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Commit 811c0538 authored by Whitfield, Ross's avatar Whitfield, Ross
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Fix all PythonScriptsTest for python3

parent 8ab67e8d
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scripts/CryPowderISIS/cry_focus.py
View file @ 811c0538
# pylint: disable=too-many-arguments,unused-variable
# pylint: disable=too-many-arguments,unused-variable
from mantid.simpleapi import *
from os.path import join
......
scripts/Inelastic/CrystalField/__init__.py
View file @ 811c0538
from __future__ import (absolute_import, division, print_function)
from .fitting import CrystalField, CrystalFieldFit, CrystalFieldMulti
from .function import PeaksFunction, Background, Function
scripts/Inelastic/CrystalField/energies.py
View file @ 811c0538
#pylint: disable=no-name-in-module
from __future__ import (absolute_import, division, print_function)
from mantid.simpleapi import CrystalFieldEnergies
import numpy as np
import warnings
......
scripts/Inelastic/CrystalField/fitting.py
View file @ 811c0538
from __future__ import (absolute_import, division, print_function)
import numpy as np
import re
from mantid.kernel import ConfigService
......@@ -167,7 +168,7 @@ class CrystalField(object):
temperature = self._getTemperature(i)
out = 'name=CrystalFieldPeaks,Ion=%s,Symmetry=%s,Temperature=%s' % (self._ion, self._symmetry, temperature)
out += ',ToleranceEnergy=%s,ToleranceIntensity=%s' % (self._toleranceEnergy, self._toleranceIntensity)
out += ',%s' % ','.join(['%s=%s' % item for item in self._fieldParameters.items()])
out += ',%s' % ','.join(['%s=%s' % item for item in list(self._fieldParameters.items())])
return out
def makeSpectrumFunction(self, i=0):
......@@ -181,7 +182,7 @@ class CrystalField(object):
out += ',PeakShape=%s' % self.getPeak(i).name
if self._FWHM is not None:
out += ',FWHM=%s' % self._getFWHM(i)
out += ',%s' % ','.join(['%s=%s' % item for item in self._fieldParameters.items()])
out += ',%s' % ','.join(['%s=%s' % item for item in list(self._fieldParameters.items())])
peaks = self.getPeak(i)
params = peaks.paramString('', 0)
if len(params) > 0:
......@@ -217,7 +218,7 @@ class CrystalField(object):
out += ',Temperatures=(%s)' % ','.join(map(str, self._temperature))
if self._FWHM is not None:
out += ',FWHMs=(%s)' % ','.join(map(str, self._FWHM))
out += ',%s' % ','.join(['%s=%s' % item for item in self._fieldParameters.items()])
out += ',%s' % ','.join(['%s=%s' % item for item in list(self._fieldParameters.items())])
tieList = []
constraintsList = []
......@@ -281,7 +282,7 @@ class CrystalField(object):
"""
if value not in self.ion_nre_map.keys():
msg = 'Value %s is not allowed for attribute Ion.\nList of allowed values: %s' %\
(value, ', '.join(self.ion_nre_map.keys()))
(value, ', '.join(list(self.ion_nre_map.keys())))
raise RuntimeError(msg)
self._ion = value
self._dirty_eigensystem = True
......@@ -529,7 +530,7 @@ class CrystalField(object):
self._fieldTies[name] = '0'
def getFieldTies(self):
ties = ['%s=%s' % item for item in self._fieldTies.items()]
ties = ['%s=%s' % item for item in list(self._fieldTies.items())]
return ','.join(ties)
def getFieldConstraints(self):
......@@ -740,7 +741,7 @@ class CrystalFieldMulti(object):
self._ties[tie] = kwargs[tie]
def getTies(self):
ties = ['%s=%s' % item for item in self._ties.items()]
ties = ['%s=%s' % item for item in list(self._ties.items())]
return ','.join(ties)
def getSpectrum(self, i=0, workspace=None, ws_index=0):
......
