source: branches/alma/python/__init__.py@ 1539

Last change on this file since 1539 was 1494, checked in by TakTsutsumi, 16 years ago

New Development: No

JIRA Issue: No

Ready to Release: Yes

Interface Changes: No

What Interface Changed: Please list interface changes

Test Programs: List test programs

Put in Release Notes: No

Module(s): Module Names change impacts.

Description: Fixed revision to set the ASAP revision

number correctly


  • Property svn:eol-style set to native
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File size: 23.0 KB
Line 
1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
5import os,sys,shutil, platform
6
7# Set up CASAPATH 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 CASAPATH if defined and "data" dir present
25if not os.environ.has_key("CASAPATH") or \
26 not os.path.exists(os.environ["CASAPATH"].split()[0]+"/data"):
27 os.environ["CASAPATH"] = "%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
350from interactivemask import interactivemask
351
352if rcParams['useplotter']:
353 try:
354 from asapplotter import asapplotter
355 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
356 if gui:
357 import pylab as xyplotter
358 plotter = asapplotter(gui)
359 del gui
360 except ImportError:
361 print "Matplotlib not installed. No plotting available"
362
363__date__ = '$Date: 2009-02-02 16:50:25 +0000 (Mon, 02 Feb 2009) $'.split()[1]
364__version__ = '2.2.0 alma'
365# nrao casapy specific, get revision number
366#__revision__ = ' unknown '
367casapath=os.environ["CASAPATH"].split()
368revinfo=casapath[0]+'/'+casapath[1]+'/python/2.5/asap/svninfo.txt'
369if os.path.isfile(revinfo):
370 f = file(revinfo)
371 f.readline()
372 revsionno=f.readline()
373 f.close()
374 __revision__ = revsionno.rstrip()
375else:
376 __revision__ = ' unknown '
377
378def is_ipython():
379 return '__IP' in dir(sys.modules["__main__"])
380if is_ipython():
381 def version(): print "ASAP %s(%s)"% (__version__, __date__)
382 def list_scans(t = scantable):
383 import types
384 globs = sys.modules['__main__'].__dict__.iteritems()
385 print "The user created scantables are:"
386 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
387 print filter(lambda x: not x.startswith('_'), sts)
388 return
389
390 def commands():
391 x = """
392 [The scan container]
393 scantable - a container for integrations/scans
394 (can open asap/rpfits/sdfits and ms files)
395 copy - returns a copy of a scan
396 get_scan - gets a specific scan out of a scantable
397 (by name or number)
398 drop_scan - drops a specific scan out of a scantable
399 (by number)
400 set_selection - set a new subselection of the data
401 get_selection - get the current selection object
402 summary - print info about the scantable contents
403 stats - get specified statistic of the spectra in
404 the scantable
405 stddev - get the standard deviation of the spectra
406 in the scantable
407 get_tsys - get the TSys
408 get_time - get the timestamps of the integrations
409 get_inttime - get the integration time
410 get_sourcename - get the source names of the scans
411 get_azimuth - get the azimuth of the scans
412 get_elevation - get the elevation of the scans
413 get_parangle - get the parallactic angle of the scans
414 get_unit - get the current unit
415 set_unit - set the abcissa unit to be used from this
416 point on
417 get_abcissa - get the abcissa values and name for a given
418 row (time)
419 get_column_names - get the names of the columns in the scantable
420 for use with selector.set_query
421 set_freqframe - set the frame info for the Spectral Axis
422 (e.g. 'LSRK')
423 set_doppler - set the doppler to be used from this point on
424 set_dirframe - set the frame for the direction on the sky
425 set_instrument - set the instrument name
426 set_feedtype - set the feed type
427 get_fluxunit - get the brightness flux unit
428 set_fluxunit - set the brightness flux unit
429 create_mask - return an mask in the current unit
430 for the given region. The specified regions
431 are NOT masked
432 get_restfreqs - get the current list of rest frequencies
433 set_restfreqs - set a list of rest frequencies
434 shift_refpix - shift the reference pixel of the IFs
435 flag - flag selected channels in the data
436 lag_flag - flag specified frequency in the data
437 save - save the scantable to disk as either 'ASAP',
438 'SDFITS' or 'ASCII'
439 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
440 nscan - the number of scans in the scantable
441 nrow - te number of spectra in the scantable
442 history - print the history of the scantable
443 get_fit - get a fit which has been stored witnh the data
444 average_time - return the (weighted) time average of a scan
445 or a list of scans
446 average_pol - average the polarisations together.
447 average_beam - average the beams together.
448 convert_pol - convert to a different polarisation type
449 auto_quotient - return the on/off quotient with
450 automatic detection of the on/off scans (closest
451 in time off is selected)
452 mx_quotient - Form a quotient using MX data (off beams)
453 scale, *, / - return a scan scaled by a given factor
454 add, +, - - return a scan with given value added
455 bin - return a scan with binned channels
456 resample - return a scan with resampled channels
457 smooth - return the spectrally smoothed scan
458 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
459 auto_poly_baseline - automatically fit a polynomial baseline
460 recalc_azel - recalculate azimuth and elevation based on
461 the pointing
462 gain_el - apply gain-elevation correction
463 opacity - apply opacity correction
464 convert_flux - convert to and from Jy and Kelvin brightness
465 units
466 freq_align - align spectra in frequency frame
467 invert_phase - Invert the phase of the cross-correlation
468 swap_linears - Swap XX and YY (or RR LL)
