[1697] | 1 | import os |
---|
[1691] | 2 | try: |
---|
| 3 | from functools import wraps as wraps_dec |
---|
| 4 | except ImportError: |
---|
| 5 | from asap.compatibility import wraps as wraps_dec |
---|
| 6 | |
---|
[1824] | 7 | from asap.env import is_casapy |
---|
[876] | 8 | from asap._asap import Scantable |
---|
[1843] | 9 | from asap._asap import filler |
---|
[1824] | 10 | from asap.parameters import rcParams |
---|
| 11 | from asap.logging import asaplog, print_log, print_log_dec |
---|
| 12 | from asap.selector import selector |
---|
| 13 | from asap.linecatalog import linecatalog |
---|
[1600] | 14 | from asap.coordinate import coordinate |
---|
[1824] | 15 | from asap.utils import _n_bools, mask_not, mask_and, mask_or |
---|
[102] | 16 | |
---|
[1689] | 17 | |
---|
| 18 | def preserve_selection(func): |
---|
[1691] | 19 | @wraps_dec(func) |
---|
[1689] | 20 | def wrap(obj, *args, **kw): |
---|
| 21 | basesel = obj.get_selection() |
---|
| 22 | val = func(obj, *args, **kw) |
---|
| 23 | obj.set_selection(basesel) |
---|
| 24 | return val |
---|
| 25 | return wrap |
---|
| 26 | |
---|
| 27 | |
---|
[1697] | 28 | def is_scantable(filename): |
---|
| 29 | return (os.path.isdir(filename) |
---|
| 30 | and not os.path.exists(filename+'/table.f1') |
---|
| 31 | and os.path.exists(filename+'/table.info')) |
---|
| 32 | |
---|
| 33 | |
---|
[876] | 34 | class scantable(Scantable): |
---|
[102] | 35 | """ |
---|
| 36 | The ASAP container for scans |
---|
| 37 | """ |
---|
[1819] | 38 | |
---|
[1589] | 39 | @print_log_dec |
---|
[1824] | 40 | def __init__(self, filename, average=None, unit=None, getpt=None, |
---|
| 41 | antenna=None, parallactify=None): |
---|
[102] | 42 | """ |
---|
| 43 | Create a scantable from a saved one or make a reference |
---|
| 44 | Parameters: |
---|
[181] | 45 | filename: the name of an asap table on disk |
---|
| 46 | or |
---|
| 47 | the name of a rpfits/sdfits/ms file |
---|
| 48 | (integrations within scans are auto averaged |
---|
| 49 | and the whole file is read) |
---|
| 50 | or |
---|
| 51 | [advanced] a reference to an existing |
---|
[102] | 52 | scantable |
---|
[484] | 53 | average: average all integrations withinb a scan on read. |
---|
| 54 | The default (True) is taken from .asaprc. |
---|
| 55 | unit: brightness unit; must be consistent with K or Jy. |
---|
[1843] | 56 | Over-rides the default selected by the filler |
---|
[340] | 57 | (input rpfits/sdfits/ms) or replaces the value |
---|
| 58 | in existing scantables |
---|
[1819] | 59 | getpt: for MeasurementSet input data only: |
---|
| 60 | If True, all pointing data are filled. |
---|
| 61 | The deafult is False, which makes time to load |
---|
| 62 | the MS data faster in some cases. |
---|
| 63 | antenna: Antenna selection. integer (id) or string (name |
---|
| 64 | or id). |
---|
[1843] | 65 | parallactify: Indicate that the data had been parallatified. |
---|
[1586] | 66 | Default is taken form rc file. |
---|
[710] | 67 | """ |
---|
[976] | 68 | if average is None: |
---|
[710] | 69 | average = rcParams['scantable.autoaverage'] |
---|
[1819] | 70 | if getpt is None: |
---|
| 71 | getpt = True |
---|
[1843] | 72 | if antenna is not None: |
---|
| 73 | asaplog.push("Antenna selection currently unsupported." |
---|
| 74 | "Using '0'") |
---|
| 75 | print_log('WARN') |
---|
[1819] | 76 | if antenna is None: |
---|
| 77 | antenna = '' |
---|
| 78 | elif type(antenna) == int: |
---|
[1843] | 79 | antenna = '%s' % antenna |
---|
[1819] | 80 | elif type(antenna) == list: |
---|
| 81 | tmpstr = '' |
---|
| 82 | for i in range( len(antenna) ): |
---|
| 83 | if type(antenna[i]) == int: |
---|
| 84 | tmpstr = tmpstr + ('%s,'%(antenna[i])) |
---|
| 85 | elif type(antenna[i]) == str: |
---|
| 86 | tmpstr=tmpstr+antenna[i]+',' |
---|
| 87 | else: |
---|
| 88 | asaplog.push('Bad antenna selection.') |
---|
| 89 | print_log('ERROR') |
---|
| 90 | return |
---|
| 91 | antenna = tmpstr.rstrip(',') |
---|
[1593] | 92 | parallactify = parallactify or rcParams['scantable.parallactify'] |
---|
[1259] | 93 | varlist = vars() |
---|
[876] | 94 | from asap._asap import stmath |
---|
[1819] | 95 | self._math = stmath( rcParams['insitu'] ) |
---|
[876] | 96 | if isinstance(filename, Scantable): |
---|
| 97 | Scantable.__init__(self, filename) |
---|
[181] | 98 | else: |
---|
[1697] | 99 | if isinstance(filename, str): |
---|
[976] | 100 | filename = os.path.expandvars(filename) |
---|
| 101 | filename = os.path.expanduser(filename) |
---|
| 102 | if not os.path.exists(filename): |
---|
| 103 | s = "File '%s' not found." % (filename) |
---|
[718] | 104 | if rcParams['verbose']: |
---|
[976] | 105 | asaplog.push(s) |
---|
[1819] | 106 | print_log('ERROR') |
---|
[718] | 107 | return |
---|
[976] | 108 | raise IOError(s) |
---|
[1697] | 109 | if is_scantable(filename): |
---|
| 110 | ondisk = rcParams['scantable.storage'] == 'disk' |
---|
| 111 | Scantable.__init__(self, filename, ondisk) |
---|
| 112 | if unit is not None: |
---|
| 113 | self.set_fluxunit(unit) |
---|
[1819] | 114 | # do not reset to the default freqframe |
---|
| 115 | #self.set_freqframe(rcParams['scantable.freqframe']) |
---|
| 116 | elif os.path.isdir(filename) \ |
---|
| 117 | and not os.path.exists(filename+'/table.f1'): |
---|
| 118 | msg = "The given file '%s'is not a valid " \ |
---|
| 119 | "asap table." % (filename) |
---|
| 120 | if rcParams['verbose']: |
---|
| 121 | #print msg |
---|
| 122 | asaplog.push( msg ) |
---|
| 123 | print_log( 'ERROR' ) |
---|
| 124 | return |
---|
| 125 | else: |
---|
| 126 | raise IOError(msg) |
---|
[226] | 127 | else: |
---|
[1819] | 128 | self._fill([filename], unit, average, getpt, antenna) |
---|
[1118] | 129 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
---|
[976] | 130 | and isinstance(filename[-1], str): |
---|
[1819] | 131 | self._fill(filename, unit, average, getpt, antenna) |
---|
[1586] | 132 | self.parallactify(parallactify) |
---|
[1259] | 133 | self._add_history("scantable", varlist) |
---|
[1819] | 134 | print_log() |
---|
[102] | 135 | |
---|
[1589] | 136 | @print_log_dec |
---|
[876] | 137 | def save(self, name=None, format=None, overwrite=False): |
---|
[116] | 138 | """ |
---|
[1280] | 139 | Store the scantable on disk. This can be an asap (aips++) Table, |
---|
| 140 | SDFITS or MS2 format. |
---|
[116] | 141 | Parameters: |
---|
[1093] | 142 | name: the name of the outputfile. For format "ASCII" |
---|
| 143 | this is the root file name (data in 'name'.txt |
---|
[497] | 144 | and header in 'name'_header.txt) |
---|
[116] | 145 | format: an optional file format. Default is ASAP. |
---|
[280] | 146 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
---|
[194] | 147 | 'SDFITS' (save as SDFITS file) |
---|
[200] | 148 | 'ASCII' (saves as ascii text file) |
---|
[226] | 149 | 'MS2' (saves as an aips++ |
---|
| 150 | MeasurementSet V2) |
---|
[1573] | 151 | 'FITS' (save as image FITS - not |
---|
[1443] | 152 | readable by class) |
---|
| 153 | 'CLASS' (save as FITS readable by CLASS) |
---|
[411] | 154 | overwrite: If the file should be overwritten if it exists. |
---|
[256] | 155 | The default False is to return with warning |
---|
[411] | 156 | without writing the output. USE WITH CARE. |
---|
[116] | 157 | Example: |
---|
| 158 | scan.save('myscan.asap') |
---|
[1118] | 159 | scan.save('myscan.sdfits', 'SDFITS') |
---|
[116] | 160 | """ |
---|
[411] | 161 | from os import path |
---|
[1593] | 162 | format = format or rcParams['scantable.save'] |
---|
[256] | 163 | suffix = '.'+format.lower() |
---|
[1118] | 164 | if name is None or name == "": |
---|
[256] | 165 | name = 'scantable'+suffix |
---|
[718] | 166 | msg = "No filename given. Using default name %s..." % name |
---|
| 167 | asaplog.push(msg) |
---|
[411] | 168 | name = path.expandvars(name) |
---|
[256] | 169 | if path.isfile(name) or path.isdir(name): |
---|
| 170 | if not overwrite: |
---|
[718] | 171 | msg = "File %s exists." % name |
---|
| 172 | if rcParams['verbose']: |
---|
[1819] | 173 | #print msg |
---|
| 174 | asaplog.push( msg ) |
---|
| 175 | print_log( 'ERROR' ) |
---|
[718] | 176 | return |
---|
| 177 | else: |
---|
| 178 | raise IOError(msg) |
---|
[451] | 179 | format2 = format.upper() |
---|
| 180 | if format2 == 'ASAP': |
---|
[116] | 181 | self._save(name) |
---|
| 182 | else: |
---|
[989] | 183 | from asap._asap import stwriter as stw |
---|
[1118] | 184 | writer = stw(format2) |
---|
| 185 | writer.write(self, name) |
---|
[1819] | 186 | print_log() |
---|
[116] | 187 | return |
---|
| 188 | |
---|
[102] | 189 | def copy(self): |
---|
| 190 | """ |
---|
| 191 | Return a copy of this scantable. |
---|
[1348] | 192 | Note: |
---|
| 193 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
---|
[102] | 194 | Parameters: |
---|
[113] | 195 | none |
---|
[102] | 196 | Example: |
---|
| 197 | copiedscan = scan.copy() |
---|
| 198 | """ |
---|
[876] | 199 | sd = scantable(Scantable._copy(self)) |
---|
[113] | 200 | return sd |
---|
| 201 | |
---|
[1093] | 202 | def drop_scan(self, scanid=None): |
---|
| 203 | """ |
---|
| 204 | Return a new scantable where the specified scan number(s) has(have) |
---|
| 205 | been dropped. |
---|
| 206 | Parameters: |
---|
| 207 | scanid: a (list of) scan number(s) |
---|
| 208 | """ |
---|
| 209 | from asap import _is_sequence_or_number as _is_valid |
---|
| 210 | from asap import _to_list |
---|
| 211 | from asap import unique |
---|
| 212 | if not _is_valid(scanid): |
---|
| 213 | if rcParams['verbose']: |
---|
[1819] | 214 | #print "Please specify a scanno to drop from the scantable" |
---|
| 215 | asaplog.push( 'Please specify a scanno to drop from the scantable' ) |
---|
| 216 | print_log( 'ERROR' ) |
---|
[1093] | 217 | return |
---|
| 218 | else: |
---|
| 219 | raise RuntimeError("No scan given") |
---|
| 220 | try: |
---|
| 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) |
---|
[1118] | 224 | if len(allscans) == 0: |
---|
| 225 | raise ValueError("Can't remove all scans") |
---|
[1093] | 226 | except ValueError: |
---|
| 227 | if rcParams['verbose']: |
---|
[1819] | 228 | #print "Couldn't find any match." |
---|
| 229 | print_log() |
---|
| 230 | asaplog.push( "Couldn't find any match." ) |
---|
| 231 | print_log( 'ERROR' ) |
---|
[1093] | 232 | return |
---|
| 233 | else: raise |
---|
| 234 | try: |
---|
[1593] | 235 | sel = selector(scans=allscans) |
---|
[1594] | 236 | return self._select_copy(sel) |
---|
[1093] | 237 | except RuntimeError: |
---|
[1118] | 238 | if rcParams['verbose']: |
---|
[1819] | 239 | #print "Couldn't find any match." |
---|
| 240 | print_log() |
---|
| 241 | asaplog.push( "Couldn't find any match." ) |
---|
| 242 | print_log( 'ERROR' ) |
---|
[1118] | 243 | else: |
---|
| 244 | raise |
---|
[1093] | 245 | |
---|
[1594] | 246 | def _select_copy(self, selection): |
---|
| 247 | orig = self.get_selection() |
---|
| 248 | self.set_selection(orig+selection) |
---|
| 249 | cp = self.copy() |
---|
| 250 | self.set_selection(orig) |
---|
| 251 | return cp |
---|
| 252 | |
---|
[102] | 253 | def get_scan(self, scanid=None): |
---|
| 254 | """ |
---|
| 255 | Return a specific scan (by scanno) or collection of scans (by |
---|
| 256 | source name) in a new scantable. |
---|
[1348] | 257 | Note: |
---|
| 258 | See scantable.drop_scan() for the inverse operation. |
---|
[102] | 259 | Parameters: |
---|
[513] | 260 | scanid: a (list of) scanno or a source name, unix-style |
---|
| 261 | patterns are accepted for source name matching, e.g. |
---|
| 262 | '*_R' gets all 'ref scans |
---|
[102] | 263 | Example: |
---|
[513] | 264 | # get all scans containing the source '323p459' |
---|
| 265 | newscan = scan.get_scan('323p459') |
---|
| 266 | # get all 'off' scans |
---|
| 267 | refscans = scan.get_scan('*_R') |
---|
| 268 | # get a susbset of scans by scanno (as listed in scan.summary()) |
---|
[1118] | 269 | newscan = scan.get_scan([0, 2, 7, 10]) |
---|
[102] | 270 | """ |
---|
| 271 | if scanid is None: |
---|
[718] | 272 | if rcParams['verbose']: |
---|
[1819] | 273 | #print "Please specify a scan no or name to " \ |
---|
| 274 | # "retrieve from the scantable" |
---|
| 275 | asaplog.push( 'Please specify a scan no or name to retrieve from the scantable' ) |
---|
| 276 | print_log( 'ERROR' ) |
---|
[718] | 277 | return |
---|
| 278 | else: |
---|
| 279 | raise RuntimeError("No scan given") |
---|
| 280 | |
---|
[102] | 281 | try: |
---|
[946] | 282 | bsel = self.get_selection() |
---|
| 283 | sel = selector() |
---|
[102] | 284 | if type(scanid) is str: |
---|
[946] | 285 | sel.set_name(scanid) |
---|
[1594] | 286 | return self._select_copy(sel) |
---|
[102] | 287 | elif type(scanid) is int: |
---|
[946] | 288 | sel.set_scans([scanid]) |
---|
[1594] | 289 | return self._select_copy(sel) |
---|
[381] | 290 | elif type(scanid) is list: |
---|
[946] | 291 | sel.set_scans(scanid) |
---|
[1594] | 292 | return self._select_copy(sel) |
---|
[381] | 293 | else: |
---|
[718] | 294 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
---|
| 295 | if rcParams['verbose']: |
---|
[1819] | 296 | #print msg |
---|
| 297 | asaplog.push( msg ) |
---|
| 298 | print_log( 'ERROR' ) |
---|
[718] | 299 | else: |
---|
| 300 | raise TypeError(msg) |
---|
[102] | 301 | except RuntimeError: |
---|
[1819] | 302 | if rcParams['verbose']: |
