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source: branches/alma/python/scantable.py@ 1655

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Last change on this file since 1655 was 1655, checked in by WataruKawasaki, 15 years ago

New Development: Yes

JIRA Issue: Yes (CAS-1433)

Ready to Release: Yes

Interface Changes: Yes

What Interface Changed: A new functionality flag_row() added

Test Programs:

Put in Release Notes: No

Module(s): sdflag

Description: Added a new functionality flag_row() to

enable row_based flagging/unflagging.

Property svn:eol-style set to native
Property svn:keywords set to Author Date Id Revision

File size: 85.3 KB

Line
1	from asap._asap import Scantable
2	from asap import rcParams
3	from asap import print_log
4	from asap import asaplog
5	from asap import selector
6	from asap import linecatalog
7	from asap import _n_bools, mask_not, mask_and, mask_or
8
9	class scantable(Scantable):
10	"""
11	The ASAP container for scans
12	"""
13
14	def __init__(self, filename, average=None, unit=None, getpt=None):
15	"""
16	Create a scantable from a saved one or make a reference
17	Parameters:
18	filename: the name of an asap table on disk
19	or
20	the name of a rpfits/sdfits/ms file
21	(integrations within scans are auto averaged
22	and the whole file is read)
23	or
24	[advanced] a reference to an existing
25	scantable
26	average: average all integrations withinb a scan on read.
27	The default (True) is taken from .asaprc.
28	unit: brightness unit; must be consistent with K or Jy.
29	Over-rides the default selected by the reader
30	(input rpfits/sdfits/ms) or replaces the value
31	in existing scantables
32	getpt: for MeasurementSet input data only:
33	If True, all pointing data are filled.
34	The deafult is False, which makes time to load
35	the MS data faster in some cases.
36	"""
37	if average is None:
38	average = rcParams['scantable.autoaverage']
39	if getpt is None:
40	getpt = False
41	varlist = vars()
42	from asap._asap import stmath
43	self._math = stmath()
44	if isinstance(filename, Scantable):
45	Scantable.__init__(self, filename)
46	else:
47	if isinstance(filename, str):# or \
48	# (isinstance(filename, list) or isinstance(filename, tuple)) \
49	# and isinstance(filename[-1], str):
50	import os.path
51	filename = os.path.expandvars(filename)
52	filename = os.path.expanduser(filename)
53	if not os.path.exists(filename):
54	s = "File '%s' not found." % (filename)
55	if rcParams['verbose']:
56	asaplog.push(s)
57	#print asaplog.pop().strip()
58	print_log('ERROR')
59	return
60	raise IOError(s)
61	if os.path.isdir(filename) \
62	and not os.path.exists(filename+'/table.f1'):
63	# crude check if asap table
64	if os.path.exists(filename+'/table.info'):
65	ondisk = rcParams['scantable.storage'] == 'disk'
66	Scantable.__init__(self, filename, ondisk)
67	if unit is not None:
68	self.set_fluxunit(unit)
69	# do not reset to the default freqframe
70	#self.set_freqframe(rcParams['scantable.freqframe'])
71	else:
72	msg = "The given file '%s'is not a valid " \
73	"asap table." % (filename)
74	if rcParams['verbose']:
75	#print msg
76	asaplog.push( msg )
77	print_log( 'ERROR' )
78	return
79	else:
80	raise IOError(msg)
81	else:
82	self._fill([filename], unit, average, getpt)
83	elif (isinstance(filename, list) or isinstance(filename, tuple)) \
84	and isinstance(filename[-1], str):
85	self._fill(filename, unit, average, getpt)
86	self._add_history("scantable", varlist)
87	print_log()
88
89	def save(self, name=None, format=None, overwrite=False):
90	"""
91	Store the scantable on disk. This can be an asap (aips++) Table,
92	SDFITS or MS2 format.
93	Parameters:
94	name: the name of the outputfile. For format "ASCII"
95	this is the root file name (data in 'name'.txt
96	and header in 'name'_header.txt)
97	format: an optional file format. Default is ASAP.
98	Allowed are - 'ASAP' (save as ASAP [aips++] Table),
99	'SDFITS' (save as SDFITS file)
100	'ASCII' (saves as ascii text file)
101	'MS2' (saves as an aips++
102	MeasurementSet V2)
103	'FITS' (save as image FITS - not
104	readable by class)
105	'CLASS' (save as FITS readable by CLASS)
106	overwrite: If the file should be overwritten if it exists.
107	The default False is to return with warning
108	without writing the output. USE WITH CARE.
109	Example:
110	scan.save('myscan.asap')
111	scan.save('myscan.sdfits', 'SDFITS')
112	"""
113	from os import path
114	if format is None: format = rcParams['scantable.save']
115	suffix = '.'+format.lower()
116	if name is None or name == "":
117	name = 'scantable'+suffix
118	msg = "No filename given. Using default name %s..." % name
119	asaplog.push(msg)
120	name = path.expandvars(name)
121	if path.isfile(name) or path.isdir(name):
122	if not overwrite:
123	msg = "File %s exists." % name
124	if rcParams['verbose']:
125	#print msg
126	asaplog.push( msg )
127	print_log( 'ERROR' )
128	return
129	else:
130	raise IOError(msg)
131	format2 = format.upper()
132	if format2 == 'ASAP':
133	self._save(name)
134	else:
135	from asap._asap import stwriter as stw
136	writer = stw(format2)
137	writer.write(self, name)
138	print_log()
139	return
140
141	def copy(self):
142	"""
143	Return a copy of this scantable.
144	Note:
145	This makes a full (deep) copy. scan2 = scan1 makes a reference.
146	Parameters:
147	none
148	Example:
149	copiedscan = scan.copy()
150	"""
151	sd = scantable(Scantable._copy(self))
152	return sd
153
154	def drop_scan(self, scanid=None):
155	"""
156	Return a new scantable where the specified scan number(s) has(have)
157	been dropped.
158	Parameters:
159	scanid: a (list of) scan number(s)
160	"""
161	from asap import _is_sequence_or_number as _is_valid
162	from asap import _to_list
163	from asap import unique
164	if not _is_valid(scanid):
165	if rcParams['verbose']:
166	#print "Please specify a scanno to drop from the scantable"
167	asaplog.push( 'Please specify a scanno to drop from the scantable' )
168	print_log( 'ERROR' )
169	return
170	else:
171	raise RuntimeError("No scan given")
172	try:
173	scanid = _to_list(scanid)
174	allscans = unique([ self.getscan(i) for i in range(self.nrow())])
175	for sid in scanid: allscans.remove(sid)
176	if len(allscans) == 0:
177	raise ValueError("Can't remove all scans")
178	except ValueError:
179	if rcParams['verbose']:
180	#print "Couldn't find any match."
181	print_log()
182	asaplog.push( "Couldn't find any match." )
183	print_log( 'ERROR' )
184	return
185	else: raise
186	try:
187	bsel = self.get_selection()
188	sel = selector()
189	sel.set_scans(allscans)
190	self.set_selection(bsel+sel)
191	scopy = self._copy()
192	self.set_selection(bsel)
193	return scantable(scopy)
194	except RuntimeError:
195	if rcParams['verbose']:
196	#print "Couldn't find any match."
197	print_log()
198	asaplog.push( "Couldn't find any match." )
199	print_log( 'ERROR' )
200	else:
201	raise
202
203
204	def get_scan(self, scanid=None):
205	"""
206	Return a specific scan (by scanno) or collection of scans (by
207	source name) in a new scantable.
208	Note:
209	See scantable.drop_scan() for the inverse operation.
210	Parameters:
211	scanid: a (list of) scanno or a source name, unix-style
212	patterns are accepted for source name matching, e.g.
213	'*_R' gets all 'ref scans
214	Example:
215	# get all scans containing the source '323p459'
216	newscan = scan.get_scan('323p459')
217	# get all 'off' scans
218	refscans = scan.get_scan('*_R')
219	# get a susbset of scans by scanno (as listed in scan.summary())
220	newscan = scan.get_scan([0, 2, 7, 10])
221	"""
222	if scanid is None:
223	if rcParams['verbose']:
224	#print "Please specify a scan no or name to " \
225	# "retrieve from the scantable"
226	asaplog.push( 'Please specify a scan no or name to retrieve from the scantable' )
227	print_log( 'ERROR' )
228	return
229	else:
230	raise RuntimeError("No scan given")
231
232	try:
233	bsel = self.get_selection()
234	sel = selector()
235	if type(scanid) is str:
236	sel.set_name(scanid)
237	self.set_selection(bsel+sel)
238	scopy = self._copy()
239	self.set_selection(bsel)
240	return scantable(scopy)
241	elif type(scanid) is int:
242	sel.set_scans([scanid])
243	self.set_selection(bsel+sel)
244	scopy = self._copy()
245	self.set_selection(bsel)
246	return scantable(scopy)
247	elif type(scanid) is list:
248	sel.set_scans(scanid)
249	self.set_selection(sel)
250	scopy = self._copy()
251	self.set_selection(bsel)
252	return scantable(scopy)
253	else:
254	msg = "Illegal scanid type, use 'int' or 'list' if ints."
255	if rcParams['verbose']:
256	#print msg
257	asaplog.push( msg )
258	print_log( 'ERROR' )
259	else:
260	raise TypeError(msg)
261	except RuntimeError:
262	if rcParams['verbose']:
263	#print "Couldn't find any match."
264	print_log()
265	asaplog.push( "Couldn't find any match." )
266	print_log( 'ERROR' )
267	else: raise
268
269	def __str__(self):
270	return Scantable._summary(self, True)
271
272	def summary(self, filename=None):
273	"""
274	Print a summary of the contents of this scantable.
275	Parameters:
