def get_vanadium(self, detector_mask, m1, colltrans, exp, indir, metadata):
"""
This function returns either (vanadium_count, vanadium_monitor, None) or
(None, None, vcorr) depending what type of file is provided by getProperty("Vanadium")
"""
if not self.getProperty("Normalise").value:
return None, None, np.ones(44)[detector_mask]
vanadium_filename = self.getProperty("Vanadium").value
if vanadium_filename:
if vanadium_filename.split('.')[-1] == 'dat':
vanadium = np.genfromtxt(vanadium_filename)
vanadium_count = vanadium[:, 5:49].sum(axis=0)[detector_mask]
vanadium_monitor = vanadium[:, 3].sum()
logger.notice(
"Using vanadium data file: {}".format(vanadium_filename))
return vanadium_count, vanadium_monitor, None
else:
vcorr_filename = vanadium_filename
else: # Find adjacent vcorr file
# m1 is the monochromator angle
# m1 = -4.375 -> Ge 117, 1.12 A
# m1 = 0 -> Ge 115, 1.54 A
# m1 = 9.45 -> Ge 113, 2.41 A
# colltrans is the collimator position, whether in or out of the beam
CONVENTION_2021_02 = np.datetime64(datetime.datetime(2021, 2, 23))
CONVENTION_2021_04 = np.datetime64(datetime.datetime(2021, 4, 25))
date_created = self.get_date(metadata)
if date_created >= CONVENTION_2021_04:
if np.isclose(m1, -4.375, atol=0.1):
ge_peak = 117
elif np.isclose(m1, 0, atol=0.1):
ge_peak = 115
else:
ge_peak = 113
vcorr_filename = 'HB2A_{}__Ge_{}_{}_vcorr.txt'.format(
exp, ge_peak,
"OUT" if np.isclose(colltrans, 0, atol=0.1) else "IN")
elif date_created >= CONVENTION_2021_02:
# Convention after `CONVENTION_2021_02`.
# colltrans = 0 -> OUT
# colltrans = +/-80 -> IN
vcorr_filename = 'HB2A_{}__Ge_{}_{}_vcorr.txt'.format(
exp, 115 if np.isclose(m1, 0, atol=0.1) else 113,
"OUT" if np.isclose(colltrans, 0, atol=0.1) else "IN")
else:
# Legacy convention.
# colltrans = +/-80 -> OUT
# colltrans = 0 -> IN
vcorr_filename = 'HB2A_{}__Ge_{}_{}_vcorr.txt'.format(
exp, 115 if np.isclose(m1, 0, atol=0.1) else 113,
"IN" if np.isclose(colltrans, 0, atol=0.1) else "OUT")
vcorr_filename = os.path.join(indir, vcorr_filename)
logger.notice("Using vcorr file: {}".format(vcorr_filename))
if not os.path.isfile(vcorr_filename):
raise RuntimeError(
"Vanadium file {} does not exist".format(vcorr_filename))
return None, None, np.genfromtxt(vcorr_filename)[detector_mask]
def _calculate_energy(self, monitor_ws, grouped_ws, red_ws):
"""
Convert the input run to energy transfer
@param monitor_ws :: name of the monitor workspace to divide by
@param grouped_ws :: name of workspace with the detectors grouped
@param red_ws :: name to call the reduced workspace
"""
x_range = self._monitor_range(monitor_ws)
Scale(InputWorkspace=monitor_ws, OutputWorkspace=monitor_ws, Factor=0.001, Operation='Multiply')
CropWorkspace(InputWorkspace=monitor_ws, OutputWorkspace=monitor_ws, Xmin=x_range[0], XMax=x_range[1])
ScaleX(InputWorkspace=monitor_ws, OutputWorkspace=monitor_ws, Factor=-x_range[0], Operation='Add')
CropWorkspace(InputWorkspace=grouped_ws, OutputWorkspace=grouped_ws, Xmin=x_range[0], XMax=x_range[1])
ScaleX(InputWorkspace=grouped_ws, OutputWorkspace=grouped_ws, Factor=-x_range[0], Operation='Add')
Divide(LHSWorkspace=grouped_ws, RHSWorkspace=monitor_ws, OutputWorkspace=grouped_ws)
formula = self._energy_range(grouped_ws)
ConvertAxisByFormula(InputWorkspace=grouped_ws, OutputWorkspace=red_ws, Axis='X', Formula=formula,
AxisTitle='Energy transfer', AxisUnits='meV')
if self._verbose:
xnew = mtd[red_ws].readX(0) # energy array
logger.notice('Energy range : %f to %f' % (xnew[0], xnew[-1]))
DeleteWorkspace(grouped_ws)
DeleteWorkspace(monitor_ws)
def IndirectTrans(inst, sfile,cfile,Verbose=False,Plot=False,Save=False):
StartTime('Transmission')
TransMon(inst,'Sam',sfile,Verbose)
TransMon(inst,'Can',cfile,Verbose)
samWS = inst + '_Sam'
canWS = inst + '_Can'
trWS = inst + '_Trans'
Divide(LHSWorkspace=samWS, RHSWorkspace=canWS, OutputWorkspace=trWS)
trans = np.average(mtd[trWS].readY(0))
transWS = inst + '_Transmission'
workdir = config['defaultsave.directory']
group = samWS +','+ canWS +','+ trWS
GroupWorkspaces(InputWorkspaces=group,OutputWorkspace=transWS)
if Verbose:
logger.notice('Transmission : '+str(trans))
path = os.path.join(workdir,transWS+'.nxs')
if Save:
SaveNexusProcessed(InputWorkspace=transWS, Filename=path)
if Verbose:
logger.notice('Output file created : '+path)
if Plot:
TransPlot(transWS)
EndTime('Transmission')
def Iblock(a,first): #read Ascii block of Integers
line1 = a[first]
line2 = a[first+1]
val = ExtractInt(line2)
numb = val[0]
lines=numb/10
last = numb-10*lines
if line1.startswith('I'):
error = ''
else:
error = 'NOT an I block starting at line ' +str(first)
logger.notice('ERROR *** ' + error)
sys.exit(error)
ival = []
for m in range(0, lines):
mm = first+2+m
val = ExtractInt(a[mm])
for n in range(0, 10):
ival.append(val[n])
mm += 1
val = ExtractInt(a[mm])
for n in range(0, last):
ival.append(val[n])
mm += 1
return mm,ival #values as list
def ReadIbackGroup(a,first): #read Ascii block of spectrum values
x = []
y = []
e = []
next = first
line1 = a[next]
next += 1
val = ExtractInt(a[next])
n1 = val[0]
ngrp = val[2]
if line1.startswith('S'):
error = ''
else:
error = 'NOT an S block starting at line ' +str(first)
logger.notice('ERROR *** ' + error)
sys.exit(error)
next += 1
next,Ival = Iblock(a,next)
for m in range(0, len(Ival)):
x.append(float(m))
yy = float(Ival[m])
y.append(yy)
ee = math.sqrt(yy)
e.append(ee)
return next,x,y,e #values of x,y,e as lists
def PyExec(self):
from IndirectDataAnalysis import furyfitMult
workdir = config['defaultsave.directory']
inType = self.getProperty('InputType').value
prefix = self.getProperty('Instrument').value
ana = self.getProperty('Analyser').value
RunNumb = self.getProperty('RunNumber').value
xMax = self.getProperty('TimeMax').value
filename = prefix + str(RunNumb) + '_' + ana
plotOp = self.getProperty('Plot').value
inWS = filename + '_iqt'
if inType == 'File':
spath = os.path.join(workdir, inWS +
'.nxs') # path name for sample nxs file
logger.notice('Input from File : ' + spath)
LoadNexusProcessed(Filename=spath, OutputWorkspace=inWS)
else:
logger.notice('Input from Workspace : ' + inWS)
CropWorkspace(InputWorkspace=inWS,
OutputWorkspace=inWS,
XMin=0.0,
XMax=xMax)
function = 'name=LinearBackground,A0=0.02,A1=0,ties=(A1=0);'
function += 'name=UserFunction,Formula=Intensity*exp(-(x/Tau)^Beta),Intensity=0.98,Tau=0.02,Beta=0.8'
furyfitMult(inWS, function, 'SSSS', 0.0, 0.2, False, plotOp, True)
def getWSprefix(wsname,runfile=None):
'''Returns a string of the form '<ins><run>_<analyser><refl>_' on which
all of our other naming conventions are built.
