diff --git a/Framework/PythonInterface/plugins/algorithms/BASISReduction.py b/Framework/PythonInterface/plugins/algorithms/BASISReduction.py
index c1794f674c9084ee9281b15ebfab65934f0ef3ad..0511f0a3e1f15889206599e628d9fcac872da7a9 100644
--- a/Framework/PythonInterface/plugins/algorithms/BASISReduction.py
+++ b/Framework/PythonInterface/plugins/algorithms/BASISReduction.py
@@ -4,7 +4,7 @@
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
-#pylint: disable=no-init
+# pylint: disable=no-init
from __future__ import (absolute_import, division, print_function)
import numpy as np
@@ -20,32 +20,34 @@ from mantid.kernel import (IntArrayProperty, StringListValidator,
from mantid import config
from os.path import join as pjoin
-TEMPERATURE_SENSOR = "SensorA"
+TEMPERATURE_SENSOR = 'SensorA'
DEFAULT_RANGE = [6.24, 6.30]
-DEFAULT_MASK_GROUP_DIR = "/SNS/BSS/shared/autoreduce/new_masks_08_12_2015"
-DEFAULT_CONFIG_DIR = config["instrumentDefinition.directory"]
+DEFAULT_MASK_GROUP_DIR = '/SNS/BSS/shared/autoreduce/new_masks_08_12_2015'
+DEFAULT_CONFIG_DIR = config['instrumentDefinition.directory']
# BASIS allows two possible reflections, with associated default properties
-#pylint: disable=line-too-long
-REFLECTIONS_DICT = {"silicon111": {"name": "silicon111",
- "energy_bins": [-150, 0.4, 500], # micro-eV
- "q_bins": [0.3, 0.2, 1.9], # inverse Angstroms
- "mask_file": "BASIS_Mask_default_111.xml",
- "parameter_file": "BASIS_silicon_111_Parameters.xml",
- "default_energy": 2.0826, # mili-eV
- "vanadium_bins": [-0.0034, 0.068, 0.0034] # mili-eV
+# pylint: disable=line-too-long
+REFLECTIONS_DICT = {'silicon111': {'name': 'silicon111',
+ 'energy_bins': [-150, 0.4, 500], # micro-eV
+ 'q_bins': [0.3, 0.2, 1.9], # inverse Angst
+ 'banks': 'bank1,bank3,bank4',
+ 'mask_file': 'BASIS_Mask_default_111.xml',
+ 'parameter_file': 'BASIS_silicon_111_Parameters.xml',
+ 'default_energy': 2.0826, # meV
+ 'vanadium_bins': [-0.0034, 0.068, 0.0034]
},
- "silicon311": {"name": "silicon311",
- "energy_bins": [-740, 1.6, 740],
- "q_bins": [0.5, 0.2, 3.7],
- "mask_file": "BASIS_Mask_default_311.xml",
- "parameter_file": "BASIS_silicon_311_Parameters.xml",
- "default_energy": 7.6368, # mili-eV
- "vanadium_bins": [-0.015, 0.030, 0.015]# mili-eV
+ 'silicon311': {'name': 'silicon311',
+ 'energy_bins': [-740, 1.6, 740],
+ 'q_bins': [0.5, 0.2, 3.7],
+ 'banks': 'bank2',
+ 'mask_file': 'BASIS_Mask_default_311.xml',
+ 'parameter_file': 'BASIS_silicon_311_Parameters.xml',
+ 'default_energy': 7.6368, # meV
+ 'vanadium_bins': [-0.015, 0.030, 0.015]
}
}
-#pylint: disable=too-many-instance-attributes
+# pylint: disable=too-many-instance-attributes
class BASISReduction(PythonAlgorithm):
@@ -114,15 +116,15 @@ class BASISReduction(PythonAlgorithm):
self.declareProperty('MonitorNorm', True,
'Normalization with wavelength-dependent monitor counts')
self.declareProperty('ExcludeTimeSegment', '',
- 'Exclude a contigous time segment; '+
- 'Examples: "71546:0-60" filter run 71546 from '+
- 'start to 60 seconds, "71546:300-600", '+
+ 'Exclude a contigous time segment; ' +
+ 'Examples: "71546:0-60" filter run 71546 from ' +
+ 'start to 60 seconds, "71546:300-600", ' +
'"71546:120-end" from 120s to the end of the run')
- grouping_type = ["None", "Low-Resolution", "By-Tube"]
- self.declareProperty("GroupDetectors", "None",
+ grouping_type = ['None', 'Low-Resolution', 'By-Tube']
+ self.declareProperty('GroupDetectors', 'None',
StringListValidator(grouping_type),
- "Switch for grouping detectors")
- self.declareProperty('NormalizeToFirst', False, 'Normalize spectra '+
+ 'Switch for grouping detectors')
+ self.declareProperty('NormalizeToFirst', False, 'Normalize spectra ' +
'to intensity of spectrum with lowest Q?')
