source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/QKK_ANSTO_Transmission.ipf @ 917

Last change on this file since 917 was 917, checked in by srkline, 10 years ago

Modified QKK files to remove the calls to the ProgressWindow? XOP, which crashed my machine (OSX 10.8), Igor 6.3

Updated event processing to add new editing features to remove outliers

Updated help file for Event Mode.

File size: 89.3 KB
Line 
1#pragma rtGlobals=1             // Use modern global access method.
2#pragma version=5.0
3#pragma IgorVersion=6.0
4
5
6//*************************
7// Vers. 1.2 092101
8//
9// - procedures for (easier) caluclation of transmissions along with
10//  simultaneous patching of the calculated transmission in designated
11//  raw sans files.
12// - transmission and empty beam files are linked to the dataset by their "Annn" suffix
13//   only (and their residence in the same data folder)
14// - unused (analysis) integer values are used to store these run numbers in the sample
15//   file headers so that transmissions can be automatically calculated, once the xy box is set
16//   in the empty beam file.
17//
18//***************************
19
20//main entry procedure for displaying the Trans input panel
21//also initializes the globals as needed
22//
23Proc CalcTrans()
24        DoWindow/F Trans_Panel
25        If(V_flag == 0)
26                InitializeTransPanel()
27                //draw panel
28                Trans_Panel()
29                AutoPositionWindow/M=1/R=Main_Panel Trans_Panel
30        Endif
31End
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.
39Proc BuildFileTables()
40
41        Variable err
42        PathInfo catPathName
43        if(v_flag==0) // PathInfo returns path doesn't exist
44                err = PickPath()//sets the local path to the data (catPathName)
45                if(err)
46                        Abort "no path to data was selected, no catalog can be made - use PickPath button"
47                Endif
48        Endif
49
50        CreateTransGlobals()   
51        Variable ScatFileTableExists
52        ScatFileTableExists = WinType("ScatterFileTable")
53        //if(v_flag==0)
54        If(!ScatFileTableExists)
55                BuildScatTableWindow()
56                ModifyTable width(Point)=18
57               
58                ModifyTable width(root:myGlobals:TransHeaderInfo:S_SDD)                 = 40
59                ModifyTable width(root:myGlobals:TransHeaderInfo:S_Lambda)                      = 40
60                ModifyTable width(root:myGlobals:TransHeaderInfo:S_Transmission)        = 60
61               
62                ModifyTable rgb(root:myGlobals:TransHeaderInfo:S_Filenames)             = (0,0,65535)
63                ModifyTable width(root:myGlobals:TransHeaderInfo:S_Filenames)           = 105
64                ModifyTable width(root:myGlobals:TransHeaderInfo:T_Filenames)           = 105
65                ModifyTable width(root:myGlobals:TransHeaderInfo:EMP_Filenames) = 105
66               
67                ModifyTable width(root:myGlobals:TransHeaderInfo:S_Labels)                      = 140
68                ModifyTable width(root:myGlobals:TransHeaderInfo:T_Labels)                      = 140
69        Endif
70
71        DoWindow/F ScatterFileTable //bring window to front
72       
73        //open xml file
74        variable fileID = getReport()
75        if(fileID<=1)
76                Abort "Cannot open experimental report file " + S_filename
77        endif
78       
79        //currently have 2 function to read the 2 types of report files, with and without sample environment
80        //trying to merge into 1.       
81       
82        //getFileAssociations(fileID)
83        getFileAssociationsSampleEnv(fileID)
84       
85        //close xml file without save
86        XMLclosefile(fileID,0)
87       
88        //Read data from datafile into globals
89        GetTransHeaderInfoToWave()
90
91        //Sort entries based on date
92        //      SortGlobals(0)
93
94        //position the windows nicely
95        //      AutoPositionWindow/M=1/R=ScatterFileTable
96        //      DoWindow/F Trans_Panel //nha Trans_Panel not required?
97       
98End
99
100Function getReport()
101        // Open the experiment report file(s) in this path
102        variable refnum
103        Open/D/R /M="Open experiment report file" /T=".xml" refnum
104        if(cmpstr(S_filename,"")==0)
105                Abort "No experimental report file selected"
106        Endif 
107        variable fileID = XMLopenFile(S_filename)
108       
109        return fileID
110
111End
112
113Function getFileAssociations(fileID)
114
115        // nha 22/1/2010 - new xml report structure, from December 2009
116        // incompatible with previous report structure
117        // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
118
119        variable fileID
120        variable ii,jj
121
122        Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
123        Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
124        Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
125        Wave/T xmlContent = $"root:M_xmlcontent"
126        Wave/T xmlContentNodes = $"root:W_xmlcontentnodes"
127
128
129        string prefix = "QKK"
130        string suffix = ".nx.hdf"
131        string full_fname, xpath, xpath_config, xpath_type, xpath_fname, xmlString, list, fname
132        variable nConfig, tSamples, sSamples
133        wave w_fname
134       
135        //determine no. of samples
136        xpath = "/report//config" //root node of report
137        XMLWaveFmXpath(fileID,xpath,"","")
138        nConfig = DimSize(xmlContentNodes,0)
139       
140        ii=1
141        do
142                xpath_config = "/report/config[" + num2str(ii) + "]"  //there may be multiple config per report
143               
144                xpath_fname = xpath_config + "/transmission//sample[@type = 'sample']/@runId" //select all sample nodes of type sample and return runId attribute
145                XMLwaveFmXpath(fileID,xpath_fname,"","")
146                tSamples = DimSize(xmlContentNodes,0)
147
148                if(tSamples>=1)  //sample exist under the transmission node - probably a more elegant way of get these values into T_Filenames
149                        jj=0
150                        do
151                                full_fname = prefix + xmlcontent[0][jj] + suffix
152                                InsertPoints jj,1,T_Filenames
153                                if(strlen(xmlcontent[0][jj])<7) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
154                                        T_Filenames[jj] = ""
155                                else
156                                        T_Filenames[jj] = full_fname
157                                endif
158                                jj+=1
159                        while (jj<tSamples)
160                endif
161               
162                xpath_fname = xpath_config + "/scattering//sample[@type = 'sample']/@runId" //select all sample nodes of type sample and return runId attribute
163                XMLwaveFmXpath(fileID,xpath_fname,"","")
164                sSamples = DimSize(xmlContentNodes,0)
165
166                if(sSamples>=1)  //sample exist under the scattering node
167                        jj=0
168                        do
169                                full_fname = prefix + xmlcontent[0][jj] + suffix
170                                InsertPoints jj,1,S_Filenames
171                                if(strlen(xmlcontent[0][jj])<7) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
172                                        S_Filenames[jj] = ""
173                                else
174                                        S_Filenames[jj] = full_fname
175                                endif
176                                jj+=1
177                        while (jj<sSamples)
178                endif
179               
180                if(sSamples!=tSamples)
181                        // the experiment model from Dec 2009 should have equal numbers of scattering and trans
182                        // sample, according to Tony Lam, although the string may be ""
183                        //abort "The number transmissions samples in the report file does not equal the number of scattering files"
184                endif
185               
186                // use empty beam for transmission, not empty cell
187                //empty beam transmission
188                xpath_fname = xpath_config + "/emptyBeamTransmissionRunId" //select all sample nodes of type sample and return runId attribute
189                XMLwaveFmXpath(fileID,xpath_fname,"","")
190                if(sSamples>=1)  //sample exist under the scattering node
191                        jj=0
192                        do
193                                full_fname = prefix + xmlcontent[0][0] + suffix
194                                InsertPoints jj,1,EMP_Filenames
195                                if(strlen(xmlcontent[0][0])<7) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
196                                        EMP_Filenames[jj] = ""
197                                else
198                                        EMP_Filenames[jj] = full_fname
199                                endif
200                                jj+=1
201                        while (jj<sSamples)
202                endif           
203                ii+=1
204        while(ii<nConfig+1) //ii is using one-based counting because xml is one-based
205       
206        //delete rows with blanks
207        ii=0
208        do
209                if(cmpstr(T_Filenames[ii],"")==0 || cmpstr(S_Filenames[ii],"")==0 || cmpstr(EMP_Filenames[ii],"")==0)
210                        print "Row is incomplete and therefore being deleted " + T_Filenames + " " + S_Filenames + " " + EMP_Filenames
211                        DeletePoints ii,1,T_Filenames,S_Filenames,EMP_Filenames
212                        ii-=1
213                endif
214                ii+=1
215        while (ii<DimSize(S_Filenames,0))
216               
217                       
218        //Check if the files in the report file are available in the path.
219        //
220       
221        //Put up a dialog of the number of missing files and their filenames. ABORT or CONTINUE
222        //
223
224End
225
226Function/S pickFileInCatPath(fileFilterStr, messageStr)
227
228        string fileFilterStr
229        string messageStr
230
231        variable refNum
232        Open/D/R /F=fileFilterStr /M=messageStr refNum
233
234        variable len = strlen(S_fileName)
235        variable lastSepIndex = strsearch(S_fileName, ":", inf, 1)
236        if (lastSepIndex == -1)
237                return S_fileName
238        else
239                svar defaultPath = root:myGlobals:gCatPathStr
240                string selectedPath
241                variable q = 0
242                                                       
243                for (selectedPath = ""; q <= lastSepIndex; q += 1)
244                        selectedPath += S_fileName[q]
245                endfor
246                                                       
247                if (cmpstr(defaultPath, selectedPath) == 0) // path does match
248               
249                        string result
250                        for (result = ""; q < len; q += 1)
251                                result += S_fileName[q]
252                        endfor
253                        return result
254                       
255                else // path doesn't match
256                        DoAlert 1, "You need to pick a file in the same location as the report file. Would you like to pick another file?"
257                       
258                        if (V_flag == 1) // answer was yes
259                                return pickFileInCatPath(fileFilterStr, messageStr)
260                        else
261                                return ""
262                        endif
263                endif
264        endif
265                                               
266End
267
268Function getFileAssociationsSampleEnv(fileID)
269
270        // nha 22/1/2010 - new xml report structure, from December 2009
271        // incompatible with previous report structure
272        // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
273
274        variable fileID
275        variable ii, jj
276        variable kkS, kkSmax, kkT, kkTmax, kkE
277        variable kkToffset
278       
279        variable s_pos, t_pos
280
281        Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
282        Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
283        Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
284       
285//      Wave/T xmlContent = $"root:Packages:NIST:M_xmlcontent"
286//      Wave/T xmlContentNodes = $"root:Packages:NIST:W_xmlcontentnodes" // this location doesn't work. Don't know why. nha ???
