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V_Protocol_Reduction.ipf @ 1073

Last change on this file since 1073 was 1073, checked in by srkline, 5 years ago

lots of changes here:
many little fixes to clean up TODO items and marke them DONE

changed the handling of the panel "gap" to split the gap evenly. Q-calculations have been re-verified with this change.

re-named the list of "bin Type" values, and added a few more choices. Streamlined how the averaging and plotting works with this list so that it can be more easily modified as different combinations of binning are envisioned. This resulted in a lot of excess code being cut out and replaced with cleaner logic. This change has also been verified to work as intended.

Attenuation is now always calculated from the table. The table also by (NEW) definition has values for the white beam (one waelength) and graphite (multiple possible wavelengths) where the wavelengths are artificially scaled (*1000) or *1e6) so that the interpolations can be done internally without the need for multiple attenuator tables.

File size: 94.1 KB

Line
1	#pragma rtGlobals=1 // Use modern global access method.
2	#pragma version=5.0
3	#pragma IgorVersion=6.1
4
5	//************************
6
7	//
8	//*************************
9	//////////////////////////////////
10	//
11	// KEYWORD=<value> lists used in protocol definitions
12	//
13	// KEYWORDS are ALWAYS capitalized, and yes, it does matter
14	//
15	// for ABSOLUTE parameters
16	// (4) possible keywords, all with numerical values
17	// TSTAND=value transmission of the standard
18	// DSTAND=value thickness of the standard, in centimeters
19	// IZERO=value I(q=0) value for the standard, in normalized neutron counts
20	// XSECT=value calibrated cross-section of the standard sample
21	//
22	// For calibration with a transmission file, set TSTAND, DSTAND, and XSECT to 1.0
23	// and set IZERO to KAPPA (defined in Tania's handout, or in documentation of MRED_KAP on VAX)
24	//
25	//
26	// For AVERAGE and for DRAWING
27	// DRAWING routines only use a subset of the total list, since saving, naming, etc. don't apply
28	// (10) possible keywords, some numerical, some string values
29	// AVTYPE=string string from set {Circular,Annular,Rectangular,Sector,2D_ASCII,QxQy_ASCII,PNG_Graphic;Sector_PlusMinus;}
30	// PHI=value azimuthal angle (-90,90)
31	// DPHI=value +/- angular range around phi for average
32	// WIDTH=value total width of rectangular section, in pixels
33	// SIDE=string string from set {left,right,both} **note NOT capitalized
34
35	// QCENTER=value q-value (1/A) of center of annulus for annular average
36	// QDELTA=value (+/-) width of annulus centered at QCENTER, in units of q
37	// DETGROUP=value string with "F" or "M" to name the detector group where the annulus lies.
38
39	// PLOT=string string from set {Yes,No} = truth of generating plot of averaged data
40	// SAVE=string string from set {Yes,No} = truth of saving averaged data to disk, now with "Concatenate" or "Individual"
41	// NAME=string string from set {Auto,Manual} = Automatic name generation or Manual(dialog)
42	//
43	//
44	// BINTYPE=string (VSANS binning type) "One;Two;Four;Slit Mode;", as defined by ksBinTypeStr
45	//
46	//
47	// For work.DRK usage:
48	// **the list is COMMA delimited, separator is =
49	// DRK=none,DRKMODE=0,
50	// DRK=name is the name of the file, must be a full name, expected to be raw data
51	// DRKMODE=value is a numeric value (0 or 10 to add to the Correct(mode) switch (unused?)
52	//
53	//////////////////////////////////
54
55
56	//main entry procedure for initialzing and displaying the protocol panel
57	// initilaizes folders and globals as needed
58	//
59	Proc V_ReductionProtocolPanel()
60	DoWindow/F V_ProtocolPanel
61	if(V_flag==0)
62	V_InitProtocolPanel()
63	V_ProtocolPanel()
64	Endif
65	End
66
67	//initialization procedure for the protocol panel
68	//note that :gAbsStr is also shared (common global) to that used in
69	//the questionnare form of the protcol (see protocol.ipf)
70	//
71	Proc V_InitProtocolPanel()
72
73	if(exists(" root:Packages:NIST:VSANS:CatVSHeaderInfo:Filenames") == 0)
74	Abort "You must generate a file catalog before building protocols"
75	endif
76
77	//set up the global variables needed for the protocol panel
78	//global strings to put in a temporary protocol textwave
79	Variable ii=0
80	String waveStr="tempProtocol"
81	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
82	Make/O/T/N=(kNumProtocolSteps) $"root:Packages:NIST:VSANS:Globals:Protocols:tempProtocol" = ""
83
84	String/G root:Packages:NIST:VSANS:Globals:Protocols:gSAM="ask"
85	String/G root:Packages:NIST:VSANS:Globals:Protocols:gBGD="ask"
86	String/G root:Packages:NIST:VSANS:Globals:Protocols:gEMP="ask"
87	String/G root:Packages:NIST:VSANS:Globals:Protocols:gDIV="ask"
88	String/G root:Packages:NIST:VSANS:Globals:Protocols:gMASK="ask"
89	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr="ask"
90	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAVE="AVTYPE=Circular;SAVE=Yes - Concatenate;NAME=Auto;PLOT=No;BINTYPE=One;"
91	String/G root:Packages:NIST:VSANS:Globals:Protocols:gDRK="DRK=none,DRKMODE=0,"
92
93	// global strings for trimming data are initialized in the main VSANS initilization
94	// in case the trimming is done before the protocol panel is opened
95
96	SetDataFolder root:
97
98	End
99
100
101	//button procedure to reset the panel seletctions/checks...etc...
102	//to reflect the choices in a previously saved protocol
103	// - parses through the protocol and resets the appropriate global strings and
104	//updates the panel display
105	//
106	Function V_RecallProtocolButton(ctrlName) : ButtonControl
107	String ctrlName
108
109	//will reset panel values based on a previously saved protocol
110	//pick a protocol wave from the Protocols folder
111	//MUST move to Protocols folder to get wavelist
112	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
113	Execute "V_PickAProtocol()"
114
115	//get the selected protocol wave choice through a global string variable
116	SVAR protocolName = root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr
117
118	//If "CreateNew" was selected, ask user to try again
119	if(cmpstr("CreateNew",protocolName) == 0)
120	Abort "CreateNew is for making a new Protocol. Select a previously saved Protocol"
121	Endif
122
123	//reset the panel based on the protocol textwave (currently a string)
124	V_ResetToSavedProtocol(protocolName)
125
126	SetDataFolder root:
127	return(0)
128	End
129
130	//deletes the selected protocol from the list and from memory
131	//
132	Function V_DeleteProtocolButton(ctrlName) : ButtonControl
133	String ctrlName
134
135	//put up a list of protocols and pick one
136	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
137	// Execute "DeleteAProtocol()"
138	String Protocol=""
139	Prompt Protocol "Delete A Protocol",popup, V_DeletableProtocols()
140	DoPrompt "Select protocol to delete",protocol
141	If(V_flag==1)
142	return(0)
143	endif
144
145	//If "CreateNew, Base, DoAll, or tempProtocol" was selected, do nothing
146	strswitch(protocol)
147	case "CreateNew":
148	break
149	case "DoAll":
150	break
151	case "Base":
152	break
153	case "tempProtocol":
154	break
155	default:
156	//delete the protocol
157	KillWaves/Z $protocol
158	endswitch
159
160	SetDataFolder root:
161	return(0)
162	End
163
164	//
165	//function that actually parses the protocol specified by nameStr
166	//which is just the name of the wave, without a datafolder path
167	//
168	// TODO
169	// -- update this for 12 steps
170	//
171	Function V_ResetToSavedProtocol(nameStr)
172	String nameStr
173
174	//allow special cases of Base and DoAll Protocols to be recalled to panel - since they "ask"
175	//and don't need paths
176
177	String catPathStr
178	PathInfo catPathName
179	catPathStr=S_path
180
181	//SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols //on windows, data folder seems to get reset (erratically) to root:
182	Wave/T w=$("root:Packages:NIST:VSANS:Globals:Protocols:" + nameStr)
183
184	String fullPath="",comma=",",list="",nameList="",PathStr="",item=""
185	Variable ii=0,numItems,checked,specialProtocol
186
187	if((cmpstr(nameStr,"Base")==0) \|\| (cmpstr(nameStr,"DoAll")==0))
188	specialProtocol = 1
189	else
190	specialProtocol = 0
191	Endif
192
193	//background
194	checked = 1
195	nameList = w[0]
196	If(cmpstr(nameList,"none") ==0)
197	checked = 0
198	Endif
199
200	//set the global string to display and checkbox
201	String/G root:Packages:NIST:VSANS:Globals:Protocols:gBGD = nameList
202	CheckBox prot_check win=V_ProtocolPanel,value=checked
203
204	//empty
205	checked = 1
206	nameList = w[1]
207	If(cmpstr(nameList,"none") ==0)
208	checked = 0
209	Endif
210
211	//set the global string to display and checkbox
212	String/G root:Packages:NIST:VSANS:Globals:Protocols:gEMP = nameList
213	CheckBox prot_check_1 win=V_ProtocolPanel,value=checked
214
215	//DIV file
216	checked = 1
217	nameList = w[2]
218	If(cmpstr(nameList,"none") ==0)
219	checked = 0
220	Endif
221
222	//set the global string to display and checkbox
223	String/G root:Packages:NIST:VSANS:Globals:Protocols:gDIV = nameList
224	CheckBox prot_check_2 win=V_ProtocolPanel,value=checked
225
226	//Mask file
227	checked = 1
228	nameList = w[3]
229	If(cmpstr(nameList,"none") ==0)
230	checked = 0
231	Endif
232
233	//set the global string to display and checkbox
234	String/G root:Packages:NIST:VSANS:Globals:Protocols:gMASK = nameList
235	CheckBox prot_check_3 win=V_ProtocolPanel,value=checked
236
237	//4 = abs parameters
238	list = w[4]
239	numItems = ItemsInList(list,";")
240	checked = 1
241	if(numitems == 4 \|\| numitems == 5) //allow for protocols with no SDEV list item
242	//correct number of parameters, assume ok
243	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr = list
244	CheckBox prot_check_9 win=V_ProtocolPanel,value=checked
245	else
246	item = StringFromList(0,list,";")
247	if(cmpstr(item,"none")==0)
248	checked = 0
249	list = "none"
250	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr = list
251	CheckBox prot_check_9 win=V_ProtocolPanel,value=checked
252	else
253	//force to "ask"
254	checked = 1
255	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr = "ask"
256	CheckBox prot_check_9 win=V_ProtocolPanel,value=checked
257	Endif
258	Endif
259
260	//5 = averaging choices
261	list = w[5]
262	item = StringByKey("AVTYPE",list,"=",";")
263	if(cmpstr(item,"none") == 0)
264	checked = 0
265	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAVE = "none"
266	CheckBox prot_check_5 win=V_ProtocolPanel,value=checked
267	else
268	checked = 1
269	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAVE = list
270	CheckBox prot_check_5 win=V_ProtocolPanel,value=checked
271	Endif
272
273	// //6 = DRK choice
274	// list = w[6]
275	// item = StringByKey("DRK",list,"=",",")
276	// //print list,item
277	// if(cmpstr(item,"none") == 0)
278	// checked = 0
279	// String/G root:Packages:NIST:VSANS:Globals:Protocols:gDRK = list
280	// CheckBox prot_check_6 win=V_ProtocolPanel,value=checked
281	// else
282	// checked = 1
283	// String/G root:Packages:NIST:VSANS:Globals:Protocols:gDRK = list
284	// CheckBox prot_check_6 win=V_ProtocolPanel,value=checked
285	// Endif
286
287	//7 = beginning trim points
288	SVAR gBegPtsStr=root:Packages:NIST:VSANS:Globals:Protocols:gBegPtsStr
289	gBegPtsStr = w[7]
290	//8 = end trim points
291	SVAR gEndPtsStr=root:Packages:NIST:VSANS:Globals:Protocols:gEndPtsStr
292	gEndPtsStr = w[8]
293
294	//9 = unused
295	//10 = unused
296	//11 = unused
297
298
299	//all has been reset, get out
300	Return (0)
301	End
302
303	//button action procedure that simply closes the panel
304	//
305	Function V_DoneProtocolButton(ctrlName) : ButtonControl
306	String ctrlName
307
308	//will gracefully close and exit the protocol panel
309
310	DoWindow/K V_ProtocolPanel
311	End
312
313	//button action procedure that saves the current choices on the panel
314	//as a named protocol, for later recall
315	//asks for a valid name, then creates a protocol from the panel choices
316	//creates a wave, and sets the current protocol name to this new protocol
317	//
318	//now allows the user the choice to overwrite a protocol
319	//
320	Function V_SaveProtocolButton(ctrlName) : ButtonControl
321	String ctrlName
322
323	Variable notDone=1, newProto=1
324	//will prompt for protocol name, and save the protocol as a text wave
325	//prompt for name of new protocol wave to save
326	do
327	Execute "V_AskForName()"
328	SVAR newProtocol = root:Packages:NIST:VSANS:Globals:Protocols:gNewStr
329
330	//make sure it's a valid IGOR name
331	newProtocol = CleanupName(newProtocol,0) //strict naming convention
332	String/G root:Packages:NIST:VSANS:Globals:Protocols:gNewStr=newProtocol //reassign, if changed
333	Print "newProtocol = ",newProtocol
334
335	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
336	if(WaveExists( $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtocol) ) == 1)
337	//wave already exists
338	DoAlert 1,"That name is already in use. Do you wish to overwrite the existing protocol?"
339	if(V_Flag==1)
340	notDone = 0
341	newProto = 0
342	else
343	notDone = 1
344	endif
345	else
346	//name is good
347	notDone = 0
348	Endif
349	while(notDone)
350
351	//current data folder is root:Packages:NIST:VSANS:Globals:Protocols
352	if(newProto)
353	Make/O/T/N=(kNumProtocolSteps) $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtocol)
354	Endif
355
356	V_MakeProtocolFromPanel( $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtocol) )
357	String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr = newProtocol
358
359	//the data folder WAS changed above, this must be reset to root:
360	SetDatafolder root:
361	End
362
363	//function that does the guts of reading the panel controls and globals
364	//to create the necessary text fields for a protocol
365	//Wave/T w (input) is an empty text wave of 8 elements for the protocol
366	//on output, w[] is filled with the protocol strings as needed from the panel
367	//
368	// TODO
369	// -- update for 12 points
370	//
371	Function V_MakeProtocolFromPanel(w)
372	Wave/T w
373
374	//construct the protocol text wave form the panel
375	//it is to be parsed by ExecuteProtocol() for the actual data reduction
376	PathInfo catPathName //this is where the files came from
377	String pathstr=S_path,tempStr,curList
378	Variable checked,ii,numItems
379
380	//look for checkbox, then take each item in list and prepend the path
381	//w[0] = background
382	ControlInfo/W=V_ProtocolPanel prot_check
383	checked = V_value
384	if(checked)
385	//build the list
386	//just read the global
387	SVAR str=root:Packages:NIST:VSANS:Globals:Protocols:gBGD
388	if(cmpstr(str,"ask")==0)
389	w[0] = str //just ask
390	else
391	tempstr = V_ParseRunNumberList(str)
392	if(strlen(tempStr)==0)
393	return(1) //error parsing list
394	else
395	w[0] = tempstr
396	str = tempstr //set the protocol and the global
397	endif
398	endif
399	else
400	//none used - set textwave (and global?)
