| 1 | from asap._asap import Scantable
|
|---|
| 2 | from asap import rcParams
|
|---|
| 3 | from asap import print_log
|
|---|
| 4 | from asap import asaplog
|
|---|
| 5 | from asap import selector
|
|---|
| 6 | from asap import NUM
|
|---|
| 7 | from asap import linecatalog
|
|---|
| 8 |
|
|---|
| 9 | class scantable(Scantable):
|
|---|
| 10 | """
|
|---|
| 11 | The ASAP container for scans
|
|---|
| 12 | """
|
|---|
| 13 |
|
|---|
| 14 | def __init__(self, filename, average=None, unit=None):
|
|---|
| 15 | """
|
|---|
| 16 | Create a scantable from a saved one or make a reference
|
|---|
| 17 | Parameters:
|
|---|
| 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
|
|---|
| 25 | scantable
|
|---|
| 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.
|
|---|
| 29 | Over-rides the default selected by the reader
|
|---|
| 30 | (input rpfits/sdfits/ms) or replaces the value
|
|---|
| 31 | in existing scantables
|
|---|
| 32 | """
|
|---|
| 33 | if average is None:
|
|---|
| 34 | average = rcParams['scantable.autoaverage']
|
|---|
| 35 | #varlist = vars()
|
|---|
| 36 | from asap._asap import stmath
|
|---|
| 37 | self._math = stmath()
|
|---|
| 38 | if isinstance(filename, Scantable):
|
|---|
| 39 | Scantable.__init__(self, filename)
|
|---|
| 40 | else:
|
|---|
| 41 | if isinstance(filename, str):
|
|---|
| 42 | import os.path
|
|---|
| 43 | filename = os.path.expandvars(filename)
|
|---|
| 44 | filename = os.path.expanduser(filename)
|
|---|
| 45 | if not os.path.exists(filename):
|
|---|
| 46 | s = "File '%s' not found." % (filename)
|
|---|
| 47 | if rcParams['verbose']:
|
|---|
| 48 | asaplog.push(s)
|
|---|
| 49 | print asaplog.pop().strip()
|
|---|
| 50 | return
|
|---|
| 51 | raise IOError(s)
|
|---|
| 52 | if os.path.isdir(filename) \
|
|---|
| 53 | and not os.path.exists(filename+'/table.f1'):
|
|---|
| 54 | # crude check if asap table
|
|---|
| 55 | if os.path.exists(filename+'/table.info'):
|
|---|
| 56 | ondisk = rcParams['scantable.storage'] == 'disk'
|
|---|
| 57 | Scantable.__init__(self, filename, ondisk)
|
|---|
| 58 | if unit is not None:
|
|---|
| 59 | self.set_fluxunit(unit)
|
|---|
| 60 | self.set_freqframe(rcParams['scantable.freqframe'])
|
|---|
| 61 | else:
|
|---|
| 62 | msg = "The given file '%s'is not a valid " \
|
|---|
| 63 | "asap table." % (filename)
|
|---|
| 64 | if rcParams['verbose']:
|
|---|
| 65 | print msg
|
|---|
| 66 | return
|
|---|
| 67 | else:
|
|---|
| 68 | raise IOError(msg)
|
|---|
| 69 | else:
|
|---|
| 70 | self._fill([filename], unit, average)
|
|---|
| 71 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \
|
|---|
| 72 | and isinstance(filename[-1], str):
|
|---|
| 73 | self._fill(filename, unit, average)
|
|---|
| 74 | print_log()
|
|---|
| 75 |
|
|---|
| 76 | def save(self, name=None, format=None, overwrite=False):
|
|---|
| 77 | """
|
|---|
| 78 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS,
|
|---|
| 79 | Image FITS or MS2 format.
|
|---|
| 80 | Parameters:
|
|---|
| 81 | name: the name of the outputfile. For format "ASCII"
|
|---|
| 82 | this is the root file name (data in 'name'.txt
|
|---|
| 83 | and header in 'name'_header.txt)
|
|---|
| 84 | format: an optional file format. Default is ASAP.
|
|---|
| 85 | Allowed are - 'ASAP' (save as ASAP [aips++] Table),
|
|---|
| 86 | 'SDFITS' (save as SDFITS file)
|
|---|
| 87 | 'ASCII' (saves as ascii text file)
|
|---|
| 88 | 'MS2' (saves as an aips++
|
|---|
| 89 | MeasurementSet V2)
|
|---|
| 90 | overwrite: If the file should be overwritten if it exists.
|
|---|
| 91 | The default False is to return with warning
|
|---|
| 92 | without writing the output. USE WITH CARE.
|
|---|
| 93 | Example:
|
|---|
| 94 | scan.save('myscan.asap')
|
|---|
| 95 | scan.save('myscan.sdfits', 'SDFITS')
|
|---|
| 96 | """
|
|---|
| 97 | from os import path
|
|---|
| 98 | if format is None: format = rcParams['scantable.save']
|
|---|
| 99 | suffix = '.'+format.lower()
|
|---|
| 100 | if name is None or name == "":
|
|---|
| 101 | name = 'scantable'+suffix
|
|---|
| 102 | msg = "No filename given. Using default name %s..." % name
|
|---|
| 103 | asaplog.push(msg)
|
|---|
| 104 | name = path.expandvars(name)
|
|---|
| 105 | if path.isfile(name) or path.isdir(name):
|
|---|
| 106 | if not overwrite:
|
|---|
| 107 | msg = "File %s exists." % name
|
|---|
| 108 | if rcParams['verbose']:
|
|---|
| 109 | print msg
|
|---|
| 110 | return
|
|---|
| 111 | else:
|
|---|
| 112 | raise IOError(msg)
|
|---|
| 113 | format2 = format.upper()
|
|---|
| 114 | if format2 == 'ASAP':
|
|---|
| 115 | self._save(name)
|
|---|
| 116 | else:
|
|---|
| 117 | from asap._asap import stwriter as stw
|
|---|
| 118 | writer = stw(format2)
|
|---|
| 119 | writer.write(self, name)
|
|---|
| 120 | print_log()
|
|---|
| 121 | return
|
|---|
| 122 |
|
|---|
| 123 | def copy(self):
|
|---|
| 124 | """
|
|---|
| 125 | Return a copy of this scantable.
|
|---|
| 126 | Parameters:
|
|---|
| 127 | none
|
|---|
| 128 | Example:
|
|---|
| 129 | copiedscan = scan.copy()
|
|---|
| 130 | """
|
|---|
| 131 | sd = scantable(Scantable._copy(self))
|
|---|
| 132 | return sd
|
|---|
| 133 |
|
|---|
| 134 | def drop_scan(self, scanid=None):
|
|---|
| 135 | """
|
|---|
| 136 | Return a new scantable where the specified scan number(s) has(have)
|
|---|
| 137 | been dropped.
|
|---|
| 138 | Parameters:
|
|---|
| 139 | scanid: a (list of) scan number(s)
|
|---|
| 140 | """
|
|---|
| 141 | from asap import _is_sequence_or_number as _is_valid
|
|---|
| 142 | from asap import _to_list
|
|---|
| 143 | from asap import unique
|
|---|
| 144 | if not _is_valid(scanid):
|
|---|
| 145 | if rcParams['verbose']:
|
|---|
| 146 | print "Please specify a scanno to drop from the scantable"
|
|---|
| 147 | return
|
|---|
| 148 | else:
|
|---|
| 149 | raise RuntimeError("No scan given")
|
|---|
| 150 | try:
|
|---|
| 151 | scanid = _to_list(scanid)
|
|---|
| 152 | allscans = unique([ self.getscan(i) for i in range(self.nrow())])
|
|---|
| 153 | for sid in scanid: allscans.remove(sid)
|
|---|
| 154 | if len(allscans) == 0:
|
|---|
| 155 | raise ValueError("Can't remove all scans")
|
|---|
| 156 | except ValueError:
|
|---|
| 157 | if rcParams['verbose']:
|
|---|
| 158 | print "Couldn't find any match."
|
|---|
| 159 | return
|
|---|
| 160 | else: raise
|
|---|
| 161 | try:
|
|---|
| 162 | bsel = self.get_selection()
|
|---|
| 163 | sel = selector()
|
|---|
| 164 | sel.set_scans(allscans)
|
|---|
| 165 | self.set_selection(bsel+sel)
|
|---|
| 166 | scopy = self._copy()
|
|---|
| 167 | self.set_selection(bsel)
|
|---|
| 168 | return scantable(scopy)
|
|---|
| 169 | except RuntimeError:
|
|---|
| 170 | if rcParams['verbose']:
|
|---|
| 171 | print "Couldn't find any match."
|
|---|
| 172 | else:
|
|---|
| 173 | raise
|
|---|
| 174 |
|
|---|
| 175 |
|
|---|
| 176 | def get_scan(self, scanid=None):
|
|---|
| 177 | """
|
|---|
| 178 | Return a specific scan (by scanno) or collection of scans (by
|
|---|
| 179 | source name) in a new scantable.
|
|---|
| 180 | Parameters:
|
|---|
| 181 | scanid: a (list of) scanno or a source name, unix-style
|
|---|
| 182 | patterns are accepted for source name matching, e.g.
|
|---|
| 183 | '*_R' gets all 'ref scans
|
|---|
| 184 | Example:
|
|---|
| 185 | # get all scans containing the source '323p459'
|
|---|
| 186 | newscan = scan.get_scan('323p459')
|
|---|
| 187 | # get all 'off' scans
|
|---|
| 188 | refscans = scan.get_scan('*_R')
|
|---|
| 189 | # get a susbset of scans by scanno (as listed in scan.summary())
|
|---|
| 190 | newscan = scan.get_scan([0, 2, 7, 10])
|
|---|
| 191 | """
|
|---|
| 192 | if scanid is None:
|
|---|
| 193 | if rcParams['verbose']:
|
|---|
| 194 | print "Please specify a scan no or name to " \
|
|---|
| 195 | "retrieve from the scantable"
|
|---|
| 196 | return
|
|---|
| 197 | else:
|
|---|
| 198 | raise RuntimeError("No scan given")
|
|---|
| 199 |
|
|---|
| 200 | try:
|
|---|
| 201 | bsel = self.get_selection()
|
|---|
| 202 | sel = selector()
|
|---|
| 203 | if type(scanid) is str:
|
|---|
| 204 | sel.set_name(scanid)
|
|---|
| 205 | self.set_selection(bsel+sel)
|
|---|
| 206 | scopy = self._copy()
|
|---|
| 207 | self.set_selection(bsel)
|
|---|
| 208 | return scantable(scopy)
|
|---|
| 209 | elif type(scanid) is int:
|
|---|
| 210 | sel.set_scans([scanid])
|
|---|
| 211 | self.set_selection(bsel+sel)
|
|---|
| 212 | scopy = self._copy()
|
|---|
| 213 | self.set_selection(bsel)
|
|---|
| 214 | return scantable(scopy)
|
|---|
| 215 | elif type(scanid) is list:
|
|---|
| 216 | sel.set_scans(scanid)
|
|---|
| 217 | self.set_selection(sel)
|
|---|
| 218 | scopy = self._copy()
|
|---|
| 219 | self.set_selection(bsel)
|
|---|
| 220 | return scantable(scopy)
|
|---|
| 221 | else:
|
|---|
| 222 | msg = "Illegal scanid type, use 'int' or 'list' if ints."
