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HDF5_ConvertVAX_to_HDF5.ipf @ 1010

Last change on this file since 1010 was 954, checked in by srkline, 8 years ago

converted and renamed VSANS files. "VC_" prefix for VCALC related files (that's all of them right now), and moved and renamed parts of files so that the ipf names are more logical now with the contents. Deleted the "V_" prefix files. Added a lengthy routine to be able to write out a VSANS file in HDF format. This is NOT the final and approved data format, only a working version so that I can test things out...

File size: 23.0 KB

Line
1	#pragma rtGlobals=1 // Use modern global access method.
2
3	//
4	// DON'T TOSS THIS FILE-- THERE ARE USEFUL PROCEDURES HERE
5	// -- some that may be in use elsewhere in reading/writing of HDF files
6
7
8
9	//
10	//
11	// crudely converts the VAX format as read into RAW into an HDF5 file
12	//
13	// Not any thought was given to HDF5 structure
14	//
15	// the simple read/write works...
16	// linear_data does not seem to need to be transposed at all
17	//
18	// -- this seems too easy. what am I doing wrong? Is something getting garbled when I
19	// write back any single values back to the file
20	//
21	// -- try a string value next
22	//
23
24
25	// lays out the tree
26
27	Function SetupStructure()
28
29	SetDataFolder root:
30
31	NewDataFolder/O root:entry1
32	NewDataFolder/O root:entry1:Run1
33	NewDataFolder/O root:entry1:Run1:Sample
34	NewDataFolder/O root:entry1:Run1:Run
35	NewDataFolder/O root:entry1:Run1:Detector
36	NewDataFolder/O root:entry1:Run1:Instrument
37	NewDataFolder/O root:entry1:Run1:Analysis
38
39
40	SetDataFolder root:entry1
41	Make/O/T/N=1 filename
42
43	SetDataFolder root:entry1:Run1
44	Make/O/T/N=1 runLabel
45
46	SetDataFolder root:entry1:Run1:Sample
47	// SAMPLE
48	Make/O/D/N=1 TRNS
49	Make/O/D/N=1 THK
50	Make/O/D/N=1 POSITION
51	Make/O/D/N=1 ROTANG
52	Make/O/I/N=1 TABLE
53	Make/O/I/N=1 HOLDER
54	Make/O/I/N=1 BLANK
55	Make/O/D/N=1 TEMP
56	Make/O/D/N=1 FIELD
57	Make/O/I/N=1 TCTRLR
58	Make/O/D/N=1 MAGNET
59	Make/O/T/N=1 TUNITS
60	Make/O/T/N=1 FUNITS
61
62	SetDataFolder root:entry1:Run1:Run
63	// RUN
64	Make/O/I/N=1 NPRE
65	Make/O/I/N=1 CTIME
66	Make/O/I/N=1 RTIME
67	Make/O/I/N=1 NUMRUNS
68	Make/O/D/N=1 MONCNT
69	Make/O/D/N=1 SAVMON
70	Make/O/D/N=1 DETCNT
71	Make/O/D/N=1 ATTEN
72	Make/O/T/N=1 TIMDAT
73	Make/O/T/N=1 TYPE
74	Make/O/T/N=1 DEFDIR
75	Make/O/T/N=1 MODE
76	Make/O/T/N=1 RESERVE
77	// Make/O/T/N=1 LOGDATIM
78
79
