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Ticket #8037: WISH_cycle_13_2_SF_9to9.py

File WISH_cycle_13_2_SF_9to9.py, 29.8 KB (added by Roman Tolchenov, 7 years ago)

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1	# Set of routines to normalise WISH data
2	from mantidsimple import *
3	import matplotlib.pyplot as p
4	import numpy as n
5	wish_dir=""
6
7	# Get the valid wavelength range, i.e. excluding regions where choppers cut
8	def WISH_getlambdarange():
9	return 0.7,10.35
10
11	def WISH_setuser(usern):
12	global username
13	username=usern
14
15	def WISH_setdatadir(directory="/archive/ndxwish/Instrument/data/cycle_09_5/"):
16	global wish_datadir
17	wish_datadir=directory
18
19	def WISH_setuserdir(directory):
20	global wish_userdir
21	wish_userdir=directory
22
23	def WISH_datadir():
24	return wish_datadir
25
26	def WISH_userdir(cycle='cycle_10_1'):
27	return wish_userdir
28
29	def WISH_calibration(cycle="11_4"):
30	#return "/home/mp43/Calibration/Cycle_"+cycle+"/"
31	return "/home/hqs74821/work/mantid_stuff/DockWidget/"
32
33	def WISH_startup(usern,cycle='10_1'):
34	global userdatadir
35	global userdataprocessed
36	global mtdplt
37	import sys
38	sys.path.append('/home/hqs74821/work/mantid_stuff/DockWidget/')
39	import Mantid_plotting as mtdplt
40	userdatadir="/archive/ndxwish/Instrument/data/cycle_"+cycle+'/'
41	WISH_setdatadir(userdatadir)
42	print "Raw Data in : ", userdatadir
43	userdataprocessed="/home/hqs74821/work/mantid_stuff/DockWidget/ProcessedData/"
44	WISH_setuserdir(directory=userdataprocessed)
45	print "Processed Data in : ",userdataprocessed
46	return
47
48
49	#Returns the calibration filename
50	def WISH_cal(panel):
51	return WISH_calibration()+"WISH_cycle_10_3_noends_9to9.cal"
52
53	# Returns the grouping filename
54	def WISH_group():
55	return WISH_calibration()+"WISH_cycle_10_3_noends_9to9.cal"
56
57	def WISH_getvana(panel,SE="candlestick",cycle="09_4"):
58	if (SE=="candlestick"):
59	if (cycle=="09_2"):
60	return WISH_calibration()+"vana318-"+str(panel)+"foc-rmbins-smooth50.nx5"
61	if (cycle=="09_3"):
62	return WISH_calibration(cycle)+"vana935-"+str(panel)+"foc-SS.nx5"
63	if (cycle=="09_4"):
64	return WISH_calibration(cycle)+"vana3123-"+str(panel)+"foc-SS.nx5"
65	if (cycle=="09_5"):
66	return WISH_calibration(cycle)+"vana3123-"+str(panel)+"foc-SS.nx5"
67	if (cycle=="11_4"):
68	return WISH_calibration(cycle)+"vana19612-"+str(panel)+"foc-SF-SS.nxs"
69	if (SE=="WISHcryo"):
70	if (cycle=="09_2"):
71	return WISH_calibration()+"vana318-"+str(panel)+"foc-rmbins-smooth50.nx5"
72	if (cycle=="09_3"):
73	return WISH_calibration(cycle)+"vana935-"+str(panel)+"foc-SS.nx5"
74	if (cycle=="09_4"):
75	return WISH_calibration(cycle)+"vana3123-"+str(panel)+"foc-SS.nx5"
76	if (cycle=="11_1"):
77	return WISH_calibration(cycle)+"vana17718-"+str(panel)+"foc-SS.nxs"
78	if (cycle=="11_2"):
79	return WISH_calibration(cycle)+"vana16812-"+str(panel)+"foc-SS.nx5"
80	if (cycle=="11_3"):
81	return WISH_calibration(cycle)+"vana18590-"+str(panel)+"foc-SS-new.nxs"
82
83
84	def split_string(t):
85	indxp=0
86	for i in range(0,len(t)):
87	if (t[i]=="+"):
88	indxp=i
89	if (indxp!=0):
90	return int(t[0:indxp]),int(t[indxp+1:len(t)])
91
92	def WISH_getemptyinstrument(panel,cycle="09_4"):
93	if (cycle=="09_4"):
94	return WISH_calibration(cycle)+"emptyinst3120-"+str(panel)+"foc.nx5"
95
96	def WISH_getempty(panel,SE="WISHcryo",cycle="09_4"):
97	if (SE=="WISHcryo"):
98	if (cycle=="09_2"):
99	return WISH_calibration(cycle)+"emptycryo322-"+str(panel)+"-smooth50.nx5"
100	if (cycle=="09_3"):
101	return WISH_calibration(cycle)+"emptycryo1725-"+str(panel)+"foc.nx5"
102	if (cycle=="09_4"):
103	return WISH_calibration(cycle)+"emptycryo3307-"+str(panel)+"foc.nx5"
