| [100] | 1 | """
|
|---|
| 2 | This is the ATNF Single Dish Analysis package.
|
|---|
| 3 |
|
|---|
| 4 | """
|
|---|
| [226] | 5 | import os,sys
|
|---|
| 6 |
|
|---|
| [513] | 7 | def _validate_bool(b):
|
|---|
| [226] | 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 |
|
|---|
| [513] | 15 | def _validate_int(s):
|
|---|
| [226] | 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 |
|
|---|
| [513] | 21 | def _asap_fname():
|
|---|
| [226] | 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 |
|
|---|
| 51 | defaultParams = {
|
|---|
| 52 | # general
|
|---|
| [513] | 53 | 'verbose' : [True, _validate_bool],
|
|---|
| 54 | 'useplotter' : [True, _validate_bool],
|
|---|
| [542] | 55 | 'insitu' : [True, _validate_bool],
|
|---|
| [466] | 56 |
|
|---|
| [226] | 57 | # plotting
|
|---|
| 58 | 'plotter.stacking' : ['p', str],
|
|---|
| 59 | 'plotter.panelling' : ['s', str],
|
|---|
| [694] | 60 | 'plotter.colours' : ['', str],
|
|---|
| 61 | 'plotter.linestyles' : ['', str],
|
|---|
| 62 |
|
|---|
| [226] | 63 | # scantable
|
|---|
| 64 | 'scantable.save' : ['ASAP', str],
|
|---|
| [513] | 65 | 'scantable.autoaverage' : [True, _validate_bool],
|
|---|
| [226] | 66 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
|
|---|
| [513] | 67 | 'scantable.allaxes' : [True, _validate_bool], # apply action to all axes
|
|---|
| 68 | 'scantable.plotter' : [True, _validate_bool], # use internal plotter
|
|---|
| 69 | 'scantable.verbosesummary' : [False, _validate_bool]
|
|---|
| [226] | 70 |
|
|---|
| 71 | # fitter
|
|---|
| 72 | }
|
|---|
| 73 |
|
|---|
| [255] | 74 | def list_rcparameters():
|
|---|
| 75 |
|
|---|
| 76 | print """
|
|---|
| 77 | # general
|
|---|
| 78 | # print verbose output
|
|---|
| [466] | 79 | verbose : True
|
|---|
| [255] | 80 |
|
|---|
| 81 | # preload a default plotter
|
|---|
| [466] | 82 | useplotter : True
|
|---|
| [255] | 83 |
|
|---|
| 84 | # apply operations on the input scantable or return new one
|
|---|
| [542] | 85 | insitu : True
|
|---|
| [255] | 86 |
|
|---|
| 87 | # plotting
|
|---|
| 88 | # default mode for colour stacking
|
|---|
| [552] | 89 | plotter.stacking : Pol
|
|---|
| [255] | 90 |
|
|---|
| 91 | # default mode for panelling
|
|---|
| [552] | 92 | plotter.panelling : scan
|
|---|
| [255] | 93 |
|
|---|
| [694] | 94 | # default colours/linestyles
|
|---|
| 95 | plotter.colours :
|
|---|
| 96 | plotter.linestyles :
|
|---|
| 97 |
|
|---|
| [255] | 98 | # scantable
|
|---|
| 99 | # default ouput format when saving
|
|---|
| [552] | 100 | scantable.save : ASAP
|
|---|
| [255] | 101 | # auto averaging on read
|
|---|
| [466] | 102 | scantable.autoaverage : True
|
|---|
| [255] | 103 |
|
|---|
| 104 | # default frequency frame to set when function
|
|---|
| 105 | # scantable.set_freqfrmae is called
|
|---|
| [552] | 106 | scantable.freqframe : LSRK
|
|---|
| [255] | 107 |
|
|---|
| 108 | # apply action to all axes not just the cursor location
|
|---|
| [466] | 109 | scantable.allaxes : True
|
|---|
| [255] | 110 |
|
|---|
| 111 | # use internal plotter
|
|---|
| [466] | 112 | scantable.plotter : True
