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QKK_ANSTO_Transmission.ipf @ 986

Last change on this file since 986 was 986, checked in by srkline, 7 years ago

fixing issues with QUOKKA reduction procedures that generate errors in Igor 7

updated the QKK_NSORT file to match the new 4-file NSORT. this was a complete, direct copy of the file as there were no Ansto -specific bits.

File size: 89.3 KB

Line
1	#pragma rtGlobals=1 // Use modern global access method.
2	#pragma version=5.0
3	#pragma IgorVersion=6.0
4
5
6	//*************************
7	// Vers. 1.2 092101
8	//
9	// - procedures for (easier) caluclation of transmissions along with
10	// simultaneous patching of the calculated transmission in designated
11	// raw sans files.
12	// - transmission and empty beam files are linked to the dataset by their "Annn" suffix
13	// only (and their residence in the same data folder)
14	// - unused (analysis) integer values are used to store these run numbers in the sample
15	// file headers so that transmissions can be automatically calculated, once the xy box is set
16	// in the empty beam file.
17	//
18	//***************************
19
20	//main entry procedure for displaying the Trans input panel
21	//also initializes the globals as needed
22	//
23	Proc CalcTrans()
24	DoWindow/F Trans_Panel
25	If(V_flag == 0)
26	InitializeTransPanel()
27	//draw panel
28	Trans_Panel()
29	AutoPositionWindow/M=1/R=Main_Panel Trans_Panel
30	Endif
31	End
32
33	// The BuildFileTables routine will build two tables: one containing the
34	// data from the headers of transmission files in the folder and one
35	// containing the header data from all other SANS data files. They will
36	// each have the first column empty for, in the case of transmission files,
37	// the empty beam file and, in the case of scattering files, the scattering
38	// run file name.
39	Proc BuildFileTables()
40
41	Variable err
42	PathInfo catPathName
43	if(v_flag==0) // PathInfo returns path doesn't exist
44	err = PickPath()//sets the local path to the data (catPathName)
45	if(err)
46	Abort "no path to data was selected, no catalog can be made - use PickPath button"
47	Endif
48	Endif
49
50	CreateTransGlobals()
51	Variable ScatFileTableExists
52	ScatFileTableExists = WinType("ScatterFileTable")
53	//if(v_flag==0)
54	If(!ScatFileTableExists)
55	BuildScatTableWindow()
56	ModifyTable width(Point)=18
57
58	ModifyTable width(root:myGlobals:TransHeaderInfo:S_SDD) = 40
59	ModifyTable width(root:myGlobals:TransHeaderInfo:S_Lambda) = 40
60	ModifyTable width(root:myGlobals:TransHeaderInfo:S_Transmission) = 60
61
62	ModifyTable rgb(root:myGlobals:TransHeaderInfo:S_Filenames) = (0,0,65535)
63	ModifyTable width(root:myGlobals:TransHeaderInfo:S_Filenames) = 105
64	ModifyTable width(root:myGlobals:TransHeaderInfo:T_Filenames) = 105
65	ModifyTable width(root:myGlobals:TransHeaderInfo:EMP_Filenames) = 105
66
67	ModifyTable width(root:myGlobals:TransHeaderInfo:S_Labels) = 140
68	ModifyTable width(root:myGlobals:TransHeaderInfo:T_Labels) = 140
69	Endif
70
71	DoWindow/F ScatterFileTable //bring window to front
72
73	//open xml file
74	variable fileID = getReport()
75	if(fileID<=1)
76	Abort "Cannot open experimental report file " + S_filename
77	endif
78
79	//currently have 2 function to read the 2 types of report files, with and without sample environment
80	//trying to merge into 1.
81
82	//getFileAssociations(fileID)
83	getFileAssociationsSampleEnv(fileID)
84
85	//close xml file without save
86	XMLclosefile(fileID,0)
87
88	//Read data from datafile into globals
89	GetTransHeaderInfoToWave()
90
91	//Sort entries based on date
92	// SortGlobals(0)
93
94	//position the windows nicely
95	// AutoPositionWindow/M=1/R=ScatterFileTable
96	// DoWindow/F Trans_Panel //nha Trans_Panel not required?
97
98	End
99
100	Function getReport()
101	// Open the experiment report file(s) in this path
102	variable refnum
103	Open/D/R /M="Open experiment report file" /T=".xml" refnum
104	if(cmpstr(S_filename,"")==0)
105	Abort "No experimental report file selected"
106	Endif
107	variable fileID = XMLopenFile(S_filename)
108
109	return fileID
110
111	End
112
113	Function getFileAssociations(fileID)
114
115	// nha 22/1/2010 - new xml report structure, from December 2009
116	// incompatible with previous report structure
117	// assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
118
119	variable fileID
120	variable ii,jj
121
122	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
123	Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
124	Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
125	Wave/T xmlContent = $"root:M_xmlcontent"
126	Wave/T xmlContentNodes = $"root:W_xmlcontentnodes"
127
128
129	string prefix = "QKK"
130	string suffix = ".nx.hdf"
131	string full_fname, xpath, xpath_config, xpath_type, xpath_fname, xmlString, list, fname
132	variable nConfig, tSamples, sSamples
133	wave w_fname
134
135	//determine no. of samples
136	xpath = "/report//config" //root node of report
137	XMLWaveFmXpath(fileID,xpath,"","")
138	nConfig = DimSize(xmlContentNodes,0)
139
140	ii=1
141	do
142	xpath_config = "/report/config[" + num2str(ii) + "]" //there may be multiple config per report
143
144	xpath_fname = xpath_config + "/transmission//sample[@type = 'sample']/@runId" //select all sample nodes of type sample and return runId attribute
145	XMLwaveFmXpath(fileID,xpath_fname,"","")
146	tSamples = DimSize(xmlContentNodes,0)
147
148	if(tSamples>=1) //sample exist under the transmission node - probably a more elegant way of get these values into T_Filenames
149	jj=0
150	do
151	full_fname = prefix + xmlcontent[0][jj] + suffix
152	InsertPoints jj,1,T_Filenames
153	if(strlen(xmlcontent[0][jj])<7) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
154	T_Filenames[jj] = ""
155	else
156	T_Filenames[jj] = full_fname
157	endif
158	jj+=1
159	while (jj<tSamples)
160	endif
161
162	xpath_fname = xpath_config + "/scattering//sample[@type = 'sample']/@runId" //select all sample nodes of type sample and return runId attribute
163	XMLwaveFmXpath(fileID,xpath_fname,"","")
164	sSamples = DimSize(xmlContentNodes,0)
165
166	if(sSamples>=1) //sample exist under the scattering node
167	jj=0
168	do
169	full_fname = prefix + xmlcontent[0][jj] + suffix
170	InsertPoints jj,1,S_Filenames
171	if(strlen(xmlcontent[0][jj])<7) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
172	S_Filenames[jj] = ""
173	else
174	S_Filenames[jj] = full_fname
175	endif
176	jj+=1
177	while (jj<sSamples)
178	endif
179
180	if(sSamples!=tSamples)
181	// the experiment model from Dec 2009 should have equal numbers of scattering and trans
182	// sample, according to Tony Lam, although the string may be ""
183	//abort "The number transmissions samples in the report file does not equal the number of scattering files"
184	endif
185
186	// use empty beam for transmission, not empty cell
187	//empty beam transmission
188	xpath_fname = xpath_config + "/emptyBeamTransmissionRunId" //select all sample nodes of type sample and return runId attribute
189	XMLwaveFmXpath(fileID,xpath_fname,"","")
190	if(sSamples>=1) //sample exist under the scattering node
191	jj=0
192	do
193	full_fname = prefix + xmlcontent[0][0] + suffix
194	InsertPoints jj,1,EMP_Filenames
195	if(strlen(xmlcontent[0][0])<7) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
196	EMP_Filenames[jj] = ""
197	else
198	EMP_Filenames[jj] = full_fname
199	endif
200	jj+=1
201	while (jj<sSamples)
202	endif
203	ii+=1
204	while(ii<nConfig+1) //ii is using one-based counting because xml is one-based
205
206	//delete rows with blanks
207	ii=0
208	do
209	if(cmpstr(T_Filenames[ii],"")==0 \|\| cmpstr(S_Filenames[ii],"")==0 \|\| cmpstr(EMP_Filenames[ii],"")==0)
210	print "Row is incomplete and therefore being deleted " + T_Filenames[ii] + " " + S_Filenames[ii] + " " + EMP_Filenames[ii]
211	DeletePoints ii,1,T_Filenames,S_Filenames,EMP_Filenames
212	ii-=1
213	endif
214	ii+=1
215	while (ii<DimSize(S_Filenames,0))
216
217
218	//Check if the files in the report file are available in the path.
219	//
220
221	//Put up a dialog of the number of missing files and their filenames. ABORT or CONTINUE
222	//
223
224	End
225
226	Function/S pickFileInCatPath(fileFilterStr, messageStr)
227
228	string fileFilterStr
229	string messageStr
230
231	variable refNum
232	Open/D/R /F=fileFilterStr /M=messageStr refNum
233
234	variable len = strlen(S_fileName)
235	variable lastSepIndex = strsearch(S_fileName, ":", inf, 1)
236	if (lastSepIndex == -1)
237	return S_fileName
238	else
239	svar defaultPath = root:myGlobals:gCatPathStr
240	string selectedPath
241	variable q = 0
242
243	for (selectedPath = ""; q <= lastSepIndex; q += 1)
244	selectedPath += S_fileName[q]
245	endfor
246
247	if (cmpstr(defaultPath, selectedPath) == 0) // path does match
248
249	string result
250	for (result = ""; q < len; q += 1)
251	result += S_fileName[q]
252	endfor
253	return result
254
255	else // path doesn't match
256	DoAlert 1, "You need to pick a file in the same location as the report file. Would you like to pick another file?"
257
258	if (V_flag == 1) // answer was yes
259	return pickFileInCatPath(fileFilterStr, messageStr)
260	else
261	return ""
262	endif
263	endif
264	endif
265
266	End
267
268	Function getFileAssociationsSampleEnv(fileID)
269
270	// nha 22/1/2010 - new xml report structure, from December 2009
271	// incompatible with previous report structure
272	// assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
273
274	variable fileID
275	variable ii, jj
276	variable kkS, kkSmax, kkT, kkTmax, kkE
277	variable kkToffset
278
279	variable s_pos, t_pos
280
281	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
282	Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
283	Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
284
285	// Wave/T xmlContent = $"root:Packages:NIST:M_xmlcontent"
286	// Wave/T xmlContentNodes = $"root:Packages:NIST:W_xmlcontentnodes" // this location doesn't work. Don't know why. nha ???
