source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/FACILITY_Utils.ipf @ 665

Last change on this file since 665 was 573, checked in by srkline, 13 years ago

Merging changes of NCNR_ in to the ILL_ files. This is mostly the :Packages:NIST: data folder structure that is new since Lionel made his changes.

Removed Lionel's InitializeILL file, and moved his specific changes (just some global variables) to the initialization routine in ILL_Utils, where it belongs.

File size: 18.4 KB
Line 
1#pragma rtGlobals=1             // Use modern global access method.
2#pragma version=5.0
3#pragma IgorVersion=6.1
4
5// this file contains globals and functions that are specific to a
6// particular facility or data file format
7// branched out 29MAR07 - SRK
8//
9// functions are either labeled with the procedure file that calls them,
10// or noted that they are local to this file
11
12
13// initializes globals that are specific to a particular facility
14// - number of XY pixels
15// - pixexl resolution [cm]
16// - detector deadtime constant [s]
17//
18// called by Initialize.ipf
19//
20Function InitFacilityGlobals()
21
22        //Detector -specific globals
23        Variable/G root:myGlobals:gNPixelsX=128                                 // number of X and Y pixels
24        Variable/G root:myGlobals:gNPixelsY=128
25       
26        // pixel dimensions are now read directly from the file header.
27//      Variable/G root:myGlobals:PixelResDefault = 0.5                 //pixel resolution in cm
28       
29        Variable/G root:myGlobals:DeadtimeDefault = 3.4e-6              //deadtime in seconds
30
31        Variable/G root:myGlobals:apOff = 5.0           // (cm) distance from sample aperture to sample position
32
33End
34
35
36//**********************
37// Resolution calculation - used by the averaging routines
38// to calculate the resolution function at each q-value
39// - the return value is not used
40//
41// equivalent to John's routine on the VAX Q_SIGMA_AVE.FOR
42// Incorporates eqn. 3-15 from J. Appl. Cryst. (1995) v. 28 p105-114
43//
44// - 21 MAR 07 uses projected BS diameter on the detector
45// - APR 07 still need to add resolution with lenses. currently there is no flag in the
46//          raw data header to indicate the presence of lenses.
47//
48// - Aug 07 - added input to switch calculation based on lenses (==1 if in)
49//
50// - called by CircSectAvg.ipf and RectAnnulAvg.ipf
51//
52// passed values are read from RealsRead
53// except DDet and apOff, which are set from globals before passing
54//
55//
56Function/S getResolution(inQ,lambda,lambdaWidth,DDet,apOff,S1,S2,L1,L2,BS,del_r,usingLenses,SigmaQ,QBar,fSubS)
57        Variable inQ, lambda, lambdaWidth, DDet, apOff, S1, S2, L1, L2, BS, del_r,usingLenses
58        Variable &fSubS, &QBar, &SigmaQ         //these are the output quantities at the input Q value
59       
60        //lots of calculation variables
61        Variable a2, q_small, lp, v_lambda, v_b, v_d, vz, yg, v_g
62        Variable r0, delta, inc_gamma, fr, fv, rmd, v_r1, rm, v_r
63
64        //Constants
65        Variable vz_1 = 3.956e5         //velocity [cm/s] of 1 A neutron
66        Variable g = 981.0                              //gravity acceleration [cm/s^2]
67
68        String results
69        results ="Failure"
70
71        S1 *= 0.5*0.1                   //convert to radius and [cm]
72        S2 *= 0.5*0.1
73
74        L1 *= 100.0                     // [cm]
75        L1 -= apOff                             //correct the distance
76
77        L2 *= 100.0
78        L2 += apOff
79        del_r *= 0.1                            //width of annulus, convert mm to [cm]
80       
81        BS *= 0.5*0.1                   //nominal BS diameter passed in, convert to radius and [cm]
82        // 21 MAR 07 SRK - use the projected BS diameter, based on a point sample aperture
83        Variable LB
84        LB = 20.1 + 1.61*BS                     //distance in cm from beamstop to anode plane (empirical)
85        BS = bs + bs*lb/(l2-lb)         //adjusted diameter of shadow from parallax
86       
87        //Start resolution calculation
88        a2 = S1*L2/L1 + S2*(L1+L2)/L1
89        q_small = 2.0*Pi*(BS-a2)*(1.0-lambdaWidth)/(lambda*L2)
90        lp = 1.0/( 1.0/L1 + 1.0/L2)
