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source: branches/alma/python/scantable.py@ 1449

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Last change on this file since 1449 was 1446, checked in by TakTsutsumi, 16 years ago
Merged recent updates (since 2007) from nrao-asap
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File size: 72.4 KB

Rev	Line
[876]	1	from asap._asap import Scantable
[226]	2	from asap import rcParams
[1118]	3	from asap import print_log
	4	from asap import asaplog
[946]	5	from asap import selector
[1153]	6	from asap import linecatalog
[1295]	7	from asap import _n_bools, mask_not, mask_and, mask_or
[102]	8
[876]	9	class scantable(Scantable):
[102]	10	"""
	11	The ASAP container for scans
	12	"""
[710]	13
[484]	14	def __init__(self, filename, average=None, unit=None):
[102]	15	"""
	16	Create a scantable from a saved one or make a reference
	17	Parameters:
[181]	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
[102]	25	scantable
[484]	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.
[340]	29	Over-rides the default selected by the reader
	30	(input rpfits/sdfits/ms) or replaces the value
	31	in existing scantables
[710]	32	"""
[976]	33	if average is None:
[710]	34	average = rcParams['scantable.autoaverage']
[1259]	35	varlist = vars()
[876]	36	from asap._asap import stmath
	37	self._math = stmath()
	38	if isinstance(filename, Scantable):
	39	Scantable.__init__(self, filename)
[181]	40	else:
[1118]	41	if isinstance(filename, str):
[976]	42	import os.path
	43	filename = os.path.expandvars(filename)
	44	filename = os.path.expanduser(filename)
	45	if not os.path.exists(filename):
	46	s = "File '%s' not found." % (filename)
[718]	47	if rcParams['verbose']:
[976]	48	asaplog.push(s)
	49	print asaplog.pop().strip()
[718]	50	return
[976]	51	raise IOError(s)
[1115]	52	if os.path.isdir(filename) \
[1118]	53	and not os.path.exists(filename+'/table.f1'):
[976]	54	# crude check if asap table
	55	if os.path.exists(filename+'/table.info'):
[1118]	56	ondisk = rcParams['scantable.storage'] == 'disk'
	57	Scantable.__init__(self, filename, ondisk)
[976]	58	if unit is not None:
	59	self.set_fluxunit(unit)
	60	self.set_freqframe(rcParams['scantable.freqframe'])
[718]	61	else:
[1118]	62	msg = "The given file '%s'is not a valid " \
	63	"asap table." % (filename)
[976]	64	if rcParams['verbose']:
	65	print msg
	66	return
	67	else:
	68	raise IOError(msg)
[226]	69	else:
[1118]	70	self._fill([filename], unit, average)
	71	elif (isinstance(filename, list) or isinstance(filename, tuple)) \
[976]	72	and isinstance(filename[-1], str):
	73	self._fill(filename, unit, average)
[1259]	74	self._add_history("scantable", varlist)
[714]	75	print_log()
[102]	76
[876]	77	def save(self, name=None, format=None, overwrite=False):
[116]	78	"""
[1280]	79	Store the scantable on disk. This can be an asap (aips++) Table,
	80	SDFITS or MS2 format.
[116]	81	Parameters:
[1093]	82	name: the name of the outputfile. For format "ASCII"
	83	this is the root file name (data in 'name'.txt
[497]	84	and header in 'name'_header.txt)
[116]	85	format: an optional file format. Default is ASAP.
[280]	86	Allowed are - 'ASAP' (save as ASAP [aips++] Table),
[194]	87	'SDFITS' (save as SDFITS file)
[200]	88	'ASCII' (saves as ascii text file)
[226]	89	'MS2' (saves as an aips++
	90	MeasurementSet V2)
[411]	91	overwrite: If the file should be overwritten if it exists.
[256]	92	The default False is to return with warning
[411]	93	without writing the output. USE WITH CARE.
[116]	94	Example:
	95	scan.save('myscan.asap')
[1118]	96	scan.save('myscan.sdfits', 'SDFITS')
[116]	97	"""
[411]	98	from os import path
[226]	99	if format is None: format = rcParams['scantable.save']
[256]	100	suffix = '.'+format.lower()
[1118]	101	if name is None or name == "":
[256]	102	name = 'scantable'+suffix
[718]	103	msg = "No filename given. Using default name %s..." % name
	104	asaplog.push(msg)
[411]	105	name = path.expandvars(name)
[256]	106	if path.isfile(name) or path.isdir(name):
	107	if not overwrite:
[718]	108	msg = "File %s exists." % name
	109	if rcParams['verbose']:
	110	print msg
	111	return
	112	else:
	113	raise IOError(msg)
[451]	114	format2 = format.upper()
	115	if format2 == 'ASAP':
[116]	116	self._save(name)
	117	else:
[989]	118	from asap._asap import stwriter as stw
[1118]	119	writer = stw(format2)
	120	writer.write(self, name)
[718]	121	print_log()
[116]	122	return
	123
[102]	124	def copy(self):
	125	"""
	126	Return a copy of this scantable.
[1348]	127	Note:
	128	This makes a full (deep) copy. scan2 = scan1 makes a reference.
[102]	129	Parameters:
[113]	130	none
[102]	131	Example:
	132	copiedscan = scan.copy()
	133	"""
[876]	134	sd = scantable(Scantable._copy(self))
[113]	135	return sd
	136
[1093]	137	def drop_scan(self, scanid=None):
	138	"""
	139	Return a new scantable where the specified scan number(s) has(have)
	140	been dropped.
	141	Parameters:
	142	scanid: a (list of) scan number(s)
	143	"""
	144	from asap import _is_sequence_or_number as _is_valid
	145	from asap import _to_list
	146	from asap import unique
	147	if not _is_valid(scanid):
	148	if rcParams['verbose']:
	149	print "Please specify a scanno to drop from the scantable"
	150	return
	151	else:
	152	raise RuntimeError("No scan given")
	153	try:
	154	scanid = _to_list(scanid)
	155	allscans = unique([ self.getscan(i) for i in range(self.nrow())])
	156	for sid in scanid: allscans.remove(sid)
[1118]	157	if len(allscans) == 0:
	158	raise ValueError("Can't remove all scans")
[1093]	159	except ValueError:
	160	if rcParams['verbose']:
	161	print "Couldn't find any match."
	162	return
	163	else: raise
	164	try:
	165	bsel = self.get_selection()
	166	sel = selector()
	167	sel.set_scans(allscans)
	168	self.set_selection(bsel+sel)
	169	scopy = self._copy()
	170	self.set_selection(bsel)
	171	return scantable(scopy)
	172	except RuntimeError:
[1118]	173	if rcParams['verbose']:
	174	print "Couldn't find any match."
	175	else:
	176	raise
[1093]	177
	178
[102]	179	def get_scan(self, scanid=None):
	180	"""
	181	Return a specific scan (by scanno) or collection of scans (by
	182	source name) in a new scantable.
[1348]	183	Note:
	184	See scantable.drop_scan() for the inverse operation.
[102]	185	Parameters:
[513]	186	scanid: a (list of) scanno or a source name, unix-style
	187	patterns are accepted for source name matching, e.g.
	188	'*_R' gets all 'ref scans
[102]	189	Example:
[513]	190	# get all scans containing the source '323p459'
	191	newscan = scan.get_scan('323p459')
	192	# get all 'off' scans
	193	refscans = scan.get_scan('*_R')
	194	# get a susbset of scans by scanno (as listed in scan.summary())
[1118]	195	newscan = scan.get_scan([0, 2, 7, 10])
[102]	196	"""
	197	if scanid is None:
[718]	198	if rcParams['verbose']:
[1118]	199	print "Please specify a scan no or name to " \
	200	"retrieve from the scantable"
[718]	201	return
	202	else:
	203	raise RuntimeError("No scan given")
	204
[102]	205	try:
[946]	206	bsel = self.get_selection()
	207	sel = selector()
[102]	208	if type(scanid) is str:
[946]	209	sel.set_name(scanid)
	210	self.set_selection(bsel+sel)
[876]	211	scopy = self._copy()
[946]	212	self.set_selection(bsel)
[876]	213	return scantable(scopy)
[102]	214	elif type(scanid) is int:
[946]	215	sel.set_scans([scanid])
	216	self.set_selection(bsel+sel)
[876]	217	scopy = self._copy()
[946]	218	self.set_selection(bsel)
[876]	219	return scantable(scopy)
[381]	220	elif type(scanid) is list:
[946]	221	sel.set_scans(scanid)
	222	self.set_selection(sel)
[876]	223	scopy = self._copy()
[946]	224	self.set_selection(bsel)
[876]	225	return scantable(scopy)
[381]	226	else:
[718]	227	msg = "Illegal scanid type, use 'int' or 'list' if ints."
	228	if rcParams['verbose']:
	229	print msg
	230	else:
	231	raise TypeError(msg)
[102]	232	except RuntimeError:
[718]	233	if rcParams['verbose']: print "Couldn't find any match."