The workspace is used to get the instrument parameters. If the runfile
string is given it is expected to be a string with instrument prefix
and run number. If it is empty then the workspace name is assumed to
contain this information
'''
if wsname == '':
return ''
if runfile is None:
runfile = wsname
ws = mtd[wsname]
facility = config['default.facility']
if facility == 'ILL':
instr = ws.getInstrument().getName()
logger.notice('Facility is '+facility)
prefix = instr + '_' + wsname[:-3]
else:
(instr, run) = getInstrRun(runfile)
run_name = instr + run
try:
analyser = ws.getInstrument().getStringParameter('analyser')[0]
reflection = ws.getInstrument().getStringParameter('reflection')[0]
except IndexError:
analyser = ''
reflection = ''
prefix = run_name + '_' + analyser + reflection + '_'
return prefix
def Iblock(a,first): #read Ascii block of Integers
line1 = a[first]
line2 = a[first+1]
val = ExtractInt(line2)
numb = val[0]
lines=numb/10
last = numb-10*lines
if line1.startswith('I'):
error = ''
else:
error = 'NOT an I block starting at line ' +str(first)
logger.notice('ERROR *** ' + error)
sys.exit(error)
ival = []
for m in range(0, lines):
mm = first+2+m
val = ExtractInt(a[mm])
for n in range(0, 10):
ival.append(val[n])
mm += 1
val = ExtractInt(a[mm])
for n in range(0, last):
ival.append(val[n])
mm += 1
return mm,ival #values as list
def startup(self, cycle='14_3'):
user_data_directory = os.path.normpath(self.use_folder + cycle)
self.set_data_directory(user_data_directory)
logger.notice("Raw Data in : {}".format(user_data_directory))
user_data_processed = self.out_folder
self.set_user_directory(directory=user_data_processed)
logger.notice("Processed Data in : {}".format(user_data_processed))
def get_vanadium(self, detector_mask, m1, colltrans, exp, indir):
"""
This function returns either (vanadium_count, vanadium_monitor, None) or
(None, None, vcorr) depending what type of file is provided by getProperty("Vanadium")
"""
if not self.getProperty("Normalise").value:
return None, None, np.ones(44)[detector_mask]
vanadium_filename = self.getProperty("Vanadium").value
if vanadium_filename:
if vanadium_filename.split('.')[-1] == 'dat':
vanadium = np.genfromtxt(vanadium_filename)
vanadium_count = vanadium[:, 5:49].sum(axis=0)[detector_mask]
vanadium_monitor = vanadium[:, 3].sum()
logger.notice("Using vanadium data file: {}".format(vanadium_filename))
return vanadium_count, vanadium_monitor, None
else:
vcorr_filename = vanadium_filename
else: # Find adjacent vcorr file
# m1 is the monochromator angle
# m1 = 0 -> Ge 115, 1.54A
# m1 = 9.45 -> Ge 113, 2.41A
# colltrans is the collimator position, whether in or out of the beam
# colltrans = 0 -> IN
# colltrans = +/-80 -> OUT
vcorr_filename = 'HB2A_{}__Ge_{}_{}_vcorr.txt'.format(exp,
115 if np.isclose(m1, 0, atol=0.1) else 113,
"IN" if np.isclose(colltrans, 0, atol=0.1) else "OUT")
vcorr_filename = os.path.join(indir, vcorr_filename)
logger.notice("Using vcorr file: {}".format(vcorr_filename))
if not os.path.isfile(vcorr_filename):
raise RuntimeError("Vanadium file {} does not exist".format(vcorr_filename))
return None, None, np.genfromtxt(vcorr_filename)[detector_mask]
def PyExec(self):
in_ws = mtd[self.getPropertyValue('InputWorkspace')]
out_ws_name = self.getPropertyValue('OutputWorkspace')
out_ws = ms.CreateEmptyTableWorkspace(OutputWOrkspace=out_ws_name)
out_ws.addColumn('str', 'statistic')
stats = {
'standard_deviation': dict(),
'maximum': dict(),
'minimum': dict(),
'mean': dict(),
'median': dict(),
}
for name in in_ws.getColumnNames():
try:
col_stats = _stats_to_dict(
Stats.getStatistics(
np.array([float(v) for v in in_ws.column(name)])))
for statname in stats.keys():
stats[statname][name] = col_stats[statname]
out_ws.addColumn('float', name)
except ValueError:
logger.notice('Column \'%s\' is not numerical, skipping' %
name)
for name, stat in stats.items():
stat1 = dict(stat)
stat1['statistic'] = name
out_ws.addRow(stat1)
self.setProperty('OutputWorkspace', out_ws_name)
def ReadWidthFile(readWidth,widthFile,numSampleGroups,Verbose):
widthY = []
widthE = []
if readWidth:
if Verbose:
logger.notice('Width file is ' + widthFile)
# read ascii based width file
try:
wfPath = FileFinder.getFullPath(widthFile)
handle = open(wfPath, 'r')
asc = []
for line in handle:
line = line.rstrip()
asc.append(line)
handle.close()
except Exception, e:
raise ValueError('Failed to read width file')
numLines = len(asc)
if numLines == 0:
raise ValueError('No groups in width file')
if numLines != numSampleGroups: # check that no. groups are the same
raise ValueError('Width groups (' +str(numLines) + ') not = Sample (' +str(numSampleGroups) +')')
def PyExec(self):
in_ws = mtd[self.getPropertyValue('InputWorkspace')]
out_ws_name = self.getPropertyValue('OutputWorkspace')
out_ws = ms.CreateEmptyTableWorkspace(OutputWorkspace=out_ws_name)
out_ws.addColumn('str', 'statistic')
stats = {
'standard_deviation': dict(),
'maximum': dict(),
'minimum': dict(),
'mean': dict(),
'median': dict(),
}
for name in in_ws.getColumnNames():
try:
col_stats = _stats_to_dict(Stats.getStatistics(np.array([float(v) for v in in_ws.column(name)])))
for statname in stats:
stats[statname][name] = col_stats[statname]
out_ws.addColumn('float', name)
except ValueError:
logger.notice('Column \'%s\' is not numerical, skipping' % name)
for name, stat in iteritems(stats):
stat1 = dict(stat)
stat1['statistic'] = name
out_ws.addRow(stat1)
self.setProperty('OutputWorkspace', out_ws)
def read_mantidplot_project(self, file_name):
"""
:param file_name: String or string castable object; the file_name of the project
:return: returns True if able to load the project, otherwise False
Will attempt to read the project file in from the file_name that is given as a mantidplot project file.
