| [100] | 1 | """
|
|---|
| 2 | This is the ATNF Single Dish Analysis package.
|
|---|
| 3 |
|
|---|
| 4 | """
|
|---|
| [1080] | 5 | import os,sys,shutil, platform
|
|---|
| [1691] | 6 | try:
|
|---|
| 7 | from functools import wraps as wraps_dec
|
|---|
| 8 | except ImportError:
|
|---|
| 9 | from asap.compatibility import wraps as wraps_dec
|
|---|
| [226] | 10 |
|
|---|
| [1080] | 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]
|
|---|
| [1171] | 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"]
|
|---|
| [1371] | 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"):
|
|---|
| [1316] | 31 | os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf)
|
|---|
| [1171] | 32 | # set up user space
|
|---|
| [1080] | 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")
|
|---|
| [1588] | 38 | shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
|
|---|
| [1434] | 39 | userdir+"/ipy_user_conf.py")
|
|---|
| [1080] | 40 | f = file(userdir+"/asapuserfuncs.py", "w")
|
|---|
| 41 | f.close()
|
|---|
| 42 | f = file(userdir+"/ipythonrc", "w")
|
|---|
| 43 | f.close()
|
|---|
| [1472] | 44 | else:
|
|---|
| 45 | # upgrade to support later ipython versions
|
|---|
| 46 | if not os.path.exists(userdir+"/ipy_user_conf.py"):
|
|---|
| [1588] | 47 | shutil.copyfile(asapdata+"/data/ipy_user_conf.py",
|
|---|
| [1472] | 48 | userdir+"/ipy_user_conf.py")
|
|---|
| 49 |
|
|---|
| [1171] | 50 | # remove from namespace
|
|---|
| [1080] | 51 | del asapdata, userdir, shutil, platform
|
|---|
| 52 |
|
|---|
| [513] | 53 | def _validate_bool(b):
|
|---|
| [226] | 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 |
|
|---|
| [513] | 61 | def _validate_int(s):
|
|---|
| [226] | 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 |
|
|---|
| [513] | 67 | def _asap_fname():
|
|---|
| [226] | 68 | """
|
|---|
| 69 | Return the path to the rc file
|
|---|
| 70 |
|
|---|
| 71 | Search order:
|
|---|
| 72 |
|
|---|
| 73 | * current working dir
|
|---|
| 74 | * environ var ASAPRC
|
|---|
| [274] | 75 | * HOME/.asaprc
|
|---|
| [706] | 76 |
|
|---|
| [226] | 77 | """
|
|---|
| 78 |
|
|---|
| 79 | fname = os.path.join( os.getcwd(), '.asaprc')
|
|---|
| 80 | if os.path.exists(fname): return fname
|
|---|
| 81 |
|
|---|
| 82 | if os.environ.has_key('ASAPRC'):
|
|---|
| 83 | path = os.environ['ASAPRC']
|
|---|
| 84 | if os.path.exists(path):
|
|---|
| 85 | fname = os.path.join(path, '.asaprc')
|
|---|
| 86 | if os.path.exists(fname):
|
|---|
| 87 | return fname
|
|---|
| 88 |
|
|---|
| 89 | if os.environ.has_key('HOME'):
|
|---|
| 90 | home = os.environ['HOME']
|
|---|
| 91 | fname = os.path.join(home, '.asaprc')
|
|---|
| 92 | if os.path.exists(fname):
|
|---|
| 93 | return fname
|
|---|
| 94 | return None
|
|---|
| 95 |
|
|---|
| [706] | 96 |
|
|---|
| [226] | 97 | defaultParams = {
|
|---|
| 98 | # general
|
|---|
| [513] | 99 | 'verbose' : [True, _validate_bool],
|
|---|
| 100 | 'useplotter' : [True, _validate_bool],
|
|---|
| [542] | 101 | 'insitu' : [True, _validate_bool],
|
|---|
| [706] | 102 |
|
|---|
| [226] | 103 | # plotting
|
|---|
| [706] | 104 | 'plotter.gui' : [True, _validate_bool],
|
|---|
| [226] | 105 | 'plotter.stacking' : ['p', str],
|
|---|
| 106 | 'plotter.panelling' : ['s', str],
|
|---|
| [700] | 107 | 'plotter.colours' : ['', str],
|
|---|
| 108 | 'plotter.linestyles' : ['', str],
|
|---|
| [710] | 109 | 'plotter.decimate' : [False, _validate_bool],
|
|---|
| 110 | 'plotter.ganged' : [True, _validate_bool],
|
|---|
