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source: branches/alma/python/scantable.py@ 1526

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Last change on this file since 1526 was 1522, checked in by TakTsutsumi, 16 years ago

New Development: No

JIRA Issue: No

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: Updated the documentation for getpt

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File size: 74.2 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
[1496]	14	def __init__(self, filename, average=None, unit=None, getpt=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
[1522]	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.
[710]	36	"""
[976]	37	if average is None:
[710]	38	average = rcParams['scantable.autoaverage']
[1496]	39	if getpt is None:
	40	getpt = False
[1259]	41	varlist = vars()
[876]	42	from asap._asap import stmath
	43	self._math = stmath()
	44	if isinstance(filename, Scantable):
	45	Scantable.__init__(self, filename)
[181]	46	else:
[1118]	47	if isinstance(filename, str):
[976]	48	import os.path
	49	filename = os.path.expandvars(filename)
	50	filename = os.path.expanduser(filename)
	51	if not os.path.exists(filename):
	52	s = "File '%s' not found." % (filename)
[718]	53	if rcParams['verbose']:
[976]	54	asaplog.push(s)
	55	print asaplog.pop().strip()
[718]	56	return
[976]	57	raise IOError(s)
[1115]	58	if os.path.isdir(filename) \
[1118]	59	and not os.path.exists(filename+'/table.f1'):
[976]	60	# crude check if asap table
	61	if os.path.exists(filename+'/table.info'):
[1118]	62	ondisk = rcParams['scantable.storage'] == 'disk'
	63	Scantable.__init__(self, filename, ondisk)
[976]	64	if unit is not None:
	65	self.set_fluxunit(unit)
[1496]	66	# do not reset to the default freqframe
	67	#self.set_freqframe(rcParams['scantable.freqframe'])
[718]	68	else:
[1118]	69	msg = "The given file '%s'is not a valid " \
	70	"asap table." % (filename)
[976]	71	if rcParams['verbose']:
	72	print msg
	73	return
	74	else:
	75	raise IOError(msg)
[226]	76	else:
[1496]	77	self._fill([filename], unit, average, getpt)
[1118]	78	elif (isinstance(filename, list) or isinstance(filename, tuple)) \
[976]	79	and isinstance(filename[-1], str):
[1496]	80	self._fill(filename, unit, average, getpt)
[1259]	81	self._add_history("scantable", varlist)
[714]	82	print_log()
[102]	83
[876]	84	def save(self, name=None, format=None, overwrite=False):
[116]	85	"""
[1280]	86	Store the scantable on disk. This can be an asap (aips++) Table,
	87	SDFITS or MS2 format.
[116]	88	Parameters:
[1093]	89	name: the name of the outputfile. For format "ASCII"
	90	this is the root file name (data in 'name'.txt
[497]	91	and header in 'name'_header.txt)
[116]	92	format: an optional file format. Default is ASAP.
[280]	93	Allowed are - 'ASAP' (save as ASAP [aips++] Table),
[194]	94	'SDFITS' (save as SDFITS file)
[200]	95	'ASCII' (saves as ascii text file)
[226]	96	'MS2' (saves as an aips++
	97	MeasurementSet V2)
[411]	98	overwrite: If the file should be overwritten if it exists.
[256]	99	The default False is to return with warning
[411]	100	without writing the output. USE WITH CARE.
[116]	101	Example:
	102	scan.save('myscan.asap')
[1118]	103	scan.save('myscan.sdfits', 'SDFITS')
[116]	104	"""
[411]	105	from os import path
[226]	106	if format is None: format = rcParams['scantable.save']
[256]	107	suffix = '.'+format.lower()
[1118]	108	if name is None or name == "":
[256]	109	name = 'scantable'+suffix
[718]	110	msg = "No filename given. Using default name %s..." % name
	111	asaplog.push(msg)
[411]	112	name = path.expandvars(name)
[256]	113	if path.isfile(name) or path.isdir(name):
	114	if not overwrite:
[718]	115	msg = "File %s exists." % name
	116	if rcParams['verbose']:
	117	print msg
	118	return
	119	else:
	120	raise IOError(msg)
[451]	121	format2 = format.upper()
	122	if format2 == 'ASAP':
[116]	123	self._save(name)
	124	else:
[989]	125	from asap._asap import stwriter as stw
[1118]	126	writer = stw(format2)
	127	writer.write(self, name)
[718]	128	print_log()
[116]	129	return
	130
[102]	131	def copy(self):
	132	"""
	133	Return a copy of this scantable.
[1348]	134	Note:
	135	This makes a full (deep) copy. scan2 = scan1 makes a reference.
[102]	136	Parameters:
[113]	137	none
[102]	138	Example:
	139	copiedscan = scan.copy()
	140	"""
[876]	141	sd = scantable(Scantable._copy(self))
[113]	142	return sd
	143
[1093]	144	def drop_scan(self, scanid=None):
	145	"""
	146	Return a new scantable where the specified scan number(s) has(have)
	147	been dropped.
	148	Parameters:
	149	scanid: a (list of) scan number(s)
	150	"""
	151	from asap import _is_sequence_or_number as _is_valid
	152	from asap import _to_list
	153	from asap import unique
	154	if not _is_valid(scanid):
	155	if rcParams['verbose']:
	156	print "Please specify a scanno to drop from the scantable"
	157	return
	158	else:
	159	raise RuntimeError("No scan given")
	160	try:
	161	scanid = _to_list(scanid)
	162	allscans = unique([ self.getscan(i) for i in range(self.nrow())])
	163	for sid in scanid: allscans.remove(sid)
[1118]	164	if len(allscans) == 0:
	165	raise ValueError("Can't remove all scans")
[1093]	166	except ValueError:
	167	if rcParams['verbose']:
	168	print "Couldn't find any match."
	169	return
	170	else: raise
	171	try:
	172	bsel = self.get_selection()
	173	sel = selector()
	174	sel.set_scans(allscans)
	175	self.set_selection(bsel+sel)
	176	scopy = self._copy()
	177	self.set_selection(bsel)
	178	return scantable(scopy)
	179	except RuntimeError:
[1118]	180	if rcParams['verbose']:
	181	print "Couldn't find any match."
	182	else:
	183	raise
[1093]	184
	185
[102]	186	def get_scan(self, scanid=None):
	187	"""
	188	Return a specific scan (by scanno) or collection of scans (by
	189	source name) in a new scantable.
[1348]	190	Note:
	191	See scantable.drop_scan() for the inverse operation.
[102]	192	Parameters:
[513]	193	scanid: a (list of) scanno or a source name, unix-style
	194	patterns are accepted for source name matching, e.g.
	195	'*_R' gets all 'ref scans
[102]	196	Example:
[513]	197	# get all scans containing the source '323p459'
	198	newscan = scan.get_scan('323p459')
	199	# get all 'off' scans
	200	refscans = scan.get_scan('*_R')
	201	# get a susbset of scans by scanno (as listed in scan.summary())
[1118]	202	newscan = scan.get_scan([0, 2, 7, 10])
[102]	203	"""
	204	if scanid is None:
[718]	205	if rcParams['verbose']:
[1118]	206	print "Please specify a scan no or name to " \
	207	"retrieve from the scantable"
[718]	208	return
	209	else:
	210	raise RuntimeError("No scan given")
	211
[102]	212	try:
[946]	213	bsel = self.get_selection()
	214	sel = selector()
[102]	215	if type(scanid) is str:
[946]	216	sel.set_name(scanid)
	217	self.set_selection(bsel+sel)
[876]	218	scopy = self._copy()
[946]	219	self.set_selection(bsel)
[876]	220	return scantable(scopy)
[102]	221	elif type(scanid) is int:
[946]	222	sel.set_scans([scanid])
	223	self.set_selection(bsel+sel)
[876]	224	scopy = self._copy()
[946]	225	self.set_selection(bsel)
[876]	226	return scantable(scopy)
[381]	227	elif type(scanid) is list:
[946]	228	sel.set_scans(scanid)
	229	self.set_selection(sel)
[876]	230	scopy = self._copy()
[946]	231	self.set_selection(bsel)
[876]	232	return scantable(scopy)
[381]	233	else:
[718]	234	msg = "Illegal scanid type, use 'int' or 'list' if ints."
	235	if rcParams['verbose']:
	236	print msg
	237	else:
	238	raise TypeError(msg)
[102]	239	except RuntimeError:
[718]	240	if rcParams['verbose']: print "Couldn't find any match."
