source: trunk/python/__init__.py@ 1096

Last change on this file since 1096 was 1093, checked in by mar637, 19 years ago

removed FITS output, added drop_scan function

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File size: 19.7 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]
20os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
21userdir = os.environ["HOME"]+"/.asap"
22if not os.path.exists(userdir):
23 print 'First time ASAP use. Setting up ~/.asap'
24 os.mkdir(userdir)
25 shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
26 f = file(userdir+"/asapuserfuncs.py", "w")
27 f.close()
28 f = file(userdir+"/ipythonrc", "w")
29 f.close()
30del asapdata, userdir, shutil, platform
31
[513]32def _validate_bool(b):
[226]33 'Convert b to a boolean or raise'
34 bl = b.lower()
35 if bl in ('f', 'no', 'false', '0', 0): return False
36 elif bl in ('t', 'yes', 'true', '1', 1): return True
37 else:
38 raise ValueError('Could not convert "%s" to boolean' % b)
39
[513]40def _validate_int(s):
[226]41 'convert s to int or raise'
42 try: return int(s)
43 except ValueError:
44 raise ValueError('Could not convert "%s" to int' % s)
45
[513]46def _asap_fname():
[226]47 """
48 Return the path to the rc file
49
50 Search order:
51
52 * current working dir
53 * environ var ASAPRC
[274]54 * HOME/.asaprc
[706]55
[226]56 """
57
58 fname = os.path.join( os.getcwd(), '.asaprc')
59 if os.path.exists(fname): return fname
60
61 if os.environ.has_key('ASAPRC'):
62 path = os.environ['ASAPRC']
63 if os.path.exists(path):
64 fname = os.path.join(path, '.asaprc')
65 if os.path.exists(fname):
66 return fname
67
68 if os.environ.has_key('HOME'):
69 home = os.environ['HOME']
70 fname = os.path.join(home, '.asaprc')
71 if os.path.exists(fname):
72 return fname
73 return None
74
[706]75
[226]76defaultParams = {
77 # general
[513]78 'verbose' : [True, _validate_bool],
79 'useplotter' : [True, _validate_bool],
[542]80 'insitu' : [True, _validate_bool],
[706]81
[226]82 # plotting
[706]83 'plotter.gui' : [True, _validate_bool],
[226]84 'plotter.stacking' : ['p', str],
85 'plotter.panelling' : ['s', str],
[700]86 'plotter.colours' : ['', str],
87 'plotter.linestyles' : ['', str],
[710]88 'plotter.decimate' : [False, _validate_bool],
89 'plotter.ganged' : [True, _validate_bool],
[1022]90 'plotter.histogram' : [False, _validate_bool],
[710]91
[226]92 # scantable
93 'scantable.save' : ['ASAP', str],
[513]94 'scantable.autoaverage' : [True, _validate_bool],
[226]95 'scantable.freqframe' : ['LSRK', str], #default frequency frame
[1076]96 'scantable.verbosesummary' : [False, _validate_bool],
97 'scantable.storage' : ['memory', str]
[226]98 # fitter
99 }
100
[255]101def list_rcparameters():
[706]102
[255]103 print """
[737]104# general
105# print verbose output
106verbose : True
[255]107
[737]108# preload a default plotter
109useplotter : True
[255]110
[737]111# apply operations on the input scantable or return new one
112insitu : True
[706]113
[737]114# plotting
[710]115
[737]116# do we want a GUI or plot to a file
117plotter.gui : True
[710]118
[737]119# default mode for colour stacking
120plotter.stacking : Pol
[255]121
[737]122# default mode for panelling
123plotter.panelling : scan
[255]124
[737]125# push panels together, to share axislabels
126plotter.ganged : True
[710]127
[737]128# decimate the number of points plotted bya afactor of
129# nchan/1024
130plotter.decimate : False
[733]131
[737]132# default colours/linestyles
133plotter.colours :
134plotter.linestyles :
[700]135
[1022]136# enable/disable histogram plotting
137plotter.histogram : False
138
[737]139# scantable
[1076]140
141# default storage of scantable (memory/disk)
142scantable.storage : memory
[737]143# default ouput format when saving
144scantable.save : ASAP
145# auto averaging on read