| [1022] | 111 | 'plotter.histogram' : [False, _validate_bool],
|
|---|
| [1097] | 112 | 'plotter.papertype' : ['A4', str],
|
|---|
| [1560] | 113 | 'plotter.axesformatting' : ['mpl', str],
|
|---|
| [710] | 114 |
|
|---|
| [226] | 115 | # scantable
|
|---|
| 116 | 'scantable.save' : ['ASAP', str],
|
|---|
| [513] | 117 | 'scantable.autoaverage' : [True, _validate_bool],
|
|---|
| [226] | 118 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame
|
|---|
| [1076] | 119 | 'scantable.verbosesummary' : [False, _validate_bool],
|
|---|
| [1422] | 120 | 'scantable.storage' : ['memory', str],
|
|---|
| [1504] | 121 | 'scantable.history' : [True, _validate_bool],
|
|---|
| [1586] | 122 | 'scantable.reference' : ['.*(e|w|_R)$', str],
|
|---|
| 123 | 'scantable.parallactify' : [False, _validate_bool]
|
|---|
| [226] | 124 | # fitter
|
|---|
| 125 | }
|
|---|
| 126 |
|
|---|
| [255] | 127 | def list_rcparameters():
|
|---|
| [706] | 128 |
|
|---|
| [255] | 129 | print """
|
|---|
| [737] | 130 | # general
|
|---|
| 131 | # print verbose output
|
|---|
| 132 | verbose : True
|
|---|
| [255] | 133 |
|
|---|
| [737] | 134 | # preload a default plotter
|
|---|
| 135 | useplotter : True
|
|---|
| [255] | 136 |
|
|---|
| [737] | 137 | # apply operations on the input scantable or return new one
|
|---|
| 138 | insitu : True
|
|---|
| [706] | 139 |
|
|---|
| [737] | 140 | # plotting
|
|---|
| [710] | 141 |
|
|---|
| [737] | 142 | # do we want a GUI or plot to a file
|
|---|
| 143 | plotter.gui : True
|
|---|
| [710] | 144 |
|
|---|
| [737] | 145 | # default mode for colour stacking
|
|---|
| 146 | plotter.stacking : Pol
|
|---|
| [255] | 147 |
|
|---|
| [737] | 148 | # default mode for panelling
|
|---|
| 149 | plotter.panelling : scan
|
|---|
| [255] | 150 |
|
|---|
| [1560] | 151 | # push panels together, to share axis labels
|
|---|
| [737] | 152 | plotter.ganged : True
|
|---|
| [710] | 153 |
|
|---|
| [1513] | 154 | # decimate the number of points plotted by a factor of
|
|---|
| [737] | 155 | # nchan/1024
|
|---|
| 156 | plotter.decimate : False
|
|---|
| [733] | 157 |
|
|---|
| [737] | 158 | # default colours/linestyles
|
|---|
| 159 | plotter.colours :
|
|---|
| 160 | plotter.linestyles :
|
|---|
| [700] | 161 |
|
|---|
| [1022] | 162 | # enable/disable histogram plotting
|
|---|
| 163 | plotter.histogram : False
|
|---|
| 164 |
|
|---|
| [1097] | 165 | # ps paper type
|
|---|
| 166 | plotter.papertype : A4
|
|---|
| 167 |
|
|---|
| [1513] | 168 | # The formatting style of the xaxis
|
|---|
| [1560] | 169 | plotter.axesformatting : 'mpl' (default) or 'asap' (for old versions of matplotlib)
|
|---|
| [1513] | 170 |
|
|---|
| [737] | 171 | # scantable
|
|---|
| [1076] | 172 |
|
|---|
| [1259] | 173 | # default storage of scantable ('memory'/'disk')
|
|---|
| [1076] | 174 | scantable.storage : memory
|
|---|
| [1422] | 175 |
|
|---|
| 176 | # write history of each call to scantable
|
|---|
| 177 | scantable.history : True
|
|---|
| 178 |
|
|---|
| [737] | 179 | # default ouput format when saving
|
|---|
| 180 | scantable.save : ASAP
|
|---|
| [1422] | 181 |
|
|---|
| [737] | 182 | # auto averaging on read
|
|---|
| 183 | scantable.autoaverage : True
|
|---|
| [255] | 184 |
|
|---|
| [737] | 185 | # default frequency frame to set when function
|
|---|
| [1097] | 186 | # scantable.set_freqframe is called
|
|---|
| [737] | 187 | scantable.freqframe : LSRK
|
|---|
| [255] | 188 |
|
|---|
| [737] | 189 | # Control the level of information printed by summary