	241	else: raise
[102]	242
	243	def __str__(self):
[1118]	244	return Scantable._summary(self, True)
[102]	245
[976]	246	def summary(self, filename=None):
[102]	247	"""
	248	Print a summary of the contents of this scantable.
	249	Parameters:
	250	filename: the name of a file to write the putput to
	251	Default - no file output
[381]	252	verbose: print extra info such as the frequency table
	253	The default (False) is taken from .asaprc
[102]	254	"""
[976]	255	info = Scantable._summary(self, True)
	256	#if verbose is None: verbose = rcParams['scantable.verbosesummary']
[102]	257	if filename is not None:
[256]	258	if filename is "":
	259	filename = 'scantable_summary.txt'
[415]	260	from os.path import expandvars, isdir
[411]	261	filename = expandvars(filename)
[415]	262	if not isdir(filename):
[413]	263	data = open(filename, 'w')
	264	data.write(info)
	265	data.close()
	266	else:
[718]	267	msg = "Illegal file name '%s'." % (filename)
	268	if rcParams['verbose']:
	269	print msg
	270	else:
	271	raise IOError(msg)
	272	if rcParams['verbose']:
[794]	273	try:
	274	from IPython.genutils import page as pager
	275	except ImportError:
	276	from pydoc import pager
	277	pager(info)
[718]	278	else:
	279	return info
[710]	280
[946]	281
	282	def get_selection(self):
	283	"""
[1005]	284	Get the selection object currently set on this scantable.
	285	Parameters:
	286	none
	287	Example:
	288	sel = scan.get_selection()
	289	sel.set_ifs(0) # select IF 0
	290	scan.set_selection(sel) # apply modified selection
[946]	291	"""
	292	return selector(self._getselection())
	293
[1005]	294	def set_selection(self, selection=selector()):
[946]	295	"""
[1005]	296	Select a subset of the data. All following operations on this scantable
	297	are only applied to thi selection.
	298	Parameters:
	299	selection: a selector object (default unset the selection)
	300	Examples:
	301	sel = selector() # create a selection object
[1118]	302	self.set_scans([0, 3]) # select SCANNO 0 and 3
[1005]	303	scan.set_selection(sel) # set the selection
	304	scan.summary() # will only print summary of scanno 0 an 3
	305	scan.set_selection() # unset the selection
[946]	306	"""
	307	self._setselection(selection)
	308
[1446]	309	def get_row(self, row=0, insitu=None):
	310	"""
	311	Select a row in the scantable.
	312	Return a scantable with single row.
	313	Parameters:
	314	row: row no of integration, default is 0.
	315	insitu: if False a new scantable is returned.
	316	Otherwise, the scaling is done in-situ
	317	The default is taken from .asaprc (False)
	318	"""
	319	if insitu is None: insitu = rcParams['insitu']
	320	if not insitu:
	321	workscan = self.copy()
	322	else:
	323	workscan = self
	324	# Select a row
	325	sel=selector()
	326	sel.set_scans([workscan.getscan(row)])
	327	sel.set_cycles([workscan.getcycle(row)])
	328	sel.set_beams([workscan.getbeam(row)])
	329	sel.set_ifs([workscan.getif(row)])
	330	sel.set_polarisations([workscan.getpol(row)])
	331	sel.set_name(workscan._getsourcename(row))
	332	workscan.set_selection(sel)
	333	if not workscan.nrow() == 1:
	334	msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow())
	335	raise RuntimeError(msg)
	336	del sel
	337	if insitu:
	338	self._assign(workscan)
	339	else:
	340	return workscan
	341
[876]	342	def stats(self, stat='stddev', mask=None):
[102]	343	"""
[135]	344	Determine the specified statistic of the current beam/if/pol
[102]	345	Takes a 'mask' as an optional parameter to specify which
	346	channels should be excluded.
[1517]	347	You can get min/max values with their
	348	channels/frequencies/velocities by selecting stat='min_abc'
	349	or 'max_abc'.
[102]	350	Parameters:
[1517]	351	stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum',
[1515]	352	'mean', 'var', 'stddev', 'avdev', 'rms', 'median'
[135]	353	mask: an optional mask specifying where the statistic
[102]	354	should be determined.
	355	Example:
[113]	356	scan.set_unit('channel')
[1118]	357	msk = scan.create_mask([100, 200], [500, 600])
[135]	358	scan.stats(stat='mean', mask=m)
[102]	359	"""
	360	if mask == None:
[876]	361	mask = []
[1118]	362	axes = ['Beam', 'IF', 'Pol', 'Time']
[876]	363	if not self._check_ifs():
[1118]	364	raise ValueError("Cannot apply mask as the IFs have different "
	365	"number of channels. Please use setselection() "
	366	"to select individual IFs")
[256]	367
[1517]	368	if stat.lower().find('_abc') == -1:
[1515]	369	statvals = self._math._stats(self, mask, stat)
[1517]	370	getchan = False
[1515]	371	sstat = str(stat)
	372	else:
[1517]	373	chan = self._math._minmaxchan(self, mask, stat)
	374	getchan = True
[1515]	375	statvals = []
[1517]	376	sstat = stat.lower().strip('_abc')
[876]	377	out = ''
	378	axes = []
	379	for i in range(self.nrow()):
	380	axis = []
	381	axis.append(self.getscan(i))
	382	axis.append(self.getbeam(i))
	383	axis.append(self.getif(i))
	384	axis.append(self.getpol(i))
	385	axis.append(self.getcycle(i))
	386	axes.append(axis)
	387	tm = self._gettime(i)
	388	src = self._getsourcename(i)
[1515]	389	xpos = ''
[1517]	390	if getchan:
	391	qx, qy = self.chan2data(rowno=i, chan=chan[i])
	392	statvals.append(qy['value'])
[1515]	393	xpos = '(x = %3.3f' % (qx['value'])+' ['+qx['unit']+'])'
[876]	394	out += 'Scan[%d] (%s) ' % (axis[0], src)
	395	out += 'Time[%s]:\n' % (tm)
	396	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
	397	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
	398	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
[1515]	399	out += '= %3.3f ' % (statvals[i]) +xpos+'\n'
[876]	400	out += "--------------------------------------------------\n"
[256]	401
[876]	402	if rcParams['verbose']:
	403	print "--------------------------------------------------"
[1515]	404	print " ", sstat
[876]	405	print "--------------------------------------------------"
	406	print out
[1295]	407	#else:
	408	#retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'],
	409	# 'axes' : axes,
	410	# 'data': statvals}
	411	return statvals
[102]	412
[1517]	413	def chan2data(self, rowno=0, chan=0):
[1515]	414	"""
[1517]	415	Returns channel/frequency/velocity and spectral value
[1515]	416	at an arbitrary row and channel in the scantable.
	417	Parameters:
	418	rowno: a row number in the scantable. Default is the
	419	first row, i.e. rowno=0
[1517]	420	chan: a channel in the scantable. Default is the first
[1515]	421	channel, i.e. pos=0
	422	"""
[1517]	423	if isinstance(rowno, int) and isinstance(chan, int):
[1515]	424	x, xlbl = self.get_abcissa(rowno)
[1517]	425	qx = {'unit': xlbl, 'value': x[chan]}
	426	qy = {'unit': self.get_fluxunit(),
	427	'value': self._getspectrum(rowno)[chan]}
	428	return qx, qy
[1515]	429
[1118]	430	def stddev(self, mask=None):
[135]	431	"""
	432	Determine the standard deviation of the current beam/if/pol
	433	Takes a 'mask' as an optional parameter to specify which
	434	channels should be excluded.
	435	Parameters:
	436	mask: an optional mask specifying where the standard
	437	deviation should be determined.
	438
	439	Example:
	440	scan.set_unit('channel')
[1118]	441	msk = scan.create_mask([100, 200], [500, 600])
[135]	442	scan.stddev(mask=m)
	443	"""
[1118]	444	return self.stats(stat='stddev', mask=mask);
[135]	445
[1003]	446
[1259]	447	def get_column_names(self):
[1003]	448	"""
	449	Return a list of column names, which can be used for selection.
	450	"""
[1259]	451	return list(Scantable.get_column_names(self))
[1003]	452
[876]	453	def get_tsys(self):
[113]	454	"""
	455	Return the System temperatures.
	456	Returns:
[876]	457	a list of Tsys values for the current selection
[113]	458	"""
[256]	459
[876]	460	return self._row_callback(self._gettsys, "Tsys")
[256]	461
[876]	462	def _row_callback(self, callback, label):
	463	axes = []
[1118]	464	axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno']
[876]	465	out = ""
[1118]	466	outvec = []
[876]	467	for i in range(self.nrow()):
	468	axis = []
	469	axis.append(self.getscan(i))
	470	axis.append(self.getbeam(i))
	471	axis.append(self.getif(i))
	472	axis.append(self.getpol(i))
	473	axis.append(self.getcycle(i))
	474	axes.append(axis)
	475	tm = self._gettime(i)
	476	src = self._getsourcename(i)
	477	out += 'Scan[%d] (%s) ' % (axis[0], src)
	478	out += 'Time[%s]:\n' % (tm)
	479	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
	480	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
	481	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
	482	outvec.append(callback(i))
	483	out += '= %3.3f\n' % (outvec[i])
	484	out += "--------------------------------------------------\n"
	485	if rcParams['verbose']:
	486	print "--------------------------------------------------"
	487	print " %s" % (label)
	488	print "--------------------------------------------------"
	489	print out
[1175]	490	# disabled because the vector seems more useful
	491	#retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
	492	return outvec
[256]	493
[1070]	494	def _get_column(self, callback, row=-1):
	495	"""
	496	"""
	497	if row == -1:
	498	return [callback(i) for i in range(self.nrow())]
	499	else:
	500	if 0 <= row < self.nrow():
	501	return callback(row)
[256]	502
[1070]	503
[1348]	504	def get_time(self, row=-1, asdatetime=False):
[113]	505	"""
	506	Get a list of time stamps for the observations.
[1348]	507	Return a datetime object for each integration time stamp in the scantable.