---|
| 303 | #print "Couldn't find any match." |
---|
| 304 | print_log() |
---|
| 305 | asaplog.push( "Couldn't find any match." ) |
---|
| 306 | print_log( 'ERROR' ) |
---|
[718] | 307 | else: raise |
---|
[102] | 308 | |
---|
| 309 | def __str__(self): |
---|
[1118] | 310 | return Scantable._summary(self, True) |
---|
[102] | 311 | |
---|
[976] | 312 | def summary(self, filename=None): |
---|
[102] | 313 | """ |
---|
| 314 | Print a summary of the contents of this scantable. |
---|
| 315 | Parameters: |
---|
| 316 | filename: the name of a file to write the putput to |
---|
| 317 | Default - no file output |
---|
| 318 | """ |
---|
[976] | 319 | info = Scantable._summary(self, True) |
---|
[102] | 320 | if filename is not None: |
---|
[256] | 321 | if filename is "": |
---|
| 322 | filename = 'scantable_summary.txt' |
---|
[415] | 323 | from os.path import expandvars, isdir |
---|
[411] | 324 | filename = expandvars(filename) |
---|
[415] | 325 | if not isdir(filename): |
---|
[413] | 326 | data = open(filename, 'w') |
---|
| 327 | data.write(info) |
---|
| 328 | data.close() |
---|
| 329 | else: |
---|
[718] | 330 | msg = "Illegal file name '%s'." % (filename) |
---|
| 331 | if rcParams['verbose']: |
---|
[1819] | 332 | #print msg |
---|
| 333 | asaplog.push( msg ) |
---|
| 334 | print_log( 'ERROR' ) |
---|
[718] | 335 | else: |
---|
| 336 | raise IOError(msg) |
---|
| 337 | if rcParams['verbose']: |
---|
[794] | 338 | try: |
---|
| 339 | from IPython.genutils import page as pager |
---|
| 340 | except ImportError: |
---|
| 341 | from pydoc import pager |
---|
| 342 | pager(info) |
---|
[718] | 343 | else: |
---|
| 344 | return info |
---|
[710] | 345 | |
---|
[1512] | 346 | def get_spectrum(self, rowno): |
---|
[1471] | 347 | """Return the spectrum for the current row in the scantable as a list. |
---|
| 348 | Parameters: |
---|
[1573] | 349 | rowno: the row number to retrieve the spectrum from |
---|
[1471] | 350 | """ |
---|
| 351 | return self._getspectrum(rowno) |
---|
[946] | 352 | |
---|
[1471] | 353 | def get_mask(self, rowno): |
---|
| 354 | """Return the mask for the current row in the scantable as a list. |
---|
| 355 | Parameters: |
---|
[1573] | 356 | rowno: the row number to retrieve the mask from |
---|
[1471] | 357 | """ |
---|
| 358 | return self._getmask(rowno) |
---|
| 359 | |
---|
| 360 | def set_spectrum(self, spec, rowno): |
---|
| 361 | """Return the spectrum for the current row in the scantable as a list. |
---|
| 362 | Parameters: |
---|
| 363 | spec: the spectrum |
---|
[1573] | 364 | rowno: the row number to set the spectrum for |
---|
[1471] | 365 | """ |
---|
| 366 | assert(len(spec) == self.nchan()) |
---|
| 367 | return self._setspectrum(spec, rowno) |
---|
| 368 | |
---|
[1600] | 369 | def get_coordinate(self, rowno): |
---|
| 370 | """Return the (spectral) coordinate for a a given 'rowno'. |
---|
| 371 | NOTE: |
---|
| 372 | * This coordinate is only valid until a scantable method modifies |
---|
| 373 | the frequency axis. |
---|
| 374 | * This coordinate does contain the original frequency set-up |
---|
| 375 | NOT the new frame. The conversions however are done using the user |
---|
| 376 | specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate, |
---|
| 377 | use scantable.freq_align first. Without it there is no closure, |
---|
| 378 | i.e. |
---|
| 379 | c = myscan.get_coordinate(0) |
---|
| 380 | c.to_frequency(c.get_reference_pixel()) != c.get_reference_value() |
---|
| 381 | |
---|
| 382 | Parameters: |
---|
| 383 | rowno: the row number for the spectral coordinate |
---|
| 384 | |
---|
| 385 | """ |
---|
| 386 | return coordinate(Scantable.get_coordinate(self, rowno)) |
---|
| 387 | |
---|
[946] | 388 | def get_selection(self): |
---|
| 389 | """ |
---|
[1005] | 390 | Get the selection object currently set on this scantable. |
---|
| 391 | Parameters: |
---|
| 392 | none |
---|
| 393 | Example: |
---|
| 394 | sel = scan.get_selection() |
---|
| 395 | sel.set_ifs(0) # select IF 0 |
---|
| 396 | scan.set_selection(sel) # apply modified selection |
---|
[946] | 397 | """ |
---|
| 398 | return selector(self._getselection()) |
---|
| 399 | |
---|
[1576] | 400 | def set_selection(self, selection=None, **kw): |
---|
[946] | 401 | """ |
---|
[1005] | 402 | Select a subset of the data. All following operations on this scantable |
---|
| 403 | are only applied to thi selection. |
---|
| 404 | Parameters: |
---|
[1697] | 405 | selection: a selector object (default unset the selection), |
---|
| 406 | |
---|
| 407 | or |
---|
| 408 | |
---|
| 409 | any combination of |
---|
| 410 | "pols", "ifs", "beams", "scans", "cycles", "name", "query" |
---|
| 411 | |
---|
[1005] | 412 | Examples: |
---|
| 413 | sel = selector() # create a selection object |
---|
[1118] | 414 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
---|
[1005] | 415 | scan.set_selection(sel) # set the selection |
---|
| 416 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 417 | scan.set_selection() # unset the selection |
---|
[1697] | 418 | # or the equivalent |
---|
| 419 | scan.set_selection(scans=[0,3]) |
---|
| 420 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 421 | scan.set_selection() # unset the selection |
---|
[946] | 422 | """ |
---|
[1576] | 423 | if selection is None: |
---|
| 424 | # reset |
---|
| 425 | if len(kw) == 0: |
---|
| 426 | selection = selector() |
---|
| 427 | else: |
---|
| 428 | # try keywords |
---|
| 429 | for k in kw: |
---|
| 430 | if k not in selector.fields: |
---|
| 431 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields)) |
---|
| 432 | selection = selector(**kw) |
---|
[946] | 433 | self._setselection(selection) |
---|
| 434 | |
---|
[1819] | 435 | def get_row(self, row=0, insitu=None): |
---|
[102] | 436 | """ |
---|
[1819] | 437 | Select a row in the scantable. |
---|
| 438 | Return a scantable with single row. |
---|
| 439 | Parameters: |
---|
| 440 | row: row no of integration, default is 0. |
---|
| 441 | insitu: if False a new scantable is returned. |
---|
| 442 | Otherwise, the scaling is done in-situ |
---|
| 443 | The default is taken from .asaprc (False) |
---|
| 444 | """ |
---|
| 445 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 446 | if not insitu: |
---|
| 447 | workscan = self.copy() |
---|
| 448 | else: |
---|
| 449 | workscan = self |
---|
| 450 | # Select a row |
---|
| 451 | sel=selector() |
---|
| 452 | sel.set_scans([workscan.getscan(row)]) |
---|
| 453 | sel.set_cycles([workscan.getcycle(row)]) |
---|
| 454 | sel.set_beams([workscan.getbeam(row)]) |
---|
| 455 | sel.set_ifs([workscan.getif(row)]) |
---|
| 456 | sel.set_polarisations([workscan.getpol(row)]) |
---|
| 457 | sel.set_name(workscan._getsourcename(row)) |
---|
| 458 | workscan.set_selection(sel) |
---|
| 459 | if not workscan.nrow() == 1: |
---|
| 460 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow()) |
---|
| 461 | raise RuntimeError(msg) |
---|
| 462 | del sel |
---|
| 463 | if insitu: |
---|
| 464 | self._assign(workscan) |
---|
| 465 | else: |
---|
| 466 | return workscan |
---|
| 467 | |
---|
| 468 | #def stats(self, stat='stddev', mask=None): |
---|
| 469 | def stats(self, stat='stddev', mask=None, form='3.3f'): |
---|
| 470 | """ |
---|
[135] | 471 | Determine the specified statistic of the current beam/if/pol |
---|
[102] | 472 | Takes a 'mask' as an optional parameter to specify which |
---|
| 473 | channels should be excluded. |
---|
| 474 | Parameters: |
---|
[1819] | 475 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum', |
---|
| 476 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
[135] | 477 | mask: an optional mask specifying where the statistic |
---|
[102] | 478 | should be determined. |
---|
[1819] | 479 | form: format string to print statistic values |
---|
[102] | 480 | Example: |
---|
[113] | 481 | scan.set_unit('channel') |
---|
[1118] | 482 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 483 | scan.stats(stat='mean', mask=m) |
---|
[102] | 484 | """ |
---|
[1593] | 485 | mask = mask or [] |
---|
[876] | 486 | if not self._check_ifs(): |
---|
[1118] | 487 | raise ValueError("Cannot apply mask as the IFs have different " |
---|
| 488 | "number of channels. Please use setselection() " |
---|
| 489 | "to select individual IFs") |
---|
[1819] | 490 | rtnabc = False |
---|
| 491 | if stat.lower().endswith('_abc'): rtnabc = True |
---|
| 492 | getchan = False |
---|
| 493 | if stat.lower().startswith('min') or stat.lower().startswith('max'): |
---|
| 494 | chan = self._math._minmaxchan(self, mask, stat) |
---|
| 495 | getchan = True |
---|
| 496 | statvals = [] |
---|
| 497 | if not rtnabc: statvals = self._math._stats(self, mask, stat) |
---|
[256] | 498 | |
---|
[1819] | 499 | #def cb(i): |
---|
| 500 | # return statvals[i] |
---|
[256] | 501 | |
---|
[1819] | 502 | #return self._row_callback(cb, stat) |
---|
[102] | 503 | |
---|
[1819] | 504 | label=stat |
---|
| 505 | #callback=cb |
---|
| 506 | out = "" |
---|
| 507 | #outvec = [] |
---|
| 508 | sep = '-'*50 |
---|
| 509 | for i in range(self.nrow()): |
---|
| 510 | refstr = '' |
---|
| 511 | statunit= '' |
---|
| 512 | if getchan: |
---|
| 513 | qx, qy = self.chan2data(rowno=i, chan=chan[i]) |
---|
| 514 | if rtnabc: |
---|
| 515 | statvals.append(qx['value']) |
---|
| 516 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])' |
---|
| 517 | statunit= '['+qx['unit']+']' |
---|
| 518 | else: |
---|
| 519 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])' |
---|
| 520 | |
---|
| 521 | tm = self._gettime(i) |
---|
| 522 | src = self._getsourcename(i) |
---|
| 523 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
| 524 | out += 'Time[%s]:\n' % (tm) |
---|
| 525 | if self.nbeam(-1) > 1: |
---|
| 526 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 527 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 528 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
| 529 | #outvec.append(callback(i)) |
---|
| 530 | #out += ('= %'+form) % (outvec[i]) +' '+refstr+'\n' |
---|
| 531 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n' |
---|
| 532 | out += sep+"\n" |
---|
| 533 | |
---|
| 534 | if rcParams['verbose']: |
---|
| 535 | import os |
---|
| 536 | if os.environ.has_key( 'USER' ): |
---|
| 537 | usr=os.environ['USER'] |
---|
| 538 | else: |
---|
| 539 | import commands |
---|
| 540 | usr=commands.getoutput( 'whoami' ) |
---|
| 541 | tmpfile='/tmp/tmp_'+usr+'_casapy_asap_scantable_stats' |
---|
| 542 | f=open(tmpfile,'w') |
---|
| 543 | print >> f, sep |
---|
| 544 | print >> f, ' %s %s' % (label, statunit) |
---|
| 545 | print >> f, sep |
---|
| 546 | print >> f, out |
---|
| 547 | f.close() |
---|
| 548 | f=open(tmpfile,'r') |
---|
| 549 | x=f.readlines() |
---|
| 550 | f.close() |
---|
| 551 | blanc='' |
---|
| 552 | asaplog.push(blanc.join(x), False) |
---|
| 553 | #for xx in x: |
---|
| 554 | # asaplog.push( xx, False ) |
---|
| 555 | print_log() |
---|
| 556 | return statvals |
---|
| 557 | |
---|
| 558 | def chan2data(self, rowno=0, chan=0): |
---|
| 559 | """ |
---|
| 560 | Returns channel/frequency/velocity and spectral value |
---|
| 561 | at an arbitrary row and channel in the scantable. |
---|
| 562 | Parameters: |
---|
| 563 | rowno: a row number in the scantable. Default is the |
---|
| 564 | first row, i.e. rowno=0 |
---|
| 565 | chan: a channel in the scantable. Default is the first |
---|
| 566 | channel, i.e. pos=0 |
---|
| 567 | """ |
---|
| 568 | if isinstance(rowno, int) and isinstance(chan, int): |
---|
| 569 | qx = {'unit': self.get_unit(), |
---|
| 570 | 'value': self._getabcissa(rowno)[chan]} |
---|
| 571 | qy = {'unit': self.get_fluxunit(), |
---|
| 572 | 'value': self._getspectrum(rowno)[chan]} |
---|
| 573 | return qx, qy |
---|
| 574 | |
---|
[1118] | 575 | def stddev(self, mask=None): |
---|
[135] | 576 | """ |
---|
| 577 | Determine the standard deviation of the current beam/if/pol |
---|
| 578 | Takes a 'mask' as an optional parameter to specify which |
---|
| 579 | channels should be excluded. |
---|
| 580 | Parameters: |
---|
| 581 | mask: an optional mask specifying where the standard |
---|
| 582 | deviation should be determined. |
---|
| 583 | |
---|
| 584 | Example: |
---|
| 585 | scan.set_unit('channel') |
---|
[1118] | 586 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 587 | scan.stddev(mask=m) |
---|
| 588 | """ |
---|
[1118] | 589 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 590 | |
---|
[1003] | 591 | |
---|
[1259] | 592 | def get_column_names(self): |
---|
[1003] | 593 | """ |
---|
| 594 | Return a list of column names, which can be used for selection. |
---|
| 595 | """ |
---|
[1259] | 596 | return list(Scantable.get_column_names(self)) |
---|
[1003] | 597 | |
---|
[1730] | 598 | def get_tsys(self, row=-1): |
---|
[113] | 599 | """ |
---|
| 600 | Return the System temperatures. |
---|
| 601 | Returns: |
---|
[876] | 602 | a list of Tsys values for the current selection |
---|
[113] | 603 | """ |
---|
[1730] | 604 | if row > -1: |
---|
| 605 | return self._get_column(self._gettsys, row) |
---|
[876] | 606 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 607 | |
---|
[1730] | 608 | |
---|
| 609 | def get_weather(self, row=-1): |
---|
| 610 | values = self._get_column(self._get_weather, row) |
---|
| 611 | if row > -1: |
---|
