source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_WorkFolderUtils.ipf @ 984

Last change on this file since 984 was 984, checked in by srkline, 7 years ago

lots of changes to 1D averaging and the plotting routines, detector corrections, and basic reads

File size: 29.2 KB
Line 
1#pragma rtGlobals=3             // Use modern global access method and strict wave access.
2#pragma version=1.0
3#pragma IgorVersion=6.1
4
5//*******************
6// Vers 1.0 JAN2016
7//
8//*******************
9//  VSANS Utility procedures for handling of workfiles (each is housed in a separate datafolder)
10//
11// - adding RAW data to a workfile
12// -- **this conversion applies the detector corrections**
13//
14// - copying workfiles to another folder
15//
16// - absolute scaling
17//
18// - (no) the WorkFile Math panel for simple image math (not done - maybe in the future?)
19// -
20// - (no) adding work.drk data without normalizing to monitor counts (the case not currently handled)
21//***************************
22
23//
24// Functions used for manipulation of the local Igor "WORK" folder
25// structure as raw data is displayed and processed.
26//
27//
28Strconstant ksDetectorListNoB = "FT;FB;FL;FR;MT;MB;ML;MR;"
29Strconstant ksDetectorListAll = "FT;FB;FL;FR;MT;MB;ML;MR;B;"
30
31
32//
33//Entry procedure from main panel
34//
35Proc CopyWorkFolder(oldType,newType)
36        String oldType,newType
37        Prompt oldType,"Source WORK data type",popup,"SAM;EMP;BGD;DIV;COR;CAL;RAW;ABS;STO;SUB;DRK;"
38        Prompt newType,"Destination WORK data type",popup,"SAM;EMP;BGD;DIV;COR;CAL;RAW;ABS;STO;SUB;DRK;"
39
40        // data folder "old" will be copied to "new" (either kills/copies or will overwrite)
41        CopyHDFToWorkFolder(oldtype,newtype)
42End
43
44//
45// copy what is needed for data processing (not the DAS_logs)
46// from the RawVSANS storage folder to the local WORK folder as needed
47//
48// TODO -- at what stage do I make copies of data in linear/log forms for data display?
49//                      -- when do I make the 2D error waves?
50//
51// TODO - decide what exactly I need to copy over. May be best to copy all, and delete
52//       what I know that I don't need
53//
54// TODO !!! DuplicateDataFolder will FAIL - in the base case of RAW data files, the
55//  data is actually in use - so it will fail every time. need an alternate solution. in SANS,
56// there are a limited number of waves to carry over, so Dupliate/O is used for rw, tw, data, etc.
57//
58// TODO : I also need a list of what is generated during processing that may be hanging around - that I need to
59//     be sure to get rid of - like the calibration waves, solidAngle, etc.
60//
61// hdfDF is the name only of the data in storage. May be full file name with extension (clean as needed)
62// type is the destination WORK folder for the copy
63//
64Function CopyHDFToWorkFolder(fromStr,toStr)
65        String fromStr,toStr
66       
67        String fromDF, toDF
68       
69        // make the DF paths - source and destination
70        fromDF = "root:Packages:NIST:VSANS:"+fromStr
71        toDF = "root:Packages:NIST:VSANS:"+toStr
72       
73//      // make a copy of the file name for my own use, since it's not in the file
74//      String/G $(toDF+":file_name") = root:
75       
76        // copy the folders
77        KillDataFolder/Z $toDF                  //DuplicateDataFolder will not overwrite, so Kill
78       
79        if(V_flag == 0)         // kill DF was OK
80                DuplicateDataFolder $("root:Packages:NIST:VSANS:"+fromStr),$("root:Packages:NIST:VSANS:"+toStr)
81               
82                // I can delete these if they came along with RAW
83                //   DAS_logs
84                //   top-level copies of data (duplicate links)
85                KillDataFolder/Z $(toDF+":entry:entry:DAS_logs")
86                KillDataFolder/Z $(toDF+":entry:entry:data")
87                KillDataFolder/Z $(toDF+":entry:entry:data_B")
88                KillDataFolder/Z $(toDF+":entry:entry:data_ML")
89                KillDataFolder/Z $(toDF+":entry:entry:data_MR")
90                KillDataFolder/Z $(toDF+":entry:entry:data_MT")
91                KillDataFolder/Z $(toDF+":entry:entry:data_MB")
92                KillDataFolder/Z $(toDF+":entry:entry:data_FL")
