[1846] | 1 | """This module defines the scantable class.""" |
---|
| 2 | |
---|
[1697] | 3 | import os |
---|
[1948] | 4 | import numpy |
---|
[1691] | 5 | try: |
---|
| 6 | from functools import wraps as wraps_dec |
---|
| 7 | except ImportError: |
---|
| 8 | from asap.compatibility import wraps as wraps_dec |
---|
| 9 | |
---|
[1824] | 10 | from asap.env import is_casapy |
---|
[876] | 11 | from asap._asap import Scantable |
---|
[1843] | 12 | from asap._asap import filler |
---|
[1824] | 13 | from asap.parameters import rcParams |
---|
[1862] | 14 | from asap.logging import asaplog, asaplog_post_dec |
---|
[1824] | 15 | from asap.selector import selector |
---|
| 16 | from asap.linecatalog import linecatalog |
---|
[1600] | 17 | from asap.coordinate import coordinate |
---|
[1859] | 18 | from asap.utils import _n_bools, mask_not, mask_and, mask_or, page |
---|
[1907] | 19 | from asap.asapfitter import fitter |
---|
[102] | 20 | |
---|
[1689] | 21 | |
---|
| 22 | def preserve_selection(func): |
---|
[1691] | 23 | @wraps_dec(func) |
---|
[1689] | 24 | def wrap(obj, *args, **kw): |
---|
| 25 | basesel = obj.get_selection() |
---|
[1857] | 26 | try: |
---|
| 27 | val = func(obj, *args, **kw) |
---|
| 28 | finally: |
---|
| 29 | obj.set_selection(basesel) |
---|
[1689] | 30 | return val |
---|
| 31 | return wrap |
---|
| 32 | |
---|
[1846] | 33 | def is_scantable(filename): |
---|
| 34 | """Is the given file a scantable? |
---|
[1689] | 35 | |
---|
[1846] | 36 | Parameters: |
---|
| 37 | |
---|
| 38 | filename: the name of the file/directory to test |
---|
| 39 | |
---|
| 40 | """ |
---|
[1883] | 41 | if ( os.path.isdir(filename) |
---|
| 42 | and os.path.exists(filename+'/table.info') |
---|
| 43 | and os.path.exists(filename+'/table.dat') ): |
---|
| 44 | f=open(filename+'/table.info') |
---|
| 45 | l=f.readline() |
---|
| 46 | f.close() |
---|
| 47 | #if ( l.find('Scantable') != -1 ): |
---|
| 48 | if ( l.find('Measurement Set') == -1 ): |
---|
| 49 | return True |
---|
| 50 | else: |
---|
| 51 | return False |
---|
| 52 | else: |
---|
| 53 | return False |
---|
| 54 | ## return (os.path.isdir(filename) |
---|
| 55 | ## and not os.path.exists(filename+'/table.f1') |
---|
| 56 | ## and os.path.exists(filename+'/table.info')) |
---|
[1697] | 57 | |
---|
[1883] | 58 | def is_ms(filename): |
---|
| 59 | """Is the given file a MeasurementSet? |
---|
[1697] | 60 | |
---|
[1883] | 61 | Parameters: |
---|
| 62 | |
---|
| 63 | filename: the name of the file/directory to test |
---|
| 64 | |
---|
| 65 | """ |
---|
| 66 | if ( os.path.isdir(filename) |
---|
| 67 | and os.path.exists(filename+'/table.info') |
---|
| 68 | and os.path.exists(filename+'/table.dat') ): |
---|
| 69 | f=open(filename+'/table.info') |
---|
| 70 | l=f.readline() |
---|
| 71 | f.close() |
---|
| 72 | if ( l.find('Measurement Set') != -1 ): |
---|
| 73 | return True |
---|
| 74 | else: |
---|
| 75 | return False |
---|
| 76 | else: |
---|
| 77 | return False |
---|
| 78 | |
---|
[876] | 79 | class scantable(Scantable): |
---|
[1846] | 80 | """\ |
---|
| 81 | The ASAP container for scans (single-dish data). |
---|
[102] | 82 | """ |
---|
[1819] | 83 | |
---|
[1862] | 84 | @asaplog_post_dec |
---|
[1916] | 85 | #def __init__(self, filename, average=None, unit=None, getpt=None, |
---|
| 86 | # antenna=None, parallactify=None): |
---|
| 87 | def __init__(self, filename, average=None, unit=None, parallactify=None, **args): |
---|
[1846] | 88 | """\ |
---|
[102] | 89 | Create a scantable from a saved one or make a reference |
---|
[1846] | 90 | |
---|
[102] | 91 | Parameters: |
---|
[1846] | 92 | |
---|
| 93 | filename: the name of an asap table on disk |
---|
| 94 | or |
---|
| 95 | the name of a rpfits/sdfits/ms file |
---|
| 96 | (integrations within scans are auto averaged |
---|
| 97 | and the whole file is read) or |
---|
| 98 | [advanced] a reference to an existing scantable |
---|
| 99 | |
---|
| 100 | average: average all integrations withinb a scan on read. |
---|
| 101 | The default (True) is taken from .asaprc. |
---|
| 102 | |
---|
[484] | 103 | unit: brightness unit; must be consistent with K or Jy. |
---|
[1846] | 104 | Over-rides the default selected by the filler |
---|
| 105 | (input rpfits/sdfits/ms) or replaces the value |
---|
| 106 | in existing scantables |
---|
| 107 | |
---|
| 108 | getpt: for MeasurementSet input data only: |
---|
| 109 | If True, all pointing data are filled. |
---|
| 110 | The deafult is False, which makes time to load |
---|
| 111 | the MS data faster in some cases. |
---|
| 112 | |
---|
[1920] | 113 | antenna: for MeasurementSet input data only: |
---|
| 114 | Antenna selection. integer (id) or string (name or id). |
---|
[1846] | 115 | |
---|
| 116 | parallactify: Indicate that the data had been parallatified. Default |
---|
| 117 | is taken from rc file. |
---|
| 118 | |
---|
[710] | 119 | """ |
---|
[976] | 120 | if average is None: |
---|
[710] | 121 | average = rcParams['scantable.autoaverage'] |
---|
[1916] | 122 | #if getpt is None: |
---|
| 123 | # getpt = True |
---|
| 124 | #if antenna is not None: |
---|
| 125 | # asaplog.push("Antenna selection currently unsupported." |
---|
| 126 | # "Using ''") |
---|
| 127 | # asaplog.post('WARN') |
---|
| 128 | #if antenna is None: |
---|
| 129 | # antenna = '' |
---|
| 130 | #elif type(antenna) == int: |
---|
| 131 | # antenna = '%s' % antenna |
---|
| 132 | #elif type(antenna) == list: |
---|
| 133 | # tmpstr = '' |
---|
| 134 | # for i in range( len(antenna) ): |
---|
| 135 | # if type(antenna[i]) == int: |
---|
| 136 | # tmpstr = tmpstr + ('%s,'%(antenna[i])) |
---|
| 137 | # elif type(antenna[i]) == str: |
---|
| 138 | # tmpstr=tmpstr+antenna[i]+',' |
---|
| 139 | # else: |
---|
| 140 | # raise TypeError('Bad antenna selection.') |
---|
| 141 | # antenna = tmpstr.rstrip(',') |
---|
[1593] | 142 | parallactify = parallactify or rcParams['scantable.parallactify'] |
---|
[1259] | 143 | varlist = vars() |
---|
[876] | 144 | from asap._asap import stmath |
---|
[1819] | 145 | self._math = stmath( rcParams['insitu'] ) |
---|
[876] | 146 | if isinstance(filename, Scantable): |
---|
| 147 | Scantable.__init__(self, filename) |
---|
[181] | 148 | else: |
---|
[1697] | 149 | if isinstance(filename, str): |
---|
[976] | 150 | filename = os.path.expandvars(filename) |
---|
| 151 | filename = os.path.expanduser(filename) |
---|
| 152 | if not os.path.exists(filename): |
---|
| 153 | s = "File '%s' not found." % (filename) |
---|
| 154 | raise IOError(s) |
---|
[1697] | 155 | if is_scantable(filename): |
---|
| 156 | ondisk = rcParams['scantable.storage'] == 'disk' |
---|
| 157 | Scantable.__init__(self, filename, ondisk) |
---|
| 158 | if unit is not None: |
---|
| 159 | self.set_fluxunit(unit) |
---|
[1819] | 160 | # do not reset to the default freqframe |
---|
| 161 | #self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[1883] | 162 | #elif os.path.isdir(filename) \ |
---|
| 163 | # and not os.path.exists(filename+'/table.f1'): |
---|
| 164 | elif is_ms(filename): |
---|
[1916] | 165 | # Measurement Set |
---|
| 166 | opts={'ms': {}} |
---|
| 167 | mskeys=['getpt','antenna'] |
---|
| 168 | for key in mskeys: |
---|
| 169 | if key in args.keys(): |
---|
| 170 | opts['ms'][key] = args[key] |
---|
| 171 | #self._fill([filename], unit, average, getpt, antenna) |
---|
| 172 | self._fill([filename], unit, average, opts) |
---|
[1893] | 173 | elif os.path.isfile(filename): |
---|
[1916] | 174 | #self._fill([filename], unit, average, getpt, antenna) |
---|
| 175 | self._fill([filename], unit, average) |
---|
[1883] | 176 | else: |
---|
[1819] | 177 | msg = "The given file '%s'is not a valid " \ |
---|
| 178 | "asap table." % (filename) |
---|
[1859] | 179 | raise IOError(msg) |
---|
[1118] | 180 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
---|
[976] | 181 | and isinstance(filename[-1], str): |
---|
[1916] | 182 | #self._fill(filename, unit, average, getpt, antenna) |
---|
| 183 | self._fill(filename, unit, average) |
---|
[1586] | 184 | self.parallactify(parallactify) |
---|
[1259] | 185 | self._add_history("scantable", varlist) |
---|
[102] | 186 | |
---|
[1862] | 187 | @asaplog_post_dec |
---|
[876] | 188 | def save(self, name=None, format=None, overwrite=False): |
---|
[1846] | 189 | """\ |
---|
[1280] | 190 | Store the scantable on disk. This can be an asap (aips++) Table, |
---|
| 191 | SDFITS or MS2 format. |
---|
[1846] | 192 | |
---|
[116] | 193 | Parameters: |
---|
[1846] | 194 | |
---|
[1093] | 195 | name: the name of the outputfile. For format "ASCII" |
---|
| 196 | this is the root file name (data in 'name'.txt |
---|
[497] | 197 | and header in 'name'_header.txt) |
---|
[1855] | 198 | |
---|
[116] | 199 | format: an optional file format. Default is ASAP. |
---|
[1855] | 200 | Allowed are: |
---|
| 201 | |
---|
| 202 | * 'ASAP' (save as ASAP [aips++] Table), |
---|
| 203 | * 'SDFITS' (save as SDFITS file) |
---|
| 204 | * 'ASCII' (saves as ascii text file) |
---|
| 205 | * 'MS2' (saves as an casacore MeasurementSet V2) |
---|
| 206 | * 'FITS' (save as image FITS - not readable by class) |
---|
| 207 | * 'CLASS' (save as FITS readable by CLASS) |
---|
| 208 | |
---|
[411] | 209 | overwrite: If the file should be overwritten if it exists. |
---|
[256] | 210 | The default False is to return with warning |
---|
[411] | 211 | without writing the output. USE WITH CARE. |
---|
[1855] | 212 | |
---|
[1846] | 213 | Example:: |
---|
| 214 | |
---|
[116] | 215 | scan.save('myscan.asap') |
---|
[1118] | 216 | scan.save('myscan.sdfits', 'SDFITS') |
---|
[1846] | 217 | |
---|
[116] | 218 | """ |
---|
[411] | 219 | from os import path |
---|
[1593] | 220 | format = format or rcParams['scantable.save'] |
---|
[256] | 221 | suffix = '.'+format.lower() |
---|
[1118] | 222 | if name is None or name == "": |
---|
[256] | 223 | name = 'scantable'+suffix |
---|
[718] | 224 | msg = "No filename given. Using default name %s..." % name |
---|
| 225 | asaplog.push(msg) |
---|
[411] | 226 | name = path.expandvars(name) |
---|
[256] | 227 | if path.isfile(name) or path.isdir(name): |
---|
| 228 | if not overwrite: |
---|
[718] | 229 | msg = "File %s exists." % name |
---|
[1859] | 230 | raise IOError(msg) |
---|
[451] | 231 | format2 = format.upper() |
---|
| 232 | if format2 == 'ASAP': |
---|
[116] | 233 | self._save(name) |
---|
| 234 | else: |
---|
[989] | 235 | from asap._asap import stwriter as stw |
---|
[1118] | 236 | writer = stw(format2) |
---|
| 237 | writer.write(self, name) |
---|
[116] | 238 | return |
---|
| 239 | |
---|
[102] | 240 | def copy(self): |
---|
[1846] | 241 | """Return a copy of this scantable. |
---|
| 242 | |
---|
| 243 | *Note*: |
---|
| 244 | |
---|
[1348] | 245 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
---|
[1846] | 246 | |
---|
| 247 | Example:: |
---|
| 248 | |
---|
[102] | 249 | copiedscan = scan.copy() |
---|
[1846] | 250 | |
---|
[102] | 251 | """ |
---|
[876] | 252 | sd = scantable(Scantable._copy(self)) |
---|
[113] | 253 | return sd |
---|
| 254 | |
---|
[1093] | 255 | def drop_scan(self, scanid=None): |
---|
[1846] | 256 | """\ |
---|
[1093] | 257 | Return a new scantable where the specified scan number(s) has(have) |
---|
| 258 | been dropped. |
---|
[1846] | 259 | |
---|
[1093] | 260 | Parameters: |
---|
[1846] | 261 | |
---|
[1093] | 262 | scanid: a (list of) scan number(s) |
---|
[1846] | 263 | |
---|
[1093] | 264 | """ |
---|
| 265 | from asap import _is_sequence_or_number as _is_valid |
---|
| 266 | from asap import _to_list |
---|
| 267 | from asap import unique |
---|
| 268 | if not _is_valid(scanid): |
---|
[1859] | 269 | raise RuntimeError( 'Please specify a scanno to drop from the scantable' ) |
---|
| 270 | scanid = _to_list(scanid) |
---|
| 271 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
---|
| 272 | for sid in scanid: allscans.remove(sid) |
---|
| 273 | if len(allscans) == 0: |
---|
| 274 | raise ValueError("Can't remove all scans") |
---|
| 275 | sel = selector(scans=allscans) |
---|
| 276 | return self._select_copy(sel) |
---|
[1093] | 277 | |
---|
[1594] | 278 | def _select_copy(self, selection): |
---|
| 279 | orig = self.get_selection() |
---|
| 280 | self.set_selection(orig+selection) |
---|
| 281 | cp = self.copy() |
---|
| 282 | self.set_selection(orig) |
---|
| 283 | return cp |
---|
| 284 | |
---|
[102] | 285 | def get_scan(self, scanid=None): |
---|
[1855] | 286 | """\ |
---|
[102] | 287 | Return a specific scan (by scanno) or collection of scans (by |
---|
| 288 | source name) in a new scantable. |
---|
[1846] | 289 | |
---|
| 290 | *Note*: |
---|
| 291 | |
---|
[1348] | 292 | See scantable.drop_scan() for the inverse operation. |
---|
[1846] | 293 | |
---|
[102] | 294 | Parameters: |
---|
[1846] | 295 | |
---|
[513] | 296 | scanid: a (list of) scanno or a source name, unix-style |
---|
| 297 | patterns are accepted for source name matching, e.g. |
---|
| 298 | '*_R' gets all 'ref scans |
---|
[1846] | 299 | |
---|
| 300 | Example:: |
---|
| 301 | |
---|
[513] | 302 | # get all scans containing the source '323p459' |
---|
| 303 | newscan = scan.get_scan('323p459') |
---|
| 304 | # get all 'off' scans |
---|
| 305 | refscans = scan.get_scan('*_R') |
---|
| 306 | # get a susbset of scans by scanno (as listed in scan.summary()) |
---|
[1118] | 307 | newscan = scan.get_scan([0, 2, 7, 10]) |
---|
[1846] | 308 | |
---|
[102] | 309 | """ |
---|
| 310 | if scanid is None: |
---|
[1859] | 311 | raise RuntimeError( 'Please specify a scan no or name to ' |
---|
| 312 | 'retrieve from the scantable' ) |
---|
[102] | 313 | try: |
---|
[946] | 314 | bsel = self.get_selection() |
---|
| 315 | sel = selector() |
---|
[102] | 316 | if type(scanid) is str: |
---|
[946] | 317 | sel.set_name(scanid) |
---|
[1594] | 318 | return self._select_copy(sel) |
---|
[102] | 319 | elif type(scanid) is int: |
---|
[946] | 320 | sel.set_scans([scanid]) |
---|
[1594] | 321 | return self._select_copy(sel) |
---|
[381] | 322 | elif type(scanid) is list: |
---|
[946] | 323 | sel.set_scans(scanid) |
---|
[1594] | 324 | return self._select_copy(sel) |
---|
[381] | 325 | else: |
---|
[718] | 326 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
---|
[1859] | 327 | raise TypeError(msg) |
---|
[102] | 328 | except RuntimeError: |
---|
[1859] | 329 | raise |
---|
[102] | 330 | |
---|
| 331 | def __str__(self): |
---|
[1118] | 332 | return Scantable._summary(self, True) |
---|
[102] | 333 | |
---|
[976] | 334 | def summary(self, filename=None): |
---|
[1846] | 335 | """\ |
---|
[102] | 336 | Print a summary of the contents of this scantable. |
---|
[1846] | 337 | |
---|
[102] | 338 | Parameters: |
---|
[1846] | 339 | |
---|
[1931] | 340 | filename: the name of a file to write the putput to |
---|
