[1846] | 1 | """This module defines the scantable class.""" |
---|
| 2 | |
---|
[1697] | 3 | import os |
---|
[1691] | 4 | try: |
---|
| 5 | from functools import wraps as wraps_dec |
---|
| 6 | except ImportError: |
---|
| 7 | from asap.compatibility import wraps as wraps_dec |
---|
| 8 | |
---|
[1824] | 9 | from asap.env import is_casapy |
---|
[876] | 10 | from asap._asap import Scantable |
---|
[1843] | 11 | from asap._asap import filler |
---|
[1824] | 12 | from asap.parameters import rcParams |
---|
| 13 | from asap.logging import asaplog, print_log, print_log_dec |
---|
| 14 | from asap.selector import selector |
---|
| 15 | from asap.linecatalog import linecatalog |
---|
[1600] | 16 | from asap.coordinate import coordinate |
---|
[1824] | 17 | from asap.utils import _n_bools, mask_not, mask_and, mask_or |
---|
[102] | 18 | |
---|
[1689] | 19 | |
---|
| 20 | def preserve_selection(func): |
---|
[1691] | 21 | @wraps_dec(func) |
---|
[1689] | 22 | def wrap(obj, *args, **kw): |
---|
| 23 | basesel = obj.get_selection() |
---|
| 24 | val = func(obj, *args, **kw) |
---|
| 25 | obj.set_selection(basesel) |
---|
| 26 | return val |
---|
| 27 | return wrap |
---|
| 28 | |
---|
[1846] | 29 | def is_scantable(filename): |
---|
| 30 | """Is the given file a scantable? |
---|
[1689] | 31 | |
---|
[1846] | 32 | Parameters: |
---|
| 33 | |
---|
| 34 | filename: the name of the file/directory to test |
---|
| 35 | |
---|
| 36 | """ |
---|
[1697] | 37 | return (os.path.isdir(filename) |
---|
| 38 | and not os.path.exists(filename+'/table.f1') |
---|
| 39 | and os.path.exists(filename+'/table.info')) |
---|
| 40 | |
---|
| 41 | |
---|
[876] | 42 | class scantable(Scantable): |
---|
[1846] | 43 | """\ |
---|
| 44 | The ASAP container for scans (single-dish data). |
---|
[102] | 45 | """ |
---|
[1819] | 46 | |
---|
[1589] | 47 | @print_log_dec |
---|
[1824] | 48 | def __init__(self, filename, average=None, unit=None, getpt=None, |
---|
| 49 | antenna=None, parallactify=None): |
---|
[1846] | 50 | """\ |
---|
[102] | 51 | Create a scantable from a saved one or make a reference |
---|
[1846] | 52 | |
---|
[102] | 53 | Parameters: |
---|
[1846] | 54 | |
---|
| 55 | filename: the name of an asap table on disk |
---|
| 56 | or |
---|
| 57 | the name of a rpfits/sdfits/ms file |
---|
| 58 | (integrations within scans are auto averaged |
---|
| 59 | and the whole file is read) or |
---|
| 60 | [advanced] a reference to an existing scantable |
---|
| 61 | |
---|
| 62 | average: average all integrations withinb a scan on read. |
---|
| 63 | The default (True) is taken from .asaprc. |
---|
| 64 | |
---|
[484] | 65 | unit: brightness unit; must be consistent with K or Jy. |
---|
[1846] | 66 | Over-rides the default selected by the filler |
---|
| 67 | (input rpfits/sdfits/ms) or replaces the value |
---|
| 68 | in existing scantables |
---|
| 69 | |
---|
| 70 | getpt: for MeasurementSet input data only: |
---|
| 71 | If True, all pointing data are filled. |
---|
| 72 | The deafult is False, which makes time to load |
---|
| 73 | the MS data faster in some cases. |
---|
| 74 | |
---|
| 75 | antenna: Antenna selection. integer (id) or string (name or id). |
---|
| 76 | |
---|
| 77 | parallactify: Indicate that the data had been parallatified. Default |
---|
| 78 | is taken from rc file. |
---|
| 79 | |
---|
[710] | 80 | """ |
---|
[976] | 81 | if average is None: |
---|
[710] | 82 | average = rcParams['scantable.autoaverage'] |
---|
[1819] | 83 | if getpt is None: |
---|
| 84 | getpt = True |
---|
[1843] | 85 | if antenna is not None: |
---|
| 86 | asaplog.push("Antenna selection currently unsupported." |
---|
| 87 | "Using '0'") |
---|
| 88 | print_log('WARN') |
---|
[1819] | 89 | if antenna is None: |
---|
| 90 | antenna = '' |
---|
| 91 | elif type(antenna) == int: |
---|
[1843] | 92 | antenna = '%s' % antenna |
---|
[1819] | 93 | elif type(antenna) == list: |
---|
| 94 | tmpstr = '' |
---|
| 95 | for i in range( len(antenna) ): |
---|
| 96 | if type(antenna[i]) == int: |
---|
| 97 | tmpstr = tmpstr + ('%s,'%(antenna[i])) |
---|
| 98 | elif type(antenna[i]) == str: |
---|
| 99 | tmpstr=tmpstr+antenna[i]+',' |
---|
| 100 | else: |
---|
| 101 | asaplog.push('Bad antenna selection.') |
---|
| 102 | print_log('ERROR') |
---|
| 103 | return |
---|
| 104 | antenna = tmpstr.rstrip(',') |
---|
[1593] | 105 | parallactify = parallactify or rcParams['scantable.parallactify'] |
---|
[1259] | 106 | varlist = vars() |
---|
[876] | 107 | from asap._asap import stmath |
---|
[1819] | 108 | self._math = stmath( rcParams['insitu'] ) |
---|
[876] | 109 | if isinstance(filename, Scantable): |
---|
| 110 | Scantable.__init__(self, filename) |
---|
[181] | 111 | else: |
---|
[1697] | 112 | if isinstance(filename, str): |
---|
[976] | 113 | filename = os.path.expandvars(filename) |
---|
| 114 | filename = os.path.expanduser(filename) |
---|
| 115 | if not os.path.exists(filename): |
---|
| 116 | s = "File '%s' not found." % (filename) |
---|
[718] | 117 | if rcParams['verbose']: |
---|
[976] | 118 | asaplog.push(s) |
---|
[1819] | 119 | print_log('ERROR') |
---|
[718] | 120 | return |
---|
[976] | 121 | raise IOError(s) |
---|
[1697] | 122 | if is_scantable(filename): |
---|
| 123 | ondisk = rcParams['scantable.storage'] == 'disk' |
---|
| 124 | Scantable.__init__(self, filename, ondisk) |
---|
| 125 | if unit is not None: |
---|
| 126 | self.set_fluxunit(unit) |
---|
[1819] | 127 | # do not reset to the default freqframe |
---|
| 128 | #self.set_freqframe(rcParams['scantable.freqframe']) |
---|
| 129 | elif os.path.isdir(filename) \ |
---|
| 130 | and not os.path.exists(filename+'/table.f1'): |
---|
| 131 | msg = "The given file '%s'is not a valid " \ |
---|
| 132 | "asap table." % (filename) |
---|
| 133 | if rcParams['verbose']: |
---|
| 134 | #print msg |
---|
| 135 | asaplog.push( msg ) |
---|
| 136 | print_log( 'ERROR' ) |
---|
| 137 | return |
---|
| 138 | else: |
---|
| 139 | raise IOError(msg) |
---|
[226] | 140 | else: |
---|
[1819] | 141 | self._fill([filename], unit, average, getpt, antenna) |
---|
[1118] | 142 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
---|
[976] | 143 | and isinstance(filename[-1], str): |
---|
[1819] | 144 | self._fill(filename, unit, average, getpt, antenna) |
---|
[1586] | 145 | self.parallactify(parallactify) |
---|
[1259] | 146 | self._add_history("scantable", varlist) |
---|
[1819] | 147 | print_log() |
---|
[102] | 148 | |
---|
[1589] | 149 | @print_log_dec |
---|
[876] | 150 | def save(self, name=None, format=None, overwrite=False): |
---|
[1846] | 151 | """\ |
---|
[1280] | 152 | Store the scantable on disk. This can be an asap (aips++) Table, |
---|
| 153 | SDFITS or MS2 format. |
---|
[1846] | 154 | |
---|
[116] | 155 | Parameters: |
---|
[1846] | 156 | |
---|
[1093] | 157 | name: the name of the outputfile. For format "ASCII" |
---|
| 158 | this is the root file name (data in 'name'.txt |
---|
[497] | 159 | and header in 'name'_header.txt) |
---|
[1855] | 160 | |
---|
[116] | 161 | format: an optional file format. Default is ASAP. |
---|
[1855] | 162 | Allowed are: |
---|
| 163 | |
---|
| 164 | * 'ASAP' (save as ASAP [aips++] Table), |
---|
| 165 | * 'SDFITS' (save as SDFITS file) |
---|
| 166 | * 'ASCII' (saves as ascii text file) |
---|
| 167 | * 'MS2' (saves as an casacore MeasurementSet V2) |
---|
| 168 | * 'FITS' (save as image FITS - not readable by class) |
---|
| 169 | * 'CLASS' (save as FITS readable by CLASS) |
---|
| 170 | |
---|
[411] | 171 | overwrite: If the file should be overwritten if it exists. |
---|
[256] | 172 | The default False is to return with warning |
---|
[411] | 173 | without writing the output. USE WITH CARE. |
---|
[1855] | 174 | |
---|
[1846] | 175 | Example:: |
---|
| 176 | |
---|
[116] | 177 | scan.save('myscan.asap') |
---|
[1118] | 178 | scan.save('myscan.sdfits', 'SDFITS') |
---|
[1846] | 179 | |
---|
[116] | 180 | """ |
---|
[411] | 181 | from os import path |
---|
[1593] | 182 | format = format or rcParams['scantable.save'] |
---|
[256] | 183 | suffix = '.'+format.lower() |
---|
[1118] | 184 | if name is None or name == "": |
---|
[256] | 185 | name = 'scantable'+suffix |
---|
[718] | 186 | msg = "No filename given. Using default name %s..." % name |
---|
| 187 | asaplog.push(msg) |
---|
[411] | 188 | name = path.expandvars(name) |
---|
[256] | 189 | if path.isfile(name) or path.isdir(name): |
---|
| 190 | if not overwrite: |
---|
[718] | 191 | msg = "File %s exists." % name |
---|
| 192 | if rcParams['verbose']: |
---|
[1819] | 193 | #print msg |
---|
| 194 | asaplog.push( msg ) |
---|
| 195 | print_log( 'ERROR' ) |
---|
[718] | 196 | return |
---|
| 197 | else: |
---|
| 198 | raise IOError(msg) |
---|
[451] | 199 | format2 = format.upper() |
---|
| 200 | if format2 == 'ASAP': |
---|
[116] | 201 | self._save(name) |
---|
| 202 | else: |
---|
[989] | 203 | from asap._asap import stwriter as stw |
---|
[1118] | 204 | writer = stw(format2) |
---|
| 205 | writer.write(self, name) |
---|
[1819] | 206 | print_log() |
---|
[116] | 207 | return |
---|
| 208 | |
---|
[102] | 209 | def copy(self): |
---|
[1846] | 210 | """Return a copy of this scantable. |
---|
| 211 | |
---|
| 212 | *Note*: |
---|
| 213 | |
---|
[1348] | 214 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
---|
[1846] | 215 | |
---|
| 216 | Example:: |
---|
| 217 | |
---|
[102] | 218 | copiedscan = scan.copy() |
---|
[1846] | 219 | |
---|
[102] | 220 | """ |
---|
[876] | 221 | sd = scantable(Scantable._copy(self)) |
---|
[113] | 222 | return sd |
---|
| 223 | |
---|
[1093] | 224 | def drop_scan(self, scanid=None): |
---|
[1846] | 225 | """\ |
---|
[1093] | 226 | Return a new scantable where the specified scan number(s) has(have) |
---|
| 227 | been dropped. |
---|
[1846] | 228 | |
---|
[1093] | 229 | Parameters: |
---|
[1846] | 230 | |
---|
[1093] | 231 | scanid: a (list of) scan number(s) |
---|
[1846] | 232 | |
---|
[1093] | 233 | """ |
---|
| 234 | from asap import _is_sequence_or_number as _is_valid |
---|
| 235 | from asap import _to_list |
---|
| 236 | from asap import unique |
---|
| 237 | if not _is_valid(scanid): |
---|
| 238 | if rcParams['verbose']: |
---|
[1819] | 239 | #print "Please specify a scanno to drop from the scantable" |
---|
| 240 | asaplog.push( 'Please specify a scanno to drop from the scantable' ) |
---|
| 241 | print_log( 'ERROR' ) |
---|
[1093] | 242 | return |
---|
| 243 | else: |
---|
| 244 | raise RuntimeError("No scan given") |
---|
| 245 | try: |
---|
| 246 | scanid = _to_list(scanid) |
---|
| 247 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
---|
| 248 | for sid in scanid: allscans.remove(sid) |
---|
[1118] | 249 | if len(allscans) == 0: |
---|
| 250 | raise ValueError("Can't remove all scans") |
---|
[1093] | 251 | except ValueError: |
---|
| 252 | if rcParams['verbose']: |
---|
[1819] | 253 | #print "Couldn't find any match." |
---|
| 254 | print_log() |
---|
| 255 | asaplog.push( "Couldn't find any match." ) |
---|
| 256 | print_log( 'ERROR' ) |
---|
[1093] | 257 | return |
---|
| 258 | else: raise |
---|
| 259 | try: |
---|
[1593] | 260 | sel = selector(scans=allscans) |
---|
[1594] | 261 | return self._select_copy(sel) |
---|
[1093] | 262 | except RuntimeError: |
---|
[1118] | 263 | if rcParams['verbose']: |
---|
[1819] | 264 | #print "Couldn't find any match." |
---|
| 265 | print_log() |
---|
| 266 | asaplog.push( "Couldn't find any match." ) |
---|
| 267 | print_log( 'ERROR' ) |
---|
[1118] | 268 | else: |
---|
| 269 | raise |
---|
[1093] | 270 | |
---|
[1594] | 271 | def _select_copy(self, selection): |
---|
| 272 | orig = self.get_selection() |
---|
| 273 | self.set_selection(orig+selection) |
---|
| 274 | cp = self.copy() |
---|
| 275 | self.set_selection(orig) |
---|
| 276 | return cp |
---|
| 277 | |
---|
[102] | 278 | def get_scan(self, scanid=None): |
---|
[1855] | 279 | """\ |
---|
[102] | 280 | Return a specific scan (by scanno) or collection of scans (by |
---|
| 281 | source name) in a new scantable. |
---|
[1846] | 282 | |
---|
| 283 | *Note*: |
---|
| 284 | |
---|
[1348] | 285 | See scantable.drop_scan() for the inverse operation. |
---|
[1846] | 286 | |
---|
[102] | 287 | Parameters: |
---|
[1846] | 288 | |
---|
[513] | 289 | scanid: a (list of) scanno or a source name, unix-style |
---|
| 290 | patterns are accepted for source name matching, e.g. |
---|
| 291 | '*_R' gets all 'ref scans |
---|
[1846] | 292 | |
---|
| 293 | Example:: |
---|
| 294 | |
---|
[513] | 295 | # get all scans containing the source '323p459' |
---|
| 296 | newscan = scan.get_scan('323p459') |
---|
| 297 | # get all 'off' scans |
---|
| 298 | refscans = scan.get_scan('*_R') |
---|
| 299 | # get a susbset of scans by scanno (as listed in scan.summary()) |
---|
[1118] | 300 | newscan = scan.get_scan([0, 2, 7, 10]) |
---|
[1846] | 301 | |
---|
[102] | 302 | """ |
---|
| 303 | if scanid is None: |
---|
[718] | 304 | if rcParams['verbose']: |
---|
[1819] | 305 | #print "Please specify a scan no or name to " \ |
---|
| 306 | # "retrieve from the scantable" |
---|
[1846] | 307 | asaplog.push( 'Please specify a scan no or name to retrieve' |
---|
| 308 | ' from the scantable' ) |
---|
[1819] | 309 | print_log( 'ERROR' ) |
---|
[718] | 310 | return |
---|
| 311 | else: |
---|
| 312 | raise RuntimeError("No scan given") |
---|
| 313 | |
---|
[102] | 314 | try: |
---|
[946] | 315 | bsel = self.get_selection() |
---|
| 316 | sel = selector() |
---|
[102] | 317 | if type(scanid) is str: |
---|
[946] | 318 | sel.set_name(scanid) |
---|
[1594] | 319 | return self._select_copy(sel) |
---|
[102] | 320 | elif type(scanid) is int: |
---|
[946] | 321 | sel.set_scans([scanid]) |
---|
[1594] | 322 | return self._select_copy(sel) |
---|
[381] | 323 | elif type(scanid) is list: |
---|
[946] | 324 | sel.set_scans(scanid) |
---|
[1594] | 325 | return self._select_copy(sel) |
---|
[381] | 326 | else: |
---|
[718] | 327 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
---|
| 328 | if rcParams['verbose']: |
---|
[1819] | 329 | #print msg |
---|
| 330 | asaplog.push( msg ) |
---|
| 331 | print_log( 'ERROR' ) |
---|
[718] | 332 | else: |
---|
| 333 | raise TypeError(msg) |
---|
[102] | 334 | except RuntimeError: |
---|
[1819] | 335 | if rcParams['verbose']: |
---|
| 336 | #print "Couldn't find any match." |
---|
| 337 | print_log() |
---|
| 338 | asaplog.push( "Couldn't find any match." ) |
---|
| 339 | print_log( 'ERROR' ) |
---|
