicted)
if self._delete_ws:
DeleteWorkspace(self._workspace)
class WISHSingleCrystalPeakPredictionTest(MantidSystemTest):
"""
At the time of writing WISH users rely quite heavily on the PredictPeaks
algorithm. As WISH has tubes rather than rectangular detectors sometimes
peaks fall between the gaps in the tubes.
Here we check that PredictPeaks works on a real WISH dataset & UB. This also
includes an example of a peak whose center is predicted to fall between two
tubes.
"""
def requiredFiles(self):
return ["WISH00038237.raw", "WISHPredictedSingleCrystalPeaks.nxs"]
def requiredMemoryMB(self):
# Need lots of memory for full WISH dataset
return 24000
def cleanup(self):
try:
os.path.remove(self._peaks_file)
except:
pass
def runTest(self):
ws = LoadRaw(Filename='WISH00038237.raw', OutputWorkspace='38237')
ws = ConvertUnits(ws, 'dSpacing', OutputWorkspace='38237')
UB = np.array([[-0.00601763, 0.07397297, 0.05865706],
[0.05373321, 0.050198, -0.05651455],
[-0.07822144, 0.0295911, -0.04489172]])
SetUB(ws, UB=UB)
self._peaks = PredictPeaks(ws,
WavelengthMin=0.1,
WavelengthMax=100,
OutputWorkspace='peaks')
# We specifically want to check peak -5 -1 -7 exists, so filter for it
self._filtered = FilterPeaks(self._peaks,
"h^2+k^2+l^2",
75,
'=',
OutputWorkspace='filtered')
SaveIsawPeaks(self._peaks, Filename='WISHSXReductionPeaksTest.peaks')
def validate(self):
self.assertEqual(self._peaks.rowCount(), 510)
self.assertEqual(self._filtered.rowCount(), 6)
# The peak at [-5 -1 -7] is known to fall between the gaps of WISH's tubes
# Specifically check this one is predicted to exist because past bugs have
# been found in the ray tracing.
BasicPeak = namedtuple('Peak', ('DetID', 'BankName', 'h', 'k', 'l'))
expected = BasicPeak(DetID=9202086,
BankName='WISHpanel09',
h=-5.0,
k=-1.0,
l=-7.0)
expected_peak_found = False
for full_peak in self._filtered:
peak = BasicPeak(DetID=full_peak.getDetectorID(),
BankName=full_peak.getBankName(),
h=full_peak.getH(),
k=full_peak.getK(),
l=full_peak.getL())
if peak == expected:
expected_peak_found = True
break
#endfor
self.assertTrue(
expected_peak_found,
msg="Peak at {} expected but it was not found".format(expected))
self._peaks_file = os.path.join(config['defaultsave.directory'],
'WISHSXReductionPeaksTest.peaks')
self.assertTrue(os.path.isfile(self._peaks_file))
return self._peaks.name(), "WISHPredictedSingleCrystalPeaks.nxs"
def PyExec(self):
input_workspaces, peak_workspaces = self._expand_groups()
output_workspace_name = self.getPropertyValue("OutputWorkspace")
peak_radius = self.getProperty("PeakRadius").value
inner_radius = self.getProperty("BackgroundInnerRadius").value
outer_radius = self.getProperty("BackgroundOuterRadius").value
remove_0_intensity = self.getProperty("RemoveZeroIntensity").value
use_lorentz = self.getProperty("ApplyLorentz").value
multi_ws = len(input_workspaces) > 1
output_workspaces = []
for input_ws, peak_ws in zip(input_workspaces, peak_workspaces):
if multi_ws:
peaks_ws_name = input_ws + '_' + output_workspace_name
output_workspaces.append(peaks_ws_name)
else:
peaks_ws_name = output_workspace_name
IntegratePeaksMD(InputWorkspace=input_ws,
PeakRadius=peak_radius,
BackgroundInnerRadius=inner_radius,
BackgroundOuterRadius=outer_radius,
PeaksWorkspace=peak_ws,
OutputWorkspace=peaks_ws_name)
if multi_ws:
peaks_ws_name = output_workspace_name
CreatePeaksWorkspace(
InstrumentWorkspace=input_workspaces[0],
NumberOfPeaks=0,
OutputWorkspace=peaks_ws_name,
OutputType=mtd[peak_workspaces[0]].id().replace(
'sWorkspace', ''))
CopySample(InputWorkspace=output_workspaces[0],
