[100] | 1 | """
|
---|
| 2 | This is the ATNF Single Dish Analysis package.
|
---|
| 3 |
|
---|
| 4 | """
|
---|
[1080] | 5 | import os,sys,shutil, platform
|
---|
[226] | 6 |
|
---|
[1080] | 7 | # Set up AIPSPATH and first time use of asap i.e. ~/.asap/*
|
---|
| 8 | plf = None
|
---|
| 9 | if sys.platform == "linux2":
|
---|
| 10 | if platform.architecture()[0] == '64bit':
|
---|
| 11 | plf = 'linux_64b'
|
---|
| 12 | else:
|
---|
| 13 | plf = 'linux_gnu'
|
---|
| 14 | elif sys.platform == 'darwin':
|
---|
| 15 | plf = 'darwin'
|
---|
| 16 | else:
|
---|
| 17 | # Shouldn't happen - default to linux
|
---|
| 18 | plf = 'linux'
|
---|
| 19 | asapdata = __path__[-1]
|
---|
[1171] | 20 | # Allow user defined data location
|
---|
| 21 | if os.environ.has_key("ASAPDATA"):
|
---|
| 22 | if os.path.exists(os.environ["ASAPDATA"]):
|
---|
| 23 | asapdata = os.environ["ASAPDATA"]
|
---|
[1080] | 24 | os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
|
---|
[1171] | 25 | # set up user space
|
---|
[1080] | 26 | userdir = os.environ["HOME"]+"/.asap"
|
---|
| 27 | if not os.path.exists(userdir):
|
---|
| 28 | print 'First time ASAP use. Setting up ~/.asap'
|
---|
| 29 | os.mkdir(userdir)
|
---|
| 30 | shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap")
|
---|
| 31 | f = file(userdir+"/asapuserfuncs.py", "w")
|
---|
| 32 | f.close()
|
---|
| 33 | f = file(userdir+"/ipythonrc", "w")
|
---|
| 34 | f.close()
|
---|
[1171] | 35 | # remove from namespace
|
---|
[1080] | 36 | del asapdata, userdir, shutil, platform
|
---|
| 37 |
|
---|
[513] | 38 | def _validate_bool(b):
|
---|
[226] | 39 | 'Convert b to a boolean or raise'
|
---|
| 40 | bl = b.lower()
|
---|
| 41 | if bl in ('f', 'no', 'false', '0', 0): return False
|
---|
| 42 | elif bl in ('t', 'yes', 'true', '1', 1): return True
|
---|
| 43 | else:
|
---|
| 44 | raise ValueError('Could not convert "%s" to boolean' % b)
|
---|
| 45 |
|
---|
[513] | 46 | def _validate_int(s):
|
---|
[226] | 47 | 'convert s to int or raise'
|
---|
| 48 | try: return int(s)
|
---|
| 49 | except ValueError:
|
---|
| 50 | raise ValueError('Could not convert "%s" to int' % s)
|
---|
| 51 |
|
---|
[513] | 52 | def _asap_fname():
|
---|
[226] | 53 | """
|
---|
| 54 | Return the path to the rc file
|
---|
| 55 |
|
---|
| 56 | Search order:
|
---|
| 57 |
|
---|
| 58 | * current working dir
|
---|
| 59 | * environ var ASAPRC
|
---|
[274] | 60 | * HOME/.asaprc
|
---|
[706] | 61 |
|
---|
[226] | 62 | """
|
---|
| 63 |
|
---|
| 64 | fname = os.path.join( os.getcwd(), '.asaprc')
|
---|
| 65 | if os.path.exists(fname): return fname
|
---|
| 66 |
|
---|
| 67 | if os.environ.has_key('ASAPRC'):
|
---|
| 68 | path = os.environ['ASAPRC']
|
---|
| 69 | if os.path.exists(path):
|
---|
| 70 | fname = os.path.join(path, '.asaprc')
|
---|
| 71 | if os.path.exists(fname):
|
---|
| 72 | return fname
|
---|
| 73 |
|
---|
| 74 | if os.environ.has_key('HOME'):
|
---|
| 75 | home = os.environ['HOME']
|
---|
| 76 | fname = os.path.join(home, '.asaprc')
|
---|
| 77 | if os.path.exists(fname):
|
---|
| 78 | return fname
|
---|
| 79 | return None
|
---|
| 80 |
|
---|
[706] | 81 |
|
---|
