[876] | 1 | from asap._asap import Scantable |
---|
[226] | 2 | from asap import rcParams |
---|
[1118] | 3 | from asap import print_log |
---|
| 4 | from asap import asaplog |
---|
[946] | 5 | from asap import selector |
---|
[1153] | 6 | from asap import linecatalog |
---|
[1295] | 7 | from asap import _n_bools, mask_not, mask_and, mask_or |
---|
[102] | 8 | |
---|
[876] | 9 | class scantable(Scantable): |
---|
[102] | 10 | """ |
---|
| 11 | The ASAP container for scans |
---|
| 12 | """ |
---|
[710] | 13 | |
---|
[484] | 14 | def __init__(self, filename, average=None, unit=None): |
---|
[102] | 15 | """ |
---|
| 16 | Create a scantable from a saved one or make a reference |
---|
| 17 | Parameters: |
---|
[181] | 18 | filename: the name of an asap table on disk |
---|
| 19 | or |
---|
| 20 | the name of a rpfits/sdfits/ms file |
---|
| 21 | (integrations within scans are auto averaged |
---|
| 22 | and the whole file is read) |
---|
| 23 | or |
---|
| 24 | [advanced] a reference to an existing |
---|
[102] | 25 | scantable |
---|
[484] | 26 | average: average all integrations withinb a scan on read. |
---|
| 27 | The default (True) is taken from .asaprc. |
---|
| 28 | unit: brightness unit; must be consistent with K or Jy. |
---|
[340] | 29 | Over-rides the default selected by the reader |
---|
| 30 | (input rpfits/sdfits/ms) or replaces the value |
---|
| 31 | in existing scantables |
---|
[710] | 32 | """ |
---|
[976] | 33 | if average is None: |
---|
[710] | 34 | average = rcParams['scantable.autoaverage'] |
---|
[1259] | 35 | varlist = vars() |
---|
[876] | 36 | from asap._asap import stmath |
---|
| 37 | self._math = stmath() |
---|
| 38 | if isinstance(filename, Scantable): |
---|
| 39 | Scantable.__init__(self, filename) |
---|
[181] | 40 | else: |
---|
[1435] | 41 | if isinstance(filename, str):# or \ |
---|
| 42 | # (isinstance(filename, list) or isinstance(filename, tuple)) \ |
---|
| 43 | # and isinstance(filename[-1], str): |
---|
[976] | 44 | import os.path |
---|
| 45 | filename = os.path.expandvars(filename) |
---|
| 46 | filename = os.path.expanduser(filename) |
---|
| 47 | if not os.path.exists(filename): |
---|
| 48 | s = "File '%s' not found." % (filename) |
---|
[718] | 49 | if rcParams['verbose']: |
---|
[976] | 50 | asaplog.push(s) |
---|
| 51 | print asaplog.pop().strip() |
---|
[718] | 52 | return |
---|
[976] | 53 | raise IOError(s) |
---|
[1115] | 54 | if os.path.isdir(filename) \ |
---|
[1118] | 55 | and not os.path.exists(filename+'/table.f1'): |
---|
[976] | 56 | # crude check if asap table |
---|
| 57 | if os.path.exists(filename+'/table.info'): |
---|
[1118] | 58 | ondisk = rcParams['scantable.storage'] == 'disk' |
---|
| 59 | Scantable.__init__(self, filename, ondisk) |
---|
[976] | 60 | if unit is not None: |
---|
| 61 | self.set_fluxunit(unit) |
---|
| 62 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[718] | 63 | else: |
---|
[1118] | 64 | msg = "The given file '%s'is not a valid " \ |
---|
| 65 | "asap table." % (filename) |
---|
[976] | 66 | if rcParams['verbose']: |
---|
| 67 | print msg |
---|
| 68 | return |
---|
| 69 | else: |
---|
| 70 | raise IOError(msg) |
---|
[226] | 71 | else: |
---|
[1118] | 72 | self._fill([filename], unit, average) |
---|
| 73 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
---|
[976] | 74 | and isinstance(filename[-1], str): |
---|
| 75 | self._fill(filename, unit, average) |
---|
[1259] | 76 | self._add_history("scantable", varlist) |
---|
[714] | 77 | print_log() |
---|
[102] | 78 | |
---|
[876] | 79 | def save(self, name=None, format=None, overwrite=False): |
---|
[116] | 80 | """ |
---|
[1280] | 81 | Store the scantable on disk. This can be an asap (aips++) Table, |
---|
| 82 | SDFITS or MS2 format. |
---|
[116] | 83 | Parameters: |
---|
[1093] | 84 | name: the name of the outputfile. For format "ASCII" |
---|
| 85 | this is the root file name (data in 'name'.txt |
---|
[497] | 86 | and header in 'name'_header.txt) |
---|
[116] | 87 | format: an optional file format. Default is ASAP. |
---|
[280] | 88 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
---|
[194] | 89 | 'SDFITS' (save as SDFITS file) |
---|
[200] | 90 | 'ASCII' (saves as ascii text file) |
---|
[226] | 91 | 'MS2' (saves as an aips++ |
---|
| 92 | MeasurementSet V2) |
---|
[1573] | 93 | 'FITS' (save as image FITS - not |
---|
[1443] | 94 | readable by class) |
---|
| 95 | 'CLASS' (save as FITS readable by CLASS) |
---|
[411] | 96 | overwrite: If the file should be overwritten if it exists. |
---|
[256] | 97 | The default False is to return with warning |
---|
[411] | 98 | without writing the output. USE WITH CARE. |
---|
[116] | 99 | Example: |
---|
| 100 | scan.save('myscan.asap') |
---|
[1118] | 101 | scan.save('myscan.sdfits', 'SDFITS') |
---|
[116] | 102 | """ |
---|
[411] | 103 | from os import path |
---|
[226] | 104 | if format is None: format = rcParams['scantable.save'] |
---|
[256] | 105 | suffix = '.'+format.lower() |
---|
[1118] | 106 | if name is None or name == "": |
---|
[256] | 107 | name = 'scantable'+suffix |
---|
[718] | 108 | msg = "No filename given. Using default name %s..." % name |
---|
| 109 | asaplog.push(msg) |
---|
[411] | 110 | name = path.expandvars(name) |
---|
[256] | 111 | if path.isfile(name) or path.isdir(name): |
---|
| 112 | if not overwrite: |
---|
[718] | 113 | msg = "File %s exists." % name |
---|
| 114 | if rcParams['verbose']: |
---|
| 115 | print msg |
---|
| 116 | return |
---|
| 117 | else: |
---|
| 118 | raise IOError(msg) |
---|
[451] | 119 | format2 = format.upper() |
---|
| 120 | if format2 == 'ASAP': |
---|
[116] | 121 | self._save(name) |
---|
| 122 | else: |
---|
[989] | 123 | from asap._asap import stwriter as stw |
---|
[1118] | 124 | writer = stw(format2) |
---|
| 125 | writer.write(self, name) |
---|
[718] | 126 | print_log() |
---|
[116] | 127 | return |
---|
| 128 | |
---|
[102] | 129 | def copy(self): |
---|
| 130 | """ |
---|
| 131 | Return a copy of this scantable. |
---|
[1348] | 132 | Note: |
---|
| 133 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
---|
[102] | 134 | Parameters: |
---|
[113] | 135 | none |
---|
[102] | 136 | Example: |
---|
| 137 | copiedscan = scan.copy() |
---|
| 138 | """ |
---|
[876] | 139 | sd = scantable(Scantable._copy(self)) |
---|
[113] | 140 | return sd |
---|
| 141 | |
---|
[1093] | 142 | def drop_scan(self, scanid=None): |
---|
| 143 | """ |
---|
| 144 | Return a new scantable where the specified scan number(s) has(have) |
---|
| 145 | been dropped. |
---|
| 146 | Parameters: |
---|
| 147 | scanid: a (list of) scan number(s) |
---|
| 148 | """ |
---|
| 149 | from asap import _is_sequence_or_number as _is_valid |
---|
| 150 | from asap import _to_list |
---|
| 151 | from asap import unique |
---|
| 152 | if not _is_valid(scanid): |
---|
| 153 | if rcParams['verbose']: |
---|
| 154 | print "Please specify a scanno to drop from the scantable" |
---|
| 155 | return |
---|
| 156 | else: |
---|
| 157 | raise RuntimeError("No scan given") |
---|
| 158 | try: |
---|
| 159 | scanid = _to_list(scanid) |
---|
| 160 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
---|
| 161 | for sid in scanid: allscans.remove(sid) |
---|
[1118] | 162 | if len(allscans) == 0: |
---|
| 163 | raise ValueError("Can't remove all scans") |
---|
[1093] | 164 | except ValueError: |
---|
| 165 | if rcParams['verbose']: |
---|
| 166 | print "Couldn't find any match." |
---|
| 167 | return |
---|
| 168 | else: raise |
---|
| 169 | try: |
---|
| 170 | bsel = self.get_selection() |
---|
| 171 | sel = selector() |
---|
| 172 | sel.set_scans(allscans) |
---|
| 173 | self.set_selection(bsel+sel) |
---|
| 174 | scopy = self._copy() |
---|
| 175 | self.set_selection(bsel) |
---|
| 176 | return scantable(scopy) |
---|
| 177 | except RuntimeError: |
---|
[1118] | 178 | if rcParams['verbose']: |
---|
| 179 | print "Couldn't find any match." |
---|
| 180 | else: |
---|
| 181 | raise |
---|
[1093] | 182 | |
---|
| 183 | |
---|
[102] | 184 | def get_scan(self, scanid=None): |
---|
| 185 | """ |
---|
| 186 | Return a specific scan (by scanno) or collection of scans (by |
---|
| 187 | source name) in a new scantable. |
---|
[1348] | 188 | Note: |
---|
| 189 | See scantable.drop_scan() for the inverse operation. |
---|
[102] | 190 | Parameters: |
---|
[513] | 191 | scanid: a (list of) scanno or a source name, unix-style |
---|
| 192 | patterns are accepted for source name matching, e.g. |
---|
| 193 | '*_R' gets all 'ref scans |
---|
[102] | 194 | Example: |
---|
[513] | 195 | # get all scans containing the source '323p459' |
---|
| 196 | newscan = scan.get_scan('323p459') |
---|
| 197 | # get all 'off' scans |
---|
| 198 | refscans = scan.get_scan('*_R') |
---|
| 199 | # get a susbset of scans by scanno (as listed in scan.summary()) |
---|
[1118] | 200 | newscan = scan.get_scan([0, 2, 7, 10]) |
---|
[102] | 201 | """ |
---|
| 202 | if scanid is None: |
---|
[718] | 203 | if rcParams['verbose']: |
---|
[1118] | 204 | print "Please specify a scan no or name to " \ |
---|
| 205 | "retrieve from the scantable" |
---|
[718] | 206 | return |
---|
| 207 | else: |
---|
| 208 | raise RuntimeError("No scan given") |
---|
| 209 | |
---|
[102] | 210 | try: |
---|
[946] | 211 | bsel = self.get_selection() |
---|
| 212 | sel = selector() |
---|
[102] | 213 | if type(scanid) is str: |
---|
[946] | 214 | sel.set_name(scanid) |
---|
| 215 | self.set_selection(bsel+sel) |
---|
[876] | 216 | scopy = self._copy() |
---|
[946] | 217 | self.set_selection(bsel) |
---|
[876] | 218 | return scantable(scopy) |
---|
[102] | 219 | elif type(scanid) is int: |
---|
[946] | 220 | sel.set_scans([scanid]) |
---|
| 221 | self.set_selection(bsel+sel) |
---|
[876] | 222 | scopy = self._copy() |
---|
[946] | 223 | self.set_selection(bsel) |
---|
[876] | 224 | return scantable(scopy) |
---|
[381] | 225 | elif type(scanid) is list: |
---|
[946] | 226 | sel.set_scans(scanid) |
---|
| 227 | self.set_selection(sel) |
---|
[876] | 228 | scopy = self._copy() |
---|
[946] | 229 | self.set_selection(bsel) |
---|
[876] | 230 | return scantable(scopy) |
---|
[381] | 231 | else: |
---|
[718] | 232 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
---|
| 233 | if rcParams['verbose']: |
---|
| 234 | print msg |
---|
| 235 | else: |
---|
| 236 | raise TypeError(msg) |
---|
