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V_Protocol_Reduction.ipf @ 1095

Last change on this file since 1095 was 1095, checked in by srkline, 4 years ago

Added two model functions for white beam smearing.

Many other small changes for processing of the back detector, shuffling of VSANS menu items, and consistent naming of V_ procedures.

File size: 94.8 KB

Line
1	#pragma TextEncoding = "MacRoman"
2	#pragma rtGlobals=1 // Use modern global access method.
3	#pragma version=5.0
4	#pragma IgorVersion=7
5
6	//************************
7
8	//
9	//*************************
10	//////////////////////////////////
11	//
12	// KEYWORD=<value> lists used in protocol definitions
13	//
14	// KEYWORDS are ALWAYS capitalized, and yes, it does matter
15	//
16	// for ABSOLUTE parameters
17	// (4) possible keywords, all with numerical values
18	// TSTAND=value transmission of the standard
19	// DSTAND=value thickness of the standard, in centimeters
20	// IZERO=value I(q=0) value for the standard, in normalized neutron counts
21	// XSECT=value calibrated cross-section of the standard sample
22	//
23	// For calibration with a transmission file, set TSTAND, DSTAND, and XSECT to 1.0
24	// and set IZERO to KAPPA (defined in Tania's handout, or in documentation of MRED_KAP on VAX)
25	//
26	//
27	// For AVERAGE and for DRAWING
28	// DRAWING routines only use a subset of the total list, since saving, naming, etc. don't apply
29	// (10) possible keywords, some numerical, some string values
30	// AVTYPE=string string from set {Circular,Annular,Rectangular,Sector,2D_ASCII,QxQy_ASCII,PNG_Graphic;Sector_PlusMinus;}
31	// PHI=value azimuthal angle (-90,90)
32	// DPHI=value +/- angular range around phi for average
33	// WIDTH=value total width of rectangular section, in pixels
34	// SIDE=string string from set {left,right,both} **note NOT capitalized
35
36	// QCENTER=value q-value (1/A) of center of annulus for annular average
37	// QDELTA=value (+/-) width of annulus centered at QCENTER, in units of q
38	// DETGROUP=value string with "F" or "M" to name the detector group where the annulus lies.
39
40	// PLOT=string string from set {Yes,No} = truth of generating plot of averaged data
41	// SAVE=string string from set {Yes,No} = truth of saving averaged data to disk, now with "Concatenate" or "Individual"
42	// NAME=string string from set {Auto,Manual} = Automatic name generation or Manual(dialog)
43	//
44	//
45	// BINTYPE=string (VSANS binning type) "One;Two;Four;Slit Mode;", as defined by ksBinTypeStr
46	//
47	//
48	// For work.DRK usage:
49	// **the list is COMMA delimited, separator is =
50	// DRK=none,DRKMODE=0,
51	// DRK=name is the name of the file, must be a full name, expected to be raw data
52	// DRKMODE=value is a numeric value (0 or 10 to add to the Correct(mode) switch (unused?)
53	//
54	//////////////////////////////////
55
56
57	//main entry procedure for initialzing and displaying the protocol panel
58	// initilaizes folders and globals as needed
59	//
60	Proc V_ReductionProtocolPanel()
61	DoWindow/F V_ProtocolPanel
62	if(V_flag==0)
63	V_InitProtocolPanel()
64	V_ProtocolPanel()
65	Endif
66	End
67
68	//initialization procedure for the protocol panel
69	//note that :gAbsStr is also shared (common global) to that used in
70	//the questionnare form of the protcol (see protocol.ipf)
71	//
72	Proc V_InitProtocolPanel()
73
74	if(exists(" root:Packages:NIST:VSANS:CatVSHeaderInfo:Filenames") == 0)
75	Abort "You must generate a file catalog before building protocols"
76	endif
77
78	//set up the global variables needed for the protocol panel
79	//global strings to put in a temporary protocol textwave
80	Variable ii=0
81	String waveStr="tempProtocol"
82	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
83	Make/O/T/N=(kNumProtocolSteps) $"root:Packages:NIST:VSANS:Globals:Protocols:tempProtocol" = ""
84
85	String/G root:Packages:NIST:VSANS:Globals:Protocols:gSAM="ask"
86	String/G root:Packages:NIST:VSANS:Globals:Protocols:gBGD="ask"
87	String/G root:Packages:NIST:VSANS:Globals:Protocols:gEMP="ask"
88	String/G root:Packages:NIST:VSANS:Globals:Protocols:gDIV="ask"
89	String/G root:Packages:NIST:VSANS:Globals:Protocols:gMASK="ask"
90	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr="ask"
91	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAVE="AVTYPE=Circular;SAVE=Yes - Concatenate;NAME=Auto;PLOT=No;BINTYPE=One;"
92	String/G root:Packages:NIST:VSANS:Globals:Protocols:gDRK="DRK=none,DRKMODE=0,"
93
94	// global strings for trimming data are initialized in the main VSANS initilization
95	// in case the trimming is done before the protocol panel is opened
96
97	SetDataFolder root:
98
99	End
100
101
102	//button procedure to reset the panel seletctions/checks...etc...
103	//to reflect the choices in a previously saved protocol
104	// - parses through the protocol and resets the appropriate global strings and
105	//updates the panel display
106	//
107	Function V_RecallProtocolButton(ctrlName) : ButtonControl
108	String ctrlName
109
110	//will reset panel values based on a previously saved protocol
111	//pick a protocol wave from the Protocols folder
112	//MUST move to Protocols folder to get wavelist
113	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
114	Execute "V_PickAProtocol()"
115
116	//get the selected protocol wave choice through a global string variable
117	SVAR protocolName = root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr
118
119	//If "CreateNew" was selected, ask user to try again
120	if(cmpstr("CreateNew",protocolName) == 0)
121	Abort "CreateNew is for making a new Protocol. Select a previously saved Protocol"
122	Endif
123
124	//reset the panel based on the protocol textwave (currently a string)
125	V_ResetToSavedProtocol(protocolName)
126
127	SetDataFolder root:
128	return(0)
129	End
130
131	//deletes the selected protocol from the list and from memory
132	//
133	Function V_DeleteProtocolButton(ctrlName) : ButtonControl
134	String ctrlName
135
136	//put up a list of protocols and pick one
137	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
138	// Execute "DeleteAProtocol()"
139	String Protocol=""
140	Prompt Protocol "Delete A Protocol",popup, V_DeletableProtocols()
141	DoPrompt "Select protocol to delete",protocol
142	If(V_flag==1)
143	return(0)
144	endif
145
146	//If "CreateNew, Base, DoAll, or tempProtocol" was selected, do nothing
147	strswitch(protocol)
148	case "CreateNew":
149	break
150	case "DoAll":
151	break
152	case "Base":
153	break
154	case "tempProtocol":
155	break
156	default:
157	//delete the protocol
158	KillWaves/Z $protocol
159	endswitch
160
161	SetDataFolder root:
162	return(0)
163	End
164
165	//
166	//function that actually parses the protocol specified by nameStr
167	//which is just the name of the wave, without a datafolder path
168	//
169	// TODO
170	// -- update this for 12 steps
171	//
172	Function V_ResetToSavedProtocol(nameStr)
173	String nameStr
174
175	//allow special cases of Base and DoAll Protocols to be recalled to panel - since they "ask"
176	//and don't need paths
177
178	String catPathStr
179	PathInfo catPathName
180	catPathStr=S_path
181
182	//SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols //on windows, data folder seems to get reset (erratically) to root:
183	Wave/T w=$("root:Packages:NIST:VSANS:Globals:Protocols:" + nameStr)
184
185	String fullPath="",comma=",",list="",nameList="",PathStr="",item=""
186	Variable ii=0,numItems,checked,specialProtocol
187
188	if((cmpstr(nameStr,"Base")==0) \|\| (cmpstr(nameStr,"DoAll")==0))
189	specialProtocol = 1
190	else
191	specialProtocol = 0
192	Endif
193
194	//background
195	checked = 1
196	nameList = w[0]
197	If(cmpstr(nameList,"none") ==0)
198	checked = 0
199	Endif
200
201	//set the global string to display and checkbox
202	String/G root:Packages:NIST:VSANS:Globals:Protocols:gBGD = nameList
203	CheckBox prot_check win=V_ProtocolPanel,value=checked
204
205	//empty
206	checked = 1
207	nameList = w[1]
208	If(cmpstr(nameList,"none") ==0)
209	checked = 0
210	Endif
211
212	//set the global string to display and checkbox
213	String/G root:Packages:NIST:VSANS:Globals:Protocols:gEMP = nameList
214	CheckBox prot_check_1 win=V_ProtocolPanel,value=checked
215
216	//DIV file
217	checked = 1
218	nameList = w[2]
219	If(cmpstr(nameList,"none") ==0)
220	checked = 0
221	Endif
222
223	//set the global string to display and checkbox
224	String/G root:Packages:NIST:VSANS:Globals:Protocols:gDIV = nameList
225	CheckBox prot_check_2 win=V_ProtocolPanel,value=checked
226
227	//Mask file
228	checked = 1
229	nameList = w[3]
230	If(cmpstr(nameList,"none") ==0)
231	checked = 0
232	Endif
233
234	//set the global string to display and checkbox
235	String/G root:Packages:NIST:VSANS:Globals:Protocols:gMASK = nameList
236	CheckBox prot_check_3 win=V_ProtocolPanel,value=checked
237
238	//4 = abs parameters
239	list = w[4]
240	numItems = ItemsInList(list,";")
241	checked = 1
242	if(numitems == 4 \|\| numitems == 5) //allow for protocols with no SDEV list item
243	//correct number of parameters, assume ok
244	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr = list
245	CheckBox prot_check_9 win=V_ProtocolPanel,value=checked
246	else
247	item = StringFromList(0,list,";")
248	if(cmpstr(item,"none")==0)
249	checked = 0
250	list = "none"
251	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr = list
252	CheckBox prot_check_9 win=V_ProtocolPanel,value=checked
253	else
254	//force to "ask"
255	checked = 1
256	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr = "ask"
257	CheckBox prot_check_9 win=V_ProtocolPanel,value=checked
258	Endif
259	Endif
260
261	//5 = averaging choices
262	list = w[5]
263	item = StringByKey("AVTYPE",list,"=",";")
264	if(cmpstr(item,"none") == 0)
265	checked = 0
266	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAVE = "none"
267	CheckBox prot_check_5 win=V_ProtocolPanel,value=checked
268	else
269	checked = 1
270	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAVE = list
271	CheckBox prot_check_5 win=V_ProtocolPanel,value=checked
272	Endif
273
274	// //6 = DRK choice
275	// list = w[6]
276	// item = StringByKey("DRK",list,"=",",")
277	// //print list,item
278	// if(cmpstr(item,"none") == 0)
279	// checked = 0
280	// String/G root:Packages:NIST:VSANS:Globals:Protocols:gDRK = list
281	// CheckBox prot_check_6 win=V_ProtocolPanel,value=checked
282	// else
283	// checked = 1
284	// String/G root:Packages:NIST:VSANS:Globals:Protocols:gDRK = list
285	// CheckBox prot_check_6 win=V_ProtocolPanel,value=checked
286	// Endif
287
288	//7 = beginning trim points
289	SVAR gBegPtsStr=root:Packages:NIST:VSANS:Globals:Protocols:gBegPtsStr
290	gBegPtsStr = w[7]
291	//8 = end trim points
292	SVAR gEndPtsStr=root:Packages:NIST:VSANS:Globals:Protocols:gEndPtsStr
293	gEndPtsStr = w[8]
294
295	//9 = unused
296	//10 = unused
297	//11 = unused
298
299
300	//all has been reset, get out
301	Return (0)
302	End
303
304	//button action procedure that simply closes the panel
305	//
306	Function V_DoneProtocolButton(ctrlName) : ButtonControl
307	String ctrlName
308
309	//will gracefully close and exit the protocol panel
310
311	DoWindow/K V_ProtocolPanel
312	End
313
314	//button action procedure that saves the current choices on the panel
315	//as a named protocol, for later recall
316	//asks for a valid name, then creates a protocol from the panel choices
317	//creates a wave, and sets the current protocol name to this new protocol
318	//
319	//now allows the user the choice to overwrite a protocol
320	//
321	Function V_SaveProtocolButton(ctrlName) : ButtonControl
322	String ctrlName
323
324	Variable notDone=1, newProto=1
325	//will prompt for protocol name, and save the protocol as a text wave
326	//prompt for name of new protocol wave to save
327	do
328	Execute "V_AskForName()"
329	SVAR newProtocol = root:Packages:NIST:VSANS:Globals:Protocols:gNewStr
330
331	//make sure it's a valid IGOR name
332	newProtocol = CleanupName(newProtocol,0) //strict naming convention
333	String/G root:Packages:NIST:VSANS:Globals:Protocols:gNewStr=newProtocol //reassign, if changed
334	Print "newProtocol = ",newProtocol
335
336	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
337	if(WaveExists( $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtocol) ) == 1)
338	//wave already exists
339	DoAlert 1,"That name is already in use. Do you wish to overwrite the existing protocol?"
340	if(V_Flag==1)
341	notDone = 0
342	newProto = 0
343	else
344	notDone = 1
345	endif
346	else
347	//name is good
348	notDone = 0
349	Endif
350	while(notDone)
351
352	//current data folder is root:Packages:NIST:VSANS:Globals:Protocols
353	if(newProto)
354	Make/O/T/N=(kNumProtocolSteps) $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtocol)
355	Endif
356
357	V_MakeProtocolFromPanel( $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtocol) )
358	String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr = newProtocol
359
360	//the data folder WAS changed above, this must be reset to root:
361	SetDatafolder root:
362	End
363
364	//function that does the guts of reading the panel controls and globals
365	//to create the necessary text fields for a protocol
366	//Wave/T w (input) is an empty text wave of 8 elements for the protocol
367	//on output, w[] is filled with the protocol strings as needed from the panel
368	//
369	// TODO
370	// -- update for 12 points
371	//
372	Function V_MakeProtocolFromPanel(w)
373	Wave/T w
374
375	//construct the protocol text wave form the panel
376	//it is to be parsed by ExecuteProtocol() for the actual data reduction
377	PathInfo catPathName //this is where the files came from
378	String pathstr=S_path,tempStr,curList
379	Variable checked,ii,numItems
380
381	//look for checkbox, then take each item in list and prepend the path
382	//w[0] = background
383	ControlInfo/W=V_ProtocolPanel prot_check
384	checked = V_value
385	if(checked)
386	//build the list
387	//just read the global
388	SVAR str=root:Packages:NIST:VSANS:Globals:Protocols:gBGD
389	if(cmpstr(str,"ask")==0)
390	w[0] = str //just ask
391	else
392	tempstr = V_ParseRunNumberList(str)
393	if(strlen(tempStr)==0)
394	return(1) //error parsing list
395	else
396	w[0] = tempstr
397	str = tempstr //set the protocol and the global
398	endif
399	endif
400	else
401	//none used - set textwave (and global?)