[102] | 341 | Default - no file output |
---|
[1846] | 342 | |
---|
[102] | 343 | """ |
---|
[976] | 344 | info = Scantable._summary(self, True) |
---|
[102] | 345 | if filename is not None: |
---|
[256] | 346 | if filename is "": |
---|
| 347 | filename = 'scantable_summary.txt' |
---|
[415] | 348 | from os.path import expandvars, isdir |
---|
[411] | 349 | filename = expandvars(filename) |
---|
[415] | 350 | if not isdir(filename): |
---|
[413] | 351 | data = open(filename, 'w') |
---|
| 352 | data.write(info) |
---|
| 353 | data.close() |
---|
| 354 | else: |
---|
[718] | 355 | msg = "Illegal file name '%s'." % (filename) |
---|
[1859] | 356 | raise IOError(msg) |
---|
| 357 | return page(info) |
---|
[710] | 358 | |
---|
[1512] | 359 | def get_spectrum(self, rowno): |
---|
[1471] | 360 | """Return the spectrum for the current row in the scantable as a list. |
---|
[1846] | 361 | |
---|
[1471] | 362 | Parameters: |
---|
[1846] | 363 | |
---|
[1573] | 364 | rowno: the row number to retrieve the spectrum from |
---|
[1846] | 365 | |
---|
[1471] | 366 | """ |
---|
| 367 | return self._getspectrum(rowno) |
---|
[946] | 368 | |
---|
[1471] | 369 | def get_mask(self, rowno): |
---|
| 370 | """Return the mask for the current row in the scantable as a list. |
---|
[1846] | 371 | |
---|
[1471] | 372 | Parameters: |
---|
[1846] | 373 | |
---|
[1573] | 374 | rowno: the row number to retrieve the mask from |
---|
[1846] | 375 | |
---|
[1471] | 376 | """ |
---|
| 377 | return self._getmask(rowno) |
---|
| 378 | |
---|
| 379 | def set_spectrum(self, spec, rowno): |
---|
[1938] | 380 | """Set the spectrum for the current row in the scantable. |
---|
[1846] | 381 | |
---|
[1471] | 382 | Parameters: |
---|
[1846] | 383 | |
---|
[1855] | 384 | spec: the new spectrum |
---|
[1846] | 385 | |
---|
[1855] | 386 | rowno: the row number to set the spectrum for |
---|
| 387 | |
---|
[1471] | 388 | """ |
---|
| 389 | assert(len(spec) == self.nchan()) |
---|
| 390 | return self._setspectrum(spec, rowno) |
---|
| 391 | |
---|
[1600] | 392 | def get_coordinate(self, rowno): |
---|
| 393 | """Return the (spectral) coordinate for a a given 'rowno'. |
---|
[1846] | 394 | |
---|
| 395 | *Note*: |
---|
| 396 | |
---|
[1600] | 397 | * This coordinate is only valid until a scantable method modifies |
---|
| 398 | the frequency axis. |
---|
| 399 | * This coordinate does contain the original frequency set-up |
---|
| 400 | NOT the new frame. The conversions however are done using the user |
---|
| 401 | specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate, |
---|
| 402 | use scantable.freq_align first. Without it there is no closure, |
---|
[1846] | 403 | i.e.:: |
---|
[1600] | 404 | |
---|
[1846] | 405 | c = myscan.get_coordinate(0) |
---|
| 406 | c.to_frequency(c.get_reference_pixel()) != c.get_reference_value() |
---|
| 407 | |
---|
[1600] | 408 | Parameters: |
---|
[1846] | 409 | |
---|
[1600] | 410 | rowno: the row number for the spectral coordinate |
---|
| 411 | |
---|
| 412 | """ |
---|
| 413 | return coordinate(Scantable.get_coordinate(self, rowno)) |
---|
| 414 | |
---|
[946] | 415 | def get_selection(self): |
---|
[1846] | 416 | """\ |
---|
[1005] | 417 | Get the selection object currently set on this scantable. |
---|
[1846] | 418 | |
---|
| 419 | Example:: |
---|
| 420 | |
---|
[1005] | 421 | sel = scan.get_selection() |
---|
| 422 | sel.set_ifs(0) # select IF 0 |
---|
| 423 | scan.set_selection(sel) # apply modified selection |
---|
[1846] | 424 | |
---|
[946] | 425 | """ |
---|
| 426 | return selector(self._getselection()) |
---|
| 427 | |
---|
[1576] | 428 | def set_selection(self, selection=None, **kw): |
---|
[1846] | 429 | """\ |
---|
[1005] | 430 | Select a subset of the data. All following operations on this scantable |
---|
| 431 | are only applied to thi selection. |
---|
[1846] | 432 | |
---|
[1005] | 433 | Parameters: |
---|
[1697] | 434 | |
---|
[1846] | 435 | selection: a selector object (default unset the selection), or |
---|
| 436 | any combination of "pols", "ifs", "beams", "scans", |
---|
| 437 | "cycles", "name", "query" |
---|
[1697] | 438 | |
---|
[1846] | 439 | Examples:: |
---|
[1697] | 440 | |
---|
[1005] | 441 | sel = selector() # create a selection object |
---|
[1118] | 442 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
---|
[1005] | 443 | scan.set_selection(sel) # set the selection |
---|
| 444 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 445 | scan.set_selection() # unset the selection |
---|
[1697] | 446 | # or the equivalent |
---|
| 447 | scan.set_selection(scans=[0,3]) |
---|
| 448 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 449 | scan.set_selection() # unset the selection |
---|
[1846] | 450 | |
---|
[946] | 451 | """ |
---|
[1576] | 452 | if selection is None: |
---|
| 453 | # reset |
---|
| 454 | if len(kw) == 0: |
---|
| 455 | selection = selector() |
---|
| 456 | else: |
---|
| 457 | # try keywords |
---|
| 458 | for k in kw: |
---|
| 459 | if k not in selector.fields: |
---|
| 460 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields)) |
---|
| 461 | selection = selector(**kw) |
---|
[946] | 462 | self._setselection(selection) |
---|
| 463 | |
---|
[1819] | 464 | def get_row(self, row=0, insitu=None): |
---|
[1846] | 465 | """\ |
---|
[1819] | 466 | Select a row in the scantable. |
---|
| 467 | Return a scantable with single row. |
---|
[1846] | 468 | |
---|
[1819] | 469 | Parameters: |
---|
[1846] | 470 | |
---|
| 471 | row: row no of integration, default is 0. |
---|
| 472 | insitu: if False a new scantable is returned. Otherwise, the |
---|
| 473 | scaling is done in-situ. The default is taken from .asaprc |
---|
| 474 | (False) |
---|
| 475 | |
---|
[1819] | 476 | """ |
---|
| 477 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 478 | if not insitu: |
---|
| 479 | workscan = self.copy() |
---|
| 480 | else: |
---|
| 481 | workscan = self |
---|
| 482 | # Select a row |
---|
| 483 | sel=selector() |
---|
[1992] | 484 | sel.set_rows([row]) |
---|
| 485 | #sel.set_scans([workscan.getscan(row)]) |
---|
| 486 | #sel.set_cycles([workscan.getcycle(row)]) |
---|
| 487 | #sel.set_beams([workscan.getbeam(row)]) |
---|
| 488 | #sel.set_ifs([workscan.getif(row)]) |
---|
| 489 | #sel.set_polarisations([workscan.getpol(row)]) |
---|
| 490 | #sel.set_name(workscan._getsourcename(row)) |
---|
[1819] | 491 | workscan.set_selection(sel) |
---|
| 492 | if not workscan.nrow() == 1: |
---|
| 493 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow()) |
---|
| 494 | raise RuntimeError(msg) |
---|
| 495 | del sel |
---|
| 496 | if insitu: |
---|
| 497 | self._assign(workscan) |
---|
| 498 | else: |
---|
| 499 | return workscan |
---|
| 500 | |
---|
[1862] | 501 | @asaplog_post_dec |
---|
[1907] | 502 | def stats(self, stat='stddev', mask=None, form='3.3f', row=None): |
---|
[1846] | 503 | """\ |
---|
[135] | 504 | Determine the specified statistic of the current beam/if/pol |
---|
[102] | 505 | Takes a 'mask' as an optional parameter to specify which |
---|
| 506 | channels should be excluded. |
---|
[1846] | 507 | |
---|
[102] | 508 | Parameters: |
---|
[1846] | 509 | |
---|
[1819] | 510 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum', |
---|
| 511 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
[1855] | 512 | |
---|
[135] | 513 | mask: an optional mask specifying where the statistic |
---|
[102] | 514 | should be determined. |
---|
[1855] | 515 | |
---|
[1819] | 516 | form: format string to print statistic values |
---|
[1846] | 517 | |
---|
[1907] | 518 | row: row number of spectrum to process. |
---|
| 519 | (default is None: for all rows) |
---|
[1846] | 520 | |
---|
[1907] | 521 | Example: |
---|
[113] | 522 | scan.set_unit('channel') |
---|
[1118] | 523 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 524 | scan.stats(stat='mean', mask=m) |
---|
[1846] | 525 | |
---|
[102] | 526 | """ |
---|
[1593] | 527 | mask = mask or [] |
---|
[876] | 528 | if not self._check_ifs(): |
---|
[1118] | 529 | raise ValueError("Cannot apply mask as the IFs have different " |
---|
| 530 | "number of channels. Please use setselection() " |
---|
| 531 | "to select individual IFs") |
---|
[1819] | 532 | rtnabc = False |
---|
| 533 | if stat.lower().endswith('_abc'): rtnabc = True |
---|
| 534 | getchan = False |
---|
| 535 | if stat.lower().startswith('min') or stat.lower().startswith('max'): |
---|
| 536 | chan = self._math._minmaxchan(self, mask, stat) |
---|
| 537 | getchan = True |
---|
| 538 | statvals = [] |
---|
[1907] | 539 | if not rtnabc: |
---|
| 540 | if row == None: |
---|
| 541 | statvals = self._math._stats(self, mask, stat) |
---|
| 542 | else: |
---|
| 543 | statvals = self._math._statsrow(self, mask, stat, int(row)) |
---|
[256] | 544 | |
---|
[1819] | 545 | #def cb(i): |
---|
| 546 | # return statvals[i] |
---|
[256] | 547 | |
---|
[1819] | 548 | #return self._row_callback(cb, stat) |
---|
[102] | 549 | |
---|
[1819] | 550 | label=stat |
---|
| 551 | #callback=cb |
---|
| 552 | out = "" |
---|
| 553 | #outvec = [] |
---|
| 554 | sep = '-'*50 |
---|
[1907] | 555 | |
---|
| 556 | if row == None: |
---|
| 557 | rows = xrange(self.nrow()) |
---|
| 558 | elif isinstance(row, int): |
---|
| 559 | rows = [ row ] |
---|
| 560 | |
---|
| 561 | for i in rows: |
---|
[1819] | 562 | refstr = '' |
---|
| 563 | statunit= '' |
---|
| 564 | if getchan: |
---|
| 565 | qx, qy = self.chan2data(rowno=i, chan=chan[i]) |
---|
| 566 | if rtnabc: |
---|
| 567 | statvals.append(qx['value']) |
---|
| 568 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])' |
---|
| 569 | statunit= '['+qx['unit']+']' |
---|
| 570 | else: |
---|
| 571 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])' |
---|
| 572 | |
---|
| 573 | tm = self._gettime(i) |
---|
| 574 | src = self._getsourcename(i) |
---|
| 575 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
| 576 | out += 'Time[%s]:\n' % (tm) |
---|
[1907] | 577 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 578 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 579 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
[1819] | 580 | #outvec.append(callback(i)) |
---|
[1907] | 581 | if len(rows) > 1: |
---|
| 582 | # out += ('= %'+form) % (outvec[i]) +' '+refstr+'\n' |
---|
| 583 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n' |
---|
| 584 | else: |
---|
| 585 | # out += ('= %'+form) % (outvec[0]) +' '+refstr+'\n' |
---|
| 586 | out += ('= %'+form) % (statvals[0]) +' '+refstr+'\n' |
---|
[1819] | 587 | out += sep+"\n" |
---|
| 588 | |
---|
[1859] | 589 | import os |
---|
| 590 | if os.environ.has_key( 'USER' ): |
---|
| 591 | usr = os.environ['USER'] |
---|
| 592 | else: |
---|
| 593 | import commands |
---|
| 594 | usr = commands.getoutput( 'whoami' ) |
---|
| 595 | tmpfile = '/tmp/tmp_'+usr+'_casapy_asap_scantable_stats' |
---|
| 596 | f = open(tmpfile,'w') |
---|
| 597 | print >> f, sep |
---|
| 598 | print >> f, ' %s %s' % (label, statunit) |
---|
| 599 | print >> f, sep |
---|
| 600 | print >> f, out |
---|
| 601 | f.close() |
---|
| 602 | f = open(tmpfile,'r') |
---|
| 603 | x = f.readlines() |
---|
| 604 | f.close() |
---|
| 605 | asaplog.push(''.join(x), False) |
---|
| 606 | |
---|
[1819] | 607 | return statvals |
---|
| 608 | |
---|
| 609 | def chan2data(self, rowno=0, chan=0): |
---|
[1846] | 610 | """\ |
---|
[1819] | 611 | Returns channel/frequency/velocity and spectral value |
---|
| 612 | at an arbitrary row and channel in the scantable. |
---|
[1846] | 613 | |
---|
[1819] | 614 | Parameters: |
---|
[1846] | 615 | |
---|
[1819] | 616 | rowno: a row number in the scantable. Default is the |
---|
| 617 | first row, i.e. rowno=0 |
---|
[1855] | 618 | |
---|
[1819] | 619 | chan: a channel in the scantable. Default is the first |
---|
| 620 | channel, i.e. pos=0 |
---|
[1846] | 621 | |
---|
[1819] | 622 | """ |
---|
| 623 | if isinstance(rowno, int) and isinstance(chan, int): |
---|
| 624 | qx = {'unit': self.get_unit(), |
---|
| 625 | 'value': self._getabcissa(rowno)[chan]} |
---|
| 626 | qy = {'unit': self.get_fluxunit(), |
---|
| 627 | 'value': self._getspectrum(rowno)[chan]} |
---|
| 628 | return qx, qy |
---|
| 629 | |
---|
[1118] | 630 | def stddev(self, mask=None): |
---|
[1846] | 631 | """\ |
---|
[135] | 632 | Determine the standard deviation of the current beam/if/pol |
---|
| 633 | Takes a 'mask' as an optional parameter to specify which |
---|
| 634 | channels should be excluded. |
---|
[1846] | 635 | |
---|
[135] | 636 | Parameters: |
---|
[1846] | 637 | |
---|
[135] | 638 | mask: an optional mask specifying where the standard |
---|
| 639 | deviation should be determined. |
---|
| 640 | |
---|
[1846] | 641 | Example:: |
---|
| 642 | |
---|
[135] | 643 | scan.set_unit('channel') |
---|
[1118] | 644 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 645 | scan.stddev(mask=m) |
---|
[1846] | 646 | |
---|
[135] | 647 | """ |
---|
[1118] | 648 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 649 | |
---|
[1003] | 650 | |
---|
[1259] | 651 | def get_column_names(self): |
---|
[1846] | 652 | """\ |
---|
[1003] | 653 | Return a list of column names, which can be used for selection. |
---|
| 654 | """ |
---|
[1259] | 655 | return list(Scantable.get_column_names(self)) |
---|
[1003] | 656 | |
---|
[1730] | 657 | def get_tsys(self, row=-1): |
---|
[1846] | 658 | """\ |
---|
[113] | 659 | Return the System temperatures. |
---|
[1846] | 660 | |
---|
| 661 | Parameters: |
---|
| 662 | |
---|
| 663 | row: the rowno to get the information for. (default all rows) |
---|
| 664 | |
---|
[113] | 665 | Returns: |
---|
[1846] | 666 | |
---|
[876] | 667 | a list of Tsys values for the current selection |
---|
[1846] | 668 | |
---|
[113] | 669 | """ |
---|
[1730] | 670 | if row > -1: |
---|
| 671 | return self._get_column(self._gettsys, row) |
---|
[876] | 672 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 673 | |
---|
[1730] | 674 | |
---|
| 675 | def get_weather(self, row=-1): |
---|
[1846] | 676 | """\ |
---|
| 677 | Return the weather informations. |
---|
| 678 | |
---|
| 679 | Parameters: |
---|
| 680 | |
---|
| 681 | row: the rowno to get the information for. (default all rows) |
---|
| 682 | |
---|
| 683 | Returns: |
---|
| 684 | |
---|
| 685 | a dict or list of of dicts of values for the current selection |
---|
| 686 | |
---|
| 687 | """ |
---|
| 688 | |
---|
[1730] | 689 | values = self._get_column(self._get_weather, row) |
---|
| 690 | if row > -1: |
---|
| 691 | return {'temperature': values[0], |
---|
| 692 | 'pressure': values[1], 'humidity' : values[2], |
---|
| 693 | 'windspeed' : values[3], 'windaz' : values[4] |
---|
| 694 | } |
---|
| 695 | else: |
---|
| 696 | out = [] |
---|
| 697 | for r in values: |
---|
| 698 | |
---|
| 699 | out.append({'temperature': r[0], |