287
288        // "root:M_xmlcontent" and "root:W_xmlcontentnodes" is not available until XMLWaveFmXpath has been called the first time! [davidm]
289        //Wave/T xmlContent = $"root:M_xmlcontent"                             // this has been move to the lines after: XMLWaveFmXpath
290        //Wave/T xmlContentNodes = $"root:W_xmlcontentnodes"
291       
292        // "root:M_listXPath" is not available until xmlListXPath(fileID,xpath,"")  has been called the first time!  [davidm]
293        // Wave/T listXPath = $"root:M_listXPath"  // this has been move to the line after: err = xmlListXPath(fileID,xpath,"")
294
295        string prefix = "QKK"
296        string suffix = ".nx.hdf"
297        string full_fname, xpath, xpath_SampleEnv, xpath_config, xpath_type, xpath_fname, xmlString, list, fname
298        variable nSampleEnv, nConfig, tSamples, sSamples
299        variable tSampleNum, sSampleNum, eSampleNum // used to accumulate the number of samples across multiple configs
300        variable noRunIds
301
302        variable hasSampleEnv
303        variable err
304       
305        // to disable asking dialogs
306        variable specifyTFile_Enabled           = 1 // 0: Disabled; 1: Enabled; 2: Always specify if missing
307        variable specifySFile_Enabled           = 1
308        variable specifyEMPFile_Enabled = 1
309       
310        //in a report there are 0..n /sampleEnvironment
311        //these have 1..n or 1..2 /config
312                //these have a /transmission /scattering
313                        //these have 1..n sample which may or maynot have a runId
314                //config also has 0..1 /emptyCellTransmissionRunId    0..1 /emptyCellScatteringRunId    0..1 /emptyBeamTransmissionRunId
315       
316        //determine no. of sampleEnvironment tags
317        hasSampleEnv = 0
318        xpath = "/report//sampleEnvironment" //root node of report - what happens if this xpath doesn't exist ???TEST
319//      xpath = "/report//config"  // for test ??? nha
320       
321        //check if the file contains the required nodes
322        //xmlelementlist(fileID)
323        err = xmlListXPath(fileID,xpath,"") // this creates a three column text wave, M_listXPath
324       
325        Wave/T listXPath = $"root:M_listXPath"
326
327        if (err != 0)
328                abort "Can't read xml file"
329        endif
330       
331        if (DimSize(listXPath,0) > 0)
332                hasSampleEnv = 1
333        else
334                xpath = "/report//config"
335        endif
336
337        nSampleEnv = 0
338        if (hasSampleEnv)
339                XMLWaveFmXpath(fileID,xpath,"","")
340               
341                Wave/T xmlContentNodes = $"root:W_xmlcontentnodes" // [davidm]
342               
343                nSampleEnv = DimSize(xmlContentNodes,0)
344        endif
345        ii=1 //sample environment iterator
346       
347        tSampleNum = 0
348        sSampleNum = 0
349        eSampleNum = 0
350
351        do
352                if (hasSampleEnv)
353                        xpath_SampleEnv = "/report/sampleEnvironment[" + num2str(ii) + "]"  //there may be multiple sampleEnvironment per report
354                else
355                        xpath_SampleEnv = "/report"
356                endif
357                       
358                //determine no. of config tags
359                xpath = xpath_SampleEnv + "//config"
360                XMLWaveFmXpath(fileID,xpath,"","")
361
362                Wave/T xmlContent = $"root:M_xmlcontent"                                // [davidm]
363                Wave/T xmlContentNodes = $"root:W_xmlcontentnodes"
364               
365                nConfig = DimSize(xmlContentNodes,0)
366                jj=1  // config iterator
367
368                do
369//                      Execute  "ProgressWindow spin"
370                        xpath_config = xpath_SampleEnv + "/config[" + num2str(jj) + "]" //there may be multiple config per report
371
372                        // get the positions of the s-samples (used to check if report file does not contain all samples)
373                        xpath_fname = xpath_config + "/scattering//sample[@type = 'sample']/@position" //select all sample nodes of type sample and return position attribute
374                        XMLwaveFmXpath(fileID,xpath_fname,"","")
375                        Duplicate /FREE/T xmlcontent, S_Positions
376                       
377                        // get the runIds of the s-sampels
378                        xpath_fname = xpath_config + "/scattering//sample[@type = 'sample']/@runId" //select all sample nodes of type sample and return runId attribute
379                        XMLwaveFmXpath(fileID,xpath_fname,"","")
380                        sSamples = DimSize(xmlContentNodes,0)
381                        kkSmax = sSamples - 1
382                       
383                        // if no runIds are specified then xmlcontent is empty
384                        noRunIds = DimSize(xmlcontent,0) == 0
385
386                        // s-sample exist under the scattering node
387                        if (sSamples > 0)
388                                for (kkS = 0; kkS <= kkSmax; kkS += 1) // scattering sample iterator
389                               
390                                        InsertPoints sSampleNum + kkS, 1, S_Filenames
391                                       
392                                        if (noRunIds)
393                                                S_Filenames[sSampleNum + kkS] = ""
394                                        else
395                                                full_fname = prefix + xmlcontent[0][kkS] + suffix
396                                                if (strlen(xmlcontent[0][kkS]) < 7) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
397                                                        S_Filenames[sSampleNum + kkS] = ""
398                                                else
399                                                        S_Filenames[sSampleNum + kkS] = full_fname
400                                                endif
401                                        endif
402                                       
403                                endfor
404                        endif
405
406                        // get the positions of the t-samples (used to check if report file does not contain samples)
407                        xpath_fname = xpath_config + "/transmission//sample[@type = 'sample']/@position" //select all sample nodes of type sample and return position attribute
408                        XMLwaveFmXpath(fileID,xpath_fname,"","")
409                        Duplicate /FREE/T xmlcontent, T_Positions
410                       
411                        // get the runIds of the t-sampels
412                        xpath_fname = xpath_config + "/transmission//sample[@type = 'sample']/@runId" //select all sample nodes of type sample and return runId attribute
413                        XMLwaveFmXpath(fileID,xpath_fname,"","")
414                        tSamples = DimSize(xmlContentNodes,0)
415                        kkTmax = tSamples - 1
416                       
417                        // if no runIds are specified then xmlcontent is empty
418                        noRunIds = DimSize(xmlcontent,0) == 0
419
420                        // we need to know how many t-samples are added (if report file does not contain all t-sampels)
421                        kkToffset = 0
422
423                        // t-sample exist under the transmission node
424                        if (tSamples > 0)
425                                for (kkS = 0, kkT = 0; kkT <= kkTmax;) // transmission sample iterator
426
427                                        // we need to compare the position of the current s- and t-sample
428                                        if (kkS <= kkSmax)
429                                                s_pos = str2num(S_Positions[0][kkS])
430                                        else
431                                                s_pos = Inf // this means that at least one s-sample is missing
432                                        endif
433                                        t_pos = str2num(T_Positions[0][kkT])
434                                       
435                                        if (s_pos < t_pos) // t-sample is missing
436                                       
437                                                if (specifyTFile_Enabled)
438                                                        DoAlert 1, "For the S-File \"" + S_Filenames[tSampleNum+kkS] + "\" (position " + S_Positions[0][kkS] + ") no T-File was specified. Would you like to select one now?"
439                                                else
440                                                        V_flag = 0 // if disabled then answer is always no
441                                                endif
442                                       
443                                                // insert new t-sample
444                                                InsertPoints tSampleNum + kkT + kkToffset, 1, T_Filenames
445                                                if (V_flag != 1) // answer was no
446                                                        T_Filenames[tSampleNum + kkT + kkToffset] = ""
447                                                       
448                                                        if (specifyTFile_Enabled == 1)
449                                                                DoAlert 1, "Would you like to specify any missing T-Files?"
450                                                                if (V_flag != 1) // answer was no
451                                                                        specifyTFile_Enabled = 0
452                                                                else
453                                                                        specifyTFile_Enabled = 2
454                                                                endif
455                                                        endif
456                                                       
457                                                else
458                                                        T_Filenames[tSampleNum + kkT + kkToffset] = pickFileInCatPath("Hierarchical Data Format (*.nx.hdf):.nx.hdf;All Files:.*;", "Select the corresponding T-File")
459                                                endif
460                                               
461                                                kkToffset += 1
462                                                kkS += 1
463                                                tSamples += 1
464                                               
465                                        else // insert t-sample from report file
466                                       
467                                                InsertPoints tSampleNum + kkT + kkToffset, 1, T_Filenames
468                                       
469                                                if (noRunIds)
470                                                        T_Filenames[tSampleNum + kkT + kkToffset] = ""
471                                                else                                   
472                                                        full_fname = prefix + xmlcontent[0][kkT] + suffix
473                                                        if(strlen(xmlcontent[0][kkT]) < 7) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
474                                                                T_Filenames[tSampleNum + kkT + kkToffset] = ""
475                                                        else
476                                                                T_Filenames[tSampleNum + kkT + kkToffset] = full_fname
477                                                        endif
478                                                endif
479                                               
480                                                kkT += 1
481                                               
482                                                if (s_pos == t_pos)
483                                                        kkS += 1
484                                                else // s-sample is missing
485                                               
486                                                        if (specifySFile_Enabled)
487                                                                DoAlert 1, "For the T-File \"" + T_Filenames[tSampleNum+kkT] + "\" (position " + T_Positions[0][kkT] + ") no S-File was specified. Would you like to select one now?"
488                                                        else
489                                                                V_flag = 0 // if disabled then answer is always no
490                                                        endif
491                                               
492                                                        // insert new s-sample
493                                                        InsertPoints tSampleNum + kkT + kkToffset, 1, S_Filenames
494                                                        if (V_flag != 1) // answer was no
495                                                                S_Filenames[tSampleNum + kkT + kkToffset] = ""
496                                                               
497                                                                if (specifySFile_Enabled == 1)
498                                                                        DoAlert 1, "Would you like to specify any missing S-Files?"
499                                                                        if (V_flag != 1) // answer was no
500                                                                                specifySFile_Enabled = 0
501                                                                        else
502                                                                                specifySFile_Enabled = 2
503                                                                        endif
504                                                                endif
505                                                       
506                                                        else
507                                                                S_Filenames[tSampleNum + kkT + kkToffset] = pickFileInCatPath("Hierarchical Data Format (*.nx.hdf):.nx.hdf;All Files:.*;", "Select the corresponding S-File")
508                                                        endif
509                                               
510                                                        sSamples += 1
511                                                endif
512                                        endif
513                                endfor
514                        endif
515
516                        if (sSamples > tSamples) // checks if t-samples are still missing
517                                do
518                                        if (specifyTFile_Enabled)
519                                                DoAlert 1, "For the S-File \"" + S_Filenames[tSampleNum+kkS] + "\" (position " + S_Positions[0][kkS] + ") no T-File was specified. Would you like to select one now?"
520                                        else
521                                                V_flag = 0 // if disabled then answer is always no
522                                        endif
523                                                       
524                                        // insert new t-sample
525                                        InsertPoints tSampleNum + kkT + kkToffset, 1, T_Filenames
526                                        if (V_flag != 1) // answer was no
527                                       
528                                                T_Filenames[tSampleNum + kkT + kkToffset] = ""
529                                               
530                                                if (specifyTFile_Enabled == 1)
531                                                        DoAlert 1, "Would you like to specify any missing T-Files?"
532                                                        if (V_flag != 1) // answer was no
533                                                                specifyTFile_Enabled = 0
534                                                        else
535                                                                specifyTFile_Enabled = 2
536                                                        endif
537                                                endif
538                                               
539                                        else
540                                                T_Filenames[tSampleNum + kkT + kkToffset] = pickFileInCatPath("Hierarchical Data Format (*.nx.hdf):.nx.hdf;All Files:.*;", "Select the corresponding T-File")
541                                        endif
542                                       
543                                        kkToffset += 1
544                                        kkS += 1
545                                        tSamples += 1
546
547                                while (sSamples > tSamples)
548                        endif
549                               
550                        tSampleNum += tSamples
551                        sSampleNum += sSamples
552
553                        // empty beam transmission
554                        xpath_fname = xpath_config + "/emptyBeamTransmissionRunId"
555                        XMLwaveFmXpath(fileID,xpath_fname,"","")
556                       
557                        if (sSamples>=1)  //sample exist under the scattering node
558                               
559                                if (WaveDims(xmlcontent) && (strlen(xmlcontent[0][0]) == 7)) // assumes the ANSTO filename convention QKKnnnnnnn.nx.hdf
560                                        full_fname = prefix + xmlcontent[0][0] + suffix
561                                else
562                                        kkS = sSampleNum-sSamples
563                                        string sFilenames = S_Filenames[kkS]
564                                       
565                                        for (kkS += 1; kkS < sSampleNum; kkS += 1)
566                                                if (strlen(S_Filenames[kkS]) > 0)
567                                                        sFilenames = sFilenames + ", " + S_Filenames[kkS]
568                                                endif
569                                        endfor
570
571                                        // only ask if sFilenames is not empty
572                                        full_fname = ""
573                                        if (strlen(sFilenames) > 0)
574                                       
575                                                if (specifyEMPFile_Enabled)
576                                                        DoAlert 1, "For the listed S-File(s), no appropriate EMP-File was specified. Would you like to select one now?\n" + sFilenames
577                                                else
578                                                        V_flag = 0 // if disabled then answer is always no
579                                                endif
580                                                       
581                                                if (V_flag == 1) // answer was yes
582                                                        full_fname = pickFileInCatPath("Hierarchical Data Format (*.nx.hdf):.nx.hdf;All Files:.*;", "Select an EMP-File")
583                                                elseif (specifyEMPFile_Enabled == 1)
584                                                        DoAlert 1, "Would you like to specify any missing EMP-Files?"
585                                                        if (V_flag != 1) // answer was no
586                                                                specifyEMPFile_Enabled = 0
587                                                        else
588                                                                specifyEMPFile_Enabled = 2
589                                                        endif
590                                                endif
591                                        endif
592                                endif
593                       
594                                kkE = 0
595                                do
596                                        InsertPoints eSampleNum + kkE,1,EMP_Filenames
597                                        EMP_Filenames[eSampleNum + kkE] = full_fname
598                                        kkE += 1
599                                while (kkE < sSamples)
600                               
601                                eSampleNum += sSamples
602                        endif
603                       
604                        jj += 1
605                while(jj<nConfig+1)
606                ii+=1
607        while(ii<nsampleEnv+1) //ii is using one-based counting because xml is one-based
608       
609        //delete rows with blanks
610        // ??? testing without removal of blanks. nha.
611//      ii=0
612//      do
613//              if(cmpstr(T_Filenames[ii],"")==0 || cmpstr(S_Filenames[ii],"")==0 || cmpstr(EMP_Filenames[ii],"")==0)
614//                      print "Row is incomplete and therefore being deleted " + T_Filenames + " " + S_Filenames + " " + EMP_Filenames
615//                      DeletePoints ii,1,T_Filenames,S_Filenames,EMP_Filenames
616//                      ii-=1
617//              endif
618//              ii+=1
619//      while (ii<DimSize(S_Filenames,0))
620               
621                       
622        //Check if the files in the report file are available in the path.
