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Transmission.ipf @ 545

Last change on this file since 545 was 545, checked in by srkline, 14 years ago

(1) changed the "guessing" of transmission files to be tolerant (within 1%) of mismatches in the wavelength. With the VAX, I had required them to be equal. ICE reports a FP number that varies in the 3rd decimal place (from the RPM?).

(2) Changed the calculation of errors and total detector count in 1D simulation to be correct.

File size: 72.4 KB

Line
1	#pragma rtGlobals=1 // Use modern global access method.
2	#pragma version=5.0
3	#pragma IgorVersion=6.0
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
161	SetWindow kwTopWin hook=GuessFromTableHook, hookevents=1 // mouse down events
162
163	String name="TransFileTable"
164	DoWindow/C $name
165
166	End
167
168	//actually creates the table of scattering files
169	// - the waves must exist
170	//
171	Function BuildScatTableWindow()
172	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
173	Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
174	Wave/T S_Suffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
175	Wave/T S_Labels = $"root:myGlobals:TransHeaderInfo:S_Labels"
176	Wave S_SDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
177	Wave S_Lambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
178	Wave S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
179
180	Edit/K=1/W=(50,50,520,270) S_TRANS_Filenames, S_Filenames, S_Labels, S_SDD, S_Lambda, S_Transmission as "ScatteringFiles"
181	String name="ScatterFileTable"
182	DoWindow/C $name
183
184	End
185
186	//sorts each of the tables by date - does this by using the suffix "Annn"
187	// which is automatically supplied by the VAX (and can't be changed)
188	// - only problem may be "Z999" -> "A001" rollover
189	//
190	Function SortTransByDate()
191	Wave/T T_GEMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
192	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
193	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
194	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
195	Wave/T T_GLabels = $"root:myGlobals:TransHeaderInfo:T_Labels"
196	Wave T_GSDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
197	Wave T_GLambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
198	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
199	Wave T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
200
201	Wave/T S_GTRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
202	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
203	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
204	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
205	Wave/T S_GLabels = $"root:myGlobals:TransHeaderInfo:S_Labels"
206	Wave S_GSDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
207	Wave S_GLambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
208	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
209	Wave S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
210
211	Sort T_GSuffix, T_GEMP_Filenames, T_GSuffix, T_GSuffices, T_GFilenames, T_GLabels, T_GSDD, T_GLambda, T_GTransmission, T_Whole
212	Sort S_GSuffix, S_GTRANS_Filenames, S_GSuffix, S_GSuffices, S_GFilenames, S_GLabels, S_GSDD, S_GLambda, S_GTransmission, S_Whole
213
214	End
215
216	// sorts files alphabetically byt the sample label
217	// - consistent and descriptive sample labels really pay off here
218	//
219	Function SortTransByLabel()
220	Wave/T T_GEMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
221	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
222	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
223	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
224	Wave/T T_GLabels = $"root:myGlobals:TransHeaderInfo:T_Labels"
225	Wave T_GSDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
226	Wave T_GLambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
227	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
228	Wave T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
229
230	Wave/T S_GTRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
231	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
232	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
233	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
234	Wave/T S_GLabels = $"root:myGlobals:TransHeaderInfo:S_Labels"
235	Wave S_GSDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
236	Wave S_GLambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
237	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
238	Wave S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
239
240	Sort T_GLabels, T_GEMP_Filenames, T_GSuffix, T_GSuffices, T_GFilenames, T_GLabels, T_GSDD, T_GLambda, T_GTransmission, T_Whole
241	Sort S_GLabels, S_GTRANS_Filenames, S_GSuffix, S_GSuffices, S_GFilenames, S_GLabels, S_GSDD, S_GLambda, S_GTransmission, S_Whole
242
243	End
244
245	//reads the file and assigns header information to the proper table
246	//
247	//fname - is the full path:name of the datafile (used by Open)
248	//sname - is the name only, used as the filename field
249	//
250	// takes care of all necessary open/close of file
251	//
252	Function GetTransHeaderInfoToWave(fname,sname)
253	String fname,sname
254
255	Variable isTrans
256
257	Variable lastPoint
258
259	isTrans = isTransFile(fname)
260	// decalre the correct set of waves
261	// S_Whole is only a place holder so the waves are of equal length
262	if (isTrans)
263	Wave/T GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
264	Wave/T G_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
265	Wave/T GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
266	Wave/T GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
267	Wave/T GLabels = $"root:myGlobals:TransHeaderInfo:T_Labels"
268	Wave GSDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
269	Wave GLambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
270	Wave GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
271	Wave GWhole = $"root:myGlobals:TransHeaderInfo:T_Whole"
272	Else
273	Wave/T GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
274	Wave/T G_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
275	Wave/T GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
276	Wave/T GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
277	Wave/T GLabels = $"root:myGlobals:TransHeaderInfo:S_Labels"
278	Wave GSDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
279	Wave GLambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
280	Wave GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
281	Wave GWhole = $"root:myGlobals:TransHeaderInfo:S_Whole"
282	Endif
283
284	lastPoint = numpnts(GLambda)
285
286	InsertPoints lastPoint,1,G_TRANS_Filenames
287	G_TRANS_Filenames[lastPoint]=""
288
289	InsertPoints lastPoint,1,GFilenames
290	GFilenames[lastPoint]=sname
291
292	//read the file suffix
293	InsertPoints lastPoint,1,GSuffix
294	GSuffix[lastPoint]=getSuffix(fname)
295
296	//read any suffix that this file is associated with
297	InsertPoints lastPoint,1,GSuffices
298	GSuffices[lastPoint]=getAssociatedFileSuffix(fname)
299
300	// read the sample.label text field
301	InsertPoints lastPoint,1,GLabels
302	GLabels[lastPoint]=getSampleLabel(fname)
303
304
305	//Transmission
306	InsertPoints lastPoint,1,GTransmission
307	GTransmission[lastPoint]=getSampleTrans(fname)
308
309	//Whole detector Transmission
310	InsertPoints lastPoint,1,GWhole
311	GWhole[lastPoint]=getSampleTransWholeDetector(fname)
312
313	//SDD
314	InsertPoints lastPoint,1,GSDD
315	GSDD[lastPoint]=getSDD(fname)
316
317	//wavelength
318	InsertPoints lastPoint,1,GLambda
319	GLambda[lastPoint]=getWavelength(fname)
320
321	return(0)
322	End
323
324	//fills in the file relations that have already been set
325	//
326	//
327	Function GetFilenamesFromSuffices()
328	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
329	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
330	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
331	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
332
333	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
334	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
335	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
336	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
337
338	Variable num_s_files, num_t_files, ii, jj
339	num_t_files = numpnts(T_GFilenames)
340	num_s_files = numpnts(S_GFilenames)
341	//print num_t_files, num_s_files
342
343	// Get transmission file relations
344	ii= 0
345	do
346	if (cmpstr(T_GSuffices[ii],"")!=0)
347	jj=0
348	do
349	if (cmpstr(T_GSuffices[ii],T_GSuffix[jj])==0)
350	T_EMP_Filenames[ii]=T_GFilenames[jj]
351	endif
352	jj+=1
353	while(jj<num_t_files)
354	endif
355	ii+=1
356	while(ii<num_t_files)
357
358	// Get scattering file relations
359	ii= 0
360	do
361	if (cmpstr(S_GSuffices[ii],"")!=0)
362	jj=0
363	do
364	if (cmpstr(S_GSuffices[ii],T_GSuffix[jj])==0)
365	S_TRANS_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_s_files)
372	End
373
374	// gets the selected transmission filename, and puts its name as the
375	//empty beam reference file
376	// lists the xy box coordinates as read from the file header (zeros if not yet assigned)
377	//
378	Function PickEMPTransButton(ctrlName) : ButtonControl
379	String ctrlName
380
381	Variable TransFileTableExists
382	TransFileTableExists = WinType("TransFileTable")
383	//??BUG?? V_flag returns 1 even if no selection?
