source: branches/Release2.1.1/python/__init__.py@ 1520

Last change on this file since 1520 was 1301, checked in by mar637, 18 years ago

version -> 2.1.1

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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"]
24os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
25# set up user space
26userdir = os.environ["HOME"]+"/.asap"
27if not os.path.exists(userdir):
28 print 'First time ASAP use. Setting up ~/.asap'
29 os.mkdir(userdir)
30 shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
31 f = file(userdir+"/asapuserfuncs.py", "w")
32 f.close()
33 f = file(userdir+"/ipythonrc", "w")
34 f.close()
35# remove from namespace
36del asapdata, userdir, shutil, platform
37
38def _validate_bool(b):
39 'Convert b to a boolean or raise'
40 bl = b.lower()
41 if bl in ('f', 'no', 'false', '0', 0): return False
42 elif bl in ('t', 'yes', 'true', '1', 1): return True
43 else:
44 raise ValueError('Could not convert "%s" to boolean' % b)
45
46def _validate_int(s):
47 'convert s to int or raise'
48 try: return int(s)
49 except ValueError:
50 raise ValueError('Could not convert "%s" to int' % s)
51
52def _asap_fname():
53 """
54 Return the path to the rc file
55
56 Search order:
57
58 * current working dir
59 * environ var ASAPRC
60 * HOME/.asaprc
61
62 """
63
64 fname = os.path.join( os.getcwd(), '.asaprc')
65 if os.path.exists(fname): return fname
66
67 if os.environ.has_key('ASAPRC'):
68 path = os.environ['ASAPRC']
69 if os.path.exists(path):
70 fname = os.path.join(path, '.asaprc')
71 if os.path.exists(fname):
72 return fname
73
74 if os.environ.has_key('HOME'):
75 home = os.environ['HOME']
76 fname = os.path.join(home, '.asaprc')
77 if os.path.exists(fname):
78 return fname
79 return None
80
81
82defaultParams = {
83 # general
84 'verbose' : [True, _validate_bool],
85 'useplotter' : [True, _validate_bool],
86 'insitu' : [True, _validate_bool],
87
88 # plotting
89 'plotter.gui' : [True, _validate_bool],
90 'plotter.stacking' : ['p', str],
91 'plotter.panelling' : ['s', str],
92 'plotter.colours' : ['', str],
93 'plotter.linestyles' : ['', str],
94 'plotter.decimate' : [False, _validate_bool],
95 'plotter.ganged' : [True, _validate_bool],
96 'plotter.histogram' : [False, _validate_bool],
97 'plotter.papertype' : ['A4', str],
98
99 # scantable
100 'scantable.save' : ['ASAP', str],
101 'scantable.autoaverage' : [True, _validate_bool],
102 'scantable.freqframe' : ['LSRK', str], #default frequency frame
103 'scantable.verbosesummary' : [False, _validate_bool],
104 'scantable.storage' : ['memory', str]
105 # fitter
106 }
107
108def list_rcparameters():
109
110 print """
111# general
112# print verbose output
113verbose : True
114
115# preload a default plotter
116useplotter : True
117
118# apply operations on the input scantable or return new one
119insitu : True
120
121# plotting
122
123# do we want a GUI or plot to a file
124plotter.gui : True
125
126# default mode for colour stacking
127plotter.stacking : Pol
128
129# default mode for panelling
130plotter.panelling : scan
131
132# push panels together, to share axislabels
133plotter.ganged : True
134
135# decimate the number of points plotted bya afactor of
136# nchan/1024
137plotter.decimate : False
138
139# default colours/linestyles
140plotter.colours :
141plotter.linestyles :
142
143# enable/disable histogram plotting
144plotter.histogram : False
145
146# ps paper type
147plotter.papertype : A4
148
149# scantable
150
151# default storage of scantable ('memory'/'disk')
152scantable.storage : memory
153# default ouput format when saving
154scantable.save : ASAP
155# auto averaging on read
156scantable.autoaverage : True
157
158# default frequency frame to set when function
159# scantable.set_freqframe is called
160scantable.freqframe : LSRK
161
162# Control the level of information printed by summary
163scantable.verbosesummary : False
164
165# Fitter
166"""
167
168def rc_params():
169 'Return the default params updated from the values in the rc file'
170
171 fname = _asap_fname()
172
173 if fname is None or not os.path.exists(fname):
174 message = 'could not find rc file; returning defaults'
175 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
176 #print message
177 return ret
178
179 cnt = 0
180 for line in file(fname):
181 cnt +=1
182 line = line.strip()
183 if not len(line): continue
184 if line.startswith('#'): continue
185 tup = line.split(':',1)
186 if len(tup) !=2:
