| 1 | """ |
|---|
| 2 | This is the ATNF Single Dish Analysis package. |
|---|
| 3 | |
|---|
| 4 | """ |
|---|
| 5 | import os,sys,shutil, platform |
|---|
| 6 | try: |
|---|
| 7 | from functools import wraps as wraps_dec |
|---|
| 8 | except ImportError: |
|---|
| 9 | from asap.compatibility import wraps as wraps_dec |
|---|
| 10 | |
|---|
| 11 | # Set up AIPSPATH and first time use of asap i.e. ~/.asap/* |
|---|
| 12 | plf = None |
|---|
| 13 | if sys.platform == "linux2": |
|---|
| 14 | if platform.architecture()[0] == '64bit': |
|---|
| 15 | plf = 'linux_64b' |
|---|
| 16 | else: |
|---|
| 17 | plf = 'linux_gnu' |
|---|
| 18 | elif sys.platform == 'darwin': |
|---|
| 19 | plf = 'darwin' |
|---|
| 20 | else: |
|---|
| 21 | # Shouldn't happen - default to linux |
|---|
| 22 | plf = 'linux' |
|---|
| 23 | asapdata = __path__[-1] |
|---|
| 24 | # Allow user defined data location |
|---|
| 25 | if os.environ.has_key("ASAPDATA"): |
|---|
| 26 | if os.path.exists(os.environ["ASAPDATA"]): |
|---|
| 27 | asapdata = os.environ["ASAPDATA"] |
|---|
| 28 | # use AIPSPATH if defined and "data" dir present |
|---|
| 29 | if not os.environ.has_key("AIPSPATH") or \ |
|---|
| 30 | not os.path.exists(os.environ["AIPSPATH"].split()[0]+"/data"): |
|---|
| 31 | os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf) |
|---|
| 32 | # set up user space |
|---|
| 33 | userdir = os.environ["HOME"]+"/.asap" |
|---|
| 34 | if not os.path.exists(userdir): |
|---|
| 35 | print 'First time ASAP use. Setting up ~/.asap' |
|---|
| 36 | os.mkdir(userdir) |
|---|
| 37 | shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap") |
|---|
| 38 | shutil.copyfile(asapdata+"/data/ipy_user_conf.py", |
|---|
| 39 | userdir+"/ipy_user_conf.py") |
|---|
| 40 | f = file(userdir+"/asapuserfuncs.py", "w") |
|---|
| 41 | f.close() |
|---|
| 42 | f = file(userdir+"/ipythonrc", "w") |
|---|
| 43 | f.close() |
|---|
| 44 | else: |
|---|
| 45 | # upgrade to support later ipython versions |
|---|
| 46 | if not os.path.exists(userdir+"/ipy_user_conf.py"): |
|---|
| 47 | shutil.copyfile(asapdata+"/data/ipy_user_conf.py", |
|---|
| 48 | userdir+"/ipy_user_conf.py") |
|---|
| 49 | |
|---|
| 50 | # remove from namespace |
|---|
| 51 | del asapdata, userdir, shutil, platform |
|---|
| 52 | |
|---|
| 53 | def _validate_bool(b): |
|---|
| 54 | 'Convert b to a boolean or raise' |
|---|
| 55 | bl = b.lower() |
|---|
| 56 | if bl in ('f', 'no', 'false', '0', 0): return False |
|---|
| 57 | elif bl in ('t', 'yes', 'true', '1', 1): return True |
|---|
| 58 | else: |
|---|
| 59 | raise ValueError('Could not convert "%s" to boolean' % b) |
|---|
| 60 | |
|---|
| 61 | def _validate_int(s): |
|---|
| 62 | 'convert s to int or raise' |
|---|
| 63 | try: return int(s) |
|---|
| 64 | except ValueError: |
|---|
| 65 | raise ValueError('Could not convert "%s" to int' % s) |
|---|
| 66 | |
|---|
| 67 | def _asap_fname(): |
|---|
| 68 | """ |
|---|
| 69 | Return the path to the rc file |
|---|
| 70 | |
|---|
| 71 | Search order: |
|---|
| 72 | |
|---|
| 73 | * current working dir |
|---|
| 74 | * environ var ASAPRC |
|---|
| 75 | * HOME/.asaprc |
|---|
| 76 | |
|---|
| 77 | """ |
|---|
| 78 | fname = os.path.join( os.getcwd(), '.asaprc') |
|---|
| 79 | if os.path.exists(fname): return fname |
|---|
| 80 | |
|---|
| 81 | if os.environ.has_key('ASAPRC'): |
|---|
| 82 | path = os.environ['ASAPRC'] |
|---|
| 83 | if os.path.exists(path): |
|---|
| 84 | fname = os.path.join(path, '.asaprc') |
|---|
| 85 | if os.path.exists(fname): |
|---|
| 86 | return fname |
|---|
| 87 | |
|---|
| 88 | if os.environ.has_key('HOME'): |
|---|
| 89 | home = os.environ['HOME'] |
|---|
| 90 | fname = os.path.join(home, '.asaprc') |
|---|
