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Commit 9eebdc83 authored by Gemma Guest's avatar Gemma Guest
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Tidy code and improve variable names 

I've left the script largely as provided by the scientists but done some tidying to improve readability
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Testing/SystemTests/tests/analysis/INTERReductionTest.py
+ 84
− 74
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...@@ -102,6 +102,7 @@ def WorkspaceName(file_path): ...@@ -102,6 +102,7 @@ def WorkspaceName(file_path):
def RegenerateReferenceFile(reference_file_directory, output_filename): def RegenerateReferenceFile(reference_file_directory, output_filename):
'''Generate the reference file from a given folder of output workspaces'''
files = os.listdir(reference_file_directory) files = os.listdir(reference_file_directory)
workspace_names = [] workspace_names = []
for file in files: for file in files:
...@@ -116,8 +117,7 @@ def RegenerateReferenceFile(reference_file_directory, output_filename): ...@@ -116,8 +117,7 @@ def RegenerateReferenceFile(reference_file_directory, output_filename):
def RegenerateRunsFile(transmission_run_names, run_numbers, event_run_numbers): def RegenerateRunsFile(transmission_run_names, run_numbers, event_run_numbers):
"This is used to generate the test input file from a range of run numbers" '''Generate the test input file from a range of run numbers and transmission runs.'''
"and transmission runs."
# Load transmission runs # Load transmission runs
for run in transmission_run_names: for run in transmission_run_names:
Load('{}.raw'.format(run), OutputWorkspace=run) Load('{}.raw'.format(run), OutputWorkspace=run)
...@@ -150,107 +150,117 @@ def CreateTransmissionWorkspaces(runs1, runs2, output_names): ...@@ -150,107 +150,117 @@ def CreateTransmissionWorkspaces(runs1, runs2, output_names):
DeleteWorkspace('TRANS_LAM_'+run2) DeleteWorkspace('TRANS_LAM_'+run2)
def EventRef(runno,angle,stop=0,start=0,DB='TRANS'): def EventRef(run_number,angle,start=0,stop=0,DB='TRANS'):
'''Event data time-slicing''' '''Event data time-slicing'''
runno=str(runno) # Filter the input workspace by the given start/stop time (or end time
w1=mtd[runno] # if stop time is not given)
total = w1.getRun().getLogData('gd_prtn_chrg').value run_name=str(run_number)
end = w1.getRun().getLogData('duration').value run_workspace=mtd[run_name]
if stop==0: if stop==0:
stoptime=end stoptime=run_workspace.getRun().getLogData('duration').value
else: else:
stoptime=stop stoptime=stop
FilterByTime(InputWorkspace=runno, OutputWorkspace=runno+'_filter', StartTime=start, StopTime=stoptime) filter_ws_name=run_name+'_filter'
wt=mtd[runno+'_filter'] FilterByTime(InputWorkspace=run_name, OutputWorkspace=filter_ws_name, StartTime=start, StopTime=stoptime)
slice = wt.getRun().getLogData('gd_prtn_chrg').value # Calculate the fraction of proton charge in this slice
fraction = slice/total filter_workspace=mtd[filter_ws_name]
duration = wt.getRun().getLogData('duration').value slice_proton_charge = filter_workspace.getRun().getLogData('gd_prtn_chrg').value
total_proton_charge = run_workspace.getRun().getLogData('gd_prtn_chrg').value
fraction = slice_proton_charge/total_proton_charge
duration = filter_workspace.getRun().getLogData('duration').value
print('Fraction:',fraction) print('Fraction:',fraction)
print('Slice:',slice) print('Slice:',slice)
print('Duration:',duration) print('Duration:',duration)
# Scale monitors by proton charge and add them to the slice workspace
Scale(InputWorkspace=runno+'_monitors',Factor=fraction,OutputWorkspace='mon_slice') Scale(InputWorkspace=run_name+'_monitors',Factor=fraction,OutputWorkspace='mon_slice')
Rebin(InputWorkspace=runno+'_filter', OutputWorkspace=runno+'_'+str(start)+'_'+str(stop), Params='0,100,100000', PreserveEvents=False)
Rebin(InputWorkspace='mon_slice', OutputWorkspace='mon_rebin', Params='0,100,100000', PreserveEvents=False) Rebin(InputWorkspace='mon_slice', OutputWorkspace='mon_rebin', Params='0,100,100000', PreserveEvents=False)
