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Transmission.ipf @ 949

Last change on this file since 949 was 949, checked in by srkline, 8 years ago
Marquee.ipf -- added procedures (to the end of the file) that are extensions of the "BoxSum?" functionality. Instead of a rectangular box, these will sum over a series of files, using a defined region that is a q-annulus (+/-), or sectors, or arcs. This is expected to be useful for event mode data.
File size: 82.6 KB

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1	#pragma rtGlobals=1 // Use modern global access method.
2	#pragma version=5.0
3	#pragma IgorVersion=6.1
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_Trans_Error"
83
84	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Whole"
85	If(V_Flag==0)
86	BuildScatTableWindow()
87	ModifyTable width(:myGlobals:TransHeaderInfo:S_SDD)=40
88	ModifyTable width(:myGlobals:TransHeaderInfo:S_Lambda)=40
89	ModifyTable width(:myGlobals:TransHeaderInfo:S_Transmission)=60
90	ModifyTable rgb(:myGlobals:TransHeaderInfo:S_Filenames)=(0,0,65535)
91
92	ModifyTable width(Point)=0
93	Endif
94
95	String temp=""
96
97	//get a list of all files in the folder, some will be junk version numbers that don't exist
98	String list,partialName,tempName
99	list = IndexedFile(catPathName,-1,"????") //get all files in folder
100	Variable numitems,ii,ok
101
102	//remove version numbers from semicolon-delimited list
103	list = RemoveVersNumsFromList(list)
104
105	numitems = ItemsInList(list,";")
106
107	//loop through all of the files in the list, reading CAT/SHORT information if the file is RAW SANS
108	//*version numbers have been removed*
109	String str,fullName
110	Variable lastPoint
111	ii=0
112
113	do
114	//get current item in the list
115	partialName = StringFromList(ii, list, ";")
116	//get a valid file based on this partialName and catPathName
117	tempName = FindValidFilename(partialName)
118	If(cmpstr(tempName,"")==0) //a null string was returned
119	//write to notebook that file was not found
120	//if string is not a number, report the error
121	if(str2num(partialName) == NaN)
122	str = "this file was not found: "+partialName+"\r\r"
123	//Notebook CatWin,font="Times",fsize=12,text=str
124	Endif
125	else
126	//prepend path to tempName for read routine
127	PathInfo catPathName
128	FullName = S_path + tempName
129	//make sure the file is really a RAW data file
130	ok = CheckIfRawData(fullName)
131	if (ok)
132	GetTransHeaderInfoToWave(fullName,tempName)
133	Endif
134	Endif
135	ii+=1
136	while(ii<numitems)
137	//Now sort them all based on the suffix data
138	SortTransByDate()
139	//Now fill in the filenames of the ones that have already had EMP or TRANS
140	//files associated with them.
141	GetFilenamesFromSuffices()
142
143	//position the windows nicely
144	AutoPositionWindow/M=1/R=TransFileTable ScatterFileTable
145	DoWindow/F Trans_Panel
146	End
147
148	//actually creates the table of transmission files
149	// - the waves must exist
150	//
151	Function BuildTransTableWindow()
152	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
153	Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
154	Wave/T T_Suffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
155	Wave/T T_Labels = $"root:myGlobals:TransHeaderInfo:T_Labels"
156	Wave T_SDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
157	Wave T_Lambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
158	Wave T_Transmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
159	Wave T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
160
161	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"
162
163	SetWindow kwTopWin hook=GuessFromTableHook, hookevents=1 // mouse down events
164
165	String name="TransFileTable"
166	DoWindow/C $name
167
168	End
169
170	//actually creates the table of scattering files
171	// - the waves must exist
172	//
173	Function BuildScatTableWindow()
174	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
175	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
176	Wave/T S_Suffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
177	Wave/T S_Labels = $"root:myGlobals:TransHeaderInfo:S_Labels"
178	Wave S_SDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
179	Wave S_Lambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
180	Wave S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
181	Wave S_GTrans_err = $"root:myGlobals:TransHeaderInfo:S_Trans_Error"
182
183
184	Edit/K=1/W=(50,50,520,270) S_TRANS_Filenames, S_Filenames, S_Labels, S_SDD, S_Lambda, S_Transmission, S_GTrans_err as "ScatteringFiles"
185	String name="ScatterFileTable"
186	DoWindow/C $name
187
188	End
189
190	//sorts each of the tables by date - does this by using the suffix "Annn"
191	// which is automatically supplied by the VAX (and can't be changed)
192	// - only problem may be "Z999" -> "A001" rollover
193	//
194	Function SortTransByDate()
195	Wave/T T_GEMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
196	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
197	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
198	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
199	Wave/T T_GLabels = $"root:myGlobals:TransHeaderInfo:T_Labels"
200	Wave T_GSDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
201	Wave T_GLambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
202	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
203	Wave T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
204
205	Wave/T S_GTRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
206	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
207	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
208	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
209	Wave/T S_GLabels = $"root:myGlobals:TransHeaderInfo:S_Labels"
210	Wave S_GSDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
211	Wave S_GLambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
212	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
213	Wave S_GTrans_err = $"root:myGlobals:TransHeaderInfo:S_Trans_Error"
214	Wave S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
215
216	Sort T_GSuffix, T_GEMP_Filenames, T_GSuffix, T_GSuffices, T_GFilenames, T_GLabels, T_GSDD, T_GLambda, T_GTransmission, T_Whole
217	Sort S_GSuffix, S_GTRANS_Filenames, S_GSuffix, S_GSuffices, S_GFilenames, S_GLabels, S_GSDD, S_GLambda, S_GTransmission, S_Whole, S_GTrans_err
218
219	End
220
221	// sorts files alphabetically byt the sample label
222	// - consistent and descriptive sample labels really pay off here
223	//
224	Function SortTransByLabel()
225	Wave/T T_GEMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
226	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
227	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
228	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
229	Wave/T T_GLabels = $"root:myGlobals:TransHeaderInfo:T_Labels"
230	Wave T_GSDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
231	Wave T_GLambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
232	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
233	Wave T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
234
235	Wave/T S_GTRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
236	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
237	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
238	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
239	Wave/T S_GLabels = $"root:myGlobals:TransHeaderInfo:S_Labels"
240	Wave S_GSDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
241	Wave S_GLambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
242	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
243	Wave S_GTrans_err = $"root:myGlobals:TransHeaderInfo:S_Trans_Error"
244	Wave S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
245
246	Sort T_GLabels, T_GEMP_Filenames, T_GSuffix, T_GSuffices, T_GFilenames, T_GLabels, T_GSDD, T_GLambda, T_GTransmission, T_Whole
247	Sort S_GLabels, S_GTRANS_Filenames, S_GSuffix, S_GSuffices, S_GFilenames, S_GLabels, S_GSDD, S_GLambda, S_GTransmission, S_Whole, S_GTrans_err
248
249	End
250
251	//reads the file and assigns header information to the proper table
252	//
253	//fname - is the full path:name of the datafile (used by Open)
254	//sname - is the name only, used as the filename field
255	//
256	// takes care of all necessary open/close of file
257	//
258	Function GetTransHeaderInfoToWave(fname,sname)
259	String fname,sname
260
261	Variable isTrans
262
263	Variable lastPoint
264
265	isTrans = isTransFile(fname)
266	// decalre the correct set of waves
267	// S_Whole is only a place holder so the waves are of equal length
268	if (isTrans)
269	Wave/T GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
270	Wave/T G_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
271	Wave/T GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
272	Wave/T GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
273	Wave/T GLabels = $"root:myGlobals:TransHeaderInfo:T_Labels"
274	Wave GSDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
275	Wave GLambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
276	Wave GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
277	Wave GWhole = $"root:myGlobals:TransHeaderInfo:T_Whole"
278	Else
279	Wave/T GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
280	Wave/T G_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
281	Wave/T GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
282	Wave/T GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
283	Wave/T GLabels = $"root:myGlobals:TransHeaderInfo:S_Labels"
284	Wave GSDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
285	Wave GLambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
286	Wave GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
287	Wave S_GTrans_err = $"root:myGlobals:TransHeaderInfo:S_Trans_Error"
288	Wave GWhole = $"root:myGlobals:TransHeaderInfo:S_Whole"
289	Endif
290
291	lastPoint = numpnts(GLambda)
292
293	InsertPoints lastPoint,1,G_TRANS_Filenames
294	G_TRANS_Filenames[lastPoint]=""
295
296	InsertPoints lastPoint,1,GFilenames
297	GFilenames[lastPoint]=sname
298
299	//read the file suffix
300	InsertPoints lastPoint,1,GSuffix
301	GSuffix[lastPoint]=getSuffix(fname)
302
303	//read any suffix that this file is associated with
304	InsertPoints lastPoint,1,GSuffices
305	GSuffices[lastPoint]=getAssociatedFileSuffix(fname)
306
307	// read the sample.label text field
308	InsertPoints lastPoint,1,GLabels
309	GLabels[lastPoint]=getSampleLabel(fname)
310
311
312	//Transmission
313	InsertPoints lastPoint,1,GTransmission
314	GTransmission[lastPoint]=getSampleTrans(fname)
315
316
317
318	//Whole detector Transmission
319	InsertPoints lastPoint,1,GWhole
320	GWhole[lastPoint]=getSampleTransWholeDetector(fname)
321
322	//SDD
323	InsertPoints lastPoint,1,GSDD
324	GSDD[lastPoint]=getSDD(fname)
325
326	//wavelength
327	InsertPoints lastPoint,1,GLambda
328	GLambda[lastPoint]=getWavelength(fname)
329
330	if(isTrans==0)
331	//Transmission error
332	InsertPoints lastPoint,1,S_GTrans_err
333	S_GTrans_err[lastPoint] = getSampleTransError(fname)
334	Endif
335
336	return(0)
337	End
338
339	//fills in the file relations that have already been set
340	//
341	//
342	Function GetFilenamesFromSuffices()
343	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
344	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
345	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
346	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
347
348	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
349	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
350	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
351	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
352
353	Variable num_s_files, num_t_files, ii, jj
354	num_t_files = numpnts(T_GFilenames)
355	num_s_files = numpnts(S_GFilenames)
356	//print num_t_files, num_s_files
357
358	// Get transmission file relations
359	ii= 0
360	do
361	if (cmpstr(T_GSuffices[ii],"")!=0)
362	jj=0
363	do
364	if (cmpstr(T_GSuffices[ii],T_GSuffix[jj])==0)
365	T_EMP_Filenames[ii]=T_GFilenames[jj]
366	endif
367	jj+=1
368	while(jj<num_t_files)
369	endif
370	ii+=1
371	while(ii<num_t_files)
372
373	// Get scattering file relations
374	ii= 0
375	do
376	if (cmpstr(S_GSuffices[ii],"")!=0)
377	jj=0
378	do
379	if (cmpstr(S_GSuffices[ii],T_GSuffix[jj])==0)
380	S_TRANS_Filenames[ii]=T_GFilenames[jj]
381	endif
382	jj+=1
383	while(jj<num_t_files)
384	endif
385	ii+=1
386	while(ii<num_s_files)
387	End
388
389	// gets the selected transmission filename, and puts its name as the
390	//empty beam reference file
391	// lists the xy box coordinates as read from the file header (zeros if not yet assigned)
392	//
393	Function PickEMPTransButton(ctrlName) : ButtonControl
394	String ctrlName
395
396	Variable TransFileTableExists
397	TransFileTableExists = WinType("TransFileTable")
398	//??BUG?? V_flag returns 1 even if no selection?
