[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 |
---|
[1862] | 13 | from asap.logging import asaplog, asaplog_post_dec |
---|
[1824] | 14 | from asap.selector import selector |
---|
| 15 | from asap.linecatalog import linecatalog |
---|
[1600] | 16 | from asap.coordinate import coordinate |
---|
[1859] | 17 | from asap.utils import _n_bools, mask_not, mask_and, mask_or, page |
---|
[1907] | 18 | from asap.asapfitter import fitter |
---|
[102] | 19 | |
---|
[1689] | 20 | |
---|
| 21 | def preserve_selection(func): |
---|
[1691] | 22 | @wraps_dec(func) |
---|
[1689] | 23 | def wrap(obj, *args, **kw): |
---|
| 24 | basesel = obj.get_selection() |
---|
[1857] | 25 | try: |
---|
| 26 | val = func(obj, *args, **kw) |
---|
| 27 | finally: |
---|
| 28 | obj.set_selection(basesel) |
---|
[1689] | 29 | return val |
---|
| 30 | return wrap |
---|
| 31 | |
---|
[1846] | 32 | def is_scantable(filename): |
---|
| 33 | """Is the given file a scantable? |
---|
[1689] | 34 | |
---|
[1846] | 35 | Parameters: |
---|
| 36 | |
---|
| 37 | filename: the name of the file/directory to test |
---|
| 38 | |
---|
| 39 | """ |
---|
[1883] | 40 | if ( os.path.isdir(filename) |
---|
| 41 | and os.path.exists(filename+'/table.info') |
---|
| 42 | and os.path.exists(filename+'/table.dat') ): |
---|
| 43 | f=open(filename+'/table.info') |
---|
| 44 | l=f.readline() |
---|
| 45 | f.close() |
---|
| 46 | #if ( l.find('Scantable') != -1 ): |
---|
| 47 | if ( l.find('Measurement Set') == -1 ): |
---|
| 48 | return True |
---|
| 49 | else: |
---|
| 50 | return False |
---|
| 51 | else: |
---|
| 52 | return False |
---|
| 53 | ## return (os.path.isdir(filename) |
---|
| 54 | ## and not os.path.exists(filename+'/table.f1') |
---|
| 55 | ## and os.path.exists(filename+'/table.info')) |
---|
[1697] | 56 | |
---|
[1883] | 57 | def is_ms(filename): |
---|
| 58 | """Is the given file a MeasurementSet? |
---|
[1697] | 59 | |
---|
[1883] | 60 | Parameters: |
---|
| 61 | |
---|
| 62 | filename: the name of the file/directory to test |
---|
| 63 | |
---|
| 64 | """ |
---|
| 65 | if ( os.path.isdir(filename) |
---|
| 66 | and os.path.exists(filename+'/table.info') |
---|
| 67 | and os.path.exists(filename+'/table.dat') ): |
---|
| 68 | f=open(filename+'/table.info') |
---|
| 69 | l=f.readline() |
---|
| 70 | f.close() |
---|
| 71 | if ( l.find('Measurement Set') != -1 ): |
---|
| 72 | return True |
---|
| 73 | else: |
---|
| 74 | return False |
---|
| 75 | else: |
---|
| 76 | return False |
---|
| 77 | |
---|
[876] | 78 | class scantable(Scantable): |
---|
[1846] | 79 | """\ |
---|
| 80 | The ASAP container for scans (single-dish data). |
---|
[102] | 81 | """ |
---|
[1819] | 82 | |
---|
[1862] | 83 | @asaplog_post_dec |
---|
[1824] | 84 | def __init__(self, filename, average=None, unit=None, getpt=None, |
---|
| 85 | antenna=None, parallactify=None): |
---|
[1846] | 86 | """\ |
---|
[102] | 87 | Create a scantable from a saved one or make a reference |
---|
[1846] | 88 | |
---|
[102] | 89 | Parameters: |
---|
[1846] | 90 | |
---|
| 91 | filename: the name of an asap table on disk |
---|
| 92 | or |
---|
| 93 | the name of a rpfits/sdfits/ms file |
---|
| 94 | (integrations within scans are auto averaged |
---|
| 95 | and the whole file is read) or |
---|
| 96 | [advanced] a reference to an existing scantable |
---|
| 97 | |
---|
| 98 | average: average all integrations withinb a scan on read. |
---|
| 99 | The default (True) is taken from .asaprc. |
---|
| 100 | |
---|
[484] | 101 | unit: brightness unit; must be consistent with K or Jy. |
---|
[1846] | 102 | Over-rides the default selected by the filler |
---|
| 103 | (input rpfits/sdfits/ms) or replaces the value |
---|
| 104 | in existing scantables |
---|
| 105 | |
---|
| 106 | getpt: for MeasurementSet input data only: |
---|
| 107 | If True, all pointing data are filled. |
---|
| 108 | The deafult is False, which makes time to load |
---|
| 109 | the MS data faster in some cases. |
---|
| 110 | |
---|
| 111 | antenna: Antenna selection. integer (id) or string (name or id). |
---|
| 112 | |
---|
| 113 | parallactify: Indicate that the data had been parallatified. Default |
---|
| 114 | is taken from rc file. |
---|
| 115 | |
---|
[710] | 116 | """ |
---|
[976] | 117 | if average is None: |
---|
[710] | 118 | average = rcParams['scantable.autoaverage'] |
---|
[1819] | 119 | if getpt is None: |
---|
| 120 | getpt = True |
---|
[1843] | 121 | if antenna is not None: |
---|
| 122 | asaplog.push("Antenna selection currently unsupported." |
---|
[1883] | 123 | "Using ''") |
---|
[1861] | 124 | asaplog.post('WARN') |
---|
[1819] | 125 | if antenna is None: |
---|
| 126 | antenna = '' |
---|
| 127 | elif type(antenna) == int: |
---|
[1843] | 128 | antenna = '%s' % antenna |
---|
[1819] | 129 | elif type(antenna) == list: |
---|
| 130 | tmpstr = '' |
---|
| 131 | for i in range( len(antenna) ): |
---|
| 132 | if type(antenna[i]) == int: |
---|
| 133 | tmpstr = tmpstr + ('%s,'%(antenna[i])) |
---|
| 134 | elif type(antenna[i]) == str: |
---|
| 135 | tmpstr=tmpstr+antenna[i]+',' |
---|
| 136 | else: |
---|
[1859] | 137 | raise TypeError('Bad antenna selection.') |
---|
[1819] | 138 | antenna = tmpstr.rstrip(',') |
---|
[1593] | 139 | parallactify = parallactify or rcParams['scantable.parallactify'] |
---|
[1259] | 140 | varlist = vars() |
---|
[876] | 141 | from asap._asap import stmath |
---|
[1819] | 142 | self._math = stmath( rcParams['insitu'] ) |
---|
[876] | 143 | if isinstance(filename, Scantable): |
---|
| 144 | Scantable.__init__(self, filename) |
---|
[181] | 145 | else: |
---|
[1697] | 146 | if isinstance(filename, str): |
---|
[976] | 147 | filename = os.path.expandvars(filename) |
---|
| 148 | filename = os.path.expanduser(filename) |
---|
| 149 | if not os.path.exists(filename): |
---|
| 150 | s = "File '%s' not found." % (filename) |
---|
| 151 | raise IOError(s) |
---|
[1697] | 152 | if is_scantable(filename): |
---|
| 153 | ondisk = rcParams['scantable.storage'] == 'disk' |
---|
| 154 | Scantable.__init__(self, filename, ondisk) |
---|
| 155 | if unit is not None: |
---|
| 156 | self.set_fluxunit(unit) |
---|
[1819] | 157 | # do not reset to the default freqframe |
---|
| 158 | #self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[1883] | 159 | #elif os.path.isdir(filename) \ |
---|
| 160 | # and not os.path.exists(filename+'/table.f1'): |
---|
| 161 | elif is_ms(filename): |
---|
| 162 | self._fill([filename], unit, average, getpt, antenna) |
---|
[1893] | 163 | elif os.path.isfile(filename): |
---|
| 164 | self._fill([filename], unit, average, getpt, antenna) |
---|
[1883] | 165 | else: |
---|
[1819] | 166 | msg = "The given file '%s'is not a valid " \ |
---|
| 167 | "asap table." % (filename) |
---|
[1859] | 168 | raise IOError(msg) |
---|
[1118] | 169 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
---|
[976] | 170 | and isinstance(filename[-1], str): |
---|
[1819] | 171 | self._fill(filename, unit, average, getpt, antenna) |
---|
[1586] | 172 | self.parallactify(parallactify) |
---|
[1259] | 173 | self._add_history("scantable", varlist) |
---|
[102] | 174 | |
---|
[1862] | 175 | @asaplog_post_dec |
---|
[876] | 176 | def save(self, name=None, format=None, overwrite=False): |
---|
[1846] | 177 | """\ |
---|
[1280] | 178 | Store the scantable on disk. This can be an asap (aips++) Table, |
---|
| 179 | SDFITS or MS2 format. |
---|
[1846] | 180 | |
---|
[116] | 181 | Parameters: |
---|
[1846] | 182 | |
---|
[1093] | 183 | name: the name of the outputfile. For format "ASCII" |
---|
| 184 | this is the root file name (data in 'name'.txt |
---|
[497] | 185 | and header in 'name'_header.txt) |
---|
[1855] | 186 | |
---|
[116] | 187 | format: an optional file format. Default is ASAP. |
---|
[1855] | 188 | Allowed are: |
---|
| 189 | |
---|
| 190 | * 'ASAP' (save as ASAP [aips++] Table), |
---|
| 191 | * 'SDFITS' (save as SDFITS file) |
---|
| 192 | * 'ASCII' (saves as ascii text file) |
---|
| 193 | * 'MS2' (saves as an casacore MeasurementSet V2) |
---|
| 194 | * 'FITS' (save as image FITS - not readable by class) |
---|
| 195 | * 'CLASS' (save as FITS readable by CLASS) |
---|
| 196 | |
---|
[411] | 197 | overwrite: If the file should be overwritten if it exists. |
---|
[256] | 198 | The default False is to return with warning |
---|
[411] | 199 | without writing the output. USE WITH CARE. |
---|
[1855] | 200 | |
---|
[1846] | 201 | Example:: |
---|
| 202 | |
---|
[116] | 203 | scan.save('myscan.asap') |
---|
[1118] | 204 | scan.save('myscan.sdfits', 'SDFITS') |
---|
[1846] | 205 | |
---|
[116] | 206 | """ |
---|
[411] | 207 | from os import path |
---|
[1593] | 208 | format = format or rcParams['scantable.save'] |
---|
[256] | 209 | suffix = '.'+format.lower() |
---|
[1118] | 210 | if name is None or name == "": |
---|
[256] | 211 | name = 'scantable'+suffix |
---|
[718] | 212 | msg = "No filename given. Using default name %s..." % name |
---|
| 213 | asaplog.push(msg) |
---|
[411] | 214 | name = path.expandvars(name) |
---|
[256] | 215 | if path.isfile(name) or path.isdir(name): |
---|
| 216 | if not overwrite: |
---|
[718] | 217 | msg = "File %s exists." % name |
---|
[1859] | 218 | raise IOError(msg) |
---|
[451] | 219 | format2 = format.upper() |
---|
| 220 | if format2 == 'ASAP': |
---|
[116] | 221 | self._save(name) |
---|
| 222 | else: |
---|
[989] | 223 | from asap._asap import stwriter as stw |
---|
[1118] | 224 | writer = stw(format2) |
---|
| 225 | writer.write(self, name) |
---|
[116] | 226 | return |
---|
| 227 | |
---|
[102] | 228 | def copy(self): |
---|
[1846] | 229 | """Return a copy of this scantable. |
---|
| 230 | |
---|
| 231 | *Note*: |
---|
| 232 | |
---|
[1348] | 233 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
---|
[1846] | 234 | |
---|
| 235 | Example:: |
---|
| 236 | |
---|
[102] | 237 | copiedscan = scan.copy() |
---|
[1846] | 238 | |
---|
[102] | 239 | """ |
---|
[876] | 240 | sd = scantable(Scantable._copy(self)) |
---|
[113] | 241 | return sd |
---|
| 242 | |
---|
[1093] | 243 | def drop_scan(self, scanid=None): |
---|
[1846] | 244 | """\ |
---|
[1093] | 245 | Return a new scantable where the specified scan number(s) has(have) |
---|
| 246 | been dropped. |
---|
[1846] | 247 | |
---|
[1093] | 248 | Parameters: |
---|
[1846] | 249 | |
---|
[1093] | 250 | scanid: a (list of) scan number(s) |
---|
[1846] | 251 | |
---|
[1093] | 252 | """ |
---|
| 253 | from asap import _is_sequence_or_number as _is_valid |
---|
| 254 | from asap import _to_list |
---|
| 255 | from asap import unique |
---|
| 256 | if not _is_valid(scanid): |
---|
[1859] | 257 | raise RuntimeError( 'Please specify a scanno to drop from the scantable' ) |
---|
| 258 | scanid = _to_list(scanid) |
---|
| 259 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
---|
| 260 | for sid in scanid: allscans.remove(sid) |
---|
| 261 | if len(allscans) == 0: |
---|
| 262 | raise ValueError("Can't remove all scans") |
---|
| 263 | sel = selector(scans=allscans) |
---|
| 264 | return self._select_copy(sel) |
---|
[1093] | 265 | |
---|
[1594] | 266 | def _select_copy(self, selection): |
---|
| 267 | orig = self.get_selection() |
---|
| 268 | self.set_selection(orig+selection) |
---|
| 269 | cp = self.copy() |
---|
| 270 | self.set_selection(orig) |
---|
| 271 | return cp |
---|
| 272 | |
---|
[102] | 273 | def get_scan(self, scanid=None): |
---|
[1855] | 274 | """\ |
---|
[102] | 275 | Return a specific scan (by scanno) or collection of scans (by |
---|
| 276 | source name) in a new scantable. |
---|
[1846] | 277 | |
---|
| 278 | *Note*: |
---|
| 279 | |
---|
[1348] | 280 | See scantable.drop_scan() for the inverse operation. |
---|
[1846] | 281 | |
---|
[102] | 282 | Parameters: |
---|
[1846] | 283 | |
---|
[513] | 284 | scanid: a (list of) scanno or a source name, unix-style |
---|
| 285 | patterns are accepted for source name matching, e.g. |
---|
| 286 | '*_R' gets all 'ref scans |
---|
[1846] | 287 | |
---|
| 288 | Example:: |
---|
| 289 | |
---|
[513] | 290 | # get all scans containing the source '323p459' |
---|
| 291 | newscan = scan.get_scan('323p459') |
---|
| 292 | # get all 'off' scans |
---|
| 293 | refscans = scan.get_scan('*_R') |
---|
| 294 | # get a susbset of scans by scanno (as listed in scan.summary()) |
---|
[1118] | 295 | newscan = scan.get_scan([0, 2, 7, 10]) |
---|
[1846] | 296 | |
---|
[102] | 297 | """ |
---|
| 298 | if scanid is None: |
---|
[1859] | 299 | raise RuntimeError( 'Please specify a scan no or name to ' |
---|
| 300 | 'retrieve from the scantable' ) |
---|
[102] | 301 | try: |
---|
[946] | 302 | bsel = self.get_selection() |
---|
| 303 | sel = selector() |
---|
[102] | 304 | if type(scanid) is str: |
---|
[946] | 305 | sel.set_name(scanid) |
---|
[1594] | 306 | return self._select_copy(sel) |
---|
[102] | 307 | elif type(scanid) is int: |
---|
[946] | 308 | sel.set_scans([scanid]) |
---|
[1594] | 309 | return self._select_copy(sel) |
---|
[381] | 310 | elif type(scanid) is list: |
---|
[946] | 311 | sel.set_scans(scanid) |
---|
[1594] | 312 | return self._select_copy(sel) |
---|
[381] | 313 | else: |
---|
[718] | 314 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
---|
[1859] | 315 | raise TypeError(msg) |
---|
[102] | 316 | except RuntimeError: |
---|
[1859] | 317 | raise |
---|
[102] | 318 | |
---|
| 319 | def __str__(self): |
---|
[1118] | 320 | return Scantable._summary(self, True) |
---|
[102] | 321 | |
---|
[976] | 322 | def summary(self, filename=None): |
---|
[1846] | 323 | """\ |
---|
[102] | 324 | Print a summary of the contents of this scantable. |
---|
[1846] | 325 | |
---|
[102] | 326 | Parameters: |
---|
[1846] | 327 | |
---|
[102] | 328 | filename: the name of a file to write the putput to |
---|
| 329 | Default - no file output |
---|
[1846] | 330 | |
---|
[102] | 331 | """ |
---|
[976] | 332 | info = Scantable._summary(self, True) |
---|
[102] | 333 | if filename is not None: |
---|
[256] | 334 | if filename is "": |
---|
| 335 | filename = 'scantable_summary.txt' |
---|
[415] | 336 | from os.path import expandvars, isdir |
---|
[411] | 337 | filename = expandvars(filename) |
---|
[415] | 338 | if not isdir(filename): |
---|
[413] | 339 | data = open(filename, 'w') |
---|
| 340 | data.write(info) |
---|
| 341 | data.close() |
---|
| 342 | else: |
---|
[718] | 343 | msg = "Illegal file name '%s'." % (filename) |
---|
[1859] | 344 | raise IOError(msg) |
---|
| 345 | return page(info) |
---|
[710] | 346 | |
---|
[1512] | 347 | def get_spectrum(self, rowno): |
