[102] | 1 | from asap._asap import sdtable |
---|
[226] | 2 | from asap import rcParams |
---|
[189] | 3 | from numarray import ones,zeros |
---|
[102] | 4 | import sys |
---|
| 5 | |
---|
| 6 | class scantable(sdtable): |
---|
| 7 | """ |
---|
| 8 | The ASAP container for scans |
---|
| 9 | """ |
---|
[113] | 10 | |
---|
[340] | 11 | def __init__(self, filename, unit=None): |
---|
[102] | 12 | """ |
---|
| 13 | Create a scantable from a saved one or make a reference |
---|
| 14 | Parameters: |
---|
[181] | 15 | filename: the name of an asap table on disk |
---|
| 16 | or |
---|
| 17 | the name of a rpfits/sdfits/ms file |
---|
| 18 | (integrations within scans are auto averaged |
---|
| 19 | and the whole file is read) |
---|
| 20 | or |
---|
| 21 | [advanced] a reference to an existing |
---|
[102] | 22 | scantable |
---|
[340] | 23 | unit: brightness unit; must be consistent with K or Jy. |
---|
| 24 | Over-rides the default selected by the reader |
---|
| 25 | (input rpfits/sdfits/ms) or replaces the value |
---|
| 26 | in existing scantables |
---|
[102] | 27 | """ |
---|
[226] | 28 | self._vb = rcParams['verbose'] |
---|
[113] | 29 | self._p = None |
---|
[181] | 30 | from os import stat as st |
---|
| 31 | import stat |
---|
| 32 | if isinstance(filename,sdtable): |
---|
| 33 | sdtable.__init__(self, filename) |
---|
[340] | 34 | if unit is not None: |
---|
[346] | 35 | self.set_fluxunit(unit) |
---|
[181] | 36 | else: |
---|
[411] | 37 | import os.path |
---|
| 38 | if not os.path.exists(filename): |
---|
| 39 | print "File '%s' not found." % (filename) |
---|
[226] | 40 | return |
---|
[411] | 41 | filename = os.path.expandvars(filename) |
---|
| 42 | if os.path.isdir(filename): |
---|
[181] | 43 | # crude check if asap table |
---|
[411] | 44 | if os.path.exists(filename+'/table.info'): |
---|
[181] | 45 | sdtable.__init__(self, filename) |
---|
[340] | 46 | if unit is not None: |
---|
| 47 | self.set_fluxunit(unit) |
---|
[181] | 48 | else: |
---|
[411] | 49 | print "The given file '%s'is not a valid asap table." % (filename) |
---|
[226] | 50 | return |
---|
| 51 | else: |
---|
| 52 | autoav = rcParams['scantable.autoaverage'] |
---|
| 53 | |
---|
[181] | 54 | from asap._asap import sdreader |
---|
[340] | 55 | ifSel = -1 |
---|
| 56 | beamSel = -1 |
---|
[345] | 57 | r = sdreader(filename,ifSel,beamSel) |
---|
[181] | 58 | print 'Importing data...' |
---|
[411] | 59 | r._read([-1]) |
---|
| 60 | tbl = r._getdata() |
---|
[346] | 61 | if unit is not None: |
---|
| 62 | tbl.set_fluxunit(unit) |
---|
[226] | 63 | if autoav: |
---|
| 64 | from asap._asap import average |
---|
| 65 | tmp = tuple([tbl]) |
---|
| 66 | print 'Auto averaging integrations...' |
---|
| 67 | tbl2 = average(tmp,(),True,'none') |
---|
| 68 | sdtable.__init__(self,tbl2) |
---|
| 69 | del r,tbl |
---|
| 70 | else: |
---|
| 71 | sdtable.__init__(self,tbl) |
---|
[102] | 72 | |
---|
[451] | 73 | def save(self, name=None, format=None, stokes=False, overwrite=False): |
---|
[116] | 74 | """ |
---|
[280] | 75 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, |
---|
| 76 | Image FITS or MS2 format. |
---|
[116] | 77 | Parameters: |
---|
[196] | 78 | name: the name of the outputfile. For format="FITS" this |
---|
[280] | 79 | is the directory file name into which all the files will |
---|
| 80 | be written (default is 'asap_FITS') |
---|
[116] | 81 | format: an optional file format. Default is ASAP. |
---|
[280] | 82 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
---|
[194] | 83 | 'SDFITS' (save as SDFITS file) |
---|
| 84 | 'FITS' (saves each row as a FITS Image) |
---|
[200] | 85 | 'ASCII' (saves as ascii text file) |
---|
[226] | 86 | 'MS2' (saves as an aips++ |
---|
| 87 | MeasurementSet V2) |
---|
[445] | 88 | stokes: Convert to Stokes parameters (only available |
---|