276	filename: the name of a file to write the putput to
277	Default - no file output
278	verbose: print extra info such as the frequency table
279	The default (False) is taken from .asaprc
280	"""
281	info = Scantable._summary(self, True)
282	#if verbose is None: verbose = rcParams['scantable.verbosesummary']
283	if filename is not None:
284	if filename is "":
285	filename = 'scantable_summary.txt'
286	from os.path import expandvars, isdir
287	filename = expandvars(filename)
288	if not isdir(filename):
289	data = open(filename, 'w')
290	data.write(info)
291	data.close()
292	else:
293	msg = "Illegal file name '%s'." % (filename)
294	if rcParams['verbose']:
295	#print msg
296	asaplog.push( msg )
297	print_log( 'ERROR' )
298	else:
299	raise IOError(msg)
300	if rcParams['verbose']:
301	try:
302	from IPython.genutils import page as pager
303	except ImportError:
304	from pydoc import pager
305	pager(info)
306	else:
307	return info
308
309	def get_spectrum(self, rowno):
310	"""Return the spectrum for the current row in the scantable as a list.
311	Parameters:
312	rowno: the row number to retrieve the spectrum from
313	"""
314	return self._getspectrum(rowno)
315
316	def get_mask(self, rowno):
317	"""Return the mask for the current row in the scantable as a list.
318	Parameters:
319	rowno: the row number to retrieve the mask from
320	"""
321	return self._getmask(rowno)
322
323	def set_spectrum(self, spec, rowno):
324	"""Return the spectrum for the current row in the scantable as a list.
325	Parameters:
326	spec: the spectrum
327	rowno: the row number to set the spectrum for
328	"""
329	assert(len(spec) == self.nchan())
330	return self._setspectrum(spec, rowno)
331
332	def get_selection(self):
333	"""
334	Get the selection object currently set on this scantable.
335	Parameters:
336	none
337	Example:
338	sel = scan.get_selection()
339	sel.set_ifs(0) # select IF 0
340	scan.set_selection(sel) # apply modified selection
341	"""
342	return selector(self._getselection())
343
344	def set_selection(self, selection=selector()):
345	"""
346	Select a subset of the data. All following operations on this scantable
347	are only applied to thi selection.
348	Parameters:
349	selection: a selector object (default unset the selection)
350	Examples:
351	sel = selector() # create a selection object
352	self.set_scans([0, 3]) # select SCANNO 0 and 3
353	scan.set_selection(sel) # set the selection
354	scan.summary() # will only print summary of scanno 0 an 3
355	scan.set_selection() # unset the selection
356	"""
357	self._setselection(selection)
358
359	def get_row(self, row=0, insitu=None):
360	"""
361	Select a row in the scantable.
362	Return a scantable with single row.
363	Parameters:
364	row: row no of integration, default is 0.
365	insitu: if False a new scantable is returned.
366	Otherwise, the scaling is done in-situ
367	The default is taken from .asaprc (False)
368	"""
369	if insitu is None: insitu = rcParams['insitu']
370	if not insitu:
371	workscan = self.copy()
372	else:
373	workscan = self
374	# Select a row
375	sel=selector()
376	sel.set_scans([workscan.getscan(row)])
377	sel.set_cycles([workscan.getcycle(row)])
378	sel.set_beams([workscan.getbeam(row)])
379	sel.set_ifs([workscan.getif(row)])
380	sel.set_polarisations([workscan.getpol(row)])
381	sel.set_name(workscan._getsourcename(row))
382	workscan.set_selection(sel)
383	if not workscan.nrow() == 1:
384	msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow())
385	raise RuntimeError(msg)
386	del sel
387	if insitu:
388	self._assign(workscan)
389	else:
390	return workscan
391
392	#def stats(self, stat='stddev', mask=None):
393	def stats(self, stat='stddev', mask=None, form='3.3f'):
394	"""
395	Determine the specified statistic of the current beam/if/pol
396	Takes a 'mask' as an optional parameter to specify which
397	channels should be excluded.
398	Parameters:
399	stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum',
400	'mean', 'var', 'stddev', 'avdev', 'rms', 'median'
401	mask: an optional mask specifying where the statistic
402	should be determined.
403	form: format string to print statistic values
404	Example:
405	scan.set_unit('channel')
406	msk = scan.create_mask([100, 200], [500, 600])
407	scan.stats(stat='mean', mask=m)
408	"""
409	if mask == None:
410	mask = []
411	axes = ['Beam', 'IF', 'Pol', 'Time']
412	if not self._check_ifs():
413	raise ValueError("Cannot apply mask as the IFs have different "
414	"number of channels. Please use setselection() "
415	"to select individual IFs")
416	rtnabc = False
417	if stat.lower().endswith('_abc'): rtnabc = True
418	getchan = False
419	if stat.lower().startswith('min') or stat.lower().startswith('max'):
420	chan = self._math._minmaxchan(self, mask, stat)
421	getchan = True
422	statvals = []
423	if not rtnabc: statvals = self._math._stats(self, mask, stat)
424
425	out = ''
426	axes = []
427	for i in range(self.nrow()):
428	axis = []
429	axis.append(self.getscan(i))
430	axis.append(self.getbeam(i))
431	axis.append(self.getif(i))
432	axis.append(self.getpol(i))
433	axis.append(self.getcycle(i))
434	axes.append(axis)
435	tm = self._gettime(i)
436	src = self._getsourcename(i)
437	refstr = ''
438	statunit= ''
439	if getchan:
440	qx, qy = self.chan2data(rowno=i, chan=chan[i])
441	if rtnabc:
442	statvals.append(qx['value'])
443	#refstr = '(value: %3.3f' % (qy['value'])+' ['+qy['unit']+'])'
444	refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])'
445	statunit= '['+qx['unit']+']'
446	else:
447	#refstr = '(@ %3.3f' % (qx['value'])+' ['+qx['unit']+'])'
448	refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])'
449	#statunit= ' ['+qy['unit']+']'
450	out += 'Scan[%d] (%s) ' % (axis[0], src)
451	out += 'Time[%s]:\n' % (tm)
452	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
453	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
454	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
455	#out += '= %3.3f ' % (statvals[i]) +refstr+'\n'
456	out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n'
457	out += "--------------------------------------------------\n"
458
459	if rcParams['verbose']:
460	import os
461	if os.environ.has_key( 'USER' ):
462	usr=os.environ['USER']
463	else:
464	import commands
465	usr=commands.getoutput( 'whoami' )
466	tmpfile='/tmp/tmp_'+usr+'_casapy_asap_scantable_stats'
467	f=open(tmpfile,'w')
468	print >> f, "--------------------------------------------------"
469	print >> f, " ", stat, statunit
470	print >> f, "--------------------------------------------------"
471	print >> f, out
472	f.close()
473	f=open(tmpfile,'r')
474	x=f.readlines()
475	f.close()
476	for xx in x:
477	asaplog.push( xx )
478	print_log()
479	#else:
480	#retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'],
481	# 'axes' : axes,
482	# 'data': statvals}
483	return statvals
484
485	def chan2data(self, rowno=0, chan=0):
486	"""
487	Returns channel/frequency/velocity and spectral value
488	at an arbitrary row and channel in the scantable.
489	Parameters:
490	rowno: a row number in the scantable. Default is the
491	first row, i.e. rowno=0
492	chan: a channel in the scantable. Default is the first
493	channel, i.e. pos=0
494	"""
495	if isinstance(rowno, int) and isinstance(chan, int):
496	qx = {'unit': self.get_unit(),
497	'value': self._getabcissa(rowno)[chan]}
498	qy = {'unit': self.get_fluxunit(),
499	'value': self._getspectrum(rowno)[chan]}
500	return qx, qy
501
502	def stddev(self, mask=None):
503	"""
504	Determine the standard deviation of the current beam/if/pol
505	Takes a 'mask' as an optional parameter to specify which
506	channels should be excluded.
507	Parameters:
508	mask: an optional mask specifying where the standard
509	deviation should be determined.
510
511	Example:
512	scan.set_unit('channel')
513	msk = scan.create_mask([100, 200], [500, 600])
514	scan.stddev(mask=m)
515	"""
516	return self.stats(stat='stddev', mask=mask);
517
518
519	def get_column_names(self):
520	"""
521	Return a list of column names, which can be used for selection.
522	"""
523	return list(Scantable.get_column_names(self))
524
525	def get_tsys(self):
526	"""
527	Return the System temperatures.
528	Returns:
529	a list of Tsys values for the current selection
530	"""
531
532	return self._row_callback(self._gettsys, "Tsys")
533
534	def _row_callback(self, callback, label):
535	axes = []
536	axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno']
537	out = ""
538	outvec = []
539	for i in range(self.nrow()):
540	axis = []
541	axis.append(self.getscan(i))
542	axis.append(self.getbeam(i))
543	axis.append(self.getif(i))
544	axis.append(self.getpol(i))
545	axis.append(self.getcycle(i))
546	axes.append(axis)
547	tm = self._gettime(i)
548	src = self._getsourcename(i)
549	out += 'Scan[%d] (%s) ' % (axis[0], src)
550	out += 'Time[%s]:\n' % (tm)
551	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
552	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
553	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
554	outvec.append(callback(i))
555	out += '= %3.3f\n' % (outvec[i])