384	//check manually for null selection
385	//Print "local v_flag = ",num2str(V_flag)
386	Wave/T LocFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
387	if (TransFileTableExists != 0)
388	String/G root:myGlobals:TransHeaderInfo:gEMP = ""
389	GetSelection table,TransFileTable,7
390	//Print S_Selection
391	if(strsearch(S_selection,"T_Filenames",0) == 0)
392	//selection OK, add to list
393	Duplicate/O/R=[V_startRow,V_endRow] LocFilenames, filenames
394	Wave/T selectedFiles = $"filenames"
395
396	SVAR temp = root:myGlobals:TransHeaderInfo:gEMP
397	//
398	temp = temp+selectedFiles[0] //take just the first file
399	UpdateBoxCoordinates()
400	Else
401	DoWindow/F TransFileTable
402	DoAlert 0,"Invalid selection from the Transmision file table. You must select a file from the T_Filenames column"
403	Endif
404	else
405	//no selection
406	DoAlert 0,"No file selected from Transmission file table or no Transmission file table available"
407	Endif
408	End
409
410	//initialize data folder and globals for the Trans panel as needed
411	//since this operation is somewhat tangled with the Patch Panel, keep all of the
412	//globals in the Patch subfolder (make sure both panels are simultaneously initialized)
413	//do not create a separate Trans folder
414	//
415	Proc InitializeTransPanel()
416	//create the global variables needed to run the Trans Panel
417	//all are kept in root:myGlobals:TransHeaderInfo
418	If( ! (DataFolderExists("root:myGlobals:TransHeaderInfo")) )
419	//create the data folder and the clobals for BOTH the Patch and Trans Panels
420	NewDataFolder/O root:myGlobals:TransHeaderInfo
421	CreateTransGlobals()
422	Endif
423	End
424
425
426	//
427	Proc CreateTransGlobals()
428
429	PathInfo catPathName
430	If(V_flag==1)
431	String dum = S_path
432	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = dum
433	else
434	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = "no path selected"
435	endif
436
437	String/G root:myGlobals:TransHeaderInfo:gEMP = "no file selected"
438	String/G root:myGlobals:TransHeaderInfo:gBox = ""
439	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Suffices"
440	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
441	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Filenames"
442	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Suffix"
443	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Labels"
444	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_SDD"
445	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Lambda"
446	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Transmission"
447	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Whole"
448
449	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Suffices"
450	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
451	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Filenames"
452	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Suffix"
453	Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Labels"
454	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_SDD"
455	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Lambda"
456	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Transmission"
457	Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Whole"
458	End
459
460
461	//function that writes out (to the header of a raw binary SANS file)
462	//characters representing the empty beam file and the sample transmission file
463	//the 4-character file suffix is written, rather than the run numbers
464	//from this, the trans files can be located, and the
465	//sample file contains all the information needed to calculate its transmission
466	//
467	//uses first 4 bytes of params.reserve (character field) starting at byte 404
468	//(previous version (AM) used run.reserve field @ byte 91, which was not empty, and not at the start of the field!)
469	//
470	Function AssignSelTransFilesToData(startRow,endRow)
471	Variable startRow,endRow
472
473	// GetSelection table,ScatterFileTable,1
474
475	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
476	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
477	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
478	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
479
480	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
481	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
482	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
483	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
484
485	Variable num_s_files, num_t_files, ii, jj
486	Variable refnum
487	num_t_files = numpnts(T_GFilenames)
488	String suffix = ""
489	PathInfo catPathName
490	String pathname = S_path
491	String filename
492
493	// Write suffix of empty beam file into transmission files
494	ii= 0
495	do
496	if (cmpstr(T_EMP_Filenames[ii],"")!=0)
497	jj=0
498	do
499	if (cmpstr(T_EMP_Filenames[ii],T_GFilenames[jj])==0)
500	suffix=T_GSuffix[jj]
501	filename = pathname + T_GFilenames[ii]
502	WriteAssocFileSuffixToHeader(filename,suffix)
503	endif
504	jj+=1
505	while(jj<num_t_files)
506	endif
507	ii+=1
508	while(ii<num_t_files)
509
510	// Write suffix of transmission files into scattering files
511	ii= startRow
512	do
513	if (cmpstr(S_TRANS_Filenames[ii],"")!=0)
514	jj=0
515	do
516	if (cmpstr(S_TRANS_Filenames[ii],T_GFilenames[jj])==0)
517	suffix=T_GSuffix[jj]
518	filename = pathname + S_GFilenames[ii]
519	WriteAssocFileSuffixToHeader(filename,suffix)
520	endif
521	jj+=1
522	while(jj<num_t_files)
523	endif
524	ii+=1
525	while(ii<=endRow)
526	return(0)
527	End
528
529	// Allows to calculate transmissions without need of a scattering file. Used with the Calculate Total Trans button.
530
531	Function AssignTotalTransFilesToData(startRow,endRow)
532	Variable startRow,endRow
533
534	// GetSelection table,ScatterFileTable,1
535
536	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
537	Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
538	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
539	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
540
541	Variable num_t_files, ii, jj
542	Variable refnum
543	num_t_files = numpnts(T_GFilenames)
544	String suffix = ""
545	PathInfo catPathName
546	String pathname = S_path
547	String filename
548
549	// Write suffix of empty beam file into transmission files
550	ii= 0
551	do
552	if (cmpstr(T_EMP_Filenames[ii],"")!=0)
553	jj=0
554	do
555	if (cmpstr(T_EMP_Filenames[ii],T_GFilenames[jj])==0)
556	suffix=T_GSuffix[jj]
557	filename = pathname + T_GFilenames[ii]
558	WriteAssocFileSuffixToHeader(filename,suffix)
559	endif
560	jj+=1
561	while(jj<num_t_files)
562	endif
563	ii+=1
564	while(ii<num_t_files)
565
566	return(0)
567	End
568
569
570	//function that clears the selected assignments of sample trans -> sample scattering
571	//also writes a trans=1 value back to the sample file
572	//
573	// DEC 2006 - now also writes blank suffix to clear trans->empty assignment, and Twhole=1
574	//
575	// target = 1 = ScatterFileTable
576	// target = 2 = TransFileTable
577	Function fClearSelectedAssignments(startRow,endRow,target)
578	Variable startRow,endRow,target
579
580	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
581	Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
582	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
583	Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
584	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
585	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
586	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
587	Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
588	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
589	Wave T_GTWhole = $"root:myGlobals:TransHeaderInfo:T_Whole"
590
591
592	Variable num_s_files, num_t_files, ii, jj
593	Variable refnum,zero=0
594	num_t_files = numpnts(T_GFilenames)
595	String suffix = " " //4 blank spaces
596	PathInfo catPathName
597	String pathname = S_path
598	String filename
599
600	// If the selection is from the TransFileTable
601	// - wipe out the box coordinates
602	// - wipe out the suffix
603	// - wipe out the transmission
604	// - wipe out T_whole
605	// - update the waves in the table
606
607	if(target == 2)
608	ii= startRow
609	do
610	filename = pathname + T_GFilenames[ii]
611
612	// write in zeros for the box coordinates
613	WriteXYBoxToHeader(filename,0,0,0,0)
614
615	// write in a null suffix
616	WriteAssocFileSuffixToHeader(filename,suffix)
617
618	//write a trans==1 to the file header of the raw data
619	WriteTransmissionToHeader(filename,1) //sample trans
620
621	WriteWholeTransToHeader(filename,1) //WholeTrans start byte is 392
622
623	//then update the table that is displayed
624	T_EMP_Filenames[ii] = ""
625	T_GTransmission[ii] = 1
626	T_GTWhole[ii] = 1
627
628	ii+=1
629	while(ii<=endRow)
630	endif
631
632
633	if(target == 1)
634	// Write null suffix of transmission files into scattering files
635	ii= startRow
636	do
637	filename = pathname + S_GFilenames[ii]
638	// write in a null suffix
639	WriteAssocFileSuffixToHeader(filename,suffix)
640
641	//write a trans==1 to the file header of the raw data (open/close done in function)
