source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/HFIR_Utils.ipf @ 750

Last change on this file since 750 was 750, checked in by srkline, 12 years ago

Some utility procedures were moved from NSORT to NCNR_Utilities. These changes were previously propogated to ANSTO_Utils, and now are propagated to HFIR and ILL_Util files.

File size: 32.2 KB
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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// initializes globals that are specific to a particular facility
13// - number of XY pixels
14// - pixexl resolution [cm]
15// - detector deadtime constant [s]
16//
17// called by Initialize.ipf
18//
19Function InitFacilityGlobals()
20
21        //Detector -specific globals
22        Variable/G root:myGlobals:gNPixelsX=192                                 // number of detector X and Y pixels
23        Variable/G root:myGlobals:gNPixelsY=192
24       
25        // pixel dimensions are now read directly from the file header.
26        Variable/G root:myGlobals:PixelResDefault = 0.51        //pixel resolution in cm
27        //No dead time measured for HFIR detector but the count rate is set very low. For now, set the detector perfect.
28        // This should be updated when the condition is changed.   JHC 09/02/09
29        Variable/G root:myGlobals:DeadtimeDefault =  0       //3.4e-6 (NIST value)      //deadtime in seconds
30
31        Variable/G root:myGlobals:apOff = 5.0           // (cm) distance from sample aperture to sample positio
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
139//Utility function that returns the detector resolution (in cm)
140//Global values are set in the Initialize procedure
141//
142// - called by CircSectAvg.ipf, RectAnnulAvg.ipf, and ProtocolAsPanel.ipf
143//
144// fileStr is passed as TextRead[3] and is the filename
145// detStr is passed as TextRead[9] and is an identifier for the detector
146//
147// depricated - pixel dimensions are read directly from the file header
148Function xDetectorPixelResolution(fileStr,detStr)
149        String fileStr,detStr
150       
151        Variable DDet
152        NVAR PixelResDefault = root:myGlobals:PixelResDefault
153        //your code here
154        DDet = PixelResDefault  //0.515 cm, typical for new ORNL detectors
155        return(DDet)
156End
157
158//Utility function that returns the detector deadtime (in seconds)
159//Global values are set in the Initialize procedure
160//
161// - called by WorkFileUtils.ipf
162//
163// fileStr is passed as TextRead[3] and is the filename
164// detStr is passed as TextRead[9] and is an identifier for the detector
165//
166Function DetectorDeadtime(fileStr,detStr)
167        String fileStr,detStr
168       
169        Variable deadtime
170        NVAR DeadtimeDefault = root:myGlobals:DeadtimeDefault
171       
172        deadtime = DeadtimeDefault      //3.4e-6 seconds, typical for new ORNL detectors //???????????????????????????
173        return(deadtime)
174End
175
176
177
178// item is a filename
179//
180// this function extracts some sort of number from the file
181// presumably some sort of automatically incrementing run number set by the
182// acquisition system
183//
184// this run number should be a unique identifier for the file
185//Because HFIR data format is w/ 2X 4digit number. We add them to get a unique number => This will cause the arrow button not working.
186Function GetRunNumFromFile(item)
187        String item
188        Variable invalid = -1   //negative numbers are invalid
189        Variable num=-1
190       
191        //find the "dot"
192        String runStr=""
193        Variable pos = strsearch(item,".",0)
194        if(pos == -1)
195                //"dot" not found
196                return (invalid)
197        else
198                //found, get the nine characters preceeding it
199                if (pos <=8)
200                        //not enough characters
201                        return (invalid)
202                else
203                        Variable pos_bio = strsearch( LowerStr(item),"biosans",0)
204                        //if  (pos_bio== -1)
205                                runStr  = item[pos-9,pos-6]     //first 4 numbers
206                        //else
207                                runStr  += item[pos-4,pos-1]    //add last 4 numbers
208                        //endif
209                        //convert to a number
210                        num = str2num(runStr)
211                       
212                        //if valid, return it
213                        if (num == NaN)
214                                //8 characters were not a number
215                                return (invalid)
216                        else
217                                //run was OK
218                                return (num)
219                        Endif
220                Endif
221        Endif
222       
223End
224
225
226// item is a filename
227//
228// this function extracts some sort of number from the file
229// presumably some sort of automatically incrementing run number set by the
230// acquisition system
231//
232// this run number should be a unique identifier for the file
233//
234// same as GetRunNumFromFile(0), just with a string return
235//
236// "ABC" returned as an invalid result
237// XXXXSANS_expXX._scan1234_5678.xmp ==> "12345678"
238// -- result is an 8-character string
239//
240Function/S GetRunNumStrFromFile(item)   //,numposition)
241        String item
242        Variable numposition
243       
244        String invalid = "ABC"  //"ABC" is not a valid run number, since it's text
245        String retStr
246        retStr=invalid
247
248        //find the "dot"
249        Variable pos = strsearch( LowerStr(item),".xml",0)
250        if(pos == -1)
251                //"dotxml" not found
252                return (retStr)
253        else
254                pos = strsearch( LowerStr(item),"_scan",0)
255               
256                if  (pos == -1)
257                        //not a raw data file
258                        return (retStr)
259                else
260                        //Variable pos_bio = strsearch( LowerStr(item),"biosans_",0)  //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
261                        //if  (numposition == 0)
262                                //Take the first four: //HiResSANS
263                                retStr = item[pos+5,pos+8]
264                        //else 
265                                //add the last four: //BioSANS
266                                retStr += item[pos+10,pos+13]
267                        //Endif
268                        return (retStr)
269                Endif
270        Endif
271       
272End
273
274//returns a string containing the full path to the file containing the
275//run number "num". The null string is returned if no valid file can be found.
