source: branches/Release2.1.2/python/__init__.py@ 1913

Last change on this file since 1913 was 1320, checked in by mar637, 18 years ago

merge from trunk, to get most recent bug fixes

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Line 
1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
5import os,sys,shutil, platform
6
7# Set up AIPSPATH and first time use of asap i.e. ~/.asap/*
8plf = None
9if sys.platform == "linux2":
10 if platform.architecture()[0] == '64bit':
11 plf = 'linux_64b'
12 else:
13 plf = 'linux_gnu'
14elif sys.platform == 'darwin':
15 plf = 'darwin'
16else:
17 # Shouldn't happen - default to linux
18 plf = 'linux'
19asapdata = __path__[-1]
20# Allow user defined data location
21if os.environ.has_key("ASAPDATA"):
22 if os.path.exists(os.environ["ASAPDATA"]):
23 asapdata = os.environ["ASAPDATA"]
24if not os.environ.has_key("AIPSPATH"):
25 os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
26# set up user space
27userdir = os.environ["HOME"]+"/.asap"
28if not os.path.exists(userdir):
29 print 'First time ASAP use. Setting up ~/.asap'
30 os.mkdir(userdir)
31 shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
32 f = file(userdir+"/asapuserfuncs.py", "w")
33 f.close()
34 f = file(userdir+"/ipythonrc", "w")
35 f.close()
36# remove from namespace
37del asapdata, userdir, shutil, platform
38
39def _validate_bool(b):
40 'Convert b to a boolean or raise'
41 bl = b.lower()
42 if bl in ('f', 'no', 'false', '0', 0): return False
43 elif bl in ('t', 'yes', 'true', '1', 1): return True
44 else:
45 raise ValueError('Could not convert "%s" to boolean' % b)
46
47def _validate_int(s):
48 'convert s to int or raise'
49 try: return int(s)
50 except ValueError:
51 raise ValueError('Could not convert "%s" to int' % s)
52
53def _asap_fname():
54 """
55 Return the path to the rc file
56
57 Search order:
58
59 * current working dir
60 * environ var ASAPRC
61 * HOME/.asaprc
62
63 """
64
65 fname = os.path.join( os.getcwd(), '.asaprc')
66 if os.path.exists(fname): return fname
67
68 if os.environ.has_key('ASAPRC'):
69 path = os.environ['ASAPRC']
70 if os.path.exists(path):
71 fname = os.path.join(path, '.asaprc')
72 if os.path.exists(fname):
73 return fname
74
75 if os.environ.has_key('HOME'):
76 home = os.environ['HOME']
77 fname = os.path.join(home, '.asaprc')
78 if os.path.exists(fname):
79 return fname
80 return None
81
82
83defaultParams = {
84 # general
85 'verbose' : [True, _validate_bool],
86 'useplotter' : [True, _validate_bool],
87 'insitu' : [True, _validate_bool],
88
89 # plotting
90 'plotter.gui' : [True, _validate_bool],
91 'plotter.stacking' : ['p', str],
92 'plotter.panelling' : ['s', str],
93 'plotter.colours' : ['', str],
94 'plotter.linestyles' : ['', str],
95 'plotter.decimate' : [False, _validate_bool],
96 'plotter.ganged' : [True, _validate_bool],
97 'plotter.histogram' : [False, _validate_bool],
98 'plotter.papertype' : ['A4', str],
99
100 # scantable
101 'scantable.save' : ['ASAP', str],
102 'scantable.autoaverage' : [True, _validate_bool],
103 'scantable.freqframe' : ['LSRK', str], #default frequency frame
104 'scantable.verbosesummary' : [False, _validate_bool],
105 'scantable.storage' : ['memory', str]
106 # fitter
107 }
108
109def list_rcparameters():
110
111 print """
112# general
113# print verbose output
114verbose : True
115
116# preload a default plotter
117useplotter : True
118
119# apply operations on the input scantable or return new one
120insitu : True
121
122# plotting
123
124# do we want a GUI or plot to a file
125plotter.gui : True
126
127# default mode for colour stacking
128plotter.stacking : Pol
129
130# default mode for panelling
131plotter.panelling : scan
132
133# push panels together, to share axislabels
134plotter.ganged : True
135
136# decimate the number of points plotted bya afactor of
137# nchan/1024
138plotter.decimate : False
139
140# default colours/linestyles
141plotter.colours :
142plotter.linestyles :
143
