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