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LakeDesmearing_JB.ipf @ 625

Last change on this file since 625 was 624, checked in by ajj, 13 years ago
Implement XML writing in USANS reduction
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1	#pragma rtGlobals=1 // Use modern global access method.
2	#pragma Version=2.20
3	#pragma IgorVersion=6.1
4
5	//////////////////////////////////////////////
6	// Igor conversion: 03 FEB 06 SRK
7	// Revision: 03 MAR 06 SRK
8	//
9	// Program uses Lake's iterative technique, J. A. Lake, Acta Cryst. 23 (1967) 191-4.
10	// to DESMEAR Infinite slit smeared USANS DATA.
11	//
12	// TO SEE DESCRIPTION, CHECK COMPUTER SOFTWARE LOGBOOK, P13,41-46, 50
13	// J. BARKER, August, 2001
14	// Switches from fast to slow convergence near target chi JGB 2/2003
15	//
16	// steps are:
17	// load
18	// mask
19	// extrapolate (find the power law of the desmeared set = smeared -1)
20	// smooth (optional)
21	// desmear based on dQv and chi^2 target
22	// save result
23	//
24	/////////
25	// Waves produced at each step: (Q/I/S with the following extensions)
26	//
27	// Load: Uses -> nothing (Kills old waves)
28	// Produces -> "_exp" and "_exp_orig"
29	//
30	// Mask: Uses -> "_exp"
31	// Produces -> "_msk"
32	//
33	// Extrapolate: Uses -> nothing
34	// Produces -> nothing
35	//
36	// Smooth: Uses -> "_smth" OR "_msk" OR "_exp" (in that order)
37	// Produces -> "_smth"
38	//
39	// Desmear: Uses -> "_smth" OR "_msk" OR "_exp" (in that order)
40	// Produces -> "_dsm"
41	//
42	////////
43
44	///*** TO FIX *****
45	// - ? power law + background extrapolation (only useful for X-ray data...)
46	//
47	// see commented code lines for Igor 4 or Igor 5
48	// - there are only a few options and calls that are not Igor 4 compatible.
49	// Igor 4 routines are currently used.
50
51	////////////////////////////////////////////////////////////////////////
52
53	// main entry routine
54	Proc Desmear()
55
56	String USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
57
58	//check for the correct data folder, initialize if necessary
59	//
60	if(DataFolderExists(USANSFolder+":DSM") == 0)
61	Execute "Init_Desmearing()"
62	endif
63
64	SetDataFolder $(USANSFolder+":DSM")
65	//always initialize these global variables
66	gStr1 = ""
67	gStr2 = ""
68	gIterStr = ""
69	SetDataFolder root:
70
71	DoWindow/F Desmear_Graph
72	if(V_flag==0)
73	Execute "Desmear_Graph()"
74	endif
75	End
76
77	Proc Init_Desmearing()
78
79	String USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
80
81	//set up the folder(s) needed
82	NewDataFolder/O $(USANSFolder+":DSM")
83	NewDataFolder/O $(USANSFolder+":myGlobals") //in case it wasn't created elsewhere
84
85	SetDataFolder $(USANSFolder+":DSM")
86
87	String/G gCurFile=""
88
89	Variable/G gMaxFastIter = 100 //max number of iter in Fast convergence
90	Variable/G gMaxSlowIter = 10000
91
92	Variable/G gNptsExtrap = 10 //points for high q extrapolation
93	Variable/G gChi2Target = 1 //chi^2 target
94	Variable/G gPowerM = -4
95	Variable/G gDqv = 0.117 //2005 measured slit height - see John
96	Variable/G gNq = 1
97	Variable/G gS = 0 // global varaible for Midpnt()
98	Variable/G gSmoothFac=0.03
99
100	Variable/G gChi2Final = 0 //chi^2 final
101	Variable/G gIterations = 0 //total number of iterations
102
103	String/G gStr1 = "" //information strings
104	String/G gStr2 = ""
105	String/G gIterStr = ""
106	Variable/G gChi2Smooth = 0
107
108	Variable/G gFreshMask=1
109
110	SetDataFolder root:
111	End
112
113	//////////// Lake desmearing routines
114
115	// Smears guess Y --> YS using weighting array
116	Function DSM_Smear(Y_wave,Ys,NQ,FW)
117	Wave Y_wave,Ys
118	Variable nq
119	Wave FW
120
121	Variable ii,jj,summ
122	for(ii=0;ii<nq;ii+=1)
123	summ=0
124	for(jj=0;jj<nq;jj+=1)
125	summ = summ + Y_wave[jj]*FW[ii][jj]
126	endfor
127	Ys[ii] = summ
128	endfor
129
130	Return (0)
131	End
132
133	// CALCULATES CHI^2
134	FUNCTION CHI2(ys_new,ys_exp,w,NQ)
135	Wave ys_new,ys_exp,w
136	Variable nq
137
138	Variable CHI2,summ,ii
139
140	SUMm = 0.0
141	for(ii=0;ii<nq;ii+=1)
142	// if(numtype(YS_EXP[ii]) == 0 && numtype(YS_NEW[ii]) == 0)
143	SUMm=SUMm+W[ii]*(YS_EXP[ii]-YS_NEW[ii])^2
144	// endif
145	endfor
146
147	CHI2=SUMm/(NQ-1)
148
149	RETURN CHI2
150	END
151
152	// Routine calculates the weights needed to convert a table
153	// representation of a scattering function I(q) into the infinite
154	// slit smeared table represented as Is(q)
155	// Is(qi) = Sum(j=i-n) Wij*I(qj)
156	// Program assumes data is extrapolated from qn to dqv using powerlaw
157	// I(q) = Aq^m
158	// Required input:
159	// N : Number of data points {in Global common block }
160	// q(N) : Array of q values {in Global common block }
161	// dqv : Limit of slit length {in Global common block }
162	// m : powerlaw for extrapolation.
163	//
164	// Routine output:
165	// W(N,N) : Weights array
166	//
167	// The weights obtained from this routine can be used to calculate
168	// Is(q) for any I(q) function.
169	//
170	// Calculation based upon linear interpolation between points.
171	// See p.44, Computer Software Log book.
172	// 11/00 JGB
173	Function Weights_L(m,FW,Q_exp) //changed input w to FW (FW is two dimensional)
174	Variable m
175	Wave FW,Q_exp
176
177	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
178
179	NVAR dqv = $(USANSFolder+":DSM:gDqv")
180	NVAR NN = $(USANSFolder+":DSM:gNq")
181
182	// Calculate Remainder fractions and put into separate array.
183	Variable lower,ii,ss,jj
184	Duplicate/O Q_exp $(USANSFolder+":DSM:R_wave")
185	wave r_wave = $(USANSFolder+":DSM:R_wave")
186
187	// Make/O/D/N=75 root:DSM:SS_save //debug
188	// wave SS_save = root:DSM:SS_save
189
190	Print "calculating remainders by integration..."
191	for(ii=0;ii<NN-1;ii+=1)
192	lower = sqrt(Q_exp[NN-1]^2-Q_exp[ii]^2)
193	ss = Qromo(lower,dqv,Q_exp[ii],m) //new parameter list for Qromo call
194	// SS_save[ii] = ss
195	R_wave[ii] = (Q_exp[NN-1]^(-m)/dqv)*SS
196	// Printf "I = %d R_wave[ii] =%g\r",ii,R_wave[ii]
197	endfor
198
199	lower = 0.0
200	ss = Qromo(lower,dqv,Q_exp[NN-1],m) //new parameter list for Qromo call
201	R_wave[NN-1] = (Q_exp[NN-1]^(-m)/dqv)*SS
202	// Printf "I = %d R_wave[ii] =%g\r",NN-1,R_wave[NN-1]
203	// SS_save[ii] = ss
204
205	// Make/O/D/N=(75,75) root:DSM:IG_save //debug
206	// wave IG_save=root:DSM:IG_save
207
208	// Zero weight matrix... then fill it
209	FW = 0
210	Print "calculating full weights...."
211	// Calculate weights
212	for(ii=0;ii<NN;ii+=1)
213	for(jj=ii+1;jj<NN-1;jj+=1)
214	FW[ii][jj] = DU(ii,jj)*(1.0+Q_exp[jj]/(Q_exp[jj+1]-Q_exp[jj]))
215	FW[ii][jj] -= (1.0/(Q_exp[jj+1]-Q_exp[jj]))*IG(ii,jj)
216	FW[ii][jj] -= DU(ii,jj-1)*Q_exp[jj-1]/(Q_exp[jj]-Q_exp[jj-1])
217	FW[ii][jj] += (1.0/(Q_exp[jj]-Q_exp[jj-1]))*IG(ii,jj-1)
218	FW[ii][jj] *= (1.0/dqv)
219	// Printf "FW[%d][%d] = %g\r",ii,jj,FW[ii][jj]
220	endfor
221	endfor
222	//
223	// special case: I=J,I=N
224	for(ii=0;ii<NN-1;ii+=1)
225	FW[ii][ii] = DU(ii,ii)*(1.0+Q_exp[ii]/(Q_exp[ii+1]-Q_exp[ii]))
226	FW[ii][ii] -= (1.0/(Q_exp[ii+1]-Q_exp[ii]))*IG(ii,ii)
227	FW[ii][ii] *= (1.0/dqv)
228	// Printf "FW[%d][%d] = %g\r",ii,jj,FW[ii][jj]
229	// following line corrected for N -> NN-1 since Igor indexes from 0! (Q_exp[NN] DNE!)