104	if (cycle=="09_5"):
105	return WISH_calibration(cycle)+"emptycryo16759-"+str(panel)+"foc.nx5"
106	if (cycle=="11_1"):
107	return WISH_calibration(cycle)+"emptycryo17712-"+str(panel)+"foc-SS.nxs"
108	if (cycle=="11_2"):
109	return WISH_calibration(cycle)+"emptycryo16759-"+str(panel)+"foc-SS.nx5"
110	if (cycle=="11_3"):
111	return WISH_calibration(cycle)+"emptycryo17712-"+str(panel)+"foc-SS-new.nxs"
112	if (cycle=="11_4"):
113	return WISH_calibration(cycle)+"empty_mag20620-"+str(panel)+"foc-HR-SF.nxs"
114	if (SE=="candlestick"):
115	if (cycle=="09_4"):
116	return WISH_calibration(cycle)+"emptyinst3120-"+str(panel)+"foc.nxs"
117	if (cycle=="09_3"):
118	return WISH_calibration(cycle)+"emptyinst1726-"+str(panel)+"foc-monitor.nxs"
119	if (cycle=="11_4"):
120	return WISH_calibration(cycle)+"emptyinst19618-"+str(panel)+"foc-SF-S.nxs"
121
122	def WISH_getfilename(run_number,ext):
123	if (ext[0]!='s'):
124	data_dir=WISH_datadir()
125	else:
126	#data_dir="/datad/ndxwish/"
127	data_dir=WISH_datadir()
128	digit=len(str(run_number))
129	filename=data_dir+"WISH"
130	for i in range(0,8-digit):
131	filename=filename+"0"
132	filename+=str(run_number)+"."+ext
133	return filename
134
135	def WISH_returnpanel(panel):
136	if (panel==1):
137	min=6
138	max=19461
139	elif (panel==2):
140	min=19462
141	max=38917
142	elif( panel==3):
143	min=38918
144	max=58373
145	elif (panel==4):
146	min=58374
147	max=77829
148	elif (panel==5):
149	min=77830
150	max=97285
151	elif (panel==6):
152	min=97286
153	max=116741
154	elif (panel==7):
155	min=116742
156	max=136197
157	elif (panel==8):
158	min=136198
159	max=155653
160	elif (panel==9):
161	min=155654
162	max=175109
163	elif (panel==0):
164	min=6
165	max=175109
166	return min,max
167
168	# Reads a wish data file return a workspace with a short name
169	def WISH_read(number,panel,ext):
170	if type(number) is int:
171	filename=WISH_getfilename(number,ext)
172	if (ext[0:9]=="nxs_event"):
173	filename=WISH_getfilename(number,"nxs")
174	print "will be reading filename..."+filename
175	min,max=WISH_returnpanel(panel)
176	if (panel!=0):
177	output="w"+str(number)+"-"+str(panel)
178	else:
179	output="w"+str(number)
180	if (ext=="raw"):
181	LoadRaw(Filename=filename,OutputWorkspace=output,SpectrumMin=str(min),SpectrumMax=str(max),LoadLogFiles="0")
182	MaskBins(output,output,XMin=99900,XMax=106000)
183	print "standard raw file loaded"
184	if (ext[0]=="s"):
185	LoadRaw(Filename=filename,OutputWorkspace=output,SpectrumMin=str(min),SpectrumMax=str(max),LoadLogFiles="0")
186	MaskBins(output,output,XMin=99900,XMax=106000)
187	print "sav file loaded"
188	if (ext=="nxs_event"):
189	LoadEventNexus(Filename=filename,OutputWorkspace=output,LoadMonitors='1')
190	RenameWorkspace(output+"_monitors","w"+str(number)+"_monitors")
191	Rebin(InputWorkspace=output,OutputWorkspace=output,Params='6000,-0.00063,110000')
192	ConvertToMatrixWorkspace(output,output)
193	min,max=WISH_returnpanel(panel)
194	CropWorkspace(InputWorkspace=output,OutputWorkspace=output,StartWorkspaceIndex=min-6,EndWorkspaceIndex=max-6)
195	MaskBins(output,output,XMin=99900,XMax=106000)
196	print "full nexus eventfile loaded"
197	if (ext[0:10]=="nxs_event_"):
198	label,tmin,tmax=split_string_event(ext)
199	output=output+"_"+label
200	if (tmax=="end"):
201	LoadEventNexus(Filename=filename,OutputWorkspace=output,FilterByTimeStart=tmin,LoadMonitors='1',MonitorsAsEvents='1',FilterMonByTimeStart=tmin)
202	else:
203	LoadEventNexus(Filename=filename,OutputWorkspace=output,FilterByTimeStart=tmin,FilterByTimeStop=tmax,LoadMonitors='1',MonitorsAsEvents='1',FilterMonByTimeStart=tmin,FilterMonByTimeStop=tmax)
204	RenameWorkspace(output+"_monitors","w"+str(number)+"_monitors")
205	print "renaming monitors done!"
