| 1 | """ |
|---|
| 2 | This is the ATNF Single Dish Analysis package. |
|---|
| 3 | |
|---|
| 4 | """ |
|---|
| 5 | import os,sys |
|---|
| 6 | |
|---|
| 7 | def _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 | |
|---|
| 15 | def _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 | |
|---|
| 21 | def _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 | |
|---|
| 51 | defaultParams = { |
|---|
| 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.plotter' : [True, _validate_bool], # use internal plotter |
|---|
| 71 | 'scantable.verbosesummary' : [False, _validate_bool] |
|---|
| 72 | |
|---|
| 73 | # fitter |
|---|
| 74 | } |
|---|
| 75 | |
|---|
| 76 | def list_rcparameters(): |
|---|
| 77 | |
|---|
| 78 | print """ |
|---|
| 79 | # general |
|---|
| 80 | # print verbose output |
|---|
| 81 | verbose : True |
|---|
| 82 | |
|---|
| 83 | # preload a default plotter |
|---|
| 84 | useplotter : True |
|---|
| 85 | |
|---|
| 86 | # apply operations on the input scantable or return new one |
|---|
| 87 | insitu : True |
|---|
| 88 | |
|---|
| 89 | # plotting |
|---|
| 90 | |
|---|
| 91 | # do we want a GUI or plot to a file |
|---|
| 92 | plotter.gui : True |
|---|
| 93 | |
|---|
| 94 | # default mode for colour stacking |
|---|
| 95 | plotter.stacking : Pol |
|---|
| 96 | |
|---|
| 97 | # default mode for panelling |
|---|
| 98 | plotter.panelling : scan |
|---|
| 99 | |
|---|
| 100 | # push panels together, to share axislabels |
|---|
| 101 | plotter.ganged : True |
|---|
| 102 | |
|---|
| 103 | # decimate the number of points plotted bya afactor of |
|---|
| 104 | # nchan/1024 |
|---|
| 105 | plotter.decimate : False |
|---|
| 106 | |
|---|
| 107 | # default colours/linestyles |
|---|
| 108 | plotter.colours : |
|---|
| 109 | plotter.linestyles : |
|---|
| 110 | |
|---|
| 111 | # scantable |
|---|
| 112 | # default ouput format when saving |
|---|
| 113 | scantable.save : ASAP |
|---|
| 114 | # auto averaging on read |
|---|
| 115 | scantable.autoaverage : True |
|---|
| 116 | |
|---|
| 117 | # default frequency frame to set when function |
|---|
| 118 | # scantable.set_freqfrmae is called |
|---|
| 119 | scantable.freqframe : LSRK |
|---|
| 120 | |
|---|
| 121 | # Control the level of information printed by summary |
|---|
| 122 | scantable.verbosesummary : False |
|---|
| 123 | |
|---|
| 124 | # Fitter |
|---|
| 125 | """ |
|---|
| 126 | |
|---|
| 127 | def rc_params(): |
|---|
| 128 | 'Return the default params updated from the values in the rc file' |
|---|
| 129 | |
|---|
| 130 | fname = _asap_fname() |
|---|
| 131 | |
|---|
| 132 | if fname is None or not os.path.exists(fname): |
|---|
| 133 | message = 'could not find rc file; returning defaults' |
|---|
| 134 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
|---|
| 135 | #print message |
|---|
| 136 | return ret |
|---|
| 137 | |
|---|
| 138 | cnt = 0 |
|---|
| 139 | for line in file(fname): |
|---|
| 140 | cnt +=1 |
|---|
| 141 | line = line.strip() |
|---|
| 142 | if not len(line): continue |
|---|
| 143 | if line.startswith('#'): continue |
|---|
| 144 | tup = line.split(':',1) |
|---|
| 145 | if len(tup) !=2: |
|---|
| 146 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
|---|
| 147 | continue |
|---|
| 148 | |
|---|
| 149 | key, val = tup |
|---|
| 150 | key = key.strip() |
|---|
| 151 | if not defaultParams.has_key(key): |
|---|
| 152 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
|---|
| 153 | continue |
|---|
| 154 | |
|---|
| 155 | default, converter = defaultParams[key] |
|---|
| 156 | |
|---|
| 157 | ind = val.find('#') |
|---|
| 158 | if ind>=0: val = val[:ind] # ignore trailing comments |
|---|
| 159 | val = val.strip() |
|---|
| 160 | try: cval = converter(val) # try to convert to proper type or raise |
|---|
| 161 | except Exception, msg: |
|---|
| 162 | print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg)) |
|---|
| 163 | continue |
|---|
| 164 | else: |
|---|
| 165 | # Alles Klar, update dict |
|---|
| 166 | defaultParams[key][0] = cval |
|---|
| 167 | |
|---|
| 168 | # strip the conveter funcs and return |
|---|
| 169 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
|---|
| 170 | print ('loaded rc file %s'%fname) |