230	FW[ii][NN-1] = -DU(ii,NN-2)*Q_exp[NN-2]/(Q_exp[NN-1]-Q_exp[NN-2])
231	FW[ii][NN-1] += (1.0/(Q_exp[NN-1]-Q_exp[NN-2]))*IG(ii,NN-2)
232	FW[ii][NN-1] *= (1.0/dqv)
233	FW[ii][NN-1] += R_wave[ii]
234	// Printf "FW[%d][%d] = %g\r",ii,NN-1,FW[ii][NN-1]
235	endfor
236	//
237	// special case: I=J=N
238	FW[NN-1][NN-1] = R_wave[NN-1]
239	//
240	Return (0)
241	End
242
243	////
244	Function Integrand_dsm(u,qi,m)
245	Variable u,qi,m
246
247	Variable integrand
248	Integrand = (u^2+qi^2)^(m/2)
249	return integrand
250	end
251
252	///
253	Function DU(ii,jj)
254	Variable ii,jj
255
256	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
257
258	Wave Q_exp = $(USANSFolder+":DSM:Q_exp")
259	Variable DU
260
261	// Wave DU_save=root:DSM:DU_save
262	If (ii == jj)
263	DU = sqrt(Q_exp[jj+1]^2-Q_exp[ii]^2)
264	Else
265	DU = sqrt(Q_exp[jj+1]^2-Q_exp[ii]^2) - sqrt(Q_exp[jj]^2-Q_exp[ii]^2)
266	EndIf
267
268	// DU_save[ii][jj] = DU
269	Return DU
270	End
271
272	Function IG(ii,jj)
273	Variable ii,jj
274
275	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
276
277	Wave Q_exp=$(USANSFolder+":DSM:Q_exp")
278	Variable IG,UL,UU
279
280	// WAVE IG_save = root:DSM:IG_save
281	If (ii == jj)
282	UL=0.0
283	Else
284	UL=sqrt(Q_exp[jj]^2-Q_exp[ii]^2)
285	EndIf
286	UU=sqrt(Q_exp[jj+1]^2-Q_exp[ii]^2)
287
288	//in FORTRAN log = natural log....
289	IG = UUQ_exp[jj+1]+Q_exp[ii]^2ln(UU+Q_exp[jj+1])
290	IG -= UL*Q_exp[jj]
291	IG -= Q_exp[ii]^2*ln(UL+Q_exp[jj])
292	IG *= 0.5
293	// IG_save[ii][jj] = IG
294
295	Return IG
296	End
297
298	//
299	Function FF(ii,jj)
300	Variable ii,jj
301
302	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
303
304	Variable FF
305	NVAR dqv = $(USANSFolder+":DSM:gDqv")
306
307	FF = (1.0/dqv)*(0.5+HH(ii,jj))
308	Return FF
309	End
310
311	//
312	Function GG(ii,jj)
313	Variable ii,jj
314
315	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
316
317	Variable GG
318	NVAR dqv = $(USANSFolder+":DSM:gDqv")
319
320	GG = (1.0/dqv)*(0.5-HH(ii,jj))
321	Return GG
322	End
323	//
324	Function HH(ii,jj)
325	Variable ii,jj
326
327	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
328
329	Wave Q_exp=$(USANSFolder+":DSM:Q_exp")
330	Variable HH
331
332	HH = 0.5*(Q_exp[jj+1]+Q_exp[jj])/(Q_exp[jj+1]-Q_exp[jj])
333	HH -= (1.0/(Q_exp[jj+1]-Q_exp[jj]))*(CC(ii,jj+1)-CC(ii,jj))
334	return HH
335	End
336	//
337	//
338	Function CC(ii,jj)
339	Variable ii,jj
340
341	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
342
343	wave Q_exp = $(USANSFolder+":DSM:Q_exp")
344	Variable CC
345
346	If (ii == jj)
347	CC = 0.0
348	Else
349	CC = (Q_exp[jj]-Q_exp[ii])^0.5
350	EndIf
351	Return CC
352	End
353
354	// QROMO is a gerneric NR routine that takes function arguments
355	// Call Qromo(Integrand,lower,dqv,Q_exp(N),m,SS,Midpnt)
356	// -- here, it is always called with Integrand and Midpnt as the functions
357	// -- so rewrite in a simpler way....
358	//
359	// SS is the returned value?
360	// H_wave, S_wave (original names H,S)
361	//
362	// modified using c-version in NR (pg 143)
363	Function QROMO(A,B,qi,m)
364	Variable A,B,qi,m
365
366	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
367
368	Variable EPS,JMAX,JMAXP,KM,K
369	EPS=1.E-6
370	JMAX=14
371	KM=4
372	K=KM+1
373
374	Make/O/D/N=(JMAX) $(USANSFolder+":DSM:S_wave")
375	Make/O/D/N=(JMAX+1) $(USANSFolder+":DSM:H_wave")
376	wave S_wave=$(USANSFolder+":DSM:S_wave")
377	wave H_wave=$(USANSFolder+":DSM:H_wave")
378	S_wave=0
379	H_wave=0
380
381	H_Wave[0] = 1
382
383	variable jj,SS,DSS
384
385	for(jj=0;jj<jmax;jj+=1)
386	S_wave[jj] = Midpnt(A,B,jj,qi,m) //remove FUNC, always call Integrand from within Midpnt
387	IF (jj>=KM) //after 1st 5 points calculated
388	POLINT(H_wave,S_wave,jj-KM,KM,0.0,SS,DSS) //ss, dss returned
389	IF (ABS(DSS) < EPS*ABS(SS))
390	RETURN ss
391	endif
392	ENDIF
393	// S_wave[jj+1]=S_wave[jj]
394	H_wave[jj+1]=H_wave[jj]/9.
395	endfor
396
397	DoAlert 0,"Too many steps in QROMO"
398	return 1 //error if you get here
399	END
400
401	//
402	// see NR pg 109
403	// - Given input arrays xa[1..n] and ya[1..n], and a given value x
404	// return a value y and an error estimate dy. if P(x) is the polynomial of
405	// degree N-1 such that P(xai) = yai, then the returned value y=P(x)
406	//
407	// arrays XA[] and YA[] are passed in with an offset of the index
408	// of where to start the interpolation
409	Function POLINT(XA,YA,offset,N,X,Y,DY)
410	Wave XA,YA
411	Variable offset,N,X,&Y,&DY
412
413	Variable ii,mm,nmax,ns,dif,den,ho,hp,wi,dift
414
415	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
416
417	NMAX=10
418
419	Make/O/D/N=(NMAX) $(USANSFolder+":DSM:Ci"),$(USANSFolder+":DSM:Di")
420	wave Ci = $(USANSFolder+":DSM:Ci")
421	wave Di = $(USANSFolder+":DSM:Di")
422
423	NS=1
424	DIF=ABS(X-XA[0])
425	for(ii=0;ii<n;ii+=1)
426	DIFT=ABS(X-XA[ii+offset])
427	IF (DIFT < DIF)
428	NS=ii
429	DIF=DIFT
430	ENDIF
431	Ci[ii]=YA[ii+offset]
432	Di[ii]=YA[ii+offset]
433	endfor
434
435	Y=YA[NS+offset]
436	NS=NS-1
437	for(mm=1;mm<n-1;mm+=1)
438	for(ii=0;ii<(n-mm);ii+=1)
439	HO=XA[ii+offset]-X
440	HP=XA[ii+offset+mm]-X
441	Wi=Ci[ii+1]-Di[ii]
442	DEN=HO-HP
443	IF(DEN == 0.)
444	print "den == 0 in POLINT - ERROR!!!"
445	endif
446	DEN=Wi/DEN
447	Di[ii]=HP*DEN
448	Ci[ii]=HO*DEN
449	endfor //ii
450	IF (2*NS < (N-mm) )
451	DY=Ci[NS+1]
452	ELSE
453	DY=Di[NS]
454	NS=NS-1
455	ENDIF
456	Y=Y+DY
457	endfor //mm
458	RETURN (0) //y and dy are returned as pass-by-reference
459	END
460
461	//
462	// FUNC is always Integrand()
463	// again, see the c-version, NR pg 142
464	Function MIDPNT(A,B,N,qi,m)
465	Variable A,B,N,qi,m
466
467	Variable it,tnm,del,ddel,x,summ,jj
468
469	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
470
471	NVAR S_ret = $(USANSFolder+":DSM:gS")
472
473	IF (N == 0)
474	S_ret=(B-A)Integrand_dsm(0.5(A+B),qi,m)
475	// Print "N==0, S_ret = ",s_ret
476	return(S_ret)
477	//IT=1
478	ELSE
479	//AJJ This code is confusing!
480	// it = 1
481	// for(jj=1;jj<n-1;jj+=1)
482	// it *= 3
483	// endfor
484	//AJJ Equivalent and simpler
485	it = 3^(N-1)
486	//
487	TNM=IT
488	DEL=(B-A)/(3.*TNM)
489	DDEL=DEL+DEL
490	X=A+0.5*DEL
491	SUMm=0.
492	for(jj=1;jj<=it;jj+=1)
493	SUMm=SUMm+Integrand_dsm(X,qi,m)
494	X=X+DDEL
495	SUMm=SUMm+Integrand_dsm(X,qi,m)
496	X=X+DEL
497	endfor
498	S_ret=(S_ret+(B-A)*SUMm/TNM)/3.
499	IT=3*IT
500	ENDIF
501	return S_ret
502	END
503
504	//////////// end of Lake desmearing routines
505
506	// - Almost everything below here is utility routines for data handling, panel
507	// controls, and all the fluff that makes this useable. Note that this is
508	// a lot more code than the actual guts of the Lake method!