80	SetDataFolder root:entry1:Run1:Detector
81	// DET
82	Make/O/T/N=1 TYP
83	Make/O/D/N=3 CALX
84	Make/O/D/N=3 CALY
85	Make/O/I/N=1 NUM
86	Make/O/I/N=1 DetSPACER
87	Make/O/D/N=1 BEAMX
88	Make/O/D/N=1 BEAMY
89	Make/O/D/N=1 DIS
90	Make/O/D/N=1 ANG
91	Make/O/D/N=1 SIZ
92	Make/O/D/N=1 BSTOP
93	Make/O/D/N=1 DetBLANK
94
95	Make/O/D/N=(128,128) data
96
97	SetDataFolder root:entry1:Run1:Instrument
98	// RESOLUTION
99	Make/O/D/N=1 AP1
100	Make/O/D/N=1 AP2
101	Make/O/D/N=1 AP12DIS
102	Make/O/D/N=1 LMDA
103	Make/O/D/N=1 DLMDA
104	Make/O/D/N=1 SAVEFlag
105	// BMSTP
106	Make/O/D/N=1 XPOS
107	Make/O/D/N=1 YPOS
108	// TIMESLICING
109	Make/O/T/N=1 SLICING
110	Make/O/I/N=1 MULTFACT
111	Make/O/I/N=1 LTSLICE
112
113	// POLARIZATION
114	Make/O/T/N=1 PRINTPOL
115	Make/O/T/N=1 FLIPPER
116	Make/O/D/N=1 HORIZ
117	Make/O/D/N=1 VERT
118	// TEMP
119	Make/O/T/N=1 PRINTEMP
120	Make/O/D/N=1 HOLD
121	// Make/O/D/N=1 ERR
122	Make/O/D/N=1 ERR_TEMP
123	Make/O/D/N=1 TempBLANK
124	Make/O/T/N=1 EXTEMP
125	Make/O/T/N=1 EXTCNTL
126	Make/O/T/N=1 TempEXTRA2
127	Make/O/I/N=1 TempRESERVE
128	// MAGNET
129	Make/O/T/N=1 PRINTMAG
130	Make/O/T/N=1 SENSOR
131	Make/O/D/N=1 CURRENT
132	Make/O/D/N=1 CONV
133	Make/O/D/N=1 FIELDLAST
134	Make/O/D/N=1 MagnetBLANK
135	Make/O/D/N=1 MagnetSPACER
136	// VOLTAGE
137	Make/O/T/N=1 PRINTVOLT
138	Make/O/D/N=1 VOLTS
139	Make/O/D/N=1 VoltBLANK
140	Make/O/I/N=1 VoltSPACER
141
142	SetDataFolder root:entry1:Run1:Analysis
143	// ANALYSIS
144	Make/O/I/N=2 ROWS
145	Make/O/I/N=2 COLS
146	Make/O/D/N=1 FACTOR
147	Make/O/D/N=1 AnalysisQMIN
148	Make/O/D/N=1 AnalysisQMAX
149	Make/O/D/N=1 IMIN
150	Make/O/D/N=1 IMAX
151
152	// PARAMS
153	Make/O/I/N=1 BLANK1
154	Make/O/I/N=1 BLANK2
155	Make/O/I/N=1 BLANK3
156	Make/O/D/N=1 TRNSCNT
157	Make/O/D/N=1 ParamEXTRA1
158	Make/O/D/N=1 ParamEXTRA2
159	Make/O/D/N=1 ParamEXTRA3
160	Make/O/T/N=1 ParamRESERVE
161
162	SetDataFolder root:
163
164	End
165
166
167	// fills the tree structure based on the RTI from RAW
168	// logicals are skipped
169	Function FillStructureFromRTI()
170
171	WAVE rw = root:Packages:NIST:RAW:RealsRead
172	WAVE iw = root:Packages:NIST:RAW:IntegersRead
173	WAVE/T tw = root:Packages:NIST:RAW:TextRead
174
175
176	SetDataFolder root:entry1
177	Wave/T filename
178
179	String newFileName= GetNameFromHeader(tw[0]) //02JUL13
180
181	//TODO - not the best choice of file name, (maybe not unique) but this is only a test...
182	filename[0] = newfilename[0,7]+".h5" //make sure the file name in the header matches that on disk!
