source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_HDF5_RW_Utils.ipf @ 1031

Last change on this file since 1031 was 1031, checked in by srkline, 6 years ago

changes for combining of 1D data sets

File size: 26.6 KB
Line 
1#pragma rtGlobals=3             // Use modern global access method and strict wave access.
2
3//
4// The base functions for R/W from HDF5 files.
5// All of the specific "get" and "write" functions call these base functions which are responsible
6// for all of the open/close mechanics.
7//
8// These VSANS file-specific functions are in:
9// V_HDF5_Read.ipf
10//               and
11// V_HDF5_Write.ipf
12//
13
14// data is read into:
15//      NewDataFolder/O/S root:Packages:NIST:VSANS:RawVSANS
16// so that the data folders of the raw data won't be lying around on the top level, looking like
17// 1D data sets and interfering.
18
19
20// the base data folder path where the raw data is loaded
21Strconstant ksBaseDFPath = "root:Packages:NIST:VSANS:RawVSANS:"
22
23// the list of WORK Folders
24Strconstant ksWorkFolderList = "RAW;SAM;EMP;BGD;COR;DIV;ABS;MSK;CAL;STO;SUB;DRK;ADJ;VCALC;RawVSANS;"
25Strconstant ksWorkFolderListShort = "RAW;SAM;EMP;BGD;COR;DIV;ABS;MSK;CAL;STO;SUB;DRK;ADJ;"
26
27
28// passing null file string presents a dialog
29Proc LoadFakeDIVData()
30        V_LoadHDF5Data("","DIV")
31End
32
33// Moved to V_MaskUtils.ipf
34// passing null file string presents a dialog
35//Proc LoadFakeMASKData()
36//      V_LoadHDF5Data("","MSK")
37//End
38
39// passing null file string presents a dialog
40Proc Read_HDF5_Raw_No_Attributes()
41        V_LoadHDF5Data("","RAW")
42End
43
44
45// TODO:
46//  x- move the initialization of the raw data folder to be in the as-yet unwritten initialization routine for
47// reduction. be sure that it's duplicated in the VCALC initialization too.
48// x- as needed, get rid of the FAKE redimension of the data from 3D->2D and from 128x128 to something else for VSANS
49//    This is a fake since I don't have anything close to correct fake data yet. (1/29/16)
50//
51// DONE: x- is there an extra "entry" heading? Am I adding this by mistake by setting base_name="entry" for RAW data?
52//                      x- as dumb as it is -- do I just leave it now, or break everything. On the plus side, removing the extra "entry"
53//          layer may catch a lot of the hard-wired junk that is present...
54//      extra entry layer is no longer generated for any WORK folders
55//
56Function V_LoadHDF5Data(file,folder)
57        String file,folder
58
59        String base_name,detStr
60        String destPath
61        Variable ii
62       
63        SetDataFolder $("root:Packages:NIST:VSANS:"+folder)
64        destPath = "root:Packages:NIST:VSANS:"+folder
65
66        Variable err= V_LoadHDF5_NoAtt(file,folder)     // reads into current folder
67       
68        // if RAW data, then generate the errors and linear data copy
69        // do this 9x
70        // then do any "massaging" needed to redimension, fake values, etc.
71        //
72        string tmpStr = "root:Packages:NIST:VSANS:RAW:entry:instrument:"
73
74        if(cmpstr(folder,"RAW")==0)
75       
76                // TODO -- once I get "real" data, get rid of this call to force the data to be proper dimensions.
77//              V_RedimFakeData()
78               
79                V_MakeDataWaves_DP(folder)
80//              V_FakeBeamCenters()
81//              V_FakeScaleToCenter()
82               
83
84                // makes data error and linear copy -- DP waves if V_MakeDataWaves_DP() called above
85                for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
86                        detStr = StringFromList(ii, ksDetectorListAll, ";")
87                        V_MakeDataError(tmpStr+"detector_"+detStr)     
88                endfor
89
90                // TODO
91                //  -- get rid of these fake calibration waves as "real" ones are filled in by NICE
92//              (currently does nothing)
93//              Execute "MakeFakeCalibrationWaves()"
94               
95                //              fMakeFakeCalibrationWaves()             //skips the alert
96
97
98                // TODO -- do I want to calculate the nonlinear x/y arrays and the q-values here?