[226] | 82 | defaultParams = {
|
---|
| 83 | # general
|
---|
[513] | 84 | 'verbose' : [True, _validate_bool],
|
---|
| 85 | 'useplotter' : [True, _validate_bool],
|
---|
[542] | 86 | 'insitu' : [True, _validate_bool],
|
---|
[706] | 87 |
|
---|
[226] | 88 | # plotting
|
---|
[706] | 89 | 'plotter.gui' : [True, _validate_bool],
|
---|
[226] | 90 | 'plotter.stacking' : ['p', str],
|
---|
| 91 | 'plotter.panelling' : ['s', str],
|
---|
[700] | 92 | 'plotter.colours' : ['', str],
|
---|
| 93 | 'plotter.linestyles' : ['', str],
|
---|
[710] | 94 | 'plotter.decimate' : [False, _validate_bool],
|
---|
| 95 | 'plotter.ganged' : [True, _validate_bool],
|
---|
[1022] | 96 | 'plotter.histogram' : [False, _validate_bool],
|
---|
[1097] | 97 | 'plotter.papertype' : ['A4', str],
|
---|
[710] | 98 |
|
---|
[226] | 99 | # scantable
|
---|
| 100 | 'scantable.save' : ['ASAP', str],
|
---|
[513] | 101 | 'scantable.autoaverage' : [True, _validate_bool],
|
---|
[226] | 102 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
|
---|
[1076] | 103 | 'scantable.verbosesummary' : [False, _validate_bool],
|
---|
| 104 | 'scantable.storage' : ['memory', str]
|
---|
[226] | 105 | # fitter
|
---|
| 106 | }
|
---|
| 107 |
|
---|
[255] | 108 | def list_rcparameters():
|
---|
[706] | 109 |
|
---|
[255] | 110 | print """
|
---|
[737] | 111 | # general
|
---|
| 112 | # print verbose output
|
---|
| 113 | verbose : True
|
---|
[255] | 114 |
|
---|
[737] | 115 | # preload a default plotter
|
---|
| 116 | useplotter : True
|
---|
[255] | 117 |
|
---|
[737] | 118 | # apply operations on the input scantable or return new one
|
---|
| 119 | insitu : True
|
---|
[706] | 120 |
|
---|
[737] | 121 | # plotting
|
---|
[710] | 122 |
|
---|
[737] | 123 | # do we want a GUI or plot to a file
|
---|
| 124 | plotter.gui : True
|
---|
[710] | 125 |
|
---|
[737] | 126 | # default mode for colour stacking
|
---|
| 127 | plotter.stacking : Pol
|
---|
[255] | 128 |
|
---|
[737] | 129 | # default mode for panelling
|
---|
| 130 | plotter.panelling : scan
|
---|
[255] | 131 |
|
---|
[737] | 132 | # push panels together, to share axislabels
|
---|
| 133 | plotter.ganged : True
|
---|
[710] | 134 |
|
---|
[737] | 135 | # decimate the number of points plotted bya afactor of
|
---|
| 136 | # nchan/1024
|
---|
| 137 | plotter.decimate : False
|
---|
[733] | 138 |
|
---|
[737] | 139 | # default colours/linestyles
|
---|
| 140 | plotter.colours :
|
---|
| 141 | plotter.linestyles :
|
---|
[700] | 142 |
|
---|
[1022] | 143 | # enable/disable histogram plotting
|
---|
| 144 | plotter.histogram : False
|
---|
| 145 |
|
---|
[1097] | 146 | # ps paper type
|
---|
| 147 | plotter.papertype : A4
|
---|
| 148 |
|
---|
[737] | 149 | # scantable
|
---|
[1076] | 150 |
|
---|
[1259] | 151 | # default storage of scantable ('memory'/'disk')
|
---|
[1076] | 152 | scantable.storage : memory
|
---|
[737] | 153 | # default ouput format when saving
|
---|
| 154 | scantable.save : ASAP
|
---|
| 155 | # auto averaging on read
|
---|
| 156 | scantable.autoaverage : True
|
---|
[255] | 157 |
|
---|
[737] | 158 | # default frequency frame to set when function
|
---|
