source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_DetectorCorrections.ipf @ 1112

Last change on this file since 1112 was 1112, checked in by srkline, 4 years ago

a few bug fixes

added menu options to apply the median filter and/or the read noise subtraction to the raw data for troubleshooting/simple analysis rather than needing to convert to normalized WORK data.

File size: 44.2 KB
Line 
1#pragma rtGlobals=3             // Use modern global access method and strict wave access.
2#pragma version=1.0
3#pragma IgorVersion=6.1
4
5
6
7//
8// functions to apply corrections to the detector panels
9//
10// these are meant to be called by the procedures that convert "raw" data to
11// "adjusted" or corrected data sets
12//
13
14
15
16
17//
18// detector dead time
19//
20// input is the data array (N tubes x M pixels)
21// input of N x 1 array of dead time values
22//
23// output is the corrected counts in data, overwriting the input data
24//
25// Note that the equation in Roe (eqn 2.15, p. 63) looks different, but it is really the
26// same old equation, just written in a more complex form.
27//
28// (DONE)
29// x- verify the direction of the tubes and indexing
30// x- decide on the appropriate functional form for the tubes
31// x- need count time as input
32// x- be sure I'm working in the right data folder (all waves are passed in)
33// x- clean up when done
34// x- calculate + return the error contribution?
35// x- verify the error propagation
36Function V_DeadTimeCorrectionTubes(dataW,data_errW,dtW,ctTime)
37        Wave dataW,data_errW,dtW
38        Variable ctTime
39       
40        // do I count on the orientation as an input, or do I just figure it out on my own?
41        String orientation
42        Variable dimX,dimY
43        dimX = DimSize(dataW,0)
44        dimY = DimSize(dataw,1)
45        if(dimX > dimY)
46                orientation = "horizontal"
47        else
48                orientation = "vertical"
49        endif
50       
51        // sum the counts in each tube and divide by time for total cr per tube
52        Variable npt
53       
54        if(cmpstr(orientation,"vertical")==0)
55                //      this is data dimensioned as (Ntubes,Npix)
56               
57                MatrixOp/O sumTubes = sumRows(dataW)            // n x 1 result
58                sumTubes /= ctTime              //now count rate per tube
59               
60                dataW[][] = dataW[p][q]/(1-sumTubes[p]*dtW[p])          //correct the data
61                data_errW[][] = data_errW[p][q]/(1-sumTubes[p]*dtW[p])          // propagate the error wave
62
63        elseif(cmpstr(orientation,"horizontal")==0)
64        //      this is data (horizontal) dimensioned as (Npix,Ntubes)
65
66                MatrixOp/O sumTubes = sumCols(dataW)            // 1 x m result
67                sumTubes /= ctTime
68               
69                dataW[][] = dataW[p][q]/(1-sumTubes[q]*dtW[q])
70                data_errW[][] = data_errW[p][q]/(1-sumTubes[q]*dtW[q])
71       
72        else           
73                DoAlert 0,"Orientation not correctly passed in DeadTimeCorrectionTubes(). No correction done."
74        endif
75       
76        return(0)
77end
78
79// test function
80Function V_testDTCor()
81
82        String detStr = ""
83        String fname = "RAW"
84        Variable ctTime
85       
86        detStr = "FR"
87        Wave w = V_getDetectorDataW(fname,detStr)
88        Wave w_err = V_getDetectorDataErrW(fname,detStr)
89        Wave w_dt = V_getDetector_deadtime(fname,detStr)
90
91        ctTime = V_getCount_time(fname)
92       
93//      ctTime = 10
94        V_DeadTimeCorrectionTubes(w,w_err,w_dt,ctTime)
95
96End
97
98
99//
100// Non-linear data correction
101//
102// DOES NOT modify the data, only calculates the spatial relationship
103//
104// input is the data array (N tubes x M pixels)
105// input of N x M array of quadratic coefficients
106//
107// output is wave of corrected real space distance corresponding to each pixel of the data
108// ** its distance from the nominal beam center of (0,0) **
109//
110//
111// (DONE)
112// x- UNITS!!!! currently this is mm, which certainly doesn't match anything else!!!
113//
114// x- verify the direction of the tubes and indexing
115// x- be sure I'm working in the right data folder (it is passed in, and the full path is used)
116// x- clean up when done
117// x- calculate + return the error contribution? (there is none for this operation)
118// x- do I want this to return a wave? (no, default names are generated)
119// x- do I need to write a separate function that returns the distance wave for later calculations?
120// x- do I want to make the distance array 3D to keep the x and y dims together? Calculate them all right now?
121// x- what else do I need to pass to the function? (fname=folder? detStr?)
122// y- (yes,see below) need a separate block or function to handle "B" detector which will be ? different
123//
124//
125Function V_NonLinearCorrection(fname,dataW,coefW,tube_width,detStr,destPath)
126        String fname            //can also be a folder such as "RAW"
127        Wave dataW,coefW
128        Variable tube_width
129        String detStr,destPath
130       
131         
132        // do I count on the orientation as an input, or do I just figure it out on my own?
133        String orientation
134        Variable dimX,dimY
135        dimX = DimSize(dataW,0)
136        dimY = DimSize(dataW,1)
137        if(dimX > dimY)
138                orientation = "horizontal"
139        else
140                orientation = "vertical"
141        endif
142
143        // make a wave of the same dimensions, in the same data folder for the distance
144        // ?? or a 3D wave?
145        Make/O/D/N=(dimX,dimY) $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistX")
146        Make/O/D/N=(dimX,dimY) $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistY")
147        Wave data_realDistX = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistX")
148        Wave data_realDistY = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistY")
149       
150        // then per tube, do the quadratic calculation to get the real space distance along the tube
151        // the distance perpendicular to the tube is n*(8.4mm) per tube index
152       
153        // TODO
154        // -- GAP IS HARD-WIRED as constant values
155        Variable offset,gap
156
157// kPanelTouchingGap is in mm   
158// the gap is split equally between the panel pairs
159// (DONE) -- replace all of this with V_getDet_panel_gap(fname,detStr) once it is added to the file
160
161        gap = V_getDet_panel_gap(fname,detStr)
162
163// TODO:
164// -- once the gap fields have been verified, this check can be removed
165// -- it should only apply to data pre-2018 when the field did not exist in the file
166// -- any VSANS data from 2018+ should read gap from the file.
167
168        if(gap < -100)          //-999999 returned if field is missing from file
169       
170                if(cmpstr(detStr,"FL") == 0 || cmpstr(detStr,"FR") == 0)
171                        gap = 3.5               //mm (measured, JB 1/4/18)
172                endif
173                if(cmpstr(detStr,"FT") == 0 || cmpstr(detStr,"FB") == 0)
174                        gap = 3.3               //mm (measured, JB 2/1/18)
175                endif
176                if(cmpstr(detStr,"ML") == 0 || cmpstr(detStr,"MR") == 0)
177                        gap = 5.9               //mm (measured, JB 1/4/18)
178                endif
179                if(cmpstr(detStr,"MT") == 0 || cmpstr(detStr,"MB") == 0)
180                        gap = 18.3              //mm (measured, JB 2/1/18)
181                endif
182       
183        endif
184
185       
186        if(cmpstr(orientation,"vertical")==0)
187                //      this is data dimensioned as (Ntubes,Npix)
188       
189                // adjust the x postion based on the beam center being nominally (0,0) in units of cm, not pixels
190                if(cmpstr(fname,"VCALC")== 0 )
191                        offset = VCALC_getPanelTranslation(detStr)
192                        offset *= 10                    // convert to units of mm
193//                      if(cmpstr("L",detStr[1]) == 0)
194//                              offset *= -1            //negative value for L
195//                      endif
196                else
197                        //normal case
198                        offset = V_getDet_LateralOffset(fname,detStr)
199                        offset *= 10 //convert cm to mm
200                endif
201               
202        // calculation is in mm, not cm
203        // offset will be a negative value for the L panel, and positive for the R panel
204                if(kBCTR_CM)
205                        if(cmpstr("L",detStr[1]) == 0)
206//                              data_realDistX[][] = offset - (dimX - p)*tube_width                     // TODO should this be dimX-1-p = 47-p?