|
|---|
| 223 | if rcParams['verbose']:
|
|---|
| 224 | print msg
|
|---|
| 225 | else:
|
|---|
| 226 | raise TypeError(msg)
|
|---|
| 227 | except RuntimeError:
|
|---|
| 228 | if rcParams['verbose']: print "Couldn't find any match."
|
|---|
| 229 | else: raise
|
|---|
| 230 |
|
|---|
| 231 | def __str__(self):
|
|---|
| 232 | return Scantable._summary(self, True)
|
|---|
| 233 |
|
|---|
| 234 | def summary(self, filename=None):
|
|---|
| 235 | """
|
|---|
| 236 | Print a summary of the contents of this scantable.
|
|---|
| 237 | Parameters:
|
|---|
| 238 | filename: the name of a file to write the putput to
|
|---|
| 239 | Default - no file output
|
|---|
| 240 | verbose: print extra info such as the frequency table
|
|---|
| 241 | The default (False) is taken from .asaprc
|
|---|
| 242 | """
|
|---|
| 243 | info = Scantable._summary(self, True)
|
|---|
| 244 | #if verbose is None: verbose = rcParams['scantable.verbosesummary']
|
|---|
| 245 | if filename is not None:
|
|---|
| 246 | if filename is "":
|
|---|
| 247 | filename = 'scantable_summary.txt'
|
|---|
| 248 | from os.path import expandvars, isdir
|
|---|
| 249 | filename = expandvars(filename)
|
|---|
| 250 | if not isdir(filename):
|
|---|
| 251 | data = open(filename, 'w')
|
|---|
| 252 | data.write(info)
|
|---|
| 253 | data.close()
|
|---|
| 254 | else:
|
|---|
| 255 | msg = "Illegal file name '%s'." % (filename)
|
|---|
| 256 | if rcParams['verbose']:
|
|---|
| 257 | print msg
|
|---|
| 258 | else:
|
|---|
| 259 | raise IOError(msg)
|
|---|
| 260 | if rcParams['verbose']:
|
|---|
| 261 | try:
|
|---|
| 262 | from IPython.genutils import page as pager
|
|---|
| 263 | except ImportError:
|
|---|
| 264 | from pydoc import pager
|
|---|
| 265 | pager(info)
|
|---|
| 266 | else:
|
|---|
| 267 | return info
|
|---|
| 268 |
|
|---|
| 269 |
|
|---|
| 270 | def get_selection(self):
|
|---|
| 271 | """
|
|---|
| 272 | Get the selection object currently set on this scantable.
|
|---|
| 273 | Parameters:
|
|---|
| 274 | none
|
|---|
| 275 | Example:
|
|---|
| 276 | sel = scan.get_selection()
|
|---|
| 277 | sel.set_ifs(0) # select IF 0
|
|---|
| 278 | scan.set_selection(sel) # apply modified selection
|
|---|
| 279 | """
|
|---|
| 280 | return selector(self._getselection())
|
|---|
| 281 |
|
|---|
| 282 | def set_selection(self, selection=selector()):
|
|---|
| 283 | """
|
|---|
| 284 | Select a subset of the data. All following operations on this scantable
|
|---|
| 285 | are only applied to thi selection.
|
|---|
| 286 | Parameters:
|
|---|
| 287 | selection: a selector object (default unset the selection)
|
|---|
| 288 | Examples:
|
|---|
| 289 | sel = selector() # create a selection object
|
|---|
| 290 | self.set_scans([0, 3]) # select SCANNO 0 and 3
|
|---|
| 291 | scan.set_selection(sel) # set the selection
|
|---|
| 292 | scan.summary() # will only print summary of scanno 0 an 3
|
|---|
| 293 | scan.set_selection() # unset the selection
|
|---|
| 294 | """
|
|---|
| 295 | self._setselection(selection)
|
|---|
| 296 |
|
|---|
| 297 | def stats(self, stat='stddev', mask=None):
|
|---|
| 298 | """
|
|---|
| 299 | Determine the specified statistic of the current beam/if/pol
|
|---|
| 300 | Takes a 'mask' as an optional parameter to specify which
|
|---|
| 301 | channels should be excluded.
|
|---|
| 302 | Parameters:
|
|---|
| 303 | stat: 'min', 'max', 'sumsq', 'sum', 'mean'
|
|---|
| 304 | 'var', 'stddev', 'avdev', 'rms', 'median'
|
|---|
| 305 | mask: an optional mask specifying where the statistic
|
|---|
| 306 | should be determined.
|
|---|
| 307 | Example:
|
|---|
| 308 | scan.set_unit('channel')
|
|---|
| 309 | msk = scan.create_mask([100, 200], [500, 600])
|
|---|
| 310 | scan.stats(stat='mean', mask=m)
|
|---|
| 311 | """
|
|---|
| 312 | if mask == None:
|
|---|
| 313 | mask = []
|
|---|
| 314 | axes = ['Beam', 'IF', 'Pol', 'Time']
|
|---|
| 315 | if not self._check_ifs():
|
|---|
| 316 | raise ValueError("Cannot apply mask as the IFs have different "
|
|---|
| 317 | "number of channels. Please use setselection() "
|
|---|
| 318 | "to select individual IFs")
|
|---|
| 319 |
|
|---|
| 320 | statvals = self._math._stats(self, mask, stat)
|
|---|
| 321 | out = ''
|
|---|
| 322 | axes = []
|
|---|
| 323 | for i in range(self.nrow()):
|
|---|
| 324 | axis = []
|
|---|
| 325 | axis.append(self.getscan(i))
|
|---|
| 326 | axis.append(self.getbeam(i))
|
|---|
| 327 | axis.append(self.getif(i))
|
|---|
| 328 | axis.append(self.getpol(i))
|
|---|
| 329 | axis.append(self.getcycle(i))
|
|---|
| 330 | axes.append(axis)
|
|---|
| 331 | tm = self._gettime(i)
|
|---|
| 332 | src = self._getsourcename(i)
|
|---|
| 333 | out += 'Scan[%d] (%s) ' % (axis[0], src)
|
|---|
| 334 | out += 'Time[%s]:\n' % (tm)
|
|---|
| 335 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
|
|---|
| 336 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
|
|---|
| 337 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
|
|---|
| 338 | out += '= %3.3f\n' % (statvals[i])
|
|---|
| 339 | out += "--------------------------------------------------\n"
|
|---|
| 340 |
|
|---|
| 341 | if rcParams['verbose']:
|
|---|
| 342 | print "--------------------------------------------------"
|
|---|
| 343 | print " ", stat
|
|---|
| 344 | print "--------------------------------------------------"
|
|---|
| 345 | print out
|
|---|
| 346 | retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'],
|
|---|
| 347 | 'axes' : axes,
|
|---|
| 348 | 'data': statvals}
|
|---|
| 349 | return retval
|
|---|
| 350 |
|
|---|
| 351 | def stddev(self, mask=None):
|
|---|
| 352 | """
|
|---|
| 353 | Determine the standard deviation of the current beam/if/pol
|
|---|
| 354 | Takes a 'mask' as an optional parameter to specify which
|
|---|
| 355 | channels should be excluded.
|
|---|
| 356 | Parameters:
|
|---|
| 357 | mask: an optional mask specifying where the standard
|
|---|
| 358 | deviation should be determined.
|
|---|
| 359 |
|
|---|
| 360 | Example:
|
|---|
| 361 | scan.set_unit('channel')
|
|---|
| 362 | msk = scan.create_mask([100, 200], [500, 600])
|
|---|
| 363 | scan.stddev(mask=m)
|
|---|
| 364 | """
|
|---|
| 365 | return self.stats(stat='stddev', mask=mask);
|
|---|
| 366 |
|
|---|
| 367 |
|
|---|
| 368 | def column_names(self):
|
|---|
| 369 | """
|
|---|
| 370 | Return a list of column names, which can be used for selection.
|
|---|
| 371 | """
|
|---|
| 372 | return list(Scantable.column_names(self))
|
|---|
| 373 |
|
|---|
| 374 | def get_tsys(self):
|
|---|
| 375 | """
|
|---|
| 376 | Return the System temperatures.
|
|---|
| 377 | Parameters:
|
|---|
| 378 |
|
|---|
| 379 | Returns:
|
|---|
| 380 | a list of Tsys values for the current selection
|
|---|
| 381 | """
|
|---|
| 382 |
|
|---|
| 383 | return self._row_callback(self._gettsys, "Tsys")
|
|---|
| 384 |
|
|---|
| 385 | def _row_callback(self, callback, label):
|
|---|
| 386 | axes = []
|
|---|
| 387 | axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno']
|
|---|
| 388 | out = ""
|
|---|
| 389 | outvec = []
|
|---|
| 390 | for i in range(self.nrow()):
|
|---|
| 391 | axis = []
|
|---|
| 392 | axis.append(self.getscan(i))
|
|---|
| 393 | axis.append(self.getbeam(i))
|
|---|
| 394 | axis.append(self.getif(i))
|
|---|
| 395 | axis.append(self.getpol(i))
|
|---|
| 396 | axis.append(self.getcycle(i))
|
|---|
| 397 | axes.append(axis)
|
|---|
| 398 | tm = self._gettime(i)
|
|---|
| 399 | src = self._getsourcename(i)
|
|---|
| 400 | out += 'Scan[%d] (%s) ' % (axis[0], src)
|
|---|
| 401 | out += 'Time[%s]:\n' % (tm)
|
|---|
| 402 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
|
|---|
| 403 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
|
|---|
| 404 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
|
|---|
| 405 | outvec.append(callback(i))
|
|---|
| 406 | out += '= %3.3f\n' % (outvec[i])
|
|---|
| 407 | out += "--------------------------------------------------\n"
|
|---|
| 408 | if rcParams['verbose']:
|
|---|
| 409 | print "--------------------------------------------------"
|
|---|
| 410 | print " %s" % (label)
|
|---|
| 411 | print "--------------------------------------------------"
|
|---|
| 412 | print out
|
|---|
| 413 | # disabled because the vector seems more useful
|
|---|
| 414 | #retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
|
|---|
| 415 | return outvec
|
|---|
| 416 |
|
|---|
| 417 | def _get_column(self, callback, row=-1):
|
|---|
| 418 | """
|
|---|
| 419 | """
|
|---|
| 420 | if row == -1:
|
|---|
| 421 | return [callback(i) for i in range(self.nrow())]
|
|---|
| 422 | else:
|
|---|
| 423 | if 0 <= row < self.nrow():
|
|---|
| 424 | return callback(row)
|
|---|
| 425 |
|
|---|
| 426 |
|
|---|
| 427 | def get_time(self, row=-1):
|
|---|
| 428 | """
|
|---|
| 429 | Get a list of time stamps for the observations.
|
|---|
| 430 | Return a string for each integration in the scantable.