399	//check manually for null selection
400	//Print "local v_flag = ",num2str(V_flag)
401	Wave/T LocFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
402	if (TransFileTableExists != 0)
403	String/G root:myGlobals:TransHeaderInfo:gEMP = ""
404	GetSelection table,TransFileTable,7
405	//Print S_Selection
406	if(strsearch(S_selection,"T_Filenames",0) == 0)
407	//selection OK, add to list
408	Duplicate/O/R=[V_startRow,V_endRow] LocFilenames, filenames
409	Wave/T selectedFiles = $"filenames"
410
411	SVAR temp = root:myGlobals:TransHeaderInfo:gEMP
412	//
413	temp = temp+selectedFiles[0] //take just the first file
414
415	UpdateBoxCoordinates()
416
417	//check to make sure that if the box is set, that the count value in the box is set too...
418	// if the box is set by a protocol, then the counts are not set -> and the transmission will be INF
419	String tempName = FindValidFilename(temp)
420	if(cmpstr(tempName,"")==0)
421	//file not found, get out
422	Abort "Empty beam file not found UpdateBoxCoordinates(ctrlName)"
423	Endif
424	//name is ok, prepend path to tempName for read routine
425	PathInfo catPathName
426	String filename = S_path + tempName
427	Variable boxCounts = getBoxCounts(filename)
428
429	variable x1,x2,y1,y2
430	getXYBoxFromFile(filename,x1,x2,y1,y2)
431
432	if( (boxCounts == 0) && (x1!=0) && (x2!=0) && (y1!=0) && (y2!=0) )
433	DoAlert 0,"Box Counts were not recorded. Please re-select the box using SetXYBox"
434	endif
435
436
437	Else
438	DoWindow/F TransFileTable
439	DoAlert 0,"Invalid selection from the Transmision file table. You must select a file from the T_Filenames column"
440	Endif
441	else
442	//no selection
443	DoAlert 0,"No file selected from Transmission file table or no Transmission file table available"
444	Endif
445	End
446
447	//initialize data folder and globals for the Trans panel as needed
448	//since this operation is somewhat tangled with the Patch Panel, keep all of the
449	//globals in the Patch subfolder (make sure both panels are simultaneously initialized)
450	//do not create a separate Trans folder
451	//
452	Proc InitializeTransPanel()
453	//create the global variables needed to run the Trans Panel
454	//all are kept in root:myGlobals:TransHeaderInfo
455	If( ! (DataFolderExists("root:myGlobals:TransHeaderInfo")) )
456	//create the data folder and the clobals for BOTH the Patch and Trans Panels
457	NewDataFolder/O root:myGlobals:TransHeaderInfo
458	CreateTransGlobals()
459	Endif
460	End
461
462
463	//
464	Proc CreateTransGlobals()
465
466	PathInfo catPathName
467	If(V_flag==1)
468	String dum = S_path
469	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = dum
470	else
471	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = "no path selected"
472	endif
473
474	String/G root:myGlobals:TransHeaderInfo:gEMP = "no file selected"
475	String/G root:myGlobals:TransHeaderInfo:gBox = ""
476	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Suffices"
477	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
478	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Filenames"
479	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Suffix"
480	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Labels"
481	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_SDD"
482	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Lambda"
483	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Transmission"
484	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Whole"
485
486	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Suffices"
487	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
488	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Filenames"
489	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Suffix"
490	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Labels"
491	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_SDD"
492	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Lambda"
493	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Transmission"
494	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Trans_Error"
495	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Whole"
496
497	String/G root:myGlobals:TransHeaderInfo:gMatchingSampleFiles = ""
498
499	End
500
501
502	//function that writes out (to the header of a raw binary SANS file)
503	//characters representing the empty beam file and the sample transmission file
504	//the 4-character file suffix is written, rather than the run numbers
505	//from this, the trans files can be located, and the
506	//sample file contains all the information needed to calculate its transmission
507	//
508	//uses first 4 bytes of params.reserve (character field) starting at byte 404
509	//(previous version (AM) used run.reserve field @ byte 91, which was not empty, and not at the start of the field!)
510	//
511	Function AssignSelTransFilesToData(startRow,endRow)
512	Variable startRow,endRow
513
514	// GetSelection table,ScatterFileTable,1
515
516	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
517	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
518	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
519	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
520
521	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
522	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
523	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
524	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
525
526	Variable num_s_files, num_t_files, ii, jj
527	Variable refnum
528	num_t_files = numpnts(T_GFilenames)
529	String suffix = ""
530	PathInfo catPathName
531	String pathname = S_path
532	String filename
533
534	// Write suffix of empty beam file into transmission files
535	ii= 0
536	do
537	if (cmpstr(T_EMP_Filenames[ii],"")!=0)
538	jj=0
539	do
540	if (cmpstr(T_EMP_Filenames[ii],T_GFilenames[jj])==0)
541	suffix=T_GSuffix[jj]
542	filename = pathname + T_GFilenames[ii]
543	WriteAssocFileSuffixToHeader(filename,suffix)
544	endif
545	jj+=1
546	while(jj<num_t_files)
547	endif
548	ii+=1
549	while(ii<num_t_files)
550
551	// Write suffix of transmission files into scattering files
552	ii= startRow
553	do
554	if (cmpstr(S_TRANS_Filenames[ii],"")!=0)
555	jj=0
556	do
557	if (cmpstr(S_TRANS_Filenames[ii],T_GFilenames[jj])==0)
558	suffix=T_GSuffix[jj]
559	filename = pathname + S_GFilenames[ii]
560	WriteAssocFileSuffixToHeader(filename,suffix)
561	endif
562	jj+=1
563	while(jj<num_t_files)
564	endif
565	ii+=1
566	while(ii<=endRow)
567	return(0)
568	End
569
570	// Allows to calculate transmissions without need of a scattering file. Used with the Calculate Total Trans button.
571
572	Function AssignTotalTransFilesToData(startRow,endRow)
573	Variable startRow,endRow
574
575	// GetSelection table,ScatterFileTable,1
576
577	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
578	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
579	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
580	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
581
582	Variable num_t_files, ii, jj
583	Variable refnum
584	num_t_files = numpnts(T_GFilenames)
585	String suffix = ""
586	PathInfo catPathName
587	String pathname = S_path
588	String filename
589
590	// Write suffix of empty beam file into transmission files
591	ii= 0
592	do
593	if (cmpstr(T_EMP_Filenames[ii],"")!=0)
594	jj=0
595	do
596	if (cmpstr(T_EMP_Filenames[ii],T_GFilenames[jj])==0)
597	suffix=T_GSuffix[jj]
598	filename = pathname + T_GFilenames[ii]
599	WriteAssocFileSuffixToHeader(filename,suffix)
600	endif
601	jj+=1
602	while(jj<num_t_files)
603	endif
604	ii+=1
605	while(ii<num_t_files)
606
607	return(0)
608	End
609
610
611	//function that clears the selected assignments of sample trans -> sample scattering
612	//also writes a trans=1 value back to the sample file
613	//
614	// DEC 2006 - now also writes blank suffix to clear trans->empty assignment, and Twhole=1
615	//
616	// target = 1 = ScatterFileTable
617	// target = 2 = TransFileTable
618	Function fClearSelectedAssignments(startRow,endRow,target)
619	Variable startRow,endRow,target
620
621	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
622	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
623	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
624	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
625	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
626	Wave S_GTrans_err = $"root:myGlobals:TransHeaderInfo:S_Trans_Error"
627	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
628	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
629	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
630	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
631	Wave T_GTWhole = $"root:myGlobals:TransHeaderInfo:T_Whole"
632
633
634	Variable num_s_files, num_t_files, ii, jj
635	Variable refnum,zero=0
636	num_t_files = numpnts(T_GFilenames)
637	String suffix = " " //4 blank spaces
638	PathInfo catPathName
639	String pathname = S_path
640	String filename
641
642	// If the selection is from the TransFileTable
643	// - wipe out the box coordinates
644	// - wipe out the suffix
645	// - wipe out the transmission
646	// - wipe out T_whole
647	// - update the waves in the table
648
649	if(target == 2)
650	ii= startRow
651	do
652	filename = pathname + T_GFilenames[ii]
653
654	// write in zeros for the box coordinates