99                // -- otherwise the mouse-over doesn't calculate the correct Q_values
100                // the display currently is not shifted or altered at all to account for the non-linearity
101                // or for display in q-values -- so why bother with this?
102                NVAR gDoNonLinearCor = root:Packages:NIST:VSANS:Globals:gDoNonLinearCor
103                // generate a distance matrix for each of the detectors
104                if (gDoNonLinearCor == 1)
105                        Print "Calculating Non-linear correction at RAW load time"// for "+ detStr
106                        for(ii=0;ii<ItemsInList(ksDetectorListNoB);ii+=1)
107                                detStr = StringFromList(ii, ksDetectorListNoB, ";")
108                                Wave w = V_getDetectorDataW(folder,detStr)
109        //                      Wave w_err = V_getDetectorDataErrW(fname,detStr)                //not here, done above w/V_MakeDataError()
110                                Wave w_calib = V_getDetTube_spatialCalib(folder,detStr)
111                                Variable tube_width = V_getDet_tubeWidth(folder,detStr)
112                                V_NonLinearCorrection(w,w_calib,tube_width,detStr,destPath)
113                               
114                               
115                                //(2.4) Convert the beam center values from pixels to mm
116                                // TODO -- there needs to be a permanent location for these values??
117                                //
118                                V_ConvertBeamCtr_to_mm(folder,detStr,destPath)
119                               
120                                // (2.5) Calculate the q-values
121                                // calculating q-values can't be done unless the non-linear corrections are calculated
122                                // so go ahead and put it in this loop.
123                                // TODO :
124                                // -- make sure that everything is present before the calculation
125                                // -- beam center must be properly defined in terms of real distance
126                                // -- distances/zero location/ etc. must be clearly documented for each detector
127                                //      ** this assumes that NonLinearCorrection() has been run to generate data_RealDistX and Y
128                                // ** this routine Makes the waves QTot, qx, qy, qz in each detector folder.
129                                //
130                                V_Detector_CalcQVals(folder,detStr,destPath)
131                               
132                        endfor
133                       
134                        //"B" is separate
135                        V_NonLinearCorrection_B(folder,"B",destPath)
136                        V_ConvertBeamCtr_to_mmB(folder,"B",destPath)
137                        V_Detector_CalcQVals(folder,"B",destPath)
138                       
139                else
140                        Print "Non-linear correction not done"
141                endif
142                                       
143                                       
144                /// END FAKE DATA CORRECTIONS           
145                       
146        endif
147       
148        SetDataFolder root:
149        return(err)
150End
151
152// fname is the folder = "RAW"
153Function V_MakeDataWaves_DP(fname)
154        String fname
155       
156        Variable ii
157        String detStr
158       
159        for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
160                detStr = StringFromList(ii, ksDetectorListAll, ";")
161                Wave w = V_getDetectorDataW(fname,detStr)
162//              Wave w_err = V_getDetectorDataErrW(fname,detStr)  //not here, done above w/V_MakeDataError()
163                Redimension/D w
164//              Redimension/D w_err
165        endfor
166       
167        return(0)
168End
169
170
171
172//
173// TODO -- this is all FAKED since all the data arrays are written to hdf as (1,128,128)
174//  -- try to fill in the bits from VCALC, if it exists (or force it)
175//
176// the SetScale parts may be useful later.
177//
178// This is NOT CALLED anymore.
179// the rescaling (SetScale) of the data sets is still done separately to a "fake" beam center
180Function xV_RedimFakeData()
181       
182        // check for fake data in VCALC folder...