402	w[0] = "none"
403	String/G root:Packages:NIST:VSANS:Globals:Protocols:gBGD = "none"
404	endif
405
406	//w[1] = empty
407	ControlInfo/W=V_ProtocolPanel prot_check_1
408	checked = V_value
409	if(checked)
410	//build the list
411	//just read the global
412	SVAR str=root:Packages:NIST:VSANS:Globals:Protocols:gEMP
413	if(cmpstr(str,"ask")==0)
414	w[1] = str
415	else
416	tempstr = V_ParseRunNumberList(str)
417	if(strlen(tempStr)==0)
418	return(1)
419	else
420	w[1] = tempstr
421	str=tempStr
422	endif
423	endif
424	else
425	//none used - set textwave (and global?)
426	w[1] = "none"
427	String/G root:Packages:NIST:VSANS:Globals:Protocols:gEMP = "none"
428	endif
429
430	//w[2] = div file
431	ControlInfo/W=V_ProtocolPanel prot_check_2
432	checked = V_value
433	if(checked)
434	//build the list
435	//just read the global
436	SVAR str=root:Packages:NIST:VSANS:Globals:Protocols:gDIV
437	if(cmpstr(str,"ask")==0)
438	w[2] = str
439	else
440	tempStr = V_ParseRunNumberList(str)
441	if(strlen(tempStr)==0)
442	return(1)
443	else
444	w[2] = tempstr
445	str=tempstr
446	endif
447	endif
448	else
449	//none used - set textwave (and global?)
450	w[2] = "none"
451	String/G root:Packages:NIST:VSANS:Globals:Protocols:gDIV = "none"
452	endif
453
454	//w[3] = mask file
455	ControlInfo/W=V_ProtocolPanel prot_check_3
456	checked = V_value
457	if(checked)
458	//build the list
459	//just read the global
460	SVAR str=root:Packages:NIST:VSANS:Globals:Protocols:gMASK
461	if(cmpstr(str,"ask")==0)
462	w[3] = str
463	else
464	tempstr = V_ParseRunNumberList(str)
465	if(strlen(tempstr)==0)
466	return(1)
467	else
468	w[3] = tempstr
469	str = tempstr
470	endif
471	endif
472	else
473	//none used - set textwave (and global?)
474	w[3] = "none"
475	String/G root:Packages:NIST:VSANS:Globals:Protocols:gMASK = "none"
476	endif
477
478	//w[4] = abs parameters
479	ControlInfo/W=V_ProtocolPanel prot_check_9
480	checked = V_value
481	if(checked)
482	//build the list
483	//just read the global
484	SVAR str=root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr
485	w[4] = str
486	else
487	//none used - set textwave (and global?)
488	w[4] = "none"
489	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr = "none"
490	endif
491
492	//w[5] = averaging choices
493	ControlInfo/W=V_ProtocolPanel prot_check_5 //do the average?
494	checked = V_value
495	if(checked)
496	//just read the global
497	SVAR avestr=root:Packages:NIST:VSANS:Globals:Protocols:gAVE
498	w[5] = avestr
499	else
500	//none used - set textwave
501	w[5] = "AVTYPE=none;"
502	endif
503
504	//w[6]
505	//work.DRK information
506	SVAR drkStr=root:Packages:NIST:VSANS:Globals:Protocols:gDRK
507	w[6] = drkStr
508
509	//w[7]
510	// beginning trim points
511	SVAR gBegPtsStr=root:Packages:NIST:VSANS:Globals:Protocols:gBegPtsStr
512	w[7] = gBegPtsStr
513
514	//w[8]
515	// End trim points
516	SVAR gEndPtsStr=root:Packages:NIST:VSANS:Globals:Protocols:gEndPtsStr
517	w[8] = gEndPtsStr
518
519	//w[9]
520	//currently unused
521	w[9] = ""
522	//w[10]
523	//currently unused
524	w[10] = ""
525	//w[11]
526	//currently unused
527	w[11] = ""
528
529	return(0)
530	End
531
532
533	//
534	Function V_PickSAMButton(ctrlName) : ButtonControl
535	String ctrlName
536
537
538	End
539
540
541
542
543	//
544	// TODO
545	// -- identifying "intent" using V_get can be very slow, since it reads in each and every data file.
546	// grep is a lot faster, but there can be a lot of false "hits" unless I do it correctly.
547	//
548	//
549	// //grep through what text I can find in the VAX binary
550	// // Grep Note: the \\b sequences limit matches to a word boundary before and after
551	// // "boondoggle", so "boondoggles" and "aboondoggle" won't match.
552	// if(gRadioVal == 2)
553	// for(ii=0;ii<num;ii+=1)
554	// item=StringFromList(ii, newList , ";")
555	//// Grep/P=catPathName/Q/E=("(?i)\\b"+match+"\\b") item
556	// Grep/P=catPathName/Q/E=("(?i)"+match) item
557	// if( V_value ) // at least one instance was found
558	//// Print "found ", item,ii
559	// list += item + ";"
560	// endif
561	// endfor
562	//
563	// newList = list
564	// endif
565
566	// match is the string to look for in the search
567	// 0 is a flag to tell it to look in the file catalog (the fastest method)
568	// Other options are to grep, or to read the intent field in every file
569	Function/S V_GetSAMList()
570
571	// String match="SAMPLE"
572	// String list = V_getFileIntentList(match,0)
573
574	String intent = "SAMPLE"
575	String purpose = "SCATTERING"
576	String list = V_getFileIntentPurposeList(intent,purpose,0)
577
578	// Printf "SAM files = %s\r",list
579	return(list)
580	end
581
582
583	Function/S V_GetBGDList()
584
585	String intent="BLOCKED BEAM"
586	String purpose="SCATTERING"
587	// String list = V_getFileIntentList(match,0)
588	String list = V_getFileIntentPurposeList(intent,purpose,0)
589
590	// Printf "BGD files = %s\r",list
591	return(list)
592	end
593
594	//
595	// V_getFileIntentPurposeList(intent,purpose,method)
596	Function/S V_GetEMPList()
597
598	String intent="EMPTY CELL"
599	String purpose="SCATTERING"
600	// String list = V_getFileIntentList(match,0)
601	String list = V_getFileIntentPurposeList(intent,purpose,0)
602
603
604	// Printf "EMP files = %s\r",list
605	return(list)
606	end
607
608
609	//
610	// TODO
611	// -- decide on the way to locate the blocked beam files. Is the enumerated text of the intent
612	// sufficiently unique to locate the file?
613	// -- can I use the Data Catalog waves to locate the files - faster?
614	// (fails if the catalog has not been read in recently enough)
615	//
616	//
617	Function/S V_PickBGDButton(ctrlName) : ButtonControl
618	String ctrlName
619
620	String list="",item="",fname,newList,intent
621	Variable ii,num
622
623	PathInfo catPathName
624	String path = S_path
625
626	String match="BLOCKED BEAM"
627
628	//v_tic()
629	// get the list from the file catalog (=0.0007s)
630	//
631	WAVE/T fileNameW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Filenames
632	WAVE/T intentW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Intent
633
634	Variable np = numpnts(intentW)
635	for(ii=0;ii<np;ii+=1)
636	if(cmpstr(intentW[ii],match)==0)
637	list += fileNameW[ii] + ";"
638	endif
639	endfor
640
641	List = SortList(List,";",0)
642	Printf "BGD files = %s\r",list
643	//v_toc()
644
645
646	////v_tic() // from grep = 3.3s
647	// newList = V_GetRawDataFileList()
648	// num=ItemsInList(newList)
649	//
650	//// for(ii=0;ii<num;ii+=1)
651	//// item=StringFromList(ii, newList , ";")
652	//// fname = path + item
653	//// intent = V_getReduction_intent(fname)
654	//// if(cmpstr(intent,"BLOCKED BEAM") == 0)
655	//// list += item + ";"
656	//// endif
657	////
658	//// endfor
659	// list = ""
660	// for(ii=0;ii<num;ii+=1)
661	// item=StringFromList(ii, newList , ";")
662	// Grep/P=catPathName/Q/E=("(?i)"+match) item
663	// if( V_value ) // at least one instance was found
664	//// Print "found ", item,ii
665	// list += item + ";"
666	// endif
667	// endfor
668	//
669	//
670	// List = SortList(List,";",0)
671	// Printf "BGD files = %s\r",list
672	////v_toc()
673
674	return(list)
675	End
676
677
678	//
679	Function/S V_PickEMPButton(ctrlName) : ButtonControl
680	String ctrlName
681	String list="",item="",fname,newList,intent
682	Variable ii,num
683
684	PathInfo catPathName
685	String path = S_path
686
687	String match="EMPTY CELL"
688
689	// get the list from the file catalog (=0.0007s)
690	//
691	WAVE/T fileNameW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Filenames
692	WAVE/T intentW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Intent
693
694	Variable np = numpnts(intentW)
695	for(ii=0;ii<np;ii+=1)
696	if(cmpstr(intentW[ii],match)==0)
697	list += fileNameW[ii] + ";"
698	endif
699	endfor
700
701	List = SortList(List,";",0)
702	Printf "EMP files = %s\r",list
703
704
705	//
706	// newList = V_GetRawDataFileList()
707	// num=ItemsInList(newList)
708	//
709	//// for(ii=0;ii<num;ii+=1)
710	//// item=StringFromList(ii, newList , ";")
711	//// fname = path + item
712	//// intent = V_getReduction_intent(fname)
713	//// if(cmpstr(intent,"EMPTY CELL") == 0)
714	//// list += item + ";"
715	//// endif
716	////
717	//// endfor
718	//
719	// for(ii=0;ii<num;ii+=1)
720	// item=StringFromList(ii, newList , ";")
721	// Grep/P=catPathName/Q/E=("(?i)"+match) item
722	// if( V_value ) // at least one instance was found
723	//// Print "found ", item,ii
724	// list += item + ";"
725	// endif
726	//
727	// endfor
728	//
729	// List = SortList(List,";",0)
730	// Printf "EMP files = %s\r",list
731
732	return(list)
733	End
734
735
736	//
737	Function/S V_PickEMPBeamButton(ctrlName) : ButtonControl
738	String ctrlName
739	String list="",item="",fname,newList,intent
740	Variable ii,num
741
742	PathInfo catPathName
743	String path = S_path
744
745	String match="OPEN BEAM"
746
747	// get the list from the file catalog (=0.0007s)
748	//
749	WAVE/T fileNameW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Filenames
750	WAVE/T intentW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Intent
751
752	Variable np = numpnts(intentW)
753	for(ii=0;ii<np;ii+=1)
754	if(cmpstr(intentW[ii],match)==0)
755	list += fileNameW[ii] + ";"
756	endif
757	endfor
758
759	List = SortList(List,";",0)
760	Printf "EMP Beam files = %s\r",list
761
762
763
764	return(list)
765	End
766
767
768	// TODO
769	// -- find proper way to search for these files
770	// -- they may be written to the file header(reduction block)
771	// -- or grep for VSANS_DIV (in the title)
772	Function/S V_GetDIVList()
773
774	String list="",item="",fname,newList,intent
775	Variable ii,num
776
777	PathInfo catPathName
778	String path = S_path
779
780	newList = V_Get_NotRawDataFileList()
781	newList = V_RemoveEXTFromList(newlist,"hst") // remove the event files
782	newList = V_RemoveEXTFromList(newlist,"ave") // remove the ave files
783	newList = V_RemoveEXTFromList(newlist,"abs") // remove the abs files
784	newList = V_RemoveEXTFromList(newlist,"pxp") // remove the pxp files
785	newList = V_RemoveEXTFromList(newlist,"DS_Store") // remove the DS_Store file (OSX only)
786
787	num=ItemsInList(newList)
788
789	// for(ii=0;ii<num;ii+=1)
790	// item=StringFromList(ii, newList , ";")
791	// fname = path + item
792	// intent = V_getReduction_intent(fname)
793	// if(cmpstr(intent,"SENSITIVITY") == 0)
794	// list += item + ";"
795	// endif
796	//
797	// endfor
798
799	String match="DIV"
800	for(ii=0;ii<num;ii+=1)
801	item=StringFromList(ii, newList , ";")
802	Grep/P=catPathName/Q/E=("(?i)\\b"+match+"\\b") item
803	// Grep/P=catPathName/Q/E=("(?i)"+match) item
804	if( V_value ) // at least one instance was found
805	// Print "found ", item,ii
806	// if(strsearch(item,"pxp",0,2) == -1) //does NOT contain .pxp (the current experiment will be a match)
807	list += item + ";"
808	// endif
809	endif
810	endfor
811
812	List = SortList(List,";",0)
813
814	return(list)
815	end
816
817
818	Function/S V_GetMSKList()
819
820	String list="",item="",fname,newList,intent
821	Variable ii,num
822
823	PathInfo catPathName
824	String path = S_path
825
826	newList = V_Get_NotRawDataFileList()
827	newList = V_RemoveEXTFromList(newlist,"hst") // remove the event files
828	newList = V_RemoveEXTFromList(newlist,"ave") // remove the ave files
829	newList = V_RemoveEXTFromList(newlist,"abs") // remove the abs files
830	newList = V_RemoveEXTFromList(newlist,"pxp") // remove the pxp files
831	newList = V_RemoveEXTFromList(newlist,"DS_Store") // remove the DS_Store file (OSX only)
832
833	num=ItemsInList(newList)
834
835	// for(ii=0;ii<num;ii+=1)
836	// item=StringFromList(ii, newList , ";")
837	// fname = path + item
838	// intent = V_getReduction_intent(fname)
839	// if(cmpstr(intent,"SENSITIVITY") == 0)
840	// list += item + ";"
841	// endif
842	//
843	// endfor
844
845	// String match="MASK" // this is part of the title of a VSANS MASK file
846	String match="VSANS_MASK" // this is part of the title of a VSANS MASK file
847	for(ii=0;ii<num;ii+=1)
848	item=StringFromList(ii, newList , ";")
849	Grep/P=catPathName/Q/E=("(?i)\\b"+match+"\\b") item
850	// Grep/P=catPathName/Q/E=("(?i)"+match) item
851	if( V_value ) // at least one instance was found
852	// Print "found ", item,ii
853	// if(strsearch(item,"pxp",0,2) == -1) //does NOT contain .pxp (the current experiment will be a match)
854	list += item + ";"
855	// endif
856	endif
857
858	endfor
859
860	List = SortList(List,";",0)
861
862	return(list)
863	end
864
865
866	//
867	// TODO
868	// -- find proper way to search for these files
869	// -- they may be written to the file header(reduction block)
870	// -- or grep for VSANS_MASK (in the title)
871	Function/S V_PickMASKButton(ctrlName) : ButtonControl
872	String ctrlName
873	String list="",item="",fname,newList,intent
874	Variable ii,num
875
876	PathInfo catPathName
877	String path = S_path
878
879	newList = V_Get_NotRawDataFileList()
880	newList = V_RemoveEXTFromList(newlist,"hst") // remove the event files
881	num=ItemsInList(newList)
882
883	// for(ii=0;ii<num;ii+=1)
884	// item=StringFromList(ii, newList , ";")
885	// fname = path + item
886	// intent = V_getReduction_intent(fname)
887	// if(cmpstr(intent,"MASK") == 0)
888	// list += item + ";"
889	// endif
890	//
891	// endfor
892
893	String match="MASK"
894	for(ii=0;ii<num;ii+=1)
895	item=StringFromList(ii, newList , ";")
896	Grep/P=catPathName/Q/E=("(?i)\\b"+match+"\\b") item
897	// Grep/P=catPathName/Q/E=("(?i)"+match) item
898	if( V_value ) // at least one instance was found
899	// Print "found ", item,ii
900	list += item + ";"
901	endif
902
903	endfor
904
905	List = SortList(List,";",0)
906	Printf "MASK files = %s\r",list
907
908	return(list)
909
910
911	End
912
913	//button action function to reduce one file with the information specified on
914	//the panel
915	//a temporary protocol is created, even if the fields correspond to a named protocol
916	//(only the protocol wave values are written to the data header, but the name is written to the
917	//schematic - this could cause some unwanted confusion)
918	//
919	//if a sample file(s) is selected, only that file(s) will be reduced
920	//if no file is selected, the user will be prompted with a standard open
921	//dialog to select sample data file(s)
922	//
923	Function V_ReduceOneButton(ctrlName) : ButtonControl
924	String ctrlName
925
926	//parse the information on the panel and assign to tempProtocol wave (in protocol folder)
927	//and execute
928	String temp="root:Packages:NIST:VSANS:Globals:Protocols:tempProtocol"
929	Wave/T w=$temp
930	Variable ii=0,num=12
931	do
932	w[ii] = ""
933	ii+=1
934	while(ii<num)
935
936	V_MakeProtocolFromPanel(w)
937
938	//the "current" protocol is the "tempProtocol" that was parsed from the panel input
939	//set the global, so that the data writing routine can find the protocol wave (fatal otherwise)
940	String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr="tempProtocol"
941
942	PathInfo catPathName //this is where the files came from
943	String pathstr=S_path,samStr
944
945	//take the string from the panel
946	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gSAM
947
948	if( (strlen(tempStr) == 0) \|\| (cmpstr(tempStr,"ask")==0) )
949	//let user select the files
950	tempStr="ask"
951	V_ExecuteProtocol(temp,tempStr)
952	return(0)
953	Else
954	//parse the list of numbers
955	//send only the filenames, without paths
956	samStr = V_ParseRunNumberList(tempStr)
957	If(strlen(samStr)==0)
958	DoAlert 0,"The SAM file number cound not be interpreted. Please enter a valid run number or filename"
959	return(1)
960	endif
961	tempStr=samStr //reset the global
962	V_ExecuteProtocol(temp,samStr)
963	return(0)
964	endif
965	End
966
967
968	//button action function will prompt user for absolute scaling parameters
969	//either from an empty beam file or by manually entering the 4 required values
970	//uses the same function and shared global string as the questionnare form of reduction
971	//in "protocol.ipf" - the string is root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr
972	//
973	Function V_SetABSParamsButton(ctrlName) : ButtonControl
974	String ctrlName
975
976	//will prompt for a list of ABS parameters (4) through a global string variable
