source: trunk/python/__init__.py@ 1505

Last change on this file since 1505 was 1504, checked in by Malte Marquarding, 16 years ago

Fix for ticket #151: added facilities to help with on/off scan identification/setting

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File size: 23.6 KB
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[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")
[1434]34 shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
35 userdir+"/ipy_user_conf.py")
[1080]36 f = file(userdir+"/asapuserfuncs.py", "w")
37 f.close()
38 f = file(userdir+"/ipythonrc", "w")
39 f.close()
[1472]40else:
41 # upgrade to support later ipython versions
42 if not os.path.exists(userdir+"/ipy_user_conf.py"):
43 shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
44 userdir+"/ipy_user_conf.py")
45
[1171]46# remove from namespace
[1080]47del asapdata, userdir, shutil, platform
48
[513]49def _validate_bool(b):
[226]50 'Convert b to a boolean or raise'
51 bl = b.lower()
52 if bl in ('f', 'no', 'false', '0', 0): return False
53 elif bl in ('t', 'yes', 'true', '1', 1): return True
54 else:
55 raise ValueError('Could not convert "%s" to boolean' % b)
56
[513]57def _validate_int(s):
[226]58 'convert s to int or raise'
59 try: return int(s)
60 except ValueError:
61 raise ValueError('Could not convert "%s" to int' % s)
62
[513]63def _asap_fname():
[226]64 """
65 Return the path to the rc file
66
67 Search order:
68
69 * current working dir
70 * environ var ASAPRC
[274]71 * HOME/.asaprc
[706]72
[226]73 """
74
75 fname = os.path.join( os.getcwd(), '.asaprc')
76 if os.path.exists(fname): return fname
77
78 if os.environ.has_key('ASAPRC'):
79 path = os.environ['ASAPRC']
80 if os.path.exists(path):
81 fname = os.path.join(path, '.asaprc')
82 if os.path.exists(fname):
83 return fname
84
85 if os.environ.has_key('HOME'):
86 home = os.environ['HOME']
87 fname = os.path.join(home, '.asaprc')
88 if os.path.exists(fname):
89 return fname
90 return None
91
[706]92
[226]93defaultParams = {
94 # general
[513]95 'verbose' : [True, _validate_bool],
96 'useplotter' : [True, _validate_bool],
[542]97 'insitu' : [True, _validate_bool],
[706]98
[226]99 # plotting
[706]100 'plotter.gui' : [True, _validate_bool],
[226]101 'plotter.stacking' : ['p', str],
102 'plotter.panelling' : ['s', str],
[700]103 'plotter.colours' : ['', str],
104 'plotter.linestyles' : ['', str],
[710]105 'plotter.decimate' : [False, _validate_bool],
106 'plotter.ganged' : [True, _validate_bool],
[1022]107 'plotter.histogram' : [False, _validate_bool],
[1097]108 'plotter.papertype' : ['A4', str],
[710]109
[226]110 # scantable
111 'scantable.save' : ['ASAP', str],
[513]112 'scantable.autoaverage' : [True, _validate_bool],
[226]113 'scantable.freqframe' : ['LSRK', str], #default frequency frame
[1076]114 'scantable.verbosesummary' : [False, _validate_bool],
[1422]115 'scantable.storage' : ['memory', str],
[1504]116 'scantable.history' : [True, _validate_bool],
117 'scantable.reference' : ['.*(e|w|_R)$', str]
[226]118 # fitter
119 }
120
[255]121def list_rcparameters():
[706]122
[255]123 print """
[737]124# general
125# print verbose output
126verbose : True
[255]127
[737]128# preload a default plotter
129useplotter : True
[255]130
[737]131# apply operations on the input scantable or return new one
132insitu : True
[706]133
[737]134# plotting
[710]135
[737]136# do we want a GUI or plot to a file
137plotter.gui : True
[710]138
[737]139# default mode for colour stacking
140plotter.stacking : Pol
[255]141
[737]142# default mode for panelling
143plotter.panelling : scan
[255]144
[737]145# push panels together, to share axislabels
146plotter.ganged : True
[710]147
[737]148# decimate the number of points plotted bya afactor of
149# nchan/1024
150plotter.decimate : False
[733]151
[737]152# default colours/linestyles
153plotter.colours :
154plotter.linestyles :
[700]155
[1022]156# enable/disable histogram plotting
157plotter.histogram : False
158
[1097]159# ps paper type
160plotter.papertype : A4
161
[737]162# scantable
[1076]163
[1259]164# default storage of scantable ('memory'/'disk')
[1076]165scantable.storage : memory
[1422]166
167# write history of each call to scantable