| 89 | currently with FITS and ASCII formats. |
---|
[451] | 90 | Default is False. |
---|
[411] | 91 | overwrite: If the file should be overwritten if it exists. |
---|
[256] | 92 | The default False is to return with warning |
---|
[411] | 93 | without writing the output. USE WITH CARE. |
---|
[116] | 94 | Example: |
---|
| 95 | scan.save('myscan.asap') |
---|
| 96 | scan.save('myscan.sdfits','SDFITS') |
---|
| 97 | """ |
---|
[411] | 98 | from os import path |
---|
[226] | 99 | if format is None: format = rcParams['scantable.save'] |
---|
[256] | 100 | suffix = '.'+format.lower() |
---|
| 101 | if name is None or name =="": |
---|
| 102 | name = 'scantable'+suffix |
---|
[283] | 103 | print "No filename given. Using default name %s..." % name |
---|
[411] | 104 | name = path.expandvars(name) |
---|
[256] | 105 | if path.isfile(name) or path.isdir(name): |
---|
| 106 | if not overwrite: |
---|
| 107 | print "File %s already exists." % name |
---|
| 108 | return |
---|
[451] | 109 | format2 = format.upper() |
---|
| 110 | if format2 == 'ASAP': |
---|
[116] | 111 | self._save(name) |
---|
| 112 | else: |
---|
| 113 | from asap._asap import sdwriter as _sw |
---|
[451] | 114 | w = _sw(format2) |
---|
[445] | 115 | w.write(self, name, stokes) |
---|
[116] | 116 | return |
---|
| 117 | |
---|
[102] | 118 | def copy(self): |
---|
| 119 | """ |
---|
| 120 | Return a copy of this scantable. |
---|
| 121 | Parameters: |
---|
[113] | 122 | none |
---|
[102] | 123 | Example: |
---|
| 124 | copiedscan = scan.copy() |
---|
| 125 | """ |
---|
[113] | 126 | sd = scantable(sdtable._copy(self)) |
---|
| 127 | return sd |
---|
| 128 | |
---|
[102] | 129 | def get_scan(self, scanid=None): |
---|
| 130 | """ |
---|
| 131 | Return a specific scan (by scanno) or collection of scans (by |
---|
| 132 | source name) in a new scantable. |
---|
| 133 | Parameters: |
---|
| 134 | scanid: a scanno or a source name |
---|
| 135 | Example: |
---|
[113] | 136 | scan.get_scan('323p459') |
---|
[102] | 137 | # gets all scans containing the source '323p459' |
---|
| 138 | """ |
---|
| 139 | if scanid is None: |
---|
| 140 | print "Please specify a scan no or name to retrieve from the scantable" |
---|
| 141 | try: |
---|
| 142 | if type(scanid) is str: |
---|
[113] | 143 | s = sdtable._getsource(self,scanid) |
---|
[102] | 144 | return scantable(s) |
---|
| 145 | elif type(scanid) is int: |
---|
[381] | 146 | s = sdtable._getscan(self,[scanid]) |
---|
| 147 | return scantable(s) |
---|
| 148 | elif type(scanid) is list: |
---|
[113] | 149 | s = sdtable._getscan(self,scanid) |
---|
[102] | 150 | return scantable(s) |
---|
[381] | 151 | else: |
---|
| 152 | print "Illegal scanid type, use 'int' or 'list' if ints." |
---|
[102] | 153 | except RuntimeError: |
---|
| 154 | print "Couldn't find any match." |
---|
| 155 | |
---|
| 156 | def __str__(self): |
---|
[381] | 157 | return sdtable._summary(self,True) |
---|
[102] | 158 | |
---|
[381] | 159 | def summary(self,filename=None, verbose=None): |
---|
[102] | 160 | """ |
---|
| 161 | Print a summary of the contents of this scantable. |
---|
| 162 | Parameters: |
---|
| 163 | filename: the name of a file to write the putput to |
---|
| 164 | Default - no file output |
---|
[381] | 165 | verbose: print extra info such as the frequency table |
---|
| 166 | The default (False) is taken from .asaprc |
---|
[102] | 167 | """ |
---|
[381] | 168 | info = sdtable._summary(self, verbose) |
---|
| 169 | if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
---|
[102] | 170 | if filename is not None: |
---|
[256] | 171 | if filename is "": |
---|
| 172 | filename = 'scantable_summary.txt' |
---|
[415] | 173 | from os.path import expandvars, isdir |
---|
[411] | 174 | filename = expandvars(filename) |
---|
[415] | 175 | if not isdir(filename): |
---|
[413] | 176 | data = open(filename, 'w') |