|
|---|
| 190 | scantable.verbosesummary : False
|
|---|
| [706] | 191 |
|
|---|
| [1504] | 192 | # Control the identification of reference (off) scans
|
|---|
| 193 | # This is has to be a regular expression
|
|---|
| [1595] | 194 | scantable.reference : .*(e|w|_R)$
|
|---|
| [1560] | 195 |
|
|---|
| [1595] | 196 | # Indicate whether the data was parallactified (total phase offest == 0.0)
|
|---|
| 197 | scantable.parallactify : False
|
|---|
| 198 |
|
|---|
| [737] | 199 | # Fitter
|
|---|
| 200 | """
|
|---|
| [706] | 201 |
|
|---|
| [226] | 202 | def rc_params():
|
|---|
| 203 | 'Return the default params updated from the values in the rc file'
|
|---|
| [706] | 204 |
|
|---|
| [513] | 205 | fname = _asap_fname()
|
|---|
| [706] | 206 |
|
|---|
| [226] | 207 | if fname is None or not os.path.exists(fname):
|
|---|
| 208 | message = 'could not find rc file; returning defaults'
|
|---|
| 209 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
|
|---|
| 210 | #print message
|
|---|
| 211 | return ret
|
|---|
| [706] | 212 |
|
|---|
| [226] | 213 | cnt = 0
|
|---|
| 214 | for line in file(fname):
|
|---|
| 215 | cnt +=1
|
|---|
| 216 | line = line.strip()
|
|---|
| 217 | if not len(line): continue
|
|---|
| 218 | if line.startswith('#'): continue
|
|---|
| 219 | tup = line.split(':',1)
|
|---|
| 220 | if len(tup) !=2:
|
|---|
| 221 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname))
|
|---|
| 222 | continue
|
|---|
| [706] | 223 |
|
|---|
| [226] | 224 | key, val = tup
|
|---|
| 225 | key = key.strip()
|
|---|
| 226 | if not defaultParams.has_key(key):
|
|---|
| 227 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname))
|
|---|
| 228 | continue
|
|---|
| [706] | 229 |
|
|---|
| [226] | 230 | default, converter = defaultParams[key]
|
|---|
| 231 |
|
|---|
| 232 | ind = val.find('#')
|
|---|
| 233 | if ind>=0: val = val[:ind] # ignore trailing comments
|
|---|
| 234 | val = val.strip()
|
|---|
| 235 | try: cval = converter(val) # try to convert to proper type or raise
|
|---|
| [1080] | 236 | except ValueError, msg:
|
|---|
| [226] | 237 | print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg))
|
|---|
| 238 | continue
|
|---|
| 239 | else:
|
|---|
| 240 | # Alles Klar, update dict
|
|---|
| 241 | defaultParams[key][0] = cval
|
|---|
| 242 |
|
|---|
| 243 | # strip the conveter funcs and return
|
|---|
| 244 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()])
|
|---|
| [466] | 245 | print ('loaded rc file %s'%fname)
|
|---|
| [226] | 246 |
|
|---|
| 247 | return ret
|
|---|
| 248 |
|
|---|
| 249 |
|
|---|
| 250 | # this is the instance used by the asap classes
|
|---|
| [706] | 251 | rcParams = rc_params()
|
|---|
| [226] | 252 |
|
|---|
| 253 | rcParamsDefault = dict(rcParams.items()) # a copy
|
|---|
| 254 |
|
|---|
| 255 | def rc(group, **kwargs):
|
|---|
| 256 | """
|
|---|
| 257 | Set the current rc params. Group is the grouping for the rc, eg
|
|---|
| [379] | 258 | for scantable.save the group is 'scantable', for plotter.stacking, the
|
|---|
| 259 | group is 'plotter', and so on. kwargs is a list of attribute
|
|---|
| [226] | 260 | name/value pairs, eg
|
|---|
| 261 |
|
|---|
| [379] | 262 | rc('scantable', save='SDFITS')
|
|---|
| [226] | 263 |
|
|---|
| 264 | sets the current rc params and is equivalent to
|
|---|
| [706] | 265 |
|
|---|
| [379] | 266 | rcParams['scantable.save'] = 'SDFITS'
|
|---|
| [226] | 267 |
|
|---|
| 268 | Use rcdefaults to restore the default rc params after changes.
