source: branches/alma/python/__init__.py@ 1623

Last change on this file since 1623 was 1614, checked in by Takeshi Nakazato, 15 years ago

New Development: No

JIRA Issue: Yes CAS-729, CAS-1147

Ready to Release: Yes

Interface Changes: No

What Interface Changed: Please list interface changes

Test Programs: List test programs

Put in Release Notes: No

Module(s): Module Names change impacts.

Description: Describe your changes here...

  1. Added level parameter to print_log()
  2. Replaced casalog.post() to asaplog.push() + print_log().


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 24.9 KB
Line 
1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
5import os,sys,shutil, platform
6
7# Set up CASAPATH 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"]
24# use CASAPATH if defined and "data" dir present
25if not os.environ.has_key("CASAPATH") or \
26 not os.path.exists(os.environ["CASAPATH"].split()[0]+"/data"):
27 os.environ["CASAPATH"] = "%s %s somwhere" % ( asapdata, plf)
28# set up user space
29userdir = os.environ["HOME"]+"/.asap"
30if not os.path.exists(userdir):
31 print 'First time ASAP use. Setting up ~/.asap'
32 os.mkdir(userdir)
33 #shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
34 # commented out by TT on 2009.06.23 for casapy use
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()
41# commented out by TT on 2009.06.23 for casapy use
42##else:
43 # upgrade to support later ipython versions
44 ##if not os.path.exists(userdir+"/ipy_user_conf.py"):
45 ## shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
46 ## userdir+"/ipy_user_conf.py")
47
48# remove from namespace
49del asapdata, userdir, shutil, platform
50
51def _validate_bool(b):
52 'Convert b to a boolean or raise'
53 bl = b.lower()
54 if bl in ('f', 'no', 'false', '0', 0): return False
55 elif bl in ('t', 'yes', 'true', '1', 1): return True
56 else:
57 raise ValueError('Could not convert "%s" to boolean' % b)
58
59def _validate_int(s):
60 'convert s to int or raise'
61 try: return int(s)
62 except ValueError:
63 raise ValueError('Could not convert "%s" to int' % s)
64
65def _asap_fname():
66 """
67 Return the path to the rc file
68
69 Search order:
70
71 * current working dir
72 * environ var ASAPRC
73 * HOME/.asaprc
74
75 """
76
77 fname = os.path.join( os.getcwd(), '.asaprc')
78 if os.path.exists(fname): return fname
79
80 if os.environ.has_key('ASAPRC'):
81 path = os.environ['ASAPRC']
82 if os.path.exists(path):
83 fname = os.path.join(path, '.asaprc')
84 if os.path.exists(fname):
85 return fname
86
87 if os.environ.has_key('HOME'):
88 home = os.environ['HOME']
89 fname = os.path.join(home, '.asaprc')
90 if os.path.exists(fname):
91 return fname
92 return None
93
94
95defaultParams = {
96 # general
97 'verbose' : [True, _validate_bool],
98 'useplotter' : [True, _validate_bool],
99 'insitu' : [True, _validate_bool],
100
101 # plotting
102 'plotter.gui' : [True, _validate_bool],
103 'plotter.stacking' : ['p', str],
104 'plotter.panelling' : ['s', str],
105 'plotter.colours' : ['', str],
106 'plotter.linestyles' : ['', str],
107 'plotter.decimate' : [False, _validate_bool],
108 'plotter.ganged' : [True, _validate_bool],
109 'plotter.histogram' : [False, _validate_bool],
110 'plotter.papertype' : ['A4', str],
111 'plotter.xaxisformatting' : ['asap', str],
112
113 # scantable
114 'scantable.save' : ['ASAP', str],
115 'scantable.autoaverage' : [True, _validate_bool],
116 'scantable.freqframe' : ['LSRK', str], #default frequency frame
117 'scantable.verbosesummary' : [False, _validate_bool],
118 'scantable.storage' : ['memory', str],
119 'scantable.history' : [True, _validate_bool],
120 'scantable.reference' : ['.*(e|w|_R)$', str]
121 # fitter
122 }
123
124def list_rcparameters():
125
126 print """
127# general
128# print verbose output
129verbose : True
130
131# preload a default plotter
132useplotter : True
133
134# apply operations on the input scantable or return new one
135insitu : True
136
137# plotting
138
139# do we want a GUI or plot to a file
140plotter.gui : True
141
142# default mode for colour stacking
143plotter.stacking : Pol
144
145# default mode for panelling
146plotter.panelling : scan
147
148# push panels together, to share axislabels
149plotter.ganged : True
150
151# decimate the number of points plotted by a factor of
152# nchan/1024
153plotter.decimate : False
154
155# default colours/linestyles
156plotter.colours :
157plotter.linestyles :
158
159# enable/disable histogram plotting
160plotter.histogram : False
161
162# ps paper type
163plotter.papertype : A4
164
165# The formatting style of the xaxis
166plotter.xaxisformatting : 'asap' or 'mpl'
167
168# scantable
169
170# default storage of scantable ('memory'/'disk')
171scantable.storage : memory
172
173# write history of each call to scantable
174scantable.history : True