	234	else: raise
[102]	235
	236	def __str__(self):
[1118]	237	return Scantable._summary(self, True)
[102]	238
[976]	239	def summary(self, filename=None):
[102]	240	"""
	241	Print a summary of the contents of this scantable.
	242	Parameters:
	243	filename: the name of a file to write the putput to
	244	Default - no file output
[381]	245	verbose: print extra info such as the frequency table
	246	The default (False) is taken from .asaprc
[102]	247	"""
[976]	248	info = Scantable._summary(self, True)
	249	#if verbose is None: verbose = rcParams['scantable.verbosesummary']
[102]	250	if filename is not None:
[256]	251	if filename is "":
	252	filename = 'scantable_summary.txt'
[415]	253	from os.path import expandvars, isdir
[411]	254	filename = expandvars(filename)
[415]	255	if not isdir(filename):
[413]	256	data = open(filename, 'w')
	257	data.write(info)
	258	data.close()
	259	else:
[718]	260	msg = "Illegal file name '%s'." % (filename)
	261	if rcParams['verbose']:
	262	print msg
	263	else:
	264	raise IOError(msg)
	265	if rcParams['verbose']:
[794]	266	try:
	267	from IPython.genutils import page as pager
	268	except ImportError:
	269	from pydoc import pager
	270	pager(info)
[718]	271	else:
	272	return info
[710]	273
[946]	274
	275	def get_selection(self):
	276	"""
[1005]	277	Get the selection object currently set on this scantable.
	278	Parameters:
	279	none
	280	Example:
	281	sel = scan.get_selection()
	282	sel.set_ifs(0) # select IF 0
	283	scan.set_selection(sel) # apply modified selection
[946]	284	"""
	285	return selector(self._getselection())
	286
[1005]	287	def set_selection(self, selection=selector()):
[946]	288	"""
[1005]	289	Select a subset of the data. All following operations on this scantable
	290	are only applied to thi selection.
	291	Parameters:
	292	selection: a selector object (default unset the selection)
	293	Examples:
	294	sel = selector() # create a selection object
[1118]	295	self.set_scans([0, 3]) # select SCANNO 0 and 3
[1005]	296	scan.set_selection(sel) # set the selection
	297	scan.summary() # will only print summary of scanno 0 an 3
	298	scan.set_selection() # unset the selection
[946]	299	"""
	300	self._setselection(selection)
	301
[1446]	302	def get_row(self, row=0, insitu=None):
	303	"""
	304	Select a row in the scantable.
	305	Return a scantable with single row.
	306	Parameters:
	307	row: row no of integration, default is 0.
	308	insitu: if False a new scantable is returned.
	309	Otherwise, the scaling is done in-situ
	310	The default is taken from .asaprc (False)
	311	"""
	312	if insitu is None: insitu = rcParams['insitu']
	313	if not insitu:
	314	workscan = self.copy()
	315	else:
	316	workscan = self
	317	# Select a row
	318	sel=selector()
	319	sel.set_scans([workscan.getscan(row)])
	320	sel.set_cycles([workscan.getcycle(row)])
	321	sel.set_beams([workscan.getbeam(row)])
	322	sel.set_ifs([workscan.getif(row)])
	323	sel.set_polarisations([workscan.getpol(row)])
	324	sel.set_name(workscan._getsourcename(row))
	325	workscan.set_selection(sel)
	326	if not workscan.nrow() == 1:
	327	msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow())
	328	raise RuntimeError(msg)
	329	del sel
	330	if insitu:
	331	self._assign(workscan)
	332	else:
	333	return workscan
	334
[876]	335	def stats(self, stat='stddev', mask=None):
[102]	336	"""
[135]	337	Determine the specified statistic of the current beam/if/pol
[102]	338	Takes a 'mask' as an optional parameter to specify which
	339	channels should be excluded.
	340	Parameters:
[135]	341	stat: 'min', 'max', 'sumsq', 'sum', 'mean'
	342	'var', 'stddev', 'avdev', 'rms', 'median'
	343	mask: an optional mask specifying where the statistic
[102]	344	should be determined.
	345	Example:
[113]	346	scan.set_unit('channel')
[1118]	347	msk = scan.create_mask([100, 200], [500, 600])
[135]	348	scan.stats(stat='mean', mask=m)
[102]	349	"""
	350	if mask == None:
[876]	351	mask = []
[1118]	352	axes = ['Beam', 'IF', 'Pol', 'Time']
[876]	353	if not self._check_ifs():
[1118]	354	raise ValueError("Cannot apply mask as the IFs have different "
	355	"number of channels. Please use setselection() "
	356	"to select individual IFs")
[256]	357
[876]	358	statvals = self._math._stats(self, mask, stat)
	359	out = ''
	360	axes = []
	361	for i in range(self.nrow()):
	362	axis = []
	363	axis.append(self.getscan(i))
	364	axis.append(self.getbeam(i))
	365	axis.append(self.getif(i))
	366	axis.append(self.getpol(i))
	367	axis.append(self.getcycle(i))
	368	axes.append(axis)
	369	tm = self._gettime(i)
	370	src = self._getsourcename(i)
	371	out += 'Scan[%d] (%s) ' % (axis[0], src)
	372	out += 'Time[%s]:\n' % (tm)
	373	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
	374	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
	375	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
	376	out += '= %3.3f\n' % (statvals[i])
	377	out += "--------------------------------------------------\n"
[256]	378
[876]	379	if rcParams['verbose']:
	380	print "--------------------------------------------------"
[1118]	381	print " ", stat
[876]	382	print "--------------------------------------------------"
	383	print out
[1295]	384	#else:
	385	#retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'],
	386	# 'axes' : axes,
	387	# 'data': statvals}
	388	return statvals
[102]	389
[1118]	390	def stddev(self, mask=None):
[135]	391	"""
	392	Determine the standard deviation of the current beam/if/pol
	393	Takes a 'mask' as an optional parameter to specify which
	394	channels should be excluded.
	395	Parameters:
	396	mask: an optional mask specifying where the standard
	397	deviation should be determined.
	398
	399	Example:
	400	scan.set_unit('channel')
[1118]	401	msk = scan.create_mask([100, 200], [500, 600])
[135]	402	scan.stddev(mask=m)
	403	"""
[1118]	404	return self.stats(stat='stddev', mask=mask);
[135]	405
[1003]	406
[1259]	407	def get_column_names(self):
[1003]	408	"""
	409	Return a list of column names, which can be used for selection.
	410	"""
[1259]	411	return list(Scantable.get_column_names(self))
[1003]	412
[876]	413	def get_tsys(self):
[113]	414	"""
	415	Return the System temperatures.
	416	Returns:
[876]	417	a list of Tsys values for the current selection
[113]	418	"""
[256]	419
[876]	420	return self._row_callback(self._gettsys, "Tsys")
[256]	421
[876]	422	def _row_callback(self, callback, label):
	423	axes = []
[1118]	424	axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno']
[876]	425	out = ""
[1118]	426	outvec = []
[876]	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	out += 'Scan[%d] (%s) ' % (axis[0], src)
	438	out += 'Time[%s]:\n' % (tm)
	439	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
	440	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
	441	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
	442	outvec.append(callback(i))
	443	out += '= %3.3f\n' % (outvec[i])
	444	out += "--------------------------------------------------\n"
	445	if rcParams['verbose']:
	446	print "--------------------------------------------------"
	447	print " %s" % (label)
	448	print "--------------------------------------------------"
	449	print out
[1175]	450	# disabled because the vector seems more useful
	451	#retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
	452	return outvec
[256]	453
[1070]	454	def _get_column(self, callback, row=-1):
	455	"""
	456	"""
	457	if row == -1:
	458	return [callback(i) for i in range(self.nrow())]
	459	else:
	460	if 0 <= row < self.nrow():
	461	return callback(row)
[256]	462
[1070]	463
[1348]	464	def get_time(self, row=-1, asdatetime=False):
[113]	465	"""
	466	Get a list of time stamps for the observations.
[1348]	467	Return a datetime object for each integration time stamp in the scantable.
[113]	468	Parameters:
[1348]	469	row: row no of integration. Default -1 return all rows
	470	asdatetime: return values as datetime objects rather than strings
[113]	471	Example:
	472	none
	473	"""
[1175]	474	from time import strptime
	475	from datetime import datetime
[1348]	476	if not asdatetime:
	477	return self._get_column(self._gettime, row)
[1175]	478	format = "%Y/%m/%d/%H:%M:%S"
	479	if isinstance(times, list):
	480	return [datetime(*strptime(i, format)[:6]) for i in times]
	481	else:
	482	return datetime(*strptime(times, format)[:6])
[102]	483
[1348]	484
	485	def get_inttime(self, row=-1):
	486	"""
	487	Get a list of integration times for the observations.
	488	Return a time in seconds for each integration in the scantable.
	489	Parameters:
	490	row: row no of integration. Default -1 return all rows.
	491	Example:
	492	none
	493	"""
	494	return self._get_column(self._getinttime, row)
	495
	496
[714]	497	def get_sourcename(self, row=-1):
	498	"""
[794]	499	Get a list source names for the observations.
[714]	500	Return a string for each integration in the scantable.
	501	Parameters:
[1348]	502	row: row no of integration. Default -1 return all rows.
[714]	503	Example:
	504	none
	505	"""
[1070]	506	return self._get_column(self._getsourcename, row)
[714]	507
[794]	508	def get_elevation(self, row=-1):
	509	"""
	510	Get a list of elevations for the observations.
	511	Return a float for each integration in the scantable.
	512	Parameters:
[1348]	513	row: row no of integration. Default -1 return all rows.