207                                data_realDistX[][] = offset - (dimX - p - 1/2)*tube_width - gap/2               // TODO should this be dimX-1-p = 47-p?
208                        else
209                        //      right
210//                              data_realDistX[][] = tube_width*(p+1) + offset + gap            //add to the Right det,
211                                data_realDistX[][] = tube_width*(p+1/2) + offset + gap/2                //add to the Right det
212                        endif
213                else
214                        data_realDistX[][] = tube_width*(p)
215                endif
216                data_realDistY[][] = coefW[0][p] + coefW[1][p]*q + coefW[2][p]*q*q
217       
218       
219        elseif(cmpstr(orientation,"horizontal")==0)
220                //      this is data (horizontal) dimensioned as (Npix,Ntubes)
221                data_realDistY[][] = tube_width*q
222
223                if(cmpstr(fname,"VCALC")== 0 )
224                        offset = VCALC_getPanelTranslation(detStr)
225                        offset *= 10                    // convert to units of mm
226//                      if(cmpstr("B",detStr[1]) == 0)
227//                              offset *= -1    // negative value for Bottom det
228//                      endif
229                else
230                        //normal case
231                        offset = V_getDet_VerticalOffset(fname,detStr)
232                        offset *= 10 //convert cm to mm
233                endif
234               
235                if(kBCTR_CM)
236                        if(cmpstr("T",detStr[1]) == 0)
237//                              data_realDistY[][] = tube_width*(q+1) + offset + gap                   
238                                data_realDistY[][] = tube_width*(q+1/2) + offset + gap/2                       
239                        else
240                                // bottom
241//                              data_realDistY[][] = offset - (dimY - q)*tube_width     // TODO should this be dimY-1-q = 47-q?
242                                data_realDistY[][] = offset - (dimY - q - 1/2)*tube_width - gap/2       // TODO should this be dimY-1-q = 47-q?
243                        endif
244                else
245                        data_realDistY[][] = tube_width*(q)
246                endif
247                data_realDistX[][] = coefW[0][q] + coefW[1][q]*p + coefW[2][q]*p*p
248
249        else           
250                DoAlert 0,"Orientation not correctly passed in NonLinearCorrection(). No correction done."
251                return(0)
252        endif
253       
254        return(0)
255end
256
257
258
259
260// TODO:
261// -- the cal_x and y coefficients are totally fake
262// -- the wave assignment may not be correct.. so beware
263//
264//
265Function V_NonLinearCorrection_B(folder,dataW,cal_x,cal_y,detStr,destPath)
266        String folder
267        Wave dataW,cal_x,cal_y
268        String detStr,destPath
269
270        if(cmpstr(detStr,"B") != 0)
271                return(0)
272        endif
273
274Print "***Cal_X and Cal_Y for Back are using file values ***"
275
276//              cal_x[0] = VCALC_getPixSizeX(detStr)*10                 // pixel size in mm  VCALC_getPixSizeX(detStr) is [cm]
277//              cal_x[1] = 1
278//              cal_x[2] = 10000
279//              cal_y[0] = VCALC_getPixSizeY(detStr)*10                 // pixel size in mm  VCALC_getPixSizeX(detStr) is [cm]
280//              cal_y[1] = 1
281//              cal_y[2] = 10000
282
283       
284        // do I count on the orientation as an input, or do I just figure it out on my own?
285        Variable dimX,dimY
286       
287//      Wave dataW = V_getDetectorDataW(folder,detStr)
288       
289        dimX = DimSize(dataW,0)
290        dimY = DimSize(dataW,1)
291
292        // make a wave of the same dimensions, in the same data folder for the distance
293        // ?? or a 3D wave?
294        Make/O/D/N=(dimX,dimY) $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistX")
295        Make/O/D/N=(dimX,dimY) $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistY")
296        Wave data_realDistX = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistX")
297        Wave data_realDistY = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistY")
298       
299//      Wave cal_x = V_getDet_cal_x(folder,detStr)
300//      Wave cal_y = V_getDet_cal_y(folder,detStr)
301       
302        data_realDistX[][] = cal_x[0]*p*10              // cal_x and cal_y are in [cm], need mm
303        data_realDistY[][] = cal_y[0]*q*10
304       
305        return(0)
306end
307
308
309//
310//
311// TODO
312// -- VERIFY the calculations
313// -- verify where this needs to be done (if the beam center is changed)
314// -- then the q-calculation needs to be re-done
315// -- the position along the tube length is referenced to tube[0], for no particular reason
316//    It may be better to take an average? but [0] is an ASSUMPTION
317// -- distance along tube is simple interpolation, or do I use the coefficients to
318//    calculate the actual value
319//
320// -- distance in the lateral direction is based on tube width, which is a fixed parameter
321//
322//
323Function V_ConvertBeamCtr_to_mm(folder,detStr,destPath)
324        String folder,detStr,destPath
325       
326        Wave data_realDistX = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistX")
327        Wave data_realDistY = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistY")     
328
329        String orientation
330        Variable dimX,dimY,xCtr,yCtr
331        dimX = DimSize(data_realDistX,0)
332        dimY = DimSize(data_realDistX,1)
333        if(dimX > dimY)
334                orientation = "horizontal"
335        else
336                orientation = "vertical"
337        endif
338       
339        xCtr = V_getDet_beam_center_x(folder,detStr)
340        yCtr = V_getDet_beam_center_y(folder,detStr)   
341       
342        Make/O/D/N=1 $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_x_mm")
343        Make/O/D/N=1 $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_y_mm")
344        WAVE x_mm = $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_x_mm")
345        WAVE y_mm = $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_y_mm")
346
347        Variable tube_width = V_getDet_tubeWidth(folder,detStr)
348
349//
350        if(cmpstr(orientation,"vertical")==0)
351                //      this is data dimensioned as (Ntubes,Npix)
352//              data_realDistX[][] = tube_width*p
353//              data_realDistY[][] = coefW[0][p] + coefW[1][p]*q + coefW[2][p]*q*q
354                x_mm[0] = tube_width*xCtr
355                y_mm[0] = data_realDistY[0][yCtr]
356        else
357                //      this is data (horizontal) dimensioned as (Npix,Ntubes)
358//              data_realDistX[][] = coefW[0][q] + coefW[1][q]*p + coefW[2][q]*p*p
359//              data_realDistY[][] = tube_width*q
360                x_mm[0] = data_realDistX[xCtr][0]
361                y_mm[0] = tube_width*yCtr
362        endif
363               
364        return(0)
365end
366
367//
368//
369// (DONE)
370// x- VERIFY the calculations
371// x- verify where this needs to be done (if the beam center is changed)
372// x- then the q-calculation needs to be re-done
373// x- the position along the tube length is referenced to tube[0], for no particular reason
374//    It may be better to take an average? but [0] is an ASSUMPTION
375// x- distance along tube is simple interpolation
376//
377// x- distance in the lateral direction is based on tube width, which is a fixed parameter
378//
379// the value in pixels is written to the local data folder, NOT to disk (it is recalculated as needed)
380//
381Function V_ConvertBeamCtr_to_pix(folder,detStr,destPath)
382        String folder,detStr,destPath
383       
384        Wave data_realDistX = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistX")
385        Wave data_realDistY = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistY")     
386
387        String orientation
388        Variable dimX,dimY,xCtr,yCtr
389        dimX = DimSize(data_realDistX,0)
390        dimY = DimSize(data_realDistX,1)
391        if(dimX > dimY)
392                orientation = "horizontal"
393        else
394                orientation = "vertical"
395        endif
396       
397        xCtr = V_getDet_beam_center_x(folder,detStr)            //these are in cm
398        yCtr = V_getDet_beam_center_y(folder,detStr)   
399       
400        Make/O/D/N=1 $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_x_pix")