| 91 | if os.path.exists(fname): |
|---|
| 92 | return fname |
|---|
| 93 | return None |
|---|
| 94 | |
|---|
| 95 | |
|---|
| 96 | defaultParams = { |
|---|
| 97 | # general |
|---|
| 98 | 'verbose' : [True, _validate_bool], |
|---|
| 99 | 'useplotter' : [True, _validate_bool], |
|---|
| 100 | 'insitu' : [True, _validate_bool], |
|---|
| 101 | |
|---|
| 102 | # plotting |
|---|
| 103 | 'plotter.gui' : [True, _validate_bool], |
|---|
| 104 | 'plotter.stacking' : ['p', str], |
|---|
| 105 | 'plotter.panelling' : ['s', str], |
|---|
| 106 | 'plotter.colours' : ['', str], |
|---|
| 107 | 'plotter.linestyles' : ['', str], |
|---|
| 108 | 'plotter.decimate' : [False, _validate_bool], |
|---|
| 109 | 'plotter.ganged' : [True, _validate_bool], |
|---|
| 110 | 'plotter.histogram' : [False, _validate_bool], |
|---|
| 111 | 'plotter.papertype' : ['A4', str], |
|---|
| 112 | 'plotter.axesformatting' : ['mpl', str], |
|---|
| 113 | |
|---|
| 114 | # scantable |
|---|
| 115 | 'scantable.save' : ['ASAP', str], |
|---|
| 116 | 'scantable.autoaverage' : [True, _validate_bool], |
|---|
| 117 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame |
|---|
| 118 | 'scantable.verbosesummary' : [False, _validate_bool], |
|---|
| 119 | 'scantable.storage' : ['memory', str], |
|---|
| 120 | 'scantable.history' : [True, _validate_bool], |
|---|
| 121 | 'scantable.reference' : ['.*(e|w|_R)$', str], |
|---|
| 122 | 'scantable.parallactify' : [False, _validate_bool] |
|---|
| 123 | # fitter |
|---|
| 124 | } |
|---|
| 125 | |
|---|
| 126 | def list_rcparameters(): |
|---|
| 127 | |
|---|
| 128 | print """ |
|---|
| 129 | # general |
|---|
| 130 | # print verbose output |
|---|
| 131 | verbose : True |
|---|
| 132 | |
|---|
| 133 | # preload a default plotter |
|---|
| 134 | useplotter : True |
|---|
| 135 | |
|---|
| 136 | # apply operations on the input scantable or return new one |
|---|
| 137 | insitu : True |
|---|
| 138 | |
|---|
| 139 | # plotting |
|---|
| 140 | |
|---|
| 141 | # do we want a GUI or plot to a file |
|---|
| 142 | plotter.gui : True |
|---|
| 143 | |
|---|
| 144 | # default mode for colour stacking |
|---|
| 145 | plotter.stacking : Pol |
|---|
| 146 | |
|---|
| 147 | # default mode for panelling |
|---|
| 148 | plotter.panelling : scan |
|---|
| 149 | |
|---|
| 150 | # push panels together, to share axis labels |
|---|
| 151 | plotter.ganged : True |
|---|
| 152 | |
|---|
| 153 | # decimate the number of points plotted by a factor of |
|---|
| 154 | # nchan/1024 |
|---|
| 155 | plotter.decimate : False |
|---|
| 156 | |
|---|
| 157 | # default colours/linestyles |
|---|
| 158 | plotter.colours : |
|---|
| 159 | plotter.linestyles : |
|---|
| 160 | |
|---|
| 161 | # enable/disable histogram plotting |
|---|
| 162 | plotter.histogram : False |
|---|
| 163 | |
|---|
| 164 | # ps paper type |
|---|
| 165 | plotter.papertype : A4 |
|---|
| 166 | |
|---|
| 167 | # The formatting style of the xaxis |
|---|
| 168 | plotter.axesformatting : 'mpl' (default) or 'asap' (for old versions of matplotlib) |
|---|
| 169 | |
|---|
| 170 | # scantable |
|---|
| 171 | |
|---|
| 172 | # default storage of scantable ('memory'/'disk') |
|---|
| 173 | scantable.storage : memory |
|---|
| 174 | |
|---|
| 175 | # write history of each call to scantable |
|---|
| 176 | scantable.history : True |
|---|
| 177 | |
|---|
| 178 | # default ouput format when saving |
|---|
| 179 | scantable.save : ASAP |
|---|
| 180 | |
|---|
| 181 | # auto averaging on read |
|---|
| 182 | scantable.autoaverage : True |
|---|
| 183 | |
|---|
| 184 | # default frequency frame to set when function |
|---|
| 185 | # scantable.set_freqframe is called |
|---|
| 186 | scantable.freqframe : LSRK |
|---|
| 187 | |