| 612 | return {'temperature': values[0], |
---|
| 613 | 'pressure': values[1], 'humidity' : values[2], |
---|
| 614 | 'windspeed' : values[3], 'windaz' : values[4] |
---|
| 615 | } |
---|
| 616 | else: |
---|
| 617 | out = [] |
---|
| 618 | for r in values: |
---|
| 619 | |
---|
| 620 | out.append({'temperature': r[0], |
---|
| 621 | 'pressure': r[1], 'humidity' : r[2], |
---|
| 622 | 'windspeed' : r[3], 'windaz' : r[4] |
---|
| 623 | }) |
---|
| 624 | return out |
---|
| 625 | |
---|
[876] | 626 | def _row_callback(self, callback, label): |
---|
| 627 | out = "" |
---|
[1118] | 628 | outvec = [] |
---|
[1590] | 629 | sep = '-'*50 |
---|
[876] | 630 | for i in range(self.nrow()): |
---|
| 631 | tm = self._gettime(i) |
---|
| 632 | src = self._getsourcename(i) |
---|
[1590] | 633 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
[876] | 634 | out += 'Time[%s]:\n' % (tm) |
---|
[1590] | 635 | if self.nbeam(-1) > 1: |
---|
| 636 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 637 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 638 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
[876] | 639 | outvec.append(callback(i)) |
---|
| 640 | out += '= %3.3f\n' % (outvec[i]) |
---|
[1590] | 641 | out += sep+'\n' |
---|
[876] | 642 | if rcParams['verbose']: |
---|
[1819] | 643 | asaplog.push(sep) |
---|
| 644 | asaplog.push(" %s" % (label)) |
---|
| 645 | asaplog.push(sep) |
---|
| 646 | asaplog.push(out) |
---|
| 647 | print_log() |
---|
[1175] | 648 | return outvec |
---|
[256] | 649 | |
---|
[1070] | 650 | def _get_column(self, callback, row=-1): |
---|
| 651 | """ |
---|
| 652 | """ |
---|
| 653 | if row == -1: |
---|
| 654 | return [callback(i) for i in range(self.nrow())] |
---|
| 655 | else: |
---|
[1819] | 656 | if 0 <= row < self.nrow(): |
---|
[1070] | 657 | return callback(row) |
---|
[256] | 658 | |
---|
[1070] | 659 | |
---|
[1348] | 660 | def get_time(self, row=-1, asdatetime=False): |
---|
[113] | 661 | """ |
---|
| 662 | Get a list of time stamps for the observations. |
---|
[1348] | 663 | Return a datetime object for each integration time stamp in the scantable. |
---|
[113] | 664 | Parameters: |
---|
[1348] | 665 | row: row no of integration. Default -1 return all rows |
---|
| 666 | asdatetime: return values as datetime objects rather than strings |
---|
[113] | 667 | Example: |
---|
| 668 | none |
---|
| 669 | """ |
---|
[1175] | 670 | from time import strptime |
---|
| 671 | from datetime import datetime |
---|
[1392] | 672 | times = self._get_column(self._gettime, row) |
---|
[1348] | 673 | if not asdatetime: |
---|
[1392] | 674 | return times |
---|
[1175] | 675 | format = "%Y/%m/%d/%H:%M:%S" |
---|
| 676 | if isinstance(times, list): |
---|
| 677 | return [datetime(*strptime(i, format)[:6]) for i in times] |
---|
| 678 | else: |
---|
| 679 | return datetime(*strptime(times, format)[:6]) |
---|
[102] | 680 | |
---|
[1348] | 681 | |
---|
| 682 | def get_inttime(self, row=-1): |
---|
| 683 | """ |
---|
| 684 | Get a list of integration times for the observations. |
---|
| 685 | Return a time in seconds for each integration in the scantable. |
---|
| 686 | Parameters: |
---|
| 687 | row: row no of integration. Default -1 return all rows. |
---|
| 688 | Example: |
---|
| 689 | none |
---|
| 690 | """ |
---|
[1573] | 691 | return self._get_column(self._getinttime, row) |
---|
[1348] | 692 | |
---|
[1573] | 693 | |
---|
[714] | 694 | def get_sourcename(self, row=-1): |
---|
| 695 | """ |
---|
[794] | 696 | Get a list source names for the observations. |
---|
[714] | 697 | Return a string for each integration in the scantable. |
---|
| 698 | Parameters: |
---|
[1348] | 699 | row: row no of integration. Default -1 return all rows. |
---|
[714] | 700 | Example: |
---|
| 701 | none |
---|
| 702 | """ |
---|
[1070] | 703 | return self._get_column(self._getsourcename, row) |
---|
[714] | 704 | |
---|
[794] | 705 | def get_elevation(self, row=-1): |
---|
| 706 | """ |
---|
| 707 | Get a list of elevations for the observations. |
---|
| 708 | Return a float for each integration in the scantable. |
---|
| 709 | Parameters: |
---|
[1348] | 710 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 711 | Example: |
---|
| 712 | none |
---|
| 713 | """ |
---|
[1070] | 714 | return self._get_column(self._getelevation, row) |
---|
[794] | 715 | |
---|
| 716 | def get_azimuth(self, row=-1): |
---|
| 717 | """ |
---|
| 718 | Get a list of azimuths for the observations. |
---|
| 719 | Return a float for each integration in the scantable. |
---|
| 720 | Parameters: |
---|
[1348] | 721 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 722 | Example: |
---|
| 723 | none |
---|
| 724 | """ |
---|
[1070] | 725 | return self._get_column(self._getazimuth, row) |
---|
[794] | 726 | |
---|
| 727 | def get_parangle(self, row=-1): |
---|
| 728 | """ |
---|
| 729 | Get a list of parallactic angles for the observations. |
---|
| 730 | Return a float for each integration in the scantable. |
---|
| 731 | Parameters: |
---|
[1348] | 732 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 733 | Example: |
---|
| 734 | none |
---|
| 735 | """ |
---|
[1070] | 736 | return self._get_column(self._getparangle, row) |
---|
[794] | 737 | |
---|
[1070] | 738 | def get_direction(self, row=-1): |
---|
| 739 | """ |
---|
| 740 | Get a list of Positions on the sky (direction) for the observations. |
---|
[1594] | 741 | Return a string for each integration in the scantable. |
---|
[1070] | 742 | Parameters: |
---|
| 743 | row: row no of integration. Default -1 return all rows |
---|
| 744 | Example: |
---|
| 745 | none |
---|
| 746 | """ |
---|
| 747 | return self._get_column(self._getdirection, row) |
---|
| 748 | |
---|
[1391] | 749 | def get_directionval(self, row=-1): |
---|
| 750 | """ |
---|
| 751 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 752 | Return a float for each integration in the scantable. |
---|
| 753 | Parameters: |
---|
| 754 | row: row no of integration. Default -1 return all rows |
---|
| 755 | Example: |
---|
| 756 | none |
---|
| 757 | """ |
---|
| 758 | return self._get_column(self._getdirectionvec, row) |
---|
| 759 | |
---|
[1730] | 760 | @print_log_dec |
---|
[102] | 761 | def set_unit(self, unit='channel'): |
---|
| 762 | """ |
---|
| 763 | Set the unit for all following operations on this scantable |
---|
| 764 | Parameters: |
---|
| 765 | unit: optional unit, default is 'channel' |
---|
[1118] | 766 | one of '*Hz', 'km/s', 'channel', '' |
---|
[102] | 767 | """ |
---|
[484] | 768 | varlist = vars() |
---|
[1118] | 769 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 770 | unit = '' |
---|
| 771 | inf = list(self._getcoordinfo()) |
---|
| 772 | inf[0] = unit |
---|
| 773 | self._setcoordinfo(inf) |
---|
[1118] | 774 | self._add_history("set_unit", varlist) |
---|
[113] | 775 | |
---|
[1589] | 776 | @print_log_dec |
---|
[484] | 777 | def set_instrument(self, instr): |
---|
[358] | 778 | """ |
---|
[1348] | 779 | Set the instrument for subsequent processing. |
---|
[358] | 780 | Parameters: |
---|
[710] | 781 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 782 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 783 | """ |
---|
| 784 | self._setInstrument(instr) |
---|
[1118] | 785 | self._add_history("set_instument", vars()) |
---|
[1819] | 786 | print_log() |
---|
[358] | 787 | |
---|
[1589] | 788 | @print_log_dec |
---|
[1190] | 789 | def set_feedtype(self, feedtype): |
---|
| 790 | """ |
---|
| 791 | Overwrite the feed type, which might not be set correctly. |
---|
| 792 | Parameters: |
---|
| 793 | feedtype: 'linear' or 'circular' |
---|
| 794 | """ |
---|
| 795 | self._setfeedtype(feedtype) |
---|
| 796 | self._add_history("set_feedtype", vars()) |
---|
[1819] | 797 | print_log() |
---|
[1190] | 798 | |
---|
[1589] | 799 | @print_log_dec |
---|
[276] | 800 | def set_doppler(self, doppler='RADIO'): |
---|
| 801 | """ |
---|
| 802 | Set the doppler for all following operations on this scantable. |
---|
| 803 | Parameters: |
---|
| 804 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 805 | """ |
---|
[484] | 806 | varlist = vars() |
---|
[276] | 807 | inf = list(self._getcoordinfo()) |
---|
| 808 | inf[2] = doppler |
---|
| 809 | self._setcoordinfo(inf) |
---|
[1118] | 810 | self._add_history("set_doppler", vars()) |
---|
[1819] | 811 | print_log() |
---|
[710] | 812 | |
---|
[1589] | 813 | @print_log_dec |
---|
[226] | 814 | def set_freqframe(self, frame=None): |
---|
[113] | 815 | """ |
---|
| 816 | Set the frame type of the Spectral Axis. |
---|
| 817 | Parameters: |
---|
[591] | 818 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1819] | 819 | 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
[1118] | 820 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[113] | 821 | Examples: |
---|
| 822 | scan.set_freqframe('BARY') |
---|
| 823 | """ |
---|
[1593] | 824 | frame = frame or rcParams['scantable.freqframe'] |
---|
[484] | 825 | varlist = vars() |
---|
[1819] | 826 | # "REST" is not implemented in casacore |
---|
| 827 | #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 828 | # 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
| 829 | valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
[1118] | 830 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 831 | |
---|
[989] | 832 | if frame in valid: |
---|
[113] | 833 | inf = list(self._getcoordinfo()) |
---|
| 834 | inf[1] = frame |
---|
| 835 | self._setcoordinfo(inf) |
---|
[1118] | 836 | self._add_history("set_freqframe", varlist) |
---|
[102] | 837 | else: |
---|
[1118] | 838 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[718] | 839 | if rcParams['verbose']: |
---|
[1819] | 840 | #print msg |
---|
| 841 | asaplog.push( msg ) |
---|
| 842 | print_log( 'ERROR' ) |
---|
[718] | 843 | else: |
---|
| 844 | raise TypeError(msg) |
---|
[1819] | 845 | print_log() |
---|
[710] | 846 | |
---|
[989] | 847 | def set_dirframe(self, frame=""): |
---|
| 848 | """ |
---|
| 849 | Set the frame type of the Direction on the sky. |
---|
| 850 | Parameters: |
---|
| 851 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 852 | 'J2000', 'B1950', 'GALACTIC' |
---|
| 853 | Examples: |
---|
| 854 | scan.set_dirframe('GALACTIC') |
---|
| 855 | """ |
---|
| 856 | varlist = vars() |
---|
| 857 | try: |
---|
| 858 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 859 | except RuntimeError, msg: |
---|
[989] | 860 | if rcParams['verbose']: |
---|
[1819] | 861 | #print msg |
---|
| 862 | print_log() |
---|
| 863 | asaplog.push( str(msg) ) |
---|
| 864 | print_log( 'ERROR' ) |
---|
[989] | 865 | else: |
---|
| 866 | raise |
---|
[1118] | 867 | self._add_history("set_dirframe", varlist) |
---|
[989] | 868 | |
---|
[113] | 869 | def get_unit(self): |
---|
| 870 | """ |
---|
| 871 | Get the default unit set in this scantable |
---|
| 872 | Returns: |
---|
| 873 | A unit string |
---|
| 874 | """ |
---|
| 875 | inf = self._getcoordinfo() |
---|
| 876 | unit = inf[0] |
---|
| 877 | if unit == '': unit = 'channel' |
---|
| 878 | return unit |
---|
[102] | 879 | |
---|
[158] | 880 | def get_abcissa(self, rowno=0): |
---|
[102] | 881 | """ |
---|
[158] | 882 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 883 | selected Beam/IF/Pol |
---|
| 884 | Parameters: |
---|
[226] | 885 | rowno: an optional row number in the scantable. Default is the |
---|
| 886 | first row, i.e. rowno=0 |
---|
[113] | 887 | Returns: |
---|
[1348] | 888 | The abcissa values and the format string (as a dictionary) |
---|
[113] | 889 | """ |
---|
[256] | 890 | abc = self._getabcissa(rowno) |
---|
[710] | 891 | lbl = self._getabcissalabel(rowno) |
---|
[1819] | 892 | print_log() |
---|
[158] | 893 | return abc, lbl |
---|
[113] | 894 | |
---|
[1819] | 895 | def flag(self, mask=None, unflag=False): |
---|
[1001] | 896 | """ |
---|
| 897 | Flag the selected data using an optional channel mask. |
---|
| 898 | Parameters: |
---|
| 899 | mask: an optional channel mask, created with create_mask. Default |
---|
| 900 | (no mask) is all channels. |
---|
[1819] | 901 | unflag: if True, unflag the data |
---|
[1001] | 902 | """ |
---|
| 903 | varlist = vars() |
---|
[1593] | 904 | mask = mask or [] |
---|
[1001] | 905 | try: |
---|
[1819] | 906 | self._flag(mask, unflag) |
---|
[1118] | 907 | except RuntimeError, msg: |
---|
[1001] | 908 | if rcParams['verbose']: |
---|
[1819] | 909 | #print msg |
---|
| 910 | print_log() |
---|
| 911 | asaplog.push( str(msg) ) |
---|
| 912 | print_log( 'ERROR' ) |
---|
[1001] | 913 | return |
---|
| 914 | else: raise |
---|
| 915 | self._add_history("flag", varlist) |
---|
| 916 | |
---|
[1819] | 917 | def flag_row(self, rows=[], unflag=False): |
---|
| 918 | """ |
---|
| 919 | Flag the selected data in row-based manner. |
---|
| 920 | Parameters: |
---|
[1843] | 921 | rows: list of row numbers to be flagged. Default is no row |
---|
| 922 | (must be explicitly specified to execute row-based flagging). |
---|
[1819] | 923 | unflag: if True, unflag the data. |
---|
| 924 | """ |
---|
| 925 | varlist = vars() |
---|
| 926 | try: |
---|
| 927 | self._flag_row(rows, unflag) |
---|
| 928 | except RuntimeError, msg: |
---|
| 929 | if rcParams['verbose']: |
---|
| 930 | print_log() |
---|
| 931 | asaplog.push( str(msg) ) |
---|
| 932 | print_log('ERROR') |
---|
| 933 | return |
