source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_Initialize.ipf @ 1166

Last change on this file since 1166 was 1166, checked in by srkline, 3 years ago

changed the file extension on VSANS QxQyASCII output to have the panel tag in th
e middle of the name to keep the .DAT extension visible for sasView

Changed the behavior of the VSANS averaging protocol. When "saving file" is selceted, choices are either to concatenate or individual. concatenate has NOT been changed. Individual save will now save each individual detector panel data in as
eparate file with the detectr panel string tagged on the end. This replaces the
tedious procedure of multiple mask files an multiple reduction passes.

The save as ITX function is still available through a menu option but is current
ly not an option for a protocol.

File size: 18.3 KB
Line 
1#pragma rtGlobals=3             // Use modern global access method and strict wave access.
2#pragma version=0.1
3#pragma IgorVersion=6.1
4
5//***********************
6// NOV 2015 Vers 0.1
7//
8// Initialization procedures that must be run before anything
9// this is accomplished by placing:
10//
11// Initialize()
12// #include "includes"
13//
14// in the built-in procedure window of the .pxt (template) experiment
15// IGOR recognizes this, and executes Initialize() immediately after
16// compiling all of the included procedures. This is all done as the blank
17// template is opened
18//
19// Choosing initialize from the VSANS menu will do the same, and no harm is done
20// to the experiment by re- initializing. no data or folders are overwritten
21//
22//************************
23
24Constant kVSANSVersion = 7.93
25
26// TODO -- need to set up a separate file of "constants" or "globals" where the actual numbers are
27//stored. If there are not a lot, that place could be here. InitFacilityGlobals() is currently in NCNR_Utils.ipf
28
29
30// for the change in July 2017 where the beam center is now defined in cm, rather than pixels.
31// this need not ever change from 1
32// the back detector is always treated as a beam center in pixels, since it is the natural definition
33Constant kBCTR_CM = 1                   //set to 1 to use beam center in cm. O to use pixels
34
35// // TODO: -- replace this constant with V_getDet_panel_gap(fname,detStr)
36//Constant kPanelTouchingGap = 10                       // TODO -- measure this gap when panels "touch", UNITS OF mm, not cm
37
38
39// the base data folder path where the raw data is loaded
40Strconstant ksBaseDFPath = "root:Packages:NIST:VSANS:RawVSANS:"
41
42
43// the list of WORK Folders
44// RawVSANS does not behave as a WORK folder, but it is local. so add it in explicitly to the list if needed
45// VCALC behaves *almost* as a WORK folder, but it is local. so add it in explicitly to the list if needed
46//Strconstant ksWorkFolderList = "RAW;SAM;EMP;BGD;COR;DIV;ABS;MSK;CAL;STO;SUB;DRK;ADJ;VCALC;RawVSANS;"
47Strconstant ksWorkFolderListShort = "RAW;SAM;EMP;BGD;COR;DIV;ABS;MSK;CAL;STO;SUB;DRK;ADJ;"
48
49
50// for defining which "bin type" corresponds to which set of extensions for I(q) data
51// !! see V_BinTypeStr2Num() for the numbering, not the order of the list
52//
53//////////////////
54//Strconstant ksBinTypeStr = "One;Two;Four;Slit Mode;"
55Strconstant ksBinTypeStr = "F4-M4-B;F2-M2-B;F1-M1-B;F2-M1-B;F1-M2xTB-B;F2-M2xTB-B;SLIT-F2-M2-B;"
56Strconstant ksBinType1 = "FT;FB;FL;FR;MT;MB;ML;MR;B;"           //these are the "active" extensions
57Strconstant ksBinType2 = "FTB;FLR;MTB;MLR;B;"
58Strconstant ksBinType3 = "FLRTB;MLRTB;B;"
59Strconstant ksBinType4 = "FL;FR;ML;MR;B;"               //in SLIT mode, disregard the T/B panels
60Strconstant ksBinType5 = "FTB;FLR;MLRTB;B;"
61Strconstant ksBinType6 = "FLRTB;MLR;B;"
