source: trunk/python/__init__.py@ 1714

Last change on this file since 1714 was 1697, checked in by Malte Marquarding, 15 years ago

Some minor tidy up and documentation

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Line 
1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
5import os,sys,shutil, platform
6try:
7 from functools import wraps as wraps_dec
8except ImportError:
9 from asap.compatibility import wraps as wraps_dec
10
11# Set up AIPSPATH and first time use of asap i.e. ~/.asap/*
12plf = None
13if sys.platform == "linux2":
14 if platform.architecture()[0] == '64bit':
15 plf = 'linux_64b'
16 else:
17 plf = 'linux_gnu'
18elif sys.platform == 'darwin':
19 plf = 'darwin'
20else:
21 # Shouldn't happen - default to linux
22 plf = 'linux'
23asapdata = __path__[-1]
24# Allow user defined data location
25if os.environ.has_key("ASAPDATA"):
26 if os.path.exists(os.environ["ASAPDATA"]):
27 asapdata = os.environ["ASAPDATA"]
28# use AIPSPATH if defined and "data" dir present
29if not os.environ.has_key("AIPSPATH") or \
30 not os.path.exists(os.environ["AIPSPATH"].split()[0]+"/data"):
31 os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
32# set up user space
33userdir = os.environ["HOME"]+"/.asap"
34if not os.path.exists(userdir):
35 print 'First time ASAP use. Setting up ~/.asap'
36 os.mkdir(userdir)
37 shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
38 shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
39 userdir+"/ipy_user_conf.py")
40 f = file(userdir+"/asapuserfuncs.py", "w")
41 f.close()
42 f = file(userdir+"/ipythonrc", "w")
43 f.close()
44else:
45 # upgrade to support later ipython versions
46 if not os.path.exists(userdir+"/ipy_user_conf.py"):
47 shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
48 userdir+"/ipy_user_conf.py")
49
50# remove from namespace
51del asapdata, userdir, shutil, platform
52
53def _validate_bool(b):
54 'Convert b to a boolean or raise'
55 bl = b.lower()
56 if bl in ('f', 'no', 'false', '0', 0): return False
57 elif bl in ('t', 'yes', 'true', '1', 1): return True
58 else:
59 raise ValueError('Could not convert "%s" to boolean' % b)
60
61def _validate_int(s):
62 'convert s to int or raise'
63 try: return int(s)
64 except ValueError:
65 raise ValueError('Could not convert "%s" to int' % s)
66
67def _asap_fname():
68 """
69 Return the path to the rc file
70
71 Search order:
72
73 * current working dir
74 * environ var ASAPRC
75 * HOME/.asaprc
76
77 """
78
79 fname = os.path.join( os.getcwd(), '.asaprc')
80 if os.path.exists(fname): return fname
81
82 if os.environ.has_key('ASAPRC'):
83 path = os.environ['ASAPRC']
84 if os.path.exists(path):
85 fname = os.path.join(path, '.asaprc')
86 if os.path.exists(fname):
87 return fname
88
89 if os.environ.has_key('HOME'):
90 home = os.environ['HOME']
91 fname = os.path.join(home, '.asaprc')
92 if os.path.exists(fname):
93 return fname
94 return None
95
96
97defaultParams = {
98 # general
99 'verbose' : [True, _validate_bool],
100 'useplotter' : [True, _validate_bool],
101 'insitu' : [True, _validate_bool],
102
103 # plotting
104 'plotter.gui' : [True, _validate_bool],
105 'plotter.stacking' : ['p', str],
106 'plotter.panelling' : ['s', str],
107 'plotter.colours' : ['', str],
108 'plotter.linestyles' : ['', str],
109 'plotter.decimate' : [False, _validate_bool],
110 'plotter.ganged' : [True, _validate_bool],
111 'plotter.histogram' : [False, _validate_bool],
112 'plotter.papertype' : ['A4', str],
113 'plotter.axesformatting' : ['mpl', str],
114
115 # scantable
116 'scantable.save' : ['ASAP', str],
117 'scantable.autoaverage' : [True, _validate_bool],
118 'scantable.freqframe' : ['LSRK', str], #default frequency frame
119 'scantable.verbosesummary' : [False, _validate_bool],
120 'scantable.storage' : ['memory', str],
121 'scantable.history' : [True, _validate_bool],