---|
| 934 | else: raise |
---|
| 935 | self._add_history("flag_row", varlist) |
---|
| 936 | |
---|
| 937 | def clip(self, uthres=None, dthres=None, clipoutside=True, unflag=False): |
---|
| 938 | """ |
---|
| 939 | Flag the selected data outside a specified range (in channel-base) |
---|
| 940 | Parameters: |
---|
| 941 | uthres: upper threshold. |
---|
| 942 | dthres: lower threshold |
---|
| 943 | clipoutside: True for flagging data outside the range [dthres:uthres]. |
---|
| 944 | False for glagging data inside the range. |
---|
| 945 | unflag : if True, unflag the data. |
---|
| 946 | """ |
---|
| 947 | varlist = vars() |
---|
| 948 | try: |
---|
| 949 | self._clip(uthres, dthres, clipoutside, unflag) |
---|
| 950 | except RuntimeError, msg: |
---|
| 951 | if rcParams['verbose']: |
---|
| 952 | print_log() |
---|
| 953 | asaplog.push(str(msg)) |
---|
| 954 | print_log('ERROR') |
---|
| 955 | return |
---|
| 956 | else: raise |
---|
| 957 | self._add_history("clip", varlist) |
---|
| 958 | |
---|
[1589] | 959 | @print_log_dec |
---|
[1584] | 960 | def lag_flag(self, start, end, unit="MHz", insitu=None): |
---|
[1819] | 961 | #def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None): |
---|
[1192] | 962 | """ |
---|
| 963 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
[1584] | 964 | Flagged data in the scantable gets interpolated over the region. |
---|
[1192] | 965 | No taper is applied. |
---|
| 966 | Parameters: |
---|
[1579] | 967 | start: the start frequency (really a period within the |
---|
| 968 | bandwidth) or period to remove |
---|
| 969 | end: the end frequency or period to remove |
---|
[1584] | 970 | unit: the frequency unit (default "MHz") or "" for |
---|
[1579] | 971 | explicit lag channels |
---|
[1203] | 972 | Notes: |
---|
[1579] | 973 | It is recommended to flag edges of the band or strong |
---|
[1348] | 974 | signals beforehand. |
---|
[1192] | 975 | """ |
---|
| 976 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 977 | self._math._setinsitu(insitu) |
---|
| 978 | varlist = vars() |
---|
[1579] | 979 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.} |
---|
| 980 | if not (unit == "" or base.has_key(unit)): |
---|
[1192] | 981 | raise ValueError("%s is not a valid unit." % unit) |
---|
| 982 | try: |
---|
[1579] | 983 | if unit == "": |
---|
| 984 | s = scantable(self._math._lag_flag(self, start, end, "lags")) |
---|
| 985 | else: |
---|
| 986 | s = scantable(self._math._lag_flag(self, start*base[unit], |
---|
| 987 | end*base[unit], "frequency")) |
---|
[1192] | 988 | except RuntimeError, msg: |
---|
| 989 | if rcParams['verbose']: |
---|
[1819] | 990 | #print msg |
---|
| 991 | print_log() |
---|
| 992 | asaplog.push( str(msg) ) |
---|
| 993 | print_log( 'ERROR' ) |
---|
[1192] | 994 | return |
---|
| 995 | else: raise |
---|
| 996 | s._add_history("lag_flag", varlist) |
---|
[1819] | 997 | print_log() |
---|
[1192] | 998 | if insitu: |
---|
| 999 | self._assign(s) |
---|
| 1000 | else: |
---|
| 1001 | return s |
---|
[1001] | 1002 | |
---|
[1589] | 1003 | @print_log_dec |
---|
[113] | 1004 | def create_mask(self, *args, **kwargs): |
---|
| 1005 | """ |
---|
[1118] | 1006 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 1007 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 1008 | applied. |
---|
[102] | 1009 | Parameters: |
---|
[1118] | 1010 | [min, max], [min2, max2], ... |
---|
[1024] | 1011 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 1012 | to be masked |
---|
[189] | 1013 | invert: optional argument. If specified as True, |
---|
| 1014 | return an inverted mask, i.e. the regions |
---|
| 1015 | specified are EXCLUDED |
---|
[513] | 1016 | row: create the mask using the specified row for |
---|
| 1017 | unit conversions, default is row=0 |
---|
| 1018 | only necessary if frequency varies over rows. |
---|
[102] | 1019 | Example: |
---|
[113] | 1020 | scan.set_unit('channel') |
---|
| 1021 | a) |
---|
[1118] | 1022 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 1023 | # masks everything outside 400 and 500 |
---|
[113] | 1024 | # and 800 and 900 in the unit 'channel' |
---|
| 1025 | |
---|
| 1026 | b) |
---|
[1118] | 1027 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 1028 | # masks the regions between 400 and 500 |
---|
[113] | 1029 | # and 800 and 900 in the unit 'channel' |
---|
[1024] | 1030 | c) |
---|
| 1031 | mask only channel 400 |
---|
[1554] | 1032 | msk = scan.create_mask([400]) |
---|
[102] | 1033 | """ |
---|
[1554] | 1034 | row = kwargs.get("row", 0) |
---|
[513] | 1035 | data = self._getabcissa(row) |
---|
[113] | 1036 | u = self._getcoordinfo()[0] |
---|
[718] | 1037 | if rcParams['verbose']: |
---|
[113] | 1038 | if u == "": u = "channel" |
---|
[718] | 1039 | msg = "The current mask window unit is %s" % u |
---|
[1118] | 1040 | i = self._check_ifs() |
---|
| 1041 | if not i: |
---|
[876] | 1042 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 1043 | asaplog.push(msg) |
---|
[102] | 1044 | n = self.nchan() |
---|
[1295] | 1045 | msk = _n_bools(n, False) |
---|
[710] | 1046 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 1047 | |
---|
[1118] | 1048 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 1049 | and args or args[0] |
---|
[710] | 1050 | for window in ws: |
---|
[1554] | 1051 | if len(window) == 1: |
---|
| 1052 | window = [window[0], window[0]] |
---|
| 1053 | if len(window) == 0 or len(window) > 2: |
---|
| 1054 | raise ValueError("A window needs to be defined as [start(, end)]") |
---|
[1545] | 1055 | if window[0] > window[1]: |
---|
| 1056 | tmp = window[0] |
---|
| 1057 | window[0] = window[1] |
---|
| 1058 | window[1] = tmp |
---|
[102] | 1059 | for i in range(n): |
---|
[1024] | 1060 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 1061 | msk[i] = True |
---|
[113] | 1062 | if kwargs.has_key('invert'): |
---|
| 1063 | if kwargs.get('invert'): |
---|
[1295] | 1064 | msk = mask_not(msk) |
---|
[1819] | 1065 | print_log() |
---|
[102] | 1066 | return msk |
---|
[710] | 1067 | |
---|
[1819] | 1068 | def get_masklist(self, mask=None, row=0): |
---|
[256] | 1069 | """ |
---|
[1819] | 1070 | Compute and return a list of mask windows, [min, max]. |
---|
| 1071 | Parameters: |
---|
| 1072 | mask: channel mask, created with create_mask. |
---|
| 1073 | row: calcutate the masklist using the specified row |
---|
| 1074 | for unit conversions, default is row=0 |
---|
| 1075 | only necessary if frequency varies over rows. |
---|
| 1076 | Returns: |
---|
| 1077 | [min, max], [min2, max2], ... |
---|
| 1078 | Pairs of start/end points (inclusive)specifying |
---|
| 1079 | the masked regions |
---|
| 1080 | """ |
---|
| 1081 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1082 | raise TypeError("The mask should be list or tuple.") |
---|
| 1083 | if len(mask) < 2: |
---|
| 1084 | raise TypeError("The mask elements should be > 1") |
---|
| 1085 | if self.nchan() != len(mask): |
---|
| 1086 | msg = "Number of channels in scantable != number of mask elements" |
---|
| 1087 | raise TypeError(msg) |
---|
| 1088 | data = self._getabcissa(row) |
---|
| 1089 | u = self._getcoordinfo()[0] |
---|
| 1090 | if rcParams['verbose']: |
---|
| 1091 | if u == "": u = "channel" |
---|
| 1092 | msg = "The current mask window unit is %s" % u |
---|
| 1093 | i = self._check_ifs() |
---|
| 1094 | if not i: |
---|
| 1095 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 1096 | asaplog.push(msg) |
---|
| 1097 | masklist=[] |
---|
| 1098 | ist, ien = None, None |
---|
| 1099 | ist, ien=self.get_mask_indices(mask) |
---|
| 1100 | if ist is not None and ien is not None: |
---|
| 1101 | for i in xrange(len(ist)): |
---|
| 1102 | range=[data[ist[i]],data[ien[i]]] |
---|
| 1103 | range.sort() |
---|
| 1104 | masklist.append([range[0],range[1]]) |
---|
| 1105 | return masklist |
---|
| 1106 | |
---|
| 1107 | def get_mask_indices(self, mask=None): |
---|
| 1108 | """ |
---|
| 1109 | Compute and Return lists of mask start indices and mask end indices. |
---|
| 1110 | Parameters: |
---|
| 1111 | mask: channel mask, created with create_mask. |
---|
| 1112 | Returns: |
---|
| 1113 | List of mask start indices and that of mask end indices, |
---|
| 1114 | i.e., [istart1,istart2,....], [iend1,iend2,....]. |
---|
| 1115 | """ |
---|
| 1116 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1117 | raise TypeError("The mask should be list or tuple.") |
---|
| 1118 | if len(mask) < 2: |
---|
| 1119 | raise TypeError("The mask elements should be > 1") |
---|
| 1120 | istart=[] |
---|
| 1121 | iend=[] |
---|
| 1122 | if mask[0]: istart.append(0) |
---|
| 1123 | for i in range(len(mask)-1): |
---|
| 1124 | if not mask[i] and mask[i+1]: |
---|
| 1125 | istart.append(i+1) |
---|
| 1126 | elif mask[i] and not mask[i+1]: |
---|
| 1127 | iend.append(i) |
---|
| 1128 | if mask[len(mask)-1]: iend.append(len(mask)-1) |
---|
| 1129 | if len(istart) != len(iend): |
---|
| 1130 | raise RuntimeError("Numbers of mask start != mask end.") |
---|
| 1131 | for i in range(len(istart)): |
---|
| 1132 | if istart[i] > iend[i]: |
---|
| 1133 | raise RuntimeError("Mask start index > mask end index") |
---|
| 1134 | break |
---|
| 1135 | return istart,iend |
---|
| 1136 | |
---|
| 1137 | # def get_restfreqs(self): |
---|
| 1138 | # """ |
---|
| 1139 | # Get the restfrequency(s) stored in this scantable. |
---|
| 1140 | # The return value(s) are always of unit 'Hz' |
---|
| 1141 | # Parameters: |
---|
| 1142 | # none |
---|
| 1143 | # Returns: |
---|
| 1144 | # a list of doubles |
---|
| 1145 | # """ |
---|
| 1146 | # return list(self._getrestfreqs()) |
---|
| 1147 | |
---|
| 1148 | def get_restfreqs(self, ids=None): |
---|
| 1149 | """ |
---|
[256] | 1150 | Get the restfrequency(s) stored in this scantable. |
---|
| 1151 | The return value(s) are always of unit 'Hz' |
---|
| 1152 | Parameters: |
---|
[1819] | 1153 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to |
---|
| 1154 | be retrieved |
---|
[256] | 1155 | Returns: |
---|
[1819] | 1156 | dictionary containing ids and a list of doubles for each id |
---|
[256] | 1157 | """ |
---|
[1819] | 1158 | if ids is None: |
---|
| 1159 | rfreqs={} |
---|
| 1160 | idlist = self.getmolnos() |
---|
| 1161 | for i in idlist: |
---|
| 1162 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1163 | return rfreqs |
---|
| 1164 | else: |
---|
| 1165 | if type(ids)==list or type(ids)==tuple: |
---|
| 1166 | rfreqs={} |
---|
| 1167 | for i in ids: |
---|
| 1168 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1169 | return rfreqs |
---|
| 1170 | else: |
---|
| 1171 | return list(self._getrestfreqs(ids)) |
---|
| 1172 | #return list(self._getrestfreqs(ids)) |
---|
[102] | 1173 | |
---|
[931] | 1174 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
| 1175 | """ |
---|
[1819] | 1176 | ********NEED TO BE UPDATED begin************ |
---|
[931] | 1177 | Set or replace the restfrequency specified and |
---|
| 1178 | If the 'freqs' argument holds a scalar, |
---|
| 1179 | then that rest frequency will be applied to all the selected |
---|
| 1180 | data. If the 'freqs' argument holds |
---|
| 1181 | a vector, then it MUST be of equal or smaller length than |
---|
| 1182 | the number of IFs (and the available restfrequencies will be |
---|
| 1183 | replaced by this vector). In this case, *all* data have |
---|
| 1184 | the restfrequency set per IF according |
---|
| 1185 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 1186 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 1187 | IF 1 gets restfreq 2e9. |
---|
[1819] | 1188 | ********NEED TO BE UPDATED end************ |
---|
[1395] | 1189 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 1190 | |
---|
[931] | 1191 | Parameters: |
---|
| 1192 | freqs: list of rest frequency values or string idenitfiers |
---|
| 1193 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 1194 | |
---|
[931] | 1195 | Example: |
---|
[1819] | 1196 | # set the given restfrequency for the all currently selected IFs |
---|
[931] | 1197 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1819] | 1198 | # set multiple restfrequencies to all the selected data |
---|
| 1199 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9]) |
---|
| 1200 | # If the number of IFs in the data is >= 2 the IF0 gets the first |
---|
| 1201 | # value IF1 the second... NOTE that freqs needs to be |
---|
| 1202 | # specified in list of list (e.g. [[],[],...] ). |
---|
| 1203 | scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]]) |
---|
[931] | 1204 | #set the given restfrequency for the whole table (by name) |
---|
| 1205 | scan.set_restfreqs(freqs="OH1667") |
---|
[391] | 1206 | |
---|
[931] | 1207 | Note: |
---|
| 1208 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 1209 | source and IF basis, use scantable.set_selection() before using |
---|
| 1210 | this function. |
---|
[1593] | 1211 | # provide your scantable is called scan |
---|
[931] | 1212 | selection = selector() |
---|
| 1213 | selection.set_name("ORION*") |
---|
| 1214 | selection.set_ifs([1]) |
---|
| 1215 | scan.set_selection(selection) |
---|
| 1216 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 1217 | |
---|
| 1218 | """ |
---|
| 1219 | varlist = vars() |
---|
[1157] | 1220 | from asap import linecatalog |
---|
| 1221 | # simple value |
---|
