def setUp(self):
ws1 = CreateSampleWorkspace()
self.ws1 = ws1
ws2 = CreateSampleWorkspace()
self.ws2 = ws2
lognames = 'run_title,deterota,wavelength,polarisation,flipper'
logvalues = 'ws1,-10.0,4.2,x,ON'
AddSampleLogMultiple(Workspace=ws1, LogNames=lognames, LogValues=logvalues, ParseType=True)
logvalues = 'ws2,-12.0,4.2,x,OFF'
AddSampleLogMultiple(Workspace=ws2, LogNames=lognames, LogValues=logvalues, ParseType=True)
def setUp(self):
input_ws = Load(Filename="TOFTOFTestdata.nxs")
self._input_ws_base = input_ws
self._input_good = input_ws
AddSampleLogMultiple(Workspace=self._input_good, LogNames=['run_number'], LogValues=[001])
self._input_bad_entry = input_ws+0
# remove a compulsory entry in Logs
DeleteLog(self._input_bad_entry, 'duration')
self._input_bad_value = input_ws+0
AddSampleLogMultiple(Workspace=self._input_bad_value, LogNames=['wavelength'], LogValues=[0.])
def prepare_background(input_md, reference_sample_mde, background_md: str):
"""Prepare background MDEventWorkspace from reduced sample Matrix
This is the previous solution to merge all the ExperimentInfo
"""
dgs_data = CloneWorkspace(input_md)
data_MDE = mtd[reference_sample_mde]
if mtd.doesExist('background_MDE'):
DeleteWorkspace('background_MDE')
for i in range(data_MDE.getNumExperimentInfo()):
phi, chi, omega = data_MDE.getExperimentInfo(
i).run().getGoniometer().getEulerAngles('YZY')
AddSampleLogMultiple(Workspace=dgs_data,
LogNames='phi, chi, omega',
LogValues='{},{},{}'.format(phi, chi, omega))
SetGoniometer(Workspace=dgs_data, Goniometers='Universal')
ConvertToMD(InputWorkspace=dgs_data,
QDimensions='Q3D',
dEAnalysisMode='Direct',
Q3DFrames="Q_sample",
MinValues='-11,-11,-11,-25',
MaxValues='11,11,11,49',
PreprocDetectorsWS='-',
OverwriteExisting=False,
OutputWorkspace=background_md)
def setUp(self):
# create sample workspace
self.xmin = 2123.33867005 + 4005.75
self.xmax = 2123.33867005 + 7995.75
self._input_ws = CreateSampleWorkspace(
Function="User Defined",
UserDefinedFunction="name=LinearBackground, \
A0=0.3;name=Gaussian, PeakCentre=8190, Height=5, Sigma=75",
NumBanks=2,
BankPixelWidth=1,
XMin=self.xmin,
XMax=self.xmax,
BinWidth=10.5,
BankDistanceFromSample=4.0,
SourceDistanceFromSample=1.4,
OutputWorkspace="ws")
lognames = "wavelength,TOF1"
logvalues = "6.0,2123.33867005"
AddSampleLogMultiple(self._input_ws, lognames, logvalues)
# create EPP table
self._table = CreateEmptyTableWorkspace(OutputWorkspace="epptable")
self._table.addColumn(type="double", name="PeakCentre")
table_row = {'PeakCentre': 8189.5}
for i in range(2):
self._table.addRow(table_row)
def PyExec(self):
input_file = self.getProperty("InputFile").value
output_ws = self.getPropertyValue("OutputWorkspace")
logs = ''
with h5py.File(input_file, 'r') as hf:
data = numpy.array(hf.get('entry1/data1/DATA'), dtype='float')
if data.ndim > 2:
raise RuntimeError(
'Data with more than 2 dimensions are not supported.')