146scantable.autoaverage : True
[255]147
[737]148# default frequency frame to set when function
149# scantable.set_freqfrmae is called
150scantable.freqframe : LSRK
[255]151
[737]152# Control the level of information printed by summary
153scantable.verbosesummary : False
[706]154
[737]155# Fitter
156"""
[706]157
[226]158def rc_params():
159 'Return the default params updated from the values in the rc file'
[706]160
[513]161 fname = _asap_fname()
[706]162
[226]163 if fname is None or not os.path.exists(fname):
164 message = 'could not find rc file; returning defaults'
165 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
166 #print message
167 return ret
[706]168
[226]169 cnt = 0
170 for line in file(fname):
171 cnt +=1
172 line = line.strip()
173 if not len(line): continue
174 if line.startswith('#'): continue
175 tup = line.split(':',1)
176 if len(tup) !=2:
177 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
178 continue
[706]179
[226]180 key, val = tup
181 key = key.strip()
182 if not defaultParams.has_key(key):
183 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
184 continue
[706]185
[226]186 default, converter = defaultParams[key]
187
188 ind = val.find('#')
189 if ind>=0: val = val[:ind] # ignore trailing comments
190 val = val.strip()
191 try: cval = converter(val) # try to convert to proper type or raise
[1080]192 except ValueError, msg:
[226]193 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
194 continue
195 else:
196 # Alles Klar, update dict
197 defaultParams[key][0] = cval
198
199 # strip the conveter funcs and return
200 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
[466]201 print ('loaded rc file %s'%fname)
[226]202
203 return ret
204
205
206# this is the instance used by the asap classes
[706]207rcParams = rc_params()
[226]208
209rcParamsDefault = dict(rcParams.items()) # a copy
210
211def rc(group, **kwargs):
212 """
213 Set the current rc params. Group is the grouping for the rc, eg
[379]214 for scantable.save the group is 'scantable', for plotter.stacking, the
215 group is 'plotter', and so on. kwargs is a list of attribute
[226]216 name/value pairs, eg
217
[379]218 rc('scantable', save='SDFITS')
[226]219
220 sets the current rc params and is equivalent to
[706]221
[379]222 rcParams['scantable.save'] = 'SDFITS'
[226]223
224 Use rcdefaults to restore the default rc params after changes.
225 """
226
[379]227 aliases = {}
[706]228
[226]229 for k,v in kwargs.items():
230 name = aliases.get(k) or k
231 key = '%s.%s' % (group, name)
232 if not rcParams.has_key(key):
233 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
[706]234
[226]235 rcParams[key] = v
236
237
238def rcdefaults():
239 """
240 Restore the default rc params - the ones that were created at
241 asap load time
242 """
243 rcParams.update(rcParamsDefault)
244
[513]245
246def _is_sequence_or_number(param, ptype=int):
247 if isinstance(param,tuple) or isinstance(param,list):
[928]248 if len(param) == 0: return True # empty list
[513]249 out = True
250 for p in param:
251 out &= isinstance(p,ptype)
252 return out
253 elif isinstance(param, ptype):
254 return True
255 return False
256
[928]257def _to_list(param, ptype=int):
258 if isinstance(param, ptype):
259 if ptype is str: return param.split()
260 else: return [param]
261 if _is_sequence_or_number(param, ptype):
262 return param
263 return None
[715]264
[944]265def unique(x):
[992]266 """
267 Return the unique values in a list
268 Parameters:
269 x: the list to reduce
270 Examples:
271 x = [1,2,3,3,4]
272 print unique(x)
273 [1,2,3,4]
274 """
[944]275 return dict([ (val, 1) for val in x]).keys()
276
[992]277def list_files(path=".",suffix="rpf"):
278 """
279 Return a list files readable by asap, such as rpf, sdfits, mbf, asap
280 Parameters:
281 path: The directory to list (default '.')