93                KillDataFolder/Z $(toDF+":entry:entry:data_FR")
94                KillDataFolder/Z $(toDF+":entry:entry:data_FT")
95                KillDataFolder/Z $(toDF+":entry:entry:data_FB")
96
97                return(0)
98        else
99                // need to do this the hard way, duplicate/O recursively
100                // see V_CopyToWorkFolder()
101               
102                // everything on the top level
103                V_DuplicateDataFolder($(fromDF+":entry:entry"),fromStr,toStr,0,"",0)    //no recursion here
104                // control
105                V_DuplicateDataFolder($(fromDF+":entry:entry:control"),fromStr,toStr,0,"",1)    //yes recursion here
106                // instrument
107                V_DuplicateDataFolder($(fromDF+":entry:entry:instrument"),fromStr,toStr,0,"",1) //yes recursion here
108                // reduction
109                V_DuplicateDataFolder($(fromDF+":entry:entry:reduction"),fromStr,toStr,0,"",1)  //yes recursion here
110                // sample
111                V_DuplicateDataFolder($(fromDF+":entry:entry:sample"),fromStr,toStr,0,"",1)     //yes recursion here
112
113        endif   
114       
115        return(0)
116end
117
118
119////////
120// see the help entry for IndexedDir for help on (possibly) how to do this faster
121// -- see the function Function ScanDirectories(pathName, printDirNames)
122//
123
124
125// from IgorExchange On July 17th, 2011 jtigor
126// started from "Recursively List Data Folder Contents"
127// Posted July 15th, 2011 by hrodstein
128//
129//
130//
131Proc V_CopyWorkFolderTest(dataFolderStr, fromStr, toStr, level, sNBName, recurse)
132        String dataFolderStr="root:Packages:NIST:VSANS:RAW"
133        String fromStr = "RAW"
134        String toStr="SAM"
135        Variable level=0
136        String sNBName="DataFolderTree"
137        Variable recurse = 1
138       
139        V_DuplicateDataFolder($dataFolderStr, fromStr, toStr, level, sNBName, recurse)
140
141
142end
143
144// ListDataFolder(dfr, level)
145// Recursively lists objects in data folder.
146// Pass data folder path for dfr and 0 for level.
147// pass level == 0 for the first call
148//  sNBName = "" prints nothing. any name will generate a notebook
149//
150// recurse == 0 will do only the specified folder, anything else will recurse all levels
151// toStr is the string name of the top-level folder only, not the full path
152//
153//
154Function V_DuplicateDataFolder(dfr, fromStr, toStr, level, sNBName,recurse)
155        DFREF dfr
156        String fromStr
157        String toStr
158        Variable level                  // Pass 0 to start
159        String sNBName
160        Variable recurse
161 
162        String name
163        String dfName
164        String sString
165       
166        String toDF = ""
167 
168        if (level == 0)         // this is the data folder, generate if needed in the destination
169                name = GetDataFolder(1, dfr)
170//              sPrintf sString, "%s (data folder)\r", name
171                toDF = ReplaceString(fromStr,name,toStr,1)              // case-sensitive replace
172                sprintf sString, "NewDataFolder/O %s\r",toDF
173                NewDataFolder/O $(RemoveEnding(toDF,":"))                       // remove trailing semicolon if it's there
174               
175                V_WriteBrowserInfo(sString, 1, sNBName)
176        endif
177 
178        dfName = GetDataFolder(1, dfr)
179        toDF = ReplaceString(fromStr,dfName,toStr,1)            // case-sensitive replace
180        Variable i
181 
182        String indentStr = "\t"
183        for(i=0; i<level; i+=1)
184                indentStr += "\t"
185        endfor
186 
187        Variable numWaves = CountObjectsDFR(dfr, 1)
188        for(i=0; i<numWaves; i+=1)
189                name = GetIndexedObjNameDFR(dfr, 1, i)
190                //
191                // wave type does not matter now. Duplicate does not care
192                //
193                sPrintf sString, "Duplicate/O  %s,  %s\r",dfName+name,toDF+name
194                Duplicate/O $(dfName+name),$(toDF+name)
195               
196                V_WriteBrowserInfo(sString, 2, sNBName)
197        endfor 
198 
199        Variable numNumericVariables = CountObjectsDFR(dfr, 2) 
200        for(i=0; i<numNumericVariables; i+=1)
