source: branches/Release-2-fixes/python/__init__.py@ 687

Last change on this file since 687 was 676, checked in by mar637, 19 years ago

reflect scantable changes - auto_quotient added to commands()

  • Property svn:eol-style set to native
  • 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
61 # scantable
62 'scantable.save' : ['ASAP', str],
63 'scantable.autoaverage' : [True, _validate_bool],
64 'scantable.freqframe' : ['LSRK', str], #default frequency frame
65 'scantable.allaxes' : [True, _validate_bool], # apply action to all axes
66 'scantable.plotter' : [True, _validate_bool], # use internal plotter
67 'scantable.verbosesummary' : [False, _validate_bool]
68
69 # fitter
70 }
71
72def list_rcparameters():
73
74 print """
75 # general
76 # print verbose output
77 verbose : True
78
79 # preload a default plotter
80 useplotter : True
81
82 # apply operations on the input scantable or return new one
83 insitu : True
84
85 # plotting
86 # default mode for colour stacking
87 plotter.stacking : Pol
88
89 # default mode for panelling
90 plotter.panelling : scan
91
92 # scantable
93 # default ouput format when saving
94 scantable.save : ASAP
95 # auto averaging on read
96 scantable.autoaverage : True
97
98 # default frequency frame to set when function
99 # scantable.set_freqfrmae is called
100 scantable.freqframe : LSRK
101
102 # apply action to all axes not just the cursor location
103 scantable.allaxes : True
104
105 # use internal plotter
106 scantable.plotter : True
107
108 # Control the level of information printed by summary
109 scantable.verbosesummary : False
110
111 # Fitter
112 """
113
114def rc_params():
115 'Return the default params updated from the values in the rc file'
116
117 fname = _asap_fname()
118
119 if fname is None or not os.path.exists(fname):
120 message = 'could not find rc file; returning defaults'
121 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
122 #print message
123 return ret
124
125 cnt = 0
126 for line in file(fname):
127 cnt +=1
128 line = line.strip()
129 if not len(line): continue
130 if line.startswith('#'): continue
131 tup = line.split(':',1)
132 if len(tup) !=2:
133 print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
134 continue
135
136 key, val = tup
137 key = key.strip()
138 if not defaultParams.has_key(key):
139 print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
140 continue
141
142 default, converter = defaultParams[key]
143
144 ind = val.find('#')
145 if ind>=0: val = val[:ind] # ignore trailing comments
146 val = val.strip()
147 try: cval = converter(val) # try to convert to proper type or raise
148 except Exception, msg:
149 print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
150 continue
151 else:
152 # Alles Klar, update dict
153 defaultParams[key][0] = cval
154
155 # strip the conveter funcs and return
156 ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
157 print ('loaded rc file %s'%fname)
158
159 return ret
160
161
162# this is the instance used by the asap classes
163rcParams = rc_params()
164
165rcParamsDefault = dict(rcParams.items()) # a copy
166
167def rc(group, **kwargs):
168 """
169 Set the current rc params. Group is the grouping for the rc, eg
170 for scantable.save the group is 'scantable', for plotter.stacking, the
171 group is 'plotter', and so on. kwargs is a list of attribute
172 name/value pairs, eg
173
174 rc('scantable', save='SDFITS')
175
176 sets the current rc params and is equivalent to
177
178 rcParams['scantable.save'] = 'SDFITS'
179
180 Use rcdefaults to restore the default rc params after changes.
181 """
182
183 aliases = {}
184
185 for k,v in kwargs.items():
186 name = aliases.get(k) or k
187 key = '%s.%s' % (group, name)
188 if not rcParams.has_key(key):
189 raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
190
191 rcParams[key] = v
192
193
194def rcdefaults():
195 """
196 Restore the default rc params - the ones that were created at
197 asap load time
198 """
199 rcParams.update(rcParamsDefault)
200
201
202def _is_sequence_or_number(param, ptype=int):
203 if isinstance(param,tuple) or isinstance(param,list):
204 out = True
205 for p in param:
206 out &= isinstance(p,ptype)
207 return out
208 elif isinstance(param, ptype):
209 return True
210 return False
211
212from asapfitter import *
213from asapreader import reader
214from asapmath import *
215from scantable import *
216from asaplinefind import *
217from asapfit import *
218
219from numarray import logical_and as mask_and
220from numarray import logical_or as mask_or
221from numarray import logical_not as mask_not
222
223if rcParams['useplotter']:
224 if os.environ.has_key('DISPLAY'):
225 print "Initialising asapplotter with the name 'plotter' ..."
226 import asapplotter
227 plotter = asapplotter.asapplotter()
228 else:
229 print "No $DISPLAY set. Disabling plotter.\n"
230
231#from numarray ones,zeros
232
233
234__date__ = '$Date: 2005-09-20 04:26:55 +0000 (Tue, 20 Sep 2005) $'.split()[1]
235__version__ = '1.1'
236
237def list_scans(t = scantable):
238 import sys, types
239 #meta_t = type(t)
240 #if meta_t == types.InstanceType:
241 # t = t.__class__
242 #elif meta_t not in [types.ClassType, types.TypeType]:
243 # t = meta_t
244 globs = sys.modules['__main__'].__dict__.iteritems()
245 print "The user created scantables are:"
246 sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
247 print filter(lambda x: not x.startswith('_'), sts)
248
249def commands():
250 x = """
251 [The scan container]
252 scantable - a container for integrations/scans
253 (can open asap/rpfits/sdfits and ms files)
254 copy - returns a copy of a scan
255 get_scan - gets a specific scan out of a scantable