168scantable.history : True
169
[737]170# default ouput format when saving
171scantable.save : ASAP
[1422]172
[737]173# auto averaging on read
174scantable.autoaverage : True
[255]175
[737]176# default frequency frame to set when function
[1097]177# scantable.set_freqframe is called
[737]178scantable.freqframe : LSRK
[255]179
[737]180# Control the level of information printed by summary
181scantable.verbosesummary : False
[706]182
[1504]183# Control the identification of reference (off) scans
184# This is has to be a regular expression
185scantable.reference : .*(e|w|_R)$
[737]186# Fitter
187"""
[706]188
[226]189def rc_params():
190 'Return the default params updated from the values in the rc file'
[706]191
[513]192 fname = _asap_fname()
[706]193
[226]194 if fname is None or not os.path.exists(fname):
195 message = 'could not find rc file; returning defaults'
196 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
197 #print message
198 return ret
[706]199
[226]200 cnt = 0
201 for line in file(fname):
202 cnt +=1
203 line = line.strip()
204 if not len(line): continue
205 if line.startswith('#'): continue
206 tup = line.split(':',1)
207 if len(tup) !=2:
208 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
209 continue
[706]210
[226]211 key, val = tup
212 key = key.strip()
213 if not defaultParams.has_key(key):
214 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
215 continue
[706]216
[226]217 default, converter = defaultParams[key]
218
219 ind = val.find('#')
220 if ind>=0: val = val[:ind] # ignore trailing comments
221 val = val.strip()
222 try: cval = converter(val) # try to convert to proper type or raise
[1080]223 except ValueError, msg:
[226]224 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
225 continue
226 else:
227 # Alles Klar, update dict
228 defaultParams[key][0] = cval
229
230 # strip the conveter funcs and return
231 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
[466]232 print ('loaded rc file %s'%fname)
[226]233
234 return ret
235
236
237# this is the instance used by the asap classes
[706]238rcParams = rc_params()
[226]239
240rcParamsDefault = dict(rcParams.items()) # a copy
241
242def rc(group, **kwargs):
243 """
244 Set the current rc params. Group is the grouping for the rc, eg
[379]245 for scantable.save the group is 'scantable', for plotter.stacking, the
246 group is 'plotter', and so on. kwargs is a list of attribute
[226]247 name/value pairs, eg
248
[379]249 rc('scantable', save='SDFITS')
[226]250
251 sets the current rc params and is equivalent to
[706]252
[379]253 rcParams['scantable.save'] = 'SDFITS'
[226]254
255 Use rcdefaults to restore the default rc params after changes.
256 """
257
[379]258 aliases = {}
[706]259
[226]260 for k,v in kwargs.items():
261 name = aliases.get(k) or k
[1422]262 if len(group):
263 key = '%s.%s' % (group, name)
264 else:
265 key = name
[226]266 if not rcParams.has_key(key):
267 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
[706]268
[226]269 rcParams[key] = v
270
271
272def rcdefaults():
273 """
274 Restore the default rc params - the ones that were created at
275 asap load time
276 """
277 rcParams.update(rcParamsDefault)
278
[1295]279def _n_bools(n, val):
280 return [ val for i in xrange(n) ]
[513]281
282def _is_sequence_or_number(param, ptype=int):
283 if isinstance(param,tuple) or isinstance(param,list):
[928]284 if len(param) == 0: return True # empty list
[513]285 out = True
286 for p in param:
287 out &= isinstance(p,ptype)
288 return out
289 elif isinstance(param, ptype):
290 return True
291 return False
292
[928]293def _to_list(param, ptype=int):
294 if isinstance(param, ptype):
295 if ptype is str: return param.split()
296 else: return [param]
297 if _is_sequence_or_number(param, ptype):
298 return param
299 return None
[715]300
[944]301def unique(x):
[992]302 """
303 Return the unique values in a list
304 Parameters:
305 x: the list to reduce
306 Examples:
307 x = [1,2,3,3,4]
308 print unique(x)
309 [1,2,3,4]
310 """
[944]311 return dict([ (val, 1) for val in x]).keys()
312
[992]313def list_files(path=".",suffix="rpf"):
314 """
315 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
316 Parameters:
317 path: The directory to list (default '.')