[718] | 340 | else: raise |
---|
[102] | 341 | |
---|
| 342 | def __str__(self): |
---|
[1118] | 343 | return Scantable._summary(self, True) |
---|
[102] | 344 | |
---|
[976] | 345 | def summary(self, filename=None): |
---|
[1846] | 346 | """\ |
---|
[102] | 347 | Print a summary of the contents of this scantable. |
---|
[1846] | 348 | |
---|
[102] | 349 | Parameters: |
---|
[1846] | 350 | |
---|
[102] | 351 | filename: the name of a file to write the putput to |
---|
| 352 | Default - no file output |
---|
[1846] | 353 | |
---|
[102] | 354 | """ |
---|
[976] | 355 | info = Scantable._summary(self, True) |
---|
[102] | 356 | if filename is not None: |
---|
[256] | 357 | if filename is "": |
---|
| 358 | filename = 'scantable_summary.txt' |
---|
[415] | 359 | from os.path import expandvars, isdir |
---|
[411] | 360 | filename = expandvars(filename) |
---|
[415] | 361 | if not isdir(filename): |
---|
[413] | 362 | data = open(filename, 'w') |
---|
| 363 | data.write(info) |
---|
| 364 | data.close() |
---|
| 365 | else: |
---|
[718] | 366 | msg = "Illegal file name '%s'." % (filename) |
---|
| 367 | if rcParams['verbose']: |
---|
[1819] | 368 | #print msg |
---|
| 369 | asaplog.push( msg ) |
---|
| 370 | print_log( 'ERROR' ) |
---|
[718] | 371 | else: |
---|
| 372 | raise IOError(msg) |
---|
| 373 | if rcParams['verbose']: |
---|
[794] | 374 | try: |
---|
| 375 | from IPython.genutils import page as pager |
---|
| 376 | except ImportError: |
---|
| 377 | from pydoc import pager |
---|
| 378 | pager(info) |
---|
[718] | 379 | else: |
---|
| 380 | return info |
---|
[710] | 381 | |
---|
[1512] | 382 | def get_spectrum(self, rowno): |
---|
[1471] | 383 | """Return the spectrum for the current row in the scantable as a list. |
---|
[1846] | 384 | |
---|
[1471] | 385 | Parameters: |
---|
[1846] | 386 | |
---|
[1573] | 387 | rowno: the row number to retrieve the spectrum from |
---|
[1846] | 388 | |
---|
[1471] | 389 | """ |
---|
| 390 | return self._getspectrum(rowno) |
---|
[946] | 391 | |
---|
[1471] | 392 | def get_mask(self, rowno): |
---|
| 393 | """Return the mask for the current row in the scantable as a list. |
---|
[1846] | 394 | |
---|
[1471] | 395 | Parameters: |
---|
[1846] | 396 | |
---|
[1573] | 397 | rowno: the row number to retrieve the mask from |
---|
[1846] | 398 | |
---|
[1471] | 399 | """ |
---|
| 400 | return self._getmask(rowno) |
---|
| 401 | |
---|
| 402 | def set_spectrum(self, spec, rowno): |
---|
| 403 | """Return the spectrum for the current row in the scantable as a list. |
---|
[1846] | 404 | |
---|
[1471] | 405 | Parameters: |
---|
[1846] | 406 | |
---|
[1855] | 407 | spec: the new spectrum |
---|
[1846] | 408 | |
---|
[1855] | 409 | rowno: the row number to set the spectrum for |
---|
| 410 | |
---|
[1471] | 411 | """ |
---|
| 412 | assert(len(spec) == self.nchan()) |
---|
| 413 | return self._setspectrum(spec, rowno) |
---|
| 414 | |
---|
[1600] | 415 | def get_coordinate(self, rowno): |
---|
| 416 | """Return the (spectral) coordinate for a a given 'rowno'. |
---|
[1846] | 417 | |
---|
| 418 | *Note*: |
---|
| 419 | |
---|
[1600] | 420 | * This coordinate is only valid until a scantable method modifies |
---|
| 421 | the frequency axis. |
---|
| 422 | * This coordinate does contain the original frequency set-up |
---|
| 423 | NOT the new frame. The conversions however are done using the user |
---|
| 424 | specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate, |
---|
| 425 | use scantable.freq_align first. Without it there is no closure, |
---|
[1846] | 426 | i.e.:: |
---|
[1600] | 427 | |
---|
[1846] | 428 | c = myscan.get_coordinate(0) |
---|
| 429 | c.to_frequency(c.get_reference_pixel()) != c.get_reference_value() |
---|
| 430 | |
---|
[1600] | 431 | Parameters: |
---|
[1846] | 432 | |
---|
[1600] | 433 | rowno: the row number for the spectral coordinate |
---|
| 434 | |
---|
| 435 | """ |
---|
| 436 | return coordinate(Scantable.get_coordinate(self, rowno)) |
---|
| 437 | |
---|
[946] | 438 | def get_selection(self): |
---|
[1846] | 439 | """\ |
---|
[1005] | 440 | Get the selection object currently set on this scantable. |
---|
[1846] | 441 | |
---|
| 442 | Example:: |
---|
| 443 | |
---|
[1005] | 444 | sel = scan.get_selection() |
---|
| 445 | sel.set_ifs(0) # select IF 0 |
---|
| 446 | scan.set_selection(sel) # apply modified selection |
---|
[1846] | 447 | |
---|
[946] | 448 | """ |
---|
| 449 | return selector(self._getselection()) |
---|
| 450 | |
---|
[1576] | 451 | def set_selection(self, selection=None, **kw): |
---|
[1846] | 452 | """\ |
---|
[1005] | 453 | Select a subset of the data. All following operations on this scantable |
---|
| 454 | are only applied to thi selection. |
---|
[1846] | 455 | |
---|
[1005] | 456 | Parameters: |
---|
[1697] | 457 | |
---|
[1846] | 458 | selection: a selector object (default unset the selection), or |
---|
| 459 | any combination of "pols", "ifs", "beams", "scans", |
---|
| 460 | "cycles", "name", "query" |
---|
[1697] | 461 | |
---|
[1846] | 462 | Examples:: |
---|
[1697] | 463 | |
---|
[1005] | 464 | sel = selector() # create a selection object |
---|
[1118] | 465 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
---|
[1005] | 466 | scan.set_selection(sel) # set the selection |
---|
| 467 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 468 | scan.set_selection() # unset the selection |
---|
[1697] | 469 | # or the equivalent |
---|
| 470 | scan.set_selection(scans=[0,3]) |
---|
| 471 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 472 | scan.set_selection() # unset the selection |
---|
[1846] | 473 | |
---|
[946] | 474 | """ |
---|
[1576] | 475 | if selection is None: |
---|
| 476 | # reset |
---|
| 477 | if len(kw) == 0: |
---|
| 478 | selection = selector() |
---|
| 479 | else: |
---|
| 480 | # try keywords |
---|
| 481 | for k in kw: |
---|
| 482 | if k not in selector.fields: |
---|
| 483 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields)) |
---|
| 484 | selection = selector(**kw) |
---|
[946] | 485 | self._setselection(selection) |
---|
| 486 | |
---|
[1819] | 487 | def get_row(self, row=0, insitu=None): |
---|
[1846] | 488 | """\ |
---|
[1819] | 489 | Select a row in the scantable. |
---|
| 490 | Return a scantable with single row. |
---|
[1846] | 491 | |
---|
[1819] | 492 | Parameters: |
---|
[1846] | 493 | |
---|
| 494 | row: row no of integration, default is 0. |
---|
| 495 | insitu: if False a new scantable is returned. Otherwise, the |
---|
| 496 | scaling is done in-situ. The default is taken from .asaprc |
---|
| 497 | (False) |
---|
| 498 | |
---|
[1819] | 499 | """ |
---|
| 500 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 501 | if not insitu: |
---|
| 502 | workscan = self.copy() |
---|
| 503 | else: |
---|
| 504 | workscan = self |
---|
| 505 | # Select a row |
---|
| 506 | sel=selector() |
---|
| 507 | sel.set_scans([workscan.getscan(row)]) |
---|
| 508 | sel.set_cycles([workscan.getcycle(row)]) |
---|
| 509 | sel.set_beams([workscan.getbeam(row)]) |
---|
| 510 | sel.set_ifs([workscan.getif(row)]) |
---|
| 511 | sel.set_polarisations([workscan.getpol(row)]) |
---|
| 512 | sel.set_name(workscan._getsourcename(row)) |
---|
| 513 | workscan.set_selection(sel) |
---|
| 514 | if not workscan.nrow() == 1: |
---|
| 515 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow()) |
---|
| 516 | raise RuntimeError(msg) |
---|
| 517 | del sel |
---|
| 518 | if insitu: |
---|
| 519 | self._assign(workscan) |
---|
| 520 | else: |
---|
| 521 | return workscan |
---|
| 522 | |
---|
| 523 | #def stats(self, stat='stddev', mask=None): |
---|
| 524 | def stats(self, stat='stddev', mask=None, form='3.3f'): |
---|
[1846] | 525 | """\ |
---|
[135] | 526 | Determine the specified statistic of the current beam/if/pol |
---|
[102] | 527 | Takes a 'mask' as an optional parameter to specify which |
---|
| 528 | channels should be excluded. |
---|
[1846] | 529 | |
---|
[102] | 530 | Parameters: |
---|
[1846] | 531 | |
---|
[1819] | 532 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum', |
---|
| 533 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
[1855] | 534 | |
---|
[135] | 535 | mask: an optional mask specifying where the statistic |
---|
[102] | 536 | should be determined. |
---|
[1855] | 537 | |
---|
[1819] | 538 | form: format string to print statistic values |
---|
[1846] | 539 | |
---|
| 540 | Example:: |
---|
| 541 | |
---|
[113] | 542 | scan.set_unit('channel') |
---|
[1118] | 543 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 544 | scan.stats(stat='mean', mask=m) |
---|
[1846] | 545 | |
---|
[102] | 546 | """ |
---|
[1593] | 547 | mask = mask or [] |
---|
[876] | 548 | if not self._check_ifs(): |
---|
[1118] | 549 | raise ValueError("Cannot apply mask as the IFs have different " |
---|
| 550 | "number of channels. Please use setselection() " |
---|
| 551 | "to select individual IFs") |
---|
[1819] | 552 | rtnabc = False |
---|
| 553 | if stat.lower().endswith('_abc'): rtnabc = True |
---|
| 554 | getchan = False |
---|
| 555 | if stat.lower().startswith('min') or stat.lower().startswith('max'): |
---|
| 556 | chan = self._math._minmaxchan(self, mask, stat) |
---|
| 557 | getchan = True |
---|
| 558 | statvals = [] |
---|
| 559 | if not rtnabc: statvals = self._math._stats(self, mask, stat) |
---|
[256] | 560 | |
---|
[1819] | 561 | #def cb(i): |
---|
| 562 | # return statvals[i] |
---|
[256] | 563 | |
---|
[1819] | 564 | #return self._row_callback(cb, stat) |
---|
[102] | 565 | |
---|
[1819] | 566 | label=stat |
---|
| 567 | #callback=cb |
---|
| 568 | out = "" |
---|
| 569 | #outvec = [] |
---|
| 570 | sep = '-'*50 |
---|
| 571 | for i in range(self.nrow()): |
---|
| 572 | refstr = '' |
---|
| 573 | statunit= '' |
---|
| 574 | if getchan: |
---|
| 575 | qx, qy = self.chan2data(rowno=i, chan=chan[i]) |
---|
| 576 | if rtnabc: |
---|
| 577 | statvals.append(qx['value']) |
---|
| 578 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])' |
---|
| 579 | statunit= '['+qx['unit']+']' |
---|
| 580 | else: |
---|
| 581 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])' |
---|
| 582 | |
---|
| 583 | tm = self._gettime(i) |
---|
| 584 | src = self._getsourcename(i) |
---|
| 585 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
| 586 | out += 'Time[%s]:\n' % (tm) |
---|
| 587 | if self.nbeam(-1) > 1: |
---|
| 588 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 589 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 590 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
| 591 | #outvec.append(callback(i)) |
---|
| 592 | #out += ('= %'+form) % (outvec[i]) +' '+refstr+'\n' |
---|
| 593 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n' |
---|
| 594 | out += sep+"\n" |
---|
| 595 | |
---|
| 596 | if rcParams['verbose']: |
---|
| 597 | import os |
---|
| 598 | if os.environ.has_key( 'USER' ): |
---|
| 599 | usr=os.environ['USER'] |
---|
| 600 | else: |
---|
| 601 | import commands |
---|
| 602 | usr=commands.getoutput( 'whoami' ) |
---|
| 603 | tmpfile='/tmp/tmp_'+usr+'_casapy_asap_scantable_stats' |
---|
| 604 | f=open(tmpfile,'w') |
---|
| 605 | print >> f, sep |
---|
| 606 | print >> f, ' %s %s' % (label, statunit) |
---|
| 607 | print >> f, sep |
---|
| 608 | print >> f, out |
---|
| 609 | f.close() |
---|
| 610 | f=open(tmpfile,'r') |
---|
| 611 | x=f.readlines() |
---|
| 612 | f.close() |
---|
| 613 | blanc='' |
---|
| 614 | asaplog.push(blanc.join(x), False) |
---|
| 615 | #for xx in x: |
---|
| 616 | # asaplog.push( xx, False ) |
---|
| 617 | print_log() |
---|
| 618 | return statvals |
---|
| 619 | |
---|
| 620 | def chan2data(self, rowno=0, chan=0): |
---|
[1846] | 621 | """\ |
---|
[1819] | 622 | Returns channel/frequency/velocity and spectral value |
---|
| 623 | at an arbitrary row and channel in the scantable. |
---|
[1846] | 624 | |
---|
[1819] | 625 | Parameters: |
---|
[1846] | 626 | |
---|
[1819] | 627 | rowno: a row number in the scantable. Default is the |
---|
| 628 | first row, i.e. rowno=0 |
---|
[1855] | 629 | |
---|
[1819] | 630 | chan: a channel in the scantable. Default is the first |
---|
| 631 | channel, i.e. pos=0 |
---|
[1846] | 632 | |
---|
[1819] | 633 | """ |
---|
| 634 | if isinstance(rowno, int) and isinstance(chan, int): |
---|
| 635 | qx = {'unit': self.get_unit(), |
---|
| 636 | 'value': self._getabcissa(rowno)[chan]} |
---|
| 637 | qy = {'unit': self.get_fluxunit(), |
---|
| 638 | 'value': self._getspectrum(rowno)[chan]} |
---|
| 639 | return qx, qy |
---|
| 640 | |
---|
[1118] | 641 | def stddev(self, mask=None): |
---|
[1846] | 642 | """\ |
---|
[135] | 643 | Determine the standard deviation of the current beam/if/pol |
---|
| 644 | Takes a 'mask' as an optional parameter to specify which |
---|
| 645 | channels should be excluded. |
---|
[1846] | 646 | |
---|
[135] | 647 | Parameters: |
---|
[1846] | 648 | |
---|
[135] | 649 | mask: an optional mask specifying where the standard |
---|
| 650 | deviation should be determined. |
---|
| 651 | |
---|
[1846] | 652 | Example:: |
---|
| 653 | |
---|
[135] | 654 | scan.set_unit('channel') |
---|
[1118] | 655 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 656 | scan.stddev(mask=m) |
---|
[1846] | 657 | |
---|
[135] | 658 | """ |
---|
[1118] | 659 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 660 | |
---|
[1003] | 661 | |
---|
[1259] | 662 | def get_column_names(self): |
---|
[1846] | 663 | """\ |
---|
[1003] | 664 | Return a list of column names, which can be used for selection. |
---|
| 665 | """ |
---|
[1259] | 666 | return list(Scantable.get_column_names(self)) |
---|
[1003] | 667 | |
---|
[1730] | 668 | def get_tsys(self, row=-1): |
---|
[1846] | 669 | """\ |
---|
[113] | 670 | Return the System temperatures. |
---|
[1846] | 671 | |
---|
| 672 | Parameters: |
---|
| 673 | |
---|
| 674 | row: the rowno to get the information for. (default all rows) |
---|
| 675 | |
---|
[113] | 676 | Returns: |
---|
[1846] | 677 | |
---|
[876] | 678 | a list of Tsys values for the current selection |
---|
[1846] | 679 | |
---|
[113] | 680 | """ |
---|
[1730] | 681 | if row > -1: |
---|
| 682 | return self._get_column(self._gettsys, row) |
---|
[876] | 683 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 684 | |
---|
[1730] | 685 | |
---|
| 686 | def get_weather(self, row=-1): |
---|
[1846] | 687 | """\ |
---|
| 688 | Return the weather informations. |
---|
| 689 | |
---|
| 690 | Parameters: |
---|
| 691 | |
---|