206	Rebin(InputWorkspace=output,OutputWorkspace=output,Params='6000,-0.00063,110000')
207	ConvertToMatrixWorkspace(output,output)
208	min,max=WISH_returnpanel(panel)
209	CropWorkspace(InputWorkspace=output,OutputWorkspace=output,StartWorkspaceIndex=min-6,EndWorkspaceIndex=max-6)
210	MaskBins(output,output,XMin=99900,XMax=106000)
211	print "nexus event file chopped"
212	if (ext=="nxs"):
213	LoadNexus(Filename=filename,OutputWorkspace=output)
214	print "standard histo nxs file loaded"
215	else:
216	n1,n2=split_string(number)
217	output="w"+str(n1)+"_"+str(n2)+"-"+str(panel)
218	filename=WISH_getfilename(n1,ext)
219	print "reading filename..."+filename
220	min,max=WISH_returnpanel(panel)
221	output1="w"+str(n1)+"-"+str(panel)
222	LoadRaw(Filename=filename,OutputWorkspace=output1,SpectrumMin=str(min),SpectrumMax=str(max),LoadLogFiles="0")
223	filename=WISH_getfilename(n2,ext)
224	print "reading filename..."+filename
225	min,max=WISH_returnpanel(panel)
226	output2="w"+str(n2)+"-"+str(panel)
227	LoadRaw(Filename=filename,OutputWorkspace=output2,SpectrumMin=str(min),SpectrumMax=str(max),LoadLogFiles="0")
228	MergeRuns(output1+","+output2,output)
229	mantid.deleteWorkspace(output1)
230	mantid.deleteWorkspace(output2)
231	ConvertUnits(output,output,"Wavelength")
232	lmin,lmax=WISH_getlambdarange()
233	CropWorkspace(output,output,XMin=lmin,XMax=lmax)
234	monitor=WISH_process_incidentmon(number,ext,spline_terms=70,debug=False)
235	print "first norm to be done"
236	NormaliseToMonitor(InputWorkspace=output,OutputWorkspace=output+"norm1",MonitorWorkspace=monitor)
237	print "second norm to be done"
238	NormaliseToMonitor(InputWorkspace=output+"norm1",OutputWorkspace=output+"norm2",MonitorWorkspace=monitor,IntegrationRangeMin=0.7,IntegrationRangeMax=10.35)
239	DeleteWorkspace(output)
240	DeleteWorkspace(output+"norm1")
241	RenameWorkspace(output+"norm2",output)
242	ConvertUnits(output,output,"TOF")
243	ReplaceSpecialValues(output,output,NaNValue=0.0,NaNError=0.0,InfinityValue=0.0,InfinityError=0.0)
244	return output
245
246	#Focus dataset for a given panel and return the workspace
247	def WISH_focus_onepanel(work,focus,panel):
248	AlignDetectors(work,work,WISH_cal(panel))
249	DiffractionFocussing(work,focus,WISH_group())
250	if (panel==5):
251	CropWorkspace(focus,focus,XMin=0.3)
252	mantid.deleteWorkspace(work)
253	return focus
254
255	def WISH_split(focus):
256	for i in range(0,10):
257	out=focus[0:len(focus)-3]+"-"+str(i+1)+"foc"
258	ExtractSingleSpectrum(focus,out,i)
259	mantid.deleteWorkspace(focus)
260	return
261
262	def WISH_focus(work,panel):
263	focus=work+"foc"
264	if (panel!=0):
265	WISH_focus_onepanel(work,focus,panel)
266	else:
267	WISH_focus_onepanel(work,focus,panel)
268	WISH_split(focus)
269
270	def WISH_process(number,panel,ext,SEsample="WISHcryo",emptySEcycle="09_4",SEvana="candlestick",cyclevana="09_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0):
271	w=WISH_read(number,panel,ext)
272	print "file read and normalized"
273	if (absorb):
274	ConvertUnits(w,w,"Wavelength")
275	CylinderAbsorption(InputWorkspace=w,OutputWorkspace="T",
276	CylinderSampleHeight=h,CylinderSampleRadius=r,AttenuationXSection=Xa,
277	ScatteringXSection=Xs,SampleNumberDensity=nd,
278	NumberOfSlices="10",NumberOfAnnuli="10",NumberOfWavelengthPoints="25",ExpMethod="Normal")
279	Divide(w,"T",w)
280	mantid.deleteWorkspace("T")
281	ConvertUnits(w,w,"TOF")
282	wfoc=WISH_focus(w,panel)
283	print "focussing done!"