[102] | 237 | except RuntimeError: |
---|
[718] | 238 | if rcParams['verbose']: print "Couldn't find any match." |
---|
| 239 | else: raise |
---|
[102] | 240 | |
---|
| 241 | def __str__(self): |
---|
[1118] | 242 | return Scantable._summary(self, True) |
---|
[102] | 243 | |
---|
[976] | 244 | def summary(self, filename=None): |
---|
[102] | 245 | """ |
---|
| 246 | Print a summary of the contents of this scantable. |
---|
| 247 | Parameters: |
---|
| 248 | filename: the name of a file to write the putput to |
---|
| 249 | Default - no file output |
---|
[381] | 250 | verbose: print extra info such as the frequency table |
---|
| 251 | The default (False) is taken from .asaprc |
---|
[102] | 252 | """ |
---|
[976] | 253 | info = Scantable._summary(self, True) |
---|
| 254 | #if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
---|
[102] | 255 | if filename is not None: |
---|
[256] | 256 | if filename is "": |
---|
| 257 | filename = 'scantable_summary.txt' |
---|
[415] | 258 | from os.path import expandvars, isdir |
---|
[411] | 259 | filename = expandvars(filename) |
---|
[415] | 260 | if not isdir(filename): |
---|
[413] | 261 | data = open(filename, 'w') |
---|
| 262 | data.write(info) |
---|
| 263 | data.close() |
---|
| 264 | else: |
---|
[718] | 265 | msg = "Illegal file name '%s'." % (filename) |
---|
| 266 | if rcParams['verbose']: |
---|
| 267 | print msg |
---|
| 268 | else: |
---|
| 269 | raise IOError(msg) |
---|
| 270 | if rcParams['verbose']: |
---|
[794] | 271 | try: |
---|
| 272 | from IPython.genutils import page as pager |
---|
| 273 | except ImportError: |
---|
| 274 | from pydoc import pager |
---|
| 275 | pager(info) |
---|
[718] | 276 | else: |
---|
| 277 | return info |
---|
[710] | 278 | |
---|
[1512] | 279 | def get_spectrum(self, rowno): |
---|
[1471] | 280 | """Return the spectrum for the current row in the scantable as a list. |
---|
| 281 | Parameters: |
---|
[1573] | 282 | rowno: the row number to retrieve the spectrum from |
---|
[1471] | 283 | """ |
---|
| 284 | return self._getspectrum(rowno) |
---|
[946] | 285 | |
---|
[1471] | 286 | def get_mask(self, rowno): |
---|
| 287 | """Return the mask for the current row in the scantable as a list. |
---|
| 288 | Parameters: |
---|
[1573] | 289 | rowno: the row number to retrieve the mask from |
---|
[1471] | 290 | """ |
---|
| 291 | return self._getmask(rowno) |
---|
| 292 | |
---|
| 293 | def set_spectrum(self, spec, rowno): |
---|
| 294 | """Return the spectrum for the current row in the scantable as a list. |
---|
| 295 | Parameters: |
---|
| 296 | spec: the spectrum |
---|
[1573] | 297 | rowno: the row number to set the spectrum for |
---|
[1471] | 298 | """ |
---|
| 299 | assert(len(spec) == self.nchan()) |
---|
| 300 | return self._setspectrum(spec, rowno) |
---|
| 301 | |
---|
[946] | 302 | def get_selection(self): |
---|
| 303 | """ |
---|
[1005] | 304 | Get the selection object currently set on this scantable. |
---|
| 305 | Parameters: |
---|
| 306 | none |
---|
| 307 | Example: |
---|
| 308 | sel = scan.get_selection() |
---|
| 309 | sel.set_ifs(0) # select IF 0 |
---|
| 310 | scan.set_selection(sel) # apply modified selection |
---|
[946] | 311 | """ |
---|
| 312 | return selector(self._getselection()) |
---|
| 313 | |
---|
[1576] | 314 | def set_selection(self, selection=None, **kw): |
---|
[946] | 315 | """ |
---|
[1005] | 316 | Select a subset of the data. All following operations on this scantable |
---|
| 317 | are only applied to thi selection. |
---|
| 318 | Parameters: |
---|
| 319 | selection: a selector object (default unset the selection) |
---|
| 320 | Examples: |
---|
| 321 | sel = selector() # create a selection object |
---|
[1118] | 322 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
---|
[1005] | 323 | scan.set_selection(sel) # set the selection |
---|
| 324 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 325 | scan.set_selection() # unset the selection |
---|
[946] | 326 | """ |
---|
[1576] | 327 | if selection is None: |
---|
| 328 | # reset |
---|
| 329 | if len(kw) == 0: |
---|
| 330 | selection = selector() |
---|
| 331 | else: |
---|
| 332 | # try keywords |
---|
| 333 | for k in kw: |
---|
| 334 | if k not in selector.fields: |
---|
| 335 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields)) |
---|
| 336 | selection = selector(**kw) |
---|
[946] | 337 | self._setselection(selection) |
---|
| 338 | |
---|
[876] | 339 | def stats(self, stat='stddev', mask=None): |
---|
[102] | 340 | """ |
---|
[135] | 341 | Determine the specified statistic of the current beam/if/pol |
---|
[102] | 342 | Takes a 'mask' as an optional parameter to specify which |
---|
| 343 | channels should be excluded. |
---|
| 344 | Parameters: |
---|
[135] | 345 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
---|
| 346 | 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
| 347 | mask: an optional mask specifying where the statistic |
---|
[102] | 348 | should be determined. |
---|
| 349 | Example: |
---|
[113] | 350 | scan.set_unit('channel') |
---|
[1118] | 351 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 352 | scan.stats(stat='mean', mask=m) |
---|
[102] | 353 | """ |
---|
| 354 | if mask == None: |
---|
[876] | 355 | mask = [] |
---|
[1118] | 356 | axes = ['Beam', 'IF', 'Pol', 'Time'] |
---|
[876] | 357 | if not self._check_ifs(): |
---|
[1118] | 358 | raise ValueError("Cannot apply mask as the IFs have different " |
---|
| 359 | "number of channels. Please use setselection() " |
---|
| 360 | "to select individual IFs") |
---|
[256] | 361 | |
---|
[876] | 362 | statvals = self._math._stats(self, mask, stat) |
---|
| 363 | out = '' |
---|
| 364 | axes = [] |
---|
| 365 | for i in range(self.nrow()): |
---|
| 366 | axis = [] |
---|
| 367 | axis.append(self.getscan(i)) |
---|
| 368 | axis.append(self.getbeam(i)) |
---|
| 369 | axis.append(self.getif(i)) |
---|
| 370 | axis.append(self.getpol(i)) |
---|
| 371 | axis.append(self.getcycle(i)) |
---|
| 372 | axes.append(axis) |
---|
| 373 | tm = self._gettime(i) |
---|
| 374 | src = self._getsourcename(i) |
---|
| 375 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
---|
| 376 | out += 'Time[%s]:\n' % (tm) |
---|
| 377 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
---|
| 378 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
---|
| 379 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
---|
| 380 | out += '= %3.3f\n' % (statvals[i]) |
---|
| 381 | out += "--------------------------------------------------\n" |
---|
[256] | 382 | |
---|
[876] | 383 | if rcParams['verbose']: |
---|
| 384 | print "--------------------------------------------------" |
---|
[1118] | 385 | print " ", stat |
---|
[876] | 386 | print "--------------------------------------------------" |
---|
| 387 | print out |
---|
[1295] | 388 | #else: |
---|
| 389 | #retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'], |
---|
| 390 | # 'axes' : axes, |
---|
| 391 | # 'data': statvals} |
---|
| 392 | return statvals |
---|
[102] | 393 | |
---|
[1118] | 394 | def stddev(self, mask=None): |
---|
[135] | 395 | """ |
---|
| 396 | Determine the standard deviation of the current beam/if/pol |
---|
| 397 | Takes a 'mask' as an optional parameter to specify which |
---|
| 398 | channels should be excluded. |
---|
| 399 | Parameters: |
---|
| 400 | mask: an optional mask specifying where the standard |
---|
| 401 | deviation should be determined. |
---|
| 402 | |
---|
| 403 | Example: |
---|
| 404 | scan.set_unit('channel') |
---|
[1118] | 405 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 406 | scan.stddev(mask=m) |
---|
| 407 | """ |
---|
[1118] | 408 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 409 | |
---|
[1003] | 410 | |
---|
[1259] | 411 | def get_column_names(self): |
---|
[1003] | 412 | """ |
---|
| 413 | Return a list of column names, which can be used for selection. |
---|
| 414 | """ |
---|
[1259] | 415 | return list(Scantable.get_column_names(self)) |
---|
[1003] | 416 | |
---|
[876] | 417 | def get_tsys(self): |
---|
[113] | 418 | """ |
---|
| 419 | Return the System temperatures. |
---|
| 420 | Returns: |
---|
[876] | 421 | a list of Tsys values for the current selection |
---|
[113] | 422 | """ |
---|
[256] | 423 | |
---|
[876] | 424 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 425 | |
---|
[876] | 426 | def _row_callback(self, callback, label): |
---|
| 427 | axes = [] |
---|
[1118] | 428 | axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'] |
---|
[876] | 429 | out = "" |
---|
[1118] | 430 | outvec = [] |
---|
[876] | 431 | for i in range(self.nrow()): |
---|
| 432 | axis = [] |
---|
| 433 | axis.append(self.getscan(i)) |
---|
| 434 | axis.append(self.getbeam(i)) |
---|
| 435 | axis.append(self.getif(i)) |
---|
| 436 | axis.append(self.getpol(i)) |
---|
| 437 | axis.append(self.getcycle(i)) |
---|
| 438 | axes.append(axis) |
---|
| 439 | tm = self._gettime(i) |
---|
| 440 | src = self._getsourcename(i) |
---|
| 441 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
---|
| 442 | out += 'Time[%s]:\n' % (tm) |
---|
| 443 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
---|
| 444 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
---|
| 445 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
---|
| 446 | outvec.append(callback(i)) |
---|
| 447 | out += '= %3.3f\n' % (outvec[i]) |
---|
| 448 | out += "--------------------------------------------------\n" |
---|
| 449 | if rcParams['verbose']: |
---|
| 450 | print "--------------------------------------------------" |
---|
| 451 | print " %s" % (label) |
---|
| 452 | print "--------------------------------------------------" |
---|
| 453 | print out |
---|
[1175] | 454 | # disabled because the vector seems more useful |
---|
| 455 | #retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec} |
---|
| 456 | return outvec |
---|
[256] | 457 | |
---|
[1070] | 458 | def _get_column(self, callback, row=-1): |
---|
| 459 | """ |
---|
| 460 | """ |
---|
| 461 | if row == -1: |
---|
| 462 | return [callback(i) for i in range(self.nrow())] |
---|
| 463 | else: |
---|
| 464 | if 0 <= row < self.nrow(): |
---|
| 465 | return callback(row) |
---|
[256] | 466 | |
---|
[1070] | 467 | |
---|
[1348] | 468 | def get_time(self, row=-1, asdatetime=False): |
---|
[113] | 469 | """ |
---|
