source: branches/Release2.1/python/__init__.py@ 2388

Last change on this file since 2388 was 1258, checked in by mar637, 18 years ago

version bump to 2.1.0

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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
255
256def _is_sequence_or_number(param, ptype=int):
257 if isinstance(param,tuple) or isinstance(param,list):
258 if len(param) == 0: return True # empty list
259 out = True
260 for p in param:
261 out &= isinstance(p,ptype)
262 return out
263 elif isinstance(param, ptype):
264 return True
265 return False
266
267def _to_list(param, ptype=int):
268 if isinstance(param, ptype):
269 if ptype is str: return param.split()
270 else: return [param]
271 if _is_sequence_or_number(param, ptype):
272 return param
273 return None
274
275def unique(x):
276 """
277 Return the unique values in a list
278 Parameters:
279 x: the list to reduce
280 Examples:
281 x = [1,2,3,3,4]
282 print unique(x)
283 [1,2,3,4]
284 """
285 return dict([ (val, 1) for val in x]).keys()
286
287def list_files(path=".",suffix="rpf"):
288 """
289 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
290 Parameters:
291 path: The directory to list (default '.')
292 suffix: The file extension (default rpf)
293 Example:
294 files = list_files("data/","sdfits")
295 print files
296 ['data/2001-09-01_0332_P363.sdfits',
297 'data/2003-04-04_131152_t0002.sdfits',
298 'data/Sgr_86p262_best_SPC.sdfits']
299 """
300 import os
301 if not os.path.isdir(path):
302 return None
303 valid = "rpf sdf sdfits mbf asap".split()
304 if not suffix in valid:
305 return None
306 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
307 return filter(lambda x: x.endswith(suffix),files)
308
309# workaround for ipython, which redirects this if banner=0 in ipythonrc
310sys.stdout = sys.__stdout__
311sys.stderr = sys.__stderr__
312
313# Logging
314from asap._asap import Log as _asaplog
315global asaplog
316asaplog=_asaplog()
317if rcParams['verbose']:
318 asaplog.enable()
319else:
320 asaplog.disable()
321
322def print_log():
323 log = asaplog.pop()
324 if len(log) and rcParams['verbose']: print log
325 return
326
327try:
328 import numpy.core as NUM
329except ImportError:
330 try:
331 import numarray as NUM
332 except ImportError:
333 raise ImportError("You need to have numpy or numarray installed")
334
335from asapfitter import fitter
336from asapreader import reader
337from selector import selector
338
339from asapmath import *
340from scantable import scantable
341from asaplinefind import linefinder
342from linecatalog import linecatalog
343
344mask_and = NUM.logical_and
345mask_or = NUM.logical_or
346mask_not = NUM.logical_not
347
348if rcParams['useplotter']:
349 from asapplotter import asapplotter
350 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
351 if gui:
352 import pylab as xyplotter
353 plotter = asapplotter(gui)
354 del gui
355
356__date__ = '$Date: 2006-09-11 05:03:57 +0000 (Mon, 11 Sep 2006) $'.split()[1]
357__version__ = '2.1'
358
359def is_ipython():
360 return '__IP' in dir(sys.modules["__main__"])
361if is_ipython():
362 def version(): print "ASAP %s(%s)"% (__version__, __date__)
363 def list_scans(t = scantable):
364 import sys, types
365 globs = sys.modules['__main__'].__dict__.iteritems()
366 print "The user created scantables are:"
367 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
368 print filter(lambda x: not x.startswith('_'), sts)
369 return
370
371 def commands():
372 x = """
373 [The scan container]
374 scantable - a container for integrations/scans
375 (can open asap/rpfits/sdfits and ms files)
376 copy - returns a copy of a scan
377 get_scan - gets a specific scan out of a scantable
378 (by name or number)
379 drop_scan - drops a specific scan out of a scantable
380 (by number)
381 set_selection - set a new subselection of the data
382 get_selection - get the current selection object
383 summary - print info about the scantable contents
384 stats - get specified statistic of the spectra in
385 the scantable
386 stddev - get the standard deviation of the spectra
387 in the scantable
388 get_tsys - get the TSys
389 get_time - get the timestamps of the integrations
390 get_sourcename - get the source names of the scans
391 get_azimuth - get the azimuth of the scans
392 get_elevation - get the elevation of the scans
393 get_parangle - get the parallactic angle of the scans
394 get_unit - get the current unit
395 set_unit - set the abcissa unit to be used from this