|
|---|
| 431 | Parameters:
|
|---|
| 432 | row: row no of integration. Default -1 return all rows
|
|---|
| 433 | Example:
|
|---|
| 434 | none
|
|---|
| 435 | """
|
|---|
| 436 | from time import strptime
|
|---|
| 437 | from datetime import datetime
|
|---|
| 438 | times = self._get_column(self._gettime, row)
|
|---|
| 439 | format = "%Y/%m/%d/%H:%M:%S"
|
|---|
| 440 | if isinstance(times, list):
|
|---|
| 441 | return [datetime(*strptime(i, format)[:6]) for i in times]
|
|---|
| 442 | else:
|
|---|
| 443 | return datetime(*strptime(times, format)[:6])
|
|---|
| 444 |
|
|---|
| 445 | def get_sourcename(self, row=-1):
|
|---|
| 446 | """
|
|---|
| 447 | Get a list source names for the observations.
|
|---|
| 448 | Return a string for each integration in the scantable.
|
|---|
| 449 | Parameters:
|
|---|
| 450 | row: row no of integration. Default -1 return all rows
|
|---|
| 451 | Example:
|
|---|
| 452 | none
|
|---|
| 453 | """
|
|---|
| 454 | return self._get_column(self._getsourcename, row)
|
|---|
| 455 |
|
|---|
| 456 | def get_elevation(self, row=-1):
|
|---|
| 457 | """
|
|---|
| 458 | Get a list of elevations for the observations.
|
|---|
| 459 | Return a float for each integration in the scantable.
|
|---|
| 460 | Parameters:
|
|---|
| 461 | row: row no of integration. Default -1 return all rows
|
|---|
| 462 | Example:
|
|---|
| 463 | none
|
|---|
| 464 | """
|
|---|
| 465 | return self._get_column(self._getelevation, row)
|
|---|
| 466 |
|
|---|
| 467 | def get_azimuth(self, row=-1):
|
|---|
| 468 | """
|
|---|
| 469 | Get a list of azimuths for the observations.
|
|---|
| 470 | Return a float for each integration in the scantable.
|
|---|
| 471 | Parameters:
|
|---|
| 472 | row: row no of integration. Default -1 return all rows
|
|---|
| 473 | Example:
|
|---|
| 474 | none
|
|---|
| 475 | """
|
|---|
| 476 | return self._get_column(self._getazimuth, row)
|
|---|
| 477 |
|
|---|
| 478 | def get_parangle(self, row=-1):
|
|---|
| 479 | """
|
|---|
| 480 | Get a list of parallactic angles for the observations.
|
|---|
| 481 | Return a float for each integration in the scantable.
|
|---|
| 482 | Parameters:
|
|---|
| 483 | row: row no of integration. Default -1 return all rows
|
|---|
| 484 | Example:
|
|---|
| 485 | none
|
|---|
| 486 | """
|
|---|
| 487 | return self._get_column(self._getparangle, row)
|
|---|
| 488 |
|
|---|
| 489 | def get_direction(self, row=-1):
|
|---|
| 490 | """
|
|---|
| 491 | Get a list of Positions on the sky (direction) for the observations.
|
|---|
| 492 | Return a float for each integration in the scantable.
|
|---|
| 493 | Parameters:
|
|---|
| 494 | row: row no of integration. Default -1 return all rows
|
|---|
| 495 | Example:
|
|---|
| 496 | none
|
|---|
| 497 | """
|
|---|
| 498 | return self._get_column(self._getdirection, row)
|
|---|
| 499 |
|
|---|
| 500 | def set_unit(self, unit='channel'):
|
|---|
| 501 | """
|
|---|
| 502 | Set the unit for all following operations on this scantable
|
|---|
| 503 | Parameters:
|
|---|
| 504 | unit: optional unit, default is 'channel'
|
|---|
| 505 | one of '*Hz', 'km/s', 'channel', ''
|
|---|
| 506 | """
|
|---|
| 507 | varlist = vars()
|
|---|
| 508 | if unit in ['', 'pixel', 'channel']:
|
|---|
| 509 | unit = ''
|
|---|
| 510 | inf = list(self._getcoordinfo())
|
|---|
| 511 | inf[0] = unit
|
|---|
| 512 | self._setcoordinfo(inf)
|
|---|
| 513 | self._add_history("set_unit", varlist)
|
|---|
| 514 |
|
|---|
| 515 | def set_instrument(self, instr):
|
|---|
| 516 | """
|
|---|
| 517 | Set the instrument for subsequent processing
|
|---|
| 518 | Parameters:
|
|---|
| 519 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
|
|---|
| 520 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
|
|---|
| 521 | """
|
|---|
| 522 | self._setInstrument(instr)
|
|---|
| 523 | self._add_history("set_instument", vars())
|
|---|
| 524 | print_log()
|
|---|
| 525 |
|
|---|
| 526 | def set_feedtype(self, feedtype):
|
|---|
| 527 | """
|
|---|
| 528 | Overwrite the feed type, which might not be set correctly.
|
|---|
| 529 | Parameters:
|
|---|
| 530 | feedtype: 'linear' or 'circular'
|
|---|
| 531 | """
|
|---|
| 532 | self._setfeedtype(feedtype)
|
|---|
| 533 | self._add_history("set_feedtype", vars())
|
|---|
| 534 | print_log()
|
|---|
| 535 |
|
|---|
| 536 | def set_doppler(self, doppler='RADIO'):
|
|---|
| 537 | """
|
|---|
| 538 | Set the doppler for all following operations on this scantable.
|
|---|
| 539 | Parameters:
|
|---|
| 540 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
|
|---|
| 541 | """
|
|---|
| 542 | varlist = vars()
|
|---|
| 543 | inf = list(self._getcoordinfo())
|
|---|
| 544 | inf[2] = doppler
|
|---|
| 545 | self._setcoordinfo(inf)
|
|---|
| 546 | self._add_history("set_doppler", vars())
|
|---|
| 547 | print_log()
|
|---|
| 548 |
|
|---|
| 549 | def set_freqframe(self, frame=None):
|
|---|
| 550 | """
|
|---|
| 551 | Set the frame type of the Spectral Axis.
|
|---|
| 552 | Parameters:
|
|---|
| 553 | frame: an optional frame type, default 'LSRK'. Valid frames are:
|
|---|
| 554 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY',
|
|---|
| 555 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'
|
|---|
| 556 | Examples:
|
|---|
| 557 | scan.set_freqframe('BARY')
|
|---|
| 558 | """
|
|---|
| 559 | if frame is None: frame = rcParams['scantable.freqframe']
|
|---|
| 560 | varlist = vars()
|
|---|
| 561 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
|
|---|
| 562 | 'GEO', 'GALACTO', 'LGROUP', 'CMB']
|
|---|
| 563 |
|
|---|
| 564 | if frame in valid:
|
|---|
| 565 | inf = list(self._getcoordinfo())
|
|---|
| 566 | inf[1] = frame
|
|---|
| 567 | self._setcoordinfo(inf)
|
|---|
| 568 | self._add_history("set_freqframe", varlist)
|
|---|
| 569 | else:
|
|---|
| 570 | msg = "Please specify a valid freq type. Valid types are:\n", valid
|
|---|
| 571 | if rcParams['verbose']:
|
|---|
| 572 | print msg
|
|---|
| 573 | else:
|
|---|
| 574 | raise TypeError(msg)
|
|---|
| 575 | print_log()
|
|---|
| 576 |
|
|---|
| 577 | def set_dirframe(self, frame=""):
|
|---|
| 578 | """
|
|---|
| 579 | Set the frame type of the Direction on the sky.
|
|---|
| 580 | Parameters:
|
|---|
| 581 | frame: an optional frame type, default ''. Valid frames are:
|
|---|
| 582 | 'J2000', 'B1950', 'GALACTIC'
|
|---|
| 583 | Examples:
|
|---|
| 584 | scan.set_dirframe('GALACTIC')
|
|---|
| 585 | """
|
|---|
| 586 | varlist = vars()
|
|---|
| 587 | try:
|
|---|
| 588 | Scantable.set_dirframe(self, frame)
|
|---|
| 589 | except RuntimeError, msg:
|
|---|
| 590 | if rcParams['verbose']:
|
|---|
| 591 | print msg
|
|---|
| 592 | else:
|
|---|
| 593 | raise
|
|---|
| 594 | self._add_history("set_dirframe", varlist)
|
|---|
| 595 |
|
|---|
| 596 | def get_unit(self):
|
|---|
| 597 | """
|
|---|
| 598 | Get the default unit set in this scantable
|
|---|
| 599 | Parameters:
|
|---|
| 600 | Returns:
|
|---|
| 601 | A unit string
|
|---|
| 602 | """
|
|---|
| 603 | inf = self._getcoordinfo()
|
|---|
| 604 | unit = inf[0]
|
|---|
| 605 | if unit == '': unit = 'channel'
|
|---|
| 606 | return unit
|
|---|
| 607 |
|
|---|
| 608 | def get_abcissa(self, rowno=0):
|
|---|
| 609 | """
|
|---|
| 610 | Get the abcissa in the current coordinate setup for the currently
|
|---|
| 611 | selected Beam/IF/Pol
|
|---|
| 612 | Parameters:
|
|---|
| 613 | rowno: an optional row number in the scantable. Default is the
|
|---|
| 614 | first row, i.e. rowno=0
|
|---|
| 615 | Returns:
|
|---|
| 616 | The abcissa values and it's format string (as a dictionary)
|
|---|
| 617 | """
|
|---|
| 618 | abc = self._getabcissa(rowno)
|
|---|
| 619 | lbl = self._getabcissalabel(rowno)
|
|---|
| 620 | print_log()
|
|---|
| 621 | return abc, lbl
|
|---|
| 622 |
|
|---|
| 623 | def flag(self, mask=None):
|
|---|
| 624 | """
|
|---|
| 625 | Flag the selected data using an optional channel mask.
|
|---|
| 626 | Parameters:
|
|---|
| 627 | mask: an optional channel mask, created with create_mask. Default
|
|---|
| 628 | (no mask) is all channels.
|
|---|
| 629 | """
|
|---|
| 630 | varlist = vars()
|
|---|
| 631 | if mask is None:
|
|---|
| 632 | mask = []
|
|---|
| 633 | try:
|
|---|
| 634 | self._flag(mask)
|
|---|
| 635 | except RuntimeError, msg:
|
|---|
| 636 | if rcParams['verbose']:
|
|---|
| 637 | print msg
|
|---|
| 638 | return
|
|---|
| 639 | else: raise
|
|---|
| 640 | self._add_history("flag", varlist)
|
|---|
| 641 |
|
|---|
| 642 | def lag_flag(self, frequency, unit="GHz", width=0.0, insitu=None):
|
|---|
| 643 | """
|
|---|
| 644 | Flag the data in 'lag' space by providing a frequency to remove.
|
|---|
| 645 | Flagged data in the scantable gets set to 0.0 before the fft.
|
|---|
| 646 | No taper is applied.