642	WriteTransmissionToHeader(filename,1) //sample trans
643
644	//then update the table that is displayed
645	S_TRANS_Filenames[ii] = ""
646	S_GTransmission[ii] = 1
647
648	ii+=1
649	while(ii<=endRow)
650	endif
651
652	return(0)
653	End
654
655	//given a selection of scattering files, calculates the transmission
656	//and writes the new transmission to the file header
657	//
658	//given the full path;name;vers (= filenmame), of a raw binary SANS file,
659	//the transmission of the sample is calculated (if possible) from information
660	//in the file header. empty beam and sample transmision run numbers are extracted
661	//and the files are located from the run number (if possible)
662	//from the header of the empty beam file, the XY box coordinates and "empty"
663	//counts are determined
664	//once all information is located, the transmission is calculated and the
665	//transmission field of the sample file is automatically "Patched"
666	// - updates the global variable that is displayed in the panel
667	//can be run in batch mode, sequentially passing each item from a list of filenames
668	//this is the single step of the batch mode
669	//
670	//in batch mode: execution will proceed through all of the files, reporting
671	//results to the history window. If no trans could be successfully calculated
672	//(for a blocked beam, for example), then that is displayed as well, and the
673	//raw data is not modified
674	//
675	// now takes the attenuation of the sample trans and empty beam trans into account, (normally this == 1)
676	// and rescales the transmission as appropriate
677	// 3/31/04 SRK
678	//
679	Function CalcSelTransFromHeader(startRow,endRow)
680	Variable startRow,endRow
681	// GetSelection table,ScatterFileTable,1
682
683	String filename
684	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
685	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
686
687	Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
688	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
689	Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
690
691	Variable num_s_files, num_t_files, ii, jj
692	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
693	Variable x1,x2,y1,y2,err,attenEmp,attenSam
694	String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
695	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
696	String strToExecute
697
698	num_t_files = numpnts(T_GFilenames)
699
700	PathInfo catPathName
701	pathname = S_path
702
703	ii= startRow
704	do
705	if (cmpstr(S_TRANS_Filenames[ii],"")!=0) //if there is a sample trans file assigned
706	jj=0
707	do
708	if (cmpstr(S_TRANS_Filenames[ii],T_GFilenames[jj])==0) //find it in the trans file table
709	if (cmpstr(T_EMP_Filenames[jj],"")!=0) //if empty beam file assigned, proceed with the calculation
710	//full path+name to access all 3 files
711	filename=pathname+S_GFilenames[ii]
712	emptyFile = pathname+T_EMP_Filenames[jj]
713	transFile = pathname+T_GFilenames[jj]
714	//////////
715	// check the empty beam file for previously selected coordinates
716	//if they exist, set the xy string , save the normalized counts somewhere
717	//the value was written to an unused r*4 header analysis.factor (@b494)
718	GetXYBoxFromFile(emptyFile,x1,x2,y1,y2)
719
720	//read the real count value
721	emptyCts = getBoxCounts(emptyFile)
722	// read the attenuator number of the empty beam file
723	attenEmp = getAttenNumber(emptyFile)
724	//
725	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
726	//no region selected -- prompt user to select box w/marquee
727	DoWindow/F TransFileTable
728	Abort "Use \"Set BCENT File\", then \"SetXYBox\" to select XY range in empty beam file "+T_EMP_Filenames[jj]
729	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
730	Endif
731
732	//read in trans file then add to SAM
733	ReadHeaderAndData(transFile)
734	//adds to SAM
735	err = Raw_to_work("SAM")
736	//sum region in SAM
737	transCts = SumCountsInBox(x1,x2,y1,y2,"SAM")
738	// get the attenuator, lambda, and sample string (to get the instrument)
739	WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
740	WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
741	samfileStr = samText[3]
742	lambda = samReals[26]
743	attenSam = samReals[3]
744	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
745	AttenRatio = AttenuationFactor(samFileStr,lambda,attenEmp)/AttenuationFactor(samFileStr,lambda,attenSam)
746	//calculate trans based on empty beam value and rescale by attenuation ratio
747	trans= transCts/emptyCts * AttenRatio
748
749	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
750	If(attenRatio==1)
751	Printf "%s\t\tTrans Counts = %g\tTrans = %g\r",S_GFilenames[ii], transCts,trans
752	else
753	Printf "%s\t\tTrans Counts = %g\tTrans = %g\tAttenuatorRatio = %g\r",S_GFilenames[ii], transCts,trans,attenRatio
754	endif
755	//write the trans to the file header of the raw data (open/close done in function)
756	WriteTransmissionToHeader(filename,trans)
757
758	//then update the global that is displayed
759	S_GTransmission[ii] = trans
760
761	else // There is no empty assigned
762	abortStr = "Empty beam file not assigned properly for " + T_GFilenames[jj]
763	Print abortStr
764	//Abort abortStr
765	return(1)
766	endif
767	endif
768	jj+=1
769	while(jj<num_t_files)
770	else //no transmission file
771	abortStr = "Transmission beam file not assigned properly for " + S_GFilenames[ii]
772	Print abortStr
773	endif
774	ii+=1
775	while(ii<=endRow)
776	print "done"
777	return(0)
778	End
779
780	//
781	// For the calculation of the Transmission using only the Trans Files screen
782	// Uses only the information on the transmissionFiles screen to calculate
783	// a "box" Transmission for comparison with the Whole Transmission
784	// updated 5/11/2006 by Bryan Greenwald
785	Function CalcTotalTrans(startRow,endRow)
786	Variable startRow,endRow
787	// GetSelection table,ScatterFileTable,1
788
789	String filename
790	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
791
792	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
793	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
794
795	// Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
796	// Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
797	// Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
798	Wave GWhole= $"root:myGlobals:TransHeaderInfo:T_Whole"
799
800	Variable num_t_files, ii, jj
801	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
802	Variable x1,x2,y1,y2,err,attenEmp,attenSam
803	String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
804	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
805	String strToExecute
806
807	num_t_files = numpnts(T_GFilenames)
808
809	PathInfo catPathName
810	pathname = S_path
811
812	ii= startRow
813	do
814	if (cmpstr(T_Emp_Filenames[ii],"")!=0) //if there is a sample trans file assigned
815	jj=0
816	do
817	if (cmpstr(T_Emp_Filenames[ii],T_GFilenames[jj])==0) //find it in the trans file table
818	if (cmpstr(T_EMP_Filenames[ii],"")!=0) //if empty beam file assigned, proceed with the calculation
819	//full path+name to access all 3 files
820	filename=pathname+T_GFilenames[ii]
821	emptyFile = pathname+T_EMP_Filenames[ii]
822	transFile = pathname+T_GFilenames[ii]
823	//////////
824	// check the empty beam file for previously selected coordinates
825	//if they exist, set the xy string , save the normalized counts somewhere
826	//the value was written to an unused r*4 header analysis.factor (@b494)
827	getXYBoxFromFile(emptyFile,x1,x2,y1,y2)
828
829	//read the real count value
830	emptyCts = getBoxCounts(emptyFile)
831	// read the attenuator number of the empty beam file
832	attenEmp = getAttenNumber(emptyFile)
833	//
834	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
835	//no region selected -- prompt user to select box w/marquee
836	DoWindow/F TransFileTable
837	Abort "Use \"Set BCENT File\", then \"SetXYBox\" to select XY range in empty beam file "+T_EMP_Filenames[jj]
838	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
839	Endif
840
841	//read in trans file then add to SAM
842	ReadHeaderAndData(transFile)
843	//adds to SAM
844	err = Raw_to_work("SAM")
845	//sum region in SAM
846	transCts = SumCountsInBox(x1,x2,y1,y2,"SAM")
847	// get the attenuator, lambda, and sample string (to get the instrument)
848	WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
849	WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
850	samfileStr = samText[3]
851	lambda = samReals[26]
852	attenSam = samReals[3]
853	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
854	AttenRatio = AttenuationFactor(samFileStr,lambda,attenEmp)/AttenuationFactor(samFileStr,lambda,attenSam)
855	//calculate trans based on empty beam value and rescale by attenuation ratio
856	trans= transCts/emptyCts * AttenRatio
857
858	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
859	If(attenRatio==1)
860	//Printf "%s\t\tTrans Counts = %g\t Actual Trans = %g\r",T_GFilenames[ii], transCts,trans
861	Printf "%s\t\tBox Counts = %g\t Trans = %g\r",T_GFilenames[ii], transCts,trans
