[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 |
---|
[1134] | 6 | from asap import NUM |
---|
[102] | 7 | |
---|
[876] | 8 | class scantable(Scantable): |
---|
[102] | 9 | """ |
---|
| 10 | The ASAP container for scans |
---|
| 11 | """ |
---|
[710] | 12 | |
---|
[484] | 13 | def __init__(self, filename, average=None, unit=None): |
---|
[102] | 14 | """ |
---|
| 15 | Create a scantable from a saved one or make a reference |
---|
| 16 | Parameters: |
---|
[181] | 17 | filename: the name of an asap table on disk |
---|
| 18 | or |
---|
| 19 | the name of a rpfits/sdfits/ms file |
---|
| 20 | (integrations within scans are auto averaged |
---|
| 21 | and the whole file is read) |
---|
| 22 | or |
---|
| 23 | [advanced] a reference to an existing |
---|
[102] | 24 | scantable |
---|
[484] | 25 | average: average all integrations withinb a scan on read. |
---|
| 26 | The default (True) is taken from .asaprc. |
---|
| 27 | unit: brightness unit; must be consistent with K or Jy. |
---|
[340] | 28 | Over-rides the default selected by the reader |
---|
| 29 | (input rpfits/sdfits/ms) or replaces the value |
---|
| 30 | in existing scantables |
---|
[710] | 31 | """ |
---|
[976] | 32 | if average is None: |
---|
[710] | 33 | average = rcParams['scantable.autoaverage'] |
---|
[1118] | 34 | #varlist = vars() |
---|
[876] | 35 | from asap._asap import stmath |
---|
| 36 | self._math = stmath() |
---|
| 37 | if isinstance(filename, Scantable): |
---|
| 38 | Scantable.__init__(self, filename) |
---|
[181] | 39 | else: |
---|
[1118] | 40 | if isinstance(filename, str): |
---|
[976] | 41 | import os.path |
---|
| 42 | filename = os.path.expandvars(filename) |
---|
| 43 | filename = os.path.expanduser(filename) |
---|
| 44 | if not os.path.exists(filename): |
---|
| 45 | s = "File '%s' not found." % (filename) |
---|
[718] | 46 | if rcParams['verbose']: |
---|
[976] | 47 | asaplog.push(s) |
---|
| 48 | print asaplog.pop().strip() |
---|
[718] | 49 | return |
---|
[976] | 50 | raise IOError(s) |
---|
[1115] | 51 | if os.path.isdir(filename) \ |
---|
[1118] | 52 | and not os.path.exists(filename+'/table.f1'): |
---|
[976] | 53 | # crude check if asap table |
---|
| 54 | if os.path.exists(filename+'/table.info'): |
---|
[1118] | 55 | ondisk = rcParams['scantable.storage'] == 'disk' |
---|
| 56 | Scantable.__init__(self, filename, ondisk) |
---|
[976] | 57 | if unit is not None: |
---|
| 58 | self.set_fluxunit(unit) |
---|
| 59 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[718] | 60 | else: |
---|
[1118] | 61 | msg = "The given file '%s'is not a valid " \ |
---|
| 62 | "asap table." % (filename) |
---|
[976] | 63 | if rcParams['verbose']: |
---|
| 64 | print msg |
---|
| 65 | return |
---|
| 66 | else: |
---|
| 67 | raise IOError(msg) |
---|
[226] | 68 | else: |
---|
[1118] | 69 | self._fill([filename], unit, average) |
---|
| 70 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
---|
[976] | 71 | and isinstance(filename[-1], str): |
---|
| 72 | self._fill(filename, unit, average) |
---|
[714] | 73 | print_log() |
---|
[102] | 74 | |
---|
[876] | 75 | def save(self, name=None, format=None, overwrite=False): |
---|
[116] | 76 | """ |
---|
[710] | 77 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, |
---|
[280] | 78 | Image FITS or MS2 format. |
---|
[116] | 79 | Parameters: |
---|
[1093] | 80 | name: the name of the outputfile. For format "ASCII" |
---|
| 81 | this is the root file name (data in 'name'.txt |
---|
[497] | 82 | and header in 'name'_header.txt) |
---|
[116] | 83 | format: an optional file format. Default is ASAP. |
---|
[280] | 84 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
---|
[194] | 85 | 'SDFITS' (save as SDFITS file) |
---|
[200] | 86 | 'ASCII' (saves as ascii text file) |
---|
[226] | 87 | 'MS2' (saves as an aips++ |
---|
| 88 | MeasurementSet V2) |
---|
[411] | 89 | overwrite: If the file should be overwritten if it exists. |
---|
[256] | 90 | The default False is to return with warning |
---|
[411] | 91 | without writing the output. USE WITH CARE. |
---|
[116] | 92 | Example: |
---|
| 93 | scan.save('myscan.asap') |
---|
[1118] | 94 | scan.save('myscan.sdfits', 'SDFITS') |
---|
[116] | 95 | """ |
---|
[411] | 96 | from os import path |
---|
[226] | 97 | if format is None: format = rcParams['scantable.save'] |
---|
[256] | 98 | suffix = '.'+format.lower() |
---|
[1118] | 99 | if name is None or name == "": |
---|
[256] | 100 | name = 'scantable'+suffix |
---|
[718] | 101 | msg = "No filename given. Using default name %s..." % name |
---|
| 102 | asaplog.push(msg) |
---|
[411] | 103 | name = path.expandvars(name) |
---|
[256] | 104 | if path.isfile(name) or path.isdir(name): |
---|
| 105 | if not overwrite: |
---|
[718] | 106 | msg = "File %s exists." % name |
---|
| 107 | if rcParams['verbose']: |
---|
| 108 | print msg |
---|
| 109 | return |
---|
| 110 | else: |
---|
| 111 | raise IOError(msg) |
---|
[451] | 112 | format2 = format.upper() |
---|
| 113 | if format2 == 'ASAP': |
---|
[116] | 114 | self._save(name) |
---|
| 115 | else: |
---|
[989] | 116 | from asap._asap import stwriter as stw |
---|
[1118] | 117 | writer = stw(format2) |
---|
| 118 | writer.write(self, name) |
---|
[718] | 119 | print_log() |
---|
[116] | 120 | return |
---|
| 121 | |
---|
[102] | 122 | def copy(self): |
---|
| 123 | """ |
---|
| 124 | Return a copy of this scantable. |
---|
| 125 | Parameters: |
---|
[113] | 126 | none |
---|
[102] | 127 | Example: |
---|
| 128 | copiedscan = scan.copy() |
---|
| 129 | """ |
---|
[876] | 130 | sd = scantable(Scantable._copy(self)) |
---|
[113] | 131 | return sd |
---|
| 132 | |
---|
[1093] | 133 | def drop_scan(self, scanid=None): |
---|
| 134 | """ |
---|
| 135 | Return a new scantable where the specified scan number(s) has(have) |
---|
| 136 | been dropped. |
---|
| 137 | Parameters: |
---|
| 138 | scanid: a (list of) scan number(s) |
---|
| 139 | """ |
---|
| 140 | from asap import _is_sequence_or_number as _is_valid |
---|
| 141 | from asap import _to_list |
---|
| 142 | from asap import unique |
---|
| 143 | if not _is_valid(scanid): |
---|
| 144 | if rcParams['verbose']: |
---|
| 145 | print "Please specify a scanno to drop from the scantable" |
---|
| 146 | return |
---|
| 147 | else: |
---|
| 148 | raise RuntimeError("No scan given") |
---|
| 149 | try: |
---|
| 150 | scanid = _to_list(scanid) |
---|
| 151 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
---|
| 152 | for sid in scanid: allscans.remove(sid) |
---|
[1118] | 153 | if len(allscans) == 0: |
---|
| 154 | raise ValueError("Can't remove all scans") |
---|
[1093] | 155 | except ValueError: |
---|
| 156 | if rcParams['verbose']: |
---|
| 157 | print "Couldn't find any match." |
---|
| 158 | return |
---|
| 159 | else: raise |
---|
| 160 | try: |
---|
| 161 | bsel = self.get_selection() |
---|
| 162 | sel = selector() |
---|
| 163 | sel.set_scans(allscans) |
---|
| 164 | self.set_selection(bsel+sel) |
---|
| 165 | scopy = self._copy() |
---|
| 166 | self.set_selection(bsel) |
---|
| 167 | return scantable(scopy) |
---|
| 168 | except RuntimeError: |
---|
[1118] | 169 | if rcParams['verbose']: |
---|
| 170 | print "Couldn't find any match." |
---|
| 171 | else: |
---|
| 172 | raise |
---|
[1093] | 173 | |
---|
| 174 | |
---|
[102] | 175 | def get_scan(self, scanid=None): |
---|
| 176 | """ |
---|
| 177 | Return a specific scan (by scanno) or collection of scans (by |
---|
| 178 | source name) in a new scantable. |
---|
| 179 | Parameters: |
---|
[513] | 180 | scanid: a (list of) scanno or a source name, unix-style |
---|
| 181 | patterns are accepted for source name matching, e.g. |
---|
| 182 | '*_R' gets all 'ref scans |
---|
[102] | 183 | Example: |
---|
[513] | 184 | # get all scans containing the source '323p459' |
---|
| 185 | newscan = scan.get_scan('323p459') |
---|
| 186 | # get all 'off' scans |
---|
| 187 | refscans = scan.get_scan('*_R') |
---|
| 188 | # get a susbset of scans by scanno (as listed in scan.summary()) |
---|
[1118] | 189 | newscan = scan.get_scan([0, 2, 7, 10]) |
---|
[102] | 190 | """ |
---|
| 191 | if scanid is None: |
---|
[718] | 192 | if rcParams['verbose']: |
---|
[1118] | 193 | print "Please specify a scan no or name to " \ |
---|
| 194 | "retrieve from the scantable" |
---|
[718] | 195 | return |
---|
| 196 | else: |
---|
| 197 | raise RuntimeError("No scan given") |
---|
| 198 | |
---|
[102] | 199 | try: |
---|
[946] | 200 | bsel = self.get_selection() |
---|
| 201 | sel = selector() |
---|
[102] | 202 | if type(scanid) is str: |
---|
