source: trunk/python/__init__.py@ 1686

Last change on this file since 1686 was 1645, checked in by Max Voronkov, 15 years ago

added a simplified version of the linefinder (largely to be used with some scripts than on real single-dish data)

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 24.6 KB
Line 
1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
5import os,sys,shutil, platform
6import functools
7
8# Set up AIPSPATH and first time use of asap i.e. ~/.asap/*
9plf = None
10if sys.platform == "linux2":
11 if platform.architecture()[0] == '64bit':
12 plf = 'linux_64b'
13 else:
14 plf = 'linux_gnu'
15elif sys.platform == 'darwin':
16 plf = 'darwin'
17else:
18 # Shouldn't happen - default to linux
19 plf = 'linux'
20asapdata = __path__[-1]
21# Allow user defined data location
22if os.environ.has_key("ASAPDATA"):
23 if os.path.exists(os.environ["ASAPDATA"]):
24 asapdata = os.environ["ASAPDATA"]
25# use AIPSPATH if defined and "data" dir present
26if not os.environ.has_key("AIPSPATH") or \
27 not os.path.exists(os.environ["AIPSPATH"].split()[0]+"/data"):
28 os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
29# set up user space
30userdir = os.environ["HOME"]+"/.asap"
31if not os.path.exists(userdir):
32 print 'First time ASAP use. Setting up ~/.asap'
33 os.mkdir(userdir)
34 shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
35 shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
36 userdir+"/ipy_user_conf.py")
37 f = file(userdir+"/asapuserfuncs.py", "w")
38 f.close()
39 f = file(userdir+"/ipythonrc", "w")
40 f.close()
41else:
42 # upgrade to support later ipython versions
43 if not os.path.exists(userdir+"/ipy_user_conf.py"):
44 shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
45 userdir+"/ipy_user_conf.py")
46
47# remove from namespace
48del asapdata, userdir, shutil, platform
49
50def _validate_bool(b):
51 'Convert b to a boolean or raise'
52 bl = b.lower()
53 if bl in ('f', 'no', 'false', '0', 0): return False
54 elif bl in ('t', 'yes', 'true', '1', 1): return True
55 else:
56 raise ValueError('Could not convert "%s" to boolean' % b)
57
58def _validate_int(s):
59 'convert s to int or raise'
60 try: return int(s)
61 except ValueError:
62 raise ValueError('Could not convert "%s" to int' % s)
63
64def _asap_fname():
65 """
66 Return the path to the rc file
67
68 Search order:
69
70 * current working dir
71 * environ var ASAPRC
72 * HOME/.asaprc
73
74 """
75
76 fname = os.path.join( os.getcwd(), '.asaprc')
77 if os.path.exists(fname): return fname
78
79 if os.environ.has_key('ASAPRC'):
80 path = os.environ['ASAPRC']
81 if os.path.exists(path):
82 fname = os.path.join(path, '.asaprc')
83 if os.path.exists(fname):
84 return fname
85
86 if os.environ.has_key('HOME'):
87 home = os.environ['HOME']
88 fname = os.path.join(home, '.asaprc')
89 if os.path.exists(fname):
90 return fname
91 return None
92
93
94defaultParams = {
95 # general
96 'verbose' : [True, _validate_bool],
97 'useplotter' : [True, _validate_bool],
98 'insitu' : [True, _validate_bool],
99
100 # plotting
101 'plotter.gui' : [True, _validate_bool],
102 'plotter.stacking' : ['p', str],
103 'plotter.panelling' : ['s', str],
104 'plotter.colours' : ['', str],
105 'plotter.linestyles' : ['', str],
106 'plotter.decimate' : [False, _validate_bool],
107 'plotter.ganged' : [True, _validate_bool],
108 'plotter.histogram' : [False, _validate_bool],
109 'plotter.papertype' : ['A4', str],
110 'plotter.axesformatting' : ['mpl', str],
111
112 # scantable
113 'scantable.save' : ['ASAP', str],
114 'scantable.autoaverage' : [True, _validate_bool],
115 'scantable.freqframe' : ['LSRK', str], #default frequency frame
116 'scantable.verbosesummary' : [False, _validate_bool],
117 'scantable.storage' : ['memory', str],
118 'scantable.history' : [True, _validate_bool],