183        wave/Z tmpw=$"root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_B:det_B"
184        if(WaveExists(tmpw) == 0)
185                Execute "VCALC_Panel()"
186        endif
187       
188        SetDataFolder root:Packages:NIST:VSANS:RAW:entry:instrument:detector_B
189        Wave det_B=data
190//      Redimension/N=(150,150)/E=1 det_B       
191        Redimension/D det_B
192        wave tmpw=$"root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_B:det_B"
193//      det_B=tmpw
194//      det_B += 2
195        Wave distance=distance
196        distance = VCALC_getSDD("B")*100                // to convert m to cm
197
198                       
199        Variable ctr=20,npix=128
200        SetDataFolder root:Packages:NIST:VSANS:RAW:entry:instrument:detector_MT
201        Wave det_MT=data
202//      Redimension/N=(npix,48)/E=1 det_MT
203        Redimension/D det_MT           
204        SetScale/I x -npix/2,npix/2,"",det_MT
205        SetScale/I y ctr,ctr+48,"",det_MT
206//      det_MT *= 10
207//      det_MT += 2
208        wave tmpw=$"root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_MT:det_MT"
209//      det_MT=tmpw
210//      det_MT += 2
211        Wave distance=distance
212        distance = VCALC_getSDD("MT")*100               // to convert m to cm
213
214       
215        SetDataFolder root:Packages:NIST:VSANS:RAW:entry:instrument:detector_MB
216        Wave det_MB=data
217//      Redimension/N=(npix,48)/E=1 det_MB             
218        Redimension/D det_MB
219        SetScale/I x -npix/2,npix/2,"",det_MB
220        SetScale/I y -ctr-48,-ctr,"",det_MB
221//      det_MB *= 5
222//      det_MB += 2
223        wave tmpw=$"root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_MB:det_MB"
224//      det_MB=tmpw
225//      det_MB += 2
226        Wave distance=distance
227        distance = VCALC_getSDD("MB")*100               // to convert m to cm
228
229       
230        ctr=30
231        SetDataFolder root:Packages:NIST:VSANS:RAW:entry:instrument:detector_ML
232        Wave det_ML=data
233//      Redimension/N=(48,npix)/E=1 det_ML             
234        Redimension/D det_ML
235        SetScale/I x -ctr-48,-ctr,"",det_ML
236        SetScale/I y -npix/2,npix/2,"",det_ML
237//      det_ML *= 2
238//      det_ML += 2
239        wave tmpw=$"root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_ML:det_ML"
240//      det_ML=tmpw
241//      det_ML += 2
242        Wave distance=distance
243        distance = VCALC_getSDD("ML")*100               // to convert m to cm
244
245               
246        SetDataFolder root:Packages:NIST:VSANS:RAW:entry:instrument:detector_MR
247        Wave det_MR=data
248//      Redimension/N=(48,npix)/E=1 det_MR             
249        Redimension/D det_MR
250        SetScale/I x ctr,ctr+48,"",det_MR
251        SetScale/I y -npix/2,npix/2,"",det_MR
252//      det_MR +=2
253        wave tmpw=$"root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_MR:det_MR"
254//      det_MR=tmpw
255//      det_MR += 2
256        Wave distance=distance
257        distance = VCALC_getSDD("MR")*100               // to convert m to cm
258       
259       
260        ctr=30
261        SetDataFolder root:Packages:NIST:VSANS:RAW:entry:instrument:detector_FT
262        Wave det_FT=data
263//      Redimension/N=(npix,48)/E=1 det_FT             
264        Redimension/D det_FT
265        SetScale/I x -npix/2,npix/2,"",det_FT
266        SetScale/I y ctr,ctr+48,"",det_FT
267        wave tmpw=$"root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FT:det_FT"
268//      det_FT=tmpw
269        Wave distance=distance
270        distance = VCALC_getSDD("FT")*100               // to convert m to cm
271
272
273        SetDataFolder root:Packages:NIST:VSANS:RAW:entry:instrument:detector_FB
274        Wave det_FB=data
275//      Redimension/N=(npix,48)/E=1 det_FB             
276        Redimension/D det_FB
277        SetScale/I x -npix/2,npix/2,"",det_FB
278        SetScale/I y -ctr-48,-ctr,"",det_FB
279        wave tmpw=$"root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FB:det_FB"
280//      det_FB=tmpw
281        Wave distance=distance
282        distance = VCALC_getSDD("FB")*100               // to convert m to cm
283
284                       
285        SetDataFolder root:Packages:NIST:VSANS:RAW:entry:instrument:detector_FL
286        Wave det_FL=data
287//      Redimension/N=(48,npix)/E=1 det_FL             
288        Redimension/D det_FL
289        SetScale/I x -ctr-48,-ctr,"",det_FL
290        SetScale/I y -npix/2,npix/2,"",det_FL