144# enable/disable histogram plotting
145plotter.histogram : False
146
147# ps paper type
148plotter.papertype : A4
149
150# scantable
151
152# default storage of scantable ('memory'/'disk')
153scantable.storage : memory
154# default ouput format when saving
155scantable.save : ASAP
156# auto averaging on read
157scantable.autoaverage : True
158
159# default frequency frame to set when function
160# scantable.set_freqframe is called
161scantable.freqframe : LSRK
162
163# Control the level of information printed by summary
164scantable.verbosesummary : False
165
166# Fitter
167"""
168
169def rc_params():
170 'Return the default params updated from the values in the rc file'
171
172 fname = _asap_fname()
173
174 if fname is None or not os.path.exists(fname):
175 message = 'could not find rc file; returning defaults'
176 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
177 #print message
178 return ret
179
180 cnt = 0
181 for line in file(fname):
182 cnt +=1
183 line = line.strip()
184 if not len(line): continue
185 if line.startswith('#'): continue
186 tup = line.split(':',1)
187 if len(tup) !=2:
188 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
189 continue
190
191 key, val = tup
192 key = key.strip()
193 if not defaultParams.has_key(key):
194 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
195 continue
196
197 default, converter = defaultParams[key]
198
199 ind = val.find('#')
200 if ind>=0: val = val[:ind] # ignore trailing comments
201 val = val.strip()
202 try: cval = converter(val) # try to convert to proper type or raise
203 except ValueError, msg:
204 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
205 continue
206 else:
207 # Alles Klar, update dict
208 defaultParams[key][0] = cval
209
210 # strip the conveter funcs and return
211 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
212 print ('loaded rc file %s'%fname)
213
214 return ret
215
216
217# this is the instance used by the asap classes
218rcParams = rc_params()
219
220rcParamsDefault = dict(rcParams.items()) # a copy
221
222def rc(group, **kwargs):
223 """
224 Set the current rc params. Group is the grouping for the rc, eg
225 for scantable.save the group is 'scantable', for plotter.stacking, the
226 group is 'plotter', and so on. kwargs is a list of attribute
227 name/value pairs, eg
228
229 rc('scantable', save='SDFITS')
230
231 sets the current rc params and is equivalent to
232
233 rcParams['scantable.save'] = 'SDFITS'
234
235 Use rcdefaults to restore the default rc params after changes.
236 """
237
238 aliases = {}
239
240 for k,v in kwargs.items():
241 name = aliases.get(k) or k
242 key = '%s.%s' % (group, name)
243 if not rcParams.has_key(key):
244 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
245
246 rcParams[key] = v
247
248
249def rcdefaults():
250 """
251 Restore the default rc params - the ones that were created at
252 asap load time
253 """
254 rcParams.update(rcParamsDefault)
255
256def _n_bools(n, val):
257 return [ val for i in xrange(n) ]
258
259def _is_sequence_or_number(param, ptype=int):
260 if isinstance(param,tuple) or isinstance(param,list):
261 if len(param) == 0: return True # empty list
262 out = True
263 for p in param:
264 out &= isinstance(p,ptype)
265 return out
266 elif isinstance(param, ptype):
267 return True
268 return False
269
270def _to_list(param, ptype=int):
271 if isinstance(param, ptype):
272 if ptype is str: return param.split()
273 else: return [param]
274 if _is_sequence_or_number(param, ptype):
275 return param
276 return None
277
278def unique(x):
279 """
280 Return the unique values in a list
281 Parameters:
282 x: the list to reduce
283 Examples:
284 x = [1,2,3,3,4]
285 print unique(x)
286 [1,2,3,4]
287 """
288 return dict([ (val, 1) for val in x]).keys()
289
290def list_files(path=".",suffix="rpf"):
291 """
292 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
293 Parameters:
294 path: The directory to list (default '.')