977
978	Execute "V_AskForAbsoluteParams_Quest()"
979
980	End
981
982
983
984	//the panel recreation macro
985	//
986	Window V_ProtocolPanel()
987	PauseUpdate; Silent 1 // building window...
988	NewPanel /W=(1280,332,1630,932) /K=1 as "VSANS Reduction Protocol"
989	ModifyPanel cbRGB=(56589,50441,50159), fixedSize=1
990	SetDrawLayer UserBack
991	DrawLine 3,65,301,65
992	DrawLine 3,157,301,157
993	DrawLine 3,208,301,208
994	DrawLine 3,257,301,257
995	DrawLine 3,305,301,305
996	DrawLine 3,350,301,350
997	DrawLine 3,445,301,445
998	DrawLine 3,513,301,513
999	DrawLine 3,396,301,396
1000
1001	//
1002	Button button_help,pos={300,2},size={25,20},proc=V_ShowProtoHelp,title="?"
1003	Button button_help,help={"Show the help file for setting up a reduction protocol"}
1004	Button button_quest,pos={20,2},size={150,20},proc=V_ProtocolQuestionnaire,title="Questions"
1005	Button button_quest,help={"Run through the questionnaire for setting up a reduction protocol"}
1006	Button button_quest,disable=2
1007
1008
1009	PopupMenu popup_sam,pos={85,68},size={51,23},proc=SAMFilePopMenuProc
1010	PopupMenu popup_sam,mode=1,value= #"V_getSAMList()"
1011	PopupMenu popup_bkg,pos={85,164},size={51,23},proc=BKGFilePopMenuProc
1012	PopupMenu popup_bkg,mode=1,value= #"V_getBGDList()"
1013	PopupMenu popup_emp,pos={85,213},size={51,23},proc=EMPFilePopMenuProc
1014	PopupMenu popup_emp,mode=1,value= #"V_getEMPList()"
1015	PopupMenu popup_div,pos={85,263},size={51,23},proc=DIVFilePopMenuProc
1016	PopupMenu popup_div,mode=1,value= #"V_getDIVList()"
1017	PopupMenu popup_msk,pos={85,356},size={51,23},proc=MSKFilePopMenuProc
1018	PopupMenu popup_msk,mode=1,value= #"V_getMSKList()"
1019
1020
1021	CheckBox prot_check,pos={6,163},size={74,14},title="Background"
1022	CheckBox prot_check,help={"If checked, the specified background file will be included in the data reduction. If the file name is \"ask\", then the user will be prompted for the file"}
1023	CheckBox prot_check,value= 1
1024	CheckBox prot_check_1,pos={6,215},size={71,14},title="Empty Cell"
1025	CheckBox prot_check_1,help={"If checked, the specified empty cell file will be included in the data reduction. If the file name is \"ask\", then the user will be prompted for the file"}
1026	CheckBox prot_check_1,value= 1
1027	CheckBox prot_check_2,pos={6,263},size={72,14},title="Sensitivity"
1028	CheckBox prot_check_2,help={"If checked, the specified detector sensitivity file will be included in the data reduction. If the file name is \"ask\", then the user will be prompted for the file"}
1029	CheckBox prot_check_2,value= 1
1030	CheckBox prot_check_3,pos={6,356},size={43,14},title="Mask"
1031	CheckBox prot_check_3,help={"If checked, the specified mask file will be included in the data reduction. If the file name is \"ask\", then the user will be prompted for the file"}
1032	CheckBox prot_check_3,value= 1
1033	CheckBox prot_check_4,pos={6,70},size={53,14},title="Sample"
1034	CheckBox prot_check_4,help={"If checked, the specified sample file will be included in the data reduction. If the file name is \"ask\", then the user will be prompted for the file"}
1035	CheckBox prot_check_4,value= 1
1036	CheckBox prot_check_5,pos={6,399},size={56,14},title="Average"
1037	CheckBox prot_check_5,help={"If checked, the specified averaging will be performed at the end of the data reduction."}
1038	CheckBox prot_check_5,value= 1
1039	CheckBox prot_check_9,pos={6,310},size={59,14},title="Absolute"
1040	CheckBox prot_check_9,help={"If checked, absolute calibration will be included in the data reduction. If the parameter list is \"ask\", then the user will be prompted for absolue parameters"}
1041	CheckBox prot_check_9,value= 1
1042
1043
1044	// Button pick_sam,pos={214,28},size={70,20},proc=V_PickSAMButton,title="set SAM"
1045	// Button pick_sam,help={"This button will set the file selected in the File Catalog table to be the sample file"}
1046	// Button pick_bgd,pos={214,75},size={70,20},proc=V_PickBGDButton,title="set BGD"
1047	// Button pick_bgd,help={"This button will set the file selected in the File Catalog table to be the background file."}
1048	// Button pick_emp,pos={214,125},size={70,20},proc=V_PickEMPButton,title="set EMP"
1049	// Button pick_emp,help={"This button will set the file selected in the File Catalog table to be the empty cell file."}
1050	// Button pick_DIV,pos={214,173},size={70,20},proc=V_PickDIVButton,title="set DIV"
1051	// Button pick_DIV,help={"This button will set the file selected in the File Catalog table to be the sensitivity file."}
1052	Button pick_ABS,pos={264,308},size={70,20},proc=V_SetABSParamsButton,title="set ABS"
1053	Button pick_ABS,help={"This button will prompt the user for absolute scaling parameters"}
1054	// Button pick_MASK,pos={214,266},size={70,20},proc=V_PickMASKButton,title="set MASK"
1055	// Button pick_MASK,help={"This button will set the file selected in the File Catalog table to be the mask file."}
1056
1057
1058	Button pick_AVE,pos={188,401},size={150,20},proc=V_SetAverageParamsButtonProc,title="set AVERAGE params"
1059	Button pick_AVE,help={"Prompts the user for the type of 1-D averaging to perform, as well as saving options"}
1060
1061
1062	Button pick_trim,pos={264,454},size={70,20},proc=V_TrimDataProtoButton,title="Trim"
1063	Button pick_trim,help={"This button will prompt the user for trimming parameters"}
1064
1065
1066	SetVariable samStr,pos={6,90},size={250,15},title="file:"
1067	SetVariable samStr,help={"Filename of the sample file(s) to be used in the data reduction"}
1068	SetVariable samStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gSAM
1069	SetVariable bgdStr,pos={7,186},size={250,15},title="file:"
1070	SetVariable bgdStr,help={"Filename of the background file(s) to be used in the data reduction"}
1071	SetVariable bgdStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gBGD
1072	SetVariable empStr,pos={8,236},size={250,15},title="file:"
1073	SetVariable empStr,help={"Filename of the empty cell file(s) to be used in the data reduction"}
1074	SetVariable empStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gEMP
1075	SetVariable divStr,pos={9,285},size={250,15},title="file:"
1076	SetVariable divStr,help={"Filename of the detector sensitivity file to be used in the data reduction"}
1077	SetVariable divStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gDIV
1078	SetVariable maskStr,pos={9,377},size={250,15},title="file:"
1079	SetVariable maskStr,help={"Filename of the mask file to be used in the data reduction"}
1080	SetVariable maskStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gMASK
1081	SetVariable absStr,pos={7,331},size={250,15},title="parameters:"
1082	SetVariable absStr,help={"Keyword-string of values necessary for absolute scaling of data. Remaining parameters are taken from the sample file."}
1083	SetVariable absStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr
1084	SetVariable aveStr,pos={9,424},size={250,15},title="parameters:"
1085	SetVariable aveStr,help={"Keyword-string of choices used for averaging and saving the 1-D data files"}
1086	SetVariable aveStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gAVE
1087
1088	SetVariable begStr,pos={9,464},size={250,15},title="Beg Trim:"
1089	SetVariable begStr,help={"Keyword-string of choices used for averaging and saving the 1-D data files"}
1090	SetVariable begStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gBegPtsStr
1091	SetVariable endStr,pos={9,484},size={250,15},title="End Trim:"
1092	SetVariable endStr,help={"Keyword-string of choices used for averaging and saving the 1-D data files"}
1093	SetVariable endStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gEndPtsStr
1094
1095
1096
1097	//only show DRK if user wants to see it
1098	//if global = 1,then show => set disable = 0
1099	// CheckBox prot_check_6,pos={6,363},size={113,14},proc=DrkCheckProc,title="Use DRK correction"
1100	// CheckBox prot_check_6,help={"If checked, the selected file will be used for DRK correction. Typically this is NOT checked"}
1101	// CheckBox prot_check_6,value= 0,disable = (!root:Packages:NIST:gAllowDRK)
1102	// SetVariable drkStr,pos={120,363},size={150,15},title="."