122 'scantable.reference' : ['.*(e|w|_R)$', str],
123 'scantable.parallactify' : [False, _validate_bool]
124 # fitter
125 }
126
127def list_rcparameters():
128
129 print """
130# general
131# print verbose output
132verbose : True
133
134# preload a default plotter
135useplotter : True
136
137# apply operations on the input scantable or return new one
138insitu : True
139
140# plotting
141
142# do we want a GUI or plot to a file
143plotter.gui : True
144
145# default mode for colour stacking
146plotter.stacking : Pol
147
148# default mode for panelling
149plotter.panelling : scan
150
151# push panels together, to share axis labels
152plotter.ganged : True
153
154# decimate the number of points plotted by a factor of
155# nchan/1024
156plotter.decimate : False
157
158# default colours/linestyles
159plotter.colours :
160plotter.linestyles :
161
162# enable/disable histogram plotting
163plotter.histogram : False
164
165# ps paper type
166plotter.papertype : A4
167
168# The formatting style of the xaxis
169plotter.axesformatting : 'mpl' (default) or 'asap' (for old versions of matplotlib)
170
171# scantable
172
173# default storage of scantable ('memory'/'disk')
174scantable.storage : memory
175
176# write history of each call to scantable
177scantable.history : True
178
179# default ouput format when saving
180scantable.save : ASAP
181
182# auto averaging on read
183scantable.autoaverage : True
184
185# default frequency frame to set when function
186# scantable.set_freqframe is called
187scantable.freqframe : LSRK
188
189# Control the level of information printed by summary
190scantable.verbosesummary : False
191
192# Control the identification of reference (off) scans
193# This is has to be a regular expression
194scantable.reference : .*(e|w|_R)$
195
196# Indicate whether the data was parallactified (total phase offest == 0.0)
197scantable.parallactify : False
198
199# Fitter
200"""
201
202def rc_params():
203 'Return the default params updated from the values in the rc file'
204
205 fname = _asap_fname()
206
207 if fname is None or not os.path.exists(fname):
208 message = 'could not find rc file; returning defaults'
209 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
210 #print message
211 return ret
212
213 cnt = 0
214 for line in file(fname):
215 cnt +=1
216 line = line.strip()
217 if not len(line): continue
218 if line.startswith('#'): continue
219 tup = line.split(':',1)
220 if len(tup) !=2:
221 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
222 continue
223
224 key, val = tup
225 key = key.strip()
226 if not defaultParams.has_key(key):
227 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
228 continue
229
230 default, converter = defaultParams[key]
231
232 ind = val.find('#')
233 if ind>=0: val = val[:ind] # ignore trailing comments
234 val = val.strip()
235 try: cval = converter(val) # try to convert to proper type or raise
236 except ValueError, msg:
237 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
238 continue
239 else:
240 # Alles Klar, update dict
241 defaultParams[key][0] = cval
242
243 # strip the conveter funcs and return
244 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
245 print ('loaded rc file %s'%fname)
246
247 return ret
248
249
250# this is the instance used by the asap classes
251rcParams = rc_params()
252
253rcParamsDefault = dict(rcParams.items()) # a copy
254
255def rc(group, **kwargs):
256 """
257 Set the current rc params. Group is the grouping for the rc, eg
258 for scantable.save the group is 'scantable', for plotter.stacking, the
259 group is 'plotter', and so on. kwargs is a list of attribute
260 name/value pairs, eg
261
262 rc('scantable', save='SDFITS')
263
264 sets the current rc params and is equivalent to
265
266 rcParams['scantable.save'] = 'SDFITS'