"""
#Get the string inside the mantidworkspaces tags, allowing for whitespace at either end
workspaces_pattern = r"<mantidworkspaces>\s*(.*?)\s*<\/mantidworkspaces>"
try:
with open(file_name) as f:
full_text = f.read()
ws_match = re.search(workspaces_pattern,full_text,re.DOTALL)
if ws_match:
#split by tab
ws_list = ws_match.group(1).split('\t')
if len(ws_list) > 1 and ws_list[0] == "WorkspaceNames":
#the first entry is just an identification tag
self.workspace_names = ws_list[1:]
logger.notice("Loading workspaces from Mantidplot project file " + file_name)
return True
logger.warning("Mantidplot project file unable to be read")
return False
except Exception:
logger.warning("Mantidplot project file unable to be loaded/read")
return False
def createQaxis(inputWS):
result = []
ws = mtd[inputWS]
nHist = ws.getNumberHistograms()
if ws.getAxis(1).isSpectra():
inst = ws.getInstrument()
samplePos = inst.getSample().getPos()
beamPos = samplePos - inst.getSource().getPos()
for i in range(0,nHist):
efixed = getEfixed(inputWS, i)
detector = ws.getDetector(i)
theta = getDetectorTwoTheta(detector, samplePos, beamPos) / 2
lamda = math.sqrt(81.787/efixed)
q = 4 * math.pi * math.sin(theta) / lamda
result.append(q)
else:
axis = ws.getAxis(1)
msg = 'Creating Axis based on Detector Q value: '
if not axis.isNumeric():
msg += 'Input workspace must have either spectra or numeric axis.'
logger.notice(msg)
sys.exit(msg)
if ( axis.getUnit().unitID() != 'MomentumTransfer' ):
msg += 'Input must have axis values of Q'
logger.notice(msg)
sys.exit(msg)
for i in range(0, nHist):
result.append(float(axis.label(i)))
return result
def ReadIbackGroup(a,first): #read Ascii block of spectrum values
x = []
y = []
e = []
next = first
line1 = a[next]
next += 1
val = ExtractInt(a[next])
n1 = val[0]
ngrp = val[2]
if line1.startswith('S'):
error = ''
else:
error = 'NOT an S block starting at line ' +str(first)
logger.notice('ERROR *** ' + error)
sys.exit(error)
next += 1
next,Ival = Iblock(a,next)
for m in range(0, len(Ival)):
x.append(float(m))
yy = float(Ival[m])
y.append(yy)
ee = math.sqrt(yy)
e.append(ee)
return next,x,y,e #values of x,y,e as lists
def ReadWidthFile(readWidth, widthFile, numSampleGroups, Verbose):
widthY = []
widthE = []
if readWidth:
if Verbose:
logger.notice('Width file is ' + widthFile)
# read ascii based width file
try:
wfPath = FileFinder.getFullPath(widthFile)
handle = open(wfPath, 'r')
asc = []
for line in handle:
line = line.rstrip()
asc.append(line)
handle.close()
except Exception, e:
raise ValueError('Failed to read width file')
numLines = len(asc)
if numLines == 0:
raise ValueError('No groups in width file')
if numLines != numSampleGroups: # check that no. groups are the same
raise ValueError('Width groups (' + str(numLines) +
') not = Sample (' + str(numSampleGroups) + ')')
def Fblock(a,first): #read Ascii block of Floats
line1 = a[first]
line2 = a[first+1]
val = ExtractInt(line2)
numb = val[0]
lines=numb/5
last = numb-5*lines
if line1.startswith('F'):
error= ''
else:
error = 'NOT an F block starting at line ' +str(first)
logger.notice('ERROR *** ' + error)
sys.exit(error)
fval = []
for m in range(0, lines):
mm = first+2+m
val = ExtractFloat(a[mm])
for n in range(0, 5):
fval.append(val[n])
mm += 1
val = ExtractFloat(a[mm])
for n in range(0, last):
fval.append(val[n])
mm += 1
return mm,fval #values as list
def startup(self, cycle='14_3'):
user_data_directory = os.path.normpath(self.use_folder + cycle)
self.set_data_directory(user_data_directory)
logger.notice("Raw Data in : {}".format(user_data_directory))
user_data_processed = self.out_folder
self.set_user_directory(directory=user_data_processed)
logger.notice("Processed Data in : {}".format(user_data_processed))
def TransMon(inst, type,file,verbose):
if verbose:
logger.notice('Raw file : '+file)
LoadRaw(Filename=file,OutputWorkspace='__m1',SpectrumMin=1,SpectrumMax=1)
LoadRaw(Filename=file,OutputWorkspace='__m2',SpectrumMin=2,SpectrumMax=2)
LoadRaw(Filename=file,OutputWorkspace='__det',SpectrumMin=3,SpectrumMax=3)
# Check for single or multiple time regimes
MonTCBstart = mtd['__m1'].readX(0)[0]
SpecTCBstart = mtd['__det'].readX(0)[0]
DeleteWorkspace('__det') # delete monWS
monWS = '__Mon'
if (SpecTCBstart == MonTCBstart):
monWS = UnwrapMon('__m1') # unwrap the monitor spectrum and convert to wavelength
RenameWorkspace(InputWorkspace=monWS, OutputWorkspace='__Mon1')
else:
ConvertUnits(InputWorkspace='__m1', OutputWorkspace='__Mon1', Target="Wavelength")
ConvertUnits(InputWorkspace='__m2', OutputWorkspace='__Mon2', Target="Wavelength")
DeleteWorkspace('__m2') # delete monWS
Xin = mtd['__Mon1'].readX(0)
xmin1 = mtd['__Mon1'].readX(0)[0]
xmax1 = mtd['__Mon1'].readX(0)[len(Xin)-1]
Xin = mtd['__Mon2'].readX(0)
xmin2 = mtd['__Mon2'].readX(0)[0]
xmax2 = mtd['__Mon2'].readX(0)[len(Xin)-1]
wmin = max(xmin1,xmin2)
wmax = min(xmax1,xmax2)
CropWorkspace(InputWorkspace='__Mon1', OutputWorkspace='__Mon1', XMin=wmin, XMax=wmax)
RebinToWorkspace(WorkspaceToRebin='__Mon2', WorkspaceToMatch='__Mon1', OutputWorkspace='__Mon2')
monWS = inst +'_'+ type
Divide(LHSWorkspace='__Mon2', RHSWorkspace='__Mon1', OutputWorkspace=monWS)
DeleteWorkspace('__Mon1') # delete monWS
DeleteWorkspace('__Mon2') # delete monWS
def PyExec(self):
run_f2py_compatibility_test()
self.log().information('Jump input')
inType = self.getPropertyValue('InputType')
prefix = self.getPropertyValue('Instrument')
ana = self.getPropertyValue('Analyser')
prog = self.getPropertyValue('QLprogram')
jump = self.getPropertyValue('Fit')
fw = self.getPropertyValue('Width')
sam = self.getPropertyValue('SamNumber')
sname = prefix+sam+'_'+ana+'_'+prog
cropOp = self.getProperty('CropQ')
if cropOp:
qmin = self.getPropertyValue('Qmin')
qmax = self.getPropertyValue('Qmax')
qrange = [qmin, qmax]
else:
qrange = [0.0, 5.0]
verbOp = self.getProperty('Verbose')
plotOp = self.getProperty('Plot')
saveOp = self.getProperty('Save')
workdir = config['defaultsave.directory']
if inType == 'File':
