[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], |
---|
[466] | 60 | |
---|
[226] | 61 | # scantable |
---|
| 62 | 'scantable.save' : ['ASAP', str], |
---|
[513] | 63 | 'scantable.autoaverage' : [True, _validate_bool], |
---|
[226] | 64 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame |
---|
[513] | 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] |
---|
[226] | 68 | |
---|
| 69 | # fitter |
---|
| 70 | } |
---|
| 71 | |
---|
[255] | 72 | def list_rcparameters(): |
---|
| 73 | |
---|
| 74 | print """ |
---|
| 75 | # general |
---|
| 76 | # print verbose output |
---|
[466] | 77 | verbose : True |
---|
[255] | 78 | |
---|
| 79 | # preload a default plotter |
---|
[466] | 80 | useplotter : True |
---|
[255] | 81 | |
---|
| 82 | # apply operations on the input scantable or return new one |
---|
[542] | 83 | insitu : True |
---|
[255] | 84 | |
---|
| 85 | # plotting |
---|
| 86 | # default mode for colour stacking |
---|
[552] | 87 | plotter.stacking : Pol |
---|
[255] | 88 | |
---|
| 89 | # default mode for panelling |
---|
[552] | 90 | plotter.panelling : scan |
---|
[255] | 91 | |
---|
| 92 | # scantable |
---|
| 93 | # default ouput format when saving |
---|
[552] | 94 | scantable.save : ASAP |
---|
[255] | 95 | # auto averaging on read |
---|
[466] | 96 | scantable.autoaverage : True |
---|
[255] | 97 | |
---|
| 98 | # default frequency frame to set when function |
---|
| 99 | # scantable.set_freqfrmae is called |
---|
[552] | 100 | scantable.freqframe : LSRK |
---|
[255] | 101 | |
---|
| 102 | # apply action to all axes not just the cursor location |
---|
[466] | 103 | scantable.allaxes : True |
---|
[255] | 104 | |
---|
| 105 | # use internal plotter |
---|
[466] | 106 | scantable.plotter : True |
---|
[255] | 107 | |
---|
[381] | 108 | # Control the level of information printed by summary |
---|
[466] | 109 | scantable.verbosesummary : False |
---|
[381] | 110 | |
---|
[255] | 111 | # Fitter |
---|
| 112 | """ |
---|
| 113 | |
---|
[226] | 114 | def rc_params(): |
---|
| 115 | 'Return the default params updated from the values in the rc file' |
---|
| 116 | |
---|
[513] | 117 | fname = _asap_fname() |
---|
[226] | 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()]) |
---|
[466] | 157 | print ('loaded rc file %s'%fname) |
---|
[226] | 158 | |
---|
| 159 | return ret |
---|
| 160 | |
---|
| 161 | |
---|
| 162 | # this is the instance used by the asap classes |
---|
| 163 | rcParams = rc_params() |
---|
| 164 | |
---|
| 165 | rcParamsDefault = dict(rcParams.items()) # a copy |
---|
| 166 | |
---|
| 167 | def 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 | |
---|
| 194 | def rcdefaults(): |
---|
| 195 | """ |
---|
| 196 | Restore the default rc params - the ones that were created at |
---|
| 197 | asap load time |
---|
| 198 | """ |
---|
| 199 | rcParams.update(rcParamsDefault) |
---|
| 200 | |
---|
[513] | 201 | |
---|
| 202 | def _is_sequence_or_number(param, ptype=int): |
---|
| 203 | if isinstance(param,tuple) or isinstance(param,list): |
---|
| 204 | out = True |
---|
| 205 | for p in param: |
---|
| 206 | out &= isinstance(p,ptype) |
---|
| 207 | return out |
---|
| 208 | elif isinstance(param, ptype): |
---|
| 209 | return True |
---|
| 210 | return False |
---|
| 211 | |
---|
[113] | 212 | from asapfitter import * |
---|
[100] | 213 | from asapreader import reader |
---|
| 214 | from asapmath import * |
---|
| 215 | from scantable import * |
---|
[297] | 216 | from asaplinefind import * |
---|
[530] | 217 | from asapfit import * |
---|
[285] | 218 | |
---|
[466] | 219 | from numarray import logical_and as mask_and |
---|
| 220 | from numarray import logical_or as mask_or |
---|
| 221 | from numarray import logical_not as mask_not |
---|
| 222 | |
---|
[226] | 223 | if rcParams['useplotter']: |
---|
[285] | 224 | if os.environ.has_key('DISPLAY'): |
---|
[378] | 225 | print "Initialising asapplotter with the name 'plotter' ..." |
---|
[285] | 226 | import asapplotter |
---|
| 227 | plotter = asapplotter.asapplotter() |
---|
| 228 | else: |
---|
[378] | 229 | print "No $DISPLAY set. Disabling plotter.\n" |
---|
[285] | 230 | |
---|
[274] | 231 | #from numarray ones,zeros |
---|
[100] | 232 | |
---|
[378] | 233 | |
---|
[100] | 234 | __date__ = '$Date: 2005-05-09 05:06:54 +0000 (Mon, 09 May 2005) $' |
---|
[631] | 235 | __version__ = '1.0.1' |
---|
[100] | 236 | |
---|
| 237 | def list_scans(t = scantable): |
---|
| 238 | import sys, types |
---|
| 239 | #meta_t = type(t) |
---|
| 240 | #if meta_t == types.InstanceType: |
---|
| 241 | # t = t.__class__ |
---|
| 242 | #elif meta_t not in [types.ClassType, types.TypeType]: |
---|
| 243 | # t = meta_t |
---|
| 244 | globs = sys.modules['__main__'].__dict__.iteritems() |
---|
[113] | 245 | print "The user created scantables are:" |
---|
[583] | 246 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
---|
| 247 | print filter(lambda x: not x.startswith('_'), sts) |
---|
[100] | 248 | |
---|
[113] | 249 | def commands(): |
---|
[210] | 250 | x = """ |
---|
[113] | 251 | [The scan container] |
---|
| 252 | scantable - a container for integrations/scans |
---|
[182] | 253 | (can open asap/rpfits/sdfits and ms files) |
---|
[113] | 254 | copy - returns a copy of a scan |
---|
| 255 | get_scan - gets a specific scan out of a scantable |
---|
| 256 | summary - print info about the scantable contents |
---|
[255] | 257 | set_cursor - set a specific Beam/IF/Pol 'cursor' for |
---|
| 258 | further use |
---|
| 259 | get_cursor - print out the current cursor position |
---|
[182] | 260 | stats - get specified statistic of the spectra in |
---|
| 261 | the scantable |
---|
| 262 | stddev - get the standard deviation of the spectra |
---|
| 263 | in the scantable |
---|
[113] | 264 | get_tsys - get the TSys |
---|
| 265 | get_time - get the timestamps of the integrations |
---|
[255] | 266 | get_unit - get the currnt unit |
---|
[513] | 267 | set_unit - set the abcissa unit to be used from this |
---|
| 268 | point on |
---|
[255] | 269 | get_abcissa - get the abcissa values and name for a given |
---|
| 270 | row (time) |
---|
[113] | 271 | set_freqframe - set the frame info for the Spectral Axis |
---|
| 272 | (e.g. 'LSRK') |
---|
[276] | 273 | set_doppler - set the doppler to be used from this point on |
---|
[240] | 274 | set_instrument - set the instrument name |
---|
[255] | 275 | get_fluxunit - get the brightness flux unit |
---|
[240] | 276 | set_fluxunit - set the brightness flux unit |
---|
[188] | 277 | create_mask - return an mask in the current unit |
---|
| 278 | for the given region. The specified regions |
---|
| 279 | are NOT masked |
---|
[255] | 280 | get_restfreqs - get the current list of rest frequencies |
---|
| 281 | set_restfreqs - set a list of rest frequencies |
---|
[403] | 282 | lines - print list of known spectral lines |
---|
[113] | 283 | flag_spectrum - flag a whole Beam/IF/Pol |
---|
[116] | 284 | save - save the scantable to disk as either 'ASAP' |
---|
| 285 | or 'SDFITS' |
---|
[486] | 286 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
---|
| 287 | history - print the history of the scantable |
---|
[530] | 288 | get_fit - get a fit which has been stored witnh the data |
---|
[513] | 289 | average_time - return the (weighted) time average of a scan |
---|
| 290 | or a list of scans |
---|
| 291 | average_pol - average the polarisations together. |
---|
[113] | 292 | The dimension won't be reduced and |
---|
| 293 | all polarisations will contain the |
---|
| 294 | averaged spectrum. |
---|
[513] | 295 | quotient - return the on/off quotient |
---|
| 296 | scale - return a scan scaled by a given factor |
---|
| 297 | add - return a scan with given value added |
---|
| 298 | bin - return a scan with binned channels |
---|
| 299 | resample - return a scan with resampled channels |
---|
| 300 | smooth - return the spectrally smoothed scan |
---|
| 301 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
---|
[547] | 302 | auto_poly_baseline - automatically fit a polynomial baseline |
---|
[513] | 303 | gain_el - apply gain-elevation correction |
---|
| 304 | opacity - apply opacity correction |
---|
| 305 | convert_flux - convert to and from Jy and Kelvin brightness |
---|
[255] | 306 | units |
---|
[513] | 307 | freq_align - align spectra in frequency frame |
---|
| 308 | rotate_xyphase - rotate XY phase of cross correlation |
---|
| 309 | rotate_linpolphase - rotate the phase of the complex |
---|