284	if type(number) is int:
285	wfocname="w"+str(number)+"-"+str(panel)+"foc"
286	if (len(ext)>9):
287	label,tmin,tmax=split_string_event(ext)
288	wfocname="w"+str(number)+"-"+str(panel)+"_"+label+"foc"
289	else:
290	n1,n2=split_string(number)
291	wfocname="w"+str(n1)+"_"+str(n2)+"-"+str(panel)+"foc"
292	if (panel==1):
293	CropWorkspace(wfocname,wfocname,XMin=0.80,XMax=53.3)
294	elif(panel==2):
295	CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=13.1)
296	elif(panel==3):
297	CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=7.77)
298	elif(panel==4):
299	CropWorkspace(wfocname,wfocname,XMin=0.40,XMax=5.86)
300	elif(panel==5):
301	CropWorkspace(wfocname,wfocname,XMin=0.35,XMax=4.99)
302	elif(panel==6):
303	CropWorkspace(wfocname,wfocname,XMin=0.35,XMax=4.99)
304	elif(panel==7):
305	CropWorkspace(wfocname,wfocname,XMin=0.40,XMax=5.86)
306	elif(panel==8):
307	CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=7.77)
308	elif(panel==9):
309	CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=13.1)
310
311	if (panel==0):
312	for i in range(1,10):
313	wfocname="w"+str(number)+"-"+str(i)+"foc"
314	CropWorkspace(wfocname,wfocname,XMin=0.80,XMax=53.3)
315	CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=13.1)
316	CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=7.77)
317	CropWorkspace(wfocname,wfocname,XMin=0.40,XMax=5.86)
318	CropWorkspace(wfocname,wfocname,XMin=0.35,XMax=4.99)
319	CropWorkspace(wfocname,wfocname,XMin=0.35,XMax=4.99)
320	CropWorkspace(wfocname,wfocname,XMin=0.40,XMax=5.86)
321	CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=7.77)
322	CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=13.1)
323	#print "will try to load an empty with the name:"
324	print WISH_getempty(panel,SEsample,emptySEcycle)
325	if (panel==0):
326	for i in range(1,10):
327	wfocname="w"+str(number)+"-"+str(i)+"foc"
328	LoadNexusProcessed(Filename=WISH_getempty(i,SEsample,emptySEcycle),OutputWorkspace="empty")
329	RebinToWorkspace("empty",wfocname,"empty")
330	Minus(wfocname,"empty",wfocname)
331	mantid.deleteWorkspace("empty")
332	print "will try to load a vanadium with the name:"+WISH_getvana(i,SEvana,cyclevana)
333	LoadNexusProcessed(Filename=WISH_getvana(i,SEvana,cyclevana),OutputWorkspace="vana")
334	RebinToWorkspace("vana",wfocname,"vana")
335	Divide(wfocname,"vana",wfocname)
336	mantid.deleteWorkspace("vana")
337	ConvertUnits(wfocname,wfocname,"TOF")
338	ReplaceSpecialValues(wfocname,wfocname,NaNValue=0.0,NaNError=0.0,InfinityValue=0.0,InfinityError=0.0)
339	SaveGSS(InputWorkspace=wfocname,Filename=WISH_userdir()+str(number)+"-"+str(i)+ext+".gss",Append=False,Bank=1)
340	SaveFocusedXYE(wfocname,WISH_userdir()+str(number)+"-"+str(i)+ext+".dat")
341	SaveNexusProcessed(wfocname,WISH_userdir()+str(number)+"-"+str(i)+ext+".nxs")
342	else:
343	LoadNexusProcessed(Filename=WISH_getempty(panel,SEsample,emptySEcycle),OutputWorkspace="empty")
344	RebinToWorkspace("empty",wfocname,"empty")
345	Minus(wfocname,"empty",wfocname)
346	mantid.deleteWorkspace("empty")
347	print "will try to load a vanadium with the name:"+WISH_getvana(panel,SEvana,cyclevana)
348	LoadNexusProcessed(Filename=WISH_getvana(panel,SEvana,cyclevana),OutputWorkspace="vana")
349	RebinToWorkspace("vana",wfocname,"vana")
350	Divide(wfocname,"vana",wfocname)
351	mantid.deleteWorkspace("vana")
352	ConvertUnits(wfocname,wfocname,"TOF")
353	ReplaceSpecialValues(wfocname,wfocname,NaNValue=0.0,NaNError=0.0,InfinityValue=0.0,InfinityError=0.0)
354	SaveGSS(InputWorkspace=wfocname,Filename=WISH_userdir()+str(number)+"-"+str(panel)+ext+".gss",Append=False,Bank=1)
355	SaveFocusedXYE(wfocname,WISH_userdir()+str(number)+"-"+str(panel)+ext+".dat")
356	SaveNexusProcessed(wfocname,WISH_userdir()+str(number)+"-"+str(panel)+ext+".nxs")
357	return wfocname
358	#Create a corrected vanadium (normalise,corrected for attenuation and empty, strip peaks) and
359	# save a a nexus processed file.
