[1757] | 1 | import os |
---|
| 2 | try: |
---|
| 3 | from functools import wraps as wraps_dec |
---|
| 4 | except ImportError: |
---|
| 5 | from asap.compatibility import wraps as wraps_dec |
---|
| 6 | |
---|
[876] | 7 | from asap._asap import Scantable |
---|
[226] | 8 | from asap import rcParams |
---|
[1757] | 9 | from asap import print_log, print_log_dec |
---|
[1118] | 10 | from asap import asaplog |
---|
[946] | 11 | from asap import selector |
---|
[1153] | 12 | from asap import linecatalog |
---|
[1757] | 13 | from asap.coordinate import coordinate |
---|
[1295] | 14 | from asap import _n_bools, mask_not, mask_and, mask_or |
---|
[102] | 15 | |
---|
[1757] | 16 | |
---|
| 17 | def preserve_selection(func): |
---|
| 18 | @wraps_dec(func) |
---|
| 19 | def wrap(obj, *args, **kw): |
---|
| 20 | basesel = obj.get_selection() |
---|
| 21 | val = func(obj, *args, **kw) |
---|
| 22 | obj.set_selection(basesel) |
---|
| 23 | return val |
---|
| 24 | return wrap |
---|
| 25 | |
---|
| 26 | |
---|
| 27 | def is_scantable(filename): |
---|
| 28 | return (os.path.isdir(filename) |
---|
| 29 | and not os.path.exists(filename+'/table.f1') |
---|
| 30 | and os.path.exists(filename+'/table.info')) |
---|
| 31 | |
---|
| 32 | |
---|
[876] | 33 | class scantable(Scantable): |
---|
[102] | 34 | """ |
---|
| 35 | The ASAP container for scans |
---|
| 36 | """ |
---|
[710] | 37 | |
---|
[1757] | 38 | #@print_log_dec |
---|
| 39 | def __init__(self, filename, average=None, unit=None, getpt=None, antenna=None, parallactify=None): |
---|
[102] | 40 | """ |
---|
| 41 | Create a scantable from a saved one or make a reference |
---|
| 42 | Parameters: |
---|
[181] | 43 | filename: the name of an asap table on disk |
---|
| 44 | or |
---|
| 45 | the name of a rpfits/sdfits/ms file |
---|
| 46 | (integrations within scans are auto averaged |
---|
| 47 | and the whole file is read) |
---|
| 48 | or |
---|
| 49 | [advanced] a reference to an existing |
---|
[102] | 50 | scantable |
---|
[484] | 51 | average: average all integrations withinb a scan on read. |
---|
| 52 | The default (True) is taken from .asaprc. |
---|
| 53 | unit: brightness unit; must be consistent with K or Jy. |
---|
[340] | 54 | Over-rides the default selected by the reader |
---|
| 55 | (input rpfits/sdfits/ms) or replaces the value |
---|
| 56 | in existing scantables |
---|
[1522] | 57 | getpt: for MeasurementSet input data only: |
---|
| 58 | If True, all pointing data are filled. |
---|
| 59 | The deafult is False, which makes time to load |
---|
[1685] | 60 | the MS data faster in some cases. |
---|
| 61 | antenna: Antenna selection. integer (id) or string (name |
---|
| 62 | or id). |
---|
[1757] | 63 | parallactify: Indcicate that the data had been parallatified. |
---|
| 64 | Default is taken form rc file. |
---|
[710] | 65 | """ |
---|
[976] | 66 | if average is None: |
---|
[710] | 67 | average = rcParams['scantable.autoaverage'] |
---|
[1496] | 68 | if getpt is None: |
---|
[1673] | 69 | getpt = True |
---|
[1684] | 70 | if antenna is None: |
---|
| 71 | antenna = '' |
---|
| 72 | elif type(antenna) == int: |
---|
| 73 | antenna = '%s'%antenna |
---|
| 74 | elif type(antenna) == list: |
---|
| 75 | tmpstr = '' |
---|
| 76 | for i in range( len(antenna) ): |
---|
| 77 | if type(antenna[i]) == int: |
---|
| 78 | tmpstr = tmpstr + ('%s,'%(antenna[i])) |
---|
| 79 | elif type(antenna[i]) == str: |
---|
| 80 | tmpstr=tmpstr+antenna[i]+',' |
---|
| 81 | else: |
---|
| 82 | asaplog.push('Bad antenna selection.') |
---|
| 83 | print_log('ERROR') |
---|
| 84 | return |
---|
| 85 | antenna = tmpstr.rstrip(',') |
---|
[1757] | 86 | parallactify = parallactify or rcParams['scantable.parallactify'] |
---|
[1259] | 87 | varlist = vars() |
---|
[876] | 88 | from asap._asap import stmath |
---|
[1680] | 89 | self._math = stmath( rcParams['insitu'] ) |
---|
[876] | 90 | if isinstance(filename, Scantable): |
---|
| 91 | Scantable.__init__(self, filename) |
---|
[181] | 92 | else: |
---|
[1757] | 93 | if isinstance(filename, str): |
---|
[976] | 94 | filename = os.path.expandvars(filename) |
---|
| 95 | filename = os.path.expanduser(filename) |
---|
| 96 | if not os.path.exists(filename): |
---|
| 97 | s = "File '%s' not found." % (filename) |
---|
[718] | 98 | if rcParams['verbose']: |
---|
[976] | 99 | asaplog.push(s) |
---|
[1614] | 100 | print_log('ERROR') |
---|
[718] | 101 | return |
---|
[976] | 102 | raise IOError(s) |
---|
[1757] | 103 | if is_scantable(filename): |
---|
| 104 | ondisk = rcParams['scantable.storage'] == 'disk' |
---|
| 105 | Scantable.__init__(self, filename, ondisk) |
---|
| 106 | if unit is not None: |
---|
| 107 | self.set_fluxunit(unit) |
---|
| 108 | # do not reset to the default freqframe |
---|
| 109 | #self.set_freqframe(rcParams['scantable.freqframe']) |
---|
| 110 | elif os.path.isdir(filename) \ |
---|
| 111 | and not os.path.exists(filename+'/table.f1'): |
---|
| 112 | msg = "The given file '%s'is not a valid " \ |
---|
| 113 | "asap table." % (filename) |
---|
| 114 | if rcParams['verbose']: |
---|
| 115 | #print msg |
---|
| 116 | asaplog.push( msg ) |
---|
| 117 | print_log( 'ERROR' ) |
---|
| 118 | return |
---|
[718] | 119 | else: |
---|
[1757] | 120 | raise IOError(msg) |
---|
[226] | 121 | else: |
---|
[1684] | 122 | self._fill([filename], unit, average, getpt, antenna) |
---|
[1118] | 123 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
---|
[976] | 124 | and isinstance(filename[-1], str): |
---|
[1684] | 125 | self._fill(filename, unit, average, getpt, antenna) |
---|
[1757] | 126 | self.parallactify(parallactify) |
---|
[1259] | 127 | self._add_history("scantable", varlist) |
---|
[714] | 128 | print_log() |
---|
[102] | 129 | |
---|
[1757] | 130 | #@print_log_dec |
---|
[876] | 131 | def save(self, name=None, format=None, overwrite=False): |
---|
[116] | 132 | """ |
---|
[1280] | 133 | Store the scantable on disk. This can be an asap (aips++) Table, |
---|
| 134 | SDFITS or MS2 format. |
---|
[116] | 135 | Parameters: |
---|
[1093] | 136 | name: the name of the outputfile. For format "ASCII" |
---|
| 137 | this is the root file name (data in 'name'.txt |
---|
[497] | 138 | and header in 'name'_header.txt) |
---|
[116] | 139 | format: an optional file format. Default is ASAP. |
---|
[280] | 140 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
---|
[194] | 141 | 'SDFITS' (save as SDFITS file) |
---|
[200] | 142 | 'ASCII' (saves as ascii text file) |
---|
[226] | 143 | 'MS2' (saves as an aips++ |
---|
| 144 | MeasurementSet V2) |
---|
[1757] | 145 | 'FITS' (save as image FITS - not |
---|
[1603] | 146 | readable by class) |
---|
| 147 | 'CLASS' (save as FITS readable by CLASS) |
---|
[411] | 148 | overwrite: If the file should be overwritten if it exists. |
---|
[256] | 149 | The default False is to return with warning |
---|
[411] | 150 | without writing the output. USE WITH CARE. |
---|
[116] | 151 | Example: |
---|
| 152 | scan.save('myscan.asap') |
---|
[1118] | 153 | scan.save('myscan.sdfits', 'SDFITS') |
---|
[116] | 154 | """ |
---|
[411] | 155 | from os import path |
---|
[1757] | 156 | format = format or rcParams['scantable.save'] |
---|
[256] | 157 | suffix = '.'+format.lower() |
---|
[1118] | 158 | if name is None or name == "": |
---|
[256] | 159 | name = 'scantable'+suffix |
---|
[718] | 160 | msg = "No filename given. Using default name %s..." % name |
---|
| 161 | asaplog.push(msg) |
---|
[411] | 162 | name = path.expandvars(name) |
---|
[256] | 163 | if path.isfile(name) or path.isdir(name): |
---|
| 164 | if not overwrite: |
---|
[718] | 165 | msg = "File %s exists." % name |
---|
| 166 | if rcParams['verbose']: |
---|
[1612] | 167 | #print msg |
---|
[1614] | 168 | asaplog.push( msg ) |
---|
| 169 | print_log( 'ERROR' ) |
---|
[718] | 170 | return |
---|
| 171 | else: |
---|
| 172 | raise IOError(msg) |
---|
[451] | 173 | format2 = format.upper() |
---|
| 174 | if format2 == 'ASAP': |
---|
[116] | 175 | self._save(name) |
---|
| 176 | else: |
---|
[989] | 177 | from asap._asap import stwriter as stw |
---|
[1118] | 178 | writer = stw(format2) |
---|
| 179 | writer.write(self, name) |
---|
[718] | 180 | print_log() |
---|
[116] | 181 | return |
---|
| 182 | |
---|
[102] | 183 | def copy(self): |
---|
| 184 | """ |
---|
| 185 | Return a copy of this scantable. |
---|
[1348] | 186 | Note: |
---|
| 187 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
---|
[102] | 188 | Parameters: |
---|
[113] | 189 | none |
---|
[102] | 190 | Example: |
---|
| 191 | copiedscan = scan.copy() |
---|
| 192 | """ |
---|
[876] | 193 | sd = scantable(Scantable._copy(self)) |
---|
[113] | 194 | return sd |
---|
| 195 | |
---|
[1093] | 196 | def drop_scan(self, scanid=None): |
---|
| 197 | """ |
---|
| 198 | Return a new scantable where the specified scan number(s) has(have) |
---|
| 199 | been dropped. |
---|
| 200 | Parameters: |
---|
| 201 | scanid: a (list of) scan number(s) |
---|
| 202 | """ |
---|
| 203 | from asap import _is_sequence_or_number as _is_valid |
---|
| 204 | from asap import _to_list |
---|
| 205 | from asap import unique |
---|
| 206 | if not _is_valid(scanid): |
---|
| 207 | if rcParams['verbose']: |
---|
[1612] | 208 | #print "Please specify a scanno to drop from the scantable" |
---|
[1614] | 209 | asaplog.push( 'Please specify a scanno to drop from the scantable' ) |
---|
| 210 | print_log( 'ERROR' ) |
---|
[1093] | 211 | return |
---|
| 212 | else: |
---|
| 213 | raise RuntimeError("No scan given") |
---|
| 214 | try: |
---|
| 215 | scanid = _to_list(scanid) |
---|
| 216 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
---|
| 217 | for sid in scanid: allscans.remove(sid) |
---|
[1118] | 218 | if len(allscans) == 0: |
---|
| 219 | raise ValueError("Can't remove all scans") |
---|
[1093] | 220 | except ValueError: |
---|
| 221 | if rcParams['verbose']: |
---|
[1612] | 222 | #print "Couldn't find any match." |
---|
[1614] | 223 | print_log() |
---|
| 224 | asaplog.push( "Couldn't find any match." ) |
---|
| 225 | print_log( 'ERROR' ) |
---|
[1093] | 226 | return |
---|
| 227 | else: raise |
---|
| 228 | try: |
---|
[1757] | 229 | sel = selector(scans=allscans) |
---|
| 230 | return self._select_copy(sel) |
---|
[1093] | 231 | except RuntimeError: |
---|
[1118] | 232 | if rcParams['verbose']: |
---|
[1612] | 233 | #print "Couldn't find any match." |
---|
[1614] | 234 | print_log() |
---|
| 235 | asaplog.push( "Couldn't find any match." ) |
---|
| 236 | print_log( 'ERROR' ) |
---|
[1118] | 237 | else: |
---|
| 238 | raise |
---|
[1093] | 239 | |
---|
[1757] | 240 | def _select_copy(self, selection): |
---|
| 241 | orig = self.get_selection() |
---|
| 242 | self.set_selection(orig+selection) |
---|
| 243 | cp = self.copy() |
---|
| 244 | self.set_selection(orig) |
---|
| 245 | return cp |
---|
[1093] | 246 | |
---|
[102] | 247 | def get_scan(self, scanid=None): |
---|
| 248 | """ |
---|
| 249 | Return a specific scan (by scanno) or collection of scans (by |
---|
| 250 | source name) in a new scantable. |
---|
[1348] | 251 | Note: |
---|
| 252 | See scantable.drop_scan() for the inverse operation. |
---|
[102] | 253 | Parameters: |
---|
[513] | 254 | scanid: a (list of) scanno or a source name, unix-style |
---|
| 255 | patterns are accepted for source name matching, e.g. |
---|
| 256 | '*_R' gets all 'ref scans |
---|
[102] | 257 | Example: |
---|
[513] | 258 | # get all scans containing the source '323p459' |
---|
| 259 | newscan = scan.get_scan('323p459') |
---|
| 260 | # get all 'off' scans |
---|
| 261 | refscans = scan.get_scan('*_R') |
---|
| 262 | # get a susbset of scans by scanno (as listed in scan.summary()) |
---|
[1118] | 263 | newscan = scan.get_scan([0, 2, 7, 10]) |
---|
[102] | 264 | """ |
---|
| 265 | if scanid is None: |
---|
[718] | 266 | if rcParams['verbose']: |
---|
[1612] | 267 | #print "Please specify a scan no or name to " \ |
---|
| 268 | # "retrieve from the scantable" |
---|
[1614] | 269 | asaplog.push( 'Please specify a scan no or name to retrieve from the scantable' ) |
---|
| 270 | print_log( 'ERROR' ) |
---|
[718] | 271 | return |
---|
| 272 | else: |
---|
| 273 | raise RuntimeError("No scan given") |
---|
| 274 | |
---|
[102] | 275 | try: |
---|
[946] | 276 | bsel = self.get_selection() |
---|
| 277 | sel = selector() |
---|
[102] | 278 | if type(scanid) is str: |
---|
[946] | 279 | sel.set_name(scanid) |
---|
[1757] | 280 | return self._select_copy(sel) |
---|
[102] | 281 | elif type(scanid) is int: |
---|
[946] | 282 | sel.set_scans([scanid]) |
---|
[1757] | 283 | return self._select_copy(sel) |
---|
[381] | 284 | elif type(scanid) is list: |
---|
[946] | 285 | sel.set_scans(scanid) |
---|
[1757] | 286 | return self._select_copy(sel) |
---|
[381] | 287 | else: |
---|
[718] | 288 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
---|
| 289 | if rcParams['verbose']: |
---|
[1612] | 290 | #print msg |
---|
[1614] | 291 | asaplog.push( msg ) |
---|
| 292 | print_log( 'ERROR' ) |
---|
[718] | 293 | else: |
---|
| 294 | raise TypeError(msg) |
---|
[102] | 295 | except RuntimeError: |
---|
[1612] | 296 | if rcParams['verbose']: |
---|
| 297 | #print "Couldn't find any match." |
---|
[1614] | 298 | print_log() |
---|
| 299 | asaplog.push( "Couldn't find any match." ) |
---|
| 300 | print_log( 'ERROR' ) |
