Context Navigation

NIST_XML_v40.ipf @ 709

Last change on this file since 709 was 709, checked in by srkline, 13 years ago
Fixed the re-writing of 1D data from Data Arithmetic panel - it was not correctly writing out the resolution information
File size: 34.4 KB

Line
1	#pragma rtGlobals=1 // Use modern global access method.
2	#pragma version=1.00
3	#pragma IgorVersion=6.1
4
5
6	#if( Exists("XmlOpenFile") )
7
8	#include "cansasXML", version >= 1.10
9
10	// The function is called "LoadNISTXMLData" but is actually more generic
11	// and will load any canSAS XML v1 dataset
12	// Dec 2008 :
13	// Caveats - Assumes Q in /A and I in /cm
14	// Takes outStr as output name. If outStr is specified then we must load only the first SASData in the firstSASEntry,
15	// since anything else doesn't make sense. This is a bit of a hack to support NSORT.
16
17
18	function LoadNISTXMLData(filestr,outStr,doPlot,forceOverwrite)
19	String filestr,outStr
20	Variable doPlot,forceOverwrite
21
22
23	Variable rr,gg,bb
24	Variable dQv
25	// NVAR/Z dQv = root:Packages:NIST:USANS_dQv //let USANS_CalcWeights set the dQv value
26
27
28	// Print "Trying to load canSAS XML format data"
29	Variable result = CS_XMLReader(filestr)
30
31	String xmlReaderFolder = "root:Packages:CS_XMLreader:"
32
33	if (result == 0)
34	SetDataFolder xmlReaderFolder
35
36	Variable i,j,numDataSets
37	Variable np
38
39	String w0,w1,w2,w3,w4,w5,basestr,fileName
40	String xmlDataFolder,xmlDataSetFolder
41
42	Variable numSASEntries
43
44	if(!cmpStr(outStr,""))
45	//no outStr defined
46	numSASEntries = CountObjects(xmlReaderFolder,4)
47	else
48	numSASEntries = 1
49	endif
50
51	for (i = 0; i < numSASEntries; i+=1)
52
53	xmlDataFolder = xmlReaderFolder+GetIndexedObjName(xmlReaderFolder,4,i)+":"
54	if (!cmpstr(outstr,""))
55	numDataSets = CountObjects(xmlDataFolder,4)
56	else
57	numDataSets = 0
58	endif
59
60	if (numDataSets > 0)
61	//Multiple SASData sets in this SASEntry
62	for (j = 0; j < numDataSets; j+=1)
63
64	xmlDataSetFolder = xmlDataFolder+GetIndexedObjName(xmlDataFolder,4,j)+":"
65
66	SetDataFolder xmlDataSetFolder
67	// enforce a short enough name here to keep Igor objects < 31 chars
68	// Multiple data sets so we need to use titles and run numbers for naming
69	basestr = ShortFileNameString(CleanupName(getXMLDataSetTitle(xmlDataSetFolder,j,useFilename=0),0))
70	baseStr = CleanupName(baseStr,0) //in case the user added odd characters
71
72	//String basestr = ParseFilePath(3, ParseFilePath(5,filestr,":",0,0),":",0,0)
73	fileName = ParseFilePath(0,ParseFilePath(5,filestr,":",0,0),":",1,0)
74
75
76	//print "In NIST XML Loader"
77	//print "fileStr: ",fileStr
78	//print "basestr: ",basestr
79	//print "fileName: ",fileName
80	//remove the semicolon AND period from files from the VAX
81	// print basestr
82	w0 = basestr + "_q"
83	w1 = basestr + "_i"
84	w2 = basestr + "_s"
85	w3 = basestr + "sq"
86	w4 = basestr + "qb"
87	w5 = basestr + "fs"
88
89	if(DataFolderExists("root:"+baseStr))
90	if(!forceOverwrite)
91	DoAlert 1,"The data set " + basestr + " from file "+fileName+" has already been loaded. Do you want to load the new data file, overwriting the data in memory?"
92	if(V_flag==2) //user selected No, don't load the data
93	SetDataFolder root:
94	if(DataFolderExists("root:Packages:NIST"))
95	String/G root:Packages:NIST:gLastFileName = filename
96	endif //set the last file loaded to the one NOT loaded
97	return 0 //quits the macro
98	endif
99	endif
100	SetDataFolder $("root:"+baseStr)
101	else
102	NewDataFolder/S $("root:"+baseStr)
103	endif
104
105	Duplicate/O $(xmlDataSetFolder+"Qsas") $w0
106	Duplicate/O $(xmlDataSetFolder+"Isas") $w1
107	Duplicate/O $(xmlDataSetFolder+"Idev") $w2
108
109
110	if (exists(xmlDataSetFolder+"Qdev"))
111	Wave Qsas = $(xmlDataSetFolder+"Qsas")
112	Wave Qdev = $(xmlDataSetFolder+"Qdev")
113
114	Duplicate/O Qdev, $w3
115	// make a resolution matrix for SANS data
116	np=numpnts($w0)
117	Make/D/O/N=(np,4) $(baseStr+"_res")
118	Wave reswave = $(baseStr+"_res")
119
120	reswave[][0] = Qdev[p] //sigQ
121	reswave[][3] = Qsas[p] //Qvalues
122	if(exists(xmlDataSetFolder+"Qmean"))
123	Wave Qmean = $(xmlDataSetFolder+"Qmean")
124	Duplicate/O Qmean,$w4
125	reswave[][1] = Qmean[p] //qBar
126	endif
127	if(exists(xmlDataSetFolder+"Shadowfactor"))
128	Wave Shadowfactor = $(xmlDataSetFolder+"Shadowfactor")
129	Duplicate/O Shadowfactor, $w5
130	reswave[][2] = Shadowfactor[p] //fShad
131	endif
132	elseif(exists(xmlDataSetFolder+"dQl"))
133	//USAS Data
134	Wave dQl = $(xmlDataSetFolder+"dQl")
135	dQv = dQl[0]
136
137	USANS_CalcWeights(baseStr,dQv)
138	else
139	//No resolution data
140	endif
141	//get rid of the resolution waves that are in the matrix
142
143	SetScale d,0,0,"1/A",$w0
144	SetScale d,0,0,"1/cm",$w1
145
146
147
148	//////
149	if(DataFolderExists("root:Packages:NIST"))
150	String/G root:Packages:NIST:gLastFileName = filename
151	endif
152
153
154	//plot if desired
155	if(doPlot)
156	// assign colors randomly
157	rr = abs(trunc(enoise(65535)))
158	gg = abs(trunc(enoise(65535)))
159	bb = abs(trunc(enoise(65535)))
160
161	// if target window is a graph, and user wants to append, do so
162	DoWindow/B Plot_Manager
163	if(WinType("") == 1)