276//
277//
278// search in the path "catPathName" (hard-wired), will abort if this path does not exist
279//the file returned will be a RAW SANS data file, other types of files are
280//filtered out.
281//
282// called by Buttons.ipf and Transmission.ipf, and locally by parsing routines
283//
284Function/S FindFileFromRunNumber(num)
285        Variable num
286
287        String fullName="",partialName="",item=""
288        //get list of raw data files in folder that match "num" (add leading zeros)
289        if( (num>99999999) || (num<0) )
290                //Print "error in  FindFileFromRunNumber(num), file number too large or too small"
291                Return ("")
292        Endif
293        //make a four character string of the run number
294        String numStr=""
295       
296        if(num > 9999999 && num < 100000000)
297                numStr = num2istr(num)
298        endif
299        if(num > 999999 && num < 10000000)
300                numStr = "0"+num2istr(num)
301        endif   
302        if(num > 99999 && num < 1000000)
303                numStr = "00"+num2istr(num)
304        endif   
305        if(num > 9999 && num < 100000)
306                numStr = "000"+num2istr(num)
307        endif
308        if(num > 999 && num < 10000)
309                numStr =  "0000"+num2istr(num)
310        endif
311        if(num > 99 && num < 1000)
312                numStr = "00000"+num2istr(num)
313        endif   
314        if(num > 9 && num < 100)
315                numStr = "000000"+num2istr(num)
316        endif   
317        if(num < 10 && num >0)
318                numStr = "0000000"+num2iStr(num)
319        endif
320        if(num == 0)
321                numStr = "00000000"
322        endif
323
324        //make sure that path exists
325        PathInfo catPathName
326        String path = S_path
327        if (V_flag == 0)
328                Abort "folder path does not exist - use Pick Path button"
329        Endif
330        String list="",newList="",testStr=""
331       
332        list = IndexedFile(catPathName,-1,"????")       //get all files in folder
333        //find (the) one with the number in the run # location in the name
334        Variable numItems,ii,runFound,isRAW
335        numItems = ItemsInList(list,";")                //get the new number of items in the list
336
337        ii=0
338        do
339                //parse through the list in this order:
340                // 1 - does item contain run number (as a string) "NAMESANS_expNN_scan####_####.xml" : Let's check the 8  nums.
341                // 2 - exclude by isRaw? (to minimize disk access)
342                item = StringFromList(ii, list  ,";" )
343               
344                if(strlen(item) != 0)
345                        //find the run number, if it exists as a 8 character string
346                        testStr = GetRunNumStrFromFile(item)    //0)
347                        runFound= cmpstr(numStr,testStr)        //compare the three character strings, 0 if equal
348                       
349                        if(runFound == 0)
350                                //the run Number was found
351                                //build valid filename
352                                partialName = FindValidFileName(item)
353                               
354                                if(strlen(partialName) != 0)            //non-null return from FindValidFileName()
355                                        fullName = path + partialName
356                                        //check if RAW, if so,this must be the file!
