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source: branches/alma/python/scantable.py @ 1614

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Last change on this file since 1614 was 1614, checked in by Takeshi Nakazato, 15 years ago

New Development: No

JIRA Issue: Yes CAS-729, CAS-1147

Ready to Release: Yes

Interface Changes: No

What Interface Changed: Please list interface changes

Test Programs: List test programs

Put in Release Notes: No

Module(s): Module Names change impacts.

Description: Describe your changes here...

Added level parameter to print_log()
Replaced casalog.post() to asaplog.push() + print_log().

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

File size: 80.9 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	"""
394	Determine the specified statistic of the current beam/if/pol
395	Takes a 'mask' as an optional parameter to specify which
396	channels should be excluded.
397	Parameters:
398	stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum',
399	'mean', 'var', 'stddev', 'avdev', 'rms', 'median'
400	mask: an optional mask specifying where the statistic
401	should be determined.
402	Example:
403	scan.set_unit('channel')
404	msk = scan.create_mask([100, 200], [500, 600])
405	scan.stats(stat='mean', mask=m)
406	"""
407	if mask == None:
408	mask = []
409	axes = ['Beam', 'IF', 'Pol', 'Time']
410	if not self._check_ifs():
411	raise ValueError("Cannot apply mask as the IFs have different "
412	"number of channels. Please use setselection() "
413	"to select individual IFs")
414	rtnabc = False
415	if stat.lower().endswith('_abc'): rtnabc = True
416	getchan = False
417	if stat.lower().startswith('min') or stat.lower().startswith('max'):
418	chan = self._math._minmaxchan(self, mask, stat)
419	getchan = True
420	statvals = []
421	if not rtnabc: statvals = self._math._stats(self, mask, stat)
422
423	out = ''
424	axes = []
425	for i in range(self.nrow()):
426	axis = []
427	axis.append(self.getscan(i))
428	axis.append(self.getbeam(i))
429	axis.append(self.getif(i))
430	axis.append(self.getpol(i))
431	axis.append(self.getcycle(i))
432	axes.append(axis)
433	tm = self._gettime(i)
434	src = self._getsourcename(i)
435	refstr = ''
436	statunit= ''
437	if getchan:
438	qx, qy = self.chan2data(rowno=i, chan=chan[i])
439	if rtnabc:
440	statvals.append(qx['value'])
441	refstr = '(value: %3.3f' % (qy['value'])+' ['+qy['unit']+'])'
442	statunit= '['+qx['unit']+']'
443	else:
444	refstr = '(@ %3.3f' % (qx['value'])+' ['+qx['unit']+'])'
445	#statunit= ' ['+qy['unit']+']'
446	out += 'Scan[%d] (%s) ' % (axis[0], src)
447	out += 'Time[%s]:\n' % (tm)
448	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
449	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
450	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
451	out += '= %3.3f ' % (statvals[i]) +refstr+'\n'
452	out += "--------------------------------------------------\n"
453
454	if rcParams['verbose']:
455	usr=os.environ['USER']
456	tmpfile='/tmp/tmp_'+usr+'_casapy_asap_scantable_stats'
457	f=open(tmpfile,'w')
458	print >> f, "--------------------------------------------------"
459	print >> f, " ", stat, statunit
460	print >> f, "--------------------------------------------------"
461	print >> f, out
462	f.close()
463	f=open(tmpfile,'r')
464	x=f.readlines()
465	f.close()
466	for xx in x:
467	asaplog.push( xx )
468	print_log()
469	#else:
470	#retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'],
471	# 'axes' : axes,
472	# 'data': statvals}
473	return statvals
474
475	def chan2data(self, rowno=0, chan=0):
476	"""
477	Returns channel/frequency/velocity and spectral value
478	at an arbitrary row and channel in the scantable.
479	Parameters:
480	rowno: a row number in the scantable. Default is the
481	first row, i.e. rowno=0
482	chan: a channel in the scantable. Default is the first
483	channel, i.e. pos=0
484	"""
485	if isinstance(rowno, int) and isinstance(chan, int):
486	qx = {'unit': self.get_unit(),
487	'value': self._getabcissa(rowno)[chan]}
488	qy = {'unit': self.get_fluxunit(),
489	'value': self._getspectrum(rowno)[chan]}
490	return qx, qy
491
492	def stddev(self, mask=None):
493	"""
494	Determine the standard deviation of the current beam/if/pol
495	Takes a 'mask' as an optional parameter to specify which
496	channels should be excluded.
497	Parameters:
498	mask: an optional mask specifying where the standard
499	deviation should be determined.
500
501	Example:
502	scan.set_unit('channel')
503	msk = scan.create_mask([100, 200], [500, 600])
504	scan.stddev(mask=m)
505	"""
506	return self.stats(stat='stddev', mask=mask);
507
508
509	def get_column_names(self):
510	"""
511	Return a list of column names, which can be used for selection.
512	"""
513	return list(Scantable.get_column_names(self))
514
515	def get_tsys(self):
516	"""
517	Return the System temperatures.
518	Returns:
519	a list of Tsys values for the current selection
520	"""
521
522	return self._row_callback(self._gettsys, "Tsys")
523
524	def _row_callback(self, callback, label):
525	axes = []
526	axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno']
527	out = ""
528	outvec = []
529	for i in range(self.nrow()):
530	axis = []
531	axis.append(self.getscan(i))
532	axis.append(self.getbeam(i))
533	axis.append(self.getif(i))
534	axis.append(self.getpol(i))
535	axis.append(self.getcycle(i))
536	axes.append(axis)
537	tm = self._gettime(i)
538	src = self._getsourcename(i)
539	out += 'Scan[%d] (%s) ' % (axis[0], src)
540	out += 'Time[%s]:\n' % (tm)
541	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
542	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
543	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
544	outvec.append(callback(i))
545	out += '= %3.3f\n' % (outvec[i])
546	out += "--------------------------------------------------\n"
547	if rcParams['verbose']:
548	usr=os.environ['USER']
549	tmpfile='/tmp/tmp_'+usr+'_casapy_asap_scantable_row_callback'
550	f=open(tmpfile,'w')
551	print >> f, "--------------------------------------------------"
552	print >> f, " %s" % (label)
553	print >> f, "--------------------------------------------------"
554	print >> f, out
555	f.close()
556	f=open(tmpfile,'r')
557	x=f.readlines()
558	f.close()
559	for xx in x:
560	asaplog.push( xx )
561	print_log()
562	# disabled because the vector seems more useful
563	#retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
564	return outvec
565
566	def _get_column(self, callback, row=-1):
567	"""
568	"""
569	if row == -1:
570	return [callback(i) for i in range(self.nrow())]
571	else:
572	if 0 <= row < self.nrow():
573	return callback(row)
574
575
576	def get_time(self, row=-1, asdatetime=False):
577	"""
578	Get a list of time stamps for the observations.
579	Return a datetime object for each integration time stamp in the scantable.
580	Parameters:
581	row: row no of integration. Default -1 return all rows
582	asdatetime: return values as datetime objects rather than strings
583	Example:
584	none
585	"""
586	from time import strptime
587	from datetime import datetime
588	times = self._get_column(self._gettime, row)
589	if not asdatetime:
590	return times
591	format = "%Y/%m/%d/%H:%M:%S"
592	if isinstance(times, list):
593	return [datetime(*strptime(i, format)[:6]) for i in times]
594	else:
595	return datetime(*strptime(times, format)[:6])
596
597
598	def get_inttime(self, row=-1):
599	"""
600	Get a list of integration times for the observations.
601	Return a time in seconds for each integration in the scantable.
602	Parameters:
603	row: row no of integration. Default -1 return all rows.