|---|
| 171 | |
|---|
| 172 | return ret |
|---|
| 173 | |
|---|
| 174 | |
|---|
| 175 | # this is the instance used by the asap classes |
|---|
| 176 | rcParams = rc_params() |
|---|
| 177 | |
|---|
| 178 | rcParamsDefault = dict(rcParams.items()) # a copy |
|---|
| 179 | |
|---|
| 180 | def rc(group, **kwargs): |
|---|
| 181 | """ |
|---|
| 182 | Set the current rc params. Group is the grouping for the rc, eg |
|---|
| 183 | for scantable.save the group is 'scantable', for plotter.stacking, the |
|---|
| 184 | group is 'plotter', and so on. kwargs is a list of attribute |
|---|
| 185 | name/value pairs, eg |
|---|
| 186 | |
|---|
| 187 | rc('scantable', save='SDFITS') |
|---|
| 188 | |
|---|
| 189 | sets the current rc params and is equivalent to |
|---|
| 190 | |
|---|
| 191 | rcParams['scantable.save'] = 'SDFITS' |
|---|
| 192 | |
|---|
| 193 | Use rcdefaults to restore the default rc params after changes. |
|---|
| 194 | """ |
|---|
| 195 | |
|---|
| 196 | aliases = {} |
|---|
| 197 | |
|---|
| 198 | for k,v in kwargs.items(): |
|---|
| 199 | name = aliases.get(k) or k |
|---|
| 200 | key = '%s.%s' % (group, name) |
|---|
| 201 | if not rcParams.has_key(key): |
|---|
| 202 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
|---|
| 203 | |
|---|
| 204 | rcParams[key] = v |
|---|
| 205 | |
|---|
| 206 | |
|---|
| 207 | def rcdefaults(): |
|---|
| 208 | """ |
|---|
| 209 | Restore the default rc params - the ones that were created at |
|---|
| 210 | asap load time |
|---|
| 211 | """ |
|---|
| 212 | rcParams.update(rcParamsDefault) |
|---|
| 213 | |
|---|
| 214 | |
|---|
| 215 | def _is_sequence_or_number(param, ptype=int): |
|---|
| 216 | if isinstance(param,tuple) or isinstance(param,list): |
|---|
| 217 | out = True |
|---|
| 218 | for p in param: |
|---|
| 219 | out &= isinstance(p,ptype) |
|---|
| 220 | return out |
|---|
| 221 | elif isinstance(param, ptype): |
|---|
| 222 | return True |
|---|
| 223 | return False |
|---|
| 224 | |
|---|
| 225 | |
|---|
| 226 | # workaround for ipython, which redirects this if banner=0 in ipythonrc |
|---|
| 227 | sys.stdout = sys.__stdout__ |
|---|
| 228 | sys.stderr = sys.__stderr__ |
|---|
| 229 | |
|---|
| 230 | # Logging |
|---|
| 231 | from asap._asap import Log as _asaplog |
|---|
| 232 | global asaplog |
|---|
| 233 | asaplog=_asaplog() |
|---|
| 234 | if rcParams['verbose']: |
|---|
| 235 | asaplog.enable() |
|---|
| 236 | else: |
|---|
| 237 | asaplog.disable() |
|---|
| 238 | |
|---|
| 239 | def print_log(): |
|---|
| 240 | log = asaplog.pop() |
|---|
| 241 | if len(log) and rcParams['verbose']: print log |
|---|
| 242 | return |
|---|
| 243 | |
|---|
| 244 | from asapfitter import * |
|---|
| 245 | from asapreader import reader |
|---|
| 246 | |
|---|
| 247 | from asapmath import * |
|---|
| 248 | from scantable import * |
|---|
| 249 | from asaplinefind import * |
|---|
| 250 | #from asapfit import * |
|---|
| 251 | |
|---|
| 252 | from numarray import logical_and as mask_and |
|---|
| 253 | from numarray import logical_or as mask_or |
|---|
| 254 | from numarray import logical_not as mask_not |
|---|
| 255 | |
|---|
| 256 | # if rcParams['useplotter']: |
|---|
| 257 | # from asapplotter import * |
|---|
| 258 | # gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui'] |
|---|
| 259 | # plotter = asapplotter(gui) |
|---|
| 260 | # del gui |
|---|
| 261 | |
|---|
| 262 | __date__ = '$Date: 2006-03-08 03:29:58 +0000 (Wed, 08 Mar 2006) $'.split()[1] |
|---|
| 263 | __version__ = '2.0a' |
|---|
| 264 | |
|---|
| 265 | if rcParams['verbose']: |
|---|
| 266 | def list_scans(t = scantable): |
|---|
| 267 | import sys, types |
|---|
| 268 | globs = sys.modules['__main__'].__dict__.iteritems() |
|---|
| 269 | print "The user created scantables are:" |
|---|
| 270 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs)) |
|---|
| 271 | print filter(lambda x: not x.startswith('_'), sts) |
|---|
| 272 | return |
|---|
| 273 | |
|---|
| 274 | def commands(): |
|---|
| 275 | x = """ |
|---|
| 276 | [The scan container] |
|---|
| 277 | scantable - a container for integrations/scans |
|---|
| 278 | (can open asap/rpfits/sdfits and ms files) |
|---|
