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Transmission.ipf @ 40

Last change on this file since 40 was 40, checked in by srkline, 16 years ago
Initial checkin of V5.00 SANSReduction files
File size: 81.2 KB

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1	#pragma rtGlobals=1 // Use modern global access method.
2	#pragma version=5.0
3	#pragma IgorVersion=4.0
4
5	//*************************
6	// Vers. 1.2 092101
7	//
8	// - procedures for (easier) caluclation of transmissions along with
9	// simultaneous patching of the calculated transmission in designated
10	// raw sans files.
11	// - transmission and empty beam files are linked to the dataset by their "Annn" suffix
12	// only (and their residence in the same data folder)
13	// - unused (analysis) integer values are used to store these run numbers in the sample
14	// file headers so that transmissions can be automatically calculated, once the xy box is set
15	// in the empty beam file.
16	//
17	//***************************
18
19	//main entry procedure for displaying the Trans input panel
20	//also initializes the globals as needed
21	//
22	Proc CalcTrans()
23
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)
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	DoWindow/F TransFileTable
51
52	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Suffices"
53	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
54	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Filenames"
55	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Suffix"
56	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Labels"
57	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_SDD"
58	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Lambda"
59	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Transmission"
60	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Whole"
61	If(V_Flag==0)
62	BuildTransTableWindow()
63	ModifyTable width(:myGlobals:TransHeaderInfo:T_SDD)=40
64	ModifyTable width(:myGlobals:TransHeaderInfo:T_Lambda)=40
65	ModifyTable rgb(:myGlobals:TransHeaderInfo:T_Filenames)=(0,0,65535)
66	ModifyTable width(:myGlobals:TransHeaderInfo:T_Transmission)=60
67	ModifyTable width(:myGlobals:TransHeaderInfo:T_Whole)=60
68
69	ModifyTable width(Point)=0
70	//ModifyTable width(:myGlobals:TransHeaderInfo:T_Transmission)=40
71	Endif
72
73	DoWindow/F ScatterFileTable
74	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Suffices"
75	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
76	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Filenames"
77	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Suffix"
78	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Labels"
79	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_SDD"
80	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Lambda"
81	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Transmission"
82	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Whole"
83	If(V_Flag==0)
84	BuildScatTableWindow()
85	ModifyTable width(:myGlobals:TransHeaderInfo:S_SDD)=40
86	ModifyTable width(:myGlobals:TransHeaderInfo:S_Lambda)=40
87	ModifyTable width(:myGlobals:TransHeaderInfo:S_Transmission)=60
88	ModifyTable rgb(:myGlobals:TransHeaderInfo:S_Filenames)=(0,0,65535)
89
90	ModifyTable width(Point)=0
91	Endif
92
93	String temp=""
94
95	//get a list of all files in the folder, some will be junk version numbers that don't exist
96	String list,partialName,tempName
97	list = IndexedFile(catPathName,-1,"????") //get all files in folder
98	Variable numitems,ii,ok
99
100	//remove version numbers from semicolon-delimited list
101	list = RemoveVersNumsFromList(list)
102
103	numitems = ItemsInList(list,";")
104
105	//loop through all of the files in the list, reading CAT/SHORT information if the file is RAW SANS
106	//*version numbers have been removed*
107	String str,fullName
108	Variable lastPoint
109	ii=0
110
111	do
112	//get current item in the list
113	partialName = StringFromList(ii, list, ";")
114	//get a valid file based on this partialName and catPathName
115	tempName = FindValidFilename(partialName)
116	If(cmpstr(tempName,"")==0) //a null string was returned
117	//write to notebook that file was not found
118	//if string is not a number, report the error
119	if(str2num(partialName) == NaN)
120	str = "this file was not found: "+partialName+"\r\r"
121	//Notebook CatWin,font="Times",fsize=12,text=str
122	Endif
123	else
124	//prepend path to tempName for read routine
125	PathInfo catPathName
126	FullName = S_path + tempName
127	//make sure the file is really a RAW data file
128	ok = CheckIfRawData(fullName)
129	if (ok)
130	GetTransHeaderInfoToWave(fullName,tempName)
131	Endif
132	Endif
133	ii+=1
134	while(ii<numitems)
135	//Now sort them all based on the suffix data
136	SortTransByDate()
137	//Now fill in the filenames of the ones that have already had EMP or TRANS
138	//files associated with them.
139	GetFilenamesFromSuffices()
140
141	//position the windows nicely
142	AutoPositionWindow/M=1/R=TransFileTable ScatterFileTable
143	DoWindow/F Trans_Panel
144	End
145
146	//actually creates the table of transmission files
147	// - the waves must exist
148	//
149	Function BuildTransTableWindow()
150	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
151	Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
152	Wave/T T_Suffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
153	Wave/T T_Labels = $"root:myGlobals:TransHeaderInfo:T_Labels"
154	Wave T_SDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
155	Wave T_Lambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
156	Wave T_Transmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
157	Wave T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
158
159	Edit/K=1/W=(30,30,500,250) T_EMP_Filenames, T_Filenames, T_Labels, T_SDD, T_Lambda, T_Transmission, T_Whole as "TransmissionFiles"
160	String name="TransFileTable"
161	DoWindow/C $name
162
163	End
164
165	//actually creates the table of scattering files
166	// - the waves must exist
167	//
168	Function BuildScatTableWindow()
169	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
170	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
171	Wave/T S_Suffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
172	Wave/T S_Labels = $"root:myGlobals:TransHeaderInfo:S_Labels"
173	Wave S_SDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
174	Wave S_Lambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
175	Wave S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
176
177	Edit/K=1/W=(50,50,520,270) S_TRANS_Filenames, S_Filenames, S_Labels, S_SDD, S_Lambda, S_Transmission as "ScatteringFiles"
178	String name="ScatterFileTable"
179	DoWindow/C $name
180
181	End
182
183	//sorts each of the tables by date - does this by using the suffix "Annn"
184	// which is automatically supplied by the VAX (and can't be changed)
185	// - only problem may be "Z999" -> "A001" rollover
186	//
187	Function SortTransByDate()
188	Wave/T T_GEMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
189	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
190	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
191	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
192	Wave/T T_GLabels = $"root:myGlobals:TransHeaderInfo:T_Labels"
193	Wave T_GSDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
194	Wave T_GLambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
195	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
196	Wave T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
197
198	Wave/T S_GTRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
199	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
200	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
201	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
202	Wave/T S_GLabels = $"root:myGlobals:TransHeaderInfo:S_Labels"
203	Wave S_GSDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
204	Wave S_GLambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
205	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
206	Wave S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
207
208	Sort T_GSuffix, T_GEMP_Filenames, T_GSuffix, T_GSuffices, T_GFilenames, T_GLabels, T_GSDD, T_GLambda, T_GTransmission, T_Whole
209	Sort S_GSuffix, S_GTRANS_Filenames, S_GSuffix, S_GSuffices, S_GFilenames, S_GLabels, S_GSDD, S_GLambda, S_GTransmission, S_Whole
210
211	End
212
213	// sorts files alphabetically byt the sample label
214	// - consistent and descriptive sample labels really pay off here
215	//
216	Function SortTransByLabel()
217	Wave/T T_GEMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
218	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
219	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
220	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
221	Wave/T T_GLabels = $"root:myGlobals:TransHeaderInfo:T_Labels"
222	Wave T_GSDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
223	Wave T_GLambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
224	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
225	Wave T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
226
227	Wave/T S_GTRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
228	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
229	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
230	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
231	Wave/T S_GLabels = $"root:myGlobals:TransHeaderInfo:S_Labels"
232	Wave S_GSDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
233	Wave S_GLambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
234	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
235	Wave S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
236
237	Sort T_GLabels, T_GEMP_Filenames, T_GSuffix, T_GSuffices, T_GFilenames, T_GLabels, T_GSDD, T_GLambda, T_GTransmission, T_Whole
238	Sort S_GLabels, S_GTRANS_Filenames, S_GSuffix, S_GSuffices, S_GFilenames, S_GLabels, S_GSDD, S_GLambda, S_GTransmission, S_Whole
239
240	End
241
242	//reads the file and assigns header information to the proper table
243	//
244	//fname - is the full path:name of the datafile (used by Open)
245	//sname - is the name only, used as the filename field
246	//
247	// takes care of all necessary open/close of file
248	//
249	Function GetTransHeaderInfoToWave(fname,sname)
250	String fname,sname
251
252	Variable isTrans, xTol= -5
253
254	String textstr,temp,labelStr,date_time,suffix,assoc
255	Variable ctime,lambda,sdd,detcnt,cntrate,refNum,trans,thick,xcenter,ycenter,numatten
256	Variable lastPoint, beamstop, Whole
257
258	isTrans = CheckIfBeamstopOut(fname, xTol)
259	// decalre the correct set of waves
260	// S_Whole is only a place holder so the waves are of equal length
261	if (isTrans)
262	Wave/T GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
263	Wave/T G_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
264	Wave/T GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
265	Wave/T GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
266	Wave/T GLabels = $"root:myGlobals:TransHeaderInfo:T_Labels"
267	Wave GSDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
268	Wave GLambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
269	Wave GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
270	Wave GWhole = $"root:myGlobals:TransHeaderInfo:T_Whole"
271	Else
272	Wave/T GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
273	Wave/T G_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
274	Wave/T GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
275	Wave/T GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
276	Wave/T GLabels = $"root:myGlobals:TransHeaderInfo:S_Labels"
277	Wave GSDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
278	Wave GLambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
279	Wave GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
280	Wave GWhole = $"root:myGlobals:TransHeaderInfo:S_Whole"
281	Endif
282
283	lastPoint = numpnts(GLambda)
284
285	Open/R refNum as fname
286
287	InsertPoints lastPoint,1,G_TRANS_Filenames
288	G_TRANS_Filenames[lastPoint]=""
289
290	InsertPoints lastPoint,1,GFilenames
291	GFilenames[lastPoint]=sname
292
293	//read the file suffix
294	FSetPos refNum,19
295	FReadLine/N=4 refNum,suffix
296	//print suffix
297	InsertPoints lastPoint,1,GSuffix
298	GSuffix[lastPoint]=suffix
299
300	//read any suffix that this file is associated with
301	//FSetPos refNum,91 //wrong position
302	FSetPos refNum,404
303	FReadLine/N=4 refNum,assoc
304	//print isTrans, assoc
305	InsertPoints lastPoint,1,GSuffices
306	GSuffices[lastPoint]=assoc
307
308	// read the sample.label text field
309	FSetPos refNum,98 //will start reading at byte 99
310	FReadLine/N=60 refNum,labelStr
311	InsertPoints lastPoint,1,GLabels
312	GLabels[lastPoint]=labelStr
313
314	Close refNum
315
316	//read the reals with GBLoadWave
317	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
318	String strToExecute
319
320	//Transmission
321	strToExecute = GBLoadStr + "/S=158/U=1" + "\"" + fname + "\""
322	Execute strToExecute
323	Wave w=$"tempGBWave0"
324	trans = w[0]
325	InsertPoints lastPoint,1,GTransmission
326	GTransmission[lastPoint]=trans
327
328	//Whole Transmission
329	strToExecute = GBLoadStr + "/S=392/U=1" + "\"" + fname + "\""
330	Execute strToExecute
331	Wave w=$"tempGBWave0"
332	Whole = w[0]
333	InsertPoints lastPoint,1,GWhole
334	GWhole[lastPoint]=Whole
335
336	//SDD
337	strToExecute = GBLoadStr + "/S=260/U=1" + "\"" + fname + "\""
338	Execute strToExecute
339	sdd = w[0]
340	InsertPoints lastPoint,1,GSDD
341	GSDD[lastPoint]=sdd
342
343	//wavelength
344	strToExecute = GBLoadStr + "/S=292/U=1" + "\"" + fname + "\""
345	Execute strToExecute
346	lambda = w[0]
347	InsertPoints lastPoint,1,GLambda
348	GLambda[lastPoint]=lambda
349
350	// InsertPoints lastPoint,1,GWhole
351	// GWhole[lastPoint]=1
352
353	KillWaves/Z w
354
355	End
356
357	//fills in the file relations that have already been set
358	//
359	//
360	Function GetFilenamesFromSuffices()
361	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
362	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
363	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
364	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
365
366	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
367	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
368	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
369	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
370
371	Variable num_s_files, num_t_files, ii, jj
372	num_t_files = numpnts(T_GFilenames)
373	num_s_files = numpnts(S_GFilenames)
374	//print num_t_files, num_s_files
375
376	// Get transmission file relations
377	ii= 0
378	do
379	if (cmpstr(T_GSuffices[ii],"")!=0)
380	jj=0
381	do
382	if (cmpstr(T_GSuffices[ii],T_GSuffix[jj])==0)
383	T_EMP_Filenames[ii]=T_GFilenames[jj]
384	endif
385	jj+=1
386	while(jj<num_t_files)
387	endif
388	ii+=1
389	while(ii<num_t_files)
390
391	// Get scattering file relations
392	ii= 0
393	do
394	if (cmpstr(S_GSuffices[ii],"")!=0)
395	jj=0
396	do
397	if (cmpstr(S_GSuffices[ii],T_GSuffix[jj])==0)
398	S_TRANS_Filenames[ii]=T_GFilenames[jj]
399	endif
400	jj+=1
401	while(jj<num_t_files)
402	endif
403	ii+=1
404	while(ii<num_s_files)
405	End
406
407	// gets the selected transmission filename, and puts its name as the
408	//empty beam reference file
409	// lists the xy box coordinates as read from the file header (zeros if not yet assigned)
410	//
411	Function PickEMPTransButton(ctrlName) : ButtonControl
412	String ctrlName
413
414	Variable TransFileTableExists
415	TransFileTableExists = WinType("TransFileTable")
416	//??BUG?? V_flag returns 1 even if no selection?
