source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/MultScatter_MonteCarlo_2D.ipf @ 596

Last change on this file since 596 was 596, checked in by srkline, 13 years ago

changes to how a fake VAX raw data file is written out. now call accepts optional parameters so that the index and label can be supplied, and the MC simulation can be very crudely scripted for unattended operation.

File size: 60.8 KB
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1#pragma rtGlobals=1             // Use modern global access method.
2#pragma IgorVersion=6.1
3
4//
5// Monte Carlo simulator for SASCALC
6// October 2008 SRK
7//
8// This code simulates the scattering for a selected model based on the instrument configuration
9// This code is based directly on John Barker's code, which includes multiple scattering effects.
10// A lot of the setup, wave creation, and post-calculations are done in SASCALC->ReCalculateInten()
11//
12//
13// at the end of the procedure fils is a *very* simple example of scripting for unattended simulations
14// - not for the casual user at all.
15
16
17
18// the RNG issue is really not worth the effort. multiple copies with different RNG is as good as I need. Plus,
19// whatever XOP crashing was happining during threading is really unlikely to be from the RNG
20//
21// *** look into erand48() as the (pseudo) random number generator (it's a standard c-lib function, at least on unix)
22//     and is apparantly thread safe. drand48() returns values [0.0,1.0)
23//http://qnxcs.unomaha.edu/help/product/neutrino/lib_ref/e/erand48.html
24//
25
26
27// - Why am I off by a factor of 2.7 - 3.7 (MC too high) relative to real data?
28//   I need to include efficiency (70%?) - do I knock these off before the simulation or do I
29//    really simulate that some fraction of neutrons on the detector don't actually get counted?
30//   Is the flux estimate up-to-date? !! Flux estimates at NG3 are out-of-date....
31// - my simulated transmission is larger than what is measured, even after correcting for the quartz cell.
32//   Why? Do I need to include absorption? Just inherent problems with incoherent cross sections?
33
34// - Most importantly, this needs to be checked for correctness of the MC simulation
35// X how can I get the "data" on absolute scale? This would be a great comparison vs. the ideal model calculation
36// X why does my integrated tau not match up with John's analytical calculations? where are the assumptions?
37// X get rid of all small angle assumptions - to make sure that the calculation is correct at all angles
38
39//
40// X at the larger angles, is the "flat" detector being properly accounted for - in terms of
41//   the solid angle and how many counts fall in that pixel. Am I implicitly defining a spherical detector
42//   so that what I see is already "corrected"?
43// X the MC will, of course benefit greatly from being XOPized. Maybe think about parallel implementation
44//   by allowing the data arrays to accumulate. First pass at the XOP is done. Not pretty, not the speediest (5.8x)
45//   but it is functional. Add spinCursor() for long calculations. See WaveAccess XOP example.
46// X the background parameter for the model MUST be zero, or the integration for scattering
47//    power will be incorrect. (now the LAST point in a copy of the coef wave is set to zero, only for the rad_dev calculation
48// X fully use the SASCALC input, most importantly, flux on sample.
49// X if no MC desired, still use the selected model
50// X better display of MC results on panel
51// X settings for "count for X seconds" or "how long to 1E6 cts on detector" (but 1E6 is typically too many counts...)
52// X warn of projected simulation time
53// - add quartz window scattering to the simulation somehow
54// -?- do smeared models make any sense?? Yes, John agrees that they do, and may be used in a more realistic simulation
55//   -?- but the random deviate can't be properly calculated...
56// - make sure that the ratio of scattering coherent/incoherent is properly adjusted for the sample composition
57//   or the volume fraction of solvent.
58//
59// X add to the results the fraction of coherently scattered neutrons that are singly scattered, different than
60//   the overall fraction of singly scattered, and maybe more important to know.
61//
62// X change the fraction reaching the detector to exclude those that don't interact. These transmitted neutrons
63//   aren't counted. Is the # that interact a better number?
64//
65// - do we want to NOT offset the data by a multiplicative factor as it is "frozen" , so that the
66//   effects on the absolute scale can be seen?
67//
68// X why is "pure" incoherent scattering giving me a q^-1 slope, even with the detector all the way back?
69// -NO- can I speed up by assuming everything interacts? This would compromise the ability to calculate multiple scattering
70// X ask John how to verify what is going on
71// - a number of models are now found to be ill-behaved when q=1e-10. Then the random deviate calculation blows up.
72//   a warning has been added - but some models need a proper limiting value, and some (power-law) are simply unuseable
73//   unless something else can be done. Using a log-spacing of points doesn't seem to help, and it introduces a lot of
74//   other problems. Not the way to go.
75// - if the MC gags on a simulation, it often gets "stuck" and can't do the normal calculation from the model, which it
76//   should always default to...
77//
78//
79
80
81
82
83
84// setting the flag to 1 == 2D simulation
85// any other value for flag == 1D simulation
86//
87// must remember to close/reopen the simulation control panel to get the correct panel
88//
89Function Set_2DMonteCarlo_Flag(value)
90        Variable value
91       
92        NVAR flag=root:Packages:NIST:SAS:gDoMonteCarlo
93        flag=value
94        return(0)
95end
96
97// threaded call to the main function, adds up the individual runs, and returns what is to be displayed
98// results is calculated and sent back for display
99Function Monte_SANS_Threaded(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
100        WAVE inputWave,ran_dev,nt,j1,j2,nn,linear_data,results
101
102        //initialize ran1 in the XOP by passing a negative integer
103        // does nothing in the Igor code
104        Duplicate/O results retWave
105
106        Variable NNeutron=inputWave[0]
107        Variable i,nthreads= ThreadProcessorCount
108        if(nthreads>2)          //only support 2 processors until I can figure out how to properly thread the XOP and to loop it
109                nthreads=2
110        endif
111       
112//      nthreads = 1
113        NVAR mt=root:myGlobals:gThreadGroupID
114        mt = ThreadGroupCreate(nthreads)
115        NVAR gInitTime = root:Packages:NIST:SAS:gRanDateTime            //time that SASCALC was started
116        Print "thread group ID = ",mt
117       
118        inputWave[0] = NNeutron/nthreads                //split up the number of neutrons
119       
120        for(i=0;i<nthreads;i+=1)
121                Duplicate/O nt $("nt"+num2istr(i))              //new instance for each thread
122                Duplicate/O j1 $("j1"+num2istr(i))
123                Duplicate/O j2 $("j2"+num2istr(i))
124                Duplicate/O nn $("nn"+num2istr(i))
125                Duplicate/O linear_data $("linear_data"+num2istr(i))
126                Duplicate/O retWave $("retWave"+num2istr(i))
127                Duplicate/O inputWave $("inputWave"+num2istr(i))
128                Duplicate/O ran_dev $("ran_dev"+num2istr(i))
129                               
130                // ?? I need explicit wave references?
131                // maybe I need to have everything in separate data folders - bu tI haven't tried that. seems like a reach.
132                // more likely there is something bad going on in the XOP code.
133                if(i==0)
134                        WAVE inputWave0,ran_dev0,nt0,j10,j20,nn0,linear_data0,retWave0
135                        retWave0 = 0            //clear the return wave
136                        retWave0[0] = -1*(datetime-gInitTime)           //to initialize ran3
137                        ThreadStart mt,i,Monte_SANS_W1(inputWave0,ran_dev0,nt0,j10,j20,nn0,linear_data0,retWave0)
138                        Print "started thread 0"
139                endif
140                if(i==1)
141                        WAVE inputWave1,ran_dev1,nt1,j11,j21,nn1,linear_data1,retWave1
142                        retWave1 = 0                    //clear the return wave
143                        retWave1[0] = -1*(datetime-gInitTime)           //to initialize ran1
144                        ThreadStart mt,i,Monte_SANS_W2(inputWave1,ran_dev1,nt1,j11,j21,nn1,linear_data1,retWave1)
145                        Print "started thread 1"
146                endif
147//              if(i==2)
148//                      WAVE inputWave2,ran_dev2,nt2,j12,j22,nn2,linear_data2,retWave2
149//                      retWave2[0] = -1*datetime               //to initialize ran3
150//                      ThreadStart mt,i,Monte_SANS_W(inputWave2,ran_dev2,nt2,j12,j22,nn2,linear_data2,retWave2)
151//              endif
152//              if(i==3)
153//                      WAVE inputWave3,ran_dev3,nt3,j13,j23,nn3,linear_data3,retWave3
154//                      retWave3[0] = -1*datetime               //to initialize ran3
155//                      ThreadStart mt,i,Monte_SANS_W(inputWave3,ran_dev3,nt3,j13,j23,nn3,linear_data3,retWave3)
156//              endif
157        endfor
158
159// wait until done
160        do
161                variable tgs= ThreadGroupWait(mt,100)
162        while( tgs != 0 )
163        variable dummy= ThreadGroupRelease(mt)
164        mt=0
165        Print "done with all threads"
166
167        // calculate all of the bits for the results
168        if(nthreads == 1)
169                nt = nt0                // add up each instance
170                j1 = j10
171                j2 = j20
172                nn = nn0
173                linear_data = linear_data0
174                retWave = retWave0
175        endif
176        if(nthreads == 2)
177                nt = nt0+nt1            // add up each instance
178                j1 = j10+j11
179                j2 = j20+j21
180                nn = nn0+nn1
181                linear_data = linear_data0+linear_data1
182                retWave = retWave0+retWave1
183        endif
184//      if(nthreads == 3)
185//              nt = nt0+nt1+nt2                // add up each instance
186//              j1 = j10+j11+j12
187//              j2 = j20+j21+j22
188//              nn = nn0+nn1+nn2
189//              linear_data = linear_data0+linear_data1+linear_data2
190//              retWave = retWave0+retWave1+retWave2
191//      endif
192//      if(nthreads == 4)
193//              nt = nt0+nt1+nt2+nt3            // add up each instance
194//              j1 = j10+j11+j12+j13
195//              j2 = j20+j21+j22+j23
196//              nn = nn0+nn1+nn2+nn3
197//              linear_data = linear_data0+linear_data1+linear_data2+linear_data3
198//              retWave = retWave0+retWave1+retWave2+retWave3
199//      endif
200       
201        // fill up the results wave
202        Variable xc,yc
203        xc=inputWave[3]
204        yc=inputWave[4]
205        results[0] = inputWave[9]+inputWave[10]         //total XS
206        results[1] = inputWave[10]                                              //SAS XS
207        results[2] = retWave[1]                                                 //number that interact n2
208        results[3] = retWave[2] - linear_data[xc][yc]                           //# reaching detector minus Q(0)
209        results[4] = retWave[3]/retWave[1]                              //avg# times scattered
210        results[5] = retWave[4]/retWave[7]                                              //single coherent fraction
211        results[6] = retWave[5]/retWave[7]                              //multiple coherent fraction
212        results[7] = retWave[6]/retWave[1]                              //multiple scatter fraction
213        results[8] = (retWave[0]-retWave[1])/retWave[0]                 //transmitted fraction
214       
215        return(0)
216End
217
218// worker function for threads, does nothing except switch between XOP and Igor versions
219//
220// uses ran3
221ThreadSafe Function Monte_SANS_W1(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
222        WAVE inputWave,ran_dev,nt,j1,j2,nn,linear_data,results
223       
224#if exists("Monte_SANSX")
225        Monte_SANSX(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
226#else
227        Monte_SANS(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
228#endif
229
230        return (0)
231End
232
233// worker function for threads, does nothing except switch between XOP and Igor versions
234//
235// uses ran1
236ThreadSafe Function Monte_SANS_W2(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
237        WAVE inputWave,ran_dev,nt,j1,j2,nn,linear_data,results
238       
239#if exists("Monte_SANSX2")
240        Monte_SANSX2(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
241#else
242        Monte_SANS(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
243#endif
244
245        return (0)
246End
247
248// NON-threaded call to the main function returns what is to be displayed
249// results is calculated and sent back for display
250Function Monte_SANS_NotThreaded(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
251        WAVE inputWave,ran_dev,nt,j1,j2,nn,linear_data,results
252
253        //initialize ran1 in the XOP by passing a negative integer
254        // does nothing in the Igor code, enoise is already initialized
255        Duplicate/O results retWave
256        WAVE retWave
257        retWave[0] = -1*abs(trunc(100000*enoise(1)))
258       
259#if exists("Monte_SANSX")
260        Monte_SANSX(inputWave,ran_dev,nt,j1,j2,nn,linear_data,retWave)
261#else
262        Monte_SANS(inputWave,ran_dev,nt,j1,j2,nn,linear_data,retWave)
263#endif
264
265        // fill up the results wave
266        Variable xc,yc
267        xc=inputWave[3]
268        yc=inputWave[4]
269        results[0] = inputWave[9]+inputWave[10]         //total XS
270        results[1] = inputWave[10]                                              //SAS XS
271        results[2] = retWave[1]                                                 //number that interact n2
272        results[3] = retWave[2] - linear_data[xc][yc]                           //# reaching detector minus Q(0)
273        results[4] = retWave[3]/retWave[1]                              //avg# times scattered
274        results[5] = retWave[4]/retWave[7]                                              //single coherent fraction
275        results[6] = retWave[5]/retWave[7]                              //double coherent fraction
276        results[7] = retWave[6]/retWave[1]                              //multiple scatter fraction
277        results[8] = (retWave[0]-retWave[1])/retWave[0]                 //transmitted fraction
278       
279        return(0)
280End
281
282
283
284//////////
285//    PROGRAM Monte_SANS
286//    PROGRAM simulates multiple SANS.