|
|---|
| 269 | """
|
|---|
| 270 |
|
|---|
| [379] | 271 | aliases = {}
|
|---|
| [706] | 272 |
|
|---|
| [226] | 273 | for k,v in kwargs.items():
|
|---|
| 274 | name = aliases.get(k) or k
|
|---|
| [1422] | 275 | if len(group):
|
|---|
| 276 | key = '%s.%s' % (group, name)
|
|---|
| 277 | else:
|
|---|
| 278 | key = name
|
|---|
| [226] | 279 | if not rcParams.has_key(key):
|
|---|
| 280 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name))
|
|---|
| [706] | 281 |
|
|---|
| [226] | 282 | rcParams[key] = v
|
|---|
| 283 |
|
|---|
| 284 |
|
|---|
| 285 | def rcdefaults():
|
|---|
| 286 | """
|
|---|
| 287 | Restore the default rc params - the ones that were created at
|
|---|
| 288 | asap load time
|
|---|
| 289 | """
|
|---|
| 290 | rcParams.update(rcParamsDefault)
|
|---|
| 291 |
|
|---|
| [1295] | 292 | def _n_bools(n, val):
|
|---|
| [1588] | 293 | return [ val for i in xrange(n) ]
|
|---|
| [513] | 294 |
|
|---|
| 295 | def _is_sequence_or_number(param, ptype=int):
|
|---|
| 296 | if isinstance(param,tuple) or isinstance(param,list):
|
|---|
| [928] | 297 | if len(param) == 0: return True # empty list
|
|---|
| [513] | 298 | out = True
|
|---|
| 299 | for p in param:
|
|---|
| 300 | out &= isinstance(p,ptype)
|
|---|
| 301 | return out
|
|---|
| 302 | elif isinstance(param, ptype):
|
|---|
| 303 | return True
|
|---|
| 304 | return False
|
|---|
| 305 |
|
|---|
| [928] | 306 | def _to_list(param, ptype=int):
|
|---|
| 307 | if isinstance(param, ptype):
|
|---|
| 308 | if ptype is str: return param.split()
|
|---|
| 309 | else: return [param]
|
|---|
| 310 | if _is_sequence_or_number(param, ptype):
|
|---|
| 311 | return param
|
|---|
| 312 | return None
|
|---|
| [715] | 313 |
|
|---|
| [944] | 314 | def unique(x):
|
|---|
| [992] | 315 | """
|
|---|
| 316 | Return the unique values in a list
|
|---|
| 317 | Parameters:
|
|---|
| 318 | x: the list to reduce
|
|---|
| 319 | Examples:
|
|---|
| 320 | x = [1,2,3,3,4]
|
|---|
| 321 | print unique(x)
|
|---|
| 322 | [1,2,3,4]
|
|---|
| 323 | """
|
|---|
| [944] | 324 | return dict([ (val, 1) for val in x]).keys()
|
|---|
| 325 |
|
|---|
| [992] | 326 | def list_files(path=".",suffix="rpf"):
|
|---|
| 327 | """
|
|---|
| 328 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap
|
|---|
| 329 | Parameters:
|
|---|
| 330 | path: The directory to list (default '.')
|
|---|
| 331 | suffix: The file extension (default rpf)
|
|---|
| 332 | Example:
|
|---|
| 333 | files = list_files("data/","sdfits")
|
|---|
| 334 | print files
|
|---|
| 335 | ['data/2001-09-01_0332_P363.sdfits',
|
|---|
| 336 | 'data/2003-04-04_131152_t0002.sdfits',
|
|---|
| 337 | 'data/Sgr_86p262_best_SPC.sdfits']
|
|---|
| 338 | """
|
|---|
| 339 | if not os.path.isdir(path):
|
|---|
| 340 | return None
|
|---|
| [1295] | 341 | valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split()
|
|---|
| [992] | 342 | if not suffix in valid:
|
|---|
| 343 | return None
|
|---|
| 344 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)]
|
|---|
| 345 | return filter(lambda x: x.endswith(suffix),files)
|
|---|
| 346 |
|
|---|
| [715] | 347 | # workaround for ipython, which redirects this if banner=0 in ipythonrc
|
|---|
| 348 | sys.stdout = sys.__stdout__
|
|---|
| 349 | sys.stderr = sys.__stderr__
|
|---|
| 350 |
|
|---|
| 351 | # Logging
|
|---|
| 352 | from asap._asap import Log as _asaplog
|
|---|
| 353 | global asaplog
|
|---|
| [710] | 354 | asaplog=_asaplog()
|
|---|
| [715] | 355 | if rcParams['verbose']:
|
|---|
| 356 | asaplog.enable()
|
|---|
| 357 | else:
|
|---|
| 358 | asaplog.disable()
|
|---|
| 359 |
|
|---|
| [1589] | 360 |
|
|---|
| 361 | def print_log_dec(f):
|
|---|
| [1691] | 362 | @wraps_dec(f)
|
|---|
| [1589] | 363 | def wrap_it(*args, **kw):
|
|---|
| 364 | val = f(*args, **kw)
|
|---|
| 365 | print_log()
|
|---|
| 366 | return val
|
|---|
| 367 | return wrap_it
|
|---|
| 368 |
|
|---|
| [715] | 369 | def print_log():
|
|---|
| [1589] | 370 | log = asaplog.pop().strip()