417	//check manually for null selection
418	//Print "local v_flag = ",num2str(V_flag)
419	Wave/T LocFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
420	if (TransFileTableExists != 0)
421	String/G root:myGlobals:TransHeaderInfo:gEMP = ""
422	GetSelection table,TransFileTable,7
423	//Print S_Selection
424	if(strsearch(S_selection,"T_Filenames",0) == 0)
425	//selection OK, add to list
426	Duplicate/O/R=[V_startRow,V_endRow] LocFilenames, filenames
427	Wave/T selectedFiles = $"filenames"
428
429	SVAR temp = root:myGlobals:TransHeaderInfo:gEMP
430	//
431	temp = temp+selectedFiles[0] //take just the first file
432	UpdateBoxCoordinates()
433	Else
434	DoWindow/F TransFileTable
435	DoAlert 0,"Invalid selection from the Transmision file table. You must select a file from the T_Filenames column"
436	Endif
437	else
438	//no selection
439	DoAlert 0,"No file selected from Transmission file table or no Transmission file table available"
440	Endif
441	End
442
443	//initialize data folder and globals for the Trans panel as needed
444	//since this operation is somewhat tangled with the Patch Panel, keep all of the
445	//globals in the Patch subfolder (make sure both panels are simultaneously initialized)
446	//do not create a separate Trans folder
447	//
448	Proc InitializeTransPanel()
449	//create the global variables needed to run the Trans Panel
450	//all are kept in root:myGlobals:TransHeaderInfo
451	If( ! (DataFolderExists("root:myGlobals:TransHeaderInfo")) )
452	//create the data folder and the clobals for BOTH the Patch and Trans Panels
453	NewDataFolder/O root:myGlobals:TransHeaderInfo
454	CreateTransGlobals()
455	Endif
456	End
457
458
459	//
460	Proc CreateTransGlobals()
461
462	PathInfo catPathName
463	If(V_flag==1)
464	String dum = S_path
465	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = dum
466	else
467	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = "no path selected"
468	endif
469
470	String/G root:myGlobals:TransHeaderInfo:gEMP = "no file selected"
471	String/G root:myGlobals:TransHeaderInfo:gBox = ""
472	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Suffices"
473	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
474	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Filenames"
475	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Suffix"
476	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Labels"
477	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_SDD"
478	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Lambda"
479	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Transmission"
480	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Whole"
481
482	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Suffices"
483	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
484	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Filenames"
485	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Suffix"
486	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Labels"
487	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_SDD"
488	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Lambda"
489	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Transmission"
490	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Whole"
491	End
492
493
494	//function that writes out (to the header of a raw binary SANS file)
495	//characters representing the empty beam file and the sample transmission file
496	//the 4-character file suffix is written, rather than the run numbers
497	//from this, the trans files can be located, and the
498	//sample file contains all the information needed to calculate its transmission
499	//
500	//uses first 4 bytes of params.reserve (character field) starting at byte 404
501	//(previous version (AM) used run.reserve field @ byte 91, which was not empty, and not at the start of the field!)
502	//
503	Function AssignSelTransFilesToData(startRow,endRow)
504	Variable startRow,endRow
505
506	// GetSelection table,ScatterFileTable,1
507
508	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
509	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
510	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
511	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
512
513	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
514	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
515	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
516	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
517
518	Variable num_s_files, num_t_files, ii, jj
519	Variable refnum
520	num_t_files = numpnts(T_GFilenames)
521	String suffix = ""
522	PathInfo catPathName
523	String pathname = S_path
524	String filename
525
526	// Write suffix of empty beam file into transmission files
527	ii= 0
528	do
529	if (cmpstr(T_EMP_Filenames[ii],"")!=0)
530	jj=0
531	do
532	if (cmpstr(T_EMP_Filenames[ii],T_GFilenames[jj])==0)
533	suffix=T_GSuffix[jj]
534	filename = pathname + T_GFilenames[ii]
535	Open/A/T="????TEXT" refnum as filename
536	//FSetPos refnum,91 //wrong position
537	FSetPos refnum,404
538	FBinWrite refnum, suffix
539	FStatus refnum
540	FSetPos refnum,V_logEOF
541	Close refnum
542	endif
543	jj+=1
544	while(jj<num_t_files)
545	endif
546	ii+=1
547	while(ii<num_t_files)
548
549	// Write suffix of transmission files into scattering files
550	ii= startRow
551	do
552	if (cmpstr(S_TRANS_Filenames[ii],"")!=0)
553	jj=0
554	do
555	if (cmpstr(S_TRANS_Filenames[ii],T_GFilenames[jj])==0)
556	suffix=T_GSuffix[jj]
557	filename = pathname + S_GFilenames[ii]
558	Open/A/T="????TEXT" refnum as filename
559	//FSetPos refnum,91 //wrong position
560	FSetPos refnum,404
561	FBinWrite refnum, suffix
562	FStatus refnum
563	FSetPos refnum,V_logEOF
564	Close refnum
565	endif
566	jj+=1
567	while(jj<num_t_files)
568	endif
569	ii+=1
570	while(ii<=endRow)
571	return(0)
572	End
573
574	// Allows to calculate transmissions without need of a scattering file. Used with the Calculate Total Trans button.
575
576	Function AssignTotalTransFilesToData(startRow,endRow)
577	Variable startRow,endRow
578
579	// GetSelection table,ScatterFileTable,1
580
581	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
582	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
583	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
584	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
585
586	Variable num_t_files, ii, jj
587	Variable refnum
588	num_t_files = numpnts(T_GFilenames)
589	String suffix = ""
590	PathInfo catPathName
591	String pathname = S_path
592	String filename
593
594	// Write suffix of empty beam file into transmission files
595	ii= 0
596	do
597	if (cmpstr(T_EMP_Filenames[ii],"")!=0)
598	jj=0
599	do
600	if (cmpstr(T_EMP_Filenames[ii],T_GFilenames[jj])==0)
601	suffix=T_GSuffix[jj]
602	filename = pathname + T_GFilenames[ii]
603	Open/A/T="????TEXT" refnum as filename
604	//FSetPos refnum,91 //wrong position
605	FSetPos refnum,404
606	FBinWrite refnum, suffix
607	FStatus refnum
608	FSetPos refnum,V_logEOF
609	Close refnum
610	endif
611	jj+=1
612	while(jj<num_t_files)
613	endif
614	ii+=1
615	while(ii<num_t_files)
616
617	return(0)
618	End
619
620
621	//function that clears the selected assignments of sample trans -> sample scattering
622	//also writes a trans=1 value back to the sample file
623	//
624	Function fClearSelectedAssignments(startRow,endRow)
625	Variable startRow,endRow
626
627	// GetSelection table,ScatterFileTable,1
628
629	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
630	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
631	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
632	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
633	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
634
635	Variable num_s_files, num_t_files, ii, jj
636	Variable refnum
637	num_t_files = numpnts(T_GFilenames)
638	String suffix = " " //4 blank spaces
639	PathInfo catPathName
640	String pathname = S_path
641	String filename
642
643	// don't do anything with the trans file -> empty beam file correspondence
644
645	// // Write suffix of empty beam file into transmission files
646	// ii= 0
647	// do
648	// if (cmpstr(T_EMP_Filenames[ii],"")!=0)
649	// jj=0
650	// do
651	// if (cmpstr(T_EMP_Filenames[ii],T_GFilenames[jj])==0)
652	// suffix=T_GSuffix[jj]
653	// filename = pathname + T_GFilenames[ii]
654	// Open/A/T="????TEXT" refnum as filename
655	// //FSetPos refnum,91 //wrong position
656	// FSetPos refnum,404
657	// FBinWrite refnum, suffix
658	// FStatus refnum
659	// FSetPos refnum,V_logEOF
660	// Close refnum
661	// endif
662	// jj+=1
663	// while(jj<num_t_files)
664	// endif
665	// ii+=1
666	// while(ii<num_t_files)
667
668	// Write null suffix of transmission files into scattering files
669	ii= startRow
670	do
671	filename = pathname + S_GFilenames[ii]
672	Open/A/T="????TEXT" refnum as filename
673	//FSetPos refnum,91 //wrong position
674	FSetPos refnum,404
675	FBinWrite refnum, suffix
676	FStatus refnum
677	FSetPos refnum,V_logEOF
678	Close refnum
679
680	//write a trans==1 to the file header of the raw data (open/close done in function)
681	ReWriteReal(filename,1,158) //transmission start byte is 158
682
683	//then update the table that is displayed
684	S_TRANS_Filenames[ii] = ""
685	S_GTransmission[ii] = 1
686
687	ii+=1
688	while(ii<=endRow)
689	return(0)
690	End
691
692
693	// assigns both the empty file to the trans file
694	// and the trans file to the scattering file
695	// - writes out 4 characters to the file headers @ byte 404
696	//
697	// assignments are only permanently made when the transmissions
698	// are actually calculated
699	//
700	// NOT USED - AssignSelTransFilestoData(first,last) has been generalized to take a range
701	// 3/31/04 SRK
702	//Function AssignTransFilesToData()
703	//
704	// Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
705	// Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
706	// Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
707	// Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
708	//
709	// Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
710	// Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
711	// Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
712	// Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
713	//
714	// Variable num_s_files, num_t_files, ii, jj
715	// Variable refnum
716	// num_t_files = numpnts(T_GFilenames)
717	// num_s_files = numpnts(S_GFilenames)
718	// String suffix = ""
719	// PathInfo catPathName
720	// String pathname = S_path
721	// String filename
722	//
723	// // Write suffix of empty beam file into transmission files