62Strconstant ksBinType7 = "FTB;FLR;MLR;B;"
63///////////////////
64
65
66// for looping over each detector
67Strconstant ksDetectorListNoB = "FL;FR;FT;FB;ML;MR;MT;MB;"
68Strconstant ksDetectorListAll = "FL;FR;FT;FB;ML;MR;MT;MB;B;"
69
70
71// for Protocols
72Constant kNumProtocolSteps = 12
73// for trimming of the I(q) data sets, and part of the protocol
74Strconstant ksPanelBinTypeList = "B;FT;FB;FL;FR;MT;MB;ML;MR;FTB;FLR;MTB;MLR;FLRTB;MLRTB;"
75Strconstant ksBinTrimBegDefault = "B=5;FT=3;FB=3;FL=3;FR=3;MT=3;MB=3;ML=3;MR=3;FTB=2;FLR=2;MTB=2;MLR=2;FLRTB=1;MLRTB=1;"
76Strconstant ksBinTrimEndDefault = "B=10;FT=5;FB=5;FL=5;FR=5;MT=5;MB=5;ML=5;MR=5;FTB=4;FLR=4;MTB=4;MLR=4;FLRTB=3;MLRTB=3;"
77
78
79
80//////// HIGH RESOLUTION DETECTOR  ///////////////
81
82
83//
84// In May 2019 - after testing with Phil's procesing, the data from the detector has a
85// larger read noise value. It can also no longer be treated  as a constant value, but rather
86// a detector file that is read in and subtracted pixel-by-pixel.
87//
88
89
90// the average read noise level of the back detector
91// taken from multiple runs with the beam off, 6-28-18
92// runs sans12324 - sans12353
93//
94// used in V_Raw_to_Work()
95// average of whole panel (tested several data files) = 208 +/- 14
96//
97// 200 appears to be a better value - (empirical, based on teflon/converging pinhole data)
98//Constant kReadNoiseLevel_bin4 = 200
99//Constant kReadNoiseLevel_Err_bin4 = 14
100// after binning/processing changes from March 2019:
101Constant kReadNoiseLevel_bin4 = 3160                    // from bkg area of sans30201 (a transmission measurement)
102Constant kReadNoiseLevel_Err_bin4 = 50          //estimated
103
104// TODOHIGHRES: these values are complete fiction
105Constant kReadNoiseLevel_bin1 = 20
106Constant kReadNoiseLevel_Err_bin1 = 1
107
108// Pixel shifts for the back detector to bring the three CCDs into registry
109// data from pinholes used to match up CCDs
110// 27 JUN 2018
111// runs 12221,12225,27,33,34,35,38,42
112// middle CCD is not moved
113// See V_ShiftBackDetImage() for implementation
114Constant        kShift_TopX_bin4 = 7
115Constant                kShift_TopY_bin4 = 105
116Constant                kShift_BottomX_bin4 = 5
117Constant                kShift_BottomY_bin4 = 35
118
119// TODOHIGHRES -- these values need to be verified. they are currently simply 4x the bin4 values
120Constant        kShift_TopX_bin1 = 28
121Constant                kShift_TopY_bin1 = 420
122Constant                kShift_BottomX_bin1 = 20
123Constant                kShift_BottomY_bin1 = 130
124
125
126
127
128
129
130
131
132Proc Initialize_VSANS()
133        V_Initialize()
134End
135
136//this is the main initialization procedure that must be the first thing
137//done when opening a new Data reduction experiment
138//
139//sets up data folders, globals, protocols, and draws the main panel
140Proc V_Initialize()
141
142        Variable curVersion = kVSANSVersion
143        Variable oldVersion = NumVarOrDefault("root:VSANS_RED_VERSION",curVersion)
144               
145        if(oldVersion == curVersion)
146                //must just be a new startup with the current version
147                Variable/G root:VSANS_RED_VERSION=kVSANSVersion
148        endif
149       
150        if(oldVersion < curVersion)
151                String str =    "This experiment was created with version "+num2str(oldVersion)+" of the macros. I'll try to make this work, but please start new work with a current template"
152                DoAlert 0,str
153        endif
154       
155        V_InitFolders()
156       
157       
158        V_InitFakeProtocols()
159        V_InitGlobals()
160        V_InitFacilityGlobals()