291        wave tmpw=$"root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FL:det_FL"
292//      det_FL=tmpw
293        Wave distance=distance
294        distance = VCALC_getSDD("FL")*100               // to convert m to cm
295
296       
297        SetDataFolder root:Packages:NIST:VSANS:RAW:entry:instrument:detector_FR
298        Wave det_FR=data
299//      Redimension/N=(48,npix)/E=1 det_FR             
300        Redimension/D det_FR
301        SetScale/I x ctr,ctr+48,"",det_FR
302        SetScale/I y -npix/2,npix/2,"",det_FR
303        wave tmpw=$"root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FR:det_FR"
304//      det_FR=tmpw
305        Wave distance=distance
306        distance = VCALC_getSDD("FR")*100               // to convert m to cm
307
308       
309// get rid of zeros
310//      det_FL += 2
311//      det_FR += 2
312//      det_FT += 2
313//      det_FB += 2
314
315
316// fake beam center values
317        V_putDet_beam_center_x("RAW","B",75)
318        V_putDet_beam_center_y("RAW","B",75)
319
320        V_putDet_beam_center_x("RAW","MB",64)
321        V_putDet_beam_center_y("RAW","MB",55)
322        V_putDet_beam_center_x("RAW","MT",64)
323        V_putDet_beam_center_y("RAW","MT",-8.7)
324        V_putDet_beam_center_x("RAW","MR",-8.1)
325        V_putDet_beam_center_y("RAW","MR",64)
326        V_putDet_beam_center_x("RAW","ML",55)
327        V_putDet_beam_center_y("RAW","ML",64)
328
329        V_putDet_beam_center_x("RAW","FB",64)
330        V_putDet_beam_center_y("RAW","FB",55)
331        V_putDet_beam_center_x("RAW","FT",64)
332        V_putDet_beam_center_y("RAW","FT",-8.7)
333        V_putDet_beam_center_x("RAW","FR",-8.1)
334        V_putDet_beam_center_y("RAW","FR",64)
335        V_putDet_beam_center_x("RAW","FL",55)
336        V_putDet_beam_center_y("RAW","FL",64)
337
338
339        V_RescaleToBeamCenter("RAW","MB",64,55)
340        V_RescaleToBeamCenter("RAW","MT",64,-8.7)
341        V_RescaleToBeamCenter("RAW","MR",-8.1,64)
342        V_RescaleToBeamCenter("RAW","ML",55,64)
343        V_RescaleToBeamCenter("RAW","FL",55,64)
344        V_RescaleToBeamCenter("RAW","FR",-8.1,64)
345        V_RescaleToBeamCenter("RAW","FT",64,-8.7)
346        V_RescaleToBeamCenter("RAW","FB",64,55)
347
348
349
350        return(0)
351End
352
353
354// This loads for speed, since loading the attributes takes a LOT of time.
355//
356// this will load in the whole HDF file all at once.
357// Attributes are NOT loaded at all.
358//
359// -- the Gateway function H5GW_ReadHDF5(parentFolder, fileName, [hdf5Path])
360//    reads in the attributes too, but is very slow
361//   -- the H5GW function is called by: H_HDF5Gate_Read_Raw(file)
362//
363// TODO:
364// -x remove the P=home restriction top make this more generic (replaced with catPathName from PickPath)
365// -- get rid of bits leftover here that I don't need
366// -- be sure I'm using all of the correct flags in the HDF5LoadGroup operation
367// -- settle on how the base_name is to be used. "entry" for the RAW, fileName for the "rawVSANS"?
368// x- error check for path existence
369//
370// passing in "" for base_name will take the name from the file name as selected
371//
372Function V_LoadHDF5_NoAtt(fileName,base_name)
373        String fileName, base_name
374       
375//      if ( ParamIsDefault(hdf5Path) )
376//              hdf5Path = "/"
377//      endif
378
379        PathInfo/S catPathName
380        if(V_flag == 0)
381                V_PickPath()
382        endif
383
384        String hdf5path = "/"           //always read from the top
385        String status = ""
386
387        Variable fileID = 0
388//      HDF5OpenFile/R/P=home/Z fileID as fileName              //read file from home directory?
389        HDF5OpenFile/R/P=catPathName/Z fileID as fileName
390        if (V_Flag != 0)
391                return 0
392        endif
393
394        String/G root:file_path = S_path
395        String/G root:file_name = S_FileName
396       
397        if ( fileID == 0 )
398                Print fileName + ": could not open as HDF5 file"
399                return (0)
400        endif
401       
402//s_tic()               //fast
403       
404        SVAR tmpStr=root:file_name
405        fileName=tmpStr         //SRK - in case the file was chosen from a dialog, I'll need access to the name later
406       
407        //   read the data (too bad that HDF5LoadGroup does not read the attributes)
408//      if(cmpstr(base_name,"") == 0)
409//              base_name = StringFromList(0,FileName,".")