[1118] | 1222 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1819] | 1223 | # TT mod |
---|
| 1224 | #self._setrestfreqs(freqs, "",unit) |
---|
| 1225 | self._setrestfreqs([freqs], [""],unit) |
---|
[1157] | 1226 | # list of values |
---|
[1118] | 1227 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 1228 | # list values are scalars |
---|
[1118] | 1229 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[1819] | 1230 | self._setrestfreqs(freqs, [""], unit) |
---|
[1157] | 1231 | # list values are tuples, (value, name) |
---|
| 1232 | elif isinstance(freqs[-1], dict): |
---|
[1819] | 1233 | #sel = selector() |
---|
| 1234 | #savesel = self._getselection() |
---|
| 1235 | #iflist = self.getifnos() |
---|
| 1236 | #for i in xrange(len(freqs)): |
---|
| 1237 | # sel.set_ifs(iflist[i]) |
---|
| 1238 | # self._setselection(sel) |
---|
| 1239 | # self._setrestfreqs(freqs[i], "",unit) |
---|
| 1240 | #self._setselection(savesel) |
---|
| 1241 | self._setrestfreqs(freqs["value"], |
---|
| 1242 | freqs["name"], unit) |
---|
| 1243 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple): |
---|
[1157] | 1244 | sel = selector() |
---|
| 1245 | savesel = self._getselection() |
---|
[1322] | 1246 | iflist = self.getifnos() |
---|
[1819] | 1247 | if len(freqs)>len(iflist): |
---|
| 1248 | raise ValueError("number of elements in list of list exeeds the current IF selections") |
---|
[1157] | 1249 | for i in xrange(len(freqs)): |
---|
[1322] | 1250 | sel.set_ifs(iflist[i]) |
---|
[1259] | 1251 | self._setselection(sel) |
---|
[1819] | 1252 | self._setrestfreqs(freqs[i], [""], unit) |
---|
[1157] | 1253 | self._setselection(savesel) |
---|
| 1254 | # freqs are to be taken from a linecatalog |
---|
[1153] | 1255 | elif isinstance(freqs, linecatalog): |
---|
| 1256 | sel = selector() |
---|
| 1257 | savesel = self._getselection() |
---|
| 1258 | for i in xrange(freqs.nrow()): |
---|
[1322] | 1259 | sel.set_ifs(iflist[i]) |
---|
[1153] | 1260 | self._setselection(sel) |
---|
| 1261 | self._setrestfreqs(freqs.get_frequency(i), |
---|
| 1262 | freqs.get_name(i), "MHz") |
---|
| 1263 | # ensure that we are not iterating past nIF |
---|
| 1264 | if i == self.nif()-1: break |
---|
| 1265 | self._setselection(savesel) |
---|
[931] | 1266 | else: |
---|
| 1267 | return |
---|
| 1268 | self._add_history("set_restfreqs", varlist) |
---|
| 1269 | |
---|
[1360] | 1270 | def shift_refpix(self, delta): |
---|
[1589] | 1271 | """ |
---|
| 1272 | Shift the reference pixel of the Spectra Coordinate by an |
---|
| 1273 | integer amount. |
---|
| 1274 | Parameters: |
---|
| 1275 | delta: the amount to shift by |
---|
[1360] | 1276 | Note: |
---|
[1589] | 1277 | Be careful using this with broadband data. |
---|
[1360] | 1278 | """ |
---|
[1731] | 1279 | Scantable.shift_refpix(self, delta) |
---|
[931] | 1280 | |
---|
[1259] | 1281 | def history(self, filename=None): |
---|
| 1282 | """ |
---|
| 1283 | Print the history. Optionally to a file. |
---|
[1348] | 1284 | Parameters: |
---|
| 1285 | filename: The name of the file to save the history to. |
---|
[1259] | 1286 | """ |
---|
[484] | 1287 | hist = list(self._gethistory()) |
---|
[794] | 1288 | out = "-"*80 |
---|
[484] | 1289 | for h in hist: |
---|
[489] | 1290 | if h.startswith("---"): |
---|
[794] | 1291 | out += "\n"+h |
---|
[489] | 1292 | else: |
---|
| 1293 | items = h.split("##") |
---|
| 1294 | date = items[0] |
---|
| 1295 | func = items[1] |
---|
| 1296 | items = items[2:] |
---|
[794] | 1297 | out += "\n"+date+"\n" |
---|
| 1298 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 1299 | for i in items: |
---|
| 1300 | s = i.split("=") |
---|
[1118] | 1301 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[794] | 1302 | out += "\n"+"-"*80 |
---|
[1259] | 1303 | if filename is not None: |
---|
| 1304 | if filename is "": |
---|
| 1305 | filename = 'scantable_history.txt' |
---|
| 1306 | import os |
---|
| 1307 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 1308 | if not os.path.isdir(filename): |
---|
| 1309 | data = open(filename, 'w') |
---|
| 1310 | data.write(out) |
---|
| 1311 | data.close() |
---|
| 1312 | else: |
---|
| 1313 | msg = "Illegal file name '%s'." % (filename) |
---|
| 1314 | if rcParams['verbose']: |
---|
[1819] | 1315 | #print msg |
---|
| 1316 | asaplog.push( msg ) |
---|
| 1317 | print_log( 'ERROR' ) |
---|
[1259] | 1318 | else: |
---|
| 1319 | raise IOError(msg) |
---|
| 1320 | if rcParams['verbose']: |
---|
| 1321 | try: |
---|
| 1322 | from IPython.genutils import page as pager |
---|
| 1323 | except ImportError: |
---|
| 1324 | from pydoc import pager |
---|
| 1325 | pager(out) |
---|
| 1326 | else: |
---|
| 1327 | return out |
---|
[484] | 1328 | return |
---|
[513] | 1329 | # |
---|
| 1330 | # Maths business |
---|
| 1331 | # |
---|
[1589] | 1332 | @print_log_dec |
---|
[931] | 1333 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[513] | 1334 | """ |
---|
[1070] | 1335 | Return the (time) weighted average of a scan. |
---|
[513] | 1336 | Note: |
---|
[1070] | 1337 | in channels only - align if necessary |
---|
[513] | 1338 | Parameters: |
---|
| 1339 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 1340 | weighting) |
---|
[558] | 1341 | scanav: True averages each scan separately |
---|
| 1342 | False (default) averages all scans together, |
---|
[1099] | 1343 | weight: Weighting scheme. |
---|
| 1344 | 'none' (mean no weight) |
---|
| 1345 | 'var' (1/var(spec) weighted) |
---|
| 1346 | 'tsys' (1/Tsys**2 weighted) |
---|
| 1347 | 'tint' (integration time weighted) |
---|
| 1348 | 'tintsys' (Tint/Tsys**2) |
---|
| 1349 | 'median' ( median averaging) |
---|
[535] | 1350 | The default is 'tint' |
---|
[931] | 1351 | align: align the spectra in velocity before averaging. It takes |
---|
| 1352 | the time of the first spectrum as reference time. |
---|
[513] | 1353 | Example: |
---|
| 1354 | # time average the scantable without using a mask |
---|
[710] | 1355 | newscan = scan.average_time() |
---|
[513] | 1356 | """ |
---|
| 1357 | varlist = vars() |
---|
[1593] | 1358 | weight = weight or 'TINT' |
---|
| 1359 | mask = mask or () |
---|
| 1360 | scanav = (scanav and 'SCAN') or 'NONE' |
---|
[1118] | 1361 | scan = (self, ) |
---|
[989] | 1362 | try: |
---|
[1118] | 1363 | if align: |
---|
| 1364 | scan = (self.freq_align(insitu=False), ) |
---|
| 1365 | s = None |
---|
| 1366 | if weight.upper() == 'MEDIAN': |
---|
| 1367 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 1368 | scanav)) |
---|
| 1369 | else: |
---|
| 1370 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 1371 | scanav)) |
---|
| 1372 | except RuntimeError, msg: |
---|
[989] | 1373 | if rcParams['verbose']: |
---|
[1819] | 1374 | #print msg |
---|
| 1375 | print_log() |
---|
| 1376 | asaplog.push( str(msg) ) |
---|
| 1377 | print_log( 'ERROR' ) |
---|
[989] | 1378 | return |
---|
| 1379 | else: raise |
---|
[1099] | 1380 | s._add_history("average_time", varlist) |
---|
[1819] | 1381 | print_log() |
---|
[513] | 1382 | return s |
---|
[710] | 1383 | |
---|
[1589] | 1384 | @print_log_dec |
---|
[876] | 1385 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[513] | 1386 | """ |
---|
| 1387 | Return a scan where all spectra are converted to either |
---|
| 1388 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 1389 | By default the function tries to look the values up internally. |
---|
| 1390 | If it can't find them (or if you want to over-ride), you must |
---|
| 1391 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 1392 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 1393 | Parameters: |
---|
| 1394 | jyperk: the Jy / K conversion factor |
---|
| 1395 | eta: the aperture efficiency |
---|
| 1396 | d: the geomtric diameter (metres) |
---|
| 1397 | insitu: if False a new scantable is returned. |
---|
| 1398 | Otherwise, the scaling is done in-situ |
---|
| 1399 | The default is taken from .asaprc (False) |
---|
| 1400 | """ |
---|
| 1401 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1402 | self._math._setinsitu(insitu) |
---|
[513] | 1403 | varlist = vars() |
---|
[1593] | 1404 | jyperk = jyperk or -1.0 |
---|
| 1405 | d = d or -1.0 |
---|
| 1406 | eta = eta or -1.0 |
---|
[876] | 1407 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 1408 | s._add_history("convert_flux", varlist) |
---|
[1819] | 1409 | print_log() |
---|
[876] | 1410 | if insitu: self._assign(s) |
---|
| 1411 | else: return s |
---|
[513] | 1412 | |
---|
[1589] | 1413 | @print_log_dec |
---|
[876] | 1414 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[513] | 1415 | """ |
---|
| 1416 | Return a scan after applying a gain-elevation correction. |
---|
| 1417 | The correction can be made via either a polynomial or a |
---|
| 1418 | table-based interpolation (and extrapolation if necessary). |
---|
| 1419 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 1420 | If you specify neither, then a polynomial correction will be made |
---|
| 1421 | with built in coefficients known for certain telescopes (an error |
---|
| 1422 | will occur if the instrument is not known). |
---|
| 1423 | The data and Tsys are *divided* by the scaling factors. |
---|
| 1424 | Parameters: |
---|
| 1425 | poly: Polynomial coefficients (default None) to compute a |
---|
| 1426 | gain-elevation correction as a function of |
---|
| 1427 | elevation (in degrees). |
---|
| 1428 | filename: The name of an ascii file holding correction factors. |
---|
| 1429 | The first row of the ascii file must give the column |
---|
| 1430 | names and these MUST include columns |
---|
| 1431 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 1432 | by this) somewhere. |
---|
| 1433 | The second row must give the data type of the |
---|
| 1434 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 1435 | An example file would be |
---|
| 1436 | (actual factors are arbitrary) : |
---|
| 1437 | |
---|
| 1438 | TIME ELEVATION FACTOR |
---|
| 1439 | R R R |
---|
| 1440 | 0.1 0 0.8 |
---|
| 1441 | 0.2 20 0.85 |
---|
| 1442 | 0.3 40 0.9 |
---|
| 1443 | 0.4 60 0.85 |
---|
| 1444 | 0.5 80 0.8 |
---|
| 1445 | 0.6 90 0.75 |
---|
| 1446 | method: Interpolation method when correcting from a table. |
---|
| 1447 | Values are "nearest", "linear" (default), "cubic" |
---|
| 1448 | and "spline" |
---|
| 1449 | insitu: if False a new scantable is returned. |
---|
| 1450 | Otherwise, the scaling is done in-situ |
---|
| 1451 | The default is taken from .asaprc (False) |
---|
| 1452 | """ |
---|
| 1453 | |
---|
| 1454 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1455 | self._math._setinsitu(insitu) |
---|
[513] | 1456 | varlist = vars() |
---|
[1593] | 1457 | poly = poly or () |
---|
[513] | 1458 | from os.path import expandvars |
---|
| 1459 | filename = expandvars(filename) |
---|
[876] | 1460 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 1461 | s._add_history("gain_el", varlist) |
---|
[1819] | 1462 | print_log() |
---|
[1593] | 1463 | if insitu: |
---|
| 1464 | self._assign(s) |
---|
| 1465 | else: |
---|
| 1466 | return s |
---|
[710] | 1467 | |
---|
[1589] | 1468 | @print_log_dec |
---|
[931] | 1469 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[513] | 1470 | """ |
---|
| 1471 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 1472 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 1473 | set_freqframe. |
---|
| 1474 | Parameters: |
---|
| 1475 | reftime: reference time to align at. By default, the time of |
---|
| 1476 | the first row of data is used. |
---|
| 1477 | method: Interpolation method for regridding the spectra. |
---|
| 1478 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 1479 | and "spline" |
---|
| 1480 | insitu: if False a new scantable is returned. |
---|
| 1481 | Otherwise, the scaling is done in-situ |
---|
| 1482 | The default is taken from .asaprc (False) |
---|
| 1483 | """ |
---|
[931] | 1484 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 1485 | self._math._setinsitu(insitu) |
---|
[513] | 1486 | varlist = vars() |
---|
[1593] | 1487 | reftime = reftime or "" |
---|
[931] | 1488 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 1489 | s._add_history("freq_align", varlist) |
---|
[1819] | 1490 | print_log() |
---|
[876] | 1491 | if insitu: self._assign(s) |
---|
| 1492 | else: return s |
---|
[513] | 1493 | |
---|
[1589] | 1494 | @print_log_dec |
---|
[1725] | 1495 | def opacity(self, tau=None, insitu=None): |
---|
[513] | 1496 | """ |
---|
| 1497 | Apply an opacity correction. The data |
---|
| 1498 | and Tsys are multiplied by the correction factor. |
---|
| 1499 | Parameters: |
---|
[1689] | 1500 | tau: (list of) opacity from which the correction factor is |
---|
[513] | 1501 | exp(tau*ZD) |
---|
[1689] | 1502 | where ZD is the zenith-distance. |
---|
| 1503 | If a list is provided, it has to be of length nIF, |
---|
| 1504 | nIF*nPol or 1 and in order of IF/POL, e.g. |
---|
| 1505 | [opif0pol0, opif0pol1, opif1pol0 ...] |
---|
[1725] | 1506 | if tau is `None` the opacities are determined from a |
---|
| 1507 | model. |
---|
[513] | 1508 | insitu: if False a new scantable is returned. |
---|
| 1509 | Otherwise, the scaling is done in-situ |
---|
| 1510 | The default is taken from .asaprc (False) |
---|
| 1511 | """ |
---|
| 1512 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1513 | self._math._setinsitu(insitu) |