287//       revised 2/12/99  JGB
288//            added calculation of random deviate, and 2D 10/2008 SRK
289
290//    N1 = NUMBER OF INCIDENT NEUTRONS.
291//    N2 = NUMBER INTERACTED IN THE SAMPLE.
292//    N3 = NUMBER ABSORBED.
293//    THETA = SCATTERING ANGLE.
294
295//        IMON = 'Enter number of neutrons to use in simulation.'
296//        NUM_BINS = 'Enter number of THETA BINS TO use. (<5000).'
297//        R1 = 'Enter beam radius. (cm)'
298//        R2 = 'Enter sample radius. (cm)'
299//        thick = 'Enter sample thickness. (cm)'
300//        wavelength = 'Enter neutron wavelength. (A)'
301//        R0 = 'Enter sphere radius. (A)'
302//
303
304ThreadSafe Function Monte_SANS(inputWave,ran_dev,nt,j1,j2,nn,MC_linear_data,results)
305        WAVE inputWave,ran_dev,nt,j1,j2,nn,MC_linear_data,results
306
307        Variable imon,r1,r2,xCtr,yCtr,sdd,pixSize,thick,wavelength,sig_incoh,sig_sas
308        Variable NUM_BINS,N_INDEX
309        Variable RHO,SIGSAS,SIGABS_0
310        Variable ii,jj,IND,idum,INDEX,IR,NQ
311        Variable qmax,theta_max,R_DAB,R0,BOUND,I0,q0,zpow
312        Variable N1,N2,N3,DTH,zz,tt,SIG_SINGLE,xx,yy,PHI,UU,SIG
313        Variable THETA,Ran,ll,D_OMEGA,RR,Tabs,Ttot,I1_sumI
314        Variable G0,E_NT,E_NN,TRANS_th,Trans_exp,rat
315        Variable GG,GG_ED,dS_dW,ds_dw_double,ds_dw_single
316        Variable DONE,FIND_THETA,err            //used as logicals
317
318        Variable Vx,Vy,Vz,Theta_z,qq
319        Variable Sig_scat,Sig_abs,Ratio,Sig_total
320        Variable isOn=0,testQ,testPhi,xPixel,yPixel
321        Variable NSingleIncoherent,NSingleCoherent,NScatterEvents,incoherentEvent,coherentEvent
322        Variable NDoubleCoherent,NMultipleScatter,countIt,detEfficiency
323        Variable NMultipleCoherent,NCoherentEvents
324       
325        detEfficiency = 1.0             //70% counting efficiency = 0.7
326       
327        imon = inputWave[0]
328        r1 = inputWave[1]
329        r2 = inputWave[2]
330        xCtr = inputWave[3]
331        yCtr = inputWave[4]
332        sdd = inputWave[5]
333        pixSize = inputWave[6]
334        thick = inputWave[7]
335        wavelength = inputWave[8]
336        sig_incoh = inputWave[9]
337        sig_sas = inputWave[10]
338       
339//      SetRandomSeed 0.1               //to get a reproduceable sequence
340
341//scattering power and maximum qvalue to bin
342//      zpow = .1               //scattering power, calculated below
343        qmax = 4*pi/wavelength          //maximum Q to bin 1D data. (A-1) (not really used, so set to a big value)
344        sigabs_0 = 0.0          // ignore absorption cross section/wavelength [1/(cm A)]
345        N_INDEX = 50            // maximum number of scattering events per neutron
346        num_bins = 200          //number of 1-D bins (not really used)
347       
348// my additions - calculate the random deviate function as needed
349// and calculate the scattering power from the model function (passed in as a wave)
350//
351        Variable left = leftx(ran_dev)
352        Variable delta = deltax(ran_dev)
353       
354//c       total SAS cross-section
355//      SIG_SAS = zpow/thick
356        zpow = sig_sas*thick                    //since I now calculate the sig_sas from the model
357        SIG_ABS = SIGABS_0 * WAVElength
358        sig_abs = 0.0           //cm-1
359        SIG_TOTAL =SIG_ABS + SIG_SAS + sig_incoh
360//      Print "The TOTAL XSECTION. (CM-1) is ",sig_total
361//      Print "The TOTAL SAS XSECTION. (CM-1) is ",sig_sas
362//      results[0] = sig_total          //assign these after everything's done
363//      results[1] = sig_sas
364//      variable ratio1,ratio2
365//      ratio1 = sig_abs/sig_total
366//      ratio2 = sig_incoh/sig_total
367//      // 0->ratio1 = abs
368//      // ratio1 -> ratio2 = incoh
369//      // > ratio2 = coherent
370        RATIO = sig_incoh / SIG_TOTAL
371       
372//c       assuming theta = sin(theta)...OK
373        theta_max = wavelength*qmax/(2*pi)
374//C     SET Theta-STEP SIZE.
375        DTH = Theta_max/NUM_BINS
376//      Print "theta bin size = dth = ",dth
377
378//C     INITIALIZE COUNTERS.
379        N1 = 0
380        N2 = 0
381        N3 = 0
382        NSingleIncoherent = 0
383        NSingleCoherent = 0
384        NDoubleCoherent = 0
385        NMultipleScatter = 0
386        NScatterEvents = 0
387        NMultipleCoherent = 0
388        NCoherentEvents = 0
389
390//C     INITIALIZE ARRAYS.
391        j1 = 0
392        j2 = 0
393        nt = 0
394        nn=0
395       
396//C     MONITOR LOOP - looping over the number of incedent neutrons
397//note that zz, is the z-position in the sample - NOT the scattering power
398
399// NOW, start the loop, throwing neutrons at the sample.
400        do
401                Vx = 0.0                        // Initialize direction vector.
402                Vy = 0.0
403                Vz = 1.0
404               
405                Theta = 0.0             //      Initialize scattering angle.
406                Phi = 0.0                       //      Intialize azimuthal angle.
407                N1 += 1                 //      Increment total number neutrons counter.
408                DONE = 0                        //      True when neutron is scattered out of the sample.
409                INDEX = 0                       //      Set counter for number of scattering events.
410                zz = 0.0                        //      Set entering dimension of sample.
411                incoherentEvent = 0
412                coherentEvent = 0
413               
414                do                                      //      Makes sure position is within circle.
415                        ran = abs(enoise(1))            //[0,1]
416                        xx = 2.0*R1*(Ran-0.5)           //X beam position of neutron entering sample.
417                        ran = abs(enoise(1))            //[0,1]
418                        yy = 2.0*R1*(Ran-0.5)           //Y beam position ...
419                        RR = SQRT(xx*xx+yy*yy)          //Radial position of neutron in incident beam.
420                while(rr>r1)
421
422                do    //Scattering Loop, will exit when "done" == 1
423                                // keep scattering multiple times until the neutron exits the sample
424                        ran = abs(enoise(1))            //[0,1]  RANDOM NUMBER FOR DETERMINING PATH LENGTH
425                        ll = PATH_len(ran,Sig_total)
426                        //Determine new scattering direction vector.
427                        err = NewDirection(vx,vy,vz,Theta,Phi)          //vx,vy,vz is updated, theta, phi unchanged by function
428
429                        //X,Y,Z-POSITION OF SCATTERING EVENT.
430                        xx += ll*vx
431                        yy += ll*vy
432                        zz += ll*vz
433                        RR = sqrt(xx*xx+yy*yy)          //radial position of scattering event.
434
435                        //Check whether interaction occurred within sample volume.
436                        IF (((zz > 0.0) && (zz < THICK)) && (rr < r2))
437                                //NEUTRON INTERACTED.