| 692 | row: the rowno to get the information for. (default all rows) |
---|
| 693 | |
---|
| 694 | Returns: |
---|
| 695 | |
---|
| 696 | a dict or list of of dicts of values for the current selection |
---|
| 697 | |
---|
| 698 | """ |
---|
| 699 | |
---|
[1730] | 700 | values = self._get_column(self._get_weather, row) |
---|
| 701 | if row > -1: |
---|
| 702 | return {'temperature': values[0], |
---|
| 703 | 'pressure': values[1], 'humidity' : values[2], |
---|
| 704 | 'windspeed' : values[3], 'windaz' : values[4] |
---|
| 705 | } |
---|
| 706 | else: |
---|
| 707 | out = [] |
---|
| 708 | for r in values: |
---|
| 709 | |
---|
| 710 | out.append({'temperature': r[0], |
---|
| 711 | 'pressure': r[1], 'humidity' : r[2], |
---|
| 712 | 'windspeed' : r[3], 'windaz' : r[4] |
---|
| 713 | }) |
---|
| 714 | return out |
---|
| 715 | |
---|
[876] | 716 | def _row_callback(self, callback, label): |
---|
| 717 | out = "" |
---|
[1118] | 718 | outvec = [] |
---|
[1590] | 719 | sep = '-'*50 |
---|
[876] | 720 | for i in range(self.nrow()): |
---|
| 721 | tm = self._gettime(i) |
---|
| 722 | src = self._getsourcename(i) |
---|
[1590] | 723 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
[876] | 724 | out += 'Time[%s]:\n' % (tm) |
---|
[1590] | 725 | if self.nbeam(-1) > 1: |
---|
| 726 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 727 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 728 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
[876] | 729 | outvec.append(callback(i)) |
---|
| 730 | out += '= %3.3f\n' % (outvec[i]) |
---|
[1590] | 731 | out += sep+'\n' |
---|
[876] | 732 | if rcParams['verbose']: |
---|
[1819] | 733 | asaplog.push(sep) |
---|
| 734 | asaplog.push(" %s" % (label)) |
---|
| 735 | asaplog.push(sep) |
---|
| 736 | asaplog.push(out) |
---|
| 737 | print_log() |
---|
[1175] | 738 | return outvec |
---|
[256] | 739 | |
---|
[1070] | 740 | def _get_column(self, callback, row=-1): |
---|
| 741 | """ |
---|
| 742 | """ |
---|
| 743 | if row == -1: |
---|
| 744 | return [callback(i) for i in range(self.nrow())] |
---|
| 745 | else: |
---|
[1819] | 746 | if 0 <= row < self.nrow(): |
---|
[1070] | 747 | return callback(row) |
---|
[256] | 748 | |
---|
[1070] | 749 | |
---|
[1348] | 750 | def get_time(self, row=-1, asdatetime=False): |
---|
[1846] | 751 | """\ |
---|
[113] | 752 | Get a list of time stamps for the observations. |
---|
[1348] | 753 | Return a datetime object for each integration time stamp in the scantable. |
---|
[1846] | 754 | |
---|
[113] | 755 | Parameters: |
---|
[1846] | 756 | |
---|
[1348] | 757 | row: row no of integration. Default -1 return all rows |
---|
[1855] | 758 | |
---|
[1348] | 759 | asdatetime: return values as datetime objects rather than strings |
---|
[1846] | 760 | |
---|
[113] | 761 | """ |
---|
[1175] | 762 | from time import strptime |
---|
| 763 | from datetime import datetime |
---|
[1392] | 764 | times = self._get_column(self._gettime, row) |
---|
[1348] | 765 | if not asdatetime: |
---|
[1392] | 766 | return times |
---|
[1175] | 767 | format = "%Y/%m/%d/%H:%M:%S" |
---|
| 768 | if isinstance(times, list): |
---|
| 769 | return [datetime(*strptime(i, format)[:6]) for i in times] |
---|
| 770 | else: |
---|
| 771 | return datetime(*strptime(times, format)[:6]) |
---|
[102] | 772 | |
---|
[1348] | 773 | |
---|
| 774 | def get_inttime(self, row=-1): |
---|
[1846] | 775 | """\ |
---|
[1348] | 776 | Get a list of integration times for the observations. |
---|
| 777 | Return a time in seconds for each integration in the scantable. |
---|
[1846] | 778 | |
---|
[1348] | 779 | Parameters: |
---|
[1846] | 780 | |
---|
[1348] | 781 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 782 | |
---|
[1348] | 783 | """ |
---|
[1573] | 784 | return self._get_column(self._getinttime, row) |
---|
[1348] | 785 | |
---|
[1573] | 786 | |
---|
[714] | 787 | def get_sourcename(self, row=-1): |
---|
[1846] | 788 | """\ |
---|
[794] | 789 | Get a list source names for the observations. |
---|
[714] | 790 | Return a string for each integration in the scantable. |
---|
| 791 | Parameters: |
---|
[1846] | 792 | |
---|
[1348] | 793 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 794 | |
---|
[714] | 795 | """ |
---|
[1070] | 796 | return self._get_column(self._getsourcename, row) |
---|
[714] | 797 | |
---|
[794] | 798 | def get_elevation(self, row=-1): |
---|
[1846] | 799 | """\ |
---|
[794] | 800 | Get a list of elevations for the observations. |
---|
| 801 | Return a float for each integration in the scantable. |
---|
[1846] | 802 | |
---|
[794] | 803 | Parameters: |
---|
[1846] | 804 | |
---|
[1348] | 805 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 806 | |
---|
[794] | 807 | """ |
---|
[1070] | 808 | return self._get_column(self._getelevation, row) |
---|
[794] | 809 | |
---|
| 810 | def get_azimuth(self, row=-1): |
---|
[1846] | 811 | """\ |
---|
[794] | 812 | Get a list of azimuths for the observations. |
---|
| 813 | Return a float for each integration in the scantable. |
---|
[1846] | 814 | |
---|
[794] | 815 | Parameters: |
---|
[1348] | 816 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 817 | |
---|
[794] | 818 | """ |
---|
[1070] | 819 | return self._get_column(self._getazimuth, row) |
---|
[794] | 820 | |
---|
| 821 | def get_parangle(self, row=-1): |
---|
[1846] | 822 | """\ |
---|
[794] | 823 | Get a list of parallactic angles for the observations. |
---|
| 824 | Return a float for each integration in the scantable. |
---|
[1846] | 825 | |
---|
[794] | 826 | Parameters: |
---|
[1846] | 827 | |
---|
[1348] | 828 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 829 | |
---|
[794] | 830 | """ |
---|
[1070] | 831 | return self._get_column(self._getparangle, row) |
---|
[794] | 832 | |
---|
[1070] | 833 | def get_direction(self, row=-1): |
---|
| 834 | """ |
---|
| 835 | Get a list of Positions on the sky (direction) for the observations. |
---|
[1594] | 836 | Return a string for each integration in the scantable. |
---|
[1855] | 837 | |
---|
[1070] | 838 | Parameters: |
---|
[1855] | 839 | |
---|
[1070] | 840 | row: row no of integration. Default -1 return all rows |
---|
[1855] | 841 | |
---|
[1070] | 842 | """ |
---|
| 843 | return self._get_column(self._getdirection, row) |
---|
| 844 | |
---|
[1391] | 845 | def get_directionval(self, row=-1): |
---|
[1846] | 846 | """\ |
---|
[1391] | 847 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 848 | Return a float for each integration in the scantable. |
---|
[1846] | 849 | |
---|
[1391] | 850 | Parameters: |
---|
[1846] | 851 | |
---|
[1391] | 852 | row: row no of integration. Default -1 return all rows |
---|
[1846] | 853 | |
---|
[1391] | 854 | """ |
---|
| 855 | return self._get_column(self._getdirectionvec, row) |
---|
| 856 | |
---|
[1730] | 857 | @print_log_dec |
---|
[102] | 858 | def set_unit(self, unit='channel'): |
---|
[1846] | 859 | """\ |
---|
[102] | 860 | Set the unit for all following operations on this scantable |
---|
[1846] | 861 | |
---|
[102] | 862 | Parameters: |
---|
[1846] | 863 | |
---|
| 864 | unit: optional unit, default is 'channel'. Use one of '*Hz', |
---|
| 865 | 'km/s', 'channel' or equivalent '' |
---|
| 866 | |
---|
[102] | 867 | """ |
---|
[484] | 868 | varlist = vars() |
---|
[1118] | 869 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 870 | unit = '' |
---|
| 871 | inf = list(self._getcoordinfo()) |
---|
| 872 | inf[0] = unit |
---|
| 873 | self._setcoordinfo(inf) |
---|
[1118] | 874 | self._add_history("set_unit", varlist) |
---|
[113] | 875 | |
---|
[1589] | 876 | @print_log_dec |
---|
[484] | 877 | def set_instrument(self, instr): |
---|
[1846] | 878 | """\ |
---|
[1348] | 879 | Set the instrument for subsequent processing. |
---|
[1846] | 880 | |
---|
[358] | 881 | Parameters: |
---|
[1846] | 882 | |
---|
[710] | 883 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 884 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[1846] | 885 | |
---|
[358] | 886 | """ |
---|
| 887 | self._setInstrument(instr) |
---|
[1118] | 888 | self._add_history("set_instument", vars()) |
---|
[1819] | 889 | print_log() |
---|
[358] | 890 | |
---|
[1589] | 891 | @print_log_dec |
---|
[1190] | 892 | def set_feedtype(self, feedtype): |
---|
[1846] | 893 | """\ |
---|
[1190] | 894 | Overwrite the feed type, which might not be set correctly. |
---|
[1846] | 895 | |
---|
[1190] | 896 | Parameters: |
---|
[1846] | 897 | |
---|
[1190] | 898 | feedtype: 'linear' or 'circular' |
---|
[1846] | 899 | |
---|
[1190] | 900 | """ |
---|
| 901 | self._setfeedtype(feedtype) |
---|
| 902 | self._add_history("set_feedtype", vars()) |
---|
[1819] | 903 | print_log() |
---|
[1190] | 904 | |
---|
[1589] | 905 | @print_log_dec |
---|
[276] | 906 | def set_doppler(self, doppler='RADIO'): |
---|
[1846] | 907 | """\ |
---|
[276] | 908 | Set the doppler for all following operations on this scantable. |
---|
[1846] | 909 | |
---|
[276] | 910 | Parameters: |
---|
[1846] | 911 | |
---|
[276] | 912 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
[1846] | 913 | |
---|
[276] | 914 | """ |
---|
[484] | 915 | varlist = vars() |
---|
[276] | 916 | inf = list(self._getcoordinfo()) |
---|
| 917 | inf[2] = doppler |
---|
| 918 | self._setcoordinfo(inf) |
---|
[1118] | 919 | self._add_history("set_doppler", vars()) |
---|
[1819] | 920 | print_log() |
---|
[710] | 921 | |
---|
[1589] | 922 | @print_log_dec |
---|
[226] | 923 | def set_freqframe(self, frame=None): |
---|
[1846] | 924 | """\ |
---|
[113] | 925 | Set the frame type of the Spectral Axis. |
---|
[1846] | 926 | |
---|
[113] | 927 | Parameters: |
---|
[1846] | 928 | |
---|
[591] | 929 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1819] | 930 | 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
[1118] | 931 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[1846] | 932 | |
---|
| 933 | Example:: |
---|
| 934 | |
---|
[113] | 935 | scan.set_freqframe('BARY') |
---|
[1846] | 936 | |
---|
[113] | 937 | """ |
---|
[1593] | 938 | frame = frame or rcParams['scantable.freqframe'] |
---|
[484] | 939 | varlist = vars() |
---|
[1819] | 940 | # "REST" is not implemented in casacore |
---|
| 941 | #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 942 | # 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
| 943 | valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
[1118] | 944 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 945 | |
---|
[989] | 946 | if frame in valid: |
---|
[113] | 947 | inf = list(self._getcoordinfo()) |
---|
| 948 | inf[1] = frame |
---|
| 949 | self._setcoordinfo(inf) |
---|
[1118] | 950 | self._add_history("set_freqframe", varlist) |
---|
[102] | 951 | else: |
---|
[1118] | 952 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[718] | 953 | if rcParams['verbose']: |
---|
[1819] | 954 | #print msg |
---|
| 955 | asaplog.push( msg ) |
---|
| 956 | print_log( 'ERROR' ) |
---|
[718] | 957 | else: |
---|
| 958 | raise TypeError(msg) |
---|
[1819] | 959 | print_log() |
---|
[710] | 960 | |
---|
[989] | 961 | def set_dirframe(self, frame=""): |
---|
[1846] | 962 | """\ |
---|
[989] | 963 | Set the frame type of the Direction on the sky. |
---|
[1846] | 964 | |
---|
[989] | 965 | Parameters: |
---|
[1846] | 966 | |
---|
[989] | 967 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 968 | 'J2000', 'B1950', 'GALACTIC' |
---|
[1846] | 969 | |
---|
| 970 | Example: |
---|
| 971 | |
---|
[989] | 972 | scan.set_dirframe('GALACTIC') |
---|
[1846] | 973 | |
---|
[989] | 974 | """ |
---|
| 975 | varlist = vars() |
---|
| 976 | try: |
---|
| 977 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 978 | except RuntimeError, msg: |
---|
[989] | 979 | if rcParams['verbose']: |
---|
[1819] | 980 | #print msg |
---|
| 981 | print_log() |
---|
| 982 | asaplog.push( str(msg) ) |
---|
| 983 | print_log( 'ERROR' ) |
---|
[989] | 984 | else: |
---|
| 985 | raise |
---|
[1118] | 986 | self._add_history("set_dirframe", varlist) |
---|
[989] | 987 | |
---|
[113] | 988 | def get_unit(self): |
---|
[1846] | 989 | """\ |
---|
[113] | 990 | Get the default unit set in this scantable |
---|
[1846] | 991 | |
---|
[113] | 992 | Returns: |
---|
[1846] | 993 | |
---|
[113] | 994 | A unit string |
---|
[1846] | 995 | |
---|
[113] | 996 | """ |
---|
| 997 | inf = self._getcoordinfo() |
---|
| 998 | unit = inf[0] |
---|
| 999 | if unit == '': unit = 'channel' |
---|
| 1000 | return unit |
---|
[102] | 1001 | |
---|
[158] | 1002 | def get_abcissa(self, rowno=0): |
---|
[1846] | 1003 | """\ |
---|
[158] | 1004 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 1005 | selected Beam/IF/Pol |
---|
[1846] | 1006 | |
---|
[113] | 1007 | Parameters: |
---|
[1846] | 1008 | |
---|
[226] | 1009 | rowno: an optional row number in the scantable. Default is the |
---|
| 1010 | first row, i.e. rowno=0 |
---|
[1846] | 1011 | |
---|
[113] | 1012 | Returns: |
---|
[1846] | 1013 | |
---|
[1348] | 1014 | The abcissa values and the format string (as a dictionary) |
---|
[1846] | 1015 | |
---|
[113] | 1016 | """ |
---|
[256] | 1017 | abc = self._getabcissa(rowno) |
---|
[710] | 1018 | lbl = self._getabcissalabel(rowno) |
---|
[1819] | 1019 | print_log() |
---|
[158] | 1020 | return abc, lbl |
---|
[113] | 1021 | |
---|
[1819] | 1022 | def flag(self, mask=None, unflag=False): |
---|
[1846] | 1023 | """\ |
---|
[1001] | 1024 | Flag the selected data using an optional channel mask. |
---|
[1846] | 1025 | |
---|
[1001] | 1026 | Parameters: |
---|
[1846] | 1027 | |
---|
[1001] | 1028 | mask: an optional channel mask, created with create_mask. Default |
---|
| 1029 | (no mask) is all channels. |
---|
[1855] | 1030 | |
---|
[1819] | 1031 | unflag: if True, unflag the data |
---|
[1846] | 1032 | |
---|
[1001] | 1033 | """ |
---|
| 1034 | varlist = vars() |
---|
[1593] | 1035 | mask = mask or [] |
---|
[1001] | 1036 | try: |
---|
[1819] | 1037 | self._flag(mask, unflag) |
---|
[1118] | 1038 | except RuntimeError, msg: |
---|
[1001] | 1039 | if rcParams['verbose']: |
---|
[1819] | 1040 | #print msg |
---|
| 1041 | print_log() |
---|
| 1042 | asaplog.push( str(msg) ) |
---|
| 1043 | print_log( 'ERROR' ) |
---|
[1001] | 1044 | return |
---|
| 1045 | else: raise |
---|
| 1046 | self._add_history("flag", varlist) |
---|
| 1047 | |
---|
[1819] | 1048 | def flag_row(self, rows=[], unflag=False): |
---|
[1846] | 1049 | """\ |
---|
[1819] | 1050 | Flag the selected data in row-based manner. |
---|
[1846] | 1051 | |