|---|
| 188 | # Control the level of information printed by summary |
|---|
| 189 | scantable.verbosesummary : False |
|---|
| 190 | |
|---|
| 191 | # Control the identification of reference (off) scans |
|---|
| 192 | # This is has to be a regular expression |
|---|
| 193 | scantable.reference : .*(e|w|_R)$ |
|---|
| 194 | |
|---|
| 195 | # Indicate whether the data was parallactified (total phase offest == 0.0) |
|---|
| 196 | scantable.parallactify : False |
|---|
| 197 | |
|---|
| 198 | # Fitter |
|---|
| 199 | """ |
|---|
| 200 | |
|---|
| 201 | def rc_params(): |
|---|
| 202 | 'Return the default params updated from the values in the rc file' |
|---|
| 203 | |
|---|
| 204 | fname = _asap_fname() |
|---|
| 205 | |
|---|
| 206 | if fname is None or not os.path.exists(fname): |
|---|
| 207 | message = 'could not find rc file; returning defaults' |
|---|
| 208 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
|---|
| 209 | #print message |
|---|
| 210 | return ret |
|---|
| 211 | |
|---|
| 212 | cnt = 0 |
|---|
| 213 | for line in file(fname): |
|---|
| 214 | cnt +=1 |
|---|
| 215 | line = line.strip() |
|---|
| 216 | if not len(line): continue |
|---|
| 217 | if line.startswith('#'): continue |
|---|
| 218 | tup = line.split(':',1) |
|---|
| 219 | if len(tup) !=2: |
|---|
| 220 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
|---|
| 221 | continue |
|---|
| 222 | |
|---|
| 223 | key, val = tup |
|---|
| 224 | key = key.strip() |
|---|
| 225 | if not defaultParams.has_key(key): |
|---|
| 226 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
|---|
| 227 | continue |
|---|
| 228 | |
|---|
| 229 | default, converter = defaultParams[key] |
|---|
| 230 | |
|---|
| 231 | ind = val.find('#') |
|---|
| 232 | if ind>=0: val = val[:ind] # ignore trailing comments |
|---|
| 233 | val = val.strip() |
|---|
| 234 | try: cval = converter(val) # try to convert to proper type or raise |
|---|
| 235 | except ValueError, msg: |
|---|
| 236 | print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg)) |
|---|
| 237 | continue |
|---|
| 238 | else: |
|---|
| 239 | # Alles Klar, update dict |
|---|
| 240 | defaultParams[key][0] = cval |
|---|
| 241 | |
|---|
| 242 | # strip the conveter funcs and return |
|---|
| 243 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
|---|
| 244 | print ('loaded rc file %s'%fname) |
|---|
| 245 | |
|---|
| 246 | return ret |
|---|
| 247 | |
|---|
| 248 | |
|---|
| 249 | # this is the instance used by the asap classes |
|---|
| 250 | rcParams = rc_params() |
|---|
| 251 | |
|---|
| 252 | rcParamsDefault = dict(rcParams.items()) # a copy |
|---|
| 253 | |
|---|
| 254 | def rc(group, **kwargs): |
|---|
| 255 | """ |
|---|
| 256 | Set the current rc params. Group is the grouping for the rc, eg |
|---|
| 257 | for scantable.save the group is 'scantable', for plotter.stacking, the |
|---|
| 258 | group is 'plotter', and so on. kwargs is a list of attribute |
|---|
| 259 | name/value pairs, eg |
|---|
| 260 | |
|---|
| 261 | rc('scantable', save='SDFITS') |
|---|
| 262 | |
|---|
| 263 | sets the current rc params and is equivalent to |
|---|
| 264 | |
|---|
| 265 | rcParams['scantable.save'] = 'SDFITS' |
|---|
| 266 | |
|---|
| 267 | Use rcdefaults to restore the default rc params after changes. |
|---|
| 268 | """ |
|---|
| 269 | |
|---|
| 270 | aliases = {} |
|---|
| 271 | |
|---|
| 272 | for k,v in kwargs.items(): |
|---|
| 273 | name = aliases.get(k) or k |
|---|
| 274 | if len(group): |
|---|
| 275 | key = '%s.%s' % (group, name) |
|---|
| 276 | else: |
|---|
| 277 | key = name |
|---|
| 278 | if not rcParams.has_key(key): |
|---|
| 279 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
|---|
| 280 | |
|---|