[794]	514	Example:
	515	none
	516	"""
[1070]	517	return self._get_column(self._getelevation, row)
[794]	518
	519	def get_azimuth(self, row=-1):
	520	"""
	521	Get a list of azimuths for the observations.
	522	Return a float for each integration in the scantable.
	523	Parameters:
[1348]	524	row: row no of integration. Default -1 return all rows.
[794]	525	Example:
	526	none
	527	"""
[1070]	528	return self._get_column(self._getazimuth, row)
[794]	529
	530	def get_parangle(self, row=-1):
	531	"""
	532	Get a list of parallactic angles for the observations.
	533	Return a float for each integration in the scantable.
	534	Parameters:
[1348]	535	row: row no of integration. Default -1 return all rows.
[794]	536	Example:
	537	none
	538	"""
[1070]	539	return self._get_column(self._getparangle, row)
[794]	540
[1070]	541	def get_direction(self, row=-1):
	542	"""
	543	Get a list of Positions on the sky (direction) for the observations.
	544	Return a float for each integration in the scantable.
	545	Parameters:
	546	row: row no of integration. Default -1 return all rows
	547	Example:
	548	none
	549	"""
	550	return self._get_column(self._getdirection, row)
	551
[1389]	552	def get_directionval(self, row=-1):
	553	"""
	554	Get a list of Positions on the sky (direction) for the observations.
	555	Return a float for each integration in the scantable.
	556	Parameters:
	557	row: row no of integration. Default -1 return all rows
	558	Example:
	559	none
	560	"""
	561	return self._get_column(self._getdirectionvec, row)
	562
[102]	563	def set_unit(self, unit='channel'):
	564	"""
	565	Set the unit for all following operations on this scantable
	566	Parameters:
	567	unit: optional unit, default is 'channel'
[1118]	568	one of '*Hz', 'km/s', 'channel', ''
[102]	569	"""
[484]	570	varlist = vars()
[1118]	571	if unit in ['', 'pixel', 'channel']:
[113]	572	unit = ''
	573	inf = list(self._getcoordinfo())
	574	inf[0] = unit
	575	self._setcoordinfo(inf)
[1118]	576	self._add_history("set_unit", varlist)
[113]	577
[484]	578	def set_instrument(self, instr):
[358]	579	"""
[1348]	580	Set the instrument for subsequent processing.
[358]	581	Parameters:
[710]	582	instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
[407]	583	'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
[358]	584	"""
	585	self._setInstrument(instr)
[1118]	586	self._add_history("set_instument", vars())
[718]	587	print_log()
[358]	588
[1190]	589	def set_feedtype(self, feedtype):
	590	"""
	591	Overwrite the feed type, which might not be set correctly.
	592	Parameters:
	593	feedtype: 'linear' or 'circular'
	594	"""
	595	self._setfeedtype(feedtype)
	596	self._add_history("set_feedtype", vars())
	597	print_log()
	598
[276]	599	def set_doppler(self, doppler='RADIO'):
	600	"""
	601	Set the doppler for all following operations on this scantable.
	602	Parameters:
	603	doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
	604	"""
[484]	605	varlist = vars()
[276]	606	inf = list(self._getcoordinfo())
	607	inf[2] = doppler
	608	self._setcoordinfo(inf)
[1118]	609	self._add_history("set_doppler", vars())
[718]	610	print_log()
[710]	611
[226]	612	def set_freqframe(self, frame=None):
[113]	613	"""
	614	Set the frame type of the Spectral Axis.
	615	Parameters:
[591]	616	frame: an optional frame type, default 'LSRK'. Valid frames are:
[1118]	617	'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY',
	618	'GEO', 'GALACTO', 'LGROUP', 'CMB'
[113]	619	Examples:
	620	scan.set_freqframe('BARY')
	621	"""
[484]	622	if frame is None: frame = rcParams['scantable.freqframe']
	623	varlist = vars()
[1118]	624	valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
	625	'GEO', 'GALACTO', 'LGROUP', 'CMB']
[591]	626
[989]	627	if frame in valid:
[113]	628	inf = list(self._getcoordinfo())
	629	inf[1] = frame
	630	self._setcoordinfo(inf)
[1118]	631	self._add_history("set_freqframe", varlist)
[102]	632	else:
[1118]	633	msg = "Please specify a valid freq type. Valid types are:\n", valid
[718]	634	if rcParams['verbose']:
	635	print msg
	636	else:
	637	raise TypeError(msg)
	638	print_log()
[710]	639
[989]	640	def set_dirframe(self, frame=""):
	641	"""
	642	Set the frame type of the Direction on the sky.
	643	Parameters:
	644	frame: an optional frame type, default ''. Valid frames are:
	645	'J2000', 'B1950', 'GALACTIC'
	646	Examples:
	647	scan.set_dirframe('GALACTIC')
	648	"""
	649	varlist = vars()
	650	try:
	651	Scantable.set_dirframe(self, frame)
[1118]	652	except RuntimeError, msg:
[989]	653	if rcParams['verbose']:
	654	print msg
	655	else:
	656	raise
[1118]	657	self._add_history("set_dirframe", varlist)
[989]	658
[113]	659	def get_unit(self):
	660	"""
	661	Get the default unit set in this scantable
	662	Returns:
	663	A unit string
	664	"""
	665	inf = self._getcoordinfo()
	666	unit = inf[0]
	667	if unit == '': unit = 'channel'
	668	return unit
[102]	669
[158]	670	def get_abcissa(self, rowno=0):
[102]	671	"""
[158]	672	Get the abcissa in the current coordinate setup for the currently
[113]	673	selected Beam/IF/Pol
	674	Parameters:
[226]	675	rowno: an optional row number in the scantable. Default is the
	676	first row, i.e. rowno=0
[113]	677	Returns:
[1348]	678	The abcissa values and the format string (as a dictionary)
[113]	679	"""
[256]	680	abc = self._getabcissa(rowno)
[710]	681	lbl = self._getabcissalabel(rowno)
[718]	682	print_log()
[158]	683	return abc, lbl
[113]	684
[1401]	685	def flag(self, mask=None, unflag=False):
[1001]	686	"""
	687	Flag the selected data using an optional channel mask.
	688	Parameters:
	689	mask: an optional channel mask, created with create_mask. Default
	690	(no mask) is all channels.
[1401]	691	unflag: if True, unflag the data
[1001]	692	"""
	693	varlist = vars()
[1118]	694	if mask is None:
	695	mask = []
[1001]	696	try:
[1401]	697	self._flag(mask, unflag)
[1118]	698	except RuntimeError, msg:
[1001]	699	if rcParams['verbose']:
	700	print msg
	701	return
	702	else: raise
	703	self._add_history("flag", varlist)
	704
[1203]	705	def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None):
[1192]	706	"""
	707	Flag the data in 'lag' space by providing a frequency to remove.
	708	Flagged data in the scantable gets set to 0.0 before the fft.
	709	No taper is applied.
	710	Parameters:
[1348]	711	frequency: the frequency (really a period within the bandwidth)
	712	to remove
	713	width: the width of the frequency to remove, to remove a
	714	range of frequencies aroung the centre.
[1203]	715	unit: the frequency unit (default "GHz")
	716	Notes:
[1348]	717	It is recommended to flag edges of the band or strong
	718	signals beforehand.
[1192]	719	"""
	720	if insitu is None: insitu = rcParams['insitu']
	721	self._math._setinsitu(insitu)
	722	varlist = vars()
[1370]	723	base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. }
[1192]	724	if not base.has_key(unit):
	725	raise ValueError("%s is not a valid unit." % unit)
	726	try:
[1200]	727	s = scantable(self._math._lag_flag(self, frequency*base[unit],
	728	width*base[unit]))
[1192]	729	except RuntimeError, msg:
	730	if rcParams['verbose']:
	731	print msg
	732	return
	733	else: raise
	734	s._add_history("lag_flag", varlist)
	735	print_log()
	736	if insitu:
	737	self._assign(s)
	738	else:
	739	return s
[1001]	740
[1192]	741
[113]	742	def create_mask(self, args, *kwargs):
	743	"""
[1118]	744	Compute and return a mask based on [min, max] windows.
[189]	745	The specified windows are to be INCLUDED, when the mask is
[113]	746	applied.
[102]	747	Parameters:
[1118]	748	[min, max], [min2, max2], ...
[1024]	749	Pairs of start/end points (inclusive)specifying the regions
[102]	750	to be masked
[189]	751	invert: optional argument. If specified as True,
	752	return an inverted mask, i.e. the regions
	753	specified are EXCLUDED
[513]	754	row: create the mask using the specified row for
	755	unit conversions, default is row=0
	756	only necessary if frequency varies over rows.
[102]	757	Example:
[113]	758	scan.set_unit('channel')
	759	a)
[1118]	760	msk = scan.create_mask([400, 500], [800, 900])
[189]	761	# masks everything outside 400 and 500
[113]	762	# and 800 and 900 in the unit 'channel'
	763
	764	b)
[1118]	765	msk = scan.create_mask([400, 500], [800, 900], invert=True)
[189]	766	# masks the regions between 400 and 500
[113]	767	# and 800 and 900 in the unit 'channel'
[1024]	768	c)
	769	mask only channel 400
[1118]	770	msk = scan.create_mask([400, 400])
[102]	771	"""
[513]	772	row = 0
	773	if kwargs.has_key("row"):
	774	row = kwargs.get("row")
	775	data = self._getabcissa(row)
[113]	776	u = self._getcoordinfo()[0]
[718]	777	if rcParams['verbose']:
[113]	778	if u == "": u = "channel"
[718]	779	msg = "The current mask window unit is %s" % u
[1118]	780	i = self._check_ifs()
	781	if not i:
[876]	782	msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
[718]	783	asaplog.push(msg)
[102]	784	n = self.nchan()
[1295]	785	msk = _n_bools(n, False)
[710]	786	# test if args is a 'list' or a 'normal *args - UGLY!!!
