source: branches/alma/python/__init__.py@ 1708

Last change on this file since 1708 was 1676, checked in by Takeshi Nakazato, 15 years ago

New Development: No

JIRA Issue: Yes CAS-1920

Ready to Release: Yes

Interface Changes: No

What Interface Changed: Please list interface changes

Test Programs: List test programs

Put in Release Notes: Yes/No

Module(s): Module Names change impacts.

Description: Describe your changes here...

Bug fix.
The object that the except block catches either Exception object or string.
Thus, .message attribute, which is proper for Exception object, should not
use. I have replaced .message attribute with str() function.


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 25.3 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, str(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 asap._asap import Log as _asaplog
352global asaplog
353asaplog=_asaplog()
354if rcParams['verbose']:
355 asaplog.enable()
356else:
357 asaplog.disable()
358
359def print_log(level='INFO'):
360 from taskinit import casalog
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: 2010-01-27 00:43:10 +0000 (Wed, 27 Jan 2010) $'.split()[1]
404__version__ = '2.3.1 alma'
405# nrao casapy specific, get revision number
406#__revision__ = ' unknown '
407casapath=os.environ["CASAPATH"].split()
408#svninfo.txt path
409if os.path.isdir(casapath[0]+'/'+casapath[1]+'/python/2.5/asap'):
410 # for casa developer environment (linux or darwin)
411 revinfo=casapath[0]+'/'+casapath[1]+'/python/2.5/asap/svninfo.txt'
412else:
413 # for end-user environments
414 if casapath[1]=='darwin':
415 revinfo=casapath[0]+'/Resources/python/asap/svninfo.txt'
416 else:
417 revinfo=casapath[0]+'/lib/python2.5/asap/svninfo.txt'
418if os.path.isfile(revinfo):
419 f = file(revinfo)
420 f.readline()
421 revsionno=f.readline()
422 f.close()
423 del f
424 __revision__ = revsionno.rstrip()
425else:
426 __revision__ = ' unknown '
427
428def is_ipython():
429 return '__IP' in dir(sys.modules["__main__"])
430if is_ipython():
431 def version(): print "ASAP %s(%s)"% (__version__, __date__)
432 def list_scans(t = scantable):
433 import types
434 globs = sys.modules['__main__'].__dict__.iteritems()
435 print "The user created scantables are:"
436 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
437 print filter(lambda x: not x.startswith('_'), sts)
438 return
439
440 def commands():
441 x = """
442 [The scan container]
443 scantable - a container for integrations/scans
444 (can open asap/rpfits/sdfits and ms files)
445 copy - returns a copy of a scan
446 get_scan - gets a specific scan out of a scantable
447 (by name or number)
448 drop_scan - drops a specific scan out of a scantable
449 (by number)
450 set_selection - set a new subselection of the data
451 get_selection - get the current selection object
452 summary - print info about the scantable contents
453 stats - get specified statistic of the spectra in
454 the scantable
455 stddev - get the standard deviation of the spectra
456 in the scantable
457 get_tsys - get the TSys
458 get_time - get the timestamps of the integrations
459 get_inttime - get the integration time
460 get_sourcename - get the source names of the scans
461 get_azimuth - get the azimuth of the scans
462 get_elevation - get the elevation of the scans
463 get_parangle - get the parallactic angle of the scans
464 get_unit - get the current unit
465 set_unit - set the abcissa unit to be used from this
466 point on
467 get_abcissa - get the abcissa values and name for a given
468 row (time)
469 get_column_names - get the names of the columns in the scantable
470 for use with selector.set_query
471 set_freqframe - set the frame info for the Spectral Axis
472 (e.g. 'LSRK')
473 set_doppler - set the doppler to be used from this point on
474 set_dirframe - set the frame for the direction on the sky
475 set_instrument - set the instrument name
476 set_feedtype - set the feed type
477 get_fluxunit - get the brightness flux unit
478 set_fluxunit - set the brightness flux unit
479 set_sourcetype - set the type of the source - source or reference
480 create_mask - return an mask in the current unit
481 for the given region. The specified regions
482 are NOT masked
483 get_restfreqs - get the current list of rest frequencies
484 set_restfreqs - set a list of rest frequencies
485 shift_refpix - shift the reference pixel of the IFs
486 set_spectrum - overwrite the spectrum for a given row
487 get_spectrum - retrieve the spectrum for a given
488 get_mask - retrieve the mask for a given
489 flag - flag selected channels in the data
490 lag_flag - flag specified frequency in the data
491 save - save the scantable to disk as either 'ASAP',
492 'SDFITS' or 'ASCII'
493 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
494 nscan - the number of scans in the scantable
495 nrow - the number of spectra in the scantable
496 history - print the history of the scantable
497 get_fit - get a fit which has been stored witnh the data
498 average_time - return the (weighted) time average of a scan
499 or a list of scans
500 average_pol - average the polarisations together.
501 average_beam - average the beams together.
502 convert_pol - convert to a different polarisation type
503 auto_quotient - return the on/off quotient with
504 automatic detection of the on/off scans (closest
505 in time off is selected)
506 mx_quotient - Form a quotient using MX data (off beams)
507 scale, *, / - return a scan scaled by a given factor
508 add, +, - - return a scan with given value added
509 bin - return a scan with binned channels
510 resample - return a scan with resampled channels
511 smooth - return the spectrally smoothed scan
512 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
513 auto_poly_baseline - automatically fit a polynomial baseline
514 recalc_azel - recalculate azimuth and elevation based on
515 the pointing
516 gain_el - apply gain-elevation correction
517 opacity - apply opacity correction
518 convert_flux - convert to and from Jy and Kelvin brightness