[946] | 203 | sel.set_name(scanid) |
---|
| 204 | self.set_selection(bsel+sel) |
---|
[876] | 205 | scopy = self._copy() |
---|
[946] | 206 | self.set_selection(bsel) |
---|
[876] | 207 | return scantable(scopy) |
---|
[102] | 208 | elif type(scanid) is int: |
---|
[946] | 209 | sel.set_scans([scanid]) |
---|
| 210 | self.set_selection(bsel+sel) |
---|
[876] | 211 | scopy = self._copy() |
---|
[946] | 212 | self.set_selection(bsel) |
---|
[876] | 213 | return scantable(scopy) |
---|
[381] | 214 | elif type(scanid) is list: |
---|
[946] | 215 | sel.set_scans(scanid) |
---|
| 216 | self.set_selection(sel) |
---|
[876] | 217 | scopy = self._copy() |
---|
[946] | 218 | self.set_selection(bsel) |
---|
[876] | 219 | return scantable(scopy) |
---|
[381] | 220 | else: |
---|
[718] | 221 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
---|
| 222 | if rcParams['verbose']: |
---|
| 223 | print msg |
---|
| 224 | else: |
---|
| 225 | raise TypeError(msg) |
---|
[102] | 226 | except RuntimeError: |
---|
[718] | 227 | if rcParams['verbose']: print "Couldn't find any match." |
---|
| 228 | else: raise |
---|
[102] | 229 | |
---|
| 230 | def __str__(self): |
---|
[1118] | 231 | return Scantable._summary(self, True) |
---|
[102] | 232 | |
---|
[976] | 233 | def summary(self, filename=None): |
---|
[102] | 234 | """ |
---|
| 235 | Print a summary of the contents of this scantable. |
---|
| 236 | Parameters: |
---|
| 237 | filename: the name of a file to write the putput to |
---|
| 238 | Default - no file output |
---|
[381] | 239 | verbose: print extra info such as the frequency table |
---|
| 240 | The default (False) is taken from .asaprc |
---|
[102] | 241 | """ |
---|
[976] | 242 | info = Scantable._summary(self, True) |
---|
| 243 | #if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
---|
[102] | 244 | if filename is not None: |
---|
[256] | 245 | if filename is "": |
---|
| 246 | filename = 'scantable_summary.txt' |
---|
[415] | 247 | from os.path import expandvars, isdir |
---|
[411] | 248 | filename = expandvars(filename) |
---|
[415] | 249 | if not isdir(filename): |
---|
[413] | 250 | data = open(filename, 'w') |
---|
| 251 | data.write(info) |
---|
| 252 | data.close() |
---|
| 253 | else: |
---|
[718] | 254 | msg = "Illegal file name '%s'." % (filename) |
---|
| 255 | if rcParams['verbose']: |
---|
| 256 | print msg |
---|
| 257 | else: |
---|
| 258 | raise IOError(msg) |
---|
| 259 | if rcParams['verbose']: |
---|
[794] | 260 | try: |
---|
| 261 | from IPython.genutils import page as pager |
---|
| 262 | except ImportError: |
---|
| 263 | from pydoc import pager |
---|
| 264 | pager(info) |
---|
[718] | 265 | else: |
---|
| 266 | return info |
---|
[710] | 267 | |
---|
[946] | 268 | |
---|
| 269 | def get_selection(self): |
---|
| 270 | """ |
---|
[1005] | 271 | Get the selection object currently set on this scantable. |
---|
| 272 | Parameters: |
---|
| 273 | none |
---|
| 274 | Example: |
---|
| 275 | sel = scan.get_selection() |
---|
| 276 | sel.set_ifs(0) # select IF 0 |
---|
| 277 | scan.set_selection(sel) # apply modified selection |
---|
[946] | 278 | """ |
---|
| 279 | return selector(self._getselection()) |
---|
| 280 | |
---|
[1005] | 281 | def set_selection(self, selection=selector()): |
---|
[946] | 282 | """ |
---|
[1005] | 283 | Select a subset of the data. All following operations on this scantable |
---|
| 284 | are only applied to thi selection. |
---|
| 285 | Parameters: |
---|
| 286 | selection: a selector object (default unset the selection) |
---|
| 287 | Examples: |
---|
| 288 | sel = selector() # create a selection object |
---|
[1118] | 289 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
---|
[1005] | 290 | scan.set_selection(sel) # set the selection |
---|
| 291 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 292 | scan.set_selection() # unset the selection |
---|
[946] | 293 | """ |
---|
| 294 | self._setselection(selection) |
---|
| 295 | |
---|
[876] | 296 | def stats(self, stat='stddev', mask=None): |
---|
[102] | 297 | """ |
---|
[135] | 298 | Determine the specified statistic of the current beam/if/pol |
---|
[102] | 299 | Takes a 'mask' as an optional parameter to specify which |
---|
| 300 | channels should be excluded. |
---|
| 301 | Parameters: |
---|
[135] | 302 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
---|
| 303 | 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
| 304 | mask: an optional mask specifying where the statistic |
---|
[102] | 305 | should be determined. |
---|
| 306 | Example: |
---|
[113] | 307 | scan.set_unit('channel') |
---|
[1118] | 308 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 309 | scan.stats(stat='mean', mask=m) |
---|
[102] | 310 | """ |
---|
| 311 | if mask == None: |
---|
[876] | 312 | mask = [] |
---|
[1118] | 313 | axes = ['Beam', 'IF', 'Pol', 'Time'] |
---|
[876] | 314 | if not self._check_ifs(): |
---|
[1118] | 315 | raise ValueError("Cannot apply mask as the IFs have different " |
---|
| 316 | "number of channels. Please use setselection() " |
---|
| 317 | "to select individual IFs") |
---|
[256] | 318 | |
---|
[876] | 319 | statvals = self._math._stats(self, mask, stat) |
---|
| 320 | out = '' |
---|
| 321 | axes = [] |
---|
| 322 | for i in range(self.nrow()): |
---|
| 323 | axis = [] |
---|
| 324 | axis.append(self.getscan(i)) |
---|
| 325 | axis.append(self.getbeam(i)) |
---|
| 326 | axis.append(self.getif(i)) |
---|
| 327 | axis.append(self.getpol(i)) |
---|
| 328 | axis.append(self.getcycle(i)) |
---|
| 329 | axes.append(axis) |
---|
| 330 | tm = self._gettime(i) |
---|
| 331 | src = self._getsourcename(i) |
---|
| 332 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
---|
| 333 | out += 'Time[%s]:\n' % (tm) |
---|
| 334 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
---|
| 335 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
---|
| 336 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
---|
| 337 | out += '= %3.3f\n' % (statvals[i]) |
---|
| 338 | out += "--------------------------------------------------\n" |
---|
[256] | 339 | |
---|
[876] | 340 | if rcParams['verbose']: |
---|
| 341 | print "--------------------------------------------------" |
---|
[1118] | 342 | print " ", stat |
---|
[876] | 343 | print "--------------------------------------------------" |
---|
| 344 | print out |
---|
[1118] | 345 | retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'], |
---|
[876] | 346 | 'axes' : axes, |
---|
| 347 | 'data': statvals} |
---|
| 348 | return retval |
---|
[102] | 349 | |
---|
[1118] | 350 | def stddev(self, mask=None): |
---|
[135] | 351 | """ |
---|
| 352 | Determine the standard deviation of the current beam/if/pol |
---|
| 353 | Takes a 'mask' as an optional parameter to specify which |
---|
| 354 | channels should be excluded. |
---|
| 355 | Parameters: |
---|
| 356 | mask: an optional mask specifying where the standard |
---|
| 357 | deviation should be determined. |
---|
| 358 | |
---|
| 359 | Example: |
---|
| 360 | scan.set_unit('channel') |
---|
[1118] | 361 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 362 | scan.stddev(mask=m) |
---|
| 363 | """ |
---|
[1118] | 364 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 365 | |
---|
[1003] | 366 | |
---|
| 367 | def column_names(self): |
---|
| 368 | """ |
---|
| 369 | Return a list of column names, which can be used for selection. |
---|
| 370 | """ |
---|
| 371 | return list(Scantable.column_names(self)) |
---|
| 372 | |
---|
[876] | 373 | def get_tsys(self): |
---|
[113] | 374 | """ |
---|
| 375 | Return the System temperatures. |
---|
| 376 | Parameters: |
---|
[876] | 377 | |
---|
[113] | 378 | Returns: |
---|
[876] | 379 | a list of Tsys values for the current selection |
---|
[113] | 380 | """ |
---|
[256] | 381 | |
---|
[876] | 382 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 383 | |
---|
[876] | 384 | def _row_callback(self, callback, label): |
---|
| 385 | axes = [] |
---|
[1118] | 386 | axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'] |
---|
[876] | 387 | out = "" |
---|
[1118] | 388 | outvec = [] |
---|
[876] | 389 | for i in range(self.nrow()): |
---|
| 390 | axis = [] |
---|
| 391 | axis.append(self.getscan(i)) |
---|
| 392 | axis.append(self.getbeam(i)) |
---|
| 393 | axis.append(self.getif(i)) |
---|
| 394 | axis.append(self.getpol(i)) |
---|
| 395 | axis.append(self.getcycle(i)) |
---|
| 396 | axes.append(axis) |
---|
| 397 | tm = self._gettime(i) |
---|
| 398 | src = self._getsourcename(i) |
---|
| 399 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
---|