623        //
624       
625        //Put up a dialog of the number of missing files and their filenames. ABORT or CONTINUE
626        //
627
628End
629
630//actually creates the table of scattering files
631// - the waves must exist
632//
633Function BuildScatTableWindow()
634        Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
635        Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
636        Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
637        Wave/T S_Labels = $"root:myGlobals:TransHeaderInfo:S_Labels"
638        Wave/T T_Labels = $"root:myGlobals:TransHeaderInfo:T_Labels"
639        Wave   S_SDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
640        Wave   S_Lambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
641        Wave   S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
642        Wave   S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
643        Wave   T_SDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
644        Wave   T_Lambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
645        //      Wave   T_Transmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
646        //      Wave   T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
647        Wave   EMP_x1= $"root:myGlobals:TransHeaderInfo:EMP_x1"
648        Wave   EMP_x2= $"root:myGlobals:TransHeaderInfo:EMP_x2"
649        Wave   EMP_y1= $"root:myGlobals:TransHeaderInfo:EMP_y1"
650        Wave   EMP_y2= $"root:myGlobals:TransHeaderInfo:EMP_y2"
651                               
652        Edit/K=1/W=(20,20,520,470) S_Filenames, T_Filenames, EMP_Filenames, S_Labels, T_Labels, S_SDD, T_SDD, S_Lambda, T_Lambda, S_Transmission, S_Whole, EMP_x1, EMP_x2, EMP_y1, EMP_y2 as "ScatteringFiles"
653       
654        String name="ScatterFileTable"
655        DoWindow/C $name
656
657End
658
659
660//sorts each of the tables by date - does this by using the suffix "Annn"
661// which is automatically supplied by the VAX (and can't be changed)
662// - only problem may be "Z999" -> "A001" rollover
663//
664// sorts files alphabetically byt the sample label
665// - consistent and descriptive sample labels really pay off here
666//
667Function SortGlobals(sortFlag)
668        Variable sortFlag
669       
670        Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
671        Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
672        Wave/T T_Labels = $"root:myGlobals:TransHeaderInfo:T_Labels"
673        Wave   T_SDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
674        Wave   T_Lambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
675        //      Wave   T_Transmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
676        //      Wave   T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
677
678        Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
679        Wave/T S_Labels = $"root:myGlobals:TransHeaderInfo:S_Labels"
680        Wave   S_SDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
681        Wave   S_Lambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
682        Wave   S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
683        Wave   S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
684       
685        Wave   EMP_x1= $"root:myGlobals:TransHeaderInfo:EMP_x1"
686        Wave   EMP_x2= $"root:myGlobals:TransHeaderInfo:EMP_x2"
687        Wave   EMP_y1= $"root:myGlobals:TransHeaderInfo:EMP_y1"
688        Wave   EMP_y2= $"root:myGlobals:TransHeaderInfo:EMP_y2"
689       
690        if(sortFlag == 0) // by date
691                Sort S_Filenames, S_Filenames, S_Labels, S_SDD, S_Lambda, S_Transmission, S_Whole, EMP_Filenames, T_Filenames, T_Labels, T_SDD, T_Lambda, EMP_x1, EMP_x2, EMP_y1, EMP_y2
692        else  //by label
693                Sort S_Labels, S_Labels, S_Filenames, S_SDD, S_Lambda, S_Transmission, S_Whole, EMP_Filenames,  T_Filenames, T_Labels, T_SDD, T_Lambda, EMP_x1, EMP_x2, EMP_y1, EMP_y2
694        endif
695End
696
697//reads the file and assigns header information to globals, which are read by the ScatteringTable.
698//assumes that associations have been found in experiment report
699//
700//scat_fname - is the full path:name of the datafile (used by Open)
701//
702// takes care of all necessary open/close of file
703//
704Function GetTransHeaderInfoToWave()
705
706        String s_fname,t_fname,emp_fname
707       
708        Variable lastPoint, ii
709
710        Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
711        Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
712        Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
713        Wave/T S_Labels = $"root:myGlobals:TransHeaderInfo:S_Labels"
714        Wave/T T_Labels = $"root:myGlobals:TransHeaderInfo:T_Labels"
715        Wave   S_SDD = $"root:myGlobals:TransHeaderInfo:S_SDD"
716        Wave   S_Lambda = $"root:myGlobals:TransHeaderInfo:S_Lambda"
717        Wave   S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
718        Wave   S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
719        Wave   T_SDD = $"root:myGlobals:TransHeaderInfo:T_SDD"
720        Wave   T_Lambda = $"root:myGlobals:TransHeaderInfo:T_Lambda"
721        //      Wave   T_Transmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
722        //      Wave   T_Whole= $"root:myGlobals:TransHeaderInfo:T_Whole"
723       
724        Wave   EMP_x1= $"root:myGlobals:TransHeaderInfo:EMP_x1"
725        Wave   EMP_x2= $"root:myGlobals:TransHeaderInfo:EMP_x2"
726        Wave   EMP_y1= $"root:myGlobals:TransHeaderInfo:EMP_y1"
727        Wave   EMP_y2= $"root:myGlobals:TransHeaderInfo:EMP_y2"
728
729        lastPoint = numpnts(S_Filenames)
730        PathInfo catPathName
731        variable x1, x2, y1, y2
732       
733        variable FilesAreMissing = 0
734
735//      Execute "ProgressWindow open, text=\"Loading Table...\""
736       
737        ii = 0
738        do
739                s_fname = S_path + S_Filenames[ii]
740                t_fname = S_path + T_Filenames[ii]
741                emp_fname = S_path + EMP_Filenames[ii]
742
743//              Execute "ProgressWindow text=\"Loading Table...\n" + S_Filenames[ii] + "\""
744               
745                InsertPoints ii,1,S_Labels
746                InsertPoints ii,1,S_Transmission
747                InsertPoints ii,1,S_Whole
748                InsertPoints ii,1,S_SDD
749                InsertPoints ii,1,S_Lambda
750                InsertPoints ii,1,T_Labels
751                //              InsertPoints ii,1,T_Transmission
752                //              InsertPoints ii,1,T_Whole
753                InsertPoints ii,1,T_SDD
754                InsertPoints ii,1,T_Lambda
755                InsertPoints ii,1,EMP_x1
756                InsertPoints ii,1,EMP_x2
757                InsertPoints ii,1,EMP_y1
758                InsertPoints ii,1,EMP_y2               
759               
760                if (CheckIfFileExists(s_fname))
761                        if (CheckIfRawData(s_fname))
762                                // read the sample.label text field - OK
763                                S_Labels[ii]=getSampleLabel(s_fname)
764                           
765                                //Transmission - OK as long as it has been patched in ???
766                                S_Transmission[ii]=getSampleTrans(s_fname)
767                       
768                                //Whole detector Transmission - Don't know where this will be in the file. Need help from epg ???
769                                S_Whole[ii]=getSampleTransWholeDetector(s_fname)
770                       
771                                //SDD - OK
772                                S_SDD[ii]=getSDD(s_fname)
773                       
774                                //wavelength - OK
775                                S_Lambda[ii]=getWavelength(s_fname)
776                        endif
777                else
778                        S_Filenames[ii] = "? " + S_Filenames[ii]
779                        FilesAreMissing = 1
780                endif
781               
782                if (CheckIfFileExists(t_fname))
783                        if (CheckIfRawData(t_fname))   
784                                // read the sample.label text field - OK
785                                T_Labels[ii]=getSampleLabel(t_fname)
786                       
787                                //Transmission - OK as long as it has been patched in ???
788                                //T_Transmission[ii]=getSampleTrans(t_fname)
789                       
790                                //Whole detector Transmission - Don't know where this will be in the file. Need help from epg ???
791                                //T_Whole[ii]=getSampleTransWholeDetector(t_fname)   
792                       
793                                //SDD - OK
794                                T_SDD[ii]=getSDD(t_fname)
795                           
796                                //wavelength - OK
797                                T_Lambda[ii]=getWavelength(t_fname)
798                        endif
799                else
800                        T_Filenames[ii] = "? " + T_Filenames[ii]
801                        FilesAreMissing = 1
802                endif
803               
804                if (CheckIfFileExists(emp_fname))
805                        if (CheckIfRawData(emp_fname))
806                                getXYBoxFromFile(emp_fname,x1,x2,y1,y2)
807                                EMP_x1[ii] = x1
808                                EMP_x2[ii] = x2
809                                EMP_y1[ii] = y1
810                                EMP_y2[ii] = y2
811                        endif
812                else
813                        EMP_Filenames[ii] = "? " + EMP_Filenames[ii]
814                        FilesAreMissing = 1
815                endif
816               
817                ii+=1
818//              Execute  "ProgressWindow percent=" + Num2Str(100*ii/lastPoint)
819               
820        while(ii<lastPoint)
821       
822//      Execute "ProgressWindow close"
823       
824        if (FilesAreMissing)
825                DoAlert /T="Warning" 0, "The files marked with \"?\" in the table could not be found.\r\n\r\nSome files listed in the XML-Catalog may be missing."
826        endif
827       
828        return(0)
829End
830
831//initialize data folder and globals for the Trans panel as needed
832//since this operation is somewhat tangled with the Patch Panel, keep all of the
833//globals in the Patch subfolder (make sure both panels are simultaneously initialized)
834//do not create a separate Trans folder
835//
836Proc InitializeTransPanel()
837        //create the global variables needed to run the Trans Panel
838        //all are kept in root:myGlobals:TransHeaderInfo
839        If( ! (DataFolderExists("root:myGlobals:TransHeaderInfo"))  )
840                //create the data folder and the clobals for BOTH the Patch and Trans Panels
841                NewDataFolder/O root:myGlobals:TransHeaderInfo
842                CreateTransGlobals()
843        Endif
844End
845
846
847//
848Proc CreateTransGlobals()
849
850        PathInfo catPathName
851        If(V_flag==1)
852                String dum = S_path
853                String/G root:myGlobals:TransHeaderInfo:gCatPathStr = dum
854        else
855                String/G root:myGlobals:TransHeaderInfo:gCatPathStr = "no path selected"
856        endif
857
858        String/G root:myGlobals:TransHeaderInfo:gEMP = "no file selected"
859        String/G root:myGlobals:TransHeaderInfo:gBox = ""
860        Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
861        Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Filenames"
862        Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:T_Labels"
863        Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_SDD"
864        Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Lambda"
865        //      Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Transmission"
866        //      Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:T_Whole"
867       
868        Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Filenames"
869        Make/O/T/N=0 $"root:myGlobals:TransHeaderInfo:S_Labels"
870        Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_SDD"
871        Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Lambda"
872        Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Transmission"
873        Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:S_Whole"
874       
875        Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:EMP_x1"
876        Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:EMP_x2"
877        Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:EMP_y1"
878        Make/O/D/N=0 $"root:myGlobals:TransHeaderInfo:EMP_y2"
879End
880
881//given a selection of scattering files, calculates the transmission
882//and writes the new transmission to the file header
883//
884//given the full path;name;vers  (= filenmame), of a raw binary SANS file,
885//the transmission of the sample is calculated (if possible) from information
886//in the file header. empty beam and sample transmision run numbers are extracted
887//and the files are located from the run number (if possible)
888//from the header of the empty beam file, the XY box coordinates and "empty"
889//counts are determined
890//once all information is located, the transmission is calculated and the
891//transmission field of the sample file is automatically "Patched"
892// - updates the global variable that is displayed in the panel
893//can be run in batch mode, sequentially passing each item from a list of filenames
894//this is the single step of the batch mode
895//
896//in batch mode: execution will proceed through all of the files, reporting
897//results to the history window. If no trans could be successfully calculated
898//(for a blocked beam, for example), then that is displayed as well, and the
899//raw data is not modified
900//
901// now takes the attenuation of the sample trans and empty beam trans into account, (normally this == 1)
902// and rescales the transmission as appropriate
903// 3/31/04  SRK
904//
905Function CalcSelTransFromHeader(startRow,endRow)
906        Variable startRow,endRow
907        //      GetSelection table,ScatterFileTable,1
908
909        String S_Filename, T_Filename, EMP_Filename
910       
911        Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
912        Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
913        Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
914
915        Wave   S_Transmission = $"root:myGlobals:TransHeaderInfo:S_Transmission"
916       
917        Variable/G $"root:Packages:quokka:IgnoreTrans"
918        NVAR IgnoreTrans = $"root:Packages:quokka:IgnoreTrans"
919       
920        Variable num_s_files, num_t_files, ii, jj
921        Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
922        Variable x1,x2,y1,y2,err,attenEmp,attenSam
923        String suffix = "",pathName,textStr,abortStr,samFileStr
924        String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
925               
926        num_t_files = numpnts(T_Filenames)
927       
928        PathInfo catPathName
929        pathname = S_path
930
931        // [davidm] restructured the following code
932        for (ii = startRow; ii<=endRow; ii += 1)
933       
934                S_Filename              = pathname + S_Filenames[ii]
935                T_Filename              = pathname + T_Filenames[ii]
936                EMP_Filename    = pathname + EMP_Filenames[ii]
937               
938                // check S-file
939                if ((cmpstr(S_Filenames[ii],"") == 0) || !CheckIfFileExists(S_Filename))
940                        Print "Scattering beam file not assigned properly in line", ii+1
941                       
942                // check T-file
943                elseif ((cmpstr(T_Filenames[ii],"") == 0) || !CheckIfFileExists(T_Filename))
944                        Print "Transmission beam file not assigned properly for", S_Filenames[ii]
945                       
946                // check EMP-file
947                elseif ((cmpstr(EMP_Filenames[ii],"") == 0) || !CheckIfFileExists(EMP_Filename))
948                        Print "Empty beam file not assigned properly for", S_Filenames[ii]
949
950                // proceed
951                else
952                        // check the empty beam file for previously selected coordinates
953                        //if they exist, set the xy string , save the normalized counts somewhere
954                        GetXYBoxFromFile(EMP_Filename,x1,x2,y1,y2)
955                                               
956                        //read the real count value
957                        //emptyCts = getBoxCounts(emptyFile)
958                        //if(emptyCts < 1) //box counts hasn't been patched to file
959                        ReadHeaderAndData(EMP_Filename)
960                        IgnoreTrans = 1 // to prevent the warning message: ***transmission is ZERO***
961                        err = Raw_to_work("SAM")
962                        IgnoreTrans = 0
963                        emptyCts =  SumCountsInBox(x1,x2,y1,y2,"SAM")
964                        //nha debug
965                        //textStr = "Box counts for " +  emptyFile + "  " + num2str(emptyCts)
966                        //print textStr
967                        //endif
968
969                        // read the attenuator number of the empty beam file
970                        attenEmp = getAttenNumber(EMP_Filename)
971                        //
972                        if( ((x1-x2)==0) || ((y1-y2)==0) )              //zero width marquee in either direction
973                                //no region selected    -- prompt user to select box w/marquee
974                                DoWindow/F ScatterFileTable
975                                Abort "Use \"Set EMP File\", then \"SetXYBox\" to select XY range in empty beam file "+EMP_Filenames[ii]
976                                //from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
977                        Endif
978               
979                        //read in trans file
980                        ReadHeaderAndData(T_Filename)