119 'scantable.reference' : ['.*(e|w|_R)$', str],
120 'scantable.parallactify' : [False, _validate_bool]
121 # fitter
122 }
123
124def list_rcparameters():
125
126 print """
127# general
128# print verbose output
129verbose : True
130
131# preload a default plotter
132useplotter : True
133
134# apply operations on the input scantable or return new one
135insitu : True
136
137# plotting
138
139# do we want a GUI or plot to a file
140plotter.gui : True
141
142# default mode for colour stacking
143plotter.stacking : Pol
144
145# default mode for panelling
146plotter.panelling : scan
147
148# push panels together, to share axis labels
149plotter.ganged : True
150
151# decimate the number of points plotted by a factor of
152# nchan/1024
153plotter.decimate : False
154
155# default colours/linestyles
156plotter.colours :
157plotter.linestyles :
158
159# enable/disable histogram plotting
160plotter.histogram : False
161
162# ps paper type
163plotter.papertype : A4
164
165# The formatting style of the xaxis
166plotter.axesformatting : 'mpl' (default) or 'asap' (for old versions of matplotlib)
167
168# scantable
169
170# default storage of scantable ('memory'/'disk')
171scantable.storage : memory
172
173# write history of each call to scantable
174scantable.history : True
175
176# default ouput format when saving
177scantable.save : ASAP
178
179# auto averaging on read
180scantable.autoaverage : True
181
182# default frequency frame to set when function
183# scantable.set_freqframe is called
184scantable.freqframe : LSRK
185
186# Control the level of information printed by summary
187scantable.verbosesummary : False
188
189# Control the identification of reference (off) scans
190# This is has to be a regular expression
191scantable.reference : .*(e|w|_R)$
192
193# Indicate whether the data was parallactified (total phase offest == 0.0)
194scantable.parallactify : False
195
196# Fitter
197"""
198
199def rc_params():
200 'Return the default params updated from the values in the rc file'
201
202 fname = _asap_fname()
203
204 if fname is None or not os.path.exists(fname):
205 message = 'could not find rc file; returning defaults'
206 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
207 #print message
208 return ret
209
210 cnt = 0
211 for line in file(fname):
212 cnt +=1
213 line = line.strip()
214 if not len(line): continue
215 if line.startswith('#'): continue
216 tup = line.split(':',1)
217 if len(tup) !=2:
218 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
219 continue
220
221 key, val = tup
222 key = key.strip()
223 if not defaultParams.has_key(key):
224 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
225 continue
226
227 default, converter = defaultParams[key]
228
229 ind = val.find('#')
230 if ind>=0: val = val[:ind] # ignore trailing comments
231 val = val.strip()
232 try: cval = converter(val) # try to convert to proper type or raise
233 except ValueError, msg:
234 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
235 continue
236 else:
237 # Alles Klar, update dict
238 defaultParams[key][0] = cval
239
240 # strip the conveter funcs and return
241 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
242 print ('loaded rc file %s'%fname)
243
244 return ret
245
246
247# this is the instance used by the asap classes
248rcParams = rc_params()
249
250rcParamsDefault = dict(rcParams.items()) # a copy
251
252def rc(group, **kwargs):
253 """
254 Set the current rc params. Group is the grouping for the rc, eg
255 for scantable.save the group is 'scantable', for plotter.stacking, the
256 group is 'plotter', and so on. kwargs is a list of attribute
257 name/value pairs, eg
258
259 rc('scantable', save='SDFITS')
260
261 sets the current rc params and is equivalent to
262
263 rcParams['scantable.save'] = 'SDFITS'