282 suffix: The file extension (default rpf)
283 Example:
284 files = list_files("data/","sdfits")
285 print files
286 ['data/2001-09-01_0332_P363.sdfits',
287 'data/2003-04-04_131152_t0002.sdfits',
288 'data/Sgr_86p262_best_SPC.sdfits']
289 """
290 import os
291 if not os.path.isdir(path):
292 return None
293 valid = "rpf sdf sdfits mbf asap".split()
294 if not suffix in valid:
295 return None
296 files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
297 return filter(lambda x: x.endswith(suffix),files)
298
[715]299# workaround for ipython, which redirects this if banner=0 in ipythonrc
300sys.stdout = sys.__stdout__
301sys.stderr = sys.__stderr__
302
303# Logging
304from asap._asap import Log as _asaplog
305global asaplog
[710]306asaplog=_asaplog()
[715]307if rcParams['verbose']:
308 asaplog.enable()
309else:
310 asaplog.disable()
311
312def print_log():
313 log = asaplog.pop()
314 if len(log) and rcParams['verbose']: print log
315 return
316
[113]317from asapfitter import *
[895]318from asapreader import reader
[944]319from selector import selector
[710]320
[100]321from asapmath import *
[1080]322from scantable import scantable
[880]323from asaplinefind import *
[876]324#from asapfit import *
[285]325
[466]326from numarray import logical_and as mask_and
327from numarray import logical_or as mask_or
328from numarray import logical_not as mask_not
329
[928]330if rcParams['useplotter']:
331 from asapplotter import *
332 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
333 plotter = asapplotter(gui)
334 del gui
[285]335
[1069]336
[574]337__date__ = '$Date: 2006-07-28 05:12:20 +0000 (Fri, 28 Jul 2006) $'.split()[1]
[1069]338__version__ = '2.1a'
[100]339
[706]340if rcParams['verbose']:
[1014]341 def version(): print "ASAP %s(%s)"% (__version__, __date__)
[706]342 def list_scans(t = scantable):
343 import sys, types
344 globs = sys.modules['__main__'].__dict__.iteritems()
345 print "The user created scantables are:"
346 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
347 print filter(lambda x: not x.startswith('_'), sts)
348 return
[100]349
[715]350 def commands():
351 x = """
[113]352 [The scan container]
353 scantable - a container for integrations/scans
[182]354 (can open asap/rpfits/sdfits and ms files)
[113]355 copy - returns a copy of a scan
356 get_scan - gets a specific scan out of a scantable
[984]357 (by name or number)
[1093]358 drop_scan - drops a specific scan out of a scantable
359 (by number)
[984]360 set_selection - set a new subselection of the data
361 get_selection - get the current selection object
[113]362 summary - print info about the scantable contents
[182]363 stats - get specified statistic of the spectra in
364 the scantable
365 stddev - get the standard deviation of the spectra
366 in the scantable
[113]367 get_tsys - get the TSys
368 get_time - get the timestamps of the integrations
[733]369 get_sourcename - get the source names of the scans
[794]370 get_azimuth - get the azimuth of the scans
371 get_elevation - get the elevation of the scans
372 get_parangle - get the parallactic angle of the scans
[876]373 get_unit - get the current unit
[513]374 set_unit - set the abcissa unit to be used from this
375 point on
[255]376 get_abcissa - get the abcissa values and name for a given
377 row (time)
[113]378 set_freqframe - set the frame info for the Spectral Axis
379 (e.g. 'LSRK')
[276]380 set_doppler - set the doppler to be used from this point on
[984]381 set_dirframe - set the frame for the direction on the sky
[240]382 set_instrument - set the instrument name
[255]383 get_fluxunit - get the brightness flux unit
[240]384 set_fluxunit - set the brightness flux unit
[188]385 create_mask - return an mask in the current unit
386 for the given region. The specified regions
387 are NOT masked
[255]388 get_restfreqs - get the current list of rest frequencies
389 set_restfreqs - set a list of rest frequencies
[1012]390 flag - flag selected channels in the data
[116]391 save - save the scantable to disk as either 'ASAP'
392 or 'SDFITS'
[486]393 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
[733]394 nscan - the number of scans in the scantable
[984]395 nrow - te number of spectra in the scantable
[486]396 history - print the history of the scantable
[530]397 get_fit - get a fit which has been stored witnh the data
[706]398 average_time - return the (weighted) time average of a scan
[513]399 or a list of scans
[1069]400 average_channel - return the (median) average of a scantable
[513]401 average_pol - average the polarisations together.
[113]402 The dimension won't be reduced and
403 all polarisations will contain the
404 averaged spectrum.
[992]405 convert_pol - convert to a different polarisation type
[690]406 auto_quotient - return the on/off quotient with
[1069]407 automatic detection of the on/off scans (closest
408 in time off is selected)
[1014]409 scale, *, / - return a scan scaled by a given factor
410 add, +, - - return a scan with given value added
[513]411 bin - return a scan with binned channels
412 resample - return a scan with resampled channels
413 smooth - return the spectrally smoothed scan
414 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
[706]415 auto_poly_baseline - automatically fit a polynomial baseline
[780]416 recalc_azel - recalculate azimuth and elevation based on
417 the pointing
[513]418 gain_el - apply gain-elevation correction
419 opacity - apply opacity correction
420 convert_flux - convert to and from Jy and Kelvin brightness
[255]421 units
[513]422 freq_align - align spectra in frequency frame
[1014]423 invert_phase - Invert the phase of the cross-correlation
424 swap_linears - Swap XX and YY
[513]425 rotate_xyphase - rotate XY phase of cross correlation
426 rotate_linpolphase - rotate the phase of the complex
427 polarization O=Q+iU correlation
[733]428 freq_switch - perform frequency switching on the data
429 stats - Determine the specified statistic, e.g. 'min'
430 'max', 'rms' etc.