# Properties affected by the reflection selected
@@ -178,7 +180,7 @@ class BASISReduction(PythonAlgorithm):
self.setPropertyGroup('NormWavelengthRange', titleDivideByVanadium)
# Properties setting the saving of NSXPE file
- title_nxspe= 'Save to NXSPE'
+ title_nxspe = 'Save to NXSPE'
self.declareProperty('SaveNXSPE', False, direction=Direction.Input,
doc='Do we save to NXSPE format?')
nxspe_enabled = EnabledWhenProperty('SaveNXSPE',
@@ -202,7 +204,7 @@ class BASISReduction(PythonAlgorithm):
doc='Output dynamic susceptibility (Xqw)')
self.setPropertyGroup('OutputSusceptibility', titleAddionalOutput)
- #pylint: disable=too-many-branches
+ # pylint: disable=too-many-branches
def PyExec(self):
config['default.facility'] = 'SNS'
config['default.instrument'] = self._long_inst
@@ -229,15 +231,15 @@ class BASISReduction(PythonAlgorithm):
self._nxspe_psi_angle_log = self.getProperty('PsiAngleLog').value
self._nxspe_offset = self.getProperty('PsiOffset').value
- datasearch = config["datasearch.searcharchive"]
- if datasearch != "On":
- config["datasearch.searcharchive"] = "On"
+ datasearch = config['datasearch.searcharchive']
+ if datasearch != 'On':
+ config['datasearch.searcharchive'] = 'On'
# Apply default mask if not supplied by user
self._overrideMask = bool(self._maskFile)
if not self._overrideMask:
config.appendDataSearchDir(DEFAULT_MASK_GROUP_DIR)
- self._maskFile = self._reflection["mask_file"]
+ self._maskFile = self._reflection['mask_file']
sapi.LoadMask(Instrument='BASIS',
OutputWorkspace='BASIS_MASK',
@@ -248,29 +250,29 @@ class BASISReduction(PythonAlgorithm):
self._dMask = _dMask[1]
sapi.DeleteWorkspace(_dMask[0])
- ############################
- ## Process the Vanadium ##
- ############################
+ ##########################
+ # Process the Vanadium #
+ ##########################
- norm_runs = self.getProperty("NormRunNumbers").value
+ norm_runs = self.getProperty('NormRunNumbers').value
if self._doNorm and bool(norm_runs):
- if ";" in norm_runs:
- raise SyntaxError("Normalization does not support run groups")
- self._normalizationType = self.getProperty("NormalizationType").value
- self.log().information("Divide by Vanadium with normalization" +
+ if ';' in norm_runs:
+ raise SyntaxError('Normalization does not support run groups')
+ self._normalizationType = self.getProperty('NormalizationType').value
+ self.log().information('Divide by Vanadium with normalization' +
self._normalizationType)
# Following steps common to all types of Vanadium normalization
# norm_runs encompasses a single set, thus _getRuns returns
# a list of only one item
- norm_set = self._getRuns(norm_runs, doIndiv=False)[0]
- normWs = self._sum_and_calibrate(norm_set, extra_extension="_norm")
+ norm_set = self._get_runs(norm_runs, doIndiv=False)[0]
+ normWs = self._sum_and_calibrate(norm_set, extra_extension='_norm')
- normRange = self.getProperty("NormWavelengthRange").value
+ normRange = self.getProperty('NormWavelengthRange').value
bin_width = normRange[1] - normRange[0]
# This rebin integrates counts onto a histogram of a single bin
- if self._normalizationType == "by detector ID":
+ if self._normalizationType == 'by detector ID':
self._normRange = [normRange[0], bin_width, normRange[1]]
sapi.Rebin(InputWorkspace=normWs,
OutputWorkspace=normWs,
@@ -284,20 +286,20 @@ class BASISReduction(PythonAlgorithm):
RangeUpper=normRange[1],
OutputWorkspace='BASIS_NORM_MASK')
# additional reduction steps when normalizing by Q slice
- if self._normalizationType == "by Q slice":
+ if self._normalizationType == 'by Q slice':
self._normWs = self._group_and_SofQW(normWs, self._etBins,
isSample=False)
- ##########################
- ## Process the sample ##
- ##########################
