source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/RectAnnulAvg.ipf @ 430

Last change on this file since 430 was 418, checked in by ajj, 14 years ago

Moving data folders into root:Packages:NIST

This could be hairy.

File size: 20.0 KB
Line 
1#pragma rtGlobals=1             // Use modern global access method.
2#pragma version=5.0
3#pragma IgorVersion=6.0
4
5//***********************
6// Vers. 1.2 092101
7//
8// functions to perform either ractangular averages (similar to sector averages)
9// or annular averages ( fixed Q, I(angle) )
10//
11// dispatched to this point by ExecuteProtocol()
12//
13//**************************
14
15////////////////////////////////////
16//
17//              For AVERAGE and for DRAWING
18//                      DRAWING routines only use a subset of the total list, since saving, naming, etc. don't apply
19//              (10) possible keywords, some numerical, some string values
20//              AVTYPE=string           string from set {Circular,Annular,Rectangular,Sector,2D_ASCII,PNG_Graphic}
21//              PHI=value                       azimuthal angle (-90,90)
22//              DPHI=value                      +/- angular range around phi for average
23//              WIDTH=value             total width of rectangular section, in pixels
24//              SIDE=string             string from set {left,right,both} **note NOT capitalized
25//              QCENTER=value           q-value (1/A) of center of annulus for annular average
26//              QDELTA=value            total width of annulus centered at QCENTER
27//              PLOT=string             string from set {Yes,No} = truth of generating plot of averaged data
28//              SAVE=string             string from set {Yes,No} = truth of saving averaged data to disk
29//              NAME=string             string from set {Auto,Manual} = Automatic name generation or Manual(dialog)
30//
31//////////////////////////////////
32
33
34//function to do average of a rectangular swath of the detector
35//a sector average seems to be more appropriate, but there may be some
36//utility in rectangular averages
37//the parameters in the global keyword-string must have already been set somewhere
38//either directly or from the protocol
39//
40// 2-D data in the folder must already be on a linear scale. The calling routine is
41//responsible for this -
42//writes out the averaged waves to the "type" data folder
43//data is not written to disk by this routine
44//
45Function RectangularAverageTo1D(type)
46        String type
47       
48        SVAR keyListStr = root:myGlobals:Protocols:gAvgInfoStr
49       
50        //type is the data type to do the averaging on, and will be set as the current folder
51        //get the current displayed data (so the correct folder is used)
52        String destPath = "root:Packages:NIST:"+type
53        //
54        Variable xcenter,ycenter,x0,y0,sx,sx3,sy,sy3,dtsize,dtdist,dr,ddr
55        Variable lambda,trans
56        Wave reals = $(destPath + ":RealsRead")
57        WAVE/T textread = $(destPath + ":TextRead")
58        String fileStr = textread[3]
59       
60        // center of detector, for non-linear corrections
61        NVAR pixelsX = root:myGlobals:gNPixelsX
62        NVAR pixelsY = root:myGlobals:gNPixelsY
63       
64        xcenter = pixelsX/2 + 0.5               // == 64.5 for 128x128 Ordela
65        ycenter = pixelsY/2 + 0.5               // == 64.5 for 128x128 Ordela
66       
67        // beam center, in pixels
68        x0 = reals[16]
69        y0 = reals[17]
70        //detector calibration constants
71        sx = reals[10]          //mm/pixel (x)
72        sx3 = reals[11]         //nonlinear coeff
73        sy = reals[13]          //mm/pixel (y)
74        sy3 = reals[14]         //nonlinear coeff
75
76       
77        dtsize = 10*reals[20]           //det size in mm
78        dtdist = 1000*reals[18] // det distance in mm
79       
80        NVAR pixelsX = root:myGlobals:gNPixelsX
81        NVAR pixelsY = root:myGlobals:gNPixelsY
82       
83        NVAR binWidth=root:myGlobals:gBinWidth
84        dr = binWidth           // annulus width set by user, default is one