[1097] | 159 | # scantable.set_freqframe is called
|
---|
[737] | 160 | scantable.freqframe : LSRK
|
---|
[255] | 161 |
|
---|
[737] | 162 | # Control the level of information printed by summary
|
---|
| 163 | scantable.verbosesummary : False
|
---|
[706] | 164 |
|
---|
[737] | 165 | # Fitter
|
---|
| 166 | """
|
---|
[706] | 167 |
|
---|
[226] | 168 | def rc_params():
|
---|
| 169 | 'Return the default params updated from the values in the rc file'
|
---|
[706] | 170 |
|
---|
[513] | 171 | fname = _asap_fname()
|
---|
[706] | 172 |
|
---|
[226] | 173 | if fname is None or not os.path.exists(fname):
|
---|
| 174 | message = 'could not find rc file; returning defaults'
|
---|
| 175 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
|
---|
| 176 | #print message
|
---|
| 177 | return ret
|
---|
[706] | 178 |
|
---|
[226] | 179 | cnt = 0
|
---|
| 180 | for line in file(fname):
|
---|
| 181 | cnt +=1
|
---|
| 182 | line = line.strip()
|
---|
| 183 | if not len(line): continue
|
---|
| 184 | if line.startswith('#'): continue
|
---|
| 185 | tup = line.split(':',1)
|
---|
| 186 | if len(tup) !=2:
|
---|
| 187 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
|
---|
| 188 | continue
|
---|
[706] | 189 |
|
---|
[226] | 190 | key, val = tup
|
---|
| 191 | key = key.strip()
|
---|
| 192 | if not defaultParams.has_key(key):
|
---|
| 193 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
|
---|
| 194 | continue
|
---|
[706] | 195 |
|
---|
[226] | 196 | default, converter = defaultParams[key]
|
---|
| 197 |
|
---|
| 198 | ind = val.find('#')
|
---|
| 199 | if ind>=0: val = val[:ind] # ignore trailing comments
|
---|
| 200 | val = val.strip()
|
---|
| 201 | try: cval = converter(val) # try to convert to proper type or raise
|
---|
[1080] | 202 | except ValueError, msg:
|
---|
[226] | 203 | print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
|
---|
| 204 | continue
|
---|
| 205 | else:
|
---|
| 206 | # Alles Klar, update dict
|
---|
| 207 | defaultParams[key][0] = cval
|
---|
| 208 |
|
---|
| 209 | # strip the conveter funcs and return
|
---|
| 210 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
|
---|
[466] | 211 | print ('loaded rc file %s'%fname)
|
---|
[226] | 212 |
|
---|
| 213 | return ret
|
---|
| 214 |
|
---|
| 215 |
|
---|
| 216 | # this is the instance used by the asap classes
|
---|
[706] | 217 | rcParams = rc_params()
|
---|
[226] | 218 |
|
---|
| 219 | rcParamsDefault = dict(rcParams.items()) # a copy
|
---|
| 220 |
|
---|
| 221 | def rc(group, **kwargs):
|
---|
| 222 | """
|
---|
| 223 | Set the current rc params. Group is the grouping for the rc, eg
|
---|
[379] | 224 | for scantable.save the group is 'scantable', for plotter.stacking, the
|
---|
| 225 | group is 'plotter', and so on. kwargs is a list of attribute
|
---|
[226] | 226 | name/value pairs, eg
|
---|
| 227 |
|
---|
[379] | 228 | rc('scantable', save='SDFITS')
|
---|
[226] | 229 |
|
---|
| 230 | sets the current rc params and is equivalent to
|
---|
[706] | 231 |
|
---|
[379] | 232 | rcParams['scantable.save'] = 'SDFITS'
|
---|
[226] | 233 |
|
---|
| 234 | Use rcdefaults to restore the default rc params after changes.
