source: trunk/python/__init__.py@ 969

Last change on this file since 969 was 944, checked in by mar637, 19 years ago

added unique; added selector

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File size: 16.2 KB
Line 
1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
5import os,sys
6
7def _validate_bool(b):
8 'Convert b to a boolean or raise'
9 bl = b.lower()
10 if bl in ('f', 'no', 'false', '0', 0): return False
11 elif bl in ('t', 'yes', 'true', '1', 1): return True
12 else:
13 raise ValueError('Could not convert "%s" to boolean' % b)
14
15def _validate_int(s):
16 'convert s to int or raise'
17 try: return int(s)
18 except ValueError:
19 raise ValueError('Could not convert "%s" to int' % s)
20
21def _asap_fname():
22 """
23 Return the path to the rc file
24
25 Search order:
26
27 * current working dir
28 * environ var ASAPRC
29 * HOME/.asaprc
30
31 """
32
33 fname = os.path.join( os.getcwd(), '.asaprc')
34 if os.path.exists(fname): return fname
35
36 if os.environ.has_key('ASAPRC'):
37 path = os.environ['ASAPRC']
38 if os.path.exists(path):
39 fname = os.path.join(path, '.asaprc')
40 if os.path.exists(fname):
41 return fname
42
43 if os.environ.has_key('HOME'):
44 home = os.environ['HOME']
45 fname = os.path.join(home, '.asaprc')
46 if os.path.exists(fname):
47 return fname
48 return None
49
50
51defaultParams = {
52 # general
53 'verbose' : [True, _validate_bool],
54 'useplotter' : [True, _validate_bool],
55 'insitu' : [True, _validate_bool],
56
57 # plotting
58 'plotter.gui' : [True, _validate_bool],
59 'plotter.stacking' : ['p', str],
60 'plotter.panelling' : ['s', str],
61 'plotter.colours' : ['', str],
62 'plotter.linestyles' : ['', str],
63 'plotter.decimate' : [False, _validate_bool],
64 'plotter.ganged' : [True, _validate_bool],
65
66 # scantable
67 'scantable.save' : ['ASAP', str],
68 'scantable.autoaverage' : [True, _validate_bool],
69 'scantable.freqframe' : ['LSRK', str], #default frequency frame
70 'scantable.verbosesummary' : [False, _validate_bool]
71
72 # fitter
73 }
74
75def list_rcparameters():
76
77 print """
78# general
79# print verbose output
80verbose : True
81
82# preload a default plotter
83useplotter : True
84
85# apply operations on the input scantable or return new one
86insitu : True
87
88# plotting
89
90# do we want a GUI or plot to a file
91plotter.gui : True
92
93# default mode for colour stacking
94plotter.stacking : Pol
95
96# default mode for panelling
97plotter.panelling : scan
98
99# push panels together, to share axislabels
100plotter.ganged : True
101
102# decimate the number of points plotted bya afactor of
103# nchan/1024
104plotter.decimate : False
105
106# default colours/linestyles
107plotter.colours :
108plotter.linestyles :
109
110# scantable
111# default ouput format when saving
112scantable.save : ASAP
113# auto averaging on read
114scantable.autoaverage : True
115
116# default frequency frame to set when function
117# scantable.set_freqfrmae is called
118scantable.freqframe : LSRK
119
120# Control the level of information printed by summary
121scantable.verbosesummary : False
122
123# Fitter
124"""
125
126def rc_params():
127 'Return the default params updated from the values in the rc file'
128
129 fname = _asap_fname()
130
131 if fname is None or not os.path.exists(fname):
132 message = 'could not find rc file; returning defaults'
133 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
134 #print message
135 return ret
136
137 cnt = 0
138 for line in file(fname):
139 cnt +=1
140 line = line.strip()
141 if not len(line): continue
142 if line.startswith('#'): continue
143 tup = line.split(':',1)
144 if len(tup) !=2:
145 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
146 continue
147
148 key, val = tup
149 key = key.strip()
150 if not defaultParams.has_key(key):
151 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
152 continue
153
154 default, converter = defaultParams[key]
155
156 ind = val.find('#')
157 if ind>=0: val = val[:ind] # ignore trailing comments
158 val = val.strip()
159 try: cval = converter(val) # try to convert to proper type or raise
160 except Exception, msg:
161 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
162 continue
163 else:
164 # Alles Klar, update dict
165 defaultParams[key][0] = cval
166
167 # strip the conveter funcs and return
168 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
169 print ('loaded rc file %s'%fname)
170
171 return ret
172
173
174# this is the instance used by the asap classes
175rcParams = rc_params()
176
177rcParamsDefault = dict(rcParams.items()) # a copy
178
179def rc(group, **kwargs):
180 """
181 Set the current rc params. Group is the grouping for the rc, eg
182 for scantable.save the group is 'scantable', for plotter.stacking, the
183 group is 'plotter', and so on. kwargs is a list of attribute
184 name/value pairs, eg
185
186 rc('scantable', save='SDFITS')
187
188 sets the current rc params and is equivalent to
189
190 rcParams['scantable.save'] = 'SDFITS'