724	// ii= 0
725	// do
726	// if (cmpstr(T_EMP_Filenames[ii],"")!=0)
727	// jj=0
728	// do
729	// if (cmpstr(T_EMP_Filenames[ii],T_GFilenames[jj])==0)
730	// suffix=T_GSuffix[jj]
731	// filename = pathname + T_GFilenames[ii]
732	// Open/A/T="????TEXT" refnum as filename
733	// //FSetPos refnum,91 //wrong position
734	// FSetPos refnum,404
735	// FBinWrite refnum, suffix
736	// FStatus refnum
737	// FSetPos refnum,V_logEOF
738	// Close refnum
739	// endif
740	// jj+=1
741	// while(jj<num_t_files)
742	// endif
743	// ii+=1
744	// while(ii<num_t_files)
745	//
746	// // Write suffix of transmission files into scattering files
747	// ii= 0
748	// do
749	// if (cmpstr(S_TRANS_Filenames[ii],"")!=0)
750	// jj=0
751	// do
752	// if (cmpstr(S_TRANS_Filenames[ii],T_GFilenames[jj])==0)
753	// suffix=T_GSuffix[jj]
754	// filename = pathname + S_GFilenames[ii]
755	// Open/A/T="????TEXT" refnum as filename
756	// //FSetPos refnum,91 //wrong position
757	// FSetPos refnum,404
758	// FBinWrite refnum, suffix
759	// FStatus refnum
760	// FSetPos refnum,V_logEOF
761	// Close refnum
762	// endif
763	// jj+=1
764	// while(jj<num_t_files)
765	// endif
766	// ii+=1
767	// while(ii<num_s_files)
768	//
769	// return(0)
770	//End
771
772
773
774	// NOT USED --- CalcSelTransFromHeader(first,last) has been generalized to accept a selection
775	// and modified to account for different attenuation factors. 3/31/04 SRK
776	//
777	//Function CalcTransFromHeader()
778	// String filename
779	// Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
780	// Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
781	//
782	// Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
783	// Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
784	// Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
785	//
786	// Variable num_s_files, num_t_files, ii, jj
787	// Variable refnum, transCts, emptyCts
788	// num_t_files = numpnts(T_GFilenames)
789	// num_s_files = numpnts(S_GFilenames)
790	// String suffix = ""
791	// PathInfo catPathName
792	// String pathname = S_path
793	// String textStr="",abortStr=""
794	// String emptyFile, transFile
795	//
796	// ii= 0
797	// do
798	// if (cmpstr(S_TRANS_Filenames[ii],"")!=0)
799	// jj=0
800	// do
801	// if (cmpstr(S_TRANS_Filenames[ii],T_GFilenames[jj])==0)
802	// //Look for an empty beam for the transmission then
803	// if (cmpstr(T_EMP_Filenames[jj],"")!=0)//Do the transmission calculation
804	// textStr = ""
805	// filename=pathname+S_GFilenames[ii]
806	// emptyFile = pathname+T_EMP_Filenames[jj]
807	// transFile = pathname+T_GFilenames[jj]
808	// //////////
809	// // check the empty beam file for previously selected coordinates
810	// //if they exist, set the xy string , save the normalized counts somewhere
811	// //the value was written to an unused r*4 header analysis.factor (@b494)
812	// Variable x1,x2,y1,y2,err
813	// Open/R refnum as emptyFile
814	// FSetPos refnum,478
815	// FBinRead/F=3/B=3 refnum, x1
816	// FBinRead/F=3/B=3 refnum, x2
817	// FBinRead/F=3/B=3 refnum, y1
818	// FBinRead/F=3/B=3 refnum, y2
819	// Close refnum
820	// //read the real count value
821	// String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
822	// String strToExecute
823	// strToExecute = GBLoadStr + "/S=494/U=1" + "\"" + emptyFile + "\""
824	// Execute strToExecute
825	// Wave w=$"tempGBWave0"
826	// Variable/G root:myGlobals:Patch:gTransCts = w[0]
827	// emptyCts = w[0]
828	//
829	// //
830	// if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
831	// //no region selected
832	// //prompt user to select box w/marquee
833	// DoWindow/F TransFileTable
834	// Abort "Use \"Set BCENT File\", then \"SetXYBox\" to select XY range in empty beam file "+T_EMP_Filenames[jj]
835	// //from here the Marquee menu selection must handle the task of setting the box
836	// //and updating the information in the file header
837	// Endif
838	//
839	// //read in trans file to add to SAM
840	// ReadHeaderAndData(transFile)
841	// //adds to SAM
842	// err = Raw_to_work("SAM")
843	// //sum region in SAM
844	// transCts = SumCountsInBox(x1,x2,y1,y2,"SAM")
845	//
846	// //calculate trans based on empty beam value
847	// Variable trans= transCts/emptyCts
848	//
849	// //write out counts and transmission
850	// textstr += " Trans counts = "+num2str(transCts) + " Trans = "+num2str(trans)
851	// Print S_GFilenames[ii], textstr
852	// //Print ii,jj
853	// //Print "Empty counts = ",emptycts, "Trans counts = "+num2str(transCts) + " Trans = "+num2str(trans)
854	//
855	// //write the trans to the file header of the raw data (open/close done in function)
856	// Variable start = 158 //transmission start byte
857	// ReWriteReal(filename,trans,start)
858	//
859	// //then update the global that is displayed
860	// S_GTransmission[ii] = trans
861	//
862	// else // There is no empty assigned
863	// abortStr = "Empty beam file not assigned properly for " + T_GFilenames[jj]
864	// Print abortStr
865	// //Abort abortStr
866	// return(1)
867	// endif
868	// endif
869	// jj+=1
870	// while(jj<num_t_files)
871	// else //no transmission file
872	// abortStr = "Transmission beam file not assigned properly for " + S_GFilenames[ii]
873	// Print abortStr
874	// endif
875	// ii+=1
876	// while(ii<num_s_files)
877	// print "done"
878	// return(0)
879	//End
880
881
882
883	//given a selection of scattering files, calculates the transmission
884	//and writes the new transmission to the file header
885	//
886	//given the full path;name;vers (= filenmame), of a raw binary SANS file,
887	//the transmission of the sample is calculated (if possible) from information
888	//in the file header. empty beam and sample transmision run numbers are extracted
889	//and the files are located from the run number (if possible)
890	//from the header of the empty beam file, the XY box coordinates and "empty"
891	//counts are determined
892	//once all information is located, the transmission is calculated and the
893	//transmission field of the sample file is automatically "Patched"
894	// - updates the global variable that is displayed in the panel
895	//can be run in batch mode, sequentially passing each item from a list of filenames
896	//this is the single step of the batch mode
897	//
898	//in batch mode: execution will proceed through all of the files, reporting
899	//results to the history window. If no trans could be successfully calculated
900	//(for a blocked beam, for example), then that is displayed as well, and the
901	//raw data is not modified
902	//
903	// now takes the attenuation of the sample trans and empty beam trans into account, (normally this == 1)
904	// and rescales the transmission as appropriate
905	// 3/31/04 SRK
906	//
907	Function CalcSelTransFromHeader(startRow,endRow)
908	Variable startRow,endRow
909	// GetSelection table,ScatterFileTable,1
910
911	String filename
912	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
913	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
914
915	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
916	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
917	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
918
919	Variable num_s_files, num_t_files, ii, jj
920	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
921	Variable x1,x2,y1,y2,err,attenEmp,attenSam
922	String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
923	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
924	String strToExecute
925
926	num_t_files = numpnts(T_GFilenames)
927
928	PathInfo catPathName
929	pathname = S_path
930
931	ii= startRow
932	do
933	if (cmpstr(S_TRANS_Filenames[ii],"")!=0) //if there is a sample trans file assigned
934	jj=0
935	do
936	if (cmpstr(S_TRANS_Filenames[ii],T_GFilenames[jj])==0) //find it in the trans file table
937	if (cmpstr(T_EMP_Filenames[jj],"")!=0) //if empty beam file assigned, proceed with the calculation
938	//full path+name to access all 3 files
939	filename=pathname+S_GFilenames[ii]
940	emptyFile = pathname+T_EMP_Filenames[jj]
941	transFile = pathname+T_GFilenames[jj]
942	//////////
943	// check the empty beam file for previously selected coordinates
944	//if they exist, set the xy string , save the normalized counts somewhere
945	//the value was written to an unused r*4 header analysis.factor (@b494)
946	Open/R refnum as emptyFile
947	FSetPos refnum,478
948	FBinRead/F=3/B=3 refnum, x1
949	FBinRead/F=3/B=3 refnum, x2
950	FBinRead/F=3/B=3 refnum, y1
951	FBinRead/F=3/B=3 refnum, y2
952	Close refnum
953	//read the real count value
954	strToExecute = GBLoadStr + "/S=494/U=1" + "\"" + emptyFile + "\""
955	Execute strToExecute
956	Wave w=$"tempGBWave0"
957	// Variable/G root:myGlobals:Patch:gTransCts = w[0]
958	emptyCts = w[0]
959	// read the attenuator number of the empty beam file
960	strToExecute = GBLoadStr + "/S=39/U=4" + "\"" + emptyFile + "\""
961	Execute strToExecute
962	attenEmp = w[3]
963	//
964	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
965	//no region selected -- prompt user to select box w/marquee
966	DoWindow/F TransFileTable
967	Abort "Use \"Set BCENT File\", then \"SetXYBox\" to select XY range in empty beam file "+T_EMP_Filenames[jj]
968	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
969	Endif
970
971	//read in trans file then add to SAM
972	ReadHeaderAndData(transFile)
973	//adds to SAM
974	err = Raw_to_work("SAM")
975	//sum region in SAM
976	transCts = SumCountsInBox(x1,x2,y1,y2,"SAM")
977	// get the attenuator, lambda, and sample string (to get the instrument)
978	WAVE/T samText = $"root:SAM:textRead"
979	WAVE samReals = $"root:SAM:realsRead"
980	samfileStr = samText[3]
981	lambda = samReals[26]
982	attenSam = samReals[3]
983	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
984	AttenRatio = AttenuationFactor(samFileStr,lambda,attenEmp)/AttenuationFactor(samFileStr,lambda,attenSam)
985	//calculate trans based on empty beam value and rescale by attenuation ratio
986	trans= transCts/emptyCts * AttenRatio
987
988	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
989	If(attenRatio==1)
990	Printf "%s\t\tTrans Counts = %g\tTrans = %g\r",S_GFilenames[ii], transCts,trans
991	else
992	Printf "%s\t\tTrans Counts = %g\tTrans = %g\tAttenuatorRatio = %g\r",S_GFilenames[ii], transCts,trans,attenRatio
993	endif
994	//write the trans to the file header of the raw data (open/close done in function)
995	ReWriteReal(filename,trans,158) //transmission start byte is 158
996
997	//then update the global that is displayed
998	S_GTransmission[ii] = trans
999
1000	else // There is no empty assigned