---|
| 177 | data.write(info) |
---|
| 178 | data.close() |
---|
| 179 | else: |
---|
| 180 | print "Illegal file name '%s'." % (filename) |
---|
[102] | 181 | print info |
---|
| 182 | |
---|
[256] | 183 | def set_cursor(self, thebeam=0,theif=0,thepol=0): |
---|
[102] | 184 | """ |
---|
| 185 | Set the spectrum for individual operations. |
---|
| 186 | Parameters: |
---|
| 187 | thebeam,theif,thepol: a number |
---|
| 188 | Example: |
---|
[256] | 189 | scan.set_cursor(0,0,1) |
---|
[135] | 190 | pol1sig = scan.stats(all=False) # returns std dev for beam=0 |
---|
[181] | 191 | # if=0, pol=1 |
---|
[102] | 192 | """ |
---|
| 193 | self.setbeam(thebeam) |
---|
| 194 | self.setpol(thepol) |
---|
| 195 | self.setif(theif) |
---|
| 196 | return |
---|
| 197 | |
---|
[256] | 198 | def get_cursor(self): |
---|
[113] | 199 | """ |
---|
| 200 | Return/print a the current 'cursor' into the Beam/IF/Pol cube. |
---|
| 201 | Parameters: |
---|
| 202 | none |
---|
| 203 | Returns: |
---|
| 204 | a list of values (currentBeam,currentIF,currentPol) |
---|
| 205 | Example: |
---|
| 206 | none |
---|
| 207 | """ |
---|
[102] | 208 | i = self.getbeam() |
---|
| 209 | j = self.getif() |
---|
| 210 | k = self.getpol() |
---|
[113] | 211 | if self._vb: |
---|
[181] | 212 | print "--------------------------------------------------" |
---|
[256] | 213 | print " Cursor position" |
---|
[181] | 214 | print "--------------------------------------------------" |
---|
[226] | 215 | out = 'Beam=%d IF=%d Pol=%d ' % (i,j,k) |
---|
[113] | 216 | print out |
---|
[102] | 217 | return i,j,k |
---|
| 218 | |
---|
[436] | 219 | def stats(self, stat='stddev', mask=None, allaxes=None): |
---|
[102] | 220 | """ |
---|
[135] | 221 | Determine the specified statistic of the current beam/if/pol |
---|
[102] | 222 | Takes a 'mask' as an optional parameter to specify which |
---|
| 223 | channels should be excluded. |
---|
| 224 | Parameters: |
---|
[135] | 225 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
---|
| 226 | 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
| 227 | mask: an optional mask specifying where the statistic |
---|
[102] | 228 | should be determined. |
---|
[436] | 229 | allaxes: if True apply to all spectra. Otherwise |
---|
| 230 | apply only to the selected (beam/pol/if)spectra only. |
---|
| 231 | The default is taken from .asaprc (True if none) |
---|
[102] | 232 | Example: |
---|
[113] | 233 | scan.set_unit('channel') |
---|
[102] | 234 | msk = scan.create_mask([100,200],[500,600]) |
---|
[135] | 235 | scan.stats(stat='mean', mask=m) |
---|
[102] | 236 | """ |
---|
[436] | 237 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
[135] | 238 | from asap._asap import stats as _stats |
---|
[256] | 239 | from numarray import array,zeros,Float |
---|
[102] | 240 | if mask == None: |
---|
| 241 | mask = ones(self.nchan()) |
---|
[256] | 242 | axes = ['Beam','IF','Pol','Time'] |
---|
| 243 | |
---|
[436] | 244 | beamSel,IFSel,polSel = (self.getbeam(),self.getif(),self.getpol()) |
---|
| 245 | if allaxes: |
---|
[256] | 246 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
---|
| 247 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
---|
| 248 | arr = array(zeros(n),shape=shp,type=Float) |
---|
| 249 | |
---|
| 250 | for i in range(self.nbeam()): |
---|
| 251 | self.setbeam(i) |
---|
| 252 | for j in range(self.nif()): |
---|
| 253 | self.setif(j) |
---|
| 254 | for k in range(self.npol()): |
---|
| 255 | self.setpol(k) |
---|
| 256 | arr[i,j,k,:] = _stats(self,mask,stat,-1) |
---|
| 257 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
---|
| 258 | tm = [self._gettime(val) for val in range(self.nrow())] |
---|
[181] | 259 | if self._vb: |
---|
[256] | 260 | self._print_values(retval,stat,tm) |
---|
[436] | 261 | self.setbeam(beamSel) |
---|