862	else
863	//Printf "%s\t\tTrans Counts = %g\t Trans = %g\tAttenuatorRatio = %g\r",T_GFilenames[ii], transCts,trans,attenRatio
864	Printf "%s\t\tBox Counts = %g\t Trans = %g\t AttenuatorRatio = %g\r",T_GFilenames[ii], transCts,trans,attenRatio
865	endif
866	//write the trans to the file header of the raw data (open/close done in function)
867	WriteTransmissionToHeader(filename,trans) //transmission start byte is 158
868
869	//then update the global that is displayed
870	T_GTransmission[ii] = trans
871
872	else // There is no empty assigned
873	abortStr = "Empty beam file not assigned properly for " + T_GFilenames[jj]
874	Print abortStr
875	//Abort abortStr
876	return(1)
877	endif
878	endif
879	jj+=1
880	while(jj<num_t_files)
881	else //no transmission file
882	abortStr = "Transmission beam file not assigned properly for " + T_GFilenames[ii]
883	Print abortStr
884	endif
885	ii+=1
886	while(ii<=endRow)
887	//print "done"
888	return(0)
889	End
890
891	//
892	// For the calculation of the Transmission using only the whole detector
893	// Used to compute the transmission for the TransmissionFiles table using
894	// the entire detector. For comparison with the "box" trans
895	// updated: 5/11/2006 by Bryan Greenwald
896	Function CalcWholeTrans(startRow,endRow)
897	Variable startRow,endRow
898	// GetSelection table,ScatterFileTable,1
899
900	NVAR pixelsX = root:myGlobals:gNPixelsX
901	NVAR pixelsY = root:myGlobals:gNPixelsY
902
903	String filename
904	Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
905
906	Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
907	Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
908
909	// Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
910	// Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
911	// Wave S_GTransmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
912	Wave GWhole= $"root:myGlobals:TransHeaderInfo:T_Whole"
913
914	Variable num_t_files, ii, jj
915	Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
916	Variable x1,x2,y1,y2,err,attenEmp,attenSam
917	String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
918	String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
919	String strToExecute
920
921	num_t_files = numpnts(T_GFilenames)
922
923	PathInfo catPathName
924	pathname = S_path
925
926	ii= startRow
927	do
928	if (cmpstr(T_Emp_Filenames[ii],"")!=0) //if there is a sample trans file assigned
929	jj=0
930	do
931	if (cmpstr(T_Emp_Filenames[ii],T_GFilenames[jj])==0) //find it in the trans file table
932	if (cmpstr(T_EMP_Filenames[ii],"")!=0) //if empty beam file assigned, proceed with the calculation
933	//full path+name to access all 3 files
934	filename=pathname+T_GFilenames[ii]
935	emptyFile = pathname+T_EMP_Filenames[ii]
936	transFile = pathname+T_GFilenames[ii]
937	//////////
938	// check the empty beam file for previously selected coordinates
939	//if they exist, set the xy string , save the normalized counts somewhere
940	//the value was written to an unused r*4 header analysis.factor (@b494)
941
942	getXYBoxFromFile(emptyFile,x1,x2,y1,y2)
943	//read the real count value
944	emptyCts = getBoxCounts(emptyFile)
945	// read the attenuator number of the empty beam file
946	attenEmp = getAttenNumber(emptyFile)
947	//
948	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
949	//no region selected -- prompt user to select box w/marquee
950	DoWindow/F TransFileTable
951	Abort "Use \"Set BCENT File\", then \"SetXYBox\" to select XY range in empty beam file "+T_EMP_Filenames[jj]
952	//from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
953	Endif
954
955	//read in trans file then add to SAM
956	ReadHeaderAndData(transFile)
957	//adds to SAM
958	err = Raw_to_work("SAM")
959	//sum region in SAM
960	transCts = SumCountsInBox(0,pixelsX-1,0,pixelsY-1,"SAM")
961	// get the attenuator, lambda, and sample string (to get the instrument)
962	WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
963	WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
964	samfileStr = samText[3]
965	lambda = samReals[26]
966	attenSam = samReals[3]
967	//calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
968	AttenRatio = AttenuationFactor(samFileStr,lambda,attenEmp)/AttenuationFactor(samFileStr,lambda,attenSam)
969	//calculate trans based on empty beam value and rescale by attenuation ratio
970	trans= transCts/emptyCts * AttenRatio
971
972	//write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
973	If(attenRatio==1)
974	//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
975	Printf "%s\t\tTotal Counts = %g\t Trans using whole detector = %g\t",T_GFilenames[ii], transCts,trans
976	else
977	//Printf "%s\t\tTrans Counts = %g\tTrans = %g\tAttenuatorRatio = %g, Tbox/Twhole = %g\r",T_GFilenames[ii], transCts,trans,attenRatio, T_GTransmission[ii]/trans
978	Printf "%s\t\tTotal Counts = %g\t Trans using whole detector = %g\t AttenuatorRatio = %g",T_GFilenames[ii], transCts,trans,attenRatio
979	endif
980	If(T_GTransmission[ii]/trans > 0.95) //95%, from conversation w/Lionel
981	printf " Tbox/Twhole = %g\r",T_GTransmission[ii]/trans
982	else
983	printf " !!! Tbox/Twhole is low !!! = %g\r",T_GTransmission[ii]/trans
984	endif
985	//write the trans to the file header of the raw data (open/close done in function)
986	WriteWholeTransToHeader(filename,trans)
987
988	//then update the global that is displayed
989	GWhole[ii] = trans
990
991	else // There is no empty assigned
992	abortStr = "Empty beam file not assigned properly for " + T_GFilenames[jj]
993	Print abortStr
994	//Abort abortStr
995	return(1)
996	endif
997	endif
998	jj+=1
999	while(jj<num_t_files)
1000	else //no transmission file
1001	abortStr = "Transmission beam file not assigned properly for " + T_GFilenames[ii]
1002	Print abortStr
1003	endif
1004	ii+=1
1005	while(ii<=endRow)
1006	print "done"
1007	return(0)
1008	End
1009
1010
1011	//window recreation macro for the Trans Panel
1012	//
1013	Proc Trans_Panel()
1014	PauseUpdate; Silent 1 // building window...
1015	NewPanel /W=(173,197,540,424)/K=1 as "Calculate Transmissions"
1016	DoWindow/C Trans_Panel
1017	ModifyPanel cbRGB=(49807,47186,38011)
1018	ModifyPanel fixedSize=1
1019	SetDrawLayer UserBack
1020	DrawLine 0,56,368,56
1021	DrawLine 0,125,368,125
1022	Button pick_emp,pos={4,65},size={105,20},proc=PickEMPTransButton,title="set BCENT file"
1023	Button pick_emp,help={"This button will set the file selected in the Transmission file table to be the empty beam file."}
1024	SetVariable empStr,pos={114,67},size={250,17},title="file:"
1025	SetVariable empStr,help={"Filename of the empty beam file(s) to be used in the transmission calculation"}
1026	SetVariable empStr,fSize=10
1027	SetVariable empStr,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gEMP
1028	Button Trn_button_1,pos={5,101},size={90,20},proc=Trn_SetXYBoxButton,title="Set XY Box"
1029	Button Trn_button_1,help={"Sets the XY box to sum over"}
1030	Button Trn_button_2,pos={174,139},size={110,20},proc=Trn_SortFilesByDate,title="Sort by Date"
1031	Button Trn_button_2,help={"Sort the scattering and transmission files by creation date."}
1032	Button Trn_button_3,pos={174,169},size={110,20},proc=Trn_SortFilesByLabel,title="Sort by Label"
1033	Button Trn_button_3,help={"Sort the scattering and transmission files by label."}
1034	Button Trn_button_4,pos={295,139},size={67,20},proc=Trn_ShowHelpProc,title="Help"
1035	Button Trn_button_4,help={"Show a help notebook for calculating transmissions."}
1036	SetVariable Trn_setvar_1,pos={135,100},size={227,17},title="Box is "
1037	SetVariable Trn_setvar_1,help={"Box coordinates to sum over"},fSize=10
1038	SetVariable Trn_setvar_1,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gBox
1039	Button Trn_button_0,pos={1,1},size={70,20},proc=Trn_PickPathButton,title="Pick Path"
1040	Button Trn_button_0,help={"Select the folder containing the SANS data files"}
1041	Button Trn_button_9,pos={335,1},size={25,20},proc=ShowTransHelp,title="?"
1042	Button Trn_button_9,help={"Show the help file for calculating sample transmissions"}
1043	SetVariable Trn_setvar_0,pos={80,4},size={250,17},title="Path"
1044	SetVariable Trn_setvar_0,help={"Currently selected data path"},fSize=10
1045	SetVariable Trn_setvar_0,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gCatPathStr
1046	Button Trn_button_5,pos={5,169},size={161,20},proc=Trn_CalcAllFilesButton,title="Calculate All Files"
1047	Button Trn_button_5,help={"Calculate transmission and patch headers of ALL files in the Scattering File Table."}
1048	Button Trn_button_6,pos={295,198},size={67,20},proc=Trn_PanelDoneButtonProc,title="Done"
1049	Button Trn_button_6,help={"Close the panel when done calculating transmissions"}
1050	Button Trn_button_7,pos={67,32},size={214,20},proc=Trn_RefreshProc,title="List Files"
1051	Button Trn_button_7,help={"Generate or refresh the tables of files."}
1052	Button Trn_button_8,pos={5,139},size={161,20},proc=Trn_CalcSelectedFilesButton,title="Calculate Selected Files"