360	# It looks like smoothing of 100 works quite well
361	def WISH_createvan(van,empty,panel,smoothing,vh,vr,cycle_van="09_3",cycle_empty="09_3"):
362	WISH_setdatadir("/archive/ndxwish/Instrument/data/cycle_"+cycle_van+"/")
363	wvan=WISH_read(van,panel,"nxs_event")
364	WISH_setdatadir("/archive/ndxwish/Instrument/data/cycle_"+cycle_empty+"/")
365	wempty=WISH_read(empty,panel,"nxs_event")
366	Minus(wvan,wempty,wvan)
367	print "read van and empty"
368	mantid.deleteWorkspace(wempty)
369	ConvertUnits(wvan,wvan,"Wavelength")
370	CylinderAbsorption(InputWorkspace=wvan,OutputWorkspace="T",
371	CylinderSampleHeight=str(vh),CylinderSampleRadius=str(vr),AttenuationXSection="4.8756",
372	ScatteringXSection="5.16",SampleNumberDensity="0.07118",
373	NumberOfSlices="10",NumberOfAnnuli="10",NumberOfWavelengthPoints="25",ExpMethod="Normal")
374	Divide(wvan,"T",wvan)
375	mantid.deleteWorkspace("T")
376	ConvertUnits(wvan,wvan,"TOF")
377	vanfoc=WISH_focus(wvan,panel)
378	mantid.deleteWorkspace(wvan)
379	#StripPeaks(vanfoc,vanfoc)
380	#SmoothData(vanfoc,vanfoc,str(smoothing))
381	return
382
383	def WISH_createempty(empty,panel):
384	wempty=WISH_read(empty,panel,"raw")
385	emptyfoc=WISH_focus(wempty,panel)
386	return emptyfoc
387
388	def WISH_monitors(rb,ext):
389	data_dir=WISH_dir()
390	file=WISH_getfilename(rb,ext)
391	wout="w"+str(rb)
392	print "reading File..."+file
393	LoadRaw(Filename=file,OutputWorkspace=wout,SpectrumMin=str(1),SpectrumMax=str(5),LoadLogFiles="0")
394	NormaliseByCurrent(wout,wout)
395	ConvertToDistribution(wout)
396	return wout
397
398	def WISH_PH_TOF(runnumber,tubemin):
399	min=6+(tubenumber-1)*128
400	max=min+128
401	file=WISH_getfilename(runnumber,tubemin)
402	output="Run"+str(runnumber)+"tube"+str(tubenumber)
403	w=WISH_read(number,panel,ext)
404	print "file read and normalized"
405	if (absorb):
406	ConvertUnits(w,w,"Wavelength")
407	CylinderAbsorption(InputWorkspace=w,OutputWorkspace="T",
408	CylinderSampleHeight=h,CylinderSampleRadius=r,AttenuationXSection=Xa,
409	ScatteringXSection=Xs,SampleNumberDensity=nd,
410	NumberOfSlices="10",NumberOfAnnuli="10",NumberOfWavelengthPoints="25",ExpMethod="Normal")
411	Divide(w,"T",w)
412	mantid.deleteWorkspace("T")
413	ConvertUnits(w,w,"TOF")
414	wfoc=WISH_focus(w,panel)
415	print "focussing done!"
416	if type(number) is int:
417	wfocname="w"+str(number)+"-"+str(panel)+"foc"
418	if (len(ext)>9):
419	label,tmin,tmax=split_string_event(ext)
420	wfocname="w"+str(number)+"-"+str(panel)+"_"+label+"foc"
421	else:
422	n1,n2=split_string(number)
423	wfocname="w"+str(n1)+"_"+str(n2)+"-"+str(panel)+"foc"
424	if (panel==1):
425	CropWorkspace(wfocname,wfocname,XMin=0.80,XMax=53.3)
426	elif(panel==2):
427	CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=13.1)
428	elif(panel==3):
429	CropWorkspace(wfocname,wfocname,XMin=0.50,XMax=7.77)
430	elif(panel==4):
431	CropWorkspace(wfocname,wfocname,XMin=0.40,XMax=5.86)
432	elif(panel==5):
433	CropWorkspace(wfocname,wfocname,XMin=0.35,XMax=4.99)
434	#print "will try to load an empty with the name:"
435	print WISH_getempty(panel,SEsample,emptySEcycle)
436	if (panel==0):
437	for i in range(1,6):
438	LoadNexusProcessed(Filename=WISH_getempty(i,SEsample,emptySEcycle),OutputWorkspace="empty")
439	RebinToWorkspace("empty",wfocname,"empty")
440	Minus(wfocname,"empty",wfocname)
441	mantid.deleteWorkspace("empty")
442	print "will try to load a vanadium with the name:"+WISH_getvana(i,SEvana,cyclevana)
443	LoadNexusProcessed(Filename=WISH_getvana(i,SEvana,cyclevana),OutputWorkspace="vana")
444	RebinToWorkspace("vana",wfocname,"vana")
445	Divide(wfocname,"vana",wfocname)
446	mantid.deleteWorkspace("vana")
447	ConvertUnits(wfocname,wfocname,"TOF")
448	# SaveGSS(InputWorkspace=wfocname,Filename=WISH_userdir()+str(number)+"-"+str(i)+ext+".gss",Append=False,Bank=1)
449	# SaveFocusedXYE(wfocname,WISH_userdir()+str(number)+"-"+str(i)+ext+".dat")
450	else:
451	LoadNexusProcessed(Filename=WISH_getempty(panel,SEsample,emptySEcycle),OutputWorkspace="empty")
452	RebinToWorkspace("empty",wfocname,"empty")
453	Minus(wfocname,"empty",wfocname)
454	mantid.deleteWorkspace("empty")
455	print "will try to load a vanadium with the name:"+WISH_getvana(panel,SEvana,cyclevana)
456	LoadNexusProcessed(Filename=WISH_getvana(panel,SEvana,cyclevana),OutputWorkspace="vana")
457	RebinToWorkspace("vana",wfocname,"vana")
458	Divide(wfocname,"vana",wfocname)
459	mantid.deleteWorkspace("vana")
460	ConvertUnits(wfocname,wfocname,"TOF")
461	# SaveGSS(InputWorkspace=wfocname,Filename=WISH_userdir()+str(number)+"-"+str(panel)+ext+".gss",Append=False,Bank=1)
462	# SaveFocusedXYE(wfocname,WISH_userdir()+str(number)+"-"+str(panel)+ext+".dat")
463	return wfocname
464	LoadRaw(Filename=file,OutputWorkspace=output,spectrummin=str(min),spectrummax=str(max),LoadLogFiles="0")
465	Integration(output,output+"int")
466	g=plotTimeBin(output+"int",0)
467
468	# Smoothing the incident beam monitor using a spline function. Regions around Bragg edges are masked, before fitting with a spline function.