|
---|
| 235 | """
|
---|
| 236 |
|
---|
[379] | 237 | aliases = {}
|
---|
[706] | 238 |
|
---|
[226] | 239 | for k,v in kwargs.items():
|
---|
| 240 | name = aliases.get(k) or k
|
---|
| 241 | key = '%s.%s' % (group, name)
|
---|
| 242 | if not rcParams.has_key(key):
|
---|
| 243 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
|
---|
[706] | 244 |
|
---|
[226] | 245 | rcParams[key] = v
|
---|
| 246 |
|
---|
| 247 |
|
---|
| 248 | def rcdefaults():
|
---|
| 249 | """
|
---|
| 250 | Restore the default rc params - the ones that were created at
|
---|
| 251 | asap load time
|
---|
| 252 | """
|
---|
| 253 | rcParams.update(rcParamsDefault)
|
---|
| 254 |
|
---|
[1295] | 255 | def _n_bools(n, val):
|
---|
| 256 | return [ val for i in xrange(n) ]
|
---|
[513] | 257 |
|
---|
| 258 | def _is_sequence_or_number(param, ptype=int):
|
---|
| 259 | if isinstance(param,tuple) or isinstance(param,list):
|
---|
[928] | 260 | if len(param) == 0: return True # empty list
|
---|
[513] | 261 | out = True
|
---|
| 262 | for p in param:
|
---|
| 263 | out &= isinstance(p,ptype)
|
---|
| 264 | return out
|
---|
| 265 | elif isinstance(param, ptype):
|
---|
| 266 | return True
|
---|
| 267 | return False
|
---|
| 268 |
|
---|
[928] | 269 | def _to_list(param, ptype=int):
|
---|
| 270 | if isinstance(param, ptype):
|
---|
| 271 | if ptype is str: return param.split()
|
---|
| 272 | else: return [param]
|
---|
| 273 | if _is_sequence_or_number(param, ptype):
|
---|
| 274 | return param
|
---|
| 275 | return None
|
---|
[715] | 276 |
|
---|
[944] | 277 | def unique(x):
|
---|
[992] | 278 | """
|
---|
| 279 | Return the unique values in a list
|
---|
| 280 | Parameters:
|
---|
| 281 | x: the list to reduce
|
---|
| 282 | Examples:
|
---|
| 283 | x = [1,2,3,3,4]
|
---|
| 284 | print unique(x)
|
---|
| 285 | [1,2,3,4]
|
---|
| 286 | """
|
---|
[944] | 287 | return dict([ (val, 1) for val in x]).keys()
|
---|
| 288 |
|
---|
[992] | 289 | def list_files(path=".",suffix="rpf"):
|
---|
| 290 | """
|
---|
| 291 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap
|
---|
| 292 | Parameters:
|
---|
| 293 | path: The directory to list (default '.')
|
---|
| 294 | suffix: The file extension (default rpf)
|
---|
| 295 | Example:
|
---|
| 296 | files = list_files("data/","sdfits")
|
---|
| 297 | print files
|
---|
| 298 | ['data/2001-09-01_0332_P363.sdfits',
|
---|
| 299 | 'data/2003-04-04_131152_t0002.sdfits',
|
---|
| 300 | 'data/Sgr_86p262_best_SPC.sdfits']
|
---|
| 301 | """
|
---|
| 302 | if not os.path.isdir(path):
|
---|
| 303 | return None
|
---|
[1295] | 304 | valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
|
---|
[992] | 305 | if not suffix in valid:
|
---|
| 306 | return None
|
---|
| 307 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
|
---|
| 308 | return filter(lambda x: x.endswith(suffix),files)
|
---|
| 309 |
|
---|
[715] | 310 | # workaround for ipython, which redirects this if banner=0 in ipythonrc
|
---|
| 311 | sys.stdout = sys.__stdout__
|
---|
| 312 | sys.stderr = sys.__stderr__
|
---|
| 313 |
|
---|
| 314 | # Logging
|
---|
| 315 | from asap._asap import Log as _asaplog
|
---|
| 316 | global asaplog
|
---|
[710] | 317 | asaplog=_asaplog()
|
---|
[715] | 318 | if rcParams['verbose']:
|
---|
| 319 | asaplog.enable()
|
---|
| 320 | else:
|
---|
| 321 | asaplog.disable()
|
---|
| 322 |
|
---|
| 323 | def print_log():
|
---|
| 324 | log = asaplog.pop()
|
---|
| 325 | if len(log) and rcParams['verbose']: print log
|
---|
| 326 | return
|
---|
| 327 |
|
---|
