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reduceData (1 call, 441.366 sec)
Generated 05-Aug-2011 13:01:02 using cpu time.
function in file /home/LeechJ/cbass_analysis/reduc/reduceData.m
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Parents (calling functions)
No parent Lines where the most time was spent
| Line Number | Code | Calls | Total Time | % Time | Time Plot |
| 259 | overfWrapper(d, plotparams, pa... | 1 | 233.050 s | 52.8% |  |
| 230 | d = mainsWrapper(d, plotparams... | 1 | 47.524 s | 10.8% | |
| 226 | d = rfiWrapper(d, plotparams, ... | 1 | 43.622 s | 9.9% | |
| 263 | rmsWrapper(d, plotparams, parm... | 1 | 22.636 s | 5.1% | |
| 192 | introPlots(d, plotparams, fiel... | 1 | 14.963 s | 3.4% | |
| All other lines | | | 79.571 s | 18.0% | |
| Totals | | | 441.366 s | 100% | |
Children (called functions)
Code Analyzer results
| Line number | Message |
| 46 | WARNING('OFF',msgID) is faster than WARNING('OFF'). |
| 52 | EXIST with two input arguments is generally faster and clearer than with one input argument. |
| 69 | EXIST with two input arguments is generally faster and clearer than with one input argument. |
| 78 | The value assigned to variable 'interactive' might be unused. |
| 85 | The value assigned to variable 'interactive' might be unused. |
| 89 | The value assigned to variable 'interactive' might be unused. |
| 91 | The value assigned to variable 'interactive' might be unused. |
| 144 | Use || instead of | as the OR operator in (scalar) conditional statements. |
| 170 | To improve performance, replace ISEMPTY(FIND(X)) with ISEMPTY(FIND( X, 1 )). |
| 189 | Variable 'time', apparently a structure, is changed but the value seems to be unused. |
| 289 | Best practice is for CATCH to be followed by an identifier that gets the error information. |
| 294 | TRY might not be aligned with its matching END (line 298). |
| 296 | Best practice is for CATCH to be followed by an identifier that gets the error information. |
| 321 | The value assigned to variable 'plotflag' might be unused. |
| 324 | The value assigned to variable 'plotflag' might be unused. |
| 330 | DISP(SPRINTF(...)) can usually be replaced by FPRINTF(...). |
Coverage results
[ Show coverage for parent directory ]
| Total lines in function | 353 |
| Non-code lines (comments, blank lines) | 130 |
| Code lines (lines that can run) | 223 |
| Code lines that did run | 124 |
| Code lines that did not run | 99 |
| Coverage (did run/can run) | 55.61 % |
Function listing
time calls line
1 function d = reduceData(d, fn, interactive, field,sched_name)
2
3 % function dcal = reduceData(d, fn, interactive, field,sched_name)
4 %
5 % VERSION 1.5
6 %
7 % Reduction Routine Using Matlab.
8 %
9 % Inputs:
10 % d - raw/partially calibrated data structure
11 % output from read_arc.m
12 %
13 % Optional:
14 % fn - reduceData auto script, *.red
15 % interactive - 1/0 for user input during the pipeline
16 % field - fieldname you want the plots to be saved to. if you leave it
17 % blank it will default to "other"
18 % sched_name - Name of the schedule if known (this will usually be passed in by
19 % % day_reduce)
20 %
21 % Stephen Muchovej
22 %
23 % Other contributors:
24 %
25 %
26 % HISTORY:
27 % version 0.0: had many different sizes for the flags
28 % version 1.0: all flagging will be done on basis of I1, all polarization,
29 % and I2 (implemented December 8, 2010)
30 % version 1.1: changed step 'rfi1' to 'rfi'. Removed step 'rfi2'.
31 % (MAS Jan 7, 2011).
32 % version 1.2: routine list is now an input in .red file; alpha correction
33 % can be specified in that file, r-factor no longer combines the data. (sjcm, 2/24/2011)
34 % version 1.3: gen, field now in script; removed 'intro' as an input
35 % (3/29/2010)
36 % version 1.4: interactive now as input. Major mods to subfunctions
37 % version 1.5: plot in only 3 colors. blah blah blah. see sjcm's email
38 % april 25,2011.
39 %
40 % define version number
1 41 REV='1.5';
42 % Add in a history field for history logging purposes.
43 %d.history={'Began Data Reduction...'};
44
45 % turn warnings off
1 46 warning off
47
48 % welcome!