|
|---|
| [715] | 371 | if len(log) and rcParams['verbose']: print log
|
|---|
| 372 | return
|
|---|
| 373 |
|
|---|
| [1295] | 374 | def mask_and(a, b):
|
|---|
| 375 | assert(len(a)==len(b))
|
|---|
| 376 | return [ a[i] & b[i] for i in xrange(len(a)) ]
|
|---|
| [1134] | 377 |
|
|---|
| [1295] | 378 | def mask_or(a, b):
|
|---|
| 379 | assert(len(a)==len(b))
|
|---|
| 380 | return [ a[i] | b[i] for i in xrange(len(a)) ]
|
|---|
| 381 |
|
|---|
| 382 | def mask_not(a):
|
|---|
| 383 | return [ not i for i in a ]
|
|---|
| 384 |
|
|---|
| [1117] | 385 | from asapfitter import fitter
|
|---|
| [895] | 386 | from asapreader import reader
|
|---|
| [944] | 387 | from selector import selector
|
|---|
| [710] | 388 |
|
|---|
| [100] | 389 | from asapmath import *
|
|---|
| [1080] | 390 | from scantable import scantable
|
|---|
| [1097] | 391 | from asaplinefind import linefinder
|
|---|
| [1645] | 392 | from simplelinefinder import simplelinefinder
|
|---|
| [1134] | 393 | from linecatalog import linecatalog
|
|---|
| [1689] | 394 | from opacity import skydip
|
|---|
| [285] | 395 |
|
|---|
| [928] | 396 | if rcParams['useplotter']:
|
|---|
| [1295] | 397 | try:
|
|---|
| [1423] | 398 | from asapplotter import asapplotter
|
|---|
| 399 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui']
|
|---|
| 400 | if gui:
|
|---|
| [1422] | 401 | import matplotlib
|
|---|
| 402 | matplotlib.use("TkAgg")
|
|---|
| [1691] | 403 | from matplotlib import pylab
|
|---|
| [1422] | 404 | xyplotter = pylab
|
|---|
| [1423] | 405 | plotter = asapplotter(gui)
|
|---|
| 406 | del gui
|
|---|
| [1295] | 407 | except ImportError:
|
|---|
| [1423] | 408 | print "Matplotlib not installed. No plotting available"
|
|---|
| [285] | 409 |
|
|---|
| [574] | 410 | __date__ = '$Date: 2010-02-11 00:46:14 +0000 (Thu, 11 Feb 2010) $'.split()[1]
|
|---|
| [1560] | 411 | __version__ = '$Revision: 1697 $'
|
|---|
| [100] | 412 |
|
|---|
| [1193] | 413 | def is_ipython():
|
|---|
| [1259] | 414 | return '__IP' in dir(sys.modules["__main__"])
|
|---|
| [1589] | 415 |
|
|---|
| [1193] | 416 | if is_ipython():
|
|---|
| [1014] | 417 | def version(): print "ASAP %s(%s)"% (__version__, __date__)
|
|---|
| [1588] | 418 |
|
|---|
| 419 | def list_scans(t = scantable):
|
|---|
| [1560] | 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
|
|---|
| [100] | 427 |
|
|---|
| [715] | 428 | def commands():
|
|---|
| 429 | x = """
|
|---|
| [113] | 430 | [The scan container]
|
|---|
| 431 | scantable - a container for integrations/scans
|
|---|
| [182] | 432 | (can open asap/rpfits/sdfits and ms files)
|
|---|
| [113] | 433 | copy - returns a copy of a scan
|
|---|
| 434 | get_scan - gets a specific scan out of a scantable
|
|---|
| [984] | 435 | (by name or number)
|
|---|
| [1093] | 436 | drop_scan - drops a specific scan out of a scantable
|
|---|
| 437 | (by number)
|
|---|
| [984] | 438 | set_selection - set a new subselection of the data
|
|---|
| 439 | get_selection - get the current selection object
|
|---|
| [113] | 440 | summary - print info about the scantable contents
|
|---|
| [182] | 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
|
|---|
| [113] | 445 | get_tsys - get the TSys
|
|---|
| 446 | get_time - get the timestamps of the integrations
|
|---|
| [1351] | 447 | get_inttime - get the integration time
|
|---|
| [733] | 448 | get_sourcename - get the source names of the scans
|
|---|
| [794] | 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
|
|---|
| [1697] | 452 | get_coordinate - get the spectral coordinate for the given row,
|
|---|
| 453 | which can be used for coordinate conversions
|
|---|
| [876] | 454 | get_unit - get the current unit
|
|---|
| [513] | 455 | set_unit - set the abcissa unit to be used from this
|
|---|
| 456 | point on
|
|---|
| [255] | 457 | get_abcissa - get the abcissa values and name for a given
|
|---|
| 458 | row (time)
|
|---|
| [1259] | 459 | get_column_names - get the names of the columns in the scantable