	787
[1118]	788	ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
	789	and args or args[0]
[710]	790	for window in ws:
[102]	791	if (len(window) != 2 or window[0] > window[1] ):
[1118]	792	raise TypeError("A window needs to be defined as [min, max]")
[102]	793	for i in range(n):
[1024]	794	if data[i] >= window[0] and data[i] <= window[1]:
[1295]	795	msk[i] = True
[113]	796	if kwargs.has_key('invert'):
	797	if kwargs.get('invert'):
[1295]	798	msk = mask_not(msk)
[718]	799	print_log()
[102]	800	return msk
[710]	801
[1446]	802	def get_masklist(self, mask=None, row=0):
[256]	803	"""
[1446]	804	Compute and return a list of mask windows, [min, max].
	805	Parameters:
	806	mask: channel mask, created with create_mask.
	807	row: calcutate the masklist using the specified row
	808	for unit conversions, default is row=0
	809	only necessary if frequency varies over rows.
	810	Returns:
	811	[min, max], [min2, max2], ...
	812	Pairs of start/end points (inclusive)specifying
	813	the masked regions
	814	"""
	815	if not (isinstance(mask,list) or isinstance(mask, tuple)):
	816	raise TypeError("The mask should be list or tuple.")
	817	if len(mask) < 2:
	818	raise TypeError("The mask elements should be > 1")
	819	if self.nchan() != len(mask):
	820	msg = "Number of channels in scantable != number of mask elements"
	821	raise TypeError(msg)
	822	data = self._getabcissa(row)
	823	u = self._getcoordinfo()[0]
	824	if rcParams['verbose']:
	825	if u == "": u = "channel"
	826	msg = "The current mask window unit is %s" % u
	827	i = self._check_ifs()
	828	if not i:
	829	msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
	830	asaplog.push(msg)
	831	masklist=[]
	832	ist, ien = None, None
	833	ist, ien=self.get_mask_indices(mask)
	834	if ist is not None and ien is not None:
	835	for i in xrange(len(ist)):
	836	range=[data[ist[i]],data[ien[i]]]
	837	range.sort()
	838	masklist.append([range[0],range[1]])
	839	return masklist
	840
	841	def get_mask_indices(self, mask=None):
	842	"""
	843	Compute and Return lists of mask start indices and mask end indices.
	844	Parameters:
	845	mask: channel mask, created with create_mask.
	846	Returns:
	847	List of mask start indices and that of mask end indices,
	848	i.e., [istart1,istart2,....], [iend1,iend2,....].
	849	"""
	850	if not (isinstance(mask,list) or isinstance(mask, tuple)):
	851	raise TypeError("The mask should be list or tuple.")
	852	if len(mask) < 2:
	853	raise TypeError("The mask elements should be > 1")
	854	istart=[]
	855	iend=[]
	856	if mask[0]: istart.append(0)
	857	for i in range(len(mask)-1):
	858	if not mask[i] and mask[i+1]:
	859	istart.append(i+1)
	860	elif mask[i] and not mask[i+1]:
	861	iend.append(i)
	862	if mask[len(mask)-1]: iend.append(len(mask)-1)
	863	if len(istart) != len(iend):
	864	raise RuntimeError("Numbers of mask start != mask end.")
	865	for i in range(len(istart)):
	866	if istart[i] > iend[i]:
	867	raise RuntimeError("Mask start index > mask end index")
	868	break
	869	return istart,iend
	870
	871	# def get_restfreqs(self):
	872	# """
	873	# Get the restfrequency(s) stored in this scantable.
	874	# The return value(s) are always of unit 'Hz'
	875	# Parameters:
	876	# none
	877	# Returns:
	878	# a list of doubles
	879	# """
	880	# return list(self._getrestfreqs())
	881
	882	def get_restfreqs(self, ids=None):
	883	"""
[256]	884	Get the restfrequency(s) stored in this scantable.
	885	The return value(s) are always of unit 'Hz'
	886	Parameters:
[1446]	887	ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to
	888	be retrieved
[256]	889	Returns:
[1446]	890	dictionary containing ids and a list of doubles for each id
[256]	891	"""
[1446]	892	if ids is None:
	893	rfreqs={}
	894	idlist = self.getmolnos()
	895	for i in idlist:
	896	rfreqs[i]=list(self._getrestfreqs(i))
	897	return rfreqs
	898	else:
	899	if type(ids)==list or type(ids)==tuple:
	900	rfreqs={}
	901	for i in ids:
	902	rfreqs[i]=list(self._getrestfreqs(i))
	903	return rfreqs
	904	else:
	905	return list(self._getrestfreqs(ids))
	906	#return list(self._getrestfreqs(ids))
[102]	907
[931]	908	def set_restfreqs(self, freqs=None, unit='Hz'):
	909	"""
[1446]	910	******NEED TO BE UPDATED begin**********
[931]	911	Set or replace the restfrequency specified and
	912	If the 'freqs' argument holds a scalar,
	913	then that rest frequency will be applied to all the selected
	914	data. If the 'freqs' argument holds
	915	a vector, then it MUST be of equal or smaller length than
	916	the number of IFs (and the available restfrequencies will be
	917	replaced by this vector). In this case, all data have
	918	the restfrequency set per IF according
	919	to the corresponding value you give in the 'freqs' vector.
[1118]	920	E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
[931]	921	IF 1 gets restfreq 2e9.
[1446]	922	******NEED TO BE UPDATED end**********
[1153]	923	You can also specify the frequencies via a linecatalog/
	924
[931]	925	Parameters:
	926	freqs: list of rest frequency values or string idenitfiers
	927	unit: unit for rest frequency (default 'Hz')
[402]	928
[931]	929	Example:
[1446]	930	# set the given restfrequency for the all currently selected IFs
[931]	931	scan.set_restfreqs(freqs=1.4e9)
[1446]	932	# set multiple restfrequencies to all the selected data
	933	scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9])
	934	# If the number of IFs in the data is >= 2 the IF0 gets the first
	935	# value IF1 the second... NOTE that freqs needs to be
	936	# specified in list of list (e.g. [[],[],...] ).
	937	scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]])
[931]	938	#set the given restfrequency for the whole table (by name)
	939	scan.set_restfreqs(freqs="OH1667")
[391]	940
[931]	941	Note:
	942	To do more sophisticate Restfrequency setting, e.g. on a
	943	source and IF basis, use scantable.set_selection() before using
	944	this function.
	945	# provide your scantable is call scan
	946	selection = selector()
	947	selection.set_name("ORION*")
	948	selection.set_ifs([1])
	949	scan.set_selection(selection)
	950	scan.set_restfreqs(freqs=86.6e9)
	951
	952	"""
	953	varlist = vars()
[1157]	954	from asap import linecatalog
	955	# simple value
[1118]	956	if isinstance(freqs, int) or isinstance(freqs, float):
[1446]	957	# TT mod
	958	#self._setrestfreqs(freqs, "",unit)
	959	self._setrestfreqs([freqs], [""],unit)
[1157]	960	# list of values
[1118]	961	elif isinstance(freqs, list) or isinstance(freqs, tuple):
[1157]	962	# list values are scalars
[1118]	963	if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
[1446]	964	self._setrestfreqs(freqs, [""],unit)
[1157]	965	# list values are tuples, (value, name)
	966	elif isinstance(freqs[-1], dict):
[1446]	967	#sel = selector()
	968	#savesel = self._getselection()
	969	#iflist = self.getifnos()
	970	#for i in xrange(len(freqs)):
	971	# sel.set_ifs(iflist[i])
	972	# self._setselection(sel)
	973	# self._setrestfreqs(freqs[i], "",unit)
	974	#self._setselection(savesel)
	975	self._setrestfreqs(freqs["value"],
	976	freqs["name"], "MHz")
	977	elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple):
[1157]	978	sel = selector()
	979	savesel = self._getselection()
[1322]	980	iflist = self.getifnos()
[1446]	981	if len(freqs)>len(iflist):
	982	raise ValueError("number of elements in list of list exeeds the current IF selections")
[1157]	983	for i in xrange(len(freqs)):
[1322]	984	sel.set_ifs(iflist[i])
[1259]	985	self._setselection(sel)
[1157]	986	self._setrestfreqs(freqs[i]["value"],
	987	freqs[i]["name"], "MHz")
	988	self._setselection(savesel)
	989	# freqs are to be taken from a linecatalog
[1153]	990	elif isinstance(freqs, linecatalog):
	991	sel = selector()
	992	savesel = self._getselection()
	993	for i in xrange(freqs.nrow()):
[1322]	994	sel.set_ifs(iflist[i])
[1153]	995	self._setselection(sel)
	996	self._setrestfreqs(freqs.get_frequency(i),
	997	freqs.get_name(i), "MHz")
	998	# ensure that we are not iterating past nIF
	999	if i == self.nif()-1: break
	1000	self._setselection(savesel)
[931]	1001	else:
	1002	return
	1003	self._add_history("set_restfreqs", varlist)
	1004
[1360]	1005	def shift_refpix(self, delta):
	1006	"""
	1007	Shift the reference pixel of the Spectra Coordinate by an
	1008	integer amount.