401        Make/O/D/N=1 $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_y_pix")
402        WAVE x_pix = $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_x_pix")
403        WAVE y_pix = $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_y_pix")
404
405        Variable tube_width = V_getDet_tubeWidth(folder,detStr)
406
407        variable edge,delta
408        Variable gap
409
410// kPanelTouchingGap is in mm   
411// the gap is split equally between the panel pairs
412// TODO -- replace all of this with V_getDet_panel_gap(fname,detStr) once it is added to the file
413// these hard-wired values were determined from 6A and WB beam centers. LR values were exactly the same for
414// both beam considitions (+/- 0.0 mm). FTB was +/- 0.8 mm, MTB +/- 2 mm
415        if(cmpstr(detStr,"FL") == 0 || cmpstr(detStr,"FR") == 0)
416                gap = 3.8               //mm
417        endif
418        if(cmpstr(detStr,"FT") == 0 || cmpstr(detStr,"FB") == 0)
419                gap = 5         //mm
420        endif
421        if(cmpstr(detStr,"ML") == 0 || cmpstr(detStr,"MR") == 0)
422                gap = 5.9               //mm
423        endif
424        if(cmpstr(detStr,"MT") == 0 || cmpstr(detStr,"MB") == 0)
425                gap = 5         //mm
426        endif
427// TODO: this is the line to keep, to replace the hard-wired values
428//      gap = V_getDet_panel_gap(fname,detStr)
429       
430//
431        if(cmpstr(orientation,"vertical")==0)
432                //      this is data dimensioned as (Ntubes,Npix)
433
434                if(kBCTR_CM)
435                        if(cmpstr("L",detStr[1]) == 0)
436                                edge = data_realDistX[47][0]            //tube 47
437                                delta = abs(xCtr*10 - edge)
438                                x_pix[0] = dimX-1 + delta/tube_width
439                        else
440                        // R panel
441                                edge = data_realDistX[0][0]
442                                delta = abs(xCtr*10 - edge + gap)
443                                x_pix[0] = -delta/tube_width            //since the left edge of the R panel is pixel 0
444                        endif
445                endif
446
447                Make/O/D/N=(dimY) tmpTube
448                tmpTube = data_RealDistY[0][p]
449                FindLevel /P/Q tmpTube, yCtr
450               
451                y_pix[0] = V_levelX
452                KillWaves/Z tmpTube
453        else
454                //      this is data (horizontal) dimensioned as (Npix,Ntubes)
455
456                if(kBCTR_CM)
457                        if(cmpstr("T",detStr[1]) == 0)
458                                edge = data_realDistY[0][0]             //tube 0
459                                delta = abs(yCtr*10 - edge + gap)
460                                y_pix[0] =  -delta/tube_width           //since the bottom edge of the T panel is pixel 0
461                        else
462                        // FM(B) panel
463                                edge = data_realDistY[0][47]            //y tube 47
464                                delta = abs(yCtr*10 - edge)
465                                y_pix[0] = dimY-1 + delta/tube_width            //since the top edge of the B panels is pixel 47               
466                        endif
467                endif
468
469               
470                Make/O/D/N=(dimX) tmpTube
471                tmpTube = data_RealDistX[p][0]
472                FindLevel /P/Q tmpTube, xCtr
473               
474                x_pix[0] = V_levelX
475                KillWaves/Z tmpTube
476               
477               
478        endif
479               
480        return(0)
481end
482
483// converts from [cm] beam center to pixels
484//
485// the value in pixels is written to the local data folder, NOT to disk (it is recalculated as needed)
486//
487Function V_ConvertBeamCtr_to_pixB(folder,detStr,destPath)
488        String folder,detStr,destPath
489       
490        Wave data_realDistX = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistX")
491        Wave data_realDistY = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistY")     
492
493        Variable dimX,dimY,xCtr,yCtr
494        dimX = DimSize(data_realDistX,0)
495        dimY = DimSize(data_realDistX,1)
496       
497        xCtr = V_getDet_beam_center_x(folder,detStr)                    //these are in cm, *10 to get mm
498        yCtr = V_getDet_beam_center_y(folder,detStr)   
499       
500        Make/O/D/N=1 $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_x_pix")
501        Make/O/D/N=1 $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_y_pix")
502        WAVE x_pix = $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_x_pix")
503        WAVE y_pix = $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_y_pix")
504
505
506// simple wave lookup
507// can't use x_pix[0] = data_RealDistX(xCtr)[0] since the data has no x-scale and (xCtr) is interpreted
508// as a point value
509
510//
511//xCtr, yCtr are in cm, *10 to get mm to compare to distance array
512
513        Make/O/D/N=(dimX) tmpTube
514        tmpTube = data_RealDistX[p][0]
515        FindLevel /P/Q tmpTube, xCtr*10
516       
517        x_pix[0] = V_levelX
518        KillWaves/Z tmpTube
519       
520       
521        Make/O/D/N=(dimY) tmpTube
522        tmpTube = data_RealDistY[0][p]
523        FindLevel /P/Q tmpTube, yCtr*10
524       
525        y_pix[0] = V_levelX
526        KillWaves/Z tmpTube
527               
528        print "pixel ctr B = ",x_pix[0],y_pix[0]
529               
530        return(0)
531end
532
533//
534//
535// TODO
536// -- VERIFY the calculations
537// -- verify where this needs to be done (if the beam center is changed)
538// -- then the q-calculation needs to be re-done
539//
540// -- not much is known about the "B" detector, so this
541//    all hinges on the non-linear corrections being done correctly for that detector
542//
543//      Variable detCtrX, detCtrY
544//      // get the pixel center of the detector (not the beam center)
545//      detCtrX = trunc( DimSize(dataW,0)/2 )           //
546//      detCtrY = trunc( DimSize(dataW,1)/2 )
547//
548//
549Function V_ConvertBeamCtr_to_mmB(folder,detStr,destPath)
550        String folder,detStr,destPath
551       
552       
553//      DoAlert 0,"Error - Beam center is being interpreted as pixels, but needs to be in cm. V_ConvertBeamCtr_to_mmB()"
554       
555        Wave data_realDistX = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistX")
556        Wave data_realDistY = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistY")     
557       
558        Variable xCtr,yCtr
559        xCtr = V_getDet_beam_center_x(folder,detStr)
560        yCtr = V_getDet_beam_center_y(folder,detStr)   
561       
562        Make/O/D/N=1 $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_x_mm")
563        Make/O/D/N=1 $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_y_mm")
564        WAVE x_mm = $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_x_mm")
565        WAVE y_mm = $(destPath + ":entry:instrument:detector_"+detStr+":beam_center_y_mm")
566
567        x_mm[0] = data_realDistX[xCtr][0]
568        y_mm[0] = data_realDistY[0][yCtr]
569               
570        return(0)
571end
572
573
574
575
576
577
578/////
579//
580// non-linear corrections to the tube pixels
581// - returns the distance in mm (although this may change)
582//
583// c0,c1,c2,pix
584// c0-c2 are the fit coefficients
585// pix is the test pixel
586//
587// returns the distance in mm (relative to ctr pixel)
588// ctr is the center pixel, as defined when fitting to quadratic was done
589//
590Function V_TubePixel_to_mm(c0,c1,c2,pix)
591        Variable c0,c1,c2,pix
592       
593        Variable dist
594        dist = c0 + c1*pix + c2*pix*pix
595       
596        return(dist)
597End
598//
599////
600
601
602//
603// TESTING ONLY
604Proc V_MakeFakeCalibrationWaves()
605        // make these in the RAW data folder, before converting to a work folder
606        // - then they will be "found" by get()
607        // -- only for the tube, not the Back det
608       
609//      DoAlert 0, "re-do this and do a better job of filling the fake calibration data"
610
611        DoAlert 0, "Calibration waves are read in from the data file"
612       
613//      V_fMakeFakeCalibrationWaves()
614End
615
616
617
618//
619// TESTING ONLY
620//
621// orientation does not matter, there are 48 tubes in each bank
622// so dimension (3,48) for everything.