161        DoWindow/F Main_VSANS_Panel
162        If(V_flag == 0)
163                //draw panel
164                Main_VSANS_Panel()
165        Endif
166//      V_ResizeCmdWindow()
167
168        VC_Initialize_Space()           //initialize folders for VCALC
169
170// TODO - be sure that NCNR is defined correctly       
171        //unload the NCNR_Package_Loader, if NCNR not defined
172        UnloadNCNR_VSANS_Procedures()
173
174End
175
176//creates all the necessary data folders in the root folder
177//does not overwrite any existing folders of the same name
178//it leaves data in them untouched
179//
180// x-- make sure that I have all of the folders that I need
181//
182Function V_InitFolders()
183       
184        NewDataFolder/O root:Packages
185        NewDataFolder/O root:Packages:NIST
186        NewDataFolder/O root:Packages:NIST:VSANS
187       
188// for the file catalog
189        NewDataFolder/O root:Packages:NIST:VSANS:CatVSHeaderInfo
190// for the globals
191        NewDataFolder/O root:Packages:NIST:VSANS:Globals
192// for the raw nexus data (so I don't need to reload to get a single value)
193        NewDataFolder/O root:Packages:NIST:VSANS:RawVSANS
194
195// folders for the reduction steps             
196        NewDataFolder/O root:Packages:NIST:VSANS:RAW
197        NewDataFolder/O root:Packages:NIST:VSANS:SAM
198        NewDataFolder/O root:Packages:NIST:VSANS:EMP
199        NewDataFolder/O root:Packages:NIST:VSANS:BGD
200        NewDataFolder/O root:Packages:NIST:VSANS:COR
201        NewDataFolder/O root:Packages:NIST:VSANS:DIV
202        NewDataFolder/O root:Packages:NIST:VSANS:MSK
203        NewDataFolder/O root:Packages:NIST:VSANS:ABS
204        NewDataFolder/O root:Packages:NIST:VSANS:CAL
205        NewDataFolder/O root:Packages:NIST:VSANS:STO
206        NewDataFolder/O root:Packages:NIST:VSANS:SUB
207        NewDataFolder/O root:Packages:NIST:VSANS:DRK
208        NewDataFolder/O root:Packages:NIST:VSANS:ADJ
209        NewDataFolder/O root:Packages:NIST:VSANS:RealTime
210        NewDataFolder/O root:Packages:NIST:VSANS:VCALC
211        NewDataFolder/O root:Packages:NIST:VSANS:ReadNoise
212
213
214// ?? anything else
215
216// for simulation
217//      NewDataFolder/O root:Packages:NIST:VSANS:SAS
218
219
220       
221        Return(0)
222End
223
224
225
226
227//
228//Global folder already exists...
229//adds appropriate globals to the newly created myGlobals folder
230//return data folder to root: before leaving
231//
232//
233Function V_InitGlobals()
234       
235       
236        Variable/G root:Packages:NIST:VSANS:Globals:gIsLogScale = 0
237        String/G root:Packages:NIST:VSANS:Globals:gCurDispType = "RAW"
238       
239        //check platform, so Angstrom can be drawn correctly
240
241        //TODO  -- this is different on Igor 7. Macintosh # has been updated, but Windows has not
242        // use Print char2num("Å") to find the magic number
243        if(cmpstr("Macintosh",IgorInfo(2)) == 0)
244                String/G root:Packages:NIST:VSANS:Globals:gAngstStr = num2char(197)
245                String/G root:Packages:NIST:gAngstStr = num2char(197)
246                Variable/G root:Packages:NIST:VSANS:Globals:gIsMac = 1
247        else
248                //either Windows or Windows NT
249                String/G root:Packages:NIST:VSANS:Globals:gAngstStr = num2char(-59)
250                String/G root:Packages:NIST:gAngstStr = num2char(-59)
251                Variable/G root:Packages:NIST:VSANS:Globals:gIsMac = 0
252                //SetIgorOption to keep some PC's (graphics cards?) from smoothing the 2D image
253                // SRK APRIL 2019 - removed this, does not exist in Igor 8 on WIN, and cause an error.