	1009	Parameters:
	1010	delta: the amount to shift by
	1011	Note:
	1012	Be careful using this with broadband data.
	1013	"""
	1014	Scantable.shift(self, delta)
[931]	1015
[1259]	1016	def history(self, filename=None):
	1017	"""
	1018	Print the history. Optionally to a file.
[1348]	1019	Parameters:
	1020	filename: The name of the file to save the history to.
[1259]	1021	"""
[484]	1022	hist = list(self._gethistory())
[794]	1023	out = "-"*80
[484]	1024	for h in hist:
[489]	1025	if h.startswith("---"):
[794]	1026	out += "\n"+h
[489]	1027	else:
	1028	items = h.split("##")
	1029	date = items[0]
	1030	func = items[1]
	1031	items = items[2:]
[794]	1032	out += "\n"+date+"\n"
	1033	out += "Function: %s\n Parameters:" % (func)
[489]	1034	for i in items:
	1035	s = i.split("=")
[1118]	1036	out += "\n %s = %s" % (s[0], s[1])
[794]	1037	out += "\n"+"-"*80
[1259]	1038	if filename is not None:
	1039	if filename is "":
	1040	filename = 'scantable_history.txt'
	1041	import os
	1042	filename = os.path.expandvars(os.path.expanduser(filename))
	1043	if not os.path.isdir(filename):
	1044	data = open(filename, 'w')
	1045	data.write(out)
	1046	data.close()
	1047	else:
	1048	msg = "Illegal file name '%s'." % (filename)
	1049	if rcParams['verbose']:
	1050	print msg
	1051	else:
	1052	raise IOError(msg)
	1053	if rcParams['verbose']:
	1054	try:
	1055	from IPython.genutils import page as pager
	1056	except ImportError:
	1057	from pydoc import pager
	1058	pager(out)
	1059	else:
	1060	return out
[484]	1061	return
[513]	1062	#
	1063	# Maths business
	1064	#
	1065
[931]	1066	def average_time(self, mask=None, scanav=False, weight='tint', align=False):
[513]	1067	"""
[1070]	1068	Return the (time) weighted average of a scan.
[513]	1069	Note:
[1070]	1070	in channels only - align if necessary
[513]	1071	Parameters:
	1072	mask: an optional mask (only used for 'var' and 'tsys'
	1073	weighting)
[558]	1074	scanav: True averages each scan separately
	1075	False (default) averages all scans together,
[1099]	1076	weight: Weighting scheme.
	1077	'none' (mean no weight)
	1078	'var' (1/var(spec) weighted)
	1079	'tsys' (1/Tsys**2 weighted)
	1080	'tint' (integration time weighted)
	1081	'tintsys' (Tint/Tsys**2)
	1082	'median' ( median averaging)
[535]	1083	The default is 'tint'
[931]	1084	align: align the spectra in velocity before averaging. It takes
	1085	the time of the first spectrum as reference time.
[513]	1086	Example:
	1087	# time average the scantable without using a mask
[710]	1088	newscan = scan.average_time()
[513]	1089	"""
	1090	varlist = vars()
[976]	1091	if weight is None: weight = 'TINT'
[513]	1092	if mask is None: mask = ()
[1099]	1093	if scanav: scanav = "SCAN"
	1094	else: scanav = "NONE"
[1118]	1095	scan = (self, )
[989]	1096	try:
[1118]	1097	if align:
	1098	scan = (self.freq_align(insitu=False), )
	1099	s = None
	1100	if weight.upper() == 'MEDIAN':
	1101	s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
	1102	scanav))
	1103	else:
	1104	s = scantable(self._math._average(scan, mask, weight.upper(),
	1105	scanav))
	1106	except RuntimeError, msg:
[989]	1107	if rcParams['verbose']:
	1108	print msg
	1109	return
	1110	else: raise
[1099]	1111	s._add_history("average_time", varlist)
[718]	1112	print_log()
[513]	1113	return s
[710]	1114
[876]	1115	def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
[513]	1116	"""
	1117	Return a scan where all spectra are converted to either
	1118	Jansky or Kelvin depending upon the flux units of the scan table.
	1119	By default the function tries to look the values up internally.
	1120	If it can't find them (or if you want to over-ride), you must
	1121	specify EITHER jyperk OR eta (and D which it will try to look up
	1122	also if you don't set it). jyperk takes precedence if you set both.
	1123	Parameters:
	1124	jyperk: the Jy / K conversion factor
	1125	eta: the aperture efficiency
	1126	d: the geomtric diameter (metres)
	1127	insitu: if False a new scantable is returned.
	1128	Otherwise, the scaling is done in-situ
	1129	The default is taken from .asaprc (False)
	1130	"""
	1131	if insitu is None: insitu = rcParams['insitu']
[876]	1132	self._math._setinsitu(insitu)
[513]	1133	varlist = vars()
	1134	if jyperk is None: jyperk = -1.0
	1135	if d is None: d = -1.0
	1136	if eta is None: eta = -1.0
[876]	1137	s = scantable(self._math._convertflux(self, d, eta, jyperk))
	1138	s._add_history("convert_flux", varlist)
	1139	print_log()
	1140	if insitu: self._assign(s)
	1141	else: return s
[513]	1142
[876]	1143	def gain_el(self, poly=None, filename="", method="linear", insitu=None):
[513]	1144	"""
	1145	Return a scan after applying a gain-elevation correction.
	1146	The correction can be made via either a polynomial or a
	1147	table-based interpolation (and extrapolation if necessary).
	1148	You specify polynomial coefficients, an ascii table or neither.
	1149	If you specify neither, then a polynomial correction will be made
	1150	with built in coefficients known for certain telescopes (an error
	1151	will occur if the instrument is not known).
	1152	The data and Tsys are divided by the scaling factors.
	1153	Parameters:
	1154	poly: Polynomial coefficients (default None) to compute a
	1155	gain-elevation correction as a function of
	1156	elevation (in degrees).
	1157	filename: The name of an ascii file holding correction factors.
	1158	The first row of the ascii file must give the column
	1159	names and these MUST include columns
	1160	"ELEVATION" (degrees) and "FACTOR" (multiply data
	1161	by this) somewhere.
	1162	The second row must give the data type of the
	1163	column. Use 'R' for Real and 'I' for Integer.
	1164	An example file would be
	1165	(actual factors are arbitrary) :
	1166
	1167	TIME ELEVATION FACTOR
	1168	R R R
	1169	0.1 0 0.8
	1170	0.2 20 0.85
	1171	0.3 40 0.9
	1172	0.4 60 0.85
	1173	0.5 80 0.8
	1174	0.6 90 0.75
	1175	method: Interpolation method when correcting from a table.
	1176	Values are "nearest", "linear" (default), "cubic"
	1177	and "spline"
	1178	insitu: if False a new scantable is returned.
	1179	Otherwise, the scaling is done in-situ
	1180	The default is taken from .asaprc (False)
	1181	"""
	1182
	1183	if insitu is None: insitu = rcParams['insitu']
[876]	1184	self._math._setinsitu(insitu)
[513]	1185	varlist = vars()
	1186	if poly is None:
[1118]	1187	poly = ()
[513]	1188	from os.path import expandvars
	1189	filename = expandvars(filename)
[876]	1190	s = scantable(self._math._gainel(self, poly, filename, method))
	1191	s._add_history("gain_el", varlist)
	1192	print_log()
	1193	if insitu: self._assign(s)
	1194	else: return s
[710]	1195
[931]	1196	def freq_align(self, reftime=None, method='cubic', insitu=None):
[513]	1197	"""
	1198	Return a scan where all rows have been aligned in frequency/velocity.
	1199	The alignment frequency frame (e.g. LSRK) is that set by function
	1200	set_freqframe.
	1201	Parameters:
	1202	reftime: reference time to align at. By default, the time of
	1203	the first row of data is used.
	1204	method: Interpolation method for regridding the spectra.
	1205	Choose from "nearest", "linear", "cubic" (default)
	1206	and "spline"
	1207	insitu: if False a new scantable is returned.
	1208	Otherwise, the scaling is done in-situ
	1209	The default is taken from .asaprc (False)
	1210	"""
[931]	1211	if insitu is None: insitu = rcParams["insitu"]
[876]	1212	self._math._setinsitu(insitu)
[513]	1213	varlist = vars()
[931]	1214	if reftime is None: reftime = ""
	1215	s = scantable(self._math._freq_align(self, reftime, method))
[876]	1216	s._add_history("freq_align", varlist)
	1217	print_log()
	1218	if insitu: self._assign(s)
	1219	else: return s
[513]	1220
[876]	1221	def opacity(self, tau, insitu=None):
[513]	1222	"""
	1223	Apply an opacity correction. The data
	1224	and Tsys are multiplied by the correction factor.
	1225	Parameters:
	1226	tau: Opacity from which the correction factor is
	1227	exp(tau*ZD)
	1228	where ZD is the zenith-distance
	1229	insitu: if False a new scantable is returned.