401	w[0] = "none"
402	String/G root:Packages:NIST:VSANS:Globals:Protocols:gBGD = "none"
403	endif
404
405	//w[1] = empty
406	ControlInfo/W=V_ProtocolPanel prot_check_1
407	checked = V_value
408	if(checked)
409	//build the list
410	//just read the global
411	SVAR str=root:Packages:NIST:VSANS:Globals:Protocols:gEMP
412	if(cmpstr(str,"ask")==0)
413	w[1] = str
414	else
415	tempstr = V_ParseRunNumberList(str)
416	if(strlen(tempStr)==0)
417	return(1)
418	else
419	w[1] = tempstr
420	str=tempStr
421	endif
422	endif
423	else
424	//none used - set textwave (and global?)
425	w[1] = "none"
426	String/G root:Packages:NIST:VSANS:Globals:Protocols:gEMP = "none"
427	endif
428
429	//w[2] = div file
430	ControlInfo/W=V_ProtocolPanel prot_check_2
431	checked = V_value
432	if(checked)
433	//build the list
434	//just read the global
435	SVAR str=root:Packages:NIST:VSANS:Globals:Protocols:gDIV
436	if(cmpstr(str,"ask")==0)
437	w[2] = str
438	else
439	tempStr = V_ParseRunNumberList(str)
440	if(strlen(tempStr)==0)
441	return(1)
442	else
443	w[2] = tempstr
444	str=tempstr
445	endif
446	endif
447	else
448	//none used - set textwave (and global?)
449	w[2] = "none"
450	String/G root:Packages:NIST:VSANS:Globals:Protocols:gDIV = "none"
451	endif
452
453	//w[3] = mask file
454	ControlInfo/W=V_ProtocolPanel prot_check_3
455	checked = V_value
456	if(checked)
457	//build the list
458	//just read the global
459	SVAR str=root:Packages:NIST:VSANS:Globals:Protocols:gMASK
460	if(cmpstr(str,"ask")==0)
461	w[3] = str
462	else
463	tempstr = V_ParseRunNumberList(str)
464	if(strlen(tempstr)==0)
465	return(1)
466	else
467	w[3] = tempstr
468	str = tempstr
469	endif
470	endif
471	else
472	//none used - set textwave (and global?)
473	w[3] = "none"
474	String/G root:Packages:NIST:VSANS:Globals:Protocols:gMASK = "none"
475	endif
476
477	//w[4] = abs parameters
478	ControlInfo/W=V_ProtocolPanel prot_check_9
479	checked = V_value
480	if(checked)
481	//build the list
482	//just read the global
483	SVAR str=root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr
484	w[4] = str
485	else
486	//none used - set textwave (and global?)
487	w[4] = "none"
488	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr = "none"
489	endif
490
491	//w[5] = averaging choices
492	ControlInfo/W=V_ProtocolPanel prot_check_5 //do the average?
493	checked = V_value
494	if(checked)
495	//just read the global
496	SVAR avestr=root:Packages:NIST:VSANS:Globals:Protocols:gAVE
497	w[5] = avestr
498	else
499	//none used - set textwave
500	w[5] = "AVTYPE=none;"
501	endif
502
503	//w[6]
504	//work.DRK information
505	SVAR drkStr=root:Packages:NIST:VSANS:Globals:Protocols:gDRK
506	w[6] = drkStr
507
508	//w[7]
509	// beginning trim points
510	SVAR gBegPtsStr=root:Packages:NIST:VSANS:Globals:Protocols:gBegPtsStr
511	w[7] = gBegPtsStr
512
513	//w[8]
514	// End trim points
515	SVAR gEndPtsStr=root:Packages:NIST:VSANS:Globals:Protocols:gEndPtsStr
516	w[8] = gEndPtsStr
517
518	//w[9]
519	//currently unused
520	w[9] = ""
521	//w[10]
522	//currently unused
523	w[10] = ""
524	//w[11]
525	//currently unused
526	w[11] = ""
527
528	return(0)
529	End
530
531
532	//
533	Function V_PickSAMButton(ctrlName) : ButtonControl
534	String ctrlName
535
536
537	End
538
539
540
541
542	//
543	// TODO
544	// -- identifying "intent" using V_get can be very slow, since it reads in each and every data file.
545	// grep is a lot faster, but there can be a lot of false "hits" unless I do it correctly.
546	//
547	//
548	// //grep through what text I can find in the VAX binary
549	// // Grep Note: the \\b sequences limit matches to a word boundary before and after
550	// // "boondoggle", so "boondoggles" and "aboondoggle" won't match.
551	// if(gRadioVal == 2)
552	// for(ii=0;ii<num;ii+=1)
553	// item=StringFromList(ii, newList , ";")
554	//// Grep/P=catPathName/Q/E=("(?i)\\b"+match+"\\b") item
555	// Grep/P=catPathName/Q/E=("(?i)"+match) item
556	// if( V_value ) // at least one instance was found
557	//// Print "found ", item,ii
558	// list += item + ";"
559	// endif
560	// endfor
561	//
562	// newList = list
563	// endif
564
565	// match is the string to look for in the search
566	// 0 is a flag to tell it to look in the file catalog (the fastest method)
567	// Other options are to grep, or to read the intent field in every file
568	Function/S V_GetSAMList()
569
570	// String match="SAMPLE"
571	// String list = V_getFileIntentList(match,0)
572
573	String intent = "SAMPLE"
574	String purpose = "SCATTERING"
575	String list = V_getFileIntentPurposeList(intent,purpose,0)
576
577	// Printf "SAM files = %s\r",list
578	return(list)
579	end
580
581
582	Function/S V_GetBGDList()
583
584	String match="BLOCKED BEAM"
585	String list = V_getFileIntentList(match,0)
586
587	// Printf "BGD files = %s\r",list
588	return(list)
589	end
590
591
592	Function/S V_GetEMPList()
593
594	String match="EMPTY CELL"
595	String list = V_getFileIntentList(match,0)
596
597	// Printf "EMP files = %s\r",list
598	return(list)
599	end
600
601
602	//
603	// TODO
604	// -- decide on the way to locate the blocked beam files. Is the enumerated text of the intent
605	// sufficiently unique to locate the file?
606	// -- can I use the Data Catalog waves to locate the files - faster?
607	// (fails if the catalog has not been read in recently enough)
608	//
609	//
610	Function/S V_PickBGDButton(ctrlName) : ButtonControl
611	String ctrlName
612
613	String list="",item="",fname,newList,intent
614	Variable ii,num
615
616	PathInfo catPathName
617	String path = S_path
618
619	String match="BLOCKED BEAM"
620
621	//v_tic()
622	// get the list from the file catalog (=0.0007s)
623	//
624	WAVE/T fileNameW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Filenames
625	WAVE/T intentW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Intent
626
627	Variable np = numpnts(intentW)
628	for(ii=0;ii<np;ii+=1)
629	if(cmpstr(intentW[ii],match)==0)
630	list += fileNameW[ii] + ";"
631	endif
632	endfor
633
634	List = SortList(List,";",0)
635	Printf "BGD files = %s\r",list
636	//v_toc()
637
638
639	////v_tic() // from grep = 3.3s
640	// newList = V_GetRawDataFileList()
641	// num=ItemsInList(newList)
642	//
643	//// for(ii=0;ii<num;ii+=1)
644	//// item=StringFromList(ii, newList , ";")
645	//// fname = path + item
646	//// intent = V_getReduction_intent(fname)
647	//// if(cmpstr(intent,"BLOCKED BEAM") == 0)
648	//// list += item + ";"
649	//// endif
650	////
651	//// endfor
652	// list = ""
653	// for(ii=0;ii<num;ii+=1)
654	// item=StringFromList(ii, newList , ";")
655	// Grep/P=catPathName/Q/E=("(?i)"+match) item
656	// if( V_value ) // at least one instance was found
657	//// Print "found ", item,ii
658	// list += item + ";"
659	// endif
660	// endfor
661	//
662	//
663	// List = SortList(List,";",0)
664	// Printf "BGD files = %s\r",list
665	////v_toc()
666
667	return(list)
668	End
669
670
671	//
672	Function/S V_PickEMPButton(ctrlName) : ButtonControl
673	String ctrlName
674	String list="",item="",fname,newList,intent
675	Variable ii,num
676
677	PathInfo catPathName
678	String path = S_path
679
680	String match="EMPTY CELL"
681
682	// get the list from the file catalog (=0.0007s)
683	//
684	WAVE/T fileNameW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Filenames
685	WAVE/T intentW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Intent
686
687	Variable np = numpnts(intentW)
688	for(ii=0;ii<np;ii+=1)
689	if(cmpstr(intentW[ii],match)==0)
690	list += fileNameW[ii] + ";"
691	endif
692	endfor
693
694	List = SortList(List,";",0)
695	Printf "EMP files = %s\r",list
696
697
698	//
699	// newList = V_GetRawDataFileList()
700	// num=ItemsInList(newList)
701	//
702	//// for(ii=0;ii<num;ii+=1)
703	//// item=StringFromList(ii, newList , ";")
704	//// fname = path + item
705	//// intent = V_getReduction_intent(fname)
706	//// if(cmpstr(intent,"EMPTY CELL") == 0)
707	//// list += item + ";"
708	//// endif
709	////
710	//// endfor
711	//
712	// for(ii=0;ii<num;ii+=1)
713	// item=StringFromList(ii, newList , ";")
714	// Grep/P=catPathName/Q/E=("(?i)"+match) item
715	// if( V_value ) // at least one instance was found
716	//// Print "found ", item,ii
717	// list += item + ";"
718	// endif
719	//
720	// endfor
721	//
722	// List = SortList(List,";",0)
723	// Printf "EMP files = %s\r",list
724
725	return(list)
726	End
727
728
729	//
730	Function/S V_PickEMPBeamButton(ctrlName) : ButtonControl
731	String ctrlName
732	String list="",item="",fname,newList,intent
733	Variable ii,num
734
735	PathInfo catPathName
736	String path = S_path
737
738	String match="EMPTY BEAM"
739
740	// get the list from the file catalog (=0.0007s)
741	//
742	WAVE/T fileNameW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Filenames
743	WAVE/T intentW = root:Packages:NIST:VSANS:CatVSHeaderInfo:Intent
744
745	Variable np = numpnts(intentW)
746	for(ii=0;ii<np;ii+=1)
747	if(cmpstr(intentW[ii],match)==0)
748	list += fileNameW[ii] + ";"
749	endif
750	endfor
751
752	List = SortList(List,";",0)
753	Printf "EMP Beam files = %s\r",list
754
755
756
757
758	return(list)
759	End
760
761	Function/S V_GetDIVList()
762
763	String list="",item="",fname,newList,intent
764	Variable ii,num
765
766	PathInfo catPathName
767	String path = S_path
768
769	newList = V_Get_NotRawDataFileList()
770	num=ItemsInList(newList)
771
772	// for(ii=0;ii<num;ii+=1)
773	// item=StringFromList(ii, newList , ";")
774	// fname = path + item
775	// intent = V_getReduction_intent(fname)
776	// if(cmpstr(intent,"SENSITIVITY") == 0)
777	// list += item + ";"
778	// endif
779	//
780	// endfor
781
782	String match="DIV"
783	for(ii=0;ii<num;ii+=1)
784	item=StringFromList(ii, newList , ";")
785	Grep/P=catPathName/Q/E=("(?i)\\b"+match+"\\b") item
786	// Grep/P=catPathName/Q/E=("(?i)"+match) item
787	if( V_value ) // at least one instance was found
788	// Print "found ", item,ii
789	if(strsearch(item,"pxp",0,2) == -1) //does NOT contain .pxp (the current experiment will be a match)
790	list += item + ";"
791	endif
792	endif
793	endfor
794
795	List = SortList(List,";",0)
796
797	return(list)
798	end
799
800	// TODO
801	// -- find proper way to search for these files
802	// -- they may be written to the file header(reduction block)
803	// -- or grep for VSANS_DIV (in the title)
804	Function/S V_PickDIVButton(ctrlName) : ButtonControl
805	String ctrlName
806	String list="",item="",fname,newList,intent
807	Variable ii,num
808
809	PathInfo catPathName
810	String path = S_path
811
812	newList = V_Get_NotRawDataFileList()
813	num=ItemsInList(newList)
814
815	// for(ii=0;ii<num;ii+=1)
816	// item=StringFromList(ii, newList , ";")
817	// fname = path + item
818	// intent = V_getReduction_intent(fname)
819	// if(cmpstr(intent,"SENSITIVITY") == 0)
820	// list += item + ";"
821	// endif
822	//
823	// endfor
824
825	String match="VSANS_DIV" //this is part of the title of a VSANS DIV file
826	for(ii=0;ii<num;ii+=1)
827	item=StringFromList(ii, newList , ";")
828	Grep/P=catPathName/Q/E=("(?i)\\b"+match+"\\b") item
829	// Grep/P=catPathName/Q/E=("(?i)"+match) item
830	if( V_value ) // at least one instance was found
831	// Print "found ", item,ii
832	list += item + ";"
833	endif
834
835	endfor
836
837	List = SortList(List,";",0)
838	Printf "DIV files = %s\r",list
839
840	return(list)
841
842	End
843
844	Function/S V_GetMSKList()
845
846	String list="",item="",fname,newList,intent
847	Variable ii,num
848
849	PathInfo catPathName
850	String path = S_path
851
852	newList = V_Get_NotRawDataFileList()
853	num=ItemsInList(newList)
854
855	// for(ii=0;ii<num;ii+=1)
856	// item=StringFromList(ii, newList , ";")
857	// fname = path + item
858	// intent = V_getReduction_intent(fname)
859	// if(cmpstr(intent,"SENSITIVITY") == 0)
860	// list += item + ";"
861	// endif
862	//
863	// endfor
