Context Navigation

source: trunk/python/scantable.py@ 1849

Visit:

Last change on this file since 1849 was 1846, checked in by Malte Marquarding, 14 years ago
Documentation update to play nicer with sphinx
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 91.6 KB

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

Note: See TracBrowser for help on using the repository browser.

Download in other formats: