[100] | 1 | """ |
---|
| 2 | This is the ATNF Single Dish Analysis package. |
---|
| 3 | |
---|
| 4 | """ |
---|
[1080] | 5 | import os,sys,shutil, platform |
---|
[1589] | 6 | import functools |
---|
[226] | 7 | |
---|
[1080] | 8 | # Set up AIPSPATH and first time use of asap i.e. ~/.asap/* |
---|
| 9 | plf = None |
---|
| 10 | if sys.platform == "linux2": |
---|
| 11 | if platform.architecture()[0] == '64bit': |
---|
| 12 | plf = 'linux_64b' |
---|
| 13 | else: |
---|
| 14 | plf = 'linux_gnu' |
---|
| 15 | elif sys.platform == 'darwin': |
---|
| 16 | plf = 'darwin' |
---|
| 17 | else: |
---|
| 18 | # Shouldn't happen - default to linux |
---|
| 19 | plf = 'linux' |
---|
| 20 | asapdata = __path__[-1] |
---|
[1171] | 21 | # Allow user defined data location |
---|
| 22 | if os.environ.has_key("ASAPDATA"): |
---|
| 23 | if os.path.exists(os.environ["ASAPDATA"]): |
---|
| 24 | asapdata = os.environ["ASAPDATA"] |
---|
[1371] | 25 | # use AIPSPATH if defined and "data" dir present |
---|
| 26 | if not os.environ.has_key("AIPSPATH") or \ |
---|
| 27 | not os.path.exists(os.environ["AIPSPATH"].split()[0]+"/data"): |
---|
[1316] | 28 | os.environ["AIPSPATH"] = "%s %s somwhere" % ( asapdata, plf) |
---|
[1171] | 29 | # set up user space |
---|
[1080] | 30 | userdir = os.environ["HOME"]+"/.asap" |
---|
| 31 | if not os.path.exists(userdir): |
---|
| 32 | print 'First time ASAP use. Setting up ~/.asap' |
---|
| 33 | os.mkdir(userdir) |
---|
| 34 | shutil.copyfile(asapdata+"/data/ipythonrc-asap", userdir+"/ipythonrc-asap") |
---|
[1588] | 35 | shutil.copyfile(asapdata+"/data/ipy_user_conf.py", |
---|
[1434] | 36 | userdir+"/ipy_user_conf.py") |
---|
[1080] | 37 | f = file(userdir+"/asapuserfuncs.py", "w") |
---|
| 38 | f.close() |
---|
| 39 | f = file(userdir+"/ipythonrc", "w") |
---|
| 40 | f.close() |
---|
[1472] | 41 | else: |
---|
| 42 | # upgrade to support later ipython versions |
---|
| 43 | if not os.path.exists(userdir+"/ipy_user_conf.py"): |
---|
[1588] | 44 | shutil.copyfile(asapdata+"/data/ipy_user_conf.py", |
---|
[1472] | 45 | userdir+"/ipy_user_conf.py") |
---|
| 46 | |
---|
[1171] | 47 | # remove from namespace |
---|
[1080] | 48 | del asapdata, userdir, shutil, platform |
---|
| 49 | |
---|
[513] | 50 | def _validate_bool(b): |
---|
[226] | 51 | 'Convert b to a boolean or raise' |
---|
| 52 | bl = b.lower() |
---|
| 53 | if bl in ('f', 'no', 'false', '0', 0): return False |
---|
| 54 | elif bl in ('t', 'yes', 'true', '1', 1): return True |
---|
| 55 | else: |
---|
| 56 | raise ValueError('Could not convert "%s" to boolean' % b) |
---|
| 57 | |
---|
[513] | 58 | def _validate_int(s): |
---|
[226] | 59 | 'convert s to int or raise' |
---|
| 60 | try: return int(s) |
---|
| 61 | except ValueError: |
---|
| 62 | raise ValueError('Could not convert "%s" to int' % s) |
---|
| 63 | |
---|
[513] | 64 | def _asap_fname(): |
---|
[226] | 65 | """ |
---|
| 66 | Return the path to the rc file |
---|
| 67 | |
---|
| 68 | Search order: |
---|
| 69 | |
---|
| 70 | * current working dir |
---|
| 71 | * environ var ASAPRC |
---|
[274] | 72 | * HOME/.asaprc |
---|
[706] | 73 | |
---|
[226] | 74 | """ |
---|
| 75 | |
---|
| 76 | fname = os.path.join( os.getcwd(), '.asaprc') |
---|
| 77 | if os.path.exists(fname): return fname |
---|
| 78 | |
---|
| 79 | if os.environ.has_key('ASAPRC'): |
---|
| 80 | path = os.environ['ASAPRC'] |
---|
| 81 | if os.path.exists(path): |
---|
| 82 | fname = os.path.join(path, '.asaprc') |
---|
| 83 | if os.path.exists(fname): |
---|
| 84 | return fname |
---|
| 85 | |
---|
| 86 | if os.environ.has_key('HOME'): |
---|
| 87 | home = os.environ['HOME'] |
---|
| 88 | fname = os.path.join(home, '.asaprc') |
---|
| 89 | if os.path.exists(fname): |
---|
| 90 | return fname |
---|
| 91 | return None |
---|
| 92 | |
---|
[706] | 93 | |
---|