	1230	Otherwise, the scaling is done in-situ
	1231	The default is taken from .asaprc (False)
	1232	"""
	1233	if insitu is None: insitu = rcParams['insitu']
[876]	1234	self._math._setinsitu(insitu)
[513]	1235	varlist = vars()
[876]	1236	s = scantable(self._math._opacity(self, tau))
	1237	s._add_history("opacity", varlist)
	1238	print_log()
	1239	if insitu: self._assign(s)
	1240	else: return s
[513]	1241
	1242	def bin(self, width=5, insitu=None):
	1243	"""
	1244	Return a scan where all spectra have been binned up.
[1348]	1245	Parameters:
[513]	1246	width: The bin width (default=5) in pixels
	1247	insitu: if False a new scantable is returned.
	1248	Otherwise, the scaling is done in-situ
	1249	The default is taken from .asaprc (False)
	1250	"""
	1251	if insitu is None: insitu = rcParams['insitu']
[876]	1252	self._math._setinsitu(insitu)
[513]	1253	varlist = vars()
[876]	1254	s = scantable(self._math._bin(self, width))
[1118]	1255	s._add_history("bin", varlist)
[876]	1256	print_log()
	1257	if insitu: self._assign(s)
	1258	else: return s
[513]	1259
[710]	1260
[513]	1261	def resample(self, width=5, method='cubic', insitu=None):
	1262	"""
[1348]	1263	Return a scan where all spectra have been binned up.
	1264
	1265	Parameters:
[513]	1266	width: The bin width (default=5) in pixels
	1267	method: Interpolation method when correcting from a table.
	1268	Values are "nearest", "linear", "cubic" (default)
	1269	and "spline"
	1270	insitu: if False a new scantable is returned.
	1271	Otherwise, the scaling is done in-situ
	1272	The default is taken from .asaprc (False)
	1273	"""
	1274	if insitu is None: insitu = rcParams['insitu']
[876]	1275	self._math._setinsitu(insitu)
[513]	1276	varlist = vars()
[876]	1277	s = scantable(self._math._resample(self, method, width))
[1118]	1278	s._add_history("resample", varlist)
[876]	1279	print_log()
	1280	if insitu: self._assign(s)
	1281	else: return s
[513]	1282
	1283
[946]	1284	def average_pol(self, mask=None, weight='none'):
	1285	"""
	1286	Average the Polarisations together.
	1287	Parameters:
	1288	mask: An optional mask defining the region, where the
	1289	averaging will be applied. The output will have all
	1290	specified points masked.
	1291	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
	1292	weighted), or 'tsys' (1/Tsys**2 weighted)
	1293	"""
	1294	varlist = vars()
	1295	if mask is None:
	1296	mask = ()
[1010]	1297	s = scantable(self._math._averagepol(self, mask, weight.upper()))
[1118]	1298	s._add_history("average_pol", varlist)
[946]	1299	print_log()
[992]	1300	return s
[513]	1301
[1145]	1302	def average_beam(self, mask=None, weight='none'):
	1303	"""
	1304	Average the Beams together.
	1305	Parameters:
	1306	mask: An optional mask defining the region, where the
	1307	averaging will be applied. The output will have all
	1308	specified points masked.
	1309	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
	1310	weighted), or 'tsys' (1/Tsys**2 weighted)
	1311	"""
	1312	varlist = vars()
	1313	if mask is None:
	1314	mask = ()
	1315	s = scantable(self._math._averagebeams(self, mask, weight.upper()))
	1316	s._add_history("average_beam", varlist)
	1317	print_log()
	1318	return s
	1319
[992]	1320	def convert_pol(self, poltype=None):
	1321	"""
	1322	Convert the data to a different polarisation type.
	1323	Parameters:
	1324	poltype: The new polarisation type. Valid types are:
	1325	"linear", "stokes" and "circular"
	1326	"""
	1327	varlist = vars()
	1328	try:
	1329	s = scantable(self._math._convertpol(self, poltype))
[1118]	1330	except RuntimeError, msg:
[992]	1331	if rcParams['verbose']:
[1118]	1332	print msg
	1333	return
[992]	1334	else:
	1335	raise
[1118]	1336	s._add_history("convert_pol", varlist)
[992]	1337	print_log()
	1338	return s
	1339
[876]	1340	def smooth(self, kernel="hanning", width=5.0, insitu=None):
[513]	1341	"""
	1342	Smooth the spectrum by the specified kernel (conserving flux).
	1343	Parameters:
	1344	kernel: The type of smoothing kernel. Select from
[1373]	1345	'hanning' (default), 'gaussian', 'boxcar' and
	1346	'rmedian'
[513]	1347	width: The width of the kernel in pixels. For hanning this is
	1348	ignored otherwise it defauls to 5 pixels.
	1349	For 'gaussian' it is the Full Width Half
	1350	Maximum. For 'boxcar' it is the full width.
[1373]	1351	For 'rmedian' it is the half width.
[513]	1352	insitu: if False a new scantable is returned.
	1353	Otherwise, the scaling is done in-situ
	1354	The default is taken from .asaprc (False)
	1355	Example:
	1356	none
	1357	"""
	1358	if insitu is None: insitu = rcParams['insitu']
[876]	1359	self._math._setinsitu(insitu)
[513]	1360	varlist = vars()
[1118]	1361	s = scantable(self._math._smooth(self, kernel.lower(), width))
[876]	1362	s._add_history("smooth", varlist)
	1363	print_log()
	1364	if insitu: self._assign(s)
	1365	else: return s
[513]	1366
[876]	1367
[1389]	1368	def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None):
[513]	1369	"""
	1370	Return a scan which has been baselined (all rows) by a polynomial.
	1371	Parameters:
[794]	1372	mask: an optional mask
	1373	order: the order of the polynomial (default is 0)
[1061]	1374	plot: plot the fit and the residual. In this each
	1375	indivual fit has to be approved, by typing 'y'
	1376	or 'n'
[1389]	1377	uselin: use linear polynomial fit
[794]	1378	insitu: if False a new scantable is returned.
	1379	Otherwise, the scaling is done in-situ
	1380	The default is taken from .asaprc (False)
[513]	1381	Example:
	1382	# return a scan baselined by a third order polynomial,
	1383	# not using a mask
	1384	bscan = scan.poly_baseline(order=3)
[579]	1385	"""
[513]	1386	if insitu is None: insitu = rcParams['insitu']
	1387	varlist = vars()
	1388	if mask is None:
[1295]	1389	mask = [True for i in xrange(self.nchan(-1))]
[513]	1390	from asap.asapfitter import fitter
[1217]	1391	try:
	1392	f = fitter()
	1393	f.set_scan(self, mask)
[1389]	1394	if uselin:
	1395	f.set_function(lpoly=order)
	1396	else:
	1397	f.set_function(poly=order)
[1217]	1398	s = f.auto_fit(insitu, plot=plot)
[1446]	1399	# Save parameters of baseline fits as a class attribute.
	1400	# NOTICE: It does not reflect changes in scantable!
	1401	self.blpars = f.blpars
[1217]	1402	s._add_history("poly_baseline", varlist)
	1403	print_log()
	1404	if insitu: self._assign(s)
	1405	else: return s
	1406	except RuntimeError:
	1407	msg = "The fit failed, possibly because it didn't converge."
	1408	if rcParams['verbose']:
	1409	print msg
	1410	return
	1411	else:
	1412	raise RuntimeError(msg)
[513]	1413
[1217]	1414
[1118]	1415	def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0,
[1280]	1416	threshold=3, chan_avg_limit=1, plot=False,
	1417	insitu=None):
[880]	1418	"""
	1419	Return a scan which has been baselined (all rows) by a polynomial.
	1420	Spectral lines are detected first using linefinder and masked out
	1421	to avoid them affecting the baseline solution.
	1422
	1423	Parameters:
	1424	mask: an optional mask retreived from scantable
	1425	edge: an optional number of channel to drop at
	1426	the edge of spectrum. If only one value is
	1427	specified, the same number will be dropped from
	1428	both sides of the spectrum. Default is to keep
[907]	1429	all channels. Nested tuples represent individual
[976]	1430	edge selection for different IFs (a number of spectral
	1431	channels can be different)
[880]	1432	order: the order of the polynomial (default is 0)
	1433	threshold: the threshold used by line finder. It is better to
	1434	keep it large as only strong lines affect the
	1435	baseline solution.
[1280]	1436	chan_avg_limit:
	1437	a maximum number of consequtive spectral channels to
	1438	average during the search of weak and broad lines.
	1439	The default is no averaging (and no search for weak
	1440	lines). If such lines can affect the fitted baseline
	1441	(e.g. a high order polynomial is fitted), increase this
	1442	parameter (usually values up to 8 are reasonable). Most
	1443	users of this method should find the default value
	1444	sufficient.
[1061]	1445	plot: plot the fit and the residual. In this each
	1446	indivual fit has to be approved, by typing 'y'
	1447	or 'n'
[880]	1448	insitu: if False a new scantable is returned.
	1449	Otherwise, the scaling is done in-situ
	1450	The default is taken from .asaprc (False)
	1451
	1452	Example:
	1453	scan2=scan.auto_poly_baseline(order=7)
	1454	"""
	1455	if insitu is None: insitu = rcParams['insitu']
	1456	varlist = vars()
	1457	from asap.asapfitter import fitter
	1458	from asap.asaplinefind import linefinder
	1459	from asap import _is_sequence_or_number as _is_valid
	1460
[976]	1461	# check whether edge is set up for each IF individually
[1118]	1462	individualedge = False;
	1463	if len(edge) > 1:
	1464	if isinstance(edge[0], list) or isinstance(edge[0], tuple):
	1465	individualedge = True;
[907]	1466
[1118]	1467	if not _is_valid(edge, int) and not individualedge:
[909]	1468	raise ValueError, "Parameter 'edge' has to be an integer or a \
[907]	1469	pair of integers specified as a tuple. Nested tuples are allowed \
	1470	to make individual selection for different IFs."