287
288	// "root:M_xmlcontent" and "root:W_xmlcontentnodes" is not available until XMLWaveFmXpath has been called the first time! [davidm]
289	//Wave/T xmlContent = $"root:M_xmlcontent" // this has been move to the lines after: XMLWaveFmXpath
290	//Wave/T xmlContentNodes = $"root:W_xmlcontentnodes"
291
292	// "root:M_listXPath" is not available until xmlListXPath(fileID,xpath,"") has been called the first time! [davidm]
293	// Wave/T listXPath = $"root:M_listXPath" // this has been move to the line after: err = xmlListXPath(fileID,xpath,"")
294
295	string prefix = "QKK"
296	string suffix = ".nx.hdf"
297	string full_fname, xpath, xpath_SampleEnv, xpath_config, xpath_type, xpath_fname, xmlString, list, fname
298	variable nSampleEnv, nConfig, tSamples, sSamples
299	variable tSampleNum, sSampleNum, eSampleNum // used to accumulate the number of samples across multiple configs
300	variable noRunIds
301
302	variable hasSampleEnv
303	variable err
304
305	// to disable asking dialogs
306	variable specifyTFile_Enabled = 1 // 0: Disabled; 1: Enabled; 2: Always specify if missing
307	variable specifySFile_Enabled = 1
308	variable specifyEMPFile_Enabled = 1
309
310	//in a report there are 0..n /sampleEnvironment
311	//these have 1..n or 1..2 /config
312	//these have a /transmission /scattering
313	//these have 1..n sample which may or maynot have a runId
314	//config also has 0..1 /emptyCellTransmissionRunId 0..1 /emptyCellScatteringRunId 0..1 /emptyBeamTransmissionRunId
315
316	//determine no. of sampleEnvironment tags
317	hasSampleEnv = 0
318	xpath = "/report//sampleEnvironment" //root node of report - what happens if this xpath doesn't exist ???TEST
319	// xpath = "/report//config" // for test ??? nha
320
321	//check if the file contains the required nodes
322	//xmlelementlist(fileID)
323	err = xmlListXPath(fileID,xpath,"") // this creates a three column text wave, M_listXPath
324
325	Wave/T listXPath = $"root:M_listXPath"
326
327	if (err != 0)
328	abort "Can't read xml file"
329	endif
330
331	if (DimSize(listXPath,0) > 0)
332	hasSampleEnv = 1
333	else
334	xpath = "/report//config"
335	endif
336
337	nSampleEnv = 0
338	if (hasSampleEnv)
339	XMLWaveFmXpath(fileID,xpath,"","")
340
341	Wave/T xmlContentNodes = $"root:W_xmlcontentnodes" // [davidm]
342
343	nSampleEnv = DimSize(xmlContentNodes,0)
344	endif
345	ii=1 //sample environment iterator
346
347	tSampleNum = 0
348	sSampleNum = 0
349	eSampleNum = 0
350
351	do
352	if (hasSampleEnv)
353	xpath_SampleEnv = "/report/sampleEnvironment[" + num2str(ii) + "]" //there may be multiple sampleEnvironment per report
354	else
355	xpath_SampleEnv = "/report"
356	endif
357
358	//determine no. of config tags
359	xpath = xpath_SampleEnv + "//config"
360	XMLWaveFmXpath(fileID,xpath,"","")
361
362	Wave/T xmlContent = $"root:M_xmlcontent" // [davidm]
363	Wave/T xmlContentNodes = $"root:W_xmlcontentnodes"
364
365	nConfig = DimSize(xmlContentNodes,0)
366	jj=1 // config iterator
367
368	do
369	// Execute "ProgressWindow spin"
370	xpath_config = xpath_SampleEnv + "/config[" + num2str(jj) + "]" //there may be multiple config per report
371
372	// get the positions of the s-samples (used to check if report file does not contain all samples)
373	xpath_fname = xpath_config + "/scattering//sample[@type = 'sample']/@position" //select all sample nodes of type sample and return position attribute
374	XMLwaveFmXpath(fileID,xpath_fname,"","")
375	Duplicate /FREE/T xmlcontent, S_Positions
376
377	// get the runIds of the s-sampels
378	xpath_fname = xpath_config + "/scattering//sample[@type = 'sample']/@runId" //select all sample nodes of type sample and return runId attribute
379	XMLwaveFmXpath(fileID,xpath_fname,"","")
380	sSamples = DimSize(xmlContentNodes,0)
381	kkSmax = sSamples - 1
382
383	// if no runIds are specified then xmlcontent is empty
384	noRunIds = DimSize(xmlcontent,0) == 0
385
386	// s-sample exist under the scattering node
387	if (sSamples > 0)
388	for (kkS = 0; kkS <= kkSmax; kkS += 1) // scattering sample iterator
389
390	InsertPoints sSampleNum + kkS, 1, S_Filenames
391
392	if (noRunIds)
393	S_Filenames[sSampleNum + kkS] = ""
394	else
395	full_fname = prefix + xmlcontent[0][kkS] + suffix
396	if (strlen(xmlcontent[0][kkS]) < 7) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
397	S_Filenames[sSampleNum + kkS] = ""
398	else
399	S_Filenames[sSampleNum + kkS] = full_fname
400	endif
401	endif
402
403	endfor
404	endif
405
406	// get the positions of the t-samples (used to check if report file does not contain samples)
407	xpath_fname = xpath_config + "/transmission//sample[@type = 'sample']/@position" //select all sample nodes of type sample and return position attribute
408	XMLwaveFmXpath(fileID,xpath_fname,"","")
409	Duplicate /FREE/T xmlcontent, T_Positions
410
411	// get the runIds of the t-sampels
412	xpath_fname = xpath_config + "/transmission//sample[@type = 'sample']/@runId" //select all sample nodes of type sample and return runId attribute
413	XMLwaveFmXpath(fileID,xpath_fname,"","")
414	tSamples = DimSize(xmlContentNodes,0)
415	kkTmax = tSamples - 1
416
417	// if no runIds are specified then xmlcontent is empty
418	noRunIds = DimSize(xmlcontent,0) == 0
419
420	// we need to know how many t-samples are added (if report file does not contain all t-sampels)
421	kkToffset = 0
422
423	// t-sample exist under the transmission node
424	if (tSamples > 0)
425	for (kkS = 0, kkT = 0; kkT <= kkTmax;) // transmission sample iterator
426
427	// we need to compare the position of the current s- and t-sample
428	if (kkS <= kkSmax)
429	s_pos = str2num(S_Positions[0][kkS])
430	else
431	s_pos = Inf // this means that at least one s-sample is missing
432	endif
433	t_pos = str2num(T_Positions[0][kkT])
434
435	if (s_pos < t_pos) // t-sample is missing
436
437	if (specifyTFile_Enabled)
438	DoAlert 1, "For the S-File \"" + S_Filenames[tSampleNum+kkS] + "\" (position " + S_Positions[0][kkS] + ") no T-File was specified. Would you like to select one now?"
439	else
440	V_flag = 0 // if disabled then answer is always no
441	endif
442
443	// insert new t-sample
444	InsertPoints tSampleNum + kkT + kkToffset, 1, T_Filenames
445	if (V_flag != 1) // answer was no
446	T_Filenames[tSampleNum + kkT + kkToffset] = ""
447
448	if (specifyTFile_Enabled == 1)
449	DoAlert 1, "Would you like to specify any missing T-Files?"
450	if (V_flag != 1) // answer was no
451	specifyTFile_Enabled = 0
452	else
453	specifyTFile_Enabled = 2
454	endif
455	endif
456
457	else
458	T_Filenames[tSampleNum + kkT + kkToffset] = pickFileInCatPath("Hierarchical Data Format (.nx.hdf):.nx.hdf;All Files:.;", "Select the corresponding T-File")
459	endif
460
461	kkToffset += 1
462	kkS += 1
463	tSamples += 1
464
465	else // insert t-sample from report file
466
467	InsertPoints tSampleNum + kkT + kkToffset, 1, T_Filenames
468
469	if (noRunIds)
470	T_Filenames[tSampleNum + kkT + kkToffset] = ""
471	else
472	full_fname = prefix + xmlcontent[0][kkT] + suffix
473	if(strlen(xmlcontent[0][kkT]) < 7) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
474	T_Filenames[tSampleNum + kkT + kkToffset] = ""
475	else
476	T_Filenames[tSampleNum + kkT + kkToffset] = full_fname
477	endif
478	endif
479
480	kkT += 1
481
482	if (s_pos == t_pos)
483	kkS += 1
484	else // s-sample is missing
485
486	if (specifySFile_Enabled)
487	DoAlert 1, "For the T-File \"" + T_Filenames[tSampleNum+kkT] + "\" (position " + T_Positions[0][kkT] + ") no S-File was specified. Would you like to select one now?"
488	else
489	V_flag = 0 // if disabled then answer is always no
490	endif
491
492	// insert new s-sample
493	InsertPoints tSampleNum + kkT + kkToffset, 1, S_Filenames
494	if (V_flag != 1) // answer was no
495	S_Filenames[tSampleNum + kkT + kkToffset] = ""
496
497	if (specifySFile_Enabled == 1)
498	DoAlert 1, "Would you like to specify any missing S-Files?"
499	if (V_flag != 1) // answer was no
500	specifySFile_Enabled = 0
501	else
502	specifySFile_Enabled = 2
503	endif
504	endif
505
506	else
507	S_Filenames[tSampleNum + kkT + kkToffset] = pickFileInCatPath("Hierarchical Data Format (.nx.hdf):.nx.hdf;All Files:.;", "Select the corresponding S-File")
508	endif
509
510	sSamples += 1
511	endif
512	endif
513	endfor
514	endif
515
516	if (sSamples > tSamples) // checks if t-samples are still missing
517	do
518	if (specifyTFile_Enabled)
519	DoAlert 1, "For the S-File \"" + S_Filenames[tSampleNum+kkS] + "\" (position " + S_Positions[0][kkS] + ") no T-File was specified. Would you like to select one now?"
520	else
521	V_flag = 0 // if disabled then answer is always no
522	endif
523
524	// insert new t-sample
525	InsertPoints tSampleNum + kkT + kkToffset, 1, T_Filenames
526	if (V_flag != 1) // answer was no
527
528	T_Filenames[tSampleNum + kkT + kkToffset] = ""
529
530	if (specifyTFile_Enabled == 1)
531	DoAlert 1, "Would you like to specify any missing T-Files?"
532	if (V_flag != 1) // answer was no
533	specifyTFile_Enabled = 0
534	else
535	specifyTFile_Enabled = 2
536	endif
537	endif
538
539	else
540	T_Filenames[tSampleNum + kkT + kkToffset] = pickFileInCatPath("Hierarchical Data Format (.nx.hdf):.nx.hdf;All Files:.;", "Select the corresponding T-File")
541	endif
542
543	kkToffset += 1
544	kkS += 1
545	tSamples += 1
546
547	while (sSamples > tSamples)
548	endif
549
550	tSampleNum += tSamples
551	sSampleNum += sSamples
552
553	// empty beam transmission
554	xpath_fname = xpath_config + "/emptyBeamTransmissionRunId"
555	XMLwaveFmXpath(fileID,xpath_fname,"","")
556
557	if (sSamples>=1) //sample exist under the scattering node
558
559	if (WaveDims(xmlcontent) && (strlen(xmlcontent[0][0]) == 7)) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
560	full_fname = prefix + xmlcontent[0][0] + suffix
561	else
562	kkS = sSampleNum-sSamples
563	string sFilenames = S_Filenames[kkS]
564
565	for (kkS += 1; kkS < sSampleNum; kkS += 1)
566	if (strlen(S_Filenames[kkS]) > 0)
567	sFilenames = sFilenames + ", " + S_Filenames[kkS]
568	endif
569	endfor
570
571	// only ask if sFilenames is not empty
572	full_fname = ""
573	if (strlen(sFilenames) > 0)
574
575	if (specifyEMPFile_Enabled)
576	DoAlert 1, "For the listed S-File(s), no appropriate EMP-File was specified. Would you like to select one now?\n" + sFilenames
577	else
578	V_flag = 0 // if disabled then answer is always no
579	endif
580
581	if (V_flag == 1) // answer was yes
582	full_fname = pickFileInCatPath("Hierarchical Data Format (.nx.hdf):.nx.hdf;All Files:.;", "Select an EMP-File")
583	elseif (specifyEMPFile_Enabled == 1)
584	DoAlert 1, "Would you like to specify any missing EMP-Files?"
585	if (V_flag != 1) // answer was no
586	specifyEMPFile_Enabled = 0
587	else
588	specifyEMPFile_Enabled = 2
589	endif
590	endif
591	endif
592	endif
593
594	kkE = 0
595	do
596	InsertPoints eSampleNum + kkE,1,EMP_Filenames
597	EMP_Filenames[eSampleNum + kkE] = full_fname
598	kkE += 1
599	while (kkE < sSamples)
600
601	eSampleNum += sSamples
602	endif
603
604	jj += 1
605	while(jj<nConfig+1)
606	ii+=1
607	while(ii<nsampleEnv+1) //ii is using one-based counting because xml is one-based
608
609	//delete rows with blanks
610	// ??? testing without removal of blanks. nha.
611	// ii=0
612	// do
613	// if(cmpstr(T_Filenames[ii],"")==0 \|\| cmpstr(S_Filenames[ii],"")==0 \|\| cmpstr(EMP_Filenames[ii],"")==0)
614	// print "Row is incomplete and therefore being deleted " + T_Filenames + " " + S_Filenames + " " + EMP_Filenames
615	// DeletePoints ii,1,T_Filenames,S_Filenames,EMP_Filenames
616	// ii-=1
617	// endif
618	// ii+=1
619	// while (ii<DimSize(S_Filenames,0))
620
621
622	//Check if the files in the report file are available in the path.
