| 1 | from asap._asap import sdtable
|
|---|
| 2 | from numarray import ones
|
|---|
| 3 | import sys
|
|---|
| 4 |
|
|---|
| 5 | class scantable(sdtable):
|
|---|
| 6 | """
|
|---|
| 7 | The ASAP container for scans
|
|---|
| 8 | """
|
|---|
| 9 |
|
|---|
| 10 | def __init__(self, filename):
|
|---|
| 11 | """
|
|---|
| 12 | Create a scantable from a saved one or make a reference
|
|---|
| 13 | Parameters:
|
|---|
| 14 | filename: the name of an asap table on disk, or
|
|---|
| 15 | [advanced] a refernce to an existing
|
|---|
| 16 | scantable
|
|---|
| 17 | """
|
|---|
| 18 | self._vb = True
|
|---|
| 19 | self._p = None
|
|---|
| 20 | sdtable.__init__(self, filename)
|
|---|
| 21 |
|
|---|
| 22 | def save(self, name, format='ASAP'):
|
|---|
| 23 | """
|
|---|
| 24 | Store the scantable on disk. This can be a asap file or SDFITS/MS2.
|
|---|
| 25 | Parameters:
|
|---|
| 26 | name: the name of the outputfile
|
|---|
| 27 | format: an optional file format. Default is ASAP.
|
|---|
| 28 | Alllowed are 'ASAP', 'SDFITS' and 'MS2'
|
|---|
| 29 | Example:
|
|---|
| 30 | scan.save('myscan.asap')
|
|---|
| 31 | scan.save('myscan.sdfits','SDFITS')
|
|---|
| 32 | """
|
|---|
| 33 | if format == 'ASAP':
|
|---|
| 34 | self._save(name)
|
|---|
| 35 | else:
|
|---|
| 36 | from asap._asap import sdwriter as _sw
|
|---|
| 37 | w = _sw()
|
|---|
| 38 | if format == 'SDFITS':
|
|---|
| 39 | w.write(self, name)
|
|---|
| 40 | return
|
|---|
| 41 |
|
|---|
| 42 | def _verbose(self, *args):
|
|---|
| 43 | """
|
|---|
| 44 | Set the verbose level True or False, to indicate if output
|
|---|
| 45 | should be printed as well as returned.
|
|---|
| 46 | """
|
|---|
| 47 | if type(args[0]) is bool:
|
|---|
| 48 | self._vb = args[0]
|
|---|
| 49 | return
|
|---|
| 50 | elif len(args) == 0:
|
|---|
| 51 | return self._vb
|
|---|
| 52 |
|
|---|
| 53 |
|
|---|
| 54 | def copy(self):
|
|---|
| 55 | """
|
|---|
| 56 | Return a copy of this scantable.
|
|---|
| 57 | Parameters:
|
|---|
| 58 | none
|
|---|
| 59 | Example:
|
|---|
| 60 | copiedscan = scan.copy()
|
|---|
| 61 | """
|
|---|
| 62 | sd = scantable(sdtable._copy(self))
|
|---|
| 63 | return sd
|
|---|
| 64 |
|
|---|
| 65 | def get_scan(self, scanid=None):
|
|---|
| 66 | """
|
|---|
| 67 | Return a specific scan (by scanno) or collection of scans (by
|
|---|
| 68 | source name) in a new scantable.
|
|---|
| 69 | Parameters:
|
|---|
| 70 | scanid: a scanno or a source name
|
|---|
| 71 | Example:
|
|---|
| 72 | scan.get_scan('323p459')
|
|---|
| 73 | # gets all scans containing the source '323p459'
|
|---|
| 74 | """
|
|---|
| 75 | if scanid is None:
|
|---|
| 76 | print "Please specify a scan no or name to retrieve from the scantable"
|
|---|
| 77 | try:
|
|---|
| 78 | if type(scanid) is str:
|
|---|
| 79 | s = sdtable._getsource(self,scanid)
|
|---|
| 80 | return scantable(s)
|
|---|
| 81 | elif type(scanid) is int:
|
|---|
| 82 | s = sdtable._getscan(self,scanid)
|
|---|
| 83 | return scantable(s)
|
|---|
| 84 | except RuntimeError:
|
|---|
| 85 | print "Couldn't find any match."