264
265 Use rcdefaults to restore the default rc params after changes.
266 """
267
268 aliases = {}
269
270 for k,v in kwargs.items():
271 name = aliases.get(k) or k
272 if len(group):
273 key = '%s.%s' % (group, name)
274 else:
275 key = name
276 if not rcParams.has_key(key):
277 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
278
279 rcParams[key] = v
280
281
282def rcdefaults():
283 """
284 Restore the default rc params - the ones that were created at
285 asap load time
286 """
287 rcParams.update(rcParamsDefault)
288
289def _n_bools(n, val):
290 return [ val for i in xrange(n) ]
291
292def _is_sequence_or_number(param, ptype=int):
293 if isinstance(param,tuple) or isinstance(param,list):
294 if len(param) == 0: return True # empty list
295 out = True
296 for p in param:
297 out &= isinstance(p,ptype)
298 return out
299 elif isinstance(param, ptype):
300 return True
301 return False
302
303def _to_list(param, ptype=int):
304 if isinstance(param, ptype):
305 if ptype is str: return param.split()
306 else: return [param]
307 if _is_sequence_or_number(param, ptype):
308 return param
309 return None
310
311def unique(x):
312 """
313 Return the unique values in a list
314 Parameters:
315 x: the list to reduce
316 Examples:
317 x = [1,2,3,3,4]
318 print unique(x)
319 [1,2,3,4]
320 """
321 return dict([ (val, 1) for val in x]).keys()
322
323def list_files(path=".",suffix="rpf"):
324 """
325 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
326 Parameters:
327 path: The directory to list (default '.')
328 suffix: The file extension (default rpf)
329 Example:
330 files = list_files("data/","sdfits")
331 print files
332 ['data/2001-09-01_0332_P363.sdfits',
333 'data/2003-04-04_131152_t0002.sdfits',
334 'data/Sgr_86p262_best_SPC.sdfits']
335 """
336 if not os.path.isdir(path):
337 return None
338 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
339 if not suffix in valid:
340 return None
341 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
342 return filter(lambda x: x.endswith(suffix),files)
343
344# workaround for ipython, which redirects this if banner=0 in ipythonrc
345sys.stdout = sys.__stdout__
346sys.stderr = sys.__stderr__
347
348# Logging
349from asap._asap import Log as _asaplog
350global asaplog
351asaplog=_asaplog()
352if rcParams['verbose']:
353 asaplog.enable()
354else:
355 asaplog.disable()
356
357
358def print_log_dec(f):
359 @functools.wraps(f)
360 def wrap_it(*args, **kw):
361 val = f(*args, **kw)
362 print_log()
363 return val
364 return wrap_it
365
366def print_log():
367 log = asaplog.pop().strip()
368 if len(log) and rcParams['verbose']: print log
369 return
370
371def mask_and(a, b):
372 assert(len(a)==len(b))
373 return [ a[i] & b[i] for i in xrange(len(a)) ]
374
375def mask_or(a, b):
376 assert(len(a)==len(b))
377 return [ a[i] | b[i] for i in xrange(len(a)) ]
378
379def mask_not(a):
380 return [ not i for i in a ]
381
382from asapfitter import fitter
383from asapreader import reader
384from selector import selector
385
386from asapmath import *
387from scantable import scantable
388from asaplinefind import linefinder
389from simplelinefinder import simplelinefinder
390from linecatalog import linecatalog
391
392if rcParams['useplotter']:
393 try:
394 from asapplotter import asapplotter
395 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
396 if gui:
397 import matplotlib
398 matplotlib.use("TkAgg")
399 import pylab
400 xyplotter = pylab
401 plotter = asapplotter(gui)
402 del gui
403 except ImportError:
404 print "Matplotlib not installed. No plotting available"
405
406__date__ = '$Date: 2009-10-04 12:24:37 +0000 (Sun, 04 Oct 2009) $'.split()[1]
407__version__ = '$Revision: 1645 $'
408
409def is_ipython():
410 return '__IP' in dir(sys.modules["__main__"])
411
412if is_ipython():
413 def version(): print "ASAP %s(%s)"% (__version__, __date__)
414
415 def list_scans(t = scantable):
416 import inspect
417 print "The user created scantables are: ",
418 globs=inspect.currentframe().f_back.f_locals.copy()
419 out = [ k for k,v in globs.iteritems() \
420 if isinstance(v, scantable) and not k.startswith("_") ]
421 print out
422 return out
423
424 def commands():
425 x = """
426 [The scan container]
427 scantable - a container for integrations/scans
428 (can open asap/rpfits/sdfits and ms files)
429 copy - returns a copy of a scan
430 get_scan - gets a specific scan out of a scantable
431 (by name or number)
432 drop_scan - drops a specific scan out of a scantable
433 (by number)
434 set_selection - set a new subselection of the data
435 get_selection - get the current selection object
436 summary - print info about the scantable contents
437 stats - get specified statistic of the spectra in
438 the scantable
439 stddev - get the standard deviation of the spectra
440 in the scantable
441 get_tsys - get the TSys
442 get_time - get the timestamps of the integrations
443 get_inttime - get the integration time
444 get_sourcename - get the source names of the scans
445 get_azimuth - get the azimuth of the scans
446 get_elevation - get the elevation of the scans