[113]	508	Parameters:
[1348]	509	row: row no of integration. Default -1 return all rows
	510	asdatetime: return values as datetime objects rather than strings
[113]	511	Example:
	512	none
	513	"""
[1175]	514	from time import strptime
	515	from datetime import datetime
[1457]	516	times = self._get_column(self._gettime, row)
[1348]	517	if not asdatetime:
[1457]	518	return times
[1175]	519	format = "%Y/%m/%d/%H:%M:%S"
	520	if isinstance(times, list):
	521	return [datetime(*strptime(i, format)[:6]) for i in times]
	522	else:
	523	return datetime(*strptime(times, format)[:6])
[102]	524
[1348]	525
	526	def get_inttime(self, row=-1):
	527	"""
	528	Get a list of integration times for the observations.
	529	Return a time in seconds for each integration in the scantable.
	530	Parameters:
	531	row: row no of integration. Default -1 return all rows.
	532	Example:
	533	none
	534	"""
	535	return self._get_column(self._getinttime, row)
	536
	537
[714]	538	def get_sourcename(self, row=-1):
	539	"""
[794]	540	Get a list source names for the observations.
[714]	541	Return a string for each integration in the scantable.
	542	Parameters:
[1348]	543	row: row no of integration. Default -1 return all rows.
[714]	544	Example:
	545	none
	546	"""
[1070]	547	return self._get_column(self._getsourcename, row)
[714]	548
[794]	549	def get_elevation(self, row=-1):
	550	"""
	551	Get a list of elevations for the observations.
	552	Return a float for each integration in the scantable.
	553	Parameters:
[1348]	554	row: row no of integration. Default -1 return all rows.
[794]	555	Example:
	556	none
	557	"""
[1070]	558	return self._get_column(self._getelevation, row)
[794]	559
	560	def get_azimuth(self, row=-1):
	561	"""
	562	Get a list of azimuths for the observations.
	563	Return a float for each integration in the scantable.
	564	Parameters:
[1348]	565	row: row no of integration. Default -1 return all rows.
[794]	566	Example:
	567	none
	568	"""
[1070]	569	return self._get_column(self._getazimuth, row)
[794]	570
	571	def get_parangle(self, row=-1):
	572	"""
	573	Get a list of parallactic angles for the observations.
	574	Return a float for each integration in the scantable.
	575	Parameters:
[1348]	576	row: row no of integration. Default -1 return all rows.
[794]	577	Example:
	578	none
	579	"""
[1070]	580	return self._get_column(self._getparangle, row)
[794]	581
[1070]	582	def get_direction(self, row=-1):
	583	"""
	584	Get a list of Positions on the sky (direction) for the observations.
	585	Return a float for each integration in the scantable.
	586	Parameters:
	587	row: row no of integration. Default -1 return all rows
	588	Example:
	589	none
	590	"""
	591	return self._get_column(self._getdirection, row)
	592
[1389]	593	def get_directionval(self, row=-1):
	594	"""
	595	Get a list of Positions on the sky (direction) for the observations.
	596	Return a float for each integration in the scantable.
	597	Parameters:
	598	row: row no of integration. Default -1 return all rows
	599	Example:
	600	none
	601	"""
	602	return self._get_column(self._getdirectionvec, row)
	603
[102]	604	def set_unit(self, unit='channel'):
	605	"""
	606	Set the unit for all following operations on this scantable
	607	Parameters:
	608	unit: optional unit, default is 'channel'
[1118]	609	one of '*Hz', 'km/s', 'channel', ''
[102]	610	"""
[484]	611	varlist = vars()
[1118]	612	if unit in ['', 'pixel', 'channel']:
[113]	613	unit = ''
	614	inf = list(self._getcoordinfo())
	615	inf[0] = unit
	616	self._setcoordinfo(inf)
[1118]	617	self._add_history("set_unit", varlist)
[113]	618
[484]	619	def set_instrument(self, instr):
[358]	620	"""
[1348]	621	Set the instrument for subsequent processing.
[358]	622	Parameters:
[710]	623	instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
[407]	624	'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
[358]	625	"""
	626	self._setInstrument(instr)
[1118]	627	self._add_history("set_instument", vars())
[718]	628	print_log()
[358]	629
[1190]	630	def set_feedtype(self, feedtype):
	631	"""
	632	Overwrite the feed type, which might not be set correctly.
	633	Parameters:
	634	feedtype: 'linear' or 'circular'
	635	"""
	636	self._setfeedtype(feedtype)
	637	self._add_history("set_feedtype", vars())
	638	print_log()
	639
[276]	640	def set_doppler(self, doppler='RADIO'):
	641	"""
	642	Set the doppler for all following operations on this scantable.
	643	Parameters:
	644	doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
	645	"""
[484]	646	varlist = vars()
[276]	647	inf = list(self._getcoordinfo())
	648	inf[2] = doppler
	649	self._setcoordinfo(inf)
[1118]	650	self._add_history("set_doppler", vars())
[718]	651	print_log()
[710]	652
[226]	653	def set_freqframe(self, frame=None):
[113]	654	"""
	655	Set the frame type of the Spectral Axis.
	656	Parameters:
[591]	657	frame: an optional frame type, default 'LSRK'. Valid frames are:
[1118]	658	'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY',
	659	'GEO', 'GALACTO', 'LGROUP', 'CMB'
[113]	660	Examples:
	661	scan.set_freqframe('BARY')
	662	"""
[484]	663	if frame is None: frame = rcParams['scantable.freqframe']
	664	varlist = vars()
[1118]	665	valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
	666	'GEO', 'GALACTO', 'LGROUP', 'CMB']
[591]	667
[989]	668	if frame in valid:
[113]	669	inf = list(self._getcoordinfo())
	670	inf[1] = frame
	671	self._setcoordinfo(inf)
[1118]	672	self._add_history("set_freqframe", varlist)
[102]	673	else:
[1118]	674	msg = "Please specify a valid freq type. Valid types are:\n", valid
[718]	675	if rcParams['verbose']:
	676	print msg
	677	else:
	678	raise TypeError(msg)
	679	print_log()
[710]	680
[989]	681	def set_dirframe(self, frame=""):
	682	"""
	683	Set the frame type of the Direction on the sky.
	684	Parameters:
	685	frame: an optional frame type, default ''. Valid frames are:
	686	'J2000', 'B1950', 'GALACTIC'
	687	Examples:
	688	scan.set_dirframe('GALACTIC')
	689	"""
	690	varlist = vars()
	691	try:
	692	Scantable.set_dirframe(self, frame)
[1118]	693	except RuntimeError, msg:
[989]	694	if rcParams['verbose']:
	695	print msg
	696	else:
	697	raise
[1118]	698	self._add_history("set_dirframe", varlist)
[989]	699
[113]	700	def get_unit(self):
	701	"""
	702	Get the default unit set in this scantable
	703	Returns:
	704	A unit string
	705	"""
	706	inf = self._getcoordinfo()
	707	unit = inf[0]
	708	if unit == '': unit = 'channel'
	709	return unit
[102]	710
[158]	711	def get_abcissa(self, rowno=0):
[102]	712	"""
[158]	713	Get the abcissa in the current coordinate setup for the currently
[113]	714	selected Beam/IF/Pol
	715	Parameters:
[226]	716	rowno: an optional row number in the scantable. Default is the
	717	first row, i.e. rowno=0
[113]	718	Returns:
[1348]	719	The abcissa values and the format string (as a dictionary)
[113]	720	"""
[256]	721	abc = self._getabcissa(rowno)
[710]	722	lbl = self._getabcissalabel(rowno)
[718]	723	print_log()
[158]	724	return abc, lbl
[113]	725
[1401]	726	def flag(self, mask=None, unflag=False):
[1001]	727	"""
	728	Flag the selected data using an optional channel mask.
	729	Parameters:
	730	mask: an optional channel mask, created with create_mask. Default
	731	(no mask) is all channels.
