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HDF5_ConvertVAX_to_HDF5.ipf @ 947

Last change on this file since 947 was 946, checked in by srkline, 9 years ago

Adding procedures that will allow read/write of raw data in HDF5 format. No Nexus file definition has been settled upon yet, so I made up my own for testing, simply converting what was present in the VAX file header. Simple read/write operations are functional, but no full scale testing.

Transmission calculation is partially broken as there are no file suffixes anymore.

Otherwise, a good starting point for the HDF5/Nexus of the future.

File size: 22.9 KB

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

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