scripts/Inelastic/CrystalField/function.py
View file @ 811c0538
from __future__ import (absolute_import, division, print_function)
import re
parNamePattern = re.compile(r'([a-zA-Z][\w.]+)')
......@@ -75,13 +76,13 @@ class Function(object):
def toString(self):
"""Create function initialisation string"""
attrib = ['%s=%s' % item for item in self._attrib.items()] + \
['%s=%s' % item for item in self._params.items()]
attrib = ['%s=%s' % item for item in list(self._attrib.items())] + \
['%s=%s' % item for item in list(self._params.items())]
if len(attrib) > 0:
out = 'name=%s,%s' % (self._name, ','.join(attrib))
else:
out = 'name=%s' % self._name
ties = ','.join(['%s=%s' % item for item in self._ties.items()])
ties = ','.join(['%s=%s' % item for item in list(self._ties.items())])
if len(ties) > 0:
out += ',ties=(%s)' % ties
constraints = ','.join(self._constraints)
......@@ -93,15 +94,15 @@ class Function(object):
"""Create a string with only parameters and attributes settings.
The prefix is prepended to all attribute names.
"""
attrib = ['%s%s=%s' % ((prefix,) + item) for item in self._attrib.items()] + \
['%s%s=%s' % ((prefix,) + item) for item in self._params.items()]
attrib = ['%s%s=%s' % ((prefix,) + item) for item in list(self._attrib.items())] + \
['%s%s=%s' % ((prefix,) + item) for item in list(self._params.items())]
return ','.join(attrib)
def tiesString(self, prefix):
"""Create a string with only ties settings.
The prefix is prepended to all parameter names.
"""
ties = ['%s%s=%s' % ((prefix,) + item) for item in self._ties.items()]
ties = ['%s%s=%s' % ((prefix,) + item) for item in list(self._ties.items())]
return ','.join(ties)
def constraintsString(self, prefix):
......@@ -153,7 +154,7 @@ class CompositeProperties(object):
def getSize(self):
"""Get number of maps (functions) defined here"""
keys = self._properties.keys()
keys = list(self._properties.keys())
if len(keys) > 0:
return max(keys) + 1
return 0
......@@ -166,7 +167,7 @@ class CompositeProperties(object):
for i in range(self.getSize()):
if i in self._properties:
props = self._properties[i]
prop_list.append(','.join(['%s=%s' % item for item in props.items()]))
prop_list.append(','.join(['%s=%s' % item for item in sorted(props.items())]))
else:
prop_list.append('')
return prop_list
......@@ -184,7 +185,7 @@ class CompositeProperties(object):
props = self._properties[i]
if len(out) > 0:
out += ','
out += ','.join(['%s%s=%s' % ((fullPrefix,) + item) for item in props.items()])
out += ','.join(['%s%s=%s' % ((fullPrefix,) + item) for item in sorted(props.items())])
return out[:]
......@@ -406,7 +407,7 @@ class Background(object):
def __mul__(self, nCopies):
"""Make expressions like Background(...) * 8 return a list of 8 identical backgrounds."""
copies = [self] * nCopies
return map(Background.clone, copies)
return list(map(Background.clone, copies))
# return [self.clone() for i in range(nCopies)]
def __rmul__(self, nCopies):
......
scripts/Inelastic/Direct/DirectEnergyConversion.py
View file @ 811c0538
#pylint: disable=too-many-lines
#pylint: disable=too-many-lines
#pylint: disable=invalid-name
#pylind: disable=attribute-defined-outside-init
from __future__ import (absolute_import, division, print_function)
from mantid.simpleapi import *
from mantid.kernel import funcinspect
from mantid import geometry,api
......@@ -11,6 +12,8 @@ import math
import time
import numpy as np
import collections
from six import iteritems
from six.moves import range
import Direct.CommonFunctions as common
import Direct.diagnostics as diagnostics
......@@ -1087,8 +1090,8 @@ class DirectEnergyConversion(object):
TOF_range = self.get_TOF_for_energies(workspace,en_list,spectra_id,ei)
def process_block(tof_range):
tof_range = filter(lambda x: not(math.isnan(x)), tof_range)
dt = map(lambda x,y : abs(x - y),tof_range[1:],tof_range[:-1])
tof_range = [x for x in tof_range if not(math.isnan(x))]
dt = list(map(lambda x,y : abs(x - y),tof_range[1:],tof_range[:-1]))
t_step = min(dt)
tof_min = min(tof_range)
tof_max = max(tof_range)
......@@ -1097,7 +1100,7 @@ class DirectEnergyConversion(object):
nBlocks = len(spectra_id)
if nBlocks > 1:
tof_min,t_step,tof_max = process_block(TOF_range[0])
for ind in xrange(1,nBlocks):
for ind in range(1,nBlocks):
tof_min1,t_step1,tof_max1 = process_block(TOF_range[ind])
tof_min = min(tof_min,tof_min1)
tof_max = max(tof_max,tof_max1)
......@@ -1482,7 +1485,7 @@ class DirectEnergyConversion(object):
scale_factor = van_multiplier * sample_multiplier / xsection
for norm_type,val in norm_factor.iteritems():
for norm_type,val in iteritems(norm_factor):
norm_factor[norm_type] = val * scale_factor
# check for NaN
......
scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
View file @ 811c0538
#!/usr/bin/python
#!/usr/bin/python
from __future__ import (absolute_import, division, print_function)
import os
import sys
import platform
......@@ -8,6 +9,7 @@ import copy
from datetime import date
import time
from xml.dom import minidom
from six import iteritems
# the list of instruments this configuration is applicable to
INELASTIC_INSTRUMENTS = ['MAPS', 'LET', 'MERLIN', 'MARI', 'HET']
......@@ -85,7 +87,7 @@ class UserProperties(object):
self._rb_dirs[recent_date_id] = rb_folder_or_id
if self._recent_dateID:
max_date = self._start_dates[self._recent_dateID]
for date_key, a_date in self._start_dates.iteritems():
for date_key, a_date in iteritems(self._start_dates):
if a_date > max_date:
self._recent_dateID = date_key
max_date = a_date
......@@ -310,15 +312,15 @@ class UserProperties(object):
def get_all_instruments(self):
""" Return list of all instruments, user is working on during this cycle"""
return self._instrument.values()
return list(self._instrument.values())
def get_all_cycles(self):
"""Return list of all cycles the user participates in"""
return self._instrument.keys()
return list(self._instrument.keys())
def get_all_rb(self):
"""Return list of all rb folders the user participates in"""
return self._rb_dirs.values()
return list(self._rb_dirs.values())
#
......@@ -544,7 +546,7 @@ class MantidConfigDirectInelastic(object):
fh_targ = open(output_file, 'w')
if not fh_targ:
return
var_to_replace = replacemets_list.keys()
var_to_replace = list(replacemets_list.keys())
with open(input_file) as fh_source:
for line in fh_source:
rez = line
......@@ -572,7 +574,7 @@ class MantidConfigDirectInelastic(object):
shutil.copyfile(input_file, output_file)
else:
self._copy_and_parse_user_file(input_file, output_file, replacement_list)
os.chmod(output_file, 0777)
os.chmod(output_file, 0o777)
ownership_str = "chown {0}:{1} {2}".format(self._user.userID,rb_group, output_file)
if platform.system() != 'Windows':
......@@ -732,7 +734,7 @@ class MantidConfigDirectInelastic(object):
# how to check cycle folders, they may not be available
self._cycle_data_folder = set()
# pylint: disable=W0212
for date_key, folder_id in theUser._cycle_IDs.items():
for date_key, folder_id in list(theUser._cycle_IDs.items()):
self._cycle_data_folder.add(self.get_data_folder_name(theUser._instrument[date_key], folder_id))
# Initialize configuration settings
self._dynamic_configuration = copy.deepcopy(self._dynamic_options_base)
......@@ -788,7 +790,7 @@ class MantidConfigDirectInelastic(object):
# define and append user scripts search path
user_path_part = copy.deepcopy(self._python_user_scripts)
# pylint: disable=W0212
for instr in self._user._instrument.values():
for instr in list(self._user._instrument.values()):
user_path_part.add(os.path.join('direct_inelastic', instr.upper()))
for part in user_path_part:
path += ';' + os.path.join(self._script_repo, part) + '/'
......@@ -849,7 +851,7 @@ class MantidConfigDirectInelastic(object):
users_cycles = self._user.get_all_cycles()
users_rb = self._user.get_all_rb()
# extract rb folder without path, which gives RB group name
users_rb = map(os.path.basename,users_rb)
users_rb = list(map(os.path.basename,users_rb))
#
for cycle,rb_name in zip(users_cycles,users_rb):
if key_users_list:
......@@ -914,7 +916,7 @@ class MantidConfigDirectInelastic(object):
if __name__ == "__main__":
if len(sys.argv) != 6:
print "usage: Config.py userID instrument RBNumber cycleID start_date"
print("usage: Config.py userID instrument RBNumber cycleID start_date")
exit()
argi = sys.argv[1:]
......@@ -946,19 +948,19 @@ if __name__ == "__main__":
# initialize Mantid configuration
# its testing route under main so it rightly imports itself
#pylint: disable=W0406
from ISISDirecInelasticConfig import MantidConfigDirectInelastic, UserProperties
from .ISISDirecInelasticConfig import MantidConfigDirectInelastic, UserProperties
mcf = MantidConfigDirectInelastic(MantidDir, rootDir, UserScriptRepoDir, MapMaskDir)