604	Example:
605	none
606	"""
607	return self._get_column(self._getinttime, row)
608
609
610	def get_sourcename(self, row=-1):
611	"""
612	Get a list source names for the observations.
613	Return a string for each integration in the scantable.
614	Parameters:
615	row: row no of integration. Default -1 return all rows.
616	Example:
617	none
618	"""
619	return self._get_column(self._getsourcename, row)
620
621	def get_elevation(self, row=-1):
622	"""
623	Get a list of elevations for the observations.
624	Return a float for each integration in the scantable.
625	Parameters:
626	row: row no of integration. Default -1 return all rows.
627	Example:
628	none
629	"""
630	return self._get_column(self._getelevation, row)
631
632	def get_azimuth(self, row=-1):
633	"""
634	Get a list of azimuths for the observations.
635	Return a float for each integration in the scantable.
636	Parameters:
637	row: row no of integration. Default -1 return all rows.
638	Example:
639	none
640	"""
641	return self._get_column(self._getazimuth, row)
642
643	def get_parangle(self, row=-1):
644	"""
645	Get a list of parallactic angles for the observations.
646	Return a float for each integration in the scantable.
647	Parameters:
648	row: row no of integration. Default -1 return all rows.
649	Example:
650	none
651	"""
652	return self._get_column(self._getparangle, row)
653
654	def get_direction(self, row=-1):
655	"""
656	Get a list of Positions on the sky (direction) for the observations.
657	Return a float for each integration in the scantable.
658	Parameters:
659	row: row no of integration. Default -1 return all rows
660	Example:
661	none
662	"""
663	return self._get_column(self._getdirection, row)
664
665	def get_directionval(self, row=-1):
666	"""
667	Get a list of Positions on the sky (direction) for the observations.
668	Return a float for each integration in the scantable.
669	Parameters:
670	row: row no of integration. Default -1 return all rows
671	Example:
672	none
673	"""
674	return self._get_column(self._getdirectionvec, row)
675
676	def set_unit(self, unit='channel'):
677	"""
678	Set the unit for all following operations on this scantable
679	Parameters:
680	unit: optional unit, default is 'channel'
681	one of '*Hz', 'km/s', 'channel', ''
682	"""
683	varlist = vars()
684	if unit in ['', 'pixel', 'channel']:
685	unit = ''
686	inf = list(self._getcoordinfo())
687	inf[0] = unit
688	self._setcoordinfo(inf)
689	self._add_history("set_unit", varlist)
690
691	def set_instrument(self, instr):
692	"""
693	Set the instrument for subsequent processing.
694	Parameters:
695	instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
696	'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
697	"""
698	self._setInstrument(instr)
699	self._add_history("set_instument", vars())
700	print_log()
701
702	def set_feedtype(self, feedtype):
703	"""
704	Overwrite the feed type, which might not be set correctly.
705	Parameters:
706	feedtype: 'linear' or 'circular'
707	"""
708	self._setfeedtype(feedtype)
709	self._add_history("set_feedtype", vars())
710	print_log()
711
712	def set_doppler(self, doppler='RADIO'):
713	"""
714	Set the doppler for all following operations on this scantable.
715	Parameters:
716	doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
717	"""
718	varlist = vars()
719	inf = list(self._getcoordinfo())
720	inf[2] = doppler
721	self._setcoordinfo(inf)
722	self._add_history("set_doppler", vars())
723	print_log()
724
725	def set_freqframe(self, frame=None):
726	"""
727	Set the frame type of the Spectral Axis.
728	Parameters:
729	frame: an optional frame type, default 'LSRK'. Valid frames are:
730	'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY',
731	'GEO', 'GALACTO', 'LGROUP', 'CMB'
732	Examples:
733	scan.set_freqframe('BARY')
734	"""
735	if frame is None: frame = rcParams['scantable.freqframe']
736	varlist = vars()
737	valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
738	'GEO', 'GALACTO', 'LGROUP', 'CMB']
739
740	if frame in valid:
741	inf = list(self._getcoordinfo())
742	inf[1] = frame
743	self._setcoordinfo(inf)
744	self._add_history("set_freqframe", varlist)
745	else:
746	msg = "Please specify a valid freq type. Valid types are:\n", valid
747	if rcParams['verbose']:
748	#print msg
749	asaplog.push( msg )
750	print_log( 'ERROR' )
751	else:
752	raise TypeError(msg)
753	print_log()
754
755	def set_dirframe(self, frame=""):
756	"""
757	Set the frame type of the Direction on the sky.
758	Parameters:
759	frame: an optional frame type, default ''. Valid frames are:
760	'J2000', 'B1950', 'GALACTIC'
761	Examples:
762	scan.set_dirframe('GALACTIC')
763	"""
764	varlist = vars()
765	try:
766	Scantable.set_dirframe(self, frame)
767	except RuntimeError, msg:
768	if rcParams['verbose']:
769	#print msg
770	print_log()
771	asaplog.push( msg )
772	print_log( 'ERROR' )
773	else:
774	raise
775	self._add_history("set_dirframe", varlist)
776
777	def get_unit(self):
778	"""
779	Get the default unit set in this scantable
780	Returns:
781	A unit string
782	"""
783	inf = self._getcoordinfo()
784	unit = inf[0]
785	if unit == '': unit = 'channel'
786	return unit
787
788	def get_abcissa(self, rowno=0):
789	"""
790	Get the abcissa in the current coordinate setup for the currently
791	selected Beam/IF/Pol
792	Parameters:
793	rowno: an optional row number in the scantable. Default is the
794	first row, i.e. rowno=0
795	Returns:
796	The abcissa values and the format string (as a dictionary)
797	"""
798	abc = self._getabcissa(rowno)
799	lbl = self._getabcissalabel(rowno)
800	print_log()
801	return abc, lbl
802
803	def flag(self, mask=None, unflag=False):
804	"""
805	Flag the selected data using an optional channel mask.
806	Parameters:
807	mask: an optional channel mask, created with create_mask. Default
808	(no mask) is all channels.
809	unflag: if True, unflag the data
810	"""
811	varlist = vars()
812	if mask is None:
813	mask = []
814	try:
815	self._flag(mask, unflag)
816	except RuntimeError, msg:
817	if rcParams['verbose']:
818	#print msg
819	print_log()
820	asaplog.push( msg )
821	print_log( 'ERROR' )
822	return
823	else: raise
824	self._add_history("flag", varlist)
825
826	def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None):
827	"""
828	Flag the data in 'lag' space by providing a frequency to remove.
829	Flagged data in the scantable gets set to 0.0 before the fft.
830	No taper is applied.
831	Parameters:
832	frequency: the frequency (really a period within the bandwidth)
833	to remove
834	width: the width of the frequency to remove, to remove a
835	range of frequencies around the centre.
836	unit: the frequency unit (default "GHz")
837	Notes:
838	It is recommended to flag edges of the band or strong
839	signals beforehand.
840	"""
841	if insitu is None: insitu = rcParams['insitu']
842	self._math._setinsitu(insitu)
843	varlist = vars()
844	base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. }
845	if not base.has_key(unit):
846	raise ValueError("%s is not a valid unit." % unit)
847	try:
848	s = scantable(self._math._lag_flag(self, frequency*base[unit],
849	width*base[unit]))
850	except RuntimeError, msg:
851	if rcParams['verbose']:
852	#print msg
853	print_log()
854	asaplog.push( msg )
855	print_log( 'ERROR' )
856	return
857	else: raise
858	s._add_history("lag_flag", varlist)
859	print_log()
860	if insitu:
861	self._assign(s)
862	else:
863	return s
864
865
866	def create_mask(self, args, *kwargs):
867	"""
868	Compute and return a mask based on [min, max] windows.
869	The specified windows are to be INCLUDED, when the mask is
870	applied.