| 470 | Get a list of time stamps for the observations. |
---|
[1348] | 471 | Return a datetime object for each integration time stamp in the scantable. |
---|
[113] | 472 | Parameters: |
---|
[1348] | 473 | row: row no of integration. Default -1 return all rows |
---|
| 474 | asdatetime: return values as datetime objects rather than strings |
---|
[113] | 475 | Example: |
---|
| 476 | none |
---|
| 477 | """ |
---|
[1175] | 478 | from time import strptime |
---|
| 479 | from datetime import datetime |
---|
[1392] | 480 | times = self._get_column(self._gettime, row) |
---|
[1348] | 481 | if not asdatetime: |
---|
[1392] | 482 | return times |
---|
[1175] | 483 | format = "%Y/%m/%d/%H:%M:%S" |
---|
| 484 | if isinstance(times, list): |
---|
| 485 | return [datetime(*strptime(i, format)[:6]) for i in times] |
---|
| 486 | else: |
---|
| 487 | return datetime(*strptime(times, format)[:6]) |
---|
[102] | 488 | |
---|
[1348] | 489 | |
---|
| 490 | def get_inttime(self, row=-1): |
---|
| 491 | """ |
---|
| 492 | Get a list of integration times for the observations. |
---|
| 493 | Return a time in seconds for each integration in the scantable. |
---|
| 494 | Parameters: |
---|
| 495 | row: row no of integration. Default -1 return all rows. |
---|
| 496 | Example: |
---|
| 497 | none |
---|
| 498 | """ |
---|
[1573] | 499 | return self._get_column(self._getinttime, row) |
---|
[1348] | 500 | |
---|
[1573] | 501 | |
---|
[714] | 502 | def get_sourcename(self, row=-1): |
---|
| 503 | """ |
---|
[794] | 504 | Get a list source names for the observations. |
---|
[714] | 505 | Return a string for each integration in the scantable. |
---|
| 506 | Parameters: |
---|
[1348] | 507 | row: row no of integration. Default -1 return all rows. |
---|
[714] | 508 | Example: |
---|
| 509 | none |
---|
| 510 | """ |
---|
[1070] | 511 | return self._get_column(self._getsourcename, row) |
---|
[714] | 512 | |
---|
[794] | 513 | def get_elevation(self, row=-1): |
---|
| 514 | """ |
---|
| 515 | Get a list of elevations for the observations. |
---|
| 516 | Return a float for each integration in the scantable. |
---|
| 517 | Parameters: |
---|
[1348] | 518 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 519 | Example: |
---|
| 520 | none |
---|
| 521 | """ |
---|
[1070] | 522 | return self._get_column(self._getelevation, row) |
---|
[794] | 523 | |
---|
| 524 | def get_azimuth(self, row=-1): |
---|
| 525 | """ |
---|
| 526 | Get a list of azimuths for the observations. |
---|
| 527 | Return a float for each integration in the scantable. |
---|
| 528 | Parameters: |
---|
[1348] | 529 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 530 | Example: |
---|
| 531 | none |
---|
| 532 | """ |
---|
[1070] | 533 | return self._get_column(self._getazimuth, row) |
---|
[794] | 534 | |
---|
| 535 | def get_parangle(self, row=-1): |
---|
| 536 | """ |
---|
| 537 | Get a list of parallactic angles for the observations. |
---|
| 538 | Return a float for each integration in the scantable. |
---|
| 539 | Parameters: |
---|
[1348] | 540 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 541 | Example: |
---|
| 542 | none |
---|
| 543 | """ |
---|
[1070] | 544 | return self._get_column(self._getparangle, row) |
---|
[794] | 545 | |
---|
[1070] | 546 | def get_direction(self, row=-1): |
---|
| 547 | """ |
---|
| 548 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 549 | Return a float for each integration in the scantable. |
---|
| 550 | Parameters: |
---|
| 551 | row: row no of integration. Default -1 return all rows |
---|
| 552 | Example: |
---|
| 553 | none |
---|
| 554 | """ |
---|
| 555 | return self._get_column(self._getdirection, row) |
---|
| 556 | |
---|
[1391] | 557 | def get_directionval(self, row=-1): |
---|
| 558 | """ |
---|
| 559 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 560 | Return a float for each integration in the scantable. |
---|
| 561 | Parameters: |
---|
| 562 | row: row no of integration. Default -1 return all rows |
---|
| 563 | Example: |
---|
| 564 | none |
---|
| 565 | """ |
---|
| 566 | return self._get_column(self._getdirectionvec, row) |
---|
| 567 | |
---|
| 568 | |
---|
[102] | 569 | def set_unit(self, unit='channel'): |
---|
| 570 | """ |
---|
| 571 | Set the unit for all following operations on this scantable |
---|
| 572 | Parameters: |
---|
| 573 | unit: optional unit, default is 'channel' |
---|
[1118] | 574 | one of '*Hz', 'km/s', 'channel', '' |
---|
[102] | 575 | """ |
---|
[484] | 576 | varlist = vars() |
---|
[1118] | 577 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 578 | unit = '' |
---|
| 579 | inf = list(self._getcoordinfo()) |
---|
| 580 | inf[0] = unit |
---|
| 581 | self._setcoordinfo(inf) |
---|
[1118] | 582 | self._add_history("set_unit", varlist) |
---|
[113] | 583 | |
---|
[484] | 584 | def set_instrument(self, instr): |
---|
[358] | 585 | """ |
---|
[1348] | 586 | Set the instrument for subsequent processing. |
---|
[358] | 587 | Parameters: |
---|
[710] | 588 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 589 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 590 | """ |
---|
| 591 | self._setInstrument(instr) |
---|
[1118] | 592 | self._add_history("set_instument", vars()) |
---|
[718] | 593 | print_log() |
---|
[358] | 594 | |
---|
[1190] | 595 | def set_feedtype(self, feedtype): |
---|
| 596 | """ |
---|
| 597 | Overwrite the feed type, which might not be set correctly. |
---|
| 598 | Parameters: |
---|
| 599 | feedtype: 'linear' or 'circular' |
---|
| 600 | """ |
---|
| 601 | self._setfeedtype(feedtype) |
---|
| 602 | self._add_history("set_feedtype", vars()) |
---|
| 603 | print_log() |
---|
| 604 | |
---|
[276] | 605 | def set_doppler(self, doppler='RADIO'): |
---|
| 606 | """ |
---|
| 607 | Set the doppler for all following operations on this scantable. |
---|
| 608 | Parameters: |
---|
| 609 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 610 | """ |
---|
[484] | 611 | varlist = vars() |
---|
[276] | 612 | inf = list(self._getcoordinfo()) |
---|
| 613 | inf[2] = doppler |
---|
| 614 | self._setcoordinfo(inf) |
---|
[1118] | 615 | self._add_history("set_doppler", vars()) |
---|
[718] | 616 | print_log() |
---|
[710] | 617 | |
---|
[226] | 618 | def set_freqframe(self, frame=None): |
---|
[113] | 619 | """ |
---|
| 620 | Set the frame type of the Spectral Axis. |
---|
| 621 | Parameters: |
---|
[591] | 622 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1118] | 623 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
| 624 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[113] | 625 | Examples: |
---|
| 626 | scan.set_freqframe('BARY') |
---|
| 627 | """ |
---|
[484] | 628 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
| 629 | varlist = vars() |
---|
[1118] | 630 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 631 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 632 | |
---|
[989] | 633 | if frame in valid: |
---|
[113] | 634 | inf = list(self._getcoordinfo()) |
---|
| 635 | inf[1] = frame |
---|
| 636 | self._setcoordinfo(inf) |
---|
[1118] | 637 | self._add_history("set_freqframe", varlist) |
---|
[102] | 638 | else: |
---|
[1118] | 639 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[718] | 640 | if rcParams['verbose']: |
---|
| 641 | print msg |
---|
| 642 | else: |
---|
| 643 | raise TypeError(msg) |
---|
| 644 | print_log() |
---|
[710] | 645 | |
---|
[989] | 646 | def set_dirframe(self, frame=""): |
---|
| 647 | """ |
---|
| 648 | Set the frame type of the Direction on the sky. |
---|
| 649 | Parameters: |
---|
| 650 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 651 | 'J2000', 'B1950', 'GALACTIC' |
---|
| 652 | Examples: |
---|
| 653 | scan.set_dirframe('GALACTIC') |
---|
| 654 | """ |
---|
| 655 | varlist = vars() |
---|
| 656 | try: |
---|
| 657 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 658 | except RuntimeError, msg: |
---|
[989] | 659 | if rcParams['verbose']: |
---|
| 660 | print msg |
---|
| 661 | else: |
---|
| 662 | raise |
---|
[1118] | 663 | self._add_history("set_dirframe", varlist) |
---|
[989] | 664 | |
---|
[113] | 665 | def get_unit(self): |
---|
| 666 | """ |
---|
| 667 | Get the default unit set in this scantable |
---|
| 668 | Returns: |
---|
| 669 | A unit string |
---|
| 670 | """ |
---|
| 671 | inf = self._getcoordinfo() |
---|
| 672 | unit = inf[0] |
---|
| 673 | if unit == '': unit = 'channel' |
---|
| 674 | return unit |
---|
[102] | 675 | |
---|
[158] | 676 | def get_abcissa(self, rowno=0): |
---|
[102] | 677 | """ |
---|
[158] | 678 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 679 | selected Beam/IF/Pol |
---|
| 680 | Parameters: |
---|
[226] | 681 | rowno: an optional row number in the scantable. Default is the |
---|
| 682 | first row, i.e. rowno=0 |
---|
[113] | 683 | Returns: |
---|
[1348] | 684 | The abcissa values and the format string (as a dictionary) |
---|
[113] | 685 | """ |
---|
[256] | 686 | abc = self._getabcissa(rowno) |
---|
[710] | 687 | lbl = self._getabcissalabel(rowno) |
---|
[718] | 688 | print_log() |
---|
[158] | 689 | return abc, lbl |
---|
[113] | 690 | |
---|
[1118] | 691 | def flag(self, mask=None): |
---|
[1001] | 692 | """ |
---|
| 693 | Flag the selected data using an optional channel mask. |
---|
| 694 | Parameters: |
---|
| 695 | mask: an optional channel mask, created with create_mask. Default |
---|
| 696 | (no mask) is all channels. |
---|
| 697 | """ |
---|
| 698 | varlist = vars() |
---|
[1118] | 699 | if mask is None: |
---|
| 700 | mask = [] |
---|
[1001] | 701 | try: |
---|
| 702 | self._flag(mask) |
---|
[1118] | 703 | except RuntimeError, msg: |
---|
[1001] | 704 | if rcParams['verbose']: |
---|
| 705 | print msg |
---|
| 706 | return |
---|
| 707 | else: raise |
---|
| 708 | self._add_history("flag", varlist) |
---|
| 709 | |
---|
[1203] | 710 | def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None): |
---|
[1192] | 711 | """ |
---|
| 712 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
| 713 | Flagged data in the scantable gets set to 0.0 before the fft. |
---|
| 714 | No taper is applied. |
---|
| 715 | Parameters: |
---|
[1348] | 716 | frequency: the frequency (really a period within the bandwidth) |
---|
| 717 | to remove |
---|
| 718 | width: the width of the frequency to remove, to remove a |
---|
[1471] | 719 | range of frequencies around the centre. |