164	DoAlert 1,"Do you want to append this data to the current graph?"
165	if(V_Flag == 1)
166	AppendToGraph $w1 vs $w0
167	ModifyGraph mode($w1)=3,marker($w1)=19,msize($w1)=2,rgb($w1) =(rr,gg,bb),tickUnit=1
168	ErrorBars/T=0 $w1 Y,wave=($w2,$w2)
169	ModifyGraph tickUnit(left)=1
170	else
171	//new graph
172	Display $w1 vs $w0
173	ModifyGraph log=1,mode($w1)=3,marker($w1)=19,msize($w1)=2,rgb($w1)=(rr,gg,bb),tickUnit=1
174	ModifyGraph grid=1,mirror=2,standoff=0
175	ErrorBars/T=0 $w1 Y,wave=($w2,$w2)
176	ModifyGraph tickUnit(left)=1
177	Label left "I(q)"
178	Label bottom "q (A\\S-1\\M)"
179	Legend
180	endif
181	else
182	// graph window was not target, make new one
183	Display $w1 vs $w0
184	ModifyGraph log=1,mode($w1)=3,marker($w1)=19,msize($w1)=2,rgb($w1)=(rr,gg,bb),tickUnit=1
185	ModifyGraph grid=1,mirror=2,standoff=0
186	ErrorBars/T=0 $w1 Y,wave=($w2,$w2)
187	ModifyGraph tickUnit(left)=1
188	Label left "I(q)"
189	Label bottom "q (A\\S-1\\M)"
190	Legend
191	endif
192	endif
193
194	endfor
195
196
197	else
198	//No multiple SASData sets for this SASEntry
199	SetDataFolder xmlDataFolder
200
201	// print xmlDataFolder
202
203	//if outstr has been specified, we'll find ourselves here....
204	//We should default to using the filename here to make life easier on people who have used the NIST reduction...
205	if (!cmpstr(outstr,""))
206	basestr = ShortFileNameString(CleanupName(getXMLDataSetTitle(xmlDataFolder,0,useFilename=1),0))
207	else
208	basestr = ShortFileNameString(CleanupName(outstr,0))
209	endif
210
211	//String basestr = ParseFilePath(3, ParseFilePath(5,filestr,":",0,0),":",0,0)
212	fileName = ParseFilePath(0,ParseFilePath(5,filestr,":",0,0),":",1,0)
213
214	//print "In NIST XML Loader"
215	//print "fileStr: ",fileStr
216	//print "basestr: ",basestr
217	//print "fileName: ",fileName
218	w0 = basestr + "_q"
219	w1 = basestr + "_i"
220	w2 = basestr + "_s"
221
222	if(DataFolderExists("root:"+baseStr))
223	if(!forceOverwrite)
224	DoAlert 1,"The data set " + basestr + " from file "+fileName+" has already been loaded. Do you want to load the new data file, overwriting the data in memory?"
225	if(V_flag==2) //user selected No, don't load the data
226	SetDataFolder root:
227	if(DataFolderExists("root:Packages:NIST"))
228	String/G root:Packages:NIST:gLastFileName = filename
229	endif //set the last file loaded to the one NOT loaded
230	return 0 //quits the macro
231	endif
232	endif
233	SetDataFolder $("root:"+baseStr)
234	else
235	NewDataFolder/S $("root:"+baseStr)
236	endif
237
238	Duplicate/O $(xmlDataFolder+"Qsas") $w0
239	Duplicate/O $(xmlDataFolder+"Isas") $w1
240	Duplicate/O $(xmlDataFolder+"Idev") $w2
241
242
243
244	if (exists(xmlDataFolder+"Qdev"))
245	Wave Qsas = $(xmlDataFolder+"Qsas")
246	Wave Qdev = $(xmlDataFolder+"Qdev")
247
248	// make a resolution matrix for SANS data
249	np=numpnts($w0)
250	Make/D/O/N=(np,4) $(baseStr+"_res")
251	Wave reswave = $(baseStr+"_res")
252
253	reswave[][0] = Qdev[p] //sigQ
254	reswave[][3] = Qsas[p] //Qvalues
255	if(exists(xmlDataFolder+"Qmean"))
256	Wave Qmean = $(xmlDataFolder+"Qmean")
257	reswave[][1] = Qmean[p] //qBar
258	endif
259	if(exists(xmlDataFolder+"Shadowfactor"))
260	Wave Shadowfactor = $(xmlDataFolder+"Shadowfactor")
261	reswave[][2] = Shadowfactor[p] //fShad
262	endif
263	elseif(exists(xmlDataFolder+"dQl"))
264	//USAS Data
265	Wave dQl = $(xmlDataFolder+"dQl")
266	dQv = - dQl[0] //make it positive again
267
268	USANS_CalcWeights(baseStr,dQv)
269	else
270	//No resolution data
271	endif
272	//get rid of the resolution waves that are in the matrix
273
274	SetScale d,0,0,"1/A",$w0
275	SetScale d,0,0,"1/cm",$w1
276
277
278
279	//////
280	if(DataFolderExists("root:Packages:NIST"))
281	String/G root:Packages:NIST:gLastFileName = filename
282	endif
283
284
285	//plot if desired
286	if(doPlot)
287	// assign colors randomly
288	rr = abs(trunc(enoise(65535)))
289	gg = abs(trunc(enoise(65535)))
290	bb = abs(trunc(enoise(65535)))
291
292	// if target window is a graph, and user wants to append, do so
293	DoWindow/B Plot_Manager
294	if(WinType("") == 1)