[226] | 94 | defaultParams = { |
---|
| 95 | # general |
---|
[513] | 96 | 'verbose' : [True, _validate_bool], |
---|
| 97 | 'useplotter' : [True, _validate_bool], |
---|
[542] | 98 | 'insitu' : [True, _validate_bool], |
---|
[706] | 99 | |
---|
[226] | 100 | # plotting |
---|
[706] | 101 | 'plotter.gui' : [True, _validate_bool], |
---|
[226] | 102 | 'plotter.stacking' : ['p', str], |
---|
| 103 | 'plotter.panelling' : ['s', str], |
---|
[700] | 104 | 'plotter.colours' : ['', str], |
---|
| 105 | 'plotter.linestyles' : ['', str], |
---|
[710] | 106 | 'plotter.decimate' : [False, _validate_bool], |
---|
| 107 | 'plotter.ganged' : [True, _validate_bool], |
---|
[1022] | 108 | 'plotter.histogram' : [False, _validate_bool], |
---|
[1097] | 109 | 'plotter.papertype' : ['A4', str], |
---|
[1560] | 110 | 'plotter.axesformatting' : ['mpl', str], |
---|
[710] | 111 | |
---|
[226] | 112 | # scantable |
---|
| 113 | 'scantable.save' : ['ASAP', str], |
---|
[513] | 114 | 'scantable.autoaverage' : [True, _validate_bool], |
---|
[226] | 115 | 'scantable.freqframe' : ['LSRK', str], #default frequency frame |
---|
[1076] | 116 | 'scantable.verbosesummary' : [False, _validate_bool], |
---|
[1422] | 117 | 'scantable.storage' : ['memory', str], |
---|
[1504] | 118 | 'scantable.history' : [True, _validate_bool], |
---|
[1586] | 119 | 'scantable.reference' : ['.*(e|w|_R)$', str], |
---|
| 120 | 'scantable.parallactify' : [False, _validate_bool] |
---|
[226] | 121 | # fitter |
---|
| 122 | } |
---|
| 123 | |
---|
[255] | 124 | def list_rcparameters(): |
---|
[706] | 125 | |
---|
[255] | 126 | print """ |
---|
[737] | 127 | # general |
---|
| 128 | # print verbose output |
---|
| 129 | verbose : True |
---|
[255] | 130 | |
---|
[737] | 131 | # preload a default plotter |
---|
| 132 | useplotter : True |
---|
[255] | 133 | |
---|
[737] | 134 | # apply operations on the input scantable or return new one |
---|
| 135 | insitu : True |
---|
[706] | 136 | |
---|
[737] | 137 | # plotting |
---|
[710] | 138 | |
---|
[737] | 139 | # do we want a GUI or plot to a file |
---|
| 140 | plotter.gui : True |
---|
[710] | 141 | |
---|
[737] | 142 | # default mode for colour stacking |
---|
| 143 | plotter.stacking : Pol |
---|
[255] | 144 | |
---|
[737] | 145 | # default mode for panelling |
---|
| 146 | plotter.panelling : scan |
---|
[255] | 147 | |
---|
[1560] | 148 | # push panels together, to share axis labels |
---|
[737] | 149 | plotter.ganged : True |
---|
[710] | 150 | |
---|
[1513] | 151 | # decimate the number of points plotted by a factor of |
---|
[737] | 152 | # nchan/1024 |
---|
| 153 | plotter.decimate : False |
---|
[733] | 154 | |
---|
[737] | 155 | # default colours/linestyles |
---|
| 156 | plotter.colours : |
---|
| 157 | plotter.linestyles : |
---|
[700] | 158 | |
---|
[1022] | 159 | # enable/disable histogram plotting |
---|
| 160 | plotter.histogram : False |
---|
| 161 | |
---|
[1097] | 162 | # ps paper type |
---|
| 163 | plotter.papertype : A4 |
---|
| 164 | |
---|
[1513] | 165 | # The formatting style of the xaxis |
---|
[1560] | 166 | plotter.axesformatting : 'mpl' (default) or 'asap' (for old versions of matplotlib) |
---|
[1513] | 167 | |
---|
[737] | 168 | # scantable |
---|
[1076] | 169 | |
---|
[1259] | 170 | # default storage of scantable ('memory'/'disk') |
---|
[1076] | 171 | scantable.storage : memory |
---|
[1422] | 172 | |
---|
| 173 | # write history of each call to scantable |
---|
| 174 | scantable.history : True |
---|
| 175 | |
---|
[737] | 176 | # default ouput format when saving |
---|
| 177 | scantable.save : ASAP |
---|
[1422] | 178 | |
---|
[737] | 179 | # auto averaging on read |
---|
| 180 | scantable.autoaverage : True |
---|
[255] | 181 | |
---|
[737] | 182 | # default frequency frame to set when function |
---|
[1097] | 183 | # scantable.set_freqframe is called |