556	out += "--------------------------------------------------\n"
557	if rcParams['verbose']:
558	asaplog.push("--------------------------------------------------")
559	asaplog.push(" %s" % (label))
560	asaplog.push("--------------------------------------------------")
561	asaplog.push(out)
562	print_log()
563	# disabled because the vector seems more useful
564	#retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
565	return outvec
566
567	def _get_column(self, callback, row=-1):
568	"""
569	"""
570	if row == -1:
571	return [callback(i) for i in range(self.nrow())]
572	else:
573	if 0 <= row < self.nrow():
574	return callback(row)
575
576
577	def get_time(self, row=-1, asdatetime=False):
578	"""
579	Get a list of time stamps for the observations.
580	Return a datetime object for each integration time stamp in the scantable.
581	Parameters:
582	row: row no of integration. Default -1 return all rows
583	asdatetime: return values as datetime objects rather than strings
584	Example:
585	none
586	"""
587	from time import strptime
588	from datetime import datetime
589	times = self._get_column(self._gettime, row)
590	if not asdatetime:
591	return times
592	format = "%Y/%m/%d/%H:%M:%S"
593	if isinstance(times, list):
594	return [datetime(*strptime(i, format)[:6]) for i in times]
595	else:
596	return datetime(*strptime(times, format)[:6])
597
598
599	def get_inttime(self, row=-1):
600	"""
601	Get a list of integration times for the observations.
602	Return a time in seconds for each integration in the scantable.
603	Parameters:
604	row: row no of integration. Default -1 return all rows.
605	Example:
606	none
607	"""
608	return self._get_column(self._getinttime, row)
609
610
611	def get_sourcename(self, row=-1):
612	"""
613	Get a list source names for the observations.
614	Return a string for each integration in the scantable.
615	Parameters:
616	row: row no of integration. Default -1 return all rows.
617	Example:
618	none
619	"""
620	return self._get_column(self._getsourcename, row)
621
622	def get_elevation(self, row=-1):
623	"""
624	Get a list of elevations for the observations.
625	Return a float for each integration in the scantable.
626	Parameters:
627	row: row no of integration. Default -1 return all rows.
628	Example:
629	none
630	"""
631	return self._get_column(self._getelevation, row)
632
633	def get_azimuth(self, row=-1):
634	"""
635	Get a list of azimuths for the observations.
636	Return a float for each integration in the scantable.
637	Parameters:
638	row: row no of integration. Default -1 return all rows.
639	Example:
640	none
641	"""
642	return self._get_column(self._getazimuth, row)
643
644	def get_parangle(self, row=-1):
645	"""
646	Get a list of parallactic angles for the observations.
647	Return a float for each integration in the scantable.
648	Parameters:
649	row: row no of integration. Default -1 return all rows.
650	Example:
651	none
652	"""
653	return self._get_column(self._getparangle, row)
654
655	def get_direction(self, row=-1):
656	"""
657	Get a list of Positions on the sky (direction) for the observations.
658	Return a float for each integration in the scantable.
659	Parameters:
660	row: row no of integration. Default -1 return all rows
661	Example:
662	none
663	"""
664	return self._get_column(self._getdirection, row)
665
666	def get_directionval(self, row=-1):
667	"""
668	Get a list of Positions on the sky (direction) for the observations.
669	Return a float for each integration in the scantable.
670	Parameters:
671	row: row no of integration. Default -1 return all rows
672	Example:
673	none
674	"""
675	return self._get_column(self._getdirectionvec, row)
676
677	def set_unit(self, unit='channel'):
678	"""
679	Set the unit for all following operations on this scantable
680	Parameters:
681	unit: optional unit, default is 'channel'
682	one of '*Hz', 'km/s', 'channel', ''
683	"""
684	varlist = vars()
685	if unit in ['', 'pixel', 'channel']:
686	unit = ''
687	inf = list(self._getcoordinfo())
688	inf[0] = unit
689	self._setcoordinfo(inf)
690	self._add_history("set_unit", varlist)
691
692	def set_instrument(self, instr):
693	"""
694	Set the instrument for subsequent processing.
695	Parameters:
696	instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
697	'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
698	"""
699	self._setInstrument(instr)
700	self._add_history("set_instument", vars())
701	print_log()
702
703	def set_feedtype(self, feedtype):
704	"""
705	Overwrite the feed type, which might not be set correctly.
706	Parameters:
707	feedtype: 'linear' or 'circular'
708	"""
709	self._setfeedtype(feedtype)
710	self._add_history("set_feedtype", vars())
711	print_log()
712
713	def set_doppler(self, doppler='RADIO'):
714	"""
715	Set the doppler for all following operations on this scantable.
716	Parameters:
717	doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
718	"""
719	varlist = vars()
720	inf = list(self._getcoordinfo())
721	inf[2] = doppler
722	self._setcoordinfo(inf)
723	self._add_history("set_doppler", vars())
724	print_log()
725
726	def set_freqframe(self, frame=None):
727	"""
728	Set the frame type of the Spectral Axis.
729	Parameters:
730	frame: an optional frame type, default 'LSRK'. Valid frames are:
731	'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY',
732	'GEO', 'GALACTO', 'LGROUP', 'CMB'
733	Examples:
734	scan.set_freqframe('BARY')
735	"""
736	if frame is None: frame = rcParams['scantable.freqframe']
737	varlist = vars()
738	valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
739	'GEO', 'GALACTO', 'LGROUP', 'CMB']
740
741	if frame in valid:
742	inf = list(self._getcoordinfo())
743	inf[1] = frame
744	self._setcoordinfo(inf)
745	self._add_history("set_freqframe", varlist)
746	else:
747	msg = "Please specify a valid freq type. Valid types are:\n", valid
748	if rcParams['verbose']:
749	#print msg
750	asaplog.push( msg )
751	print_log( 'ERROR' )
752	else:
753	raise TypeError(msg)
754	print_log()
755
756	def set_dirframe(self, frame=""):
757	"""
758	Set the frame type of the Direction on the sky.
759	Parameters:
760	frame: an optional frame type, default ''. Valid frames are:
761	'J2000', 'B1950', 'GALACTIC'
762	Examples:
763	scan.set_dirframe('GALACTIC')
764	"""
765	varlist = vars()
766	try:
767	Scantable.set_dirframe(self, frame)
768	except RuntimeError, msg:
769	if rcParams['verbose']:
770	#print msg
771	print_log()
772	asaplog.push( msg.message )
773	print_log( 'ERROR' )
774	else:
775	raise
776	self._add_history("set_dirframe", varlist)
777
778	def get_unit(self):
779	"""
780	Get the default unit set in this scantable
781	Returns:
782	A unit string
783	"""
784	inf = self._getcoordinfo()
785	unit = inf[0]
786	if unit == '': unit = 'channel'
787	return unit
788
789	def get_abcissa(self, rowno=0):
790	"""
791	Get the abcissa in the current coordinate setup for the currently
792	selected Beam/IF/Pol
793	Parameters:
794	rowno: an optional row number in the scantable. Default is the
795	first row, i.e. rowno=0
796	Returns:
797	The abcissa values and the format string (as a dictionary)
798	"""
799	abc = self._getabcissa(rowno)
800	lbl = self._getabcissalabel(rowno)
801	print_log()
802	return abc, lbl
803
804	def flag(self, mask=None, unflag=False):
805	"""
806	Flag the selected data using an optional channel mask.
807	Parameters:
808	mask: an optional channel mask, created with create_mask. Default
809	(no mask) is all channels.
810	unflag: if True, unflag the data
811	"""
812	varlist = vars()
813	if mask is None:
814	mask = []
815	try:
816	self._flag(mask, unflag)
817	except RuntimeError, msg:
818	if rcParams['verbose']:
819	#print msg
820	print_log()
821	asaplog.push( msg.message )
822	print_log( 'ERROR' )
823	return
824	else: raise
825	self._add_history("flag", varlist)
826
827	def flag_row(self, rows=[], unflag=False):
828	"""
829	Flag the selected data in row-based manner.
830	Parameters:
831	rows: list of row numbers to be flagged. Default is no row (must be explicitly specified to execute row-based flagging).
832	unflag: if True, unflag the data.
833	"""
834	varlist = vars()
835	try:
836	self._flag_row(rows, unflag)
837	except RuntimeError, msg:
838	if rcParams['verbose']:
839	print_log()
840	asaplog.push(msg.message)
841	print_log('ERROR')
842	return
843	else: raise
844	self._add_history("flag_row", varlist)
845
846
847	def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None):
848	"""
849	Flag the data in 'lag' space by providing a frequency to remove.
850	Flagged data in the scantable gets set to 0.0 before the fft.
851	No taper is applied.
852	Parameters:
853	frequency: the frequency (really a period within the bandwidth)
854	to remove
855	width: the width of the frequency to remove, to remove a
856	range of frequencies around the centre.
857	unit: the frequency unit (default "GHz")
858	Notes:
859	It is recommended to flag edges of the band or strong
860	signals beforehand.
861	"""
862	if insitu is None: insitu = rcParams['insitu']
863	self._math._setinsitu(insitu)
