source: trunk/python/__init__.py@ 1492

Last change on this file since 1492 was 1472, checked in by Malte Marquarding, 16 years ago

allow upgrade of ipython rc

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File size: 23.4 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()
40else:
41 # upgrade to support later ipython versions
42 if not os.path.exists(userdir+"/ipy_user_conf.py"):
43 shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
44 userdir+"/ipy_user_conf.py")
45
46# remove from namespace
47del asapdata, userdir, shutil, platform
48
49def _validate_bool(b):
50 'Convert b to a boolean or raise'
51 bl = b.lower()
52 if bl in ('f', 'no', 'false', '0', 0): return False
53 elif bl in ('t', 'yes', 'true', '1', 1): return True
54 else:
55 raise ValueError('Could not convert "%s" to boolean' % b)
56
57def _validate_int(s):
58 'convert s to int or raise'
59 try: return int(s)
60 except ValueError:
61 raise ValueError('Could not convert "%s" to int' % s)
62
63def _asap_fname():
64 """
65 Return the path to the rc file
66
67 Search order:
68
69 * current working dir
70 * environ var ASAPRC
71 * HOME/.asaprc
72
73 """
74
75 fname = os.path.join( os.getcwd(), '.asaprc')
76 if os.path.exists(fname): return fname
77
78 if os.environ.has_key('ASAPRC'):
79 path = os.environ['ASAPRC']
80 if os.path.exists(path):
81 fname = os.path.join(path, '.asaprc')
82 if os.path.exists(fname):
83 return fname
84
85 if os.environ.has_key('HOME'):
86 home = os.environ['HOME']
87 fname = os.path.join(home, '.asaprc')
88 if os.path.exists(fname):
89 return fname
90 return None
91
92
93defaultParams = {
94 # general
95 'verbose' : [True, _validate_bool],
96 'useplotter' : [True, _validate_bool],
97 'insitu' : [True, _validate_bool],
98
99 # plotting
100 'plotter.gui' : [True, _validate_bool],
101 'plotter.stacking' : ['p', str],
102 'plotter.panelling' : ['s', str],
103 'plotter.colours' : ['', str],
104 'plotter.linestyles' : ['', str],
105 'plotter.decimate' : [False, _validate_bool],
106 'plotter.ganged' : [True, _validate_bool],
107 'plotter.histogram' : [False, _validate_bool],
108 'plotter.papertype' : ['A4', str],
109
110 # scantable
111 'scantable.save' : ['ASAP', str],
112 'scantable.autoaverage' : [True, _validate_bool],
113 'scantable.freqframe' : ['LSRK', str], #default frequency frame
114 'scantable.verbosesummary' : [False, _validate_bool],
115 'scantable.storage' : ['memory', str],
116 'scantable.history' : [True, _validate_bool]
117 # fitter
118 }
119
120def list_rcparameters():
121
122 print """
123# general
124# print verbose output
125verbose : True
126
127# preload a default plotter
128useplotter : True
129
130# apply operations on the input scantable or return new one
131insitu : True
132
133# plotting
134
135# do we want a GUI or plot to a file
136plotter.gui : True
137
138# default mode for colour stacking
139plotter.stacking : Pol
140
141# default mode for panelling
142plotter.panelling : scan
143
144# push panels together, to share axislabels
145plotter.ganged : True
146
147# decimate the number of points plotted bya afactor of
148# nchan/1024
149plotter.decimate : False
150
151# default colours/linestyles
152plotter.colours :
153plotter.linestyles :
154
155# enable/disable histogram plotting
156plotter.histogram : False
157
158# ps paper type
159plotter.papertype : A4
160
161# scantable
162
163# default storage of scantable ('memory'/'disk')
164scantable.storage : memory
165
166# write history of each call to scantable
167scantable.history : True
168
169# default ouput format when saving
170scantable.save : ASAP
171
172# auto averaging on read
173scantable.autoaverage : True
174
175# default frequency frame to set when function
176# scantable.set_freqframe is called
177scantable.freqframe : LSRK
178
179# Control the level of information printed by summary
180scantable.verbosesummary : False
181
182# Fitter
183"""
184
185def rc_params():
186 'Return the default params updated from the values in the rc file'
187
188 fname = _asap_fname()
189
190 if fname is None or not os.path.exists(fname):
191 message = 'could not find rc file; returning defaults'
192 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
193 #print message
194 return ret
195
196 cnt = 0
197 for line in file(fname):
198 cnt +=1
199 line = line.strip()
200 if not len(line): continue
201 if line.startswith('#'): continue
202 tup = line.split(':',1)
203 if len(tup) !=2:
204 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
205 continue
206
207 key, val = tup
208 key = key.strip()
209 if not defaultParams.has_key(key):
210 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
211 continue
212
213 default, converter = defaultParams[key]
214
215 ind = val.find('#')
216 if ind>=0: val = val[:ind] # ignore trailing comments
217 val = val.strip()
218 try: cval = converter(val) # try to convert to proper type or raise
219 except ValueError, msg:
220 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
221 continue
222 else:
223 # Alles Klar, update dict
224 defaultParams[key][0] = cval
225
226 # strip the conveter funcs and return
227 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
228 print ('loaded rc file %s'%fname)
229
230 return ret
231
232
233# this is the instance used by the asap classes
234rcParams = rc_params()
235
236rcParamsDefault = dict(rcParams.items()) # a copy
237
238def rc(group, **kwargs):
239 """
240 Set the current rc params. Group is the grouping for the rc, eg
241 for scantable.save the group is 'scantable', for plotter.stacking, the
242 group is 'plotter', and so on. kwargs is a list of attribute
243 name/value pairs, eg
244
245 rc('scantable', save='SDFITS')
246
247 sets the current rc params and is equivalent to
248
249 rcParams['scantable.save'] = 'SDFITS'