---|
[737] | 184 | scantable.freqframe : LSRK |
---|
[255] | 185 | |
---|
[737] | 186 | # Control the level of information printed by summary |
---|
| 187 | scantable.verbosesummary : False |
---|
[706] | 188 | |
---|
[1504] | 189 | # Control the identification of reference (off) scans |
---|
| 190 | # This is has to be a regular expression |
---|
| 191 | scantable.reference : .*(e|w|_R)$ |
---|
[1560] | 192 | |
---|
[737] | 193 | # Fitter |
---|
| 194 | """ |
---|
[706] | 195 | |
---|
[226] | 196 | def rc_params(): |
---|
| 197 | 'Return the default params updated from the values in the rc file' |
---|
[706] | 198 | |
---|
[513] | 199 | fname = _asap_fname() |
---|
[706] | 200 | |
---|
[226] | 201 | if fname is None or not os.path.exists(fname): |
---|
| 202 | message = 'could not find rc file; returning defaults' |
---|
| 203 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
---|
| 204 | #print message |
---|
| 205 | return ret |
---|
[706] | 206 | |
---|
[226] | 207 | cnt = 0 |
---|
| 208 | for line in file(fname): |
---|
| 209 | cnt +=1 |
---|
| 210 | line = line.strip() |
---|
| 211 | if not len(line): continue |
---|
| 212 | if line.startswith('#'): continue |
---|
| 213 | tup = line.split(':',1) |
---|
| 214 | if len(tup) !=2: |
---|
| 215 | print ('Illegal line #%d\n\t%s\n\tin file "%s"' % (cnt, line, fname)) |
---|
| 216 | continue |
---|
[706] | 217 | |
---|
[226] | 218 | key, val = tup |
---|
| 219 | key = key.strip() |
---|
| 220 | if not defaultParams.has_key(key): |
---|
| 221 | print ('Bad key "%s" on line %d in %s' % (key, cnt, fname)) |
---|
| 222 | continue |
---|
[706] | 223 | |
---|
[226] | 224 | default, converter = defaultParams[key] |
---|
| 225 | |
---|
| 226 | ind = val.find('#') |
---|
| 227 | if ind>=0: val = val[:ind] # ignore trailing comments |
---|
| 228 | val = val.strip() |
---|
| 229 | try: cval = converter(val) # try to convert to proper type or raise |
---|
[1080] | 230 | except ValueError, msg: |
---|
[226] | 231 | print ('Bad val "%s" on line #%d\n\t"%s"\n\tin file "%s"\n\t%s' % (val, cnt, line, fname, msg)) |
---|
| 232 | continue |
---|
| 233 | else: |
---|
| 234 | # Alles Klar, update dict |
---|
| 235 | defaultParams[key][0] = cval |
---|
| 236 | |
---|
| 237 | # strip the conveter funcs and return |
---|
| 238 | ret = dict([ (key, tup[0]) for key, tup in defaultParams.items()]) |
---|
[466] | 239 | print ('loaded rc file %s'%fname) |
---|
[226] | 240 | |
---|
| 241 | return ret |
---|
| 242 | |
---|
| 243 | |
---|
| 244 | # this is the instance used by the asap classes |
---|
[706] | 245 | rcParams = rc_params() |
---|
[226] | 246 | |
---|
| 247 | rcParamsDefault = dict(rcParams.items()) # a copy |
---|
| 248 | |
---|
| 249 | def rc(group, **kwargs): |
---|
| 250 | """ |
---|
| 251 | Set the current rc params. Group is the grouping for the rc, eg |
---|
[379] | 252 | for scantable.save the group is 'scantable', for plotter.stacking, the |
---|
| 253 | group is 'plotter', and so on. kwargs is a list of attribute |
---|
[226] | 254 | name/value pairs, eg |
---|
| 255 | |
---|
[379] | 256 | rc('scantable', save='SDFITS') |
---|
[226] | 257 | |
---|
| 258 | sets the current rc params and is equivalent to |
---|
[706] | 259 | |
---|
[379] | 260 | rcParams['scantable.save'] = 'SDFITS' |
---|
[226] | 261 | |
---|
| 262 | Use rcdefaults to restore the default rc params after changes. |
---|
| 263 | """ |
---|
| 264 | |
---|
[379] | 265 | aliases = {} |
---|
[706] | 266 | |
---|
[226] | 267 | for k,v in kwargs.items(): |
---|
| 268 | name = aliases.get(k) or k |
---|
[1422] | 269 | if len(group): |
---|
| 270 | key = '%s.%s' % (group, name) |
---|
| 271 | else: |
---|
| 272 | key = name |
---|
[226] | 273 | if not rcParams.has_key(key): |
---|
| 274 | raise KeyError('Unrecognized key "%s" for group "%s" and name "%s"' % (key, group, name)) |