864	varlist = vars()
865	base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. }
866	if not base.has_key(unit):
867	raise ValueError("%s is not a valid unit." % unit)
868	try:
869	s = scantable(self._math._lag_flag(self, frequency*base[unit],
870	width*base[unit]))
871	except RuntimeError, msg:
872	if rcParams['verbose']:
873	#print msg
874	print_log()
875	asaplog.push( msg.message )
876	print_log( 'ERROR' )
877	return
878	else: raise
879	s._add_history("lag_flag", varlist)
880	print_log()
881	if insitu:
882	self._assign(s)
883	else:
884	return s
885
886
887	def create_mask(self, args, *kwargs):
888	"""
889	Compute and return a mask based on [min, max] windows.
890	The specified windows are to be INCLUDED, when the mask is
891	applied.
892	Parameters:
893	[min, max], [min2, max2], ...
894	Pairs of start/end points (inclusive)specifying the regions
895	to be masked
896	invert: optional argument. If specified as True,
897	return an inverted mask, i.e. the regions
898	specified are EXCLUDED
899	row: create the mask using the specified row for
900	unit conversions, default is row=0
901	only necessary if frequency varies over rows.
902	Example:
903	scan.set_unit('channel')
904	a)
905	msk = scan.create_mask([400, 500], [800, 900])
906	# masks everything outside 400 and 500
907	# and 800 and 900 in the unit 'channel'
908
909	b)
910	msk = scan.create_mask([400, 500], [800, 900], invert=True)
911	# masks the regions between 400 and 500
912	# and 800 and 900 in the unit 'channel'
913	c)
914	mask only channel 400
915	msk = scan.create_mask([400, 400])
916	"""
917	row = 0
918	if kwargs.has_key("row"):
919	row = kwargs.get("row")
920	data = self._getabcissa(row)
921	u = self._getcoordinfo()[0]
922	if rcParams['verbose']:
923	if u == "": u = "channel"
924	msg = "The current mask window unit is %s" % u
925	i = self._check_ifs()
926	if not i:
927	msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
928	asaplog.push(msg)
929	n = self.nchan()
930	msk = _n_bools(n, False)
931	# test if args is a 'list' or a 'normal *args - UGLY!!!
932
933	ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
934	and args or args[0]
935	for window in ws:
936	if (len(window) != 2 or window[0] > window[1] ):
937	raise TypeError("A window needs to be defined as [min, max]")
938	for i in range(n):
939	if data[i] >= window[0] and data[i] <= window[1]:
940	msk[i] = True
941	if kwargs.has_key('invert'):
942	if kwargs.get('invert'):
943	msk = mask_not(msk)
944	print_log()
945	return msk
946
947	def get_masklist(self, mask=None, row=0):
948	"""
949	Compute and return a list of mask windows, [min, max].
950	Parameters:
951	mask: channel mask, created with create_mask.
952	row: calcutate the masklist using the specified row
953	for unit conversions, default is row=0
954	only necessary if frequency varies over rows.
955	Returns:
956	[min, max], [min2, max2], ...
957	Pairs of start/end points (inclusive)specifying
958	the masked regions
959	"""
960	if not (isinstance(mask,list) or isinstance(mask, tuple)):
961	raise TypeError("The mask should be list or tuple.")
962	if len(mask) < 2:
963	raise TypeError("The mask elements should be > 1")
964	if self.nchan() != len(mask):
965	msg = "Number of channels in scantable != number of mask elements"
966	raise TypeError(msg)
967	data = self._getabcissa(row)
968	u = self._getcoordinfo()[0]
969	if rcParams['verbose']:
970	if u == "": u = "channel"
971	msg = "The current mask window unit is %s" % u
972	i = self._check_ifs()
973	if not i:
974	msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
975	asaplog.push(msg)
976	masklist=[]
977	ist, ien = None, None
978	ist, ien=self.get_mask_indices(mask)
979	if ist is not None and ien is not None:
980	for i in xrange(len(ist)):
981	range=[data[ist[i]],data[ien[i]]]
982	range.sort()
983	masklist.append([range[0],range[1]])
984	return masklist
985
986	def get_mask_indices(self, mask=None):
987	"""
988	Compute and Return lists of mask start indices and mask end indices.
989	Parameters:
990	mask: channel mask, created with create_mask.
991	Returns:
992	List of mask start indices and that of mask end indices,
993	i.e., [istart1,istart2,....], [iend1,iend2,....].
994	"""
995	if not (isinstance(mask,list) or isinstance(mask, tuple)):
996	raise TypeError("The mask should be list or tuple.")
997	if len(mask) < 2:
998	raise TypeError("The mask elements should be > 1")
999	istart=[]
1000	iend=[]
1001	if mask[0]: istart.append(0)
1002	for i in range(len(mask)-1):
1003	if not mask[i] and mask[i+1]:
1004	istart.append(i+1)
1005	elif mask[i] and not mask[i+1]:
1006	iend.append(i)
1007	if mask[len(mask)-1]: iend.append(len(mask)-1)
1008	if len(istart) != len(iend):
1009	raise RuntimeError("Numbers of mask start != mask end.")
1010	for i in range(len(istart)):
1011	if istart[i] > iend[i]:
1012	raise RuntimeError("Mask start index > mask end index")
1013	break
1014	return istart,iend
1015
1016	# def get_restfreqs(self):
1017	# """
1018	# Get the restfrequency(s) stored in this scantable.
1019	# The return value(s) are always of unit 'Hz'
1020	# Parameters:
1021	# none
1022	# Returns:
1023	# a list of doubles
1024	# """
1025	# return list(self._getrestfreqs())
1026
1027	def get_restfreqs(self, ids=None):
1028	"""
1029	Get the restfrequency(s) stored in this scantable.
1030	The return value(s) are always of unit 'Hz'
1031	Parameters:
1032	ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to
1033	be retrieved
1034	Returns:
1035	dictionary containing ids and a list of doubles for each id
1036	"""
1037	if ids is None:
1038	rfreqs={}
1039	idlist = self.getmolnos()
1040	for i in idlist:
1041	rfreqs[i]=list(self._getrestfreqs(i))
1042	return rfreqs
1043	else:
1044	if type(ids)==list or type(ids)==tuple:
1045	rfreqs={}
1046	for i in ids:
1047	rfreqs[i]=list(self._getrestfreqs(i))
1048	return rfreqs
1049	else:
1050	return list(self._getrestfreqs(ids))
1051	#return list(self._getrestfreqs(ids))
1052
1053	def set_restfreqs(self, freqs=None, unit='Hz'):
1054	"""
1055	******NEED TO BE UPDATED begin**********
1056	Set or replace the restfrequency specified and
1057	If the 'freqs' argument holds a scalar,
1058	then that rest frequency will be applied to all the selected
1059	data. If the 'freqs' argument holds
1060	a vector, then it MUST be of equal or smaller length than
1061	the number of IFs (and the available restfrequencies will be
1062	replaced by this vector). In this case, all data have
1063	the restfrequency set per IF according
1064	to the corresponding value you give in the 'freqs' vector.
1065	E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
1066	IF 1 gets restfreq 2e9.
1067	******NEED TO BE UPDATED end**********
1068	You can also specify the frequencies via a linecatalog.
1069
1070	Parameters:
1071	freqs: list of rest frequency values or string idenitfiers
1072	unit: unit for rest frequency (default 'Hz')
1073
1074	Example:
1075	# set the given restfrequency for the all currently selected IFs
1076	scan.set_restfreqs(freqs=1.4e9)
1077	# set multiple restfrequencies to all the selected data
1078	scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9])
1079	# If the number of IFs in the data is >= 2 the IF0 gets the first
1080	# value IF1 the second... NOTE that freqs needs to be
1081	# specified in list of list (e.g. [[],[],...] ).
1082	scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]])
1083	#set the given restfrequency for the whole table (by name)
1084	scan.set_restfreqs(freqs="OH1667")
1085
1086	Note:
1087	To do more sophisticate Restfrequency setting, e.g. on a
1088	source and IF basis, use scantable.set_selection() before using
1089	this function.
1090	# provide your scantable is call scan
1091	selection = selector()
1092	selection.set_name("ORION*")
1093	selection.set_ifs([1])
1094	scan.set_selection(selection)
1095	scan.set_restfreqs(freqs=86.6e9)
1096
1097	"""
1098	varlist = vars()
1099	from asap import linecatalog
1100	# simple value
1101	if isinstance(freqs, int) or isinstance(freqs, float):
1102	# TT mod
1103	#self._setrestfreqs(freqs, "",unit)
1104	self._setrestfreqs([freqs], [""],unit)
1105	# list of values
1106	elif isinstance(freqs, list) or isinstance(freqs, tuple):
1107	# list values are scalars
1108	if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
1109	self._setrestfreqs(freqs, [""],unit)
1110	# list values are tuples, (value, name)
1111	elif isinstance(freqs[-1], dict):
1112	#sel = selector()
1113	#savesel = self._getselection()
1114	#iflist = self.getifnos()
1115	#for i in xrange(len(freqs)):
1116	# sel.set_ifs(iflist[i])
1117	# self._setselection(sel)
1118	# self._setrestfreqs(freqs[i], "",unit)
1119	#self._setselection(savesel)
1120	self._setrestfreqs(freqs["value"],
1121	freqs["name"], "MHz")
1122	elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple):
1123	sel = selector()
1124	savesel = self._getselection()
1125	iflist = self.getifnos()
1126	if len(freqs)>len(iflist):
1127	raise ValueError("number of elements in list of list exeeds the current IF selections")