655	WriteXYBoxToHeader(filename,0,0,0,0)
656
657	// write in a null suffix
658	WriteAssocFileSuffixToHeader(filename,suffix)
659
660	//write a trans==1 to the file header of the raw data
661	WriteTransmissionToHeader(filename,1) //sample trans
662
663	WriteWholeTransToHeader(filename,1) //WholeTrans start byte is 392
664
665	WriteTransmissionErrorToHeader(filename,0) //reset transmission error to zero
666	WriteBoxCountsErrorToHeader(filename,0)
667
668	//then update the table that is displayed
669	T_EMP_Filenames[ii] = ""
670	T_GTransmission[ii] = 1
671	T_GTWhole[ii] = 1
672
673	ii+=1
674	while(ii<=endRow)
675	endif
676
677
678	if(target == 1)
679	// Write null suffix of transmission files into scattering files
680	ii= startRow
681	do
682	filename = pathname + S_GFilenames[ii]
683	// write in a null suffix
684	WriteAssocFileSuffixToHeader(filename,suffix)
685
686	//write a trans==1 to the file header of the raw data (open/close done in function)
687	WriteTransmissionToHeader(filename,1) //sample trans
688	WriteTransmissionErrorToHeader(filename,0) //reset transmission error to zero
689	WriteBoxCountsErrorToHeader(filename,0)
690
691	//then update the table that is displayed
692	S_TRANS_Filenames[ii] = ""
693	S_GTransmission[ii] = 1
694	S_GTrans_err[ii] = 0
695
696	ii+=1
697	while(ii<=endRow)
698	endif
699
700	return(0)
701	End
702
703	//given a selection of scattering files, calculates the transmission
704	//and writes the new transmission to the file header
705	//
706	//given the full path;name;vers (= filenmame), of a raw binary SANS file,
707	//the transmission of the sample is calculated (if possible) from information
708	//in the file header. empty beam and sample transmision run numbers are extracted
709	//and the files are located from the run number (if possible)
710	//from the header of the empty beam file, the XY box coordinates and "empty"
711	//counts are determined
712	//once all information is located, the transmission is calculated and the
713	//transmission field of the sample file is automatically "Patched"
714	// - updates the global variable that is displayed in the panel
715	//can be run in batch mode, sequentially passing each item from a list of filenames
716	//this is the single step of the batch mode
717	//
718	//in batch mode: execution will proceed through all of the files, reporting
719	//results to the history window. If no trans could be successfully calculated
720	//(for a blocked beam, for example), then that is displayed as well, and the
721	//raw data is not modified
722	//
723	// now takes the attenuation of the sample trans and empty beam trans into account, (normally this == 1)
724	// and rescales the transmission as appropriate
725	// 3/31/04 SRK
726	//
727	Function CalcSelTransFromHeader(startRow,endRow)
728	Variable startRow,endRow
729	// GetSelection table,ScatterFileTable,1
730
731	String filename
732	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
733	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
734
735	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
736	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
737	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
738	Wave S_GTrans_err = $"root:myGlobals:TransHeaderInfo:S_Trans_Error"
739
740	Variable num_s_files, num_t_files, ii, jj
741	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans,sam_atten_err,emp_atten_err
742	Variable x1,x2,y1,y2,err,attenEmp,attenSam,empty_ct_err,sam_ct_err,samAttenFactor,empAttenFactor,trans_err
743	String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
744	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
745	String strToExecute
746
747	num_t_files = numpnts(T_GFilenames)
748
749	PathInfo catPathName
750	pathname = S_path
751
752	ii= startRow
753	do
754	if (cmpstr(S_TRANS_Filenames[ii],"")!=0) //if there is a sample trans file assigned
755	jj=0
756	do
757	if (cmpstr(S_TRANS_Filenames[ii],T_GFilenames[jj])==0) //find it in the trans file table
758	if (cmpstr(T_EMP_Filenames[jj],"")!=0) //if empty beam file assigned, proceed with the calculation
759	//full path+name to access all 3 files
760	filename=pathname+S_GFilenames[ii]
761	emptyFile = pathname+T_EMP_Filenames[jj]
762	transFile = pathname+T_GFilenames[jj]
763	//////////
764	// check the empty beam file for previously selected coordinates
765	//if they exist, set the xy string , save the normalized counts somewhere
766	//the value was written to an unused r*4 header analysis.factor (@b494)
767	GetXYBoxFromFile(emptyFile,x1,x2,y1,y2)
768
769	//read the real count value
770	emptyCts = getBoxCounts(emptyFile)
771	// get the error in count value
772	empty_ct_err = getBoxCountsError(emptyFile)
773
774	// read the attenuator number of the empty beam file
775	attenEmp = getAttenNumber(emptyFile)
776	//
777	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
778	//no region selected -- prompt user to select box w/marquee
779	DoWindow/F TransFileTable
780	Abort "Use \"Set BCENT File\", then \"SetXYBox\" to select XY range in empty beam file "+T_EMP_Filenames[jj]
781	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
782	Endif
783
784	//read in trans file then add to SAM
785	ReadHeaderAndData(transFile)
786	//adds to SAM
787	err = Raw_to_work("SAM")
788	//sum region in SAM
789	transCts = SumCountsInBox(x1,x2,y1,y2,sam_ct_err,"SAM")
790	// get the attenuator, lambda, and sample string (to get the instrument)
791	WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
792	WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
793	samfileStr = samText[3]
794	lambda = samReals[26]
795	attenSam = samReals[3]
796
797	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
798	samAttenFactor = AttenuationFactor(samFileStr,lambda,attenSam,sam_atten_err)
799	empAttenFactor = AttenuationFactor(samFileStr,lambda,attenEmp,emp_atten_err)
800	AttenRatio = empAttenFactor/samAttenFactor
801	//calculate trans based on empty beam value and rescale by attenuation ratio
802	trans= transCts/emptyCts * AttenRatio
803
804	// squared, relative error
805	if(AttenRatio == 1)
806	trans_err = (sam_ct_err/transCts)^2 + (empty_ct_err/emptyCts)^2 //same atten, att_err drops out
807	else
808	trans_err = (sam_ct_err/transCts)^2 + (empty_ct_err/emptyCts)^2 + (sam_atten_err/samAttenFactor)^2 + (emp_atten_err/empAttenFactor)^2
809	endif
810	trans_err = sqrt(trans_err)
811	trans_err *= trans // now, one std deviation
812
813	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
814	If(attenRatio==1)
815	Printf "%s\t\tTrans Counts = %g\tTrans = %g +/- %g\r",S_GFilenames[ii], transCts,trans,trans_err
816	else
817	Printf "%s\t\tTrans Counts = %g\tTrans = %g +/- %g\tAttenuatorRatio = %g\r",S_GFilenames[ii], transCts,trans,trans_err,attenRatio
818	endif
819	//write the trans to the file header of the raw data (open/close done in function)
820	WriteTransmissionToHeader(filename,trans)
821
822	WriteTransmissionErrorToHeader(filename,trans_err)
823	/////
824	//then update the global that is displayed
825	S_GTransmission[ii] = trans
826	S_GTrans_err[ii] = trans_err
827
828
829	else // There is no empty assigned
830	abortStr = "Empty beam file not assigned properly for " + T_GFilenames[jj]
831	Print abortStr
832	//Abort abortStr
833	return(1)
834	endif
835	endif
836	jj+=1
837	while(jj<num_t_files)
838	else //no transmission file
839	abortStr = "Transmission beam file not assigned properly for " + S_GFilenames[ii]
840	Print abortStr
841	endif
842	ii+=1
843	while(ii<=endRow)
844	print "done"
845	return(0)
846	End
847
848	//
849	// For the calculation of the Transmission using only the Trans Files screen
850	// Uses only the information on the transmissionFiles screen to calculate
851	// a "box" Transmission for comparison with the Whole Transmission
852	// updated 5/11/2006 by Bryan Greenwald
853	Function CalcTotalTrans(startRow,endRow)
854	Variable startRow,endRow
855	// GetSelection table,ScatterFileTable,1
856
857	String filename
858	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
859
860	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
861	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
862
863	// Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
864	// Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
865	// Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
866	Wave GWhole= $"root:myGlobals:TransHeaderInfo:T_Whole"
867
868	Variable num_t_files, ii, jj
869	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans,samAttenFactor,empAttenFactor,trans_err
870	Variable x1,x2,y1,y2,err,attenEmp,attenSam,empty_ct_err,sam_ct_err,emp_atten_err,sam_atten_err
871	String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
872	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
873	String strToExecute
874
875	num_t_files = numpnts(T_GFilenames)
876
877	PathInfo catPathName
878	pathname = S_path
879
880	ii= startRow
881	do
882	if (cmpstr(T_Emp_Filenames[ii],"")!=0) //if there is a sample trans file assigned
883	jj=0
884	do
885	if (cmpstr(T_Emp_Filenames[ii],T_GFilenames[jj])==0) //find it in the trans file table
886	if (cmpstr(T_EMP_Filenames[ii],"")!=0) //if empty beam file assigned, proceed with the calculation
887	//full path+name to access all 3 files
888	filename=pathname+T_GFilenames[ii]