175
176# default ouput format when saving
177scantable.save : ASAP
178
179# auto averaging on read
180scantable.autoaverage : True
181
182# default frequency frame to set when function
183# scantable.set_freqframe is called
184scantable.freqframe : LSRK
185
186# Control the level of information printed by summary
187scantable.verbosesummary : False
188
189# Control the identification of reference (off) scans
190# This is has to be a regular expression
191scantable.reference : .*(e|w|_R)$
192# Fitter
193"""
194
195def rc_params():
196 'Return the default params updated from the values in the rc file'
197
198 fname = _asap_fname()
199
200 if fname is None or not os.path.exists(fname):
201 message = 'could not find rc file; returning defaults'
202 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
203 #print message
204 return ret
205
206 cnt = 0
207 for line in file(fname):
208 cnt +=1
209 line = line.strip()
210 if not len(line): continue
211 if line.startswith('#'): continue
212 tup = line.split(':',1)
213 if len(tup) !=2:
214 #print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
215 asaplog.push('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
216 print_log('WARN')
217 continue
218
219 key, val = tup
220 key = key.strip()
221 if not defaultParams.has_key(key):
222 #print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
223 asaplog.push('Bad key "%s" on line %d in %s' % (key, cnt, fname))
224 print_log('WARN')
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 asaplog.push('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
236 print_log('WARN')
237 continue
238 else:
239 # Alles Klar, update dict
240 defaultParams[key][0] = cval
241
242 # strip the conveter funcs and return
243 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
244 print ('loaded rc file %s'%fname)
245
246 return ret
247
248
249# this is the instance used by the asap classes
250rcParams = rc_params()
251
252rcParamsDefault = dict(rcParams.items()) # a copy
253
254def rc(group, **kwargs):
255 """
256 Set the current rc params. Group is the grouping for the rc, eg
257 for scantable.save the group is 'scantable', for plotter.stacking, the
258 group is 'plotter', and so on. kwargs is a list of attribute
259 name/value pairs, eg
260
261 rc('scantable', save='SDFITS')
262
263 sets the current rc params and is equivalent to
264
265 rcParams['scantable.save'] = 'SDFITS'
266
267 Use rcdefaults to restore the default rc params after changes.
268 """
269
270 aliases = {}
271
272 for k,v in kwargs.items():
273 name = aliases.get(k) or k
274 if len(group):
275 key = '%s.%s' % (group, name)
276 else:
277 key = name
278 if not rcParams.has_key(key):
279 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
280
281 rcParams[key] = v
282
283
284def rcdefaults():
285 """
286 Restore the default rc params - the ones that were created at
287 asap load time
288 """
289 rcParams.update(rcParamsDefault)
290
291def _n_bools(n, val):
292 return [ val for i in xrange(n) ]
293
294def _is_sequence_or_number(param, ptype=int):
295 if isinstance(param,tuple) or isinstance(param,list):
296 if len(param) == 0: return True # empty list
297 out = True
298 for p in param:
299 out &= isinstance(p,ptype)
300 return out
301 elif isinstance(param, ptype):
302 return True
303 return False
304
305def _to_list(param, ptype=int):
306 if isinstance(param, ptype):
307 if ptype is str: return param.split()
308 else: return [param]
309 if _is_sequence_or_number(param, ptype):
310 return param
311 return None
312
313def unique(x):
314 """
315 Return the unique values in a list
316 Parameters:
317 x: the list to reduce
318 Examples:
319 x = [1,2,3,3,4]
320 print unique(x)
321 [1,2,3,4]
322 """
323 return dict([ (val, 1) for val in x]).keys()
324
325def list_files(path=".",suffix="rpf"):
326 """
327 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
328 Parameters:
329 path: The directory to list (default '.')
330 suffix: The file extension (default rpf)
331 Example:
332 files = list_files("data/","sdfits")
333 print files
334 ['data/2001-09-01_0332_P363.sdfits',
335 'data/2003-04-04_131152_t0002.sdfits',
336 'data/Sgr_86p262_best_SPC.sdfits']
337 """
338 if not os.path.isdir(path):
339 return None
340 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
341 if not suffix in valid:
342 return None
343 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
344 return filter(lambda x: x.endswith(suffix),files)
345
346# workaround for ipython, which redirects this if banner=0 in ipythonrc
347sys.stdout = sys.__stdout__
348sys.stderr = sys.__stderr__
349
350# Logging
351from taskinit import *
352from asap._asap import Log as _asaplog
353global asaplog
354asaplog=_asaplog()
355if rcParams['verbose']:
356 asaplog.enable()
357else:
358 asaplog.disable()
359
360def print_log(level='INFO'):