| 281 | rcParams[key] = v |
|---|
| 282 | |
|---|
| 283 | |
|---|
| 284 | def rcdefaults(): |
|---|
| 285 | """ |
|---|
| 286 | Restore the default rc params - the ones that were created at |
|---|
| 287 | asap load time |
|---|
| 288 | """ |
|---|
| 289 | rcParams.update(rcParamsDefault) |
|---|
| 290 | |
|---|
| 291 | def _n_bools(n, val): |
|---|
| 292 | return [ val for i in xrange(n) ] |
|---|
| 293 | |
|---|
| 294 | def _is_sequence_or_number(param, ptype=int): |
|---|
| 295 | if isinstance(param,tuple) or isinstance(param,list): |
|---|
| 296 | if len(param) == 0: return True # empty list |
|---|
| 297 | out = True |
|---|
| 298 | for p in param: |
|---|
| 299 | out &= isinstance(p,ptype) |
|---|
| 300 | return out |
|---|
| 301 | elif isinstance(param, ptype): |
|---|
| 302 | return True |
|---|
| 303 | return False |
|---|
| 304 | |
|---|
| 305 | def _to_list(param, ptype=int): |
|---|
| 306 | if isinstance(param, ptype): |
|---|
| 307 | if ptype is str: return param.split() |
|---|
| 308 | else: return [param] |
|---|
| 309 | if _is_sequence_or_number(param, ptype): |
|---|
| 310 | return param |
|---|
| 311 | return None |
|---|
| 312 | |
|---|
| 313 | def unique(x): |
|---|
| 314 | """ |
|---|
| 315 | Return the unique values in a list |
|---|
| 316 | Parameters: |
|---|
| 317 | x: the list to reduce |
|---|
| 318 | Examples: |
|---|
| 319 | x = [1,2,3,3,4] |
|---|
| 320 | print unique(x) |
|---|
| 321 | [1,2,3,4] |
|---|
| 322 | """ |
|---|
| 323 | return dict([ (val, 1) for val in x]).keys() |
|---|
| 324 | |
|---|
| 325 | def list_files(path=".",suffix="rpf"): |
|---|
| 326 | """ |
|---|
| 327 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap |
|---|
| 328 | Parameters: |
|---|
| 329 | path: The directory to list (default '.') |
|---|
| 330 | suffix: The file extension (default rpf) |
|---|
| 331 | Example: |
|---|
| 332 | files = list_files("data/","sdfits") |
|---|
| 333 | print files |
|---|
| 334 | ['data/2001-09-01_0332_P363.sdfits', |
|---|
| 335 | 'data/2003-04-04_131152_t0002.sdfits', |
|---|
| 336 | 'data/Sgr_86p262_best_SPC.sdfits'] |
|---|
| 337 | """ |
|---|
| 338 | if not os.path.isdir(path): |
|---|
| 339 | return None |
|---|
| 340 | valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split() |
|---|
| 341 | if not suffix in valid: |
|---|
| 342 | return None |
|---|
| 343 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)] |
|---|
| 344 | return filter(lambda x: x.endswith(suffix),files) |
|---|
| 345 | |
|---|
| 346 | # workaround for ipython, which redirects this if banner=0 in ipythonrc |
|---|
| 347 | sys.stdout = sys.__stdout__ |
|---|
| 348 | sys.stderr = sys.__stderr__ |
|---|
| 349 | |
|---|
| 350 | # Logging |
|---|
| 351 | from asap._asap import Log as _asaplog |
|---|
| 352 | global asaplog |
|---|
| 353 | asaplog=_asaplog() |
|---|
| 354 | if rcParams['verbose']: |
|---|
| 355 | asaplog.enable() |
|---|
| 356 | else: |
|---|
| 357 | asaplog.disable() |
|---|
| 358 | |
|---|
| 359 | |
|---|
| 360 | def print_log_dec(f): |
|---|
| 361 | @wraps_dec(f) |
|---|
| 362 | def wrap_it(*args, **kw): |
|---|
| 363 | val = f(*args, **kw) |
|---|
| 364 | print_log() |
|---|
| 365 | return val |
|---|
| 366 | return wrap_it |
|---|
| 367 | |
|---|
| 368 | def print_log(): |
|---|
| 369 | log = asaplog.pop().strip() |
|---|
| 370 | if len(log) and rcParams['verbose']: print log |
|---|
| 371 | return |
|---|
| 372 | |
|---|
| 373 | def mask_and(a, b): |
|---|
| 374 | assert(len(a)==len(b)) |
|---|
| 375 | return [ a[i] & b[i] for i in xrange(len(a)) ] |
|---|
| 376 | |
|---|
| 377 | def mask_or(a, b): |
|---|
| 378 | assert(len(a)==len(b)) |
|---|
| 379 | return [ a[i] | b[i] for i in xrange(len(a)) ] |
|---|
| 380 | |