889	emptyFile = pathname+T_EMP_Filenames[ii]
890	transFile = pathname+T_GFilenames[ii]
891	//////////
892	// check the empty beam file for previously selected coordinates
893	//if they exist, set the xy string , save the normalized counts somewhere
894	//the value was written to an unused r*4 header analysis.factor (@b494)
895	getXYBoxFromFile(emptyFile,x1,x2,y1,y2)
896
897	//read the real count value
898	emptyCts = getBoxCounts(emptyFile)
899	// get the count error
900	empty_ct_err = getBoxCountsError(emptyFile)
901
902	// read the attenuator number of the empty beam file
903	attenEmp = getAttenNumber(emptyFile)
904
905	//
906	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
907	//no region selected -- prompt user to select box w/marquee
908	DoWindow/F TransFileTable
909	Abort "Use \"Set BCENT File\", then \"SetXYBox\" to select XY range in empty beam file "+T_EMP_Filenames[jj]
910	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
911	Endif
912
913	//read in trans file then add to SAM
914	ReadHeaderAndData(transFile)
915	//adds to SAM
916	err = Raw_to_work("SAM")
917	//sum region in SAM
918	transCts = SumCountsInBox(x1,x2,y1,y2,sam_ct_err,"SAM")
919	// get the attenuator, lambda, and sample string (to get the instrument)
920	WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
921	WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
922	samfileStr = samText[3]
923	lambda = samReals[26]
924	attenSam = samReals[3]
925
926	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
927	samAttenFactor = AttenuationFactor(samFileStr,lambda,attenSam,sam_atten_err)
928	empAttenFactor = AttenuationFactor(samFileStr,lambda,attenEmp,emp_atten_err)
929	AttenRatio = empAttenFactor/samAttenFactor
930	//calculate trans based on empty beam value and rescale by attenuation ratio
931	trans= transCts/emptyCts * AttenRatio
932
933	// squared, relative error
934	if(AttenRatio == 1)
935	trans_err = (sam_ct_err/transCts)^2 + (empty_ct_err/emptyCts)^2 //same atten, att_err drops out
936	else
937	trans_err = (sam_ct_err/transCts)^2 + (empty_ct_err/emptyCts)^2 + (sam_atten_err/samAttenFactor)^2 + (emp_atten_err/empAttenFactor)^2
938	endif
939	trans_err = sqrt(trans_err)
940	trans_err *= trans // now, one std deviation
941
942	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
943	If(attenRatio==1)
944	//Printf "%s\t\tTrans Counts = %g\t Actual Trans = %g\r",T_GFilenames[ii], transCts,trans
945	Printf "%s\t\tBox Counts = %g\t Trans = %g +/- %g\r",T_GFilenames[ii], transCts,trans,trans_err
946	else
947	//Printf "%s\t\tTrans Counts = %g\t Trans = %g\tAttenuatorRatio = %g\r",T_GFilenames[ii], transCts,trans,attenRatio
948	Printf "%s\t\tBox Counts = %g\t Trans = %g +/- %g\t AttenuatorRatio = %g\r",T_GFilenames[ii], transCts,trans,trans_err,attenRatio
949	endif
950	//write the trans to the file header of the raw data (open/close done in function)
951	WriteTransmissionToHeader(filename,trans) //transmission start byte is 158
952
953	WriteTransmissionErrorToHeader(filename,trans_err)
954
955	//then update the global that is displayed
956	T_GTransmission[ii] = trans
957
958	else // There is no empty assigned
959	abortStr = "Empty beam file not assigned properly for " + T_GFilenames[jj]
960	Print abortStr
961	//Abort abortStr
962	return(1)
963	endif
964	endif
965	jj+=1
966	while(jj<num_t_files)
967	else //no transmission file
968	abortStr = "Transmission beam file not assigned properly for " + T_GFilenames[ii]
969	Print abortStr
970	endif
971	ii+=1
972	while(ii<=endRow)
973	//print "done"
974	return(0)
975	End
976
977	//
978	// For the calculation of the Transmission using only the whole detector
979	// Used to compute the transmission for the TransmissionFiles table using
980	// the entire detector. For comparison with the "box" trans
981	// updated: 5/11/2006 by Bryan Greenwald
982	Function CalcWholeTrans(startRow,endRow)
983	Variable startRow,endRow
984	// GetSelection table,ScatterFileTable,1
985
986	NVAR pixelsX = root:myGlobals:gNPixelsX
987	NVAR pixelsY = root:myGlobals:gNPixelsY
988
989	String filename
990	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
991
992	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
993	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
994
995	// Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
996	// Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
997	// Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
998	Wave GWhole= $"root:myGlobals:TransHeaderInfo:T_Whole"
999
1000	Variable num_t_files, ii, jj
1001	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
1002	Variable x1,x2,y1,y2,err,attenEmp,attenSam,empty_ct_err,sam_ct_err,emp_atten_err,sam_atten_err
1003	String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
1004	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
1005	String strToExecute
1006
1007	num_t_files = numpnts(T_GFilenames)
1008
1009	PathInfo catPathName
1010	pathname = S_path
1011
1012	ii= startRow
1013	do
1014	if (cmpstr(T_Emp_Filenames[ii],"")!=0) //if there is a sample trans file assigned
1015	jj=0
1016	do
1017	if (cmpstr(T_Emp_Filenames[ii],T_GFilenames[jj])==0) //find it in the trans file table
1018	if (cmpstr(T_EMP_Filenames[ii],"")!=0) //if empty beam file assigned, proceed with the calculation
1019	//full path+name to access all 3 files
1020	filename=pathname+T_GFilenames[ii]
1021	emptyFile = pathname+T_EMP_Filenames[ii]
1022	transFile = pathname+T_GFilenames[ii]
1023	//////////
1024	// check the empty beam file for previously selected coordinates
1025	//if they exist, set the xy string , save the normalized counts somewhere
1026	//the value was written to an unused r*4 header analysis.factor (@b494)
1027
1028	getXYBoxFromFile(emptyFile,x1,x2,y1,y2)
1029	//read the real count value
1030	emptyCts = getBoxCounts(emptyFile)
1031	// get the box count error
1032	empty_ct_err = getBoxCountsError(emptyFile)
1033
1034	// read the attenuator number of the empty beam file
1035	attenEmp = getAttenNumber(emptyFile)
1036
1037	//
1038	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
1039	//no region selected -- prompt user to select box w/marquee
1040	DoWindow/F TransFileTable
1041	Abort "Use \"Set BCENT File\", then \"SetXYBox\" to select XY range in empty beam file "+T_EMP_Filenames[jj]
1042	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
1043	Endif
1044
1045	//read in trans file then add to SAM
1046	ReadHeaderAndData(transFile)
1047	//adds to SAM
1048	err = Raw_to_work("SAM")
1049	//sum region in SAM
1050	transCts = SumCountsInBox(0,pixelsX-1,0,pixelsY-1,sam_ct_err,"SAM")
1051	// get the attenuator, lambda, and sample string (to get the instrument)
1052	WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
1053	WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
1054	samfileStr = samText[3]
1055	lambda = samReals[26]
1056	attenSam = samReals[3]
1057
1058	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
1059	AttenRatio = AttenuationFactor(samFileStr,lambda,attenEmp,emp_atten_err)/AttenuationFactor(samFileStr,lambda,attenSam,sam_atten_err)
1060	//calculate trans based on empty beam value and rescale by attenuation ratio
1061	trans= transCts/emptyCts * AttenRatio
1062
1063	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
1064	If(attenRatio==1)
1065	//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
1066	Printf "%s\t\tTotal Counts = %g\t Trans using whole detector = %g\t",T_GFilenames[ii], transCts,trans
1067	else
1068	//Printf "%s\t\tTrans Counts = %g\tTrans = %g\tAttenuatorRatio = %g, Tbox/Twhole = %g\r",T_GFilenames[ii], transCts,trans,attenRatio, T_GTransmission[ii]/trans
1069	Printf "%s\t\tTotal Counts = %g\t Trans using whole detector = %g\t AttenuatorRatio = %g",T_GFilenames[ii], transCts,trans,attenRatio
1070	endif
1071	If(T_GTransmission[ii]/trans > 0.95) //95%, from conversation w/Lionel
1072	printf " Tbox/Twhole = %g\r",T_GTransmission[ii]/trans
1073	else
1074	printf " !!! Tbox/Twhole is low !!! = %g\r",T_GTransmission[ii]/trans
1075	endif
1076	//write the trans to the file header of the raw data (open/close done in function)
1077	WriteWholeTransToHeader(filename,trans)
1078
1079	//then update the global that is displayed
1080	GWhole[ii] = trans
1081
1082	else // There is no empty assigned
1083	abortStr = "Empty beam file not assigned properly for " + T_GFilenames[jj]
1084	Print abortStr
1085	//Abort abortStr
1086	return(1)
1087	endif
1088	endif
1089	jj+=1
1090	while(jj<num_t_files)
1091	else //no transmission file
1092	abortStr = "Transmission beam file not assigned properly for " + T_GFilenames[ii]
1093	Print abortStr
1094	endif
1095	ii+=1
1096	while(ii<=endRow)
1097	print "done"
1098	return(0)
1099	End
1100
1101
1102	//window recreation macro for the Trans Panel
1103	//
1104	Proc Trans_Panel()
1105	PauseUpdate; Silent 1 // building window...
1106	NewPanel /W=(173,197,548,444) /K=1 as "Calculate Transmissions"
1107	DoWindow/C Trans_Panel
1108	ModifyPanel cbRGB=(49807,47186,38011)
1109	ModifyPanel fixedSize=1
1110	SetDrawLayer UserBack
1111	DrawLine 0,56,368,56
1112	DrawLine 0,142,368,142
1113	Button pick_emp,pos={4,65},size={105,20},proc=PickEMPTransButton,title="set EMPTY file"
1114	Button pick_emp,help={"This button will set the file selected in the Transmission file table to be the empty beam file."}