871	Parameters:
872	[min, max], [min2, max2], ...
873	Pairs of start/end points (inclusive)specifying the regions
874	to be masked
875	invert: optional argument. If specified as True,
876	return an inverted mask, i.e. the regions
877	specified are EXCLUDED
878	row: create the mask using the specified row for
879	unit conversions, default is row=0
880	only necessary if frequency varies over rows.
881	Example:
882	scan.set_unit('channel')
883	a)
884	msk = scan.create_mask([400, 500], [800, 900])
885	# masks everything outside 400 and 500
886	# and 800 and 900 in the unit 'channel'
887
888	b)
889	msk = scan.create_mask([400, 500], [800, 900], invert=True)
890	# masks the regions between 400 and 500
891	# and 800 and 900 in the unit 'channel'
892	c)
893	mask only channel 400
894	msk = scan.create_mask([400, 400])
895	"""
896	row = 0
897	if kwargs.has_key("row"):
898	row = kwargs.get("row")
899	data = self._getabcissa(row)
900	u = self._getcoordinfo()[0]
901	if rcParams['verbose']:
902	if u == "": u = "channel"
903	msg = "The current mask window unit is %s" % u
904	i = self._check_ifs()
905	if not i:
906	msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
907	asaplog.push(msg)
908	n = self.nchan()
909	msk = _n_bools(n, False)
910	# test if args is a 'list' or a 'normal *args - UGLY!!!
911
912	ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
913	and args or args[0]
914	for window in ws:
915	if (len(window) != 2 or window[0] > window[1] ):
916	raise TypeError("A window needs to be defined as [min, max]")
917	for i in range(n):
918	if data[i] >= window[0] and data[i] <= window[1]:
919	msk[i] = True
920	if kwargs.has_key('invert'):
921	if kwargs.get('invert'):
922	msk = mask_not(msk)
923	print_log()
924	return msk
925
926	def get_masklist(self, mask=None, row=0):
927	"""
928	Compute and return a list of mask windows, [min, max].
929	Parameters:
930	mask: channel mask, created with create_mask.
931	row: calcutate the masklist using the specified row
932	for unit conversions, default is row=0
933	only necessary if frequency varies over rows.
934	Returns:
935	[min, max], [min2, max2], ...
936	Pairs of start/end points (inclusive)specifying
937	the masked regions
938	"""
939	if not (isinstance(mask,list) or isinstance(mask, tuple)):
940	raise TypeError("The mask should be list or tuple.")
941	if len(mask) < 2:
942	raise TypeError("The mask elements should be > 1")
943	if self.nchan() != len(mask):
944	msg = "Number of channels in scantable != number of mask elements"
945	raise TypeError(msg)
946	data = self._getabcissa(row)
947	u = self._getcoordinfo()[0]
948	if rcParams['verbose']:
949	if u == "": u = "channel"
950	msg = "The current mask window unit is %s" % u
951	i = self._check_ifs()
952	if not i:
953	msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
954	asaplog.push(msg)
955	masklist=[]
956	ist, ien = None, None
957	ist, ien=self.get_mask_indices(mask)
958	if ist is not None and ien is not None:
959	for i in xrange(len(ist)):
960	range=[data[ist[i]],data[ien[i]]]
961	range.sort()
962	masklist.append([range[0],range[1]])
963	return masklist
964
965	def get_mask_indices(self, mask=None):
966	"""
967	Compute and Return lists of mask start indices and mask end indices.
968	Parameters:
969	mask: channel mask, created with create_mask.
970	Returns:
971	List of mask start indices and that of mask end indices,
972	i.e., [istart1,istart2,....], [iend1,iend2,....].
973	"""
974	if not (isinstance(mask,list) or isinstance(mask, tuple)):
975	raise TypeError("The mask should be list or tuple.")
976	if len(mask) < 2:
977	raise TypeError("The mask elements should be > 1")
978	istart=[]
979	iend=[]
980	if mask[0]: istart.append(0)
981	for i in range(len(mask)-1):
982	if not mask[i] and mask[i+1]:
983	istart.append(i+1)
984	elif mask[i] and not mask[i+1]:
985	iend.append(i)
986	if mask[len(mask)-1]: iend.append(len(mask)-1)
987	if len(istart) != len(iend):
988	raise RuntimeError("Numbers of mask start != mask end.")
989	for i in range(len(istart)):
990	if istart[i] > iend[i]:
991	raise RuntimeError("Mask start index > mask end index")
992	break
993	return istart,iend
994
995	# def get_restfreqs(self):
996	# """
997	# Get the restfrequency(s) stored in this scantable.
998	# The return value(s) are always of unit 'Hz'
999	# Parameters:
1000	# none
1001	# Returns:
1002	# a list of doubles
1003	# """
1004	# return list(self._getrestfreqs())
1005
1006	def get_restfreqs(self, ids=None):
1007	"""
1008	Get the restfrequency(s) stored in this scantable.
1009	The return value(s) are always of unit 'Hz'
1010	Parameters:
1011	ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to
1012	be retrieved
1013	Returns:
1014	dictionary containing ids and a list of doubles for each id
1015	"""
1016	if ids is None:
1017	rfreqs={}
1018	idlist = self.getmolnos()
1019	for i in idlist:
1020	rfreqs[i]=list(self._getrestfreqs(i))
1021	return rfreqs
1022	else:
1023	if type(ids)==list or type(ids)==tuple:
1024	rfreqs={}
1025	for i in ids:
1026	rfreqs[i]=list(self._getrestfreqs(i))
1027	return rfreqs
1028	else:
1029	return list(self._getrestfreqs(ids))
1030	#return list(self._getrestfreqs(ids))
1031
1032	def set_restfreqs(self, freqs=None, unit='Hz'):
1033	"""
1034	******NEED TO BE UPDATED begin**********
1035	Set or replace the restfrequency specified and
1036	If the 'freqs' argument holds a scalar,
1037	then that rest frequency will be applied to all the selected
1038	data. If the 'freqs' argument holds
1039	a vector, then it MUST be of equal or smaller length than
1040	the number of IFs (and the available restfrequencies will be
1041	replaced by this vector). In this case, all data have
1042	the restfrequency set per IF according
1043	to the corresponding value you give in the 'freqs' vector.
1044	E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
1045	IF 1 gets restfreq 2e9.
1046	******NEED TO BE UPDATED end**********
1047	You can also specify the frequencies via a linecatalog.
1048
1049	Parameters:
1050	freqs: list of rest frequency values or string idenitfiers
1051	unit: unit for rest frequency (default 'Hz')
1052
1053	Example:
1054	# set the given restfrequency for the all currently selected IFs
1055	scan.set_restfreqs(freqs=1.4e9)
1056	# set multiple restfrequencies to all the selected data
1057	scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9])
1058	# If the number of IFs in the data is >= 2 the IF0 gets the first
1059	# value IF1 the second... NOTE that freqs needs to be
1060	# specified in list of list (e.g. [[],[],...] ).
1061	scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]])
1062	#set the given restfrequency for the whole table (by name)
1063	scan.set_restfreqs(freqs="OH1667")
1064
1065	Note:
1066	To do more sophisticate Restfrequency setting, e.g. on a
1067	source and IF basis, use scantable.set_selection() before using
1068	this function.