256 summary - print info about the scantable contents
257 set_cursor - set a specific Beam/IF/Pol 'cursor' for
258 further use
259 get_cursor - print out the current cursor position
260 stats - get specified statistic of the spectra in
261 the scantable
262 stddev - get the standard deviation of the spectra
263 in the scantable
264 get_tsys - get the TSys
265 get_time - get the timestamps of the integrations
266 get_unit - get the currnt unit
267 set_unit - set the abcissa unit to be used from this
268 point on
269 get_abcissa - get the abcissa values and name for a given
270 row (time)
271 set_freqframe - set the frame info for the Spectral Axis
272 (e.g. 'LSRK')
273 set_doppler - set the doppler to be used from this point on
274 set_instrument - set the instrument name
275 get_fluxunit - get the brightness flux unit
276 set_fluxunit - set the brightness flux unit
277 create_mask - return an mask in the current unit
278 for the given region. The specified regions
279 are NOT masked
280 get_restfreqs - get the current list of rest frequencies
281 set_restfreqs - set a list of rest frequencies
282 lines - print list of known spectral lines
283 flag_spectrum - flag a whole Beam/IF/Pol
284 save - save the scantable to disk as either 'ASAP'
285 or 'SDFITS'
286 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
287 history - print the history of the scantable
288 get_fit - get a fit which has been stored witnh the data
289 average_time - return the (weighted) time average of a scan
290 or a list of scans
291 average_pol - average the polarisations together.
292 The dimension won't be reduced and
293 all polarisations will contain the
294 averaged spectrum.
295 auto_quotient - return the on/off quotient with
296 automatic detection of the on/off scans
297 quotient - return the on/off quotient
298 scale - return a scan scaled by a given factor
299 add - return a scan with given value added
300 bin - return a scan with binned channels
301 resample - return a scan with resampled channels
302 smooth - return the spectrally smoothed scan
303 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
304 auto_poly_baseline - automatically fit a polynomial baseline
305 gain_el - apply gain-elevation correction
306 opacity - apply opacity correction
307 convert_flux - convert to and from Jy and Kelvin brightness
308 units
309 freq_align - align spectra in frequency frame
310 rotate_xyphase - rotate XY phase of cross correlation
311 rotate_linpolphase - rotate the phase of the complex
312 polarization O=Q+iU correlation
313 [Math] Mainly functions which operate on more than one scantable
314
315 average_time - return the (weighted) time average
316 of a list of scans
317 quotient - return the on/off quotient
318 simple_math - simple mathematical operations on two scantables,
319 'add', 'sub', 'mul', 'div'
320 [Fitting]
321 fitter
322 auto_fit - return a scan where the function is
323 applied to all Beams/IFs/Pols.
324 commit - return a new scan where the fits have been
325 commited.
326 fit - execute the actual fitting process
327 store_fit - store the fit paramaters in the data (scantable)
328 get_chi2 - get the Chi^2
329 set_scan - set the scantable to be fit
330 set_function - set the fitting function
331 set_parameters - set the parameters for the function(s), and
332 set if they should be held fixed during fitting
333 set_gauss_parameters - same as above but specialised for individual
334 gaussian components
335 get_parameters - get the fitted parameters
336 plot - plot the resulting fit and/or components and
337 residual
338 [Plotter]
339 asapplotter - a plotter for asap, default plotter is
340 called 'plotter'
341 plot - plot a (list of) scantable
342 save - save the plot to a file ('png' ,'ps' or 'eps')
343 set_mode - set the state of the plotter, i.e.
344 what is to be plotted 'colour stacked'
345 and what 'panelled'
346 set_cursor - only plot a selected part of the data
347 set_range - set a 'zoom' window
348 set_legend - specify user labels for the legend indeces
349 set_title - specify user labels for the panel indeces
350 set_ordinate - specify a user label for the ordinate
351 set_abcissa - specify a user label for the abcissa
352 set_layout - specify the multi-panel layout (rows,cols)
353
354 [Reading files]
355 reader - access rpfits/sdfits files
356 read - read in integrations
357 summary - list info about all integrations
358
359 [General]
360 commands - this command
361 print - print details about a variable
362 list_scans - list all scantables created bt the user
363 del - delete the given variable from memory
364 range - create a list of values, e.g.
365 range(3) = [0,1,2], range(2,5) = [2,3,4]
366 help - print help for one of the listed functions
367 execfile - execute an asap script, e.g. execfile('myscript')
368 list_rcparameters - print out a list of possible values to be
369 put into $HOME/.asaprc
370 mask_and,mask_or,
371 mask_not - boolean operations on masks created with
372 scantable.create_mask
373
374 Note:
375 How to use this with help:
376 # function 'summary'
377 [xxx] is just a category
378 Every 'sub-level' in this list should be replaces by a '.' Period when
379 using help
380 Example:
381 ASAP> help scantable # to get info on ths scantable
382 ASAP> help scantable.summary # to get help on the scantable's
383 ASAP> help average_time
384
385 """
386 print x
387 return
388
389print """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
390
391Please report any bugs to:
392asap@atnf.csiro.au
393
394[IMPORTANT: ASAP is 0-based]
395Type commands() to get a list of all available ASAP commands.
396""" % (__version__, __date__)
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