|
|---|
| 647 | Parameters:
|
|---|
| 648 | frequency: the frequency to remove
|
|---|
| 649 | unit: the frequency unit ()default "GHz")
|
|---|
| 650 | width: the width of the frequency to remove
|
|---|
| 651 | """
|
|---|
| 652 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 653 | self._math._setinsitu(insitu)
|
|---|
| 654 | varlist = vars()
|
|---|
| 655 | base = { "GHz": 100000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. }
|
|---|
| 656 | if not base.has_key(unit):
|
|---|
| 657 | raise ValueError("%s is not a valid unit." % unit)
|
|---|
| 658 | try:
|
|---|
| 659 | s = scantable(self._math._lag_flag(self, frequency*base[unit],
|
|---|
| 660 | width*base[unit]))
|
|---|
| 661 | except RuntimeError, msg:
|
|---|
| 662 | if rcParams['verbose']:
|
|---|
| 663 | print msg
|
|---|
| 664 | return
|
|---|
| 665 | else: raise
|
|---|
| 666 | s._add_history("lag_flag", varlist)
|
|---|
| 667 | print_log()
|
|---|
| 668 | if insitu:
|
|---|
| 669 | self._assign(s)
|
|---|
| 670 | else:
|
|---|
| 671 | return s
|
|---|
| 672 |
|
|---|
| 673 |
|
|---|
| 674 | def create_mask(self, *args, **kwargs):
|
|---|
| 675 | """
|
|---|
| 676 | Compute and return a mask based on [min, max] windows.
|
|---|
| 677 | The specified windows are to be INCLUDED, when the mask is
|
|---|
| 678 | applied.
|
|---|
| 679 | Parameters:
|
|---|
| 680 | [min, max], [min2, max2], ...
|
|---|
| 681 | Pairs of start/end points (inclusive)specifying the regions
|
|---|
| 682 | to be masked
|
|---|
| 683 | invert: optional argument. If specified as True,
|
|---|
| 684 | return an inverted mask, i.e. the regions
|
|---|
| 685 | specified are EXCLUDED
|
|---|
| 686 | row: create the mask using the specified row for
|
|---|
| 687 | unit conversions, default is row=0
|
|---|
| 688 | only necessary if frequency varies over rows.
|
|---|
| 689 | Example:
|
|---|
| 690 | scan.set_unit('channel')
|
|---|
| 691 | a)
|
|---|
| 692 | msk = scan.create_mask([400, 500], [800, 900])
|
|---|
| 693 | # masks everything outside 400 and 500
|
|---|
| 694 | # and 800 and 900 in the unit 'channel'
|
|---|
| 695 |
|
|---|
| 696 | b)
|
|---|
| 697 | msk = scan.create_mask([400, 500], [800, 900], invert=True)
|
|---|
| 698 | # masks the regions between 400 and 500
|
|---|
| 699 | # and 800 and 900 in the unit 'channel'
|
|---|
| 700 | c)
|
|---|
| 701 | mask only channel 400
|
|---|
| 702 | msk = scan.create_mask([400, 400])
|
|---|
| 703 | """
|
|---|
| 704 | row = 0
|
|---|
| 705 | if kwargs.has_key("row"):
|
|---|
| 706 | row = kwargs.get("row")
|
|---|
| 707 | data = self._getabcissa(row)
|
|---|
| 708 | u = self._getcoordinfo()[0]
|
|---|
| 709 | if rcParams['verbose']:
|
|---|
| 710 | if u == "": u = "channel"
|
|---|
| 711 | msg = "The current mask window unit is %s" % u
|
|---|
| 712 | i = self._check_ifs()
|
|---|
| 713 | if not i:
|
|---|
| 714 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
|---|
| 715 | asaplog.push(msg)
|
|---|
| 716 | n = self.nchan()
|
|---|
| 717 | msk = NUM.zeros(n)
|
|---|
| 718 | # test if args is a 'list' or a 'normal *args - UGLY!!!
|
|---|
| 719 |
|
|---|
| 720 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
|
|---|
| 721 | and args or args[0]
|
|---|
| 722 | for window in ws:
|
|---|
| 723 | if (len(window) != 2 or window[0] > window[1] ):
|
|---|
| 724 | raise TypeError("A window needs to be defined as [min, max]")
|
|---|
| 725 | for i in range(n):
|
|---|
| 726 | if data[i] >= window[0] and data[i] <= window[1]:
|
|---|
| 727 | msk[i] = 1
|
|---|
| 728 | if kwargs.has_key('invert'):
|
|---|
| 729 | if kwargs.get('invert'):
|
|---|
| 730 | msk = NUM.logical_not(msk)
|
|---|
| 731 | print_log()
|
|---|
| 732 | return msk
|
|---|
| 733 |
|
|---|
| 734 | def get_restfreqs(self):
|
|---|
| 735 | """
|
|---|
| 736 | Get the restfrequency(s) stored in this scantable.
|
|---|
| 737 | The return value(s) are always of unit 'Hz'
|
|---|
| 738 | Parameters:
|
|---|
| 739 | none
|
|---|
| 740 | Returns:
|
|---|
| 741 | a list of doubles
|
|---|
| 742 | """
|
|---|
| 743 | return list(self._getrestfreqs())
|
|---|
| 744 |
|
|---|
| 745 |
|
|---|
| 746 | def set_restfreqs(self, freqs=None, unit='Hz'):
|
|---|
| 747 | """
|
|---|
| 748 | Set or replace the restfrequency specified and
|
|---|
| 749 | If the 'freqs' argument holds a scalar,
|
|---|
| 750 | then that rest frequency will be applied to all the selected
|
|---|
| 751 | data. If the 'freqs' argument holds
|
|---|
| 752 | a vector, then it MUST be of equal or smaller length than
|
|---|
| 753 | the number of IFs (and the available restfrequencies will be
|
|---|
| 754 | replaced by this vector). In this case, *all* data have
|
|---|
| 755 | the restfrequency set per IF according
|
|---|
| 756 | to the corresponding value you give in the 'freqs' vector.
|
|---|
| 757 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
|
|---|
| 758 | IF 1 gets restfreq 2e9.
|
|---|
| 759 | You can also specify the frequencies via a linecatalog/
|
|---|
| 760 |
|
|---|
| 761 | Parameters:
|
|---|
| 762 | freqs: list of rest frequency values or string idenitfiers
|
|---|
| 763 | unit: unit for rest frequency (default 'Hz')
|
|---|
| 764 |
|
|---|
| 765 | Example:
|
|---|
| 766 | # set the given restfrequency for the whole table
|
|---|
| 767 | scan.set_restfreqs(freqs=1.4e9)
|
|---|
| 768 | # If thee number of IFs in the data is >= 2 the IF0 gets the first
|
|---|
| 769 | # value IF1 the second...
|
|---|
| 770 | scan.set_restfreqs(freqs=[1.4e9, 1.67e9])
|
|---|
| 771 | #set the given restfrequency for the whole table (by name)
|
|---|
| 772 | scan.set_restfreqs(freqs="OH1667")
|
|---|
| 773 |
|
|---|
| 774 | Note:
|
|---|
| 775 | To do more sophisticate Restfrequency setting, e.g. on a
|
|---|
| 776 | source and IF basis, use scantable.set_selection() before using
|
|---|
| 777 | this function.
|
|---|
| 778 | # provide your scantable is call scan
|
|---|
| 779 | selection = selector()
|
|---|
| 780 | selection.set_name("ORION*")
|
|---|
| 781 | selection.set_ifs([1])
|
|---|
| 782 | scan.set_selection(selection)
|
|---|
| 783 | scan.set_restfreqs(freqs=86.6e9)
|
|---|
| 784 |
|
|---|
| 785 | """
|
|---|
| 786 | varlist = vars()
|
|---|
| 787 | from asap import linecatalog
|
|---|
| 788 | # simple value
|
|---|
| 789 | if isinstance(freqs, int) or isinstance(freqs, float):
|
|---|
| 790 | self._setrestfreqs(freqs, "",unit)
|
|---|
| 791 | # list of values
|
|---|
| 792 | elif isinstance(freqs, list) or isinstance(freqs, tuple):
|
|---|
| 793 | # list values are scalars
|
|---|
| 794 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
|
|---|
| 795 | sel = selector()
|
|---|
| 796 | savesel = self._getselection()
|
|---|
| 797 | for i in xrange(len(freqs)):
|
|---|
| 798 | sel.set_ifs([i])
|
|---|
| 799 | self._setselection(sel)
|
|---|
| 800 | self._setrestfreqs(freqs[i], "",unit)
|
|---|
| 801 | self._setselection(savesel)
|
|---|
| 802 | # list values are tuples, (value, name)
|
|---|
| 803 | elif isinstance(freqs[-1], dict):
|
|---|
| 804 | sel = selector()
|
|---|
| 805 | savesel = self._getselection()
|
|---|
| 806 | for i in xrange(len(freqs)):
|
|---|
| 807 | sel.set_ifs([i])
|
|---|
| 808 | self._setrestfreqs(freqs[i]["value"],
|
|---|
| 809 | freqs[i]["name"], "MHz")
|
|---|
| 810 | self._setselection(sel)
|
|---|
| 811 | self._setselection(savesel)
|
|---|
| 812 | # freqs are to be taken from a linecatalog
|
|---|
| 813 | elif isinstance(freqs, linecatalog):
|
|---|
| 814 | sel = selector()
|
|---|
| 815 | savesel = self._getselection()
|
|---|
| 816 | for i in xrange(freqs.nrow()):
|
|---|
| 817 | sel.set_ifs([i])
|
|---|
| 818 | self._setselection(sel)
|
|---|
| 819 | self._setrestfreqs(freqs.get_frequency(i),
|
|---|
| 820 | freqs.get_name(i), "MHz")
|
|---|
| 821 | # ensure that we are not iterating past nIF
|
|---|
| 822 | if i == self.nif()-1: break
|
|---|
| 823 | self._setselection(savesel)
|
|---|
| 824 | else:
|
|---|
| 825 | return
|
|---|
| 826 | self._add_history("set_restfreqs", varlist)
|
|---|
| 827 |
|
|---|
| 828 |
|
|---|
| 829 |
|
|---|
| 830 | def history(self):
|
|---|
| 831 | hist = list(self._gethistory())
|
|---|
| 832 | out = "-"*80
|
|---|
| 833 | for h in hist:
|
|---|
| 834 | if h.startswith("---"):
|
|---|
| 835 | out += "\n"+h
|
|---|
| 836 | else:
|
|---|
| 837 | items = h.split("##")
|
|---|
| 838 | date = items[0]
|
|---|
| 839 | func = items[1]
|
|---|
| 840 | items = items[2:]
|
|---|
| 841 | out += "\n"+date+"\n"
|
|---|
| 842 | out += "Function: %s\n Parameters:" % (func)
|
|---|
| 843 | for i in items:
|
|---|
| 844 | s = i.split("=")
|
|---|
| 845 | out += "\n %s = %s" % (s[0], s[1])
|
|---|
| 846 | out += "\n"+"-"*80
|
|---|
| 847 | try:
|
|---|
| 848 | from IPython.genutils import page as pager
|
|---|
| 849 | except ImportError:
|
|---|
| 850 | from pydoc import pager
|
|---|
| 851 | pager(out)
|
|---|
| 852 | return
|
|---|
| 853 |
|
|---|
| 854 | #
|
|---|
| 855 | # Maths business
|
|---|
| 856 | #
|
|---|
| 857 |
|
|---|
| 858 | def average_time(self, mask=None, scanav=False, weight='tint', align=False):
|
|---|
| 859 | """
|
|---|
| 860 | Return the (time) weighted average of a scan.