357                                        isRAW = CheckIfRawData(fullName)
358                                        if(isRaw)
359                                                //stop here
360                                                return(fullname)
361                                        Endif
362                                Endif
363                        Endif
364                       
365                Endif
366                ii+=1
367        while(ii<numItems)              //process all items in list
368        print "The run number (", numStr, " +- 1 ) does not exist... (Note: The run number is defined as 12345678 if the file name is NameSANS_exp##_scan1234_5678.xml)"
369        Return ("")     //null return if file not found in list
370End
371
372
373//make an (N) character string of the run number
374//Moved to facility utils
375//
376// same scheme to get 8-character string as in GetRunNumStrFromFile(item)
377//
378Function/S RunDigitString(num)
379        Variable num
380
381        String numStr=""
382
383        //make 8 digit string from run number
384        sprintf numStr,"%08u",num
385       
386        if(strlen(numStr) > 8)
387                return("")
388        else
389                return(numstr)
390        endif
391       
392End
393
394//given a filename of a SANS data filename of the form
395//TTTTTnnn.SAn_TTT_Txxx
396//returns the prefix "TTTTT" as some number of characters
397//returns "" as an invalid file prefix
398//
399// HFIR writes out files with a "prefix" of the following -- since there is really no "prefix"
400// like in the VAX scheme:
401//                      newFileName = ReplaceString(".xml",textPath[0],"")              //removes 4 chars
402//                      newFileName = ReplaceString("SANS",newFileName,"")              //removes 4 more chars = 8
403//                      newFileName = ReplaceString("exp",newFileName,"")                       //removes 3 more chars = 11
404//                      newFileName = ReplaceString("scan",newFileName,"")              //removes 4 more chars = 15, should be enough?
405//
406//
407// -- so the raw data:          BioSANS_exp9_scan1828_0001.xml
408// -- translates to:            Bio_9_1828_0001.AVE     
409//
410//
411// NCNR-specifc, does not really belong here - it's a beta procedure used for the
412// Combine Files Panel, and I'm not sure of how I'm really going to get this to work properly
413// since the .ABS file written is not of the form that NSORT->Set3NSORTFiles(low,med,hi,pref)
414// is trying to construct
415//
416// changed (Oct 2010) the naming for HFIR from ExecuteProtocol to:
417//                      newFileName = GetPrefixStrFromFile(textPath[0])+GetRunNumStrFromFile(textPath[0])
418// -- translates to:            BioSANS18280001.AVE
419//
420Function/S GetPrefixStrFromFile(item)
421        String item
422        String invalid = ""     //"" is not a valid run prefix, since it's text
423        Variable num=-1
424       
425        //find the "dash"
426        String runStr=""
427        Variable pos = strsearch(item,"_",0)
428        if(pos == -1)
429                //"dot" not found
430                return (invalid)
431        else
432                //found
433                if (pos <=3)
434                        //not enough characters
435                        return (invalid)
436                else
437                        runStr = item[0,pos-1]
438                        return (runStr)
439                Endif
440        Endif
441End
442
443
444
445//function to test a binary file to see if it is a RAW binary SANS file
446//first checks the total bytes in the file (which for raw data is 33316 bytes)
447//**note that the "DIV" file will also show up as a raw file by the run field
448//should be listed in CAT/SHORT and in patch windows
449//
450//Function then checks the file fname (full path:file) for "RAW" run.type field
451//if not found, the data is not raw data and zero is returned
452//
453// called by many procedures (both external and local)
454//
455Function CheckIfRawData(fname)
456        String fname
457             
458        String tempheadhfir                                           
459        Variable ind=0
460        Variable refNum
461       
462        //If not have .xml extension, return 0.
463        if (stringmatch(fname,"*.xml") <1)
464                print fname+": Failed. Not a *.xml file."
465                return 0                                //Not *.xml. Do nothing...
466        endif
467        //actually open the file
468        refNum = XmlOpenFile(fname)     
469        if (refNum < 0)
470                print "==> "+ fname+ "\r  ==> Failed to load: Not a standard xml file format or broken.. Please check the file if properly written..."
471                return 0                                //Not a xml file. Do nothing...