---|
[718] | 301 | else: raise |
---|
[102] | 302 | |
---|
| 303 | def __str__(self): |
---|
[1118] | 304 | return Scantable._summary(self, True) |
---|
[102] | 305 | |
---|
[976] | 306 | def summary(self, filename=None): |
---|
[102] | 307 | """ |
---|
| 308 | Print a summary of the contents of this scantable. |
---|
| 309 | Parameters: |
---|
| 310 | filename: the name of a file to write the putput to |
---|
| 311 | Default - no file output |
---|
| 312 | """ |
---|
[976] | 313 | info = Scantable._summary(self, True) |
---|
[102] | 314 | if filename is not None: |
---|
[256] | 315 | if filename is "": |
---|
| 316 | filename = 'scantable_summary.txt' |
---|
[415] | 317 | from os.path import expandvars, isdir |
---|
[411] | 318 | filename = expandvars(filename) |
---|
[415] | 319 | if not isdir(filename): |
---|
[413] | 320 | data = open(filename, 'w') |
---|
| 321 | data.write(info) |
---|
| 322 | data.close() |
---|
| 323 | else: |
---|
[718] | 324 | msg = "Illegal file name '%s'." % (filename) |
---|
| 325 | if rcParams['verbose']: |
---|
[1612] | 326 | #print msg |
---|
[1614] | 327 | asaplog.push( msg ) |
---|
| 328 | print_log( 'ERROR' ) |
---|
[718] | 329 | else: |
---|
| 330 | raise IOError(msg) |
---|
| 331 | if rcParams['verbose']: |
---|
[794] | 332 | try: |
---|
| 333 | from IPython.genutils import page as pager |
---|
| 334 | except ImportError: |
---|
| 335 | from pydoc import pager |
---|
| 336 | pager(info) |
---|
[718] | 337 | else: |
---|
| 338 | return info |
---|
[710] | 339 | |
---|
[1603] | 340 | def get_spectrum(self, rowno): |
---|
| 341 | """Return the spectrum for the current row in the scantable as a list. |
---|
| 342 | Parameters: |
---|
[1757] | 343 | rowno: the row number to retrieve the spectrum from |
---|
[1603] | 344 | """ |
---|
| 345 | return self._getspectrum(rowno) |
---|
[946] | 346 | |
---|
[1603] | 347 | def get_mask(self, rowno): |
---|
| 348 | """Return the mask for the current row in the scantable as a list. |
---|
| 349 | Parameters: |
---|
[1757] | 350 | rowno: the row number to retrieve the mask from |
---|
[1603] | 351 | """ |
---|
| 352 | return self._getmask(rowno) |
---|
| 353 | |
---|
| 354 | def set_spectrum(self, spec, rowno): |
---|
| 355 | """Return the spectrum for the current row in the scantable as a list. |
---|
| 356 | Parameters: |
---|
| 357 | spec: the spectrum |
---|
[1757] | 358 | rowno: the row number to set the spectrum for |
---|
[1603] | 359 | """ |
---|
| 360 | assert(len(spec) == self.nchan()) |
---|
| 361 | return self._setspectrum(spec, rowno) |
---|
| 362 | |
---|
[1757] | 363 | def get_coordinate(self, rowno): |
---|
| 364 | """Return the (spectral) coordinate for a a given 'rowno'. |
---|
| 365 | NOTE: |
---|
| 366 | * This coordinate is only valid until a scantable method modifies |
---|
| 367 | the frequency axis. |
---|
| 368 | * This coordinate does contain the original frequency set-up |
---|
| 369 | NOT the new frame. The conversions however are done using the user |
---|
| 370 | specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate, |
---|
| 371 | use scantable.freq_align first. Without it there is no closure, |
---|
| 372 | i.e. |
---|
| 373 | c = myscan.get_coordinate(0) |
---|
| 374 | c.to_frequency(c.get_reference_pixel()) != c.get_reference_value() |
---|
| 375 | |
---|
| 376 | Parameters: |
---|
| 377 | rowno: the row number for the spectral coordinate |
---|
| 378 | |
---|
| 379 | """ |
---|
| 380 | return coordinate(Scantable.get_coordinate(self, rowno)) |
---|
| 381 | |
---|
[946] | 382 | def get_selection(self): |
---|
| 383 | """ |
---|
[1005] | 384 | Get the selection object currently set on this scantable. |
---|
| 385 | Parameters: |
---|
| 386 | none |
---|
| 387 | Example: |
---|
| 388 | sel = scan.get_selection() |
---|
| 389 | sel.set_ifs(0) # select IF 0 |
---|
| 390 | scan.set_selection(sel) # apply modified selection |
---|
[946] | 391 | """ |
---|
| 392 | return selector(self._getselection()) |
---|
| 393 | |
---|
[1757] | 394 | def set_selection(self, selection=None, **kw): |
---|
[946] | 395 | """ |
---|
[1005] | 396 | Select a subset of the data. All following operations on this scantable |
---|
| 397 | are only applied to thi selection. |
---|
| 398 | Parameters: |
---|
[1757] | 399 | selection: a selector object (default unset the selection), |
---|
| 400 | |
---|
| 401 | or |
---|
| 402 | |
---|
| 403 | any combination of |
---|
| 404 | "pols", "ifs", "beams", "scans", "cycles", "name", "query" |
---|
| 405 | |
---|
[1005] | 406 | Examples: |
---|
| 407 | sel = selector() # create a selection object |
---|
[1118] | 408 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
---|
[1005] | 409 | scan.set_selection(sel) # set the selection |
---|
| 410 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 411 | scan.set_selection() # unset the selection |
---|
[1757] | 412 | # or the equivalent |
---|
| 413 | scan.set_selection(scans=[0,3]) |
---|
| 414 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 415 | scan.set_selection() # unset the selection |
---|
[946] | 416 | """ |
---|
[1757] | 417 | if selection is None: |
---|
| 418 | # reset |
---|
| 419 | if len(kw) == 0: |
---|
| 420 | selection = selector() |
---|
| 421 | else: |
---|
| 422 | # try keywords |
---|
| 423 | for k in kw: |
---|
| 424 | if k not in selector.fields: |
---|
| 425 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields)) |
---|
| 426 | selection = selector(**kw) |
---|
[946] | 427 | self._setselection(selection) |
---|
| 428 | |
---|
[1446] | 429 | def get_row(self, row=0, insitu=None): |
---|
| 430 | """ |
---|
| 431 | Select a row in the scantable. |
---|
| 432 | Return a scantable with single row. |
---|
| 433 | Parameters: |
---|
| 434 | row: row no of integration, default is 0. |
---|
| 435 | insitu: if False a new scantable is returned. |
---|
| 436 | Otherwise, the scaling is done in-situ |
---|
| 437 | The default is taken from .asaprc (False) |
---|
| 438 | """ |
---|
| 439 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 440 | if not insitu: |
---|
| 441 | workscan = self.copy() |
---|
| 442 | else: |
---|
| 443 | workscan = self |
---|
| 444 | # Select a row |
---|
| 445 | sel=selector() |
---|
| 446 | sel.set_scans([workscan.getscan(row)]) |
---|
| 447 | sel.set_cycles([workscan.getcycle(row)]) |
---|
| 448 | sel.set_beams([workscan.getbeam(row)]) |
---|
| 449 | sel.set_ifs([workscan.getif(row)]) |
---|
| 450 | sel.set_polarisations([workscan.getpol(row)]) |
---|
| 451 | sel.set_name(workscan._getsourcename(row)) |
---|
| 452 | workscan.set_selection(sel) |
---|
| 453 | if not workscan.nrow() == 1: |
---|
| 454 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow()) |
---|
| 455 | raise RuntimeError(msg) |
---|
| 456 | del sel |
---|
| 457 | if insitu: |
---|
| 458 | self._assign(workscan) |
---|
| 459 | else: |
---|
| 460 | return workscan |
---|
| 461 | |
---|
[1629] | 462 | #def stats(self, stat='stddev', mask=None): |
---|
| 463 | def stats(self, stat='stddev', mask=None, form='3.3f'): |
---|
[102] | 464 | """ |
---|
[135] | 465 | Determine the specified statistic of the current beam/if/pol |
---|
[102] | 466 | Takes a 'mask' as an optional parameter to specify which |
---|
| 467 | channels should be excluded. |
---|
| 468 | Parameters: |
---|
[1517] | 469 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum', |
---|
[1515] | 470 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
[135] | 471 | mask: an optional mask specifying where the statistic |
---|
[102] | 472 | should be determined. |
---|
[1629] | 473 | form: format string to print statistic values |
---|
[102] | 474 | Example: |
---|
[113] | 475 | scan.set_unit('channel') |
---|
[1118] | 476 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 477 | scan.stats(stat='mean', mask=m) |
---|
[102] | 478 | """ |
---|
[1757] | 479 | mask = mask or [] |
---|
[876] | 480 | if not self._check_ifs(): |
---|
[1118] | 481 | raise ValueError("Cannot apply mask as the IFs have different " |
---|
| 482 | "number of channels. Please use setselection() " |
---|
| 483 | "to select individual IFs") |
---|
[1530] | 484 | rtnabc = False |
---|
| 485 | if stat.lower().endswith('_abc'): rtnabc = True |
---|
| 486 | getchan = False |
---|
| 487 | if stat.lower().startswith('min') or stat.lower().startswith('max'): |
---|
[1517] | 488 | chan = self._math._minmaxchan(self, mask, stat) |
---|
| 489 | getchan = True |
---|
[1515] | 490 | statvals = [] |
---|
[1530] | 491 | if not rtnabc: statvals = self._math._stats(self, mask, stat) |
---|
| 492 | |
---|
[1757] | 493 | #def cb(i): |
---|
| 494 | # return statvals[i] |
---|
| 495 | |
---|
| 496 | #return self._row_callback(cb, stat) |
---|
| 497 | |
---|
| 498 | label=stat |
---|
| 499 | #callback=cb |
---|
| 500 | out = "" |
---|
| 501 | #outvec = [] |
---|
| 502 | sep = '-'*50 |
---|
[876] | 503 | for i in range(self.nrow()): |
---|
[1530] | 504 | refstr = '' |
---|
| 505 | statunit= '' |
---|
[1517] | 506 | if getchan: |
---|
| 507 | qx, qy = self.chan2data(rowno=i, chan=chan[i]) |
---|
[1530] | 508 | if rtnabc: |
---|
| 509 | statvals.append(qx['value']) |
---|
[1629] | 510 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])' |
---|
[1530] | 511 | statunit= '['+qx['unit']+']' |
---|
| 512 | else: |
---|
[1629] | 513 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])' |
---|
[1757] | 514 | |
---|
| 515 | tm = self._gettime(i) |
---|
| 516 | src = self._getsourcename(i) |
---|
| 517 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
[876] | 518 | out += 'Time[%s]:\n' % (tm) |
---|
[1757] | 519 | if self.nbeam(-1) > 1: |
---|
| 520 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 521 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 522 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
| 523 | #outvec.append(callback(i)) |
---|
| 524 | #out += ('= %'+form) % (outvec[i]) +' '+refstr+'\n' |
---|
[1629] | 525 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n' |
---|
[1757] | 526 | out += sep+"\n" |
---|
[256] | 527 | |
---|
[876] | 528 | if rcParams['verbose']: |
---|
[1615] | 529 | import os |
---|
[1625] | 530 | if os.environ.has_key( 'USER' ): |
---|
| 531 | usr=os.environ['USER'] |
---|
| 532 | else: |
---|
| 533 | import commands |
---|
| 534 | usr=commands.getoutput( 'whoami' ) |
---|
[1613] | 535 | tmpfile='/tmp/tmp_'+usr+'_casapy_asap_scantable_stats' |
---|
[1612] | 536 | f=open(tmpfile,'w') |
---|
[1757] | 537 | print >> f, sep |
---|
| 538 | print >> f, ' %s %s' % (label, statunit) |
---|
| 539 | print >> f, sep |
---|
[1612] | 540 | print >> f, out |
---|
| 541 | f.close() |
---|
| 542 | f=open(tmpfile,'r') |
---|
| 543 | x=f.readlines() |
---|
| 544 | f.close() |
---|
[1757] | 545 | blanc='' |
---|
| 546 | asaplog.push(blanc.join(x), False) |
---|
| 547 | #for xx in x: |
---|
| 548 | # asaplog.push( xx, False ) |
---|
[1614] | 549 | print_log() |
---|
[1295] | 550 | return statvals |
---|
[102] | 551 | |
---|
[1517] | 552 | def chan2data(self, rowno=0, chan=0): |
---|
[1515] | 553 | """ |
---|
[1517] | 554 | Returns channel/frequency/velocity and spectral value |
---|
[1515] | 555 | at an arbitrary row and channel in the scantable. |
---|
| 556 | Parameters: |
---|
| 557 | rowno: a row number in the scantable. Default is the |
---|
| 558 | first row, i.e. rowno=0 |
---|
[1517] | 559 | chan: a channel in the scantable. Default is the first |
---|
[1515] | 560 | channel, i.e. pos=0 |
---|
| 561 | """ |
---|
[1517] | 562 | if isinstance(rowno, int) and isinstance(chan, int): |
---|
[1530] | 563 | qx = {'unit': self.get_unit(), |
---|
| 564 | 'value': self._getabcissa(rowno)[chan]} |
---|
[1517] | 565 | qy = {'unit': self.get_fluxunit(), |
---|
| 566 | 'value': self._getspectrum(rowno)[chan]} |
---|
| 567 | return qx, qy |
---|
[1515] | 568 | |
---|
[1118] | 569 | def stddev(self, mask=None): |
---|
[135] | 570 | """ |
---|
| 571 | Determine the standard deviation of the current beam/if/pol |
---|
| 572 | Takes a 'mask' as an optional parameter to specify which |
---|
| 573 | channels should be excluded. |
---|
| 574 | Parameters: |
---|
| 575 | mask: an optional mask specifying where the standard |
---|
| 576 | deviation should be determined. |
---|
| 577 | |
---|
| 578 | Example: |
---|
| 579 | scan.set_unit('channel') |
---|
[1118] | 580 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 581 | scan.stddev(mask=m) |
---|
| 582 | """ |
---|
[1118] | 583 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 584 | |
---|
[1003] | 585 | |
---|
[1259] | 586 | def get_column_names(self): |
---|
[1003] | 587 | """ |
---|
| 588 | Return a list of column names, which can be used for selection. |
---|
| 589 | """ |
---|
[1259] | 590 | return list(Scantable.get_column_names(self)) |
---|
[1003] | 591 | |
---|
[1757] | 592 | def get_tsys(self, row=-1): |
---|
[113] | 593 | """ |
---|
| 594 | Return the System temperatures. |
---|
| 595 | Returns: |
---|
[876] | 596 | a list of Tsys values for the current selection |
---|
[113] | 597 | """ |
---|
[1757] | 598 | if row > -1: |
---|
| 599 | return self._get_column(self._gettsys, row) |
---|
[876] | 600 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 601 | |
---|
[1757] | 602 | |
---|
| 603 | def get_weather(self, row=-1): |
---|