187 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
188 continue
189
190 key, val = tup
191 key = key.strip()
192 if not defaultParams.has_key(key):
193 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
194 continue
195
196 default, converter = defaultParams[key]
197
198 ind = val.find('#')
199 if ind>=0: val = val[:ind] # ignore trailing comments
200 val = val.strip()
201 try: cval = converter(val) # try to convert to proper type or raise
202 except ValueError, msg:
203 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
204 continue
205 else:
206 # Alles Klar, update dict
207 defaultParams[key][0] = cval
208
209 # strip the conveter funcs and return
210 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
211 print ('loaded rc file %s'%fname)
212
213 return ret
214
215
216# this is the instance used by the asap classes
217rcParams = rc_params()
218
219rcParamsDefault = dict(rcParams.items()) # a copy
220
221def rc(group, **kwargs):
222 """
223 Set the current rc params. Group is the grouping for the rc, eg
224 for scantable.save the group is 'scantable', for plotter.stacking, the
225 group is 'plotter', and so on. kwargs is a list of attribute
226 name/value pairs, eg
227
228 rc('scantable', save='SDFITS')
229
230 sets the current rc params and is equivalent to
231
232 rcParams['scantable.save'] = 'SDFITS'
233
234 Use rcdefaults to restore the default rc params after changes.
235 """
236
237 aliases = {}
238
239 for k,v in kwargs.items():
240 name = aliases.get(k) or k
241 key = '%s.%s' % (group, name)
242 if not rcParams.has_key(key):
243 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
244
245 rcParams[key] = v
246
247
248def rcdefaults():
249 """
250 Restore the default rc params - the ones that were created at
251 asap load time
252 """
253 rcParams.update(rcParamsDefault)
254
255def _n_bools(n, val):
256 return [ val for i in xrange(n) ]
257
258def _is_sequence_or_number(param, ptype=int):
259 if isinstance(param,tuple) or isinstance(param,list):
260 if len(param) == 0: return True # empty list
261 out = True
262 for p in param:
263 out &= isinstance(p,ptype)
264 return out
265 elif isinstance(param, ptype):
266 return True
267 return False
268
269def _to_list(param, ptype=int):
270 if isinstance(param, ptype):
271 if ptype is str: return param.split()
272 else: return [param]
273 if _is_sequence_or_number(param, ptype):
274 return param
275 return None
276
277def unique(x):
278 """
279 Return the unique values in a list
280 Parameters:
281 x: the list to reduce
282 Examples:
283 x = [1,2,3,3,4]
284 print unique(x)
285 [1,2,3,4]
286 """
287 return dict([ (val, 1) for val in x]).keys()
288
289def list_files(path=".",suffix="rpf"):
290 """
291 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
292 Parameters:
293 path: The directory to list (default '.')
294 suffix: The file extension (default rpf)
295 Example:
296 files = list_files("data/","sdfits")
297 print files
298 ['data/2001-09-01_0332_P363.sdfits',
299 'data/2003-04-04_131152_t0002.sdfits',
300 'data/Sgr_86p262_best_SPC.sdfits']
301 """
302 if not os.path.isdir(path):
303 return None
304 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
305 if not suffix in valid:
306 return None
307 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
308 return filter(lambda x: x.endswith(suffix),files)
309
310# workaround for ipython, which redirects this if banner=0 in ipythonrc
311sys.stdout = sys.__stdout__
312sys.stderr = sys.__stderr__
313
314# Logging
315from asap._asap import Log as _asaplog
316global asaplog
317asaplog=_asaplog()
318if rcParams['verbose']:
319 asaplog.enable()
320else:
321 asaplog.disable()
322
323def print_log():
324 log = asaplog.pop()
325 if len(log) and rcParams['verbose']: print log
326 return
327
328def mask_and(a, b):
329 assert(len(a)==len(b))
330 return [ a[i] & b[i] for i in xrange(len(a)) ]
331
332def mask_or(a, b):
333 assert(len(a)==len(b))
334 return [ a[i] | b[i] for i in xrange(len(a)) ]
335
336def mask_not(a):
337 return [ not i for i in a ]
338
339from asapfitter import fitter
340from asapreader import reader
341from selector import selector
342
343from asapmath import *
344from scantable import scantable
345from asaplinefind import linefinder
346from linecatalog import linecatalog
347
348if rcParams['useplotter']:
349 try:
350 from asapplotter import asapplotter
351 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
352 if gui:
353 import pylab as xyplotter