---|
[1471] | 348 | """Return the spectrum for the current row in the scantable as a list. |
---|
[1846] | 349 | |
---|
[1471] | 350 | Parameters: |
---|
[1846] | 351 | |
---|
[1573] | 352 | rowno: the row number to retrieve the spectrum from |
---|
[1846] | 353 | |
---|
[1471] | 354 | """ |
---|
| 355 | return self._getspectrum(rowno) |
---|
[946] | 356 | |
---|
[1471] | 357 | def get_mask(self, rowno): |
---|
| 358 | """Return the mask for the current row in the scantable as a list. |
---|
[1846] | 359 | |
---|
[1471] | 360 | Parameters: |
---|
[1846] | 361 | |
---|
[1573] | 362 | rowno: the row number to retrieve the mask from |
---|
[1846] | 363 | |
---|
[1471] | 364 | """ |
---|
| 365 | return self._getmask(rowno) |
---|
| 366 | |
---|
| 367 | def set_spectrum(self, spec, rowno): |
---|
| 368 | """Return the spectrum for the current row in the scantable as a list. |
---|
[1846] | 369 | |
---|
[1471] | 370 | Parameters: |
---|
[1846] | 371 | |
---|
[1855] | 372 | spec: the new spectrum |
---|
[1846] | 373 | |
---|
[1855] | 374 | rowno: the row number to set the spectrum for |
---|
| 375 | |
---|
[1471] | 376 | """ |
---|
| 377 | assert(len(spec) == self.nchan()) |
---|
| 378 | return self._setspectrum(spec, rowno) |
---|
| 379 | |
---|
[1600] | 380 | def get_coordinate(self, rowno): |
---|
| 381 | """Return the (spectral) coordinate for a a given 'rowno'. |
---|
[1846] | 382 | |
---|
| 383 | *Note*: |
---|
| 384 | |
---|
[1600] | 385 | * This coordinate is only valid until a scantable method modifies |
---|
| 386 | the frequency axis. |
---|
| 387 | * This coordinate does contain the original frequency set-up |
---|
| 388 | NOT the new frame. The conversions however are done using the user |
---|
| 389 | specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate, |
---|
| 390 | use scantable.freq_align first. Without it there is no closure, |
---|
[1846] | 391 | i.e.:: |
---|
[1600] | 392 | |
---|
[1846] | 393 | c = myscan.get_coordinate(0) |
---|
| 394 | c.to_frequency(c.get_reference_pixel()) != c.get_reference_value() |
---|
| 395 | |
---|
[1600] | 396 | Parameters: |
---|
[1846] | 397 | |
---|
[1600] | 398 | rowno: the row number for the spectral coordinate |
---|
| 399 | |
---|
| 400 | """ |
---|
| 401 | return coordinate(Scantable.get_coordinate(self, rowno)) |
---|
| 402 | |
---|
[946] | 403 | def get_selection(self): |
---|
[1846] | 404 | """\ |
---|
[1005] | 405 | Get the selection object currently set on this scantable. |
---|
[1846] | 406 | |
---|
| 407 | Example:: |
---|
| 408 | |
---|
[1005] | 409 | sel = scan.get_selection() |
---|
| 410 | sel.set_ifs(0) # select IF 0 |
---|
| 411 | scan.set_selection(sel) # apply modified selection |
---|
[1846] | 412 | |
---|
[946] | 413 | """ |
---|
| 414 | return selector(self._getselection()) |
---|
| 415 | |
---|
[1576] | 416 | def set_selection(self, selection=None, **kw): |
---|
[1846] | 417 | """\ |
---|
[1005] | 418 | Select a subset of the data. All following operations on this scantable |
---|
| 419 | are only applied to thi selection. |
---|
[1846] | 420 | |
---|
[1005] | 421 | Parameters: |
---|
[1697] | 422 | |
---|
[1846] | 423 | selection: a selector object (default unset the selection), or |
---|
| 424 | any combination of "pols", "ifs", "beams", "scans", |
---|
| 425 | "cycles", "name", "query" |
---|
[1697] | 426 | |
---|
[1846] | 427 | Examples:: |
---|
[1697] | 428 | |
---|
[1005] | 429 | sel = selector() # create a selection object |
---|
[1118] | 430 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
---|
[1005] | 431 | scan.set_selection(sel) # set the selection |
---|
| 432 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 433 | scan.set_selection() # unset the selection |
---|
[1697] | 434 | # or the equivalent |
---|
| 435 | scan.set_selection(scans=[0,3]) |
---|
| 436 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 437 | scan.set_selection() # unset the selection |
---|
[1846] | 438 | |
---|
[946] | 439 | """ |
---|
[1576] | 440 | if selection is None: |
---|
| 441 | # reset |
---|
| 442 | if len(kw) == 0: |
---|
| 443 | selection = selector() |
---|
| 444 | else: |
---|
| 445 | # try keywords |
---|
| 446 | for k in kw: |
---|
| 447 | if k not in selector.fields: |
---|
| 448 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields)) |
---|
| 449 | selection = selector(**kw) |
---|
[946] | 450 | self._setselection(selection) |
---|
| 451 | |
---|
[1819] | 452 | def get_row(self, row=0, insitu=None): |
---|
[1846] | 453 | """\ |
---|
[1819] | 454 | Select a row in the scantable. |
---|
| 455 | Return a scantable with single row. |
---|
[1846] | 456 | |
---|
[1819] | 457 | Parameters: |
---|
[1846] | 458 | |
---|
| 459 | row: row no of integration, default is 0. |
---|
| 460 | insitu: if False a new scantable is returned. Otherwise, the |
---|
| 461 | scaling is done in-situ. The default is taken from .asaprc |
---|
| 462 | (False) |
---|
| 463 | |
---|
[1819] | 464 | """ |
---|
| 465 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 466 | if not insitu: |
---|
| 467 | workscan = self.copy() |
---|
| 468 | else: |
---|
| 469 | workscan = self |
---|
| 470 | # Select a row |
---|
| 471 | sel=selector() |
---|
| 472 | sel.set_scans([workscan.getscan(row)]) |
---|
| 473 | sel.set_cycles([workscan.getcycle(row)]) |
---|
| 474 | sel.set_beams([workscan.getbeam(row)]) |
---|
| 475 | sel.set_ifs([workscan.getif(row)]) |
---|
| 476 | sel.set_polarisations([workscan.getpol(row)]) |
---|
| 477 | sel.set_name(workscan._getsourcename(row)) |
---|
| 478 | workscan.set_selection(sel) |
---|
| 479 | if not workscan.nrow() == 1: |
---|
| 480 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow()) |
---|
| 481 | raise RuntimeError(msg) |
---|
| 482 | del sel |
---|
| 483 | if insitu: |
---|
| 484 | self._assign(workscan) |
---|
| 485 | else: |
---|
| 486 | return workscan |
---|
| 487 | |
---|
[1862] | 488 | @asaplog_post_dec |
---|
[1907] | 489 | def stats(self, stat='stddev', mask=None, form='3.3f', row=None): |
---|
[1846] | 490 | """\ |
---|
[135] | 491 | Determine the specified statistic of the current beam/if/pol |
---|
[102] | 492 | Takes a 'mask' as an optional parameter to specify which |
---|
| 493 | channels should be excluded. |
---|
[1846] | 494 | |
---|
[102] | 495 | Parameters: |
---|
[1846] | 496 | |
---|
[1819] | 497 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum', |
---|
| 498 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
[1855] | 499 | |
---|
[135] | 500 | mask: an optional mask specifying where the statistic |
---|
[102] | 501 | should be determined. |
---|
[1855] | 502 | |
---|
[1819] | 503 | form: format string to print statistic values |
---|
[1846] | 504 | |
---|
[1907] | 505 | row: row number of spectrum to process. |
---|
| 506 | (default is None: for all rows) |
---|
[1846] | 507 | |
---|
[1907] | 508 | Example: |
---|
[113] | 509 | scan.set_unit('channel') |
---|
[1118] | 510 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 511 | scan.stats(stat='mean', mask=m) |
---|
[1846] | 512 | |
---|
[102] | 513 | """ |
---|
[1593] | 514 | mask = mask or [] |
---|
[876] | 515 | if not self._check_ifs(): |
---|
[1118] | 516 | raise ValueError("Cannot apply mask as the IFs have different " |
---|
| 517 | "number of channels. Please use setselection() " |
---|
| 518 | "to select individual IFs") |
---|
[1819] | 519 | rtnabc = False |
---|
| 520 | if stat.lower().endswith('_abc'): rtnabc = True |
---|
| 521 | getchan = False |
---|
| 522 | if stat.lower().startswith('min') or stat.lower().startswith('max'): |
---|
| 523 | chan = self._math._minmaxchan(self, mask, stat) |
---|
| 524 | getchan = True |
---|
| 525 | statvals = [] |
---|
[1907] | 526 | if not rtnabc: |
---|
| 527 | if row == None: |
---|
| 528 | statvals = self._math._stats(self, mask, stat) |
---|
| 529 | else: |
---|
| 530 | statvals = self._math._statsrow(self, mask, stat, int(row)) |
---|
[256] | 531 | |
---|
[1819] | 532 | #def cb(i): |
---|
| 533 | # return statvals[i] |
---|
[256] | 534 | |
---|
[1819] | 535 | #return self._row_callback(cb, stat) |
---|
[102] | 536 | |
---|
[1819] | 537 | label=stat |
---|
| 538 | #callback=cb |
---|
| 539 | out = "" |
---|
| 540 | #outvec = [] |
---|
| 541 | sep = '-'*50 |
---|
[1907] | 542 | |
---|
| 543 | if row == None: |
---|
| 544 | rows = xrange(self.nrow()) |
---|
| 545 | elif isinstance(row, int): |
---|
| 546 | rows = [ row ] |
---|
| 547 | |
---|
| 548 | for i in rows: |
---|
[1819] | 549 | refstr = '' |
---|
| 550 | statunit= '' |
---|
| 551 | if getchan: |
---|
| 552 | qx, qy = self.chan2data(rowno=i, chan=chan[i]) |
---|
| 553 | if rtnabc: |
---|
| 554 | statvals.append(qx['value']) |
---|
| 555 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])' |
---|
| 556 | statunit= '['+qx['unit']+']' |
---|
| 557 | else: |
---|
| 558 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])' |
---|
| 559 | |
---|
| 560 | tm = self._gettime(i) |
---|
| 561 | src = self._getsourcename(i) |
---|
| 562 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
| 563 | out += 'Time[%s]:\n' % (tm) |
---|
[1907] | 564 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 565 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 566 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
[1819] | 567 | #outvec.append(callback(i)) |
---|
[1907] | 568 | if len(rows) > 1: |
---|
| 569 | # out += ('= %'+form) % (outvec[i]) +' '+refstr+'\n' |
---|
| 570 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n' |
---|
| 571 | else: |
---|
| 572 | # out += ('= %'+form) % (outvec[0]) +' '+refstr+'\n' |
---|
| 573 | out += ('= %'+form) % (statvals[0]) +' '+refstr+'\n' |
---|
[1819] | 574 | out += sep+"\n" |
---|
| 575 | |
---|
[1859] | 576 | import os |
---|
| 577 | if os.environ.has_key( 'USER' ): |
---|
| 578 | usr = os.environ['USER'] |
---|
| 579 | else: |
---|
| 580 | import commands |
---|
| 581 | usr = commands.getoutput( 'whoami' ) |
---|
| 582 | tmpfile = '/tmp/tmp_'+usr+'_casapy_asap_scantable_stats' |
---|
| 583 | f = open(tmpfile,'w') |
---|
| 584 | print >> f, sep |
---|
| 585 | print >> f, ' %s %s' % (label, statunit) |
---|
| 586 | print >> f, sep |
---|
| 587 | print >> f, out |
---|
| 588 | f.close() |
---|
| 589 | f = open(tmpfile,'r') |
---|
| 590 | x = f.readlines() |
---|
| 591 | f.close() |
---|
| 592 | asaplog.push(''.join(x), False) |
---|
| 593 | |
---|
[1819] | 594 | return statvals |
---|
| 595 | |
---|
| 596 | def chan2data(self, rowno=0, chan=0): |
---|
[1846] | 597 | """\ |
---|
[1819] | 598 | Returns channel/frequency/velocity and spectral value |
---|
| 599 | at an arbitrary row and channel in the scantable. |
---|
[1846] | 600 | |
---|
[1819] | 601 | Parameters: |
---|
[1846] | 602 | |
---|
[1819] | 603 | rowno: a row number in the scantable. Default is the |
---|
| 604 | first row, i.e. rowno=0 |
---|
[1855] | 605 | |
---|
[1819] | 606 | chan: a channel in the scantable. Default is the first |
---|
| 607 | channel, i.e. pos=0 |
---|
[1846] | 608 | |
---|
[1819] | 609 | """ |
---|
| 610 | if isinstance(rowno, int) and isinstance(chan, int): |
---|
| 611 | qx = {'unit': self.get_unit(), |
---|
| 612 | 'value': self._getabcissa(rowno)[chan]} |
---|
| 613 | qy = {'unit': self.get_fluxunit(), |
---|
| 614 | 'value': self._getspectrum(rowno)[chan]} |
---|
| 615 | return qx, qy |
---|
| 616 | |
---|
[1118] | 617 | def stddev(self, mask=None): |
---|
[1846] | 618 | """\ |
---|
[135] | 619 | Determine the standard deviation of the current beam/if/pol |
---|
| 620 | Takes a 'mask' as an optional parameter to specify which |
---|
| 621 | channels should be excluded. |
---|
[1846] | 622 | |
---|
[135] | 623 | Parameters: |
---|
[1846] | 624 | |
---|
[135] | 625 | mask: an optional mask specifying where the standard |
---|
| 626 | deviation should be determined. |
---|
| 627 | |
---|
[1846] | 628 | Example:: |
---|
| 629 | |
---|
[135] | 630 | scan.set_unit('channel') |
---|
[1118] | 631 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 632 | scan.stddev(mask=m) |
---|
[1846] | 633 | |
---|
[135] | 634 | """ |
---|
[1118] | 635 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 636 | |
---|
[1003] | 637 | |
---|
[1259] | 638 | def get_column_names(self): |
---|
[1846] | 639 | """\ |
---|
[1003] | 640 | Return a list of column names, which can be used for selection. |
---|
| 641 | """ |
---|
[1259] | 642 | return list(Scantable.get_column_names(self)) |
---|
[1003] | 643 | |
---|
[1730] | 644 | def get_tsys(self, row=-1): |
---|
[1846] | 645 | """\ |
---|
[113] | 646 | Return the System temperatures. |
---|
[1846] | 647 | |
---|
| 648 | Parameters: |
---|
| 649 | |
---|
| 650 | row: the rowno to get the information for. (default all rows) |
---|
| 651 | |
---|
[113] | 652 | Returns: |
---|
[1846] | 653 | |
---|
[876] | 654 | a list of Tsys values for the current selection |
---|
[1846] | 655 | |
---|
[113] | 656 | """ |
---|
[1730] | 657 | if row > -1: |
---|
| 658 | return self._get_column(self._gettsys, row) |
---|
[876] | 659 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 660 | |
---|
[1730] | 661 | |
---|
| 662 | def get_weather(self, row=-1): |
---|
[1846] | 663 | """\ |
---|
| 664 | Return the weather informations. |
---|
| 665 | |
---|
| 666 | Parameters: |
---|
| 667 | |
---|
| 668 | row: the rowno to get the information for. (default all rows) |
---|
| 669 | |
---|
| 670 | Returns: |
---|
| 671 | |
---|
| 672 | a dict or list of of dicts of values for the current selection |
---|
| 673 | |
---|
| 674 | """ |
---|
| 675 | |
---|
[1730] | 676 | values = self._get_column(self._get_weather, row) |
---|
| 677 | if row > -1: |
---|
| 678 | return {'temperature': values[0], |
---|
| 679 | 'pressure': values[1], 'humidity' : values[2], |
---|
| 680 | 'windspeed' : values[3], 'windaz' : values[4] |
---|
| 681 | } |
---|
| 682 | else: |
---|
| 683 | out = [] |
---|
| 684 | for r in values: |
---|
| 685 | |
---|
| 686 | out.append({'temperature': r[0], |
---|
| 687 | 'pressure': r[1], 'humidity' : r[2], |
---|
| 688 | 'windspeed' : r[3], 'windaz' : r[4] |
---|
| 689 | }) |
---|
| 690 | return out |
---|
| 691 | |
---|
[876] | 692 | def _row_callback(self, callback, label): |
---|
| 693 | out = "" |
---|
[1118] | 694 | outvec = [] |
---|
[1590] | 695 | sep = '-'*50 |
---|
[876] | 696 | for i in range(self.nrow()): |
---|
| 697 | tm = self._gettime(i) |
---|
| 698 | src = self._getsourcename(i) |
---|
[1590] | 699 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