| 604 | values = self._get_column(self._get_weather, row) |
---|
| 605 | if row > -1: |
---|
| 606 | return {'temperature': values[0], |
---|
| 607 | 'pressure': values[1], 'humidity' : values[2], |
---|
| 608 | 'windspeed' : values[3], 'windaz' : values[4] |
---|
| 609 | } |
---|
| 610 | else: |
---|
| 611 | out = [] |
---|
| 612 | for r in values: |
---|
| 613 | |
---|
| 614 | out.append({'temperature': r[0], |
---|
| 615 | 'pressure': r[1], 'humidity' : r[2], |
---|
| 616 | 'windspeed' : r[3], 'windaz' : r[4] |
---|
| 617 | }) |
---|
| 618 | return out |
---|
| 619 | |
---|
[876] | 620 | def _row_callback(self, callback, label): |
---|
| 621 | out = "" |
---|
[1118] | 622 | outvec = [] |
---|
[1757] | 623 | sep = '-'*50 |
---|
[876] | 624 | for i in range(self.nrow()): |
---|
| 625 | tm = self._gettime(i) |
---|
| 626 | src = self._getsourcename(i) |
---|
[1757] | 627 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
[876] | 628 | out += 'Time[%s]:\n' % (tm) |
---|
[1757] | 629 | if self.nbeam(-1) > 1: |
---|
| 630 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 631 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 632 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
[876] | 633 | outvec.append(callback(i)) |
---|
| 634 | out += '= %3.3f\n' % (outvec[i]) |
---|
[1757] | 635 | out += sep+'\n' |
---|
[876] | 636 | if rcParams['verbose']: |
---|
[1757] | 637 | asaplog.push(sep) |
---|
[1615] | 638 | asaplog.push(" %s" % (label)) |
---|
[1757] | 639 | asaplog.push(sep) |
---|
[1615] | 640 | asaplog.push(out) |
---|
[1614] | 641 | print_log() |
---|
[1175] | 642 | return outvec |
---|
[256] | 643 | |
---|
[1070] | 644 | def _get_column(self, callback, row=-1): |
---|
| 645 | """ |
---|
| 646 | """ |
---|
| 647 | if row == -1: |
---|
| 648 | return [callback(i) for i in range(self.nrow())] |
---|
| 649 | else: |
---|
| 650 | if 0 <= row < self.nrow(): |
---|
| 651 | return callback(row) |
---|
[256] | 652 | |
---|
[1070] | 653 | |
---|
[1348] | 654 | def get_time(self, row=-1, asdatetime=False): |
---|
[113] | 655 | """ |
---|
| 656 | Get a list of time stamps for the observations. |
---|
[1348] | 657 | Return a datetime object for each integration time stamp in the scantable. |
---|
[113] | 658 | Parameters: |
---|
[1348] | 659 | row: row no of integration. Default -1 return all rows |
---|
| 660 | asdatetime: return values as datetime objects rather than strings |
---|
[113] | 661 | Example: |
---|
| 662 | none |
---|
| 663 | """ |
---|
[1175] | 664 | from time import strptime |
---|
| 665 | from datetime import datetime |
---|
[1457] | 666 | times = self._get_column(self._gettime, row) |
---|
[1348] | 667 | if not asdatetime: |
---|
[1603] | 668 | return times |
---|
[1175] | 669 | format = "%Y/%m/%d/%H:%M:%S" |
---|
| 670 | if isinstance(times, list): |
---|
| 671 | return [datetime(*strptime(i, format)[:6]) for i in times] |
---|
| 672 | else: |
---|
| 673 | return datetime(*strptime(times, format)[:6]) |
---|
[102] | 674 | |
---|
[1348] | 675 | |
---|
| 676 | def get_inttime(self, row=-1): |
---|
| 677 | """ |
---|
| 678 | Get a list of integration times for the observations. |
---|
| 679 | Return a time in seconds for each integration in the scantable. |
---|
| 680 | Parameters: |
---|
| 681 | row: row no of integration. Default -1 return all rows. |
---|
| 682 | Example: |
---|
| 683 | none |
---|
| 684 | """ |
---|
[1757] | 685 | return self._get_column(self._getinttime, row) |
---|
[1348] | 686 | |
---|
[1757] | 687 | |
---|
[714] | 688 | def get_sourcename(self, row=-1): |
---|
| 689 | """ |
---|
[794] | 690 | Get a list source names for the observations. |
---|
[714] | 691 | Return a string for each integration in the scantable. |
---|
| 692 | Parameters: |
---|
[1348] | 693 | row: row no of integration. Default -1 return all rows. |
---|
[714] | 694 | Example: |
---|
| 695 | none |
---|
| 696 | """ |
---|
[1070] | 697 | return self._get_column(self._getsourcename, row) |
---|
[714] | 698 | |
---|
[794] | 699 | def get_elevation(self, row=-1): |
---|
| 700 | """ |
---|
| 701 | Get a list of elevations for the observations. |
---|
| 702 | Return a float for each integration in the scantable. |
---|
| 703 | Parameters: |
---|
[1348] | 704 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 705 | Example: |
---|
| 706 | none |
---|
| 707 | """ |
---|
[1070] | 708 | return self._get_column(self._getelevation, row) |
---|
[794] | 709 | |
---|
| 710 | def get_azimuth(self, row=-1): |
---|
| 711 | """ |
---|
| 712 | Get a list of azimuths for the observations. |
---|
| 713 | Return a float for each integration in the scantable. |
---|
| 714 | Parameters: |
---|
[1348] | 715 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 716 | Example: |
---|
| 717 | none |
---|
| 718 | """ |
---|
[1070] | 719 | return self._get_column(self._getazimuth, row) |
---|
[794] | 720 | |
---|
| 721 | def get_parangle(self, row=-1): |
---|
| 722 | """ |
---|
| 723 | Get a list of parallactic angles for the observations. |
---|
| 724 | Return a float for each integration in the scantable. |
---|
| 725 | Parameters: |
---|
[1348] | 726 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 727 | Example: |
---|
| 728 | none |
---|
| 729 | """ |
---|
[1070] | 730 | return self._get_column(self._getparangle, row) |
---|
[794] | 731 | |
---|
[1070] | 732 | def get_direction(self, row=-1): |
---|
| 733 | """ |
---|
| 734 | Get a list of Positions on the sky (direction) for the observations. |
---|
[1757] | 735 | Return a string for each integration in the scantable. |
---|
[1070] | 736 | Parameters: |
---|
| 737 | row: row no of integration. Default -1 return all rows |
---|
| 738 | Example: |
---|
| 739 | none |
---|
| 740 | """ |
---|
| 741 | return self._get_column(self._getdirection, row) |
---|
| 742 | |
---|
[1389] | 743 | def get_directionval(self, row=-1): |
---|
| 744 | """ |
---|
| 745 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 746 | Return a float for each integration in the scantable. |
---|
| 747 | Parameters: |
---|
| 748 | row: row no of integration. Default -1 return all rows |
---|
| 749 | Example: |
---|
| 750 | none |
---|
| 751 | """ |
---|
| 752 | return self._get_column(self._getdirectionvec, row) |
---|
| 753 | |
---|
[1757] | 754 | #@print_log_dec |
---|
[102] | 755 | def set_unit(self, unit='channel'): |
---|
| 756 | """ |
---|
| 757 | Set the unit for all following operations on this scantable |
---|
| 758 | Parameters: |
---|
| 759 | unit: optional unit, default is 'channel' |
---|
[1118] | 760 | one of '*Hz', 'km/s', 'channel', '' |
---|
[102] | 761 | """ |
---|
[484] | 762 | varlist = vars() |
---|
[1118] | 763 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 764 | unit = '' |
---|
| 765 | inf = list(self._getcoordinfo()) |
---|
| 766 | inf[0] = unit |
---|
| 767 | self._setcoordinfo(inf) |
---|
[1118] | 768 | self._add_history("set_unit", varlist) |
---|
[113] | 769 | |
---|
[1757] | 770 | #@print_log_dec |
---|
[484] | 771 | def set_instrument(self, instr): |
---|
[358] | 772 | """ |
---|
[1348] | 773 | Set the instrument for subsequent processing. |
---|
[358] | 774 | Parameters: |
---|
[710] | 775 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 776 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 777 | """ |
---|
| 778 | self._setInstrument(instr) |
---|
[1118] | 779 | self._add_history("set_instument", vars()) |
---|
[718] | 780 | print_log() |
---|
[358] | 781 | |
---|
[1757] | 782 | #@print_log_dec |
---|
[1190] | 783 | def set_feedtype(self, feedtype): |
---|
| 784 | """ |
---|
| 785 | Overwrite the feed type, which might not be set correctly. |
---|
| 786 | Parameters: |
---|
| 787 | feedtype: 'linear' or 'circular' |
---|
| 788 | """ |
---|
| 789 | self._setfeedtype(feedtype) |
---|
| 790 | self._add_history("set_feedtype", vars()) |
---|
| 791 | print_log() |
---|
| 792 | |
---|
[1757] | 793 | #@print_log_dec |
---|
[276] | 794 | def set_doppler(self, doppler='RADIO'): |
---|
| 795 | """ |
---|
| 796 | Set the doppler for all following operations on this scantable. |
---|
| 797 | Parameters: |
---|
| 798 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 799 | """ |
---|
[484] | 800 | varlist = vars() |
---|
[276] | 801 | inf = list(self._getcoordinfo()) |
---|
| 802 | inf[2] = doppler |
---|
| 803 | self._setcoordinfo(inf) |
---|
[1118] | 804 | self._add_history("set_doppler", vars()) |
---|
[718] | 805 | print_log() |
---|
[710] | 806 | |
---|
[1757] | 807 | #@print_log_dec |
---|
[226] | 808 | def set_freqframe(self, frame=None): |
---|
[113] | 809 | """ |
---|
| 810 | Set the frame type of the Spectral Axis. |
---|
| 811 | Parameters: |
---|
[591] | 812 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1757] | 813 | 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
[1118] | 814 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[113] | 815 | Examples: |
---|
| 816 | scan.set_freqframe('BARY') |
---|
| 817 | """ |
---|
[1757] | 818 | frame = frame or rcParams['scantable.freqframe'] |
---|
[484] | 819 | varlist = vars() |
---|
[1757] | 820 | # "REST" is not implemented in casacore |
---|
| 821 | #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 822 | # 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
| 823 | valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
[1118] | 824 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 825 | |
---|
[989] | 826 | if frame in valid: |
---|
[113] | 827 | inf = list(self._getcoordinfo()) |
---|
| 828 | inf[1] = frame |
---|
| 829 | self._setcoordinfo(inf) |
---|
[1118] | 830 | self._add_history("set_freqframe", varlist) |
---|
[102] | 831 | else: |
---|
[1118] | 832 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[718] | 833 | if rcParams['verbose']: |
---|
[1612] | 834 | #print msg |
---|
[1614] | 835 | asaplog.push( msg ) |
---|
| 836 | print_log( 'ERROR' ) |
---|
[718] | 837 | else: |
---|
| 838 | raise TypeError(msg) |
---|
| 839 | print_log() |
---|
[710] | 840 | |
---|
[989] | 841 | def set_dirframe(self, frame=""): |
---|
| 842 | """ |
---|
| 843 | Set the frame type of the Direction on the sky. |
---|
| 844 | Parameters: |
---|
| 845 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 846 | 'J2000', 'B1950', 'GALACTIC' |
---|
| 847 | Examples: |
---|
| 848 | scan.set_dirframe('GALACTIC') |
---|
| 849 | """ |
---|
| 850 | varlist = vars() |
---|
| 851 | try: |
---|
| 852 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 853 | except RuntimeError, msg: |
---|
[989] | 854 | if rcParams['verbose']: |
---|
[1612] | 855 | #print msg |
---|
[1614] | 856 | print_log() |
---|
[1676] | 857 | asaplog.push( str(msg) ) |
---|
[1614] | 858 | print_log( 'ERROR' ) |
---|
[989] | 859 | else: |
---|
| 860 | raise |
---|
[1118] | 861 | self._add_history("set_dirframe", varlist) |
---|
[989] | 862 | |
---|
[113] | 863 | def get_unit(self): |
---|
| 864 | """ |
---|
| 865 | Get the default unit set in this scantable |
---|
| 866 | Returns: |
---|
| 867 | A unit string |
---|
| 868 | """ |
---|
| 869 | inf = self._getcoordinfo() |
---|
| 870 | unit = inf[0] |
---|
| 871 | if unit == '': unit = 'channel' |
---|
| 872 | return unit |
---|
[102] | 873 | |
---|
[158] | 874 | def get_abcissa(self, rowno=0): |
---|
[102] | 875 | """ |
---|
[158] | 876 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 877 | selected Beam/IF/Pol |
---|
| 878 | Parameters: |
---|
[226] | 879 | rowno: an optional row number in the scantable. Default is the |
---|
| 880 | first row, i.e. rowno=0 |
---|
[113] | 881 | Returns: |
---|
[1348] | 882 | The abcissa values and the format string (as a dictionary) |
---|
[113] | 883 | """ |
---|
[256] | 884 | abc = self._getabcissa(rowno) |
---|
[710] | 885 | lbl = self._getabcissalabel(rowno) |
---|
[718] | 886 | print_log() |
---|
[158] | 887 | return abc, lbl |
---|
[113] | 888 | |
---|
[1401] | 889 | def flag(self, mask=None, unflag=False): |
---|
[1001] | 890 | """ |
---|
| 891 | Flag the selected data using an optional channel mask. |
---|
| 892 | Parameters: |
---|
| 893 | mask: an optional channel mask, created with create_mask. Default |
---|
| 894 | (no mask) is all channels. |
---|
[1401] | 895 | unflag: if True, unflag the data |
---|
[1001] | 896 | """ |
---|
| 897 | varlist = vars() |
---|
[1757] | 898 | mask = mask or [] |
---|
[1001] | 899 | try: |
---|
[1401] | 900 | self._flag(mask, unflag) |
---|
[1118] | 901 | except RuntimeError, msg: |
---|
[1001] | 902 | if rcParams['verbose']: |
---|
[1612] | 903 | #print msg |
---|
[1614] | 904 | print_log() |
---|
[1676] | 905 | asaplog.push( str(msg) ) |
---|
[1614] | 906 | print_log( 'ERROR' ) |
---|
[1001] | 907 | return |
---|
| 908 | else: raise |
---|
| 909 | self._add_history("flag", varlist) |
---|
| 910 | |
---|
[1655] | 911 | def flag_row(self, rows=[], unflag=False): |
---|
| 912 | """ |
---|
| 913 | Flag the selected data in row-based manner. |
---|
| 914 | Parameters: |
---|
| 915 | rows: list of row numbers to be flagged. Default is no row (must be explicitly specified to execute row-based flagging). |
---|
| 916 | unflag: if True, unflag the data. |
---|
| 917 | """ |
---|
| 918 | varlist = vars() |
---|
| 919 | try: |
---|
| 920 | self._flag_row(rows, unflag) |
---|
| 921 | except RuntimeError, msg: |
---|
| 922 | if rcParams['verbose']: |
---|