183
184	SetDataFolder root:entry1:Run1
185	Wave/T runLabel
186
187	runLabel[0] = tw[6]
188
189	SetDataFolder root:entry1:Run1:Sample
190	// SAMPLE
191	Wave TRNS
192	Wave THK
193	Wave POSITION
194	Wave ROTANG
195	Wave TABLE
196	Wave HOLDER
197	Wave BLANK
198	Wave TEMP
199	Wave FIELD
200	Wave TCTRLR
201	Wave MAGNET
202	Wave/T TUNITS
203	Wave/T FUNITS
204
205	TRNS[0] = rw[4]
206	THK[0] = rw[5]
207	POSITION[0] = rw[6]
208	ROTANG[0] = rw[7]
209	TABLE[0] = iw[4]
210	HOLDER[0] = iw[5]
211	BLANK[0] = iw[6]
212	TEMP[0] = rw[8]
213	FIELD[0] = rw[9]
214	TCTRLR[0] = iw[7]
215	MAGNET[0] = iw[8]
216	TUNITS[0] = tw[7]
217	FUNITS[0] = tw[8]
218
219
220	SetDataFolder root:entry1:Run1:Run
221	// RUN
222	Wave NPRE
223	Wave CTIME
224	Wave RTIME
225	Wave NUMRUNS
226	Wave MONCNT
227	Wave SAVMON
228	Wave DETCNT
229	Wave ATTEN
230	Wave/T TIMDAT
231	Wave/T TYPE
232	Wave/T DEFDIR
233	Wave/T MODE
234	Wave/T RESERVE
235	// Wave/T LOGDATIM
236
237
238	NPRE[0] = iw[0]
239	CTIME[0] = iw[1]
240	RTIME[0] = iw[2]
241	NUMRUNS[0] = iw[3]
242	MONCNT[0] = rw[0]
243	SAVMON[0] = rw[1]
244	DETCNT[0] = rw[2]
245	ATTEN[0] = rw[3]
246	TIMDAT[0] = tw[1]
247	TYPE[0] = tw[2]
248	DEFDIR[0] = tw[3]
249	MODE[0] = tw[4]
250	RESERVE[0] = tw[5]
251	// LOGDATIM
252
253
254	SetDataFolder root:entry1:Run1:Detector
255	// DET
256	Wave/T TYP
257	Wave CALX
258	Wave CALY
259	Wave NUM
260	Wave DetSPACER
261	Wave BEAMX
262	Wave BEAMY
263	Wave DIS
264	Wave ANG
265	Wave SIZ
266	Wave BSTOP
267	Wave DetBLANK
268
269	Wave data
270
271	//CALX is 3 pts
272	//CALY is 3 pts
273	//data is 128,128
274
275	TYP[0] = tw[9]
276	CALX[0] = rw[10]
277	CALX[1] = rw[11]
278	CALX[2] = rw[12]
279	CALY[0] = rw[13]
280	CALY[1] = rw[14]
281	CALY[2] = rw[15]
282	NUM[0] = iw[9]
283	DetSPACER[0] = iw[10]
284	BEAMX[0] = rw[16]
285	BEAMY[0] = rw[17]
286	DIS[0] = rw[18]
287	ANG[0] = rw[19]
288	SIZ[0] = rw[20]
289	BSTOP[0] = rw[21]
290	DetBLANK[0] = rw[22]
291
292	Wave linear_data = root:Packages:NIST:RAW:linear_data
293	data = linear_data
294
295
296	SetDataFolder root:entry1:Run1:Instrument
297	// RESOLUTION
298	Wave AP1
299	Wave AP2
300	Wave AP12DIS
301	Wave LMDA
302	Wave DLMDA
303	Wave SAVEFlag
304	// BMSTP
305	Wave XPOS
306	Wave YPOS
307	// TIMESLICING
308	Wave/T SLICING //logical
309	Wave MULTFACT
310	Wave LTSLICE
311
312	// POLARIZATION
313	Wave/T PRINTPOL //logical
314	Wave/T FLIPPER //logical
315	Wave HORIZ
316	Wave VERT
317	// TEMP
318	Wave/T PRINTEMP //logical
319	Wave HOLD
320	Wave ERR_TEMP
321	Wave TempBLANK
322	Wave/T EXTEMP //logical
323	Wave/T EXTCNTL //logical
324	Wave/T TempEXTRA2 //logical
325	Wave TempRESERVE
326	// MAGNET
327	Wave/T PRINTMAG //logical
328	Wave/T SENSOR //logical
329	Wave CURRENT
330	Wave CONV
331	Wave FIELDLAST
332	Wave MagnetBLANK
333	Wave MagnetSPACER
334	// VOLTAGE
