1 | """ |
---|
2 | This is the ATNF Single Dish Analysis package. |
---|
3 | |
---|
4 | """ |
---|
5 | import os,sys |
---|
6 | |
---|
7 | def _validate_bool(b): |
---|
8 | 'Convert b to a boolean or raise' |
---|
9 | bl = b.lower() |
---|
10 | if bl in ('f', 'no', 'false', '0', 0): return False |
---|
11 | elif bl in ('t', 'yes', 'true', '1', 1): return True |
---|
12 | else: |
---|
13 | raise ValueError('Could not convert "%s" to boolean' % b) |
---|
14 | |
---|
15 | def _validate_int(s): |
---|
16 | 'convert s to int or raise' |
---|
17 | try: return int(s) |
---|
18 | except ValueError: |
---|
19 | raise ValueError('Could not convert "%s" to int' % s) |
---|
20 | |
---|
21 | def _asap_fname(): |
---|
22 | """ |
---|
23 | Return the path to the rc file |
---|
24 | |
---|
25 | Search order: |
---|
26 | |
---|
27 | * current working dir |
---|
28 | * environ var ASAPRC |
---|
29 | * HOME/.asaprc |
---|
30 | |
---|
31 | """ |
---|
32 | |
---|
33 | fname = os.path.join( os.getcwd(), '.asaprc') |
---|
34 | if os.path.exists(fname): return fname |
---|
35 | |
---|
36 | if os.environ.has_key('ASAPRC'): |
---|
37 | path = os.environ['ASAPRC'] |
---|
38 | if os.path.exists(path): |
---|
39 | fname = os.path.join(path, '.asaprc') |
---|
40 | if os.path.exists(fname): |
---|
41 | return fname |
---|
42 | |
---|
43 | if os.environ.has_key('HOME'): |
---|
44 | home = os.environ['HOME'] |
---|
45 | fname = os.path.join(home, '.asaprc') |
---|
46 | if os.path.exists(fname): |
---|
47 | return fname |
---|
48 | return None |
---|
49 | |
---|
50 | |
---|
51 | defaultParams = { |
---|
52 | # general |
---|
53 | 'verbose' : [True, _validate_bool], |
---|
54 | 'useplotter' : [True, _validate_bool], |
---|
55 | 'insitu' : [True, _validate_bool], |
---|
56 | |
---|
57 | # plotting |
---|
58 | 'plotter.gui' : [True, _validate_bool], |
---|
59 | 'plotter.stacking' : ['p', str], |
---|
60 | 'plotter.panelling' : ['s', str], |
---|
61 | 'plotter.colours' : ['', str], |
---|
62 | 'plotter.linestyles' : ['', str], |
---|
63 | 'plotter.decimate' : [False, _validate_bool], |
---|
64 | 'plotter.ganged' : [True, _validate_bool], |
---|
65 | |
---|
66 | # scantable |
---|
67 | 'scantable.save' : ['ASAP', str], |
---|
68 | 'scantable.autoaverage' : [True, _validate_bool], |
---|
69 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame |
---|
70 | 'scantable.verbosesummary' : [False, _validate_bool] |
---|
71 | |
---|
72 | # fitter |
---|
73 | } |
---|
74 | |
---|
75 | def list_rcparameters(): |
---|
76 | |
---|
77 | print """ |
---|
78 | # general |
---|
79 | # print verbose output |
---|
80 | verbose : True |
---|
81 | |
---|
82 | # preload a default plotter |
---|
83 | useplotter : True |
---|
84 | |
---|
85 | # apply operations on the input scantable or return new one |
---|
86 | insitu : True |
---|
87 | |
---|
88 | # plotting |
---|
89 | |
---|
90 | # do we want a GUI or plot to a file |
---|
91 | plotter.gui : True |
---|
92 | |
---|
93 | # default mode for colour stacking |
---|
94 | plotter.stacking : Pol |
---|
95 | |
---|
96 | # default mode for panelling |
---|
97 | plotter.panelling : scan |
---|
98 | |
---|
99 | # push panels together, to share axislabels |
---|
100 | plotter.ganged : True |
---|
101 | |
---|
102 | # decimate the number of points plotted bya afactor of |
---|
103 | # nchan/1024 |
---|
104 | plotter.decimate : False |
---|
105 | |
---|
106 | # default colours/linestyles |
---|
107 | plotter.colours : |
---|
108 | plotter.linestyles : |
---|
109 | |
---|
110 | # scantable |
---|
111 | # default ouput format when saving |
---|
112 | scantable.save : ASAP |
---|
113 | # auto averaging on read |
---|
114 | scantable.autoaverage : True |
---|
115 | |
---|
116 | # default frequency frame to set when function |
---|
117 | # scantable.set_freqfrmae is called |
---|
118 | scantable.freqframe : LSRK |
---|
119 | |
---|