864
865	// String match="MASK" // this is part of the title of a VSANS MASK file
866	String match="VSANS_MASK" // this is part of the title of a VSANS MASK file
867	for(ii=0;ii<num;ii+=1)
868	item=StringFromList(ii, newList , ";")
869	Grep/P=catPathName/Q/E=("(?i)\\b"+match+"\\b") item
870	// Grep/P=catPathName/Q/E=("(?i)"+match) item
871	if( V_value ) // at least one instance was found
872	// Print "found ", item,ii
873	if(strsearch(item,"pxp",0,2) == -1) //does NOT contain .pxp (the current experiment will be a match)
874	list += item + ";"
875	endif
876	endif
877
878	endfor
879
880	List = SortList(List,";",0)
881
882	return(list)
883	end
884
885
886	//
887	// TODO
888	// -- find proper way to search for these files
889	// -- they may be written to the file header(reduction block)
890	// -- or grep for VSANS_MASK (in the title)
891	Function/S V_PickMASKButton(ctrlName) : ButtonControl
892	String ctrlName
893	String list="",item="",fname,newList,intent
894	Variable ii,num
895
896	PathInfo catPathName
897	String path = S_path
898
899	newList = V_Get_NotRawDataFileList()
900	num=ItemsInList(newList)
901
902	// for(ii=0;ii<num;ii+=1)
903	// item=StringFromList(ii, newList , ";")
904	// fname = path + item
905	// intent = V_getReduction_intent(fname)
906	// if(cmpstr(intent,"MASK") == 0)
907	// list += item + ";"
908	// endif
909	//
910	// endfor
911
912	String match="MASK"
913	for(ii=0;ii<num;ii+=1)
914	item=StringFromList(ii, newList , ";")
915	Grep/P=catPathName/Q/E=("(?i)\\b"+match+"\\b") item
916	// Grep/P=catPathName/Q/E=("(?i)"+match) item
917	if( V_value ) // at least one instance was found
918	// Print "found ", item,ii
919	list += item + ";"
920	endif
921
922	endfor
923
924	List = SortList(List,";",0)
925	Printf "MASK files = %s\r",list
926
927	return(list)
928
929
930	End
931
932	//button action function to reduce one file with the information specified on
933	//the panel
934	//a temporary protocol is created, even if the fields correspond to a named protocol
935	//(only the protocol wave values are written to the data header, but the name is written to the
936	//schematic - this could cause some unwanted confusion)
937	//
938	//if a sample file(s) is selected, only that file(s) will be reduced
939	//if no file is selected, the user will be prompted with a standard open
940	//dialog to select sample data file(s)
941	//
942	Function V_ReduceOneButton(ctrlName) : ButtonControl
943	String ctrlName
944
945	//parse the information on the panel and assign to tempProtocol wave (in protocol folder)
946	//and execute
947	String temp="root:Packages:NIST:VSANS:Globals:Protocols:tempProtocol"
948	Wave/T w=$temp
949	Variable ii=0,num=12
950	do
951	w[ii] = ""
952	ii+=1
953	while(ii<num)
954
955	V_MakeProtocolFromPanel(w)
956
957	//the "current" protocol is the "tempProtocol" that was parsed from the panel input
958	//set the global, so that the data writing routine can find the protocol wave (fatal otherwise)
959	String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr="tempProtocol"
960
961	PathInfo catPathName //this is where the files came from
962	String pathstr=S_path,samStr
963
964	//take the string from the panel
965	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gSAM
966
967	if( (strlen(tempStr) == 0) \|\| (cmpstr(tempStr,"ask")==0) )
968	//let user select the files
969	tempStr="ask"
970	V_ExecuteProtocol(temp,tempStr)
971	return(0)
972	Else
973	//parse the list of numbers
974	//send only the filenames, without paths
975	samStr = V_ParseRunNumberList(tempStr)
976	If(strlen(samStr)==0)
977	DoAlert 0,"The SAM file number cound not be interpreted. Please enter a valid run number or filename"
978	return(1)
979	endif
980	tempStr=samStr //reset the global
981	V_ExecuteProtocol(temp,samStr)
982	return(0)
983	endif
984	End
985
986
987	//button action function will prompt user for absolute scaling parameters
988	//either from an empty beam file or by manually entering the 4 required values
989	//uses the same function and shared global string as the questionnare form of reduction
990	//in "protocol.ipf" - the string is root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr
991	//
992	Function V_SetABSParamsButton(ctrlName) : ButtonControl
993	String ctrlName
994
995	//will prompt for a list of ABS parameters (4) through a global string variable
996
997	Execute "V_AskForAbsoluteParams_Quest()"
998
999	End
1000
1001
1002
1003	//the panel recreation macro
1004	//
1005	Window V_ProtocolPanel()
1006	PauseUpdate; Silent 1 // building window...
1007	NewPanel /W=(1280,332,1630,932) /K=1 as "VSANS Reduction Protocol"
1008	ModifyPanel cbRGB=(56589,50441,50159), fixedSize=1
1009	SetDrawLayer UserBack
1010	DrawLine 3,65,301,65
1011	DrawLine 3,157,301,157
1012	DrawLine 3,208,301,208
1013	DrawLine 3,257,301,257
1014	DrawLine 3,305,301,305
1015	DrawLine 3,350,301,350
1016	DrawLine 3,445,301,445
1017	DrawLine 3,513,301,513
1018	DrawLine 3,396,301,396
1019
1020	//
1021	Button button_help,pos={300,2},size={25,20},proc=V_ShowProtoHelp,title="?"
1022	Button button_help,help={"Show the help file for setting up a reduction protocol"}
1023	Button button_quest,pos={20,2},size={150,20},proc=V_ProtocolQuestionnaire,title="Questions"
1024	Button button_quest,help={"Run through the questionnaire for setting up a reduction protocol"}
1025	Button button_quest,disable=2
1026
1027
1028	PopupMenu popup_sam,pos={85,68},size={51,23},proc=SAMFilePopMenuProc
1029	PopupMenu popup_sam,mode=1,value= #"V_getSAMList()"
1030	PopupMenu popup_bkg,pos={85,164},size={51,23},proc=BKGFilePopMenuProc
1031	PopupMenu popup_bkg,mode=1,value= #"V_getBGDList()"
1032	PopupMenu popup_emp,pos={85,213},size={51,23},proc=EMPFilePopMenuProc
1033	PopupMenu popup_emp,mode=1,value= #"V_getEMPList()"
1034	PopupMenu popup_div,pos={85,263},size={51,23},proc=DIVFilePopMenuProc
1035	PopupMenu popup_div,mode=1,value= #"V_getDIVList()"
1036	PopupMenu popup_msk,pos={85,356},size={51,23},proc=MSKFilePopMenuProc
1037	PopupMenu popup_msk,mode=1,value= #"V_getMSKList()"
1038
1039
1040	CheckBox prot_check,pos={6,163},size={74,14},title="Background"
1041	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"}
1042	CheckBox prot_check,value= 1
1043	CheckBox prot_check_1,pos={6,215},size={71,14},title="Empty Cell"
1044	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"}
1045	CheckBox prot_check_1,value= 1
1046	CheckBox prot_check_2,pos={6,263},size={72,14},title="Sensitivity"
1047	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"}
1048	CheckBox prot_check_2,value= 1
1049	CheckBox prot_check_3,pos={6,356},size={43,14},title="Mask"
1050	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"}
1051	CheckBox prot_check_3,value= 1
1052	CheckBox prot_check_4,pos={6,70},size={53,14},title="Sample"
1053	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"}
1054	CheckBox prot_check_4,value= 1
1055	CheckBox prot_check_5,pos={6,399},size={56,14},title="Average"
1056	CheckBox prot_check_5,help={"If checked, the specified averaging will be performed at the end of the data reduction."}
1057	CheckBox prot_check_5,value= 1
1058	CheckBox prot_check_9,pos={6,310},size={59,14},title="Absolute"
1059	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"}
1060	CheckBox prot_check_9,value= 1
1061
1062
1063	// Button pick_sam,pos={214,28},size={70,20},proc=V_PickSAMButton,title="set SAM"
1064	// Button pick_sam,help={"This button will set the file selected in the File Catalog table to be the sample file"}
1065	// Button pick_bgd,pos={214,75},size={70,20},proc=V_PickBGDButton,title="set BGD"
1066	// Button pick_bgd,help={"This button will set the file selected in the File Catalog table to be the background file."}
1067	// Button pick_emp,pos={214,125},size={70,20},proc=V_PickEMPButton,title="set EMP"
1068	// Button pick_emp,help={"This button will set the file selected in the File Catalog table to be the empty cell file."}
1069	// Button pick_DIV,pos={214,173},size={70,20},proc=V_PickDIVButton,title="set DIV"
1070	// Button pick_DIV,help={"This button will set the file selected in the File Catalog table to be the sensitivity file."}
1071	Button pick_ABS,pos={264,308},size={70,20},proc=V_SetABSParamsButton,title="set ABS"
1072	Button pick_ABS,help={"This button will prompt the user for absolute scaling parameters"}
1073	// Button pick_MASK,pos={214,266},size={70,20},proc=V_PickMASKButton,title="set MASK"
1074	// Button pick_MASK,help={"This button will set the file selected in the File Catalog table to be the mask file."}
1075
1076
1077	Button pick_AVE,pos={188,401},size={150,20},proc=V_SetAverageParamsButtonProc,title="set AVERAGE params"
1078	Button pick_AVE,help={"Prompts the user for the type of 1-D averaging to perform, as well as saving options"}
1079
1080
1081	Button pick_trim,pos={264,454},size={70,20},proc=V_TrimDataProtoButton,title="Trim"
1082	Button pick_trim,help={"This button will prompt the user for trimming parameters"}
1083
1084
1085	SetVariable samStr,pos={6,90},size={250,15},title="file:"
1086	SetVariable samStr,help={"Filename of the sample file(s) to be used in the data reduction"}
1087	SetVariable samStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gSAM
1088	SetVariable bgdStr,pos={7,186},size={250,15},title="file:"
1089	SetVariable bgdStr,help={"Filename of the background file(s) to be used in the data reduction"}
1090	SetVariable bgdStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gBGD
1091	SetVariable empStr,pos={8,236},size={250,15},title="file:"
1092	SetVariable empStr,help={"Filename of the empty cell file(s) to be used in the data reduction"}
1093	SetVariable empStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gEMP
1094	SetVariable divStr,pos={9,285},size={250,15},title="file:"
1095	SetVariable divStr,help={"Filename of the detector sensitivity file to be used in the data reduction"}
1096	SetVariable divStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gDIV
1097	SetVariable maskStr,pos={9,377},size={250,15},title="file:"
1098	SetVariable maskStr,help={"Filename of the mask file to be used in the data reduction"}
1099	SetVariable maskStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gMASK
1100	SetVariable absStr,pos={7,331},size={250,15},title="parameters:"
1101	SetVariable absStr,help={"Keyword-string of values necessary for absolute scaling of data. Remaining parameters are taken from the sample file."}
1102	SetVariable absStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr
1103	SetVariable aveStr,pos={9,424},size={250,15},title="parameters:"
1104	SetVariable aveStr,help={"Keyword-string of choices used for averaging and saving the 1-D data files"}
1105	SetVariable aveStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gAVE
1106
1107	SetVariable begStr,pos={9,464},size={250,15},title="Beg Trim:"
1108	SetVariable begStr,help={"Keyword-string of choices used for averaging and saving the 1-D data files"}
1109	SetVariable begStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gBegPtsStr
1110	SetVariable endStr,pos={9,484},size={250,15},title="End Trim:"
1111	SetVariable endStr,help={"Keyword-string of choices used for averaging and saving the 1-D data files"}
1112	SetVariable endStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gEndPtsStr
1113
1114
1115
1116	//only show DRK if user wants to see it
1117	//if global = 1,then show => set disable = 0
1118	// CheckBox prot_check_6,pos={6,363},size={113,14},proc=DrkCheckProc,title="Use DRK correction"
1119	// CheckBox prot_check_6,help={"If checked, the selected file will be used for DRK correction. Typically this is NOT checked"}
1120	// CheckBox prot_check_6,value= 0,disable = (!root:Packages:NIST:gAllowDRK)
1121	// SetVariable drkStr,pos={120,363},size={150,15},title="."
