source: branches/polybatch/python/scantable.py@ 2151

Last change on this file since 2151 was 1924, checked in by Malte Marquarding, 14 years ago

Ticket #206: use STFitEntry as return objetc instead of pointer wrnagling.

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Line 
1"""This module defines the scantable class."""
2
3import os
4try:
5 from functools import wraps as wraps_dec
6except ImportError:
7 from asap.compatibility import wraps as wraps_dec
8
9from asap.env import is_casapy
10from asap._asap import Scantable
11from asap._asap import filler
12from asap.parameters import rcParams
13from asap.logging import asaplog, asaplog_post_dec
14from asap.selector import selector
15from asap.linecatalog import linecatalog
16from asap.coordinate import coordinate
17from asap.utils import _n_bools, mask_not, mask_and, mask_or, page
18from asap.asapfitter import fitter
19
20
21def preserve_selection(func):
22 @wraps_dec(func)
23 def wrap(obj, *args, **kw):
24 basesel = obj.get_selection()
25 try:
26 val = func(obj, *args, **kw)
27 finally:
28 obj.set_selection(basesel)
29 return val
30 return wrap
31
32def is_scantable(filename):
33 """Is the given file a scantable?
34
35 Parameters:
36
37 filename: the name of the file/directory to test
38
39 """
40 if ( os.path.isdir(filename)
41 and os.path.exists(filename+'/table.info')
42 and os.path.exists(filename+'/table.dat') ):
43 f=open(filename+'/table.info')
44 l=f.readline()
45 f.close()
46 #if ( l.find('Scantable') != -1 ):
47 if ( l.find('Measurement Set') == -1 ):
48 return True
49 else:
50 return False
51 else:
52 return False
53## return (os.path.isdir(filename)
54## and not os.path.exists(filename+'/table.f1')
55## and os.path.exists(filename+'/table.info'))
56
57def is_ms(filename):
58 """Is the given file a MeasurementSet?
59
60 Parameters:
61
62 filename: the name of the file/directory to test
63
64 """
65 if ( os.path.isdir(filename)
66 and os.path.exists(filename+'/table.info')
67 and os.path.exists(filename+'/table.dat') ):
68 f=open(filename+'/table.info')
69 l=f.readline()
70 f.close()
71 if ( l.find('Measurement Set') != -1 ):
72 return True
73 else:
74 return False
75 else:
76 return False
77
78class scantable(Scantable):
79 """\
80 The ASAP container for scans (single-dish data).
81 """
82
83 @asaplog_post_dec
84 #def __init__(self, filename, average=None, unit=None, getpt=None,
85 # antenna=None, parallactify=None):
86 def __init__(self, filename, average=None, unit=None, parallactify=None, **args):
87 """\
88 Create a scantable from a saved one or make a reference
89
90 Parameters:
91
92 filename: the name of an asap table on disk
93 or
94 the name of a rpfits/sdfits/ms file
95 (integrations within scans are auto averaged
96 and the whole file is read) or
97 [advanced] a reference to an existing scantable
98
99 average: average all integrations withinb a scan on read.
100 The default (True) is taken from .asaprc.
101
102 unit: brightness unit; must be consistent with K or Jy.
103 Over-rides the default selected by the filler
104 (input rpfits/sdfits/ms) or replaces the value
105 in existing scantables
106
107 getpt: for MeasurementSet input data only:
108 If True, all pointing data are filled.
109 The deafult is False, which makes time to load
110 the MS data faster in some cases.
111
112 antenna: for MeasurementSet input data only:
113 Antenna selection. integer (id) or string (name or id).
114
115 parallactify: Indicate that the data had been parallatified. Default
116 is taken from rc file.
117
118 """
119 if average is None:
120 average = rcParams['scantable.autoaverage']
121 #if getpt is None:
122 # getpt = True
123 #if antenna is not None:
124 # asaplog.push("Antenna selection currently unsupported."
125 # "Using ''")
126 # asaplog.post('WARN')
127 #if antenna is None:
128 # antenna = ''
129 #elif type(antenna) == int:
130 # antenna = '%s' % antenna
131 #elif type(antenna) == list:
132 # tmpstr = ''
133 # for i in range( len(antenna) ):
134 # if type(antenna[i]) == int:
135 # tmpstr = tmpstr + ('%s,'%(antenna[i]))
136 # elif type(antenna[i]) == str:
137 # tmpstr=tmpstr+antenna[i]+','
138 # else:
139 # raise TypeError('Bad antenna selection.')
140 # antenna = tmpstr.rstrip(',')
141 parallactify = parallactify or rcParams['scantable.parallactify']
142 varlist = vars()
143 from asap._asap import stmath
144 self._math = stmath( rcParams['insitu'] )
145 if isinstance(filename, Scantable):
146 Scantable.__init__(self, filename)
147 else:
148 if isinstance(filename, str):
149 filename = os.path.expandvars(filename)
150 filename = os.path.expanduser(filename)
151 if not os.path.exists(filename):
152 s = "File '%s' not found." % (filename)
153 raise IOError(s)
154 if is_scantable(filename):
155 ondisk = rcParams['scantable.storage'] == 'disk'
156 Scantable.__init__(self, filename, ondisk)
157 if unit is not None:
158 self.set_fluxunit(unit)
159 # do not reset to the default freqframe
160 #self.set_freqframe(rcParams['scantable.freqframe'])
161 #elif os.path.isdir(filename) \
162 # and not os.path.exists(filename+'/table.f1'):
163 elif is_ms(filename):
164 # Measurement Set
165 opts={'ms': {}}
166 mskeys=['getpt','antenna']
167 for key in mskeys:
168 if key in args.keys():
169 opts['ms'][key] = args[key]
170 #self._fill([filename], unit, average, getpt, antenna)
171 self._fill([filename], unit, average, opts)
172 elif os.path.isfile(filename):
173 #self._fill([filename], unit, average, getpt, antenna)
174 self._fill([filename], unit, average)
175 else:
176 msg = "The given file '%s'is not a valid " \
177 "asap table." % (filename)
178 raise IOError(msg)
179 elif (isinstance(filename, list) or isinstance(filename, tuple)) \
180 and isinstance(filename[-1], str):
181 #self._fill(filename, unit, average, getpt, antenna)
182 self._fill(filename, unit, average)
183 self.parallactify(parallactify)
184 self._add_history("scantable", varlist)
185
186 @asaplog_post_dec
187 def save(self, name=None, format=None, overwrite=False):
188 """\
189 Store the scantable on disk. This can be an asap (aips++) Table,
190 SDFITS or MS2 format.
191
192 Parameters:
193
194 name: the name of the outputfile. For format "ASCII"
195 this is the root file name (data in 'name'.txt
196 and header in 'name'_header.txt)
197
198 format: an optional file format. Default is ASAP.
199 Allowed are:
200
201 * 'ASAP' (save as ASAP [aips++] Table),
202 * 'SDFITS' (save as SDFITS file)
203 * 'ASCII' (saves as ascii text file)
204 * 'MS2' (saves as an casacore MeasurementSet V2)
205 * 'FITS' (save as image FITS - not readable by class)
206 * 'CLASS' (save as FITS readable by CLASS)
207
208 overwrite: If the file should be overwritten if it exists.
209 The default False is to return with warning
210 without writing the output. USE WITH CARE.
211
212 Example::
213
214 scan.save('myscan.asap')
215 scan.save('myscan.sdfits', 'SDFITS')
216
217 """
218 from os import path
219 format = format or rcParams['scantable.save']
220 suffix = '.'+format.lower()
221 if name is None or name == "":
222 name = 'scantable'+suffix
223 msg = "No filename given. Using default name %s..." % name
224 asaplog.push(msg)
225 name = path.expandvars(name)
226 if path.isfile(name) or path.isdir(name):
227 if not overwrite:
228 msg = "File %s exists." % name
229 raise IOError(msg)
230 format2 = format.upper()
231 if format2 == 'ASAP':
232 self._save(name)
233 else:
234 from asap._asap import stwriter as stw
235 writer = stw(format2)
236 writer.write(self, name)
237 return
238
239 def copy(self):
240 """Return a copy of this scantable.
241
242 *Note*:
243
244 This makes a full (deep) copy. scan2 = scan1 makes a reference.
245
246 Example::
247
248 copiedscan = scan.copy()
249
250 """
251 sd = scantable(Scantable._copy(self))
252 return sd
253
254 def drop_scan(self, scanid=None):
255 """\
256 Return a new scantable where the specified scan number(s) has(have)
257 been dropped.
258
259 Parameters:
260
261 scanid: a (list of) scan number(s)
262
263 """
264 from asap import _is_sequence_or_number as _is_valid
265 from asap import _to_list
266 from asap import unique
267 if not _is_valid(scanid):
268 raise RuntimeError( 'Please specify a scanno to drop from the scantable' )
269 scanid = _to_list(scanid)
270 allscans = unique([ self.getscan(i) for i in range(self.nrow())])
271 for sid in scanid: allscans.remove(sid)
272 if len(allscans) == 0:
273 raise ValueError("Can't remove all scans")
274 sel = selector(scans=allscans)
275 return self._select_copy(sel)
276
277 def _select_copy(self, selection):
278 orig = self.get_selection()
279 self.set_selection(orig+selection)
280 cp = self.copy()
281 self.set_selection(orig)
282 return cp
283
284 def get_scan(self, scanid=None):
285 """\
286 Return a specific scan (by scanno) or collection of scans (by
287 source name) in a new scantable.
288
289 *Note*:
290
291 See scantable.drop_scan() for the inverse operation.
292
293 Parameters:
294
295 scanid: a (list of) scanno or a source name, unix-style
296 patterns are accepted for source name matching, e.g.
297 '*_R' gets all 'ref scans
298
299 Example::
300
301 # get all scans containing the source '323p459'
302 newscan = scan.get_scan('323p459')
303 # get all 'off' scans
304 refscans = scan.get_scan('*_R')
305 # get a susbset of scans by scanno (as listed in scan.summary())
306 newscan = scan.get_scan([0, 2, 7, 10])
307
308 """
309 if scanid is None:
310 raise RuntimeError( 'Please specify a scan no or name to '
311 'retrieve from the scantable' )
312 try:
313 bsel = self.get_selection()
314 sel = selector()
315 if type(scanid) is str:
316 sel.set_name(scanid)
317 return self._select_copy(sel)
318 elif type(scanid) is int:
319 sel.set_scans([scanid])
320 return self._select_copy(sel)
321 elif type(scanid) is list:
322 sel.set_scans(scanid)
323 return self._select_copy(sel)
324 else:
325 msg = "Illegal scanid type, use 'int' or 'list' if ints."