1128	for i in xrange(len(freqs)):
1129	sel.set_ifs(iflist[i])
1130	self._setselection(sel)
1131	self._setrestfreqs(freqs[i]["value"],
1132	freqs[i]["name"], "MHz")
1133	self._setselection(savesel)
1134	# freqs are to be taken from a linecatalog
1135	elif isinstance(freqs, linecatalog):
1136	sel = selector()
1137	savesel = self._getselection()
1138	for i in xrange(freqs.nrow()):
1139	sel.set_ifs(iflist[i])
1140	self._setselection(sel)
1141	self._setrestfreqs(freqs.get_frequency(i),
1142	freqs.get_name(i), "MHz")
1143	# ensure that we are not iterating past nIF
1144	if i == self.nif()-1: break
1145	self._setselection(savesel)
1146	else:
1147	return
1148	self._add_history("set_restfreqs", varlist)
1149
1150	def shift_refpix(self, delta):
1151	"""
1152	Shift the reference pixel of the Spectra Coordinate by an
1153	integer amount.
1154	Parameters:
1155	delta: the amount to shift by
1156	Note:
1157	Be careful using this with broadband data.
1158	"""
1159	Scantable.shift(self, delta)
1160
1161	def history(self, filename=None):
1162	"""
1163	Print the history. Optionally to a file.
1164	Parameters:
1165	filename: The name of the file to save the history to.
1166	"""
1167	hist = list(self._gethistory())
1168	out = "-"*80
1169	for h in hist:
1170	if h.startswith("---"):
1171	out += "\n"+h
1172	else:
1173	items = h.split("##")
1174	date = items[0]
1175	func = items[1]
1176	items = items[2:]
1177	out += "\n"+date+"\n"
1178	out += "Function: %s\n Parameters:" % (func)
1179	for i in items:
1180	s = i.split("=")
1181	out += "\n %s = %s" % (s[0], s[1])
1182	out += "\n"+"-"*80
1183	if filename is not None:
1184	if filename is "":
1185	filename = 'scantable_history.txt'
1186	import os
1187	filename = os.path.expandvars(os.path.expanduser(filename))
1188	if not os.path.isdir(filename):
1189	data = open(filename, 'w')
1190	data.write(out)
1191	data.close()
1192	else:
1193	msg = "Illegal file name '%s'." % (filename)
1194	if rcParams['verbose']:
1195	#print msg
1196	asaplog.push( msg )
1197	print_log( 'ERROR' )
1198	else:
1199	raise IOError(msg)
1200	if rcParams['verbose']:
1201	try:
1202	from IPython.genutils import page as pager
1203	except ImportError:
1204	from pydoc import pager
1205	pager(out)
1206	else:
1207	return out
1208	return
1209	#
1210	# Maths business
1211	#
1212
1213	def average_time(self, mask=None, scanav=False, weight='tint', align=False):
1214	"""
1215	Return the (time) weighted average of a scan.
1216	Note:
1217	in channels only - align if necessary
1218	Parameters:
1219	mask: an optional mask (only used for 'var' and 'tsys'
1220	weighting)
1221	scanav: True averages each scan separately
1222	False (default) averages all scans together,
1223	weight: Weighting scheme.
1224	'none' (mean no weight)
1225	'var' (1/var(spec) weighted)
1226	'tsys' (1/Tsys**2 weighted)
1227	'tint' (integration time weighted)
1228	'tintsys' (Tint/Tsys**2)
1229	'median' ( median averaging)
1230	The default is 'tint'
1231	align: align the spectra in velocity before averaging. It takes
1232	the time of the first spectrum as reference time.
1233	Example:
1234	# time average the scantable without using a mask
1235	newscan = scan.average_time()
1236	"""
1237	varlist = vars()
1238	if weight is None: weight = 'TINT'
1239	if mask is None: mask = ()
1240	if scanav: scanav = "SCAN"
1241	else: scanav = "NONE"
1242	scan = (self, )
1243	try:
1244	if align:
1245	scan = (self.freq_align(insitu=False), )
1246	s = None
1247	if weight.upper() == 'MEDIAN':
1248	s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
1249	scanav))
1250	else:
1251	s = scantable(self._math._average(scan, mask, weight.upper(),
1252	scanav))
1253	except RuntimeError, msg:
1254	if rcParams['verbose']:
1255	#print msg
1256	print_log()
1257	asaplog.push( msg.message )
1258	print_log( 'ERROR' )
1259	return
1260	else: raise
1261	s._add_history("average_time", varlist)
1262	print_log()
1263	return s
1264
1265	def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
1266	"""
1267	Return a scan where all spectra are converted to either
1268	Jansky or Kelvin depending upon the flux units of the scan table.
1269	By default the function tries to look the values up internally.
1270	If it can't find them (or if you want to over-ride), you must
1271	specify EITHER jyperk OR eta (and D which it will try to look up
1272	also if you don't set it). jyperk takes precedence if you set both.
1273	Parameters:
1274	jyperk: the Jy / K conversion factor
1275	eta: the aperture efficiency
1276	d: the geomtric diameter (metres)
1277	insitu: if False a new scantable is returned.
1278	Otherwise, the scaling is done in-situ
1279	The default is taken from .asaprc (False)
1280	"""
1281	if insitu is None: insitu = rcParams['insitu']
1282	self._math._setinsitu(insitu)
1283	varlist = vars()
1284	if jyperk is None: jyperk = -1.0
1285	if d is None: d = -1.0
1286	if eta is None: eta = -1.0
1287	s = scantable(self._math._convertflux(self, d, eta, jyperk))
1288	s._add_history("convert_flux", varlist)
1289	print_log()
1290	if insitu: self._assign(s)
1291	else: return s
1292
1293	def gain_el(self, poly=None, filename="", method="linear", insitu=None):
1294	"""
1295	Return a scan after applying a gain-elevation correction.
1296	The correction can be made via either a polynomial or a
1297	table-based interpolation (and extrapolation if necessary).
1298	You specify polynomial coefficients, an ascii table or neither.
1299	If you specify neither, then a polynomial correction will be made
1300	with built in coefficients known for certain telescopes (an error
1301	will occur if the instrument is not known).
1302	The data and Tsys are divided by the scaling factors.
1303	Parameters:
1304	poly: Polynomial coefficients (default None) to compute a
1305	gain-elevation correction as a function of
1306	elevation (in degrees).
1307	filename: The name of an ascii file holding correction factors.
1308	The first row of the ascii file must give the column
1309	names and these MUST include columns
1310	"ELEVATION" (degrees) and "FACTOR" (multiply data
1311	by this) somewhere.
1312	The second row must give the data type of the
1313	column. Use 'R' for Real and 'I' for Integer.
1314	An example file would be
1315	(actual factors are arbitrary) :
1316
1317	TIME ELEVATION FACTOR
1318	R R R
1319	0.1 0 0.8
1320	0.2 20 0.85
1321	0.3 40 0.9
1322	0.4 60 0.85
1323	0.5 80 0.8
1324	0.6 90 0.75
1325	method: Interpolation method when correcting from a table.
1326	Values are "nearest", "linear" (default), "cubic"
1327	and "spline"
1328	insitu: if False a new scantable is returned.
1329	Otherwise, the scaling is done in-situ
1330	The default is taken from .asaprc (False)
1331	"""
1332
1333	if insitu is None: insitu = rcParams['insitu']
1334	self._math._setinsitu(insitu)
1335	varlist = vars()
1336	if poly is None:
1337	poly = ()
1338	from os.path import expandvars
1339	filename = expandvars(filename)
1340	s = scantable(self._math._gainel(self, poly, filename, method))
1341	s._add_history("gain_el", varlist)
1342	print_log()
1343	if insitu: self._assign(s)
1344	else: return s
1345
1346	def freq_align(self, reftime=None, method='cubic', insitu=None):
1347	"""
1348	Return a scan where all rows have been aligned in frequency/velocity.
1349	The alignment frequency frame (e.g. LSRK) is that set by function
1350	set_freqframe.
1351	Parameters:
1352	reftime: reference time to align at. By default, the time of
1353	the first row of data is used.
1354	method: Interpolation method for regridding the spectra.
1355	Choose from "nearest", "linear", "cubic" (default)
1356	and "spline"
1357	insitu: if False a new scantable is returned.
1358	Otherwise, the scaling is done in-situ
1359	The default is taken from .asaprc (False)
1360	"""
1361	if insitu is None: insitu = rcParams["insitu"]
1362	self._math._setinsitu(insitu)
1363	varlist = vars()
1364	if reftime is None: reftime = ""
1365	s = scantable(self._math._freq_align(self, reftime, method))
1366	s._add_history("freq_align", varlist)
1367	print_log()
1368	if insitu: self._assign(s)
1369	else: return s
1370
1371	def opacity(self, tau, insitu=None):
1372	"""
1373	Apply an opacity correction. The data
1374	and Tsys are multiplied by the correction factor.
1375	Parameters:
1376	tau: Opacity from which the correction factor is
1377	exp(tau*ZD)
1378	where ZD is the zenith-distance
1379	insitu: if False a new scantable is returned.
1380	Otherwise, the scaling is done in-situ
1381	The default is taken from .asaprc (False)
1382	"""
1383	if insitu is None: insitu = rcParams['insitu']
1384	self._math._setinsitu(insitu)
1385	varlist = vars()
1386	s = scantable(self._math._opacity(self, tau))
1387	s._add_history("opacity", varlist)
1388	print_log()
1389	if insitu: self._assign(s)
1390	else: return s
1391
1392	def bin(self, width=5, insitu=None):
1393	"""
1394	Return a scan where all spectra have been binned up.
1395	Parameters:
1396	width: The bin width (default=5) in pixels
1397	insitu: if False a new scantable is returned.