---|
[1819] | 1052 | Parameters: |
---|
[1846] | 1053 | |
---|
[1843] | 1054 | rows: list of row numbers to be flagged. Default is no row |
---|
| 1055 | (must be explicitly specified to execute row-based flagging). |
---|
[1855] | 1056 | |
---|
[1819] | 1057 | unflag: if True, unflag the data. |
---|
[1846] | 1058 | |
---|
[1819] | 1059 | """ |
---|
| 1060 | varlist = vars() |
---|
| 1061 | try: |
---|
| 1062 | self._flag_row(rows, unflag) |
---|
| 1063 | except RuntimeError, msg: |
---|
| 1064 | if rcParams['verbose']: |
---|
| 1065 | print_log() |
---|
| 1066 | asaplog.push( str(msg) ) |
---|
| 1067 | print_log('ERROR') |
---|
| 1068 | return |
---|
| 1069 | else: raise |
---|
| 1070 | self._add_history("flag_row", varlist) |
---|
| 1071 | |
---|
| 1072 | def clip(self, uthres=None, dthres=None, clipoutside=True, unflag=False): |
---|
[1846] | 1073 | """\ |
---|
[1819] | 1074 | Flag the selected data outside a specified range (in channel-base) |
---|
[1846] | 1075 | |
---|
[1819] | 1076 | Parameters: |
---|
[1846] | 1077 | |
---|
[1819] | 1078 | uthres: upper threshold. |
---|
[1855] | 1079 | |
---|
[1819] | 1080 | dthres: lower threshold |
---|
[1846] | 1081 | |
---|
[1819] | 1082 | clipoutside: True for flagging data outside the range [dthres:uthres]. |
---|
| 1083 | False for glagging data inside the range. |
---|
[1855] | 1084 | |
---|
[1846] | 1085 | unflag: if True, unflag the data. |
---|
| 1086 | |
---|
[1819] | 1087 | """ |
---|
| 1088 | varlist = vars() |
---|
| 1089 | try: |
---|
| 1090 | self._clip(uthres, dthres, clipoutside, unflag) |
---|
| 1091 | except RuntimeError, msg: |
---|
| 1092 | if rcParams['verbose']: |
---|
| 1093 | print_log() |
---|
| 1094 | asaplog.push(str(msg)) |
---|
| 1095 | print_log('ERROR') |
---|
| 1096 | return |
---|
| 1097 | else: raise |
---|
| 1098 | self._add_history("clip", varlist) |
---|
| 1099 | |
---|
[1589] | 1100 | @print_log_dec |
---|
[1584] | 1101 | def lag_flag(self, start, end, unit="MHz", insitu=None): |
---|
[1846] | 1102 | """\ |
---|
[1192] | 1103 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
[1584] | 1104 | Flagged data in the scantable gets interpolated over the region. |
---|
[1192] | 1105 | No taper is applied. |
---|
[1846] | 1106 | |
---|
[1192] | 1107 | Parameters: |
---|
[1846] | 1108 | |
---|
[1579] | 1109 | start: the start frequency (really a period within the |
---|
| 1110 | bandwidth) or period to remove |
---|
[1855] | 1111 | |
---|
[1579] | 1112 | end: the end frequency or period to remove |
---|
[1855] | 1113 | |
---|
[1584] | 1114 | unit: the frequency unit (default "MHz") or "" for |
---|
[1579] | 1115 | explicit lag channels |
---|
[1846] | 1116 | |
---|
| 1117 | *Notes*: |
---|
| 1118 | |
---|
[1579] | 1119 | It is recommended to flag edges of the band or strong |
---|
[1348] | 1120 | signals beforehand. |
---|
[1846] | 1121 | |
---|
[1192] | 1122 | """ |
---|
| 1123 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1124 | self._math._setinsitu(insitu) |
---|
| 1125 | varlist = vars() |
---|
[1579] | 1126 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.} |
---|
| 1127 | if not (unit == "" or base.has_key(unit)): |
---|
[1192] | 1128 | raise ValueError("%s is not a valid unit." % unit) |
---|
| 1129 | try: |
---|
[1579] | 1130 | if unit == "": |
---|
| 1131 | s = scantable(self._math._lag_flag(self, start, end, "lags")) |
---|
| 1132 | else: |
---|
| 1133 | s = scantable(self._math._lag_flag(self, start*base[unit], |
---|
| 1134 | end*base[unit], "frequency")) |
---|
[1192] | 1135 | except RuntimeError, msg: |
---|
| 1136 | if rcParams['verbose']: |
---|
[1819] | 1137 | #print msg |
---|
| 1138 | print_log() |
---|
| 1139 | asaplog.push( str(msg) ) |
---|
| 1140 | print_log( 'ERROR' ) |
---|
[1192] | 1141 | return |
---|
| 1142 | else: raise |
---|
| 1143 | s._add_history("lag_flag", varlist) |
---|
[1819] | 1144 | print_log() |
---|
[1192] | 1145 | if insitu: |
---|
| 1146 | self._assign(s) |
---|
| 1147 | else: |
---|
| 1148 | return s |
---|
[1001] | 1149 | |
---|
[1589] | 1150 | @print_log_dec |
---|
[113] | 1151 | def create_mask(self, *args, **kwargs): |
---|
[1846] | 1152 | """\ |
---|
[1118] | 1153 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 1154 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 1155 | applied. |
---|
[1846] | 1156 | |
---|
[102] | 1157 | Parameters: |
---|
[1846] | 1158 | |
---|
[1118] | 1159 | [min, max], [min2, max2], ... |
---|
[1024] | 1160 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 1161 | to be masked |
---|
[1855] | 1162 | |
---|
[189] | 1163 | invert: optional argument. If specified as True, |
---|
| 1164 | return an inverted mask, i.e. the regions |
---|
| 1165 | specified are EXCLUDED |
---|
[1855] | 1166 | |
---|
[513] | 1167 | row: create the mask using the specified row for |
---|
| 1168 | unit conversions, default is row=0 |
---|
| 1169 | only necessary if frequency varies over rows. |
---|
[1846] | 1170 | |
---|
| 1171 | Examples:: |
---|
| 1172 | |
---|
[113] | 1173 | scan.set_unit('channel') |
---|
[1846] | 1174 | # a) |
---|
[1118] | 1175 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 1176 | # masks everything outside 400 and 500 |
---|
[113] | 1177 | # and 800 and 900 in the unit 'channel' |
---|
| 1178 | |
---|
[1846] | 1179 | # b) |
---|
[1118] | 1180 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 1181 | # masks the regions between 400 and 500 |
---|
[113] | 1182 | # and 800 and 900 in the unit 'channel' |
---|
[1846] | 1183 | |
---|
| 1184 | # c) |
---|
| 1185 | #mask only channel 400 |
---|
[1554] | 1186 | msk = scan.create_mask([400]) |
---|
[1846] | 1187 | |
---|
[102] | 1188 | """ |
---|
[1554] | 1189 | row = kwargs.get("row", 0) |
---|
[513] | 1190 | data = self._getabcissa(row) |
---|
[113] | 1191 | u = self._getcoordinfo()[0] |
---|
[718] | 1192 | if rcParams['verbose']: |
---|
[113] | 1193 | if u == "": u = "channel" |
---|
[718] | 1194 | msg = "The current mask window unit is %s" % u |
---|
[1118] | 1195 | i = self._check_ifs() |
---|
| 1196 | if not i: |
---|
[876] | 1197 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 1198 | asaplog.push(msg) |
---|
[102] | 1199 | n = self.nchan() |
---|
[1295] | 1200 | msk = _n_bools(n, False) |
---|
[710] | 1201 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 1202 | |
---|
[1118] | 1203 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 1204 | and args or args[0] |
---|
[710] | 1205 | for window in ws: |
---|
[1554] | 1206 | if len(window) == 1: |
---|
| 1207 | window = [window[0], window[0]] |
---|
| 1208 | if len(window) == 0 or len(window) > 2: |
---|
| 1209 | raise ValueError("A window needs to be defined as [start(, end)]") |
---|
[1545] | 1210 | if window[0] > window[1]: |
---|
| 1211 | tmp = window[0] |
---|
| 1212 | window[0] = window[1] |
---|
| 1213 | window[1] = tmp |
---|
[102] | 1214 | for i in range(n): |
---|
[1024] | 1215 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 1216 | msk[i] = True |
---|
[113] | 1217 | if kwargs.has_key('invert'): |
---|
| 1218 | if kwargs.get('invert'): |
---|
[1295] | 1219 | msk = mask_not(msk) |
---|
[1819] | 1220 | print_log() |
---|
[102] | 1221 | return msk |
---|
[710] | 1222 | |
---|
[1819] | 1223 | def get_masklist(self, mask=None, row=0): |
---|
[1846] | 1224 | """\ |
---|
[1819] | 1225 | Compute and return a list of mask windows, [min, max]. |
---|
[1846] | 1226 | |
---|
[1819] | 1227 | Parameters: |
---|
[1846] | 1228 | |
---|
[1819] | 1229 | mask: channel mask, created with create_mask. |
---|
[1855] | 1230 | |
---|
[1819] | 1231 | row: calcutate the masklist using the specified row |
---|
| 1232 | for unit conversions, default is row=0 |
---|
| 1233 | only necessary if frequency varies over rows. |
---|
[1846] | 1234 | |
---|
[1819] | 1235 | Returns: |
---|
[1846] | 1236 | |
---|
[1819] | 1237 | [min, max], [min2, max2], ... |
---|
| 1238 | Pairs of start/end points (inclusive)specifying |
---|
| 1239 | the masked regions |
---|
[1846] | 1240 | |
---|
[1819] | 1241 | """ |
---|
| 1242 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1243 | raise TypeError("The mask should be list or tuple.") |
---|
| 1244 | if len(mask) < 2: |
---|
| 1245 | raise TypeError("The mask elements should be > 1") |
---|
| 1246 | if self.nchan() != len(mask): |
---|
| 1247 | msg = "Number of channels in scantable != number of mask elements" |
---|
| 1248 | raise TypeError(msg) |
---|
| 1249 | data = self._getabcissa(row) |
---|
| 1250 | u = self._getcoordinfo()[0] |
---|
| 1251 | if rcParams['verbose']: |
---|
| 1252 | if u == "": u = "channel" |
---|
| 1253 | msg = "The current mask window unit is %s" % u |
---|
| 1254 | i = self._check_ifs() |
---|
| 1255 | if not i: |
---|
| 1256 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 1257 | asaplog.push(msg) |
---|
| 1258 | masklist=[] |
---|
| 1259 | ist, ien = None, None |
---|
| 1260 | ist, ien=self.get_mask_indices(mask) |
---|
| 1261 | if ist is not None and ien is not None: |
---|
| 1262 | for i in xrange(len(ist)): |
---|
| 1263 | range=[data[ist[i]],data[ien[i]]] |
---|
| 1264 | range.sort() |
---|
| 1265 | masklist.append([range[0],range[1]]) |
---|
| 1266 | return masklist |
---|
| 1267 | |
---|
| 1268 | def get_mask_indices(self, mask=None): |
---|
[1846] | 1269 | """\ |
---|
[1819] | 1270 | Compute and Return lists of mask start indices and mask end indices. |
---|
[1855] | 1271 | |
---|
| 1272 | Parameters: |
---|
| 1273 | |
---|
[1819] | 1274 | mask: channel mask, created with create_mask. |
---|
[1846] | 1275 | |
---|
[1819] | 1276 | Returns: |
---|
[1846] | 1277 | |
---|
[1819] | 1278 | List of mask start indices and that of mask end indices, |
---|
| 1279 | i.e., [istart1,istart2,....], [iend1,iend2,....]. |
---|
[1846] | 1280 | |
---|
[1819] | 1281 | """ |
---|
| 1282 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1283 | raise TypeError("The mask should be list or tuple.") |
---|
| 1284 | if len(mask) < 2: |
---|
| 1285 | raise TypeError("The mask elements should be > 1") |
---|
| 1286 | istart=[] |
---|
| 1287 | iend=[] |
---|
| 1288 | if mask[0]: istart.append(0) |
---|
| 1289 | for i in range(len(mask)-1): |
---|
| 1290 | if not mask[i] and mask[i+1]: |
---|
| 1291 | istart.append(i+1) |
---|
| 1292 | elif mask[i] and not mask[i+1]: |
---|
| 1293 | iend.append(i) |
---|
| 1294 | if mask[len(mask)-1]: iend.append(len(mask)-1) |
---|
| 1295 | if len(istart) != len(iend): |
---|
| 1296 | raise RuntimeError("Numbers of mask start != mask end.") |
---|
| 1297 | for i in range(len(istart)): |
---|
| 1298 | if istart[i] > iend[i]: |
---|
| 1299 | raise RuntimeError("Mask start index > mask end index") |
---|
| 1300 | break |
---|
| 1301 | return istart,iend |
---|
| 1302 | |
---|
| 1303 | # def get_restfreqs(self): |
---|
| 1304 | # """ |
---|
| 1305 | # Get the restfrequency(s) stored in this scantable. |
---|
| 1306 | # The return value(s) are always of unit 'Hz' |
---|
| 1307 | # Parameters: |
---|
| 1308 | # none |
---|
| 1309 | # Returns: |
---|
| 1310 | # a list of doubles |
---|
| 1311 | # """ |
---|
| 1312 | # return list(self._getrestfreqs()) |
---|
| 1313 | |
---|
| 1314 | def get_restfreqs(self, ids=None): |
---|
[1846] | 1315 | """\ |
---|
[256] | 1316 | Get the restfrequency(s) stored in this scantable. |
---|
| 1317 | The return value(s) are always of unit 'Hz' |
---|
[1846] | 1318 | |
---|
[256] | 1319 | Parameters: |
---|
[1846] | 1320 | |
---|
[1819] | 1321 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to |
---|
| 1322 | be retrieved |
---|
[1846] | 1323 | |
---|
[256] | 1324 | Returns: |
---|
[1846] | 1325 | |
---|
[1819] | 1326 | dictionary containing ids and a list of doubles for each id |
---|
[1846] | 1327 | |
---|
[256] | 1328 | """ |
---|
[1819] | 1329 | if ids is None: |
---|
| 1330 | rfreqs={} |
---|
| 1331 | idlist = self.getmolnos() |
---|
| 1332 | for i in idlist: |
---|
| 1333 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1334 | return rfreqs |
---|
| 1335 | else: |
---|
| 1336 | if type(ids)==list or type(ids)==tuple: |
---|
| 1337 | rfreqs={} |
---|
| 1338 | for i in ids: |
---|
| 1339 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1340 | return rfreqs |
---|
| 1341 | else: |
---|
| 1342 | return list(self._getrestfreqs(ids)) |
---|
| 1343 | #return list(self._getrestfreqs(ids)) |
---|
[102] | 1344 | |
---|
[931] | 1345 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
[1846] | 1346 | """\ |
---|
[931] | 1347 | Set or replace the restfrequency specified and |
---|
| 1348 | If the 'freqs' argument holds a scalar, |
---|
| 1349 | then that rest frequency will be applied to all the selected |
---|
| 1350 | data. If the 'freqs' argument holds |
---|
| 1351 | a vector, then it MUST be of equal or smaller length than |
---|
| 1352 | the number of IFs (and the available restfrequencies will be |
---|
| 1353 | replaced by this vector). In this case, *all* data have |
---|
| 1354 | the restfrequency set per IF according |
---|
| 1355 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 1356 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 1357 | IF 1 gets restfreq 2e9. |
---|
[1846] | 1358 | |
---|
[1395] | 1359 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 1360 | |
---|
[931] | 1361 | Parameters: |
---|
[1846] | 1362 | |
---|
[931] | 1363 | freqs: list of rest frequency values or string idenitfiers |
---|
[1855] | 1364 | |
---|
[931] | 1365 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 1366 | |
---|
[1846] | 1367 | |
---|
| 1368 | Example:: |
---|
| 1369 | |
---|
[1819] | 1370 | # set the given restfrequency for the all currently selected IFs |
---|
[931] | 1371 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1845] | 1372 | # set restfrequencies for the n IFs (n > 1) in the order of the |
---|
| 1373 | # list, i.e |
---|
| 1374 | # IF0 -> 1.4e9, IF1 -> 1.41e9, IF3 -> 1.42e9 |
---|
| 1375 | # len(list_of_restfreqs) == nIF |
---|
| 1376 | # for nIF == 1 the following will set multiple restfrequency for |
---|
| 1377 | # that IF |
---|
[1819] | 1378 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9]) |
---|
[1845] | 1379 | # set multiple restfrequencies per IF. as a list of lists where |
---|
| 1380 | # the outer list has nIF elements, the inner s arbitrary |
---|
| 1381 | scan.set_restfreqs(freqs=[[1.4e9, 1.41e9], [1.67e9]]) |
---|
[391] | 1382 | |
---|
[1846] | 1383 | *Note*: |
---|
[1845] | 1384 | |
---|
