source: trunk/python/__init__.py@ 1412

Last change on this file since 1412 was 1408, checked in by Malte Marquarding, 17 years ago

use pylab as a reference

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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"]
24# use AIPSPATH if defined and "data" dir present
25if not os.environ.has_key("AIPSPATH") or \
26 not os.path.exists(os.environ["AIPSPATH"].split()[0]+"/data"):
27 os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
28# set up user space
29userdir = os.environ["HOME"]+"/.asap"
30if not os.path.exists(userdir):
31 print 'First time ASAP use. Setting up ~/.asap'
32 os.mkdir(userdir)
33 shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
34 f = file(userdir+"/asapuserfuncs.py", "w")
35 f.close()
36 f = file(userdir+"/ipythonrc", "w")
37 f.close()
38# remove from namespace
39del asapdata, userdir, shutil, platform
40
41def _validate_bool(b):
42 'Convert b to a boolean or raise'
43 bl = b.lower()
44 if bl in ('f', 'no', 'false', '0', 0): return False
45 elif bl in ('t', 'yes', 'true', '1', 1): return True
46 else:
47 raise ValueError('Could not convert "%s" to boolean' % b)
48
49def _validate_int(s):
50 'convert s to int or raise'
51 try: return int(s)
52 except ValueError:
53 raise ValueError('Could not convert "%s" to int' % s)
54
55def _asap_fname():
56 """
57 Return the path to the rc file
58
59 Search order:
60
61 * current working dir
62 * environ var ASAPRC
63 * HOME/.asaprc
64
65 """
66
67 fname = os.path.join( os.getcwd(), '.asaprc')
68 if os.path.exists(fname): return fname
69
70 if os.environ.has_key('ASAPRC'):
71 path = os.environ['ASAPRC']
72 if os.path.exists(path):
73 fname = os.path.join(path, '.asaprc')
74 if os.path.exists(fname):
75 return fname
76
77 if os.environ.has_key('HOME'):
78 home = os.environ['HOME']
79 fname = os.path.join(home, '.asaprc')
80 if os.path.exists(fname):
81 return fname
82 return None
83
84
85defaultParams = {
86 # general
87 'verbose' : [True, _validate_bool],
88 'useplotter' : [True, _validate_bool],
89 'insitu' : [True, _validate_bool],
90
91 # plotting
92 'plotter.gui' : [True, _validate_bool],
93 'plotter.stacking' : ['p', str],
94 'plotter.panelling' : ['s', str],
95 'plotter.colours' : ['', str],
96 'plotter.linestyles' : ['', str],
97 'plotter.decimate' : [False, _validate_bool],
98 'plotter.ganged' : [True, _validate_bool],
99 'plotter.histogram' : [False, _validate_bool],
100 'plotter.papertype' : ['A4', str],
101
102 # scantable
103 'scantable.save' : ['ASAP', str],
104 'scantable.autoaverage' : [True, _validate_bool],
105 'scantable.freqframe' : ['LSRK', str], #default frequency frame
106 'scantable.verbosesummary' : [False, _validate_bool],
107 'scantable.storage' : ['memory', str]
108 # fitter
109 }
110
111def list_rcparameters():
112
113 print """
114# general
115# print verbose output
116verbose : True
117
118# preload a default plotter
119useplotter : True
120
121# apply operations on the input scantable or return new one
122insitu : True
123
124# plotting
125
126# do we want a GUI or plot to a file
127plotter.gui : True
128
129# default mode for colour stacking
130plotter.stacking : Pol
131
132# default mode for panelling
133plotter.panelling : scan
134
135# push panels together, to share axislabels
136plotter.ganged : True
137
138# decimate the number of points plotted bya afactor of
139# nchan/1024
140plotter.decimate : False
141
142# default colours/linestyles
143plotter.colours :
144plotter.linestyles :
145
146# enable/disable histogram plotting
147plotter.histogram : False
148
149# ps paper type
150plotter.papertype : A4
151
152# scantable
153
154# default storage of scantable ('memory'/'disk')
155scantable.storage : memory
156# default ouput format when saving
157scantable.save : ASAP
158# auto averaging on read
159scantable.autoaverage : True
160
161# default frequency frame to set when function
162# scantable.set_freqframe is called
163scantable.freqframe : LSRK
164
165# Control the level of information printed by summary
166scantable.verbosesummary : False
167
168# Fitter
169"""
170
171def rc_params():
172 'Return the default params updated from the values in the rc file'
173
174 fname = _asap_fname()
175
176 if fname is None or not os.path.exists(fname):
177 message = 'could not find rc file; returning defaults'
178 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
179 #print message
180 return ret
181
182 cnt = 0
183 for line in file(fname):
184 cnt +=1
185 line = line.strip()
186 if not len(line): continue
187 if line.startswith('#'): continue