438                                ran = abs(enoise(1))            //[0,1]
439                               
440//                              if(ran<ratio1)
441//                                      //absorption event
442//                                      n3 +=1
443//                                      done=1
444//                              else
445
446                                INDEX += 1                      //Increment counter of scattering events.
447                                IF(INDEX == 1)
448                                        N2 += 1                 //Increment # of scat. neutrons
449                                Endif
450                                //Split neutron interactions into scattering and absorption events
451//                              IF(ran > (ratio1+ratio2) )              //C             NEUTRON SCATTERED coherently
452                                IF(ran > ratio)         //C             NEUTRON SCATTERED coherently
453                                        coherentEvent += 1
454                                        FIND_THETA = 0                  //false
455                                        DO
456                                                //ran = abs(enoise(1))          //[0,1]
457                                                //theta = Scat_angle(Ran,R_DAB,wavelength)      // CHOOSE DAB ANGLE -- this is 2Theta
458                                                //Q0 = 2*PI*THETA/WAVElength                                    // John chose theta, calculated Q
459
460                                                // pick a q-value from the deviate function
461                                                // pnt2x truncates the point to an integer before returning the x
462                                                // so get it from the wave scaling instead
463                                                Q0 =left + binarysearchinterp(ran_dev,abs(enoise(1)))*delta
464                                                theta = Q0/2/Pi*wavelength              //SAS approximation. 1% error at theta=30 deg (theta/2=15deg)
465                                               
466                                                //Print "q0, theta = ",q0,theta
467                                               
468                                                FIND_THETA = 1          //always accept
469
470                                        while(!find_theta)
471                                        ran = abs(enoise(1))            //[0,1]
472                                        PHI = 2.0*PI*Ran                        //Chooses azimuthal scattering angle.
473                                ELSE
474                                        //NEUTRON scattered incoherently
475                   // N3 += 1
476                  // DONE = 1
477                  // phi and theta are random over the entire sphere of scattering
478                  // !can't just choose random theta and phi, won't be random over sphere solid angle
479                        incoherentEvent += 1
480                       
481                        ran = abs(enoise(1))            //[0,1]
482                                        theta = acos(2*ran-1)           
483                       
484                        ran = abs(enoise(1))            //[0,1]
485                                        PHI = 2.0*PI*Ran                        //Chooses azimuthal scattering angle.
486                                ENDIF           //(ran > ratio)
487//                              endif           // event was absorption
488                        ELSE
489                                //NEUTRON ESCAPES FROM SAMPLE -- bin it somewhere
490                                DONE = 1                //done = true, will exit from loop
491                               
492//                              countIt = 1
493//                              if(abs(enoise(1)) > detEfficiency)              //efficiency of 70% wired @top
494//                                      countIt = 0                                     //detector does not register
495//                              endif
496                               
497                                //Increment #scattering events array
498                                If (index <= N_Index)
499                                        NN[INDEX] += 1
500                                Endif
501                               
502                                if(index != 0)          //the neutron interacted at least once, figure out where it ends up
503
504                                        Theta_z = acos(Vz)              // Angle WITH respect to z axis.
505                                        testQ = 2*pi*sin(theta_z)/wavelength
506                                       
507                                        // pick a random phi angle, and see if it lands on the detector
508                                        // since the scattering is isotropic, I can safely pick a new, random value
509                                        // this would not be true if simulating anisotropic scattering.
510                                        //testPhi = abs(enoise(1))*2*Pi
511                                        testPhi = MC_FindPhi(Vx,Vy)             //use the exiting phi value as defined by Vx and Vy
512                                       
513                                        // is it on the detector?       
514                                        FindPixel(testQ,testPhi,wavelength,sdd,pixSize,xCtr,yCtr,xPixel,yPixel)
515                                       
516                                        if(xPixel != -1 && yPixel != -1)
517                                                //if(index==1)  // only the single scattering events
518                                                        MC_linear_data[xPixel][yPixel] += 1             //this is the total scattering, including multiple scattering
519                                                //endif
520                                                        isOn += 1               // neutron that lands on detector
521                                        endif
522       
523                                        If(theta_z < theta_max)
524                                                //Choose index for scattering angle array.
525                                                //IND = NINT(THETA_z/DTH + 0.4999999)
526                                                ind = round(THETA_z/DTH + 0.4999999)            //round is eqivalent to nint()
527                                                NT[ind] += 1                    //Increment bin for angle.
528                                                //Increment angle array for single scattering events.
529                                                IF(INDEX == 1)
530                                                        j1[ind] += 1
531                                                Endif
532                                                //Increment angle array for double scattering events.
533                                                IF (INDEX == 2)
534                                                        j2[ind] += 1
535                                                Endif
536                                        EndIf
537                                       
538                                        // increment all of the counters now since done==1 here and I'm sure to exit and get another neutron
539                                        NScatterEvents += index         //total number of scattering events
540                                        if(index == 1 && incoherentEvent == 1)
541                                                NSingleIncoherent += 1
542                                        endif
543                                        if(index == 1 && coherentEvent == 1)
544                                                NSingleCoherent += 1
545                                        endif
546                                        if(index == 2 && coherentEvent == 1 && incoherentEvent == 0)
547                                                NDoubleCoherent += 1
548                                        endif
549                                        if(index > 1)
550                                                NMultipleScatter += 1
551                                        endif
552                                        if(coherentEvent >= 1 && incoherentEvent == 0)
553                                                NCoherentEvents += 1
554                                        endif
555                                        if(coherentEvent > 1 && incoherentEvent == 0)
556                                                NMultipleCoherent += 1
557                                        endif
558                                       
559                                       
560                                        //Print "n1,index (x,y) = ",n1,index, xpixel,ypixel
561                                       
562                                else    // if neutron escaped without interacting
563                               
564                                        // then it must be a transmitted neutron
565                                        // don't need to calculate, just increment the proper counters
566                                       
567                                        MC_linear_data[xCtr+xx/pixsize][yCtr+yy/pixsize] += 1
568                                        isOn += 1
569                                        nt[0] += 1
570                                       
571                                endif           //if interacted
572                        ENDIF
573                while (!done)
574        while(n1 < imon)
575
576//      Print "Monte Carlo Done"
577        results[0] = n1
578        results[1] = n2
579        results[2] = isOn
580        results[3] = NScatterEvents             //sum of # of times that neutrons scattered (coh+incoh)
581        results[4] = NSingleCoherent            //# of events that are single, coherent
582        results[5] = NMultipleCoherent  //# of scattered neutrons that are coherently scattered more than once
583        results[6] = NMultipleScatter           //# of scattered neutrons that are scattered more than once (coh and/or incoh)
584        results[7] = NCoherentEvents            //# of scattered neutrons that are scattered coherently one or more times
585       
586//      Print "# absorbed = ",n3
587
588//      trans_th = exp(-sig_total*thick)
589//      TRANS_exp = (N1-N2) / N1                        // Transmission
590        // dsigma/domega assuming isotropic scattering, with no absorption.
591//      Print "trans_exp = ",trans_exp
592//      Print "total # of neutrons reaching 2D detector",isOn
593//      Print "fraction of incident neutrons reaching detector ",isOn/iMon
594       
595//      Print "Total number of neutrons = ",N1
596//      Print "Total number of neutrons that interact = ",N2
597//      Print "Fraction of singly scattered neutrons = ",sum(j1,-inf,inf)/N2
598//      results[2] = N2                                         //number that scatter
599//      results[3] = isOn - MC_linear_data[xCtr][yCtr]                  //# scattered reaching detector minus zero angle
600
601       
602//      Tabs = (N1-N3)/N1
603//      Ttot = (N1-N2)/N1
604//      I1_sumI = NN[0]/(N2-N3)
605//      Print "Tabs = ",Tabs
606//      Print "Transmitted neutrons = ",Ttot
607//      results[8] = Ttot
608//      Print "I1 / all I1 = ", I1_sumI
609
610End
611////////        end of main function for calculating multiple scattering
612
613
614// returns the random deviate as a wave
615// and the total SAS cross-section [1/cm] sig_sas
616Function CalculateRandomDeviate(func,coef,lam,outWave,SASxs)
617        FUNCREF SANSModelAAO_MCproto func
618        WAVE coef
619        Variable lam
620        String outWave
621        Variable &SASxs
622
623        Variable nPts_ran=10000,qu
624        qu = 4*pi/lam           
625       
626// hard-wired into the Simulation directory rather than the SAS folder.
627// plotting resolution-smeared models won't work any other way
628        Make/O/N=(nPts_ran)/D root:Simulation:Gq,root:Simulation:xw             // if these waves are 1000 pts, the results are "pixelated"
629        WAVE Gq = root:Simulation:gQ
630        WAVE xw = root:Simulation:xw
631        SetScale/I x (0+1e-4),qu*(1-1e-10),"", Gq,xw                    //don't start at zero or run up all the way to qu to avoid numerical errors
632
633/// if all of the coefficients are well-behaved, then the last point is the background
634// and I can set it to zero here (only for the calculation)
635        Duplicate/O coef,tmp_coef
636        Variable num=numpnts(coef)
637        tmp_coef[num-1] = 0
638       
639        xw=x                                                                                            //for the AAO
640        func(tmp_coef,Gq,xw)                                                                    //call as AAO
641
642//      Gq = x*Gq                                                                                                       // SAS approximation
643        Gq = Gq*sin(2*asin(x/qu))/sqrt(1-(x/qu))                        // exact
644        //
645        //
646        Integrate/METH=1 Gq/D=Gq_INT
647       
648//      SASxs = lam*lam/2/pi*Gq_INT[nPts_ran-1]                 //if the approximation is used
649        SASxs = lam*Gq_INT[nPts_ran-1]
650       
651        Gq_INT /= Gq_INT[nPts_ran-1]
652       
653        Duplicate/O Gq_INT $outWave
654
655        return(0)
656End
657
658// returns the random deviate as a wave
659// and the total SAS cross-section [1/cm] sig_sas
660//
661// uses a log spacing of x for better coverage
662// downside is that it doesn't use built-in integrate, which is automatically cumulative
663//
664// --- Currently does not work - since the usage of the random deviate in the MC routine is based on the
665// wave properties of ran_dev, that is it must have the proper scaling and be equally spaced.
666//
667// -- not really sure that this will solve any of the problems with some functions (notably those with power-laws)
668// giving unreasonably large SAS cross sections. (>>10)
669//
670Function CalculateRandomDeviate_log(func,coef,lam,outWave,SASxs)
671        FUNCREF SANSModelAAO_MCproto func
672        WAVE coef
673        Variable lam
674        String outWave
675        Variable &SASxs
676
677        Variable nPts_ran=1000,qu,qmin,ii
678        qmin=1e-5
679        qu = 4*pi/lam           
680
681// hard-wired into the Simulation directory rather than the SAS folder.