1001	abortStr = "Empty beam file not assigned properly for " + T_GFilenames[jj]
1002	Print abortStr
1003	//Abort abortStr
1004	return(1)
1005	endif
1006	endif
1007	jj+=1
1008	while(jj<num_t_files)
1009	else //no transmission file
1010	abortStr = "Transmission beam file not assigned properly for " + S_GFilenames[ii]
1011	Print abortStr
1012	endif
1013	ii+=1
1014	while(ii<=endRow)
1015	print "done"
1016	return(0)
1017	End
1018
1019	//
1020	// For the calculation of the Transmission using only the Trans Files screen
1021	// Uses only the information on the transmissionFiles screen to calculate
1022	// a "box" Transmission for comparison with the Whole Transmission
1023	// updated 5/11/2006 by Bryan Greenwald
1024	Function CalcTotalTrans(startRow,endRow)
1025	Variable startRow,endRow
1026	// GetSelection table,ScatterFileTable,1
1027
1028	String filename
1029	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
1030
1031	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
1032	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
1033
1034	// Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
1035	// Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1036	// Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
1037	Wave GWhole= $"root:myGlobals:TransHeaderInfo:T_Whole"
1038
1039	Variable num_t_files, ii, jj
1040	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
1041	Variable x1,x2,y1,y2,err,attenEmp,attenSam
1042	String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
1043	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
1044	String strToExecute
1045
1046	num_t_files = numpnts(T_GFilenames)
1047
1048	PathInfo catPathName
1049	pathname = S_path
1050
1051	ii= startRow
1052	do
1053	if (cmpstr(T_Emp_Filenames[ii],"")!=0) //if there is a sample trans file assigned
1054	jj=0
1055	do
1056	if (cmpstr(T_Emp_Filenames[ii],T_GFilenames[jj])==0) //find it in the trans file table
1057	if (cmpstr(T_EMP_Filenames[ii],"")!=0) //if empty beam file assigned, proceed with the calculation
1058	//full path+name to access all 3 files
1059	filename=pathname+T_GFilenames[ii]
1060	emptyFile = pathname+T_EMP_Filenames[ii]
1061	transFile = pathname+T_GFilenames[ii]
1062	//////////
1063	// check the empty beam file for previously selected coordinates
1064	//if they exist, set the xy string , save the normalized counts somewhere
1065	//the value was written to an unused r*4 header analysis.factor (@b494)
1066	Open/R refnum as emptyFile
1067	FSetPos refnum,478
1068	FBinRead/F=3/B=3 refnum, x1
1069	FBinRead/F=3/B=3 refnum, x2
1070	FBinRead/F=3/B=3 refnum, y1
1071	FBinRead/F=3/B=3 refnum, y2
1072	Close refnum
1073	//read the real count value
1074	strToExecute = GBLoadStr + "/S=494/U=1" + "\"" + emptyFile + "\""
1075	Execute strToExecute
1076	Wave w=$"tempGBWave0"
1077	// Variable/G root:myGlobals:Patch:gTransCts = w[0]
1078	emptyCts = w[0]
1079	// read the attenuator number of the empty beam file
1080	strToExecute = GBLoadStr + "/S=39/U=4" + "\"" + emptyFile + "\""
1081	Execute strToExecute
1082	attenEmp = w[3]
1083	//
1084	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
1085	//no region selected -- prompt user to select box w/marquee
1086	DoWindow/F TransFileTable
1087	Abort "Use \"Set BCENT File\", then \"SetXYBox\" to select XY range in empty beam file "+T_EMP_Filenames[jj]
1088	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
1089	Endif
1090
1091	//read in trans file then add to SAM
1092	ReadHeaderAndData(transFile)
1093	//adds to SAM
1094	err = Raw_to_work("SAM")
1095	//sum region in SAM
1096	transCts = SumCountsInBox(x1,x2,y1,y2,"SAM")
1097	// get the attenuator, lambda, and sample string (to get the instrument)
1098	WAVE/T samText = $"root:SAM:textRead"
1099	WAVE samReals = $"root:SAM:realsRead"
1100	samfileStr = samText[3]
1101	lambda = samReals[26]
1102	attenSam = samReals[3]
1103	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
1104	AttenRatio = AttenuationFactor(samFileStr,lambda,attenEmp)/AttenuationFactor(samFileStr,lambda,attenSam)
1105	//calculate trans based on empty beam value and rescale by attenuation ratio
1106	trans= transCts/emptyCts * AttenRatio
1107
1108	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
1109	If(attenRatio==1)
1110	//Printf "%s\t\tTrans Counts = %g\t Actual Trans = %g\r",T_GFilenames[ii], transCts,trans
1111	Printf "%s\t\tBox Counts = %g\t Trans = %g\r",T_GFilenames[ii], transCts,trans
1112	else
1113	//Printf "%s\t\tTrans Counts = %g\t Trans = %g\tAttenuatorRatio = %g\r",T_GFilenames[ii], transCts,trans,attenRatio
1114	Printf "%s\t\tBox Counts = %g\t Trans = %g\t AttenuatorRatio = %g\r",T_GFilenames[ii], transCts,trans,attenRatio
1115	endif
1116	//write the trans to the file header of the raw data (open/close done in function)
1117	ReWriteReal(filename,trans,158) //transmission start byte is 158
1118
1119	//then update the global that is displayed
1120	T_GTransmission[ii] = trans
1121
1122	else // There is no empty assigned
1123	abortStr = "Empty beam file not assigned properly for " + T_GFilenames[jj]
1124	Print abortStr
1125	//Abort abortStr
1126	return(1)
1127	endif
1128	endif
1129	jj+=1
1130	while(jj<num_t_files)
1131	else //no transmission file
1132	abortStr = "Transmission beam file not assigned properly for " + T_GFilenames[ii]
1133	Print abortStr
1134	endif
1135	ii+=1
1136	while(ii<=endRow)
1137	//print "done"
1138	return(0)
1139	End
1140
1141	//
1142	// For the calculation of the Transmission using only the whole detector
1143	// Used to compute the transmission for the TransmissionFiles table using
1144	// the entire computer. For comparison with the "box" trans
1145	// updated: 5/11/2006 bo Bryan Greenwald
1146	Function CalcWholeTrans(startRow,endRow)
1147	Variable startRow,endRow
1148	// GetSelection table,ScatterFileTable,1
1149
1150	String filename
1151	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
1152
1153	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
1154	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
1155
1156	// Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
1157	// Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1158	// Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
1159	Wave GWhole= $"root:myGlobals:TransHeaderInfo:T_Whole"
1160
1161	Variable num_t_files, ii, jj
1162	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
1163	Variable x1,x2,y1,y2,err,attenEmp,attenSam
1164	String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
1165	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
1166	String strToExecute
1167
1168	num_t_files = numpnts(T_GFilenames)
1169
1170	PathInfo catPathName
1171	pathname = S_path
1172
1173	ii= startRow
1174	do
1175	if (cmpstr(T_Emp_Filenames[ii],"")!=0) //if there is a sample trans file assigned
1176	jj=0
1177	do
1178	if (cmpstr(T_Emp_Filenames[ii],T_GFilenames[jj])==0) //find it in the trans file table
1179	if (cmpstr(T_EMP_Filenames[ii],"")!=0) //if empty beam file assigned, proceed with the calculation
1180	//full path+name to access all 3 files
1181	filename=pathname+T_GFilenames[ii]
1182	emptyFile = pathname+T_EMP_Filenames[ii]
1183	transFile = pathname+T_GFilenames[ii]
1184	//////////
1185	// check the empty beam file for previously selected coordinates
1186	//if they exist, set the xy string , save the normalized counts somewhere
1187	//the value was written to an unused r*4 header analysis.factor (@b494)
1188	Open/R refnum as emptyFile
1189	FSetPos refnum,478
1190	FBinRead/F=3/B=3 refnum, x1
1191	FBinRead/F=3/B=3 refnum, x2
1192	FBinRead/F=3/B=3 refnum, y1
1193	FBinRead/F=3/B=3 refnum, y2
1194	Close refnum
1195	//read the real count value
1196	strToExecute = GBLoadStr + "/S=494/U=1" + "\"" + emptyFile + "\""
1197	Execute strToExecute
1198	Wave w=$"tempGBWave0"
1199	// Variable/G root:myGlobals:Patch:gTransCts = w[0]
1200	emptyCts = w[0]
1201	// read the attenuator number of the empty beam file
1202	strToExecute = GBLoadStr + "/S=39/U=4" + "\"" + emptyFile + "\""
1203	Execute strToExecute
1204	attenEmp = w[3]
1205	//
1206	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
1207	//no region selected -- prompt user to select box w/marquee
1208	DoWindow/F TransFileTable
1209	Abort "Use \"Set BCENT File\", then \"SetXYBox\" to select XY range in empty beam file "+T_EMP_Filenames[jj]
1210	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
1211	Endif
1212
1213	//read in trans file then add to SAM
1214	ReadHeaderAndData(transFile)
1215	//adds to SAM
1216	err = Raw_to_work("SAM")
1217	//sum region in SAM
1218	transCts = SumTotalCounts("SAM")
1219	// get the attenuator, lambda, and sample string (to get the instrument)
1220	WAVE/T samText = $"root:SAM:textRead"
1221	WAVE samReals = $"root:SAM:realsRead"
1222	samfileStr = samText[3]
1223	lambda = samReals[26]
1224	attenSam = samReals[3]
1225	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
1226	AttenRatio = AttenuationFactor(samFileStr,lambda,attenEmp)/AttenuationFactor(samFileStr,lambda,attenSam)
1227	//calculate trans based on empty beam value and rescale by attenuation ratio
1228	trans= transCts/emptyCts * AttenRatio
1229
1230	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
1231	If(attenRatio==1)
1232	//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
1233	Printf "%s\t\tTotal Counts = %g\t Trans using whole detector = %g\t",T_GFilenames[ii], transCts,trans
1234	else
1235	//Printf "%s\t\tTrans Counts = %g\tTrans = %g\tAttenuatorRatio = %g, Tbox/Twhole = %g\r",T_GFilenames[ii], transCts,trans,attenRatio, T_GTransmission[ii]/trans
1236	Printf "%s\t\tTotal Counts = %g\t Trans using whole detector = %g\t AttenuatorRatio = %g",T_GFilenames[ii], transCts,trans,attenRatio
1237	endif
1238	If(T_GTransmission[ii]/trans > 0.97)
1239	printf " Tbox/Twhole = %g\r",T_GTransmission[ii]/trans
1240	else
1241	printf " !!! Tbox/Twhole is low !!! = %g\r",T_GTransmission[ii]/trans
1242	endif
1243	//write the trans to the file header of the raw data (open/close done in function)
1244	ReWriteReal(filename,trans,392) //WholeTrans start byte is 392
1245
1246	//then update the global that is displayed
1247	GWhole[ii] = trans
1248
1249	else // There is no empty assigned
1250	abortStr = "Empty beam file not assigned properly for " + T_GFilenames[jj]
1251	Print abortStr
1252	//Abort abortStr
1253	return(1)
1254	endif
1255	endif
1256	jj+=1
1257	while(jj<num_t_files)
1258	else //no transmission file
1259	abortStr = "Transmission beam file not assigned properly for " + T_GFilenames[ii]
1260	Print abortStr
1261	endif
1262	ii+=1
1263	while(ii<=endRow)
1264	print "done"
1265	return(0)