188 tup = line.split(':',1)
189 if len(tup) !=2:
190 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
191 continue
192
193 key, val = tup
194 key = key.strip()
195 if not defaultParams.has_key(key):
196 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
197 continue
198
199 default, converter = defaultParams[key]
200
201 ind = val.find('#')
202 if ind>=0: val = val[:ind] # ignore trailing comments
203 val = val.strip()
204 try: cval = converter(val) # try to convert to proper type or raise
205 except ValueError, msg:
206 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
207 continue
208 else:
209 # Alles Klar, update dict
210 defaultParams[key][0] = cval
211
212 # strip the conveter funcs and return
213 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
214 print ('loaded rc file %s'%fname)
215
216 return ret
217
218
219# this is the instance used by the asap classes
220rcParams = rc_params()
221
222rcParamsDefault = dict(rcParams.items()) # a copy
223
224def rc(group, **kwargs):
225 """
226 Set the current rc params. Group is the grouping for the rc, eg
227 for scantable.save the group is 'scantable', for plotter.stacking, the
228 group is 'plotter', and so on. kwargs is a list of attribute
229 name/value pairs, eg
230
231 rc('scantable', save='SDFITS')
232
233 sets the current rc params and is equivalent to
234
235 rcParams['scantable.save'] = 'SDFITS'
236
237 Use rcdefaults to restore the default rc params after changes.
238 """
239
240 aliases = {}
241
242 for k,v in kwargs.items():
243 name = aliases.get(k) or k
244 key = '%s.%s' % (group, name)
245 if not rcParams.has_key(key):
246 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
247
248 rcParams[key] = v
249
250
251def rcdefaults():
252 """
253 Restore the default rc params - the ones that were created at
254 asap load time
255 """
256 rcParams.update(rcParamsDefault)
257
258def _n_bools(n, val):
259 return [ val for i in xrange(n) ]
260
261def _is_sequence_or_number(param, ptype=int):
262 if isinstance(param,tuple) or isinstance(param,list):
263 if len(param) == 0: return True # empty list
264 out = True
265 for p in param:
266 out &= isinstance(p,ptype)
267 return out
268 elif isinstance(param, ptype):
269 return True
270 return False
271
272def _to_list(param, ptype=int):
273 if isinstance(param, ptype):
274 if ptype is str: return param.split()
275 else: return [param]
276 if _is_sequence_or_number(param, ptype):
277 return param
278 return None
279
280def unique(x):
281 """
282 Return the unique values in a list
283 Parameters:
284 x: the list to reduce
285 Examples:
286 x = [1,2,3,3,4]
287 print unique(x)
288 [1,2,3,4]
289 """
290 return dict([ (val, 1) for val in x]).keys()
291
292def list_files(path=".",suffix="rpf"):
293 """
294 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
295 Parameters:
296 path: The directory to list (default '.')
297 suffix: The file extension (default rpf)
298 Example:
299 files = list_files("data/","sdfits")
300 print files
301 ['data/2001-09-01_0332_P363.sdfits',
302 'data/2003-04-04_131152_t0002.sdfits',
303 'data/Sgr_86p262_best_SPC.sdfits']
304 """
305 if not os.path.isdir(path):
306 return None
307 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
308 if not suffix in valid:
309 return None
310 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
311 return filter(lambda x: x.endswith(suffix),files)
312
313# workaround for ipython, which redirects this if banner=0 in ipythonrc
314sys.stdout = sys.__stdout__
315sys.stderr = sys.__stderr__
316
317# Logging
318from asap._asap import Log as _asaplog
319global asaplog
320asaplog=_asaplog()
321if rcParams['verbose']:
322 asaplog.enable()
323else:
324 asaplog.disable()
325
326def print_log():
327 log = asaplog.pop()
328 if len(log) and rcParams['verbose']: print log
329 return
330
331def mask_and(a, b):
332 assert(len(a)==len(b))
333 return [ a[i] & b[i] for i in xrange(len(a)) ]
334
335def mask_or(a, b):
336 assert(len(a)==len(b))
337 return [ a[i] | b[i] for i in xrange(len(a)) ]
338
339def mask_not(a):
340 return [ not i for i in a ]
341
342from asapfitter import fitter
343from asapreader import reader
344from selector import selector
345
346from asapmath import *
347from scantable import scantable
348from asaplinefind import linefinder
349from linecatalog import linecatalog
350
351if rcParams['useplotter']:
352 try:
353 from asapplotter import asapplotter
354 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
355 if gui:
356 import pylab
357 xyplotter = pylab
358 plotter = asapplotter(gui)