85        ddr = dr*sx             //step size, in mm (this is the value to pass to the resolution calculation, not dr 18NOV03)
86               
87        Variable rcentr,large_num,small_num,dtdis2,nq,xoffst,dxbm,dybm,ii
88        Variable phi_rad,dphi_rad,phi_x,phi_y
89        Variable forward,mirror
90       
91        String side = StringByKey("SIDE",keyListStr,"=",";")
92//      Print "side = ",side
93
94        //convert from degrees to radians
95        phi_rad = (Pi/180)*NumberByKey("PHI",keyListStr,"=",";")
96        dphi_rad = (Pi/180)*NumberByKey("DPHI",keyListStr,"=",";")
97        //create cartesian values for unit vector in phi direction
98        phi_x = cos(phi_rad)
99        phi_y = sin(phi_rad)
100       
101        //get (total) width of band
102        Variable width = NumberByKey("WIDTH",keyListStr,"=",";")
103
104        /// data wave is data in the current folder which was set at the top of the function
105        Wave data=$(destPath + ":data")
106        //Check for the existence of the mask, if not, make one (local to this folder) that is null
107       
108        if(WaveExists($"root:Packages:NIST:MSK:data") == 0)
109                Print "There is no mask file loaded (WaveExists)- the data is not masked"
110                Make/O/N=(pixelsX,pixelsY) $(destPath + ":mask")
111                WAVE mask = $(destPath + ":mask")
112                mask = 0
113        else
114                Wave mask=$"root:Packages:NIST:MSK:data"
115        Endif
116       
117        rcentr = 100            //pixels within rcentr of beam center are broken into 9 parts
118        // values for error if unable to estimate value
119        //large_num = 1e10
120        large_num = 1           //1e10 value (typically sig of last data point) plots poorly, arb set to 1
121        small_num = 1e-10
122       
123        // output wave are expected to exist (?) initialized to zero, what length?
124        // 300 points on VAX ---
125        Variable wavePts=500
126        Make/O/N=(wavePts) $(destPath + ":qval"),$(destPath + ":aveint")
127        Make/O/N=(wavePts) $(destPath + ":ncells"),$(destPath + ":dsq"),$(destPath + ":sigave")
128        Make/O/N=(wavePts) $(destPath + ":SigmaQ"),$(destPath + ":fSubS"),$(destPath + ":QBar")
129        WAVE qval = $(destPath + ":qval")
130        WAVE aveint = $(destPath + ":aveint")
131        WAVE ncells = $(destPath + ":ncells")
132        WAVE dsq = $(destPath + ":dsq")
133        WAVE sigave = $(destPath + ":sigave")
134        WAVE qbar = $(destPath + ":QBar")
135        WAVE sigmaq = $(destPath + ":SigmaQ")
136        WAVE fsubs = $(destPath + ":fSubS")
137
138        qval = 0
139        aveint = 0
140        ncells = 0
141        dsq = 0
142        sigave = 0
143        qbar = 0
144        sigmaq = 0
145        fsubs = 0
146
147        dtdis2 = dtdist^2
148        nq = 1
149        xoffst=0
150        //distance of beam center from detector center
151        dxbm = FX(x0,sx3,xcenter,sx)
152        dybm = FY(y0,sy3,ycenter,sy)
153               
154        //BEGIN AVERAGE **********
155        Variable xi,dxi,dx,jj,data_pixel,yj,dyj,dy,mask_val=0.1
156        Variable dr2,nd,fd,nd2,ll,kk,dxx,dyy,ir,dphi_p,d_per,d_pll
157        Make/O/N=2 $(destPath + ":par")
158        WAVE par = $(destPath + ":par")
159       
160        // IGOR arrays are indexed from [0][0], FORTAN from (1,1) (and the detector too)
161        // loop index corresponds to FORTRAN (old code)
162        // and the IGOR array indices must be adjusted (-1) to the correct address
163        ii=1
164        do
165                xi = ii
166                dxi = FX(xi,sx3,xcenter,sx)
167                dx = dxi-dxbm           //dx and dy are in mm
168               
169                jj = 1
170                do
171                        data_pixel = data[ii-1][jj-1]           //assign to local variable
172                        yj = jj
173                        dyj = FY(yj,sy3,ycenter,sy)
174                        dy = dyj - dybm
175                        if(!(mask[ii][jj]))                     //masked pixels = 1, skip if masked (this way works...)