472        endif
473       
474        // Check if  it is the SPICE version = 1.1
475        Variable  item,i,ns = 0
476        String thislocation
477        if (refNum >0)
478                ns = str2num(XMLstrFmXpath(refNum, "//SPICErack/@SPICE_version","",""))
479        endif
480        XmlCloseFile(refNum,0)
481        if (ns <1.1)
482                ns =0
483        else
484                ns =1
485        endif
486       
487        return ns
488End
489
490// for HFIR data, both DIV and RAW are determined by looking for "*.xml"
491Function CheckIfDIVData(fname)
492        String fname
493        return(CheckIfRawData(fname))
494End
495
496// function returns 1 if file is a transmission file, 0 if not
497//
498// called by Transmission.ipf, CatVSTable.ipf, NSORT.ipf
499//
500// SRK MAR 2010 - apparently from what I can see in the files, the beam stop "out"
501// position is 25 mm for all four beam stop Y POSITIONS
502// - if one is larger, (in the hundreds of mm) then it's in, and the run is not a transmission
503// - so if all four y positions are less than (tol) 30 mm, call it a trans file
504//
505// there is a field for this in the header, write "True", so I don't need to guess again.
506// -- but this field is often incorrect - for some sample data ALL FILES were "True"
507// -- better to check the physical location every time
508//
509// tol changed to 401 per Gernot's experience 6/24/10
510//
511Function isTransFile(fName)   ///  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
512        String fname
513       
514        Variable beamtrap_1y=0,beamtrap_2y=0,beamtrap_3y=0,beamtrap_4y=0,tol=401
515        //Check by key "transsmission"
516//      if (stringmatch( getIsTrans(fName),"True")>0)
517//              return (1)
518//      else
519                //Check from beam stop motor position
520        //      if(your test here)
521                beamtrap_1y=getRealValueFromHeader(fname,"//Motor_Positions/trap_y_101mm","mm")
522                beamtrap_2y=getRealValueFromHeader(fname,"//Motor_Positions/trap_y_25mm","mm")
523                beamtrap_3y=getRealValueFromHeader(fname,"//Motor_Positions/trap_y_50mm","mm")
524                beamtrap_4y=getRealValueFromHeader(fname,"//Motor_Positions/trap_y_76mm","mm")
525
526                if (beamtrap_1y < tol && beamtrap_2y < tol && beamtrap_3y < tol && beamtrap_4y < tol)   
527                        //Write the flag ON
528                        Write_isTransmissionToHeader(fName,"True")
529                        return (1)
530                else
531                        //some other file
532                        Write_isTransmissionToHeader(fName,"False")
533                        return (0)
534                endif
535               
536//      endif
537
538        return (0)
539End
540
541
542
543//function to remove all spaces from names when searching for filenames
544//the filename (as saved) will never have interior spaces (TTTTTnnn_AB _Bnnn)
545//but the text field in the header WILL, if less than 3 characters were used for the
546//user's initials, and can have leading spaces if prefix was less than 5 characters
547//
548//returns a string identical to the original string, except with the interior spaces removed
549//
550// local function for file name manipulation
551//
552// NO CHANGE NEEDED
553//
554Function/S RemoveAllSpaces(str)
555        String str
556       
557        String tempstr = str
558        Variable ii,spc,len             //should never be more than 2 or 3 trailing spaces in a filename
559        ii=0
560        do
561                len = strlen(tempStr)
562                spc = strsearch(tempStr," ",0)          //is the last character a space?
563                if (spc == -1)
564                        break           //no more spaces found, get out
565                endif
566                str = tempstr
567                tempStr = str[0,(spc-1)] + str[(spc+1),(len-1)] //remove the space from the string
568        While(1)        //should never be more than 2 or 3
569       
570        If(strlen(tempStr) < 1)
571                tempStr = ""            //be sure to return a null string if problem found
572        Endif
573       
574        //Print strlen(tempstr)
575       
576        Return(tempStr)
577               
578End
579
580
581
582//Function attempts to find valid filename from partial name by checking for
583// the existence of the file on disk
584//
585// returns a valid filename (No path prepended) or a null string
586//
587// called by any functions, both external and local
588//
589Function/S FindValidFilename(partialName)
590        String PartialName
591       
592        String retStr=partialName
593
594        //your code here
595        //try name with no changes - to allow for ABS files that have spaces in the names 12APR04
596        retStr = ValidFileString(partialName)
597        if(cmpstr(retStr,"") !=0)
598                return(retStr)
599        endif
600       
601        //if the partial name is derived from the file header, there can be spaces at the beginning
602        //or in the middle of the filename - depending on the prefix and initials used
603        //
604        //remove any leading spaces from the name before starting
605        partialName = RemoveAllSpaces(partialName)
606       
607        //try name with no spaces
608        retStr = ValidFileString(partialName)
609        if(cmpstr(retStr,"") !=0)
610                //non-null return