[876] | 700 | out += 'Time[%s]:\n' % (tm) |
---|
[1590] | 701 | if self.nbeam(-1) > 1: |
---|
| 702 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 703 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 704 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
[876] | 705 | outvec.append(callback(i)) |
---|
| 706 | out += '= %3.3f\n' % (outvec[i]) |
---|
[1590] | 707 | out += sep+'\n' |
---|
[1859] | 708 | |
---|
| 709 | asaplog.push(sep) |
---|
| 710 | asaplog.push(" %s" % (label)) |
---|
| 711 | asaplog.push(sep) |
---|
| 712 | asaplog.push(out) |
---|
[1861] | 713 | asaplog.post() |
---|
[1175] | 714 | return outvec |
---|
[256] | 715 | |
---|
[1070] | 716 | def _get_column(self, callback, row=-1): |
---|
| 717 | """ |
---|
| 718 | """ |
---|
| 719 | if row == -1: |
---|
| 720 | return [callback(i) for i in range(self.nrow())] |
---|
| 721 | else: |
---|
[1819] | 722 | if 0 <= row < self.nrow(): |
---|
[1070] | 723 | return callback(row) |
---|
[256] | 724 | |
---|
[1070] | 725 | |
---|
[1348] | 726 | def get_time(self, row=-1, asdatetime=False): |
---|
[1846] | 727 | """\ |
---|
[113] | 728 | Get a list of time stamps for the observations. |
---|
[1348] | 729 | Return a datetime object for each integration time stamp in the scantable. |
---|
[1846] | 730 | |
---|
[113] | 731 | Parameters: |
---|
[1846] | 732 | |
---|
[1348] | 733 | row: row no of integration. Default -1 return all rows |
---|
[1855] | 734 | |
---|
[1348] | 735 | asdatetime: return values as datetime objects rather than strings |
---|
[1846] | 736 | |
---|
[113] | 737 | """ |
---|
[1175] | 738 | from time import strptime |
---|
| 739 | from datetime import datetime |
---|
[1392] | 740 | times = self._get_column(self._gettime, row) |
---|
[1348] | 741 | if not asdatetime: |
---|
[1392] | 742 | return times |
---|
[1175] | 743 | format = "%Y/%m/%d/%H:%M:%S" |
---|
| 744 | if isinstance(times, list): |
---|
| 745 | return [datetime(*strptime(i, format)[:6]) for i in times] |
---|
| 746 | else: |
---|
| 747 | return datetime(*strptime(times, format)[:6]) |
---|
[102] | 748 | |
---|
[1348] | 749 | |
---|
| 750 | def get_inttime(self, row=-1): |
---|
[1846] | 751 | """\ |
---|
[1348] | 752 | Get a list of integration times for the observations. |
---|
| 753 | Return a time in seconds for each integration in the scantable. |
---|
[1846] | 754 | |
---|
[1348] | 755 | Parameters: |
---|
[1846] | 756 | |
---|
[1348] | 757 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 758 | |
---|
[1348] | 759 | """ |
---|
[1573] | 760 | return self._get_column(self._getinttime, row) |
---|
[1348] | 761 | |
---|
[1573] | 762 | |
---|
[714] | 763 | def get_sourcename(self, row=-1): |
---|
[1846] | 764 | """\ |
---|
[794] | 765 | Get a list source names for the observations. |
---|
[714] | 766 | Return a string for each integration in the scantable. |
---|
| 767 | Parameters: |
---|
[1846] | 768 | |
---|
[1348] | 769 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 770 | |
---|
[714] | 771 | """ |
---|
[1070] | 772 | return self._get_column(self._getsourcename, row) |
---|
[714] | 773 | |
---|
[794] | 774 | def get_elevation(self, row=-1): |
---|
[1846] | 775 | """\ |
---|
[794] | 776 | Get a list of elevations for the observations. |
---|
| 777 | Return a float for each integration in the scantable. |
---|
[1846] | 778 | |
---|
[794] | 779 | Parameters: |
---|
[1846] | 780 | |
---|
[1348] | 781 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 782 | |
---|
[794] | 783 | """ |
---|
[1070] | 784 | return self._get_column(self._getelevation, row) |
---|
[794] | 785 | |
---|
| 786 | def get_azimuth(self, row=-1): |
---|
[1846] | 787 | """\ |
---|
[794] | 788 | Get a list of azimuths for the observations. |
---|
| 789 | Return a float for each integration in the scantable. |
---|
[1846] | 790 | |
---|
[794] | 791 | Parameters: |
---|
[1348] | 792 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 793 | |
---|
[794] | 794 | """ |
---|
[1070] | 795 | return self._get_column(self._getazimuth, row) |
---|
[794] | 796 | |
---|
| 797 | def get_parangle(self, row=-1): |
---|
[1846] | 798 | """\ |
---|
[794] | 799 | Get a list of parallactic angles for the observations. |
---|
| 800 | Return a float for each integration in the scantable. |
---|
[1846] | 801 | |
---|
[794] | 802 | Parameters: |
---|
[1846] | 803 | |
---|
[1348] | 804 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 805 | |
---|
[794] | 806 | """ |
---|
[1070] | 807 | return self._get_column(self._getparangle, row) |
---|
[794] | 808 | |
---|
[1070] | 809 | def get_direction(self, row=-1): |
---|
| 810 | """ |
---|
| 811 | Get a list of Positions on the sky (direction) for the observations. |
---|
[1594] | 812 | Return a string for each integration in the scantable. |
---|
[1855] | 813 | |
---|
[1070] | 814 | Parameters: |
---|
[1855] | 815 | |
---|
[1070] | 816 | row: row no of integration. Default -1 return all rows |
---|
[1855] | 817 | |
---|
[1070] | 818 | """ |
---|
| 819 | return self._get_column(self._getdirection, row) |
---|
| 820 | |
---|
[1391] | 821 | def get_directionval(self, row=-1): |
---|
[1846] | 822 | """\ |
---|
[1391] | 823 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 824 | Return a float for each integration in the scantable. |
---|
[1846] | 825 | |
---|
[1391] | 826 | Parameters: |
---|
[1846] | 827 | |
---|
[1391] | 828 | row: row no of integration. Default -1 return all rows |
---|
[1846] | 829 | |
---|
[1391] | 830 | """ |
---|
| 831 | return self._get_column(self._getdirectionvec, row) |
---|
| 832 | |
---|
[1862] | 833 | @asaplog_post_dec |
---|
[102] | 834 | def set_unit(self, unit='channel'): |
---|
[1846] | 835 | """\ |
---|
[102] | 836 | Set the unit for all following operations on this scantable |
---|
[1846] | 837 | |
---|
[102] | 838 | Parameters: |
---|
[1846] | 839 | |
---|
| 840 | unit: optional unit, default is 'channel'. Use one of '*Hz', |
---|
| 841 | 'km/s', 'channel' or equivalent '' |
---|
| 842 | |
---|
[102] | 843 | """ |
---|
[484] | 844 | varlist = vars() |
---|
[1118] | 845 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 846 | unit = '' |
---|
| 847 | inf = list(self._getcoordinfo()) |
---|
| 848 | inf[0] = unit |
---|
| 849 | self._setcoordinfo(inf) |
---|
[1118] | 850 | self._add_history("set_unit", varlist) |
---|
[113] | 851 | |
---|
[1862] | 852 | @asaplog_post_dec |
---|
[484] | 853 | def set_instrument(self, instr): |
---|
[1846] | 854 | """\ |
---|
[1348] | 855 | Set the instrument for subsequent processing. |
---|
[1846] | 856 | |
---|
[358] | 857 | Parameters: |
---|
[1846] | 858 | |
---|
[710] | 859 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 860 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[1846] | 861 | |
---|
[358] | 862 | """ |
---|
| 863 | self._setInstrument(instr) |
---|
[1118] | 864 | self._add_history("set_instument", vars()) |
---|
[358] | 865 | |
---|
[1862] | 866 | @asaplog_post_dec |
---|
[1190] | 867 | def set_feedtype(self, feedtype): |
---|
[1846] | 868 | """\ |
---|
[1190] | 869 | Overwrite the feed type, which might not be set correctly. |
---|
[1846] | 870 | |
---|
[1190] | 871 | Parameters: |
---|
[1846] | 872 | |
---|
[1190] | 873 | feedtype: 'linear' or 'circular' |
---|
[1846] | 874 | |
---|
[1190] | 875 | """ |
---|
| 876 | self._setfeedtype(feedtype) |
---|
| 877 | self._add_history("set_feedtype", vars()) |
---|
| 878 | |
---|
[1862] | 879 | @asaplog_post_dec |
---|
[276] | 880 | def set_doppler(self, doppler='RADIO'): |
---|
[1846] | 881 | """\ |
---|
[276] | 882 | Set the doppler for all following operations on this scantable. |
---|
[1846] | 883 | |
---|
[276] | 884 | Parameters: |
---|
[1846] | 885 | |
---|
[276] | 886 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
[1846] | 887 | |
---|
[276] | 888 | """ |
---|
[484] | 889 | varlist = vars() |
---|
[276] | 890 | inf = list(self._getcoordinfo()) |
---|
| 891 | inf[2] = doppler |
---|
| 892 | self._setcoordinfo(inf) |
---|
[1118] | 893 | self._add_history("set_doppler", vars()) |
---|
[710] | 894 | |
---|
[1862] | 895 | @asaplog_post_dec |
---|
[226] | 896 | def set_freqframe(self, frame=None): |
---|
[1846] | 897 | """\ |
---|
[113] | 898 | Set the frame type of the Spectral Axis. |
---|
[1846] | 899 | |
---|
[113] | 900 | Parameters: |
---|
[1846] | 901 | |
---|
[591] | 902 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1819] | 903 | 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
[1118] | 904 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[1846] | 905 | |
---|
| 906 | Example:: |
---|
| 907 | |
---|
[113] | 908 | scan.set_freqframe('BARY') |
---|
[1846] | 909 | |
---|
[113] | 910 | """ |
---|
[1593] | 911 | frame = frame or rcParams['scantable.freqframe'] |
---|
[484] | 912 | varlist = vars() |
---|
[1819] | 913 | # "REST" is not implemented in casacore |
---|
| 914 | #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 915 | # 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
| 916 | valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
[1118] | 917 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 918 | |
---|
[989] | 919 | if frame in valid: |
---|
[113] | 920 | inf = list(self._getcoordinfo()) |
---|
| 921 | inf[1] = frame |
---|
| 922 | self._setcoordinfo(inf) |
---|
[1118] | 923 | self._add_history("set_freqframe", varlist) |
---|
[102] | 924 | else: |
---|
[1118] | 925 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[1859] | 926 | raise TypeError(msg) |
---|
[710] | 927 | |
---|
[1862] | 928 | @asaplog_post_dec |
---|
[989] | 929 | def set_dirframe(self, frame=""): |
---|
[1846] | 930 | """\ |
---|
[989] | 931 | Set the frame type of the Direction on the sky. |
---|
[1846] | 932 | |
---|
[989] | 933 | Parameters: |
---|
[1846] | 934 | |
---|
[989] | 935 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 936 | 'J2000', 'B1950', 'GALACTIC' |
---|
[1846] | 937 | |
---|
| 938 | Example: |
---|
| 939 | |
---|
[989] | 940 | scan.set_dirframe('GALACTIC') |
---|
[1846] | 941 | |
---|
[989] | 942 | """ |
---|
| 943 | varlist = vars() |
---|
[1859] | 944 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 945 | self._add_history("set_dirframe", varlist) |
---|
[989] | 946 | |
---|
[113] | 947 | def get_unit(self): |
---|
[1846] | 948 | """\ |
---|
[113] | 949 | Get the default unit set in this scantable |
---|
[1846] | 950 | |
---|
[113] | 951 | Returns: |
---|
[1846] | 952 | |
---|
[113] | 953 | A unit string |
---|
[1846] | 954 | |
---|
[113] | 955 | """ |
---|
| 956 | inf = self._getcoordinfo() |
---|
| 957 | unit = inf[0] |
---|
| 958 | if unit == '': unit = 'channel' |
---|
| 959 | return unit |
---|
[102] | 960 | |
---|
[1862] | 961 | @asaplog_post_dec |
---|
[158] | 962 | def get_abcissa(self, rowno=0): |
---|
[1846] | 963 | """\ |
---|
[158] | 964 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 965 | selected Beam/IF/Pol |
---|
[1846] | 966 | |
---|
[113] | 967 | Parameters: |
---|
[1846] | 968 | |
---|
[226] | 969 | rowno: an optional row number in the scantable. Default is the |
---|
| 970 | first row, i.e. rowno=0 |
---|
[1846] | 971 | |
---|
[113] | 972 | Returns: |
---|
[1846] | 973 | |
---|
[1348] | 974 | The abcissa values and the format string (as a dictionary) |
---|
[1846] | 975 | |
---|
[113] | 976 | """ |
---|
[256] | 977 | abc = self._getabcissa(rowno) |
---|
[710] | 978 | lbl = self._getabcissalabel(rowno) |
---|
[158] | 979 | return abc, lbl |
---|
[113] | 980 | |
---|
[1862] | 981 | @asaplog_post_dec |
---|
[1819] | 982 | def flag(self, mask=None, unflag=False): |
---|
[1846] | 983 | """\ |
---|
[1001] | 984 | Flag the selected data using an optional channel mask. |
---|
[1846] | 985 | |
---|
[1001] | 986 | Parameters: |
---|
[1846] | 987 | |
---|
[1001] | 988 | mask: an optional channel mask, created with create_mask. Default |
---|
| 989 | (no mask) is all channels. |
---|
[1855] | 990 | |
---|
[1819] | 991 | unflag: if True, unflag the data |
---|
[1846] | 992 | |
---|
[1001] | 993 | """ |
---|
| 994 | varlist = vars() |
---|
[1593] | 995 | mask = mask or [] |
---|
[1859] | 996 | self._flag(mask, unflag) |
---|
[1001] | 997 | self._add_history("flag", varlist) |
---|
| 998 | |
---|
[1862] | 999 | @asaplog_post_dec |
---|
[1819] | 1000 | def flag_row(self, rows=[], unflag=False): |
---|
[1846] | 1001 | """\ |
---|
[1819] | 1002 | Flag the selected data in row-based manner. |
---|
[1846] | 1003 | |
---|
[1819] | 1004 | Parameters: |
---|
[1846] | 1005 | |
---|
[1843] | 1006 | rows: list of row numbers to be flagged. Default is no row |
---|
| 1007 | (must be explicitly specified to execute row-based flagging). |
---|
[1855] | 1008 | |
---|
[1819] | 1009 | unflag: if True, unflag the data. |
---|
[1846] | 1010 | |
---|
[1819] | 1011 | """ |
---|
| 1012 | varlist = vars() |
---|
[1859] | 1013 | self._flag_row(rows, unflag) |
---|
[1819] | 1014 | self._add_history("flag_row", varlist) |
---|
| 1015 | |
---|
[1862] | 1016 | @asaplog_post_dec |
---|
[1819] | 1017 | def clip(self, uthres=None, dthres=None, clipoutside=True, unflag=False): |
---|
[1846] | 1018 | """\ |
---|
[1819] | 1019 | Flag the selected data outside a specified range (in channel-base) |
---|
[1846] | 1020 | |
---|
[1819] | 1021 | Parameters: |
---|
[1846] | 1022 | |
---|
[1819] | 1023 | uthres: upper threshold. |
---|
[1855] | 1024 | |
---|
[1819] | 1025 | dthres: lower threshold |
---|
[1846] | 1026 | |
---|
[1819] | 1027 | clipoutside: True for flagging data outside the range [dthres:uthres]. |
---|
| 1028 | False for glagging data inside the range. |
---|
[1855] | 1029 | |
---|
[1846] | 1030 | unflag: if True, unflag the data. |
---|
| 1031 | |
---|
[1819] | 1032 | """ |
---|
| 1033 | varlist = vars() |
---|
[1859] | 1034 | self._clip(uthres, dthres, clipoutside, unflag) |
---|
[1819] | 1035 | self._add_history("clip", varlist) |
---|
| 1036 | |
---|
[1862] | 1037 | @asaplog_post_dec |
---|
[1584] | 1038 | def lag_flag(self, start, end, unit="MHz", insitu=None): |
---|
[1846] | 1039 | """\ |
---|
[1192] | 1040 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
[1584] | 1041 | Flagged data in the scantable gets interpolated over the region. |
---|
[1192] | 1042 | No taper is applied. |
---|
[1846] | 1043 | |
---|
[1192] | 1044 | Parameters: |
---|
[1846] | 1045 | |
---|
[1579] | 1046 | start: the start frequency (really a period within the |
---|
| 1047 | bandwidth) or period to remove |
---|
[1855] | 1048 | |
---|
[1579] | 1049 | end: the end frequency or period to remove |