---|
[706] | 275 | |
---|
[226] | 276 | rcParams[key] = v |
---|
| 277 | |
---|
| 278 | |
---|
| 279 | def rcdefaults(): |
---|
| 280 | """ |
---|
| 281 | Restore the default rc params - the ones that were created at |
---|
| 282 | asap load time |
---|
| 283 | """ |
---|
| 284 | rcParams.update(rcParamsDefault) |
---|
| 285 | |
---|
[1295] | 286 | def _n_bools(n, val): |
---|
[1588] | 287 | return [ val for i in xrange(n) ] |
---|
[513] | 288 | |
---|
| 289 | def _is_sequence_or_number(param, ptype=int): |
---|
| 290 | if isinstance(param,tuple) or isinstance(param,list): |
---|
[928] | 291 | if len(param) == 0: return True # empty list |
---|
[513] | 292 | out = True |
---|
| 293 | for p in param: |
---|
| 294 | out &= isinstance(p,ptype) |
---|
| 295 | return out |
---|
| 296 | elif isinstance(param, ptype): |
---|
| 297 | return True |
---|
| 298 | return False |
---|
| 299 | |
---|
[928] | 300 | def _to_list(param, ptype=int): |
---|
| 301 | if isinstance(param, ptype): |
---|
| 302 | if ptype is str: return param.split() |
---|
| 303 | else: return [param] |
---|
| 304 | if _is_sequence_or_number(param, ptype): |
---|
| 305 | return param |
---|
| 306 | return None |
---|
[715] | 307 | |
---|
[944] | 308 | def unique(x): |
---|
[992] | 309 | """ |
---|
| 310 | Return the unique values in a list |
---|
| 311 | Parameters: |
---|
| 312 | x: the list to reduce |
---|
| 313 | Examples: |
---|
| 314 | x = [1,2,3,3,4] |
---|
| 315 | print unique(x) |
---|
| 316 | [1,2,3,4] |
---|
| 317 | """ |
---|
[944] | 318 | return dict([ (val, 1) for val in x]).keys() |
---|
| 319 | |
---|
[992] | 320 | def list_files(path=".",suffix="rpf"): |
---|
| 321 | """ |
---|
| 322 | Return a list files readable by asap, such as rpf, sdfits, mbf, asap |
---|
| 323 | Parameters: |
---|
| 324 | path: The directory to list (default '.') |
---|
| 325 | suffix: The file extension (default rpf) |
---|
| 326 | Example: |
---|
| 327 | files = list_files("data/","sdfits") |
---|
| 328 | print files |
---|
| 329 | ['data/2001-09-01_0332_P363.sdfits', |
---|
| 330 | 'data/2003-04-04_131152_t0002.sdfits', |
---|
| 331 | 'data/Sgr_86p262_best_SPC.sdfits'] |
---|
| 332 | """ |
---|
| 333 | if not os.path.isdir(path): |
---|
| 334 | return None |
---|
[1295] | 335 | valid = "rpf rpf.1 rpf.2 sdf sdfits mbf asap".split() |
---|
[992] | 336 | if not suffix in valid: |
---|
| 337 | return None |
---|
| 338 | files = [os.path.expanduser(os.path.expandvars(path+"/"+f)) for f in os.listdir(path)] |
---|
| 339 | return filter(lambda x: x.endswith(suffix),files) |
---|
| 340 | |
---|
[715] | 341 | # workaround for ipython, which redirects this if banner=0 in ipythonrc |
---|
| 342 | sys.stdout = sys.__stdout__ |
---|
| 343 | sys.stderr = sys.__stderr__ |
---|
| 344 | |
---|
| 345 | # Logging |
---|
| 346 | from asap._asap import Log as _asaplog |
---|
| 347 | global asaplog |
---|
[710] | 348 | asaplog=_asaplog() |
---|
[715] | 349 | if rcParams['verbose']: |
---|
| 350 | asaplog.enable() |
---|
| 351 | else: |
---|
| 352 | asaplog.disable() |
---|
| 353 | |
---|
[1589] | 354 | |
---|
| 355 | def print_log_dec(f): |
---|
| 356 | @functools.wraps(f) |
---|
| 357 | def wrap_it(*args, **kw): |
---|
| 358 | val = f(*args, **kw) |
---|
| 359 | print_log() |
---|
| 360 | return val |
---|
| 361 | return wrap_it |
---|
| 362 | |
---|
[715] | 363 | def print_log(): |
---|
[1589] | 364 | log = asaplog.pop().strip() |
---|
[715] | 365 | if len(log) and rcParams['verbose']: print log |
---|
| 366 | return |
---|
| 367 | |
---|
[1295] | 368 | def mask_and(a, b): |
---|
| 369 | assert(len(a)==len(b)) |
---|
| 370 | return [ a[i] & b[i] for i in xrange(len(a)) ] |
---|
[1134] | 371 | |
---|
[1295] | 372 | def mask_or(a, b): |
---|
| 373 | assert(len(a)==len(b)) |
---|