509	// (the guts of the iteration are in the DemsearButtonProc)
510
511
512	// add three "fake" resolution columns to the output file so that it
513	// looks like a regular SANS data set, but make the sigQ column 100x smaller than Q
514	// so that there is effectively no resolution smearing. Set Qbar = Q, and fs = 1
515	//
516	// SRK 06 FEB 06
517	//
518	Function WriteUSANSDesmeared(fullpath,lo,hi,dialog)
519	String fullpath
520	Variable lo,hi,dialog //=1 will present dialog for name
521
522	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
523
524	String termStr="\r\n"
525	String destStr = USANSFolder+":DSM:"
526	String formatStr = "%15.6g %15.6g %15.6g %15.6g %15.6g %15.6g"+termStr
527
528	Variable refNum,integer,realval
529
530	//***these waves MUST EXIST, or IGOR Pro will crash, with a type 2 error**
531	WAVE Q_dsm =$(destStr + "Q_dsm")
532	WAVE I_dsm=$(destStr + "I_dsm")
533	WAVE S_dsm=$(destStr + "S_dsm")
534
535	//check each wave
536	If(!(WaveExists(Q_dsm)))
537	Abort "Q_dsm DNExist in WriteUSANSDesmeared()"
538	Endif
539	If(!(WaveExists(I_dsm)))
540	Abort "I_dsm DNExist in WriteUSANSDesmeared()"
541	Endif
542	If(!(WaveExists(S_dsm)))
543	Abort "S_dsm DNExist in WriteUSANSDesmeared()"
544	Endif
545
546	// 06 FEB 06 SRK
547	// make dummy waves to hold the "fake" resolution, and write it as the last 3 columns
548	//
549	Duplicate/O Q_dsm,res1,res2,res3
550	res3 = 1 // "fake" beamstop shadowing
551	res1 /= 100 //make the sigmaQ so small that there is no smearing
552
553	if(dialog)
554	Open/D refnum as fullpath+".dsm" //won't actually open the file
555	If(cmpstr(S_filename,"")==0)
556	//user cancel, don't write out a file
557	Close/A
558	Abort "no data file was written"
559	Endif
560	fullpath = S_filename
561	Endif
562
563	//write out partial set?
564	Duplicate/O Q_dsm,tq,ti,te
565	ti=I_dsm
566	te=S_dsm
567	if( (lo!=hi) && (lo<hi))
568	redimension/N=(hi-lo+1) tq,ti,te,res1,res2,res3 //lo to hi, inclusive
569	tq=Q_dsm[p+lo]
570	ti=I_dsm[p+lo]
571	te=S_dsm[p+lo]
572	endif
573
574	//tailor the output given the type of data written out...
575	String samStr="",dateStr="",str1,str2
576
577	NVAR m = $(USANSFolder+":DSM:gPowerM") // power law exponent
578	NVAR chiFinal = $(USANSFolder+":DSM:gChi2Final") //chi^2 final
579	NVAR iter = $(USANSFolder+":DSM:gIterations") //total number of iterations
580
581	//get the number of spline passes from the wave note
582	String noteStr
583	Variable boxPass,SplinePass
584	noteStr=note(I_dsm)
585	BoxPass = NumberByKey("BOX", noteStr, "=", ";")
586	splinePass = NumberByKey("SPLINE", noteStr, "=", ";")
587
588	samStr = fullpath
589	dateStr="CREATED: "+date()+" at "+time()
590	sprintf str1,"Chi^2 = %g PowerLaw m = %4.2f Iterations = %d",chiFinal,m,iter
591	sprintf str2,"%d box smooth passes and %d smoothing spline passes",boxPass,splinePass
592
593
594	//actually open the file
595	Open refNum as fullpath
596
597	fprintf refnum,"%s"+termStr,samStr
598	fprintf refnum,"%s"+termStr,str1
599	fprintf refnum,"%s"+termStr,str2
600	fprintf refnum,"%s"+termStr,dateStr
601
602	wfprintf refnum, formatStr, tq,ti,te,res1,res2,res3
603
604	Close refnum
605
606	Killwaves/Z ti,tq,te,res1,res2,res3
607
608	Return(0)
609	End
610
611	/// procedures to do the extrapolation to high Q
612	// very similar to the procedures in the Invariant package
613	//
614	//create the wave to extrapolate
615	// w is the input q-values
616	Function DSM_SetExtrWaves(w)
617	Wave w
618
619	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
620
621	Variable num_extr=25
622
623	SetDataFolder $(USANSFolder+":DSM")
624
625	Make/O/D/N=(num_extr) extr_hqq,extr_hqi
626	extr_hqi=1 //default values
627
628	//set the q-range
629	Variable qmax,num
630	// qmax=0.03
631
632	num=numpnts(w)
633	qmax=6*w[num-1]
634
635	extr_hqq = w[num-1] + x * (qmax-w[num-1])/num_extr
636
637	SetDataFolder root:
638	return(0)
639	End
640
641	//creates I_ext,Q_ext,S_ext with extended q-values
642	//
643	// if num_extr == 0 , the input waves are returned as _ext
644	//
645	// !! uses simple linear extrapolation at low Q - just need something
646	// reasonable in the waves to keep from getting smoothing artifacts
647	// - uses power law at high q
648	Function ExtendToSmooth(qw,iw,sw,nbeg,nend,num_extr)
649	Wave qw,iw,sw
650	Variable nbeg,nend,num_extr
651
652	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
653
654	Variable/G V_FitMaxIters=300
655	Variable/G V_fitOptions=4 //suppress the iteration window
656	Variable num_new,qmax,num,qmin
657	num=numpnts(qw)
658
659	num_new = num + 2*num_extr
660
661	// Print "num,num_new",num,num_new
662
663	SetDataFolder $(USANSFolder+":DSM")
664	Make/O/D/N=(num_new) Q_ext,I_ext,S_ext
665
666	if(num_extr == 0) //the extended waves are the input, get out
667	Q_ext = qw
668	I_ext = iw
669	S_ext = sw
670	setDatafolder root:
671	return (0)
672	endif
673
674	//make the extensions
675	Make/O/D/N=(num_extr) hqq,hqi,lqq,lqi
676	hqi=1 //default values
677	lqi=0
678	//set the q-range based on the high/low values of the data set
679	// qmin=1e-6
680	qmin= qw[0]*0.5
681	qmax = qw[num-1]*2
682
683	hqq = qw[num-1] + x * (qmax-qw[num-1])/num_extr
684	lqq = qmin + x * (qw[0]-qmin)/num_extr
685
686	//do the fits
687	Duplicate/O iw dummy //use this as the destination to suppress fit_ from being appended
688
689	//Use simple linear fits line: y = K0+K1*x
690	CurveFit/Q line iw[0,(nbeg-1)] /X=qw /W=sw /D=dummy
691	Wave W_coef=W_coef
692	lqi=W_coef[0]+W_coef[1]*lqq
693	//
694	// Guinier or Power-law fits
695	//
696	// Make/O/D G_coef={100,-100} //input
697	// FuncFit DSM_Guinier_Fit G_coef iw[0,(nbeg-1)] /X=qw /W=sw /D
698	// lqi= DSM_Guinier_Fit(G_coef,lqq)
699
700	// Printf "I(q=0) = %g (1/cm)\r",G_coef[0]
701	// Printf "Rg = %g (A)\r",sqrt(-3*G_coef[1])
702
703	Make/O/D P_coef={0,1,-4} //input --- (set background to zero and hold fixed)
704	CurveFit/Q/N/H="100" Power kwCWave=P_coef iw[(num-1-nend),(num-1)] /X=qw /W=sw /D=dummy
705	hqi=P_coef[0]+P_coef[1]*hqq^P_coef[2]
706
707	// Printf "Power law exponent = %g\r",P_coef[2]
708	// Printf "Pre-exponential = %g\r",P_coef[1]
709
710	// concatenate the extensions
711	Q_ext[0,(num_extr-1)] = lqq[p]
712	Q_ext[num_extr,(num_extr+num-1)] = qw[p-num_extr]
713	Q_ext[(num_extr+num),(2*num_extr+num-1)] = hqq[p-num_extr-num]
714	I_ext[0,(num_extr-1)] = lqi[p]
715	I_ext[num_extr,(num_extr+num-1)] = iw[p-num_extr]
716	I_ext[(num_extr+num),(2*num_extr+num-1)] = hqi[p-num_extr-num]
717	S_ext[0,(num_extr-1)] = sw[0]
718	S_ext[num_extr,(num_extr+num-1)] = sw[p-num_extr]
719	S_ext[(num_extr+num),(2*num_extr+num-1)] = sw[num-1]
720
721	killwaves/z dummy
722	SetDataFolder root:
723	return(0)
724	End
725
726	// pass in the (smeared) experimental data and find the power-law extrapolation
727	// 10 points is usually good enough, unless the data is crummy
728	// returns the prediction for the exponent
729	//
730	Function DSM_DoExtrapolate(qw,iw,sw,nend)
731	Wave qw,iw,sw
732	Variable nend
733
734	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
735
736	Setdatafolder $(USANSFolder+":DSM")
737
738	// Wave extr_lqi=extr_lqi
739	// Wave extr_lqq=extr_lqq
740	Wave extr_hqi=extr_hqi
741	Wave extr_hqq=extr_hqq
742	Variable/G V_FitMaxIters=300
743	Variable/G V_fitOptions=4 //suppress the iteration window
744	Variable num=numpnts(iw),retVal
745
746	Make/O/D P_coef={0,1,-4} //input
747	// Make/O/T Constr={"K2<0","K2 > -20"}
748	//(set background to zero and hold fixed)
749	CurveFit/H="100" Power kwCWave=P_coef iw[(num-1-nend),(num-1)] /X=qw /W=sw /D
750	extr_hqi=P_coef[0]+P_coef[1]*extr_hqq^P_coef[2]
751
752	// for the case of data with a background
753	// Make/O/D P_coef={0,1,-4} //input
754	// //(set background to iw[num-1], let it be a free parameter
755	// P_coef[0] = iw[num-1]
756	// CurveFit Power kwCWave=P_coef iw[(num-1-nend),(num-1)] /X=qw /W=sw /D
757	// extr_hqi=P_coef[0]+P_coef[1]*extr_hqq^P_coef[2]
758
759
760	Printf "Smeared Power law exponent = %g\r",P_coef[2]
761	Printf "**** For Desmearing, use a Power law exponent of %5.1f\r",P_coef[2]-1
762
763	retVal = P_coef[2]-1
764	SetDataFolder root:
765	return(retVal)
766	End
767
768	Function DSM_Guinier_Fit(w,x) //: FitFunc
769	Wave w
770	Variable x
771
772	//fit data to I(q) = Aexp(Bq^2)
773	// (B will be negative)
774	//two parameters
775	Variable a,b,ans
776	a=w[0]
777	b=w[1]
778	ans = aexp(bx*x)
779	return(ans)
780	End
781
782	Proc Desmear_Graph()
783	String USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
784
785	PauseUpdate; Silent 1 // building window...
786	Display /W=(5,44,408,558) /K=1
787	ModifyGraph cbRGB=(51664,44236,58982)
788	DoWindow/C Desmear_Graph
789	ControlBar 160
790	// break into tabs
791	TabControl DSM_Tab,pos={5,3},size={392,128},proc=DSM_TabProc
792	TabControl DSM_Tab,labelBack=(49151,49152,65535),tabLabel(0)="Load"
793	TabControl DSM_Tab,tabLabel(1)="Mask",tabLabel(2)="Extrapolate"
794	TabControl DSM_Tab,tabLabel(3)="Smooth",tabLabel(4)="Desmear",value= 0
795
796	//always visible - revert and save
797	//maybe the wrong place here?