---|
[1855] | 1050 | |
---|
[1584] | 1051 | unit: the frequency unit (default "MHz") or "" for |
---|
[1579] | 1052 | explicit lag channels |
---|
[1846] | 1053 | |
---|
| 1054 | *Notes*: |
---|
| 1055 | |
---|
[1579] | 1056 | It is recommended to flag edges of the band or strong |
---|
[1348] | 1057 | signals beforehand. |
---|
[1846] | 1058 | |
---|
[1192] | 1059 | """ |
---|
| 1060 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1061 | self._math._setinsitu(insitu) |
---|
| 1062 | varlist = vars() |
---|
[1579] | 1063 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.} |
---|
| 1064 | if not (unit == "" or base.has_key(unit)): |
---|
[1192] | 1065 | raise ValueError("%s is not a valid unit." % unit) |
---|
[1859] | 1066 | if unit == "": |
---|
| 1067 | s = scantable(self._math._lag_flag(self, start, end, "lags")) |
---|
| 1068 | else: |
---|
| 1069 | s = scantable(self._math._lag_flag(self, start*base[unit], |
---|
| 1070 | end*base[unit], "frequency")) |
---|
[1192] | 1071 | s._add_history("lag_flag", varlist) |
---|
| 1072 | if insitu: |
---|
| 1073 | self._assign(s) |
---|
| 1074 | else: |
---|
| 1075 | return s |
---|
[1001] | 1076 | |
---|
[1862] | 1077 | @asaplog_post_dec |
---|
[113] | 1078 | def create_mask(self, *args, **kwargs): |
---|
[1846] | 1079 | """\ |
---|
[1118] | 1080 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 1081 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 1082 | applied. |
---|
[1846] | 1083 | |
---|
[102] | 1084 | Parameters: |
---|
[1846] | 1085 | |
---|
[1118] | 1086 | [min, max], [min2, max2], ... |
---|
[1024] | 1087 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 1088 | to be masked |
---|
[1855] | 1089 | |
---|
[189] | 1090 | invert: optional argument. If specified as True, |
---|
| 1091 | return an inverted mask, i.e. the regions |
---|
| 1092 | specified are EXCLUDED |
---|
[1855] | 1093 | |
---|
[513] | 1094 | row: create the mask using the specified row for |
---|
| 1095 | unit conversions, default is row=0 |
---|
| 1096 | only necessary if frequency varies over rows. |
---|
[1846] | 1097 | |
---|
| 1098 | Examples:: |
---|
| 1099 | |
---|
[113] | 1100 | scan.set_unit('channel') |
---|
[1846] | 1101 | # a) |
---|
[1118] | 1102 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 1103 | # masks everything outside 400 and 500 |
---|
[113] | 1104 | # and 800 and 900 in the unit 'channel' |
---|
| 1105 | |
---|
[1846] | 1106 | # b) |
---|
[1118] | 1107 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 1108 | # masks the regions between 400 and 500 |
---|
[113] | 1109 | # and 800 and 900 in the unit 'channel' |
---|
[1846] | 1110 | |
---|
| 1111 | # c) |
---|
| 1112 | #mask only channel 400 |
---|
[1554] | 1113 | msk = scan.create_mask([400]) |
---|
[1846] | 1114 | |
---|
[102] | 1115 | """ |
---|
[1554] | 1116 | row = kwargs.get("row", 0) |
---|
[513] | 1117 | data = self._getabcissa(row) |
---|
[113] | 1118 | u = self._getcoordinfo()[0] |
---|
[1859] | 1119 | if u == "": |
---|
| 1120 | u = "channel" |
---|
| 1121 | msg = "The current mask window unit is %s" % u |
---|
| 1122 | i = self._check_ifs() |
---|
| 1123 | if not i: |
---|
| 1124 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 1125 | asaplog.push(msg) |
---|
[102] | 1126 | n = self.nchan() |
---|
[1295] | 1127 | msk = _n_bools(n, False) |
---|
[710] | 1128 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 1129 | |
---|
[1118] | 1130 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 1131 | and args or args[0] |
---|
[710] | 1132 | for window in ws: |
---|
[1554] | 1133 | if len(window) == 1: |
---|
| 1134 | window = [window[0], window[0]] |
---|
| 1135 | if len(window) == 0 or len(window) > 2: |
---|
| 1136 | raise ValueError("A window needs to be defined as [start(, end)]") |
---|
[1545] | 1137 | if window[0] > window[1]: |
---|
| 1138 | tmp = window[0] |
---|
| 1139 | window[0] = window[1] |
---|
| 1140 | window[1] = tmp |
---|
[102] | 1141 | for i in range(n): |
---|
[1024] | 1142 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 1143 | msk[i] = True |
---|
[113] | 1144 | if kwargs.has_key('invert'): |
---|
| 1145 | if kwargs.get('invert'): |
---|
[1295] | 1146 | msk = mask_not(msk) |
---|
[102] | 1147 | return msk |
---|
[710] | 1148 | |
---|
[1819] | 1149 | def get_masklist(self, mask=None, row=0): |
---|
[1846] | 1150 | """\ |
---|
[1819] | 1151 | Compute and return a list of mask windows, [min, max]. |
---|
[1846] | 1152 | |
---|
[1819] | 1153 | Parameters: |
---|
[1846] | 1154 | |
---|
[1819] | 1155 | mask: channel mask, created with create_mask. |
---|
[1855] | 1156 | |
---|
[1819] | 1157 | row: calcutate the masklist using the specified row |
---|
| 1158 | for unit conversions, default is row=0 |
---|
| 1159 | only necessary if frequency varies over rows. |
---|
[1846] | 1160 | |
---|
[1819] | 1161 | Returns: |
---|
[1846] | 1162 | |
---|
[1819] | 1163 | [min, max], [min2, max2], ... |
---|
| 1164 | Pairs of start/end points (inclusive)specifying |
---|
| 1165 | the masked regions |
---|
[1846] | 1166 | |
---|
[1819] | 1167 | """ |
---|
| 1168 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1169 | raise TypeError("The mask should be list or tuple.") |
---|
| 1170 | if len(mask) < 2: |
---|
| 1171 | raise TypeError("The mask elements should be > 1") |
---|
| 1172 | if self.nchan() != len(mask): |
---|
| 1173 | msg = "Number of channels in scantable != number of mask elements" |
---|
| 1174 | raise TypeError(msg) |
---|
| 1175 | data = self._getabcissa(row) |
---|
| 1176 | u = self._getcoordinfo()[0] |
---|
[1859] | 1177 | if u == "": |
---|
| 1178 | u = "channel" |
---|
| 1179 | msg = "The current mask window unit is %s" % u |
---|
| 1180 | i = self._check_ifs() |
---|
| 1181 | if not i: |
---|
| 1182 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 1183 | asaplog.push(msg) |
---|
[1819] | 1184 | masklist=[] |
---|
| 1185 | ist, ien = None, None |
---|
| 1186 | ist, ien=self.get_mask_indices(mask) |
---|
| 1187 | if ist is not None and ien is not None: |
---|
| 1188 | for i in xrange(len(ist)): |
---|
| 1189 | range=[data[ist[i]],data[ien[i]]] |
---|
| 1190 | range.sort() |
---|
| 1191 | masklist.append([range[0],range[1]]) |
---|
| 1192 | return masklist |
---|
| 1193 | |
---|
| 1194 | def get_mask_indices(self, mask=None): |
---|
[1846] | 1195 | """\ |
---|
[1819] | 1196 | Compute and Return lists of mask start indices and mask end indices. |
---|
[1855] | 1197 | |
---|
| 1198 | Parameters: |
---|
| 1199 | |
---|
[1819] | 1200 | mask: channel mask, created with create_mask. |
---|
[1846] | 1201 | |
---|
[1819] | 1202 | Returns: |
---|
[1846] | 1203 | |
---|
[1819] | 1204 | List of mask start indices and that of mask end indices, |
---|
| 1205 | i.e., [istart1,istart2,....], [iend1,iend2,....]. |
---|
[1846] | 1206 | |
---|
[1819] | 1207 | """ |
---|
| 1208 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1209 | raise TypeError("The mask should be list or tuple.") |
---|
| 1210 | if len(mask) < 2: |
---|
| 1211 | raise TypeError("The mask elements should be > 1") |
---|
| 1212 | istart=[] |
---|
| 1213 | iend=[] |
---|
| 1214 | if mask[0]: istart.append(0) |
---|
| 1215 | for i in range(len(mask)-1): |
---|
| 1216 | if not mask[i] and mask[i+1]: |
---|
| 1217 | istart.append(i+1) |
---|
| 1218 | elif mask[i] and not mask[i+1]: |
---|
| 1219 | iend.append(i) |
---|
| 1220 | if mask[len(mask)-1]: iend.append(len(mask)-1) |
---|
| 1221 | if len(istart) != len(iend): |
---|
| 1222 | raise RuntimeError("Numbers of mask start != mask end.") |
---|
| 1223 | for i in range(len(istart)): |
---|
| 1224 | if istart[i] > iend[i]: |
---|
| 1225 | raise RuntimeError("Mask start index > mask end index") |
---|
| 1226 | break |
---|
| 1227 | return istart,iend |
---|
| 1228 | |
---|
| 1229 | # def get_restfreqs(self): |
---|
| 1230 | # """ |
---|
| 1231 | # Get the restfrequency(s) stored in this scantable. |
---|
| 1232 | # The return value(s) are always of unit 'Hz' |
---|
| 1233 | # Parameters: |
---|
| 1234 | # none |
---|
| 1235 | # Returns: |
---|
| 1236 | # a list of doubles |
---|
| 1237 | # """ |
---|
| 1238 | # return list(self._getrestfreqs()) |
---|
| 1239 | |
---|
| 1240 | def get_restfreqs(self, ids=None): |
---|
[1846] | 1241 | """\ |
---|
[256] | 1242 | Get the restfrequency(s) stored in this scantable. |
---|
| 1243 | The return value(s) are always of unit 'Hz' |
---|
[1846] | 1244 | |
---|
[256] | 1245 | Parameters: |
---|
[1846] | 1246 | |
---|
[1819] | 1247 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to |
---|
| 1248 | be retrieved |
---|
[1846] | 1249 | |
---|
[256] | 1250 | Returns: |
---|
[1846] | 1251 | |
---|
[1819] | 1252 | dictionary containing ids and a list of doubles for each id |
---|
[1846] | 1253 | |
---|
[256] | 1254 | """ |
---|
[1819] | 1255 | if ids is None: |
---|
| 1256 | rfreqs={} |
---|
| 1257 | idlist = self.getmolnos() |
---|
| 1258 | for i in idlist: |
---|
| 1259 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1260 | return rfreqs |
---|
| 1261 | else: |
---|
| 1262 | if type(ids)==list or type(ids)==tuple: |
---|
| 1263 | rfreqs={} |
---|
| 1264 | for i in ids: |
---|
| 1265 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1266 | return rfreqs |
---|
| 1267 | else: |
---|
| 1268 | return list(self._getrestfreqs(ids)) |
---|
| 1269 | #return list(self._getrestfreqs(ids)) |
---|
[102] | 1270 | |
---|
[931] | 1271 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
[1846] | 1272 | """\ |
---|
[931] | 1273 | Set or replace the restfrequency specified and |
---|
| 1274 | If the 'freqs' argument holds a scalar, |
---|
| 1275 | then that rest frequency will be applied to all the selected |
---|
| 1276 | data. If the 'freqs' argument holds |
---|
| 1277 | a vector, then it MUST be of equal or smaller length than |
---|
| 1278 | the number of IFs (and the available restfrequencies will be |
---|
| 1279 | replaced by this vector). In this case, *all* data have |
---|
| 1280 | the restfrequency set per IF according |
---|
| 1281 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 1282 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 1283 | IF 1 gets restfreq 2e9. |
---|
[1846] | 1284 | |
---|
[1395] | 1285 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 1286 | |
---|
[931] | 1287 | Parameters: |
---|
[1846] | 1288 | |
---|
[931] | 1289 | freqs: list of rest frequency values or string idenitfiers |
---|
[1855] | 1290 | |
---|
[931] | 1291 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 1292 | |
---|
[1846] | 1293 | |
---|
| 1294 | Example:: |
---|
| 1295 | |
---|
[1819] | 1296 | # set the given restfrequency for the all currently selected IFs |
---|
[931] | 1297 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1845] | 1298 | # set restfrequencies for the n IFs (n > 1) in the order of the |
---|
| 1299 | # list, i.e |
---|
| 1300 | # IF0 -> 1.4e9, IF1 -> 1.41e9, IF3 -> 1.42e9 |
---|
| 1301 | # len(list_of_restfreqs) == nIF |
---|
| 1302 | # for nIF == 1 the following will set multiple restfrequency for |
---|
| 1303 | # that IF |
---|
[1819] | 1304 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9]) |
---|
[1845] | 1305 | # set multiple restfrequencies per IF. as a list of lists where |
---|
| 1306 | # the outer list has nIF elements, the inner s arbitrary |
---|
| 1307 | scan.set_restfreqs(freqs=[[1.4e9, 1.41e9], [1.67e9]]) |
---|
[391] | 1308 | |
---|
[1846] | 1309 | *Note*: |
---|
[1845] | 1310 | |
---|
[931] | 1311 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 1312 | source and IF basis, use scantable.set_selection() before using |
---|
[1846] | 1313 | this function:: |
---|
[931] | 1314 | |
---|
[1846] | 1315 | # provided your scantable is called scan |
---|
| 1316 | selection = selector() |
---|
| 1317 | selection.set_name("ORION*") |
---|
| 1318 | selection.set_ifs([1]) |
---|
| 1319 | scan.set_selection(selection) |
---|
| 1320 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 1321 | |
---|
[931] | 1322 | """ |
---|
| 1323 | varlist = vars() |
---|
[1157] | 1324 | from asap import linecatalog |
---|
| 1325 | # simple value |
---|
[1118] | 1326 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1845] | 1327 | self._setrestfreqs([freqs], [""], unit) |
---|
[1157] | 1328 | # list of values |
---|
[1118] | 1329 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 1330 | # list values are scalars |
---|
[1118] | 1331 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[1845] | 1332 | if len(freqs) == 1: |
---|
| 1333 | self._setrestfreqs(freqs, [""], unit) |
---|
| 1334 | else: |
---|
| 1335 | # allow the 'old' mode of setting mulitple IFs |
---|
| 1336 | sel = selector() |
---|
| 1337 | savesel = self._getselection() |
---|
| 1338 | iflist = self.getifnos() |
---|
| 1339 | if len(freqs)>len(iflist): |
---|
| 1340 | raise ValueError("number of elements in list of list " |
---|
| 1341 | "exeeds the current IF selections") |
---|
| 1342 | iflist = self.getifnos() |
---|
| 1343 | for i, fval in enumerate(freqs): |
---|
| 1344 | sel.set_ifs(iflist[i]) |
---|
| 1345 | self._setselection(sel) |
---|
| 1346 | self._setrestfreqs([fval], [""], unit) |
---|
| 1347 | self._setselection(savesel) |
---|
| 1348 | |
---|
| 1349 | # list values are dict, {'value'=, 'name'=) |
---|
[1157] | 1350 | elif isinstance(freqs[-1], dict): |
---|
[1845] | 1351 | values = [] |
---|
| 1352 | names = [] |
---|
| 1353 | for d in freqs: |
---|
| 1354 | values.append(d["value"]) |
---|
| 1355 | names.append(d["name"]) |
---|
| 1356 | self._setrestfreqs(values, names, unit) |
---|
[1819] | 1357 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple): |
---|
[1157] | 1358 | sel = selector() |
---|
| 1359 | savesel = self._getselection() |
---|
[1322] | 1360 | iflist = self.getifnos() |
---|
[1819] | 1361 | if len(freqs)>len(iflist): |
---|
[1845] | 1362 | raise ValueError("number of elements in list of list exeeds" |
---|
| 1363 | " the current IF selections") |
---|
| 1364 | for i, fval in enumerate(freqs): |
---|
[1322] | 1365 | sel.set_ifs(iflist[i]) |
---|
[1259] | 1366 | self._setselection(sel) |
---|
[1845] | 1367 | self._setrestfreqs(fval, [""], unit) |
---|
[1157] | 1368 | self._setselection(savesel) |
---|
| 1369 | # freqs are to be taken from a linecatalog |
---|
[1153] | 1370 | elif isinstance(freqs, linecatalog): |
---|
| 1371 | sel = selector() |
---|
| 1372 | savesel = self._getselection() |
---|
| 1373 | for i in xrange(freqs.nrow()): |
---|
[1322] | 1374 | sel.set_ifs(iflist[i]) |