201                name = GetIndexedObjNameDFR(dfr, 2, i)
202                sPrintf sString, "%s%s (numeric variable)\r", indentStr, name
203                V_WriteBrowserInfo(sString, 3, sNBName)
204        endfor 
205 
206        Variable numStringVariables = CountObjectsDFR(dfr, 3)   
207        for(i=0; i<numStringVariables; i+=1)
208                name = GetIndexedObjNameDFR(dfr, 3, i)
209                sPrintf sString, "%s%s (string variable)\r", indentStr, name
210                V_WriteBrowserInfo(sString, 4, sNBName)
211        endfor 
212
213        if(recurse)
214                Variable numDataFolders = CountObjectsDFR(dfr, 4)       
215                for(i=0; i<numDataFolders; i+=1)
216                        name = GetIndexedObjNameDFR(dfr, 4, i)
217//                      sPrintf sString, "%s%s (data folder)\r", indentStr, name
218                         dfName = GetDataFolder(1, dfr)
219                         
220                        toDF = ReplaceString(fromStr,dfName,toStr,1)            // case-sensitive replace
221                        sprintf sString, "NewDataFolder/O %s\r",toDF+name
222                        NewDataFolder/O $(toDF+name)
223                       
224                       
225                        V_WriteBrowserInfo(sString, 1, sNBName)
226                        DFREF childDFR = dfr:$(name)
227                        V_DuplicateDataFolder(childDFR, fromStr, toStr, level+1, sNBName, recurse)
228                endfor 
229        endif
230         
231//when finished walking tree, save as RTF with dialog   
232//      if(level == 0 && strlen(sNBName) != 0)
233//              SaveNotebook /I /S=4  $sNBName
234//      endif
235End
236 
237Function V_WriteBrowserInfo(sString, vType, sNBName)
238        String sString
239        Variable vType
240        String sNBName
241 
242        if(strlen(sNBName) == 0)
243//              print sString
244                return 0
245        endif
246        DoWindow $sNBName
247        if(V_flag != 1)
248                NewNoteBook/F=0 /N=$sNBName /V=1 as sNBName
249        else
250                DoWindow/F $sNBName
251        endif
252        Notebook $sNBName selection={endOfFile, endOfFile}
253        if(vType == 1)          // a data folder
254//              Notebook $sNBName fstyle=1
255                Notebook $sNBName text=sString
256//              Notebook $sNBName fstyle=-1
257        else
258                Notebook $sNBName text=sString 
259        endif
260 
261End
262
263///////////////////////////////
264
265
266//
267// given the folder, duplicate the data -> linear_data and generate the error
268// TODO
269// -- do I want to use different names here? If it turns out that I don't need to drag a copy of
270//    the data around as "linear_data", then I can eliminate that, and rename the error wave
271// -- be sure the data is either properly written as 2D in the file, or converted to 2D before
272//    duplicating here
273// -- ? do I recast to DP here. Probably necessary since I'm doing a DP calculation, but Redimension
274//    is done in the Raw_to_Work step too. very confusing.
275Function V_MakeDataError(folderStr)
276        String folderStr
277       
278        SetDataFolder $folderStr
279        Wave data=data
280        Duplicate/O data linear_data                    // at this point, the data is still the raw data, and is linear_data
281       
282        // proper error for counting statistics, good for low count values too
283        // rather than just sqrt(n)
284        // see N. Gehrels, Astrophys. J., 303 (1986) 336-346, equation (7)
285        // for S = 1 in eq (7), this corresponds to one sigma error bars
286        Duplicate/O linear_data linear_data_error
287        linear_data_error = 1 + sqrt(linear_data + 0.75)                               
288        //
289       
290        SetDataFolder root:
291        return(0)
292End
293
294
295/////////////////////
296
297
298
299//testing procedure
300// TODO -- can't duplicate this with another proceudre, but if I change the name of the variable
301//   "newType" to "type", then when Raw_to_work() gets to CopyHDFToWorkFolder(), the KillDataFolder/Z
302//   line fails (but reports no error), then DuplicateDataFolder fails, and reports an error. Trying
303//   to simplify this condition, I can't duplicate the error for WM...
