source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_Initialize.ipf @ 1111

Last change on this file since 1111 was 1111, checked in by srkline, 4 years ago

two significant changes:

1- in the averaging, before the data is finally written out, duplicate q-values (within 0.1%) are averaged so that duplicate q-values do not appear in the data file. This has a very bad effect on the calculation of the smearing matrix (dq=0).

2-for the data from the back (high res) detector, two steps have been added to the processing at the point where the data is converted to WORK. First, a constant read noise value of 200 cts/pixel is subtracted (found from average of multiple runs with beam off) Second, a 3x3 median filter is applied to the whole image to eliminate the stray bright pixels. Some are saturatd, some are simply outliers. Very effective.

File size: 16.9 KB
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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
24
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
32Constant kBCTR_CM = 1                   //set to 1 to use beam center in cm. O to use pixels
33
34// // TODO: -- replace this constant with V_getDet_panel_gap(fname,detStr)
35//Constant kPanelTouchingGap = 10                       // TODO -- measure this gap when panels "touch", UNITS OF mm, not cm
36
37
38// the base data folder path where the raw data is loaded
39Strconstant ksBaseDFPath = "root:Packages:NIST:VSANS:RawVSANS:"
40
41
42// the list of WORK Folders
43// RawVSANS does not behave as a WORK folder, but it is local. so add it in explicitly to the list if needed
44// VCALC behaves *almost* as a WORK folder, but it is local. so add it in explicitly to the list if needed
45//Strconstant ksWorkFolderList = "RAW;SAM;EMP;BGD;COR;DIV;ABS;MSK;CAL;STO;SUB;DRK;ADJ;VCALC;RawVSANS;"
46Strconstant ksWorkFolderListShort = "RAW;SAM;EMP;BGD;COR;DIV;ABS;MSK;CAL;STO;SUB;DRK;ADJ;"
47
48
49// for defining which "bin type" corresponds to which set of extensions for I(q) data
50// !! see V_BinTypeStr2Num() for the numbering, not the order of the list
51//
52//////////////////
53//Strconstant ksBinTypeStr = "One;Two;Four;Slit Mode;"
54Strconstant ksBinTypeStr = "F4-M4-B;F2-M2-B;F1-M1-B;F2-M1-B;F1-M2xTB-B;F2-M2xTB-B;SLIT-F2-M2-B;"
55Strconstant ksBinType1 = "FT;FB;FL;FR;MT;MB;ML;MR;B;"           //these are the "active" extensions
56Strconstant ksBinType2 = "FTB;FLR;MTB;MLR;B;"
57Strconstant ksBinType3 = "FLRTB;MLRTB;B;"
58//Strconstant ksBinType4 = "FT;FB;FL;FR;MT;MB;ML;MR;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// the average read noise level of the back detector
79// taken from multiple runs with the beam off, 6-28-18
80// runs sans12324 - sans12353
81//
82// used in V_Raw_to_Work()
83// average of whole panel (tested several data files) = 208 +/- 14
84//
85// 200 appears to be a better value - (empirical, based on teflon/converging pinhole data)
86Constant kReadNoiseLevel = 200
87//Constant kReadNoiseLevel = 208
88Constant kReadNoiseLevel_Err = 14
89
90
91
92// Pixel shifts for the back detector to bring the three CCDs into registry
93// data from pinholes used to match up CCDs
94// 27 JUN 2018
95// runs 12221,12225,27,33,34,35,38,42
96// middle CCD is not moved
97// See V_ShiftBackDetImage() for implementation
98Constant        kShift_TopX = 7