---|
| 700 | 'pressure': r[1], 'humidity' : r[2], |
---|
| 701 | 'windspeed' : r[3], 'windaz' : r[4] |
---|
| 702 | }) |
---|
| 703 | return out |
---|
| 704 | |
---|
[876] | 705 | def _row_callback(self, callback, label): |
---|
| 706 | out = "" |
---|
[1118] | 707 | outvec = [] |
---|
[1590] | 708 | sep = '-'*50 |
---|
[876] | 709 | for i in range(self.nrow()): |
---|
| 710 | tm = self._gettime(i) |
---|
| 711 | src = self._getsourcename(i) |
---|
[1590] | 712 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
[876] | 713 | out += 'Time[%s]:\n' % (tm) |
---|
[1590] | 714 | if self.nbeam(-1) > 1: |
---|
| 715 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 716 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 717 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
[876] | 718 | outvec.append(callback(i)) |
---|
| 719 | out += '= %3.3f\n' % (outvec[i]) |
---|
[1590] | 720 | out += sep+'\n' |
---|
[1859] | 721 | |
---|
| 722 | asaplog.push(sep) |
---|
| 723 | asaplog.push(" %s" % (label)) |
---|
| 724 | asaplog.push(sep) |
---|
| 725 | asaplog.push(out) |
---|
[1861] | 726 | asaplog.post() |
---|
[1175] | 727 | return outvec |
---|
[256] | 728 | |
---|
[1947] | 729 | def _get_column(self, callback, row=-1, *args): |
---|
[1070] | 730 | """ |
---|
| 731 | """ |
---|
| 732 | if row == -1: |
---|
[1947] | 733 | return [callback(i, *args) for i in range(self.nrow())] |
---|
[1070] | 734 | else: |
---|
[1819] | 735 | if 0 <= row < self.nrow(): |
---|
[1947] | 736 | return callback(row, *args) |
---|
[256] | 737 | |
---|
[1070] | 738 | |
---|
[1948] | 739 | def get_time(self, row=-1, asdatetime=False, prec=-1): |
---|
[1846] | 740 | """\ |
---|
[113] | 741 | Get a list of time stamps for the observations. |
---|
[1938] | 742 | Return a datetime object or a string (default) for each |
---|
| 743 | integration time stamp in the scantable. |
---|
[1846] | 744 | |
---|
[113] | 745 | Parameters: |
---|
[1846] | 746 | |
---|
[1348] | 747 | row: row no of integration. Default -1 return all rows |
---|
[1855] | 748 | |
---|
[1348] | 749 | asdatetime: return values as datetime objects rather than strings |
---|
[1846] | 750 | |
---|
[1948] | 751 | prec: number of digits shown. Default -1 to automatic calculation. |
---|
| 752 | Note this number is equals to the digits of MVTime, |
---|
| 753 | i.e., 0<prec<3: dates with hh:: only, |
---|
| 754 | <5: with hh:mm:, <7 or 0: with hh:mm:ss, |
---|
[1947] | 755 | and 6> : with hh:mm:ss.tt... (prec-6 t's added) |
---|
| 756 | |
---|
[113] | 757 | """ |
---|
[1175] | 758 | from datetime import datetime |
---|
[1948] | 759 | if prec < 0: |
---|
| 760 | # automagically set necessary precision +1 |
---|
[1950] | 761 | prec = 7 - numpy.floor(numpy.log10(numpy.min(self.get_inttime(row)))) |
---|
[1948] | 762 | prec = max(6, int(prec)) |
---|
| 763 | else: |
---|
| 764 | prec = max(0, prec) |
---|
| 765 | if asdatetime: |
---|
| 766 | #precision can be 1 millisecond at max |
---|
| 767 | prec = min(12, prec) |
---|
| 768 | |
---|
[1947] | 769 | times = self._get_column(self._gettime, row, prec) |
---|
[1348] | 770 | if not asdatetime: |
---|
[1392] | 771 | return times |
---|
[1947] | 772 | format = "%Y/%m/%d/%H:%M:%S.%f" |
---|
| 773 | if prec < 7: |
---|
| 774 | nsub = 1 + (((6-prec)/2) % 3) |
---|
| 775 | substr = [".%f","%S","%M"] |
---|
| 776 | for i in range(nsub): |
---|
| 777 | format = format.replace(substr[i],"") |
---|
[1175] | 778 | if isinstance(times, list): |
---|
[1947] | 779 | return [datetime.strptime(i, format) for i in times] |
---|
[1175] | 780 | else: |
---|
[1947] | 781 | return datetime.strptime(times, format) |
---|
[102] | 782 | |
---|
[1348] | 783 | |
---|
| 784 | def get_inttime(self, row=-1): |
---|
[1846] | 785 | """\ |
---|
[1348] | 786 | Get a list of integration times for the observations. |
---|
| 787 | Return a time in seconds for each integration in the scantable. |
---|
[1846] | 788 | |
---|
[1348] | 789 | Parameters: |
---|
[1846] | 790 | |
---|
[1348] | 791 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 792 | |
---|
[1348] | 793 | """ |
---|
[1573] | 794 | return self._get_column(self._getinttime, row) |
---|
[1348] | 795 | |
---|
[1573] | 796 | |
---|
[714] | 797 | def get_sourcename(self, row=-1): |
---|
[1846] | 798 | """\ |
---|
[794] | 799 | Get a list source names for the observations. |
---|
[714] | 800 | Return a string for each integration in the scantable. |
---|
| 801 | Parameters: |
---|
[1846] | 802 | |
---|
[1348] | 803 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 804 | |
---|
[714] | 805 | """ |
---|
[1070] | 806 | return self._get_column(self._getsourcename, row) |
---|
[714] | 807 | |
---|
[794] | 808 | def get_elevation(self, row=-1): |
---|
[1846] | 809 | """\ |
---|
[794] | 810 | Get a list of elevations for the observations. |
---|
| 811 | Return a float for each integration in the scantable. |
---|
[1846] | 812 | |
---|
[794] | 813 | Parameters: |
---|
[1846] | 814 | |
---|
[1348] | 815 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 816 | |
---|
[794] | 817 | """ |
---|
[1070] | 818 | return self._get_column(self._getelevation, row) |
---|
[794] | 819 | |
---|
| 820 | def get_azimuth(self, row=-1): |
---|
[1846] | 821 | """\ |
---|
[794] | 822 | Get a list of azimuths for the observations. |
---|
| 823 | Return a float for each integration in the scantable. |
---|
[1846] | 824 | |
---|
[794] | 825 | Parameters: |
---|
[1348] | 826 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 827 | |
---|
[794] | 828 | """ |
---|
[1070] | 829 | return self._get_column(self._getazimuth, row) |
---|
[794] | 830 | |
---|
| 831 | def get_parangle(self, row=-1): |
---|
[1846] | 832 | """\ |
---|
[794] | 833 | Get a list of parallactic angles for the observations. |
---|
| 834 | Return a float for each integration in the scantable. |
---|
[1846] | 835 | |
---|
[794] | 836 | Parameters: |
---|
[1846] | 837 | |
---|
[1348] | 838 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 839 | |
---|
[794] | 840 | """ |
---|
[1070] | 841 | return self._get_column(self._getparangle, row) |
---|
[794] | 842 | |
---|
[1070] | 843 | def get_direction(self, row=-1): |
---|
| 844 | """ |
---|
| 845 | Get a list of Positions on the sky (direction) for the observations. |
---|
[1594] | 846 | Return a string for each integration in the scantable. |
---|
[1855] | 847 | |
---|
[1070] | 848 | Parameters: |
---|
[1855] | 849 | |
---|
[1070] | 850 | row: row no of integration. Default -1 return all rows |
---|
[1855] | 851 | |
---|
[1070] | 852 | """ |
---|
| 853 | return self._get_column(self._getdirection, row) |
---|
| 854 | |
---|
[1391] | 855 | def get_directionval(self, row=-1): |
---|
[1846] | 856 | """\ |
---|
[1391] | 857 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 858 | Return a float for each integration in the scantable. |
---|
[1846] | 859 | |
---|
[1391] | 860 | Parameters: |
---|
[1846] | 861 | |
---|
[1391] | 862 | row: row no of integration. Default -1 return all rows |
---|
[1846] | 863 | |
---|
[1391] | 864 | """ |
---|
| 865 | return self._get_column(self._getdirectionvec, row) |
---|
| 866 | |
---|
[1862] | 867 | @asaplog_post_dec |
---|
[102] | 868 | def set_unit(self, unit='channel'): |
---|
[1846] | 869 | """\ |
---|
[102] | 870 | Set the unit for all following operations on this scantable |
---|
[1846] | 871 | |
---|
[102] | 872 | Parameters: |
---|
[1846] | 873 | |
---|
| 874 | unit: optional unit, default is 'channel'. Use one of '*Hz', |
---|
| 875 | 'km/s', 'channel' or equivalent '' |
---|
| 876 | |
---|
[102] | 877 | """ |
---|
[484] | 878 | varlist = vars() |
---|
[1118] | 879 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 880 | unit = '' |
---|
| 881 | inf = list(self._getcoordinfo()) |
---|
| 882 | inf[0] = unit |
---|
| 883 | self._setcoordinfo(inf) |
---|
[1118] | 884 | self._add_history("set_unit", varlist) |
---|
[113] | 885 | |
---|
[1862] | 886 | @asaplog_post_dec |
---|
[484] | 887 | def set_instrument(self, instr): |
---|
[1846] | 888 | """\ |
---|
[1348] | 889 | Set the instrument for subsequent processing. |
---|
[1846] | 890 | |
---|
[358] | 891 | Parameters: |
---|
[1846] | 892 | |
---|
[710] | 893 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 894 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[1846] | 895 | |
---|
[358] | 896 | """ |
---|
| 897 | self._setInstrument(instr) |
---|
[1118] | 898 | self._add_history("set_instument", vars()) |
---|
[358] | 899 | |
---|
[1862] | 900 | @asaplog_post_dec |
---|
[1190] | 901 | def set_feedtype(self, feedtype): |
---|
[1846] | 902 | """\ |
---|
[1190] | 903 | Overwrite the feed type, which might not be set correctly. |
---|
[1846] | 904 | |
---|
[1190] | 905 | Parameters: |
---|
[1846] | 906 | |
---|
[1190] | 907 | feedtype: 'linear' or 'circular' |
---|
[1846] | 908 | |
---|
[1190] | 909 | """ |
---|
| 910 | self._setfeedtype(feedtype) |
---|
| 911 | self._add_history("set_feedtype", vars()) |
---|
| 912 | |
---|
[1862] | 913 | @asaplog_post_dec |
---|
[276] | 914 | def set_doppler(self, doppler='RADIO'): |
---|
[1846] | 915 | """\ |
---|
[276] | 916 | Set the doppler for all following operations on this scantable. |
---|
[1846] | 917 | |
---|
[276] | 918 | Parameters: |
---|
[1846] | 919 | |
---|
[276] | 920 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
[1846] | 921 | |
---|
[276] | 922 | """ |
---|
[484] | 923 | varlist = vars() |
---|
[276] | 924 | inf = list(self._getcoordinfo()) |
---|
| 925 | inf[2] = doppler |
---|
| 926 | self._setcoordinfo(inf) |
---|
[1118] | 927 | self._add_history("set_doppler", vars()) |
---|
[710] | 928 | |
---|
[1862] | 929 | @asaplog_post_dec |
---|
[226] | 930 | def set_freqframe(self, frame=None): |
---|
[1846] | 931 | """\ |
---|
[113] | 932 | Set the frame type of the Spectral Axis. |
---|
[1846] | 933 | |
---|
[113] | 934 | Parameters: |
---|
[1846] | 935 | |
---|
[591] | 936 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1819] | 937 | 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
[1118] | 938 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[1846] | 939 | |
---|
| 940 | Example:: |
---|
| 941 | |
---|
[113] | 942 | scan.set_freqframe('BARY') |
---|
[1846] | 943 | |
---|
[113] | 944 | """ |
---|
[1593] | 945 | frame = frame or rcParams['scantable.freqframe'] |
---|
[484] | 946 | varlist = vars() |
---|
[1819] | 947 | # "REST" is not implemented in casacore |
---|
| 948 | #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 949 | # 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
| 950 | valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
[1118] | 951 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 952 | |
---|
[989] | 953 | if frame in valid: |
---|
[113] | 954 | inf = list(self._getcoordinfo()) |
---|
| 955 | inf[1] = frame |
---|
| 956 | self._setcoordinfo(inf) |
---|
[1118] | 957 | self._add_history("set_freqframe", varlist) |
---|
[102] | 958 | else: |
---|
[1118] | 959 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[1859] | 960 | raise TypeError(msg) |
---|
[710] | 961 | |
---|
[1862] | 962 | @asaplog_post_dec |
---|
[989] | 963 | def set_dirframe(self, frame=""): |
---|
[1846] | 964 | """\ |
---|
[989] | 965 | Set the frame type of the Direction on the sky. |
---|
[1846] | 966 | |
---|
[989] | 967 | Parameters: |
---|
[1846] | 968 | |
---|
[989] | 969 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 970 | 'J2000', 'B1950', 'GALACTIC' |
---|
[1846] | 971 | |
---|
| 972 | Example: |
---|
| 973 | |
---|
[989] | 974 | scan.set_dirframe('GALACTIC') |
---|
[1846] | 975 | |
---|
[989] | 976 | """ |
---|
| 977 | varlist = vars() |
---|
[1859] | 978 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 979 | self._add_history("set_dirframe", varlist) |
---|
[989] | 980 | |
---|
[113] | 981 | def get_unit(self): |
---|
[1846] | 982 | """\ |
---|
[113] | 983 | Get the default unit set in this scantable |
---|
[1846] | 984 | |
---|
[113] | 985 | Returns: |
---|
[1846] | 986 | |
---|
[113] | 987 | A unit string |
---|
[1846] | 988 | |
---|
[113] | 989 | """ |
---|
| 990 | inf = self._getcoordinfo() |
---|
| 991 | unit = inf[0] |
---|
| 992 | if unit == '': unit = 'channel' |
---|
| 993 | return unit |
---|
[102] | 994 | |
---|
[1862] | 995 | @asaplog_post_dec |
---|
[158] | 996 | def get_abcissa(self, rowno=0): |
---|
[1846] | 997 | """\ |
---|
[158] | 998 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 999 | selected Beam/IF/Pol |
---|
[1846] | 1000 | |
---|
[113] | 1001 | Parameters: |
---|
[1846] | 1002 | |
---|
[226] | 1003 | rowno: an optional row number in the scantable. Default is the |
---|
| 1004 | first row, i.e. rowno=0 |
---|
[1846] | 1005 | |
---|
[113] | 1006 | Returns: |
---|
[1846] | 1007 | |
---|
[1348] | 1008 | The abcissa values and the format string (as a dictionary) |
---|
[1846] | 1009 | |
---|
[113] | 1010 | """ |
---|
[256] | 1011 | abc = self._getabcissa(rowno) |
---|
[710] | 1012 | lbl = self._getabcissalabel(rowno) |
---|
[158] | 1013 | return abc, lbl |
---|
[113] | 1014 | |
---|
[1862] | 1015 | @asaplog_post_dec |
---|
[1819] | 1016 | def flag(self, mask=None, unflag=False): |
---|
[1846] | 1017 | """\ |
---|
[1001] | 1018 | Flag the selected data using an optional channel mask. |
---|
[1846] | 1019 | |
---|
[1001] | 1020 | Parameters: |
---|
[1846] | 1021 | |
---|
[1001] | 1022 | mask: an optional channel mask, created with create_mask. Default |
---|
| 1023 | (no mask) is all channels. |
---|
[1855] | 1024 | |
---|
[1819] | 1025 | unflag: if True, unflag the data |
---|
[1846] | 1026 | |
---|
[1001] | 1027 | """ |
---|
| 1028 | varlist = vars() |
---|
[1593] | 1029 | mask = mask or [] |
---|
[1859] | 1030 | self._flag(mask, unflag) |
---|
[1001] | 1031 | self._add_history("flag", varlist) |
---|
| 1032 | |
---|
[1862] | 1033 | @asaplog_post_dec |
---|
[1819] | 1034 | def flag_row(self, rows=[], unflag=False): |
---|
[1846] | 1035 | """\ |
---|
[1819] | 1036 | Flag the selected data in row-based manner. |
---|
[1846] | 1037 | |
---|
[1819] | 1038 | Parameters: |
---|
[1846] | 1039 | |
---|
[1843] | 1040 | rows: list of row numbers to be flagged. Default is no row |
---|
| 1041 | (must be explicitly specified to execute row-based flagging). |
---|
[1855] | 1042 | |
---|
[1819] | 1043 | unflag: if True, unflag the data. |
---|
[1846] | 1044 | |
---|
[1819] | 1045 | """ |
---|
| 1046 | varlist = vars() |
---|
[1859] | 1047 | self._flag_row(rows, unflag) |
---|
[1819] | 1048 | self._add_history("flag_row", varlist) |
---|
| 1049 | |
---|
[1862] | 1050 | @asaplog_post_dec |
---|
[1819] | 1051 | def clip(self, uthres=None, dthres=None, clipoutside=True, unflag=False): |
---|
[1846] | 1052 | """\ |
---|
[1819] | 1053 | Flag the selected data outside a specified range (in channel-base) |