798	Button DSMControlA,pos={225,135},size={80,20},proc=DSM_RevertButtonProc,title="Revert"
799	Button DSMControlA,help={"Revert the smeared data to its original state and start over"}
800	Button DSMControlB,pos={325,135},size={50,20},proc=DSM_SaveButtonProc,title="Save"
801	Button DSMControlB,help={"Save the desmeared data set"}
802	Button DSMControlC,pos={25,135},size={50,20},proc=DSM_HelpButtonProc,title="Help"
803	Button DSMControlC,help={"Show the help file for desmearing"}
804
805	// add the controls to each tab ---- all names start with "DSMControl_"
806
807	//tab(0) Load - initially visible
808	Button DSMControl_0a,pos={23,39},size={80,20},proc=DSM_LoadButtonProc,title="Load Data"
809	Button DSMControl_0a,help={"Load slit-smeared USANS data = \".cor\" files"}
810	CheckBox DSMControl_0b,pos={26,74},size={80,14},proc=DSM_LoadCheckProc,title="Log Axes?"
811	CheckBox DSMControl_0b,help={"Toggle Log/Lin Q display"},value= 1
812	TitleBox DSMControl_0c,pos={120,37},size={104,19},font="Courier",fSize=10
813	TitleBox DSMControl_0c,variable= $(USANSFolder+":DSM:gStr1")
814	//second message string not used currently
815	// TitleBox DSMControl_0d,pos={120,57},size={104,19},font="Courier",fSize=10
816	// TitleBox DSMControl_0d,variable= root:DSM:gStr2
817
818	//tab(1) Mask
819	Button DSMControl_1a,pos={20,35},size={90,20},proc=DSM_MyMaskProc,title="Mask Point" //bMask
820	Button DSMControl_1a,help={"Toggles the masking of the selected data point"}
821	Button DSMControl_1a,disable=1
822	Button DSMControl_1b,pos={20,65},size={140,20},proc=DSM_MaskGTCursor,title="Mask Q >= Cursor" //bMask
823	Button DSMControl_1b,help={"Toggles the masking of all q-values GREATER than the current cursor location"}
824	Button DSMControl_1b,disable=1
825	Button DSMControl_1c,pos={20,95},size={140,20},proc=DSM_MaskLTCursor,title="Mask Q <= Cursor" //bMask
826	Button DSMControl_1c,help={"Toggles the masking of all q-values LESS than the current cursor location"}
827	Button DSMControl_1c,disable=1
828	Button DSMControl_1d,pos={180,35},size={90,20},proc=DSM_ClearMaskProc,title="Clear Mask" //bMask
829	Button DSMControl_1d,help={"Clears all mask points"}
830	Button DSMControl_1d,disable=1
831	// Button DSMControl_1b,pos={144,66},size={110,20},proc=DSM_MaskDoneButton,title="Done Masking"
832	// Button DSMControl_1b,disable=1
833
834	//tab(2) Extrapolate
835	Button DSMControl_2a,pos={31,42},size={90,20},proc=DSM_ExtrapolateButtonProc,title="Extrapolate"
836	Button DSMControl_2a,help={"Extrapolate the high-q region with a power-law"}
837	Button DSMControl_2a,disable=1
838	SetVariable DSMControl_2b,pos={31,70},size={100,15},title="# of points"
839	SetVariable DSMControl_2b,help={"Set the number of points for the power-law extrapolation"}
840	SetVariable DSMControl_2b,limits={5,100,1},value= $(USANSFolder+":DSM:gNptsExtrap")
841	SetVariable DSMControl_2b,disable=1
842	CheckBox DSMControl_2c,pos={157,45},size={105,14},proc=DSM_ExtrapolationCheckProc,title="Show Extrapolation"
843	CheckBox DSMControl_2c,help={"Show or hide the high q extrapolation"},value= 1
844	CheckBox DSMControl_2c,disable=1
845	SetVariable DSMControl_2d,pos={31,96},size={150,15},title="Power Law Exponent"
846	SetVariable DSMControl_2d,help={"Power Law exponent from the fit = the DESMEARED slope - override as needed"}
847	SetVariable DSMControl_2d format="%5.2f"
848	SetVariable DSMControl_2d,limits={-inf,inf,0},value= $(USANSFolder+":DSM:gPowerM")
849	SetVariable DSMControl_2d,disable=1
850
851	//tab(3) Smooth
852	Button DSMControl_3a,pos={34,97},size={70,20},proc=DSM_SmoothButtonProc,title="Smooth"
853	Button DSMControl_3a,disable=1
854	//BoxCheck
855	CheckBox DSMControl_3b,pos={34,39},size={35,14},title="Box",value= 1
856	CheckBox DSMControl_3b,help={"Use a single pass of 3-point box smoothing"}
857	CheckBox DSMControl_3b,disable=1
858	//SSCheck
859	CheckBox DSMControl_3c,pos={34,60},size={45,14},title="Spline",value= 0
860	CheckBox DSMControl_3c,help={"Use a single pass of a smoothing spline"}
861	CheckBox DSMControl_3c,disable=1
862	//extendCheck
863	CheckBox DSMControl_3d,pos={268,60},size={71,14},title="Extend Data"
864	CheckBox DSMControl_3d,help={"extends the data at both low q and high q to avoid end effects in smoothing"}
865	CheckBox DSMControl_3d,value= 0
866	CheckBox DSMControl_3d,disable=1
867	Button DSMControl_3e,pos={125,97},size={90,20},proc=DSM_SmoothUndoButtonProc,title="Start Over"
868	Button DSMControl_3e,help={"Start the smoothing over again without needing to re-mask the data set"}
869	Button DSMControl_3e,disable=1
870	SetVariable DSMControl_3f,pos={94,60},size={150,15},title="Smoothing factor"
871	SetVariable DSMControl_3f,help={"Smoothing factor for the smoothing spline"}
872	SetVariable DSMControl_3f format="%5.4f"
873	SetVariable DSMControl_3f,limits={0.01,2,0.01},value= $(USANSFolder+":DSM:gSmoothFac")
874	SetVariable DSMControl_3f,disable=1
875	CheckBox DSMControl_3g,pos={268,39},size={90,14},title="Log-scale smoothing?"
876	CheckBox DSMControl_3g,help={"Use log-scaled intensity during smoothing (reverts to linear if negative intensity points found)"}
877	CheckBox DSMControl_3g,value=0
878	CheckBox DSMControl_3g,disable=1
879	ValDisplay DSMControl_3h pos={235,97},title="Chi^2",size={80,20},value=root:Packages:NIST:USANS:DSM:gChi2Smooth
880	ValDisplay DSMControl_3h,help={"This is the Chi^2 value for the smoothed data vs experimental data"}
881	ValDisplay DSMControl_3h,disable=1
882
883	//tab(4) Desmear
884	Button DSMControl_4a,pos={35,93},size={80,20},proc=DSM_DesmearButtonProc,title="Desmear"
885	Button DSMControl_4a,help={"Do the desmearing - the result is in I_dsm"}
886	Button DSMControl_4a,disable=1
887	SetVariable DSMControl_4b,pos={35,63},size={120,15},title="Chi^2 target"
888	SetVariable DSMControl_4b,help={"Set the targetchi^2 for convergence (recommend chi^2=1)"}
889	SetVariable DSMControl_4b,limits={0,inf,0.1},value= $(USANSFolder+":DSM:gChi2Target")
890	SetVariable DSMControl_4b,disable=1
891	SetVariable DSMControl_4c,pos={35,35},size={80,15},title="dQv"
892	SetVariable DSMControl_4c,help={"Slit height as read in from the data file. 0.117 is the NIST value, override if necessary"}
893	SetVariable DSMControl_4c,limits={-inf,inf,0},value= $(USANSFolder+":DSM:gDqv")
894	SetVariable DSMControl_4c,disable=1
895	TitleBox DSMControl_4d,pos={160,37},size={104,19},font="Courier",fSize=10
896	TitleBox DSMControl_4d,variable= $(USANSFolder+":DSM:gIterStr")
897	TitleBox DSMControl_4d,disable=1
898
899
900	SetDataFolder root:
901	EndMacro
902
903	// function to control the drawing of buttons in the TabControl on the main panel
904	// Naming scheme for the buttons MUST be strictly adhered to... else buttons will
905	// appear in odd places...
906	// all buttons are named DSMControl_NA where N is the tab number and A is the letter denoting
907	// the button's position on that particular tab.
