source: trunk/python/__init__.py@ 439

Last change on this file since 439 was 425, checked in by kil064, 20 years ago

add rotate_xyphase
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File size: 12.8 KB
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[100]1"""
2This is the ATNF Single Dish Analysis package.
3
4"""
[226]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
[274]29 * HOME/.asaprc
[226]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],
[255]55 'insitu' : [False, validate_bool],
[226]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
[381]67 'scantable.verbosesummary' : [False, validate_bool]
[226]68
69 # fitter
70 }
71
[255]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
[381]108 # Control the level of information printed by summary
109 'scantable.verbosesummary' : False
110
[255]111 # Fitter
112 """
113
[226]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()])
[274]157 verbose.report('loaded rc file %s'%fname)
[226]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
[379]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
[226]172 name/value pairs, eg
173
[379]174 rc('scantable', save='SDFITS')
[226]175
176 sets the current rc params and is equivalent to
177
[379]178 rcParams['scantable.save'] = 'SDFITS'
[226]179
180 Use rcdefaults to restore the default rc params after changes.
181 """
182
[379]183 aliases = {}
[226]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
[113]201from asapfitter import *
[100]202from asapreader import reader
203from asapmath import *
204from scantable import *
[297]205from asaplinefind import *
[285]206
[226]207if rcParams['useplotter']:
[285]208 if os.environ.has_key('DISPLAY'):
[378]209 print "Initialising asapplotter with the name 'plotter' ..."
[285]210 import asapplotter
211 plotter = asapplotter.asapplotter()
212 else:
[378]213 print "No $DISPLAY set. Disabling plotter.\n"
[285]214
[274]215#from numarray ones,zeros
[100]216
[378]217
[100]218__date__ = '$Date: 2005-02-14 02:10:41 +0000 (Mon, 14 Feb 2005) $'
[278]219__version__ = '0.2'
[100]220
221def list_scans(t = scantable):
222 import sys, types
223 #meta_t = type(t)
224 #if meta_t == types.InstanceType:
225 # t = t.__class__
226 #elif meta_t not in [types.ClassType, types.TypeType]:
227 # t = meta_t
228 globs = sys.modules['__main__'].__dict__.iteritems()
[113]229 print "The user created scantables are:"
230 x = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
231 print x
[100]232
[113]233def commands():
[210]234 x = """
[113]235 [The scan container]
236 scantable - a container for integrations/scans
[182]237 (can open asap/rpfits/sdfits and ms files)
[113]238 copy - returns a copy of a scan
239 get_scan - gets a specific scan out of a scantable
240 summary - print info about the scantable contents
[255]241 set_cursor - set a specific Beam/IF/Pol 'cursor' for
242 further use
243 get_cursor - print out the current cursor position
[182]244 stats - get specified statistic of the spectra in
245 the scantable
246 stddev - get the standard deviation of the spectra
247 in the scantable
[113]248 get_tsys - get the TSys
249 get_time - get the timestamps of the integrations
[255]250 get_unit - get the currnt unit
[276]251 set_unit - set the abcissa unit to be used from this point on
[255]252 get_abcissa - get the abcissa values and name for a given
253 row (time)
[113]254 set_freqframe - set the frame info for the Spectral Axis
255 (e.g. 'LSRK')
[276]256 set_doppler - set the doppler to be used from this point on
[240]257 set_instrument - set the instrument name
[255]258 get_fluxunit - get the brightness flux unit
[240]259 set_fluxunit - set the brightness flux unit
[188]260 create_mask - return an mask in the current unit
261 for the given region. The specified regions
262 are NOT masked
[255]263 get_restfreqs - get the current list of rest frequencies
264 set_restfreqs - set a list of rest frequencies
[403]265 lines - print list of known spectral lines
[113]266 flag_spectrum - flag a whole Beam/IF/Pol
[116]267 save - save the scantable to disk as either 'ASAP'
268 or 'SDFITS'
[113]269 nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
270 [Math]
[142]271 average_time - return the (weighted) time average of a scan
272 or a list of scans
[128]273 average_pol - average the polarisations together.
[113]274 The dimension won't be reduced and
275 all polarisations will contain the
276 averaged spectrum.
277 quotient - return the on/off quotient
[255]278 simple_math - simple mathematical operations on two scantables,
279 'add', 'sub', 'mul', 'div'
[301]280 scale - return a scan scaled by a given factor
281 add - return a scan with given value added
[113]282 bin - return a scan with binned channels
[301]283 resample - return a scan with resampled channels
[179]284 smooth - return the spectrally smoothed scan
[113]285 poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
[240]286 gain_el - apply gain-elevation correction
287 opacity - apply opacity correction
[255]288 convert_flux - convert to and from Jy and Kelvin brightness
289 units
[425]290 rotate_xyphase - rotate XY phase of cross correlation
[100]291
[113]292 fitter
293 auto_fit - return a scan where the function is
294 applied to all Beams/IFs/Pols.
295 commit - return a new scan where the fits have been
296 commited.
297 fit - execute the actual fitting process
298 get_chi2 - get the Chi^2
299 set_scan - set the scantable to be fit
300 set_function - set the fitting function
301 set_parameters - set the parameters for the function(s), and
302 set if they should be held fixed during fitting
303 get_parameters - get the fitted parameters
[210]304 [Plotter]
305 asapplotter - a plotter for asap, default plotter is
306 called 'plotter'
307 plot - plot a (list of) scantable
[378]308 save - save the plot to a file ('png' ,'ps' or 'eps')
[210]309 set_mode - set the state of the plotter, i.e.
310 what is to be plotted 'colour stacked'
311 and what 'panelled'
312 set_range - set the abcissa 'zoom' range
[255]313 set_legend - specify user labels for the legend indeces
314 set_title - specify user labels for the panel indeces
315 set_ordinate - specify a user label for the ordinate
316 set_abcissa - specify a user label for the abcissa
[378]317 set_layout - specify the multi-panel layout (rows,cols)
[210]318
[182]319 [Reading files]
320 reader - access rpfits/sdfits files
321 read - read in integrations
322 summary - list info about all integrations
323
[113]324 [General]
325 commands - this command
326 print - print details about a variable
327 list_scans - list all scantables created bt the user
328 del - delete the given variable from memory
329 range - create a list of values, e.g.
330 range(3) = [0,1,2], range(2,5) = [2,3,4]
331 help - print help for one of the listed functions
332 execfile - execute an asap script, e.g. execfile('myscript')
[255]333 list_rcparameters - print out a list of possible values to be
[274]334 put into $HOME/.asaprc
[210]335 Note:
336 How to use this with help:
337 # function 'summary'
338 [xxx] is just a category
339 Every 'sub-level' in this list should be replaces by a '.' Period when
340 using help
341 Example:
342 ASAP> help scantable # to get info on ths scantable
343 ASAP> help scantable.summary # to get help on the scantable's
344 ASAP> help average_time
345
[113]346 """
347 print x
348 return
349
350print """Welcome to ASAP - the ATNF Single Dish Analysis Package
[378]351This is a testing pre-release %s
[100]352
353Please report any bugs to:
[128]354Malte.Marquarding@csiro.au
[100]355
[378]356[IMPORTANT: ASAP is 0-based]
[113]357Type commands() to get a list of all available ASAP commands.
[378]358""" % (__version__)
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