682// plotting resolution-smeared models won't work any other way
683        Make/O/N=(nPts_ran)/D root:Simulation:Gq,root:Simulation:xw             // if these waves are 1000 pts, the results are "pixelated"
684        WAVE Gq = root:Simulation:gQ
685        WAVE xw = root:Simulation:xw
686//      SetScale/I x (0+1e-4),qu*(1-1e-10),"", Gq,xw                    //don't start at zero or run up all the way to qu to avoid numerical errors
687        xw =  alog(log(qmin) + x*((log(qu)-log(qmin))/nPts_ran))
688
689/// if all of the coefficients are well-behaved, then the last point is the background
690// and I can set it to zero here (only for the calculation)
691        Duplicate/O coef,tmp_coef
692        Variable num=numpnts(coef)
693        tmp_coef[num-1] = 0
694       
695        func(tmp_coef,Gq,xw)                                                                    //call as AAO
696        Gq = Gq*sin(2*asin(xw/qu))/sqrt(1-(xw/qu))                      // exact
697
698       
699        Duplicate/O Gq Gq_INT
700        Gq_INT = 0
701        for(ii=0;ii<nPts_ran;ii+=1)
702                Gq_INT[ii] = AreaXY(xw,Gq,qmin,xw[ii])
703        endfor
704       
705        SASxs = lam*Gq_INT[nPts_ran-1]
706       
707        Gq_INT /= Gq_INT[nPts_ran-1]
708       
709        Duplicate/O Gq_INT $outWave
710
711        return(0)
712End
713
714ThreadSafe Function FindPixel(testQ,testPhi,lam,sdd,pixSize,xCtr,yCtr,xPixel,yPixel)
715        Variable testQ,testPhi,lam,sdd,pixSize,xCtr,yCtr,&xPixel,&yPixel
716
717        Variable theta,dy,dx,qx,qy
718        //decompose to qx,qy
719        qx = testQ*cos(testPhi)
720        qy = testQ*sin(testPhi)
721
722        //convert qx,qy to pixel locations relative to # of pixels x, y from center
723        theta = 2*asin(qy*lam/4/pi)
724        dy = sdd*tan(theta)
725        yPixel = round(yCtr + dy/pixSize)
726       
727        theta = 2*asin(qx*lam/4/pi)
728        dx = sdd*tan(theta)
729        xPixel = round(xCtr + dx/pixSize)
730
731        NVAR pixelsX = root:myGlobals:gNPixelsX
732        NVAR pixelsY = root:myGlobals:gNPixelsY
733       
734        //if on detector, return xPix and yPix values, otherwise -1
735        if(yPixel > pixelsY || yPixel < 0)
736                yPixel = -1
737        endif
738        if(xPixel > pixelsX || xPixel < 0)
739                xPixel = -1
740        endif
741       
742        return(0)
743End
744
745Function MC_CheckFunctionAndCoef(funcStr,coefStr)
746        String funcStr,coefStr
747       
748        SVAR/Z listStr=root:Packages:NIST:coefKWStr
749        if(SVAR_Exists(listStr) == 1)
750                String properCoefStr = StringByKey(funcStr, listStr  ,"=",";",0)
751                if(cmpstr("",properCoefStr)==0)
752                        return(0)               //false, no match found, so properCoefStr is returned null
753                endif
754                if(cmpstr(coefStr,properCoefStr)==0)
755                        return(1)               //true, the coef is the correct match
756                endif
757        endif
758        return(0)                       //false, wrong coef
759End
760
761Function/S MC_getFunctionCoef(funcStr)
762        String funcStr
763
764        SVAR/Z listStr=root:Packages:NIST:coefKWStr
765        String coefStr=""
766        if(SVAR_Exists(listStr) == 1)
767                coefStr = StringByKey(funcStr, listStr  ,"=",";",0)
768        endif
769        return(coefStr)
770End
771
772Function SANSModelAAO_MCproto(w,yw,xw)
773        Wave w,yw,xw
774       
775        Print "in SANSModelAAO_MCproto function"
776        return(1)
777end
778
779Function/S MC_FunctionPopupList()
780        String list,tmp
781        list = User_FunctionPopupList()
782       
783        //simplify the display, forcing smeared calculations behind the scenes
784        tmp = FunctionList("Smear*",";","NPARAMS:1")            //smeared dependency calculations
785        list = RemoveFromList(tmp, list,";")
786
787
788        if(strlen(list)==0)
789                list = "No functions plotted"
790        endif
791       
792        list = SortList(list)
793       
794        return(list)
795End             
796
797
798//Function Scat_Angle(Ran,R_DAB,wavelength)
799//      Variable Ran,r_dab,wavelength
800//
801//      Variable qq,arg,theta
802//      qq = 1. / ( R_DAB*sqrt(1.0/Ran - 1.0) )
803//      arg = qq*wavelength/(4*pi)
804//      If (arg < 1.0)
805//              theta = 2.*asin(arg)
806//      else
807//              theta = pi
808//      endif
809//      Return (theta)
810//End
811
812//calculates new direction (xyz) from an old direction
813//theta and phi don't change
814ThreadSafe Function NewDirection(vx,vy,vz,theta,phi)
815        Variable &vx,&vy,&vz
816        Variable theta,phi
817       
818        Variable err=0,vx0,vy0,vz0
819        Variable nx,ny,mag_xy,tx,ty,tz
820       
821        //store old direction vector
822        vx0 = vx
823        vy0 = vy
824        vz0 = vz
825       
826        mag_xy = sqrt(vx0*vx0 + vy0*vy0)
827        if(mag_xy < 1e-12)
828                //old vector lies along beam direction
829                nx = 0
830                ny = 1
831                tx = 1
832                ty = 0
833                tz = 0
834        else
835                Nx = -Vy0 / Mag_XY
836                Ny = Vx0 / Mag_XY
837                Tx = -Vz0*Vx0 / Mag_XY
838                Ty = -Vz0*Vy0 / Mag_XY
839                Tz = Mag_XY
840        endif
841       
842        //new scattered direction vector
843        Vx = cos(phi)*sin(theta)*Tx + sin(phi)*sin(theta)*Nx + cos(theta)*Vx0
844        Vy = cos(phi)*sin(theta)*Ty + sin(phi)*sin(theta)*Ny + cos(theta)*Vy0
845        Vz = cos(phi)*sin(theta)*Tz + cos(theta)*Vz0
846       
847        Return(err)
848End
849
850ThreadSafe Function path_len(aval,sig_tot)
851        Variable aval,sig_tot
852       
853        Variable retval
854       
855        retval = -1*ln(1-aval)/sig_tot
856       
857        return(retval)
858End
859
860// globals are initialized in SASCALC.ipf
861// coordinates if I make this part of the panel - but this breaks other things...
862//
863//Proc MC_SASCALC()
864////    PauseUpdate; Silent 1           // building window...
865//
866////    NewPanel /W=(92,556,390,1028)/K=1 as "SANS Simulator"
867//      SetVariable MC_setvar0,pos={491,73},size={144,15},bodyWidth=80,title="# of neutrons"
868//      SetVariable MC_setvar0,format="%5.4g"
869//      SetVariable MC_setvar0,limits={-inf,inf,100},value= root:Packages:NIST:SAS:gImon
870//      SetVariable MC_setvar0_1,pos={491,119},size={131,15},bodyWidth=60,title="Thickness (cm)"
871//      SetVariable MC_setvar0_1,limits={-inf,inf,0.1},value= root:Packages:NIST:SAS:gThick
872//      SetVariable MC_setvar0_2,pos={491,96},size={149,15},bodyWidth=60,title="Incoherent XS (cm)"
873//      SetVariable MC_setvar0_2,limits={-inf,inf,0.1},value= root:Packages:NIST:SAS:gSig_incoh
874//      SetVariable MC_setvar0_3,pos={491,142},size={150,15},bodyWidth=60,title="Sample Radius (cm)"
875//      SetVariable MC_setvar0_3,limits={-inf,inf,0.1},value= root:Packages:NIST:SAS:gR2
876//      PopupMenu MC_popup0,pos={476,13},size={165,20},proc=MC_ModelPopMenuProc,title="Model Function"
877//      PopupMenu MC_popup0,mode=1,value= #"MC_FunctionPopupList()"
878//      Button MC_button0,pos={480,181},size={130,20},proc=MC_DoItButtonProc,title="Do MC Simulation"
879//      Button MC_button1,pos={644,181},size={80,20},proc=MC_Display2DButtonProc,title="Show 2D"
880//      SetVariable setvar0_3,pos={568,484},size={50,20},disable=1
881//      GroupBox group0,pos={478,42},size={267,130},title="Monte Carlo"
882//      SetVariable cntVar,pos={653,73},size={80,15},proc=CountTimeSetVarProc,title="time(s)"
883//      SetVariable cntVar,format="%d"
884//      SetVariable cntVar,limits={1,10,1},value= root:Packages:NIST:SAS:gCntTime
885//     
886//      String fldrSav0= GetDataFolder(1)
887//      SetDataFolder root:Packages:NIST:SAS:
888//      Edit/W=(476,217,746,450)/HOST=#  results_desc,results
889//      ModifyTable format(Point)=1,width(Point)=0,width(results_desc)=150
890//      SetDataFolder fldrSav0
891//      RenameWindow #,T_results
892//      SetActiveSubwindow ##
893//EndMacro
894
895// as a stand-alone panel, extra control bar  (right) and subwindow implementations don't work right
896// for various reasons...