[1295] | 328 | def mask_and(a, b):
|
---|
| 329 | assert(len(a)==len(b))
|
---|
| 330 | return [ a[i] & b[i] for i in xrange(len(a)) ]
|
---|
[1134] | 331 |
|
---|
[1295] | 332 | def mask_or(a, b):
|
---|
| 333 | assert(len(a)==len(b))
|
---|
| 334 | return [ a[i] | b[i] for i in xrange(len(a)) ]
|
---|
| 335 |
|
---|
| 336 | def mask_not(a):
|
---|
| 337 | return [ not i for i in a ]
|
---|
| 338 |
|
---|
[1117] | 339 | from asapfitter import fitter
|
---|
[895] | 340 | from asapreader import reader
|
---|
[944] | 341 | from selector import selector
|
---|
[710] | 342 |
|
---|
[100] | 343 | from asapmath import *
|
---|
[1080] | 344 | from scantable import scantable
|
---|
[1097] | 345 | from asaplinefind import linefinder
|
---|
[1134] | 346 | from linecatalog import linecatalog
|
---|
[285] | 347 |
|
---|
[928] | 348 | if rcParams['useplotter']:
|
---|
[1295] | 349 | try:
|
---|
| 350 | from asapplotter import asapplotter
|
---|
| 351 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
|
---|
| 352 | if gui:
|
---|
| 353 | import pylab as xyplotter
|
---|
| 354 | plotter = asapplotter(gui)
|
---|
| 355 | del gui
|
---|
| 356 | except ImportError:
|
---|
| 357 | print "Matplotlib not installed. No plotting available"
|
---|
[285] | 358 |
|
---|
[574] | 359 | __date__ = '$Date: 2006-11-29 01:02:15 +0000 (Wed, 29 Nov 2006) $'.split()[1]
|
---|
[1305] | 360 | __version__ = '2.1.1'
|
---|
[100] | 361 |
|
---|
[1193] | 362 | def is_ipython():
|
---|
[1259] | 363 | return '__IP' in dir(sys.modules["__main__"])
|
---|
[1193] | 364 | if is_ipython():
|
---|
[1014] | 365 | def version(): print "ASAP %s(%s)"% (__version__, __date__)
|
---|
[706] | 366 | def list_scans(t = scantable):
|
---|
[1295] | 367 | import types
|
---|
[706] | 368 | globs = sys.modules['__main__'].__dict__.iteritems()
|
---|
| 369 | print "The user created scantables are:"
|
---|
| 370 | sts = map(lambda x: x[0], filter(lambda x: isinstance(x[1], t), globs))
|
---|
| 371 | print filter(lambda x: not x.startswith('_'), sts)
|
---|
| 372 | return
|
---|
[100] | 373 |
|
---|
[715] | 374 | def commands():
|
---|
| 375 | x = """
|
---|
[113] | 376 | [The scan container]
|
---|
| 377 | scantable - a container for integrations/scans
|
---|
[182] | 378 | (can open asap/rpfits/sdfits and ms files)
|
---|
[113] | 379 | copy - returns a copy of a scan
|
---|
| 380 | get_scan - gets a specific scan out of a scantable
|
---|
[984] | 381 | (by name or number)
|
---|
[1093] | 382 | drop_scan - drops a specific scan out of a scantable
|
---|
| 383 | (by number)
|
---|
[984] | 384 | set_selection - set a new subselection of the data
|
---|
| 385 | get_selection - get the current selection object
|
---|
[113] | 386 | summary - print info about the scantable contents
|
---|
[182] | 387 | stats - get specified statistic of the spectra in
|
---|
| 388 | the scantable
|
---|
| 389 | stddev - get the standard deviation of the spectra
|
---|
| 390 | in the scantable
|
---|
[113] | 391 | get_tsys - get the TSys
|
---|
| 392 | get_time - get the timestamps of the integrations
|
---|
[733] | 393 | get_sourcename - get the source names of the scans
|
---|
[794] | 394 | get_azimuth - get the azimuth of the scans
|
---|
| 395 | get_elevation - get the elevation of the scans
|
---|
| 396 | get_parangle - get the parallactic angle of the scans
|
---|
[876] | 397 | get_unit - get the current unit
|
---|
[513] | 398 | set_unit - set the abcissa unit to be used from this
|
---|
| 399 | point on
|
---|
[255] | 400 | get_abcissa - get the abcissa values and name for a given
