def create_fake_dns_workspace(wsname, angle=-7.53, flipper='ON', dataY=None, loadinstrument=False):
"""
creates DNS workspace with fake data
@param angle Angle of detector bank rotation
@param flipper Flipper state (ON/OFF)
@param dataY Data array to set as DataY of the created workspace, will be set to np.ones if None
@param loadinstrument If True api.LoadInstrument will be executed, needed for DNSMergeRuns
"""
ndet = 24
dataX = np.zeros(2*ndet)
dataX.fill(4.2 + 0.00001)
dataX[::2] -= 0.000002
if dataY is None:
dataY = np.ones(ndet)
dataE = np.sqrt(dataY)
# create workspace
api.CreateWorkspace(OutputWorkspace=wsname, DataX=dataX, DataY=dataY,
DataE=dataE, NSpec=ndet, UnitX="Wavelength")
outws = api.mtd[wsname]
p_names = 'deterota,wavelength,slit_i_left_blade_position,slit_i_right_blade_position,normalized,\
slit_i_lower_blade_position,slit_i_upper_blade_position,polarisation,polarisation_comment,flipper'
p_values = str(angle) + ',4.2,10,10,duration,5,20,x,7a,' + flipper
api.AddSampleLogMultiple(Workspace=outws, LogNames=p_names, LogValues=p_values, ParseType=True)
# rotate instrument component
if loadinstrument:
api.LoadInstrument(outws, InstrumentName='DNS', RewriteSpectraMap=True)
api.RotateInstrumentComponent(outws, "bank0", X=0, Y=1, Z=0, Angle=angle)
return outws
def adjustComponent(self, component, pos, rot):
wks_name = self.wks_name
if pos:
msa.MoveInstrumentComponent(wks_name, component, X=pos[0], Y=pos[1], Z=pos[2], RelativePosition=False)
if rot:
(rotw, rotx, roty, rotz) = eulerToAngleAxis(rot[0], rot[1], rot[2], self.eulerConvention)
msa.RotateInstrumentComponent(
wks_name, component, X=rotx, Y=roty, Z=rotz, Angle=rotw, RelativeRotation=False)
return
def _minimisation_func(self, x_0, wks_name, component, firstIndex,
lastIndex, difc, mask):
"""
Basic minimization function used. Returns the chisquared difference between the expected
difc and the new difc after the component has been moved or rotated.
"""
xmap = self._mapOptions(x_0)
if self._move:
api.MoveInstrumentComponent(wks_name,
component,
X=xmap[0],
Y=xmap[1],
Z=xmap[2],
RelativePosition=False)
if self._rotate:
(rotw, rotx, roty,
rotz) = self._eulerToAngleAxis(xmap[3], xmap[4], xmap[5],
self._eulerConvention) # YZX
api.RotateInstrumentComponent(wks_name,
component,
X=rotx,
Y=roty,
Z=rotz,
Angle=rotw,
RelativeRotation=False)
api.CalculateDIFC(InputWorkspace=wks_name, OutputWorkspace=wks_name)
difc_new = api.mtd[wks_name].extractY().flatten(
)[firstIndex:lastIndex + 1]
if self._masking:
difc_new = np.ma.masked_array(difc_new, mask)
return chisquare(f_obs=difc, f_exp=difc_new)[0]
def test_DNSTwoTheta(self):
outputWorkspaceName = "DNSFlippingRatioCorrTest_Test5"
# rotate detector bank to different angles
dataws_sf = self.__sf_nicrws - self.__sf_bkgrws
dataws_nsf = self.__nsf_nicrws - self.__nsf_bkgrws
wslist = [dataws_sf, dataws_nsf, self.__sf_nicrws, self.__nsf_nicrws, self.__sf_bkgrws, self.__nsf_bkgrws]
for wks in wslist:
api.LoadInstrument(wks, InstrumentName='DNS', RewriteSpectraMap=True)
api.RotateInstrumentComponent(dataws_sf, "bank0", X=0, Y=1, Z=0, Angle=-7.53)
api.RotateInstrumentComponent(dataws_nsf, "bank0", X=0, Y=1, Z=0, Angle=-7.53)
api.RotateInstrumentComponent(self.__sf_nicrws, "bank0", X=0, Y=1, Z=0, Angle=-8.02)
api.RotateInstrumentComponent(self.__nsf_nicrws, "bank0", X=0, Y=1, Z=0, Angle=-8.02)
api.RotateInstrumentComponent(self.__sf_bkgrws, "bank0", X=0, Y=1, Z=0, Angle=-8.54)
api.RotateInstrumentComponent(self.__nsf_bkgrws, "bank0", X=0, Y=1, Z=0, Angle=-8.54)
# apply correction
alg_test = run_algorithm("DNSFlippingRatioCorr", SFDataWorkspace=dataws_sf,
NSFDataWorkspace=dataws_nsf, SFNiCrWorkspace=self.__sf_nicrws.getName(),
