source: trunk/python/__init__.py@ 1444

Last change on this file since 1444 was 1434, checked in by Malte Marquarding, 16 years ago

work with ipython >= 0.8

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 23.0 KB
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"]
24# use AIPSPATH if defined and "data" dir present
25if not os.environ.has_key("AIPSPATH") or \
26 not os.path.exists(os.environ["AIPSPATH"].split()[0]+"/data"):
27 os.environ["AIPSPATH"] = "%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 shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
35 userdir+"/ipy_user_conf.py")
36 f = file(userdir+"/asapuserfuncs.py", "w")
37 f.close()
38 f = file(userdir+"/ipythonrc", "w")
39 f.close()
40# remove from namespace
41del asapdata, userdir, shutil, platform
42
43def _validate_bool(b):
44 'Convert b to a boolean or raise'
45 bl = b.lower()
46 if bl in ('f', 'no', 'false', '0', 0): return False
47 elif bl in ('t', 'yes', 'true', '1', 1): return True
48 else:
49 raise ValueError('Could not convert "%s" to boolean' % b)
50
51def _validate_int(s):
52 'convert s to int or raise'
53 try: return int(s)
54 except ValueError:
55 raise ValueError('Could not convert "%s" to int' % s)
56
57def _asap_fname():
58 """
59 Return the path to the rc file
60
61 Search order:
62
63 * current working dir
64 * environ var ASAPRC
65 * HOME/.asaprc
66
67 """
68
69 fname = os.path.join( os.getcwd(), '.asaprc')
70 if os.path.exists(fname): return fname
71
72 if os.environ.has_key('ASAPRC'):
73 path = os.environ['ASAPRC']
74 if os.path.exists(path):
75 fname = os.path.join(path, '.asaprc')
76 if os.path.exists(fname):
77 return fname
78
79 if os.environ.has_key('HOME'):
80 home = os.environ['HOME']
81 fname = os.path.join(home, '.asaprc')
82 if os.path.exists(fname):
83 return fname
84 return None
85
86
87defaultParams = {
88 # general
89 'verbose' : [True, _validate_bool],
90 'useplotter' : [True, _validate_bool],
91 'insitu' : [True, _validate_bool],
92
93 # plotting
94 'plotter.gui' : [True, _validate_bool],
95 'plotter.stacking' : ['p', str],
96 'plotter.panelling' : ['s', str],
97 'plotter.colours' : ['', str],
98 'plotter.linestyles' : ['', str],
99 'plotter.decimate' : [False, _validate_bool],
100 'plotter.ganged' : [True, _validate_bool],
101 'plotter.histogram' : [False, _validate_bool],
102 'plotter.papertype' : ['A4', str],
103
104 # scantable
105 'scantable.save' : ['ASAP', str],
106 'scantable.autoaverage' : [True, _validate_bool],
107 'scantable.freqframe' : ['LSRK', str], #default frequency frame
108 'scantable.verbosesummary' : [False, _validate_bool],
109 'scantable.storage' : ['memory', str],
110 'scantable.history' : [True, _validate_bool]
111 # fitter
112 }
113
114def list_rcparameters():
115
116 print """
117# general
118# print verbose output
119verbose : True
120
121# preload a default plotter
122useplotter : True
123
124# apply operations on the input scantable or return new one
125insitu : True
126
127# plotting
128
129# do we want a GUI or plot to a file
130plotter.gui : True
131
132# default mode for colour stacking
133plotter.stacking : Pol
134
135# default mode for panelling
136plotter.panelling : scan
137
138# push panels together, to share axislabels
139plotter.ganged : True
140
141# decimate the number of points plotted bya afactor of
142# nchan/1024
143plotter.decimate : False
144
145# default colours/linestyles
146plotter.colours :
147plotter.linestyles :
148
149# enable/disable histogram plotting
150plotter.histogram : False
151
152# ps paper type
153plotter.papertype : A4
154
155# scantable
156
157# default storage of scantable ('memory'/'disk')
158scantable.storage : memory
159
160# write history of each call to scantable
161scantable.history : True
162
163# default ouput format when saving
164scantable.save : ASAP
165
166# auto averaging on read
167scantable.autoaverage : True
168
169# default frequency frame to set when function
170# scantable.set_freqframe is called
171scantable.freqframe : LSRK
172
173# Control the level of information printed by summary
174scantable.verbosesummary : False
175
176# Fitter
177"""
178
179def rc_params():
180 'Return the default params updated from the values in the rc file'
181
182 fname = _asap_fname()
183
184 if fname is None or not os.path.exists(fname):
185 message = 'could not find rc file; returning defaults'
186 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
187 #print message
188 return ret
189
190 cnt = 0
191 for line in file(fname):
192 cnt +=1
193 line = line.strip()
194 if not len(line): continue
195 if line.startswith('#'): continue