295	DoAlert 1,"Do you want to append this data to the current graph?"
296	if(V_Flag == 1)
297	AppendToGraph $w1 vs $w0
298	ModifyGraph mode($w1)=3,marker($w1)=19,msize($w1)=2,rgb($w1) =(rr,gg,bb),tickUnit=1
299	ErrorBars/T=0 $w1 Y,wave=($w2,$w2)
300	ModifyGraph tickUnit(left)=1
301	else
302	//new graph
303	Display $w1 vs $w0
304	ModifyGraph log=1,mode($w1)=3,marker($w1)=19,msize($w1)=2,rgb($w1)=(rr,gg,bb),tickUnit=1
305	ModifyGraph grid=1,mirror=2,standoff=0
306	ErrorBars/T=0 $w1 Y,wave=($w2,$w2)
307	ModifyGraph tickUnit(left)=1
308	Label left "I(q)"
309	Label bottom "q (A\\S-1\\M)"
310	Legend
311	endif
312	else
313	// graph window was not target, make new one
314	Display $w1 vs $w0
315	ModifyGraph log=1,mode($w1)=3,marker($w1)=19,msize($w1)=2,rgb($w1)=(rr,gg,bb),tickUnit=1
316	ModifyGraph grid=1,mirror=2,standoff=0
317	ErrorBars/T=0 $w1 Y,wave=($w2,$w2)
318	ModifyGraph tickUnit(left)=1
319	Label left "I(q)"
320	Label bottom "q (A\\S-1\\M)"
321	Legend
322	endif
323	endif
324
325	endif
326	endfor
327	endif
328
329	//go back to the root folder and clean up before leaving
330	SetDataFolder root:
331	//KillDataFolder xmlReaderFolder
332
333
334	end
335
336
337	function/S getXMLDataSetTitle(xmlDF,dsNum,[useFilename])
338	String xmlDF
339	Variable dsNum
340	Variable useFilename
341
342	SVAR title = root:Packages:NIST:gXMLLoader_Title
343
344	String mdstring = xmlDF+"metadata"
345	String filename
346
347	Wave/T meta = $mdstring
348
349	//Get filename to use if useFilename is specified or as a fall back if title is missing.
350	FindValue/TEXT="xmlFile"/TXOP=4/Z meta
351	filename = ParseFilePath(0,TrimWS(meta[V_Value][1]),":",1,0)
352
353	if (useFilename)
354	return filename
355	endif
356
357	//Check for value when there are multiple datasets
358	//Note that the use of FindValue here assumes that the tag is in column 0 so that V_Value
359	//represents the row number
360	//This will almost certainly break if your title was "Title" or "Run"
361	FindValue/TEXT="Title"/TXOP=4/Z meta
362	if (V_Value >= 0)
363	//This should always be true as title is required in canSAS XML format
364	title = TrimWS(meta[V_Value][1])
365	else
366	title = filename
367	endif
368	//Check for Run value
369	//If you get a run value, put it at the start of the string so it isn't lost if there is truncation
370	//One hopes that the run number will be unique...
371	FindValue/TEXT="Run_"+num2str(dsNum)/TXOP=4/Z meta
372	if (V_Value >= 0)
373	title = TrimWS(meta[V_Value][1])+" "+title
374	//print title
375	else
376	FindValue/TEXT="Run"/TXOP=4/Z meta
377	if (V_Value >= 0)
378	title = TrimWS(meta[V_Value][1])+" "+title
379	//print title
380	endif
381	endif
382
383	return title
384	end
385
386
387	//AJJ 12/5/08
388
389	//Define struct for file contents
390	Structure NISTXMLfile
391	// string filename
392	string Run
393	string title
394
395	//<SASdata>
396	Wave Q,I,Idev,Qdev,Qmean,Shadowfactor,dQl
397	string unitsQ,unitsI,unitsIdev,unitsQdev,unitsQmean,unitsShadowfactor,unitsdQl
398
399	// Variable flux_monitor
400	// string Q_resolution
401
402	//<SASsample>
403	string sample_ID
404	variable sample_thickness
405	string unitssample_thickness
406	variable sample_transmission
407
408	//SASinstrument
409	string nameSASinstrument
410	// SASinstrument/SASsource
411	string radiation
412	// string beam_shape
413	variable wavelength
414	string unitswavelength
415	variable wavelength_spread
416	string unitswavelength_spread
417
418	//<SAScollimation>
419	// variable collimation_length
420	// string unitscollimation_length
421	variable source_aperture
422	string unitssource_aperture
423	string typesource_aperture
424	variable sample_aperture
425	string unitssample_aperture
426	string typesample_aperture
427
428	//SASdetector <SASdetector>
429	string detector_name
430	variable offset_angle
431	string unitsoffset_angle
432	variable SDD
433	string unitsSDD
434	variable beamcenter_X
435	string unitsbeamcenter_X
436	variable beamcenter_Y
437	string unitsbeamcenter_Y
438	// variable pixel_sizeX
439	// string unitspixel_sizeX
440	// variable pixel_sizeY
441	// string unitspixel_sizeY
442	// string detectortype
443
444	// <SASprocess name="NCNR-IGOR">
445	string nameSASprocess
446	string SASprocessnote
447	// string SASprocessdate
448	// string average_type
449	// string SAM_file
450	// string BKD_file
451	// string EMP_file
452	// string DIV_file
453	// string MASK_file
454	// string ABS_parameters
455	// variable TSTAND
456	// variable DSTAND
457	// string unitsDSTAND
458	// variable IZERO
459	// variable XSECT
460	// string unitsXSECT
461	string SASnote
462	Endstructure
463
464
465	//Function to write NIST canSAS XML files
466	//Minimalist XML file - AJJ Dec 2008
467	function writeNISTXML(fileName, NISTfile)
468	String fileName
469	Struct NISTXMLfile &NISTfile
470