|
|---|
| 861 | Note:
|
|---|
| 862 | in channels only - align if necessary
|
|---|
| 863 | Parameters:
|
|---|
| 864 | mask: an optional mask (only used for 'var' and 'tsys'
|
|---|
| 865 | weighting)
|
|---|
| 866 | scanav: True averages each scan separately
|
|---|
| 867 | False (default) averages all scans together,
|
|---|
| 868 | weight: Weighting scheme.
|
|---|
| 869 | 'none' (mean no weight)
|
|---|
| 870 | 'var' (1/var(spec) weighted)
|
|---|
| 871 | 'tsys' (1/Tsys**2 weighted)
|
|---|
| 872 | 'tint' (integration time weighted)
|
|---|
| 873 | 'tintsys' (Tint/Tsys**2)
|
|---|
| 874 | 'median' ( median averaging)
|
|---|
| 875 | The default is 'tint'
|
|---|
| 876 | align: align the spectra in velocity before averaging. It takes
|
|---|
| 877 | the time of the first spectrum as reference time.
|
|---|
| 878 | Example:
|
|---|
| 879 | # time average the scantable without using a mask
|
|---|
| 880 | newscan = scan.average_time()
|
|---|
| 881 | """
|
|---|
| 882 | varlist = vars()
|
|---|
| 883 | if weight is None: weight = 'TINT'
|
|---|
| 884 | if mask is None: mask = ()
|
|---|
| 885 | if scanav: scanav = "SCAN"
|
|---|
| 886 | else: scanav = "NONE"
|
|---|
| 887 | scan = (self, )
|
|---|
| 888 | try:
|
|---|
| 889 | if align:
|
|---|
| 890 | scan = (self.freq_align(insitu=False), )
|
|---|
| 891 | s = None
|
|---|
| 892 | if weight.upper() == 'MEDIAN':
|
|---|
| 893 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
|
|---|
| 894 | scanav))
|
|---|
| 895 | else:
|
|---|
| 896 | s = scantable(self._math._average(scan, mask, weight.upper(),
|
|---|
| 897 | scanav))
|
|---|
| 898 | except RuntimeError, msg:
|
|---|
| 899 | if rcParams['verbose']:
|
|---|
| 900 | print msg
|
|---|
| 901 | return
|
|---|
| 902 | else: raise
|
|---|
| 903 | s._add_history("average_time", varlist)
|
|---|
| 904 | print_log()
|
|---|
| 905 | return s
|
|---|
| 906 |
|
|---|
| 907 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
|
|---|
| 908 | """
|
|---|
| 909 | Return a scan where all spectra are converted to either
|
|---|
| 910 | Jansky or Kelvin depending upon the flux units of the scan table.
|
|---|
| 911 | By default the function tries to look the values up internally.
|
|---|
| 912 | If it can't find them (or if you want to over-ride), you must
|
|---|
| 913 | specify EITHER jyperk OR eta (and D which it will try to look up
|
|---|
| 914 | also if you don't set it). jyperk takes precedence if you set both.
|
|---|
| 915 | Parameters:
|
|---|
| 916 | jyperk: the Jy / K conversion factor
|
|---|
| 917 | eta: the aperture efficiency
|
|---|
| 918 | d: the geomtric diameter (metres)
|
|---|
| 919 | insitu: if False a new scantable is returned.
|
|---|
| 920 | Otherwise, the scaling is done in-situ
|
|---|
| 921 | The default is taken from .asaprc (False)
|
|---|
| 922 | allaxes: if True apply to all spectra. Otherwise
|
|---|
| 923 | apply only to the selected (beam/pol/if)spectra only
|
|---|
| 924 | The default is taken from .asaprc (True if none)
|
|---|
| 925 | """
|
|---|
| 926 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 927 | self._math._setinsitu(insitu)
|
|---|
| 928 | varlist = vars()
|
|---|
| 929 | if jyperk is None: jyperk = -1.0
|
|---|
| 930 | if d is None: d = -1.0
|
|---|
| 931 | if eta is None: eta = -1.0
|
|---|
| 932 | s = scantable(self._math._convertflux(self, d, eta, jyperk))
|
|---|
| 933 | s._add_history("convert_flux", varlist)
|
|---|
| 934 | print_log()
|
|---|
| 935 | if insitu: self._assign(s)
|
|---|
| 936 | else: return s
|
|---|
| 937 |
|
|---|
| 938 | def gain_el(self, poly=None, filename="", method="linear", insitu=None):
|
|---|
| 939 | """
|
|---|
| 940 | Return a scan after applying a gain-elevation correction.
|
|---|
| 941 | The correction can be made via either a polynomial or a
|
|---|
| 942 | table-based interpolation (and extrapolation if necessary).
|
|---|
| 943 | You specify polynomial coefficients, an ascii table or neither.
|
|---|
| 944 | If you specify neither, then a polynomial correction will be made
|
|---|
| 945 | with built in coefficients known for certain telescopes (an error
|
|---|
| 946 | will occur if the instrument is not known).
|
|---|
| 947 | The data and Tsys are *divided* by the scaling factors.
|
|---|
| 948 | Parameters:
|
|---|
| 949 | poly: Polynomial coefficients (default None) to compute a
|
|---|
| 950 | gain-elevation correction as a function of
|
|---|
| 951 | elevation (in degrees).
|
|---|
| 952 | filename: The name of an ascii file holding correction factors.
|
|---|
| 953 | The first row of the ascii file must give the column
|
|---|
| 954 | names and these MUST include columns
|
|---|
| 955 | "ELEVATION" (degrees) and "FACTOR" (multiply data
|
|---|
| 956 | by this) somewhere.
|
|---|
| 957 | The second row must give the data type of the
|
|---|
| 958 | column. Use 'R' for Real and 'I' for Integer.
|
|---|
| 959 | An example file would be
|
|---|
| 960 | (actual factors are arbitrary) :
|
|---|
| 961 |
|
|---|
| 962 | TIME ELEVATION FACTOR
|
|---|
| 963 | R R R
|
|---|
| 964 | 0.1 0 0.8
|
|---|
| 965 | 0.2 20 0.85
|
|---|
| 966 | 0.3 40 0.9
|
|---|
| 967 | 0.4 60 0.85
|
|---|
| 968 | 0.5 80 0.8
|
|---|
| 969 | 0.6 90 0.75
|
|---|
| 970 | method: Interpolation method when correcting from a table.
|
|---|
| 971 | Values are "nearest", "linear" (default), "cubic"
|
|---|
| 972 | and "spline"
|
|---|
| 973 | insitu: if False a new scantable is returned.
|
|---|
| 974 | Otherwise, the scaling is done in-situ
|
|---|
| 975 | The default is taken from .asaprc (False)
|
|---|
| 976 | """
|
|---|
| 977 |
|
|---|
| 978 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 979 | self._math._setinsitu(insitu)
|
|---|
| 980 | varlist = vars()
|
|---|
| 981 | if poly is None:
|
|---|
| 982 | poly = ()
|
|---|
| 983 | from os.path import expandvars
|
|---|
| 984 | filename = expandvars(filename)
|
|---|
| 985 | s = scantable(self._math._gainel(self, poly, filename, method))
|
|---|
| 986 | s._add_history("gain_el", varlist)
|
|---|
| 987 | print_log()
|
|---|
| 988 | if insitu: self._assign(s)
|
|---|
| 989 | else: return s
|
|---|
| 990 |
|
|---|
| 991 | def freq_align(self, reftime=None, method='cubic', insitu=None):
|
|---|
| 992 | """
|
|---|
| 993 | Return a scan where all rows have been aligned in frequency/velocity.
|
|---|
| 994 | The alignment frequency frame (e.g. LSRK) is that set by function
|
|---|
| 995 | set_freqframe.
|
|---|
| 996 | Parameters:
|
|---|
| 997 | reftime: reference time to align at. By default, the time of
|
|---|
| 998 | the first row of data is used.
|
|---|
| 999 | method: Interpolation method for regridding the spectra.
|
|---|
| 1000 | Choose from "nearest", "linear", "cubic" (default)
|
|---|
| 1001 | and "spline"
|
|---|
| 1002 | insitu: if False a new scantable is returned.
|
|---|
| 1003 | Otherwise, the scaling is done in-situ
|
|---|
| 1004 | The default is taken from .asaprc (False)
|
|---|
| 1005 | """
|
|---|
| 1006 | if insitu is None: insitu = rcParams["insitu"]
|
|---|
| 1007 | self._math._setinsitu(insitu)
|
|---|
| 1008 | varlist = vars()
|
|---|
| 1009 | if reftime is None: reftime = ""
|
|---|
| 1010 | s = scantable(self._math._freq_align(self, reftime, method))
|
|---|
| 1011 | s._add_history("freq_align", varlist)
|
|---|
| 1012 | print_log()
|
|---|
| 1013 | if insitu: self._assign(s)
|
|---|
| 1014 | else: return s
|
|---|
| 1015 |
|
|---|
| 1016 | def opacity(self, tau, insitu=None):
|
|---|
| 1017 | """
|
|---|
| 1018 | Apply an opacity correction. The data
|
|---|
| 1019 | and Tsys are multiplied by the correction factor.
|
|---|
| 1020 | Parameters:
|
|---|
| 1021 | tau: Opacity from which the correction factor is
|
|---|
| 1022 | exp(tau*ZD)
|
|---|
| 1023 | where ZD is the zenith-distance
|
|---|
| 1024 | insitu: if False a new scantable is returned.
|
|---|
| 1025 | Otherwise, the scaling is done in-situ
|
|---|
| 1026 | The default is taken from .asaprc (False)
|
|---|
| 1027 | """
|
|---|
| 1028 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1029 | self._math._setinsitu(insitu)
|
|---|
| 1030 | varlist = vars()
|
|---|
| 1031 | s = scantable(self._math._opacity(self, tau))
|
|---|
| 1032 | s._add_history("opacity", varlist)
|
|---|
| 1033 | print_log()
|
|---|
| 1034 | if insitu: self._assign(s)
|
|---|
| 1035 | else: return s
|
|---|
| 1036 |
|
|---|
| 1037 | def bin(self, width=5, insitu=None):
|
|---|
| 1038 | """
|
|---|
| 1039 | Return a scan where all spectra have been binned up.
|
|---|
| 1040 | width: The bin width (default=5) in pixels
|
|---|
| 1041 | insitu: if False a new scantable is returned.