897Window MC_SASCALC() : Panel
898
899        // when opening the panel, set the raw counts check to 1
900        root:Packages:NIST:SAS:gRawCounts = 1
901       
902        PauseUpdate; Silent 1           // building window...
903        NewPanel /W=(92,556,713,818)/K=1 as "SANS Simulator"
904        SetVariable MC_setvar0,pos={28,73},size={144,15},bodyWidth=80,title="# of neutrons"
905        SetVariable MC_setvar0,format="%5.4g"
906        SetVariable MC_setvar0,limits={0,inf,100},value= root:Packages:NIST:SAS:gImon
907        SetVariable MC_setvar0_1,pos={28,119},size={131,15},bodyWidth=60,title="Thickness (cm)"
908        SetVariable MC_setvar0_1,limits={0,inf,0.1},value= root:Packages:NIST:SAS:gThick
909        SetVariable MC_setvar0_2,pos={28,96},size={149,15},bodyWidth=60,title="Incoherent XS (cm)"
910        SetVariable MC_setvar0_2,limits={0,inf,0.1},value= root:Packages:NIST:SAS:gSig_incoh
911        SetVariable MC_setvar0_3,pos={28,142},size={150,15},bodyWidth=60,title="Sample Radius (cm)"
912        SetVariable MC_setvar0_3,limits={-inf,inf,0.1},value= root:Packages:NIST:SAS:gR2
913        PopupMenu MC_popup0,pos={13,13},size={165,20},proc=MC_ModelPopMenuProc,title="Model Function"
914        PopupMenu MC_popup0,mode=1,value= #"MC_FunctionPopupList()"
915        Button MC_button0,pos={17,181},size={130,20},proc=MC_DoItButtonProc,title="Do MC Simulation"
916        Button MC_button0,fColor=(3,52428,1)
917        Button MC_button1,pos={17,208},size={80,20},proc=MC_Display2DButtonProc,title="Show 2D"
918        SetVariable setvar0_3,pos={105,484},size={50,20},disable=1
919        GroupBox group0,pos={15,42},size={267,130},title="Monte Carlo"
920        SetVariable cntVar,pos={185,73},size={90,15},proc=CountTimeSetVarProc,title="time(s)"
921        SetVariable cntVar,format="%d"
922        SetVariable cntVar,limits={1,3600,1},value= root:Packages:NIST:SAS:gCntTime
923        Button MC_button2,pos={17,234},size={100,20},proc=SaveAsVAXButtonProc,title="Save 2D VAX"
924        CheckBox check0,pos={216,180},size={68,14},title="Raw counts",variable = root:Packages:NIST:SAS:gRawCounts
925        CheckBox check0_1,pos={216,199},size={60,14},title="Yes Offset",variable= root:Packages:NIST:SAS:gDoTraceOffset
926        CheckBox check0_2,pos={216,199+19},size={60,14},title="Beam Stop in",variable= root:Packages:NIST:SAS:gBeamStopIn
927        CheckBox check0_3,pos={216,199+2*19},size={60,14},title="use XOP",variable= root:Packages:NIST:SAS:gUse_MC_XOP
928       
929        String fldrSav0= GetDataFolder(1)
930        SetDataFolder root:Packages:NIST:SAS:
931        Edit/W=(344,23,606,248)/HOST=#  results_desc,results
932        ModifyTable format(Point)=1,width(Point)=0,width(results_desc)=150
933        SetDataFolder fldrSav0
934        RenameWindow #,T_results
935        SetActiveSubwindow ##
936EndMacro
937
938Function CountTimeSetVarProc(sva) : SetVariableControl
939        STRUCT WMSetVariableAction &sva
940
941        switch( sva.eventCode )
942                case 1: // mouse up
943                case 2: // Enter key
944                case 3: // Live update
945                        Variable dval = sva.dval
946
947                        // get the neutron flux, multiply, and reset the global for # neutrons
948                        NVAR imon=root:Packages:NIST:SAS:gImon
949                        imon = dval*beamIntensity()
950                       
951                        break
952        endswitch
953
954        return 0
955End
956
957
958Function MC_ModelPopMenuProc(pa) : PopupMenuControl
959        STRUCT WMPopupAction &pa
960
961        switch( pa.eventCode )
962                case 2: // mouse up
963                        Variable popNum = pa.popNum
964                        String popStr = pa.popStr
965                        SVAR gStr = root:Packages:NIST:SAS:gFuncStr
966                        gStr = popStr
967                       
968                        break
969        endswitch
970
971        return 0
972End
973
974Function MC_DoItButtonProc(ba) : ButtonControl
975        STRUCT WMButtonAction &ba
976
977        switch( ba.eventCode )
978                case 2: // mouse up
979                        // click code here
980                        NVAR doMC = root:Packages:NIST:SAS:gDoMonteCarlo
981                        doMC = 1
982                        ReCalculateInten(1)
983                        doMC = 0                //so the next time won't be MC
984                        break
985        endswitch
986
987        return 0
988End
989
990
991Function MC_Display2DButtonProc(ba) : ButtonControl
992        STRUCT WMButtonAction &ba
993
994        switch( ba.eventCode )
995                case 2: // mouse up
996                        // click code here
997                        Execute "ChangeDisplay(\"SAS\")"
998                        break
999        endswitch
1000
1001        return 0
1002End
1003
1004// after a 2d data image is averaged in the usual way, take the waves and generate a "fake" folder of the 1d
1005// data, to appear as if it was loaded from a real data file.
1006//
1007// ---- use FakeUSANSDataFolder() if you want to fake a 1D USANS data set ----
1008//
1009Function        Fake1DDataFolder(qval,aveint,sigave,sigmaQ,qbar,fSubs,dataFolder)
1010        WAVE qval,aveint,sigave,sigmaQ,qbar,fSubs
1011        String dataFolder
1012
1013        String baseStr=dataFolder
1014        if(DataFolderExists("root:"+baseStr))
1015                SetDataFolder $("root:"+baseStr)
1016        else
1017                NewDataFolder/S $("root:"+baseStr)
1018        endif
1019
1020        ////overwrite the existing data, if it exists
1021        Duplicate/O qval, $(baseStr+"_q")
1022        Duplicate/O aveint, $(baseStr+"_i")
1023        Duplicate/O sigave, $(baseStr+"_s")
1024
1025
1026        // make a resolution matrix for SANS data
1027        Variable np=numpnts(qval)
1028        Make/D/O/N=(np,4) $(baseStr+"_res")
1029        Wave res=$(baseStr+"_res")
1030       
1031        res[][0] = sigmaQ[p]            //sigQ
1032        res[][1] = qBar[p]              //qBar
1033        res[][2] = fSubS[p]             //fShad
1034        res[][3] = qval[p]              //Qvalues
1035       
1036        // keep a copy of everything in SAS too... the smearing wrapper function looks for
1037        // data in folders based on waves it is passed - an I lose control of that
1038        Duplicate/O res, $("root:Packages:NIST:SAS:"+baseStr+"_res")
1039        Duplicate/O qval,  $("root:Packages:NIST:SAS:"+baseStr+"_q")
1040        Duplicate/O aveint,  $("root:Packages:NIST:SAS:"+baseStr+"_i")
1041        Duplicate/O sigave,  $("root:Packages:NIST:SAS:"+baseStr+"_s")
1042       
1043        //clean up             
1044        SetDataFolder root:
1045       
1046End
1047
1048// writes out a VAX binary data file
1049// automatically generates a name
1050// will prompt for the sample label
1051//
1052// currently hard-wired for SAS data folder
1053//
1054Function SaveAsVAXButtonProc(ctrlName,[runIndex,simLabel])
1055        String ctrlName
1056        Variable runIndex
1057        String simLabel
1058
1059       
1060        // if default parameters were passed in, use them
1061        // if not, set them to "bad" values so that the user will be prompted later     
1062        NVAR autoSaveIndex = root:Packages:NIST:SAS:gAutoSaveIndex
1063        SVAR autoSaveLabel = root:Packages:NIST:SAS:gAutoSaveLabel
1064       
1065        // Determine if the optional parameters were supplied
1066        if( ParamIsDefault(runIndex))           //==1 if parameter was NOT specified
1067                print "runIndex not specified"
1068                autoSaveIndex=0                                 // 0 == bad value, test for this later
1069        else
1070                autoSaveIndex=runIndex
1071        endif
1072       
1073        if( ParamIsDefault(simLabel))           //==1 if parameter was NOT specified
1074                print "simLabel not specified"
1075                autoSaveLabel=""                                        // "" == bad value, test for this later
1076        else
1077                autoSaveLabel=simLabel
1078        endif
1079       
1080        String fullpath="",destStr=""
1081        Variable refnum
1082       
1083        fullpath = Write_RawData_File("SAS","",0)
1084       
1085        // write out the results into a text file
1086        destStr = "root:Packages:NIST:SAS:"
1087        SetDataFolder $destStr
1088
1089        WAVE results=results
1090        WAVE/T results_desc=results_desc
1091       
1092        //check each wave
1093        If(!(WaveExists(results)))
1094                Abort "results DNExist WriteVAXData()"
1095        Endif
1096        If(!(WaveExists(results_desc)))
1097                Abort "results_desc DNExist WriteVAXData()"
1098        Endif
1099       
1100        Open refNum as fullpath+".txt"
1101                wfprintf refNum, "%30s\t\t%g\r",results_desc,results
1102                FStatus refNum
1103                FSetPos refNum,V_logEOF
1104        Close refNum
1105       
1106        ///////////////////////////////
1107       
1108        // could also automatically do the average here, but probably not worth the the effort...
1109       
1110        SetDataFolder root:
1111       
1112        return(0)
1113End
1114
1115// calculates the fraction of the scattering that reaches the detector, given the random deviate function
1116// and qmin and qmax
1117//
1118//
1119// still some question of the corners and number of pixels per q-bin
1120Function FractionReachingDetector(ran_dev,Qmin,Qmax)
1121        wave ran_dev
1122        Variable Qmin,Qmax
1123       
1124        Variable r1,r2,frac
1125        r1=x2pnt(ran_dev,Qmin)
1126        r2=x2pnt(ran_dev,Qmax)
1127       
1128        // no normalization needed - the full q-range is defined as [0,1]
1129        frac = ran_dev[r2] - ran_dev[r1]
1130       
1131        return frac
1132End
1133
1134
1135/// called in SASCALC:ReCalculateInten()
1136Function        Simulate_2D_MC(funcStr,aveint,qval,sigave,sigmaq,qbar,fsubs)
1137        String funcStr
1138        WAVE aveint,qval,sigave,sigmaq,qbar,fsubs
1139
1140        NVAR doMonteCarlo = root:Packages:NIST:SAS:gDoMonteCarlo                // == 1 if 2D MonteCarlo set by hidden flag
1141        WAVE rw=root:Packages:NIST:SAS:realsRead
1142       
1143// Try to nicely exit from a threading error, if possible
1144        Variable err=0
1145        if(!exists("root:myGlobals:gThreadGroupID"))
1146                Variable/G root:myGlobals:gThreadGroupID=0
1147        endif
1148        NVAR mt=root:myGlobals:gThreadGroupID
1149
1150        if(mt!=0)       //there was an error with the stopping of the threads, possibly user abort
1151                err = ThreadGroupRelease(mt)
1152                Print "threading err = ",err
1153                if(err == 0)
1154                        // all *should* be OK
1155                else
1156                        return(0)
1157                endif
1158        endif
1159
1160        NVAR imon = root:Packages:NIST:SAS:gImon
1161        NVAR thick = root:Packages:NIST:SAS:gThick
1162        NVAR sig_incoh = root:Packages:NIST:SAS:gSig_incoh
1163        NVAR r2 = root:Packages:NIST:SAS:gR2
1164
1165        // do the simulation here, or not
1166        Variable r1,xCtr,yCtr,sdd,pixSize,wavelength
1167        String coefStr,abortStr,str
1168
1169        r1 = rw[24]/2/10                // sample diameter convert diam in [mm] to radius in cm
1170        xCtr = rw[16]
1171        yCtr = rw[17]
1172        sdd = rw[18]*100                //conver header of [m] to [cm]
1173        pixSize = rw[10]/10             // convert pix size in mm to cm
1174        wavelength = rw[26]
1175        coefStr = MC_getFunctionCoef(funcStr)
1176       
1177        if(!MC_CheckFunctionAndCoef(funcStr,coefStr))
1178                doMonteCarlo = 0                //we're getting out now, reset the flag so we don't continually end up here
1179                Abort "The coefficients and function type do not match. Please correct the selections in the popup menus."