---|
[1203] | 720 | unit: the frequency unit (default "GHz") |
---|
| 721 | Notes: |
---|
[1348] | 722 | It is recommended to flag edges of the band or strong |
---|
| 723 | signals beforehand. |
---|
[1192] | 724 | """ |
---|
| 725 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 726 | self._math._setinsitu(insitu) |
---|
| 727 | varlist = vars() |
---|
[1370] | 728 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. } |
---|
[1192] | 729 | if not base.has_key(unit): |
---|
| 730 | raise ValueError("%s is not a valid unit." % unit) |
---|
| 731 | try: |
---|
[1200] | 732 | s = scantable(self._math._lag_flag(self, frequency*base[unit], |
---|
| 733 | width*base[unit])) |
---|
[1192] | 734 | except RuntimeError, msg: |
---|
| 735 | if rcParams['verbose']: |
---|
| 736 | print msg |
---|
| 737 | return |
---|
| 738 | else: raise |
---|
| 739 | s._add_history("lag_flag", varlist) |
---|
| 740 | print_log() |
---|
| 741 | if insitu: |
---|
| 742 | self._assign(s) |
---|
| 743 | else: |
---|
| 744 | return s |
---|
[1001] | 745 | |
---|
[1192] | 746 | |
---|
[113] | 747 | def create_mask(self, *args, **kwargs): |
---|
| 748 | """ |
---|
[1118] | 749 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 750 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 751 | applied. |
---|
[102] | 752 | Parameters: |
---|
[1118] | 753 | [min, max], [min2, max2], ... |
---|
[1024] | 754 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 755 | to be masked |
---|
[189] | 756 | invert: optional argument. If specified as True, |
---|
| 757 | return an inverted mask, i.e. the regions |
---|
| 758 | specified are EXCLUDED |
---|
[513] | 759 | row: create the mask using the specified row for |
---|
| 760 | unit conversions, default is row=0 |
---|
| 761 | only necessary if frequency varies over rows. |
---|
[102] | 762 | Example: |
---|
[113] | 763 | scan.set_unit('channel') |
---|
| 764 | a) |
---|
[1118] | 765 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 766 | # masks everything outside 400 and 500 |
---|
[113] | 767 | # and 800 and 900 in the unit 'channel' |
---|
| 768 | |
---|
| 769 | b) |
---|
[1118] | 770 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 771 | # masks the regions between 400 and 500 |
---|
[113] | 772 | # and 800 and 900 in the unit 'channel' |
---|
[1024] | 773 | c) |
---|
| 774 | mask only channel 400 |
---|
[1554] | 775 | msk = scan.create_mask([400]) |
---|
[102] | 776 | """ |
---|
[1554] | 777 | row = kwargs.get("row", 0) |
---|
[513] | 778 | data = self._getabcissa(row) |
---|
[113] | 779 | u = self._getcoordinfo()[0] |
---|
[718] | 780 | if rcParams['verbose']: |
---|
[113] | 781 | if u == "": u = "channel" |
---|
[718] | 782 | msg = "The current mask window unit is %s" % u |
---|
[1118] | 783 | i = self._check_ifs() |
---|
| 784 | if not i: |
---|
[876] | 785 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 786 | asaplog.push(msg) |
---|
[102] | 787 | n = self.nchan() |
---|
[1295] | 788 | msk = _n_bools(n, False) |
---|
[710] | 789 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 790 | |
---|
[1118] | 791 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 792 | and args or args[0] |
---|
[710] | 793 | for window in ws: |
---|
[1554] | 794 | if len(window) == 1: |
---|
| 795 | window = [window[0], window[0]] |
---|
| 796 | if len(window) == 0 or len(window) > 2: |
---|
| 797 | raise ValueError("A window needs to be defined as [start(, end)]") |
---|
[1545] | 798 | if window[0] > window[1]: |
---|
| 799 | tmp = window[0] |
---|
| 800 | window[0] = window[1] |
---|
| 801 | window[1] = tmp |
---|
[102] | 802 | for i in range(n): |
---|
[1024] | 803 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 804 | msk[i] = True |
---|
[113] | 805 | if kwargs.has_key('invert'): |
---|
| 806 | if kwargs.get('invert'): |
---|
[1295] | 807 | msk = mask_not(msk) |
---|
[718] | 808 | print_log() |
---|
[102] | 809 | return msk |
---|
[710] | 810 | |
---|
[256] | 811 | def get_restfreqs(self): |
---|
| 812 | """ |
---|
| 813 | Get the restfrequency(s) stored in this scantable. |
---|
| 814 | The return value(s) are always of unit 'Hz' |
---|
| 815 | Parameters: |
---|
| 816 | none |
---|
| 817 | Returns: |
---|
| 818 | a list of doubles |
---|
| 819 | """ |
---|
| 820 | return list(self._getrestfreqs()) |
---|
[102] | 821 | |
---|
[402] | 822 | |
---|
[931] | 823 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
| 824 | """ |
---|
| 825 | Set or replace the restfrequency specified and |
---|
| 826 | If the 'freqs' argument holds a scalar, |
---|
| 827 | then that rest frequency will be applied to all the selected |
---|
| 828 | data. If the 'freqs' argument holds |
---|
| 829 | a vector, then it MUST be of equal or smaller length than |
---|
| 830 | the number of IFs (and the available restfrequencies will be |
---|
| 831 | replaced by this vector). In this case, *all* data have |
---|
| 832 | the restfrequency set per IF according |
---|
| 833 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 834 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 835 | IF 1 gets restfreq 2e9. |
---|
[1395] | 836 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 837 | |
---|
[931] | 838 | Parameters: |
---|
| 839 | freqs: list of rest frequency values or string idenitfiers |
---|
| 840 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 841 | |
---|
[931] | 842 | Example: |
---|
| 843 | # set the given restfrequency for the whole table |
---|
| 844 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1348] | 845 | # If thee number of IFs in the data is >= 2 IF0 gets the first |
---|
[931] | 846 | # value IF1 the second... |
---|
[1118] | 847 | scan.set_restfreqs(freqs=[1.4e9, 1.67e9]) |
---|
[931] | 848 | #set the given restfrequency for the whole table (by name) |
---|
| 849 | scan.set_restfreqs(freqs="OH1667") |
---|
[391] | 850 | |
---|
[931] | 851 | Note: |
---|
| 852 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 853 | source and IF basis, use scantable.set_selection() before using |
---|
| 854 | this function. |
---|
| 855 | # provide your scantable is call scan |
---|
| 856 | selection = selector() |
---|
| 857 | selection.set_name("ORION*") |
---|
| 858 | selection.set_ifs([1]) |
---|
| 859 | scan.set_selection(selection) |
---|
| 860 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 861 | |
---|
| 862 | """ |
---|
| 863 | varlist = vars() |
---|
[1157] | 864 | from asap import linecatalog |
---|
| 865 | # simple value |
---|
[1118] | 866 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1153] | 867 | self._setrestfreqs(freqs, "",unit) |
---|
[1157] | 868 | # list of values |
---|
[1118] | 869 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 870 | # list values are scalars |
---|
[1118] | 871 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[931] | 872 | sel = selector() |
---|
| 873 | savesel = self._getselection() |
---|
[1322] | 874 | iflist = self.getifnos() |
---|
[931] | 875 | for i in xrange(len(freqs)): |
---|
[1322] | 876 | sel.set_ifs(iflist[i]) |
---|
[931] | 877 | self._setselection(sel) |
---|
[1153] | 878 | self._setrestfreqs(freqs[i], "",unit) |
---|
[931] | 879 | self._setselection(savesel) |
---|
[1157] | 880 | # list values are tuples, (value, name) |
---|
| 881 | elif isinstance(freqs[-1], dict): |
---|
| 882 | sel = selector() |
---|
| 883 | savesel = self._getselection() |
---|
[1322] | 884 | iflist = self.getifnos() |
---|
[1157] | 885 | for i in xrange(len(freqs)): |
---|
[1322] | 886 | sel.set_ifs(iflist[i]) |
---|
[1259] | 887 | self._setselection(sel) |
---|
[1157] | 888 | self._setrestfreqs(freqs[i]["value"], |
---|
| 889 | freqs[i]["name"], "MHz") |
---|
| 890 | self._setselection(savesel) |
---|
| 891 | # freqs are to be taken from a linecatalog |
---|
[1153] | 892 | elif isinstance(freqs, linecatalog): |
---|
| 893 | sel = selector() |
---|
| 894 | savesel = self._getselection() |
---|
[1322] | 895 | iflist = self.getifnos() |
---|
[1153] | 896 | for i in xrange(freqs.nrow()): |
---|
[1322] | 897 | sel.set_ifs(iflist[i]) |
---|
[1153] | 898 | self._setselection(sel) |
---|
| 899 | self._setrestfreqs(freqs.get_frequency(i), |
---|
| 900 | freqs.get_name(i), "MHz") |
---|
| 901 | # ensure that we are not iterating past nIF |
---|
| 902 | if i == self.nif()-1: break |
---|
| 903 | self._setselection(savesel) |
---|
[931] | 904 | else: |
---|
| 905 | return |
---|
| 906 | self._add_history("set_restfreqs", varlist) |
---|
| 907 | |
---|
[1360] | 908 | def shift_refpix(self, delta): |
---|
| 909 | """ |
---|
[1573] | 910 | Shift the reference pixel of the Spectra Coordinate by an |
---|
[1360] | 911 | integer amount. |
---|
| 912 | Parameters: |
---|
| 913 | delta: the amount to shift by |
---|
| 914 | Note: |
---|
| 915 | Be careful using this with broadband data. |
---|
| 916 | """ |
---|
| 917 | Scantable.shift(self, delta) |
---|
[931] | 918 | |
---|
[1259] | 919 | def history(self, filename=None): |
---|
| 920 | """ |
---|
| 921 | Print the history. Optionally to a file. |
---|
[1348] | 922 | Parameters: |
---|
| 923 | filename: The name of the file to save the history to. |
---|
[1259] | 924 | """ |
---|
[484] | 925 | hist = list(self._gethistory()) |
---|
[794] | 926 | out = "-"*80 |
---|
[484] | 927 | for h in hist: |
---|
[489] | 928 | if h.startswith("---"): |
---|
[794] | 929 | out += "\n"+h |
---|
[489] | 930 | else: |
---|
| 931 | items = h.split("##") |
---|
| 932 | date = items[0] |
---|
| 933 | func = items[1] |
---|
| 934 | items = items[2:] |
---|
[794] | 935 | out += "\n"+date+"\n" |
---|
| 936 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 937 | for i in items: |
---|
| 938 | s = i.split("=") |
---|
[1118] | 939 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[794] | 940 | out += "\n"+"-"*80 |
---|
[1259] | 941 | if filename is not None: |
---|
| 942 | if filename is "": |
---|
| 943 | filename = 'scantable_history.txt' |
---|
| 944 | import os |
---|
| 945 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 946 | if not os.path.isdir(filename): |
---|
| 947 | data = open(filename, 'w') |
---|
| 948 | data.write(out) |
---|
| 949 | data.close() |
---|
| 950 | else: |
---|
| 951 | msg = "Illegal file name '%s'." % (filename) |
---|
| 952 | if rcParams['verbose']: |
---|
| 953 | print msg |
---|
| 954 | else: |
---|