196 tup = line.split(':',1)
197 if len(tup) !=2:
198 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
199 continue
200
201 key, val = tup
202 key = key.strip()
203 if not defaultParams.has_key(key):
204 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
205 continue
206
207 default, converter = defaultParams[key]
208
209 ind = val.find('#')
210 if ind>=0: val = val[:ind] # ignore trailing comments
211 val = val.strip()
212 try: cval = converter(val) # try to convert to proper type or raise
213 except ValueError, msg:
214 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
215 continue
216 else:
217 # Alles Klar, update dict
218 defaultParams[key][0] = cval
219
220 # strip the conveter funcs and return
221 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
222 print ('loaded rc file %s'%fname)
223
224 return ret
225
226
227# this is the instance used by the asap classes
228rcParams = rc_params()
229
230rcParamsDefault = dict(rcParams.items()) # a copy
231
232def rc(group, **kwargs):
233 """
234 Set the current rc params. Group is the grouping for the rc, eg
235 for scantable.save the group is 'scantable', for plotter.stacking, the
236 group is 'plotter', and so on. kwargs is a list of attribute
237 name/value pairs, eg
238
239 rc('scantable', save='SDFITS')
240
241 sets the current rc params and is equivalent to
242
243 rcParams['scantable.save'] = 'SDFITS'
244
245 Use rcdefaults to restore the default rc params after changes.
246 """
247
248 aliases = {}
249
250 for k,v in kwargs.items():
251 name = aliases.get(k) or k
252 if len(group):
253 key = '%s.%s' % (group, name)
254 else:
255 key = name
256 if not rcParams.has_key(key):
257 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
258
259 rcParams[key] = v
260
261
262def rcdefaults():
263 """
264 Restore the default rc params - the ones that were created at
265 asap load time
266 """
267 rcParams.update(rcParamsDefault)
268
269def _n_bools(n, val):
270 return [ val for i in xrange(n) ]
271
272def _is_sequence_or_number(param, ptype=int):
273 if isinstance(param,tuple) or isinstance(param,list):
274 if len(param) == 0: return True # empty list
275 out = True
276 for p in param:
277 out &= isinstance(p,ptype)
278 return out
279 elif isinstance(param, ptype):
280 return True
281 return False
282
283def _to_list(param, ptype=int):
284 if isinstance(param, ptype):
285 if ptype is str: return param.split()
286 else: return [param]
287 if _is_sequence_or_number(param, ptype):
288 return param
289 return None
290
291def unique(x):
292 """
293 Return the unique values in a list
294 Parameters:
295 x: the list to reduce
296 Examples:
297 x = [1,2,3,3,4]
298 print unique(x)
299 [1,2,3,4]
300 """
301 return dict([ (val, 1) for val in x]).keys()
302
303def list_files(path=".",suffix="rpf"):
304 """
305 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
306 Parameters:
307 path: The directory to list (default '.')
308 suffix: The file extension (default rpf)
309 Example:
310 files = list_files("data/","sdfits")
311 print files
312 ['data/2001-09-01_0332_P363.sdfits',
313 'data/2003-04-04_131152_t0002.sdfits',
314 'data/Sgr_86p262_best_SPC.sdfits']
315 """
316 if not os.path.isdir(path):
317 return None
318 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
319 if not suffix in valid:
320 return None
321 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
322 return filter(lambda x: x.endswith(suffix),files)
323
324# workaround for ipython, which redirects this if banner=0 in ipythonrc
325sys.stdout = sys.__stdout__
326sys.stderr = sys.__stderr__
327
328# Logging
329from asap._asap import Log as _asaplog
330global asaplog
331asaplog=_asaplog()
332if rcParams['verbose']:
333 asaplog.enable()
334else:
335 asaplog.disable()
336
337def print_log():
338 log = asaplog.pop()
339 if len(log) and rcParams['verbose']: print log
340 return
341
342def mask_and(a, b):
343 assert(len(a)==len(b))
344 return [ a[i] & b[i] for i in xrange(len(a)) ]
345
346def mask_or(a, b):
347 assert(len(a)==len(b))
348 return [ a[i] | b[i] for i in xrange(len(a)) ]
349
350def mask_not(a):
351 return [ not i for i in a ]
352
353from asapfitter import fitter
354from asapreader import reader
355from selector import selector
356
357from asapmath import *
358from scantable import scantable
359from asaplinefind import linefinder
360from linecatalog import linecatalog
361
362if rcParams['useplotter']:
363 try:
364 from asapplotter import asapplotter
365 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
366 if gui:
367 import matplotlib
368 matplotlib.use("TkAgg")
369 import pylab