908	// in this way, buttons will always be drawn correctly :-)
909	//
910	Function DSM_TabProc(ctrlName,tab) //: TabControl
911	String ctrlName
912	Variable tab
913
914	String ctrlList = ControlNameList("",";"),item="",nameStr=""
915	Variable num = ItemsinList(ctrlList,";"),ii,onTab
916	for(ii=0;ii<num;ii+=1)
917	//items all start w/"DSMControl_" //11 characters
918	item=StringFromList(ii, ctrlList ,";")
919	nameStr=item[0,10]
920	if(cmpstr(nameStr,"DSMControl_")==0)
921	onTab = str2num(item[11]) //12th is a number
922	ControlInfo $item
923	switch(abs(V_flag))
924	case 1:
925	Button $item,disable=(tab!=onTab)
926	break
927	case 2:
928	CheckBox $item,disable=(tab!=onTab)
929	break
930	case 5:
931	SetVariable $item,disable=(tab!=onTab)
932	break
933	case 10:
934	TitleBox $item,disable=(tab!=onTab)
935	break
936	case 4:
937	ValDisplay $item,disable=(tab!=onTab)
938	break
939	// add more items to the switch if different control types are used
940	endswitch
941
942	endif
943	endfor
944
945	if(tab==1)
946	DSM_MyMaskProc("") //start maksing if you click on the tab
947	else
948	DSM_MaskDoneButton("") //masking is done if you click off the tab
949	endif
950
951	return 0
952	End
953
954	Proc AppendSmeared()
955	String USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
956
957	SetDataFolder $(USANSFolder+":DSM")
958	// if( strsearch(TraceNameList("Desmear_Graph", "", 1),"I_exp_orig",0,2) == -1) //Igor 5
959	if( strsearch(TraceNameList("Desmear_Graph", "", 1),"I_exp_orig",0) == -1)
960	AppendToGraph/W=Desmear_Graph I_exp_orig vs Q_exp_orig
961	ModifyGraph mode=4,marker=19 //3 is markers, 4 is markers and lines
962	ModifyGraph rgb(I_exp_orig)=(0,0,0)
963	ModifyGraph msize=2,grid=1,log=1,mirror=2,standoff=0,tickunit=1
964	ErrorBars/T=0 I_exp_orig Y,wave=(S_exp_orig,S_exp_orig)
965	Legend/N=text0/J "\\F'Courier'\\s(I_exp_orig) I_exp_orig"
966	Label left "Intensity"
967	Label bottom "Q (1/A)"
968	endif
969	//always update the textbox - kill the old one first
970	TextBox/K/N=text1
971	// TextBox/C/N=text1/F=0/A=MT/E=2/X=5.50/Y=0.00 root:DSM:gCurFile //Igor 5
972	TextBox/C/N=text1/F=0/A=MT/E=1/X=5.50/Y=0.00 $(USANSFolder+":DSM:gCurFile")
973	End
974
975	Proc AppendMask()
976	String USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
977
978	// if( strsearch(TraceNameList("Desmear_Graph", "", 1),"MaskData",0,2) == -1) //Igor 5
979	if( strsearch(TraceNameList("Desmear_Graph", "", 1),"MaskData",0) == -1)
980	SetDataFolder $(USANSFolder+":DSM:")
981	AppendToGraph/W=Desmear_Graph MaskData vs Q_exp_orig
982	ModifyGraph mode(MaskData)=3,marker(MaskData)=8,msize(MaskData)=2.5,opaque(MaskData)=1
983	ModifyGraph rgb(MaskData)=(65535,16385,16385)
984	setdatafolder root:
985	endif
986	end
987
988	Proc AppendSmoothed()
989	String USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
990
991	// if( strsearch(TraceNameList("Desmear_Graph", "", 1),"I_smth",0,2) == -1) //Igor 5
992	if( strsearch(TraceNameList("Desmear_Graph", "", 1),"I_smth",0) == -1)
993	SetDataFolder $(USANSFolder+":DSM:")
994	AppendToGraph/W=Desmear_Graph I_smth vs Q_smth
995	ModifyGraph/W=Desmear_Graph rgb(I_smth)=(3,52428,1),lsize(I_smth)=2
996	setdatafolder root:
997	endif
998	end
999
1000	Function RemoveSmoothed()
1001	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1002
1003	SetDataFolder $(USANSFolder+":DSM:")
1004	RemoveFromGraph/W=Desmear_Graph/Z I_smth
1005	setdatafolder root:
1006	end
1007
1008	Function RemoveMask()
1009	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1010
1011	SetDataFolder $(USANSFolder+":DSM:")
1012	RemoveFromGraph/W=Desmear_Graph/Z MaskData
1013	setdatafolder root:
1014	end
1015
1016	Proc AppendDesmeared()
1017	String USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1018
1019	// if( strsearch(TraceNameList("Desmear_Graph", "", 1),"I_dsm",0,2) == -1) //Igor 5
1020	if( strsearch(TraceNameList("Desmear_Graph", "", 1),"I_dsm",0) == -1)
1021	SetDataFolder $(USANSFolder+":DSM:")
1022	AppendToGraph/W=Desmear_Graph I_dsm vs Q_dsm
1023	ModifyGraph mode(I_dsm)=3,marker(I_dsm)=19
1024	ModifyGraph rgb(I_dsm)=(1,16019,65535),msize(I_dsm)=2
1025	ErrorBars/T=0 I_dsm Y,wave=(S_dsm,S_dsm)
1026	setdatafolder root:
1027	endif
1028	end
1029
1030	Function RemoveDesmeared()
1031	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1032
1033	SetDataFolder $(USANSFolder+":DSM:")
1034	RemoveFromGraph/W=Desmear_Graph/Z I_dsm
1035	setdatafolder root:
1036	end
1037
1038	Function AppendExtrapolation()
1039	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1040
1041	// if( strsearch(TraceNameList("Desmear_Graph", "", 1),"extr_hqi",0,2) == -1) //Igor 5
1042	if( strsearch(TraceNameList("Desmear_Graph", "", 1),"extr_hqi",0) == -1)
1043	SetDataFolder $(USANSFolder+":DSM:")
1044	AppendToGraph/W=Desmear_Graph extr_hqi vs extr_hqq
1045	ModifyGraph/W=Desmear_Graph lSize(extr_hqi)=2
1046	setdatafolder root:
1047	endif
1048	end
1049
1050	Function RemoveExtrapolation()
1051	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1052
1053	SetDataFolder $(USANSFolder+":DSM:")
1054	RemoveFromGraph/W=Desmear_Graph/Z extr_hqi
1055	setdatafolder root:
1056	end
1057
1058	// step (1) - read in the data, and plot it
1059	// clear out all of the "old" waves, remove them from the graph first
1060	// reads in a fresh copy of the data
1061	//
1062	// produces Q_exp, I_exp, S_exp waves (and originals "_orig")
1063	// add a dummy wave note that can be changed on later steps
1064	//
1065	Function DSM_LoadButtonProc(ctrlName) : ButtonControl
1066	String ctrlName
1067
1068	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1069
1070	String qStr,iStr,sStr,sqStr
1071	Variable nq,dqv,numBad,val
1072
1073	// remove any of the old traces on the graph and delete the waves
1074	CleanUpJunk()
1075
1076	SetDataFolder root:
1077	Execute "A_LoadOneDDataWithName(\"\",0)"
1078	//define the waves that the smoothing will be looking for...
1079	SVAR fname = $("root:Packages:NIST:gLastFileName") //this changes as any data is loaded
1080	SVAR curFile = $(USANSFolder+":DSM:gCurFile") //keep this for title, save
1081	curFile = fname
1082
1083	qStr = CleanupName((fName + "_q"),0) //the q-wave
1084	iStr = CleanupName((fName + "_i"),0) //the i-wave
1085	sStr = CleanupName((fName + "_s"),0) //the s-wave
1086	sqStr = CleanupName((fName + "sq"),0) //the sq-wave, which should have -dQv as the elements
1087
1088	String DFStr= CleanupName(fname,0)
1089
1090	Duplicate/O $("root:"+DFStr+":"+qStr) $(USANSFolder+":DSM:Q_exp ")
1091	Duplicate/O $("root:"+DFStr+":"+iStr) $(USANSFolder+":DSM:I_exp")
1092	Duplicate/O $("root:"+DFStr+":"+sStr) $(USANSFolder+":DSM:S_exp ")
1093	wave Q_exp = $(USANSFolder+":DSM:Q_exp")
1094	Wave I_exp = $(USANSFolder+":DSM:I_exp")
1095	Wave S_exp = $(USANSFolder+":DSM:S_exp")
1096
1097	// remove any negative q-values (and q=0 values!)(and report this)
1098	// ? and trim the low q to be >= 3.0e-5 (1/A), below this USANS is not reliable.