304Macro Convert_to_Workfile(newtype, doadd)
305        String newtype,doadd
306        Prompt newtype,"WORK data type",popup,"SAM;EMP;BGD;ADJ;"
307        Prompt doadd,"Add to current WORK contents?",popup,"No;Yes;"
308       
309        //macro will take whatever is in RAW folder and "ADD" it to the folder specified
310        //in the popup menu
311       
312        //"add" = yes/no, don't add to previous runs
313        //switch here - two separate functions to avoid (my) confusion
314        Variable err// = Raw_to_work(newtype)
315        if(cmpstr(doadd,"No")==0)
316                //don't add to prev work contents, copy RAW contents to work and convert
317                err = Raw_to_work(newtype)
318        else
319                //yes, add RAW to the current work folder contents
320                Abort "Adding RAW data files is currently unsupported"
321                err = Add_raw_to_work(newtype)
322        endif
323       
324        String newTitle = "WORK_"+newtype
325        DoWindow/F VSANS_Data
326        DoWindow/T VSANS_Data, newTitle
327        KillStrings/Z newTitle
328       
329        //need to update the display with "data" from the correct dataFolder
330        UpdateDisplayInformation(newtype)
331       
332End
333
334
335//
336// THIS IS THE MAJOR ROUTINE TO APPLY DATA CORRECTIONS
337//
338//will copy the current contents of the RAW folder to the newType work folder
339//and do the geometric corrections and normalization to monitor counts
340//(the function Add_Raw_to_work(type) adds multiple runs together - and is LOW priority)
341//
342//the current display type is updated to newType (global)
343//
344Function Raw_to_work(newType)
345        String newType
346       
347        Variable deadTime,defmon,total_mon,total_det,total_trn,total_numruns,total_rtime
348        Variable ii,jj,itim,cntrate,dscale,scale,uscale
349        String destPath
350       
351        String fname = newType
352        String detStr
353        Variable ctTime
354
355        //initialize values before normalization
356        total_mon=0
357        total_det=0
358        total_trn=0
359        total_numruns=0
360        total_rtime=0
361       
362        //Not adding multiple runs, so wipe out the old contents of the work folder and
363        // replace with the contents of raw
364
365        destPath = "root:Packages:NIST:VSANS:" + newType
366       
367        //copy from current dir (RAW) to work, defined by newType
368        CopyHDFToWorkFolder("RAW",newType)
369       
370        // now work with the waves from the destination folder.
371       
372        // apply corrections ---
373        // switches to control what is done, don't do the transmission correction for the BGD measurement
374        // start with the DIV correction, before conversion to mm
375        // then do all of the other corrections, order doesn't matter.
376        // rescaling to default monitor counts however, must be LAST.
377
378// each correction must loop over each detector. tedious.
379
380        // (0) Redimension the data waves in the destination folder
381        //     so that they are DP, not integer
382        // TODO
383        // -- currently only redimensioning the data and linear_data_error - What else???
384        // -- ?? some of this is done at load time for RAW data
385        for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
386                detStr = StringFromList(ii, ksDetectorListAll, ";")
387                Wave w = V_getDetectorDataW(fname,detStr)
388                Wave w_err = V_getDetectorDataErrW(fname,detStr)
389                Redimension/D w,w_err
390        endfor
391       
392       
393        // (1) DIV correction
394        // do this in terms of pixels.
395        // TODO : This must also exist at the time the first work folder is generated.
396        //   So it must be in the user folder at the start of the experiment, and defined.
397        NVAR gDoDIVCor = root:Packages:NIST:VSANS:Globals:gDoDIVCor
398        if (gDoDIVCor == 1)
399                // need extra check here for file existence
400                // if not in DIV folder, load.
401                // if unable to load, skip correction and report error (Alert?) (Ask to Load?)
402                Print "Doing DIV correction"// for "+ detStr
403                for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
404                        detStr = StringFromList(ii, ksDetectorListAll, ";")
405                        Wave w = V_getDetectorDataW(fname,detStr)
406                        Wave w_err = V_getDetectorDataErrW(fname,detStr)
407                       
408                        DIVCorrection(w,w_err,detStr,newType)
409                endfor
410        else
411                Print "DIV correction not done"         // not an error since correction was unchecked
412        endif
413       
414        // (2) non-linear correction   
415        // TODO:
416        // -- currently, the "B" detector is skipped
417        // -- document what is generated here:
418        //    **in each detector folder: data_realDistX and data_realDistY (2D waves of the mm? position of the pixel)
419        // -- still not sure whether to duplicate these calculations as the RAW data is loaded. It would allow the RAW
420        //    data to be properly displayed, but without all of the (complete) set of corrections
421        // * the corrected distances are calculated into arrays, but nothing is done with them yet
422        // * there is enough information now to calculate the q-arrays -other corrections modify the data
423        NVAR gDoNonLinearCor = root:Packages:NIST:VSANS:Globals:gDoNonLinearCor
424        // generate a distance matrix for each of the detectors
425        if (gDoNonLinearCor == 1)
426                Print "Doing Non-linear correction"// for "+ detStr
427                for(ii=0;ii<ItemsInList(ksDetectorListNoB);ii+=1)
428                        detStr = StringFromList(ii, ksDetectorListNoB, ";")
429                        Wave w = V_getDetectorDataW(fname,detStr)
430//                      Wave w_err = V_getDetectorDataErrW(fname,detStr)
431                        Wave w_calib = V_getDetTube_spatialCalib(fname,detStr)
432                        Variable tube_width = V_getDet_tubeWidth(fname,detStr)
433                        NonLinearCorrection(w,w_calib,tube_width,detStr,destPath)
434
435                        //(2.4) Convert the beam center values from pixels to mm
436                        // TODO -- there needs to be a permanent location for these values??