- self._run_list = self._getRuns(self.getProperty("RunNumbers").value,
- doIndiv=self._doIndiv)
+ ########################
+ # Process the sample #
+ ########################
+ self._run_list = self._get_runs(self.getProperty('RunNumbers').value,
+ doIndiv=self._doIndiv)
for run_set in self._run_list:
self._samWs = self._sum_and_calibrate(run_set)
self._samWsRun = str(run_set[0])
# Divide by Vanadium detector ID, if pertinent
- if self._normalizationType == "by detector ID":
+ if self._normalizationType == 'by detector ID':
# Mask detectors with insufficient Vanadium signal before dividing
sapi.MaskDetectors(Workspace=self._samWs,
MaskedWorkspace='BASIS_NORM_MASK')
@@ -310,7 +312,7 @@ class BASISReduction(PythonAlgorithm):
if not self._debugMode:
sapi.DeleteWorkspace(self._samWs) # delete events file
# Divide by Vanadium Q slice, if pertinent
- if self._normalizationType == "by Q slice":
+ if self._normalizationType == 'by Q slice':
sapi.Divide(LHSWorkspace=self._samSqwWs,
RHSWorkspace=self._normWs,
OutputWorkspace=self._samSqwWs)
@@ -333,49 +335,49 @@ class BASISReduction(PythonAlgorithm):
OutputWorkspace=self._samSqwWs)
self.serialize_in_log(self._samSqwWs) # store the call
# Output Dave and Nexus files
- extension = "_divided.dat" if self._doNorm else ".dat"
- dave_grp_filename = self._makeRunName(self._samWsRun, False) +\
+ extension = '_divided.dat' if self._doNorm else '.dat'
+ dave_grp_filename = self._make_run_name(self._samWsRun, False) + \
extension
sapi.SaveDaveGrp(Filename=dave_grp_filename,
InputWorkspace=self._samSqwWs,
ToMicroEV=True)
- extension = "_divided_sqw.nxs" if self._doNorm else "_sqw.nxs"
- processed_filename = self._makeRunName(self._samWsRun, False) +\
+ extension = '_divided_sqw.nxs' if self._doNorm else '_sqw.nxs'
+ processed_filename = self._make_run_name(self._samWsRun, False) + \
extension
sapi.SaveNexus(Filename=processed_filename,
InputWorkspace=self._samSqwWs)
# additional output
- if self.getProperty("OutputSusceptibility").value:
+ if self.getProperty('OutputSusceptibility').value:
temperature = mtd[self._samSqwWs].getRun().\
getProperty(TEMPERATURE_SENSOR).getStatistics().mean
- samXqsWs = self._samSqwWs.replace("sqw", "Xqw")
+ samXqsWs = self._samSqwWs.replace('sqw', 'Xqw')
sapi.ApplyDetailedBalance(InputWorkspace=self._samSqwWs,
OutputWorkspace=samXqsWs,
Temperature=str(temperature))
sapi.ConvertUnits(InputWorkspace=samXqsWs,
OutputWorkspace=samXqsWs,
- Target="DeltaE_inFrequency",
- Emode="Indirect")
+ Target='DeltaE_inFrequency',
+ Emode='Indirect')
self.serialize_in_log(samXqsWs)
- susceptibility_filename = processed_filename.replace("sqw", "Xqw")
+ susceptibility_filename = processed_filename.replace('sqw', 'Xqw')
sapi.SaveNexus(Filename=susceptibility_filename,
InputWorkspace=samXqsWs)
if not self._debugMode:
- sapi.DeleteWorkspace("BASIS_MASK") # delete the mask
+ sapi.DeleteWorkspace('BASIS_MASK') # delete the mask
if self._doNorm and bool(norm_runs):
- sapi.DeleteWorkspace("BASIS_NORM_MASK") # delete vanadium mask
+ sapi.DeleteWorkspace('BASIS_NORM_MASK') # delete vanadium mask
sapi.DeleteWorkspace(self._normWs) # Delete vanadium S(Q)
- if self._normalizationType == "by Q slice":
+ if self._normalizationType == 'by Q slice':
sapi.DeleteWorkspace(normWs) # Delete vanadium events file
- if self.getProperty("ExcludeTimeSegment").value:
+ if self.getProperty('ExcludeTimeSegment').value:
sapi.DeleteWorkspace('splitter')
[sapi.DeleteWorkspace(name) for name in
('splitted_unfiltered', 'TOFCorrectWS') if
AnalysisDataService.doesExist(name)]
- def _getRuns(self, rlist, doIndiv=True):
+ def _get_runs(self, rlist, doIndiv=True):
"""
Create sets of run numbers for analysis. A semicolon indicates a
separate group of runs to be processed together.