[919]	1471
[1118]	1472	curedge = (0, 0)
	1473	if individualedge:
	1474	for edgepar in edge:
	1475	if not _is_valid(edgepar, int):
	1476	raise ValueError, "Each element of the 'edge' tuple has \
	1477	to be a pair of integers or an integer."
[907]	1478	else:
[1118]	1479	curedge = edge;
[880]	1480
	1481	# setup fitter
	1482	f = fitter()
	1483	f.set_function(poly=order)
	1484
	1485	# setup line finder
[1118]	1486	fl = linefinder()
[1268]	1487	fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
[880]	1488
	1489	if not insitu:
[1118]	1490	workscan = self.copy()
[880]	1491	else:
[1118]	1492	workscan = self
[880]	1493
[907]	1494	fl.set_scan(workscan)
	1495
[1118]	1496	rows = range(workscan.nrow())
[1446]	1497	# Save parameters of baseline fits & masklists as a class attribute.
	1498	# NOTICE: It does not reflect changes in scantable!
	1499	if len(rows) > 0:
	1500	self.blpars=[]
	1501	self.masklists=[]
[880]	1502	asaplog.push("Processing:")
	1503	for r in rows:
[1118]	1504	msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
	1505	(workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
	1506	workscan.getpol(r), workscan.getcycle(r))
[880]	1507	asaplog.push(msg, False)
[907]	1508
[976]	1509	# figure out edge parameter
[1118]	1510	if individualedge:
	1511	if len(edge) >= workscan.getif(r):
	1512	raise RuntimeError, "Number of edge elements appear to " \
	1513	"be less than the number of IFs"
	1514	curedge = edge[workscan.getif(r)]
[919]	1515
[976]	1516	# setup line finder
[1118]	1517	fl.find_lines(r, mask, curedge)
[1446]	1518	outmask=fl.get_mask()
[880]	1519	f.set_scan(workscan, fl.get_mask())
	1520	f.x = workscan._getabcissa(r)
	1521	f.y = workscan._getspectrum(r)
	1522	f.data = None
	1523	f.fit()
[1446]	1524
	1525	# Show mask list
	1526	masklist=workscan.get_masklist(fl.get_mask(),row=r)
	1527	msg = "mask range: "+str(masklist)
	1528	asaplog.push(msg, False)
	1529
	1530	fpar = f.get_parameters()
[1061]	1531	if plot:
	1532	f.plot(residual=True)
	1533	x = raw_input("Accept fit ( [y]/n ): ")
	1534	if x.upper() == 'N':
[1446]	1535	self.blpars.append(None)
	1536	self.masklists.append(None)
[1061]	1537	continue
[880]	1538	workscan._setspectrum(f.fitter.getresidual(), r)
[1446]	1539	self.blpars.append(fpar)
	1540	self.masklists.append(masklist)
[1061]	1541	if plot:
	1542	f._p.unmap()
	1543	f._p = None
	1544	workscan._add_history("auto_poly_baseline", varlist)
[880]	1545	if insitu:
	1546	self._assign(workscan)
	1547	else:
	1548	return workscan
	1549
[914]	1550	def rotate_linpolphase(self, angle):
	1551	"""
	1552	Rotate the phase of the complex polarization O=Q+iU correlation.
	1553	This is always done in situ in the raw data. So if you call this
	1554	function more than once then each call rotates the phase further.
	1555	Parameters:
	1556	angle: The angle (degrees) to rotate (add) by.
	1557	Examples:
	1558	scan.rotate_linpolphase(2.3)
	1559	"""
	1560	varlist = vars()
[936]	1561	self._math._rotate_linpolphase(self, angle)
[914]	1562	self._add_history("rotate_linpolphase", varlist)
	1563	print_log()
	1564	return
[710]	1565
[513]	1566
[914]	1567	def rotate_xyphase(self, angle):
	1568	"""
	1569	Rotate the phase of the XY correlation. This is always done in situ
	1570	in the data. So if you call this function more than once
	1571	then each call rotates the phase further.
	1572	Parameters:
	1573	angle: The angle (degrees) to rotate (add) by.
	1574	Examples:
	1575	scan.rotate_xyphase(2.3)
	1576	"""
	1577	varlist = vars()
[936]	1578	self._math._rotate_xyphase(self, angle)
[914]	1579	self._add_history("rotate_xyphase", varlist)
	1580	print_log()
	1581	return
	1582
	1583	def swap_linears(self):
	1584	"""
[1348]	1585	Swap the linear polarisations XX and YY, or better the first two
	1586	polarisations as this also works for ciculars.
[914]	1587	"""
	1588	varlist = vars()
[936]	1589	self._math._swap_linears(self)
[914]	1590	self._add_history("swap_linears", varlist)
	1591	print_log()
	1592	return
	1593
	1594	def invert_phase(self):
	1595	"""
	1596	Invert the phase of the complex polarisation
	1597	"""
	1598	varlist = vars()
[936]	1599	self._math._invert_phase(self)
[914]	1600	self._add_history("invert_phase", varlist)
	1601	print_log()
	1602	return
	1603
[876]	1604	def add(self, offset, insitu=None):
[513]	1605	"""
	1606	Return a scan where all spectra have the offset added
	1607	Parameters:
	1608	offset: the offset
	1609	insitu: if False a new scantable is returned.
	1610	Otherwise, the scaling is done in-situ
	1611	The default is taken from .asaprc (False)
	1612	"""
	1613	if insitu is None: insitu = rcParams['insitu']
[876]	1614	self._math._setinsitu(insitu)
[513]	1615	varlist = vars()
[876]	1616	s = scantable(self._math._unaryop(self, offset, "ADD", False))
[1118]	1617	s._add_history("add", varlist)
[876]	1618	print_log()
	1619	if insitu:
	1620	self._assign(s)
	1621	else:
[513]	1622	return s
	1623
[1308]	1624	def scale(self, factor, tsys=True, insitu=None):
[513]	1625	"""
	1626	Return a scan where all spectra are scaled by the give 'factor'
	1627	Parameters:
	1628	factor: the scaling factor
	1629	insitu: if False a new scantable is returned.
	1630	Otherwise, the scaling is done in-situ
	1631	The default is taken from .asaprc (False)
	1632	tsys: if True (default) then apply the operation to Tsys
	1633	as well as the data
	1634	"""
	1635	if insitu is None: insitu = rcParams['insitu']
[876]	1636	self._math._setinsitu(insitu)
[513]	1637	varlist = vars()
[876]	1638	s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
[1118]	1639	s._add_history("scale", varlist)
[876]	1640	print_log()
	1641	if insitu:
	1642	self._assign(s)
	1643	else:
[513]	1644	return s
	1645
[1348]	1646	def auto_quotient(self, preserve=True, mode='paired'):
[670]	1647	"""
	1648	This function allows to build quotients automatically.
	1649	It assumes the observation to have the same numer of
	1650	"ons" and "offs"
	1651	Parameters:
[710]	1652	preserve: you can preserve (default) the continuum or
	1653	remove it. The equations used are
[670]	1654	preserve: Output = Toff * (on/off) - Toff
[1070]	1655	remove: Output = Toff * (on/off) - Ton
[1348]	1656	mode: the on/off detection mode
	1657	'paired' (default)
	1658	identifies 'off' scans by the
	1659	trailing '_R' (Mopra/Parkes) or
	1660	'_e'/'_w' (Tid) and matches
	1661	on/off pairs from the observing pattern
	1662	'time'
	1663	finds the closest off in time
	1664
[670]	1665	"""
[1348]	1666	modes = ["time", "paired"]
[670]	1667	if not mode in modes:
[876]	1668	msg = "please provide valid mode. Valid modes are %s" % (modes)
	1669	raise ValueError(msg)
	1670	varlist = vars()
[1348]	1671	s = None
	1672	if mode.lower() == "paired":
	1673	basesel = self.get_selection()
[1356]	1674	sel = selector()+basesel
	1675	sel.set_query("SRCTYPE==1")
	1676	self.set_selection(sel)
[1348]	1677	offs = self.copy()
	1678	sel.set_query("SRCTYPE==0")
[1356]	1679	self.set_selection(sel)
[1348]	1680	ons = self.copy()
	1681	s = scantable(self._math._quotient(ons, offs, preserve))
	1682	self.set_selection(basesel)
	1683	elif mode.lower() == "time":
	1684	s = scantable(self._math._auto_quotient(self, mode, preserve))
[1118]	1685	s._add_history("auto_quotient", varlist)
[876]	1686	print_log()
	1687	return s
[710]	1688
[1145]	1689	def mx_quotient(self, mask = None, weight='median', preserve=True):
[1141]	1690	"""
[1143]	1691	Form a quotient using "off" beams when observing in "MX" mode.
	1692	Parameters:
[1145]	1693	mask: an optional mask to be used when weight == 'stddev'
[1143]	1694	weight: How to average the off beams. Default is 'median'.