120 | # Control the level of information printed by summary |
---|
121 | scantable.verbosesummary : False |
---|
122 | |
---|
123 | # Fitter |
---|
124 | """ |
---|
125 | |
---|
126 | def rc_params(): |
---|
127 | 'Return the default params updated from the values in the rc file' |
---|
128 | |
---|
129 | fname = _asap_fname() |
---|
130 | |
---|
131 | if fname is None or not os.path.exists(fname): |
---|
132 | message = 'could not find rc file; returning defaults' |
---|
133 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
---|
134 | #print message |
---|
135 | return ret |
---|
136 | |
---|
137 | cnt = 0 |
---|
138 | for line in file(fname): |
---|
139 | cnt +=1 |
---|
140 | line = line.strip() |
---|
141 | if not len(line): continue |
---|
142 | if line.startswith('#'): continue |
---|
143 | tup = line.split(':',1) |
---|
144 | if len(tup) !=2: |
---|
145 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
---|
146 | continue |
---|
147 | |
---|
148 | key, val = tup |
---|
149 | key = key.strip() |
---|
150 | if not defaultParams.has_key(key): |
---|
151 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
---|
152 | continue |
---|
153 | |
---|
154 | default, converter = defaultParams[key] |
---|
155 | |
---|
156 | ind = val.find('#') |
---|
157 | if ind>=0: val = val[:ind] # ignore trailing comments |
---|
158 | val = val.strip() |
---|
159 | try: cval = converter(val) # try to convert to proper type or raise |
---|
160 | except Exception, msg: |
---|
161 | print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg)) |
---|
162 | continue |
---|
163 | else: |
---|
164 | # Alles Klar, update dict |
---|
165 | defaultParams[key][0] = cval |
---|
166 | |
---|
167 | # strip the conveter funcs and return |
---|
168 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
---|
169 | print ('loaded rc file %s'%fname) |
---|
170 | |
---|
171 | return ret |
---|
172 | |
---|
173 | |
---|
174 | # this is the instance used by the asap classes |
---|
175 | rcParams = rc_params() |
---|
176 | |
---|
177 | rcParamsDefault = dict(rcParams.items()) # a copy |
---|
178 | |
---|
179 | def rc(group, **kwargs): |
---|
180 | """ |
---|
181 | Set the current rc params. Group is the grouping for the rc, eg |
---|
182 | for scantable.save the group is 'scantable', for plotter.stacking, the |
---|
183 | group is 'plotter', and so on. kwargs is a list of attribute |
---|
184 | name/value pairs, eg |
---|
185 | |
---|
186 | rc('scantable', save='SDFITS') |
---|
187 | |
---|
188 | sets the current rc params and is equivalent to |
---|
189 | |
---|
190 | rcParams['scantable.save'] = 'SDFITS' |
---|
191 | |
---|
192 | Use rcdefaults to restore the default rc params after changes. |
---|
193 | """ |
---|
194 | |
---|
195 | aliases = {} |
---|
196 | |
---|
197 | for k,v in kwargs.items(): |
---|
198 | name = aliases.get(k) or k |
---|
199 | key = '%s.%s' % (group, name) |
---|
200 | if not rcParams.has_key(key): |
---|
201 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
---|
202 | |
---|
203 | rcParams[key] = v |
---|
204 | |
---|
205 | |
---|
206 | def rcdefaults(): |
---|
207 | """ |
---|
208 | Restore the default rc params - the ones that were created at |
---|
209 | asap load time |
---|
210 | """ |
---|
211 | rcParams.update(rcParamsDefault) |
---|
212 | |
---|
213 | |
---|
214 | def _is_sequence_or_number(param, ptype=int): |
---|
215 | if isinstance(param,tuple) or isinstance(param,list): |
---|
216 | if len(param) == 0: return True # empty list |
---|
217 | out = True |
---|
218 | for p in param: |
---|
219 | out &= isinstance(p,ptype) |
---|
220 | return out |
---|
221 | elif isinstance(param, ptype): |
---|
222 | return True |
---|
223 | return False |
---|
224 | |
---|
225 | def _to_list(param, ptype=int): |
---|
226 | if isinstance(param, ptype): |
---|
227 | if ptype is str: return param.split() |
---|