410//      endif
411       
412        // if base_name is from my list of WORK folders, then base_name = ""
413        // use a stringSwitch? WhichListItem?
414        Variable isFolder = WhichListItem(base_name,ksWorkFolderList)
415        if(isFolder != -1)
416                base_name = ""
417        else
418                base_name = StringFromList(0,FileName,".")
419        endif
420       
421        HDF5LoadGroup/Z/L=7/O/R/T=$base_name  :, fileID, hdf5Path               //      recursive
422        if ( V_Flag != 0 )
423                Print fileName + ": could not open as HDF5 file"
424                setdatafolder root:
425                return (0)
426        endif
427
428        HDF5CloseFile fileID
429       
430//s_toc()
431        return(0)
432end     
433
434
435// read a single real value
436// - fname passed in is the full path to the file on disk
437// - path is the path to the value in the HDF tree
438//
439// check to see if the value exists (It will be a wave)
440// -- if it does, return the value from the local folder
441// -- if not, read the file in, then return the value
442//
443// TODO:
444// currently, the work folders have the following path - so passing in "RAW" as fname
445// will take some re-configuring.
446//  root:Packages:NIST:VSANS:RAW:entry:instrument:detector_FL:distance
447// -- be sure this read from work folders is not broken in the future, and is passed to ALL of the
448//    top-level R/W routines. (Write is necessary ONLY for SIM data files. Patch is direct to disk.)
449Function V_getRealValueFromHDF5(fname,path)
450        String fname,path
451
452        String folderStr=""
453        Variable valExists=0
454       
455        folderStr = V_RemoveDotExtension(V_GetFileNameFromPathNoSemi(fname))
456
457// check for a work folder first (note that "entry" is now NOT doubled)
458        if(Exists("root:Packages:NIST:VSANS:"+folderStr+":"+path))
459                Wave/Z w = $("root:Packages:NIST:VSANS:"+folderStr+":"+path)
460                return(w[0])
461        endif
462       
463        if(Exists(ksBaseDFPath+folderStr+":"+path))
464                valExists=1
465        endif
466       
467        if(!valExists)
468                //then read in the file, putting the data in RawVSANS
469                SetDataFolder ksBaseDFPath
470                V_LoadHDF5_NoAtt(fname,"")
471                SetDataFolder root:
472        endif
473
474// this should exist now - if not, I need to see the error
475        Wave/Z w = $(ksBaseDFPath+folderStr+":"+path)
476       
477        if(WaveExists(w))
478                return(w[0])
479        else
480                return(-999999)
481        endif   
482End
483
484// Returns a wave reference, not just a single value
485// ---then you pick what you need from the wave
486//
487// - fname passed in is the full path to the file on disk
488// - path is the path to the value in the HDF tree
489//
490// check to see if the value exists (It will be a wave)
491// -- if it does, return the value from the local folder
492// -- if not, read the file in, then return the value
493//
494Function/WAVE V_getRealWaveFromHDF5(fname,path)
495        String fname,path
496
497        String folderStr=""
498        Variable valExists=0
499       
500        folderStr = V_RemoveDotExtension(V_GetFileNameFromPathNoSemi(fname))
501
502// check for a work folder first (note that "entry" is NOT doubled)
503        if(Exists("root:Packages:NIST:VSANS:"+folderStr+":"+path))
504                Wave wOut = $("root:Packages:NIST:VSANS:"+folderStr+":"+path)
505                return wOut
506        endif
507               
508        if(Exists(ksBaseDFPath+folderStr+":"+path))
509                valExists=1
510        endif
511
512        if(!valExists)
513                //then read in the file, putting the data in RawVSANS
514                SetDataFolder ksBaseDFPath
515                V_LoadHDF5_NoAtt(fname,"")
516                SetDataFolder root:
517        endif
518               
519// this should exist now - if not, I need to see the error
520        Wave wOut = $(ksBaseDFPath+folderStr+":"+path)
521       
522        return wOut
523       
524End
525
526// Returns a wave reference, not just a single value
527// ---then you pick what you need from the wave
528//
529// - fname passed in is the full path to the file on disk
530// - path is the path to the value in the HDF tree
531//
532// check to see if the value exists (It will be a wave)
533// -- if it does, return the value from the local folder
534// -- if not, read the file in, then return the value
535//
536Function/WAVE V_getTextWaveFromHDF5(fname,path)
537        String fname,path
538
539        String folderStr=""
540        Variable valExists=0
541       
542        folderStr = V_RemoveDotExtension(V_GetFileNameFromPathNoSemi(fname))
543
544// check for a work folder first (note that "entry" is NOT doubled)
545        if(Exists("root:Packages:NIST:VSANS:"+folderStr+":"+path))
546                Wave/T wOut = $("root:Packages:NIST:VSANS:"+folderStr+":"+path)
547                return wOut
548        endif
549       
550        if(Exists(ksBaseDFPath+folderStr+":"+path))
551                valExists=1
552        endif
553       
554        if(!valExists)
555                //then read in the file, putting the data in RawVSANS
556                SetDataFolder ksBaseDFPath
557                V_LoadHDF5_NoAtt(fname,"")
558                SetDataFolder root:
559        endif
560
561// this should exist now - if not, I need to see the error
562        Wave/T wOut = $(ksBaseDFPath+folderStr+":"+path)
563       
564        return wOut
565       
566End
567
568
569//
570//   TODO
571// depricated? in HDF5 - store all of the values as real?