1053	Button Trn_button_8,help={"Calculate transmission and patch headers of selected files in the Scattering File Table."}
1054	Button Trn_button_10,pos={5,198}, size={161,20},proc=TotalTransButtonProc
1055	Button Trn_button_10 title="Calculate Total Trans"
1056	Button Trn_button_10 help={"Calculate transmission over the whole detector and patch headers of ALL files in the data folder."}
1057	EndMacro
1058
1059
1060	Function TotalTransButtonProc(ctrlName) : ButtonControl
1061	String ctrlName
1062	TotalTrans(ctrlName)
1063	End
1064
1065
1066	Proc ShowTransHelp(ctrlName) : ButtonControl
1067	String ctrlName
1068	DisplayHelpTopic/K=1 "SANS Data Reduction Tutorial[Calculate Transmissions]"
1069	if(V_flag !=0)
1070	DoAlert 0,"The SANS Data Reduction Tutorial Help file could not be found"
1071	endif
1072	End
1073
1074
1075	//generates the file tables of scattering files and transmission files
1076	//
1077	// if the tables already exist, they will be updated
1078	//
1079	Proc Trn_RefreshProc(ctrlName) : ButtonControl
1080	String ctrlName
1081	BuildFileTables()
1082	End
1083
1084	//shows a noteboox of help text describing how to calculate transmissions
1085	// - better that the user read the igor or pdf file, but it's a victory to get
1086	//users to read anything at all
1087	//
1088	Proc Trn_ShowHelpProc(ctrlName) : ButtonControl
1089	String ctrlName
1090	DisplayTransHelp()
1091	End
1092
1093	//sorts the tables by date
1094	//
1095	Proc Trn_SortFilesByDate(ctrlName) : ButtonControl
1096	String ctrlName
1097	SortTransByDate()
1098	End
1099
1100	//sorts the tables alphabetically by the sample label field
1101	//
1102	Proc Trn_SortFilesByLabel(ctrlName) : ButtonControl
1103	String ctrlName
1104	SortTransByLabel()
1105	End
1106
1107	//button action procedure to select the local path to the
1108	//folder containing the RAW SANS data files
1109	// - once the data folder is selected, all of the popup file menus are
1110	//forced to update with fresh file lists
1111	//
1112	Function Trn_PickPathButton(PathButton) : ButtonControl
1113	String PathButton
1114
1115	//set the global string to the selected pathname
1116	Variable err
1117	err = PickPath()
1118	if(err)
1119	return(1) //some problem with path or user cancelled, get out
1120	endif
1121
1122	PathInfo/S catPathName
1123	String path = S_path
1124	if (V_flag == 0)
1125	//path does not exist - no folder selected
1126	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = "no folder selected"
1127	else
1128	String/G root:myGlobals:TransHeaderInfo:gCatPathStr = path
1129	endif
1130
1131	//Update the pathStr variable box
1132	ControlUpdate/W=Trans_Panel $"Trn_setvar_0"
1133	//Generate tables
1134	Execute "BuildFileTables()"
1135
1136	End
1137
1138	//button action function that asks the user to set the XY box to sum over
1139	//for all transmission calculations
1140	//
1141	// requires the user to set the box coordinates with the marquee popup
1142	//that wil properly set the keyword string, and write the values to the empty beam header
1143	//
1144	Function Trn_SetXYBoxButton(ctrlName) : ButtonControl
1145	String ctrlName
1146
1147	String msgStr = "Select the Empty Beam File"
1148	String filename=""
1149
1150	//get the filename from the popup menu
1151	//and construct a full path to it
1152	SVAR partialName = root:myGlobals:TransHeaderInfo:gEMP
1153	print partialName
1154	//get a valid file based on this partialName and catPathName
1155	String tempName = FindValidFilename(partialName)
1156	if(cmpstr(tempName,"")==0)
1157	//file not found, get out
1158	Abort "Empty beam file not found Trn_SetXYBoxButton(ctrlName)"
1159	Endif
1160	//name is ok, prepend path to tempName for read routine
1161	PathInfo catPathName
1162	filename = S_path + tempName
1163
1164	//read the file in - check for previous coordinates
1165	ReadHeaderAndData(filename)
1166	//data is displayed here (go through the normal display steps, so all is created properly
1167	String/G root:myGlobals:gDataDisplayType="RAW"
1168	fRawWindowHook()
1169
1170	// check the empty beam file for previously selected coordinates
1171	//if they exist, set the xy string , save the normalized counts somewhere
1172	//the value was written to an unused r*4 header analysis.factor (@b494)
1173	Variable refnum,x1,x2,y1,y2,err
1174	getXYBoxFromFile(filename,x1,x2,y1,y2)
1175
1176	//read the real count value, assign to a global
1177	Variable/G root:myGlobals:gTransCts = getBoxCounts(filename) //***NOTE this is NOT in the Trans sub-folder
1178	//
1179	if( ((x1-x2)==0) \|\| ((y1-y2)==0) ) //zero width marquee in either direction
1180	//no region selected
1181
1182	//add the empty beam file to work.SAM
1183	err = Raw_to_work("SAM")
1184
1185	//the calling macro must change the display type
1186	String/G root:myGlobals:gDataDisplayType="SAM" //displayed data type is sam
1187
1188	//data is displayed here
1189	fRawWindowHook()
1190
1191	//prompt user to select box w/marquee
1192	DoAlert 0,"Select the region to sum with the Marquee"
1193
1194	//from here the Marquee menu selection must handle the task of setting the box
1195	//and updating the information in the file header
1196	else
1197	// region already selected, just put up the values from the file header
1198	//allow user the option of overriding the current box region
1199	msgStr = "X1="+num2str(x1)+";"
1200	msgStr += "X2="+num2str(x2)+";"
1201	msgStr += "Y1="+num2str(y1)+";"
1202	msgStr += "Y2="+num2str(y2)+";"
1203	String textStr
1204	textStr = "Override current box "+msgStr+" ?"
1205	DoAlert 1,textStr
1206	If((V_flag)==1)
1207	//get new box coordinates, same procedure as above
1208	//add the empty beam file to work.SAM
1209	err = Raw_to_work("SAM")
1210
1211	//the calling macro must change the display type
1212	String/G root:myGlobals:gDataDisplayType="SAM" //displayed data type is sam
1213
1214	//data is displayed here
1215	fRawWindowHook()
1216
1217	//prompt user to select box w/marquee
1218	DoAlert 0,"Select the region to sum with the Marquee"
1219
1220	//from here the Marquee menu selection must handle the task of setting the box
1221	//and updating the information in the file header
1222	else
1223	String/G root:myGlobals:TransHeaderInfo:gBox = msgStr
1224	Endif
1225	Endif
1226
1227	UpdateBoxCoordinates()
1228	Return (0)
1229	End
1230
1231
1232	//button action function that assigns the selected empty beam file (run number only)
1233	//and the sample trnansmissionfile (run number only) to the popup list of sample scattering
1234	//files (ALL of the list items). Assignment is done by writing the integer run numbers of
1235	//trans files to the header of each of the scattering files, in a batchwise processing
1236	//of the popup list
1237	//
1238	//transmission are not calculated here - only the file numbers are set
1239	//
1240	//*******unused*********
1241	//Function Trn_AssignAllFilesButton(ctrlName) : ButtonControl
1242	// String ctrlName
1243	//
1244	// AssignTransFilesToData()
1245	//
1246	//End
1247
1248	//button action procedure to calculate the transmission of all of the sample files in the
1249	//sample popup list, based on the information in EACH sample header and in the empty beam file
1250	//the box must be set properly in the empty beam file, AND the empty and trans
1251	//run number must also be set properly in EACH scattering file,
1252	//If run numbers are not properly assigned, no trans is calculated and the
1253	//header is not modified
1254	//
1255	//The RAW data header of EACH sample file IS modified, with the newly calculated transmission
1256	//
1257	//not very friendly, but forces users to assign the files before continuing
1258	//
1259	Function Trn_CalcAllFilesButton(ctrlName) : ButtonControl
1260	String ctrlName
1261
1262	//calculate the transmission and Patch the header (if possible)
1263	Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1264	Variable num_s_files = numpnts(S_GFilenames)
1265	AssignSelTransFilesToData(0,num_s_files-1) //do all the files (points 0 to n-1, inclusive)
1266	CalcSelTransFromHeader(0,num_s_files-1)
1267
1268	End
1269
1270	//for selected scattering files in the scattering table,
1271	// the "Annn" association of trans file is written to the data file,
1272	// the the transmission is actually calculated
1273	//
1274	Function Trn_CalcSelectedFilesButton(ctrlName) : ButtonControl
1275	String ctrlName
1276
1277	Variable scatterTableExists
1278	scatterTableExists = WinType("ScatterFileTable")
1279	if (scatterTableExists != 0)
1280	GetSelection table,ScatterFileTable,1
1281	if(V_Flag != 0)
1282	AssignSelTransFilesToData(V_StartRow,V_EndRow)
1283	//calculate the transmission and Patch the header (if possible)
1284	CalcSelTransFromHeader(V_StartRow,V_EndRow)
1285	Else
1286	DoAlert 0,"No selection from Scattering Files table"
1287	Endif
1288	Else
1289	DoAlert 0,"No file selected from Scattering Files table or no Scattering Files table available"
1290	Endif
1291	End
1292
1293	//
1294	// I am not sure what the difference is inthe function of CalcTotalTrans and CalcWholeTrans ?
1295	// do they really do anything different?
1296	// is it a useful calculation at all?