OutputWorkspace=peaks_ws_name,
CopyName=False,
CopyMaterial=False,
CopyEnvironment=False,
CopyShape=False,
CopyLattice=True)
for peak_ws in output_workspaces:
CombinePeaksWorkspaces(peaks_ws_name,
peak_ws,
OutputWorkspace=peaks_ws_name)
DeleteWorkspace(peak_ws)
if use_lorentz:
# Apply Lorentz correction:
peaks = AnalysisDataService[peaks_ws_name]
for p in range(peaks.getNumberPeaks()):
peak = peaks.getPeak(p)
lorentz = abs(
np.sin(peak.getScattering() * np.cos(peak.getAzimuthal())))
peak.setIntensity(peak.getIntensity() * lorentz)
if remove_0_intensity:
FilterPeaks(InputWorkspace=peaks_ws_name,
OutputWorkspace=peaks_ws_name,
FilterVariable='Intensity',
FilterValue=0,
Operator='>')
# Write output only if a file path was provided
if not self.getProperty("OutputFile").isDefault:
out_format = self.getProperty("OutputFormat").value
filename = self.getProperty("OutputFile").value
if out_format == "SHELX":
SaveHKL(InputWorkspace=peaks_ws_name,
Filename=filename,
DirectionCosines=True,
OutputWorkspace="__tmp")
DeleteWorkspace("__tmp")
elif out_format == "Fullprof":
SaveReflections(InputWorkspace=peaks_ws_name,
Filename=filename,
Format="Fullprof")
else:
# This shouldn't happen
RuntimeError("Invalid output format given")
self.setProperty("OutputWorkspace", AnalysisDataService[peaks_ws_name])
class WISHSingleCrystalPeakPredictionTest(MantidSystemTest):
"""
At the time of writing WISH users rely quite heavily on the PredictPeaks
algorithm. As WISH has tubes rather than rectangular detectors sometimes
peaks fall between the gaps in the tubes.
Here we check that PredictPeaks works on a real WISH dataset & UB. This also
includes an example of a peak whose center is predicted to fall between two
tubes.
"""
def requiredFiles(self):
return ["WISH00038237.raw", "WISHPredictedSingleCrystalPeaks.nxs"]
def requiredMemoryMB(self):
# Need lots of memory for full WISH dataset
return 16000
def cleanup(self):
try:
os.path.remove(self._peaks_file)
except:
pass
def runTest(self):
ws = LoadRaw(Filename='WISH00038237.raw', OutputWorkspace='38237')
ws = ConvertUnits(ws, 'dSpacing', OutputWorkspace='38237')
UB = np.array([[-0.00601763, 0.07397297, 0.05865706],
[ 0.05373321, 0.050198, -0.05651455],
[-0.07822144, 0.0295911, -0.04489172]])
SetUB(ws, UB=UB)
self._peaks = PredictPeaks(ws, WavelengthMin=0.1, WavelengthMax=100,
OutputWorkspace='peaks')
# We specifically want to check peak -5 -1 -7 exists, so filter for it
self._filtered = FilterPeaks(self._peaks, "h^2+k^2+l^2", 75, '=',
OutputWorkspace='filtered')
SaveIsawPeaks(self._peaks, Filename='WISHSXReductionPeaksTest.peaks')
def validate(self):
self.assertEqual(self._peaks.rowCount(), 510)
self.assertEqual(self._filtered.rowCount(), 6)
# The peak at [-5 -1 -7] is known to fall between the gaps of WISH's tubes
# Specifically check this one is predicted to exist because past bugs have
# been found in the ray tracing.
Peak = namedtuple('Peak', ('DetID', 'BankName', 'h', 'k', 'l'))
expected = Peak(DetID=9202086, BankName='WISHpanel09', h=-5.0, k=-1.0, l=-7.0)
expected_peak_found = False
for row in self._filtered:
peak = Peak(DetID=row['DetID'], BankName=row['BankName'], h=row['h'], k=row['k'], l=row['l'])
if peak == expected:
expected_peak_found = True
break
#endfor
self.assertTrue(expected_peak_found, msg="Peak at {} expected but it was not found".format(expected))
self._peaks_file = os.path.join(config['defaultsave.directory'], 'WISHSXReductionPeaksTest.peaks')
self.assertTrue(os.path.isfile(self._peaks_file))
return self._peaks.name(), "WISHPredictedSingleCrystalPeaks.nxs"