---|
[1846] | 1054 | |
---|
[1819] | 1055 | Parameters: |
---|
[1846] | 1056 | |
---|
[1819] | 1057 | uthres: upper threshold. |
---|
[1855] | 1058 | |
---|
[1819] | 1059 | dthres: lower threshold |
---|
[1846] | 1060 | |
---|
[1819] | 1061 | clipoutside: True for flagging data outside the range [dthres:uthres]. |
---|
[1928] | 1062 | False for flagging data inside the range. |
---|
[1855] | 1063 | |
---|
[1846] | 1064 | unflag: if True, unflag the data. |
---|
| 1065 | |
---|
[1819] | 1066 | """ |
---|
| 1067 | varlist = vars() |
---|
[1859] | 1068 | self._clip(uthres, dthres, clipoutside, unflag) |
---|
[1819] | 1069 | self._add_history("clip", varlist) |
---|
| 1070 | |
---|
[1862] | 1071 | @asaplog_post_dec |
---|
[1584] | 1072 | def lag_flag(self, start, end, unit="MHz", insitu=None): |
---|
[1846] | 1073 | """\ |
---|
[1192] | 1074 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
[1584] | 1075 | Flagged data in the scantable gets interpolated over the region. |
---|
[1192] | 1076 | No taper is applied. |
---|
[1846] | 1077 | |
---|
[1192] | 1078 | Parameters: |
---|
[1846] | 1079 | |
---|
[1579] | 1080 | start: the start frequency (really a period within the |
---|
| 1081 | bandwidth) or period to remove |
---|
[1855] | 1082 | |
---|
[1579] | 1083 | end: the end frequency or period to remove |
---|
[1855] | 1084 | |
---|
[1584] | 1085 | unit: the frequency unit (default "MHz") or "" for |
---|
[1579] | 1086 | explicit lag channels |
---|
[1846] | 1087 | |
---|
| 1088 | *Notes*: |
---|
| 1089 | |
---|
[1579] | 1090 | It is recommended to flag edges of the band or strong |
---|
[1348] | 1091 | signals beforehand. |
---|
[1846] | 1092 | |
---|
[1192] | 1093 | """ |
---|
| 1094 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1095 | self._math._setinsitu(insitu) |
---|
| 1096 | varlist = vars() |
---|
[1579] | 1097 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.} |
---|
| 1098 | if not (unit == "" or base.has_key(unit)): |
---|
[1192] | 1099 | raise ValueError("%s is not a valid unit." % unit) |
---|
[1859] | 1100 | if unit == "": |
---|
| 1101 | s = scantable(self._math._lag_flag(self, start, end, "lags")) |
---|
| 1102 | else: |
---|
| 1103 | s = scantable(self._math._lag_flag(self, start*base[unit], |
---|
| 1104 | end*base[unit], "frequency")) |
---|
[1192] | 1105 | s._add_history("lag_flag", varlist) |
---|
| 1106 | if insitu: |
---|
| 1107 | self._assign(s) |
---|
| 1108 | else: |
---|
| 1109 | return s |
---|
[1001] | 1110 | |
---|
[1862] | 1111 | @asaplog_post_dec |
---|
[113] | 1112 | def create_mask(self, *args, **kwargs): |
---|
[1846] | 1113 | """\ |
---|
[1118] | 1114 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 1115 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 1116 | applied. |
---|
[1846] | 1117 | |
---|
[102] | 1118 | Parameters: |
---|
[1846] | 1119 | |
---|
[1118] | 1120 | [min, max], [min2, max2], ... |
---|
[1024] | 1121 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 1122 | to be masked |
---|
[1855] | 1123 | |
---|
[189] | 1124 | invert: optional argument. If specified as True, |
---|
| 1125 | return an inverted mask, i.e. the regions |
---|
| 1126 | specified are EXCLUDED |
---|
[1855] | 1127 | |
---|
[513] | 1128 | row: create the mask using the specified row for |
---|
| 1129 | unit conversions, default is row=0 |
---|
| 1130 | only necessary if frequency varies over rows. |
---|
[1846] | 1131 | |
---|
| 1132 | Examples:: |
---|
| 1133 | |
---|
[113] | 1134 | scan.set_unit('channel') |
---|
[1846] | 1135 | # a) |
---|
[1118] | 1136 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 1137 | # masks everything outside 400 and 500 |
---|
[113] | 1138 | # and 800 and 900 in the unit 'channel' |
---|
| 1139 | |
---|
[1846] | 1140 | # b) |
---|
[1118] | 1141 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 1142 | # masks the regions between 400 and 500 |
---|
[113] | 1143 | # and 800 and 900 in the unit 'channel' |
---|
[1846] | 1144 | |
---|
| 1145 | # c) |
---|
| 1146 | #mask only channel 400 |
---|
[1554] | 1147 | msk = scan.create_mask([400]) |
---|
[1846] | 1148 | |
---|
[102] | 1149 | """ |
---|
[1554] | 1150 | row = kwargs.get("row", 0) |
---|
[513] | 1151 | data = self._getabcissa(row) |
---|
[113] | 1152 | u = self._getcoordinfo()[0] |
---|
[1859] | 1153 | if u == "": |
---|
| 1154 | u = "channel" |
---|
| 1155 | msg = "The current mask window unit is %s" % u |
---|
| 1156 | i = self._check_ifs() |
---|
| 1157 | if not i: |
---|
| 1158 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 1159 | asaplog.push(msg) |
---|
[102] | 1160 | n = self.nchan() |
---|
[1295] | 1161 | msk = _n_bools(n, False) |
---|
[710] | 1162 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 1163 | |
---|
[1118] | 1164 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 1165 | and args or args[0] |
---|
[710] | 1166 | for window in ws: |
---|
[1554] | 1167 | if len(window) == 1: |
---|
| 1168 | window = [window[0], window[0]] |
---|
| 1169 | if len(window) == 0 or len(window) > 2: |
---|
| 1170 | raise ValueError("A window needs to be defined as [start(, end)]") |
---|
[1545] | 1171 | if window[0] > window[1]: |
---|
| 1172 | tmp = window[0] |
---|
| 1173 | window[0] = window[1] |
---|
| 1174 | window[1] = tmp |
---|
[102] | 1175 | for i in range(n): |
---|
[1024] | 1176 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 1177 | msk[i] = True |
---|
[113] | 1178 | if kwargs.has_key('invert'): |
---|
| 1179 | if kwargs.get('invert'): |
---|
[1295] | 1180 | msk = mask_not(msk) |
---|
[102] | 1181 | return msk |
---|
[710] | 1182 | |
---|
[1931] | 1183 | def get_masklist(self, mask=None, row=0, silent=False): |
---|
[1846] | 1184 | """\ |
---|
[1819] | 1185 | Compute and return a list of mask windows, [min, max]. |
---|
[1846] | 1186 | |
---|
[1819] | 1187 | Parameters: |
---|
[1846] | 1188 | |
---|
[1819] | 1189 | mask: channel mask, created with create_mask. |
---|
[1855] | 1190 | |
---|
[1819] | 1191 | row: calcutate the masklist using the specified row |
---|
| 1192 | for unit conversions, default is row=0 |
---|
| 1193 | only necessary if frequency varies over rows. |
---|
[1846] | 1194 | |
---|
[1819] | 1195 | Returns: |
---|
[1846] | 1196 | |
---|
[1819] | 1197 | [min, max], [min2, max2], ... |
---|
| 1198 | Pairs of start/end points (inclusive)specifying |
---|
| 1199 | the masked regions |
---|
[1846] | 1200 | |
---|
[1819] | 1201 | """ |
---|
| 1202 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1203 | raise TypeError("The mask should be list or tuple.") |
---|
| 1204 | if len(mask) < 2: |
---|
| 1205 | raise TypeError("The mask elements should be > 1") |
---|
| 1206 | if self.nchan() != len(mask): |
---|
| 1207 | msg = "Number of channels in scantable != number of mask elements" |
---|
| 1208 | raise TypeError(msg) |
---|
| 1209 | data = self._getabcissa(row) |
---|
| 1210 | u = self._getcoordinfo()[0] |
---|
[1859] | 1211 | if u == "": |
---|
| 1212 | u = "channel" |
---|
| 1213 | msg = "The current mask window unit is %s" % u |
---|
| 1214 | i = self._check_ifs() |
---|
| 1215 | if not i: |
---|
| 1216 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[1931] | 1217 | if not silent: |
---|
| 1218 | asaplog.push(msg) |
---|
[1819] | 1219 | masklist=[] |
---|
| 1220 | ist, ien = None, None |
---|
| 1221 | ist, ien=self.get_mask_indices(mask) |
---|
| 1222 | if ist is not None and ien is not None: |
---|
| 1223 | for i in xrange(len(ist)): |
---|
| 1224 | range=[data[ist[i]],data[ien[i]]] |
---|
| 1225 | range.sort() |
---|
| 1226 | masklist.append([range[0],range[1]]) |
---|
| 1227 | return masklist |
---|
| 1228 | |
---|
| 1229 | def get_mask_indices(self, mask=None): |
---|
[1846] | 1230 | """\ |
---|
[1819] | 1231 | Compute and Return lists of mask start indices and mask end indices. |
---|
[1855] | 1232 | |
---|
| 1233 | Parameters: |
---|
| 1234 | |
---|
[1819] | 1235 | mask: channel mask, created with create_mask. |
---|
[1846] | 1236 | |
---|
[1819] | 1237 | Returns: |
---|
[1846] | 1238 | |
---|
[1819] | 1239 | List of mask start indices and that of mask end indices, |
---|
| 1240 | i.e., [istart1,istart2,....], [iend1,iend2,....]. |
---|
[1846] | 1241 | |
---|
[1819] | 1242 | """ |
---|
| 1243 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1244 | raise TypeError("The mask should be list or tuple.") |
---|
| 1245 | if len(mask) < 2: |
---|
| 1246 | raise TypeError("The mask elements should be > 1") |
---|
| 1247 | istart=[] |
---|
| 1248 | iend=[] |
---|
| 1249 | if mask[0]: istart.append(0) |
---|
| 1250 | for i in range(len(mask)-1): |
---|
| 1251 | if not mask[i] and mask[i+1]: |
---|
| 1252 | istart.append(i+1) |
---|
| 1253 | elif mask[i] and not mask[i+1]: |
---|
| 1254 | iend.append(i) |
---|
| 1255 | if mask[len(mask)-1]: iend.append(len(mask)-1) |
---|
| 1256 | if len(istart) != len(iend): |
---|
| 1257 | raise RuntimeError("Numbers of mask start != mask end.") |
---|
| 1258 | for i in range(len(istart)): |
---|
| 1259 | if istart[i] > iend[i]: |
---|
| 1260 | raise RuntimeError("Mask start index > mask end index") |
---|
| 1261 | break |
---|
| 1262 | return istart,iend |
---|
| 1263 | |
---|
| 1264 | # def get_restfreqs(self): |
---|
| 1265 | # """ |
---|
| 1266 | # Get the restfrequency(s) stored in this scantable. |
---|
| 1267 | # The return value(s) are always of unit 'Hz' |
---|
| 1268 | # Parameters: |
---|
| 1269 | # none |
---|
| 1270 | # Returns: |
---|
| 1271 | # a list of doubles |
---|
| 1272 | # """ |
---|
| 1273 | # return list(self._getrestfreqs()) |
---|
| 1274 | |
---|
| 1275 | def get_restfreqs(self, ids=None): |
---|
[1846] | 1276 | """\ |
---|
[256] | 1277 | Get the restfrequency(s) stored in this scantable. |
---|
| 1278 | The return value(s) are always of unit 'Hz' |
---|
[1846] | 1279 | |
---|
[256] | 1280 | Parameters: |
---|
[1846] | 1281 | |
---|
[1819] | 1282 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to |
---|
| 1283 | be retrieved |
---|
[1846] | 1284 | |
---|
[256] | 1285 | Returns: |
---|
[1846] | 1286 | |
---|
[1819] | 1287 | dictionary containing ids and a list of doubles for each id |
---|
[1846] | 1288 | |
---|
[256] | 1289 | """ |
---|
[1819] | 1290 | if ids is None: |
---|
| 1291 | rfreqs={} |
---|
| 1292 | idlist = self.getmolnos() |
---|
| 1293 | for i in idlist: |
---|
| 1294 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1295 | return rfreqs |
---|
| 1296 | else: |
---|
| 1297 | if type(ids)==list or type(ids)==tuple: |
---|
| 1298 | rfreqs={} |
---|
| 1299 | for i in ids: |
---|
| 1300 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1301 | return rfreqs |
---|
| 1302 | else: |
---|
| 1303 | return list(self._getrestfreqs(ids)) |
---|
| 1304 | #return list(self._getrestfreqs(ids)) |
---|
[102] | 1305 | |
---|
[931] | 1306 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
[1846] | 1307 | """\ |
---|
[931] | 1308 | Set or replace the restfrequency specified and |
---|
[1938] | 1309 | if the 'freqs' argument holds a scalar, |
---|
[931] | 1310 | then that rest frequency will be applied to all the selected |
---|
| 1311 | data. If the 'freqs' argument holds |
---|
| 1312 | a vector, then it MUST be of equal or smaller length than |
---|
| 1313 | the number of IFs (and the available restfrequencies will be |
---|
| 1314 | replaced by this vector). In this case, *all* data have |
---|
| 1315 | the restfrequency set per IF according |
---|
| 1316 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 1317 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 1318 | IF 1 gets restfreq 2e9. |
---|
[1846] | 1319 | |
---|
[1395] | 1320 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 1321 | |
---|
[931] | 1322 | Parameters: |
---|
[1846] | 1323 | |
---|
[931] | 1324 | freqs: list of rest frequency values or string idenitfiers |
---|
[1855] | 1325 | |
---|
[931] | 1326 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 1327 | |
---|
[1846] | 1328 | |
---|
| 1329 | Example:: |
---|
| 1330 | |
---|
[1819] | 1331 | # set the given restfrequency for the all currently selected IFs |
---|
[931] | 1332 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1845] | 1333 | # set restfrequencies for the n IFs (n > 1) in the order of the |
---|
| 1334 | # list, i.e |
---|
| 1335 | # IF0 -> 1.4e9, IF1 -> 1.41e9, IF3 -> 1.42e9 |
---|
| 1336 | # len(list_of_restfreqs) == nIF |
---|
| 1337 | # for nIF == 1 the following will set multiple restfrequency for |
---|
| 1338 | # that IF |
---|
[1819] | 1339 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9]) |
---|
[1845] | 1340 | # set multiple restfrequencies per IF. as a list of lists where |
---|
| 1341 | # the outer list has nIF elements, the inner s arbitrary |
---|
| 1342 | scan.set_restfreqs(freqs=[[1.4e9, 1.41e9], [1.67e9]]) |
---|
[391] | 1343 | |
---|
[1846] | 1344 | *Note*: |
---|
[1845] | 1345 | |
---|
[931] | 1346 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 1347 | source and IF basis, use scantable.set_selection() before using |
---|
[1846] | 1348 | this function:: |
---|
[931] | 1349 | |
---|
[1846] | 1350 | # provided your scantable is called scan |
---|
| 1351 | selection = selector() |
---|
| 1352 | selection.set_name("ORION*") |
---|
| 1353 | selection.set_ifs([1]) |
---|
| 1354 | scan.set_selection(selection) |
---|
| 1355 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 1356 | |
---|
[931] | 1357 | """ |
---|
| 1358 | varlist = vars() |
---|
[1157] | 1359 | from asap import linecatalog |
---|
| 1360 | # simple value |
---|
[1118] | 1361 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1845] | 1362 | self._setrestfreqs([freqs], [""], unit) |
---|
[1157] | 1363 | # list of values |
---|
[1118] | 1364 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 1365 | # list values are scalars |
---|
[1118] | 1366 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[1845] | 1367 | if len(freqs) == 1: |
---|
| 1368 | self._setrestfreqs(freqs, [""], unit) |
---|
| 1369 | else: |
---|
| 1370 | # allow the 'old' mode of setting mulitple IFs |
---|
| 1371 | sel = selector() |
---|
| 1372 | savesel = self._getselection() |
---|
| 1373 | iflist = self.getifnos() |
---|
| 1374 | if len(freqs)>len(iflist): |
---|
| 1375 | raise ValueError("number of elements in list of list " |
---|
| 1376 | "exeeds the current IF selections") |
---|
| 1377 | iflist = self.getifnos() |
---|
| 1378 | for i, fval in enumerate(freqs): |
---|
| 1379 | sel.set_ifs(iflist[i]) |
---|
| 1380 | self._setselection(sel) |
---|
| 1381 | self._setrestfreqs([fval], [""], unit) |
---|
| 1382 | self._setselection(savesel) |
---|
| 1383 | |
---|
| 1384 | # list values are dict, {'value'=, 'name'=) |
---|
[1157] | 1385 | elif isinstance(freqs[-1], dict): |
---|
[1845] | 1386 | values = [] |