1069	# provide your scantable is call scan
1070	selection = selector()
1071	selection.set_name("ORION*")
1072	selection.set_ifs([1])
1073	scan.set_selection(selection)
1074	scan.set_restfreqs(freqs=86.6e9)
1075
1076	"""
1077	varlist = vars()
1078	from asap import linecatalog
1079	# simple value
1080	if isinstance(freqs, int) or isinstance(freqs, float):
1081	# TT mod
1082	#self._setrestfreqs(freqs, "",unit)
1083	self._setrestfreqs([freqs], [""],unit)
1084	# list of values
1085	elif isinstance(freqs, list) or isinstance(freqs, tuple):
1086	# list values are scalars
1087	if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
1088	self._setrestfreqs(freqs, [""],unit)
1089	# list values are tuples, (value, name)
1090	elif isinstance(freqs[-1], dict):
1091	#sel = selector()
1092	#savesel = self._getselection()
1093	#iflist = self.getifnos()
1094	#for i in xrange(len(freqs)):
1095	# sel.set_ifs(iflist[i])
1096	# self._setselection(sel)
1097	# self._setrestfreqs(freqs[i], "",unit)
1098	#self._setselection(savesel)
1099	self._setrestfreqs(freqs["value"],
1100	freqs["name"], "MHz")
1101	elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple):
1102	sel = selector()
1103	savesel = self._getselection()
1104	iflist = self.getifnos()
1105	if len(freqs)>len(iflist):
1106	raise ValueError("number of elements in list of list exeeds the current IF selections")
1107	for i in xrange(len(freqs)):
1108	sel.set_ifs(iflist[i])
1109	self._setselection(sel)
1110	self._setrestfreqs(freqs[i]["value"],
1111	freqs[i]["name"], "MHz")
1112	self._setselection(savesel)
1113	# freqs are to be taken from a linecatalog
1114	elif isinstance(freqs, linecatalog):
1115	sel = selector()
1116	savesel = self._getselection()
1117	for i in xrange(freqs.nrow()):
1118	sel.set_ifs(iflist[i])
1119	self._setselection(sel)
1120	self._setrestfreqs(freqs.get_frequency(i),
1121	freqs.get_name(i), "MHz")
1122	# ensure that we are not iterating past nIF
1123	if i == self.nif()-1: break
1124	self._setselection(savesel)
1125	else:
1126	return
1127	self._add_history("set_restfreqs", varlist)
1128
1129	def shift_refpix(self, delta):
1130	"""
1131	Shift the reference pixel of the Spectra Coordinate by an
1132	integer amount.
1133	Parameters:
1134	delta: the amount to shift by
1135	Note:
1136	Be careful using this with broadband data.
1137	"""
1138	Scantable.shift(self, delta)
1139
1140	def history(self, filename=None):
1141	"""
1142	Print the history. Optionally to a file.
1143	Parameters:
1144	filename: The name of the file to save the history to.
1145	"""
1146	hist = list(self._gethistory())
1147	out = "-"*80
1148	for h in hist:
1149	if h.startswith("---"):
1150	out += "\n"+h
1151	else:
1152	items = h.split("##")
1153	date = items[0]
1154	func = items[1]
1155	items = items[2:]
1156	out += "\n"+date+"\n"
1157	out += "Function: %s\n Parameters:" % (func)
1158	for i in items:
1159	s = i.split("=")
1160	out += "\n %s = %s" % (s[0], s[1])
1161	out += "\n"+"-"*80
1162	if filename is not None:
1163	if filename is "":
1164	filename = 'scantable_history.txt'
1165	import os
1166	filename = os.path.expandvars(os.path.expanduser(filename))
1167	if not os.path.isdir(filename):
1168	data = open(filename, 'w')
1169	data.write(out)
1170	data.close()
1171	else:
1172	msg = "Illegal file name '%s'." % (filename)
1173	if rcParams['verbose']:
1174	#print msg
1175	asaplog.push( msg )
1176	print_log( 'ERROR' )
1177	else:
1178	raise IOError(msg)
1179	if rcParams['verbose']:
1180	try:
1181	from IPython.genutils import page as pager
1182	except ImportError:
1183	from pydoc import pager
1184	pager(out)
1185	else:
1186	return out
1187	return
1188	#
1189	# Maths business
1190	#
1191
1192	def average_time(self, mask=None, scanav=False, weight='tint', align=False):
1193	"""
1194	Return the (time) weighted average of a scan.
1195	Note:
1196	in channels only - align if necessary
1197	Parameters:
1198	mask: an optional mask (only used for 'var' and 'tsys'
1199	weighting)
1200	scanav: True averages each scan separately
1201	False (default) averages all scans together,
1202	weight: Weighting scheme.
1203	'none' (mean no weight)
1204	'var' (1/var(spec) weighted)
1205	'tsys' (1/Tsys**2 weighted)
1206	'tint' (integration time weighted)
1207	'tintsys' (Tint/Tsys**2)
1208	'median' ( median averaging)
1209	The default is 'tint'
1210	align: align the spectra in velocity before averaging. It takes
1211	the time of the first spectrum as reference time.
1212	Example:
1213	# time average the scantable without using a mask
1214	newscan = scan.average_time()
1215	"""
1216	varlist = vars()
1217	if weight is None: weight = 'TINT'
1218	if mask is None: mask = ()
1219	if scanav: scanav = "SCAN"
1220	else: scanav = "NONE"
1221	scan = (self, )
1222	try:
1223	if align:
1224	scan = (self.freq_align(insitu=False), )
1225	s = None
1226	if weight.upper() == 'MEDIAN':
1227	s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
1228	scanav))
1229	else:
1230	s = scantable(self._math._average(scan, mask, weight.upper(),
1231	scanav))
1232	except RuntimeError, msg:
1233	if rcParams['verbose']:
1234	#print msg
1235	print_log()
1236	asaplog.push( msg )
1237	print_log( 'ERROR' )
1238	return
1239	else: raise
1240	s._add_history("average_time", varlist)
1241	print_log()
1242	return s
1243
1244	def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
1245	"""
1246	Return a scan where all spectra are converted to either
1247	Jansky or Kelvin depending upon the flux units of the scan table.
1248	By default the function tries to look the values up internally.
1249	If it can't find them (or if you want to over-ride), you must
1250	specify EITHER jyperk OR eta (and D which it will try to look up
1251	also if you don't set it). jyperk takes precedence if you set both.
1252	Parameters:
1253	jyperk: the Jy / K conversion factor
1254	eta: the aperture efficiency
1255	d: the geomtric diameter (metres)
1256	insitu: if False a new scantable is returned.
1257	Otherwise, the scaling is done in-situ
1258	The default is taken from .asaprc (False)
1259	"""
1260	if insitu is None: insitu = rcParams['insitu']
1261	self._math._setinsitu(insitu)
1262	varlist = vars()
1263	if jyperk is None: jyperk = -1.0
1264	if d is None: d = -1.0
1265	if eta is None: eta = -1.0
1266	s = scantable(self._math._convertflux(self, d, eta, jyperk))
1267	s._add_history("convert_flux", varlist)
1268	print_log()
1269	if insitu: self._assign(s)
1270	else: return s
1271
1272	def gain_el(self, poly=None, filename="", method="linear", insitu=None):
1273	"""
1274	Return a scan after applying a gain-elevation correction.
1275	The correction can be made via either a polynomial or a
1276	table-based interpolation (and extrapolation if necessary).
1277	You specify polynomial coefficients, an ascii table or neither.
1278	If you specify neither, then a polynomial correction will be made
1279	with built in coefficients known for certain telescopes (an error
1280	will occur if the instrument is not known).
