source: trunk/python/__init__.py@ 1422

Last change on this file since 1422 was 1422, checked in by Malte Marquarding, 16 years ago

added scantable.history rc parameter to optionally suppress history generation. Fixed warning in matplotlib re backend import

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 22.9 KB
RevLine 
[100]1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
[1080]5import os,sys,shutil, platform
[226]6
[1080]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]
[1171]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"]
[1371]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"):
[1316]27 os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
[1171]28# set up user space
[1080]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()
[1171]38# remove from namespace
[1080]39del asapdata, userdir, shutil, platform
40
[513]41def _validate_bool(b):
[226]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
[513]49def _validate_int(s):
[226]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
[513]55def _asap_fname():
[226]56 """
57 Return the path to the rc file
58
59 Search order:
60
61 * current working dir
62 * environ var ASAPRC
[274]63 * HOME/.asaprc
[706]64
[226]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
[706]84
[226]85defaultParams = {
86 # general
[513]87 'verbose' : [True, _validate_bool],
88 'useplotter' : [True, _validate_bool],
[542]89 'insitu' : [True, _validate_bool],
[706]90
[226]91 # plotting
[706]92 'plotter.gui' : [True, _validate_bool],
[226]93 'plotter.stacking' : ['p', str],
94 'plotter.panelling' : ['s', str],
[700]95 'plotter.colours' : ['', str],
96 'plotter.linestyles' : ['', str],
[710]97 'plotter.decimate' : [False, _validate_bool],
98 'plotter.ganged' : [True, _validate_bool],
[1022]99 'plotter.histogram' : [False, _validate_bool],
[1097]100 'plotter.papertype' : ['A4', str],
[710]101
[226]102 # scantable
103 'scantable.save' : ['ASAP', str],
[513]104 'scantable.autoaverage' : [True, _validate_bool],
[226]105 'scantable.freqframe' : ['LSRK', str], #default frequency frame
[1076]106 'scantable.verbosesummary' : [False, _validate_bool],
[1422]107 'scantable.storage' : ['memory', str],
108 'scantable.history' : [True, _validate_bool]
[226]109 # fitter
110 }
111
[255]112def list_rcparameters():
[706]113
[255]114 print """
[737]115# general
116# print verbose output
117verbose : True
[255]118
[737]119# preload a default plotter
120useplotter : True
[255]121
[737]122# apply operations on the input scantable or return new one
123insitu : True
[706]124
[737]125# plotting
[710]126
[737]127# do we want a GUI or plot to a file
128plotter.gui : True
[710]129
[737]130# default mode for colour stacking
131plotter.stacking : Pol
[255]132
[737]133# default mode for panelling
134plotter.panelling : scan
[255]135
[737]136# push panels together, to share axislabels
137plotter.ganged : True
[710]138
[737]139# decimate the number of points plotted bya afactor of
140# nchan/1024
141plotter.decimate : False
[733]142
[737]143# default colours/linestyles
144plotter.colours :
145plotter.linestyles :
[700]146
[1022]147# enable/disable histogram plotting
148plotter.histogram : False
149
[1097]150# ps paper type
151plotter.papertype : A4
152
[737]153# scantable
[1076]154
[1259]155# default storage of scantable ('memory'/'disk')
[1076]156scantable.storage : memory
[1422]157
158# write history of each call to scantable
159scantable.history : True
160
[737]161# default ouput format when saving
162scantable.save : ASAP
[1422]163
[737]164# auto averaging on read
165scantable.autoaverage : True
[255]166
[737]167# default frequency frame to set when function
[1097]168# scantable.set_freqframe is called
[737]169scantable.freqframe : LSRK
[255]170