326 raise TypeError(msg)
327 except RuntimeError:
328 raise
329
330 def __str__(self):
331 return Scantable._summary(self, True)
332
333 def summary(self, filename=None):
334 """\
335 Print a summary of the contents of this scantable.
336
337 Parameters:
338
339 filename: the name of a file to write the putput to
340 Default - no file output
341
342 """
343 info = Scantable._summary(self, True)
344 if filename is not None:
345 if filename is "":
346 filename = 'scantable_summary.txt'
347 from os.path import expandvars, isdir
348 filename = expandvars(filename)
349 if not isdir(filename):
350 data = open(filename, 'w')
351 data.write(info)
352 data.close()
353 else:
354 msg = "Illegal file name '%s'." % (filename)
355 raise IOError(msg)
356 return page(info)
357
358 def get_spectrum(self, rowno):
359 """Return the spectrum for the current row in the scantable as a list.
360
361 Parameters:
362
363 rowno: the row number to retrieve the spectrum from
364
365 """
366 return self._getspectrum(rowno)
367
368 def get_mask(self, rowno):
369 """Return the mask for the current row in the scantable as a list.
370
371 Parameters:
372
373 rowno: the row number to retrieve the mask from
374
375 """
376 return self._getmask(rowno)
377
378 def set_spectrum(self, spec, rowno):
379 """Return the spectrum for the current row in the scantable as a list.
380
381 Parameters:
382
383 spec: the new spectrum
384
385 rowno: the row number to set the spectrum for
386
387 """
388 assert(len(spec) == self.nchan())
389 return self._setspectrum(spec, rowno)
390
391 def get_coordinate(self, rowno):
392 """Return the (spectral) coordinate for a a given 'rowno'.
393
394 *Note*:
395
396 * This coordinate is only valid until a scantable method modifies
397 the frequency axis.
398 * This coordinate does contain the original frequency set-up
399 NOT the new frame. The conversions however are done using the user
400 specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate,
401 use scantable.freq_align first. Without it there is no closure,
402 i.e.::
403
404 c = myscan.get_coordinate(0)
405 c.to_frequency(c.get_reference_pixel()) != c.get_reference_value()
406
407 Parameters:
408
409 rowno: the row number for the spectral coordinate
410
411 """
412 return coordinate(Scantable.get_coordinate(self, rowno))
413
414 def get_selection(self):
415 """\
416 Get the selection object currently set on this scantable.
417
418 Example::
419
420 sel = scan.get_selection()
421 sel.set_ifs(0) # select IF 0
422 scan.set_selection(sel) # apply modified selection
423
424 """
425 return selector(self._getselection())
426
427 def set_selection(self, selection=None, **kw):
428 """\
429 Select a subset of the data. All following operations on this scantable
430 are only applied to thi selection.
431
432 Parameters:
433
434 selection: a selector object (default unset the selection), or
435 any combination of "pols", "ifs", "beams", "scans",
436 "cycles", "name", "query"
437
438 Examples::
439
440 sel = selector() # create a selection object
441 self.set_scans([0, 3]) # select SCANNO 0 and 3
442 scan.set_selection(sel) # set the selection
443 scan.summary() # will only print summary of scanno 0 an 3
444 scan.set_selection() # unset the selection
445 # or the equivalent
446 scan.set_selection(scans=[0,3])
447 scan.summary() # will only print summary of scanno 0 an 3
448 scan.set_selection() # unset the selection
449
450 """
451 if selection is None:
452 # reset
453 if len(kw) == 0:
454 selection = selector()
455 else:
456 # try keywords
457 for k in kw:
458 if k not in selector.fields:
459 raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields))
460 selection = selector(**kw)
461 self._setselection(selection)
462
463 def get_row(self, row=0, insitu=None):
464 """\
465 Select a row in the scantable.
466 Return a scantable with single row.
467
468 Parameters:
469
470 row: row no of integration, default is 0.
471 insitu: if False a new scantable is returned. Otherwise, the
472 scaling is done in-situ. The default is taken from .asaprc
473 (False)
474
475 """
476 if insitu is None: insitu = rcParams['insitu']
477 if not insitu:
478 workscan = self.copy()
479 else:
480 workscan = self
481 # Select a row
482 sel=selector()
483 sel.set_scans([workscan.getscan(row)])
484 sel.set_cycles([workscan.getcycle(row)])
485 sel.set_beams([workscan.getbeam(row)])
486 sel.set_ifs([workscan.getif(row)])
487 sel.set_polarisations([workscan.getpol(row)])
488 sel.set_name(workscan._getsourcename(row))
489 workscan.set_selection(sel)
490 if not workscan.nrow() == 1:
491 msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow())
492 raise RuntimeError(msg)
493 del sel
494 if insitu:
495 self._assign(workscan)
496 else:
497 return workscan
498
499 @asaplog_post_dec
500 def stats(self, stat='stddev', mask=None, form='3.3f', row=None):
501 """\
502 Determine the specified statistic of the current beam/if/pol
503 Takes a 'mask' as an optional parameter to specify which
504 channels should be excluded.
505
506 Parameters:
507
508 stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum',
509 'mean', 'var', 'stddev', 'avdev', 'rms', 'median'
510
511 mask: an optional mask specifying where the statistic
512 should be determined.
513
514 form: format string to print statistic values
515
516 row: row number of spectrum to process.
517 (default is None: for all rows)
518
519 Example:
520 scan.set_unit('channel')
521 msk = scan.create_mask([100, 200], [500, 600])
522 scan.stats(stat='mean', mask=m)
523
524 """
525 mask = mask or []
526 if not self._check_ifs():
527 raise ValueError("Cannot apply mask as the IFs have different "
528 "number of channels. Please use setselection() "
529 "to select individual IFs")
530 rtnabc = False
531 if stat.lower().endswith('_abc'): rtnabc = True
532 getchan = False
533 if stat.lower().startswith('min') or stat.lower().startswith('max'):
534 chan = self._math._minmaxchan(self, mask, stat)
535 getchan = True
536 statvals = []
537 if not rtnabc:
538 if row == None:
539 statvals = self._math._stats(self, mask, stat)
540 else:
541 statvals = self._math._statsrow(self, mask, stat, int(row))
542
543 #def cb(i):
544 # return statvals[i]
545
546 #return self._row_callback(cb, stat)
547
548 label=stat
549 #callback=cb
550 out = ""
551 #outvec = []
552 sep = '-'*50
553
554 if row == None:
555 rows = xrange(self.nrow())
556 elif isinstance(row, int):
557 rows = [ row ]
558
559 for i in rows:
560 refstr = ''
561 statunit= ''
562 if getchan:
563 qx, qy = self.chan2data(rowno=i, chan=chan[i])
564 if rtnabc:
565 statvals.append(qx['value'])
566 refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])'
567 statunit= '['+qx['unit']+']'
568 else:
569 refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])'
570
571 tm = self._gettime(i)
572 src = self._getsourcename(i)
573 out += 'Scan[%d] (%s) ' % (self.getscan(i), src)
574 out += 'Time[%s]:\n' % (tm)
575 if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (self.getbeam(i))
576 if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i))
577 if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i))
578 #outvec.append(callback(i))
579 if len(rows) > 1:
580 # out += ('= %'+form) % (outvec[i]) +' '+refstr+'\n'
581 out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n'
582 else:
583 # out += ('= %'+form) % (outvec[0]) +' '+refstr+'\n'
584 out += ('= %'+form) % (statvals[0]) +' '+refstr+'\n'
585 out += sep+"\n"
586
587 import os
588 if os.environ.has_key( 'USER' ):
589 usr = os.environ['USER']
590 else:
591 import commands
592 usr = commands.getoutput( 'whoami' )
593 tmpfile = '/tmp/tmp_'+usr+'_casapy_asap_scantable_stats'
594 f = open(tmpfile,'w')
595 print >> f, sep
596 print >> f, ' %s %s' % (label, statunit)
597 print >> f, sep
598 print >> f, out
599 f.close()
600 f = open(tmpfile,'r')
601 x = f.readlines()
602 f.close()
603 asaplog.push(''.join(x), False)
604
605 return statvals
606
607 def chan2data(self, rowno=0, chan=0):
608 """\
609 Returns channel/frequency/velocity and spectral value
610 at an arbitrary row and channel in the scantable.
611
612 Parameters:
613
614 rowno: a row number in the scantable. Default is the
615 first row, i.e. rowno=0
616
617 chan: a channel in the scantable. Default is the first
618 channel, i.e. pos=0
619
620 """
621 if isinstance(rowno, int) and isinstance(chan, int):
622 qx = {'unit': self.get_unit(),
623 'value': self._getabcissa(rowno)[chan]}
624 qy = {'unit': self.get_fluxunit(),
625 'value': self._getspectrum(rowno)[chan]}
626 return qx, qy
627
628 def stddev(self, mask=None):
629 """\
630 Determine the standard deviation of the current beam/if/pol
631 Takes a 'mask' as an optional parameter to specify which
632 channels should be excluded.
633
634 Parameters:
635
636 mask: an optional mask specifying where the standard
637 deviation should be determined.
638
639 Example::
640
641 scan.set_unit('channel')
642 msk = scan.create_mask([100, 200], [500, 600])
643 scan.stddev(mask=m)
644
645 """
646 return self.stats(stat='stddev', mask=mask);
647
648
649 def get_column_names(self):
650 """\
651 Return a list of column names, which can be used for selection.
652 """
653 return list(Scantable.get_column_names(self))
654
655 def get_tsys(self, row=-1):
656 """\
657 Return the System temperatures.
658
659 Parameters:
660
661 row: the rowno to get the information for. (default all rows)
662
663 Returns:
664
665 a list of Tsys values for the current selection
666
667 """
668 if row > -1:
669 return self._get_column(self._gettsys, row)
670 return self._row_callback(self._gettsys, "Tsys")
671
672
673 def get_weather(self, row=-1):
674 """\
675 Return the weather informations.
676
677 Parameters:
678
679 row: the rowno to get the information for. (default all rows)
680
681 Returns:
682
683 a dict or list of of dicts of values for the current selection
684
685 """
686
687 values = self._get_column(self._get_weather, row)
688 if row > -1:
689 return {'temperature': values[0],
690 'pressure': values[1], 'humidity' : values[2],
691 'windspeed' : values[3], 'windaz' : values[4]
692 }
693 else:
694 out = []
695 for r in values:
696
697 out.append({'temperature': r[0],
698 'pressure': r[1], 'humidity' : r[2],
699 'windspeed' : r[3], 'windaz' : r[4]
700 })
701 return out
702
703 def _row_callback(self, callback, label):
704 out = ""
705 outvec = []
706 sep = '-'*50
707 for i in range(self.nrow()):
708 tm = self._gettime(i)
709 src = self._getsourcename(i)
710 out += 'Scan[%d] (%s) ' % (self.getscan(i), src)
711 out += 'Time[%s]:\n' % (tm)
712 if self.nbeam(-1) > 1:
713 out += ' Beam[%d] ' % (self.getbeam(i))
714 if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i))
715 if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i))
716 outvec.append(callback(i))
717 out += '= %3.3f\n' % (outvec[i])
718 out += sep+'\n'
719
720 asaplog.push(sep)
721 asaplog.push(" %s" % (label))
722 asaplog.push(sep)
723 asaplog.push(out)
724 asaplog.post()
725 return outvec
726
727 def _get_column(self, callback, row=-1):
728 """
729 """
730 if row == -1:
731 return [callback(i) for i in range(self.nrow())]
732 else:
733 if 0 <= row < self.nrow():
734 return callback(row)
735
736
737 def get_time(self, row=-1, asdatetime=False):
738 """\
739 Get a list of time stamps for the observations.
740 Return a datetime object for each integration time stamp in the scantable.
741
742 Parameters:
743
744 row: row no of integration. Default -1 return all rows
745
746 asdatetime: return values as datetime objects rather than strings
747
748 """
749 from time import strptime
750 from datetime import datetime
751 times = self._get_column(self._gettime, row)
752 if not asdatetime:
753 return times
754 format = "%Y/%m/%d/%H:%M:%S"
755 if isinstance(times, list):
756 return [datetime(*strptime(i, format)[:6]) for i in times]
757 else:
758 return datetime(*strptime(times, format)[:6])
759
760
761 def get_inttime(self, row=-1):
762 """\
763 Get a list of integration times for the observations.
764 Return a time in seconds for each integration in the scantable.
765
766 Parameters:
767
768 row: row no of integration. Default -1 return all rows.