---|
| 1387 | names = [] |
---|
| 1388 | for d in freqs: |
---|
| 1389 | values.append(d["value"]) |
---|
| 1390 | names.append(d["name"]) |
---|
| 1391 | self._setrestfreqs(values, names, unit) |
---|
[1819] | 1392 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple): |
---|
[1157] | 1393 | sel = selector() |
---|
| 1394 | savesel = self._getselection() |
---|
[1322] | 1395 | iflist = self.getifnos() |
---|
[1819] | 1396 | if len(freqs)>len(iflist): |
---|
[1845] | 1397 | raise ValueError("number of elements in list of list exeeds" |
---|
| 1398 | " the current IF selections") |
---|
| 1399 | for i, fval in enumerate(freqs): |
---|
[1322] | 1400 | sel.set_ifs(iflist[i]) |
---|
[1259] | 1401 | self._setselection(sel) |
---|
[1845] | 1402 | self._setrestfreqs(fval, [""], unit) |
---|
[1157] | 1403 | self._setselection(savesel) |
---|
| 1404 | # freqs are to be taken from a linecatalog |
---|
[1153] | 1405 | elif isinstance(freqs, linecatalog): |
---|
| 1406 | sel = selector() |
---|
| 1407 | savesel = self._getselection() |
---|
| 1408 | for i in xrange(freqs.nrow()): |
---|
[1322] | 1409 | sel.set_ifs(iflist[i]) |
---|
[1153] | 1410 | self._setselection(sel) |
---|
[1845] | 1411 | self._setrestfreqs([freqs.get_frequency(i)], |
---|
| 1412 | [freqs.get_name(i)], "MHz") |
---|
[1153] | 1413 | # ensure that we are not iterating past nIF |
---|
| 1414 | if i == self.nif()-1: break |
---|
| 1415 | self._setselection(savesel) |
---|
[931] | 1416 | else: |
---|
| 1417 | return |
---|
| 1418 | self._add_history("set_restfreqs", varlist) |
---|
| 1419 | |
---|
[1360] | 1420 | def shift_refpix(self, delta): |
---|
[1846] | 1421 | """\ |
---|
[1589] | 1422 | Shift the reference pixel of the Spectra Coordinate by an |
---|
| 1423 | integer amount. |
---|
[1846] | 1424 | |
---|
[1589] | 1425 | Parameters: |
---|
[1846] | 1426 | |
---|
[1589] | 1427 | delta: the amount to shift by |
---|
[1846] | 1428 | |
---|
| 1429 | *Note*: |
---|
| 1430 | |
---|
[1589] | 1431 | Be careful using this with broadband data. |
---|
[1846] | 1432 | |
---|
[1360] | 1433 | """ |
---|
[1731] | 1434 | Scantable.shift_refpix(self, delta) |
---|
[931] | 1435 | |
---|
[1862] | 1436 | @asaplog_post_dec |
---|
[1259] | 1437 | def history(self, filename=None): |
---|
[1846] | 1438 | """\ |
---|
[1259] | 1439 | Print the history. Optionally to a file. |
---|
[1846] | 1440 | |
---|
[1348] | 1441 | Parameters: |
---|
[1846] | 1442 | |
---|
[1928] | 1443 | filename: The name of the file to save the history to. |
---|
[1846] | 1444 | |
---|
[1259] | 1445 | """ |
---|
[484] | 1446 | hist = list(self._gethistory()) |
---|
[794] | 1447 | out = "-"*80 |
---|
[484] | 1448 | for h in hist: |
---|
[489] | 1449 | if h.startswith("---"): |
---|
[1857] | 1450 | out = "\n".join([out, h]) |
---|
[489] | 1451 | else: |
---|
| 1452 | items = h.split("##") |
---|
| 1453 | date = items[0] |
---|
| 1454 | func = items[1] |
---|
| 1455 | items = items[2:] |
---|
[794] | 1456 | out += "\n"+date+"\n" |
---|
| 1457 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 1458 | for i in items: |
---|
[1938] | 1459 | if i == '': |
---|
| 1460 | continue |
---|
[489] | 1461 | s = i.split("=") |
---|
[1118] | 1462 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[1857] | 1463 | out = "\n".join([out, "-"*80]) |
---|
[1259] | 1464 | if filename is not None: |
---|
| 1465 | if filename is "": |
---|
| 1466 | filename = 'scantable_history.txt' |
---|
| 1467 | import os |
---|
| 1468 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 1469 | if not os.path.isdir(filename): |
---|
| 1470 | data = open(filename, 'w') |
---|
| 1471 | data.write(out) |
---|
| 1472 | data.close() |
---|
| 1473 | else: |
---|
| 1474 | msg = "Illegal file name '%s'." % (filename) |
---|
[1859] | 1475 | raise IOError(msg) |
---|
| 1476 | return page(out) |
---|
[513] | 1477 | # |
---|
| 1478 | # Maths business |
---|
| 1479 | # |
---|
[1862] | 1480 | @asaplog_post_dec |
---|
[931] | 1481 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[1846] | 1482 | """\ |
---|
[1070] | 1483 | Return the (time) weighted average of a scan. |
---|
[1846] | 1484 | |
---|
| 1485 | *Note*: |
---|
| 1486 | |
---|
[1070] | 1487 | in channels only - align if necessary |
---|
[1846] | 1488 | |
---|
[513] | 1489 | Parameters: |
---|
[1846] | 1490 | |
---|
[513] | 1491 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 1492 | weighting) |
---|
[1855] | 1493 | |
---|
[558] | 1494 | scanav: True averages each scan separately |
---|
| 1495 | False (default) averages all scans together, |
---|
[1855] | 1496 | |
---|
[1099] | 1497 | weight: Weighting scheme. |
---|
| 1498 | 'none' (mean no weight) |
---|
| 1499 | 'var' (1/var(spec) weighted) |
---|
| 1500 | 'tsys' (1/Tsys**2 weighted) |
---|
| 1501 | 'tint' (integration time weighted) |
---|
| 1502 | 'tintsys' (Tint/Tsys**2) |
---|
| 1503 | 'median' ( median averaging) |
---|
[535] | 1504 | The default is 'tint' |
---|
[1855] | 1505 | |
---|
[931] | 1506 | align: align the spectra in velocity before averaging. It takes |
---|
| 1507 | the time of the first spectrum as reference time. |
---|
[1846] | 1508 | |
---|
| 1509 | Example:: |
---|
| 1510 | |
---|
[513] | 1511 | # time average the scantable without using a mask |
---|
[710] | 1512 | newscan = scan.average_time() |
---|
[1846] | 1513 | |
---|
[513] | 1514 | """ |
---|
| 1515 | varlist = vars() |
---|
[1593] | 1516 | weight = weight or 'TINT' |
---|
| 1517 | mask = mask or () |
---|
| 1518 | scanav = (scanav and 'SCAN') or 'NONE' |
---|
[1118] | 1519 | scan = (self, ) |
---|
[1859] | 1520 | |
---|
| 1521 | if align: |
---|
| 1522 | scan = (self.freq_align(insitu=False), ) |
---|
| 1523 | s = None |
---|
| 1524 | if weight.upper() == 'MEDIAN': |
---|
| 1525 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 1526 | scanav)) |
---|
| 1527 | else: |
---|
| 1528 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 1529 | scanav)) |
---|
[1099] | 1530 | s._add_history("average_time", varlist) |
---|
[513] | 1531 | return s |
---|
[710] | 1532 | |
---|
[1862] | 1533 | @asaplog_post_dec |
---|
[876] | 1534 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[1846] | 1535 | """\ |
---|
[513] | 1536 | Return a scan where all spectra are converted to either |
---|
| 1537 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 1538 | By default the function tries to look the values up internally. |
---|
| 1539 | If it can't find them (or if you want to over-ride), you must |
---|
| 1540 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 1541 | also if you don't set it). jyperk takes precedence if you set both. |
---|
[1846] | 1542 | |
---|
[513] | 1543 | Parameters: |
---|
[1846] | 1544 | |
---|
[513] | 1545 | jyperk: the Jy / K conversion factor |
---|
[1855] | 1546 | |
---|
[513] | 1547 | eta: the aperture efficiency |
---|
[1855] | 1548 | |
---|
[1928] | 1549 | d: the geometric diameter (metres) |
---|
[1855] | 1550 | |
---|
[513] | 1551 | insitu: if False a new scantable is returned. |
---|
| 1552 | Otherwise, the scaling is done in-situ |
---|
| 1553 | The default is taken from .asaprc (False) |
---|
[1846] | 1554 | |
---|
[513] | 1555 | """ |
---|
| 1556 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1557 | self._math._setinsitu(insitu) |
---|
[513] | 1558 | varlist = vars() |
---|
[1593] | 1559 | jyperk = jyperk or -1.0 |
---|
| 1560 | d = d or -1.0 |
---|
| 1561 | eta = eta or -1.0 |
---|
[876] | 1562 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 1563 | s._add_history("convert_flux", varlist) |
---|
| 1564 | if insitu: self._assign(s) |
---|
| 1565 | else: return s |
---|
[513] | 1566 | |
---|
[1862] | 1567 | @asaplog_post_dec |
---|
[876] | 1568 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[1846] | 1569 | """\ |
---|
[513] | 1570 | Return a scan after applying a gain-elevation correction. |
---|
| 1571 | The correction can be made via either a polynomial or a |
---|
| 1572 | table-based interpolation (and extrapolation if necessary). |
---|
| 1573 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 1574 | If you specify neither, then a polynomial correction will be made |
---|
| 1575 | with built in coefficients known for certain telescopes (an error |
---|
| 1576 | will occur if the instrument is not known). |
---|
| 1577 | The data and Tsys are *divided* by the scaling factors. |
---|
[1846] | 1578 | |
---|
[513] | 1579 | Parameters: |
---|
[1846] | 1580 | |
---|
[513] | 1581 | poly: Polynomial coefficients (default None) to compute a |
---|
| 1582 | gain-elevation correction as a function of |
---|
| 1583 | elevation (in degrees). |
---|
[1855] | 1584 | |
---|
[513] | 1585 | filename: The name of an ascii file holding correction factors. |
---|
| 1586 | The first row of the ascii file must give the column |
---|
| 1587 | names and these MUST include columns |
---|
| 1588 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 1589 | by this) somewhere. |
---|
| 1590 | The second row must give the data type of the |
---|
| 1591 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 1592 | An example file would be |
---|
| 1593 | (actual factors are arbitrary) : |
---|
| 1594 | |
---|
| 1595 | TIME ELEVATION FACTOR |
---|
| 1596 | R R R |
---|
| 1597 | 0.1 0 0.8 |
---|
| 1598 | 0.2 20 0.85 |
---|
| 1599 | 0.3 40 0.9 |
---|
| 1600 | 0.4 60 0.85 |
---|
| 1601 | 0.5 80 0.8 |
---|
| 1602 | 0.6 90 0.75 |
---|
[1855] | 1603 | |
---|
[513] | 1604 | method: Interpolation method when correcting from a table. |
---|
| 1605 | Values are "nearest", "linear" (default), "cubic" |
---|
| 1606 | and "spline" |
---|
[1855] | 1607 | |
---|
[513] | 1608 | insitu: if False a new scantable is returned. |
---|
| 1609 | Otherwise, the scaling is done in-situ |
---|
| 1610 | The default is taken from .asaprc (False) |
---|
[1846] | 1611 | |
---|
[513] | 1612 | """ |
---|
| 1613 | |
---|
| 1614 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1615 | self._math._setinsitu(insitu) |
---|
[513] | 1616 | varlist = vars() |
---|
[1593] | 1617 | poly = poly or () |
---|
[513] | 1618 | from os.path import expandvars |
---|
| 1619 | filename = expandvars(filename) |
---|
[876] | 1620 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 1621 | s._add_history("gain_el", varlist) |
---|
[1593] | 1622 | if insitu: |
---|
| 1623 | self._assign(s) |
---|
| 1624 | else: |
---|
| 1625 | return s |
---|
[710] | 1626 | |
---|
[1862] | 1627 | @asaplog_post_dec |
---|
[931] | 1628 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[1846] | 1629 | """\ |
---|
[513] | 1630 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 1631 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 1632 | set_freqframe. |
---|
[1846] | 1633 | |
---|
[513] | 1634 | Parameters: |
---|
[1855] | 1635 | |
---|
[513] | 1636 | reftime: reference time to align at. By default, the time of |
---|
| 1637 | the first row of data is used. |
---|
[1855] | 1638 | |
---|
[513] | 1639 | method: Interpolation method for regridding the spectra. |
---|
| 1640 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 1641 | and "spline" |
---|
[1855] | 1642 | |
---|
[513] | 1643 | insitu: if False a new scantable is returned. |
---|
| 1644 | Otherwise, the scaling is done in-situ |
---|
| 1645 | The default is taken from .asaprc (False) |
---|
[1846] | 1646 | |
---|
[513] | 1647 | """ |
---|
[931] | 1648 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 1649 | self._math._setinsitu(insitu) |
---|
[513] | 1650 | varlist = vars() |
---|
[1593] | 1651 | reftime = reftime or "" |
---|
[931] | 1652 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 1653 | s._add_history("freq_align", varlist) |
---|
| 1654 | if insitu: self._assign(s) |
---|
| 1655 | else: return s |
---|
[513] | 1656 | |
---|
[1862] | 1657 | @asaplog_post_dec |
---|
[1725] | 1658 | def opacity(self, tau=None, insitu=None): |
---|
[1846] | 1659 | """\ |
---|
[513] | 1660 | Apply an opacity correction. The data |
---|
| 1661 | and Tsys are multiplied by the correction factor. |
---|
[1846] | 1662 | |
---|
[513] | 1663 | Parameters: |
---|
[1855] | 1664 | |
---|
[1689] | 1665 | tau: (list of) opacity from which the correction factor is |
---|
[513] | 1666 | exp(tau*ZD) |
---|
[1689] | 1667 | where ZD is the zenith-distance. |
---|
| 1668 | If a list is provided, it has to be of length nIF, |
---|
| 1669 | nIF*nPol or 1 and in order of IF/POL, e.g. |
---|
| 1670 | [opif0pol0, opif0pol1, opif1pol0 ...] |
---|
[1725] | 1671 | if tau is `None` the opacities are determined from a |
---|
| 1672 | model. |
---|
[1855] | 1673 | |
---|
[513] | 1674 | insitu: if False a new scantable is returned. |
---|
| 1675 | Otherwise, the scaling is done in-situ |
---|
| 1676 | The default is taken from .asaprc (False) |
---|
[1846] | 1677 | |
---|
[513] | 1678 | """ |
---|
| 1679 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1680 | self._math._setinsitu(insitu) |
---|
[513] | 1681 | varlist = vars() |
---|
[1689] | 1682 | if not hasattr(tau, "__len__"): |
---|
| 1683 | tau = [tau] |
---|
[876] | 1684 | s = scantable(self._math._opacity(self, tau)) |
---|
| 1685 | s._add_history("opacity", varlist) |
---|
| 1686 | if insitu: self._assign(s) |
---|
| 1687 | else: return s |
---|
[513] | 1688 | |
---|
[1862] | 1689 | @asaplog_post_dec |
---|
[513] | 1690 | def bin(self, width=5, insitu=None): |
---|
[1846] | 1691 | """\ |
---|
[513] | 1692 | Return a scan where all spectra have been binned up. |
---|
[1846] | 1693 | |
---|
[1348] | 1694 | Parameters: |
---|
[1846] | 1695 | |
---|
[513] | 1696 | width: The bin width (default=5) in pixels |
---|
[1855] | 1697 | |
---|
[513] | 1698 | insitu: if False a new scantable is returned. |
---|
| 1699 | Otherwise, the scaling is done in-situ |
---|
| 1700 | The default is taken from .asaprc (False) |
---|
[1846] | 1701 | |
---|
[513] | 1702 | """ |
---|
| 1703 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1704 | self._math._setinsitu(insitu) |
---|
[513] | 1705 | varlist = vars() |
---|
[876] | 1706 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1707 | s._add_history("bin", varlist) |
---|
[1589] | 1708 | if insitu: |
---|
| 1709 | self._assign(s) |
---|
| 1710 | else: |
---|
| 1711 | return s |
---|
[513] | 1712 | |
---|
[1862] | 1713 | @asaplog_post_dec |
---|
[513] | 1714 | def resample(self, width=5, method='cubic', insitu=None): |
---|
[1846] | 1715 | """\ |
---|
[1348] | 1716 | Return a scan where all spectra have been binned up. |
---|
[1573] | 1717 | |
---|
[1348] | 1718 | Parameters: |
---|
[1846] | 1719 | |
---|
[513] | 1720 | width: The bin width (default=5) in pixels |
---|
[1855] | 1721 | |
---|
[513] | 1722 | method: Interpolation method when correcting from a table. |
---|
| 1723 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1724 | and "spline" |