611                return(retStr)
612        endif
613       
614        //try all UPPERCASE
615        partialName = UpperStr(partialName)
616        retStr = ValidFileString(partialName)
617        if(cmpstr(retStr,"") !=0)
618                //non-null return
619                return(retStr)
620        endif
621       
622        //try all lowercase (ret null if failure)
623        partialName = LowerStr(partialName)
624        retStr = ValidFileString(partialName)
625        if(cmpstr(retStr,"") !=0)
626                //non-null return
627                return(retStr)
628        else
629                return(retStr)
630        endif
631End
632
633// Function checks for the existence of a file
634
635// *** the PATH is hard-wired to catPathName (which is assumed to exist)
636// version numers up to ;10 are tried
637// only the "name;vers" is returned if successful. The path is not prepended
638//
639// local function
640//
641Function/S ValidFileString(partialName)
642        String partialName
643       
644        String tempName = "",msg=""
645        Variable ii,refnum
646
647        ii=0
648        do
649                if(ii==0)
650                        //first pass, try the partialName
651                        tempName = partialName
652                        Open/Z/R/T="????TEXT"/P=catPathName refnum tempName     //Does open file (/Z flag)
653                        if(V_flag == 0)
654                                //file exists
655                                Close refnum            //YES needed,
656                                break
657                        endif
658                else
659                        tempName = partialName + ";" + num2str(ii)
660                        Open/Z/R/T="????TEXT"/P=catPathName refnum tempName
661                        if(V_flag == 0)
662                                //file exists
663                                Close refnum
664                                break
665                        endif
666                Endif
667                ii+=1
668
669        while(ii<11)
670        //go get the selected bits of information, using tempName, which exists
671        if(ii>=11)
672                //msg = partialName + " not found. is version number > 11?"
673                //DoAlert 0, msg
674                //PathInfo catPathName
675                //Print S_Path
676                Return ("")             //use null string as error condition
677        Endif
678               
679        Return (tempName)
680End
681
682
683//returns a string containing filename (WITHOUT the ;vers)
684//the input string is a full path to the file (Mac-style, still works on Win in IGOR)
685//with the folders separated by colons
686//
687// called by MaskUtils.ipf, ProtocolAsPanel.ipf, WriteQIS.ipf
688//
689// NO CHANGE NEEDED
690//
691
692Function/S GetFileNameFromPathNoSemi(fullPath)
693        String fullPath
694       
695        Variable offset1,offset2
696        String filename=""
697        //String PartialPath
698        offset1 = 0
699        do
700                offset2 = StrSearch(fullPath, ":", offset1)
701                if (offset2 == -1)                              // no more colons ?
702                        fileName = FullPath[offset1,strlen(FullPath) ]
703                        //PartialPath = FullPath[0, offset1-1]
704                        break
705                endif
706                offset1 = offset2+1
707        while (1)
708       
709        //remove version number from name, if it's there - format should be: filename;N
710        filename =  StringFromList(0,filename,";")              //returns null if error
711       
712        Return filename
713End
714
715//returns a string containing filename (INCLUDING the ;vers)
716//the input string is a full path to the file (Mac-style, still works on Win in IGOR)
717//with the folders separated by colons
718//
719// local, currently unused
720//
721// NO CHANGE NEEDED
722//
723
724Function/S GetFileNameFromPathKeepSemi(fullPath)
725        String fullPath
726       
727        Variable offset1,offset2
728        String filename
729        //String PartialPath
730        offset1 = 0
731        do
732                offset2 = StrSearch(fullPath, ":", offset1)
733                if (offset2 == -1)                              // no more colons ?
734                        fileName = FullPath[offset1,strlen(FullPath) ]
735                        //PartialPath = FullPath[0, offset1-1]
736                        break
737                endif
738                offset1 = offset2+1
739        while (1)
740       
741        //keep version number from name, if it's there - format should be: filename;N
742       
743        Return filename
744End
745
746//given the full path and filename (fullPath), strips the data path
747//(Mac-style, separated by colons) and returns this path
748//this partial path is the same string that would be returned from PathInfo, for example
749//
750// - allows the user to save to a different path than catPathName
751//
752// called by WriteQIS.ipf
753//
754// NO CHANGE NEEDED
755//
756
757Function/S GetPathStrFromfullName(fullPath)
758        String fullPath
759       
760        Variable offset1,offset2
761        //String filename
762        String PartialPath
763        offset1 = 0
764        do
765                offset2 = StrSearch(fullPath, ":", offset1)
766                if (offset2 == -1)                              // no more colons ?