354 plotter = asapplotter(gui)
355 del gui
356 except ImportError:
357 print "Matplotlib not installed. No plotting available"
358
359__date__ = '$Date: 2006-11-09 03:06:26 +0000 (Thu, 09 Nov 2006) $'.split()[1]
360__version__ = '2.1.1'
361
362def is_ipython():
363 return '__IP' in dir(sys.modules["__main__"])
364if is_ipython():
365 def version(): print "ASAP %s(%s)"% (__version__, __date__)
366 def list_scans(t = scantable):
367 import types
368 globs = sys.modules['__main__'].__dict__.iteritems()
369 print "The user created scantables are:"
370 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
371 print filter(lambda x: not x.startswith('_'), sts)
372 return
373
374 def commands():
375 x = """
376 [The scan container]
377 scantable - a container for integrations/scans
378 (can open asap/rpfits/sdfits and ms files)
379 copy - returns a copy of a scan
380 get_scan - gets a specific scan out of a scantable
381 (by name or number)
382 drop_scan - drops a specific scan out of a scantable
383 (by number)
384 set_selection - set a new subselection of the data
385 get_selection - get the current selection object
386 summary - print info about the scantable contents
387 stats - get specified statistic of the spectra in
388 the scantable
389 stddev - get the standard deviation of the spectra
390 in the scantable
391 get_tsys - get the TSys
392 get_time - get the timestamps of the integrations
393 get_sourcename - get the source names of the scans
394 get_azimuth - get the azimuth of the scans
395 get_elevation - get the elevation of the scans
396 get_parangle - get the parallactic angle of the scans
397 get_unit - get the current unit
398 set_unit - set the abcissa unit to be used from this
399 point on
400 get_abcissa - get the abcissa values and name for a given
401 row (time)
402 get_column_names - get the names of the columns in the scantable
403 for use with selector.set_query
404 set_freqframe - set the frame info for the Spectral Axis
405 (e.g. 'LSRK')
406 set_doppler - set the doppler to be used from this point on
407 set_dirframe - set the frame for the direction on the sky
408 set_instrument - set the instrument name
409 set_feedtype - set the feed type
410 get_fluxunit - get the brightness flux unit
411 set_fluxunit - set the brightness flux unit
412 create_mask - return an mask in the current unit
413 for the given region. The specified regions
414 are NOT masked
415 get_restfreqs - get the current list of rest frequencies
416 set_restfreqs - set a list of rest frequencies
417 flag - flag selected channels in the data
418 lag_flag - flag specified frequency in the data
419 save - save the scantable to disk as either 'ASAP',
420 'SDFITS' or 'ASCII'
421 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
422 nscan - the number of scans in the scantable
423 nrow - te number of spectra in the scantable
424 history - print the history of the scantable
425 get_fit - get a fit which has been stored witnh the data
426 average_time - return the (weighted) time average of a scan
427 or a list of scans
428 average_pol - average the polarisations together.
429 average_beam - average the beams together.
430 convert_pol - convert to a different polarisation type
431 auto_quotient - return the on/off quotient with
432 automatic detection of the on/off scans (closest
433 in time off is selected)
434 mx_quotient - Form a quotient using MX data (off beams)
435 scale, *, / - return a scan scaled by a given factor
436 add, +, - - return a scan with given value added
437 bin - return a scan with binned channels
438 resample - return a scan with resampled channels
439 smooth - return the spectrally smoothed scan
440 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
441 auto_poly_baseline - automatically fit a polynomial baseline
442 recalc_azel - recalculate azimuth and elevation based on
443 the pointing
444 gain_el - apply gain-elevation correction
445 opacity - apply opacity correction
446 convert_flux - convert to and from Jy and Kelvin brightness
447 units
448 freq_align - align spectra in frequency frame
449 invert_phase - Invert the phase of the cross-correlation
450 swap_linears - Swap XX and YY
451 rotate_xyphase - rotate XY phase of cross correlation
452 rotate_linpolphase - rotate the phase of the complex
453 polarization O=Q+iU correlation
454 freq_switch - perform frequency switching on the data
455 stats - Determine the specified statistic, e.g. 'min'
456 'max', 'rms' etc.