437                        //
438                        ConvertBeamCtr_to_mm(fname,detStr,destPath)
439                                                       
440                        // (2.5) Calculate the q-values
441                        // calculating q-values can't be done unless the non-linear corrections are calculated
442                        // so go ahead and put it in this loop.
443                        // TODO :
444                        // -- make sure that everything is present before the calculation
445                        // -- beam center must be properly defined in terms of real distance
446                        // -- distances/zero location/ etc. must be clearly documented for each detector
447                        //      ** this assumes that NonLinearCorrection() has been run to generate data_RealDistX and Y
448                        // ** this routine Makes the waves QTot, qx, qy, qz in each detector folder.
449                        //
450                        V_Detector_CalcQVals(fname,detStr,destPath)
451                       
452                endfor
453               
454                //"B" is separate
455                NonLinearCorrection_B(fname,"B",destPath)
456                ConvertBeamCtr_to_mmB(fname,"B",destPath)
457                V_Detector_CalcQVals(fname,"B",destPath)
458               
459        else
460                Print "Non-linear correction not done"
461        endif
462
463        // (3) solid angle correction
464        NVAR gDoSolidAngleCor = root:Packages:NIST:VSANS:Globals:gDoSolidAngleCor
465        if (gDoSolidAngleCor == 1)
466                Print "Doing Solid Angle correction"// for "+ detStr
467                for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
468                        detStr = StringFromList(ii, ksDetectorListAll, ";")
469                        Wave w = V_getDetectorDataW(fname,detStr)
470                        Wave w_err = V_getDetectorDataErrW(fname,detStr)
471                        Wave w_dt = V_getDetector_deadtime(fname,detStr)
472//                      SolidAngleCorrection(fill this in)
473                       
474                endfor
475        else
476                Print "Solid Angle correction not done"
477        endif   
478       
479        // (4) dead time correction
480        // TODO: -- remove the hard-wired test
481        // -- test for correct operation
482        // -- loop over all of the detectors
483        // -- B detector is a special case (do separately, then loop over NoB)
484        NVAR gDoDeadTimeCor = root:Packages:NIST:VSANS:Globals:gDoDeadTimeCor
485        ctTime = V_getCount_time(fname)
486        if (gDoDeadTimeCor == 1)
487                Print "Doing DeadTime correction"// for "+ detStr
488                for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
489                        detStr = StringFromList(ii, ksDetectorListAll, ";")
490                        Wave w = V_getDetectorDataW(fname,detStr)
491                        Wave w_err = V_getDetectorDataErrW(fname,detStr)
492                        Wave w_dt = V_getDetector_deadtime(fname,detStr)
493//                      DeadTimeCorrectionTubes(w,w_err,w_dt,ctTime)
494                                //deadtime corrections
495//      itim = integersread[2]
496//      cntrate = sum(data,-inf,inf)/itim               //use sum of detector counts rather than scaler value
497//      //TODO - do correct dead time correction for tubes
498//      deadtime = 1//DetectorDeadtime(textread[3],textread[9],dateAndTimeStr=textRead[1],dtime=realsRead[48])  //pick the correct deadtime
499//      dscale = 1/(1-deadTime*cntrate)
500//     
501       
502// dead time correction
503//      data *= dscale          //deadtime correction for everyone else, including NCNR
504//      data_err *= dscale
505
506                endfor
507        else
508                Print "Dead Time correction not done"
509        endif   
510       
511        // (5) angle-dependent tube shadowing
512        NVAR gDoTubeShadowCor = root:Packages:NIST:VSANS:Globals:gDoTubeShadowCor
513        if (gDoTubeShadowCor == 1)
514       
515        else
516                Print "Tube shadowing correction not done"
517        endif   
518               
519        // (6) angle dependent transmission correction
520        NVAR gDoTrans = root:Packages:NIST:VSANS:Globals:gDoTransmissionCor
521        if (gDoTrans == 1)
522                Print "Doing Large-angle transmission correction"// for "+ detStr
523                for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
524                        detStr = StringFromList(ii, ksDetectorListAll, ";")
525                        Wave w = V_getDetectorDataW(fname,detStr)
526                        Wave w_err = V_getDetectorDataErrW(fname,detStr)
527                        Wave w_dt = V_getDetector_deadtime(fname,detStr)
528//                      TransmissionCorrection(fill this in)
529                       
530                endfor
531        else
532                Print "Sample Transmission correction not done"
533        endif   
534       
535        // (7) normalize to default monitor counts
536        // TODO -- each detector is rescaled separately, but the rescaling factor is global (only one monitor!)
