source: trunk/python/__init__.py@ 885

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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.allaxes' : [True, _validate_bool], # apply action to all axes
71 'scantable.plotter' : [True, _validate_bool], # use internal plotter
72 'scantable.verbosesummary' : [False, _validate_bool]
73
74 # fitter
75 }
76
77def list_rcparameters():
78
79 print """
80# general
81# print verbose output
82verbose : True
83
84# preload a default plotter
85useplotter : True
86
87# apply operations on the input scantable or return new one
88insitu : True
89
90# plotting
91
92# do we want a GUI or plot to a file
93plotter.gui : True
94
95# default mode for colour stacking
96plotter.stacking : Pol
97
98# default mode for panelling
99plotter.panelling : scan
100
101# push panels together, to share axislabels
102plotter.ganged : True
103
104# decimate the number of points plotted bya afactor of
105# nchan/1024
106plotter.decimate : False
107
108# default colours/linestyles
109plotter.colours :
110plotter.linestyles :
111
112# scantable
113# default ouput format when saving
114scantable.save : ASAP
115# auto averaging on read
116scantable.autoaverage : True
117
118# default frequency frame to set when function
119# scantable.set_freqfrmae is called
120scantable.freqframe : LSRK
121
122# apply action to all axes not just the cursor location
123scantable.allaxes : True
124
125# use internal plotter
126scantable.plotter : True
127
128# Control the level of information printed by summary
129scantable.verbosesummary : False
130
131# Fitter
132"""
133
134def rc_params():
135 'Return the default params updated from the values in the rc file'
136
137 fname = _asap_fname()
138
139 if fname is None or not os.path.exists(fname):
140 message = 'could not find rc file; returning defaults'
141 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
142 #print message
143 return ret
144
145 cnt = 0
146 for line in file(fname):
147 cnt +=1
148 line = line.strip()
149 if not len(line): continue
150 if line.startswith('#'): continue
151 tup = line.split(':',1)
152 if len(tup) !=2:
153 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
154 continue
155
156 key, val = tup
157 key = key.strip()
158 if not defaultParams.has_key(key):
159 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
160 continue
161
162 default, converter = defaultParams[key]
163
164 ind = val.find('#')
165 if ind>=0: val = val[:ind] # ignore trailing comments
166 val = val.strip()
167 try: cval = converter(val) # try to convert to proper type or raise
168 except Exception, msg:
169 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
170 continue
171 else:
172 # Alles Klar, update dict
173 defaultParams[key][0] = cval
174
175 # strip the conveter funcs and return
176 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
177 print ('loaded rc file %s'%fname)
178
179 return ret
180
181
182# this is the instance used by the asap classes
183rcParams = rc_params()
184
185rcParamsDefault = dict(rcParams.items()) # a copy
186
187def rc(group, **kwargs):
188 """
189 Set the current rc params. Group is the grouping for the rc, eg
190 for scantable.save the group is 'scantable', for plotter.stacking, the
191 group is 'plotter', and so on. kwargs is a list of attribute
192 name/value pairs, eg
193
194 rc('scantable', save='SDFITS')
195
196 sets the current rc params and is equivalent to
197
198 rcParams['scantable.save'] = 'SDFITS'
199
200 Use rcdefaults to restore the default rc params after changes.
201 """
202
203 aliases = {}
204
205 for k,v in kwargs.items():
206 name = aliases.get(k) or k
207 key = '%s.%s' % (group, name)
208 if not rcParams.has_key(key):
209 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
210
211 rcParams[key] = v
212
213
214def rcdefaults():
215 """
216 Restore the default rc params - the ones that were created at
217 asap load time
218 """
219 rcParams.update(rcParamsDefault)
220
221
222def _is_sequence_or_number(param, ptype=int):
223 if isinstance(param,tuple) or isinstance(param,list):
224 out = True
225 for p in param:
226 out &= isinstance(p,ptype)
227 return out
228 elif isinstance(param, ptype):
229 return True
230 return False
231
232
233# workaround for ipython, which redirects this if banner=0 in ipythonrc
234sys.stdout = sys.__stdout__
235sys.stderr = sys.__stderr__
236
237# Logging
238from asap._asap import Log as _asaplog
239global asaplog
240asaplog=_asaplog()
241if rcParams['verbose']:
242 asaplog.enable()
243else:
244 asaplog.disable()
245
246def print_log():
247 log = asaplog.pop()
248 if len(log) and rcParams['verbose']: print log
249 return
250
251from asapfitter import *
252#from asapreader import reader
253
254from asapmath import *
255from scantable import *
256from asaplinefind import *
257#from asapfit import *
258
259from numarray import logical_and as mask_and
260from numarray import logical_or as mask_or
261from numarray import logical_not as mask_not
262
263# if rcParams['useplotter']:
264# from asapplotter import *
265# gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
266# plotter = asapplotter(gui)
267# del gui
268
269__date__ = '$Date: 2006-03-08 00:57:12 +0000 (Wed, 08 Mar 2006) $'.split()[1]
270__version__ = '2.0a'
271
272if rcParams['verbose']:
273 def list_scans(t = scantable):
274 import sys, types
275 globs = sys.modules['__main__'].__dict__.iteritems()
276 print "The user created scantables are:"
277 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
278 print filter(lambda x: not x.startswith('_'), sts)
279 return
280
281 def commands():
282 x = """
283 [The scan container]
284 scantable - a container for integrations/scans
285 (can open asap/rpfits/sdfits and ms files)
286 copy - returns a copy of a scan
287 get_scan - gets a specific scan out of a scantable
288 (by name or number) [deprecated]
289 summary - print info about the scantable contents
290 stats - get specified statistic of the spectra in
291 the scantable
292 stddev - get the standard deviation of the spectra
293 in the scantable
294 get_tsys - get the TSys
295 get_time - get the timestamps of the integrations
296 get_sourcename - get the source names of the scans
297 get_azimuth - get the azimuth of the scans
298 get_elevation - get the elevation of the scans
299 get_parangle - get the parallactic angle of the scans
300 get_unit - get the current unit
301 set_unit - set the abcissa unit to be used from this
302 point on
303 get_abcissa - get the abcissa values and name for a given
304 row (time)
305 set_freqframe - set the frame info for the Spectral Axis
306 (e.g. 'LSRK')
307 set_doppler - set the doppler to be used from this point on
308 set_instrument - set the instrument name
309 get_fluxunit - get the brightness flux unit
310 set_fluxunit - set the brightness flux unit
311 create_mask - return an mask in the current unit
312 for the given region. The specified regions
313 are NOT masked
314 get_restfreqs - get the current list of rest frequencies
315 set_restfreqs - set a list of rest frequencies
316 lines - print list of known spectral lines
317 flag_spectrum - flag a whole Beam/IF/Pol
318 save - save the scantable to disk as either 'ASAP'
319 or 'SDFITS'
320 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
321 nscan - the number of scans in the scantable
322 nrow - te number of integrations in the scantable
323 history - print the history of the scantable
324 get_fit - get a fit which has been stored witnh the data
325 average_time - return the (weighted) time average of a scan
326 or a list of scans
327 average_pol - average the polarisations together.