1266	End
1267
1268
1269	//window recreation macro for the Trans Panel
1270	//
1271	Proc Trans_Panel()
1272	PauseUpdate; Silent 1 // building window...
1273	NewPanel /W=(173,197,540,424)/K=1 as "Calculate Transmissions"
1274	DoWindow/C Trans_Panel
1275	ModifyPanel cbRGB=(49807,47186,38011)
1276	ModifyPanel fixedSize=1
1277	SetDrawLayer UserBack
1278	DrawLine 0,56,368,56
1279	DrawLine 0,125,368,125
1280	Button pick_emp,pos={4,65},size={105,20},proc=PickEMPTransButton,title="set BCENT file"
1281	Button pick_emp,help={"This button will set the file selected in the Transmission file table to be the empty beam file."}
1282	SetVariable empStr,pos={114,67},size={250,17},title="file:"
1283	SetVariable empStr,help={"Filename of the empty beam file(s) to be used in the transmission calculation"}
1284	SetVariable empStr,fSize=10
1285	SetVariable empStr,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gEMP
1286	Button Trn_button_1,pos={5,101},size={90,20},proc=Trn_SetXYBoxButton,title="Set XY Box"
1287	Button Trn_button_1,help={"Sets the XY box to sum over"}
1288	Button Trn_button_2,pos={174,139},size={110,20},proc=Trn_SortFilesByDate,title="Sort by Date"
1289	Button Trn_button_2,help={"Sort the scattering and transmission files by creation date."}
1290	Button Trn_button_3,pos={174,169},size={110,20},proc=Trn_SortFilesByLabel,title="Sort by Label"
1291	Button Trn_button_3,help={"Sort the scattering and transmission files by label."}
1292	Button Trn_button_4,pos={295,139},size={67,20},proc=Trn_ShowHelpProc,title="Help"
1293	Button Trn_button_4,help={"Show a help notebook for calculating transmissions."}
1294	SetVariable Trn_setvar_1,pos={135,100},size={227,17},title="Box is "
1295	SetVariable Trn_setvar_1,help={"Box coordinates to sum over"},fSize=10
1296	SetVariable Trn_setvar_1,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gBox
1297	Button Trn_button_0,pos={1,1},size={70,20},proc=Trn_PickPathButton,title="Pick Path"
1298	Button Trn_button_0,help={"Select the folder containing the SANS data files"}
1299	Button Trn_button_9,pos={335,1},size={25,20},proc=ShowTransHelp,title="?"
1300	Button Trn_button_9,help={"Show the help file for calculating sample transmissions"}
1301	SetVariable Trn_setvar_0,pos={80,4},size={250,17},title="Path"
1302	SetVariable Trn_setvar_0,help={"Currently selected data path"},fSize=10
1303	SetVariable Trn_setvar_0,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gCatPathStr
1304	Button Trn_button_5,pos={5,169},size={161,20},proc=Trn_CalcAllFilesButton,title="Calculate All Files"
1305	Button Trn_button_5,help={"Calculate transmission and patch headers of ALL files in the Scattering File Table."}
1306	Button Trn_button_6,pos={295,198},size={67,20},proc=Trn_PanelDoneButtonProc,title="Done"
1307	Button Trn_button_6,help={"Close the panel when done calculating transmissions"}
1308	Button Trn_button_7,pos={67,32},size={214,20},proc=Trn_RefreshProc,title="List Files"
1309	Button Trn_button_7,help={"Generate or refresh the tables of files."}
1310	Button Trn_button_8,pos={5,139},size={161,20},proc=Trn_CalcSelectedFilesButton,title="Calculate Selected Files"
1311	Button Trn_button_8,help={"Calculate transmission and patch headers of selected files in the Scattering File Table."}
1312	Button Trn_button_10,pos={5,198}, size={161,20},proc=TotalTransButtonProc
1313	Button Trn_button_10 title="Calculate Total Trans"
1314	Button Trn_button_10 help={"Calculate transmission over the whole detector and patch headers of ALL files in the data folder."}
1315	EndMacro
1316
1317
1318	Function TotalTransButtonProc(ctrlName) : ButtonControl
1319	String ctrlName
1320	TotalTrans(ctrlName)
1321	End
1322
1323
1324	Proc ShowTransHelp(ctrlName) : ButtonControl
1325	String ctrlName
1326	DisplayHelpTopic/K=1 "SANS Data Reduction Tutorial[Calculate Transmissions]"
1327	End
1328
1329
1330	//generates the file tables of scattering files and transmission files
1331	//
1332	// if the tables already exist, they will be updated
1333	//
1334	Proc Trn_RefreshProc(ctrlName) : ButtonControl
1335	String ctrlName
1336	BuildFileTables()
1337	End
1338
1339	//shows a noteboox of help text describing how to calculate transmissions
1340	// - better that the user read the igor or pdf file, but it's a victory to get
1341	//users to read anything at all
1342	//
1343	Proc Trn_ShowHelpProc(ctrlName) : ButtonControl
1344	String ctrlName
1345	DisplayTransHelp()
1346	End
1347
1348	//sorts the tables by date
1349	//
1350	Proc Trn_SortFilesByDate(ctrlName) : ButtonControl
1351	String ctrlName
1352	SortTransByDate()
1353	End
1354
1355	//sorts the tables alphabetically by the sample label field
1356	//
1357	Proc Trn_SortFilesByLabel(ctrlName) : ButtonControl
1358	String ctrlName
1359	SortTransByLabel()
1360	End
1361
1362	//button action procedure to select the local path to the
1363	//folder containing the RAW SANS data files
1364	// - once the data folder is selected, all of the popup file menus are
1365	//forced to update with fresh file lists
1366	//
1367	Function Trn_PickPathButton(PathButton) : ButtonControl
1368	String PathButton
1369
1370	//set the global string to the selected pathname
1371	Variable err
1372	err = PickPath()
1373	if(err)
1374	return(1) //some problem with path or user cancelled, get out
1375	endif
1376
1377	PathInfo/S catPathName
1378	String path = S_path
1379	if (V_flag == 0)
1380	//path does not exist - no folder selected
1381	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = "no folder selected"
1382	else
1383	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = path
1384	endif
1385
1386	//Update the pathStr variable box
1387	ControlUpdate/W=Trans_Panel $"Trn_setvar_0"
1388	//Generate tables
1389	Execute "BuildFileTables()"
1390
1391	End
1392
1393	//button action function that asks the user to set the XY box to sum over
1394	//for all transmission calculations
1395	//
1396	// requires the user to set the box coordinates with the marquee popup
1397	//that wil properly set the keyword string, and write the values to the empty beam header
1398	//
1399	Function Trn_SetXYBoxButton(ctrlName) : ButtonControl
1400	String ctrlName
1401
1402	String msgStr = "Select the Empty Beam File"
1403	String filename=""
1404
1405	//get the filename from the popup menu
1406	//and construct a full path to it
1407	SVAR partialName = root:myGlobals:TransHeaderInfo:gEMP
1408	print partialName
1409	//get a valid file based on this partialName and catPathName
1410	String tempName = FindValidFilename(partialName)
1411	if(cmpstr(tempName,"")==0)
1412	//file not found, get out
1413	Abort "Empty beam file not found Trn_SetXYBoxButton(ctrlName)"
1414	Endif
1415	//name is ok, prepend path to tempName for read routine
1416	PathInfo catPathName
1417	filename = S_path + tempName
1418
1419	//read the file in - check for previous coordinates
1420	ReadHeaderAndData(filename)
1421	//data is displayed here (go through the normal display steps, so all is created properly
1422	String/G root:myGlobals:gDataDisplayType="RAW"
1423	fRawWindowHook()
1424
1425	// check the empty beam file for previously selected coordinates
1426	//if they exist, set the xy string , save the normalized counts somewhere
1427	//the value was written to an unused r*4 header analysis.factor (@b494)
1428	Variable refnum,x1,x2,y1,y2,err
1429	Open/R refnum as filename
1430	FSetPos refnum,478
1431	FBinRead/F=3/B=3 refnum, x1
1432	FBinRead/F=3/B=3 refnum, x2
1433	FBinRead/F=3/B=3 refnum, y1
1434	FBinRead/F=3/B=3 refnum, y2
1435	Close refnum
1436	//read the real count value
1437	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
1438	String strToExecute
1439	strToExecute = GBLoadStr + "/S=494/U=1" + "\"" + filename + "\""
1440	Execute strToExecute
1441	Wave w=$"tempGBWave0"
1442	Variable/G root:myGlobals:gTransCts = w[0] //***NOTE this is NOT in the Trans sub-folder
1443	//
1444	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
1445	//no region selected
1446
1447	//add the empty beam file to work.SAM
1448	err = Raw_to_work("SAM")
1449
1450	//the calling macro must change the display type
1451	String/G root:myGlobals:gDataDisplayType="SAM" //displayed data type is sam
1452
1453	//data is displayed here
1454	fRawWindowHook()
1455
1456	//prompt user to select box w/marquee
1457	DoAlert 0,"Select the region to sum with the Marquee"
1458
1459	//from here the Marquee menu selection must handle the task of setting the box
1460	//and updating the information in the file header
1461	else
1462	// region already selected, just put up the values from the file header
1463	//allow user the option of overriding the current box region
1464	msgStr = "X1="+num2str(x1)+";"
1465	msgStr += "X2="+num2str(x2)+";"
1466	msgStr += "Y1="+num2str(y1)+";"
1467	msgStr += "Y2="+num2str(y2)+";"
1468	String textStr
1469	textStr = "Override current box "+msgStr+" ?"