335	Wave/T PRINTVOLT //logical
336	Wave VOLTS
337	Wave VoltBLANK
338	Wave VoltSPACER
339
340
341	AP1[0] = rw[23]
342	AP2[0] = rw[24]
343	AP12DIS[0] = rw[25]
344	LMDA[0] = rw[26]
345	DLMDA[0] = rw[27]
346	SAVEFlag[0] = rw[28]
347
348	XPOS[0] = rw[37]
349	YPOS[0] = rw[38]
350
351	MULTFACT[0] = iw[11]
352	LTSLICE[0] = iw[12]
353
354	HORIZ[0] = rw[45]
355	VERT[0] = rw[46]
356	// TEMP
357	HOLD[0] = rw[29]
358	ERR_TEMP[0] = rw[30]
359	TempBLANK[0] = rw[31]
360	TempRESERVE[0] = iw[14]
361	// MAGNET
362	CURRENT[0] = rw[32]
363	CONV[0] = rw[33]
364	FIELDLAST[0] = rw[34]
365	MagnetBLANK[0] = rw[35]
366	MagnetSPACER[0] = rw[36]
367	// VOLTAGE
368	VOLTS[0] = rw[43]
369	VoltBLANK[0] = rw[44]
370	VoltSPACER[0] = iw[18]
371
372	SetDataFolder root:entry1:Run1:Analysis
373	// ANALYSIS
374	Wave ROWS
375	Wave COLS
376	Wave FACTOR
377	Wave AnalysisQMIN
378	Wave AnalysisQMAX
379	Wave IMIN
380	Wave IMAX
381
382	// PARAMS
383	Wave BLANK1
384	Wave BLANK2
385	Wave BLANK3
386	Wave TRNSCNT
387	Wave ParamEXTRA1
388	Wave ParamEXTRA2
389	Wave ParamEXTRA3
390	Wave/T ParamRESERVE
391
392	// ROWS is 2 pts
393	// COLS is 2 pts
394
395	// ANALYSIS
396	ROWS[0] = iw[19]
397	ROWS[1] = iw[20]
398	COLS[0] = iw[21]
399	COLS[1] = iw[22]
400
401	FACTOR[0] = rw[47]
402	AnalysisQMIN[0] = rw[48]
403	AnalysisQMAX[0] = rw[49]
404	IMIN[0] = rw[50]
405	IMAX[0] = rw[51]
406
407	// PARAMS
408	BLANK1[0] = iw[15]
409	BLANK2[0] = iw[16]
410	BLANK3[0] = iw[17]
411	TRNSCNT[0] = rw[39]
412	ParamEXTRA1[0] = rw[40]
413	ParamEXTRA2[0] = rw[41]
414	ParamEXTRA3[0] = rw[42]
415	ParamRESERVE[0] = tw[10]
416
417
418	SetDataFolder root:
419
420	return(0)
421	End
422
423
424
425	Function Test_HDFWriteTrans(fname,val)
426	String fname
427	Variable val
428
429
430	String str
431	PathInfo home
432	str = S_path
433
434	WriteTransmissionToHeader(str+fname,val)
435
436	return(0)
437	End
438
439	//Function WriteTransmissionToHeader(fname,trans)
440	// String fname
441	// Variable trans
442	//
443	// Make/O/D/N=1 wTmpWrite
444	// String groupName = "/Sample" // /Run1/Sample becomes groupName /Run1/Run1/Sample
445	// String varName = "TRNS"
446	// wTmpWrite[0] = trans //
447	//
448	// variable err
449	// err = HDFWrite_Wave(fname, groupName, varName, wTmpWrite)
450	// KillWaves wTmpWrite
451	//
452	// //err not handled here
453	//
454	// return(0)
455	//End
456
457
458
459	Function Test_ListAttributes(fname,groupName)
460	String fname,groupName
461	Variable trans
462
463	// Make/O/D/N=1 wTmpWrite
464	// String groupName = "/Sample" // /Run1/Sample becomes groupName /Run1/Run1/Sample
465	// String varName = "TRNS"
466	// wTmpWrite[0] = trans //
467	String str
468	PathInfo home
469	str = S_path
470
471	variable err
472	err = HDF_ListAttributes(str+fname, groupName)
473
474	//err not handled here
475
476	return(0)
