source: trunk/python/scantable.py@ 315

Last change on this file since 315 was 283, checked in by mar637, 20 years ago

Added deafult filename warning.
Added warning to internal plotter.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 21.4 KB
Line 
1from asap._asap import sdtable
2from asap import rcParams
3from numarray import ones,zeros
4import sys
5
6class scantable(sdtable):
7 """
8 The ASAP container for scans
9 """
10
11 def __init__(self, filename):
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 """
24 self._vb = rcParams['verbose']
25 self._p = None
26 from os import stat as st
27 import stat
28 if isinstance(filename,sdtable):
29 sdtable.__init__(self, filename)
30 else:
31 try:
32 mode = st(filename)[stat.ST_MODE]
33 except OSError:
34 print "File not found"
35 return
36 if stat.S_ISDIR(mode):
37 # crude check if asap table
38 if stat.S_ISREG(st(filename+'/table.info')[stat.ST_MODE]):
39 sdtable.__init__(self, filename)
40 else:
41 print 'The given file is not a valid asap table'
42 return
43 else:
44 autoav = rcParams['scantable.autoaverage']
45
46 from asap._asap import sdreader
47 r = sdreader(filename)
48 print 'Importing data...'
49 r.read([-1])
50 tbl = r.getdata()
51 if autoav:
52 from asap._asap import average
53 tmp = tuple([tbl])
54 print 'Auto averaging integrations...'
55 tbl2 = average(tmp,(),True,'none')
56 sdtable.__init__(self,tbl2)
57 del r,tbl
58 else:
59 sdtable.__init__(self,tbl)
60
61 def save(self, name=None, format=None, overwrite=False):
62 """
63 Store the scantable on disk. This can be an asap (aips++) Table, SDFITS,
64 Image FITS or MS2 format.
65 Parameters:
66 name: the name of the outputfile. For format="FITS" this
67 is the directory file name into which all the files will
68 be written (default is 'asap_FITS')
69 format: an optional file format. Default is ASAP.
70 Allowed are - 'ASAP' (save as ASAP [aips++] Table),
71 'SDFITS' (save as SDFITS file)
72 'FITS' (saves each row as a FITS Image)
73 'ASCII' (saves as ascii text file)
74 'MS2' (saves as an aips++
75 MeasurementSet V2)
76 overwrite: if the file should be overwritten if it exists.
77 The default False is to return with warning
78 without writing the output
79 Example:
80 scan.save('myscan.asap')
81 scan.save('myscan.sdfits','SDFITS')
82 """
83 if format is None: format = rcParams['scantable.save']
84 suffix = '.'+format.lower()
85 if name is None or name =="":
86 name = 'scantable'+suffix
87 print "No filename given. Using default name %s..." % name
88 from os import path
89 if path.isfile(name) or path.isdir(name):
90 if not overwrite:
91 print "File %s already exists." % name
92 return
93 if format == 'ASAP':
94 self._save(name)
95 else:
96 from asap._asap import sdwriter as _sw
97 w = _sw(format)
98 w.write(self, name)
99 return
100
101 def copy(self):
102 """
103 Return a copy of this scantable.
104 Parameters:
105 none
106 Example:
107 copiedscan = scan.copy()
108 """
109 sd = scantable(sdtable._copy(self))
110 return sd
111
112 def get_scan(self, scanid=None):
113 """
114 Return a specific scan (by scanno) or collection of scans (by
115 source name) in a new scantable.
116 Parameters:
117 scanid: a scanno or a source name
118 Example:
119 scan.get_scan('323p459')
120 # gets all scans containing the source '323p459'
121 """
122 if scanid is None:
123 print "Please specify a scan no or name to retrieve from the scantable"
124 try:
125 if type(scanid) is str:
126 s = sdtable._getsource(self,scanid)
127 return scantable(s)
128 elif type(scanid) is int:
129 s = sdtable._getscan(self,scanid)
130 return scantable(s)
131 except RuntimeError:
132 print "Couldn't find any match."