469 rotate_xyphase - rotate XY phase of cross correlation
470 rotate_linpolphase - rotate the phase of the complex
471 polarization O=Q+iU correlation
472 freq_switch - perform frequency switching on the data
473 stats - Determine the specified statistic, e.g. 'min'
474 'max', 'rms' etc.
475 stddev - Determine the standard deviation of the current
476 beam/if/pol
477 [Selection]
478 selector - a selection object to set a subset of a scantable
479 set_scans - set (a list of) scans by index
480 set_cycles - set (a list of) cycles by index
481 set_beams - set (a list of) beamss by index
482 set_ifs - set (a list of) ifs by index
483 set_polarisations - set (a list of) polarisations by name
484 or by index
485 set_names - set a selection by name (wildcards allowed)
486 set_tsys - set a selection by tsys thresholds
487 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
488 ( also get_ functions for all these )
489 reset - unset all selections
490 + - merge two selections
491
492 [Math] Mainly functions which operate on more than one scantable
493
494 average_time - return the (weighted) time average
495 of a list of scans
496 quotient - return the on/off quotient
497 simple_math - simple mathematical operations on two scantables,
498 'add', 'sub', 'mul', 'div'
499 quotient - build quotient of the given on and off scans
500 (matched pairs and 1 off - n on are valid)
501 merge - merge a list of scantables
502
503 [Line Catalog]
504 linecatalog - a linecatalog wrapper, taking an ASCII or
505 internal format table
506 summary - print a summary of the current selection
507 set_name - select a subset by name pattern, e.g. '*OH*'
508 set_strength_limits - select a subset by line strength limits
509 set_frequency_limits - select a subset by frequency limits
510 reset - unset all selections
511 save - save the current subset to a table (internal
512 format)
513 get_row - get the name and frequency from a specific
514 row in the table
515 [Fitting]
516 fitter
517 auto_fit - return a scan where the function is
518 applied to all Beams/IFs/Pols.
519 commit - return a new scan where the fits have been
520 commited.
521 fit - execute the actual fitting process
522 store_fit - store the fit parameters in the data (scantable)
523 get_chi2 - get the Chi^2
524 set_scan - set the scantable to be fit
525 set_function - set the fitting function
526 set_parameters - set the parameters for the function(s), and
527 set if they should be held fixed during fitting
528 set_gauss_parameters - same as above but specialised for individual
529 gaussian components
530 get_parameters - get the fitted parameters
531 plot - plot the resulting fit and/or components and
532 residual
533 [Plotter]
534 asapplotter - a plotter for asap, default plotter is
535 called 'plotter'
536 plot - plot a scantable
537 plot_lines - plot a linecatalog overlay
538 save - save the plot to a file ('png' ,'ps' or 'eps')
539 set_mode - set the state of the plotter, i.e.
540 what is to be plotted 'colour stacked'
541 and what 'panelled'
542 set_selection - only plot a selected part of the data
543 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
544 set_legend - specify user labels for the legend indeces
545 set_title - specify user labels for the panel indeces
546 set_abcissa - specify a user label for the abcissa
547 set_ordinate - specify a user label for the ordinate
548 set_layout - specify the multi-panel layout (rows,cols)
549 set_colors - specify a set of colours to use
550 set_linestyles - specify a set of linestyles to use if only
551 using one color
552 set_font - set general font properties, e.g. 'family'
553 set_histogram - plot in historam style
554 set_mask - set a plotting mask for a specific polarization
555 text - draw text annotations either in data or relative
556 coordinates
557 arrow - draw arrow annotations either in data or relative
558 coordinates
559 axhline,axvline - draw horizontal/vertical lines
560 axhspan,axvspan - draw horizontal/vertical regions
561
562 xyplotter - matplotlib/pylab plotting functions
563
564 [Reading files]
565 reader - access rpfits/sdfits files
566 open - attach reader to a file
567 close - detach reader from file
568 read - read in integrations
569 summary - list info about all integrations
570
571 [General]
572 commands - this command
573 print - print details about a variable
574 list_scans - list all scantables created bt the user
575 list_files - list all files readable by asap (default rpf)
576 del - delete the given variable from memory
577 range - create a list of values, e.g.
578 range(3) = [0,1,2], range(2,5) = [2,3,4]
579 help - print help for one of the listed functions
580 execfile - execute an asap script, e.g. execfile('myscript')
581 list_rcparameters - print out a list of possible values to be
582 put into $HOME/.asaprc
583 rc - set rc parameters from within asap
584 mask_and,mask_or,
585 mask_not - boolean operations on masks created with
586 scantable.create_mask
587
588 Note:
589 How to use this with help:
590 # function 'summary'
591 [xxx] is just a category
592 Every 'sub-level' in this list should be replaces by a '.' Period when
593 using help
594 Example:
595 ASAP> help scantable # to get info on ths scantable
596 ASAP> help scantable.summary # to get help on the scantable's
597 ASAP> help average_time
598
599 """
600 if rcParams['verbose']:
601 try:
602 from IPython.genutils import page as pager
603 except ImportError:
604 from pydoc import pager
605 pager(x)
606 else:
607 print x
608 return
609
610def welcome():
611 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
612
613Please report any bugs via:
614http://svn.atnf.csiro.au/trac/asap/simpleticket
615
616[IMPORTANT: ASAP is 0-based]
617Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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