| 923 | print_log() |
---|
[1676] | 924 | asaplog.push( str(msg) ) |
---|
[1655] | 925 | print_log('ERROR') |
---|
| 926 | return |
---|
| 927 | else: raise |
---|
| 928 | self._add_history("flag_row", varlist) |
---|
| 929 | |
---|
[1701] | 930 | def clip(self, uthres=None, dthres=None, clipoutside=True, unflag=False): |
---|
| 931 | """ |
---|
| 932 | Flag the selected data outside a specified range (in channel-base) |
---|
| 933 | Parameters: |
---|
| 934 | uthres: upper threshold. |
---|
| 935 | dthres: lower threshold |
---|
| 936 | clipoutside: True for flagging data outside the range [dthres:uthres]. |
---|
| 937 | False for glagging data inside the range. |
---|
| 938 | unflag : if True, unflag the data. |
---|
| 939 | """ |
---|
| 940 | varlist = vars() |
---|
| 941 | try: |
---|
| 942 | self._clip(uthres, dthres, clipoutside, unflag) |
---|
| 943 | except RuntimeError, msg: |
---|
| 944 | if rcParams['verbose']: |
---|
| 945 | print_log() |
---|
| 946 | asaplog.push(str(msg)) |
---|
| 947 | print_log('ERROR') |
---|
| 948 | return |
---|
| 949 | else: raise |
---|
| 950 | self._add_history("clip", varlist) |
---|
[1757] | 951 | |
---|
| 952 | #@print_log_dec |
---|
| 953 | def lag_flag(self, start, end, unit="MHz", insitu=None): |
---|
| 954 | #def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None): |
---|
[1192] | 955 | """ |
---|
| 956 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
[1757] | 957 | Flagged data in the scantable gets interpolated over the region. |
---|
[1192] | 958 | No taper is applied. |
---|
| 959 | Parameters: |
---|
[1757] | 960 | start: the start frequency (really a period within the |
---|
| 961 | bandwidth) or period to remove |
---|
| 962 | end: the end frequency or period to remove |
---|
| 963 | unit: the frequency unit (default "MHz") or "" for |
---|
| 964 | explicit lag channels |
---|
[1203] | 965 | Notes: |
---|
[1757] | 966 | It is recommended to flag edges of the band or strong |
---|
[1348] | 967 | signals beforehand. |
---|
[1192] | 968 | """ |
---|
| 969 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 970 | self._math._setinsitu(insitu) |
---|
| 971 | varlist = vars() |
---|
[1757] | 972 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.} |
---|
| 973 | if not (unit == "" or base.has_key(unit)): |
---|
[1192] | 974 | raise ValueError("%s is not a valid unit." % unit) |
---|
| 975 | try: |
---|
[1757] | 976 | if unit == "": |
---|
| 977 | s = scantable(self._math._lag_flag(self, start, end, "lags")) |
---|
| 978 | else: |
---|
| 979 | s = scantable(self._math._lag_flag(self, start*base[unit], |
---|
| 980 | end*base[unit], "frequency")) |
---|
[1192] | 981 | except RuntimeError, msg: |
---|
| 982 | if rcParams['verbose']: |
---|
[1612] | 983 | #print msg |
---|
[1614] | 984 | print_log() |
---|
[1676] | 985 | asaplog.push( str(msg) ) |
---|
[1614] | 986 | print_log( 'ERROR' ) |
---|
[1192] | 987 | return |
---|
| 988 | else: raise |
---|
| 989 | s._add_history("lag_flag", varlist) |
---|
| 990 | print_log() |
---|
| 991 | if insitu: |
---|
| 992 | self._assign(s) |
---|
| 993 | else: |
---|
| 994 | return s |
---|
[1001] | 995 | |
---|
[1757] | 996 | #@print_log_dec |
---|
[113] | 997 | def create_mask(self, *args, **kwargs): |
---|
| 998 | """ |
---|
[1118] | 999 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 1000 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 1001 | applied. |
---|
[102] | 1002 | Parameters: |
---|
[1118] | 1003 | [min, max], [min2, max2], ... |
---|
[1024] | 1004 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 1005 | to be masked |
---|
[189] | 1006 | invert: optional argument. If specified as True, |
---|
| 1007 | return an inverted mask, i.e. the regions |
---|
| 1008 | specified are EXCLUDED |
---|
[513] | 1009 | row: create the mask using the specified row for |
---|
| 1010 | unit conversions, default is row=0 |
---|
| 1011 | only necessary if frequency varies over rows. |
---|
[102] | 1012 | Example: |
---|
[113] | 1013 | scan.set_unit('channel') |
---|
| 1014 | a) |
---|
[1118] | 1015 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 1016 | # masks everything outside 400 and 500 |
---|
[113] | 1017 | # and 800 and 900 in the unit 'channel' |
---|
| 1018 | |
---|
| 1019 | b) |
---|
[1118] | 1020 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 1021 | # masks the regions between 400 and 500 |
---|
[113] | 1022 | # and 800 and 900 in the unit 'channel' |
---|
[1024] | 1023 | c) |
---|
| 1024 | mask only channel 400 |
---|
[1757] | 1025 | msk = scan.create_mask([400]) |
---|
[102] | 1026 | """ |
---|
[1757] | 1027 | row = kwargs.get("row", 0) |
---|
[513] | 1028 | data = self._getabcissa(row) |
---|
[113] | 1029 | u = self._getcoordinfo()[0] |
---|
[718] | 1030 | if rcParams['verbose']: |
---|
[113] | 1031 | if u == "": u = "channel" |
---|
[718] | 1032 | msg = "The current mask window unit is %s" % u |
---|
[1118] | 1033 | i = self._check_ifs() |
---|
| 1034 | if not i: |
---|
[876] | 1035 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 1036 | asaplog.push(msg) |
---|
[102] | 1037 | n = self.nchan() |
---|
[1295] | 1038 | msk = _n_bools(n, False) |
---|
[710] | 1039 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 1040 | |
---|
[1118] | 1041 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 1042 | and args or args[0] |
---|
[710] | 1043 | for window in ws: |
---|
[1757] | 1044 | if len(window) == 1: |
---|
| 1045 | window = [window[0], window[0]] |
---|
| 1046 | if len(window) == 0 or len(window) > 2: |
---|
| 1047 | raise ValueError("A window needs to be defined as [start(, end)]") |
---|
| 1048 | if window[0] > window[1]: |
---|
| 1049 | tmp = window[0] |
---|
| 1050 | window[0] = window[1] |
---|
| 1051 | window[1] = tmp |
---|
[102] | 1052 | for i in range(n): |
---|
[1024] | 1053 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 1054 | msk[i] = True |
---|
[113] | 1055 | if kwargs.has_key('invert'): |
---|
| 1056 | if kwargs.get('invert'): |
---|
[1295] | 1057 | msk = mask_not(msk) |
---|
[718] | 1058 | print_log() |
---|
[102] | 1059 | return msk |
---|
[710] | 1060 | |
---|
[1446] | 1061 | def get_masklist(self, mask=None, row=0): |
---|
[256] | 1062 | """ |
---|
[1446] | 1063 | Compute and return a list of mask windows, [min, max]. |
---|
| 1064 | Parameters: |
---|
| 1065 | mask: channel mask, created with create_mask. |
---|
| 1066 | row: calcutate the masklist using the specified row |
---|
| 1067 | for unit conversions, default is row=0 |
---|
| 1068 | only necessary if frequency varies over rows. |
---|
| 1069 | Returns: |
---|
| 1070 | [min, max], [min2, max2], ... |
---|
| 1071 | Pairs of start/end points (inclusive)specifying |
---|
| 1072 | the masked regions |
---|
| 1073 | """ |
---|
| 1074 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1075 | raise TypeError("The mask should be list or tuple.") |
---|
| 1076 | if len(mask) < 2: |
---|
| 1077 | raise TypeError("The mask elements should be > 1") |
---|
| 1078 | if self.nchan() != len(mask): |
---|
| 1079 | msg = "Number of channels in scantable != number of mask elements" |
---|
| 1080 | raise TypeError(msg) |
---|
| 1081 | data = self._getabcissa(row) |
---|
| 1082 | u = self._getcoordinfo()[0] |
---|
| 1083 | if rcParams['verbose']: |
---|
| 1084 | if u == "": u = "channel" |
---|
| 1085 | msg = "The current mask window unit is %s" % u |
---|
| 1086 | i = self._check_ifs() |
---|
| 1087 | if not i: |
---|
| 1088 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 1089 | asaplog.push(msg) |
---|
| 1090 | masklist=[] |
---|
| 1091 | ist, ien = None, None |
---|
| 1092 | ist, ien=self.get_mask_indices(mask) |
---|
| 1093 | if ist is not None and ien is not None: |
---|
| 1094 | for i in xrange(len(ist)): |
---|
| 1095 | range=[data[ist[i]],data[ien[i]]] |
---|
| 1096 | range.sort() |
---|
| 1097 | masklist.append([range[0],range[1]]) |
---|
| 1098 | return masklist |
---|
| 1099 | |
---|
| 1100 | def get_mask_indices(self, mask=None): |
---|
| 1101 | """ |
---|
| 1102 | Compute and Return lists of mask start indices and mask end indices. |
---|
| 1103 | Parameters: |
---|
| 1104 | mask: channel mask, created with create_mask. |
---|
| 1105 | Returns: |
---|
| 1106 | List of mask start indices and that of mask end indices, |
---|
| 1107 | i.e., [istart1,istart2,....], [iend1,iend2,....]. |
---|
| 1108 | """ |
---|
| 1109 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1110 | raise TypeError("The mask should be list or tuple.") |
---|
| 1111 | if len(mask) < 2: |
---|
| 1112 | raise TypeError("The mask elements should be > 1") |
---|
| 1113 | istart=[] |
---|
| 1114 | iend=[] |
---|
| 1115 | if mask[0]: istart.append(0) |
---|
| 1116 | for i in range(len(mask)-1): |
---|
| 1117 | if not mask[i] and mask[i+1]: |
---|
| 1118 | istart.append(i+1) |
---|
| 1119 | elif mask[i] and not mask[i+1]: |
---|
| 1120 | iend.append(i) |
---|
| 1121 | if mask[len(mask)-1]: iend.append(len(mask)-1) |
---|
| 1122 | if len(istart) != len(iend): |
---|
| 1123 | raise RuntimeError("Numbers of mask start != mask end.") |
---|
| 1124 | for i in range(len(istart)): |
---|
| 1125 | if istart[i] > iend[i]: |
---|
| 1126 | raise RuntimeError("Mask start index > mask end index") |
---|
| 1127 | break |
---|
| 1128 | return istart,iend |
---|
| 1129 | |
---|
| 1130 | # def get_restfreqs(self): |
---|
| 1131 | # """ |
---|
| 1132 | # Get the restfrequency(s) stored in this scantable. |
---|
| 1133 | # The return value(s) are always of unit 'Hz' |
---|
| 1134 | # Parameters: |
---|
| 1135 | # none |
---|
| 1136 | # Returns: |
---|
| 1137 | # a list of doubles |
---|
| 1138 | # """ |
---|
| 1139 | # return list(self._getrestfreqs()) |
---|
| 1140 | |
---|
| 1141 | def get_restfreqs(self, ids=None): |
---|
| 1142 | """ |
---|
[256] | 1143 | Get the restfrequency(s) stored in this scantable. |
---|
| 1144 | The return value(s) are always of unit 'Hz' |
---|
| 1145 | Parameters: |
---|
[1446] | 1146 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to |
---|
| 1147 | be retrieved |
---|
[256] | 1148 | Returns: |
---|
[1446] | 1149 | dictionary containing ids and a list of doubles for each id |
---|
[256] | 1150 | """ |
---|
[1446] | 1151 | if ids is None: |
---|
| 1152 | rfreqs={} |
---|
| 1153 | idlist = self.getmolnos() |
---|
| 1154 | for i in idlist: |
---|
| 1155 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1156 | return rfreqs |
---|
| 1157 | else: |
---|
| 1158 | if type(ids)==list or type(ids)==tuple: |
---|
| 1159 | rfreqs={} |
---|
| 1160 | for i in ids: |
---|
| 1161 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1162 | return rfreqs |
---|
| 1163 | else: |
---|
| 1164 | return list(self._getrestfreqs(ids)) |
---|
| 1165 | #return list(self._getrestfreqs(ids)) |
---|
[102] | 1166 | |
---|
[931] | 1167 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
| 1168 | """ |
---|
[1446] | 1169 | ********NEED TO BE UPDATED begin************ |
---|
[931] | 1170 | Set or replace the restfrequency specified and |
---|
| 1171 | If the 'freqs' argument holds a scalar, |
---|
| 1172 | then that rest frequency will be applied to all the selected |
---|
| 1173 | data. If the 'freqs' argument holds |
---|
| 1174 | a vector, then it MUST be of equal or smaller length than |
---|
| 1175 | the number of IFs (and the available restfrequencies will be |
---|
| 1176 | replaced by this vector). In this case, *all* data have |
---|
| 1177 | the restfrequency set per IF according |
---|
| 1178 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 1179 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 1180 | IF 1 gets restfreq 2e9. |
---|
[1446] | 1181 | ********NEED TO BE UPDATED end************ |
---|
[1603] | 1182 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 1183 | |
---|
[931] | 1184 | Parameters: |
---|
| 1185 | freqs: list of rest frequency values or string idenitfiers |
---|
| 1186 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 1187 | |
---|
[931] | 1188 | Example: |
---|
[1446] | 1189 | # set the given restfrequency for the all currently selected IFs |
---|
[931] | 1190 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1446] | 1191 | # set multiple restfrequencies to all the selected data |
---|
| 1192 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9]) |
---|
| 1193 | # If the number of IFs in the data is >= 2 the IF0 gets the first |
---|
| 1194 | # value IF1 the second... NOTE that freqs needs to be |
---|
| 1195 | # specified in list of list (e.g. [[],[],...] ). |
---|
| 1196 | scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]]) |
---|
[931] | 1197 | #set the given restfrequency for the whole table (by name) |
---|
| 1198 | scan.set_restfreqs(freqs="OH1667") |
---|
[391] | 1199 | |
---|
[931] | 1200 | Note: |
---|
| 1201 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 1202 | source and IF basis, use scantable.set_selection() before using |
---|
| 1203 | this function. |
---|
[1757] | 1204 | # provide your scantable is called scan |
---|
[931] | 1205 | selection = selector() |
---|
| 1206 | selection.set_name("ORION*") |
---|
| 1207 | selection.set_ifs([1]) |
---|
| 1208 | scan.set_selection(selection) |
---|
| 1209 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 1210 | |
---|
| 1211 | """ |
---|
| 1212 | varlist = vars() |
