source: trunk/python/__init__.py@ 1173

Last change on this file since 1173 was 1171, checked in by mar637, 18 years ago

re-introduced custom ASAPDAT environment variable. Some more commands().

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File size: 21.7 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 plotter = asapplotter(gui)
352 del gui
353
354__date__ = '$Date: 2006-08-22 23:45:12 +0000 (Tue, 22 Aug 2006) $'.split()[1]
355__version__ = '2.1b'
356
357if rcParams['verbose']:
358 def version(): print "ASAP %s(%s)"% (__version__, __date__)
359 def list_scans(t = scantable):
360 import sys, types
361 globs = sys.modules['__main__'].__dict__.iteritems()
362 print "The user created scantables are:"
363 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
364 print filter(lambda x: not x.startswith('_'), sts)
365 return
366
367 def commands():
368 x = """
369 [The scan container]
370 scantable - a container for integrations/scans
371 (can open asap/rpfits/sdfits and ms files)
372 copy - returns a copy of a scan
373 get_scan - gets a specific scan out of a scantable
374 (by name or number)
375 drop_scan - drops a specific scan out of a scantable
376 (by number)
377 set_selection - set a new subselection of the data
378 get_selection - get the current selection object
379 summary - print info about the scantable contents
380 stats - get specified statistic of the spectra in
381 the scantable
382 stddev - get the standard deviation of the spectra
383 in the scantable
384 get_tsys - get the TSys
385 get_time - get the timestamps of the integrations
386 get_sourcename - get the source names of the scans
387 get_azimuth - get the azimuth of the scans
388 get_elevation - get the elevation of the scans
389 get_parangle - get the parallactic angle of the scans
390 get_unit - get the current unit
391 set_unit - set the abcissa unit to be used from this
392 point on
393 get_abcissa - get the abcissa values and name for a given
394 row (time)
395 set_freqframe - set the frame info for the Spectral Axis
396 (e.g. 'LSRK')
397 set_doppler - set the doppler to be used from this point on
398 set_dirframe - set the frame for the direction on the sky
399 set_instrument - set the instrument name
400 get_fluxunit - get the brightness flux unit
401 set_fluxunit - set the brightness flux unit
402 create_mask - return an mask in the current unit
403 for the given region. The specified regions
404 are NOT masked
405 get_restfreqs - get the current list of rest frequencies
406 set_restfreqs - set a list of rest frequencies
407 flag - flag selected channels in the data
408 save - save the scantable to disk as either 'ASAP',
409 'SDFITS' or 'ASCII'
410 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
411 nscan - the number of scans in the scantable
412 nrow - te number of spectra in the scantable
413 history - print the history of the scantable
414 get_fit - get a fit which has been stored witnh the data
415 average_time - return the (weighted) time average of a scan
416 or a list of scans
417 average_pol - average the polarisations together.
418 average_beam - average the beams together.
419 convert_pol - convert to a different polarisation type
420 auto_quotient - return the on/off quotient with
421 automatic detection of the on/off scans (closest
422 in time off is selected)
423 mx_quotient - Form a quotient using MX data (off beams)
424 scale, *, / - return a scan scaled by a given factor
425 add, +, - - return a scan with given value added
426 bin - return a scan with binned channels
427 resample - return a scan with resampled channels
428 smooth - return the spectrally smoothed scan
429 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
430 auto_poly_baseline - automatically fit a polynomial baseline
431 recalc_azel - recalculate azimuth and elevation based on
432 the pointing
433 gain_el - apply gain-elevation correction
434 opacity - apply opacity correction
435 convert_flux - convert to and from Jy and Kelvin brightness
436 units
437 freq_align - align spectra in frequency frame
438 invert_phase - Invert the phase of the cross-correlation
439 swap_linears - Swap XX and YY
440 rotate_xyphase - rotate XY phase of cross correlation
441 rotate_linpolphase - rotate the phase of the complex
442 polarization O=Q+iU correlation
443 freq_switch - perform frequency switching on the data
444 stats - Determine the specified statistic, e.g. 'min'
445 'max', 'rms' etc.
446 stddev - Determine the standard deviation of the current
447 beam/if/pol
448 [Selection]
449 selector - a selection object to set a subset of a scantable
450 set_scans - set (a list of) scans by index
451 set_cycles - set (a list of) cycles by index
452 set_beams - set (a list of) beamss by index
453 set_ifs - set (a list of) ifs by index
454 set_polarisations - set (a list of) polarisations by name
455 or by index
456 set_names - set a selection by name (wildcards allowed)
