source: trunk/python/__init__.py@ 1530

Last change on this file since 1530 was 1529, checked in by Malte Marquarding, 16 years ago

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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 'plotter.xaxisformatting' : ['asap', str],
110
111 # scantable
112 'scantable.save' : ['ASAP', str],
113 'scantable.autoaverage' : [True, _validate_bool],
114 'scantable.freqframe' : ['LSRK', str], #default frequency frame
115 'scantable.verbosesummary' : [False, _validate_bool],
116 'scantable.storage' : ['memory', str],
117 'scantable.history' : [True, _validate_bool],
118 'scantable.reference' : ['.*(e|w|_R)$', str]
119 # fitter
120 }
121
122def list_rcparameters():
123
124 print """
125# general
126# print verbose output
127verbose : True
128
129# preload a default plotter
130useplotter : True
131
132# apply operations on the input scantable or return new one
133insitu : True
134
135# plotting
136
137# do we want a GUI or plot to a file
138plotter.gui : True
139
140# default mode for colour stacking
141plotter.stacking : Pol
142
143# default mode for panelling
144plotter.panelling : scan
145
146# push panels together, to share axislabels
147plotter.ganged : True
148
149# decimate the number of points plotted by a factor of
150# nchan/1024
151plotter.decimate : False
152
153# default colours/linestyles
154plotter.colours :
155plotter.linestyles :
156
157# enable/disable histogram plotting
158plotter.histogram : False
159
160# ps paper type
161plotter.papertype : A4
162
163# The formatting style of the xaxis
164plotter.xaxisformatting : 'asap' or 'mpl'
165
166# scantable
167
168# default storage of scantable ('memory'/'disk')
169scantable.storage : memory
170
171# write history of each call to scantable
172scantable.history : True
173
174# default ouput format when saving
175scantable.save : ASAP
176
177# auto averaging on read
178scantable.autoaverage : True
179
180# default frequency frame to set when function
181# scantable.set_freqframe is called
182scantable.freqframe : LSRK
183
184# Control the level of information printed by summary
185scantable.verbosesummary : False
186
187# Control the identification of reference (off) scans
188# This is has to be a regular expression
189scantable.reference : .*(e|w|_R)$
190# Fitter
191"""
192
193def rc_params():
194 'Return the default params updated from the values in the rc file'
195
196 fname = _asap_fname()
197
198 if fname is None or not os.path.exists(fname):
199 message = 'could not find rc file; returning defaults'
200 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
201 #print message
202 return ret
203
204 cnt = 0
205 for line in file(fname):
206 cnt +=1
207 line = line.strip()
208 if not len(line): continue
209 if line.startswith('#'): continue
210 tup = line.split(':',1)
211 if len(tup) !=2:
212 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
213 continue
214
215 key, val = tup
216 key = key.strip()
217 if not defaultParams.has_key(key):
218 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
219 continue
220
221 default, converter = defaultParams[key]
222
223 ind = val.find('#')
224 if ind>=0: val = val[:ind] # ignore trailing comments
225 val = val.strip()
226 try: cval = converter(val) # try to convert to proper type or raise
227 except ValueError, msg:
228 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
229 continue
230 else:
231 # Alles Klar, update dict
232 defaultParams[key][0] = cval
233
234 # strip the conveter funcs and return
235 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
236 print ('loaded rc file %s'%fname)
237
238 return ret
239
240
241# this is the instance used by the asap classes
242rcParams = rc_params()
243
244rcParamsDefault = dict(rcParams.items()) # a copy
245
246def rc(group, **kwargs):
247 """
248 Set the current rc params. Group is the grouping for the rc, eg
249 for scantable.save the group is 'scantable', for plotter.stacking, the
250 group is 'plotter', and so on. kwargs is a list of attribute
251 name/value pairs, eg
252
253 rc('scantable', save='SDFITS')
254
255 sets the current rc params and is equivalent to
256
257 rcParams['scantable.save'] = 'SDFITS'