errors = numpy.array(hf.get('entry1/data1/errors'), dtype='float')
x = numpy.array(hf.get('entry1/data1/X'), dtype='float')
if "entry1/data1/PARAMETERS" in hf:
logs = str(
hf.get('entry1/data1/PARAMETERS')[0].decode('UTF-8'))
y = numpy.array([0])
nspec = 1
if data.ndim == 2:
y = numpy.array(hf.get('entry1/data1/Y'), dtype='float')
nspec = data.shape[0]
if x.ndim == 1:
x = numpy.tile(x, nspec)
CreateWorkspace(DataX=x,
DataY=data,
DataE=errors,
NSpec=nspec,
VerticalAxisUnit='Label',
VerticalAxisValues=y,
OutputWorkspace=output_ws)
if logs:
log_names = []
log_values = []
for log in logs.split('\n'):
split = log.strip().split('=')
if len(split) == 2:
name = split[0]
value = split[1]
if name and value:
log_names.append(name)
log_values.append(value)
if log_names:
try:
AddSampleLogMultiple(Workspace=output_ws,
LogNames=log_names,
LogValues=log_values)
except RuntimeError as e:
self.log().warning(
'Unable to set the sample logs, reason: ' + str(e))
self.setProperty('OutputWorkspace', output_ws)
def setUp(self):
# create sample workspace
ws_tof = CreateSampleWorkspace(
Function="User Defined",
UserDefinedFunction="name=LinearBackground, \
A0=0.3;name=Gaussian, PeakCentre=6000, Height=5, Sigma=75",
NumBanks=2,
BankPixelWidth=1,
XMin=4005.75,
XMax=7995.75,
BinWidth=10.5,
BankDistanceFromSample=4.0)
# add required sample logs
lognames = "channel_width,chopper_ratio,chopper_speed,Ei,wavelength,EPP"
logvalues = "10.5,5,14000,2.27,6,190.0"
AddSampleLogMultiple(ws_tof, lognames, logvalues)
self._input_ws = ws_tof
def setUp(self):
# create sample workspace
ws_tof = CreateSampleWorkspace(
Function="User Defined",
UserDefinedFunction="name=LinearBackground, \
A0=0.3;name=Gaussian, PeakCentre=8000, Height=5, Sigma=75",
NumBanks=2,
BankPixelWidth=1,
XMin=6005.75,
XMax=9995.75,
BinWidth=10.5,
BankDistanceFromSample=4.0,
SourceDistanceFromSample=8.0)
# add required sample logs
lognames = "channel_width,EPP,TOF1"
logvalues = "10.5,190.0,2000.0"
AddSampleLogMultiple(ws_tof, lognames, logvalues)
self._input_ws = ws_tof
def PyExec(self):
fn = self.getPropertyValue("Filename")
wsn = self.getPropertyValue("OutputWorkspace")
#print (fn, wsn)
self.fxml = self.getPropertyValue("InstrumentXML")
#load data
parms_dict, det_udet, det_count, det_tbc, data = self.read_file(fn)
nrows = int(parms_dict['NDET'])
#nbins=int(parms_dict['NTC'])
xdata = np.array(det_tbc)
xdata_mon = np.linspace(xdata[0], xdata[-1], len(xdata))
ydata = data.astype(np.float)
ydata = ydata.reshape(nrows, -1)
edata = np.sqrt(ydata)
#CreateWorkspace(OutputWorkspace=wsn,DataX=xdata,DataY=ydata,DataE=edata,
# NSpec=nrows,UnitX='TOF',WorkspaceTitle='Data',YUnitLabel='Counts')
nr, nc = ydata.shape
ws = WorkspaceFactory.create("Workspace2D",
NVectors=nr,
XLength=nc + 1,
YLength=nc)
for i in range(nrows):
ws.setX(i, xdata)
ws.setY(i, ydata[i])
ws.setE(i, edata[i])
ws.getAxis(0).setUnit('tof')
AnalysisDataService.addOrReplace(wsn, ws)
#self.setProperty("OutputWorkspace", wsn)
#print ("ws:", wsn)
#ws=mtd[wsn]
# fix the x values for the monitor
for i in range(nrows - 2, nrows):
ws.setX(i, xdata_mon)
self.log().information("set detector IDs")
#set detetector IDs
for i in range(nrows):
ws.getSpectrum(i).setDetectorID(det_udet[i])
#Sample_logs the header values are written into the sample logs
log_names = [sl.encode('ascii', 'ignore') for sl in parms_dict.keys()]
log_values = [
sl.encode('ascii', 'ignore')
if isinstance(sl, types.UnicodeType) else str(sl)
for sl in parms_dict.values()
]
AddSampleLogMultiple(Workspace=wsn,
LogNames=log_names,
LogValues=log_values)
SetGoniometer(Workspace=wsn, Goniometers='Universal')
if (self.fxml == ""):
LoadInstrument(Workspace=wsn,
InstrumentName="Exed",
RewriteSpectraMap=True)
else:
LoadInstrument(Workspace=wsn,
Filename=self.fxml,
RewriteSpectraMap=True)