1281	The data and Tsys are divided by the scaling factors.
1282	Parameters:
1283	poly: Polynomial coefficients (default None) to compute a
1284	gain-elevation correction as a function of
1285	elevation (in degrees).
1286	filename: The name of an ascii file holding correction factors.
1287	The first row of the ascii file must give the column
1288	names and these MUST include columns
1289	"ELEVATION" (degrees) and "FACTOR" (multiply data
1290	by this) somewhere.
1291	The second row must give the data type of the
1292	column. Use 'R' for Real and 'I' for Integer.
1293	An example file would be
1294	(actual factors are arbitrary) :
1295
1296	TIME ELEVATION FACTOR
1297	R R R
1298	0.1 0 0.8
1299	0.2 20 0.85
1300	0.3 40 0.9
1301	0.4 60 0.85
1302	0.5 80 0.8
1303	0.6 90 0.75
1304	method: Interpolation method when correcting from a table.
1305	Values are "nearest", "linear" (default), "cubic"
1306	and "spline"
1307	insitu: if False a new scantable is returned.
1308	Otherwise, the scaling is done in-situ
1309	The default is taken from .asaprc (False)
1310	"""
1311
1312	if insitu is None: insitu = rcParams['insitu']
1313	self._math._setinsitu(insitu)
1314	varlist = vars()
1315	if poly is None:
1316	poly = ()
1317	from os.path import expandvars
1318	filename = expandvars(filename)
1319	s = scantable(self._math._gainel(self, poly, filename, method))
1320	s._add_history("gain_el", varlist)
1321	print_log()
1322	if insitu: self._assign(s)
1323	else: return s
1324
1325	def freq_align(self, reftime=None, method='cubic', insitu=None):
1326	"""
1327	Return a scan where all rows have been aligned in frequency/velocity.
1328	The alignment frequency frame (e.g. LSRK) is that set by function
1329	set_freqframe.
1330	Parameters:
1331	reftime: reference time to align at. By default, the time of
1332	the first row of data is used.
1333	method: Interpolation method for regridding the spectra.
1334	Choose from "nearest", "linear", "cubic" (default)
1335	and "spline"
1336	insitu: if False a new scantable is returned.
1337	Otherwise, the scaling is done in-situ
1338	The default is taken from .asaprc (False)
1339	"""
1340	if insitu is None: insitu = rcParams["insitu"]
1341	self._math._setinsitu(insitu)
1342	varlist = vars()
1343	if reftime is None: reftime = ""
1344	s = scantable(self._math._freq_align(self, reftime, method))
1345	s._add_history("freq_align", varlist)
1346	print_log()
1347	if insitu: self._assign(s)
1348	else: return s
1349
1350	def opacity(self, tau, insitu=None):
1351	"""
1352	Apply an opacity correction. The data
1353	and Tsys are multiplied by the correction factor.
1354	Parameters:
1355	tau: Opacity from which the correction factor is
1356	exp(tau*ZD)
1357	where ZD is the zenith-distance
1358	insitu: if False a new scantable is returned.
1359	Otherwise, the scaling is done in-situ
1360	The default is taken from .asaprc (False)
1361	"""
1362	if insitu is None: insitu = rcParams['insitu']
1363	self._math._setinsitu(insitu)
1364	varlist = vars()
1365	s = scantable(self._math._opacity(self, tau))
1366	s._add_history("opacity", varlist)
1367	print_log()
1368	if insitu: self._assign(s)
1369	else: return s
1370
1371	def bin(self, width=5, insitu=None):
1372	"""
1373	Return a scan where all spectra have been binned up.
1374	Parameters:
1375	width: The bin width (default=5) in pixels
1376	insitu: if False a new scantable is returned.
1377	Otherwise, the scaling is done in-situ
1378	The default is taken from .asaprc (False)
1379	"""
1380	if insitu is None: insitu = rcParams['insitu']
1381	self._math._setinsitu(insitu)
1382	varlist = vars()
1383	s = scantable(self._math._bin(self, width))
1384	s._add_history("bin", varlist)
1385	print_log()
1386	if insitu: self._assign(s)
1387	else: return s
1388
1389
1390	def resample(self, width=5, method='cubic', insitu=None):
1391	"""
1392	Return a scan where all spectra have been binned up.
1393
1394	Parameters:
1395	width: The bin width (default=5) in pixels
1396	method: Interpolation method when correcting from a table.
1397	Values are "nearest", "linear", "cubic" (default)
1398	and "spline"
1399	insitu: if False a new scantable is returned.
1400	Otherwise, the scaling is done in-situ
1401	The default is taken from .asaprc (False)
1402	"""
1403	if insitu is None: insitu = rcParams['insitu']
1404	self._math._setinsitu(insitu)
1405	varlist = vars()
1406	s = scantable(self._math._resample(self, method, width))
1407	s._add_history("resample", varlist)
1408	print_log()
1409	if insitu: self._assign(s)
1410	else: return s
1411
1412
1413	def average_pol(self, mask=None, weight='none'):
1414	"""
1415	Average the Polarisations together.
1416	Parameters:
1417	mask: An optional mask defining the region, where the
1418	averaging will be applied. The output will have all
1419	specified points masked.
1420	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
1421	weighted), or 'tsys' (1/Tsys**2 weighted)
1422	"""
1423	varlist = vars()
1424	if mask is None:
1425	mask = ()
1426	s = scantable(self._math._averagepol(self, mask, weight.upper()))
1427	s._add_history("average_pol", varlist)
1428	print_log()
1429	return s
1430
1431	def average_beam(self, mask=None, weight='none'):
1432	"""
1433	Average the Beams together.
1434	Parameters:
1435	mask: An optional mask defining the region, where the
1436	averaging will be applied. The output will have all
1437	specified points masked.
1438	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
1439	weighted), or 'tsys' (1/Tsys**2 weighted)
1440	"""
1441	varlist = vars()
1442	if mask is None:
1443	mask = ()
1444	s = scantable(self._math._averagebeams(self, mask, weight.upper()))
1445	s._add_history("average_beam", varlist)
1446	print_log()
1447	return s
1448
1449	def convert_pol(self, poltype=None):
1450	"""
1451	Convert the data to a different polarisation type.
1452	Parameters:
1453	poltype: The new polarisation type. Valid types are:
1454	"linear", "stokes" and "circular"
1455	"""
1456	varlist = vars()
1457	try:
1458	s = scantable(self._math._convertpol(self, poltype))
1459	except RuntimeError, msg:
1460	if rcParams['verbose']:
1461	#print msg
1462	print_log()
1463	asaplog.push( msg )
1464	print_log( 'ERROR' )
1465	return
1466	else:
1467	raise
1468	s._add_history("convert_pol", varlist)
1469	print_log()
1470	return s
1471
1472	def smooth(self, kernel="hanning", width=5.0, insitu=None):
1473	"""
1474	Smooth the spectrum by the specified kernel (conserving flux).
1475	Parameters:
1476	kernel: The type of smoothing kernel. Select from
1477	'hanning' (default), 'gaussian', 'boxcar' and
1478	'rmedian'
1479	width: The width of the kernel in pixels. For hanning this is
1480	ignored otherwise it defauls to 5 pixels.
1481	For 'gaussian' it is the Full Width Half
1482	Maximum. For 'boxcar' it is the full width.
1483	For 'rmedian' it is the half width.
1484	insitu: if False a new scantable is returned.