228 | else: return [param] |
---|
229 | if _is_sequence_or_number(param, ptype): |
---|
230 | return param |
---|
231 | return None |
---|
232 | |
---|
233 | def unique(x): |
---|
234 | """ |
---|
235 | Return the unique values in a list |
---|
236 | Parameters: |
---|
237 | x: the list to reduce |
---|
238 | Examples: |
---|
239 | x = [1,2,3,3,4] |
---|
240 | print unique(x) |
---|
241 | [1,2,3,4] |
---|
242 | """ |
---|
243 | return dict([ (val, 1) for val in x]).keys() |
---|
244 | |
---|
245 | def list_files(path=".",suffix="rpf"): |
---|
246 | """ |
---|
247 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap |
---|
248 | Parameters: |
---|
249 | path: The directory to list (default '.') |
---|
250 | suffix: The file extension (default rpf) |
---|
251 | Example: |
---|
252 | files = list_files("data/","sdfits") |
---|
253 | print files |
---|
254 | ['data/2001-09-01_0332_P363.sdfits', |
---|
255 | 'data/2003-04-04_131152_t0002.sdfits', |
---|
256 | 'data/Sgr_86p262_best_SPC.sdfits'] |
---|
257 | """ |
---|
258 | import os |
---|
259 | if not os.path.isdir(path): |
---|
260 | return None |
---|
261 | valid = "rpf sdf sdfits mbf asap".split() |
---|
262 | if not suffix in valid: |
---|
263 | return None |
---|
264 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)] |
---|
265 | return filter(lambda x: x.endswith(suffix),files) |
---|
266 | |
---|
267 | # workaround for ipython, which redirects this if banner=0 in ipythonrc |
---|
268 | sys.stdout = sys.__stdout__ |
---|
269 | sys.stderr = sys.__stderr__ |
---|
270 | |
---|
271 | # Logging |
---|
272 | from asap._asap import Log as _asaplog |
---|
273 | global asaplog |
---|
274 | asaplog=_asaplog() |
---|
275 | if rcParams['verbose']: |
---|
276 | asaplog.enable() |
---|
277 | else: |
---|
278 | asaplog.disable() |
---|
279 | |
---|
280 | def print_log(): |
---|
281 | log = asaplog.pop() |
---|
282 | if len(log) and rcParams['verbose']: print log |
---|
283 | return |
---|
284 | |
---|
285 | from asapfitter import * |
---|
286 | from asapreader import reader |
---|
287 | from selector import selector |
---|
288 | |
---|
289 | from asapmath import * |
---|
290 | from scantable import * |
---|
291 | from asaplinefind import * |
---|
292 | #from asapfit import * |
---|
293 | |
---|
294 | from numarray import logical_and as mask_and |
---|
295 | from numarray import logical_or as mask_or |
---|
296 | from numarray import logical_not as mask_not |
---|
297 | |
---|
298 | if rcParams['useplotter']: |
---|
299 | from asapplotter import * |
---|
300 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui'] |
---|
301 | plotter = asapplotter(gui) |
---|
302 | del gui |
---|
303 | |
---|
304 | __date__ = '$Date: 2006-04-11 04:54:45 +0000 (Tue, 11 Apr 2006) $'.split()[1] |
---|
305 | __version__ = '2.0b' |
---|
306 | |
---|
307 | if rcParams['verbose']: |
---|
308 | def list_scans(t = scantable): |
---|
309 | import sys, types |
---|
310 | globs = sys.modules['__main__'].__dict__.iteritems() |
---|
311 | print "The user created scantables are:" |
---|
312 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
---|
313 | print filter(lambda x: not x.startswith('_'), sts) |
---|
314 | return |
---|
315 | |
---|
316 | def commands(): |
---|
317 | x = """ |
---|
318 | [The scan container] |
---|
319 | scantable - a container for integrations/scans |
---|
320 | (can open asap/rpfits/sdfits and ms files) |
---|
321 | copy - returns a copy of a scan |
---|
322 | get_scan - gets a specific scan out of a scantable |
---|
323 | (by name or number) |
---|
324 | set_selection - set a new subselection of the data |
---|
325 | get_selection - get the current selection object |
---|
326 | summary - print info about the scantable contents |
---|
327 | stats - get specified statistic of the spectra in |
---|
328 | the scantable |
---|
329 | stddev - get the standard deviation of the spectra |