537        // TODO -- but there are TWO monitors - so how to switch?
538        // TODO -- what do I really need to save?
539        Print "Doing monitor normalization"// for "+ detStr
540
541        defmon=1e8                      //default monitor counts
542        for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
543                detStr = StringFromList(ii, ksDetectorListAll, ";")
544                Wave w = V_getDetectorDataW(fname,detStr)
545                Wave w_err = V_getDetectorDataErrW(fname,detStr)
546                Variable monCt = V_getBeamMonNormData(fname)
547//                      MonitorNormalization(fill this in)
548        //scale the data to the default montor counts
549       
550        // TODO -- un-comment these three lines once monitor counts are reasonable - currently monCt = 9!!!
551//              scale = defmon/monCt
552//              w *= scale
553//              w_err *= scale          //assumes total monitor count is so large there is essentially no error
554
555// TODO
556// -- to write back to the local value, get the wave reference rather than the value, then I can
557//    re-assign the value directly, rather than this method (which is not terrible)     
558                // V_getBeamMonNormSaved_count()
559                // save the true monitor counts? save the scaling factor?
560                String path = "entry:instrument:beam_monitor_norm:saved_count"
561                Wave/Z savW = $("root:Packages:NIST:VSANS:"+fname+":entry:"+path)
562                savW[0] = scale
563        endfor
564       
565       
566        // (not done) angle dependent efficiency correction
567        NVAR doEfficiency = root:Packages:NIST:VSANS:Globals:gDoDetectorEffCor
568
569       
570// this function, in the past did the non-linear, solid angle, transmission, and efficiency corrections all at once
571//      DetCorr(data,data_err,realsread,doEfficiency,doTrans)           //the parameters are waves, and will be changed by the function
572
573
574       
575        //update totals to put in the work header (at the end of the function)
576//      total_mon += realsread[0]
577//
578//      total_det += dscale*realsread[2]
579//
580//      total_trn += realsread[39]
581//      total_rtime += integersread[2]
582//      total_numruns +=1
583//     
584
585        //all is done, except for the bookkeeping, updating the header information in the work folder
586
587//      integersread[3] = total_numruns                                         //numruns = 1
588//      realsread[1] = total_mon                        //save the true monitor count
589//      realsread[0] = defmon                                   //monitor ct = defmon
590//      realsread[2] = scale*total_det                  //scaled detector counts
591//     
592        //reset the current displaytype to "newtype"
593        String/G root:Packages:NIST:VSANS:Globals:gCurDispType=newType
594       
595        //return to root folder (redundant)
596        SetDataFolder root:
597       
598        Return(0)
599End
600
601
602//will "ADD" the current contents of the RAW folder to the newType work folder
603//and will ADD the RAW contents to the existing content of the newType folder
604// - used when adding multiple runs together
605//(the function Raw_to_work(type) makes a fresh workfile)
606//
607//the current display type is updated to newType (global)
608Function Add_raw_to_work(newType)
609        String newType
610       
611        // NEW OCT 2014
612        // this corrects for adding raw data files with different attenuation   
613        // does nothing if the attenuation of RAW and destination are the same
614        NVAR doAdjustRAW_Atten = root:Packages:NIST:gDoAdjustRAW_Atten
615        if(doAdjustRAW_Atten)
616                Adjust_RAW_Attenuation(newType)
617        endif
618       
619        String destPath=""
620       
621        // if the desired workfile doesn't exist, let the user know, and just make a new one
622        if(WaveExists($("root:Packages:NIST:"+newType + ":data")) == 0)
623                Print "There is no old work file to add to - a new one will be created"
624                //call Raw_to_work(), then return from this function
625                Raw_to_Work(newType)
626                Return(0)               //does not generate an error - a single file was converted to work.newtype
627        Endif
628       
629        NVAR pixelsX = root:myGlobals:gNPixelsX
630        NVAR pixelsY = root:myGlobals:gNPixelsY
631       
632        //now make references to data in newType folder
633        DestPath="root:Packages:NIST:"+newType 
634        WAVE data=$(destPath +":linear_data")                   // these wave references point to the EXISTING work data
635        WAVE data_copy=$(destPath +":data")                     // these wave references point to the EXISTING work data