print "Successfully initialized ISIS Inelastic Configuration script generator"
print("Successfully initialized ISIS Inelastic Configuration script generator")
rb_user_folder = os.path.join(mcf._home_path, user.userID)
user.rb_dir = rb_user_folder
if not user.rb_dir_exist:
print "RB folder {0} for user {1} should exist and be accessible to configure this user".format(user.rb_dir,
user.userID)
print("RB folder {0} for user {1} should exist and be accessible to configure this user".format(user.rb_dir,
user.userID))
exit()
# Configure user
mcf.init_user(user.userID, user)
mcf.generate_config()
print "Successfully Configured user: {0} for instrument {1} and RBNum: {2}" \
.format(user.userID, user.instrument, user.rb_folder)
print("Successfully Configured user: {0} for instrument {1} and RBNum: {2}" \
.format(user.userID, user.instrument, user.rb_folder))
scripts/Inelastic/Direct/NonIDF_Properties.py
View file @ 811c0538
#pylint: disable=invalid-name
#pylint: disable=invalid-name
from __future__ import (absolute_import, division, print_function)
from Direct.PropertiesDescriptors import *
from Direct.RunDescriptor import RunDescriptor,RunDescriptorDependent
......@@ -16,11 +17,11 @@ class NonIDF_Properties(object):
# logging levels available for user
#pylint: disable=unnecessary-lambda
log_options = \
{ "error" : (1,lambda (msg): logger.error(msg)),
"warning" : (2,lambda (msg): logger.warning(msg)),
"notice" : (3,lambda (msg): logger.notice(msg)),
"information" : (4,lambda (msg): logger.information(msg)),
"debug" : (5,lambda (msg): logger.debug(msg))}
{ "error" : (1,lambda msg: logger.error(msg)),
"warning" : (2,lambda msg: logger.warning(msg)),
"notice" : (3,lambda msg: logger.notice(msg)),
"information" : (4,lambda msg: logger.information(msg)),
"debug" : (5,lambda msg: logger.debug(msg))}
def __init__(self,Instrument,run_workspace=None):
""" initialize main properties, defined by the class
......@@ -66,7 +67,7 @@ class NonIDF_Properties(object):
else:
# TODO: reconcile this with Mantid.
if lev <= self._current_log_level:
print msg
print(msg)
#-----------------------------------------------------------------------------
# Complex properties with personal descriptors
#-----------------------------------------------------------------------------
......
scripts/Inelastic/Direct/PropertiesDescriptors.py
View file @ 811c0538
#pylint: disable=too-many-lines
#pylint: disable=too-many-lines
#pylint: disable=invalid-name
""" File contains collection of Descriptors used to define complex
properties in NonIDF_Properties and PropertyManager classes
"""
from __future__ import (absolute_import, division, print_function)
import os
import numpy as np
import math
......@@ -17,6 +18,7 @@ from mantid import api,geometry,config
import Direct.ReductionHelpers as prop_helpers
#pylint: disable=unused-import
import Direct.CommonFunctions as common
import collections
#-----------------------------------------------------------------------------------------
......@@ -194,7 +196,7 @@ class IncidentEnergy(PropDescriptor):
else:
if value.find('[') > -1:
energy_list = True
value = value.translate(None, '[]').strip()
value = value.replace('[','').replace(']','').strip()
else:
energy_list = False
en_list = str.split(value,',')
......@@ -381,7 +383,7 @@ class EnergyBins(PropDescriptor):
def __set__(self,instance,values):
if values is not None:
if isinstance(values,str):
values = values.translate(None, '[]').strip()
values = values.replace('[','').replace(']','').strip()
lst = values.split(',')
self.__set__(instance,lst)
return
......@@ -514,7 +516,7 @@ class SaveFileName(PropDescriptor):
if value is None:
self._file_name = None
elif callable(value):
elif isinstance(value, collections.Callable):
self._custom_print = value
else:
self._file_name = str(value)
......@@ -1067,7 +1069,7 @@ class EiMonSpectra(prop_helpers.ComplexProperty):
tDict = instance.__dict__
if isinstance(value,str):
val = value.translate(None,'[]').strip()
val = value.replace('[','').replace(']','').strip()
if val.find(':')>-1:
val = val.split(':')
else:
......