NSFNiCrWorkspace=self.__nsf_nicrws.getName(), SFBkgrWorkspace=self.__sf_bkgrws.getName(),
NSFBkgrWorkspace=self.__nsf_bkgrws.getName(), SFOutputWorkspace=outputWorkspaceName+'SF',
NSFOutputWorkspace=outputWorkspaceName+'NSF')
self.assertTrue(alg_test.isExecuted())
ws_sf = AnalysisDataService.retrieve(outputWorkspaceName + 'SF')
ws_nsf = AnalysisDataService.retrieve(outputWorkspaceName + 'NSF')
# dimensions
self.assertEqual(24, ws_sf.getNumberHistograms())
self.assertEqual(24, ws_nsf.getNumberHistograms())
self.assertEqual(2, ws_sf.getNumDims())
self.assertEqual(2, ws_nsf.getNumDims())
# 2theta angles must not change after correction has been applied
tthetas = np.array([7.53 + i*5 for i in range(24)])
for i in range(24):
det = ws_sf.getDetector(i)
self.assertAlmostEqual(tthetas[i], np.degrees(ws_sf.detectorSignedTwoTheta(det)))
det = ws_nsf.getDetector(i)
self.assertAlmostEqual(tthetas[i], np.degrees(ws_nsf.detectorSignedTwoTheta(det)))
run_algorithm("DeleteWorkspace", Workspace=outputWorkspaceName + 'SF')
run_algorithm("DeleteWorkspace", Workspace=outputWorkspaceName + 'NSF')
run_algorithm("DeleteWorkspace", Workspace=dataws_sf)
run_algorithm("DeleteWorkspace", Workspace=dataws_nsf)
return
def PyExec(self):
self._eulerConvention = self.getProperty('EulerConvention').value
calWS = self.getProperty('CalibrationTable').value
calWS = api.SortTableWorkspace(calWS, Columns='detid')
maskWS = self.getProperty("MaskWorkspace").value
difc = calWS.column('difc')
if maskWS is not None:
self._masking = True
mask = maskWS.extractY().flatten()
difc = np.ma.masked_array(difc, mask)
detID = calWS.column('detid')
if self.getProperty("Workspace").value is not None:
wks_name = self.getProperty("Workspace").value.name()
else:
wks_name = "alignedWorkspace"
api.LoadEmptyInstrument(
Filename=self.getProperty("InstrumentFilename").value,
OutputWorkspace=wks_name)
# Make a dictionary of what options are being refined for sample/source. No rotation.
for opt in self._optionsList[:3]:
self._optionsDict[opt] = self.getProperty(opt).value
for opt in self._optionsList[3:]:
self._optionsDict[opt] = False
# First fit L1 if selected for Source and/or Sample
for component in "Source", "Sample":
if self.getProperty("Fit" + component + "Position").value:
self._move = True
if component == "Sample":
comp = api.mtd[wks_name].getInstrument().getSample()
else:
comp = api.mtd[wks_name].getInstrument().getSource()
componentName = comp.getFullName()
logger.notice("Working on " + componentName +
" Starting position is " + str(comp.getPos()))
firstIndex = 0
lastIndex = len(difc)
if self._masking:
mask_out = mask[firstIndex:lastIndex + 1]
else:
mask_out = None
self._initialPos = [
comp.getPos().getX(),
comp.getPos().getY(),
comp.getPos().getZ(), 0, 0, 0
]
# Set up x0 and bounds lists
x0List = []
boundsList = []
for iopt, opt in enumerate(self._optionsList[:3]):
if self._optionsDict[opt]:
x0List.append(self._initialPos[iopt])
boundsList.append(
(self._initialPos[iopt] +
self.getProperty("Min" + opt).value,
self._initialPos[iopt] +
self.getProperty("Max" + opt).value))
results = minimize(self._minimisation_func,
x0=x0List,
method='L-BFGS-B',
args=(wks_name, componentName, firstIndex,
lastIndex, difc[firstIndex:lastIndex +
1], mask_out),
bounds=boundsList)
# Apply the results to the output workspace
xmap = self._mapOptions(results.x)
# Need to grab the component again, as things have changed
api.MoveInstrumentComponent(wks_name,
componentName,
X=xmap[0],
Y=xmap[1],
Z=xmap[2],
RelativePosition=False)
comp = api.mtd[wks_name].getInstrument().getComponentByName(
componentName)
logger.notice("Finished " + componentName +
" Final position is " + str(comp.getPos()))