path = os.path.join(workdir, sname+'_Parameters.nxs') # path name for nxs file
LoadNexusProcessed(Filename=path, OutputWorkspace=sname+'_Parameters')
message = 'Input from File : '+path
else:
message = 'Input from Workspace : '+sname
if verbOp:
logger.notice(message)
Main.JumpRun(sname,jump,prog,fw,cropOp,qrange,verbOp,plotOp,saveOp)
def Fblock(a,first): #read Ascii block of Floats
line1 = a[first]
line2 = a[first+1]
val = ExtractInt(line2)
numb = val[0]
lines=numb/5
last = numb-5*lines
if line1.startswith('F'):
error= ''
else:
error = 'NOT an F block starting at line ' +str(first)
logger.notice('ERROR *** ' + error)
sys.exit(error)
fval = []
for m in range(0, lines):
mm = first+2+m
val = ExtractFloat(a[mm])
for n in range(0, 5):
fval.append(val[n])
mm += 1
val = ExtractFloat(a[mm])
for n in range(0, last):
fval.append(val[n])
mm += 1
return mm,fval #values as list
def unwrap_monitor(workspace_name):
"""
Unwrap monitor if required based on value of Workflow.UnwrapMonitor parameter
@param workspace_name Name of workspace
@return True if the monitor was unwrapped
"""
from mantid.simpleapi import (UnwrapMonitor, RemoveBins, FFTSmooth)
monitor_workspace_name = workspace_name + '_mon'
instrument = mtd[monitor_workspace_name].getInstrument()
# Determine if the monitor should be unwrapped
try:
unwrap = instrument.getStringParameter('Workflow.UnwrapMonitor')[0]
if unwrap == 'Always':
should_unwrap = True
elif unwrap == 'BaseOnTimeRegime':
mon_time = mtd[monitor_workspace_name].readX(0)[0]
det_time = mtd[workspace_name].readX(0)[0]
logger.notice(str(mon_time) + " " + str(det_time))
should_unwrap = mon_time == det_time
else:
should_unwrap = False
except IndexError:
should_unwrap = False
logger.debug('Need to unwrap monitor for %s: %s' % (workspace_name, str(should_unwrap)))
if should_unwrap:
sample = instrument.getSample()
sample_to_source = sample.getPos() - instrument.getSource().getPos()
radius = mtd[workspace_name].getDetector(0).getDistance(sample)
z_dist = sample_to_source.getZ()
l_ref = z_dist + radius
logger.debug('For workspace %s: radius=%d, z_dist=%d, l_ref=%d' %
(workspace_name, radius, z_dist, l_ref))
_, join = UnwrapMonitor(InputWorkspace=monitor_workspace_name,
OutputWorkspace=monitor_workspace_name,
LRef=l_ref)
RemoveBins(InputWorkspace=monitor_workspace_name,
OutputWorkspace=monitor_workspace_name,
XMin=join - 0.001, XMax=join + 0.001,
Interpolation='Linear')
try:
FFTSmooth(InputWorkspace=monitor_workspace_name,
OutputWorkspace=monitor_workspace_name,
WorkspaceIndex=0,
IgnoreXBins=True)
except ValueError:
raise ValueError('Uneven bin widths are not supported.')
return should_unwrap
def unwrap_monitor(workspace_name):
"""
Unwrap monitor if required based on value of Workflow.UnwrapMonitor parameter
@param workspace_name Name of workspace
@return True if the monitor was unwrapped
"""
from mantid.simpleapi import (UnwrapMonitor, RemoveBins, FFTSmooth)
monitor_workspace_name = workspace_name + '_mon'
instrument = mtd[monitor_workspace_name].getInstrument()
# Determine if the monitor should be unwrapped
try:
unwrap = instrument.getStringParameter('Workflow.UnwrapMonitor')[0]
if unwrap == 'Always':
should_unwrap = True
elif unwrap == 'BaseOnTimeRegime':
mon_time = mtd[monitor_workspace_name].readX(0)[0]
det_time = mtd[workspace_name].readX(0)[0]
logger.notice(str(mon_time) + " " + str(det_time))
should_unwrap = mon_time == det_time
else:
should_unwrap = False
except IndexError:
should_unwrap = False
logger.debug('Need to unwrap monitor for %s: %s' % (workspace_name, str(should_unwrap)))
if should_unwrap:
sample = instrument.getSample()
sample_to_source = sample.getPos() - instrument.getSource().getPos()
radius = mtd[workspace_name].getDetector(0).getDistance(sample)
z_dist = sample_to_source.getZ()
l_ref = z_dist + radius
logger.debug('For workspace %s: radius=%d, z_dist=%d, l_ref=%d' %
(workspace_name, radius, z_dist, l_ref))
_, join = UnwrapMonitor(InputWorkspace=monitor_workspace_name,
OutputWorkspace=monitor_workspace_name,
LRef=l_ref)
RemoveBins(InputWorkspace=monitor_workspace_name,
OutputWorkspace=monitor_workspace_name,
XMin=join - 0.001, XMax=join + 0.001,
Interpolation='Linear')
try:
FFTSmooth(InputWorkspace=monitor_workspace_name,
OutputWorkspace=monitor_workspace_name,
WorkspaceIndex=0,
IgnoreXBins=True)
except ValueError:
raise ValueError('Uneven bin widths are not supported.')
return should_unwrap
def load_multi_run_part(self, extension, run, panel):
filename = self.get_file_name(run, extension)
logger.notice("reading filename... {}".format(filename))
spectra_min, spectra_max = self.return_panel.get(panel)
output1 = "w{0}-{1}".format(run, panel)
simple.LoadRaw(Filename=filename, OutputWorkspace=output1, SpectrumMin=str(spectra_min),
SpectrumMax=str(spectra_max), LoadLogFiles="0")
return output1
def _post_process(self):
"""
Handles adding logs, saving and plotting.
"""
use_scale_factor = self._scale_factor == 1.0
AddSampleLog(Workspace=self._out_ws,
LogName='scale',
LogType='String',
LogText=str(use_scale_factor))
if use_scale_factor:
AddSampleLog(Workspace=self._out_ws,
LogName='scale_factor',
LogType='Number',
LogText=str(self._scale_factor))
AddSampleLog(Workspace=self._out_ws,
LogName='res_smoothing_applied',
LogType='String',
LogText=str(self._smooth))
AddSampleLog(Workspace=self._out_ws,
LogName='back_start',
LogType='Number',
LogText=str(self._background[0]))
AddSampleLog(Workspace=self._out_ws,
LogName='back_end',
LogType='Number',
LogText=str(self._background[1]))
rebin_params = self._rebin_string.split(',')
if len(rebin_params) == 3:
AddSampleLog(Workspace=self._out_ws,
LogName='rebin_low',
LogType='Number',
LogText=rebin_params[0])
AddSampleLog(Workspace=self._out_ws,
LogName='rebin_width',
LogType='Number',
LogText=rebin_params[1])
AddSampleLog(Workspace=self._out_ws,
LogName='rebin_high',
LogType='Number',
LogText=rebin_params[2])
self.setProperty('OutputWorkspace', self._out_ws)
if self._save:
if self._verbose:
logger.notice(
"Resolution file saved to default save directory.")