1485	Otherwise, the scaling is done in-situ
1486	The default is taken from .asaprc (False)
1487	Example:
1488	none
1489	"""
1490	if insitu is None: insitu = rcParams['insitu']
1491	self._math._setinsitu(insitu)
1492	varlist = vars()
1493	s = scantable(self._math._smooth(self, kernel.lower(), width))
1494	s._add_history("smooth", varlist)
1495	print_log()
1496	if insitu: self._assign(s)
1497	else: return s
1498
1499
1500	def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None):
1501	"""
1502	Return a scan which has been baselined (all rows) by a polynomial.
1503	Parameters:
1504	mask: an optional mask
1505	order: the order of the polynomial (default is 0)
1506	plot: plot the fit and the residual. In this each
1507	indivual fit has to be approved, by typing 'y'
1508	or 'n'
1509	uselin: use linear polynomial fit
1510	insitu: if False a new scantable is returned.
1511	Otherwise, the scaling is done in-situ
1512	The default is taken from .asaprc (False)
1513	Example:
1514	# return a scan baselined by a third order polynomial,
1515	# not using a mask
1516	bscan = scan.poly_baseline(order=3)
1517	"""
1518	if insitu is None: insitu = rcParams['insitu']
1519	varlist = vars()
1520	if mask is None:
1521	mask = [True for i in xrange(self.nchan(-1))]
1522	from asap.asapfitter import fitter
1523	try:
1524	f = fitter()
1525	f.set_scan(self, mask)
1526	if uselin:
1527	f.set_function(lpoly=order)
1528	else:
1529	f.set_function(poly=order)
1530	s = f.auto_fit(insitu, plot=plot)
1531	# Save parameters of baseline fits as a class attribute.
1532	# NOTICE: It does not reflect changes in scantable!
1533	self.blpars = f.blpars
1534	s._add_history("poly_baseline", varlist)
1535	print_log()
1536	if insitu: self._assign(s)
1537	else: return s
1538	except RuntimeError:
1539	msg = "The fit failed, possibly because it didn't converge."
1540	if rcParams['verbose']:
1541	#print msg
1542	print_log()
1543	asaplog.push( msg )
1544	print_log( 'ERROR' )
1545	return
1546	else:
1547	raise RuntimeError(msg)
1548
1549
1550	def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0,
1551	threshold=3, chan_avg_limit=1, plot=False,
1552	insitu=None):
1553	"""
1554	Return a scan which has been baselined (all rows) by a polynomial.
1555	Spectral lines are detected first using linefinder and masked out
1556	to avoid them affecting the baseline solution.
1557
1558	Parameters:
1559	mask: an optional mask retreived from scantable
1560	edge: an optional number of channel to drop at
1561	the edge of spectrum. If only one value is
1562	specified, the same number will be dropped from
1563	both sides of the spectrum. Default is to keep
1564	all channels. Nested tuples represent individual
1565	edge selection for different IFs (a number of spectral
1566	channels can be different)
1567	order: the order of the polynomial (default is 0)
1568	threshold: the threshold used by line finder. It is better to
1569	keep it large as only strong lines affect the
1570	baseline solution.
1571	chan_avg_limit:
1572	a maximum number of consequtive spectral channels to
1573	average during the search of weak and broad lines.
1574	The default is no averaging (and no search for weak
1575	lines). If such lines can affect the fitted baseline
1576	(e.g. a high order polynomial is fitted), increase this
1577	parameter (usually values up to 8 are reasonable). Most
1578	users of this method should find the default value
1579	sufficient.
1580	plot: plot the fit and the residual. In this each
1581	indivual fit has to be approved, by typing 'y'
1582	or 'n'
1583	insitu: if False a new scantable is returned.
1584	Otherwise, the scaling is done in-situ
1585	The default is taken from .asaprc (False)
1586
1587	Example:
1588	scan2=scan.auto_poly_baseline(order=7)
1589	"""
1590	if insitu is None: insitu = rcParams['insitu']
1591	varlist = vars()
1592	from asap.asapfitter import fitter
1593	from asap.asaplinefind import linefinder
1594	from asap import _is_sequence_or_number as _is_valid
1595
1596	# check whether edge is set up for each IF individually
1597	individualedge = False;
1598	if len(edge) > 1:
1599	if isinstance(edge[0], list) or isinstance(edge[0], tuple):
1600	individualedge = True;
1601
1602	if not _is_valid(edge, int) and not individualedge:
1603	raise ValueError, "Parameter 'edge' has to be an integer or a \
1604	pair of integers specified as a tuple. Nested tuples are allowed \
1605	to make individual selection for different IFs."
1606
1607	curedge = (0, 0)
1608	if individualedge:
1609	for edgepar in edge:
1610	if not _is_valid(edgepar, int):
1611	raise ValueError, "Each element of the 'edge' tuple has \
1612	to be a pair of integers or an integer."
1613	else:
1614	curedge = edge;
1615
1616	# setup fitter
1617	f = fitter()
1618	f.set_function(poly=order)
1619
1620	# setup line finder
1621	fl = linefinder()
1622	fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
1623
1624	if not insitu:
1625	workscan = self.copy()
1626	else:
1627	workscan = self
1628
1629	fl.set_scan(workscan)
1630
1631	rows = range(workscan.nrow())
1632	# Save parameters of baseline fits & masklists as a class attribute.
1633	# NOTICE: It does not reflect changes in scantable!
1634	if len(rows) > 0:
1635	self.blpars=[]
1636	self.masklists=[]
1637	asaplog.push("Processing:")
1638	for r in rows:
1639	msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
1640	(workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
1641	workscan.getpol(r), workscan.getcycle(r))
1642	asaplog.push(msg, False)
1643
1644	# figure out edge parameter
1645	if individualedge:
1646	if len(edge) >= workscan.getif(r):
1647	raise RuntimeError, "Number of edge elements appear to " \
1648	"be less than the number of IFs"
1649	curedge = edge[workscan.getif(r)]
1650
1651	# setup line finder
1652	fl.find_lines(r, mask, curedge)
1653	outmask=fl.get_mask()
1654	f.set_scan(workscan, fl.get_mask())
1655	f.x = workscan._getabcissa(r)
1656	f.y = workscan._getspectrum(r)
1657	f.data = None
1658	f.fit()
1659
1660	# Show mask list
1661	masklist=workscan.get_masklist(fl.get_mask(),row=r)
1662	msg = "mask range: "+str(masklist)
1663	asaplog.push(msg, False)
1664
1665	fpar = f.get_parameters()
1666	if plot:
1667	f.plot(residual=True)
1668	x = raw_input("Accept fit ( [y]/n ): ")
1669	if x.upper() == 'N':
1670	self.blpars.append(None)
1671	self.masklists.append(None)
1672	continue
1673	workscan._setspectrum(f.fitter.getresidual(), r)
1674	self.blpars.append(fpar)
1675	self.masklists.append(masklist)
1676	if plot:
1677	f._p.unmap()
1678	f._p = None
1679	workscan._add_history("auto_poly_baseline", varlist)
1680	if insitu:
1681	self._assign(workscan)
1682	else:
1683	return workscan
1684
1685	def rotate_linpolphase(self, angle):
1686	"""
1687	Rotate the phase of the complex polarization O=Q+iU correlation.
1688	This is always done in situ in the raw data. So if you call this
1689	function more than once then each call rotates the phase further.
1690	Parameters:
1691	angle: The angle (degrees) to rotate (add) by.
1692	Examples:
1693	scan.rotate_linpolphase(2.3)
1694	"""
1695	varlist = vars()
1696	self._math._rotate_linpolphase(self, angle)
1697	self._add_history("rotate_linpolphase", varlist)
1698	print_log()
1699	return
1700
1701
1702	def rotate_xyphase(self, angle):
1703	"""
1704	Rotate the phase of the XY correlation. This is always done in situ
1705	in the data. So if you call this function more than once
1706	then each call rotates the phase further.