1103	// SetVariable drkStr,help={"DRK detector count file"},disable = (!root:Packages:NIST:gAllowDRK)
1104	// SetVariable drkStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gDRK
1105
1106
1107	Button export_button, size={120,20},pos={125,540},title="Export to Data",proc=V_ExportFileProtocol
1108	Button export_button, help={"Exports the protocol to data file on disk for Importing into another experiment"}
1109	Button import_button, size={120,20},pos={125,562},title="Import from Data",proc=V_ImportFileProtocol
1110	Button import_button,help={"Imports a protocol from a data file on disk for use in this experiment"}
1111	Button recallProt,pos={7,540},size={107,20},proc=V_RecallProtocolButton,title="Recall Protocol"
1112	Button recallProt,help={"Resets the panel to the file choices in a previously saved protocol"}
1113	Button del_protocol,pos={7,562},size={110,20},proc=V_DeleteProtocolButton,title="Delete Protocol"
1114	Button del_protocol,help={"Use this to delete a previously saved protocol."}
1115	Button done_protocol,pos={285,562},size={45,20},proc=V_DoneProtocolButton,title="Done"
1116	Button done_protocol,help={"This button will close the panel. The panel can be recalled at any time from the SANS menu."}
1117	Button saveProtocol,pos={7,518},size={100,20},proc=V_SaveProtocolButton,title="Save Protocol"
1118	Button saveProtocol,help={"Saves the cerrent selections in the panel to a protocol which can be later recalled"}
1119	Button ReduceOne,pos={240,518},size={100,20},proc=V_ReduceOneButton,title="Reduce A File"
1120	Button ReduceOne,help={"Using the panel selections, the specified sample file will be reduced. If none is specified, the user will be prompted for a sample file"}
1121
1122	EndMacro
1123
1124
1125
1126
1127
1128	Function SAMFilePopMenuProc(pa) : PopupMenuControl
1129	STRUCT WMPopupAction &pa
1130
1131	switch( pa.eventCode )
1132	case 2: // mouse up
1133	Variable popNum = pa.popNum
1134	String popStr = pa.popStr
1135	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gSAM
1136	tempStr = popStr
1137	break
1138	case -1: // control being killed
1139	break
1140	endswitch
1141
1142	return 0
1143	End
1144
1145
1146	Function BKGFilePopMenuProc(pa) : PopupMenuControl
1147	STRUCT WMPopupAction &pa
1148
1149	switch( pa.eventCode )
1150	case 2: // mouse up
1151	Variable popNum = pa.popNum
1152	String popStr = pa.popStr
1153	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gBGD
1154	tempStr = popStr
1155	break
1156	case -1: // control being killed
1157	break
1158	endswitch
1159
1160	return 0
1161	End
1162
1163	Function EMPFilePopMenuProc(pa) : PopupMenuControl
1164	STRUCT WMPopupAction &pa
1165
1166	switch( pa.eventCode )
1167	case 2: // mouse up
1168	Variable popNum = pa.popNum
1169	String popStr = pa.popStr
1170	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gEMP
1171	tempStr = popStr
1172	break
1173	case -1: // control being killed
1174	break
1175	endswitch
1176
1177	return 0
1178	End
1179
1180	Function DIVFilePopMenuProc(pa) : PopupMenuControl
1181	STRUCT WMPopupAction &pa
1182
1183	switch( pa.eventCode )
1184	case 2: // mouse up
1185	Variable popNum = pa.popNum
1186	String popStr = pa.popStr
1187	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gDIV
1188	tempStr = popStr
1189	break
1190	case -1: // control being killed
1191	break
1192	endswitch
1193
1194	return 0
1195	End
1196
1197	Function MSKFilePopMenuProc(pa) : PopupMenuControl
1198	STRUCT WMPopupAction &pa
1199
1200	switch( pa.eventCode )
1201	case 2: // mouse up
1202	Variable popNum = pa.popNum
1203	String popStr = pa.popStr
1204	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gMASK
1205	tempStr = popStr
1206	break
1207	case -1: // control being killed
1208	break
1209	endswitch
1210
1211	return 0
1212	End
1213
1214	////activated when user checks/unchecks the box
1215	////either prompts for a file using a standard dialog, or removes the current file
1216	//Function V_DrkCheckProc(ctrlName,checked) : CheckBoxControl
1217	// String ctrlName
1218	// Variable checked //Desired state, not previous state
1219	//
1220	// SVAR drkStr=root:Packages:NIST:VSANS:Globals:Protocols:gDRK
1221	// if(checked==1)
1222	// //print "Unchecked on call"
1223	// //this just asks for the filename, doesn't open the file
1224	// String msgStr="Select the DRK file",fullPath="",fileStr=""
1225	// Variable refnum
1226	//
1227	// Open/D/R/T="????"/M=(msgStr)/P=catPathName refNum
1228	// fullPath = S_FileName //fname is the full path
1229	// if(cmpstr(fullpath,"")==0)
1230	// //user cancelled
1231	// CheckBox prot_check_6,value=0 //keep box unchecked
1232	// return(0)
1233	// Endif
1234	// fileStr=V_GetFileNameFromPathNoSemi(fullPath)
1235	// //Print fileStr
1236	// //update the global string
1237	// drkStr = ReplaceStringByKey("DRK",drkStr,fileStr,"=",",")
1238	// drkStr = ReplaceNumberByKey("DRKMODE", drkStr, 10 ,"=",",")
1239	// else
1240	// //print "checked on call"
1241	// drkStr="DRK=none,DRKMODE=0," //change the global
1242	// endif
1243	//
1244	//End
1245
1246
1247	Function V_ShowProtoHelp(ctrlName) : ButtonControl
1248	String ctrlName
1249	DisplayHelpTopic/Z/K=1 "VSANS Data Reduction Tutorial[VSANS Reduction Protocol]"
1250	if(V_flag !=0)
1251	DoAlert 0,"The VSANS Data Reduction Tutorial Help file could not be found"
1252	endif
1253	End
1254
1255	//button action procedure to get the type of average requested by the user
1256	//presented as a missing parameter dialog, which is really user-UN-friendly
1257	//and will need to be re-thought. Defaults of dialog are set for normal
1258	//circular average, so typically click "continue" and proceed
1259	//
1260	Function V_SetAverageParamsButtonProc(ctrlName) : ButtonControl
1261	String ctrlName
1262
1263	// Execute "V_GetAvgInfo_Full()"
1264	Execute "V_GetAvgInfo()"
1265
1266	//set the global string
1267	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr
1268	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAVE = tempStr
1269
1270	End
1271
1272	// TODO
1273	// -- this is a trimmed down version of the "full" set of averaging options
1274	// add to this as needed as I figure out what functionality is appropriate
1275	//
1276	//procedure called by protocol panel to ask user for average type choices
1277	// somewhat confusing and complex, but may be as good as it gets.
1278	//
1279	//Proc V_GetAvgInfo(av_typ,autoSave,autoName,autoPlot,side,phi,dphi,width,QCtr,QDelta)
1280	Proc V_GetAvgInfo(av_typ,autoSave,autoName,binType,qCtr,qDelta,detGroup)
1281	String av_typ,autoSave,AutoName,binType
1282	// Variable phi=0,dphi=10,width=10,Qctr = 0.01,qDelta=10
1283	Variable Qctr=0.1,qDelta=0.01
1284	String detGroup="F"
1285
1286	// Prompt av_typ, "Type of Average",popup,"Circular;Sector;Rectangular;Annular;2D_ASCII;QxQy_ASCII;PNG_Graphic;Sector_PlusMinus;"
1287	Prompt av_typ, "Type of Average",popup,"Circular;Annular;"
1288
1289	// comment out above line in DEMO_MODIFIED version, and uncomment the line below (to disable PNG save)
1290	// Prompt av_typ, "Type of Average",popup,"Circular;Sector;Rectangular;Annular;2D_ASCII;QxQy_ASCII"
1291	Prompt autoSave,"Save files to disk?",popup,"Yes - Concatenate;Yes - Individual;No"
1292	Prompt autoName,"Auto-Name files?",popup,"Auto;Manual"
1293	// Prompt autoPlot,"Plot the averaged Data?",popup,"Yes;No"
1294	// Prompt side,"Include detector halves?",popup,"both;right;left"
1295	// Prompt phi,"Orientation Angle (-90,90) degrees (Rectangular or Sector)"
1296	// Prompt dphi, "Azimuthal range (0,45) degrees (Sector only)"
1297	// Prompt width, "Width of Rectangular average (1,128)"
1298	Prompt binType,"Binning Type?",popup,ksBinTypeStr
1299
1300	Prompt Qctr, "q-value of center of annulus"
1301	Prompt Qdelta,"(+/-) q-width of annulus"
1302	Prompt detGroup,"Group for annulus"
1303
1304	//assign results of dialog to key=value string, semicolon separated
1305	//do only what is necessary, based on av_typ
1306	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr=""
1307
1308	// TODO:
1309	// hard wired value
1310	String autoPlot = "No"
1311
1312
1313	// all averages need these values
1314	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "AVTYPE=" + av_typ + ";"
1315	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SAVE=" + autoSave + ";"
1316	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "NAME=" + autoName + ";"
1317	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PLOT=" + autoPlot + ";"
1318	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "BINTYPE=" + binType + ";"
1319
1320	// if(cmpstr(av_typ,"Sector")==0 \|\| cmpstr(av_typ,"Sector_PlusMinus")==0)
1321	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SIDE=" + side + ";"
1322	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PHI=" + num2str(phi) + ";"
1323	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "DPHI=" + num2str(dphi) + ";"
1324	// Endif
1325	//
1326	// if(cmpstr(av_typ,"Rectangular")==0)
1327	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SIDE=" + side + ";"
1328	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PHI=" + num2str(phi) + ";"
1329	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "WIDTH=" + num2str(width) + ";"
1330	// Endif
1331	//
1332	if(cmpstr(av_typ,"Annular")==0)
1333	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "QCENTER=" + num2str(QCtr) + ";"
1334	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "QDELTA=" + num2str(QDelta) + ";"
1335	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "DETGROUP=" + detGroup + ";"
1336	Endif
1337	End
1338
1339
1340	// TODO
1341	// -- this is the original(SANS) version, and needs to be updated for VSANS as the averaging options are
1342	// worked out
1343	// -- there have been changes made to V_GetAvgInfo() above -- so work from that version, NOT this one.
1344	//
1345	//
1346	//procedure called by protocol panel to ask user for average type choices
1347	// somewhat confusing and complex, but may be as good as it gets.
1348	//
1349	Proc V_GetAvgInfo_Full(av_typ,autoSave,autoName,autoPlot,side,phi,dphi,width,QCtr,QDelta)
1350	String av_typ,autoSave,AutoName,autoPlot,side
1351	Variable phi=0,dphi=10,width=10,Qctr = 0.01,qDelta=10
1352	Prompt av_typ, "Type of Average",popup,"Circular;Sector;Rectangular;Annular;2D_ASCII;QxQy_ASCII;PNG_Graphic;Sector_PlusMinus;"
1353	// comment out above line in DEMO_MODIFIED version, and uncomment the line below (to disable PNG save)
1354	// Prompt av_typ, "Type of Average",popup,"Circular;Sector;Rectangular;Annular;2D_ASCII;QxQy_ASCII"
1355	Prompt autoSave,"Save files to disk?",popup,"Yes;No"
1356	Prompt autoName,"Auto-Name files?",popup,"Auto;Manual"
1357	Prompt autoPlot,"Plot the averaged Data?",popup,"Yes;No"
1358	Prompt side,"Include detector halves?",popup,"both;right;left"
1359	Prompt phi,"Orientation Angle (-90,90) degrees (Rectangular or Sector)"
1360	Prompt dphi, "Azimuthal range (0,45) degrees (Sector only)"
1361	Prompt width, "Width of Rectangular average (1,128)"
1362	Prompt Qctr, "q-value of center of annulus"
1363	Prompt Qdelta,"Pixel width of annulus"
1364
1365	//assign results of dialog to key=value string, semicolon separated
1366	//do only what is necessary, based on av_typ
1367	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr=""
1368
1369	// all averages need these four values
1370	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "AVTYPE=" + av_typ + ";"
1371	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SAVE=" + autoSave + ";"
1372	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "NAME=" + autoName + ";"
1373	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PLOT=" + autoPlot + ";"
1374
1375	if(cmpstr(av_typ,"Sector")==0 \|\| cmpstr(av_typ,"Sector_PlusMinus")==0)
1376	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SIDE=" + side + ";"
1377	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PHI=" + num2str(phi) + ";"
1378	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "DPHI=" + num2str(dphi) + ";"
1379	Endif
1380
1381	if(cmpstr(av_typ,"Rectangular")==0)
1382	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SIDE=" + side + ";"
1383	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PHI=" + num2str(phi) + ";"
1384	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "WIDTH=" + num2str(width) + ";"
1385	Endif
1386
1387	if(cmpstr(av_typ,"Annular")==0)
1388	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "QCENTER=" + num2str(QCtr) + ";"
1389	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "QDELTA=" + num2str(QDelta) + ";"
1390	Endif
1391	End
1392
1393
1394	//prompts the user to pick a previously created protocol from a popup list
1395	//of given the option to create a new protocol
1396	//the chosen protocol is passed back to the calling procedure by a global string
1397	//the popup is presented as a missing parameter dialog (called with empty parameter list)
1398	//
1399	// MAXROWS is present to exclude the PanelNameW from appearing as a protocol
1400	Proc V_PickAProtocol(protocol)
1401	String Protocol
1402	Prompt Protocol "Pick A Protocol",popup, V_RecallableProtocols()
1403
1404	String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr = protocol
1405	End
1406
1407	Proc V_DeleteAProtocol(protocol)
1408	String Protocol
1409	// Prompt Protocol "Delete A Protocol",popup, WaveList("*",";","TEXT:1")
1410	Prompt Protocol "Delete A Protocol",popup, V_DeletableProtocols()
1411
1412	String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr = protocol
1413	End
1414
1415	Function/S V_DeletableProtocols()
1416	String list=WaveList("*",";","TEXT:1,MAXROWS:13")
1417
1418	list= RemoveFromList("Base", list , ";")
1419	list= RemoveFromList("DoAll", list , ";")
1420	list= RemoveFromList("CreateNew", list , ";")
1421	list= RemoveFromList("tempProtocol", list , ";")
1422	list= RemoveFromList("wTTmpWrite", list , ";")
1423	if(cmpstr(list,"")==0)
1424	list = "_no_protocols_;"
1425	endif
1426
1427	return(list)
1428	End
1429
1430	Function/S V_RecallableProtocols()
1431	String list=WaveList("*",";","TEXT:1,MAXROWS:13")
1432
1433	// list= RemoveFromList("Base", list , ";")
1434	// list= RemoveFromList("DoAll", list , ";")
1435	list= RemoveFromList("CreateNew", list , ";")
1436	list= RemoveFromList("tempProtocol", list , ";")
1437	list= RemoveFromList("wTTmpWrite", list , ";")
1438	if(cmpstr(list,"")==0)
1439	list = "_no_protocols_;"
1440	endif
1441
1442	return(list)
1443	End
1444
1445
1446	//missing parameter dialog to solicit user for a waveStr for the protocol
1447	//about to be created
1448	//name is passed back as a global string and calling procedure is responsible for
1449	//checking for wave conflicts and valid names
1450	//
1451	Proc V_AskForName(protocol)
1452	String Protocol
1453	Prompt Protocol "Enter a new name for your protocol (no extension)"
1454
1455	String/G root:Packages:NIST:VSANS:Globals:Protocols:gNewStr = protocol
1456	End
1457
1458	//this is a lengthy procedure for sequentially polling the user about what data
1459	//reduction steps they want to be performed during the protocol
1460	//ensures that a valid protocol name was chosen, then fills out each "item"
1461	//(6 total) needed for reduction
1462	//it the user cancels at any point, the partial protocol will be deleted
1463	//
1464	Function V_ProtocolQuestionnaire(ctrlName)
1465	String ctrlName
1466
1467	String filename,cmd
1468	Variable notDone,refnum
1469
1470	//prompt for name of new protocol wave to save
1471	do
1472	Execute "V_AskForName()"
1473	SVAR newProtoStr = root:Packages:NIST:VSANS:Globals:Protocols:gNewStr
1474
1475	//make sure it's a valid IGOR name
1476	newProtoStr = CleanupName(newProtoStr,0) //strict naming convention
1477	String/G root:Packages:NIST:VSANS:Globals:Protocols:gNewStr=newProtoStr //reassign, if changed
1478	//Print "newProtoStr = ",newProtoStr
1479
1480	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
1481	if(WaveExists( $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtoStr) ) == 1)
1482	//wave already exists
1483	DoAlert 0,"that name is already in use. Please pick a new name"
1484	notDone = 1
1485	else
1486	//name is good
1487	notDone = 0
1488	Endif
1489	while(notDone)
1490
1491	//Print "protocol questionnaire is "+newProtocol
1492
1493	//make a new text wave (12 points) and fill it in, in response to questions
1494	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols //(redundant - full wave specs are used)
1495	Make/O/T/N=(kNumProtocolSteps) $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtoStr)
1496	Wave/T newProtocol = $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtoStr)
1497	newProtocol = ""
1498
1499	//ask the questions
1500	/////
1501	//*****Multiple files in these lists are full paths/filenames which may or may not
1502	//have semicolon version numbers in the filename. Therefore, construct the list with
1503	//COMMAS as separators - to avoid messy parsing
1504	///////
1505
1506	String fileFilters = "VSANS Data Files (.ngv,.h5):.ngv,.h5;"
1507	// fileFilters += "HTML Files (.htm,.html):.htm,.html;"
1508	fileFilters += "All Files:.*;"
1509	//////////////////////////
1510	String drkStr="",fileStr=""
1511
1512
1513	//////////////////////////
1514	// DoAlert 1,"Do you want to correct your data for DRK (beam off) counts?"