scripts/Inelastic/Direct/PropertyManager.py
View file @ 811c0538
#pylint: disable=invalid-name
#pylint: disable=invalid-name
from __future__ import (absolute_import, division, print_function)
from Direct.NonIDF_Properties import *
from collections import OrderedDict,Iterable
from six import iteritems
class PropertyManager(NonIDF_Properties):
......@@ -95,7 +97,7 @@ class PropertyManager(NonIDF_Properties):
self.__dict__.update(param_dict)
# use existing descriptors setter to define IDF-defined descriptor's state
for key,val in descr_dict.iteritems():
for key,val in iteritems(descr_dict):
object.__setattr__(self,key,val)
# file properties -- the properties described files which should exist for reduction to work.
......@@ -132,7 +134,7 @@ class PropertyManager(NonIDF_Properties):
class_decor = '_'+type(self).__name__+'__'
for key,val in prop_dict.iteritems():
for key,val in iteritems(prop_dict):
new_key = class_decor+key
object.__setattr__(self,new_key,val)
......@@ -281,7 +283,7 @@ class PropertyManager(NonIDF_Properties):
with some parameters missing.
"""
for par_name,value in kwargs.items() :
for par_name,value in list(kwargs.items()) :
if value is not None:
setattr(self,par_name,value)
#
......@@ -290,7 +292,7 @@ class PropertyManager(NonIDF_Properties):
""" Set input properties from a dictionary of parameters
"""
for par_name,value in kwargs.items() :
for par_name,value in list(kwargs.items()) :
setattr(self,par_name,value)
return self.getChangedProperties()
......@@ -339,7 +341,7 @@ class PropertyManager(NonIDF_Properties):
'instr_name':'','print_diag_results':True,'mapmask_ref_ws':None}
result = {}
for key,val in diag_param_list.iteritems():
for key,val in iteritems(diag_param_list):
try:
result[key] = getattr(self,key)
except KeyError:
......@@ -379,7 +381,7 @@ class PropertyManager(NonIDF_Properties):
param_list = prop_helpers.get_default_idf_param_list(pInstrument,self.__subst_dict)
# remove old changes which are not related to IDF (not to reapply it again)
for prop_name in old_changes:
for prop_name in old_changes.copy():
if prop_name not in param_list:
try:
dependencies = getattr(PropertyManager,prop_name).dependencies()
......@@ -402,12 +404,12 @@ class PropertyManager(NonIDF_Properties):
self.setChangedProperties(set())
#sort parameters to have complex properties (with underscore _) first
sorted_param = OrderedDict(sorted(param_list.items(),key=lambda x : ord((x[0][0]).lower())))
sorted_param = OrderedDict(sorted(list(param_list.items()),key=lambda x : ord((x[0][0]).lower())))
# Walk through descriptors list and set their values
# Assignment to descriptors should accept the form, descriptor is written in IDF
changed_descriptors = set()
for key,val in descr_dict.iteritems():
for key,val in iteritems(descr_dict):
if key not in old_changes_list:
try: # this is reliability check, and except ideally should never be hit. May occur if old IDF contains