| 955 | raise IOError(msg) |
---|
| 956 | if rcParams['verbose']: |
---|
| 957 | try: |
---|
| 958 | from IPython.genutils import page as pager |
---|
| 959 | except ImportError: |
---|
| 960 | from pydoc import pager |
---|
| 961 | pager(out) |
---|
| 962 | else: |
---|
| 963 | return out |
---|
[484] | 964 | return |
---|
[513] | 965 | # |
---|
| 966 | # Maths business |
---|
| 967 | # |
---|
| 968 | |
---|
[931] | 969 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[513] | 970 | """ |
---|
[1070] | 971 | Return the (time) weighted average of a scan. |
---|
[513] | 972 | Note: |
---|
[1070] | 973 | in channels only - align if necessary |
---|
[513] | 974 | Parameters: |
---|
| 975 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 976 | weighting) |
---|
[558] | 977 | scanav: True averages each scan separately |
---|
| 978 | False (default) averages all scans together, |
---|
[1099] | 979 | weight: Weighting scheme. |
---|
| 980 | 'none' (mean no weight) |
---|
| 981 | 'var' (1/var(spec) weighted) |
---|
| 982 | 'tsys' (1/Tsys**2 weighted) |
---|
| 983 | 'tint' (integration time weighted) |
---|
| 984 | 'tintsys' (Tint/Tsys**2) |
---|
| 985 | 'median' ( median averaging) |
---|
[535] | 986 | The default is 'tint' |
---|
[931] | 987 | align: align the spectra in velocity before averaging. It takes |
---|
| 988 | the time of the first spectrum as reference time. |
---|
[513] | 989 | Example: |
---|
| 990 | # time average the scantable without using a mask |
---|
[710] | 991 | newscan = scan.average_time() |
---|
[513] | 992 | """ |
---|
| 993 | varlist = vars() |
---|
[976] | 994 | if weight is None: weight = 'TINT' |
---|
[513] | 995 | if mask is None: mask = () |
---|
[1099] | 996 | if scanav: scanav = "SCAN" |
---|
| 997 | else: scanav = "NONE" |
---|
[1118] | 998 | scan = (self, ) |
---|
[989] | 999 | try: |
---|
[1118] | 1000 | if align: |
---|
| 1001 | scan = (self.freq_align(insitu=False), ) |
---|
| 1002 | s = None |
---|
| 1003 | if weight.upper() == 'MEDIAN': |
---|
| 1004 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 1005 | scanav)) |
---|
| 1006 | else: |
---|
| 1007 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 1008 | scanav)) |
---|
| 1009 | except RuntimeError, msg: |
---|
[989] | 1010 | if rcParams['verbose']: |
---|
| 1011 | print msg |
---|
| 1012 | return |
---|
| 1013 | else: raise |
---|
[1099] | 1014 | s._add_history("average_time", varlist) |
---|
[718] | 1015 | print_log() |
---|
[513] | 1016 | return s |
---|
[710] | 1017 | |
---|
[876] | 1018 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[513] | 1019 | """ |
---|
| 1020 | Return a scan where all spectra are converted to either |
---|
| 1021 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 1022 | By default the function tries to look the values up internally. |
---|
| 1023 | If it can't find them (or if you want to over-ride), you must |
---|
| 1024 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 1025 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 1026 | Parameters: |
---|
| 1027 | jyperk: the Jy / K conversion factor |
---|
| 1028 | eta: the aperture efficiency |
---|
| 1029 | d: the geomtric diameter (metres) |
---|
| 1030 | insitu: if False a new scantable is returned. |
---|
| 1031 | Otherwise, the scaling is done in-situ |
---|
| 1032 | The default is taken from .asaprc (False) |
---|
| 1033 | """ |
---|
| 1034 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1035 | self._math._setinsitu(insitu) |
---|
[513] | 1036 | varlist = vars() |
---|
| 1037 | if jyperk is None: jyperk = -1.0 |
---|
| 1038 | if d is None: d = -1.0 |
---|
| 1039 | if eta is None: eta = -1.0 |
---|
[876] | 1040 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 1041 | s._add_history("convert_flux", varlist) |
---|
| 1042 | print_log() |
---|
| 1043 | if insitu: self._assign(s) |
---|
| 1044 | else: return s |
---|
[513] | 1045 | |
---|
[876] | 1046 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[513] | 1047 | """ |
---|
| 1048 | Return a scan after applying a gain-elevation correction. |
---|
| 1049 | The correction can be made via either a polynomial or a |
---|
| 1050 | table-based interpolation (and extrapolation if necessary). |
---|
| 1051 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 1052 | If you specify neither, then a polynomial correction will be made |
---|
| 1053 | with built in coefficients known for certain telescopes (an error |
---|
| 1054 | will occur if the instrument is not known). |
---|
| 1055 | The data and Tsys are *divided* by the scaling factors. |
---|
| 1056 | Parameters: |
---|
| 1057 | poly: Polynomial coefficients (default None) to compute a |
---|
| 1058 | gain-elevation correction as a function of |
---|
| 1059 | elevation (in degrees). |
---|
| 1060 | filename: The name of an ascii file holding correction factors. |
---|
| 1061 | The first row of the ascii file must give the column |
---|
| 1062 | names and these MUST include columns |
---|
| 1063 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 1064 | by this) somewhere. |
---|
| 1065 | The second row must give the data type of the |
---|
| 1066 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 1067 | An example file would be |
---|
| 1068 | (actual factors are arbitrary) : |
---|
| 1069 | |
---|
| 1070 | TIME ELEVATION FACTOR |
---|
| 1071 | R R R |
---|
| 1072 | 0.1 0 0.8 |
---|
| 1073 | 0.2 20 0.85 |
---|
| 1074 | 0.3 40 0.9 |
---|
| 1075 | 0.4 60 0.85 |
---|
| 1076 | 0.5 80 0.8 |
---|
| 1077 | 0.6 90 0.75 |
---|
| 1078 | method: Interpolation method when correcting from a table. |
---|
| 1079 | Values are "nearest", "linear" (default), "cubic" |
---|
| 1080 | and "spline" |
---|
| 1081 | insitu: if False a new scantable is returned. |
---|
| 1082 | Otherwise, the scaling is done in-situ |
---|
| 1083 | The default is taken from .asaprc (False) |
---|
| 1084 | """ |
---|
| 1085 | |
---|
| 1086 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1087 | self._math._setinsitu(insitu) |
---|
[513] | 1088 | varlist = vars() |
---|
| 1089 | if poly is None: |
---|
[1118] | 1090 | poly = () |
---|
[513] | 1091 | from os.path import expandvars |
---|
| 1092 | filename = expandvars(filename) |
---|
[876] | 1093 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 1094 | s._add_history("gain_el", varlist) |
---|
| 1095 | print_log() |
---|
| 1096 | if insitu: self._assign(s) |
---|
| 1097 | else: return s |
---|
[710] | 1098 | |
---|
[931] | 1099 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[513] | 1100 | """ |
---|
| 1101 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 1102 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 1103 | set_freqframe. |
---|
| 1104 | Parameters: |
---|
| 1105 | reftime: reference time to align at. By default, the time of |
---|
| 1106 | the first row of data is used. |
---|
| 1107 | method: Interpolation method for regridding the spectra. |
---|
| 1108 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 1109 | and "spline" |
---|
| 1110 | insitu: if False a new scantable is returned. |
---|
| 1111 | Otherwise, the scaling is done in-situ |
---|
| 1112 | The default is taken from .asaprc (False) |
---|
| 1113 | """ |
---|
[931] | 1114 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 1115 | self._math._setinsitu(insitu) |
---|
[513] | 1116 | varlist = vars() |
---|
[931] | 1117 | if reftime is None: reftime = "" |
---|
| 1118 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 1119 | s._add_history("freq_align", varlist) |
---|
| 1120 | print_log() |
---|
| 1121 | if insitu: self._assign(s) |
---|
| 1122 | else: return s |
---|
[513] | 1123 | |
---|
[876] | 1124 | def opacity(self, tau, insitu=None): |
---|
[513] | 1125 | """ |
---|
| 1126 | Apply an opacity correction. The data |
---|
| 1127 | and Tsys are multiplied by the correction factor. |
---|
| 1128 | Parameters: |
---|
| 1129 | tau: Opacity from which the correction factor is |
---|
| 1130 | exp(tau*ZD) |
---|
| 1131 | where ZD is the zenith-distance |
---|
| 1132 | insitu: if False a new scantable is returned. |
---|
| 1133 | Otherwise, the scaling is done in-situ |
---|
| 1134 | The default is taken from .asaprc (False) |
---|
| 1135 | """ |
---|
| 1136 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1137 | self._math._setinsitu(insitu) |
---|
[513] | 1138 | varlist = vars() |
---|
[876] | 1139 | s = scantable(self._math._opacity(self, tau)) |
---|
| 1140 | s._add_history("opacity", varlist) |
---|
| 1141 | print_log() |
---|
| 1142 | if insitu: self._assign(s) |
---|
| 1143 | else: return s |
---|
[513] | 1144 | |
---|
| 1145 | def bin(self, width=5, insitu=None): |
---|
| 1146 | """ |
---|
| 1147 | Return a scan where all spectra have been binned up. |
---|
[1348] | 1148 | Parameters: |
---|
[513] | 1149 | width: The bin width (default=5) in pixels |
---|
| 1150 | insitu: if False a new scantable is returned. |
---|
| 1151 | Otherwise, the scaling is done in-situ |
---|
| 1152 | The default is taken from .asaprc (False) |
---|
| 1153 | """ |
---|
| 1154 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1155 | self._math._setinsitu(insitu) |
---|
[513] | 1156 | varlist = vars() |
---|
[876] | 1157 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1158 | s._add_history("bin", varlist) |
---|
[876] | 1159 | print_log() |
---|
| 1160 | if insitu: self._assign(s) |
---|
| 1161 | else: return s |
---|
[513] | 1162 | |
---|
[710] | 1163 | |
---|
[513] | 1164 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 1165 | """ |
---|
[1348] | 1166 | Return a scan where all spectra have been binned up. |
---|
[1573] | 1167 | |
---|
[1348] | 1168 | Parameters: |
---|
[513] | 1169 | width: The bin width (default=5) in pixels |
---|
| 1170 | method: Interpolation method when correcting from a table. |
---|
| 1171 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1172 | and "spline" |
---|
| 1173 | insitu: if False a new scantable is returned. |
---|
| 1174 | Otherwise, the scaling is done in-situ |
---|
| 1175 | The default is taken from .asaprc (False) |
---|
| 1176 | """ |
---|
| 1177 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1178 | self._math._setinsitu(insitu) |
---|
[513] | 1179 | varlist = vars() |
---|
[876] | 1180 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1181 | s._add_history("resample", varlist) |