91
92        v_lambda = lambdaWidth^2/6.0
93       
94//      if(usingLenses==1)                      //SRK 2007
95        if(usingLenses != 0)                    //SRK 2008 allows for the possibility of different numbers of lenses in header
96                v_b = 0.25*(S1*L2/L1)^2 +0.25*(2/3)*(lambdaWidth/lambda)^2*(S2*L2/lp)^2         //correction to 2nd term
97        else
98                v_b = 0.25*(S1*L2/L1)^2 +0.25*(S2*L2/lp)^2              //original form
99        endif
100       
101        v_d = (DDet/2.3548)^2 + del_r^2/12.0
102        vz = vz_1 / lambda
103        yg = 0.5*g*L2*(L1+L2)/vz^2
104        v_g = 2.0*(2.0*yg^2*v_lambda)                                   //factor of 2 correction, B. Hammouda, 2007
105
106        r0 = L2*tan(2.0*asin(lambda*inQ/(4.0*Pi) ))
107        delta = 0.5*(BS - r0)^2/v_d
108
109        if (r0 < BS)
110                inc_gamma=exp(gammln(1.5))*(1-gammp(1.5,delta))
111        else
112                inc_gamma=exp(gammln(1.5))*(1+gammp(1.5,delta))
113        endif
114
115        fSubS = 0.5*(1.0+erf( (r0-BS)/sqrt(2.0*v_d) ) )
116        if (fSubS <= 0.0)
117                fSubS = 1.e-10
118        endif
119        fr = 1.0 + sqrt(v_d)*exp(-1.0*delta) /(r0*fSubS*sqrt(2.0*Pi))
120        fv = inc_gamma/(fSubS*sqrt(Pi)) - r0^2*(fr-1.0)^2/v_d
121
122        rmd = fr*r0
123        v_r1 = v_b + fv*v_d +v_g
124
125        rm = rmd + 0.5*v_r1/rmd
126        v_r = v_r1 - 0.5*(v_r1/rmd)^2
127        if (v_r < 0.0)
128                v_r = 0.0
129        endif
130        QBar = (4.0*Pi/lambda)*sin(0.5*atan(rm/L2))
131        SigmaQ = QBar*sqrt(v_r/rmd^2 +v_lambda)
132
133        results = "success"
134        Return results
135End
136
137
138//Utility function that returns the detector resolution (in cm)
139//Global values are set in the Initialize procedure
140//
141//
142// - called by CircSectAvg.ipf, RectAnnulAvg.ipf, and ProtocolAsPanel.ipf
143//
144// fileStr is passed as TextRead[3]
145// detStr is passed as TextRead[9]
146//
147// *** as of Jan 2008, depricated. Now detector pixel sizes are read from the file header
148// rw[10] = x size (mm); rw[13] = y size (mm)
149//
150// depricated - pixel dimensions are read directly from the file header
151Function xDetectorPixelResolution(fileStr,detStr)
152        String fileStr,detStr
153       
154        Variable DDet
155
156        //your code here
157       
158        return(DDet)
159End
160
161//Utility function that returns the detector deadtime (in seconds)
162//Global values are set in the Initialize procedure
163//
164// - called by WorkFileUtils.ipf
165//
166// fileStr is passed as TextRead[3] and is the filename
167// detStr is passed as TextRead[9] and is an identifier for the detector
168//
169Function DetectorDeadtime(fileStr,detStr)
170        String fileStr,detStr
171       
172        Variable deadtime
173       
174// your code here
175
176        return(deadtime)
177End
178
179
180// item is a filename
181//
182// this function extracts some sort of number from the file
183// presumably some sort of automatically incrementing run number set by the
184// acquisition system
185//
186// this run number should be a unique identifier for the file
187//
188Function GetRunNumFromFile(item)
189        String item
190
191        Variable num=-1         // an invalid return value
192       
193        //your code here
194       
195        return (num)
196End
197
198// item is a filename
199//
200// this function extracts some sort of number from the file
201// presumably some sort of automatically incrementing run number set by the
202// acquisition system
203//
204// this run number should be a unique identifier for the file
205//
206// same as GetRunNumFromFile(0), just with a string return
207//
208// "ABC" returned as an invalid result
209Function/S GetRunNumStrFromFile(item)
210        String item
211       
212        String invalid = "ABC"  //"ABC" is not a valid run number, since it's text
213        String retStr
214        retStr=invalid
215       
216        //your code here
217       
218        return(retStr)
219End
220
221//returns a string containing the full path to the file containing the
222//run number "num". The null string is returned if no valid file can be found.