623//
624// -- but the orientation does indicate TB vs LR, which has implications for
625//  the (fictional) dimension of the pixel along the tube axis, at least as far
626// as for making the fake coefficients.
627//
628Function V_fMakeFakeCalibrationWaves()
629
630        Variable ii,pixSize
631        String detStr,fname="RAW",orientation
632       
633        for(ii=0;ii<ItemsInList(ksDetectorListNoB);ii+=1)
634                detStr = StringFromList(ii, ksDetectorListNoB, ";")
635//              Wave w = V_getDetectorDataW(fname,detStr)
636                Make/O/D/N=(3,48) $("root:Packages:NIST:VSANS:RAW:entry:instrument:detector_"+detStr+":spatial_calibration")
637                Wave calib = $("root:Packages:NIST:VSANS:RAW:entry:instrument:detector_"+detStr+":spatial_calibration")
638                // !!!! this overwrites what is there
639
640                orientation = V_getDet_tubeOrientation(fname,detStr)
641                if(cmpstr(orientation,"vertical")==0)
642                //      this is vertical tube data dimensioned as (Ntubes,Npix)
643                        pixSize = 8.4           //V_getDet_y_pixel_size(fname,detStr)
644                       
645                elseif(cmpstr(orientation,"horizontal")==0)
646                //      this is data (horizontal) dimensioned as (Npix,Ntubes)
647                        pixSize = 4                     //V_getDet_x_pixel_size(fname,detStr)
648                       
649                else           
650                        DoAlert 0,"Orientation not correctly passed in NonLinearCorrection(). No correction done."
651                endif
652               
653                calib[0][] = -(128/2)*pixSize                   //approx (n/2)*pixSixe
654                calib[1][] = pixSize
655                calib[2][] = 2e-4
656               
657        endfor
658       
659        // now fake calibration for "B"
660        Wave cal_x = V_getDet_cal_x("RAW","B")
661        Wave cal_y = V_getDet_cal_y("RAW","B")
662       
663        cal_x = .34             // mm, ignore the other 2 values
664        cal_y = .34             // mm
665        return(0)
666End
667
668//
669// (DONE)
670// x- MUST VERIFY the definition of SDD and how (if) setback is written to the data files
671// x- currently I'm assuming that the SDD is the "nominal" value which is correct for the
672//    L/R panels, but is not correct for the T/B panels (must add in the setback)
673//
674//
675//
676// data_realDistX, Y must be previously generated from running NonLinearCorrection()
677//
678// call with:
679// fname as the WORK folder, "RAW"
680// detStr = detector String, "FL"
681// destPath = path to destination WORK folder ("root:Packages:NIST:VSANS:"+folder)
682//
683Function V_Detector_CalcQVals(fname,detStr,destPath)
684        String fname,detStr,destPath
685
686        String orientation
687        Variable xCtr,yCtr,lambda,sdd
688       
689// get all of the geometry information 
690        orientation = V_getDet_tubeOrientation(fname,detStr)
691
692
693        sdd = V_getDet_ActualDistance(fname,detStr)             //sdd derived, including setback [cm]
694
695        // this is the ctr in pixels --xx-- (now it is in cm!)
696//      xCtr = V_getDet_beam_center_x(fname,detStr)
697//      yCtr = V_getDet_beam_center_y(fname,detStr)
698        // this is ctr in mm
699        xCtr = V_getDet_beam_center_x_mm(fname,detStr)
700        yCtr = V_getDet_beam_center_y_mm(fname,detStr)
701        lambda = V_getWavelength(fname)
702        Wave data_realDistX = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistX")
703        Wave data_realDistY = $(destPath + ":entry:instrument:detector_"+detStr+":data_realDistY")
704
705// make the new waves
706        Duplicate/O data_realDistX $(destPath + ":entry:instrument:detector_"+detStr+":qTot_"+detStr)
707        Duplicate/O data_realDistX $(destPath + ":entry:instrument:detector_"+detStr+":qx_"+detStr)
708        Duplicate/O data_realDistX $(destPath + ":entry:instrument:detector_"+detStr+":qy_"+detStr)
709        Duplicate/O data_realDistX $(destPath + ":entry:instrument:detector_"+detStr+":qz_"+detStr)
710        Wave qTot = $(destPath + ":entry:instrument:detector_"+detStr+":qTot_"+detStr)
711        Wave qx = $(destPath + ":entry:instrument:detector_"+detStr+":qx_"+detStr)
712        Wave qy = $(destPath + ":entry:instrument:detector_"+detStr+":qy_"+detStr)
713        Wave qz = $(destPath + ":entry:instrument:detector_"+detStr+":qz_"+detStr)
714
715// calculate all of the q-values
716// sdd is passed in [cm]
717
718
719// after adding in the 680x1656 back detector, load time was 7.8s, without multithreading
720// with multithreading, 1.9s
721//       qTot = V_CalcQval(p,q,xCtr,yCtr,sdd,lambda,data_realDistX,data_realDistY)
722//              qx = V_CalcQX(p,q,xCtr,yCtr,sdd,lambda,data_realDistX,data_realDistY)
723//              qy = V_CalcQY(p,q,xCtr,yCtr,sdd,lambda,data_realDistX,data_realDistY)
724//              qz = V_CalcQZ(p,q,xCtr,yCtr,sdd,lambda,data_realDistX,data_realDistY)   
725
726        MultiThread qTot = V_CalcQval(p,q,xCtr,yCtr,sdd,lambda,data_realDistX,data_realDistY)
727        MultiThread     qx = V_CalcQX(p,q,xCtr,yCtr,sdd,lambda,data_realDistX,data_realDistY)
728        MultiThread     qy = V_CalcQY(p,q,xCtr,yCtr,sdd,lambda,data_realDistX,data_realDistY)
729        MultiThread     qz = V_CalcQZ(p,q,xCtr,yCtr,sdd,lambda,data_realDistX,data_realDistY)
730       
731        return(0)
732End
733
734
735//function to calculate the overall q-value, given all of the necesary trig inputs
736//
737// (DONE)
738// x- verify the calculation (accuracy - in all input conditions)