1122	// SetVariable drkStr,help={"DRK detector count file"},disable = (!root:Packages:NIST:gAllowDRK)
1123	// SetVariable drkStr,limits={-Inf,Inf,0},value= root:Packages:NIST:VSANS:Globals:Protocols:gDRK
1124
1125
1126	Button export_button, size={120,20},pos={125,540},title="Export to Data",proc=V_ExportFileProtocol
1127	Button export_button, help={"Exports the protocol to data file on disk for Importing into another experiment"}
1128	Button import_button, size={120,20},pos={125,562},title="Import from Data",proc=V_ImportFileProtocol
1129	Button import_button,help={"Imports a protocol from a data file on disk for use in this experiment"}
1130	Button recallProt,pos={7,540},size={107,20},proc=V_RecallProtocolButton,title="Recall Protocol"
1131	Button recallProt,help={"Resets the panel to the file choices in a previously saved protocol"}
1132	Button del_protocol,pos={7,562},size={110,20},proc=V_DeleteProtocolButton,title="Delete Protocol"
1133	Button del_protocol,help={"Use this to delete a previously saved protocol."}
1134	Button done_protocol,pos={285,562},size={45,20},proc=V_DoneProtocolButton,title="Done"
1135	Button done_protocol,help={"This button will close the panel. The panel can be recalled at any time from the SANS menu."}
1136	Button saveProtocol,pos={7,518},size={100,20},proc=V_SaveProtocolButton,title="Save Protocol"
1137	Button saveProtocol,help={"Saves the cerrent selections in the panel to a protocol which can be later recalled"}
1138	Button ReduceOne,pos={240,518},size={100,20},proc=V_ReduceOneButton,title="Reduce A File"
1139	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"}
1140
1141	EndMacro
1142
1143
1144
1145
1146
1147	Function SAMFilePopMenuProc(pa) : PopupMenuControl
1148	STRUCT WMPopupAction &pa
1149
1150	switch( pa.eventCode )
1151	case 2: // mouse up
1152	Variable popNum = pa.popNum
1153	String popStr = pa.popStr
1154	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gSAM
1155	tempStr = popStr
1156	break
1157	case -1: // control being killed
1158	break
1159	endswitch
1160
1161	return 0
1162	End
1163
1164
1165	Function BKGFilePopMenuProc(pa) : PopupMenuControl
1166	STRUCT WMPopupAction &pa
1167
1168	switch( pa.eventCode )
1169	case 2: // mouse up
1170	Variable popNum = pa.popNum
1171	String popStr = pa.popStr
1172	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gBGD
1173	tempStr = popStr
1174	break
1175	case -1: // control being killed
1176	break
1177	endswitch
1178
1179	return 0
1180	End
1181
1182	Function EMPFilePopMenuProc(pa) : PopupMenuControl
1183	STRUCT WMPopupAction &pa
1184
1185	switch( pa.eventCode )
1186	case 2: // mouse up
1187	Variable popNum = pa.popNum
1188	String popStr = pa.popStr
1189	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gEMP
1190	tempStr = popStr
1191	break
1192	case -1: // control being killed
1193	break
1194	endswitch
1195
1196	return 0
1197	End
1198
1199	Function DIVFilePopMenuProc(pa) : PopupMenuControl
1200	STRUCT WMPopupAction &pa
1201
1202	switch( pa.eventCode )
1203	case 2: // mouse up
1204	Variable popNum = pa.popNum
1205	String popStr = pa.popStr
1206	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gDIV
1207	tempStr = popStr
1208	break
1209	case -1: // control being killed
1210	break
1211	endswitch
1212
1213	return 0
1214	End
1215
1216	Function MSKFilePopMenuProc(pa) : PopupMenuControl
1217	STRUCT WMPopupAction &pa
1218
1219	switch( pa.eventCode )
1220	case 2: // mouse up
1221	Variable popNum = pa.popNum
1222	String popStr = pa.popStr
1223	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gMASK
1224	tempStr = popStr
1225	break
1226	case -1: // control being killed
1227	break
1228	endswitch
1229
1230	return 0
1231	End
1232
1233	////activated when user checks/unchecks the box
1234	////either prompts for a file using a standard dialog, or removes the current file
1235	//Function V_DrkCheckProc(ctrlName,checked) : CheckBoxControl
1236	// String ctrlName
1237	// Variable checked //Desired state, not previous state
1238	//
1239	// SVAR drkStr=root:Packages:NIST:VSANS:Globals:Protocols:gDRK
1240	// if(checked==1)
1241	// //print "Unchecked on call"
1242	// //this just asks for the filename, doesn't open the file
1243	// String msgStr="Select the DRK file",fullPath="",fileStr=""
1244	// Variable refnum
1245	//
1246	// Open/D/R/T="????"/M=(msgStr)/P=catPathName refNum
1247	// fullPath = S_FileName //fname is the full path
1248	// if(cmpstr(fullpath,"")==0)
1249	// //user cancelled
1250	// CheckBox prot_check_6,value=0 //keep box unchecked
1251	// return(0)
1252	// Endif
1253	// fileStr=V_GetFileNameFromPathNoSemi(fullPath)
1254	// //Print fileStr
1255	// //update the global string
1256	// drkStr = ReplaceStringByKey("DRK",drkStr,fileStr,"=",",")
1257	// drkStr = ReplaceNumberByKey("DRKMODE", drkStr, 10 ,"=",",")
1258	// else
1259	// //print "checked on call"
1260	// drkStr="DRK=none,DRKMODE=0," //change the global
1261	// endif
1262	//
1263	//End
1264
1265
1266	Function V_ShowProtoHelp(ctrlName) : ButtonControl
1267	String ctrlName
1268	DisplayHelpTopic/Z/K=1 "VSANS Data Reduction Tutorial[VSANS Reduction Protocol]"
1269	if(V_flag !=0)
1270	DoAlert 0,"The VSANS Data Reduction Tutorial Help file could not be found"
1271	endif
1272	End
1273
1274	//button action procedure to get the type of average requested by the user
1275	//presented as a missing parameter dialog, which is really user-UN-friendly
1276	//and will need to be re-thought. Defaults of dialog are set for normal
1277	//circular average, so typically click "continue" and proceed
1278	//
1279	Function V_SetAverageParamsButtonProc(ctrlName) : ButtonControl
1280	String ctrlName
1281
1282	// Execute "V_GetAvgInfo_Full()"
1283	Execute "V_GetAvgInfo()"
1284
1285	//set the global string
1286	SVAR tempStr = root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr
1287	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAVE = tempStr
1288
1289	End
1290
1291	// TODO
1292	// -- this is a trimmed down version of the "full" set of averaging options
1293	// add to this as needed as I figure out what functionality is appropriate
1294	//
1295	//procedure called by protocol panel to ask user for average type choices
1296	// somewhat confusing and complex, but may be as good as it gets.
1297	//
1298	//Proc V_GetAvgInfo(av_typ,autoSave,autoName,autoPlot,side,phi,dphi,width,QCtr,QDelta)
1299	Proc V_GetAvgInfo(av_typ,autoSave,autoName,binType,qCtr,qDelta,detGroup)
1300	String av_typ,autoSave,AutoName,binType
1301	// Variable phi=0,dphi=10,width=10,Qctr = 0.01,qDelta=10
1302	Variable Qctr=0.1,qDelta=0.01
1303	String detGroup="F"
1304
1305	// Prompt av_typ, "Type of Average",popup,"Circular;Sector;Rectangular;Annular;2D_ASCII;QxQy_ASCII;PNG_Graphic;Sector_PlusMinus;"
1306	Prompt av_typ, "Type of Average",popup,"Circular;Annular;"
1307
1308	// comment out above line in DEMO_MODIFIED version, and uncomment the line below (to disable PNG save)
1309	// Prompt av_typ, "Type of Average",popup,"Circular;Sector;Rectangular;Annular;2D_ASCII;QxQy_ASCII"
1310	Prompt autoSave,"Save files to disk?",popup,"Yes - Concatenate;Yes - Individual;No"
1311	Prompt autoName,"Auto-Name files?",popup,"Auto;Manual"
1312	// Prompt autoPlot,"Plot the averaged Data?",popup,"Yes;No"
1313	// Prompt side,"Include detector halves?",popup,"both;right;left"
1314	// Prompt phi,"Orientation Angle (-90,90) degrees (Rectangular or Sector)"
1315	// Prompt dphi, "Azimuthal range (0,45) degrees (Sector only)"
1316	// Prompt width, "Width of Rectangular average (1,128)"
1317	Prompt binType,"Binning Type?",popup,ksBinTypeStr
1318
1319	Prompt Qctr, "q-value of center of annulus"
1320	Prompt Qdelta,"(+/-) q-width of annulus"
1321	Prompt detGroup,"Group for annulus"
1322
1323	//assign results of dialog to key=value string, semicolon separated
1324	//do only what is necessary, based on av_typ
1325	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr=""
1326
1327	// TODO:
1328	// hard wired value
1329	String autoPlot = "No"
1330
1331
1332	// all averages need these values
1333	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "AVTYPE=" + av_typ + ";"
1334	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SAVE=" + autoSave + ";"
1335	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "NAME=" + autoName + ";"
1336	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PLOT=" + autoPlot + ";"
1337	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "BINTYPE=" + binType + ";"
1338
1339	// if(cmpstr(av_typ,"Sector")==0 \|\| cmpstr(av_typ,"Sector_PlusMinus")==0)
1340	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SIDE=" + side + ";"
1341	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PHI=" + num2str(phi) + ";"
1342	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "DPHI=" + num2str(dphi) + ";"
1343	// Endif
1344	//
1345	// if(cmpstr(av_typ,"Rectangular")==0)
1346	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SIDE=" + side + ";"
1347	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PHI=" + num2str(phi) + ";"
1348	// root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "WIDTH=" + num2str(width) + ";"
1349	// Endif
1350	//
1351	if(cmpstr(av_typ,"Annular")==0)
1352	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "QCENTER=" + num2str(QCtr) + ";"
1353	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "QDELTA=" + num2str(QDelta) + ";"
1354	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "DETGROUP=" + detGroup + ";"
1355	Endif
1356	End
1357
1358
1359	// TODO
1360	// -- this is the original(SANS) version, and needs to be updated for VSANS as the averaging options are
1361	// worked out
1362	// -- there have been changes made to V_GetAvgInfo() above -- so work from that version, NOT this one.
1363	//
1364	//
1365	//procedure called by protocol panel to ask user for average type choices
1366	// somewhat confusing and complex, but may be as good as it gets.
1367	//
1368	Proc V_GetAvgInfo_Full(av_typ,autoSave,autoName,autoPlot,side,phi,dphi,width,QCtr,QDelta)
1369	String av_typ,autoSave,AutoName,autoPlot,side
1370	Variable phi=0,dphi=10,width=10,Qctr = 0.01,qDelta=10
1371	Prompt av_typ, "Type of Average",popup,"Circular;Sector;Rectangular;Annular;2D_ASCII;QxQy_ASCII;PNG_Graphic;Sector_PlusMinus;"
1372	// comment out above line in DEMO_MODIFIED version, and uncomment the line below (to disable PNG save)
1373	// Prompt av_typ, "Type of Average",popup,"Circular;Sector;Rectangular;Annular;2D_ASCII;QxQy_ASCII"
1374	Prompt autoSave,"Save files to disk?",popup,"Yes;No"
1375	Prompt autoName,"Auto-Name files?",popup,"Auto;Manual"
1376	Prompt autoPlot,"Plot the averaged Data?",popup,"Yes;No"
1377	Prompt side,"Include detector halves?",popup,"both;right;left"
1378	Prompt phi,"Orientation Angle (-90,90) degrees (Rectangular or Sector)"
1379	Prompt dphi, "Azimuthal range (0,45) degrees (Sector only)"
1380	Prompt width, "Width of Rectangular average (1,128)"
1381	Prompt Qctr, "q-value of center of annulus"
1382	Prompt Qdelta,"Pixel width of annulus"
1383
1384	//assign results of dialog to key=value string, semicolon separated
1385	//do only what is necessary, based on av_typ
1386	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr=""
1387
1388	// all averages need these four values
1389	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "AVTYPE=" + av_typ + ";"
1390	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SAVE=" + autoSave + ";"
1391	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "NAME=" + autoName + ";"
1392	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PLOT=" + autoPlot + ";"
1393
1394	if(cmpstr(av_typ,"Sector")==0 \|\| cmpstr(av_typ,"Sector_PlusMinus")==0)
1395	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SIDE=" + side + ";"
1396	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PHI=" + num2str(phi) + ";"
1397	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "DPHI=" + num2str(dphi) + ";"
1398	Endif
1399
1400	if(cmpstr(av_typ,"Rectangular")==0)
1401	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "SIDE=" + side + ";"
1402	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "PHI=" + num2str(phi) + ";"
1403	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "WIDTH=" + num2str(width) + ";"
1404	Endif
1405
1406	if(cmpstr(av_typ,"Annular")==0)
1407	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "QCENTER=" + num2str(QCtr) + ";"
1408	root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr += "QDELTA=" + num2str(QDelta) + ";"
1409	Endif
1410	End
1411
1412
1413	//prompts the user to pick a previously created protocol from a popup list
1414	//of given the option to create a new protocol
1415	//the chosen protocol is passed back to the calling procedure by a global string
1416	//the popup is presented as a missing parameter dialog (called with empty parameter list)
1417	//
1418	// MAXROWS is present to exclude the PanelNameW from appearing as a protocol
1419	Proc V_PickAProtocol(protocol)
1420	String Protocol
1421	Prompt Protocol "Pick A Protocol",popup, V_RecallableProtocols()
1422
1423	String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr = protocol
1424	End
1425
1426	Proc V_DeleteAProtocol(protocol)
1427	String Protocol
1428	// Prompt Protocol "Delete A Protocol",popup, WaveList("*",";","TEXT:1")
1429	Prompt Protocol "Delete A Protocol",popup, V_DeletableProtocols()
1430
1431	String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr = protocol
1432	End
1433
1434	Function/S V_DeletableProtocols()
1435	String list=WaveList("*",";","TEXT:1,MAXROWS:13")
1436
1437	list= RemoveFromList("Base", list , ";")
1438	list= RemoveFromList("DoAll", list , ";")
1439	list= RemoveFromList("CreateNew", list , ";")
1440	list= RemoveFromList("tempProtocol", list , ";")
1441	list= RemoveFromList("wTTmpWrite", list , ";")
1442	if(cmpstr(list,"")==0)
1443	list = "_no_protocols_;"
1444	endif
1445
1446	return(list)
1447	End
1448
1449	Function/S V_RecallableProtocols()
1450	String list=WaveList("*",";","TEXT:1,MAXROWS:13")
1451
1452	// list= RemoveFromList("Base", list , ";")
1453	// list= RemoveFromList("DoAll", list , ";")
1454	list= RemoveFromList("CreateNew", list , ";")
1455	list= RemoveFromList("tempProtocol", list , ";")
1456	list= RemoveFromList("wTTmpWrite", list , ";")
1457	if(cmpstr(list,"")==0)
1458	list = "_no_protocols_;"
1459	endif
1460
1461	return(list)
1462	End
1463
1464
1465	//missing parameter dialog to solicit user for a waveStr for the protocol
1466	//about to be created
1467	//name is passed back as a global string and calling procedure is responsible for
1468	//checking for wave conflicts and valid names
1469	//
1470	Proc V_AskForName(protocol)
1471	String Protocol
1472	Prompt Protocol "Enter a new name for your protocol (no extension)"
1473
1474	String/G root:Packages:NIST:VSANS:Globals:Protocols:gNewStr = protocol
1475	End
1476
1477	//this is a lengthy procedure for sequentially polling the user about what data
1478	//reduction steps they want to be performed during the protocol
1479	//ensures that a valid protocol name was chosen, then fills out each "item"
1480	//(6 total) needed for reduction
1481	//it the user cancels at any point, the partial protocol will be deleted
1482	//
1483	Function V_ProtocolQuestionnaire(ctrlName)
1484	String ctrlName
1485
1486	String filename,cmd
1487	Variable notDone,refnum
1488
1489	//prompt for name of new protocol wave to save
1490	do
1491	Execute "V_AskForName()"
1492	SVAR newProtoStr = root:Packages:NIST:VSANS:Globals:Protocols:gNewStr
1493
1494	//make sure it's a valid IGOR name
1495	newProtoStr = CleanupName(newProtoStr,0) //strict naming convention
1496	String/G root:Packages:NIST:VSANS:Globals:Protocols:gNewStr=newProtoStr //reassign, if changed
1497	//Print "newProtoStr = ",newProtoStr
1498
1499	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
1500	if(WaveExists( $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtoStr) ) == 1)
1501	//wave already exists
1502	DoAlert 0,"that name is already in use. Please pick a new name"
1503	notDone = 1
1504	else
1505	//name is good
1506	notDone = 0
1507	Endif
1508	while(notDone)
1509
1510	//Print "protocol questionnaire is "+newProtocol
1511
1512	//make a new text wave (12 points) and fill it in, in response to questions
1513	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols //(redundant - full wave specs are used)
1514	Make/O/T/N=(kNumProtocolSteps) $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtoStr)
1515	Wave/T newProtocol = $("root:Packages:NIST:VSANS:Globals:Protocols:" + newProtoStr)
1516	newProtocol = ""
1517
1518	//ask the questions
1519	/////
1520	//*****Multiple files in these lists are full paths/filenames which may or may not
1521	//have semicolon version numbers in the filename. Therefore, construct the list with
1522	//COMMAS as separators - to avoid messy parsing
1523	///////
1524
1525	String fileFilters = "VSANS Data Files (.ngv,.h5):.ngv,.h5;"
1526	// fileFilters += "HTML Files (.htm,.html):.htm,.html;"
1527	fileFilters += "All Files:.*;"
1528	//////////////////////////
1529	String drkStr="",fileStr=""
1530
1531
1532	//////////////////////////
1533	// DoAlert 1,"Do you want to correct your data for DRK (beam off) counts?"