|---|
| 381 | def mask_not(a): |
|---|
| 382 | return [ not i for i in a ] |
|---|
| 383 | |
|---|
| 384 | from asapfitter import fitter |
|---|
| 385 | from asapreader import reader |
|---|
| 386 | from selector import selector |
|---|
| 387 | |
|---|
| 388 | from asapmath import * |
|---|
| 389 | from scantable import scantable |
|---|
| 390 | from asaplinefind import linefinder |
|---|
| 391 | from simplelinefinder import simplelinefinder |
|---|
| 392 | from linecatalog import linecatalog |
|---|
| 393 | from opacity import skydip |
|---|
| 394 | from opacity import model as opacity_model |
|---|
| 395 | |
|---|
| 396 | if rcParams['useplotter']: |
|---|
| 397 | try: |
|---|
| 398 | from asapplotter import asapplotter |
|---|
| 399 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui'] |
|---|
| 400 | if gui: |
|---|
| 401 | import matplotlib |
|---|
| 402 | matplotlib.use("TkAgg") |
|---|
| 403 | from matplotlib import pylab |
|---|
| 404 | xyplotter = pylab |
|---|
| 405 | plotter = asapplotter(gui) |
|---|
| 406 | del gui |
|---|
| 407 | except ImportError: |
|---|
| 408 | print "Matplotlib not installed. No plotting available" |
|---|
| 409 | |
|---|
| 410 | __date__ = '$Date: 2010-05-04 02:42:40 +0000 (Tue, 04 May 2010) $'.split()[1] |
|---|
| 411 | __version__ = '$Revision: 1739 $' |
|---|
| 412 | |
|---|
| 413 | def is_ipython(): |
|---|
| 414 | return 'IPython' in sys.modules.keys() |
|---|
| 415 | |
|---|
| 416 | if is_ipython(): |
|---|
| 417 | def version(): print "ASAP %s(%s)"% (__version__, __date__) |
|---|
| 418 | |
|---|
| 419 | def list_scans(t = scantable): |
|---|
| 420 | import inspect |
|---|
| 421 | print "The user created scantables are: ", |
|---|
| 422 | globs=inspect.currentframe().f_back.f_locals.copy() |
|---|
| 423 | out = [ k for k,v in globs.iteritems() \ |
|---|
| 424 | if isinstance(v, scantable) and not k.startswith("_") ] |
|---|
| 425 | print out |
|---|
| 426 | return out |
|---|
| 427 | |
|---|
| 428 | def commands(): |
|---|
| 429 | x = """ |
|---|
| 430 | [The scan container] |
|---|
| 431 | scantable - a container for integrations/scans |
|---|
| 432 | (can open asap/rpfits/sdfits and ms files) |
|---|
| 433 | copy - returns a copy of a scan |
|---|
| 434 | get_scan - gets a specific scan out of a scantable |
|---|
| 435 | (by name or number) |
|---|
| 436 | drop_scan - drops a specific scan out of a scantable |
|---|
| 437 | (by number) |
|---|
| 438 | set_selection - set a new subselection of the data |
|---|
| 439 | get_selection - get the current selection object |
|---|
| 440 | summary - print info about the scantable contents |
|---|
| 441 | stats - get specified statistic of the spectra in |
|---|
| 442 | the scantable |
|---|
| 443 | stddev - get the standard deviation of the spectra |
|---|
| 444 | in the scantable |
|---|
| 445 | get_tsys - get the TSys |
|---|
| 446 | get_time - get the timestamps of the integrations |
|---|
| 447 | get_inttime - get the integration time |
|---|
| 448 | get_sourcename - get the source names of the scans |
|---|
| 449 | get_azimuth - get the azimuth of the scans |
|---|
| 450 | get_elevation - get the elevation of the scans |
|---|
| 451 | get_parangle - get the parallactic angle of the scans |
|---|
| 452 | get_coordinate - get the spectral coordinate for the given row, |
|---|
| 453 | which can be used for coordinate conversions |
|---|
| 454 | get_weather - get the weather condition parameters |
|---|
| 455 | get_unit - get the current unit |
|---|
| 456 | set_unit - set the abcissa unit to be used from this |
|---|
| 457 | point on |
|---|
| 458 | get_abcissa - get the abcissa values and name for a given |
|---|
| 459 | row (time) |
|---|