739// x- verify the units of everything here, it's currently all jumbled and wrong... and repeated
740// x- the input data_realDistX and Y are essentially lookup tables of the real space distance corresponding
741//    to each pixel
742//
743//sdd is in [cm]
744// distX and distY are in [mm]
745//wavelength is in Angstroms
746//
747//returned magnitude of Q is in 1/Angstroms
748//
749ThreadSafe Function V_CalcQval(xaxval,yaxval,xctr,yctr,sdd,lam,distX,distY)
750        Variable xaxval,yaxval,xctr,yctr,sdd,lam
751        Wave distX,distY
752       
753        Variable dx,dy,qval,two_theta,dist
754               
755
756        dx = (distX[xaxval][yaxval] - xctr)             //delta x in mm
757        dy = (distY[xaxval][yaxval] - yctr)             //delta y in mm
758        dist = sqrt(dx^2 + dy^2)
759       
760        dist /= 10  // convert mm to cm
761       
762        two_theta = atan(dist/sdd)
763
764        qval = 4*Pi/lam*sin(two_theta/2)
765       
766        return qval
767End
768
769//calculates just the q-value in the x-direction on the detector
770// (DONE)
771// x- verify the calculation (accuracy - in all input conditions)
772// x- verify the units of everything here, it's currently all jumbled and wrong... and repeated
773// x- the input data_realDistX and Y are essentially lookup tables of the real space distance corresponding
774//    to each pixel
775//
776//
777// this properly accounts for qz
778//
779ThreadSafe Function V_CalcQX(xaxval,yaxval,xctr,yctr,sdd,lam,distX,distY)
780        Variable xaxval,yaxval,xctr,yctr,sdd,lam
781        Wave distX,distY
782
783        Variable qx,qval,phi,dx,dy,dist,two_theta
784       
785        qval = V_CalcQval(xaxval,yaxval,xctr,yctr,sdd,lam,distX,distY)
786       
787
788        dx = (distX[xaxval][yaxval] - xctr)             //delta x in mm
789        dy = (distY[xaxval][yaxval] - yctr)             //delta y in mm
790        phi = V_FindPhi(dx,dy)
791       
792        //get scattering angle to project onto flat detector => Qr = qval*cos(theta)
793        dist = sqrt(dx^2 + dy^2)
794        dist /= 10  // convert mm to cm
795
796        two_theta = atan(dist/sdd)
797
798        qx = qval*cos(two_theta/2)*cos(phi)
799       
800        return qx
801End
802
803//calculates just the q-value in the y-direction on the detector
804// (DONE)
805// x- verify the calculation (accuracy - in all input conditions)
806// x- verify the units of everything here, it's currently all jumbled and wrong... and repeated
807// x- the input data_realDistX and Y are essentially lookup tables of the real space distance corresponding
808//    to each pixel
809//
810//
811// this properly accounts for qz
812//
813ThreadSafe Function V_CalcQY(xaxval,yaxval,xctr,yctr,sdd,lam,distX,distY)
814        Variable xaxval,yaxval,xctr,yctr,sdd,lam
815        Wave distX,distY
816
817        Variable qy,qval,phi,dx,dy,dist,two_theta
818       
819        qval = V_CalcQval(xaxval,yaxval,xctr,yctr,sdd,lam,distX,distY)
820       
821
822        dx = (distX[xaxval][yaxval] - xctr)             //delta x in mm
823        dy = (distY[xaxval][yaxval] - yctr)             //delta y in mm
824        phi = V_FindPhi(dx,dy)
825       
826        //get scattering angle to project onto flat detector => Qr = qval*cos(theta)
827        dist = sqrt(dx^2 + dy^2)
828        dist /= 10  // convert mm to cm
829
830        two_theta = atan(dist/sdd)
831
832        qy = qval*cos(two_theta/2)*sin(phi)
833       
834        return qy
835End
836
837//calculates just the q-value in the z-direction on the detector
838// (DONE)
839// x- verify the calculation (accuracy - in all input conditions)
840// x- verify the units of everything here, it's currently all jumbled and wrong... and repeated
841// x- the input data_realDistX and Y are essentially lookup tables of the real space distance corresponding
842//    to each pixel
843//
844// not actually used for any calculations, but here for completeness if anyone asks, or for 2D data export
845//
846// this properly accounts for qz, because it is qz
847//
848ThreadSafe Function V_CalcQZ(xaxval,yaxval,xctr,yctr,sdd,lam,distX,distY)
849        Variable xaxval,yaxval,xctr,yctr,sdd,lam
850        Wave distX,distY
851
852        Variable qz,qval,phi,dx,dy,dist,two_theta
853       
854        qval = V_CalcQval(xaxval,yaxval,xctr,yctr,sdd,lam,distX,distY)
855       
856
857        dx = (distX[xaxval][yaxval] - xctr)             //delta x in mm
858        dy = (distY[xaxval][yaxval] - yctr)             //delta y in mm
859       
860        //get scattering angle to project onto flat detector => Qr = qval*cos(theta)
861        dist = sqrt(dx^2 + dy^2)
862        dist /= 10  // convert mm to cm
863
864        two_theta = atan(dist/sdd)
865
866        qz = qval*sin(two_theta/2)
867       
868        return qz
869End
870
871
872//
873// (DONE)
874// x- VERIFY calculations
875// x- This is the actual solid angle per pixel, not a ratio vs. some "unit SA"
876//    Do I just correct for the different area vs. the "nominal" central area?
877// x- decide how to implement - YES - directly change the data values (as was done in the past)
878//    or (NOT done this way...use this as a weighting for when the data is binned to I(q). In the second method, 2D data
879//    would need this to be applied before exporting)
880// x- do I keep a wave note indicating that this correction has been applied to the data
881//    so that it can be "un-applied"? NO
882// x- do I calculate theta from geometry directly, or get it from Q (Assuming it's present?)
883//    (YES just from geometry, since I need SDD and dx and dy values...)