SaveNexusProcessed(InputWorkspace=self._out_ws,
Filename=self._out_ws + '.nxs')
if self._plot:
from IndirectImport import import_mantidplot
mtd_plot = import_mantidplot()
mtd_plot.plotSpectrum(self._out_ws, 0)
def MomentStart(inType,sname,erange,factor,Verbose,Plot,Save):
workdir = config['defaultsave.directory']
if inType == 'File':
spath = os.path.join(workdir, sname+'.nxs') # path name for sample nxs file
logger.notice('Input from File : '+spath)
LoadNexusProcessed(Filename=spath, OutputWorkspace=sname)
else:
logger.notice('Input from Workspace : '+sname)
MomentRun(sname,erange,factor,Verbose,Plot,Save)
def CheckSam(sam):
if sam[1] <1e-8:
error = 'Sample density is Zero'
logger.notice('ERROR *** ' + error)
sys.exit(error)
if (sam[2]+sam[3]) <1e-8:
error = 'Sample total scattering cross-section (scat+abs) is Zero'
logger.notice('ERROR *** ' + error)
sys.exit(error)
def PyExec(self):
from IndirectImport import run_f2py_compatibility_test, is_supported_f2py_platform
if is_supported_f2py_platform():
import IndirectBayes as Main
run_f2py_compatibility_test()
self.log().information('Quest input')
inType = self.getPropertyValue('InputType')
prefix = self.getPropertyValue('Instrument')
ana = self.getPropertyValue('Analyser')
sam = self.getPropertyValue('SamNumber')
rinType = self.getPropertyValue('ResInputType')
res = self.getPropertyValue('ResNumber')
elastic = self.getProperty('ElasticOption').value
bgd = self.getPropertyValue('BackgroundOption')
emin = self.getPropertyValue('EnergyMin')
emax = self.getPropertyValue('EnergyMax')
nbin = self.getPropertyValue('SamBinning')
nbins = [nbin, 1]
nbet = self.getProperty('NumberBeta').value
nsig = self.getProperty('NumberSigma').value
nbs = [nbet, nsig]
sname = prefix+sam+'_'+ana + '_red'
rname = prefix+res+'_'+ana + '_res'
erange = [float(emin), float(emax)]
if elastic:
o_el = 1
else:
o_el = 0
fitOp = [o_el, bgd, 0, 0]
loopOp = self.getProperty('Sequence').value
verbOp = self.getProperty('Verbose').value
plotOp = self.getPropertyValue('Plot')
saveOp = self.getProperty('Save').value
workdir = config['defaultsave.directory']
if inType == 'File':
spath = os.path.join(workdir, sname+'.nxs') # path name for sample nxs file
LoadNexusProcessed(Filename=spath, OutputWorkspace=sname)
Smessage = 'Sample from File : '+spath
else:
Smessage = 'Sample from Workspace : '+sname
if rinType == 'File':
rpath = os.path.join(workdir, rname+'.nxs') # path name for res nxs file
LoadNexusProcessed(Filename=rpath, OutputWorkspace=rname)
Rmessage = 'Resolution from File : '+rpath
else:
Rmessage = 'Resolution from Workspace : '+rname
if verbOp:
logger.notice(Smessage)
logger.notice(Rmessage)
Main.QuestRun(sname,rname,nbs,erange,nbins,fitOp,loopOp,plotOp,saveOp)
def PyExec(self):
from IndirectImport import run_f2py_compatibility_test, is_supported_f2py_platform
if is_supported_f2py_platform():
import IndirectBayes as Main
run_f2py_compatibility_test()
self.log().information('Quest input')
inType = self.getPropertyValue('InputType')
prefix = self.getPropertyValue('Instrument')
ana = self.getPropertyValue('Analyser')
sam = self.getPropertyValue('SamNumber')
rinType = self.getPropertyValue('ResInputType')
res = self.getPropertyValue('ResNumber')
elastic = self.getProperty('ElasticOption').value
bgd = self.getPropertyValue('BackgroundOption')
emin = self.getPropertyValue('EnergyMin')
emax = self.getPropertyValue('EnergyMax')
nbin = self.getPropertyValue('SamBinning')
nbins = [nbin, 1]
nbet = self.getProperty('NumberBeta').value
nsig = self.getProperty('NumberSigma').value
nbs = [nbet, nsig]
sname = prefix+sam+'_'+ana + '_red'
rname = prefix+res+'_'+ana + '_res'
erange = [float(emin), float(emax)]
if elastic:
o_el = 1
else:
o_el = 0
fitOp = [o_el, bgd, 0, 0]
loopOp = self.getProperty('Sequence').value
verbOp = self.getProperty('Verbose').value
plotOp = self.getPropertyValue('Plot')
saveOp = self.getProperty('Save').value
workdir = config['defaultsave.directory']
if inType == 'File':
spath = os.path.join(workdir, sname+'.nxs') # path name for sample nxs file
LoadNexusProcessed(Filename=spath, OutputWorkspace=sname)
Smessage = 'Sample from File : '+spath
else:
Smessage = 'Sample from Workspace : '+sname
if rinType == 'File':
rpath = os.path.join(workdir, rname+'.nxs') # path name for res nxs file
LoadNexusProcessed(Filename=rpath, OutputWorkspace=rname)
Rmessage = 'Resolution from File : '+rpath
else:
Rmessage = 'Resolution from Workspace : '+rname
if verbOp:
logger.notice(Smessage)
logger.notice(Rmessage)
Main.QuestRun(sname,rname,nbs,erange,nbins,fitOp,loopOp,plotOp,saveOp)
def CheckSam(sam):
if sam[1] < 1e-8:
error = 'Sample density is Zero'
logger.notice('ERROR *** ' + error)
sys.exit(error)
if (sam[2] + sam[3]) < 1e-8:
error = 'Sample total scattering cross-section (scat+abs) is Zero'
logger.notice('ERROR *** ' + error)
sys.exit(error)
def PyExec(self):
run_f2py_compatibility_test()
self.log().information("Quest input")
inType = self.getPropertyValue("InputType")
prefix = self.getPropertyValue("Instrument")
ana = self.getPropertyValue("Analyser")
sam = self.getPropertyValue("SamNumber")
rinType = self.getPropertyValue("ResInputType")
res = self.getPropertyValue("ResNumber")
elastic = self.getProperty("ElasticOption")
bgd = self.getPropertyValue("BackgroundOption")
emin = self.getPropertyValue("EnergyMin")
emax = self.getPropertyValue("EnergyMax")
nbin = self.getPropertyValue("SamBinning")
nbins = [nbin, 1]
nbet = self.getPropertyValue("NumberBeta")
nsig = self.getPropertyValue("NumberSigma")
nbs = [nbet, nsig]
sname = prefix + sam + "_" + ana + "_red"
rname = prefix + res + "_" + ana + "_res"
erange = [float(emin), float(emax)]
if elastic:
o_el = 1
else:
o_el = 0
if bgd == "Sloping":
o_bgd = 2
if bgd == "Flat":
o_bgd = 1
if bgd == "Zero":
o_bgd = 0
fitOp = [o_el, o_bgd, 0, 0]
loopOp = self.getProperty("Sequence")
verbOp = self.getProperty("Verbose")
plotOp = self.getPropertyValue("Plot")
saveOp = self.getProperty("Save")
workdir = config["defaultsave.directory"]
if inType == "File":
spath = os.path.join(workdir, sname + ".nxs") # path name for sample nxs file
LoadNexusProcessed(Filename=spath, OutputWorkspace=sname)
Smessage = "Sample from File : " + spath
else:
Smessage = "Sample from Workspace : " + sname
if rinType == "File":
rpath = os.path.join(workdir, rname + ".nxs") # path name for res nxs file
LoadNexusProcessed(Filename=rpath, OutputWorkspace=rname)
Rmessage = "Resolution from File : " + rpath
else:
Rmessage = "Resolution from Workspace : " + rname
if verbOp:
logger.notice(Smessage)
logger.notice(Rmessage)
Main.QuestRun(sname, rname, nbs, erange, nbins, fitOp, loopOp, verbOp, plotOp, saveOp)
def C2Se(sname):
prog = 'QSe'
outWS = sname+'_Result'
asc = readASCIIFile(sname+'.qse')
lasc = len(asc)
var = asc[3].split() #split line on spaces
nspec = var[0]
ndat = var[1]
var = ExtractInt(asc[6])
first = 7
Xout = []
Yf = []
Ef = []
Yi = []
Ei = []
Yb = []
Eb = []
ns = int(nspec)
dataX = np.array([])
dataY = np.array([])
dataE = np.array([])
for m in range(0,ns):
first,Q,int0,fw,it,be = SeBlock(asc,first)
Xout.append(Q)
Yf.append(fw[0])
Ef.append(fw[1])
Yi.append(it[0])
Ei.append(it[1])
Yb.append(be[0])
Eb.append(be[1])
Vaxis = []
dataX = np.append(dataX,np.array(Xout))
dataY = np.append(dataY,np.array(Yi))
dataE = np.append(dataE,np.array(Ei))
nhist = 1
Vaxis.append('f1.Amplitude')
dataX = np.append(dataX, np.array(Xout))
dataY = np.append(dataY, np.array(Yf))
dataE = np.append(dataE, np.array(Ef))
nhist += 1
Vaxis.append('f1.FWHM')
dataX = np.append(dataX,np.array(Xout))
dataY = np.append(dataY,np.array(Yb))
dataE = np.append(dataE,np.array(Eb))
nhist += 1
Vaxis.append('f1.Beta')
logger.notice('Vaxis=' + str(Vaxis))
CreateWorkspace(OutputWorkspace=outWS, DataX=dataX, DataY=dataY, DataE=dataE, Nspec=nhist,
UnitX='MomentumTransfer', VerticalAxisUnit='Text', VerticalAxisValues=Vaxis, YUnitLabel='')
return outWS
def CheckDensity(density,ncan):
if density[0] < 1e-5:
error = 'Sample density is zero'
logger.notice('ERROR *** '+error)
sys.exit(error)
if ncan == 2:
if density[1] < 1e-5:
error = 'Can density is zero'
logger.notice('ERROR *** '+error)
sys.exit(error)
def restore_figure_data(self, fig, dic):
self.restore_fig_properties(fig, dic["properties"])
axes_list = dic["axes"]
for index, ax in enumerate(fig.axes):
try:
self.restore_fig_axes(ax, axes_list[index])
except IndexError as e:
if not self.color_bar_remade:
raise IndexError(e)
except KeyError:
logger.notice("Not adding data to blank axis.")