[737]171# Control the level of information printed by summary
172scantable.verbosesummary : False
[706]173
[737]174# Fitter
175"""
[706]176
[226]177def rc_params():
178 'Return the default params updated from the values in the rc file'
[706]179
[513]180 fname = _asap_fname()
[706]181
[226]182 if fname is None or not os.path.exists(fname):
183 message = 'could not find rc file; returning defaults'
184 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
185 #print message
186 return ret
[706]187
[226]188 cnt = 0
189 for line in file(fname):
190 cnt +=1
191 line = line.strip()
192 if not len(line): continue
193 if line.startswith('#'): continue
194 tup = line.split(':',1)
195 if len(tup) !=2:
196 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
197 continue
[706]198
[226]199 key, val = tup
200 key = key.strip()
201 if not defaultParams.has_key(key):
202 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
203 continue
[706]204
[226]205 default, converter = defaultParams[key]
206
207 ind = val.find('#')
208 if ind>=0: val = val[:ind] # ignore trailing comments
209 val = val.strip()
210 try: cval = converter(val) # try to convert to proper type or raise
[1080]211 except ValueError, msg:
[226]212 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
213 continue
214 else:
215 # Alles Klar, update dict
216 defaultParams[key][0] = cval
217
218 # strip the conveter funcs and return
219 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
[466]220 print ('loaded rc file %s'%fname)
[226]221
222 return ret
223
224
225# this is the instance used by the asap classes
[706]226rcParams = rc_params()
[226]227
228rcParamsDefault = dict(rcParams.items()) # a copy
229
230def rc(group, **kwargs):
231 """
232 Set the current rc params. Group is the grouping for the rc, eg
[379]233 for scantable.save the group is 'scantable', for plotter.stacking, the
234 group is 'plotter', and so on. kwargs is a list of attribute
[226]235 name/value pairs, eg
236
[379]237 rc('scantable', save='SDFITS')
[226]238
239 sets the current rc params and is equivalent to
[706]240
[379]241 rcParams['scantable.save'] = 'SDFITS'
[226]242
243 Use rcdefaults to restore the default rc params after changes.
244 """
245
[379]246 aliases = {}
[706]247
[226]248 for k,v in kwargs.items():
249 name = aliases.get(k) or k
[1422]250 if len(group):
251 key = '%s.%s' % (group, name)
252 else:
253 key = name
[226]254 if not rcParams.has_key(key):
255 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
[706]256
[226]257 rcParams[key] = v
258
259
260def rcdefaults():
261 """
262 Restore the default rc params - the ones that were created at
263 asap load time
264 """
265 rcParams.update(rcParamsDefault)
266
[1295]267def _n_bools(n, val):
268 return [ val for i in xrange(n) ]
[513]269
270def _is_sequence_or_number(param, ptype=int):
271 if isinstance(param,tuple) or isinstance(param,list):
[928]272 if len(param) == 0: return True # empty list
[513]273 out = True
274 for p in param:
275 out &= isinstance(p,ptype)
276 return out
277 elif isinstance(param, ptype):
278 return True
279 return False
280
[928]281def _to_list(param, ptype=int):
282 if isinstance(param, ptype):
283 if ptype is str: return param.split()
284 else: return [param]
285 if _is_sequence_or_number(param, ptype):
286 return param
287 return None
[715]288
[944]289def unique(x):
[992]290 """
291 Return the unique values in a list
292 Parameters:
293 x: the list to reduce
294 Examples:
295 x = [1,2,3,3,4]
296 print unique(x)
297 [1,2,3,4]
298 """
[944]299 return dict([ (val, 1) for val in x]).keys()
300
[992]301def list_files(path=".",suffix="rpf"):
302 """
303 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
304 Parameters:
305 path: The directory to list (default '.')