|
|---|
| 86 |
|
|---|
| 87 | def __str__(self):
|
|---|
| 88 | return sdtable.summary(self)
|
|---|
| 89 |
|
|---|
| 90 | def summary(self,filename=None):
|
|---|
| 91 | """
|
|---|
| 92 | Print a summary of the contents of this scantable.
|
|---|
| 93 | Parameters:
|
|---|
| 94 | filename: the name of a file to write the putput to
|
|---|
| 95 | Default - no file output
|
|---|
| 96 | """
|
|---|
| 97 | info = sdtable.summary(self)
|
|---|
| 98 | if filename is not None:
|
|---|
| 99 | data = open(filename, 'w')
|
|---|
| 100 | data.write(info)
|
|---|
| 101 | data.close()
|
|---|
| 102 | print info
|
|---|
| 103 |
|
|---|
| 104 | def set_selection(self, thebeam=0,theif=0,thepol=0):
|
|---|
| 105 | """
|
|---|
| 106 | Set the spectrum for individual operations.
|
|---|
| 107 | Parameters:
|
|---|
| 108 | thebeam,theif,thepol: a number
|
|---|
| 109 | Example:
|
|---|
| 110 | scan.set_selection(0,0,1)
|
|---|
| 111 | pol1rms = scan.rms(all=False) # returns rms for beam=0
|
|---|
| 112 | # if=0, pol=1
|
|---|
| 113 | """
|
|---|
| 114 | self.setbeam(thebeam)
|
|---|
| 115 | self.setpol(thepol)
|
|---|
| 116 | self.setif(theif)
|
|---|
| 117 | return
|
|---|
| 118 |
|
|---|
| 119 | def get_selection(self):
|
|---|
| 120 | """
|
|---|
| 121 | Return/print a the current 'cursor' into the Beam/IF/Pol cube.
|
|---|
| 122 | Parameters:
|
|---|
| 123 | none
|
|---|
| 124 | Returns:
|
|---|
| 125 | a list of values (currentBeam,currentIF,currentPol)
|
|---|
| 126 | Example:
|
|---|
| 127 | none
|
|---|
| 128 | """
|
|---|
| 129 | i = self.getbeam()
|
|---|
| 130 | j = self.getif()
|
|---|
| 131 | k = self.getpol()
|
|---|
| 132 | if self._vb:
|
|---|
| 133 | out = 'Beam=%d IF=%d Pol=%d '% (i,j,k)
|
|---|
| 134 | print out
|
|---|
| 135 | return i,j,k
|
|---|
| 136 |
|
|---|
| 137 | def rms(self,mask=None, all=True):
|
|---|
| 138 | """
|
|---|
| 139 | Determine the root mean square of the current beam/if/pol
|
|---|
| 140 | Takes a 'mask' as an optional parameter to specify which
|
|---|
| 141 | channels should be excluded.
|
|---|
| 142 | Parameters:
|
|---|
| 143 | mask: an optional mask specifying where the rms
|
|---|
| 144 | should be determined.