self._move = False
# Now fit all the components if any
components = self.getProperty("ComponentList").value
# Make a dictionary of what options are being refined.
for opt in self._optionsList:
self._optionsDict[opt] = self.getProperty(opt).value
self._move = (self._optionsDict["Xposition"]
or self._optionsDict["Yposition"]
or self._optionsDict["Zposition"])
self._rotate = (self._optionsDict["AlphaRotation"]
or self._optionsDict["BetaRotation"]
or self._optionsDict["GammaRotation"])
prog = Progress(self, start=0, end=1, nreports=len(components))
for component in components:
comp = api.mtd[wks_name].getInstrument().getComponentByName(
component)
firstDetID = self._getFirstDetID(comp)
firstIndex = detID.index(firstDetID)
lastDetID = self._getLastDetID(comp)
lastIndex = detID.index(lastDetID)
if lastDetID - firstDetID != lastIndex - firstIndex:
raise RuntimeError(
"Calibration detid doesn't match instrument")
eulerAngles = comp.getRotation().getEulerAngles(
self._eulerConvention)
logger.notice("Working on " + comp.getFullName() +
" Starting position is " + str(comp.getPos()) +
" Starting rotation is " + str(eulerAngles))
x0List = []
self._initialPos = [
comp.getPos().getX(),
comp.getPos().getY(),
comp.getPos().getZ(), eulerAngles[0], eulerAngles[1],
eulerAngles[2]
]
boundsList = []
if self._masking:
mask_out = mask[firstIndex:lastIndex + 1]
if mask_out.sum() == mask_out.size:
self.log().warning(
"All pixels in '%s' are masked. Skipping calibration."
% component)
continue
else:
mask_out = None
for iopt, opt in enumerate(self._optionsList):
if self._optionsDict[opt]:
x0List.append(self._initialPos[iopt])
boundsList.append((self._initialPos[iopt] +
self.getProperty("Min" + opt).value,
self._initialPos[iopt] +
self.getProperty("Max" + opt).value))
results = minimize(self._minimisation_func,
x0=x0List,
method='L-BFGS-B',
args=(wks_name, component, firstIndex,
lastIndex, difc[firstIndex:lastIndex + 1],
mask_out),
bounds=boundsList)
# Apply the results to the output workspace
xmap = self._mapOptions(results.x)
if self._move:
api.MoveInstrumentComponent(wks_name,
component,
X=xmap[0],
Y=xmap[1],
Z=xmap[2],
RelativePosition=False)
if self._rotate:
(rotw, rotx, roty,
rotz) = self._eulerToAngleAxis(xmap[3], xmap[4], xmap[5],
self._eulerConvention)
api.RotateInstrumentComponent(wks_name,
component,
X=rotx,
Y=roty,
Z=rotz,
Angle=rotw,
RelativeRotation=False)
# Need to grab the component again, as things have changed
comp = api.mtd[wks_name].getInstrument().getComponentByName(
component)
logger.notice(
"Finshed " + comp.getFullName() + " Final position is " +
str(comp.getPos()) + " Final rotation is " +
str(comp.getRotation().getEulerAngles(self._eulerConvention)))
prog.report()
logger.notice("Results applied to workspace " + wks_name)
def PyExec(self):
# Input
filename = self.getPropertyValue("Filename")
outws_name = self.getPropertyValue("OutputWorkspace")
norm = self.getPropertyValue("Normalization")
# load data array from the given file
data_array = np.loadtxt(filename)
if not data_array.size:
message = "File " + filename + " does not contain any data!"
self.log().error(message)
raise RuntimeError(message)
# sample logs
logs = {"names": [], "values": [], "units": []}
# load run information
metadata = DNSdata()
try:
metadata.read_legacy(filename)
except RuntimeError as err:
message = "Error of loading of file " + filename + ": " + str(err)
self.log().error(message)
raise RuntimeError(message)
tmp = api.LoadEmptyInstrument(InstrumentName='DNS')
self.instrument = tmp.getInstrument()
api.DeleteWorkspace(tmp)
# load polarisation table and determine polarisation
poltable = self.get_polarisation_table()
pol = self.get_polarisation(metadata, poltable)
if not pol:
pol = ['0', 'undefined']
self.log().warning("Failed to determine polarisation for " +
filename +
". Values have been set to undefined.")
ndet = 24
unitX = "Wavelength"
if metadata.tof_channel_number < 2:
dataX = np.zeros(2 * ndet)
dataX.fill(metadata.wavelength + 0.00001)
dataX[::2] -= 0.000002
else:
unitX = "TOF"
# get instrument parameters
l1 = np.linalg.norm(self.instrument.getSample().getPos() -
self.instrument.getSource().getPos())
self.log().notice("L1 = {} m".format(l1))
dt_factor = float(
self.instrument.getStringParameter("channel_width_factor")[0])
# channel width
dt = metadata.tof_channel_width * dt_factor
# calculate tof1
velocity = h / (m_n * metadata.wavelength * 1e-10) # m/s
tof1 = 1e+06 * l1 / velocity # microseconds
self.log().debug("TOF1 = {} microseconds".format(tof1))
self.log().debug("Delay time = {} microsecond".format(
metadata.tof_delay_time))
# create dataX array
x0 = tof1 + metadata.tof_delay_time
self.log().debug("TOF1 = {} microseconds".format(tof1))
dataX = np.linspace(x0, x0 + metadata.tof_channel_number * dt,
metadata.tof_channel_number + 1)
# sample logs
logs["names"].extend(
["channel_width", "TOF1", "delay_time", "tof_channels"])
logs["values"].extend([
dt, tof1, metadata.tof_delay_time, metadata.tof_channel_number
])
logs["units"].extend(
["microseconds", "microseconds", "microseconds", ""])
if metadata.tof_elastic_channel:
logs["names"].append("EPP")
logs["values"].append(metadata.tof_elastic_channel)
logs["units"].append("")
if metadata.chopper_rotation_speed:
logs["names"].append("chopper_speed")
logs["values"].append(metadata.chopper_rotation_speed)
logs["units"].append("Hz")
if metadata.chopper_slits:
logs["names"].append("chopper_slits")
logs["values"].append(metadata.chopper_slits)
logs["units"].append("")
# data normalization
factor = 1.0
yunit = "Counts"
ylabel = "Intensity"
if norm == 'duration':
factor = metadata.duration
yunit = "Counts/s"
ylabel = "Intensity normalized to duration"
if factor <= 0:
raise RuntimeError("Duration is invalid for file " + filename +
". Cannot normalize.")
