source: branches/Release12/python/__init__.py@ 937

Last change on this file since 937 was 800, checked in by mar637, 19 years ago

Request: added channel based flagging

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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 *
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: 2006-01-10 04:11:58 +0000 (Tue, 10 Jan 2006) $'.split()[1]
270__version__ = '1.2.2a'
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_azimuth - get the azimuth of the scans
301 get_elevation - get the elevation of the scans
302 get_parangle - get the parallactic angle of the scans
303 get_unit - get the currnt unit
304 set_unit - set the abcissa unit to be used from this
305 point on
306 get_abcissa - get the abcissa values and name for a given
307 row (time)
308 set_freqframe - set the frame info for the Spectral Axis
309 (e.g. 'LSRK')
310 set_doppler - set the doppler to be used from this point on
311 set_instrument - set the instrument name
312 get_fluxunit - get the brightness flux unit
313 set_fluxunit - set the brightness flux unit
314 create_mask - return an mask in the current unit
315 for the given region. The specified regions
316 are NOT masked
317 get_restfreqs - get the current list of rest frequencies
318 set_restfreqs - set a list of rest frequencies
319 lines - print list of known spectral lines
320 flag_spectrum - flag spectral channels
321 save - save the scantable to disk as either 'ASAP'
322 or 'SDFITS'
323 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
324 nscan - the number of scans in the scantable
325 nrow - te number of integrations in the scantable
326 history - print the history of the scantable
327 get_fit - get a fit which has been stored witnh the data
328 average_time - return the (weighted) time average of a scan
329 or a list of scans
330 average_pol - average the polarisations together.
331 The dimension won't be reduced and
332 all polarisations will contain the
333 averaged spectrum.
334 auto_quotient - return the on/off quotient with
335 automatic detection of the on/off scans
336 (matched pairs and 1 off - n on)
337 quotient - return the on/off quotient
338 scale - return a scan scaled by a given factor
339 add - return a scan with given value added
340 bin - return a scan with binned channels
341 resample - return a scan with resampled channels
342 smooth - return the spectrally smoothed scan
343 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
344 auto_poly_baseline - automatically fit a polynomial baseline
345 recalc_azel - recalculate azimuth and elevation based on
346 the pointing
347 gain_el - apply gain-elevation correction
348 opacity - apply opacity correction
349 convert_flux - convert to and from Jy and Kelvin brightness
350 units
351 freq_align - align spectra in frequency frame
352 rotate_xyphase - rotate XY phase of cross correlation
353 rotate_linpolphase - rotate the phase of the complex
354 polarization O=Q+iU correlation
355 invert_phase - take the complex conjugate of the cross correlation
356 swap_pol - swap the order of the parallel polarisations
357 freq_switch - perform frequency switching on the data
358 stats - Determine the specified statistic, e.g. 'min'
359 'max', 'rms' etc.
360 stddev - Determine the standard deviation of the current
361 beam/if/pol
362
363 [Math] Mainly functions which operate on more than one scantable
364
365 average_time - return the (weighted) time average
366 of a list of scans
367 quotient - return the on/off quotient
368 simple_math - simple mathematical operations on two scantables,
369 'add', 'sub', 'mul', 'div'
370 [Fitting]
371 fitter
372 auto_fit - return a scan where the function is
373 applied to all Beams/IFs/Pols.
374 commit - return a new scan where the fits have been
375 commited.
376 fit - execute the actual fitting process
377 store_fit - store the fit paramaters in the data (scantable)
378 get_chi2 - get the Chi^2
379 set_scan - set the scantable to be fit
380 set_function - set the fitting function
381 set_parameters - set the parameters for the function(s), and
382 set if they should be held fixed during fitting
383 set_gauss_parameters - same as above but specialised for individual
384 gaussian components
385 get_parameters - get the fitted parameters
386 plot - plot the resulting fit and/or components and
387 residual
388 [Plotter]
389 asapplotter - a plotter for asap, default plotter is
390 called 'plotter'
391 plot - plot a (list of) scantable
392 save - save the plot to a file ('png' ,'ps' or 'eps')
393 set_mode - set the state of the plotter, i.e.
394 what is to be plotted 'colour stacked'
395 and what 'panelled'
396 set_cursor - only plot a selected part of the data
397 set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
398 set_legend - specify user labels for the legend indeces
399 set_title - specify user labels for the panel indeces
400 set_abcissa - specify a user label for the abcissa
401 set_ordinate - specify a user label for the ordinate
402 set_layout - specify the multi-panel layout (rows,cols)
403 set_colors - specify a set of colours to use
404 set_linestyles - specify a set of linestyles to use if only
405 using one color
406 set_mask - set a plotting mask for a specific polarization
407
408 [Reading files]
409 reader - access rpfits/sdfits files
410 read - read in integrations
411 summary - list info about all integrations
412
413 [General]
414 commands - this command
415 print - print details about a variable
416 list_scans - list all scantables created bt the user
417 del - delete the given variable from memory
418 range - create a list of values, e.g.
419 range(3) = [0,1,2], range(2,5) = [2,3,4]
420 help - print help for one of the listed functions
421 execfile - execute an asap script, e.g. execfile('myscript')
422 list_rcparameters - print out a list of possible values to be
423 put into $HOME/.asaprc
424 mask_and,mask_or,
425 mask_not - boolean operations on masks created with
426 scantable.create_mask
427
428 Note:
429 How to use this with help:
430 # function 'summary'
431 [xxx] is just a category
432 Every 'sub-level' in this list should be replaces by a '.' Period when
433 using help
434 Example:
435 ASAP> help scantable # to get info on ths scantable
436 ASAP> help scantable.summary # to get help on the scantable's
437 ASAP> help average_time
438
439 """
440 print x
441 return
442
443def welcome():
444 return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
445
446Please report any bugs to:
447asap@atnf.csiro.au
448
449[IMPORTANT: ASAP is 0-based]
450Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
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