---|
[1153] | 1375 | self._setselection(sel) |
---|
[1845] | 1376 | self._setrestfreqs([freqs.get_frequency(i)], |
---|
| 1377 | [freqs.get_name(i)], "MHz") |
---|
[1153] | 1378 | # ensure that we are not iterating past nIF |
---|
| 1379 | if i == self.nif()-1: break |
---|
| 1380 | self._setselection(savesel) |
---|
[931] | 1381 | else: |
---|
| 1382 | return |
---|
| 1383 | self._add_history("set_restfreqs", varlist) |
---|
| 1384 | |
---|
[1360] | 1385 | def shift_refpix(self, delta): |
---|
[1846] | 1386 | """\ |
---|
[1589] | 1387 | Shift the reference pixel of the Spectra Coordinate by an |
---|
| 1388 | integer amount. |
---|
[1846] | 1389 | |
---|
[1589] | 1390 | Parameters: |
---|
[1846] | 1391 | |
---|
[1589] | 1392 | delta: the amount to shift by |
---|
[1846] | 1393 | |
---|
| 1394 | *Note*: |
---|
| 1395 | |
---|
[1589] | 1396 | Be careful using this with broadband data. |
---|
[1846] | 1397 | |
---|
[1360] | 1398 | """ |
---|
[1731] | 1399 | Scantable.shift_refpix(self, delta) |
---|
[931] | 1400 | |
---|
[1862] | 1401 | @asaplog_post_dec |
---|
[1259] | 1402 | def history(self, filename=None): |
---|
[1846] | 1403 | """\ |
---|
[1259] | 1404 | Print the history. Optionally to a file. |
---|
[1846] | 1405 | |
---|
[1348] | 1406 | Parameters: |
---|
[1846] | 1407 | |
---|
[1348] | 1408 | filename: The name of the file to save the history to. |
---|
[1846] | 1409 | |
---|
[1259] | 1410 | """ |
---|
[484] | 1411 | hist = list(self._gethistory()) |
---|
[794] | 1412 | out = "-"*80 |
---|
[484] | 1413 | for h in hist: |
---|
[489] | 1414 | if h.startswith("---"): |
---|
[1857] | 1415 | out = "\n".join([out, h]) |
---|
[489] | 1416 | else: |
---|
| 1417 | items = h.split("##") |
---|
| 1418 | date = items[0] |
---|
| 1419 | func = items[1] |
---|
| 1420 | items = items[2:] |
---|
[794] | 1421 | out += "\n"+date+"\n" |
---|
| 1422 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 1423 | for i in items: |
---|
| 1424 | s = i.split("=") |
---|
[1118] | 1425 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[1857] | 1426 | out = "\n".join([out, "-"*80]) |
---|
[1259] | 1427 | if filename is not None: |
---|
| 1428 | if filename is "": |
---|
| 1429 | filename = 'scantable_history.txt' |
---|
| 1430 | import os |
---|
| 1431 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 1432 | if not os.path.isdir(filename): |
---|
| 1433 | data = open(filename, 'w') |
---|
| 1434 | data.write(out) |
---|
| 1435 | data.close() |
---|
| 1436 | else: |
---|
| 1437 | msg = "Illegal file name '%s'." % (filename) |
---|
[1859] | 1438 | raise IOError(msg) |
---|
| 1439 | return page(out) |
---|
[513] | 1440 | # |
---|
| 1441 | # Maths business |
---|
| 1442 | # |
---|
[1862] | 1443 | @asaplog_post_dec |
---|
[931] | 1444 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[1846] | 1445 | """\ |
---|
[1070] | 1446 | Return the (time) weighted average of a scan. |
---|
[1846] | 1447 | |
---|
| 1448 | *Note*: |
---|
| 1449 | |
---|
[1070] | 1450 | in channels only - align if necessary |
---|
[1846] | 1451 | |
---|
[513] | 1452 | Parameters: |
---|
[1846] | 1453 | |
---|
[513] | 1454 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 1455 | weighting) |
---|
[1855] | 1456 | |
---|
[558] | 1457 | scanav: True averages each scan separately |
---|
| 1458 | False (default) averages all scans together, |
---|
[1855] | 1459 | |
---|
[1099] | 1460 | weight: Weighting scheme. |
---|
| 1461 | 'none' (mean no weight) |
---|
| 1462 | 'var' (1/var(spec) weighted) |
---|
| 1463 | 'tsys' (1/Tsys**2 weighted) |
---|
| 1464 | 'tint' (integration time weighted) |
---|
| 1465 | 'tintsys' (Tint/Tsys**2) |
---|
| 1466 | 'median' ( median averaging) |
---|
[535] | 1467 | The default is 'tint' |
---|
[1855] | 1468 | |
---|
[931] | 1469 | align: align the spectra in velocity before averaging. It takes |
---|
| 1470 | the time of the first spectrum as reference time. |
---|
[1846] | 1471 | |
---|
| 1472 | Example:: |
---|
| 1473 | |
---|
[513] | 1474 | # time average the scantable without using a mask |
---|
[710] | 1475 | newscan = scan.average_time() |
---|
[1846] | 1476 | |
---|
[513] | 1477 | """ |
---|
| 1478 | varlist = vars() |
---|
[1593] | 1479 | weight = weight or 'TINT' |
---|
| 1480 | mask = mask or () |
---|
| 1481 | scanav = (scanav and 'SCAN') or 'NONE' |
---|
[1118] | 1482 | scan = (self, ) |
---|
[1859] | 1483 | |
---|
| 1484 | if align: |
---|
| 1485 | scan = (self.freq_align(insitu=False), ) |
---|
| 1486 | s = None |
---|
| 1487 | if weight.upper() == 'MEDIAN': |
---|
| 1488 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 1489 | scanav)) |
---|
| 1490 | else: |
---|
| 1491 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 1492 | scanav)) |
---|
[1099] | 1493 | s._add_history("average_time", varlist) |
---|
[513] | 1494 | return s |
---|
[710] | 1495 | |
---|
[1862] | 1496 | @asaplog_post_dec |
---|
[876] | 1497 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[1846] | 1498 | """\ |
---|
[513] | 1499 | Return a scan where all spectra are converted to either |
---|
| 1500 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 1501 | By default the function tries to look the values up internally. |
---|
| 1502 | If it can't find them (or if you want to over-ride), you must |
---|
| 1503 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 1504 | also if you don't set it). jyperk takes precedence if you set both. |
---|
[1846] | 1505 | |
---|
[513] | 1506 | Parameters: |
---|
[1846] | 1507 | |
---|
[513] | 1508 | jyperk: the Jy / K conversion factor |
---|
[1855] | 1509 | |
---|
[513] | 1510 | eta: the aperture efficiency |
---|
[1855] | 1511 | |
---|
[513] | 1512 | d: the geomtric diameter (metres) |
---|
[1855] | 1513 | |
---|
[513] | 1514 | insitu: if False a new scantable is returned. |
---|
| 1515 | Otherwise, the scaling is done in-situ |
---|
| 1516 | The default is taken from .asaprc (False) |
---|
[1846] | 1517 | |
---|
[513] | 1518 | """ |
---|
| 1519 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1520 | self._math._setinsitu(insitu) |
---|
[513] | 1521 | varlist = vars() |
---|
[1593] | 1522 | jyperk = jyperk or -1.0 |
---|
| 1523 | d = d or -1.0 |
---|
| 1524 | eta = eta or -1.0 |
---|
[876] | 1525 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 1526 | s._add_history("convert_flux", varlist) |
---|
| 1527 | if insitu: self._assign(s) |
---|
| 1528 | else: return s |
---|
[513] | 1529 | |
---|
[1862] | 1530 | @asaplog_post_dec |
---|
[876] | 1531 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[1846] | 1532 | """\ |
---|
[513] | 1533 | Return a scan after applying a gain-elevation correction. |
---|
| 1534 | The correction can be made via either a polynomial or a |
---|
| 1535 | table-based interpolation (and extrapolation if necessary). |
---|
| 1536 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 1537 | If you specify neither, then a polynomial correction will be made |
---|
| 1538 | with built in coefficients known for certain telescopes (an error |
---|
| 1539 | will occur if the instrument is not known). |
---|
| 1540 | The data and Tsys are *divided* by the scaling factors. |
---|
[1846] | 1541 | |
---|
[513] | 1542 | Parameters: |
---|
[1846] | 1543 | |
---|
[513] | 1544 | poly: Polynomial coefficients (default None) to compute a |
---|
| 1545 | gain-elevation correction as a function of |
---|
| 1546 | elevation (in degrees). |
---|
[1855] | 1547 | |
---|
[513] | 1548 | filename: The name of an ascii file holding correction factors. |
---|
| 1549 | The first row of the ascii file must give the column |
---|
| 1550 | names and these MUST include columns |
---|
| 1551 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 1552 | by this) somewhere. |
---|
| 1553 | The second row must give the data type of the |
---|
| 1554 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 1555 | An example file would be |
---|
| 1556 | (actual factors are arbitrary) : |
---|
| 1557 | |
---|
| 1558 | TIME ELEVATION FACTOR |
---|
| 1559 | R R R |
---|
| 1560 | 0.1 0 0.8 |
---|
| 1561 | 0.2 20 0.85 |
---|
| 1562 | 0.3 40 0.9 |
---|
| 1563 | 0.4 60 0.85 |
---|
| 1564 | 0.5 80 0.8 |
---|
| 1565 | 0.6 90 0.75 |
---|
[1855] | 1566 | |
---|
[513] | 1567 | method: Interpolation method when correcting from a table. |
---|
| 1568 | Values are "nearest", "linear" (default), "cubic" |
---|
| 1569 | and "spline" |
---|
[1855] | 1570 | |
---|
[513] | 1571 | insitu: if False a new scantable is returned. |
---|
| 1572 | Otherwise, the scaling is done in-situ |
---|
| 1573 | The default is taken from .asaprc (False) |
---|
[1846] | 1574 | |
---|
[513] | 1575 | """ |
---|
| 1576 | |
---|
| 1577 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1578 | self._math._setinsitu(insitu) |
---|
[513] | 1579 | varlist = vars() |
---|
[1593] | 1580 | poly = poly or () |
---|
[513] | 1581 | from os.path import expandvars |
---|
| 1582 | filename = expandvars(filename) |
---|
[876] | 1583 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 1584 | s._add_history("gain_el", varlist) |
---|
[1593] | 1585 | if insitu: |
---|
| 1586 | self._assign(s) |
---|
| 1587 | else: |
---|
| 1588 | return s |
---|
[710] | 1589 | |
---|
[1862] | 1590 | @asaplog_post_dec |
---|
[931] | 1591 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[1846] | 1592 | """\ |
---|
[513] | 1593 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 1594 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 1595 | set_freqframe. |
---|
[1846] | 1596 | |
---|
[513] | 1597 | Parameters: |
---|
[1855] | 1598 | |
---|
[513] | 1599 | reftime: reference time to align at. By default, the time of |
---|
| 1600 | the first row of data is used. |
---|
[1855] | 1601 | |
---|
[513] | 1602 | method: Interpolation method for regridding the spectra. |
---|
| 1603 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 1604 | and "spline" |
---|
[1855] | 1605 | |
---|
[513] | 1606 | insitu: if False a new scantable is returned. |
---|
| 1607 | Otherwise, the scaling is done in-situ |
---|
| 1608 | The default is taken from .asaprc (False) |
---|
[1846] | 1609 | |
---|
[513] | 1610 | """ |
---|
[931] | 1611 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 1612 | self._math._setinsitu(insitu) |
---|
[513] | 1613 | varlist = vars() |
---|
[1593] | 1614 | reftime = reftime or "" |
---|
[931] | 1615 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 1616 | s._add_history("freq_align", varlist) |
---|
| 1617 | if insitu: self._assign(s) |
---|
| 1618 | else: return s |
---|
[513] | 1619 | |
---|
[1862] | 1620 | @asaplog_post_dec |
---|
[1725] | 1621 | def opacity(self, tau=None, insitu=None): |
---|
[1846] | 1622 | """\ |
---|
[513] | 1623 | Apply an opacity correction. The data |
---|
| 1624 | and Tsys are multiplied by the correction factor. |
---|
[1846] | 1625 | |
---|
[513] | 1626 | Parameters: |
---|
[1855] | 1627 | |
---|
[1689] | 1628 | tau: (list of) opacity from which the correction factor is |
---|
[513] | 1629 | exp(tau*ZD) |
---|
[1689] | 1630 | where ZD is the zenith-distance. |
---|
| 1631 | If a list is provided, it has to be of length nIF, |
---|
| 1632 | nIF*nPol or 1 and in order of IF/POL, e.g. |
---|
| 1633 | [opif0pol0, opif0pol1, opif1pol0 ...] |
---|
[1725] | 1634 | if tau is `None` the opacities are determined from a |
---|
| 1635 | model. |
---|
[1855] | 1636 | |
---|
[513] | 1637 | insitu: if False a new scantable is returned. |
---|
| 1638 | Otherwise, the scaling is done in-situ |
---|
| 1639 | The default is taken from .asaprc (False) |
---|
[1846] | 1640 | |
---|
[513] | 1641 | """ |
---|
| 1642 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1643 | self._math._setinsitu(insitu) |
---|
[513] | 1644 | varlist = vars() |
---|
[1689] | 1645 | if not hasattr(tau, "__len__"): |
---|
| 1646 | tau = [tau] |
---|
[876] | 1647 | s = scantable(self._math._opacity(self, tau)) |
---|
| 1648 | s._add_history("opacity", varlist) |
---|
| 1649 | if insitu: self._assign(s) |
---|
| 1650 | else: return s |
---|
[513] | 1651 | |
---|
[1862] | 1652 | @asaplog_post_dec |
---|
[513] | 1653 | def bin(self, width=5, insitu=None): |
---|
[1846] | 1654 | """\ |
---|
[513] | 1655 | Return a scan where all spectra have been binned up. |
---|
[1846] | 1656 | |
---|
[1348] | 1657 | Parameters: |
---|
[1846] | 1658 | |
---|
[513] | 1659 | width: The bin width (default=5) in pixels |
---|
[1855] | 1660 | |
---|
[513] | 1661 | insitu: if False a new scantable is returned. |
---|
| 1662 | Otherwise, the scaling is done in-situ |
---|
| 1663 | The default is taken from .asaprc (False) |
---|
[1846] | 1664 | |
---|
[513] | 1665 | """ |
---|
| 1666 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1667 | self._math._setinsitu(insitu) |
---|
[513] | 1668 | varlist = vars() |
---|
[876] | 1669 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1670 | s._add_history("bin", varlist) |
---|
[1589] | 1671 | if insitu: |
---|
| 1672 | self._assign(s) |
---|
| 1673 | else: |
---|
| 1674 | return s |
---|
[513] | 1675 | |
---|
[1862] | 1676 | @asaplog_post_dec |
---|
[513] | 1677 | def resample(self, width=5, method='cubic', insitu=None): |
---|
[1846] | 1678 | """\ |
---|
[1348] | 1679 | Return a scan where all spectra have been binned up. |
---|
[1573] | 1680 | |
---|
[1348] | 1681 | Parameters: |
---|
[1846] | 1682 | |
---|
[513] | 1683 | width: The bin width (default=5) in pixels |
---|
[1855] | 1684 | |
---|
[513] | 1685 | method: Interpolation method when correcting from a table. |
---|
| 1686 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1687 | and "spline" |
---|
[1855] | 1688 | |
---|
[513] | 1689 | insitu: if False a new scantable is returned. |
---|
| 1690 | Otherwise, the scaling is done in-situ |
---|
| 1691 | The default is taken from .asaprc (False) |
---|
[1846] | 1692 | |
---|
[513] | 1693 | """ |
---|
| 1694 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1695 | self._math._setinsitu(insitu) |
---|
[513] | 1696 | varlist = vars() |
---|
[876] | 1697 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1698 | s._add_history("resample", varlist) |
---|
[876] | 1699 | if insitu: self._assign(s) |
---|
| 1700 | else: return s |
---|
[513] | 1701 | |
---|
[1862] | 1702 | @asaplog_post_dec |
---|
[946] | 1703 | def average_pol(self, mask=None, weight='none'): |
---|
[1846] | 1704 | """\ |
---|
[946] | 1705 | Average the Polarisations together. |
---|
[1846] | 1706 | |
---|
[946] | 1707 | Parameters: |
---|
[1846] | 1708 | |