623	//
624
625	//Put up a dialog of the number of missing files and their filenames. ABORT or CONTINUE
626	//
627
628	End
629
630	//actually creates the table of scattering files
631	// - the waves must exist
632	//
633	Function BuildScatTableWindow()
634	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
635	Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
636	Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
637	Wave/T S_Labels = $"root:myGlobals:TransHeaderInfo:S_Labels"
638	Wave/T T_Labels = $"root:myGlobals:TransHeaderInfo:T_Labels"
639	Wave S_SDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
640	Wave S_Lambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
641	Wave S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
642	Wave S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
643	Wave T_SDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
644	Wave T_Lambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
645	// Wave T_Transmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
646	// Wave T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
647	Wave EMP_x1= $"root:myGlobals:TransHeaderInfo:EMP_x1"
648	Wave EMP_x2= $"root:myGlobals:TransHeaderInfo:EMP_x2"
649	Wave EMP_y1= $"root:myGlobals:TransHeaderInfo:EMP_y1"
650	Wave EMP_y2= $"root:myGlobals:TransHeaderInfo:EMP_y2"
651
652	Edit/K=1/W=(20,20,520,470) S_Filenames, T_Filenames, EMP_Filenames, S_Labels, T_Labels, S_SDD, T_SDD, S_Lambda, T_Lambda, S_Transmission, S_Whole, EMP_x1, EMP_x2, EMP_y1, EMP_y2 as "ScatteringFiles"
653
654	String name="ScatterFileTable"
655	DoWindow/C $name
656
657	End
658
659
660	//sorts each of the tables by date - does this by using the suffix "Annn"
661	// which is automatically supplied by the VAX (and can't be changed)
662	// - only problem may be "Z999" -> "A001" rollover
663	//
664	// sorts files alphabetically byt the sample label
665	// - consistent and descriptive sample labels really pay off here
666	//
667	Function SortGlobals(sortFlag)
668	Variable sortFlag
669
670	Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
671	Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
672	Wave/T T_Labels = $"root:myGlobals:TransHeaderInfo:T_Labels"
673	Wave T_SDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
674	Wave T_Lambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
675	// Wave T_Transmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
676	// Wave T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
677
678	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
679	Wave/T S_Labels = $"root:myGlobals:TransHeaderInfo:S_Labels"
680	Wave S_SDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
681	Wave S_Lambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
682	Wave S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
683	Wave S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
684
685	Wave EMP_x1= $"root:myGlobals:TransHeaderInfo:EMP_x1"
686	Wave EMP_x2= $"root:myGlobals:TransHeaderInfo:EMP_x2"
687	Wave EMP_y1= $"root:myGlobals:TransHeaderInfo:EMP_y1"
688	Wave EMP_y2= $"root:myGlobals:TransHeaderInfo:EMP_y2"
689
690	if(sortFlag == 0) // by date
691	Sort S_Filenames, S_Filenames, S_Labels, S_SDD, S_Lambda, S_Transmission, S_Whole, EMP_Filenames, T_Filenames, T_Labels, T_SDD, T_Lambda, EMP_x1, EMP_x2, EMP_y1, EMP_y2
692	else //by label
693	Sort S_Labels, S_Labels, S_Filenames, S_SDD, S_Lambda, S_Transmission, S_Whole, EMP_Filenames, T_Filenames, T_Labels, T_SDD, T_Lambda, EMP_x1, EMP_x2, EMP_y1, EMP_y2
694	endif
695	End
696
697	//reads the file and assigns header information to globals, which are read by the ScatteringTable.
698	//assumes that associations have been found in experiment report
699	//
700	//scat_fname - is the full path:name of the datafile (used by Open)
701	//
702	// takes care of all necessary open/close of file
703	//
704	Function GetTransHeaderInfoToWave()
705
706	String s_fname,t_fname,emp_fname
707
708	Variable lastPoint, ii
709
710	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
711	Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
712	Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
713	Wave/T S_Labels = $"root:myGlobals:TransHeaderInfo:S_Labels"
714	Wave/T T_Labels = $"root:myGlobals:TransHeaderInfo:T_Labels"
715	Wave S_SDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
716	Wave S_Lambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
717	Wave S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
718	Wave S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
719	Wave T_SDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
720	Wave T_Lambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
721	// Wave T_Transmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
722	// Wave T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
723
724	Wave EMP_x1= $"root:myGlobals:TransHeaderInfo:EMP_x1"
725	Wave EMP_x2= $"root:myGlobals:TransHeaderInfo:EMP_x2"
726	Wave EMP_y1= $"root:myGlobals:TransHeaderInfo:EMP_y1"
727	Wave EMP_y2= $"root:myGlobals:TransHeaderInfo:EMP_y2"
728
729	lastPoint = numpnts(S_Filenames)
730	PathInfo catPathName
731	variable x1, x2, y1, y2
732
733	variable FilesAreMissing = 0
734
735	// Execute "ProgressWindow open, text=\"Loading Table...\""
736
737	ii = 0
738	do
739	s_fname = S_path + S_Filenames[ii]
740	t_fname = S_path + T_Filenames[ii]
741	emp_fname = S_path + EMP_Filenames[ii]
742
743	// Execute "ProgressWindow text=\"Loading Table...\n" + S_Filenames[ii] + "\""
744
745	InsertPoints ii,1,S_Labels
746	InsertPoints ii,1,S_Transmission
747	InsertPoints ii,1,S_Whole
748	InsertPoints ii,1,S_SDD
749	InsertPoints ii,1,S_Lambda
750	InsertPoints ii,1,T_Labels
751	// InsertPoints ii,1,T_Transmission
752	// InsertPoints ii,1,T_Whole
753	InsertPoints ii,1,T_SDD
754	InsertPoints ii,1,T_Lambda
755	InsertPoints ii,1,EMP_x1
756	InsertPoints ii,1,EMP_x2
757	InsertPoints ii,1,EMP_y1
758	InsertPoints ii,1,EMP_y2
759
760	if (CheckIfFileExists(s_fname))
761	if (CheckIfRawData(s_fname))
762	// read the sample.label text field - OK
763	S_Labels[ii]=getSampleLabel(s_fname)
764
765	//Transmission - OK as long as it has been patched in ???
766	S_Transmission[ii]=getSampleTrans(s_fname)
767
768	//Whole detector Transmission - Don't know where this will be in the file. Need help from epg ???
769	S_Whole[ii]=getSampleTransWholeDetector(s_fname)
770
771	//SDD - OK
772	S_SDD[ii]=getSDD(s_fname)
773
774	//wavelength - OK
775	S_Lambda[ii]=getWavelength(s_fname)
776	endif
777	else
778	S_Filenames[ii] = "? " + S_Filenames[ii]
779	FilesAreMissing = 1
780	endif
781
782	if (CheckIfFileExists(t_fname))
783	if (CheckIfRawData(t_fname))
784	// read the sample.label text field - OK
785	T_Labels[ii]=getSampleLabel(t_fname)
786
787	//Transmission - OK as long as it has been patched in ???
788	//T_Transmission[ii]=getSampleTrans(t_fname)
789
790	//Whole detector Transmission - Don't know where this will be in the file. Need help from epg ???
791	//T_Whole[ii]=getSampleTransWholeDetector(t_fname)
792
793	//SDD - OK
794	T_SDD[ii]=getSDD(t_fname)
795
796	//wavelength - OK
797	T_Lambda[ii]=getWavelength(t_fname)
798	endif
799	else
800	T_Filenames[ii] = "? " + T_Filenames[ii]
801	FilesAreMissing = 1
802	endif
803
804	if (CheckIfFileExists(emp_fname))
805	if (CheckIfRawData(emp_fname))
806	getXYBoxFromFile(emp_fname,x1,x2,y1,y2)
807	EMP_x1[ii] = x1
808	EMP_x2[ii] = x2
809	EMP_y1[ii] = y1
810	EMP_y2[ii] = y2
811	endif
812	else
813	EMP_Filenames[ii] = "? " + EMP_Filenames[ii]
814	FilesAreMissing = 1
815	endif
816
817	ii+=1
818	// Execute "ProgressWindow percent=" + Num2Str(100*ii/lastPoint)
819
820	while(ii<lastPoint)
821
822	// Execute "ProgressWindow close"
823
824	if (FilesAreMissing)
825	DoAlert /T="Warning" 0, "The files marked with \"?\" in the table could not be found.\r\n\r\nSome files listed in the XML-Catalog may be missing."
826	endif
827
828	return(0)
829	End
830
831	//initialize data folder and globals for the Trans panel as needed
832	//since this operation is somewhat tangled with the Patch Panel, keep all of the
833	//globals in the Patch subfolder (make sure both panels are simultaneously initialized)
834	//do not create a separate Trans folder
835	//
836	Proc InitializeTransPanel()
837	//create the global variables needed to run the Trans Panel
838	//all are kept in root:myGlobals:TransHeaderInfo
839	If( ! (DataFolderExists("root:myGlobals:TransHeaderInfo")) )
840	//create the data folder and the clobals for BOTH the Patch and Trans Panels
841	NewDataFolder/O root:myGlobals:TransHeaderInfo
842	CreateTransGlobals()
843	Endif
844	End
845
846
847	//
848	Proc CreateTransGlobals()
849
850	PathInfo catPathName
851	If(V_flag==1)
852	String dum = S_path
853	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = dum
854	else
855	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = "no path selected"
856	endif
857
858	String/G root:myGlobals:TransHeaderInfo:gEMP = "no file selected"
859	String/G root:myGlobals:TransHeaderInfo:gBox = ""
860	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
861	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Filenames"
862	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Labels"
863	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_SDD"
864	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Lambda"
865	// Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Transmission"
866	// Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Whole"
867
868	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Filenames"
869	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Labels"
870	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_SDD"
871	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Lambda"
872	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Transmission"
873	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Whole"
874
875	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:EMP_x1"
876	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:EMP_x2"
877	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:EMP_y1"
878	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:EMP_y2"
879	End
880
881	//given a selection of scattering files, calculates the transmission
882	//and writes the new transmission to the file header
883	//
884	//given the full path;name;vers (= filenmame), of a raw binary SANS file,
885	//the transmission of the sample is calculated (if possible) from information
886	//in the file header. empty beam and sample transmision run numbers are extracted
887	//and the files are located from the run number (if possible)
888	//from the header of the empty beam file, the XY box coordinates and "empty"
889	//counts are determined
890	//once all information is located, the transmission is calculated and the
891	//transmission field of the sample file is automatically "Patched"
892	// - updates the global variable that is displayed in the panel
893	//can be run in batch mode, sequentially passing each item from a list of filenames
894	//this is the single step of the batch mode
895	//
896	//in batch mode: execution will proceed through all of the files, reporting
897	//results to the history window. If no trans could be successfully calculated
898	//(for a blocked beam, for example), then that is displayed as well, and the
899	//raw data is not modified
900	//
901	// now takes the attenuation of the sample trans and empty beam trans into account, (normally this == 1)
902	// and rescales the transmission as appropriate
903	// 3/31/04 SRK
904	//
905	Function CalcSelTransFromHeader(startRow,endRow)
906	Variable startRow,endRow
907	// GetSelection table,ScatterFileTable,1
908
909	String S_Filename, T_Filename, EMP_Filename
910
911	Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
912	Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
913	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
914
915	Wave S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
916
917	Variable/G $"root:Packages:quokka:IgnoreTrans"
918	NVAR IgnoreTrans = $"root:Packages:quokka:IgnoreTrans"
919
920	Variable num_s_files, num_t_files, ii, jj
921	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
922	Variable x1,x2,y1,y2,err,attenEmp,attenSam
923	String suffix = "",pathName,textStr,abortStr,samFileStr
924	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
925
926	num_t_files = numpnts(T_Filenames)
927
928	PathInfo catPathName
929	pathname = S_path
930
931	// [davidm] restructured the following code
932	for (ii = startRow; ii<=endRow; ii += 1)
933
934	S_Filename = pathname + S_Filenames[ii]
935	T_Filename = pathname + T_Filenames[ii]
936	EMP_Filename = pathname + EMP_Filenames[ii]
937
938	// check S-file
939	if ((cmpstr(S_Filenames[ii],"") == 0) \|\| !CheckIfFileExists(S_Filename))
940	Print "Scattering beam file not assigned properly in line", ii+1
941
942	// check T-file
943	elseif ((cmpstr(T_Filenames[ii],"") == 0) \|\| !CheckIfFileExists(T_Filename))
944	Print "Transmission beam file not assigned properly for", S_Filenames[ii]
945
946	// check EMP-file
947	elseif ((cmpstr(EMP_Filenames[ii],"") == 0) \|\| !CheckIfFileExists(EMP_Filename))