250
251 Use rcdefaults to restore the default rc params after changes.
252 """
253
254 aliases = {}
255
256 for k,v in kwargs.items():
257 name = aliases.get(k) or k
258 if len(group):
259 key = '%s.%s' % (group, name)
260 else:
261 key = name
262 if not rcParams.has_key(key):
263 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
264
265 rcParams[key] = v
266
267
268def rcdefaults():
269 """
270 Restore the default rc params - the ones that were created at
271 asap load time
272 """
273 rcParams.update(rcParamsDefault)
274
275def _n_bools(n, val):
276 return [ val for i in xrange(n) ]
277
278def _is_sequence_or_number(param, ptype=int):
279 if isinstance(param,tuple) or isinstance(param,list):
280 if len(param) == 0: return True # empty list
281 out = True
282 for p in param:
283 out &= isinstance(p,ptype)
284 return out
285 elif isinstance(param, ptype):
286 return True
287 return False
288
289def _to_list(param, ptype=int):
290 if isinstance(param, ptype):
291 if ptype is str: return param.split()
292 else: return [param]
293 if _is_sequence_or_number(param, ptype):
294 return param
295 return None
296
297def unique(x):
298 """
299 Return the unique values in a list
300 Parameters:
301 x: the list to reduce
302 Examples:
303 x = [1,2,3,3,4]
304 print unique(x)
305 [1,2,3,4]
306 """
307 return dict([ (val, 1) for val in x]).keys()
308
309def list_files(path=".",suffix="rpf"):
310 """
311 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
312 Parameters:
313 path: The directory to list (default '.')
314 suffix: The file extension (default rpf)
315 Example:
316 files = list_files("data/","sdfits")
317 print files
318 ['data/2001-09-01_0332_P363.sdfits',
319 'data/2003-04-04_131152_t0002.sdfits',
320 'data/Sgr_86p262_best_SPC.sdfits']
321 """
322 if not os.path.isdir(path):
323 return None
324 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
325 if not suffix in valid:
326 return None
327 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
328 return filter(lambda x: x.endswith(suffix),files)
329
330# workaround for ipython, which redirects this if banner=0 in ipythonrc
331sys.stdout = sys.__stdout__
332sys.stderr = sys.__stderr__
333
334# Logging
335from asap._asap import Log as _asaplog
336global asaplog
337asaplog=_asaplog()
338if rcParams['verbose']:
339 asaplog.enable()
340else:
341 asaplog.disable()
342
343def print_log():
344 log = asaplog.pop()
345 if len(log) and rcParams['verbose']: print log
346 return
347
348def mask_and(a, b):
349 assert(len(a)==len(b))
350 return [ a[i] & b[i] for i in xrange(len(a)) ]
351
352def mask_or(a, b):
353 assert(len(a)==len(b))
354 return [ a[i] | b[i] for i in xrange(len(a)) ]
355
356def mask_not(a):
357 return [ not i for i in a ]
358
359from asapfitter import fitter
360from asapreader import reader
361from selector import selector
362
363from asapmath import *
364from scantable import scantable
365from asaplinefind import linefinder
366from linecatalog import linecatalog
367
368if rcParams['useplotter']:
369 try:
370 from asapplotter import asapplotter
371 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
372 if gui:
373 import matplotlib
374 matplotlib.use("TkAgg")
375 import pylab
376 xyplotter = pylab
377 plotter = asapplotter(gui)
378 del gui
379 except ImportError:
380 print "Matplotlib not installed. No plotting available"
381
382__date__ = '$Date: 2009-01-15 01:16:08 +0000 (Thu, 15 Jan 2009) $'.split()[1]
383__version__ = 'trunk'
384
385def is_ipython():
386 return '__IP' in dir(sys.modules["__main__"])
387if is_ipython():
388 def version(): print "ASAP %s(%s)"% (__version__, __date__)
389
390 def list_scans(t = scantable):
391 import types
392 globs = sys.modules['__main__'].__dict__.iteritems()
393 print "The user created scantables are:"
394 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
395 print filter(lambda x: not x.startswith('_'), sts)
396 return
397
398 def commands():
399 x = """
400 [The scan container]