---|
[946] | 1709 | mask: An optional mask defining the region, where the |
---|
| 1710 | averaging will be applied. The output will have all |
---|
| 1711 | specified points masked. |
---|
[1855] | 1712 | |
---|
[946] | 1713 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1714 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 1715 | |
---|
[946] | 1716 | """ |
---|
| 1717 | varlist = vars() |
---|
[1593] | 1718 | mask = mask or () |
---|
[1010] | 1719 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1720 | s._add_history("average_pol", varlist) |
---|
[992] | 1721 | return s |
---|
[513] | 1722 | |
---|
[1862] | 1723 | @asaplog_post_dec |
---|
[1145] | 1724 | def average_beam(self, mask=None, weight='none'): |
---|
[1846] | 1725 | """\ |
---|
[1145] | 1726 | Average the Beams together. |
---|
[1846] | 1727 | |
---|
[1145] | 1728 | Parameters: |
---|
| 1729 | mask: An optional mask defining the region, where the |
---|
| 1730 | averaging will be applied. The output will have all |
---|
| 1731 | specified points masked. |
---|
[1855] | 1732 | |
---|
[1145] | 1733 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1734 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 1735 | |
---|
[1145] | 1736 | """ |
---|
| 1737 | varlist = vars() |
---|
[1593] | 1738 | mask = mask or () |
---|
[1145] | 1739 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1740 | s._add_history("average_beam", varlist) |
---|
| 1741 | return s |
---|
| 1742 | |
---|
[1586] | 1743 | def parallactify(self, pflag): |
---|
[1846] | 1744 | """\ |
---|
[1843] | 1745 | Set a flag to indicate whether this data should be treated as having |
---|
[1617] | 1746 | been 'parallactified' (total phase == 0.0) |
---|
[1846] | 1747 | |
---|
[1617] | 1748 | Parameters: |
---|
[1855] | 1749 | |
---|
[1843] | 1750 | pflag: Bool indicating whether to turn this on (True) or |
---|
[1617] | 1751 | off (False) |
---|
[1846] | 1752 | |
---|
[1617] | 1753 | """ |
---|
[1586] | 1754 | varlist = vars() |
---|
| 1755 | self._parallactify(pflag) |
---|
| 1756 | self._add_history("parallactify", varlist) |
---|
| 1757 | |
---|
[1862] | 1758 | @asaplog_post_dec |
---|
[992] | 1759 | def convert_pol(self, poltype=None): |
---|
[1846] | 1760 | """\ |
---|
[992] | 1761 | Convert the data to a different polarisation type. |
---|
[1565] | 1762 | Note that you will need cross-polarisation terms for most conversions. |
---|
[1846] | 1763 | |
---|
[992] | 1764 | Parameters: |
---|
[1855] | 1765 | |
---|
[992] | 1766 | poltype: The new polarisation type. Valid types are: |
---|
[1565] | 1767 | "linear", "circular", "stokes" and "linpol" |
---|
[1846] | 1768 | |
---|
[992] | 1769 | """ |
---|
| 1770 | varlist = vars() |
---|
[1859] | 1771 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1772 | s._add_history("convert_pol", varlist) |
---|
[992] | 1773 | return s |
---|
| 1774 | |
---|
[1862] | 1775 | @asaplog_post_dec |
---|
[1819] | 1776 | def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, insitu=None): |
---|
[1846] | 1777 | """\ |
---|
[513] | 1778 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
[1846] | 1779 | |
---|
[513] | 1780 | Parameters: |
---|
[1846] | 1781 | |
---|
[513] | 1782 | kernel: The type of smoothing kernel. Select from |
---|
[1574] | 1783 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian' |
---|
| 1784 | or 'poly' |
---|
[1855] | 1785 | |
---|
[513] | 1786 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1787 | ignored otherwise it defauls to 5 pixels. |
---|
| 1788 | For 'gaussian' it is the Full Width Half |
---|
| 1789 | Maximum. For 'boxcar' it is the full width. |
---|
[1574] | 1790 | For 'rmedian' and 'poly' it is the half width. |
---|
[1855] | 1791 | |
---|
[1574] | 1792 | order: Optional parameter for 'poly' kernel (default is 2), to |
---|
| 1793 | specify the order of the polnomial. Ignored by all other |
---|
| 1794 | kernels. |
---|
[1855] | 1795 | |
---|
[1819] | 1796 | plot: plot the original and the smoothed spectra. |
---|
| 1797 | In this each indivual fit has to be approved, by |
---|
| 1798 | typing 'y' or 'n' |
---|
[1855] | 1799 | |
---|
[513] | 1800 | insitu: if False a new scantable is returned. |
---|
| 1801 | Otherwise, the scaling is done in-situ |
---|
| 1802 | The default is taken from .asaprc (False) |
---|
[1846] | 1803 | |
---|
[513] | 1804 | """ |
---|
| 1805 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1806 | self._math._setinsitu(insitu) |
---|
[513] | 1807 | varlist = vars() |
---|
[1819] | 1808 | |
---|
| 1809 | if plot: orgscan = self.copy() |
---|
| 1810 | |
---|
[1574] | 1811 | s = scantable(self._math._smooth(self, kernel.lower(), width, order)) |
---|
[876] | 1812 | s._add_history("smooth", varlist) |
---|
[1819] | 1813 | |
---|
| 1814 | if plot: |
---|
| 1815 | if rcParams['plotter.gui']: |
---|
| 1816 | from asap.asaplotgui import asaplotgui as asaplot |
---|
| 1817 | else: |
---|
| 1818 | from asap.asaplot import asaplot |
---|
| 1819 | self._p=asaplot() |
---|
| 1820 | self._p.set_panels() |
---|
| 1821 | ylab=s._get_ordinate_label() |
---|
| 1822 | #self._p.palette(0,["#777777","red"]) |
---|
| 1823 | for r in xrange(s.nrow()): |
---|
| 1824 | xsm=s._getabcissa(r) |
---|
| 1825 | ysm=s._getspectrum(r) |
---|
| 1826 | xorg=orgscan._getabcissa(r) |
---|
| 1827 | yorg=orgscan._getspectrum(r) |
---|
| 1828 | self._p.clear() |
---|
| 1829 | self._p.hold() |
---|
| 1830 | self._p.set_axes('ylabel',ylab) |
---|
| 1831 | self._p.set_axes('xlabel',s._getabcissalabel(r)) |
---|
| 1832 | self._p.set_axes('title',s._getsourcename(r)) |
---|
| 1833 | self._p.set_line(label='Original',color="#777777") |
---|
| 1834 | self._p.plot(xorg,yorg) |
---|
| 1835 | self._p.set_line(label='Smoothed',color="red") |
---|
| 1836 | self._p.plot(xsm,ysm) |
---|
| 1837 | ### Ugly part for legend |
---|
| 1838 | for i in [0,1]: |
---|
| 1839 | self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]]) |
---|
| 1840 | self._p.release() |
---|
| 1841 | ### Ugly part for legend |
---|
| 1842 | self._p.subplots[0]['lines']=[] |
---|
| 1843 | res = raw_input("Accept smoothing ([y]/n): ") |
---|
| 1844 | if res.upper() == 'N': |
---|
| 1845 | s._setspectrum(yorg, r) |
---|
| 1846 | self._p.unmap() |
---|
| 1847 | self._p = None |
---|
| 1848 | del orgscan |
---|
| 1849 | |
---|
[876] | 1850 | if insitu: self._assign(s) |
---|
| 1851 | else: return s |
---|
[513] | 1852 | |
---|
[1862] | 1853 | @asaplog_post_dec |
---|
[1907] | 1854 | def old_poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None, rows=None): |
---|
[1846] | 1855 | """\ |
---|
[513] | 1856 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
[1907] | 1857 | |
---|
[513] | 1858 | Parameters: |
---|
[1846] | 1859 | |
---|
[794] | 1860 | mask: an optional mask |
---|
[1855] | 1861 | |
---|
[794] | 1862 | order: the order of the polynomial (default is 0) |
---|
[1855] | 1863 | |
---|
[1061] | 1864 | plot: plot the fit and the residual. In this each |
---|
| 1865 | indivual fit has to be approved, by typing 'y' |
---|
| 1866 | or 'n' |
---|
[1855] | 1867 | |
---|
[1391] | 1868 | uselin: use linear polynomial fit |
---|
[1855] | 1869 | |
---|
[794] | 1870 | insitu: if False a new scantable is returned. |
---|
| 1871 | Otherwise, the scaling is done in-situ |
---|
| 1872 | The default is taken from .asaprc (False) |
---|
[1846] | 1873 | |
---|
[1907] | 1874 | rows: row numbers of spectra to be processed. |
---|
| 1875 | (default is None: for all rows) |
---|
| 1876 | |
---|
| 1877 | Example: |
---|
[513] | 1878 | # return a scan baselined by a third order polynomial, |
---|
| 1879 | # not using a mask |
---|
| 1880 | bscan = scan.poly_baseline(order=3) |
---|
[1846] | 1881 | |
---|
[579] | 1882 | """ |
---|
[513] | 1883 | if insitu is None: insitu = rcParams['insitu'] |
---|
[1819] | 1884 | if not insitu: |
---|
| 1885 | workscan = self.copy() |
---|
| 1886 | else: |
---|
| 1887 | workscan = self |
---|
[513] | 1888 | varlist = vars() |
---|
| 1889 | if mask is None: |
---|
[1907] | 1890 | mask = [True for i in xrange(self.nchan())] |
---|
[1819] | 1891 | |
---|
[1217] | 1892 | try: |
---|
| 1893 | f = fitter() |
---|
[1391] | 1894 | if uselin: |
---|
| 1895 | f.set_function(lpoly=order) |
---|
| 1896 | else: |
---|
| 1897 | f.set_function(poly=order) |
---|
[1819] | 1898 | |
---|
[1907] | 1899 | if rows == None: |
---|
| 1900 | rows = xrange(workscan.nrow()) |
---|
| 1901 | elif isinstance(rows, int): |
---|
| 1902 | rows = [ rows ] |
---|
| 1903 | |
---|
[1819] | 1904 | if len(rows) > 0: |
---|
| 1905 | self.blpars = [] |
---|
[1907] | 1906 | self.masklists = [] |
---|
| 1907 | self.actualmask = [] |
---|
| 1908 | |
---|
[1819] | 1909 | for r in rows: |
---|
| 1910 | f.x = workscan._getabcissa(r) |
---|
| 1911 | f.y = workscan._getspectrum(r) |
---|
[1907] | 1912 | f.mask = mask_and(mask, workscan._getmask(r)) # (CAS-1434) |
---|
[1819] | 1913 | f.data = None |
---|
| 1914 | f.fit() |
---|
| 1915 | if plot: |
---|
| 1916 | f.plot(residual=True) |
---|
| 1917 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1918 | if x.upper() == 'N': |
---|
| 1919 | self.blpars.append(None) |
---|
[1907] | 1920 | self.masklists.append(None) |
---|
| 1921 | self.actualmask.append(None) |
---|
[1819] | 1922 | continue |
---|
| 1923 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
| 1924 | self.blpars.append(f.get_parameters()) |
---|
[1907] | 1925 | self.masklists.append(workscan.get_masklist(f.mask, row=r)) |
---|
| 1926 | self.actualmask.append(f.mask) |
---|
[1819] | 1927 | |
---|
| 1928 | if plot: |
---|
| 1929 | f._p.unmap() |
---|
| 1930 | f._p = None |
---|
| 1931 | workscan._add_history("poly_baseline", varlist) |
---|
[1856] | 1932 | if insitu: |
---|
| 1933 | self._assign(workscan) |
---|
| 1934 | else: |
---|
| 1935 | return workscan |
---|
[1217] | 1936 | except RuntimeError: |
---|
| 1937 | msg = "The fit failed, possibly because it didn't converge." |
---|
[1859] | 1938 | raise RuntimeError(msg) |
---|
[513] | 1939 | |
---|
[1819] | 1940 | |
---|
[1907] | 1941 | def poly_baseline(self, mask=None, order=0, plot=False, batch=False, insitu=None, rows=None): |
---|
| 1942 | """\ |
---|
| 1943 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1944 | Parameters: |
---|
| 1945 | mask: an optional mask |
---|
| 1946 | order: the order of the polynomial (default is 0) |
---|
| 1947 | plot: plot the fit and the residual. In this each |
---|
| 1948 | indivual fit has to be approved, by typing 'y' |
---|
| 1949 | or 'n'. Ignored if batch = True. |
---|
| 1950 | batch: if True a faster algorithm is used and logs |
---|
| 1951 | including the fit results are not output |
---|
| 1952 | (default is False) |
---|
| 1953 | insitu: if False a new scantable is returned. |
---|
| 1954 | Otherwise, the scaling is done in-situ |
---|
| 1955 | The default is taken from .asaprc (False) |
---|
| 1956 | rows: row numbers of spectra to be processed. |
---|
| 1957 | (default is None: for all rows) |
---|
| 1958 | Example: |
---|
| 1959 | # return a scan baselined by a third order polynomial, |
---|
| 1960 | # not using a mask |
---|
| 1961 | bscan = scan.poly_baseline(order=3) |
---|
| 1962 | """ |
---|
| 1963 | if insitu is None: insitu = rcParams["insitu"] |
---|
| 1964 | if insitu: |
---|
| 1965 | workscan = self |
---|
| 1966 | else: |
---|
| 1967 | workscan = self.copy() |
---|
| 1968 | |
---|
| 1969 | varlist = vars() |
---|
| 1970 | nchan = workscan.nchan() |
---|
| 1971 | |
---|
| 1972 | if mask is None: |
---|
| 1973 | mask = [True for i in xrange(nchan)] |
---|
| 1974 | |
---|
| 1975 | try: |
---|
| 1976 | if rows == None: |
---|
| 1977 | rows = xrange(workscan.nrow()) |
---|
| 1978 | elif isinstance(rows, int): |
---|
| 1979 | rows = [ rows ] |
---|
| 1980 | |
---|
| 1981 | if len(rows) > 0: |
---|
| 1982 | self.blpars = [] |
---|
| 1983 | self.masklists = [] |
---|
| 1984 | self.actualmask = [] |
---|
| 1985 | |
---|
| 1986 | if batch: |
---|
| 1987 | for r in rows: |
---|
[1908] | 1988 | workscan._poly_baseline_batch(mask, order, r) |
---|
[1907] | 1989 | elif plot: |
---|
| 1990 | f = fitter() |
---|
| 1991 | f.set_function(lpoly=order) |
---|
| 1992 | for r in rows: |
---|
| 1993 | f.x = workscan._getabcissa(r) |
---|
| 1994 | f.y = workscan._getspectrum(r) |
---|
| 1995 | f.mask = mask_and(mask, workscan._getmask(r)) # (CAS-1434) |
---|
| 1996 | f.data = None |
---|
| 1997 | f.fit() |
---|
| 1998 | |
---|
| 1999 | f.plot(residual=True) |
---|
| 2000 | accept_fit = raw_input("Accept fit ( [y]/n ): ") |
---|
| 2001 | if accept_fit.upper() == "N": |
---|
| 2002 | self.blpars.append(None) |
---|
| 2003 | self.masklists.append(None) |
---|
| 2004 | self.actualmask.append(None) |
---|
| 2005 | continue |
---|
| 2006 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
| 2007 | self.blpars.append(f.get_parameters()) |
---|
| 2008 | self.masklists.append(workscan.get_masklist(f.mask, row=r)) |
---|
| 2009 | self.actualmask.append(f.mask) |
---|
| 2010 | |
---|
| 2011 | f._p.unmap() |
---|
| 2012 | f._p = None |
---|
| 2013 | else: |
---|
| 2014 | import array |
---|
| 2015 | for r in rows: |
---|
| 2016 | pars = array.array("f", [0.0 for i in range(order+1)]) |
---|
| 2017 | pars_adr = pars.buffer_info()[0] |
---|
| 2018 | pars_len = pars.buffer_info()[1] |
---|
| 2019 | |
---|
| 2020 | errs = array.array("f", [0.0 for i in range(order+1)]) |
---|
| 2021 | errs_adr = errs.buffer_info()[0] |
---|
| 2022 | errs_len = errs.buffer_info()[1] |
---|
| 2023 | |
---|
| 2024 | fmsk = array.array("i", [1 for i in range(nchan)]) |
---|
| 2025 | fmsk_adr = fmsk.buffer_info()[0] |
---|
| 2026 | fmsk_len = fmsk.buffer_info()[1] |
---|
| 2027 | |
---|
| 2028 | workscan._poly_baseline(mask, order, r, pars_adr, pars_len, errs_adr, errs_len, fmsk_adr, fmsk_len) |
---|
| 2029 | |
---|
| 2030 | params = pars.tolist() |
---|
| 2031 | fmtd = "" |
---|
| 2032 | for i in xrange(len(params)): fmtd += " p%d= %3.6f," % (i, params[i]) |
---|
| 2033 | fmtd = fmtd[:-1] # remove trailing "," |
---|
| 2034 | errors = errs.tolist() |
---|
| 2035 | fmask = fmsk.tolist() |
---|
| 2036 | for i in xrange(len(fmask)): fmask[i] = (fmask[i] > 0) # transform (1/0) -> (True/False) |
---|
| 2037 | |
---|
| 2038 | self.blpars.append({"params":params, "fixed":[], "formatted":fmtd, "errors":errors}) |
---|
| 2039 | self.masklists.append(workscan.get_masklist(fmask, r)) |
---|
| 2040 | self.actualmask.append(fmask) |
---|
| 2041 | |
---|
| 2042 | asaplog.push(str(fmtd)) |
---|
| 2043 | |