767                        //fileName = FullPath[offset1,strlen(FullPath) ]
768                        PartialPath = FullPath[0, offset1-1]
769                        break
770                endif
771                offset1 = offset2+1
772        while (1)
773       
774        Return PartialPath
775End
776
777//given the filename trim or modify the filename to get a new
778//file string that can be used for naming averaged 1-d files
779//
780// called by ProtocolAsPanel.ipf and Tile_2D.ipf
781//
782Function/S GetNameFromHeader(fName)
783        String fName
784        String temp, newName = ""
785        Variable spc,ii=0
786       
787        //filename is 31-33 characters INSTRNAMESANS_exp##_scan####_####.xml (where # : numbers)
788        //returns a null string if no name can be found
789        Variable iimax =  strlen(fName)
790        do
791                temp = fname[ii,iimax-1-4]              //characters ii,all of the name
792                spc = strsearch(temp," ",0)
793                if (spc == -1)
794                        break           //no more spaces found
795                endif
796                ii+=1
797        While(ii<iimax)
798       
799        If(strlen(temp) < 1)
800                newName = ""            //be sure to return a null string if problem found
801        else
802                newName = temp
803        Endif
804       
805        Return(newName)
806End
807
808//list (input) is a list, typically returned from IndexedFile()
809//which is semicolon-delimited, and may contain filenames from the VAX
810//that contain version numbers, where the version number appears as a separate list item
811//(and also as a non-existent file)
812//these numbers must be purged from the list, especially for display in a popup
813//or list processing of filenames
814//the function returns the list, cleaned of version numbers (up to 11)
815//raw data files will typically never have a version number other than 1.
816//
817// if there are no version numbers in the list, the input list is returned
818//
819// called by CatVSTable.ipf, NSORT.ipf, Transmission.ipf, WorkFileUtils.ipf
820//
821// NO CHANGE NEEDED
822//
823
824Function/S RemoveVersNumsFromList(list)
825        String list
826       
827        //get rid of version numbers first (up to 11)
828        Variable ii,num
829        String item
830        num = ItemsInList(list,";")
831        ii=1
832        do
833                item = num2str(ii)
834                list = RemoveFromList(item, list ,";" )
835                ii+=1
836        while(ii<12)
837       
838        return (list)
839End
840
841//input is a list of run numbers, and output is a list of filenames (not the full path)
842//*** input list must be COMMA delimited***
843//output is equivalent to selecting from the CAT table
844//if some or all of the list items are valid filenames, keep them...
845//if an error is encountered, notify of the offending element and return a null list
846//
847//output is COMMA delimited
848//
849// this routine is expecting that the "ask", "none" special cases are handled elsewhere
850//and not passed here
851//
852// called by Marquee.ipf, MultipleReduce.ipf, ProtocolAsPanel.ipf
853//
854// NO CHANGE NEEDED
855//
856
857Function/S ParseRunNumberList(list)
858        String list
859       
860        String newList="",item="",tempStr=""
861        Variable num,ii,runNum
862       
863        //expand number ranges, if any
864        list = ExpandNumRanges(list)
865       
866        num=itemsinlist(list,",")
867       
868        for(ii=0;ii<num;ii+=1)
869                //get the item
870                item = StringFromList(ii,list,",")
871                //is it already a valid filename?
872               
873                tempStr=FindValidFilename(item) //returns filename if good, null if error
874                if(strlen(tempstr)!=0)
875                        //valid name, add to list
876                        //Print "it's a file"
877                        newList += tempStr + ","
878                else
879                        //not a valid name
880                        //is it a number?
881                        runNum=str2num(item)
882
883                        if(numtype(runNum) != 0)
884                                //not a number -  maybe an error                       
885                                DoAlert 0,"List item "+item+" is not a valid run number or filename. Please enter a valid number or filename."
886                                return("")
887                        else
888                                //a run number or an error
889                                tempStr = GetFileNameFromPathNoSemi( FindFileFromRunNumber(runNum) )
890                                if(strlen(tempstr)==0)
891                                        //file not found, error
892                                        DoAlert 0,"List item "+item+" is not a valid run number. Please enter a valid number."
893                                        return("")
894                                else
895                                        newList += tempStr + ","
896                                endif
897                        endif
898                endif
899        endfor          //loop over all items in list
900
901        return(newList)
902End
903
904//takes a comma delimited list that MAY contain number range, and
905//expands any range of run numbers into a comma-delimited list...