99Constant                kShift_TopY = 105
100Constant                kShift_BottomX = 5
101Constant                kShift_BottomY = 35
102
103
104
105
106
107
108Proc Initialize_VSANS()
109        V_Initialize()
110End
111
112//this is the main initualization procedure that must be the first thing
113//done when opening a new Data reduction experiment
114//
115//sets up data folders, globals, protocols, and draws the main panel
116Proc V_Initialize()
117
118        Variable curVersion = 0.1
119        Variable oldVersion = NumVarOrDefault("root:VSANS_RED_VERSION",curVersion)
120               
121        if(oldVersion == curVersion)
122                //must just be a new startup with the current version
123                Variable/G root:VSANS_RED_VERSION=0.1
124        endif
125       
126        if(oldVersion < curVersion)
127                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"
128                DoAlert 0,str
129        endif
130       
131        V_InitFolders()
132       
133        VC_Initialize_Space()           //initialize folders for VCALC
134       
135        V_InitFakeProtocols()
136        V_InitGlobals()
137        V_InitFacilityGlobals()
138        DoWindow/F Main_VSANS_Panel
139        If(V_flag == 0)
140                //draw panel
141                Main_VSANS_Panel()
142        Endif
143//      V_ResizeCmdWindow()
144
145// TODO - be sure that NCNR is defined correctly       
146        //unload the NCNR_Package_Loader, if NCNR not defined
147        UnloadNCNR_VSANS_Procedures()
148
149End
150
151//creates all the necessary data folders in the root folder
152//does not overwrite any existing folders of the same name
153//it leaves data in them untouched
154//
155// x-- make sure that I have all of the folders that I need
156//
157Function V_InitFolders()
158       
159        NewDataFolder/O root:Packages
160        NewDataFolder/O root:Packages:NIST
161        NewDataFolder/O root:Packages:NIST:VSANS
162       
163// for the file catalog
164        NewDataFolder/O root:Packages:NIST:VSANS:CatVSHeaderInfo
165// for the globals
166        NewDataFolder/O root:Packages:NIST:VSANS:Globals
167// for the raw nexus data (so I don't need to reload to get a single value)
168        NewDataFolder/O root:Packages:NIST:VSANS:RawVSANS
169
170// folders for the reduction steps             
171        NewDataFolder/O root:Packages:NIST:VSANS:RAW
172        NewDataFolder/O root:Packages:NIST:VSANS:SAM
173        NewDataFolder/O root:Packages:NIST:VSANS:EMP
174        NewDataFolder/O root:Packages:NIST:VSANS:BGD
175        NewDataFolder/O root:Packages:NIST:VSANS:COR
176        NewDataFolder/O root:Packages:NIST:VSANS:DIV
177        NewDataFolder/O root:Packages:NIST:VSANS:MSK
178        NewDataFolder/O root:Packages:NIST:VSANS:ABS
179        NewDataFolder/O root:Packages:NIST:VSANS:CAL
180        NewDataFolder/O root:Packages:NIST:VSANS:STO
181        NewDataFolder/O root:Packages:NIST:VSANS:SUB
182        NewDataFolder/O root:Packages:NIST:VSANS:DRK
183        NewDataFolder/O root:Packages:NIST:VSANS:ADJ
184
185
186// ?? anything else
187
188// for simulation
189//      NewDataFolder/O root:Packages:NIST:VSANS:SAS
190
191
192       
193        Return(0)
194End
195
196
197
198
199//
200//Global folder already exists...