| 374 | return [ a[i] | b[i] for i in xrange(len(a)) ] |
---|
| 375 | |
---|
| 376 | def mask_not(a): |
---|
| 377 | return [ not i for i in a ] |
---|
| 378 | |
---|
[1117] | 379 | from asapfitter import fitter |
---|
[895] | 380 | from asapreader import reader |
---|
[944] | 381 | from selector import selector |
---|
[710] | 382 | |
---|
[100] | 383 | from asapmath import * |
---|
[1080] | 384 | from scantable import scantable |
---|
[1097] | 385 | from asaplinefind import linefinder |
---|
[1134] | 386 | from linecatalog import linecatalog |
---|
[285] | 387 | |
---|
[928] | 388 | if rcParams['useplotter']: |
---|
[1295] | 389 | try: |
---|
[1423] | 390 | from asapplotter import asapplotter |
---|
| 391 | gui = os.environ.has_key('DISPLAY') and rcParams['plotter.gui'] |
---|
| 392 | if gui: |
---|
[1422] | 393 | import matplotlib |
---|
| 394 | matplotlib.use("TkAgg") |
---|
[1423] | 395 | import pylab |
---|
[1422] | 396 | xyplotter = pylab |
---|
[1423] | 397 | plotter = asapplotter(gui) |
---|
| 398 | del gui |
---|
[1295] | 399 | except ImportError: |
---|
[1423] | 400 | print "Matplotlib not installed. No plotting available" |
---|
[285] | 401 | |
---|
[574] | 402 | __date__ = '$Date: 2009-07-02 02:17:20 +0000 (Thu, 02 Jul 2009) $'.split()[1] |
---|
[1560] | 403 | __version__ = '$Revision: 1589 $' |
---|
[100] | 404 | |
---|
[1193] | 405 | def is_ipython(): |
---|
[1259] | 406 | return '__IP' in dir(sys.modules["__main__"]) |
---|
[1589] | 407 | |
---|
[1193] | 408 | if is_ipython(): |
---|
[1014] | 409 | def version(): print "ASAP %s(%s)"% (__version__, __date__) |
---|
[1588] | 410 | |
---|
| 411 | def list_scans(t = scantable): |
---|
[1560] | 412 | import inspect |
---|
| 413 | print "The user created scantables are: ", |
---|
| 414 | globs=inspect.currentframe().f_back.f_locals.copy() |
---|
| 415 | out = [ k for k,v in globs.iteritems() \ |
---|
| 416 | if isinstance(v, scantable) and not k.startswith("_") ] |
---|
| 417 | print out |
---|
| 418 | return out |
---|
[100] | 419 | |
---|
[715] | 420 | def commands(): |
---|
| 421 | x = """ |
---|
[113] | 422 | [The scan container] |
---|
| 423 | scantable - a container for integrations/scans |
---|
[182] | 424 | (can open asap/rpfits/sdfits and ms files) |
---|
[113] | 425 | copy - returns a copy of a scan |
---|
| 426 | get_scan - gets a specific scan out of a scantable |
---|
[984] | 427 | (by name or number) |
---|
[1093] | 428 | drop_scan - drops a specific scan out of a scantable |
---|
| 429 | (by number) |
---|
[984] | 430 | set_selection - set a new subselection of the data |
---|
| 431 | get_selection - get the current selection object |
---|
[113] | 432 | summary - print info about the scantable contents |
---|
[182] | 433 | stats - get specified statistic of the spectra in |
---|
| 434 | the scantable |
---|
| 435 | stddev - get the standard deviation of the spectra |
---|
| 436 | in the scantable |
---|
[113] | 437 | get_tsys - get the TSys |
---|
| 438 | get_time - get the timestamps of the integrations |
---|
[1351] | 439 | get_inttime - get the integration time |
---|
[733] | 440 | get_sourcename - get the source names of the scans |
---|
[794] | 441 | get_azimuth - get the azimuth of the scans |
---|
| 442 | get_elevation - get the elevation of the scans |
---|
| 443 | get_parangle - get the parallactic angle of the scans |
---|
[876] | 444 | get_unit - get the current unit |
---|
[513] | 445 | set_unit - set the abcissa unit to be used from this |
---|
| 446 | point on |
---|
[255] | 447 | get_abcissa - get the abcissa values and name for a given |
---|
| 448 | row (time) |
---|
[1259] | 449 | get_column_names - get the names of the columns in the scantable |
---|
| 450 | for use with selector.set_query |
---|
[113] | 451 | set_freqframe - set the frame info for the Spectral Axis |