457 stddev - Determine the standard deviation of the current
458 beam/if/pol
459 [Selection]
460 selector - a selection object to set a subset of a scantable
461 set_scans - set (a list of) scans by index
462 set_cycles - set (a list of) cycles by index
463 set_beams - set (a list of) beamss by index
464 set_ifs - set (a list of) ifs by index
465 set_polarisations - set (a list of) polarisations by name
466 or by index
467 set_names - set a selection by name (wildcards allowed)
468 set_tsys - set a selection by tsys thresholds
469 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
470 reset - unset all selections
471 + - merge to selections
472
473 [Math] Mainly functions which operate on more than one scantable
474
475 average_time - return the (weighted) time average
476 of a list of scans
477 quotient - return the on/off quotient
478 simple_math - simple mathematical operations on two scantables,
479 'add', 'sub', 'mul', 'div'
480 quotient - build quotient of the given on and off scans
481 (matched pairs and 1 off/n on are valid)
482 merge - merge a list of scantables
483
484 [Line Catalog]
485 linecatalog - a linecatalog wrapper, taking an ASCII or
486 internal format table
487 summary - print a summary of the current selection
488 set_name - select a subset by name pattern, e.g. '*OH*'
489 set_strength_limits - select a subset by line strength limits
490 set_frequency_limits - select a subset by frequency limits
491 reset - unset all selections
492 save - save the current subset to a table (internal
493 format)
494 get_row - get the name and frequency from a specific
495 row in the table
496 [Fitting]
497 fitter
498 auto_fit - return a scan where the function is
499 applied to all Beams/IFs/Pols.
500 commit - return a new scan where the fits have been
501 commited.
502 fit - execute the actual fitting process
503 store_fit - store the fit parameters in the data (scantable)
504 get_chi2 - get the Chi^2
505 set_scan - set the scantable to be fit
506 set_function - set the fitting function
507 set_parameters - set the parameters for the function(s), and
508 set if they should be held fixed during fitting
509 set_gauss_parameters - same as above but specialised for individual
510 gaussian components
511 get_parameters - get the fitted parameters
512 plot - plot the resulting fit and/or components and
513 residual
514 [Plotter]
515 asapplotter - a plotter for asap, default plotter is
516 called 'plotter'
517 plot - plot a scantable
518 plot_lines - plot a linecatalog overlay
519 save - save the plot to a file ('png' ,'ps' or 'eps')
520 set_mode - set the state of the plotter, i.e.
521 what is to be plotted 'colour stacked'
522 and what 'panelled'
523 set_selection - only plot a selected part of the data
524 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
525 set_legend - specify user labels for the legend indeces
526 set_title - specify user labels for the panel indeces
527 set_abcissa - specify a user label for the abcissa
528 set_ordinate - specify a user label for the ordinate
529 set_layout - specify the multi-panel layout (rows,cols)
530 set_colors - specify a set of colours to use
531 set_linestyles - specify a set of linestyles to use if only
532 using one color
533 set_font - set general font properties, e.g. 'family'
534 set_histogram - plot in historam style
535 set_mask - set a plotting mask for a specific polarization
536 text - draw text annotations either in data or relative
537 coordinates
538 arrow - draw arrow annotations either in data or relative
539 coordinates
540 axhline,axvline - draw horizontal/vertical lines
541 axhspan,axvspan - draw horizontal/vertical regions
542
543 xyplotter - matplotlib/pylab plotting functions
544
545 [Reading files]
546 reader - access rpfits/sdfits files
547 open - attach reader to a file
548 close - detach reader from file
549 read - read in integrations
550 summary - list info about all integrations
551
552 [General]
553 commands - this command
554 print - print details about a variable
555 list_scans - list all scantables created bt the user
556 list_files - list all files readable by asap (default rpf)
557 del - delete the given variable from memory
558 range - create a list of values, e.g.
559 range(3) = [0,1,2], range(2,5) = [2,3,4]
560 help - print help for one of the listed functions
561 execfile - execute an asap script, e.g. execfile('myscript')
562 list_rcparameters - print out a list of possible values to be
563 put into $HOME/.asaprc
564 rc - set rc parameters from within asap
565 mask_and,mask_or,
566 mask_not - boolean operations on masks created with
567 scantable.create_mask
568
569 Note:
570 How to use this with help:
571 # function 'summary'
572 [xxx] is just a category
573 Every 'sub-level' in this list should be replaces by a '.' Period when
574 using help
575 Example:
576 ASAP> help scantable # to get info on ths scantable
577 ASAP> help scantable.summary # to get help on the scantable's
578 ASAP> help average_time
579
580 """
581 if rcParams['verbose']:
582 try:
583 from IPython.genutils import page as pager
584 except ImportError:
585 from pydoc import pager
586 pager(x)
587 else:
588 print x
589 return
590
591def welcome():
592 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
593
594Please report any bugs via:
595http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
596
597[IMPORTANT: ASAP is 0-based]
598Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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