|
|---|
| 460 | for use with selector.set_query
|
|---|
| [113] | 461 | set_freqframe - set the frame info for the Spectral Axis
|
|---|
| 462 | (e.g. 'LSRK')
|
|---|
| [276] | 463 | set_doppler - set the doppler to be used from this point on
|
|---|
| [984] | 464 | set_dirframe - set the frame for the direction on the sky
|
|---|
| [240] | 465 | set_instrument - set the instrument name
|
|---|
| [1190] | 466 | set_feedtype - set the feed type
|
|---|
| [255] | 467 | get_fluxunit - get the brightness flux unit
|
|---|
| [240] | 468 | set_fluxunit - set the brightness flux unit
|
|---|
| [1508] | 469 | set_sourcetype - set the type of the source - source or reference
|
|---|
| [188] | 470 | create_mask - return an mask in the current unit
|
|---|
| 471 | for the given region. The specified regions
|
|---|
| 472 | are NOT masked
|
|---|
| [255] | 473 | get_restfreqs - get the current list of rest frequencies
|
|---|
| 474 | set_restfreqs - set a list of rest frequencies
|
|---|
| [1471] | 475 | shift_refpix - shift the reference pixel of the IFs
|
|---|
| 476 | set_spectrum - overwrite the spectrum for a given row
|
|---|
| 477 | get_spectrum - retrieve the spectrum for a given
|
|---|
| 478 | get_mask - retrieve the mask for a given
|
|---|
| [1012] | 479 | flag - flag selected channels in the data
|
|---|
| [1192] | 480 | lag_flag - flag specified frequency in the data
|
|---|
| [1151] | 481 | save - save the scantable to disk as either 'ASAP',
|
|---|
| 482 | 'SDFITS' or 'ASCII'
|
|---|
| [486] | 483 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
|
|---|
| [733] | 484 | nscan - the number of scans in the scantable
|
|---|
| [1422] | 485 | nrow - the number of spectra in the scantable
|
|---|
| [486] | 486 | history - print the history of the scantable
|
|---|
| [530] | 487 | get_fit - get a fit which has been stored witnh the data
|
|---|
| [706] | 488 | average_time - return the (weighted) time average of a scan
|
|---|
| [513] | 489 | or a list of scans
|
|---|
| 490 | average_pol - average the polarisations together.
|
|---|
| [1144] | 491 | average_beam - average the beams together.
|
|---|
| [992] | 492 | convert_pol - convert to a different polarisation type
|
|---|
| [690] | 493 | auto_quotient - return the on/off quotient with
|
|---|
| [1069] | 494 | automatic detection of the on/off scans (closest
|
|---|
| 495 | in time off is selected)
|
|---|
| [1144] | 496 | mx_quotient - Form a quotient using MX data (off beams)
|
|---|
| [1014] | 497 | scale, *, / - return a scan scaled by a given factor
|
|---|
| [1560] | 498 | add, + - return a scan with given value added
|
|---|
| 499 | sub, - - return a scan with given value subtracted
|
|---|
| [513] | 500 | bin - return a scan with binned channels
|
|---|
| 501 | resample - return a scan with resampled channels
|
|---|
| 502 | smooth - return the spectrally smoothed scan
|
|---|
| 503 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols
|
|---|
| [706] | 504 | auto_poly_baseline - automatically fit a polynomial baseline
|
|---|
| [780] | 505 | recalc_azel - recalculate azimuth and elevation based on
|
|---|
| 506 | the pointing
|
|---|
| [513] | 507 | gain_el - apply gain-elevation correction
|
|---|
| 508 | opacity - apply opacity correction
|
|---|
| 509 | convert_flux - convert to and from Jy and Kelvin brightness
|
|---|
| [255] | 510 | units
|
|---|
| [513] | 511 | freq_align - align spectra in frequency frame
|
|---|
| [1014] | 512 | invert_phase - Invert the phase of the cross-correlation
|
|---|
| [1351] | 513 | swap_linears - Swap XX and YY (or RR LL)
|
|---|
| [513] | 514 | rotate_xyphase - rotate XY phase of cross correlation
|
|---|
| 515 | rotate_linpolphase - rotate the phase of the complex
|
|---|
| 516 | polarization O=Q+iU correlation
|
|---|
| [733] | 517 | freq_switch - perform frequency switching on the data
|
|---|
| 518 | stats - Determine the specified statistic, e.g. 'min'
|
|---|
| 519 | 'max', 'rms' etc.