981                        //adds to SAM
982                        IgnoreTrans = 1 // to prevent the warning message: ***transmission is ZERO***
983                        err = Raw_to_work("SAM")
984                        IgnoreTrans = 0
985                        //sum region in SAM
986                        transCts =  SumCountsInBox(x1,x2,y1,y2,"SAM")   
987                        // get the attenuator, lambda, and sample string (to get the instrument)
988                        //                              WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
989                        WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
990                        //                              samfileStr = samText[3]
991                        lambda = samReals[26]
992                        attenSam = samReals[3]
993                        //nha debug
994                        //variable attenSamFromFile
995                        //attenSamFromFile = getAttenNumber(transFile)
996                        //textStr = num2str(attenSam) + "  "+ num2str(attenSamFromFile)
997                        //print textStr
998                        //calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
999                        AttenRatio = AttenuationFactor("",lambda,attenEmp)/AttenuationFactor("",lambda,attenSam)
1000                        //calculate trans based on empty beam value and rescale by attenuation ratio
1001                        trans= transCts/emptyCts * AttenRatio
1002                                               
1003                        //write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
1004                        If(attenRatio==1)
1005                                Printf "%s\t\tTrans Counts = %g\tTrans = %g\r",S_Filenames[ii], transCts,trans
1006                        else
1007                                Printf "%s\t\tTrans Counts = %g\tTrans = %g\tAttenuatorRatio = %g\r",S_Filenames[ii], transCts,trans,attenRatio
1008                        endif
1009                        //write the trans to the file header of the raw data (open/close done in function)
1010                        WriteTransmissionToHeader(S_Filename,trans)
1011       
1012                        // after patching, the file needs to be removed from the DataFolder
1013                        // so that it will be reloaded if it is needed again [davidm]
1014                        string partialName = S_Filenames[ii]
1015                        variable index = strsearch(partialName, ".", 0)
1016                        if (index != -1)
1017                                partialName = partialName[0,index-1]
1018                        endif
1019                        KillDataFolder/Z $"root:Packages:quokka:"+partialName
1020               
1021                        //then update the global that is displayed
1022                        S_Transmission[ii] = trans
1023                endif
1024        endfor
1025       
1026        print "done"
1027        return 0
1028End
1029
1030//
1031// For the calculation of the Transmission using only the Trans Files screen
1032// Uses only the information on the transmissionFiles screen to calculate
1033// a "box" Transmission for comparison with the Whole Transmission
1034// updated 5/11/2006 by Bryan Greenwald
1035Function CalcTotalTrans(startRow,endRow)
1036        Variable startRow,endRow
1037        //      GetSelection table,ScatterFileTable,1
1038
1039        String filename
1040        Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
1041        Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
1042        //      Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
1043       
1044        Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1045        //      Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1046        //      Wave S_GTransmission =  $"root:myGlobals:TransHeaderInfo:S_Transmission"
1047        //      Wave GWhole= $"root:myGlobals:TransHeaderInfo:T_Whole"
1048       
1049        Variable num_t_files, ii, jj
1050        Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
1051        Variable x1,x2,y1,y2,err,attenEmp,attenSam
1052        String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
1053        String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
1054        String strToExecute
1055       
1056        //      num_t_files = numpnts(T_Filenames)
1057       
1058        PathInfo catPathName
1059        pathname = S_path
1060
1061        ii= startRow
1062        do
1063                if (cmpstr(T_Filenames[ii],"")!=0)      //if there is a sample trans file assigned
1064                        if (cmpstr(EMP_Filenames[ii],"")!=0)            //if empty beam file assigned, proceed with the calculation
1065
1066                                //full path+name to access all 3 files
1067                                filename=pathname+S_Filenames[ii]
1068                                emptyFile = pathname+ EMP_Filenames[ii]
1069                                transFile = pathname+T_Filenames[ii]
1070                                //////////
1071                                // check the empty beam file for previously selected coordinates
1072                                //if they exist, set the xy string , save the normalized counts somewhere
1073                                //the value was written to an unused r*4 header analysis.factor (@b494)
1074                                getXYBoxFromFile(emptyFile,x1,x2,y1,y2)
1075                                               
1076                                //read the real count value
1077                                emptyCts = getBoxCounts(emptyFile)
1078                                // read the attenuator number of the empty beam file
1079                                attenEmp = getAttenNumber(emptyFile)
1080                                //
1081                                if( ((x1-x2)==0) || ((y1-y2)==0) )              //zero width marquee in either direction
1082                                        //no region selected    -- prompt user to select box w/marquee
1083                                        DoWindow/F TransFileTable
1084                                        Abort "Use \"Set EMP File\", then \"SetXYBox\" to select XY range in empty beam file "+EMP_Filenames[ii]
1085                                        //from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
1086                                Endif
1087               
1088                                //read in trans file then add to SAM
1089                                ReadHeaderAndData(transFile)
1090                                //adds to SAM
1091                                err = Raw_to_work("SAM")
1092                                //sum region in SAM
1093                                transCts =  SumCountsInBox(x1,x2,y1,y2,"SAM")   
1094                                // get the attenuator, lambda, and sample string (to get the instrument)
1095                                WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
1096                                WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
1097                                samfileStr = samText[3]
1098                                lambda = samReals[26]
1099                                attenSam = samReals[3]
1100                                //calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
1101                                AttenRatio = AttenuationFactor("",lambda,attenEmp)/AttenuationFactor("",lambda,attenSam)
1102                                //calculate trans based on empty beam value and rescale by attenuation ratio
1103                                trans= transCts/emptyCts * AttenRatio
1104                                               
1105                                //write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
1106                                If(attenRatio==1)
1107                                        //Printf "%s\t\tTrans Counts = %g\t Actual Trans = %g\r",T_GFilenames[ii], transCts,trans
1108                                        Printf "%s\t\tBox Counts = %g\t Trans = %g\r",T_Filenames[ii], transCts,trans
1109                                else
1110                                        //Printf "%s\t\tTrans Counts = %g\t Trans = %g\tAttenuatorRatio = %g\r",T_GFilenames[ii], transCts,trans,attenRatio
1111                                        Printf "%s\t\tBox Counts = %g\t Trans = %g\t AttenuatorRatio = %g\r",T_Filenames[ii], transCts,trans,attenRatio
1112                                endif
1113                                //write the trans to the file header of the raw data (open/close done in function)
1114                                WriteTransmissionToHeader(filename,trans)               //transmission start byte is 158
1115                               
1116                                // after patching, the file needs to be removed from the DataFolder
1117                                // so that it will be reloaded if it is needed again [davidm]
1118                                string partialName = S_Filenames[ii]
1119                                variable index = strsearch(partialName, ".", 0)
1120                                if (index != -1)
1121                                        partialName = partialName[0,index-1]
1122                                endif
1123                                KillDataFolder/Z $"root:Packages:quokka:"+partialName
1124                               
1125                                //then update the global that is displayed
1126                                //                                              T_GTransmission[ii] = trans
1127                                               
1128                        else  // There is no empty assigned
1129                                abortStr = "Empty beam file not assigned properly for " + S_Filenames[jj]
1130                                Print abortStr
1131                                //Abort abortStr
1132                                return(1)
1133                        endif
1134                else //no transmission file
1135                        abortStr = "Transmission beam file not assigned properly for " + S_Filenames[ii]
1136                        Print abortStr
1137                endif
1138                ii+=1
1139        while(ii<=endRow)
1140        //print "done"
1141        return(0)
1142End
1143
1144//
1145// For the calculation of the Transmission using only the whole detector
1146// Used to compute the transmission for the TransmissionFiles table using
1147// the entire detector. For comparison with the "box" trans
1148// updated: 5/11/2006 by Bryan Greenwald
1149Function CalcWholeTrans(startRow,endRow)
1150        Variable startRow,endRow
1151        //      GetSelection table,ScatterFileTable,1
1152
1153        NVAR pixelsX = root:myGlobals:gNPixelsX
1154        NVAR pixelsY = root:myGlobals:gNPixelsY
1155       
1156        String filename
1157        Wave/T EMP_Filenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
1158       
1159        Wave/T T_Filenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
1160        //      Wave T_GTransmission = $"root:myGlobals:TransHeaderInfo:T_Transmission"
1161       
1162        Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1163        //      Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1164        Wave S_Transmission =  $"root:myGlobals:TransHeaderInfo:S_Transmission"
1165        Wave S_Whole= $"root:myGlobals:TransHeaderInfo:S_Whole"
1166       
1167        Variable num_t_files, ii, jj
1168        Variable refnum, transCts, emptyCts,attenRatio,lambda,trans
1169        Variable x1,x2,y1,y2,err,attenEmp,attenSam
1170        String suffix = "",pathName,textStr,abortStr,emptyFile,transFile,samFileStr
1171        String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
1172        String strToExecute
1173       
1174        //      num_t_files = numpnts(T_GFilenames)
1175       
1176        PathInfo catPathName
1177        pathname = S_path
1178
1179        ii= startRow
1180        do
1181                if (cmpstr(T_Filenames[ii],"")!=0)      //if there is a sample trans file assigned
1182                        if (cmpstr(EMP_Filenames[ii],"")!=0)            //if empty beam file assigned, proceed with the calculation
1183                                //full path+name to access all 3 files
1184                                filename=pathname+ S_Filenames[ii]
1185                                emptyFile = pathname+EMP_Filenames[ii]
1186                                transFile = pathname+T_Filenames[ii]
1187                                //////////
1188                                // check the empty beam file for previously selected coordinates
1189                                //if they exist, set the xy string , save the normalized counts somewhere
1190                                //the value was written to an unused r*4 header analysis.factor (@b494)
1191                                               
1192                                getXYBoxFromFile(emptyFile,x1,x2,y1,y2)
1193                                //read the real count value
1194                                emptyCts = getBoxCounts(emptyFile)
1195                                // read the attenuator number of the empty beam file
1196                                attenEmp = getAttenNumber(emptyFile)
1197                                //
1198                                if( ((x1-x2)==0) || ((y1-y2)==0) )              //zero width marquee in either direction
1199                                        //no region selected    -- prompt user to select box w/marquee
1200                                        DoWindow/F TransFileTable
1201                                        Abort "Use \"Set EMP File\", then \"SetXYBox\" to select XY range in empty beam file "+EMP_Filenames[ii]
1202                                        //from here the Marquee menu selection must handle the task of setting the box and updating the information in the file header
1203                                Endif
1204               
1205                                //read in trans file then add to SAM
1206                                ReadHeaderAndData(transFile)
1207                                //adds to SAM
1208                                err = Raw_to_work("SAM")
1209                                //sum region in SAM
1210                                transCts =  SumCountsInBox(0,pixelsX-1,0,pixelsY-1,"SAM")       
1211                                // get the attenuator, lambda, and sample string (to get the instrument)
1212                                WAVE/T samText = $"root:Packages:NIST:SAM:textRead"
1213                                WAVE samReals = $"root:Packages:NIST:SAM:realsRead"
1214                                samfileStr = samText[3]
1215                                lambda = samReals[26]
1216                                attenSam = samReals[3]
1217                                //calculate the ratio of attenuation factors - assumes that same instrument used for each, AND same lambda
1218                                AttenRatio = AttenuationFactor("",lambda,attenEmp)/AttenuationFactor("",lambda,attenSam)
1219                                //calculate trans based on empty beam value and rescale by attenuation ratio
1220                                trans= transCts/emptyCts * AttenRatio
1221                                               
1222                                //write out counts and transmission to history window, showing the attenuator ratio, if it is not unity
1223                                If(attenRatio==1)
1224                                        //Printf "%s\t\tTrans Counts = %g\tTrans using whole detector = %g\t Tbox/Twhole = %g\r",T_GFilenames[ii], transCts,trans,T_GTransmission[ii]/trans
1225                                        Printf "%s\t\tTotal Counts = %g\t Trans using whole detector = %g\t",T_Filenames[ii], transCts,trans
1226                                else
1227                                        //Printf "%s\t\tTrans Counts = %g\tTrans = %g\tAttenuatorRatio = %g, Tbox/Twhole = %g\r",T_GFilenames[ii], transCts,trans,attenRatio, T_GTransmission[ii]/trans
1228                                        Printf "%s\t\tTotal Counts = %g\t Trans using whole detector = %g\t AttenuatorRatio = %g",T_Filenames[ii], transCts,trans,attenRatio
1229                                endif
1230                                If(S_Transmission[ii]/trans > 0.97)
1231                                        printf " Tbox/Twhole = %g\r",S_Transmission[ii]/trans
1232                                else
1233                                        printf " !!! Tbox/Twhole is low !!! = %g\r",S_Transmission[ii]/trans
1234                                endif
1235                                //write the trans to the file header of the raw data (open/close done in function)
1236                                WriteWholeTransToHeader(filename,trans)
1237                                               
1238                                //then update the global that is displayed
1239                                S_Whole[ii] = trans
1240                                               
1241                        else  // There is no empty assigned
1242                                abortStr = "Empty beam file not assigned properly for " + S_Filenames[ii]
1243                                Print abortStr
1244                                //Abort abortStr
1245                                return(1)
1246                        endif
1247               
1248                else //no transmission file
1249                        abortStr = "Transmission beam file not assigned properly for " + S_Filenames[ii]
1250                        Print abortStr
1251                endif
1252                ii+=1
1253        while(ii<=endRow)
1254        print "done"
1255        return(0)
1256End
1257
1258Function PickEMPTransButton(ctrlName) : ButtonControl
1259        String ctrlName
1260       
1261        Variable ScatFileTableExists
1262        ScatFileTableExists = WinType("ScatterFileTable")
1263        //??BUG?? V_flag returns 1 even if no selection?