AppendSpectra(InputWorkspace1='mon_rebin', InputWorkspace2=runno+'_'+str(start)+'_'+str(stop), slice_name = str(run_number) + '_' + str(start) + '_' + str(stop)
OutputWorkspace=runno+'_'+str(start)+'_'+str(stop), MergeLogs=False) Rebin(InputWorkspace=filter_ws_name, OutputWorkspace=slice_name, Params='0,100,100000', PreserveEvents=False)
ReflectometryReductionOneAuto(InputWorkspace=runno+'_'+str(start)+'_'+str(stop), FirstTransmissionRun=DB, AppendSpectra(InputWorkspace1='mon_rebin', InputWorkspace2=slice_name,
OutputWorkspaceBinned=runno+'_'+str(start)+'_'+str(stop)+'_ref_binned', OutputWorkspace=slice_name, MergeLogs=False)
OutputWorkspace=runno+'_'+str(start)+'_'+str(stop)+'_ref', # Reduce this slice
OutputWorkspaceWavelength=runno+'_'+str(start)+'_'+str(stop)+'_lam',Debug=True) ReflectometryReductionOneAuto(InputWorkspace=slice_name, FirstTransmissionRun=DB,
OutputWorkspaceBinned=slice_name+'_ref_binned',
OutputWorkspace=slice_name+'_ref',
def QuickRef(runs=[], trans=[], angles=[]): OutputWorkspaceWavelength=slice_name+'_lam',Debug=True)
# Delete interim workspaces
DeleteWorkspace(slice_name+'_lam')
DeleteWorkspace(slice_name)
DeleteWorkspace(slice_name+'_ref')
DeleteWorkspace('mon_slice')
DeleteWorkspace('mon_rebin')
def QuickRef(run_numbers=[], trans_workspace_names=[], angles=[]):
'''Use of "QuickRef" - scripted reduction''' '''Use of "QuickRef" - scripted reduction'''
list='' list=''
if not angles: if not angles:
for i in range(len(runs)): for run_index in range(len(run_numbers)):
run1=runs[i] run_number=run_numbers[run_index]
trans1=trans[i] run_name=str(run_number)
ReflectometryReductionOneAuto(InputWorkspace=str(run1)+'.raw', FirstTransmissionRun=str(trans1), trans_workspace_name=str(trans_workspace_names[run_index])
OutputWorkspaceBinned=str(run1)+'_IvsQ_binned', OutputWorkspace=str(run1)+'_IvsQ', ReflectometryReductionOneAuto(InputWorkspace=run_name+'.raw', FirstTransmissionRun=trans_workspace_name,
OutputWorkspaceWavelength=str(run1)+'_IvsLam',Debug=True) OutputWorkspaceBinned=run_name+'_IvsQ_binned', OutputWorkspace=run_name+'_IvsQ',
list=list+str(run1)+'_IvsQ_binned'+',' OutputWorkspaceWavelength=run_name+'_IvsLam',Debug=True)
list=list+run_name+'_IvsQ_binned'+','
else: else:
for i in range(len(runs)): for run_index in range(len(run_numbers)):
run1=runs[i] run_number=run_numbers[run_index]
trans1=trans[i] run_name=str(run_number)
theta=angles[i] trans_workspace_name=str(trans_workspace_names[run_index])
theta=angles[run_index]
if theta == 0.8: if theta == 0.8:
ReflectometryReductionOneAuto(InputWorkspace=str(run1)+'.raw', FirstTransmissionRun=str(trans1), ReflectometryReductionOneAuto(InputWorkspace=run_name+'.raw', FirstTransmissionRun=trans_workspace_name,
OutputWorkspaceBinned=str(run1)+'_IvsQ_binned', OutputWorkspace=str(run1)+'_IvsQ', OutputWorkspaceBinned=run_name+'_IvsQ_binned', OutputWorkspace=run_name+'_IvsQ',
OutputWorkspaceWavelength=str(run1)+'_IvsLam', ThetaIn=theta, WavelengthMin=2.6,Debug=True) OutputWorkspaceWavelength=run_name+'_IvsLam', ThetaIn=theta, WavelengthMin=2.6,Debug=True)
else: else:
ReflectometryReductionOneAuto(InputWorkspace=str(run1)+'.raw', FirstTransmissionRun=str(trans1), ReflectometryReductionOneAuto(InputWorkspace=run_name+'.raw', FirstTransmissionRun=trans_workspace_name,
OutputWorkspaceBinned=str(run1)+'_IvsQ_binned', OutputWorkspace=str(run1)+'_IvsQ', OutputWorkspaceBinned=run_name+'_IvsQ_binned', OutputWorkspace=run_name+'_IvsQ',
OutputWorkspaceWavelength=str(run1)+'_IvsLam', ThetaIn=theta,Debug=True) OutputWorkspaceWavelength=run_name+'_IvsLam', ThetaIn=theta,Debug=True)
if i == len(runs)-1: if run_index == len(run_numbers)-1:
list=list+str(run1)+'_IvsQ_binned' list=list+run_name+'_IvsQ_binned'
else: else:
list=list+str(run1)+'_IvsQ_binned'+',' list=list+run_name+'_IvsQ_binned'+','
runno2=str(runs[-1]) first_run_name=str(run_numbers[0])
runno2=runno2[-2:] last_run_name=str(run_numbers[-1])