|
|---|
| 520 | stddev - Determine the standard deviation of the current
|
|---|
| 521 | beam/if/pol
|
|---|
| [1588] | 522 | get_row_selector - get the selection object for a specified row
|
|---|
| 523 | number
|
|---|
| [1014] | 524 | [Selection]
|
|---|
| 525 | selector - a selection object to set a subset of a scantable
|
|---|
| 526 | set_scans - set (a list of) scans by index
|
|---|
| 527 | set_cycles - set (a list of) cycles by index
|
|---|
| 528 | set_beams - set (a list of) beamss by index
|
|---|
| 529 | set_ifs - set (a list of) ifs by index
|
|---|
| 530 | set_polarisations - set (a list of) polarisations by name
|
|---|
| 531 | or by index
|
|---|
| 532 | set_names - set a selection by name (wildcards allowed)
|
|---|
| 533 | set_tsys - set a selection by tsys thresholds
|
|---|
| [1259] | 534 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1
|
|---|
| [1351] | 535 | ( also get_ functions for all these )
|
|---|
| [1014] | 536 | reset - unset all selections
|
|---|
| [1351] | 537 | + - merge two selections
|
|---|
| [733] | 538 |
|
|---|
| [513] | 539 | [Math] Mainly functions which operate on more than one scantable
|
|---|
| [100] | 540 |
|
|---|
| [706] | 541 | average_time - return the (weighted) time average
|
|---|
| [513] | 542 | of a list of scans
|
|---|
| 543 | quotient - return the on/off quotient
|
|---|
| 544 | simple_math - simple mathematical operations on two scantables,
|
|---|
| 545 | 'add', 'sub', 'mul', 'div'
|
|---|
| [1069] | 546 | quotient - build quotient of the given on and off scans
|
|---|
| [1351] | 547 | (matched pairs and 1 off - n on are valid)
|
|---|
| [1117] | 548 | merge - merge a list of scantables
|
|---|
| [1069] | 549 |
|
|---|
| [1151] | 550 | [Line Catalog]
|
|---|
| 551 | linecatalog - a linecatalog wrapper, taking an ASCII or
|
|---|
| 552 | internal format table
|
|---|
| 553 | summary - print a summary of the current selection
|
|---|
| 554 | set_name - select a subset by name pattern, e.g. '*OH*'
|
|---|
| 555 | set_strength_limits - select a subset by line strength limits
|
|---|
| 556 | set_frequency_limits - select a subset by frequency limits
|
|---|
| 557 | reset - unset all selections
|
|---|
| 558 | save - save the current subset to a table (internal
|
|---|
| 559 | format)
|
|---|
| 560 | get_row - get the name and frequency from a specific
|
|---|
| 561 | row in the table
|
|---|
| [513] | 562 | [Fitting]
|
|---|
| [113] | 563 | fitter
|
|---|
| 564 | auto_fit - return a scan where the function is
|
|---|
| 565 | applied to all Beams/IFs/Pols.
|
|---|
| 566 | commit - return a new scan where the fits have been
|
|---|
| 567 | commited.
|
|---|
| 568 | fit - execute the actual fitting process
|
|---|
| [984] | 569 | store_fit - store the fit parameters in the data (scantable)
|
|---|
| [113] | 570 | get_chi2 - get the Chi^2
|
|---|
| 571 | set_scan - set the scantable to be fit
|
|---|
| 572 | set_function - set the fitting function
|
|---|
| 573 | set_parameters - set the parameters for the function(s), and
|
|---|
| 574 | set if they should be held fixed during fitting
|
|---|
| [513] | 575 | set_gauss_parameters - same as above but specialised for individual
|
|---|
| 576 | gaussian components
|
|---|
| [113] | 577 | get_parameters - get the fitted parameters
|
|---|
| [513] | 578 | plot - plot the resulting fit and/or components and
|
|---|
| 579 | residual
|
|---|
| [210] | 580 | [Plotter]
|
|---|
| 581 | asapplotter - a plotter for asap, default plotter is
|
|---|
| 582 | called 'plotter'
|
|---|
| [984] | 583 | plot - plot a scantable
|
|---|
| [1151] | 584 | plot_lines - plot a linecatalog overlay
|
|---|
| [1697] | 585 | plotazel - plot azimuth and elevation versus time
|
|---|
| 586 | plotpointing - plot telescope pointings
|
|---|
| [378] | 587 | save - save the plot to a file ('png' ,'ps' or 'eps')
|
|---|
| [210] | 588 | set_mode - set the state of the plotter, i.e.