370 xyplotter = pylab
371 plotter = asapplotter(gui)
372 del gui
373 except ImportError:
374 print "Matplotlib not installed. No plotting available"
375
376__date__ = '$Date: 2008-08-28 03:55:49 +0000 (Thu, 28 Aug 2008) $'.split()[1]
377__version__ = 'trunk'
378
379def is_ipython():
380 return '__IP' in dir(sys.modules["__main__"])
381if is_ipython():
382 def version(): print "ASAP %s(%s)"% (__version__, __date__)
383
384 def list_scans(t = scantable):
385 import types
386 globs = sys.modules['__main__'].__dict__.iteritems()
387 print "The user created scantables are:"
388 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
389 print filter(lambda x: not x.startswith('_'), sts)
390 return
391
392 def commands():
393 x = """
394 [The scan container]
395 scantable - a container for integrations/scans
396 (can open asap/rpfits/sdfits and ms files)
397 copy - returns a copy of a scan
398 get_scan - gets a specific scan out of a scantable
399 (by name or number)
400 drop_scan - drops a specific scan out of a scantable
401 (by number)
402 set_selection - set a new subselection of the data
403 get_selection - get the current selection object
404 summary - print info about the scantable contents
405 stats - get specified statistic of the spectra in
406 the scantable
407 stddev - get the standard deviation of the spectra
408 in the scantable
409 get_tsys - get the TSys
410 get_time - get the timestamps of the integrations
411 get_inttime - get the integration time
412 get_sourcename - get the source names of the scans
413 get_azimuth - get the azimuth of the scans
414 get_elevation - get the elevation of the scans
415 get_parangle - get the parallactic angle of the scans
416 get_unit - get the current unit
417 set_unit - set the abcissa unit to be used from this
418 point on
419 get_abcissa - get the abcissa values and name for a given
420 row (time)
421 get_column_names - get the names of the columns in the scantable
422 for use with selector.set_query
423 set_freqframe - set the frame info for the Spectral Axis
424 (e.g. 'LSRK')
425 set_doppler - set the doppler to be used from this point on
426 set_dirframe - set the frame for the direction on the sky
427 set_instrument - set the instrument name
428 set_feedtype - set the feed type
429 get_fluxunit - get the brightness flux unit
430 set_fluxunit - set the brightness flux unit
431 create_mask - return an mask in the current unit
432 for the given region. The specified regions
433 are NOT masked
434 get_restfreqs - get the current list of rest frequencies
435 set_restfreqs - set a list of rest frequencies
436 shift_refpix - shift the reference pixel of the IFs
437 flag - flag selected channels in the data
438 lag_flag - flag specified frequency in the data
439 save - save the scantable to disk as either 'ASAP',
440 'SDFITS' or 'ASCII'
441 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
442 nscan - the number of scans in the scantable
443 nrow - the number of spectra in the scantable
444 history - print the history of the scantable
445 get_fit - get a fit which has been stored witnh the data
446 average_time - return the (weighted) time average of a scan
447 or a list of scans
448 average_pol - average the polarisations together.
449 average_beam - average the beams together.
450 convert_pol - convert to a different polarisation type
451 auto_quotient - return the on/off quotient with
452 automatic detection of the on/off scans (closest
453 in time off is selected)
454 mx_quotient - Form a quotient using MX data (off beams)
455 scale, *, / - return a scan scaled by a given factor
456 add, +, - - return a scan with given value added
457 bin - return a scan with binned channels
458 resample - return a scan with resampled channels
459 smooth - return the spectrally smoothed scan
460 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
461 auto_poly_baseline - automatically fit a polynomial baseline
462 recalc_azel - recalculate azimuth and elevation based on
463 the pointing
464 gain_el - apply gain-elevation correction
465 opacity - apply opacity correction
466 convert_flux - convert to and from Jy and Kelvin brightness
467 units
468 freq_align - align spectra in frequency frame
469 invert_phase - Invert the phase of the cross-correlation
470 swap_linears - Swap XX and YY (or RR LL)
471 rotate_xyphase - rotate XY phase of cross correlation
472 rotate_linpolphase - rotate the phase of the complex
473 polarization O=Q+iU correlation
474 freq_switch - perform frequency switching on the data
475 stats - Determine the specified statistic, e.g. 'min'
476 'max', 'rms' etc.