201//adds appropriate globals to the newly created myGlobals folder
202//return data folder to root: before leaving
203//
204//
205Function V_InitGlobals()
206       
207       
208        Variable/G root:Packages:NIST:VSANS:Globals:gIsLogScale = 0
209        String/G root:Packages:NIST:VSANS:Globals:gCurDispType = "RAW"
210       
211        //check platform, so Angstrom can be drawn correctly
212
213        //TODO  -- this is different on Igor 7. Macintosh # has been updated, but Windows has not
214        // use Print char2num("Å") to find the magic number
215        if(cmpstr("Macintosh",IgorInfo(2)) == 0)
216                String/G root:Packages:NIST:VSANS:Globals:gAngstStr = num2char(197)
217                String/G root:Packages:NIST:gAngstStr = num2char(197)
218                Variable/G root:Packages:NIST:VSANS:Globals:gIsMac = 1
219        else
220                //either Windows or Windows NT
221                String/G root:Packages:NIST:VSANS:Globals:gAngstStr = num2char(-59)
222                String/G root:Packages:NIST:gAngstStr = num2char(-59)
223                Variable/G root:Packages:NIST:VSANS:Globals:gIsMac = 0
224                //SetIgorOption to keep some PC's (graphics cards?) from smoothing the 2D image
225                Execute "SetIgorOption WinDraw,forceCOLORONCOLOR=1"
226        endif
227       
228        // TODO x- find the SANS preferences, copy over and update for VSANS
229        // x- these are all in PlotUtilsMacro_v40.ipf as the preferences are set up as common
230        // to all packages. I'm not sure that I want to do this with VSANS, but make the packages
231        // separate entities. I'm seeing little benefit of the crossover, especially now that
232        // Analysis is not mine. So for VSANS, there is a new, separate file: V_VSANS_Preferences.ipf
233
234        //this is critical to initialize now - as it has the y/n flags for the detector correction steps
235        Execute "Initialize_VSANSPreferences()"
236
237       
238        // set the lookup waves for log/lin display of the detector images
239        V_MakeImageLookupTables(10000,0,1)
240
241
242
243        //set flag if Demo Version is detected
244        Variable/G root:Packages:NIST:VSANS:Globals:isDemoVersion = V_isDemo()
245       
246        //set XML globals
247//      String/G root:Packages:NIST:gXMLLoader_Title = ""
248       
249        Return(0)
250End
251
252//
253//num = number of points (10000 seeems to be a good number so far)
254// lo = lower value (between 0 and 1)
255// hi = upper value (between 0 and 1)
256//
257// note that it is currenty NOT OK for lo > hi (!= reversed color scale, right now log(negative) == bad)
258//
259// TODO hi, lo not used properly here, seems to mangle log display now that I'm switching the lo,hi of the ctab
260//
261Function V_MakeImageLookupTables(num,lo,hi)
262        Variable num,lo,hi
263
264                // lookup waves for log and linear display of images
265        // this is used for the main data display. With this, I can use the original
266        // detector data (no copy) and the zeros in the data set are tolerated when displaying
267        // on log scale
268        SetDataFolder root:Packages:NIST:VSANS:Globals
269        Variable val,offset
270       
271        offset = 1/num          //can't use 1/lo if lo == 0
272       
273        Make/O/D/N=(num) logLookupWave,linearLookupWave
274       
275        linearLookupWave = (p+1)/num
276       
277       
278        logLookupWave = log(linearLookupWave)
279        val = logLookupWave[0]
280        logLookupWave += -val + offset
281        val = logLookupWave[num-1]
282        logLookupWave /= val
283       
284        SetDataFolder root:
285       
286        return(0)
287end
288
289//
290// initializes globals that are specific to VSANS
291//
292// there really should be nothing here... all of this should now be in the Nexus data file
293// and not tethered to hard-wired constants.
