diff --git a/Code/Mantid/Framework/Algorithms/src/CalculateTransmission.cpp b/Code/Mantid/Framework/Algorithms/src/CalculateTransmission.cpp
index 735362b49e1b6443a9d7fd8ccaa569d64dcd0828..89b9b78b242b336c747305beeab5db139686196c 100644
--- a/Code/Mantid/Framework/Algorithms/src/CalculateTransmission.cpp
+++ b/Code/Mantid/Framework/Algorithms/src/CalculateTransmission.cpp
@@ -92,7 +92,7 @@ void CalculateTransmission::exec()
{
if (indices.size() == 1)
{
- g_log.error() << "Incident and transmitted spectra can't be set to the same value (they were both set to " << indices.front() << ")\n";
+ g_log.error() << "Incident and transmitted spectra must be set to different spectra that exist in the workspaces. Only found one valid index " << indices.front() << std::endl;
}
else
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp
index b364ffb79235b183cdb27c194d7663bf55256fc5..d934e778492d1626f5d7339d50611dd8d95f65b8 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp
@@ -734,13 +734,13 @@ bool SANSRunWindow::loadUserFile(QString & errors)
//Monitor spectra
m_uiForm.monitor_spec->setText(runReduceScriptFunction(
- "print i.ReductionSingleton().instrument.get_incident_mon()"));
+ "print i.ReductionSingleton().instrument.get_incident_mon()").trimmed());
m_uiForm.trans_monitor->setText(runReduceScriptFunction(
- "print i.ReductionSingleton().instrument.incid_mon_4_trans_calc"));
+ "print i.ReductionSingleton().instrument.incid_mon_4_trans_calc").trimmed());
m_uiForm.monitor_interp->setChecked(runReduceScriptFunction(
"print i.ReductionSingleton().instrument.is_interpolating_norm()").trimmed() == "True");
m_uiForm.trans_interp->setChecked(runReduceScriptFunction(
- "print i.ReductionSingleton().instrument.use_interpol_trans_calc"
+ "print i.ReductionSingleton().transmission_calculator.interpolate"
).trimmed() == "True");
//Direct efficiency correction
diff --git a/Code/Mantid/scripts/SANS/isis_instrument.py b/Code/Mantid/scripts/SANS/isis_instrument.py
index 2615d4d1400cb03fd9f87bc9162301391585f880..9386478d6f16efac365a690ee96072c0a717e93f 100644
--- a/Code/Mantid/scripts/SANS/isis_instrument.py
+++ b/Code/Mantid/scripts/SANS/isis_instrument.py
@@ -256,7 +256,6 @@ class ISISInstrument(instrument.Instrument):
self.setDefaultDetector()
# if this is set InterpolationRebin will be used on the monitor spectrum used to normalize the sample, useful because wavelength resolution in the monitor spectrum can be course in the range of interest
self._use_interpol_norm = False
- self.use_interpol_trans_calc = False
# the sample will be moved this distance a long the beam axis
self.SAMPLE_Z_CORR = 0
diff --git a/Code/Mantid/scripts/SANS/isis_reducer.py b/Code/Mantid/scripts/SANS/isis_reducer.py
index d8b4babab44ba7207148afe71e524dd0c40ce1a4..71b31707fee420953ca1498da71d056b4258c829 100644
--- a/Code/Mantid/scripts/SANS/isis_reducer.py
+++ b/Code/Mantid/scripts/SANS/isis_reducer.py
@@ -317,9 +317,11 @@ class ISISReducer(SANSReducer):
self.instrument.set_incident_mon(specNum)
self.instrument.set_interpolating_norm(interp)
- def set_trans_spectrum(self, specNum, interp=False):
+ def set_trans_spectrum(self, specNum, interp=False, override=True):
self.instrument.incid_mon_4_trans_calc = int(specNum)
- self.instrument.use_interpol_trans_calc = interp
+
+ if (interp == None) or override:
+ self.transmission_calculator.interpolate = interp
def get_trans_lambdamin(self):
"""
diff --git a/Code/Mantid/scripts/SANS/isis_reduction_steps.py b/Code/Mantid/scripts/SANS/isis_reduction_steps.py
index b2d8ed613c66fb7eeb83c2f9a74e7f43d069e4d2..1976fadb730c705300afa8744e39736e031623d7 100644