1534	// if(V_flag == 1) //1=yes
1535	// //prompt for DRK file, but don't actually open it (/D flag)
1536	// Open/D/R/F=fileFilters/M="Select the DRK file"/P=catPathName refnum
1537	// //check for cancel
1538	// if(strlen(S_filename)==0)
1539	// //user cancelled, abort
1540	// KillWaves/Z newProtocol
1541	// SetDataFolder root:
1542	// Abort "Incomplete protocol has been deleted"
1543	// Endif
1544	// //assign filename (just the name) to [6]
1545	// fileStr = V_GetFileNameFromPathNoSemi(S_filename)
1546	// drkStr = "DRK=none,DRKMODE=0,"
1547	// drkStr = ReplaceStringByKey("DRK",drkStr,fileStr,"=",",")
1548	// drkStr = ReplaceNumberByKey("DRKMODE", drkStr, 10 ,"=",",")
1549	// newProtocol[6] = drkStr
1550	// else
1551	// //no Work.DRK desired
1552	// newProtocol[6] = "DRK=none,DRKMODE=0,"
1553	// Endif
1554	//
1555	////////////
1556
1557
1558	// TODO:
1559	// -- there is a lag in the V_pick() routine as it greps through all of the files. Several seconds even when there
1560	// are 20-ish files. Pre-search for the strings? When to refresh them for new data?
1561	/////////////////
1562	DoAlert 1,"Do you want to subtract background from your data?"
1563	if(V_flag == 1) //1=yes
1564
1565	Prompt filename,"BKG File",popup,V_PickBGDButton("")
1566	DoPrompt "Select File",filename
1567	if (V_Flag)
1568	return 0 // user canceled
1569	endif
1570	// //assign filename to [0]
1571	newProtocol[0] = V_GetFileNameFromPathNoSemi(fileName)
1572
1573
1574	// OLD way, using an open file dialog
1575	// and allowing for multiple files to be added together
1576	//
1577	// //prompt for background file, but don't actually open it (/D flag)
1578	// Open/D/R/F=fileFilters/M="Select the Background data file"/P=catPathName refnum
1579	// //check for cancel
1580	// if(strlen(S_filename)==0)
1581	// //user cancelled, abort
1582	// KillWaves/Z newProtocol
1583	// SetDataFolder root:
1584	// Abort "Incomplete protocol has been deleted"
1585	// Endif
1586	// //assign filename (full path) to [0]
1587	// newProtocol[0] = V_GetFileNameFromPathNoSemi(S_filename)
1588
1589	// notDone=1
1590	// do
1591	// //prompt for additional background files
1592	// DoAlert 1,"Do you want to add another background file?"
1593	// if(V_flag == 1) //yes
1594	// Open/D/R/F=fileFilters/M="Select another Background data file"/P=catPathName refnum
1595	// //check for cancel
1596	// if(strlen(S_filename)==0)
1597	// //user cancelled, abort ********maybe just break out of the loop here
1598	// KillWaves/Z newProtocol
1599	// SetDataFolder root:
1600	// Abort "Incomplete protocol has been deleted"
1601	// Endif
1602	// //assign filename (full path) to [0]
1603	// newProtocol[0] += "," + V_GetFileNameFromPathNoSemi(S_filename) //***COMMA separated list
1604	// notDone = 1 //keep going
1605	// else
1606	// notDone = 0 //no more to add
1607	// Endif
1608	// While(notDone)
1609	//////
1610
1611	else //no background desired
1612	newProtocol[0] = "none"
1613	Endif
1614
1615
1616	//////////////////////
1617	DoAlert 1,"Do you want to subtract empty cell scattering from your data?"
1618	if(V_flag == 1) //1=yes
1619
1620	Prompt filename,"EMP File",popup,V_PickEMPButton("")
1621	DoPrompt "Select File",filename
1622	if (V_Flag)
1623	return 0 // user canceled
1624	endif
1625	// //assign filename to [1]
1626	newProtocol[1] = V_GetFileNameFromPathNoSemi(fileName)
1627
1628
1629
1630	// //prompt for Empty cell file, but don't actually open it (/D flag)
1631	// Open/D/R/F=fileFilters/M="Select the Empty Cell data file"/P=catPathName refnum
1632	// //check for cancel
1633	// if(strlen(S_filename)==0)
1634	// //user cancelled, abort
1635	// KillWaves/Z newProtocol
1636	// SetDataFolder root:
1637	// Abort "Incomplete protocol has been deleted"
1638	// Endif
1639	// //assign filename (full path) to [1]
1640	// newProtocol[1] = V_GetFileNameFromPathNoSemi(S_filename)
1641	//
1642	// notDone=1
1643	// do
1644	// //prompt for additional Empty Cell files
1645	// DoAlert 1,"Do you want to add another Empty Cell file?"
1646	// if(V_flag == 1) //yes
1647	// Open/D/R/F=fileFilters/M="Select another Empty Cell data file"/P=catPathName refnum
1648	// //check for cancel
1649	// if(strlen(S_filename)==0)
1650	// //user cancelled, abort ********maybe just break out of the loop here
1651	// KillWaves/Z newProtocol
1652	// SetDataFolder root:
1653	// Abort "Incomplete protocol has been deleted"
1654	// Endif
1655	// //assign filename (full path) to [1]
1656	// newProtocol[1] += "," + V_GetFileNameFromPathNoSemi(S_filename) //***COMMA separated list
1657	// notDone = 1 //keep going
1658	// else
1659	// notDone = 0 //no more to add
1660	// Endif
1661	// While(notDone)
1662
1663
1664	else //no background desired
1665	newProtocol[1] = "none"
1666	Endif
1667
1668
1669	//////////////////////////
1670	DoAlert 1,"Do you want to correct your data for detector sensitivity?"
1671
1672	if(V_flag == 1) //1=yes
1673
1674	Prompt filename,"DIV File",popup,V_PickDIVButton("")
1675	DoPrompt "Select File",filename
1676	if (V_Flag)
1677	return 0 // user canceled
1678	endif
1679	// //assign filename to [2]
1680	newProtocol[2] = V_GetFileNameFromPathNoSemi(fileName)
1681
1682	// //prompt for DIV file, but don't actually open it (/D flag)
1683	// Open/D/R/F=fileFilters/M="Select the detector sensitivity file"/P=catPathName refnum
1684	// //check for cancel
1685	// if(strlen(S_filename)==0)
1686	// //user cancelled, abort
1687	// KillWaves/Z newProtocol
1688	// SetDataFolder root:
1689	// Abort "Incomplete protocol has been deleted"
1690	// Endif
1691	// //assign filename (full path) to [2]
1692	// newProtocol[2] = V_GetFileNameFromPathNoSemi(S_filename)
1693
1694
1695	else
1696	//no Work.DIV desired
1697	newProtocol[2] = "none"
1698	Endif
1699	//////////////////////////
1700	DoAlert 1,"Do you want to mask your files before averaging?"
1701
1702	if(V_flag == 1) //1=yes
1703
1704	Prompt filename,"MASK File",popup,V_PickMASKButton("")
1705	DoPrompt "Select File",filename
1706	if (V_Flag)
1707	return 0 // user canceled
1708	endif
1709	// //assign filename to [3]
1710	newProtocol[3] = V_GetFileNameFromPathNoSemi(fileName)
1711
1712	// //prompt for mask file, but don't actually open it (/D flag)
1713	// Open/D/R/F=fileFilters/M="Select the mask file"/P=catPathName refnum
1714	// //check for cancel
1715	// if(strlen(S_filename)==0)
1716	// //user cancelled, abort
1717	// KillWaves/Z newProtocol
1718	// SetDataFolder root:
1719	// Abort "Incomplete protocol has been deleted"
1720	// Endif
1721	// //assign filename (full path) to [3]
1722	// newProtocol[3] = V_GetFileNameFromPathNoSemi(S_filename)
1723
1724
1725	else
1726	//no MASK desired
1727	newProtocol[3] = "none"
1728	Endif
1729
1730	//absolute scaling
1731
1732	//////////////////////////
1733	//ABS parameters stored as keyword=value string
1734	DoAlert 1,"Do you want absolute scaling?"
1735	if(V_flag == 1) //1=yes
1736	//missing param - prompt for values, put in semicolon-separated list
1737	Execute "V_AskForAbsoluteParams_Quest()"
1738	SVAR absStr = root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr
1739	newProtocol[4] = absStr
1740	else
1741	//no absolute scaling desired
1742	newProtocol[4] = "none"
1743	Endif
1744
1745	//type of average, plot?, auto/manual naming/saving... put in semicolon separated string
1746	//of KEY=<value> format for easy parsing
1747	//Kewords are: AVTYPE,PHI,DPHI,PLOT,SAVE,NAME,SIDE,WIDTH
1748	//note that AVTYPE,NAME,SIDE have string values, others have numerical values
1749	///////////////////////
1750	DoAlert 1,"Do you want to average your data to I vs. q?"
1751	if(V_flag == 1) //1=yes
1752	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr = ""
1753	Execute "V_GetAvgInfo()" //will put up missing paramter dialog and do all the work
1754	//:gAvgInfo is reset by the Proc(), copy this string tot he protocol
1755	SVAR tempStr=root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr
1756
1757	//get a file path for saving files, if desired
1758	/////no - save files to the same data folder as the one with the raw data
1759	//then only one path to manage.
1760	//String yesNo = StringByKey("SAVE", tempStr,"=", ";")
1761	//if(cmpstr("Yes",yesNo) == 0) //0=yes
1762	//NewPath/C/M="Select Folder"/O Save_path //Save_path is the symbolic path
1763	//Endif
1764
1765	newProtocol[5] = tempStr
1766	KillStrings/Z tempStr
1767	else
1768	//no averaging desired
1769	newProtocol[5] = "AVTYPE=none"
1770	Endif
1771
1772	//returns the name of the newly created (= currently in use) protocol wave through a global
1773	String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr = newProtoStr
1774
1775	//reset the panel based on the protocol textwave (currently a string)
1776	V_ResetToSavedProtocol(newProtoStr)
1777
1778	SetDataFolder root:
1779
1780	return(0)
1781	End
1782
1783
1784	// TODO
1785	// -- this function may not work properly for VSANS, but I haven't tested it yet
1786	// -- I'd rather have some sort of display to show the current content of the WORK folders
1787	//
1788	// -- the global string fileList does not exist, so this will always fail and return zero
1789	//
1790	//
1791	//function to check the work files (to see what's already there)
1792	//and compare that with the files that are supposed to be there, according to the
1793	//current protocol (to save unnecessary time re-loading files)
1794	//
1795	//the "type" folder is checked for all files in the list req(ested)Files
1796	//note that the list of files is a full path:name;ver, while the
1797	//fileList in the folder is just the name (or a list of names)
1798	//
1799	//returns 0 false, if files are NOT present
1800	//or 1 = true, yes, the files are there as requested
1801	//
1802	Function V_AreFilesThere(type,reqFiles)
1803	String type,reqFiles
1804
1805	//in general, reqFiles is a list of full paths to files - which MAY include semicolon version numbers
1806	//reqFiles MUST be constructed with COMMAS as list separators, to avoid disaster
1807	//when the version numbers are interpreted as filenames
1808
1809	//get the number of files requested
1810	Variable nReq,nCur,match,ii
1811	nReq = ItemsInList(reqFiles,",")
1812
1813	//get the name of the file currently in BGD - in the global fileList
1814	//fileList has NAMES ONLY - since it was derived from the file header
1815	String testStr
1816	testStr = "root:Packages:NIST:"+type+":fileList"
1817	if(Exists(testStr) == 2) //2 if string variable exists
1818	SVAR curFiles = $testStr
1819	else
1820	//no files currently in type folder, return zero
1821	Return (0)
1822	Endif
1823	//get the number of files already in folder
1824	nCur = ItemsInList(curFiles,";")
1825	If(nCur != nReq)
1826	Return (0) //quit now, the wrong number of files present
1827	Endif
1828	//right number of files... are the names right...
1829	//check for a match (case-sensitive!!) of each requested file in the curFile string
1830	//need to extract filenames from reqFiles, since they're the full path and name
1831
1832	ii=0
1833	do
1834	testStr = StringFromList(ii,reqFiles,",") //testStr is the Nth full path and filename
1835	//testStr = GetFileNameFromPathNoSemi(testStr) //testStr will now be just the filename
1836	match = stringmatch(curFiles,testStr)
1837	If(!match)
1838	Return (0) //req file was not found in curFile list - get out now
1839	Endif
1840	ii+=1
1841	while(ii<nreq)
1842
1843	Return (1) //indicate that files are OK, no changes needed
1844	End
1845
1846
1847	//
1848	//will add the files specified in the protocol to the "type" folder
1849	//will add multiple files together if more than one file is requested
1850	//(list is a comma delimited list of filenames, with NO path information)
1851	//
1852	// This routine NOW DOES check for the possibility that the filenames may have ";vers" from the
1853	// VAX - data should be picked up from Charlotte, where it won't have version numbers.