| 279 | copy - returns a copy of a scan |
|---|
| 280 | get_scan - gets a specific scan out of a scantable |
|---|
| 281 | (by name or number) [deprecated] |
|---|
| 282 | summary - print info about the scantable contents |
|---|
| 283 | stats - get specified statistic of the spectra in |
|---|
| 284 | the scantable |
|---|
| 285 | stddev - get the standard deviation of the spectra |
|---|
| 286 | in the scantable |
|---|
| 287 | get_tsys - get the TSys |
|---|
| 288 | get_time - get the timestamps of the integrations |
|---|
| 289 | get_sourcename - get the source names of the scans |
|---|
| 290 | get_azimuth - get the azimuth of the scans |
|---|
| 291 | get_elevation - get the elevation of the scans |
|---|
| 292 | get_parangle - get the parallactic angle of the scans |
|---|
| 293 | get_unit - get the current unit |
|---|
| 294 | set_unit - set the abcissa unit to be used from this |
|---|
| 295 | point on |
|---|
| 296 | get_abcissa - get the abcissa values and name for a given |
|---|
| 297 | row (time) |
|---|
| 298 | set_freqframe - set the frame info for the Spectral Axis |
|---|
| 299 | (e.g. 'LSRK') |
|---|
| 300 | set_doppler - set the doppler to be used from this point on |
|---|
| 301 | set_instrument - set the instrument name |
|---|
| 302 | get_fluxunit - get the brightness flux unit |
|---|
| 303 | set_fluxunit - set the brightness flux unit |
|---|
| 304 | create_mask - return an mask in the current unit |
|---|
| 305 | for the given region. The specified regions |
|---|
| 306 | are NOT masked |
|---|
| 307 | get_restfreqs - get the current list of rest frequencies |
|---|
| 308 | set_restfreqs - set a list of rest frequencies |
|---|
| 309 | lines - print list of known spectral lines |
|---|
| 310 | flag_spectrum - flag a whole Beam/IF/Pol |
|---|
| 311 | save - save the scantable to disk as either 'ASAP' |
|---|
| 312 | or 'SDFITS' |
|---|
| 313 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
|---|
| 314 | nscan - the number of scans in the scantable |
|---|
| 315 | nrow - te number of integrations in the scantable |
|---|
| 316 | history - print the history of the scantable |
|---|
| 317 | get_fit - get a fit which has been stored witnh the data |
|---|
| 318 | average_time - return the (weighted) time average of a scan |
|---|
| 319 | or a list of scans |
|---|
| 320 | average_pol - average the polarisations together. |
|---|
| 321 | The dimension won't be reduced and |
|---|
| 322 | all polarisations will contain the |
|---|
| 323 | averaged spectrum. |
|---|
| 324 | auto_quotient - return the on/off quotient with |
|---|
| 325 | automatic detection of the on/off scans |
|---|
| 326 | (matched pairs and 1 off - n on) |
|---|
| 327 | quotient - return the on/off quotient |
|---|
| 328 | scale - return a scan scaled by a given factor |
|---|
| 329 | add - return a scan with given value added |
|---|
| 330 | bin - return a scan with binned channels |
|---|
| 331 | resample - return a scan with resampled channels |
|---|
| 332 | smooth - return the spectrally smoothed scan |
|---|
| 333 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
|---|
| 334 | auto_poly_baseline - automatically fit a polynomial baseline |
|---|
| 335 | recalc_azel - recalculate azimuth and elevation based on |
|---|
| 336 | the pointing |
|---|
| 337 | gain_el - apply gain-elevation correction |
|---|
| 338 | opacity - apply opacity correction |
|---|
| 339 | convert_flux - convert to and from Jy and Kelvin brightness |
|---|
| 340 | units |
|---|
| 341 | freq_align - align spectra in frequency frame |
|---|
| 342 | rotate_xyphase - rotate XY phase of cross correlation |
|---|
| 343 | rotate_linpolphase - rotate the phase of the complex |
|---|
| 344 | polarization O=Q+iU correlation |
|---|
| 345 | freq_switch - perform frequency switching on the data |
|---|
| 346 | stats - Determine the specified statistic, e.g. 'min' |
|---|
| 347 | 'max', 'rms' etc. |
|---|
| 348 | stddev - Determine the standard deviation of the current |
|---|
| 349 | beam/if/pol |
|---|
| 350 | |
|---|
| 351 | [Math] Mainly functions which operate on more than one scantable |
|---|
| 352 | |
|---|
| 353 | average_time - return the (weighted) time average |