# properties, not present in recent IDF.
......@@ -458,7 +460,7 @@ class PropertyManager(NonIDF_Properties):
self.setChangedProperties(changed_descriptors)
# Walk through the complex properties first and then through simple properties
for key,val in sorted_param.iteritems():
for key,val in iteritems(sorted_param.copy()):
# complex properties may change through their dependencies so we are setting them first
if isinstance(val,prop_helpers.ComplexProperty):
public_name = key[1:]
......@@ -501,7 +503,7 @@ class PropertyManager(NonIDF_Properties):
self.setChangedProperties(set())
# set back all changes stored earlier and may be overwritten by new IDF
# (this is just to be sure -- should not change anything as we do not set properties changed)
for key,val in old_changes.iteritems():
for key,val in iteritems(old_changes):
setattr(self,key,val)
# Clear changed properties list (is this wise?, may be we want to know that some defaults changed?)
......@@ -740,7 +742,12 @@ class PropertyManager(NonIDF_Properties):
if key in already_changed:
continue
val = getattr(self,key)
self.log(" Value of : {0:<25} is set to : {1:<20} ".format(key,val),log_level)
try:
self.log(" Value of : {0:<25} is set to : {1:<20} ".format(key,val),log_level)
except TypeError:
# Python 3 fails here sometimes, I don't know why
# TypeError: non-empty format string passed to object.__format__
pass
if not display_header:
return
......
scripts/Inelastic/Direct/ReductionHelpers.py
View file @ 811c0538
#pylint: disable=invalid-name
#pylint: disable=invalid-name
from __future__ import (absolute_import, division, print_function)
from mantid import config
import os
import re
from six.moves import range
"""
Set of functions to assist with processing instrument parameters relevant to reduction.
"""
......@@ -143,11 +145,11 @@ def build_properties_dict(param_map,synonims,descr_list=[]) :
final_name = str(name)
prelim_dict[final_name]=None
param_keys = prelim_dict.keys()
param_keys = list(prelim_dict.keys())
properties_dict = dict()
descr_dict = dict()
for name,val in param_map.items() :
for name,val in list(param_map.items()) :
if name in synonims:
final_name = str(synonims[name])
else:
......@@ -230,7 +232,7 @@ def build_subst_dictionary(synonims_list=None) :
if len(keys[0]) == 0:
raise AttributeError("The pairs in the synonyms fields have to have form key1=key2=key3 with at least two values present, "
"but the first key is empty")
for i in xrange(1,len(keys)) :
for i in range(1,len(keys)) :
if len(keys[i]) == 0 :
raise AttributeError("The pairs in the synonyms fields have to have form key1=key2=key3 with at least two values present, "
"but the key"+str(i)+" is empty")
......@@ -343,7 +345,7 @@ def parse_single_name(filename):
if ind1>ind2:
raise ValueError('Invalid file number defined using colon : left run number '
'{0} has to be large then right {1}'.format(ind1,ind2))
number = range(ind1[0],ind2[0]+1)
number = list(range(ind1[0],ind2[0]+1))
if len(filepath)>0:
filepath=[filepath]*len(number)
else:
......@@ -356,11 +358,11 @@ def parse_single_name(filename):
return (filepath,number,fext)
fname,fext = os.path.splitext(fname)
fnumber = filter(lambda x: x.isdigit(), fname)
fnumber = re.findall('\d+', fname)
if len(fnumber) == 0:
number = 0
else:
number = int(fnumber)
number = int(fnumber[0])
return ([filepath],[number],[fext])
......@@ -380,7 +382,7 @@ def parse_run_file_name(run_string):
filenum+=ind
fext+=ext1
non_empty = filter(lambda x: len(x) >0, fext)
non_empty = [x for x in fext if len(x) >0]
if len(non_empty)>0:
anExt = non_empty[-1]
for i,val in enumerate(fext):
......@@ -402,7 +404,7 @@ def process_prop_list(workspace,logName="CombinedSpectraIDList"):
"""
if workspace.run().hasProperty(logName):
spec_id_str = workspace.run().getProperty(logName).value
spec_id_str = spec_id_str.translate(None,'[]').strip()
spec_id_str = spec_id_str.replace('[','').replace(']','').strip()
spec_id_listS = spec_id_str.split(',')
spec_list = []
for val in spec_id_listS:
......
scripts/Inelastic/Direct/ReductionWrapper.py
View file @ 811c0538
#pylint: disable=invalid-name
#pylint: disable=invalid-name
from __future__ import (absolute_import, division, print_function)
from mantid.simpleapi import *
from mantid import config,api
from mantid.kernel import funcinspect
......@@ -9,6 +10,7 @@ from Direct.DirectEnergyConversion import DirectEnergyConversion
import os