[931] | 1385 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 1386 | source and IF basis, use scantable.set_selection() before using |
---|
[1846] | 1387 | this function:: |
---|
[931] | 1388 | |
---|
[1846] | 1389 | # provided your scantable is called scan |
---|
| 1390 | selection = selector() |
---|
| 1391 | selection.set_name("ORION*") |
---|
| 1392 | selection.set_ifs([1]) |
---|
| 1393 | scan.set_selection(selection) |
---|
| 1394 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 1395 | |
---|
[931] | 1396 | """ |
---|
| 1397 | varlist = vars() |
---|
[1157] | 1398 | from asap import linecatalog |
---|
| 1399 | # simple value |
---|
[1118] | 1400 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1845] | 1401 | self._setrestfreqs([freqs], [""], unit) |
---|
[1157] | 1402 | # list of values |
---|
[1118] | 1403 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 1404 | # list values are scalars |
---|
[1118] | 1405 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[1845] | 1406 | if len(freqs) == 1: |
---|
| 1407 | self._setrestfreqs(freqs, [""], unit) |
---|
| 1408 | else: |
---|
| 1409 | # allow the 'old' mode of setting mulitple IFs |
---|
| 1410 | sel = selector() |
---|
| 1411 | savesel = self._getselection() |
---|
| 1412 | iflist = self.getifnos() |
---|
| 1413 | if len(freqs)>len(iflist): |
---|
| 1414 | raise ValueError("number of elements in list of list " |
---|
| 1415 | "exeeds the current IF selections") |
---|
| 1416 | iflist = self.getifnos() |
---|
| 1417 | for i, fval in enumerate(freqs): |
---|
| 1418 | sel.set_ifs(iflist[i]) |
---|
| 1419 | self._setselection(sel) |
---|
| 1420 | self._setrestfreqs([fval], [""], unit) |
---|
| 1421 | self._setselection(savesel) |
---|
| 1422 | |
---|
| 1423 | # list values are dict, {'value'=, 'name'=) |
---|
[1157] | 1424 | elif isinstance(freqs[-1], dict): |
---|
[1845] | 1425 | values = [] |
---|
| 1426 | names = [] |
---|
| 1427 | for d in freqs: |
---|
| 1428 | values.append(d["value"]) |
---|
| 1429 | names.append(d["name"]) |
---|
| 1430 | self._setrestfreqs(values, names, unit) |
---|
[1819] | 1431 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple): |
---|
[1157] | 1432 | sel = selector() |
---|
| 1433 | savesel = self._getselection() |
---|
[1322] | 1434 | iflist = self.getifnos() |
---|
[1819] | 1435 | if len(freqs)>len(iflist): |
---|
[1845] | 1436 | raise ValueError("number of elements in list of list exeeds" |
---|
| 1437 | " the current IF selections") |
---|
| 1438 | for i, fval in enumerate(freqs): |
---|
[1322] | 1439 | sel.set_ifs(iflist[i]) |
---|
[1259] | 1440 | self._setselection(sel) |
---|
[1845] | 1441 | self._setrestfreqs(fval, [""], unit) |
---|
[1157] | 1442 | self._setselection(savesel) |
---|
| 1443 | # freqs are to be taken from a linecatalog |
---|
[1153] | 1444 | elif isinstance(freqs, linecatalog): |
---|
| 1445 | sel = selector() |
---|
| 1446 | savesel = self._getselection() |
---|
| 1447 | for i in xrange(freqs.nrow()): |
---|
[1322] | 1448 | sel.set_ifs(iflist[i]) |
---|
[1153] | 1449 | self._setselection(sel) |
---|
[1845] | 1450 | self._setrestfreqs([freqs.get_frequency(i)], |
---|
| 1451 | [freqs.get_name(i)], "MHz") |
---|
[1153] | 1452 | # ensure that we are not iterating past nIF |
---|
| 1453 | if i == self.nif()-1: break |
---|
| 1454 | self._setselection(savesel) |
---|
[931] | 1455 | else: |
---|
| 1456 | return |
---|
| 1457 | self._add_history("set_restfreqs", varlist) |
---|
| 1458 | |
---|
[1360] | 1459 | def shift_refpix(self, delta): |
---|
[1846] | 1460 | """\ |
---|
[1589] | 1461 | Shift the reference pixel of the Spectra Coordinate by an |
---|
| 1462 | integer amount. |
---|
[1846] | 1463 | |
---|
[1589] | 1464 | Parameters: |
---|
[1846] | 1465 | |
---|
[1589] | 1466 | delta: the amount to shift by |
---|
[1846] | 1467 | |
---|
| 1468 | *Note*: |
---|
| 1469 | |
---|
[1589] | 1470 | Be careful using this with broadband data. |
---|
[1846] | 1471 | |
---|
[1360] | 1472 | """ |
---|
[1731] | 1473 | Scantable.shift_refpix(self, delta) |
---|
[931] | 1474 | |
---|
[1259] | 1475 | def history(self, filename=None): |
---|
[1846] | 1476 | """\ |
---|
[1259] | 1477 | Print the history. Optionally to a file. |
---|
[1846] | 1478 | |
---|
[1348] | 1479 | Parameters: |
---|
[1846] | 1480 | |
---|
[1348] | 1481 | filename: The name of the file to save the history to. |
---|
[1846] | 1482 | |
---|
[1259] | 1483 | """ |
---|
[484] | 1484 | hist = list(self._gethistory()) |
---|
[794] | 1485 | out = "-"*80 |
---|
[484] | 1486 | for h in hist: |
---|
[489] | 1487 | if h.startswith("---"): |
---|
[794] | 1488 | out += "\n"+h |
---|
[489] | 1489 | else: |
---|
| 1490 | items = h.split("##") |
---|
| 1491 | date = items[0] |
---|
| 1492 | func = items[1] |
---|
| 1493 | items = items[2:] |
---|
[794] | 1494 | out += "\n"+date+"\n" |
---|
| 1495 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 1496 | for i in items: |
---|
| 1497 | s = i.split("=") |
---|
[1118] | 1498 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[794] | 1499 | out += "\n"+"-"*80 |
---|
[1259] | 1500 | if filename is not None: |
---|
| 1501 | if filename is "": |
---|
| 1502 | filename = 'scantable_history.txt' |
---|
| 1503 | import os |
---|
| 1504 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 1505 | if not os.path.isdir(filename): |
---|
| 1506 | data = open(filename, 'w') |
---|
| 1507 | data.write(out) |
---|
| 1508 | data.close() |
---|
| 1509 | else: |
---|
| 1510 | msg = "Illegal file name '%s'." % (filename) |
---|
| 1511 | if rcParams['verbose']: |
---|
[1819] | 1512 | #print msg |
---|
| 1513 | asaplog.push( msg ) |
---|
| 1514 | print_log( 'ERROR' ) |
---|
[1259] | 1515 | else: |
---|
| 1516 | raise IOError(msg) |
---|
| 1517 | if rcParams['verbose']: |
---|
| 1518 | try: |
---|
| 1519 | from IPython.genutils import page as pager |
---|
| 1520 | except ImportError: |
---|
| 1521 | from pydoc import pager |
---|
| 1522 | pager(out) |
---|
| 1523 | else: |
---|
| 1524 | return out |
---|
[484] | 1525 | return |
---|
[513] | 1526 | # |
---|
| 1527 | # Maths business |
---|
| 1528 | # |
---|
[1589] | 1529 | @print_log_dec |
---|
[931] | 1530 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[1846] | 1531 | """\ |
---|
[1070] | 1532 | Return the (time) weighted average of a scan. |
---|
[1846] | 1533 | |
---|
| 1534 | *Note*: |
---|
| 1535 | |
---|
[1070] | 1536 | in channels only - align if necessary |
---|
[1846] | 1537 | |
---|
[513] | 1538 | Parameters: |
---|
[1846] | 1539 | |
---|
[513] | 1540 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 1541 | weighting) |
---|
[1855] | 1542 | |
---|
[558] | 1543 | scanav: True averages each scan separately |
---|
| 1544 | False (default) averages all scans together, |
---|
[1855] | 1545 | |
---|
[1099] | 1546 | weight: Weighting scheme. |
---|
| 1547 | 'none' (mean no weight) |
---|
| 1548 | 'var' (1/var(spec) weighted) |
---|
| 1549 | 'tsys' (1/Tsys**2 weighted) |
---|
| 1550 | 'tint' (integration time weighted) |
---|
| 1551 | 'tintsys' (Tint/Tsys**2) |
---|
| 1552 | 'median' ( median averaging) |
---|
[535] | 1553 | The default is 'tint' |
---|
[1855] | 1554 | |
---|
[931] | 1555 | align: align the spectra in velocity before averaging. It takes |
---|
| 1556 | the time of the first spectrum as reference time. |
---|
[1846] | 1557 | |
---|
| 1558 | Example:: |
---|
| 1559 | |
---|
[513] | 1560 | # time average the scantable without using a mask |
---|
[710] | 1561 | newscan = scan.average_time() |
---|
[1846] | 1562 | |
---|
[513] | 1563 | """ |
---|
| 1564 | varlist = vars() |
---|
[1593] | 1565 | weight = weight or 'TINT' |
---|
| 1566 | mask = mask or () |
---|
| 1567 | scanav = (scanav and 'SCAN') or 'NONE' |
---|
[1118] | 1568 | scan = (self, ) |
---|
[989] | 1569 | try: |
---|
[1118] | 1570 | if align: |
---|
| 1571 | scan = (self.freq_align(insitu=False), ) |
---|
| 1572 | s = None |
---|
| 1573 | if weight.upper() == 'MEDIAN': |
---|
| 1574 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 1575 | scanav)) |
---|
| 1576 | else: |
---|
| 1577 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 1578 | scanav)) |
---|
| 1579 | except RuntimeError, msg: |
---|
[989] | 1580 | if rcParams['verbose']: |
---|
[1819] | 1581 | #print msg |
---|
| 1582 | print_log() |
---|
| 1583 | asaplog.push( str(msg) ) |
---|
| 1584 | print_log( 'ERROR' ) |
---|
[989] | 1585 | return |
---|
| 1586 | else: raise |
---|
[1099] | 1587 | s._add_history("average_time", varlist) |
---|
[1819] | 1588 | print_log() |
---|
[513] | 1589 | return s |
---|
[710] | 1590 | |
---|
[1589] | 1591 | @print_log_dec |
---|
[876] | 1592 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[1846] | 1593 | """\ |
---|
[513] | 1594 | Return a scan where all spectra are converted to either |
---|
| 1595 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 1596 | By default the function tries to look the values up internally. |
---|
| 1597 | If it can't find them (or if you want to over-ride), you must |
---|
| 1598 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 1599 | also if you don't set it). jyperk takes precedence if you set both. |
---|
[1846] | 1600 | |
---|
[513] | 1601 | Parameters: |
---|
[1846] | 1602 | |
---|
[513] | 1603 | jyperk: the Jy / K conversion factor |
---|
[1855] | 1604 | |
---|
[513] | 1605 | eta: the aperture efficiency |
---|
[1855] | 1606 | |
---|
[513] | 1607 | d: the geomtric diameter (metres) |
---|
[1855] | 1608 | |
---|
[513] | 1609 | insitu: if False a new scantable is returned. |
---|
| 1610 | Otherwise, the scaling is done in-situ |
---|
| 1611 | The default is taken from .asaprc (False) |
---|
[1846] | 1612 | |
---|
[513] | 1613 | """ |
---|
| 1614 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1615 | self._math._setinsitu(insitu) |
---|
[513] | 1616 | varlist = vars() |
---|
[1593] | 1617 | jyperk = jyperk or -1.0 |
---|
| 1618 | d = d or -1.0 |
---|
| 1619 | eta = eta or -1.0 |
---|
[876] | 1620 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 1621 | s._add_history("convert_flux", varlist) |
---|
[1819] | 1622 | print_log() |
---|
[876] | 1623 | if insitu: self._assign(s) |
---|
| 1624 | else: return s |
---|
[513] | 1625 | |
---|
[1589] | 1626 | @print_log_dec |
---|
[876] | 1627 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[1846] | 1628 | """\ |
---|
[513] | 1629 | Return a scan after applying a gain-elevation correction. |
---|
| 1630 | The correction can be made via either a polynomial or a |
---|
| 1631 | table-based interpolation (and extrapolation if necessary). |
---|
| 1632 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 1633 | If you specify neither, then a polynomial correction will be made |
---|
| 1634 | with built in coefficients known for certain telescopes (an error |
---|
| 1635 | will occur if the instrument is not known). |
---|
| 1636 | The data and Tsys are *divided* by the scaling factors. |
---|
[1846] | 1637 | |
---|
[513] | 1638 | Parameters: |
---|
[1846] | 1639 | |
---|
[513] | 1640 | poly: Polynomial coefficients (default None) to compute a |
---|
| 1641 | gain-elevation correction as a function of |
---|
| 1642 | elevation (in degrees). |
---|
[1855] | 1643 | |
---|
[513] | 1644 | filename: The name of an ascii file holding correction factors. |
---|
| 1645 | The first row of the ascii file must give the column |
---|
| 1646 | names and these MUST include columns |
---|
| 1647 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 1648 | by this) somewhere. |
---|
| 1649 | The second row must give the data type of the |
---|
| 1650 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 1651 | An example file would be |
---|
| 1652 | (actual factors are arbitrary) : |
---|
| 1653 | |
---|
| 1654 | TIME ELEVATION FACTOR |
---|
| 1655 | R R R |
---|
| 1656 | 0.1 0 0.8 |
---|
| 1657 | 0.2 20 0.85 |
---|
| 1658 | 0.3 40 0.9 |
---|
| 1659 | 0.4 60 0.85 |
---|
| 1660 | 0.5 80 0.8 |
---|
| 1661 | 0.6 90 0.75 |
---|
[1855] | 1662 | |
---|
[513] | 1663 | method: Interpolation method when correcting from a table. |
---|
| 1664 | Values are "nearest", "linear" (default), "cubic" |
---|
| 1665 | and "spline" |
---|
[1855] | 1666 | |
---|
[513] | 1667 | insitu: if False a new scantable is returned. |
---|
| 1668 | Otherwise, the scaling is done in-situ |
---|
| 1669 | The default is taken from .asaprc (False) |
---|
[1846] | 1670 | |
---|
[513] | 1671 | """ |
---|
| 1672 | |
---|
| 1673 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1674 | self._math._setinsitu(insitu) |
---|
[513] | 1675 | varlist = vars() |
---|
[1593] | 1676 | poly = poly or () |
---|
[513] | 1677 | from os.path import expandvars |
---|
| 1678 | filename = expandvars(filename) |
---|
[876] | 1679 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 1680 | s._add_history("gain_el", varlist) |
---|
[1819] | 1681 | print_log() |
---|
[1593] | 1682 | if insitu: |
---|
| 1683 | self._assign(s) |
---|
| 1684 | else: |
---|
| 1685 | return s |
---|
[710] | 1686 | |
---|
[1589] | 1687 | @print_log_dec |
---|
[931] | 1688 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[1846] | 1689 | """\ |
---|
[513] | 1690 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 1691 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 1692 | set_freqframe. |
---|
[1846] | 1693 | |
---|
[513] | 1694 | Parameters: |
---|
[1855] | 1695 | |
---|
[513] | 1696 | reftime: reference time to align at. By default, the time of |
---|
| 1697 | the first row of data is used. |
---|
[1855] | 1698 | |
---|
[513] | 1699 | method: Interpolation method for regridding the spectra. |
---|
| 1700 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 1701 | and "spline" |
---|
[1855] | 1702 | |
---|
[513] | 1703 | insitu: if False a new scantable is returned. |
---|
| 1704 | Otherwise, the scaling is done in-situ |
---|
| 1705 | The default is taken from .asaprc (False) |
---|
[1846] | 1706 | |
---|
[513] | 1707 | """ |
---|
[931] | 1708 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 1709 | self._math._setinsitu(insitu) |
---|
[513] | 1710 | varlist = vars() |
---|
[1593] | 1711 | reftime = reftime or "" |
---|
[931] | 1712 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 1713 | s._add_history("freq_align", varlist) |
---|
[1819] | 1714 | print_log() |
---|
[876] | 1715 | if insitu: self._assign(s) |
---|
| 1716 | else: return s |
---|
[513] | 1717 | |
---|
[1589] | 1718 | @print_log_dec |
---|