471	variable fileID
472
473	//create the sasXML file with SASroot
474	//no namespace, no prefix
475	fileID = xmlcreatefile(fileName,"SASroot","cansas1d/1.0","")
476
477	//create a version attribute for the root element
478	xmlsetAttr(fileID,"/SASroot","","version","1.0")
479	xmlsetAttr(fileID,"/SASroot","","xmlns:xsi","http://www.w3.org/2001/XMLSchema-instance")
480	xmlsetAttr(fileID,"/SASroot","","xsi:schemaLocation","cansas1d/1.0 http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd")
481
482
483	//create the SASentry node
484	xmladdnode(fileID,"/SASroot","","SASentry","",1)
485
486	//create the Title node
487	xmladdnode(fileID,"/SASroot/SASentry","","Title",NISTfile.Title,1)
488
489	//create the Run node
490	xmladdnode(fileID,"/SASroot/SASentry","","Run",NISTfile.Run,1)
491
492	//create the SASdata node
493	xmladdnode(fileID,"/SASroot/SASentry","","SASdata","",1)
494
495	variable ii
496
497	if (WaveExists(NISTfile.dQl) == 1)
498	for(ii=0 ; ii<numpnts(NISTfile.Q) ; ii+=1)
499	xmladdnode(fileID,"/SASroot/SASentry/SASdata","","Idata","",1)
500	xmladdnode(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]","","Q",num2str(NISTfile.Q[ii]),1)
501	xmlsetAttr(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]/Q","","unit",NISTfile.unitsQ)
502
503	xmladdnode(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]","","I",num2str(NISTfile.I[ii]),1)
504	xmlsetAttr(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]/I","","unit",NISTfile.unitsI)
505
506	xmladdnode(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]","","Idev",num2str(NISTfile.Idev[ii]),1)
507	xmlsetAttr(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]/Idev","","unit",NISTfile.unitsIdev)
508
509	xmladdnode(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]","","dQl",num2str(NISTfile.dQl[ii]),1)
510	xmlsetAttr(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]/dQl","","unit",NISTfile.unitsdQl)
511	endfor
512	else
513	for(ii=0 ; ii<numpnts(NISTfile.Q) ; ii+=1)
514	xmladdnode(fileID,"/SASroot/SASentry/SASdata","","Idata","",1)
515	xmladdnode(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]","","Q",num2str(NISTfile.Q[ii]),1)
516	xmlsetAttr(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]/Q","","unit",NISTfile.unitsQ)
517
518	xmladdnode(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]","","I",num2str(NISTfile.I[ii]),1)
519	xmlsetAttr(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]/I","","unit",NISTfile.unitsI)
520
521	xmladdnode(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]","","Idev",num2str(NISTfile.Idev[ii]),1)
522	xmlsetAttr(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]/Idev","","unit",NISTfile.unitsIdev)
523
524	xmladdnode(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]","","Qdev",num2str(NISTfile.Qdev[ii]),1)
525	xmlsetAttr(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]/Qdev","","unit",NISTfile.unitsQdev)
526
527	xmladdnode(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]","","Qmean",num2str(NISTfile.Qmean[ii]),1)
528	xmlsetAttr(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]/Qmean","","unit",NISTfile.unitsQmean)
529
530	xmladdnode(fileID,"/SASroot/SASentry/SASdata/Idata["+num2istr(ii+1)+"]","","Shadowfactor",num2str(NISTfile.shadowfactor[ii]),1)
531	endfor
532	endif
533
534	//SASsample node
535	xmladdnode(fileID,"/SASroot/SASentry","","SASsample","",1)
536	xmladdnode(fileID,"/SASroot/SASentry/SASsample","","ID",NISTfile.sample_ID,1)
537
538	//SASInstrument node
539	xmladdnode(fileID,"/SASroot/SASentry","","SASinstrument","",1)
540	xmladdnode(fileID,"/SASroot/SASentry/SASinstrument","","name",NISTfile.nameSASinstrument,1)
541
542	//SASsource
543	xmladdnode(fileID,"/SASroot/SASentry/SASinstrument","","SASsource","",1)
544	xmladdnode(fileID,"/SASroot/SASentry/SASinstrument/SASsource","","radiation",NISTfile.radiation,1)
545
546	//SAScollimation
547	xmladdnode(fileID,"/SASroot/SASentry/SASinstrument","","SAScollimation","",1)
548
549	//SASdetector
550	xmladdnode(fileID,"/SASroot/SASentry/SASinstrument","","SASdetector","",1)
551	xmladdnode(fileID,"/SASroot/SASentry/SASinstrument/SASdetector","","name",NISTfile.detector_name,1)
552
553
554	//SASprocess
555	xmladdnode(fileID,"/SASroot/SASentry","","SASprocess","",1)
556	xmlsetAttr(fileID,"/SASroot/SASentry/SASprocess","","name",NISTfile.nameSASprocess)
557	xmladdnode(fileID,"/SASroot/SASentry/SASprocess","","SASprocessnote",NISTfile.SASprocessnote,1)
558
559	//SASnote
560	xmladdnode(fileID,"/SASroot/SASentry","","SASnote",NISTfile.SASnote,1)
561
562	xmlsavefile(fileID)
563	xmlclosefile(fileID,0)
564
565	end
566
567	Function convertNISTtoNISTXML(fileStr)
568	String fileStr
569
570	Struct NISTXMLfile nf
571
572	Variable rr,gg,bb,refnum,dQv
573	SetDataFolder root:
574
575	if (cmpStr(fileStr,"") == 0)