RotateInstrumentComponent(
Workspace=wsn,
ComponentName='Tank',
Y=1,
Angle=-float(parms_dict['phi'].encode('ascii', 'ignore')),
RelativeRotation=False)
# Separate monitors into seperate workspace
ExtractSpectra(InputWorkspace=wsn,
WorkspaceIndexList=','.join(
[str(s) for s in range(nrows - 2, nrows)]),
OutputWorkspace=wsn + '_Monitors')
MaskDetectors(Workspace=wsn,
WorkspaceIndexList=','.join(
[str(s) for s in range(nrows - 2, nrows)]))
RemoveMaskedSpectra(InputWorkspace=wsn, OutputWorkspace=wsn)
self.setProperty("OutputWorkspace", wsn)
def PyExec(self):
fn = self.getPropertyValue("Filename")
wsn = self.getPropertyValue("OutputWorkspace")
monitor_workspace_name = self.getPropertyValue(
"OutputMonitorWorkspace")
if monitor_workspace_name == "":
self.setPropertyValue("OutputMonitorWorkspace", wsn + '_Monitors')
# print (fn, wsn)
self.override_angle = self.getPropertyValue("AngleOverride")
self.fxml = self.getPropertyValue("InstrumentXML")
# load data
parms_dict, det_udet, det_count, det_tbc, data = self.read_file(fn)
nrows = int(parms_dict['NDET'])
# nbins=int(parms_dict['NTC'])
xdata = np.array(det_tbc)
xdata_mon = np.linspace(xdata[0], xdata[-1], len(xdata))
ydata = data.astype(float)
ydata = ydata.reshape(nrows, -1)
edata = np.sqrt(ydata)
# CreateWorkspace(OutputWorkspace=wsn,DataX=xdata,DataY=ydata,DataE=edata,
# NSpec=nrows,UnitX='TOF',WorkspaceTitle='Data',YUnitLabel='Counts')
nr, nc = ydata.shape
ws = WorkspaceFactory.create("Workspace2D",
NVectors=nr,
XLength=nc + 1,
YLength=nc)
for i in range(nrows):
ws.setX(i, xdata)
ws.setY(i, ydata[i])
ws.setE(i, edata[i])
ws.getAxis(0).setUnit('tof')
AnalysisDataService.addOrReplace(wsn, ws)
# self.setProperty("OutputWorkspace", wsn)
# print ("ws:", wsn)
# ws=mtd[wsn]
# fix the x values for the monitor
for i in range(nrows - 2, nrows):
ws.setX(i, xdata_mon)
self.log().information("set detector IDs")
# set detetector IDs
for i in range(nrows):
ws.getSpectrum(i).setDetectorID(det_udet[i])
# Sample_logs the header values are written into the sample logs
log_names = [
str(sl.encode('ascii', 'ignore').decode())
for sl in parms_dict.keys()
]
log_values = [
str(sl.encode('ascii', 'ignore').decode()) if isinstance(
sl, UnicodeType) else str(sl) for sl in parms_dict.values()
]
for i in range(len(log_values)):
if ('nan' in log_values[i]) or ('NaN' in log_values[i]):
log_values[i] = '-1.0'
AddSampleLogMultiple(Workspace=wsn,
LogNames=log_names,
LogValues=log_values)
SetGoniometer(Workspace=wsn, Goniometers='Universal')
if (self.fxml == ""):
LoadInstrument(Workspace=wsn,
InstrumentName="Exed",
RewriteSpectraMap=True)
else:
LoadInstrument(Workspace=wsn,
Filename=self.fxml,
RewriteSpectraMap=True)
try:
RotateInstrumentComponent(
Workspace=wsn,
ComponentName='Tank',
Y=1,
Angle=-float(parms_dict['phi'].encode('ascii', 'ignore')),
RelativeRotation=False)
except:
self.log().warning(
"The instrument does not contain a 'Tank' component. "
"This means that you are using a custom XML instrument definition. "
"OMEGA_MAG will be ignored.")
self.log().warning(
"Please make sure that the detector positions in the instrument definition are correct."
)
# Separate monitors into seperate workspace
__temp_monitors = ExtractSpectra(
InputWorkspace=wsn,
WorkspaceIndexList=','.join(
[str(s) for s in range(nrows - 2, nrows)]),
OutputWorkspace=self.getPropertyValue("OutputMonitorWorkspace"))
# ExtractSpectra(InputWorkspace = wsn, WorkspaceIndexList = ','.join([str(s) for s in range(nrows-2, nrows)]),
# OutputWorkspace = wsn + '_Monitors')
MaskDetectors(Workspace=wsn,
WorkspaceIndexList=','.join(
[str(s) for s in range(nrows - 2, nrows)]))
RemoveMaskedSpectra(InputWorkspace=wsn, OutputWorkspace=wsn)
self.setProperty("OutputWorkspace", wsn)
self.setProperty("OutputMonitorWorkspace", __temp_monitors)