191
192 Use rcdefaults to restore the default rc params after changes.
193 """
194
195 aliases = {}
196
197 for k,v in kwargs.items():
198 name = aliases.get(k) or k
199 key = '%s.%s' % (group, name)
200 if not rcParams.has_key(key):
201 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
202
203 rcParams[key] = v
204
205
206def rcdefaults():
207 """
208 Restore the default rc params - the ones that were created at
209 asap load time
210 """
211 rcParams.update(rcParamsDefault)
212
213
214def _is_sequence_or_number(param, ptype=int):
215 if isinstance(param,tuple) or isinstance(param,list):
216 if len(param) == 0: return True # empty list
217 out = True
218 for p in param:
219 out &= isinstance(p,ptype)
220 return out
221 elif isinstance(param, ptype):
222 return True
223 return False
224
225def _to_list(param, ptype=int):
226 if isinstance(param, ptype):
227 if ptype is str: return param.split()
228 else: return [param]
229 if _is_sequence_or_number(param, ptype):
230 return param
231 return None
232
233def unique(x):
234 return dict([ (val, 1) for val in x]).keys()
235
236# workaround for ipython, which redirects this if banner=0 in ipythonrc
237sys.stdout = sys.__stdout__
238sys.stderr = sys.__stderr__
239
240# Logging
241from asap._asap import Log as _asaplog
242global asaplog
243asaplog=_asaplog()
244if rcParams['verbose']:
245 asaplog.enable()
246else:
247 asaplog.disable()
248
249def print_log():
250 log = asaplog.pop()
251 if len(log) and rcParams['verbose']: print log
252 return
253
254from asapfitter import *
255from asapreader import reader
256from selector import selector
257
258from asapmath import *
259from scantable import *
260from asaplinefind import *
261#from asapfit import *
262
263from numarray import logical_and as mask_and
264from numarray import logical_or as mask_or
265from numarray import logical_not as mask_not
266
267if rcParams['useplotter']:
268 from asapplotter import *
269 gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
270 plotter = asapplotter(gui)
271 del gui
272
273__date__ = '$Date: 2006-03-30 04:38:02 +0000 (Thu, 30 Mar 2006) $'.split()[1]
274__version__ = '2.0a'
275
276if rcParams['verbose']:
277 def list_scans(t = scantable):
278 import sys, types
279 globs = sys.modules['__main__'].__dict__.iteritems()
280 print "The user created scantables are:"
281 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
282 print filter(lambda x: not x.startswith('_'), sts)
283 return
284
285 def commands():
286 x = """
287 [The scan container]
288 scantable - a container for integrations/scans
289 (can open asap/rpfits/sdfits and ms files)
290 copy - returns a copy of a scan
291 get_scan - gets a specific scan out of a scantable
292 (by name or number) [deprecated]
293 summary - print info about the scantable contents
294 stats - get specified statistic of the spectra in
295 the scantable
296 stddev - get the standard deviation of the spectra
297 in the scantable
298 get_tsys - get the TSys
299 get_time - get the timestamps of the integrations
300 get_sourcename - get the source names of the scans
301 get_azimuth - get the azimuth of the scans
302 get_elevation - get the elevation of the scans
303 get_parangle - get the parallactic angle of the scans
304 get_unit - get the current unit
305 set_unit - set the abcissa unit to be used from this
306 point on
307 get_abcissa - get the abcissa values and name for a given
308 row (time)
309 set_freqframe - set the frame info for the Spectral Axis
310 (e.g. 'LSRK')
311 set_doppler - set the doppler to be used from this point on
312 set_instrument - set the instrument name
313 get_fluxunit - get the brightness flux unit
314 set_fluxunit - set the brightness flux unit
315 create_mask - return an mask in the current unit
316 for the given region. The specified regions
317 are NOT masked
318 get_restfreqs - get the current list of rest frequencies
319 set_restfreqs - set a list of rest frequencies
320 lines - print list of known spectral lines
321 flag_spectrum - flag a whole Beam/IF/Pol
322 save - save the scantable to disk as either 'ASAP'
323 or 'SDFITS'
324 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
325 nscan - the number of scans in the scantable
326 nrow - te number of integrations in the scantable
327 history - print the history of the scantable
328 get_fit - get a fit which has been stored witnh the data
329 average_time - return the (weighted) time average of a scan
330 or a list of scans
331 average_pol - average the polarisations together.