1854	//
1855	Function V_AddFilesInList(type,list)
1856	String type,list
1857
1858	//type is the work folder to put the data into, and list is a COMMA delimited list of paths/names
1859	Variable num,ii,err=0,refNum
1860	String filename,pathStr=""
1861	PathInfo catPathName //this is where the files are
1862	pathstr=S_path
1863
1864	num = ItemsInList(list,",") // comma delimited list
1865
1866	ii=0
1867	do
1868	//FindValidFilename only needed in case of vax version numbers
1869	filename = pathStr + V_FindValidFilename(StringFromList(ii,list,","))
1870	Open/Z/R refnum as filename
1871	if(V_flag != 0) //file not found
1872	//Print "file not found AddFilesInList()"
1873	//Print filename
1874	err = 1
1875	return(err)
1876	Endif
1877	Close refnum //file was found and opened, so close it
1878
1879	// Abort "Find equivalent to ReadHeaderAndData(filename)"
1880	// ReadHeaderAndData(filename)
1881	err = V_LoadHDF5Data(filename,"RAW")
1882
1883	if(ii == 0)
1884	//first pass, wipe out the old contents of the work file
1885	err = V_Raw_to_work(type)
1886	else
1887	err = V_Add_raw_to_work(type)
1888	Endif
1889	ii+=1
1890	while(ii<num)
1891	return(err)
1892	End
1893
1894	//function will reduce a sample file (or ask for file(s))
1895	//using the protocol named as "protoStr" in the Protocols subfolder
1896	//samStr is the file(s) or "ask" to force prompt
1897	//sequentially proceeds through flowchart, doing reduction steps as needed
1898	//show Schematic to debug what steps/values were used
1899	//
1900	//function is long, but straightforward logic
1901	//
1902	Function V_ExecuteProtocol(protStr,samStr)
1903	String protStr,samStr
1904	//protStr is the full path to the selected protocol wave
1905	//samStr is either "ask" or the name ONLY ofthe desired sample data file(s) (NO PATH)
1906	WAVE/T prot = $protStr
1907	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
1908
1909	Variable filesOK,err,notDone
1910	String activeType, msgStr, junkStr, pathStr=""
1911	PathInfo catPathName //this is where the files are
1912	pathStr=S_path
1913
1914	// NVAR useXMLOutput = root:Packages:NIST:gXML_Write
1915
1916	//Parse the instructions in the prot wave
1917	//0 - bkg
1918	//1 - emp
1919	//2 - div
1920	//3 - mask
1921	//4 - abs params c2-c5
1922	//5 - average params
1923	//6 = DRK file (**out of sequence)
1924	//7 = beginning trim points
1925	//8 = end trim points
1926	//9 = unused
1927	//10 = unused
1928	//11 = unused
1929
1930	// for VSANS, DIV is used on each data file as it is converted to WORK, so it needs to be
1931	// the first thing in place, before any data or backgrounds are loaded
1932
1933
1934	//
1935	// TODO:
1936	// x- this is no longer done after the COR step, and CAL is not produced as output of DIV
1937	// x- needs to be aware of the file name passed in
1938	// x- PromptForPath does not exist in VSANS. Need a better (automated) way to find the file.
1939
1940	//check for work.div file (prot[2])
1941	//load in if needed
1942	// no math is done here, DIV is applied as files are converted to WORK (the first operation in VSANS)
1943	//
1944	String divFileName = ""
1945
1946	If(cmpstr("none",prot[2])!=0) // if !0, then there's a file requested
1947	If(cmpstr("ask",prot[2]) == 0)
1948	//ask user for file
1949	// junkStr = PromptForPath("Select the detector sensitivity file")
1950	Prompt divFileName,"DIV File",popup,V_PickDIVButton("")
1951	DoPrompt "Select File",divFileName
1952
1953	If(strlen(divFileName)==0)
1954	SetDataFolder root:
1955	Abort "No file selected, data reduction aborted"
1956	Endif
1957	V_LoadHDF5Data(divFileName,"DIV")
1958	else
1959	//assume it's a path, and that the first (and only) item is the path:file
1960	//list processing is necessary to remove any final comma
1961	junkStr = pathStr + StringFromList(0, prot[2],"," )
1962	V_LoadHDF5Data(junkStr,"DIV")
1963	Endif
1964
1965	else
1966	// DIV step is being skipped
1967	NVAR gDoDIVCor = root:Packages:NIST:VSANS:Globals:gDoDIVCor
1968	Variable saved_gDoDIVCor = gDoDIVCor
1969	gDoDIVCor = 0 // protocol says to turn it off for now (reset later)
1970	Endif
1971
1972
1973	// TODO:
1974	// -- currently does not allow adding RAW data files together, so no parsing is done
1975	// -- NOTE detector corrections (including DIV) are done at the V_Raw_to_Work() step
1976	// So if the DIV is not part of the protocol, be sure to set/reset the global preference
1977	//
1978	//prompt for sam data => read raw data, add to sam folder
1979	//or parse file(s) from the input paramter string
1980	activeType = "SAM"
1981	msgStr = "Select sample data"
1982	//Ask for SAM file or parse
1983	do
1984	if((cmpstr(samStr,"ask") == 0) \|\| (cmpstr(samStr,"")==0) ) //zero if strings are equal
1985	err = V_LoadHDF5Data("","RAW") //will prompt for file
1986	if(err)
1987	PathInfo/S catPathName
1988	Abort "reduction sequence aborted"
1989	endif
1990	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
1991	err = V_Raw_to_work(activeType) //this is the first file (default)
1992	//Ask for another SAM file
1993	do
1994	DoAlert 1,"Do you want to add another Sample file?"
1995	if(V_flag == 1) //yes
1996	err = V_LoadHDF5Data("","RAW") //will prompt for file
1997	if(err)
1998	PathInfo/S catPathName
1999	Abort "reduction sequence aborted"
2000	endif
2001	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
2002	err = V_Add_raw_to_work(activeType)
2003	notDone = 1
2004	else
2005	notDone = 0
2006	endif
2007	while(notDone)
2008	break
2009	Endif
2010	//"none" is not an option - you always need a sample file - "none" will never return zero
2011	//if not "ask" AND not "none" then try to parse the filenames
2012	If((cmpstr(samStr,"none") != 0) && (cmpstr(samStr,"ask") != 0))
2013	//filesOK = AreFilesThere(activeType,samStr) //return 1 if correct files are already there
2014	filesOK = 0 // Feb 2008, always force a reload of files. Maybe slow, but always correct
2015	if(!filesOK)
2016	//add the correct file(s) to SAM
2017
2018	// TODO: only one file is allowed currently
2019	err = V_AddFilesInList(activeType,samStr)
2020
2021	if(err)
2022	//Print "samstr = ",samStr
2023	Abort "SAM file not found, reset SAM file"
2024	Endif
2025	Endif
2026	Endif
2027	While(0)
2028	// TODO
2029	// -- this may not be the most reliable way to pass the file name (for naming of the saved file later)
2030	SVAR file_name = root:file_Name
2031	String samFileLoaded = file_name //keep a copy of the sample file loaded
2032
2033	//always update
2034	V_UpdateDisplayInformation(ActiveType)
2035
2036	//check for bkg file -- "ask" might not fail - "ask?" will - ? not allowed in VAX filenames
2037	// add if needed
2038	//use a "case" statement
2039	msgStr = "Select background file"
2040	activeType = "BGD"
2041	do
2042	if(cmpstr(prot[0],"ask") == 0) //zero if strings are equal
2043	err = V_LoadHDF5Data("","RAW") //will prompt for file
2044	if(err)
2045	PathInfo/S catPathName
2046	Abort "reduction sequence aborted"
2047	endif
2048	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
2049	err = V_Raw_to_work(activeType) //this is the first file (default)
2050	//Ask for another BGD file
2051	do
2052	DoAlert 1,"Do you want to add another Background file?"
2053	if(V_flag == 1) //yes
2054	err = V_LoadHDF5Data("","RAW") //will prompt for file
2055	if(err)
2056	PathInfo/S catPathName
2057	Abort "reduction sequence aborted"
2058	endif
2059	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
2060	err = V_Add_raw_to_work(activeType)
2061	notDone = 1
2062	else
2063	notDone = 0
2064	endif
2065	while(notDone)
2066	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2067	break
2068	Endif
2069	If(cmpstr(prot[0],"none") == 0)
2070	//clean out the BKG folder?
2071	//KillDataFolder root:BKG
2072	//NewDataFolder/O root:BKG
2073	break
2074	Endif
2075	//if not "ask" AND not "none" then try to parse the filenames
2076	If((cmpstr(prot[0],"none") != 0) && (cmpstr(prot[0],"ask") != 0))
2077	//filesOK = AreFilesThere(activeType,prot[0])
2078	filesOK = 0 // Feb 2008, always force a reload of files. Maybe slow, but always correct
2079	if(!filesOK)
2080	//add the correct file(s) to BGD
2081	string bgdStr = prot[0]
2082	err = V_AddFilesInList(activeType,bgdStr)
2083	If(err)
2084	Abort "BGD file not found. Reset BGD file list"
2085	Endif
2086	Endif
2087	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2088	Endif
2089	While(0)
2090
2091
2092	//check for emp file (prot[1])
2093	// add if needed
2094	msgStr = "Select empty cell data"
2095	activeType = "EMP"
2096	do
2097	if(cmpstr(prot[1],"ask") == 0)
2098	err = V_LoadHDF5Data("","RAW") //will prompt for file
2099	if(err)
2100	PathInfo/S catPathName
2101	Abort "reduction sequence aborted"
2102	endif
2103	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
2104	err = V_Raw_to_work(activeType) //this is the first file (default)
2105	//Ask for another EMP file
2106	do
2107	DoAlert 1,"Do you want to add another Empty Cell file?"
2108	if(V_flag == 1) //yes
2109	err = V_LoadHDF5Data("","RAW") //will prompt for file
2110	if(err)
2111	PathInfo/S catPathName
2112	Abort "reduction sequence aborted"
2113	endif
2114	V_UpdateDisplayInformation("RAW") //display the new type of data that was loaded
2115	err = V_Add_raw_to_work(activeType)
2116	notDone = 1
2117	else
2118	notDone = 0
2119	endif
2120	while(notDone)
2121	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2122	break
2123	Endif
2124	If(cmpstr(prot[1],"none") == 0)
2125	//clean out the EMP folder?