|
|---|
| [255] | 113 |
|
|---|
| [381] | 114 | # Control the level of information printed by summary
|
|---|
| [466] | 115 | scantable.verbosesummary : False
|
|---|
| [381] | 116 |
|
|---|
| [255] | 117 | # Fitter
|
|---|
| 118 | """
|
|---|
| 119 |
|
|---|
| [226] | 120 | def rc_params():
|
|---|
| 121 | 'Return the default params updated from the values in the rc file'
|
|---|
| 122 |
|
|---|
| [513] | 123 | fname = _asap_fname()
|
|---|
| [226] | 124 |
|
|---|
| 125 | if fname is None or not os.path.exists(fname):
|
|---|
| 126 | message = 'could not find rc file; returning defaults'
|
|---|
| 127 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
|
|---|
| 128 | #print message
|
|---|
| 129 | return ret
|
|---|
| 130 |
|
|---|
| 131 | cnt = 0
|
|---|
| 132 | for line in file(fname):
|
|---|
| 133 | cnt +=1
|
|---|
| 134 | line = line.strip()
|
|---|
| 135 | if not len(line): continue
|
|---|
| 136 | if line.startswith('#'): continue
|
|---|
| 137 | tup = line.split(':',1)
|
|---|
| 138 | if len(tup) !=2:
|
|---|
| 139 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
|
|---|
| 140 | continue
|
|---|
| 141 |
|
|---|
| 142 | key, val = tup
|
|---|
| 143 | key = key.strip()
|
|---|
| 144 | if not defaultParams.has_key(key):
|
|---|
| 145 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
|
|---|
| 146 | continue
|
|---|
| 147 |
|
|---|
| 148 | default, converter = defaultParams[key]
|
|---|
| 149 |
|
|---|
| 150 | ind = val.find('#')
|
|---|
| 151 | if ind>=0: val = val[:ind] # ignore trailing comments
|
|---|
| 152 | val = val.strip()
|
|---|
| 153 | try: cval = converter(val) # try to convert to proper type or raise
|
|---|
| 154 | except Exception, msg:
|
|---|
| 155 | print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
|
|---|
| 156 | continue
|
|---|
| 157 | else:
|
|---|
| 158 | # Alles Klar, update dict
|
|---|
| 159 | defaultParams[key][0] = cval
|
|---|
| 160 |
|
|---|
| 161 | # strip the conveter funcs and return
|
|---|
| 162 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
|
|---|
| [466] | 163 | print ('loaded rc file %s'%fname)
|
|---|
| [226] | 164 |
|
|---|
| 165 | return ret
|
|---|
| 166 |
|
|---|
| 167 |
|
|---|
| 168 | # this is the instance used by the asap classes
|
|---|
| 169 | rcParams = rc_params()
|
|---|
| 170 |
|
|---|
| 171 | rcParamsDefault = dict(rcParams.items()) # a copy
|
|---|
| 172 |
|
|---|
| 173 | def rc(group, **kwargs):
|
|---|
| 174 | """
|
|---|
| 175 | Set the current rc params. Group is the grouping for the rc, eg
|
|---|
| [379] | 176 | for scantable.save the group is 'scantable', for plotter.stacking, the
|
|---|
| 177 | group is 'plotter', and so on. kwargs is a list of attribute
|
|---|
| [226] | 178 | name/value pairs, eg
|
|---|
| 179 |
|
|---|
| [379] | 180 | rc('scantable', save='SDFITS')
|
|---|
| [226] | 181 |
|
|---|
| 182 | sets the current rc params and is equivalent to
|
|---|
| 183 |
|
|---|
| [379] | 184 | rcParams['scantable.save'] = 'SDFITS'
|
|---|
| [226] | 185 |
|
|---|
| 186 | Use rcdefaults to restore the default rc params after changes.