---|
[1855] | 1725 | |
---|
[513] | 1726 | insitu: if False a new scantable is returned. |
---|
| 1727 | Otherwise, the scaling is done in-situ |
---|
| 1728 | The default is taken from .asaprc (False) |
---|
[1846] | 1729 | |
---|
[513] | 1730 | """ |
---|
| 1731 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1732 | self._math._setinsitu(insitu) |
---|
[513] | 1733 | varlist = vars() |
---|
[876] | 1734 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1735 | s._add_history("resample", varlist) |
---|
[876] | 1736 | if insitu: self._assign(s) |
---|
| 1737 | else: return s |
---|
[513] | 1738 | |
---|
[1862] | 1739 | @asaplog_post_dec |
---|
[946] | 1740 | def average_pol(self, mask=None, weight='none'): |
---|
[1846] | 1741 | """\ |
---|
[946] | 1742 | Average the Polarisations together. |
---|
[1846] | 1743 | |
---|
[946] | 1744 | Parameters: |
---|
[1846] | 1745 | |
---|
[946] | 1746 | mask: An optional mask defining the region, where the |
---|
| 1747 | averaging will be applied. The output will have all |
---|
| 1748 | specified points masked. |
---|
[1855] | 1749 | |
---|
[946] | 1750 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1751 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 1752 | |
---|
[946] | 1753 | """ |
---|
| 1754 | varlist = vars() |
---|
[1593] | 1755 | mask = mask or () |
---|
[1010] | 1756 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1757 | s._add_history("average_pol", varlist) |
---|
[992] | 1758 | return s |
---|
[513] | 1759 | |
---|
[1862] | 1760 | @asaplog_post_dec |
---|
[1145] | 1761 | def average_beam(self, mask=None, weight='none'): |
---|
[1846] | 1762 | """\ |
---|
[1145] | 1763 | Average the Beams together. |
---|
[1846] | 1764 | |
---|
[1145] | 1765 | Parameters: |
---|
| 1766 | mask: An optional mask defining the region, where the |
---|
| 1767 | averaging will be applied. The output will have all |
---|
| 1768 | specified points masked. |
---|
[1855] | 1769 | |
---|
[1145] | 1770 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1771 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 1772 | |
---|
[1145] | 1773 | """ |
---|
| 1774 | varlist = vars() |
---|
[1593] | 1775 | mask = mask or () |
---|
[1145] | 1776 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1777 | s._add_history("average_beam", varlist) |
---|
| 1778 | return s |
---|
| 1779 | |
---|
[1586] | 1780 | def parallactify(self, pflag): |
---|
[1846] | 1781 | """\ |
---|
[1843] | 1782 | Set a flag to indicate whether this data should be treated as having |
---|
[1617] | 1783 | been 'parallactified' (total phase == 0.0) |
---|
[1846] | 1784 | |
---|
[1617] | 1785 | Parameters: |
---|
[1855] | 1786 | |
---|
[1843] | 1787 | pflag: Bool indicating whether to turn this on (True) or |
---|
[1617] | 1788 | off (False) |
---|
[1846] | 1789 | |
---|
[1617] | 1790 | """ |
---|
[1586] | 1791 | varlist = vars() |
---|
| 1792 | self._parallactify(pflag) |
---|
| 1793 | self._add_history("parallactify", varlist) |
---|
| 1794 | |
---|
[1862] | 1795 | @asaplog_post_dec |
---|
[992] | 1796 | def convert_pol(self, poltype=None): |
---|
[1846] | 1797 | """\ |
---|
[992] | 1798 | Convert the data to a different polarisation type. |
---|
[1565] | 1799 | Note that you will need cross-polarisation terms for most conversions. |
---|
[1846] | 1800 | |
---|
[992] | 1801 | Parameters: |
---|
[1855] | 1802 | |
---|
[992] | 1803 | poltype: The new polarisation type. Valid types are: |
---|
[1565] | 1804 | "linear", "circular", "stokes" and "linpol" |
---|
[1846] | 1805 | |
---|
[992] | 1806 | """ |
---|
| 1807 | varlist = vars() |
---|
[1859] | 1808 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1809 | s._add_history("convert_pol", varlist) |
---|
[992] | 1810 | return s |
---|
| 1811 | |
---|
[1862] | 1812 | @asaplog_post_dec |
---|
[1819] | 1813 | def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, insitu=None): |
---|
[1846] | 1814 | """\ |
---|
[513] | 1815 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
[1846] | 1816 | |
---|
[513] | 1817 | Parameters: |
---|
[1846] | 1818 | |
---|
[513] | 1819 | kernel: The type of smoothing kernel. Select from |
---|
[1574] | 1820 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian' |
---|
| 1821 | or 'poly' |
---|
[1855] | 1822 | |
---|
[513] | 1823 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1824 | ignored otherwise it defauls to 5 pixels. |
---|
| 1825 | For 'gaussian' it is the Full Width Half |
---|
| 1826 | Maximum. For 'boxcar' it is the full width. |
---|
[1574] | 1827 | For 'rmedian' and 'poly' it is the half width. |
---|
[1855] | 1828 | |
---|
[1574] | 1829 | order: Optional parameter for 'poly' kernel (default is 2), to |
---|
| 1830 | specify the order of the polnomial. Ignored by all other |
---|
| 1831 | kernels. |
---|
[1855] | 1832 | |
---|
[1819] | 1833 | plot: plot the original and the smoothed spectra. |
---|
| 1834 | In this each indivual fit has to be approved, by |
---|
| 1835 | typing 'y' or 'n' |
---|
[1855] | 1836 | |
---|
[513] | 1837 | insitu: if False a new scantable is returned. |
---|
| 1838 | Otherwise, the scaling is done in-situ |
---|
| 1839 | The default is taken from .asaprc (False) |
---|
[1846] | 1840 | |
---|
[513] | 1841 | """ |
---|
| 1842 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1843 | self._math._setinsitu(insitu) |
---|
[513] | 1844 | varlist = vars() |
---|
[1819] | 1845 | |
---|
| 1846 | if plot: orgscan = self.copy() |
---|
| 1847 | |
---|
[1574] | 1848 | s = scantable(self._math._smooth(self, kernel.lower(), width, order)) |
---|
[876] | 1849 | s._add_history("smooth", varlist) |
---|
[1819] | 1850 | |
---|
| 1851 | if plot: |
---|
| 1852 | if rcParams['plotter.gui']: |
---|
| 1853 | from asap.asaplotgui import asaplotgui as asaplot |
---|
| 1854 | else: |
---|
| 1855 | from asap.asaplot import asaplot |
---|
| 1856 | self._p=asaplot() |
---|
| 1857 | self._p.set_panels() |
---|
| 1858 | ylab=s._get_ordinate_label() |
---|
| 1859 | #self._p.palette(0,["#777777","red"]) |
---|
| 1860 | for r in xrange(s.nrow()): |
---|
| 1861 | xsm=s._getabcissa(r) |
---|
| 1862 | ysm=s._getspectrum(r) |
---|
| 1863 | xorg=orgscan._getabcissa(r) |
---|
| 1864 | yorg=orgscan._getspectrum(r) |
---|
| 1865 | self._p.clear() |
---|
| 1866 | self._p.hold() |
---|
| 1867 | self._p.set_axes('ylabel',ylab) |
---|
| 1868 | self._p.set_axes('xlabel',s._getabcissalabel(r)) |
---|
| 1869 | self._p.set_axes('title',s._getsourcename(r)) |
---|
| 1870 | self._p.set_line(label='Original',color="#777777") |
---|
| 1871 | self._p.plot(xorg,yorg) |
---|
| 1872 | self._p.set_line(label='Smoothed',color="red") |
---|
| 1873 | self._p.plot(xsm,ysm) |
---|
| 1874 | ### Ugly part for legend |
---|
| 1875 | for i in [0,1]: |
---|
| 1876 | self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]]) |
---|
| 1877 | self._p.release() |
---|
| 1878 | ### Ugly part for legend |
---|
| 1879 | self._p.subplots[0]['lines']=[] |
---|
| 1880 | res = raw_input("Accept smoothing ([y]/n): ") |
---|
| 1881 | if res.upper() == 'N': |
---|
| 1882 | s._setspectrum(yorg, r) |
---|
| 1883 | self._p.unmap() |
---|
| 1884 | self._p = None |
---|
| 1885 | del orgscan |
---|
| 1886 | |
---|
[876] | 1887 | if insitu: self._assign(s) |
---|
| 1888 | else: return s |
---|
[513] | 1889 | |
---|
[1862] | 1890 | @asaplog_post_dec |
---|
[1907] | 1891 | def old_poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None, rows=None): |
---|
[1846] | 1892 | """\ |
---|
[513] | 1893 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
[1907] | 1894 | |
---|
[513] | 1895 | Parameters: |
---|
[1846] | 1896 | |
---|
[794] | 1897 | mask: an optional mask |
---|
[1855] | 1898 | |
---|
[794] | 1899 | order: the order of the polynomial (default is 0) |
---|
[1855] | 1900 | |
---|
[1061] | 1901 | plot: plot the fit and the residual. In this each |
---|
| 1902 | indivual fit has to be approved, by typing 'y' |
---|
| 1903 | or 'n' |
---|
[1855] | 1904 | |
---|
[1391] | 1905 | uselin: use linear polynomial fit |
---|
[1855] | 1906 | |
---|
[794] | 1907 | insitu: if False a new scantable is returned. |
---|
| 1908 | Otherwise, the scaling is done in-situ |
---|
| 1909 | The default is taken from .asaprc (False) |
---|
[1846] | 1910 | |
---|
[1907] | 1911 | rows: row numbers of spectra to be processed. |
---|
| 1912 | (default is None: for all rows) |
---|
| 1913 | |
---|
| 1914 | Example: |
---|
[513] | 1915 | # return a scan baselined by a third order polynomial, |
---|
| 1916 | # not using a mask |
---|
| 1917 | bscan = scan.poly_baseline(order=3) |
---|
[1846] | 1918 | |
---|
[579] | 1919 | """ |
---|
[513] | 1920 | if insitu is None: insitu = rcParams['insitu'] |
---|
[1819] | 1921 | if not insitu: |
---|
| 1922 | workscan = self.copy() |
---|
| 1923 | else: |
---|
| 1924 | workscan = self |
---|
[513] | 1925 | varlist = vars() |
---|
| 1926 | if mask is None: |
---|
[1907] | 1927 | mask = [True for i in xrange(self.nchan())] |
---|
[1819] | 1928 | |
---|
[1217] | 1929 | try: |
---|
| 1930 | f = fitter() |
---|
[1391] | 1931 | if uselin: |
---|
| 1932 | f.set_function(lpoly=order) |
---|
| 1933 | else: |
---|
| 1934 | f.set_function(poly=order) |
---|
[1819] | 1935 | |
---|
[1907] | 1936 | if rows == None: |
---|
| 1937 | rows = xrange(workscan.nrow()) |
---|
| 1938 | elif isinstance(rows, int): |
---|
| 1939 | rows = [ rows ] |
---|
| 1940 | |
---|
[1819] | 1941 | if len(rows) > 0: |
---|
| 1942 | self.blpars = [] |
---|
[1907] | 1943 | self.masklists = [] |
---|
| 1944 | self.actualmask = [] |
---|
| 1945 | |
---|
[1819] | 1946 | for r in rows: |
---|
| 1947 | f.x = workscan._getabcissa(r) |
---|
| 1948 | f.y = workscan._getspectrum(r) |
---|
[1907] | 1949 | f.mask = mask_and(mask, workscan._getmask(r)) # (CAS-1434) |
---|
[1819] | 1950 | f.data = None |
---|
| 1951 | f.fit() |
---|
| 1952 | if plot: |
---|
| 1953 | f.plot(residual=True) |
---|
| 1954 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1955 | if x.upper() == 'N': |
---|
| 1956 | self.blpars.append(None) |
---|
[1907] | 1957 | self.masklists.append(None) |
---|
| 1958 | self.actualmask.append(None) |
---|
[1819] | 1959 | continue |
---|
| 1960 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
| 1961 | self.blpars.append(f.get_parameters()) |
---|
[1931] | 1962 | self.masklists.append(workscan.get_masklist(f.mask, row=r, silent=True)) |
---|
[1907] | 1963 | self.actualmask.append(f.mask) |
---|
[1819] | 1964 | |
---|
| 1965 | if plot: |
---|
| 1966 | f._p.unmap() |
---|
| 1967 | f._p = None |
---|
| 1968 | workscan._add_history("poly_baseline", varlist) |
---|
[1856] | 1969 | if insitu: |
---|
| 1970 | self._assign(workscan) |
---|
| 1971 | else: |
---|
| 1972 | return workscan |
---|
[1217] | 1973 | except RuntimeError: |
---|
| 1974 | msg = "The fit failed, possibly because it didn't converge." |
---|
[1859] | 1975 | raise RuntimeError(msg) |
---|
[513] | 1976 | |
---|
[1931] | 1977 | @asaplog_post_dec |
---|
[1907] | 1978 | def poly_baseline(self, mask=None, order=0, plot=False, batch=False, insitu=None, rows=None): |
---|
| 1979 | """\ |
---|
| 1980 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1981 | Parameters: |
---|
| 1982 | mask: an optional mask |
---|
| 1983 | order: the order of the polynomial (default is 0) |
---|
| 1984 | plot: plot the fit and the residual. In this each |
---|
| 1985 | indivual fit has to be approved, by typing 'y' |
---|
| 1986 | or 'n'. Ignored if batch = True. |
---|
| 1987 | batch: if True a faster algorithm is used and logs |
---|
| 1988 | including the fit results are not output |
---|
| 1989 | (default is False) |
---|
| 1990 | insitu: if False a new scantable is returned. |
---|
| 1991 | Otherwise, the scaling is done in-situ |
---|
| 1992 | The default is taken from .asaprc (False) |
---|
[1931] | 1993 | rows: row numbers of spectra to be baselined. |
---|
[1907] | 1994 | (default is None: for all rows) |
---|
| 1995 | Example: |
---|
| 1996 | # return a scan baselined by a third order polynomial, |
---|
| 1997 | # not using a mask |
---|
| 1998 | bscan = scan.poly_baseline(order=3) |
---|
| 1999 | """ |
---|
[1931] | 2000 | |
---|
| 2001 | varlist = vars() |
---|
| 2002 | |
---|
[1907] | 2003 | if insitu is None: insitu = rcParams["insitu"] |
---|
| 2004 | if insitu: |
---|
| 2005 | workscan = self |
---|
| 2006 | else: |
---|
| 2007 | workscan = self.copy() |
---|
| 2008 | |
---|
| 2009 | nchan = workscan.nchan() |
---|
| 2010 | |
---|
| 2011 | if mask is None: |
---|
| 2012 | mask = [True for i in xrange(nchan)] |
---|
| 2013 | |
---|
| 2014 | try: |
---|
| 2015 | if rows == None: |
---|
| 2016 | rows = xrange(workscan.nrow()) |
---|
| 2017 | elif isinstance(rows, int): |
---|
| 2018 | rows = [ rows ] |
---|
| 2019 | |
---|
| 2020 | if len(rows) > 0: |
---|
[1931] | 2021 | workscan.blpars = [] |
---|
| 2022 | workscan.masklists = [] |
---|
| 2023 | workscan.actualmask = [] |
---|
[1907] | 2024 | |
---|
| 2025 | if batch: |
---|
[1931] | 2026 | workscan._poly_baseline_batch(mask, order) |
---|
[1907] | 2027 | elif plot: |
---|
| 2028 | f = fitter() |
---|
| 2029 | f.set_function(lpoly=order) |
---|
| 2030 | for r in rows: |
---|
| 2031 | f.x = workscan._getabcissa(r) |
---|
| 2032 | f.y = workscan._getspectrum(r) |
---|
| 2033 | f.mask = mask_and(mask, workscan._getmask(r)) # (CAS-1434) |
---|
| 2034 | f.data = None |
---|
| 2035 | f.fit() |
---|
| 2036 | |
---|
| 2037 | f.plot(residual=True) |
---|
| 2038 | accept_fit = raw_input("Accept fit ( [y]/n ): ") |
---|
| 2039 | if accept_fit.upper() == "N": |
---|
| 2040 | self.blpars.append(None) |
---|
| 2041 | self.masklists.append(None) |
---|
| 2042 | self.actualmask.append(None) |
---|
| 2043 | continue |
---|
| 2044 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1931] | 2045 | workscan.blpars.append(f.get_parameters()) |
---|
| 2046 | workscan.masklists.append(workscan.get_masklist(f.mask, row=r)) |
---|
| 2047 | workscan.actualmask.append(f.mask) |
---|
[1907] | 2048 | |
---|
| 2049 | f._p.unmap() |
---|
| 2050 | f._p = None |
---|
| 2051 | else: |
---|
| 2052 | for r in rows: |
---|
[1931] | 2053 | fitparams = workscan._poly_baseline(mask, order, r) |
---|
| 2054 | params = fitparams.getparameters() |
---|
| 2055 | fmtd = ", ".join(["p%d = %3.6f" % (i, v) for i, v in enumerate(params)]) |
---|
| 2056 | errors = fitparams.geterrors() |
---|
| 2057 | fmask = mask_and(mask, workscan._getmask(r)) |
---|
| 2058 | |
---|
| 2059 | workscan.blpars.append({"params":params, |
---|
| 2060 | "fixed": fitparams.getfixedparameters(), |
---|
| 2061 | "formatted":fmtd, "errors":errors}) |
---|
| 2062 | workscan.masklists.append(workscan.get_masklist(fmask, r, silent=True)) |
---|
| 2063 | workscan.actualmask.append(fmask) |
---|