1 49 welcome(REV);
50
51 % Check the inputs
1 52 if (exist('fn'))
1 53 if (~isempty(fn))
1 54 disp('Reading script')
0.03 1 55 pause(1)
56
0.07 1 57 parm=readScript(fn);
0.03 1 58 if (~matchRev(parm,REV))
59 return
60 end
0.02 1 61 pause(1)
62 else
63 parm = [];
64 end
65 else
66 parm = [];
67 end
68
1 69 if (~exist('sched_name'))
1 70 sched_name = 'not supplied';
1 71 end;
72
73 % check the inputs, and set defaults
1 74 if(nargin==1)
75 display('Interactive mode with only one input');
76 display('Setting default values');
77 parm = [];
78 interactive = 1;
79 field = 'other';
1 80 elseif(nargin==2)
81 % check if script was read properly
82 if(isempty(parm))
83 display('WARNING: script bad');
84 display('Giving you interactive mode');
85 interactive = 1;
86 field = 'other';
87 else
88 if(isfield(parm, 'interactive'));
89 interactive = parm.interactive.flag;
90 else
91 interactive = 1;
92 parm.interactive.flag = 1;
93 end
94 if(isfield(parm, 'field'))
95 field = parm.field.name;
96 else
97 field = 'other';
98 parm.field.name = 'other';
99 end
100 end
1 101 elseif(nargin==3)
102 display('interactive variable in function call will supersede one in script');
103 parm.interactive.flag = interactive;
104 if(isfield(parm, 'field'))
105 field = parm.field.name;
106 else
107 field = 'other';
108 parm.field.name = field;
109 end
1 110 elseif(nargin==4)
1 111 display('interactive and field variable in function call will supersed one in script');
1 112 parm.interactive.flag = interactive;
1 113 if(isempty(field))
114 field = 'other';
115 end
1 116 parm.field.name = field;
1 117 end
118 % done checking inputs
119
0.01 1 120 d.par = parm;
121
122 % tag version to data
1 123 d.rev=REV;
124
125 % make sure the alpha database is uptodate
2.92 1 126 isup2date = checkAlphaDatabase((d.array.frame.utc(1)));
1 127 if(~isup2date)
128 display('Your alpha database is not up to date');
129 if(parm.interactive.flag)
130 display('You will update the database');
131 display('Don''t fudge it up');
132 updateAlphaDatabase_DD(last(d.array.frame.utc));
133 else
134 display('Proceeding with last valid value');
135 end
136 end
137
138
139 % check run flags
1 140 [plotparams, autorun]=setRunFlags(parm); % from the file
141
142
143 % check if we actually have any data.
1 144 if(isempty(d.array.frame.utc) | all(d.array.frame.features==0))
145 display('You have no data in this structure');
146 display('Why would you try to calibrate it?');
147 return;
148 end
149
150
1 151 if (plotparams.save)
0.56 1 152 createDir(d,field);
1 153 end
154
155
156
157 % perform the first level of flagging
1 158 if(plotparams.save)
1 159 maindir = getMainDir(d, field);
0.01 1 160 fn = strcat(maindir, '/flags.txt');
1 161 diary(fn);
1 162 diary on;
12.06 1 163 d = checkFlags(d, parm);
1 164 diary off;
165 else
166 d = checkFlags(d, parm);
167 end
168
169 % if there's no noise source diode events, you can't calibrate.