447 get_parangle - get the parallactic angle of the scans
448 get_unit - get the current unit
449 set_unit - set the abcissa unit to be used from this
450 point on
451 get_abcissa - get the abcissa values and name for a given
452 row (time)
453 get_column_names - get the names of the columns in the scantable
454 for use with selector.set_query
455 set_freqframe - set the frame info for the Spectral Axis
456 (e.g. 'LSRK')
457 set_doppler - set the doppler to be used from this point on
458 set_dirframe - set the frame for the direction on the sky
459 set_instrument - set the instrument name
460 set_feedtype - set the feed type
461 get_fluxunit - get the brightness flux unit
462 set_fluxunit - set the brightness flux unit
463 set_sourcetype - set the type of the source - source or reference
464 create_mask - return an mask in the current unit
465 for the given region. The specified regions
466 are NOT masked
467 get_restfreqs - get the current list of rest frequencies
468 set_restfreqs - set a list of rest frequencies
469 shift_refpix - shift the reference pixel of the IFs
470 set_spectrum - overwrite the spectrum for a given row
471 get_spectrum - retrieve the spectrum for a given
472 get_mask - retrieve the mask for a given
473 flag - flag selected channels in the data
474 lag_flag - flag specified frequency in the data
475 save - save the scantable to disk as either 'ASAP',
476 'SDFITS' or 'ASCII'
477 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
478 nscan - the number of scans in the scantable
479 nrow - the number of spectra in the scantable
480 history - print the history of the scantable
481 get_fit - get a fit which has been stored witnh the data
482 average_time - return the (weighted) time average of a scan
483 or a list of scans
484 average_pol - average the polarisations together.
485 average_beam - average the beams together.
486 convert_pol - convert to a different polarisation type
487 auto_quotient - return the on/off quotient with
488 automatic detection of the on/off scans (closest
489 in time off is selected)
490 mx_quotient - Form a quotient using MX data (off beams)
491 scale, *, / - return a scan scaled by a given factor
492 add, + - return a scan with given value added
493 sub, - - return a scan with given value subtracted
494 bin - return a scan with binned channels
495 resample - return a scan with resampled channels
496 smooth - return the spectrally smoothed scan
497 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
498 auto_poly_baseline - automatically fit a polynomial baseline
499 recalc_azel - recalculate azimuth and elevation based on
500 the pointing
501 gain_el - apply gain-elevation correction
502 opacity - apply opacity correction
503 convert_flux - convert to and from Jy and Kelvin brightness
504 units
505 freq_align - align spectra in frequency frame
506 invert_phase - Invert the phase of the cross-correlation
507 swap_linears - Swap XX and YY (or RR LL)
508 rotate_xyphase - rotate XY phase of cross correlation
509 rotate_linpolphase - rotate the phase of the complex
510 polarization O=Q+iU correlation
511 freq_switch - perform frequency switching on the data
512 stats - Determine the specified statistic, e.g. 'min'
513 'max', 'rms' etc.
514 stddev - Determine the standard deviation of the current
515 beam/if/pol
516 get_row_selector - get the selection object for a specified row
517 number
518 [Selection]
519 selector - a selection object to set a subset of a scantable
520 set_scans - set (a list of) scans by index
521 set_cycles - set (a list of) cycles by index
522 set_beams - set (a list of) beamss by index
523 set_ifs - set (a list of) ifs by index
524 set_polarisations - set (a list of) polarisations by name
525 or by index
526 set_names - set a selection by name (wildcards allowed)
527 set_tsys - set a selection by tsys thresholds
528 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
529 ( also get_ functions for all these )
530 reset - unset all selections
531 + - merge two selections
532
533 [Math] Mainly functions which operate on more than one scantable
534
535 average_time - return the (weighted) time average
536 of a list of scans
537 quotient - return the on/off quotient
538 simple_math - simple mathematical operations on two scantables,
539 'add', 'sub', 'mul', 'div'
540 quotient - build quotient of the given on and off scans
541 (matched pairs and 1 off - n on are valid)
542 merge - merge a list of scantables
543
544 [Line Catalog]
545 linecatalog - a linecatalog wrapper, taking an ASCII or
546 internal format table
547 summary - print a summary of the current selection
548 set_name - select a subset by name pattern, e.g. '*OH*'
549 set_strength_limits - select a subset by line strength limits
550 set_frequency_limits - select a subset by frequency limits
551 reset - unset all selections
552 save - save the current subset to a table (internal
553 format)
554 get_row - get the name and frequency from a specific
555 row in the table
556 [Fitting]
557 fitter
558 auto_fit - return a scan where the function is
559 applied to all Beams/IFs/Pols.