254//              Execute "SetIgorOption WinDraw,forceCOLORONCOLOR=1"
255        endif
256       
257        // TODO x- find the SANS preferences, copy over and update for VSANS
258        // x- these are all in PlotUtilsMacro_v40.ipf as the preferences are set up as common
259        // to all packages. I'm not sure that I want to do this with VSANS, but make the packages
260        // separate entities. I'm seeing little benefit of the crossover, especially now that
261        // Analysis is not mine. So for VSANS, there is a new, separate file: V_VSANS_Preferences.ipf
262
263        //this is critical to initialize now - as it has the y/n flags for the detector correction steps
264        Execute "Initialize_VSANSPreferences()"
265
266        Execute "V_TubeZeroPointTables()"                       // correction to the beam center
267       
268        // set the lookup waves for log/lin display of the detector images
269        V_MakeImageLookupTables(10000,0,1)
270
271
272
273        //set flag if Demo Version is detected
274        Variable/G root:Packages:NIST:VSANS:Globals:isDemoVersion = V_isDemo()
275
276       
277        //set XML globals
278//      String/G root:Packages:NIST:gXMLLoader_Title = ""
279       
280        Return(0)
281End
282
283//
284//num = number of points (10000 seeems to be a good number so far)
285// lo = lower value (between 0 and 1)
286// hi = upper value (between 0 and 1)
287//
288// note that it is currenty NOT OK for lo > hi (!= reversed color scale, right now log(negative) == bad)
289//
290// TODO hi, lo not used properly here, seems to mangle log display now that I'm switching the lo,hi of the ctab
291//
292Function V_MakeImageLookupTables(num,lo,hi)
293        Variable num,lo,hi
294
295                // lookup waves for log and linear display of images
296        // this is used for the main data display. With this, I can use the original
297        // detector data (no copy) and the zeros in the data set are tolerated when displaying
298        // on log scale
299        SetDataFolder root:Packages:NIST:VSANS:Globals
300        Variable val,offset
301       
302        offset = 1/num          //can't use 1/lo if lo == 0
303       
304        Make/O/D/N=(num) logLookupWave,linearLookupWave
305       
306        linearLookupWave = (p+1)/num
307       
308       
309        logLookupWave = log(linearLookupWave)
310        val = logLookupWave[0]
311        logLookupWave += -val + offset
312        val = logLookupWave[num-1]
313        logLookupWave /= val
314       
315        SetDataFolder root:
316       
317        return(0)
318end
319
320//
321// initializes globals that are specific to VSANS
322//
323// there really should be nothing here... all of this should now be in the Nexus data file
324// and not tethered to hard-wired constants.
325//
326// -- what was here was:
327// number of detector pixels
328// pixel size
329// deadtime
330// beamstop "tolerance" to identify Trans files
331// sample aperture offset
332//
333Function V_InitFacilityGlobals()
334
335//      //Detector -specific globals
336//      Variable/G root:myGlobals:gNPixelsX=128
337//      Variable/G root:myGlobals:gNPixelsY=128
338//     
339//      // as of Jan2008, detector pixel sizes are read directly from the file header, so they MUST
340//      // be set correctly in instr.cfg - these values are not used, but declared to avoid errors
341//      Variable/G root:myGlobals:PixelResNG3_ILL = 1.0         //pixel resolution in cm
342//      Variable/G root:myGlobals:PixelResNG5_ILL = 1.0
343//      Variable/G root:myGlobals:PixelResNG7_ILL = 1.0
344//      Variable/G root:myGlobals:PixelResNG3_ORNL = 0.5
345//      Variable/G root:myGlobals:PixelResNG5_ORNL = 0.5
346//      Variable/G root:myGlobals:PixelResNG7_ORNL = 0.5
347//      Variable/G root:myGlobals:PixelResNGB_ORNL = 0.5
348////    Variable/G root:myGlobals:PixelResCGB_ORNL = 0.5                // fiction
349//
350//      Variable/G root:myGlobals:PixelResDefault = 0.5
351//     
352//      Variable/G root:myGlobals:DeadtimeNG3_ILL = 3.0e-6              //deadtime in seconds
353//      Variable/G root:myGlobals:DeadtimeNG5_ILL = 3.0e-6
354//      Variable/G root:myGlobals:DeadtimeNG7_ILL = 3.0e-6
355//      Variable/G root:myGlobals:DeadtimeNGB_ILL = 4.0e-6              // fictional
356//      Variable/G root:myGlobals:DeadtimeNG3_ORNL_VAX = 3.4e-6         //pre - 23-JUL-2009 used VAX
357//      Variable/G root:myGlobals:DeadtimeNG3_ORNL_ICE = 1.5e-6         //post - 23-JUL-2009 used ICE
358//      Variable/G root:myGlobals:DeadtimeNG5_ORNL = 0.6e-6                     //as of 9 MAY 2002