318 suffix: The file extension (default rpf)
319 Example:
320 files = list_files("data/","sdfits")
321 print files
322 ['data/2001-09-01_0332_P363.sdfits',
323 'data/2003-04-04_131152_t0002.sdfits',
324 'data/Sgr_86p262_best_SPC.sdfits']
325 """
326 if not os.path.isdir(path):
327 return None
[1295]328 valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
[992]329 if not suffix in valid:
330 return None
331 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
332 return filter(lambda x: x.endswith(suffix),files)
333
[715]334# workaround for ipython, which redirects this if banner=0 in ipythonrc
335sys.stdout = sys.__stdout__
336sys.stderr = sys.__stderr__
337
338# Logging
339from asap._asap import Log as _asaplog
340global asaplog
[710]341asaplog=_asaplog()
[715]342if rcParams['verbose']:
343 asaplog.enable()
344else:
345 asaplog.disable()
346
347def print_log():
348 log = asaplog.pop()
349 if len(log) and rcParams['verbose']: print log
350 return
351
[1295]352def mask_and(a, b):
353 assert(len(a)==len(b))
354 return [ a[i] & b[i] for i in xrange(len(a)) ]
[1134]355
[1295]356def mask_or(a, b):
357 assert(len(a)==len(b))
358 return [ a[i] | b[i] for i in xrange(len(a)) ]
359
360def mask_not(a):
361 return [ not i for i in a ]
362
[1117]363from asapfitter import fitter
[895]364from asapreader import reader
[944]365from selector import selector
[710]366
[100]367from asapmath import *
[1080]368from scantable import scantable
[1097]369from asaplinefind import linefinder
[1134]370from linecatalog import linecatalog
[285]371
[928]372if rcParams['useplotter']:
[1295]373 try:
[1423]374 from asapplotter import asapplotter
375 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
376 if gui:
[1422]377 import matplotlib
378 matplotlib.use("TkAgg")
[1423]379 import pylab
[1422]380 xyplotter = pylab
[1423]381 plotter = asapplotter(gui)
382 del gui
[1295]383 except ImportError:
[1423]384 print "Matplotlib not installed. No plotting available"
[285]385
[574]386__date__ = '$Date: 2009-02-13 00:27:42 +0000 (Fri, 13 Feb 2009) $'.split()[1]
[1371]387__version__ = 'trunk'
[100]388
[1193]389def is_ipython():
[1259]390 return '__IP' in dir(sys.modules["__main__"])
[1193]391if is_ipython():
[1014]392 def version(): print "ASAP %s(%s)"% (__version__, __date__)
[1422]393
[706]394 def list_scans(t = scantable):
[1295]395 import types
[706]396 globs = sys.modules['__main__'].__dict__.iteritems()
397 print "The user created scantables are:"
398 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
399 print filter(lambda x: not x.startswith('_'), sts)
400 return
[100]401
[715]402 def commands():
403 x = """
[113]404 [The scan container]
405 scantable - a container for integrations/scans
[182]406 (can open asap/rpfits/sdfits and ms files)
[113]407 copy - returns a copy of a scan
408 get_scan - gets a specific scan out of a scantable
[984]409 (by name or number)
[1093]410 drop_scan - drops a specific scan out of a scantable
411 (by number)
[984]412 set_selection - set a new subselection of the data
413 get_selection - get the current selection object
[113]414 summary - print info about the scantable contents
[182]415 stats - get specified statistic of the spectra in
416 the scantable
417 stddev - get the standard deviation of the spectra
418 in the scantable
[113]419 get_tsys - get the TSys
420 get_time - get the timestamps of the integrations
[1351]421 get_inttime - get the integration time
[733]422 get_sourcename - get the source names of the scans
[794]423 get_azimuth - get the azimuth of the scans
424 get_elevation - get the elevation of the scans
425 get_parangle - get the parallactic angle of the scans
[876]426 get_unit - get the current unit
[513]427 set_unit - set the abcissa unit to be used from this
428 point on
[255]429 get_abcissa - get the abcissa values and name for a given
430 row (time)
[1259]431 get_column_names - get the names of the columns in the scantable
432 for use with selector.set_query
[113]433 set_freqframe - set the frame info for the Spectral Axis
434 (e.g. 'LSRK')
[276]435 set_doppler - set the doppler to be used from this point on
[984]436 set_dirframe - set the frame for the direction on the sky
[240]437 set_instrument - set the instrument name
[1190]438 set_feedtype - set the feed type
[255]439 get_fluxunit - get the brightness flux unit
[240]440 set_fluxunit - set the brightness flux unit