---|
| 452 | (e.g. 'LSRK') |
---|
[276] | 453 | set_doppler - set the doppler to be used from this point on |
---|
[984] | 454 | set_dirframe - set the frame for the direction on the sky |
---|
[240] | 455 | set_instrument - set the instrument name |
---|
[1190] | 456 | set_feedtype - set the feed type |
---|
[255] | 457 | get_fluxunit - get the brightness flux unit |
---|
[240] | 458 | set_fluxunit - set the brightness flux unit |
---|
[1508] | 459 | set_sourcetype - set the type of the source - source or reference |
---|
[188] | 460 | create_mask - return an mask in the current unit |
---|
| 461 | for the given region. The specified regions |
---|
| 462 | are NOT masked |
---|
[255] | 463 | get_restfreqs - get the current list of rest frequencies |
---|
| 464 | set_restfreqs - set a list of rest frequencies |
---|
[1471] | 465 | shift_refpix - shift the reference pixel of the IFs |
---|
| 466 | set_spectrum - overwrite the spectrum for a given row |
---|
| 467 | get_spectrum - retrieve the spectrum for a given |
---|
| 468 | get_mask - retrieve the mask for a given |
---|
[1012] | 469 | flag - flag selected channels in the data |
---|
[1192] | 470 | lag_flag - flag specified frequency in the data |
---|
[1151] | 471 | save - save the scantable to disk as either 'ASAP', |
---|
| 472 | 'SDFITS' or 'ASCII' |
---|
[486] | 473 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
---|
[733] | 474 | nscan - the number of scans in the scantable |
---|
[1422] | 475 | nrow - the number of spectra in the scantable |
---|
[486] | 476 | history - print the history of the scantable |
---|
[530] | 477 | get_fit - get a fit which has been stored witnh the data |
---|
[706] | 478 | average_time - return the (weighted) time average of a scan |
---|
[513] | 479 | or a list of scans |
---|
| 480 | average_pol - average the polarisations together. |
---|
[1144] | 481 | average_beam - average the beams together. |
---|
[992] | 482 | convert_pol - convert to a different polarisation type |
---|
[690] | 483 | auto_quotient - return the on/off quotient with |
---|
[1069] | 484 | automatic detection of the on/off scans (closest |
---|
| 485 | in time off is selected) |
---|
[1144] | 486 | mx_quotient - Form a quotient using MX data (off beams) |
---|
[1014] | 487 | scale, *, / - return a scan scaled by a given factor |
---|
[1560] | 488 | add, + - return a scan with given value added |
---|
| 489 | sub, - - return a scan with given value subtracted |
---|
[513] | 490 | bin - return a scan with binned channels |
---|
| 491 | resample - return a scan with resampled channels |
---|
| 492 | smooth - return the spectrally smoothed scan |
---|
| 493 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
---|
[706] | 494 | auto_poly_baseline - automatically fit a polynomial baseline |
---|
[780] | 495 | recalc_azel - recalculate azimuth and elevation based on |
---|
| 496 | the pointing |
---|
[513] | 497 | gain_el - apply gain-elevation correction |
---|
| 498 | opacity - apply opacity correction |
---|
| 499 | convert_flux - convert to and from Jy and Kelvin brightness |
---|
[255] | 500 | units |
---|
[513] | 501 | freq_align - align spectra in frequency frame |
---|
[1014] | 502 | invert_phase - Invert the phase of the cross-correlation |
---|
[1351] | 503 | swap_linears - Swap XX and YY (or RR LL) |
---|
[513] | 504 | rotate_xyphase - rotate XY phase of cross correlation |
---|
| 505 | rotate_linpolphase - rotate the phase of the complex |
---|
| 506 | polarization O=Q+iU correlation |
---|
[733] | 507 | freq_switch - perform frequency switching on the data |
---|
| 508 | stats - Determine the specified statistic, e.g. 'min' |
---|
| 509 | 'max', 'rms' etc. |
---|
| 510 | stddev - Determine the standard deviation of the current |
---|
| 511 | beam/if/pol |
---|