359//      Variable/G root:myGlobals:DeadtimeNG7_ORNL_VAX = 3.4e-6         //pre 25-FEB-2010 used VAX
360//      Variable/G root:myGlobals:DeadtimeNG7_ORNL_ICE = 2.3e-6         //post 25-FEB-2010 used ICE
361//      Variable/G root:myGlobals:DeadtimeNGB_ORNL_ICE = 4.0e-6         //per JGB 16-JAN-2013, best value we have for the oscillating data
362//
363////    Variable/G root:myGlobals:DeadtimeCGB_ORNL_ICE = 1.5e-6         // fiction
364//
365//      Variable/G root:myGlobals:DeadtimeDefault = 3.4e-6
366//
367//      //new 11APR07
368//      Variable/G root:myGlobals:BeamstopXTol = -8                     // (cm) is BS Xpos is -5 cm or less, it's a trans measurement
369//      // sample aperture offset is NOT stored in the VAX header, but it should be
370//      // - when it is, remove the global and write an accessor AND make a place for
371//      // it in the RealsRead
372//      Variable/G root:myGlobals:apOff = 5.0                           // (cm) distance from sample aperture to sample position
373
374End
375
376///////////////////////////////////////////////
377// TODO
378////////////// everything below needs to be re-written for VSANS
379//
380//////////////////////////////////////////////
381
382
383//
384// do I need to make the protocols any longer for VSANS? (yes -- now 12 points)
385// What other options for processing / averaging / saving are needed??
386//  TODO
387// x- likely that I'll want to have #pts to cut from I(q) as input to NSORT within the protocol so that the
388// entire reduction can be automatic
389//
390//
391// x- creates the "base" protocols that should be available, after creating the data folder
392// x- all protocols are kept in the root:Packages:NIST:VSANS:Globals:Protocols folder, created here
393//
394//
395//*****as of 05_2017, protocols are 12 points long, [6] is used for work.drk, [7,8] are for trimmig points, and [9,11] are currently unused
396//
397Function V_InitFakeProtocols()
398       
399        NewDataFolder/O root:Packages:NIST:VSANS:Globals:Protocols
400        Make/O/T $"root:Packages:NIST:VSANS:Globals:Protocols:Base"={"none","none","ask","ask","none","AVTYPE=Circular;SAVE=Yes;NAME=Auto;PLOT=Yes;BINTYPE=F4-M4-B;","DRK=none,DRKMODE=0,","","","","",""}
401        Make/O/T $"root:Packages:NIST:VSANS:Globals:Protocols:DoAll"={"ask","ask","ask","ask","ask","AVTYPE=Circular;SAVE=Yes;NAME=Auto;PLOT=Yes;BINTYPE=F4-M4-B;","DRK=none,DRKMODE=0,","","","","",""}
402        Make/O/T/N=(kNumProtocolSteps) $"root:Packages:NIST:VSANS:Globals:Protocols:CreateNew"                  //null wave
403        //Initialize waves to store values in
404       
405        String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr=""
406        String/G root:Packages:NIST:VSANS:Globals:Protocols:gNewStr=""
407        String/G root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr = "AVTYPE=Circular;SAVE=Yes;NAME=Auto;PLOT=Yes;BINTYPE=F4-M4-B;"
408       
409        String/G root:Packages:NIST:VSANS:Globals:Protocols:gBegPtsStr=""
410        String/G root:Packages:NIST:VSANS:Globals:Protocols:gEndPtsStr=""
411        String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr=""
412       
413        Return(0)
414End
415
416//simple function to resize the comand window to a nice size, no matter what the resolution
417//need to test out on several different monitors and both platforms
418//
419// could easily be incorporated into the initialization routines to ensure that the
420// command window is always visible at startup of the macros. No need for a hook function
421//
422Function V_ResizeCmdWindow()
423
424        String str=IgorInfo(0),rect="",platform=igorinfo(2)
425        Variable depth,left,top,right,bottom,factor
426       
427        if(cmpstr(platform,"Macintosh")==0)
428                factor=1
429        else
430                factor = 0.6            //fudge factor to get command window on-screen on Windows
431        endif
432        rect = StringByKey("SCREEN1", str  ,":",";")   
433        sscanf rect,"DEPTH=%d,RECT=%d,%d,%d,%d",depth, left,top,right,bottom
434        MoveWindow/C  (left+3)*factor,(bottom-150)*factor,(right-50)*factor,(bottom-10)*factor
435End
436
437// since the NCNR procedures can't be loaded concurrently with the other facility functions,
438// unload this procedure file, and add this to the functions that run at initialization of the
439// experiment
440//
441// TODO - be sure that this unloads correctly
442Function UnloadNCNR_VSANS_Procedures()
443
444#if (exists("NCNR_VSANS")==6)                   //defined in the main #includes file.