560 commit - return a new scan where the fits have been
561 commited.
562 fit - execute the actual fitting process
563 store_fit - store the fit parameters in the data (scantable)
564 get_chi2 - get the Chi^2
565 set_scan - set the scantable to be fit
566 set_function - set the fitting function
567 set_parameters - set the parameters for the function(s), and
568 set if they should be held fixed during fitting
569 set_gauss_parameters - same as above but specialised for individual
570 gaussian components
571 get_parameters - get the fitted parameters
572 plot - plot the resulting fit and/or components and
573 residual
574 [Plotter]
575 asapplotter - a plotter for asap, default plotter is
576 called 'plotter'
577 plot - plot a scantable
578 plot_lines - plot a linecatalog overlay
579 save - save the plot to a file ('png' ,'ps' or 'eps')
580 set_mode - set the state of the plotter, i.e.
581 what is to be plotted 'colour stacked'
582 and what 'panelled'
583 set_selection - only plot a selected part of the data
584 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
585 set_legend - specify user labels for the legend indeces
586 set_title - specify user labels for the panel indeces
587 set_abcissa - specify a user label for the abcissa
588 set_ordinate - specify a user label for the ordinate
589 set_layout - specify the multi-panel layout (rows,cols)
590 set_colors - specify a set of colours to use
591 set_linestyles - specify a set of linestyles to use if only
592 using one color
593 set_font - set general font properties, e.g. 'family'
594 set_histogram - plot in historam style
595 set_mask - set a plotting mask for a specific polarization
596 text - draw text annotations either in data or relative
597 coordinates
598 arrow - draw arrow annotations either in data or relative
599 coordinates
600 axhline,axvline - draw horizontal/vertical lines
601 axhspan,axvspan - draw horizontal/vertical regions
602 annotate - draw an arrow with label
603 create_mask - create a scnatble mask interactively
604
605 xyplotter - matplotlib/pylab plotting functions
606
607 [Reading files]
608 reader - access rpfits/sdfits files
609 open - attach reader to a file
610 close - detach reader from file
611 read - read in integrations
612 summary - list info about all integrations
613
614 [General]
615 commands - this command
616 print - print details about a variable
617 list_scans - list all scantables created by the user
618 list_files - list all files readable by asap (default rpf)
619 del - delete the given variable from memory
620 range - create a list of values, e.g.
621 range(3) = [0,1,2], range(2,5) = [2,3,4]
622 help - print help for one of the listed functions
623 execfile - execute an asap script, e.g. execfile('myscript')
624 list_rcparameters - print out a list of possible values to be
625 put into $HOME/.asaprc
626 rc - set rc parameters from within asap
627 mask_and,mask_or,
628 mask_not - boolean operations on masks created with
629 scantable.create_mask
630
631 Note:
632 How to use this with help:
633 # function 'summary'
634 [xxx] is just a category
635 Every 'sub-level' in this list should be replaces by a '.' Period when
636 using help
637 Example:
638 ASAP> help scantable # to get info on ths scantable
639 ASAP> help scantable.summary # to get help on the scantable's
640 ASAP> help average_time
641
642 """
643 if rcParams['verbose']:
644 try:
645 from IPython.genutils import page as pager
646 except ImportError:
647 from pydoc import pager
648 pager(x)
649 else:
650 print x
651 return
652
653def welcome():
654 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
655
656Please report any bugs via:
657http://svn.atnf.csiro.au/trac/asap/simpleticket
658
659[IMPORTANT: ASAP is 0-based]
660Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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