906//and returns the new list - if not a range, return unchanged
907//
908// local function
909//
910// NO CHANGE NEEDED
911//
912
913Function/S ExpandNumRanges(list)
914        String list
915       
916        String newList="",dash="-",item,str
917        Variable num,ii,hasDash
918       
919        num=itemsinlist(list,",")
920
921        for(ii=0;ii<num;ii+=1)
922                //get the item
923                item = StringFromList(ii,list,",")
924                //does it contain a dash?
925                hasDash = strsearch(item,dash,0)                //-1 if no dash found
926                if(hasDash == -1)
927                        //not a range, keep it in the list
928                        newList += item + ","
929                else
930                        //has a dash (so it's a range), expand (or add null)
931                        newList += ListFromDash(item)           
932                endif
933        endfor
934       
935        return newList
936End
937
938//be sure to add a trailing comma to the return string...
939//
940// local function
941//
942// NO CHANGE NEEDED
943//
944Function/S ListFromDash(item)
945        String item
946       
947        String numList="",loStr="",hiStr=""
948        Variable lo,hi,ii
949       
950        loStr=StringFromList(0,item,"-")        //treat the range as a list
951        hiStr=StringFromList(1,item,"-")
952        lo=str2num(loStr)
953        hi=str2num(hiStr)
954        if( (numtype(lo) != 0) || (numtype(hi) !=0 ) || (lo > hi) )
955                numList=""
956                return numList
957        endif
958        for(ii=lo;ii<=hi;ii+=1)
959                numList += num2str(ii) + ","
960        endfor
961       
962        Return numList
963End
964
965
966//returns the proper attenuation factor based on the instrument
967//
968// filestr is passed from TextRead[3] = the default directory, used to identify the instrument
969// lam is passed from RealsRead[26]
970// AttenNo is passed from ReaslRead[3]
971//
972// Attenuation factor as defined here is <= 1
973//
974// Facilities can pass ("",1,attenuationFactor) and have this function simply
975// spit back the attenuationFactor (that was read into rw[3])
976//
977// called by Correct.ipf, ProtocolAsPanel.ipf, Transmission.ipf
978//
979Function AttenuationFactor(fileStr,lam,attenuation)
980        String fileStr
981        Variable lam,attenuation  //    0 =< attenuation <= 100 (%) : where no attenuator stands for 0.
982       
983        Variable attenFactor=1
984       
985        // your code here
986        attenFactor = 1- attenuation*0.01  //???Attenuate transmission
987
988        return(attenFactor)
989End
990
991//function called by the popups to get a file list of data that can be sorted
992// this procedure simply removes the raw data files from the string - there
993//can be lots of other junk present, but this is very fast...
994//
995// could also use the alternate procedure of keeping only file with the proper extension
996//
997// another possibility is to get a listing of the text files, but is unreliable on
998// Windows, where the data file must be .txt (and possibly OSX)
999//
1000// called by FIT_Ops.ipf, NSORT.ipf, PlotUtils.ipf
1001//
1002Function/S ReducedDataFileList(ctrlName)
1003        String ctrlName
1004
1005        String list="",newList="",item=""
1006        Variable num,ii
1007       
1008        //check for the path
1009        PathInfo catPathName
1010        if(V_Flag==0)
1011                DoAlert 0, "Data path does not exist - pick the data path from the button on the main panel"
1012                Return("")
1013        Endif
1014       
1015        list = IndexedFile(catpathName,-1,"????")
1016        num=ItemsInList(list,";")
1017
1018        for(ii=(num-1);ii>=0;ii-=1)
1019                item = StringFromList(ii, list  ,";")
1020                //simply remove all that are not raw data files (SA1 SA2 SA3)
1021                //if( !stringmatch(item,"*HiResSANS*.xml") && !stringmatch(item,"*BioSANS*.xml"))
1022                        if( !stringmatch(item,".*") && !stringmatch(item,"*.pxp") && !stringmatch(item,"*.DIV"))                //eliminate mac "hidden" files, pxp, and div files
1023                                newlist += (item) + ";"   
1024                        endif
1025                //endif
1026        endfor
1027        //remove VAX version numbers
1028        newList = RemoveVersNumsFromList(newList)
1029        //sort
1030        newList = SortList(newList,";",0)
1031
1032        return newlist
1033End
1034
1035// returns a list of raw data files in the catPathName directory on disk
1036// - list is SEMICOLON-delimited
1037//
1038// does it the "cheap" way, simply finding the ".SAn" in the file name
1039// = does not check for proper byte length.