if norm == 'monitor':
factor = metadata.monitor_counts
yunit = "Counts/monitor"
ylabel = "Intensity normalized to monitor"
if factor <= 0:
raise RuntimeError("Monitor counts are invalid for file " +
filename + ". Cannot normalize.")
# set values for dataY and dataE
dataY = data_array[0:ndet, 1:] / factor
dataE = np.sqrt(data_array[0:ndet, 1:]) / factor
# create workspace
api.CreateWorkspace(OutputWorkspace=outws_name,
DataX=dataX,
DataY=dataY,
DataE=dataE,
NSpec=ndet,
UnitX=unitX)
outws = api.AnalysisDataService.retrieve(outws_name)
api.LoadInstrument(outws, InstrumentName='DNS', RewriteSpectraMap=True)
run = outws.mutableRun()
if metadata.start_time and metadata.end_time:
run.setStartAndEndTime(DateAndTime(metadata.start_time),
DateAndTime(metadata.end_time))
# add name of file as a run title
fname = os.path.splitext(os.path.split(filename)[1])[0]
run.addProperty('run_title', fname, True)
# rotate the detector bank to the proper position
api.RotateInstrumentComponent(outws,
"bank0",
X=0,
Y=1,
Z=0,
Angle=metadata.deterota)
# add sample log Ei and wavelength
logs["names"].extend(["Ei", "wavelength"])
logs["values"].extend([metadata.incident_energy, metadata.wavelength])
logs["units"].extend(["meV", "Angstrom"])
# add other sample logs
logs["names"].extend([
"deterota", "mon_sum", "duration", "huber", "omega", "T1", "T2",
"Tsp"
])
logs["values"].extend([
metadata.deterota, metadata.monitor_counts, metadata.duration,
metadata.huber, metadata.huber - metadata.deterota, metadata.temp1,
metadata.temp2, metadata.tsp
])
logs["units"].extend([
"Degrees", "Counts", "Seconds", "Degrees", "Degrees", "K", "K", "K"
])
# flipper, coil currents and polarisation
flipper_status = 'OFF' # flipper OFF
if abs(metadata.flipper_precession_current) > sys.float_info.epsilon:
flipper_status = 'ON' # flipper ON
logs["names"].extend([
"flipper_precession", "flipper_z_compensation", "flipper", "C_a",
"C_b", "C_c", "C_z", "polarisation", "polarisation_comment"
])
logs["values"].extend([
metadata.flipper_precession_current,
metadata.flipper_z_compensation_current, flipper_status,
metadata.a_coil_current, metadata.b_coil_current,
metadata.c_coil_current, metadata.z_coil_current,
str(pol[0]),
str(pol[1])
])
logs["units"].extend(["A", "A", "", "A", "A", "A", "A", "", ""])
# slits
logs["names"].extend([
"slit_i_upper_blade_position", "slit_i_lower_blade_position",
"slit_i_left_blade_position", "slit_i_right_blade_position"
])
logs["values"].extend([
metadata.slit_i_upper_blade_position,
metadata.slit_i_lower_blade_position,
metadata.slit_i_left_blade_position,
metadata.slit_i_right_blade_position
])
logs["units"].extend(["mm", "mm", "mm", "mm"])
# add information whether the data are normalized (duration/monitor/no):
api.AddSampleLog(outws,
LogName='normalized',
LogText=norm,
LogType='String')
api.AddSampleLogMultiple(outws,
LogNames=logs["names"],
LogValues=logs["values"],
LogUnits=logs["units"])
outws.setYUnit(yunit)
outws.setYUnitLabel(ylabel)
self.setProperty("OutputWorkspace", outws)
self.log().debug('LoadDNSLegacy: data are loaded to the workspace ' +
outws_name)
return
def PyExec(self):
# Input
filename = self.getPropertyValue("Filename")
outws_name = self.getPropertyValue("OutputWorkspace")
norm = self.getPropertyValue("Normalization")
# load data array from the given file
data_array = np.loadtxt(filename)
if not data_array.size:
message = "File " + filename + " does not contain any data!"
self.log().error(message)
raise RuntimeError(message)
# load run information
metadata = DNSdata()
try:
metadata.read_legacy(filename)
except RuntimeError as err:
message = "Error of loading of file " + filename + ": " + str(err)
self.log().error(message)
raise RuntimeError(message)
# load polarisation table and determine polarisation
poltable = self.get_polarisation_table()
pol = self.get_polarisation(metadata, poltable)
if not pol:
pol = ['0', 'undefined']
self.log().warning("Failed to determine polarisation for " + filename +
". Values have been set to undefined.")