|
|---|
| 589 | what is to be plotted 'colour stacked'
|
|---|
| 590 | and what 'panelled'
|
|---|
| [984] | 591 | set_selection - only plot a selected part of the data
|
|---|
| [733] | 592 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax]
|
|---|
| [255] | 593 | set_legend - specify user labels for the legend indeces
|
|---|
| 594 | set_title - specify user labels for the panel indeces
|
|---|
| [733] | 595 | set_abcissa - specify a user label for the abcissa
|
|---|
| [255] | 596 | set_ordinate - specify a user label for the ordinate
|
|---|
| [378] | 597 | set_layout - specify the multi-panel layout (rows,cols)
|
|---|
| [733] | 598 | set_colors - specify a set of colours to use
|
|---|
| 599 | set_linestyles - specify a set of linestyles to use if only
|
|---|
| 600 | using one color
|
|---|
| [1151] | 601 | set_font - set general font properties, e.g. 'family'
|
|---|
| [1054] | 602 | set_histogram - plot in historam style
|
|---|
| [733] | 603 | set_mask - set a plotting mask for a specific polarization
|
|---|
| [1171] | 604 | text - draw text annotations either in data or relative
|
|---|
| 605 | coordinates
|
|---|
| 606 | arrow - draw arrow annotations either in data or relative
|
|---|
| 607 | coordinates
|
|---|
| 608 | axhline,axvline - draw horizontal/vertical lines
|
|---|
| 609 | axhspan,axvspan - draw horizontal/vertical regions
|
|---|
| [1560] | 610 | annotate - draw an arrow with label
|
|---|
| 611 | create_mask - create a scnatble mask interactively
|
|---|
| [1175] | 612 |
|
|---|
| 613 | xyplotter - matplotlib/pylab plotting functions
|
|---|
| 614 |
|
|---|
| [182] | 615 | [Reading files]
|
|---|
| 616 | reader - access rpfits/sdfits files
|
|---|
| [984] | 617 | open - attach reader to a file
|
|---|
| 618 | close - detach reader from file
|
|---|
| [182] | 619 | read - read in integrations
|
|---|
| 620 | summary - list info about all integrations
|
|---|
| 621 |
|
|---|
| [113] | 622 | [General]
|
|---|
| 623 | commands - this command
|
|---|
| 624 | print - print details about a variable
|
|---|
| [1560] | 625 | list_scans - list all scantables created by the user
|
|---|
| [992] | 626 | list_files - list all files readable by asap (default rpf)
|
|---|
| [113] | 627 | del - delete the given variable from memory
|
|---|
| 628 | range - create a list of values, e.g.
|
|---|
| 629 | range(3) = [0,1,2], range(2,5) = [2,3,4]
|
|---|
| 630 | help - print help for one of the listed functions
|
|---|
| 631 | execfile - execute an asap script, e.g. execfile('myscript')
|
|---|
| [255] | 632 | list_rcparameters - print out a list of possible values to be
|
|---|
| [274] | 633 | put into $HOME/.asaprc
|
|---|
| [1171] | 634 | rc - set rc parameters from within asap
|
|---|
| [466] | 635 | mask_and,mask_or,
|
|---|
| 636 | mask_not - boolean operations on masks created with
|
|---|
| 637 | scantable.create_mask
|
|---|
| [1697] | 638 | skydip - gain opacity values from a sky dip observation
|
|---|
| [706] | 639 |
|
|---|
| [210] | 640 | Note:
|
|---|
| 641 | How to use this with help:
|
|---|
| 642 | # function 'summary'
|
|---|
| 643 | [xxx] is just a category
|
|---|
| 644 | Every 'sub-level' in this list should be replaces by a '.' Period when
|
|---|
| [706] | 645 | using help
|
|---|
| [210] | 646 | Example:
|
|---|
| 647 | ASAP> help scantable # to get info on ths scantable
|
|---|
| 648 | ASAP> help scantable.summary # to get help on the scantable's
|
|---|
| 649 | ASAP> help average_time
|
|---|
| 650 |
|
|---|
| [715] | 651 | """
|
|---|
| [1151] | 652 | if rcParams['verbose']:
|
|---|
| 653 | try:
|
|---|
| 654 | from IPython.genutils import page as pager
|
|---|
| 655 | except ImportError:
|
|---|
| 656 | from pydoc import pager
|
|---|
| 657 | pager(x)
|
|---|
| 658 | else:
|
|---|
| 659 | print x
|
|---|
| [715] | 660 | return
|
|---|
| [113] | 661 |
|
|---|
| [706] | 662 | def welcome():
|
|---|
| 663 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package
|
|---|
| [100] | 664 |
|
|---|
| [1035] | 665 | Please report any bugs via:
|
|---|
| [1378] | 666 | http://svn.atnf.csiro.au/trac/asap/simpleticket
|
|---|
| [100] | 667 |
|
|---|
| [378] | 668 | [IMPORTANT: ASAP is 0-based]
|
|---|
| [706] | 669 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__)
|
|---|