1264        //check manually for null selection
1265        //Print "local v_flag = ",num2str(V_flag)
1266        Wave/T LocFilenames = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
1267        if (ScatFileTableExists != 0)
1268                String/G root:myGlobals:TransHeaderInfo:gEMP = ""
1269                GetSelection table,ScatterFileTable,7
1270                //Print S_Selection
1271                if(strsearch(S_selection,"EMP_Filenames",0) == 0)
1272                        //selection OK, add to list
1273                        Duplicate/O/R=[V_startRow,V_endRow] LocFilenames, filenames
1274                        Wave/T selectedFiles = $"filenames"
1275
1276                        SVAR temp = root:myGlobals:TransHeaderInfo:gEMP
1277                        //
1278                        temp = temp+selectedFiles[0]            //take just the first file
1279                        UpdateBoxCoordinates()
1280                Else
1281                        DoWindow/F ScatterFileTable
1282                        DoAlert 0,"Invalid selection from the Scattering file table. You must select a file from the EMP_Filenames column"
1283                Endif
1284        else
1285                //no selection
1286                DoAlert 0,"No file selected from Scattering file table or no Scattering file table available"
1287        Endif
1288End
1289
1290
1291//window recreation macro for the Trans Panel
1292//
1293Proc Trans_Panel()
1294        PauseUpdate; Silent 1           // building window...
1295        NewPanel /W=(173,197,540,424)/K=1 as "Calculate Transmissions"
1296        DoWindow/C Trans_Panel
1297        ModifyPanel cbRGB=(49807,47186,38011)
1298        ModifyPanel fixedSize=1
1299        SetDrawLayer UserBack
1300        DrawLine 0,56,368,56
1301        DrawLine 0,125,368,125
1302        Button pick_emp,pos={4,65},size={105,20},proc=PickEMPTransButton,title="set EMP file"
1303        Button pick_emp,help={"This button will set the file selected in the Transmission file table to be the empty beam file."}
1304        SetVariable empStr,pos={114,67},size={250,17},title="file:"
1305        SetVariable empStr,help={"Filename of the empty beam file(s) to be used in the transmission calculation"}
1306        SetVariable empStr,fSize=10
1307        SetVariable empStr,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gEMP
1308        Button Trn_button_1,pos={5,101},size={90,20},proc=Trn_SetXYBoxButton,title="Set XY Box"
1309        Button Trn_button_1,help={"Sets the XY box to sum over"}
1310        Button Trn_button_2,pos={174,139},size={110,20},proc=Trn_SortFilesByDate,title="Sort by Date"
1311        Button Trn_button_2,help={"Sort the scattering and transmission files by creation date."}
1312        Button Trn_button_3,pos={174,169},size={110,20},proc=Trn_SortFilesByLabel,title="Sort by Label"
1313        Button Trn_button_3,help={"Sort the scattering and transmission files by label."}
1314        Button Trn_button_4,pos={295,139},size={67,20},proc=Trn_ShowHelpProc,title="Help"
1315        Button Trn_button_4,help={"Show a help notebook for calculating transmissions."}
1316        SetVariable Trn_setvar_1,pos={135,100},size={227,17},title="Box is "
1317        SetVariable Trn_setvar_1,help={"Box coordinates to sum over"},fSize=10
1318        SetVariable Trn_setvar_1,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gBox
1319        Button Trn_button_0,pos={1,1},size={70,20},proc=Trn_PickPathButton,title="Pick Path"
1320        Button Trn_button_0,help={"Select the folder containing the SANS data files"}
1321        Button Trn_button_9,pos={335,1},size={25,20},proc=ShowTransHelp,title="?"
1322        Button Trn_button_9,help={"Show the help file for calculating sample transmissions"}
1323        SetVariable Trn_setvar_0,pos={80,4},size={250,17},title="Path"
1324        SetVariable Trn_setvar_0,help={"Currently selected data path"},fSize=10
1325        SetVariable Trn_setvar_0,limits={-Inf,Inf,0},value= root:myGlobals:TransHeaderInfo:gCatPathStr
1326        Button Trn_button_5,pos={5,169},size={161,20},proc=Trn_CalcAllFilesButton,title="Calculate All Files"
1327        Button Trn_button_5,help={"Calculate transmission and patch headers of ALL files in the Scattering File Table."}
1328        Button Trn_button_6,pos={295,198},size={67,20},proc=Trn_PanelDoneButtonProc,title="Done"
1329        Button Trn_button_6,help={"Close the panel when done calculating transmissions"}
1330       
1331        Button Trn_button_7,pos={67,32},size={114,20},proc=Trn_RefreshProc,title="List Files"
1332        Button Trn_button_7,help={"Generate or refresh the tables of files."}
1333       
1334        Button Trn_button_7b, pos={67+114+5,32},size={114,20},proc=Trn_AutoCompleteProc,title="Auto Complete"
1335        Button Trn_button_7b, help={"???"}
1336       
1337        Button Trn_button_8,pos={5,139},size={161,20},proc=Trn_CalcSelectedFilesButton,title="Calculate Selected Files"
1338        Button Trn_button_8,help={"Calculate transmission and patch headers of selected files in the Scattering File Table."}
1339        Button Trn_button_10,pos={5,198}, size={161,20},proc=TotalTransButtonProc
1340        Button Trn_button_10 title="Calculate Total Trans"
1341        Button Trn_button_10 help={"Calculate transmission over the whole detector and patch headers of ALL files in the data folder."}
1342EndMacro
1343
1344
1345Function TotalTransButtonProc(ctrlName) : ButtonControl
1346        String ctrlName
1347        TotalTrans(ctrlName)
1348End
1349
1350
1351Proc ShowTransHelp(ctrlName) : ButtonControl
1352        String ctrlName
1353        DisplayHelpTopic/K=1 "SANS Data Reduction Tutorial[Calculate Transmissions]"
1354        if(V_flag !=0)
1355                DoAlert 0,"The SANS Data Reduction Tutorial Help file could not be found"
1356        endif
1357End
1358
1359
1360//generates the file tables of scattering files and transmission files
1361//
1362// if the tables already exist, they will be updated
1363//
1364Proc Trn_RefreshProc(ctrlName) : ButtonControl
1365        String ctrlName
1366        BuildFileTables()
1367End
1368
1369Function Example2()
1370        String browserCmd,cmd1,cmd2,promptStr
1371
1372        cmd1="Display %s"
1373        cmd2="AppendToGraph %s"
1374        promptStr="Select Waves for Graph"
1375        sprintf browserCmd, "CreateBrowser prompt=\"%s\", executeMode=2, command1=\"%s\", command2=\"%s\"",promptStr,cmd1,cmd2
1376        Execute browserCmd
1377End
1378
1379//improves the file tables of scattering files and transmission files
1380Function Trn_AutoCompleteProc(ctrlName) : ButtonControl
1381        String ctrlName
1382
1383        Variable i, in
1384        Variable j, jn
1385        Variable row
1386       
1387        Wave/T S_Filenames              = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1388        Wave/T T_Filenames              = $"root:myGlobals:TransHeaderInfo:T_Filenames"
1389        Wave/T EMP_Filenames    = $"root:myGlobals:TransHeaderInfo:EMP_Filenames"
1390        Wave/T S_Labels                 = $"root:myGlobals:TransHeaderInfo:S_Labels"
1391
1392        String Pathname, S_Filename, T_Filename, EMP_Filename, S_Label
1393        String safeLabel
1394       
1395        String dicValidRows             = "" // [safeLabel] -> [[row1],[row2],...]
1396        String dicCandidates            = "" // [safeLabel] -> [[row1],[row2],...]      // candidates to be auto completed
1397       
1398        String validRows                // [[row1],[row2],...]
1399        String candidateRows    // [[row1],[row2],...]
1400       
1401        String title, message, selection
1402
1403//      String selection
1404//      Prompt selection, "titleStr", popup, "hallo\tTest;nein\tJa;danke"
1405//      DoPrompt "hello", selection
1406
1407        PathInfo catPathName
1408        Pathname = S_path
1409       
1410        // check if ScatterFileTable exists
1411        if (WinType("ScatterFileTable") == 2)
1412
1413                //
1414                // first step: find valid rows and find rows which potentially could be auto fixed
1415                //
1416               
1417                in = DimSize(S_Filenames, 0)
1418                for (i = 0; i < in; i += 1)
1419                        S_Filename              = Pathname + S_Filenames[i]
1420                        T_Filename              = Pathname + T_Filenames[i]
1421                        EMP_Filename    = Pathname + EMP_Filenames[i]
1422                        S_Label                 = S_Labels[i]
1423
1424                        // check S-file
1425                        if ((strlen(S_Filenames[i]) != 0) && CheckIfFileExists(S_Filename) && (strlen(S_Label) != 0))
1426                       
1427                                // make sure that label doesn't interfere with list and dictionary symbols
1428                                safeLabel = S_Label
1429                                safeLabel = ReplaceString("\\", safeLabel, "\\1") // ReplaceString("\", safeLabel, "\1")
1430                                safeLabel = ReplaceString(":",  safeLabel, "\\2")
1431                                safeLabel = ReplaceString(";",  safeLabel, "\\3")
1432                               
1433                                // check T-file and EMP-file
1434                                if ((strlen(T_Filenames[i]) != 0) && CheckIfFileExists(T_Filename) && (strlen(EMP_Filenames[i]) != 0) && CheckIfFileExists(EMP_Filename))
1435                                        // check if sample is already marked as valid row
1436                                        if (-1 != strsearch(dicValidRows, safeLabel, 0))
1437                                                // add row-index
1438                                                validRows = StringByKey(safeLabel, dicValidRows)
1439                                                sprintf validRows, "%s, %g", validRows, i
1440                                        else
1441                                                // set first row-index
1442                                                sprintf validRows, "%g", i
1443                                        endif
1444                                        dicValidRows = ReplaceStringByKey(safeLabel, dicValidRows, validRows)
1445                                       
1446                                // S-file seemed fine but problems occurred with T- and EMP-file
1447                                else
1448                                        // check if sample is already marked as possible candidate
1449                                        if (-1 != strsearch(dicCandidates, safeLabel, 0))
1450                                                // add row-index
1451                                                candidateRows = StringByKey(safeLabel, dicCandidates)
1452                                                sprintf candidateRows, "%s, %g", candidateRows, i
1453                                        else
1454                                                // set first row-index
1455                                                sprintf candidateRows, "%g", i
1456                                        endif
1457                                        dicCandidates = ReplaceStringByKey(safeLabel, dicCandidates, candidateRows)
1458                                endif                   
1459                        endif
1460                endfor
1461               
1462                //
1463                // second step: fix invalid rows
1464                //
1465               
1466                jn = ItemsInList(dicCandidates)
1467                for (j = 0; j < jn; j += 1)
1468                        safeLabel = StringFromList(0, StringFromList(j, dicCandidates), ":")
1469
1470                        // check if invalid rows of current sample can be fixed
1471                        if (-1 != strsearch(dicValidRows, safeLabel, 0))
1472                                validRows               = StringByKey(safeLabel, dicValidRows)
1473                                candidateRows   = StringByKey(safeLabel, dicCandidates)
1474                               
1475                                // check if more than one row can be used to fix current candidates
1476                                if (-1 != strsearch(validRows, ",", 0))
1477                       
1478                                        sprintf message, "Select row you want to use to update all incomplete rows with that sample."