[1588] | 512 | get_row_selector - get the selection object for a specified row |
---|
| 513 | number |
---|
[1014] | 514 | [Selection] |
---|
| 515 | selector - a selection object to set a subset of a scantable |
---|
| 516 | set_scans - set (a list of) scans by index |
---|
| 517 | set_cycles - set (a list of) cycles by index |
---|
| 518 | set_beams - set (a list of) beamss by index |
---|
| 519 | set_ifs - set (a list of) ifs by index |
---|
| 520 | set_polarisations - set (a list of) polarisations by name |
---|
| 521 | or by index |
---|
| 522 | set_names - set a selection by name (wildcards allowed) |
---|
| 523 | set_tsys - set a selection by tsys thresholds |
---|
[1259] | 524 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1 |
---|
[1351] | 525 | ( also get_ functions for all these ) |
---|
[1014] | 526 | reset - unset all selections |
---|
[1351] | 527 | + - merge two selections |
---|
[733] | 528 | |
---|
[513] | 529 | [Math] Mainly functions which operate on more than one scantable |
---|
[100] | 530 | |
---|
[706] | 531 | average_time - return the (weighted) time average |
---|
[513] | 532 | of a list of scans |
---|
| 533 | quotient - return the on/off quotient |
---|
| 534 | simple_math - simple mathematical operations on two scantables, |
---|
| 535 | 'add', 'sub', 'mul', 'div' |
---|
[1069] | 536 | quotient - build quotient of the given on and off scans |
---|
[1351] | 537 | (matched pairs and 1 off - n on are valid) |
---|
[1117] | 538 | merge - merge a list of scantables |
---|
[1069] | 539 | |
---|
[1151] | 540 | [Line Catalog] |
---|
| 541 | linecatalog - a linecatalog wrapper, taking an ASCII or |
---|
| 542 | internal format table |
---|
| 543 | summary - print a summary of the current selection |
---|
| 544 | set_name - select a subset by name pattern, e.g. '*OH*' |
---|
| 545 | set_strength_limits - select a subset by line strength limits |
---|
| 546 | set_frequency_limits - select a subset by frequency limits |
---|
| 547 | reset - unset all selections |
---|
| 548 | save - save the current subset to a table (internal |
---|
| 549 | format) |
---|
| 550 | get_row - get the name and frequency from a specific |
---|
| 551 | row in the table |
---|
[513] | 552 | [Fitting] |
---|
[113] | 553 | fitter |
---|
| 554 | auto_fit - return a scan where the function is |
---|
| 555 | applied to all Beams/IFs/Pols. |
---|
| 556 | commit - return a new scan where the fits have been |
---|
| 557 | commited. |
---|
| 558 | fit - execute the actual fitting process |
---|
[984] | 559 | store_fit - store the fit parameters in the data (scantable) |
---|
[113] | 560 | get_chi2 - get the Chi^2 |
---|
| 561 | set_scan - set the scantable to be fit |
---|
| 562 | set_function - set the fitting function |
---|
| 563 | set_parameters - set the parameters for the function(s), and |
---|
| 564 | set if they should be held fixed during fitting |
---|
[513] | 565 | set_gauss_parameters - same as above but specialised for individual |
---|
| 566 | gaussian components |
---|
[113] | 567 | get_parameters - get the fitted parameters |
---|
[513] | 568 | plot - plot the resulting fit and/or components and |
---|
| 569 | residual |
---|
[210] | 570 | [Plotter] |
---|
| 571 | asapplotter - a plotter for asap, default plotter is |
---|
| 572 | called 'plotter' |
---|
[984] | 573 | plot - plot a scantable |
---|
[1151] | 574 | plot_lines - plot a linecatalog overlay |
---|
[378] | 575 | save - save the plot to a file ('png' ,'ps' or 'eps') |
---|
[210] | 576 | set_mode - set the state of the plotter, i.e. |
---|
| 577 | what is to be plotted 'colour stacked' |
---|
| 578 | and what 'panelled' |
---|
[984] | 579 | set_selection - only plot a selected part of the data |
---|
[733] | 580 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
---|