[1401]	732	unflag: if True, unflag the data
[1001]	733	"""
	734	varlist = vars()
[1118]	735	if mask is None:
	736	mask = []
[1001]	737	try:
[1401]	738	self._flag(mask, unflag)
[1118]	739	except RuntimeError, msg:
[1001]	740	if rcParams['verbose']:
	741	print msg
	742	return
	743	else: raise
	744	self._add_history("flag", varlist)
	745
[1203]	746	def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None):
[1192]	747	"""
	748	Flag the data in 'lag' space by providing a frequency to remove.
	749	Flagged data in the scantable gets set to 0.0 before the fft.
	750	No taper is applied.
	751	Parameters:
[1348]	752	frequency: the frequency (really a period within the bandwidth)
	753	to remove
	754	width: the width of the frequency to remove, to remove a
	755	range of frequencies aroung the centre.
[1203]	756	unit: the frequency unit (default "GHz")
	757	Notes:
[1348]	758	It is recommended to flag edges of the band or strong
	759	signals beforehand.
[1192]	760	"""
	761	if insitu is None: insitu = rcParams['insitu']
	762	self._math._setinsitu(insitu)
	763	varlist = vars()
[1370]	764	base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. }
[1192]	765	if not base.has_key(unit):
	766	raise ValueError("%s is not a valid unit." % unit)
	767	try:
[1200]	768	s = scantable(self._math._lag_flag(self, frequency*base[unit],
	769	width*base[unit]))
[1192]	770	except RuntimeError, msg:
	771	if rcParams['verbose']:
	772	print msg
	773	return
	774	else: raise
	775	s._add_history("lag_flag", varlist)
	776	print_log()
	777	if insitu:
	778	self._assign(s)
	779	else:
	780	return s
[1001]	781
[1192]	782
[113]	783	def create_mask(self, args, *kwargs):
	784	"""
[1118]	785	Compute and return a mask based on [min, max] windows.
[189]	786	The specified windows are to be INCLUDED, when the mask is
[113]	787	applied.
[102]	788	Parameters:
[1118]	789	[min, max], [min2, max2], ...
[1024]	790	Pairs of start/end points (inclusive)specifying the regions
[102]	791	to be masked
[189]	792	invert: optional argument. If specified as True,
	793	return an inverted mask, i.e. the regions
	794	specified are EXCLUDED
[513]	795	row: create the mask using the specified row for
	796	unit conversions, default is row=0
	797	only necessary if frequency varies over rows.
[102]	798	Example:
[113]	799	scan.set_unit('channel')
	800	a)
[1118]	801	msk = scan.create_mask([400, 500], [800, 900])
[189]	802	# masks everything outside 400 and 500
[113]	803	# and 800 and 900 in the unit 'channel'
	804
	805	b)
[1118]	806	msk = scan.create_mask([400, 500], [800, 900], invert=True)
[189]	807	# masks the regions between 400 and 500
[113]	808	# and 800 and 900 in the unit 'channel'
[1024]	809	c)
	810	mask only channel 400
[1118]	811	msk = scan.create_mask([400, 400])
[102]	812	"""
[513]	813	row = 0
	814	if kwargs.has_key("row"):
	815	row = kwargs.get("row")
	816	data = self._getabcissa(row)
[113]	817	u = self._getcoordinfo()[0]
[718]	818	if rcParams['verbose']:
[113]	819	if u == "": u = "channel"
[718]	820	msg = "The current mask window unit is %s" % u
[1118]	821	i = self._check_ifs()
	822	if not i:
[876]	823	msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
[718]	824	asaplog.push(msg)
[102]	825	n = self.nchan()
[1295]	826	msk = _n_bools(n, False)
[710]	827	# test if args is a 'list' or a 'normal *args - UGLY!!!
	828
[1118]	829	ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
	830	and args or args[0]
[710]	831	for window in ws:
[102]	832	if (len(window) != 2 or window[0] > window[1] ):
[1118]	833	raise TypeError("A window needs to be defined as [min, max]")
[102]	834	for i in range(n):
[1024]	835	if data[i] >= window[0] and data[i] <= window[1]:
[1295]	836	msk[i] = True
[113]	837	if kwargs.has_key('invert'):
	838	if kwargs.get('invert'):
[1295]	839	msk = mask_not(msk)
[718]	840	print_log()
[102]	841	return msk
[710]	842
[1446]	843	def get_masklist(self, mask=None, row=0):
[256]	844	"""
[1446]	845	Compute and return a list of mask windows, [min, max].
	846	Parameters:
	847	mask: channel mask, created with create_mask.
	848	row: calcutate the masklist using the specified row
	849	for unit conversions, default is row=0
	850	only necessary if frequency varies over rows.
	851	Returns:
	852	[min, max], [min2, max2], ...
	853	Pairs of start/end points (inclusive)specifying
	854	the masked regions
	855	"""
	856	if not (isinstance(mask,list) or isinstance(mask, tuple)):
	857	raise TypeError("The mask should be list or tuple.")
	858	if len(mask) < 2:
	859	raise TypeError("The mask elements should be > 1")
	860	if self.nchan() != len(mask):
	861	msg = "Number of channels in scantable != number of mask elements"
	862	raise TypeError(msg)
	863	data = self._getabcissa(row)
	864	u = self._getcoordinfo()[0]
	865	if rcParams['verbose']:
	866	if u == "": u = "channel"
	867	msg = "The current mask window unit is %s" % u
	868	i = self._check_ifs()
	869	if not i:
	870	msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
	871	asaplog.push(msg)
	872	masklist=[]
	873	ist, ien = None, None
	874	ist, ien=self.get_mask_indices(mask)
	875	if ist is not None and ien is not None:
	876	for i in xrange(len(ist)):
	877	range=[data[ist[i]],data[ien[i]]]
	878	range.sort()
	879	masklist.append([range[0],range[1]])
	880	return masklist
	881
	882	def get_mask_indices(self, mask=None):
	883	"""
	884	Compute and Return lists of mask start indices and mask end indices.
	885	Parameters:
	886	mask: channel mask, created with create_mask.
	887	Returns:
	888	List of mask start indices and that of mask end indices,
	889	i.e., [istart1,istart2,....], [iend1,iend2,....].
	890	"""
	891	if not (isinstance(mask,list) or isinstance(mask, tuple)):
	892	raise TypeError("The mask should be list or tuple.")
	893	if len(mask) < 2:
	894	raise TypeError("The mask elements should be > 1")
	895	istart=[]
	896	iend=[]
	897	if mask[0]: istart.append(0)
	898	for i in range(len(mask)-1):
	899	if not mask[i] and mask[i+1]:
	900	istart.append(i+1)
	901	elif mask[i] and not mask[i+1]:
	902	iend.append(i)
	903	if mask[len(mask)-1]: iend.append(len(mask)-1)
	904	if len(istart) != len(iend):
	905	raise RuntimeError("Numbers of mask start != mask end.")
	906	for i in range(len(istart)):
	907	if istart[i] > iend[i]:
	908	raise RuntimeError("Mask start index > mask end index")
	909	break
	910	return istart,iend
	911
	912	# def get_restfreqs(self):
	913	# """
	914	# Get the restfrequency(s) stored in this scantable.
	915	# The return value(s) are always of unit 'Hz'
	916	# Parameters:
	917	# none
	918	# Returns:
	919	# a list of doubles
	920	# """
	921	# return list(self._getrestfreqs())
	922
	923	def get_restfreqs(self, ids=None):
	924	"""
[256]	925	Get the restfrequency(s) stored in this scantable.
	926	The return value(s) are always of unit 'Hz'
	927	Parameters:
[1446]	928	ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to
	929	be retrieved
[256]	930	Returns:
[1446]	931	dictionary containing ids and a list of doubles for each id
[256]	932	"""
[1446]	933	if ids is None:
	934	rfreqs={}
	935	idlist = self.getmolnos()
	936	for i in idlist:
	937	rfreqs[i]=list(self._getrestfreqs(i))
	938	return rfreqs
	939	else:
	940	if type(ids)==list or type(ids)==tuple:
	941	rfreqs={}
	942	for i in ids:
	943	rfreqs[i]=list(self._getrestfreqs(i))
	944	return rfreqs
	945	else:
	946	return list(self._getrestfreqs(ids))
	947	#return list(self._getrestfreqs(ids))
[102]	948
[931]	949	def set_restfreqs(self, freqs=None, unit='Hz'):
	950	"""
[1446]	951	******NEED TO BE UPDATED begin**********
[931]	952	Set or replace the restfrequency specified and
	953	If the 'freqs' argument holds a scalar,
	954	then that rest frequency will be applied to all the selected
	955	data. If the 'freqs' argument holds
	956	a vector, then it MUST be of equal or smaller length than
	957	the number of IFs (and the available restfrequencies will be
	958	replaced by this vector). In this case, all data have
	959	the restfrequency set per IF according
	960	to the corresponding value you give in the 'freqs' vector.