519 units
520 freq_align - align spectra in frequency frame
521 invert_phase - Invert the phase of the cross-correlation
522 swap_linears - Swap XX and YY (or RR LL)
523 rotate_xyphase - rotate XY phase of cross correlation
524 rotate_linpolphase - rotate the phase of the complex
525 polarization O=Q+iU correlation
526 freq_switch - perform frequency switching on the data
527 stats - Determine the specified statistic, e.g. 'min'
528 'max', 'rms' etc.
529 stddev - Determine the standard deviation of the current
530 beam/if/pol
531 [Selection]
532 selector - a selection object to set a subset of a scantable
533 set_scans - set (a list of) scans by index
534 set_cycles - set (a list of) cycles by index
535 set_beams - set (a list of) beamss by index
536 set_ifs - set (a list of) ifs by index
537 set_polarisations - set (a list of) polarisations by name
538 or by index
539 set_names - set a selection by name (wildcards allowed)
540 set_tsys - set a selection by tsys thresholds
541 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
542 ( also get_ functions for all these )
543 reset - unset all selections
544 + - merge two selections
545
546 [Math] Mainly functions which operate on more than one scantable
547
548 average_time - return the (weighted) time average
549 of a list of scans
550 quotient - return the on/off quotient
551 simple_math - simple mathematical operations on two scantables,
552 'add', 'sub', 'mul', 'div'
553 quotient - build quotient of the given on and off scans
554 (matched pairs and 1 off - n on are valid)
555 merge - merge a list of scantables
556
557 [Line Catalog]
558 linecatalog - a linecatalog wrapper, taking an ASCII or
559 internal format table
560 summary - print a summary of the current selection
561 set_name - select a subset by name pattern, e.g. '*OH*'
562 set_strength_limits - select a subset by line strength limits
563 set_frequency_limits - select a subset by frequency limits
564 reset - unset all selections
565 save - save the current subset to a table (internal
566 format)
567 get_row - get the name and frequency from a specific
568 row in the table
569 [Fitting]
570 fitter
571 auto_fit - return a scan where the function is
572 applied to all Beams/IFs/Pols.
573 commit - return a new scan where the fits have been
574 commited.
575 fit - execute the actual fitting process
576 store_fit - store the fit parameters in the data (scantable)
577 get_chi2 - get the Chi^2
578 set_scan - set the scantable to be fit
579 set_function - set the fitting function
580 set_parameters - set the parameters for the function(s), and
581 set if they should be held fixed during fitting
582 set_gauss_parameters - same as above but specialised for individual
583 gaussian components
584 get_parameters - get the fitted parameters
585 plot - plot the resulting fit and/or components and
586 residual
587 [Plotter]
588 asapplotter - a plotter for asap, default plotter is
589 called 'plotter'
590 plot - plot a scantable
591 plot_lines - plot a linecatalog overlay
592 save - save the plot to a file ('png' ,'ps' or 'eps')
593 set_mode - set the state of the plotter, i.e.
594 what is to be plotted 'colour stacked'
595 and what 'panelled'
596 set_selection - only plot a selected part of the data
597 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
598 set_legend - specify user labels for the legend indeces
599 set_title - specify user labels for the panel indeces
600 set_abcissa - specify a user label for the abcissa
601 set_ordinate - specify a user label for the ordinate
602 set_layout - specify the multi-panel layout (rows,cols)
603 set_colors - specify a set of colours to use
604 set_linestyles - specify a set of linestyles to use if only
605 using one color
606 set_font - set general font properties, e.g. 'family'
607 set_histogram - plot in historam style
608 set_mask - set a plotting mask for a specific polarization
609 text - draw text annotations either in data or relative
610 coordinates
611 arrow - draw arrow annotations either in data or relative
612 coordinates
613 axhline,axvline - draw horizontal/vertical lines
614 axhspan,axvspan - draw horizontal/vertical regions
615
616 xyplotter - matplotlib/pylab plotting functions
617
618 [Reading files]
619 reader - access rpfits/sdfits files
620 open - attach reader to a file
621 close - detach reader from file
622 read - read in integrations
623 summary - list info about all integrations
624
625 [General]
626 commands - this command
627 print - print details about a variable
628 list_scans - list all scantables created bt the user
629 list_files - list all files readable by asap (default rpf)
630 del - delete the given variable from memory
631 range - create a list of values, e.g.
632 range(3) = [0,1,2], range(2,5) = [2,3,4]
633 help - print help for one of the listed functions
634 execfile - execute an asap script, e.g. execfile('myscript')
635 list_rcparameters - print out a list of possible values to be
636 put into $HOME/.asaprc
637 rc - set rc parameters from within asap
638 mask_and,mask_or,
639 mask_not - boolean operations on masks created with
640 scantable.create_mask
641
642 Note:
643 How to use this with help:
644 # function 'summary'
645 [xxx] is just a category
646 Every 'sub-level' in this list should be replaces by a '.' Period when
647 using help
648 Example:
649 ASAP> help scantable # to get info on ths scantable
650 ASAP> help scantable.summary # to get help on the scantable's
651 ASAP> help average_time
652
653 """
654 if rcParams['verbose']:
655 try:
656 from IPython.genutils import page as pager
657 except ImportError:
658 from pydoc import pager
659 pager(x)
660 else:
661 print x
662 return
663
664def welcome():
665 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
666
667Please report any bugs via:
668http://svn.atnf.csiro.au/trac/asap/simpleticket
669
670[IMPORTANT: ASAP is 0-based]
671Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
Note: See TracBrowser for help on using the repository browser.