1040//
1041// called by PatchFiles.ipf, Tile_2D.ipf
1042//
1043Function/S GetRawDataFileList()
1044       
1045        //make sure that path exists
1046        PathInfo catPathName
1047        if (V_flag == 0)
1048                Abort "Folder path does not exist - use Pick Path button on Main Panel"
1049        Endif
1050       
1051        String list=IndexedFile(catPathName,-1,"????")
1052        String newList="",item=""
1053        Variable num=ItemsInList(list,";"),ii
1054        for(ii=0;ii<num;ii+=1)
1055                item = StringFromList(ii, list  ,";")
1056                if( stringmatch(item,"*.xml") )
1057                        if (CheckIfRawData(S_path+item) >0)
1058                                newlist += item + ";"
1059                        endif
1060                endif
1061                // if condition is in here twice, not sure why since they are both "*.xml"
1062//              if( stringmatch(item,"*.xml") )
1063//                      if (CheckIfRawData(S_path+item) >0)
1064//                              newlist += item + ";"
1065//                      endif
1066//              endif
1067        endfor
1068        newList = SortList(newList,";",0)
1069        return(newList)
1070End
1071
1072//**********************
1073// 2D resolution function calculation - in terms of X and Y
1074//
1075// based on notes from David Mildner, 2008
1076//
1077// the final NCNR version is located in NCNR_Utils.ipf
1078//
1079Function/S get2DResolution(inQ,phi,lambda,lambdaWidth,DDet,apOff,S1,S2,L1,L2,BS,del_r,usingLenses,r_dist,SigmaQX,SigmaQY,fSubS)
1080        Variable inQ, phi,lambda, lambdaWidth, DDet, apOff, S1, S2, L1, L2, BS, del_r,usingLenses,r_dist
1081        Variable &SigmaQX,&SigmaQY,&fSubS               //these are the output quantities at the input Q value
1082       
1083        return("Function Empty")
1084End
1085
1086
1087
1088
1089// Return the filename that represents the previous or next file.
1090// Input is current filename and increment.
1091// Increment should be -1 or 1
1092// -1 => previous file
1093// 1 => next file
1094Function/S GetPrevNextRawFile(curfilename, prevnext)
1095        String curfilename
1096        Variable prevnext
1097
1098        String filename
1099       
1100        //get the run number
1101        Variable num = GetRunNumFromFile(curfilename)
1102               
1103        //find the next specified file by number
1104        fileName = FindPrevNextRawFile(curfilename, prevnext)
1105
1106        if(cmpstr(fileName,"")==0)
1107                //null return, do nothing
1108                fileName = FindFileFromRunNumber(num)
1109        Endif
1110
1111        //print "in FU "+filename
1112
1113        Return filename
1114End
1115
1116// Find next or previous file name w/ current file name given.
1117// Sort the list of files and get the next/previous file name.
1118Function/S FindPrevNextRawFile(curfilename, prevnext)
1119        String curfilename
1120        Variable prevnext
1121       
1122        String fullName="",partialName="",item="", list=""
1123        Variable numItems,isRAW
1124                       
1125        //make sure that path exists
1126        PathInfo catPathName
1127        String path = S_path
1128       
1129        if (V_flag == 0)
1130                Abort "folder path does not exist - use Pick Path button"
1131        Endif
1132
1133       
1134        list = SortList(IndexedFile(catPathName,-1,"????"),";") //get all files in folder and make sure it is sorted.
1135       
1136        //find (the) one with the number in the run # location in the name
1137
1138        numItems = ItemsInList(list,";")                //get the new number of items in the list
1139        //index of curfilename
1140        Variable index = WhichListItem(curfilename,list,";",0,0)
1141        //get the prenextitem in the list
1142        item = StringFromList(index+prevnext, list  ,";")
1143        partialName = FindValidFileName(item)
1144       
1145        if(strlen(partialName) != 0)            //non-null return from FindValidFileName()
1146                fullName = path + partialName
1147                //check if RAW, if so,this must be the file!
1148                isRAW = CheckIfRawData(fullName)
1149                if(isRaw)
1150                        //stop here
1151                        return(fullname)
1152                Endif
1153        Endif
1154
1155        print "Please type 'scan number(s)' from your file name..."
1156        Return ("")     //null return if file not found in list
1157End
1158
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