133
134 def __str__(self):
135 return sdtable._summary(self)
136
137 def summary(self,filename=None):
138 """
139 Print a summary of the contents of this scantable.
140 Parameters:
141 filename: the name of a file to write the putput to
142 Default - no file output
143 """
144 info = sdtable._summary(self)
145 if filename is not None:
146 if filename is "":
147 filename = 'scantable_summary.txt'
148 data = open(filename, 'w')
149 data.write(info)
150 data.close()
151 print info
152
153 def set_cursor(self, thebeam=0,theif=0,thepol=0):
154 """
155 Set the spectrum for individual operations.
156 Parameters:
157 thebeam,theif,thepol: a number
158 Example:
159 scan.set_cursor(0,0,1)
160 pol1sig = scan.stats(all=False) # returns std dev for beam=0
161 # if=0, pol=1
162 """
163 self.setbeam(thebeam)
164 self.setpol(thepol)
165 self.setif(theif)
166 return
167
168 def get_cursor(self):
169 """
170 Return/print a the current 'cursor' into the Beam/IF/Pol cube.
171 Parameters:
172 none
173 Returns:
174 a list of values (currentBeam,currentIF,currentPol)
175 Example:
176 none
177 """
178 i = self.getbeam()
179 j = self.getif()
180 k = self.getpol()
181 if self._vb:
182 print "--------------------------------------------------"
183 print " Cursor position"
184 print "--------------------------------------------------"
185 out = 'Beam=%d IF=%d Pol=%d ' % (i,j,k)
186 print out
187 return i,j,k
188
189 def stats(self, stat='stddev', mask=None, all=None):
190 """
191 Determine the specified statistic of the current beam/if/pol
192 Takes a 'mask' as an optional parameter to specify which
193 channels should be excluded.
194 Parameters:
195 stat: 'min', 'max', 'sumsq', 'sum', 'mean'
196 'var', 'stddev', 'avdev', 'rms', 'median'
197 mask: an optional mask specifying where the statistic
198 should be determined.
199 all: if true show all (default or .asaprc) rather
200 that the cursor selected spectrum of Beam/IF/Pol
201
202 Example:
203 scan.set_unit('channel')
204 msk = scan.create_mask([100,200],[500,600])
205 scan.stats(stat='mean', mask=m)
206 """
207 if all is None: all = rcParams['scantable.allaxes']
208 from asap._asap import stats as _stats
209 from numarray import array,zeros,Float
210 if mask == None:
211 mask = ones(self.nchan())
212 axes = ['Beam','IF','Pol','Time']
213
214 if all:
215 n = self.nbeam()*self.nif()*self.npol()*self.nrow()
216 shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()]
217 arr = array(zeros(n),shape=shp,type=Float)
218
219 for i in range(self.nbeam()):
220 self.setbeam(i)
221 for j in range(self.nif()):
222 self.setif(j)
223 for k in range(self.npol()):
224 self.setpol(k)
225 arr[i,j,k,:] = _stats(self,mask,stat,-1)
226 retval = {'axes': axes, 'data': arr, 'cursor':None}
227 tm = [self._gettime(val) for val in range(self.nrow())]
228 if self._vb:
229 self._print_values(retval,stat,tm)
230 return retval
231
232 else:
233 i,j,k = (self.getbeam(),self.getif(),self.getpol())
234 statval = _stats(self,mask,stat,-1)
235 out = ''
236 for l in range(self.nrow()):
237 tm = self._gettime(l)
238 out += 'Time[%s]:\n' % (tm)
239 if self.nbeam() > 1: out += ' Beam[%d] ' % (i)
240 if self.nif() > 1: out += ' IF[%d] ' % (j)
241 if self.npol() > 1: out += ' Pol[%d] ' % (k)
242 out += '= %3.3f\n' % (statval[l])
243 out += "--------------------------------------------------\n"
244
245 if self._vb:
246 print "--------------------------------------------------"
247 print " ",stat
248 print "--------------------------------------------------"
249 print out
250 retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)}
251 return retval
252
253 def stddev(self,mask=None, all=None):
254 """
255 Determine the standard deviation of the current beam/if/pol
256 Takes a 'mask' as an optional parameter to specify which
257 channels should be excluded.