1707	Parameters:
1708	angle: The angle (degrees) to rotate (add) by.
1709	Examples:
1710	scan.rotate_xyphase(2.3)
1711	"""
1712	varlist = vars()
1713	self._math._rotate_xyphase(self, angle)
1714	self._add_history("rotate_xyphase", varlist)
1715	print_log()
1716	return
1717
1718	def swap_linears(self):
1719	"""
1720	Swap the linear polarisations XX and YY, or better the first two
1721	polarisations as this also works for ciculars.
1722	"""
1723	varlist = vars()
1724	self._math._swap_linears(self)
1725	self._add_history("swap_linears", varlist)
1726	print_log()
1727	return
1728
1729	def invert_phase(self):
1730	"""
1731	Invert the phase of the complex polarisation
1732	"""
1733	varlist = vars()
1734	self._math._invert_phase(self)
1735	self._add_history("invert_phase", varlist)
1736	print_log()
1737	return
1738
1739	def add(self, offset, insitu=None):
1740	"""
1741	Return a scan where all spectra have the offset added
1742	Parameters:
1743	offset: the offset
1744	insitu: if False a new scantable is returned.
1745	Otherwise, the scaling is done in-situ
1746	The default is taken from .asaprc (False)
1747	"""
1748	if insitu is None: insitu = rcParams['insitu']
1749	self._math._setinsitu(insitu)
1750	varlist = vars()
1751	s = scantable(self._math._unaryop(self, offset, "ADD", False))
1752	s._add_history("add", varlist)
1753	print_log()
1754	if insitu:
1755	self._assign(s)
1756	else:
1757	return s
1758
1759	def scale(self, factor, tsys=True, insitu=None):
1760	"""
1761	Return a scan where all spectra are scaled by the give 'factor'
1762	Parameters:
1763	factor: the scaling factor
1764	insitu: if False a new scantable is returned.
1765	Otherwise, the scaling is done in-situ
1766	The default is taken from .asaprc (False)
1767	tsys: if True (default) then apply the operation to Tsys
1768	as well as the data
1769	"""
1770	if insitu is None: insitu = rcParams['insitu']
1771	self._math._setinsitu(insitu)
1772	varlist = vars()
1773	s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
1774	s._add_history("scale", varlist)
1775	print_log()
1776	if insitu:
1777	self._assign(s)
1778	else:
1779	return s
1780
1781	def set_sourcetype(self, match, matchtype="pattern",
1782	sourcetype="reference"):
1783	"""
1784	Set the type of the source to be an source or reference scan
1785	using the provided pattern:
1786	Parameters:
1787	match: a Unix style pattern, regular expression or selector
1788	matchtype: 'pattern' (default) UNIX style pattern or
1789	'regex' regular expression
1790	sourcetype: the type of the source to use (source/reference)
1791	"""
1792	varlist = vars()
1793	basesel = self.get_selection()
1794	stype = -1
1795	if sourcetype.lower().startswith("r"):
1796	stype = 1
1797	elif sourcetype.lower().startswith("s"):
1798	stype = 0
1799	else:
1800	raise ValueError("Illegal sourcetype use s(ource) or r(eference)")
1801	if matchtype.lower().startswith("p"):
1802	matchtype = "pattern"
1803	elif matchtype.lower().startswith("r"):
1804	matchtype = "regex"
1805	else:
1806	raise ValueError("Illegal matchtype, use p(attern) or r(egex)")
1807	sel = selector()
1808	if isinstance(match, selector):
1809	sel = match
1810	else:
1811	sel.set_query("SRCNAME == %s('%s')" % (matchtype, match))
1812	self.set_selection(basesel+sel)
1813	self._setsourcetype(stype)
1814	self.set_selection(basesel)
1815	s._add_history("set_sourcetype", varlist)
1816
1817	def auto_quotient(self, preserve=True, mode='paired'):
1818	"""
1819	This function allows to build quotients automatically.
1820	It assumes the observation to have the same numer of
1821	"ons" and "offs"
1822	Parameters:
1823	preserve: you can preserve (default) the continuum or
1824	remove it. The equations used are
1825	preserve: Output = Toff * (on/off) - Toff
1826	remove: Output = Toff * (on/off) - Ton
1827	mode: the on/off detection mode
1828	'paired' (default)
1829	identifies 'off' scans by the
1830	trailing '_R' (Mopra/Parkes) or
1831	'_e'/'_w' (Tid) and matches
1832	on/off pairs from the observing pattern
1833	'time'
1834	finds the closest off in time
1835
1836	"""
1837	modes = ["time", "paired"]
1838	if not mode in modes:
1839	msg = "please provide valid mode. Valid modes are %s" % (modes)
1840	raise ValueError(msg)
1841	varlist = vars()
1842	s = None
1843	if mode.lower() == "paired":
1844	basesel = self.get_selection()
1845	sel = selector()+basesel
1846	sel.set_query("SRCTYPE==1")
1847	self.set_selection(sel)
1848	offs = self.copy()
1849	sel.set_query("SRCTYPE==0")
1850	self.set_selection(sel)
1851	ons = self.copy()
1852	s = scantable(self._math._quotient(ons, offs, preserve))
1853	self.set_selection(basesel)
1854	elif mode.lower() == "time":
1855	s = scantable(self._math._auto_quotient(self, mode, preserve))
1856	s._add_history("auto_quotient", varlist)
1857	print_log()
1858	return s
1859
1860	def mx_quotient(self, mask = None, weight='median', preserve=True):
1861	"""
1862	Form a quotient using "off" beams when observing in "MX" mode.
1863	Parameters:
1864	mask: an optional mask to be used when weight == 'stddev'
1865	weight: How to average the off beams. Default is 'median'.
1866	preserve: you can preserve (default) the continuum or
1867	remove it. The equations used are
1868	preserve: Output = Toff * (on/off) - Toff
1869	remove: Output = Toff * (on/off) - Ton
1870	"""
1871	if mask is None: mask = ()
1872	varlist = vars()
1873	on = scantable(self._math._mx_extract(self, 'on'))
1874	preoff = scantable(self._math._mx_extract(self, 'off'))
1875	off = preoff.average_time(mask=mask, weight=weight, scanav=False)
1876	from asapmath import quotient
1877	q = quotient(on, off, preserve)
1878	q._add_history("mx_quotient", varlist)
1879	print_log()
1880	return q
1881
1882	def freq_switch(self, insitu=None):
1883	"""
1884	Apply frequency switching to the data.
1885	Parameters:
1886	insitu: if False a new scantable is returned.