469	# Returns a smooth monitor spectrum
470
471
472	def WISH_process_incidentmon(number,ext,spline_terms=20,debug=False):
473	if type(number) is int:
474	fname=WISH_getfilename(number,ext)
475	works="monitor"+str(number)
476	if (ext=="raw"):
477	works="monitor"+str(number)
478	LoadRaw(Filename=fname,OutputWorkspace=works,SpectrumMin=4,SpectrumMax=4,LoadLogFiles="0")
479	if (ext[0]=="s"):
480	works="monitor"+str(number)
481	LoadRaw(Filename=fname,OutputWorkspace=works,SpectrumMin=4,SpectrumMax=4,LoadLogFiles="0")
482	if (ext=="nxs"):
483	works="monitor"+str(number)
484	LoadNexus(Filename=fname,OutputWorkspace=works,SpectrumMin=4,SpectrumMax=4)
485	if (ext[0:9]=="nxs_event"):
486	temp="w"+str(number)+"_monitors"
487	works="w"+str(number)+"_monitor4"
488	Rebin(temp,temp,Params='6000,-0.00063,110000',PreserveEvents=False)
489	ExtractSingleSpectrum(temp,works,3)
490	else:
491	n1,n2=split_string(number)
492	works="monitor"+str(n1)+"_"+str(n2)
493	fname=WISH_getfilename(n1,ext)
494	works1="monitor"+str(n1)
495	LoadRaw(Filename=fname,OutputWorkspace=works1,SpectrumMin=4,SpectrumMax=4,LoadLogFiles="0")
496	fname=WISH_getfilename(n2,ext)
497	works2="monitor"+str(n2)
498	LoadRaw(Filename=fname,OutputWorkspace=works2,SpectrumMin=4,SpectrumMax=4,LoadLogFiles="0")
499	MergeRuns(works1+","+works2,works)
500	mantid.deleteWorkspace(works1)
501	mantid.deleteWorkspace(works2)
502	ConvertUnits(works,works,"Wavelength")
503	lmin,lmax=WISH_getlambdarange()
504	CropWorkspace(works,works,XMin=lmin,XMax=lmax)
505	ex_regions=n.zeros((2,4))
506	ex_regions[:,0]=[4.57,4.76]
507	ex_regions[:,1]=[3.87,4.12]
508	ex_regions[:,2]=[2.75,2.91]
509	ex_regions[:,3]=[2.24,2.50]
510	ConvertToDistribution(works)
511	if (debug):
512	x,y,z=mtdplt.getnarray(works,0)
513	p.plot(x,y)
514	for reg in range(0,4):
515	MaskBins(works,works,XMin=ex_regions[0,reg],XMax=ex_regions[1,reg])
516	if (debug):
517	x,y,z=mtdplt.getnarray(works,LoadRaw0)
518	p.plot(x,y)
519	SplineBackground(works,works,0,spline_terms)
520	if (debug):
521	x,y,z=mtdplt.getnarray(works,0)
522	p.plot(x,y)
523	p.show()
524	SmoothData(works,works,40)
525	ConvertFromDistribution(works)
526	return works
527
528	#removes the peaks in a vanadium run, then performs a spline and a smooth
529	def Removepeaks_spline_smooth_empty(works,panel,debug=False):
530	if (panel==1):
531	splineterms=0
532	smoothterms=30
533	if (panel==2):
534	splineterms=0
535	smoothterms=10
536	if (panel==3):
537	splineterms=0
538	smoothterms=15
539	if (panel==4):
540	splineterms=0
541	smoothterms=15
542	if (panel==5):
543	splineterms=0
544	smoothterms=10
545	if (debug):
546	x,y,z=getnarray(works,0)
547	p.plot(x,y)
548	if (splineterms!=0):
549	SplineBackground(works,works,0,splineterms)
550	if (debug):
551	x,y,z=getnarray(works,0)
552	p.plot(x,y)
553	SmoothData(works,works,smoothterms)
554	if (debug):
555	x,y,z=getnarray(works,0)
556	p.plot(x,y)
557	p.show()
558	return works
559
560	def split_string_event(t):
561	#this assumes the form nxs_event_label_tmin_tmax
562	indx_=[]
563	for i in range(10,len(t)):
564	if (t[i]=="_"):
565	indx_.append(i)
566	label=t[10:indx_[0]]
567	tmin=t[indx_[0]+1:indx_[1]]
568	tmax=t[indx_[1]+1:len(t)]
569	return label,tmin,tmax
570
571	#test="nxs_event_1_300.00_600.00"
572	#print split_string_event(test)
573
574	# #####################################################################
575	# ##### USER SPECIFIC PART STARTS BELOW ##
576	# ##### IN CASE LINES ABOVE HAVE BEEN EDITED AND SCRIPTS NO LONGER WORK ##
577	# ##### LOG OUT AND BACK IN TO THE MACHINE ##
578	# #####################################################################
579	# ########### SETTING the paths automatically : WISH_startup(username,cycle_name) ##############
580	WISH_startup("mp43","13_3")
581	# # WISH PROCESS ROUTINES TO EDIT (penultimate line optional but useful for recovering data later on) #
582	# To add two raw files together, replace runno (integer, eg. 16800) by a string "int1+int2" (eg "16800+16801" note quotes)
583	# ##############################################################################################