1180        endif
1181       
1182        Variable sig_sas
1183//              FUNCREF SANSModelAAO_MCproto func=$("fSmeared"+funcStr)         //a wrapper for the structure version
1184        FUNCREF SANSModelAAO_MCproto func=$(funcStr)            //unsmeared
1185        WAVE results = root:Packages:NIST:SAS:results
1186        WAVE linear_data = root:Packages:NIST:SAS:linear_data
1187        WAVE data = root:Packages:NIST:SAS:data
1188
1189        results = 0
1190        linear_data = 0
1191       
1192        CalculateRandomDeviate(func,$coefStr,wavelength,"root:Packages:NIST:SAS:ran_dev",SIG_SAS)
1193        if(sig_sas > 100)
1194                sprintf abortStr,"sig_sas = %g. Please check that the model coefficients have a zero background, or the low q is well-behaved.",sig_sas
1195                Abort abortStr
1196        endif
1197       
1198        WAVE ran_dev=$"root:Packages:NIST:SAS:ran_dev"
1199       
1200        Make/O/D/N=5000 root:Packages:NIST:SAS:nt=0,root:Packages:NIST:SAS:j1=0,root:Packages:NIST:SAS:j2=0
1201        Make/O/D/N=100 root:Packages:NIST:SAS:nn=0
1202        Make/O/D/N=11 root:Packages:NIST:SAS:inputWave=0
1203       
1204        WAVE nt = root:Packages:NIST:SAS:nt
1205        WAVE j1 = root:Packages:NIST:SAS:j1
1206        WAVE j2 = root:Packages:NIST:SAS:j2
1207        WAVE nn = root:Packages:NIST:SAS:nn
1208        WAVE inputWave = root:Packages:NIST:SAS:inputWave
1209
1210        inputWave[0] = imon
1211        inputWave[1] = r1
1212        inputWave[2] = r2
1213        inputWave[3] = xCtr
1214        inputWave[4] = yCtr
1215        inputWave[5] = sdd
1216        inputWave[6] = pixSize
1217        inputWave[7] = thick
1218        inputWave[8] = wavelength
1219        inputWave[9] = sig_incoh
1220        inputWave[10] = sig_sas
1221
1222        linear_data = 0         //initialize
1223
1224        Variable t0,trans
1225       
1226        // get a time estimate, and give the user a chance to exit if they're unsure.
1227        t0 = stopMStimer(-2)
1228        inputWave[0] = 1000
1229        NVAR useXOP = root:Packages:NIST:SAS:gUse_MC_XOP                //if zero, will use non-threaded Igor code
1230       
1231        if(useXOP)
1232                //use a single thread, otherwise time is dominated by overhead
1233                Monte_SANS_NotThreaded(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
1234        else
1235                Monte_SANS(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
1236        endif
1237       
1238        t0 = (stopMSTimer(-2) - t0)*1e-6
1239        t0 *= imon/1000/ThreadProcessorCount                    //projected time, in seconds (using threads for the calculation)
1240        inputWave[0] = imon             //reset
1241       
1242        if(t0>10)
1243                sprintf str,"The simulation will take approximately %d seconds.\r- Proceed?",t0
1244                DoAlert 1,str
1245                if(V_flag == 2)
1246                        doMonteCarlo = 0
1247                        reCalculateInten(1)             //come back in and do the smeared calculation
1248                        return(0)
1249                endif
1250        endif
1251       
1252        linear_data = 0         //initialize
1253// threading crashes!! - there must be some operation in the XOP that is not threadSafe. What, I don't know...
1254// I think it's the ran() calls, being "non-reentrant". So the XOP now defines two separate functions, that each
1255// use a different rng. This works. 1.75x speedup.     
1256        t0 = stopMStimer(-2)
1257
1258        if(useXOP)
1259                Monte_SANS_Threaded(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
1260        else
1261                Monte_SANS_NotThreaded(inputWave,ran_dev,nt,j1,j2,nn,linear_data,results)
1262        endif
1263       
1264        t0 = (stopMSTimer(-2) - t0)*1e-6
1265        Printf  "MC sim time = %g seconds\r",t0
1266       
1267        trans = results[8]                      //(n1-n2)/n1
1268        if(trans == 0)
1269                trans = 1
1270        endif
1271
1272        Print "counts on detector, including transmitted = ",sum(linear_data,-inf,inf)
1273       
1274//              linear_data[xCtr][yCtr] = 0                     //snip out the transmitted spike
1275//              Print "counts on detector not transmitted = ",sum(linear_data,-inf,inf)
1276
1277        // or simulate a beamstop
1278        NVAR MC_BS_in = root:Packages:NIST:SAS:gBeamStopIn              //if zero, beam stop is "out", as in a transmission measurement
1279       
1280        Variable rad=beamstopDiam()/2           //beamstop radius in cm
1281        if(MC_BS_in)
1282                rad /= 0.5                              //convert cm to pixels
1283                rad += 0.                                       // (no - it cuts off the low Q artificially) add an extra pixel to each side to account for edge
1284                Duplicate/O linear_data,root:Packages:NIST:SAS:tmp_mask//,root:Packages:NIST:SAS:MC_linear_data
1285                WAVE tmp_mask = root:Packages:NIST:SAS:tmp_mask
1286                tmp_mask = (sqrt((p-xCtr)^2+(q-yCtr)^2) < rad) ? 0 : 1          //behind beamstop = 0, away = 1
1287               
1288                linear_data *= tmp_mask
1289        endif
1290       
1291        results[9] = sum(linear_data,-inf,inf)
1292        //              Print "counts on detector not behind beamstop = ",results[9]
1293       
1294        // convert to absolute scale
1295        Variable kappa          //,beaminten = beamIntensity()
1296//              kappa = beamInten*pi*r1*r1*thick*(pixSize/sdd)^2*trans*(iMon/beaminten)
1297        kappa = thick*(pixSize/sdd)^2*trans*iMon
1298       
1299        //use kappa to get back to counts => linear_data = round(linear_data*kappa)
1300        Note/K linear_data ,"KAPPA="+num2str(kappa)+";"
1301       
1302        NVAR rawCts = root:Packages:NIST:SAS:gRawCounts
1303        if(!rawCts)                     //go ahead and do the linear scaling
1304                linear_data = linear_data / kappa
1305        endif           
1306        data = linear_data
1307       
1308        // re-average the 2D data
1309        S_CircularAverageTo1D("SAS")
1310       
1311        // put the new result into the simulation folder
1312        Fake1DDataFolder(qval,aveint,sigave,sigmaQ,qbar,fSubs,"Simulation")     
1313                               
1314
1315        return(0)
1316end
1317
1318//phi is defined from +x axis, proceeding CCW around [0,2Pi]
1319ThreadSafe Function MC_FindPhi(vx,vy)
1320        variable vx,vy
1321       
1322        variable phi
1323       
1324        phi = atan(vy/vx)               //returns a value from -pi/2 to pi/2
1325       
1326        // special cases
1327        if(vx==0 && vy > 0)
1328                return(pi/2)
1329        endif
1330        if(vx==0 && vy < 0)
1331                return(3*pi/2)
1332        endif
1333        if(vx >= 0 && vy == 0)
1334                return(0)
1335        endif
1336        if(vx < 0 && vy == 0)
1337                return(pi)
1338        endif
1339       
1340       
1341        if(vx > 0 && vy > 0)
1342                return(phi)
1343        endif
1344        if(vx < 0 && vy > 0)
1345                return(phi + pi)
1346        endif
1347        if(vx < 0 && vy < 0)
1348                return(phi + pi)
1349        endif
1350        if( vx > 0 && vy < 0)
1351                return(phi + 2*pi)
1352        endif
1353       
1354        return(phi)