294//
295// -- what was here was:
296// number of detector pixels
297// pixel size
298// deadtime
299// beamstop "tolerance" to identify Trans files
300// sample aperture offset
301//
302Function V_InitFacilityGlobals()
303
304//      //Detector -specific globals
305//      Variable/G root:myGlobals:gNPixelsX=128
306//      Variable/G root:myGlobals:gNPixelsY=128
307//     
308//      // as of Jan2008, detector pixel sizes are read directly from the file header, so they MUST
309//      // be set correctly in instr.cfg - these values are not used, but declared to avoid errors
310//      Variable/G root:myGlobals:PixelResNG3_ILL = 1.0         //pixel resolution in cm
311//      Variable/G root:myGlobals:PixelResNG5_ILL = 1.0
312//      Variable/G root:myGlobals:PixelResNG7_ILL = 1.0
313//      Variable/G root:myGlobals:PixelResNG3_ORNL = 0.5
314//      Variable/G root:myGlobals:PixelResNG5_ORNL = 0.5
315//      Variable/G root:myGlobals:PixelResNG7_ORNL = 0.5
316//      Variable/G root:myGlobals:PixelResNGB_ORNL = 0.5
317////    Variable/G root:myGlobals:PixelResCGB_ORNL = 0.5                // fiction
318//
319//      Variable/G root:myGlobals:PixelResDefault = 0.5
320//     
321//      Variable/G root:myGlobals:DeadtimeNG3_ILL = 3.0e-6              //deadtime in seconds
322//      Variable/G root:myGlobals:DeadtimeNG5_ILL = 3.0e-6
323//      Variable/G root:myGlobals:DeadtimeNG7_ILL = 3.0e-6
324//      Variable/G root:myGlobals:DeadtimeNGB_ILL = 4.0e-6              // fictional
325//      Variable/G root:myGlobals:DeadtimeNG3_ORNL_VAX = 3.4e-6         //pre - 23-JUL-2009 used VAX
326//      Variable/G root:myGlobals:DeadtimeNG3_ORNL_ICE = 1.5e-6         //post - 23-JUL-2009 used ICE
327//      Variable/G root:myGlobals:DeadtimeNG5_ORNL = 0.6e-6                     //as of 9 MAY 2002
328//      Variable/G root:myGlobals:DeadtimeNG7_ORNL_VAX = 3.4e-6         //pre 25-FEB-2010 used VAX
329//      Variable/G root:myGlobals:DeadtimeNG7_ORNL_ICE = 2.3e-6         //post 25-FEB-2010 used ICE
330//      Variable/G root:myGlobals:DeadtimeNGB_ORNL_ICE = 4.0e-6         //per JGB 16-JAN-2013, best value we have for the oscillating data
331//
332////    Variable/G root:myGlobals:DeadtimeCGB_ORNL_ICE = 1.5e-6         // fiction
333//
334//      Variable/G root:myGlobals:DeadtimeDefault = 3.4e-6
335//
336//      //new 11APR07
337//      Variable/G root:myGlobals:BeamstopXTol = -8                     // (cm) is BS Xpos is -5 cm or less, it's a trans measurement
338//      // sample aperture offset is NOT stored in the VAX header, but it should be
339//      // - when it is, remove the global and write an accessor AND make a place for
340//      // it in the RealsRead
341//      Variable/G root:myGlobals:apOff = 5.0                           // (cm) distance from sample aperture to sample position
342
343End
344
345///////////////////////////////////////////////
346// TODO
347////////////// everything below needs to be re-written for VSANS
348//
349//////////////////////////////////////////////
350
351
352//
353// do I need to make the protocols any longer for VSANS? (yes -- now 12 points)
354// What other options for processing / averaging / saving are needed??
355//  TODO
356// x- likely that I'll want to have #pts to cut from I(q) as input to NSORT within the protocol so that the
357// entire reduction can be automatic
358//
359//
360// x- creates the "base" protocols that should be available, after creating the data folder
361// x- all protocols are kept in the root:Packages:NIST:VSANS:Globals:Protocols folder, created here
362//
363//
364//*****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
365//
366Function V_InitFakeProtocols()
367       
368        NewDataFolder/O root:Packages:NIST:VSANS:Globals:Protocols
369        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,","","","","",""}
370        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,","","","","",""}
371        Make/O/T/N=(kNumProtocolSteps) $"root:Packages:NIST:VSANS:Globals:Protocols:CreateNew"                  //null wave
372        //Initialize waves to store values in
373       
374        String/G root:Packages:NIST:VSANS:Globals:Protocols:gProtoStr=""