176                                dr2 = (dx^2 + dy^2)^(0.5)               //distance from beam center NOTE dr2 used here - dr used above
177                                if(dr2>rcentr)          //keep pixel whole
178                                        nd = 1
179                                        fd = 1
180                                else                            //break pixel into 9 equal parts
181                                        nd = 3
182                                        fd = 2
183                                endif
184                                nd2 = nd^2
185                                ll = 1          //"el-el" loop index
186                                do
187                                        dxx = dx + (ll - fd)*sx/3
188                                        kk = 1
189                                        do
190                                                dyy = dy + (kk - fd)*sy/3
191                                                //determine distance pixel is from beam center (d_pll)
192                                                //and distance off-line (d_per) and if in forward direction
193                                                par = 0                 //initialize the wave
194                                                forward = distance(dxx,dyy,phi_x,phi_y,par)
195                                                d_per = par[0]
196                                                d_pll = par[1]
197                                                //check whether pixel lies within width band
198                                                if(d_per <= (0.5*width*ddr))
199                                                        //check if pixel lies within allowed sector(s)
200                                                        if(cmpstr(side,"both")==0)              //both sectors
201                                                                        //increment
202                                                                        nq = IncrementPixel_Rec(data_pixel,ddr,d_pll,aveint,dsq,ncells,nq,nd2)
203                                                        else
204                                                                if(cmpstr(side,"right")==0)             //forward sector only
205                                                                        if(forward)
206                                                                                //increment
207                                                                                nq = IncrementPixel_Rec(data_pixel,ddr,d_pll,aveint,dsq,ncells,nq,nd2)
208                                                                        Endif
209                                                                else                    //mirror sector only
210                                                                        if(!forward)
211                                                                                //increment
212                                                                                nq = IncrementPixel_Rec(data_pixel,ddr,d_pll,aveint,dsq,ncells,nq,nd2)
213                                                                        Endif
214                                                                Endif
215                                                        Endif           //allowable sectors
216                                                Endif           //check if in band
217                                                kk+=1
218                                        while(kk<=nd)
219                                        ll += 1
220                                while(ll<=nd)
221                        Endif           //masked pixel check
222                        jj += 1
223                while (jj<=pixelsY)
224                ii += 1
225        while(ii<=pixelsX)              //end of the averaging
226               
227        //compute q-values and errors
228        Variable ntotal,rr,theta,avesq,aveisq,var
229       
230        lambda = reals[26]
231        ntotal = 0
232        kk = 1
233        do
234                rr = (2*kk-1)*ddr/2
235                theta = 0.5*atan(rr/dtdist)
236                qval[kk-1] = (4*Pi/lambda)*sin(theta)
237                if(ncells[kk-1] == 0)
238                        //no pixels in annuli, data unknown
239                        aveint[kk-1] = 0
240                        sigave[kk-1] = large_num
241                else
242                        if(ncells[kk-1] <= 1)
243                                //need more than one pixel to determine error
244                                aveint[kk-1] = aveint[kk-1]/ncells[kk-1]
245                                sigave[kk-1] = large_num
246                        else
247                                //assume that the intensity in each pixel in annuli is normally
248                                // distributed about mean...