dqq = NRCalculateSlitResolution(Workspace=str(runs[0])+'_IvsQ') last_run_short_name=last_run_name[-2:]
Stitch1DMany(InputWorkspaces=list, OutputWorkspace=str(runs[0])+'_'+str(runno2), Params='-'+str(dqq), ScaleRHSWorkspace=1) dqq = NRCalculateSlitResolution(Workspace=first_run_name+'_IvsQ')
Stitch1DMany(InputWorkspaces=list, OutputWorkspace=first_run_name+'_'+last_run_short_name, Params='-'+str(dqq), ScaleRHSWorkspace=1)
def twoangfit(run1,run2,scalefactor):
runno=str(run2) def TwoAngleFit(run1_number,run2_number,scalefactor):
runno=runno[-2:] run1_name=str(run1_number)
Scale(InputWorkspace=str(run1)+'_'+str(runno), OutputWorkspace=str(run1)+'_'+str(runno)+'_scaled', Factor=(1.0/scalefactor)) run2_name=str(run2_number)
run2_short_name=run2_name[-2:]
combined_name=run1_name+'_'+run2_short_name
Scale(InputWorkspace=combined_name, OutputWorkspace=combined_name+'_scaled', Factor=(1.0/scalefactor))
function_name='name=ReflectivityMulf,nlayer=1,Theta=2.3,ScaleFactor=1,AirSLD=0,BulkSLD=0,Roughness=0,BackGround=6.8e-06,'\ function_name='name=ReflectivityMulf,nlayer=1,Theta=2.3,ScaleFactor=1,AirSLD=0,BulkSLD=0,Roughness=0,BackGround=6.8e-06,'\
'Resolution=5.0,SLD_Layer0=1.0e-6,d_Layer0=20.0,Rough_Layer0=0.0,constraints=(0<SLD_Layer0,0<d_Layer0),'\ 'Resolution=5.0,SLD_Layer0=1.0e-6,d_Layer0=20.0,Rough_Layer0=0.0,constraints=(0<SLD_Layer0,0<d_Layer0),'\
'ties=(Theta=2.3,AirSLD=0,BulkSLD=0,Resolution=5.0,ScaleFactor=1.0,Roughness=0,Rough_Layer0=0)' 'ties=(Theta=2.3,AirSLD=0,BulkSLD=0,Resolution=5.0,ScaleFactor=1.0,Roughness=0,Rough_Layer0=0)'
Fit(Function=function_name, Fit(Function=function_name,
InputWorkspace=str(run1)+'_'+str(runno)+'_scaled',IgnoreInvalidData='1', InputWorkspace=combined_name+'_scaled',IgnoreInvalidData='1',
Output=str(run1)+'_'+str(runno)+'_fit',OutputCompositeMembers='1',ConvolveMembers='1') Output=combined_name+'_fit',OutputCompositeMembers='1',ConvolveMembers='1')
sld=round(mtd[str(run1)+'_'+str(runno)+'_fit_Parameters'].cell(7,1),9) sld=round(mtd[combined_name+'_fit_Parameters'].cell(7,1),9)
thick=round(mtd[str(run1)+'_'+str(runno)+'_fit_Parameters'].cell(8,1),2) thick=round(mtd[combined_name+'_fit_Parameters'].cell(8,1),2)
dNb=sld*thick dNb=sld*thick
print('run ',str(run1)) print('run ',run1_name)
print('dNb ',dNb) print('dNb ',dNb)
print('SLD ',sld) print('SLD ',sld)
print('Thick ',thick) print('Thick ',thick)
print('-----------') print('-----------')
def GenerateTimeSlices(run): def GenerateTimeSlices(run_number):
'''Generate 60sec time slices''' '''Generate 60sec time slices'''
grouped='' for slice_index in range(5):
for ii in range(5): start=slice_index*60
slice_name = str(run) + '_' + str(60*ii) + '_' + str(60*(ii+1)) stop=(slice_index+1)*60
EventRef(run,0.5,(ii+1)*60,ii*60,DB='TRANS') EventRef(run_number,0.5,start,stop,DB='TRANS')
grouped=grouped+', ' + slice_name + '_ref_binned'
DeleteWorkspace(slice_name+'_lam')
DeleteWorkspace(slice_name)
DeleteWorkspace(slice_name+'_ref')
DeleteWorkspace('mon_slice')
DeleteWorkspace('mon_rebin')
def TestEventDataTimeSlicing(event_run_numbers): def TestEventDataTimeSlicing(event_run_numbers):
for run in event_run_numbers: for run_number in event_run_numbers:
GenerateTimeSlices(run) GenerateTimeSlices(run_number)
def TestReductionOfThreeAngleFringedSolidLiquidExample(): def TestReductionOfThreeAngleFringedSolidLiquidExample():
...@@ -274,7 +284,7 @@ def TestFittingOfReducedData(): ...@@ -274,7 +284,7 @@ def TestFittingOfReducedData():
#Create reduced workspace for test: #Create reduced workspace for test:
QuickRef([44990,44991],['TRANS_SM','TRANS_noSM'], angles=[0.8,2.3]) QuickRef([44990,44991],['TRANS_SM','TRANS_noSM'], angles=[0.8,2.3])
#Test fitting: #Test fitting:
twoangfit(44990,44991,scalefactor) TwoAngleFit(44990,44991,scalefactor)
# If you want to re-run the test and save the result as a reference... # If you want to re-run the test and save the result as a reference...
......
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