948	Print "Empty beam file not assigned properly for", S_Filenames[ii]
949
950	// proceed
951	else
952	// check the empty beam file for previously selected coordinates
953	//if they exist, set the xy string , save the normalized counts somewhere
954	GetXYBoxFromFile(EMP_Filename,x1,x2,y1,y2)
955
956	//read the real count value
957	//emptyCts = getBoxCounts(emptyFile)
958	//if(emptyCts < 1) //box counts hasn't been patched to file
959	ReadHeaderAndData(EMP_Filename)
960	IgnoreTrans = 1 // to prevent the warning message: *transmission is ZERO*
961	err = Raw_to_work("SAM")
962	IgnoreTrans = 0
963	emptyCts = SumCountsInBox(x1,x2,y1,y2,"SAM")
964	//nha debug
965	//textStr = "Box counts for " + emptyFile + " " + num2str(emptyCts)
966	//print textStr
967	//endif
968
969	// read the attenuator number of the empty beam file
970	attenEmp = getAttenNumber(EMP_Filename)
971	//
972	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
973	//no region selected -- prompt user to select box w/marquee
974	DoWindow/F ScatterFileTable
975	Abort "Use \"Set EMP File\", then \"SetXYBox\" to select XY range in empty beam file "+EMP_Filenames[ii]
976	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
977	Endif
978
979	//read in trans file
980	ReadHeaderAndData(T_Filename)
981	//adds to SAM
982	IgnoreTrans = 1 // to prevent the warning message: *transmission is ZERO*
983	err = Raw_to_work("SAM")
984	IgnoreTrans = 0
985	//sum region in SAM
986	transCts = SumCountsInBox(x1,x2,y1,y2,"SAM")
987	// get the attenuator, lambda, and sample string (to get the instrument)
988	// WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
989	WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
990	// samfileStr = samText[3]
991	lambda = samReals[26]
992	attenSam = samReals[3]
993	//nha debug
994	//variable attenSamFromFile
995	//attenSamFromFile = getAttenNumber(transFile)
996	//textStr = num2str(attenSam) + " "+ num2str(attenSamFromFile)
997	//print textStr
998	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
999	AttenRatio = AttenuationFactor("",lambda,attenEmp)/AttenuationFactor("",lambda,attenSam)
1000	//calculate trans based on empty beam value and rescale by attenuation ratio
1001	trans= transCts/emptyCts * AttenRatio
1002
1003	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
1004	If(attenRatio==1)
1005	Printf "%s\t\tTrans Counts = %g\tTrans = %g\r",S_Filenames[ii], transCts,trans
1006	else
1007	Printf "%s\t\tTrans Counts = %g\tTrans = %g\tAttenuatorRatio = %g\r",S_Filenames[ii], transCts,trans,attenRatio
1008	endif
1009	//write the trans to the file header of the raw data (open/close done in function)
1010	WriteTransmissionToHeader(S_Filename,trans)
1011
1012	// after patching, the file needs to be removed from the DataFolder
1013	// so that it will be reloaded if it is needed again [davidm]
1014	string partialName = S_Filenames[ii]
1015	variable index = strsearch(partialName, ".", 0)
1016	if (index != -1)
1017	partialName = partialName[0,index-1]
1018	endif
1019	KillDataFolder/Z $"root:Packages:quokka:"+partialName
1020
1021	//then update the global that is displayed
1022	S_Transmission[ii] = trans
1023	endif
1024	endfor
1025
1026	print "done"
1027	return 0
1028	End
1029
1030	//
1031	// For the calculation of the Transmission using only the Trans Files screen
1032	// Uses only the information on the transmissionFiles screen to calculate
1033	// a "box" Transmission for comparison with the Whole Transmission
1034	// updated 5/11/2006 by Bryan Greenwald
1035	Function CalcTotalTrans(startRow,endRow)
1036	Variable startRow,endRow
1037	// GetSelection table,ScatterFileTable,1
1038
1039	String filename
1040	Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
1041	Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
1042	// Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
1043
1044	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1045	// Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1046	// Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
1047	// Wave GWhole= $"root:myGlobals:TransHeaderInfo:T_Whole"
1048
1049	Variable num_t_files, ii, jj
1050	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
1051	Variable x1,x2,y1,y2,err,attenEmp,attenSam
1052	String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
1053	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
1054	String strToExecute
1055
1056	// num_t_files = numpnts(T_Filenames)
1057
1058	PathInfo catPathName
1059	pathname = S_path
1060
1061	ii= startRow
1062	do
1063	if (cmpstr(T_Filenames[ii],"")!=0) //if there is a sample trans file assigned
1064	if (cmpstr(EMP_Filenames[ii],"")!=0) //if empty beam file assigned, proceed with the calculation
1065
1066	//full path+name to access all 3 files
1067	filename=pathname+S_Filenames[ii]
1068	emptyFile = pathname+ EMP_Filenames[ii]
1069	transFile = pathname+T_Filenames[ii]
1070	//////////
1071	// check the empty beam file for previously selected coordinates
1072	//if they exist, set the xy string , save the normalized counts somewhere
1073	//the value was written to an unused r*4 header analysis.factor (@b494)
1074	getXYBoxFromFile(emptyFile,x1,x2,y1,y2)
1075
1076	//read the real count value
1077	emptyCts = getBoxCounts(emptyFile)
1078	// read the attenuator number of the empty beam file
1079	attenEmp = getAttenNumber(emptyFile)
1080	//
1081	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
1082	//no region selected -- prompt user to select box w/marquee
1083	DoWindow/F TransFileTable
1084	Abort "Use \"Set EMP File\", then \"SetXYBox\" to select XY range in empty beam file "+EMP_Filenames[ii]
1085	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
1086	Endif
1087
1088	//read in trans file then add to SAM
1089	ReadHeaderAndData(transFile)
1090	//adds to SAM
1091	err = Raw_to_work("SAM")
1092	//sum region in SAM
1093	transCts = SumCountsInBox(x1,x2,y1,y2,"SAM")
1094	// get the attenuator, lambda, and sample string (to get the instrument)
1095	WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
1096	WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
1097	samfileStr = samText[3]
1098	lambda = samReals[26]
1099	attenSam = samReals[3]
1100	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
1101	AttenRatio = AttenuationFactor("",lambda,attenEmp)/AttenuationFactor("",lambda,attenSam)
1102	//calculate trans based on empty beam value and rescale by attenuation ratio
1103	trans= transCts/emptyCts * AttenRatio
1104
1105	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
1106	If(attenRatio==1)
1107	//Printf "%s\t\tTrans Counts = %g\t Actual Trans = %g\r",T_GFilenames[ii], transCts,trans
1108	Printf "%s\t\tBox Counts = %g\t Trans = %g\r",T_Filenames[ii], transCts,trans
1109	else
1110	//Printf "%s\t\tTrans Counts = %g\t Trans = %g\tAttenuatorRatio = %g\r",T_GFilenames[ii], transCts,trans,attenRatio
1111	Printf "%s\t\tBox Counts = %g\t Trans = %g\t AttenuatorRatio = %g\r",T_Filenames[ii], transCts,trans,attenRatio
1112	endif
1113	//write the trans to the file header of the raw data (open/close done in function)
1114	WriteTransmissionToHeader(filename,trans) //transmission start byte is 158
1115
1116	// after patching, the file needs to be removed from the DataFolder
1117	// so that it will be reloaded if it is needed again [davidm]
1118	string partialName = S_Filenames[ii]
1119	variable index = strsearch(partialName, ".", 0)
1120	if (index != -1)
1121	partialName = partialName[0,index-1]
1122	endif
1123	KillDataFolder/Z $"root:Packages:quokka:"+partialName
1124
1125	//then update the global that is displayed
1126	// T_GTransmission[ii] = trans
1127
1128	else // There is no empty assigned
1129	abortStr = "Empty beam file not assigned properly for " + S_Filenames[jj]
1130	Print abortStr
1131	//Abort abortStr
1132	return(1)
1133	endif
1134	else //no transmission file
1135	abortStr = "Transmission beam file not assigned properly for " + S_Filenames[ii]
1136	Print abortStr
1137	endif
1138	ii+=1
1139	while(ii<=endRow)
1140	//print "done"
1141	return(0)
1142	End
1143
1144	//
1145	// For the calculation of the Transmission using only the whole detector
1146	// Used to compute the transmission for the TransmissionFiles table using
1147	// the entire detector. For comparison with the "box" trans
1148	// updated: 5/11/2006 by Bryan Greenwald
1149	Function CalcWholeTrans(startRow,endRow)
1150	Variable startRow,endRow
1151	// GetSelection table,ScatterFileTable,1
1152
1153	NVAR pixelsX = root:myGlobals:gNPixelsX
1154	NVAR pixelsY = root:myGlobals:gNPixelsY
1155
1156	String filename
1157	Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
1158
1159	Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
1160	// Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
1161
1162	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1163	// Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1164	Wave S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
1165	Wave S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
1166
1167	Variable num_t_files, ii, jj
1168	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
1169	Variable x1,x2,y1,y2,err,attenEmp,attenSam
1170	String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
1171	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
1172	String strToExecute
1173
1174	// num_t_files = numpnts(T_GFilenames)
1175
1176	PathInfo catPathName
1177	pathname = S_path
1178
1179	ii= startRow
1180	do
1181	if (cmpstr(T_Filenames[ii],"")!=0) //if there is a sample trans file assigned
1182	if (cmpstr(EMP_Filenames[ii],"")!=0) //if empty beam file assigned, proceed with the calculation
1183	//full path+name to access all 3 files
1184	filename=pathname+ S_Filenames[ii]
1185	emptyFile = pathname+EMP_Filenames[ii]
1186	transFile = pathname+T_Filenames[ii]
1187	//////////
1188	// check the empty beam file for previously selected coordinates
1189	//if they exist, set the xy string , save the normalized counts somewhere
1190	//the value was written to an unused r*4 header analysis.factor (@b494)
1191
1192	getXYBoxFromFile(emptyFile,x1,x2,y1,y2)
1193	//read the real count value
1194	emptyCts = getBoxCounts(emptyFile)
1195	// read the attenuator number of the empty beam file
1196	attenEmp = getAttenNumber(emptyFile)
1197	//
1198	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
1199	//no region selected -- prompt user to select box w/marquee
1200	DoWindow/F TransFileTable
1201	Abort "Use \"Set EMP File\", then \"SetXYBox\" to select XY range in empty beam file "+EMP_Filenames[ii]
1202	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
1203	Endif
1204
1205	//read in trans file then add to SAM
1206	ReadHeaderAndData(transFile)
1207	//adds to SAM
1208	err = Raw_to_work("SAM")
1209	//sum region in SAM
1210	transCts = SumCountsInBox(0,pixelsX-1,0,pixelsY-1,"SAM")
1211	// get the attenuator, lambda, and sample string (to get the instrument)
1212	WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
1213	WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
1214	samfileStr = samText[3]
1215	lambda = samReals[26]
1216	attenSam = samReals[3]
1217	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
1218	AttenRatio = AttenuationFactor("",lambda,attenEmp)/AttenuationFactor("",lambda,attenSam)
1219	//calculate trans based on empty beam value and rescale by attenuation ratio
1220	trans= transCts/emptyCts * AttenRatio
1221
1222	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
1223	If(attenRatio==1)
1224	//Printf "%s\t\tTrans Counts = %g\tTrans using whole detector = %g\t Tbox/Twhole = %g\r",T_GFilenames[ii], transCts,trans,T_GTransmission[ii]/trans
1225	Printf "%s\t\tTotal Counts = %g\t Trans using whole detector = %g\t",T_Filenames[ii], transCts,trans
1226	else
1227	//Printf "%s\t\tTrans Counts = %g\tTrans = %g\tAttenuatorRatio = %g, Tbox/Twhole = %g\r",T_GFilenames[ii], transCts,trans,attenRatio, T_GTransmission[ii]/trans
1228	Printf "%s\t\tTotal Counts = %g\t Trans using whole detector = %g\t AttenuatorRatio = %g",T_Filenames[ii], transCts,trans,attenRatio
1229	endif
1230	If(S_Transmission[ii]/trans > 0.97)
1231	printf " Tbox/Twhole = %g\r",S_Transmission[ii]/trans
1232	else
1233	printf " !!! Tbox/Twhole is low !!! = %g\r",S_Transmission[ii]/trans
1234	endif
1235	//write the trans to the file header of the raw data (open/close done in function)
1236	WriteWholeTransToHeader(filename,trans)
1237
1238	//then update the global that is displayed
1239	S_Whole[ii] = trans
1240
1241	else // There is no empty assigned
1242	abortStr = "Empty beam file not assigned properly for " + S_Filenames[ii]
1243	Print abortStr
1244	//Abort abortStr
1245	return(1)
1246	endif
1247
1248	else //no transmission file
1249	abortStr = "Transmission beam file not assigned properly for " + S_Filenames[ii]
1250	Print abortStr
1251	endif
1252	ii+=1
1253	while(ii<=endRow)
1254	print "done"
1255	return(0)
1256	End
1257
1258	Function PickEMPTransButton(ctrlName) : ButtonControl
1259	String ctrlName
1260
1261	Variable ScatFileTableExists
1262	ScatFileTableExists = WinType("ScatterFileTable")
1263	//??BUG?? V_flag returns 1 even if no selection?