ndet = 24
# this needed to be able to use ConvertToMD
dataX = np.zeros(2*ndet)
dataX.fill(metadata.wavelength + 0.00001)
dataX[::2] -= 0.000002
# data normalization
factor = 1.0
yunit = "Counts"
ylabel = "Intensity"
if norm == 'duration':
factor = metadata.duration
yunit = "Counts/s"
ylabel = "Intensity normalized to duration"
if factor <= 0:
raise RuntimeError("Duration is invalid for file " + filename + ". Cannot normalize.")
if norm == 'monitor':
factor = metadata.monitor_counts
yunit = "Counts/monitor"
ylabel = "Intensity normalized to monitor"
if factor <= 0:
raise RuntimeError("Monitor counts are invalid for file " + filename + ". Cannot normalize.")
# set values for dataY and dataE
dataY = data_array[0:ndet, 1:]/factor
dataE = np.sqrt(data_array[0:ndet, 1:])/factor
# create workspace
api.CreateWorkspace(OutputWorkspace=outws_name, DataX=dataX, DataY=dataY,
DataE=dataE, NSpec=ndet, UnitX="Wavelength")
outws = api.AnalysisDataService.retrieve(outws_name)
api.LoadInstrument(outws, InstrumentName='DNS', RewriteSpectraMap=True)
run = outws.mutableRun()
if metadata.start_time and metadata.end_time:
run.setStartAndEndTime(DateAndTime(metadata.start_time),
DateAndTime(metadata.end_time))
# add name of file as a run title
fname = os.path.splitext(os.path.split(filename)[1])[0]
run.addProperty('run_title', fname, True)
# rotate the detector bank to the proper position
api.RotateInstrumentComponent(outws, "bank0", X=0, Y=1, Z=0, Angle=metadata.deterota)
# add sample log Ei and wavelength
api.AddSampleLog(outws, LogName='Ei', LogText=str(metadata.incident_energy),
LogType='Number', LogUnit='meV')
api.AddSampleLog(outws, LogName='wavelength', LogText=str(metadata.wavelength),
LogType='Number', LogUnit='Angstrom')
# add other sample logs
api.AddSampleLog(outws, LogName='deterota', LogText=str(metadata.deterota),
LogType='Number', LogUnit='Degrees')
api.AddSampleLog(outws, 'mon_sum',
LogText=str(float(metadata.monitor_counts)), LogType='Number')
api.AddSampleLog(outws, LogName='duration', LogText=str(metadata.duration),
LogType='Number', LogUnit='Seconds')
api.AddSampleLog(outws, LogName='huber', LogText=str(metadata.huber),
LogType='Number', LogUnit='Degrees')
api.AddSampleLog(outws, LogName='omega', LogText=str(metadata.huber - metadata.deterota),
LogType='Number', LogUnit='Degrees')
api.AddSampleLog(outws, LogName='T1', LogText=str(metadata.temp1),
LogType='Number', LogUnit='K')
api.AddSampleLog(outws, LogName='T2', LogText=str(metadata.temp2),
LogType='Number', LogUnit='K')
api.AddSampleLog(outws, LogName='Tsp', LogText=str(metadata.tsp),
LogType='Number', LogUnit='K')
# flipper
api.AddSampleLog(outws, LogName='flipper_precession',
LogText=str(metadata.flipper_precession_current),
LogType='Number', LogUnit='A')
api.AddSampleLog(outws, LogName='flipper_z_compensation',
LogText=str(metadata.flipper_z_compensation_current),
LogType='Number', LogUnit='A')
flipper_status = 'OFF' # flipper OFF
if abs(metadata.flipper_precession_current) > sys.float_info.epsilon:
flipper_status = 'ON' # flipper ON
api.AddSampleLog(outws, LogName='flipper',
LogText=flipper_status, LogType='String')
# coil currents
api.AddSampleLog(outws, LogName='C_a', LogText=str(metadata.a_coil_current),
LogType='Number', LogUnit='A')
api.AddSampleLog(outws, LogName='C_b', LogText=str(metadata.b_coil_current),
LogType='Number', LogUnit='A')
api.AddSampleLog(outws, LogName='C_c', LogText=str(metadata.c_coil_current),
LogType='Number', LogUnit='A')
api.AddSampleLog(outws, LogName='C_z', LogText=str(metadata.z_coil_current),
LogType='Number', LogUnit='A')
# type of polarisation
api.AddSampleLog(outws, 'polarisation', LogText=pol[0], LogType='String')
api.AddSampleLog(outws, 'polarisation_comment', LogText=str(pol[1]), LogType='String')
# slits
api.AddSampleLog(outws, LogName='slit_i_upper_blade_position',
LogText=str(metadata.slit_i_upper_blade_position),
LogType='Number', LogUnit='mm')
api.AddSampleLog(outws, LogName='slit_i_lower_blade_position',
LogText=str(metadata.slit_i_lower_blade_position),
LogType='Number', LogUnit='mm')
api.AddSampleLog(outws, LogName='slit_i_left_blade_position',
LogText=str(metadata.slit_i_left_blade_position),
LogType='Number', LogUnit='mm')
api.AddSampleLog(outws, 'slit_i_right_blade_position',
LogText=str(metadata.slit_i_right_blade_position),
LogType='Number', LogUnit='mm')
# data normalization
# add information whether the data are normalized (duration/monitor/no):
api.AddSampleLog(outws, LogName='normalized', LogText=norm, LogType='String')