584	#beg=0
585	#end=1800
586	#nbslices=int(end/180)
587	#suffix=[]
588	#for k in range(0,nbslices):
589	# suffix.append("nxs_event_slice"+str(k)+"_"+str(int(k180))+"_"+str((k+1)180))
590
591	#print len(suffix)
592	#print suffix[0], suffix[k]
593
594	#for i in range(24901,24902):
595	# for j in range(2,3):
596	# for k in range(0,len(suffix)):
597	# wout=WISH_process(i,j,suffix[k],"candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
598	# ConvertUnits(wout,wout+"-d","dSpacing")
599	# ##############################################################################################
600	#for i in range(24895,24896):
601	# for j in range(5,6):
602	# wout=WISH_process(i,j,"nxs_event_slice1_0_300","candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
603	# ConvertUnits(wout,wout+"-d","dSpacing")
604	# wout=WISH_process(i,j,"nxs_event_slice2_300_600","candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
605	# ConvertUnits(wout,wout+"-d","dSpacing")
606	# wout=WISH_process(i,j,"nxs_event_slice3_600_900","candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
607	# ConvertUnits(wout,wout+"-d","dSpacing")
608	# wout=WISH_process(i,j,"nxs_event_slice4_900_1200","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
609	# ConvertUnits(wout,wout+"-d","dSpacing")
610	# wout=WISH_process(i,j,"nxs_event_slice5_1200_1500","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
611	# ConvertUnits(wout,wout+"-d","dSpacing")
612	# wout=WISH_process(i,j,"nxs_event_slice6_1500_1800","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
613	# ConvertUnits(wout,wout+"-d","dSpacing")
614	# wout=WISH_process(i,j,"nxs_event_slice7_1800_2100","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
615	# ConvertUnits(wout,wout+"-d","dSpacing")
616	# wout=WISH_process(i,j,"nxs_event_slice8_2100_2400","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
617	# ConvertUnits(wout,wout+"-d","dSpacing")
618	# wout=WISH_process(i,j,"nxs_event_slice9_2400_2700","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
619	# ConvertUnits(wout,wout+"-d","dSpacing")
620	# wout=WISH_process(i,j,"nxs_event_slice10_2700_3000","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
621	# ConvertUnits(wout,wout+"-d","dSpacing")
622	# wout=WISH_process(i,j,"nxs_event_slice11_3000_3300","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
623	# ConvertUnits(wout,wout+"-d","dSpacing")
624	# wout=WISH_process(i,j,"nxs_event_slice12_3300_end","WISHcryo","11_3","WISHcryo","11_3",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
625
626	for i in range(25449,25450):
627	for j in range(1,10):
628	wout=WISH_process(i,j,"raw","candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
629	ConvertUnits(wout,wout+"-d","dSpacing")
630	# SaveGSS("w"+str(i)+"-1foc",WISH_userdir()+str(i)+"-1foc"+".gss",Append=False,Bank=1)
631	# SaveFocusedXYE("w"+str(i)+"-1foc",WISH_userdir()+str(i)+"-1foc"+".dat")
632	# SaveGSS("w"+str(i)+"-2foc",WISH_userdir()+str(i)+"-2foc"+".gss",Append=False,Bank=1)
633	# SaveFocusedXYE("w"+str(i)+"-2foc",WISH_userdir()+str(i)+"-2foc"+".dat")
634	RebinToWorkspace("w"+str(i)+"-6foc","w"+str(i)+"-5foc","w"+str(i)+"-6foc")
635	Plus("w"+str(i)+"-5foc","w"+str(i)+"-6foc","w"+str(i)+"-5_6foc")
636	ConvertUnits("w"+str(i)+"-5_6foc","w"+str(i)+"-5_6foc"+"-d","dSpacing")
637	SaveGSS("w"+str(i)+"-5_6foc",WISH_userdir()+str(i)+"-5_6foc"+".gss",Append=False,Bank=1)
638	SaveFocusedXYE("w"+str(i)+"-5_6foc",WISH_userdir()+str(i)+"-5_6foc"+".dat")
639	SaveNexusProcessed("w"+str(i)+"-5_6foc",WISH_userdir()+str(i)+"-5_6foc"+".nxs")
640	RebinToWorkspace("w"+str(i)+"-7foc","w"+str(i)+"-4foc","w"+str(i)+"-7foc")
641	Plus("w"+str(i)+"-4foc","w"+str(i)+"-7foc","w"+str(i)+"-4_7foc")
642	ConvertUnits("w"+str(i)+"-4_7foc","w"+str(i)+"-4_7foc"+"-d","dSpacing")
643	SaveGSS("w"+str(i)+"-4_7foc",WISH_userdir()+str(i)+"-4_7foc"+".gss",Append=False,Bank=1)
644	SaveFocusedXYE("w"+str(i)+"-4_7foc",WISH_userdir()+str(i)+"-4_7foc"+".dat")
645	SaveNexusProcessed("w"+str(i)+"-4_7foc",WISH_userdir()+str(i)+"-4_7foc"+".nxs")