1264	//check manually for null selection
1265	//Print "local v_flag = ",num2str(V_flag)
1266	Wave/T LocFilenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
1267	if (ScatFileTableExists != 0)
1268	String/G root:myGlobals:TransHeaderInfo:gEMP = ""
1269	GetSelection table,ScatterFileTable,7
1270	//Print S_Selection
1271	if(strsearch(S_selection,"EMP_Filenames",0) == 0)
1272	//selection OK, add to list
1273	Duplicate/O/R=[V_startRow,V_endRow] LocFilenames, filenames
1274	Wave/T selectedFiles = $"filenames"
1275
1276	SVAR temp = root:myGlobals:TransHeaderInfo:gEMP
1277	//
1278	temp = temp+selectedFiles[0] //take just the first file
1279	UpdateBoxCoordinates()
1280	Else
1281	DoWindow/F ScatterFileTable
1282	DoAlert 0,"Invalid selection from the Scattering file table. You must select a file from the EMP_Filenames column"
1283	Endif
1284	else
1285	//no selection
1286	DoAlert 0,"No file selected from Scattering file table or no Scattering file table available"
1287	Endif
1288	End
1289
1290
1291	//window recreation macro for the Trans Panel
1292	//
1293	Proc Trans_Panel()
1294	PauseUpdate; Silent 1 // building window...
1295	NewPanel /W=(173,197,540,424)/K=1 as "Calculate Transmissions"
1296	DoWindow/C Trans_Panel
1297	ModifyPanel cbRGB=(49807,47186,38011)
1298	ModifyPanel fixedSize=1
1299	SetDrawLayer UserBack
1300	DrawLine 0,56,368,56
1301	DrawLine 0,125,368,125
1302	Button pick_emp,pos={4,65},size={105,20},proc=PickEMPTransButton,title="set EMP file"
1303	Button pick_emp,help={"This button will set the file selected in the Transmission file table to be the empty beam file."}
1304	SetVariable empStr,pos={114,67},size={250,17},title="file:"
1305	SetVariable empStr,help={"Filename of the empty beam file(s) to be used in the transmission calculation"}
1306	SetVariable empStr,fSize=10
1307	SetVariable empStr,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gEMP
1308	Button Trn_button_1,pos={5,101},size={90,20},proc=Trn_SetXYBoxButton,title="Set XY Box"
1309	Button Trn_button_1,help={"Sets the XY box to sum over"}
1310	Button Trn_button_2,pos={174,139},size={110,20},proc=Trn_SortFilesByDate,title="Sort by Date"
1311	Button Trn_button_2,help={"Sort the scattering and transmission files by creation date."}
1312	Button Trn_button_3,pos={174,169},size={110,20},proc=Trn_SortFilesByLabel,title="Sort by Label"
1313	Button Trn_button_3,help={"Sort the scattering and transmission files by label."}
1314	Button Trn_button_4,pos={295,139},size={67,20},proc=Trn_ShowHelpProc,title="Help"
1315	Button Trn_button_4,help={"Show a help notebook for calculating transmissions."}
1316	SetVariable Trn_setvar_1,pos={135,100},size={227,17},title="Box is "
1317	SetVariable Trn_setvar_1,help={"Box coordinates to sum over"},fSize=10
1318	SetVariable Trn_setvar_1,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gBox
1319	Button Trn_button_0,pos={1,1},size={70,20},proc=Trn_PickPathButton,title="Pick Path"
1320	Button Trn_button_0,help={"Select the folder containing the SANS data files"}
1321	Button Trn_button_9,pos={335,1},size={25,20},proc=ShowTransHelp,title="?"
1322	Button Trn_button_9,help={"Show the help file for calculating sample transmissions"}
1323	SetVariable Trn_setvar_0,pos={80,4},size={250,17},title="Path"
1324	SetVariable Trn_setvar_0,help={"Currently selected data path"},fSize=10
1325	SetVariable Trn_setvar_0,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gCatPathStr
1326	Button Trn_button_5,pos={5,169},size={161,20},proc=Trn_CalcAllFilesButton,title="Calculate All Files"
1327	Button Trn_button_5,help={"Calculate transmission and patch headers of ALL files in the Scattering File Table."}
1328	Button Trn_button_6,pos={295,198},size={67,20},proc=Trn_PanelDoneButtonProc,title="Done"
1329	Button Trn_button_6,help={"Close the panel when done calculating transmissions"}
1330
1331	Button Trn_button_7,pos={67,32},size={114,20},proc=Trn_RefreshProc,title="List Files"
1332	Button Trn_button_7,help={"Generate or refresh the tables of files."}
1333
1334	Button Trn_button_7b, pos={67+114+5,32},size={114,20},proc=Trn_AutoCompleteProc,title="Auto Complete"
1335	Button Trn_button_7b, help={"???"}
1336
1337	Button Trn_button_8,pos={5,139},size={161,20},proc=Trn_CalcSelectedFilesButton,title="Calculate Selected Files"
1338	Button Trn_button_8,help={"Calculate transmission and patch headers of selected files in the Scattering File Table."}
1339	Button Trn_button_10,pos={5,198}, size={161,20},proc=TotalTransButtonProc
1340	Button Trn_button_10 title="Calculate Total Trans"
1341	Button Trn_button_10 help={"Calculate transmission over the whole detector and patch headers of ALL files in the data folder."}
1342	EndMacro
1343
1344
1345	Function TotalTransButtonProc(ctrlName) : ButtonControl
1346	String ctrlName
1347	TotalTrans(ctrlName)
1348	End
1349
1350
1351	Proc ShowTransHelp(ctrlName) : ButtonControl
1352	String ctrlName
1353	DisplayHelpTopic/K=1 "SANS Data Reduction Tutorial[Calculate Transmissions]"
1354	if(V_flag !=0)
1355	DoAlert 0,"The SANS Data Reduction Tutorial Help file could not be found"
1356	endif
1357	End
1358
1359
1360	//generates the file tables of scattering files and transmission files
1361	//
1362	// if the tables already exist, they will be updated
1363	//
1364	Proc Trn_RefreshProc(ctrlName) : ButtonControl
1365	String ctrlName
1366	BuildFileTables()
1367	End
1368
1369	Function Example2()
1370	String browserCmd,cmd1,cmd2,promptStr
1371
1372	cmd1="Display %s"
1373	cmd2="AppendToGraph %s"
1374	promptStr="Select Waves for Graph"
1375	sprintf browserCmd, "CreateBrowser prompt=\"%s\", executeMode=2, command1=\"%s\", command2=\"%s\"",promptStr,cmd1,cmd2
1376	Execute browserCmd
1377	End
1378
1379	//improves the file tables of scattering files and transmission files
1380	Function Trn_AutoCompleteProc(ctrlName) : ButtonControl
1381	String ctrlName
1382
1383	Variable i, in
1384	Variable j, jn
1385	Variable row
1386
1387	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1388	Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
1389	Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
1390	Wave/T S_Labels = $"root:myGlobals:TransHeaderInfo:S_Labels"
1391
1392	String Pathname, S_Filename, T_Filename, EMP_Filename, S_Label
1393	String safeLabel
1394
1395	String dicValidRows = "" // [safeLabel] -> [[row1],[row2],...]
1396	String dicCandidates = "" // [safeLabel] -> [[row1],[row2],...] // candidates to be auto completed
1397
1398	String validRows // [[row1],[row2],...]
1399	String candidateRows // [[row1],[row2],...]
1400
1401	String title, message, selection
1402
1403	// String selection
1404	// Prompt selection, "titleStr", popup, "hallo\tTest;nein\tJa;danke"
1405	// DoPrompt "hello", selection
1406
1407	PathInfo catPathName
1408	Pathname = S_path
1409
1410	// check if ScatterFileTable exists
1411	if (WinType("ScatterFileTable") == 2)
1412
1413	//
1414	// first step: find valid rows and find rows which potentially could be auto fixed
1415	//
1416
1417	in = DimSize(S_Filenames, 0)
1418	for (i = 0; i < in; i += 1)
1419	S_Filename = Pathname + S_Filenames[i]
1420	T_Filename = Pathname + T_Filenames[i]
1421	EMP_Filename = Pathname + EMP_Filenames[i]
1422	S_Label = S_Labels[i]
1423
1424	// check S-file
1425	if ((strlen(S_Filenames[i]) != 0) && CheckIfFileExists(S_Filename) && (strlen(S_Label) != 0))
1426
1427	// make sure that label doesn't interfere with list and dictionary symbols
1428	safeLabel = S_Label
1429	safeLabel = ReplaceString("\\", safeLabel, "\\1") // ReplaceString("\", safeLabel, "\1")
1430	safeLabel = ReplaceString(":", safeLabel, "\\2")
1431	safeLabel = ReplaceString(";", safeLabel, "\\3")
1432
1433	// check T-file and EMP-file
1434	if ((strlen(T_Filenames[i]) != 0) && CheckIfFileExists(T_Filename) && (strlen(EMP_Filenames[i]) != 0) && CheckIfFileExists(EMP_Filename))
1435	// check if sample is already marked as valid row
1436	if (-1 != strsearch(dicValidRows, safeLabel, 0))
1437	// add row-index
1438	validRows = StringByKey(safeLabel, dicValidRows)
1439	sprintf validRows, "%s, %g", validRows, i
1440	else
1441	// set first row-index
1442	sprintf validRows, "%g", i
1443	endif
1444	dicValidRows = ReplaceStringByKey(safeLabel, dicValidRows, validRows)
1445
1446	// S-file seemed fine but problems occurred with T- and EMP-file
1447	else
1448	// check if sample is already marked as possible candidate
1449	if (-1 != strsearch(dicCandidates, safeLabel, 0))
1450	// add row-index
1451	candidateRows = StringByKey(safeLabel, dicCandidates)
1452	sprintf candidateRows, "%s, %g", candidateRows, i
1453	else
1454	// set first row-index
1455	sprintf candidateRows, "%g", i
1456	endif
1457	dicCandidates = ReplaceStringByKey(safeLabel, dicCandidates, candidateRows)
1458	endif
1459	endif
1460	endfor
1461
1462	//
1463	// second step: fix invalid rows
1464	//
1465
1466	jn = ItemsInList(dicCandidates)
1467	for (j = 0; j < jn; j += 1)
1468	safeLabel = StringFromList(0, StringFromList(j, dicCandidates), ":")
1469
1470	// check if invalid rows of current sample can be fixed
1471	if (-1 != strsearch(dicValidRows, safeLabel, 0))
1472	validRows = StringByKey(safeLabel, dicValidRows)
1473	candidateRows = StringByKey(safeLabel, dicCandidates)
1474
1475	// check if more than one row can be used to fix current candidates
1476	if (-1 != strsearch(validRows, ",", 0))
1477
1478	sprintf message, "Select row you want to use to update all incomplete rows with that sample."