572// Igor sees no difference in real and integer variables (waves are different)
573// BUT-- Igor 7 will have integer variables
574//
575// truncate to integer before returning??
576//
577//  TODO
578// write a "getIntegerWave" function??
579//
580//////  integer values
581// reads 32 bit integer
582Function V_getIntegerFromHDF5(fname,path)
583        String fname                            //full path+name
584        String path                             //path to the hdf5 location
585       
586        Variable val = V_getRealValueFromHDF5(fname,path)
587       
588        val = round(val)
589        return(val)
590End
591
592
593// read a single string
594// - fname passed in is the full path to the file on disk
595// - path is the path to the value in the HDF tree
596// - num is the number of characters in the VAX string
597// check to see if the value exists (It will be a wave)
598// -- if it does, return the value from the local folder
599// -- if not, read the file in, then return the value
600//
601// TODO -- string could be checked for length, but returned right or wrong
602//
603// -- currently num is completely ignored
604//
605Function/S V_getStringFromHDF5(fname,path,num)
606        String fname,path
607        Variable num
608
609        String folderStr=""
610        Variable valExists=0
611       
612        folderStr = V_RemoveDotExtension(V_GetFileNameFromPathNoSemi(fname))
613
614// check for a work folder first (note that "entry" is NOT doubled)
615        if(Exists("root:Packages:NIST:VSANS:"+folderStr+":"+path))
616                Wave/Z/T tw = $("root:Packages:NIST:VSANS:"+folderStr+":"+path)
617                return(tw[0])
618        endif
619       
620        if(Exists(ksBaseDFPath+folderStr+":"+path))
621                valExists=1
622        endif
623
624        if(!valExists)
625                //then read in the file, putting the data in RawVSANS
626                SetDataFolder ksBaseDFPath
627                V_LoadHDF5_NoAtt(fname,"")
628                SetDataFolder root:
629        endif
630
631// this should exist now - if not, I need to see the error
632        Wave/T/Z tw = $(ksBaseDFPath+folderStr+":"+path)
633       
634        if(WaveExists(tw))
635       
636        //      if(strlen(tw[0]) != num)
637        //              Print "string is not the specified length"
638        //      endif
639               
640                return(tw[0])
641        else
642                return("The specified wave does not exist: " + path)
643        endif
644End
645
646
647
648///////////////////////////////
649
650//
651//Write Wave 'wav' to hdf5 file 'fname'
652//Based on code from ANSTO (N. Hauser. nha 8/1/09)
653//
654// TODO:
655// -- figure out if this will write in the native format of the
656//     wave as passed in, or if it will only write as DP.
657// -- do I need to write separate functions for real, integer, etc.?
658// -- the lines to create a missing group have been commented out to avoid filling
659//    in missing fields that should have been generated by the data writer. Need to make
660//    a separate function that will write and generate if needed, and use this in specific cases
661//    only if I really have to force it.