1479                                       
1480                                        // check if more than one row is afftected
1481                                        if (-1 != strsearch(candidateRows, ",", 0))
1482                                                sprintf title, "\"%s\" (Affected rows: %s)", S_Labels[str2num(StringFromList(0, validRows, ","))], candidateRows
1483                                        else
1484                                                sprintf title, " \"%s\" (Affected row: %s)", S_Labels[str2num(StringFromList(0, validRows, ","))], candidateRows
1485                                        endif
1486                                       
1487                                        selection = StringFromList(0, validRows, ",")
1488                                        Prompt selection, message, popup, ReplaceString(", ", validRows, ";")
1489                                        DoPrompt /HELP="" title, selection
1490                               
1491                                        // evaluate result
1492                                        switch (V_flag)
1493                                                case 0: // yes
1494                                                        row = str2num(selection)  // use selected row value
1495                                                        break
1496                                                       
1497                                                case 1: // cancel
1498                                                        row = -1 // skip
1499                                                        break
1500                               
1501                                                default:
1502                                                        return 0
1503                                        endswitch
1504                                else
1505                                        // only one row can be used to fix current candidates
1506                                        row = str2num(validRows)
1507                                       
1508                                        // check if more than one row is afftected
1509                                        if (-1 != strsearch(candidateRows, ",", 0))
1510                                                sprintf message, "The transmission value of \"%s\" can be determined with the information provided in row %g.\rWould you like to apply the information to all rows with that sample? (Affected rows: %s)", S_Labels[row], row, candidateRows
1511                                        else
1512                                                sprintf message, "The transmission value of \"%s\" can be determined with the information provided in row %g.\rWould you like to apply the information to all rows with that sample? (Affected row: %s)", S_Labels[row], row, candidateRows
1513                                        endif
1514                                        DoAlert 2, message
1515                                       
1516                                        // evaluate result
1517                                        switch (V_flag)
1518                                                case 1: // yes
1519                                                        break // use selected row value
1520                                                       
1521                                                case 2: // no
1522                                                        row = -1 // skip
1523                                                        break
1524                               
1525                                                default: // cancel
1526                                                        return 0
1527                                        endswitch
1528                                endif
1529                               
1530                                // fix current candidates if source row is specified
1531                                if (row != -1)
1532                                        // these are the values to be used to fix current candidates
1533                                        T_Filename              = T_Filenames[row]
1534                                        EMP_Filename    = EMP_Filenames[row]
1535               
1536                                        // fix all invalid rows of current sample
1537                                        in = ItemsInList(candidateRows, ",")
1538                                        for (i = 0; i < in; i += 1)
1539                                                row = str2num(StringFromList(i, candidateRows, ","))
1540                                                T_Filenames[row]                = T_Filename
1541                                                EMP_Filenames[row]      = EMP_Filename
1542                                        endfor
1543                                endif
1544                        endif
1545                       
1546                       
1547                                               
1548//                      // if dicValidRows contains row number for current sample, then transmission can be determined
1549//                      row = NumberByKey(safeLabel, dicValidRows) // if item is not in dicValidRows then row is set to NaN
1550//                      if (numtype(row) == 0) // check for normal number
1551//                              S_Label         = S_Labels[row]
1552//                              if (-1 != strsearch(rowSelection, ",", 0)) // check if more than one row is afftected
1553//                                      sprintf message, "The transmission value of \"%s\" can be determined with the information provided in row %g.\rWould you like to apply the information to all rows with that sample? (Affected rows: %s)", S_Label, row, rowSelection
1554//                              else
1555//                                      sprintf message, "The transmission value of \"%s\" can be determined with the information provided in row %g.\rWould you like to apply the information to all rows with that sample? (Affected row: %s)", S_Label, row, rowSelection
1556//                              endif
1557//                              DoAlert 2, message
1558//                             
1559//                              switch (V_flag)
1560//                                      case 1: // yes
1561//                                              T_Filename              = T_Filenames[row]
1562//                                              EMP_Filename    = EMP_Filenames[row]
1563//                                              // find sample and replace T- and EMP-Filename
1564//                                              for (i = 0; i < in; i += 1)
1565//                                                      // check S-file
1566//                                                      if ((strlen(S_Filenames[i]) != 0) && CheckIfFileExists(Pathname + S_Filenames[i]) && (cmpstr(S_Label, S_Labels[i]) == 0))
1567//                                                              T_Filenames[i]          = T_Filename
1568//                                                              EMP_Filenames[i]        = EMP_Filename
1569//                                                      endif
1570//                                              endfor
1571//                                              break
1572//                                             
1573//                                      case 3: // cancel
1574//                                              return 0
1575//                              endswitch
1576//                             
1577//                      // check if transmission of current sample could be determined
1578//                      elseif (-1 != strsearch(listUnclearSamples, safeLabel, 0))
1579//                              S_Label = safeLabel
1580//                              S_Label = ReplaceString("\\3",  S_Label, ";")
1581//                              S_Label = ReplaceString("\\2",  S_Label, ":")
1582//                              S_Label = ReplaceString("\\1",  S_Label, "\\")
1583//                              if (-1 != strsearch(rowSelection, ",", 0)) // check if more than one row is afftected
1584//                                      sprintf message, "The transmission value of \"%s\" can be determined with the information provided by multiple rows.\rPlease complete the report file manually for that sample. (Affected rows: %s)", S_Label, rowSelection
1585//                              else
1586//                                      sprintf message, "The transmission value of \"%s\" can be determined with the information provided by multiple rows.\rPlease complete the report file manually for that sample. (Affected row: %s)", S_Label, rowSelection
1587//                              endif
1588//                              DoAlert 0, message
1589//                             
1590//                             
1591//                              Example2()
1592//                      endif
1593                endfor
1594        else
1595                DoAlert 0,"No file selected from Scattering Files table or no Scattering Files table available"
1596        endif
1597End
1598
1599//shows a noteboox of help text describing how to calculate transmissions
1600// - better that the user read the igor or pdf file, but it's a victory to get
1601//users to read anything at all
1602//
1603Proc Trn_ShowHelpProc(ctrlName) : ButtonControl
1604        String ctrlName
1605        DisplayTransHelp()
1606End
1607
1608//sorts the tables by date
1609//
1610Proc Trn_SortFilesByDate(ctrlName) : ButtonControl
1611        String ctrlName
1612        SortGlobals(0)
1613End
1614
1615//sorts the tables alphabetically by the sample label field
1616//
1617Proc Trn_SortFilesByLabel(ctrlName) : ButtonControl
1618        String ctrlName
1619        SortGlobals(1)
1620End
1621
1622//button action procedure to select the local path to the
1623//folder containing the RAW SANS data files
1624// - once the data folder is selected, all of the popup file menus are
1625//forced to update with fresh file lists
1626//
1627Function Trn_PickPathButton(PathButton) : ButtonControl
1628        String PathButton
1629       
1630        //set the global string to the selected pathname
1631        Variable err
1632        err = PickPath()
1633        if(err)
1634                return(1)               //some problem with path or user cancelled, get out
1635        endif
1636       
1637        PathInfo/S catPathName
1638        String path = S_path
1639        if (V_flag == 0)
1640                //path does not exist - no folder selected
1641                String/G root:myGlobals:TransHeaderInfo:gCatPathStr = "no folder selected"
1642        else
1643                String/G root:myGlobals:TransHeaderInfo:gCatPathStr = path
1644        endif
1645       
1646        //Update the pathStr variable box
1647        ControlUpdate/W=Trans_Panel $"Trn_setvar_0"
1648        //Generate tables
1649        Execute "BuildFileTables()"
1650       
1651End
1652
1653//button action function that asks the user to set the XY box to sum over
1654//for all transmission calculations
1655//
1656// requires the user to set the box coordinates with the marquee popup
1657//that wil properly set the keyword string, and write the values to the empty beam header
1658//
1659Function Trn_SetXYBoxButton(ctrlName) : ButtonControl
1660        String ctrlName
1661
1662        String msgStr = "Select the Empty Beam File"
1663        String filename=""
1664       
1665        //get the filename from the popup menu
1666        //and construct a full path to it
1667        SVAR partialName = root:myGlobals:TransHeaderInfo:gEMP
1668        print partialName
1669        //get a valid file based on this partialName and catPathName
1670        String tempName = FindValidFilename(partialName)
1671        if(cmpstr(tempName,"")==0)
1672                //file not found, get out
1673                Abort "Empty beam file not found Trn_SetXYBoxButton(ctrlName)"
1674        Endif
1675        //name is ok, prepend path to tempName for read routine
1676        PathInfo catPathName
1677        filename = S_path + tempName
1678       
1679        //read the file in - check for previous coordinates
1680        ReadHeaderAndData(filename)
1681
1682        Wave realw=$"root:Packages:NIST:RAW:RealsRead"
1683        if (realw[26] == 0)
1684                DoAlert /T="Warning" 0, "Lambda for this file is zero! You might need to patch this file again before you continue to work with it."
1685        endif
1686               
1687        //data is displayed here (go through the normal display steps, so all is created properly
1688        String/G root:myGlobals:gDataDisplayType="RAW"
1689        fRawWindowHook()
1690       
1691        // check the empty beam file for previously selected coordinates
1692        //if they exist, set the xy string , save the normalized counts somewhere
1693        //the value was written to an unused r*4 header analysis.factor (@b494)
1694        Variable refnum,x1,x2,y1,y2,err
1695        getXYBoxFromFile(filename,x1,x2,y1,y2)
1696       
1697        //read the real count value, assign to a global
1698        Variable/G root:myGlobals:gTransCts = getBoxCounts(filename)                    //***NOTE this is NOT in the Trans sub-folder
1699        //
1700        if( ((x1-x2)==0) || ((y1-y2)==0) )              //zero width marquee in either direction
1701                //no region selected
1702               
1703                //add the empty beam file to work.SAM
1704                err = Raw_to_work("SAM")
1705       
1706                //the calling macro must change the display type
1707                String/G root:myGlobals:gDataDisplayType="SAM"          //displayed data type is sam
1708       
1709                //data is displayed here
1710                fRawWindowHook()
1711       
1712                //prompt user to select box w/marquee
1713                DoAlert 0,"(1) Select the region to sum with the Marquee.\n(2) Right click into the selected region.\n(3) Click on SetXYBoxCoords"
1714                // DoAlert 0,"Select the region to sum with the Marquee"
1715                       
1716                //from here the Marquee menu selection must handle the task of setting the box
1717                //and updating the information in the file header
1718        else
1719                // region already selected, just put up the values from the file header
1720                //allow user the option of overriding the current box region
1721                msgStr = "X1="+num2str(x1)+";"
1722                msgStr += "X2="+num2str(x2)+";"
1723                msgStr += "Y1="+num2str(y1)+";"
1724                msgStr += "Y2="+num2str(y2)+";"
1725                String textStr
1726                textStr = "Override current box  "+msgStr+" ?"
1727                DoAlert 1,textStr
1728                If((V_flag)==1)
1729                        //get new box coordinates, same procedure as above
1730                        //add the empty beam file to work.SAM
1731                        err = Raw_to_work("SAM")
1732       
1733                        //the calling macro must change the display type
1734                        String/G root:myGlobals:gDataDisplayType="SAM"          //displayed data type is sam
1735       
1736                        //data is displayed here
1737                        fRawWindowHook()
1738       
1739                        //prompt user to select box w/marquee
1740                        DoAlert 0,"(1) Select the region to sum with the Marquee.\n(2) Right click into the selected region.\n(3) Click on SetXYBoxCoords"
1741                        // DoAlert 0,"Select the region to sum with the Marquee"
1742       
1743                        //from here the Marquee menu selection must handle the task of setting the box
1744                        //and updating the information in the file header
1745                else
1746                        String/G root:myGlobals:TransHeaderInfo:gBox = msgStr
1747                Endif
1748        Endif
1749       
1750        UpdateBoxCoordinates()
1751        Return (0)
1752End
1753
1754
1755//button action function that assigns the selected empty beam file (run number only)
1756//and the sample trnansmissionfile (run number only) to the popup list of  sample scattering
1757//files (ALL of the list items). Assignment is done by writing the integer run numbers of
1758//trans files to the header of each of the  scattering files, in a batchwise processing
1759//of the popup list
1760//
1761//transmission are not calculated here - only the file numbers are set
1762//
1763//*********unused***********
1764//Function Trn_AssignAllFilesButton(ctrlName) : ButtonControl
1765//      String ctrlName
1766//
1767//      AssignTransFilesToData()
1768//             
1769//End
1770
1771//button action procedure to calculate the transmission of all of the sample files in the
1772//sample popup list, based on the information in EACH sample header and in the empty beam file
1773//the box must be set properly in the empty beam file, AND the empty and trans
1774//run number must also be set properly in EACH scattering file,
1775//If run numbers are not properly assigned, no trans is calculated and the
1776//header is not modified
1777//
1778//The RAW data header of EACH sample file IS modified, with the newly calculated transmission
1779//
1780//not very friendly, but forces users to assign the files before continuing
1781//
1782Function Trn_CalcAllFilesButton(ctrlName) : ButtonControl
1783        String ctrlName
1784
1785        //calculate the transmission and Patch the header (if possible)
1786        Wave/T S_Filenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
1787        Variable num_s_files = numpnts(S_Filenames)
1788        CalcSelTransFromHeader(0,num_s_files-1)
1789       
1790End
1791
1792//for selected scattering files in the scattering table,
1793// the "Annn" association of trans file is written to the data file,
1794// the the transmission is actually calculated
1795//
1796Function Trn_CalcSelectedFilesButton(ctrlName) : ButtonControl
1797        String ctrlName
1798 
1799        Variable scatterTableExists
1800        scatterTableExists = WinType("ScatterFileTable")
1801        if (scatterTableExists != 0)
1802                GetSelection table,ScatterFileTable,1
1803                if(V_Flag != 0)
1804                        //AssignSelTransFilesToData(V_StartRow,V_EndRow)
1805                        //calculate the transmission and Patch the header (if possible)
1806                        CalcSelTransFromHeader(V_StartRow,V_EndRow)
1807                Else
1808                        DoAlert 0,"No selection from Scattering Files table"
1809                Endif
1810        Else
1811                DoAlert 0,"No file selected from Scattering Files table or no Scattering Files table available"
1812        Endif
1813End
1814
1815//
1816// I am not sure what the difference is inthe function of CalcTotalTrans and CalcWholeTrans ?
1817// do they really do anything different?
1818// is it a useful calculation at all?