| 400 | out += 'Time[%s]:\n' % (tm) |
---|
| 401 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
---|
| 402 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
---|
| 403 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
---|
| 404 | outvec.append(callback(i)) |
---|
| 405 | out += '= %3.3f\n' % (outvec[i]) |
---|
| 406 | out += "--------------------------------------------------\n" |
---|
| 407 | if rcParams['verbose']: |
---|
| 408 | print "--------------------------------------------------" |
---|
| 409 | print " %s" % (label) |
---|
| 410 | print "--------------------------------------------------" |
---|
| 411 | print out |
---|
| 412 | retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec} |
---|
| 413 | return retval |
---|
[256] | 414 | |
---|
[1070] | 415 | def _get_column(self, callback, row=-1): |
---|
| 416 | """ |
---|
| 417 | """ |
---|
| 418 | if row == -1: |
---|
| 419 | return [callback(i) for i in range(self.nrow())] |
---|
| 420 | else: |
---|
| 421 | if 0 <= row < self.nrow(): |
---|
| 422 | return callback(row) |
---|
[256] | 423 | |
---|
[1070] | 424 | |
---|
[407] | 425 | def get_time(self, row=-1): |
---|
[113] | 426 | """ |
---|
| 427 | Get a list of time stamps for the observations. |
---|
[181] | 428 | Return a string for each integration in the scantable. |
---|
[113] | 429 | Parameters: |
---|
[407] | 430 | row: row no of integration. Default -1 return all rows |
---|
[113] | 431 | Example: |
---|
| 432 | none |
---|
| 433 | """ |
---|
[1070] | 434 | return self._get_column(self._gettime, row) |
---|
[102] | 435 | |
---|
[714] | 436 | def get_sourcename(self, row=-1): |
---|
| 437 | """ |
---|
[794] | 438 | Get a list source names for the observations. |
---|
[714] | 439 | Return a string for each integration in the scantable. |
---|
| 440 | Parameters: |
---|
| 441 | row: row no of integration. Default -1 return all rows |
---|
| 442 | Example: |
---|
| 443 | none |
---|
| 444 | """ |
---|
[1070] | 445 | return self._get_column(self._getsourcename, row) |
---|
[714] | 446 | |
---|
[794] | 447 | def get_elevation(self, row=-1): |
---|
| 448 | """ |
---|
| 449 | Get a list of elevations for the observations. |
---|
| 450 | Return a float for each integration in the scantable. |
---|
| 451 | Parameters: |
---|
| 452 | row: row no of integration. Default -1 return all rows |
---|
| 453 | Example: |
---|
| 454 | none |
---|
| 455 | """ |
---|
[1070] | 456 | return self._get_column(self._getelevation, row) |
---|
[794] | 457 | |
---|
| 458 | def get_azimuth(self, row=-1): |
---|
| 459 | """ |
---|
| 460 | Get a list of azimuths for the observations. |
---|
| 461 | Return a float for each integration in the scantable. |
---|
| 462 | Parameters: |
---|
| 463 | row: row no of integration. Default -1 return all rows |
---|
| 464 | Example: |
---|
| 465 | none |
---|
| 466 | """ |
---|
[1070] | 467 | return self._get_column(self._getazimuth, row) |
---|
[794] | 468 | |
---|
| 469 | def get_parangle(self, row=-1): |
---|
| 470 | """ |
---|
| 471 | Get a list of parallactic angles for the observations. |
---|
| 472 | Return a float for each integration in the scantable. |
---|
| 473 | Parameters: |
---|
| 474 | row: row no of integration. Default -1 return all rows |
---|
| 475 | Example: |
---|
| 476 | none |
---|
| 477 | """ |
---|
[1070] | 478 | return self._get_column(self._getparangle, row) |
---|
[794] | 479 | |
---|
[1070] | 480 | def get_direction(self, row=-1): |
---|
| 481 | """ |
---|
| 482 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 483 | Return a float for each integration in the scantable. |
---|
| 484 | Parameters: |
---|
| 485 | row: row no of integration. Default -1 return all rows |
---|
| 486 | Example: |
---|
| 487 | none |
---|
| 488 | """ |
---|
| 489 | return self._get_column(self._getdirection, row) |
---|
| 490 | |
---|
[102] | 491 | def set_unit(self, unit='channel'): |
---|
| 492 | """ |
---|
| 493 | Set the unit for all following operations on this scantable |
---|
| 494 | Parameters: |
---|
| 495 | unit: optional unit, default is 'channel' |
---|
[1118] | 496 | one of '*Hz', 'km/s', 'channel', '' |
---|
[102] | 497 | """ |
---|
[484] | 498 | varlist = vars() |
---|
[1118] | 499 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 500 | unit = '' |
---|
| 501 | inf = list(self._getcoordinfo()) |
---|
| 502 | inf[0] = unit |
---|
| 503 | self._setcoordinfo(inf) |
---|
[1118] | 504 | self._add_history("set_unit", varlist) |
---|
[113] | 505 | |
---|
[484] | 506 | def set_instrument(self, instr): |
---|
[358] | 507 | """ |
---|
| 508 | Set the instrument for subsequent processing |
---|
| 509 | Parameters: |
---|
[710] | 510 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 511 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 512 | """ |
---|
| 513 | self._setInstrument(instr) |
---|
[1118] | 514 | self._add_history("set_instument", vars()) |
---|
[718] | 515 | print_log() |
---|
[358] | 516 | |
---|
[276] | 517 | def set_doppler(self, doppler='RADIO'): |
---|
| 518 | """ |
---|
| 519 | Set the doppler for all following operations on this scantable. |
---|
| 520 | Parameters: |
---|
| 521 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 522 | """ |
---|
[484] | 523 | varlist = vars() |
---|
[276] | 524 | inf = list(self._getcoordinfo()) |
---|
| 525 | inf[2] = doppler |
---|
| 526 | self._setcoordinfo(inf) |
---|
[1118] | 527 | self._add_history("set_doppler", vars()) |
---|
[718] | 528 | print_log() |
---|
[710] | 529 | |
---|
[226] | 530 | def set_freqframe(self, frame=None): |
---|
[113] | 531 | """ |
---|
| 532 | Set the frame type of the Spectral Axis. |
---|
| 533 | Parameters: |
---|
[591] | 534 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1118] | 535 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
| 536 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[113] | 537 | Examples: |
---|
| 538 | scan.set_freqframe('BARY') |
---|
| 539 | """ |
---|
[484] | 540 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
| 541 | varlist = vars() |
---|
[1118] | 542 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 543 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 544 | |
---|
[989] | 545 | if frame in valid: |
---|
[113] | 546 | inf = list(self._getcoordinfo()) |
---|
| 547 | inf[1] = frame |
---|
| 548 | self._setcoordinfo(inf) |
---|
[1118] | 549 | self._add_history("set_freqframe", varlist) |
---|
[102] | 550 | else: |
---|
[1118] | 551 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[718] | 552 | if rcParams['verbose']: |
---|
| 553 | print msg |
---|
| 554 | else: |
---|
| 555 | raise TypeError(msg) |
---|
| 556 | print_log() |
---|
[710] | 557 | |
---|
[989] | 558 | def set_dirframe(self, frame=""): |
---|
| 559 | """ |
---|
| 560 | Set the frame type of the Direction on the sky. |
---|
| 561 | Parameters: |
---|
| 562 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 563 | 'J2000', 'B1950', 'GALACTIC' |
---|
| 564 | Examples: |
---|
| 565 | scan.set_dirframe('GALACTIC') |
---|
| 566 | """ |
---|
| 567 | varlist = vars() |
---|
| 568 | try: |
---|
| 569 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 570 | except RuntimeError, msg: |
---|
[989] | 571 | if rcParams['verbose']: |
---|
| 572 | print msg |
---|
| 573 | else: |
---|
| 574 | raise |
---|
[1118] | 575 | self._add_history("set_dirframe", varlist) |
---|
[989] | 576 | |
---|
[113] | 577 | def get_unit(self): |
---|
| 578 | """ |
---|
| 579 | Get the default unit set in this scantable |
---|
| 580 | Parameters: |
---|
| 581 | Returns: |
---|
| 582 | A unit string |
---|
| 583 | """ |
---|
| 584 | inf = self._getcoordinfo() |
---|
| 585 | unit = inf[0] |
---|
| 586 | if unit == '': unit = 'channel' |
---|
| 587 | return unit |
---|
[102] | 588 | |
---|
[158] | 589 | def get_abcissa(self, rowno=0): |
---|
[102] | 590 | """ |
---|
[158] | 591 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 592 | selected Beam/IF/Pol |
---|
| 593 | Parameters: |
---|
[226] | 594 | rowno: an optional row number in the scantable. Default is the |
---|
| 595 | first row, i.e. rowno=0 |
---|
[113] | 596 | Returns: |
---|
[407] | 597 | The abcissa values and it's format string (as a dictionary) |
---|
[113] | 598 | """ |
---|
[256] | 599 | abc = self._getabcissa(rowno) |
---|
[710] | 600 | lbl = self._getabcissalabel(rowno) |
---|
[718] | 601 | print_log() |
---|
[158] | 602 | return abc, lbl |
---|
[113] | 603 | |
---|
[1118] | 604 | def flag(self, mask=None): |
---|
[1001] | 605 | """ |
---|
| 606 | Flag the selected data using an optional channel mask. |