[1118]	961	E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
[931]	962	IF 1 gets restfreq 2e9.
[1446]	963	******NEED TO BE UPDATED end**********
[1153]	964	You can also specify the frequencies via a linecatalog/
	965
[931]	966	Parameters:
	967	freqs: list of rest frequency values or string idenitfiers
	968	unit: unit for rest frequency (default 'Hz')
[402]	969
[931]	970	Example:
[1446]	971	# set the given restfrequency for the all currently selected IFs
[931]	972	scan.set_restfreqs(freqs=1.4e9)
[1446]	973	# set multiple restfrequencies to all the selected data
	974	scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9])
	975	# If the number of IFs in the data is >= 2 the IF0 gets the first
	976	# value IF1 the second... NOTE that freqs needs to be
	977	# specified in list of list (e.g. [[],[],...] ).
	978	scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]])
[931]	979	#set the given restfrequency for the whole table (by name)
	980	scan.set_restfreqs(freqs="OH1667")
[391]	981
[931]	982	Note:
	983	To do more sophisticate Restfrequency setting, e.g. on a
	984	source and IF basis, use scantable.set_selection() before using
	985	this function.
	986	# provide your scantable is call scan
	987	selection = selector()
	988	selection.set_name("ORION*")
	989	selection.set_ifs([1])
	990	scan.set_selection(selection)
	991	scan.set_restfreqs(freqs=86.6e9)
	992
	993	"""
	994	varlist = vars()
[1157]	995	from asap import linecatalog
	996	# simple value
[1118]	997	if isinstance(freqs, int) or isinstance(freqs, float):
[1446]	998	# TT mod
	999	#self._setrestfreqs(freqs, "",unit)
	1000	self._setrestfreqs([freqs], [""],unit)
[1157]	1001	# list of values
[1118]	1002	elif isinstance(freqs, list) or isinstance(freqs, tuple):
[1157]	1003	# list values are scalars
[1118]	1004	if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
[1446]	1005	self._setrestfreqs(freqs, [""],unit)
[1157]	1006	# list values are tuples, (value, name)
	1007	elif isinstance(freqs[-1], dict):
[1446]	1008	#sel = selector()
	1009	#savesel = self._getselection()
	1010	#iflist = self.getifnos()
	1011	#for i in xrange(len(freqs)):
	1012	# sel.set_ifs(iflist[i])
	1013	# self._setselection(sel)
	1014	# self._setrestfreqs(freqs[i], "",unit)
	1015	#self._setselection(savesel)
	1016	self._setrestfreqs(freqs["value"],
	1017	freqs["name"], "MHz")
	1018	elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple):
[1157]	1019	sel = selector()
	1020	savesel = self._getselection()
[1322]	1021	iflist = self.getifnos()
[1446]	1022	if len(freqs)>len(iflist):
	1023	raise ValueError("number of elements in list of list exeeds the current IF selections")
[1157]	1024	for i in xrange(len(freqs)):
[1322]	1025	sel.set_ifs(iflist[i])
[1259]	1026	self._setselection(sel)
[1157]	1027	self._setrestfreqs(freqs[i]["value"],
	1028	freqs[i]["name"], "MHz")
	1029	self._setselection(savesel)
	1030	# freqs are to be taken from a linecatalog
[1153]	1031	elif isinstance(freqs, linecatalog):
	1032	sel = selector()
	1033	savesel = self._getselection()
	1034	for i in xrange(freqs.nrow()):
[1322]	1035	sel.set_ifs(iflist[i])
[1153]	1036	self._setselection(sel)
	1037	self._setrestfreqs(freqs.get_frequency(i),
	1038	freqs.get_name(i), "MHz")
	1039	# ensure that we are not iterating past nIF
	1040	if i == self.nif()-1: break
	1041	self._setselection(savesel)
[931]	1042	else:
	1043	return
	1044	self._add_history("set_restfreqs", varlist)
	1045
[1360]	1046	def shift_refpix(self, delta):
	1047	"""
	1048	Shift the reference pixel of the Spectra Coordinate by an
	1049	integer amount.
	1050	Parameters:
	1051	delta: the amount to shift by
	1052	Note:
	1053	Be careful using this with broadband data.
	1054	"""
	1055	Scantable.shift(self, delta)
[931]	1056
[1259]	1057	def history(self, filename=None):
	1058	"""
	1059	Print the history. Optionally to a file.
[1348]	1060	Parameters:
	1061	filename: The name of the file to save the history to.
[1259]	1062	"""
[484]	1063	hist = list(self._gethistory())
[794]	1064	out = "-"*80
[484]	1065	for h in hist:
[489]	1066	if h.startswith("---"):
[794]	1067	out += "\n"+h
[489]	1068	else:
	1069	items = h.split("##")
	1070	date = items[0]
	1071	func = items[1]
	1072	items = items[2:]
[794]	1073	out += "\n"+date+"\n"
	1074	out += "Function: %s\n Parameters:" % (func)
[489]	1075	for i in items:
	1076	s = i.split("=")
[1118]	1077	out += "\n %s = %s" % (s[0], s[1])
[794]	1078	out += "\n"+"-"*80
[1259]	1079	if filename is not None:
	1080	if filename is "":
	1081	filename = 'scantable_history.txt'
	1082	import os
	1083	filename = os.path.expandvars(os.path.expanduser(filename))
	1084	if not os.path.isdir(filename):
	1085	data = open(filename, 'w')
	1086	data.write(out)
	1087	data.close()
	1088	else:
	1089	msg = "Illegal file name '%s'." % (filename)
	1090	if rcParams['verbose']:
	1091	print msg
	1092	else:
	1093	raise IOError(msg)
	1094	if rcParams['verbose']:
	1095	try:
	1096	from IPython.genutils import page as pager
	1097	except ImportError:
	1098	from pydoc import pager
	1099	pager(out)
	1100	else:
	1101	return out
[484]	1102	return
[513]	1103	#
	1104	# Maths business
	1105	#
	1106
[931]	1107	def average_time(self, mask=None, scanav=False, weight='tint', align=False):
[513]	1108	"""
[1070]	1109	Return the (time) weighted average of a scan.
[513]	1110	Note:
[1070]	1111	in channels only - align if necessary
[513]	1112	Parameters:
	1113	mask: an optional mask (only used for 'var' and 'tsys'
	1114	weighting)
[558]	1115	scanav: True averages each scan separately
	1116	False (default) averages all scans together,
[1099]	1117	weight: Weighting scheme.
	1118	'none' (mean no weight)
	1119	'var' (1/var(spec) weighted)
	1120	'tsys' (1/Tsys**2 weighted)
	1121	'tint' (integration time weighted)
	1122	'tintsys' (Tint/Tsys**2)
	1123	'median' ( median averaging)
[535]	1124	The default is 'tint'
[931]	1125	align: align the spectra in velocity before averaging. It takes
	1126	the time of the first spectrum as reference time.
[513]	1127	Example:
	1128	# time average the scantable without using a mask
[710]	1129	newscan = scan.average_time()
[513]	1130	"""
	1131	varlist = vars()
[976]	1132	if weight is None: weight = 'TINT'
[513]	1133	if mask is None: mask = ()
[1099]	1134	if scanav: scanav = "SCAN"
	1135	else: scanav = "NONE"
[1118]	1136	scan = (self, )
[989]	1137	try:
[1118]	1138	if align:
	1139	scan = (self.freq_align(insitu=False), )
	1140	s = None
	1141	if weight.upper() == 'MEDIAN':
	1142	s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
	1143	scanav))
	1144	else:
	1145	s = scantable(self._math._average(scan, mask, weight.upper(),
	1146	scanav))
	1147	except RuntimeError, msg:
[989]	1148	if rcParams['verbose']:
	1149	print msg
	1150	return
	1151	else: raise
[1099]	1152	s._add_history("average_time", varlist)
[718]	1153	print_log()
[513]	1154	return s
[710]	1155
[876]	1156	def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
[513]	1157	"""
	1158	Return a scan where all spectra are converted to either
	1159	Jansky or Kelvin depending upon the flux units of the scan table.
	1160	By default the function tries to look the values up internally.
	1161	If it can't find them (or if you want to over-ride), you must
	1162	specify EITHER jyperk OR eta (and D which it will try to look up
	1163	also if you don't set it). jyperk takes precedence if you set both.