884//
885//
886Function V_SolidAngleCorrection(w,w_err,fname,detStr,destPath)
887        Wave w,w_err
888        String fname,detStr,destPath
889
890        Variable sdd,xCtr,yCtr,lambda
891
892// get all of the geometry information 
893//      orientation = V_getDet_tubeOrientation(fname,detStr)
894        sdd = V_getDet_ActualDistance(fname,detStr)
895
896
897        // this is ctr in mm
898        xCtr = V_getDet_beam_center_x_mm(fname,detStr)
899        yCtr = V_getDet_beam_center_y_mm(fname,detStr)
900        lambda = V_getWavelength(fname)
901       
902        SetDataFolder $(destPath + ":entry:instrument:detector_"+detStr)
903       
904        Wave data_realDistX = data_realDistX
905        Wave data_realDistY = data_realDistY
906
907        Duplicate/O w solid_angle,tmp_theta,tmp_dist            //in the current df
908
909//// calculate the scattering angle
910//      dx = (distX - xctr)             //delta x in mm
911//      dy = (distY - yctr)             //delta y in mm
912        tmp_dist = sqrt((data_realDistX - xctr)^2 + (data_realDistY - yctr)^2)
913       
914        tmp_dist /= 10  // convert mm to cm
915        // sdd is in [cm]
916
917        tmp_theta = atan(tmp_dist/sdd)          //this is two_theta, the scattering angle
918
919        Variable ii,jj,numx,numy,dx,dy
920        numx = DimSize(tmp_theta,0)
921        numy = DimSize(tmp_theta,1)
922       
923        for(ii=0        ;ii<numx;ii+=1)
924                for(jj=0;jj<numy;jj+=1)
925                       
926                        if(ii==0)               //do a forward difference if ii==0
927                                dx = (data_realDistX[ii+1][jj] - data_realDistX[ii][jj])        //delta x for the pixel
928                        else
929                                dx = (data_realDistX[ii][jj] - data_realDistX[ii-1][jj])        //delta x for the pixel
930                        endif
931                       
932                       
933                        if(jj==0)
934                                dy = (data_realDistY[ii][jj+1] - data_realDistY[ii][jj])        //delta y for the pixel
935                        else
936                                dy = (data_realDistY[ii][jj] - data_realDistY[ii][jj-1])        //delta y for the pixel
937                        endif
938       
939                        dx /= 10
940                        dy /= 10                // convert mm to cm (since sdd is in cm)
941                        solid_angle[ii][jj] = dx*dy             //this is in cm^2
942                endfor
943        endfor
944       
945        // to cover up any issues w/negative dx or dy
946        solid_angle = abs(solid_angle)
947       
948        // solid_angle correction
949        // == dx*dy*cos^3/sdd^2
950        solid_angle *= (cos(tmp_theta))^3
951        solid_angle /= sdd^2
952       
953        // Here it is! Apply the correction to the intensity (I divide -- to get the counts per solid angle!!)
954        w /= solid_angle
955       
956        //
957        // correctly apply the correction to the error wave (assume a perfect value?)
958        w_err /= solid_angle            //
959
960// DONE x- clean up after I'm satisfied computations are correct               
961        KillWaves/Z tmp_theta,tmp_dist
962       
963        return(0)
964end
965
966
967
968
969//
970// Large angle transmission correction
971//
972// DIVIDE the intensity by this correction to get the right answer
973//
974//
975// Apply the large angle transmssion correction as the data is converted to WORK
976// so that whether the data is saved as 2D or 1D, the correction has properly been done.
977//
978// This is, however, a SAMPLE dependent calculation, not purely instrument geometry.
979//
980Function V_LargeAngleTransmissionCorr(w,w_err,fname,detStr,destPath)
981        Wave w,w_err
982        String fname,detStr,destPath
983
984        Variable sdd,xCtr,yCtr,trans,trans_err,uval
985
986// get all of the geometry information 
987//      orientation = V_getDet_tubeOrientation(fname,detStr)
988        sdd = V_getDet_ActualDistance(fname,detStr)
989
990        // this is ctr in mm
991        xCtr = V_getDet_beam_center_x_mm(fname,detStr)
992        yCtr = V_getDet_beam_center_y_mm(fname,detStr)
993        trans = V_getSampleTransmission(fname)
994        trans_err = V_getSampleTransError(fname)
995       
996        SetDataFolder $(destPath + ":entry:instrument:detector_"+detStr)
997       
998        Wave data_realDistX = data_realDistX
999        Wave data_realDistY = data_realDistY
1000
1001        Duplicate/O w lat_corr,tmp_theta,tmp_dist,lat_err,tmp_err               //in the current df
1002
1003//// calculate the scattering angle
1004//      dx = (distX - xctr)             //delta x in mm
1005//      dy = (distY - yctr)             //delta y in mm
1006        tmp_dist = sqrt((data_realDistX - xctr)^2 + (data_realDistY - yctr)^2)
1007       
1008        tmp_dist /= 10  // convert mm to cm
1009        // sdd is in [cm]
1010
1011        tmp_theta = atan(tmp_dist/sdd)          //this is two_theta, the scattering angle
1012
1013        Variable ii,jj,numx,numy,dx,dy,cos_th,arg,tmp
1014        numx = DimSize(tmp_theta,0)
1015        numy = DimSize(tmp_theta,1)
1016       
1017       
1018        //optical thickness
1019        uval = -ln(trans)               //use natural logarithm
1020       
1021        for(ii=0        ;ii<numx;ii+=1)
1022                for(jj=0;jj<numy;jj+=1)
1023                       
1024                        cos_th = cos(tmp_theta[ii][jj])
1025                        arg = (1-cos_th)/cos_th
1026                       
1027                        // a Taylor series around uval*arg=0 only needs about 4 terms for very good accuracy
1028                        //                      correction= 1 - 0.5*uval*arg + (uval*arg)^2/6 - (uval*arg)^3/24 + (uval*arg)^4/120
1029                        // OR
1030                        if((uval<0.01) || (cos_th>0.99))       
1031                                //small arg, approx correction
1032                                lat_corr[ii][jj] = 1-0.5*uval*arg
1033                        else
1034                                //large arg, exact correction
1035                                lat_corr[ii][jj] = (1-exp(-uval*arg))/(uval*arg)
1036                        endif
1037                         
1038                        // (DONE)
1039                        // x- properly calculate and apply the 2D error propagation
1040                        if(trans == 1)
1041                                lat_err[ii][jj] = 0             //no correction, no error
1042                        else
1043                                //sigT, calculated from the Taylor expansion
1044                                tmp = (1/trans)*(arg/2-arg^2/3*uval+arg^3/8*uval^2-arg^4/30*uval^3)
1045                                tmp *= tmp
1046                                tmp *= trans_err^2
1047                                tmp = sqrt(tmp)         //sigT
1048                               
1049                                lat_err[ii][jj] = tmp
1050                        endif
1051                         
1052 
1053                endfor
1054        endfor
1055       
1056
1057       
1058        // Here it is! Apply the correction to the intensity (divide -- to get the proper correction)
1059        w /= lat_corr
1060
1061        // relative errors add in quadrature to the current 2D error
1062        tmp_err = (w_err/lat_corr)^2 + (lat_err/lat_corr)^2*w*w/lat_corr^2
1063        tmp_err = sqrt(tmp_err)
1064       
1065        w_err = tmp_err
1066       
1067
1068        // DONE x- clean up after I'm satisfied computations are correct               
1069        KillWaves/Z tmp_theta,tmp_dist,tmp_err,lat_err
1070       
1071        return(0)
1072end
1073
1074
1075
1076//
1077//test procedure, not called anymore
1078Proc V_AbsoluteScaling(type,c0,c1,c2,c3,c4,c5,I_err)
1079        String type
1080        Variable c0=1,c1=0.1,c2=0.95,c3=0.1,c4=1,c5=32.0,I_err=0.32
1081        Prompt type,"WORK data type",popup,"CAL;COR;SAM"
1082        Prompt c0, "Sample Transmission"
1083        Prompt c1, "Sample Thickness (cm)"
1084        Prompt c2, "Standard Transmission"
1085        Prompt c3, "Standard Thickness (cm)"
1086        Prompt c4, "I(0) from standard fit (normalized to 1E8 monitor cts)"
1087        Prompt c5, "Standard Cross-Section (cm-1)"
1088        Prompt I_err, "error in I(q=0) (one std dev)"
1089
1090        Variable err
1091        //call the function to do the math
1092        //data from "type" will be scaled and deposited in ABS
1093        err = V_Absolute_Scale(type,c0,c1,c2,c3,c4,c5,I_err)
1094       
1095        if(err)
