source: branches/Release-2-fixes/python/__init__.py@ 2303

Last change on this file since 2303 was 694, checked in by mar637, 19 years ago

added user customisable colors and linestyles.

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  • Property svn:keywords set to Author Date Id Revision
File size: 14.5 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.stacking' : ['p', str],
59 'plotter.panelling' : ['s', str],
60 'plotter.colours' : ['', str],
61 'plotter.linestyles' : ['', str],
62
63 # scantable
64 'scantable.save' : ['ASAP', str],
65 'scantable.autoaverage' : [True, _validate_bool],
66 'scantable.freqframe' : ['LSRK', str], #default frequency frame
67 'scantable.allaxes' : [True, _validate_bool], # apply action to all axes
68 'scantable.plotter' : [True, _validate_bool], # use internal plotter
69 'scantable.verbosesummary' : [False, _validate_bool]
70
71 # fitter
72 }
73
74def list_rcparameters():
75
76 print """
77 # general
78 # print verbose output
79 verbose : True
80
81 # preload a default plotter
82 useplotter : True
83
84 # apply operations on the input scantable or return new one
85 insitu : True
86
87 # plotting
88 # default mode for colour stacking
89 plotter.stacking : Pol
90
91 # default mode for panelling
92 plotter.panelling : scan
93
94 # default colours/linestyles
95 plotter.colours :
96 plotter.linestyles :
97
98 # scantable
99 # default ouput format when saving
100 scantable.save : ASAP
101 # auto averaging on read
102 scantable.autoaverage : True
103
104 # default frequency frame to set when function
105 # scantable.set_freqfrmae is called
106 scantable.freqframe : LSRK
107
108 # apply action to all axes not just the cursor location
109 scantable.allaxes : True
110
111 # use internal plotter
112 scantable.plotter : True
113
114 # Control the level of information printed by summary
115 scantable.verbosesummary : False
116
117 # Fitter
118 """
119
120def rc_params():
121 'Return the default params updated from the values in the rc file'
122
123 fname = _asap_fname()
124
125 if fname is None or not os.path.exists(fname):
126 message = 'could not find rc file; returning defaults'
127 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
128 #print message
129 return ret
130
131 cnt = 0
132 for line in file(fname):
133 cnt +=1
134 line = line.strip()
135 if not len(line): continue
136 if line.startswith('#'): continue
137 tup = line.split(':',1)
138 if len(tup) !=2:
139 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
140 continue
141
142 key, val = tup
143 key = key.strip()
144 if not defaultParams.has_key(key):
145 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
146 continue
147
148 default, converter = defaultParams[key]
149
150 ind = val.find('#')
151 if ind>=0: val = val[:ind] # ignore trailing comments
152 val = val.strip()
153 try: cval = converter(val) # try to convert to proper type or raise
154 except Exception, msg:
155 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
156 continue
157 else:
158 # Alles Klar, update dict
159 defaultParams[key][0] = cval
160
161 # strip the conveter funcs and return
162 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
163 print ('loaded rc file %s'%fname)
164
165 return ret
166
167
168# this is the instance used by the asap classes
169rcParams = rc_params()
170
171rcParamsDefault = dict(rcParams.items()) # a copy
172
173def rc(group, **kwargs):
174 """
175 Set the current rc params. Group is the grouping for the rc, eg
176 for scantable.save the group is 'scantable', for plotter.stacking, the
177 group is 'plotter', and so on. kwargs is a list of attribute
178 name/value pairs, eg
179
180 rc('scantable', save='SDFITS')
181
182 sets the current rc params and is equivalent to
183
184 rcParams['scantable.save'] = 'SDFITS'
185
186 Use rcdefaults to restore the default rc params after changes.
187 """
188
189 aliases = {}
190
191 for k,v in kwargs.items():
192 name = aliases.get(k) or k
193 key = '%s.%s' % (group, name)
194 if not rcParams.has_key(key):
195 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
196
197 rcParams[key] = v
198
199
200def rcdefaults():
201 """
202 Restore the default rc params - the ones that were created at
203 asap load time
204 """
205 rcParams.update(rcParamsDefault)
206
207
208def _is_sequence_or_number(param, ptype=int):
209 if isinstance(param,tuple) or isinstance(param,list):
210 out = True
211 for p in param:
212 out &= isinstance(p,ptype)
213 return out
214 elif isinstance(param, ptype):
215 return True
216 return False
217
218from asapfitter import *
219from asapreader import reader
220from asapmath import *
221from scantable import *
222from asaplinefind import *
223from asapfit import *
224
225from numarray import logical_and as mask_and
226from numarray import logical_or as mask_or
227from numarray import logical_not as mask_not
228
229if rcParams['useplotter']:
230 if os.environ.has_key('DISPLAY'):
231 print "Initialising asapplotter with the name 'plotter' ..."
232 import asapplotter
233 plotter = asapplotter.asapplotter()
234 else:
235 print "No $DISPLAY set. Disabling plotter.\n"
236
237#from numarray ones,zeros
238
239
240__date__ = '$Date: 2005-09-29 06:36:56 +0000 (Thu, 29 Sep 2005) $'.split()[1]
241__version__ = '1.1'
242
243def list_scans(t = scantable):
244 import sys, types
245 globs = sys.modules['__main__'].__dict__.iteritems()
246 print "The user created scantables are:"
247 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
248 print filter(lambda x: not x.startswith('_'), sts)
249
250def commands():
251 x = """
252 [The scan container]
253 scantable - a container for integrations/scans
254 (can open asap/rpfits/sdfits and ms files)
255 copy - returns a copy of a scan