---|
[1157] | 1213 | from asap import linecatalog |
---|
| 1214 | # simple value |
---|
[1118] | 1215 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1446] | 1216 | # TT mod |
---|
| 1217 | #self._setrestfreqs(freqs, "",unit) |
---|
| 1218 | self._setrestfreqs([freqs], [""],unit) |
---|
[1157] | 1219 | # list of values |
---|
[1118] | 1220 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 1221 | # list values are scalars |
---|
[1118] | 1222 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[1446] | 1223 | self._setrestfreqs(freqs, [""],unit) |
---|
[1157] | 1224 | # list values are tuples, (value, name) |
---|
| 1225 | elif isinstance(freqs[-1], dict): |
---|
[1446] | 1226 | #sel = selector() |
---|
| 1227 | #savesel = self._getselection() |
---|
| 1228 | #iflist = self.getifnos() |
---|
| 1229 | #for i in xrange(len(freqs)): |
---|
| 1230 | # sel.set_ifs(iflist[i]) |
---|
| 1231 | # self._setselection(sel) |
---|
| 1232 | # self._setrestfreqs(freqs[i], "",unit) |
---|
| 1233 | #self._setselection(savesel) |
---|
| 1234 | self._setrestfreqs(freqs["value"], |
---|
| 1235 | freqs["name"], "MHz") |
---|
| 1236 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple): |
---|
[1157] | 1237 | sel = selector() |
---|
| 1238 | savesel = self._getselection() |
---|
[1322] | 1239 | iflist = self.getifnos() |
---|
[1446] | 1240 | if len(freqs)>len(iflist): |
---|
| 1241 | raise ValueError("number of elements in list of list exeeds the current IF selections") |
---|
[1157] | 1242 | for i in xrange(len(freqs)): |
---|
[1322] | 1243 | sel.set_ifs(iflist[i]) |
---|
[1259] | 1244 | self._setselection(sel) |
---|
[1157] | 1245 | self._setrestfreqs(freqs[i]["value"], |
---|
| 1246 | freqs[i]["name"], "MHz") |
---|
| 1247 | self._setselection(savesel) |
---|
| 1248 | # freqs are to be taken from a linecatalog |
---|
[1153] | 1249 | elif isinstance(freqs, linecatalog): |
---|
| 1250 | sel = selector() |
---|
| 1251 | savesel = self._getselection() |
---|
| 1252 | for i in xrange(freqs.nrow()): |
---|
[1322] | 1253 | sel.set_ifs(iflist[i]) |
---|
[1153] | 1254 | self._setselection(sel) |
---|
| 1255 | self._setrestfreqs(freqs.get_frequency(i), |
---|
| 1256 | freqs.get_name(i), "MHz") |
---|
| 1257 | # ensure that we are not iterating past nIF |
---|
| 1258 | if i == self.nif()-1: break |
---|
| 1259 | self._setselection(savesel) |
---|
[931] | 1260 | else: |
---|
| 1261 | return |
---|
| 1262 | self._add_history("set_restfreqs", varlist) |
---|
| 1263 | |
---|
[1360] | 1264 | def shift_refpix(self, delta): |
---|
[1757] | 1265 | """ |
---|
| 1266 | Shift the reference pixel of the Spectra Coordinate by an |
---|
| 1267 | integer amount. |
---|
| 1268 | Parameters: |
---|
| 1269 | delta: the amount to shift by |
---|
[1360] | 1270 | Note: |
---|
[1757] | 1271 | Be careful using this with broadband data. |
---|
[1360] | 1272 | """ |
---|
[1757] | 1273 | Scantable.shift_refpix(self, delta) |
---|
[931] | 1274 | |
---|
[1259] | 1275 | def history(self, filename=None): |
---|
| 1276 | """ |
---|
| 1277 | Print the history. Optionally to a file. |
---|
[1348] | 1278 | Parameters: |
---|
| 1279 | filename: The name of the file to save the history to. |
---|
[1259] | 1280 | """ |
---|
[484] | 1281 | hist = list(self._gethistory()) |
---|
[794] | 1282 | out = "-"*80 |
---|
[484] | 1283 | for h in hist: |
---|
[489] | 1284 | if h.startswith("---"): |
---|
[794] | 1285 | out += "\n"+h |
---|
[489] | 1286 | else: |
---|
| 1287 | items = h.split("##") |
---|
| 1288 | date = items[0] |
---|
| 1289 | func = items[1] |
---|
| 1290 | items = items[2:] |
---|
[794] | 1291 | out += "\n"+date+"\n" |
---|
| 1292 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 1293 | for i in items: |
---|
| 1294 | s = i.split("=") |
---|
[1118] | 1295 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[794] | 1296 | out += "\n"+"-"*80 |
---|
[1259] | 1297 | if filename is not None: |
---|
| 1298 | if filename is "": |
---|
| 1299 | filename = 'scantable_history.txt' |
---|
| 1300 | import os |
---|
| 1301 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 1302 | if not os.path.isdir(filename): |
---|
| 1303 | data = open(filename, 'w') |
---|
| 1304 | data.write(out) |
---|
| 1305 | data.close() |
---|
| 1306 | else: |
---|
| 1307 | msg = "Illegal file name '%s'." % (filename) |
---|
| 1308 | if rcParams['verbose']: |
---|
[1612] | 1309 | #print msg |
---|
[1614] | 1310 | asaplog.push( msg ) |
---|
| 1311 | print_log( 'ERROR' ) |
---|
[1259] | 1312 | else: |
---|
| 1313 | raise IOError(msg) |
---|
| 1314 | if rcParams['verbose']: |
---|
| 1315 | try: |
---|
| 1316 | from IPython.genutils import page as pager |
---|
| 1317 | except ImportError: |
---|
| 1318 | from pydoc import pager |
---|
| 1319 | pager(out) |
---|
| 1320 | else: |
---|
| 1321 | return out |
---|
[484] | 1322 | return |
---|
[513] | 1323 | # |
---|
| 1324 | # Maths business |
---|
| 1325 | # |
---|
[1757] | 1326 | #@print_log_dec |
---|
[931] | 1327 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[513] | 1328 | """ |
---|
[1070] | 1329 | Return the (time) weighted average of a scan. |
---|
[513] | 1330 | Note: |
---|
[1070] | 1331 | in channels only - align if necessary |
---|
[513] | 1332 | Parameters: |
---|
| 1333 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 1334 | weighting) |
---|
[558] | 1335 | scanav: True averages each scan separately |
---|
| 1336 | False (default) averages all scans together, |
---|
[1099] | 1337 | weight: Weighting scheme. |
---|
| 1338 | 'none' (mean no weight) |
---|
| 1339 | 'var' (1/var(spec) weighted) |
---|
| 1340 | 'tsys' (1/Tsys**2 weighted) |
---|
| 1341 | 'tint' (integration time weighted) |
---|
| 1342 | 'tintsys' (Tint/Tsys**2) |
---|
| 1343 | 'median' ( median averaging) |
---|
[535] | 1344 | The default is 'tint' |
---|
[931] | 1345 | align: align the spectra in velocity before averaging. It takes |
---|
| 1346 | the time of the first spectrum as reference time. |
---|
[513] | 1347 | Example: |
---|
| 1348 | # time average the scantable without using a mask |
---|
[710] | 1349 | newscan = scan.average_time() |
---|
[513] | 1350 | """ |
---|
| 1351 | varlist = vars() |
---|
[1757] | 1352 | weight = weight or 'TINT' |
---|
| 1353 | mask = mask or () |
---|
| 1354 | scanav = (scanav and 'SCAN') or 'NONE' |
---|
[1118] | 1355 | scan = (self, ) |
---|
[989] | 1356 | try: |
---|
[1118] | 1357 | if align: |
---|
| 1358 | scan = (self.freq_align(insitu=False), ) |
---|
| 1359 | s = None |
---|
| 1360 | if weight.upper() == 'MEDIAN': |
---|
| 1361 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 1362 | scanav)) |
---|
| 1363 | else: |
---|
| 1364 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 1365 | scanav)) |
---|
| 1366 | except RuntimeError, msg: |
---|
[989] | 1367 | if rcParams['verbose']: |
---|
[1612] | 1368 | #print msg |
---|
[1614] | 1369 | print_log() |
---|
[1676] | 1370 | asaplog.push( str(msg) ) |
---|
[1614] | 1371 | print_log( 'ERROR' ) |
---|
[989] | 1372 | return |
---|
| 1373 | else: raise |
---|
[1099] | 1374 | s._add_history("average_time", varlist) |
---|
[718] | 1375 | print_log() |
---|
[513] | 1376 | return s |
---|
[710] | 1377 | |
---|
[1757] | 1378 | #@print_log_dec |
---|
[876] | 1379 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[513] | 1380 | """ |
---|
| 1381 | Return a scan where all spectra are converted to either |
---|
| 1382 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 1383 | By default the function tries to look the values up internally. |
---|
| 1384 | If it can't find them (or if you want to over-ride), you must |
---|
| 1385 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 1386 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 1387 | Parameters: |
---|
| 1388 | jyperk: the Jy / K conversion factor |
---|
| 1389 | eta: the aperture efficiency |
---|
| 1390 | d: the geomtric diameter (metres) |
---|
| 1391 | insitu: if False a new scantable is returned. |
---|
| 1392 | Otherwise, the scaling is done in-situ |
---|
| 1393 | The default is taken from .asaprc (False) |
---|
| 1394 | """ |
---|
| 1395 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1396 | self._math._setinsitu(insitu) |
---|
[513] | 1397 | varlist = vars() |
---|
[1757] | 1398 | jyperk = jyperk or -1.0 |
---|
| 1399 | d = d or -1.0 |
---|
| 1400 | eta = eta or -1.0 |
---|
[876] | 1401 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 1402 | s._add_history("convert_flux", varlist) |
---|
| 1403 | print_log() |
---|
| 1404 | if insitu: self._assign(s) |
---|
| 1405 | else: return s |
---|
[513] | 1406 | |
---|
[1757] | 1407 | #@print_log_dec |
---|
[876] | 1408 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[513] | 1409 | """ |
---|
| 1410 | Return a scan after applying a gain-elevation correction. |
---|
| 1411 | The correction can be made via either a polynomial or a |
---|
| 1412 | table-based interpolation (and extrapolation if necessary). |
---|
| 1413 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 1414 | If you specify neither, then a polynomial correction will be made |
---|
| 1415 | with built in coefficients known for certain telescopes (an error |
---|
| 1416 | will occur if the instrument is not known). |
---|
| 1417 | The data and Tsys are *divided* by the scaling factors. |
---|
| 1418 | Parameters: |
---|
| 1419 | poly: Polynomial coefficients (default None) to compute a |
---|
| 1420 | gain-elevation correction as a function of |
---|
| 1421 | elevation (in degrees). |
---|
| 1422 | filename: The name of an ascii file holding correction factors. |
---|
| 1423 | The first row of the ascii file must give the column |
---|
| 1424 | names and these MUST include columns |
---|
| 1425 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 1426 | by this) somewhere. |
---|
| 1427 | The second row must give the data type of the |
---|
| 1428 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 1429 | An example file would be |
---|
| 1430 | (actual factors are arbitrary) : |
---|
| 1431 | |
---|
| 1432 | TIME ELEVATION FACTOR |
---|
| 1433 | R R R |
---|
| 1434 | 0.1 0 0.8 |
---|
| 1435 | 0.2 20 0.85 |
---|
| 1436 | 0.3 40 0.9 |
---|
| 1437 | 0.4 60 0.85 |
---|
| 1438 | 0.5 80 0.8 |
---|
| 1439 | 0.6 90 0.75 |
---|
| 1440 | method: Interpolation method when correcting from a table. |
---|
| 1441 | Values are "nearest", "linear" (default), "cubic" |
---|
| 1442 | and "spline" |
---|
| 1443 | insitu: if False a new scantable is returned. |
---|
| 1444 | Otherwise, the scaling is done in-situ |
---|
| 1445 | The default is taken from .asaprc (False) |
---|
| 1446 | """ |
---|
| 1447 | |
---|
| 1448 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1449 | self._math._setinsitu(insitu) |
---|
[513] | 1450 | varlist = vars() |
---|
[1757] | 1451 | poly = poly or () |
---|
[513] | 1452 | from os.path import expandvars |
---|
| 1453 | filename = expandvars(filename) |
---|
[876] | 1454 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 1455 | s._add_history("gain_el", varlist) |
---|
| 1456 | print_log() |
---|
[1757] | 1457 | if insitu: |
---|
| 1458 | self._assign(s) |
---|
| 1459 | else: |
---|
| 1460 | return s |
---|
[710] | 1461 | |
---|
[1757] | 1462 | #@print_log_dec |
---|
[931] | 1463 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[513] | 1464 | """ |
---|
| 1465 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 1466 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 1467 | set_freqframe. |
---|
| 1468 | Parameters: |
---|
| 1469 | reftime: reference time to align at. By default, the time of |
---|
| 1470 | the first row of data is used. |
---|
| 1471 | method: Interpolation method for regridding the spectra. |
---|
| 1472 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 1473 | and "spline" |
---|
| 1474 | insitu: if False a new scantable is returned. |
---|
| 1475 | Otherwise, the scaling is done in-situ |
---|
| 1476 | The default is taken from .asaprc (False) |
---|
| 1477 | """ |
---|
[931] | 1478 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 1479 | self._math._setinsitu(insitu) |
---|
[513] | 1480 | varlist = vars() |
---|
[1757] | 1481 | reftime = reftime or "" |
---|
[931] | 1482 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 1483 | s._add_history("freq_align", varlist) |
---|
| 1484 | print_log() |
---|
| 1485 | if insitu: self._assign(s) |
---|
| 1486 | else: return s |
---|
[513] | 1487 | |
---|
[1757] | 1488 | #@print_log_dec |
---|
| 1489 | def opacity(self, tau=None, insitu=None): |
---|
[513] | 1490 | """ |
---|
| 1491 | Apply an opacity correction. The data |
---|
| 1492 | and Tsys are multiplied by the correction factor. |
---|
| 1493 | Parameters: |
---|
[1757] | 1494 | tau: (list of) opacity from which the correction factor is |
---|
[513] | 1495 | exp(tau*ZD) |
---|
[1757] | 1496 | where ZD is the zenith-distance. |
---|
| 1497 | If a list is provided, it has to be of length nIF, |
---|
| 1498 | nIF*nPol or 1 and in order of IF/POL, e.g. |
---|
| 1499 | [opif0pol0, opif0pol1, opif1pol0 ...] |
---|
| 1500 | if tau is `None` the opacities are determined from a |
---|
| 1501 | model. |
---|
[513] | 1502 | insitu: if False a new scantable is returned. |
---|
| 1503 | Otherwise, the scaling is done in-situ |
---|
| 1504 | The default is taken from .asaprc (False) |