306 suffix: The file extension (default rpf)
307 Example:
308 files = list_files("data/","sdfits")
309 print files
310 ['data/2001-09-01_0332_P363.sdfits',
311 'data/2003-04-04_131152_t0002.sdfits',
312 'data/Sgr_86p262_best_SPC.sdfits']
313 """
314 if not os.path.isdir(path):
315 return None
[1295]316 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
[992]317 if not suffix in valid:
318 return None
319 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
320 return filter(lambda x: x.endswith(suffix),files)
321
[715]322# workaround for ipython, which redirects this if banner=0 in ipythonrc
323sys.stdout = sys.__stdout__
324sys.stderr = sys.__stderr__
325
326# Logging
327from asap._asap import Log as _asaplog
328global asaplog
[710]329asaplog=_asaplog()
[715]330if rcParams['verbose']:
331 asaplog.enable()
332else:
333 asaplog.disable()
334
335def print_log():
336 log = asaplog.pop()
337 if len(log) and rcParams['verbose']: print log
338 return
339
[1295]340def mask_and(a, b):
341 assert(len(a)==len(b))
342 return [ a[i] & b[i] for i in xrange(len(a)) ]
[1134]343
[1295]344def mask_or(a, b):
345 assert(len(a)==len(b))
346 return [ a[i] | b[i] for i in xrange(len(a)) ]
347
348def mask_not(a):
349 return [ not i for i in a ]
350
[1117]351from asapfitter import fitter
[895]352from asapreader import reader
[944]353from selector import selector
[710]354
[100]355from asapmath import *
[1080]356from scantable import scantable
[1097]357from asaplinefind import linefinder
[1134]358from linecatalog import linecatalog
[285]359
[928]360if rcParams['useplotter']:
[1295]361 try:
[1422]362 from asapplotter import asapplotter
363 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
364 if gui:
365 import matplotlib
366 matplotlib.use("TkAgg")
[1408]367 import pylab
[1422]368 xyplotter = pylab
[1295]369 plotter = asapplotter(gui)
370 del gui
371 except ImportError:
[1422]372 print "Matplotlib not installed. No plotting available"
[285]373
[574]374__date__ = '$Date: 2008-05-22 06:38:44 +0000 (Thu, 22 May 2008) $'.split()[1]
[1371]375__version__ = 'trunk'
[100]376
[1193]377def is_ipython():
[1259]378 return '__IP' in dir(sys.modules["__main__"])
[1193]379if is_ipython():
[1014]380 def version(): print "ASAP %s(%s)"% (__version__, __date__)
[1422]381
[706]382 def list_scans(t = scantable):
[1295]383 import types
[706]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
[100]389
[715]390 def commands():
391 x = """
[113]392 [The scan container]
393 scantable - a container for integrations/scans
[182]394 (can open asap/rpfits/sdfits and ms files)
[113]395 copy - returns a copy of a scan
396 get_scan - gets a specific scan out of a scantable
[984]397 (by name or number)
[1093]398 drop_scan - drops a specific scan out of a scantable
399 (by number)
[984]400 set_selection - set a new subselection of the data
401 get_selection - get the current selection object
[113]402 summary - print info about the scantable contents
[182]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
[113]407 get_tsys - get the TSys
408 get_time - get the timestamps of the integrations
[1351]409 get_inttime - get the integration time
[733]410 get_sourcename - get the source names of the scans
[794]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
[876]414 get_unit - get the current unit
[513]415 set_unit - set the abcissa unit to be used from this
416 point on
[255]417 get_abcissa - get the abcissa values and name for a given
418 row (time)
[1259]419 get_column_names - get the names of the columns in the scantable
420 for use with selector.set_query
[113]421 set_freqframe - set the frame info for the Spectral Axis
422 (e.g. 'LSRK')
[276]423 set_doppler - set the doppler to be used from this point on
[984]424 set_dirframe - set the frame for the direction on the sky
[240]425 set_instrument - set the instrument name
[1190]426 set_feedtype - set the feed type
[255]427 get_fluxunit - get the brightness flux unit
[240]428 set_fluxunit - set the brightness flux unit
[188]429 create_mask - return an mask in the current unit
430 for the given region. The specified regions
431 are NOT masked
[255]432 get_restfreqs - get the current list of rest frequencies
433 set_restfreqs - set a list of rest frequencies
[1422]434 shift_refpix - shift the reference pixel of the IFs
[1012]435 flag - flag selected channels in the data
[1192]436 lag_flag - flag specified frequency in the data
[1151]437 save - save the scantable to disk as either 'ASAP',
438 'SDFITS' or 'ASCII'
[486]439 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
[733]440 nscan - the number of scans in the scantable
[1422]441 nrow - the number of spectra in the scantable
[486]442 history - print the history of the scantable
[530]443 get_fit - get a fit which has been stored witnh the data
[706]444 average_time - return the (weighted) time average of a scan
[513]445 or a list of scans
446 average_pol - average the polarisations together.