|
---|
| 401 | row (time)
|
---|
[1259] | 402 | get_column_names - get the names of the columns in the scantable
|
---|
| 403 | for use with selector.set_query
|
---|
[113] | 404 | set_freqframe - set the frame info for the Spectral Axis
|
---|
| 405 | (e.g. 'LSRK')
|
---|
[276] | 406 | set_doppler - set the doppler to be used from this point on
|
---|
[984] | 407 | set_dirframe - set the frame for the direction on the sky
|
---|
[240] | 408 | set_instrument - set the instrument name
|
---|
[1190] | 409 | set_feedtype - set the feed type
|
---|
[255] | 410 | get_fluxunit - get the brightness flux unit
|
---|
[240] | 411 | set_fluxunit - set the brightness flux unit
|
---|
[188] | 412 | create_mask - return an mask in the current unit
|
---|
| 413 | for the given region. The specified regions
|
---|
| 414 | are NOT masked
|
---|
[255] | 415 | get_restfreqs - get the current list of rest frequencies
|
---|
| 416 | set_restfreqs - set a list of rest frequencies
|
---|
[1012] | 417 | flag - flag selected channels in the data
|
---|
[1192] | 418 | lag_flag - flag specified frequency in the data
|
---|
[1151] | 419 | save - save the scantable to disk as either 'ASAP',
|
---|
| 420 | 'SDFITS' or 'ASCII'
|
---|
[486] | 421 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
|
---|
[733] | 422 | nscan - the number of scans in the scantable
|
---|
[984] | 423 | nrow - te number of spectra in the scantable
|
---|
[486] | 424 | history - print the history of the scantable
|
---|
[530] | 425 | get_fit - get a fit which has been stored witnh the data
|
---|
[706] | 426 | average_time - return the (weighted) time average of a scan
|
---|
[513] | 427 | or a list of scans
|
---|
| 428 | average_pol - average the polarisations together.
|
---|
[1144] | 429 | average_beam - average the beams together.
|
---|
[992] | 430 | convert_pol - convert to a different polarisation type
|
---|
[690] | 431 | auto_quotient - return the on/off quotient with
|
---|
[1069] | 432 | automatic detection of the on/off scans (closest
|
---|
| 433 | in time off is selected)
|
---|
[1144] | 434 | mx_quotient - Form a quotient using MX data (off beams)
|
---|
[1014] | 435 | scale, *, / - return a scan scaled by a given factor
|
---|
| 436 | add, +, - - return a scan with given value added
|
---|
[513] | 437 | bin - return a scan with binned channels
|
---|
| 438 | resample - return a scan with resampled channels
|
---|
| 439 | smooth - return the spectrally smoothed scan
|
---|
| 440 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
|
---|
[706] | 441 | auto_poly_baseline - automatically fit a polynomial baseline
|
---|
[780] | 442 | recalc_azel - recalculate azimuth and elevation based on
|
---|
| 443 | the pointing
|
---|
[513] | 444 | gain_el - apply gain-elevation correction
|
---|
| 445 | opacity - apply opacity correction
|
---|
| 446 | convert_flux - convert to and from Jy and Kelvin brightness
|
---|
[255] | 447 | units
|
---|
[513] | 448 | freq_align - align spectra in frequency frame
|
---|
[1014] | 449 | invert_phase - Invert the phase of the cross-correlation
|
---|
| 450 | swap_linears - Swap XX and YY
|
---|
[513] | 451 | rotate_xyphase - rotate XY phase of cross correlation
|
---|
| 452 | rotate_linpolphase - rotate the phase of the complex
|
---|
| 453 | polarization O=Q+iU correlation
|
---|
[733] | 454 | freq_switch - perform frequency switching on the data
|
---|
| 455 | stats - Determine the specified statistic, e.g. 'min'
|
---|
| 456 | 'max', 'rms' etc.