outws.setYUnit(yunit)
outws.setYUnitLabel(ylabel)
self.setProperty("OutputWorkspace", outws)
self.log().debug('LoadDNSLegacy: data are loaded to the workspace ' + outws_name)
return
print("=========================================")
# Create workspace for current frame
ws_for_this_frame = createWorkspace(data_x=[f.wavelength],
data_y=f.IntensityUp,
data_e=np.sqrt(f.IntensityUp),
n_spec=f.x*f.y,
unit="Wavelength")
# Register the workspace in the mantid ADS
mantid.mtd.addOrReplace("ws_for_this_frame", ws_for_this_frame)
# Load the instrument from the definition file
mantid.LoadInstrument(ws_for_this_frame, FileName="5C1_Definition.xml",
RewriteSpectraMap=True)
# Rotate the instrument to the current gamma angle (in degrees)
mantid.RotateInstrumentComponent(ws_for_this_frame, "detector_panel",
X=0, Y=1, Z=0, Angle=f.Gamma,
RelativeRotation=False)
# Normalise by monitor counts
normalised = ws_for_this_frame / f.totalmonitorcount
# Convert to d-spacing
dspacing = mantid.ConvertUnits(InputWorkspace=normalised,
Target="dSpacing", EMode="Elastic")
# 1. Naive accumulation of workspace data: this does not seem to work
rebinned = mantid.Rebin(dspacing, "0.5,0.01,5.0")
if final is None:
final = mantid.CloneWorkspace(rebinned)
else:
final += rebinned
# 2. Try to extract 1D profile from equatorial plane
def _minimisation_func(self, x_0, wks_name, component, firstIndex,
lastIndex):
"""
Basic minimization function used. Returns the sum of the absolute values for the fractional peak
deviations:
.. math::
\\sum_i^{N_d}\\sum_j^{N_p} (1 - m_{i,j}) \\frac{|d_{i,j} - d_j^*|}{d_j^*}
where :math:`N_d` is the number of detectors in the bank, :math:`N_p` is the number of reference peaks, and
:math:`m_{i,j}` is the mask for peak :math:`j` and detector :math:`i`. The mask evaluates to 1 if the
detector is defective or the peak is missing in the detector, otherwise the mask evaluates to zero.
There's an implicit one-to-correspondence between array index of ``difc`` and workspace index of ``wks_name``,
that is, between row index of the input TOFS table and workspace index of ``wks_name``.
@param x_0 :: list of length 3 (new XYZ coordinates of the component) or length 6 (XYZ and rotation coords)
@param wks_name :: name of a workspace with an embedded instrument. The instrument will be adjusted according to
the new coordinates ``x_0`` for instrument component ``component``. It's pixel spectra will contain the new DIFC
@param component :: name of the instrument component to be optimized
@param firstIndex :: workspace index of first index of ``difc`` array to be considered when comparing old
and new DIFC values. When fitting the source or sample, this is the first spectrum index.
@param lastIndex :: workspace index of last index of ``difc`` array to be considered when comparing old
and new DIFC values. When fitting the source or sample, this is the last row number of the input
TOFS table.
@return Chi-square value between old and new DIFC values for the unmasked spectra
"""
xmap = self._mapOptions(
x_0) # pad null rotations when x_0 contains only translations
if self._move:
api.MoveInstrumentComponent(wks_name,
component,
X=xmap[0],
Y=xmap[1],
Z=xmap[2],
RelativePosition=False,
EnableLogging=False)
if self._rotate:
(rotw, rotx, roty,
rotz) = self._eulerToAngleAxis(xmap[3], xmap[4], xmap[5],
self._eulerConvention) # YZX
api.RotateInstrumentComponent(wks_name,
component,
X=rotx,
Y=roty,
Z=rotz,
Angle=rotw,
RelativeRotation=False,
EnableLogging=False)
api.CalculateDIFC(InputWorkspace=wks_name,
OutputWorkspace=wks_name,
EnableLogging=False)
difc = api.mtd[wks_name].extractY().flatten()[firstIndex:lastIndex + 1]
peaks_d = self.peaks_tof[
firstIndex:lastIndex +
1] / difc[:, np.newaxis] # peak centers in d-spacing units
# calculate the fractional peak center deviations, then sum their absolute values
return np.sum(np.abs((peaks_d - self.peaks_ref) / self.peaks_ref))
def PyExec(self):
table_tof = self.getProperty('PeakCentersTofTable').value
self.peaks_tof = self._extract_tofs(table_tof)
detector_count, peak_count = self.peaks_tof.shape
table_tof = api.SortTableWorkspace(table_tof, Columns='detid')
detID = table_tof.column('detid')
peaks_ref = np.sort(self.getProperty(
'PeakPositions').value) # sort by increasing value
self.peaks_ref = peaks_ref[np.newaxis, :] # shape = (1, peak_count)
# Process input mask
maskWS = self.getProperty("MaskWorkspace").value
if maskWS is not None:
mask = maskWS.extractY().flatten() # shape=(detector_count,)