1398	Otherwise, the scaling is done in-situ
1399	The default is taken from .asaprc (False)
1400	"""
1401	if insitu is None: insitu = rcParams['insitu']
1402	self._math._setinsitu(insitu)
1403	varlist = vars()
1404	s = scantable(self._math._bin(self, width))
1405	s._add_history("bin", varlist)
1406	print_log()
1407	if insitu: self._assign(s)
1408	else: return s
1409
1410
1411	def resample(self, width=5, method='cubic', insitu=None):
1412	"""
1413	Return a scan where all spectra have been binned up.
1414
1415	Parameters:
1416	width: The bin width (default=5) in pixels
1417	method: Interpolation method when correcting from a table.
1418	Values are "nearest", "linear", "cubic" (default)
1419	and "spline"
1420	insitu: if False a new scantable is returned.
1421	Otherwise, the scaling is done in-situ
1422	The default is taken from .asaprc (False)
1423	"""
1424	if insitu is None: insitu = rcParams['insitu']
1425	self._math._setinsitu(insitu)
1426	varlist = vars()
1427	s = scantable(self._math._resample(self, method, width))
1428	s._add_history("resample", varlist)
1429	print_log()
1430	if insitu: self._assign(s)
1431	else: return s
1432
1433
1434	def average_pol(self, mask=None, weight='none'):
1435	"""
1436	Average the Polarisations together.
1437	Parameters:
1438	mask: An optional mask defining the region, where the
1439	averaging will be applied. The output will have all
1440	specified points masked.
1441	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
1442	weighted), or 'tsys' (1/Tsys**2 weighted)
1443	"""
1444	varlist = vars()
1445	if mask is None:
1446	mask = ()
1447	s = scantable(self._math._averagepol(self, mask, weight.upper()))
1448	s._add_history("average_pol", varlist)
1449	print_log()
1450	return s
1451
1452	def average_beam(self, mask=None, weight='none'):
1453	"""
1454	Average the Beams together.
1455	Parameters:
1456	mask: An optional mask defining the region, where the
1457	averaging will be applied. The output will have all
1458	specified points masked.
1459	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
1460	weighted), or 'tsys' (1/Tsys**2 weighted)
1461	"""
1462	varlist = vars()
1463	if mask is None:
1464	mask = ()
1465	s = scantable(self._math._averagebeams(self, mask, weight.upper()))
1466	s._add_history("average_beam", varlist)
1467	print_log()
1468	return s
1469
1470	def convert_pol(self, poltype=None):
1471	"""
1472	Convert the data to a different polarisation type.
1473	Parameters:
1474	poltype: The new polarisation type. Valid types are:
1475	"linear", "stokes" and "circular"
1476	"""
1477	varlist = vars()
1478	try:
1479	s = scantable(self._math._convertpol(self, poltype))
1480	except RuntimeError, msg:
1481	if rcParams['verbose']:
1482	#print msg
1483	print_log()
1484	asaplog.push( msg.message )
1485	print_log( 'ERROR' )
1486	return
1487	else:
1488	raise
1489	s._add_history("convert_pol", varlist)
1490	print_log()
1491	return s
1492
1493	#def smooth(self, kernel="hanning", width=5.0, insitu=None):
1494	def smooth(self, kernel="hanning", width=5.0, plot=False, insitu=None):
1495	"""
1496	Smooth the spectrum by the specified kernel (conserving flux).
1497	Parameters:
1498	kernel: The type of smoothing kernel. Select from
1499	'hanning' (default), 'gaussian', 'boxcar' and
1500	'rmedian'
1501	width: The width of the kernel in pixels. For hanning this is
1502	ignored otherwise it defauls to 5 pixels.
1503	For 'gaussian' it is the Full Width Half
1504	Maximum. For 'boxcar' it is the full width.
1505	For 'rmedian' it is the half width.
1506	plot: plot the original and the smoothed spectra.
1507	In this each indivual fit has to be approved, by
1508	typing 'y' or 'n'
1509	insitu: if False a new scantable is returned.
1510	Otherwise, the scaling is done in-situ
1511	The default is taken from .asaprc (False)
1512	Example:
1513	none
1514	"""
1515	if insitu is None: insitu = rcParams['insitu']
1516	self._math._setinsitu(insitu)
1517	varlist = vars()
1518
1519	if plot: orgscan = self.copy()
1520
1521	s = scantable(self._math._smooth(self, kernel.lower(), width))
1522	s._add_history("smooth", varlist)
1523
1524	if plot:
1525	if rcParams['plotter.gui']:
1526	from asap.asaplotgui import asaplotgui as asaplot
1527	else:
1528	from asap.asaplot import asaplot
1529	self._p=asaplot()
1530	self._p.set_panels()
1531	ylab=s._get_ordinate_label()
1532	#self._p.palette(0,["#777777","red"])
1533	for r in xrange(s.nrow()):
1534	xsm=s._getabcissa(r)
1535	ysm=s._getspectrum(r)
1536	xorg=orgscan._getabcissa(r)
1537	yorg=orgscan._getspectrum(r)
1538	self._p.clear()
1539	self._p.hold()
1540	self._p.set_axes('ylabel',ylab)
1541	self._p.set_axes('xlabel',s._getabcissalabel(r))
1542	self._p.set_axes('title',s._getsourcename(r))
1543	self._p.set_line(label='Original',color="#777777")
1544	self._p.plot(xorg,yorg)
1545	self._p.set_line(label='Smoothed',color="red")
1546	self._p.plot(xsm,ysm)
1547	### Ugly part for legend
1548	for i in [0,1]:
1549	self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]])
1550	self._p.release()
1551	### Ugly part for legend
1552	self._p.subplots[0]['lines']=[]
1553	res = raw_input("Accept smoothing ([y]/n): ")
1554	if res.upper() == 'N':
1555	s._setspectrum(yorg, r)
1556	self._p.unmap()
1557	self._p = None
1558	del orgscan
1559
1560	print_log()
1561	if insitu: self._assign(s)
1562	else: return s
1563
1564
1565	def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None):
1566	"""
1567	Return a scan which has been baselined (all rows) by a polynomial.
1568	Parameters:
1569	mask: an optional mask
1570	order: the order of the polynomial (default is 0)
1571	plot: plot the fit and the residual. In this each
1572	indivual fit has to be approved, by typing 'y'
1573	or 'n'
1574	uselin: use linear polynomial fit
1575	insitu: if False a new scantable is returned.
1576	Otherwise, the scaling is done in-situ
1577	The default is taken from .asaprc (False)
1578	Example:
1579	# return a scan baselined by a third order polynomial,
1580	# not using a mask
1581	bscan = scan.poly_baseline(order=3)
1582	"""
1583	if insitu is None: insitu = rcParams['insitu']
1584	if not insitu:
1585	workscan = self.copy()
1586	else:
1587	workscan = self
1588	varlist = vars()
1589	if mask is None:
1590	mask = [True for i in xrange(self.nchan(-1))]
1591
1592	from asap.asapfitter import fitter
1593	try:
1594	f = fitter()
1595	if uselin:
1596	f.set_function(lpoly=order)
1597	else:
1598	f.set_function(poly=order)
1599
1600	rows = range(workscan.nrow())
1601	if len(rows) > 0:
1602	self.blpars = []
1603
1604	for r in rows:
1605	# take into account flagtra info (CAS-1434)
1606	flagtra = workscan._getmask(r)
1607	actualmask = mask[:]
1608	if len(actualmask) == 0:
1609	actualmask = list(flagtra[:])
1610	else:
1611	if len(actualmask) != len(flagtra):
1612	raise RuntimeError, "Mask and flagtra have different length"
1613	else:
1614	for i in range(0, len(actualmask)):
1615	actualmask[i] = actualmask[i] and flagtra[i]
1616	f.set_scan(workscan, actualmask)
1617	f.x = workscan._getabcissa(r)
1618	f.y = workscan._getspectrum(r)
1619	f.data = None
1620	f.fit()
1621	if plot:
1622	f.plot(residual=True)
1623	x = raw_input("Accept fit ( [y]/n ): ")
1624	if x.upper() == 'N':
1625	self.blpars.append(None)
1626	continue
1627	workscan._setspectrum(f.fitter.getresidual(), r)
1628	self.blpars.append(f.get_parameters())
1629
1630	if plot:
1631	f._p.unmap()
1632	f._p = None
1633	workscan._add_history("poly_baseline", varlist)
1634	print_log()
1635	if insitu: self._assign(workscan)
1636	else: return workscan
1637	except RuntimeError:
1638	msg = "The fit failed, possibly because it didn't converge."
1639	if rcParams['verbose']:
1640	#print msg
1641	print_log()
1642	asaplog.push( msg.message )
1643	print_log( 'ERROR' )
1644	return
1645	else:
1646	raise RuntimeError(msg)
1647
1648
1649	def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0,
1650	threshold=3, chan_avg_limit=1, plot=False,
1651	insitu=None):
1652	"""
1653	Return a scan which has been baselined (all rows) by a polynomial.
1654	Spectral lines are detected first using linefinder and masked out
1655	to avoid them affecting the baseline solution.
1656
1657	Parameters:
1658	mask: an optional mask retreived from scantable
1659	edge: an optional number of channel to drop at
1660	the edge of spectrum. If only one value is
1661	specified, the same number will be dropped from
1662	both sides of the spectrum. Default is to keep
1663	all channels. Nested tuples represent individual
1664	edge selection for different IFs (a number of spectral
1665	channels can be different)
1666	order: the order of the polynomial (default is 0)
1667	threshold: the threshold used by line finder. It is better to
1668	keep it large as only strong lines affect the
1669	baseline solution.
1670	chan_avg_limit:
1671	a maximum number of consequtive spectral channels to
1672	average during the search of weak and broad lines.
1673	The default is no averaging (and no search for weak
1674	lines). If such lines can affect the fitted baseline