258 Parameters:
259 mask: an optional mask specifying where the standard
260 deviation should be determined.
261 all: optional flag to show all or a cursor selected
262 spectrum of Beam/IF/Pol. Default is all or taken
263 from .asaprc
264
265 Example:
266 scan.set_unit('channel')
267 msk = scan.create_mask([100,200],[500,600])
268 scan.stddev(mask=m)
269 """
270 if all is None: all = rcParams['scantable.allaxes']
271 return self.stats(stat='stddev',mask=mask, all=all);
272
273 def get_tsys(self, all=None):
274 """
275 Return the System temperatures.
276 Parameters:
277 all: optional parameter to get the Tsys values for all
278 Beams/IFs/Pols (default) or just the one selected
279 with scantable.set_cursor()
280 [True or False]
281 Returns:
282 a list of Tsys values.
283 """
284 if all is None: all = rcParams['scantable.allaxes']
285 from numarray import array,zeros,Float
286 axes = ['Beam','IF','Pol','Time']
287
288 if all:
289 n = self.nbeam()*self.nif()*self.npol()*self.nrow()
290 shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()]
291 arr = array(zeros(n),shape=shp,type=Float)
292
293 for i in range(self.nbeam()):
294 self.setbeam(i)
295 for j in range(self.nif()):
296 self.setif(j)
297 for k in range(self.npol()):
298 self.setpol(k)
299 arr[i,j,k,:] = self._gettsys()
300 retval = {'axes': axes, 'data': arr, 'cursor':None}
301 tm = [self._gettime(val) for val in range(self.nrow())]
302 if self._vb:
303 self._print_values(retval,'Tsys',tm)
304 return retval
305
306 else:
307 i,j,k = (self.getbeam(),self.getif(),self.getpol())
308 statval = self._gettsys()
309 out = ''
310 for l in range(self.nrow()):
311 tm = self._gettime(l)
312 out += 'Time[%s]:\n' % (tm)
313 if self.nbeam() > 1: out += ' Beam[%d] ' % (i)
314 if self.nif() > 1: out += ' IF[%d] ' % (j)
315 if self.npol() > 1: out += ' Pol[%d] ' % (k)
316 out += '= %3.3f\n' % (statval[l])
317 out += "--------------------------------------------------\n"
318
319 if self._vb:
320 print "--------------------------------------------------"
321 print " TSys"
322 print "--------------------------------------------------"
323 print out
324 retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)}
325 return retval
326
327 def get_time(self):
328 """
329 Get a list of time stamps for the observations.
330 Return a string for each integration in the scantable.
331 Parameters:
332 none
333 Example:
334 none
335 """
336 out = []
337 for i in range(self.nrow()):
338 out.append(self._gettime(i))
339 return out
340
341 def set_unit(self, unit='channel'):
342 """
343 Set the unit for all following operations on this scantable
344 Parameters:
345 unit: optional unit, default is 'channel'
346 one of '*Hz','km/s','channel', ''
347 """
348
349 if unit in ['','pixel', 'channel']:
350 unit = ''
351 inf = list(self._getcoordinfo())
352 inf[0] = unit
353 self._setcoordinfo(inf)
354 if self._p: self.plot()
355
356 def set_doppler(self, doppler='RADIO'):
357 """
358 Set the doppler for all following operations on this scantable.
359 Parameters:
360 doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
361 """
362
363 inf = list(self._getcoordinfo())
364 inf[2] = doppler
365 self._setcoordinfo(inf)
366 if self._p: self.plot()
367
368 def set_freqframe(self, frame=None):
369 """
370 Set the frame type of the Spectral Axis.
371 Parameters:
372 frame: an optional frame type, default 'LSRK'.