359 del gui
360 except ImportError:
361 print "Matplotlib not installed. No plotting available"
362
363__date__ = '$Date: 2008-01-31 04:07:57 +0000 (Thu, 31 Jan 2008) $'.split()[1]
364__version__ = 'trunk'
365
366def is_ipython():
367 return '__IP' in dir(sys.modules["__main__"])
368if is_ipython():
369 def version(): print "ASAP %s(%s)"% (__version__, __date__)
370 def list_scans(t = scantable):
371 import types
372 globs = sys.modules['__main__'].__dict__.iteritems()
373 print "The user created scantables are:"
374 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
375 print filter(lambda x: not x.startswith('_'), sts)
376 return
377
378 def commands():
379 x = """
380 [The scan container]
381 scantable - a container for integrations/scans
382 (can open asap/rpfits/sdfits and ms files)
383 copy - returns a copy of a scan
384 get_scan - gets a specific scan out of a scantable
385 (by name or number)
386 drop_scan - drops a specific scan out of a scantable
387 (by number)
388 set_selection - set a new subselection of the data
389 get_selection - get the current selection object
390 summary - print info about the scantable contents
391 stats - get specified statistic of the spectra in
392 the scantable
393 stddev - get the standard deviation of the spectra
394 in the scantable
395 get_tsys - get the TSys
396 get_time - get the timestamps of the integrations
397 get_inttime - get the integration time
398 get_sourcename - get the source names of the scans
399 get_azimuth - get the azimuth of the scans
400 get_elevation - get the elevation of the scans
401 get_parangle - get the parallactic angle of the scans
402 get_unit - get the current unit
403 set_unit - set the abcissa unit to be used from this
404 point on
405 get_abcissa - get the abcissa values and name for a given
406 row (time)
407 get_column_names - get the names of the columns in the scantable
408 for use with selector.set_query
409 set_freqframe - set the frame info for the Spectral Axis
410 (e.g. 'LSRK')
411 set_doppler - set the doppler to be used from this point on
412 set_dirframe - set the frame for the direction on the sky
413 set_instrument - set the instrument name
414 set_feedtype - set the feed type
415 get_fluxunit - get the brightness flux unit
416 set_fluxunit - set the brightness flux unit
417 create_mask - return an mask in the current unit
418 for the given region. The specified regions
419 are NOT masked
420 get_restfreqs - get the current list of rest frequencies
421 set_restfreqs - set a list of rest frequencies
422 shift_refpix - shift the reference pixel of the IFs
423 flag - flag selected channels in the data
424 lag_flag - flag specified frequency in the data
425 save - save the scantable to disk as either 'ASAP',
426 'SDFITS' or 'ASCII'
427 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
428 nscan - the number of scans in the scantable
429 nrow - te number of spectra in the scantable
430 history - print the history of the scantable
431 get_fit - get a fit which has been stored witnh the data
432 average_time - return the (weighted) time average of a scan
433 or a list of scans
434 average_pol - average the polarisations together.
435 average_beam - average the beams together.
436 convert_pol - convert to a different polarisation type
437 auto_quotient - return the on/off quotient with
438 automatic detection of the on/off scans (closest
439 in time off is selected)
440 mx_quotient - Form a quotient using MX data (off beams)
441 scale, *, / - return a scan scaled by a given factor
442 add, +, - - return a scan with given value added
443 bin - return a scan with binned channels
444 resample - return a scan with resampled channels
445 smooth - return the spectrally smoothed scan
446 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
447 auto_poly_baseline - automatically fit a polynomial baseline
448 recalc_azel - recalculate azimuth and elevation based on
449 the pointing
450 gain_el - apply gain-elevation correction
451 opacity - apply opacity correction
452 convert_flux - convert to and from Jy and Kelvin brightness
453 units
454 freq_align - align spectra in frequency frame
455 invert_phase - Invert the phase of the cross-correlation
456 swap_linears - Swap XX and YY (or RR LL)
457 rotate_xyphase - rotate XY phase of cross correlation
458 rotate_linpolphase - rotate the phase of the complex
459 polarization O=Q+iU correlation
460 freq_switch - perform frequency switching on the data
461 stats - Determine the specified statistic, e.g. 'min'
462 'max', 'rms' etc.