| 262 | self.setif(IFSel) |
---|
| 263 | self.setpol(polSel) |
---|
[256] | 264 | return retval |
---|
[102] | 265 | |
---|
| 266 | else: |
---|
[241] | 267 | statval = _stats(self,mask,stat,-1) |
---|
[181] | 268 | out = '' |
---|
| 269 | for l in range(self.nrow()): |
---|
| 270 | tm = self._gettime(l) |
---|
| 271 | out += 'Time[%s]:\n' % (tm) |
---|
[436] | 272 | if self.nbeam() > 1: out += ' Beam[%d] ' % (beamSel) |
---|
| 273 | if self.nif() > 1: out += ' IF[%d] ' % (IFSel) |
---|
| 274 | if self.npol() > 1: out += ' Pol[%d] ' % (polSel) |
---|
[181] | 275 | out += '= %3.3f\n' % (statval[l]) |
---|
| 276 | out += "--------------------------------------------------\n" |
---|
[226] | 277 | |
---|
[181] | 278 | if self._vb: |
---|
| 279 | print "--------------------------------------------------" |
---|
| 280 | print " ",stat |
---|
| 281 | print "--------------------------------------------------" |
---|
| 282 | print out |
---|
[256] | 283 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
---|
| 284 | return retval |
---|
[102] | 285 | |
---|
[436] | 286 | def stddev(self,mask=None, allaxes=None): |
---|
[135] | 287 | """ |
---|
| 288 | Determine the standard deviation of the current beam/if/pol |
---|
| 289 | Takes a 'mask' as an optional parameter to specify which |
---|
| 290 | channels should be excluded. |
---|
| 291 | Parameters: |
---|
| 292 | mask: an optional mask specifying where the standard |
---|
| 293 | deviation should be determined. |
---|
[436] | 294 | allaxes: optional flag to show all or a cursor selected |
---|
[226] | 295 | spectrum of Beam/IF/Pol. Default is all or taken |
---|
| 296 | from .asaprc |
---|
[135] | 297 | |
---|
| 298 | Example: |
---|
| 299 | scan.set_unit('channel') |
---|
| 300 | msk = scan.create_mask([100,200],[500,600]) |
---|
| 301 | scan.stddev(mask=m) |
---|
| 302 | """ |
---|
[436] | 303 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 304 | return self.stats(stat='stddev',mask=mask, allaxes=allaxes); |
---|
[135] | 305 | |
---|
[436] | 306 | def get_tsys(self, allaxes=None): |
---|
[113] | 307 | """ |
---|
| 308 | Return the System temperatures. |
---|
| 309 | Parameters: |
---|
[436] | 310 | allaxes: if True apply to all spectra. Otherwise |
---|
| 311 | apply only to the selected (beam/pol/if)spectra only. |
---|
| 312 | The default is taken from .asaprc (True if none) |
---|
[113] | 313 | Returns: |
---|
| 314 | a list of Tsys values. |
---|
| 315 | """ |
---|
[436] | 316 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
[256] | 317 | from numarray import array,zeros,Float |
---|
| 318 | axes = ['Beam','IF','Pol','Time'] |
---|
| 319 | |
---|
[436] | 320 | if allaxes: |
---|
[256] | 321 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
---|
| 322 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
---|
| 323 | arr = array(zeros(n),shape=shp,type=Float) |
---|
| 324 | |
---|
| 325 | for i in range(self.nbeam()): |
---|
| 326 | self.setbeam(i) |
---|
| 327 | for j in range(self.nif()): |
---|
| 328 | self.setif(j) |
---|
| 329 | for k in range(self.npol()): |
---|
| 330 | self.setpol(k) |
---|
| 331 | arr[i,j,k,:] = self._gettsys() |
---|
| 332 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
---|
| 333 | tm = [self._gettime(val) for val in range(self.nrow())] |
---|
[181] | 334 | if self._vb: |
---|
[256] | 335 | self._print_values(retval,'Tsys',tm) |
---|
| 336 | return retval |
---|
| 337 | |
---|
[102] | 338 | else: |
---|
[256] | 339 | i,j,k = (self.getbeam(),self.getif(),self.getpol()) |
---|
| 340 | statval = self._gettsys() |
---|
[181] | 341 | out = '' |
---|
| 342 | for l in range(self.nrow()): |
---|
| 343 | tm = self._gettime(l) |
---|
| 344 | out += 'Time[%s]:\n' % (tm) |
---|
| 345 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i) |
---|
| 346 | if self.nif() > 1: out += ' IF[%d] ' % (j) |