267
268 Use rcdefaults to restore the default rc params after changes.
269 """
270
271 aliases = {}
272
273 for k,v in kwargs.items():
274 name = aliases.get(k) or k
275 if len(group):
276 key = '%s.%s' % (group, name)
277 else:
278 key = name
279 if not rcParams.has_key(key):
280 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
281
282 rcParams[key] = v
283
284
285def rcdefaults():
286 """
287 Restore the default rc params - the ones that were created at
288 asap load time
289 """
290 rcParams.update(rcParamsDefault)
291
292def _n_bools(n, val):
293 return [ val for i in xrange(n) ]
294
295def _is_sequence_or_number(param, ptype=int):
296 if isinstance(param,tuple) or isinstance(param,list):
297 if len(param) == 0: return True # empty list
298 out = True
299 for p in param:
300 out &= isinstance(p,ptype)
301 return out
302 elif isinstance(param, ptype):
303 return True
304 return False
305
306def _to_list(param, ptype=int):
307 if isinstance(param, ptype):
308 if ptype is str: return param.split()
309 else: return [param]
310 if _is_sequence_or_number(param, ptype):
311 return param
312 return None
313
314def unique(x):
315 """
316 Return the unique values in a list
317 Parameters:
318 x: the list to reduce
319 Examples:
320 x = [1,2,3,3,4]
321 print unique(x)
322 [1,2,3,4]
323 """
324 return dict([ (val, 1) for val in x]).keys()
325
326def list_files(path=".",suffix="rpf"):
327 """
328 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
329 Parameters:
330 path: The directory to list (default '.')
331 suffix: The file extension (default rpf)
332 Example:
333 files = list_files("data/","sdfits")
334 print files
335 ['data/2001-09-01_0332_P363.sdfits',
336 'data/2003-04-04_131152_t0002.sdfits',
337 'data/Sgr_86p262_best_SPC.sdfits']
338 """
339 if not os.path.isdir(path):
340 return None
341 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
342 if not suffix in valid:
343 return None
344 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
345 return filter(lambda x: x.endswith(suffix),files)
346
347# workaround for ipython, which redirects this if banner=0 in ipythonrc
348sys.stdout = sys.__stdout__
349sys.stderr = sys.__stderr__
350
351# Logging
352from asap._asap import Log as _asaplog
353global asaplog
354asaplog=_asaplog()
355if rcParams['verbose']:
356 asaplog.enable()
357else:
358 asaplog.disable()
359
360
361def print_log_dec(f):
362 @wraps_dec(f)
363 def wrap_it(*args, **kw):
364 val = f(*args, **kw)
365 print_log()
366 return val
367 return wrap_it
368
369def print_log():
370 log = asaplog.pop().strip()
371 if len(log) and rcParams['verbose']: print log
372 return
373
374def mask_and(a, b):
375 assert(len(a)==len(b))
376 return [ a[i] & b[i] for i in xrange(len(a)) ]
377
378def mask_or(a, b):
379 assert(len(a)==len(b))
380 return [ a[i] | b[i] for i in xrange(len(a)) ]
381
382def mask_not(a):
383 return [ not i for i in a ]
384
385from asapfitter import fitter
386from asapreader import reader
387from selector import selector
388
389from asapmath import *
390from scantable import scantable
391from asaplinefind import linefinder
392from simplelinefinder import simplelinefinder
393from linecatalog import linecatalog
394from opacity import skydip
395
396if rcParams['useplotter']:
397 try:
398 from asapplotter import asapplotter
399 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
400 if gui:
401 import matplotlib
402 matplotlib.use("TkAgg")
403 from matplotlib import pylab
404 xyplotter = pylab
405 plotter = asapplotter(gui)
406 del gui
407 except ImportError:
408 print "Matplotlib not installed. No plotting available"
409
410__date__ = '$Date: 2010-02-11 00:46:14 +0000 (Thu, 11 Feb 2010) $'.split()[1]
411__version__ = '$Revision: 1697 $'
412
413def is_ipython():
414 return '__IP' in dir(sys.modules["__main__"])
415
416if is_ipython():
417 def version(): print "ASAP %s(%s)"% (__version__, __date__)
418
419 def list_scans(t = scantable):
420 import inspect
421 print "The user created scantables are: ",
422 globs=inspect.currentframe().f_back.f_locals.copy()
423 out = [ k for k,v in globs.iteritems() \
424 if isinstance(v, scantable) and not k.startswith("_") ]
425 print out
426 return out
427
428 def commands():
429 x = """
430 [The scan container]
431 scantable - a container for integrations/scans
432 (can open asap/rpfits/sdfits and ms files)
433 copy - returns a copy of a scan
434 get_scan - gets a specific scan out of a scantable
435 (by name or number)
436 drop_scan - drops a specific scan out of a scantable
437 (by number)
438 set_selection - set a new subselection of the data
439 get_selection - get the current selection object
440 summary - print info about the scantable contents
441 stats - get specified statistic of the spectra in
442 the scantable
443 stddev - get the standard deviation of the spectra
444 in the scantable
445 get_tsys - get the TSys
446 get_time - get the timestamps of the integrations
447 get_inttime - get the integration time
448 get_sourcename - get the source names of the scans
449 get_azimuth - get the azimuth of the scans
450 get_elevation - get the elevation of the scans
451 get_parangle - get the parallactic angle of the scans