|
---|
| 457 | stddev - Determine the standard deviation of the current
|
---|
| 458 | beam/if/pol
|
---|
[1014] | 459 | [Selection]
|
---|
| 460 | selector - a selection object to set a subset of a scantable
|
---|
| 461 | set_scans - set (a list of) scans by index
|
---|
| 462 | set_cycles - set (a list of) cycles by index
|
---|
| 463 | set_beams - set (a list of) beamss by index
|
---|
| 464 | set_ifs - set (a list of) ifs by index
|
---|
| 465 | set_polarisations - set (a list of) polarisations by name
|
---|
| 466 | or by index
|
---|
| 467 | set_names - set a selection by name (wildcards allowed)
|
---|
| 468 | set_tsys - set a selection by tsys thresholds
|
---|
[1259] | 469 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1
|
---|
[1014] | 470 | reset - unset all selections
|
---|
| 471 | + - merge to selections
|
---|
[733] | 472 |
|
---|
[513] | 473 | [Math] Mainly functions which operate on more than one scantable
|
---|
[100] | 474 |
|
---|
[706] | 475 | average_time - return the (weighted) time average
|
---|
[513] | 476 | of a list of scans
|
---|
| 477 | quotient - return the on/off quotient
|
---|
| 478 | simple_math - simple mathematical operations on two scantables,
|
---|
| 479 | 'add', 'sub', 'mul', 'div'
|
---|
[1069] | 480 | quotient - build quotient of the given on and off scans
|
---|
| 481 | (matched pairs and 1 off/n on are valid)
|
---|
[1117] | 482 | merge - merge a list of scantables
|
---|
[1069] | 483 |
|
---|
[1151] | 484 | [Line Catalog]
|
---|
| 485 | linecatalog - a linecatalog wrapper, taking an ASCII or
|
---|
| 486 | internal format table
|
---|
| 487 | summary - print a summary of the current selection
|
---|
| 488 | set_name - select a subset by name pattern, e.g. '*OH*'
|
---|
| 489 | set_strength_limits - select a subset by line strength limits
|
---|
| 490 | set_frequency_limits - select a subset by frequency limits
|
---|
| 491 | reset - unset all selections
|
---|
| 492 | save - save the current subset to a table (internal
|
---|
| 493 | format)
|
---|
| 494 | get_row - get the name and frequency from a specific
|
---|
| 495 | row in the table
|
---|
[513] | 496 | [Fitting]
|
---|
[113] | 497 | fitter
|
---|
| 498 | auto_fit - return a scan where the function is
|
---|
| 499 | applied to all Beams/IFs/Pols.
|
---|
| 500 | commit - return a new scan where the fits have been
|
---|
| 501 | commited.
|
---|
| 502 | fit - execute the actual fitting process
|
---|
[984] | 503 | store_fit - store the fit parameters in the data (scantable)
|
---|
[113] | 504 | get_chi2 - get the Chi^2
|
---|
| 505 | set_scan - set the scantable to be fit
|
---|
| 506 | set_function - set the fitting function
|
---|
| 507 | set_parameters - set the parameters for the function(s), and
|
---|
| 508 | set if they should be held fixed during fitting
|
---|
[513] | 509 | set_gauss_parameters - same as above but specialised for individual
|
---|
| 510 | gaussian components
|
---|
[113] | 511 | get_parameters - get the fitted parameters
|
---|
[513] | 512 | plot - plot the resulting fit and/or components and
|
---|
| 513 | residual
|
---|
[210] | 514 | [Plotter]
|
---|
| 515 | asapplotter - a plotter for asap, default plotter is
|
---|
| 516 | called 'plotter'
|
---|
[984] | 517 | plot - plot a scantable
|
---|
[1151] | 518 | plot_lines - plot a linecatalog overlay
|
---|
[378] | 519 | save - save the plot to a file ('png' ,'ps' or 'eps')
|
---|
[210] | 520 | set_mode - set the state of the plotter, i.e.