[1907] | 2064 | |
---|
[1931] | 2065 | asaplog.push(fmtd) |
---|
[1907] | 2066 | |
---|
| 2067 | workscan._add_history("poly_baseline", varlist) |
---|
| 2068 | |
---|
| 2069 | if insitu: |
---|
| 2070 | self._assign(workscan) |
---|
| 2071 | else: |
---|
| 2072 | return workscan |
---|
| 2073 | |
---|
[1919] | 2074 | except RuntimeError, e: |
---|
[1907] | 2075 | msg = "The fit failed, possibly because it didn't converge." |
---|
| 2076 | if rcParams["verbose"]: |
---|
[1919] | 2077 | asaplog.push(str(e)) |
---|
[1907] | 2078 | asaplog.push(str(msg)) |
---|
| 2079 | return |
---|
| 2080 | else: |
---|
[1919] | 2081 | raise RuntimeError(str(e)+'\n'+msg) |
---|
[1907] | 2082 | |
---|
| 2083 | |
---|
| 2084 | def auto_poly_baseline(self, mask=None, edge=(0, 0), order=0, |
---|
[1280] | 2085 | threshold=3, chan_avg_limit=1, plot=False, |
---|
[1907] | 2086 | insitu=None, rows=None): |
---|
[1846] | 2087 | """\ |
---|
[1931] | 2088 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
[880] | 2089 | Spectral lines are detected first using linefinder and masked out |
---|
| 2090 | to avoid them affecting the baseline solution. |
---|
| 2091 | |
---|
| 2092 | Parameters: |
---|
[1846] | 2093 | |
---|
[880] | 2094 | mask: an optional mask retreived from scantable |
---|
[1846] | 2095 | |
---|
| 2096 | edge: an optional number of channel to drop at the edge of |
---|
| 2097 | spectrum. If only one value is |
---|
[880] | 2098 | specified, the same number will be dropped from |
---|
| 2099 | both sides of the spectrum. Default is to keep |
---|
[907] | 2100 | all channels. Nested tuples represent individual |
---|
[976] | 2101 | edge selection for different IFs (a number of spectral |
---|
| 2102 | channels can be different) |
---|
[1846] | 2103 | |
---|
[880] | 2104 | order: the order of the polynomial (default is 0) |
---|
[1846] | 2105 | |
---|
[880] | 2106 | threshold: the threshold used by line finder. It is better to |
---|
| 2107 | keep it large as only strong lines affect the |
---|
| 2108 | baseline solution. |
---|
[1846] | 2109 | |
---|
[1280] | 2110 | chan_avg_limit: |
---|
| 2111 | a maximum number of consequtive spectral channels to |
---|
| 2112 | average during the search of weak and broad lines. |
---|
| 2113 | The default is no averaging (and no search for weak |
---|
| 2114 | lines). If such lines can affect the fitted baseline |
---|
| 2115 | (e.g. a high order polynomial is fitted), increase this |
---|
| 2116 | parameter (usually values up to 8 are reasonable). Most |
---|
| 2117 | users of this method should find the default value |
---|
| 2118 | sufficient. |
---|
[1846] | 2119 | |
---|
[1061] | 2120 | plot: plot the fit and the residual. In this each |
---|
| 2121 | indivual fit has to be approved, by typing 'y' |
---|
| 2122 | or 'n' |
---|
[1846] | 2123 | |
---|
[880] | 2124 | insitu: if False a new scantable is returned. |
---|
| 2125 | Otherwise, the scaling is done in-situ |
---|
| 2126 | The default is taken from .asaprc (False) |
---|
[1907] | 2127 | rows: row numbers of spectra to be processed. |
---|
| 2128 | (default is None: for all rows) |
---|
[880] | 2129 | |
---|
[1846] | 2130 | |
---|
| 2131 | Example:: |
---|
| 2132 | |
---|
| 2133 | scan2 = scan.auto_poly_baseline(order=7, insitu=False) |
---|
| 2134 | |
---|
[880] | 2135 | """ |
---|
| 2136 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 2137 | varlist = vars() |
---|
| 2138 | from asap.asaplinefind import linefinder |
---|
| 2139 | from asap import _is_sequence_or_number as _is_valid |
---|
| 2140 | |
---|
[976] | 2141 | # check whether edge is set up for each IF individually |
---|
[1118] | 2142 | individualedge = False; |
---|
| 2143 | if len(edge) > 1: |
---|
| 2144 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 2145 | individualedge = True; |
---|
[907] | 2146 | |
---|
[1118] | 2147 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 2148 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 2149 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 2150 | to make individual selection for different IFs." |
---|
[919] | 2151 | |
---|
[1118] | 2152 | curedge = (0, 0) |
---|
| 2153 | if individualedge: |
---|
| 2154 | for edgepar in edge: |
---|
| 2155 | if not _is_valid(edgepar, int): |
---|
| 2156 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 2157 | to be a pair of integers or an integer." |
---|
[907] | 2158 | else: |
---|
[1118] | 2159 | curedge = edge; |
---|
[880] | 2160 | |
---|
[1907] | 2161 | if not insitu: |
---|
| 2162 | workscan = self.copy() |
---|
| 2163 | else: |
---|
| 2164 | workscan = self |
---|
| 2165 | |
---|
[880] | 2166 | # setup fitter |
---|
| 2167 | f = fitter() |
---|
[1907] | 2168 | f.set_function(lpoly=order) |
---|
[880] | 2169 | |
---|
| 2170 | # setup line finder |
---|
[1118] | 2171 | fl = linefinder() |
---|
[1268] | 2172 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
[880] | 2173 | |
---|
[907] | 2174 | fl.set_scan(workscan) |
---|
| 2175 | |
---|
[1907] | 2176 | if mask is None: |
---|
| 2177 | mask = _n_bools(workscan.nchan(), True) |
---|
| 2178 | |
---|
| 2179 | if rows is None: |
---|
| 2180 | rows = xrange(workscan.nrow()) |
---|
| 2181 | elif isinstance(rows, int): |
---|
| 2182 | rows = [ rows ] |
---|
| 2183 | |
---|
[1819] | 2184 | # Save parameters of baseline fits & masklists as a class attribute. |
---|
| 2185 | # NOTICE: It does not reflect changes in scantable! |
---|
| 2186 | if len(rows) > 0: |
---|
| 2187 | self.blpars=[] |
---|
| 2188 | self.masklists=[] |
---|
[1907] | 2189 | self.actualmask=[] |
---|
[880] | 2190 | asaplog.push("Processing:") |
---|
| 2191 | for r in rows: |
---|
[1118] | 2192 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 2193 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 2194 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 2195 | asaplog.push(msg, False) |
---|
[907] | 2196 | |
---|
[976] | 2197 | # figure out edge parameter |
---|
[1118] | 2198 | if individualedge: |
---|
| 2199 | if len(edge) >= workscan.getif(r): |
---|
| 2200 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 2201 | "be less than the number of IFs" |
---|
| 2202 | curedge = edge[workscan.getif(r)] |
---|
[919] | 2203 | |
---|
[1907] | 2204 | actualmask = mask_and(mask, workscan._getmask(r)) # (CAS-1434) |
---|
[1819] | 2205 | |
---|
[976] | 2206 | # setup line finder |
---|
[1819] | 2207 | fl.find_lines(r, actualmask, curedge) |
---|
[1907] | 2208 | |
---|
[1819] | 2209 | f.x = workscan._getabcissa(r) |
---|
| 2210 | f.y = workscan._getspectrum(r) |
---|
[1907] | 2211 | f.mask = fl.get_mask() |
---|
[1819] | 2212 | f.data = None |
---|
[880] | 2213 | f.fit() |
---|
[1819] | 2214 | |
---|
| 2215 | # Show mask list |
---|
[1931] | 2216 | masklist=workscan.get_masklist(f.mask, row=r, silent=True) |
---|
[1819] | 2217 | msg = "mask range: "+str(masklist) |
---|
| 2218 | asaplog.push(msg, False) |
---|
| 2219 | |
---|
[1061] | 2220 | if plot: |
---|
| 2221 | f.plot(residual=True) |
---|
| 2222 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 2223 | if x.upper() == 'N': |
---|
[1819] | 2224 | self.blpars.append(None) |
---|
| 2225 | self.masklists.append(None) |
---|
[1907] | 2226 | self.actualmask.append(None) |
---|
[1061] | 2227 | continue |
---|
[1819] | 2228 | |
---|
[880] | 2229 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1819] | 2230 | self.blpars.append(f.get_parameters()) |
---|
| 2231 | self.masklists.append(masklist) |
---|
[1907] | 2232 | self.actualmask.append(f.mask) |
---|
[1061] | 2233 | if plot: |
---|
| 2234 | f._p.unmap() |
---|
| 2235 | f._p = None |
---|
| 2236 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 2237 | if insitu: |
---|
| 2238 | self._assign(workscan) |
---|
| 2239 | else: |
---|
| 2240 | return workscan |
---|
| 2241 | |
---|
[1862] | 2242 | @asaplog_post_dec |
---|
[914] | 2243 | def rotate_linpolphase(self, angle): |
---|
[1846] | 2244 | """\ |
---|
[914] | 2245 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 2246 | This is always done in situ in the raw data. So if you call this |
---|
| 2247 | function more than once then each call rotates the phase further. |
---|
[1846] | 2248 | |
---|
[914] | 2249 | Parameters: |
---|
[1846] | 2250 | |
---|
[914] | 2251 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 2252 | |
---|
| 2253 | Example:: |
---|
| 2254 | |
---|
[914] | 2255 | scan.rotate_linpolphase(2.3) |
---|
[1846] | 2256 | |
---|
[914] | 2257 | """ |
---|
| 2258 | varlist = vars() |
---|
[936] | 2259 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 2260 | self._add_history("rotate_linpolphase", varlist) |
---|
| 2261 | return |
---|
[710] | 2262 | |
---|
[1862] | 2263 | @asaplog_post_dec |
---|
[914] | 2264 | def rotate_xyphase(self, angle): |
---|
[1846] | 2265 | """\ |
---|
[914] | 2266 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 2267 | in the data. So if you call this function more than once |
---|
| 2268 | then each call rotates the phase further. |
---|
[1846] | 2269 | |
---|
[914] | 2270 | Parameters: |
---|
[1846] | 2271 | |
---|
[914] | 2272 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 2273 | |
---|
| 2274 | Example:: |
---|
| 2275 | |
---|
[914] | 2276 | scan.rotate_xyphase(2.3) |
---|
[1846] | 2277 | |
---|
[914] | 2278 | """ |
---|
| 2279 | varlist = vars() |
---|
[936] | 2280 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 2281 | self._add_history("rotate_xyphase", varlist) |
---|
| 2282 | return |
---|
| 2283 | |
---|
[1862] | 2284 | @asaplog_post_dec |
---|
[914] | 2285 | def swap_linears(self): |
---|
[1846] | 2286 | """\ |
---|
[1573] | 2287 | Swap the linear polarisations XX and YY, or better the first two |
---|
[1348] | 2288 | polarisations as this also works for ciculars. |
---|
[914] | 2289 | """ |
---|
| 2290 | varlist = vars() |
---|
[936] | 2291 | self._math._swap_linears(self) |
---|
[914] | 2292 | self._add_history("swap_linears", varlist) |
---|
| 2293 | return |
---|
| 2294 | |
---|
[1862] | 2295 | @asaplog_post_dec |
---|
[914] | 2296 | def invert_phase(self): |
---|
[1846] | 2297 | """\ |
---|
[914] | 2298 | Invert the phase of the complex polarisation |
---|
| 2299 | """ |
---|
| 2300 | varlist = vars() |
---|
[936] | 2301 | self._math._invert_phase(self) |
---|
[914] | 2302 | self._add_history("invert_phase", varlist) |
---|
| 2303 | return |
---|
| 2304 | |
---|
[1862] | 2305 | @asaplog_post_dec |
---|
[876] | 2306 | def add(self, offset, insitu=None): |
---|
[1846] | 2307 | """\ |
---|
[513] | 2308 | Return a scan where all spectra have the offset added |
---|
[1846] | 2309 | |
---|
[513] | 2310 | Parameters: |
---|
[1846] | 2311 | |
---|
[513] | 2312 | offset: the offset |
---|
[1855] | 2313 | |
---|
[513] | 2314 | insitu: if False a new scantable is returned. |
---|
| 2315 | Otherwise, the scaling is done in-situ |
---|
| 2316 | The default is taken from .asaprc (False) |
---|
[1846] | 2317 | |
---|
[513] | 2318 | """ |
---|
| 2319 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2320 | self._math._setinsitu(insitu) |
---|
[513] | 2321 | varlist = vars() |
---|
[876] | 2322 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 2323 | s._add_history("add", varlist) |
---|
[876] | 2324 | if insitu: |
---|
| 2325 | self._assign(s) |
---|
| 2326 | else: |
---|
[513] | 2327 | return s |
---|
| 2328 | |
---|
[1862] | 2329 | @asaplog_post_dec |
---|
[1308] | 2330 | def scale(self, factor, tsys=True, insitu=None): |
---|
[1846] | 2331 | """\ |
---|
| 2332 | |
---|
[1938] | 2333 | Return a scan where all spectra are scaled by the given 'factor' |
---|
[1846] | 2334 | |
---|
[513] | 2335 | Parameters: |
---|
[1846] | 2336 | |
---|
[1819] | 2337 | factor: the scaling factor (float or 1D float list) |
---|
[1855] | 2338 | |
---|
[513] | 2339 | insitu: if False a new scantable is returned. |
---|
| 2340 | Otherwise, the scaling is done in-situ |
---|
| 2341 | The default is taken from .asaprc (False) |
---|
[1855] | 2342 | |
---|
[513] | 2343 | tsys: if True (default) then apply the operation to Tsys |
---|
| 2344 | as well as the data |
---|
[1846] | 2345 | |
---|
[513] | 2346 | """ |
---|
| 2347 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2348 | self._math._setinsitu(insitu) |
---|
[513] | 2349 | varlist = vars() |
---|
[1819] | 2350 | s = None |
---|
| 2351 | import numpy |
---|
| 2352 | if isinstance(factor, list) or isinstance(factor, numpy.ndarray): |
---|
| 2353 | if isinstance(factor[0], list) or isinstance(factor[0], numpy.ndarray): |
---|
| 2354 | from asapmath import _array2dOp |
---|
| 2355 | s = _array2dOp( self.copy(), factor, "MUL", tsys ) |
---|
| 2356 | else: |
---|
| 2357 | s = scantable( self._math._arrayop( self.copy(), factor, "MUL", tsys ) ) |
---|
| 2358 | else: |
---|
| 2359 | s = scantable(self._math._unaryop(self.copy(), factor, "MUL", tsys)) |
---|
[1118] | 2360 | s._add_history("scale", varlist) |
---|
[876] | 2361 | if insitu: |
---|
| 2362 | self._assign(s) |
---|
| 2363 | else: |
---|
[513] | 2364 | return s |
---|
| 2365 | |
---|
[1504] | 2366 | def set_sourcetype(self, match, matchtype="pattern", |
---|
| 2367 | sourcetype="reference"): |
---|
[1846] | 2368 | """\ |
---|
[1502] | 2369 | Set the type of the source to be an source or reference scan |
---|
[1846] | 2370 | using the provided pattern. |
---|
| 2371 | |
---|
[1502] | 2372 | Parameters: |
---|
[1846] | 2373 | |
---|
[1504] | 2374 | match: a Unix style pattern, regular expression or selector |
---|
[1855] | 2375 | |
---|
[1504] | 2376 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
| 2377 | 'regex' regular expression |
---|
[1855] | 2378 | |
---|
[1502] | 2379 | sourcetype: the type of the source to use (source/reference) |
---|
[1846] | 2380 | |
---|
[1502] | 2381 | """ |
---|
| 2382 | varlist = vars() |
---|
| 2383 | basesel = self.get_selection() |
---|
| 2384 | stype = -1 |
---|
| 2385 | if sourcetype.lower().startswith("r"): |
---|
| 2386 | stype = 1 |
---|
| 2387 | elif sourcetype.lower().startswith("s"): |
---|
| 2388 | stype = 0 |
---|
[1504] | 2389 | else: |
---|
[1502] | 2390 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)") |
---|
[1504] | 2391 | if matchtype.lower().startswith("p"): |
---|
| 2392 | matchtype = "pattern" |
---|
| 2393 | elif matchtype.lower().startswith("r"): |
---|
| 2394 | matchtype = "regex" |
---|
| 2395 | else: |
---|
| 2396 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
[1502] | 2397 | sel = selector() |
---|
| 2398 | if isinstance(match, selector): |
---|
| 2399 | sel = match |
---|
| 2400 | else: |
---|
[1504] | 2401 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match)) |
---|
[1502] | 2402 | self.set_selection(basesel+sel) |
---|
| 2403 | self._setsourcetype(stype) |
---|
| 2404 | self.set_selection(basesel) |
---|