peaks_mask = np.tile(
mask[:, np.newaxis],
peak_count) # shape=(detector_count, peak_count)
else:
peaks_mask = np.zeros(
(detector_count, peak_count)) # no detectors are masked
peaks_mask[np.isnan(self.peaks_tof)] = True
# mask the defective detectors and missing peaks
self.peaks_tof = np.ma.masked_array(self.peaks_tof, peaks_mask)
input_workspace = self.getProperty('InputWorkspace').value
# Table containing the optimized absolute locations and orientations for each component
adjustments_table_name = self.getProperty('AdjustmentsTable').value
if len(adjustments_table_name) > 0:
adjustments_table = self._initialize_adjustments_table(
adjustments_table_name)
saving_adjustments = True
else:
saving_adjustments = False
# Table containing the relative changes in position and euler angles for each bank component
displacements_table_name = self.getProperty('DisplacementsTable').value
if len(displacements_table_name) > 0:
displacements_table = self._initialize_displacements_table(
displacements_table_name)
saving_displacements = True
else:
saving_displacements = False
self._eulerConvention = self.getProperty('EulerConvention').value
output_workspace = self.getPropertyValue("OutputWorkspace")
wks_name = '__alignedworkspace' # workspace whose counts will be DIFC values
if bool(input_workspace) is True:
api.CloneWorkspace(InputWorkspace=input_workspace,
OutputWorkspace=wks_name)
if output_workspace != str(input_workspace):
api.CloneWorkspace(InputWorkspace=input_workspace,
OutputWorkspace=output_workspace)
else:
api.LoadEmptyInstrument(
Filename=self.getProperty("InstrumentFilename").value,
OutputWorkspace=wks_name)
# Make a dictionary of what options are being refined for sample/source. No rotation.
for translation_option in self._optionsList[:3]:
self._optionsDict[translation_option] = self.getProperty(
translation_option).value
for rotation_option in self._optionsList[3:]:
self._optionsDict[rotation_option] = False
# First fit L1 if selected for Source and/or Sample
sample_position_begin = api.mtd[wks_name].getInstrument().getSample(
).getPos()
for component in "Source", "Sample": # fit first the source position, then the sample position
if self.getProperty("Fit" + component + "Position").value:
self._move = True
if component == "Sample":
comp = api.mtd[wks_name].getInstrument().getSample()
else:
comp = api.mtd[wks_name].getInstrument().getSource()
componentName = comp.getFullName()
logger.notice("Working on " + componentName +
" Starting position is " + str(comp.getPos()))
firstIndex = 0
lastIndex = detector_count - 1
self._initialPos = [
comp.getPos().getX(),
comp.getPos().getY(),
comp.getPos().getZ(), 0, 0, 0
] # no rotation
# Set up x0 and bounds lists
x0List = [] # initial X, Y, Z coordinates
boundsList = [] # [(minX, maxX), (minZ, maxZ), (minZ, maxZ)]
for iopt, translation_option in enumerate(
self._optionsList[:3]): # iterate over X, Y, and Z
if self._optionsDict[translation_option]:
x0List.append(self._initialPos[iopt])
# default range for X is (x0 - 0.1m, x0 + 0.1m), same for Y and Z
boundsList.append((
self._initialPos[iopt] +
self.getProperty("Min" + translation_option).value,
self._initialPos[iopt] +
self.getProperty("Max" +
translation_option).value))
# scipy.opimize.minimize with the L-BFGS-B algorithm
results: OptimizeResult = minimize(
self._minimisation_func,
x0=x0List,
method='L-BFGS-B',
args=(wks_name, componentName, firstIndex, lastIndex),
bounds=boundsList)
# Apply the results to the output workspace
xmap = self._mapOptions(results.x)
# Save translation and rotations, if requested
if saving_adjustments:
instrument = api.mtd[wks_name].getInstrument()
name_finder = {
'Source': instrument.getSource().getName(),
'Sample': instrument.getSample().getName()
}
component_adjustments = [
name_finder[component]
] + xmap[:3] + [0.0] * 4 # no rotations
adjustments_table.addRow(component_adjustments)
# Need to grab the component again, as things have changed
kwargs = dict(X=xmap[0],
Y=xmap[1],
Z=xmap[2],
RelativePosition=False,
EnableLogging=False)
api.MoveInstrumentComponent(wks_name, componentName,
**kwargs) # adjust workspace
api.MoveInstrumentComponent(output_workspace, componentName,
**kwargs) # adjust workspace
comp = api.mtd[wks_name].getInstrument().getComponentByName(
componentName)
logger.notice("Finished " + componentName +
" Final position is " + str(comp.getPos()))
self._move = False
sample_position_end = api.mtd[wks_name].getInstrument().getSample(
).getPos()