256 get_scan - gets a specific scan out of a scantable
257 summary - print info about the scantable contents
258 set_cursor - set a specific Beam/IF/Pol 'cursor' for
259 further use
260 get_cursor - print out the current cursor position
261 stats - get specified statistic of the spectra in
262 the scantable
263 stddev - get the standard deviation of the spectra
264 in the scantable
265 get_tsys - get the TSys
266 get_time - get the timestamps of the integrations
267 get_unit - get the currnt unit
268 set_unit - set the abcissa unit to be used from this
269 point on
270 get_abcissa - get the abcissa values and name for a given
271 row (time)
272 set_freqframe - set the frame info for the Spectral Axis
273 (e.g. 'LSRK')
274 set_doppler - set the doppler to be used from this point on
275 set_instrument - set the instrument name
276 get_fluxunit - get the brightness flux unit
277 set_fluxunit - set the brightness flux unit
278 create_mask - return an mask in the current unit
279 for the given region. The specified regions
280 are NOT masked
281 get_restfreqs - get the current list of rest frequencies
282 set_restfreqs - set a list of rest frequencies
283 lines - print list of known spectral lines
284 flag_spectrum - flag a whole Beam/IF/Pol
285 save - save the scantable to disk as either 'ASAP'
286 or 'SDFITS'
287 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
288 history - print the history of the scantable
289 get_fit - get a fit which has been stored witnh the data
290 average_time - return the (weighted) time average of a scan
291 or a list of scans
292 average_pol - average the polarisations together.
293 The dimension won't be reduced and
294 all polarisations will contain the
295 averaged spectrum.
296 auto_quotient - return the on/off quotient with
297 automatic detection of the on/off scans
298 quotient - return the on/off quotient
299 scale - return a scan scaled by a given factor
300 add - return a scan with given value added
301 bin - return a scan with binned channels
302 resample - return a scan with resampled channels
303 smooth - return the spectrally smoothed scan
304 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
305 auto_poly_baseline - automatically fit a polynomial baseline
306 gain_el - apply gain-elevation correction
307 opacity - apply opacity correction
308 convert_flux - convert to and from Jy and Kelvin brightness
309 units
310 freq_align - align spectra in frequency frame
311 rotate_xyphase - rotate XY phase of cross correlation
312 rotate_linpolphase - rotate the phase of the complex
313 polarization O=Q+iU correlation
314 [Math] Mainly functions which operate on more than one scantable
315
316 average_time - return the (weighted) time average
317 of a list of scans
318 quotient - return the on/off quotient
319 simple_math - simple mathematical operations on two scantables,
320 'add', 'sub', 'mul', 'div'
321 [Fitting]
322 fitter
323 auto_fit - return a scan where the function is
324 applied to all Beams/IFs/Pols.
325 commit - return a new scan where the fits have been
326 commited.
327 fit - execute the actual fitting process
328 store_fit - store the fit paramaters in the data (scantable)
329 get_chi2 - get the Chi^2
330 set_scan - set the scantable to be fit
331 set_function - set the fitting function
332 set_parameters - set the parameters for the function(s), and
333 set if they should be held fixed during fitting
334 set_gauss_parameters - same as above but specialised for individual
335 gaussian components
336 get_parameters - get the fitted parameters
337 plot - plot the resulting fit and/or components and
338 residual
339 [Plotter]
340 asapplotter - a plotter for asap, default plotter is
341 called 'plotter'
342 plot - plot a (list of) scantable
343 save - save the plot to a file ('png' ,'ps' or 'eps')
344 set_mode - set the state of the plotter, i.e.
345 what is to be plotted 'colour stacked'
346 and what 'panelled'
347 set_cursor - only plot a selected part of the data
348 set_range - set a 'zoom' window
349 set_legend - specify user labels for the legend indeces
350 set_title - specify user labels for the panel indeces
351 set_ordinate - specify a user label for the ordinate
352 set_abcissa - specify a user label for the abcissa
353 set_layout - specify the multi-panel layout (rows,cols)
354
355 [Reading files]
356 reader - access rpfits/sdfits files
357 read - read in integrations
358 summary - list info about all integrations
359
360 [General]
361 commands - this command
362 print - print details about a variable
363 list_scans - list all scantables created bt the user
364 del - delete the given variable from memory
365 range - create a list of values, e.g.
366 range(3) = [0,1,2], range(2,5) = [2,3,4]
367 help - print help for one of the listed functions
368 execfile - execute an asap script, e.g. execfile('myscript')
369 list_rcparameters - print out a list of possible values to be
370 put into $HOME/.asaprc
371 mask_and,mask_or,
372 mask_not - boolean operations on masks created with
373 scantable.create_mask
374
375 Note:
376 How to use this with help:
377 # function 'summary'
378 [xxx] is just a category
379 Every 'sub-level' in this list should be replaces by a '.' Period when
380 using help
381 Example:
382 ASAP> help scantable # to get info on ths scantable
383 ASAP> help scantable.summary # to get help on the scantable's
384 ASAP> help average_time
385
386 """
387 print x
388 return
389
390print """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
391
392Please report any bugs to:
393asap@atnf.csiro.au
394
395[IMPORTANT: ASAP is 0-based]
396Type commands() to get a list of all available ASAP commands.
397""" % (__version__, __date__)
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