---|
| 347 | if self.npol() > 1: out += ' Pol[%d] ' % (k) |
---|
[256] | 348 | out += '= %3.3f\n' % (statval[l]) |
---|
| 349 | out += "--------------------------------------------------\n" |
---|
| 350 | |
---|
[181] | 351 | if self._vb: |
---|
| 352 | print "--------------------------------------------------" |
---|
[256] | 353 | print " TSys" |
---|
[181] | 354 | print "--------------------------------------------------" |
---|
| 355 | print out |
---|
[256] | 356 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
---|
| 357 | return retval |
---|
[113] | 358 | |
---|
[407] | 359 | def get_time(self, row=-1): |
---|
[113] | 360 | """ |
---|
| 361 | Get a list of time stamps for the observations. |
---|
[181] | 362 | Return a string for each integration in the scantable. |
---|
[113] | 363 | Parameters: |
---|
[407] | 364 | row: row no of integration. Default -1 return all rows |
---|
[113] | 365 | Example: |
---|
| 366 | none |
---|
| 367 | """ |
---|
| 368 | out = [] |
---|
[407] | 369 | if row == -1: |
---|
| 370 | for i in range(self.nrow()): |
---|
| 371 | out.append(self._gettime(i)) |
---|
| 372 | return out |
---|
| 373 | else: |
---|
| 374 | if row < self.nrow(): |
---|
| 375 | return self._gettime(row) |
---|
[102] | 376 | |
---|
| 377 | def set_unit(self, unit='channel'): |
---|
| 378 | """ |
---|
| 379 | Set the unit for all following operations on this scantable |
---|
| 380 | Parameters: |
---|
| 381 | unit: optional unit, default is 'channel' |
---|
[113] | 382 | one of '*Hz','km/s','channel', '' |
---|
[102] | 383 | """ |
---|
[113] | 384 | |
---|
| 385 | if unit in ['','pixel', 'channel']: |
---|
| 386 | unit = '' |
---|
| 387 | inf = list(self._getcoordinfo()) |
---|
| 388 | inf[0] = unit |
---|
| 389 | self._setcoordinfo(inf) |
---|
| 390 | if self._p: self.plot() |
---|
| 391 | |
---|
[358] | 392 | def set_instrument (self, instr): |
---|
| 393 | """ |
---|
| 394 | Set the instrument for subsequent processing |
---|
| 395 | Parameters: |
---|
[407] | 396 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
| 397 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 398 | """ |
---|
| 399 | self._setInstrument(instr) |
---|
| 400 | |
---|
[276] | 401 | def set_doppler(self, doppler='RADIO'): |
---|
| 402 | """ |
---|
| 403 | Set the doppler for all following operations on this scantable. |
---|
| 404 | Parameters: |
---|
| 405 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 406 | """ |
---|
| 407 | |
---|
| 408 | inf = list(self._getcoordinfo()) |
---|
| 409 | inf[2] = doppler |
---|
| 410 | self._setcoordinfo(inf) |
---|
| 411 | if self._p: self.plot() |
---|
[432] | 412 | |
---|
[226] | 413 | def set_freqframe(self, frame=None): |
---|
[113] | 414 | """ |
---|
| 415 | Set the frame type of the Spectral Axis. |
---|
| 416 | Parameters: |
---|
| 417 | frame: an optional frame type, default 'LSRK'. |
---|
| 418 | Examples: |
---|
| 419 | scan.set_freqframe('BARY') |
---|
| 420 | """ |
---|
[226] | 421 | if not frame: frame = rcParams['scantable.freqframe'] |
---|
[113] | 422 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
---|
| 423 | 'GEO','GALACTO','LGROUP','CMB'] |
---|
| 424 | if frame in valid: |
---|
| 425 | inf = list(self._getcoordinfo()) |
---|
| 426 | inf[1] = frame |
---|
| 427 | self._setcoordinfo(inf) |
---|
[102] | 428 | else: |
---|
[113] | 429 | print "Please specify a valid freq type. Valid types are:\n",valid |
---|
| 430 | |
---|
| 431 | def get_unit(self): |
---|
| 432 | """ |
---|
| 433 | Get the default unit set in this scantable |
---|
| 434 | Parameters: |
---|
| 435 | Returns: |
---|
| 436 | A unit string |
---|
| 437 | """ |
---|
| 438 | inf = self._getcoordinfo() |
---|
| 439 | unit = inf[0] |
---|
| 440 | if unit == '': unit = 'channel' |
---|
| 441 | return unit |
---|
[102] | 442 | |
---|