--- a/Code/Mantid/scripts/SANS/isis_reduction_steps.py
+++ b/Code/Mantid/scripts/SANS/isis_reduction_steps.py
@@ -1056,6 +1056,8 @@ class TransmissionCalc(sans_reduction_steps.BaseTransmission):
self.loader = loader
# this contains the spectrum number of the monitor that comes after the sample from which the transmission calculation is done
self._trans_spec = None
+ # use InterpolatingRebin
+ self.interpolate = None
def get_lambdamin(self, instrum):
"""
@@ -1100,37 +1102,40 @@ class TransmissionCalc(sans_reduction_steps.BaseTransmission):
def set_loader(self, loader):
self.loader = loader
- def setup_wksp(self, inputWS, inst, backmon_start, backmon_end, wavbining, interpolate):
+ def setup_wksp(self, inputWS, inst, backmon_start, backmon_end, wavbining, pre_monitor, post_monitor):
"""
Creates a new workspace removing any background from the monitor spectra, converting units
- and re-binning. Optionally removes between the x-values 19900 and 20500
+ and re-bins. If the instrument is LOQ it zeros values between the x-values 19900 and 20500
@param inputWS: contains the monitor spectra
@param inst: the selected instrument
@param backmon_start: the start of the region that we'll assume is just background
@param backmon_end: the end of the background region
@param wavbinning: the re-bin string to use after convert units
- @param interpolate: apply cubic interpolation to the output from convert units
+ @param pre_monitor: DETECTOR ID of the incident monitor
+ @param post_monitor: DETECTOR ID of the transmission monitor
@return the name of the workspace created
"""
inst.load_transmission_inst(inputWS)
+ #the workspace is forked, below is its new name
tmpWS = inputWS + '_tmp'
- CropWorkspace(inputWS,tmpWS, StartWorkspaceIndex=0, EndWorkspaceIndex=2)
+
+ #exclude unused spectra because the empty spectra can cause errors, use the index numbers (one less than spectrum number) to crop
+ index1 = min(pre_monitor, post_monitor)-1
+ index2 = max(pre_monitor, post_monitor)-1
+ CropWorkspace(inputWS, tmpWS,
+ StartWorkspaceIndex=index1, EndWorkspaceIndex=index2)
if inst.name() == 'LOQ':
- RemoveBins(tmpWS,tmpWS, 19900, 20500, Interpolation='Linear')
- # Load in the instrument setup used for LOQ transmission runs
+ RemoveBins(tmpWS, tmpWS, 19900, 20500, Interpolation='Linear')[0]
if backmon_start != None and backmon_end != None:
- #only remove the background from the monitor spectra that are going to be used
- spec_list = '1,2'
- FlatBackground(tmpWS, tmpWS, StartX=backmon_start, EndX=backmon_end, WorkspaceIndexList=spec_list, Mode='Mean')
+ FlatBackground(tmpWS, tmpWS, StartX=backmon_start, EndX=backmon_end, Mode='Mean')[0]
- # Convert and rebin
- ConvertUnits(tmpWS,tmpWS,"Wavelength")
+ ConvertUnits(tmpWS, tmpWS,"Wavelength")
- if interpolate:
+ if self.interpolate:
InterpolatingRebin(tmpWS, tmpWS, wavbining)
else :
Rebin(tmpWS, tmpWS, wavbining)
@@ -1163,9 +1168,10 @@ class TransmissionCalc(sans_reduction_steps.BaseTransmission):
fit_type = fit_meth
if self._trans_spec:
- trans = self._trans_spec
+ post_sample = self._trans_spec
else:
- trans = reducer.instrument.trans_monitor
+ post_sample = reducer.instrument.trans_monitor
+ pre_sample = reducer.instrument.incid_mon_4_trans_calc
if self._use_full_range is None:
use_full_range = reducer.full_trans_wav
@@ -1183,21 +1189,19 @@ class TransmissionCalc(sans_reduction_steps.BaseTransmission):
wavbin = str(reducer.to_wavelen.get_rebin())
- fittedtransws, unfittedtransws = self.get_wksp_names(
- trans_raw, translambda_min, translambda_max)
-
trans_tmp_out = self.setup_wksp(trans_raw, reducer.instrument,
reducer.BACKMON_START, reducer.BACKMON_END, wavbin,