|
---|
| 521 | what is to be plotted 'colour stacked'
|
---|
| 522 | and what 'panelled'
|
---|
[984] | 523 | set_selection - only plot a selected part of the data
|
---|
[733] | 524 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
|
---|
[255] | 525 | set_legend - specify user labels for the legend indeces
|
---|
| 526 | set_title - specify user labels for the panel indeces
|
---|
[733] | 527 | set_abcissa - specify a user label for the abcissa
|
---|
[255] | 528 | set_ordinate - specify a user label for the ordinate
|
---|
[378] | 529 | set_layout - specify the multi-panel layout (rows,cols)
|
---|
[733] | 530 | set_colors - specify a set of colours to use
|
---|
| 531 | set_linestyles - specify a set of linestyles to use if only
|
---|
| 532 | using one color
|
---|
[1151] | 533 | set_font - set general font properties, e.g. 'family'
|
---|
[1054] | 534 | set_histogram - plot in historam style
|
---|
[733] | 535 | set_mask - set a plotting mask for a specific polarization
|
---|
[1171] | 536 | text - draw text annotations either in data or relative
|
---|
| 537 | coordinates
|
---|
| 538 | arrow - draw arrow annotations either in data or relative
|
---|
| 539 | coordinates
|
---|
| 540 | axhline,axvline - draw horizontal/vertical lines
|
---|
| 541 | axhspan,axvspan - draw horizontal/vertical regions
|
---|
[1175] | 542 |
|
---|
| 543 | xyplotter - matplotlib/pylab plotting functions
|
---|
| 544 |
|
---|
[182] | 545 | [Reading files]
|
---|
| 546 | reader - access rpfits/sdfits files
|
---|
[984] | 547 | open - attach reader to a file
|
---|
| 548 | close - detach reader from file
|
---|
[182] | 549 | read - read in integrations
|
---|
| 550 | summary - list info about all integrations
|
---|
| 551 |
|
---|
[113] | 552 | [General]
|
---|
| 553 | commands - this command
|
---|
| 554 | print - print details about a variable
|
---|
| 555 | list_scans - list all scantables created bt the user
|
---|
[992] | 556 | list_files - list all files readable by asap (default rpf)
|
---|
[113] | 557 | del - delete the given variable from memory
|
---|
| 558 | range - create a list of values, e.g.
|
---|
| 559 | range(3) = [0,1,2], range(2,5) = [2,3,4]
|
---|
| 560 | help - print help for one of the listed functions
|
---|
| 561 | execfile - execute an asap script, e.g. execfile('myscript')
|
---|
[255] | 562 | list_rcparameters - print out a list of possible values to be
|
---|
[274] | 563 | put into $HOME/.asaprc
|
---|
[1171] | 564 | rc - set rc parameters from within asap
|
---|
[466] | 565 | mask_and,mask_or,
|
---|
| 566 | mask_not - boolean operations on masks created with
|
---|
| 567 | scantable.create_mask
|
---|
[706] | 568 |
|
---|
[210] | 569 | Note:
|
---|
| 570 | How to use this with help:
|
---|
| 571 | # function 'summary'
|
---|
| 572 | [xxx] is just a category
|
---|
| 573 | Every 'sub-level' in this list should be replaces by a '.' Period when
|
---|
[706] | 574 | using help
|
---|
[210] | 575 | Example:
|
---|
| 576 | ASAP> help scantable # to get info on ths scantable
|
---|
| 577 | ASAP> help scantable.summary # to get help on the scantable's
|
---|
| 578 | ASAP> help average_time
|
---|
| 579 |
|
---|
[715] | 580 | """
|
---|
[1151] | 581 | if rcParams['verbose']:
|
---|
| 582 | try:
|
---|
| 583 | from IPython.genutils import page as pager
|
---|
| 584 | except ImportError:
|
---|
| 585 | from pydoc import pager
|
---|
| 586 | pager(x)
|
---|
| 587 | else:
|
---|
| 588 | print x
|
---|
[715] | 589 | return
|
---|
[113] | 590 |
|
---|
[706] | 591 | def welcome():
|
---|
| 592 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
|
---|
[100] | 593 |
|
---|
[1035] | 594 | Please report any bugs via:
|
---|
| 595 | http://sourcecode.atnf.csiro.au/cgi-bin/trac_asap.cgi/newticket
|
---|
[100] | 596 |
|
---|
[378] | 597 | [IMPORTANT: ASAP is 0-based]
|
---|
[706] | 598 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
|
---|