---|
| 607 | Parameters: |
---|
| 608 | mask: an optional channel mask, created with create_mask. Default |
---|
| 609 | (no mask) is all channels. |
---|
| 610 | """ |
---|
| 611 | varlist = vars() |
---|
[1118] | 612 | if mask is None: |
---|
| 613 | mask = [] |
---|
[1001] | 614 | try: |
---|
| 615 | self._flag(mask) |
---|
[1118] | 616 | except RuntimeError, msg: |
---|
[1001] | 617 | if rcParams['verbose']: |
---|
| 618 | print msg |
---|
| 619 | return |
---|
| 620 | else: raise |
---|
| 621 | self._add_history("flag", varlist) |
---|
| 622 | |
---|
| 623 | |
---|
[113] | 624 | def create_mask(self, *args, **kwargs): |
---|
| 625 | """ |
---|
[1118] | 626 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 627 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 628 | applied. |
---|
[102] | 629 | Parameters: |
---|
[1118] | 630 | [min, max], [min2, max2], ... |
---|
[1024] | 631 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 632 | to be masked |
---|
[189] | 633 | invert: optional argument. If specified as True, |
---|
| 634 | return an inverted mask, i.e. the regions |
---|
| 635 | specified are EXCLUDED |
---|
[513] | 636 | row: create the mask using the specified row for |
---|
| 637 | unit conversions, default is row=0 |
---|
| 638 | only necessary if frequency varies over rows. |
---|
[102] | 639 | Example: |
---|
[113] | 640 | scan.set_unit('channel') |
---|
| 641 | a) |
---|
[1118] | 642 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 643 | # masks everything outside 400 and 500 |
---|
[113] | 644 | # and 800 and 900 in the unit 'channel' |
---|
| 645 | |
---|
| 646 | b) |
---|
[1118] | 647 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 648 | # masks the regions between 400 and 500 |
---|
[113] | 649 | # and 800 and 900 in the unit 'channel' |
---|
[1024] | 650 | c) |
---|
| 651 | mask only channel 400 |
---|
[1118] | 652 | msk = scan.create_mask([400, 400]) |
---|
[102] | 653 | """ |
---|
[513] | 654 | row = 0 |
---|
| 655 | if kwargs.has_key("row"): |
---|
| 656 | row = kwargs.get("row") |
---|
| 657 | data = self._getabcissa(row) |
---|
[113] | 658 | u = self._getcoordinfo()[0] |
---|
[718] | 659 | if rcParams['verbose']: |
---|
[113] | 660 | if u == "": u = "channel" |
---|
[718] | 661 | msg = "The current mask window unit is %s" % u |
---|
[1118] | 662 | i = self._check_ifs() |
---|
| 663 | if not i: |
---|
[876] | 664 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 665 | asaplog.push(msg) |
---|
[102] | 666 | n = self.nchan() |
---|
[1134] | 667 | msk = NUM.zeros(n) |
---|
[710] | 668 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 669 | |
---|
[1118] | 670 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 671 | and args or args[0] |
---|
[710] | 672 | for window in ws: |
---|
[102] | 673 | if (len(window) != 2 or window[0] > window[1] ): |
---|
[1118] | 674 | raise TypeError("A window needs to be defined as [min, max]") |
---|
[102] | 675 | for i in range(n): |
---|
[1024] | 676 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[189] | 677 | msk[i] = 1 |
---|
[113] | 678 | if kwargs.has_key('invert'): |
---|
| 679 | if kwargs.get('invert'): |
---|
[1134] | 680 | msk = NUM.logical_not(msk) |
---|
[718] | 681 | print_log() |
---|
[102] | 682 | return msk |
---|
[710] | 683 | |
---|
[256] | 684 | def get_restfreqs(self): |
---|
| 685 | """ |
---|
| 686 | Get the restfrequency(s) stored in this scantable. |
---|
| 687 | The return value(s) are always of unit 'Hz' |
---|
| 688 | Parameters: |
---|
| 689 | none |
---|
| 690 | Returns: |
---|
| 691 | a list of doubles |
---|
| 692 | """ |
---|
| 693 | return list(self._getrestfreqs()) |
---|
[102] | 694 | |
---|
[402] | 695 | |
---|
[931] | 696 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
| 697 | """ |
---|
| 698 | Set or replace the restfrequency specified and |
---|
| 699 | If the 'freqs' argument holds a scalar, |
---|
| 700 | then that rest frequency will be applied to all the selected |
---|
| 701 | data. If the 'freqs' argument holds |
---|
| 702 | a vector, then it MUST be of equal or smaller length than |
---|
| 703 | the number of IFs (and the available restfrequencies will be |
---|
| 704 | replaced by this vector). In this case, *all* data have |
---|
| 705 | the restfrequency set per IF according |
---|
| 706 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 707 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 708 | IF 1 gets restfreq 2e9. |
---|
| 709 | You can also specify the frequencies via known line names |
---|
| 710 | from the built-in Lovas table. |
---|
| 711 | Parameters: |
---|
| 712 | freqs: list of rest frequency values or string idenitfiers |
---|
| 713 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 714 | |
---|
[931] | 715 | Example: |
---|
| 716 | # set the given restfrequency for the whole table |
---|
| 717 | scan.set_restfreqs(freqs=1.4e9) |
---|
| 718 | # If thee number of IFs in the data is >= 2 the IF0 gets the first |
---|
| 719 | # value IF1 the second... |
---|
[1118] | 720 | scan.set_restfreqs(freqs=[1.4e9, 1.67e9]) |
---|
[931] | 721 | #set the given restfrequency for the whole table (by name) |
---|
| 722 | scan.set_restfreqs(freqs="OH1667") |
---|
[391] | 723 | |
---|
[931] | 724 | Note: |
---|
| 725 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 726 | source and IF basis, use scantable.set_selection() before using |
---|
| 727 | this function. |
---|
| 728 | # provide your scantable is call scan |
---|
| 729 | selection = selector() |
---|
| 730 | selection.set_name("ORION*") |
---|
| 731 | selection.set_ifs([1]) |
---|
| 732 | scan.set_selection(selection) |
---|
| 733 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 734 | |
---|
| 735 | """ |
---|
| 736 | varlist = vars() |
---|
| 737 | |
---|
| 738 | t = type(freqs) |
---|
[1118] | 739 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
| 740 | self._setrestfreqs(freqs, unit) |
---|
| 741 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
| 742 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[931] | 743 | sel = selector() |
---|
| 744 | savesel = self._getselection() |
---|
| 745 | for i in xrange(len(freqs)): |
---|
[946] | 746 | sel.set_ifs([i]) |
---|
[931] | 747 | self._setselection(sel) |
---|
| 748 | self._setrestfreqs(freqs[i], unit) |
---|
| 749 | self._setselection(savesel) |
---|
| 750 | elif isinstance(freqs[-1], str): |
---|
| 751 | # not yet implemented |
---|
| 752 | pass |
---|
| 753 | else: |
---|
| 754 | return |
---|
| 755 | self._add_history("set_restfreqs", varlist) |
---|
| 756 | |
---|
| 757 | |
---|
| 758 | |
---|
[484] | 759 | def history(self): |
---|
| 760 | hist = list(self._gethistory()) |
---|
[794] | 761 | out = "-"*80 |
---|
[484] | 762 | for h in hist: |
---|
[489] | 763 | if h.startswith("---"): |
---|
[794] | 764 | out += "\n"+h |
---|
[489] | 765 | else: |
---|
| 766 | items = h.split("##") |
---|
| 767 | date = items[0] |
---|
| 768 | func = items[1] |
---|
| 769 | items = items[2:] |
---|
[794] | 770 | out += "\n"+date+"\n" |
---|
| 771 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 772 | for i in items: |
---|
| 773 | s = i.split("=") |
---|
[1118] | 774 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[794] | 775 | out += "\n"+"-"*80 |
---|
| 776 | try: |
---|
| 777 | from IPython.genutils import page as pager |
---|
| 778 | except ImportError: |
---|
| 779 | from pydoc import pager |
---|
| 780 | pager(out) |
---|
[484] | 781 | return |
---|
| 782 | |
---|
[513] | 783 | # |
---|
| 784 | # Maths business |
---|
| 785 | # |
---|
| 786 | |
---|
[931] | 787 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[513] | 788 | """ |
---|
[1070] | 789 | Return the (time) weighted average of a scan. |
---|
[513] | 790 | Note: |
---|
[1070] | 791 | in channels only - align if necessary |
---|
[513] | 792 | Parameters: |
---|
| 793 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 794 | weighting) |
---|
[558] | 795 | scanav: True averages each scan separately |
---|
| 796 | False (default) averages all scans together, |
---|
[1099] | 797 | weight: Weighting scheme. |
---|
| 798 | 'none' (mean no weight) |
---|
| 799 | 'var' (1/var(spec) weighted) |
---|
| 800 | 'tsys' (1/Tsys**2 weighted) |
---|
| 801 | 'tint' (integration time weighted) |
---|
| 802 | 'tintsys' (Tint/Tsys**2) |
---|
| 803 | 'median' ( median averaging) |
---|
[535] | 804 | The default is 'tint' |
---|
[931] | 805 | align: align the spectra in velocity before averaging. It takes |
---|
| 806 | the time of the first spectrum as reference time. |
---|