| 460 | get_column_names - get the names of the columns in the scantable |
|---|
| 461 | for use with selector.set_query |
|---|
| 462 | set_freqframe - set the frame info for the Spectral Axis |
|---|
| 463 | (e.g. 'LSRK') |
|---|
| 464 | set_doppler - set the doppler to be used from this point on |
|---|
| 465 | set_dirframe - set the frame for the direction on the sky |
|---|
| 466 | set_instrument - set the instrument name |
|---|
| 467 | set_feedtype - set the feed type |
|---|
| 468 | get_fluxunit - get the brightness flux unit |
|---|
| 469 | set_fluxunit - set the brightness flux unit |
|---|
| 470 | set_sourcetype - set the type of the source - source or reference |
|---|
| 471 | create_mask - return an mask in the current unit |
|---|
| 472 | for the given region. The specified regions |
|---|
| 473 | are NOT masked |
|---|
| 474 | get_restfreqs - get the current list of rest frequencies |
|---|
| 475 | set_restfreqs - set a list of rest frequencies |
|---|
| 476 | shift_refpix - shift the reference pixel of the IFs |
|---|
| 477 | set_spectrum - overwrite the spectrum for a given row |
|---|
| 478 | get_spectrum - retrieve the spectrum for a given |
|---|
| 479 | get_mask - retrieve the mask for a given |
|---|
| 480 | flag - flag selected channels in the data |
|---|
| 481 | lag_flag - flag specified frequency in the data |
|---|
| 482 | save - save the scantable to disk as either 'ASAP', |
|---|
| 483 | 'SDFITS' or 'ASCII' |
|---|
| 484 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
|---|
| 485 | nscan - the number of scans in the scantable |
|---|
| 486 | nrow - the number of spectra in the scantable |
|---|
| 487 | history - print the history of the scantable |
|---|
| 488 | get_fit - get a fit which has been stored witnh the data |
|---|
| 489 | average_time - return the (weighted) time average of a scan |
|---|
| 490 | or a list of scans |
|---|
| 491 | average_pol - average the polarisations together. |
|---|
| 492 | average_beam - average the beams together. |
|---|
| 493 | convert_pol - convert to a different polarisation type |
|---|
| 494 | auto_quotient - return the on/off quotient with |
|---|
| 495 | automatic detection of the on/off scans (closest |
|---|
| 496 | in time off is selected) |
|---|
| 497 | mx_quotient - Form a quotient using MX data (off beams) |
|---|
| 498 | scale, *, / - return a scan scaled by a given factor |
|---|
| 499 | add, + - return a scan with given value added |
|---|
| 500 | sub, - - return a scan with given value subtracted |
|---|
| 501 | bin - return a scan with binned channels |
|---|
| 502 | resample - return a scan with resampled channels |
|---|
| 503 | smooth - return the spectrally smoothed scan |
|---|
| 504 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
|---|
| 505 | auto_poly_baseline - automatically fit a polynomial baseline |
|---|
| 506 | recalc_azel - recalculate azimuth and elevation based on |
|---|
| 507 | the pointing |
|---|
| 508 | gain_el - apply gain-elevation correction |
|---|
| 509 | opacity - apply opacity correction |
|---|
| 510 | convert_flux - convert to and from Jy and Kelvin brightness |
|---|
| 511 | units |
|---|
| 512 | freq_align - align spectra in frequency frame |
|---|
| 513 | invert_phase - Invert the phase of the cross-correlation |
|---|
| 514 | swap_linears - Swap XX and YY (or RR LL) |
|---|
| 515 | rotate_xyphase - rotate XY phase of cross correlation |
|---|
| 516 | rotate_linpolphase - rotate the phase of the complex |
|---|
| 517 | polarization O=Q+iU correlation |
|---|
| 518 | freq_switch - perform frequency switching on the data |
|---|
| 519 | stats - Determine the specified statistic, e.g. 'min' |
|---|
| 520 | 'max', 'rms' etc. |
|---|