---|
[876] | 1182 | print_log() |
---|
| 1183 | if insitu: self._assign(s) |
---|
| 1184 | else: return s |
---|
[513] | 1185 | |
---|
| 1186 | |
---|
[946] | 1187 | def average_pol(self, mask=None, weight='none'): |
---|
| 1188 | """ |
---|
| 1189 | Average the Polarisations together. |
---|
| 1190 | Parameters: |
---|
| 1191 | mask: An optional mask defining the region, where the |
---|
| 1192 | averaging will be applied. The output will have all |
---|
| 1193 | specified points masked. |
---|
| 1194 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1195 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1196 | """ |
---|
| 1197 | varlist = vars() |
---|
| 1198 | if mask is None: |
---|
| 1199 | mask = () |
---|
[1010] | 1200 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1201 | s._add_history("average_pol", varlist) |
---|
[946] | 1202 | print_log() |
---|
[992] | 1203 | return s |
---|
[513] | 1204 | |
---|
[1145] | 1205 | def average_beam(self, mask=None, weight='none'): |
---|
| 1206 | """ |
---|
| 1207 | Average the Beams together. |
---|
| 1208 | Parameters: |
---|
| 1209 | mask: An optional mask defining the region, where the |
---|
| 1210 | averaging will be applied. The output will have all |
---|
| 1211 | specified points masked. |
---|
| 1212 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1213 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1214 | """ |
---|
| 1215 | varlist = vars() |
---|
| 1216 | if mask is None: |
---|
| 1217 | mask = () |
---|
| 1218 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1219 | s._add_history("average_beam", varlist) |
---|
| 1220 | print_log() |
---|
| 1221 | return s |
---|
| 1222 | |
---|
[992] | 1223 | def convert_pol(self, poltype=None): |
---|
| 1224 | """ |
---|
| 1225 | Convert the data to a different polarisation type. |
---|
[1565] | 1226 | Note that you will need cross-polarisation terms for most conversions. |
---|
[992] | 1227 | Parameters: |
---|
| 1228 | poltype: The new polarisation type. Valid types are: |
---|
[1565] | 1229 | "linear", "circular", "stokes" and "linpol" |
---|
[992] | 1230 | """ |
---|
| 1231 | varlist = vars() |
---|
| 1232 | try: |
---|
| 1233 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1234 | except RuntimeError, msg: |
---|
[992] | 1235 | if rcParams['verbose']: |
---|
[1118] | 1236 | print msg |
---|
| 1237 | return |
---|
[992] | 1238 | else: |
---|
| 1239 | raise |
---|
[1118] | 1240 | s._add_history("convert_pol", varlist) |
---|
[992] | 1241 | print_log() |
---|
| 1242 | return s |
---|
| 1243 | |
---|
[1574] | 1244 | def smooth(self, kernel="hanning", width=5.0, order=2, insitu=None): |
---|
[513] | 1245 | """ |
---|
| 1246 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 1247 | Parameters: |
---|
| 1248 | kernel: The type of smoothing kernel. Select from |
---|
[1574] | 1249 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian' |
---|
| 1250 | or 'poly' |
---|
[513] | 1251 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1252 | ignored otherwise it defauls to 5 pixels. |
---|
| 1253 | For 'gaussian' it is the Full Width Half |
---|
| 1254 | Maximum. For 'boxcar' it is the full width. |
---|
[1574] | 1255 | For 'rmedian' and 'poly' it is the half width. |
---|
| 1256 | order: Optional parameter for 'poly' kernel (default is 2), to |
---|
| 1257 | specify the order of the polnomial. Ignored by all other |
---|
| 1258 | kernels. |
---|
[513] | 1259 | insitu: if False a new scantable is returned. |
---|
| 1260 | Otherwise, the scaling is done in-situ |
---|
| 1261 | The default is taken from .asaprc (False) |
---|
| 1262 | Example: |
---|
| 1263 | none |
---|
| 1264 | """ |
---|
| 1265 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1266 | self._math._setinsitu(insitu) |
---|
[513] | 1267 | varlist = vars() |
---|
[1574] | 1268 | s = scantable(self._math._smooth(self, kernel.lower(), width, order)) |
---|
[876] | 1269 | s._add_history("smooth", varlist) |
---|
| 1270 | print_log() |
---|
| 1271 | if insitu: self._assign(s) |
---|
| 1272 | else: return s |
---|
[513] | 1273 | |
---|
[876] | 1274 | |
---|
[1391] | 1275 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None): |
---|
[513] | 1276 | """ |
---|
| 1277 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1278 | Parameters: |
---|
[794] | 1279 | mask: an optional mask |
---|
| 1280 | order: the order of the polynomial (default is 0) |
---|
[1061] | 1281 | plot: plot the fit and the residual. In this each |
---|
| 1282 | indivual fit has to be approved, by typing 'y' |
---|
| 1283 | or 'n' |
---|
[1391] | 1284 | uselin: use linear polynomial fit |
---|
[794] | 1285 | insitu: if False a new scantable is returned. |
---|
| 1286 | Otherwise, the scaling is done in-situ |
---|
| 1287 | The default is taken from .asaprc (False) |
---|
[513] | 1288 | Example: |
---|
| 1289 | # return a scan baselined by a third order polynomial, |
---|
| 1290 | # not using a mask |
---|
| 1291 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1292 | """ |
---|
[513] | 1293 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1294 | varlist = vars() |
---|
| 1295 | if mask is None: |
---|
[1295] | 1296 | mask = [True for i in xrange(self.nchan(-1))] |
---|
[513] | 1297 | from asap.asapfitter import fitter |
---|
[1217] | 1298 | try: |
---|
| 1299 | f = fitter() |
---|
| 1300 | f.set_scan(self, mask) |
---|
[1391] | 1301 | #f.set_function(poly=order) |
---|
| 1302 | if uselin: |
---|
| 1303 | f.set_function(lpoly=order) |
---|
| 1304 | else: |
---|
| 1305 | f.set_function(poly=order) |
---|
[1217] | 1306 | s = f.auto_fit(insitu, plot=plot) |
---|
| 1307 | s._add_history("poly_baseline", varlist) |
---|
| 1308 | print_log() |
---|
| 1309 | if insitu: self._assign(s) |
---|
| 1310 | else: return s |
---|
| 1311 | except RuntimeError: |
---|
| 1312 | msg = "The fit failed, possibly because it didn't converge." |
---|
| 1313 | if rcParams['verbose']: |
---|
| 1314 | print msg |
---|
| 1315 | return |
---|
| 1316 | else: |
---|
| 1317 | raise RuntimeError(msg) |
---|
[513] | 1318 | |
---|
[1217] | 1319 | |
---|
[1118] | 1320 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
[1280] | 1321 | threshold=3, chan_avg_limit=1, plot=False, |
---|
| 1322 | insitu=None): |
---|
[880] | 1323 | """ |
---|
| 1324 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1325 | Spectral lines are detected first using linefinder and masked out |
---|
| 1326 | to avoid them affecting the baseline solution. |
---|
| 1327 | |
---|
| 1328 | Parameters: |
---|
| 1329 | mask: an optional mask retreived from scantable |
---|
| 1330 | edge: an optional number of channel to drop at |
---|
| 1331 | the edge of spectrum. If only one value is |
---|
| 1332 | specified, the same number will be dropped from |
---|
| 1333 | both sides of the spectrum. Default is to keep |
---|
[907] | 1334 | all channels. Nested tuples represent individual |
---|
[976] | 1335 | edge selection for different IFs (a number of spectral |
---|
| 1336 | channels can be different) |
---|
[880] | 1337 | order: the order of the polynomial (default is 0) |
---|
| 1338 | threshold: the threshold used by line finder. It is better to |
---|
| 1339 | keep it large as only strong lines affect the |
---|
| 1340 | baseline solution. |
---|
[1280] | 1341 | chan_avg_limit: |
---|
| 1342 | a maximum number of consequtive spectral channels to |
---|
| 1343 | average during the search of weak and broad lines. |
---|
| 1344 | The default is no averaging (and no search for weak |
---|
| 1345 | lines). If such lines can affect the fitted baseline |
---|
| 1346 | (e.g. a high order polynomial is fitted), increase this |
---|
| 1347 | parameter (usually values up to 8 are reasonable). Most |
---|
| 1348 | users of this method should find the default value |
---|
| 1349 | sufficient. |
---|
[1061] | 1350 | plot: plot the fit and the residual. In this each |
---|
| 1351 | indivual fit has to be approved, by typing 'y' |
---|
| 1352 | or 'n' |
---|
[880] | 1353 | insitu: if False a new scantable is returned. |
---|
| 1354 | Otherwise, the scaling is done in-situ |
---|
| 1355 | The default is taken from .asaprc (False) |
---|
| 1356 | |
---|
| 1357 | Example: |
---|
| 1358 | scan2=scan.auto_poly_baseline(order=7) |
---|
| 1359 | """ |
---|
| 1360 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1361 | varlist = vars() |
---|
| 1362 | from asap.asapfitter import fitter |
---|
| 1363 | from asap.asaplinefind import linefinder |
---|
| 1364 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1365 | |
---|
[976] | 1366 | # check whether edge is set up for each IF individually |
---|
[1118] | 1367 | individualedge = False; |
---|
| 1368 | if len(edge) > 1: |
---|
| 1369 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 1370 | individualedge = True; |
---|
[907] | 1371 | |
---|
[1118] | 1372 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 1373 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1374 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1375 | to make individual selection for different IFs." |
---|
[919] | 1376 | |
---|
[1118] | 1377 | curedge = (0, 0) |
---|
| 1378 | if individualedge: |
---|
| 1379 | for edgepar in edge: |
---|
| 1380 | if not _is_valid(edgepar, int): |
---|
| 1381 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 1382 | to be a pair of integers or an integer." |
---|
[907] | 1383 | else: |
---|
[1118] | 1384 | curedge = edge; |
---|
[880] | 1385 | |
---|
| 1386 | # setup fitter |
---|
| 1387 | f = fitter() |
---|
| 1388 | f.set_function(poly=order) |
---|
| 1389 | |
---|
| 1390 | # setup line finder |
---|
[1118] | 1391 | fl = linefinder() |
---|
[1268] | 1392 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
[880] | 1393 | |
---|
| 1394 | if not insitu: |
---|
[1118] | 1395 | workscan = self.copy() |
---|
[880] | 1396 | else: |
---|
[1118] | 1397 | workscan = self |
---|
[880] | 1398 | |
---|
[907] | 1399 | fl.set_scan(workscan) |
---|
| 1400 | |
---|
[1118] | 1401 | rows = range(workscan.nrow()) |
---|
[880] | 1402 | asaplog.push("Processing:") |
---|
| 1403 | for r in rows: |
---|
[1118] | 1404 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 1405 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 1406 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 1407 | asaplog.push(msg, False) |