|
|---|
| 145 | all: optional flag to show all or a selected
|
|---|
| 146 | spectrum of Beam/IF/Pol
|
|---|
| 147 |
|
|---|
| 148 | Example:
|
|---|
| 149 | scan.set_unit('channel')
|
|---|
| 150 | msk = scan.create_mask([100,200],[500,600])
|
|---|
| 151 | scan.rms(mask=m)
|
|---|
| 152 | """
|
|---|
| 153 | from asap._asap import rms as _rms
|
|---|
| 154 | if mask == None:
|
|---|
| 155 | mask = ones(self.nchan())
|
|---|
| 156 | if all:
|
|---|
| 157 | out = ''
|
|---|
| 158 | tmp = []
|
|---|
| 159 | for i in range(self.nbeam()):
|
|---|
| 160 | self.setbeam(i)
|
|---|
| 161 | for j in range(self.nif()):
|
|---|
| 162 | self.setif(j)
|
|---|
| 163 | for k in range(self.npol()):
|
|---|
| 164 | self.setpol(k)
|
|---|
| 165 | rmsval = _rms(self,mask)
|
|---|
| 166 | tmp.append(rmsval)
|
|---|
| 167 | out += 'Beam[%d], IF[%d], Pol[%d] = %3.3f\n' % (i,j,k,rmsval)
|
|---|
| 168 | if self._vb:
|
|---|
| 169 | print out
|
|---|
| 170 | return tmp
|
|---|
| 171 |
|
|---|
| 172 | else:
|
|---|
| 173 | i = self.getbeam()
|
|---|
| 174 | j = self.getif()
|
|---|
| 175 | k = self.getpol()
|
|---|
| 176 | rmsval = _rms(self,mask)
|
|---|
| 177 | out = 'Beam[%d], IF[%d], Pol[%d] = %3.3f' % (i,j,k,rmsval)
|
|---|
| 178 | if self._vb:
|
|---|
| 179 | print out
|
|---|
| 180 | return rmsval
|
|---|
| 181 |
|
|---|
| 182 | def get_tsys(self, all=True):
|
|---|
| 183 | """
|
|---|
| 184 | Return the System temperatures.
|
|---|
| 185 | Parameters:
|
|---|
| 186 | all: optional parameter to get the Tsys values for all
|
|---|
| 187 | Beams/IFs/Pols (default) or just the one selected
|
|---|
| 188 | with scantable.set_selection()
|
|---|
| 189 | [True or False]
|
|---|
| 190 | Returns:
|
|---|
| 191 | a list of Tsys values.
|
|---|
| 192 | """
|
|---|
| 193 | if all:
|
|---|
| 194 | tmp = []
|
|---|
| 195 | out = ''
|
|---|
| 196 | for i in range(self.nbeam()):
|
|---|
| 197 | self.setbeam(i)
|
|---|
| 198 | for j in range(self.nif()):
|
|---|
| 199 | self.setif(j)
|
|---|
| 200 | for k in range(self.npol()):
|
|---|
| 201 | self.setpol(k)
|
|---|
| 202 | ts = self._gettsys()
|
|---|
| 203 | tmp.append(ts)
|
|---|
| 204 | out += 'TSys: Beam[%d], IF[%d], Pol[%d] = %3.3f\n' % (i,j,k,ts)
|
|---|
| 205 | if self._vb:
|
|---|
| 206 | print out
|
|---|
| 207 | return tmp
|
|---|
| 208 | else:
|
|---|
| 209 | i = self.getbeam()
|
|---|
| 210 | j = self.getif()
|
|---|
| 211 | k = self.getpol()
|
|---|
| 212 | ts = self._gettsys()
|
|---|
| 213 | out = 'TSys: Beam[%d], IF[%d], Pol[%d] = %3.3f' % (i,j,k,ts)
|
|---|
| 214 | if self._vb:
|
|---|
| 215 | print out
|
|---|
| 216 | return ts
|
|---|
| 217 |
|
|---|
| 218 | def get_time(self):
|
|---|
| 219 | """
|
|---|
| 220 | Get a list of time stamps for the observations.
|
|---|
| 221 | Return a string for each intergration in the scantable.