373 Examples:
374 scan.set_freqframe('BARY')
375 """
376 if not frame: frame = rcParams['scantable.freqframe']
377 valid = ['REST','TOPO','LSRD','LSRK','BARY', \
378 'GEO','GALACTO','LGROUP','CMB']
379 if frame in valid:
380 inf = list(self._getcoordinfo())
381 inf[1] = frame
382 self._setcoordinfo(inf)
383 else:
384 print "Please specify a valid freq type. Valid types are:\n",valid
385
386 def get_unit(self):
387 """
388 Get the default unit set in this scantable
389 Parameters:
390 Returns:
391 A unit string
392 """
393 inf = self._getcoordinfo()
394 unit = inf[0]
395 if unit == '': unit = 'channel'
396 return unit
397
398 def get_abcissa(self, rowno=0):
399 """
400 Get the abcissa in the current coordinate setup for the currently
401 selected Beam/IF/Pol
402 Parameters:
403 rowno: an optional row number in the scantable. Default is the
404 first row, i.e. rowno=0
405 Returns:
406 The abcissa values and it's format string.
407 """
408 abc = self._getabcissa(rowno)
409 lbl = self._getabcissalabel(rowno)
410 return abc, lbl
411
412 def create_mask(self, *args, **kwargs):
413 """
414 Compute and return a mask based on [min,max] windows.
415 The specified windows are to be INCLUDED, when the mask is
416 applied.
417 Parameters:
418 [min,max],[min2,max2],...
419 Pairs of start/end points specifying the regions
420 to be masked
421 invert: optional argument. If specified as True,
422 return an inverted mask, i.e. the regions
423 specified are EXCLUDED
424 Example:
425 scan.set_unit('channel')
426
427 a)
428 msk = scan.set_mask([400,500],[800,900])
429 # masks everything outside 400 and 500
430 # and 800 and 900 in the unit 'channel'
431
432 b)
433 msk = scan.set_mask([400,500],[800,900], invert=True)
434 # masks the regions between 400 and 500
435 # and 800 and 900 in the unit 'channel'
436
437 """
438 u = self._getcoordinfo()[0]
439 if self._vb:
440 if u == "": u = "channel"
441 print "The current mask window unit is", u
442 n = self.nchan()
443 data = self._getabcissa()
444 msk = zeros(n)
445 for window in args:
446 if (len(window) != 2 or window[0] > window[1] ):
447 print "A window needs to be defined as [min,max]"
448 return
449 for i in range(n):
450 if data[i] >= window[0] and data[i] < window[1]:
451 msk[i] = 1
452 if kwargs.has_key('invert'):
453 if kwargs.get('invert'):
454 from numarray import logical_not
455 msk = logical_not(msk)
456 return msk
457
458 def set_restfreqs(self, freqs, unit='Hz'):
459 """
460 Set the restfrequency(s) for this scantable.
461 Parameters:
462 freqs: one or more frequencies
463 unit: optional 'unit', default 'Hz'
464 Example:
465 scan.set_restfreqs([1000000000.0])
466 """
467 if type(freqs) is float or int:
468 freqs = (freqs)
469 sdtable._setrestfreqs(self,freqs, unit)
470 return
471 def get_restfreqs(self):
472 """
473 Get the restfrequency(s) stored in this scantable.
474 The return value(s) are always of unit 'Hz'
475 Parameters:
476 none
477 Returns:
478 a list of doubles
479 """
480 return list(self._getrestfreqs())
481
482 def flag_spectrum(self, thebeam, theif, thepol):
483 """