def load_multi_run_part(self, extension, run, panel):
filename = self.get_file_name(run, extension)
logger.notice("reading filename... {}".format(filename))
spectra_min, spectra_max = self.return_panel.get(panel)
output1 = "w{0}-{1}".format(run, panel)
simple.LoadRaw(Filename=filename,
OutputWorkspace=output1,
SpectrumMin=str(spectra_min),
SpectrumMax=str(spectra_max),
LoadLogFiles="0")
return output1
def sliceReadRawFile(fname, Verbose):
if Verbose:
logger.notice('Reading file :'+fname)
#Load the raw file
(dir, filename) = os.path.split(fname)
(root, ext) = os.path.splitext(filename)
Load(Filename=fname, OutputWorkspace=root, LoadLogFiles=False)
return root
def CreateSqw(disp,coeff,grid,Verbose):
CheckCoeff(disp,coeff)
if Verbose:
logger.notice('Dispersion is '+disp)
logger.notice('Coefficients : '+str(coeff))
nq,dq,nw,dw = CheckQw(grid)
q0,w0,e0 = CalcW0(nq,dq,disp,coeff)
CreateWorkspace(OutputWorkspace=disp, DataX=q0, DataY=w0, DataE=e0,\
Nspec=1, UnitX='MomentumTransfer')
nw2 = 2*nw+1
nel= nw+1
CalcSqw(q0,nw2,nel,dw,w0)
def CreateSqw(disp,coeff,grid,Verbose):
CheckCoeff(disp,coeff)
if Verbose:
logger.notice('Dispersion is '+disp)
logger.notice('Coefficients : '+str(coeff))
nq,dq,nw,dw = CheckQw(grid)
q0,w0,e0 = CalcW0(nq,dq,disp,coeff)
CreateWorkspace(OutputWorkspace=disp, DataX=q0, DataY=w0, DataE=e0,\
Nspec=1, UnitX='MomentumTransfer')
nw2 = 2*nw+1
nel= nw+1
CalcSqw(q0,nw2,nel,dw,w0)
def _save_output(self):
"""
Save the output workspace to the user's default working directory
"""
from IndirectCommon import getDefaultWorkingDirectory
workdir = getDefaultWorkingDirectory()
file_path = os.path.join(workdir, self._output_workspace + '.nxs')
SaveNexusProcessed(InputWorkspace=self._output_workspace,
Filename=file_path)
if self._verbose:
logger.notice('Output file : ' + file_path)
def MuscatFuncStart(sname,geom,neut,beam,sam,grid,disp,coeff,kr1,Verbose,Plot,Save):
StartTime('Muscat Function')
workdir = config['defaultsave.directory']
sname = sname+'_red'
spath = os.path.join(workdir, sname+'.nxs') # path name for sample nxs file
LoadNexusProcessed(FileName=spath, OutputWorkspace=sname)
sqw = 'S(Q,w)'
CreateSqw(disp,coeff,grid,Verbose)
if Verbose:
logger.notice('Sample run : '+spath)
logger.notice('S(Q,w) from : '+disp)
MuscatRun(sname,geom,neut,beam,sam,sqw,kr1,Verbose,Plot,Save)
EndTime('Muscat Function')
def SymmStart(inType,sname,cut,Verbose,Plot,Save):
StartTime('Symmetrise')
workdir = config['defaultsave.directory']
if inType == 'File':
spath = os.path.join(workdir, sname+'.nxs') # path name for sample nxs file
LoadNexusProcessed(FileName=spath, OutputWorkspace=sname)
message = 'Input from File : '+spath
else:
message = 'Input from Workspace : '+sname
if Verbose:
logger.notice(message)
SymmRun(sname,cut,Verbose,Plot,Save)
EndTime('Symmetrise')
def CheckHistZero(inWS):
nhist = mtd[inWS].getNumberHistograms() # no. of hist/groups in WS
if nhist == 0:
error = 'Workspace '+inWS+' has NO histograms'
logger.notice('ERROR *** ' + error)
sys.exit(error)
Xin = mtd[inWS].readX(0)
ntc = len(Xin)-1 # no. points from length of x array
if ntc == 0:
error = 'Workspace '+inWS+' has NO points'
logger.notice('ERROR *** ' + error)
sys.exit(error)
return nhist,ntc
def MuscatFuncStart(sname,geom,neut,beam,sam,grid,disp,coeff,kr1,Verbose,Plot,Save):
StartTime('Muscat Function')
workdir = config['defaultsave.directory']
sname = sname+'_red'
spath = os.path.join(workdir, sname+'.nxs') # path name for sample nxs file
LoadNexusProcessed(FileName=spath, OutputWorkspace=sname)
sqw = 'S(Q,w)'
CreateSqw(disp,coeff,grid,Verbose)
if Verbose:
logger.notice('Sample run : '+spath)
logger.notice('S(Q,w) from : '+disp)
MuscatRun(sname,geom,neut,beam,sam,sqw,kr1,Verbose,Plot,Save)
EndTime('Muscat Function')
def slice(inputfiles, calib, xRange, spec, suffix, Save=False, Verbose=False, Plot=False):
StartTime('Slice')
CheckXrange(xRange,'Time')
workdir = config['defaultsave.directory']
outWSlist = []
useTwoRanges = (len(xRange) != 2)
useCalib = (calib != '')
calibWsName = '__calibration'
#load the calibration file
if useCalib:
Load(Filename=calib, OutputWorkspace=calibWsName)
if Verbose:
logger.notice('Using Calibration file: %s' % calib)
for index, file in enumerate(inputfiles):
rawFile = sliceReadRawFile(file, Verbose)
#only need to process the calib file once
if(index == 0 and useCalib):
sliceProcessCalib(rawFile, calibWsName, spec)
sfile = sliceProcessRawFile(rawFile, calibWsName, useCalib, xRange, useTwoRanges, spec, suffix, Verbose)
Transpose(InputWorkspace=sfile, OutputWorkspace=sfile)
unit = mtd[sfile].getAxis(0).setUnit("Label")
unit.setLabel("Spectrum Number", "")
outWSlist.append(sfile)
DeleteWorkspace(rawFile)
if Save:
# path name for nxs file
o_path = os.path.join(workdir, sfile+'.nxs')
SaveNexusProcessed(InputWorkspace=sfile, Filename=o_path)
if Verbose:
logger.notice('Output file :'+o_path)
if useCalib:
DeleteWorkspace(Workspace=calibWsName)
if Plot:
try:
graph = mp.plotSpectrum(sfile, 0)
except RuntimeError, e:
#User clicked cancel on plot so don't do anything
pass
def read(self, number, panel, extension):
if type(number) is int:
filename = self.datafile
logger.notice("will be reading filename...{}".format(filename))
spectra_min, spectra_max = self.return_panel_van.get(panel) if self.is_vanadium else \
self.return_panel.get(panel)
if panel != 0:
output = "w{0}-{1}".format(number, panel)
else:
output = "w{}".format(number)
shared_load_files(extension, filename, output, spectra_max, spectra_min, False)
if extension == "nxs_event":
simple.LoadEventNexus(Filename=filename, OutputWorkspace=output, LoadMonitors='1')