1297	//
1298	Function TotalTrans(ctrlName) : ButtonControl
1299	String ctrlName
1300
1301	Variable transTableExists
1302	transTableExists = WinType("TransFileTable")
1303	if (transTableExists != 0)
1304	GetSelection table,transFileTable,1
1305	if(V_Flag != 0)
1306	AssignTotalTransFilesToData(V_StartRow,V_EndRow)
1307	//calculate the transmission and Patch the header (if possible)
1308	CalcTotalTrans(V_StartRow,V_EndRow)
1309	CalcWholeTrans(V_StartRow,V_EndRow)
1310	Else
1311	DoAlert 0,"No selection from Trans Files table"
1312	Endif
1313	Else
1314	DoAlert 0,"No file selected from Trans Files table or no Trans Files table available"
1315	Endif
1316	End
1317
1318
1319	//simple button procedure to close the trans panel
1320	// - automatically kills the two tables as well
1321	//
1322	Function Trn_PanelDoneButtonProc(ctrlName) : ButtonControl
1323	String ctrlName
1324
1325	// this button will make sure all files are closed
1326	//and close the panel
1327
1328	Close/A
1329	DoWindow/K Trans_Panel
1330	DoWindow/K ScatterFileTable
1331	DoWindow/K TransFileTable
1332	End
1333
1334
1335	//function to update the box coordinates of the file selected as the
1336	//empty beam file - takes the file that is currently popped from the list
1337	//reads the 4 "analysis" integers that hold the box coordinates
1338	//resets the globals string that is displayed with the new values
1339	//should be called whenever the "empty" popup is popped, to ensure
1340	//that current header information is displayed
1341	//
1342	Function UpdateBoxCoordinates()
1343
1344	//construct a full name, and read in the label from the file
1345	//and set the global
1346	String textstr=""
1347	ControlInfo empStr
1348	SVAR item = root:myGlobals:TransHeaderInfo:gEMP
1349	String tempName = FindValidFilename(item)
1350	if(cmpstr(tempName,"")==0)
1351	//file not found, get out
1352	Abort "Empty beam file not found UpdateBoxCoordinates(ctrlName)"
1353	Endif
1354	//name is ok, prepend path to tempName for read routine
1355	PathInfo catPathName
1356	String filename = S_path + tempName
1357
1358	Variable refnum,x1,x2,y1,y2,err
1359	GetXYBoxFromFile(filename,x1,x2,y1,y2)
1360
1361	//and update the global string
1362	String msgStr=""
1363	msgStr = "X1="+num2str(x1)+";"
1364	msgStr += "X2="+num2str(x2)+";"
1365	msgStr += "Y1="+num2str(y1)+";"
1366	msgStr += "Y2="+num2str(y2)+";"
1367
1368	String/G root:myGlobals:TransHeaderInfo:gBox = msgStr
1369
1370	ControlUpdate/W=Trans_panel Trn_setvar_1
1371	End
1372
1373	//crude procedure to display a notebook of help information for users
1374	//
1375	Proc DisplayTransHelp()
1376	String nb = "Notebook0"
1377	NewNotebook/N=$nb/F=1/V=1/W=(342,302,868,674) as "Notebook0:Transmission Help"
1378	Notebook $nb defaultTab=36, statusWidth=238, pageMargins={36,72,36,72}
1379	Notebook $nb showRuler=1, rulerUnits=1, updating={1, 3600}
1380	Notebook $nb newRuler=Normal, justification=0, margins={0,0,468}, spacing={0,0,0}, tabs={}, rulerDefaults={"Geneva",10,0,(0,0,0)}
1381	Notebook $nb ruler=Normal; Notebook $nb justification=1, fSize=14, fStyle=1, text="Transmission Help\r"
1382	Notebook $nb ruler=Normal, fSize=-1, fStyle=-1, text="\r"
1383	Notebook $nb text="This panel allows quick and easy calculation of sample transmission. The neutron transmission of a sampl"
1384	Notebook $nb text="e must be calculated and entered into the header of each sample scattering file before proper background"
1385	Notebook $nb text=" corrections or absolute scaling can be done.\r"
1386	Notebook $nb text="\r"
1387	Notebook $nb text="During data collection, you measured an empty beam - that is a measurement with heavy attenuation of th"
1388	Notebook $nb text="e neutron beam and the beamstop mover out of line with the direct beam. Then without changing the attenu"
1389	Notebook $nb text="ation or replacing the beamstop, you put a sample in the beam, and repeated the measurement (a sample tr"
1390	Notebook $nb text="ansmission measurement). The neutron transmission of the sample is simply the ratio of the number of neu"
1391	Notebook $nb text="tron counts from the sample transmission measurement normalized by the number of neutron counts from the"
1392	Notebook $nb text=" empty beam measurement. In this way, each sample transmission file is \"linked\" to the same empty beam t"
1393	Notebook $nb text="ransmission file.\r"
1394	Notebook $nb text="\r"
1395	Notebook $nb text="This calculated transmission value must be entered into the header of the sample scattering measurement "
1396	Notebook $nb text="- that is the measurement of the sample with the beamstop covering the primary (transmitted) beam, and n"
1397	Notebook $nb text="o (or few) attenuators in place. In this way, the sample transmission file is \"linked\" to its correspond"
1398	Notebook $nb text="ing sample scattering file. This panel allows you to set up the links and calculate the transmission.Tra"
1399	Notebook $nb text="nsmisison values are automatically patched to the scattering file headers as they are calculated.\r"
1400	Notebook $nb text="\r"
1401	Notebook $nb text="To Calculate Transmissions:\r"
1402	Notebook $nb text="\r"
1403	Notebook $nb text="1) Click \"List Files\" to get two lists (tables) - one of all the sample scattering files in the folder, "
1404	Notebook $nb text="and one of the transmission files.\r"
1405	Notebook $nb text="\r"
1406	Notebook $nb text="2) Select the region of the detector to sum over from the empty beam transmission file. Do theis by clic"
1407	Notebook $nb text="king on the filename of the empty beam transmision file (from the TransmissionFiles window, in the blue "
1408	Notebook $nb text="\"T_Filenames\" column). Return to the panel, and click the \"set EMP file\" button\", and the filename shoul"
1409	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"
1410	Notebook $nb text="et XY Box\" button. The empty beam file will be displayed, and you will be instructed to select the regio"
1411	Notebook $nb text="n to sum with the marquee. On the data, click and drag a rectangle that encompasses the primary beam. Mo"
1412	Notebook $nb text="ve the cursor inside the selection, to get an \"upside-down hat\" cursor. Click to get a menu, and near th"
1413	Notebook $nb text="e bottom, select \"Set XY Box Coords\". The pixel values should be updated to the Transmission panel, and "
1414	Notebook $nb text="are written to the empty beam header for future calculations. Note that the marquee selection can also b"
1415	Notebook $nb text="e used to measure the beam center, or centroid of any selected region.\r"
1416	Notebook $nb text="\r"
1417	Notebook $nb text="3) Now you need to \"link\" the ", fStyle=2, text="sample", fStyle=-1, text=" transmission files to the "
1418	Notebook $nb fStyle=2, text="empty", fStyle=-1, text=" ", fStyle=2, text="beam", fStyle=-1
1419	Notebook $nb text=" transmission file. Do this in the TransmissionFiles window by selecting the filename (in the blue T_Fil"
1420	Notebook $nb text="enames column) and pasing it to the corresponding row(s) in the T_EMP_Filenames column. This links the e"
1421	Notebook $nb text="mpty beam transmission with the sample transmission file. Do this for every sample transmission file.\r"
1422	Notebook $nb text="\r"
1423	Notebook $nb text="4) Now you need to link the sample ", fStyle=2, text="transmission", fStyle=-1
1424	Notebook $nb text=" file to the sample ", fStyle=2, text="scattering", fStyle=-1
1425	Notebook $nb text=" file. Do this by selecting the name of the transmission file (from the blue T_Filenames column) and pas"
1426	Notebook $nb text="ting it into the corresponding row of the S_TRANS_Filenames column of the ScatteringFiles window. This l"
1427	Notebook $nb text="inks the scattering file to its corresponding sample transmission file. This for all of the sample scatt"
1428	Notebook $nb text="ering files.\r"
1429	Notebook $nb text="\r"
1430	Notebook $nb text="5) Calculate the transmissions (and automatically write the transmission value to the satterng file head"
1431	Notebook $nb text="er) by clicking \"Calculate All Files\" from the Transmission Panel. The results will be printed to the co"
1432	Notebook $nb text="mmand window at the bottom of the screen. Any improperly assigned files will be listed. For example, blo"
1433	Notebook $nb text="cked beam scattering files will return an error, since the transmssion known to be zero, and is not meas"
1434	Notebook $nb text="ured (and no files are \"linked\"). Rather than calculating the transmission of all of the files, a range"
1435	Notebook $nb text=" of S_Filenames can be selected, then calculated by clicking \"Calculate Selected Files\".\r"
1436	Notebook $nb text="\r"
1437	Notebook $nb text="By default the lists are sorted by run number (= chronological). In some cases it may be easier to sort "
1438	Notebook $nb text="by the sample label to group several of the same sample scattering files collected at different sample-t"
1439	Notebook $nb text="o-detector distances. Its utility depends, of course, on how consistent and unique your sample labels ar"
1440	Notebook $nb text="e.\r"
1441	Notebook $nb text="\r"
1442	Notebook $nb text="The \"links\" are stored in the corresponding files, and wil be re-generated when the lists are re-generat"
1443	Notebook $nb text="ed. Unassigned links will appear as blank elements in the T_EMP_Filenames or S_TRANS_Filenames columns.\r"
1444	Notebook $nb text="\r"
1445	Notebook $nb, selection={startOfFile,startOfFile}
1446	Notebook $nb text="\r"
1447	End
1448
1449
1450
1451	//*******************
1452	//************
1453	// A simple panel to allow users of the NG1 SANS instrument to make their
1454	// transmission files "look" like a transmission measurement to the data reduction
1455	// program. Transmission files are designated by an x-position of the beamstop of
1456	// < -5 (cm). this simple procedure sets xpos=-10 for individual files. files
1457	// con be "un-converted", which set the xpos=0.