1515	// if(V_flag == 1) //1=yes
1516	// //prompt for DRK file, but don't actually open it (/D flag)
1517	// Open/D/R/F=fileFilters/M="Select the DRK file"/P=catPathName refnum
1518	// //check for cancel
1519	// if(strlen(S_filename)==0)
1520	// //user cancelled, abort
1521	// KillWaves/Z newProtocol
1522	// SetDataFolder root:
1523	// Abort "Incomplete protocol has been deleted"
1524	// Endif
1525	// //assign filename (just the name) to [6]
1526	// fileStr = V_GetFileNameFromPathNoSemi(S_filename)
1527	// drkStr = "DRK=none,DRKMODE=0,"
1528	// drkStr = ReplaceStringByKey("DRK",drkStr,fileStr,"=",",")
1529	// drkStr = ReplaceNumberByKey("DRKMODE", drkStr, 10 ,"=",",")
1530	// newProtocol[6] = drkStr
1531	// else
1532	// //no Work.DRK desired
1533	// newProtocol[6] = "DRK=none,DRKMODE=0,"
1534	// Endif
1535	//
1536	////////////
1537
1538
1539	// TODO:
1540	// -- there is a lag in the V_pick() routine as it greps through all of the files. Several seconds even when there
1541	// are 20-ish files. Pre-search for the strings? When to refresh them for new data?
1542	/////////////////
1543	DoAlert 1,"Do you want to subtract background from your data?"
1544	if(V_flag == 1) //1=yes
1545
1546	Prompt filename,"BKG File",popup,V_PickBGDButton("")
1547	DoPrompt "Select File",filename
1548	if (V_Flag)
1549	return 0 // user canceled
1550	endif
1551	// //assign filename to [0]
1552	newProtocol[0] = V_GetFileNameFromPathNoSemi(fileName)
1553
1554
1555	// OLD way, using an open file dialog
1556	// and allowing for multiple files to be added together
1557	//
1558	// //prompt for background file, but don't actually open it (/D flag)
1559	// Open/D/R/F=fileFilters/M="Select the Background data file"/P=catPathName refnum
1560	// //check for cancel
1561	// if(strlen(S_filename)==0)
1562	// //user cancelled, abort
1563	// KillWaves/Z newProtocol
1564	// SetDataFolder root:
1565	// Abort "Incomplete protocol has been deleted"
1566	// Endif
1567	// //assign filename (full path) to [0]
1568	// newProtocol[0] = V_GetFileNameFromPathNoSemi(S_filename)
1569
1570	// notDone=1
1571	// do
1572	// //prompt for additional background files
1573	// DoAlert 1,"Do you want to add another background file?"
1574	// if(V_flag == 1) //yes
1575	// Open/D/R/F=fileFilters/M="Select another Background data file"/P=catPathName refnum
1576	// //check for cancel
1577	// if(strlen(S_filename)==0)
1578	// //user cancelled, abort ********maybe just break out of the loop here
1579	// KillWaves/Z newProtocol
1580	// SetDataFolder root:
1581	// Abort "Incomplete protocol has been deleted"
1582	// Endif
1583	// //assign filename (full path) to [0]
1584	// newProtocol[0] += "," + V_GetFileNameFromPathNoSemi(S_filename) //***COMMA separated list
1585	// notDone = 1 //keep going
1586	// else
1587	// notDone = 0 //no more to add
1588	// Endif
1589	// While(notDone)
1590	//////
1591
1592	else //no background desired
1593	newProtocol[0] = "none"
1594	Endif
1595
1596
1597	//////////////////////
1598	DoAlert 1,"Do you want to subtract empty cell scattering from your data?"
1599	if(V_flag == 1) //1=yes
1600
1601	Prompt filename,"EMP File",popup,V_PickEMPButton("")
1602	DoPrompt "Select File",filename
1603	if (V_Flag)
1604	return 0 // user canceled
1605	endif
1606	// //assign filename to [1]
1607	newProtocol[1] = V_GetFileNameFromPathNoSemi(fileName)
1608
1609
1610
1611	// //prompt for Empty cell file, but don't actually open it (/D flag)
1612	// Open/D/R/F=fileFilters/M="Select the Empty Cell data file"/P=catPathName refnum
1613	// //check for cancel
1614	// if(strlen(S_filename)==0)
1615	// //user cancelled, abort
1616	// KillWaves/Z newProtocol
1617	// SetDataFolder root:
1618	// Abort "Incomplete protocol has been deleted"
1619	// Endif
1620	// //assign filename (full path) to [1]
1621	// newProtocol[1] = V_GetFileNameFromPathNoSemi(S_filename)
1622	//
1623	// notDone=1
1624	// do
1625	// //prompt for additional Empty Cell files
1626	// DoAlert 1,"Do you want to add another Empty Cell file?"
1627	// if(V_flag == 1) //yes
1628	// Open/D/R/F=fileFilters/M="Select another Empty Cell data file"/P=catPathName refnum
1629	// //check for cancel
1630	// if(strlen(S_filename)==0)
1631	// //user cancelled, abort ********maybe just break out of the loop here
1632	// KillWaves/Z newProtocol
1633	// SetDataFolder root:
1634	// Abort "Incomplete protocol has been deleted"
1635	// Endif
1636	// //assign filename (full path) to [1]
1637	// newProtocol[1] += "," + V_GetFileNameFromPathNoSemi(S_filename) //***COMMA separated list
1638	// notDone = 1 //keep going
1639	// else
1640	// notDone = 0 //no more to add
1641	// Endif
1642	// While(notDone)
1643
1644
1645	else //no background desired
1646	newProtocol[1] = "none"
1647	Endif
1648
1649
1650	//////////////////////////
1651	DoAlert 1,"Do you want to correct your data for detector sensitivity?"
1652
1653	if(V_flag == 1) //1=yes
1654
1655	Prompt filename,"DIV File",popup,V_GetDIVList()
1656	DoPrompt "Select File",filename
1657	if (V_Flag)
1658	return 0 // user canceled
1659	endif
1660	// //assign filename to [2]
1661	newProtocol[2] = V_GetFileNameFromPathNoSemi(fileName)
1662
1663	// //prompt for DIV file, but don't actually open it (/D flag)
1664	// Open/D/R/F=fileFilters/M="Select the detector sensitivity file"/P=catPathName refnum
1665	// //check for cancel
1666	// if(strlen(S_filename)==0)
1667	// //user cancelled, abort
1668	// KillWaves/Z newProtocol
1669	// SetDataFolder root:
1670	// Abort "Incomplete protocol has been deleted"
1671	// Endif
1672	// //assign filename (full path) to [2]
1673	// newProtocol[2] = V_GetFileNameFromPathNoSemi(S_filename)
1674
1675
1676	else
1677	//no Work.DIV desired
1678	newProtocol[2] = "none"
1679	Endif
1680	//////////////////////////
1681	DoAlert 1,"Do you want to mask your files before averaging?"
1682
1683	if(V_flag == 1) //1=yes
1684
1685	Prompt filename,"MASK File",popup,V_PickMASKButton("")
1686	DoPrompt "Select File",filename
1687	if (V_Flag)
1688	return 0 // user canceled
1689	endif
1690	// //assign filename to [3]
1691	newProtocol[3] = V_GetFileNameFromPathNoSemi(fileName)
1692
1693	// //prompt for mask file, but don't actually open it (/D flag)
1694	// Open/D/R/F=fileFilters/M="Select the mask file"/P=catPathName refnum
1695	// //check for cancel
1696	// if(strlen(S_filename)==0)
1697	// //user cancelled, abort
1698	// KillWaves/Z newProtocol
1699	// SetDataFolder root:
1700	// Abort "Incomplete protocol has been deleted"
1701	// Endif
1702	// //assign filename (full path) to [3]
1703	// newProtocol[3] = V_GetFileNameFromPathNoSemi(S_filename)
1704
1705
1706	else
1707	//no MASK desired
1708	newProtocol[3] = "none"
1709	Endif
1710
1711	//absolute scaling
1712
1713	//////////////////////////
1714	//ABS parameters stored as keyword=value string
1715	DoAlert 1,"Do you want absolute scaling?"
1716	if(V_flag == 1) //1=yes
1717	//missing param - prompt for values, put in semicolon-separated list
1718	Execute "V_AskForAbsoluteParams_Quest()"
1719	SVAR absStr = root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr
1720	newProtocol[4] = absStr
1721	else
1722	//no absolute scaling desired
1723	newProtocol[4] = "none"
1724	Endif
1725
1726	//type of average, plot?, auto/manual naming/saving... put in semicolon separated string
1727	//of KEY=<value> format for easy parsing
1728	//Kewords are: AVTYPE,PHI,DPHI,PLOT,SAVE,NAME,SIDE,WIDTH
1729	//note that AVTYPE,NAME,SIDE have string values, others have numerical values
1730	///////////////////////
1731	DoAlert 1,"Do you want to average your data to I vs. q?"
1732	if(V_flag == 1) //1=yes
1733	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr = ""
1734	Execute "V_GetAvgInfo()" //will put up missing paramter dialog and do all the work
1735	//:gAvgInfo is reset by the Proc(), copy this string tot he protocol
1736	SVAR tempStr=root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr
1737
1738	//get a file path for saving files, if desired
1739	/////no - save files to the same data folder as the one with the raw data
1740	//then only one path to manage.
1741	//String yesNo = StringByKey("SAVE", tempStr,"=", ";")
1742	//if(cmpstr("Yes",yesNo) == 0) //0=yes
1743	//NewPath/C/M="Select Folder"/O Save_path //Save_path is the symbolic path
1744	//Endif
1745
1746	newProtocol[5] = tempStr
1747	KillStrings/Z tempStr
1748	else
1749	//no averaging desired
1750	newProtocol[5] = "AVTYPE=none"
1751	Endif
1752
1753	//returns the name of the newly created (= currently in use) protocol wave through a global
1754	String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr = newProtoStr
1755
1756	//reset the panel based on the protocol textwave (currently a string)
1757	V_ResetToSavedProtocol(newProtoStr)
1758
1759	SetDataFolder root:
1760
1761	return(0)
1762	End
1763
1764
1765	// TODO
1766	// -- this function may not work properly for VSANS, but I haven't tested it yet
1767	// -- I'd rather have some sort of display to show the current content of the WORK folders
1768	//
1769	// -- the global string fileList does not exist, so this will always fail and return zero
1770	//
1771	//
1772	//function to check the work files (to see what's already there)
1773	//and compare that with the files that are supposed to be there, according to the
1774	//current protocol (to save unnecessary time re-loading files)
1775	//
1776	//the "type" folder is checked for all files in the list req(ested)Files
1777	//note that the list of files is a full path:name;ver, while the
1778	//fileList in the folder is just the name (or a list of names)
1779	//
1780	//returns 0 false, if files are NOT present
1781	//or 1 = true, yes, the files are there as requested
1782	//
1783	Function V_AreFilesThere(type,reqFiles)
1784	String type,reqFiles
1785
1786	//in general, reqFiles is a list of full paths to files - which MAY include semicolon version numbers
1787	//reqFiles MUST be constructed with COMMAS as list separators, to avoid disaster
1788	//when the version numbers are interpreted as filenames
1789
1790	//get the number of files requested
1791	Variable nReq,nCur,match,ii
1792	nReq = ItemsInList(reqFiles,",")
1793
1794	//get the name of the file currently in BGD - in the global fileList
1795	//fileList has NAMES ONLY - since it was derived from the file header
1796	String testStr
1797	testStr = "root:Packages:NIST:"+type+":fileList"
1798	if(Exists(testStr) == 2) //2 if string variable exists
1799	SVAR curFiles = $testStr
1800	else
1801	//no files currently in type folder, return zero
1802	Return (0)
1803	Endif
1804	//get the number of files already in folder
1805	nCur = ItemsInList(curFiles,";")
1806	If(nCur != nReq)
1807	Return (0) //quit now, the wrong number of files present
1808	Endif
1809	//right number of files... are the names right...
1810	//check for a match (case-sensitive!!) of each requested file in the curFile string
1811	//need to extract filenames from reqFiles, since they're the full path and name
1812
1813	ii=0
1814	do
1815	testStr = StringFromList(ii,reqFiles,",") //testStr is the Nth full path and filename
1816	//testStr = GetFileNameFromPathNoSemi(testStr) //testStr will now be just the filename
1817	match = stringmatch(curFiles,testStr)
1818	If(!match)
1819	Return (0) //req file was not found in curFile list - get out now
1820	Endif
1821	ii+=1
1822	while(ii<nreq)
1823
1824	Return (1) //indicate that files are OK, no changes needed
1825	End
1826
1827
1828	//
1829	//will add the files specified in the protocol to the "type" folder
1830	//will add multiple files together if more than one file is requested
1831	//(list is a comma delimited list of filenames, with NO path information)
1832	//
1833	// This routine NOW DOES check for the possibility that the filenames may have ";vers" from the
1834	// VAX - data should be picked up from Charlotte, where it won't have version numbers.