223//
224//
225// search in the path "catPathName" (hard-wired), will abort if this path does not exist
226//the file returned will be a RAW SANS data file, other types of files are
227//filtered out.
228//
229// called by Buttons.ipf and Transmission.ipf, and locally by parsing routines
230//
231Function/S FindFileFromRunNumber(num)
232        Variable num
233       
234        String fullName="",partialName="",item=""
235       
236        //make sure that path exists
237        PathInfo catPathName
238        String path = S_path
239        if (V_flag == 0)
240                Abort "folder path does not exist - use Pick Path button"
241        Endif
242
243        //your code here       
244
245        return(fullname)
246       
247End
248
249//function to test a file to see if it is a RAW SANS file
250//
251// returns truth 0/1
252//
253// called by many procedures (both external and local)
254//
255Function CheckIfRawData(fname)
256        String fname
257       
258
259//      if(your test here)
260//              //true, is raw data file
261//              Return(1)
262//      else
263//              //some other file
264//              Return(0)
265//      Endif
266
267End
268
269
270// function returns 1 if file is a transmission file, 0 if not
271//
272// called by Transmission.ipf, CatVSTable.ipf, NSORT.ipf
273//
274Function isTransFile(fName)
275        String fname
276       
277//      if(your test here)
278//              //yes, its a transmisison file
279//              Return(1)
280//      else
281//              //some other file
282//              Return(0)
283//      Endif
284End
285
286
287//function to remove all spaces from names when searching for filenames
288//the filename (as saved) will never have interior spaces (TTTTTnnn_AB _Bnnn)
289//but the text field in the header may
290//
291//returns a string identical to the original string, except with the interior spaces removed
292//
293// local function for file name manipulation
294//
295// no change needed here
296Function/S RemoveAllSpaces(str)
297        String str
298       
299        String tempstr = str
300        Variable ii,spc,len             //should never be more than 2 or 3 trailing spaces in a filename
301        ii=0
302        do
303                len = strlen(tempStr)
304                spc = strsearch(tempStr," ",0)          //is the last character a space?
305                if (spc == -1)
306                        break           //no more spaces found, get out
307                endif
308                str = tempstr
309                tempStr = str[0,(spc-1)] + str[(spc+1),(len-1)] //remove the space from the string
310        While(1)        //should never be more than 2 or 3
311       
312        If(strlen(tempStr) < 1)
313                tempStr = ""            //be sure to return a null string if problem found
314        Endif
315       
316        //Print strlen(tempstr)
317       
318        Return(tempStr)
319               
320End
321
322
323//Function attempts to find valid filename from partial name by checking for
324// the existence of the file on disk
325//
326// returns a valid filename (No path prepended) or a null string
327//
328// called by any functions, both external and local
329//
330Function/S FindValidFilename(partialName)
331        String PartialName
332       
333        String retStr=""
334       
335        //your code here
336       
337        return(retStr)
338End
339
340
341//returns a string containing filename (WITHOUT the ;vers)
342//the input string is a full path to the file (Mac-style, still works on Win in IGOR)
343//with the folders separated by colons
344//
345// called by MaskUtils.ipf, ProtocolAsPanel.ipf, WriteQIS.ipf
346//
347// NEEDS NO CHANGES
348//
349Function/S GetFileNameFromPathNoSemi(fullPath)
350        String fullPath
351       
352        Variable offset1,offset2
353        String filename=""
354        //String PartialPath
355        offset1 = 0
356        do
357                offset2 = StrSearch(fullPath, ":", offset1)
358                if (offset2 == -1)                              // no more colons ?