# Now fit all the remaining components, if any
components = self.getProperty("ComponentList").value
# Make a dictionary of what translational and rotational options are being refined.
for opt in self._optionsList:
self._optionsDict[opt] = self.getProperty(opt).value
self._move = any([
self._optionsDict[t]
for t in ('Xposition', 'Yposition', 'Zposition')
])
self._rotate = any([
self._optionsDict[r]
for r in ('AlphaRotation', 'BetaRotation', 'GammaRotation')
])
prog = Progress(self, start=0, end=1, nreports=len(components))
for component in components:
comp = api.mtd[wks_name].getInstrument().getComponentByName(
component)
firstDetID = self._getFirstDetID(comp)
firstIndex = detID.index(
firstDetID) # a row index in the input TOFS table
lastDetID = self._getLastDetID(comp)
lastIndex = detID.index(
lastDetID) # a row index in the input TOFS table
if lastDetID - firstDetID != lastIndex - firstIndex:
raise RuntimeError("TOFS detid doesn't match instrument")
eulerAngles: List[float] = comp.getRotation().getEulerAngles(
self._eulerConvention)
logger.notice("Working on " + comp.getFullName() +
" Starting position is " + str(comp.getPos()) +
" Starting rotation is " + str(eulerAngles))
x0List = []
self._initialPos = [
comp.getPos().getX(),
comp.getPos().getY(),
comp.getPos().getZ(), eulerAngles[0], eulerAngles[1],
eulerAngles[2]
]
# Distance between the original position of the sample and the original position of the component
comp_sample_distance_begin = (comp.getPos() -
sample_position_begin).norm()
boundsList = []
if np.all(peaks_mask[firstIndex:lastIndex + 1].astype(bool)):
self.log().warning(
"All pixels in '%s' are masked. Skipping calibration." %
component)
continue
for iopt, opt in enumerate(self._optionsList):
if self._optionsDict[opt]:
x0List.append(self._initialPos[iopt])
boundsList.append((self._initialPos[iopt] +
self.getProperty("Min" + opt).value,
self._initialPos[iopt] +
self.getProperty("Max" + opt).value))
minimizer_selection = self.getProperty('Minimizer').value
if minimizer_selection == 'L-BFGS-B':
# scipy.opimize.minimize with the L-BFGS-B algorithm
results: OptimizeResult = minimize(self._minimisation_func,
x0=x0List,
method='L-BFGS-B',
args=(wks_name, component,
firstIndex,
lastIndex),
bounds=boundsList)
elif minimizer_selection == 'differential_evolution':
results: OptimizeResult = differential_evolution(
self._minimisation_func,
bounds=boundsList,
args=(wks_name, component, firstIndex, lastIndex),
maxiter=self.getProperty('MaxIterations').value)
# Apply the results to the output workspace
xmap = self._mapOptions(results.x)
comp = api.mtd[wks_name].getInstrument().getComponentByName(
component) # adjusted component
# Distance between the adjusted position of the sample and the adjusted position of the component
comp_sample_distance_end = (comp.getPos() -
sample_position_end).norm()
component_adjustments = [
0.
] * 7 # 3 for translation, 3 for rotation axis, 1 for rotation angle
component_displacements = [
0.
] * 7 # 1 for distnace, 3 for translation, 3 for Euler angles
component_displacements[0] = 1000 * (
comp_sample_distance_end - comp_sample_distance_begin
) # in mili-meters
if self._move:
kwargs = dict(X=xmap[0],
Y=xmap[1],
Z=xmap[2],
RelativePosition=False,
EnableLogging=False)
api.MoveInstrumentComponent(wks_name, component,
**kwargs) # adjust workspace
api.MoveInstrumentComponent(output_workspace, component,
**kwargs) # adjust workspace
component_adjustments[:3] = xmap[:3]
for i in range(3):
component_displacements[i + 1] = 1000 * (
xmap[i] - self._initialPos[i]) # in mili-meters
if self._rotate:
(rotw, rotx, roty,
rotz) = self._eulerToAngleAxis(xmap[3], xmap[4], xmap[5],
self._eulerConvention)
kwargs = dict(X=rotx,
Y=roty,
Z=rotz,
Angle=rotw,
RelativeRotation=False,
EnableLogging=False)
api.RotateInstrumentComponent(wks_name, component,
**kwargs) # adjust workspace
api.RotateInstrumentComponent(output_workspace, component,
**kwargs) # adjust workspace
component_adjustments[3:] = [rotx, roty, rotz, rotw]
for i in range(3, 6):
component_displacements[
i + 1] = xmap[i] - self._initialPos[i] # in degrees
if saving_adjustments and (self._move or self._rotate):
adjustments_table.addRow([component] + component_adjustments)
if saving_displacements and (self._move or self._rotate):
displacements_table.addRow([component] +
component_displacements)
# Need to grab the component object again, as things have changed
logger.notice(
"Finished " + comp.getFullName() + " Final position is " +
str(comp.getPos()) + " Final rotation is " +
str(comp.getRotation().getEulerAngles(self._eulerConvention)))
prog.report()
api.DeleteWorkspace(wks_name)
self.setProperty("OutputWorkspace", output_workspace)
logger.notice("Results applied to workspace " + wks_name)