636        WAVE dest_data_err=$(destPath +":linear_data_error")                    // these wave references point to the EXISTING work data
637        WAVE/T textread=$(destPath + ":textread")
638        WAVE integersread=$(destPath + ":integersread")
639        WAVE realsread=$(destPath + ":realsread")
640       
641        Variable deadTime,defmon,total_mon,total_det,total_trn,total_numruns,total_rtime
642        Variable ii,jj,itim,cntrate,dscale,scale,uscale,wrk_beamx,wrk_beamy,xshift,yshift
643
644
645        defmon=1e8                      //default monitor counts
646       
647        //Yes, add to previous run(s) in work, that does exist
648        //use the actual monitor count run.savmon rather than the normalized monitor count
649        //in run.moncnt and unscale the work data
650       
651        total_mon = realsread[1]        //saved monitor count
652        uscale = total_mon/defmon               //unscaling factor
653        total_det = uscale*realsread[2]         //unscaled detector count
654        total_trn = uscale*realsread[39]        //unscaled trans det count
655        total_numruns = integersread[3] //number of runs in workfile
656        total_rtime = integersread[2]           //total counting time in workfile
657        //retrieve workfile beamcenter
658        wrk_beamx = realsread[16]
659        wrk_beamy = realsread[17]
660        //unscale the workfile data in "newType"
661        //
662        //check for log-scaling and adjust if necessary
663        // should not be needed now - using display flag instead
664//      ConvertFolderToLinearScale(newType)
665        //
666        //then unscale the data array
667        data *= uscale
668        dest_data_err *= uscale
669       
670        //DetCorr() has not been applied to the data in RAW , do it now in a local reference to the raw data
671        WAVE raw_data = $"root:Packages:NIST:RAW:linear_data"
672        WAVE raw_data_err = $"root:Packages:NIST:RAW:linear_data_error"
673        WAVE raw_reals =  $"root:Packages:NIST:RAW:realsread"
674        WAVE/T raw_text = $"root:Packages:NIST:RAW:textread"
675        WAVE raw_ints = $"root:Packages:NIST:RAW:integersread"
676       
677        //check for log-scaling of the raw data - make sure it's linear
678        // should not be needed now - using display flag instead
679//      ConvertFolderToLinearScale("RAW")
680       
681        // switches to control what is done, don't do the transmission correction for the BGD measurement
682        NVAR doEfficiency = root:Packages:NIST:gDoDetectorEffCorr
683        NVAR gDoTrans = root:Packages:NIST:gDoTransmissionCorr
684        Variable doTrans = gDoTrans
685        if(cmpstr("BGD",newtype) == 0)
686                doTrans = 0             //skip the trans correction for the BGD file but don't change the value of the global
687        endif   
688       
689        DetCorr(raw_data,raw_data_err,raw_reals,doEfficiency,doTrans)   //applies correction to raw_data, and overwrites it
690       
691        //deadtime corrections to raw data
692        // TODO - do the tube correction for dead time now
693        deadTime = 1//DetectorDeadtime(raw_text[3],raw_text[9],dateAndTimeStr=raw_text[1],dtime=raw_reals[48])          //pick the correct detector deadtime, switch on date too
694        itim = raw_ints[2]
695        cntrate = sum(raw_data,-inf,inf)/itim           //080802 use data sum, rather than scaler value
696        dscale = 1/(1-deadTime*cntrate)
697
698#if (exists("ILL_D22")==6)
699        Variable tubeSum
700        // for D22 detector might need to use cntrate/128 as it is the tube response
701        for(ii=0;ii<pixelsX;ii+=1)
702                //sum the counts in each tube
703                tubeSum = 0
704                for(jj=0;jj<pixelsY;jj+=1)
705                        tubeSum += data[jj][ii]
706                endfor
707                // countrate in tube ii
708                cntrate = tubeSum/itim
709                // deadtime scaling in tube ii
710                dscale = 1/(1-deadTime*cntrate)
711                // multiply data[ii][] by the dead time
712                raw_data[][ii] *= dscale
713                raw_data_err[][ii] *= dscale
714        endfor
715#else
716        // dead time correction on all other RAW data, including NCNR
717        raw_data *= dscale
718        raw_data_err *= dscale
719#endif
720
721        //update totals by adding RAW values to the local ones (write to work header at end of function)
722        total_mon += raw_reals[0]
723
724        total_det += dscale*raw_reals[2]
725
726        total_trn += raw_reals[39]
727        total_rtime += raw_ints[2]
728        total_numruns +=1
729       
730        //do the beamcenter shifting if there is a mismatch
731        //and then add the two data sets together, changing "data" since it is the workfile data