769
770 """
771 return self._get_column(self._getinttime, row)
772
773
774 def get_sourcename(self, row=-1):
775 """\
776 Get a list source names for the observations.
777 Return a string for each integration in the scantable.
778 Parameters:
779
780 row: row no of integration. Default -1 return all rows.
781
782 """
783 return self._get_column(self._getsourcename, row)
784
785 def get_elevation(self, row=-1):
786 """\
787 Get a list of elevations for the observations.
788 Return a float for each integration in the scantable.
789
790 Parameters:
791
792 row: row no of integration. Default -1 return all rows.
793
794 """
795 return self._get_column(self._getelevation, row)
796
797 def get_azimuth(self, row=-1):
798 """\
799 Get a list of azimuths for the observations.
800 Return a float for each integration in the scantable.
801
802 Parameters:
803 row: row no of integration. Default -1 return all rows.
804
805 """
806 return self._get_column(self._getazimuth, row)
807
808 def get_parangle(self, row=-1):
809 """\
810 Get a list of parallactic angles for the observations.
811 Return a float for each integration in the scantable.
812
813 Parameters:
814
815 row: row no of integration. Default -1 return all rows.
816
817 """
818 return self._get_column(self._getparangle, row)
819
820 def get_direction(self, row=-1):
821 """
822 Get a list of Positions on the sky (direction) for the observations.
823 Return a string for each integration in the scantable.
824
825 Parameters:
826
827 row: row no of integration. Default -1 return all rows
828
829 """
830 return self._get_column(self._getdirection, row)
831
832 def get_directionval(self, row=-1):
833 """\
834 Get a list of Positions on the sky (direction) for the observations.
835 Return a float for each integration in the scantable.
836
837 Parameters:
838
839 row: row no of integration. Default -1 return all rows
840
841 """
842 return self._get_column(self._getdirectionvec, row)
843
844 @asaplog_post_dec
845 def set_unit(self, unit='channel'):
846 """\
847 Set the unit for all following operations on this scantable
848
849 Parameters:
850
851 unit: optional unit, default is 'channel'. Use one of '*Hz',
852 'km/s', 'channel' or equivalent ''
853
854 """
855 varlist = vars()
856 if unit in ['', 'pixel', 'channel']:
857 unit = ''
858 inf = list(self._getcoordinfo())
859 inf[0] = unit
860 self._setcoordinfo(inf)
861 self._add_history("set_unit", varlist)
862
863 @asaplog_post_dec
864 def set_instrument(self, instr):
865 """\
866 Set the instrument for subsequent processing.
867
868 Parameters:
869
870 instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
871 'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
872
873 """
874 self._setInstrument(instr)
875 self._add_history("set_instument", vars())
876
877 @asaplog_post_dec
878 def set_feedtype(self, feedtype):
879 """\
880 Overwrite the feed type, which might not be set correctly.
881
882 Parameters:
883
884 feedtype: 'linear' or 'circular'
885
886 """
887 self._setfeedtype(feedtype)
888 self._add_history("set_feedtype", vars())
889
890 @asaplog_post_dec
891 def set_doppler(self, doppler='RADIO'):
892 """\
893 Set the doppler for all following operations on this scantable.
894
895 Parameters:
896
897 doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
898
899 """
900 varlist = vars()
901 inf = list(self._getcoordinfo())
902 inf[2] = doppler
903 self._setcoordinfo(inf)
904 self._add_history("set_doppler", vars())
905
906 @asaplog_post_dec
907 def set_freqframe(self, frame=None):
908 """\
909 Set the frame type of the Spectral Axis.
910
911 Parameters:
912
913 frame: an optional frame type, default 'LSRK'. Valid frames are:
914 'TOPO', 'LSRD', 'LSRK', 'BARY',
915 'GEO', 'GALACTO', 'LGROUP', 'CMB'
916
917 Example::
918
919 scan.set_freqframe('BARY')
920
921 """
922 frame = frame or rcParams['scantable.freqframe']
923 varlist = vars()
924 # "REST" is not implemented in casacore
925 #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
926 # 'GEO', 'GALACTO', 'LGROUP', 'CMB']
927 valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \
928 'GEO', 'GALACTO', 'LGROUP', 'CMB']
929
930 if frame in valid:
931 inf = list(self._getcoordinfo())
932 inf[1] = frame
933 self._setcoordinfo(inf)
934 self._add_history("set_freqframe", varlist)
935 else:
936 msg = "Please specify a valid freq type. Valid types are:\n", valid
937 raise TypeError(msg)
938
939 @asaplog_post_dec
940 def set_dirframe(self, frame=""):
941 """\
942 Set the frame type of the Direction on the sky.
943
944 Parameters:
945
946 frame: an optional frame type, default ''. Valid frames are:
947 'J2000', 'B1950', 'GALACTIC'
948
949 Example:
950
951 scan.set_dirframe('GALACTIC')
952
953 """
954 varlist = vars()
955 Scantable.set_dirframe(self, frame)
956 self._add_history("set_dirframe", varlist)
957
958 def get_unit(self):
959 """\
960 Get the default unit set in this scantable
961
962 Returns:
963
964 A unit string
965
966 """
967 inf = self._getcoordinfo()
968 unit = inf[0]
969 if unit == '': unit = 'channel'
970 return unit
971
972 @asaplog_post_dec
973 def get_abcissa(self, rowno=0):
974 """\
975 Get the abcissa in the current coordinate setup for the currently
976 selected Beam/IF/Pol
977
978 Parameters:
979
980 rowno: an optional row number in the scantable. Default is the
981 first row, i.e. rowno=0
982
983 Returns:
984
985 The abcissa values and the format string (as a dictionary)
986
987 """
988 abc = self._getabcissa(rowno)
989 lbl = self._getabcissalabel(rowno)
990 return abc, lbl
991
992 @asaplog_post_dec
993 def flag(self, mask=None, unflag=False):
994 """\
995 Flag the selected data using an optional channel mask.
996
997 Parameters:
998
999 mask: an optional channel mask, created with create_mask. Default
1000 (no mask) is all channels.
1001
1002 unflag: if True, unflag the data
1003
1004 """
1005 varlist = vars()
1006 mask = mask or []
1007 self._flag(mask, unflag)
1008 self._add_history("flag", varlist)
1009
1010 @asaplog_post_dec
1011 def flag_row(self, rows=[], unflag=False):
1012 """\
1013 Flag the selected data in row-based manner.
1014
1015 Parameters:
1016
1017 rows: list of row numbers to be flagged. Default is no row
1018 (must be explicitly specified to execute row-based flagging).
1019
1020 unflag: if True, unflag the data.
1021
1022 """
1023 varlist = vars()
1024 self._flag_row(rows, unflag)
1025 self._add_history("flag_row", varlist)
1026
1027 @asaplog_post_dec
1028 def clip(self, uthres=None, dthres=None, clipoutside=True, unflag=False):
1029 """\
1030 Flag the selected data outside a specified range (in channel-base)
1031
1032 Parameters:
1033
1034 uthres: upper threshold.
1035
1036 dthres: lower threshold
1037
1038 clipoutside: True for flagging data outside the range [dthres:uthres].
1039 False for glagging data inside the range.
1040
1041 unflag: if True, unflag the data.
1042
1043 """
1044 varlist = vars()
1045 self._clip(uthres, dthres, clipoutside, unflag)
1046 self._add_history("clip", varlist)
1047
1048 @asaplog_post_dec
1049 def lag_flag(self, start, end, unit="MHz", insitu=None):
1050 """\
1051 Flag the data in 'lag' space by providing a frequency to remove.
1052 Flagged data in the scantable gets interpolated over the region.
1053 No taper is applied.
1054
1055 Parameters:
1056
1057 start: the start frequency (really a period within the
1058 bandwidth) or period to remove
1059
1060 end: the end frequency or period to remove
1061
1062 unit: the frequency unit (default "MHz") or "" for
1063 explicit lag channels
1064
1065 *Notes*:
1066
1067 It is recommended to flag edges of the band or strong
1068 signals beforehand.
1069
1070 """
1071 if insitu is None: insitu = rcParams['insitu']
1072 self._math._setinsitu(insitu)
1073 varlist = vars()
1074 base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.}
1075 if not (unit == "" or base.has_key(unit)):
1076 raise ValueError("%s is not a valid unit." % unit)
1077 if unit == "":
1078 s = scantable(self._math._lag_flag(self, start, end, "lags"))
1079 else:
1080 s = scantable(self._math._lag_flag(self, start*base[unit],
1081 end*base[unit], "frequency"))
1082 s._add_history("lag_flag", varlist)
1083 if insitu:
1084 self._assign(s)
1085 else:
1086 return s
1087
1088 @asaplog_post_dec
1089 def create_mask(self, *args, **kwargs):
1090 """\
1091 Compute and return a mask based on [min, max] windows.
1092 The specified windows are to be INCLUDED, when the mask is
1093 applied.
1094
1095 Parameters:
1096
1097 [min, max], [min2, max2], ...
1098 Pairs of start/end points (inclusive)specifying the regions
1099 to be masked
1100
1101 invert: optional argument. If specified as True,
1102 return an inverted mask, i.e. the regions
1103 specified are EXCLUDED
1104
1105 row: create the mask using the specified row for
1106 unit conversions, default is row=0
1107 only necessary if frequency varies over rows.