---|
[513] | 1514 | varlist = vars() |
---|
[1689] | 1515 | if not hasattr(tau, "__len__"): |
---|
| 1516 | tau = [tau] |
---|
[876] | 1517 | s = scantable(self._math._opacity(self, tau)) |
---|
| 1518 | s._add_history("opacity", varlist) |
---|
[1819] | 1519 | print_log() |
---|
[876] | 1520 | if insitu: self._assign(s) |
---|
| 1521 | else: return s |
---|
[513] | 1522 | |
---|
[1589] | 1523 | @print_log_dec |
---|
[513] | 1524 | def bin(self, width=5, insitu=None): |
---|
| 1525 | """ |
---|
| 1526 | Return a scan where all spectra have been binned up. |
---|
[1348] | 1527 | Parameters: |
---|
[513] | 1528 | width: The bin width (default=5) in pixels |
---|
| 1529 | insitu: if False a new scantable is returned. |
---|
| 1530 | Otherwise, the scaling is done in-situ |
---|
| 1531 | The default is taken from .asaprc (False) |
---|
| 1532 | """ |
---|
| 1533 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1534 | self._math._setinsitu(insitu) |
---|
[513] | 1535 | varlist = vars() |
---|
[876] | 1536 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1537 | s._add_history("bin", varlist) |
---|
[1819] | 1538 | print_log() |
---|
[1589] | 1539 | if insitu: |
---|
| 1540 | self._assign(s) |
---|
| 1541 | else: |
---|
| 1542 | return s |
---|
[513] | 1543 | |
---|
[1589] | 1544 | @print_log_dec |
---|
[513] | 1545 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 1546 | """ |
---|
[1348] | 1547 | Return a scan where all spectra have been binned up. |
---|
[1573] | 1548 | |
---|
[1348] | 1549 | Parameters: |
---|
[513] | 1550 | width: The bin width (default=5) in pixels |
---|
| 1551 | method: Interpolation method when correcting from a table. |
---|
| 1552 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1553 | and "spline" |
---|
| 1554 | insitu: if False a new scantable is returned. |
---|
| 1555 | Otherwise, the scaling is done in-situ |
---|
| 1556 | The default is taken from .asaprc (False) |
---|
| 1557 | """ |
---|
| 1558 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1559 | self._math._setinsitu(insitu) |
---|
[513] | 1560 | varlist = vars() |
---|
[876] | 1561 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1562 | s._add_history("resample", varlist) |
---|
[1819] | 1563 | print_log() |
---|
[876] | 1564 | if insitu: self._assign(s) |
---|
| 1565 | else: return s |
---|
[513] | 1566 | |
---|
[1589] | 1567 | @print_log_dec |
---|
[946] | 1568 | def average_pol(self, mask=None, weight='none'): |
---|
| 1569 | """ |
---|
| 1570 | Average the Polarisations together. |
---|
| 1571 | Parameters: |
---|
| 1572 | mask: An optional mask defining the region, where the |
---|
| 1573 | averaging will be applied. The output will have all |
---|
| 1574 | specified points masked. |
---|
| 1575 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1576 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1577 | """ |
---|
| 1578 | varlist = vars() |
---|
[1593] | 1579 | mask = mask or () |
---|
[1010] | 1580 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1581 | s._add_history("average_pol", varlist) |
---|
[1819] | 1582 | print_log() |
---|
[992] | 1583 | return s |
---|
[513] | 1584 | |
---|
[1589] | 1585 | @print_log_dec |
---|
[1145] | 1586 | def average_beam(self, mask=None, weight='none'): |
---|
| 1587 | """ |
---|
| 1588 | Average the Beams together. |
---|
| 1589 | Parameters: |
---|
| 1590 | mask: An optional mask defining the region, where the |
---|
| 1591 | averaging will be applied. The output will have all |
---|
| 1592 | specified points masked. |
---|
| 1593 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1594 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1595 | """ |
---|
| 1596 | varlist = vars() |
---|
[1593] | 1597 | mask = mask or () |
---|
[1145] | 1598 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1599 | s._add_history("average_beam", varlist) |
---|
[1819] | 1600 | print_log() |
---|
[1145] | 1601 | return s |
---|
| 1602 | |
---|
[1586] | 1603 | def parallactify(self, pflag): |
---|
[1617] | 1604 | """ |
---|
[1843] | 1605 | Set a flag to indicate whether this data should be treated as having |
---|
[1617] | 1606 | been 'parallactified' (total phase == 0.0) |
---|
| 1607 | Parameters: |
---|
[1843] | 1608 | pflag: Bool indicating whether to turn this on (True) or |
---|
[1617] | 1609 | off (False) |
---|
| 1610 | """ |
---|
[1586] | 1611 | varlist = vars() |
---|
| 1612 | self._parallactify(pflag) |
---|
| 1613 | self._add_history("parallactify", varlist) |
---|
| 1614 | |
---|
[1589] | 1615 | @print_log_dec |
---|
[992] | 1616 | def convert_pol(self, poltype=None): |
---|
| 1617 | """ |
---|
| 1618 | Convert the data to a different polarisation type. |
---|
[1565] | 1619 | Note that you will need cross-polarisation terms for most conversions. |
---|
[992] | 1620 | Parameters: |
---|
| 1621 | poltype: The new polarisation type. Valid types are: |
---|
[1565] | 1622 | "linear", "circular", "stokes" and "linpol" |
---|
[992] | 1623 | """ |
---|
| 1624 | varlist = vars() |
---|
| 1625 | try: |
---|
| 1626 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1627 | except RuntimeError, msg: |
---|
[992] | 1628 | if rcParams['verbose']: |
---|
[1819] | 1629 | #print msg |
---|
| 1630 | print_log() |
---|
| 1631 | asaplog.push( str(msg) ) |
---|
| 1632 | print_log( 'ERROR' ) |
---|
[1118] | 1633 | return |
---|
[992] | 1634 | else: |
---|
| 1635 | raise |
---|
[1118] | 1636 | s._add_history("convert_pol", varlist) |
---|
[1819] | 1637 | print_log() |
---|
[992] | 1638 | return s |
---|
| 1639 | |
---|
[1589] | 1640 | @print_log_dec |
---|
[1819] | 1641 | def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, insitu=None): |
---|
[513] | 1642 | """ |
---|
| 1643 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 1644 | Parameters: |
---|
| 1645 | kernel: The type of smoothing kernel. Select from |
---|
[1574] | 1646 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian' |
---|
| 1647 | or 'poly' |
---|
[513] | 1648 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1649 | ignored otherwise it defauls to 5 pixels. |
---|
| 1650 | For 'gaussian' it is the Full Width Half |
---|
| 1651 | Maximum. For 'boxcar' it is the full width. |
---|
[1574] | 1652 | For 'rmedian' and 'poly' it is the half width. |
---|
| 1653 | order: Optional parameter for 'poly' kernel (default is 2), to |
---|
| 1654 | specify the order of the polnomial. Ignored by all other |
---|
| 1655 | kernels. |
---|
[1819] | 1656 | plot: plot the original and the smoothed spectra. |
---|
| 1657 | In this each indivual fit has to be approved, by |
---|
| 1658 | typing 'y' or 'n' |
---|
[513] | 1659 | insitu: if False a new scantable is returned. |
---|
| 1660 | Otherwise, the scaling is done in-situ |
---|
| 1661 | The default is taken from .asaprc (False) |
---|
| 1662 | Example: |
---|
| 1663 | none |
---|
| 1664 | """ |
---|
| 1665 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1666 | self._math._setinsitu(insitu) |
---|
[513] | 1667 | varlist = vars() |
---|
[1819] | 1668 | |
---|
| 1669 | if plot: orgscan = self.copy() |
---|
| 1670 | |
---|
[1574] | 1671 | s = scantable(self._math._smooth(self, kernel.lower(), width, order)) |
---|
[876] | 1672 | s._add_history("smooth", varlist) |
---|
[1819] | 1673 | |
---|
| 1674 | if plot: |
---|
| 1675 | if rcParams['plotter.gui']: |
---|
| 1676 | from asap.asaplotgui import asaplotgui as asaplot |
---|
| 1677 | else: |
---|
| 1678 | from asap.asaplot import asaplot |
---|
| 1679 | self._p=asaplot() |
---|
| 1680 | self._p.set_panels() |
---|
| 1681 | ylab=s._get_ordinate_label() |
---|
| 1682 | #self._p.palette(0,["#777777","red"]) |
---|
| 1683 | for r in xrange(s.nrow()): |
---|
| 1684 | xsm=s._getabcissa(r) |
---|
| 1685 | ysm=s._getspectrum(r) |
---|
| 1686 | xorg=orgscan._getabcissa(r) |
---|
| 1687 | yorg=orgscan._getspectrum(r) |
---|
| 1688 | self._p.clear() |
---|
| 1689 | self._p.hold() |
---|
| 1690 | self._p.set_axes('ylabel',ylab) |
---|
| 1691 | self._p.set_axes('xlabel',s._getabcissalabel(r)) |
---|
| 1692 | self._p.set_axes('title',s._getsourcename(r)) |
---|
| 1693 | self._p.set_line(label='Original',color="#777777") |
---|
| 1694 | self._p.plot(xorg,yorg) |
---|
| 1695 | self._p.set_line(label='Smoothed',color="red") |
---|
| 1696 | self._p.plot(xsm,ysm) |
---|
| 1697 | ### Ugly part for legend |
---|
| 1698 | for i in [0,1]: |
---|
| 1699 | self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]]) |
---|
| 1700 | self._p.release() |
---|
| 1701 | ### Ugly part for legend |
---|
| 1702 | self._p.subplots[0]['lines']=[] |
---|
| 1703 | res = raw_input("Accept smoothing ([y]/n): ") |
---|
| 1704 | if res.upper() == 'N': |
---|
| 1705 | s._setspectrum(yorg, r) |
---|
| 1706 | self._p.unmap() |
---|
| 1707 | self._p = None |
---|
| 1708 | del orgscan |
---|
| 1709 | |
---|
| 1710 | print_log() |
---|
[876] | 1711 | if insitu: self._assign(s) |
---|
| 1712 | else: return s |
---|
[513] | 1713 | |
---|
[1589] | 1714 | @print_log_dec |
---|
[1617] | 1715 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, |
---|
| 1716 | insitu=None): |
---|
[513] | 1717 | """ |
---|
| 1718 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1719 | Parameters: |
---|
[794] | 1720 | mask: an optional mask |
---|
| 1721 | order: the order of the polynomial (default is 0) |
---|
[1061] | 1722 | plot: plot the fit and the residual. In this each |
---|
| 1723 | indivual fit has to be approved, by typing 'y' |
---|
| 1724 | or 'n' |
---|
[1391] | 1725 | uselin: use linear polynomial fit |
---|
[794] | 1726 | insitu: if False a new scantable is returned. |
---|
| 1727 | Otherwise, the scaling is done in-situ |
---|
| 1728 | The default is taken from .asaprc (False) |
---|
[513] | 1729 | Example: |
---|
| 1730 | # return a scan baselined by a third order polynomial, |
---|
| 1731 | # not using a mask |
---|
| 1732 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1733 | """ |
---|
[513] | 1734 | if insitu is None: insitu = rcParams['insitu'] |
---|
[1819] | 1735 | if not insitu: |
---|
| 1736 | workscan = self.copy() |
---|
| 1737 | else: |
---|
| 1738 | workscan = self |
---|
[513] | 1739 | varlist = vars() |
---|
| 1740 | if mask is None: |
---|
[1295] | 1741 | mask = [True for i in xrange(self.nchan(-1))] |
---|
[1819] | 1742 | |
---|
[513] | 1743 | from asap.asapfitter import fitter |
---|
[1217] | 1744 | try: |
---|
| 1745 | f = fitter() |
---|
[1391] | 1746 | if uselin: |
---|
| 1747 | f.set_function(lpoly=order) |
---|
| 1748 | else: |
---|
| 1749 | f.set_function(poly=order) |
---|
[1819] | 1750 | |
---|
| 1751 | rows = range(workscan.nrow()) |
---|
| 1752 | if len(rows) > 0: |
---|
| 1753 | self.blpars = [] |
---|
| 1754 | |
---|
| 1755 | for r in rows: |
---|
| 1756 | # take into account flagtra info (CAS-1434) |
---|
| 1757 | flagtra = workscan._getmask(r) |
---|
| 1758 | actualmask = mask[:] |
---|
| 1759 | if len(actualmask) == 0: |
---|
| 1760 | actualmask = list(flagtra[:]) |
---|
| 1761 | else: |
---|
| 1762 | if len(actualmask) != len(flagtra): |
---|
| 1763 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 1764 | else: |
---|
| 1765 | for i in range(0, len(actualmask)): |
---|
| 1766 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 1767 | f.set_scan(workscan, actualmask) |
---|
| 1768 | f.x = workscan._getabcissa(r) |
---|
| 1769 | f.y = workscan._getspectrum(r) |
---|
| 1770 | f.data = None |
---|
| 1771 | f.fit() |
---|
| 1772 | if plot: |
---|
| 1773 | f.plot(residual=True) |
---|
| 1774 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1775 | if x.upper() == 'N': |
---|
| 1776 | self.blpars.append(None) |
---|
| 1777 | continue |
---|
| 1778 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
| 1779 | self.blpars.append(f.get_parameters()) |
---|
| 1780 | |
---|
| 1781 | if plot: |
---|
| 1782 | f._p.unmap() |
---|
| 1783 | f._p = None |
---|
| 1784 | workscan._add_history("poly_baseline", varlist) |
---|
| 1785 | print_log() |
---|
| 1786 | if insitu: self._assign(workscan) |
---|
| 1787 | else: return workscan |
---|
[1217] | 1788 | except RuntimeError: |
---|
| 1789 | msg = "The fit failed, possibly because it didn't converge." |
---|
| 1790 | if rcParams['verbose']: |
---|
[1819] | 1791 | #print msg |
---|
| 1792 | print_log() |
---|
| 1793 | asaplog.push( str(msg) ) |
---|
| 1794 | print_log( 'ERROR' ) |
---|
[1217] | 1795 | return |
---|
| 1796 | else: |
---|
| 1797 | raise RuntimeError(msg) |
---|
[513] | 1798 | |
---|
[1819] | 1799 | |
---|
[1118] | 1800 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
[1280] | 1801 | threshold=3, chan_avg_limit=1, plot=False, |
---|
| 1802 | insitu=None): |
---|
[880] | 1803 | """ |
---|
| 1804 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1805 | Spectral lines are detected first using linefinder and masked out |
---|
| 1806 | to avoid them affecting the baseline solution. |
---|
| 1807 | |
---|
| 1808 | Parameters: |
---|
| 1809 | mask: an optional mask retreived from scantable |
---|
| 1810 | edge: an optional number of channel to drop at |
---|
| 1811 | the edge of spectrum. If only one value is |
---|
| 1812 | specified, the same number will be dropped from |
---|
| 1813 | both sides of the spectrum. Default is to keep |
---|
[907] | 1814 | all channels. Nested tuples represent individual |