1355end
1356
1357
1358
1359
1360
1361Window Sim_1D_Panel() : Panel
1362        PauseUpdate; Silent 1           // building window...
1363        NewPanel /W=(92,556,713,818)/K=1 as "1D SANS Simulator"
1364        SetVariable cntVar,pos={26,68},size={160,15},title="Counting time(s)",format="%d"
1365        SetVariable cntVar,limits={1,36000,10},value= root:Packages:NIST:SAS:gCntTime
1366        SetVariable cntVar, proc=Sim_1D_CountTimeSetVarProc
1367        SetVariable MC_setvar0_1,pos={26,91},size={160,15},title="Thickness (cm)"
1368        SetVariable MC_setvar0_1,limits={0,inf,0.1},value= root:Packages:NIST:SAS:gThick
1369        SetVariable MC_setvar0_1, proc=Sim_1D_SamThickSetVarProc
1370
1371        SetVariable MC_setvar0_3,pos={26,114},size={160,15},title="Sample Transmission"
1372        SetVariable MC_setvar0_3,limits={0,1,0.01},value= root:Packages:NIST:SAS:gSamTrans
1373        SetVariable MC_setvar0_3, proc=Sim_1D_SamTransSetVarProc
1374
1375        PopupMenu MC_popup0,pos={13,13},size={165,20},proc=Sim_1D_ModelPopMenuProc,title="Model Function"
1376        PopupMenu MC_popup0,mode=1,value= #"MC_FunctionPopupList()"
1377        Button MC_button0,pos={17,181},size={130,20},proc=Sim_1D_DoItButtonProc,title="Do 1D Simulation"
1378        Button MC_button0,fColor=(3,52428,1)
1379        Button MC_button1,pos={17,211},size={150,20},proc=Save_1DSimData,title="Save Simulated Data"
1380        GroupBox group0,pos={15,42},size={280,130},title="Sample Setup"
1381        CheckBox check0_1,pos={216,179},size={60,14},title="Yes Offset",variable= root:Packages:NIST:SAS:gDoTraceOffset
1382        CheckBox check0_2,pos={216,199},size={60,14},title="Abs scale?",variable= root:Packages:NIST:SAS:g_1D_DoABS
1383        CheckBox check0_3,pos={216,219},size={60,14},title="Noise?",variable= root:Packages:NIST:SAS:g_1D_AddNoise
1384       
1385// a box for the results
1386        GroupBox group1,pos={314,23},size={277,163},title="Simulation Results"
1387        ValDisplay valdisp0,pos={326,48},size={220,13},title="Total detector counts"
1388        ValDisplay valdisp0,limits={0,0,0},barmisc={0,1000},value= root:Packages:NIST:SAS:g_1DTotCts
1389        ValDisplay valdisp0_1,pos={326,72},size={220,13},title="Estimated count rate (1/s)"
1390        ValDisplay valdisp0_1,limits={0,0,0},barmisc={0,1000},value=root:Packages:NIST:SAS:g_1DEstDetCR
1391        ValDisplay valdisp0_2,pos={326,96},size={220,13},title="Fraction of beam scattered"
1392        ValDisplay valdisp0_2,limits={0,0,0},barmisc={0,1000},value= root:Packages:NIST:SAS:g_1DFracScatt
1393        ValDisplay valdisp0_3,pos={326,121},size={220,13},title="Estimated transmission"
1394        ValDisplay valdisp0_3,limits={0,0,0},barmisc={0,1000},value=root:Packages:NIST:SAS:g_1DEstTrans
1395        ValDisplay valdisp0_4,pos={326,145},size={220,13},title="Multiple Coherent Scattering"
1396        ValDisplay valdisp0_4,limits={0,0,0},barmisc={0,1000},value=root:Packages:NIST:SAS:g_MultScattFraction
1397        // set the flags here -- do the simulation, but not 2D
1398       
1399        root:Packages:NIST:SAS:doSimulation     = 1     // == 1 if 1D simulated data, 0 if other from the checkbox
1400        root:Packages:NIST:SAS:gDoMonteCarlo     = 0  // == 1 if 2D MonteCarlo set by hidden flag
1401
1402       
1403EndMacro
1404
1405Function Sim_1D_CountTimeSetVarProc(sva) : SetVariableControl
1406        STRUCT WMSetVariableAction &sva
1407
1408        switch( sva.eventCode )
1409                case 1: // mouse up
1410                case 2: // Enter key
1411                case 3: // Live update
1412                        Variable dval = sva.dval
1413
1414                        ReCalculateInten(1)
1415                       
1416                        break
1417        endswitch
1418
1419        return 0
1420End
1421
1422Function Sim_1D_SamThickSetVarProc(sva) : SetVariableControl
1423        STRUCT WMSetVariableAction &sva
1424
1425        switch( sva.eventCode )
1426                case 1: // mouse up
1427                case 2: // Enter key
1428                case 3: // Live update
1429                        Variable dval = sva.dval
1430
1431                        ReCalculateInten(1)
1432                       
1433                        break
1434        endswitch
1435
1436        return 0
1437End
1438
1439Function Sim_1D_SamTransSetVarProc(sva) : SetVariableControl
1440        STRUCT WMSetVariableAction &sva
1441
1442        switch( sva.eventCode )
1443                case 1: // mouse up
1444                case 2: // Enter key
1445                case 3: // Live update
1446                        Variable dval = sva.dval
1447
1448                        ReCalculateInten(1)
1449                       
1450                        break
1451        endswitch
1452
1453        return 0
1454End
1455
1456
1457Function Sim_1D_ModelPopMenuProc(pa) : PopupMenuControl
1458        STRUCT WMPopupAction &pa
1459
1460        switch( pa.eventCode )
1461                case 2: // mouse up
1462                        Variable popNum = pa.popNum
1463                        String popStr = pa.popStr
1464                        SVAR gStr = root:Packages:NIST:SAS:gFuncStr
1465                        gStr = popStr
1466                       
1467                        break
1468        endswitch
1469
1470        return 0
1471End
1472
1473
1474Function Sim_1D_DoItButtonProc(ba) : ButtonControl
1475        STRUCT WMButtonAction &ba
1476
1477        switch( ba.eventCode )
1478                case 2: // mouse up
1479               
1480                        ReCalculateInten(1)
1481                       
1482                        break
1483        endswitch
1484
1485        return 0
1486End
1487
1488
1489//
1490//
1491//
1492Function Save_1DSimData(ctrlName) : ButtonControl
1493        String ctrlName
1494
1495        String type="SAS",fullpath=""
1496        Variable dialog=1               //=1 will present dialog for name
1497       
1498        String destStr=""
1499        destStr = "root:Packages:NIST:"+type
1500       
1501        Variable refNum
1502        String formatStr = "%15.4g %15.4g %15.4g %15.4g %15.4g %15.4g\r\n"
1503        String fname,ave="C",hdrStr1="",hdrStr2=""
1504        Variable step=1
1505       
1506        If(1)
1507                //setup a "fake protocol" wave, sice I have no idea of the current state of the data
1508                Make/O/T/N=8 root:myGlobals:Protocols:SIMProtocol
1509                Wave/T SIMProtocol = $"root:myGlobals:Protocols:SIMProtocol"
1510                String junk="****SIMULATED DATA****"
1511                //stick in the fake protocol...
1512                NVAR ctTime = root:Packages:NIST:SAS:gCntTime
1513                NVAR totalCts = root:Packages:NIST:SAS:g_1DTotCts                       //summed counts (simulated)
1514                NVAR detCR = root:Packages:NIST:SAS:g_1DEstDetCR                // estimated detector count rate
1515                NVAR fractScat = root:Packages:NIST:SAS:g_1DFracScatt
1516                NVAR mScat = root:Packages:NIST:SAS:g_MultScattFraction
1517       
1518                SIMProtocol[0] = junk
1519                SIMProtocol[1] = "\tCounting time (s) = "+num2str(ctTime)
1520                SIMProtocol[2] = "\tTotal detector counts = "+num2str(totalCts)
1521                SIMProtocol[3] = "\tDetector countrate (1/s) = "+num2str(detCR)
1522                SIMProtocol[4] = "\tFraction of beam scattered coherently = "+num2str(fractScat)
1523                SIMProtocol[5] = "\tFraction of multiple coherent scattering = "+num2str(mScat)
1524                SIMProtocol[6] = ""
1525                SIMProtocol[7] = ""
1526                //set the global
1527                String/G root:myGlobals:Protocols:gProtoStr = "SIMProtocol"
1528        Endif
1529       
1530       
1531        //*****these waves MUST EXIST, or IGOR Pro will crash, with a type 2 error****
1532        WAVE intw=$(destStr + ":integersRead")
1533        WAVE rw=$(destStr + ":realsRead")
1534        WAVE/T textw=$(destStr + ":textRead")
1535        WAVE qvals =$(destStr + ":qval")
1536        WAVE inten=$(destStr + ":aveint")
1537        WAVE sig=$(destStr + ":sigave")
1538        WAVE qbar = $(destStr + ":QBar")
1539        WAVE sigmaq = $(destStr + ":SigmaQ")
1540        WAVE fsubs = $(destStr + ":fSubS")
1541
1542        SVAR gProtoStr = root:myGlobals:Protocols:gProtoStr
1543        Wave/T proto=$("root:myGlobals:Protocols:"+gProtoStr)
1544       
1545        //check each wave
1546        If(!(WaveExists(intw)))
1547                Abort "intw DNExist Save_1DSimData()"
1548        Endif
1549        If(!(WaveExists(rw)))
1550                Abort "rw DNExist Save_1DSimData()"
1551        Endif
1552        If(!(WaveExists(textw)))
1553                Abort "textw DNExist Save_1DSimData()"
1554        Endif
1555        If(!(WaveExists(qvals)))
1556                Abort "qvals DNExist Save_1DSimData()"
1557        Endif
1558        If(!(WaveExists(inten)))
1559                Abort "inten DNExist Save_1DSimData()"
1560        Endif
1561        If(!(WaveExists(sig)))
1562                Abort "sig DNExist Save_1DSimData()"
1563        Endif
1564        If(!(WaveExists(qbar)))
1565                Abort "qbar DNExist Save_1DSimData()"
1566        Endif
1567        If(!(WaveExists(sigmaq)))
1568                Abort "sigmaq DNExist Save_1DSimData()"
1569        Endif
1570        If(!(WaveExists(fsubs)))
1571                Abort "fsubs DNExist Save_1DSimData()"
1572        Endif
1573        If(!(WaveExists(proto)))
1574                Abort "current protocol wave DNExist Save_1DSimData()"
1575        Endif
1576
1577        //strings can be too long to print-- must trim to 255 chars
1578        Variable ii,num=8
1579        Make/O/T/N=(num) tempShortProto
1580        for(ii=0;ii<num;ii+=1)
1581                tempShortProto[ii] = (proto[ii])[0,240]
1582        endfor
1583       
1584        if(dialog)
1585                PathInfo/S catPathName
1586                fullPath = DoSaveFileDialog("Save data as")
1587                If(cmpstr(fullPath,"")==0)
1588                        //user cancel, don't write out a file
1589                        Close/A
1590                        Abort "no data file was written"
1591                Endif
1592                //Print "dialog fullpath = ",fullpath
1593        Endif
1594       
1595        NVAR monCt = root:Packages:NIST:SAS:gImon
1596        NVAR thick = root:Packages:NIST:SAS:gThick
1597        NVAR trans = root:Packages:NIST:SAS:gSamTrans                   //for 1D, default value
1598       
1599
1600       
1601        hdrStr1 = num2str(monCt)+"  "+num2str(rw[26])+"       "+num2str(rw[19])+"     "+num2str(rw[18])
1602        hdrStr1 += "     "+num2str(trans)+"     "+num2str(thick) + ave +"   "+num2str(step) + "\r\n"
1603
1604        hdrStr2 = num2str(rw[16])+"  "+num2str(rw[17])+"  "+num2str(rw[23])+"    "+num2str(rw[24])+"    "
1605        hdrStr2 += num2str(rw[25])+"    "+num2str(rw[27])+"    "+num2str(rw[21])+"    "+"ORNL  " + "\r\n"
1606       
1607        //actually open the file here
1608        Open refNum as fullpath
1609       
1610        //write out the standard header information
1611        fprintf refnum,"FILE: %s\t\t CREATED: %s\r\n","SIMULATED DATA",(date() +"  "+ time())
1612        fprintf refnum,"LABEL: %s\r\n","SIMULATED DATA"
1613        fprintf refnum,"MON CNT   LAMBDA   DET ANG   DET DIST   TRANS   THICK   AVE   STEP\r\n"
1614        fprintf refnum,hdrStr1
1615        fprintf refnum,"BCENT(X,Y)   A1(mm)   A2(mm)   A1A2DIST(m)   DL/L   BSTOP(mm)   DET_TYP \r\n"
1616        fprintf refnum,hdrStr2
1617//      fprintf refnum,headerFormat,rw[0],rw[26],rw[19],rw[18],rw[4],rw[5],ave,step
1618
1619        //insert protocol information here
1620        //-1 list of sample files
1621        //0 - bkg
1622        //1 - emp
1623        //2 - div
1624        //3 - mask
1625        //4 - abs params c2-c5
1626        //5 - average params
1627        fprintf refnum, "SAM: %s\r\n",tempShortProto[0]
1628        fprintf refnum, "BGD: %s\r\n",tempShortProto[1]
1629        fprintf refnum, "EMP: %s\r\n",tempShortProto[2]
1630        fprintf refnum, "DIV: %s\r\n",tempShortProto[3]
1631        fprintf refnum, "MASK: %s\r\n",tempShortProto[4]
1632        fprintf refnum, "ABS: %s\r\n",tempShortProto[5]
1633        fprintf refnum, "Average Choices: %s\r\n",tempShortProto[6]
1634       
1635        //write out the data columns
1636        fprintf refnum,"The 6 columns are | Q (1/A) | I(Q) (1/cm) | std. dev. I(Q) (1/cm) | sigmaQ | meanQ | ShadowFactor|\r\n"
1637        wfprintf refnum, formatStr, qvals,inten,sig,sigmaq,qbar,fsubs
1638       
1639        Close refnum
1640       
1641        SetDataFolder root:             //(redundant)
1642       
1643        //write confirmation of write operation to history area
1644        Print "Averaged File written: ", GetFileNameFromPathNoSemi(fullPath)
1645        KillWaves/Z tempShortProto
1646
1647        //clear the stuff that was created for case of saving files
1648        If(1)
1649                Killwaves/Z root:myGlobals:Protocols:SIMProtocol
1650                String/G root:myGlobals:Protocols:gProtoStr = ""
1651        Endif
1652       
1653       
1654        return(0)
1655       
1656End
1657
1658
1659/// called in SASCALC:ReCalculateInten()
1660Function Simulate_1D(funcStr,aveint,qval,sigave,sigmaq,qbar,fsubs)
1661        String funcStr
1662        WAVE aveint,qval,sigave,sigmaq,qbar,fsubs
1663
1664        Variable r1,xCtr,yCtr,sdd,pixSize,wavelength
1665        String coefStr,abortStr,str     
1666
1667        FUNCREF SANSModelAAO_MCproto func=$("fSmeared"+funcStr)                 //a wrapper for the structure version
1668        FUNCREF SANSModelAAO_MCproto funcUnsmeared=$(funcStr)           //unsmeared
1669        coefStr = MC_getFunctionCoef(funcStr)
1670       
1671        if(!MC_CheckFunctionAndCoef(funcStr,coefStr))
1672                Abort "Function and coefficients do not match. You must plot the unsmeared function before simulation."