[1725] | 1719 | def opacity(self, tau=None, insitu=None): |
---|
[1846] | 1720 | """\ |
---|
[513] | 1721 | Apply an opacity correction. The data |
---|
| 1722 | and Tsys are multiplied by the correction factor. |
---|
[1846] | 1723 | |
---|
[513] | 1724 | Parameters: |
---|
[1855] | 1725 | |
---|
[1689] | 1726 | tau: (list of) opacity from which the correction factor is |
---|
[513] | 1727 | exp(tau*ZD) |
---|
[1689] | 1728 | where ZD is the zenith-distance. |
---|
| 1729 | If a list is provided, it has to be of length nIF, |
---|
| 1730 | nIF*nPol or 1 and in order of IF/POL, e.g. |
---|
| 1731 | [opif0pol0, opif0pol1, opif1pol0 ...] |
---|
[1725] | 1732 | if tau is `None` the opacities are determined from a |
---|
| 1733 | model. |
---|
[1855] | 1734 | |
---|
[513] | 1735 | insitu: if False a new scantable is returned. |
---|
| 1736 | Otherwise, the scaling is done in-situ |
---|
| 1737 | The default is taken from .asaprc (False) |
---|
[1846] | 1738 | |
---|
[513] | 1739 | """ |
---|
| 1740 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1741 | self._math._setinsitu(insitu) |
---|
[513] | 1742 | varlist = vars() |
---|
[1689] | 1743 | if not hasattr(tau, "__len__"): |
---|
| 1744 | tau = [tau] |
---|
[876] | 1745 | s = scantable(self._math._opacity(self, tau)) |
---|
| 1746 | s._add_history("opacity", varlist) |
---|
[1819] | 1747 | print_log() |
---|
[876] | 1748 | if insitu: self._assign(s) |
---|
| 1749 | else: return s |
---|
[513] | 1750 | |
---|
[1589] | 1751 | @print_log_dec |
---|
[513] | 1752 | def bin(self, width=5, insitu=None): |
---|
[1846] | 1753 | """\ |
---|
[513] | 1754 | Return a scan where all spectra have been binned up. |
---|
[1846] | 1755 | |
---|
[1348] | 1756 | Parameters: |
---|
[1846] | 1757 | |
---|
[513] | 1758 | width: The bin width (default=5) in pixels |
---|
[1855] | 1759 | |
---|
[513] | 1760 | insitu: if False a new scantable is returned. |
---|
| 1761 | Otherwise, the scaling is done in-situ |
---|
| 1762 | The default is taken from .asaprc (False) |
---|
[1846] | 1763 | |
---|
[513] | 1764 | """ |
---|
| 1765 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1766 | self._math._setinsitu(insitu) |
---|
[513] | 1767 | varlist = vars() |
---|
[876] | 1768 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1769 | s._add_history("bin", varlist) |
---|
[1819] | 1770 | print_log() |
---|
[1589] | 1771 | if insitu: |
---|
| 1772 | self._assign(s) |
---|
| 1773 | else: |
---|
| 1774 | return s |
---|
[513] | 1775 | |
---|
[1589] | 1776 | @print_log_dec |
---|
[513] | 1777 | def resample(self, width=5, method='cubic', insitu=None): |
---|
[1846] | 1778 | """\ |
---|
[1348] | 1779 | Return a scan where all spectra have been binned up. |
---|
[1573] | 1780 | |
---|
[1348] | 1781 | Parameters: |
---|
[1846] | 1782 | |
---|
[513] | 1783 | width: The bin width (default=5) in pixels |
---|
[1855] | 1784 | |
---|
[513] | 1785 | method: Interpolation method when correcting from a table. |
---|
| 1786 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1787 | and "spline" |
---|
[1855] | 1788 | |
---|
[513] | 1789 | insitu: if False a new scantable is returned. |
---|
| 1790 | Otherwise, the scaling is done in-situ |
---|
| 1791 | The default is taken from .asaprc (False) |
---|
[1846] | 1792 | |
---|
[513] | 1793 | """ |
---|
| 1794 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1795 | self._math._setinsitu(insitu) |
---|
[513] | 1796 | varlist = vars() |
---|
[876] | 1797 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1798 | s._add_history("resample", varlist) |
---|
[1819] | 1799 | print_log() |
---|
[876] | 1800 | if insitu: self._assign(s) |
---|
| 1801 | else: return s |
---|
[513] | 1802 | |
---|
[1589] | 1803 | @print_log_dec |
---|
[946] | 1804 | def average_pol(self, mask=None, weight='none'): |
---|
[1846] | 1805 | """\ |
---|
[946] | 1806 | Average the Polarisations together. |
---|
[1846] | 1807 | |
---|
[946] | 1808 | Parameters: |
---|
[1846] | 1809 | |
---|
[946] | 1810 | mask: An optional mask defining the region, where the |
---|
| 1811 | averaging will be applied. The output will have all |
---|
| 1812 | specified points masked. |
---|
[1855] | 1813 | |
---|
[946] | 1814 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1815 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 1816 | |
---|
[946] | 1817 | """ |
---|
| 1818 | varlist = vars() |
---|
[1593] | 1819 | mask = mask or () |
---|
[1010] | 1820 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1821 | s._add_history("average_pol", varlist) |
---|
[1819] | 1822 | print_log() |
---|
[992] | 1823 | return s |
---|
[513] | 1824 | |
---|
[1589] | 1825 | @print_log_dec |
---|
[1145] | 1826 | def average_beam(self, mask=None, weight='none'): |
---|
[1846] | 1827 | """\ |
---|
[1145] | 1828 | Average the Beams together. |
---|
[1846] | 1829 | |
---|
[1145] | 1830 | Parameters: |
---|
| 1831 | mask: An optional mask defining the region, where the |
---|
| 1832 | averaging will be applied. The output will have all |
---|
| 1833 | specified points masked. |
---|
[1855] | 1834 | |
---|
[1145] | 1835 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1836 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 1837 | |
---|
[1145] | 1838 | """ |
---|
| 1839 | varlist = vars() |
---|
[1593] | 1840 | mask = mask or () |
---|
[1145] | 1841 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1842 | s._add_history("average_beam", varlist) |
---|
[1819] | 1843 | print_log() |
---|
[1145] | 1844 | return s |
---|
| 1845 | |
---|
[1586] | 1846 | def parallactify(self, pflag): |
---|
[1846] | 1847 | """\ |
---|
[1843] | 1848 | Set a flag to indicate whether this data should be treated as having |
---|
[1617] | 1849 | been 'parallactified' (total phase == 0.0) |
---|
[1846] | 1850 | |
---|
[1617] | 1851 | Parameters: |
---|
[1855] | 1852 | |
---|
[1843] | 1853 | pflag: Bool indicating whether to turn this on (True) or |
---|
[1617] | 1854 | off (False) |
---|
[1846] | 1855 | |
---|
[1617] | 1856 | """ |
---|
[1586] | 1857 | varlist = vars() |
---|
| 1858 | self._parallactify(pflag) |
---|
| 1859 | self._add_history("parallactify", varlist) |
---|
| 1860 | |
---|
[1589] | 1861 | @print_log_dec |
---|
[992] | 1862 | def convert_pol(self, poltype=None): |
---|
[1846] | 1863 | """\ |
---|
[992] | 1864 | Convert the data to a different polarisation type. |
---|
[1565] | 1865 | Note that you will need cross-polarisation terms for most conversions. |
---|
[1846] | 1866 | |
---|
[992] | 1867 | Parameters: |
---|
[1855] | 1868 | |
---|
[992] | 1869 | poltype: The new polarisation type. Valid types are: |
---|
[1565] | 1870 | "linear", "circular", "stokes" and "linpol" |
---|
[1846] | 1871 | |
---|
[992] | 1872 | """ |
---|
| 1873 | varlist = vars() |
---|
| 1874 | try: |
---|
| 1875 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1876 | except RuntimeError, msg: |
---|
[992] | 1877 | if rcParams['verbose']: |
---|
[1819] | 1878 | #print msg |
---|
| 1879 | print_log() |
---|
| 1880 | asaplog.push( str(msg) ) |
---|
| 1881 | print_log( 'ERROR' ) |
---|
[1118] | 1882 | return |
---|
[992] | 1883 | else: |
---|
| 1884 | raise |
---|
[1118] | 1885 | s._add_history("convert_pol", varlist) |
---|
[1819] | 1886 | print_log() |
---|
[992] | 1887 | return s |
---|
| 1888 | |
---|
[1589] | 1889 | @print_log_dec |
---|
[1819] | 1890 | def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, insitu=None): |
---|
[1846] | 1891 | """\ |
---|
[513] | 1892 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
[1846] | 1893 | |
---|
[513] | 1894 | Parameters: |
---|
[1846] | 1895 | |
---|
[513] | 1896 | kernel: The type of smoothing kernel. Select from |
---|
[1574] | 1897 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian' |
---|
| 1898 | or 'poly' |
---|
[1855] | 1899 | |
---|
[513] | 1900 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1901 | ignored otherwise it defauls to 5 pixels. |
---|
| 1902 | For 'gaussian' it is the Full Width Half |
---|
| 1903 | Maximum. For 'boxcar' it is the full width. |
---|
[1574] | 1904 | For 'rmedian' and 'poly' it is the half width. |
---|
[1855] | 1905 | |
---|
[1574] | 1906 | order: Optional parameter for 'poly' kernel (default is 2), to |
---|
| 1907 | specify the order of the polnomial. Ignored by all other |
---|
| 1908 | kernels. |
---|
[1855] | 1909 | |
---|
[1819] | 1910 | plot: plot the original and the smoothed spectra. |
---|
| 1911 | In this each indivual fit has to be approved, by |
---|
| 1912 | typing 'y' or 'n' |
---|
[1855] | 1913 | |
---|
[513] | 1914 | insitu: if False a new scantable is returned. |
---|
| 1915 | Otherwise, the scaling is done in-situ |
---|
| 1916 | The default is taken from .asaprc (False) |
---|
[1846] | 1917 | |
---|
[513] | 1918 | """ |
---|
| 1919 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1920 | self._math._setinsitu(insitu) |
---|
[513] | 1921 | varlist = vars() |
---|
[1819] | 1922 | |
---|
| 1923 | if plot: orgscan = self.copy() |
---|
| 1924 | |
---|
[1574] | 1925 | s = scantable(self._math._smooth(self, kernel.lower(), width, order)) |
---|
[876] | 1926 | s._add_history("smooth", varlist) |
---|
[1819] | 1927 | |
---|
| 1928 | if plot: |
---|
| 1929 | if rcParams['plotter.gui']: |
---|
| 1930 | from asap.asaplotgui import asaplotgui as asaplot |
---|
| 1931 | else: |
---|
| 1932 | from asap.asaplot import asaplot |
---|
| 1933 | self._p=asaplot() |
---|
| 1934 | self._p.set_panels() |
---|
| 1935 | ylab=s._get_ordinate_label() |
---|
| 1936 | #self._p.palette(0,["#777777","red"]) |
---|
| 1937 | for r in xrange(s.nrow()): |
---|
| 1938 | xsm=s._getabcissa(r) |
---|
| 1939 | ysm=s._getspectrum(r) |
---|
| 1940 | xorg=orgscan._getabcissa(r) |
---|
| 1941 | yorg=orgscan._getspectrum(r) |
---|
| 1942 | self._p.clear() |
---|
| 1943 | self._p.hold() |
---|
| 1944 | self._p.set_axes('ylabel',ylab) |
---|
| 1945 | self._p.set_axes('xlabel',s._getabcissalabel(r)) |
---|
| 1946 | self._p.set_axes('title',s._getsourcename(r)) |
---|
| 1947 | self._p.set_line(label='Original',color="#777777") |
---|
| 1948 | self._p.plot(xorg,yorg) |
---|
| 1949 | self._p.set_line(label='Smoothed',color="red") |
---|
| 1950 | self._p.plot(xsm,ysm) |
---|
| 1951 | ### Ugly part for legend |
---|
| 1952 | for i in [0,1]: |
---|
| 1953 | self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]]) |
---|
| 1954 | self._p.release() |
---|
| 1955 | ### Ugly part for legend |
---|
| 1956 | self._p.subplots[0]['lines']=[] |
---|
| 1957 | res = raw_input("Accept smoothing ([y]/n): ") |
---|
| 1958 | if res.upper() == 'N': |
---|
| 1959 | s._setspectrum(yorg, r) |
---|
| 1960 | self._p.unmap() |
---|
| 1961 | self._p = None |
---|
| 1962 | del orgscan |
---|
| 1963 | |
---|
| 1964 | print_log() |
---|
[876] | 1965 | if insitu: self._assign(s) |
---|
| 1966 | else: return s |
---|
[513] | 1967 | |
---|
[1589] | 1968 | @print_log_dec |
---|
[1617] | 1969 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, |
---|
| 1970 | insitu=None): |
---|
[1846] | 1971 | """\ |
---|
[513] | 1972 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
[1846] | 1973 | |
---|
[513] | 1974 | Parameters: |
---|
[1846] | 1975 | |
---|
[794] | 1976 | mask: an optional mask |
---|
[1855] | 1977 | |
---|
[794] | 1978 | order: the order of the polynomial (default is 0) |
---|
[1855] | 1979 | |
---|
[1061] | 1980 | plot: plot the fit and the residual. In this each |
---|
| 1981 | indivual fit has to be approved, by typing 'y' |
---|
| 1982 | or 'n' |
---|
[1855] | 1983 | |
---|
[1391] | 1984 | uselin: use linear polynomial fit |
---|
[1855] | 1985 | |
---|
[794] | 1986 | insitu: if False a new scantable is returned. |
---|
| 1987 | Otherwise, the scaling is done in-situ |
---|
| 1988 | The default is taken from .asaprc (False) |
---|
[1846] | 1989 | |
---|
| 1990 | Example:: |
---|
| 1991 | |
---|
[513] | 1992 | # return a scan baselined by a third order polynomial, |
---|
| 1993 | # not using a mask |
---|
| 1994 | bscan = scan.poly_baseline(order=3) |
---|
[1846] | 1995 | |
---|
[579] | 1996 | """ |
---|
[513] | 1997 | if insitu is None: insitu = rcParams['insitu'] |
---|
[1819] | 1998 | if not insitu: |
---|
| 1999 | workscan = self.copy() |
---|
| 2000 | else: |
---|
| 2001 | workscan = self |
---|
[513] | 2002 | varlist = vars() |
---|
| 2003 | if mask is None: |
---|
[1295] | 2004 | mask = [True for i in xrange(self.nchan(-1))] |
---|
[1819] | 2005 | |
---|
[513] | 2006 | from asap.asapfitter import fitter |
---|
[1217] | 2007 | try: |
---|
| 2008 | f = fitter() |
---|
[1391] | 2009 | if uselin: |
---|
| 2010 | f.set_function(lpoly=order) |
---|
| 2011 | else: |
---|
| 2012 | f.set_function(poly=order) |
---|
[1819] | 2013 | |
---|
| 2014 | rows = range(workscan.nrow()) |
---|
| 2015 | if len(rows) > 0: |
---|
| 2016 | self.blpars = [] |
---|
| 2017 | |
---|
| 2018 | for r in rows: |
---|
| 2019 | # take into account flagtra info (CAS-1434) |
---|
| 2020 | flagtra = workscan._getmask(r) |
---|
| 2021 | actualmask = mask[:] |
---|
| 2022 | if len(actualmask) == 0: |
---|
| 2023 | actualmask = list(flagtra[:]) |
---|
| 2024 | else: |
---|
| 2025 | if len(actualmask) != len(flagtra): |
---|
| 2026 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 2027 | else: |
---|
| 2028 | for i in range(0, len(actualmask)): |
---|
| 2029 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 2030 | f.set_scan(workscan, actualmask) |
---|
| 2031 | f.x = workscan._getabcissa(r) |
---|
| 2032 | f.y = workscan._getspectrum(r) |
---|
| 2033 | f.data = None |
---|
| 2034 | f.fit() |
---|
| 2035 | if plot: |
---|
| 2036 | f.plot(residual=True) |
---|
| 2037 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 2038 | if x.upper() == 'N': |
---|
| 2039 | self.blpars.append(None) |
---|
| 2040 | continue |
---|
| 2041 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
| 2042 | self.blpars.append(f.get_parameters()) |
---|
| 2043 | |
---|
| 2044 | if plot: |
---|
| 2045 | f._p.unmap() |
---|
| 2046 | f._p = None |
---|
| 2047 | workscan._add_history("poly_baseline", varlist) |
---|
| 2048 | print_log() |
---|
| 2049 | if insitu: self._assign(workscan) |
---|
| 2050 | else: return workscan |
---|
[1217] | 2051 | except RuntimeError: |
---|
| 2052 | msg = "The fit failed, possibly because it didn't converge." |
---|
| 2053 | if rcParams['verbose']: |
---|
[1819] | 2054 | #print msg |
---|
| 2055 | print_log() |
---|
| 2056 | asaplog.push( str(msg) ) |
---|
| 2057 | print_log( 'ERROR' ) |