1835	//
1836	Function V_AddFilesInList(type,list)
1837	String type,list
1838
1839	//type is the work folder to put the data into, and list is a COMMA delimited list of paths/names
1840	Variable num,ii,err=0,refNum
1841	String filename,pathStr=""
1842	PathInfo catPathName //this is where the files are
1843	pathstr=S_path
1844
1845	num = ItemsInList(list,",") // comma delimited list
1846
1847	ii=0
1848	do
1849	//FindValidFilename only needed in case of vax version numbers
1850	filename = pathStr + V_FindValidFilename(StringFromList(ii,list,","))
1851	Open/Z/R refnum as filename
1852	if(V_flag != 0) //file not found
1853	//Print "file not found AddFilesInList()"
1854	//Print filename
1855	err = 1
1856	return(err)
1857	Endif
1858	Close refnum //file was found and opened, so close it
1859
1860	// Abort "Find equivalent to ReadHeaderAndData(filename)"
1861	// ReadHeaderAndData(filename)
1862	err = V_LoadHDF5Data(filename,"RAW")
1863
1864	if(ii == 0)
1865	//first pass, wipe out the old contents of the work file
1866	err = V_Raw_to_work(type)
1867	else
1868	err = V_Add_raw_to_work(type)
1869	Endif
1870	ii+=1
1871	while(ii<num)
1872	return(err)
1873	End
1874
1875	//function will reduce a sample file (or ask for file(s))
1876	//using the protocol named as "protoStr" in the Protocols subfolder
1877	//samStr is the file(s) or "ask" to force prompt
1878	//sequentially proceeds through flowchart, doing reduction steps as needed
1879	//show Schematic to debug what steps/values were used
1880	//
1881	//function is long, but straightforward logic
1882	//
1883	Function V_ExecuteProtocol(protStr,samStr)
1884	String protStr,samStr
1885	//protStr is the full path to the selected protocol wave
1886	//samStr is either "ask" or the name ONLY ofthe desired sample data file(s) (NO PATH)
1887	WAVE/T prot = $protStr
1888	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
1889
1890	Variable filesOK,err,notDone
1891	String activeType, msgStr, junkStr, pathStr=""
1892	PathInfo catPathName //this is where the files are
1893	pathStr=S_path
1894
1895	// NVAR useXMLOutput = root:Packages:NIST:gXML_Write
1896
1897	//Parse the instructions in the prot wave
1898	//0 - bkg
1899	//1 - emp
1900	//2 - div
1901	//3 - mask
1902	//4 - abs params c2-c5
1903	//5 - average params
1904	//6 = DRK file (**out of sequence)
1905	//7 = beginning trim points
1906	//8 = end trim points
1907	//9 = unused
1908	//10 = unused
1909	//11 = unused
1910
1911	// for VSANS, DIV is used on each data file as it is converted to WORK, so it needs to be
1912	// the first thing in place, before any data or backgrounds are loaded
1913
1914
1915	//
1916	// DONE:
1917	// x- this is no longer done after the COR step, and CAL is not produced as output of DIV
1918	// x- needs to be aware of the file name passed in
1919	// x- PromptForPath does not exist in VSANS. Need a better (automated) way to find the file.
1920
1921	//check for work.div file (prot[2])
1922	//load in if needed
1923	// no math is done here, DIV is applied as files are converted to WORK (the first operation in VSANS)
1924	//
1925	String divFileName = ""
1926
1927	If(cmpstr("none",prot[2])!=0) // if !0, then there's a file requested
1928	If(cmpstr("ask",prot[2]) == 0)
1929	//ask user for file
1930	// junkStr = PromptForPath("Select the detector sensitivity file")
1931	Prompt divFileName,"DIV File",popup,V_GetDIVList()
1932	DoPrompt "Select File",divFileName
1933
1934	If(strlen(divFileName)==0)
1935	SetDataFolder root:
1936	Abort "No file selected, data reduction aborted"
1937	Endif
1938	V_LoadHDF5Data(divFileName,"DIV")
1939	else
1940	//assume it's a path, and that the first (and only) item is the path:file
1941	//list processing is necessary to remove any final comma
1942	junkStr = pathStr + StringFromList(0, prot[2],"," )
1943	V_LoadHDF5Data(junkStr,"DIV")
1944	Endif
1945
1946	else
1947	// DIV step is being skipped
1948	NVAR gDoDIVCor = root:Packages:NIST:VSANS:Globals:gDoDIVCor
1949	Variable saved_gDoDIVCor = gDoDIVCor
1950	gDoDIVCor = 0 // protocol says to turn it off for now (reset later)
1951	Endif
1952
1953
1954	// TODO:
1955	// -- currently does not allow adding RAW data files together, so no parsing is done
1956	// -- NOTE detector corrections (including DIV) are done at the V_Raw_to_Work() step
1957	// So if the DIV is not part of the protocol, be sure to set/reset the global preference
1958	//
1959	//prompt for sam data => read raw data, add to sam folder
1960	//or parse file(s) from the input paramter string
1961	activeType = "SAM"
1962	msgStr = "Select sample data"
1963	//Ask for SAM file or parse
1964	do
1965	if((cmpstr(samStr,"ask") == 0) \|\| (cmpstr(samStr,"")==0) ) //zero if strings are equal
1966	err = V_LoadHDF5Data("","RAW") //will prompt for file
1967	if(err)
1968	PathInfo/S catPathName
1969	Abort "reduction sequence aborted"
1970	endif
1971	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
1972	err = V_Raw_to_work(activeType) //this is the first file (default)
1973	//Ask for another SAM file
1974	do
1975	DoAlert 1,"Do you want to add another Sample file?"
1976	if(V_flag == 1) //yes
1977	err = V_LoadHDF5Data("","RAW") //will prompt for file
1978	if(err)
1979	PathInfo/S catPathName
1980	Abort "reduction sequence aborted"
1981	endif
1982	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
1983	err = V_Add_raw_to_work(activeType)
1984	notDone = 1
1985	else
1986	notDone = 0
1987	endif
1988	while(notDone)
1989	break
1990	Endif
1991	//"none" is not an option - you always need a sample file - "none" will never return zero
1992	//if not "ask" AND not "none" then try to parse the filenames
1993	If((cmpstr(samStr,"none") != 0) && (cmpstr(samStr,"ask") != 0))
1994	//filesOK = AreFilesThere(activeType,samStr) //return 1 if correct files are already there
1995	filesOK = 0 // Feb 2008, always force a reload of files. Maybe slow, but always correct
1996	if(!filesOK)
1997	//add the correct file(s) to SAM
1998
1999	// TODO: only one file is allowed currently
2000	err = V_AddFilesInList(activeType,samStr)
2001
2002	if(err)
2003	//Print "samstr = ",samStr
2004	Abort "SAM file not found, reset SAM file"
2005	Endif
2006	Endif
2007	Endif
2008	While(0)
2009	// TODO
2010	// -- this may not be the most reliable way to pass the file name (for naming of the saved file later)
2011	SVAR file_name = root:file_Name
2012	String samFileLoaded = file_name //keep a copy of the sample file loaded
2013
2014	//always update
2015	V_UpdateDisplayInformation(ActiveType)
2016
2017	//check for bkg file -- "ask" might not fail - "ask?" will - ? not allowed in VAX filenames
2018	// add if needed
2019	//use a "case" statement
2020	msgStr = "Select background file"
2021	activeType = "BGD"
2022	do
2023	if(cmpstr(prot[0],"ask") == 0) //zero if strings are equal
2024	err = V_LoadHDF5Data("","RAW") //will prompt for file
2025	if(err)
2026	PathInfo/S catPathName
2027	Abort "reduction sequence aborted"
2028	endif
2029	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
2030	err = V_Raw_to_work(activeType) //this is the first file (default)
2031	//Ask for another BGD file
2032	do
2033	DoAlert 1,"Do you want to add another Background file?"
2034	if(V_flag == 1) //yes
2035	err = V_LoadHDF5Data("","RAW") //will prompt for file
2036	if(err)
2037	PathInfo/S catPathName
2038	Abort "reduction sequence aborted"
2039	endif
2040	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
2041	err = V_Add_raw_to_work(activeType)
2042	notDone = 1
2043	else
2044	notDone = 0
2045	endif
2046	while(notDone)
2047	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2048	break
2049	Endif
2050	If(cmpstr(prot[0],"none") == 0)
2051	//clean out the BKG folder?
2052	//KillDataFolder root:BKG
2053	//NewDataFolder/O root:BKG
2054	break
2055	Endif
2056	//if not "ask" AND not "none" then try to parse the filenames
2057	If((cmpstr(prot[0],"none") != 0) && (cmpstr(prot[0],"ask") != 0))
2058	//filesOK = AreFilesThere(activeType,prot[0])
2059	filesOK = 0 // Feb 2008, always force a reload of files. Maybe slow, but always correct
2060	if(!filesOK)
2061	//add the correct file(s) to BGD
2062	string bgdStr = prot[0]
2063	err = V_AddFilesInList(activeType,bgdStr)
2064	If(err)
2065	Abort "BGD file not found. Reset BGD file list"
2066	Endif
2067	Endif
2068	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2069	Endif
2070	While(0)
2071
2072
2073	//check for emp file (prot[1])
2074	// add if needed
2075	msgStr = "Select empty cell data"
2076	activeType = "EMP"
2077	do
2078	if(cmpstr(prot[1],"ask") == 0)
2079	err = V_LoadHDF5Data("","RAW") //will prompt for file
2080	if(err)
2081	PathInfo/S catPathName
2082	Abort "reduction sequence aborted"
2083	endif
2084	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
2085	err = V_Raw_to_work(activeType) //this is the first file (default)
2086	//Ask for another EMP file
2087	do
2088	DoAlert 1,"Do you want to add another Empty Cell file?"
2089	if(V_flag == 1) //yes
2090	err = V_LoadHDF5Data("","RAW") //will prompt for file
2091	if(err)
2092	PathInfo/S catPathName
2093	Abort "reduction sequence aborted"
2094	endif
2095	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
2096	err = V_Add_raw_to_work(activeType)
2097	notDone = 1
2098	else
2099	notDone = 0
2100	endif
2101	while(notDone)
2102	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2103	break
2104	Endif
2105	If(cmpstr(prot[1],"none") == 0)
2106	//clean out the EMP folder?
2107	//KillDataFolder root:Packages:NIST:EMP
2108	//NewDataFolder/O root:Packages:NIST:EMP
2109	break
2110	Endif
2111	//if not "ask" AND not "none" then try to parse the filenames
2112	If((cmpstr(prot[1],"none") != 0) && (cmpstr(prot[1],"ask") != 0))
2113	//filesOK = AreFilesThere(activeType,prot[1])
2114	filesOK = 0 // Feb 2008, always force a reload of files. Maybe slow, but always correct
2115	if(!filesOK)
2116	//add the correct file(s) to BGD
2117	err = V_AddFilesInList(activeType,prot[1])
2118	If(err)
2119	Abort "EMP file not found. Reset EMP file list"
2120	Endif
2121	Endif
2122	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2123	Endif
2124	While(0)
2125
2126	//do the CORRECT step based on the answers to emp and bkg subtraction
2127	//by setting the proper"mode"
2128	//1 = both emp and bgd subtraction
2129	//2 = only bgd subtraction
2130	//3 = only emp subtraction
2131	//4 = no subtraction
2132	//additional modes 091301
2133	//11 = emp, bgd, drk
2134	//12 = bgd and drk
2135	//13 = emp and drk
2136	//14 = no subtractions
2137	//work.drk is from proto[6]
2138	//
2139	//subtracting just the DRK data is NOT an option - it doesnt' really make any physical sense
2140	// - in this case, DRK is skipped (equivalent to mode==4)
2141	// automatically accounts for attenuators given the lookup tables and the
2142	//desired subtractions
2143	//Attenuator lookup tables are alredy implemented (NG1 = NG7)
2144	//
2145
2146
2147	/////// DRK is SKIPPED
2148
2149	// //read in the DRK data if necessary
2150	// //only one file, assumed to be RAW data
2151	// //
2152	// String fname="",drkStr=""
2153	// drkStr=StringByKey("DRK",prot[6],"=",",")
2154	// if(cmpstr(drkStr,"none") != 0)
2155	// err = ReadHeaderAndData( (pathStr+drkStr) )
2156	// if(err)
2157	// PathInfo/S catPathName
2158	// Abort "reduction sequence aborted"
2159	// endif
2160	// err = V_Raw_to_Work_NoNorm("DRK")
2161	// endif
2162
2163
2164
2165	//dispatch to the proper "mode" of Correct()
2166	Variable mode=4,val
2167	do
2168	if( (cmpstr("none",prot[0]) == 0) && (cmpstr("none",prot[1]) == 0) )
2169	//no subtraction (mode = 4),
2170	mode = 4
2171	Endif
2172	If((cmpstr(prot[0],"none") != 0) && (cmpstr(prot[1],"none") == 0))
2173	//subtract BGD only
2174	mode=2
2175	Endif
2176	If((cmpstr(prot[0],"none") == 0) && (cmpstr(prot[1],"none") != 0))
2177	//subtract EMP only
2178	mode=3
2179	Endif
2180	If((cmpstr(prot[0],"none") != 0) && (cmpstr(prot[1],"none") != 0))
2181	// bkg and emp subtraction are to be done (BOTH not "none")
2182	mode=1
2183	Endif
2184	activeType = "COR"
2185	//add in DRK mode (0= no used, 10 = used)
2186	val = NumberByKey("DRKMODE",prot[6],"=","," )
2187	mode += val
2188	// print "mode = ",mode
2189	err = V_Correct(mode)
2190	if(err)
2191	SetDataFolder root:
2192	Abort "error in Correct, called from executeprotocol, normal cor"
2193	endif
2194	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2195	While(0)
2196
2197
2198	////////////////////////////////////////////////////////
2199	// Absolute scale
2200
2201	// x- calculation works, needs proper inputs (solid angle aware)
2202	// x- Open beam method needs to be verified in V_AskForAbsoluteParams_Quest()
2203	Variable c2,c3,c4,c5,kappa_err
2204	//do absolute scaling if desired
2205	// DoAlert 0,"Abs step incomplete"
2206
2207	if(cmpstr("none",prot[4])!=0)
2208	if(cmpstr("ask",prot[4])==0)
2209	//get the params from the user
2210	Execute "V_AskForAbsoluteParams_Quest()"
2211	//then from the list
2212	SVAR junkAbsStr = root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr
2213	c2 = NumberByKey("TSTAND", junkAbsStr, "=", ";") //parse the list of values
2214	c3 = NumberByKey("DSTAND", junkAbsStr, "=", ";")
2215	c4 = NumberByKey("IZERO", junkAbsStr, "=", ";")
2216	c5 = NumberByKey("XSECT", junkAbsStr, "=", ";")
2217	kappa_err = NumberByKey("SDEV", junkAbsStr, "=", ";")
2218	else
2219	//get the parames from the list
2220	c2 = NumberByKey("TSTAND", prot[4], "=", ";") //parse the list of values
2221	c3 = NumberByKey("DSTAND", prot[4], "=", ";")
2222	c4 = NumberByKey("IZERO", prot[4], "=", ";")
2223	c5 = NumberByKey("XSECT", prot[4], "=", ";")
2224	kappa_err = NumberByKey("SDEV", prot[4], "=", ";")
2225	Endif
2226	//get the sample trans and thickness from the activeType folder
2227	Variable c0 = V_getSampleTransmission(activeType) //sample transmission
2228	Variable c1 = V_getSampleThickness(activeType) //sample thickness
2229
2230	err = V_Absolute_Scale(activeType,c0,c1,c2,c3,c4,c5,kappa_err)
2231	if(err)
2232	SetDataFolder root:
2233	Abort "Error in V_Absolute_Scale(), called from V_ExecuteProtocol"
2234	endif
2235	activeType = "ABS"
2236	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2237	Endif
2238
2239	//
2240	// DONE
2241	// x- fill in the "ask" step
2242	// x- none is OK, except if the kill fails for any reason
2243	// x- the regular case of the file name specified by the protocol works correctly
2244	// x- don't create a null mask if not used, it will handle the error and print out that the mask is missing
2245
2246	//mask data if desired (this is done automatically when the data is binned to I(q)) and is
2247	//not done explicitly here
2248
2249	//check for mask
2250	//doesn't change the activeType
2251	String mskFileName=""
2252
2253	if(cmpstr("none",prot[3])!=0)
2254	If(cmpstr("ask",prot[3])==0)
2255	//get file from user
2256	// x- fill in the get file prompt, and handle the result
2257	Prompt mskFileName,"MASK File",popup,V_PickMASKButton("")
2258	DoPrompt "Select File",mskFileName
2259	// if (V_Flag)
2260	// return 0 // user cancelled
2261	// endif
2262
2263	If(strlen(mskFileName)==0) //use cancelled
2264	//if none desired, make sure that the old mask is deleted
2265	KillDataFolder/Z root:Packages:NIST:VSANS:MSK:
2266	NewDataFolder/O root:Packages:NIST:VSANS:MSK
2267
2268	DoAlert 0,"No Mask file selected, data not masked"
2269	else
2270	//read in the file from the selection
2271	V_LoadHDF5Data(mskFileName,"MSK")
2272	Endif
2273	else
2274	//just read it in from the protocol
2275	//list processing is necessary to remove any final comma
2276	mskFileName = pathStr + StringFromList(0, prot[3],"," )
2277	V_LoadHDF5Data(mskFileName,"MSK")
2278	Endif
2279
2280	else
2281	//if none desired, make sure that the old mask is deleted
2282	// TODO
2283	// x- clean out the data folder
2284	// x- note that V_KillNamedDataFolder() points to RawVSANS, and won't work
2285	// -- what happens if the kill fails? need error handling
2286	//
2287	KillDataFolder/Z root:Packages:NIST:VSANS:MSK:
2288	NewDataFolder/O root:Packages:NIST:VSANS:MSK
2289
2290	Endif
2291
2292
2293	// average/save data as specified
2294	//Parse the keyword=<Value> string as needed, based on AVTYPE
2295
2296	//average/plot first
2297	String av_type = StringByKey("AVTYPE",prot[5],"=",";")
2298	If(cmpstr(av_type,"none") != 0)
2299	If (cmpstr(av_type,"")==0) //if the key could not be found... (if "ask" the string)
2300	//get the averaging parameters from the user, as if the set button was hit in the panel
2301	V_SetAverageParamsButtonProc("dummy") //from "ProtocolAsPanel"
2302	SVAR tempAveStr = root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr
2303	av_type = StringByKey("AVTYPE",tempAveStr,"=",";")
2304	else
2305	//there is info in the string, use the protocol
2306	//set the global keyword-string to prot[5]
2307	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr = prot[5]
2308	Endif
2309	Endif
2310
2311	//convert the folder to linear scale before averaging, then revert by calling the window hook
2312	// (not needed for VSANS, data is always linear scale)
2313
2314	// bin and plot the data
2315
2316	//
2317	// x- need to convert BINTYPE keyword into a numerical value to pass
2318	//
2319
2320	//
2321	// (DONE)
2322	// -x this generates a "Bin Type Not Found" error if reducing only to a 2D level (like for DIV)
2323	// because binTypeStr is null
2324	String binTypeStr = StringByKey("BINTYPE",prot[5],"=",";")
2325	// plotting is not really necessary, and the graph may not be open - so skip for now?
2326	Variable binType
2327	// only get the binning type if user asks for averaging
2328	If(cmpstr(av_type,"none") != 0)
2329	binType = V_BinTypeStr2Num(binTypeStr)
2330	if(binType == 0)
2331	Abort "Binning mode not found in V_QBinAllPanels() "// when no case matches
2332	endif
2333	endif
2334
2335	//
2336	// TODO:
2337	// -- do I calculate the proper resolution here? I've already decoded the binning type
2338	// and the averaging type has been specified by the protocol.
2339	//
2340	// currently, the resolution is calculated every time that the data is averaged (in VC_fDoBinning_QxQy2D)
2341	//
2342	// -- if I calculate the resolution here, then the Trimming routines must be updated
2343	// to trim the resolution waves also. This will work for the columns present in
2344	// pinhole resolution, but anything using the matrix method - it won't work - and I'll need
2345	// a different solution
2346	//
2347	strswitch(av_type) //dispatch to the proper routine to average to 1D data
2348	case "none":
2349	//still do nothing
2350	break
2351	case "2D_ASCII":
2352	//do nothing
2353	break
2354	case "QxQy_ASCII":
2355	//do nothing
2356	break
2357	case "PNG_Graphic":
2358	//do nothing
2359	break
2360	case "Rectangular":
2361	// RectangularAverageTo1D(activeType)
2362	break
2363	case "Annular":
2364	// AnnularAverageTo1D(activeType)
2365	String detGroup = StringByKey("DETGROUP",prot[5],"=",";")
2366	Variable qCtr_Ann = NumberByKey("QCENTER",prot[5],"=",";")
2367	Variable qWidth = NumberByKey("QDELTA",prot[5],"=",";")
2368	V_QBinAllPanels_Annular(activeType,detGroup,qCtr_Ann,qWidth)
2369	break
2370	case "Circular":
2371
2372	V_QBinAllPanels_Circular(activeType,binType) // this does a default circular average
2373	break
2374	case "Sector":
2375	// CircularAverageTo1D(activeType)
2376	break
2377	case "Sector_PlusMinus":
2378	// Sector_PlusMinus1D(activeType)
2379	break
2380	default:
2381	//do nothing
2382	endswitch
2383
2384	// DONE
2385	// x- this call will bin the active type, then the next call bins the active type
2386	// x- then later, I dispatch to bin the active type...
2387	// x- !!!need to split out the panel draw and the binning calls from V_PlotData_Panel
2388	//
2389	// TODO:
2390	// -- BAD logic here, skipping the normal graph if annular is chosen. Go back and see how I do this
2391	// in SANS for a better and more foolproof way to do this
2392	// x- don't draw the graph if "none" is the average type!
2393	//
2394	if(cmpstr(av_type,"Annular") != 0 && (cmpstr(av_type,"none") != 0) )
2395	V_PlotData_Panel() //this brings the plot window to the front, or draws it (ONLY)
2396	V_Update1D_Graph(activeType,binType) //update the graph, data was already binned
2397	endif
2398	///// end of averaging dispatch
2399
2400
2401	//
2402	// x- how do I get the sample file name?
2403	// local variable samFileLoaded is the file name loaded (contains the extension)
2404	//
2405	//save data if desired - dispatch as needed
2406	String fullpath = "", newfileName=""
2407	String saveType = StringByKey("SAVE",prot[5],"=",";") //does user want to save data?
2408
2409	If( (cmpstr(saveType[0,2],"Yes")==0) && (cmpstr(av_type,"none") != 0) )
2410	//then save
2411	newFileName = RemoveEnding(samFileLoaded,".nxs.ngv")
2412
2413	//pick ABS or AVE extension
2414	String exten = activeType
2415	if(cmpstr(exten,"ABS") != 0)
2416	exten = "AVE"
2417	endif
2418	if(cmpstr(av_type,"2D_ASCII") == 0)
2419	exten = "ASC"
2420	endif
2421	if(cmpstr(av_type,"QxQy_ASCII") == 0)
2422	exten = "DAT"
2423	endif
2424
2425	// // add an "x" to the file extension if the output is XML
2426	// // currently (2010), only for ABS and AVE (1D) output
2427	// if( cmpstr(exten,"ABS") == 0 \|\| cmpstr(exten,"AVE") == 0 )
2428	// if(useXMLOutput == 1)
2429	// exten += "x"
2430	// endif
2431	// endif
2432
2433	//Path is catPathName, symbolic path
2434	//if this doesn't exist, a dialog will be presented by setting dialog = 1
2435	//
2436	Variable dialog = 0
2437
2438	PathInfo/S catPathName
2439	String item = StringByKey("NAME",prot[5],"=",";") //Auto or Manual naming
2440	String autoname = StringByKey("AUTONAME",prot[5],"=",";") //autoname - will get empty string if not present
2441	If((cmpstr(item,"Manual")==0) \|\| (cmpstr(newFileName,"") == 0))
2442	//manual name if requested or if no name can be derived from header
2443	fullPath = newfileName + "."+ exten //puts possible new name or null string in dialog
2444	dialog = 1 //force dialog for user to enter name
2445	else
2446	//auto-generate name and prepend path - won't put up any dialogs since it has all it needs
2447	//use autoname if present
2448	if (cmpstr(autoname,"") != 0)
2449	fullPath = S_Path + autoname + "." +exten
2450	else
2451	fullPath = S_Path + newFileName+"." + exten
2452	endif
2453	Endif
2454	//
2455	strswitch(av_type)
2456	case "Annular":
2457	// WritePhiave_W_Protocol(activeType,fullPath,dialog)
2458	V_fWrite1DAnnular("root:Packages:NIST:VSANS:",activeType,detGroup,newFileName+".phi")
2459	Print "data written to: "+ newFileName+".phi"
2460
2461	break
2462	case "2D_ASCII":
2463	// Fast2DExport(activeType,fullPath,dialog)
2464	break
2465	case "QxQy_ASCII":
2466	// QxQy_Export(activeType,fullPath,dialog)
2467	break
2468	case "PNG_Graphic":
2469	// SaveAsPNG(activeType,fullpath,dialog)
2470	break
2471	case "Circular": //in SANS, this was the default, but is dangerous, so make it explicit here
2472	// if (useXMLOutput == 1)
2473	// WriteXMLWaves_W_Protocol(activeType,fullPath,dialog)
2474	// else
2475	// WriteWaves_W_Protocol(activeType,fullpath,dialog)
2476	// endif
2477	//
2478	// x- get the trim strings from somewhere-- from the file or from the protocol??
2479	// then replace the null strings being passed
2480
2481	if(cmpstr(saveType,"Yes - Concatenate")==0)
2482	V_Trim1DDataStr(activeType,binType,prot[7],prot[8]) // x- passing null strings uses global or default trim values
2483
2484	V_ConcatenateForSave("root:Packages:NIST:VSANS:",activeType,"",binType) // this removes q=0 point, concatenates, sorts
2485	V_Write1DData("root:Packages:NIST:VSANS:",activeType,newFileName+"."+exten) //don't pass the full path, just the name
2486	else
2487	// remove the q=0 point from the back detector, if it's there
2488	// does not trim any of the data
2489	V_RemoveQ0_B(activeType)
2490	V_Write1DData_ITX("root:Packages:NIST:VSANS:",activeType,newFileName,binType)
2491	endif
2492	Print "data written to: "+ newFileName+"."+exten
2493
2494	break
2495	default:
2496	DoAlert 0, "av_type not found in dispatch to write file"
2497
2498	endswitch
2499
2500	Endif
2501
2502	//done with everything in protocol list
2503
2504
2505	// reset any global preferences that I had changed
2506	gDoDIVCor = saved_gDoDIVCor
2507
2508
2509	Return(0)
2510	End
2511
2512
2513
2514
2515
2516	//missing parameter dialog to solicit the 4 absolute intensity parameters
2517	//from the user
2518	//values are passed back as a global string variable (keyword=value)
2519	//
2520	Proc V_AskForAbsoluteParams(c2,c3,c4,c5,I_err)
2521	Variable c2=1,c3=1,c4=1e8,c5=1,I_err=1
2522	Prompt c2, "Standard Transmission"
2523	Prompt c3, "Standard Thickness (cm)"
2524	Prompt c4, "I(0) from standard fit (normalized to 1E8 monitor cts)"
2525	Prompt c5, "Standard Cross-Section (cm-1)"
2526	Prompt I_err, "error in I(q=0) (one std dev)"
2527
2528	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr=""
2529
2530	root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr = "TSTAND="+num2str(c2)
2531	root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr += ";" + "DSTAND="+num2str(c3)
2532	root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr += ";" + "IZERO="+num2str(c4)
2533	root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr += ";" + "XSECT="+num2str(c5)
2534	root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr += ";" + "SDEV="+num2str(I_err)
2535
2536	End
2537
2538
2539	//
2540	// DONE
2541	// x- fill in all of the functionality for calculation from direct beam
2542	// and verify that the calculations are numerically correct
2543	//
2544	//asks the user for absolute scaling information. the user can either
2545	//enter the necessary values in manually (missing parameter dialog)
2546	//or the user can select an empty beam file from a standard open dialog
2547	//if an empty beam file is selected, the "kappa" value is automatically calculated
2548	//in either case, the global keyword=value string is set.