452 get_coordinate - get the spectral coordinate for the given row,
453 which can be used for coordinate conversions
454 get_unit - get the current unit
455 set_unit - set the abcissa unit to be used from this
456 point on
457 get_abcissa - get the abcissa values and name for a given
458 row (time)
459 get_column_names - get the names of the columns in the scantable
460 for use with selector.set_query
461 set_freqframe - set the frame info for the Spectral Axis
462 (e.g. 'LSRK')
463 set_doppler - set the doppler to be used from this point on
464 set_dirframe - set the frame for the direction on the sky
465 set_instrument - set the instrument name
466 set_feedtype - set the feed type
467 get_fluxunit - get the brightness flux unit
468 set_fluxunit - set the brightness flux unit
469 set_sourcetype - set the type of the source - source or reference
470 create_mask - return an mask in the current unit
471 for the given region. The specified regions
472 are NOT masked
473 get_restfreqs - get the current list of rest frequencies
474 set_restfreqs - set a list of rest frequencies
475 shift_refpix - shift the reference pixel of the IFs
476 set_spectrum - overwrite the spectrum for a given row
477 get_spectrum - retrieve the spectrum for a given
478 get_mask - retrieve the mask for a given
479 flag - flag selected channels in the data
480 lag_flag - flag specified frequency in the data
481 save - save the scantable to disk as either 'ASAP',
482 'SDFITS' or 'ASCII'
483 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
484 nscan - the number of scans in the scantable
485 nrow - the number of spectra in the scantable
486 history - print the history of the scantable
487 get_fit - get a fit which has been stored witnh the data
488 average_time - return the (weighted) time average of a scan
489 or a list of scans
490 average_pol - average the polarisations together.
491 average_beam - average the beams together.
492 convert_pol - convert to a different polarisation type
493 auto_quotient - return the on/off quotient with
494 automatic detection of the on/off scans (closest
495 in time off is selected)
496 mx_quotient - Form a quotient using MX data (off beams)
497 scale, *, / - return a scan scaled by a given factor
498 add, + - return a scan with given value added
499 sub, - - return a scan with given value subtracted
500 bin - return a scan with binned channels
501 resample - return a scan with resampled channels
502 smooth - return the spectrally smoothed scan
503 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
504 auto_poly_baseline - automatically fit a polynomial baseline
505 recalc_azel - recalculate azimuth and elevation based on
506 the pointing
507 gain_el - apply gain-elevation correction
508 opacity - apply opacity correction
509 convert_flux - convert to and from Jy and Kelvin brightness
510 units
511 freq_align - align spectra in frequency frame
512 invert_phase - Invert the phase of the cross-correlation
513 swap_linears - Swap XX and YY (or RR LL)
514 rotate_xyphase - rotate XY phase of cross correlation
515 rotate_linpolphase - rotate the phase of the complex
516 polarization O=Q+iU correlation
517 freq_switch - perform frequency switching on the data
518 stats - Determine the specified statistic, e.g. 'min'
519 'max', 'rms' etc.
520 stddev - Determine the standard deviation of the current
521 beam/if/pol
522 get_row_selector - get the selection object for a specified row
523 number
524 [Selection]
525 selector - a selection object to set a subset of a scantable
526 set_scans - set (a list of) scans by index
527 set_cycles - set (a list of) cycles by index
528 set_beams - set (a list of) beamss by index
529 set_ifs - set (a list of) ifs by index
530 set_polarisations - set (a list of) polarisations by name
531 or by index
532 set_names - set a selection by name (wildcards allowed)
533 set_tsys - set a selection by tsys thresholds
534 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
535 ( also get_ functions for all these )
536 reset - unset all selections
537 + - merge two selections
538
539 [Math] Mainly functions which operate on more than one scantable
540
541 average_time - return the (weighted) time average
542 of a list of scans
543 quotient - return the on/off quotient
544 simple_math - simple mathematical operations on two scantables,
545 'add', 'sub', 'mul', 'div'
546 quotient - build quotient of the given on and off scans
547 (matched pairs and 1 off - n on are valid)
548 merge - merge a list of scantables
549
550 [Line Catalog]
551 linecatalog - a linecatalog wrapper, taking an ASCII or
552 internal format table
553 summary - print a summary of the current selection
554 set_name - select a subset by name pattern, e.g. '*OH*'
555 set_strength_limits - select a subset by line strength limits
556 set_frequency_limits - select a subset by frequency limits
557 reset - unset all selections
558 save - save the current subset to a table (internal
559 format)
560 get_row - get the name and frequency from a specific
561 row in the table
562 [Fitting]
563 fitter
564 auto_fit - return a scan where the function is
565 applied to all Beams/IFs/Pols.
