source: trunk/python/__init__.py@ 1184

Last change on this file since 1184 was 1175, checked in by mar637, 18 years ago

various changes to support the pylab plotter 'xyplotter'

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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: 2006-08-23 03:15:32 +0000 (Wed, 23 Aug 2006) $'.split()[1]
357__version__ = '2.1b'
358
359if rcParams['verbose']:
360 def version(): print "ASAP %s(%s)"% (__version__, __date__)
361 def list_scans(t = scantable):
362 import sys, types
363 globs = sys.modules['__main__'].__dict__.iteritems()
364 print "The user created scantables are:"
365 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
366 print filter(lambda x: not x.startswith('_'), sts)
367 return
368
369 def commands():
370 x = """
371 [The scan container]
372 scantable - a container for integrations/scans
373 (can open asap/rpfits/sdfits and ms files)
374 copy - returns a copy of a scan
375 get_scan - gets a specific scan out of a scantable
376 (by name or number)
377 drop_scan - drops a specific scan out of a scantable
378 (by number)
379 set_selection - set a new subselection of the data
380 get_selection - get the current selection object
381 summary - print info about the scantable contents
382 stats - get specified statistic of the spectra in
383 the scantable
384 stddev - get the standard deviation of the spectra
385 in the scantable
386 get_tsys - get the TSys
387 get_time - get the timestamps of the integrations
388 get_sourcename - get the source names of the scans
389 get_azimuth - get the azimuth of the scans
390 get_elevation - get the elevation of the scans
391 get_parangle - get the parallactic angle of the scans
392 get_unit - get the current unit
393 set_unit - set the abcissa unit to be used from this
394 point on
395 get_abcissa - get the abcissa values and name for a given
396 row (time)
397 set_freqframe - set the frame info for the Spectral Axis
398 (e.g. 'LSRK')
399 set_doppler - set the doppler to be used from this point on
400 set_dirframe - set the frame for the direction on the sky
401 set_instrument - set the instrument name
402 get_fluxunit - get the brightness flux unit
403 set_fluxunit - set the brightness flux unit
404 create_mask - return an mask in the current unit
405 for the given region. The specified regions
406 are NOT masked
407 get_restfreqs - get the current list of rest frequencies
408 set_restfreqs - set a list of rest frequencies
409 flag - flag selected channels in the data
410 save - save the scantable to disk as either 'ASAP',
411 'SDFITS' or 'ASCII'
412 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
413 nscan - the number of scans in the scantable
414 nrow - te number of spectra in the scantable
415 history - print the history of the scantable
416 get_fit - get a fit which has been stored witnh the data
417 average_time - return the (weighted) time average of a scan
418 or a list of scans
419 average_pol - average the polarisations together.
420 average_beam - average the beams together.
421 convert_pol - convert to a different polarisation type
422 auto_quotient - return the on/off quotient with
423 automatic detection of the on/off scans (closest
424 in time off is selected)
425 mx_quotient - Form a quotient using MX data (off beams)
426 scale, *, / - return a scan scaled by a given factor
427 add, +, - - return a scan with given value added
428 bin - return a scan with binned channels
429 resample - return a scan with resampled channels
430 smooth - return the spectrally smoothed scan
431 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
432 auto_poly_baseline - automatically fit a polynomial baseline
433 recalc_azel - recalculate azimuth and elevation based on
434 the pointing
435 gain_el - apply gain-elevation correction
436 opacity - apply opacity correction
437 convert_flux - convert to and from Jy and Kelvin brightness
438 units
439 freq_align - align spectra in frequency frame
440 invert_phase - Invert the phase of the cross-correlation
441 swap_linears - Swap XX and YY
442 rotate_xyphase - rotate XY phase of cross correlation
443 rotate_linpolphase - rotate the phase of the complex
444 polarization O=Q+iU correlation
445 freq_switch - perform frequency switching on the data
446 stats - Determine the specified statistic, e.g. 'min'
447 'max', 'rms' etc.
448 stddev - Determine the standard deviation of the current
449 beam/if/pol
450 [Selection]
451 selector - a selection object to set a subset of a scantable
452 set_scans - set (a list of) scans by index
453 set_cycles - set (a list of) cycles by index
454 set_beams - set (a list of) beamss by index
455 set_ifs - set (a list of) ifs by index
456 set_polarisations - set (a list of) polarisations by name
457 or by index
458 set_names - set a selection by name (wildcards allowed)
459 set_tsys - set a selection by tsys thresholds
460 reset - unset all selections