396 point on
397 get_abcissa - get the abcissa values and name for a given
398 row (time)
399 get_column_names - get the names of the columns in the scantable
400 for use with selector.set_query
401 set_freqframe - set the frame info for the Spectral Axis
402 (e.g. 'LSRK')
403 set_doppler - set the doppler to be used from this point on
404 set_dirframe - set the frame for the direction on the sky
405 set_instrument - set the instrument name
406 set_feedtype - set the feed type
407 get_fluxunit - get the brightness flux unit
408 set_fluxunit - set the brightness flux unit
409 create_mask - return an mask in the current unit
410 for the given region. The specified regions
411 are NOT masked
412 get_restfreqs - get the current list of rest frequencies
413 set_restfreqs - set a list of rest frequencies
414 flag - flag selected channels in the data
415 lag_flag - flag specified frequency in the data
416 save - save the scantable to disk as either 'ASAP',
417 'SDFITS' or 'ASCII'
418 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
419 nscan - the number of scans in the scantable
420 nrow - te number of spectra in the scantable
421 history - print the history of the scantable
422 get_fit - get a fit which has been stored witnh the data
423 average_time - return the (weighted) time average of a scan
424 or a list of scans
425 average_pol - average the polarisations together.
426 average_beam - average the beams together.
427 convert_pol - convert to a different polarisation type
428 auto_quotient - return the on/off quotient with
429 automatic detection of the on/off scans (closest
430 in time off is selected)
431 mx_quotient - Form a quotient using MX data (off beams)
432 scale, *, / - return a scan scaled by a given factor
433 add, +, - - return a scan with given value added
434 bin - return a scan with binned channels
435 resample - return a scan with resampled channels
436 smooth - return the spectrally smoothed scan
437 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
438 auto_poly_baseline - automatically fit a polynomial baseline
439 recalc_azel - recalculate azimuth and elevation based on
440 the pointing
441 gain_el - apply gain-elevation correction
442 opacity - apply opacity correction
443 convert_flux - convert to and from Jy and Kelvin brightness
444 units
445 freq_align - align spectra in frequency frame
446 invert_phase - Invert the phase of the cross-correlation
447 swap_linears - Swap XX and YY
448 rotate_xyphase - rotate XY phase of cross correlation
449 rotate_linpolphase - rotate the phase of the complex
450 polarization O=Q+iU correlation
451 freq_switch - perform frequency switching on the data
452 stats - Determine the specified statistic, e.g. 'min'
453 'max', 'rms' etc.
454 stddev - Determine the standard deviation of the current
455 beam/if/pol
456 [Selection]
457 selector - a selection object to set a subset of a scantable
458 set_scans - set (a list of) scans by index
459 set_cycles - set (a list of) cycles by index
460 set_beams - set (a list of) beamss by index
461 set_ifs - set (a list of) ifs by index
462 set_polarisations - set (a list of) polarisations by name
463 or by index
464 set_names - set a selection by name (wildcards allowed)
465 set_tsys - set a selection by tsys thresholds
466 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
467 reset - unset all selections
468 + - merge to selections
469
470 [Math] Mainly functions which operate on more than one scantable
471
472 average_time - return the (weighted) time average
473 of a list of scans
474 quotient - return the on/off quotient
475 simple_math - simple mathematical operations on two scantables,
476 'add', 'sub', 'mul', 'div'
477 quotient - build quotient of the given on and off scans
478 (matched pairs and 1 off/n on are valid)
479 merge - merge a list of scantables
480
481 [Line Catalog]
482 linecatalog - a linecatalog wrapper, taking an ASCII or
483 internal format table
484 summary - print a summary of the current selection
485 set_name - select a subset by name pattern, e.g. '*OH*'
486 set_strength_limits - select a subset by line strength limits
487 set_frequency_limits - select a subset by frequency limits
488 reset - unset all selections
489 save - save the current subset to a table (internal
490 format)
491 get_row - get the name and frequency from a specific
492 row in the table
493 [Fitting]
494 fitter
495 auto_fit - return a scan where the function is
496 applied to all Beams/IFs/Pols.