|
|---|
| 1042 | Otherwise, the scaling is done in-situ
|
|---|
| 1043 | The default is taken from .asaprc (False)
|
|---|
| 1044 | """
|
|---|
| 1045 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1046 | self._math._setinsitu(insitu)
|
|---|
| 1047 | varlist = vars()
|
|---|
| 1048 | s = scantable(self._math._bin(self, width))
|
|---|
| 1049 | s._add_history("bin", varlist)
|
|---|
| 1050 | print_log()
|
|---|
| 1051 | if insitu: self._assign(s)
|
|---|
| 1052 | else: return s
|
|---|
| 1053 |
|
|---|
| 1054 |
|
|---|
| 1055 | def resample(self, width=5, method='cubic', insitu=None):
|
|---|
| 1056 | """
|
|---|
| 1057 | Return a scan where all spectra have been binned up
|
|---|
| 1058 | width: The bin width (default=5) in pixels
|
|---|
| 1059 | method: Interpolation method when correcting from a table.
|
|---|
| 1060 | Values are "nearest", "linear", "cubic" (default)
|
|---|
| 1061 | and "spline"
|
|---|
| 1062 | insitu: if False a new scantable is returned.
|
|---|
| 1063 | Otherwise, the scaling is done in-situ
|
|---|
| 1064 | The default is taken from .asaprc (False)
|
|---|
| 1065 | """
|
|---|
| 1066 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1067 | self._math._setinsitu(insitu)
|
|---|
| 1068 | varlist = vars()
|
|---|
| 1069 | s = scantable(self._math._resample(self, method, width))
|
|---|
| 1070 | s._add_history("resample", varlist)
|
|---|
| 1071 | print_log()
|
|---|
| 1072 | if insitu: self._assign(s)
|
|---|
| 1073 | else: return s
|
|---|
| 1074 |
|
|---|
| 1075 |
|
|---|
| 1076 | def average_pol(self, mask=None, weight='none'):
|
|---|
| 1077 | """
|
|---|
| 1078 | Average the Polarisations together.
|
|---|
| 1079 | Parameters:
|
|---|
| 1080 | mask: An optional mask defining the region, where the
|
|---|
| 1081 | averaging will be applied. The output will have all
|
|---|
| 1082 | specified points masked.
|
|---|
| 1083 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
|---|
| 1084 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
|---|
| 1085 | """
|
|---|
| 1086 | varlist = vars()
|
|---|
| 1087 | if mask is None:
|
|---|
| 1088 | mask = ()
|
|---|
| 1089 | s = scantable(self._math._averagepol(self, mask, weight.upper()))
|
|---|
| 1090 | s._add_history("average_pol", varlist)
|
|---|
| 1091 | print_log()
|
|---|
| 1092 | return s
|
|---|
| 1093 |
|
|---|
| 1094 | def average_beam(self, mask=None, weight='none'):
|
|---|
| 1095 | """
|
|---|
| 1096 | Average the Beams together.
|
|---|
| 1097 | Parameters:
|
|---|
| 1098 | mask: An optional mask defining the region, where the
|
|---|
| 1099 | averaging will be applied. The output will have all
|
|---|
| 1100 | specified points masked.
|
|---|
| 1101 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
|---|
| 1102 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
|---|
| 1103 | """
|
|---|
| 1104 | varlist = vars()
|
|---|
| 1105 | if mask is None:
|
|---|
| 1106 | mask = ()
|
|---|
| 1107 | s = scantable(self._math._averagebeams(self, mask, weight.upper()))
|
|---|
| 1108 | s._add_history("average_beam", varlist)
|
|---|
| 1109 | print_log()
|
|---|
| 1110 | return s
|
|---|
| 1111 |
|
|---|
| 1112 | def convert_pol(self, poltype=None):
|
|---|
| 1113 | """
|
|---|
| 1114 | Convert the data to a different polarisation type.
|
|---|
| 1115 | Parameters:
|
|---|
| 1116 | poltype: The new polarisation type. Valid types are:
|
|---|
| 1117 | "linear", "stokes" and "circular"
|
|---|
| 1118 | """
|
|---|
| 1119 | varlist = vars()
|
|---|
| 1120 | try:
|
|---|
| 1121 | s = scantable(self._math._convertpol(self, poltype))
|
|---|
| 1122 | except RuntimeError, msg:
|
|---|
| 1123 | if rcParams['verbose']:
|
|---|
| 1124 | print msg
|
|---|
| 1125 | return
|
|---|
| 1126 | else:
|
|---|
| 1127 | raise
|
|---|
| 1128 | s._add_history("convert_pol", varlist)
|
|---|
| 1129 | print_log()
|
|---|
| 1130 | return s
|
|---|
| 1131 |
|
|---|
| 1132 | def smooth(self, kernel="hanning", width=5.0, insitu=None):
|
|---|
| 1133 | """
|
|---|
| 1134 | Smooth the spectrum by the specified kernel (conserving flux).
|
|---|
| 1135 | Parameters:
|
|---|
| 1136 | scan: The input scan
|
|---|
| 1137 | kernel: The type of smoothing kernel. Select from
|
|---|
| 1138 | 'hanning' (default), 'gaussian' and 'boxcar'.
|
|---|
| 1139 | The first three characters are sufficient.
|
|---|
| 1140 | width: The width of the kernel in pixels. For hanning this is
|
|---|
| 1141 | ignored otherwise it defauls to 5 pixels.
|
|---|
| 1142 | For 'gaussian' it is the Full Width Half
|
|---|
| 1143 | Maximum. For 'boxcar' it is the full width.
|
|---|
| 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 | Example:
|
|---|
| 1148 | none
|
|---|
| 1149 | """
|
|---|
| 1150 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1151 | self._math._setinsitu(insitu)
|
|---|
| 1152 | varlist = vars()
|
|---|
| 1153 | s = scantable(self._math._smooth(self, kernel.lower(), width))
|
|---|
| 1154 | s._add_history("smooth", varlist)
|
|---|
| 1155 | print_log()
|
|---|
| 1156 | if insitu: self._assign(s)
|
|---|
| 1157 | else: return s
|
|---|
| 1158 |
|
|---|
| 1159 |
|
|---|
| 1160 | def poly_baseline(self, mask=None, order=0, plot=False, insitu=None):
|
|---|
| 1161 | """
|
|---|
| 1162 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 1163 | Parameters:
|
|---|
| 1164 | scan: a scantable
|
|---|
| 1165 | mask: an optional mask
|
|---|
| 1166 | order: the order of the polynomial (default is 0)
|
|---|
| 1167 | plot: plot the fit and the residual. In this each
|
|---|
| 1168 | indivual fit has to be approved, by typing 'y'
|
|---|
| 1169 | or 'n'
|
|---|
| 1170 | insitu: if False a new scantable is returned.
|
|---|
| 1171 | Otherwise, the scaling is done in-situ
|
|---|
| 1172 | The default is taken from .asaprc (False)
|
|---|
| 1173 | Example:
|
|---|
| 1174 | # return a scan baselined by a third order polynomial,
|
|---|
| 1175 | # not using a mask
|
|---|
| 1176 | bscan = scan.poly_baseline(order=3)
|
|---|
| 1177 | """
|
|---|
| 1178 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1179 | varlist = vars()
|
|---|
| 1180 | if mask is None:
|
|---|
| 1181 | mask = list(NUM.ones(self.nchan(-1)))
|
|---|
| 1182 | from asap.asapfitter import fitter
|
|---|
| 1183 | f = fitter()
|
|---|
| 1184 | f.set_scan(self, mask)
|
|---|
| 1185 | f.set_function(poly=order)
|
|---|
| 1186 | s = f.auto_fit(insitu, plot=plot)
|
|---|
| 1187 | s._add_history("poly_baseline", varlist)
|
|---|
| 1188 | print_log()
|
|---|
| 1189 | if insitu: self._assign(s)
|
|---|
| 1190 | else: return s
|
|---|
| 1191 |
|
|---|
| 1192 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0,
|
|---|
| 1193 | threshold=3, plot=False, insitu=None):
|
|---|
| 1194 | """
|
|---|
| 1195 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 1196 | Spectral lines are detected first using linefinder and masked out
|
|---|
| 1197 | to avoid them affecting the baseline solution.
|
|---|
| 1198 |
|
|---|
| 1199 | Parameters:
|
|---|
| 1200 | mask: an optional mask retreived from scantable
|
|---|
| 1201 | edge: an optional number of channel to drop at
|
|---|
| 1202 | the edge of spectrum. If only one value is
|
|---|
| 1203 | specified, the same number will be dropped from
|
|---|
| 1204 | both sides of the spectrum. Default is to keep
|
|---|
| 1205 | all channels. Nested tuples represent individual
|
|---|
| 1206 | edge selection for different IFs (a number of spectral
|
|---|
| 1207 | channels can be different)
|
|---|
| 1208 | order: the order of the polynomial (default is 0)
|
|---|
| 1209 | threshold: the threshold used by line finder. It is better to
|
|---|
| 1210 | keep it large as only strong lines affect the
|
|---|
| 1211 | baseline solution.
|
|---|
| 1212 | plot: plot the fit and the residual. In this each
|
|---|
| 1213 | indivual fit has to be approved, by typing 'y'
|
|---|
| 1214 | or 'n'
|
|---|
| 1215 | insitu: if False a new scantable is returned.
|
|---|
| 1216 | Otherwise, the scaling is done in-situ
|
|---|
| 1217 | The default is taken from .asaprc (False)
|
|---|
| 1218 |
|
|---|
| 1219 | Example:
|
|---|
| 1220 | scan2=scan.auto_poly_baseline(order=7)
|
|---|
| 1221 | """
|
|---|
| 1222 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1223 | varlist = vars()
|
|---|
| 1224 | from asap.asapfitter import fitter
|
|---|
| 1225 | from asap.asaplinefind import linefinder
|
|---|
| 1226 | from asap import _is_sequence_or_number as _is_valid
|
|---|
| 1227 |
|
|---|
| 1228 | # check whether edge is set up for each IF individually
|
|---|
| 1229 | individualedge = False;
|
|---|
| 1230 | if len(edge) > 1:
|
|---|
| 1231 | if isinstance(edge[0], list) or isinstance(edge[0], tuple):
|
|---|
| 1232 | individualedge = True;
|
|---|
| 1233 |
|
|---|
| 1234 | if not _is_valid(edge, int) and not individualedge:
|
|---|
| 1235 | raise ValueError, "Parameter 'edge' has to be an integer or a \
|
|---|
| 1236 | pair of integers specified as a tuple. Nested tuples are allowed \
|
|---|
| 1237 | to make individual selection for different IFs."
|
|---|
| 1238 |
|
|---|
| 1239 | curedge = (0, 0)
|
|---|
| 1240 | if individualedge:
|
|---|
| 1241 | for edgepar in edge:
|
|---|
| 1242 | if not _is_valid(edgepar, int):
|
|---|
| 1243 | raise ValueError, "Each element of the 'edge' tuple has \
|
|---|
| 1244 | to be a pair of integers or an integer."