1458	// 1/30/01 SRK
1459	//************
1460
1461	Proc TransformToTransFile()
1462	Variable/G root:myGlobals:gConvTrans=1
1463	DoWindow/F Convert_to_Trans
1464	if(V_flag==0)
1465	Convert2Trans()
1466	endif
1467	End
1468
1469	//fname must be the full path and name for the file
1470	Function ChangeBSXPos(fname,xpos)
1471	String fname
1472	Variable xpos
1473
1474	Variable start
1475	//x-position starts after byte 368 in VAX files
1476	WriteBSXPosToHeader(fname,xpos)
1477	return(0)
1478	End
1479
1480	//sets the beamstop position to zero NOT the original position
1481	Function UnConvertButtonProc(ctrlName) : ButtonControl
1482	String ctrlName
1483
1484	//Print "UnConvert"
1485	String fullname=""
1486	ControlInfo fileNum
1487	Variable num = V_Value //run number to find
1488
1489	fullname = FindFileFromRunNumber(num)
1490	Print fullname
1491	//report error or change the file
1492	if(cmpstr(fullname,"")==0)
1493	Print "Unconvert - file not found"
1494	else
1495	//Print "Unconvert",fullname
1496	ChangeBSXPos(fullName,0)
1497	Endif
1498	return(0)
1499	End
1500
1501	//button procedure to do the conversion
1502	// writes fake beamstop position to the data file
1503	//
1504	Function ConvertButtonProc(ctrlName) : ButtonControl
1505	String ctrlName
1506
1507	String fullname=""
1508	ControlInfo fileNum
1509	Variable num = V_Value //run number to find
1510
1511	fullname = FindFileFromRunNumber(num)
1512	print fullname
1513	//report error or change the file
1514	if(cmpstr(fullname,"")==0)
1515	Print "Convert - file not found"
1516	else
1517	//Print "Convert",fullname
1518	ChangeBSXPos(fullName,-10)
1519	Endif
1520	return(0)
1521	End
1522
1523	//simple panel recreation macro
1524	//
1525	Proc Convert2Trans()
1526	PauseUpdate; Silent 1 // building window...
1527	NewPanel /W=(434,74,671,216) /K=1
1528	DoWindow/C Convert_to_Trans
1529	SetDrawLayer UserBack
1530	DrawText 18,22,"Convert files to be recognized"
1531	DrawText 43,39,"as transmission files"
1532	SetVariable fileNum,pos={43,58},size={130,15},title="File Number"
1533	SetVariable fileNum,limits={1,Inf,1},value=root:myGlobals:gConvTrans
1534	SetVariable fileNum,help={"Sets the run number of the file that is to be converted"}
1535	Button ConvButton,pos={73,79},size={80,20},proc=ConvertButtonProc,title="Convert"
1536	Button ConvButton,help={"Converts the chosen file to appear as a transmission file"}
1537	Button UndoButton,pos={68,105},size={90,20},proc=UnConvertButtonProc,title="Un-Convert"
1538	Button UndoButton,help={"Converts the chosen file to appear as a scattering file"}
1539	EndMacro
1540
1541
1542	/////
1543	// A quick way to fill all the T_EMP_Filenames with the selected empty beam file
1544	// Note that you must go back and clear or reassign any files that are special cases
1545	//
1546	// IMPORTANT - this will overwrite any other file assignments (typically not a problem
1547	// if you are using only one wavelength)
1548	//
1549	/////
1550	Function FillEMPFilenameWSelection()
1551
1552	GetSelection table,TransFileTable,3
1553	Variable row=V_startRow //ony need the selected row, we know the column names and location
1554	Wave/T fw = root:myGlobals:TransHeaderInfo:T_FileNames //trans files
1555	Wave/T ew = root:myGlobals:TransHeaderInfo:T_EMP_FileNames //empty beam reference files
1556
1557	ew[] = fw[row]
1558
1559	return(0)
1560	End
1561
1562	//given a selection of the SAMPLE files, try to find the corresponding transmission file
1563	//
1564	Function GuessTransFile(charsToUse,row)
1565	Variable charsToUse,row //number of characers to use from the beginning of the label, and the row of the sample file
1566
1567	// GetSelection table,ScatterFileTable,3
1568	// Variable row=V_startRow //ony need the selected row, we know the column names and location
1569	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
1570	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
1571	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
1572	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
1573
1574	Variable num,ii,found
1575	String samStr = "",testStr=""
1576
1577	samStr = (sw[row])[0,charsToUse-1] //string to try and match
1578	samStr += "*"
1579	// Print samStr
1580	num=numpnts(tw)
1581	ii=0
1582	do
1583	testStr=tw[ii]
1584	found = stringmatch(testStr, samStr )
1585	if(found == 1)
1586	Print "Match Found at: ",samStr,tnam[ii],tw[ii]
1587	snam[row] = tnam[ii] //write the file name into the table
1588	return(0)
1589	endif
1590	ii+=1
1591	while(ii<num)
1592
1593	//method 2
1594	// samStr = (sw[row])[0,charsToUse-1] //string to try and match
1595	//// Print samStr
1596	// num=numpnts(tw)
1597	// ii=0
1598	// do
1599	// testStr=tw[ii]
1600	// found = strsearch(testStr,samStr,0) //start from zero, Need Igor 5 to allow 4th parameter to ignore case
1601	// if(found != -1)
1602	// Print "Match Found at: ",samStr,tnam[ii],tw[ii]
1603	// snam[row] = tnam[ii] //write the file name into the table
1604	// return(0)
1605	// endif
1606	// ii+=1
1607	// while(ii<num)
1608
1609	Print "No Match found"
1610	return(0)
1611	End
1612
1613	//given a single transmission file, try to find the corresponding scattering file(s)
1614	//
1615	// apply TWO criteria
1616	// (1) the label must match "well enough"
1617	// (2) the wavelength must be the same "enough", given the unnecessary precision reported by ICE
1618	//
1619	// (for example, "6" can be anything from 6.0008 to 6.0020 in a recent experiment)
1620	//
1621	// passes the matching rows in the sample table back
1622	//
1623	Function GuessTransToScattFiles(charsToUse,row,matchRows)
1624	Variable charsToUse,row //number of characers to use from the beginning of the label, and the row of the transmission file
1625	Wave matchRows //rows where (potential) matches found. initially zero points
1626
1627	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
1628	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
1629	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
1630	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
1631	Wave sLam = root:myGlobals:TransHeaderInfo:S_Lambda //Scattering file wavelength
1632	Wave tLam = root:myGlobals:TransHeaderInfo:T_Lambda //Transmission file wavelength
1633
1634	Variable num,ii,found,tolerance=0.01 //0.01 = 1% tolerance
1635	String transStr = "",testStr=""
1636
1637	transStr = (tw[row])[0,charsToUse-1] //string to try and match
1638	transStr += "*"
1639
1640	//loop over ALL sample files
1641	num=numpnts(sw)
1642	ii=0
1643	do
1644	testStr=sw[ii]
1645	found = stringmatch(testStr, transStr )
1646	if( (found == 1) && (abs(sLam[ii] - tLam[row]) < tolerance) ) // both must match
1647	Print "Match Found at: ",transStr,snam[ii],sw[ii]
1648	InsertPoints numpnts(matchRows), 1, matchRows
1649	matchRows[numpnts(matchRows)-1] = ii
1650	endif
1651	ii+=1
1652	while(ii<num)
1653
1654	//method 2 UNTESTED
1655	// transStr = (tw[row])[0,charsToUse-1] //string to try and match
1656	// num=numpnts(sw)
1657	// ii=0
1658	// do
1659	// testStr=sw[ii]
1660	// found = strsearch(testStr,transStr,0,2) //start from zero, ignore case
1661	// if(found != -1)
1662	// Print "Match Found at: ",transStr,snam[ii],sw[ii]
1663	// InsertPoints numpnts(matchRows), 1, matchRows
1664	// matchRows[numpnts(matchRows)-1] = ii
1665	//// snam[ii] = tnam[row] //write the file name into the table
1666	// endif
1667	// ii+=1
1668	// while(ii<num)
1669
1670	// Print "No Match found"
1671	return(0)
1672	End
1673
1674	//get a single selection from the Trans table
1675	// find all of the matching scattering files (rows)
1676	// ask the user if the selections are OK
1677	// if NOT OK, do nothing
1678	// if OK: make the assignments, and immediately calculate the transmission
1679	//
1680	Function fGuessTransToScattFiles(numChars)
1681	Variable numChars
1682
1683	Variable ii,row
1684	Variable transTableExists
1685	Make/O/D/N=0 root:myGlobals:TransHeaderInfo:matchRows
1686	Wave matchRows=root:myGlobals:TransHeaderInfo:matchRows
1687
1688	transTableExists = WinType("TransFileTable")
1689	if (transTableExists != 0)
1690	GetSelection table,transFileTable,1
1691	row = V_startRow
1692	GuessTransToScattFiles(numChars,row,matchRows)
1693	else
1694	Print "Transmission->Scattering File table is not open"
1695	return (1)
1696	endif
1697
1698	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
1699	Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels //trans file labels
1700	Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames //trans file names
1701	Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames //Scattering - trans correspondence
1702	Wave/T samfile = root:myGlobals:TransHeaderInfo:S_FileNames //Scattering file name
1703
1704	// can do fancy formatted string with ...
