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V_HDF5_RW_Utils.ipf @ 995

Last change on this file since 995 was 995, checked in by srkline, 6 years ago
more changes, bug fixes, detector dead time fix
File size: 25.4 KB

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

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