| 310 | polarization O=Q+iU correlation |
---|
| 311 | [Math] Mainly functions which operate on more than one scantable |
---|
[100] | 312 | |
---|
[513] | 313 | average_time - return the (weighted) time average |
---|
| 314 | of a list of scans |
---|
| 315 | quotient - return the on/off quotient |
---|
| 316 | simple_math - simple mathematical operations on two scantables, |
---|
| 317 | 'add', 'sub', 'mul', 'div' |
---|
| 318 | [Fitting] |
---|
[113] | 319 | fitter |
---|
| 320 | auto_fit - return a scan where the function is |
---|
| 321 | applied to all Beams/IFs/Pols. |
---|
| 322 | commit - return a new scan where the fits have been |
---|
| 323 | commited. |
---|
| 324 | fit - execute the actual fitting process |
---|
[530] | 325 | store_fit - store the fit paramaters in the data (scantable) |
---|
[113] | 326 | get_chi2 - get the Chi^2 |
---|
| 327 | set_scan - set the scantable to be fit |
---|
| 328 | set_function - set the fitting function |
---|
| 329 | set_parameters - set the parameters for the function(s), and |
---|
| 330 | set if they should be held fixed during fitting |
---|
[513] | 331 | set_gauss_parameters - same as above but specialised for individual |
---|
| 332 | gaussian components |
---|
[113] | 333 | get_parameters - get the fitted parameters |
---|
[513] | 334 | plot - plot the resulting fit and/or components and |
---|
| 335 | residual |
---|
[210] | 336 | [Plotter] |
---|
| 337 | asapplotter - a plotter for asap, default plotter is |
---|
| 338 | called 'plotter' |
---|
| 339 | plot - plot a (list of) scantable |
---|
[378] | 340 | save - save the plot to a file ('png' ,'ps' or 'eps') |
---|
[210] | 341 | set_mode - set the state of the plotter, i.e. |
---|
| 342 | what is to be plotted 'colour stacked' |
---|
| 343 | and what 'panelled' |
---|
[530] | 344 | set_cursor - only plot a selected part of the data |
---|
| 345 | set_range - set a 'zoom' window |
---|
[255] | 346 | set_legend - specify user labels for the legend indeces |
---|
| 347 | set_title - specify user labels for the panel indeces |
---|
| 348 | set_ordinate - specify a user label for the ordinate |
---|
| 349 | set_abcissa - specify a user label for the abcissa |
---|
[378] | 350 | set_layout - specify the multi-panel layout (rows,cols) |
---|
[210] | 351 | |
---|
[182] | 352 | [Reading files] |
---|
| 353 | reader - access rpfits/sdfits files |
---|
| 354 | read - read in integrations |
---|
| 355 | summary - list info about all integrations |
---|
| 356 | |
---|
[113] | 357 | [General] |
---|
| 358 | commands - this command |
---|
| 359 | print - print details about a variable |
---|
| 360 | list_scans - list all scantables created bt the user |
---|
| 361 | del - delete the given variable from memory |
---|
| 362 | range - create a list of values, e.g. |
---|
| 363 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
---|
| 364 | help - print help for one of the listed functions |
---|
| 365 | execfile - execute an asap script, e.g. execfile('myscript') |
---|
[255] | 366 | list_rcparameters - print out a list of possible values to be |
---|
[274] | 367 | put into $HOME/.asaprc |
---|
[466] | 368 | mask_and,mask_or, |
---|
| 369 | mask_not - boolean operations on masks created with |
---|
| 370 | scantable.create_mask |
---|
| 371 | |
---|
[210] | 372 | Note: |
---|
| 373 | How to use this with help: |
---|
| 374 | # function 'summary' |
---|
| 375 | [xxx] is just a category |
---|
| 376 | Every 'sub-level' in this list should be replaces by a '.' Period when |
---|
| 377 | using help |
---|
| 378 | Example: |
---|
| 379 | ASAP> help scantable # to get info on ths scantable |
---|
| 380 | ASAP> help scantable.summary # to get help on the scantable's |
---|
| 381 | ASAP> help average_time |
---|
| 382 | |
---|
[113] | 383 | """ |
---|
| 384 | print x |
---|
| 385 | return |
---|
| 386 | |
---|
[559] | 387 | print """Welcome to ASAP v%s - the ATNF Spectral Analysis Package |
---|
[100] | 388 | |
---|
| 389 | Please report any bugs to: |
---|
[555] | 390 | asap@atnf.csiro.au |
---|
[100] | 391 | |
---|
[378] | 392 | [IMPORTANT: ASAP is 0-based] |
---|
[113] | 393 | Type commands() to get a list of all available ASAP commands. |
---|
[378] | 394 | """ % (__version__) |
---|