1675	(e.g. a high order polynomial is fitted), increase this
1676	parameter (usually values up to 8 are reasonable). Most
1677	users of this method should find the default value
1678	sufficient.
1679	plot: plot the fit and the residual. In this each
1680	indivual fit has to be approved, by typing 'y'
1681	or 'n'
1682	insitu: if False a new scantable is returned.
1683	Otherwise, the scaling is done in-situ
1684	The default is taken from .asaprc (False)
1685
1686	Example:
1687	scan2=scan.auto_poly_baseline(order=7)
1688	"""
1689	if insitu is None: insitu = rcParams['insitu']
1690	varlist = vars()
1691	from asap.asapfitter import fitter
1692	from asap.asaplinefind import linefinder
1693	from asap import _is_sequence_or_number as _is_valid
1694
1695	# check whether edge is set up for each IF individually
1696	individualedge = False;
1697	if len(edge) > 1:
1698	if isinstance(edge[0], list) or isinstance(edge[0], tuple):
1699	individualedge = True;
1700
1701	if not _is_valid(edge, int) and not individualedge:
1702	raise ValueError, "Parameter 'edge' has to be an integer or a \
1703	pair of integers specified as a tuple. Nested tuples are allowed \
1704	to make individual selection for different IFs."
1705
1706	curedge = (0, 0)
1707	if individualedge:
1708	for edgepar in edge:
1709	if not _is_valid(edgepar, int):
1710	raise ValueError, "Each element of the 'edge' tuple has \
1711	to be a pair of integers or an integer."
1712	else:
1713	curedge = edge;
1714
1715	# setup fitter
1716	f = fitter()
1717	f.set_function(poly=order)
1718
1719	# setup line finder
1720	fl = linefinder()
1721	fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
1722
1723	if not insitu:
1724	workscan = self.copy()
1725	else:
1726	workscan = self
1727
1728	fl.set_scan(workscan)
1729
1730	rows = range(workscan.nrow())
1731	# Save parameters of baseline fits & masklists as a class attribute.
1732	# NOTICE: It does not reflect changes in scantable!
1733	if len(rows) > 0:
1734	self.blpars=[]
1735	self.masklists=[]
1736	asaplog.push("Processing:")
1737	for r in rows:
1738	msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
1739	(workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
1740	workscan.getpol(r), workscan.getcycle(r))
1741	asaplog.push(msg, False)
1742
1743	# figure out edge parameter
1744	if individualedge:
1745	if len(edge) >= workscan.getif(r):
1746	raise RuntimeError, "Number of edge elements appear to " \
1747	"be less than the number of IFs"
1748	curedge = edge[workscan.getif(r)]
1749
1750	# take into account flagtra info (CAS-1434)
1751	flagtra = workscan._getmask(r)
1752	actualmask = mask[:]
1753	if len(actualmask) == 0:
1754	actualmask = list(flagtra[:])
1755	else:
1756	if len(actualmask) != len(flagtra):
1757	raise RuntimeError, "Mask and flagtra have different length"
1758	else:
1759	for i in range(0, len(actualmask)):
1760	actualmask[i] = actualmask[i] and flagtra[i]
1761
1762	# setup line finder
1763	fl.find_lines(r, actualmask, curedge)
1764	outmask=fl.get_mask()
1765	f.set_scan(workscan, fl.get_mask())
1766	f.x = workscan._getabcissa(r)
1767	f.y = workscan._getspectrum(r)
1768	f.data = None
1769	f.fit()
1770
1771	# Show mask list
1772	masklist=workscan.get_masklist(fl.get_mask(),row=r)
1773	msg = "mask range: "+str(masklist)
1774	asaplog.push(msg, False)
1775
1776	if plot:
1777	f.plot(residual=True)
1778	x = raw_input("Accept fit ( [y]/n ): ")
1779	if x.upper() == 'N':
1780	self.blpars.append(None)
1781	self.masklists.append(None)
1782	continue
1783
1784	workscan._setspectrum(f.fitter.getresidual(), r)
1785	self.blpars.append(f.get_parameters())
1786	self.masklists.append(masklist)
1787	if plot:
1788	f._p.unmap()
1789	f._p = None
1790	workscan._add_history("auto_poly_baseline", varlist)
1791	if insitu:
1792	self._assign(workscan)
1793	else:
1794	return workscan
1795
1796	def rotate_linpolphase(self, angle):
1797	"""
1798	Rotate the phase of the complex polarization O=Q+iU correlation.
1799	This is always done in situ in the raw data. So if you call this
1800	function more than once then each call rotates the phase further.
1801	Parameters:
1802	angle: The angle (degrees) to rotate (add) by.
1803	Examples:
1804	scan.rotate_linpolphase(2.3)
1805	"""
1806	varlist = vars()
1807	self._math._rotate_linpolphase(self, angle)
1808	self._add_history("rotate_linpolphase", varlist)
1809	print_log()
1810	return
1811
1812
1813	def rotate_xyphase(self, angle):
1814	"""
1815	Rotate the phase of the XY correlation. This is always done in situ
1816	in the data. So if you call this function more than once
1817	then each call rotates the phase further.
1818	Parameters:
1819	angle: The angle (degrees) to rotate (add) by.
1820	Examples:
1821	scan.rotate_xyphase(2.3)
1822	"""
1823	varlist = vars()
1824	self._math._rotate_xyphase(self, angle)
1825	self._add_history("rotate_xyphase", varlist)
1826	print_log()
1827	return
1828
1829	def swap_linears(self):
1830	"""
1831	Swap the linear polarisations XX and YY, or better the first two
1832	polarisations as this also works for ciculars.
1833	"""
1834	varlist = vars()
1835	self._math._swap_linears(self)
1836	self._add_history("swap_linears", varlist)
1837	print_log()
1838	return
1839
1840	def invert_phase(self):
1841	"""
1842	Invert the phase of the complex polarisation
1843	"""
1844	varlist = vars()
1845	self._math._invert_phase(self)
1846	self._add_history("invert_phase", varlist)
1847	print_log()
1848	return
1849
1850	def add(self, offset, insitu=None):
1851	"""
1852	Return a scan where all spectra have the offset added
1853	Parameters:
1854	offset: the offset
1855	insitu: if False a new scantable is returned.
1856	Otherwise, the scaling is done in-situ
1857	The default is taken from .asaprc (False)
1858	"""
1859	if insitu is None: insitu = rcParams['insitu']
1860	self._math._setinsitu(insitu)
1861	varlist = vars()
1862	s = scantable(self._math._unaryop(self, offset, "ADD", False))
1863	s._add_history("add", varlist)
1864	print_log()
1865	if insitu:
1866	self._assign(s)
1867	else:
1868	return s
1869
1870	def scale(self, factor, tsys=True, insitu=None):
1871	"""
1872	Return a scan where all spectra are scaled by the give 'factor'
1873	Parameters:
1874	factor: the scaling factor
1875	insitu: if False a new scantable is returned.
1876	Otherwise, the scaling is done in-situ
1877	The default is taken from .asaprc (False)
1878	tsys: if True (default) then apply the operation to Tsys
1879	as well as the data
1880	"""
1881	if insitu is None: insitu = rcParams['insitu']
1882	self._math._setinsitu(insitu)
1883	varlist = vars()
1884	s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
1885	s._add_history("scale", varlist)
1886	print_log()
1887	if insitu:
1888	self._assign(s)
1889	else:
1890	return s
1891
1892	def set_sourcetype(self, match, matchtype="pattern",
1893	sourcetype="reference"):
1894	"""
1895	Set the type of the source to be an source or reference scan
1896	using the provided pattern:
1897	Parameters:
1898	match: a Unix style pattern, regular expression or selector
1899	matchtype: 'pattern' (default) UNIX style pattern or
1900	'regex' regular expression
1901	sourcetype: the type of the source to use (source/reference)
1902	"""
1903	varlist = vars()
1904	basesel = self.get_selection()
1905	stype = -1
1906	if sourcetype.lower().startswith("r"):
1907	stype = 1
1908	elif sourcetype.lower().startswith("s"):
1909	stype = 0
1910	else:
1911	raise ValueError("Illegal sourcetype use s(ource) or r(eference)")
1912	if matchtype.lower().startswith("p"):
1913	matchtype = "pattern"
1914	elif matchtype.lower().startswith("r"):
1915	matchtype = "regex"
1916	else:
1917	raise ValueError("Illegal matchtype, use p(attern) or r(egex)")
1918	sel = selector()
1919	if isinstance(match, selector):
1920	sel = match
1921	else:
1922	sel.set_query("SRCNAME == %s('%s')" % (matchtype, match))
1923	self.set_selection(basesel+sel)
1924	self._setsourcetype(stype)
1925	self.set_selection(basesel)
1926	s._add_history("set_sourcetype", varlist)
1927
1928	def auto_quotient(self, preserve=True, mode='paired', verify=False):
1929	"""
1930	This function allows to build quotients automatically.
1931	It assumes the observation to have the same number of
1932	"ons" and "offs"
1933	Parameters:
1934	preserve: you can preserve (default) the continuum or
1935	remove it. The equations used are
1936	preserve: Output = Toff * (on/off) - Toff
1937	remove: Output = Toff * (on/off) - Ton
1938	mode: the on/off detection mode
1939	'paired' (default)
1940	identifies 'off' scans by the
1941	trailing '_R' (Mopra/Parkes) or
1942	'_e'/'_w' (Tid) and matches
1943	on/off pairs from the observing pattern
1944	'time'
1945	finds the closest off in time
1946
1947	"""
1948	modes = ["time", "paired"]
1949	if not mode in modes:
1950	msg = "please provide valid mode. Valid modes are %s" % (modes)
1951	raise ValueError(msg)
1952	varlist = vars()
1953	s = None
1954	if mode.lower() == "paired":
1955	basesel = self.get_selection()
1956	sel = selector()+basesel