461 + - merge to selections
462
463 [Math] Mainly functions which operate on more than one scantable
464
465 average_time - return the (weighted) time average
466 of a list of scans
467 quotient - return the on/off quotient
468 simple_math - simple mathematical operations on two scantables,
469 'add', 'sub', 'mul', 'div'
470 quotient - build quotient of the given on and off scans
471 (matched pairs and 1 off/n on are valid)
472 merge - merge a list of scantables
473
474 [Line Catalog]
475 linecatalog - a linecatalog wrapper, taking an ASCII or
476 internal format table
477 summary - print a summary of the current selection
478 set_name - select a subset by name pattern, e.g. '*OH*'
479 set_strength_limits - select a subset by line strength limits
480 set_frequency_limits - select a subset by frequency limits
481 reset - unset all selections
482 save - save the current subset to a table (internal
483 format)
484 get_row - get the name and frequency from a specific
485 row in the table
486 [Fitting]
487 fitter
488 auto_fit - return a scan where the function is
489 applied to all Beams/IFs/Pols.
490 commit - return a new scan where the fits have been
491 commited.
492 fit - execute the actual fitting process
493 store_fit - store the fit parameters in the data (scantable)
494 get_chi2 - get the Chi^2
495 set_scan - set the scantable to be fit
496 set_function - set the fitting function
497 set_parameters - set the parameters for the function(s), and
498 set if they should be held fixed during fitting
499 set_gauss_parameters - same as above but specialised for individual
500 gaussian components
501 get_parameters - get the fitted parameters
502 plot - plot the resulting fit and/or components and
503 residual
504 [Plotter]
505 asapplotter - a plotter for asap, default plotter is
506 called 'plotter'
507 plot - plot a scantable
508 plot_lines - plot a linecatalog overlay
509 save - save the plot to a file ('png' ,'ps' or 'eps')
510 set_mode - set the state of the plotter, i.e.
511 what is to be plotted 'colour stacked'
512 and what 'panelled'
513 set_selection - only plot a selected part of the data
514 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
515 set_legend - specify user labels for the legend indeces
516 set_title - specify user labels for the panel indeces
517 set_abcissa - specify a user label for the abcissa
518 set_ordinate - specify a user label for the ordinate
519 set_layout - specify the multi-panel layout (rows,cols)
520 set_colors - specify a set of colours to use
521 set_linestyles - specify a set of linestyles to use if only
522 using one color
523 set_font - set general font properties, e.g. 'family'
524 set_histogram - plot in historam style
525 set_mask - set a plotting mask for a specific polarization
526 text - draw text annotations either in data or relative
527 coordinates
528 arrow - draw arrow annotations either in data or relative
529 coordinates
530 axhline,axvline - draw horizontal/vertical lines
531 axhspan,axvspan - draw horizontal/vertical regions
532
533 xyplotter - matplotlib/pylab plotting functions
534
535 [Reading files]
536 reader - access rpfits/sdfits files
537 open - attach reader to a file
538 close - detach reader from file
539 read - read in integrations
540 summary - list info about all integrations
541
542 [General]
543 commands - this command
544 print - print details about a variable
545 list_scans - list all scantables created bt the user
546 list_files - list all files readable by asap (default rpf)
547 del - delete the given variable from memory
548 range - create a list of values, e.g.
549 range(3) = [0,1,2], range(2,5) = [2,3,4]
550 help - print help for one of the listed functions
551 execfile - execute an asap script, e.g. execfile('myscript')
552 list_rcparameters - print out a list of possible values to be
553 put into $HOME/.asaprc
554 rc - set rc parameters from within asap
555 mask_and,mask_or,
556 mask_not - boolean operations on masks created with
557 scantable.create_mask
558
559 Note:
560 How to use this with help:
561 # function 'summary'
562 [xxx] is just a category
563 Every 'sub-level' in this list should be replaces by a '.' Period when
564 using help
565 Example:
566 ASAP> help scantable # to get info on ths scantable
567 ASAP> help scantable.summary # to get help on the scantable's
568 ASAP> help average_time
569
570 """
571 if rcParams['verbose']:
572 try:
573 from IPython.genutils import page as pager
574 except ImportError:
575 from pydoc import pager
576 pager(x)
577 else:
578 print x
579 return
580
581def welcome():
582 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
583
584Please report any bugs via:
585http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
586
587[IMPORTANT: ASAP is 0-based]
588Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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