258
259 Use rcdefaults to restore the default rc params after changes.
260 """
261
262 aliases = {}
263
264 for k,v in kwargs.items():
265 name = aliases.get(k) or k
266 if len(group):
267 key = '%s.%s' % (group, name)
268 else:
269 key = name
270 if not rcParams.has_key(key):
271 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
272
273 rcParams[key] = v
274
275
276def rcdefaults():
277 """
278 Restore the default rc params - the ones that were created at
279 asap load time
280 """
281 rcParams.update(rcParamsDefault)
282
283def _n_bools(n, val):
284 return [ val for i in xrange(n) ]
285
286def _is_sequence_or_number(param, ptype=int):
287 if isinstance(param,tuple) or isinstance(param,list):
288 if len(param) == 0: return True # empty list
289 out = True
290 for p in param:
291 out &= isinstance(p,ptype)
292 return out
293 elif isinstance(param, ptype):
294 return True
295 return False
296
297def _to_list(param, ptype=int):
298 if isinstance(param, ptype):
299 if ptype is str: return param.split()
300 else: return [param]
301 if _is_sequence_or_number(param, ptype):
302 return param
303 return None
304
305def unique(x):
306 """
307 Return the unique values in a list
308 Parameters:
309 x: the list to reduce
310 Examples:
311 x = [1,2,3,3,4]
312 print unique(x)
313 [1,2,3,4]
314 """
315 return dict([ (val, 1) for val in x]).keys()
316
317def list_files(path=".",suffix="rpf"):
318 """
319 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
320 Parameters:
321 path: The directory to list (default '.')
322 suffix: The file extension (default rpf)
323 Example:
324 files = list_files("data/","sdfits")
325 print files
326 ['data/2001-09-01_0332_P363.sdfits',
327 'data/2003-04-04_131152_t0002.sdfits',
328 'data/Sgr_86p262_best_SPC.sdfits']
329 """
330 if not os.path.isdir(path):
331 return None
332 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
333 if not suffix in valid:
334 return None
335 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
336 return filter(lambda x: x.endswith(suffix),files)
337
338# workaround for ipython, which redirects this if banner=0 in ipythonrc
339sys.stdout = sys.__stdout__
340sys.stderr = sys.__stderr__
341
342# Logging
343from asap._asap import Log as _asaplog
344global asaplog
345asaplog=_asaplog()
346if rcParams['verbose']:
347 asaplog.enable()
348else:
349 asaplog.disable()
350
351def print_log():
352 log = asaplog.pop()
353 if len(log) and rcParams['verbose']: print log
354 return
355
356def mask_and(a, b):
357 assert(len(a)==len(b))
358 return [ a[i] & b[i] for i in xrange(len(a)) ]
359
360def mask_or(a, b):
361 assert(len(a)==len(b))
362 return [ a[i] | b[i] for i in xrange(len(a)) ]
363
364def mask_not(a):
365 return [ not i for i in a ]
366
367from asapfitter import fitter
368from asapreader import reader
369from selector import selector
370
371from asapmath import *
372from scantable import scantable
373from asaplinefind import linefinder
374from linecatalog import linecatalog
375
376if rcParams['useplotter']:
377 try:
378 from asapplotter import asapplotter
379 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
380 if gui:
381 import matplotlib
382 matplotlib.use("TkAgg")
383 import pylab
384 xyplotter = pylab
385 plotter = asapplotter(gui)
386 del gui
387 except ImportError:
388 print "Matplotlib not installed. No plotting available"
389
390__date__ = '$Date: 2009-03-13 01:01:23 +0000 (Fri, 13 Mar 2009) $'.split()[1]
391__version__ = 'trunk'
392
393def is_ipython():
394 return '__IP' in dir(sys.modules["__main__"])
395if is_ipython():
396 def version(): print "ASAP %s(%s)"% (__version__, __date__)
397
398 def list_scans(t = scantable):
399 import types
400 globs = sys.modules['__main__'].__dict__.iteritems()
401 print "The user created scantables are:"
402 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
403 print filter(lambda x: not x.startswith('_'), sts)
404 return
405
406 def commands():
407 x = """
408 [The scan container]
409 scantable - a container for integrations/scans
410 (can open asap/rpfits/sdfits and ms files)
411 copy - returns a copy of a scan
412 get_scan - gets a specific scan out of a scantable
413 (by name or number)
414 drop_scan - drops a specific scan out of a scantable
415 (by number)
416 set_selection - set a new subselection of the data
417 get_selection - get the current selection object
418 summary - print info about the scantable contents
419 stats - get specified statistic of the spectra in
420 the scantable
421 stddev - get the standard deviation of the spectra
422 in the scantable
423 get_tsys - get the TSys
424 get_time - get the timestamps of the integrations
425 get_inttime - get the integration time
426 get_sourcename - get the source names of the scans
427 get_azimuth - get the azimuth of the scans
428 get_elevation - get the elevation of the scans
429 get_parangle - get the parallactic angle of the scans