1470	DoAlert 1,textStr
1471	If((V_flag)==1)
1472	//get new box coordinates, same procedure as above
1473	//add the empty beam file to work.SAM
1474	err = Raw_to_work("SAM")
1475
1476	//the calling macro must change the display type
1477	String/G root:myGlobals:gDataDisplayType="SAM" //displayed data type is sam
1478
1479	//data is displayed here
1480	fRawWindowHook()
1481
1482	//prompt user to select box w/marquee
1483	DoAlert 0,"Select the region to sum with the Marquee"
1484
1485	//from here the Marquee menu selection must handle the task of setting the box
1486	//and updating the information in the file header
1487	else
1488	String/G root:myGlobals:TransHeaderInfo:gBox = msgStr
1489	Endif
1490	Endif
1491
1492	UpdateBoxCoordinates()
1493	KillWaves/Z w
1494	Return (0)
1495	End
1496
1497
1498	//button action function that assigns the selected empty beam file (run number only)
1499	//and the sample trnansmissionfile (run number only) to the popup list of sample scattering
1500	//files (ALL of the list items). Assignment is done by writing the integer run numbers of
1501	//trans files to the header of each of the scattering files, in a batchwise processing
1502	//of the popup list
1503	//
1504	//transmission are not calculated here - only the file numbers are set
1505	//
1506	//*******unused*********
1507	//Function Trn_AssignAllFilesButton(ctrlName) : ButtonControl
1508	// String ctrlName
1509	//
1510	// AssignTransFilesToData()
1511	//
1512	//End
1513
1514	//button action procedure to calculate the transmission of all of the sample files in the
1515	//sample popup list, based on the information in EACH sample header and in the empty beam file
1516	//the box must be set properly in the empty beam file, AND the empty and trans
1517	//run number must also be set properly in EACH scattering file,
1518	//If run numbers are not properly assigned, no trans is calculated and the
1519	//header is not modified
1520	//
1521	//The RAW data header of EACH sample file IS modified, with the newly calculated transmission
1522	//
1523	//not very friendly, but forces users to assign the files before continuing
1524	//
1525	Function Trn_CalcAllFilesButton(ctrlName) : ButtonControl
1526	String ctrlName
1527
1528	//calculate the transmission and Patch the header (if possible)
1529	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1530	Variable num_s_files = numpnts(S_GFilenames)
1531	AssignSelTransFilesToData(0,num_s_files-1) //do all the files (points 0 to n-1, inclusive)
1532	CalcSelTransFromHeader(0,num_s_files-1)
1533
1534	End
1535
1536	//for selected scattering files in the scattering table,
1537	// the "Annn" association of trans file is written to the data file,
1538	// the the transmission is actually calculated
1539	//
1540	Function Trn_CalcSelectedFilesButton(ctrlName) : ButtonControl
1541	String ctrlName
1542
1543	Variable scatterTableExists
1544	scatterTableExists = WinType("ScatterFileTable")
1545	if (scatterTableExists != 0)
1546	GetSelection table,ScatterFileTable,1
1547	if(V_Flag != 0)
1548	AssignSelTransFilesToData(V_StartRow,V_EndRow)
1549	//calculate the transmission and Patch the header (if possible)
1550	CalcSelTransFromHeader(V_StartRow,V_EndRow)
1551	Else
1552	DoAlert 0,"No selection from Scattering Files table"
1553	Endif
1554	Else
1555	DoAlert 0,"No file selected from Scattering Files table or no Scattering Files table available"
1556	Endif
1557	End
1558
1559	// b BGtoFix -comment to describe the workings of the function
1560	// since it's different than calculating the regular transmission
1561	//
1562	// I am not sure what the difference is inthe function of CalcTotalTrans and CalcWholeTrans ?
1563	// do they really do anything different?
1564	//
1565	Function TotalTrans(ctrlName) : ButtonControl
1566	String ctrlName
1567
1568	Variable transTableExists
1569	transTableExists = WinType("ScatterFileTable") // b BGtoFix -checking for the existence of the wrong table
1570	if (transTableExists != 0)
1571	GetSelection table,transFileTable,1
1572	if(V_Flag != 0)
1573	AssignTotalTransFilesToData(V_StartRow,V_EndRow)
1574	//calculate the transmission and Patch the header (if possible)
1575	CalcTotalTrans(V_StartRow,V_EndRow)
1576	CalcWholeTrans(V_StartRow,V_EndRow)
1577	Else
1578	DoAlert 0,"No selection from Scattering Files table" // b BGtoFix - really looking for files from the Trans Table...
1579	Endif
1580	Else
1581	DoAlert 0,"No file selected from Scattering Files table or no Scattering Files table available" // b BGtoFix - really looking for files from the Trans Table...
1582	Endif
1583	End
1584
1585
1586	//simple button procedure to close the trans panel
1587	// - automatically kills the two tables as well
1588	//
1589	Function Trn_PanelDoneButtonProc(ctrlName) : ButtonControl
1590	String ctrlName
1591
1592	// this button will make sure all files are closed
1593	//and close the panel
1594
1595	Close/A
1596	DoWindow/K Trans_Panel
1597	DoWindow/K ScatterFileTable
1598	DoWindow/K TransFileTable
1599	End
1600
1601
1602	//function to check the header of a raw data file (full path specified by fname)
1603	//checks the field of the x-position of the beamstop during data collection
1604	//if the x-position is more negatice (farther to the left) than xTol(input)
1605	//the the beamstop is "out" and the file is a transmission run and not a scattering run
1606	//xtol typically set at -5 (cm) - trans runs have bs(x) at -10 to -15 cm
1607	// function returns 1 if beamstop is out, 0 if beamstop is in
1608	//
1609	Function CheckIfBeamstopOut(fName,xTol)
1610	String fname
1611	Variable xTol
1612
1613	Variable refnum,xpos
1614	//pos = 369, read one real value
1615
1616	SetDataFolder root:
1617	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
1618	String strToExecute=""
1619	// 1 R*4 value
1620	strToExecute = GBLoadStr + "/S=368/U=1" + "\"" + fname + "\""
1621	Execute strToExecute
1622	Wave w=$"root:tempGBWave0"
1623	xPos = w[0]
1624	KillWaves/Z w
1625	//Print "xPos = ",xpos
1626
1627	if(xpos<=xTol)
1628	//xpos is farther left (more negative) than xtol (currently -5 cm)
1629	Return(1)
1630	else
1631	//some other file
1632	Return(0)
1633	Endif
1634	End
1635
1636	//function to update the box coordinates of the file selected as the
1637	//empty beam file - takes the file that is currently popped from the list
1638	//reads the 4 "analysis" integers that hold the box coordinates
1639	//resets the globals string that is displayed with the new values
1640	//should be called whenever the "empty" popup is popped, to ensure
1641	//that current header information is displayed
1642	//
1643	Function UpdateBoxCoordinates()
1644
1645	//construct a full name, and read in the label from the file
1646	//and set the global
1647	String textstr=""
1648	ControlInfo empStr
1649	SVAR item = root:myGlobals:TransHeaderInfo:gEMP
1650	String tempName = FindValidFilename(item)
1651	if(cmpstr(tempName,"")==0)
1652	//file not found, get out
1653	Abort "Empty beam file not found UpdateBoxCoordinates(ctrlName)"
1654	Endif
1655	//name is ok, prepend path to tempName for read routine
1656	PathInfo catPathName
1657	String filename = S_path + tempName
1658
1659	Variable refnum,x1,x2,y1,y2,err
1660	Open/R refnum as filename
1661	FSetPos refnum,478
1662	FBinRead/F=3/B=3 refnum, x1
1663	FBinRead/F=3/B=3 refnum, x2
1664	FBinRead/F=3/B=3 refnum, y1
1665	FBinRead/F=3/B=3 refnum, y2
1666	Close refnum
1667
1668	//and update the global string
1669	String msgStr=""
1670	msgStr = "X1="+num2str(x1)+";"
1671	msgStr += "X2="+num2str(x2)+";"
1672	msgStr += "Y1="+num2str(y1)+";"
1673	msgStr += "Y2="+num2str(y2)+";"
1674
1675	String/G root:myGlobals:TransHeaderInfo:gBox = msgStr
1676
1677	ControlUpdate/W=Trans_panel Trn_setvar_1
1678	End
1679
1680	//crude procedure to display a notebook of help information for users
1681	//
1682	Proc DisplayTransHelp()
1683	String nb = "Notebook0"
1684	NewNotebook/N=$nb/F=1/V=1/W=(342,302,868,674) as "Notebook0:Transmission Help"
1685	Notebook $nb defaultTab=36, statusWidth=238, pageMargins={36,72,36,72}
1686	Notebook $nb showRuler=1, rulerUnits=1, updating={1, 3600}
1687	Notebook $nb newRuler=Normal, justification=0, margins={0,0,468}, spacing={0,0,0}, tabs={}, rulerDefaults={"Geneva",10,0,(0,0,0)}
1688	Notebook $nb ruler=Normal; Notebook $nb justification=1, fSize=14, fStyle=1, text="Transmission Help\r"
1689	Notebook $nb ruler=Normal, fSize=-1, fStyle=-1, text="\r"
1690	Notebook $nb text="This panel allows quick and easy calculation of sample transmission. The neutron transmission of a sampl"
1691	Notebook $nb text="e must be calculated and entered into the header of each sample scattering file before proper background"
1692	Notebook $nb text=" corrections or absolute scaling can be done.\r"
1693	Notebook $nb text="\r"
1694	Notebook $nb text="During data collection, you measured an empty beam - that is a measurement with heavy attenuation of th"
1695	Notebook $nb text="e neutron beam and the beamstop mover out of line with the direct beam. Then without changing the attenu"
1696	Notebook $nb text="ation or replacing the beamstop, you put a sample in the beam, and repeated the measurement (a sample tr"
1697	Notebook $nb text="ansmission measurement). The neutron transmission of the sample is simply the ratio of the number of neu"
1698	Notebook $nb text="tron counts from the sample transmission measurement normalized by the number of neutron counts from the"
1699	Notebook $nb text=" empty beam measurement. In this way, each sample transmission file is \"linked\" to the same empty beam t"
1700	Notebook $nb text="ransmission file.\r"
1701	Notebook $nb text="\r"
1702	Notebook $nb text="This calculated transmission value must be entered into the header of the sample scattering measurement "
1703	Notebook $nb text="- that is the measurement of the sample with the beamstop covering the primary (transmitted) beam, and n"
1704	Notebook $nb text="o (or few) attenuators in place. In this way, the sample transmission file is \"linked\" to its correspond"
1705	Notebook $nb text="ing sample scattering file. This panel allows you to set up the links and calculate the transmission.Tra"