249                                aveint[kk-1] = aveint[kk-1]/ncells[kk-1]
250                                avesq = aveint[kk-1]^2
251                                aveisq = dsq[kk-1]/ncells[kk-1]
252                                var = aveisq-avesq
253                                if(var<=0)
254                                        sigave[kk-1] = small_num
255                                else
256                                        sigave[kk-1] = sqrt(var/(ncells[kk-1] - 1))
257                                endif
258                        endif
259                endif
260                ntotal += ncells[kk-1]
261                kk+=1
262        while(kk<=nq)
263       
264        //Print "NQ = ",nq
265        // data waves were defined as 200 points (=wavePts), but now have less than that (nq) points
266        // use DeletePoints to remove junk from end of waves
267        //WaveStats would be a more foolproof implementation, to get the # points in the wave
268        Variable startElement,numElements
269        startElement = nq
270        numElements = wavePts - startElement
271        DeletePoints startElement,numElements, qval,aveint,ncells,dsq,sigave
272       
273        //////////////end of VAX sector_ave()
274               
275        //angle dependent transmission correction
276        Variable uval,arg,cos_th
277        lambda = reals[26]
278        trans = reals[4]
279//
280//  The transmission correction is now done at the ADD step, in DetCorr()
281//             
282//      ////this section is the trans_correct() VAX routine
283//      if(trans<0.1)
284//              Print "***transmission is less than 0.1*** and is a significant correction"
285//      endif
286//      if(trans==0)
287//              Print "***transmission is ZERO*** and has been reset to 1.0 for the averaging calculation"
288//              trans = 1
289//      endif
290//      //optical thickness
291//      uval = -ln(trans)
292//      //apply correction to aveint[]
293//      //index from zero here, since only working with IGOR waves
294//      ii=0
295//      do
296//              theta = 2*asin(lambda*qval[ii]/(4*pi))
297//              cos_th = cos(theta)
298//              arg = (1-cos_th)/cos_th
299//              if((uval<0.01) || (cos_th>0.99))                //OR
300//                      //small arg, approx correction
301//                      aveint[ii] /= 1-0.5*uval*arg
302//              else
303//                      //large arg, exact correction
304//                      aveint[ii] /= (1-exp(-uval*arg))/(uval*arg)
305//              endif
306//              ii+=1
307//      while(ii<nq)
308//      //end of transmission/pathlength correction
309//     
310// ***************************************************************
311//
312// Do the extra 3 columns of resolution calculations starting here.
313//
314// ***************************************************************
315
316        Variable L2 = reals[18]
317        Variable BS = reals[21]
318        Variable S1 = reals[23]
319        Variable S2 = reals[24]
320        Variable L1 = reals[25]
321        lambda = reals[26]
322        Variable lambdaWidth = reals[27]
323        String detStr=textRead[9]
324       
325        Variable usingLenses = reals[28]                //new 2007
326
327        //Two parameters DDET and APOFF are instrument dependent.  Determine
328        //these from the instrument name in the header.
329        //From conversation with JB on 01.06.99 these are the current
330        //good values
331
332        Variable DDet
333        NVAR apOff = root:myGlobals:apOff               //in cm
334       
335//      DDet = DetectorPixelResolution(fileStr,detStr)          //needs detector type and beamline
336        //note that reading the detector pixel size from the header ASSUMES SQUARE PIXELS! - Jan2008
337        DDet = reals[10]/10                     // header value (X) is in mm, want cm here
338       
339        //Width of annulus used for the average is gotten from the
340        //input dialog before.  This also must be passed to the resol
341        //calculator. Currently the default is dr=1 so just keeping that.