1819//
1820Function TotalTrans(ctrlName) : ButtonControl
1821        String ctrlName
1822 
1823        Variable scatTableExists
1824        scatTableExists = WinType("ScatterFileTable")
1825        if (scatTableExists != 0)
1826                GetSelection table,ScatterFileTable,1
1827                if(V_Flag != 0)
1828                        //AssignTotalTransFilesToData(V_StartRow,V_EndRow)
1829                        //calculate the transmission and Patch the header (if possible)
1830                        CalcTotalTrans(V_StartRow,V_EndRow)
1831                        CalcWholeTrans(V_StartRow,V_EndRow)
1832                Else
1833                        DoAlert 0,"No selection from Trans Files table"
1834                Endif
1835        Else
1836                DoAlert 0,"No file selected from Trans Files table or no Trans Files table available"
1837        Endif
1838End
1839
1840
1841//simple button procedure to close the trans panel
1842// - automatically kills the two tables as well
1843//
1844Function Trn_PanelDoneButtonProc(ctrlName) : ButtonControl
1845        String ctrlName
1846
1847        // this button will make sure all files are closed
1848        //and close the panel
1849       
1850        Close/A
1851        DoWindow/K Trans_Panel
1852        DoWindow/K ScatterFileTable
1853        DoWindow/K TransFileTable
1854End
1855
1856
1857//function to update the box coordinates of the file selected as the
1858//empty beam file - takes the file that is currently popped from the list
1859//reads the 4 "analysis" integers that hold the box coordinates
1860//resets the globals string that is displayed with the new values
1861//should be called whenever the "empty" popup is popped, to ensure
1862//that current header information is displayed
1863//
1864Function UpdateBoxCoordinates()
1865
1866        //construct a full name, and read in the label from the file
1867        //and set the global
1868        String textstr=""
1869        ControlInfo empStr
1870        SVAR item = root:myGlobals:TransHeaderInfo:gEMP
1871        String tempName = FindValidFilename(item)
1872        if(cmpstr(tempName,"")==0)
1873                //file not found, get out
1874                Abort "Empty beam file not found UpdateBoxCoordinates(ctrlName)"
1875        Endif
1876        //name is ok, prepend path to tempName for read routine
1877        PathInfo catPathName
1878        String filename = S_path + tempName
1879       
1880        Variable refnum,x1,x2,y1,y2,err
1881        GetXYBoxFromFile(filename,x1,x2,y1,y2)
1882               
1883        //and update the global string
1884        String msgStr=""
1885        msgStr = "X1="+num2str(x1)+";"
1886        msgStr += "X2="+num2str(x2)+";"
1887        msgStr += "Y1="+num2str(y1)+";"
1888        msgStr += "Y2="+num2str(y2)+";"
1889       
1890        String/G root:myGlobals:TransHeaderInfo:gBox = msgStr
1891       
1892        ControlUpdate/W=Trans_panel Trn_setvar_1
1893End
1894
1895//crude procedure to display a notebook of help information for users
1896//
1897Proc DisplayTransHelp()
1898        String nb = "Notebook0"
1899        NewNotebook/N=$nb/F=1/V=1/W=(342,302,868,674) as "Notebook0:Transmission Help"
1900        Notebook $nb defaultTab=36, statusWidth=238, pageMargins={36,72,36,72}
1901        Notebook $nb showRuler=1, rulerUnits=1, updating={1, 3600}
1902        Notebook $nb newRuler=Normal, justification=0, margins={0,0,468}, spacing={0,0,0}, tabs={}, rulerDefaults={"Geneva",10,0,(0,0,0)}
1903        Notebook $nb ruler=Normal; Notebook $nb  justification=1, fSize=14, fStyle=1, text="Transmission Help\r"
1904        Notebook $nb ruler=Normal, fSize=-1, fStyle=-1, text="\r"
1905        Notebook $nb text="This panel allows quick and easy calculation of sample transmission. The neutron transmission of a sampl"
1906        Notebook $nb text="e must be calculated and entered into the header of each sample scattering file before proper background"
1907        Notebook $nb text=" corrections or absolute scaling can be done.\r"
1908        Notebook $nb text="\r"
1909        Notebook $nb text="During data collection, you measured an empty beam  - that is a measurement with heavy attenuation of th"
1910        Notebook $nb text="e neutron beam and the beamstop mover out of line with the direct beam. Then without changing the attenu"
1911        Notebook $nb text="ation or replacing the beamstop, you put a sample in the beam, and repeated the measurement (a sample tr"
1912        Notebook $nb text="ansmission measurement). The neutron transmission of the sample is simply the ratio of the number of neu"
1913        Notebook $nb text="tron counts from the sample transmission measurement normalized by the number of neutron counts from the"
1914        Notebook $nb text=" empty beam measurement. In this way, each sample transmission file is \"linked\" to the same empty beam t"
1915        Notebook $nb text="ransmission file.\r"
1916        Notebook $nb text="\r"
1917        Notebook $nb text="This calculated transmission value must be entered into the header of the sample scattering measurement "
1918        Notebook $nb text="- that is the measurement of the sample with the beamstop covering the primary (transmitted) beam, and n"
1919        Notebook $nb text="o (or few) attenuators in place. In this way, the sample transmission file is \"linked\" to its correspond"
1920        Notebook $nb text="ing sample scattering file. This panel allows you to set up the links and calculate the transmission.Tra"
1921        Notebook $nb text="nsmisison values are automatically patched to the scattering file headers as they are calculated.\r"
1922        Notebook $nb text="\r"
1923        Notebook $nb text="To Calculate Transmissions:\r"
1924        Notebook $nb text="\r"
1925        Notebook $nb text="1) Click \"List Files\" to get two lists (tables) - one of all the sample scattering files in the folder, "
1926        Notebook $nb text="and one of the transmission files.\r"
1927        Notebook $nb text="\r"
1928        Notebook $nb text="2) Select the region of the detector to sum over from the empty beam transmission file. Do theis by clic"
1929        Notebook $nb text="king on the filename of the empty beam transmision file (from the TransmissionFiles window, in the blue "
1930        Notebook $nb text="\"T_Filenames\" column). Return to the panel, and click the \"set EMP file\" button\", and the filename shoul"
1931        Notebook $nb text="d appear in the file box. The \"Box is\" field should have zeros for the x and y coordinates. Click the \"S"
1932        Notebook $nb text="et XY Box\" button. The empty beam file will be displayed, and you will be instructed to select the regio"
1933        Notebook $nb text="n to sum with the marquee. On the data, click and drag a rectangle that encompasses the primary beam. Mo"
1934        Notebook $nb text="ve the cursor inside the selection, to get an \"upside-down hat\" cursor. Click to get a menu, and near th"
1935        Notebook $nb text="e bottom, select \"Set XY Box Coords\". The pixel values should be updated to the Transmission panel, and "
1936        Notebook $nb text="are written to the empty beam header for future calculations. Note that the marquee selection can also b"
1937        Notebook $nb text="e used to measure the beam center, or centroid of any selected region.\r"
1938        Notebook $nb text="\r"
1939        Notebook $nb text="3) Now you need to \"link\" the ", fStyle=2, text="sample", fStyle=-1, text=" transmission files to the "
1940        Notebook $nb fStyle=2, text="empty", fStyle=-1, text=" ", fStyle=2, text="beam", fStyle=-1
1941        Notebook $nb text=" transmission file. Do this in the TransmissionFiles window by selecting the filename (in the blue T_Fil"
1942        Notebook $nb text="enames column) and pasing it to the corresponding row(s) in the T_EMP_Filenames column. This links the e"
1943        Notebook $nb text="mpty beam transmission with the sample transmission file. Do this for every sample transmission file.\r"
1944        Notebook $nb text="\r"
1945        Notebook $nb text="4) Now you need to link the sample ", fStyle=2, text="transmission", fStyle=-1
1946        Notebook $nb text=" file to the sample ", fStyle=2, text="scattering", fStyle=-1
1947        Notebook $nb text=" file. Do this by selecting the name of the transmission file (from the blue T_Filenames column) and pas"
1948        Notebook $nb text="ting it into the corresponding row of the S_TRANS_Filenames column of the ScatteringFiles window. This l"
1949        Notebook $nb text="inks the scattering file to its corresponding sample transmission file. This for all of the sample scatt"
1950        Notebook $nb text="ering files.\r"
1951        Notebook $nb text="\r"
1952        Notebook $nb text="5) Calculate the transmissions (and automatically write the transmission value to the satterng file head"
1953        Notebook $nb text="er) by clicking \"Calculate All Files\" from the Transmission Panel. The results will be printed to the co"
1954        Notebook $nb text="mmand window at the bottom of the screen. Any improperly assigned files will be listed. For example, blo"
1955        Notebook $nb text="cked beam scattering files will return an error, since the transmssion known to be zero, and is not meas"
1956        Notebook $nb text="ured (and no files are \"linked\"). Rather than calculating the transmission of all of the files,  a range"
1957        Notebook $nb text=" of S_Filenames can be selected, then calculated by clicking \"Calculate Selected Files\".\r"
1958        Notebook $nb text="\r"
1959        Notebook $nb text="By default the lists are sorted by run number (= chronological). In some cases it may be easier to sort "
1960        Notebook $nb text="by the sample label to group several of the same sample scattering files collected at different sample-t"
1961        Notebook $nb text="o-detector distances. Its utility depends, of course, on how consistent and unique your sample labels ar"
1962        Notebook $nb text="e.\r"
1963        Notebook $nb text="\r"
1964        Notebook $nb text="The \"links\" are stored in the corresponding files, and wil be re-generated when the lists are re-generat"
1965        Notebook $nb text="ed. Unassigned links will appear as blank elements in the T_EMP_Filenames or S_TRANS_Filenames columns.\r"
1966        Notebook $nb text="\r"
1967        Notebook $nb, selection={startOfFile,startOfFile}
1968        Notebook $nb text="\r"
1969End
1970
1971
1972
1973//*******************
1974//************
1975//   A simple panel to allow users of the NG1 SANS instrument to make their
1976// transmission files "look" like a transmission measurement to the data reduction
1977// program. Transmission files are designated by an x-position of the beamstop of
1978// < -5 (cm). this simple procedure sets xpos=-10 for individual files. files
1979// con be "un-converted", which set the xpos=0.
1980// 1/30/01 SRK
1981//************
1982
1983Proc TransformToTransFile()
1984        Variable/G root:myGlobals:gConvTrans=1
1985        DoWindow/F Convert_to_Trans
1986        if(V_flag==0)
1987                Convert2Trans()
1988        endif
1989End
1990
1991//fname must be the full path and name for the file
1992Function ChangeBSXPos(fname,xpos)
1993        String fname
1994        Variable xpos
1995       
1996        Variable start
1997        //x-position starts after byte 368 in VAX files
1998        WriteBSXPosToHeader(fname,xpos)
1999        return(0)
2000End
2001
2002//sets the beamstop position to zero NOT the original position
2003Function UnConvertButtonProc(ctrlName) : ButtonControl
2004        String ctrlName
2005       
2006        //Print "UnConvert"
2007        String fullname=""
2008        ControlInfo fileNum
2009        Variable num = V_Value  //run number to find
2010       
2011        fullname = FindFileFromRunNumber(num)
2012        Print fullname
2013        //report error or change the file
2014        if(cmpstr(fullname,"")==0)
2015                Print "Unconvert - file not found"
2016        else
2017                //Print "Unconvert",fullname
2018                ChangeBSXPos(fullName,0)
2019        Endif
2020        return(0)
2021End
2022
2023//button procedure to do the conversion
2024// writes fake beamstop position to the data file
2025//
2026Function ConvertButtonProc(ctrlName) : ButtonControl
2027        String ctrlName
2028       
2029        String fullname=""
2030        ControlInfo fileNum
2031        Variable num = V_Value  //run number to find
2032       
2033        fullname = FindFileFromRunNumber(num)
2034        print fullname
2035        //report error or change the file
2036        if(cmpstr(fullname,"")==0)
2037                Print "Convert - file not found"
2038        else
2039                //Print "Convert",fullname
2040                ChangeBSXPos(fullName,-10)
2041        Endif
2042        return(0)
2043End
2044
2045//simple panel recreation macro
2046//
2047Proc Convert2Trans()