1673        endif
1674       
1675        Wave inten=$"root:Simulation:Simulation_i"              // this will exist and send the smeared calculation to the corect DF
1676       
1677        // the resolution-smeared intensity is calculated, including the incoherent background
1678        func($coefStr,inten,qval)
1679
1680        NVAR imon = root:Packages:NIST:SAS:gImon
1681        NVAR ctTime = root:Packages:NIST:SAS:gCntTime
1682        NVAR thick = root:Packages:NIST:SAS:gThick
1683        NVAR trans = root:Packages:NIST:SAS:gSamTrans
1684        NVAR SimDetCts = root:Packages:NIST:SAS:g_1DTotCts                      //summed counts (simulated)
1685        NVAR estDetCR = root:Packages:NIST:SAS:g_1DEstDetCR                     // estimated detector count rate
1686        NVAR fracScat = root:Packages:NIST:SAS:g_1DFracScatt            // fraction of beam captured on detector
1687        NVAR estTrans = root:Packages:NIST:SAS:g_1DEstTrans             // estimated transmission of sample
1688        NVAR mScat = root:Packages:NIST:SAS:g_MultScattFraction
1689       
1690        WAVE rw=root:Packages:NIST:SAS:realsRead
1691        WAVE nCells=root:Packages:NIST:SAS:nCells                               
1692                                       
1693        pixSize = rw[10]/10             // convert pix size in mm to cm
1694        sdd = rw[18]*100                //convert header of [m] to [cm]
1695        wavelength = rw[26]             // in 1/A
1696       
1697        imon = beamIntensity()*ctTime
1698       
1699        // calculate the scattering cross section simply to be able to estimate the transmission
1700        Variable sig_sas=0
1701       
1702        // remember that the random deviate is the coherent portion ONLY - the incoherent background is
1703        // subtracted before the calculation.
1704        CalculateRandomDeviate(funcUnsmeared,$coefStr,wavelength,"root:Packages:NIST:SAS:ran_dev",sig_sas)
1705       
1706//                              if(sig_sas > 100)
1707//                                      sprintf abortStr,"sig_sas = %g. Please check that the model coefficients have a zero background, or the low q is well-behaved.",sig_sas
1708//                              endif
1709
1710        // calculate the multiple scattering fraction for display (10/2009)
1711        Variable ii,nMax=10,tau
1712        mScat=0
1713        tau = thick*sig_sas
1714        // this sums the normalized scattering P', so the result is the fraction of multiply coherently scattered
1715        // neutrons out of those that were scattered
1716        for(ii=2;ii<nMax;ii+=1)
1717                mScat += tau^(ii)/factorial(ii)
1718//              print tau^(ii)/factorial(ii)
1719        endfor
1720        estTrans = exp(-1*thick*sig_sas)                //thickness and sigma both in units of cm
1721        mscat *= (estTrans)/(1-estTrans)
1722
1723        if(mScat > 0.1)         //  /Z to supress error if this was a 1D calc with the 2D panel open
1724                ValDisplay/Z valdisp0_4 win=Sim_1D_Panel,labelBack=(65535,32768,32768)
1725        else
1726                ValDisplay/Z valdisp0_4 win=Sim_1D_Panel,labelBack=0
1727        endif
1728
1729
1730        Print "Sig_sas = ",sig_sas
1731       
1732        Duplicate/O qval prob_i,countsInAnnulus
1733       
1734        // not needed - nCells takes care of this when the error is correctly calculated
1735//                              Duplicate/O qval circle_fraction,rval,nCells_expected
1736//                              rval = sdd*tan(2*asin(qval*wavelength/4/pi))            //radial distance in cm
1737//                              nCells_expected = 2*pi*rval/pixSize                                     //does this need to be an integer?
1738//                              circle_fraction = nCells / nCells_expected
1739       
1740                               
1741//                              prob_i = trans*thick*nCells*(pixSize/sdd)^2*inten                       //probability of a neutron in q-bin(i) that has nCells
1742        prob_i = trans*thick*(pixSize/sdd)^2*inten                      //probability of a neutron in q-bin(i)
1743       
1744        Variable P_on = sum(prob_i,-inf,inf)
1745        Print "P_on = ",P_on
1746       
1747//                              fracScat = P_on
1748        fracScat = 1-estTrans
1749       
1750//                              aveint = (Imon)*prob_i / circle_fraction / nCells_expected
1751        aveint = (Imon)*prob_i
1752
1753        countsInAnnulus = aveint*nCells
1754        SimDetCts = sum(countsInAnnulus,-inf,inf)
1755        estDetCR = SimDetCts/ctTime
1756       
1757       
1758        NVAR doABS = root:Packages:NIST:SAS:g_1D_DoABS
1759        NVAR addNoise = root:Packages:NIST:SAS:g_1D_AddNoise
1760       
1761        // this is where the number of cells comes in - the calculation of the error bars
1762        // sigma[i] = SUM(sigma[ij]^2) / nCells^2
1763        // and since in the simulation, SUM(sigma[ij]^2) = nCells*sigma[ij]^2 = nCells*Inten
1764        // then...
1765        sigave = sqrt(aveint/nCells)            // corrected based on John's memo, from 8/9/99
1766       
1767        // add in random error in aveint based on the sigave
1768        if(addNoise)
1769                aveint += gnoise(sigave)
1770        endif
1771
1772        // signature in the standard deviation, do this after the noise is added
1773        // start at 10 to be out of the beamstop (makes for nicer plotting)
1774        // end at 50 to leave the natural statistics at the end of the set (may have a total of 80+ points if no offset)
1775        sigave[10,50;10] = 10*sigave[p]
1776
1777        // convert to absolute scale
1778        if(doABS)
1779                Variable kappa = thick*(pixSize/sdd)^2*trans*iMon
1780                aveint /= kappa
1781                sigave /= kappa
1782        endif
1783                               
1784                               
1785        return(0)
1786End
1787
1788/// for testing only
1789Function testProbability(sas,thick)
1790        Variable sas,thick
1791       
1792        Variable tau,trans,p2p,p3p,p4p
1793       
1794        tau = sas*thick
1795        trans = exp(-tau)
1796       
1797        Print "tau = ",tau
1798        Print "trans = ",trans
1799       
1800        p2p = tau^2/factorial(2)*trans/(1-trans)
1801        p3p = tau^3/factorial(3)*trans/(1-trans)
1802        p4p = tau^4/factorial(4)*trans/(1-trans)
1803       
1804        Print "double scattering = ",p2p
1805        Print "triple scattering = ",p3p
1806        Print "quadruple scattering = ",p4p
1807       
1808        Variable ii,nMax=10,mScat=0
1809        for(ii=2;ii<nMax;ii+=1)
1810                mScat += tau^(ii)/factorial(ii)
1811//              print tau^(ii)/factorial(ii)
1812        endfor
1813        mscat *= (Trans)/(1-Trans)
1814
1815        Print "Total fraction of multiple scattering = ",mScat
1816
1817        return(mScat)
1818End
1819
1820
1821//// this is a very simple example of how to script the MC simulation to run unattended
1822//
1823//  you need to supply for each "run":  the run index (you increment manually)
1824//                                                                                              the sample label (as a string)
1825//
1826// changing the various configuration paramters will have to be done on a case-by-case basis
1827// looking into SASCALC to see what is really changed,
1828// or the configuration parameters of the MC_SASCALC panel
1829//
1830//
1831//Function Script_2DMC()
1832//
1833//      STRUCT WMButtonAction ba
1834//      ba.eventCode = 2                        //fake mouse click on button
1835//     
1836//      NVAR detDist = root:Packages:NIST:SAS:gDetDist
1837//     
1838//      detDist = 200           //set directly in cm
1839//      MC_DoItButtonProc(ba)
1840//      SaveAsVAXButtonProc("",runIndex=105,simLabel="this is run 105, SDD = 200")
1841//     
1842//      detDist = 300           //set directly in cm
1843//      MC_DoItButtonProc(ba)
1844//      SaveAsVAXButtonProc("",runIndex=106,simLabel="this is run 106, SDD = 300")
1845//
1846//      detDist = 400           //set directly in cm
1847//      MC_DoItButtonProc(ba)
1848//      SaveAsVAXButtonProc("",runIndex=107,simLabel="this is run 107, SDD = 400")
1849//     
1850//      return(0)
1851//end
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