1479
1480	// check if more than one row is afftected
1481	if (-1 != strsearch(candidateRows, ",", 0))
1482	sprintf title, "\"%s\" (Affected rows: %s)", S_Labels[str2num(StringFromList(0, validRows, ","))], candidateRows
1483	else
1484	sprintf title, " \"%s\" (Affected row: %s)", S_Labels[str2num(StringFromList(0, validRows, ","))], candidateRows
1485	endif
1486
1487	selection = StringFromList(0, validRows, ",")
1488	Prompt selection, message, popup, ReplaceString(", ", validRows, ";")
1489	DoPrompt /HELP="" title, selection
1490
1491	// evaluate result
1492	switch (V_flag)
1493	case 0: // yes
1494	row = str2num(selection) // use selected row value
1495	break
1496
1497	case 1: // cancel
1498	row = -1 // skip
1499	break
1500
1501	default:
1502	return 0
1503	endswitch
1504	else
1505	// only one row can be used to fix current candidates
1506	row = str2num(validRows)
1507
1508	// check if more than one row is afftected
1509	if (-1 != strsearch(candidateRows, ",", 0))
1510	sprintf message, "The transmission value of \"%s\" can be determined with the information provided in row %g.\rWould you like to apply the information to all rows with that sample? (Affected rows: %s)", S_Labels[row], row, candidateRows
1511	else
1512	sprintf message, "The transmission value of \"%s\" can be determined with the information provided in row %g.\rWould you like to apply the information to all rows with that sample? (Affected row: %s)", S_Labels[row], row, candidateRows
1513	endif
1514	DoAlert 2, message
1515
1516	// evaluate result
1517	switch (V_flag)
1518	case 1: // yes
1519	break // use selected row value
1520
1521	case 2: // no
1522	row = -1 // skip
1523	break
1524
1525	default: // cancel
1526	return 0
1527	endswitch
1528	endif
1529
1530	// fix current candidates if source row is specified
1531	if (row != -1)
1532	// these are the values to be used to fix current candidates
1533	T_Filename = T_Filenames[row]
1534	EMP_Filename = EMP_Filenames[row]
1535
1536	// fix all invalid rows of current sample
1537	in = ItemsInList(candidateRows, ",")
1538	for (i = 0; i < in; i += 1)
1539	row = str2num(StringFromList(i, candidateRows, ","))
1540	T_Filenames[row] = T_Filename
1541	EMP_Filenames[row] = EMP_Filename
1542	endfor
1543	endif
1544	endif
1545
1546
1547
1548	// // if dicValidRows contains row number for current sample, then transmission can be determined
1549	// row = NumberByKey(safeLabel, dicValidRows) // if item is not in dicValidRows then row is set to NaN
1550	// if (numtype(row) == 0) // check for normal number
1551	// S_Label = S_Labels[row]
1552	// if (-1 != strsearch(rowSelection, ",", 0)) // check if more than one row is afftected
1553	// sprintf message, "The transmission value of \"%s\" can be determined with the information provided in row %g.\rWould you like to apply the information to all rows with that sample? (Affected rows: %s)", S_Label, row, rowSelection
1554	// else
1555	// sprintf message, "The transmission value of \"%s\" can be determined with the information provided in row %g.\rWould you like to apply the information to all rows with that sample? (Affected row: %s)", S_Label, row, rowSelection
1556	// endif
1557	// DoAlert 2, message
1558	//
1559	// switch (V_flag)
1560	// case 1: // yes
1561	// T_Filename = T_Filenames[row]
1562	// EMP_Filename = EMP_Filenames[row]
1563	// // find sample and replace T- and EMP-Filename
1564	// for (i = 0; i < in; i += 1)
1565	// // check S-file
1566	// if ((strlen(S_Filenames[i]) != 0) && CheckIfFileExists(Pathname + S_Filenames[i]) && (cmpstr(S_Label, S_Labels[i]) == 0))
1567	// T_Filenames[i] = T_Filename
1568	// EMP_Filenames[i] = EMP_Filename
1569	// endif
1570	// endfor
1571	// break
1572	//
1573	// case 3: // cancel
1574	// return 0
1575	// endswitch
1576	//
1577	// // check if transmission of current sample could be determined
1578	// elseif (-1 != strsearch(listUnclearSamples, safeLabel, 0))
1579	// S_Label = safeLabel
1580	// S_Label = ReplaceString("\\3", S_Label, ";")
1581	// S_Label = ReplaceString("\\2", S_Label, ":")
1582	// S_Label = ReplaceString("\\1", S_Label, "\\")
1583	// if (-1 != strsearch(rowSelection, ",", 0)) // check if more than one row is afftected
1584	// sprintf message, "The transmission value of \"%s\" can be determined with the information provided by multiple rows.\rPlease complete the report file manually for that sample. (Affected rows: %s)", S_Label, rowSelection
1585	// else
1586	// sprintf message, "The transmission value of \"%s\" can be determined with the information provided by multiple rows.\rPlease complete the report file manually for that sample. (Affected row: %s)", S_Label, rowSelection
1587	// endif
1588	// DoAlert 0, message
1589	//
1590	//
1591	// Example2()
1592	// endif
1593	endfor
1594	else
1595	DoAlert 0,"No file selected from Scattering Files table or no Scattering Files table available"
1596	endif
1597	End
1598
1599	//shows a noteboox of help text describing how to calculate transmissions
1600	// - better that the user read the igor or pdf file, but it's a victory to get
1601	//users to read anything at all
1602	//
1603	Proc Trn_ShowHelpProc(ctrlName) : ButtonControl
1604	String ctrlName
1605	DisplayTransHelp()
1606	End
1607
1608	//sorts the tables by date
1609	//
1610	Proc Trn_SortFilesByDate(ctrlName) : ButtonControl
1611	String ctrlName
1612	SortGlobals(0)
1613	End
1614
1615	//sorts the tables alphabetically by the sample label field
1616	//
1617	Proc Trn_SortFilesByLabel(ctrlName) : ButtonControl
1618	String ctrlName
1619	SortGlobals(1)
1620	End
1621
1622	//button action procedure to select the local path to the
1623	//folder containing the RAW SANS data files
1624	// - once the data folder is selected, all of the popup file menus are
1625	//forced to update with fresh file lists
1626	//
1627	Function Trn_PickPathButton(PathButton) : ButtonControl
1628	String PathButton
1629
1630	//set the global string to the selected pathname
1631	Variable err
1632	err = PickPath()
1633	if(err)
1634	return(1) //some problem with path or user cancelled, get out
1635	endif
1636
1637	PathInfo/S catPathName
1638	String path = S_path
1639	if (V_flag == 0)
1640	//path does not exist - no folder selected
1641	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = "no folder selected"
1642	else
1643	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = path
1644	endif
1645
1646	//Update the pathStr variable box
1647	ControlUpdate/W=Trans_Panel $"Trn_setvar_0"
1648	//Generate tables
1649	Execute "BuildFileTables()"
1650
1651	End
1652
1653	//button action function that asks the user to set the XY box to sum over
1654	//for all transmission calculations
1655	//
1656	// requires the user to set the box coordinates with the marquee popup
1657	//that wil properly set the keyword string, and write the values to the empty beam header
1658	//
1659	Function Trn_SetXYBoxButton(ctrlName) : ButtonControl
1660	String ctrlName
1661
1662	String msgStr = "Select the Empty Beam File"
1663	String filename=""
1664
1665	//get the filename from the popup menu
1666	//and construct a full path to it
1667	SVAR partialName = root:myGlobals:TransHeaderInfo:gEMP
1668	print partialName
1669	//get a valid file based on this partialName and catPathName
1670	String tempName = FindValidFilename(partialName)
1671	if(cmpstr(tempName,"")==0)
1672	//file not found, get out
1673	Abort "Empty beam file not found Trn_SetXYBoxButton(ctrlName)"
1674	Endif
1675	//name is ok, prepend path to tempName for read routine
1676	PathInfo catPathName
1677	filename = S_path + tempName
1678
1679	//read the file in - check for previous coordinates
1680	ReadHeaderAndData(filename)
1681
1682	Wave realw=$"root:Packages:NIST:RAW:RealsRead"
1683	if (realw[26] == 0)
1684	DoAlert /T="Warning" 0, "Lambda for this file is zero! You might need to patch this file again before you continue to work with it."
1685	endif
1686
1687	//data is displayed here (go through the normal display steps, so all is created properly
1688	String/G root:myGlobals:gDataDisplayType="RAW"
1689	fRawWindowHook()
1690
1691	// check the empty beam file for previously selected coordinates
1692	//if they exist, set the xy string , save the normalized counts somewhere
1693	//the value was written to an unused r*4 header analysis.factor (@b494)
1694	Variable refnum,x1,x2,y1,y2,err
1695	getXYBoxFromFile(filename,x1,x2,y1,y2)
1696
1697	//read the real count value, assign to a global
1698	Variable/G root:myGlobals:gTransCts = getBoxCounts(filename) //***NOTE this is NOT in the Trans sub-folder
1699	//
1700	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
1701	//no region selected
1702
1703	//add the empty beam file to work.SAM
1704	err = Raw_to_work("SAM")
1705
1706	//the calling macro must change the display type
1707	String/G root:myGlobals:gDataDisplayType="SAM" //displayed data type is sam
1708
1709	//data is displayed here
1710	fRawWindowHook()
1711
1712	//prompt user to select box w/marquee
1713	DoAlert 0,"(1) Select the region to sum with the Marquee.\n(2) Right click into the selected region.\n(3) Click on SetXYBoxCoords"
1714	// DoAlert 0,"Select the region to sum with the Marquee"
1715
1716	//from here the Marquee menu selection must handle the task of setting the box
1717	//and updating the information in the file header
1718	else
1719	// region already selected, just put up the values from the file header
1720	//allow user the option of overriding the current box region
1721	msgStr = "X1="+num2str(x1)+";"
1722	msgStr += "X2="+num2str(x2)+";"
1723	msgStr += "Y1="+num2str(y1)+";"
1724	msgStr += "Y2="+num2str(y2)+";"
1725	String textStr
1726	textStr = "Override current box "+msgStr+" ?"
1727	DoAlert 1,textStr
1728	If((V_flag)==1)
1729	//get new box coordinates, same procedure as above
1730	//add the empty beam file to work.SAM
1731	err = Raw_to_work("SAM")
1732
1733	//the calling macro must change the display type
1734	String/G root:myGlobals:gDataDisplayType="SAM" //displayed data type is sam
1735
1736	//data is displayed here
1737	fRawWindowHook()
1738
1739	//prompt user to select box w/marquee
1740	DoAlert 0,"(1) Select the region to sum with the Marquee.\n(2) Right click into the selected region.\n(3) Click on SetXYBoxCoords"
1741	// DoAlert 0,"Select the region to sum with the Marquee"
1742
1743	//from here the Marquee menu selection must handle the task of setting the box
1744	//and updating the information in the file header
1745	else
1746	String/G root:myGlobals:TransHeaderInfo:gBox = msgStr
1747	Endif
1748	Endif
1749
1750	UpdateBoxCoordinates()
1751	Return (0)
1752	End
1753
1754
1755	//button action function that assigns the selected empty beam file (run number only)
1756	//and the sample trnansmissionfile (run number only) to the popup list of sample scattering
1757	//files (ALL of the list items). Assignment is done by writing the integer run numbers of
1758	//trans files to the header of each of the scattering files, in a batchwise processing
1759	//of the popup list
1760	//
1761	//transmission are not calculated here - only the file numbers are set
1762	//
1763	//*******unused*********
1764	//Function Trn_AssignAllFilesButton(ctrlName) : ButtonControl
1765	// String ctrlName
1766	//
1767	// AssignTransFilesToData()
1768	//
1769	//End
1770
1771	//button action procedure to calculate the transmission of all of the sample files in the
1772	//sample popup list, based on the information in EACH sample header and in the empty beam file
1773	//the box must be set properly in the empty beam file, AND the empty and trans
1774	//run number must also be set properly in EACH scattering file,
1775	//If run numbers are not properly assigned, no trans is calculated and the
1776	//header is not modified
1777	//
1778	//The RAW data header of EACH sample file IS modified, with the newly calculated transmission
1779	//
1780	//not very friendly, but forces users to assign the files before continuing
1781	//
1782	Function Trn_CalcAllFilesButton(ctrlName) : ButtonControl
1783	String ctrlName
1784
1785	//calculate the transmission and Patch the header (if possible)
1786	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1787	Variable num_s_files = numpnts(S_Filenames)
1788	CalcSelTransFromHeader(0,num_s_files-1)
1789
1790	End
1791
1792	//for selected scattering files in the scattering table,
1793	// the "Annn" association of trans file is written to the data file,
1794	// the the transmission is actually calculated
1795	//
1796	Function Trn_CalcSelectedFilesButton(ctrlName) : ButtonControl
1797	String ctrlName
1798
1799	Variable scatterTableExists
1800	scatterTableExists = WinType("ScatterFileTable")
1801	if (scatterTableExists != 0)
1802	GetSelection table,ScatterFileTable,1
1803	if(V_Flag != 0)
1804	//AssignSelTransFilesToData(V_StartRow,V_EndRow)
1805	//calculate the transmission and Patch the header (if possible)
1806	CalcSelTransFromHeader(V_StartRow,V_EndRow)
1807	Else
1808	DoAlert 0,"No selection from Scattering Files table"
1809	Endif
1810	Else
1811	DoAlert 0,"No file selected from Scattering Files table or no Scattering Files table available"
1812	Endif
1813	End
1814
1815	//
1816	// I am not sure what the difference is inthe function of CalcTotalTrans and CalcWholeTrans ?
1817	// do they really do anything different?
1818	// is it a useful calculation at all?