484 This flags a selected spectrum in the scan 'for good'.
485 USE WITH CARE - not reversible.
486 Use masks for non-permanent exclusion of channels.
487 Parameters:
488 thebeam,theif,thepol: all have to be explicitly
489 specified
490 Example:
491 scan.flag_spectrum(0,0,1)
492 flags the spectrum for Beam=0, IF=0, Pol=1
493 """
494 if (thebeam < self.nbeam() and theif < self.nif() and thepol < self.npol()):
495 stable.setbeam(thebeam)
496 stable.setif(theif)
497 stable.setpol(thepol)
498 stable._flag(self)
499 else:
500 print "Please specify a valid (Beam/IF/Pol)"
501 return
502
503 def plot(self, what='spectrum',col='Pol', panel=None):
504 """
505 Plot the spectra contained in the scan. Alternatively you can also
506 Plot Tsys vs Time
507 Parameters:
508 what: a choice of 'spectrum' (default) or 'tsys'
509 col: which out of Beams/IFs/Pols should be colour stacked
510 panel: set up multiple panels, currently not working.
511 """
512 print "Warning! Not fully functional. Use plotter.plot() instead"
513
514 validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()}
515
516 validyax = ['spectrum','tsys']
517 from asap.asaplot import ASAPlot
518 if not self._p:
519 self._p = ASAPlot()
520 #print "Plotting not enabled"
521 #return
522 if self._p.is_dead:
523 del self._p
524 self._p = ASAPlot()
525 npan = 1
526 x = None
527 if what == 'tsys':
528 n = self.nrow()
529 if n < 2:
530 print "Only one integration. Can't plot."
531 return
532 self._p.hold()
533 self._p.clear()
534 if panel == 'Time':
535 npan = self.nrow()
536 self._p.set_panels(rows=npan)
537 xlab,ylab,tlab = None,None,None
538 self._vb = False
539 sel = self.get_cursor()
540 for i in range(npan):
541 if npan > 1:
542 self._p.subplot(i)
543 for j in range(validcol[col]):
544 x = None
545 y = None
546 m = None
547 tlab = self._getsourcename(i)
548 import re
549 tlab = re.sub('_S','',tlab)
550 if col == 'Beam':
551 self.setbeam(j)
552 elif col == 'IF':
553 self.setif(j)
554 elif col == 'Pol':
555 self.setpol(j)
556 if what == 'tsys':
557 x = range(self.nrow())
558 xlab = 'Time [pixel]'
559 m = list(ones(len(x)))
560 y = []
561 ylab = r'$T_{sys}$'
562 for k in range(len(x)):
563 y.append(self._gettsys(k))
564 else:
565 x,xlab = self.get_abcissa(i)
566 y = self._getspectrum(i)
567 ylab = r'Flux'
568 m = self._getmask(i)
569 llab = col+' '+str(j)
570 self._p.set_line(label=llab)
571 self._p.plot(x,y,m)
572 self._p.set_axes('xlabel',xlab)
573 self._p.set_axes('ylabel',ylab)
574 self._p.set_axes('title',tlab)
575 self._p.release()
576 self.set_cursor(sel[0],sel[1],sel[2])
577 self._vb = rcParams['verbose']
578 return
579
580 print out
581
582 def _print_values(self, dat, label='', timestamps=[]):
583 d = dat['data']
584 a = dat['axes']
585 shp = d.getshape()
586 out = ''
587 for i in range(shp[3]):
588 out += '%s [%s]:\n' % (a[3],timestamps[i])
589 t = d[:,:,:,i]
590 for j in range(shp[0]):
591 if shp[0] > 1: out += ' %s[%d] ' % (a[0],j)
592 for k in range(shp[1]):
593 if shp[1] > 1: out += ' %s[%d] ' % (a[1],k)
594 for l in range(shp[2]):
595 if shp[2] > 1: out += ' %s[%d] ' % (a[2],l)
596 out += '= %3.3f\n' % (t[j,k,l])
597 out += "--------------------------------------------------\n"
598 print "--------------------------------------------------"
599 print " ", label
600 print "--------------------------------------------------"
601 print out
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