---|
[907] | 1408 | |
---|
[976] | 1409 | # figure out edge parameter |
---|
[1118] | 1410 | if individualedge: |
---|
| 1411 | if len(edge) >= workscan.getif(r): |
---|
| 1412 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 1413 | "be less than the number of IFs" |
---|
| 1414 | curedge = edge[workscan.getif(r)] |
---|
[919] | 1415 | |
---|
[976] | 1416 | # setup line finder |
---|
[1118] | 1417 | fl.find_lines(r, mask, curedge) |
---|
[1536] | 1418 | f.set_data(workscan._getabcissa(r), workscan._getspectrum(r), |
---|
| 1419 | mask_and(workscan._getmask(r), fl.get_mask())) |
---|
[880] | 1420 | f.fit() |
---|
| 1421 | x = f.get_parameters() |
---|
[1061] | 1422 | if plot: |
---|
| 1423 | f.plot(residual=True) |
---|
| 1424 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1425 | if x.upper() == 'N': |
---|
| 1426 | continue |
---|
[880] | 1427 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1061] | 1428 | if plot: |
---|
| 1429 | f._p.unmap() |
---|
| 1430 | f._p = None |
---|
| 1431 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 1432 | if insitu: |
---|
| 1433 | self._assign(workscan) |
---|
| 1434 | else: |
---|
| 1435 | return workscan |
---|
| 1436 | |
---|
[914] | 1437 | def rotate_linpolphase(self, angle): |
---|
| 1438 | """ |
---|
| 1439 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1440 | This is always done in situ in the raw data. So if you call this |
---|
| 1441 | function more than once then each call rotates the phase further. |
---|
| 1442 | Parameters: |
---|
| 1443 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1444 | Examples: |
---|
| 1445 | scan.rotate_linpolphase(2.3) |
---|
| 1446 | """ |
---|
| 1447 | varlist = vars() |
---|
[936] | 1448 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 1449 | self._add_history("rotate_linpolphase", varlist) |
---|
| 1450 | print_log() |
---|
| 1451 | return |
---|
[710] | 1452 | |
---|
[513] | 1453 | |
---|
[914] | 1454 | def rotate_xyphase(self, angle): |
---|
| 1455 | """ |
---|
| 1456 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1457 | in the data. So if you call this function more than once |
---|
| 1458 | then each call rotates the phase further. |
---|
| 1459 | Parameters: |
---|
| 1460 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1461 | Examples: |
---|
| 1462 | scan.rotate_xyphase(2.3) |
---|
| 1463 | """ |
---|
| 1464 | varlist = vars() |
---|
[936] | 1465 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 1466 | self._add_history("rotate_xyphase", varlist) |
---|
| 1467 | print_log() |
---|
| 1468 | return |
---|
| 1469 | |
---|
| 1470 | def swap_linears(self): |
---|
| 1471 | """ |
---|
[1573] | 1472 | Swap the linear polarisations XX and YY, or better the first two |
---|
[1348] | 1473 | polarisations as this also works for ciculars. |
---|
[914] | 1474 | """ |
---|
| 1475 | varlist = vars() |
---|
[936] | 1476 | self._math._swap_linears(self) |
---|
[914] | 1477 | self._add_history("swap_linears", varlist) |
---|
| 1478 | print_log() |
---|
| 1479 | return |
---|
| 1480 | |
---|
| 1481 | def invert_phase(self): |
---|
| 1482 | """ |
---|
| 1483 | Invert the phase of the complex polarisation |
---|
| 1484 | """ |
---|
| 1485 | varlist = vars() |
---|
[936] | 1486 | self._math._invert_phase(self) |
---|
[914] | 1487 | self._add_history("invert_phase", varlist) |
---|
| 1488 | print_log() |
---|
| 1489 | return |
---|
| 1490 | |
---|
[876] | 1491 | def add(self, offset, insitu=None): |
---|
[513] | 1492 | """ |
---|
| 1493 | Return a scan where all spectra have the offset added |
---|
| 1494 | Parameters: |
---|
| 1495 | offset: the offset |
---|
| 1496 | insitu: if False a new scantable is returned. |
---|
| 1497 | Otherwise, the scaling is done in-situ |
---|
| 1498 | The default is taken from .asaprc (False) |
---|
| 1499 | """ |
---|
| 1500 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1501 | self._math._setinsitu(insitu) |
---|
[513] | 1502 | varlist = vars() |
---|
[876] | 1503 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 1504 | s._add_history("add", varlist) |
---|
[876] | 1505 | print_log() |
---|
| 1506 | if insitu: |
---|
| 1507 | self._assign(s) |
---|
| 1508 | else: |
---|
[513] | 1509 | return s |
---|
| 1510 | |
---|
[1308] | 1511 | def scale(self, factor, tsys=True, insitu=None): |
---|
[513] | 1512 | """ |
---|
| 1513 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 1514 | Parameters: |
---|
| 1515 | factor: the scaling factor |
---|
| 1516 | insitu: if False a new scantable is returned. |
---|
| 1517 | Otherwise, the scaling is done in-situ |
---|
| 1518 | The default is taken from .asaprc (False) |
---|
| 1519 | tsys: if True (default) then apply the operation to Tsys |
---|
| 1520 | as well as the data |
---|
| 1521 | """ |
---|
| 1522 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1523 | self._math._setinsitu(insitu) |
---|
[513] | 1524 | varlist = vars() |
---|
[876] | 1525 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
[1118] | 1526 | s._add_history("scale", varlist) |
---|
[876] | 1527 | print_log() |
---|
| 1528 | if insitu: |
---|
| 1529 | self._assign(s) |
---|
| 1530 | else: |
---|
[513] | 1531 | return s |
---|
| 1532 | |
---|
[1504] | 1533 | def set_sourcetype(self, match, matchtype="pattern", |
---|
| 1534 | sourcetype="reference"): |
---|
[1502] | 1535 | """ |
---|
| 1536 | Set the type of the source to be an source or reference scan |
---|
| 1537 | using the provided pattern: |
---|
| 1538 | Parameters: |
---|
[1504] | 1539 | match: a Unix style pattern, regular expression or selector |
---|
| 1540 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
| 1541 | 'regex' regular expression |
---|
[1502] | 1542 | sourcetype: the type of the source to use (source/reference) |
---|
| 1543 | """ |
---|
| 1544 | varlist = vars() |
---|
| 1545 | basesel = self.get_selection() |
---|
| 1546 | stype = -1 |
---|
| 1547 | if sourcetype.lower().startswith("r"): |
---|
| 1548 | stype = 1 |
---|
| 1549 | elif sourcetype.lower().startswith("s"): |
---|
| 1550 | stype = 0 |
---|
[1504] | 1551 | else: |
---|
[1502] | 1552 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)") |
---|
[1504] | 1553 | if matchtype.lower().startswith("p"): |
---|
| 1554 | matchtype = "pattern" |
---|
| 1555 | elif matchtype.lower().startswith("r"): |
---|
| 1556 | matchtype = "regex" |
---|
| 1557 | else: |
---|
| 1558 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
[1502] | 1559 | sel = selector() |
---|
| 1560 | if isinstance(match, selector): |
---|
| 1561 | sel = match |
---|
| 1562 | else: |
---|
[1504] | 1563 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match)) |
---|
[1502] | 1564 | self.set_selection(basesel+sel) |
---|
| 1565 | self._setsourcetype(stype) |
---|
| 1566 | self.set_selection(basesel) |
---|
[1573] | 1567 | self._add_history("set_sourcetype", varlist) |
---|
[1502] | 1568 | |
---|
[1348] | 1569 | def auto_quotient(self, preserve=True, mode='paired'): |
---|
[670] | 1570 | """ |
---|
| 1571 | This function allows to build quotients automatically. |
---|
| 1572 | It assumes the observation to have the same numer of |
---|
| 1573 | "ons" and "offs" |
---|
| 1574 | Parameters: |
---|
[710] | 1575 | preserve: you can preserve (default) the continuum or |
---|
| 1576 | remove it. The equations used are |
---|
[670] | 1577 | preserve: Output = Toff * (on/off) - Toff |
---|
[1070] | 1578 | remove: Output = Toff * (on/off) - Ton |
---|
[1573] | 1579 | mode: the on/off detection mode |
---|
[1348] | 1580 | 'paired' (default) |
---|
| 1581 | identifies 'off' scans by the |
---|
| 1582 | trailing '_R' (Mopra/Parkes) or |
---|
| 1583 | '_e'/'_w' (Tid) and matches |
---|
| 1584 | on/off pairs from the observing pattern |
---|
[1502] | 1585 | 'time' |
---|
| 1586 | finds the closest off in time |
---|
[1348] | 1587 | |
---|
[670] | 1588 | """ |
---|
[1348] | 1589 | modes = ["time", "paired"] |
---|
[670] | 1590 | if not mode in modes: |
---|
[876] | 1591 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 1592 | raise ValueError(msg) |
---|
| 1593 | varlist = vars() |
---|
[1348] | 1594 | s = None |
---|
| 1595 | if mode.lower() == "paired": |
---|
| 1596 | basesel = self.get_selection() |
---|
[1356] | 1597 | sel = selector()+basesel |
---|
| 1598 | sel.set_query("SRCTYPE==1") |
---|
| 1599 | self.set_selection(sel) |
---|
[1348] | 1600 | offs = self.copy() |
---|
| 1601 | sel.set_query("SRCTYPE==0") |
---|
[1356] | 1602 | self.set_selection(sel) |
---|
[1348] | 1603 | ons = self.copy() |
---|
| 1604 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 1605 | self.set_selection(basesel) |
---|
| 1606 | elif mode.lower() == "time": |
---|
| 1607 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 1608 | s._add_history("auto_quotient", varlist) |
---|
[876] | 1609 | print_log() |
---|
| 1610 | return s |
---|
[710] | 1611 | |
---|
[1145] | 1612 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1141] | 1613 | """ |
---|
[1143] | 1614 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
| 1615 | Parameters: |
---|
[1145] | 1616 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1143] | 1617 | weight: How to average the off beams. Default is 'median'. |
---|
[1145] | 1618 | preserve: you can preserve (default) the continuum or |
---|
| 1619 | remove it. The equations used are |
---|
| 1620 | preserve: Output = Toff * (on/off) - Toff |
---|
| 1621 | remove: Output = Toff * (on/off) - Ton |
---|
[1217] | 1622 | """ |
---|
[1143] | 1623 | if mask is None: mask = () |
---|
[1141] | 1624 | varlist = vars() |
---|
| 1625 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 1626 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 1627 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 1628 | from asapmath import quotient |
---|
[1145] | 1629 | q = quotient(on, off, preserve) |
---|
[1143] | 1630 | q._add_history("mx_quotient", varlist) |
---|
[1145] | 1631 | print_log() |
---|
[1217] | 1632 | return q |
---|
[513] | 1633 | |
---|
[718] | 1634 | def freq_switch(self, insitu=None): |
---|
| 1635 | """ |
---|
| 1636 | Apply frequency switching to the data. |
---|
| 1637 | Parameters: |
---|
| 1638 | insitu: if False a new scantable is returned. |
---|
| 1639 | Otherwise, the swictching is done in-situ |
---|
| 1640 | The default is taken from .asaprc (False) |