477	End
478
479	Function HDF_ListAttributes(fname, groupName)
480	String fname, groupName
481
482	variable err=0, fileID,groupID
483	String cDF = getDataFolder(1), temp
484	String NXentry_name, attrValue=""
485
486	STRUCT HDF5DataInfo di // Defined in HDF5 Browser.ipf.
487	InitHDF5DataInfo(di) // Initialize structure.
488
489	try
490	HDF5OpenFile /Z fileID as fname //open file read-write
491	if(!fileID)
492	err = 1
493	abort "HDF5 file does not exist"
494	endif
495
496	HDF5OpenGroup /Z fileID , groupName, groupID
497
498	// !! At the moment, there is no entry for sample thickness in our data file
499	// therefore create new HDF5 group to enable write / patch command
500	// comment out the following group creation once thickness appears in revised file
501
502	if(!groupID)
503	HDF5CreateGroup /Z fileID, groupName, groupID
504	//err = 1
505	//abort "HDF5 group does not exist"
506	else
507
508	// HDF5AttributeInfo(fileID, "/", 1, "file_name", 0, di)
509	HDF5AttributeInfo(fileID, "/", 1, "NeXus_version", 0, di)
510	Print di
511
512	// see the HDF5 Browser for how to get the actual <value> of the attribute. See GetPreviewString in
513	// or in FillGroupAttributesList or in FillDatasetAttributesList (from FillLists)
514	// it seems to be ridiculously complex to get such a simple bit of information - the HDF5BrowserData STRUCT
515	// needs to be filled first. Ugh.
516	attrValue = GetPreviewString(fileID, 1, di, "/entry", "cucumber")
517	Print "attrValue = ",attrValue
518
519
520	//get attributes and save them
521	HDF5ListAttributes/TYPE=1 /Z fileID, groupName //TYPE=1 means that we're referencing a group, not a dataset
522	Print "S_HDF5ListAttributes = ", S_HDF5ListAttributes
523
524	// passing the groupID works too, then the group name is not needed
525	HDF5ListAttributes/TYPE=1 /Z groupID, "." //TYPE=1 means that we're referencing a group, not a dataset
526	Print "S_HDF5ListAttributes = ", S_HDF5ListAttributes
527	endif
528	catch
529
530	// catch any aborts here
531
532	endtry
533
534	if(groupID)
535	HDF5CloseGroup /Z groupID
536	endif
537
538	if(fileID)
539	HDF5CloseFile /Z fileID
540	endif
541
542	setDataFolder $cDF
543	return err
544	end
545
546	// this is my procedure to save VAX to HDF5, once I've filled the folder tree
547	//
548	Function VAXSaveGroupAsHDF5(dfPath, filename)
549	String dfPath // e.g., "root:FolderA" or ":"
550	String filename
551
552	Variable result = 0 // 0 means no error
553
554	Variable fileID
555	HDF5CreateFile/P=home /O /Z fileID as filename
556	if (V_flag != 0)
557	Print "HDF5CreateFile failed"
558	return -1
559	endif
560
561	HDF5SaveGroup /IGOR=0 /O /R /Z $dfPath, fileID, "."
562	// HDF5SaveGroup /O /R /Z $dfPath, fileID, "."
563	if (V_flag != 0)
564	Print "HDF5SaveGroup failed"
565	result = -1
566	endif
567
568	HDF5CloseFile fileID
569
570	return result
571	End
572
573
574
575	//////// Two procedures that test out Pete Jemain's HDF5Gateway
576	//
577	// This works fine, but it may not be terribly compatible with the way NICE will eventually
578	// write out the data files. I'll have very little control over that and I'll need to cobble together
579	// a bunch of fixes to cover up their mistakes.
580	//
581	// Using Nick Hauser's code as a starting point may be a lot more painful, but more flexible in the end.
582	//
583	// I'm completely baffled about what to do with attributes. Are they needed, is this the best way to deal
584	// with them, do I care about reading them in, and if I do, why?
585	//
586	Proc HDF5Gate_WriteTest()
587
588	// create the folder structure
589	NewDataFolder/O/S root:mydata
590	NewDataFolder/O sasentry
591	NewDataFolder/O :sasentry:sasdata
592
593	// create the waves
594	Make/O :sasentry:sasdata:I0
595	Make/O :sasentry:sasdata:Q0
596
597	Make/O/N=0 Igor___folder_attributes
598	Make/O/N=0 :sasentry:Igor___folder_attributes
599	Make/O/N=0 :sasentry:sasdata:Igor___folder_attributes
600
601	// create the attributes
602	Note/K Igor___folder_attributes, "producer=IgorPro\rNX_class=NXroot"
603	Note/K :sasentry:Igor___folder_attributes, "NX_class=NXentry"
604	Note/K :sasentry:sasdata:Igor___folder_attributes, "NX_class=NXdata"
605	Note/K :sasentry:sasdata:I0, "units=1/cm\rsignal=1\rtitle=reduced intensity"
606	Note/K :sasentry:sasdata:Q0, "units=1/A\rtitle=\|scattering vector\|"
607
608	// create the cross-reference mapping
609	Make/O/T/N=(5,2) HDF5___xref
610	Edit/K=0 'HDF5___xref';DelayUpdate
611	HDF5___xref[0][1] = ":"
612	HDF5___xref[1][1] = ":sasentry"
613	HDF5___xref[2][1] = ":sasentry:sasdata"
614	HDF5___xref[3][1] = ":sasentry:sasdata:I0"
615	HDF5___xref[4][1] = ":sasentry:sasdata:Q0"
616	HDF5___xref[0][0] = "/"
617	HDF5___xref[1][0] = "/sasentry"
618	HDF5___xref[2][0] = "/sasentry/sasdata"
619	HDF5___xref[3][0] = "/sasentry/sasdata/I"
620	HDF5___xref[4][0] = "/sasentry/sasdata/Q"
621
622	// Check our work so far.