---|
[1217] | 2058 | return |
---|
| 2059 | else: |
---|
| 2060 | raise RuntimeError(msg) |
---|
[513] | 2061 | |
---|
[1819] | 2062 | |
---|
[1118] | 2063 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
[1280] | 2064 | threshold=3, chan_avg_limit=1, plot=False, |
---|
| 2065 | insitu=None): |
---|
[1846] | 2066 | """\ |
---|
[880] | 2067 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 2068 | Spectral lines are detected first using linefinder and masked out |
---|
| 2069 | to avoid them affecting the baseline solution. |
---|
| 2070 | |
---|
| 2071 | Parameters: |
---|
[1846] | 2072 | |
---|
[880] | 2073 | mask: an optional mask retreived from scantable |
---|
[1846] | 2074 | |
---|
| 2075 | edge: an optional number of channel to drop at the edge of |
---|
| 2076 | spectrum. If only one value is |
---|
[880] | 2077 | specified, the same number will be dropped from |
---|
| 2078 | both sides of the spectrum. Default is to keep |
---|
[907] | 2079 | all channels. Nested tuples represent individual |
---|
[976] | 2080 | edge selection for different IFs (a number of spectral |
---|
| 2081 | channels can be different) |
---|
[1846] | 2082 | |
---|
[880] | 2083 | order: the order of the polynomial (default is 0) |
---|
[1846] | 2084 | |
---|
[880] | 2085 | threshold: the threshold used by line finder. It is better to |
---|
| 2086 | keep it large as only strong lines affect the |
---|
| 2087 | baseline solution. |
---|
[1846] | 2088 | |
---|
[1280] | 2089 | chan_avg_limit: |
---|
| 2090 | a maximum number of consequtive spectral channels to |
---|
| 2091 | average during the search of weak and broad lines. |
---|
| 2092 | The default is no averaging (and no search for weak |
---|
| 2093 | lines). If such lines can affect the fitted baseline |
---|
| 2094 | (e.g. a high order polynomial is fitted), increase this |
---|
| 2095 | parameter (usually values up to 8 are reasonable). Most |
---|
| 2096 | users of this method should find the default value |
---|
| 2097 | sufficient. |
---|
[1846] | 2098 | |
---|
[1061] | 2099 | plot: plot the fit and the residual. In this each |
---|
| 2100 | indivual fit has to be approved, by typing 'y' |
---|
| 2101 | or 'n' |
---|
[1846] | 2102 | |
---|
[880] | 2103 | insitu: if False a new scantable is returned. |
---|
| 2104 | Otherwise, the scaling is done in-situ |
---|
| 2105 | The default is taken from .asaprc (False) |
---|
| 2106 | |
---|
[1846] | 2107 | |
---|
| 2108 | Example:: |
---|
| 2109 | |
---|
| 2110 | scan2 = scan.auto_poly_baseline(order=7, insitu=False) |
---|
| 2111 | |
---|
[880] | 2112 | """ |
---|
| 2113 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 2114 | varlist = vars() |
---|
| 2115 | from asap.asapfitter import fitter |
---|
| 2116 | from asap.asaplinefind import linefinder |
---|
| 2117 | from asap import _is_sequence_or_number as _is_valid |
---|
| 2118 | |
---|
[976] | 2119 | # check whether edge is set up for each IF individually |
---|
[1118] | 2120 | individualedge = False; |
---|
| 2121 | if len(edge) > 1: |
---|
| 2122 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 2123 | individualedge = True; |
---|
[907] | 2124 | |
---|
[1118] | 2125 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 2126 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 2127 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 2128 | to make individual selection for different IFs." |
---|
[919] | 2129 | |
---|
[1118] | 2130 | curedge = (0, 0) |
---|
| 2131 | if individualedge: |
---|
| 2132 | for edgepar in edge: |
---|
| 2133 | if not _is_valid(edgepar, int): |
---|
| 2134 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 2135 | to be a pair of integers or an integer." |
---|
[907] | 2136 | else: |
---|
[1118] | 2137 | curedge = edge; |
---|
[880] | 2138 | |
---|
| 2139 | # setup fitter |
---|
| 2140 | f = fitter() |
---|
| 2141 | f.set_function(poly=order) |
---|
| 2142 | |
---|
| 2143 | # setup line finder |
---|
[1118] | 2144 | fl = linefinder() |
---|
[1268] | 2145 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
[880] | 2146 | |
---|
| 2147 | if not insitu: |
---|
[1118] | 2148 | workscan = self.copy() |
---|
[880] | 2149 | else: |
---|
[1118] | 2150 | workscan = self |
---|
[880] | 2151 | |
---|
[907] | 2152 | fl.set_scan(workscan) |
---|
| 2153 | |
---|
[1118] | 2154 | rows = range(workscan.nrow()) |
---|
[1819] | 2155 | # Save parameters of baseline fits & masklists as a class attribute. |
---|
| 2156 | # NOTICE: It does not reflect changes in scantable! |
---|
| 2157 | if len(rows) > 0: |
---|
| 2158 | self.blpars=[] |
---|
| 2159 | self.masklists=[] |
---|
[880] | 2160 | asaplog.push("Processing:") |
---|
| 2161 | for r in rows: |
---|
[1118] | 2162 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 2163 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 2164 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 2165 | asaplog.push(msg, False) |
---|
[907] | 2166 | |
---|
[976] | 2167 | # figure out edge parameter |
---|
[1118] | 2168 | if individualedge: |
---|
| 2169 | if len(edge) >= workscan.getif(r): |
---|
| 2170 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 2171 | "be less than the number of IFs" |
---|
| 2172 | curedge = edge[workscan.getif(r)] |
---|
[919] | 2173 | |
---|
[1819] | 2174 | # take into account flagtra info (CAS-1434) |
---|
| 2175 | flagtra = workscan._getmask(r) |
---|
| 2176 | actualmask = mask[:] |
---|
| 2177 | if len(actualmask) == 0: |
---|
| 2178 | actualmask = list(flagtra[:]) |
---|
| 2179 | else: |
---|
| 2180 | if len(actualmask) != len(flagtra): |
---|
| 2181 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 2182 | else: |
---|
| 2183 | for i in range(0, len(actualmask)): |
---|
| 2184 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 2185 | |
---|
[976] | 2186 | # setup line finder |
---|
[1819] | 2187 | fl.find_lines(r, actualmask, curedge) |
---|
| 2188 | outmask=fl.get_mask() |
---|
| 2189 | f.set_scan(workscan, fl.get_mask()) |
---|
| 2190 | f.x = workscan._getabcissa(r) |
---|
| 2191 | f.y = workscan._getspectrum(r) |
---|
| 2192 | f.data = None |
---|
[880] | 2193 | f.fit() |
---|
[1819] | 2194 | |
---|
| 2195 | # Show mask list |
---|
| 2196 | masklist=workscan.get_masklist(fl.get_mask(),row=r) |
---|
| 2197 | msg = "mask range: "+str(masklist) |
---|
| 2198 | asaplog.push(msg, False) |
---|
| 2199 | |
---|
[1061] | 2200 | if plot: |
---|
| 2201 | f.plot(residual=True) |
---|
| 2202 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 2203 | if x.upper() == 'N': |
---|
[1819] | 2204 | self.blpars.append(None) |
---|
| 2205 | self.masklists.append(None) |
---|
[1061] | 2206 | continue |
---|
[1819] | 2207 | |
---|
[880] | 2208 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1819] | 2209 | self.blpars.append(f.get_parameters()) |
---|
| 2210 | self.masklists.append(masklist) |
---|
[1061] | 2211 | if plot: |
---|
| 2212 | f._p.unmap() |
---|
| 2213 | f._p = None |
---|
| 2214 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 2215 | if insitu: |
---|
| 2216 | self._assign(workscan) |
---|
| 2217 | else: |
---|
| 2218 | return workscan |
---|
| 2219 | |
---|
[1589] | 2220 | @print_log_dec |
---|
[914] | 2221 | def rotate_linpolphase(self, angle): |
---|
[1846] | 2222 | """\ |
---|
[914] | 2223 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 2224 | This is always done in situ in the raw data. So if you call this |
---|
| 2225 | function more than once then each call rotates the phase further. |
---|
[1846] | 2226 | |
---|
[914] | 2227 | Parameters: |
---|
[1846] | 2228 | |
---|
[914] | 2229 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 2230 | |
---|
| 2231 | Example:: |
---|
| 2232 | |
---|
[914] | 2233 | scan.rotate_linpolphase(2.3) |
---|
[1846] | 2234 | |
---|
[914] | 2235 | """ |
---|
| 2236 | varlist = vars() |
---|
[936] | 2237 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 2238 | self._add_history("rotate_linpolphase", varlist) |
---|
[1819] | 2239 | print_log() |
---|
[914] | 2240 | return |
---|
[710] | 2241 | |
---|
[1589] | 2242 | @print_log_dec |
---|
[914] | 2243 | def rotate_xyphase(self, angle): |
---|
[1846] | 2244 | """\ |
---|
[914] | 2245 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 2246 | in the data. So if you call this function more than once |
---|
| 2247 | then each call rotates the phase further. |
---|
[1846] | 2248 | |
---|
[914] | 2249 | Parameters: |
---|
[1846] | 2250 | |
---|
[914] | 2251 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 2252 | |
---|
| 2253 | Example:: |
---|
| 2254 | |
---|
[914] | 2255 | scan.rotate_xyphase(2.3) |
---|
[1846] | 2256 | |
---|
[914] | 2257 | """ |
---|
| 2258 | varlist = vars() |
---|
[936] | 2259 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 2260 | self._add_history("rotate_xyphase", varlist) |
---|
[1819] | 2261 | print_log() |
---|
[914] | 2262 | return |
---|
| 2263 | |
---|
[1589] | 2264 | @print_log_dec |
---|
[914] | 2265 | def swap_linears(self): |
---|
[1846] | 2266 | """\ |
---|
[1573] | 2267 | Swap the linear polarisations XX and YY, or better the first two |
---|
[1348] | 2268 | polarisations as this also works for ciculars. |
---|
[914] | 2269 | """ |
---|
| 2270 | varlist = vars() |
---|
[936] | 2271 | self._math._swap_linears(self) |
---|
[914] | 2272 | self._add_history("swap_linears", varlist) |
---|
[1819] | 2273 | print_log() |
---|
[914] | 2274 | return |
---|
| 2275 | |
---|
[1589] | 2276 | @print_log_dec |
---|
[914] | 2277 | def invert_phase(self): |
---|
[1846] | 2278 | """\ |
---|
[914] | 2279 | Invert the phase of the complex polarisation |
---|
| 2280 | """ |
---|
| 2281 | varlist = vars() |
---|
[936] | 2282 | self._math._invert_phase(self) |
---|
[914] | 2283 | self._add_history("invert_phase", varlist) |
---|
| 2284 | return |
---|
| 2285 | |
---|
[1589] | 2286 | @print_log_dec |
---|
[876] | 2287 | def add(self, offset, insitu=None): |
---|
[1846] | 2288 | """\ |
---|
[513] | 2289 | Return a scan where all spectra have the offset added |
---|
[1846] | 2290 | |
---|
[513] | 2291 | Parameters: |
---|
[1846] | 2292 | |
---|
[513] | 2293 | offset: the offset |
---|
[1855] | 2294 | |
---|
[513] | 2295 | insitu: if False a new scantable is returned. |
---|
| 2296 | Otherwise, the scaling is done in-situ |
---|
| 2297 | The default is taken from .asaprc (False) |
---|
[1846] | 2298 | |
---|
[513] | 2299 | """ |
---|
| 2300 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2301 | self._math._setinsitu(insitu) |
---|
[513] | 2302 | varlist = vars() |
---|
[876] | 2303 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 2304 | s._add_history("add", varlist) |
---|
[876] | 2305 | if insitu: |
---|
| 2306 | self._assign(s) |
---|
| 2307 | else: |
---|
[513] | 2308 | return s |
---|
| 2309 | |
---|
[1589] | 2310 | @print_log_dec |
---|
[1308] | 2311 | def scale(self, factor, tsys=True, insitu=None): |
---|
[1846] | 2312 | """\ |
---|
| 2313 | |
---|
[513] | 2314 | Return a scan where all spectra are scaled by the give 'factor' |
---|
[1846] | 2315 | |
---|
[513] | 2316 | Parameters: |
---|
[1846] | 2317 | |
---|
[1819] | 2318 | factor: the scaling factor (float or 1D float list) |
---|
[1855] | 2319 | |
---|
[513] | 2320 | insitu: if False a new scantable is returned. |
---|
| 2321 | Otherwise, the scaling is done in-situ |
---|
| 2322 | The default is taken from .asaprc (False) |
---|
[1855] | 2323 | |
---|
[513] | 2324 | tsys: if True (default) then apply the operation to Tsys |
---|
| 2325 | as well as the data |
---|
[1846] | 2326 | |
---|
[513] | 2327 | """ |
---|
| 2328 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2329 | self._math._setinsitu(insitu) |
---|
[513] | 2330 | varlist = vars() |
---|
[1819] | 2331 | s = None |
---|
| 2332 | import numpy |
---|
| 2333 | if isinstance(factor, list) or isinstance(factor, numpy.ndarray): |
---|
| 2334 | if isinstance(factor[0], list) or isinstance(factor[0], numpy.ndarray): |
---|
| 2335 | from asapmath import _array2dOp |
---|
| 2336 | s = _array2dOp( self.copy(), factor, "MUL", tsys ) |
---|
| 2337 | else: |
---|
| 2338 | s = scantable( self._math._arrayop( self.copy(), factor, "MUL", tsys ) ) |
---|
| 2339 | else: |
---|
| 2340 | s = scantable(self._math._unaryop(self.copy(), factor, "MUL", tsys)) |
---|
[1118] | 2341 | s._add_history("scale", varlist) |
---|
[1819] | 2342 | print_log() |
---|
[876] | 2343 | if insitu: |
---|
| 2344 | self._assign(s) |
---|
| 2345 | else: |
---|
[513] | 2346 | return s |
---|
| 2347 | |
---|
[1504] | 2348 | def set_sourcetype(self, match, matchtype="pattern", |
---|
| 2349 | sourcetype="reference"): |
---|
[1846] | 2350 | """\ |
---|
[1502] | 2351 | Set the type of the source to be an source or reference scan |
---|
[1846] | 2352 | using the provided pattern. |
---|
| 2353 | |
---|
[1502] | 2354 | Parameters: |
---|
[1846] | 2355 | |
---|
[1504] | 2356 | match: a Unix style pattern, regular expression or selector |
---|
[1855] | 2357 | |
---|
[1504] | 2358 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
| 2359 | 'regex' regular expression |
---|
[1855] | 2360 | |
---|
[1502] | 2361 | sourcetype: the type of the source to use (source/reference) |
---|
[1846] | 2362 | |
---|
[1502] | 2363 | """ |
---|
| 2364 | varlist = vars() |
---|
| 2365 | basesel = self.get_selection() |
---|
| 2366 | stype = -1 |
---|
| 2367 | if sourcetype.lower().startswith("r"): |
---|
| 2368 | stype = 1 |
---|
| 2369 | elif sourcetype.lower().startswith("s"): |
---|
| 2370 | stype = 0 |
---|
[1504] | 2371 | else: |
---|
[1502] | 2372 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)") |
---|
[1504] | 2373 | if matchtype.lower().startswith("p"): |
---|
| 2374 | matchtype = "pattern" |
---|
| 2375 | elif matchtype.lower().startswith("r"): |
---|
| 2376 | matchtype = "regex" |
---|
| 2377 | else: |
---|
| 2378 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
[1502] | 2379 | sel = selector() |
---|
| 2380 | if isinstance(match, selector): |
---|
| 2381 | sel = match |
---|
| 2382 | else: |
---|
[1504] | 2383 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match)) |
---|
[1502] | 2384 | self.set_selection(basesel+sel) |
---|
| 2385 | self._setsourcetype(stype) |
---|
| 2386 | self.set_selection(basesel) |
---|
[1573] | 2387 | self._add_history("set_sourcetype", varlist) |
---|
[1502] | 2388 | |
---|
[1589] | 2389 | @print_log_dec |
---|
[1819] | 2390 | def auto_quotient(self, preserve=True, mode='paired', verify=False): |