1108
1109 Examples::
1110
1111 scan.set_unit('channel')
1112 # a)
1113 msk = scan.create_mask([400, 500], [800, 900])
1114 # masks everything outside 400 and 500
1115 # and 800 and 900 in the unit 'channel'
1116
1117 # b)
1118 msk = scan.create_mask([400, 500], [800, 900], invert=True)
1119 # masks the regions between 400 and 500
1120 # and 800 and 900 in the unit 'channel'
1121
1122 # c)
1123 #mask only channel 400
1124 msk = scan.create_mask([400])
1125
1126 """
1127 row = kwargs.get("row", 0)
1128 data = self._getabcissa(row)
1129 u = self._getcoordinfo()[0]
1130 if u == "":
1131 u = "channel"
1132 msg = "The current mask window unit is %s" % u
1133 i = self._check_ifs()
1134 if not i:
1135 msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
1136 asaplog.push(msg)
1137 n = self.nchan()
1138 msk = _n_bools(n, False)
1139 # test if args is a 'list' or a 'normal *args - UGLY!!!
1140
1141 ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
1142 and args or args[0]
1143 for window in ws:
1144 if len(window) == 1:
1145 window = [window[0], window[0]]
1146 if len(window) == 0 or len(window) > 2:
1147 raise ValueError("A window needs to be defined as [start(, end)]")
1148 if window[0] > window[1]:
1149 tmp = window[0]
1150 window[0] = window[1]
1151 window[1] = tmp
1152 for i in range(n):
1153 if data[i] >= window[0] and data[i] <= window[1]:
1154 msk[i] = True
1155 if kwargs.has_key('invert'):
1156 if kwargs.get('invert'):
1157 msk = mask_not(msk)
1158 return msk
1159
1160 def get_masklist(self, mask=None, row=0, silent=False):
1161 """\
1162 Compute and return a list of mask windows, [min, max].
1163
1164 Parameters:
1165
1166 mask: channel mask, created with create_mask.
1167
1168 row: calcutate the masklist using the specified row
1169 for unit conversions, default is row=0
1170 only necessary if frequency varies over rows.
1171
1172 Returns:
1173
1174 [min, max], [min2, max2], ...
1175 Pairs of start/end points (inclusive)specifying
1176 the masked regions
1177
1178 """
1179 if not (isinstance(mask,list) or isinstance(mask, tuple)):
1180 raise TypeError("The mask should be list or tuple.")
1181 if len(mask) < 2:
1182 raise TypeError("The mask elements should be > 1")
1183 if self.nchan() != len(mask):
1184 msg = "Number of channels in scantable != number of mask elements"
1185 raise TypeError(msg)
1186 data = self._getabcissa(row)
1187 u = self._getcoordinfo()[0]
1188 if u == "":
1189 u = "channel"
1190 msg = "The current mask window unit is %s" % u
1191 i = self._check_ifs()
1192 if not i:
1193 msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
1194 if not silent:
1195 asaplog.push(msg)
1196 masklist=[]
1197 ist, ien = None, None
1198 ist, ien=self.get_mask_indices(mask)
1199 if ist is not None and ien is not None:
1200 for i in xrange(len(ist)):
1201 range=[data[ist[i]],data[ien[i]]]
1202 range.sort()
1203 masklist.append([range[0],range[1]])
1204 return masklist
1205
1206 def get_mask_indices(self, mask=None):
1207 """\
1208 Compute and Return lists of mask start indices and mask end indices.
1209
1210 Parameters:
1211
1212 mask: channel mask, created with create_mask.
1213
1214 Returns:
1215
1216 List of mask start indices and that of mask end indices,
1217 i.e., [istart1,istart2,....], [iend1,iend2,....].
1218
1219 """
1220 if not (isinstance(mask,list) or isinstance(mask, tuple)):
1221 raise TypeError("The mask should be list or tuple.")
1222 if len(mask) < 2:
1223 raise TypeError("The mask elements should be > 1")
1224 istart=[]
1225 iend=[]
1226 if mask[0]: istart.append(0)
1227 for i in range(len(mask)-1):
1228 if not mask[i] and mask[i+1]:
1229 istart.append(i+1)
1230 elif mask[i] and not mask[i+1]:
1231 iend.append(i)
1232 if mask[len(mask)-1]: iend.append(len(mask)-1)
1233 if len(istart) != len(iend):
1234 raise RuntimeError("Numbers of mask start != mask end.")
1235 for i in range(len(istart)):
1236 if istart[i] > iend[i]:
1237 raise RuntimeError("Mask start index > mask end index")
1238 break
1239 return istart,iend
1240
1241# def get_restfreqs(self):
1242# """
1243# Get the restfrequency(s) stored in this scantable.
1244# The return value(s) are always of unit 'Hz'
1245# Parameters:
1246# none
1247# Returns:
1248# a list of doubles
1249# """
1250# return list(self._getrestfreqs())
1251
1252 def get_restfreqs(self, ids=None):
1253 """\
1254 Get the restfrequency(s) stored in this scantable.
1255 The return value(s) are always of unit 'Hz'
1256
1257 Parameters:
1258
1259 ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to
1260 be retrieved
1261
1262 Returns:
1263
1264 dictionary containing ids and a list of doubles for each id
1265
1266 """
1267 if ids is None:
1268 rfreqs={}
1269 idlist = self.getmolnos()
1270 for i in idlist:
1271 rfreqs[i]=list(self._getrestfreqs(i))
1272 return rfreqs
1273 else:
1274 if type(ids)==list or type(ids)==tuple:
1275 rfreqs={}
1276 for i in ids:
1277 rfreqs[i]=list(self._getrestfreqs(i))
1278 return rfreqs
1279 else:
1280 return list(self._getrestfreqs(ids))
1281 #return list(self._getrestfreqs(ids))
1282
1283 def set_restfreqs(self, freqs=None, unit='Hz'):
1284 """\
1285 Set or replace the restfrequency specified and
1286 If the 'freqs' argument holds a scalar,
1287 then that rest frequency will be applied to all the selected
1288 data. If the 'freqs' argument holds
1289 a vector, then it MUST be of equal or smaller length than
1290 the number of IFs (and the available restfrequencies will be
1291 replaced by this vector). In this case, *all* data have
1292 the restfrequency set per IF according
1293 to the corresponding value you give in the 'freqs' vector.
1294 E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
1295 IF 1 gets restfreq 2e9.
1296
1297 You can also specify the frequencies via a linecatalog.
1298
1299 Parameters:
1300
1301 freqs: list of rest frequency values or string idenitfiers
1302
1303 unit: unit for rest frequency (default 'Hz')
1304
1305
1306 Example::
1307
1308 # set the given restfrequency for the all currently selected IFs
1309 scan.set_restfreqs(freqs=1.4e9)
1310 # set restfrequencies for the n IFs (n > 1) in the order of the
1311 # list, i.e
1312 # IF0 -> 1.4e9, IF1 -> 1.41e9, IF3 -> 1.42e9
1313 # len(list_of_restfreqs) == nIF
1314 # for nIF == 1 the following will set multiple restfrequency for
1315 # that IF
1316 scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9])
1317 # set multiple restfrequencies per IF. as a list of lists where
1318 # the outer list has nIF elements, the inner s arbitrary
1319 scan.set_restfreqs(freqs=[[1.4e9, 1.41e9], [1.67e9]])
1320
1321 *Note*:
1322
1323 To do more sophisticate Restfrequency setting, e.g. on a
1324 source and IF basis, use scantable.set_selection() before using
1325 this function::
1326
1327 # provided your scantable is called scan
1328 selection = selector()
1329 selection.set_name("ORION*")
1330 selection.set_ifs([1])
1331 scan.set_selection(selection)
1332 scan.set_restfreqs(freqs=86.6e9)
1333
1334 """
1335 varlist = vars()
1336 from asap import linecatalog
1337 # simple value
1338 if isinstance(freqs, int) or isinstance(freqs, float):
1339 self._setrestfreqs([freqs], [""], unit)
1340 # list of values
1341 elif isinstance(freqs, list) or isinstance(freqs, tuple):
1342 # list values are scalars
1343 if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
1344 if len(freqs) == 1:
1345 self._setrestfreqs(freqs, [""], unit)
1346 else:
1347 # allow the 'old' mode of setting mulitple IFs
1348 sel = selector()
1349 savesel = self._getselection()
1350 iflist = self.getifnos()
1351 if len(freqs)>len(iflist):
1352 raise ValueError("number of elements in list of list "
1353 "exeeds the current IF selections")
1354 iflist = self.getifnos()
1355 for i, fval in enumerate(freqs):
1356 sel.set_ifs(iflist[i])
1357 self._setselection(sel)
1358 self._setrestfreqs([fval], [""], unit)
1359 self._setselection(savesel)
1360
1361 # list values are dict, {'value'=, 'name'=)
1362 elif isinstance(freqs[-1], dict):
1363 values = []
1364 names = []
1365 for d in freqs:
1366 values.append(d["value"])
1367 names.append(d["name"])
1368 self._setrestfreqs(values, names, unit)
1369 elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple):
1370 sel = selector()
1371 savesel = self._getselection()
1372 iflist = self.getifnos()
1373 if len(freqs)>len(iflist):
1374 raise ValueError("number of elements in list of list exeeds"
1375 " the current IF selections")
1376 for i, fval in enumerate(freqs):
1377 sel.set_ifs(iflist[i])
1378 self._setselection(sel)
1379 self._setrestfreqs(fval, [""], unit)
1380 self._setselection(savesel)
1381 # freqs are to be taken from a linecatalog
1382 elif isinstance(freqs, linecatalog):
1383 sel = selector()
1384 savesel = self._getselection()
1385 for i in xrange(freqs.nrow()):
1386 sel.set_ifs(iflist[i])
1387 self._setselection(sel)
1388 self._setrestfreqs([freqs.get_frequency(i)],
1389 [freqs.get_name(i)], "MHz")
1390 # ensure that we are not iterating past nIF
1391 if i == self.nif()-1: break
1392 self._setselection(savesel)
1393 else:
1394 return
1395 self._add_history("set_restfreqs", varlist)
1396
1397 def shift_refpix(self, delta):
1398 """\
1399 Shift the reference pixel of the Spectra Coordinate by an
1400 integer amount.
1401
1402 Parameters:
1403
1404 delta: the amount to shift by
1405
1406 *Note*:
1407
1408 Be careful using this with broadband data.
1409
1410 """
1411 Scantable.shift_refpix(self, delta)
1412
1413 @asaplog_post_dec
1414 def history(self, filename=None):
1415 """\
1416 Print the history. Optionally to a file.
1417
1418 Parameters:
1419
1420 filename: The name of the file to save the history to.