---|
[976] | 1815 | edge selection for different IFs (a number of spectral |
---|
| 1816 | channels can be different) |
---|
[880] | 1817 | order: the order of the polynomial (default is 0) |
---|
| 1818 | threshold: the threshold used by line finder. It is better to |
---|
| 1819 | keep it large as only strong lines affect the |
---|
| 1820 | baseline solution. |
---|
[1280] | 1821 | chan_avg_limit: |
---|
| 1822 | a maximum number of consequtive spectral channels to |
---|
| 1823 | average during the search of weak and broad lines. |
---|
| 1824 | The default is no averaging (and no search for weak |
---|
| 1825 | lines). If such lines can affect the fitted baseline |
---|
| 1826 | (e.g. a high order polynomial is fitted), increase this |
---|
| 1827 | parameter (usually values up to 8 are reasonable). Most |
---|
| 1828 | users of this method should find the default value |
---|
| 1829 | sufficient. |
---|
[1061] | 1830 | plot: plot the fit and the residual. In this each |
---|
| 1831 | indivual fit has to be approved, by typing 'y' |
---|
| 1832 | or 'n' |
---|
[880] | 1833 | insitu: if False a new scantable is returned. |
---|
| 1834 | Otherwise, the scaling is done in-situ |
---|
| 1835 | The default is taken from .asaprc (False) |
---|
| 1836 | |
---|
| 1837 | Example: |
---|
| 1838 | scan2=scan.auto_poly_baseline(order=7) |
---|
| 1839 | """ |
---|
| 1840 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1841 | varlist = vars() |
---|
| 1842 | from asap.asapfitter import fitter |
---|
| 1843 | from asap.asaplinefind import linefinder |
---|
| 1844 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1845 | |
---|
[976] | 1846 | # check whether edge is set up for each IF individually |
---|
[1118] | 1847 | individualedge = False; |
---|
| 1848 | if len(edge) > 1: |
---|
| 1849 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 1850 | individualedge = True; |
---|
[907] | 1851 | |
---|
[1118] | 1852 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 1853 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1854 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1855 | to make individual selection for different IFs." |
---|
[919] | 1856 | |
---|
[1118] | 1857 | curedge = (0, 0) |
---|
| 1858 | if individualedge: |
---|
| 1859 | for edgepar in edge: |
---|
| 1860 | if not _is_valid(edgepar, int): |
---|
| 1861 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 1862 | to be a pair of integers or an integer." |
---|
[907] | 1863 | else: |
---|
[1118] | 1864 | curedge = edge; |
---|
[880] | 1865 | |
---|
| 1866 | # setup fitter |
---|
| 1867 | f = fitter() |
---|
| 1868 | f.set_function(poly=order) |
---|
| 1869 | |
---|
| 1870 | # setup line finder |
---|
[1118] | 1871 | fl = linefinder() |
---|
[1268] | 1872 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
[880] | 1873 | |
---|
| 1874 | if not insitu: |
---|
[1118] | 1875 | workscan = self.copy() |
---|
[880] | 1876 | else: |
---|
[1118] | 1877 | workscan = self |
---|
[880] | 1878 | |
---|
[907] | 1879 | fl.set_scan(workscan) |
---|
| 1880 | |
---|
[1118] | 1881 | rows = range(workscan.nrow()) |
---|
[1819] | 1882 | # Save parameters of baseline fits & masklists as a class attribute. |
---|
| 1883 | # NOTICE: It does not reflect changes in scantable! |
---|
| 1884 | if len(rows) > 0: |
---|
| 1885 | self.blpars=[] |
---|
| 1886 | self.masklists=[] |
---|
[880] | 1887 | asaplog.push("Processing:") |
---|
| 1888 | for r in rows: |
---|
[1118] | 1889 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 1890 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 1891 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 1892 | asaplog.push(msg, False) |
---|
[907] | 1893 | |
---|
[976] | 1894 | # figure out edge parameter |
---|
[1118] | 1895 | if individualedge: |
---|
| 1896 | if len(edge) >= workscan.getif(r): |
---|
| 1897 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 1898 | "be less than the number of IFs" |
---|
| 1899 | curedge = edge[workscan.getif(r)] |
---|
[919] | 1900 | |
---|
[1819] | 1901 | # take into account flagtra info (CAS-1434) |
---|
| 1902 | flagtra = workscan._getmask(r) |
---|
| 1903 | actualmask = mask[:] |
---|
| 1904 | if len(actualmask) == 0: |
---|
| 1905 | actualmask = list(flagtra[:]) |
---|
| 1906 | else: |
---|
| 1907 | if len(actualmask) != len(flagtra): |
---|
| 1908 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 1909 | else: |
---|
| 1910 | for i in range(0, len(actualmask)): |
---|
| 1911 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 1912 | |
---|
[976] | 1913 | # setup line finder |
---|
[1819] | 1914 | fl.find_lines(r, actualmask, curedge) |
---|
| 1915 | outmask=fl.get_mask() |
---|
| 1916 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1917 | f.x = workscan._getabcissa(r) |
---|
| 1918 | f.y = workscan._getspectrum(r) |
---|
| 1919 | f.data = None |
---|
[880] | 1920 | f.fit() |
---|
[1819] | 1921 | |
---|
| 1922 | # Show mask list |
---|
| 1923 | masklist=workscan.get_masklist(fl.get_mask(),row=r) |
---|
| 1924 | msg = "mask range: "+str(masklist) |
---|
| 1925 | asaplog.push(msg, False) |
---|
| 1926 | |
---|
[1061] | 1927 | if plot: |
---|
| 1928 | f.plot(residual=True) |
---|
| 1929 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1930 | if x.upper() == 'N': |
---|
[1819] | 1931 | self.blpars.append(None) |
---|
| 1932 | self.masklists.append(None) |
---|
[1061] | 1933 | continue |
---|
[1819] | 1934 | |
---|
[880] | 1935 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1819] | 1936 | self.blpars.append(f.get_parameters()) |
---|
| 1937 | self.masklists.append(masklist) |
---|
[1061] | 1938 | if plot: |
---|
| 1939 | f._p.unmap() |
---|
| 1940 | f._p = None |
---|
| 1941 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 1942 | if insitu: |
---|
| 1943 | self._assign(workscan) |
---|
| 1944 | else: |
---|
| 1945 | return workscan |
---|
| 1946 | |
---|
[1589] | 1947 | @print_log_dec |
---|
[914] | 1948 | def rotate_linpolphase(self, angle): |
---|
| 1949 | """ |
---|
| 1950 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1951 | This is always done in situ in the raw data. So if you call this |
---|
| 1952 | function more than once then each call rotates the phase further. |
---|
| 1953 | Parameters: |
---|
| 1954 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1955 | Examples: |
---|
| 1956 | scan.rotate_linpolphase(2.3) |
---|
| 1957 | """ |
---|
| 1958 | varlist = vars() |
---|
[936] | 1959 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 1960 | self._add_history("rotate_linpolphase", varlist) |
---|
[1819] | 1961 | print_log() |
---|
[914] | 1962 | return |
---|
[710] | 1963 | |
---|
[1589] | 1964 | @print_log_dec |
---|
[914] | 1965 | def rotate_xyphase(self, angle): |
---|
| 1966 | """ |
---|
| 1967 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1968 | in the data. So if you call this function more than once |
---|
| 1969 | then each call rotates the phase further. |
---|
| 1970 | Parameters: |
---|
| 1971 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1972 | Examples: |
---|
| 1973 | scan.rotate_xyphase(2.3) |
---|
| 1974 | """ |
---|
| 1975 | varlist = vars() |
---|
[936] | 1976 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 1977 | self._add_history("rotate_xyphase", varlist) |
---|
[1819] | 1978 | print_log() |
---|
[914] | 1979 | return |
---|
| 1980 | |
---|
[1589] | 1981 | @print_log_dec |
---|
[914] | 1982 | def swap_linears(self): |
---|
| 1983 | """ |
---|
[1573] | 1984 | Swap the linear polarisations XX and YY, or better the first two |
---|
[1348] | 1985 | polarisations as this also works for ciculars. |
---|
[914] | 1986 | """ |
---|
| 1987 | varlist = vars() |
---|
[936] | 1988 | self._math._swap_linears(self) |
---|
[914] | 1989 | self._add_history("swap_linears", varlist) |
---|
[1819] | 1990 | print_log() |
---|
[914] | 1991 | return |
---|
| 1992 | |
---|
[1589] | 1993 | @print_log_dec |
---|
[914] | 1994 | def invert_phase(self): |
---|
| 1995 | """ |
---|
| 1996 | Invert the phase of the complex polarisation |
---|
| 1997 | """ |
---|
| 1998 | varlist = vars() |
---|
[936] | 1999 | self._math._invert_phase(self) |
---|
[914] | 2000 | self._add_history("invert_phase", varlist) |
---|
[1819] | 2001 | print_log() |
---|
[914] | 2002 | return |
---|
| 2003 | |
---|
[1589] | 2004 | @print_log_dec |
---|
[876] | 2005 | def add(self, offset, insitu=None): |
---|
[513] | 2006 | """ |
---|
| 2007 | Return a scan where all spectra have the offset added |
---|
| 2008 | Parameters: |
---|
| 2009 | offset: the offset |
---|
| 2010 | insitu: if False a new scantable is returned. |
---|
| 2011 | Otherwise, the scaling is done in-situ |
---|
| 2012 | The default is taken from .asaprc (False) |
---|
| 2013 | """ |
---|
| 2014 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2015 | self._math._setinsitu(insitu) |
---|
[513] | 2016 | varlist = vars() |
---|
[876] | 2017 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 2018 | s._add_history("add", varlist) |
---|
[1819] | 2019 | print_log() |
---|
[876] | 2020 | if insitu: |
---|
| 2021 | self._assign(s) |
---|
| 2022 | else: |
---|
[513] | 2023 | return s |
---|
| 2024 | |
---|
[1589] | 2025 | @print_log_dec |
---|
[1308] | 2026 | def scale(self, factor, tsys=True, insitu=None): |
---|
[513] | 2027 | """ |
---|
| 2028 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 2029 | Parameters: |
---|
[1819] | 2030 | factor: the scaling factor (float or 1D float list) |
---|
[513] | 2031 | insitu: if False a new scantable is returned. |
---|
| 2032 | Otherwise, the scaling is done in-situ |
---|
| 2033 | The default is taken from .asaprc (False) |
---|
| 2034 | tsys: if True (default) then apply the operation to Tsys |
---|
| 2035 | as well as the data |
---|
| 2036 | """ |
---|
| 2037 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2038 | self._math._setinsitu(insitu) |
---|
[513] | 2039 | varlist = vars() |
---|
[1819] | 2040 | s = None |
---|
| 2041 | import numpy |
---|
| 2042 | if isinstance(factor, list) or isinstance(factor, numpy.ndarray): |
---|
| 2043 | if isinstance(factor[0], list) or isinstance(factor[0], numpy.ndarray): |
---|
| 2044 | from asapmath import _array2dOp |
---|
| 2045 | s = _array2dOp( self.copy(), factor, "MUL", tsys ) |
---|
| 2046 | else: |
---|
| 2047 | s = scantable( self._math._arrayop( self.copy(), factor, "MUL", tsys ) ) |
---|
| 2048 | else: |
---|
| 2049 | s = scantable(self._math._unaryop(self.copy(), factor, "MUL", tsys)) |
---|
[1118] | 2050 | s._add_history("scale", varlist) |
---|
[1819] | 2051 | print_log() |
---|
[876] | 2052 | if insitu: |
---|
| 2053 | self._assign(s) |
---|
| 2054 | else: |
---|
[513] | 2055 | return s |
---|
| 2056 | |
---|
[1504] | 2057 | def set_sourcetype(self, match, matchtype="pattern", |
---|
| 2058 | sourcetype="reference"): |
---|
[1502] | 2059 | """ |
---|
| 2060 | Set the type of the source to be an source or reference scan |
---|
| 2061 | using the provided pattern: |
---|
| 2062 | Parameters: |
---|
[1504] | 2063 | match: a Unix style pattern, regular expression or selector |
---|
| 2064 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
| 2065 | 'regex' regular expression |
---|
[1502] | 2066 | sourcetype: the type of the source to use (source/reference) |
---|
| 2067 | """ |
---|
| 2068 | varlist = vars() |
---|
| 2069 | basesel = self.get_selection() |
---|
| 2070 | stype = -1 |
---|
| 2071 | if sourcetype.lower().startswith("r"): |
---|
| 2072 | stype = 1 |
---|
| 2073 | elif sourcetype.lower().startswith("s"): |
---|
| 2074 | stype = 0 |
---|
[1504] | 2075 | else: |
---|
[1502] | 2076 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)") |
---|
[1504] | 2077 | if matchtype.lower().startswith("p"): |
---|
| 2078 | matchtype = "pattern" |
---|
| 2079 | elif matchtype.lower().startswith("r"): |
---|
| 2080 | matchtype = "regex" |
---|
| 2081 | else: |
---|
| 2082 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
[1502] | 2083 | sel = selector() |
---|
| 2084 | if isinstance(match, selector): |
---|
| 2085 | sel = match |
---|
| 2086 | else: |
---|
[1504] | 2087 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match)) |
---|
[1502] | 2088 | self.set_selection(basesel+sel) |
---|
| 2089 | self._setsourcetype(stype) |
---|
| 2090 | self.set_selection(basesel) |
---|
[1573] | 2091 | self._add_history("set_sourcetype", varlist) |
---|
[1502] | 2092 | |
---|
[1589] | 2093 | @print_log_dec |
---|
[1819] | 2094 | def auto_quotient(self, preserve=True, mode='paired', verify=False): |
---|
[670] | 2095 | """ |
---|
| 2096 | This function allows to build quotients automatically. |
---|
[1819] | 2097 | It assumes the observation to have the same number of |
---|
[670] | 2098 | "ons" and "offs" |
---|
| 2099 | Parameters: |
---|
[710] | 2100 | preserve: you can preserve (default) the continuum or |
---|
| 2101 | remove it. The equations used are |
---|
[670] | 2102 | preserve: Output = Toff * (on/off) - Toff |
---|
[1070] | 2103 | remove: Output = Toff * (on/off) - Ton |
---|
[1573] | 2104 | mode: the on/off detection mode |
---|
[1348] | 2105 | 'paired' (default) |
---|
| 2106 | identifies 'off' scans by the |
---|
| 2107 | trailing '_R' (Mopra/Parkes) or |
---|
| 2108 | '_e'/'_w' (Tid) and matches |
---|