|---|
| 354 | of a list of scans |
|---|
| 355 | quotient - return the on/off quotient |
|---|
| 356 | simple_math - simple mathematical operations on two scantables, |
|---|
| 357 | 'add', 'sub', 'mul', 'div' |
|---|
| 358 | [Fitting] |
|---|
| 359 | fitter |
|---|
| 360 | auto_fit - return a scan where the function is |
|---|
| 361 | applied to all Beams/IFs/Pols. |
|---|
| 362 | commit - return a new scan where the fits have been |
|---|
| 363 | commited. |
|---|
| 364 | fit - execute the actual fitting process |
|---|
| 365 | store_fit - store the fit paramaters in the data (scantable) |
|---|
| 366 | get_chi2 - get the Chi^2 |
|---|
| 367 | set_scan - set the scantable to be fit |
|---|
| 368 | set_function - set the fitting function |
|---|
| 369 | set_parameters - set the parameters for the function(s), and |
|---|
| 370 | set if they should be held fixed during fitting |
|---|
| 371 | set_gauss_parameters - same as above but specialised for individual |
|---|
| 372 | gaussian components |
|---|
| 373 | get_parameters - get the fitted parameters |
|---|
| 374 | plot - plot the resulting fit and/or components and |
|---|
| 375 | residual |
|---|
| 376 | [Plotter] |
|---|
| 377 | asapplotter - a plotter for asap, default plotter is |
|---|
| 378 | called 'plotter' |
|---|
| 379 | plot - plot a (list of) scantable |
|---|
| 380 | save - save the plot to a file ('png' ,'ps' or 'eps') |
|---|
| 381 | set_mode - set the state of the plotter, i.e. |
|---|
| 382 | what is to be plotted 'colour stacked' |
|---|
| 383 | and what 'panelled' |
|---|
| 384 | set_cursor - only plot a selected part of the data |
|---|
| 385 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
|---|
| 386 | set_legend - specify user labels for the legend indeces |
|---|
| 387 | set_title - specify user labels for the panel indeces |
|---|
| 388 | set_abcissa - specify a user label for the abcissa |
|---|
| 389 | set_ordinate - specify a user label for the ordinate |
|---|
| 390 | set_layout - specify the multi-panel layout (rows,cols) |
|---|
| 391 | set_colors - specify a set of colours to use |
|---|
| 392 | set_linestyles - specify a set of linestyles to use if only |
|---|
| 393 | using one color |
|---|
| 394 | set_mask - set a plotting mask for a specific polarization |
|---|
| 395 | |
|---|
| 396 | [Reading files] |
|---|
| 397 | reader - access rpfits/sdfits files |
|---|
| 398 | read - read in integrations |
|---|
| 399 | summary - list info about all integrations |
|---|
| 400 | |
|---|
| 401 | [General] |
|---|
| 402 | commands - this command |
|---|
| 403 | print - print details about a variable |
|---|
| 404 | list_scans - list all scantables created bt the user |
|---|
| 405 | del - delete the given variable from memory |
|---|
| 406 | range - create a list of values, e.g. |
|---|
| 407 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
|---|
| 408 | help - print help for one of the listed functions |
|---|
| 409 | execfile - execute an asap script, e.g. execfile('myscript') |
|---|
| 410 | list_rcparameters - print out a list of possible values to be |
|---|
| 411 | put into $HOME/.asaprc |
|---|
| 412 | mask_and,mask_or, |
|---|
| 413 | mask_not - boolean operations on masks created with |
|---|
| 414 | scantable.create_mask |
|---|
| 415 | |
|---|
| 416 | Note: |
|---|
| 417 | How to use this with help: |
|---|
| 418 | # function 'summary' |
|---|
| 419 | [xxx] is just a category |
|---|
| 420 | Every 'sub-level' in this list should be replaces by a '.' Period when |
|---|
| 421 | using help |
|---|
| 422 | Example: |
|---|
| 423 | ASAP> help scantable # to get info on ths scantable |
|---|
| 424 | ASAP> help scantable.summary # to get help on the scantable's |
|---|
| 425 | ASAP> help average_time |
|---|
| 426 | |
|---|
| 427 | """ |
|---|
| 428 | print x |
|---|
| 429 | return |
|---|
| 430 | |
|---|
| 431 | def welcome(): |
|---|
| 432 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package |
|---|
| 433 | |
|---|
| 434 | Please report any bugs to: |
|---|
| 435 | asap@atnf.csiro.au |
|---|
| 436 | |
|---|
| 437 | [IMPORTANT: ASAP is 0-based] |
|---|
| 438 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__) |
|---|