[255] | 581 | set_legend - specify user labels for the legend indeces |
---|
| 582 | set_title - specify user labels for the panel indeces |
---|
[733] | 583 | set_abcissa - specify a user label for the abcissa |
---|
[255] | 584 | set_ordinate - specify a user label for the ordinate |
---|
[378] | 585 | set_layout - specify the multi-panel layout (rows,cols) |
---|
[733] | 586 | set_colors - specify a set of colours to use |
---|
| 587 | set_linestyles - specify a set of linestyles to use if only |
---|
| 588 | using one color |
---|
[1151] | 589 | set_font - set general font properties, e.g. 'family' |
---|
[1054] | 590 | set_histogram - plot in historam style |
---|
[733] | 591 | set_mask - set a plotting mask for a specific polarization |
---|
[1171] | 592 | text - draw text annotations either in data or relative |
---|
| 593 | coordinates |
---|
| 594 | arrow - draw arrow annotations either in data or relative |
---|
| 595 | coordinates |
---|
| 596 | axhline,axvline - draw horizontal/vertical lines |
---|
| 597 | axhspan,axvspan - draw horizontal/vertical regions |
---|
[1560] | 598 | annotate - draw an arrow with label |
---|
| 599 | create_mask - create a scnatble mask interactively |
---|
[1175] | 600 | |
---|
| 601 | xyplotter - matplotlib/pylab plotting functions |
---|
| 602 | |
---|
[182] | 603 | [Reading files] |
---|
| 604 | reader - access rpfits/sdfits files |
---|
[984] | 605 | open - attach reader to a file |
---|
| 606 | close - detach reader from file |
---|
[182] | 607 | read - read in integrations |
---|
| 608 | summary - list info about all integrations |
---|
| 609 | |
---|
[113] | 610 | [General] |
---|
| 611 | commands - this command |
---|
| 612 | print - print details about a variable |
---|
[1560] | 613 | list_scans - list all scantables created by the user |
---|
[992] | 614 | list_files - list all files readable by asap (default rpf) |
---|
[113] | 615 | del - delete the given variable from memory |
---|
| 616 | range - create a list of values, e.g. |
---|
| 617 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
---|
| 618 | help - print help for one of the listed functions |
---|
| 619 | execfile - execute an asap script, e.g. execfile('myscript') |
---|
[255] | 620 | list_rcparameters - print out a list of possible values to be |
---|
[274] | 621 | put into $HOME/.asaprc |
---|
[1171] | 622 | rc - set rc parameters from within asap |
---|
[466] | 623 | mask_and,mask_or, |
---|
| 624 | mask_not - boolean operations on masks created with |
---|
| 625 | scantable.create_mask |
---|
[706] | 626 | |
---|
[210] | 627 | Note: |
---|
| 628 | How to use this with help: |
---|
| 629 | # function 'summary' |
---|
| 630 | [xxx] is just a category |
---|
| 631 | Every 'sub-level' in this list should be replaces by a '.' Period when |
---|
[706] | 632 | using help |
---|
[210] | 633 | Example: |
---|
| 634 | ASAP> help scantable # to get info on ths scantable |
---|
| 635 | ASAP> help scantable.summary # to get help on the scantable's |
---|
| 636 | ASAP> help average_time |
---|
| 637 | |
---|
[715] | 638 | """ |
---|
[1151] | 639 | if rcParams['verbose']: |
---|
| 640 | try: |
---|
| 641 | from IPython.genutils import page as pager |
---|
| 642 | except ImportError: |
---|
| 643 | from pydoc import pager |
---|
| 644 | pager(x) |
---|
| 645 | else: |
---|
| 646 | print x |
---|
[715] | 647 | return |
---|
[113] | 648 | |
---|
[706] | 649 | def welcome(): |
---|
| 650 | return """Welcome to ASAP v%s (%s) - the ATNF Spectral Analysis Package |
---|
[100] | 651 | |
---|
[1035] | 652 | Please report any bugs via: |
---|
[1378] | 653 | http://svn.atnf.csiro.au/trac/asap/simpleticket |
---|
[100] | 654 | |
---|
[378] | 655 | [IMPORTANT: ASAP is 0-based] |
---|
[706] | 656 | Type commands() to get a list of all available ASAP commands.""" % (__version__, __date__) |
---|