	1164	Parameters:
	1165	jyperk: the Jy / K conversion factor
	1166	eta: the aperture efficiency
	1167	d: the geomtric diameter (metres)
	1168	insitu: if False a new scantable is returned.
	1169	Otherwise, the scaling is done in-situ
	1170	The default is taken from .asaprc (False)
	1171	"""
	1172	if insitu is None: insitu = rcParams['insitu']
[876]	1173	self._math._setinsitu(insitu)
[513]	1174	varlist = vars()
	1175	if jyperk is None: jyperk = -1.0
	1176	if d is None: d = -1.0
	1177	if eta is None: eta = -1.0
[876]	1178	s = scantable(self._math._convertflux(self, d, eta, jyperk))
	1179	s._add_history("convert_flux", varlist)
	1180	print_log()
	1181	if insitu: self._assign(s)
	1182	else: return s
[513]	1183
[876]	1184	def gain_el(self, poly=None, filename="", method="linear", insitu=None):
[513]	1185	"""
	1186	Return a scan after applying a gain-elevation correction.
	1187	The correction can be made via either a polynomial or a
	1188	table-based interpolation (and extrapolation if necessary).
	1189	You specify polynomial coefficients, an ascii table or neither.
	1190	If you specify neither, then a polynomial correction will be made
	1191	with built in coefficients known for certain telescopes (an error
	1192	will occur if the instrument is not known).
	1193	The data and Tsys are divided by the scaling factors.
	1194	Parameters:
	1195	poly: Polynomial coefficients (default None) to compute a
	1196	gain-elevation correction as a function of
	1197	elevation (in degrees).
	1198	filename: The name of an ascii file holding correction factors.
	1199	The first row of the ascii file must give the column
	1200	names and these MUST include columns
	1201	"ELEVATION" (degrees) and "FACTOR" (multiply data
	1202	by this) somewhere.
	1203	The second row must give the data type of the
	1204	column. Use 'R' for Real and 'I' for Integer.
	1205	An example file would be
	1206	(actual factors are arbitrary) :
	1207
	1208	TIME ELEVATION FACTOR
	1209	R R R
	1210	0.1 0 0.8
	1211	0.2 20 0.85
	1212	0.3 40 0.9
	1213	0.4 60 0.85
	1214	0.5 80 0.8
	1215	0.6 90 0.75
	1216	method: Interpolation method when correcting from a table.
	1217	Values are "nearest", "linear" (default), "cubic"
	1218	and "spline"
	1219	insitu: if False a new scantable is returned.
	1220	Otherwise, the scaling is done in-situ
	1221	The default is taken from .asaprc (False)
	1222	"""
	1223
	1224	if insitu is None: insitu = rcParams['insitu']
[876]	1225	self._math._setinsitu(insitu)
[513]	1226	varlist = vars()
	1227	if poly is None:
[1118]	1228	poly = ()
[513]	1229	from os.path import expandvars
	1230	filename = expandvars(filename)
[876]	1231	s = scantable(self._math._gainel(self, poly, filename, method))
	1232	s._add_history("gain_el", varlist)
	1233	print_log()
	1234	if insitu: self._assign(s)
	1235	else: return s
[710]	1236
[931]	1237	def freq_align(self, reftime=None, method='cubic', insitu=None):
[513]	1238	"""
	1239	Return a scan where all rows have been aligned in frequency/velocity.
	1240	The alignment frequency frame (e.g. LSRK) is that set by function
	1241	set_freqframe.
	1242	Parameters:
	1243	reftime: reference time to align at. By default, the time of
	1244	the first row of data is used.
	1245	method: Interpolation method for regridding the spectra.
	1246	Choose from "nearest", "linear", "cubic" (default)
	1247	and "spline"
	1248	insitu: if False a new scantable is returned.
	1249	Otherwise, the scaling is done in-situ
	1250	The default is taken from .asaprc (False)
	1251	"""
[931]	1252	if insitu is None: insitu = rcParams["insitu"]
[876]	1253	self._math._setinsitu(insitu)
[513]	1254	varlist = vars()
[931]	1255	if reftime is None: reftime = ""
	1256	s = scantable(self._math._freq_align(self, reftime, method))
[876]	1257	s._add_history("freq_align", varlist)
	1258	print_log()
	1259	if insitu: self._assign(s)
	1260	else: return s
[513]	1261
[876]	1262	def opacity(self, tau, insitu=None):
[513]	1263	"""
	1264	Apply an opacity correction. The data
	1265	and Tsys are multiplied by the correction factor.
	1266	Parameters:
	1267	tau: Opacity from which the correction factor is
	1268	exp(tau*ZD)
	1269	where ZD is the zenith-distance
	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._opacity(self, tau))
	1278	s._add_history("opacity", varlist)
	1279	print_log()
	1280	if insitu: self._assign(s)
	1281	else: return s
[513]	1282
	1283	def bin(self, width=5, insitu=None):
	1284	"""
	1285	Return a scan where all spectra have been binned up.
[1348]	1286	Parameters:
[513]	1287	width: The bin width (default=5) in pixels
	1288	insitu: if False a new scantable is returned.
	1289	Otherwise, the scaling is done in-situ
	1290	The default is taken from .asaprc (False)
	1291	"""
	1292	if insitu is None: insitu = rcParams['insitu']
[876]	1293	self._math._setinsitu(insitu)
[513]	1294	varlist = vars()
[876]	1295	s = scantable(self._math._bin(self, width))
[1118]	1296	s._add_history("bin", varlist)
[876]	1297	print_log()
	1298	if insitu: self._assign(s)
	1299	else: return s
[513]	1300
[710]	1301
[513]	1302	def resample(self, width=5, method='cubic', insitu=None):
	1303	"""
[1348]	1304	Return a scan where all spectra have been binned up.
	1305
	1306	Parameters:
[513]	1307	width: The bin width (default=5) in pixels
	1308	method: Interpolation method when correcting from a table.
	1309	Values are "nearest", "linear", "cubic" (default)
	1310	and "spline"
	1311	insitu: if False a new scantable is returned.
	1312	Otherwise, the scaling is done in-situ
	1313	The default is taken from .asaprc (False)
	1314	"""
	1315	if insitu is None: insitu = rcParams['insitu']
[876]	1316	self._math._setinsitu(insitu)
[513]	1317	varlist = vars()
[876]	1318	s = scantable(self._math._resample(self, method, width))
[1118]	1319	s._add_history("resample", varlist)
[876]	1320	print_log()
	1321	if insitu: self._assign(s)
	1322	else: return s
[513]	1323
	1324
[946]	1325	def average_pol(self, mask=None, weight='none'):
	1326	"""
	1327	Average the Polarisations together.
	1328	Parameters:
	1329	mask: An optional mask defining the region, where the
	1330	averaging will be applied. The output will have all
	1331	specified points masked.
	1332	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
	1333	weighted), or 'tsys' (1/Tsys**2 weighted)
	1334	"""
	1335	varlist = vars()
	1336	if mask is None:
	1337	mask = ()
[1010]	1338	s = scantable(self._math._averagepol(self, mask, weight.upper()))
[1118]	1339	s._add_history("average_pol", varlist)
[946]	1340	print_log()
[992]	1341	return s
[513]	1342
[1145]	1343	def average_beam(self, mask=None, weight='none'):
	1344	"""
	1345	Average the Beams together.
	1346	Parameters:
	1347	mask: An optional mask defining the region, where the
	1348	averaging will be applied. The output will have all
	1349	specified points masked.
	1350	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
	1351	weighted), or 'tsys' (1/Tsys**2 weighted)
	1352	"""
	1353	varlist = vars()
	1354	if mask is None:
	1355	mask = ()
	1356	s = scantable(self._math._averagebeams(self, mask, weight.upper()))
	1357	s._add_history("average_beam", varlist)
	1358	print_log()
	1359	return s
	1360
[992]	1361	def convert_pol(self, poltype=None):
	1362	"""
	1363	Convert the data to a different polarisation type.
	1364	Parameters:
	1365	poltype: The new polarisation type. Valid types are:
	1366	"linear", "stokes" and "circular"
	1367	"""
	1368	varlist = vars()
	1369	try:
	1370	s = scantable(self._math._convertpol(self, poltype))
[1118]	1371	except RuntimeError, msg:
[992]	1372	if rcParams['verbose']:
[1118]	1373	print msg
	1374	return
[992]	1375	else:
	1376	raise
[1118]	1377	s._add_history("convert_pol", varlist)
[992]	1378	print_log()
	1379	return s
	1380
[876]	1381	def smooth(self, kernel="hanning", width=5.0, insitu=None):
[513]	1382	"""
	1383	Smooth the spectrum by the specified kernel (conserving flux).
	1384	Parameters:
	1385	kernel: The type of smoothing kernel. Select from
[1373]	1386	'hanning' (default), 'gaussian', 'boxcar' and
	1387	'rmedian'
[513]	1388	width: The width of the kernel in pixels. For hanning this is
	1389	ignored otherwise it defauls to 5 pixels.