576	//No filename given, open dialog
577	Open/D/R refnum
578	if (cmpstr(S_filename,"") == 0)
579	return 0
580	else
581	fileStr = S_filename
582	endif
583	endif
584
585	//Load the waves, using default waveX names
586	//if no path or file is specified for LoadWave, the default Mac open dialog will appear
587	LoadWave/G/D/A/Q fileStr
588	String fileNamePath = S_Path+S_fileName
589	String basestr = CleanupName(ParseFilePath(3,ParseFilePath(5,fileNamePath,":",0,0),":",0,0),0)
590	// String baseStr = CleanupName(S_fileName,0)
591	// print "basestr :"+basestr
592	String fileName = ParseFilePath(0,ParseFilePath(5,filestr,":",0,0),":",1,0)
593	// print "filename :"+filename
594	Variable numCols = V_flag
595	String outfileName = S_Path+basestr+".xml"
596
597
598	if(numCols==3) //simple 3-column data with no resolution information
599
600	Wave nf.Q = $(StringFromList(0, S_waveNames ,";" ))
601	Wave nf.I = $(StringFromList(1, S_waveNames ,";" ))
602	Wave nf.Idev = $(StringFromList(2, S_waveNames ,";" ))
603
604	//Set units
605	nf.unitsQ = "1/A"
606	nf.unitsI = "1/cm"
607	nf.unitsIdev = "1/cm"
608
609	endif //3-col data
610
611	if(numCols == 6) //6-column SANS or USANS data that has resolution information
612
613	// put the names of the (default named) loaded waves into local names
614	Wave nf.Q = $(StringFromList(0, S_waveNames ,";" ))
615	Wave nf.I = $(StringFromList(1, S_waveNames ,";" ))
616	Wave nf.Idev = $(StringFromList(2, S_waveNames ,";" ))
617
618	//Set units
619	nf.unitsQ = "1/A"
620	nf.unitsI = "1/cm"
621	nf.unitsIdev = "1/cm"
622
623	WAVE resTest = $(StringFromList(3, S_waveNames ,";" ))
624
625	// need to switch based on SANS/USANS
626	if (isSANSResolution(resTest[0])) //checks to see if the first point of the wave is <0]
627	Wave nf.Qdev = $(StringFromList(3, S_waveNames ,";" ))
628	Wave nf.Qmean = $(StringFromList(4, S_waveNames ,";" ))
629	Wave nf.Shadowfactor = $(StringFromList(5, S_waveNames ,";" ))
630
631	//Set units
632	nf.unitsQdev = "1/A"
633	nf.unitsQmean = "1/A"
634	else
635	Wave nf.dQl = $(StringFromList(3, S_waveNames ,";" ))
636
637	//Set units
638	nf.unitsdQl = "1/A"
639
640	endif
641
642	//Tidy up
643	Variable i = 0
644	do
645	WAVE/Z wv= $(StringFromList(i,S_waveNames,";"))
646	if( WaveExists(wv) == 0 )
647	break
648	endif
649	KillWaves wv
650	i += 1
651	while (1) // exit is via break statement
652
653
654	endif //6-col data
655
656	//Get file header
657	setmetadataFromASCHeader(fileStr,nf)
658
659	//Set required metadata that we can't get from these files
660	nf.detector_name = "Ordela 128x128"
661	nf.nameSASinstrument = "NIST NG3/NG7 SANS"
662	nf.radiation = "neutron"
663	nf.sample_ID = nf.title
664	nf.nameSASProcess = "NIST Data Converter"
665	nf.sasnote = "Data converted from previous NIST format. SASProcessnote contains header from original text file."
666
667	writeNISTXML(outfileName, nf)
668
669	end
670
671	function setmetadataFromASCHeader(fileStr,NISTfile)
672	String fileStr
673	Struct NISTXMLfile &NISTfile
674
675	String hdr="",buffer=""
676	Variable lineNum = 0, fileref
677	Variable num
678
679	Open/R fileref as fileStr
680	do
681	FReadLine fileref, buffer
682	if (stringmatch(buffer,"The 6 columns are") == 1)
683	break
684	endif
685	buffer = RemoveEnding(buffer)
686	// print buffer
687	//Get run value
688	if (stringmatch(buffer,"file:") == 1)
689	NISTfile.run = TrimWS(StringFromList(0,StringFromList(1, buffer, ":"),"C"))
690	elseif (stringmatch(buffer,"combined file*") == 1)
691	NISTfile.run = "Combined Data"
692	endif
693
694	//Get title value
695	if (stringmatch(buffer,"FIRST File LABEL:") == 1)
696	NISTfile.title = TrimWS(StringFromList(1,buffer, ":"))
697	elseif(stringmatch(buffer,"LABEL:") == 1)
698	NISTfile.title = TrimWS(StringFromList(1,buffer, ":"))
699	endif
700
701	hdr += buffer+"\n"
702	while(strlen(buffer) > 0)
703
704	if (strlen(NISTfile.title) == 0)
705	NISTfile.title = CleanupName(ParseFilePath(3,ParseFilePath(5,fileStr,":",0,0),":",0,0),0)
706	endif
707	if (strlen(NISTfile.run) == 0)
708	NISTfile.run = "Unknown"
709	endif
710
711	NISTfile.sasprocessnote = RemoveEnding(hdr)
712
713	end
714
715	//for writing out data (q-i-s) from the "type" folder, and including reduction information
716	//if fullpath is a complete HD path:filename, no dialog will be presented
717	//if fullpath is just a filename, the save dialog will be presented
718	//if dialog = 1, a dialog will always be presented
719	//
720	// root:myGlobals:Protocols:gProtoStr is the name of the currently active protocol
721	//
722	//AJJ Nov 2009 : This version of the function currently only works for Circular, Sector and Rectangular averages
723	//i.e. anything that produces I vs Q. Need to add ability to handle Annular (I vs theta) but that requires namespace addition to XML format
724	//and handling on load.