2549	//
2550	Function V_AskForAbsoluteParams_Quest()
2551
2552	Variable err,loc,refnum
2553
2554	Variable ii
2555
2556	Variable kappa=1
2557	Variable kappa_err
2558
2559	//get the necessary variables for the calculation of kappa
2560	Variable countTime,monCnt,sdd,pixel_x,pixel_y
2561	String detStr,junkStr,errStr
2562
2563	Variable empAttenFactor, emp_atten_err
2564
2565	//get the XY box and files
2566	Variable x1,x2,y1,y2,emptyCts,empty_ct_err
2567	String emptyFileName,tempStr,divFileName,detPanel_toSum
2568
2569	//ask user if he wants to use a transmision file for absolute scaling
2570	//or if he wants to enter his own information
2571	err = V_UseStdOrEmpForABS()
2572	//DoAlert 1,"<Yes> to enter your own values, <No> to select an empty beam flux file"
2573	If ( err==1 )
2574	//secondary standard selected, prompt for values
2575	Execute "V_AskForAbsoluteParams()" //missing parameters
2576	else
2577	//empty beam flux file selected, prompt for file, and use this to calculate KAPPA
2578
2579	// DONE
2580	// x- need an empty beam file name
2581	//
2582	Prompt emptyFileName,"Empty Beam File",popup,V_PickEMPBeamButton("")
2583	DoPrompt "Select File",emptyFileName
2584	if (V_Flag)
2585	return 0 // user canceled
2586	endif
2587
2588	// DONE
2589	// x- need panel
2590	// x- now, look for the value in the file, if not there, ask
2591
2592	detPanel_toSum = V_getReduction_BoxPanel(emptyFileName)
2593	if(strlen(detPanel_toSum) > 2)
2594	// it's the error message
2595	Prompt detPanel_toSum,"Panel with Direct Beam",popup,ksDetectorListAll
2596	DoPrompt "Select Panel",detPanel_toSum
2597	if (V_Flag)
2598	return 0 // user canceled
2599	endif
2600	endif
2601
2602	//need the detector sensitivity file - make a guess, allow to override
2603	Prompt divFileName,"DIV File",popup,V_GetDIVList()
2604	DoPrompt "Select File",divFileName
2605	if (V_Flag)
2606	return 0 // user canceled
2607	endif
2608	V_LoadHDF5Data(divFileName,"DIV")
2609
2610
2611	WAVE xyBoxW = V_getBoxCoordinates(emptyFileName)
2612
2613
2614	// load in the data, and use all of the corrections, especially DIV
2615	// (be sure the corrections are actually set to "on", don't assume that they are)
2616	// save preferences for file loading
2617	Variable savDivPref,savSAPref
2618	NVAR gDoDIVCor = root:Packages:NIST:VSANS:Globals:gDoDIVCor
2619	savDivPref = gDoDIVCor
2620	NVAR gDoSolidAngleCor = root:Packages:NIST:VSANS:Globals:gDoSolidAngleCor
2621	savSAPref = gDoSolidAngleCor
2622
2623	// set local preferences
2624	gDoDIVCor = 1
2625	gDoSolidAngleCor = 1
2626
2627	V_LoadAndPlotRAW_wName(emptyFileName)
2628	// convert raw->SAM
2629	// V_Raw_to_work("SAM")
2630	// V_UpdateDisplayInformation("SAM")
2631	V_UpdateDisplayInformation("RAW")
2632
2633	// do the DIV correction
2634	if (gDoDIVCor == 1)
2635	// need extra check here for file existence
2636	// if not in DIV folder, load.
2637	// if unable to load, skip correction and report error (Alert?) (Ask to Load?)
2638	Print "Doing DIV correction"// for "+ detStr
2639	for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
2640	detStr = StringFromList(ii, ksDetectorListAll, ";")
2641	Wave w = V_getDetectorDataW("RAW",detStr)
2642	Wave w_err = V_getDetectorDataErrW("RAW",detStr)
2643
2644	V_DIVCorrection(w,w_err,detStr,"RAW") // do the correction in-place
2645	endfor
2646	else
2647	Print "DIV correction NOT DONE" // not an error since correction was unchecked
2648	endif
2649
2650	// and determine box sum and error
2651	// store these locally
2652
2653
2654	// x- need to get the panel string for the sum.
2655	// x- the detector string is currently hard-wired
2656	// detStr = "MR"
2657
2658	emptyCts = V_SumCountsInBox(xyBoxW[0],xyBoxW[1],xyBoxW[2],xyBoxW[3],empty_ct_err,"RAW",detPanel_toSum)
2659
2660	Print "empty counts = ",emptyCts
2661	Print "empty err/counts = ",empty_ct_err/emptyCts
2662
2663	//
2664	// x- get all of the proper values for the calculation
2665	// -x currently the attenuation is incorrect
2666	// such that kappa_err = 1*kappa
2667	// x- verify the calculation (no solid angle needed??)
2668
2669	// get the attenuation factor for the empty beam
2670	// -- the attenuation is not written by NICE to the file
2671	// so I need to calculate it myself from the tables
2672	//
2673	// empAttenFactor = V_getAttenuator_transmission(emptyFileName)
2674	// emp_atten_err = V_getAttenuator_trans_err(emptyFileName)
2675	empAttenFactor = V_CalculateAttenuationFactor(emptyFileName)
2676	emp_atten_err = V_CalculateAttenuationError(emptyFileName)
2677
2678	countTime = V_getCount_time(emptyFileName)
2679
2680	// TODO
2681	// -- not sure if this is the correct monitor count to use
2682	monCnt = V_getBeamMonNormData("RAW")
2683
2684	pixel_x = V_getDet_x_pixel_size("RAW",detPanel_toSum)
2685	pixel_x /= 10 //convert mm to cm, since sdd in cm
2686	pixel_y = V_getDet_y_pixel_size("RAW",detPanel_toSum)
2687	pixel_y /= 10 //convert mm to cm, since sdd in cm
2688	sdd = V_getDet_ActualDistance("RAW",detPanel_toSum)
2689
2690	// kappa = emptyCts/countTime/empAttenFactor1.0e8/(monCnt/countTime)(pixel_x*pixel_y/sdd^2)
2691	kappa = emptyCts/countTime/empAttenFactor*1.0e8/(monCnt/countTime)
2692
2693
2694	kappa_err = (empty_ct_err/emptyCts)^2 + (emp_atten_err/empAttenFactor)^2
2695	kappa_err = sqrt(kappa_err) * kappa
2696
2697	// x- set the parameters in the global string
2698	junkStr = num2str(kappa)
2699	errStr = num2Str(kappa_err)
2700	Execute "V_AskForAbsoluteParams(1,1,"+junkStr+",1,"+errStr+")" //no missing parameters, no dialog
2701
2702
2703	Printf "Kappa was successfully calculated as = %g +/- %g (%g %)\r",kappa,kappa_err,(kappa_err/kappa)*100
2704
2705	// restore preferences on exit
2706	gDoDIVCor = savDivPref
2707	gDoSolidAngleCor = savSAPref
2708
2709	Endif
2710
2711	End
2712
2713	Function V_UserSelectBox_Continue(ctrlName) :buttonControl
2714	String ctrlName
2715
2716	DoWindow/K junkWindow //kill panel
2717	end
2718
2719	Function V_SelectABS_XYBox(x1,x2,y1,y2)
2720	Variable &x1,&x2,&y1,&y2
2721
2722	Variable err=0
2723
2724	Variable/G root:V_marquee=1 //sets the sneaky bit to automatically update marquee coords
2725	Variable/G root:V_left,root:V_right,root:V_bottom,root:V_top //must be global for auto-update
2726	DoWindow/F SANS_Data
2727	NewPanel/K=2 /W=(139,341,382,432) as "Select the primary beam"
2728	DoWindow/C junkWindow
2729	AutoPositionWindow/E/M=1/R=SANS_Data
2730
2731	Drawtext 21,20 ,"Select the primary beam with the"
2732	DrawText 21,40, "marquee and press continue"
2733	Button button0,pos={80,58},size={92,20},title="Continue"
2734	Button button0,proc=V_UserSelectBox_Continue
2735
2736	PauseForUser junkWindow,SANS_Data
2737
2738	DoWindow/F SANS_Data
2739
2740	//GetMarquee left,bottom //not needed
2741	NVAR V_left=V_left
2742	NVAR V_right=V_right
2743	NVAR V_bottom=V_bottom
2744	NVAR V_top=V_top
2745
2746	x1 = V_left
2747	x2 = V_right
2748	y1 = V_bottom
2749	y2 = V_top
2750	// Print "new values,before rounding = ",x1,x2,y1,y2
2751
2752	// TODO -- replace this call
2753	// KeepSelectionInBounds(x1,x2,y1,y2)
2754	//Print "new values = ",x1,x2,y1,y2
2755
2756	KillVariables/Z root:V_Marquee,root:V_left,root:V_right,root:V_bottom,root:V_top
2757	if((x1-x2)==0 \|\| (y1-y2)==0)
2758	err=1
2759	endif
2760	return(err)
2761	End
2762
2763	Function V_UseStdOrEmpForABS()
2764
2765	NewPanel/K=2 /W=(139,341,402,448) as "Absolute Scaling"
2766	DoWindow/C junkABSWindow
2767	ModifyPanel cbRGB=(57346,65535,49151)
2768	SetDrawLayer UserBack
2769	SetDrawEnv fstyle= 1
2770	DrawText 21,20,"Method of absolute calibration"
2771	Button button0,pos={52,33},size={150,20},proc=V_UserSelectABS_Continue,title="Empty Beam Flux"
2772	Button button1,pos={52,65},size={150,20},proc=V_UserSelectABS_Continue,title="Secondary Standard"
2773
2774	PauseForUser junkABSWindow
2775	NVAR val = root:Packages:NIST:VSANS:Globals:tmpAbsVal
2776	return(val)
2777	End
2778
2779	//returns 0 if button0 (empty beam flux)
2780	// or 1 if secondary standard
2781	Function V_UserSelectABS_Continue(ctrlName) :buttonControl
2782	String ctrlName
2783
2784	variable val=0
2785	If(cmpstr(ctrlName,"button0")==0)
2786	val=0
2787	else
2788	val=1
2789	endif
2790	// print "val = ",ctrlName,val
2791	Variable/G root:Packages:NIST:VSANS:Globals:tmpAbsVal = val
2792	DoWindow/K junkABSWindow //kill panel
2793	return(0)
2794	end
2795
2796
2797	Function V_TrimDataProtoButton(ctrlName) :buttonControl
2798	String ctrlName
2799
2800	Execute "V_CombineDataGraph()"
2801	return(0)
2802	end
2803
2804	//
2805	// export protocol to a data file
2806	//
2807	//
2808	Function V_ExportFileProtocol(ctrlName) : ButtonControl
2809	String ctrlName
2810	// get a list of protocols
2811	String Protocol=""
2812	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
2813	Prompt Protocol "Pick A Protocol",popup, V_DeletableProtocols()
2814	DoPrompt "Pick A Protocol to Export",Protocol
2815	if(V_flag==1)
2816	//Print "user cancel"
2817	SetDatafolder root:
2818	return(1)
2819	endif
2820
2821	String fileName = V_DoSaveFileDialog("pick the file to write to")
2822	print fileName
2823	//
2824	if(strlen(fileName) == 0)
2825	return(0)
2826	endif
2827
2828	V_writeReductionProtocolWave(fileName,$("root:Packages:NIST:VSANS:Globals:Protocols:"+Protocol) )
2829
2830	setDataFolder root:
2831	return(0)
2832
2833	End
2834
2835	//
2836	// imports a protocol from a file on disk into the protocols folder
2837	//
2838	//
2839	Function V_ImportFileProtocol(ctrlName) : ButtonControl
2840	String ctrlName
2841
2842	// SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
2843
2844	String fullPath,fileName
2845	fullPath = DoOpenFileDialog("Import Protocol from file")
2846	print fullPath
2847	//
2848	if(strlen(fullPath) == 0)
2849	return(0)
2850	endif
2851
2852	fileName = ParseFilePath(0, fullPath, ":", 1, 0) //just the file name at the end of the full path
2853
2854	Wave/T tmpW = V_getReductionProtocolWave(fileName)
2855	if(numpnts(tmpW) == 0)
2856	DoAlert 0,"No protocol wave has been saved to this data file"
2857	return(0)
2858	endif
2859
2860	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
2861	String newName
2862	newName = CleanupName(fileName,0) + "_proto"
2863	duplicate/o tmpw $newName
2864
2865
2866	SetDataFolder root:
2867	return(0)
2868	end
2869
2870
2871	// currently not used - and not updated to 12 point protocols (5/2017)
2872	//
2873	//save the protocol as an IGOR text wave (.itx)
2874	//
2875	//
2876	Function V_ExportProtocol(ctrlName) : ButtonControl
2877	String ctrlName
2878	// get a list of protocols
2879	String Protocol=""
2880	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
2881	Prompt Protocol "Pick A Protocol",popup, WaveList("*",";","")
2882	DoPrompt "Pick A Protocol to Export",Protocol
2883	if(V_flag==1)
2884	//Print "user cancel"
2885	SetDatafolder root:
2886	return(1)
2887	endif
2888	//get the selection, or exit
2889	Wave/T pW= $protocol
2890	Make/O/T/N=13 tw
2891	// save in the proper format (must write manually, for demo version)
2892	tw[0] = "IGOR"
2893	tw[1] = "WAVES/T \t"+protocol
2894	tw[2] = "BEGIN"
2895	tw[3,10] = "\t\""+pW[p-3]+"\""
2896	tw[11] = "END"
2897	tw[12] = "X SetScale/P x 0,1,\"\","+protocol+"; SetScale y 0,0,\"\","+protocol
2898
2899	Variable refnum
2900	String fullPath
2901
2902	PathInfo/S catPathName
2903	fullPath = DoSaveFileDialog("Export Protocol as",fname=Protocol,suffix="")
2904	If(cmpstr(fullPath,"")==0)
2905	//user cancel, don't write out a file
2906	Close/A
2907	Abort "no Protocol file was written"
2908	Endif
2909
2910	//actually open the file
2911	Open refNum as fullpath+".itx"
2912
2913	wfprintf refnum, "%s\r", tw
2914	Close refnum
2915	//Print "all is well ",protocol
2916	KillWaves/Z tw
2917	setDataFolder root:
2918	return(0)
2919
2920	End
2921
2922
2923	// currently not used - and not updated to 12 point protocols (5/2017)
2924	//imports a protocol from disk into the protocols folder
2925	//
2926	// will overwrite existing protocols if necessary
2927	//
2928	//
2929	Function V_ImportProtocol(ctrlName) : ButtonControl
2930	String ctrlName
2931
2932	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
2933
2934	String fullPath
2935
2936	PathInfo/S catPathName
2937	fullPath = DoOpenFileDialog("Import Protocol")
2938	If(cmpstr(fullPath,"")==0)
2939	//user cancel, don't write out a file
2940	Close/A
2941	Abort "no protocol was loaded"
2942	Endif
2943
2944	LoadWave/O/T fullPath
2945
2946	SetDataFolder root:
2947	return(0)
2948	end

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