566 commit - return a new scan where the fits have been
567 commited.
568 fit - execute the actual fitting process
569 store_fit - store the fit parameters in the data (scantable)
570 get_chi2 - get the Chi^2
571 set_scan - set the scantable to be fit
572 set_function - set the fitting function
573 set_parameters - set the parameters for the function(s), and
574 set if they should be held fixed during fitting
575 set_gauss_parameters - same as above but specialised for individual
576 gaussian components
577 get_parameters - get the fitted parameters
578 plot - plot the resulting fit and/or components and
579 residual
580 [Plotter]
581 asapplotter - a plotter for asap, default plotter is
582 called 'plotter'
583 plot - plot a scantable
584 plot_lines - plot a linecatalog overlay
585 plotazel - plot azimuth and elevation versus time
586 plotpointing - plot telescope pointings
587 save - save the plot to a file ('png' ,'ps' or 'eps')
588 set_mode - set the state of the plotter, i.e.
589 what is to be plotted 'colour stacked'
590 and what 'panelled'
591 set_selection - only plot a selected part of the data
592 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
593 set_legend - specify user labels for the legend indeces
594 set_title - specify user labels for the panel indeces
595 set_abcissa - specify a user label for the abcissa
596 set_ordinate - specify a user label for the ordinate
597 set_layout - specify the multi-panel layout (rows,cols)
598 set_colors - specify a set of colours to use
599 set_linestyles - specify a set of linestyles to use if only
600 using one color
601 set_font - set general font properties, e.g. 'family'
602 set_histogram - plot in historam style
603 set_mask - set a plotting mask for a specific polarization
604 text - draw text annotations either in data or relative
605 coordinates
606 arrow - draw arrow annotations either in data or relative
607 coordinates
608 axhline,axvline - draw horizontal/vertical lines
609 axhspan,axvspan - draw horizontal/vertical regions
610 annotate - draw an arrow with label
611 create_mask - create a scnatble mask interactively
612
613 xyplotter - matplotlib/pylab plotting functions
614
615 [Reading files]
616 reader - access rpfits/sdfits files
617 open - attach reader to a file
618 close - detach reader from file
619 read - read in integrations
620 summary - list info about all integrations
621
622 [General]
623 commands - this command
624 print - print details about a variable
625 list_scans - list all scantables created by the user
626 list_files - list all files readable by asap (default rpf)
627 del - delete the given variable from memory
628 range - create a list of values, e.g.
629 range(3) = [0,1,2], range(2,5) = [2,3,4]
630 help - print help for one of the listed functions
631 execfile - execute an asap script, e.g. execfile('myscript')
632 list_rcparameters - print out a list of possible values to be
633 put into $HOME/.asaprc
634 rc - set rc parameters from within asap
635 mask_and,mask_or,
636 mask_not - boolean operations on masks created with
637 scantable.create_mask
638 skydip - gain opacity values from a sky dip observation
639
640 Note:
641 How to use this with help:
642 # function 'summary'
643 [xxx] is just a category
644 Every 'sub-level' in this list should be replaces by a '.' Period when
645 using help
646 Example:
647 ASAP> help scantable # to get info on ths scantable
648 ASAP> help scantable.summary # to get help on the scantable's
649 ASAP> help average_time
650
651 """
652 if rcParams['verbose']:
653 try:
654 from IPython.genutils import page as pager
655 except ImportError:
656 from pydoc import pager
657 pager(x)
658 else:
659 print x
660 return
661
662def welcome():
663 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
664
665Please report any bugs via:
666http://svn.atnf.csiro.au/trac/asap/simpleticket
667
668[IMPORTANT: ASAP is 0-based]
669Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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