source: trunk/python/__init__.py@ 509

Last change on this file since 509 was 487, checked in by kil064, 20 years ago

add freq_align

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  • Property svn:keywords set to Author Date Id Revision
File size: 13.1 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' : [False, 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 : False
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
201from asapfitter import *
202from asapreader import reader
203from asapmath import *
204from scantable import *
205from asaplinefind import *
206
207from numarray import logical_and as mask_and
208from numarray import logical_or as mask_or
209from numarray import logical_not as mask_not
210
211if rcParams['useplotter']:
212 if os.environ.has_key('DISPLAY'):
213 print "Initialising asapplotter with the name 'plotter' ..."
214 import asapplotter
215 plotter = asapplotter.asapplotter()
216 else:
217 print "No $DISPLAY set. Disabling plotter.\n"
218
219#from numarray ones,zeros
220
221
222__date__ = '$Date: 2005-02-20 23:58:43 +0000 (Sun, 20 Feb 2005) $'
223__version__ = '0.2'
224
225def list_scans(t = scantable):
226 import sys, types
227 #meta_t = type(t)
228 #if meta_t == types.InstanceType:
229 # t = t.__class__
230 #elif meta_t not in [types.ClassType, types.TypeType]:
231 # t = meta_t
232 globs = sys.modules['__main__'].__dict__.iteritems()
233 print "The user created scantables are:"
234 x = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
235 print x
236
237def commands():
238 x = """
239 [The scan container]
240 scantable - a container for integrations/scans
241 (can open asap/rpfits/sdfits and ms files)
242 copy - returns a copy of a scan
243 get_scan - gets a specific scan out of a scantable
244 summary - print info about the scantable contents
245 set_cursor - set a specific Beam/IF/Pol 'cursor' for
246 further use
247 get_cursor - print out the current cursor position
248 stats - get specified statistic of the spectra in
249 the scantable
250 stddev - get the standard deviation of the spectra
251 in the scantable
252 get_tsys - get the TSys
253 get_time - get the timestamps of the integrations
254 get_unit - get the currnt unit
255 set_unit - set the abcissa unit to be used from this point on
256 get_abcissa - get the abcissa values and name for a given
257 row (time)
258 set_freqframe - set the frame info for the Spectral Axis
259 (e.g. 'LSRK')
260 set_doppler - set the doppler to be used from this point on
261 set_instrument - set the instrument name
262 get_fluxunit - get the brightness flux unit
263 set_fluxunit - set the brightness flux unit
264 create_mask - return an mask in the current unit
265 for the given region. The specified regions
266 are NOT masked
267 get_restfreqs - get the current list of rest frequencies
268 set_restfreqs - set a list of rest frequencies
269 lines - print list of known spectral lines
270 flag_spectrum - flag a whole Beam/IF/Pol
271 save - save the scantable to disk as either 'ASAP'
272 or 'SDFITS'
273 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
274 history - print the history of the scantable
275 [Math]
276 average_time - return the (weighted) time average of a scan
277 or a list of scans
278 average_pol - average the polarisations together.
279 The dimension won't be reduced and
280 all polarisations will contain the
281 averaged spectrum.
282 quotient - return the on/off quotient
283 simple_math - simple mathematical operations on two scantables,
284 'add', 'sub', 'mul', 'div'
285 scale - return a scan scaled by a given factor
286 add - return a scan with given value added
287 bin - return a scan with binned channels
288 resample - return a scan with resampled channels
289 smooth - return the spectrally smoothed scan
290 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
291 gain_el - apply gain-elevation correction
292 opacity - apply opacity correction
293 convert_flux - convert to and from Jy and Kelvin brightness
294 units
295 freq_align - align spectra in frequency frame
296 rotate_xyphase - rotate XY phase of cross correlation
297
298 fitter
299 auto_fit - return a scan where the function is
300 applied to all Beams/IFs/Pols.
301 commit - return a new scan where the fits have been
302 commited.
303 fit - execute the actual fitting process
304 get_chi2 - get the Chi^2
305 set_scan - set the scantable to be fit
306 set_function - set the fitting function
307 set_parameters - set the parameters for the function(s), and
308 set if they should be held fixed during fitting
309 get_parameters - get the fitted parameters
310 [Plotter]
311 asapplotter - a plotter for asap, default plotter is
312 called 'plotter'
313 plot - plot a (list of) scantable
314 save - save the plot to a file ('png' ,'ps' or 'eps')
315 set_mode - set the state of the plotter, i.e.
316 what is to be plotted 'colour stacked'
317 and what 'panelled'
318 set_range - set the abcissa 'zoom' range
319 set_legend - specify user labels for the legend indeces
320 set_title - specify user labels for the panel indeces
321 set_ordinate - specify a user label for the ordinate
322 set_abcissa - specify a user label for the abcissa
323 set_layout - specify the multi-panel layout (rows,cols)
324
325 [Reading files]
326 reader - access rpfits/sdfits files
327 read - read in integrations
328 summary - list info about all integrations
329
330 [General]
331 commands - this command
332 print - print details about a variable
333 list_scans - list all scantables created bt the user
334 del - delete the given variable from memory
335 range - create a list of values, e.g.
336 range(3) = [0,1,2], range(2,5) = [2,3,4]
337 help - print help for one of the listed functions
338 execfile - execute an asap script, e.g. execfile('myscript')
339 list_rcparameters - print out a list of possible values to be
340 put into $HOME/.asaprc
341 mask_and,mask_or,
342 mask_not - boolean operations on masks created with
343 scantable.create_mask
344
345 Note:
346 How to use this with help:
347 # function 'summary'
348 [xxx] is just a category
349 Every 'sub-level' in this list should be replaces by a '.' Period when
350 using help
351 Example:
352 ASAP> help scantable # to get info on ths scantable
353 ASAP> help scantable.summary # to get help on the scantable's
354 ASAP> help average_time
355
356 """
357 print x
358 return
359
360print """Welcome to ASAP - the ATNF Single Dish Analysis Package
361This is a testing pre-release %s
362
363Please report any bugs to:
364Malte.Marquarding@csiro.au
365
366[IMPORTANT: ASAP is 0-based]
367Type commands() to get a list of all available ASAP commands.
368""" % (__version__)
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