430 get_unit - get the current unit
431 set_unit - set the abcissa unit to be used from this
432 point on
433 get_abcissa - get the abcissa values and name for a given
434 row (time)
435 get_column_names - get the names of the columns in the scantable
436 for use with selector.set_query
437 set_freqframe - set the frame info for the Spectral Axis
438 (e.g. 'LSRK')
439 set_doppler - set the doppler to be used from this point on
440 set_dirframe - set the frame for the direction on the sky
441 set_instrument - set the instrument name
442 set_feedtype - set the feed type
443 get_fluxunit - get the brightness flux unit
444 set_fluxunit - set the brightness flux unit
445 set_sourcetype - set the type of the source - source or reference
446 create_mask - return an mask in the current unit
447 for the given region. The specified regions
448 are NOT masked
449 get_restfreqs - get the current list of rest frequencies
450 set_restfreqs - set a list of rest frequencies
451 shift_refpix - shift the reference pixel of the IFs
452 set_spectrum - overwrite the spectrum for a given row
453 get_spectrum - retrieve the spectrum for a given
454 get_mask - retrieve the mask for a given
455 flag - flag selected channels in the data
456 lag_flag - flag specified frequency in the data
457 save - save the scantable to disk as either 'ASAP',
458 'SDFITS' or 'ASCII'
459 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
460 nscan - the number of scans in the scantable
461 nrow - the number of spectra in the scantable
462 history - print the history of the scantable
463 get_fit - get a fit which has been stored witnh the data
464 average_time - return the (weighted) time average of a scan
465 or a list of scans
466 average_pol - average the polarisations together.
467 average_beam - average the beams together.
468 convert_pol - convert to a different polarisation type
469 auto_quotient - return the on/off quotient with
470 automatic detection of the on/off scans (closest
471 in time off is selected)
472 mx_quotient - Form a quotient using MX data (off beams)
473 scale, *, / - return a scan scaled by a given factor
474 add, +, - - return a scan with given value added
475 bin - return a scan with binned channels
476 resample - return a scan with resampled channels
477 smooth - return the spectrally smoothed scan
478 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
479 auto_poly_baseline - automatically fit a polynomial baseline
480 recalc_azel - recalculate azimuth and elevation based on
481 the pointing
482 gain_el - apply gain-elevation correction
483 opacity - apply opacity correction
484 convert_flux - convert to and from Jy and Kelvin brightness
485 units
486 freq_align - align spectra in frequency frame
487 invert_phase - Invert the phase of the cross-correlation
488 swap_linears - Swap XX and YY (or RR LL)
489 rotate_xyphase - rotate XY phase of cross correlation
490 rotate_linpolphase - rotate the phase of the complex
491 polarization O=Q+iU correlation
492 freq_switch - perform frequency switching on the data
493 stats - Determine the specified statistic, e.g. 'min'
494 'max', 'rms' etc.
495 stddev - Determine the standard deviation of the current
496 beam/if/pol
497 [Selection]
498 selector - a selection object to set a subset of a scantable
499 set_scans - set (a list of) scans by index
500 set_cycles - set (a list of) cycles by index
501 set_beams - set (a list of) beamss by index
502 set_ifs - set (a list of) ifs by index
503 set_polarisations - set (a list of) polarisations by name
504 or by index
505 set_names - set a selection by name (wildcards allowed)
506 set_tsys - set a selection by tsys thresholds
507 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
508 ( also get_ functions for all these )
509 reset - unset all selections
510 + - merge two selections
511
512 [Math] Mainly functions which operate on more than one scantable
513
514 average_time - return the (weighted) time average
515 of a list of scans
516 quotient - return the on/off quotient
517 simple_math - simple mathematical operations on two scantables,
518 'add', 'sub', 'mul', 'div'
519 quotient - build quotient of the given on and off scans
520 (matched pairs and 1 off - n on are valid)
521 merge - merge a list of scantables
522
523 [Line Catalog]
524 linecatalog - a linecatalog wrapper, taking an ASCII or
525 internal format table
526 summary - print a summary of the current selection
527 set_name - select a subset by name pattern, e.g. '*OH*'
528 set_strength_limits - select a subset by line strength limits
529 set_frequency_limits - select a subset by frequency limits
530 reset - unset all selections
531 save - save the current subset to a table (internal
532 format)
533 get_row - get the name and frequency from a specific
534 row in the table
535 [Fitting]
536 fitter
537 auto_fit - return a scan where the function is
538 applied to all Beams/IFs/Pols.