342
343        //Go from 0 to nq doing the calc for all three values at
344        //every Q value
345
346        ii=0
347
348        Variable ret1,ret2,ret3
349        do
350                getResolution(qval[ii],lambda,lambdaWidth,DDet,apOff,S1,S2,L1,L2,BS,ddr,usingLenses,ret1,ret2,ret3)
351                sigmaq[ii] = ret1
352                qbar[ii] = ret2
353                fsubs[ii] = ret3
354                ii+=1
355        while(ii<nq)
356
357        DeletePoints startElement,numElements, sigmaq, qbar, fsubs
358
359// ***************************************************************
360//
361// End of resolution calculations
362//
363// ***************************************************************
364
365        Avg_1D_Graph(aveint,qval,sigave)
366
367        //get rid of the default mask, if one was created (it is in the current folder)
368        //don't just kill "mask" since it might be pointing to the one in the MSK folder
369        Killwaves/Z $(destPath+":mask")
370       
371        KillWaves/Z $(destPath+":par")          //parameter wave used in function distance()
372       
373        //return to root folder (redundant)
374        SetDataFolder root:
375       
376        Return 0
377End
378
379//returns nq, new number of q-values
380//arrays aveint,dsq,ncells are also changed by this function
381//
382Function IncrementPixel_Rec(dataPixel,ddr,d_pll,aveint,dsq,ncells,nq,nd2)
383        Variable dataPixel,ddr,d_pll
384        Wave aveint,dsq,ncells
385        Variable nq,nd2
386       
387        Variable ir
388       
389        ir = trunc(abs(d_pll)/ddr)+1
390        if (ir>nq)
391                nq = ir         //resets maximum number of q-values
392        endif
393        aveint[ir-1] += dataPixel/nd2           //ir-1 must be used, since ir is physical
394        dsq[ir-1] += dataPixel*dataPixel/nd2
395        ncells[ir-1] += 1/nd2
396       
397        Return nq
398End
399
400//function determines disatnce in mm  that pixel is from line
401//intersecting cetner of detector and direction phi
402//at chosen azimuthal angle phi -> [cos(phi),sin(phi0] = [phi_x,phi_y]
403//distance is always positive
404//
405// distances are returned in  a wave
406// forward (truth) is the function return value
407//
408Function distance(dxx,dyy,phi_x,phi_y,par)
409        Variable dxx,dyy,phi_x,phi_y
410        Wave par                //par[0] = d_per
411                                        //par[1] = d_pll        , both are returned values
412       
413        Variable val,rr,dot_prod,forward,d_per,d_pll,dphi_pixel
414       
415        rr = sqrt(dxx^2 + dyy^2)
416        dot_prod = (dxx*phi_x + dyy*phi_y)/rr
417        if(dot_prod >= 0)
418                forward = 1
419        else
420                forward = 0
421        Endif
422        //? correct for roundoff error? - is this necessary in IGOR, w/ double precision?
423        if(dot_prod > 1)
424                dot_prod =1
425        Endif
426        if(dot_prod < -1)
427                dot_prod = -1
428        Endif
429        dphi_pixel = acos(dot_prod)
430       
431        //distance (in mm) that pixel is from  line (perpendicular)
432        d_per = sin(dphi_pixel)*rr
433        //distance (in mm) that pixel projected onto line is from beam center (parallel)
434        d_pll = cos(dphi_pixel)*rr
435       
436        //assign to wave for return
437        par[0] = d_per
438        par[1] = d_pll
439       
440        return (forward)
441
442End
443
444//performs an average around an annulus of specified width, centered on a
445//specified q-value (Intensity vs. angle)
446//the parameters in the global keyword-string must have already been set somewhere
447//either directly or from the protocol
448//
449//the input (data in the "type" folder) must be on linear scale - the calling routine is
450//responsible for this
451//averaged data is written to the data folder and plotted. data is not written
452//to disk from this routine.