---|
| 1505 | """ |
---|
| 1506 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1507 | self._math._setinsitu(insitu) |
---|
[513] | 1508 | varlist = vars() |
---|
[1757] | 1509 | if not hasattr(tau, "__len__"): |
---|
| 1510 | tau = [tau] |
---|
[876] | 1511 | s = scantable(self._math._opacity(self, tau)) |
---|
| 1512 | s._add_history("opacity", varlist) |
---|
| 1513 | print_log() |
---|
| 1514 | if insitu: self._assign(s) |
---|
| 1515 | else: return s |
---|
[513] | 1516 | |
---|
[1757] | 1517 | #@print_log_dec |
---|
[513] | 1518 | def bin(self, width=5, insitu=None): |
---|
| 1519 | """ |
---|
| 1520 | Return a scan where all spectra have been binned up. |
---|
[1348] | 1521 | Parameters: |
---|
[513] | 1522 | width: The bin width (default=5) in pixels |
---|
| 1523 | insitu: if False a new scantable is returned. |
---|
| 1524 | Otherwise, the scaling is done in-situ |
---|
| 1525 | The default is taken from .asaprc (False) |
---|
| 1526 | """ |
---|
| 1527 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1528 | self._math._setinsitu(insitu) |
---|
[513] | 1529 | varlist = vars() |
---|
[876] | 1530 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1531 | s._add_history("bin", varlist) |
---|
[876] | 1532 | print_log() |
---|
[1757] | 1533 | if insitu: |
---|
| 1534 | self._assign(s) |
---|
| 1535 | else: |
---|
| 1536 | return s |
---|
[513] | 1537 | |
---|
[1757] | 1538 | #@print_log_dec |
---|
[513] | 1539 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 1540 | """ |
---|
[1348] | 1541 | Return a scan where all spectra have been binned up. |
---|
| 1542 | |
---|
| 1543 | Parameters: |
---|
[513] | 1544 | width: The bin width (default=5) in pixels |
---|
| 1545 | method: Interpolation method when correcting from a table. |
---|
| 1546 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1547 | and "spline" |
---|
| 1548 | insitu: if False a new scantable is returned. |
---|
| 1549 | Otherwise, the scaling is done in-situ |
---|
| 1550 | The default is taken from .asaprc (False) |
---|
| 1551 | """ |
---|
| 1552 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1553 | self._math._setinsitu(insitu) |
---|
[513] | 1554 | varlist = vars() |
---|
[876] | 1555 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1556 | s._add_history("resample", varlist) |
---|
[876] | 1557 | print_log() |
---|
| 1558 | if insitu: self._assign(s) |
---|
| 1559 | else: return s |
---|
[513] | 1560 | |
---|
[1757] | 1561 | #@print_log_dec |
---|
[946] | 1562 | def average_pol(self, mask=None, weight='none'): |
---|
| 1563 | """ |
---|
| 1564 | Average the Polarisations together. |
---|
| 1565 | Parameters: |
---|
| 1566 | mask: An optional mask defining the region, where the |
---|
| 1567 | averaging will be applied. The output will have all |
---|
| 1568 | specified points masked. |
---|
| 1569 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1570 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1571 | """ |
---|
| 1572 | varlist = vars() |
---|
[1757] | 1573 | mask = mask or () |
---|
[1010] | 1574 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1575 | s._add_history("average_pol", varlist) |
---|
[946] | 1576 | print_log() |
---|
[992] | 1577 | return s |
---|
[513] | 1578 | |
---|
[1757] | 1579 | #@print_log_dec |
---|
[1145] | 1580 | def average_beam(self, mask=None, weight='none'): |
---|
| 1581 | """ |
---|
| 1582 | Average the Beams together. |
---|
| 1583 | Parameters: |
---|
| 1584 | mask: An optional mask defining the region, where the |
---|
| 1585 | averaging will be applied. The output will have all |
---|
| 1586 | specified points masked. |
---|
| 1587 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1588 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1589 | """ |
---|
| 1590 | varlist = vars() |
---|
[1757] | 1591 | mask = mask or () |
---|
[1145] | 1592 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1593 | s._add_history("average_beam", varlist) |
---|
| 1594 | print_log() |
---|
| 1595 | return s |
---|
| 1596 | |
---|
[1757] | 1597 | def parallactify(self, pflag): |
---|
| 1598 | """ |
---|
| 1599 | Set a flag to inidcate whether this data should be treated as having |
---|
| 1600 | been 'parallactified' (total phase == 0.0) |
---|
| 1601 | Parameters: |
---|
| 1602 | pflag: Bool inidcating whether to turn this on (True) or |
---|
| 1603 | off (False) |
---|
| 1604 | """ |
---|
| 1605 | varlist = vars() |
---|
| 1606 | self._parallactify(pflag) |
---|
| 1607 | self._add_history("parallactify", varlist) |
---|
| 1608 | |
---|
| 1609 | #@print_log_dec |
---|
[992] | 1610 | def convert_pol(self, poltype=None): |
---|
| 1611 | """ |
---|
| 1612 | Convert the data to a different polarisation type. |
---|
[1757] | 1613 | Note that you will need cross-polarisation terms for most conversions. |
---|
[992] | 1614 | Parameters: |
---|
| 1615 | poltype: The new polarisation type. Valid types are: |
---|
[1757] | 1616 | "linear", "circular", "stokes" and "linpol" |
---|
[992] | 1617 | """ |
---|
| 1618 | varlist = vars() |
---|
| 1619 | try: |
---|
| 1620 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1621 | except RuntimeError, msg: |
---|
[992] | 1622 | if rcParams['verbose']: |
---|
[1612] | 1623 | #print msg |
---|
[1614] | 1624 | print_log() |
---|
[1676] | 1625 | asaplog.push( str(msg) ) |
---|
[1614] | 1626 | print_log( 'ERROR' ) |
---|
[1118] | 1627 | return |
---|
[992] | 1628 | else: |
---|
| 1629 | raise |
---|
[1118] | 1630 | s._add_history("convert_pol", varlist) |
---|
[992] | 1631 | print_log() |
---|
| 1632 | return s |
---|
| 1633 | |
---|
[1757] | 1634 | #@print_log_dec |
---|
| 1635 | def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, insitu=None): |
---|
[513] | 1636 | """ |
---|
| 1637 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 1638 | Parameters: |
---|
| 1639 | kernel: The type of smoothing kernel. Select from |
---|
[1757] | 1640 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian' |
---|
| 1641 | or 'poly' |
---|
[513] | 1642 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1643 | ignored otherwise it defauls to 5 pixels. |
---|
| 1644 | For 'gaussian' it is the Full Width Half |
---|
| 1645 | Maximum. For 'boxcar' it is the full width. |
---|
[1757] | 1646 | For 'rmedian' and 'poly' it is the half width. |
---|
| 1647 | order: Optional parameter for 'poly' kernel (default is 2), to |
---|
| 1648 | specify the order of the polnomial. Ignored by all other |
---|
| 1649 | kernels. |
---|
[1653] | 1650 | plot: plot the original and the smoothed spectra. |
---|
| 1651 | In this each indivual fit has to be approved, by |
---|
| 1652 | typing 'y' or 'n' |
---|
[513] | 1653 | insitu: if False a new scantable is returned. |
---|
| 1654 | Otherwise, the scaling is done in-situ |
---|
| 1655 | The default is taken from .asaprc (False) |
---|
| 1656 | Example: |
---|
| 1657 | none |
---|
| 1658 | """ |
---|
| 1659 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1660 | self._math._setinsitu(insitu) |
---|
[513] | 1661 | varlist = vars() |
---|
[1653] | 1662 | |
---|
| 1663 | if plot: orgscan = self.copy() |
---|
| 1664 | |
---|
[1757] | 1665 | s = scantable(self._math._smooth(self, kernel.lower(), width, order)) |
---|
[876] | 1666 | s._add_history("smooth", varlist) |
---|
[1653] | 1667 | |
---|
| 1668 | if plot: |
---|
| 1669 | if rcParams['plotter.gui']: |
---|
| 1670 | from asap.asaplotgui import asaplotgui as asaplot |
---|
| 1671 | else: |
---|
| 1672 | from asap.asaplot import asaplot |
---|
| 1673 | self._p=asaplot() |
---|
| 1674 | self._p.set_panels() |
---|
| 1675 | ylab=s._get_ordinate_label() |
---|
| 1676 | #self._p.palette(0,["#777777","red"]) |
---|
| 1677 | for r in xrange(s.nrow()): |
---|
| 1678 | xsm=s._getabcissa(r) |
---|
| 1679 | ysm=s._getspectrum(r) |
---|
| 1680 | xorg=orgscan._getabcissa(r) |
---|
| 1681 | yorg=orgscan._getspectrum(r) |
---|
| 1682 | self._p.clear() |
---|
| 1683 | self._p.hold() |
---|
| 1684 | self._p.set_axes('ylabel',ylab) |
---|
| 1685 | self._p.set_axes('xlabel',s._getabcissalabel(r)) |
---|
| 1686 | self._p.set_axes('title',s._getsourcename(r)) |
---|
| 1687 | self._p.set_line(label='Original',color="#777777") |
---|
| 1688 | self._p.plot(xorg,yorg) |
---|
| 1689 | self._p.set_line(label='Smoothed',color="red") |
---|
| 1690 | self._p.plot(xsm,ysm) |
---|
| 1691 | ### Ugly part for legend |
---|
| 1692 | for i in [0,1]: |
---|
| 1693 | self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]]) |
---|
| 1694 | self._p.release() |
---|
| 1695 | ### Ugly part for legend |
---|
| 1696 | self._p.subplots[0]['lines']=[] |
---|
| 1697 | res = raw_input("Accept smoothing ([y]/n): ") |
---|
| 1698 | if res.upper() == 'N': |
---|
| 1699 | s._setspectrum(yorg, r) |
---|
| 1700 | self._p.unmap() |
---|
| 1701 | self._p = None |
---|
| 1702 | del orgscan |
---|
| 1703 | |
---|
[876] | 1704 | print_log() |
---|
| 1705 | if insitu: self._assign(s) |
---|
| 1706 | else: return s |
---|
[513] | 1707 | |
---|
[1757] | 1708 | #@print_log_dec |
---|
| 1709 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, |
---|
| 1710 | insitu=None): |
---|
[513] | 1711 | """ |
---|
| 1712 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1713 | Parameters: |
---|
[794] | 1714 | mask: an optional mask |
---|
| 1715 | order: the order of the polynomial (default is 0) |
---|
[1061] | 1716 | plot: plot the fit and the residual. In this each |
---|
| 1717 | indivual fit has to be approved, by typing 'y' |
---|
| 1718 | or 'n' |
---|
[1389] | 1719 | uselin: use linear polynomial fit |
---|
[794] | 1720 | insitu: if False a new scantable is returned. |
---|
| 1721 | Otherwise, the scaling is done in-situ |
---|
| 1722 | The default is taken from .asaprc (False) |
---|
[513] | 1723 | Example: |
---|
| 1724 | # return a scan baselined by a third order polynomial, |
---|
| 1725 | # not using a mask |
---|
| 1726 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1727 | """ |
---|
[513] | 1728 | if insitu is None: insitu = rcParams['insitu'] |
---|
[1649] | 1729 | if not insitu: |
---|
| 1730 | workscan = self.copy() |
---|
| 1731 | else: |
---|
| 1732 | workscan = self |
---|
[513] | 1733 | varlist = vars() |
---|
| 1734 | if mask is None: |
---|
[1295] | 1735 | mask = [True for i in xrange(self.nchan(-1))] |
---|
[1637] | 1736 | |
---|
[513] | 1737 | from asap.asapfitter import fitter |
---|
[1217] | 1738 | try: |
---|
| 1739 | f = fitter() |
---|
[1389] | 1740 | if uselin: |
---|
| 1741 | f.set_function(lpoly=order) |
---|
| 1742 | else: |
---|
| 1743 | f.set_function(poly=order) |
---|
[1637] | 1744 | |
---|
[1655] | 1745 | rows = range(workscan.nrow()) |
---|
[1637] | 1746 | if len(rows) > 0: |
---|
| 1747 | self.blpars = [] |
---|
| 1748 | |
---|
| 1749 | for r in rows: |
---|
| 1750 | # take into account flagtra info (CAS-1434) |
---|
[1655] | 1751 | flagtra = workscan._getmask(r) |
---|
[1637] | 1752 | actualmask = mask[:] |
---|
| 1753 | if len(actualmask) == 0: |
---|
| 1754 | actualmask = list(flagtra[:]) |
---|
| 1755 | else: |
---|
| 1756 | if len(actualmask) != len(flagtra): |
---|
| 1757 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 1758 | else: |
---|
| 1759 | for i in range(0, len(actualmask)): |
---|
| 1760 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
[1655] | 1761 | f.set_scan(workscan, actualmask) |
---|
| 1762 | f.x = workscan._getabcissa(r) |
---|
| 1763 | f.y = workscan._getspectrum(r) |
---|
[1637] | 1764 | f.data = None |
---|
| 1765 | f.fit() |
---|
[1653] | 1766 | if plot: |
---|
| 1767 | f.plot(residual=True) |
---|
| 1768 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1769 | if x.upper() == 'N': |
---|
| 1770 | self.blpars.append(None) |
---|
| 1771 | continue |
---|
[1649] | 1772 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1655] | 1773 | self.blpars.append(f.get_parameters()) |
---|
| 1774 | |
---|
[1653] | 1775 | if plot: |
---|
| 1776 | f._p.unmap() |
---|
| 1777 | f._p = None |
---|
[1649] | 1778 | workscan._add_history("poly_baseline", varlist) |
---|
[1217] | 1779 | print_log() |
---|
[1649] | 1780 | if insitu: self._assign(workscan) |
---|
| 1781 | else: return workscan |
---|
[1217] | 1782 | except RuntimeError: |
---|
| 1783 | msg = "The fit failed, possibly because it didn't converge." |
---|
| 1784 | if rcParams['verbose']: |
---|
[1612] | 1785 | #print msg |
---|
[1614] | 1786 | print_log() |
---|
[1676] | 1787 | asaplog.push( str(msg) ) |
---|
[1614] | 1788 | print_log( 'ERROR' ) |
---|
[1217] | 1789 | return |
---|
| 1790 | else: |
---|
| 1791 | raise RuntimeError(msg) |
---|
[513] | 1792 | |
---|
[1217] | 1793 | |
---|
[1118] | 1794 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
[1280] | 1795 | threshold=3, chan_avg_limit=1, plot=False, |
---|
| 1796 | insitu=None): |
---|
[880] | 1797 | """ |
---|
| 1798 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1799 | Spectral lines are detected first using linefinder and masked out |
---|
| 1800 | to avoid them affecting the baseline solution. |
---|
| 1801 | |
---|
| 1802 | Parameters: |
---|
| 1803 | mask: an optional mask retreived from scantable |
---|
| 1804 | edge: an optional number of channel to drop at |
---|
| 1805 | the edge of spectrum. If only one value is |
---|