1 170 if(isempty(find(d.index.noise_event.fast)))
171 display('There are no Noise Source diode events in your data');
172 display('Can not calibrate this data set');
173 return;
174 end
175
176
177
178 % check for the integration shortfall correction
179 %[d,q] = logcal(d, 'shortfall');
180 %if(~q)
181 % display('Correcting for the Integration Shortfall');
182 % d = shortfallCorr(d);
183 %end
184
185
186
187 % log start time
1 188 time.startTime=d.array.frame.utc(1);
1 189 time.stopTime=d.array.frame.utc(length(d.array.frame.utc));
190
191 % plot the intro plots
14.96 1 192 introPlots(d, plotparams, field);
193
194 % set autoflag false
1 195 autoflag=0;
1 196 par=[];
1 197 lastpar='auto';
1 198 disp(' ')
199
200
201 % now the meat of the function
1 202 while (1)
17 203 if (autorun)
0.03 17 204 [par,lastpar,autorun]=go(par,lastpar,autorun, parm);
205 else
206 [par,lastpar,autoflag]=prompt(par,lastpar,autoflag, parm);
207 end
208
17 209 switch par
17 210 case 'help'
211 menu;
212
17 213 case 'intro'
214 introPlots(d, plotparams, field);
215
17 216 case 'pointing'
0.01 1 217 display('Checking the pointing');
0.02 1 218 pointingWrapper(d, plotparams, parm, field);
219
16 220 case 'deglitch'
1 221 display('Deglitching data');
7.85 1 222 d = deglitchWrapper(d, plotparams, parm, field);
223
15 224 case 'rfi'
1 225 display('RFI Flagging');
43.62 1 226 d = rfiWrapper(d, plotparams, parm, field);
227
14 228 case 'mains'
1 229 display('60Hz Mains correction');
47.52 1 230 d = mainsWrapper(d, plotparams, parm, field);
231
13 232 case 'alpha'
1 233 display('Alpha Correction');
11.63 1 234 d = alphaWrapper(d, plotparams, parm, field);
235
12 236 case 'rfactor'
237 display('R-factor correction');
238 d = rfactorWrapper(d, plotparams, parm, field);
239
12 240 case 'load'
1 241 display('Cold Load fluctuation Removal');
12.22 1 242 d = loadWrapper(d, plotparams, parm, field);
243
11 244 case 'tau'
1 245 display('Calculating the atmospheric opacity');
2.39 1 246 d = tauCalWrapper(d, plotparams, parm, field);
247
10 248 case 'astro'
1 249 display('Applying Astronomical Calibration');
1 250 display('not done yet');
251 %d = astroCalWrapper(d, plotparams, parm, field);
252
9 253 case 'power'
1 254 display('Power Spectrum Plot');
4.18 1 255 powerSpecWrapper(d, plotparams, parm, field);
256
8 257 case 'overf'
1 258 display('1/f plot');
233.05 1 259 overfWrapper(d, plotparams, parm, field);
260
0.01 7 261 case 'rms'
1 262 display('RMS calculation');
22.64 1 263 rmsWrapper(d, plotparams, parm, field);
264
6 265 case 'tsys'
1 266 display('Calculating system temperature of data');
3.42 1 267 d = tsysWrapper(d, plotparams, parm, field);
268
5 269 case 'noise'
1 270 display('Calculating temperature of noise diode');
0.43 1 271 d = noiseWrapper(d, plotparams, parm, field);
272
4 273 case 'gain'
1 274 display('Calculating time-varying gain');
0.74 1 275 d = gainWrapper(d, plotparams, parm, field);
276
3 277 case 'summary'
1 278 display('Displaying the summary of all the flags');
8.39 1 279 flagSummary(d, plotparams, parm, field);
280
2 281 case 'fits'
1 282 if(searchStruct(d, {'correction', 'tsys', 'allbad'}))
1 283 if(d.correction.tsys.allbad == 1)
284 display('Not writing out this crap data');
1 285 else
1 286 display('Writing out data to fits file');
1 287 try
7.84 1 288 writeOutFits(maindir, d, parm);
289 catch
290 disp('Failed to write to fits data')
291 end
1 292 end
293 else
294 try
295 writeOutFits(maindir, d, parm);
296 catch
297 disp('Failed to write to fits data')
298 end
299 end
300
301
1 302 case 'auto'
303 disp(' ')
304 disp('********Auto mode***********')
305 disp('After each step any standard')
306 disp('command will work')
307 disp(' ')
308 disp('To continue with calibration')
309 disp('Hit RETURN without typing anything')
310 disp(' ')
311 autoflag=1;
312 close all;
313
1 314 case 'key'
315 keyboard;
316
1 317 case 'close'
318 close all
319
1 320 case 'plot off'
321 plotflag=0;
322
1 323 case 'plot on'
324 plotflag=1;
325
1 326 case 'save'
327 save dataRed.mat
328
1 329 case 'exit'
1 330 disp(sprintf('Thank you for using Cbass Data Reduction. Now go away\n'))
1 331 break;
332
333 otherwise
334 disp('Unknown command');
335 disp(' ')
336
337 end
16 338 end
339
340 % next, if we generated the plots, we should generate the pages.
1 341 if(plotparams.save)
1 342 display('Generating webpages of all previous plots');
4.68 1 343 webpipe(d, field,0,sched_name);
1 344 end
345
346 % make sure your plots appear from now on
1 347 if(plotparams.plot==0)
0.02 1 348 close all;
1 349 end
350
351
352
1 353 return;
Other subfunctions in this file are not included in this listing.