self.read_event_nexus(number, output, panel)
if extension[:10] == "nxs_event_":
label, tmin, tmax = split_string_event(extension)
output = output + "_" + label
if tmax == "end":
simple.LoadEventNexus(Filename=filename, OutputWorkspace=output, FilterByTimeStart=tmin,
LoadMonitors='1', MonitorsAsEvents='1', FilterMonByTimeStart=tmin)
else:
simple.LoadEventNexus(Filename=filename, OutputWorkspace=output, FilterByTimeStart=tmin,
FilterByTimeStop=tmax, LoadMonitors='1', MonitorsAsEvents='1',
FilterMonByTimeStart=tmin, FilterMonByTimeStop=tmax)
self.read_event_nexus(number, output, panel)
else:
num_1, num_2 = split_run_string(number)
output = "w{0}_{1}-{2}".format(num_1, num_2, panel)
output1 = self.load_multi_run_part(extension, num_1, panel)
output2 = self.load_multi_run_part(extension, num_2, panel)
simple.MergeRuns(output1 + "," + output2, output)
simple.DeleteWorkspace(output1)
simple.DeleteWorkspace(output2)
simple.ConvertUnits(InputWorkspace=output, OutputWorkspace=output, Target="Wavelength", Emode="Elastic")
lmin, lmax = Wish.LAMBDA_RANGE
simple.CropWorkspace(InputWorkspace=output, OutputWorkspace=output, XMin=lmin, XMax=lmax)
monitor_run = "monitor{}".format(number)
if monitor_run not in simple.mtd:
monitor = self.process_incidentmon(number, extension, spline_terms=70)
else:
monitor = simple.mtd[monitor_run]
simple.NormaliseToMonitor(InputWorkspace=output, OutputWorkspace=output + "norm1", MonitorWorkspace=monitor)
simple.NormaliseToMonitor(InputWorkspace=output + "norm1", OutputWorkspace=output + "norm2",
MonitorWorkspace=monitor, IntegrationRangeMin=0.7, IntegrationRangeMax=10.35)
simple.DeleteWorkspace(output)
simple.DeleteWorkspace(output + "norm1")
simple.RenameWorkspace(InputWorkspace=output + "norm2", OutputWorkspace=output)
simple.ConvertUnits(InputWorkspace=output, OutputWorkspace=output, Target="TOF", EMode="Elastic")
simple.ReplaceSpecialValues(InputWorkspace=output, OutputWorkspace=output, NaNValue=0.0, NaNError=0.0,
InfinityValue=0.0, InfinityError=0.0)
return output
def MuscatDataStart(sname,geom,neut,beam,sam,sqw,kr1,Verbose,Plot,Save):
StartTime('Muscat Data')
workdir = config['defaultsave.directory']
sname = sname+'_red'
spath = os.path.join(workdir, sname+'.nxs') # path name for sample nxs file
LoadNexusProcessed(FileName=spath, OutputWorkspace=sname)
sqw = sqw+'_sqw'
qpath = os.path.join(workdir, sqw+'.nxs') # path name for S(Q,w) nxs file
LoadNexusProcessed(FileName=qpath, OutputWorkspace=sqw)
if Verbose:
logger.notice('Sample run : '+spath)
logger.notice('S(Q,w) file : '+qpath)
MuscatRun(sname,geom,neut,beam,sam,sqw,kr1,Verbose,Plot,Save)
EndTime('Muscat Data')
def CheckSize(size, geom, ncan, Verbose):
if geom == 'cyl':
if (size[1] - size[0]) < 1e-4:
raise ValueError('Sample outer radius not > inner radius')
else:
if Verbose:
message = 'Sam : inner radius = ' + str(
size[0]) + ' ; outer radius = ' + str(size[1])
logger.notice(message)
if geom == 'flt':
if size[0] < 1e-4:
raise ValueError('Sample thickness is zero')
else:
if Verbose:
logger.notice('Sam : thickness = ' + str(size[0]))
if ncan == 2:
if geom == 'cyl':
if (size[2] - size[1]) < 1e-4:
raise ValueError('Can inner radius not > sample outer radius')
else:
if Verbose:
message = 'Can : inner radius = ' + str(
size[1]) + ' ; outer radius = ' + str(size[2])
logger.notice(message)
if geom == 'flt':
if size[1] < 1e-4:
raise ValueError('Can thickness is zero')
else:
if Verbose:
logger.notice('Can : thickness = ' + str(size[1]))
def PyExec(self):
from IndirectCommon import StartTime, EndTime
self._setup()
StartTime('IndirectTransmissionMonitor')
ws_basename = str(self._sample_ws_in)
self._trans_mon(ws_basename, 'Sam', self._sample_ws_in)
self._trans_mon(ws_basename, 'Can', self._can_ws_in)
# Generate workspace names
sam_ws = ws_basename + '_Sam'
can_ws = ws_basename + '_Can'
trans_ws = ws_basename + '_Trans'
# Divide sample and can workspaces
Divide(LHSWorkspace=sam_ws,
RHSWorkspace=can_ws,
OutputWorkspace=trans_ws)
trans = numpy.average(mtd[trans_ws].readY(0))
AddSampleLog(Workspace=trans_ws,
LogName='can_workspace',
LogType='String',
LogText=self._can_ws_in)
# Group workspaces
group = sam_ws + ',' + can_ws + ',' + trans_ws
GroupWorkspaces(InputWorkspaces=group, OutputWorkspace=self._out_ws)
self.setProperty('OutputWorkspace', self._out_ws)
if self._verbose:
logger.notice('Transmission : ' + str(trans))
# Save the tranmissin workspace group to a nexus file
if self._save:
workdir = config['defaultsave.directory']
path = os.path.join(workdir, self._out_ws + '.nxs')
SaveNexusProcessed(InputWorkspace=self._out_ws, Filename=path)
if self._verbose:
logger.notice('Output file created : ' + path)
# Plot spectra from transmission workspace
if self._plot:
mtd_plot = import_mantidplot()
mtd_plot.plotSpectrum(self._out_ws, 0)
EndTime('IndirectTransmissionMonitor')
def MuscatDataStart(sname,geom,neut,beam,sam,sqw,kr1,Verbose,Plot,Save):
StartTime('Muscat Data')
workdir = config['defaultsave.directory']
sname = sname+'_red'
spath = os.path.join(workdir, sname+'.nxs') # path name for sample nxs file
LoadNexusProcessed(FileName=spath, OutputWorkspace=sname)
sqw = sqw+'_sqw'
qpath = os.path.join(workdir, sqw+'.nxs') # path name for S(Q,w) nxs file
LoadNexusProcessed(FileName=qpath, OutputWorkspace=sqw)
if Verbose:
logger.notice('Sample run : '+spath)
logger.notice('S(Q,w) file : '+qpath)
MuscatRun(sname,geom,neut,beam,sam,sqw,kr1,Verbose,Plot,Save)
EndTime('Muscat Data')
def CubicFit(inputWS, spec, Verbose=False):
'''Uses the Mantid Fit Algorithm to fit a quadratic to the inputWS
parameter. Returns a list containing the fitted parameter values.'''