---|
330 | in the scantable |
---|
331 | get_tsys - get the TSys |
---|
332 | get_time - get the timestamps of the integrations |
---|
333 | get_sourcename - get the source names of the scans |
---|
334 | get_azimuth - get the azimuth of the scans |
---|
335 | get_elevation - get the elevation of the scans |
---|
336 | get_parangle - get the parallactic angle of the scans |
---|
337 | get_unit - get the current unit |
---|
338 | set_unit - set the abcissa unit to be used from this |
---|
339 | point on |
---|
340 | get_abcissa - get the abcissa values and name for a given |
---|
341 | row (time) |
---|
342 | set_freqframe - set the frame info for the Spectral Axis |
---|
343 | (e.g. 'LSRK') |
---|
344 | set_doppler - set the doppler to be used from this point on |
---|
345 | set_dirframe - set the frame for the direction on the sky |
---|
346 | set_instrument - set the instrument name |
---|
347 | get_fluxunit - get the brightness flux unit |
---|
348 | set_fluxunit - set the brightness flux unit |
---|
349 | create_mask - return an mask in the current unit |
---|
350 | for the given region. The specified regions |
---|
351 | are NOT masked |
---|
352 | get_restfreqs - get the current list of rest frequencies |
---|
353 | set_restfreqs - set a list of rest frequencies |
---|
354 | flag - flag selected channels in the data |
---|
355 | save - save the scantable to disk as either 'ASAP' |
---|
356 | or 'SDFITS' |
---|
357 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
---|
358 | nscan - the number of scans in the scantable |
---|
359 | nrow - te number of spectra in the scantable |
---|
360 | history - print the history of the scantable |
---|
361 | get_fit - get a fit which has been stored witnh the data |
---|
362 | average_time - return the (weighted) time average of a scan |
---|
363 | or a list of scans |
---|
364 | average_pol - average the polarisations together. |
---|
365 | The dimension won't be reduced and |
---|
366 | all polarisations will contain the |
---|
367 | averaged spectrum. |
---|
368 | convert_pol - convert to a different polarisation type |
---|
369 | auto_quotient - return the on/off quotient with |
---|
370 | automatic detection of the on/off scans |
---|
371 | (matched pairs and 1 off - n on) |
---|
372 | scale - return a scan scaled by a given factor |
---|
373 | add - return a scan with given value added |
---|
374 | bin - return a scan with binned channels |
---|
375 | resample - return a scan with resampled channels |
---|
376 | smooth - return the spectrally smoothed scan |
---|
377 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
---|
378 | auto_poly_baseline - automatically fit a polynomial baseline |
---|
379 | recalc_azel - recalculate azimuth and elevation based on |
---|
380 | the pointing |
---|
381 | gain_el - apply gain-elevation correction |
---|
382 | opacity - apply opacity correction |
---|
383 | convert_flux - convert to and from Jy and Kelvin brightness |
---|
384 | units |
---|
385 | freq_align - align spectra in frequency frame |
---|
386 | rotate_xyphase - rotate XY phase of cross correlation |
---|
387 | rotate_linpolphase - rotate the phase of the complex |
---|
388 | polarization O=Q+iU correlation |
---|
389 | freq_switch - perform frequency switching on the data |
---|
390 | stats - Determine the specified statistic, e.g. 'min' |
---|
391 | 'max', 'rms' etc. |
---|
392 | stddev - Determine the standard deviation of the current |
---|
393 | beam/if/pol |
---|
394 | |
---|
395 | [Math] Mainly functions which operate on more than one scantable |
---|
396 | |
---|
397 | average_time - return the (weighted) time average |
---|
398 | of a list of scans |
---|
399 | quotient - return the on/off quotient |
---|
400 | simple_math - simple mathematical operations on two scantables, |
---|
401 | 'add', 'sub', 'mul', 'div' |
---|
402 | [Fitting] |