401 scantable - a container for integrations/scans
402 (can open asap/rpfits/sdfits and ms files)
403 copy - returns a copy of a scan
404 get_scan - gets a specific scan out of a scantable
405 (by name or number)
406 drop_scan - drops a specific scan out of a scantable
407 (by number)
408 set_selection - set a new subselection of the data
409 get_selection - get the current selection object
410 summary - print info about the scantable contents
411 stats - get specified statistic of the spectra in
412 the scantable
413 stddev - get the standard deviation of the spectra
414 in the scantable
415 get_tsys - get the TSys
416 get_time - get the timestamps of the integrations
417 get_inttime - get the integration time
418 get_sourcename - get the source names of the scans
419 get_azimuth - get the azimuth of the scans
420 get_elevation - get the elevation of the scans
421 get_parangle - get the parallactic angle of the scans
422 get_unit - get the current unit
423 set_unit - set the abcissa unit to be used from this
424 point on
425 get_abcissa - get the abcissa values and name for a given
426 row (time)
427 get_column_names - get the names of the columns in the scantable
428 for use with selector.set_query
429 set_freqframe - set the frame info for the Spectral Axis
430 (e.g. 'LSRK')
431 set_doppler - set the doppler to be used from this point on
432 set_dirframe - set the frame for the direction on the sky
433 set_instrument - set the instrument name
434 set_feedtype - set the feed type
435 get_fluxunit - get the brightness flux unit
436 set_fluxunit - set the brightness flux unit
437 create_mask - return an mask in the current unit
438 for the given region. The specified regions
439 are NOT masked
440 get_restfreqs - get the current list of rest frequencies
441 set_restfreqs - set a list of rest frequencies
442 shift_refpix - shift the reference pixel of the IFs
443 set_spectrum - overwrite the spectrum for a given row
444 get_spectrum - retrieve the spectrum for a given
445 get_mask - retrieve the mask for a given
446 flag - flag selected channels in the data
447 lag_flag - flag specified frequency in the data
448 save - save the scantable to disk as either 'ASAP',
449 'SDFITS' or 'ASCII'
450 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
451 nscan - the number of scans in the scantable
452 nrow - the number of spectra in the scantable
453 history - print the history of the scantable
454 get_fit - get a fit which has been stored witnh the data
455 average_time - return the (weighted) time average of a scan
456 or a list of scans
457 average_pol - average the polarisations together.
458 average_beam - average the beams together.
459 convert_pol - convert to a different polarisation type
460 auto_quotient - return the on/off quotient with
461 automatic detection of the on/off scans (closest
462 in time off is selected)
463 mx_quotient - Form a quotient using MX data (off beams)
464 scale, *, / - return a scan scaled by a given factor
465 add, +, - - return a scan with given value added
466 bin - return a scan with binned channels
467 resample - return a scan with resampled channels
468 smooth - return the spectrally smoothed scan
469 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
470 auto_poly_baseline - automatically fit a polynomial baseline
471 recalc_azel - recalculate azimuth and elevation based on
472 the pointing
473 gain_el - apply gain-elevation correction
474 opacity - apply opacity correction
475 convert_flux - convert to and from Jy and Kelvin brightness
476 units
477 freq_align - align spectra in frequency frame
478 invert_phase - Invert the phase of the cross-correlation
479 swap_linears - Swap XX and YY (or RR LL)
480 rotate_xyphase - rotate XY phase of cross correlation
481 rotate_linpolphase - rotate the phase of the complex
482 polarization O=Q+iU correlation
483 freq_switch - perform frequency switching on the data
484 stats - Determine the specified statistic, e.g. 'min'
485 'max', 'rms' etc.