	1390	For 'gaussian' it is the Full Width Half
	1391	Maximum. For 'boxcar' it is the full width.
[1373]	1392	For 'rmedian' it is the half width.
[513]	1393	insitu: if False a new scantable is returned.
	1394	Otherwise, the scaling is done in-situ
	1395	The default is taken from .asaprc (False)
	1396	Example:
	1397	none
	1398	"""
	1399	if insitu is None: insitu = rcParams['insitu']
[876]	1400	self._math._setinsitu(insitu)
[513]	1401	varlist = vars()
[1118]	1402	s = scantable(self._math._smooth(self, kernel.lower(), width))
[876]	1403	s._add_history("smooth", varlist)
	1404	print_log()
	1405	if insitu: self._assign(s)
	1406	else: return s
[513]	1407
[876]	1408
[1389]	1409	def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None):
[513]	1410	"""
	1411	Return a scan which has been baselined (all rows) by a polynomial.
	1412	Parameters:
[794]	1413	mask: an optional mask
	1414	order: the order of the polynomial (default is 0)
[1061]	1415	plot: plot the fit and the residual. In this each
	1416	indivual fit has to be approved, by typing 'y'
	1417	or 'n'
[1389]	1418	uselin: use linear polynomial fit
[794]	1419	insitu: if False a new scantable is returned.
	1420	Otherwise, the scaling is done in-situ
	1421	The default is taken from .asaprc (False)
[513]	1422	Example:
	1423	# return a scan baselined by a third order polynomial,
	1424	# not using a mask
	1425	bscan = scan.poly_baseline(order=3)
[579]	1426	"""
[513]	1427	if insitu is None: insitu = rcParams['insitu']
	1428	varlist = vars()
	1429	if mask is None:
[1295]	1430	mask = [True for i in xrange(self.nchan(-1))]
[513]	1431	from asap.asapfitter import fitter
[1217]	1432	try:
	1433	f = fitter()
	1434	f.set_scan(self, mask)
[1389]	1435	if uselin:
	1436	f.set_function(lpoly=order)
	1437	else:
	1438	f.set_function(poly=order)
[1217]	1439	s = f.auto_fit(insitu, plot=plot)
[1446]	1440	# Save parameters of baseline fits as a class attribute.
	1441	# NOTICE: It does not reflect changes in scantable!
	1442	self.blpars = f.blpars
[1217]	1443	s._add_history("poly_baseline", varlist)
	1444	print_log()
	1445	if insitu: self._assign(s)
	1446	else: return s
	1447	except RuntimeError:
	1448	msg = "The fit failed, possibly because it didn't converge."
	1449	if rcParams['verbose']:
	1450	print msg
	1451	return
	1452	else:
	1453	raise RuntimeError(msg)
[513]	1454
[1217]	1455
[1118]	1456	def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0,
[1280]	1457	threshold=3, chan_avg_limit=1, plot=False,
	1458	insitu=None):
[880]	1459	"""
	1460	Return a scan which has been baselined (all rows) by a polynomial.
	1461	Spectral lines are detected first using linefinder and masked out
	1462	to avoid them affecting the baseline solution.
	1463
	1464	Parameters:
	1465	mask: an optional mask retreived from scantable
	1466	edge: an optional number of channel to drop at
	1467	the edge of spectrum. If only one value is
	1468	specified, the same number will be dropped from
	1469	both sides of the spectrum. Default is to keep
[907]	1470	all channels. Nested tuples represent individual
[976]	1471	edge selection for different IFs (a number of spectral
	1472	channels can be different)
[880]	1473	order: the order of the polynomial (default is 0)
	1474	threshold: the threshold used by line finder. It is better to
	1475	keep it large as only strong lines affect the
	1476	baseline solution.
[1280]	1477	chan_avg_limit:
	1478	a maximum number of consequtive spectral channels to
	1479	average during the search of weak and broad lines.
	1480	The default is no averaging (and no search for weak
	1481	lines). If such lines can affect the fitted baseline
	1482	(e.g. a high order polynomial is fitted), increase this
	1483	parameter (usually values up to 8 are reasonable). Most
	1484	users of this method should find the default value
	1485	sufficient.
[1061]	1486	plot: plot the fit and the residual. In this each
	1487	indivual fit has to be approved, by typing 'y'
	1488	or 'n'
[880]	1489	insitu: if False a new scantable is returned.
	1490	Otherwise, the scaling is done in-situ
	1491	The default is taken from .asaprc (False)
	1492
	1493	Example:
	1494	scan2=scan.auto_poly_baseline(order=7)
	1495	"""
	1496	if insitu is None: insitu = rcParams['insitu']
	1497	varlist = vars()
	1498	from asap.asapfitter import fitter
	1499	from asap.asaplinefind import linefinder
	1500	from asap import _is_sequence_or_number as _is_valid
	1501
[976]	1502	# check whether edge is set up for each IF individually
[1118]	1503	individualedge = False;
	1504	if len(edge) > 1:
	1505	if isinstance(edge[0], list) or isinstance(edge[0], tuple):
	1506	individualedge = True;
[907]	1507
[1118]	1508	if not _is_valid(edge, int) and not individualedge:
[909]	1509	raise ValueError, "Parameter 'edge' has to be an integer or a \
[907]	1510	pair of integers specified as a tuple. Nested tuples are allowed \
	1511	to make individual selection for different IFs."
[919]	1512
[1118]	1513	curedge = (0, 0)
	1514	if individualedge:
	1515	for edgepar in edge:
	1516	if not _is_valid(edgepar, int):
	1517	raise ValueError, "Each element of the 'edge' tuple has \
	1518	to be a pair of integers or an integer."
[907]	1519	else:
[1118]	1520	curedge = edge;
[880]	1521
	1522	# setup fitter
	1523	f = fitter()
	1524	f.set_function(poly=order)
	1525
	1526	# setup line finder
[1118]	1527	fl = linefinder()
[1268]	1528	fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
[880]	1529
	1530	if not insitu:
[1118]	1531	workscan = self.copy()
[880]	1532	else:
[1118]	1533	workscan = self
[880]	1534
[907]	1535	fl.set_scan(workscan)
	1536
[1118]	1537	rows = range(workscan.nrow())
[1446]	1538	# Save parameters of baseline fits & masklists as a class attribute.
	1539	# NOTICE: It does not reflect changes in scantable!
	1540	if len(rows) > 0:
	1541	self.blpars=[]
	1542	self.masklists=[]
[880]	1543	asaplog.push("Processing:")
	1544	for r in rows:
[1118]	1545	msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
	1546	(workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
	1547	workscan.getpol(r), workscan.getcycle(r))
[880]	1548	asaplog.push(msg, False)
[907]	1549
[976]	1550	# figure out edge parameter
[1118]	1551	if individualedge:
	1552	if len(edge) >= workscan.getif(r):
	1553	raise RuntimeError, "Number of edge elements appear to " \
	1554	"be less than the number of IFs"
	1555	curedge = edge[workscan.getif(r)]
[919]	1556
[976]	1557	# setup line finder
[1118]	1558	fl.find_lines(r, mask, curedge)
[1446]	1559	outmask=fl.get_mask()
[880]	1560	f.set_scan(workscan, fl.get_mask())
	1561	f.x = workscan._getabcissa(r)
	1562	f.y = workscan._getspectrum(r)
	1563	f.data = None
	1564	f.fit()
[1446]	1565
	1566	# Show mask list
	1567	masklist=workscan.get_masklist(fl.get_mask(),row=r)
	1568	msg = "mask range: "+str(masklist)
	1569	asaplog.push(msg, False)
	1570
	1571	fpar = f.get_parameters()
[1061]	1572	if plot:
	1573	f.plot(residual=True)
	1574	x = raw_input("Accept fit ( [y]/n ): ")
	1575	if x.upper() == 'N':
[1446]	1576	self.blpars.append(None)
	1577	self.masklists.append(None)
[1061]	1578	continue
[880]	1579	workscan._setspectrum(f.fitter.getresidual(), r)
[1446]	1580	self.blpars.append(fpar)
	1581	self.masklists.append(masklist)
[1061]	1582	if plot:
	1583	f._p.unmap()
	1584	f._p = None
	1585	workscan._add_history("auto_poly_baseline", varlist)
[880]	1586	if insitu:
	1587	self._assign(workscan)
	1588	else:
	1589	return workscan
	1590
[914]	1591	def rotate_linpolphase(self, angle):
	1592	"""
	1593	Rotate the phase of the complex polarization O=Q+iU correlation.
	1594	This is always done in situ in the raw data. So if you call this
	1595	function more than once then each call rotates the phase further.