497 commit - return a new scan where the fits have been
498 commited.
499 fit - execute the actual fitting process
500 store_fit - store the fit parameters in the data (scantable)
501 get_chi2 - get the Chi^2
502 set_scan - set the scantable to be fit
503 set_function - set the fitting function
504 set_parameters - set the parameters for the function(s), and
505 set if they should be held fixed during fitting
506 set_gauss_parameters - same as above but specialised for individual
507 gaussian components
508 get_parameters - get the fitted parameters
509 plot - plot the resulting fit and/or components and
510 residual
511 [Plotter]
512 asapplotter - a plotter for asap, default plotter is
513 called 'plotter'
514 plot - plot a scantable
515 plot_lines - plot a linecatalog overlay
516 save - save the plot to a file ('png' ,'ps' or 'eps')
517 set_mode - set the state of the plotter, i.e.
518 what is to be plotted 'colour stacked'
519 and what 'panelled'
520 set_selection - only plot a selected part of the data
521 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
522 set_legend - specify user labels for the legend indeces
523 set_title - specify user labels for the panel indeces
524 set_abcissa - specify a user label for the abcissa
525 set_ordinate - specify a user label for the ordinate
526 set_layout - specify the multi-panel layout (rows,cols)
527 set_colors - specify a set of colours to use
528 set_linestyles - specify a set of linestyles to use if only
529 using one color
530 set_font - set general font properties, e.g. 'family'
531 set_histogram - plot in historam style
532 set_mask - set a plotting mask for a specific polarization
533 text - draw text annotations either in data or relative
534 coordinates
535 arrow - draw arrow annotations either in data or relative
536 coordinates
537 axhline,axvline - draw horizontal/vertical lines
538 axhspan,axvspan - draw horizontal/vertical regions
539
540 xyplotter - matplotlib/pylab plotting functions
541
542 [Reading files]
543 reader - access rpfits/sdfits files
544 open - attach reader to a file
545 close - detach reader from file
546 read - read in integrations
547 summary - list info about all integrations
548
549 [General]
550 commands - this command
551 print - print details about a variable
552 list_scans - list all scantables created bt the user
553 list_files - list all files readable by asap (default rpf)
554 del - delete the given variable from memory
555 range - create a list of values, e.g.
556 range(3) = [0,1,2], range(2,5) = [2,3,4]
557 help - print help for one of the listed functions
558 execfile - execute an asap script, e.g. execfile('myscript')
559 list_rcparameters - print out a list of possible values to be
560 put into $HOME/.asaprc
561 rc - set rc parameters from within asap
562 mask_and,mask_or,
563 mask_not - boolean operations on masks created with
564 scantable.create_mask
565
566 Note:
567 How to use this with help:
568 # function 'summary'
569 [xxx] is just a category
570 Every 'sub-level' in this list should be replaces by a '.' Period when
571 using help
572 Example:
573 ASAP> help scantable # to get info on ths scantable
574 ASAP> help scantable.summary # to get help on the scantable's
575 ASAP> help average_time
576
577 """
578 if rcParams['verbose']:
579 try:
580 from IPython.genutils import page as pager
581 except ImportError:
582 from pydoc import pager
583 pager(x)
584 else:
585 print x
586 return
587
588def welcome():
589 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
590
591Please report any bugs via:
592http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
593
594[IMPORTANT: ASAP is 0-based]
595Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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