---|
| 1641 | Example: |
---|
| 1642 | none |
---|
| 1643 | """ |
---|
| 1644 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1645 | self._math._setinsitu(insitu) |
---|
[718] | 1646 | varlist = vars() |
---|
[876] | 1647 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 1648 | s._add_history("freq_switch", varlist) |
---|
[876] | 1649 | print_log() |
---|
| 1650 | if insitu: self._assign(s) |
---|
| 1651 | else: return s |
---|
[718] | 1652 | |
---|
[780] | 1653 | def recalc_azel(self): |
---|
| 1654 | """ |
---|
| 1655 | Recalculate the azimuth and elevation for each position. |
---|
| 1656 | Parameters: |
---|
| 1657 | none |
---|
| 1658 | Example: |
---|
| 1659 | """ |
---|
| 1660 | varlist = vars() |
---|
[876] | 1661 | self._recalcazel() |
---|
[780] | 1662 | self._add_history("recalc_azel", varlist) |
---|
| 1663 | print_log() |
---|
| 1664 | return |
---|
| 1665 | |
---|
[513] | 1666 | def __add__(self, other): |
---|
| 1667 | varlist = vars() |
---|
| 1668 | s = None |
---|
| 1669 | if isinstance(other, scantable): |
---|
[1573] | 1670 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
[513] | 1671 | elif isinstance(other, float): |
---|
[876] | 1672 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 1673 | else: |
---|
[718] | 1674 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1675 | s._add_history("operator +", varlist) |
---|
[718] | 1676 | print_log() |
---|
[513] | 1677 | return s |
---|
| 1678 | |
---|
| 1679 | def __sub__(self, other): |
---|
| 1680 | """ |
---|
| 1681 | implicit on all axes and on Tsys |
---|
| 1682 | """ |
---|
| 1683 | varlist = vars() |
---|
| 1684 | s = None |
---|
| 1685 | if isinstance(other, scantable): |
---|
[1308] | 1686 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
[513] | 1687 | elif isinstance(other, float): |
---|
[876] | 1688 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 1689 | else: |
---|
[718] | 1690 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1691 | s._add_history("operator -", varlist) |
---|
[718] | 1692 | print_log() |
---|
[513] | 1693 | return s |
---|
[710] | 1694 | |
---|
[513] | 1695 | def __mul__(self, other): |
---|
| 1696 | """ |
---|
| 1697 | implicit on all axes and on Tsys |
---|
| 1698 | """ |
---|
| 1699 | varlist = vars() |
---|
| 1700 | s = None |
---|
| 1701 | if isinstance(other, scantable): |
---|
[1308] | 1702 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
[513] | 1703 | elif isinstance(other, float): |
---|
[876] | 1704 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 1705 | else: |
---|
[718] | 1706 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1707 | s._add_history("operator *", varlist) |
---|
[718] | 1708 | print_log() |
---|
[513] | 1709 | return s |
---|
| 1710 | |
---|
[710] | 1711 | |
---|
[513] | 1712 | def __div__(self, other): |
---|
| 1713 | """ |
---|
| 1714 | implicit on all axes and on Tsys |
---|
| 1715 | """ |
---|
| 1716 | varlist = vars() |
---|
| 1717 | s = None |
---|
| 1718 | if isinstance(other, scantable): |
---|
[1308] | 1719 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
[513] | 1720 | elif isinstance(other, float): |
---|
| 1721 | if other == 0.0: |
---|
[718] | 1722 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 1723 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 1724 | else: |
---|
[718] | 1725 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1726 | s._add_history("operator /", varlist) |
---|
[718] | 1727 | print_log() |
---|
[513] | 1728 | return s |
---|
| 1729 | |
---|
[530] | 1730 | def get_fit(self, row=0): |
---|
| 1731 | """ |
---|
| 1732 | Print or return the stored fits for a row in the scantable |
---|
| 1733 | Parameters: |
---|
| 1734 | row: the row which the fit has been applied to. |
---|
| 1735 | """ |
---|
| 1736 | if row > self.nrow(): |
---|
| 1737 | return |
---|
[976] | 1738 | from asap.asapfit import asapfit |
---|
[530] | 1739 | fit = asapfit(self._getfit(row)) |
---|
[718] | 1740 | if rcParams['verbose']: |
---|
[530] | 1741 | print fit |
---|
| 1742 | return |
---|
| 1743 | else: |
---|
| 1744 | return fit.as_dict() |
---|
| 1745 | |
---|
[1483] | 1746 | def flag_nans(self): |
---|
| 1747 | """ |
---|
| 1748 | Utility function to flag NaN values in the scantable. |
---|
| 1749 | """ |
---|
| 1750 | import numpy |
---|
| 1751 | basesel = self.get_selection() |
---|
| 1752 | for i in range(self.nrow()): |
---|
| 1753 | sel = selector()+basesel |
---|
| 1754 | sel.set_scans(self.getscan(i)) |
---|
| 1755 | sel.set_beams(self.getbeam(i)) |
---|
| 1756 | sel.set_ifs(self.getif(i)) |
---|
| 1757 | sel.set_polarisations(self.getpol(i)) |
---|
| 1758 | self.set_selection(sel) |
---|
| 1759 | nans = numpy.isnan(self._getspectrum(0)) |
---|
| 1760 | if numpy.any(nans): |
---|
| 1761 | bnans = [ bool(v) for v in nans] |
---|
| 1762 | self.flag(bnans) |
---|
| 1763 | self.set_selection(basesel) |
---|
| 1764 | |
---|
[1573] | 1765 | |
---|
[484] | 1766 | def _add_history(self, funcname, parameters): |
---|
[1435] | 1767 | if not rcParams['scantable.history']: |
---|
| 1768 | return |
---|
[484] | 1769 | # create date |
---|
| 1770 | sep = "##" |
---|
| 1771 | from datetime import datetime |
---|
| 1772 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 1773 | hist = dstr+sep |
---|
| 1774 | hist += funcname+sep#cdate+sep |
---|
| 1775 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 1776 | for k, v in parameters.iteritems(): |
---|
[484] | 1777 | if type(v) is dict: |
---|
[1118] | 1778 | for k2, v2 in v.iteritems(): |
---|
[484] | 1779 | hist += k2 |
---|
| 1780 | hist += "=" |
---|
[1118] | 1781 | if isinstance(v2, scantable): |
---|
[484] | 1782 | hist += 'scantable' |
---|
| 1783 | elif k2 == 'mask': |
---|
[1118] | 1784 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 1785 | hist += str(self._zip_mask(v2)) |
---|
| 1786 | else: |
---|
| 1787 | hist += str(v2) |
---|
[484] | 1788 | else: |
---|
[513] | 1789 | hist += str(v2) |
---|
[484] | 1790 | else: |
---|
| 1791 | hist += k |
---|
| 1792 | hist += "=" |
---|
[1118] | 1793 | if isinstance(v, scantable): |
---|
[484] | 1794 | hist += 'scantable' |
---|
| 1795 | elif k == 'mask': |
---|
[1118] | 1796 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 1797 | hist += str(self._zip_mask(v)) |
---|
| 1798 | else: |
---|
| 1799 | hist += str(v) |
---|
[484] | 1800 | else: |
---|
| 1801 | hist += str(v) |
---|
| 1802 | hist += sep |
---|
| 1803 | hist = hist[:-2] # remove trailing '##' |
---|
| 1804 | self._addhistory(hist) |
---|
| 1805 | |
---|
[710] | 1806 | |
---|
[484] | 1807 | def _zip_mask(self, mask): |
---|
| 1808 | mask = list(mask) |
---|
| 1809 | i = 0 |
---|
| 1810 | segments = [] |
---|
| 1811 | while mask[i:].count(1): |
---|
| 1812 | i += mask[i:].index(1) |
---|
| 1813 | if mask[i:].count(0): |
---|
| 1814 | j = i + mask[i:].index(0) |
---|
| 1815 | else: |
---|
[710] | 1816 | j = len(mask) |
---|
[1118] | 1817 | segments.append([i, j]) |
---|
[710] | 1818 | i = j |
---|
[484] | 1819 | return segments |
---|
[714] | 1820 | |
---|
[626] | 1821 | def _get_ordinate_label(self): |
---|
| 1822 | fu = "("+self.get_fluxunit()+")" |
---|
| 1823 | import re |
---|
| 1824 | lbl = "Intensity" |
---|
[1118] | 1825 | if re.match(".K.", fu): |
---|
[626] | 1826 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 1827 | elif re.match(".Jy.", fu): |
---|
[626] | 1828 | lbl = "Flux density "+ fu |
---|
| 1829 | return lbl |
---|
[710] | 1830 | |
---|
[876] | 1831 | def _check_ifs(self): |
---|
| 1832 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 1833 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 1834 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 1835 | |
---|
| 1836 | def _fill(self, names, unit, average): |
---|
| 1837 | import os |
---|
| 1838 | from asap._asap import stfiller |
---|
| 1839 | first = True |
---|
| 1840 | fullnames = [] |
---|
| 1841 | for name in names: |
---|
| 1842 | name = os.path.expandvars(name) |
---|
| 1843 | name = os.path.expanduser(name) |
---|
| 1844 | if not os.path.exists(name): |
---|
| 1845 | msg = "File '%s' does not exists" % (name) |
---|
| 1846 | if rcParams['verbose']: |
---|
| 1847 | asaplog.push(msg) |
---|
| 1848 | print asaplog.pop().strip() |
---|
| 1849 | return |
---|
| 1850 | raise IOError(msg) |
---|
| 1851 | fullnames.append(name) |
---|
| 1852 | if average: |
---|
| 1853 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 1854 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 1855 | for name in fullnames: |
---|
[1073] | 1856 | tbl = Scantable(stype) |
---|
| 1857 | r = stfiller(tbl) |
---|
[1504] | 1858 | rx = rcParams['scantable.reference'] |
---|
| 1859 | r._setreferenceexpr(rx) |
---|
[976] | 1860 | msg = "Importing %s..." % (name) |
---|
[1118] | 1861 | asaplog.push(msg, False) |
---|
[976] | 1862 | print_log() |
---|
[1118] | 1863 | r._open(name, -1, -1) |
---|
[976] | 1864 | r._read() |
---|
| 1865 | if average: |
---|
[1118] | 1866 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 1867 | if not first: |
---|
| 1868 | tbl = self._math._merge([self, tbl]) |
---|
| 1869 | Scantable.__init__(self, tbl) |
---|
| 1870 | r._close() |
---|
[1118] | 1871 | del r, tbl |
---|
[976] | 1872 | first = False |
---|
| 1873 | if unit is not None: |
---|
| 1874 | self.set_fluxunit(unit) |
---|
| 1875 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
| 1876 | |
---|
[1402] | 1877 | def __getitem__(self, key): |
---|
| 1878 | if key < 0: |
---|
| 1879 | key += self.nrow() |
---|
| 1880 | if key >= self.nrow(): |
---|
| 1881 | raise IndexError("Row index out of range.") |
---|
| 1882 | return self._getspectrum(key) |
---|
| 1883 | |
---|
| 1884 | def __setitem__(self, key, value): |
---|
| 1885 | if key < 0: |
---|
| 1886 | key += self.nrow() |
---|
| 1887 | if key >= self.nrow(): |
---|
| 1888 | raise IndexError("Row index out of range.") |
---|
| 1889 | if not hasattr(value, "__len__") or \ |
---|
| 1890 | len(value) > self.nchan(self.getif(key)): |
---|
| 1891 | raise ValueError("Spectrum length doesn't match.") |
---|
| 1892 | return self._setspectrum(value, key) |
---|
| 1893 | |
---|
| 1894 | def __len__(self): |
---|
| 1895 | return self.nrow() |
---|
| 1896 | |
---|
| 1897 | def __iter__(self): |
---|
| 1898 | for i in range(len(self)): |
---|
| 1899 | yield self[i] |
---|