477 stddev - Determine the standard deviation of the current
478 beam/if/pol
479 [Selection]
480 selector - a selection object to set a subset of a scantable
481 set_scans - set (a list of) scans by index
482 set_cycles - set (a list of) cycles by index
483 set_beams - set (a list of) beamss by index
484 set_ifs - set (a list of) ifs by index
485 set_polarisations - set (a list of) polarisations by name
486 or by index
487 set_names - set a selection by name (wildcards allowed)
488 set_tsys - set a selection by tsys thresholds
489 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
490 ( also get_ functions for all these )
491 reset - unset all selections
492 + - merge two selections
493
494 [Math] Mainly functions which operate on more than one scantable
495
496 average_time - return the (weighted) time average
497 of a list of scans
498 quotient - return the on/off quotient
499 simple_math - simple mathematical operations on two scantables,
500 'add', 'sub', 'mul', 'div'
501 quotient - build quotient of the given on and off scans
502 (matched pairs and 1 off - n on are valid)
503 merge - merge a list of scantables
504
505 [Line Catalog]
506 linecatalog - a linecatalog wrapper, taking an ASCII or
507 internal format table
508 summary - print a summary of the current selection
509 set_name - select a subset by name pattern, e.g. '*OH*'
510 set_strength_limits - select a subset by line strength limits
511 set_frequency_limits - select a subset by frequency limits
512 reset - unset all selections
513 save - save the current subset to a table (internal
514 format)
515 get_row - get the name and frequency from a specific
516 row in the table
517 [Fitting]
518 fitter
519 auto_fit - return a scan where the function is
520 applied to all Beams/IFs/Pols.
521 commit - return a new scan where the fits have been
522 commited.
523 fit - execute the actual fitting process
524 store_fit - store the fit parameters in the data (scantable)
525 get_chi2 - get the Chi^2
526 set_scan - set the scantable to be fit
527 set_function - set the fitting function
528 set_parameters - set the parameters for the function(s), and
529 set if they should be held fixed during fitting
530 set_gauss_parameters - same as above but specialised for individual
531 gaussian components
532 get_parameters - get the fitted parameters
533 plot - plot the resulting fit and/or components and
534 residual
535 [Plotter]
536 asapplotter - a plotter for asap, default plotter is
537 called 'plotter'
538 plot - plot a scantable
539 plot_lines - plot a linecatalog overlay
540 save - save the plot to a file ('png' ,'ps' or 'eps')
541 set_mode - set the state of the plotter, i.e.
542 what is to be plotted 'colour stacked'
543 and what 'panelled'
544 set_selection - only plot a selected part of the data
545 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
546 set_legend - specify user labels for the legend indeces
547 set_title - specify user labels for the panel indeces
548 set_abcissa - specify a user label for the abcissa
549 set_ordinate - specify a user label for the ordinate
550 set_layout - specify the multi-panel layout (rows,cols)
551 set_colors - specify a set of colours to use
552 set_linestyles - specify a set of linestyles to use if only
553 using one color
554 set_font - set general font properties, e.g. 'family'
555 set_histogram - plot in historam style
556 set_mask - set a plotting mask for a specific polarization
557 text - draw text annotations either in data or relative
558 coordinates
559 arrow - draw arrow annotations either in data or relative
560 coordinates
561 axhline,axvline - draw horizontal/vertical lines
562 axhspan,axvspan - draw horizontal/vertical regions
563
564 xyplotter - matplotlib/pylab plotting functions
565
566 [Reading files]
567 reader - access rpfits/sdfits files
568 open - attach reader to a file
569 close - detach reader from file
570 read - read in integrations
571 summary - list info about all integrations
572
573 [General]
574 commands - this command
575 print - print details about a variable
576 list_scans - list all scantables created bt the user
577 list_files - list all files readable by asap (default rpf)
578 del - delete the given variable from memory
579 range - create a list of values, e.g.
580 range(3) = [0,1,2], range(2,5) = [2,3,4]
581 help - print help for one of the listed functions
582 execfile - execute an asap script, e.g. execfile('myscript')
583 list_rcparameters - print out a list of possible values to be
584 put into $HOME/.asaprc
585 rc - set rc parameters from within asap
586 mask_and,mask_or,
587 mask_not - boolean operations on masks created with
588 scantable.create_mask
589
590 Note:
591 How to use this with help:
592 # function 'summary'
593 [xxx] is just a category
594 Every 'sub-level' in this list should be replaces by a '.' Period when
595 using help
596 Example:
597 ASAP> help scantable # to get info on ths scantable
598 ASAP> help scantable.summary # to get help on the scantable's
599 ASAP> help average_time
600
601 """
602 if rcParams['verbose']:
603 try:
604 from IPython.genutils import page as pager
605 except ImportError:
606 from pydoc import pager
607 pager(x)
608 else:
609 print x
610 return
611
612def welcome():
613 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
614
615Please report any bugs via:
616http://svn.atnf.csiro.au/trac/asap/simpleticket
617
618[IMPORTANT: ASAP is 0-based]
619Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
Note: See TracBrowser for help on using the repository browser.