source: trunk/python/__init__.py@ 735

Last change on this file since 735 was 733, checked in by mar637, 19 years ago

documentation fixes

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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
82 verbose : True
83
84 # preload a default plotter
85 useplotter : True
86
87 # apply operations on the input scantable or return new one
88 insitu : True
89
90 # plotting
91
92 # do we want a GUI or plot to a file
93 plotter.gui : True
94
95 # default mode for colour stacking
96 plotter.stacking : Pol
97
98 # default mode for panelling
99 plotter.panelling : scan
100
101 # push panels together, to share axislabels
102 plotter.ganged : True
103
104 # decimate the number of points plotted bya afactor of
105 # nchan/1024
106 plotter.decimate : False
107
108 # default colours/linestyles
109 plotter.colours :
110 plotter.linestyles :
111
112 # scantable
113 # default ouput format when saving
114 scantable.save : ASAP
115 # auto averaging on read
116 scantable.autoaverage : True
117
118 # default frequency frame to set when function
119 # scantable.set_freqfrmae is called
120 scantable.freqframe : LSRK
121
122 # apply action to all axes not just the cursor location
123 scantable.allaxes : True
124
125 # use internal plotter
126 scantable.plotter : True
127
128 # Control the level of information printed by summary
129 scantable.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 *
252from asapreader import reader
253
254from asapmath import *
255from scantable import *
256from asaplinefind import *
257from 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
263if 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: 2005-11-24 03:12:33 +0000 (Thu, 24 Nov 2005) $'.split()[1]
270__version__ = '1.2'
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)
289 summary - print info about the scantable contents
290 set_cursor - set a specific Beam/IF/Pol 'cursor' for
291 further use
292 get_cursor - print out the current cursor position
293 stats - get specified statistic of the spectra in
294 the scantable
295 stddev - get the standard deviation of the spectra
296 in the scantable
297 get_tsys - get the TSys
298 get_time - get the timestamps of the integrations
299 get_sourcename - get the source names of the scans
300 get_unit - get the currnt 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 gain_el - apply gain-elevation correction
343 opacity - apply opacity correction
344 convert_flux - convert to and from Jy and Kelvin brightness
345 units
346 freq_align - align spectra in frequency frame
347 rotate_xyphase - rotate XY phase of cross correlation
348 rotate_linpolphase - rotate the phase of the complex
349 polarization O=Q+iU correlation
350 freq_switch - perform frequency switching on the data
351 stats - Determine the specified statistic, e.g. 'min'
352 'max', 'rms' etc.
353 stddev - Determine the standard deviation of the current
354 beam/if/pol
355
356 [Math] Mainly functions which operate on more than one scantable
357
358 average_time - return the (weighted) time average
359 of a list of scans
360 quotient - return the on/off quotient
361 simple_math - simple mathematical operations on two scantables,
362 'add', 'sub', 'mul', 'div'
363 [Fitting]
364 fitter
365 auto_fit - return a scan where the function is
366 applied to all Beams/IFs/Pols.
367 commit - return a new scan where the fits have been
368 commited.
369 fit - execute the actual fitting process
370 store_fit - store the fit paramaters in the data (scantable)
371 get_chi2 - get the Chi^2
372 set_scan - set the scantable to be fit
373 set_function - set the fitting function
374 set_parameters - set the parameters for the function(s), and
375 set if they should be held fixed during fitting
376 set_gauss_parameters - same as above but specialised for individual
377 gaussian components
378 get_parameters - get the fitted parameters
379 plot - plot the resulting fit and/or components and
380 residual
381 [Plotter]
382 asapplotter - a plotter for asap, default plotter is
383 called 'plotter'
384 plot - plot a (list of) scantable
385 save - save the plot to a file ('png' ,'ps' or 'eps')
386 set_mode - set the state of the plotter, i.e.
387 what is to be plotted 'colour stacked'
388 and what 'panelled'
389 set_cursor - only plot a selected part of the data
390 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
391 set_legend - specify user labels for the legend indeces
392 set_title - specify user labels for the panel indeces
393 set_abcissa - specify a user label for the abcissa
394 set_ordinate - specify a user label for the ordinate
395 set_layout - specify the multi-panel layout (rows,cols)
396 set_colors - specify a set of colours to use
397 set_linestyles - specify a set of linestyles to use if only
398 using one color
399 set_mask - set a plotting mask for a specific polarization
400
401 [Reading files]
402 reader - access rpfits/sdfits files
403 read - read in integrations
404 summary - list info about all integrations
405
406 [General]
407 commands - this command
408 print - print details about a variable
409 list_scans - list all scantables created bt the user
410 del - delete the given variable from memory
411 range - create a list of values, e.g.
412 range(3) = [0,1,2], range(2,5) = [2,3,4]
413 help - print help for one of the listed functions
414 execfile - execute an asap script, e.g. execfile('myscript')
415 list_rcparameters - print out a list of possible values to be
416 put into $HOME/.asaprc
417 mask_and,mask_or,
418 mask_not - boolean operations on masks created with
419 scantable.create_mask
420
421 Note:
422 How to use this with help:
423 # function 'summary'
424 [xxx] is just a category
425 Every 'sub-level' in this list should be replaces by a '.' Period when
426 using help
427 Example:
428 ASAP> help scantable # to get info on ths scantable
429 ASAP> help scantable.summary # to get help on the scantable's
430 ASAP> help average_time
431
432 """
433 print x
434 return
435
436def welcome():
437 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
438
439Please report any bugs to:
440asap@atnf.csiro.au
441
442[IMPORTANT: ASAP is 0-based]
443Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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