1421
1422 """
1423 hist = list(self._gethistory())
1424 out = "-"*80
1425 for h in hist:
1426 if h.startswith("---"):
1427 out = "\n".join([out, h])
1428 else:
1429 items = h.split("##")
1430 date = items[0]
1431 func = items[1]
1432 items = items[2:]
1433 out += "\n"+date+"\n"
1434 out += "Function: %s\n Parameters:" % (func)
1435 for i in items:
1436 s = i.split("=")
1437 out += "\n %s = %s" % (s[0], s[1])
1438 out = "\n".join([out, "-"*80])
1439 if filename is not None:
1440 if filename is "":
1441 filename = 'scantable_history.txt'
1442 import os
1443 filename = os.path.expandvars(os.path.expanduser(filename))
1444 if not os.path.isdir(filename):
1445 data = open(filename, 'w')
1446 data.write(out)
1447 data.close()
1448 else:
1449 msg = "Illegal file name '%s'." % (filename)
1450 raise IOError(msg)
1451 return page(out)
1452 #
1453 # Maths business
1454 #
1455 @asaplog_post_dec
1456 def average_time(self, mask=None, scanav=False, weight='tint', align=False):
1457 """\
1458 Return the (time) weighted average of a scan.
1459
1460 *Note*:
1461
1462 in channels only - align if necessary
1463
1464 Parameters:
1465
1466 mask: an optional mask (only used for 'var' and 'tsys'
1467 weighting)
1468
1469 scanav: True averages each scan separately
1470 False (default) averages all scans together,
1471
1472 weight: Weighting scheme.
1473 'none' (mean no weight)
1474 'var' (1/var(spec) weighted)
1475 'tsys' (1/Tsys**2 weighted)
1476 'tint' (integration time weighted)
1477 'tintsys' (Tint/Tsys**2)
1478 'median' ( median averaging)
1479 The default is 'tint'
1480
1481 align: align the spectra in velocity before averaging. It takes
1482 the time of the first spectrum as reference time.
1483
1484 Example::
1485
1486 # time average the scantable without using a mask
1487 newscan = scan.average_time()
1488
1489 """
1490 varlist = vars()
1491 weight = weight or 'TINT'
1492 mask = mask or ()
1493 scanav = (scanav and 'SCAN') or 'NONE'
1494 scan = (self, )
1495
1496 if align:
1497 scan = (self.freq_align(insitu=False), )
1498 s = None
1499 if weight.upper() == 'MEDIAN':
1500 s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
1501 scanav))
1502 else:
1503 s = scantable(self._math._average(scan, mask, weight.upper(),
1504 scanav))
1505 s._add_history("average_time", varlist)
1506 return s
1507
1508 @asaplog_post_dec
1509 def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
1510 """\
1511 Return a scan where all spectra are converted to either
1512 Jansky or Kelvin depending upon the flux units of the scan table.
1513 By default the function tries to look the values up internally.
1514 If it can't find them (or if you want to over-ride), you must
1515 specify EITHER jyperk OR eta (and D which it will try to look up
1516 also if you don't set it). jyperk takes precedence if you set both.
1517
1518 Parameters:
1519
1520 jyperk: the Jy / K conversion factor
1521
1522 eta: the aperture efficiency
1523
1524 d: the geomtric diameter (metres)
1525
1526 insitu: if False a new scantable is returned.
1527 Otherwise, the scaling is done in-situ
1528 The default is taken from .asaprc (False)
1529
1530 """
1531 if insitu is None: insitu = rcParams['insitu']
1532 self._math._setinsitu(insitu)
1533 varlist = vars()
1534 jyperk = jyperk or -1.0
1535 d = d or -1.0
1536 eta = eta or -1.0
1537 s = scantable(self._math._convertflux(self, d, eta, jyperk))
1538 s._add_history("convert_flux", varlist)
1539 if insitu: self._assign(s)
1540 else: return s
1541
1542 @asaplog_post_dec
1543 def gain_el(self, poly=None, filename="", method="linear", insitu=None):
1544 """\
1545 Return a scan after applying a gain-elevation correction.
1546 The correction can be made via either a polynomial or a
1547 table-based interpolation (and extrapolation if necessary).
1548 You specify polynomial coefficients, an ascii table or neither.
1549 If you specify neither, then a polynomial correction will be made
1550 with built in coefficients known for certain telescopes (an error
1551 will occur if the instrument is not known).
1552 The data and Tsys are *divided* by the scaling factors.
1553
1554 Parameters:
1555
1556 poly: Polynomial coefficients (default None) to compute a
1557 gain-elevation correction as a function of
1558 elevation (in degrees).
1559
1560 filename: The name of an ascii file holding correction factors.
1561 The first row of the ascii file must give the column
1562 names and these MUST include columns
1563 "ELEVATION" (degrees) and "FACTOR" (multiply data
1564 by this) somewhere.
1565 The second row must give the data type of the
1566 column. Use 'R' for Real and 'I' for Integer.
1567 An example file would be
1568 (actual factors are arbitrary) :
1569
1570 TIME ELEVATION FACTOR
1571 R R R
1572 0.1 0 0.8
1573 0.2 20 0.85
1574 0.3 40 0.9
1575 0.4 60 0.85
1576 0.5 80 0.8
1577 0.6 90 0.75
1578
1579 method: Interpolation method when correcting from a table.
1580 Values are "nearest", "linear" (default), "cubic"
1581 and "spline"
1582
1583 insitu: if False a new scantable is returned.
1584 Otherwise, the scaling is done in-situ
1585 The default is taken from .asaprc (False)
1586
1587 """
1588
1589 if insitu is None: insitu = rcParams['insitu']
1590 self._math._setinsitu(insitu)
1591 varlist = vars()
1592 poly = poly or ()
1593 from os.path import expandvars
1594 filename = expandvars(filename)
1595 s = scantable(self._math._gainel(self, poly, filename, method))
1596 s._add_history("gain_el", varlist)
1597 if insitu:
1598 self._assign(s)
1599 else:
1600 return s
1601
1602 @asaplog_post_dec
1603 def freq_align(self, reftime=None, method='cubic', insitu=None):
1604 """\
1605 Return a scan where all rows have been aligned in frequency/velocity.
1606 The alignment frequency frame (e.g. LSRK) is that set by function
1607 set_freqframe.
1608
1609 Parameters:
1610
1611 reftime: reference time to align at. By default, the time of
1612 the first row of data is used.
1613
1614 method: Interpolation method for regridding the spectra.
1615 Choose from "nearest", "linear", "cubic" (default)
1616 and "spline"
1617
1618 insitu: if False a new scantable is returned.
1619 Otherwise, the scaling is done in-situ
1620 The default is taken from .asaprc (False)
1621
1622 """
1623 if insitu is None: insitu = rcParams["insitu"]
1624 self._math._setinsitu(insitu)
1625 varlist = vars()
1626 reftime = reftime or ""
1627 s = scantable(self._math._freq_align(self, reftime, method))
1628 s._add_history("freq_align", varlist)
1629 if insitu: self._assign(s)
1630 else: return s
1631
1632 @asaplog_post_dec
1633 def opacity(self, tau=None, insitu=None):
1634 """\
1635 Apply an opacity correction. The data
1636 and Tsys are multiplied by the correction factor.
1637
1638 Parameters:
1639
1640 tau: (list of) opacity from which the correction factor is
1641 exp(tau*ZD)
1642 where ZD is the zenith-distance.
1643 If a list is provided, it has to be of length nIF,
1644 nIF*nPol or 1 and in order of IF/POL, e.g.
1645 [opif0pol0, opif0pol1, opif1pol0 ...]
1646 if tau is `None` the opacities are determined from a
1647 model.
1648
1649 insitu: if False a new scantable is returned.
1650 Otherwise, the scaling is done in-situ
1651 The default is taken from .asaprc (False)
1652
1653 """
1654 if insitu is None: insitu = rcParams['insitu']
1655 self._math._setinsitu(insitu)
1656 varlist = vars()
1657 if not hasattr(tau, "__len__"):
1658 tau = [tau]
1659 s = scantable(self._math._opacity(self, tau))
1660 s._add_history("opacity", varlist)
1661 if insitu: self._assign(s)
1662 else: return s
1663
1664 @asaplog_post_dec
1665 def bin(self, width=5, insitu=None):
1666 """\
1667 Return a scan where all spectra have been binned up.
1668
1669 Parameters:
1670
1671 width: The bin width (default=5) in pixels
1672
1673 insitu: if False a new scantable is returned.
1674 Otherwise, the scaling is done in-situ
1675 The default is taken from .asaprc (False)
1676
1677 """
1678 if insitu is None: insitu = rcParams['insitu']
1679 self._math._setinsitu(insitu)
1680 varlist = vars()
1681 s = scantable(self._math._bin(self, width))
1682 s._add_history("bin", varlist)
1683 if insitu:
1684 self._assign(s)
1685 else:
1686 return s
1687
1688 @asaplog_post_dec
1689 def resample(self, width=5, method='cubic', insitu=None):
1690 """\
1691 Return a scan where all spectra have been binned up.
1692
1693 Parameters:
1694
1695 width: The bin width (default=5) in pixels
1696
1697 method: Interpolation method when correcting from a table.
1698 Values are "nearest", "linear", "cubic" (default)
1699 and "spline"
1700
1701 insitu: if False a new scantable is returned.
1702 Otherwise, the scaling is done in-situ
1703 The default is taken from .asaprc (False)
1704
1705 """
1706 if insitu is None: insitu = rcParams['insitu']
1707 self._math._setinsitu(insitu)
1708 varlist = vars()
1709 s = scantable(self._math._resample(self, method, width))
1710 s._add_history("resample", varlist)
1711 if insitu: self._assign(s)
1712 else: return s
1713
1714 @asaplog_post_dec
1715 def average_pol(self, mask=None, weight='none'):
1716 """\
1717 Average the Polarisations together.
1718
1719 Parameters:
1720
1721 mask: An optional mask defining the region, where the
1722 averaging will be applied. The output will have all
1723 specified points masked.
1724
1725 weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
1726 weighted), or 'tsys' (1/Tsys**2 weighted)
1727
1728 """
1729 varlist = vars()
1730 mask = mask or ()
1731 s = scantable(self._math._averagepol(self, mask, weight.upper()))
1732 s._add_history("average_pol", varlist)
1733 return s
1734
1735 @asaplog_post_dec
1736 def average_beam(self, mask=None, weight='none'):
1737 """\
1738 Average the Beams together.
1739
1740 Parameters:
1741 mask: An optional mask defining the region, where the
1742 averaging will be applied. The output will have all
1743 specified points masked.