359                        fileName = FullPath[offset1,strlen(FullPath) ]
360                        //PartialPath = FullPath[0, offset1-1]
361                        break
362                endif
363                offset1 = offset2+1
364        while (1)
365       
366        //remove version number from name, if it's there - format should be: filename;N
367        filename =  StringFromList(0,filename,";")              //returns null if error
368       
369        Return filename
370End
371
372//returns a string containing filename (INCLUDING the ;vers)
373//the input string is a full path to the file (Mac-style, still works on Win in IGOR)
374//with the folders separated by colons
375//
376// local, currently unused
377//
378// NEEDS NO CHANGES
379//
380Function/S GetFileNameFromPathKeepSemi(fullPath)
381        String fullPath
382       
383        Variable offset1,offset2
384        String filename
385        //String PartialPath
386        offset1 = 0
387        do
388                offset2 = StrSearch(fullPath, ":", offset1)
389                if (offset2 == -1)                              // no more colons ?
390                        fileName = FullPath[offset1,strlen(FullPath) ]
391                        //PartialPath = FullPath[0, offset1-1]
392                        break
393                endif
394                offset1 = offset2+1
395        while (1)
396       
397        //keep version number from name, if it's there - format should be: filename;N
398       
399        Return filename
400End
401
402//given the full path and filename (fullPath), strips the data path
403//(Mac-style, separated by colons) and returns this path
404//this partial path is the same string that would be returned from PathInfo, for example
405//
406// - allows the user to save to a different path than catPathName
407//
408// called by WriteQIS.ipf
409//
410// NEEDS NO CHANGES
411//
412Function/S GetPathStrFromfullName(fullPath)
413        String fullPath
414       
415        Variable offset1,offset2
416        //String filename
417        String PartialPath
418        offset1 = 0
419        do
420                offset2 = StrSearch(fullPath, ":", offset1)
421                if (offset2 == -1)                              // no more colons ?
422                        //fileName = FullPath[offset1,strlen(FullPath) ]
423                        PartialPath = FullPath[0, offset1-1]
424                        break
425                endif
426                offset1 = offset2+1
427        while (1)
428       
429        Return PartialPath
430End
431
432//given the filename trim or modify the filename to get a new
433//file string that can be used for naming averaged 1-d files
434//
435// called by ProtocolAsPanel.ipf and Tile_2D.ipf
436//
437Function/S GetNameFromHeader(fullName)
438        String fullName
439        String newName = ""
440
441        //your code here
442       
443        Return(newName)
444End
445
446//list (input) is a list, typically returned from IndexedFile()
447//which is semicolon-delimited, and may contain filenames from the VAX
448//that contain version numbers, where the version number appears as a separate list item
449//(and also as a non-existent file)
450//these numbers must be purged from the list, especially for display in a popup
451//or list processing of filenames
452//the function returns the list, cleaned of version numbers (up to 11)
453//raw data files will typically never have a version number other than 1.