[1144]447 average_beam - average the beams together.
[992]448 convert_pol - convert to a different polarisation type
[690]449 auto_quotient - return the on/off quotient with
[1069]450 automatic detection of the on/off scans (closest
451 in time off is selected)
[1144]452 mx_quotient - Form a quotient using MX data (off beams)
[1014]453 scale, *, / - return a scan scaled by a given factor
454 add, +, - - return a scan with given value added
[513]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
[706]459 auto_poly_baseline - automatically fit a polynomial baseline
[780]460 recalc_azel - recalculate azimuth and elevation based on
461 the pointing
[513]462 gain_el - apply gain-elevation correction
463 opacity - apply opacity correction
464 convert_flux - convert to and from Jy and Kelvin brightness
[255]465 units
[513]466 freq_align - align spectra in frequency frame
[1014]467 invert_phase - Invert the phase of the cross-correlation
[1351]468 swap_linears - Swap XX and YY (or RR LL)
[513]469 rotate_xyphase - rotate XY phase of cross correlation
470 rotate_linpolphase - rotate the phase of the complex
471 polarization O=Q+iU correlation
[733]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
[1014]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
[1259]487 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
[1351]488 ( also get_ functions for all these )
[1014]489 reset - unset all selections
[1351]490 + - merge two selections
[733]491
[513]492 [Math] Mainly functions which operate on more than one scantable
[100]493
[706]494 average_time - return the (weighted) time average
[513]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'
[1069]499 quotient - build quotient of the given on and off scans
[1351]500 (matched pairs and 1 off - n on are valid)
[1117]501 merge - merge a list of scantables
[1069]502
[1151]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
[513]515 [Fitting]
[113]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
[984]522 store_fit - store the fit parameters in the data (scantable)
[113]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
[513]528 set_gauss_parameters - same as above but specialised for individual
529 gaussian components
[113]530 get_parameters - get the fitted parameters
[513]531 plot - plot the resulting fit and/or components and
532 residual
[210]533 [Plotter]
534 asapplotter - a plotter for asap, default plotter is
535 called 'plotter'
[984]536 plot - plot a scantable
[1151]537 plot_lines - plot a linecatalog overlay
[378]538 save - save the plot to a file ('png' ,'ps' or 'eps')
[210]539 set_mode - set the state of the plotter, i.e.
540 what is to be plotted 'colour stacked'
541 and what 'panelled'
[984]542 set_selection - only plot a selected part of the data
[733]543 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
[255]544 set_legend - specify user labels for the legend indeces
545 set_title - specify user labels for the panel indeces
[733]546 set_abcissa - specify a user label for the abcissa
[255]547 set_ordinate - specify a user label for the ordinate
[378]548 set_layout - specify the multi-panel layout (rows,cols)
[733]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
[1151]552 set_font - set general font properties, e.g. 'family'
[1054]553 set_histogram - plot in historam style
[733]554 set_mask - set a plotting mask for a specific polarization
[1171]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
[1175]561
562 xyplotter - matplotlib/pylab plotting functions
563
[182]564 [Reading files]
565 reader - access rpfits/sdfits files
[984]566 open - attach reader to a file
567 close - detach reader from file
[182]568 read - read in integrations
569 summary - list info about all integrations
570
[113]571 [General]
572 commands - this command
573 print - print details about a variable
574 list_scans - list all scantables created bt the user
[992]575 list_files - list all files readable by asap (default rpf)
[113]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')
[255]581 list_rcparameters - print out a list of possible values to be
[274]582 put into $HOME/.asaprc
[1171]583 rc - set rc parameters from within asap
[466]584 mask_and,mask_or,
585 mask_not - boolean operations on masks created with
586 scantable.create_mask
[706]587
[210]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
[706]593 using help
[210]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
[715]599 """
[1151]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
[715]608 return
[113]609
[706]610def welcome():
611 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
[100]612
[1035]613Please report any bugs via:
[1378]614http://svn.atnf.csiro.au/trac/asap/simpleticket
[100]615
[378]616[IMPORTANT: ASAP is 0-based]
[706]617Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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