623	// If something prints, there was an error above.
624	print H5GW_ValidateFolder("root:mydata")
625
626	// set I0 and Q0 to your data
627
628	print H5GW_WriteHDF5("root:mydata", "mydata.h5")
629
630	SetDataFolder root:
631	End
632
633	Proc HDF5Gate_ReadTest(file)
634	String file
635	// NewDataFolder/O/S root:newdata
636	Print H5GW_ReadHDF5("", file) // reads into current folder
637	SetDataFolder root:
638	End
639
640
641
642	//// after reading in an HDF file, convert it into something I can use with data reduction
643	//
644	// This is to be an integral part of the file loader
645	//
646	// I guess I need to load the file into a temporary location, and then copy what I need to the local RTI
647	// and then get rid of the temp dump. ANSTO keeps all of the loads around, but this may get too large
648	// especially if NICE dumps all of the logs into the data file.
649	//
650	// -- and I may need to have a couple of these, at least for testing to be able to convert the
651	// minimal VAX file to HDF, and also to write out/ have a container/ for what NICE calls a data file.
652	//
653	//
654
655	// From the HDF5 tree as read in from a (converted) raw VAX file,
656	// put everything back into its proper place in the RTI waves
657	// (and the data!)
658	//
659	Function FillRTIFromHDFTree(folderStr)
660	String folderStr
661
662	WAVE rw = root:Packages:NIST:RAW:RealsRead
663	WAVE iw = root:Packages:NIST:RAW:IntegersRead
664	WAVE/T tw = root:Packages:NIST:RAW:TextRead
665
666	rw = -999
667	iw = 11111
668	tw = "jibberish"
669
670	folderStr = RemoveDotExtension(folderStr) // to make sure that the ".h5" or any other extension is removed
671	// folderStr = RemoveEnding(folderStr,".h5") // to make sure that the ".h5" or any other extension is removed
672
673	String base="root:"+folderStr+":"
674	SetDataFolder $base
675	Wave/T filename
676
677	tw[0] = filename[0]
678
679	SetDataFolder $(base+"Run1")
680	Wave/T runLabel
681
682	tw[6] = runLabel[0]
683
684	SetDataFolder $(base+"Run1:Sample")
685	// SAMPLE
686	Wave TRNS
687	Wave THK
688	Wave POSITION
689	Wave ROTANG
690	Wave TABLE
691	Wave HOLDER
692	Wave BLANK
693	Wave TEMP
694	Wave FIELD
695	Wave TCTRLR
696	Wave MAGNET
697	Wave/T TUNITS
698	Wave/T FUNITS
699
700	rw[4] = TRNS[0]
701	rw[5] = THK[0]
702	rw[6] = POSITION[0]
703	rw[7] = ROTANG[0]
704	iw[4] = TABLE[0]
705	iw[5] = HOLDER[0]
706	iw[6] = BLANK[0]
707	rw[8] = TEMP[0]
708	rw[9] = FIELD[0]
709	iw[7] = TCTRLR[0]
710	iw[8] = MAGNET[0]
711	tw[7] = TUNITS[0]
712	tw[8] = FUNITS[0]
713
714
715	SetDataFolder $(base+"Run1:Run")
716	// RUN
717	Wave NPRE
718	Wave CTIME
719	Wave RTIME
720	Wave NUMRUNS
721	Wave MONCNT
722	Wave SAVMON
723	Wave DETCNT
724	Wave ATTEN
725	Wave/T TIMDAT
726	Wave/T TYPE
727	Wave/T DEFDIR
728	Wave/T MODE
729	Wave/T RESERVE