@@ -386,33 +388,33 @@ class BASISReduction(PythonAlgorithm):
each string is a run number.
"""
run_list = []
- # ";" separates the runs into substrings. Each substring
+ # ';' separates the runs into substrings. Each substring
# represents a set of runs
rlvals = rlist.split(';')
for rlval in rlvals:
- iap = IntArrayProperty("", rlval) # split the substring
+ iap = IntArrayProperty('', rlval) # split the substring
if doIndiv:
run_list.extend([[x] for x in iap.value])
else:
run_list.append(iap.value)
return run_list
- def _makeRunName(self, run, useShort=True):
+ def _make_run_name(self, run, useShort=True):
"""
Make name like BSS_24234
"""
if useShort:
- return self._short_inst + "_" + str(run)
+ return self._short_inst + '_' + str(run)
else:
- return self._long_inst + "_" + str(run)
+ return self._long_inst + '_' + str(run)
- def _makeRunFile(self, run):
+ def _make_run_file(self, run):
"""
Make name like BSS_24234_event.nxs
"""
- return "{0}_{1}_event.nxs".format(self._short_inst,str(run))
+ return '{0}_{1}_event.nxs'.format(self._short_inst, str(run))
- def _sumRuns(self, run_set, sam_ws, mon_ws, extra_ext=None):
+ def _sum_runs(self, run_set, sam_ws, mon_ws, extra_ext=None):
"""
Aggregate the set of runs
@param run_set: list of run numbers
@@ -421,21 +423,16 @@ class BASISReduction(PythonAlgorithm):
@param extra_ext: string to be added to the temporary workspaces
"""
for run in run_set:
- ws_name = self._makeRunName(run)
+ ws_name = self._make_run_name(run)
if extra_ext is not None:
ws_name += extra_ext
- mon_ws_name = ws_name + "_monitors"
- run_file = self._makeRunFile(run)
-
- # Faster loading for the 311 reflection
- if self._reflection["name"] == "silicon311":
- kwargs = {"BankName": "bank2"} # 311 analyzers only in bank2
- else:
- kwargs = {}
+ mon_ws_name = ws_name + '_monitors'
+ run_file = self._make_run_file(run)
sapi.LoadEventNexus(Filename=run_file,
- OutputWorkspace=ws_name, **kwargs)
- if str(run)+':' in self.getProperty("ExcludeTimeSegment").value:
+ OutputWorkspace=ws_name,
+ BankName=self._reflection['banks'])
+ if str(run)+':' in self.getProperty('ExcludeTimeSegment').value:
self._filterEvents(str(run), ws_name)
if self._MonNorm:
@@ -453,14 +450,14 @@ class BASISReduction(PythonAlgorithm):
OutputWorkspace=mon_ws)
sapi.DeleteWorkspace(mon_ws_name)
- def _calibData(self, sam_ws, mon_ws):
+ def _calibrate_data(self, sam_ws, mon_ws):
sapi.MaskDetectors(Workspace=sam_ws,
DetectorList=self._dMask)
sapi.ModeratorTzeroLinear(InputWorkspace=sam_ws,
OutputWorkspace=sam_ws)
sapi.LoadParameterFile(Workspace=sam_ws,
Filename=pjoin(DEFAULT_CONFIG_DIR,
- self._reflection["parameter_file"]))
+ self._reflection['parameter_file']))
sapi.ConvertUnits(InputWorkspace=sam_ws,
OutputWorkspace=sam_ws,
Target='Wavelength',
@@ -490,18 +487,18 @@ class BASISReduction(PythonAlgorithm):
RHSWorkspace=mon_ws,
OutputWorkspace=sam_ws)
- def _sum_and_calibrate(self, run_set, extra_extension=""):
+ def _sum_and_calibrate(self, run_set, extra_extension=''):
"""
Aggregate the set of runs and calibrate
@param run_set: list of run numbers
@param extra_extension: string to be added to the workspace names