453//
454Function AnnularAverageTo1D(type)
455        String type
456       
457        SVAR keyListStr = root:myGlobals:Protocols:gAvgInfoStr
458       
459        //type is the data type to do the averaging on, and will be set as the current folder
460        //get the current displayed data (so the correct folder is used)
461        String destPath = "root:Packages:NIST:"+type
462       
463        Variable xcenter,ycenter,x0,y0,sx,sx3,sy,sy3,dtsize,dtdist
464        Variable rcentr,large_num,small_num,dtdis2,nq,xoffst,xbm,ybm,ii
465        Variable rc,delr,rlo,rhi,dphi,nphi,dr
466        Variable lambda,trans
467        Wave reals = $(destPath + ":RealsRead")
468
469        // center of detector, for non-linear corrections
470        NVAR pixelsX = root:myGlobals:gNPixelsX
471        NVAR pixelsY = root:myGlobals:gNPixelsY
472       
473        xcenter = pixelsX/2 + 0.5               // == 64.5 for 128x128 Ordela
474        ycenter = pixelsY/2 + 0.5               // == 64.5 for 128x128 Ordela
475       
476        // beam center, in pixels
477        x0 = reals[16]
478        y0 = reals[17]
479        //detector calibration constants
480        sx = reals[10]          //mm/pixel (x)
481        sx3 = reals[11]         //nonlinear coeff
482        sy = reals[13]          //mm/pixel (y)
483        sy3 = reals[14]         //nonlinear coeff
484       
485        dtsize = 10*reals[20]           //det size in mm
486        dtdist = 1000*reals[18] // det distance in mm
487        lambda = reals[26]
488       
489        Variable qc = NumberByKey("QCENTER",keyListStr,"=",";")
490        Variable nw = NumberByKey("QDELTA",keyListStr,"=",";")
491       
492        dr = 1                  //minimum annulus width, keep this fixed at one
493        NVAR numPhiSteps = root:myGlobals:gNPhiSteps
494        nphi = numPhiSteps              //number of anular sectors is set by users
495       
496        rc = 2*dtdist*asin(qc*lambda/4/Pi)              //in mm
497        delr = nw*sx/2
498        rlo = rc-delr
499        rhi = rc + delr
500        dphi = 360/nphi
501
502        /// data wave is data in the current folder which was set at the top of the function
503        Wave data=$(destPath + ":data")
504        //Check for the existence of the mask, if not, make one (local to this folder) that is null
505       
506        if(WaveExists($"root:Packages:NIST:MSK:data") == 0)
507                Print "There is no mask file loaded (WaveExists)- the data is not masked"
508                Make/O/N=(pixelsX,pixelsY) $(destPath + ":mask")
509                WAVE mask = $(destPath + ":mask")
510                mask = 0
511        else
512                Wave mask=$"root:Packages:NIST:MSK:data"
513        Endif
514       
515        rcentr = 150            //pixels within rcentr of beam center are broken into 9 parts
516        // values for error if unable to estimate value
517        //large_num = 1e10
518        large_num = 1           //1e10 value (typically sig of last data point) plots poorly, arb set to 1
519        small_num = 1e-10
520       
521        // output wave are expected to exist (?) initialized to zero, what length?
522        // 300 points on VAX ---
523        Variable wavePts=500
524        Make/O/N=(wavePts) $(destPath + ":phival"),$(destPath + ":aveint")
525        Make/O/N=(wavePts) $(destPath + ":ncells"),$(destPath + ":sig"),$(destPath + ":sigave")
526        WAVE phival = $(destPath + ":phival")
527        WAVE aveint = $(destPath + ":aveint")
528        WAVE ncells = $(destPath + ":ncells")
529        WAVE sig = $(destPath + ":sig")
530        WAVE sigave = $(destPath + ":sigave")
531
532        phival = 0
533        aveint = 0
534        ncells = 0
535        sig = 0
536        sigave = 0
537
538        dtdis2 = dtdist^2
539        nq = 1
540        xoffst=0
541        //distance of beam center from detector center
542        xbm = FX(x0,sx3,xcenter,sx)
543        ybm = FY(y0,sy3,ycenter,sy)
544               
545        //BEGIN AVERAGE **********
546        Variable xi,xd,x,y,yd,yj,nd,fd,nd2,iphi,ntotal,var
547        Variable jj,data_pixel,xx,yy,ll,kk,rij,phiij,avesq,aveisq
548
549        // IGOR arrays are indexed from [0][0], FORTAN from (1,1) (and the detector too)
550        // loop index corresponds to FORTRAN (old code)
551        // and the IGOR array indices must be adjusted (-1) to the correct address
552        ntotal = 0
553        ii=1
554        do
555                xi = ii
556                xd = FX(xi,sx3,xcenter,sx)
557                x = xoffst + xd -xbm            //x and y are in mm
558               
559                jj = 1
560                do
561                        data_pixel = data[ii-1][jj-1]           //assign to local variable
562                        yj = jj
563                        yd = FY(yj,sy3,ycenter,sy)
564                        y = yd - ybm
565                        if(!(mask[ii-1][jj-1]))                 //masked pixels = 1, skip if masked (this way works...)