1115	SetVariable empStr,pos={114,67},size={250,17},title="file:"
1116	SetVariable empStr,help={"Filename of the empty beam file(s) to be used in the transmission calculation"}
1117	SetVariable empStr,fSize=10
1118	SetVariable empStr,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gEMP
1119	Button Trn_button_1,pos={5,91},size={90,20},proc=Trn_SetXYBoxButton,title="Set XY Box"
1120	Button Trn_button_1,help={"Sets the XY box to sum over"}
1121	Button Trn_button_2,pos={174,156},size={110,20},proc=Trn_SortFilesByDate,title="Sort by Date"
1122	Button Trn_button_2,help={"Sort the scattering and transmission files by creation date."}
1123	Button Trn_button_3,pos={174,186},size={110,20},proc=Trn_SortFilesByLabel,title="Sort by Label"
1124	Button Trn_button_3,help={"Sort the scattering and transmission files by label."}
1125	SetVariable Trn_setvar_1,pos={135,90},size={227,17},title="Box is "
1126	SetVariable Trn_setvar_1,help={"Box coordinates to sum over"},fSize=10
1127	SetVariable Trn_setvar_1,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gBox
1128	Button Trn_button_0,pos={1,1},size={70,20},proc=Trn_PickPathButton,title="Pick Path"
1129	Button Trn_button_0,help={"Select the folder containing the SANS data files"}
1130	Button Trn_button_9,pos={335,1},size={25,20},proc=ShowTransHelp,title="?"
1131	Button Trn_button_9,help={"Show the help file for calculating sample transmissions"}
1132	SetVariable Trn_setvar_0,pos={80,4},size={250,17},title="Path"
1133	SetVariable Trn_setvar_0,help={"Currently selected data path"},fSize=10
1134	SetVariable Trn_setvar_0,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gCatPathStr
1135	Button Trn_button_5,pos={5,186},size={161,20},proc=Trn_CalcAllFilesButton,title="Calculate All Files"
1136	Button Trn_button_5,help={"Calculate transmission and patch headers of ALL files in the Scattering File Table."}
1137	Button Trn_button_6,pos={295,215},size={67,20},proc=Trn_PanelDoneButtonProc,title="Done"
1138	Button Trn_button_6,help={"Close the panel when done calculating transmissions"}
1139	Button Trn_button_7,pos={67,32},size={214,20},proc=Trn_RefreshProc,title="List Files"
1140	Button Trn_button_7,help={"Generate or refresh the tables of files."}
1141	Button Trn_button_8,pos={5,156},size={161,20},proc=Trn_CalcSelectedFilesButton,title="Calculate Selected Files"
1142	Button Trn_button_8,help={"Calculate transmission and patch headers of selected files in the Scattering File Table."}
1143	Button Trn_button_10,pos={5,215}, size={161,20},proc=TotalTransButtonProc
1144	Button Trn_button_10 title="Calculate Total Trans"
1145	Button Trn_button_10 help={"Calculate transmission over the whole detector and patch headers of ALL files in the data folder."}
1146	Button setEmpForAll,pos={4,117},size={120,20},proc=FillEMPFilenameWSelection,title="Use EMP for ALL"
1147	Button setEmpForAll,help={"This button will set the file selected in the Transmission file table to be the empty beam file."}
1148	Button ClearTrans,pos={175,215},size={110,20},proc=ClearSelectedAssignments,title="Clear Selection"
1149	Button ClearTrans,help={"This button will set the file selected in the Transmission file table to be the empty beam file."}
1150	EndMacro
1151
1152
1153	Function TotalTransButtonProc(ctrlName) : ButtonControl
1154	String ctrlName
1155	TotalTrans(ctrlName)
1156	End
1157
1158
1159	Proc ShowTransHelp(ctrlName) : ButtonControl
1160	String ctrlName
1161	DisplayHelpTopic/Z/K=1 "SANS Data Reduction Tutorial[Calculate Transmissions]"
1162	if(V_flag !=0)
1163	DoAlert 0,"The SANS Data Reduction Tutorial Help file could not be found"
1164	endif
1165	End
1166
1167
1168	//generates the file tables of scattering files and transmission files
1169	//
1170	// if the tables already exist, they will be updated
1171	//
1172	Proc Trn_RefreshProc(ctrlName) : ButtonControl
1173	String ctrlName
1174	BuildFileTables()
1175	End
1176
1177	//shows a noteboox of help text describing how to calculate transmissions
1178	// - better that the user read the igor or pdf file, but it's a victory to get
1179	//users to read anything at all
1180	//
1181	Proc Trn_ShowHelpProc(ctrlName) : ButtonControl
1182	String ctrlName
1183	DisplayTransHelp()
1184	End
1185
1186	//sorts the tables by date
1187	//
1188	Proc Trn_SortFilesByDate(ctrlName) : ButtonControl
1189	String ctrlName
1190	SortTransByDate()
1191	End
1192
1193	//sorts the tables alphabetically by the sample label field
1194	//
1195	Proc Trn_SortFilesByLabel(ctrlName) : ButtonControl
1196	String ctrlName
1197	SortTransByLabel()
1198	End
1199
1200	//button action procedure to select the local path to the
1201	//folder containing the RAW SANS data files
1202	// - once the data folder is selected, all of the popup file menus are
1203	//forced to update with fresh file lists
1204	//
1205	Function Trn_PickPathButton(PathButton) : ButtonControl
1206	String PathButton
1207
1208	//set the global string to the selected pathname
1209	Variable err
1210	err = PickPath()
1211	if(err)
1212	return(1) //some problem with path or user cancelled, get out
1213	endif
1214
1215	PathInfo/S catPathName
1216	String path = S_path
1217	if (V_flag == 0)
1218	//path does not exist - no folder selected
1219	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = "no folder selected"
1220	else
1221	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = path
1222	endif
1223
1224	//Update the pathStr variable box
1225	ControlUpdate/W=Trans_Panel $"Trn_setvar_0"
1226	//Generate tables
1227	Execute "BuildFileTables()"
1228
1229	End
1230
1231	//button action function that asks the user to set the XY box to sum over
1232	//for all transmission calculations
1233	//
1234	// requires the user to set the box coordinates with the marquee popup
1235	//that wil properly set the keyword string, and write the values to the empty beam header
1236	//
1237	Function Trn_SetXYBoxButton(ctrlName) : ButtonControl
1238	String ctrlName
1239
1240	String msgStr = "Select the Empty Beam File"
1241	String filename=""
1242
1243	//get the filename from the popup menu
1244	//and construct a full path to it
1245	SVAR partialName = root:myGlobals:TransHeaderInfo:gEMP
1246	print partialName
1247	//get a valid file based on this partialName and catPathName
1248	String tempName = FindValidFilename(partialName)
1249	if(cmpstr(tempName,"")==0)
1250	//file not found, get out
1251	Abort "Empty beam file not found Trn_SetXYBoxButton(ctrlName)"
1252	Endif
1253	//name is ok, prepend path to tempName for read routine
1254	PathInfo catPathName
1255	filename = S_path + tempName
1256
1257	//read the file in - check for previous coordinates
1258	ReadHeaderAndData(filename)
1259	//data is displayed here (go through the normal display steps, so all is created properly
1260	String/G root:myGlobals:gDataDisplayType="RAW"
1261	fRawWindowHook()
1262
1263	// check the empty beam file for previously selected coordinates
1264	//if they exist, set the xy string , save the normalized counts somewhere
1265	//the value was written to an unused r*4 header analysis.factor (@b494)
1266	Variable refnum,x1,x2,y1,y2,err
1267	getXYBoxFromFile(filename,x1,x2,y1,y2)
1268
1269	//read the real count value, assign to a global
1270	Variable/G root:myGlobals:gTransCts = getBoxCounts(filename) //***NOTE this is NOT in the Trans sub-folder
1271	//
1272	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
1273	//no region selected
1274
1275	//add the empty beam file to work.SAM
1276	err = Raw_to_work("SAM")
1277
1278	//the calling macro must change the display type
1279	String/G root:myGlobals:gDataDisplayType="SAM" //displayed data type is sam
1280
1281	//data is displayed here
1282	fRawWindowHook()
1283
1284	//prompt user to select box w/marquee
1285	DoAlert 0,"Select the region to sum with the Marquee"
1286
1287	//from here the Marquee menu selection must handle the task of setting the box
1288	//and updating the information in the file header
1289	else
1290	// region already selected, just put up the values from the file header
1291	//allow user the option of overriding the current box region
1292	msgStr = "X1="+num2str(x1)+";"
1293	msgStr += "X2="+num2str(x2)+";"
1294	msgStr += "Y1="+num2str(y1)+";"
1295	msgStr += "Y2="+num2str(y2)+";"
1296	String textStr
1297	textStr = "Override current box "+msgStr+" ?"
1298	DoAlert 1,textStr
1299	If((V_flag)==1)
1300	//get new box coordinates, same procedure as above
1301	//add the empty beam file to work.SAM
1302	err = Raw_to_work("SAM")
1303
1304	//the calling macro must change the display type
1305	String/G root:myGlobals:gDataDisplayType="SAM" //displayed data type is sam
1306
1307	//data is displayed here
1308	fRawWindowHook()
1309
1310	//prompt user to select box w/marquee
1311	DoAlert 0,"Select the region to sum with the Marquee"
1312
1313	//from here the Marquee menu selection must handle the task of setting the box
1314	//and updating the information in the file header
1315	else
1316	String/G root:myGlobals:TransHeaderInfo:gBox = msgStr
1317	Endif
1318	Endif
1319
1320	UpdateBoxCoordinates()
1321	Return (0)
1322	End
1323
1324
1325	//button action function that assigns the selected empty beam file (run number only)
1326	//and the sample trnansmissionfile (run number only) to the popup list of sample scattering
1327	//files (ALL of the list items). Assignment is done by writing the integer run numbers of
1328	//trans files to the header of each of the scattering files, in a batchwise processing
1329	//of the popup list
1330	//
1331	//transmission are not calculated here - only the file numbers are set
1332	//
1333	//*******unused*********
1334	//Function Trn_AssignAllFilesButton(ctrlName) : ButtonControl
1335	// String ctrlName
1336	//
1337	// AssignTransFilesToData()
1338	//
1339	//End
1340
1341	//button action procedure to calculate the transmission of all of the sample files in the
1342	//sample popup list, based on the information in EACH sample header and in the empty beam file
1343	//the box must be set properly in the empty beam file, AND the empty and trans
1344	//run number must also be set properly in EACH scattering file,
1345	//If run numbers are not properly assigned, no trans is calculated and the
1346	//header is not modified
1347	//
1348	//The RAW data header of EACH sample file IS modified, with the newly calculated transmission
1349	//
1350	//not very friendly, but forces users to assign the files before continuing
1351	//
1352	Function Trn_CalcAllFilesButton(ctrlName) : ButtonControl
1353	String ctrlName
1354
1355	//calculate the transmission and Patch the header (if possible)
1356	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1357	Variable num_s_files = numpnts(S_GFilenames)
1358	AssignSelTransFilesToData(0,num_s_files-1) //do all the files (points 0 to n-1, inclusive)
1359	CalcSelTransFromHeader(0,num_s_files-1)
1360
1361	End
1362
1363	//for selected scattering files in the scattering table,
1364	// the "Annn" association of trans file is written to the data file,
1365	// the the transmission is actually calculated
1366	//
1367	Function Trn_CalcSelectedFilesButton(ctrlName) : ButtonControl
1368	String ctrlName
1369
1370	Variable scatterTableExists
1371	scatterTableExists = WinType("ScatterFileTable")
1372	if (scatterTableExists != 0)
1373	GetSelection table,ScatterFileTable,1
1374	if(V_Flag != 0)
1375	AssignSelTransFilesToData(V_StartRow,V_EndRow)
1376	//calculate the transmission and Patch the header (if possible)
1377	CalcSelTransFromHeader(V_StartRow,V_EndRow)
1378	Else
1379	DoAlert 0,"No selection from Scattering Files table"
1380	Endif
1381	Else
1382	DoAlert 0,"No file selected from Scattering Files table or no Scattering Files table available"
1383	Endif
1384	End
1385
1386	//
1387	// I am not sure what the difference is inthe function of CalcTotalTrans and CalcWholeTrans ?
1388	// do they really do anything different?
1389	// is it a useful calculation at all?