| 521 | stddev - Determine the standard deviation of the current |
|---|
| 522 | beam/if/pol |
|---|
| 523 | get_row_selector - get the selection object for a specified row |
|---|
| 524 | number |
|---|
| 525 | [Selection] |
|---|
| 526 | selector - a selection object to set a subset of a scantable |
|---|
| 527 | set_scans - set (a list of) scans by index |
|---|
| 528 | set_cycles - set (a list of) cycles by index |
|---|
| 529 | set_beams - set (a list of) beamss by index |
|---|
| 530 | set_ifs - set (a list of) ifs by index |
|---|
| 531 | set_polarisations - set (a list of) polarisations by name |
|---|
| 532 | or by index |
|---|
| 533 | set_names - set a selection by name (wildcards allowed) |
|---|
| 534 | set_tsys - set a selection by tsys thresholds |
|---|
| 535 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1 |
|---|
| 536 | ( also get_ functions for all these ) |
|---|
| 537 | reset - unset all selections |
|---|
| 538 | + - merge two selections |
|---|
| 539 | |
|---|
| 540 | [Math] Mainly functions which operate on more than one scantable |
|---|
| 541 | |
|---|
| 542 | average_time - return the (weighted) time average |
|---|
| 543 | of a list of scans |
|---|
| 544 | quotient - return the on/off quotient |
|---|
| 545 | simple_math - simple mathematical operations on two scantables, |
|---|
| 546 | 'add', 'sub', 'mul', 'div' |
|---|
| 547 | quotient - build quotient of the given on and off scans |
|---|
| 548 | (matched pairs and 1 off - n on are valid) |
|---|
| 549 | merge - merge a list of scantables |
|---|
| 550 | |
|---|
| 551 | [Line Catalog] |
|---|
| 552 | linecatalog - a linecatalog wrapper, taking an ASCII or |
|---|
| 553 | internal format table |
|---|
| 554 | summary - print a summary of the current selection |
|---|
| 555 | set_name - select a subset by name pattern, e.g. '*OH*' |
|---|
| 556 | set_strength_limits - select a subset by line strength limits |
|---|
| 557 | set_frequency_limits - select a subset by frequency limits |
|---|
| 558 | reset - unset all selections |
|---|
| 559 | save - save the current subset to a table (internal |
|---|
| 560 | format) |
|---|
| 561 | get_row - get the name and frequency from a specific |
|---|
| 562 | row in the table |
|---|
| 563 | [Fitting] |
|---|
| 564 | fitter |
|---|
| 565 | auto_fit - return a scan where the function is |
|---|
| 566 | applied to all Beams/IFs/Pols. |
|---|
| 567 | commit - return a new scan where the fits have been |
|---|
| 568 | commited. |
|---|
| 569 | fit - execute the actual fitting process |
|---|
| 570 | store_fit - store the fit parameters in the data (scantable) |
|---|
| 571 | get_chi2 - get the Chi^2 |
|---|
| 572 | set_scan - set the scantable to be fit |
|---|
| 573 | set_function - set the fitting function |
|---|
| 574 | set_parameters - set the parameters for the function(s), and |
|---|
| 575 | set if they should be held fixed during fitting |
|---|
| 576 | set_gauss_parameters - same as above but specialised for individual |
|---|
| 577 | gaussian components |
|---|
| 578 | get_parameters - get the fitted parameters |
|---|
| 579 | plot - plot the resulting fit and/or components and |
|---|
| 580 | residual |
|---|
| 581 | [Plotter] |
|---|
| 582 | asapplotter - a plotter for asap, default plotter is |
|---|
| 583 | called 'plotter' |
|---|
| 584 | plot - plot a scantable |
|---|
| 585 | plot_lines - plot a linecatalog overlay |
|---|
| 586 | plotazel - plot azimuth and elevation versus time |
|---|
| 587 | plotpointing - plot telescope pointings |
|---|
| 588 | save - save the plot to a file ('png' ,'ps' or 'eps') |
|---|
| 589 | set_mode - set the state of the plotter, i.e. |
|---|
| 590 | what is to be plotted 'colour stacked' |