[1145]	1695	preserve: you can preserve (default) the continuum or
	1696	remove it. The equations used are
	1697	preserve: Output = Toff * (on/off) - Toff
	1698	remove: Output = Toff * (on/off) - Ton
[1217]	1699	"""
[1143]	1700	if mask is None: mask = ()
[1141]	1701	varlist = vars()
	1702	on = scantable(self._math._mx_extract(self, 'on'))
[1143]	1703	preoff = scantable(self._math._mx_extract(self, 'off'))
	1704	off = preoff.average_time(mask=mask, weight=weight, scanav=False)
[1217]	1705	from asapmath import quotient
[1145]	1706	q = quotient(on, off, preserve)
[1143]	1707	q._add_history("mx_quotient", varlist)
[1145]	1708	print_log()
[1217]	1709	return q
[513]	1710
[718]	1711	def freq_switch(self, insitu=None):
	1712	"""
	1713	Apply frequency switching to the data.
	1714	Parameters:
	1715	insitu: if False a new scantable is returned.
	1716	Otherwise, the swictching is done in-situ
	1717	The default is taken from .asaprc (False)
	1718	Example:
	1719	none
	1720	"""
	1721	if insitu is None: insitu = rcParams['insitu']
[876]	1722	self._math._setinsitu(insitu)
[718]	1723	varlist = vars()
[876]	1724	s = scantable(self._math._freqswitch(self))
[1118]	1725	s._add_history("freq_switch", varlist)
[876]	1726	print_log()
	1727	if insitu: self._assign(s)
	1728	else: return s
[718]	1729
[780]	1730	def recalc_azel(self):
	1731	"""
	1732	Recalculate the azimuth and elevation for each position.
	1733	Parameters:
	1734	none
	1735	Example:
	1736	"""
	1737	varlist = vars()
[876]	1738	self._recalcazel()
[780]	1739	self._add_history("recalc_azel", varlist)
	1740	print_log()
	1741	return
	1742
[513]	1743	def __add__(self, other):
	1744	varlist = vars()
	1745	s = None
	1746	if isinstance(other, scantable):
[1308]	1747	s = scantable(self._math._binaryop(self, other, "ADD"))
[513]	1748	elif isinstance(other, float):
[876]	1749	s = scantable(self._math._unaryop(self, other, "ADD", False))
[513]	1750	else:
[718]	1751	raise TypeError("Other input is not a scantable or float value")
[513]	1752	s._add_history("operator +", varlist)
[718]	1753	print_log()
[513]	1754	return s
	1755
	1756	def __sub__(self, other):
	1757	"""
	1758	implicit on all axes and on Tsys
	1759	"""
	1760	varlist = vars()
	1761	s = None
	1762	if isinstance(other, scantable):
[1308]	1763	s = scantable(self._math._binaryop(self, other, "SUB"))
[513]	1764	elif isinstance(other, float):
[876]	1765	s = scantable(self._math._unaryop(self, other, "SUB", False))
[513]	1766	else:
[718]	1767	raise TypeError("Other input is not a scantable or float value")
[513]	1768	s._add_history("operator -", varlist)
[718]	1769	print_log()
[513]	1770	return s
[710]	1771
[513]	1772	def __mul__(self, other):
	1773	"""
	1774	implicit on all axes and on Tsys
	1775	"""
	1776	varlist = vars()
	1777	s = None
	1778	if isinstance(other, scantable):
[1308]	1779	s = scantable(self._math._binaryop(self, other, "MUL"))
[513]	1780	elif isinstance(other, float):
[876]	1781	s = scantable(self._math._unaryop(self, other, "MUL", False))
[513]	1782	else:
[718]	1783	raise TypeError("Other input is not a scantable or float value")
[513]	1784	s._add_history("operator *", varlist)
[718]	1785	print_log()
[513]	1786	return s
	1787
[710]	1788
[513]	1789	def __div__(self, other):
	1790	"""
	1791	implicit on all axes and on Tsys
	1792	"""
	1793	varlist = vars()
	1794	s = None
	1795	if isinstance(other, scantable):
[1308]	1796	s = scantable(self._math._binaryop(self, other, "DIV"))
[513]	1797	elif isinstance(other, float):
	1798	if other == 0.0:
[718]	1799	raise ZeroDivisionError("Dividing by zero is not recommended")
[876]	1800	s = scantable(self._math._unaryop(self, other, "DIV", False))
[513]	1801	else:
[718]	1802	raise TypeError("Other input is not a scantable or float value")
[513]	1803	s._add_history("operator /", varlist)
[718]	1804	print_log()
[513]	1805	return s
	1806
[530]	1807	def get_fit(self, row=0):
	1808	"""
	1809	Print or return the stored fits for a row in the scantable
	1810	Parameters:
	1811	row: the row which the fit has been applied to.
	1812	"""
	1813	if row > self.nrow():
	1814	return
[976]	1815	from asap.asapfit import asapfit
[530]	1816	fit = asapfit(self._getfit(row))
[718]	1817	if rcParams['verbose']:
[530]	1818	print fit
	1819	return
	1820	else:
	1821	return fit.as_dict()
	1822
[484]	1823	def _add_history(self, funcname, parameters):
	1824	# create date
	1825	sep = "##"
	1826	from datetime import datetime
	1827	dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
	1828	hist = dstr+sep
	1829	hist += funcname+sep#cdate+sep
	1830	if parameters.has_key('self'): del parameters['self']
[1118]	1831	for k, v in parameters.iteritems():
[484]	1832	if type(v) is dict:
[1118]	1833	for k2, v2 in v.iteritems():
[484]	1834	hist += k2
	1835	hist += "="
[1118]	1836	if isinstance(v2, scantable):
[484]	1837	hist += 'scantable'
	1838	elif k2 == 'mask':
[1118]	1839	if isinstance(v2, list) or isinstance(v2, tuple):
[513]	1840	hist += str(self._zip_mask(v2))
	1841	else:
	1842	hist += str(v2)
[484]	1843	else:
[513]	1844	hist += str(v2)
[484]	1845	else:
	1846	hist += k
	1847	hist += "="
[1118]	1848	if isinstance(v, scantable):
[484]	1849	hist += 'scantable'
	1850	elif k == 'mask':
[1118]	1851	if isinstance(v, list) or isinstance(v, tuple):
[513]	1852	hist += str(self._zip_mask(v))
	1853	else:
	1854	hist += str(v)
[484]	1855	else:
	1856	hist += str(v)
	1857	hist += sep
	1858	hist = hist[:-2] # remove trailing '##'
	1859	self._addhistory(hist)
	1860
[710]	1861
[484]	1862	def _zip_mask(self, mask):
	1863	mask = list(mask)
	1864	i = 0
	1865	segments = []
	1866	while mask[i:].count(1):
	1867	i += mask[i:].index(1)
	1868	if mask[i:].count(0):
	1869	j = i + mask[i:].index(0)
	1870	else:
[710]	1871	j = len(mask)
[1118]	1872	segments.append([i, j])
[710]	1873	i = j
[484]	1874	return segments
[714]	1875
[626]	1876	def _get_ordinate_label(self):
	1877	fu = "("+self.get_fluxunit()+")"
	1878	import re
	1879	lbl = "Intensity"
[1118]	1880	if re.match(".K.", fu):
[626]	1881	lbl = "Brightness Temperature "+ fu
[1118]	1882	elif re.match(".Jy.", fu):
[626]	1883	lbl = "Flux density "+ fu
	1884	return lbl
[710]	1885
[876]	1886	def _check_ifs(self):
	1887	nchans = [self.nchan(i) for i in range(self.nif(-1))]
[889]	1888	nchans = filter(lambda t: t > 0, nchans)
[876]	1889	return (sum(nchans)/len(nchans) == nchans[0])
[976]	1890
	1891	def _fill(self, names, unit, average):
	1892	import os
	1893	from asap._asap import stfiller
	1894	first = True
	1895	fullnames = []
	1896	for name in names:
	1897	name = os.path.expandvars(name)
	1898	name = os.path.expanduser(name)
	1899	if not os.path.exists(name):
	1900	msg = "File '%s' does not exists" % (name)
	1901	if rcParams['verbose']:
	1902	asaplog.push(msg)
	1903	print asaplog.pop().strip()
	1904	return
	1905	raise IOError(msg)
	1906	fullnames.append(name)
	1907	if average:
	1908	asaplog.push('Auto averaging integrations')
[1079]	1909	stype = int(rcParams['scantable.storage'].lower() == 'disk')
[976]	1910	for name in fullnames:
[1073]	1911	tbl = Scantable(stype)
	1912	r = stfiller(tbl)
[976]	1913	msg = "Importing %s..." % (name)
[1118]	1914	asaplog.push(msg, False)
[976]	1915	print_log()
[1118]	1916	r._open(name, -1, -1)
[976]	1917	r._read()
[1073]	1918	#tbl = r._getdata()
[976]	1919	if average:
[1118]	1920	tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
[976]	1921	#tbl = tbl2
	1922	if not first:
	1923	tbl = self._math._merge([self, tbl])
	1924	#tbl = tbl2
	1925	Scantable.__init__(self, tbl)
	1926	r._close()
[1118]	1927	del r, tbl
[976]	1928	first = False
	1929	if unit is not None:
	1930	self.set_fluxunit(unit)
[1446]	1931	#self.set_freqframe(rcParams['scantable.freqframe'])
[976]	1932

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