1819	//
1820	Function TotalTrans(ctrlName) : ButtonControl
1821	String ctrlName
1822
1823	Variable scatTableExists
1824	scatTableExists = WinType("ScatterFileTable")
1825	if (scatTableExists != 0)
1826	GetSelection table,ScatterFileTable,1
1827	if(V_Flag != 0)
1828	//AssignTotalTransFilesToData(V_StartRow,V_EndRow)
1829	//calculate the transmission and Patch the header (if possible)
1830	CalcTotalTrans(V_StartRow,V_EndRow)
1831	CalcWholeTrans(V_StartRow,V_EndRow)
1832	Else
1833	DoAlert 0,"No selection from Trans Files table"
1834	Endif
1835	Else
1836	DoAlert 0,"No file selected from Trans Files table or no Trans Files table available"
1837	Endif
1838	End
1839
1840
1841	//simple button procedure to close the trans panel
1842	// - automatically kills the two tables as well
1843	//
1844	Function Trn_PanelDoneButtonProc(ctrlName) : ButtonControl
1845	String ctrlName
1846
1847	// this button will make sure all files are closed
1848	//and close the panel
1849
1850	Close/A
1851	DoWindow/K Trans_Panel
1852	DoWindow/K ScatterFileTable
1853	DoWindow/K TransFileTable
1854	End
1855
1856
1857	//function to update the box coordinates of the file selected as the
1858	//empty beam file - takes the file that is currently popped from the list
1859	//reads the 4 "analysis" integers that hold the box coordinates
1860	//resets the globals string that is displayed with the new values
1861	//should be called whenever the "empty" popup is popped, to ensure
1862	//that current header information is displayed
1863	//
1864	Function UpdateBoxCoordinates()
1865
1866	//construct a full name, and read in the label from the file
1867	//and set the global
1868	String textstr=""
1869	ControlInfo empStr
1870	SVAR item = root:myGlobals:TransHeaderInfo:gEMP
1871	String tempName = FindValidFilename(item)
1872	if(cmpstr(tempName,"")==0)
1873	//file not found, get out
1874	Abort "Empty beam file not found UpdateBoxCoordinates(ctrlName)"
1875	Endif
1876	//name is ok, prepend path to tempName for read routine
1877	PathInfo catPathName
1878	String filename = S_path + tempName
1879
1880	Variable refnum,x1,x2,y1,y2,err
1881	GetXYBoxFromFile(filename,x1,x2,y1,y2)
1882
1883	//and update the global string
1884	String msgStr=""
1885	msgStr = "X1="+num2str(x1)+";"
1886	msgStr += "X2="+num2str(x2)+";"
1887	msgStr += "Y1="+num2str(y1)+";"
1888	msgStr += "Y2="+num2str(y2)+";"
1889
1890	String/G root:myGlobals:TransHeaderInfo:gBox = msgStr
1891
1892	ControlUpdate/W=Trans_panel Trn_setvar_1
1893	End
1894
1895	//crude procedure to display a notebook of help information for users
1896	//
1897	Proc DisplayTransHelp()
1898	String nb = "Notebook0"
1899	NewNotebook/N=$nb/F=1/V=1/W=(342,302,868,674) as "Notebook0:Transmission Help"
1900	Notebook $nb defaultTab=36, statusWidth=238, pageMargins={36,72,36,72}
1901	Notebook $nb showRuler=1, rulerUnits=1, updating={1, 3600}
1902	Notebook $nb newRuler=Normal, justification=0, margins={0,0,468}, spacing={0,0,0}, tabs={}, rulerDefaults={"Geneva",10,0,(0,0,0)}
1903	Notebook $nb ruler=Normal; Notebook $nb justification=1, fSize=14, fStyle=1, text="Transmission Help\r"
1904	Notebook $nb ruler=Normal, fSize=-1, fStyle=-1, text="\r"
1905	Notebook $nb text="This panel allows quick and easy calculation of sample transmission. The neutron transmission of a sampl"
1906	Notebook $nb text="e must be calculated and entered into the header of each sample scattering file before proper background"
1907	Notebook $nb text=" corrections or absolute scaling can be done.\r"
1908	Notebook $nb text="\r"
1909	Notebook $nb text="During data collection, you measured an empty beam - that is a measurement with heavy attenuation of th"
1910	Notebook $nb text="e neutron beam and the beamstop mover out of line with the direct beam. Then without changing the attenu"
1911	Notebook $nb text="ation or replacing the beamstop, you put a sample in the beam, and repeated the measurement (a sample tr"
1912	Notebook $nb text="ansmission measurement). The neutron transmission of the sample is simply the ratio of the number of neu"
1913	Notebook $nb text="tron counts from the sample transmission measurement normalized by the number of neutron counts from the"
1914	Notebook $nb text=" empty beam measurement. In this way, each sample transmission file is \"linked\" to the same empty beam t"
1915	Notebook $nb text="ransmission file.\r"
1916	Notebook $nb text="\r"
1917	Notebook $nb text="This calculated transmission value must be entered into the header of the sample scattering measurement "
1918	Notebook $nb text="- that is the measurement of the sample with the beamstop covering the primary (transmitted) beam, and n"
1919	Notebook $nb text="o (or few) attenuators in place. In this way, the sample transmission file is \"linked\" to its correspond"
1920	Notebook $nb text="ing sample scattering file. This panel allows you to set up the links and calculate the transmission.Tra"
1921	Notebook $nb text="nsmisison values are automatically patched to the scattering file headers as they are calculated.\r"
1922	Notebook $nb text="\r"
1923	Notebook $nb text="To Calculate Transmissions:\r"
1924	Notebook $nb text="\r"
1925	Notebook $nb text="1) Click \"List Files\" to get two lists (tables) - one of all the sample scattering files in the folder, "
1926	Notebook $nb text="and one of the transmission files.\r"
1927	Notebook $nb text="\r"
1928	Notebook $nb text="2) Select the region of the detector to sum over from the empty beam transmission file. Do theis by clic"
1929	Notebook $nb text="king on the filename of the empty beam transmision file (from the TransmissionFiles window, in the blue "
1930	Notebook $nb text="\"T_Filenames\" column). Return to the panel, and click the \"set EMP file\" button\", and the filename shoul"
1931	Notebook $nb text="d appear in the file box. The \"Box is\" field should have zeros for the x and y coordinates. Click the \"S"
1932	Notebook $nb text="et XY Box\" button. The empty beam file will be displayed, and you will be instructed to select the regio"
1933	Notebook $nb text="n to sum with the marquee. On the data, click and drag a rectangle that encompasses the primary beam. Mo"
1934	Notebook $nb text="ve the cursor inside the selection, to get an \"upside-down hat\" cursor. Click to get a menu, and near th"
1935	Notebook $nb text="e bottom, select \"Set XY Box Coords\". The pixel values should be updated to the Transmission panel, and "
1936	Notebook $nb text="are written to the empty beam header for future calculations. Note that the marquee selection can also b"
1937	Notebook $nb text="e used to measure the beam center, or centroid of any selected region.\r"
1938	Notebook $nb text="\r"
1939	Notebook $nb text="3) Now you need to \"link\" the ", fStyle=2, text="sample", fStyle=-1, text=" transmission files to the "
1940	Notebook $nb fStyle=2, text="empty", fStyle=-1, text=" ", fStyle=2, text="beam", fStyle=-1
1941	Notebook $nb text=" transmission file. Do this in the TransmissionFiles window by selecting the filename (in the blue T_Fil"
1942	Notebook $nb text="enames column) and pasing it to the corresponding row(s) in the T_EMP_Filenames column. This links the e"
1943	Notebook $nb text="mpty beam transmission with the sample transmission file. Do this for every sample transmission file.\r"
1944	Notebook $nb text="\r"
1945	Notebook $nb text="4) Now you need to link the sample ", fStyle=2, text="transmission", fStyle=-1
1946	Notebook $nb text=" file to the sample ", fStyle=2, text="scattering", fStyle=-1
1947	Notebook $nb text=" file. Do this by selecting the name of the transmission file (from the blue T_Filenames column) and pas"
1948	Notebook $nb text="ting it into the corresponding row of the S_TRANS_Filenames column of the ScatteringFiles window. This l"
1949	Notebook $nb text="inks the scattering file to its corresponding sample transmission file. This for all of the sample scatt"
1950	Notebook $nb text="ering files.\r"
1951	Notebook $nb text="\r"
1952	Notebook $nb text="5) Calculate the transmissions (and automatically write the transmission value to the satterng file head"
1953	Notebook $nb text="er) by clicking \"Calculate All Files\" from the Transmission Panel. The results will be printed to the co"
1954	Notebook $nb text="mmand window at the bottom of the screen. Any improperly assigned files will be listed. For example, blo"
1955	Notebook $nb text="cked beam scattering files will return an error, since the transmssion known to be zero, and is not meas"
1956	Notebook $nb text="ured (and no files are \"linked\"). Rather than calculating the transmission of all of the files, a range"
1957	Notebook $nb text=" of S_Filenames can be selected, then calculated by clicking \"Calculate Selected Files\".\r"
1958	Notebook $nb text="\r"
1959	Notebook $nb text="By default the lists are sorted by run number (= chronological). In some cases it may be easier to sort "
1960	Notebook $nb text="by the sample label to group several of the same sample scattering files collected at different sample-t"
1961	Notebook $nb text="o-detector distances. Its utility depends, of course, on how consistent and unique your sample labels ar"
1962	Notebook $nb text="e.\r"
1963	Notebook $nb text="\r"
1964	Notebook $nb text="The \"links\" are stored in the corresponding files, and wil be re-generated when the lists are re-generat"
1965	Notebook $nb text="ed. Unassigned links will appear as blank elements in the T_EMP_Filenames or S_TRANS_Filenames columns.\r"
1966	Notebook $nb text="\r"
1967	Notebook $nb, selection={startOfFile,startOfFile}
1968	Notebook $nb text="\r"
1969	End
1970
1971
1972
1973	//*******************
1974	//************
1975	// A simple panel to allow users of the NG1 SANS instrument to make their
1976	// transmission files "look" like a transmission measurement to the data reduction
1977	// program. Transmission files are designated by an x-position of the beamstop of
1978	// < -5 (cm). this simple procedure sets xpos=-10 for individual files. files
1979	// con be "un-converted", which set the xpos=0.
1980	// 1/30/01 SRK
1981	//************
1982
1983	Proc TransformToTransFile()
1984	Variable/G root:myGlobals:gConvTrans=1
1985	DoWindow/F Convert_to_Trans
1986	if(V_flag==0)
1987	Convert2Trans()
1988	endif
1989	End
1990
1991	//fname must be the full path and name for the file
1992	Function ChangeBSXPos(fname,xpos)
1993	String fname
1994	Variable xpos
1995
1996	Variable start
1997	//x-position starts after byte 368 in VAX files
1998	WriteBSXPosToHeader(fname,xpos)
1999	return(0)
2000	End
2001
2002	//sets the beamstop position to zero NOT the original position
2003	Function UnConvertButtonProc(ctrlName) : ButtonControl
2004	String ctrlName
2005
2006	//Print "UnConvert"
2007	String fullname=""
2008	ControlInfo fileNum
2009	Variable num = V_Value //run number to find
2010
2011	fullname = FindFileFromRunNumber(num)
2012	Print fullname
2013	//report error or change the file
2014	if(cmpstr(fullname,"")==0)
2015	Print "Unconvert - file not found"
2016	else
2017	//Print "Unconvert",fullname
2018	ChangeBSXPos(fullName,0)
2019	Endif
2020	return(0)
2021	End
2022
2023	//button procedure to do the conversion
2024	// writes fake beamstop position to the data file
2025	//
2026	Function ConvertButtonProc(ctrlName) : ButtonControl
2027	String ctrlName
2028
2029	String fullname=""
2030	ControlInfo fileNum
2031	Variable num = V_Value //run number to find
2032
2033	fullname = FindFileFromRunNumber(num)
2034	print fullname
2035	//report error or change the file
2036	if(cmpstr(fullname,"")==0)
2037	Print "Convert - file not found"
2038	else
2039	//Print "Convert",fullname
2040	ChangeBSXPos(fullName,-10)
2041	Endif
2042	return(0)