[513] | 807 | Example: |
---|
| 808 | # time average the scantable without using a mask |
---|
[710] | 809 | newscan = scan.average_time() |
---|
[513] | 810 | """ |
---|
| 811 | varlist = vars() |
---|
[976] | 812 | if weight is None: weight = 'TINT' |
---|
[513] | 813 | if mask is None: mask = () |
---|
[1099] | 814 | if scanav: scanav = "SCAN" |
---|
| 815 | else: scanav = "NONE" |
---|
[1118] | 816 | scan = (self, ) |
---|
[989] | 817 | try: |
---|
[1118] | 818 | if align: |
---|
| 819 | scan = (self.freq_align(insitu=False), ) |
---|
| 820 | s = None |
---|
| 821 | if weight.upper() == 'MEDIAN': |
---|
| 822 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 823 | scanav)) |
---|
| 824 | else: |
---|
| 825 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 826 | scanav)) |
---|
| 827 | except RuntimeError, msg: |
---|
[989] | 828 | if rcParams['verbose']: |
---|
| 829 | print msg |
---|
| 830 | return |
---|
| 831 | else: raise |
---|
[1099] | 832 | s._add_history("average_time", varlist) |
---|
[718] | 833 | print_log() |
---|
[513] | 834 | return s |
---|
[710] | 835 | |
---|
[876] | 836 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[513] | 837 | """ |
---|
| 838 | Return a scan where all spectra are converted to either |
---|
| 839 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 840 | By default the function tries to look the values up internally. |
---|
| 841 | If it can't find them (or if you want to over-ride), you must |
---|
| 842 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 843 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 844 | Parameters: |
---|
| 845 | jyperk: the Jy / K conversion factor |
---|
| 846 | eta: the aperture efficiency |
---|
| 847 | d: the geomtric diameter (metres) |
---|
| 848 | insitu: if False a new scantable is returned. |
---|
| 849 | Otherwise, the scaling is done in-situ |
---|
| 850 | The default is taken from .asaprc (False) |
---|
| 851 | allaxes: if True apply to all spectra. Otherwise |
---|
| 852 | apply only to the selected (beam/pol/if)spectra only |
---|
| 853 | The default is taken from .asaprc (True if none) |
---|
| 854 | """ |
---|
| 855 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 856 | self._math._setinsitu(insitu) |
---|
[513] | 857 | varlist = vars() |
---|
| 858 | if jyperk is None: jyperk = -1.0 |
---|
| 859 | if d is None: d = -1.0 |
---|
| 860 | if eta is None: eta = -1.0 |
---|
[876] | 861 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 862 | s._add_history("convert_flux", varlist) |
---|
| 863 | print_log() |
---|
| 864 | if insitu: self._assign(s) |
---|
| 865 | else: return s |
---|
[513] | 866 | |
---|
[876] | 867 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[513] | 868 | """ |
---|
| 869 | Return a scan after applying a gain-elevation correction. |
---|
| 870 | The correction can be made via either a polynomial or a |
---|
| 871 | table-based interpolation (and extrapolation if necessary). |
---|
| 872 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 873 | If you specify neither, then a polynomial correction will be made |
---|
| 874 | with built in coefficients known for certain telescopes (an error |
---|
| 875 | will occur if the instrument is not known). |
---|
| 876 | The data and Tsys are *divided* by the scaling factors. |
---|
| 877 | Parameters: |
---|
| 878 | poly: Polynomial coefficients (default None) to compute a |
---|
| 879 | gain-elevation correction as a function of |
---|
| 880 | elevation (in degrees). |
---|
| 881 | filename: The name of an ascii file holding correction factors. |
---|
| 882 | The first row of the ascii file must give the column |
---|
| 883 | names and these MUST include columns |
---|
| 884 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 885 | by this) somewhere. |
---|
| 886 | The second row must give the data type of the |
---|
| 887 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 888 | An example file would be |
---|
| 889 | (actual factors are arbitrary) : |
---|
| 890 | |
---|
| 891 | TIME ELEVATION FACTOR |
---|
| 892 | R R R |
---|
| 893 | 0.1 0 0.8 |
---|
| 894 | 0.2 20 0.85 |
---|
| 895 | 0.3 40 0.9 |
---|
| 896 | 0.4 60 0.85 |
---|
| 897 | 0.5 80 0.8 |
---|
| 898 | 0.6 90 0.75 |
---|
| 899 | method: Interpolation method when correcting from a table. |
---|
| 900 | Values are "nearest", "linear" (default), "cubic" |
---|
| 901 | and "spline" |
---|
| 902 | insitu: if False a new scantable is returned. |
---|
| 903 | Otherwise, the scaling is done in-situ |
---|
| 904 | The default is taken from .asaprc (False) |
---|
| 905 | """ |
---|
| 906 | |
---|
| 907 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 908 | self._math._setinsitu(insitu) |
---|
[513] | 909 | varlist = vars() |
---|
| 910 | if poly is None: |
---|
[1118] | 911 | poly = () |
---|
[513] | 912 | from os.path import expandvars |
---|
| 913 | filename = expandvars(filename) |
---|
[876] | 914 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 915 | s._add_history("gain_el", varlist) |
---|
| 916 | print_log() |
---|
| 917 | if insitu: self._assign(s) |
---|
| 918 | else: return s |
---|
[710] | 919 | |
---|
[931] | 920 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[513] | 921 | """ |
---|
| 922 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 923 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 924 | set_freqframe. |
---|
| 925 | Parameters: |
---|
| 926 | reftime: reference time to align at. By default, the time of |
---|
| 927 | the first row of data is used. |
---|
| 928 | method: Interpolation method for regridding the spectra. |
---|
| 929 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 930 | and "spline" |
---|
| 931 | insitu: if False a new scantable is returned. |
---|
| 932 | Otherwise, the scaling is done in-situ |
---|
| 933 | The default is taken from .asaprc (False) |
---|
| 934 | """ |
---|
[931] | 935 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 936 | self._math._setinsitu(insitu) |
---|
[513] | 937 | varlist = vars() |
---|
[931] | 938 | if reftime is None: reftime = "" |
---|
| 939 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 940 | s._add_history("freq_align", varlist) |
---|
| 941 | print_log() |
---|
| 942 | if insitu: self._assign(s) |
---|
| 943 | else: return s |
---|
[513] | 944 | |
---|
[876] | 945 | def opacity(self, tau, insitu=None): |
---|
[513] | 946 | """ |
---|
| 947 | Apply an opacity correction. The data |
---|
| 948 | and Tsys are multiplied by the correction factor. |
---|
| 949 | Parameters: |
---|
| 950 | tau: Opacity from which the correction factor is |
---|
| 951 | exp(tau*ZD) |
---|
| 952 | where ZD is the zenith-distance |
---|
| 953 | insitu: if False a new scantable is returned. |
---|
| 954 | Otherwise, the scaling is done in-situ |
---|
| 955 | The default is taken from .asaprc (False) |
---|
| 956 | """ |
---|
| 957 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 958 | self._math._setinsitu(insitu) |
---|
[513] | 959 | varlist = vars() |
---|
[876] | 960 | s = scantable(self._math._opacity(self, tau)) |
---|
| 961 | s._add_history("opacity", varlist) |
---|
| 962 | print_log() |
---|
| 963 | if insitu: self._assign(s) |
---|
| 964 | else: return s |
---|
[513] | 965 | |
---|
| 966 | def bin(self, width=5, insitu=None): |
---|
| 967 | """ |
---|
| 968 | Return a scan where all spectra have been binned up. |
---|
| 969 | width: The bin width (default=5) in pixels |
---|
| 970 | insitu: if False a new scantable is returned. |
---|
| 971 | Otherwise, the scaling is done in-situ |
---|
| 972 | The default is taken from .asaprc (False) |
---|
| 973 | """ |
---|
| 974 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 975 | self._math._setinsitu(insitu) |
---|
[513] | 976 | varlist = vars() |
---|
[876] | 977 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 978 | s._add_history("bin", varlist) |
---|
[876] | 979 | print_log() |
---|
| 980 | if insitu: self._assign(s) |
---|
| 981 | else: return s |
---|
[513] | 982 | |
---|
[710] | 983 | |
---|
[513] | 984 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 985 | """ |
---|
| 986 | Return a scan where all spectra have been binned up |
---|
| 987 | width: The bin width (default=5) in pixels |
---|
| 988 | method: Interpolation method when correcting from a table. |
---|
| 989 | Values are "nearest", "linear", "cubic" (default) |
---|
| 990 | and "spline" |
---|
| 991 | insitu: if False a new scantable is returned. |
---|
| 992 | Otherwise, the scaling is done in-situ |
---|
| 993 | The default is taken from .asaprc (False) |