1390	//
1391	Function TotalTrans(ctrlName) : ButtonControl
1392	String ctrlName
1393
1394	Variable transTableExists
1395	transTableExists = WinType("TransFileTable")
1396	if (transTableExists != 0)
1397	GetSelection table,transFileTable,1
1398	if(V_Flag != 0)
1399	AssignTotalTransFilesToData(V_StartRow,V_EndRow)
1400	//calculate the transmission and Patch the header (if possible)
1401	CalcTotalTrans(V_StartRow,V_EndRow)
1402	CalcWholeTrans(V_StartRow,V_EndRow)
1403	Else
1404	DoAlert 0,"No selection from Trans Files table"
1405	Endif
1406	Else
1407	DoAlert 0,"No file selected from Trans Files table or no Trans Files table available"
1408	Endif
1409	End
1410
1411
1412	//simple button procedure to close the trans panel
1413	// - automatically kills the two tables as well
1414	//
1415	Function Trn_PanelDoneButtonProc(ctrlName) : ButtonControl
1416	String ctrlName
1417
1418	// this button will make sure all files are closed
1419	//and close the panel
1420
1421	Close/A
1422	DoWindow/K Trans_Panel
1423	DoWindow/K ScatterFileTable
1424	DoWindow/K TransFileTable
1425	End
1426
1427
1428	//function to update the box coordinates of the file selected as the
1429	//empty beam file - takes the file that is currently popped from the list
1430	//reads the 4 "analysis" integers that hold the box coordinates
1431	//resets the globals string that is displayed with the new values
1432	//should be called whenever the "empty" popup is popped, to ensure
1433	//that current header information is displayed
1434	//
1435	Function UpdateBoxCoordinates()
1436
1437	//construct a full name, and read in the label from the file
1438	//and set the global
1439	String textstr=""
1440	ControlInfo empStr
1441	SVAR item = root:myGlobals:TransHeaderInfo:gEMP
1442	String tempName = FindValidFilename(item)
1443	if(cmpstr(tempName,"")==0)
1444	//file not found, get out
1445	Abort "Empty beam file not found UpdateBoxCoordinates(ctrlName)"
1446	Endif
1447	//name is ok, prepend path to tempName for read routine
1448	PathInfo catPathName
1449	String filename = S_path + tempName
1450
1451	Variable refnum,x1,x2,y1,y2,err
1452	GetXYBoxFromFile(filename,x1,x2,y1,y2)
1453
1454	//and update the global string
1455	String msgStr=""
1456	msgStr = "X1="+num2str(x1)+";"
1457	msgStr += "X2="+num2str(x2)+";"
1458	msgStr += "Y1="+num2str(y1)+";"
1459	msgStr += "Y2="+num2str(y2)+";"
1460
1461	String/G root:myGlobals:TransHeaderInfo:gBox = msgStr
1462
1463	ControlUpdate/W=Trans_panel Trn_setvar_1
1464	End
1465
1466	//crude procedure to display a notebook of help information for users
1467	//
1468	Proc DisplayTransHelp()
1469	String nb = "Notebook0"
1470	NewNotebook/N=$nb/F=1/V=1/W=(342,302,868,674) as "Notebook0:Transmission Help"
1471	Notebook $nb defaultTab=36, statusWidth=238, pageMargins={36,72,36,72}
1472	Notebook $nb showRuler=1, rulerUnits=1, updating={1, 3600}
1473	Notebook $nb newRuler=Normal, justification=0, margins={0,0,468}, spacing={0,0,0}, tabs={}, rulerDefaults={"Geneva",10,0,(0,0,0)}
1474	Notebook $nb ruler=Normal; Notebook $nb justification=1, fSize=14, fStyle=1, text="Transmission Help\r"
1475	Notebook $nb ruler=Normal, fSize=-1, fStyle=-1, text="\r"
1476	Notebook $nb text="This panel allows quick and easy calculation of sample transmission. The neutron transmission of a sampl"
1477	Notebook $nb text="e must be calculated and entered into the header of each sample scattering file before proper background"
1478	Notebook $nb text=" corrections or absolute scaling can be done.\r"
1479	Notebook $nb text="\r"
1480	Notebook $nb text="During data collection, you measured an empty beam - that is a measurement with heavy attenuation of th"
1481	Notebook $nb text="e neutron beam and the beamstop mover out of line with the direct beam. Then without changing the attenu"
1482	Notebook $nb text="ation or replacing the beamstop, you put a sample in the beam, and repeated the measurement (a sample tr"
1483	Notebook $nb text="ansmission measurement). The neutron transmission of the sample is simply the ratio of the number of neu"
1484	Notebook $nb text="tron counts from the sample transmission measurement normalized by the number of neutron counts from the"
1485	Notebook $nb text=" empty beam measurement. In this way, each sample transmission file is \"linked\" to the same empty beam t"
1486	Notebook $nb text="ransmission file.\r"
1487	Notebook $nb text="\r"
1488	Notebook $nb text="This calculated transmission value must be entered into the header of the sample scattering measurement "
1489	Notebook $nb text="- that is the measurement of the sample with the beamstop covering the primary (transmitted) beam, and n"
1490	Notebook $nb text="o (or few) attenuators in place. In this way, the sample transmission file is \"linked\" to its correspond"
1491	Notebook $nb text="ing sample scattering file. This panel allows you to set up the links and calculate the transmission.Tra"
1492	Notebook $nb text="nsmisison values are automatically patched to the scattering file headers as they are calculated.\r"
1493	Notebook $nb text="\r"
1494	Notebook $nb text="To Calculate Transmissions:\r"
1495	Notebook $nb text="\r"
1496	Notebook $nb text="1) Click \"List Files\" to get two lists (tables) - one of all the sample scattering files in the folder, "
1497	Notebook $nb text="and one of the transmission files.\r"
1498	Notebook $nb text="\r"
1499	Notebook $nb text="2) Select the region of the detector to sum over from the empty beam transmission file. Do theis by clic"
1500	Notebook $nb text="king on the filename of the empty beam transmision file (from the TransmissionFiles window, in the blue "
1501	Notebook $nb text="\"T_Filenames\" column). Return to the panel, and click the \"set EMP file\" button\", and the filename shoul"
1502	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"
1503	Notebook $nb text="et XY Box\" button. The empty beam file will be displayed, and you will be instructed to select the regio"
1504	Notebook $nb text="n to sum with the marquee. On the data, click and drag a rectangle that encompasses the primary beam. Mo"
1505	Notebook $nb text="ve the cursor inside the selection, to get an \"upside-down hat\" cursor. Click to get a menu, and near th"
1506	Notebook $nb text="e bottom, select \"Set XY Box Coords\". The pixel values should be updated to the Transmission panel, and "
1507	Notebook $nb text="are written to the empty beam header for future calculations. Note that the marquee selection can also b"
1508	Notebook $nb text="e used to measure the beam center, or centroid of any selected region.\r"
1509	Notebook $nb text="\r"
1510	Notebook $nb text="3) Now you need to \"link\" the ", fStyle=2, text="sample", fStyle=-1, text=" transmission files to the "
1511	Notebook $nb fStyle=2, text="empty", fStyle=-1, text=" ", fStyle=2, text="beam", fStyle=-1
1512	Notebook $nb text=" transmission file. Do this in the TransmissionFiles window by selecting the filename (in the blue T_Fil"
1513	Notebook $nb text="enames column) and pasing it to the corresponding row(s) in the T_EMP_Filenames column. This links the e"
1514	Notebook $nb text="mpty beam transmission with the sample transmission file. Do this for every sample transmission file.\r"
1515	Notebook $nb text="\r"
1516	Notebook $nb text="4) Now you need to link the sample ", fStyle=2, text="transmission", fStyle=-1
1517	Notebook $nb text=" file to the sample ", fStyle=2, text="scattering", fStyle=-1
1518	Notebook $nb text=" file. Do this by selecting the name of the transmission file (from the blue T_Filenames column) and pas"
1519	Notebook $nb text="ting it into the corresponding row of the S_TRANS_Filenames column of the ScatteringFiles window. This l"
1520	Notebook $nb text="inks the scattering file to its corresponding sample transmission file. This for all of the sample scatt"
1521	Notebook $nb text="ering files.\r"
1522	Notebook $nb text="\r"
1523	Notebook $nb text="5) Calculate the transmissions (and automatically write the transmission value to the satterng file head"
1524	Notebook $nb text="er) by clicking \"Calculate All Files\" from the Transmission Panel. The results will be printed to the co"
1525	Notebook $nb text="mmand window at the bottom of the screen. Any improperly assigned files will be listed. For example, blo"
1526	Notebook $nb text="cked beam scattering files will return an error, since the transmssion known to be zero, and is not meas"
1527	Notebook $nb text="ured (and no files are \"linked\"). Rather than calculating the transmission of all of the files, a range"
1528	Notebook $nb text=" of S_Filenames can be selected, then calculated by clicking \"Calculate Selected Files\".\r"
1529	Notebook $nb text="\r"
1530	Notebook $nb text="By default the lists are sorted by run number (= chronological). In some cases it may be easier to sort "
1531	Notebook $nb text="by the sample label to group several of the same sample scattering files collected at different sample-t"
1532	Notebook $nb text="o-detector distances. Its utility depends, of course, on how consistent and unique your sample labels ar"
1533	Notebook $nb text="e.\r"
1534	Notebook $nb text="\r"
1535	Notebook $nb text="The \"links\" are stored in the corresponding files, and wil be re-generated when the lists are re-generat"
1536	Notebook $nb text="ed. Unassigned links will appear as blank elements in the T_EMP_Filenames or S_TRANS_Filenames columns.\r"
1537	Notebook $nb text="\r"
1538	Notebook $nb, selection={startOfFile,startOfFile}
1539	Notebook $nb text="\r"
1540	End
1541
1542
1543
1544	//*******************
1545	//************
1546	// A simple panel to allow users of the NG1 SANS instrument to make their
1547	// transmission files "look" like a transmission measurement to the data reduction
1548	// program. Transmission files are designated by an x-position of the beamstop of
1549	// < -5 (cm). this simple procedure sets xpos=-10 for individual files. files
1550	// con be "un-converted", which set the xpos=0.
1551	// 1/30/01 SRK
1552	//************
1553
1554	Proc TransformToTransFile()
1555	Variable/G root:myGlobals:gConvTrans=1
1556	DoWindow/F Convert_to_Trans
1557	if(V_flag==0)
1558	Convert2Trans()
1559	endif
1560	End
1561
1562	//fname must be the full path and name for the file
1563	Function ChangeBSXPos(fname,xpos)
1564	String fname
1565	Variable xpos
1566
1567	Variable start
1568	//x-position starts after byte 368 in VAX files
1569	WriteBSXPosToHeader(fname,xpos)
1570	return(0)
1571	End
1572
1573	//sets the beamstop position to zero NOT the original position
1574	Function UnConvertButtonProc(ctrlName) : ButtonControl
1575	String ctrlName
1576
1577	//Print "UnConvert"
1578	String fullname=""
1579	ControlInfo fileNum
1580	Variable num = V_Value //run number to find
1581
1582	fullname = FindFileFromRunNumber(num)
1583	Print fullname
1584	//report error or change the file
1585	if(cmpstr(fullname,"")==0)
1586	Print "Unconvert - file not found"
1587	else
1588	//Print "Unconvert",fullname
1589	ChangeBSXPos(fullName,0)
1590	Endif
1591	return(0)
1592	End
1593
1594	//button procedure to do the conversion
1595	// writes fake beamstop position to the data file
1596	//
1597	Function ConvertButtonProc(ctrlName) : ButtonControl
1598	String ctrlName
1599
1600	String fullname=""
1601	ControlInfo fileNum
1602	Variable num = V_Value //run number to find
1603
1604	fullname = FindFileFromRunNumber(num)
1605	print fullname
1606	//report error or change the file
1607	if(cmpstr(fullname,"")==0)
1608	Print "Convert - file not found"
1609	else
1610	//Print "Convert",fullname
1611	ChangeBSXPos(fullName,-10)
1612	Endif
1613	return(0)