725	Function WriteXMLWaves_W_Protocol(type,fullpath,dialog)
726	String type,fullpath
727	Variable dialog //=1 will present dialog for name
728
729	Struct NISTXMLfile nf
730
731	String destStr=""
732	destStr = "root:Packages:NIST:"+type
733
734	Variable refNum
735	// String fname,ave="C",hdrStr1="",hdrStr2=""
736	// Variable step=1
737
738	//***these waves MUST EXIST, or IGOR Pro will crash, with a type 2 error**
739	WAVE intw=$(destStr + ":integersRead")
740	WAVE rw=$(destStr + ":realsRead")
741	WAVE/T textw=$(destStr + ":textRead")
742	WAVE qvals =$(destStr + ":qval")
743	WAVE inten=$(destStr + ":aveint")
744	WAVE sig=$(destStr + ":sigave")
745	WAVE qbar = $(destStr + ":QBar")
746	WAVE sigmaq = $(destStr + ":SigmaQ")
747	WAVE fsubs = $(destStr + ":fSubS")
748
749
750	SVAR gProtoStr = root:myGlobals:Protocols:gProtoStr
751	Wave/T proto=$("root:myGlobals:Protocols:"+gProtoStr)
752
753
754	//check each wave
755	If(!(WaveExists(intw)))
756	Abort "intw DNExist BinaryWrite_W_Protocol()"
757	Endif
758	If(!(WaveExists(rw)))
759	Abort "rw DNExist BinaryWrite_W_Protocol()"
760	Endif
761	If(!(WaveExists(textw)))
762	Abort "textw DNExist BinaryWrite_W_Protocol()"
763	Endif
764	If(!(WaveExists(qvals)))
765	Abort "qvals DNExist BinaryWrite_W_Protocol()"
766	Endif
767	If(!(WaveExists(inten)))
768	Abort "inten DNExist BinaryWrite_W_Protocol()"
769	Endif
770	If(!(WaveExists(sig)))
771	Abort "sig DNExist BinaryWrite_W_Protocol()"
772	Endif
773	If(!(WaveExists(qbar)))
774	Abort "qbar DNExist BinaryWrite_W_Protocol()"
775	Endif
776	If(!(WaveExists(sigmaq)))
777	Abort "sigmaq DNExist BinaryWrite_W_Protocol()"
778	Endif
779	If(!(WaveExists(fsubs)))
780	Abort "fsubs DNExist BinaryWrite_W_Protocol()"
781	Endif
782	If(!(WaveExists(proto)))
783	Abort "current protocol wave DNExist BinaryWrite_W_Protocol()"
784	Endif
785
786	if(dialog)
787	PathInfo/S catPathName
788	fullPath = DoSaveFileDialog("Save data as")
789	If(cmpstr(fullPath,"")==0)
790	//user cancel, don't write out a file
791	Close/A
792	Abort "no data file was written"
793	Endif
794	//Print "dialog fullpath = ",fullpath
795	Endif
796
797	SVAR samFiles = $("root:Packages:NIST:"+type+":fileList")
798	//actually open the file here
799	//Open refNum as fullpath
800
801	//Data
802	Wave nf.Q = qvals
803	nf.unitsQ = "1/A"
804	Wave nf.I = inten
805	nf.unitsI = "1/cm"
806	Wave nf.Idev = sig
807	nf.unitsIdev = "1/cm"
808	Wave nf.Qdev = sigmaq
809	nf.unitsQdev = "1/A"
810	Wave nf.Qmean = qbar
811	nf.unitsQmean = "1/A"
812	Wave nf.Shadowfactor = fSubS
813	nf.unitsShadowfactor = "none"
814
815
816	//write out the standard header information
817	//fprintf refnum,"FILE: %s\t\t CREATED: %s\r\n",textw[0],textw[1]
818
819	//AJJ to fix with sensible values
820	nf.run = "Test"
821	String acct = textw[3]
822	nf.nameSASinstrument = acct[1,3]
823	nf.SASnote = ""
824	//
825	nf.sample_ID = textw[6]
826	nf.title = textw[6]
827	nf.radiation = "neutron"
828	nf.wavelength = rw[26]
829	nf.unitswavelength = "A"
830	nf.offset_angle = rw[19]
831	nf.unitsoffset_angle = "cm"
832	nf.SDD = rw[18]
833	nf.unitsSDD = "m"
834	nf.sample_transmission = rw[4]
835	nf.sample_thickness = rw[5]
836	nf.unitssample_thickness = "mm"
837
838	nf.beamcenter_X = rw[16]
839	nf.beamcenter_Y = rw[17]
840	nf.unitsbeamcenter_X = "pixels"
841	nf.unitsbeamcenter_Y = "pixels"
842	nf.source_aperture = rw[23]
843	nf.typesource_aperture = "pinhole"
844	nf.unitssource_aperture = "mm"
845	nf.sample_aperture = rw[24]
846	nf.typesample_aperture = "pinhole"
847	nf.unitssample_aperture = "mm"
848	//nf.collimation_length = total length - rw[25]
849	nf.wavelength_spread = rw[27]
850	nf.unitswavelength_spread = "percent"
851	//Do something with beamstop (rw[21])
852	nf.detector_name = textW[9]
853	// fprintf refnum,"MON CNT LAMBDA DET ANG DET DIST TRANS THICK AVE STEP\r\n"
854	// fprintf refnum,hdrStr1
855
856	// fprintf refnum,"BCENT(X,Y) A1(mm) A2(mm) A1A2DIST(m) DL/L BSTOP(mm) DET_TYP \r\n"
857	// fprintf refnum,hdrStr2
858
859	//insert protocol information here
860	//-1 list of sample files
861	//0 - bkg
862	//1 - emp
863	//2 - div
864	//3 - mask
865	//4 - abs params c2-c5
866	//5 - average params
867	nf.SASprocessnote = "SAM: "+samFiles+"\n"
868	nf.SASprocessnote += "BGD: "+proto[0]+"\n"
869	nf.SASprocessnote += "EMP: "+Proto[1]+"\n"
870	nf.SASprocessnote += "DIV: "+Proto[2]+"\n"
871	nf.SASprocessnote += "MASK: "+Proto[3]+"\n"
872	nf.SASprocessnote += "ABS Parameters (3-6): "+Proto[4]+"\n"
873	nf.SASprocessnote += "Average Choices: "+Proto[5]+"\n"
874
875	nf.nameSASProcess = "NIST IGOR"