539 commit - return a new scan where the fits have been
540 commited.
541 fit - execute the actual fitting process
542 store_fit - store the fit parameters in the data (scantable)
543 get_chi2 - get the Chi^2
544 set_scan - set the scantable to be fit
545 set_function - set the fitting function
546 set_parameters - set the parameters for the function(s), and
547 set if they should be held fixed during fitting
548 set_gauss_parameters - same as above but specialised for individual
549 gaussian components
550 get_parameters - get the fitted parameters
551 plot - plot the resulting fit and/or components and
552 residual
553 [Plotter]
554 asapplotter - a plotter for asap, default plotter is
555 called 'plotter'
556 plot - plot a scantable
557 plot_lines - plot a linecatalog overlay
558 save - save the plot to a file ('png' ,'ps' or 'eps')
559 set_mode - set the state of the plotter, i.e.
560 what is to be plotted 'colour stacked'
561 and what 'panelled'
562 set_selection - only plot a selected part of the data
563 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
564 set_legend - specify user labels for the legend indeces
565 set_title - specify user labels for the panel indeces
566 set_abcissa - specify a user label for the abcissa
567 set_ordinate - specify a user label for the ordinate
568 set_layout - specify the multi-panel layout (rows,cols)
569 set_colors - specify a set of colours to use
570 set_linestyles - specify a set of linestyles to use if only
571 using one color
572 set_font - set general font properties, e.g. 'family'
573 set_histogram - plot in historam style
574 set_mask - set a plotting mask for a specific polarization
575 text - draw text annotations either in data or relative
576 coordinates
577 arrow - draw arrow annotations either in data or relative
578 coordinates
579 axhline,axvline - draw horizontal/vertical lines
580 axhspan,axvspan - draw horizontal/vertical regions
581
582 xyplotter - matplotlib/pylab plotting functions
583
584 [Reading files]
585 reader - access rpfits/sdfits files
586 open - attach reader to a file
587 close - detach reader from file
588 read - read in integrations
589 summary - list info about all integrations
590
591 [General]
592 commands - this command
593 print - print details about a variable
594 list_scans - list all scantables created bt the user
595 list_files - list all files readable by asap (default rpf)
596 del - delete the given variable from memory
597 range - create a list of values, e.g.
598 range(3) = [0,1,2], range(2,5) = [2,3,4]
599 help - print help for one of the listed functions
600 execfile - execute an asap script, e.g. execfile('myscript')
601 list_rcparameters - print out a list of possible values to be
602 put into $HOME/.asaprc
603 rc - set rc parameters from within asap
604 mask_and,mask_or,
605 mask_not - boolean operations on masks created with
606 scantable.create_mask
607
608 Note:
609 How to use this with help:
610 # function 'summary'
611 [xxx] is just a category
612 Every 'sub-level' in this list should be replaces by a '.' Period when
613 using help
614 Example:
615 ASAP> help scantable # to get info on ths scantable
616 ASAP> help scantable.summary # to get help on the scantable's
617 ASAP> help average_time
618
619 """
620 if rcParams['verbose']:
621 try:
622 from IPython.genutils import page as pager
623 except ImportError:
624 from pydoc import pager
625 pager(x)
626 else:
627 print x
628 return
629
630def welcome():
631 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
632
633Please report any bugs via:
634http://svn.atnf.csiro.au/trac/asap/simpleticket
635
636[IMPORTANT: ASAP is 0-based]
637Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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