2043	End
2044
2045	//simple panel recreation macro
2046	//
2047	Proc Convert2Trans()
2048	PauseUpdate; Silent 1 // building window...
2049	NewPanel /W=(434,74,671,216) /K=1
2050	DoWindow/C Convert_to_Trans
2051	SetDrawLayer UserBack
2052	DrawText 18,22,"Convert files to be recognized"
2053	DrawText 43,39,"as transmission files"
2054	SetVariable fileNum,pos={43,58},size={130,15},title="File Number"
2055	SetVariable fileNum,limits={1,Inf,1},value=root:myGlobals:gConvTrans
2056	SetVariable fileNum,help={"Sets the run number of the file that is to be converted"}
2057	Button ConvButton,pos={73,79},size={80,20},proc=ConvertButtonProc,title="Convert"
2058	Button ConvButton,help={"Converts the chosen file to appear as a transmission file"}
2059	Button UndoButton,pos={68,105},size={90,20},proc=UnConvertButtonProc,title="Un-Convert"
2060	Button UndoButton,help={"Converts the chosen file to appear as a scattering file"}
2061	EndMacro
2062
2063
2064	/////
2065	// A quick way to fill all the T_EMP_Filenames with the selected empty beam file
2066	// Note that you must go back and clear or reassign any files that are special cases
2067	//
2068	// IMPORTANT - this will overwrite any other file assignments (typically not a problem
2069	// if you are using only one wavelength)
2070	//
2071	/////
2072	Function FillEMPFilenameWSelection()
2073
2074	GetSelection table,TransFileTable,3
2075	Variable row=V_startRow //ony need the selected row, we know the column names and location
2076	Wave/T fw = root:myGlobals:TransHeaderInfo:T_FileNames //trans files
2077	Wave/T ew = root:myGlobals:TransHeaderInfo:T_EMP_FileNames //empty beam reference files
2078
2079	ew[] = fw[row]
2080
2081	return(0)
2082	End
2083
2084	//given a selection of the SAMPLE files, try to find the corresponding transmission file
2085	//
2086	Function GuessTransFile(charsToUse,row)
2087	Variable charsToUse,row //number of characers to use from the beginning of the label, and the row of the sample file
2088
2089	// GetSelection table,ScatterFileTable,3
2090	// Variable row=V_startRow //ony need the selected row, we know the column names and location
2091	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
2092	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
2093	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
2094	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
2095
2096	Variable num,ii,found
2097	String samStr = "",testStr=""
2098
2099	samStr = (sw[row])[0,charsToUse-1] //string to try and match
2100	samStr += "*"
2101	// Print samStr
2102	num=numpnts(tw)
2103	ii=0
2104	do
2105	testStr=tw[ii]
2106	found = stringmatch(testStr, samStr )
2107	if(found == 1)
2108	Print "Match Found at: ",samStr,tnam[ii],tw[ii]
2109	snam[row] = tnam[ii] //write the file name into the table
2110	return(0)
2111	endif
2112	ii+=1
2113	while(ii<num)
2114
2115	//method 2
2116	// samStr = (sw[row])[0,charsToUse-1] //string to try and match
2117	//// Print samStr
2118	// num=numpnts(tw)
2119	// ii=0
2120	// do
2121	// testStr=tw[ii]
2122	// found = strsearch(testStr,samStr,0) //start from zero, Need Igor 5 to allow 4th parameter to ignore case
2123	// if(found != -1)
2124	// Print "Match Found at: ",samStr,tnam[ii],tw[ii]
2125	// snam[row] = tnam[ii] //write the file name into the table
2126	// return(0)
2127	// endif
2128	// ii+=1
2129	// while(ii<num)
2130
2131	Print "No Match found"
2132	return(0)
2133	End
2134
2135	//given a single transmission file, try to find the corresponding scattering file(s)
2136	//
2137	// apply TWO criteria
2138	// (1) the label must match "well enough"
2139	// (2) the wavelength must be the same
2140	//
2141	// passes the matching rows in the sample table back
2142	//
2143	Function GuessTransToScattFiles(charsToUse,row,matchRows)
2144	Variable charsToUse,row //number of characers to use from the beginning of the label, and the row of the transmission file
2145	Wave matchRows //rows where (potential) matches found. initially zero points
2146
2147	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
2148	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
2149	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
2150	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
2151	Wave sLam = root:myGlobals:TransHeaderInfo:S_Lambda //Scattering file wavelength
2152	Wave tLam = root:myGlobals:TransHeaderInfo:T_Lambda //Transmission file wavelength
2153
2154	Variable num,ii,found
2155	String transStr = "",testStr=""
2156
2157	transStr = (tw[row])[0,charsToUse-1] //string to try and match
2158	transStr += "*"
2159
2160	//loop over ALL sample files
2161	num=numpnts(sw)
2162	ii=0
2163	do
2164	testStr=sw[ii]
2165	found = stringmatch(testStr, transStr )
2166	if( (found == 1) && (sLam[ii] == tLam[row]) ) // both must match
2167	Print "Match Found at: ",transStr,snam[ii],sw[ii]
2168	InsertPoints numpnts(matchRows), 1, matchRows
2169	matchRows[numpnts(matchRows)-1] = ii
2170	endif
2171	ii+=1
2172	while(ii<num)
2173
2174	//method 2 UNTESTED
2175	// transStr = (tw[row])[0,charsToUse-1] //string to try and match
2176	// num=numpnts(sw)
2177	// ii=0
2178	// do
2179	// testStr=sw[ii]
2180	// found = strsearch(testStr,transStr,0,2) //start from zero, ignore case
2181	// if(found != -1)
2182	// Print "Match Found at: ",transStr,snam[ii],sw[ii]
2183	// InsertPoints numpnts(matchRows), 1, matchRows
2184	// matchRows[numpnts(matchRows)-1] = ii
2185	//// snam[ii] = tnam[row] //write the file name into the table
2186	// endif
2187	// ii+=1
2188	// while(ii<num)
2189
2190	// Print "No Match found"
2191	return(0)
2192	End
2193
2194	//get a single selection from the Trans table
2195	// find all of the matching scattering files (rows)
2196	// ask the user if the selections are OK
2197	// if NOT OK, do nothing
2198	// if OK: make the assignments, and immediately calculate the transmission
2199	//
2200	Function fGuessTransToScattFiles(numChars)
2201	Variable numChars
2202
2203	Variable ii,row
2204	Variable transTableExists
2205	Make/O/D/N=0 root:myGlobals:TransHeaderInfo:matchRows
2206	Wave matchRows=root:myGlobals:TransHeaderInfo:matchRows
2207
2208	transTableExists = WinType("TransFileTable")
2209	if (transTableExists != 0)
2210	GetSelection table,transFileTable,1
2211	row = V_startRow
2212	GuessTransToScattFiles(numChars,row,matchRows)
2213	else
2214	Print "Transmission->Scattering File table is not open"
2215	return (1)
2216	endif
2217
2218	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
2219	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
2220	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
2221	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
2222	Wave/T samfile = root:myGlobals:TransHeaderInfo:S_FileNames //Scattering file name
2223
2224	// can do fancy formatted string with ...
2225	//"asdf* matches file: \\f01filen\\f00 \\K(52428,1,1)\\f01afdsfdd\\f00\\K(0,0,0)asdfasdfs"
2226	Variable num=numpnts(matchRows)
2227	String result="",tmpStr
2228	for(ii=0;ii<num;ii+=1)
2229	sprintf tmpStr,"\\f01\\K(52428,1,1)%s\\K(0,0,0)\\f00* Matches file: \\f01%s\\f00 \| \\K(52428,1,1)\\f01%s\\f00\\K(0,0,0)%s\r",(tw[row])[0,numChars-1],samfile[matchRows[ii]],(sw[matchRows[ii]])[0,numchars-1],(sw[matchRows[ii]])[numchars,59]
2230	result += tmpStr
2231	endfor
2232
2233	if(cmpstr(result,"")==0)
2234	result = "No match found for "+ (tw[row])[0,numChars-1]
2235	endif
2236
2237	// Print result
2238	Print "*******"
2239
2240	String/G root:myGlobals:TransHeaderInfo:gResultStr = result
2241
2242	DoWindow/F ConfirmGuess //it really shouldn't exist...
2243	if(V_flag==1)
2244	TitleBox title0,pos={9,5},variable=root:myGlobals:TransHeaderInfo:gResultStr
2245	else
2246	NewPanel /W=(578,44,1263,214) as "Confirm Guess"
2247	DoWindow/C ConfirmGuess
2248	TitleBox title0,pos={9,5},size={501,32}
2249	TitleBox title0,variable= root:myGlobals:TransHeaderInfo:gResultStr
2250	Button button0,pos={9,107},size={190,20},proc=DoAssignTransButtonProc,title="Assign Transmission Files"
2251	Button button2,pos={341,108},size={90,20},proc=DoTryAgainButtonProc,title="Try Again"
2252	ToolsGrid snap=1,visible=1
2253	endif
2254
2255	PauseForUser ConfirmGuess
2256
2257	// figure out from the return code what the user did...
2258	// 1 = OK, accept guess (assign, and calculate immediately)
2259	// 2 = try again
2260	// 0 = cancel, don't do anything (not used, simply try again)
2261	NVAR guessOK = root:myGlobals:TransHeaderInfo:GuessOK
2262
2263	// switch here...
2264	switch(guessOK) // numeric switch
2265	case 1:
2266	// accept guess (assign, and calculate immediately)
2267	for(ii=0;ii<num;ii+=1)
2268	snam[matchRows[ii]] = tnam[row]
2269	//AssignSelTransFilesToData(matchRows[ii],matchRows[ii])
2270	CalcSelTransFromHeader(matchRows[ii],matchRows[ii]) //does only that sample file
2271	endfor
2272	break
2273	case 2: //try again (with more / fewer characters?)
2274	// does nothing right now
2275	break
2276	case 0:
2277	// do nothing
2278	break
2279	default:
2280	// do nothing
2281	endswitch
2282
2283	return(0)
2284	End
2285
2286	// a hook attached to the Transmission Files Table
2287	// given a single selected Trans File, popup gives choices
2288	// to guess using "n" characters, then dispatch accordingly
2289	Function GuessFromTableHook(infoStr)
2290	String infoStr
2291	String event= StringByKey("EVENT",infoStr)
2292	// Print "EVENT= ",event
2293
2294	String menuStr=""
2295	menuStr += "Guess using 3 characters;"
2296	menuStr += "Guess using 6 characters;"
2297	menuStr += "Guess using 9 characters;"
2298	menuStr += "Guess using 12 characters;"
2299	menuStr += "Guess using 15 characters;"
2300	menuStr += "Guess using 18 characters;"
2301	menuStr += "Guess using 21 characters;"
2302	menuStr += "Guess using 24 characters;"
2303
2304	strswitch(event)
2305	case "mousedown":
2306	Variable xpix= NumberByKey("MOUSEX",infoStr)
2307	Variable ypix= NumberByKey("MOUSEY",infoStr)
2308	Variable modif= NumberByKey("MODIFIERS",infoStr)
2309	//print modif
2310	if(modif & 2^1) //bit 1 set, shift key is down
2311	PopupContextualMenu/C=(xpix, ypix) menuStr
2312	strswitch(S_selection)
2313	case "Guess using 3 characters":
2314	fGuessTransToScattFiles(3)
2315	break
2316	case "Guess using 6 characters":
2317	fGuessTransToScattFiles(6)
2318	break
2319	case "Guess using 9 characters":
2320	fGuessTransToScattFiles(9)
2321	break
2322	case "Guess using 12 characters":
2323	fGuessTransToScattFiles(12)
2324	break
2325	case "Guess using 15 characters":
2326	fGuessTransToScattFiles(15)
2327	break
2328	case "Guess using 18 characters":
2329	fGuessTransToScattFiles(18)
2330	break
2331	case "Guess using 21 characters":
2332	fGuessTransToScattFiles(21)
2333	break
2334	case "Guess using 24 characters":
2335	fGuessTransToScattFiles(24)
2336	break
2337	endswitch //on selection
2338	endif
2339	endswitch // on event
2340
2341	return 0
2342	End
2343
2344	// sets a flag if the user thinks that the guess was correct, and wants to use the
2345	// identified files for the transmission
2346	Function DoAssignTransButtonProc(ba) : ButtonControl
2347	STRUCT WMButtonAction &ba
2348
2349	switch( ba.eventCode )
2350	case 2: // mouse up
2351	// click code here
2352	//Print "Assigned stuff, and left."
2353	Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 1
2354	DoWindow/K ConfirmGuess
2355	break
2356	endswitch
2357
2358
2359	return 0
2360	End
2361
2362	// files are wrong, let the user try it again
2363	// sets a flag, nothing else
2364	Function DoTryAgainButtonProc(ba) : ButtonControl
2365	STRUCT WMButtonAction &ba
2366
2367	switch( ba.eventCode )
2368	case 2: // mouse up
2369	// click code here
2370	Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 2
2371	DoWindow/K ConfirmGuess
2372	//Print "Try Again"
2373	break
2374	endswitch
2375
2376	return 0
2377	End
2378
2379	// not used
2380	Function DoCancelGuessButtonProc(ba) : ButtonControl
2381	STRUCT WMButtonAction &ba
2382
2383	switch( ba.eventCode )
2384	case 2: // mouse up
2385	// click code here
2386	//just kill the panel, don't do anything
2387	Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 0
2388	DoWindow/K ConfirmGuess
2389	break
2390	endswitch
2391
2392	return 0
2393	End
2394
2395	Function GuessAllTransFiles(numChars)
2396	Variable numChars
2397
2398	if(WinType("ScatterFileTable") ==0 )
2399	return(1)
2400	endif
2401
2402	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
2403	Variable ii,num=numpnts(sw)
2404
2405	for(ii=0;ii<num;ii+=1)
2406	GuessTransFile(numChars,ii)
2407	endfor
2408
2409	return(0)
2410	End
2411
2412	Function fGuessSelectedTransFiles(numChars)
2413	Variable numChars
2414
2415	Variable ii
2416	Variable scatterTableExists
2417	scatterTableExists = WinType("ScatterFileTable")
2418	if (scatterTableExists != 0)
2419	GetSelection table,ScatterFileTable,1
2420	for(ii=V_StartRow;ii<=V_EndRow;ii+=1)
2421	GuessTransFile(numChars,ii)
2422	endfor
2423	else
2424	Print "Transmission->Scattering File table is not open"
2425	endif
2426	return(0)
2427	End
2428
2429	Function ClearSelectedAssignments()
2430
2431	// String winStr = WinList("*", ";", "WIN:" ) //returns the target window
2432	// Variable scatterTableExists, transTableExists
2433	// Print winStr
2434	// scatterTableExists = cmpstr(winStr,"ScatterFileTable;")
2435	// if (scatterTableExists == 0)
2436	// GetSelection table,ScatterFileTable,1
2437	// fClearSelectedAssignments(V_startRow,V_endRow,1)
2438	// endif
2439	//
2440	// transTableExists = cmpstr(winStr,"TransFileTable;")
2441	// if (transTableExists == 0)
2442	// GetSelection table,TransFileTable,1
2443	// fClearSelectedAssignments(V_startRow,V_endRow,2)
2444	// endif
2445
2446	// return(0)
2447	End

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