1706	Notebook $nb text="nsmisison values are automatically patched to the scattering file headers as they are calculated.\r"
1707	Notebook $nb text="\r"
1708	Notebook $nb text="To Calculate Transmissions:\r"
1709	Notebook $nb text="\r"
1710	Notebook $nb text="1) Click \"List Files\" to get two lists (tables) - one of all the sample scattering files in the folder, "
1711	Notebook $nb text="and one of the transmission files.\r"
1712	Notebook $nb text="\r"
1713	Notebook $nb text="2) Select the region of the detector to sum over from the empty beam transmission file. Do theis by clic"
1714	Notebook $nb text="king on the filename of the empty beam transmision file (from the TransmissionFiles window, in the blue "
1715	Notebook $nb text="\"T_Filenames\" column). Return to the panel, and click the \"set EMP file\" button\", and the filename shoul"
1716	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"
1717	Notebook $nb text="et XY Box\" button. The empty beam file will be displayed, and you will be instructed to select the regio"
1718	Notebook $nb text="n to sum with the marquee. On the data, click and drag a rectangle that encompasses the primary beam. Mo"
1719	Notebook $nb text="ve the cursor inside the selection, to get an \"upside-down hat\" cursor. Click to get a menu, and near th"
1720	Notebook $nb text="e bottom, select \"Set XY Box Coords\". The pixel values should be updated to the Transmission panel, and "
1721	Notebook $nb text="are written to the empty beam header for future calculations. Note that the marquee selection can also b"
1722	Notebook $nb text="e used to measure the beam center, or centroid of any selected region.\r"
1723	Notebook $nb text="\r"
1724	Notebook $nb text="3) Now you need to \"link\" the ", fStyle=2, text="sample", fStyle=-1, text=" transmission files to the "
1725	Notebook $nb fStyle=2, text="empty", fStyle=-1, text=" ", fStyle=2, text="beam", fStyle=-1
1726	Notebook $nb text=" transmission file. Do this in the TransmissionFiles window by selecting the filename (in the blue T_Fil"
1727	Notebook $nb text="enames column) and pasing it to the corresponding row(s) in the T_EMP_Filenames column. This links the e"
1728	Notebook $nb text="mpty beam transmission with the sample transmission file. Do this for every sample transmission file.\r"
1729	Notebook $nb text="\r"
1730	Notebook $nb text="4) Now you need to link the sample ", fStyle=2, text="transmission", fStyle=-1
1731	Notebook $nb text=" file to the sample ", fStyle=2, text="scattering", fStyle=-1
1732	Notebook $nb text=" file. Do this by selecting the name of the transmission file (from the blue T_Filenames column) and pas"
1733	Notebook $nb text="ting it into the corresponding row of the S_TRANS_Filenames column of the ScatteringFiles window. This l"
1734	Notebook $nb text="inks the scattering file to its corresponding sample transmission file. This for all of the sample scatt"
1735	Notebook $nb text="ering files.\r"
1736	Notebook $nb text="\r"
1737	Notebook $nb text="5) Calculate the transmissions (and automatically write the transmission value to the satterng file head"
1738	Notebook $nb text="er) by clicking \"Calculate All Files\" from the Transmission Panel. The results will be printed to the co"
1739	Notebook $nb text="mmand window at the bottom of the screen. Any improperly assigned files will be listed. For example, blo"
1740	Notebook $nb text="cked beam scattering files will return an error, since the transmssion known to be zero, and is not meas"
1741	Notebook $nb text="ured (and no files are \"linked\"). Rather than calculating the transmission of all of the files, a range"
1742	Notebook $nb text=" of S_Filenames can be selected, then calculated by clicking \"Calculate Selected Files\".\r"
1743	Notebook $nb text="\r"
1744	Notebook $nb text="By default the lists are sorted by run number (= chronological). In some cases it may be easier to sort "
1745	Notebook $nb text="by the sample label to group several of the same sample scattering files collected at different sample-t"
1746	Notebook $nb text="o-detector distances. Its utility depends, of course, on how consistent and unique your sample labels ar"
1747	Notebook $nb text="e.\r"
1748	Notebook $nb text="\r"
1749	Notebook $nb text="The \"links\" are stored in the corresponding files, and wil be re-generated when the lists are re-generat"
1750	Notebook $nb text="ed. Unassigned links will appear as blank elements in the T_EMP_Filenames or S_TRANS_Filenames columns.\r"
1751	Notebook $nb text="\r"
1752	Notebook $nb, selection={startOfFile,startOfFile}
1753	Notebook $nb text="\r"
1754	End
1755
1756	//******************
1757	//lookup tables for attenuator transmissions
1758	//NG3 and NG7 attenuators are physically different, so the transmissions are slightly different
1759	//NG1 - (8m SANS) is not supported
1760
1761	Proc MakeNG3AttenTable()
1762
1763	NewDataFolder/O root:myGlobals:Attenuators
1764	//do explicitly to avoid data folder problems, redundant, but it must work without fail
1765	Make/O/N=9 root:myGlobals:Attenuators:ng3att0
1766	Make/O/N=9 root:myGlobals:Attenuators:ng3att1
1767	Make/O/N=9 root:myGlobals:Attenuators:ng3att2
1768	Make/O/N=9 root:myGlobals:Attenuators:ng3att3
1769	Make/O/N=9 root:myGlobals:Attenuators:ng3att4
1770	Make/O/N=9 root:myGlobals:Attenuators:ng3att5
1771	Make/O/N=9 root:myGlobals:Attenuators:ng3att6
1772	Make/O/N=9 root:myGlobals:Attenuators:ng3att7
1773	Make/O/N=9 root:myGlobals:Attenuators:ng3att8
1774	Make/O/N=9 root:myGlobals:Attenuators:ng3att9
1775	Make/O/N=9 root:myGlobals:Attenuators:ng3att10
1776
1777	//each wave has 8 elements, the transmission of att# at the wavelengths
1778	//lambda = 5,6,7,8,10,12,14,17
1779	Make/O/N=9 root:myGlobals:Attenuators:ng3lambda={5,6,7,8,10,12,14,17,20}
1780	root:myGlobals:Attenuators:ng3att0 = {1, 1, 1, 1, 1, 1, 1, 1,1 }
1781	root:myGlobals:Attenuators:ng3att1 = {0.421, 0.394, 0.371, 0.349, 0.316, 0.293, 0.274, 0.245,0.220}
1782	root:myGlobals:Attenuators:ng3att2 = {0.187, 0.164, 0.145, 0.130, 0.106, 0.0916, 0.0808, 0.0651,0.0531}
1783	root:myGlobals:Attenuators:ng3att3 = {0.0777, 0.0636, 0.0534, 0.0446, 0.0330, 0.0262, 0.0217, 0.0157 ,0.0116}
1784	root:myGlobals:Attenuators:ng3att4 = {0.0328, 0.0252, 0.0195, 0.0156, 0.0104, 7.68e-3, 5.98e-3, 3.91e-3,0.00262}
1785	root:myGlobals:Attenuators:ng3att5 = {0.0139, 9.94e-3, 7.34e-3, 5.44e-3, 3.29e-3, 2.25e-3, 1.66e-3, 9.95e-4, 6.12e-4}
1786	root:myGlobals:Attenuators:ng3att6 = {5.95e-3, 3.97e-3, 2.77e-3, 1.95e-3, 1.06e-3, 6.81e-4, 4.71e-4, 2.59e-4 , 1.45e-4}
1787	root:myGlobals:Attenuators:ng3att7 = {1.07e-3, 6.24e-4, 3.90e-4, 2.44e-4, 1.14e-4, 6.55e-5, 4.10e-5, 1.64e-5 , 7.26e-6}
1788	root:myGlobals:Attenuators:ng3att8 = {1.90e-4, 9.84e-5, 5.60e-5, 3.25e-5, 1.55e-5, 6.60e-6, 3.42e-6, 1.04e-6 , 3.48e-7}
1789	root:myGlobals:Attenuators:ng3att9 = {3.61e-5, 1.74e-5, 9.90e-6, 6.45e-6, 2.35e-6, 6.35e-7, 2.86e-7, 6.61e-8 , 1.73e-8}
1790	root:myGlobals:Attenuators:ng3att10 = {7.60e-6, 3.99e-6, 2.96e-6, 2.03e-6, 3.34e-7, 6.11e-8, 2.39e-8, 4.19e-9 , 8.60e-10}
1791
1792	End
1793
1794	Proc MakeNG7AttenTable()
1795
1796	NewDataFolder/O root:myGlobals:Attenuators
1797
1798	Make/O/N=9 root:myGlobals:Attenuators:ng7att0
1799	Make/O/N=9 root:myGlobals:Attenuators:ng7att1
1800	Make/O/N=9 root:myGlobals:Attenuators:ng7att2
1801	Make/O/N=9 root:myGlobals:Attenuators:ng7att3
1802	Make/O/N=9 root:myGlobals:Attenuators:ng7att4
1803	Make/O/N=9 root:myGlobals:Attenuators:ng7att5
1804	Make/O/N=9 root:myGlobals:Attenuators:ng7att6
1805	Make/O/N=9 root:myGlobals:Attenuators:ng7att7
1806	Make/O/N=9 root:myGlobals:Attenuators:ng7att8
1807	Make/O/N=9 root:myGlobals:Attenuators:ng7att9
1808	Make/O/N=9 root:myGlobals:Attenuators:ng7att10
1809
1810	//each wave has 8 elements, the transmission of att# at the wavelengths
1811	//lambda = 5,6,7,8,10,12,14,17
1812	Make/O/N=9 root:myGlobals:Attenuators:ng7lambda={5,6,7,8,10,12,14,17,20}
1813	root:myGlobals:Attenuators:ng7att0 = {1, 1, 1, 1, 1, 1, 1, 1 ,1}
1814	root:myGlobals:Attenuators:ng7att1 = {0.418, 0.393, 0.369, 0.347, 0.313, 0.291, 0.271, 0.244, 0.219 }
1815	root:myGlobals:Attenuators:ng7att2 = {0.189, 0.167, 0.148, 0.132, 0.109, 0.0945, 0.0830, 0.0681, 0.0560}
1816	root:myGlobals:Attenuators:ng7att3 = {0.0784, 0.0651, 0.0541, 0.0456, 0.0340, 0.0273, 0.0223, 0.0164 , 0.0121}
1817	root:myGlobals:Attenuators:ng7att4 = {0.0328, 0.0256, 0.0200, 0.0159, 0.0107, 7.98e-3, 6.14e-3, 4.09e-3 , 0.00274}
1818	root:myGlobals:Attenuators:ng7att5 = {0.0139, 0.0101, 7.43e-3, 5.58e-3, 3.42e-3, 2.36e-3, 1.70e-3, 1.03e-3 , 6.27e-4}
1819	root:myGlobals:Attenuators:ng7att6 = {5.90e-3, 4.07e-3, 2.79e-3, 1.99e-3, 1.11e-3, 7.13e-4, 4.91e-4, 2.59e-4 , 1.42e-4}
1820	root:myGlobals:Attenuators:ng7att7 = {1.04e-3, 6.37e-4, 3.85e-4, 2.46e-4, 1.16e-4, 6.86e-5, 4.10e-5, 1.64e-5 ,7.02e-6}
1821	root:myGlobals:Attenuators:ng7att8 = {1.90e-4, 1.03e-4, 5.71e-5, 3.44e-5, 1.65e-5, 6.60e-6, 3.42e-6, 1.04e-6 , 3.48e-7}
1822	root:myGlobals:Attenuators:ng7att9 = {3.58e-5, 1.87e-5, 1.05e-5, 7.00e-6, 2.35e-6, 6.35e-7, 2.86e-7, 6.61e-8 , 1.73e-8}
1823	root:myGlobals:Attenuators:ng7att10 = {7.76e-6, 4.56e-6, 3.25e-6, 2.03e-6, 3.34e-7, 6.11e-8, 2.39e-8, 4.19e-9, 8.60e-10}
1824
1825	End
1826
1827	//returns the transmission of the attenuator (at NG3) given the attenuator number
1828	//which must be an integer(to select the wave) and given the wavelength.
1829	//the wavelength may be any value between 5 and 20 (A), and is interpolated
1830	//between calibrated wavelengths for a given attenuator
1831	Function LookupAttenNG3(lambda,attenNo)
1832	Variable lambda, attenNo
1833
1834	Variable trans
1835	String attStr="root:myGlobals:Attenuators:ng3att"+num2str(trunc(attenNo))
1836	String lamStr = "root:myGlobals:Attenuators:ng3lambda"
1837
1838	if(attenNo == 0)
1839	return (1) //no attenuation, return trans == 1
1840	endif
1841
1842	if( (lambda < 5) \|\| (lambda > 20 ) )
1843	Abort "Wavelength out of calibration range (5,20). You must manually enter the absolute parameters"
1844	Endif
1845
1846	if(!(WaveExists($attStr)) \|\| !(WaveExists($lamStr)) )
1847	Execute "MakeNG3AttenTable()"
1848	Endif
1849	//just in case creating the tables fails....