876
877	//Close refnum
878
879	writeNISTXML(fullpath, nf)
880
881	SetDataFolder root: //(redundant)
882
883	//write confirmation of write operation to history area
884	Print "Averaged XML File written: ", GetFileNameFromPathNoSemi(fullPath)
885	KillWaves/Z tempShortProto
886	Return(0)
887	End
888
889	Function WriteNSORTedXMLFile(qw,iw,sw,firstFileName,secondFileName,thirdFileName,normTo,norm12,norm23,[res])
890	Wave qw,iw,sw,res
891	String firstFileName,secondFileName,thirdFileName,normTo
892	Variable norm12,norm23
893
894	Variable err=0,refNum,numCols,dialog=1
895	String fullPath="",formatStr="",str2
896	//check each wave - else REALLY FATAL error when writing file
897	If(!(WaveExists(qw)))
898	err = 1
899	return err
900	Endif
901	If(!(WaveExists(iw)))
902	err = 1
903	return err
904	Endif
905	If(!(WaveExists(sw)))
906	err = 1
907	return err
908	Endif
909
910	if(WaveExists(res))
911	numCols = 6
912	else
913	numCols = 3
914	endif
915
916	// 05SEP05 SRK -- added to automatically combine files from a table - see the end of NSORT.ipf for details
917	// - use the flag set in DoCombineFiles() to decide if the table entries should be used
918	//Ê Êroot:myGlobals:CombineTable:useTable= (1) (0)
919	//if(exists("root:myGlobals:CombineTable:SaveName"))
920	NVAR/Z useTable = root:myGlobals:CombineTable:useTable
921	if(NVAR_Exists(useTable) && useTable==1)
922	SVAR str=root:myGlobals:CombineTable:SaveNameStr //messy, but pass in as a global
923	fullPath = str
924	// str2 = "Is the file name "+str+" correct?"
925	// DoAlert 1,str2
926	// if(V_flag==1)
927	dialog=0 //bypass the dialog if the name is good (assumed, since DoAlert is bypassed)
928	// endif
929	endif
930
931	if(dialog)
932	PathInfo/S catPathName
933	fullPath = DoSaveFileDialog("Save XML data as",fname="",suffix=".ABSx") //won't actually open the file
934	If(cmpstr(fullPath,"")==0)
935	//user cancel, don't write out a file
936	Close/A
937	Abort "no data file was written"
938	Endif
939	//Print "dialog fullpath = ",fullpath
940	Endif
941
942	Struct NISTxmlfile nf
943
944	//Data
945	Wave nf.Q = qw
946	nf.unitsQ = "1/A"
947	Wave nf.I = iw
948	nf.unitsI = "1/cm"
949	Wave nf.Idev = sw
950	nf.unitsIdev = "1/cm"
951
952	//write out the standard header information
953	//fprintf refnum,"FILE: %s\t\t CREATED: %s\r\n",textw[0],textw[1]
954
955	//AJJ to fix with sensible values
956	nf.run = ""
957	nf.nameSASinstrument = "NIST IGOR"
958	nf.SASnote = ""
959	//
960	nf.sample_ID = ParseFilePath(3, fullPath, ":", 0, 0)
961	nf.title = ParseFilePath(3, fullPath, ":", 0, 0)
962	nf.radiation = "neutron"
963	//Do something with beamstop (rw[21])
964	nf.detector_name = "NSORTed Data"
965	nf.nameSASProcess = "NIST IGOR"
966
967	nf.sasProcessNote = "COMBINED FILE CREATED: "+date()+"\n"
968	nf.sasProcessNote += "NSORT-ed : " +firstFileName+";"+secondFileName+";"+thirdFileName+"\n"
969	nf.sasProcessNote += "normalized to "+normTo+"\n"
970	fprintf refNum, "multiplicative factor 1-2 = "+num2str(norm12)+" multiplicative factor 2-3 = "+num2str(norm23)+"\n"
971
972	if (numCols == 3)
973	writeNISTXML(fullpath,nf)
974	elseif (numCols == 6)
975	Make/O/N=(dimsize(res,0)) sigq = res[p][0]
976	Make/O/N=(dimsize(res,0)) qbar = res[p][1]
977	Make/O/N=(dimsize(res,0)) fs = res[p][2]
978
979	Wave nf.Qdev = sigQ
980	nf.unitsQdev = "1/A"
981	Wave nf.Qmean = qbar
982	nf.unitsQmean = "1/A"
983	Wave nf.Shadowfactor = fs
984	nf.unitsShadowfactor = "none"
985
986	writeNISTXML(fullpath,nf)
987
988	Killwaves/Z sigq,qbar,fs
989	endif
990
991	Return err
992	End
993
994
995
996	/// See WriteModelData_v40.ipf for 6 column equivalent
997	//
998	// this only handles 6-column data, will abort if resolution wave is missing
999	//
1000	Function ReWrite1DXMLData(folderStr)
1001	String folderStr
1002
1003	String fullpath=""
1004	Variable dialog=1
1005	String dataSetFolderParent,basestr,fullBase
1006
1007	Struct NISTXMLfile nf
1008
1009	//Abuse ParseFilePath to get path without folder name
1010	dataSetFolderParent = ParseFilePath(1,folderStr,":",1,0)
1011	//Abuse ParseFilePath to get basestr
1012	basestr = ParseFilePath(0,folderStr,":",1,0)
1013
1014	SetDataFolder $(dataSetFolderParent+basestr)
1015	WAVE/Z qw = $(baseStr+"_q")
1016	WAVE/Z iw = $(baseStr+"_i")
1017	WAVE/Z sw = $(baseStr+"_s")
1018	WAVE/Z resw = $(baseStr+"_res")
1019
1020	if(WaveExists(qw) == 0)
1021	Abort "q is missing"
1022	endif
1023	if(WaveExists(iw) == 0)
1024	Abort "i is missing"
1025	endif
1026	if(WaveExists(sw) == 0)
1027	Abort "s is missing"
1028	endif
1029	if(WaveExists(resw) == 0)