662//
663// --Attributes are not currently saved. Fix this, maybe make it optional? See the help file for
664//  DemoAttributes(w) example under the HDF5SaveData operation
665//     
666// -x change the /P=home to the user-defined data path (catPathName)           
667//
668Function V_WriteWaveToHDF(fname, groupName, varName, wav)
669        String fname, groupName, varName
670        Wave wav
671       
672       
673        // try a local folder first, then try to save to disk
674        //
675        String folderStr = V_RemoveDotExtension(V_GetFileNameFromPathNoSemi(fname))
676       
677        String localPath = "root:Packages:NIST:VSANS:"+folderStr//+":entry"
678        localPath += groupName + "/" + varName
679        // make everything colons for local data folders
680        localPath = ReplaceString("/", localPath, ":")
681       
682        Wave/Z w = $localPath
683        if(waveExists(w) == 1)
684                w = wav
685//              Print "write to local folder done"
686                return(0)               //we're done, get out
687        endif
688       
689       
690        // if the local wave did not exist, then we proceed to write to disk
691
692       
693        variable err=0, fileID,groupID
694        String cDF = getDataFolder(1), temp
695        String NXentry_name
696       
697        try     
698                HDF5OpenFile/P=catPathName /Z fileID  as fname  //open file read-write
699                if(!fileID)
700                        err = 1
701                        abort "HDF5 file does not exist"
702                endif
703               
704                //get the NXentry node name
705                HDF5ListGroup /TYPE=1 fileID, "/"
706                //remove trailing ; from S_HDF5ListGroup
707               
708                Print "S_HDF5ListGroup = ",S_HDF5ListGroup
709               
710                NXentry_name = S_HDF5ListGroup
711                NXentry_name = ReplaceString(";",NXentry_name,"")
712                if(strsearch(NXentry_name,":",0)!=-1) //more than one entry under the root node
713                        err = 1
714                        abort "More than one entry under the root node. Ambiguous"
715                endif
716                //concatenate NXentry node name and groupName   
717                // SRK - NOV2015 - dropped this and require the full group name passed in
718//              groupName = "/" + NXentry_name + groupName
719                Print "groupName = ",groupName
720                HDF5OpenGroup /Z fileID , groupName, groupID
721
722                if(!groupID)
723                // don't create the group if the name isn't right -- throw up an error
724                        //HDF5CreateGroup /Z fileID, groupName, groupID
725                        err = 1
726                        HDF5CloseFile /Z fileID
727                        DoAlert 0, "HDF5 group does not exist "+groupName+varname
728                        return(err)
729                else
730                        // get attributes and save them
731                        //HDF5ListAttributes /Z fileID, groupName    this is returning null. expect it to return semicolon delimited list of attributes
732                        //Wave attributes = S_HDF5ListAttributes
733                endif
734       
735                HDF5SaveData /O /Z /IGOR=0 wav, groupID, varName
736                if (V_flag != 0)
737                        err = 1
738                        abort "Cannot save wave to HDF5 dataset " + varName
739                endif   
740               
741               
742                //attributes - something could be added here as optional parameters and flagged
743//              String attributes = "units"
744//              Make/O/T/N=1 tmp
745//              tmp[0] = "dimensionless"
746//              HDF5SaveData /O /Z /IGOR=0 /A=attributes tmp, groupID, varName
747//              if (V_flag != 0)
748//                      err = 1
749//                      abort "Cannot save attributes to HDF5 dataset"
750//              endif   
751        catch
752
753        endtry
754
755// it is not necessary to close the group here. HDF5CloseFile will close the group as well     
756        if(groupID)
757                HDF5CloseGroup /Z groupID
758        endif
759       
760        if(fileID)
761                HDF5CloseFile /Z fileID
762        endif
763
764        setDataFolder $cDF
765        return err
766end
767
768//Write Wave 'wav' to hdf5 file 'fname'
769//Based on code from ANSTO (N. Hauser. nha 8/1/09)
770//
771// TODO
772//
773// -x change the /P=home to the user-defined data path (catPathName)           
774//
775Function V_WriteTextWaveToHDF(fname, groupName, varName, wav)
776        String fname, groupName, varName
777        Wave/T wav
778
779        // try a local folder first, then try to save to disk
780        //
781        String folderStr = V_RemoveDotExtension(V_GetFileNameFromPathNoSemi(fname))
782       
783        String localPath = "root:Packages:NIST:VSANS:"+folderStr//+":entry"
784        localPath += groupName + "/" + varName
785        // make everything colons for local data folders