454//
455// if there are no version numbers in the list, the input list is returned
456//
457// called by CatVSTable.ipf, NSORT.ipf, Transmission.ipf, WorkFileUtils.ipf
458//
459//
460// NO CHANGE NEEDED
461//
462Function/S RemoveVersNumsFromList(list)
463        String list
464       
465        //get rid of version numbers first (up to 11)
466        Variable ii,num
467        String item
468        num = ItemsInList(list,";")
469        ii=1
470        do
471                item = num2str(ii)
472                list = RemoveFromList(item, list ,";" )
473                ii+=1
474        while(ii<12)
475       
476        return (list)
477End
478
479//input is a list of run numbers, and output is a list of filenames (not the full path)
480//*** input list must be COMMA delimited***
481//output is equivalent to selecting from the CAT table
482//if some or all of the list items are valid filenames, keep them...
483//if an error is encountered, notify of the offending element and return a null list
484//
485//output is COMMA delimited
486//
487// this routine is expecting that the "ask", "none" special cases are handled elsewhere
488//and not passed here
489//
490// called by Marquee.ipf, MultipleReduce.ipf, ProtocolAsPanel.ipf
491//
492// NO CHANGE NEEDED
493//
494Function/S ParseRunNumberList(list)
495        String list
496       
497        String newList="",item="",tempStr=""
498        Variable num,ii,runNum
499       
500        //expand number ranges, if any
501        list = ExpandNumRanges(list)
502       
503        num=itemsinlist(list,",")
504       
505        for(ii=0;ii<num;ii+=1)
506                //get the item
507                item = StringFromList(ii,list,",")
508                //is it already a valid filename?
509                tempStr=FindValidFilename(item) //returns filename if good, null if error
510                if(strlen(tempstr)!=0)
511                        //valid name, add to list
512                        //Print "it's a file"
513                        newList += tempStr + ","
514                else
515                        //not a valid name
516                        //is it a number?
517                        runNum=str2num(item)
518                        //print runnum
519                        if(numtype(runNum) != 0)
520                                //not a number -  maybe an error                       
521                                DoAlert 0,"List item "+item+" is not a valid run number or filename. Please enter a valid number or filename."
522                                return("")
523                        else
524                                //a run number or an error
525                                tempStr = GetFileNameFromPathNoSemi( FindFileFromRunNumber(runNum) )
526                                if(strlen(tempstr)==0)
527                                        //file not found, error
528                                        DoAlert 0,"List item "+item+" is not a valid run number. Please enter a valid number."
529                                        return("")
530                                else
531                                        newList += tempStr + ","
532                                endif
533                        endif
534                endif
535        endfor          //loop over all items in list
536       
537        return(newList)
538End
539
540//takes a comma delimited list that MAY contain number range, and
541//expands any range of run numbers into a comma-delimited list...
542//and returns the new list - if not a range, return unchanged
543//
544// local function
545//
546// NO CHANGE NEEDED
547//
548Function/S ExpandNumRanges(list)
549        String list
550       
551        String newList="",dash="-",item,str
552        Variable num,ii,hasDash
553       
554        num=itemsinlist(list,",")
555//      print num
556        for(ii=0;ii<num;ii+=1)
557                //get the item
558                item = StringFromList(ii,list,",")
559                //does it contain a dash?
560                hasDash = strsearch(item,dash,0)                //-1 if no dash found
561                if(hasDash == -1)
562                        //not a range, keep it in the list
563                        newList += item + ","
564                else
565                        //has a dash (so it's a range), expand (or add null)
566                        newList += ListFromDash(item)           
567                endif
568        endfor
569       
570        return newList
571End
572
573//be sure to add a trailing comma to the return string...