566                                nd = 1
567                                fd = 1
568                                if( (abs(x) > rcentr) || (abs(y) > rcentr))     //break pixel into 9 equal parts
569                                        nd = 3
570                                        fd = 2
571                                Endif
572                                nd2 = nd^2
573                                ll = 1          //"el-el" loop index
574                                do
575                                        xx = x + (ll - fd)*sx/3
576                                        kk = 1
577                                        do
578                                                yy = y + (kk - fd)*sy/3
579                                                //test to see if center of pixel (i,j) lies in annulus
580                                                rij = sqrt(x*x + y*y)/dr + 1.001
581                                                //check whether pixel lies within width band
582                                                if((rij > rlo) && (rij < rhi))
583                                                        //in the annulus, do something
584                                                        if (yy >= 0)
585                                                                //phiij is in degrees
586                                                                phiij = atan2(yy,xx)*180/Pi             //0 to 180 deg
587                                                        else
588                                                                phiij = 360 + atan2(yy,xx)*180/Pi               //180 to 360 deg
589                                                        Endif
590                                                        if (phiij > (360-0.5*dphi))
591                                                                phiij -= 360
592                                                        Endif
593                                                        iphi = trunc(phiij/dphi + 1.501)
594                                                        aveint[iphi-1] += 9*data_pixel/nd2
595                                                        sig[iphi-1] += 9*data_pixel*data_pixel/nd2
596                                                        ncells[iphi-1] += 9/nd2
597                                                        ntotal += 9/nd2
598                                                Endif           //check if in annulus
599                                                kk+=1
600                                        while(kk<=nd)
601                                        ll += 1
602                                while(ll<=nd)
603                        Endif           //masked pixel check
604                        jj += 1
605                while (jj<=pixelsY)
606                ii += 1
607        while(ii<=pixelsX)              //end of the averaging
608               
609        //compute phi-values and errors
610       
611        ntotal /=9
612       
613        kk = 1
614        do
615                phival[kk-1] = dphi*(kk-1)
616                if(ncells[kk-1] != 0)
617                        aveint[kk-1] = aveint[kk-1]/ncells[kk-1]
618                        avesq = aveint[kk-1]*aveint[kk-1]
619                        aveisq = sig[kk-1]/ncells[kk-1]
620                        var = aveisq - avesq
621                        if (var <=0 )
622                                sig[kk-1] = 0
623                                sigave[kk-1] = 0
624                                ncells[kk-1] /=9
625                        else
626                                if(ncells[kk-1] > 9)
627                                        sigave[kk-1] = sqrt(9*var/(ncells[kk-1]-9))
628                                        sig[kk-1] = sqrt( abs(aveint[kk-1])/(ncells[kk-1]/9) )
629                                        ncells[kk-1] /=9
630                                else
631                                        sig[kk-1] = 0
632                                        sigave[kk-1] = 0
633                                        ncells[kk-1] /=9
634                                Endif
635                        Endif
636                Endif
637                kk+=1
638        while(kk<=nphi)
639       
640        // data waves were defined as 200 points (=wavePts), but now have less than that (nphi) points
641        // use DeletePoints to remove junk from end of waves
642        Variable startElement,numElements
643        startElement = nphi
644        numElements = wavePts - startElement
645        DeletePoints startElement,numElements, phival,aveint,ncells,sig,sigave
646       
647        //////////////end of VAX Phibin.for
648               
649        //angle dependent transmission correction is not done in phiave
650        Ann_1D_Graph(aveint,phival,sigave)
651       
652        //get rid of the default mask, if one was created (it is in the current folder)
653        //don't just kill "mask" since it might be pointing to the one in the MSK folder
654        Killwaves/z $(destPath+":mask")
655               
656        //return to root folder (redundant)
657        SetDataFolder root:
658       
659        Return 0
660End
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