2126	//KillDataFolder root:Packages:NIST:EMP
2127	//NewDataFolder/O root:Packages:NIST:EMP
2128	break
2129	Endif
2130	//if not "ask" AND not "none" then try to parse the filenames
2131	If((cmpstr(prot[1],"none") != 0) && (cmpstr(prot[1],"ask") != 0))
2132	//filesOK = AreFilesThere(activeType,prot[1])
2133	filesOK = 0 // Feb 2008, always force a reload of files. Maybe slow, but always correct
2134	if(!filesOK)
2135	//add the correct file(s) to BGD
2136	err = V_AddFilesInList(activeType,prot[1])
2137	If(err)
2138	Abort "EMP file not found. Reset EMP file list"
2139	Endif
2140	Endif
2141	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2142	Endif
2143	While(0)
2144
2145	//do the CORRECT step based on the answers to emp and bkg subtraction
2146	//by setting the proper"mode"
2147	//1 = both emp and bgd subtraction
2148	//2 = only bgd subtraction
2149	//3 = only emp subtraction
2150	//4 = no subtraction
2151	//additional modes 091301
2152	//11 = emp, bgd, drk
2153	//12 = bgd and drk
2154	//13 = emp and drk
2155	//14 = no subtractions
2156	//work.drk is from proto[6]
2157	//
2158	//subtracting just the DRK data is NOT an option - it doesnt' really make any physical sense
2159	// - in this case, DRK is skipped (equivalent to mode==4)
2160	// automatically accounts for attenuators given the lookup tables and the
2161	//desired subtractions
2162	//Attenuator lookup tables are alredy implemented (NG1 = NG7)
2163	//
2164
2165
2166	/////// DRK is SKIPPED
2167
2168	// //read in the DRK data if necessary
2169	// //only one file, assumed to be RAW data
2170	// //
2171	// String fname="",drkStr=""
2172	// drkStr=StringByKey("DRK",prot[6],"=",",")
2173	// if(cmpstr(drkStr,"none") != 0)
2174	// err = ReadHeaderAndData( (pathStr+drkStr) )
2175	// if(err)
2176	// PathInfo/S catPathName
2177	// Abort "reduction sequence aborted"
2178	// endif
2179	// err = V_Raw_to_Work_NoNorm("DRK")
2180	// endif
2181
2182
2183
2184	//dispatch to the proper "mode" of Correct()
2185	Variable mode=4,val
2186	do
2187	if( (cmpstr("none",prot[0]) == 0) && (cmpstr("none",prot[1]) == 0) )
2188	//no subtraction (mode = 4),
2189	mode = 4
2190	Endif
2191	If((cmpstr(prot[0],"none") != 0) && (cmpstr(prot[1],"none") == 0))
2192	//subtract BGD only
2193	mode=2
2194	Endif
2195	If((cmpstr(prot[0],"none") == 0) && (cmpstr(prot[1],"none") != 0))
2196	//subtract EMP only
2197	mode=3
2198	Endif
2199	If((cmpstr(prot[0],"none") != 0) && (cmpstr(prot[1],"none") != 0))
2200	// bkg and emp subtraction are to be done (BOTH not "none")
2201	mode=1
2202	Endif
2203	activeType = "COR"
2204	//add in DRK mode (0= no used, 10 = used)
2205	val = NumberByKey("DRKMODE",prot[6],"=","," )
2206	mode += val
2207	// print "mode = ",mode
2208	err = V_Correct(mode)
2209	if(err)
2210	SetDataFolder root:
2211	Abort "error in Correct, called from executeprotocol, normal cor"
2212	endif
2213	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2214	While(0)
2215
2216
2217	////////////////////////////////////////////////////////
2218	// Absolute scale
2219
2220	// x- calculation works, needs proper inputs (solid angle aware)
2221	// x- Open beam method needs to be verified in V_AskForAbsoluteParams_Quest()
2222	Variable c2,c3,c4,c5,kappa_err
2223	//do absolute scaling if desired
2224	// DoAlert 0,"Abs step incomplete"
2225
2226	if(cmpstr("none",prot[4])!=0)
2227	if(cmpstr("ask",prot[4])==0)
2228	//get the params from the user
2229	Execute "V_AskForAbsoluteParams_Quest()"
2230	//then from the list
2231	SVAR junkAbsStr = root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr
2232	c2 = NumberByKey("TSTAND", junkAbsStr, "=", ";") //parse the list of values
2233	c3 = NumberByKey("DSTAND", junkAbsStr, "=", ";")
2234	c4 = NumberByKey("IZERO", junkAbsStr, "=", ";")
2235	c5 = NumberByKey("XSECT", junkAbsStr, "=", ";")
2236	kappa_err = NumberByKey("SDEV", junkAbsStr, "=", ";")
2237	else
2238	//get the parames from the list
2239	c2 = NumberByKey("TSTAND", prot[4], "=", ";") //parse the list of values
2240	c3 = NumberByKey("DSTAND", prot[4], "=", ";")
2241	c4 = NumberByKey("IZERO", prot[4], "=", ";")
2242	c5 = NumberByKey("XSECT", prot[4], "=", ";")
2243	kappa_err = NumberByKey("SDEV", prot[4], "=", ";")
2244	Endif
2245	//get the sample trans and thickness from the activeType folder
2246	Variable c0 = V_getSampleTransmission(activeType) //sample transmission
2247	Variable c1 = V_getSampleThickness(activeType) //sample thickness
2248
2249	err = V_Absolute_Scale(activeType,c0,c1,c2,c3,c4,c5,kappa_err)
2250	if(err)
2251	SetDataFolder root:
2252	Abort "Error in V_Absolute_Scale(), called from V_ExecuteProtocol"
2253	endif
2254	activeType = "ABS"
2255	V_UpdateDisplayInformation(ActiveType) //update before breaking from loop
2256	Endif
2257
2258	//
2259	// TODO
2260	// x- fill in the "ask" step
2261	// -- none is OK, except if the kill fails for any reason
2262	// x- the regular case of the file name specified by the protocol works correctly
2263	// x- don't create a null mask if not used, it will handle the error and print out that the mask is missing
2264
2265	//mask data if desired (this is done automatically when the data is binned to I(q)) and is
2266	//not done explicitly here
2267
2268	//check for mask
2269	//doesn't change the activeType
2270	String mskFileName=""
2271
2272	if(cmpstr("none",prot[3])!=0)
2273	If(cmpstr("ask",prot[3])==0)
2274	//get file from user
2275	// x- fill in the get file prompt, and handle the result
2276	Prompt mskFileName,"MASK File",popup,V_PickMASKButton("")
2277	DoPrompt "Select File",mskFileName
2278	// if (V_Flag)
2279	// return 0 // user cancelled
2280	// endif
2281
2282	If(strlen(mskFileName)==0) //use cancelled
2283	//if none desired, make sure that the old mask is deleted
2284	KillDataFolder/Z root:Packages:NIST:VSANS:MSK:
2285	NewDataFolder/O root:Packages:NIST:VSANS:MSK
2286
2287	DoAlert 0,"No Mask file selected, data not masked"
2288	else
2289	//read in the file from the selection
2290	V_LoadHDF5Data(mskFileName,"MSK")
2291	Endif
2292	else
2293	//just read it in from the protocol
2294	//list processing is necessary to remove any final comma
2295	mskFileName = pathStr + StringFromList(0, prot[3],"," )
2296	V_LoadHDF5Data(mskFileName,"MSK")
2297	Endif
2298
2299	else
2300	//if none desired, make sure that the old mask is deleted
2301	// TODO
2302	// x- clean out the data folder
2303	// x- note that V_KillNamedDataFolder() points to RawVSANS, and won't work
2304	// -- what happens if the kill fails? need error handling
2305	//
2306	KillDataFolder/Z root:Packages:NIST:VSANS:MSK:
2307	NewDataFolder/O root:Packages:NIST:VSANS:MSK
2308
2309	Endif
2310
2311
2312	// average/save data as specified
2313	//Parse the keyword=<Value> string as needed, based on AVTYPE
2314
2315	//average/plot first
2316	String av_type = StringByKey("AVTYPE",prot[5],"=",";")
2317	If(cmpstr(av_type,"none") != 0)
2318	If (cmpstr(av_type,"")==0) //if the key could not be found... (if "ask" the string)
2319	//get the averaging parameters from the user, as if the set button was hit in the panel
2320	V_SetAverageParamsButtonProc("dummy") //from "ProtocolAsPanel"
2321	SVAR tempAveStr = root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr
2322	av_type = StringByKey("AVTYPE",tempAveStr,"=",";")
2323	else
2324	//there is info in the string, use the protocol
2325	//set the global keyword-string to prot[5]
2326	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr = prot[5]
2327	Endif
2328	Endif
2329
2330	//convert the folder to linear scale before averaging, then revert by calling the window hook
2331	// (not needed for VSANS, data is always linear scale)
2332
2333	// bin and plot the data
2334
2335	//
2336	// x- need to convert BINTYPE keyword into a numerical value to pass
2337	//
2338
2339	String binTypeStr = StringByKey("BINTYPE",prot[5],"=",";")
2340	// plotting is not really necessary, and the graph may not be open - so skip for now?
2341	Variable binType
2342	binType = V_BinTypeStr2Num(binTypeStr)
2343	if(binType == 0)
2344	Abort "Binning mode not found in V_QBinAllPanels() "// when no case matches
2345	endif
2346
2347
2348	//
2349	// TODO:
2350	// -- do I calculate the proper resolution here? I've already decoded the binning type
2351	// and the averaging type has been specified by the protocol.
2352	//
2353	// currently, the resolution is calculated every time that the data is averaged (in VC_fDoBinning_QxQy2D)
2354	//
2355	// -- if I calculate the resolution here, then the Trimming routines must be updated
2356	// to trim the resolution waves also. This will work for the columns present in
2357	// pinhole resolution, but anything using the matrix method - it won't work - and I'll need
2358	// a different solution
2359	//
2360	strswitch(av_type) //dispatch to the proper routine to average to 1D data
2361	case "none":
2362	//still do nothing
2363	break
2364	case "2D_ASCII":
2365	//do nothing
2366	break
2367	case "QxQy_ASCII":
2368	//do nothing
2369	break
2370	case "PNG_Graphic":
2371	//do nothing
2372	break
2373	case "Rectangular":
2374	// RectangularAverageTo1D(activeType)
2375	break
2376	case "Annular":
2377	// AnnularAverageTo1D(activeType)
2378	String detGroup = StringByKey("DETGROUP",prot[5],"=",";")
2379	Variable qCtr_Ann = NumberByKey("QCENTER",prot[5],"=",";")
2380	Variable qWidth = NumberByKey("QDELTA",prot[5],"=",";")
2381	V_QBinAllPanels_Annular(activeType,detGroup,qCtr_Ann,qWidth)
2382	break
2383	case "Circular":
2384
2385	V_QBinAllPanels_Circular(activeType,binType) // this does a default circular average
2386	break
2387	case "Sector":
2388	// CircularAverageTo1D(activeType)
2389	break
2390	case "Sector_PlusMinus":
2391	// Sector_PlusMinus1D(activeType)
2392	break
2393	default:
2394	//do nothing
2395	endswitch
2396
2397	// TODO
2398	// x- this call will bin the active type, then the next call bins the active type
2399	// x- then later, I dispatch to bin the active type...
2400	// x- !!!need to split out the panel draw and the binning calls from V_PlotData_Panel
2401	//
2402	// TODO:
2403	// -- BAD logic here, skipping the normal graph if annular is chosen. Go back and see how I do this
2404	// in SANS for a better and more foolproof way to do this
2405	//
2406	if(cmpstr(av_type,"Annular") != 0)
2407	V_PlotData_Panel() //this brings the plot window to the front, or draws it (ONLY)
2408	V_Update1D_Graph(activeType,binType) //update the graph, data was already binned
2409	endif
2410	///// end of averaging dispatch
2411
2412
2413	//
2414	// x- how do I get the sample file name?
2415	// local variable samFileLoaded is the file name loaded (contains the extension)
2416	//
2417	//save data if desired - dispatch as needed
2418	String fullpath = "", newfileName=""
2419	String saveType = StringByKey("SAVE",prot[5],"=",";") //does user want to save data?
2420
2421	If( (cmpstr(saveType[0,2],"Yes")==0) && (cmpstr(av_type,"none") != 0) )
2422	//then save
2423	newFileName = RemoveEnding(samFileLoaded,".nxs.ngv")
2424
2425	//pick ABS or AVE extension
2426	String exten = activeType
2427	if(cmpstr(exten,"ABS") != 0)
2428	exten = "AVE"
2429	endif
2430	if(cmpstr(av_type,"2D_ASCII") == 0)
2431	exten = "ASC"
2432	endif
2433	if(cmpstr(av_type,"QxQy_ASCII") == 0)
2434	exten = "DAT"
2435	endif
2436
2437	// // add an "x" to the file extension if the output is XML
2438	// // currently (2010), only for ABS and AVE (1D) output
2439	// if( cmpstr(exten,"ABS") == 0 \|\| cmpstr(exten,"AVE") == 0 )
2440	// if(useXMLOutput == 1)
2441	// exten += "x"
2442	// endif
2443	// endif
2444
2445	//Path is catPathName, symbolic path
2446	//if this doesn't exist, a dialog will be presented by setting dialog = 1
2447	//
2448	Variable dialog = 0
2449
2450	PathInfo/S catPathName
2451	String item = StringByKey("NAME",prot[5],"=",";") //Auto or Manual naming
2452	String autoname = StringByKey("AUTONAME",prot[5],"=",";") //autoname - will get empty string if not present
2453	If((cmpstr(item,"Manual")==0) \|\| (cmpstr(newFileName,"") == 0))
2454	//manual name if requested or if no name can be derived from header
2455	fullPath = newfileName + "."+ exten //puts possible new name or null string in dialog
2456	dialog = 1 //force dialog for user to enter name
2457	else
2458	//auto-generate name and prepend path - won't put up any dialogs since it has all it needs
2459	//use autoname if present
2460	if (cmpstr(autoname,"") != 0)
2461	fullPath = S_Path + autoname + "." +exten
2462	else
2463	fullPath = S_Path + newFileName+"." + exten
2464	endif
2465	Endif
2466	//
2467	strswitch(av_type)
2468	case "Annular":
2469	// WritePhiave_W_Protocol(activeType,fullPath,dialog)
2470	V_fWrite1DAnnular("root:Packages:NIST:VSANS:",activeType,detGroup,newFileName+".phi")
2471	Print "data written to: "+ newFileName+".phi"
2472
2473	break
2474	case "2D_ASCII":
2475	// Fast2DExport(activeType,fullPath,dialog)
2476	break
2477	case "QxQy_ASCII":
2478	// QxQy_Export(activeType,fullPath,dialog)
2479	break
2480	case "PNG_Graphic":
2481	// SaveAsPNG(activeType,fullpath,dialog)
2482	break
2483	case "Circular": //in SANS, this was the default, but is dangerous, so make it explicit here
2484	// if (useXMLOutput == 1)
2485	// WriteXMLWaves_W_Protocol(activeType,fullPath,dialog)
2486	// else
2487	// WriteWaves_W_Protocol(activeType,fullpath,dialog)
2488	// endif
2489	//
2490	// x- get the trim strings from somewhere-- from the file or from the protocol??
2491	// then replace the null strings being passed
2492
2493	if(cmpstr(saveType,"Yes - Concatenate")==0)
2494	V_Trim1DDataStr(activeType,binType,prot[7],prot[8]) // x- passing null strings uses global or default trim values
2495
2496	V_ConcatenateForSave("root:Packages:NIST:VSANS:",activeType,"",binType) // this removes q=0 point, concatenates, sorts
2497	V_Write1DData("root:Packages:NIST:VSANS:",activeType,newFileName+"."+exten) //don't pass the full path, just the name
2498	else
2499	// remove the q=0 point from the back detector, if it's there
2500	// does not trim any of the data
2501	V_RemoveQ0_B(activeType)
2502	V_Write1DData_ITX("root:Packages:NIST:VSANS:",activeType,newFileName,binType)
2503	endif
2504	Print "data written to: "+ newFileName+"."+exten
2505
2506	break
2507	default:
2508	DoAlert 0, "av_type not found in dispatch to write file"
2509
2510	endswitch
2511
2512	Endif
2513
2514	//done with everything in protocol list
2515
2516
2517	// reset any global preferences that I had changed
2518	gDoDIVCor = saved_gDoDIVCor
2519
2520
2521	Return(0)
2522	End
2523
2524
2525
2526
2527
2528	//missing parameter dialog to solicit the 4 absolute intensity parameters
2529	//from the user
2530	//values are passed back as a global string variable (keyword=value)
2531	//
2532	Proc V_AskForAbsoluteParams(c2,c3,c4,c5,I_err)
2533	Variable c2=1,c3=1,c4=1e8,c5=1,I_err=1
2534	Prompt c2, "Standard Transmission"
2535	Prompt c3, "Standard Thickness (cm)"
2536	Prompt c4, "I(0) from standard fit (normalized to 1E8 monitor cts)"
2537	Prompt c5, "Standard Cross-Section (cm-1)"
2538	Prompt I_err, "error in I(q=0) (one std dev)"
2539
2540	String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr=""
2541
2542	root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr = "TSTAND="+num2str(c2)
2543	root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr += ";" + "DSTAND="+num2str(c3)
2544	root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr += ";" + "IZERO="+num2str(c4)
2545	root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr += ";" + "XSECT="+num2str(c5)
2546	root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr += ";" + "SDEV="+num2str(I_err)
2547
2548	End
2549
2550
2551	//
2552	// TODO
2553	// -- fill in all of the functionality for calculation from direct beam
2554	// and verify that the calculations are numerically correct
2555	//
2556	//asks the user for absolute scaling information. the user can either
2557	//enter the necessary values in manually (missing parameter dialog)
2558	//or the user can select an empty beam file from a standard open dialog
2559	//if an empty beam file is selected, the "kappa" value is automatically calculated
2560	//in either case, the global keyword=value string is set.