1030	Abort "Resolution information is missing."
1031	endif
1032
1033	Duplicate/O qw qbar,sigQ,fs
1034	sigq = resw[p][0]
1035	qbar = resw[p][1]
1036	fs = resw[p][2]
1037
1038
1039	//Data
1040	Wave nf.Q = qw
1041	nf.unitsQ = "1/A"
1042	Wave nf.I = iw
1043	nf.unitsI = "1/cm"
1044	Wave nf.Idev = sw
1045	nf.unitsIdev = "1/cm"
1046	Wave nf.Qdev = sigQ
1047	nf.unitsQdev = "1/A"
1048	Wave nf.Qmean = qbar
1049	nf.unitsQmean = "1/A"
1050	Wave nf.Shadowfactor = fs
1051	nf.unitsShadowfactor = "none"
1052
1053
1054	//write out the standard header information
1055	//fprintf refnum,"FILE: %s\t\t CREATED: %s\r\n",textw[0],textw[1]
1056
1057	//AJJ to fix with sensible values
1058	nf.run = ""
1059	nf.nameSASinstrument = "NIST IGOR Procedures"
1060	nf.SASnote = ""
1061	//
1062	nf.sample_ID = baseStr
1063	nf.title = baseStr
1064	nf.radiation = "neutron"
1065	//Do something with beamstop (rw[21])
1066	nf.detector_name = "Re-written data"
1067
1068	nf.SASprocessnote = "Modified data written from folder "+baseStr+" on "+(date()+" "+time())
1069
1070	nf.nameSASProcess = "NIST IGOR"
1071
1072	//Close refnum
1073
1074	if(dialog)
1075	PathInfo/S catPathName
1076	fullPath = DoSaveFileDialog("Save data as",fname=baseStr+".xml")
1077	If(cmpstr(fullPath,"")==0)
1078	//user cancel, don't write out a file
1079	Close/A
1080	Abort "no data file was written"
1081	Endif
1082	//Print "dialog fullpath = ",fullpath
1083	Endif
1084
1085
1086	writeNISTXML(fullpath,nf)
1087	//write confirmation of write operation to history area
1088	Print "XML File written: ", GetFileNameFromPathNoSemi(fullPath)
1089	KillWaves/Z tempShortProto
1090	Return(0)
1091	End
1092
1093
1094
1095
1096	#else // if( Exists("XmlOpenFile") )
1097	// No XMLutils XOP: provide dummy function so that IgorPro can compile dependent support code
1098	FUNCTION LoadNISTXMLData(fileName,doPlot)
1099	String fileName
1100	Variable doPlot
1101	Abort "XML function provided by XMLutils XOP is not available, get the XOP from : http://www.igorexchange.com/project/XMLutils (see http://www.smallangles.net/wgwiki/index.php/cansas1d_binding_IgorPro for details)"
1102	RETURN(-6)
1103	END
1104
1105
1106	Function writeNISTXML(fileName, NISTfile)
1107	String fileName, NISTfile
1108	Abort "XML function provided by XMLutils XOP is not available, get the XOP from : http://www.igorexchange.com/project/XMLutils (see http://www.smallangles.net/wgwiki/index.php/cansas1d_binding_IgorPro for details)"
1109	RETURN(-6)
1110	End
1111
1112	Function WriteXMLWaves_W_Protocol(type,fullpath,dialog)
1113	String type,fullpath
1114	Variable dialog //=1 will present dialog for name
1115
1116	Abort "XML function provided by XMLutils XOP is not available, get the XOP from : http://www.igorexchange.com/project/XMLutils (see http://www.smallangles.net/wgwiki/index.php/cansas1d_binding_IgorPro for details)"
1117	return(-6)
1118	end
1119
1120	Function WriteNSORTedXMLFile(q3,i3,sig3,firstFileName,secondFileName,thirdFileName,normTo,norm12,norm23,[res])
1121	Wave q3,i3,sig3,res
1122	String firstFileName,secondFileName,thirdFileName,normTo
1123	Variable norm12,norm23
1124
1125	Abort "XML function provided by XMLutils XOP is not available, get the XOP from : http://www.igorexchange.com/project/XMLutils (see http://www.smallangles.net/wgwiki/index.php/cansas1d_binding_IgorPro for details)"
1126	return(-6)
1127	End
1128
1129	Function ReWrite1DXMLData(folderStr)
1130	String folderStr
1131
1132	Abort "XML function provided by XMLutils XOP is not available, get the XOP from : http://www.igorexchange.com/project/XMLutils (see http://www.smallangles.net/wgwiki/index.php/cansas1d_binding_IgorPro for details)"
1133	return(-6)
1134	end
1135	#endif
1136
1137	// if( Exists("XmlOpenFile")
1138	//Needed to test whether file is XML. The load routine will then either give an error if XMLutils is not present or load the file if it is.
1139	function isXML(filestr)
1140	String filestr
1141
1142	String line
1143	Variable fileref
1144
1145	Open/R fileref as filestr
1146	FReadLine fileref, line
1147	Close fileref
1148
1149	//Hopefully this will distinguish between other formats and the XML
1150	//Previous string match would match normal files that have a .xml file as their progenitor...
1151	return GrepString(line, "(?iU).\<.xml.*")
1152
1153	end

Note: See TracBrowser for help on using the repository browser.

Download in other formats:

Original Format