1099	NumBad = RemoveBadQPoints(Q_exp,I_exp,S_exp,0)
1100	SVAR str1 = $(USANSFolder+":DSM:gStr1")
1101	sprintf str1,"%d negative q-values were removed",numBad
1102
1103	// don't trim off any positive q-values
1104	// val = 3e-5 //lowest "good" q-value from USANS
1105	// NumBad = RemoveBadQPoints(Q_exp,I_exp,S_exp,val-1e-8)
1106	// SVAR str2 = root:DSM:gStr2
1107	// sprintf str2,"%d q-values below q = %g were removed",numBad,val
1108
1109	Duplicate/O $(USANSFolder+":DSM:Q_exp") $(USANSFolder+":DSM:Q_exp_orig")
1110	Duplicate/O $(USANSFolder+":DSM:I_exp") $(USANSFolder+":DSM:I_exp_orig")
1111	Duplicate/O $(USANSFolder+":DSM:S_exp") $(USANSFolder+":DSM:S_exp_orig")
1112	wave I_exp_orig = $(USANSFolder+":DSM:I_exp_orig")
1113
1114	nq = numpnts($(USANSFolder+":DSM:Q_exp"))
1115
1116	dQv = NumVarOrDefault("root:"+DFStr+":USANS_dQv", 0.117 )
1117	// if(WaveExists(sigQ)) //try to read dQv
1118	//// dqv = -sigQ[0][0]
1119	//// DoAlert 0,"Found dQv value of " + num2str(dqv)
1120	// else
1121	// dqv = 0.117
1122	// // dqv = 0.037 //old value
1123	// DoAlert 0,"Could not find dQv in the data file - using " + num2str(dqv)
1124	// endif
1125	NVAR gDqv = $(USANSFolder+":DSM:gDqv") //needs to be global for Weights_L()
1126	NVAR gNq = $(USANSFolder+":DSM:gNq")
1127	//reset the globals
1128	gDqv = dqv
1129	gNq = nq
1130
1131	// append the (blank) wave note to the intensity wave
1132	Note I_exp,"BOX=0;SPLINE=0;"
1133	Note I_exp_orig,"BOX=0;SPLINE=0;"
1134
1135	//draw the graph
1136	Execute "AppendSmeared()"
1137
1138	SetDataFolder root:
1139	End
1140
1141	// remove any q-values <= val
1142	Function RemoveBadQPoints(qw,iw,sw,val)
1143	Wave qw,iw,sw
1144	Variable val
1145
1146	Variable ii,num,numBad,qval
1147	num = numpnts(qw)
1148
1149	ii=0
1150	numBad=0
1151	do
1152	qval = qw[ii]
1153	if(qval <= val)
1154	numBad += 1
1155	else //keep the points
1156	qw[ii-numBad] = qval
1157	iw[ii-numBad] = iw[ii]
1158	sw[ii-numBad] = sw[ii]
1159	endif
1160	ii += 1
1161	while(ii<num)
1162	//trim the end of the waves
1163	DeletePoints num-numBad, numBad, qw,iw,sw
1164	return(numBad)
1165	end
1166
1167	// if mw = Nan, keep the point, if a numerical value, delete it
1168	Function RemoveMaskedPoints(mw,qw,iw,sw)
1169	Wave mw,qw,iw,sw
1170
1171	Variable ii,num,numBad,mask
1172	num = numpnts(qw)
1173
1174	ii=0
1175	numBad=0
1176	do
1177	mask = mw[ii]
1178	if(numtype(mask) != 2) //if not NaN
1179	numBad += 1
1180	else //keep the points that are NaN
1181	qw[ii-numBad] = qw[ii]
1182	iw[ii-numBad] = iw[ii]
1183	sw[ii-numBad] = sw[ii]
1184	endif
1185	ii += 1
1186	while(ii<num)
1187	//trim the end of the waves
1188	DeletePoints num-numBad, numBad, qw,iw,sw
1189	return(numBad)
1190	end
1191
1192	// produces the _msk waves that have the new number of data points
1193	//
1194	Function DSM_MaskDoneButton(ctrlName) : ButtonControl
1195	String ctrlName
1196
1197	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1198
1199	// Variable aExists= strlen(CsrInfo(A)) > 0 //Igor 5
1200	Variable aExists= strlen(CsrWave(A)) > 0 //Igor 4
1201	if(!aExists)
1202	return(1) //possibly reverted data, no cursor, no Mask wave
1203	endif
1204
1205	Duplicate/O $(USANSFolder+":DSM:Q_exp_orig"),$(USANSFolder+":DSM:Q_msk")
1206	Duplicate/O $(USANSFolder+":DSM:I_exp_orig"),$(USANSFolder+":DSM:I_msk")
1207	Duplicate/O $(USANSFolder+":DSM:S_exp_orig"),$(USANSFolder+":DSM:S_msk")
1208	Wave Q_msk=$(USANSFolder+":DSM:Q_msk")
1209	Wave I_msk=$(USANSFolder+":DSM:I_msk")
1210	Wave S_msk=$(USANSFolder+":DSM:S_msk")
1211
1212	//finish up - trim the data sets and reassign the working set
1213	Wave MaskData=$(USANSFolder+":DSM:MaskData")
1214
1215	RemoveMaskedPoints(MaskData,Q_msk,I_msk,S_msk)
1216
1217	//reset the number of points
1218	NVAR gNq = $(USANSFolder+":DSM:gNq")
1219	gNq = numpnts(Q_msk)
1220
1221	Cursor/K A
1222	HideInfo
1223
1224	return(0)
1225	End
1226
1227
1228	// not quite the same as revert
1229	Function DSM_ClearMaskProc(ctrlName) : ButtonControl
1230	String ctrlName
1231
1232	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1233
1234	Wave MaskData=$(USANSFolder+":DSM:MaskData")
1235	MaskData = NaN
1236
1237	return(0)
1238	end
1239
1240	// when the mask button is pressed, A must be on the graph
1241	// Displays MaskData wave on the graph
1242	//
1243	Function DSM_MyMaskProc(ctrlName) : ButtonControl
1244	String ctrlName
1245
1246	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1247
1248	Wave data=$(USANSFolder+":DSM:I_exp_orig")
1249
1250	// Variable aExists= strlen(CsrInfo(A)) > 0 //Igor 5
1251	Variable aExists= strlen(CsrWave(A)) > 0 //Igor 4
1252
1253	// need to get rid of old smoothed data if data is re-masked
1254	Execute "RemoveSmoothed()"
1255	SetDataFolder $(USANSFolder+":DSM")
1256	Killwaves/Z I_smth,Q_smth,S_smth
1257
1258	if(aExists) //mask the selected point
1259	// toggle NaN (keep) or Data value (= masked)
1260	Wave MaskData
1261	MaskData[pcsr(A)] = (numType(MaskData[pcsr(A)])==0) ? NaN : data[pcsr(A)] //if NaN, doesn't plot
1262	else
1263	Cursor /A=1/H=1/L=1/P/W=Desmear_Graph A I_exp_orig leftx(I_exp_orig)
1264	ShowInfo
1265	//if the mask wave does not exist, make one
1266	if(exists("MaskData") != 1)
1267	Duplicate/O Q_exp_orig MaskData
1268	MaskData = NaN //use all data
1269	endif
1270	Execute "AppendMask()"
1271	endif
1272
1273	SetDataFolder root:
1274
1275	return(0)
1276	End
1277
1278	// when the mask button is pressed, A must be on the graph
1279	// Displays MaskData wave on the graph
1280	//
1281	Function DSM_MaskLTCursor(ctrlName) : ButtonControl
1282	String ctrlName
1283
1284	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1285
1286	// Variable aExists= strlen(CsrInfo(A)) > 0 //Igor 5
1287	Variable aExists= strlen(CsrWave(A)) > 0 //Igor 4
1288
1289	if(!aExists)
1290	return(1)
1291	endif
1292	// need to get rid of old smoothed data if data is re-masked
1293	Execute "RemoveSmoothed()"
1294	SetDataFolder $(USANSFolder+":DSM")
1295	Killwaves/Z I_smth,Q_smth,S_smth
1296
1297	Wave data=I_exp_orig
1298
1299	Variable pt,ii
1300	pt = pcsr(A)
1301	for(ii=pt;ii>=0;ii-=1)
1302	// toggle NaN (keep) or Data value (= masked)
1303	Wave MaskData
1304	MaskData[ii] = (numType(MaskData[ii])==0) ? NaN : data[ii] //if NaN, doesn't plot
1305	endfor
1306
1307	SetDataFolder root:
1308	return(0)
1309	End
1310
1311	// when the mask button is pressed, A must be on the graph
1312	// Displays MaskData wave on the graph
1313	//
1314	Function DSM_MaskGTCursor(ctrlName) : ButtonControl
1315	String ctrlName
1316
1317	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1318
1319
1320	// Variable aExists= strlen(CsrInfo(A)) > 0 //Igor 5
1321	Variable aExists= strlen(CsrWave(A)) > 0 //Igor 4
1322
1323	if(!aExists)
1324	return(1)
1325	endif
1326	// need to get rid of old smoothed data if data is re-masked
1327	Execute "RemoveSmoothed()"
1328	SetDataFolder $(USANSFolder+":DSM")
1329	Killwaves/Z I_smth,Q_smth,S_smth
1330
1331	Wave data=I_exp_orig
1332
1333	Variable pt,ii,endPt
1334	endPt=numpnts(MaskData)
1335	pt = pcsr(A)
1336	for(ii=pt;ii<endPt;ii+=1)
1337	// toggle NaN (keep) or Data value (= masked)
1338	Wave MaskData
1339	MaskData[ii] = (numType(MaskData[ii])==0) ? NaN : data[ii] //if NaN, doesn't plot
1340	endfor
1341
1342	SetDataFolder root:
1343
1344	return(0)
1345	End
1346
1347	Function CleanUpJunk()
1348	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1349
1350	// clean up the old junk on the graph, /Z for no error
1351	Execute "RemoveExtrapolation()"
1352	Execute "RemoveDesmeared()"
1353	Execute "RemoveSmoothed()"
1354	Execute "RemoveMask()"
1355
1356	//remove the cursor
1357	Cursor/K A
1358
1359	//always initialize these
1360	String/G $(USANSFolder+":DSM:gStr1") = ""
1361	String/G $(USANSFolder+":DSM:gStr2") = ""
1362	String/G $(USANSFolder+":DSM:gIterStr") = ""
1363
1364	// clean up the old waves from smoothing and desmearing steps
1365	SetDataFolder $(USANSFolder+":DSM")
1366	Killwaves/Z I_smth,I_dsm,I_dsm_sm,Q_smth,Q_dsm,S_smth,S_dsm,Yi_SS,Yq_SS
1367	Killwaves/Z Weights,FW,R_wave,S_wave,H_wave,Di,Ci
1368	Killwaves/Z Is_old,I_old,err
1369	Killwaves/Z Q_ext,I_ext,S_ext,hqq,hqi,lqq,lqi
1370	Killwaves/Z MaskData,Q_msk,I_msk,S_msk
1371	Killwaves/Z Q_work,I_work,S_work //working waves for desmearing step
1372	SetDataFolder root:
1373	End
1374
1375	// does not alter the data sets - reports a power law
1376	// exponent and makes it global so it will automatically
1377	// be used during the desmearing
1378	//
1379	// generates extr_hqi vs extr_hqq that are Appended to the graph
1380	Function DSM_ExtrapolateButtonProc(ctrlName) : ButtonControl
1381	String ctrlName
1382
1383	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1384
1385	NVAR nend = $(USANSFolder+":DSM:gNptsExtrap")
1386	NVAR m_pred = $(USANSFolder+":DSM:gPowerM")
1387
1388	SetDataFolder $(USANSFolder+":DSM")
1389	//use masked data if it exists
1390	if(exists("I_msk")==1 && exists("Q_msk")==1 && exists("S_msk")==1)
1391	wave Qw = $(USANSFolder+":DSM:Q_msk")
1392	Wave Iw = $(USANSFolder+":DSM:I_msk")
1393	Wave Sw = $(USANSFolder+":DSM:S_msk")
1394	else
1395	//start from the "_exp" waves
1396	if(exists("I_exp")==1 && exists("Q_exp")==1 && exists("S_exp")==1)
1397	wave Qw = $(USANSFolder+":DSM:Q_exp")
1398	Wave Iw = $(USANSFolder+":DSM:I_exp")
1399	Wave Sw = $(USANSFolder+":DSM:S_exp")
1400	endif
1401	endif
1402	SetDataFolder root:
1403
1404	DSM_SetExtrWaves(Qw)
1405	m_pred = DSM_DoExtrapolate(Qw,Iw,Sw,nend)
1406	AppendExtrapolation()
1407
1408	return(0)
1409	End
1410
1411	//smooths the data in steps as requested...