1705	//"asdf* matches file: \\f01filen\\f00 \\K(52428,1,1)\\f01afdsfdd\\f00\\K(0,0,0)asdfasdfs"
1706	Variable num=numpnts(matchRows)
1707	String result="",tmpStr
1708	for(ii=0;ii<num;ii+=1)
1709	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]
1710	result += tmpStr
1711	endfor
1712
1713	if(cmpstr(result,"")==0)
1714	result = "No match found for "+ (tw[row])[0,numChars-1]
1715	endif
1716
1717	// Print result
1718	Print "*******"
1719
1720	String/G root:myGlobals:TransHeaderInfo:gResultStr = result
1721
1722	DoWindow/F ConfirmGuess //it really shouldn't exist...
1723	if(V_flag==1)
1724	TitleBox title0,pos={9,5},variable=root:myGlobals:TransHeaderInfo:gResultStr
1725	else
1726	NewPanel /W=(578,44,1263,214) as "Confirm Guess"
1727	DoWindow/C ConfirmGuess
1728	TitleBox title0,pos={9,5},size={501,32}
1729	TitleBox title0,variable= root:myGlobals:TransHeaderInfo:gResultStr
1730	Button button0,pos={9,107},size={190,20},proc=DoAssignTransButtonProc,title="Assign Transmission Files"
1731	Button button2,pos={341,108},size={90,20},proc=DoTryAgainButtonProc,title="Try Again"
1732	ToolsGrid snap=1,visible=1
1733	endif
1734
1735	PauseForUser ConfirmGuess
1736
1737	// figure out from the return code what the user did...
1738	// 1 = OK, accept guess (assign, and calculate immediately)
1739	// 2 = try again
1740	// 0 = cancel, don't do anything (not used, simply try again)
1741	NVAR guessOK = root:myGlobals:TransHeaderInfo:GuessOK
1742
1743	// switch here...
1744	switch(guessOK) // numeric switch
1745	case 1:
1746	// accept guess (assign, and calculate immediately)
1747	for(ii=0;ii<num;ii+=1)
1748	snam[matchRows[ii]] = tnam[row]
1749	AssignSelTransFilesToData(matchRows[ii],matchRows[ii])
1750	CalcSelTransFromHeader(matchRows[ii],matchRows[ii]) //does only that sample file
1751	endfor
1752	break
1753	case 2: //try again (with more / fewer characters?)
1754	// does nothing right now
1755	break
1756	case 0:
1757	// do nothing
1758	break
1759	default:
1760	// do nothing
1761	endswitch
1762
1763	return(0)
1764	End
1765
1766	// a hook attached to the Transmission Files Table
1767	// given a single selected Trans File, popup gives choices
1768	// to guess using "n" characters, then dispatch accordingly
1769	Function GuessFromTableHook(infoStr)
1770	String infoStr
1771	String event= StringByKey("EVENT",infoStr)
1772	// Print "EVENT= ",event
1773
1774	String menuStr=""
1775	menuStr += "Guess using N characters;"
1776	menuStr += "Guess using 3 characters;"
1777	menuStr += "Guess using 6 characters;"
1778	menuStr += "Guess using 9 characters;"
1779	menuStr += "Guess using 12 characters;"
1780	menuStr += "Guess using 15 characters;"
1781	menuStr += "Guess using 18 characters;"
1782	menuStr += "Guess using 21 characters;"
1783	menuStr += "Guess using 24 characters;"
1784
1785	strswitch(event)
1786	case "mousedown":
1787	Variable xpix= NumberByKey("MOUSEX",infoStr)
1788	Variable ypix= NumberByKey("MOUSEY",infoStr)
1789	Variable modif= NumberByKey("MODIFIERS",infoStr)
1790	//print modif
1791	if(modif & 2^1) //bit 1 set, shift key is down
1792	PopupContextualMenu/C=(xpix, ypix) menuStr
1793	strswitch(S_selection)
1794	case "Guess using 3 characters":
1795	fGuessTransToScattFiles(3)
1796	break
1797	case "Guess using 6 characters":
1798	fGuessTransToScattFiles(6)
1799	break
1800	case "Guess using 9 characters":
1801	fGuessTransToScattFiles(9)
1802	break
1803	case "Guess using 12 characters":
1804	fGuessTransToScattFiles(12)
1805	break
1806	case "Guess using 15 characters":
1807	fGuessTransToScattFiles(15)
1808	break
1809	case "Guess using 18 characters":
1810	fGuessTransToScattFiles(18)
1811	break
1812	case "Guess using 21 characters":
1813	fGuessTransToScattFiles(21)
1814	break
1815	case "Guess using 24 characters":
1816	fGuessTransToScattFiles(24)
1817	break
1818	case "Guess using N characters":
1819	Variable num=10
1820	Prompt num, "Number of characters"
1821	DoPrompt "Enter the number of characters to match", num
1822	if (V_Flag)
1823	break //user cancel, do nothing
1824	endif
1825	fGuessTransToScattFiles(num)
1826	break
1827	endswitch //on selection
1828	endif
1829	endswitch // on event
1830
1831	return 0
1832	End
1833
1834	// sets a flag if the user thinks that the guess was correct, and wants to use the
1835	// identified files for the transmission
1836	Function DoAssignTransButtonProc(ba) : ButtonControl
1837	STRUCT WMButtonAction &ba
1838
1839	switch( ba.eventCode )
1840	case 2: // mouse up
1841	// click code here
1842	//Print "Assigned stuff, and left."
1843	Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 1
1844	DoWindow/K ConfirmGuess
1845	break
1846	endswitch
1847
1848
1849	return 0
1850	End
1851
1852	// files are wrong, let the user try it again
1853	// sets a flag, nothing else
1854	Function DoTryAgainButtonProc(ba) : ButtonControl
1855	STRUCT WMButtonAction &ba
1856
1857	switch( ba.eventCode )
1858	case 2: // mouse up
1859	// click code here
1860	Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 2
1861	DoWindow/K ConfirmGuess
1862	//Print "Try Again"
1863	break
1864	endswitch
1865
1866	return 0
1867	End
1868
1869	// not used
1870	Function DoCancelGuessButtonProc(ba) : ButtonControl
1871	STRUCT WMButtonAction &ba
1872
1873	switch( ba.eventCode )
1874	case 2: // mouse up
1875	// click code here
1876	//just kill the panel, don't do anything
1877	Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 0
1878	DoWindow/K ConfirmGuess
1879	break
1880	endswitch
1881
1882	return 0
1883	End
1884
1885	Function GuessAllTransFiles(numChars)
1886	Variable numChars
1887
1888	if(WinType("ScatterFileTable") ==0 )
1889	return(1)
1890	endif
1891
1892	Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels //Sample file labels
1893	Variable ii,num=numpnts(sw)
1894
1895	for(ii=0;ii<num;ii+=1)
1896	GuessTransFile(numChars,ii)
1897	endfor
1898
1899	return(0)
1900	End
1901
1902	Function fGuessSelectedTransFiles(numChars)
1903	Variable numChars
1904
1905	Variable ii
1906	Variable scatterTableExists
1907	scatterTableExists = WinType("ScatterFileTable")
1908	if (scatterTableExists != 0)
1909	GetSelection table,ScatterFileTable,1
1910	for(ii=V_StartRow;ii<=V_EndRow;ii+=1)
1911	GuessTransFile(numChars,ii)
1912	endfor
1913	else
1914	Print "Transmission->Scattering File table is not open"
1915	endif
1916	return(0)
1917	End
1918
1919	Function ClearSelectedAssignments()
1920
1921	String winStr = WinList("*", ";", "WIN:" ) //returns the target window
1922	Variable scatterTableExists, transTableExists
1923	Print winStr
1924	scatterTableExists = cmpstr(winStr,"ScatterFileTable;")
1925	if (scatterTableExists == 0)
1926	GetSelection table,ScatterFileTable,1
1927	fClearSelectedAssignments(V_startRow,V_endRow,1)
1928	endif
1929
1930	transTableExists = cmpstr(winStr,"TransFileTable;")
1931	if (transTableExists == 0)
1932	GetSelection table,TransFileTable,1
1933	fClearSelectedAssignments(V_startRow,V_endRow,2)
1934	endif
1935
1936	return(0)
1937	End

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