|
|---|
| 222 | Parameters:
|
|---|
| 223 | none
|
|---|
| 224 | Example:
|
|---|
| 225 | none
|
|---|
| 226 | """
|
|---|
| 227 | out = []
|
|---|
| 228 | for i in range(self.nrow()):
|
|---|
| 229 | out.append(self._gettime(i))
|
|---|
| 230 | return out
|
|---|
| 231 |
|
|---|
| 232 | def set_unit(self, unit='channel'):
|
|---|
| 233 | """
|
|---|
| 234 | Set the unit for all following operations on this scantable
|
|---|
| 235 | Parameters:
|
|---|
| 236 | unit: optional unit, default is 'channel'
|
|---|
| 237 | one of '*Hz','km/s','channel', ''
|
|---|
| 238 | """
|
|---|
| 239 |
|
|---|
| 240 | if unit in ['','pixel', 'channel']:
|
|---|
| 241 | unit = ''
|
|---|
| 242 | inf = list(self._getcoordinfo())
|
|---|
| 243 | inf[0] = unit
|
|---|
| 244 | self._setcoordinfo(inf)
|
|---|
| 245 | if self._p: self.plot()
|
|---|
| 246 |
|
|---|
| 247 | def set_freqframe(self, frame='LSRK'):
|
|---|
| 248 | """
|
|---|
| 249 | Set the frame type of the Spectral Axis.
|
|---|
| 250 | Parameters:
|
|---|
| 251 | frame: an optional frame type, default 'LSRK'.
|
|---|
| 252 | Examples:
|
|---|
| 253 | scan.set_freqframe('BARY')
|
|---|
| 254 | """
|
|---|
| 255 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \
|
|---|
| 256 | 'GEO','GALACTO','LGROUP','CMB']
|
|---|
| 257 | if frame in valid:
|
|---|
| 258 | inf = list(self._getcoordinfo())
|
|---|
| 259 | inf[1] = frame
|
|---|
| 260 | self._setcoordinfo(inf)
|
|---|
| 261 | else:
|
|---|
| 262 | print "Please specify a valid freq type. Valid types are:\n",valid
|
|---|
| 263 |
|
|---|
| 264 | def get_unit(self):
|
|---|
| 265 | """
|
|---|
| 266 | Get the default unit set in this scantable
|
|---|
| 267 | Parameters:
|
|---|
| 268 | Returns:
|
|---|
| 269 | A unit string
|
|---|
| 270 | """
|
|---|
| 271 | inf = self._getcoordinfo()
|
|---|
| 272 | unit = inf[0]
|
|---|
| 273 | if unit == '': unit = 'channel'
|
|---|
| 274 | return unit
|
|---|
| 275 |
|
|---|
| 276 | def get_abscissa(self, rowno=0):
|
|---|
| 277 | """
|
|---|
| 278 | Get the abscissa in the current coordinate setup for the currently
|
|---|
| 279 | selected Beam/IF/Pol
|
|---|
| 280 | Parameters:
|
|---|
| 281 | none
|
|---|
| 282 | Returns:
|
|---|
| 283 | The abscissa values and it's format string.
|
|---|
| 284 | """
|
|---|
| 285 | absc = self.getabscissa(rowno)
|
|---|
| 286 | lbl = self.getabscissalabel(rowno)
|
|---|
| 287 | return absc, lbl
|
|---|
| 288 |
|
|---|
| 289 | def create_mask(self, *args, **kwargs):
|
|---|
| 290 | """
|
|---|
| 291 | Compute and return a mask based on [min,max] windows.
|
|---|
| 292 | The specified windows are to be EXCLUDED, when the mask is
|
|---|
| 293 | applied.
|
|---|
| 294 | Parameters:
|
|---|
| 295 | [min,max],[min2,max2],...