| 1806 | specified, the same number will be dropped from |
---|
| 1807 | both sides of the spectrum. Default is to keep |
---|
[907] | 1808 | all channels. Nested tuples represent individual |
---|
[976] | 1809 | edge selection for different IFs (a number of spectral |
---|
| 1810 | channels can be different) |
---|
[880] | 1811 | order: the order of the polynomial (default is 0) |
---|
| 1812 | threshold: the threshold used by line finder. It is better to |
---|
| 1813 | keep it large as only strong lines affect the |
---|
| 1814 | baseline solution. |
---|
[1280] | 1815 | chan_avg_limit: |
---|
| 1816 | a maximum number of consequtive spectral channels to |
---|
| 1817 | average during the search of weak and broad lines. |
---|
| 1818 | The default is no averaging (and no search for weak |
---|
| 1819 | lines). If such lines can affect the fitted baseline |
---|
| 1820 | (e.g. a high order polynomial is fitted), increase this |
---|
| 1821 | parameter (usually values up to 8 are reasonable). Most |
---|
| 1822 | users of this method should find the default value |
---|
| 1823 | sufficient. |
---|
[1061] | 1824 | plot: plot the fit and the residual. In this each |
---|
| 1825 | indivual fit has to be approved, by typing 'y' |
---|
| 1826 | or 'n' |
---|
[880] | 1827 | insitu: if False a new scantable is returned. |
---|
| 1828 | Otherwise, the scaling is done in-situ |
---|
| 1829 | The default is taken from .asaprc (False) |
---|
| 1830 | |
---|
| 1831 | Example: |
---|
| 1832 | scan2=scan.auto_poly_baseline(order=7) |
---|
| 1833 | """ |
---|
| 1834 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1835 | varlist = vars() |
---|
| 1836 | from asap.asapfitter import fitter |
---|
| 1837 | from asap.asaplinefind import linefinder |
---|
| 1838 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1839 | |
---|
[976] | 1840 | # check whether edge is set up for each IF individually |
---|
[1118] | 1841 | individualedge = False; |
---|
| 1842 | if len(edge) > 1: |
---|
| 1843 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 1844 | individualedge = True; |
---|
[907] | 1845 | |
---|
[1118] | 1846 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 1847 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1848 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1849 | to make individual selection for different IFs." |
---|
[919] | 1850 | |
---|
[1118] | 1851 | curedge = (0, 0) |
---|
| 1852 | if individualedge: |
---|
| 1853 | for edgepar in edge: |
---|
| 1854 | if not _is_valid(edgepar, int): |
---|
| 1855 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 1856 | to be a pair of integers or an integer." |
---|
[907] | 1857 | else: |
---|
[1118] | 1858 | curedge = edge; |
---|
[880] | 1859 | |
---|
| 1860 | # setup fitter |
---|
| 1861 | f = fitter() |
---|
| 1862 | f.set_function(poly=order) |
---|
| 1863 | |
---|
| 1864 | # setup line finder |
---|
[1118] | 1865 | fl = linefinder() |
---|
[1268] | 1866 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
[880] | 1867 | |
---|
| 1868 | if not insitu: |
---|
[1118] | 1869 | workscan = self.copy() |
---|
[880] | 1870 | else: |
---|
[1118] | 1871 | workscan = self |
---|
[880] | 1872 | |
---|
[907] | 1873 | fl.set_scan(workscan) |
---|
| 1874 | |
---|
[1118] | 1875 | rows = range(workscan.nrow()) |
---|
[1446] | 1876 | # Save parameters of baseline fits & masklists as a class attribute. |
---|
| 1877 | # NOTICE: It does not reflect changes in scantable! |
---|
| 1878 | if len(rows) > 0: |
---|
| 1879 | self.blpars=[] |
---|
| 1880 | self.masklists=[] |
---|
[880] | 1881 | asaplog.push("Processing:") |
---|
| 1882 | for r in rows: |
---|
[1118] | 1883 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 1884 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 1885 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 1886 | asaplog.push(msg, False) |
---|
[907] | 1887 | |
---|
[976] | 1888 | # figure out edge parameter |
---|
[1118] | 1889 | if individualedge: |
---|
| 1890 | if len(edge) >= workscan.getif(r): |
---|
| 1891 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 1892 | "be less than the number of IFs" |
---|
| 1893 | curedge = edge[workscan.getif(r)] |
---|
[919] | 1894 | |
---|
[1637] | 1895 | # take into account flagtra info (CAS-1434) |
---|
| 1896 | flagtra = workscan._getmask(r) |
---|
| 1897 | actualmask = mask[:] |
---|
| 1898 | if len(actualmask) == 0: |
---|
| 1899 | actualmask = list(flagtra[:]) |
---|
| 1900 | else: |
---|
| 1901 | if len(actualmask) != len(flagtra): |
---|
| 1902 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 1903 | else: |
---|
| 1904 | for i in range(0, len(actualmask)): |
---|
| 1905 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 1906 | |
---|
[976] | 1907 | # setup line finder |
---|
[1637] | 1908 | fl.find_lines(r, actualmask, curedge) |
---|
[1446] | 1909 | outmask=fl.get_mask() |
---|
[880] | 1910 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1911 | f.x = workscan._getabcissa(r) |
---|
| 1912 | f.y = workscan._getspectrum(r) |
---|
| 1913 | f.data = None |
---|
| 1914 | f.fit() |
---|
[1446] | 1915 | |
---|
| 1916 | # Show mask list |
---|
| 1917 | masklist=workscan.get_masklist(fl.get_mask(),row=r) |
---|
| 1918 | msg = "mask range: "+str(masklist) |
---|
| 1919 | asaplog.push(msg, False) |
---|
| 1920 | |
---|
[1061] | 1921 | if plot: |
---|
| 1922 | f.plot(residual=True) |
---|
| 1923 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1924 | if x.upper() == 'N': |
---|
[1446] | 1925 | self.blpars.append(None) |
---|
| 1926 | self.masklists.append(None) |
---|
[1061] | 1927 | continue |
---|
[1655] | 1928 | |
---|
[880] | 1929 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1655] | 1930 | self.blpars.append(f.get_parameters()) |
---|
[1446] | 1931 | self.masklists.append(masklist) |
---|
[1061] | 1932 | if plot: |
---|
| 1933 | f._p.unmap() |
---|
| 1934 | f._p = None |
---|
| 1935 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 1936 | if insitu: |
---|
| 1937 | self._assign(workscan) |
---|
| 1938 | else: |
---|
| 1939 | return workscan |
---|
| 1940 | |
---|
[1757] | 1941 | #@print_log_dec |
---|
[914] | 1942 | def rotate_linpolphase(self, angle): |
---|
| 1943 | """ |
---|
| 1944 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1945 | This is always done in situ in the raw data. So if you call this |
---|
| 1946 | function more than once then each call rotates the phase further. |
---|
| 1947 | Parameters: |
---|
| 1948 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1949 | Examples: |
---|
| 1950 | scan.rotate_linpolphase(2.3) |
---|
| 1951 | """ |
---|
| 1952 | varlist = vars() |
---|
[936] | 1953 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 1954 | self._add_history("rotate_linpolphase", varlist) |
---|
| 1955 | print_log() |
---|
| 1956 | return |
---|
[710] | 1957 | |
---|
[1757] | 1958 | #@print_log_dec |
---|
[914] | 1959 | def rotate_xyphase(self, angle): |
---|
| 1960 | """ |
---|
| 1961 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1962 | in the data. So if you call this function more than once |
---|
| 1963 | then each call rotates the phase further. |
---|
| 1964 | Parameters: |
---|
| 1965 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1966 | Examples: |
---|
| 1967 | scan.rotate_xyphase(2.3) |
---|
| 1968 | """ |
---|
| 1969 | varlist = vars() |
---|
[936] | 1970 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 1971 | self._add_history("rotate_xyphase", varlist) |
---|
| 1972 | print_log() |
---|
| 1973 | return |
---|
| 1974 | |
---|
[1757] | 1975 | #@print_log_dec |
---|
[914] | 1976 | def swap_linears(self): |
---|
| 1977 | """ |
---|
[1757] | 1978 | Swap the linear polarisations XX and YY, or better the first two |
---|
[1348] | 1979 | polarisations as this also works for ciculars. |
---|
[914] | 1980 | """ |
---|
| 1981 | varlist = vars() |
---|
[936] | 1982 | self._math._swap_linears(self) |
---|
[914] | 1983 | self._add_history("swap_linears", varlist) |
---|
| 1984 | print_log() |
---|
| 1985 | return |
---|
| 1986 | |
---|
[1757] | 1987 | #@print_log_dec |
---|
[914] | 1988 | def invert_phase(self): |
---|
| 1989 | """ |
---|
| 1990 | Invert the phase of the complex polarisation |
---|
| 1991 | """ |
---|
| 1992 | varlist = vars() |
---|
[936] | 1993 | self._math._invert_phase(self) |
---|
[914] | 1994 | self._add_history("invert_phase", varlist) |
---|
| 1995 | print_log() |
---|
| 1996 | return |
---|
| 1997 | |
---|
[1757] | 1998 | #@print_log_dec |
---|
[876] | 1999 | def add(self, offset, insitu=None): |
---|
[513] | 2000 | """ |
---|
| 2001 | Return a scan where all spectra have the offset added |
---|
| 2002 | Parameters: |
---|
| 2003 | offset: the offset |
---|
| 2004 | insitu: if False a new scantable is returned. |
---|
| 2005 | Otherwise, the scaling is done in-situ |
---|
| 2006 | The default is taken from .asaprc (False) |
---|
| 2007 | """ |
---|
| 2008 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2009 | self._math._setinsitu(insitu) |
---|
[513] | 2010 | varlist = vars() |
---|
[876] | 2011 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 2012 | s._add_history("add", varlist) |
---|
[876] | 2013 | print_log() |
---|
| 2014 | if insitu: |
---|
| 2015 | self._assign(s) |
---|
| 2016 | else: |
---|
[513] | 2017 | return s |
---|
| 2018 | |
---|
[1757] | 2019 | #@print_log_dec |
---|
[1680] | 2020 | def scale(self, factor, tsys=True, insitu=None): |
---|
[513] | 2021 | """ |
---|
| 2022 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 2023 | Parameters: |
---|
[1677] | 2024 | factor: the scaling factor (float or 1D float list) |
---|
[513] | 2025 | insitu: if False a new scantable is returned. |
---|
| 2026 | Otherwise, the scaling is done in-situ |
---|
| 2027 | The default is taken from .asaprc (False) |
---|
| 2028 | tsys: if True (default) then apply the operation to Tsys |
---|
| 2029 | as well as the data |
---|
| 2030 | """ |
---|
| 2031 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2032 | self._math._setinsitu(insitu) |
---|
[513] | 2033 | varlist = vars() |
---|
[1680] | 2034 | s = None |
---|
[1681] | 2035 | import numpy |
---|
| 2036 | if isinstance(factor, list) or isinstance(factor, numpy.ndarray): |
---|
| 2037 | if isinstance(factor[0], list) or isinstance(factor[0], numpy.ndarray): |
---|
[1680] | 2038 | from asapmath import _array2dOp |
---|
| 2039 | s = _array2dOp( self.copy(), factor, "MUL", tsys ) |
---|
[1677] | 2040 | else: |
---|
[1681] | 2041 | s = scantable( self._math._arrayop( self.copy(), factor, "MUL", tsys ) ) |
---|
[1677] | 2042 | else: |
---|
| 2043 | s = scantable(self._math._unaryop(self.copy(), factor, "MUL", tsys)) |
---|
[1118] | 2044 | s._add_history("scale", varlist) |
---|
[876] | 2045 | print_log() |
---|
| 2046 | if insitu: |
---|
| 2047 | self._assign(s) |
---|
| 2048 | else: |
---|
[513] | 2049 | return s |
---|
| 2050 | |
---|
[1603] | 2051 | def set_sourcetype(self, match, matchtype="pattern", |
---|
| 2052 | sourcetype="reference"): |
---|
| 2053 | """ |
---|
| 2054 | Set the type of the source to be an source or reference scan |
---|
| 2055 | using the provided pattern: |
---|
| 2056 | Parameters: |
---|
| 2057 | match: a Unix style pattern, regular expression or selector |
---|
| 2058 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
| 2059 | 'regex' regular expression |
---|
| 2060 | sourcetype: the type of the source to use (source/reference) |
---|
| 2061 | """ |
---|
| 2062 | varlist = vars() |
---|
| 2063 | basesel = self.get_selection() |
---|
| 2064 | stype = -1 |
---|
| 2065 | if sourcetype.lower().startswith("r"): |
---|
| 2066 | stype = 1 |
---|
| 2067 | elif sourcetype.lower().startswith("s"): |
---|
| 2068 | stype = 0 |
---|
| 2069 | else: |
---|
| 2070 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)") |
---|
| 2071 | if matchtype.lower().startswith("p"): |
---|
| 2072 | matchtype = "pattern" |
---|
| 2073 | elif matchtype.lower().startswith("r"): |
---|
| 2074 | matchtype = "regex" |
---|
| 2075 | else: |
---|
| 2076 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
| 2077 | sel = selector() |
---|
| 2078 | if isinstance(match, selector): |
---|
| 2079 | sel = match |
---|
| 2080 | else: |
---|
| 2081 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match)) |
---|
| 2082 | self.set_selection(basesel+sel) |
---|
| 2083 | self._setsourcetype(stype) |
---|
| 2084 | self.set_selection(basesel) |
---|
[1757] | 2085 | self._add_history("set_sourcetype", varlist) |
---|
[1603] | 2086 | |
---|
[1757] | 2087 | #@print_log_dec |
---|
[1631] | 2088 | def auto_quotient(self, preserve=True, mode='paired', verify=False): |
---|
[670] | 2089 | """ |
---|
| 2090 | This function allows to build quotients automatically. |
---|
[1631] | 2091 | It assumes the observation to have the same number of |
---|
[670] | 2092 | "ons" and "offs" |
---|
| 2093 | Parameters: |
---|
[710] | 2094 | preserve: you can preserve (default) the continuum or |
---|
| 2095 | remove it. The equations used are |
---|
[670] | 2096 | preserve: Output = Toff * (on/off) - Toff |
---|
[1070] | 2097 | remove: Output = Toff * (on/off) - Ton |
---|
[1757] | 2098 | mode: the on/off detection mode |
---|
[1348] | 2099 | 'paired' (default) |
---|
| 2100 | identifies 'off' scans by the |
---|