328 The dimension won't be reduced and
329 all polarisations will contain the
330 averaged spectrum.
331 auto_quotient - return the on/off quotient with
332 automatic detection of the on/off scans
333 (matched pairs and 1 off - n on)
334 quotient - return the on/off quotient
335 scale - return a scan scaled by a given factor
336 add - return a scan with given value added
337 bin - return a scan with binned channels
338 resample - return a scan with resampled channels
339 smooth - return the spectrally smoothed scan
340 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
341 auto_poly_baseline - automatically fit a polynomial baseline
342 recalc_azel - recalculate azimuth and elevation based on
343 the pointing
344 gain_el - apply gain-elevation correction
345 opacity - apply opacity correction
346 convert_flux - convert to and from Jy and Kelvin brightness
347 units
348 freq_align - align spectra in frequency frame
349 rotate_xyphase - rotate XY phase of cross correlation
350 rotate_linpolphase - rotate the phase of the complex
351 polarization O=Q+iU correlation
352 freq_switch - perform frequency switching on the data
353 stats - Determine the specified statistic, e.g. 'min'
354 'max', 'rms' etc.
355 stddev - Determine the standard deviation of the current
356 beam/if/pol
357
358 [Math] Mainly functions which operate on more than one scantable
359
360 average_time - return the (weighted) time average
361 of a list of scans
362 quotient - return the on/off quotient
363 simple_math - simple mathematical operations on two scantables,
364 'add', 'sub', 'mul', 'div'
365 [Fitting]
366 fitter
367 auto_fit - return a scan where the function is
368 applied to all Beams/IFs/Pols.
369 commit - return a new scan where the fits have been
370 commited.
371 fit - execute the actual fitting process
372 store_fit - store the fit paramaters in the data (scantable)
373 get_chi2 - get the Chi^2
374 set_scan - set the scantable to be fit
375 set_function - set the fitting function
376 set_parameters - set the parameters for the function(s), and
377 set if they should be held fixed during fitting
378 set_gauss_parameters - same as above but specialised for individual
379 gaussian components
380 get_parameters - get the fitted parameters
381 plot - plot the resulting fit and/or components and
382 residual
383 [Plotter]
384 asapplotter - a plotter for asap, default plotter is
385 called 'plotter'
386 plot - plot a (list of) scantable
387 save - save the plot to a file ('png' ,'ps' or 'eps')
388 set_mode - set the state of the plotter, i.e.
389 what is to be plotted 'colour stacked'
390 and what 'panelled'
391 set_cursor - only plot a selected part of the data
392 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
393 set_legend - specify user labels for the legend indeces
394 set_title - specify user labels for the panel indeces
395 set_abcissa - specify a user label for the abcissa
396 set_ordinate - specify a user label for the ordinate
397 set_layout - specify the multi-panel layout (rows,cols)
398 set_colors - specify a set of colours to use
399 set_linestyles - specify a set of linestyles to use if only
400 using one color
401 set_mask - set a plotting mask for a specific polarization
402
403 [Reading files]
404 reader - access rpfits/sdfits files
405 read - read in integrations
406 summary - list info about all integrations
407
408 [General]
409 commands - this command
410 print - print details about a variable
411 list_scans - list all scantables created bt the user
412 del - delete the given variable from memory
413 range - create a list of values, e.g.
414 range(3) = [0,1,2], range(2,5) = [2,3,4]
415 help - print help for one of the listed functions
416 execfile - execute an asap script, e.g. execfile('myscript')
417 list_rcparameters - print out a list of possible values to be
418 put into $HOME/.asaprc
419 mask_and,mask_or,
420 mask_not - boolean operations on masks created with
421 scantable.create_mask
422
423 Note:
424 How to use this with help:
425 # function 'summary'
426 [xxx] is just a category
427 Every 'sub-level' in this list should be replaces by a '.' Period when
428 using help
429 Example:
430 ASAP> help scantable # to get info on ths scantable
431 ASAP> help scantable.summary # to get help on the scantable's
432 ASAP> help average_time
433
434 """
435 print x
436 return
437
438def welcome():
439 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
440
441Please report any bugs to:
442asap@atnf.csiro.au
443
444[IMPORTANT: ASAP is 0-based]
445Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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