[1573] | 2405 | self._add_history("set_sourcetype", varlist) |
---|
[1502] | 2406 | |
---|
[1862] | 2407 | @asaplog_post_dec |
---|
[1857] | 2408 | @preserve_selection |
---|
[1819] | 2409 | def auto_quotient(self, preserve=True, mode='paired', verify=False): |
---|
[1846] | 2410 | """\ |
---|
[670] | 2411 | This function allows to build quotients automatically. |
---|
[1819] | 2412 | It assumes the observation to have the same number of |
---|
[670] | 2413 | "ons" and "offs" |
---|
[1846] | 2414 | |
---|
[670] | 2415 | Parameters: |
---|
[1846] | 2416 | |
---|
[710] | 2417 | preserve: you can preserve (default) the continuum or |
---|
| 2418 | remove it. The equations used are |
---|
[1857] | 2419 | |
---|
[670] | 2420 | preserve: Output = Toff * (on/off) - Toff |
---|
[1857] | 2421 | |
---|
[1070] | 2422 | remove: Output = Toff * (on/off) - Ton |
---|
[1855] | 2423 | |
---|
[1573] | 2424 | mode: the on/off detection mode |
---|
[1348] | 2425 | 'paired' (default) |
---|
| 2426 | identifies 'off' scans by the |
---|
| 2427 | trailing '_R' (Mopra/Parkes) or |
---|
| 2428 | '_e'/'_w' (Tid) and matches |
---|
| 2429 | on/off pairs from the observing pattern |
---|
[1502] | 2430 | 'time' |
---|
| 2431 | finds the closest off in time |
---|
[1348] | 2432 | |
---|
[1857] | 2433 | .. todo:: verify argument is not implemented |
---|
| 2434 | |
---|
[670] | 2435 | """ |
---|
[1857] | 2436 | varlist = vars() |
---|
[1348] | 2437 | modes = ["time", "paired"] |
---|
[670] | 2438 | if not mode in modes: |
---|
[876] | 2439 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 2440 | raise ValueError(msg) |
---|
[1348] | 2441 | s = None |
---|
| 2442 | if mode.lower() == "paired": |
---|
[1857] | 2443 | sel = self.get_selection() |
---|
[1875] | 2444 | sel.set_query("SRCTYPE==psoff") |
---|
[1356] | 2445 | self.set_selection(sel) |
---|
[1348] | 2446 | offs = self.copy() |
---|
[1875] | 2447 | sel.set_query("SRCTYPE==pson") |
---|
[1356] | 2448 | self.set_selection(sel) |
---|
[1348] | 2449 | ons = self.copy() |
---|
| 2450 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 2451 | elif mode.lower() == "time": |
---|
| 2452 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 2453 | s._add_history("auto_quotient", varlist) |
---|
[876] | 2454 | return s |
---|
[710] | 2455 | |
---|
[1862] | 2456 | @asaplog_post_dec |
---|
[1145] | 2457 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1846] | 2458 | """\ |
---|
[1143] | 2459 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
[1846] | 2460 | |
---|
[1143] | 2461 | Parameters: |
---|
[1846] | 2462 | |
---|
[1145] | 2463 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1855] | 2464 | |
---|
[1143] | 2465 | weight: How to average the off beams. Default is 'median'. |
---|
[1855] | 2466 | |
---|
[1145] | 2467 | preserve: you can preserve (default) the continuum or |
---|
[1855] | 2468 | remove it. The equations used are: |
---|
[1846] | 2469 | |
---|
[1855] | 2470 | preserve: Output = Toff * (on/off) - Toff |
---|
| 2471 | |
---|
| 2472 | remove: Output = Toff * (on/off) - Ton |
---|
| 2473 | |
---|
[1217] | 2474 | """ |
---|
[1593] | 2475 | mask = mask or () |
---|
[1141] | 2476 | varlist = vars() |
---|
| 2477 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 2478 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 2479 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 2480 | from asapmath import quotient |
---|
[1145] | 2481 | q = quotient(on, off, preserve) |
---|
[1143] | 2482 | q._add_history("mx_quotient", varlist) |
---|
[1217] | 2483 | return q |
---|
[513] | 2484 | |
---|
[1862] | 2485 | @asaplog_post_dec |
---|
[718] | 2486 | def freq_switch(self, insitu=None): |
---|
[1846] | 2487 | """\ |
---|
[718] | 2488 | Apply frequency switching to the data. |
---|
[1846] | 2489 | |
---|
[718] | 2490 | Parameters: |
---|
[1846] | 2491 | |
---|
[718] | 2492 | insitu: if False a new scantable is returned. |
---|
| 2493 | Otherwise, the swictching is done in-situ |
---|
| 2494 | The default is taken from .asaprc (False) |
---|
[1846] | 2495 | |
---|
[718] | 2496 | """ |
---|
| 2497 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2498 | self._math._setinsitu(insitu) |
---|
[718] | 2499 | varlist = vars() |
---|
[876] | 2500 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 2501 | s._add_history("freq_switch", varlist) |
---|
[1856] | 2502 | if insitu: |
---|
| 2503 | self._assign(s) |
---|
| 2504 | else: |
---|
| 2505 | return s |
---|
[718] | 2506 | |
---|
[1862] | 2507 | @asaplog_post_dec |
---|
[780] | 2508 | def recalc_azel(self): |
---|
[1846] | 2509 | """Recalculate the azimuth and elevation for each position.""" |
---|
[780] | 2510 | varlist = vars() |
---|
[876] | 2511 | self._recalcazel() |
---|
[780] | 2512 | self._add_history("recalc_azel", varlist) |
---|
| 2513 | return |
---|
| 2514 | |
---|
[1862] | 2515 | @asaplog_post_dec |
---|
[513] | 2516 | def __add__(self, other): |
---|
| 2517 | varlist = vars() |
---|
| 2518 | s = None |
---|
| 2519 | if isinstance(other, scantable): |
---|
[1573] | 2520 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
[513] | 2521 | elif isinstance(other, float): |
---|
[876] | 2522 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 2523 | else: |
---|
[718] | 2524 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2525 | s._add_history("operator +", varlist) |
---|
| 2526 | return s |
---|
| 2527 | |
---|
[1862] | 2528 | @asaplog_post_dec |
---|
[513] | 2529 | def __sub__(self, other): |
---|
| 2530 | """ |
---|
| 2531 | implicit on all axes and on Tsys |
---|
| 2532 | """ |
---|
| 2533 | varlist = vars() |
---|
| 2534 | s = None |
---|
| 2535 | if isinstance(other, scantable): |
---|
[1588] | 2536 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
[513] | 2537 | elif isinstance(other, float): |
---|
[876] | 2538 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 2539 | else: |
---|
[718] | 2540 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2541 | s._add_history("operator -", varlist) |
---|
| 2542 | return s |
---|
[710] | 2543 | |
---|
[1862] | 2544 | @asaplog_post_dec |
---|
[513] | 2545 | def __mul__(self, other): |
---|
| 2546 | """ |
---|
| 2547 | implicit on all axes and on Tsys |
---|
| 2548 | """ |
---|
| 2549 | varlist = vars() |
---|
| 2550 | s = None |
---|
| 2551 | if isinstance(other, scantable): |
---|
[1588] | 2552 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
[513] | 2553 | elif isinstance(other, float): |
---|
[876] | 2554 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 2555 | else: |
---|
[718] | 2556 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2557 | s._add_history("operator *", varlist) |
---|
| 2558 | return s |
---|
| 2559 | |
---|
[710] | 2560 | |
---|
[1862] | 2561 | @asaplog_post_dec |
---|
[513] | 2562 | def __div__(self, other): |
---|
| 2563 | """ |
---|
| 2564 | implicit on all axes and on Tsys |
---|
| 2565 | """ |
---|
| 2566 | varlist = vars() |
---|
| 2567 | s = None |
---|
| 2568 | if isinstance(other, scantable): |
---|
[1589] | 2569 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
[513] | 2570 | elif isinstance(other, float): |
---|
| 2571 | if other == 0.0: |
---|
[718] | 2572 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 2573 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 2574 | else: |
---|
[718] | 2575 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2576 | s._add_history("operator /", varlist) |
---|
| 2577 | return s |
---|
| 2578 | |
---|
[1862] | 2579 | @asaplog_post_dec |
---|
[530] | 2580 | def get_fit(self, row=0): |
---|
[1846] | 2581 | """\ |
---|
[530] | 2582 | Print or return the stored fits for a row in the scantable |
---|
[1846] | 2583 | |
---|
[530] | 2584 | Parameters: |
---|
[1846] | 2585 | |
---|
[530] | 2586 | row: the row which the fit has been applied to. |
---|
[1846] | 2587 | |
---|
[530] | 2588 | """ |
---|
| 2589 | if row > self.nrow(): |
---|
| 2590 | return |
---|
[976] | 2591 | from asap.asapfit import asapfit |
---|
[530] | 2592 | fit = asapfit(self._getfit(row)) |
---|
[1859] | 2593 | asaplog.push( '%s' %(fit) ) |
---|
| 2594 | return fit.as_dict() |
---|
[530] | 2595 | |
---|
[1483] | 2596 | def flag_nans(self): |
---|
[1846] | 2597 | """\ |
---|
[1483] | 2598 | Utility function to flag NaN values in the scantable. |
---|
| 2599 | """ |
---|
| 2600 | import numpy |
---|
| 2601 | basesel = self.get_selection() |
---|
| 2602 | for i in range(self.nrow()): |
---|
[1589] | 2603 | sel = self.get_row_selector(i) |
---|
| 2604 | self.set_selection(basesel+sel) |
---|
[1483] | 2605 | nans = numpy.isnan(self._getspectrum(0)) |
---|
| 2606 | if numpy.any(nans): |
---|
| 2607 | bnans = [ bool(v) for v in nans] |
---|
| 2608 | self.flag(bnans) |
---|
| 2609 | self.set_selection(basesel) |
---|
| 2610 | |
---|
[1588] | 2611 | def get_row_selector(self, rowno): |
---|
[1992] | 2612 | #return selector(beams=self.getbeam(rowno), |
---|
| 2613 | # ifs=self.getif(rowno), |
---|
| 2614 | # pols=self.getpol(rowno), |
---|
| 2615 | # scans=self.getscan(rowno), |
---|
| 2616 | # cycles=self.getcycle(rowno)) |
---|
| 2617 | return selector(rows=[rowno]) |
---|
[1573] | 2618 | |
---|
[484] | 2619 | def _add_history(self, funcname, parameters): |
---|
[1435] | 2620 | if not rcParams['scantable.history']: |
---|
| 2621 | return |
---|
[484] | 2622 | # create date |
---|
| 2623 | sep = "##" |
---|
| 2624 | from datetime import datetime |
---|
| 2625 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 2626 | hist = dstr+sep |
---|
| 2627 | hist += funcname+sep#cdate+sep |
---|
| 2628 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 2629 | for k, v in parameters.iteritems(): |
---|
[484] | 2630 | if type(v) is dict: |
---|
[1118] | 2631 | for k2, v2 in v.iteritems(): |
---|
[484] | 2632 | hist += k2 |
---|
| 2633 | hist += "=" |
---|
[1118] | 2634 | if isinstance(v2, scantable): |
---|
[484] | 2635 | hist += 'scantable' |
---|
| 2636 | elif k2 == 'mask': |
---|
[1118] | 2637 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 2638 | hist += str(self._zip_mask(v2)) |
---|
| 2639 | else: |
---|
| 2640 | hist += str(v2) |
---|
[484] | 2641 | else: |
---|
[513] | 2642 | hist += str(v2) |
---|
[484] | 2643 | else: |
---|
| 2644 | hist += k |
---|
| 2645 | hist += "=" |
---|
[1118] | 2646 | if isinstance(v, scantable): |
---|
[484] | 2647 | hist += 'scantable' |
---|
| 2648 | elif k == 'mask': |
---|
[1118] | 2649 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 2650 | hist += str(self._zip_mask(v)) |
---|
| 2651 | else: |
---|
| 2652 | hist += str(v) |
---|
[484] | 2653 | else: |
---|
| 2654 | hist += str(v) |
---|
| 2655 | hist += sep |
---|
| 2656 | hist = hist[:-2] # remove trailing '##' |
---|
| 2657 | self._addhistory(hist) |
---|
| 2658 | |
---|
[710] | 2659 | |
---|
[484] | 2660 | def _zip_mask(self, mask): |
---|
| 2661 | mask = list(mask) |
---|
| 2662 | i = 0 |
---|
| 2663 | segments = [] |
---|
| 2664 | while mask[i:].count(1): |
---|
| 2665 | i += mask[i:].index(1) |
---|
| 2666 | if mask[i:].count(0): |
---|
| 2667 | j = i + mask[i:].index(0) |
---|
| 2668 | else: |
---|
[710] | 2669 | j = len(mask) |
---|
[1118] | 2670 | segments.append([i, j]) |
---|
[710] | 2671 | i = j |
---|
[484] | 2672 | return segments |
---|
[714] | 2673 | |
---|
[626] | 2674 | def _get_ordinate_label(self): |
---|
| 2675 | fu = "("+self.get_fluxunit()+")" |
---|
| 2676 | import re |
---|
| 2677 | lbl = "Intensity" |
---|
[1118] | 2678 | if re.match(".K.", fu): |
---|
[626] | 2679 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 2680 | elif re.match(".Jy.", fu): |
---|
[626] | 2681 | lbl = "Flux density "+ fu |
---|
| 2682 | return lbl |
---|
[710] | 2683 | |
---|
[876] | 2684 | def _check_ifs(self): |
---|
[1986] | 2685 | #nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
| 2686 | #nchans = filter(lambda t: t > 0, nchans) |
---|
| 2687 | nchans = [self.nchan(i) for i in self.getifnos()] |
---|
[876] | 2688 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 2689 | |
---|
[1862] | 2690 | @asaplog_post_dec |
---|
[1916] | 2691 | #def _fill(self, names, unit, average, getpt, antenna): |
---|
| 2692 | def _fill(self, names, unit, average, opts={}): |
---|
[976] | 2693 | first = True |
---|
| 2694 | fullnames = [] |
---|
| 2695 | for name in names: |
---|
| 2696 | name = os.path.expandvars(name) |
---|
| 2697 | name = os.path.expanduser(name) |
---|
| 2698 | if not os.path.exists(name): |
---|
| 2699 | msg = "File '%s' does not exists" % (name) |
---|
| 2700 | raise IOError(msg) |
---|
| 2701 | fullnames.append(name) |
---|
| 2702 | if average: |
---|
| 2703 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 2704 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 2705 | for name in fullnames: |
---|
[1073] | 2706 | tbl = Scantable(stype) |
---|
[1843] | 2707 | r = filler(tbl) |
---|
[1504] | 2708 | rx = rcParams['scantable.reference'] |
---|
[1843] | 2709 | r.setreferenceexpr(rx) |
---|
[976] | 2710 | msg = "Importing %s..." % (name) |
---|
[1118] | 2711 | asaplog.push(msg, False) |
---|
[1916] | 2712 | #opts = {'ms': {'antenna' : antenna, 'getpt': getpt} } |
---|
[1904] | 2713 | r.open(name, opts)# antenna, -1, -1, getpt) |
---|
[1843] | 2714 | r.fill() |
---|
[976] | 2715 | if average: |
---|
[1118] | 2716 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 2717 | if not first: |
---|
| 2718 | tbl = self._math._merge([self, tbl]) |
---|
| 2719 | Scantable.__init__(self, tbl) |
---|
[1843] | 2720 | r.close() |
---|
[1118] | 2721 | del r, tbl |
---|
[976] | 2722 | first = False |
---|
[1861] | 2723 | #flush log |
---|
| 2724 | asaplog.post() |
---|
[976] | 2725 | if unit is not None: |
---|
| 2726 | self.set_fluxunit(unit) |
---|
[1824] | 2727 | if not is_casapy(): |
---|
| 2728 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[976] | 2729 | |
---|
[1402] | 2730 | def __getitem__(self, key): |
---|
| 2731 | if key < 0: |
---|
| 2732 | key += self.nrow() |
---|
| 2733 | if key >= self.nrow(): |
---|
| 2734 | raise IndexError("Row index out of range.") |
---|
| 2735 | return self._getspectrum(key) |
---|
| 2736 | |
---|
| 2737 | def __setitem__(self, key, value): |
---|
| 2738 | if key < 0: |
---|
| 2739 | key += self.nrow() |
---|
| 2740 | if key >= self.nrow(): |
---|
| 2741 | raise IndexError("Row index out of range.") |
---|
| 2742 | if not hasattr(value, "__len__") or \ |
---|
| 2743 | len(value) > self.nchan(self.getif(key)): |
---|
| 2744 | raise ValueError("Spectrum length doesn't match.") |
---|
| 2745 | return self._setspectrum(value, key) |
---|
| 2746 | |
---|
| 2747 | def __len__(self): |
---|
| 2748 | return self.nrow() |
---|
| 2749 | |
---|
| 2750 | def __iter__(self): |
---|
| 2751 | for i in range(len(self)): |
---|
| 2752 | yield self[i] |
---|