1614	End
1615
1616	//simple panel recreation macro
1617	//
1618	Proc Convert2Trans()
1619	PauseUpdate; Silent 1 // building window...
1620	NewPanel /W=(434,74,671,216) /K=1
1621	DoWindow/C Convert_to_Trans
1622	SetDrawLayer UserBack
1623	DrawText 18,22,"Convert files to be recognized"
1624	DrawText 43,39,"as transmission files"
1625	SetVariable fileNum,pos={43,58},size={130,15},title="File Number"
1626	SetVariable fileNum,limits={1,Inf,1},value=root:myGlobals:gConvTrans
1627	SetVariable fileNum,help={"Sets the run number of the file that is to be converted"}
1628	Button ConvButton,pos={73,79},size={80,20},proc=ConvertButtonProc,title="Convert"
1629	Button ConvButton,help={"Converts the chosen file to appear as a transmission file"}
1630	Button UndoButton,pos={68,105},size={90,20},proc=UnConvertButtonProc,title="Un-Convert"
1631	Button UndoButton,help={"Converts the chosen file to appear as a scattering file"}
1632	EndMacro
1633
1634	//
1635	// The proper list of transmission files MUST be present in the Patch Popup list
1636	// -- using Grep for "trans" is a possible choice
1637	//
1638	// testing only TODO_10m -- a quick fix for the missing BS xpos to identify trans
1639	Function BatchConvert_10mTrans(xPos)
1640	Variable xPos //pass -10 to make it trans, pass 0 to make it scattering again
1641
1642	//this will change (checked) values in ALL of the headers in the popup list
1643	SVAR list = root:myGlobals:Patch:gPatchList
1644	String partialName="", tempName = ""
1645	Variable numitems,ii,ok
1646	numitems = ItemsInList(list,";")
1647
1648	//loop through all of the files in the list, applying changes as dictated by w and wt waves
1649	ii=0
1650	do
1651	//get current item in the list
1652	partialName = StringFromList(ii, list, ";")
1653
1654	//get a valid file based on this partialName and catPathName
1655	tempName = FindValidFilename(partialName)
1656
1657	//prepend path to tempName for read routine
1658	PathInfo catPathName
1659	tempName = S_path + tempName
1660
1661	//make sure the file is really a RAW data file
1662	ok = CheckIfRawData(tempName)
1663	if (!ok)
1664	Print "this file is not recognized as a RAW SANS data file = ",tempName
1665	else
1666	//go write the changes to the file
1667	ChangeBSXPos(tempName,xPos)
1668	Endif
1669
1670	ii+=1
1671	while(ii<numitems)
1672
1673	End
1674
1675	/////
1676	// A quick way to fill all the T_EMP_Filenames with the selected empty beam file
1677	// Note that you must go back and clear or reassign any files that are special cases
1678	//
1679	// IMPORTANT - this will overwrite any other file assignments (typically not a problem
1680	// if you are using only one wavelength)
1681	//
1682	/////
1683	// March 2010:
1684	// changed from the previous beta menu operation, now uses the text from the file name box
1685	// rather than requiring a selection on the table (since you just set the box...)
1686	//
1687	Function FillEMPFilenameWSelection(ctrlName)
1688	String ctrlName
1689
1690	// GetSelection table,TransFileTable,3
1691	// Variable row=V_startRow //ony need the selected row, we know the column names and location
1692
1693	SVAR empName = root:myGlobals:TransHeaderInfo:gEMP
1694	if(strlen(empName)==0 \|\| cmpstr(empName,"no path selected")==0)
1695	DoAlert 0,"Please select and set an empty beam file"
1696	return(0)
1697	endif
1698	Wave/T fw = root:myGlobals:TransHeaderInfo:T_FileNames //trans files
1699	Wave/T ew = root:myGlobals:TransHeaderInfo:T_EMP_FileNames //empty beam reference files
1700
1701	ew[] = empName
1702
1703	return(0)
1704	End
1705
1706	//given a selection of the SAMPLE files, try to find the corresponding transmission file
1707	//
1708	Function GuessTransFile(charsToUse,row)
1709	Variable charsToUse,row //number of characers to use from the beginning of the label, and the row of the sample file
1710
1711	// GetSelection table,ScatterFileTable,3
1712	// Variable row=V_startRow //ony need the selected row, we know the column names and location
1713	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
1714	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
1715	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
1716	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
1717
1718	Variable num,ii,found
1719	String samStr = "",testStr=""
1720
1721	samStr = (sw[row])[0,charsToUse-1] //string to try and match
1722	samStr += "*"
1723	// Print samStr
1724	num=numpnts(tw)
1725	ii=0
1726	do
1727	testStr=tw[ii]
1728	found = stringmatch(testStr, samStr )
1729	if(found == 1)
1730	Print "Match Found at: ",samStr,tnam[ii],tw[ii]
1731	snam[row] = tnam[ii] //write the file name into the table
1732	return(0)
1733	endif
1734	ii+=1
1735	while(ii<num)
1736
1737	//method 2
1738	// samStr = (sw[row])[0,charsToUse-1] //string to try and match
1739	//// Print samStr
1740	// num=numpnts(tw)
1741	// ii=0
1742	// do
1743	// testStr=tw[ii]
1744	// found = strsearch(testStr,samStr,0) //start from zero, Need Igor 5 to allow 4th parameter to ignore case
1745	// if(found != -1)
1746	// Print "Match Found at: ",samStr,tnam[ii],tw[ii]
1747	// snam[row] = tnam[ii] //write the file name into the table
1748	// return(0)
1749	// endif
1750	// ii+=1
1751	// while(ii<num)
1752
1753	Print "No Match found"
1754	return(0)
1755	End
1756
1757	//given a single transmission file, try to find the corresponding scattering file(s)
1758	//
1759	// apply TWO criteria
1760	// (1) the label must match "well enough"
1761	// (2) the wavelength must be the same "enough", given the unnecessary precision reported by ICE
1762	//
1763	// (for example, "6" can be anything from 6.0008 to 6.0020 in a recent experiment)
1764	//
1765	// passes the matching rows in the sample table back
1766	//
1767	Function GuessTransToScattFiles(charsToUse,row,matchRows)
1768	Variable charsToUse,row //number of characers to use from the beginning of the label, and the row of the transmission file
1769	Wave matchRows //rows where (potential) matches found. initially zero points
1770
1771	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
1772	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
1773	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
1774	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
1775	Wave sLam = root:myGlobals:TransHeaderInfo:S_Lambda //Scattering file wavelength
1776	Wave tLam = root:myGlobals:TransHeaderInfo:T_Lambda //Transmission file wavelength
1777
1778	Variable num,ii,found,tolerance=0.01 //0.01 = 1% tolerance
1779	String transStr = "",testStr=""
1780
1781	transStr = (tw[row])[0,charsToUse-1] //string to try and match
1782	transStr += "*"
1783
1784	//loop over ALL sample files
1785	num=numpnts(sw)
1786	ii=0
1787	do
1788	testStr=sw[ii]
1789	found = stringmatch(testStr, transStr )
1790	if( (found == 1) && (abs(sLam[ii] - tLam[row]) < tolerance) ) // both must match
1791	Print "Match Found at: ",transStr,snam[ii],sw[ii]
1792	InsertPoints numpnts(matchRows), 1, matchRows
1793	matchRows[numpnts(matchRows)-1] = ii
1794	endif
1795	ii+=1
1796	while(ii<num)
1797
1798	//method 2 UNTESTED
1799	// transStr = (tw[row])[0,charsToUse-1] //string to try and match
1800	// num=numpnts(sw)
1801	// ii=0
1802	// do
1803	// testStr=sw[ii]
1804	// found = strsearch(testStr,transStr,0,2) //start from zero, ignore case
1805	// if(found != -1)
1806	// Print "Match Found at: ",transStr,snam[ii],sw[ii]
1807	// InsertPoints numpnts(matchRows), 1, matchRows
1808	// matchRows[numpnts(matchRows)-1] = ii
1809	//// snam[ii] = tnam[row] //write the file name into the table
1810	// endif
1811	// ii+=1
1812	// while(ii<num)
1813
1814	// Print "No Match found"
1815	return(0)
1816	End
1817
1818	//get a single selection from the Trans table
1819	// find all of the matching scattering files (rows)
1820	// ask the user if the selections are OK
1821	// if NOT OK, do nothing
1822	// if OK: make the assignments, and immediately calculate the transmission
1823	//
1824	Function fGuessTransToScattFiles(numChars)
1825	Variable numChars
1826
1827	Variable ii,row
1828	Variable transTableExists
1829
1830	Variable/G root:myGlobals:TransHeaderInfo:gNumMatchChars = numChars
1831	SVAR gMatchSamStr = root:myGlobals:TransHeaderInfo:gMatchingSampleFiles
1832
1833	Make/O/D/N=0 root:myGlobals:TransHeaderInfo:matchRows
1834	Wave matchRows=root:myGlobals:TransHeaderInfo:matchRows
1835
1836	transTableExists = WinType("TransFileTable")
1837	if (transTableExists != 0)
1838	GetSelection table,transFileTable,1
1839	row = V_startRow
1840	GuessTransToScattFiles(numChars,row,matchRows)
1841	else
1842	Print "Transmission->Scattering File table is not open"
1843	return (1)
1844	endif
1845
1846	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
1847	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
1848	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
1849	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
1850	Wave/T samfile = root:myGlobals:TransHeaderInfo:S_FileNames //Scattering file name
1851
1852	// can do fancy formatted string with ...
1853	//"asdf* matches file: \\f01filen\\f00 \\K(52428,1,1)\\f01afdsfdd\\f00\\K(0,0,0)asdfasdfs"
1854	Variable num=numpnts(matchRows)
1855	String result="",tmpStr
1856	for(ii=0;ii<num;ii+=1)
1857	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]
1858	result += tmpStr
1859	endfor
1860
1861	if(cmpstr(result,"")==0)
1862	result = "No match found for "+ (tw[row])[0,numChars-1]
1863	endif
1864
1865	// Print result
1866	Print "*******"
1867
1868	String/G root:myGlobals:TransHeaderInfo:gResultStr = result
1869
1870	DoWindow/F ConfirmGuess //if being called recursively, the panel is already up
1871	if(V_flag==1)
1872	TitleBox title0,pos={9,5},variable=root:myGlobals:TransHeaderInfo:gResultStr
1873	else
1874	NewPanel /W=(600,44,1150,225) as "Confirm Guess"
1875	DoWindow/C ConfirmGuess
1876	TitleBox title0,pos={15,8},size={560,32}
1877	TitleBox title0,variable= root:myGlobals:TransHeaderInfo:gResultStr
1878	Button button0,pos={240,150},size={190,20},proc=DoAssignTransButtonProc,title="Assign Transmission Files"
1879	Button button1,pos={10,150},size={100,20},proc=DoTryAgainMoreButtonProc,title="Try Again (+)"
1880	Button button2,pos={120,150},size={100,20},proc=DoTryAgainFewerButtonProc,title="Try Again (-)"
1881	Button button3,pos={450,150},size={70,20},proc=SkipTransButtonProc,title="Skip"
1882	endif
1883
1884	PauseForUser ConfirmGuess
1885
1886	// figure out from the return code what the user did...
1887	// 1 = OK, accept guess (assign, and calculate immediately)
1888	// 2 = try again (+) // NO - not an "exit" code
1889	// 3 = try again (-) //NO - not an "exit" code
1890	// 0 = cancel, don't do anything, drop out of case
1891	NVAR guessOK = root:myGlobals:TransHeaderInfo:GuessOK
1892
1893	// switch here...