1744
1745 weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
1746 weighted), or 'tsys' (1/Tsys**2 weighted)
1747
1748 """
1749 varlist = vars()
1750 mask = mask or ()
1751 s = scantable(self._math._averagebeams(self, mask, weight.upper()))
1752 s._add_history("average_beam", varlist)
1753 return s
1754
1755 def parallactify(self, pflag):
1756 """\
1757 Set a flag to indicate whether this data should be treated as having
1758 been 'parallactified' (total phase == 0.0)
1759
1760 Parameters:
1761
1762 pflag: Bool indicating whether to turn this on (True) or
1763 off (False)
1764
1765 """
1766 varlist = vars()
1767 self._parallactify(pflag)
1768 self._add_history("parallactify", varlist)
1769
1770 @asaplog_post_dec
1771 def convert_pol(self, poltype=None):
1772 """\
1773 Convert the data to a different polarisation type.
1774 Note that you will need cross-polarisation terms for most conversions.
1775
1776 Parameters:
1777
1778 poltype: The new polarisation type. Valid types are:
1779 "linear", "circular", "stokes" and "linpol"
1780
1781 """
1782 varlist = vars()
1783 s = scantable(self._math._convertpol(self, poltype))
1784 s._add_history("convert_pol", varlist)
1785 return s
1786
1787 @asaplog_post_dec
1788 def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, insitu=None):
1789 """\
1790 Smooth the spectrum by the specified kernel (conserving flux).
1791
1792 Parameters:
1793
1794 kernel: The type of smoothing kernel. Select from
1795 'hanning' (default), 'gaussian', 'boxcar', 'rmedian'
1796 or 'poly'
1797
1798 width: The width of the kernel in pixels. For hanning this is
1799 ignored otherwise it defauls to 5 pixels.
1800 For 'gaussian' it is the Full Width Half
1801 Maximum. For 'boxcar' it is the full width.
1802 For 'rmedian' and 'poly' it is the half width.
1803
1804 order: Optional parameter for 'poly' kernel (default is 2), to
1805 specify the order of the polnomial. Ignored by all other
1806 kernels.
1807
1808 plot: plot the original and the smoothed spectra.
1809 In this each indivual fit has to be approved, by
1810 typing 'y' or 'n'
1811
1812 insitu: if False a new scantable is returned.
1813 Otherwise, the scaling is done in-situ
1814 The default is taken from .asaprc (False)
1815
1816 """
1817 if insitu is None: insitu = rcParams['insitu']
1818 self._math._setinsitu(insitu)
1819 varlist = vars()
1820
1821 if plot: orgscan = self.copy()
1822
1823 s = scantable(self._math._smooth(self, kernel.lower(), width, order))
1824 s._add_history("smooth", varlist)
1825
1826 if plot:
1827 if rcParams['plotter.gui']:
1828 from asap.asaplotgui import asaplotgui as asaplot
1829 else:
1830 from asap.asaplot import asaplot
1831 self._p=asaplot()
1832 self._p.set_panels()
1833 ylab=s._get_ordinate_label()
1834 #self._p.palette(0,["#777777","red"])
1835 for r in xrange(s.nrow()):
1836 xsm=s._getabcissa(r)
1837 ysm=s._getspectrum(r)
1838 xorg=orgscan._getabcissa(r)
1839 yorg=orgscan._getspectrum(r)
1840 self._p.clear()
1841 self._p.hold()
1842 self._p.set_axes('ylabel',ylab)
1843 self._p.set_axes('xlabel',s._getabcissalabel(r))
1844 self._p.set_axes('title',s._getsourcename(r))
1845 self._p.set_line(label='Original',color="#777777")
1846 self._p.plot(xorg,yorg)
1847 self._p.set_line(label='Smoothed',color="red")
1848 self._p.plot(xsm,ysm)
1849 ### Ugly part for legend
1850 for i in [0,1]:
1851 self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]])
1852 self._p.release()
1853 ### Ugly part for legend
1854 self._p.subplots[0]['lines']=[]
1855 res = raw_input("Accept smoothing ([y]/n): ")
1856 if res.upper() == 'N':
1857 s._setspectrum(yorg, r)
1858 self._p.unmap()
1859 self._p = None
1860 del orgscan
1861
1862 if insitu: self._assign(s)
1863 else: return s
1864
1865 @asaplog_post_dec
1866 def old_poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None, rows=None):
1867 """\
1868 Return a scan which has been baselined (all rows) by a polynomial.
1869
1870 Parameters:
1871
1872 mask: an optional mask
1873
1874 order: the order of the polynomial (default is 0)
1875
1876 plot: plot the fit and the residual. In this each
1877 indivual fit has to be approved, by typing 'y'
1878 or 'n'
1879
1880 uselin: use linear polynomial fit
1881
1882 insitu: if False a new scantable is returned.
1883 Otherwise, the scaling is done in-situ
1884 The default is taken from .asaprc (False)
1885
1886 rows: row numbers of spectra to be processed.
1887 (default is None: for all rows)
1888
1889 Example:
1890 # return a scan baselined by a third order polynomial,
1891 # not using a mask
1892 bscan = scan.poly_baseline(order=3)
1893
1894 """
1895 if insitu is None: insitu = rcParams['insitu']
1896 if not insitu:
1897 workscan = self.copy()
1898 else:
1899 workscan = self
1900 varlist = vars()
1901 if mask is None:
1902 mask = [True for i in xrange(self.nchan())]
1903
1904 try:
1905 f = fitter()
1906 if uselin:
1907 f.set_function(lpoly=order)
1908 else:
1909 f.set_function(poly=order)
1910
1911 if rows == None:
1912 rows = xrange(workscan.nrow())
1913 elif isinstance(rows, int):
1914 rows = [ rows ]
1915
1916 if len(rows) > 0:
1917 self.blpars = []
1918 self.masklists = []
1919 self.actualmask = []
1920
1921 for r in rows:
1922 f.x = workscan._getabcissa(r)
1923 f.y = workscan._getspectrum(r)
1924 f.mask = mask_and(mask, workscan._getmask(r)) # (CAS-1434)
1925 f.data = None
1926 f.fit()
1927 if plot:
1928 f.plot(residual=True)
1929 x = raw_input("Accept fit ( [y]/n ): ")
1930 if x.upper() == 'N':
1931 self.blpars.append(None)
1932 self.masklists.append(None)
1933 self.actualmask.append(None)
1934 continue
1935 workscan._setspectrum(f.fitter.getresidual(), r)
1936 self.blpars.append(f.get_parameters())
1937 self.masklists.append(workscan.get_masklist(f.mask, row=r, silent=True))
1938 self.actualmask.append(f.mask)
1939
1940 if plot:
1941 f._p.unmap()
1942 f._p = None
1943 workscan._add_history("poly_baseline", varlist)
1944 if insitu:
1945 self._assign(workscan)
1946 else:
1947 return workscan
1948 except RuntimeError:
1949 msg = "The fit failed, possibly because it didn't converge."
1950 raise RuntimeError(msg)
1951
1952 @asaplog_post_dec
1953 def poly_baseline(self, mask=None, order=0, plot=False, batch=False,
1954 insitu=None, rows=None):
1955 """\
1956 Return a scan which has been baselined (all rows) by a polynomial.
1957 Parameters:
1958 mask: an optional mask
1959 order: the order of the polynomial (default is 0)
1960 plot: plot the fit and the residual. In this each
1961 indivual fit has to be approved, by typing 'y'
1962 or 'n'. Ignored if batch = True.
1963 batch: if True a faster algorithm is used and logs
1964 including the fit results are not output
1965 (default is False)
1966 insitu: if False a new scantable is returned.
1967 Otherwise, the scaling is done in-situ
1968 The default is taken from .asaprc (False)
1969 rows: row numbers of spectra to be processed.
1970 (default is None: for all rows)
1971 Example:
1972 # return a scan baselined by a third order polynomial,
1973 # not using a mask
1974 bscan = scan.poly_baseline(order=3)
1975 """
1976 if insitu is None: insitu = rcParams["insitu"]
1977 varlist = vars()
1978 if insitu:
1979 workscan = self
1980 else:
1981 workscan = self.copy()
1982
1983 nchan = workscan.nchan()
1984
1985 if mask is None:
1986 mask = [True for i in xrange(nchan)]
1987
1988 try:
1989 if rows == None:
1990 rows = xrange(workscan.nrow())
1991 elif isinstance(rows, int):
1992 rows = [ rows ]
1993
1994 if len(rows) > 0:
1995 workscan.blpars = []
1996 workscan.masklists = []
1997 workscan.actualmask = []
1998
1999 if batch:
2000 workscan._poly_baseline_batch(mask, order)
2001 elif plot:
2002 f = fitter()
2003 f.set_function(lpoly=order)
2004 for r in rows:
2005 f.x = workscan._getabcissa(r)
2006 f.y = workscan._getspectrum(r)
2007 f.mask = mask_and(mask, workscan._getmask(r)) # (CAS-1434)
2008 f.data = None
2009 f.fit()
2010
2011 f.plot(residual=True)
2012 accept_fit = raw_input("Accept fit ( [y]/n ): ")
2013 if accept_fit.upper() == "N":
2014 self.blpars.append(None)
2015 self.masklists.append(None)
2016 self.actualmask.append(None)
2017 continue
2018 workscan._setspectrum(f.fitter.getresidual(), r)
2019 workscan.blpars.append(f.get_parameters())
2020 workscan.masklists.append(workscan.get_masklist(f.mask, row=r))
2021 workscan.actualmask.append(f.mask)
2022
2023 f._p.unmap()
2024 f._p = None
2025 else:
2026 for r in rows:
2027 fitparams = workscan._poly_baseline(mask, order, r)
2028 params = fitparams.getparameters()
2029 fmtd = ", ".join(["p%d = %3.6f" % (i, v) for i, v in enumerate(params)])
2030 errors = fitparams.geterrors()
2031 fmask = mask_and(mask, workscan._getmask(r))
2032
2033 workscan.blpars.append({"params":params,
2034 "fixed": fitparams.getfixedparameters(),
2035 "formatted":fmtd, "errors":errors})
2036 workscan.masklists.append(workscan.get_masklist(fmask, r, silent=True))
2037 workscan.actualmask.append(fmask)
2038
2039 asaplog.push(fmtd)
2040
2041 workscan._add_history("poly_baseline", varlist)
2042
2043 if insitu:
2044 self._assign(workscan)
2045 else:
2046 return workscan
2047
2048 except RuntimeError, e:
2049 msg = "The fit failed, possibly because it didn't converge."
2050 if rcParams["verbose"]:
2051 asaplog.push(str(e))
2052 asaplog.push(str(msg))
2053 return
2054 else:
2055 raise RuntimeError(str(e)+'\n'+msg)
2056
2057
2058 def auto_poly_baseline(self, mask=None, edge=(0, 0), order=0,
2059 threshold=3, chan_avg_limit=1, plot=False,
2060 insitu=None, rows=None):
2061 """\
2062 Return a scan which has been baselined (all rows) by a polynomial.
2063 Spectral lines are detected first using linefinder and masked out
2064 to avoid them affecting the baseline solution.