445        //do nothing if an NCNR reduction experiment
446#else
447        if(ItemsInList(WinList("NCNR_Package_Loader.ipf", ";","WIN:128")))
448                Execute/P "CloseProc /NAME=\"NCNR_Package_Loader.ipf\""
449                Execute/P "COMPILEPROCEDURES "
450        endif
451#endif
452
453End
454
455//returns 1 if demo version, 0 if full version
456Function V_IsDemo()
457
458        // create small offscreen graph
459        Display/W=(3000,3000,3010,3010)
460        DoWindow/C IsDemoGraph
461
462        // try to save a PICT or bitmap of it to the clipboard
463        SavePICT/Z  as "Clipboard"
464        Variable isDemo= V_Flag != 0    // if error: must be demo
465        DoWindow/K IsDemoGraph
466        return isDemo
467End
468
469// Clean out the RawVSANS folder before saving
470Function BeforeExperimentSaveHook(rN,fileName,path,type,creator,kind)
471        Variable rN,kind
472        String fileName,path,type,creator
473
474        // clean out, so that the file SAVE is not slow due to the large experiment size
475        // TODO -- decide if this is really necessary
476//     
477//      V_CleanOutRawVSANS()
478// present a progress window
479        V_CleanupData_w_Progress(0,1)
480        Printf "Hook cleaned out RawVSANS, experiment saved\r"
481
482        NVAR/Z gHighResBinning = root:Packages:NIST:VSANS:Globals:gHighResBinning
483        if(gHighResBinning == 1)
484// these KillDF are a bad idea - it wipes out all of the current work
485// whenever a save is done - which is the opposite of what you want
486// to happen when you save!
487       
488                Printf "Hook cleaned out WORK folders, experiment saved\r"
489
490                KillDataFolder/Z root:Packages:NIST:VSANS:RAW
491                KillDataFolder/Z root:Packages:NIST:VSANS:SAM
492                KillDataFolder/Z root:Packages:NIST:VSANS:EMP
493                KillDataFolder/Z root:Packages:NIST:VSANS:BGD
494                KillDataFolder/Z root:Packages:NIST:VSANS:COR
495                KillDataFolder/Z root:Packages:NIST:VSANS:DIV
496                KillDataFolder/Z root:Packages:NIST:VSANS:MSK
497                KillDataFolder/Z root:Packages:NIST:VSANS:ABS
498                KillDataFolder/Z root:Packages:NIST:VSANS:CAL
499                KillDataFolder/Z root:Packages:NIST:VSANS:STO
500                KillDataFolder/Z root:Packages:NIST:VSANS:SUB
501                KillDataFolder/Z root:Packages:NIST:VSANS:DRK
502                KillDataFolder/Z root:Packages:NIST:VSANS:ADJ
503                KillDataFolder/Z root:Packages:NIST:VSANS:VCALC
504
505        endif
506// re-create anthing that was killed
507        V_initFolders()
508
509End
Note: See TracBrowser for help on using the repository browser.