source: trunk/python/__init__.py@ 1222

Last change on this file since 1222 was 1193, checked in by mar637, 18 years ago

added ipython detection to set up ipython specific things

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File size: 21.9 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"]
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: 2006-08-28 23:24:47 +0000 (Mon, 28 Aug 2006) $'.split()[1]
357__version__ = '2.1b'
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 set_freqframe - set the frame info for the Spectral Axis
400 (e.g. 'LSRK')
401 set_doppler - set the doppler to be used from this point on
402 set_dirframe - set the frame for the direction on the sky
403 set_instrument - set the instrument name
404 set_feedtype - set the feed type
405 get_fluxunit - get the brightness flux unit
406 set_fluxunit - set the brightness flux unit
407 create_mask - return an mask in the current unit
408 for the given region. The specified regions
409 are NOT masked
410 get_restfreqs - get the current list of rest frequencies
411 set_restfreqs - set a list of rest frequencies
412 flag - flag selected channels in the data
413 lag_flag - flag specified frequency in the data
414 save - save the scantable to disk as either 'ASAP',
415 'SDFITS' or 'ASCII'
416 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
417 nscan - the number of scans in the scantable
418 nrow - te number of spectra in the scantable
419 history - print the history of the scantable
420 get_fit - get a fit which has been stored witnh the data
421 average_time - return the (weighted) time average of a scan
422 or a list of scans
423 average_pol - average the polarisations together.
424 average_beam - average the beams together.
425 convert_pol - convert to a different polarisation type
426 auto_quotient - return the on/off quotient with
427 automatic detection of the on/off scans (closest
428 in time off is selected)
429 mx_quotient - Form a quotient using MX data (off beams)
430 scale, *, / - return a scan scaled by a given factor
431 add, +, - - return a scan with given value added
432 bin - return a scan with binned channels
433 resample - return a scan with resampled channels
434 smooth - return the spectrally smoothed scan
435 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
436 auto_poly_baseline - automatically fit a polynomial baseline
437 recalc_azel - recalculate azimuth and elevation based on
438 the pointing
439 gain_el - apply gain-elevation correction
440 opacity - apply opacity correction
441 convert_flux - convert to and from Jy and Kelvin brightness
442 units
443 freq_align - align spectra in frequency frame
444 invert_phase - Invert the phase of the cross-correlation
445 swap_linears - Swap XX and YY
446 rotate_xyphase - rotate XY phase of cross correlation
447 rotate_linpolphase - rotate the phase of the complex
448 polarization O=Q+iU correlation
449 freq_switch - perform frequency switching on the data
450 stats - Determine the specified statistic, e.g. 'min'
451 'max', 'rms' etc.
452 stddev - Determine the standard deviation of the current
453 beam/if/pol
454 [Selection]
455 selector - a selection object to set a subset of a scantable
456 set_scans - set (a list of) scans by index
457 set_cycles - set (a list of) cycles by index
458 set_beams - set (a list of) beamss by index
459 set_ifs - set (a list of) ifs by index
460 set_polarisations - set (a list of) polarisations by name
461 or by index
462 set_names - set a selection by name (wildcards allowed)
463 set_tsys - set a selection by tsys thresholds
464 reset - unset all selections
465 + - merge to selections
466
467 [Math] Mainly functions which operate on more than one scantable
468
469 average_time - return the (weighted) time average
470 of a list of scans
471 quotient - return the on/off quotient
472 simple_math - simple mathematical operations on two scantables,
473 'add', 'sub', 'mul', 'div'
474 quotient - build quotient of the given on and off scans
475 (matched pairs and 1 off/n on are valid)
476 merge - merge a list of scantables
477
478 [Line Catalog]
479 linecatalog - a linecatalog wrapper, taking an ASCII or
480 internal format table
481 summary - print a summary of the current selection
482 set_name - select a subset by name pattern, e.g. '*OH*'
483 set_strength_limits - select a subset by line strength limits
484 set_frequency_limits - select a subset by frequency limits
485 reset - unset all selections
486 save - save the current subset to a table (internal
487 format)
488 get_row - get the name and frequency from a specific
489 row in the table
490 [Fitting]
491 fitter
492 auto_fit - return a scan where the function is
493 applied to all Beams/IFs/Pols.
494 commit - return a new scan where the fits have been
495 commited.
496 fit - execute the actual fitting process
497 store_fit - store the fit parameters in the data (scantable)
498 get_chi2 - get the Chi^2
499 set_scan - set the scantable to be fit
500 set_function - set the fitting function
501 set_parameters - set the parameters for the function(s), and
502 set if they should be held fixed during fitting
503 set_gauss_parameters - same as above but specialised for individual
504 gaussian components
505 get_parameters - get the fitted parameters
506 plot - plot the resulting fit and/or components and
507 residual
508 [Plotter]
509 asapplotter - a plotter for asap, default plotter is
510 called 'plotter'
511 plot - plot a scantable
512 plot_lines - plot a linecatalog overlay
513 save - save the plot to a file ('png' ,'ps' or 'eps')
514 set_mode - set the state of the plotter, i.e.
515 what is to be plotted 'colour stacked'
516 and what 'panelled'
517 set_selection - only plot a selected part of the data
518 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
519 set_legend - specify user labels for the legend indeces
520 set_title - specify user labels for the panel indeces
521 set_abcissa - specify a user label for the abcissa
522 set_ordinate - specify a user label for the ordinate
523 set_layout - specify the multi-panel layout (rows,cols)
524 set_colors - specify a set of colours to use
525 set_linestyles - specify a set of linestyles to use if only
526 using one color
527 set_font - set general font properties, e.g. 'family'
528 set_histogram - plot in historam style
529 set_mask - set a plotting mask for a specific polarization
530 text - draw text annotations either in data or relative
531 coordinates
532 arrow - draw arrow annotations either in data or relative
533 coordinates
534 axhline,axvline - draw horizontal/vertical lines
535 axhspan,axvspan - draw horizontal/vertical regions
536
537 xyplotter - matplotlib/pylab plotting functions
538
539 [Reading files]
540 reader - access rpfits/sdfits files
541 open - attach reader to a file
542 close - detach reader from file
543 read - read in integrations
544 summary - list info about all integrations
545
546 [General]
547 commands - this command
548 print - print details about a variable
549 list_scans - list all scantables created bt the user
550 list_files - list all files readable by asap (default rpf)
551 del - delete the given variable from memory
552 range - create a list of values, e.g.
553 range(3) = [0,1,2], range(2,5) = [2,3,4]
554 help - print help for one of the listed functions
555 execfile - execute an asap script, e.g. execfile('myscript')
556 list_rcparameters - print out a list of possible values to be
557 put into $HOME/.asaprc
558 rc - set rc parameters from within asap
559 mask_and,mask_or,
560 mask_not - boolean operations on masks created with
561 scantable.create_mask
562
563 Note:
564 How to use this with help:
565 # function 'summary'
566 [xxx] is just a category
567 Every 'sub-level' in this list should be replaces by a '.' Period when
568 using help
569 Example:
570 ASAP> help scantable # to get info on ths scantable
571 ASAP> help scantable.summary # to get help on the scantable's
572 ASAP> help average_time
573
574 """
575 if rcParams['verbose']:
576 try:
577 from IPython.genutils import page as pager
578 except ImportError:
579 from pydoc import pager
580 pager(x)
581 else:
582 print x
583 return
584
585def welcome():
586 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
587
588Please report any bugs via:
589http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
590
591[IMPORTANT: ASAP is 0-based]
592Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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