786        localPath = ReplaceString("/", localPath, ":")
787       
788        Wave/Z/T w = $localPath
789        if(waveExists(w) == 1)
790                w = wav
791                Print "write to local folder done"
792                return(0)               //we're done, get out
793        endif
794       
795       
796        // if the local wave did not exist, then we proceed to write to disk
797
798
799       
800        variable err=0, fileID,groupID
801        String cDF = getDataFolder(1), temp
802        String NXentry_name
803       
804        try     
805                HDF5OpenFile/P=catPathName /Z fileID  as fname  //open file read-write
806                if(!fileID)
807                        err = 1
808                        abort "HDF5 file does not exist"
809                endif
810               
811                //get the NXentry node name
812                HDF5ListGroup /TYPE=1 fileID, "/"
813                //remove trailing ; from S_HDF5ListGroup
814               
815                Print "S_HDF5ListGroup = ",S_HDF5ListGroup
816               
817                NXentry_name = S_HDF5ListGroup
818                NXentry_name = ReplaceString(";",NXentry_name,"")
819                if(strsearch(NXentry_name,":",0)!=-1) //more than one entry under the root node
820                        err = 1
821                        abort "More than one entry under the root node. Ambiguous"
822                endif
823
824                //concatenate NXentry node name and groupName
825                // SRK - NOV2015 - dropped this and require the full group name passed in
826//              groupName = "/" + NXentry_name + groupName
827                Print "groupName = ",groupName
828
829                HDF5OpenGroup /Z fileID , groupName, groupID
830
831                if(!groupID)
832                // don't create the group it the name isn't right -- throw up an error
833                        //HDF5CreateGroup /Z fileID, groupName, groupID
834                        err = 1
835                        HDF5CloseFile /Z fileID
836                        DoAlert 0, "HDF5 group does not exist "+groupName+varname
837                        return(err)
838                else
839                        // get attributes and save them
840                        //HDF5ListAttributes /Z fileID, groupName    this is returning null. expect it to return semicolon delimited list of attributes
841                        //Wave attributes = S_HDF5ListAttributes
842                endif
843       
844                HDF5SaveData /O /Z /IGOR=0 wav, groupID, varName
845                if (V_flag != 0)
846                        err = 1
847                        abort "Cannot save wave to HDF5 dataset " + varName
848                endif   
849               
850               
851                //attributes - something could be added here as optional parameters and flagged
852//              String attributes = "units"
853//              Make/O/T/N=1 tmp
854//              tmp[0] = "dimensionless"
855//              HDF5SaveData /O /Z /IGOR=0 /A=attributes tmp, groupID, varName
856//              if (V_flag != 0)
857//                      err = 1
858//                      abort "Cannot save attributes to HDF5 dataset"
859//              endif   
860        catch
861
862        endtry
863       
864        if(groupID)
865                HDF5CloseGroup /Z groupID
866        endif
867       
868        if(fileID)
869                HDF5CloseFile /Z fileID
870        endif
871
872        setDataFolder $cDF
873        return err
874end
875
876//////////////////////////////
877//////////////////////////////
878//////////////////////////////
879
880
881
882
883
884
885//////////
886//
887// These procedures are needed to write out MASK and DIV files
888//
889////////
890
891
892//
893// saves a specified folder, with a given filename.
894// saves to the home path
895//
896Proc Save_VSANS_file(dfPath, filename)
897        String dfPath   ="root:VSANS_file"              // e.g., "root:FolderA" or ":"
898        String filename = "Test_VSANS_file.h5"
899       
900        H_NXSANS_SaveGroupAsHDF5(dfPath, filename)
901End
902
903
904//     
905// this is my procedure to save the folders to HDF5, once I've filled the folder tree
906//
907// this does NOT save attributes, but gets the folder structure correct
908//
909Function H_NXSANS_SaveGroupAsHDF5(dfPath, filename)
910        String dfPath   // e.g., "root:FolderA" or ":"
911        String filename
912
913        Variable result = 0     // 0 means no error
914       
915        Variable fileID
916        HDF5CreateFile/P=home /O /Z fileID as filename
917        if (V_flag != 0)
918                Print "HDF5CreateFile failed"
919                return -1
920        endif
921
922        HDF5SaveGroup /IGOR=0 /O /R /Z $dfPath, fileID, "."
923//      HDF5SaveGroup /O /R /Z $dfPath, fileID, "."
924        if (V_flag != 0)
925                Print "HDF5SaveGroup failed"
926                result = -1
927        endif
928       
929        HDF5CloseFile fileID
930
931        return result
932End
933
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