431 stddev - Determine the standard deviation of the current
432 beam/if/pol
[1014]433 [Selection]
434 selector - a selection object to set a subset of a scantable
435 set_scans - set (a list of) scans by index
436 set_cycles - set (a list of) cycles by index
437 set_beams - set (a list of) beamss by index
438 set_ifs - set (a list of) ifs by index
439 set_polarisations - set (a list of) polarisations by name
440 or by index
441 set_names - set a selection by name (wildcards allowed)
442 set_tsys - set a selection by tsys thresholds
443 reset - unset all selections
444 + - merge to selections
[733]445
[513]446 [Math] Mainly functions which operate on more than one scantable
[100]447
[706]448 average_time - return the (weighted) time average
[513]449 of a list of scans
450 quotient - return the on/off quotient
451 simple_math - simple mathematical operations on two scantables,
452 'add', 'sub', 'mul', 'div'
[1069]453 quotient - build quotient of the given on and off scans
454 (matched pairs and 1 off/n on are valid)
455
[513]456 [Fitting]
[113]457 fitter
458 auto_fit - return a scan where the function is
459 applied to all Beams/IFs/Pols.
460 commit - return a new scan where the fits have been
461 commited.
462 fit - execute the actual fitting process
[984]463 store_fit - store the fit parameters in the data (scantable)
[113]464 get_chi2 - get the Chi^2
465 set_scan - set the scantable to be fit
466 set_function - set the fitting function
467 set_parameters - set the parameters for the function(s), and
468 set if they should be held fixed during fitting
[513]469 set_gauss_parameters - same as above but specialised for individual
470 gaussian components
[113]471 get_parameters - get the fitted parameters
[513]472 plot - plot the resulting fit and/or components and
473 residual
[210]474 [Plotter]
475 asapplotter - a plotter for asap, default plotter is
476 called 'plotter'
[984]477 plot - plot a scantable
[378]478 save - save the plot to a file ('png' ,'ps' or 'eps')
[210]479 set_mode - set the state of the plotter, i.e.
480 what is to be plotted 'colour stacked'
481 and what 'panelled'
[984]482 set_selection - only plot a selected part of the data
[733]483 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
[255]484 set_legend - specify user labels for the legend indeces
485 set_title - specify user labels for the panel indeces
[733]486 set_abcissa - specify a user label for the abcissa
[255]487 set_ordinate - specify a user label for the ordinate
[378]488 set_layout - specify the multi-panel layout (rows,cols)
[733]489 set_colors - specify a set of colours to use
490 set_linestyles - specify a set of linestyles to use if only
491 using one color
[1054]492 set_histogram - plot in historam style
[733]493 set_mask - set a plotting mask for a specific polarization
[706]494
[182]495 [Reading files]
496 reader - access rpfits/sdfits files
[984]497 open - attach reader to a file
498 close - detach reader from file
[182]499 read - read in integrations
500 summary - list info about all integrations
501
[113]502 [General]
503 commands - this command
504 print - print details about a variable
505 list_scans - list all scantables created bt the user
[992]506 list_files - list all files readable by asap (default rpf)
[113]507 del - delete the given variable from memory
508 range - create a list of values, e.g.
509 range(3) = [0,1,2], range(2,5) = [2,3,4]
510 help - print help for one of the listed functions
511 execfile - execute an asap script, e.g. execfile('myscript')
[255]512 list_rcparameters - print out a list of possible values to be
[274]513 put into $HOME/.asaprc
[466]514 mask_and,mask_or,
515 mask_not - boolean operations on masks created with
516 scantable.create_mask
[706]517
[210]518 Note:
519 How to use this with help:
520 # function 'summary'
521 [xxx] is just a category
522 Every 'sub-level' in this list should be replaces by a '.' Period when
[706]523 using help
[210]524 Example:
525 ASAP> help scantable # to get info on ths scantable
526 ASAP> help scantable.summary # to get help on the scantable's
527 ASAP> help average_time
528
[715]529 """
530 print x
531 return
[113]532
[706]533def welcome():
534 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
[100]535
[1035]536Please report any bugs via:
537http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
[100]538
[378]539[IMPORTANT: ASAP is 0-based]
[706]540Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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