730	// Wave/T LOGDATIM
731
732
733	iw[0] = NPRE[0]
734	iw[1] = CTIME[0]
735	iw[2] = RTIME[0]
736	iw[3] = NUMRUNS[0]
737	rw[0] = MONCNT[0]
738	rw[1] = SAVMON[0]
739	rw[2] = DETCNT[0]
740	rw[3] = ATTEN[0]
741	tw[1] = TIMDAT[0]
742	tw[2] = TYPE[0]
743	tw[3] = DEFDIR[0]
744	tw[4] = MODE[0]
745	tw[5] = RESERVE[0]
746	// LOGDATIM
747
748
749	SetDataFolder $(base+"Run1:Detector")
750	// DET
751	Wave/T TYP
752	Wave CALX
753	Wave CALY
754	Wave NUM
755	Wave DetSPACER
756	Wave BEAMX
757	Wave BEAMY
758	Wave DIS
759	Wave ANG
760	Wave SIZ
761	Wave BSTOP
762	Wave DetBLANK
763
764	Wave data
765
766	//CALX is 3 pts
767	//CALY is 3 pts
768	//data is 128,128
769
770	tw[9] = TYP[0]
771	rw[10] = CALX[0]
772	rw[11] = CALX[1]
773	rw[12] = CALX[2]
774	rw[13] = CALY[0]
775	rw[14] = CALY[1]
776	rw[15] = CALY[2]
777	iw[9] = NUM[0]
778	iw[10] = DetSPACER[0]
779	rw[16] = BEAMX[0]
780	rw[17] = BEAMY[0]
781	rw[18] = DIS[0]
782	rw[19] = ANG[0]
783	rw[20] = SIZ[0]
784	rw[21] = BSTOP[0]
785	rw[22] = DetBLANK[0]
786
787	// Wave linear_data = root:Packages:NIST:RAW:linear_data
788	// Wave raw_data = root:Packages:NIST:RAW:data
789	// linear_data = data
790	// raw_data = data
791
792	/// **** what about the error wave?
793
794
795
796	SetDataFolder $(base+"Run1:Instrument")
797	// RESOLUTION
798	Wave AP1
799	Wave AP2
800	Wave AP12DIS
801	Wave LMDA
802	Wave DLMDA
803	Wave SAVEFlag
804	// BMSTP
805	Wave XPOS
806	Wave YPOS
807	// TIMESLICING
808	Wave/T SLICING //logical
809	Wave MULTFACT
810	Wave LTSLICE
811
812	// POLARIZATION
813	Wave/T PRINTPOL //logical
814	Wave/T FLIPPER //logical
815	Wave HORIZ
816	Wave VERT
817	// TEMP
818	Wave/T PRINTEMP //logical
819	Wave HOLD
820	Wave ERR_TEMP
821	// Wave ERR0
822	Wave TempBLANK
823	Wave/T EXTEMP //logical
824	Wave/T EXTCNTL //logical
825	Wave/T TempEXTRA2 //logical
826	Wave TempRESERVE
827	// MAGNET
828	Wave/T PRINTMAG //logical
829	Wave/T SENSOR //logical
830	Wave CURRENT
831	Wave CONV
832	Wave FIELDLAST
833	Wave MagnetBLANK
834	Wave MagnetSPACER
835	// VOLTAGE
836	Wave/T PRINTVOLT //logical
837	Wave VOLTS
838	Wave VoltBLANK
839	Wave VoltSPACER
840
841
842	rw[23] = AP1[0]
843	rw[24] = AP2[0]
844	rw[25] = AP12DIS[0]
845	rw[26] = LMDA[0]
846	rw[27] = DLMDA[0]
847	rw[28] = SAVEFlag[0]
848
849	rw[37] = XPOS[0]
850	rw[38] = YPOS[0]
851
852	iw[11] = MULTFACT[0]
853	iw[12] = LTSLICE[0]
854
855	rw[45] = HORIZ[0]
856	rw[46] = VERT[0]
857	// TEMP
858	rw[29] = HOLD[0]
859	rw[30] = ERR_TEMP[0]
860	// rw[30] = ERR0[0]
861	rw[31] = TempBLANK[0]
862	iw[14] = TempRESERVE[0]
863	// MAGNET
864	rw[32] = CURRENT[0]
865	rw[33] = CONV[0]
866	rw[34] = FIELDLAST[0]
867	rw[35] = MagnetBLANK[0]
868	rw[36] = MagnetSPACER[0]
869	// VOLTAGE
870	rw[43] = VOLTS[0]
871	rw[44] = VoltBLANK[0]
872	iw[18] = VoltSPACER[0]
873
874	SetDataFolder $(base+"Run1:Analysis")