[188]441 create_mask - return an mask in the current unit
442 for the given region. The specified regions
443 are NOT masked
[255]444 get_restfreqs - get the current list of rest frequencies
445 set_restfreqs - set a list of rest frequencies
[1471]446 shift_refpix - shift the reference pixel of the IFs
447 set_spectrum - overwrite the spectrum for a given row
448 get_spectrum - retrieve the spectrum for a given
449 get_mask - retrieve the mask for a given
[1012]450 flag - flag selected channels in the data
[1192]451 lag_flag - flag specified frequency in the data
[1151]452 save - save the scantable to disk as either 'ASAP',
453 'SDFITS' or 'ASCII'
[486]454 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
[733]455 nscan - the number of scans in the scantable
[1422]456 nrow - the number of spectra in the scantable
[486]457 history - print the history of the scantable
[530]458 get_fit - get a fit which has been stored witnh the data
[706]459 average_time - return the (weighted) time average of a scan
[513]460 or a list of scans
461 average_pol - average the polarisations together.
[1144]462 average_beam - average the beams together.
[992]463 convert_pol - convert to a different polarisation type
[690]464 auto_quotient - return the on/off quotient with
[1069]465 automatic detection of the on/off scans (closest
466 in time off is selected)
[1144]467 mx_quotient - Form a quotient using MX data (off beams)
[1014]468 scale, *, / - return a scan scaled by a given factor
469 add, +, - - return a scan with given value added
[513]470 bin - return a scan with binned channels
471 resample - return a scan with resampled channels
472 smooth - return the spectrally smoothed scan
473 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
[706]474 auto_poly_baseline - automatically fit a polynomial baseline
[780]475 recalc_azel - recalculate azimuth and elevation based on
476 the pointing
[513]477 gain_el - apply gain-elevation correction
478 opacity - apply opacity correction
479 convert_flux - convert to and from Jy and Kelvin brightness
[255]480 units
[513]481 freq_align - align spectra in frequency frame
[1014]482 invert_phase - Invert the phase of the cross-correlation
[1351]483 swap_linears - Swap XX and YY (or RR LL)
[513]484 rotate_xyphase - rotate XY phase of cross correlation
485 rotate_linpolphase - rotate the phase of the complex
486 polarization O=Q+iU correlation
[733]487 freq_switch - perform frequency switching on the data
488 stats - Determine the specified statistic, e.g. 'min'
489 'max', 'rms' etc.
490 stddev - Determine the standard deviation of the current
491 beam/if/pol
[1014]492 [Selection]
493 selector - a selection object to set a subset of a scantable
494 set_scans - set (a list of) scans by index
495 set_cycles - set (a list of) cycles by index
496 set_beams - set (a list of) beamss by index
497 set_ifs - set (a list of) ifs by index
498 set_polarisations - set (a list of) polarisations by name
499 or by index
500 set_names - set a selection by name (wildcards allowed)
501 set_tsys - set a selection by tsys thresholds
[1259]502 set_query - set a selection by SQL-like query, e.g. BEAMNO==1
[1351]503 ( also get_ functions for all these )
[1014]504 reset - unset all selections
[1351]505 + - merge two selections
[733]506
[513]507 [Math] Mainly functions which operate on more than one scantable
[100]508
[706]509 average_time - return the (weighted) time average
[513]510 of a list of scans
511 quotient - return the on/off quotient
512 simple_math - simple mathematical operations on two scantables,
513 'add', 'sub', 'mul', 'div'
[1069]514 quotient - build quotient of the given on and off scans
[1351]515 (matched pairs and 1 off - n on are valid)
[1117]516 merge - merge a list of scantables
[1069]517
[1151]518 [Line Catalog]
519 linecatalog - a linecatalog wrapper, taking an ASCII or
520 internal format table
521 summary - print a summary of the current selection
522 set_name - select a subset by name pattern, e.g. '*OH*'
523 set_strength_limits - select a subset by line strength limits
524 set_frequency_limits - select a subset by frequency limits
525 reset - unset all selections
526 save - save the current subset to a table (internal
527 format)
528 get_row - get the name and frequency from a specific
529 row in the table
[513]530 [Fitting]
[113]531 fitter
532 auto_fit - return a scan where the function is
533 applied to all Beams/IFs/Pols.
