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