486 stddev - Determine the standard deviation of the current
487 beam/if/pol
488 [Selection]
489 selector - a selection object to set a subset of a scantable
490 set_scans - set (a list of) scans by index
491 set_cycles - set (a list of) cycles by index
492 set_beams - set (a list of) beamss by index
493 set_ifs - set (a list of) ifs by index
494 set_polarisations - set (a list of) polarisations by name
495 or by index
496 set_names - set a selection by name (wildcards allowed)
497 set_tsys - set a selection by tsys thresholds
498 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
499 ( also get_ functions for all these )
500 reset - unset all selections
501 + - merge two selections
502
503 [Math] Mainly functions which operate on more than one scantable
504
505 average_time - return the (weighted) time average
506 of a list of scans
507 quotient - return the on/off quotient
508 simple_math - simple mathematical operations on two scantables,
509 'add', 'sub', 'mul', 'div'
510 quotient - build quotient of the given on and off scans
511 (matched pairs and 1 off - n on are valid)
512 merge - merge a list of scantables
513
514 [Line Catalog]
515 linecatalog - a linecatalog wrapper, taking an ASCII or
516 internal format table
517 summary - print a summary of the current selection
518 set_name - select a subset by name pattern, e.g. '*OH*'
519 set_strength_limits - select a subset by line strength limits
520 set_frequency_limits - select a subset by frequency limits
521 reset - unset all selections
522 save - save the current subset to a table (internal
523 format)
524 get_row - get the name and frequency from a specific
525 row in the table
526 [Fitting]
527 fitter
528 auto_fit - return a scan where the function is
529 applied to all Beams/IFs/Pols.
530 commit - return a new scan where the fits have been
531 commited.
532 fit - execute the actual fitting process
533 store_fit - store the fit parameters in the data (scantable)
534 get_chi2 - get the Chi^2
535 set_scan - set the scantable to be fit
536 set_function - set the fitting function
537 set_parameters - set the parameters for the function(s), and
538 set if they should be held fixed during fitting
539 set_gauss_parameters - same as above but specialised for individual
540 gaussian components
541 get_parameters - get the fitted parameters
542 plot - plot the resulting fit and/or components and
543 residual
544 [Plotter]
545 asapplotter - a plotter for asap, default plotter is
546 called 'plotter'
547 plot - plot a scantable
548 plot_lines - plot a linecatalog overlay
549 save - save the plot to a file ('png' ,'ps' or 'eps')
550 set_mode - set the state of the plotter, i.e.
551 what is to be plotted 'colour stacked'
552 and what 'panelled'
553 set_selection - only plot a selected part of the data
554 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
555 set_legend - specify user labels for the legend indeces
556 set_title - specify user labels for the panel indeces
557 set_abcissa - specify a user label for the abcissa
558 set_ordinate - specify a user label for the ordinate
559 set_layout - specify the multi-panel layout (rows,cols)
560 set_colors - specify a set of colours to use
561 set_linestyles - specify a set of linestyles to use if only
562 using one color
563 set_font - set general font properties, e.g. 'family'
564 set_histogram - plot in historam style
565 set_mask - set a plotting mask for a specific polarization
566 text - draw text annotations either in data or relative
567 coordinates
568 arrow - draw arrow annotations either in data or relative
569 coordinates
570 axhline,axvline - draw horizontal/vertical lines
571 axhspan,axvspan - draw horizontal/vertical regions
572
573 xyplotter - matplotlib/pylab plotting functions
574
575 [Reading files]
576 reader - access rpfits/sdfits files
577 open - attach reader to a file
578 close - detach reader from file
579 read - read in integrations
580 summary - list info about all integrations
581
582 [General]
583 commands - this command
584 print - print details about a variable
585 list_scans - list all scantables created bt the user
586 list_files - list all files readable by asap (default rpf)
587 del - delete the given variable from memory
588 range - create a list of values, e.g.
589 range(3) = [0,1,2], range(2,5) = [2,3,4]
590 help - print help for one of the listed functions
591 execfile - execute an asap script, e.g. execfile('myscript')
592 list_rcparameters - print out a list of possible values to be
593 put into $HOME/.asaprc
594 rc - set rc parameters from within asap
595 mask_and,mask_or,
596 mask_not - boolean operations on masks created with
597 scantable.create_mask
598
599 Note:
600 How to use this with help:
601 # function 'summary'
602 [xxx] is just a category
603 Every 'sub-level' in this list should be replaces by a '.' Period when
604 using help
605 Example:
606 ASAP> help scantable # to get info on ths scantable
607 ASAP> help scantable.summary # to get help on the scantable's
608 ASAP> help average_time
609
610 """
611 if rcParams['verbose']:
612 try:
613 from IPython.genutils import page as pager
614 except ImportError:
615 from pydoc import pager
616 pager(x)
617 else:
618 print x
619 return
620
621def welcome():
622 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
623
624Please report any bugs via:
625http://svn.atnf.csiro.au/trac/asap/simpleticket
626
627[IMPORTANT: ASAP is 0-based]
628Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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