| 2101 | trailing '_R' (Mopra/Parkes) or |
---|
| 2102 | '_e'/'_w' (Tid) and matches |
---|
| 2103 | on/off pairs from the observing pattern |
---|
[1603] | 2104 | 'time' |
---|
| 2105 | finds the closest off in time |
---|
[1348] | 2106 | |
---|
[670] | 2107 | """ |
---|
[1348] | 2108 | modes = ["time", "paired"] |
---|
[670] | 2109 | if not mode in modes: |
---|
[876] | 2110 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 2111 | raise ValueError(msg) |
---|
| 2112 | varlist = vars() |
---|
[1348] | 2113 | s = None |
---|
| 2114 | if mode.lower() == "paired": |
---|
| 2115 | basesel = self.get_selection() |
---|
[1356] | 2116 | sel = selector()+basesel |
---|
| 2117 | sel.set_query("SRCTYPE==1") |
---|
| 2118 | self.set_selection(sel) |
---|
[1348] | 2119 | offs = self.copy() |
---|
| 2120 | sel.set_query("SRCTYPE==0") |
---|
[1356] | 2121 | self.set_selection(sel) |
---|
[1348] | 2122 | ons = self.copy() |
---|
| 2123 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 2124 | self.set_selection(basesel) |
---|
| 2125 | elif mode.lower() == "time": |
---|
| 2126 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 2127 | s._add_history("auto_quotient", varlist) |
---|
[876] | 2128 | print_log() |
---|
| 2129 | return s |
---|
[710] | 2130 | |
---|
[1757] | 2131 | #@print_log_dec |
---|
[1145] | 2132 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1141] | 2133 | """ |
---|
[1143] | 2134 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
| 2135 | Parameters: |
---|
[1145] | 2136 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1143] | 2137 | weight: How to average the off beams. Default is 'median'. |
---|
[1145] | 2138 | preserve: you can preserve (default) the continuum or |
---|
| 2139 | remove it. The equations used are |
---|
| 2140 | preserve: Output = Toff * (on/off) - Toff |
---|
| 2141 | remove: Output = Toff * (on/off) - Ton |
---|
[1217] | 2142 | """ |
---|
[1757] | 2143 | mask = mask or () |
---|
[1141] | 2144 | varlist = vars() |
---|
| 2145 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 2146 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 2147 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 2148 | from asapmath import quotient |
---|
[1145] | 2149 | q = quotient(on, off, preserve) |
---|
[1143] | 2150 | q._add_history("mx_quotient", varlist) |
---|
[1145] | 2151 | print_log() |
---|
[1217] | 2152 | return q |
---|
[513] | 2153 | |
---|
[1757] | 2154 | #@print_log_dec |
---|
[718] | 2155 | def freq_switch(self, insitu=None): |
---|
| 2156 | """ |
---|
| 2157 | Apply frequency switching to the data. |
---|
| 2158 | Parameters: |
---|
| 2159 | insitu: if False a new scantable is returned. |
---|
| 2160 | Otherwise, the swictching is done in-situ |
---|
| 2161 | The default is taken from .asaprc (False) |
---|
| 2162 | Example: |
---|
| 2163 | none |
---|
| 2164 | """ |
---|
| 2165 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2166 | self._math._setinsitu(insitu) |
---|
[718] | 2167 | varlist = vars() |
---|
[876] | 2168 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 2169 | s._add_history("freq_switch", varlist) |
---|
[876] | 2170 | print_log() |
---|
| 2171 | if insitu: self._assign(s) |
---|
| 2172 | else: return s |
---|
[718] | 2173 | |
---|
[1757] | 2174 | #@print_log_dec |
---|
[780] | 2175 | def recalc_azel(self): |
---|
| 2176 | """ |
---|
| 2177 | Recalculate the azimuth and elevation for each position. |
---|
| 2178 | Parameters: |
---|
| 2179 | none |
---|
| 2180 | Example: |
---|
| 2181 | """ |
---|
| 2182 | varlist = vars() |
---|
[876] | 2183 | self._recalcazel() |
---|
[780] | 2184 | self._add_history("recalc_azel", varlist) |
---|
| 2185 | print_log() |
---|
| 2186 | return |
---|
| 2187 | |
---|
[1757] | 2188 | #@print_log_dec |
---|
[513] | 2189 | def __add__(self, other): |
---|
[1681] | 2190 | """ |
---|
| 2191 | implicit on all axes and on Tsys |
---|
| 2192 | """ |
---|
| 2193 | return self._operation( other, "ADD" ) |
---|
[513] | 2194 | |
---|
[1757] | 2195 | #@print_log_dec |
---|
[513] | 2196 | def __sub__(self, other): |
---|
| 2197 | """ |
---|
| 2198 | implicit on all axes and on Tsys |
---|
| 2199 | """ |
---|
[1681] | 2200 | return self._operation( other, 'SUB' ) |
---|
[710] | 2201 | |
---|
[1757] | 2202 | #@print_log_dec |
---|
[513] | 2203 | def __mul__(self, other): |
---|
| 2204 | """ |
---|
| 2205 | implicit on all axes and on Tsys |
---|
| 2206 | """ |
---|
[1681] | 2207 | return self._operation( other, 'MUL' ) |
---|
[513] | 2208 | |
---|
[1757] | 2209 | #@print_log_dec |
---|
[513] | 2210 | def __div__(self, other): |
---|
| 2211 | """ |
---|
| 2212 | implicit on all axes and on Tsys |
---|
| 2213 | """ |
---|
[1681] | 2214 | return self._operation( other, 'DIV' ) |
---|
[513] | 2215 | |
---|
[530] | 2216 | def get_fit(self, row=0): |
---|
| 2217 | """ |
---|
| 2218 | Print or return the stored fits for a row in the scantable |
---|
| 2219 | Parameters: |
---|
| 2220 | row: the row which the fit has been applied to. |
---|
| 2221 | """ |
---|
| 2222 | if row > self.nrow(): |
---|
| 2223 | return |
---|
[976] | 2224 | from asap.asapfit import asapfit |
---|
[530] | 2225 | fit = asapfit(self._getfit(row)) |
---|
[718] | 2226 | if rcParams['verbose']: |
---|
[1612] | 2227 | #print fit |
---|
[1614] | 2228 | asaplog.push( '%s' %(fit) ) |
---|
| 2229 | print_log() |
---|
[530] | 2230 | return |
---|
| 2231 | else: |
---|
| 2232 | return fit.as_dict() |
---|
| 2233 | |
---|
[1603] | 2234 | def flag_nans(self): |
---|
| 2235 | """ |
---|
| 2236 | Utility function to flag NaN values in the scantable. |
---|
| 2237 | """ |
---|
| 2238 | import numpy |
---|
| 2239 | basesel = self.get_selection() |
---|
| 2240 | for i in range(self.nrow()): |
---|
[1757] | 2241 | sel = self.get_row_selector(i) |
---|
| 2242 | self.set_selection(basesel+sel) |
---|
[1603] | 2243 | nans = numpy.isnan(self._getspectrum(0)) |
---|
| 2244 | if numpy.any(nans): |
---|
| 2245 | bnans = [ bool(v) for v in nans] |
---|
| 2246 | self.flag(bnans) |
---|
| 2247 | self.set_selection(basesel) |
---|
| 2248 | |
---|
[1757] | 2249 | def get_row_selector(self, rowno): |
---|
| 2250 | return selector(beams=self.getbeam(rowno), |
---|
| 2251 | ifs=self.getif(rowno), |
---|
| 2252 | pols=self.getpol(rowno), |
---|
| 2253 | scans=self.getscan(rowno), |
---|
| 2254 | cycles=self.getcycle(rowno)) |
---|
| 2255 | |
---|
[484] | 2256 | def _add_history(self, funcname, parameters): |
---|
[1603] | 2257 | if not rcParams['scantable.history']: |
---|
| 2258 | return |
---|
[484] | 2259 | # create date |
---|
| 2260 | sep = "##" |
---|
| 2261 | from datetime import datetime |
---|
| 2262 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 2263 | hist = dstr+sep |
---|
| 2264 | hist += funcname+sep#cdate+sep |
---|
| 2265 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 2266 | for k, v in parameters.iteritems(): |
---|
[484] | 2267 | if type(v) is dict: |
---|
[1118] | 2268 | for k2, v2 in v.iteritems(): |
---|
[484] | 2269 | hist += k2 |
---|
| 2270 | hist += "=" |
---|
[1118] | 2271 | if isinstance(v2, scantable): |
---|
[484] | 2272 | hist += 'scantable' |
---|
| 2273 | elif k2 == 'mask': |
---|
[1118] | 2274 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 2275 | hist += str(self._zip_mask(v2)) |
---|
| 2276 | else: |
---|
| 2277 | hist += str(v2) |
---|
[484] | 2278 | else: |
---|
[513] | 2279 | hist += str(v2) |
---|
[484] | 2280 | else: |
---|
| 2281 | hist += k |
---|
| 2282 | hist += "=" |
---|
[1118] | 2283 | if isinstance(v, scantable): |
---|
[484] | 2284 | hist += 'scantable' |
---|
| 2285 | elif k == 'mask': |
---|
[1118] | 2286 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 2287 | hist += str(self._zip_mask(v)) |
---|
| 2288 | else: |
---|
| 2289 | hist += str(v) |
---|
[484] | 2290 | else: |
---|
| 2291 | hist += str(v) |
---|
| 2292 | hist += sep |
---|
| 2293 | hist = hist[:-2] # remove trailing '##' |
---|
| 2294 | self._addhistory(hist) |
---|
| 2295 | |
---|
[710] | 2296 | |
---|
[484] | 2297 | def _zip_mask(self, mask): |
---|
| 2298 | mask = list(mask) |
---|
| 2299 | i = 0 |
---|
| 2300 | segments = [] |
---|
| 2301 | while mask[i:].count(1): |
---|
| 2302 | i += mask[i:].index(1) |
---|
| 2303 | if mask[i:].count(0): |
---|
| 2304 | j = i + mask[i:].index(0) |
---|
| 2305 | else: |
---|
[710] | 2306 | j = len(mask) |
---|
[1118] | 2307 | segments.append([i, j]) |
---|
[710] | 2308 | i = j |
---|
[484] | 2309 | return segments |
---|
[714] | 2310 | |
---|
[626] | 2311 | def _get_ordinate_label(self): |
---|
| 2312 | fu = "("+self.get_fluxunit()+")" |
---|
| 2313 | import re |
---|
| 2314 | lbl = "Intensity" |
---|
[1118] | 2315 | if re.match(".K.", fu): |
---|
[626] | 2316 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 2317 | elif re.match(".Jy.", fu): |
---|
[626] | 2318 | lbl = "Flux density "+ fu |
---|
| 2319 | return lbl |
---|
[710] | 2320 | |
---|
[876] | 2321 | def _check_ifs(self): |
---|
| 2322 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 2323 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 2324 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 2325 | |
---|
[1684] | 2326 | def _fill(self, names, unit, average, getpt, antenna): |
---|
[976] | 2327 | import os |
---|
| 2328 | from asap._asap import stfiller |
---|
| 2329 | first = True |
---|
| 2330 | fullnames = [] |
---|
| 2331 | for name in names: |
---|
| 2332 | name = os.path.expandvars(name) |
---|
| 2333 | name = os.path.expanduser(name) |
---|
| 2334 | if not os.path.exists(name): |
---|
| 2335 | msg = "File '%s' does not exists" % (name) |
---|
| 2336 | if rcParams['verbose']: |
---|
| 2337 | asaplog.push(msg) |
---|
[1612] | 2338 | #print asaplog.pop().strip() |
---|
[1614] | 2339 | print_log( 'ERROR' ) |
---|
[976] | 2340 | return |
---|
| 2341 | raise IOError(msg) |
---|
| 2342 | fullnames.append(name) |
---|
| 2343 | if average: |
---|
| 2344 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 2345 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 2346 | for name in fullnames: |
---|
[1073] | 2347 | tbl = Scantable(stype) |
---|
| 2348 | r = stfiller(tbl) |
---|
[1603] | 2349 | rx = rcParams['scantable.reference'] |
---|
| 2350 | r._setreferenceexpr(rx) |
---|
[976] | 2351 | msg = "Importing %s..." % (name) |
---|
[1118] | 2352 | asaplog.push(msg, False) |
---|
[976] | 2353 | print_log() |
---|
[1684] | 2354 | r._open(name, antenna, -1, -1, getpt) |
---|
[976] | 2355 | r._read() |
---|
| 2356 | if average: |
---|
[1118] | 2357 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 2358 | if not first: |
---|
| 2359 | tbl = self._math._merge([self, tbl]) |
---|
| 2360 | Scantable.__init__(self, tbl) |
---|
| 2361 | r._close() |
---|
[1118] | 2362 | del r, tbl |
---|
[976] | 2363 | first = False |
---|
| 2364 | if unit is not None: |
---|
| 2365 | self.set_fluxunit(unit) |
---|
[1446] | 2366 | #self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[976] | 2367 | |
---|
[1603] | 2368 | def __getitem__(self, key): |
---|
| 2369 | if key < 0: |
---|
| 2370 | key += self.nrow() |
---|
| 2371 | if key >= self.nrow(): |
---|
| 2372 | raise IndexError("Row index out of range.") |
---|
| 2373 | return self._getspectrum(key) |
---|
| 2374 | |
---|
| 2375 | def __setitem__(self, key, value): |
---|
| 2376 | if key < 0: |
---|
| 2377 | key += self.nrow() |
---|
| 2378 | if key >= self.nrow(): |
---|
| 2379 | raise IndexError("Row index out of range.") |
---|
| 2380 | if not hasattr(value, "__len__") or \ |
---|
| 2381 | len(value) > self.nchan(self.getif(key)): |
---|
| 2382 | raise ValueError("Spectrum length doesn't match.") |
---|
| 2383 | return self._setspectrum(value, key) |
---|
| 2384 | |
---|
| 2385 | def __len__(self): |
---|
| 2386 | return self.nrow() |
---|
| 2387 | |
---|
| 2388 | def __iter__(self): |
---|
| 2389 | for i in range(len(self)): |
---|
| 2390 | yield self[i] |
---|
[1681] | 2391 | |
---|
| 2392 | def _operation(self, other, opmode): |
---|
| 2393 | varlist = vars() |
---|
| 2394 | s = None |
---|
| 2395 | import numpy |
---|
| 2396 | if isinstance(other, scantable): |
---|
| 2397 | s = scantable(self._math._binaryop(self.copy(), other, opmode)) |
---|
| 2398 | elif isinstance(other, float) or isinstance(other, int): |
---|
| 2399 | if opmode == 'DIV' and float(other) == 0.0: |
---|
| 2400 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
| 2401 | s = scantable(self._math._unaryop(self.copy(), other, opmode, False)) |
---|
| 2402 | elif isinstance(other, list) or isinstance(other, numpy.ndarray): |
---|
| 2403 | if isinstance(other[0], list) or isinstance(other[0], numpy.ndarray): |
---|
| 2404 | from asapmath import _array2dOp |
---|
| 2405 | s = _array2dOp( self.copy(), other, opmode, False ) |
---|
| 2406 | else: |
---|
| 2407 | s = scantable(self._math._arrayop(self.copy(), other, opmode, False)) |
---|
| 2408 | else: |
---|
| 2409 | raise TypeError("Other input is not a scantable or float value or float list") |
---|
| 2410 | opdic = {} |
---|
| 2411 | opdic['ADD'] = '+' |
---|
| 2412 | opdic['SUB'] = '-' |
---|
| 2413 | opdic['MUL'] = '*' |
---|
| 2414 | opdic['DIV'] = '/' |
---|
| 2415 | s._add_history("operator %s" % opdic[opmode], varlist) |
---|
| 2416 | print_log() |
---|
| 2417 | return s |
---|
| 2418 | |
---|
| 2419 | |
---|