[158] | 443 | def get_abcissa(self, rowno=0): |
---|
[102] | 444 | """ |
---|
[158] | 445 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 446 | selected Beam/IF/Pol |
---|
| 447 | Parameters: |
---|
[226] | 448 | rowno: an optional row number in the scantable. Default is the |
---|
| 449 | first row, i.e. rowno=0 |
---|
[113] | 450 | Returns: |
---|
[407] | 451 | The abcissa values and it's format string (as a dictionary) |
---|
[113] | 452 | """ |
---|
[256] | 453 | abc = self._getabcissa(rowno) |
---|
[407] | 454 | lbl = self._getabcissalabel(rowno) |
---|
[158] | 455 | return abc, lbl |
---|
[407] | 456 | #return {'abcissa':abc,'label':lbl} |
---|
[113] | 457 | |
---|
| 458 | def create_mask(self, *args, **kwargs): |
---|
| 459 | """ |
---|
[102] | 460 | Compute and return a mask based on [min,max] windows. |
---|
[189] | 461 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 462 | applied. |
---|
[102] | 463 | Parameters: |
---|
| 464 | [min,max],[min2,max2],... |
---|
| 465 | Pairs of start/end points specifying the regions |
---|
| 466 | to be masked |
---|
[189] | 467 | invert: optional argument. If specified as True, |
---|
| 468 | return an inverted mask, i.e. the regions |
---|
| 469 | specified are EXCLUDED |
---|
[102] | 470 | Example: |
---|
[113] | 471 | scan.set_unit('channel') |
---|
| 472 | |
---|
| 473 | a) |
---|
[102] | 474 | msk = scan.set_mask([400,500],[800,900]) |
---|
[189] | 475 | # masks everything outside 400 and 500 |
---|
[113] | 476 | # and 800 and 900 in the unit 'channel' |
---|
| 477 | |
---|
| 478 | b) |
---|
| 479 | msk = scan.set_mask([400,500],[800,900], invert=True) |
---|
[189] | 480 | # masks the regions between 400 and 500 |
---|
[113] | 481 | # and 800 and 900 in the unit 'channel' |
---|
| 482 | |
---|
[102] | 483 | """ |
---|
[113] | 484 | u = self._getcoordinfo()[0] |
---|
| 485 | if self._vb: |
---|
| 486 | if u == "": u = "channel" |
---|
| 487 | print "The current mask window unit is", u |
---|
[102] | 488 | n = self.nchan() |
---|
[256] | 489 | data = self._getabcissa() |
---|
[189] | 490 | msk = zeros(n) |
---|
[102] | 491 | for window in args: |
---|
| 492 | if (len(window) != 2 or window[0] > window[1] ): |
---|
| 493 | print "A window needs to be defined as [min,max]" |
---|
| 494 | return |
---|
| 495 | for i in range(n): |
---|
[113] | 496 | if data[i] >= window[0] and data[i] < window[1]: |
---|
[189] | 497 | msk[i] = 1 |
---|
[113] | 498 | if kwargs.has_key('invert'): |
---|
| 499 | if kwargs.get('invert'): |
---|
| 500 | from numarray import logical_not |
---|
| 501 | msk = logical_not(msk) |
---|
[102] | 502 | return msk |
---|
[113] | 503 | |
---|
[256] | 504 | def get_restfreqs(self): |
---|
| 505 | """ |
---|
| 506 | Get the restfrequency(s) stored in this scantable. |
---|
| 507 | The return value(s) are always of unit 'Hz' |
---|
| 508 | Parameters: |
---|
| 509 | none |
---|
| 510 | Returns: |
---|
| 511 | a list of doubles |
---|
| 512 | """ |
---|
| 513 | return list(self._getrestfreqs()) |
---|
[102] | 514 | |
---|
[402] | 515 | def lines(self): |
---|
[391] | 516 | """ |
---|
[402] | 517 | Print the list of known spectral lines |
---|
| 518 | """ |
---|
| 519 | sdtable._lines(self) |
---|
| 520 | |
---|
| 521 | def set_restfreqs(self, freqs=None, unit='Hz', lines=None, source=None, theif=None): |
---|
| 522 | """ |
---|
[393] | 523 | Select the restfrequency for the specified source and IF OR |
---|
| 524 | replace for all IFs. If the 'freqs' argument holds a scalar, |
---|
| 525 | then that rest frequency will be applied to the selected |
---|
| 526 | data (and added to the list of available rest frequencies). |
---|
| 527 | In this way, you can set a rest frequency for each |
---|
| 528 | source and IF combination. If the 'freqs' argument holds |
---|
| 529 | a vector, then it MUST be of length the number of IFs |