332 The dimension won't be reduced and
333 all polarisations will contain the
334 averaged spectrum.
335 auto_quotient - return the on/off quotient with
336 automatic detection of the on/off scans
337 (matched pairs and 1 off - n on)
338 quotient - return the on/off quotient
339 scale - return a scan scaled by a given factor
340 add - return a scan with given value added
341 bin - return a scan with binned channels
342 resample - return a scan with resampled channels
343 smooth - return the spectrally smoothed scan
344 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
345 auto_poly_baseline - automatically fit a polynomial baseline
346 recalc_azel - recalculate azimuth and elevation based on
347 the pointing
348 gain_el - apply gain-elevation correction
349 opacity - apply opacity correction
350 convert_flux - convert to and from Jy and Kelvin brightness
351 units
352 freq_align - align spectra in frequency frame
353 rotate_xyphase - rotate XY phase of cross correlation
354 rotate_linpolphase - rotate the phase of the complex
355 polarization O=Q+iU correlation
356 freq_switch - perform frequency switching on the data
357 stats - Determine the specified statistic, e.g. 'min'
358 'max', 'rms' etc.
359 stddev - Determine the standard deviation of the current
360 beam/if/pol
361
362 [Math] Mainly functions which operate on more than one scantable
363
364 average_time - return the (weighted) time average
365 of a list of scans
366 quotient - return the on/off quotient
367 simple_math - simple mathematical operations on two scantables,
368 'add', 'sub', 'mul', 'div'
369 [Fitting]
370 fitter
371 auto_fit - return a scan where the function is
372 applied to all Beams/IFs/Pols.
373 commit - return a new scan where the fits have been
374 commited.
375 fit - execute the actual fitting process
376 store_fit - store the fit paramaters in the data (scantable)
377 get_chi2 - get the Chi^2
378 set_scan - set the scantable to be fit
379 set_function - set the fitting function
380 set_parameters - set the parameters for the function(s), and
381 set if they should be held fixed during fitting
382 set_gauss_parameters - same as above but specialised for individual
383 gaussian components
384 get_parameters - get the fitted parameters
385 plot - plot the resulting fit and/or components and
386 residual
387 [Plotter]
388 asapplotter - a plotter for asap, default plotter is
389 called 'plotter'
390 plot - plot a (list of) scantable
391 save - save the plot to a file ('png' ,'ps' or 'eps')
392 set_mode - set the state of the plotter, i.e.
393 what is to be plotted 'colour stacked'
394 and what 'panelled'
395 set_cursor - only plot a selected part of the data
396 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
397 set_legend - specify user labels for the legend indeces
398 set_title - specify user labels for the panel indeces
399 set_abcissa - specify a user label for the abcissa
400 set_ordinate - specify a user label for the ordinate
401 set_layout - specify the multi-panel layout (rows,cols)
402 set_colors - specify a set of colours to use
403 set_linestyles - specify a set of linestyles to use if only
404 using one color
405 set_mask - set a plotting mask for a specific polarization
406
407 [Reading files]
408 reader - access rpfits/sdfits files
409 read - read in integrations
410 summary - list info about all integrations
411
412 [General]
413 commands - this command
414 print - print details about a variable
415 list_scans - list all scantables created bt the user
416 del - delete the given variable from memory
417 range - create a list of values, e.g.
418 range(3) = [0,1,2], range(2,5) = [2,3,4]
419 help - print help for one of the listed functions
420 execfile - execute an asap script, e.g. execfile('myscript')
421 list_rcparameters - print out a list of possible values to be
422 put into $HOME/.asaprc
423 mask_and,mask_or,
424 mask_not - boolean operations on masks created with
425 scantable.create_mask
426
427 Note:
428 How to use this with help:
429 # function 'summary'
430 [xxx] is just a category
431 Every 'sub-level' in this list should be replaces by a '.' Period when
432 using help
433 Example:
434 ASAP> help scantable # to get info on ths scantable
435 ASAP> help scantable.summary # to get help on the scantable's
436 ASAP> help average_time
437
438 """
439 print x
440 return
441
442def welcome():
443 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
444
445Please report any bugs to:
446asap@atnf.csiro.au
447
448[IMPORTANT: ASAP is 0-based]
449Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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