|
|---|
| 296 | Pairs of start/end points specifying the regions
|
|---|
| 297 | to be masked
|
|---|
| 298 | invert: return an inverted mask, i.e. the regions
|
|---|
| 299 | specified are not masked (INCLUDED)
|
|---|
| 300 | Example:
|
|---|
| 301 | scan.set_unit('channel')
|
|---|
| 302 |
|
|---|
| 303 | a)
|
|---|
| 304 | msk = scan.set_mask([400,500],[800,900])
|
|---|
| 305 | # masks the regions between 400 and 500
|
|---|
| 306 | # and 800 and 900 in the unit 'channel'
|
|---|
| 307 |
|
|---|
| 308 | b)
|
|---|
| 309 | msk = scan.set_mask([400,500],[800,900], invert=True)
|
|---|
| 310 | # masks the regions outside 400 and 500
|
|---|
| 311 | # and 800 and 900 in the unit 'channel'
|
|---|
| 312 |
|
|---|
| 313 | """
|
|---|
| 314 | u = self._getcoordinfo()[0]
|
|---|
| 315 | if self._vb:
|
|---|
| 316 | if u == "": u = "channel"
|
|---|
| 317 | print "The current mask window unit is", u
|
|---|
| 318 | n = self.nchan()
|
|---|
| 319 | data = self.getabscissa()
|
|---|
| 320 | msk = ones(n)
|
|---|
| 321 | for window in args:
|
|---|
| 322 | if (len(window) != 2 or window[0] > window[1] ):
|
|---|
| 323 | print "A window needs to be defined as [min,max]"
|
|---|
| 324 | return
|
|---|
| 325 | for i in range(n):
|
|---|
| 326 | if data[i] >= window[0] and data[i] < window[1]:
|
|---|
| 327 | msk[i] = 0
|
|---|
| 328 | if kwargs.has_key('invert'):
|
|---|
| 329 | if kwargs.get('invert'):
|
|---|
| 330 | from numarray import logical_not
|
|---|
| 331 | msk = logical_not(msk)
|
|---|
| 332 | return msk
|
|---|
| 333 |
|
|---|
| 334 | def set_restfreqs(self, freqs, unit='Hz'):
|
|---|
| 335 | """
|
|---|
| 336 | Set the restfrequency(s) for this scantable.
|
|---|
| 337 | Parameters:
|
|---|
| 338 | freqs: one or more frequencies
|
|---|
| 339 | unit: optional 'unit', default 'Hz'
|
|---|
| 340 | Example:
|
|---|
| 341 | scan.set_restfreqs([1000000000.0])
|
|---|
| 342 | """
|
|---|
| 343 | if type(freqs) is float or int:
|
|---|
| 344 | freqs = (freqs)
|
|---|
| 345 | sdtable._setrestfreqs(self,freqs, unit)
|
|---|
| 346 | return
|
|---|
| 347 |
|
|---|
| 348 | def flag_spectrum(self, thebeam, theif, thepol):
|
|---|
| 349 | """
|
|---|
| 350 | This flags a selected spectrum in the scan 'for good'.
|
|---|
| 351 | USE WITH CARE - not reversible.
|
|---|
| 352 | Use masks for non-permanent exclusion of channels.
|
|---|
| 353 | Parameters:
|
|---|
| 354 | thebeam,theif,thepol: all have to be explicitly
|
|---|
| 355 | specified
|
|---|
| 356 | Example:
|
|---|
| 357 | scan.flag_spectrum(0,0,1)
|
|---|
| 358 | flags the spectrum for Beam=0, IF=0, Pol=1
|
|---|
| 359 | """
|
|---|
| 360 | if (thebeam < self.nbeam() and theif < self.nif() and thepol < self.npol()):
|
|---|
| 361 | stable.setbeam(thebeam)
|
|---|
| 362 | stable.setif(theif)
|
|---|
| 363 | stable.setpol(thepol)
|
|---|
| 364 | stable._flag(self)
|
|---|
| 365 | else:
|
|---|
| 366 | print "Please specify a valid (Beam/IF/Pol)"
|
|---|
| 367 | return
|
|---|
| 368 |
|
|---|
| 369 | def plot(self, what='spectrum',col='Pol', panel=None):
|
|---|
| 370 | """
|
|---|
| 371 | Plot the spectra contained in the scan. Alternatively you can also
|
|---|
| 372 | Plot Tsys vs Time
|
|---|
| 373 | Parameters:
|
|---|
| 374 | what: a choice of 'spectrum' (default) or 'tsys'
|
|---|
| 375 | col: which out of Beams/IFs/Pols should be colour stacked
|
|---|
| 376 | panel: set up multiple panels, currently not working.