1096                Abort "Error in V_Absolute_Scale()"
1097        endif
1098       
1099        //contents are always dumped to ABS
1100        type = "ABS"
1101       
1102        //need to update the display with "data" from the correct dataFolder
1103        //reset the current display type to "type"
1104        SVAR gCurDispType = root:Packages:NIST:VSANS:Globals:gCurDispType
1105        gCurDispType = Type     
1106       
1107        V_UpdateDisplayInformation(Type)
1108       
1109End
1110
1111//
1112//
1113// kappa comes in as s_izero, so be sure to use 1/kappa_err
1114//
1115//convert the "type" data to absolute scale using the given standard information
1116//s_ is the standard
1117//w_ is the "work" file
1118//both are work files and should already be normalized to 10^8 monitor counts
1119Function V_Absolute_Scale(type,absStr)
1120        String type,absStr
1121       
1122       
1123        Variable w_trans,w_thick,s_trans,s_thick,s_izero,s_cross,kappa_err
1124
1125        Variable defmon = 1e8,w_moncount,s1,s2,s3,s4
1126        Variable scale,trans_err
1127        Variable err,ii
1128        String detStr
1129       
1130        // be sure that the starting data exists
1131        err = V_WorkDataExists(type)
1132        if(err==1)
1133                return(err)
1134        endif
1135               
1136        //copy from current dir (type) to ABS
1137        V_CopyHDFToWorkFolder(type,"ABS")       
1138
1139// TODO: -- which monitor to use? Here, I think it should already be normalized to 10^8
1140//     
1141//      w_moncount = V_getMonitorCount(type)            //monitor count in "type"
1142       
1143        w_moncount = V_getBeamMonNormData(type)
1144               
1145        if(w_moncount == 0)
1146                //zero monitor counts will give divide by zero ---
1147                DoAlert 0,"Total monitor count in data file is zero. No rescaling of data"
1148                Return(1)               //report error
1149        Endif
1150
1151        w_trans = V_getSampleTransmission(type)         //sample transmission
1152        w_thick = V_getSampleThickness(type)            //sample thickness
1153        trans_err = V_getSampleTransError(type)
1154       
1155       
1156        //get the parames from the list
1157        s_trans = NumberByKey("TSTAND", absStr, "=", ";")       //parse the list of values
1158        s_thick = NumberByKey("DSTAND", absStr, "=", ";")
1159        s_izero = NumberByKey("IZERO", absStr, "=", ";")
1160        s_cross = NumberByKey("XSECT", absStr, "=", ";")
1161        kappa_err = NumberByKey("SDEV", absStr, "=", ";")
1162
1163       
1164        //calculate scale factor
1165        s1 = defmon/w_moncount          // monitor count (s1 should be 1)
1166        s2 = s_thick/w_thick
1167        s3 = s_trans/w_trans
1168        s4 = s_cross/s_izero
1169        scale = s1*s2*s3*s4
1170
1171       
1172        // kappa comes in as s_izero, so be sure to use 1/kappa_err
1173
1174        // and now loop through all of the detectors
1175        //do the actual absolute scaling here, modifying the data in ABS
1176        for(ii=0;ii<ItemsInList(ksDetectorListNoB);ii+=1)
1177                detStr = StringFromList(ii, ksDetectorListNoB, ";")
1178                Wave data = V_getDetectorDataW("ABS",detStr)
1179                Wave data_err = V_getDetectorDataErrW("ABS",detStr)
1180               
1181                data *= scale
1182                data_err = sqrt(scale^2*data_err^2 + scale^2*data^2*(kappa_err^2/s_izero^2 +trans_err^2/w_trans^2))
1183        endfor
1184
1185        // do the back detector separately, if it is set to be used
1186        NVAR gIgnoreDetB = root:Packages:NIST:VSANS:Globals:gIgnoreDetB
1187        if(gIgnoreDetB == 0)
1188                detStr = "B"
1189                Wave data = V_getDetectorDataW("ABS",detStr)
1190                Wave data_err = V_getDetectorDataErrW("ABS",detStr)
1191               
1192                //get the parames from the list
1193                s_trans = NumberByKey("TSTAND_B", absStr, "=", ";")     //parse the list of values
1194                s_thick = NumberByKey("DSTAND_B", absStr, "=", ";")
1195                s_izero = NumberByKey("IZERO_B", absStr, "=", ";")
1196                s_cross = NumberByKey("XSECT_B", absStr, "=", ";")
1197                kappa_err = NumberByKey("SDEV_B", absStr, "=", ";")
1198
1199                //calculate scale factor
1200                s1 = defmon/w_moncount          // monitor count (s1 should be 1)
1201                s2 = s_thick/w_thick
1202                s3 = s_trans/w_trans
1203                s4 = s_cross/s_izero
1204                scale = s1*s2*s3*s4
1205               
1206                data *= scale
1207                data_err = sqrt(scale^2*data_err^2 + scale^2*data^2*(kappa_err^2/s_izero^2 +trans_err^2/w_trans^2))
1208        endif
1209       
1210        //********* 15APR02
1211        // DO NOT correct for atenuators here - the COR step already does this, putting all of the data on equal
1212        // footing (zero atten) before doing the subtraction.
1213       
1214        Return (0) //no error
1215End
1216
1217
1218//
1219// TODO:
1220//   --         DoAlert 0,"This has not yet been updated for VSANS"
1221//
1222//
1223// match the attenuation of the RAW data to the "type" data
1224// so that they can be properly added
1225//
1226// are the attenuator numbers the same? if so exit
1227//
1228// if not, find the attenuator number for type
1229// - find both attenuation factors
1230//
1231// rescale the raw data to match the ratio of the two attenuation factors
1232// -- adjust the detector count (rw)
1233// -- the linear data
1234//
1235//
1236Function V_Adjust_RAW_Attenuation(type)
1237        String type
1238
1239        DoAlert 0,"This has not yet been updated for VSANS"
1240       
1241        WAVE rw=$("root:Packages:NIST:RAW:realsread")
1242        WAVE linear_data=$("root:Packages:NIST:RAW:linear_data")
1243        WAVE data=$("root:Packages:NIST:RAW:data")
1244        WAVE data_err=$("root:Packages:NIST:RAW:linear_data_error")
1245        WAVE/T tw = $("root:Packages:NIST:RAW:textRead")
1246       
1247        WAVE dest_reals=$("root:Packages:NIST:"+type+":realsread")
1248
1249        Variable dest_atten,raw_atten,tol
1250        Variable lambda,raw_atten_err,raw_AttenFactor,dest_attenFactor,dest_atten_err
1251        String fileStr
1252
1253        dest_atten = dest_reals[3]
1254        raw_atten = rw[3]
1255       
1256        tol = 0.1               // within 0.1 atten units is OK
1257        if(abs(dest_atten - raw_atten) < tol )
1258                return(0)
1259        endif
1260
1261        fileStr = tw[3]
1262        lambda = rw[26]
1263        // TODO access correct values
1264        raw_AttenFactor = 1//AttenuationFactor(fileStr,lambda,raw_atten,raw_atten_err)
1265        dest_AttenFactor = 1//AttenuationFactor(fileStr,lambda,dest_atten,dest_atten_err)
1266               
1267        rw[2] *= dest_AttenFactor/raw_AttenFactor
1268        linear_data *= dest_AttenFactor/raw_AttenFactor
1269       
1270        // to keep "data" and linear_data in sync
1271        data = linear_data
1272       
1273        return(0)
1274End
1275
1276//
1277// testing procedure, called from a menu selection
1278//
1279Proc V_DIV_a_Workfile(type)
1280        String type
1281        Prompt type,"WORK data type",popup,"SAM;EMP;BGD;ADJ;"
1282       
1283        //macro will take whatever is in SELECTED folder and DIVide it by the current
1284        //contents of the DIV folder - the function will check for existence
1285        //before proceeding
1286
1287        Abort "This has not yet been updated for VSANS"
1288       
1289        Variable err
1290        err = V_DIVCorrection(type)             //returns err = 1 if data doesn't exist in specified folders
1291       
1292        if(err)
1293                Abort "error in V_DIVCorrection()"
1294        endif
1295       
1296        //contents are NOT always dumped to CAL, but are in the new type folder
1297       
1298        String newTitle = "WORK_"+type
1299        DoWindow/F VSANS_Data
1300        DoWindow/T VSANS_Data, newTitle
1301        KillStrings/Z newTitle
1302       
1303        //need to update the display with "data" from the correct dataFolder
1304        //reset the current displaytype to "type"
1305        String/G root:Packages:NIST:VSANS:Globals:gCurDispType=Type
1306       
1307        V_UpdateDisplayInformation(type)
1308       
1309End
1310
1311
1312//
1313// TODO:
1314//   x-         DoAlert 0,"This has not yet been updated for VSANS"
1315//   -- how is the error propagation handled? Be sure it is calculated correctly when DIV is generated
1316//      and is applied correctly here...