875	// ANALYSIS
876	Wave ROWS
877	Wave COLS
878	Wave FACTOR
879	Wave AnalysisQMIN
880	Wave AnalysisQMAX
881	Wave IMIN
882	Wave IMAX
883
884	// PARAMS
885	Wave BLANK1
886	Wave BLANK2
887	Wave BLANK3
888	Wave TRNSCNT
889	Wave ParamEXTRA1
890	Wave ParamEXTRA2
891	Wave ParamEXTRA3
892	Wave/T ParamRESERVE
893
894	// ROWS is 2 pts
895	// COLS is 2 pts
896
897	// ANALYSIS
898	iw[19] = ROWS[0]
899	iw[20] = ROWS[1]
900	iw[21] = COLS[0]
901	iw[22] = COLS[1]
902
903	rw[47] = FACTOR[0]
904	rw[48] = AnalysisQMIN[0]
905	rw[49] = AnalysisQMAX[0]
906	rw[50] = IMIN[0]
907	rw[51] = IMAX[0]
908
909	// PARAMS
910	iw[15] = BLANK1[0]
911	iw[16] = BLANK2[0]
912	iw[17] = BLANK3[0]
913	rw[39] = TRNSCNT[0]
914	rw[40] = ParamEXTRA1[0]
915	rw[41] = ParamEXTRA2[0]
916	rw[42] = ParamEXTRA3[0]
917	tw[10] = ParamRESERVE[0]
918
919
920	SetDataFolder root:
921
922	return(0)
923	End
924
925
926	//given a filename of a SANS data filename of the form
927	// name.anything
928	//returns the name as a string without the ".fbdfasga" extension
929	//
930	// returns the input string if a"." can't be found (maybe it wasn't there"
931	Function/S RemoveDotExtension(item)
932	String item
933	String invalid = item //
934	Variable num=-1
935
936	//find the "dot"
937	String runStr=""
938	Variable pos = strsearch(item,".",0)
939	if(pos == -1)
940	//"dot" not found
941	return (invalid)
942	else
943	//found, get all of the characters preceeding it
944	runStr = item[0,pos-1]
945	return (runStr)
946	Endif
947	End
948
949
950
951
952	//////////////////////////////////////////////////
953
954
955
956	Macro BatchConvertToHDF5(firstFile,lastFile)
957	Variable firstFile=1,lastFile=100
958
959	SetupStructure()
960	fBatchConvertToHDF5(firstFile,lastFile)
961
962	End
963
964	// lo is the first file number
965	// hi is the last file number (inclusive)
966	//
967	Function fBatchConvertToHDF5(lo,hi)
968	Variable lo,hi
969
970	Variable ii
971	String file
972
973	String fname="",pathStr="",fullPath="",newFileName=""
974
975	PathInfo catPathName //this is where the files are
976	pathStr=S_path
977
978	//loop over all files
979	for(ii=lo;ii<=hi;ii+=1)
980	file = FindFileFromRunNumber(ii)
981	if(strlen(file) != 0)
982	// load the data
983	ReadHeaderAndData(file) //file is the full path
984	String/G root:myGlobals:gDataDisplayType="RAW"
985	fRawWindowHook()
986	WAVE/T/Z tw = $"root:Packages:NIST:RAW:textRead" //to be sure that wave exists if no data was ever displayed
987	newFileName= GetNameFromHeader(tw[0]) //02JUL13
988
989	// convert it
990	FillStructureFromRTI()
991
992	// save it
993	VAXSaveGroupAsHDF5("root:entry1", newfilename[0,7]+".h5")
994
995	else
996	printf "run number %d not found\r",ii
997	endif
998	endfor
999
1000	return(0)
1001	End
1002

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