|
|---|
| 1245 | else:
|
|---|
| 1246 | curedge = edge;
|
|---|
| 1247 |
|
|---|
| 1248 | # setup fitter
|
|---|
| 1249 | f = fitter()
|
|---|
| 1250 | f.set_function(poly=order)
|
|---|
| 1251 |
|
|---|
| 1252 | # setup line finder
|
|---|
| 1253 | fl = linefinder()
|
|---|
| 1254 | fl.set_options(threshold=threshold)
|
|---|
| 1255 |
|
|---|
| 1256 | if not insitu:
|
|---|
| 1257 | workscan = self.copy()
|
|---|
| 1258 | else:
|
|---|
| 1259 | workscan = self
|
|---|
| 1260 |
|
|---|
| 1261 | fl.set_scan(workscan)
|
|---|
| 1262 |
|
|---|
| 1263 | rows = range(workscan.nrow())
|
|---|
| 1264 | asaplog.push("Processing:")
|
|---|
| 1265 | for r in rows:
|
|---|
| 1266 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
|
|---|
| 1267 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
|
|---|
| 1268 | workscan.getpol(r), workscan.getcycle(r))
|
|---|
| 1269 | asaplog.push(msg, False)
|
|---|
| 1270 |
|
|---|
| 1271 | # figure out edge parameter
|
|---|
| 1272 | if individualedge:
|
|---|
| 1273 | if len(edge) >= workscan.getif(r):
|
|---|
| 1274 | raise RuntimeError, "Number of edge elements appear to " \
|
|---|
| 1275 | "be less than the number of IFs"
|
|---|
| 1276 | curedge = edge[workscan.getif(r)]
|
|---|
| 1277 |
|
|---|
| 1278 | # setup line finder
|
|---|
| 1279 | fl.find_lines(r, mask, curedge)
|
|---|
| 1280 | f.set_scan(workscan, fl.get_mask())
|
|---|
| 1281 | f.x = workscan._getabcissa(r)
|
|---|
| 1282 | f.y = workscan._getspectrum(r)
|
|---|
| 1283 | f.data = None
|
|---|
| 1284 | f.fit()
|
|---|
| 1285 | x = f.get_parameters()
|
|---|
| 1286 | if plot:
|
|---|
| 1287 | f.plot(residual=True)
|
|---|
| 1288 | x = raw_input("Accept fit ( [y]/n ): ")
|
|---|
| 1289 | if x.upper() == 'N':
|
|---|
| 1290 | continue
|
|---|
| 1291 | workscan._setspectrum(f.fitter.getresidual(), r)
|
|---|
| 1292 | if plot:
|
|---|
| 1293 | f._p.unmap()
|
|---|
| 1294 | f._p = None
|
|---|
| 1295 | workscan._add_history("auto_poly_baseline", varlist)
|
|---|
| 1296 | if insitu:
|
|---|
| 1297 | self._assign(workscan)
|
|---|
| 1298 | else:
|
|---|
| 1299 | return workscan
|
|---|
| 1300 |
|
|---|
| 1301 | def rotate_linpolphase(self, angle):
|
|---|
| 1302 | """
|
|---|
| 1303 | Rotate the phase of the complex polarization O=Q+iU correlation.
|
|---|
| 1304 | This is always done in situ in the raw data. So if you call this
|
|---|
| 1305 | function more than once then each call rotates the phase further.
|
|---|
| 1306 | Parameters:
|
|---|
| 1307 | angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1308 | Examples:
|
|---|
| 1309 | scan.rotate_linpolphase(2.3)
|
|---|
| 1310 | """
|
|---|
| 1311 | varlist = vars()
|
|---|
| 1312 | self._math._rotate_linpolphase(self, angle)
|
|---|
| 1313 | self._add_history("rotate_linpolphase", varlist)
|
|---|
| 1314 | print_log()
|
|---|
| 1315 | return
|
|---|
| 1316 |
|
|---|
| 1317 |
|
|---|
| 1318 | def rotate_xyphase(self, angle):
|
|---|
| 1319 | """
|
|---|
| 1320 | Rotate the phase of the XY correlation. This is always done in situ
|
|---|
| 1321 | in the data. So if you call this function more than once
|
|---|
| 1322 | then each call rotates the phase further.
|
|---|
| 1323 | Parameters:
|
|---|
| 1324 | angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1325 | Examples:
|
|---|
| 1326 | scan.rotate_xyphase(2.3)
|
|---|
| 1327 | """
|
|---|
| 1328 | varlist = vars()
|
|---|
| 1329 | self._math._rotate_xyphase(self, angle)
|
|---|
| 1330 | self._add_history("rotate_xyphase", varlist)
|
|---|
| 1331 | print_log()
|
|---|
| 1332 | return
|
|---|
| 1333 |
|
|---|
| 1334 | def swap_linears(self):
|
|---|
| 1335 | """
|
|---|
| 1336 | Swap the linear polarisations XX and YY
|
|---|
| 1337 | """
|
|---|
| 1338 | varlist = vars()
|
|---|
| 1339 | self._math._swap_linears(self)
|
|---|
| 1340 | self._add_history("swap_linears", varlist)
|
|---|
| 1341 | print_log()
|
|---|
| 1342 | return
|
|---|
| 1343 |
|
|---|
| 1344 | def invert_phase(self):
|
|---|
| 1345 | """
|
|---|
| 1346 | Invert the phase of the complex polarisation
|
|---|
| 1347 | """
|
|---|
| 1348 | varlist = vars()
|
|---|
| 1349 | self._math._invert_phase(self)
|
|---|
| 1350 | self._add_history("invert_phase", varlist)
|
|---|
| 1351 | print_log()
|
|---|
| 1352 | return
|
|---|
| 1353 |
|
|---|
| 1354 | def add(self, offset, insitu=None):
|
|---|
| 1355 | """
|
|---|
| 1356 | Return a scan where all spectra have the offset added
|
|---|
| 1357 | Parameters:
|
|---|
| 1358 | offset: the offset
|
|---|
| 1359 | insitu: if False a new scantable is returned.
|
|---|
| 1360 | Otherwise, the scaling is done in-situ
|
|---|
| 1361 | The default is taken from .asaprc (False)
|
|---|
| 1362 | """
|
|---|
| 1363 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1364 | self._math._setinsitu(insitu)
|
|---|
| 1365 | varlist = vars()
|
|---|
| 1366 | s = scantable(self._math._unaryop(self, offset, "ADD", False))
|
|---|
| 1367 | s._add_history("add", varlist)
|
|---|
| 1368 | print_log()
|
|---|
| 1369 | if insitu:
|
|---|
| 1370 | self._assign(s)
|
|---|
| 1371 | else:
|
|---|
| 1372 | return s
|
|---|
| 1373 |
|
|---|
| 1374 | def scale(self, factor, tsys=True, insitu=None, ):
|
|---|
| 1375 | """
|
|---|
| 1376 | Return a scan where all spectra are scaled by the give 'factor'
|
|---|
| 1377 | Parameters:
|
|---|
| 1378 | factor: the scaling factor
|
|---|
| 1379 | insitu: if False a new scantable is returned.
|
|---|
| 1380 | Otherwise, the scaling is done in-situ
|
|---|
| 1381 | The default is taken from .asaprc (False)
|
|---|
| 1382 | tsys: if True (default) then apply the operation to Tsys
|
|---|
| 1383 | as well as the data
|
|---|
| 1384 | """
|
|---|
| 1385 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1386 | self._math._setinsitu(insitu)
|
|---|
| 1387 | varlist = vars()
|
|---|
| 1388 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
|
|---|
| 1389 | s._add_history("scale", varlist)
|
|---|
| 1390 | print_log()
|
|---|
| 1391 | if insitu:
|
|---|
| 1392 | self._assign(s)
|
|---|
| 1393 | else:
|
|---|
| 1394 | return s
|
|---|
| 1395 |
|
|---|
| 1396 | def auto_quotient(self, mode='time', preserve=True):
|
|---|
| 1397 | """
|
|---|
| 1398 | This function allows to build quotients automatically.
|
|---|
| 1399 | It assumes the observation to have the same numer of
|
|---|
| 1400 | "ons" and "offs"
|
|---|
| 1401 | It will support "closest off in time" in the future
|
|---|
| 1402 | Parameters:
|
|---|
| 1403 | mode: the on/off detection mode; 'suffix' (default)
|
|---|
| 1404 | 'suffix' identifies 'off' scans by the
|
|---|
| 1405 | trailing '_R' (Mopra/Parkes) or
|
|---|
| 1406 | '_e'/'_w' (Tid)
|
|---|
| 1407 | preserve: you can preserve (default) the continuum or
|
|---|
| 1408 | remove it. The equations used are
|
|---|
| 1409 | preserve: Output = Toff * (on/off) - Toff
|
|---|
| 1410 | remove: Output = Toff * (on/off) - Ton
|
|---|
| 1411 | """
|
|---|
| 1412 | modes = ["time"]
|
|---|
| 1413 | if not mode in modes:
|
|---|
| 1414 | msg = "please provide valid mode. Valid modes are %s" % (modes)
|
|---|
| 1415 | raise ValueError(msg)
|
|---|
| 1416 | varlist = vars()
|
|---|
| 1417 | s = scantable(self._math._auto_quotient(self, mode, preserve))
|
|---|
| 1418 | s._add_history("auto_quotient", varlist)
|
|---|
| 1419 | print_log()
|
|---|
| 1420 | return s
|
|---|
| 1421 |
|
|---|
| 1422 | def mx_quotient(self, mask = None, weight='median', preserve=True):
|
|---|
| 1423 | """
|
|---|
| 1424 | Form a quotient using "off" beams when observing in "MX" mode.
|
|---|
| 1425 | Parameters:
|
|---|
| 1426 | mask: an optional mask to be used when weight == 'stddev'
|
|---|
| 1427 | weight: How to average the off beams. Default is 'median'.
|
|---|
| 1428 | preserve: you can preserve (default) the continuum or
|
|---|
| 1429 | remove it. The equations used are
|
|---|
| 1430 | preserve: Output = Toff * (on/off) - Toff
|
|---|
| 1431 | remove: Output = Toff * (on/off) - Ton
|
|---|
| 1432 | """
|
|---|
| 1433 | if mask is None: mask = ()
|
|---|
| 1434 | varlist = vars()
|
|---|
| 1435 | on = scantable(self._math._mx_extract(self, 'on'))
|
|---|
| 1436 | preoff = scantable(self._math._mx_extract(self, 'off'))
|
|---|
| 1437 | off = preoff.average_time(mask=mask, weight=weight, scanav=False)
|
|---|
| 1438 | from asapmath import quotient
|
|---|
| 1439 | q = quotient(on, off, preserve)
|
|---|
| 1440 | q._add_history("mx_quotient", varlist)
|
|---|
| 1441 | print_log()
|
|---|
| 1442 | return q
|
|---|
| 1443 |
|
|---|
| 1444 | def freq_switch(self, insitu=None):
|
|---|
| 1445 | """
|
|---|
| 1446 | Apply frequency switching to the data.
|
|---|
| 1447 | Parameters:
|
|---|
| 1448 | insitu: if False a new scantable is returned.
|
|---|
| 1449 | Otherwise, the swictching is done in-situ
|
|---|
| 1450 | The default is taken from .asaprc (False)
|
|---|
| 1451 | Example:
|
|---|
| 1452 | none
|
|---|
| 1453 | """
|
|---|
| 1454 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1455 | self._math._setinsitu(insitu)
|
|---|
| 1456 | varlist = vars()
|
|---|
| 1457 | s = scantable(self._math._freqswitch(self))
|
|---|
| 1458 | s._add_history("freq_switch", varlist)
|
|---|
| 1459 | print_log()
|
|---|
| 1460 | if insitu: self._assign(s)
|
|---|
| 1461 | else: return s
|
|---|
| 1462 |
|
|---|
| 1463 | def recalc_azel(self):
|
|---|
| 1464 | """
|
|---|
| 1465 | Recalculate the azimuth and elevation for each position.