---|
| 994 | """ |
---|
| 995 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 996 | self._math._setinsitu(insitu) |
---|
[513] | 997 | varlist = vars() |
---|
[876] | 998 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 999 | s._add_history("resample", varlist) |
---|
[876] | 1000 | print_log() |
---|
| 1001 | if insitu: self._assign(s) |
---|
| 1002 | else: return s |
---|
[513] | 1003 | |
---|
| 1004 | |
---|
[946] | 1005 | def average_pol(self, mask=None, weight='none'): |
---|
| 1006 | """ |
---|
| 1007 | Average the Polarisations together. |
---|
| 1008 | Parameters: |
---|
| 1009 | mask: An optional mask defining the region, where the |
---|
| 1010 | averaging will be applied. The output will have all |
---|
| 1011 | specified points masked. |
---|
| 1012 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1013 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1014 | """ |
---|
| 1015 | varlist = vars() |
---|
| 1016 | if mask is None: |
---|
| 1017 | mask = () |
---|
[1010] | 1018 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1019 | s._add_history("average_pol", varlist) |
---|
[946] | 1020 | print_log() |
---|
[992] | 1021 | return s |
---|
[513] | 1022 | |
---|
[1145] | 1023 | def average_beam(self, mask=None, weight='none'): |
---|
| 1024 | """ |
---|
| 1025 | Average the Beams together. |
---|
| 1026 | Parameters: |
---|
| 1027 | mask: An optional mask defining the region, where the |
---|
| 1028 | averaging will be applied. The output will have all |
---|
| 1029 | specified points masked. |
---|
| 1030 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1031 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1032 | """ |
---|
| 1033 | varlist = vars() |
---|
| 1034 | if mask is None: |
---|
| 1035 | mask = () |
---|
| 1036 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1037 | s._add_history("average_beam", varlist) |
---|
| 1038 | print_log() |
---|
| 1039 | return s |
---|
| 1040 | |
---|
[992] | 1041 | def convert_pol(self, poltype=None): |
---|
| 1042 | """ |
---|
| 1043 | Convert the data to a different polarisation type. |
---|
| 1044 | Parameters: |
---|
| 1045 | poltype: The new polarisation type. Valid types are: |
---|
| 1046 | "linear", "stokes" and "circular" |
---|
| 1047 | """ |
---|
| 1048 | varlist = vars() |
---|
| 1049 | try: |
---|
| 1050 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1051 | except RuntimeError, msg: |
---|
[992] | 1052 | if rcParams['verbose']: |
---|
[1118] | 1053 | print msg |
---|
| 1054 | return |
---|
[992] | 1055 | else: |
---|
| 1056 | raise |
---|
[1118] | 1057 | s._add_history("convert_pol", varlist) |
---|
[992] | 1058 | print_log() |
---|
| 1059 | return s |
---|
| 1060 | |
---|
[876] | 1061 | def smooth(self, kernel="hanning", width=5.0, insitu=None): |
---|
[513] | 1062 | """ |
---|
| 1063 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 1064 | Parameters: |
---|
| 1065 | scan: The input scan |
---|
| 1066 | kernel: The type of smoothing kernel. Select from |
---|
| 1067 | 'hanning' (default), 'gaussian' and 'boxcar'. |
---|
| 1068 | The first three characters are sufficient. |
---|
| 1069 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1070 | ignored otherwise it defauls to 5 pixels. |
---|
| 1071 | For 'gaussian' it is the Full Width Half |
---|
| 1072 | Maximum. For 'boxcar' it is the full width. |
---|
| 1073 | insitu: if False a new scantable is returned. |
---|
| 1074 | Otherwise, the scaling is done in-situ |
---|
| 1075 | The default is taken from .asaprc (False) |
---|
| 1076 | Example: |
---|
| 1077 | none |
---|
| 1078 | """ |
---|
| 1079 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1080 | self._math._setinsitu(insitu) |
---|
[513] | 1081 | varlist = vars() |
---|
[1118] | 1082 | s = scantable(self._math._smooth(self, kernel.lower(), width)) |
---|
[876] | 1083 | s._add_history("smooth", varlist) |
---|
| 1084 | print_log() |
---|
| 1085 | if insitu: self._assign(s) |
---|
| 1086 | else: return s |
---|
[513] | 1087 | |
---|
[876] | 1088 | |
---|
[1061] | 1089 | def poly_baseline(self, mask=None, order=0, plot=False, insitu=None): |
---|
[513] | 1090 | """ |
---|
| 1091 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1092 | Parameters: |
---|
[794] | 1093 | scan: a scantable |
---|
| 1094 | mask: an optional mask |
---|
| 1095 | order: the order of the polynomial (default is 0) |
---|
[1061] | 1096 | plot: plot the fit and the residual. In this each |
---|
| 1097 | indivual fit has to be approved, by typing 'y' |
---|
| 1098 | or 'n' |
---|
[794] | 1099 | insitu: if False a new scantable is returned. |
---|
| 1100 | Otherwise, the scaling is done in-situ |
---|
| 1101 | The default is taken from .asaprc (False) |
---|
[513] | 1102 | Example: |
---|
| 1103 | # return a scan baselined by a third order polynomial, |
---|
| 1104 | # not using a mask |
---|
| 1105 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1106 | """ |
---|
[513] | 1107 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1108 | varlist = vars() |
---|
| 1109 | if mask is None: |
---|
[1134] | 1110 | mask = list(NUM.ones(self.nchan(-1))) |
---|
[513] | 1111 | from asap.asapfitter import fitter |
---|
| 1112 | f = fitter() |
---|
| 1113 | f.set_scan(self, mask) |
---|
| 1114 | f.set_function(poly=order) |
---|
[1061] | 1115 | s = f.auto_fit(insitu, plot=plot) |
---|
[876] | 1116 | s._add_history("poly_baseline", varlist) |
---|
[718] | 1117 | print_log() |
---|
[876] | 1118 | if insitu: self._assign(s) |
---|
| 1119 | else: return s |
---|
[513] | 1120 | |
---|
[1118] | 1121 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
[1061] | 1122 | threshold=3, plot=False, insitu=None): |
---|
[880] | 1123 | """ |
---|
| 1124 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1125 | Spectral lines are detected first using linefinder and masked out |
---|
| 1126 | to avoid them affecting the baseline solution. |
---|
| 1127 | |
---|
| 1128 | Parameters: |
---|
| 1129 | mask: an optional mask retreived from scantable |
---|
| 1130 | edge: an optional number of channel to drop at |
---|
| 1131 | the edge of spectrum. If only one value is |
---|
| 1132 | specified, the same number will be dropped from |
---|
| 1133 | both sides of the spectrum. Default is to keep |
---|
[907] | 1134 | all channels. Nested tuples represent individual |
---|
[976] | 1135 | edge selection for different IFs (a number of spectral |
---|
| 1136 | channels can be different) |
---|
[880] | 1137 | order: the order of the polynomial (default is 0) |
---|
| 1138 | threshold: the threshold used by line finder. It is better to |
---|
| 1139 | keep it large as only strong lines affect the |
---|
| 1140 | baseline solution. |
---|
[1061] | 1141 | plot: plot the fit and the residual. In this each |
---|
| 1142 | indivual fit has to be approved, by typing 'y' |
---|
| 1143 | or 'n' |
---|
[880] | 1144 | insitu: if False a new scantable is returned. |
---|
| 1145 | Otherwise, the scaling is done in-situ |
---|
| 1146 | The default is taken from .asaprc (False) |
---|
| 1147 | |
---|
| 1148 | Example: |
---|
| 1149 | scan2=scan.auto_poly_baseline(order=7) |
---|
| 1150 | """ |
---|
| 1151 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1152 | varlist = vars() |
---|
| 1153 | from asap.asapfitter import fitter |
---|
| 1154 | from asap.asaplinefind import linefinder |
---|
| 1155 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1156 | |
---|
[976] | 1157 | # check whether edge is set up for each IF individually |
---|
[1118] | 1158 | individualedge = False; |
---|
| 1159 | if len(edge) > 1: |
---|
| 1160 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 1161 | individualedge = True; |
---|
[907] | 1162 | |
---|
[1118] | 1163 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 1164 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1165 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1166 | to make individual selection for different IFs." |
---|
[919] | 1167 | |
---|
[1118] | 1168 | curedge = (0, 0) |
---|
| 1169 | if individualedge: |
---|
| 1170 | for edgepar in edge: |
---|
| 1171 | if not _is_valid(edgepar, int): |
---|
| 1172 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 1173 | to be a pair of integers or an integer." |
---|
[907] | 1174 | else: |
---|
[1118] | 1175 | curedge = edge; |
---|
[880] | 1176 | |
---|
| 1177 | # setup fitter |
---|
| 1178 | f = fitter() |
---|
| 1179 | f.set_function(poly=order) |
---|
| 1180 | |
---|
| 1181 | # setup line finder |
---|
[1118] | 1182 | fl = linefinder() |