295 suffix: The file extension (default rpf)
296 Example:
297 files = list_files("data/","sdfits")
298 print files
299 ['data/2001-09-01_0332_P363.sdfits',
300 'data/2003-04-04_131152_t0002.sdfits',
301 'data/Sgr_86p262_best_SPC.sdfits']
302 """
303 if not os.path.isdir(path):
304 return None
305 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
306 if not suffix in valid:
307 return None
308 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
309 return filter(lambda x: x.endswith(suffix),files)
310
311# workaround for ipython, which redirects this if banner=0 in ipythonrc
312sys.stdout = sys.__stdout__
313sys.stderr = sys.__stderr__
314
315# Logging
316from asap._asap import Log as _asaplog
317global asaplog
318asaplog=_asaplog()
319if rcParams['verbose']:
320 asaplog.enable()
321else:
322 asaplog.disable()
323
324def print_log():
325 log = asaplog.pop()
326 if len(log) and rcParams['verbose']: print log
327 return
328
329def mask_and(a, b):
330 assert(len(a)==len(b))
331 return [ a[i] & b[i] for i in xrange(len(a)) ]
332
333def mask_or(a, b):
334 assert(len(a)==len(b))
335 return [ a[i] | b[i] for i in xrange(len(a)) ]
336
337def mask_not(a):
338 return [ not i for i in a ]
339
340from asapfitter import fitter
341from asapreader import reader
342from selector import selector
343
344from asapmath import *
345from scantable import scantable
346from asaplinefind import linefinder
347from linecatalog import linecatalog
348
349if rcParams['useplotter']:
350 try:
351 from asapplotter import asapplotter
352 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
353 if gui:
354 import pylab as xyplotter
355 plotter = asapplotter(gui)
356 del gui
357 except ImportError:
358 print "Matplotlib not installed. No plotting available"
359
360__date__ = '$Date: 2007-03-02 00:02:27 +0000 (Fri, 02 Mar 2007) $'.split()[1]
361__version__ = '2.1.2'
362
363def is_ipython():
364 return '__IP' in dir(sys.modules["__main__"])
365if is_ipython():
366 def version(): print "ASAP %s(%s)"% (__version__, __date__)
367 def list_scans(t = scantable):
368 import types
369 globs = sys.modules['__main__'].__dict__.iteritems()
370 print "The user created scantables are:"
371 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
372 print filter(lambda x: not x.startswith('_'), sts)
373 return
374
375 def commands():
376 x = """
377 [The scan container]
378 scantable - a container for integrations/scans
379 (can open asap/rpfits/sdfits and ms files)
380 copy - returns a copy of a scan
381 get_scan - gets a specific scan out of a scantable
382 (by name or number)
383 drop_scan - drops a specific scan out of a scantable
384 (by number)
385 set_selection - set a new subselection of the data
386 get_selection - get the current selection object
387 summary - print info about the scantable contents
388 stats - get specified statistic of the spectra in
389 the scantable
390 stddev - get the standard deviation of the spectra
391 in the scantable
392 get_tsys - get the TSys
393 get_time - get the timestamps of the integrations
394 get_sourcename - get the source names of the scans
395 get_azimuth - get the azimuth of the scans
396 get_elevation - get the elevation of the scans
397 get_parangle - get the parallactic angle of the scans
398 get_unit - get the current unit
399 set_unit - set the abcissa unit to be used from this
400 point on
401 get_abcissa - get the abcissa values and name for a given
402 row (time)
403 get_column_names - get the names of the columns in the scantable
404 for use with selector.set_query
405 set_freqframe - set the frame info for the Spectral Axis
406 (e.g. 'LSRK')
407 set_doppler - set the doppler to be used from this point on
408 set_dirframe - set the frame for the direction on the sky
409 set_instrument - set the instrument name
410 set_feedtype - set the feed type
411 get_fluxunit - get the brightness flux unit
412 set_fluxunit - set the brightness flux unit
413 create_mask - return an mask in the current unit
414 for the given region. The specified regions
415 are NOT masked
416 get_restfreqs - get the current list of rest frequencies
417 set_restfreqs - set a list of rest frequencies
418 flag - flag selected channels in the data
419 lag_flag - flag specified frequency in the data
420 save - save the scantable to disk as either 'ASAP',
421 'SDFITS' or 'ASCII'
422 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
423 nscan - the number of scans in the scantable
424 nrow - te number of spectra in the scantable
425 history - print the history of the scantable
426 get_fit - get a fit which has been stored witnh the data
427 average_time - return the (weighted) time average of a scan
428 or a list of scans
429 average_pol - average the polarisations together.
430 average_beam - average the beams together.
431 convert_pol - convert to a different polarisation type
432 auto_quotient - return the on/off quotient with
433 automatic detection of the on/off scans (closest
434 in time off is selected)
435 mx_quotient - Form a quotient using MX data (off beams)
436 scale, *, / - return a scan scaled by a given factor
437 add, +, - - return a scan with given value added
438 bin - return a scan with binned channels
439 resample - return a scan with resampled channels
440 smooth - return the spectrally smoothed scan
441 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
442 auto_poly_baseline - automatically fit a polynomial baseline
443 recalc_azel - recalculate azimuth and elevation based on
444 the pointing
445 gain_el - apply gain-elevation correction
446 opacity - apply opacity correction
447 convert_flux - convert to and from Jy and Kelvin brightness
448 units
449 freq_align - align spectra in frequency frame
450 invert_phase - Invert the phase of the cross-correlation
451 swap_linears - Swap XX and YY
452 rotate_xyphase - rotate XY phase of cross correlation
453 rotate_linpolphase - rotate the phase of the complex
454 polarization O=Q+iU correlation
455 freq_switch - perform frequency switching on the data
456 stats - Determine the specified statistic, e.g. 'min'
457 'max', 'rms' etc.