---|
| 530 | (and the available restfrequencies will be replaced by |
---|
| 531 | this vector). In this case, *all* data ('source' and |
---|
| 532 | 'theif' are ignored) have the restfrequency set per IF according |
---|
| 533 | to the corresponding value you give in the 'freqs' vector. |
---|
| 534 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
| 535 | IF 1 gets restfreq 2e9. |
---|
[402] | 536 | |
---|
| 537 | You can also specify the frequencies via known line names |
---|
| 538 | in the argument 'lines'. Use 'freqs' or 'lines'. 'freqs' |
---|
| 539 | takes precedence. See the list of known names via function |
---|
| 540 | scantable.lines() |
---|
[391] | 541 | Parameters: |
---|
[402] | 542 | freqs: list of rest frequencies |
---|
[393] | 543 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 544 | lines: list of known spectral lines names (alternative to freqs). |
---|
| 545 | See possible list via scantable.lines() |
---|
[391] | 546 | source: Source name (blank means all) |
---|
| 547 | theif: IF (-1 means all) |
---|
| 548 | Example: |
---|
[393] | 549 | scan.set_restfreqs(freqs=1.4e9, source='NGC253', theif=2) |
---|
| 550 | scan.set_restfreqs(freqs=[1.4e9,1.67e9]) |
---|
[391] | 551 | """ |
---|
| 552 | if source is None: |
---|
| 553 | source = "" |
---|
| 554 | if theif is None: |
---|
| 555 | theif = -1 |
---|
[393] | 556 | t = type(freqs) |
---|
| 557 | if t is int or t is float: |
---|
| 558 | freqs = [freqs] |
---|
[402] | 559 | if freqs is None: |
---|
| 560 | freqs = [] |
---|
| 561 | t = type(lines) |
---|
| 562 | if t is str: |
---|
| 563 | lines = [lines] |
---|
| 564 | if lines is None: |
---|
| 565 | lines = [] |
---|
| 566 | sdtable._setrestfreqs(self, freqs, unit, lines, source, theif) |
---|
[391] | 567 | return |
---|
| 568 | |
---|
| 569 | |
---|
[102] | 570 | def flag_spectrum(self, thebeam, theif, thepol): |
---|
| 571 | """ |
---|
| 572 | This flags a selected spectrum in the scan 'for good'. |
---|
| 573 | USE WITH CARE - not reversible. |
---|
| 574 | Use masks for non-permanent exclusion of channels. |
---|
| 575 | Parameters: |
---|
| 576 | thebeam,theif,thepol: all have to be explicitly |
---|
| 577 | specified |
---|
| 578 | Example: |
---|
| 579 | scan.flag_spectrum(0,0,1) |
---|
| 580 | flags the spectrum for Beam=0, IF=0, Pol=1 |
---|
| 581 | """ |
---|
[407] | 582 | if (thebeam < self.nbeam() and |
---|
| 583 | theif < self.nif() and |
---|
| 584 | thepol < self.npol()): |
---|
| 585 | sdtable.setbeam(self, thebeam) |
---|
| 586 | sdtable.setif(self, theif) |
---|
| 587 | sdtable.setpol(self, thepol) |
---|
| 588 | sdtable._flag(self) |
---|
[102] | 589 | else: |
---|
| 590 | print "Please specify a valid (Beam/IF/Pol)" |
---|
| 591 | return |
---|
[113] | 592 | |
---|
[436] | 593 | def rotate_xyphase (self, angle, allaxes=None): |
---|
[432] | 594 | """ |
---|
| 595 | Rotate the phase of the XY correlation. This is done in situ |
---|
| 596 | in the data. So if you call this function more than once |
---|
| 597 | then each call rotates the phase further. |
---|
| 598 | Parameters: |
---|
| 599 | angle: The angle (degrees) to rotate (add) by. |
---|
[436] | 600 | allaxes: If True apply to all spectra. Otherwise |
---|
| 601 | apply only to the selected (beam/pol/if)spectra only. |
---|
| 602 | The default is taken from .asaprc (True if none) |
---|
[432] | 603 | Examples: |
---|
| 604 | scan.rotate_xyphase(2.3) |
---|
| 605 | """ |
---|
[436] | 606 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 607 | sdtable._rotate_xyphase(self, angle, allaxes) |
---|
[432] | 608 | |
---|
[113] | 609 | def plot(self, what='spectrum',col='Pol', panel=None): |
---|
| 610 | """ |
---|
| 611 | Plot the spectra contained in the scan. Alternatively you can also |
---|
| 612 | Plot Tsys vs Time |
---|