|
|---|
| 187 | """
|
|---|
| 188 |
|
|---|
| [379] | 189 | aliases = {}
|
|---|
| [226] | 190 |
|
|---|
| 191 | for k,v in kwargs.items():
|
|---|
| 192 | name = aliases.get(k) or k
|
|---|
| 193 | key = '%s.%s' % (group, name)
|
|---|
| 194 | if not rcParams.has_key(key):
|
|---|
| 195 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
|
|---|
| 196 |
|
|---|
| 197 | rcParams[key] = v
|
|---|
| 198 |
|
|---|
| 199 |
|
|---|
| 200 | def rcdefaults():
|
|---|
| 201 | """
|
|---|
| 202 | Restore the default rc params - the ones that were created at
|
|---|
| 203 | asap load time
|
|---|
| 204 | """
|
|---|
| 205 | rcParams.update(rcParamsDefault)
|
|---|
| 206 |
|
|---|
| [513] | 207 |
|
|---|
| 208 | def _is_sequence_or_number(param, ptype=int):
|
|---|
| 209 | if isinstance(param,tuple) or isinstance(param,list):
|
|---|
| 210 | out = True
|
|---|
| 211 | for p in param:
|
|---|
| 212 | out &= isinstance(p,ptype)
|
|---|
| 213 | return out
|
|---|
| 214 | elif isinstance(param, ptype):
|
|---|
| 215 | return True
|
|---|
| 216 | return False
|
|---|
| 217 |
|
|---|
| [113] | 218 | from asapfitter import *
|
|---|
| [100] | 219 | from asapreader import reader
|
|---|
| 220 | from asapmath import *
|
|---|
| 221 | from scantable import *
|
|---|
| [297] | 222 | from asaplinefind import *
|
|---|
| [530] | 223 | from asapfit import *
|
|---|
| [285] | 224 |
|
|---|
| [466] | 225 | from numarray import logical_and as mask_and
|
|---|
| 226 | from numarray import logical_or as mask_or
|
|---|
| 227 | from numarray import logical_not as mask_not
|
|---|
| 228 |
|
|---|
| [226] | 229 | if rcParams['useplotter']:
|
|---|
| [285] | 230 | if os.environ.has_key('DISPLAY'):
|
|---|
| [378] | 231 | print "Initialising asapplotter with the name 'plotter' ..."
|
|---|
| [285] | 232 | import asapplotter
|
|---|
| 233 | plotter = asapplotter.asapplotter()
|
|---|
| 234 | else:
|
|---|
| [378] | 235 | print "No $DISPLAY set. Disabling plotter.\n"
|
|---|
| [285] | 236 |
|
|---|
| [274] | 237 | #from numarray ones,zeros
|
|---|
| [100] | 238 |
|
|---|
| [378] | 239 |
|
|---|
| [574] | 240 | __date__ = '$Date: 2005-09-29 06:36:56 +0000 (Thu, 29 Sep 2005) $'.split()[1]
|
|---|
| [660] | 241 | __version__ = '1.1'
|
|---|
| [100] | 242 |
|
|---|
| 243 | def list_scans(t = scantable):
|
|---|
| 244 | import sys, types
|
|---|
| 245 | globs = sys.modules['__main__'].__dict__.iteritems()
|
|---|
| [113] | 246 | print "The user created scantables are:"
|
|---|
| [585] | 247 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
|
|---|
| 248 | print filter(lambda x: not x.startswith('_'), sts)
|
|---|
| [100] | 249 |
|
|---|
| [113] | 250 | def commands():
|
|---|
| [210] | 251 | x = """
|
|---|
| [113] | 252 | [The scan container]
|
|---|
| 253 | scantable - a container for integrations/scans
|
|---|
| [182] | 254 | (can open asap/rpfits/sdfits and ms files)
|
|---|
| [113] | 255 | copy - returns a copy of a scan
|
|---|
| 256 | get_scan - gets a specific scan out of a scantable
|
|---|
| 257 | summary - print info about the scantable contents
|
|---|
| [255] | 258 | set_cursor - set a specific Beam/IF/Pol 'cursor' for
|
|---|
| 259 | further use
|
|---|
| 260 | get_cursor - print out the current cursor position
|
|---|
| [182] | 261 | stats - get specified statistic of the spectra in
|
|---|
| 262 | the scantable
|
|---|
| 263 | stddev - get the standard deviation of the spectra
|
|---|
| 264 | in the scantable
|
|---|
| [113] | 265 | get_tsys - get the TSys
|
|---|
| 266 | get_time - get the timestamps of the integrations