646	RebinToWorkspace("w"+str(i)+"-8foc","w"+str(i)+"-3foc","w"+str(i)+"-8foc")
647	Plus("w"+str(i)+"-3foc","w"+str(i)+"-8foc","w"+str(i)+"-3_8foc")
648	ConvertUnits("w"+str(i)+"-3_8foc","w"+str(i)+"-3_8foc"+"-d","dSpacing")
649	SaveGSS("w"+str(i)+"-3_8foc",WISH_userdir()+str(i)+"-3_8foc"+".gss",Append=False,Bank=1)
650	SaveFocusedXYE("w"+str(i)+"-3_8foc",WISH_userdir()+str(i)+"-3_8foc"+".dat")
651	SaveNexusProcessed("w"+str(i)+"-3_8foc",WISH_userdir()+str(i)+"-3_8foc"+".nxs")
652	RebinToWorkspace("w"+str(i)+"-9foc","w"+str(i)+"-2foc","w"+str(i)+"-9foc")
653	Plus("w"+str(i)+"-2foc","w"+str(i)+"-9foc","w"+str(i)+"-2_9foc")
654	ConvertUnits("w"+str(i)+"-2_9foc","w"+str(i)+"-2_9foc"+"-d","dSpacing")
655	SaveGSS("w"+str(i)+"-2_9foc",WISH_userdir()+str(i)+"-2_9foc"+".gss",Append=False,Bank=1)
656	SaveFocusedXYE("w"+str(i)+"-2_9foc",WISH_userdir()+str(i)+"-2_9foc"+".dat")
657	SaveNexusProcessed("w"+str(i)+"-2_9foc",WISH_userdir()+str(i)+"-2_9foc"+".nxs")
658	# #############################################################################################
659	#for i in range(23840,23841):
660	# for j in range(5,0,-1):
661	# wout=WISH_process(i,j,"raw","candlestick","11_4","candlestick","11_4",absorb=False,nd=0.0,Xs=0.0,Xa=0.0,h=0.0,r=0.0)
662	# SaveNexusProcessed(wout,WISH_userdir()+wout+".nxs")
663	# ConvertUnits(wout,wout+"-d","dSpacing")
664
665
666	# ###########################################################################################
667	#for i in range(18880,18881):
668	# for j in range(1,6):
669	# wout=WISH_process(i,j,"raw","WISHcryo","11_3","WISHcryo","11_3",absorb=True,nd=0.0035,Xs=62.27,Xa=429.95,h=4.0,r=0.15)
670	# ###########################################################################################
671	# ######### END OF WISH PROCESS ROUTINES ##################
672
673	# #####################################################################
674	# How to retrieve already processed Data without having to reprocess it (in case Mantid session has been closed #
675	#for runno in range(24122,24130):
676	# for j in range(1,6):
677	# wr=str(runno)+"-"+str(j)+"raw-0"
678	# LoadNexusProcessed(WISH_userdir()+wr+".nxs",wr)
679	# ConvertUnits(wr,wr+"-d","dSpacing")
680
681	#####################################################################
682	#for runno in range(22678,22686):
683	#for j in range(1,6):
684	#wr="w"+str(runno)+"-"+str(j)+"foc"
685
686	#for j in range(1,6):
687	# Plus("w22663"+"-"+str(j)+"foc","w22664"+"-"+str(j)+"foc","vancan"+"-"+str(j)+"foc")
688	# SaveGSS(InputWorkspace="vancan"+"-"+str(j)+"foc",Filename=WISH_userdir()+"vancan"+"-"+str(j)+"foc.gss",Append=False,Bank=1)
689
690
691
692
693	# ####################################################################
694	# If you don't have a correct empty, either use the most suitable one or use the lines below ####
695	#for i in range(1197,1410):
696	# for j in range(1,6):
697	# wout=WISH_read(i,j,"raw")
698	# wfoc=WISH_focus(wout,j)
699	# ####################################################################
700	# use the lines below to manually set the paths if needed
701	#WISH_setdatadir("/archive/ndxwish/Instrument/data/cycle_10_1/")
702	#WISH_setuserdir("/home/mp43/ProcessedData/")WISHcryo
703	# ######### use the lines below to process a LoadRawvanadium run ##################
704	#for j in range(1,2):
705	# WISH_createvan(19612,19618,j,100,4.0,0.15,cycle_van="11_4",cycle_empty="11_4")
706	# CropWorkspace(InputWorkspace="w19612-"+str(j)+"foc",OutputWorkspace="w19612-"+str(j)+"foc",XMin='0.35',XMax='5.0')
707	# Removepeaks_spline_smooth_vana("w18904-"+str(j)+"foc",j,debug=False)
708	# SaveNexusProcessed("w16847-"+str(i)+"foc",WISH_userdir()+"vana16847-"+str(i)+"foc.nx5")
709	# ######## use the lines below to create a processed empty (instrument, cryostat, can..) run ########
710	#for i in range(4,5):
711	# WISH_createempty(20620,i)
712	#SaveNexusProcessed("w16748-"+str(i)+"foc",WISH_userdir()+"emptyinst16748-"+str(i)+"foc.nx5")
713
714

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