361 log = asaplog.pop()
362 #if len(log) and rcParams['verbose']: print log
363 if len(log) and rcParams['verbose']: casalog.post( log, priority=level )
364 return
365
366def mask_and(a, b):
367 assert(len(a)==len(b))
368 return [ a[i] & b[i] for i in xrange(len(a)) ]
369
370def mask_or(a, b):
371 assert(len(a)==len(b))
372 return [ a[i] | b[i] for i in xrange(len(a)) ]
373
374def mask_not(a):
375 return [ not i for i in a ]
376
377from asapfitter import fitter
378from asapreader import reader
379from selector import selector
380
381from asapmath import *
382from scantable import scantable
383from asaplinefind import linefinder
384from linecatalog import linecatalog
385from interactivemask import interactivemask
386
387if rcParams['useplotter']:
388 try:
389 from asapplotter import asapplotter
390 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
391 if gui:
392 import matplotlib
393 matplotlib.use("TkAgg")
394 import pylab
395 xyplotter = pylab
396 plotter = asapplotter(gui)
397 del gui
398 except ImportError:
399 #print "Matplotlib not installed. No plotting available"
400 asaplog.post( "Matplotlib not installed. No plotting available")
401 print_log('WARN')
402
403__date__ = '$Date: 2009-08-06 05:48:39 +0000 (Thu, 06 Aug 2009) $'.split()[1]
404__version__ = '2.3.1 alma'
405# nrao casapy specific, get revision number
406#__revision__ = ' unknown '
407casapath=os.environ["CASAPATH"].split()
408revinfo=casapath[0]+'/'+casapath[1]+'/python/2.5/asap/svninfo.txt'
409if os.path.isfile(revinfo):
410 f = file(revinfo)
411 f.readline()
412 revsionno=f.readline()
413 f.close()
414 __revision__ = revsionno.rstrip()
415else:
416 __revision__ = ' unknown '
417
418def is_ipython():
419 return '__IP' in dir(sys.modules["__main__"])
420if is_ipython():
421 def version(): print "ASAP %s(%s)"% (__version__, __date__)
422 def list_scans(t = scantable):
423 import types
424 globs = sys.modules['__main__'].__dict__.iteritems()
425 print "The user created scantables are:"
426 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
427 print filter(lambda x: not x.startswith('_'), sts)
428 return
429
430 def commands():
431 x = """
432 [The scan container]
433 scantable - a container for integrations/scans
434 (can open asap/rpfits/sdfits and ms files)
435 copy - returns a copy of a scan
436 get_scan - gets a specific scan out of a scantable
437 (by name or number)
438 drop_scan - drops a specific scan out of a scantable
439 (by number)
440 set_selection - set a new subselection of the data
441 get_selection - get the current selection object
442 summary - print info about the scantable contents
443 stats - get specified statistic of the spectra in
444 the scantable
445 stddev - get the standard deviation of the spectra
446 in the scantable
447 get_tsys - get the TSys
448 get_time - get the timestamps of the integrations
449 get_inttime - get the integration time
450 get_sourcename - get the source names of the scans
451 get_azimuth - get the azimuth of the scans
452 get_elevation - get the elevation of the scans
453 get_parangle - get the parallactic angle of the scans
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 bin - return a scan with binned channels
500 resample - return a scan with resampled channels
501 smooth - return the spectrally smoothed scan
502 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
503 auto_poly_baseline - automatically fit a polynomial baseline
504 recalc_azel - recalculate azimuth and elevation based on
505 the pointing
506 gain_el - apply gain-elevation correction
507 opacity - apply opacity correction
508 convert_flux - convert to and from Jy and Kelvin brightness
509 units
510 freq_align - align spectra in frequency frame
511 invert_phase - Invert the phase of the cross-correlation
512 swap_linears - Swap XX and YY (or RR LL)
513 rotate_xyphase - rotate XY phase of cross correlation
514 rotate_linpolphase - rotate the phase of the complex
515 polarization O=Q+iU correlation
516 freq_switch - perform frequency switching on the data
517 stats - Determine the specified statistic, e.g. 'min'
518 'max', 'rms' etc.
519 stddev - Determine the standard deviation of the current
520 beam/if/pol
521 [Selection]
522 selector - a selection object to set a subset of a scantable
523 set_scans - set (a list of) scans by index
524 set_cycles - set (a list of) cycles by index
525 set_beams - set (a list of) beamss by index
526 set_ifs - set (a list of) ifs by index
527 set_polarisations - set (a list of) polarisations by name
528 or by index
529 set_names - set a selection by name (wildcards allowed)
530 set_tsys - set a selection by tsys thresholds
531 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
532 ( also get_ functions for all these )
533 reset - unset all selections
534 + - merge two selections
535