---|
[1846] | 2391 | """\ |
---|
[670] | 2392 | This function allows to build quotients automatically. |
---|
[1819] | 2393 | It assumes the observation to have the same number of |
---|
[670] | 2394 | "ons" and "offs" |
---|
[1846] | 2395 | |
---|
[670] | 2396 | Parameters: |
---|
[1846] | 2397 | |
---|
[710] | 2398 | preserve: you can preserve (default) the continuum or |
---|
| 2399 | remove it. The equations used are |
---|
[670] | 2400 | preserve: Output = Toff * (on/off) - Toff |
---|
[1070] | 2401 | remove: Output = Toff * (on/off) - Ton |
---|
[1855] | 2402 | |
---|
[1573] | 2403 | mode: the on/off detection mode |
---|
[1348] | 2404 | 'paired' (default) |
---|
| 2405 | identifies 'off' scans by the |
---|
| 2406 | trailing '_R' (Mopra/Parkes) or |
---|
| 2407 | '_e'/'_w' (Tid) and matches |
---|
| 2408 | on/off pairs from the observing pattern |
---|
[1502] | 2409 | 'time' |
---|
| 2410 | finds the closest off in time |
---|
[1348] | 2411 | |
---|
[670] | 2412 | """ |
---|
[1348] | 2413 | modes = ["time", "paired"] |
---|
[670] | 2414 | if not mode in modes: |
---|
[876] | 2415 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 2416 | raise ValueError(msg) |
---|
| 2417 | varlist = vars() |
---|
[1348] | 2418 | s = None |
---|
| 2419 | if mode.lower() == "paired": |
---|
| 2420 | basesel = self.get_selection() |
---|
[1356] | 2421 | sel = selector()+basesel |
---|
| 2422 | sel.set_query("SRCTYPE==1") |
---|
| 2423 | self.set_selection(sel) |
---|
[1348] | 2424 | offs = self.copy() |
---|
| 2425 | sel.set_query("SRCTYPE==0") |
---|
[1356] | 2426 | self.set_selection(sel) |
---|
[1348] | 2427 | ons = self.copy() |
---|
| 2428 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 2429 | self.set_selection(basesel) |
---|
| 2430 | elif mode.lower() == "time": |
---|
| 2431 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 2432 | s._add_history("auto_quotient", varlist) |
---|
[1819] | 2433 | print_log() |
---|
[876] | 2434 | return s |
---|
[710] | 2435 | |
---|
[1589] | 2436 | @print_log_dec |
---|
[1145] | 2437 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1846] | 2438 | """\ |
---|
[1143] | 2439 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
[1846] | 2440 | |
---|
[1143] | 2441 | Parameters: |
---|
[1846] | 2442 | |
---|
[1145] | 2443 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1855] | 2444 | |
---|
[1143] | 2445 | weight: How to average the off beams. Default is 'median'. |
---|
[1855] | 2446 | |
---|
[1145] | 2447 | preserve: you can preserve (default) the continuum or |
---|
[1855] | 2448 | remove it. The equations used are: |
---|
[1846] | 2449 | |
---|
[1855] | 2450 | preserve: Output = Toff * (on/off) - Toff |
---|
| 2451 | |
---|
| 2452 | remove: Output = Toff * (on/off) - Ton |
---|
| 2453 | |
---|
[1217] | 2454 | """ |
---|
[1593] | 2455 | mask = mask or () |
---|
[1141] | 2456 | varlist = vars() |
---|
| 2457 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 2458 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 2459 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 2460 | from asapmath import quotient |
---|
[1145] | 2461 | q = quotient(on, off, preserve) |
---|
[1143] | 2462 | q._add_history("mx_quotient", varlist) |
---|
[1819] | 2463 | print_log() |
---|
[1217] | 2464 | return q |
---|
[513] | 2465 | |
---|
[1589] | 2466 | @print_log_dec |
---|
[718] | 2467 | def freq_switch(self, insitu=None): |
---|
[1846] | 2468 | """\ |
---|
[718] | 2469 | Apply frequency switching to the data. |
---|
[1846] | 2470 | |
---|
[718] | 2471 | Parameters: |
---|
[1846] | 2472 | |
---|
[718] | 2473 | insitu: if False a new scantable is returned. |
---|
| 2474 | Otherwise, the swictching is done in-situ |
---|
| 2475 | The default is taken from .asaprc (False) |
---|
[1846] | 2476 | |
---|
[718] | 2477 | """ |
---|
| 2478 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2479 | self._math._setinsitu(insitu) |
---|
[718] | 2480 | varlist = vars() |
---|
[876] | 2481 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 2482 | s._add_history("freq_switch", varlist) |
---|
[1819] | 2483 | print_log() |
---|
[876] | 2484 | if insitu: self._assign(s) |
---|
| 2485 | else: return s |
---|
[718] | 2486 | |
---|
[1589] | 2487 | @print_log_dec |
---|
[780] | 2488 | def recalc_azel(self): |
---|
[1846] | 2489 | """Recalculate the azimuth and elevation for each position.""" |
---|
[780] | 2490 | varlist = vars() |
---|
[876] | 2491 | self._recalcazel() |
---|
[780] | 2492 | self._add_history("recalc_azel", varlist) |
---|
[1819] | 2493 | print_log() |
---|
[780] | 2494 | return |
---|
| 2495 | |
---|
[1589] | 2496 | @print_log_dec |
---|
[513] | 2497 | def __add__(self, other): |
---|
| 2498 | varlist = vars() |
---|
| 2499 | s = None |
---|
| 2500 | if isinstance(other, scantable): |
---|
[1573] | 2501 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
[513] | 2502 | elif isinstance(other, float): |
---|
[876] | 2503 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 2504 | else: |
---|
[718] | 2505 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2506 | s._add_history("operator +", varlist) |
---|
| 2507 | return s |
---|
| 2508 | |
---|
[1589] | 2509 | @print_log_dec |
---|
[513] | 2510 | def __sub__(self, other): |
---|
| 2511 | """ |
---|
| 2512 | implicit on all axes and on Tsys |
---|
| 2513 | """ |
---|
| 2514 | varlist = vars() |
---|
| 2515 | s = None |
---|
| 2516 | if isinstance(other, scantable): |
---|
[1588] | 2517 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
[513] | 2518 | elif isinstance(other, float): |
---|
[876] | 2519 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 2520 | else: |
---|
[718] | 2521 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2522 | s._add_history("operator -", varlist) |
---|
| 2523 | return s |
---|
[710] | 2524 | |
---|
[1589] | 2525 | @print_log_dec |
---|
[513] | 2526 | def __mul__(self, other): |
---|
| 2527 | """ |
---|
| 2528 | implicit on all axes and on Tsys |
---|
| 2529 | """ |
---|
| 2530 | varlist = vars() |
---|
| 2531 | s = None |
---|
| 2532 | if isinstance(other, scantable): |
---|
[1588] | 2533 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
[513] | 2534 | elif isinstance(other, float): |
---|
[876] | 2535 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 2536 | else: |
---|
[718] | 2537 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2538 | s._add_history("operator *", varlist) |
---|
| 2539 | return s |
---|
| 2540 | |
---|
[710] | 2541 | |
---|
[1589] | 2542 | @print_log_dec |
---|
[513] | 2543 | def __div__(self, other): |
---|
| 2544 | """ |
---|
| 2545 | implicit on all axes and on Tsys |
---|
| 2546 | """ |
---|
| 2547 | varlist = vars() |
---|
| 2548 | s = None |
---|
| 2549 | if isinstance(other, scantable): |
---|
[1589] | 2550 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
[513] | 2551 | elif isinstance(other, float): |
---|
| 2552 | if other == 0.0: |
---|
[718] | 2553 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 2554 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 2555 | else: |
---|
[718] | 2556 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2557 | s._add_history("operator /", varlist) |
---|
| 2558 | return s |
---|
| 2559 | |
---|
[530] | 2560 | def get_fit(self, row=0): |
---|
[1846] | 2561 | """\ |
---|
[530] | 2562 | Print or return the stored fits for a row in the scantable |
---|
[1846] | 2563 | |
---|
[530] | 2564 | Parameters: |
---|
[1846] | 2565 | |
---|
[530] | 2566 | row: the row which the fit has been applied to. |
---|
[1846] | 2567 | |
---|
[530] | 2568 | """ |
---|
| 2569 | if row > self.nrow(): |
---|
| 2570 | return |
---|
[976] | 2571 | from asap.asapfit import asapfit |
---|
[530] | 2572 | fit = asapfit(self._getfit(row)) |
---|
[718] | 2573 | if rcParams['verbose']: |
---|
[1819] | 2574 | #print fit |
---|
| 2575 | asaplog.push( '%s' %(fit) ) |
---|
| 2576 | print_log() |
---|
[530] | 2577 | return |
---|
| 2578 | else: |
---|
| 2579 | return fit.as_dict() |
---|
| 2580 | |
---|
[1483] | 2581 | def flag_nans(self): |
---|
[1846] | 2582 | """\ |
---|
[1483] | 2583 | Utility function to flag NaN values in the scantable. |
---|
| 2584 | """ |
---|
| 2585 | import numpy |
---|
| 2586 | basesel = self.get_selection() |
---|
| 2587 | for i in range(self.nrow()): |
---|
[1589] | 2588 | sel = self.get_row_selector(i) |
---|
| 2589 | self.set_selection(basesel+sel) |
---|
[1483] | 2590 | nans = numpy.isnan(self._getspectrum(0)) |
---|
| 2591 | if numpy.any(nans): |
---|
| 2592 | bnans = [ bool(v) for v in nans] |
---|
| 2593 | self.flag(bnans) |
---|
| 2594 | self.set_selection(basesel) |
---|
| 2595 | |
---|
[1588] | 2596 | def get_row_selector(self, rowno): |
---|
| 2597 | return selector(beams=self.getbeam(rowno), |
---|
| 2598 | ifs=self.getif(rowno), |
---|
| 2599 | pols=self.getpol(rowno), |
---|
| 2600 | scans=self.getscan(rowno), |
---|
| 2601 | cycles=self.getcycle(rowno)) |
---|
[1573] | 2602 | |
---|
[484] | 2603 | def _add_history(self, funcname, parameters): |
---|
[1435] | 2604 | if not rcParams['scantable.history']: |
---|
| 2605 | return |
---|
[484] | 2606 | # create date |
---|
| 2607 | sep = "##" |
---|
| 2608 | from datetime import datetime |
---|
| 2609 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 2610 | hist = dstr+sep |
---|
| 2611 | hist += funcname+sep#cdate+sep |
---|
| 2612 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 2613 | for k, v in parameters.iteritems(): |
---|
[484] | 2614 | if type(v) is dict: |
---|
[1118] | 2615 | for k2, v2 in v.iteritems(): |
---|
[484] | 2616 | hist += k2 |
---|
| 2617 | hist += "=" |
---|
[1118] | 2618 | if isinstance(v2, scantable): |
---|
[484] | 2619 | hist += 'scantable' |
---|
| 2620 | elif k2 == 'mask': |
---|
[1118] | 2621 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 2622 | hist += str(self._zip_mask(v2)) |
---|
| 2623 | else: |
---|
| 2624 | hist += str(v2) |
---|
[484] | 2625 | else: |
---|
[513] | 2626 | hist += str(v2) |
---|
[484] | 2627 | else: |
---|
| 2628 | hist += k |
---|
| 2629 | hist += "=" |
---|
[1118] | 2630 | if isinstance(v, scantable): |
---|
[484] | 2631 | hist += 'scantable' |
---|
| 2632 | elif k == 'mask': |
---|
[1118] | 2633 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 2634 | hist += str(self._zip_mask(v)) |
---|
| 2635 | else: |
---|
| 2636 | hist += str(v) |
---|
[484] | 2637 | else: |
---|
| 2638 | hist += str(v) |
---|
| 2639 | hist += sep |
---|
| 2640 | hist = hist[:-2] # remove trailing '##' |
---|
| 2641 | self._addhistory(hist) |
---|
| 2642 | |
---|
[710] | 2643 | |
---|
[484] | 2644 | def _zip_mask(self, mask): |
---|
| 2645 | mask = list(mask) |
---|
| 2646 | i = 0 |
---|
| 2647 | segments = [] |
---|
| 2648 | while mask[i:].count(1): |
---|
| 2649 | i += mask[i:].index(1) |
---|
| 2650 | if mask[i:].count(0): |
---|
| 2651 | j = i + mask[i:].index(0) |
---|
| 2652 | else: |
---|
[710] | 2653 | j = len(mask) |
---|
[1118] | 2654 | segments.append([i, j]) |
---|
[710] | 2655 | i = j |
---|
[484] | 2656 | return segments |
---|
[714] | 2657 | |
---|
[626] | 2658 | def _get_ordinate_label(self): |
---|
| 2659 | fu = "("+self.get_fluxunit()+")" |
---|
| 2660 | import re |
---|
| 2661 | lbl = "Intensity" |
---|
[1118] | 2662 | if re.match(".K.", fu): |
---|
[626] | 2663 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 2664 | elif re.match(".Jy.", fu): |
---|
[626] | 2665 | lbl = "Flux density "+ fu |
---|
| 2666 | return lbl |
---|
[710] | 2667 | |
---|
[876] | 2668 | def _check_ifs(self): |
---|
| 2669 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 2670 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 2671 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 2672 | |
---|
[1819] | 2673 | def _fill(self, names, unit, average, getpt, antenna): |
---|
[976] | 2674 | first = True |
---|
| 2675 | fullnames = [] |
---|
| 2676 | for name in names: |
---|
| 2677 | name = os.path.expandvars(name) |
---|
| 2678 | name = os.path.expanduser(name) |
---|
| 2679 | if not os.path.exists(name): |
---|
| 2680 | msg = "File '%s' does not exists" % (name) |
---|
| 2681 | if rcParams['verbose']: |
---|
| 2682 | asaplog.push(msg) |
---|
[1819] | 2683 | print_log( 'ERROR' ) |
---|
[976] | 2684 | return |
---|
| 2685 | raise IOError(msg) |
---|
| 2686 | fullnames.append(name) |
---|
| 2687 | if average: |
---|
| 2688 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 2689 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 2690 | for name in fullnames: |
---|
[1073] | 2691 | tbl = Scantable(stype) |
---|
[1843] | 2692 | r = filler(tbl) |
---|
[1504] | 2693 | rx = rcParams['scantable.reference'] |
---|
[1843] | 2694 | r.setreferenceexpr(rx) |
---|
[976] | 2695 | msg = "Importing %s..." % (name) |
---|
[1118] | 2696 | asaplog.push(msg, False) |
---|
[976] | 2697 | print_log() |
---|
[1843] | 2698 | r.open(name)# antenna, -1, -1, getpt) |
---|
| 2699 | r.fill() |
---|
[976] | 2700 | if average: |
---|
[1118] | 2701 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 2702 | if not first: |
---|
| 2703 | tbl = self._math._merge([self, tbl]) |
---|
| 2704 | Scantable.__init__(self, tbl) |
---|
[1843] | 2705 | r.close() |
---|
[1118] | 2706 | del r, tbl |
---|
[976] | 2707 | first = False |
---|
| 2708 | if unit is not None: |
---|
| 2709 | self.set_fluxunit(unit) |
---|
[1824] | 2710 | if not is_casapy(): |
---|
| 2711 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[976] | 2712 | |
---|
[1402] | 2713 | def __getitem__(self, key): |
---|
| 2714 | if key < 0: |
---|
| 2715 | key += self.nrow() |
---|
| 2716 | if key >= self.nrow(): |
---|
| 2717 | raise IndexError("Row index out of range.") |
---|
| 2718 | return self._getspectrum(key) |
---|
| 2719 | |
---|
| 2720 | def __setitem__(self, key, value): |
---|
| 2721 | if key < 0: |
---|
| 2722 | key += self.nrow() |
---|
| 2723 | if key >= self.nrow(): |
---|
| 2724 | raise IndexError("Row index out of range.") |
---|
| 2725 | if not hasattr(value, "__len__") or \ |
---|
| 2726 | len(value) > self.nchan(self.getif(key)): |
---|
| 2727 | raise ValueError("Spectrum length doesn't match.") |
---|
| 2728 | return self._setspectrum(value, key) |
---|
| 2729 | |
---|
| 2730 | def __len__(self): |
---|
| 2731 | return self.nrow() |
---|
| 2732 | |
---|
| 2733 | def __iter__(self): |
---|
| 2734 | for i in range(len(self)): |
---|
| 2735 | yield self[i] |
---|