1317//
1318//function will divide the contents of "workType" folder with the contents of
1319//the DIV folder + detStr
1320// all data is linear scale for the calculation
1321//
1322Function V_DIVCorrection(data,data_err,detStr,workType)
1323        Wave data,data_err
1324        String detStr,workType
1325       
1326        //check for existence of data in type and DIV
1327        // if the desired data doesn't exist, let the user know, and abort
1328        String destPath=""
1329
1330        NVAR gIgnoreDetB = root:Packages:NIST:VSANS:Globals:gIgnoreDetB
1331        if(cmpstr(detStr,"B")==0 && gIgnoreDetB)
1332                return(0)
1333        endif
1334
1335
1336        if(WaveExists(data) == 0)
1337                Print "The data wave does not exist in V_DIVCorrection()"
1338                Return(1)               //error condition
1339        Endif
1340       
1341        //check for DIV
1342        // if the DIV workfile doesn't exist, let the user know,and abort
1343        // !! be sure to check first, before trying to access the wave
1344       
1345//      WAVE/Z div_data = $("root:Packages:NIST:VSANS:DIV:entry:instrument:detector_"+detStr+":data")
1346        if(WaveExists($("root:Packages:NIST:VSANS:DIV:entry:instrument:detector_"+detStr+":data")) == 0)
1347                Print "The DIV wave does not exist in V_DIVCorrection()"
1348                Return(1)               //error condition
1349        Endif
1350        if(WaveExists($("root:Packages:NIST:VSANS:DIV:entry:instrument:detector_"+detStr+":linear_data_error")) == 0)
1351                Print "The DIV error wave does not exist in V_DIVCorrection()"
1352                Return(1)               //error condition
1353        Endif
1354        //files exist, proceed
1355
1356        WAVE/Z div_data_err = V_getDetectorDataErrW("DIV",detStr)
1357        WAVE/Z div_data = V_getDetectorDataW("DIV",detStr)
1358
1359
1360
1361// do the error propagation first, since data is changed by the correction
1362        data_err = sqrt(data_err^2/div_data^2 + div_data_err^2 * data^2/div_data^4 )
1363
1364// then the correction
1365        data /= div_data
1366
1367       
1368        Return(0)
1369End
1370
1371
1372//////////////////////////
1373// detector corrections to stitch the back detector into one proper image
1374//
1375//
1376//
1377
1378
1379//
1380// to register the image on the back detector panel
1381//
1382// middle portion (552 pix in Y) is held fixed
1383// top portion of image is shifted right and down
1384// bottom portion of image is shifted right and up
1385//
1386// remainder of image is filled with Zero (NaN causes problems converting to WORK)
1387//
1388// currently, data is not added together and averaged, but it could be
1389//
1390Function V_ShiftBackDetImage(w,adjW)
1391        Wave w,adjW
1392
1393// this is necessary for some old data with the 150x150 back (dummy) panel
1394        NVAR gIgnoreDetB = root:Packages:NIST:VSANS:Globals:gIgnoreDetB
1395        if(gIgnoreDetB == 1)
1396                adjW=w
1397                return(0)
1398        endif
1399       
1400        adjW=0
1401       
1402//      Variable topX,bottomX
1403//      Variable topY,bottomY
1404       
1405//      topX = 7
1406//      topY = 105
1407       
1408//      bottomX = 5
1409//      bottomY = 35
1410       
1411        // middle
1412        adjW[][552,552+552] = w[p][q]
1413
1414        //top
1415        adjW[0+kShift_topX,679][552+552,1655-kShift_topY] = w[p-kShift_topX][q+kShift_topY]
1416       
1417        //bottom
1418        adjW[0+kShift_bottomX,679][0+kShift_bottomY,551] = w[p-kShift_bottomX][q-kShift_bottomY]
1419       
1420        return(0)
1421End
1422
1423
1424Proc pV_MedianFilterBack(folder)
1425        String folder="RAW"
1426       
1427        V_MedianFilterBack(folder)
1428end
1429
1430Function V_MedianFilterBack(folder)
1431        String folder
1432
1433        Wave w = V_getDetectorDataW(folder,"B")
1434//              w -= kReadNoiseLevel            // a constant value
1435       
1436        MatrixFilter /N=3 median w
1437        Print "*** median noise filter applied to the back detector***"
1438       
1439        return(0)
1440End
1441
1442
1443Proc pV_SubtractReadNoiseBack(folder,ReadNoise)
1444        String folder="RAW"
1445        Variable readNoise=200
1446       
1447        V_SubtractReadNoiseBack(folder,readNoise)
1448end
1449
1450Function V_SubtractReadNoiseBack(folder,readNoise)
1451        String folder
1452        Variable readNoise
1453
1454                Wave w = V_getDetectorDataW(folder,"B")
1455                w -= readNoise          // a constant value
1456               
1457//              MatrixFilter /N=3 median w
1458//              Print "*** median noise filter applied to the back detector***"
1459       
1460        return(0)
1461End
1462
1463
1464Proc pV_MedianAndReadNoiseBack(folder,ReadNoise)
1465        String folder="RAW"
1466        Variable readNoise=200
1467       
1468        V_MedianAndReadNoiseBack(folder,readNoise)
1469end
1470
1471Function V_MedianAndReadNoiseBack(folder,readNoise)
1472        String folder
1473        Variable readNoise
1474
1475                Wave w = V_getDetectorDataW(folder,"B")
1476                w -= readNoise          // a constant value
1477               
1478                MatrixFilter /N=3 median w
1479                Print "*** median noise filter applied to the back detector***"
1480       
1481        return(0)
1482End
1483
Note: See TracBrowser for help on using the repository browser.