| 2109 | on/off pairs from the observing pattern |
---|
[1502] | 2110 | 'time' |
---|
| 2111 | finds the closest off in time |
---|
[1348] | 2112 | |
---|
[670] | 2113 | """ |
---|
[1348] | 2114 | modes = ["time", "paired"] |
---|
[670] | 2115 | if not mode in modes: |
---|
[876] | 2116 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 2117 | raise ValueError(msg) |
---|
| 2118 | varlist = vars() |
---|
[1348] | 2119 | s = None |
---|
| 2120 | if mode.lower() == "paired": |
---|
| 2121 | basesel = self.get_selection() |
---|
[1356] | 2122 | sel = selector()+basesel |
---|
| 2123 | sel.set_query("SRCTYPE==1") |
---|
| 2124 | self.set_selection(sel) |
---|
[1348] | 2125 | offs = self.copy() |
---|
| 2126 | sel.set_query("SRCTYPE==0") |
---|
[1356] | 2127 | self.set_selection(sel) |
---|
[1348] | 2128 | ons = self.copy() |
---|
| 2129 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 2130 | self.set_selection(basesel) |
---|
| 2131 | elif mode.lower() == "time": |
---|
| 2132 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 2133 | s._add_history("auto_quotient", varlist) |
---|
[1819] | 2134 | print_log() |
---|
[876] | 2135 | return s |
---|
[710] | 2136 | |
---|
[1589] | 2137 | @print_log_dec |
---|
[1145] | 2138 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1141] | 2139 | """ |
---|
[1143] | 2140 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
| 2141 | Parameters: |
---|
[1145] | 2142 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1143] | 2143 | weight: How to average the off beams. Default is 'median'. |
---|
[1145] | 2144 | preserve: you can preserve (default) the continuum or |
---|
| 2145 | remove it. The equations used are |
---|
| 2146 | preserve: Output = Toff * (on/off) - Toff |
---|
| 2147 | remove: Output = Toff * (on/off) - Ton |
---|
[1217] | 2148 | """ |
---|
[1593] | 2149 | mask = mask or () |
---|
[1141] | 2150 | varlist = vars() |
---|
| 2151 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 2152 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 2153 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 2154 | from asapmath import quotient |
---|
[1145] | 2155 | q = quotient(on, off, preserve) |
---|
[1143] | 2156 | q._add_history("mx_quotient", varlist) |
---|
[1819] | 2157 | print_log() |
---|
[1217] | 2158 | return q |
---|
[513] | 2159 | |
---|
[1589] | 2160 | @print_log_dec |
---|
[718] | 2161 | def freq_switch(self, insitu=None): |
---|
| 2162 | """ |
---|
| 2163 | Apply frequency switching to the data. |
---|
| 2164 | Parameters: |
---|
| 2165 | insitu: if False a new scantable is returned. |
---|
| 2166 | Otherwise, the swictching is done in-situ |
---|
| 2167 | The default is taken from .asaprc (False) |
---|
| 2168 | Example: |
---|
| 2169 | none |
---|
| 2170 | """ |
---|
| 2171 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2172 | self._math._setinsitu(insitu) |
---|
[718] | 2173 | varlist = vars() |
---|
[876] | 2174 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 2175 | s._add_history("freq_switch", varlist) |
---|
[1819] | 2176 | print_log() |
---|
[876] | 2177 | if insitu: self._assign(s) |
---|
| 2178 | else: return s |
---|
[718] | 2179 | |
---|
[1589] | 2180 | @print_log_dec |
---|
[780] | 2181 | def recalc_azel(self): |
---|
| 2182 | """ |
---|
| 2183 | Recalculate the azimuth and elevation for each position. |
---|
| 2184 | Parameters: |
---|
| 2185 | none |
---|
| 2186 | Example: |
---|
| 2187 | """ |
---|
| 2188 | varlist = vars() |
---|
[876] | 2189 | self._recalcazel() |
---|
[780] | 2190 | self._add_history("recalc_azel", varlist) |
---|
[1819] | 2191 | print_log() |
---|
[780] | 2192 | return |
---|
| 2193 | |
---|
[1589] | 2194 | @print_log_dec |
---|
[513] | 2195 | def __add__(self, other): |
---|
| 2196 | varlist = vars() |
---|
| 2197 | s = None |
---|
| 2198 | if isinstance(other, scantable): |
---|
[1573] | 2199 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
[513] | 2200 | elif isinstance(other, float): |
---|
[876] | 2201 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 2202 | else: |
---|
[718] | 2203 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2204 | s._add_history("operator +", varlist) |
---|
| 2205 | return s |
---|
| 2206 | |
---|
[1589] | 2207 | @print_log_dec |
---|
[513] | 2208 | def __sub__(self, other): |
---|
| 2209 | """ |
---|
| 2210 | implicit on all axes and on Tsys |
---|
| 2211 | """ |
---|
| 2212 | varlist = vars() |
---|
| 2213 | s = None |
---|
| 2214 | if isinstance(other, scantable): |
---|
[1588] | 2215 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
[513] | 2216 | elif isinstance(other, float): |
---|
[876] | 2217 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 2218 | else: |
---|
[718] | 2219 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2220 | s._add_history("operator -", varlist) |
---|
| 2221 | return s |
---|
[710] | 2222 | |
---|
[1589] | 2223 | @print_log_dec |
---|
[513] | 2224 | def __mul__(self, other): |
---|
| 2225 | """ |
---|
| 2226 | implicit on all axes and on Tsys |
---|
| 2227 | """ |
---|
| 2228 | varlist = vars() |
---|
| 2229 | s = None |
---|
| 2230 | if isinstance(other, scantable): |
---|
[1588] | 2231 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
[513] | 2232 | elif isinstance(other, float): |
---|
[876] | 2233 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 2234 | else: |
---|
[718] | 2235 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2236 | s._add_history("operator *", varlist) |
---|
| 2237 | return s |
---|
| 2238 | |
---|
[710] | 2239 | |
---|
[1589] | 2240 | @print_log_dec |
---|
[513] | 2241 | def __div__(self, other): |
---|
| 2242 | """ |
---|
| 2243 | implicit on all axes and on Tsys |
---|
| 2244 | """ |
---|
| 2245 | varlist = vars() |
---|
| 2246 | s = None |
---|
| 2247 | if isinstance(other, scantable): |
---|
[1589] | 2248 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
[513] | 2249 | elif isinstance(other, float): |
---|
| 2250 | if other == 0.0: |
---|
[718] | 2251 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 2252 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 2253 | else: |
---|
[718] | 2254 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2255 | s._add_history("operator /", varlist) |
---|
| 2256 | return s |
---|
| 2257 | |
---|
[530] | 2258 | def get_fit(self, row=0): |
---|
| 2259 | """ |
---|
| 2260 | Print or return the stored fits for a row in the scantable |
---|
| 2261 | Parameters: |
---|
| 2262 | row: the row which the fit has been applied to. |
---|
| 2263 | """ |
---|
| 2264 | if row > self.nrow(): |
---|
| 2265 | return |
---|
[976] | 2266 | from asap.asapfit import asapfit |
---|
[530] | 2267 | fit = asapfit(self._getfit(row)) |
---|
[718] | 2268 | if rcParams['verbose']: |
---|
[1819] | 2269 | #print fit |
---|
| 2270 | asaplog.push( '%s' %(fit) ) |
---|
| 2271 | print_log() |
---|
[530] | 2272 | return |
---|
| 2273 | else: |
---|
| 2274 | return fit.as_dict() |
---|
| 2275 | |
---|
[1483] | 2276 | def flag_nans(self): |
---|
| 2277 | """ |
---|
| 2278 | Utility function to flag NaN values in the scantable. |
---|
| 2279 | """ |
---|
| 2280 | import numpy |
---|
| 2281 | basesel = self.get_selection() |
---|
| 2282 | for i in range(self.nrow()): |
---|
[1589] | 2283 | sel = self.get_row_selector(i) |
---|
| 2284 | self.set_selection(basesel+sel) |
---|
[1483] | 2285 | nans = numpy.isnan(self._getspectrum(0)) |
---|
| 2286 | if numpy.any(nans): |
---|
| 2287 | bnans = [ bool(v) for v in nans] |
---|
| 2288 | self.flag(bnans) |
---|
| 2289 | self.set_selection(basesel) |
---|
| 2290 | |
---|
[1588] | 2291 | def get_row_selector(self, rowno): |
---|
| 2292 | return selector(beams=self.getbeam(rowno), |
---|
| 2293 | ifs=self.getif(rowno), |
---|
| 2294 | pols=self.getpol(rowno), |
---|
| 2295 | scans=self.getscan(rowno), |
---|
| 2296 | cycles=self.getcycle(rowno)) |
---|
[1573] | 2297 | |
---|
[484] | 2298 | def _add_history(self, funcname, parameters): |
---|
[1435] | 2299 | if not rcParams['scantable.history']: |
---|
| 2300 | return |
---|
[484] | 2301 | # create date |
---|
| 2302 | sep = "##" |
---|
| 2303 | from datetime import datetime |
---|
| 2304 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 2305 | hist = dstr+sep |
---|
| 2306 | hist += funcname+sep#cdate+sep |
---|
| 2307 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 2308 | for k, v in parameters.iteritems(): |
---|
[484] | 2309 | if type(v) is dict: |
---|
[1118] | 2310 | for k2, v2 in v.iteritems(): |
---|
[484] | 2311 | hist += k2 |
---|
| 2312 | hist += "=" |
---|
[1118] | 2313 | if isinstance(v2, scantable): |
---|
[484] | 2314 | hist += 'scantable' |
---|
| 2315 | elif k2 == 'mask': |
---|
[1118] | 2316 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 2317 | hist += str(self._zip_mask(v2)) |
---|
| 2318 | else: |
---|
| 2319 | hist += str(v2) |
---|
[484] | 2320 | else: |
---|
[513] | 2321 | hist += str(v2) |
---|
[484] | 2322 | else: |
---|
| 2323 | hist += k |
---|
| 2324 | hist += "=" |
---|
[1118] | 2325 | if isinstance(v, scantable): |
---|
[484] | 2326 | hist += 'scantable' |
---|
| 2327 | elif k == 'mask': |
---|
[1118] | 2328 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 2329 | hist += str(self._zip_mask(v)) |
---|
| 2330 | else: |
---|
| 2331 | hist += str(v) |
---|
[484] | 2332 | else: |
---|
| 2333 | hist += str(v) |
---|
| 2334 | hist += sep |
---|
| 2335 | hist = hist[:-2] # remove trailing '##' |
---|
| 2336 | self._addhistory(hist) |
---|
| 2337 | |
---|
[710] | 2338 | |
---|
[484] | 2339 | def _zip_mask(self, mask): |
---|
| 2340 | mask = list(mask) |
---|
| 2341 | i = 0 |
---|
| 2342 | segments = [] |
---|
| 2343 | while mask[i:].count(1): |
---|
| 2344 | i += mask[i:].index(1) |
---|
| 2345 | if mask[i:].count(0): |
---|
| 2346 | j = i + mask[i:].index(0) |
---|
| 2347 | else: |
---|
[710] | 2348 | j = len(mask) |
---|
[1118] | 2349 | segments.append([i, j]) |
---|
[710] | 2350 | i = j |
---|
[484] | 2351 | return segments |
---|
[714] | 2352 | |
---|
[626] | 2353 | def _get_ordinate_label(self): |
---|
| 2354 | fu = "("+self.get_fluxunit()+")" |
---|
| 2355 | import re |
---|
| 2356 | lbl = "Intensity" |
---|
[1118] | 2357 | if re.match(".K.", fu): |
---|
[626] | 2358 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 2359 | elif re.match(".Jy.", fu): |
---|
[626] | 2360 | lbl = "Flux density "+ fu |
---|
| 2361 | return lbl |
---|
[710] | 2362 | |
---|
[876] | 2363 | def _check_ifs(self): |
---|
| 2364 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 2365 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 2366 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 2367 | |
---|
[1819] | 2368 | def _fill(self, names, unit, average, getpt, antenna): |
---|
[976] | 2369 | first = True |
---|
| 2370 | fullnames = [] |
---|
| 2371 | for name in names: |
---|
| 2372 | name = os.path.expandvars(name) |
---|
| 2373 | name = os.path.expanduser(name) |
---|
| 2374 | if not os.path.exists(name): |
---|
| 2375 | msg = "File '%s' does not exists" % (name) |
---|
| 2376 | if rcParams['verbose']: |
---|
| 2377 | asaplog.push(msg) |
---|
[1819] | 2378 | print_log( 'ERROR' ) |
---|
[976] | 2379 | return |
---|
| 2380 | raise IOError(msg) |
---|
| 2381 | fullnames.append(name) |
---|
| 2382 | if average: |
---|
| 2383 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 2384 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 2385 | for name in fullnames: |
---|
[1073] | 2386 | tbl = Scantable(stype) |
---|
[1843] | 2387 | r = filler(tbl) |
---|
[1504] | 2388 | rx = rcParams['scantable.reference'] |
---|
[1843] | 2389 | r.setreferenceexpr(rx) |
---|
[976] | 2390 | msg = "Importing %s..." % (name) |
---|
[1118] | 2391 | asaplog.push(msg, False) |
---|
[976] | 2392 | print_log() |
---|
[1843] | 2393 | r.open(name)# antenna, -1, -1, getpt) |
---|
| 2394 | r.fill() |
---|
[976] | 2395 | if average: |
---|
[1118] | 2396 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 2397 | if not first: |
---|
| 2398 | tbl = self._math._merge([self, tbl]) |
---|
| 2399 | Scantable.__init__(self, tbl) |
---|
[1843] | 2400 | r.close() |
---|
[1118] | 2401 | del r, tbl |
---|
[976] | 2402 | first = False |
---|
| 2403 | if unit is not None: |
---|
| 2404 | self.set_fluxunit(unit) |
---|
[1824] | 2405 | if not is_casapy(): |
---|
| 2406 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[976] | 2407 | |
---|
[1402] | 2408 | def __getitem__(self, key): |
---|
| 2409 | if key < 0: |
---|
| 2410 | key += self.nrow() |
---|
| 2411 | if key >= self.nrow(): |
---|
| 2412 | raise IndexError("Row index out of range.") |
---|
| 2413 | return self._getspectrum(key) |
---|
| 2414 | |
---|
| 2415 | def __setitem__(self, key, value): |
---|
| 2416 | if key < 0: |
---|
| 2417 | key += self.nrow() |
---|
| 2418 | if key >= self.nrow(): |
---|
| 2419 | raise IndexError("Row index out of range.") |
---|
| 2420 | if not hasattr(value, "__len__") or \ |
---|
| 2421 | len(value) > self.nchan(self.getif(key)): |
---|
| 2422 | raise ValueError("Spectrum length doesn't match.") |
---|
| 2423 | return self._setspectrum(value, key) |
---|
| 2424 | |
---|
| 2425 | def __len__(self): |
---|
| 2426 | return self.nrow() |
---|
| 2427 | |
---|
| 2428 | def __iter__(self): |
---|
| 2429 | for i in range(len(self)): |
---|
| 2430 | yield self[i] |
---|