2065
2066 Parameters:
2067
2068 mask: an optional mask retreived from scantable
2069
2070 edge: an optional number of channel to drop at the edge of
2071 spectrum. If only one value is
2072 specified, the same number will be dropped from
2073 both sides of the spectrum. Default is to keep
2074 all channels. Nested tuples represent individual
2075 edge selection for different IFs (a number of spectral
2076 channels can be different)
2077
2078 order: the order of the polynomial (default is 0)
2079
2080 threshold: the threshold used by line finder. It is better to
2081 keep it large as only strong lines affect the
2082 baseline solution.
2083
2084 chan_avg_limit:
2085 a maximum number of consequtive spectral channels to
2086 average during the search of weak and broad lines.
2087 The default is no averaging (and no search for weak
2088 lines). If such lines can affect the fitted baseline
2089 (e.g. a high order polynomial is fitted), increase this
2090 parameter (usually values up to 8 are reasonable). Most
2091 users of this method should find the default value
2092 sufficient.
2093
2094 plot: plot the fit and the residual. In this each
2095 indivual fit has to be approved, by typing 'y'
2096 or 'n'
2097
2098 insitu: if False a new scantable is returned.
2099 Otherwise, the scaling is done in-situ
2100 The default is taken from .asaprc (False)
2101 rows: row numbers of spectra to be processed.
2102 (default is None: for all rows)
2103
2104
2105 Example::
2106
2107 scan2 = scan.auto_poly_baseline(order=7, insitu=False)
2108
2109 """
2110 if insitu is None: insitu = rcParams['insitu']
2111 varlist = vars()
2112 from asap.asaplinefind import linefinder
2113 from asap import _is_sequence_or_number as _is_valid
2114
2115 # check whether edge is set up for each IF individually
2116 individualedge = False;
2117 if len(edge) > 1:
2118 if isinstance(edge[0], list) or isinstance(edge[0], tuple):
2119 individualedge = True;
2120
2121 if not _is_valid(edge, int) and not individualedge:
2122 raise ValueError, "Parameter 'edge' has to be an integer or a \
2123 pair of integers specified as a tuple. Nested tuples are allowed \
2124 to make individual selection for different IFs."
2125
2126 curedge = (0, 0)
2127 if individualedge:
2128 for edgepar in edge:
2129 if not _is_valid(edgepar, int):
2130 raise ValueError, "Each element of the 'edge' tuple has \
2131 to be a pair of integers or an integer."
2132 else:
2133 curedge = edge;
2134
2135 if not insitu:
2136 workscan = self.copy()
2137 else:
2138 workscan = self
2139
2140 # setup fitter
2141 f = fitter()
2142 f.set_function(lpoly=order)
2143
2144 # setup line finder
2145 fl = linefinder()
2146 fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
2147
2148 fl.set_scan(workscan)
2149
2150 if mask is None:
2151 mask = _n_bools(workscan.nchan(), True)
2152
2153 if rows is None:
2154 rows = xrange(workscan.nrow())
2155 elif isinstance(rows, int):
2156 rows = [ rows ]
2157
2158 # Save parameters of baseline fits & masklists as a class attribute.
2159 # NOTICE: It does not reflect changes in scantable!
2160 if len(rows) > 0:
2161 self.blpars=[]
2162 self.masklists=[]
2163 self.actualmask=[]
2164 asaplog.push("Processing:")
2165 for r in rows:
2166 msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
2167 (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
2168 workscan.getpol(r), workscan.getcycle(r))
2169 asaplog.push(msg, False)
2170
2171 # figure out edge parameter
2172 if individualedge:
2173 if len(edge) >= workscan.getif(r):
2174 raise RuntimeError, "Number of edge elements appear to " \
2175 "be less than the number of IFs"
2176 curedge = edge[workscan.getif(r)]
2177
2178 actualmask = mask_and(mask, workscan._getmask(r)) # (CAS-1434)
2179
2180 # setup line finder
2181 fl.find_lines(r, actualmask, curedge)
2182
2183 f.x = workscan._getabcissa(r)
2184 f.y = workscan._getspectrum(r)
2185 f.mask = fl.get_mask()
2186 f.data = None
2187 f.fit()
2188
2189 # Show mask list
2190 masklist=workscan.get_masklist(f.mask, row=r, silent=True)
2191 msg = "mask range: "+str(masklist)
2192 asaplog.push(msg, False)
2193
2194 if plot:
2195 f.plot(residual=True)
2196 x = raw_input("Accept fit ( [y]/n ): ")
2197 if x.upper() == 'N':
2198 self.blpars.append(None)
2199 self.masklists.append(None)
2200 self.actualmask.append(None)
2201 continue
2202
2203 workscan._setspectrum(f.fitter.getresidual(), r)
2204 self.blpars.append(f.get_parameters())
2205 self.masklists.append(masklist)
2206 self.actualmask.append(f.mask)
2207 if plot:
2208 f._p.unmap()
2209 f._p = None
2210 workscan._add_history("auto_poly_baseline", varlist)
2211 if insitu:
2212 self._assign(workscan)
2213 else:
2214 return workscan
2215
2216 @asaplog_post_dec
2217 def rotate_linpolphase(self, angle):
2218 """\
2219 Rotate the phase of the complex polarization O=Q+iU correlation.
2220 This is always done in situ in the raw data. So if you call this
2221 function more than once then each call rotates the phase further.
2222
2223 Parameters:
2224
2225 angle: The angle (degrees) to rotate (add) by.
2226
2227 Example::
2228
2229 scan.rotate_linpolphase(2.3)
2230
2231 """
2232 varlist = vars()
2233 self._math._rotate_linpolphase(self, angle)
2234 self._add_history("rotate_linpolphase", varlist)
2235 return
2236
2237 @asaplog_post_dec
2238 def rotate_xyphase(self, angle):
2239 """\
2240 Rotate the phase of the XY correlation. This is always done in situ
2241 in the data. So if you call this function more than once
2242 then each call rotates the phase further.
2243
2244 Parameters:
2245
2246 angle: The angle (degrees) to rotate (add) by.
2247
2248 Example::
2249
2250 scan.rotate_xyphase(2.3)
2251
2252 """
2253 varlist = vars()
2254 self._math._rotate_xyphase(self, angle)
2255 self._add_history("rotate_xyphase", varlist)
2256 return
2257
2258 @asaplog_post_dec
2259 def swap_linears(self):
2260 """\
2261 Swap the linear polarisations XX and YY, or better the first two
2262 polarisations as this also works for ciculars.
2263 """
2264 varlist = vars()
2265 self._math._swap_linears(self)
2266 self._add_history("swap_linears", varlist)
2267 return
2268
2269 @asaplog_post_dec
2270 def invert_phase(self):
2271 """\
2272 Invert the phase of the complex polarisation
2273 """
2274 varlist = vars()
2275 self._math._invert_phase(self)
2276 self._add_history("invert_phase", varlist)
2277 return
2278
2279 @asaplog_post_dec
2280 def add(self, offset, insitu=None):
2281 """\
2282 Return a scan where all spectra have the offset added
2283
2284 Parameters:
2285
2286 offset: the offset
2287
2288 insitu: if False a new scantable is returned.
2289 Otherwise, the scaling is done in-situ
2290 The default is taken from .asaprc (False)
2291
2292 """
2293 if insitu is None: insitu = rcParams['insitu']
2294 self._math._setinsitu(insitu)
2295 varlist = vars()
2296 s = scantable(self._math._unaryop(self, offset, "ADD", False))
2297 s._add_history("add", varlist)
2298 if insitu:
2299 self._assign(s)
2300 else:
2301 return s
2302
2303 @asaplog_post_dec
2304 def scale(self, factor, tsys=True, insitu=None):
2305 """\
2306
2307 Return a scan where all spectra are scaled by the give 'factor'
2308
2309 Parameters:
2310
2311 factor: the scaling factor (float or 1D float list)
2312
2313 insitu: if False a new scantable is returned.
2314 Otherwise, the scaling is done in-situ
2315 The default is taken from .asaprc (False)
2316
2317 tsys: if True (default) then apply the operation to Tsys
2318 as well as the data
2319
2320 """
2321 if insitu is None: insitu = rcParams['insitu']
2322 self._math._setinsitu(insitu)
2323 varlist = vars()
2324 s = None
2325 import numpy
2326 if isinstance(factor, list) or isinstance(factor, numpy.ndarray):
2327 if isinstance(factor[0], list) or isinstance(factor[0], numpy.ndarray):
2328 from asapmath import _array2dOp
2329 s = _array2dOp( self.copy(), factor, "MUL", tsys )
2330 else:
2331 s = scantable( self._math._arrayop( self.copy(), factor, "MUL", tsys ) )
2332 else:
2333 s = scantable(self._math._unaryop(self.copy(), factor, "MUL", tsys))
2334 s._add_history("scale", varlist)
2335 if insitu:
2336 self._assign(s)
2337 else:
2338 return s
2339
2340 def set_sourcetype(self, match, matchtype="pattern",
2341 sourcetype="reference"):
2342 """\
2343 Set the type of the source to be an source or reference scan
2344 using the provided pattern.
2345
2346 Parameters:
2347
2348 match: a Unix style pattern, regular expression or selector
2349
2350 matchtype: 'pattern' (default) UNIX style pattern or
2351 'regex' regular expression
2352
2353 sourcetype: the type of the source to use (source/reference)
2354
2355 """
2356 varlist = vars()
2357 basesel = self.get_selection()
2358 stype = -1
2359 if sourcetype.lower().startswith("r"):
2360 stype = 1
2361 elif sourcetype.lower().startswith("s"):
2362 stype = 0
2363 else:
2364 raise ValueError("Illegal sourcetype use s(ource) or r(eference)")
2365 if matchtype.lower().startswith("p"):
2366 matchtype = "pattern"
2367 elif matchtype.lower().startswith("r"):
2368 matchtype = "regex"
2369 else:
2370 raise ValueError("Illegal matchtype, use p(attern) or r(egex)")
2371 sel = selector()
2372 if isinstance(match, selector):
2373 sel = match
2374 else:
2375 sel.set_query("SRCNAME == %s('%s')" % (matchtype, match))
2376 self.set_selection(basesel+sel)
2377 self._setsourcetype(stype)
2378 self.set_selection(basesel)
2379 self._add_history("set_sourcetype", varlist)
2380
2381 @asaplog_post_dec
2382 @preserve_selection
2383 def auto_quotient(self, preserve=True, mode='paired', verify=False):
2384 """\
2385 This function allows to build quotients automatically.
2386 It assumes the observation to have the same number of
2387 "ons" and "offs"
2388
2389 Parameters:
2390
2391 preserve: you can preserve (default) the continuum or
2392 remove it. The equations used are
2393
2394 preserve: Output = Toff * (on/off) - Toff
2395
2396 remove: Output = Toff * (on/off) - Ton
2397
2398 mode: the on/off detection mode
2399 'paired' (default)
2400 identifies 'off' scans by the
2401 trailing '_R' (Mopra/Parkes) or
2402 '_e'/'_w' (Tid) and matches
2403 on/off pairs from the observing pattern
2404 'time'
2405 finds the closest off in time
2406
2407 .. todo:: verify argument is not implemented
2408
2409 """
2410 varlist = vars()
2411 modes = ["time", "paired"]
2412 if not mode in modes:
2413 msg = "please provide valid mode. Valid modes are %s" % (modes)
2414 raise ValueError(msg)
2415 s = None
2416 if mode.lower() == "paired":
2417 sel = self.get_selection()
2418 sel.set_query("SRCTYPE==psoff")
2419 self.set_selection(sel)
2420 offs = self.copy()
2421 sel.set_query("SRCTYPE==pson")
2422 self.set_selection(sel)
2423 ons = self.copy()
2424 s = scantable(self._math._quotient(ons, offs, preserve))
2425 elif mode.lower() == "time":
2426 s = scantable(self._math._auto_quotient(self, mode, preserve))
2427 s._add_history("auto_quotient", varlist)
2428 return s
2429
2430 @asaplog_post_dec
2431 def mx_quotient(self, mask = None, weight='median', preserve=True):
2432 """\
2433 Form a quotient using "off" beams when observing in "MX" mode.
2434
2435 Parameters:
2436
2437 mask: an optional mask to be used when weight == 'stddev'
2438
2439 weight: How to average the off beams. Default is 'median'.