574//
575// local function
576//
577// NO CHANGE NEEDED
578//
579Function/S ListFromDash(item)
580        String item
581       
582        String numList="",loStr="",hiStr=""
583        Variable lo,hi,ii
584       
585        loStr=StringFromList(0,item,"-")        //treat the range as a list
586        hiStr=StringFromList(1,item,"-")
587        lo=str2num(loStr)
588        hi=str2num(hiStr)
589        if( (numtype(lo) != 0) || (numtype(hi) !=0 ) || (lo > hi) )
590                numList=""
591                return numList
592        endif
593        for(ii=lo;ii<=hi;ii+=1)
594                numList += num2str(ii) + ","
595        endfor
596       
597        Return numList
598End
599
600
601//returns the proper attenuation factor based on the instrument
602//
603// filestr is passed from TextRead[3] = the default directory, used to identify the instrument
604// lam is passed from RealsRead[26]
605// AttenNo is passed from ReaslRead[3]
606//
607// Attenuation factor as defined here is <= 1
608//
609// Facilities can pass ("",1,attenuationFactor) and have this function simply
610// spit back the attenuationFactor (that was read into rw[3])
611//
612// called by Correct.ipf, ProtocolAsPanel.ipf, Transmission.ipf
613//
614Function AttenuationFactor(fileStr,lam,attenNo)
615        String fileStr
616        Variable lam,attenNo
617       
618        Variable attenFactor=1
619       
620        // your code here
621
622        return(attenFactor)
623End
624
625//function called by the popups to get a file list of data that can be sorted
626// this procedure simply removes the raw data files from the string - there
627//can be lots of other junk present, but this is very fast...
628//
629// could also use the alternate procedure of keeping only file with the proper extension
630//
631// another possibility is to get a listing of the text files, but is unreliable on
632// Windows, where the data file must be .txt (and possibly OSX)
633//
634// called by FIT_Ops.ipf, NSORT.ipf, PlotUtils.ipf
635//
636// modify for specific facilities by changing the "*.SA1*","*.SA2*","*.SA3*" stringmatch
637// items which are specific to NCNR
638//
639Function/S ReducedDataFileList(ctrlName)
640        String ctrlName
641
642        String list="",newList="",item=""
643        Variable num,ii
644       
645        //check for the path
646        PathInfo catPathName
647        if(V_Flag==0)
648                DoAlert 0, "Data path does not exist - pick the data path from the button on the main panel"
649                Return("")
650        Endif
651       
652        list = IndexedFile(catpathName,-1,"????")
653        num=ItemsInList(list,";")
654        //print "num = ",num
655        for(ii=(num-1);ii>=0;ii-=1)
656                item = StringFromList(ii, list  ,";")
657                //simply remove all that are not raw data files (SA1 SA2 SA3)
658                if( !stringmatch(item,"*.SA1*") && !stringmatch(item,"*.SA2*") && !stringmatch(item,"*.SA3*") )
659                        if( !stringmatch(item,".*") && !stringmatch(item,"*.pxp") && !stringmatch(item,"*.DIV"))                //eliminate mac "hidden" files, pxp, and div files
660                                newlist += item + ";"
661                        endif
662                endif
663        endfor
664        //remove VAX version numbers
665        newList = RemoveVersNumsFromList(newList)
666        //sort
667        newList = SortList(newList,";",0)
668
669        return newlist
670End
671
672// returns a list of raw data files in the catPathName directory on disk
673// - list is SEMICOLON-delimited
674//
675// called by PatchFiles.ipf, Tile_2D.ipf
676//
677Function/S GetRawDataFileList()
678       
679        //make sure that path exists
680        PathInfo catPathName
681        if (V_flag == 0)
682                Abort "Folder path does not exist - use Pick Path button on Main Panel"
683        Endif
684       
685        String list=""
686       
687        // your code here
688       
689        return(list)
690End
691
692//**********************
693// 2D resolution function calculation - in terms of X and Y
694//
695// based on notes from David Mildner, 2008
696//
697// the final NCNR version is located in NCNR_Utils.ipf
698//
699Function/S get2DResolution(inQ,phi,lambda,lambdaWidth,DDet,apOff,S1,S2,L1,L2,BS,del_r,usingLenses,r_dist,SigmaQX,SigmaQY,fSubS)
700        Variable inQ, phi,lambda, lambdaWidth, DDet, apOff, S1, S2, L1, L2, BS, del_r,usingLenses,r_dist
701        Variable &SigmaQX,&SigmaQY,&fSubS               //these are the output quantities at the input Q value
702       
703        return("Function Empty")
704End
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