375        String/G root:Packages:NIST:VSANS:Globals:Protocols:gNewStr=""
376        String/G root:Packages:NIST:VSANS:Globals:Protocols:gAvgInfoStr = "AVTYPE=Circular;SAVE=Yes;NAME=Auto;PLOT=Yes;BINTYPE=F4-M4-B;"
377       
378        String/G root:Packages:NIST:VSANS:Globals:Protocols:gBegPtsStr=""
379        String/G root:Packages:NIST:VSANS:Globals:Protocols:gEndPtsStr=""
380        String/G root:Packages:NIST:VSANS:Globals:Protocols:gAbsStr=""
381       
382        Return(0)
383End
384
385//simple function to resize the comand window to a nice size, no matter what the resolution
386//need to test out on several different monitors and both platforms
387//
388// could easily be incorporated into the initialization routines to ensure that the
389// command window is always visible at startup of the macros. No need for a hook function
390//
391Function V_ResizeCmdWindow()
392
393        String str=IgorInfo(0),rect="",platform=igorinfo(2)
394        Variable depth,left,top,right,bottom,factor
395       
396        if(cmpstr(platform,"Macintosh")==0)
397                factor=1
398        else
399                factor = 0.6            //fudge factor to get command window on-screen on Windows
400        endif
401        rect = StringByKey("SCREEN1", str  ,":",";")   
402        sscanf rect,"DEPTH=%d,RECT=%d,%d,%d,%d",depth, left,top,right,bottom
403        MoveWindow/C  (left+3)*factor,(bottom-150)*factor,(right-50)*factor,(bottom-10)*factor
404End
405
406// since the NCNR procedures can't be loaded concurrently with the other facility functions,
407// unload this procedure file, and add this to the functions that run at initialization of the
408// experiment
409//
410// TODO - be sure that this unloads correctly
411Function UnloadNCNR_VSANS_Procedures()
412
413#if (exists("NCNR_VSANS")==6)                   //defined in the main #includes file.
414        //do nothing if an NCNR reduction experiment
415#else
416        if(ItemsInList(WinList("NCNR_Package_Loader.ipf", ";","WIN:128")))
417                Execute/P "CloseProc /NAME=\"NCNR_Package_Loader.ipf\""
418                Execute/P "COMPILEPROCEDURES "
419        endif
420#endif
421
422End
423
424//returns 1 if demo version, 0 if full version
425Function V_IsDemo()
426
427        // create small offscreen graph
428        Display/W=(3000,3000,3010,3010)
429        DoWindow/C IsDemoGraph
430
431        // try to save a PICT or bitmap of it to the clipboard
432        SavePICT/Z  as "Clipboard"
433        Variable isDemo= V_Flag != 0    // if error: must be demo
434        DoWindow/K IsDemoGraph
435        return isDemo
436End
437
438// Clean out the RawVSANS folder before saving
439Function BeforeExperimentSaveHook(rN,fileName,path,type,creator,kind)
440        Variable rN,kind
441        String fileName,path,type,creator
442
443        // clean out, so that the file SAVE is not slow due to the large experiment size
444        // TODO -- decide if this is really necessary
445//     
446//      V_CleanOutRawVSANS()
447// present a progress window
448        V_CleanupData_w_Progress(0,1)
449        Printf "Hook cleaned out RawVSANS, experiment saved\r"
450
451
452// these KillDF are a bad idea - it wipes out all of the current work
453// whenever a save is done - which is the opposite of what you want
454// to happen when you save!
455
456//      KillDataFolder/Z root:Packages:NIST:VSANS:RAW
457//      KillDataFolder/Z root:Packages:NIST:VSANS:SAM
458//      KillDataFolder/Z root:Packages:NIST:VSANS:EMP
459//      KillDataFolder/Z root:Packages:NIST:VSANS:BGD
460//      KillDataFolder/Z root:Packages:NIST:VSANS:COR
461//      KillDataFolder/Z root:Packages:NIST:VSANS:DIV
462//      KillDataFolder/Z root:Packages:NIST:VSANS:MSK
463//      KillDataFolder/Z root:Packages:NIST:VSANS:ABS
464//      KillDataFolder/Z root:Packages:NIST:VSANS:CAL
465//      KillDataFolder/Z root:Packages:NIST:VSANS:STO
466//      KillDataFolder/Z root:Packages:NIST:VSANS:SUB
467//      KillDataFolder/Z root:Packages:NIST:VSANS:DRK
468//      KillDataFolder/Z root:Packages:NIST:VSANS:ADJ
469
470// re-create anthing that was killed
471        V_initFolders()
472
473End
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