---|
[880] | 1183 | fl.set_options(threshold=threshold) |
---|
| 1184 | |
---|
| 1185 | if not insitu: |
---|
[1118] | 1186 | workscan = self.copy() |
---|
[880] | 1187 | else: |
---|
[1118] | 1188 | workscan = self |
---|
[880] | 1189 | |
---|
[907] | 1190 | fl.set_scan(workscan) |
---|
| 1191 | |
---|
[1118] | 1192 | rows = range(workscan.nrow()) |
---|
[880] | 1193 | asaplog.push("Processing:") |
---|
| 1194 | for r in rows: |
---|
[1118] | 1195 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 1196 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 1197 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 1198 | asaplog.push(msg, False) |
---|
[907] | 1199 | |
---|
[976] | 1200 | # figure out edge parameter |
---|
[1118] | 1201 | if individualedge: |
---|
| 1202 | if len(edge) >= workscan.getif(r): |
---|
| 1203 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 1204 | "be less than the number of IFs" |
---|
| 1205 | curedge = edge[workscan.getif(r)] |
---|
[919] | 1206 | |
---|
[976] | 1207 | # setup line finder |
---|
[1118] | 1208 | fl.find_lines(r, mask, curedge) |
---|
[880] | 1209 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1210 | f.x = workscan._getabcissa(r) |
---|
| 1211 | f.y = workscan._getspectrum(r) |
---|
| 1212 | f.data = None |
---|
| 1213 | f.fit() |
---|
| 1214 | x = f.get_parameters() |
---|
[1061] | 1215 | if plot: |
---|
| 1216 | f.plot(residual=True) |
---|
| 1217 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1218 | if x.upper() == 'N': |
---|
| 1219 | continue |
---|
[880] | 1220 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1061] | 1221 | if plot: |
---|
| 1222 | f._p.unmap() |
---|
| 1223 | f._p = None |
---|
| 1224 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 1225 | if insitu: |
---|
| 1226 | self._assign(workscan) |
---|
| 1227 | else: |
---|
| 1228 | return workscan |
---|
| 1229 | |
---|
[914] | 1230 | def rotate_linpolphase(self, angle): |
---|
| 1231 | """ |
---|
| 1232 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1233 | This is always done in situ in the raw data. So if you call this |
---|
| 1234 | function more than once then each call rotates the phase further. |
---|
| 1235 | Parameters: |
---|
| 1236 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1237 | Examples: |
---|
| 1238 | scan.rotate_linpolphase(2.3) |
---|
| 1239 | """ |
---|
| 1240 | varlist = vars() |
---|
[936] | 1241 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 1242 | self._add_history("rotate_linpolphase", varlist) |
---|
| 1243 | print_log() |
---|
| 1244 | return |
---|
[710] | 1245 | |
---|
[513] | 1246 | |
---|
[914] | 1247 | def rotate_xyphase(self, angle): |
---|
| 1248 | """ |
---|
| 1249 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1250 | in the data. So if you call this function more than once |
---|
| 1251 | then each call rotates the phase further. |
---|
| 1252 | Parameters: |
---|
| 1253 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1254 | Examples: |
---|
| 1255 | scan.rotate_xyphase(2.3) |
---|
| 1256 | """ |
---|
| 1257 | varlist = vars() |
---|
[936] | 1258 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 1259 | self._add_history("rotate_xyphase", varlist) |
---|
| 1260 | print_log() |
---|
| 1261 | return |
---|
| 1262 | |
---|
| 1263 | def swap_linears(self): |
---|
| 1264 | """ |
---|
| 1265 | Swap the linear polarisations XX and YY |
---|
| 1266 | """ |
---|
| 1267 | varlist = vars() |
---|
[936] | 1268 | self._math._swap_linears(self) |
---|
[914] | 1269 | self._add_history("swap_linears", varlist) |
---|
| 1270 | print_log() |
---|
| 1271 | return |
---|
| 1272 | |
---|
| 1273 | def invert_phase(self): |
---|
| 1274 | """ |
---|
| 1275 | Invert the phase of the complex polarisation |
---|
| 1276 | """ |
---|
| 1277 | varlist = vars() |
---|
[936] | 1278 | self._math._invert_phase(self) |
---|
[914] | 1279 | self._add_history("invert_phase", varlist) |
---|
| 1280 | print_log() |
---|
| 1281 | return |
---|
| 1282 | |
---|
[876] | 1283 | def add(self, offset, insitu=None): |
---|
[513] | 1284 | """ |
---|
| 1285 | Return a scan where all spectra have the offset added |
---|
| 1286 | Parameters: |
---|
| 1287 | offset: the offset |
---|
| 1288 | insitu: if False a new scantable is returned. |
---|
| 1289 | Otherwise, the scaling is done in-situ |
---|
| 1290 | The default is taken from .asaprc (False) |
---|
| 1291 | """ |
---|
| 1292 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1293 | self._math._setinsitu(insitu) |
---|
[513] | 1294 | varlist = vars() |
---|
[876] | 1295 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 1296 | s._add_history("add", varlist) |
---|
[876] | 1297 | print_log() |
---|
| 1298 | if insitu: |
---|
| 1299 | self._assign(s) |
---|
| 1300 | else: |
---|
[513] | 1301 | return s |
---|
| 1302 | |
---|
[1118] | 1303 | def scale(self, factor, tsys=True, insitu=None, ): |
---|
[513] | 1304 | """ |
---|
| 1305 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 1306 | Parameters: |
---|
| 1307 | factor: the scaling factor |
---|
| 1308 | insitu: if False a new scantable is returned. |
---|
| 1309 | Otherwise, the scaling is done in-situ |
---|
| 1310 | The default is taken from .asaprc (False) |
---|
| 1311 | tsys: if True (default) then apply the operation to Tsys |
---|
| 1312 | as well as the data |
---|
| 1313 | """ |
---|
| 1314 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1315 | self._math._setinsitu(insitu) |
---|
[513] | 1316 | varlist = vars() |
---|
[876] | 1317 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
[1118] | 1318 | s._add_history("scale", varlist) |
---|
[876] | 1319 | print_log() |
---|
| 1320 | if insitu: |
---|
| 1321 | self._assign(s) |
---|
| 1322 | else: |
---|
[513] | 1323 | return s |
---|
| 1324 | |
---|
[876] | 1325 | def auto_quotient(self, mode='time', preserve=True): |
---|
[670] | 1326 | """ |
---|
| 1327 | This function allows to build quotients automatically. |
---|
| 1328 | It assumes the observation to have the same numer of |
---|
| 1329 | "ons" and "offs" |
---|
| 1330 | It will support "closest off in time" in the future |
---|
| 1331 | Parameters: |
---|
| 1332 | mode: the on/off detection mode; 'suffix' (default) |
---|
| 1333 | 'suffix' identifies 'off' scans by the |
---|
| 1334 | trailing '_R' (Mopra/Parkes) or |
---|
| 1335 | '_e'/'_w' (Tid) |
---|
[710] | 1336 | preserve: you can preserve (default) the continuum or |
---|
| 1337 | remove it. The equations used are |
---|
[670] | 1338 | preserve: Output = Toff * (on/off) - Toff |
---|
[1070] | 1339 | remove: Output = Toff * (on/off) - Ton |
---|
[670] | 1340 | """ |
---|
[876] | 1341 | modes = ["time"] |
---|
[670] | 1342 | if not mode in modes: |
---|
[876] | 1343 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 1344 | raise ValueError(msg) |
---|
| 1345 | varlist = vars() |
---|
[1070] | 1346 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 1347 | s._add_history("auto_quotient", varlist) |
---|
[876] | 1348 | print_log() |
---|
| 1349 | return s |
---|
[710] | 1350 | |
---|
[1145] | 1351 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1141] | 1352 | """ |
---|
[1143] | 1353 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
| 1354 | Parameters: |
---|
[1145] | 1355 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1143] | 1356 | weight: How to average the off beams. Default is 'median'. |
---|
[1145] | 1357 | preserve: you can preserve (default) the continuum or |
---|
| 1358 | remove it. The equations used are |
---|
| 1359 | preserve: Output = Toff * (on/off) - Toff |
---|
| 1360 | remove: Output = Toff * (on/off) - Ton |
---|
[1141] | 1361 | """ |
---|
[1143] | 1362 | if mask is None: mask = () |
---|
[1141] | 1363 | varlist = vars() |
---|
| 1364 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 1365 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 1366 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1141] | 1367 | from asapmath import quotient |
---|
[1145] | 1368 | q = quotient(on, off, preserve) |
---|
[1143] | 1369 | q._add_history("mx_quotient", varlist) |
---|
[1145] | 1370 | print_log() |
---|
[1143] | 1371 | return q |
---|
[513] | 1372 | |
---|
[718] | 1373 | def freq_switch(self, insitu=None): |
---|
| 1374 | """ |
---|
| 1375 | Apply frequency switching to the data. |
---|
| 1376 | Parameters: |
---|
| 1377 | insitu: if False a new scantable is returned. |
---|
| 1378 | Otherwise, the swictching is done in-situ |
---|
| 1379 | The default is taken from .asaprc (False) |
---|
| 1380 | Example: |
---|