---|
| 2044 | workscan._add_history("poly_baseline", varlist) |
---|
| 2045 | |
---|
| 2046 | if insitu: |
---|
| 2047 | self._assign(workscan) |
---|
| 2048 | else: |
---|
| 2049 | return workscan |
---|
| 2050 | |
---|
| 2051 | except RuntimeError: |
---|
| 2052 | msg = "The fit failed, possibly because it didn't converge." |
---|
| 2053 | if rcParams["verbose"]: |
---|
| 2054 | asaplog.push(str(msg)) |
---|
| 2055 | return |
---|
| 2056 | else: |
---|
| 2057 | raise RuntimeError(msg) |
---|
| 2058 | |
---|
| 2059 | |
---|
| 2060 | def auto_poly_baseline(self, mask=None, edge=(0, 0), order=0, |
---|
[1280] | 2061 | threshold=3, chan_avg_limit=1, plot=False, |
---|
[1907] | 2062 | insitu=None, rows=None): |
---|
[1846] | 2063 | """\ |
---|
[880] | 2064 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 2065 | Spectral lines are detected first using linefinder and masked out |
---|
| 2066 | to avoid them affecting the baseline solution. |
---|
| 2067 | |
---|
| 2068 | Parameters: |
---|
[1846] | 2069 | |
---|
[880] | 2070 | mask: an optional mask retreived from scantable |
---|
[1846] | 2071 | |
---|
| 2072 | edge: an optional number of channel to drop at the edge of |
---|
| 2073 | spectrum. If only one value is |
---|
[880] | 2074 | specified, the same number will be dropped from |
---|
| 2075 | both sides of the spectrum. Default is to keep |
---|
[907] | 2076 | all channels. Nested tuples represent individual |
---|
[976] | 2077 | edge selection for different IFs (a number of spectral |
---|
| 2078 | channels can be different) |
---|
[1846] | 2079 | |
---|
[880] | 2080 | order: the order of the polynomial (default is 0) |
---|
[1846] | 2081 | |
---|
[880] | 2082 | threshold: the threshold used by line finder. It is better to |
---|
| 2083 | keep it large as only strong lines affect the |
---|
| 2084 | baseline solution. |
---|
[1846] | 2085 | |
---|
[1280] | 2086 | chan_avg_limit: |
---|
| 2087 | a maximum number of consequtive spectral channels to |
---|
| 2088 | average during the search of weak and broad lines. |
---|
| 2089 | The default is no averaging (and no search for weak |
---|
| 2090 | lines). If such lines can affect the fitted baseline |
---|
| 2091 | (e.g. a high order polynomial is fitted), increase this |
---|
| 2092 | parameter (usually values up to 8 are reasonable). Most |
---|
| 2093 | users of this method should find the default value |
---|
| 2094 | sufficient. |
---|
[1846] | 2095 | |
---|
[1061] | 2096 | plot: plot the fit and the residual. In this each |
---|
| 2097 | indivual fit has to be approved, by typing 'y' |
---|
| 2098 | or 'n' |
---|
[1846] | 2099 | |
---|
[880] | 2100 | insitu: if False a new scantable is returned. |
---|
| 2101 | Otherwise, the scaling is done in-situ |
---|
| 2102 | The default is taken from .asaprc (False) |
---|
[1907] | 2103 | rows: row numbers of spectra to be processed. |
---|
| 2104 | (default is None: for all rows) |
---|
[880] | 2105 | |
---|
[1846] | 2106 | |
---|
| 2107 | Example:: |
---|
| 2108 | |
---|
| 2109 | scan2 = scan.auto_poly_baseline(order=7, insitu=False) |
---|
| 2110 | |
---|
[880] | 2111 | """ |
---|
| 2112 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 2113 | varlist = vars() |
---|
| 2114 | from asap.asaplinefind import linefinder |
---|
| 2115 | from asap import _is_sequence_or_number as _is_valid |
---|
| 2116 | |
---|
[976] | 2117 | # check whether edge is set up for each IF individually |
---|
[1118] | 2118 | individualedge = False; |
---|
| 2119 | if len(edge) > 1: |
---|
| 2120 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 2121 | individualedge = True; |
---|
[907] | 2122 | |
---|
[1118] | 2123 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 2124 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 2125 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 2126 | to make individual selection for different IFs." |
---|
[919] | 2127 | |
---|
[1118] | 2128 | curedge = (0, 0) |
---|
| 2129 | if individualedge: |
---|
| 2130 | for edgepar in edge: |
---|
| 2131 | if not _is_valid(edgepar, int): |
---|
| 2132 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 2133 | to be a pair of integers or an integer." |
---|
[907] | 2134 | else: |
---|
[1118] | 2135 | curedge = edge; |
---|
[880] | 2136 | |
---|
[1907] | 2137 | if not insitu: |
---|
| 2138 | workscan = self.copy() |
---|
| 2139 | else: |
---|
| 2140 | workscan = self |
---|
| 2141 | |
---|
[880] | 2142 | # setup fitter |
---|
| 2143 | f = fitter() |
---|
[1907] | 2144 | f.set_function(lpoly=order) |
---|
[880] | 2145 | |
---|
| 2146 | # setup line finder |
---|
[1118] | 2147 | fl = linefinder() |
---|
[1268] | 2148 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
[880] | 2149 | |
---|
[907] | 2150 | fl.set_scan(workscan) |
---|
| 2151 | |
---|
[1907] | 2152 | if mask is None: |
---|
| 2153 | mask = _n_bools(workscan.nchan(), True) |
---|
| 2154 | |
---|
| 2155 | if rows is None: |
---|
| 2156 | rows = xrange(workscan.nrow()) |
---|
| 2157 | elif isinstance(rows, int): |
---|
| 2158 | rows = [ rows ] |
---|
| 2159 | |
---|
[1819] | 2160 | # Save parameters of baseline fits & masklists as a class attribute. |
---|
| 2161 | # NOTICE: It does not reflect changes in scantable! |
---|
| 2162 | if len(rows) > 0: |
---|
| 2163 | self.blpars=[] |
---|
| 2164 | self.masklists=[] |
---|
[1907] | 2165 | self.actualmask=[] |
---|
[880] | 2166 | asaplog.push("Processing:") |
---|
| 2167 | for r in rows: |
---|
[1118] | 2168 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 2169 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 2170 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 2171 | asaplog.push(msg, False) |
---|
[907] | 2172 | |
---|
[976] | 2173 | # figure out edge parameter |
---|
[1118] | 2174 | if individualedge: |
---|
| 2175 | if len(edge) >= workscan.getif(r): |
---|
| 2176 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 2177 | "be less than the number of IFs" |
---|
| 2178 | curedge = edge[workscan.getif(r)] |
---|
[919] | 2179 | |
---|
[1907] | 2180 | actualmask = mask_and(mask, workscan._getmask(r)) # (CAS-1434) |
---|
[1819] | 2181 | |
---|
[976] | 2182 | # setup line finder |
---|
[1819] | 2183 | fl.find_lines(r, actualmask, curedge) |
---|
[1907] | 2184 | |
---|
[1819] | 2185 | f.x = workscan._getabcissa(r) |
---|
| 2186 | f.y = workscan._getspectrum(r) |
---|
[1907] | 2187 | f.mask = fl.get_mask() |
---|
[1819] | 2188 | f.data = None |
---|
[880] | 2189 | f.fit() |
---|
[1819] | 2190 | |
---|
| 2191 | # Show mask list |
---|
[1907] | 2192 | masklist=workscan.get_masklist(f.mask, row=r) |
---|
[1819] | 2193 | msg = "mask range: "+str(masklist) |
---|
| 2194 | asaplog.push(msg, False) |
---|
| 2195 | |
---|
[1061] | 2196 | if plot: |
---|
| 2197 | f.plot(residual=True) |
---|
| 2198 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 2199 | if x.upper() == 'N': |
---|
[1819] | 2200 | self.blpars.append(None) |
---|
| 2201 | self.masklists.append(None) |
---|
[1907] | 2202 | self.actualmask.append(None) |
---|
[1061] | 2203 | continue |
---|
[1819] | 2204 | |
---|
[880] | 2205 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1819] | 2206 | self.blpars.append(f.get_parameters()) |
---|
| 2207 | self.masklists.append(masklist) |
---|
[1907] | 2208 | self.actualmask.append(f.mask) |
---|
[1061] | 2209 | if plot: |
---|
| 2210 | f._p.unmap() |
---|
| 2211 | f._p = None |
---|
| 2212 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 2213 | if insitu: |
---|
| 2214 | self._assign(workscan) |
---|
| 2215 | else: |
---|
| 2216 | return workscan |
---|
| 2217 | |
---|
[1862] | 2218 | @asaplog_post_dec |
---|
[914] | 2219 | def rotate_linpolphase(self, angle): |
---|
[1846] | 2220 | """\ |
---|
[914] | 2221 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 2222 | This is always done in situ in the raw data. So if you call this |
---|
| 2223 | function more than once then each call rotates the phase further. |
---|
[1846] | 2224 | |
---|
[914] | 2225 | Parameters: |
---|
[1846] | 2226 | |
---|
[914] | 2227 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 2228 | |
---|
| 2229 | Example:: |
---|
| 2230 | |
---|
[914] | 2231 | scan.rotate_linpolphase(2.3) |
---|
[1846] | 2232 | |
---|
[914] | 2233 | """ |
---|
| 2234 | varlist = vars() |
---|
[936] | 2235 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 2236 | self._add_history("rotate_linpolphase", varlist) |
---|
| 2237 | return |
---|
[710] | 2238 | |
---|
[1862] | 2239 | @asaplog_post_dec |
---|
[914] | 2240 | def rotate_xyphase(self, angle): |
---|
[1846] | 2241 | """\ |
---|
[914] | 2242 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 2243 | in the data. So if you call this function more than once |
---|
| 2244 | then each call rotates the phase further. |
---|
[1846] | 2245 | |
---|
[914] | 2246 | Parameters: |
---|
[1846] | 2247 | |
---|
[914] | 2248 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 2249 | |
---|
| 2250 | Example:: |
---|
| 2251 | |
---|
[914] | 2252 | scan.rotate_xyphase(2.3) |
---|
[1846] | 2253 | |
---|
[914] | 2254 | """ |
---|
| 2255 | varlist = vars() |
---|
[936] | 2256 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 2257 | self._add_history("rotate_xyphase", varlist) |
---|
| 2258 | return |
---|
| 2259 | |
---|
[1862] | 2260 | @asaplog_post_dec |
---|
[914] | 2261 | def swap_linears(self): |
---|
[1846] | 2262 | """\ |
---|
[1573] | 2263 | Swap the linear polarisations XX and YY, or better the first two |
---|
[1348] | 2264 | polarisations as this also works for ciculars. |
---|
[914] | 2265 | """ |
---|
| 2266 | varlist = vars() |
---|
[936] | 2267 | self._math._swap_linears(self) |
---|
[914] | 2268 | self._add_history("swap_linears", varlist) |
---|
| 2269 | return |
---|
| 2270 | |
---|
[1862] | 2271 | @asaplog_post_dec |
---|
[914] | 2272 | def invert_phase(self): |
---|
[1846] | 2273 | """\ |
---|
[914] | 2274 | Invert the phase of the complex polarisation |
---|
| 2275 | """ |
---|
| 2276 | varlist = vars() |
---|
[936] | 2277 | self._math._invert_phase(self) |
---|
[914] | 2278 | self._add_history("invert_phase", varlist) |
---|
| 2279 | return |
---|
| 2280 | |
---|
[1862] | 2281 | @asaplog_post_dec |
---|
[876] | 2282 | def add(self, offset, insitu=None): |
---|
[1846] | 2283 | """\ |
---|
[513] | 2284 | Return a scan where all spectra have the offset added |
---|
[1846] | 2285 | |
---|
[513] | 2286 | Parameters: |
---|
[1846] | 2287 | |
---|
[513] | 2288 | offset: the offset |
---|
[1855] | 2289 | |
---|
[513] | 2290 | insitu: if False a new scantable is returned. |
---|
| 2291 | Otherwise, the scaling is done in-situ |
---|
| 2292 | The default is taken from .asaprc (False) |
---|
[1846] | 2293 | |
---|
[513] | 2294 | """ |
---|
| 2295 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2296 | self._math._setinsitu(insitu) |
---|
[513] | 2297 | varlist = vars() |
---|
[876] | 2298 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 2299 | s._add_history("add", varlist) |
---|
[876] | 2300 | if insitu: |
---|
| 2301 | self._assign(s) |
---|
| 2302 | else: |
---|
[513] | 2303 | return s |
---|
| 2304 | |
---|
[1862] | 2305 | @asaplog_post_dec |
---|
[1308] | 2306 | def scale(self, factor, tsys=True, insitu=None): |
---|
[1846] | 2307 | """\ |
---|
| 2308 | |
---|
[513] | 2309 | Return a scan where all spectra are scaled by the give 'factor' |
---|
[1846] | 2310 | |
---|
[513] | 2311 | Parameters: |
---|
[1846] | 2312 | |
---|
[1819] | 2313 | factor: the scaling factor (float or 1D float list) |
---|
[1855] | 2314 | |
---|
[513] | 2315 | insitu: if False a new scantable is returned. |
---|
| 2316 | Otherwise, the scaling is done in-situ |
---|
| 2317 | The default is taken from .asaprc (False) |
---|
[1855] | 2318 | |
---|
[513] | 2319 | tsys: if True (default) then apply the operation to Tsys |
---|
| 2320 | as well as the data |
---|
[1846] | 2321 | |
---|
[513] | 2322 | """ |
---|
| 2323 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2324 | self._math._setinsitu(insitu) |
---|
[513] | 2325 | varlist = vars() |
---|
[1819] | 2326 | s = None |
---|
| 2327 | import numpy |
---|
| 2328 | if isinstance(factor, list) or isinstance(factor, numpy.ndarray): |
---|
| 2329 | if isinstance(factor[0], list) or isinstance(factor[0], numpy.ndarray): |
---|
| 2330 | from asapmath import _array2dOp |
---|
| 2331 | s = _array2dOp( self.copy(), factor, "MUL", tsys ) |
---|
| 2332 | else: |
---|
| 2333 | s = scantable( self._math._arrayop( self.copy(), factor, "MUL", tsys ) ) |
---|
| 2334 | else: |
---|
| 2335 | s = scantable(self._math._unaryop(self.copy(), factor, "MUL", tsys)) |
---|
[1118] | 2336 | s._add_history("scale", varlist) |
---|
[876] | 2337 | if insitu: |
---|
| 2338 | self._assign(s) |
---|
| 2339 | else: |
---|
[513] | 2340 | return s |
---|
| 2341 | |
---|
[1504] | 2342 | def set_sourcetype(self, match, matchtype="pattern", |
---|
| 2343 | sourcetype="reference"): |
---|
[1846] | 2344 | """\ |
---|
[1502] | 2345 | Set the type of the source to be an source or reference scan |
---|
[1846] | 2346 | using the provided pattern. |
---|
| 2347 | |
---|
[1502] | 2348 | Parameters: |
---|
[1846] | 2349 | |
---|
[1504] | 2350 | match: a Unix style pattern, regular expression or selector |
---|
[1855] | 2351 | |
---|
[1504] | 2352 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
| 2353 | 'regex' regular expression |
---|
[1855] | 2354 | |
---|
[1502] | 2355 | sourcetype: the type of the source to use (source/reference) |
---|
[1846] | 2356 | |
---|
[1502] | 2357 | """ |
---|
| 2358 | varlist = vars() |
---|
| 2359 | basesel = self.get_selection() |
---|
| 2360 | stype = -1 |
---|
| 2361 | if sourcetype.lower().startswith("r"): |
---|
| 2362 | stype = 1 |
---|
| 2363 | elif sourcetype.lower().startswith("s"): |
---|
| 2364 | stype = 0 |
---|
[1504] | 2365 | else: |
---|
[1502] | 2366 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)") |
---|
[1504] | 2367 | if matchtype.lower().startswith("p"): |
---|
| 2368 | matchtype = "pattern" |
---|
| 2369 | elif matchtype.lower().startswith("r"): |
---|
| 2370 | matchtype = "regex" |
---|
| 2371 | else: |
---|
| 2372 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
[1502] | 2373 | sel = selector() |
---|
| 2374 | if isinstance(match, selector): |
---|
| 2375 | sel = match |
---|
| 2376 | else: |
---|
[1504] | 2377 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match)) |
---|
[1502] | 2378 | self.set_selection(basesel+sel) |
---|