| 613 | Parameters: |
---|
| 614 | what: a choice of 'spectrum' (default) or 'tsys' |
---|
[135] | 615 | col: which out of Beams/IFs/Pols should be colour stacked |
---|
[113] | 616 | panel: set up multiple panels, currently not working. |
---|
| 617 | """ |
---|
[283] | 618 | print "Warning! Not fully functional. Use plotter.plot() instead" |
---|
| 619 | |
---|
[113] | 620 | validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()} |
---|
[124] | 621 | |
---|
[113] | 622 | validyax = ['spectrum','tsys'] |
---|
[189] | 623 | from asap.asaplot import ASAPlot |
---|
[113] | 624 | if not self._p: |
---|
| 625 | self._p = ASAPlot() |
---|
[189] | 626 | #print "Plotting not enabled" |
---|
| 627 | #return |
---|
| 628 | if self._p.is_dead: |
---|
| 629 | del self._p |
---|
| 630 | self._p = ASAPlot() |
---|
[113] | 631 | npan = 1 |
---|
| 632 | x = None |
---|
| 633 | if what == 'tsys': |
---|
| 634 | n = self.nrow() |
---|
| 635 | if n < 2: |
---|
| 636 | print "Only one integration. Can't plot." |
---|
| 637 | return |
---|
[124] | 638 | self._p.hold() |
---|
| 639 | self._p.clear() |
---|
[113] | 640 | if panel == 'Time': |
---|
| 641 | npan = self.nrow() |
---|
[124] | 642 | self._p.set_panels(rows=npan) |
---|
[113] | 643 | xlab,ylab,tlab = None,None,None |
---|
[226] | 644 | self._vb = False |
---|
[256] | 645 | sel = self.get_cursor() |
---|
[113] | 646 | for i in range(npan): |
---|
[226] | 647 | if npan > 1: |
---|
| 648 | self._p.subplot(i) |
---|
[113] | 649 | for j in range(validcol[col]): |
---|
| 650 | x = None |
---|
| 651 | y = None |
---|
| 652 | m = None |
---|
| 653 | tlab = self._getsourcename(i) |
---|
[124] | 654 | import re |
---|
| 655 | tlab = re.sub('_S','',tlab) |
---|
[113] | 656 | if col == 'Beam': |
---|
| 657 | self.setbeam(j) |
---|
| 658 | elif col == 'IF': |
---|
| 659 | self.setif(j) |
---|
| 660 | elif col == 'Pol': |
---|
| 661 | self.setpol(j) |
---|
| 662 | if what == 'tsys': |
---|
| 663 | x = range(self.nrow()) |
---|
| 664 | xlab = 'Time [pixel]' |
---|
| 665 | m = list(ones(len(x))) |
---|
| 666 | y = [] |
---|
| 667 | ylab = r'$T_{sys}$' |
---|
| 668 | for k in range(len(x)): |
---|
| 669 | y.append(self._gettsys(k)) |
---|
| 670 | else: |
---|
[158] | 671 | x,xlab = self.get_abcissa(i) |
---|
[256] | 672 | y = self._getspectrum(i) |
---|
[113] | 673 | ylab = r'Flux' |
---|
[256] | 674 | m = self._getmask(i) |
---|
[113] | 675 | llab = col+' '+str(j) |
---|
| 676 | self._p.set_line(label=llab) |
---|
| 677 | self._p.plot(x,y,m) |
---|
[124] | 678 | self._p.set_axes('xlabel',xlab) |
---|
| 679 | self._p.set_axes('ylabel',ylab) |
---|
| 680 | self._p.set_axes('title',tlab) |
---|
[113] | 681 | self._p.release() |
---|
[256] | 682 | self.set_cursor(sel[0],sel[1],sel[2]) |
---|
[226] | 683 | self._vb = rcParams['verbose'] |
---|
[113] | 684 | return |
---|
[256] | 685 | |
---|
| 686 | print out |
---|
| 687 | |
---|
| 688 | def _print_values(self, dat, label='', timestamps=[]): |
---|
| 689 | d = dat['data'] |
---|
| 690 | a = dat['axes'] |
---|
| 691 | shp = d.getshape() |
---|
| 692 | out = '' |
---|
| 693 | for i in range(shp[3]): |
---|
| 694 | out += '%s [%s]:\n' % (a[3],timestamps[i]) |
---|
| 695 | t = d[:,:,:,i] |
---|
| 696 | for j in range(shp[0]): |
---|
| 697 | if shp[0] > 1: out += ' %s[%d] ' % (a[0],j) |
---|
| 698 | for k in range(shp[1]): |
---|
| 699 | if shp[1] > 1: out += ' %s[%d] ' % (a[1],k) |
---|
| 700 | for l in range(shp[2]): |
---|
| 701 | if shp[2] > 1: out += ' %s[%d] ' % (a[2],l) |
---|
| 702 | out += '= %3.3f\n' % (t[j,k,l]) |
---|
| 703 | out += "--------------------------------------------------\n" |
---|
| 704 | print "--------------------------------------------------" |
---|
| 705 | print " ", label |
---|
| 706 | print "--------------------------------------------------" |
---|
| 707 | print out |
---|