458 stddev - Determine the standard deviation of the current
459 beam/if/pol
460 [Selection]
461 selector - a selection object to set a subset of a scantable
462 set_scans - set (a list of) scans by index
463 set_cycles - set (a list of) cycles by index
464 set_beams - set (a list of) beamss by index
465 set_ifs - set (a list of) ifs by index
466 set_polarisations - set (a list of) polarisations by name
467 or by index
468 set_names - set a selection by name (wildcards allowed)
469 set_tsys - set a selection by tsys thresholds
470 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
471 reset - unset all selections
472 + - merge to selections
473
474 [Math] Mainly functions which operate on more than one scantable
475
476 average_time - return the (weighted) time average
477 of a list of scans
478 quotient - return the on/off quotient
479 simple_math - simple mathematical operations on two scantables,
480 'add', 'sub', 'mul', 'div'
481 quotient - build quotient of the given on and off scans
482 (matched pairs and 1 off/n on are valid)
483 merge - merge a list of scantables
484
485 [Line Catalog]
486 linecatalog - a linecatalog wrapper, taking an ASCII or
487 internal format table
488 summary - print a summary of the current selection
489 set_name - select a subset by name pattern, e.g. '*OH*'
490 set_strength_limits - select a subset by line strength limits
491 set_frequency_limits - select a subset by frequency limits
492 reset - unset all selections
493 save - save the current subset to a table (internal
494 format)
495 get_row - get the name and frequency from a specific
496 row in the table
497 [Fitting]
498 fitter
499 auto_fit - return a scan where the function is
500 applied to all Beams/IFs/Pols.
501 commit - return a new scan where the fits have been
502 commited.
503 fit - execute the actual fitting process
504 store_fit - store the fit parameters in the data (scantable)
505 get_chi2 - get the Chi^2
506 set_scan - set the scantable to be fit
507 set_function - set the fitting function
508 set_parameters - set the parameters for the function(s), and
509 set if they should be held fixed during fitting
510 set_gauss_parameters - same as above but specialised for individual
511 gaussian components
512 get_parameters - get the fitted parameters
513 plot - plot the resulting fit and/or components and
514 residual
515 [Plotter]
516 asapplotter - a plotter for asap, default plotter is
517 called 'plotter'
518 plot - plot a scantable
519 plot_lines - plot a linecatalog overlay
520 save - save the plot to a file ('png' ,'ps' or 'eps')
521 set_mode - set the state of the plotter, i.e.
522 what is to be plotted 'colour stacked'
523 and what 'panelled'
524 set_selection - only plot a selected part of the data
525 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
526 set_legend - specify user labels for the legend indeces
527 set_title - specify user labels for the panel indeces
528 set_abcissa - specify a user label for the abcissa
529 set_ordinate - specify a user label for the ordinate
530 set_layout - specify the multi-panel layout (rows,cols)
531 set_colors - specify a set of colours to use
532 set_linestyles - specify a set of linestyles to use if only
533 using one color
534 set_font - set general font properties, e.g. 'family'
535 set_histogram - plot in historam style
536 set_mask - set a plotting mask for a specific polarization
537 text - draw text annotations either in data or relative
538 coordinates
539 arrow - draw arrow annotations either in data or relative
540 coordinates
541 axhline,axvline - draw horizontal/vertical lines
542 axhspan,axvspan - draw horizontal/vertical regions
543
544 xyplotter - matplotlib/pylab plotting functions
545
546 [Reading files]
547 reader - access rpfits/sdfits files
548 open - attach reader to a file
549 close - detach reader from file
550 read - read in integrations
551 summary - list info about all integrations
552
553 [General]
554 commands - this command
555 print - print details about a variable
556 list_scans - list all scantables created bt the user
557 list_files - list all files readable by asap (default rpf)
558 del - delete the given variable from memory
559 range - create a list of values, e.g.
560 range(3) = [0,1,2], range(2,5) = [2,3,4]
561 help - print help for one of the listed functions
562 execfile - execute an asap script, e.g. execfile('myscript')
563 list_rcparameters - print out a list of possible values to be
564 put into $HOME/.asaprc
565 rc - set rc parameters from within asap
566 mask_and,mask_or,
567 mask_not - boolean operations on masks created with
568 scantable.create_mask
569
570 Note:
571 How to use this with help:
572 # function 'summary'
573 [xxx] is just a category
574 Every 'sub-level' in this list should be replaces by a '.' Period when
575 using help
576 Example:
577 ASAP> help scantable # to get info on ths scantable
578 ASAP> help scantable.summary # to get help on the scantable's
579 ASAP> help average_time
580
581 """
582 if rcParams['verbose']:
583 try:
584 from IPython.genutils import page as pager
585 except ImportError:
586 from pydoc import pager
587 pager(x)
588 else:
589 print x
590 return
591
592def welcome():
593 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
594
595Please report any bugs via:
596http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
597
598[IMPORTANT: ASAP is 0-based]
599Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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