1957	sel.set_query("SRCTYPE==1")
1958	self.set_selection(sel)
1959	offs = self.copy()
1960	sel.set_query("SRCTYPE==0")
1961	self.set_selection(sel)
1962	ons = self.copy()
1963	s = scantable(self._math._quotient(ons, offs, preserve))
1964	self.set_selection(basesel)
1965	elif mode.lower() == "time":
1966	s = scantable(self._math._auto_quotient(self, mode, preserve))
1967	s._add_history("auto_quotient", varlist)
1968	print_log()
1969	return s
1970
1971	def mx_quotient(self, mask = None, weight='median', preserve=True):
1972	"""
1973	Form a quotient using "off" beams when observing in "MX" mode.
1974	Parameters:
1975	mask: an optional mask to be used when weight == 'stddev'
1976	weight: How to average the off beams. Default is 'median'.
1977	preserve: you can preserve (default) the continuum or
1978	remove it. The equations used are
1979	preserve: Output = Toff * (on/off) - Toff
1980	remove: Output = Toff * (on/off) - Ton
1981	"""
1982	if mask is None: mask = ()
1983	varlist = vars()
1984	on = scantable(self._math._mx_extract(self, 'on'))
1985	preoff = scantable(self._math._mx_extract(self, 'off'))
1986	off = preoff.average_time(mask=mask, weight=weight, scanav=False)
1987	from asapmath import quotient
1988	q = quotient(on, off, preserve)
1989	q._add_history("mx_quotient", varlist)
1990	print_log()
1991	return q
1992
1993	def freq_switch(self, insitu=None):
1994	"""
1995	Apply frequency switching to the data.
1996	Parameters:
1997	insitu: if False a new scantable is returned.
1998	Otherwise, the swictching is done in-situ
1999	The default is taken from .asaprc (False)
2000	Example:
2001	none
2002	"""
2003	if insitu is None: insitu = rcParams['insitu']
2004	self._math._setinsitu(insitu)
2005	varlist = vars()
2006	s = scantable(self._math._freqswitch(self))
2007	s._add_history("freq_switch", varlist)
2008	print_log()
2009	if insitu: self._assign(s)
2010	else: return s
2011
2012	def recalc_azel(self):
2013	"""
2014	Recalculate the azimuth and elevation for each position.
2015	Parameters:
2016	none
2017	Example:
2018	"""
2019	varlist = vars()
2020	self._recalcazel()
2021	self._add_history("recalc_azel", varlist)
2022	print_log()
2023	return
2024
2025	def __add__(self, other):
2026	varlist = vars()
2027	s = None
2028	if isinstance(other, scantable):
2029	s = scantable(self._math._binaryop(self, other, "ADD"))
2030	elif isinstance(other, float):
2031	s = scantable(self._math._unaryop(self, other, "ADD", False))
2032	else:
2033	raise TypeError("Other input is not a scantable or float value")
2034	s._add_history("operator +", varlist)
2035	print_log()
2036	return s
2037
2038	def __sub__(self, other):
2039	"""
2040	implicit on all axes and on Tsys
2041	"""
2042	varlist = vars()
2043	s = None
2044	if isinstance(other, scantable):
2045	s = scantable(self._math._binaryop(self, other, "SUB"))
2046	elif isinstance(other, float):
2047	s = scantable(self._math._unaryop(self, other, "SUB", False))
2048	else:
2049	raise TypeError("Other input is not a scantable or float value")
2050	s._add_history("operator -", varlist)
2051	print_log()
2052	return s
2053
2054	def __mul__(self, other):
2055	"""
2056	implicit on all axes and on Tsys
2057	"""
2058	varlist = vars()
2059	s = None
2060	if isinstance(other, scantable):
2061	s = scantable(self._math._binaryop(self, other, "MUL"))
2062	elif isinstance(other, float):
2063	s = scantable(self._math._unaryop(self, other, "MUL", False))
2064	else:
2065	raise TypeError("Other input is not a scantable or float value")
2066	s._add_history("operator *", varlist)
2067	print_log()
2068	return s
2069
2070
2071	def __div__(self, other):
2072	"""
2073	implicit on all axes and on Tsys
2074	"""
2075	varlist = vars()
2076	s = None
2077	if isinstance(other, scantable):
2078	s = scantable(self._math._binaryop(self, other, "DIV"))
2079	elif isinstance(other, float):
2080	if other == 0.0:
2081	raise ZeroDivisionError("Dividing by zero is not recommended")
2082	s = scantable(self._math._unaryop(self, other, "DIV", False))
2083	else:
2084	raise TypeError("Other input is not a scantable or float value")
2085	s._add_history("operator /", varlist)
2086	print_log()
2087	return s
2088
2089	def get_fit(self, row=0):
2090	"""
2091	Print or return the stored fits for a row in the scantable
2092	Parameters:
2093	row: the row which the fit has been applied to.
2094	"""
2095	if row > self.nrow():
2096	return
2097	from asap.asapfit import asapfit
2098	fit = asapfit(self._getfit(row))
2099	if rcParams['verbose']:
2100	#print fit
2101	asaplog.push( '%s' %(fit) )
2102	print_log()
2103	return
2104	else:
2105	return fit.as_dict()
2106
2107	def flag_nans(self):
2108	"""
2109	Utility function to flag NaN values in the scantable.
2110	"""
2111	import numpy
2112	basesel = self.get_selection()
2113	for i in range(self.nrow()):
2114	sel = selector()+basesel
2115	sel.set_scans(self.getscan(i))
2116	sel.set_beams(self.getbeam(i))
2117	sel.set_ifs(self.getif(i))
2118	sel.set_polarisations(self.getpol(i))
2119	self.set_selection(sel)
2120	nans = numpy.isnan(self._getspectrum(0))
2121	if numpy.any(nans):
2122	bnans = [ bool(v) for v in nans]
2123	self.flag(bnans)
2124	self.set_selection(basesel)
2125
2126
2127	def _add_history(self, funcname, parameters):
2128	if not rcParams['scantable.history']:
2129	return
2130	# create date
2131	sep = "##"
2132	from datetime import datetime
2133	dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
2134	hist = dstr+sep
2135	hist += funcname+sep#cdate+sep
2136	if parameters.has_key('self'): del parameters['self']
2137	for k, v in parameters.iteritems():
2138	if type(v) is dict:
2139	for k2, v2 in v.iteritems():
2140	hist += k2
2141	hist += "="
2142	if isinstance(v2, scantable):
2143	hist += 'scantable'
2144	elif k2 == 'mask':
2145	if isinstance(v2, list) or isinstance(v2, tuple):
2146	hist += str(self._zip_mask(v2))
2147	else:
2148	hist += str(v2)
2149	else:
2150	hist += str(v2)
2151	else:
2152	hist += k
2153	hist += "="
2154	if isinstance(v, scantable):
2155	hist += 'scantable'
2156	elif k == 'mask':
2157	if isinstance(v, list) or isinstance(v, tuple):
2158	hist += str(self._zip_mask(v))
2159	else:
2160	hist += str(v)
2161	else:
2162	hist += str(v)
2163	hist += sep
2164	hist = hist[:-2] # remove trailing '##'
2165	self._addhistory(hist)
2166
2167
2168	def _zip_mask(self, mask):
2169	mask = list(mask)
2170	i = 0
2171	segments = []
2172	while mask[i:].count(1):
2173	i += mask[i:].index(1)
2174	if mask[i:].count(0):
2175	j = i + mask[i:].index(0)
2176	else:
2177	j = len(mask)
2178	segments.append([i, j])
2179	i = j
2180	return segments
2181
2182	def _get_ordinate_label(self):
2183	fu = "("+self.get_fluxunit()+")"
2184	import re
2185	lbl = "Intensity"
2186	if re.match(".K.", fu):
2187	lbl = "Brightness Temperature "+ fu
2188	elif re.match(".Jy.", fu):
2189	lbl = "Flux density "+ fu
2190	return lbl
2191
2192	def _check_ifs(self):
2193	nchans = [self.nchan(i) for i in range(self.nif(-1))]
2194	nchans = filter(lambda t: t > 0, nchans)
2195	return (sum(nchans)/len(nchans) == nchans[0])
2196
2197	def _fill(self, names, unit, average, getpt):
2198	import os
2199	from asap._asap import stfiller
2200	first = True
2201	fullnames = []
2202	for name in names:
2203	name = os.path.expandvars(name)
2204	name = os.path.expanduser(name)
2205	if not os.path.exists(name):
2206	msg = "File '%s' does not exists" % (name)
2207	if rcParams['verbose']:
2208	asaplog.push(msg)
2209	#print asaplog.pop().strip()
2210	print_log( 'ERROR' )
2211	return
2212	raise IOError(msg)
2213	fullnames.append(name)
2214	if average:
2215	asaplog.push('Auto averaging integrations')
2216	stype = int(rcParams['scantable.storage'].lower() == 'disk')
2217	for name in fullnames:
2218	tbl = Scantable(stype)
2219	r = stfiller(tbl)
2220	rx = rcParams['scantable.reference']
2221	r._setreferenceexpr(rx)
2222	msg = "Importing %s..." % (name)
2223	asaplog.push(msg, False)
2224	print_log()
2225	r._open(name, -1, -1, getpt)
2226	r._read()
2227	if average:
2228	tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
2229	if not first:
2230	tbl = self._math._merge([self, tbl])
2231	Scantable.__init__(self, tbl)
2232	r._close()
2233	del r, tbl
2234	first = False
2235	if unit is not None:
2236	self.set_fluxunit(unit)
2237	#self.set_freqframe(rcParams['scantable.freqframe'])
2238
2239	def __getitem__(self, key):
2240	if key < 0:
2241	key += self.nrow()
2242	if key >= self.nrow():
2243	raise IndexError("Row index out of range.")
2244	return self._getspectrum(key)
2245
2246	def __setitem__(self, key, value):
2247	if key < 0:
2248	key += self.nrow()
2249	if key >= self.nrow():
2250	raise IndexError("Row index out of range.")
2251	if not hasattr(value, "__len__") or \
2252	len(value) > self.nchan(self.getif(key)):
2253	raise ValueError("Spectrum length doesn't match.")
2254	return self._setspectrum(value, key)
2255
2256	def __len__(self):
2257	return self.nrow()
2258
2259	def __iter__(self):
2260	for i in range(len(self)):
2261	yield self[i]

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