1412	//
1413	// typically do a simple Box smooth first,
1414	// then do a smoothing spline, keeping the same number of data points
1415	//
1416	// chi-squared is reported - so you can see how "bad" the smoothing is
1417	// smoothing of the data is done on a log(I) scale if requested
1418	// setting doLog variable to 0 will return to linear smoothing
1419	// (I see little difference)
1420	//
1421	// start from the "_smth" waves if they exist
1422	// otheriwse start from the working waves
1423	//
1424	// create Q_smth, I_smth, S_smth
1425	// keep track of the smoothing types and passes in the wave note
1426	//
1427	Function DSM_SmoothButtonProc(ctrlName) : ButtonControl
1428	String ctrlName
1429
1430	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1431
1432	SetDataFolder $(USANSFolder+":DSM")
1433
1434	Variable ii,new_n,pass,nq_ext,offset,doLog=1
1435	String noteStr=""
1436
1437	// want log scaling of intensity during smoothing?
1438	ControlInfo DSMControl_3g
1439	doLog = V_value
1440
1441	//// if(exists("I_smth")==1 && exists("Q_smth")==1 && exists("S_smth")==1 && ! freshMask)
1442	if(exists("I_smth")==1 && exists("Q_smth")==1 && exists("S_smth")==1)
1443	//start from the smoothed waves --- just need the wave references
1444	else
1445	//start from the "msk", creating smth waves
1446	if(exists("I_msk")==1 && exists("Q_msk")==1 && exists("S_msk")==1)
1447	wave Q_msk,I_msk,S_msk
1448	Duplicate/O I_msk,I_smth,Q_smth,S_smth
1449	I_smth = I_msk
1450	Q_smth = Q_msk
1451	S_smth = S_msk
1452	else
1453	//start from the "_exp" waves
1454	if(exists("I_exp")==1 && exists("Q_exp")==1 && exists("S_exp")==1)
1455	wave Q_exp,I_exp,S_exp
1456	Duplicate/O I_exp,I_smth,Q_smth,S_smth
1457	I_smth = I_exp
1458	Q_smth = Q_exp
1459	S_smth = S_exp
1460	endif
1461	endif
1462	endif
1463
1464	wave Q_smth,I_smth,S_smth
1465
1466	// extend the data to avoid end effects
1467	//creates I_ext,Q_ext,S_ext with extended q-values
1468	// fit 15 pts at each end, typically add 10 pts to each end
1469	// does nothing if num_extr = 0
1470	ControlInfo/W=Desmear_Graph DSMControl_3d //extendCheck
1471	if(V_value == 1)
1472	ExtendToSmooth(Q_smth,I_smth,S_smth,15,15,10)
1473	else
1474	ExtendToSmooth(Q_smth,I_smth,S_smth,15,15,0) //don't extend, just use the original data
1475	endif
1476
1477	//whether extending or not, the working data is "_ext", set by ExtendToSmooth()
1478	SetDataFolder $(USANSFolder+":DSM")
1479	wave Q_ext,I_ext ,S_ext
1480
1481	noteStr=note(I_smth)
1482	Note I_ext , noteStr
1483
1484	WaveStats/Q I_ext
1485	if(V_min<=0)
1486	Print "negative itensity found, using linear scale for smoothing"
1487	doLog = 0
1488	endif
1489
1490	if(doLog)
1491	//convert to log scale
1492	Duplicate/O I_ext I_log,I_log_err
1493	Wave I_log ,I_log_err
1494	I_log = log(I_ext)
1495	WaveStats/Q I_log
1496	offset = 2*(-V_min)
1497	I_log += offset
1498	I_log_err = S_ext/(2.30*I_ext)
1499	I_ext = I_log
1500	endif
1501	//
1502
1503	ControlInfo/W=Desmear_Graph DSMControl_3b //BoxCheck
1504	if(V_value == 1)
1505	//do a simple Box smooth first - number of points does not change
1506	// fills ends with neighboring value (E=3) (n=3 points in smoothing window)
1507	Smooth/E=3/B 3, I_ext
1508
1509	noteStr=note(I_ext)
1510	pass = NumberByKey("BOX", noteStr, "=", ";")
1511	noteStr = ReplaceNumberByKey("BOX", noteStr, pass+1, "=", ";")
1512	Note/K I_ext
1513	Note I_ext , noteStr
1514	// Print "box = ",noteStr
1515	endif
1516
1517	NVAR sParam = gSmoothFac //already in the right DF
1518
1519	ControlInfo/W=Desmear_Graph DSMControl_3c //SSCheck
1520	if(V_value == 1)
1521	// Interpolate2/T=3/N=(nq)/I=2/F=1/SWAV=S_ext/Y=Yi_SS/X=Yq_SS Q_ext, I_ext //Igor 5
1522	// Interpolate/T=3/N=(nq)/I=2/F=1/S=S_ext/Y=Yi_SS/X=Yq_SS I_ext /X=Q_ext //Igor 4
1523	//Igor 4
1524	String str=""
1525	nq_ext = numpnts(Q_ext)
1526	str = "Interpolate/T=3/N=("+num2str(nq_ext)+")/I=1/F=("+num2str(sParam)+")/Y=Yi_SS/X=Yq_SS I_ext /X=Q_ext"
1527	Execute str
1528	// Print Str
1529	// Interpolate2/T=3/N=(nq_ext)/I=1/F=(sParam)/Y=Yi_SS/X=Yq_SS Q_ext, I_ext
1530	// end Igor 4
1531	wave yi_ss = yi_ss // already in the right DF
1532	wave yq_ss = yq_ss
1533	// reassign the "working" waves with the result of interpolate, which has the same I/Q values
1534	I_ext = yi_ss
1535	Q_ext = yq_ss
1536
1537	noteStr=note(I_ext)
1538	pass = NumberByKey("SPLINE", noteStr, "=", ";")
1539	noteStr = ReplaceNumberByKey("SPLINE", noteStr, pass+1, "=", ";")
1540	Note/K I_ext
1541	Note I_ext , noteStr
1542	// Print "spline = ",noteStr
1543	endif
1544
1545	//undo the scaling
1546	If(doLog)
1547	I_ext -= offset
1548	I_ext = 10^I_ext
1549	endif
1550
1551	// at this point, I_ext has too many points - and we need to just return the
1552	// center chunk that is the original q-values
1553	// as assign this to the working set for the desmear step
1554	// and to the _smth set in case another smoothng pass is desired
1555	// Q_smth has not changed, S_smth has not changed
1556	I_smth = interp(Q_smth[p], Q_ext, I_ext )
1557
1558	Note/K I_smth
1559	Note I_smth , noteStr
1560	// Print "end of smoothed, note = ",note(I_smth)
1561
1562	Variable nq = numpnts($(USANSFolder+":DSM:Q_smth"))
1563	// Print "nq after smoothing = ",nq
1564
1565	//reset the global
1566	NVAR gNq = gNq
1567	gNq = nq
1568	//report the chi^2 difference between the smoothed curve and the experimental data
1569	NVAR chi2 = gChi2Smooth
1570	chi2 = SmoothedChi2(I_smth)
1571
1572	Execute "AppendSmoothed()"
1573
1574	setDataFolder root:
1575	return(0)
1576	End
1577
1578	// undo the smoothing and start over - useful if you've smoothed
1579	// too aggressively and need to back off
1580	Function DSM_SmoothUndoButtonProc(ctrlName) : ButtonControl
1581	String ctrlName
1582
1583	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1584
1585	Execute "RemoveSmoothed()"
1586	SetDataFolder $(USANSFolder+":DSM")
1587	Killwaves/Z I_smth,Q_smth,S_smth,Q_ext,I_ext,S_ext,Yi_SS,Yq_SS
1588	SetDataFolder root:
1589	return (0)
1590	end
1591
1592	//calculate the chi^2 value for the smoothed data
1593	Function SmoothedChi2(I_smth)
1594	Wave I_smth
1595
1596	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1597
1598	//start from the "msk", if they exist
1599	if(exists("I_msk")==1 && exists("Q_msk")==1 && exists("S_msk")==1)
1600	Wave iw = $(USANSFolder+":DSM:I_msk")
1601	Wave sw = $(USANSFolder+":DSM:S_msk")
1602	else
1603	//start from the "_exp" waves
1604	if(exists("I_exp")==1 && exists("Q_exp")==1 && exists("S_exp")==1)
1605	Wave iw = $(USANSFolder+":DSM:I_exp")
1606	Wave sw = $(USANSFolder+":DSM:S_exp")
1607	endif
1608	endif
1609
1610	Variable ii,chi2,num
1611	chi2=0
1612	num = numpnts(iw)
1613	for(ii=0;ii<num;ii+=1)
1614	chi2 += (iw[ii] - I_smth[ii])^2 / (sw[ii])^2
1615	endfor
1616	Chi2 /= (num-1)
1617	return (chi2)
1618	end
1619
1620	// I_dsm is the desmeared data
1621	//