457 set_tsys - set a selection by tsys thresholds
458 reset - unset all selections
459 + - merge to selections
460
461 [Math] Mainly functions which operate on more than one scantable
462
463 average_time - return the (weighted) time average
464 of a list of scans
465 quotient - return the on/off quotient
466 simple_math - simple mathematical operations on two scantables,
467 'add', 'sub', 'mul', 'div'
468 quotient - build quotient of the given on and off scans
469 (matched pairs and 1 off/n on are valid)
470 merge - merge a list of scantables
471
472 [Line Catalog]
473 linecatalog - a linecatalog wrapper, taking an ASCII or
474 internal format table
475 summary - print a summary of the current selection
476 set_name - select a subset by name pattern, e.g. '*OH*'
477 set_strength_limits - select a subset by line strength limits
478 set_frequency_limits - select a subset by frequency limits
479 reset - unset all selections
480 save - save the current subset to a table (internal
481 format)
482 get_row - get the name and frequency from a specific
483 row in the table
484 [Fitting]
485 fitter
486 auto_fit - return a scan where the function is
487 applied to all Beams/IFs/Pols.
488 commit - return a new scan where the fits have been
489 commited.
490 fit - execute the actual fitting process
491 store_fit - store the fit parameters in the data (scantable)
492 get_chi2 - get the Chi^2
493 set_scan - set the scantable to be fit
494 set_function - set the fitting function
495 set_parameters - set the parameters for the function(s), and
496 set if they should be held fixed during fitting
497 set_gauss_parameters - same as above but specialised for individual
498 gaussian components
499 get_parameters - get the fitted parameters
500 plot - plot the resulting fit and/or components and
501 residual
502 [Plotter]
503 asapplotter - a plotter for asap, default plotter is
504 called 'plotter'
505 plot - plot a scantable
506 plot_lines - plot a linecatalog overlay
507 save - save the plot to a file ('png' ,'ps' or 'eps')
508 set_mode - set the state of the plotter, i.e.
509 what is to be plotted 'colour stacked'
510 and what 'panelled'
511 set_selection - only plot a selected part of the data
512 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
513 set_legend - specify user labels for the legend indeces
514 set_title - specify user labels for the panel indeces
515 set_abcissa - specify a user label for the abcissa
516 set_ordinate - specify a user label for the ordinate
517 set_layout - specify the multi-panel layout (rows,cols)
518 set_colors - specify a set of colours to use
519 set_linestyles - specify a set of linestyles to use if only
520 using one color
521 set_font - set general font properties, e.g. 'family'
522 set_histogram - plot in historam style
523 set_mask - set a plotting mask for a specific polarization
524 text - draw text annotations either in data or relative
525 coordinates
526 arrow - draw arrow annotations either in data or relative
527 coordinates
528 axhline,axvline - draw horizontal/vertical lines
529 axhspan,axvspan - draw horizontal/vertical regions
530
531 [Reading files]
532 reader - access rpfits/sdfits files
533 open - attach reader to a file
534 close - detach reader from file
535 read - read in integrations
536 summary - list info about all integrations
537
538 [General]
539 commands - this command
540 print - print details about a variable
541 list_scans - list all scantables created bt the user
542 list_files - list all files readable by asap (default rpf)
543 del - delete the given variable from memory
544 range - create a list of values, e.g.
545 range(3) = [0,1,2], range(2,5) = [2,3,4]
546 help - print help for one of the listed functions
547 execfile - execute an asap script, e.g. execfile('myscript')
548 list_rcparameters - print out a list of possible values to be
549 put into $HOME/.asaprc
550 rc - set rc parameters from within asap
551 mask_and,mask_or,
552 mask_not - boolean operations on masks created with
553 scantable.create_mask
554
555 Note:
556 How to use this with help:
557 # function 'summary'
558 [xxx] is just a category
559 Every 'sub-level' in this list should be replaces by a '.' Period when
560 using help
561 Example:
562 ASAP> help scantable # to get info on ths scantable
563 ASAP> help scantable.summary # to get help on the scantable's
564 ASAP> help average_time
565
566 """
567 if rcParams['verbose']:
568 try:
569 from IPython.genutils import page as pager
570 except ImportError:
571 from pydoc import pager
572 pager(x)
573 else:
574 print x
575 return
576
577def welcome():
578 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
579
580Please report any bugs via:
581http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
582
583[IMPORTANT: ASAP is 0-based]
584Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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