|
|---|
| 377 | """
|
|---|
| 378 | validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()}
|
|---|
| 379 |
|
|---|
| 380 | validyax = ['spectrum','tsys']
|
|---|
| 381 | if not self._p:
|
|---|
| 382 | from asap.asaplot import ASAPlot
|
|---|
| 383 | self._p = ASAPlot()
|
|---|
| 384 | # print "Plotting not enabled"
|
|---|
| 385 | # return
|
|---|
| 386 | npan = 1
|
|---|
| 387 | x = None
|
|---|
| 388 | if what == 'tsys':
|
|---|
| 389 | n = self.nrow()
|
|---|
| 390 | if n < 2:
|
|---|
| 391 | print "Only one integration. Can't plot."
|
|---|
| 392 | return
|
|---|
| 393 | self._p.hold()
|
|---|
| 394 | self._p.clear()
|
|---|
| 395 | if panel == 'Time':
|
|---|
| 396 | npan = self.nrow()
|
|---|
| 397 | self._p.set_panels(rows=npan)
|
|---|
| 398 | xlab,ylab,tlab = None,None,None
|
|---|
| 399 | vb = self._verbose()
|
|---|
| 400 | self._verbose(False)
|
|---|
| 401 | sel = self.get_selection()
|
|---|
| 402 | for i in range(npan):
|
|---|
| 403 | self._p.subplot(i)
|
|---|
| 404 | for j in range(validcol[col]):
|
|---|
| 405 | x = None
|
|---|
| 406 | y = None
|
|---|
| 407 | m = None
|
|---|
| 408 | tlab = self._getsourcename(i)
|
|---|
| 409 | import re
|
|---|
| 410 | tlab = re.sub('_S','',tlab)
|
|---|
| 411 | if col == 'Beam':
|
|---|
| 412 | self.setbeam(j)
|
|---|
| 413 | elif col == 'IF':
|
|---|
| 414 | self.setif(j)
|
|---|
| 415 | elif col == 'Pol':
|
|---|
| 416 | self.setpol(j)
|
|---|
| 417 | if what == 'tsys':
|
|---|
| 418 | x = range(self.nrow())
|
|---|
| 419 | xlab = 'Time [pixel]'
|
|---|
| 420 | m = list(ones(len(x)))
|
|---|
| 421 | y = []
|
|---|
| 422 | ylab = r'$T_{sys}$'
|
|---|
| 423 | for k in range(len(x)):
|
|---|
| 424 | y.append(self._gettsys(k))
|
|---|
| 425 | else:
|
|---|
| 426 | x,xlab = self.get_abscissa(i)
|
|---|
| 427 | y = self.getspectrum(i)
|
|---|
| 428 | ylab = r'Flux'
|
|---|
| 429 | m = self.getmask(i)
|
|---|
| 430 | llab = col+' '+str(j)
|
|---|
| 431 | self._p.set_line(label=llab)
|
|---|
| 432 | self._p.plot(x,y,m)
|
|---|
| 433 | self._p.set_axes('xlabel',xlab)
|
|---|
| 434 | self._p.set_axes('ylabel',ylab)
|
|---|
| 435 | self._p.set_axes('title',tlab)
|
|---|
| 436 | self._p.release()
|
|---|
| 437 | self.set_selection(sel[0],sel[1],sel[2])
|
|---|
| 438 | self._verbose(vb)
|
|---|
| 439 | return
|
|---|