534 commit - return a new scan where the fits have been
535 commited.
536 fit - execute the actual fitting process
[984]537 store_fit - store the fit parameters in the data (scantable)
[113]538 get_chi2 - get the Chi^2
539 set_scan - set the scantable to be fit
540 set_function - set the fitting function
541 set_parameters - set the parameters for the function(s), and
542 set if they should be held fixed during fitting
[513]543 set_gauss_parameters - same as above but specialised for individual
544 gaussian components
[113]545 get_parameters - get the fitted parameters
[513]546 plot - plot the resulting fit and/or components and
547 residual
[210]548 [Plotter]
549 asapplotter - a plotter for asap, default plotter is
550 called 'plotter'
[984]551 plot - plot a scantable
[1151]552 plot_lines - plot a linecatalog overlay
[378]553 save - save the plot to a file ('png' ,'ps' or 'eps')
[210]554 set_mode - set the state of the plotter, i.e.
555 what is to be plotted 'colour stacked'
556 and what 'panelled'
[984]557 set_selection - only plot a selected part of the data
[733]558 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
[255]559 set_legend - specify user labels for the legend indeces
560 set_title - specify user labels for the panel indeces
[733]561 set_abcissa - specify a user label for the abcissa
[255]562 set_ordinate - specify a user label for the ordinate
[378]563 set_layout - specify the multi-panel layout (rows,cols)
[733]564 set_colors - specify a set of colours to use
565 set_linestyles - specify a set of linestyles to use if only
566 using one color
[1151]567 set_font - set general font properties, e.g. 'family'
[1054]568 set_histogram - plot in historam style
[733]569 set_mask - set a plotting mask for a specific polarization
[1171]570 text - draw text annotations either in data or relative
571 coordinates
572 arrow - draw arrow annotations either in data or relative
573 coordinates
574 axhline,axvline - draw horizontal/vertical lines
575 axhspan,axvspan - draw horizontal/vertical regions
[1175]576
577 xyplotter - matplotlib/pylab plotting functions
578
[182]579 [Reading files]
580 reader - access rpfits/sdfits files
[984]581 open - attach reader to a file
582 close - detach reader from file
[182]583 read - read in integrations
584 summary - list info about all integrations
585
[113]586 [General]
587 commands - this command
588 print - print details about a variable
589 list_scans - list all scantables created bt the user
[992]590 list_files - list all files readable by asap (default rpf)
[113]591 del - delete the given variable from memory
592 range - create a list of values, e.g.
593 range(3) = [0,1,2], range(2,5) = [2,3,4]
594 help - print help for one of the listed functions
595 execfile - execute an asap script, e.g. execfile('myscript')
[255]596 list_rcparameters - print out a list of possible values to be
[274]597 put into $HOME/.asaprc
[1171]598 rc - set rc parameters from within asap
[466]599 mask_and,mask_or,
600 mask_not - boolean operations on masks created with
601 scantable.create_mask
[706]602
[210]603 Note:
604 How to use this with help:
605 # function 'summary'
606 [xxx] is just a category
607 Every 'sub-level' in this list should be replaces by a '.' Period when
[706]608 using help
[210]609 Example:
610 ASAP> help scantable # to get info on ths scantable
611 ASAP> help scantable.summary # to get help on the scantable's
612 ASAP> help average_time
613
[715]614 """
[1151]615 if rcParams['verbose']:
616 try:
617 from IPython.genutils import page as pager
618 except ImportError:
619 from pydoc import pager
620 pager(x)
621 else:
622 print x
[715]623 return
[113]624
[706]625def welcome():
626 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
[100]627
[1035]628Please report any bugs via:
[1378]629http://svn.atnf.csiro.au/trac/asap/simpleticket
[100]630
[378]631[IMPORTANT: ASAP is 0-based]
[706]632Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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