2561	//
2562	Function V_AskForAbsoluteParams_Quest()
2563
2564	Variable err,loc,refnum
2565
2566	Variable ii
2567
2568	Variable kappa=1
2569	Variable kappa_err
2570
2571	//get the necessary variables for the calculation of kappa
2572	Variable countTime,monCnt,sdd,pixel_x,pixel_y
2573	String detStr,junkStr,errStr
2574
2575	Variable empAttenFactor, emp_atten_err
2576
2577	//get the XY box and files
2578	Variable x1,x2,y1,y2,emptyCts,empty_ct_err
2579	String emptyFileName,tempStr,divFileName,detPanel_toSum
2580
2581	//ask user if he wants to use a transmision file for absolute scaling
2582	//or if he wants to enter his own information
2583	err = V_UseStdOrEmpForABS()
2584	//DoAlert 1,"<Yes> to enter your own values, <No> to select an empty beam flux file"
2585	If ( err==1 )
2586	//secondary standard selected, prompt for values
2587	Execute "V_AskForAbsoluteParams()" //missing parameters
2588	else
2589	//empty beam flux file selected, prompt for file, and use this to calculate KAPPA
2590
2591	// TODO
2592	// x- need an empty beam file name
2593	//
2594	Prompt emptyFileName,"Empty Beam File",popup,V_PickEMPBeamButton("")
2595	DoPrompt "Select File",emptyFileName
2596	if (V_Flag)
2597	return 0 // user canceled
2598	endif
2599
2600	// TODO
2601	// x- need panel
2602	//
2603	Prompt detPanel_toSum,"Panel with Direct Beam",popup,ksDetectorListAll
2604	DoPrompt "Select Panel",detPanel_toSum
2605	if (V_Flag)
2606	return 0 // user canceled
2607	endif
2608
2609	//need the detector sensitivity file - make a guess, allow to override
2610	Prompt divFileName,"DIV File",popup,V_PickDIVButton("")
2611	DoPrompt "Select File",divFileName
2612	if (V_Flag)
2613	return 0 // user canceled
2614	endif
2615	V_LoadHDF5Data(divFileName,"DIV")
2616
2617
2618	WAVE xyBoxW = V_getBoxCoordinates(emptyFileName)
2619
2620
2621	// load in the data, and use all of the corrections, especially DIV
2622	// (be sure the corrections are actually set to "on", don't assume that they are)
2623	// save preferences for file loading
2624	Variable savDivPref,savSAPref
2625	NVAR gDoDIVCor = root:Packages:NIST:VSANS:Globals:gDoDIVCor
2626	savDivPref = gDoDIVCor
2627	NVAR gDoSolidAngleCor = root:Packages:NIST:VSANS:Globals:gDoSolidAngleCor
2628	savSAPref = gDoSolidAngleCor
2629
2630	// set local preferences
2631	gDoDIVCor = 1
2632	gDoSolidAngleCor = 1
2633
2634	V_LoadAndPlotRAW_wName(emptyFileName)
2635	// convert raw->SAM
2636	// V_Raw_to_work("SAM")
2637	// V_UpdateDisplayInformation("SAM")
2638	V_UpdateDisplayInformation("RAW")
2639
2640	// do the DIV correction
2641	if (gDoDIVCor == 1)
2642	// need extra check here for file existence
2643	// if not in DIV folder, load.
2644	// if unable to load, skip correction and report error (Alert?) (Ask to Load?)
2645	Print "Doing DIV correction"// for "+ detStr
2646	for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
2647	detStr = StringFromList(ii, ksDetectorListAll, ";")
2648	Wave w = V_getDetectorDataW("RAW",detStr)
2649	Wave w_err = V_getDetectorDataErrW("RAW",detStr)
2650
2651	V_DIVCorrection(w,w_err,detStr,"RAW") // do the correction in-place
2652	endfor
2653	else
2654	Print "DIV correction NOT DONE" // not an error since correction was unchecked
2655	endif
2656
2657	// and determine box sum and error
2658	// store these locally
2659
2660
2661	// x- need to get the panel string for the sum.
2662	// x- the detector string is currently hard-wired
2663	// detStr = "MR"
2664
2665	emptyCts = V_SumCountsInBox(xyBoxW[0],xyBoxW[1],xyBoxW[2],xyBoxW[3],empty_ct_err,"RAW",detPanel_toSum)
2666
2667	Print "empty counts = ",emptyCts
2668	Print "empty err/counts = ",empty_ct_err/emptyCts
2669
2670	//
2671	// x- get all of the proper values for the calculation
2672	// -x currently the attenuation is incorrect
2673	// such that kappa_err = 1*kappa
2674	// x- verify the calculation (no solid angle needed??)
2675
2676	// get the attenuation factor for the empty beam
2677	// -- the attenuation is not written by NICE to the file
2678	// so I need to calculate it myself from the tables
2679	//
2680	// empAttenFactor = V_getAttenuator_transmission(emptyFileName)
2681	// emp_atten_err = V_getAttenuator_trans_err(emptyFileName)
2682	empAttenFactor = V_CalculateAttenuationFactor(emptyFileName)
2683	emp_atten_err = V_CalculateAttenuationError(emptyFileName)
2684
2685	countTime = V_getCount_time(emptyFileName)
2686
2687	// TODO
2688	// -- not sure if this is the correct monitor count to use
2689	monCnt = V_getBeamMonNormData("RAW")
2690
2691	pixel_x = V_getDet_x_pixel_size("RAW",detPanel_toSum)
2692	pixel_x /= 10 //convert mm to cm, since sdd in cm
2693	pixel_y = V_getDet_y_pixel_size("RAW",detPanel_toSum)
2694	pixel_y /= 10 //convert mm to cm, since sdd in cm
2695	sdd = V_getDet_ActualDistance("RAW",detPanel_toSum)
2696
2697	// kappa = emptyCts/countTime/empAttenFactor1.0e8/(monCnt/countTime)(pixel_x*pixel_y/sdd^2)
2698	kappa = emptyCts/countTime/empAttenFactor*1.0e8/(monCnt/countTime)
2699
2700
2701	kappa_err = (empty_ct_err/emptyCts)^2 + (emp_atten_err/empAttenFactor)^2
2702	kappa_err = sqrt(kappa_err) * kappa
2703
2704	// x- set the parameters in the global string
2705	junkStr = num2str(kappa)
2706	errStr = num2Str(kappa_err)
2707	Execute "V_AskForAbsoluteParams(1,1,"+junkStr+",1,"+errStr+")" //no missing parameters, no dialog
2708
2709
2710	Printf "Kappa was successfully calculated as = %g +/- %g (%g %)\r",kappa,kappa_err,(kappa_err/kappa)*100
2711
2712	// restore preferences on exit
2713	gDoDIVCor = savDivPref
2714	gDoSolidAngleCor = savSAPref
2715
2716	Endif
2717
2718	End
2719
2720	Function V_UserSelectBox_Continue(ctrlName) :buttonControl
2721	String ctrlName
2722
2723	DoWindow/K junkWindow //kill panel
2724	end
2725
2726	Function V_SelectABS_XYBox(x1,x2,y1,y2)
2727	Variable &x1,&x2,&y1,&y2
2728
2729	Variable err=0
2730
2731	Variable/G root:V_marquee=1 //sets the sneaky bit to automatically update marquee coords
2732	Variable/G root:V_left,root:V_right,root:V_bottom,root:V_top //must be global for auto-update
2733	DoWindow/F SANS_Data
2734	NewPanel/K=2 /W=(139,341,382,432) as "Select the primary beam"
2735	DoWindow/C junkWindow
2736	AutoPositionWindow/E/M=1/R=SANS_Data
2737
2738	Drawtext 21,20 ,"Select the primary beam with the"
2739	DrawText 21,40, "marquee and press continue"
2740	Button button0,pos={80,58},size={92,20},title="Continue"
2741	Button button0,proc=V_UserSelectBox_Continue
2742
2743	PauseForUser junkWindow,SANS_Data
2744
2745	DoWindow/F SANS_Data
2746
2747	//GetMarquee left,bottom //not needed
2748	NVAR V_left=V_left
2749	NVAR V_right=V_right
2750	NVAR V_bottom=V_bottom
2751	NVAR V_top=V_top
2752
2753	x1 = V_left
2754	x2 = V_right
2755	y1 = V_bottom
2756	y2 = V_top
2757	// Print "new values,before rounding = ",x1,x2,y1,y2
2758
2759	// TODO -- replace this call
2760	// KeepSelectionInBounds(x1,x2,y1,y2)
2761	//Print "new values = ",x1,x2,y1,y2
2762
2763	KillVariables/Z root:V_Marquee,root:V_left,root:V_right,root:V_bottom,root:V_top
2764	if((x1-x2)==0 \|\| (y1-y2)==0)
2765	err=1
2766	endif
2767	return(err)
2768	End
2769
2770	Function V_UseStdOrEmpForABS()
2771
2772	NewPanel/K=2 /W=(139,341,402,448) as "Absolute Scaling"
2773	DoWindow/C junkABSWindow
2774	ModifyPanel cbRGB=(57346,65535,49151)
2775	SetDrawLayer UserBack
2776	SetDrawEnv fstyle= 1
2777	DrawText 21,20,"Method of absolute calibration"
2778	Button button0,pos={52,33},size={150,20},proc=V_UserSelectABS_Continue,title="Empty Beam Flux"
2779	Button button1,pos={52,65},size={150,20},proc=V_UserSelectABS_Continue,title="Secondary Standard"
2780
2781	PauseForUser junkABSWindow
2782	NVAR val = root:Packages:NIST:VSANS:Globals:tmpAbsVal
2783	return(val)
2784	End
2785
2786	//returns 0 if button0 (empty beam flux)
2787	// or 1 if secondary standard
2788	Function V_UserSelectABS_Continue(ctrlName) :buttonControl
2789	String ctrlName
2790
2791	variable val=0
2792	If(cmpstr(ctrlName,"button0")==0)
2793	val=0
2794	else
2795	val=1
2796	endif
2797	// print "val = ",ctrlName,val
2798	Variable/G root:Packages:NIST:VSANS:Globals:tmpAbsVal = val
2799	DoWindow/K junkABSWindow //kill panel
2800	return(0)
2801	end
2802
2803
2804	Function V_TrimDataProtoButton(ctrlName) :buttonControl
2805	String ctrlName
2806
2807	Execute "V_CombineDataGraph()"
2808	return(0)
2809	end
2810
2811	//
2812	// export protocol to a data file
2813	//
2814	//
2815	Function V_ExportFileProtocol(ctrlName) : ButtonControl
2816	String ctrlName
2817	// get a list of protocols
2818	String Protocol=""
2819	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
2820	Prompt Protocol "Pick A Protocol",popup, V_DeletableProtocols()
2821	DoPrompt "Pick A Protocol to Export",Protocol
2822	if(V_flag==1)
2823	//Print "user cancel"
2824	SetDatafolder root:
2825	return(1)
2826	endif
2827
2828	String fileName = V_DoSaveFileDialog("pick the file to write to")
2829	print fileName
2830	//
2831	if(strlen(fileName) == 0)
2832	return(0)
2833	endif
2834
2835	V_writeReductionProtocolWave(fileName,$("root:Packages:NIST:VSANS:Globals:Protocols:"+Protocol) )
2836
2837	setDataFolder root:
2838	return(0)
2839
2840	End
2841
2842	//
2843	// imports a protocol from a file on disk into the protocols folder
2844	//
2845	//
2846	Function V_ImportFileProtocol(ctrlName) : ButtonControl
2847	String ctrlName
2848
2849	// SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
2850
2851	String fullPath,fileName
2852	fullPath = DoOpenFileDialog("Import Protocol from file")
2853	print fullPath
2854	//
2855	if(strlen(fullPath) == 0)
2856	return(0)
2857	endif
2858
2859	fileName = ParseFilePath(0, fullPath, ":", 1, 0) //just the file name at the end of the full path
2860
2861	Wave/T tmpW = V_getReductionProtocolWave(fileName)
2862	if(numpnts(tmpW) == 0)
2863	DoAlert 0,"No protocol wave has been saved to this data file"
2864	return(0)
2865	endif
2866
2867	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
2868	String newName
2869	newName = CleanupName(fileName,0) + "_proto"
2870	duplicate/o tmpw $newName
2871
2872
2873	SetDataFolder root:
2874	return(0)
2875	end
2876
2877
2878	// currently not used - and not updated to 12 point protocols (5/2017)
2879	//
2880	//save the protocol as an IGOR text wave (.itx)
2881	//
2882	//
2883	Function V_ExportProtocol(ctrlName) : ButtonControl
2884	String ctrlName
2885	// get a list of protocols
2886	String Protocol=""
2887	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
2888	Prompt Protocol "Pick A Protocol",popup, WaveList("*",";","")
2889	DoPrompt "Pick A Protocol to Export",Protocol
2890	if(V_flag==1)
2891	//Print "user cancel"
2892	SetDatafolder root:
2893	return(1)
2894	endif
2895	//get the selection, or exit
2896	Wave/T pW= $protocol
2897	Make/O/T/N=13 tw
2898	// save in the proper format (must write manually, for demo version)
2899	tw[0] = "IGOR"
2900	tw[1] = "WAVES/T \t"+protocol
2901	tw[2] = "BEGIN"
2902	tw[3,10] = "\t\""+pW[p-3]+"\""
2903	tw[11] = "END"
2904	tw[12] = "X SetScale/P x 0,1,\"\","+protocol+"; SetScale y 0,0,\"\","+protocol
2905
2906	Variable refnum
2907	String fullPath
2908
2909	PathInfo/S catPathName
2910	fullPath = DoSaveFileDialog("Export Protocol as",fname=Protocol,suffix="")
2911	If(cmpstr(fullPath,"")==0)
2912	//user cancel, don't write out a file
2913	Close/A
2914	Abort "no Protocol file was written"
2915	Endif
2916
2917	//actually open the file
2918	Open refNum as fullpath+".itx"
2919
2920	wfprintf refnum, "%s\r", tw
2921	Close refnum
2922	//Print "all is well ",protocol
2923	KillWaves/Z tw
2924	setDataFolder root:
2925	return(0)
2926
2927	End
2928
2929
2930	// currently not used - and not updated to 12 point protocols (5/2017)
2931	//imports a protocol from disk into the protocols folder
2932	//
2933	// will overwrite existing protocols if necessary
2934	//
2935	//
2936	Function V_ImportProtocol(ctrlName) : ButtonControl
2937	String ctrlName
2938
2939	SetDataFolder root:Packages:NIST:VSANS:Globals:Protocols
2940
2941	String fullPath
2942
2943	PathInfo/S catPathName
2944	fullPath = DoOpenFileDialog("Import Protocol")
2945	If(cmpstr(fullPath,"")==0)
2946	//user cancel, don't write out a file
2947	Close/A
2948	Abort "no protocol was loaded"
2949	Endif
2950
2951	LoadWave/O/T fullPath
2952
2953	SetDataFolder root:
2954	return(0)
2955	end

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