2440
2441 preserve: you can preserve (default) the continuum or
2442 remove it. The equations used are:
2443
2444 preserve: Output = Toff * (on/off) - Toff
2445
2446 remove: Output = Toff * (on/off) - Ton
2447
2448 """
2449 mask = mask or ()
2450 varlist = vars()
2451 on = scantable(self._math._mx_extract(self, 'on'))
2452 preoff = scantable(self._math._mx_extract(self, 'off'))
2453 off = preoff.average_time(mask=mask, weight=weight, scanav=False)
2454 from asapmath import quotient
2455 q = quotient(on, off, preserve)
2456 q._add_history("mx_quotient", varlist)
2457 return q
2458
2459 @asaplog_post_dec
2460 def freq_switch(self, insitu=None):
2461 """\
2462 Apply frequency switching to the data.
2463
2464 Parameters:
2465
2466 insitu: if False a new scantable is returned.
2467 Otherwise, the swictching is done in-situ
2468 The default is taken from .asaprc (False)
2469
2470 """
2471 if insitu is None: insitu = rcParams['insitu']
2472 self._math._setinsitu(insitu)
2473 varlist = vars()
2474 s = scantable(self._math._freqswitch(self))
2475 s._add_history("freq_switch", varlist)
2476 if insitu:
2477 self._assign(s)
2478 else:
2479 return s
2480
2481 @asaplog_post_dec
2482 def recalc_azel(self):
2483 """Recalculate the azimuth and elevation for each position."""
2484 varlist = vars()
2485 self._recalcazel()
2486 self._add_history("recalc_azel", varlist)
2487 return
2488
2489 @asaplog_post_dec
2490 def __add__(self, other):
2491 varlist = vars()
2492 s = None
2493 if isinstance(other, scantable):
2494 s = scantable(self._math._binaryop(self, other, "ADD"))
2495 elif isinstance(other, float):
2496 s = scantable(self._math._unaryop(self, other, "ADD", False))
2497 else:
2498 raise TypeError("Other input is not a scantable or float value")
2499 s._add_history("operator +", varlist)
2500 return s
2501
2502 @asaplog_post_dec
2503 def __sub__(self, other):
2504 """
2505 implicit on all axes and on Tsys
2506 """
2507 varlist = vars()
2508 s = None
2509 if isinstance(other, scantable):
2510 s = scantable(self._math._binaryop(self, other, "SUB"))
2511 elif isinstance(other, float):
2512 s = scantable(self._math._unaryop(self, other, "SUB", False))
2513 else:
2514 raise TypeError("Other input is not a scantable or float value")
2515 s._add_history("operator -", varlist)
2516 return s
2517
2518 @asaplog_post_dec
2519 def __mul__(self, other):
2520 """
2521 implicit on all axes and on Tsys
2522 """
2523 varlist = vars()
2524 s = None
2525 if isinstance(other, scantable):
2526 s = scantable(self._math._binaryop(self, other, "MUL"))
2527 elif isinstance(other, float):
2528 s = scantable(self._math._unaryop(self, other, "MUL", False))
2529 else:
2530 raise TypeError("Other input is not a scantable or float value")
2531 s._add_history("operator *", varlist)
2532 return s
2533
2534
2535 @asaplog_post_dec
2536 def __div__(self, other):
2537 """
2538 implicit on all axes and on Tsys
2539 """
2540 varlist = vars()
2541 s = None
2542 if isinstance(other, scantable):
2543 s = scantable(self._math._binaryop(self, other, "DIV"))
2544 elif isinstance(other, float):
2545 if other == 0.0:
2546 raise ZeroDivisionError("Dividing by zero is not recommended")
2547 s = scantable(self._math._unaryop(self, other, "DIV", False))
2548 else:
2549 raise TypeError("Other input is not a scantable or float value")
2550 s._add_history("operator /", varlist)
2551 return s
2552
2553 @asaplog_post_dec
2554 def get_fit(self, row=0):
2555 """\
2556 Print or return the stored fits for a row in the scantable
2557
2558 Parameters:
2559
2560 row: the row which the fit has been applied to.
2561
2562 """
2563 if row > self.nrow():
2564 return
2565 from asap.asapfit import asapfit
2566 fit = asapfit(self._getfit(row))
2567 asaplog.push( '%s' %(fit) )
2568 return fit.as_dict()
2569
2570 def flag_nans(self):
2571 """\
2572 Utility function to flag NaN values in the scantable.
2573 """
2574 import numpy
2575 basesel = self.get_selection()
2576 for i in range(self.nrow()):
2577 sel = self.get_row_selector(i)
2578 self.set_selection(basesel+sel)
2579 nans = numpy.isnan(self._getspectrum(0))
2580 if numpy.any(nans):
2581 bnans = [ bool(v) for v in nans]
2582 self.flag(bnans)
2583 self.set_selection(basesel)
2584
2585 def get_row_selector(self, rowno):
2586 return selector(beams=self.getbeam(rowno),
2587 ifs=self.getif(rowno),
2588 pols=self.getpol(rowno),
2589 scans=self.getscan(rowno),
2590 cycles=self.getcycle(rowno))
2591
2592 def _add_history(self, funcname, parameters):
2593 if not rcParams['scantable.history']:
2594 return
2595 # create date
2596 sep = "##"
2597 from datetime import datetime
2598 dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
2599 hist = dstr+sep
2600 hist += funcname+sep#cdate+sep
2601 if parameters.has_key('self'): del parameters['self']
2602 for k, v in parameters.iteritems():
2603 if type(v) is dict:
2604 for k2, v2 in v.iteritems():
2605 hist += k2
2606 hist += "="
2607 if isinstance(v2, scantable):
2608 hist += 'scantable'
2609 elif k2 == 'mask':
2610 if isinstance(v2, list) or isinstance(v2, tuple):
2611 hist += str(self._zip_mask(v2))
2612 else:
2613 hist += str(v2)
2614 else:
2615 hist += str(v2)
2616 else:
2617 hist += k
2618 hist += "="
2619 if isinstance(v, scantable):
2620 hist += 'scantable'
2621 elif k == 'mask':
2622 if isinstance(v, list) or isinstance(v, tuple):
2623 hist += str(self._zip_mask(v))
2624 else:
2625 hist += str(v)
2626 else:
2627 hist += str(v)
2628 hist += sep
2629 hist = hist[:-2] # remove trailing '##'
2630 self._addhistory(hist)
2631
2632
2633 def _zip_mask(self, mask):
2634 mask = list(mask)
2635 i = 0
2636 segments = []
2637 while mask[i:].count(1):
2638 i += mask[i:].index(1)
2639 if mask[i:].count(0):
2640 j = i + mask[i:].index(0)
2641 else:
2642 j = len(mask)
2643 segments.append([i, j])
2644 i = j
2645 return segments
2646
2647 def _get_ordinate_label(self):
2648 fu = "("+self.get_fluxunit()+")"
2649 import re
2650 lbl = "Intensity"
2651 if re.match(".K.", fu):
2652 lbl = "Brightness Temperature "+ fu
2653 elif re.match(".Jy.", fu):
2654 lbl = "Flux density "+ fu
2655 return lbl
2656
2657 def _check_ifs(self):
2658 nchans = [self.nchan(i) for i in range(self.nif(-1))]
2659 nchans = filter(lambda t: t > 0, nchans)
2660 return (sum(nchans)/len(nchans) == nchans[0])
2661
2662 @asaplog_post_dec
2663 #def _fill(self, names, unit, average, getpt, antenna):
2664 def _fill(self, names, unit, average, opts={}):
2665 first = True
2666 fullnames = []
2667 for name in names:
2668 name = os.path.expandvars(name)
2669 name = os.path.expanduser(name)
2670 if not os.path.exists(name):
2671 msg = "File '%s' does not exists" % (name)
2672 raise IOError(msg)
2673 fullnames.append(name)
2674 if average:
2675 asaplog.push('Auto averaging integrations')
2676 stype = int(rcParams['scantable.storage'].lower() == 'disk')
2677 for name in fullnames:
2678 tbl = Scantable(stype)
2679 r = filler(tbl)
2680 rx = rcParams['scantable.reference']
2681 r.setreferenceexpr(rx)
2682 msg = "Importing %s..." % (name)
2683 asaplog.push(msg, False)
2684 #opts = {'ms': {'antenna' : antenna, 'getpt': getpt} }
2685 r.open(name, opts)# antenna, -1, -1, getpt)
2686 r.fill()
2687 if average:
2688 tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
2689 if not first:
2690 tbl = self._math._merge([self, tbl])
2691 Scantable.__init__(self, tbl)
2692 r.close()
2693 del r, tbl
2694 first = False
2695 #flush log
2696 asaplog.post()
2697 if unit is not None:
2698 self.set_fluxunit(unit)
2699 if not is_casapy():
2700 self.set_freqframe(rcParams['scantable.freqframe'])
2701
2702 def __getitem__(self, key):
2703 if key < 0:
2704 key += self.nrow()
2705 if key >= self.nrow():
2706 raise IndexError("Row index out of range.")
2707 return self._getspectrum(key)
2708
2709 def __setitem__(self, key, value):
2710 if key < 0:
2711 key += self.nrow()
2712 if key >= self.nrow():
2713 raise IndexError("Row index out of range.")
2714 if not hasattr(value, "__len__") or \
2715 len(value) > self.nchan(self.getif(key)):
2716 raise ValueError("Spectrum length doesn't match.")
2717 return self._setspectrum(value, key)
2718
2719 def __len__(self):
2720 return self.nrow()
2721
2722 def __iter__(self):
2723 for i in range(len(self)):
2724 yield self[i]
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