| 2379 | self._setsourcetype(stype) |
---|
| 2380 | self.set_selection(basesel) |
---|
[1573] | 2381 | self._add_history("set_sourcetype", varlist) |
---|
[1502] | 2382 | |
---|
[1862] | 2383 | @asaplog_post_dec |
---|
[1857] | 2384 | @preserve_selection |
---|
[1819] | 2385 | def auto_quotient(self, preserve=True, mode='paired', verify=False): |
---|
[1846] | 2386 | """\ |
---|
[670] | 2387 | This function allows to build quotients automatically. |
---|
[1819] | 2388 | It assumes the observation to have the same number of |
---|
[670] | 2389 | "ons" and "offs" |
---|
[1846] | 2390 | |
---|
[670] | 2391 | Parameters: |
---|
[1846] | 2392 | |
---|
[710] | 2393 | preserve: you can preserve (default) the continuum or |
---|
| 2394 | remove it. The equations used are |
---|
[1857] | 2395 | |
---|
[670] | 2396 | preserve: Output = Toff * (on/off) - Toff |
---|
[1857] | 2397 | |
---|
[1070] | 2398 | remove: Output = Toff * (on/off) - Ton |
---|
[1855] | 2399 | |
---|
[1573] | 2400 | mode: the on/off detection mode |
---|
[1348] | 2401 | 'paired' (default) |
---|
| 2402 | identifies 'off' scans by the |
---|
| 2403 | trailing '_R' (Mopra/Parkes) or |
---|
| 2404 | '_e'/'_w' (Tid) and matches |
---|
| 2405 | on/off pairs from the observing pattern |
---|
[1502] | 2406 | 'time' |
---|
| 2407 | finds the closest off in time |
---|
[1348] | 2408 | |
---|
[1857] | 2409 | .. todo:: verify argument is not implemented |
---|
| 2410 | |
---|
[670] | 2411 | """ |
---|
[1857] | 2412 | varlist = vars() |
---|
[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) |
---|
[1348] | 2417 | s = None |
---|
| 2418 | if mode.lower() == "paired": |
---|
[1857] | 2419 | sel = self.get_selection() |
---|
[1875] | 2420 | sel.set_query("SRCTYPE==psoff") |
---|
[1356] | 2421 | self.set_selection(sel) |
---|
[1348] | 2422 | offs = self.copy() |
---|
[1875] | 2423 | sel.set_query("SRCTYPE==pson") |
---|
[1356] | 2424 | self.set_selection(sel) |
---|
[1348] | 2425 | ons = self.copy() |
---|
| 2426 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 2427 | elif mode.lower() == "time": |
---|
| 2428 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 2429 | s._add_history("auto_quotient", varlist) |
---|
[876] | 2430 | return s |
---|
[710] | 2431 | |
---|
[1862] | 2432 | @asaplog_post_dec |
---|
[1145] | 2433 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1846] | 2434 | """\ |
---|
[1143] | 2435 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
[1846] | 2436 | |
---|
[1143] | 2437 | Parameters: |
---|
[1846] | 2438 | |
---|
[1145] | 2439 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1855] | 2440 | |
---|
[1143] | 2441 | weight: How to average the off beams. Default is 'median'. |
---|
[1855] | 2442 | |
---|
[1145] | 2443 | preserve: you can preserve (default) the continuum or |
---|
[1855] | 2444 | remove it. The equations used are: |
---|
[1846] | 2445 | |
---|
[1855] | 2446 | preserve: Output = Toff * (on/off) - Toff |
---|
| 2447 | |
---|
| 2448 | remove: Output = Toff * (on/off) - Ton |
---|
| 2449 | |
---|
[1217] | 2450 | """ |
---|
[1593] | 2451 | mask = mask or () |
---|
[1141] | 2452 | varlist = vars() |
---|
| 2453 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 2454 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 2455 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 2456 | from asapmath import quotient |
---|
[1145] | 2457 | q = quotient(on, off, preserve) |
---|
[1143] | 2458 | q._add_history("mx_quotient", varlist) |
---|
[1217] | 2459 | return q |
---|
[513] | 2460 | |
---|
[1862] | 2461 | @asaplog_post_dec |
---|
[718] | 2462 | def freq_switch(self, insitu=None): |
---|
[1846] | 2463 | """\ |
---|
[718] | 2464 | Apply frequency switching to the data. |
---|
[1846] | 2465 | |
---|
[718] | 2466 | Parameters: |
---|
[1846] | 2467 | |
---|
[718] | 2468 | insitu: if False a new scantable is returned. |
---|
| 2469 | Otherwise, the swictching is done in-situ |
---|
| 2470 | The default is taken from .asaprc (False) |
---|
[1846] | 2471 | |
---|
[718] | 2472 | """ |
---|
| 2473 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2474 | self._math._setinsitu(insitu) |
---|
[718] | 2475 | varlist = vars() |
---|
[876] | 2476 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 2477 | s._add_history("freq_switch", varlist) |
---|
[1856] | 2478 | if insitu: |
---|
| 2479 | self._assign(s) |
---|
| 2480 | else: |
---|
| 2481 | return s |
---|
[718] | 2482 | |
---|
[1862] | 2483 | @asaplog_post_dec |
---|
[780] | 2484 | def recalc_azel(self): |
---|
[1846] | 2485 | """Recalculate the azimuth and elevation for each position.""" |
---|
[780] | 2486 | varlist = vars() |
---|
[876] | 2487 | self._recalcazel() |
---|
[780] | 2488 | self._add_history("recalc_azel", varlist) |
---|
| 2489 | return |
---|
| 2490 | |
---|
[1862] | 2491 | @asaplog_post_dec |
---|
[513] | 2492 | def __add__(self, other): |
---|
| 2493 | varlist = vars() |
---|
| 2494 | s = None |
---|
| 2495 | if isinstance(other, scantable): |
---|
[1573] | 2496 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
[513] | 2497 | elif isinstance(other, float): |
---|
[876] | 2498 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 2499 | else: |
---|
[718] | 2500 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2501 | s._add_history("operator +", varlist) |
---|
| 2502 | return s |
---|
| 2503 | |
---|
[1862] | 2504 | @asaplog_post_dec |
---|
[513] | 2505 | def __sub__(self, other): |
---|
| 2506 | """ |
---|
| 2507 | implicit on all axes and on Tsys |
---|
| 2508 | """ |
---|
| 2509 | varlist = vars() |
---|
| 2510 | s = None |
---|
| 2511 | if isinstance(other, scantable): |
---|
[1588] | 2512 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
[513] | 2513 | elif isinstance(other, float): |
---|
[876] | 2514 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 2515 | else: |
---|
[718] | 2516 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2517 | s._add_history("operator -", varlist) |
---|
| 2518 | return s |
---|
[710] | 2519 | |
---|
[1862] | 2520 | @asaplog_post_dec |
---|
[513] | 2521 | def __mul__(self, other): |
---|
| 2522 | """ |
---|
| 2523 | implicit on all axes and on Tsys |
---|
| 2524 | """ |
---|
| 2525 | varlist = vars() |
---|
| 2526 | s = None |
---|
| 2527 | if isinstance(other, scantable): |
---|
[1588] | 2528 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
[513] | 2529 | elif isinstance(other, float): |
---|
[876] | 2530 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 2531 | else: |
---|
[718] | 2532 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2533 | s._add_history("operator *", varlist) |
---|
| 2534 | return s |
---|
| 2535 | |
---|
[710] | 2536 | |
---|
[1862] | 2537 | @asaplog_post_dec |
---|
[513] | 2538 | def __div__(self, other): |
---|
| 2539 | """ |
---|
| 2540 | implicit on all axes and on Tsys |
---|
| 2541 | """ |
---|
| 2542 | varlist = vars() |
---|
| 2543 | s = None |
---|
| 2544 | if isinstance(other, scantable): |
---|
[1589] | 2545 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
[513] | 2546 | elif isinstance(other, float): |
---|
| 2547 | if other == 0.0: |
---|
[718] | 2548 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 2549 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 2550 | else: |
---|
[718] | 2551 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2552 | s._add_history("operator /", varlist) |
---|
| 2553 | return s |
---|
| 2554 | |
---|
[1862] | 2555 | @asaplog_post_dec |
---|
[530] | 2556 | def get_fit(self, row=0): |
---|
[1846] | 2557 | """\ |
---|
[530] | 2558 | Print or return the stored fits for a row in the scantable |
---|
[1846] | 2559 | |
---|
[530] | 2560 | Parameters: |
---|
[1846] | 2561 | |
---|
[530] | 2562 | row: the row which the fit has been applied to. |
---|
[1846] | 2563 | |
---|
[530] | 2564 | """ |
---|
| 2565 | if row > self.nrow(): |
---|
| 2566 | return |
---|
[976] | 2567 | from asap.asapfit import asapfit |
---|
[530] | 2568 | fit = asapfit(self._getfit(row)) |
---|
[1859] | 2569 | asaplog.push( '%s' %(fit) ) |
---|
| 2570 | return fit.as_dict() |
---|
[530] | 2571 | |
---|
[1483] | 2572 | def flag_nans(self): |
---|
[1846] | 2573 | """\ |
---|
[1483] | 2574 | Utility function to flag NaN values in the scantable. |
---|
| 2575 | """ |
---|
| 2576 | import numpy |
---|
| 2577 | basesel = self.get_selection() |
---|
| 2578 | for i in range(self.nrow()): |
---|
[1589] | 2579 | sel = self.get_row_selector(i) |
---|
| 2580 | self.set_selection(basesel+sel) |
---|
[1483] | 2581 | nans = numpy.isnan(self._getspectrum(0)) |
---|
| 2582 | if numpy.any(nans): |
---|
| 2583 | bnans = [ bool(v) for v in nans] |
---|
| 2584 | self.flag(bnans) |
---|
| 2585 | self.set_selection(basesel) |
---|
| 2586 | |
---|
[1588] | 2587 | def get_row_selector(self, rowno): |
---|
| 2588 | return selector(beams=self.getbeam(rowno), |
---|
| 2589 | ifs=self.getif(rowno), |
---|
| 2590 | pols=self.getpol(rowno), |
---|
| 2591 | scans=self.getscan(rowno), |
---|
| 2592 | cycles=self.getcycle(rowno)) |
---|
[1573] | 2593 | |
---|
[484] | 2594 | def _add_history(self, funcname, parameters): |
---|
[1435] | 2595 | if not rcParams['scantable.history']: |
---|
| 2596 | return |
---|
[484] | 2597 | # create date |
---|
| 2598 | sep = "##" |
---|
| 2599 | from datetime import datetime |
---|
| 2600 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 2601 | hist = dstr+sep |
---|
| 2602 | hist += funcname+sep#cdate+sep |
---|
| 2603 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 2604 | for k, v in parameters.iteritems(): |
---|
[484] | 2605 | if type(v) is dict: |
---|
[1118] | 2606 | for k2, v2 in v.iteritems(): |
---|
[484] | 2607 | hist += k2 |
---|
| 2608 | hist += "=" |
---|
[1118] | 2609 | if isinstance(v2, scantable): |
---|
[484] | 2610 | hist += 'scantable' |
---|
| 2611 | elif k2 == 'mask': |
---|
[1118] | 2612 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 2613 | hist += str(self._zip_mask(v2)) |
---|
| 2614 | else: |
---|
| 2615 | hist += str(v2) |
---|
[484] | 2616 | else: |
---|
[513] | 2617 | hist += str(v2) |
---|
[484] | 2618 | else: |
---|
| 2619 | hist += k |
---|
| 2620 | hist += "=" |
---|
[1118] | 2621 | if isinstance(v, scantable): |
---|
[484] | 2622 | hist += 'scantable' |
---|
| 2623 | elif k == 'mask': |
---|
[1118] | 2624 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 2625 | hist += str(self._zip_mask(v)) |
---|
| 2626 | else: |
---|
| 2627 | hist += str(v) |
---|
[484] | 2628 | else: |
---|
| 2629 | hist += str(v) |
---|
| 2630 | hist += sep |
---|
| 2631 | hist = hist[:-2] # remove trailing '##' |
---|
| 2632 | self._addhistory(hist) |
---|
| 2633 | |
---|
[710] | 2634 | |
---|
[484] | 2635 | def _zip_mask(self, mask): |
---|
| 2636 | mask = list(mask) |
---|
| 2637 | i = 0 |
---|
| 2638 | segments = [] |
---|
| 2639 | while mask[i:].count(1): |
---|
| 2640 | i += mask[i:].index(1) |
---|
| 2641 | if mask[i:].count(0): |
---|
| 2642 | j = i + mask[i:].index(0) |
---|
| 2643 | else: |
---|
[710] | 2644 | j = len(mask) |
---|
[1118] | 2645 | segments.append([i, j]) |
---|
[710] | 2646 | i = j |
---|
[484] | 2647 | return segments |
---|
[714] | 2648 | |
---|
[626] | 2649 | def _get_ordinate_label(self): |
---|
| 2650 | fu = "("+self.get_fluxunit()+")" |
---|
| 2651 | import re |
---|
| 2652 | lbl = "Intensity" |
---|
[1118] | 2653 | if re.match(".K.", fu): |
---|
[626] | 2654 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 2655 | elif re.match(".Jy.", fu): |
---|
[626] | 2656 | lbl = "Flux density "+ fu |
---|
| 2657 | return lbl |
---|
[710] | 2658 | |
---|
[876] | 2659 | def _check_ifs(self): |
---|
| 2660 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 2661 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 2662 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 2663 | |
---|
[1862] | 2664 | @asaplog_post_dec |
---|
[1819] | 2665 | def _fill(self, names, unit, average, getpt, antenna): |
---|
[976] | 2666 | first = True |
---|
| 2667 | fullnames = [] |
---|
| 2668 | for name in names: |
---|
| 2669 | name = os.path.expandvars(name) |
---|
| 2670 | name = os.path.expanduser(name) |
---|
| 2671 | if not os.path.exists(name): |
---|
| 2672 | msg = "File '%s' does not exists" % (name) |
---|
| 2673 | raise IOError(msg) |
---|
| 2674 | fullnames.append(name) |
---|
| 2675 | if average: |
---|
| 2676 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 2677 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 2678 | for name in fullnames: |
---|
[1073] | 2679 | tbl = Scantable(stype) |
---|
[1843] | 2680 | r = filler(tbl) |
---|
[1504] | 2681 | rx = rcParams['scantable.reference'] |
---|
[1843] | 2682 | r.setreferenceexpr(rx) |
---|
[976] | 2683 | msg = "Importing %s..." % (name) |
---|
[1118] | 2684 | asaplog.push(msg, False) |
---|
[1904] | 2685 | opts = {'ms': {'antenna' : antenna, 'getpt': getpt} } |
---|
| 2686 | r.open(name, opts)# antenna, -1, -1, getpt) |
---|
[1843] | 2687 | r.fill() |
---|
[976] | 2688 | if average: |
---|
[1118] | 2689 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 2690 | if not first: |
---|
| 2691 | tbl = self._math._merge([self, tbl]) |
---|
| 2692 | Scantable.__init__(self, tbl) |
---|
[1843] | 2693 | r.close() |
---|
[1118] | 2694 | del r, tbl |
---|
[976] | 2695 | first = False |
---|
[1861] | 2696 | #flush log |
---|
| 2697 | asaplog.post() |
---|
[976] | 2698 | if unit is not None: |
---|
| 2699 | self.set_fluxunit(unit) |
---|
[1824] | 2700 | if not is_casapy(): |
---|
| 2701 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[976] | 2702 | |
---|
[1402] | 2703 | def __getitem__(self, key): |
---|
| 2704 | if key < 0: |
---|
| 2705 | key += self.nrow() |
---|
| 2706 | if key >= self.nrow(): |
---|
| 2707 | raise IndexError("Row index out of range.") |
---|
| 2708 | return self._getspectrum(key) |
---|
| 2709 | |
---|
| 2710 | def __setitem__(self, key, value): |
---|
| 2711 | if key < 0: |
---|
| 2712 | key += self.nrow() |
---|
| 2713 | if key >= self.nrow(): |
---|
| 2714 | raise IndexError("Row index out of range.") |
---|
| 2715 | if not hasattr(value, "__len__") or \ |
---|
| 2716 | len(value) > self.nchan(self.getif(key)): |
---|
| 2717 | raise ValueError("Spectrum length doesn't match.") |
---|
| 2718 | return self._setspectrum(value, key) |
---|
| 2719 | |
---|
| 2720 | def __len__(self): |
---|
| 2721 | return self.nrow() |
---|
| 2722 | |
---|
| 2723 | def __iter__(self): |
---|
| 2724 | for i in range(len(self)): |
---|
| 2725 | yield self[i] |
---|