| 1381 | none |
---|
| 1382 | """ |
---|
| 1383 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1384 | self._math._setinsitu(insitu) |
---|
[718] | 1385 | varlist = vars() |
---|
[876] | 1386 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 1387 | s._add_history("freq_switch", varlist) |
---|
[876] | 1388 | print_log() |
---|
| 1389 | if insitu: self._assign(s) |
---|
| 1390 | else: return s |
---|
[718] | 1391 | |
---|
[780] | 1392 | def recalc_azel(self): |
---|
| 1393 | """ |
---|
| 1394 | Recalculate the azimuth and elevation for each position. |
---|
| 1395 | Parameters: |
---|
| 1396 | none |
---|
| 1397 | Example: |
---|
| 1398 | """ |
---|
| 1399 | varlist = vars() |
---|
[876] | 1400 | self._recalcazel() |
---|
[780] | 1401 | self._add_history("recalc_azel", varlist) |
---|
| 1402 | print_log() |
---|
| 1403 | return |
---|
| 1404 | |
---|
[513] | 1405 | def __add__(self, other): |
---|
| 1406 | varlist = vars() |
---|
| 1407 | s = None |
---|
| 1408 | if isinstance(other, scantable): |
---|
[876] | 1409 | print "scantable + scantable NYI" |
---|
| 1410 | return |
---|
[513] | 1411 | elif isinstance(other, float): |
---|
[876] | 1412 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 1413 | else: |
---|
[718] | 1414 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1415 | s._add_history("operator +", varlist) |
---|
[718] | 1416 | print_log() |
---|
[513] | 1417 | return s |
---|
| 1418 | |
---|
| 1419 | def __sub__(self, other): |
---|
| 1420 | """ |
---|
| 1421 | implicit on all axes and on Tsys |
---|
| 1422 | """ |
---|
| 1423 | varlist = vars() |
---|
| 1424 | s = None |
---|
| 1425 | if isinstance(other, scantable): |
---|
[876] | 1426 | print "scantable - scantable NYI" |
---|
| 1427 | return |
---|
[513] | 1428 | elif isinstance(other, float): |
---|
[876] | 1429 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 1430 | else: |
---|
[718] | 1431 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1432 | s._add_history("operator -", varlist) |
---|
[718] | 1433 | print_log() |
---|
[513] | 1434 | return s |
---|
[710] | 1435 | |
---|
[513] | 1436 | def __mul__(self, other): |
---|
| 1437 | """ |
---|
| 1438 | implicit on all axes and on Tsys |
---|
| 1439 | """ |
---|
| 1440 | varlist = vars() |
---|
| 1441 | s = None |
---|
| 1442 | if isinstance(other, scantable): |
---|
[876] | 1443 | print "scantable * scantable NYI" |
---|
| 1444 | return |
---|
[513] | 1445 | elif isinstance(other, float): |
---|
[876] | 1446 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 1447 | else: |
---|
[718] | 1448 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1449 | s._add_history("operator *", varlist) |
---|
[718] | 1450 | print_log() |
---|
[513] | 1451 | return s |
---|
| 1452 | |
---|
[710] | 1453 | |
---|
[513] | 1454 | def __div__(self, other): |
---|
| 1455 | """ |
---|
| 1456 | implicit on all axes and on Tsys |
---|
| 1457 | """ |
---|
| 1458 | varlist = vars() |
---|
| 1459 | s = None |
---|
| 1460 | if isinstance(other, scantable): |
---|
[876] | 1461 | print "scantable / scantable NYI" |
---|
| 1462 | return |
---|
[513] | 1463 | elif isinstance(other, float): |
---|
| 1464 | if other == 0.0: |
---|
[718] | 1465 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 1466 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 1467 | else: |
---|
[718] | 1468 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1469 | s._add_history("operator /", varlist) |
---|
[718] | 1470 | print_log() |
---|
[513] | 1471 | return s |
---|
| 1472 | |
---|
[530] | 1473 | def get_fit(self, row=0): |
---|
| 1474 | """ |
---|
| 1475 | Print or return the stored fits for a row in the scantable |
---|
| 1476 | Parameters: |
---|
| 1477 | row: the row which the fit has been applied to. |
---|
| 1478 | """ |
---|
| 1479 | if row > self.nrow(): |
---|
| 1480 | return |
---|
[976] | 1481 | from asap.asapfit import asapfit |
---|
[530] | 1482 | fit = asapfit(self._getfit(row)) |
---|
[718] | 1483 | if rcParams['verbose']: |
---|
[530] | 1484 | print fit |
---|
| 1485 | return |
---|
| 1486 | else: |
---|
| 1487 | return fit.as_dict() |
---|
| 1488 | |
---|
[484] | 1489 | def _add_history(self, funcname, parameters): |
---|
| 1490 | # create date |
---|
| 1491 | sep = "##" |
---|
| 1492 | from datetime import datetime |
---|
| 1493 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 1494 | hist = dstr+sep |
---|
| 1495 | hist += funcname+sep#cdate+sep |
---|
| 1496 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 1497 | for k, v in parameters.iteritems(): |
---|
[484] | 1498 | if type(v) is dict: |
---|
[1118] | 1499 | for k2, v2 in v.iteritems(): |
---|
[484] | 1500 | hist += k2 |
---|
| 1501 | hist += "=" |
---|
[1118] | 1502 | if isinstance(v2, scantable): |
---|
[484] | 1503 | hist += 'scantable' |
---|
| 1504 | elif k2 == 'mask': |
---|
[1118] | 1505 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 1506 | hist += str(self._zip_mask(v2)) |
---|
| 1507 | else: |
---|
| 1508 | hist += str(v2) |
---|
[484] | 1509 | else: |
---|
[513] | 1510 | hist += str(v2) |
---|
[484] | 1511 | else: |
---|
| 1512 | hist += k |
---|
| 1513 | hist += "=" |
---|
[1118] | 1514 | if isinstance(v, scantable): |
---|
[484] | 1515 | hist += 'scantable' |
---|
| 1516 | elif k == 'mask': |
---|
[1118] | 1517 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 1518 | hist += str(self._zip_mask(v)) |
---|
| 1519 | else: |
---|
| 1520 | hist += str(v) |
---|
[484] | 1521 | else: |
---|
| 1522 | hist += str(v) |
---|
| 1523 | hist += sep |
---|
| 1524 | hist = hist[:-2] # remove trailing '##' |
---|
| 1525 | self._addhistory(hist) |
---|
| 1526 | |
---|
[710] | 1527 | |
---|
[484] | 1528 | def _zip_mask(self, mask): |
---|
| 1529 | mask = list(mask) |
---|
| 1530 | i = 0 |
---|
| 1531 | segments = [] |
---|
| 1532 | while mask[i:].count(1): |
---|
| 1533 | i += mask[i:].index(1) |
---|
| 1534 | if mask[i:].count(0): |
---|
| 1535 | j = i + mask[i:].index(0) |
---|
| 1536 | else: |
---|
[710] | 1537 | j = len(mask) |
---|
[1118] | 1538 | segments.append([i, j]) |
---|
[710] | 1539 | i = j |
---|
[484] | 1540 | return segments |
---|
[714] | 1541 | |
---|
[626] | 1542 | def _get_ordinate_label(self): |
---|
| 1543 | fu = "("+self.get_fluxunit()+")" |
---|
| 1544 | import re |
---|
| 1545 | lbl = "Intensity" |
---|
[1118] | 1546 | if re.match(".K.", fu): |
---|
[626] | 1547 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 1548 | elif re.match(".Jy.", fu): |
---|
[626] | 1549 | lbl = "Flux density "+ fu |
---|
| 1550 | return lbl |
---|
[710] | 1551 | |
---|
[876] | 1552 | def _check_ifs(self): |
---|
| 1553 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 1554 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 1555 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 1556 | |
---|
| 1557 | def _fill(self, names, unit, average): |
---|
| 1558 | import os |
---|
| 1559 | from asap._asap import stfiller |
---|
| 1560 | first = True |
---|
| 1561 | fullnames = [] |
---|
| 1562 | for name in names: |
---|
| 1563 | name = os.path.expandvars(name) |
---|
| 1564 | name = os.path.expanduser(name) |
---|
| 1565 | if not os.path.exists(name): |
---|
| 1566 | msg = "File '%s' does not exists" % (name) |
---|
| 1567 | if rcParams['verbose']: |
---|
| 1568 | asaplog.push(msg) |
---|
| 1569 | print asaplog.pop().strip() |
---|
| 1570 | return |
---|
| 1571 | raise IOError(msg) |
---|
| 1572 | fullnames.append(name) |
---|
| 1573 | if average: |
---|
| 1574 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 1575 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 1576 | for name in fullnames: |
---|
[1073] | 1577 | tbl = Scantable(stype) |
---|
| 1578 | r = stfiller(tbl) |
---|
[976] | 1579 | msg = "Importing %s..." % (name) |
---|
[1118] | 1580 | asaplog.push(msg, False) |
---|
[976] | 1581 | print_log() |
---|
[1118] | 1582 | r._open(name, -1, -1) |
---|
[976] | 1583 | r._read() |
---|
[1073] | 1584 | #tbl = r._getdata() |
---|
[976] | 1585 | if average: |
---|
[1118] | 1586 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 1587 | #tbl = tbl2 |
---|
| 1588 | if not first: |
---|
| 1589 | tbl = self._math._merge([self, tbl]) |
---|
| 1590 | #tbl = tbl2 |
---|
| 1591 | Scantable.__init__(self, tbl) |
---|
| 1592 | r._close() |
---|
[1118] | 1593 | del r, tbl |
---|
[976] | 1594 | first = False |
---|
| 1595 | if unit is not None: |
---|
| 1596 | self.set_fluxunit(unit) |
---|
| 1597 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
| 1598 | #self._add_history("scantable", varlist) |
---|
| 1599 | |
---|