|
|---|
| [255] | 267 | get_unit - get the currnt unit
|
|---|
| [513] | 268 | set_unit - set the abcissa unit to be used from this
|
|---|
| 269 | point on
|
|---|
| [255] | 270 | get_abcissa - get the abcissa values and name for a given
|
|---|
| 271 | row (time)
|
|---|
| [113] | 272 | set_freqframe - set the frame info for the Spectral Axis
|
|---|
| 273 | (e.g. 'LSRK')
|
|---|
| [276] | 274 | set_doppler - set the doppler to be used from this point on
|
|---|
| [240] | 275 | set_instrument - set the instrument name
|
|---|
| [255] | 276 | get_fluxunit - get the brightness flux unit
|
|---|
| [240] | 277 | set_fluxunit - set the brightness flux unit
|
|---|
| [188] | 278 | create_mask - return an mask in the current unit
|
|---|
| 279 | for the given region. The specified regions
|
|---|
| 280 | are NOT masked
|
|---|
| [255] | 281 | get_restfreqs - get the current list of rest frequencies
|
|---|
| 282 | set_restfreqs - set a list of rest frequencies
|
|---|
| [403] | 283 | lines - print list of known spectral lines
|
|---|
| [113] | 284 | flag_spectrum - flag a whole Beam/IF/Pol
|
|---|
| [116] | 285 | save - save the scantable to disk as either 'ASAP'
|
|---|
| 286 | or 'SDFITS'
|
|---|
| [486] | 287 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
|
|---|
| 288 | history - print the history of the scantable
|
|---|
| [530] | 289 | get_fit - get a fit which has been stored witnh the data
|
|---|
| [513] | 290 | average_time - return the (weighted) time average of a scan
|
|---|
| 291 | or a list of scans
|
|---|
| 292 | average_pol - average the polarisations together.
|
|---|
| [113] | 293 | The dimension won't be reduced and
|
|---|
| 294 | all polarisations will contain the
|
|---|
| 295 | averaged spectrum.
|
|---|
| [676] | 296 | auto_quotient - return the on/off quotient with
|
|---|
| 297 | automatic detection of the on/off scans
|
|---|
| [513] | 298 | quotient - return the on/off quotient
|
|---|
| 299 | scale - return a scan scaled by a given factor
|
|---|
| 300 | add - return a scan with given value added
|
|---|
| 301 | bin - return a scan with binned channels
|
|---|
| 302 | resample - return a scan with resampled channels
|
|---|
| 303 | smooth - return the spectrally smoothed scan
|
|---|
| 304 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
|
|---|
| [547] | 305 | auto_poly_baseline - automatically fit a polynomial baseline
|
|---|
| [513] | 306 | gain_el - apply gain-elevation correction
|
|---|
| 307 | opacity - apply opacity correction
|
|---|
| 308 | convert_flux - convert to and from Jy and Kelvin brightness
|
|---|
| [255] | 309 | units
|
|---|
| [513] | 310 | freq_align - align spectra in frequency frame
|
|---|
| 311 | rotate_xyphase - rotate XY phase of cross correlation
|
|---|
| 312 | rotate_linpolphase - rotate the phase of the complex
|
|---|
| 313 | polarization O=Q+iU correlation
|
|---|
| 314 | [Math] Mainly functions which operate on more than one scantable
|
|---|
| [100] | 315 |
|
|---|
| [513] | 316 | average_time - return the (weighted) time average
|
|---|
| 317 | of a list of scans
|
|---|
| 318 | quotient - return the on/off quotient
|
|---|
| 319 | simple_math - simple mathematical operations on two scantables,
|
|---|
| 320 | 'add', 'sub', 'mul', 'div'
|
|---|
| 321 | [Fitting]
|
|---|
| [113] | 322 | fitter
|
|---|
| 323 | auto_fit - return a scan where the function is
|
|---|
| 324 | applied to all Beams/IFs/Pols.
|
|---|
| 325 | commit - return a new scan where the fits have been
|
|---|
| 326 | commited.