---|
403 | fitter |
---|
404 | auto_fit - return a scan where the function is |
---|
405 | applied to all Beams/IFs/Pols. |
---|
406 | commit - return a new scan where the fits have been |
---|
407 | commited. |
---|
408 | fit - execute the actual fitting process |
---|
409 | store_fit - store the fit parameters in the data (scantable) |
---|
410 | get_chi2 - get the Chi^2 |
---|
411 | set_scan - set the scantable to be fit |
---|
412 | set_function - set the fitting function |
---|
413 | set_parameters - set the parameters for the function(s), and |
---|
414 | set if they should be held fixed during fitting |
---|
415 | set_gauss_parameters - same as above but specialised for individual |
---|
416 | gaussian components |
---|
417 | get_parameters - get the fitted parameters |
---|
418 | plot - plot the resulting fit and/or components and |
---|
419 | residual |
---|
420 | [Plotter] |
---|
421 | asapplotter - a plotter for asap, default plotter is |
---|
422 | called 'plotter' |
---|
423 | plot - plot a scantable |
---|
424 | save - save the plot to a file ('png' ,'ps' or 'eps') |
---|
425 | set_mode - set the state of the plotter, i.e. |
---|
426 | what is to be plotted 'colour stacked' |
---|
427 | and what 'panelled' |
---|
428 | set_selection - only plot a selected part of the data |
---|
429 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
---|
430 | set_legend - specify user labels for the legend indeces |
---|
431 | set_title - specify user labels for the panel indeces |
---|
432 | set_abcissa - specify a user label for the abcissa |
---|
433 | set_ordinate - specify a user label for the ordinate |
---|
434 | set_layout - specify the multi-panel layout (rows,cols) |
---|
435 | set_colors - specify a set of colours to use |
---|
436 | set_linestyles - specify a set of linestyles to use if only |
---|
437 | using one color |
---|
438 | set_mask - set a plotting mask for a specific polarization |
---|
439 | |
---|
440 | [Reading files] |
---|
441 | reader - access rpfits/sdfits files |
---|
442 | open - attach reader to a file |
---|
443 | close - detach reader from file |
---|
444 | read - read in integrations |
---|
445 | summary - list info about all integrations |
---|
446 | |
---|
447 | [General] |
---|
448 | commands - this command |
---|
449 | print - print details about a variable |
---|
450 | list_scans - list all scantables created bt the user |
---|
451 | list_files - list all files readable by asap (default rpf) |
---|
452 | del - delete the given variable from memory |
---|
453 | range - create a list of values, e.g. |
---|
454 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
---|
455 | help - print help for one of the listed functions |
---|
456 | execfile - execute an asap script, e.g. execfile('myscript') |
---|
457 | list_rcparameters - print out a list of possible values to be |
---|
458 | put into $HOME/.asaprc |
---|
459 | mask_and,mask_or, |
---|
460 | mask_not - boolean operations on masks created with |
---|
461 | scantable.create_mask |
---|
462 | |
---|
463 | Note: |
---|
464 | How to use this with help: |
---|
465 | # function 'summary' |
---|
466 | [xxx] is just a category |
---|
467 | Every 'sub-level' in this list should be replaces by a '.' Period when |
---|
468 | using help |
---|
469 | Example: |
---|
470 | ASAP> help scantable # to get info on ths scantable |
---|
471 | ASAP> help scantable.summary # to get help on the scantable's |
---|
472 | ASAP> help average_time |
---|
473 | |
---|
474 | """ |
---|
475 | print x |
---|
476 | return |
---|
477 | |
---|
478 | def welcome(): |
---|
479 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package |
---|
480 | |
---|
481 | Please report any bugs to: |
---|
482 | asap@atnf.csiro.au |
---|
483 | |
---|
484 | [IMPORTANT: ASAP is 0-based] |
---|
485 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__) |
---|