|---|
| 591 | and what 'panelled' |
|---|
| 592 | set_selection - only plot a selected part of the data |
|---|
| 593 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
|---|
| 594 | set_legend - specify user labels for the legend indeces |
|---|
| 595 | set_title - specify user labels for the panel indeces |
|---|
| 596 | set_abcissa - specify a user label for the abcissa |
|---|
| 597 | set_ordinate - specify a user label for the ordinate |
|---|
| 598 | set_layout - specify the multi-panel layout (rows,cols) |
|---|
| 599 | set_colors - specify a set of colours to use |
|---|
| 600 | set_linestyles - specify a set of linestyles to use if only |
|---|
| 601 | using one color |
|---|
| 602 | set_font - set general font properties, e.g. 'family' |
|---|
| 603 | set_histogram - plot in historam style |
|---|
| 604 | set_mask - set a plotting mask for a specific polarization |
|---|
| 605 | text - draw text annotations either in data or relative |
|---|
| 606 | coordinates |
|---|
| 607 | arrow - draw arrow annotations either in data or relative |
|---|
| 608 | coordinates |
|---|
| 609 | axhline,axvline - draw horizontal/vertical lines |
|---|
| 610 | axhspan,axvspan - draw horizontal/vertical regions |
|---|
| 611 | annotate - draw an arrow with label |
|---|
| 612 | create_mask - create a scnatble mask interactively |
|---|
| 613 | |
|---|
| 614 | xyplotter - matplotlib/pylab plotting functions |
|---|
| 615 | |
|---|
| 616 | [General] |
|---|
| 617 | commands - this command |
|---|
| 618 | print - print details about a variable |
|---|
| 619 | list_scans - list all scantables created by the user |
|---|
| 620 | list_files - list all files readable by asap (default rpf) |
|---|
| 621 | del - delete the given variable from memory |
|---|
| 622 | range - create a list of values, e.g. |
|---|
| 623 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
|---|
| 624 | help - print help for one of the listed functions |
|---|
| 625 | execfile - execute an asap script, e.g. execfile('myscript') |
|---|
| 626 | list_rcparameters - print out a list of possible values to be |
|---|
| 627 | put into $HOME/.asaprc |
|---|
| 628 | rc - set rc parameters from within asap |
|---|
| 629 | mask_and,mask_or, |
|---|
| 630 | mask_not - boolean operations on masks created with |
|---|
| 631 | scantable.create_mask |
|---|
| 632 | skydip - gain opacity values from a sky dip observation |
|---|
| 633 | opacity_model - compute opacities fro given frequencies based on |
|---|
| 634 | atmospheric model |
|---|
| 635 | |
|---|
| 636 | Note: |
|---|
| 637 | How to use this with help: |
|---|
| 638 | # function 'summary' |
|---|
| 639 | [xxx] is just a category |
|---|
| 640 | Every 'sub-level' in this list should be replaces by a '.' Period when |
|---|
| 641 | using help |
|---|
| 642 | Example: |
|---|
| 643 | ASAP> help scantable # to get info on ths scantable |
|---|
| 644 | ASAP> help scantable.summary # to get help on the scantable's |
|---|
| 645 | ASAP> help average_time |
|---|
| 646 | |
|---|
| 647 | """ |
|---|
| 648 | if rcParams['verbose']: |
|---|
| 649 | try: |
|---|
| 650 | from IPython.genutils import page as pager |
|---|
| 651 | except ImportError: |
|---|
| 652 | from pydoc import pager |
|---|
| 653 | pager(x) |
|---|
| 654 | else: |
|---|
| 655 | print x |
|---|
| 656 | return |
|---|
| 657 | |
|---|
| 658 | def welcome(): |
|---|
| 659 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package |
|---|
| 660 | |
|---|
| 661 | Please report any bugs via: |
|---|
| 662 | http://svn.atnf.csiro.au/trac/asap/simpleticket |
|---|
| 663 | |
|---|
| 664 | [IMPORTANT: ASAP is 0-based] |
|---|
| 665 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__) |
|---|