|
|---|
| 327 | fit - execute the actual fitting process
|
|---|
| [530] | 328 | store_fit - store the fit paramaters in the data (scantable)
|
|---|
| [113] | 329 | get_chi2 - get the Chi^2
|
|---|
| 330 | set_scan - set the scantable to be fit
|
|---|
| 331 | set_function - set the fitting function
|
|---|
| 332 | set_parameters - set the parameters for the function(s), and
|
|---|
| 333 | set if they should be held fixed during fitting
|
|---|
| [513] | 334 | set_gauss_parameters - same as above but specialised for individual
|
|---|
| 335 | gaussian components
|
|---|
| [113] | 336 | get_parameters - get the fitted parameters
|
|---|
| [513] | 337 | plot - plot the resulting fit and/or components and
|
|---|
| 338 | residual
|
|---|
| [210] | 339 | [Plotter]
|
|---|
| 340 | asapplotter - a plotter for asap, default plotter is
|
|---|
| 341 | called 'plotter'
|
|---|
| 342 | plot - plot a (list of) scantable
|
|---|
| [378] | 343 | save - save the plot to a file ('png' ,'ps' or 'eps')
|
|---|
| [210] | 344 | set_mode - set the state of the plotter, i.e.
|
|---|
| 345 | what is to be plotted 'colour stacked'
|
|---|
| 346 | and what 'panelled'
|
|---|
| [530] | 347 | set_cursor - only plot a selected part of the data
|
|---|
| 348 | set_range - set a 'zoom' window
|
|---|
| [255] | 349 | set_legend - specify user labels for the legend indeces
|
|---|
| 350 | set_title - specify user labels for the panel indeces
|
|---|
| 351 | set_ordinate - specify a user label for the ordinate
|
|---|
| 352 | set_abcissa - specify a user label for the abcissa
|
|---|
| [378] | 353 | set_layout - specify the multi-panel layout (rows,cols)
|
|---|
| [210] | 354 |
|
|---|
| [182] | 355 | [Reading files]
|
|---|
| 356 | reader - access rpfits/sdfits files
|
|---|
| 357 | read - read in integrations
|
|---|
| 358 | summary - list info about all integrations
|
|---|
| 359 |
|
|---|
| [113] | 360 | [General]
|
|---|
| 361 | commands - this command
|
|---|
| 362 | print - print details about a variable
|
|---|
| 363 | list_scans - list all scantables created bt the user
|
|---|
| 364 | del - delete the given variable from memory
|
|---|
| 365 | range - create a list of values, e.g.
|
|---|
| 366 | range(3) = [0,1,2], range(2,5) = [2,3,4]
|
|---|
| 367 | help - print help for one of the listed functions
|
|---|
| 368 | execfile - execute an asap script, e.g. execfile('myscript')
|
|---|
| [255] | 369 | list_rcparameters - print out a list of possible values to be
|
|---|
| [274] | 370 | put into $HOME/.asaprc
|
|---|
| [466] | 371 | mask_and,mask_or,
|
|---|
| 372 | mask_not - boolean operations on masks created with
|
|---|
| 373 | scantable.create_mask
|
|---|
| 374 |
|
|---|
| [210] | 375 | Note:
|
|---|
| 376 | How to use this with help:
|
|---|
| 377 | # function 'summary'
|
|---|
| 378 | [xxx] is just a category
|
|---|
| 379 | Every 'sub-level' in this list should be replaces by a '.' Period when
|
|---|
| 380 | using help
|
|---|
| 381 | Example:
|
|---|
| 382 | ASAP> help scantable # to get info on ths scantable
|
|---|
| 383 | ASAP> help scantable.summary # to get help on the scantable's
|
|---|
| 384 | ASAP> help average_time
|
|---|
| 385 |
|
|---|
| [113] | 386 | """
|
|---|
| 387 | print x
|
|---|
| 388 | return
|
|---|
| 389 |
|
|---|
| [573] | 390 | print """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
|
|---|
| [100] | 391 |
|
|---|
| 392 | Please report any bugs to:
|
|---|
| [555] | 393 | asap@atnf.csiro.au
|
|---|
| [100] | 394 |
|
|---|
| [378] | 395 | [IMPORTANT: ASAP is 0-based]
|
|---|
| [113] | 396 | Type commands() to get a list of all available ASAP commands.
|
|---|
| [573] | 397 | """ % (__version__, __date__)
|
|---|