|
|---|
| 1466 | Parameters:
|
|---|
| 1467 | none
|
|---|
| 1468 | Example:
|
|---|
| 1469 | """
|
|---|
| 1470 | varlist = vars()
|
|---|
| 1471 | self._recalcazel()
|
|---|
| 1472 | self._add_history("recalc_azel", varlist)
|
|---|
| 1473 | print_log()
|
|---|
| 1474 | return
|
|---|
| 1475 |
|
|---|
| 1476 | def __add__(self, other):
|
|---|
| 1477 | varlist = vars()
|
|---|
| 1478 | s = None
|
|---|
| 1479 | if isinstance(other, scantable):
|
|---|
| 1480 | print "scantable + scantable NYI"
|
|---|
| 1481 | return
|
|---|
| 1482 | elif isinstance(other, float):
|
|---|
| 1483 | s = scantable(self._math._unaryop(self, other, "ADD", False))
|
|---|
| 1484 | else:
|
|---|
| 1485 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1486 | s._add_history("operator +", varlist)
|
|---|
| 1487 | print_log()
|
|---|
| 1488 | return s
|
|---|
| 1489 |
|
|---|
| 1490 | def __sub__(self, other):
|
|---|
| 1491 | """
|
|---|
| 1492 | implicit on all axes and on Tsys
|
|---|
| 1493 | """
|
|---|
| 1494 | varlist = vars()
|
|---|
| 1495 | s = None
|
|---|
| 1496 | if isinstance(other, scantable):
|
|---|
| 1497 | print "scantable - scantable NYI"
|
|---|
| 1498 | return
|
|---|
| 1499 | elif isinstance(other, float):
|
|---|
| 1500 | s = scantable(self._math._unaryop(self, other, "SUB", False))
|
|---|
| 1501 | else:
|
|---|
| 1502 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1503 | s._add_history("operator -", varlist)
|
|---|
| 1504 | print_log()
|
|---|
| 1505 | return s
|
|---|
| 1506 |
|
|---|
| 1507 | def __mul__(self, other):
|
|---|
| 1508 | """
|
|---|
| 1509 | implicit on all axes and on Tsys
|
|---|
| 1510 | """
|
|---|
| 1511 | varlist = vars()
|
|---|
| 1512 | s = None
|
|---|
| 1513 | if isinstance(other, scantable):
|
|---|
| 1514 | print "scantable * scantable NYI"
|
|---|
| 1515 | return
|
|---|
| 1516 | elif isinstance(other, float):
|
|---|
| 1517 | s = scantable(self._math._unaryop(self, other, "MUL", False))
|
|---|
| 1518 | else:
|
|---|
| 1519 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1520 | s._add_history("operator *", varlist)
|
|---|
| 1521 | print_log()
|
|---|
| 1522 | return s
|
|---|
| 1523 |
|
|---|
| 1524 |
|
|---|
| 1525 | def __div__(self, other):
|
|---|
| 1526 | """
|
|---|
| 1527 | implicit on all axes and on Tsys
|
|---|
| 1528 | """
|
|---|
| 1529 | varlist = vars()
|
|---|
| 1530 | s = None
|
|---|
| 1531 | if isinstance(other, scantable):
|
|---|
| 1532 | print "scantable / scantable NYI"
|
|---|
| 1533 | return
|
|---|
| 1534 | elif isinstance(other, float):
|
|---|
| 1535 | if other == 0.0:
|
|---|
| 1536 | raise ZeroDivisionError("Dividing by zero is not recommended")
|
|---|
| 1537 | s = scantable(self._math._unaryop(self, other, "DIV", False))
|
|---|
| 1538 | else:
|
|---|
| 1539 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1540 | s._add_history("operator /", varlist)
|
|---|
| 1541 | print_log()
|
|---|
| 1542 | return s
|
|---|
| 1543 |
|
|---|
| 1544 | def get_fit(self, row=0):
|
|---|
| 1545 | """
|
|---|
| 1546 | Print or return the stored fits for a row in the scantable
|
|---|
| 1547 | Parameters:
|
|---|
| 1548 | row: the row which the fit has been applied to.
|
|---|
| 1549 | """
|
|---|
| 1550 | if row > self.nrow():
|
|---|
| 1551 | return
|
|---|
| 1552 | from asap.asapfit import asapfit
|
|---|
| 1553 | fit = asapfit(self._getfit(row))
|
|---|
| 1554 | if rcParams['verbose']:
|
|---|
| 1555 | print fit
|
|---|
| 1556 | return
|
|---|
| 1557 | else:
|
|---|
| 1558 | return fit.as_dict()
|
|---|
| 1559 |
|
|---|
| 1560 | def _add_history(self, funcname, parameters):
|
|---|
| 1561 | # create date
|
|---|
| 1562 | sep = "##"
|
|---|
| 1563 | from datetime import datetime
|
|---|
| 1564 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
|
|---|
| 1565 | hist = dstr+sep
|
|---|
| 1566 | hist += funcname+sep#cdate+sep
|
|---|
| 1567 | if parameters.has_key('self'): del parameters['self']
|
|---|
| 1568 | for k, v in parameters.iteritems():
|
|---|
| 1569 | if type(v) is dict:
|
|---|
| 1570 | for k2, v2 in v.iteritems():
|
|---|
| 1571 | hist += k2
|
|---|
| 1572 | hist += "="
|
|---|
| 1573 | if isinstance(v2, scantable):
|
|---|
| 1574 | hist += 'scantable'
|
|---|
| 1575 | elif k2 == 'mask':
|
|---|
| 1576 | if isinstance(v2, list) or isinstance(v2, tuple):
|
|---|
| 1577 | hist += str(self._zip_mask(v2))
|
|---|
| 1578 | else:
|
|---|
| 1579 | hist += str(v2)
|
|---|
| 1580 | else:
|
|---|
| 1581 | hist += str(v2)
|
|---|
| 1582 | else:
|
|---|
| 1583 | hist += k
|
|---|
| 1584 | hist += "="
|
|---|
| 1585 | if isinstance(v, scantable):
|
|---|
| 1586 | hist += 'scantable'
|
|---|
| 1587 | elif k == 'mask':
|
|---|
| 1588 | if isinstance(v, list) or isinstance(v, tuple):
|
|---|
| 1589 | hist += str(self._zip_mask(v))
|
|---|
| 1590 | else:
|
|---|
| 1591 | hist += str(v)
|
|---|
| 1592 | else:
|
|---|
| 1593 | hist += str(v)
|
|---|
| 1594 | hist += sep
|
|---|
| 1595 | hist = hist[:-2] # remove trailing '##'
|
|---|
| 1596 | self._addhistory(hist)
|
|---|
| 1597 |
|
|---|
| 1598 |
|
|---|
| 1599 | def _zip_mask(self, mask):
|
|---|
| 1600 | mask = list(mask)
|
|---|
| 1601 | i = 0
|
|---|
| 1602 | segments = []
|
|---|
| 1603 | while mask[i:].count(1):
|
|---|
| 1604 | i += mask[i:].index(1)
|
|---|
| 1605 | if mask[i:].count(0):
|
|---|
| 1606 | j = i + mask[i:].index(0)
|
|---|
| 1607 | else:
|
|---|
| 1608 | j = len(mask)
|
|---|
| 1609 | segments.append([i, j])
|
|---|
| 1610 | i = j
|
|---|
| 1611 | return segments
|
|---|
| 1612 |
|
|---|
| 1613 | def _get_ordinate_label(self):
|
|---|
| 1614 | fu = "("+self.get_fluxunit()+")"
|
|---|
| 1615 | import re
|
|---|
| 1616 | lbl = "Intensity"
|
|---|
| 1617 | if re.match(".K.", fu):
|
|---|
| 1618 | lbl = "Brightness Temperature "+ fu
|
|---|
| 1619 | elif re.match(".Jy.", fu):
|
|---|
| 1620 | lbl = "Flux density "+ fu
|
|---|
| 1621 | return lbl
|
|---|
| 1622 |
|
|---|
| 1623 | def _check_ifs(self):
|
|---|
| 1624 | nchans = [self.nchan(i) for i in range(self.nif(-1))]
|
|---|
| 1625 | nchans = filter(lambda t: t > 0, nchans)
|
|---|
| 1626 | return (sum(nchans)/len(nchans) == nchans[0])
|
|---|
| 1627 |
|
|---|
| 1628 | def _fill(self, names, unit, average):
|
|---|
| 1629 | import os
|
|---|
| 1630 | from asap._asap import stfiller
|
|---|
| 1631 | first = True
|
|---|
| 1632 | fullnames = []
|
|---|
| 1633 | for name in names:
|
|---|
| 1634 | name = os.path.expandvars(name)
|
|---|
| 1635 | name = os.path.expanduser(name)
|
|---|
| 1636 | if not os.path.exists(name):
|
|---|
| 1637 | msg = "File '%s' does not exists" % (name)
|
|---|
| 1638 | if rcParams['verbose']:
|
|---|
| 1639 | asaplog.push(msg)
|
|---|
| 1640 | print asaplog.pop().strip()
|
|---|
| 1641 | return
|
|---|
| 1642 | raise IOError(msg)
|
|---|
| 1643 | fullnames.append(name)
|
|---|
| 1644 | if average:
|
|---|
| 1645 | asaplog.push('Auto averaging integrations')
|
|---|
| 1646 | stype = int(rcParams['scantable.storage'].lower() == 'disk')
|
|---|
| 1647 | for name in fullnames:
|
|---|
| 1648 | tbl = Scantable(stype)
|
|---|
| 1649 | r = stfiller(tbl)
|
|---|
| 1650 | msg = "Importing %s..." % (name)
|
|---|
| 1651 | asaplog.push(msg, False)
|
|---|
| 1652 | print_log()
|
|---|
| 1653 | r._open(name, -1, -1)
|
|---|
| 1654 | r._read()
|
|---|
| 1655 | #tbl = r._getdata()
|
|---|
| 1656 | if average:
|
|---|
| 1657 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
|
|---|
| 1658 | #tbl = tbl2
|
|---|
| 1659 | if not first:
|
|---|
| 1660 | tbl = self._math._merge([self, tbl])
|
|---|
| 1661 | #tbl = tbl2
|
|---|
| 1662 | Scantable.__init__(self, tbl)
|
|---|
| 1663 | r._close()
|
|---|
| 1664 | del r, tbl
|
|---|
| 1665 | first = False
|
|---|
| 1666 | if unit is not None:
|
|---|
| 1667 | self.set_fluxunit(unit)
|
|---|
| 1668 | self.set_freqframe(rcParams['scantable.freqframe'])
|
|---|
| 1669 | #self._add_history("scantable", varlist)
|
|---|
| 1670 |
|
|---|