1622	// step (7) - desmearing is done, write out the result
1623	//
1624	Function DSM_SaveButtonProc(ctrlName) : ButtonControl
1625	String ctrlName
1626
1627	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1628	NVAR useXMLOutput = root:Packages:NIST:gXML_Write
1629
1630	String saveStr
1631	SVAR curFile = $(USANSFolder+":DSM:gCurFile")
1632	saveStr = CleanupName((curFile),0) //the output filename
1633	//
1634
1635	if (useXMLOutput == 1)
1636	WriteXMLUSANSDesmeared(saveStr,0,0,1)
1637	else
1638	WriteUSANSDesmeared(saveStr,0,0,1) //use the full set (lo=hi=0) and present a dialog
1639	endif
1640
1641	SetDataFolder root:
1642	return(0)
1643	End
1644
1645	Function DSM_HelpButtonProc(ctrlName) : ButtonControl
1646	String ctrlName
1647
1648	DisplayHelpTopic/Z/K=1 "Desmearing USANS Data"
1649	if(V_flag !=0)
1650	DoAlert 0,"The Desmearing USANS Data Help file could not be found"
1651	endif
1652	return(0)
1653	End
1654
1655
1656	//toggles the log/lin display of the loaded data set
1657	Function DSM_LoadCheckProc(ctrlName,checked) : CheckBoxControl
1658	String ctrlName
1659	Variable checked
1660
1661	ModifyGraph log=(checked)
1662	return(0)
1663	End
1664
1665
1666	Function DSM_ExtrapolationCheckProc(ctrlName,checked) : CheckBoxControl
1667	String ctrlName
1668	Variable checked
1669
1670	if(checked)
1671	AppendExtrapolation()
1672	else
1673	RemoveExtrapolation()
1674	endif
1675	return(0)
1676	End
1677
1678
1679	// takes as input the "working waves"
1680	//
1681	// creates intermediate waves to work on
1682	//
1683	// output of Q_dsm,I_dsm,S_dsm (and I_dsm_sm, the result of smearing I_dsm)
1684	//
1685	Function DSM_DesmearButtonProc(ctrlName) : ButtonControl
1686	String ctrlName
1687
1688	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1689
1690	SetDataFolder $(USANSFolder+":DSM")
1691	if(exists("I_smth")==1 && exists("Q_smth")==1 && exists("S_smth")==1)
1692	wave Q_smth , I_smth ,S_smth
1693	Duplicate/O I_smth,I_work,Q_work,S_work
1694	I_work = I_smth
1695	Q_work = Q_smth
1696	S_work = S_smth
1697	else
1698	//start from the "msk", creating work waves
1699	if(exists("I_msk")==1 && exists("Q_msk")==1 && exists("S_msk")==1)
1700	wave Q_msk,I_msk,S_msk
1701	Duplicate/O I_msk,I_work,Q_work,S_work
1702	I_work = I_msk
1703	Q_work = Q_msk
1704	S_work = S_msk
1705	else
1706	//start from the "_exp" waves
1707	if(exists("I_exp")==1 && exists("Q_exp")==1 && exists("S_exp")==1)
1708	wave Q_exp,I_exp,S_exp
1709	Duplicate/O I_exp,I_work,Q_work,S_work
1710	I_work = I_exp
1711	Q_work = Q_exp
1712	S_work = S_exp
1713	endif
1714	endif
1715	endif
1716	//SetDataFolder root:
1717
1718	NVAR nq = gNq
1719	NVAR m = gPowerM
1720	NVAR chi2_target = gChi2Target
1721	NVAR maxFastIter = gMaxFastIter
1722	NVAR maxSlowIter = gMaxSlowIter
1723
1724	// SET WEIGHTING OF EXPERIMENTAL DATA.
1725	Duplicate/O Q_work weights
1726	Wave weights = weights
1727	weights = 1/S_work^2
1728
1729	// calculate weighting array for smearing of data
1730	Make/O/D/N=(nq,nq) FW
1731	Wave FW
1732	Weights_L(m,FW,Q_work)
1733
1734	// ^^^^ Iterative desmearing ^^^^*
1735	Variable chi2_old,chi2_new,done,iter
1736	// FOR 0TH ITERATION, EXPERIMENTAL DATA IS USED FOR Y_OLD, create ys_old for result
1737	// y_old = I_old, y_new = I_dsm, I_dsm_sm = ys_new,
1738	// duplicate preserves the wave note!
1739	Duplicate/O I_work I_old,Is_old,I_dsm,I_dsm_sm
1740	Duplicate/O Q_work Q_dsm,S_dsm //sets Q_dsm correctly
1741	wave S_dsm,I_old,Is_old,I_dsm,I_dsm_sm
1742	I_old = I_work
1743	Is_old = 0
1744	I_dsm = 0
1745	I_dsm_sm = 0
1746
1747	// Smear 0TH iter guess Y --> YS
1748	DSM_Smear(I_old,Is_old,NQ,FW)
1749	chi2_OLD = chi2(Is_old,I_work,weights,NQ)
1750
1751	printf "starting chi^2 = %g\r",chi2_old
1752	Print "Starting fast convergence..... "
1753
1754	done = 0 //false
1755	iter = 0
1756	Do // while not done, use Fast convergence
1757	I_dsm = I_work * I_old / Is_old // Calculate corrected guess (no need for do-loop)
1758
1759	// Smear iter guess I_dsm --> I_dsm_sm and see how well I_dsm_sm matches experimental data
1760	DSM_Smear(I_dsm,I_dsm_sm,NQ,FW)
1761	chi2_new = chi2(I_dsm_sm,I_work,weights,NQ)
1762
1763	// Stop iteration if fit from new iteration has worse fit...
1764	If (chi2_new > chi2_old)
1765	Done = 1
1766	Endif
1767
1768	// Stop iteration if fit is better than target value...
1769	If (chi2_new < chi2_target)
1770	Done = 1
1771	Else
1772	Iter += 1
1773	Printf "Iteration %d, Chi^2(new) = %g\r", Iter,chi2_new
1774	I_old = I_dsm
1775	Is_old = I_dsm_sm
1776	if(iter>maxFastIter)
1777	break
1778	endif
1779	CHI2_OLD = CHI2_NEW
1780	EndIf
1781	while( !done )
1782
1783	// append I_dsm,I_exp to the graph
1784	Execute "AppendDesmeared()"
1785	DoUpdate
1786
1787	SetDataFolder $(USANSFolder+":DSM")
1788
1789
1790	// step (6) - refine the desmearing using slow convergence
1791	Print "Starting slow convergence..... "
1792	done = 0 // ! reset flag for slow convergence
1793	Do
1794	I_dsm = I_old + (I_work - Is_old) // Calculate corrected guess
1795
1796	// Smear iter guess Y --> YS
1797	DSM_Smear(I_dsm,I_dsm_sm,NQ,FW)
1798	chi2_new = chi2(I_dsm_sm,I_work,weights,NQ)
1799
1800	// Stop iteration if fit from new iteration has worse fit...
1801	If (chi2_new > chi2_old)
1802	Done = 1
1803	Endif
1804
1805	// Stop iteration if fit is better than target value...
1806	If (chi2_new < chi2_target)
1807	Done = 1
1808	Else
1809	Iter += 1
1810
1811	if(mod(iter, 50 ) ==0 )
1812	Printf "Iteration %d, Chi^2(new) = %g\r", Iter,chi2_new
1813	DoUpdate
1814	endif
1815	I_old = I_dsm
1816	Is_old = I_dsm_sm
1817
1818	CHI2_OLD = CHI2_NEW
1819	EndIf
1820	if(iter>maxSlowIter)
1821	break
1822	endif
1823	While ( !done )
1824
1825	Printf "Iteration %d, Chi^2(new) = %g\r", Iter,chi2_new
1826
1827	// adjust the error
1828	SetDataFolder $(USANSFolder+":DSM")
1829	Duplicate/O S_work err
1830	S_dsm = abs(err/I_work*I_dsm) //proportional error
1831	//John simply keeps the same error as was read in from the smeared data set - is this right?
1832	// S_dsm = S_Work
1833
1834	NVAR gChi = gChi2Final //chi^2 final
1835	NVAR gIter = gIterations //total number of iterations
1836	gChi = chi2_new
1837	gIter = Iter
1838
1839	SVAR str = gIterStr
1840	sprintf str,"%d iterations required",iter
1841
1842	SetDataFolder root:
1843	return(0)
1844	End
1845
1846	Function DSM_RevertButtonProc(ctrlName) : ButtonControl
1847	String ctrlName
1848
1849	SVAR USANSFolder = root:Packages:NIST:USANS:Globals:gUSANSFolder
1850
1851
1852	CleanUpJunk()
1853
1854	SetDataFolder $(USANSFolder+":DSM")
1855
1856	//reset the working waves to the original
1857	wave Q_exp_orig,I_exp_orig,S_exp_orig
1858
1859	Duplicate/O Q_exp_orig Q_exp
1860	Duplicate/O I_exp_orig I_exp
1861	Duplicate/O S_exp_orig S_exp
1862	// kill the data folder
1863	// re-initialize?
1864
1865	SetDataFolder root:
1866
1867	return(0)
1868	End

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