2048        PauseUpdate; Silent 1           // building window...
2049        NewPanel /W=(434,74,671,216) /K=1
2050        DoWindow/C Convert_to_Trans
2051        SetDrawLayer UserBack
2052        DrawText 18,22,"Convert files to be recognized"
2053        DrawText 43,39,"as transmission files"
2054        SetVariable fileNum,pos={43,58},size={130,15},title="File Number"
2055        SetVariable fileNum,limits={1,Inf,1},value=root:myGlobals:gConvTrans
2056        SetVariable fileNum,help={"Sets the run number of the file that is to be converted"}
2057        Button ConvButton,pos={73,79},size={80,20},proc=ConvertButtonProc,title="Convert"
2058        Button ConvButton,help={"Converts the chosen file to appear as a transmission file"}
2059        Button UndoButton,pos={68,105},size={90,20},proc=UnConvertButtonProc,title="Un-Convert"
2060        Button UndoButton,help={"Converts the chosen file to appear as a scattering file"}
2061EndMacro
2062
2063
2064/////
2065//  A quick way to fill all the T_EMP_Filenames with the selected empty beam file
2066// Note that you must go back and clear or reassign any files that are special cases
2067//
2068// IMPORTANT - this will overwrite any other file assignments (typically not a problem
2069// if you  are using only one wavelength)
2070//
2071/////
2072Function FillEMPFilenameWSelection()
2073
2074        GetSelection table,TransFileTable,3
2075        Variable row=V_startRow                 //ony need the selected row, we know the column names and location
2076        Wave/T fw = root:myGlobals:TransHeaderInfo:T_FileNames          //trans files
2077        Wave/T ew = root:myGlobals:TransHeaderInfo:T_EMP_FileNames              //empty beam reference files
2078       
2079        ew[] = fw[row]
2080       
2081        return(0)
2082End
2083
2084//given a selection of the SAMPLE files, try to find the corresponding transmission file
2085//
2086Function GuessTransFile(charsToUse,row)
2087        Variable charsToUse,row                 //number of characers to use from the beginning of the label, and the row of the sample file
2088       
2089        //      GetSelection table,ScatterFileTable,3
2090        //      Variable row=V_startRow                 //ony need the selected row, we know the column names and location
2091        Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels             //Sample file labels
2092        Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels             //trans file labels
2093        Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames        //trans file names
2094        Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames  //Scattering - trans correspondence
2095       
2096        Variable num,ii,found
2097        String samStr = "",testStr=""
2098       
2099        samStr = (sw[row])[0,charsToUse-1]              //string to try and match
2100        samStr += "*"
2101        //      Print samStr
2102        num=numpnts(tw)
2103        ii=0
2104        do
2105                testStr=tw[ii]
2106                found = stringmatch(testStr, samStr )
2107                if(found == 1)
2108                        Print "Match Found at:  ",samStr,tnam[ii],tw[ii]
2109                        snam[row] = tnam[ii]                    //write the file name into the table
2110                        return(0)       
2111                endif
2112                ii+=1
2113        while(ii<num)
2114       
2115        //method 2
2116        //      samStr = (sw[row])[0,charsToUse-1]              //string to try and match
2117        ////    Print samStr
2118        //      num=numpnts(tw)
2119        //      ii=0
2120        //      do
2121        //              testStr=tw[ii]
2122        //              found = strsearch(testStr,samStr,0)             //start from zero, Need Igor 5 to allow 4th parameter to ignore case
2123        //              if(found != -1)
2124        //                      Print "Match Found at:  ",samStr,tnam[ii],tw[ii]
2125        //                      snam[row] = tnam[ii]                    //write the file name into the table
2126        //                      return(0)       
2127        //              endif
2128        //              ii+=1
2129        //      while(ii<num)
2130       
2131        Print "No Match found"
2132        return(0)
2133End
2134
2135//given a single transmission file, try to find the corresponding scattering file(s)
2136//
2137// apply TWO criteria
2138// (1) the label must match "well enough"
2139// (2) the wavelength must be the same
2140//
2141// passes the matching rows in the sample table back
2142//
2143Function GuessTransToScattFiles(charsToUse,row,matchRows)
2144        Variable charsToUse,row                 //number of characers to use from the beginning of the label, and the row of the transmission file
2145        Wave matchRows          //rows where (potential) matches found. initially zero points
2146       
2147        Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels             //Sample file labels
2148        Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels             //trans file labels
2149        Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames        //trans file names
2150        Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames  //Scattering - trans correspondence
2151        Wave sLam = root:myGlobals:TransHeaderInfo:S_Lambda             //Scattering file wavelength
2152        Wave tLam = root:myGlobals:TransHeaderInfo:T_Lambda             //Transmission file wavelength
2153       
2154        Variable num,ii,found
2155        String transStr = "",testStr=""
2156       
2157        transStr = (tw[row])[0,charsToUse-1]            //string to try and match
2158        transStr += "*"
2159       
2160        //loop over ALL sample files
2161        num=numpnts(sw)
2162        ii=0
2163        do
2164                testStr=sw[ii]
2165                found = stringmatch(testStr, transStr )
2166                if( (found == 1) && (sLam[ii] == tLam[row]) )           // both must match
2167                        Print "Match Found at:  ",transStr,snam[ii],sw[ii]
2168                        InsertPoints numpnts(matchRows), 1, matchRows
2169                        matchRows[numpnts(matchRows)-1] = ii
2170                endif
2171                ii+=1
2172        while(ii<num)
2173       
2174        //method 2 *UNTESTED*
2175        //      transStr = (tw[row])[0,charsToUse-1]            //string to try and match
2176        //      num=numpnts(sw)
2177        //      ii=0
2178        //      do
2179        //              testStr=sw[ii]
2180        //              found = strsearch(testStr,transStr,0,2)         //start from zero, ignore case
2181        //              if(found != -1)
2182        //                      Print "Match Found at:  ",transStr,snam[ii],sw[ii]
2183        //                      InsertPoints numpnts(matchRows), 1, matchRows
2184        //                      matchRows[numpnts(matchRows)-1] = ii
2185        ////                    snam[ii] = tnam[row]                    //write the file name into the table
2186        //              endif
2187        //              ii+=1
2188        //      while(ii<num)
2189       
2190        //      Print "No Match found"
2191        return(0)
2192End
2193
2194//get a single selection from the Trans table
2195// find all of the matching scattering files (rows)
2196// ask the user if the selections are OK
2197// if NOT OK, do nothing
2198// if OK: make the assignments, and immediately calculate the transmission
2199//
2200Function fGuessTransToScattFiles(numChars)
2201        Variable numChars
2202       
2203        Variable ii,row
2204        Variable transTableExists
2205        Make/O/D/N=0 root:myGlobals:TransHeaderInfo:matchRows
2206        Wave matchRows=root:myGlobals:TransHeaderInfo:matchRows
2207       
2208        transTableExists = WinType("TransFileTable")
2209        if (transTableExists != 0)
2210                GetSelection table,transFileTable,1     
2211                row = V_startRow
2212                GuessTransToScattFiles(numChars,row,matchRows)
2213        else
2214                Print "Transmission->Scattering File table is not open"
2215                return (1)
2216        endif
2217       
2218        Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels             //Sample file labels
2219        Wave/T tw = root:myGlobals:TransHeaderInfo:T_Labels             //trans file labels
2220        Wave/T tnam = root:myGlobals:TransHeaderInfo:T_FileNames        //trans file names
2221        Wave/T snam = root:myGlobals:TransHeaderInfo:S_TRANS_FileNames  //Scattering - trans correspondence
2222        Wave/T samfile = root:myGlobals:TransHeaderInfo:S_FileNames     //Scattering file name
2223       
2224        // can do fancy formatted string with ...
2225        //"asdf* matches file: \\f01filen\\f00 \\K(52428,1,1)\\f01afdsfdd\\f00\\K(0,0,0)asdfasdfs"
2226        Variable num=numpnts(matchRows)
2227        String result="",tmpStr
2228        for(ii=0;ii<num;ii+=1)
2229                sprintf tmpStr,"\\f01\\K(52428,1,1)%s\\K(0,0,0)\\f00* Matches file: \\f01%s\\f00 | \\K(52428,1,1)\\f01%s\\f00\\K(0,0,0)%s\r",(tw[row])[0,numChars-1],samfile[matchRows[ii]],(sw[matchRows[ii]])[0,numchars-1],(sw[matchRows[ii]])[numchars,59]
2230                result += tmpStr
2231        endfor
2232       
2233        if(cmpstr(result,"")==0)
2234                result = "No match found for "+ (tw[row])[0,numChars-1]
2235        endif
2236       
2237        //      Print result
2238        Print "*******"
2239       
2240        String/G root:myGlobals:TransHeaderInfo:gResultStr = result
2241       
2242        DoWindow/F ConfirmGuess         //it really shouldn't exist...
2243        if(V_flag==1)
2244                TitleBox title0,pos={9,5},variable=root:myGlobals:TransHeaderInfo:gResultStr
2245        else
2246                NewPanel /W=(578,44,1263,214) as "Confirm Guess"
2247                DoWindow/C ConfirmGuess
2248                TitleBox title0,pos={9,5},size={501,32}
2249                TitleBox title0,variable= root:myGlobals:TransHeaderInfo:gResultStr
2250                Button button0,pos={9,107},size={190,20},proc=DoAssignTransButtonProc,title="Assign Transmission Files"
2251                Button button2,pos={341,108},size={90,20},proc=DoTryAgainButtonProc,title="Try Again"
2252                ToolsGrid snap=1,visible=1
2253        endif
2254       
2255        PauseForUser ConfirmGuess
2256
2257        // figure out from the return code what the user did...
2258        // 1 = OK, accept guess (assign, and calculate immediately)
2259        // 2 = try again
2260        // 0 = cancel, don't do anything (not used, simply try again)
2261        NVAR guessOK = root:myGlobals:TransHeaderInfo:GuessOK
2262       
2263        // switch here...
2264        switch(guessOK) // numeric switch
2265                case 1:         
2266                        // accept guess (assign, and calculate immediately)
2267                        for(ii=0;ii<num;ii+=1)
2268                                snam[matchRows[ii]] = tnam[row]
2269                                //AssignSelTransFilesToData(matchRows[ii],matchRows[ii])
2270                                CalcSelTransFromHeader(matchRows[ii],matchRows[ii])             //does only that sample file
2271                        endfor                 
2272                        break                                           
2273                case 2: //try again (with more / fewer characters?)     
2274                        //              does nothing right now
2275                        break
2276                case 0:
2277                        // do nothing
2278                        break
2279                default:                                                       
2280                        //      do nothing                                     
2281        endswitch
2282       
2283        return(0)
2284End
2285
2286// a hook attached to the Transmission Files Table
2287// given a single selected Trans File, popup gives choices
2288// to guess using "n" characters, then dispatch accordingly
2289Function GuessFromTableHook(infoStr)
2290        String infoStr
2291        String event= StringByKey("EVENT",infoStr)
2292        //      Print "EVENT= ",event
2293
2294        String menuStr=""
2295        menuStr += "Guess using 3 characters;"
2296        menuStr += "Guess using 6 characters;"
2297        menuStr += "Guess using 9 characters;"
2298        menuStr += "Guess using 12 characters;"
2299        menuStr += "Guess using 15 characters;"
2300        menuStr += "Guess using 18 characters;"
2301        menuStr += "Guess using 21 characters;"
2302        menuStr += "Guess using 24 characters;"
2303       
2304        strswitch(event)
2305                case "mousedown":
2306                        Variable xpix= NumberByKey("MOUSEX",infoStr)
2307                        Variable ypix= NumberByKey("MOUSEY",infoStr)
2308                        Variable modif= NumberByKey("MODIFIERS",infoStr)
2309                        //print modif
2310                        if(modif & 2^1)         //bit 1 set, shift key is down
2311                                PopupContextualMenu/C=(xpix, ypix) menuStr
2312                                strswitch(S_selection)
2313                                        case "Guess using 3 characters":
2314                                                fGuessTransToScattFiles(3)
2315                                                break
2316                                        case "Guess using 6 characters":
2317                                                fGuessTransToScattFiles(6)
2318                                                break
2319                                        case "Guess using 9 characters":
2320                                                fGuessTransToScattFiles(9)
2321                                                break
2322                                        case "Guess using 12 characters":
2323                                                fGuessTransToScattFiles(12)
2324                                                break
2325                                        case "Guess using 15 characters":
2326                                                fGuessTransToScattFiles(15)
2327                                                break
2328                                        case "Guess using 18 characters":
2329                                                fGuessTransToScattFiles(18)
2330                                                break
2331                                        case "Guess using 21 characters":
2332                                                fGuessTransToScattFiles(21)
2333                                                break
2334                                        case "Guess using 24 characters":
2335                                                fGuessTransToScattFiles(24)
2336                                                break
2337                                endswitch               //on selection
2338                        endif
2339        endswitch       // on event
2340       
2341        return 0
2342End
2343
2344// sets a flag if the user thinks that the guess was correct, and wants to use the
2345// identified files for the transmission
2346Function DoAssignTransButtonProc(ba) : ButtonControl
2347        STRUCT WMButtonAction &ba
2348
2349        switch( ba.eventCode )
2350                case 2: // mouse up
2351                        // click code here
2352                        //Print "Assigned stuff, and left."
2353                        Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 1
2354                        DoWindow/K ConfirmGuess
2355                        break
2356        endswitch
2357
2358
2359        return 0
2360End
2361
2362// files are wrong, let the user try it again
2363// sets a flag, nothing else
2364Function DoTryAgainButtonProc(ba) : ButtonControl
2365        STRUCT WMButtonAction &ba
2366
2367        switch( ba.eventCode )
2368                case 2: // mouse up
2369                        // click code here
2370                        Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 2
2371                        DoWindow/K ConfirmGuess
2372                        //Print "Try Again"
2373                        break
2374        endswitch
2375       
2376        return 0
2377End
2378
2379// not used
2380Function DoCancelGuessButtonProc(ba) : ButtonControl
2381        STRUCT WMButtonAction &ba
2382
2383        switch( ba.eventCode )
2384                case 2: // mouse up
2385                        // click code here
2386                        //just kill the panel, don't do anything
2387                        Variable/G root:myGlobals:TransHeaderInfo:GuessOK= 0
2388                        DoWindow/K ConfirmGuess
2389                        break
2390        endswitch
2391       
2392        return 0
2393End
2394
2395Function GuessAllTransFiles(numChars)
2396        Variable numChars
2397       
2398        if(WinType("ScatterFileTable") ==0 )
2399                return(1)
2400        endif
2401       
2402        Wave/T sw = root:myGlobals:TransHeaderInfo:S_Labels             //Sample file labels
2403        Variable ii,num=numpnts(sw)
2404       
2405        for(ii=0;ii<num;ii+=1)
2406                GuessTransFile(numChars,ii)
2407        endfor
2408       
2409        return(0)
2410End
2411
2412Function fGuessSelectedTransFiles(numChars)
2413        Variable numChars
2414       
2415        Variable ii
2416        Variable scatterTableExists
2417        scatterTableExists = WinType("ScatterFileTable")
2418        if (scatterTableExists != 0)
2419                GetSelection table,ScatterFileTable,1   
2420                for(ii=V_StartRow;ii<=V_EndRow;ii+=1)
2421                        GuessTransFile(numChars,ii)
2422                endfor
2423        else
2424                Print "Transmission->Scattering File table is not open"
2425        endif
2426        return(0)
2427End
2428
2429Function ClearSelectedAssignments()
2430       
2431        //      String winStr = WinList("*", ";", "WIN:" )              //returns the target window
2432        //      Variable scatterTableExists, transTableExists
2433        //      Print winStr
2434        //      scatterTableExists = cmpstr(winStr,"ScatterFileTable;")
2435        //      if (scatterTableExists == 0)
2436        //              GetSelection table,ScatterFileTable,1   
2437        //              fClearSelectedAssignments(V_startRow,V_endRow,1)
2438        //      endif
2439        //     
2440        //      transTableExists = cmpstr(winStr,"TransFileTable;")
2441        //      if (transTableExists == 0)
2442        //              GetSelection table,TransFileTable,1     
2443        //              fClearSelectedAssignments(V_startRow,V_endRow,2)
2444        //      endif
2445       
2446        //      return(0)
2447End
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