function = 'name=Quadratic, A0=1, A1=0, A2=0'
fit = Fit(Function=function, InputWorkspace=inputWS, WorkspaceIndex=spec,
CreateOutput=True, Output='Fit')
table = mtd['Fit_Parameters']
A0 = table.cell(0,1)
A1 = table.cell(1,1)
A2 = table.cell(2,1)
Abs = [A0, A1, A2]
if Verbose:
logger.notice('Group '+str(spec)+' of '+inputWS+' ; fit coefficients are : '+str(Abs))
return Abs
def _calculate_energy(self, monitor_ws, grouped_ws, red_ws):
"""
Convert the input run to energy transfer
@param monitor_ws :: name of the monitor workspace to divide by
@param grouped_ws :: name of workspace with the detectors grouped
@param red_ws :: name to call the reduced workspace
"""
x_range = self._monitor_range(monitor_ws)
Scale(InputWorkspace=monitor_ws,
OutputWorkspace=monitor_ws,
Factor=0.001,
Operation='Multiply')
CropWorkspace(InputWorkspace=monitor_ws,
OutputWorkspace=monitor_ws,
Xmin=x_range[0],
XMax=x_range[1])
ScaleX(InputWorkspace=monitor_ws,
OutputWorkspace=monitor_ws,
Factor=-x_range[0],
Operation='Add')
CropWorkspace(InputWorkspace=grouped_ws,
OutputWorkspace=grouped_ws,
Xmin=x_range[0],
XMax=x_range[1])
ScaleX(InputWorkspace=grouped_ws,
OutputWorkspace=grouped_ws,
Factor=-x_range[0],
Operation='Add')
Divide(LHSWorkspace=grouped_ws,
RHSWorkspace=monitor_ws,
OutputWorkspace=grouped_ws)
formula = self._energy_range(grouped_ws)
ConvertAxisByFormula(InputWorkspace=grouped_ws,
OutputWorkspace=red_ws,
Axis='X',
Formula=formula,
AxisTitle='Energy transfer',
AxisUnits='meV')
if self._verbose:
xnew = mtd[red_ws].readX(0) # energy array
logger.notice('Energy range : %f to %f' % (xnew[0], xnew[-1]))
DeleteWorkspace(grouped_ws)
DeleteWorkspace(monitor_ws)
def loadData(rawfiles, outWS='RawFile', Sum=False, SpecMin=-1, SpecMax=-1,
Suffix=''):
workspaces = []
for file in rawfiles:
( dir, filename ) = os.path.split(file)
( name, ext ) = os.path.splitext(filename)
try:
if ( SpecMin == -1 ) and ( SpecMax == -1 ):
Load(Filename=file, OutputWorkspace=name+Suffix, LoadLogFiles=False)
else:
Load(Filename=file, OutputWorkspace=name+Suffix, SpectrumMin=SpecMin,
SpectrumMax=SpecMax, LoadLogFiles=False)
workspaces.append(name+Suffix)
except ValueError, message:
logger.notice(message)
sys.exit(message)
def ChangeAngles(inWS,instr,theta,Verbose):
workdir = config['defaultsave.directory']
file = instr+'_angles.txt'
path = os.path.join(workdir, file)
if Verbose:
logger.notice('Creating angles file : ' + path)
handle = open(path, 'w')
head = 'spectrum,theta'
handle.write(head +" \n" )
for n in range(0,len(theta)):
handle.write(str(n+1) +' '+ str(theta[n]) +"\n" )
if Verbose:
logger.notice('Spectrum ' +str(n+1)+ ' = '+str(theta[n]))
handle.close()
UpdateInstrumentFromFile(Workspace=inWS, Filename=path, MoveMonitors=False, IgnorePhi=False,
AsciiHeader=head)
def RejectZero(inWS,tot,Verbose):
nin = mtd[inWS].getNumberHistograms() # no. of hist/groups in sam
nout = 0
outWS = inWS[:-3]+'red'
for n in range(0, nin):
if tot[n] > 0:
ExtractSingleSpectrum(InputWorkspace=inWS, OutputWorkspace='__tmp',
WorkspaceIndex=n)
if nout == 0:
RenameWorkspace(InputWorkspace='__tmp', OutputWorkspace=outWS)
else:
ConjoinWorkspaces(InputWorkspace1=outWS, InputWorkspace2='__tmp',CheckOverlapping=False)
nout += 1
else:
if Verbose:
logger.notice('** spectrum '+str(n+1)+' rejected')
def _plot(self):
"""
Plots results.
"""
if self._plot_type == 'spectra':
from mantidplot import plotSpectrum
num_spectra = mtd[self._plot_ws].getNumberHistograms()
try:
plotSpectrum(self._plot_ws, range(0, num_spectra))
except RuntimeError:
logger.notice('Spectrum plotting canceled by user')
if self._plot_type == 'contour':
from mantidplot import importMatrixWorkspace
plot_workspace = importMatrixWorkspace(self._plot_ws)
plot_workspace.plotGraph2D()
def get_detector_mask(self, exp, indir):
"""Returns an anode mask"""
detector_mask = np.ones(44, dtype=bool)
if len(self.getProperty("ExcludeDetectors").value) == 0:
exclude_filename = os.path.join(indir, 'HB2A_{}__exclude_detectors.txt'.format(exp))
if os.path.isfile(exclude_filename):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
exclude_detectors = np.loadtxt(exclude_filename, ndmin=1, dtype=int)
else:
exclude_detectors=np.empty(0, dtype=int)
else:
exclude_detectors = np.array(self.getProperty("ExcludeDetectors").value)
if len(exclude_detectors) > 0:
logger.notice("Excluding anodes: {}".format(exclude_detectors))
detector_mask[exclude_detectors-1] = False
return detector_mask
def PyExec(self):
in_ws = mtd[self.getPropertyValue('InputWorkspace')]
indices_list = self.getPropertyValue('ColumnIndices')
out_ws_name = self.getPropertyValue('OutputWorkspace')
column_names = in_ws.getColumnNames()
# If column indices are not provided, then default to _ALL_ columns
if len(indices_list) > 0:
indices_list = [int(x) for x in indices_list.split(',')]
else:
indices_list = range(len(column_names))
out_ws = ms.CreateEmptyTableWorkspace(OutputWorkspace=out_ws_name)
out_ws.addColumn('str', 'Statistic')
stats = collections.OrderedDict([
('StandardDev', collections.OrderedDict()),
('Minimum', collections.OrderedDict()),
('Median', collections.OrderedDict()),
('Maximum', collections.OrderedDict()),
('Mean', collections.OrderedDict()),
])
for index in indices_list:
column_name = column_names[index]
try:
column_data = np.array([float(v) for v in in_ws.column(index)])
col_stats = _stats_to_dict(Stats.getStatistics(column_data))
for stat_name in stats:
stats[stat_name][column_name] = col_stats[stat_name]
out_ws.addColumn('float', column_name)
except RuntimeError:
logger.notice('Column \'%s\' is not numerical, skipping' %
column_name)
except:
logger.notice('Column \'%s\' is not numerical, skipping' %
column_name)
for index, stat_name in iteritems(stats):
stat = collections.OrderedDict(stat_name)
stat['Statistic'] = index
out_ws.addRow(stat)
self.setProperty('OutputWorkspace', out_ws)