1894	switch(guessOK) // numeric switch
1895	case 1:
1896	// accept guess (assign, and calculate immediately)
1897	gMatchSamStr=""
1898	num=numpnts(matchRows) //this may have changed
1899	for(ii=0;ii<num;ii+=1)
1900	snam[matchRows[ii]] = tnam[row]
1901	AssignSelTransFilesToData(matchRows[ii],matchRows[ii])
1902	CalcSelTransFromHeader(matchRows[ii],matchRows[ii]) //does only that sample file
1903	gMatchSamStr += samfile(matchRows[ii]) + ";"
1904	endfor
1905	break
1906	case 2: //try again (with more characters)
1907	// not an exit code, does nothing
1908	break
1909	case 3: //try again (with fewer characters)
1910	// not an exit code, can't do anything
1911	break
1912	case 0: // cancel
1913	gMatchSamStr = ""
1914	// do nothing
1915	break
1916	default:
1917	// do nothing
1918	endswitch
1919
1920	return(0)
1921	End
1922
1923	// a hook attached to the Transmission Files Table
1924	// given a single selected Trans File, popup gives choices
1925	// to guess using "n" characters, then dispatch accordingly
1926	Function GuessFromTableHook(infoStr)
1927	String infoStr
1928	String event= StringByKey("EVENT",infoStr)
1929	// Print "EVENT= ",event
1930
1931	String menuStr=""
1932	menuStr += "Guess using N characters;"
1933	menuStr += "Guess using 3 characters;"
1934	menuStr += "Guess using 6 characters;"
1935	menuStr += "Guess using 9 characters;"
1936	menuStr += "Guess using 12 characters;"
1937	menuStr += "Guess using 15 characters;"
1938	menuStr += "Guess using 18 characters;"
1939	menuStr += "Guess using 21 characters;"
1940	menuStr += "Guess using 24 characters;"
1941
1942	strswitch(event)
1943	case "mousedown":
1944	Variable xpix= NumberByKey("MOUSEX",infoStr)
1945	Variable ypix= NumberByKey("MOUSEY",infoStr)
1946	Variable modif= NumberByKey("MODIFIERS",infoStr)
1947	//print modif
1948	if(modif & 2^1) //bit 1 set, shift key is down
1949	PopupContextualMenu/C=(xpix, ypix) menuStr
1950	strswitch(S_selection)
1951	case "Guess using 3 characters":
1952	fGuessTransToScattFiles(3)
1953	break
1954	case "Guess using 6 characters":
1955	fGuessTransToScattFiles(6)
1956	break
1957	case "Guess using 9 characters":
1958	fGuessTransToScattFiles(9)
1959	break
1960	case "Guess using 12 characters":
1961	fGuessTransToScattFiles(12)
1962	break
1963	case "Guess using 15 characters":
1964	fGuessTransToScattFiles(15)
1965	break
1966	case "Guess using 18 characters":
1967	fGuessTransToScattFiles(18)
1968	break
1969	case "Guess using 21 characters":
1970	fGuessTransToScattFiles(21)
1971	break
1972	case "Guess using 24 characters":
1973	fGuessTransToScattFiles(24)
1974	break
1975	case "Guess using N characters":
1976	Variable num=10
1977	Prompt num, "Number of characters"
1978	DoPrompt "Enter the number of characters to match", num
1979	if (V_Flag)
1980	break //user cancel, do nothing
1981	endif
1982	fGuessTransToScattFiles(num)
1983	break
1984	endswitch //on selection
1985	endif
1986	endswitch // on event
1987
1988	return 0
1989	End
1990
1991	// sets a flag if the user thinks that the guess was correct, and wants to use the
1992	// identified files for the transmission
1993	Function DoAssignTransButtonProc(ba) : ButtonControl
1994	STRUCT WMButtonAction &ba
1995
1996	switch( ba.eventCode )
1997	case 2: // mouse up
1998	// click code here
1999	//Print "Assigned stuff, and left."
2000	Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 1
2001	DoWindow/K ConfirmGuess
2002	break
2003	endswitch
2004
2005
2006	return 0
2007	End
2008
2009	// files are wrong, let the user try it again
2010	// sets a flag, nothing else
2011	Function DoTryAgainMoreButtonProc(ba) : ButtonControl
2012	STRUCT WMButtonAction &ba
2013
2014	Variable row,ii,num
2015	String tmpStr
2016
2017	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
2018	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
2019	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
2020	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
2021	Wave/T samfile = root:myGlobals:TransHeaderInfo:S_FileNames //Scattering file name
2022
2023	switch( ba.eventCode )
2024	case 2: // mouse up
2025	// click code here
2026	Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 2
2027	NVAR numChars = root:myGlobals:TransHeaderInfo:gNumMatchChars
2028	SVAR resultStr = root:myGlobals:TransHeaderInfo:gResultStr
2029
2030	numChars += 1
2031
2032	Make/O/D/N=0 root:myGlobals:TransHeaderInfo:matchRows
2033	Wave matchRows=root:myGlobals:TransHeaderInfo:matchRows
2034
2035	//transTableExists = WinType("TransFileTable")
2036	//if (transTableExists != 0)
2037	GetSelection table,transFileTable,1
2038	row = V_startRow
2039	GuessTransToScattFiles(numChars,row,matchRows)
2040
2041	num=numpnts(matchRows)
2042
2043	resultStr = ""
2044	for(ii=0;ii<num;ii+=1)
2045	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]
2046	resultStr += tmpStr
2047	endfor
2048
2049	if(cmpstr(resultStr,"")==0)
2050	resultStr = "No match found for "+ (tw[row])[0,numChars-1]
2051	endif
2052
2053	// DoWindow/K ConfirmGuess
2054	//Print "Try Again"
2055	break
2056	endswitch
2057
2058	return 0
2059	End
2060
2061	// files are wrong, let the user try it again
2062	// sets a flag, nothing else
2063	Function DoTryAgainFewerButtonProc(ba) : ButtonControl
2064	STRUCT WMButtonAction &ba
2065
2066	Variable row,ii,num
2067	String tmpStr
2068
2069	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
2070	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
2071	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
2072	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
2073	Wave/T samfile = root:myGlobals:TransHeaderInfo:S_FileNames //Scattering file name
2074
2075	switch( ba.eventCode )
2076	case 2: // mouse up
2077	// click code here
2078	Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 3
2079
2080	NVAR numChars = root:myGlobals:TransHeaderInfo:gNumMatchChars
2081	SVAR resultStr = root:myGlobals:TransHeaderInfo:gResultStr
2082
2083	numChars -= 1
2084
2085	Make/O/D/N=0 root:myGlobals:TransHeaderInfo:matchRows
2086	Wave matchRows=root:myGlobals:TransHeaderInfo:matchRows
2087
2088	//transTableExists = WinType("TransFileTable")
2089	//if (transTableExists != 0)
2090	GetSelection table,transFileTable,1
2091	row = V_startRow
2092	GuessTransToScattFiles(numChars,row,matchRows)
2093
2094	num=numpnts(matchRows)
2095
2096	resultStr = ""
2097	for(ii=0;ii<num;ii+=1)
2098	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]
2099	resultStr += tmpStr
2100	endfor
2101
2102	if(cmpstr(resultStr,"")==0)
2103	resultStr = "No match found for "+ (tw[row])[0,numChars-1]
2104	endif
2105	// DoWindow/K ConfirmGuess
2106	//Print "Try Again"
2107	break
2108	endswitch
2109
2110	return 0
2111	End
2112
2113
2114	// cancel, skip this set of trans
2115	Function SkipTransButtonProc(ba) : ButtonControl
2116	STRUCT WMButtonAction &ba
2117
2118	switch( ba.eventCode )
2119	case 2: // mouse up
2120	// click code here
2121	//just kill the panel, don't do anything
2122	Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 0
2123	DoWindow/K ConfirmGuess
2124	break
2125	endswitch
2126
2127	return 0
2128	End
2129
2130	Function GuessAllTransFiles(numChars)
2131	Variable numChars
2132
2133	if(WinType("ScatterFileTable") ==0 )
2134	return(1)
2135	endif
2136
2137	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
2138	Variable ii,num=numpnts(sw)
2139
2140	for(ii=0;ii<num;ii+=1)
2141	GuessTransFile(numChars,ii)
2142	endfor
2143
2144	return(0)
2145	End
2146
2147	Function fGuessSelectedTransFiles(numChars)
2148	Variable numChars
2149
2150	Variable ii
2151	Variable scatterTableExists
2152	scatterTableExists = WinType("ScatterFileTable")
2153	if (scatterTableExists != 0)
2154	GetSelection table,ScatterFileTable,1
2155	for(ii=V_StartRow;ii<=V_EndRow;ii+=1)
2156	GuessTransFile(numChars,ii)
2157	endfor
2158	else
2159	Print "Transmission->Scattering File table is not open"
2160	endif
2161	return(0)
2162	End
2163
2164	// now a button on the Transmission Panel
2165	Function ClearSelectedAssignments(ctrlName)
2166	String ctrlName
2167
2168	/// old way, from the menu - takes the selection from the top window, have it now return the top table.
2169	// String winStr = WinList("*", ";", "WIN:" ) //returns the top window (with a trailing semicolon!)
2170	String winStr = WinName(0,2,1) //returns the top visible table
2171	Variable scatterTableExists, transTableExists
2172	// Print winStr
2173	scatterTableExists = cmpstr(winStr,"ScatterFileTable")
2174	if (scatterTableExists == 0)
2175	GetSelection table,ScatterFileTable,1
2176	fClearSelectedAssignments(V_startRow,V_endRow,1)
2177	endif
2178
2179	transTableExists = cmpstr(winStr,"TransFileTable")
2180	if (transTableExists == 0)
2181	GetSelection table,TransFileTable,1
2182	fClearSelectedAssignments(V_startRow,V_endRow,2)
2183	endif
2184
2185	///////// new method, presents a clunky dialog - don't use this way unless I absolutely need to
2186	// Variable whichTable=1
2187	// Prompt whichTable,"Which Table?",popup,"Transmission Files;Scattering Files;"
2188	// DoPrompt "Which Selection to Clear",whichTable
2189	// if (V_Flag)
2190	// return 0 // user canceled
2191	// endif
2192	//
2193	// if (whichTable == 1) //the Transmission Table
2194	// GetSelection table,TransFileTable,1
2195	// fClearSelectedAssignments(V_startRow,V_endRow,2)
2196	// else
2197	// //the Scattering Files table
2198	// GetSelection table,ScatterFileTable,1
2199	// fClearSelectedAssignments(V_startRow,V_endRow,1)
2200	// endif
2201	return(0)
2202	End

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