536 [Math] Mainly functions which operate on more than one scantable
537
538 average_time - return the (weighted) time average
539 of a list of scans
540 quotient - return the on/off quotient
541 simple_math - simple mathematical operations on two scantables,
542 'add', 'sub', 'mul', 'div'
543 quotient - build quotient of the given on and off scans
544 (matched pairs and 1 off - n on are valid)
545 merge - merge a list of scantables
546
547 [Line Catalog]
548 linecatalog - a linecatalog wrapper, taking an ASCII or
549 internal format table
550 summary - print a summary of the current selection
551 set_name - select a subset by name pattern, e.g. '*OH*'
552 set_strength_limits - select a subset by line strength limits
553 set_frequency_limits - select a subset by frequency limits
554 reset - unset all selections
555 save - save the current subset to a table (internal
556 format)
557 get_row - get the name and frequency from a specific
558 row in the table
559 [Fitting]
560 fitter
561 auto_fit - return a scan where the function is
562 applied to all Beams/IFs/Pols.
563 commit - return a new scan where the fits have been
564 commited.
565 fit - execute the actual fitting process
566 store_fit - store the fit parameters in the data (scantable)
567 get_chi2 - get the Chi^2
568 set_scan - set the scantable to be fit
569 set_function - set the fitting function
570 set_parameters - set the parameters for the function(s), and
571 set if they should be held fixed during fitting
572 set_gauss_parameters - same as above but specialised for individual
573 gaussian components
574 get_parameters - get the fitted parameters
575 plot - plot the resulting fit and/or components and
576 residual
577 [Plotter]
578 asapplotter - a plotter for asap, default plotter is
579 called 'plotter'
580 plot - plot a scantable
581 plot_lines - plot a linecatalog overlay
582 save - save the plot to a file ('png' ,'ps' or 'eps')
583 set_mode - set the state of the plotter, i.e.
584 what is to be plotted 'colour stacked'
585 and what 'panelled'
586 set_selection - only plot a selected part of the data
587 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
588 set_legend - specify user labels for the legend indeces
589 set_title - specify user labels for the panel indeces
590 set_abcissa - specify a user label for the abcissa
591 set_ordinate - specify a user label for the ordinate
592 set_layout - specify the multi-panel layout (rows,cols)
593 set_colors - specify a set of colours to use
594 set_linestyles - specify a set of linestyles to use if only
595 using one color
596 set_font - set general font properties, e.g. 'family'
597 set_histogram - plot in historam style
598 set_mask - set a plotting mask for a specific polarization
599 text - draw text annotations either in data or relative
600 coordinates
601 arrow - draw arrow annotations either in data or relative
602 coordinates
603 axhline,axvline - draw horizontal/vertical lines
604 axhspan,axvspan - draw horizontal/vertical regions
605
606 xyplotter - matplotlib/pylab plotting functions
607
608 [Reading files]
609 reader - access rpfits/sdfits files
610 open - attach reader to a file
611 close - detach reader from file
612 read - read in integrations
613 summary - list info about all integrations
614
615 [General]
616 commands - this command
617 print - print details about a variable
618 list_scans - list all scantables created bt the user
619 list_files - list all files readable by asap (default rpf)
620 del - delete the given variable from memory
621 range - create a list of values, e.g.
622 range(3) = [0,1,2], range(2,5) = [2,3,4]
623 help - print help for one of the listed functions
624 execfile - execute an asap script, e.g. execfile('myscript')
625 list_rcparameters - print out a list of possible values to be
626 put into $HOME/.asaprc
627 rc - set rc parameters from within asap
628 mask_and,mask_or,
629 mask_not - boolean operations on masks created with
630 scantable.create_mask
631
632 Note:
633 How to use this with help:
634 # function 'summary'
635 [xxx] is just a category
636 Every 'sub-level' in this list should be replaces by a '.' Period when
637 using help
638 Example:
639 ASAP> help scantable # to get info on ths scantable
640 ASAP> help scantable.summary # to get help on the scantable's
641 ASAP> help average_time
642
643 """
644 if rcParams['verbose']:
645 try:
646 from IPython.genutils import page as pager
647 except ImportError:
648 from pydoc import pager
649 pager(x)
650 else:
651 print x
652 return
653
654def welcome():
655 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
656
657Please report any bugs via:
658http://svn.atnf.csiro.au/trac/asap/simpleticket
659
660[IMPORTANT: ASAP is 0-based]
661Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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