463 stddev - Determine the standard deviation of the current
464 beam/if/pol
465 [Selection]
466 selector - a selection object to set a subset of a scantable
467 set_scans - set (a list of) scans by index
468 set_cycles - set (a list of) cycles by index
469 set_beams - set (a list of) beamss by index
470 set_ifs - set (a list of) ifs by index
471 set_polarisations - set (a list of) polarisations by name
472 or by index
473 set_names - set a selection by name (wildcards allowed)
474 set_tsys - set a selection by tsys thresholds
475 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
476 ( also get_ functions for all these )
477 reset - unset all selections
478 + - merge two selections
479
480 [Math] Mainly functions which operate on more than one scantable
481
482 average_time - return the (weighted) time average
483 of a list of scans
484 quotient - return the on/off quotient
485 simple_math - simple mathematical operations on two scantables,
486 'add', 'sub', 'mul', 'div'
487 quotient - build quotient of the given on and off scans
488 (matched pairs and 1 off - n on are valid)
489 merge - merge a list of scantables
490
491 [Line Catalog]
492 linecatalog - a linecatalog wrapper, taking an ASCII or
493 internal format table
494 summary - print a summary of the current selection
495 set_name - select a subset by name pattern, e.g. '*OH*'
496 set_strength_limits - select a subset by line strength limits
497 set_frequency_limits - select a subset by frequency limits
498 reset - unset all selections
499 save - save the current subset to a table (internal
500 format)
501 get_row - get the name and frequency from a specific
502 row in the table
503 [Fitting]
504 fitter
505 auto_fit - return a scan where the function is
506 applied to all Beams/IFs/Pols.
507 commit - return a new scan where the fits have been
508 commited.
509 fit - execute the actual fitting process
510 store_fit - store the fit parameters in the data (scantable)
511 get_chi2 - get the Chi^2
512 set_scan - set the scantable to be fit
513 set_function - set the fitting function
514 set_parameters - set the parameters for the function(s), and
515 set if they should be held fixed during fitting
516 set_gauss_parameters - same as above but specialised for individual
517 gaussian components
518 get_parameters - get the fitted parameters
519 plot - plot the resulting fit and/or components and
520 residual
521 [Plotter]
522 asapplotter - a plotter for asap, default plotter is
523 called 'plotter'
524 plot - plot a scantable
525 plot_lines - plot a linecatalog overlay
526 save - save the plot to a file ('png' ,'ps' or 'eps')
527 set_mode - set the state of the plotter, i.e.
528 what is to be plotted 'colour stacked'
529 and what 'panelled'
530 set_selection - only plot a selected part of the data
531 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
532 set_legend - specify user labels for the legend indeces
533 set_title - specify user labels for the panel indeces
534 set_abcissa - specify a user label for the abcissa
535 set_ordinate - specify a user label for the ordinate
536 set_layout - specify the multi-panel layout (rows,cols)
537 set_colors - specify a set of colours to use
538 set_linestyles - specify a set of linestyles to use if only
539 using one color
540 set_font - set general font properties, e.g. 'family'
541 set_histogram - plot in historam style
542 set_mask - set a plotting mask for a specific polarization
543 text - draw text annotations either in data or relative
544 coordinates
545 arrow - draw arrow annotations either in data or relative
546 coordinates
547 axhline,axvline - draw horizontal/vertical lines
548 axhspan,axvspan - draw horizontal/vertical regions
549
550 xyplotter - matplotlib/pylab plotting functions
551
552 [Reading files]
553 reader - access rpfits/sdfits files
554 open - attach reader to a file
555 close - detach reader from file
556 read - read in integrations
557 summary - list info about all integrations
558
559 [General]
560 commands - this command
561 print - print details about a variable
562 list_scans - list all scantables created bt the user
563 list_files - list all files readable by asap (default rpf)
564 del - delete the given variable from memory
565 range - create a list of values, e.g.
566 range(3) = [0,1,2], range(2,5) = [2,3,4]
567 help - print help for one of the listed functions
568 execfile - execute an asap script, e.g. execfile('myscript')
569 list_rcparameters - print out a list of possible values to be
570 put into $HOME/.asaprc
571 rc - set rc parameters from within asap
572 mask_and,mask_or,
573 mask_not - boolean operations on masks created with
574 scantable.create_mask
575
576 Note:
577 How to use this with help:
578 # function 'summary'
579 [xxx] is just a category
580 Every 'sub-level' in this list should be replaces by a '.' Period when
581 using help
582 Example:
583 ASAP> help scantable # to get info on ths scantable
584 ASAP> help scantable.summary # to get help on the scantable's
585 ASAP> help average_time
586
587 """
588 if rcParams['verbose']:
589 try:
590 from IPython.genutils import page as pager
591 except ImportError:
592 from pydoc import pager
593 pager(x)
594 else:
595 print x
596 return
597
598def welcome():
599 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
600
601Please report any bugs via:
602http://svn.atnf.csiro.au/trac/asap/simpleticket
603
604[IMPORTANT: ASAP is 0-based]
605Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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