@return: workspace name of the aggregated and calibrated data
"""
- wsName = self._makeRunName(run_set[0])
+ wsName = self._make_run_name(run_set[0])
wsName += extra_extension
- wsName_mon = wsName + "_monitors"
- self._sumRuns(run_set, wsName, wsName_mon, extra_extension)
- self._calibData(wsName, wsName_mon)
+ wsName_mon = wsName + '_monitors'
+ self._sum_runs(run_set, wsName, wsName_mon, extra_extension)
+ self._calibrate_data(wsName, wsName_mon)
if not self._debugMode:
if self._MonNorm:
sapi.DeleteWorkspace(wsName_mon) # delete monitors
@@ -524,11 +521,11 @@ class BASISReduction(PythonAlgorithm):
sapi.Rebin(InputWorkspace=wsName,
OutputWorkspace=wsName,
Params=etRebins)
- if self._groupDetOpt != "None":
- if self._groupDetOpt == "Low-Resolution":
- grp_file = "BASIS_Grouping_LR.xml"
+ if self._groupDetOpt != 'None':
+ if self._groupDetOpt == 'Low-Resolution':
+ grp_file = 'BASIS_Grouping_LR.xml'
else:
- grp_file = "BASIS_Grouping.xml"
+ grp_file = 'BASIS_Grouping.xml'
# If mask override used, we need to add default grouping file
# location to search paths
if self._overrideMask:
@@ -536,7 +533,7 @@ class BASISReduction(PythonAlgorithm):
sapi.GroupDetectors(InputWorkspace=wsName,
OutputWorkspace=wsName,
MapFile=grp_file,
- Behaviour="Sum")
+ Behaviour='Sum')
# Output NXSPE file (must be done before transforming the
# vertical axis to point data)
@@ -564,13 +561,13 @@ class BASISReduction(PythonAlgorithm):
sapi.SofQW3(InputWorkspace=wsName,
QAxisBinning=self._qBins,
EMode='Indirect',
- EFixed=self._reflection["default_energy"],
+ EFixed=self._reflection['default_energy'],
OutputWorkspace=wsSqwName)
# Rebin the vanadium within the elastic line
if not isSample:
sapi.Rebin(InputWorkspace=wsSqwName,
OutputWorkspace=wsSqwName,
- Params=self._reflection["vanadium_bins"])
+ Params=self._reflection['vanadium_bins'])
return wsSqwName
def _ScaleY(self, wsName):
@@ -584,7 +581,7 @@ class BASISReduction(PythonAlgorithm):
sapi.Scale(InputWorkspace=wsName,
OutputWorkspace=wsName,
Factor=1./maximumYvalue,
- Operation="Multiply")
+ Operation='Multiply')
def generateSplitterWorkspace(self, fragment):
r"""Create a table workspace with time intervals to keep
@@ -601,7 +598,7 @@ class BASISReduction(PythonAlgorithm):
splitter = sapi.CreateEmptyTableWorkspace(OutputWorkspace='splitter')
splitter.addColumn('double', 'start')
splitter.addColumn('double', 'stop')
- splitter.addColumn('str', 'target') #, 'str')
+ splitter.addColumn('str', 'target')
if a == 0.0:
splitter.addRow([b, inf, '0'])
elif b == inf:
@@ -620,7 +617,7 @@ class BASISReduction(PythonAlgorithm):
ws_name : str
name of the workspace to filter
"""
- for run_fragment in self.getProperty("ExcludeTimeSegment").value.split(';'):
+ for run_fragment in self.getProperty('ExcludeTimeSegment').value.split(';'):
if run+':' in run_fragment:
self.generateSplitterWorkspace(run_fragment.split(':')[1])
sapi.FilterEvents(InputWorkspace=ws_name,
@@ -661,5 +658,6 @@ class BASISReduction(PythonAlgorithm):
r = mtd[ws_name].mutableRun()
r.addProperty('asString', json.dumps(self._as_json), True)
+
# Register algorithm with Mantid.
AlgorithmFactory.subscribe(BASISReduction)