1850	if(!(WaveExists($attStr)) \|\| !(WaveExists($lamStr)) )
1851	Abort "Attenuator lookup waves could not be found. You must manually enter the absolute parameters"
1852	Endif
1853
1854	//lookup the value by interpolating the wavelength
1855	//the attenuator must always be an integer
1856	Wave att = $attStr
1857	Wave lam = $lamstr
1858	trans = interp(lambda,lam,att)
1859
1860	// Print "trans = ",trans
1861
1862	return trans
1863	End
1864
1865	//returns the transmission of the attenuator (at NG7) given the attenuator number
1866	//which must be an integer(to select the wave) and given the wavelength.
1867	//the wavelength may be any value between 5 and 20 (A), and is interpolated
1868	//between calibrated wavelengths for a given attenuator
1869	//
1870	// this set of tables is also used for NG5 (NG1) SANS instrument - as the attenuator has yet to be calibrated
1871	Function LookupAttenNG7(lambda,attenNo)
1872	Variable lambda, attenNo
1873
1874	Variable trans
1875	String attStr="root:myGlobals:Attenuators:ng7att"+num2str(trunc(attenNo))
1876	String lamStr = "root:myGlobals:Attenuators:ng7lambda"
1877
1878	if(attenNo == 0)
1879	return (1) //no attenuation, return trans == 1
1880	endif
1881
1882	if( (lambda < 5) \|\| (lambda > 20 ) )
1883	Abort "Wavelength out of calibration range (5,20). You must manually enter the absolute parameters"
1884	Endif
1885
1886	if(!(WaveExists($attStr)) \|\| !(WaveExists($lamStr)) )
1887	Execute "MakeNG7AttenTable()"
1888	Endif
1889	//just in case creating the tables fails....
1890	if(!(WaveExists($attStr)) \|\| !(WaveExists($lamStr)) )
1891	Abort "Attenuator lookup waves could not be found. You must manually enter the absolute parameters"
1892	Endif
1893
1894	//lookup the value by interpolating the wavelength
1895	//the attenuator must always be an integer
1896	Wave att = $attStr
1897	Wave lam = $lamstr
1898	trans = interp(lambda,lam,att)
1899
1900	//Print "trans = ",trans
1901
1902	return trans
1903
1904	End
1905
1906	//returns the proper attenuation factor based on the instrument (NG3, NG5, or NG7)
1907	//NG5 values are taken from the NG7 tables (there is very little difference in the
1908	//values, and NG5 attenuators have not been calibrated (as of 8/01)
1909	//filestr as passed is textread[3], the default directory
1910	Function AttenuationFactor(fileStr,lam,attenNo)
1911	String fileStr
1912	Variable lam,attenNo
1913
1914	Variable attenFactor=1,loc
1915	String instr=fileStr[1,3] //filestr is "[NGnSANSn] " or "[NGnSANSnn]" (11 characters total)
1916
1917	strswitch(instr)
1918	case "NG3":
1919	attenFactor = LookupAttenNG3(lam,attenNo)
1920	break
1921	case "NG5":
1922	//using NG7 lookup Table
1923	attenFactor = LookupAttenNG7(lam,attenNo)
1924	break
1925	case "NG7":
1926	attenFactor = LookupAttenNG7(lam,attenNo)
1927	break
1928	default:
1929	//return error?
1930	attenFactor=1
1931	endswitch
1932	// print "instr, lambda, attenNo,attenFactor = ",instr,lam,attenNo,attenFactor
1933	return(attenFactor)
1934	End
1935
1936	//*******************
1937	//************
1938	// A simple panel to allow users of the NG1 SANS instrument to make their
1939	// transmission files "look" like a transmission measurement to the data reduction
1940	// program. Transmission files are designated by an x-position of the beamstop of
1941	// < -5 (cm). this simple procedure sets xpos=-10 for individual files. files
1942	// con be "un-converted", which set the xpos=0.
1943	// 1/30/01 SRK
1944	//************
1945
1946	Proc TransformToTransFile()
1947	Variable/G root:myGlobals:gConvTrans=1
1948	DoWindow/F Convert_to_Trans
1949	if(V_flag==0)
1950	Convert2Trans()
1951	endif
1952	End
1953
1954	//fname must be the full path and name for the file
1955	Function ChangeBSXPos(fname,xpos)
1956	String fname
1957	Variable xpos
1958
1959	Variable start
1960	//x-position starts after byte 368
1961	//ReWriteReal() takes care of open/close on its own
1962	start = 368 //BS x-position
1963	ReWriteReal(fname,xpos,start)
1964	return(0)
1965	End
1966
1967	//sets the beamstop position to zero NOT the original position
1968	Function UnConvertButtonProc(ctrlName) : ButtonControl
1969	String ctrlName
1970
1971	//Print "UnConvert"
1972	String fullname=""
1973	ControlInfo fileNum
1974	Variable num = V_Value //run number to find
1975
1976	fullname = FindFileFromRunNumber(num)
1977	Print fullname
1978	//report error or change the file
1979	if(cmpstr(fullname,"")==0)
1980	Print "Unconvert - file not found"
1981	else
1982	//Print "Unconvert",fullname
1983	ChangeBSXPos(fullName,0)
1984	Endif
1985	return(0)
1986	End
1987
1988	//button procedure to do the conversion
1989	// writes fake beamstop position to the data file
1990	//
1991	Function ConvertButtonProc(ctrlName) : ButtonControl
1992	String ctrlName
1993
1994	String fullname=""
1995	ControlInfo fileNum
1996	Variable num = V_Value //run number to find
1997
1998	fullname = FindFileFromRunNumber(num)
1999	print fullname
2000	//report error or change the file
2001	if(cmpstr(fullname,"")==0)
2002	Print "Convert - file not found"
2003	else
2004	//Print "Convert",fullname
2005	ChangeBSXPos(fullName,-10)
2006	Endif
2007	return(0)
2008	End
2009
2010	//simple panel recreation macro
2011	//
2012	Proc Convert2Trans()
2013	PauseUpdate; Silent 1 // building window...
2014	NewPanel /W=(434,74,671,216) /K=1
2015	DoWindow/C Convert_to_Trans
2016	SetDrawLayer UserBack
2017	DrawText 18,22,"Convert files to be recognized"
2018	DrawText 43,39,"as transmission files"
2019	SetVariable fileNum,pos={43,58},size={130,15},title="File Number"
2020	SetVariable fileNum,limits={1,Inf,1},value=root:myGlobals:gConvTrans
2021	SetVariable fileNum,help={"Sets the run number of the file that is to be converted"}
2022	Button ConvButton,pos={73,79},size={80,20},proc=ConvertButtonProc,title="Convert"
2023	Button ConvButton,help={"Converts the chosen file to appear as a transmission file"}
2024	Button UndoButton,pos={68,105},size={90,20},proc=UnConvertButtonProc,title="Un-Convert"
2025	Button UndoButton,help={"Converts the chosen file to appear as a scattering file"}
2026	EndMacro
2027
2028
2029	/////
2030	// A quick way to fill all the T_EMP_Filenames with the selected empty beam file
2031	// Note that you must go back and clear or reassign any files that are special cases
2032	//
2033	// IMPORTANT - this will overwrite any other file assignments (typically not a problem
2034	// if you are using only one wavelength)
2035	//
2036	/////
2037	Function FillEMPFilenameWSelection()
2038
2039	GetSelection table,TransFileTable,3
2040	Variable row=V_startRow //ony need the selected row, we know the column names and location
2041	Wave/T fw = root:myGlobals:TransHeaderInfo:T_FileNames //trans files
2042	Wave/T ew = root:myGlobals:TransHeaderInfo:T_EMP_FileNames //empty beam reference files
2043
2044	ew[] = fw[row]
2045
2046	return(0)
2047	End
2048
2049	//given a selection of the sample files, try to find the corresponding transmission file
2050	//
2051	Function GuessTransFile(charsToUse,row)
2052	Variable charsToUse,row //number of characers to use from the beginning of the label, and the row of the sample file
2053
2054	// GetSelection table,ScatterFileTable,3
2055	// Variable row=V_startRow //ony need the selected row, we know the column names and location
2056	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
2057	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
2058	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
2059	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
2060
2061	Variable num,ii,found
2062	String samStr = "",testStr=""
2063
2064	samStr = (sw[row])[0,charsToUse-1] //string to try and match
2065	samStr += "*"
2066	// Print samStr
2067	num=numpnts(tw)
2068	ii=0
2069	do
2070	testStr=tw[ii]
2071	found = stringmatch(testStr, samStr )
2072	if(found == 1)
2073	Print "Match Found at: ",samStr,tnam[ii],tw[ii]
2074	snam[row] = tnam[ii] //write the file name into the table
2075	return(0)
2076	endif
2077	ii+=1
2078	while(ii<num)
2079
2080	//method 2
2081	// samStr = (sw[row])[0,charsToUse-1] //string to try and match
2082	//// Print samStr
2083	// num=numpnts(tw)
2084	// ii=0
2085	// do
2086	// testStr=tw[ii]
2087	// found = strsearch(testStr,samStr,0) //start from zero, Need Igor 5 to allow 4th parameter to ignore case
2088	// if(found != -1)
2089	// Print "Match Found at: ",samStr,tnam[ii],tw[ii]
2090	// snam[row] = tnam[ii] //write the file name into the table
2091	// return(0)
2092	// endif
2093	// ii+=1
2094	// while(ii<num)
2095
2096	Print "No Match found"
2097	return(0)
2098	End
2099
2100	Function GuessAllTransFiles(numChars)
2101	Variable numChars
2102
2103	if(WinType("ScatterFileTable") ==0 )
2104	return(1)
2105	endif
2106
2107	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
2108	Variable ii,num=numpnts(sw)
2109
2110	for(ii=0;ii<num;ii+=1)
2111	GuessTransFile(numChars,ii)
2112	endfor
2113
2114	return(0)
2115	End
2116
2117	Function fGuessSelectedTransFiles(numChars)
2118	Variable numChars
2119
2120	Variable ii
2121	Variable scatterTableExists
2122	scatterTableExists = WinType("ScatterFileTable")
2123	if (scatterTableExists != 0)
2124	GetSelection table,ScatterFileTable,1
2125	for(ii=V_StartRow;ii<=V_EndRow;ii+=1)
2126	GuessTransFile(numChars,ii)
2127	endfor
2128	else
2129	Print "Transmission->Scattering File table is not open"
2130	endif
2131	return(0)
2132	End
2133
2134	Function ClearSelectedAssignments()
2135
2136	Variable ii
2137	Variable scatterTableExists
2138	scatterTableExists = WinType("ScatterFileTable")
2139	if (scatterTableExists != 0)
2140	GetSelection table,ScatterFileTable,1
2141	fClearSelectedAssignments(V_startRow,V_endRow)
2142	endif
2143	return(0)
2144	End

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