1887	Otherwise, the swictching is done in-situ
1888	The default is taken from .asaprc (False)
1889	Example:
1890	none
1891	"""
1892	if insitu is None: insitu = rcParams['insitu']
1893	self._math._setinsitu(insitu)
1894	varlist = vars()
1895	s = scantable(self._math._freqswitch(self))
1896	s._add_history("freq_switch", varlist)
1897	print_log()
1898	if insitu: self._assign(s)
1899	else: return s
1900
1901	def recalc_azel(self):
1902	"""
1903	Recalculate the azimuth and elevation for each position.
1904	Parameters:
1905	none
1906	Example:
1907	"""
1908	varlist = vars()
1909	self._recalcazel()
1910	self._add_history("recalc_azel", varlist)
1911	print_log()
1912	return
1913
1914	def __add__(self, other):
1915	varlist = vars()
1916	s = None
1917	if isinstance(other, scantable):
1918	s = scantable(self._math._binaryop(self, other, "ADD"))
1919	elif isinstance(other, float):
1920	s = scantable(self._math._unaryop(self, other, "ADD", False))
1921	else:
1922	raise TypeError("Other input is not a scantable or float value")
1923	s._add_history("operator +", varlist)
1924	print_log()
1925	return s
1926
1927	def __sub__(self, other):
1928	"""
1929	implicit on all axes and on Tsys
1930	"""
1931	varlist = vars()
1932	s = None
1933	if isinstance(other, scantable):
1934	s = scantable(self._math._binaryop(self, other, "SUB"))
1935	elif isinstance(other, float):
1936	s = scantable(self._math._unaryop(self, other, "SUB", False))
1937	else:
1938	raise TypeError("Other input is not a scantable or float value")
1939	s._add_history("operator -", varlist)
1940	print_log()
1941	return s
1942
1943	def __mul__(self, other):
1944	"""
1945	implicit on all axes and on Tsys
1946	"""
1947	varlist = vars()
1948	s = None
1949	if isinstance(other, scantable):
1950	s = scantable(self._math._binaryop(self, other, "MUL"))
1951	elif isinstance(other, float):
1952	s = scantable(self._math._unaryop(self, other, "MUL", False))
1953	else:
1954	raise TypeError("Other input is not a scantable or float value")
1955	s._add_history("operator *", varlist)
1956	print_log()
1957	return s
1958
1959
1960	def __div__(self, other):
1961	"""
1962	implicit on all axes and on Tsys
1963	"""
1964	varlist = vars()
1965	s = None
1966	if isinstance(other, scantable):
1967	s = scantable(self._math._binaryop(self, other, "DIV"))
1968	elif isinstance(other, float):
1969	if other == 0.0:
1970	raise ZeroDivisionError("Dividing by zero is not recommended")
1971	s = scantable(self._math._unaryop(self, other, "DIV", False))
1972	else:
1973	raise TypeError("Other input is not a scantable or float value")
1974	s._add_history("operator /", varlist)
1975	print_log()
1976	return s
1977
1978	def get_fit(self, row=0):
1979	"""
1980	Print or return the stored fits for a row in the scantable
1981	Parameters:
1982	row: the row which the fit has been applied to.
1983	"""
1984	if row > self.nrow():
1985	return
1986	from asap.asapfit import asapfit
1987	fit = asapfit(self._getfit(row))
1988	if rcParams['verbose']:
1989	#print fit
1990	asaplog.push( '%s' %(fit) )
1991	print_log()
1992	return
1993	else:
1994	return fit.as_dict()
1995
1996	def flag_nans(self):
1997	"""
1998	Utility function to flag NaN values in the scantable.
1999	"""
2000	import numpy
2001	basesel = self.get_selection()
2002	for i in range(self.nrow()):
2003	sel = selector()+basesel
2004	sel.set_scans(self.getscan(i))
2005	sel.set_beams(self.getbeam(i))
2006	sel.set_ifs(self.getif(i))
2007	sel.set_polarisations(self.getpol(i))
2008	self.set_selection(sel)
2009	nans = numpy.isnan(self._getspectrum(0))
2010	if numpy.any(nans):
2011	bnans = [ bool(v) for v in nans]
2012	self.flag(bnans)
2013	self.set_selection(basesel)
2014
2015
2016	def _add_history(self, funcname, parameters):
2017	if not rcParams['scantable.history']:
2018	return
2019	# create date
2020	sep = "##"
2021	from datetime import datetime
2022	dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
2023	hist = dstr+sep
2024	hist += funcname+sep#cdate+sep
2025	if parameters.has_key('self'): del parameters['self']
2026	for k, v in parameters.iteritems():
2027	if type(v) is dict:
2028	for k2, v2 in v.iteritems():
2029	hist += k2
2030	hist += "="
2031	if isinstance(v2, scantable):
2032	hist += 'scantable'
2033	elif k2 == 'mask':
2034	if isinstance(v2, list) or isinstance(v2, tuple):
2035	hist += str(self._zip_mask(v2))
2036	else:
2037	hist += str(v2)
2038	else:
2039	hist += str(v2)
2040	else:
2041	hist += k
2042	hist += "="
2043	if isinstance(v, scantable):
2044	hist += 'scantable'
2045	elif k == 'mask':
2046	if isinstance(v, list) or isinstance(v, tuple):
2047	hist += str(self._zip_mask(v))
2048	else:
2049	hist += str(v)
2050	else:
2051	hist += str(v)
2052	hist += sep
2053	hist = hist[:-2] # remove trailing '##'
2054	self._addhistory(hist)
2055
2056
2057	def _zip_mask(self, mask):
2058	mask = list(mask)
2059	i = 0
2060	segments = []
2061	while mask[i:].count(1):
2062	i += mask[i:].index(1)
2063	if mask[i:].count(0):
2064	j = i + mask[i:].index(0)
2065	else:
2066	j = len(mask)
2067	segments.append([i, j])
2068	i = j
2069	return segments
2070
2071	def _get_ordinate_label(self):
2072	fu = "("+self.get_fluxunit()+")"
2073	import re
2074	lbl = "Intensity"
2075	if re.match(".K.", fu):
2076	lbl = "Brightness Temperature "+ fu
2077	elif re.match(".Jy.", fu):
2078	lbl = "Flux density "+ fu
2079	return lbl
2080
2081	def _check_ifs(self):
2082	nchans = [self.nchan(i) for i in range(self.nif(-1))]
2083	nchans = filter(lambda t: t > 0, nchans)
2084	return (sum(nchans)/len(nchans) == nchans[0])
2085
2086	def _fill(self, names, unit, average, getpt):
2087	import os
2088	from asap._asap import stfiller
2089	first = True
2090	fullnames = []
2091	for name in names:
2092	name = os.path.expandvars(name)
2093	name = os.path.expanduser(name)
2094	if not os.path.exists(name):
2095	msg = "File '%s' does not exists" % (name)
2096	if rcParams['verbose']:
2097	asaplog.push(msg)
2098	#print asaplog.pop().strip()
2099	print_log( 'ERROR' )
2100	return
2101	raise IOError(msg)
2102	fullnames.append(name)
2103	if average:
2104	asaplog.push('Auto averaging integrations')
2105	stype = int(rcParams['scantable.storage'].lower() == 'disk')
2106	for name in fullnames:
2107	tbl = Scantable(stype)
2108	r = stfiller(tbl)
2109	rx = rcParams['scantable.reference']
2110	r._setreferenceexpr(rx)
2111	msg = "Importing %s..." % (name)
2112	asaplog.push(msg, False)
2113	print_log()
2114	r._open(name, -1, -1, getpt)
2115	r._read()
2116	if average:
2117	tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
2118	if not first:
2119	tbl = self._math._merge([self, tbl])
2120	Scantable.__init__(self, tbl)
2121	r._close()
2122	del r, tbl
2123	first = False
2124	if unit is not None:
2125	self.set_fluxunit(unit)
2126	#self.set_freqframe(rcParams['scantable.freqframe'])
2127
2128	def __getitem__(self, key):
2129	if key < 0:
2130	key += self.nrow()
2131	if key >= self.nrow():
2132	raise IndexError("Row index out of range.")
2133	return self._getspectrum(key)
2134
2135	def __setitem__(self, key, value):
2136	if key < 0:
2137	key += self.nrow()
2138	if key >= self.nrow():
2139	raise IndexError("Row index out of range.")
2140	if not hasattr(value, "__len__") or \
2141	len(value) > self.nchan(self.getif(key)):
2142	raise ValueError("Spectrum length doesn't match.")
2143	return self._setspectrum(value, key)
2144
2145	def __len__(self):
2146	return self.nrow()
2147
2148	def __iter__(self):
2149	for i in range(len(self)):
2150	yield self[i]

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