- reducer.instrument.use_interpol_trans_calc)
+ pre_sample, post_sample)
direct_tmp_out = self.setup_wksp(direct_raw, reducer.instrument,
reducer.BACKMON_START, reducer.BACKMON_END, wavbin,
- reducer.instrument.use_interpol_trans_calc)
+ pre_sample, post_sample)
+ fittedtransws, unfittedtransws = self.get_wksp_names(
+ trans_raw, translambda_min, translambda_max)
CalculateTransmission(trans_tmp_out,direct_tmp_out, fittedtransws,
- reducer.instrument.incid_mon_4_trans_calc, trans,
- MinWavelength = translambda_min, MaxWavelength = translambda_max,
- FitMethod = fit_type, OutputUnfittedData=True)
+ pre_sample, post_sample, MinWavelength=translambda_min,
+ MaxWavelength=translambda_max, FitMethod=fit_type, OutputUnfittedData=True)
# Remove temporaries
mantid.deleteWorkspace(trans_tmp_out)
@@ -1453,13 +1457,13 @@ class UserFile(ReductionStep):
_issueWarning("L/SP lines are ignored")
return
+ rebin_str = None
if not ',' in limit_line:
# Split with no arguments defaults to any whitespace character and in particular
# multiple spaces are include
elements = limits.split()
if len(elements) == 4:
limit_type, minval, maxval, step = elements[0], elements[1], elements[2], elements[3]
- rebin_str = None
step_details = step.split('/')
if len(step_details) == 2:
step_size = step_details[0]
@@ -1475,16 +1479,27 @@ class UserFile(ReductionStep):
limit_type, minval, maxval = elements[0], elements[1], elements[2]
else:
_issueWarning("Incorrectly formatted limit line ignored \"" + limit_line + "\"")
+ return
else:
- limit_type = limits[0].lstrip().rstrip()
- rebin_str = limits[1:].lstrip().rstrip()
+ blocks = limits.split()
+ limit_type = blocks[0].lstrip().rstrip()
+ try:
+ rebin_str = limits.split(limit_type)[1]
+ except:
+ _issueWarning("Incorrectly formatted limit line ignored \"" + limit_line + "\"")
+ return
+
minval = maxval = step_type = step_size = None
if limit_type.upper() == 'WAV':
- reducer.to_wavelen.set_rebin(
- minval, step_type + step_size, maxval, override=False)
+ if rebin_str:
+ _issueWarning("General wave re-bin lines are not implemented, line ignored \"" + limit_line + "\"")
+ return
+ else:
+ reducer.to_wavelen.set_rebin(
+ minval, step_type + step_size, maxval, override=False)
elif limit_type.upper() == 'Q':
- if not rebin_str is None:
+ if rebin_str:
reducer.Q_REBIN = rebin_str
else:
reducer.Q_REBIN = minval + "," + step_type + step_size + "," + maxval
@@ -1495,12 +1510,13 @@ class UserFile(ReductionStep):
reducer.mask.set_radi(minval, maxval)
reducer.CENT_FIND_RMIN = float(minval)/1000.
reducer.CENT_FIND_RMAX = float(maxval)/1000.
- elif limit_type.upper() == 'PHI':
- reducer.mask.set_phi_limit(
- float(minval), float(maxval), True, override=False)
- elif limit_type.upper() == 'PHI/NOMIRROR':
+ elif (limit_type.upper() == 'PHI') or (limit_type.upper() == 'PHI/NOMIRROR'):
+ mirror = limit_type.upper() != 'PHI/NOMIRROR'
+ if maxval.endswith('/NOMIRROR'):
+ maxval = maxval.split('/NOMIRROR')[0]
+ mirror = False
reducer.mask.set_phi_limit(
- float(minval), float(maxval), False, override=False)
+ float(minval), float(maxval), mirror, override=False)
else:
_issueWarning('Error in user file after L/, "%s" is not a valid limit line' % limit_type.upper())
@@ -1529,7 +1545,7 @@ class UserFile(ReductionStep):
parts = details.split('=')
if len(parts) < 2 or parts[0].upper() != 'TRANS/SPECTRUM' :
_issueWarning('Unable to parse MON/TRANS line, needs MON/TRANS/SPECTRUM=')
- reducer.set_trans_spectrum(int(parts[1]), interpolate)
+ reducer.set_trans_spectrum(int(parts[1]), interpolate, override=False)
elif 'DIRECT' in details.upper() or details.upper().startswith('FLAT'):
parts = details.split("=")