732        xshift = raw_reals[16] - wrk_beamx
733        yshift = raw_reals[17] - wrk_beamy
734       
735        If((xshift != 0) || (yshift != 0))
736                DoAlert 1,"Do you want to ignore the beam center mismatch?"
737                if(V_flag==1)
738                        xshift=0
739                        yshift=0
740                endif
741        endif
742       
743        If((xshift == 0) && (yshift == 0))              //no shift, just add them
744                data += raw_data                //deadtime correction has already been done to the raw data
745                dest_data_err = sqrt(dest_data_err^2 + raw_data_err^2)                  // error of the sum
746        Endif
747       
748        //scale the data to the default montor counts
749        scale = defmon/total_mon
750        data *= scale
751        dest_data_err *= scale
752       
753        // keep "data" and linear_data in sync in the destination folder
754        data_copy = data
755       
756        //all is done, except for the bookkeeping of updating the header info in the work folder
757        textread[1] = date() + " " + time()             //date + time stamp
758        integersread[3] = total_numruns                                         //numruns = more than one
759        realsread[1] = total_mon                        //save the true monitor count
760        realsread[0] = defmon                                   //monitor ct = defmon
761        integersread[2] = total_rtime                   // total counting time
762        realsread[2] = scale*total_det                  //scaled detector counts
763        realsread[39] = scale*total_trn                 //scaled transmission counts
764       
765        //Add the added raw filename to the list of files in the workfile
766        String newfile = ";" + raw_text[0]
767        SVAR oldList = $(destPath + ":fileList")
768        String/G $(destPath + ":fileList") = oldList + newfile
769       
770        //reset the current displaytype to "newtype"
771        String/G root:myGlobals:gDataDisplayType=newType
772       
773        //return to root folder (redundant)
774        SetDataFolder root:
775       
776        Return(0)
777End
778
779
780//used for adding DRK (beam shutter CLOSED) data to a workfile
781//force the monitor count to 1, since it's irrelevant
782// run data through normal "add" step, then unscale default monitor counts
783//to get the data back on a simple time basis
784//
785Function Raw_to_Work_NoNorm(type)
786        String type
787       
788        WAVE reals=$("root:Packages:NIST:RAW:realsread")
789        reals[1]=1              //true monitor counts, still in raw
790        Raw_to_work(type)
791        //data is now in "type" folder
792        WAVE data=$("root:Packages:NIST:"+type+":linear_data")
793        WAVE data_copy=$("root:Packages:NIST:"+type+":data")
794        WAVE data_err=$("root:Packages:NIST:"+type+":linear_data_error")
795        WAVE new_reals=$("root:Packages:NIST:"+type+":realsread")
796       
797        Variable norm_mon,tot_mon,scale
798       
799        norm_mon = new_reals[0]         //should be 1e8
800        tot_mon = new_reals[1]          //should be 1
801        scale= norm_mon/tot_mon
802       
803        data /= scale           //unscale the data
804        data_err /= scale
805       
806        // to keep "data" and linear_data in sync
807        data_copy = data
808       
809        return(0)
810End
811
812//used for adding DRK (beam shutter CLOSED) data to a workfile
813//force the monitor count to 1, since it's irrelevant
814// run data through normal "add" step, then unscale default monitor counts
815//to get the data back on a simple time basis
816//
817Function Add_Raw_to_Work_NoNorm(type)
818        String type
819       
820        WAVE reals=$("root:Packages:NIST:RAW:realsread")
821        reals[1]=1              //true monitor counts, still in raw
822        Add_Raw_to_work(type)
823        //data is now in "type" folder
824        WAVE data=$("root:Packages:NIST:"+type+":linear_data")
825        WAVE data_copy=$("root:Packages:NIST:"+type+":data")
826        WAVE data_err=$("root:Packages:NIST:"+type+":linear_data_error")
827        WAVE new_reals=$("root:Packages:NIST:"+type+":realsread")
828       
829        Variable norm_mon,tot_mon,scale
830       
831        norm_mon = new_reals[0]         //should be 1e8
832        tot_mon = new_reals[1]          //should be equal to the number of runs (1 count per run)
833        scale= norm_mon/tot_mon
834       
835        data /= scale           //unscale the data
836        data_err /= scale
837       
838        // to keep "data" and linear_data in sync
839        data_copy = data
840       
841        return(0)
842End
843
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