	1596	Parameters:
	1597	angle: The angle (degrees) to rotate (add) by.
	1598	Examples:
	1599	scan.rotate_linpolphase(2.3)
	1600	"""
	1601	varlist = vars()
[936]	1602	self._math._rotate_linpolphase(self, angle)
[914]	1603	self._add_history("rotate_linpolphase", varlist)
	1604	print_log()
	1605	return
[710]	1606
[513]	1607
[914]	1608	def rotate_xyphase(self, angle):
	1609	"""
	1610	Rotate the phase of the XY correlation. This is always done in situ
	1611	in the data. So if you call this function more than once
	1612	then each call rotates the phase further.
	1613	Parameters:
	1614	angle: The angle (degrees) to rotate (add) by.
	1615	Examples:
	1616	scan.rotate_xyphase(2.3)
	1617	"""
	1618	varlist = vars()
[936]	1619	self._math._rotate_xyphase(self, angle)
[914]	1620	self._add_history("rotate_xyphase", varlist)
	1621	print_log()
	1622	return
	1623
	1624	def swap_linears(self):
	1625	"""
[1348]	1626	Swap the linear polarisations XX and YY, or better the first two
	1627	polarisations as this also works for ciculars.
[914]	1628	"""
	1629	varlist = vars()
[936]	1630	self._math._swap_linears(self)
[914]	1631	self._add_history("swap_linears", varlist)
	1632	print_log()
	1633	return
	1634
	1635	def invert_phase(self):
	1636	"""
	1637	Invert the phase of the complex polarisation
	1638	"""
	1639	varlist = vars()
[936]	1640	self._math._invert_phase(self)
[914]	1641	self._add_history("invert_phase", varlist)
	1642	print_log()
	1643	return
	1644
[876]	1645	def add(self, offset, insitu=None):
[513]	1646	"""
	1647	Return a scan where all spectra have the offset added
	1648	Parameters:
	1649	offset: the offset
	1650	insitu: if False a new scantable is returned.
	1651	Otherwise, the scaling is done in-situ
	1652	The default is taken from .asaprc (False)
	1653	"""
	1654	if insitu is None: insitu = rcParams['insitu']
[876]	1655	self._math._setinsitu(insitu)
[513]	1656	varlist = vars()
[876]	1657	s = scantable(self._math._unaryop(self, offset, "ADD", False))
[1118]	1658	s._add_history("add", varlist)
[876]	1659	print_log()
	1660	if insitu:
	1661	self._assign(s)
	1662	else:
[513]	1663	return s
	1664
[1308]	1665	def scale(self, factor, tsys=True, insitu=None):
[513]	1666	"""
	1667	Return a scan where all spectra are scaled by the give 'factor'
	1668	Parameters:
	1669	factor: the scaling factor
	1670	insitu: if False a new scantable is returned.
	1671	Otherwise, the scaling is done in-situ
	1672	The default is taken from .asaprc (False)
	1673	tsys: if True (default) then apply the operation to Tsys
	1674	as well as the data
	1675	"""
	1676	if insitu is None: insitu = rcParams['insitu']
[876]	1677	self._math._setinsitu(insitu)
[513]	1678	varlist = vars()
[876]	1679	s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
[1118]	1680	s._add_history("scale", varlist)
[876]	1681	print_log()
	1682	if insitu:
	1683	self._assign(s)
	1684	else:
[513]	1685	return s
	1686
[1348]	1687	def auto_quotient(self, preserve=True, mode='paired'):
[670]	1688	"""
	1689	This function allows to build quotients automatically.
	1690	It assumes the observation to have the same numer of
	1691	"ons" and "offs"
	1692	Parameters:
[710]	1693	preserve: you can preserve (default) the continuum or
	1694	remove it. The equations used are
[670]	1695	preserve: Output = Toff * (on/off) - Toff
[1070]	1696	remove: Output = Toff * (on/off) - Ton
[1348]	1697	mode: the on/off detection mode
	1698	'paired' (default)
	1699	identifies 'off' scans by the
	1700	trailing '_R' (Mopra/Parkes) or
	1701	'_e'/'_w' (Tid) and matches
	1702	on/off pairs from the observing pattern
	1703	'time'
	1704	finds the closest off in time
	1705
[670]	1706	"""
[1348]	1707	modes = ["time", "paired"]
[670]	1708	if not mode in modes:
[876]	1709	msg = "please provide valid mode. Valid modes are %s" % (modes)
	1710	raise ValueError(msg)
	1711	varlist = vars()
[1348]	1712	s = None
	1713	if mode.lower() == "paired":
	1714	basesel = self.get_selection()
[1356]	1715	sel = selector()+basesel
	1716	sel.set_query("SRCTYPE==1")
	1717	self.set_selection(sel)
[1348]	1718	offs = self.copy()
	1719	sel.set_query("SRCTYPE==0")
[1356]	1720	self.set_selection(sel)
[1348]	1721	ons = self.copy()
	1722	s = scantable(self._math._quotient(ons, offs, preserve))
	1723	self.set_selection(basesel)
	1724	elif mode.lower() == "time":
	1725	s = scantable(self._math._auto_quotient(self, mode, preserve))
[1118]	1726	s._add_history("auto_quotient", varlist)
[876]	1727	print_log()
	1728	return s
[710]	1729
[1145]	1730	def mx_quotient(self, mask = None, weight='median', preserve=True):
[1141]	1731	"""
[1143]	1732	Form a quotient using "off" beams when observing in "MX" mode.
	1733	Parameters:
[1145]	1734	mask: an optional mask to be used when weight == 'stddev'
[1143]	1735	weight: How to average the off beams. Default is 'median'.
[1145]	1736	preserve: you can preserve (default) the continuum or
	1737	remove it. The equations used are
	1738	preserve: Output = Toff * (on/off) - Toff
	1739	remove: Output = Toff * (on/off) - Ton
[1217]	1740	"""
[1143]	1741	if mask is None: mask = ()
[1141]	1742	varlist = vars()
	1743	on = scantable(self._math._mx_extract(self, 'on'))
[1143]	1744	preoff = scantable(self._math._mx_extract(self, 'off'))
	1745	off = preoff.average_time(mask=mask, weight=weight, scanav=False)
[1217]	1746	from asapmath import quotient
[1145]	1747	q = quotient(on, off, preserve)
[1143]	1748	q._add_history("mx_quotient", varlist)
[1145]	1749	print_log()
[1217]	1750	return q
[513]	1751
[718]	1752	def freq_switch(self, insitu=None):
	1753	"""
	1754	Apply frequency switching to the data.
	1755	Parameters:
	1756	insitu: if False a new scantable is returned.
	1757	Otherwise, the swictching is done in-situ
	1758	The default is taken from .asaprc (False)
	1759	Example:
	1760	none
	1761	"""
	1762	if insitu is None: insitu = rcParams['insitu']
[876]	1763	self._math._setinsitu(insitu)
[718]	1764	varlist = vars()
[876]	1765	s = scantable(self._math._freqswitch(self))
[1118]	1766	s._add_history("freq_switch", varlist)
[876]	1767	print_log()
	1768	if insitu: self._assign(s)
	1769	else: return s
[718]	1770
[780]	1771	def recalc_azel(self):
	1772	"""
	1773	Recalculate the azimuth and elevation for each position.
	1774	Parameters:
	1775	none
	1776	Example:
	1777	"""
	1778	varlist = vars()
[876]	1779	self._recalcazel()
[780]	1780	self._add_history("recalc_azel", varlist)
	1781	print_log()
	1782	return
	1783
[513]	1784	def __add__(self, other):
	1785	varlist = vars()
	1786	s = None
	1787	if isinstance(other, scantable):
[1308]	1788	s = scantable(self._math._binaryop(self, other, "ADD"))
[513]	1789	elif isinstance(other, float):
[876]	1790	s = scantable(self._math._unaryop(self, other, "ADD", False))
[513]	1791	else:
[718]	1792	raise TypeError("Other input is not a scantable or float value")
[513]	1793	s._add_history("operator +", varlist)
[718]	1794	print_log()
[513]	1795	return s
	1796
	1797	def __sub__(self, other):
	1798	"""
	1799	implicit on all axes and on Tsys
	1800	"""
	1801	varlist = vars()
	1802	s = None
	1803	if isinstance(other, scantable):
[1308]	1804	s = scantable(self._math._binaryop(self, other, "SUB"))
[513]	1805	elif isinstance(other, float):
[876]	1806	s = scantable(self._math._unaryop(self, other, "SUB", False))
[513]	1807	else:
[718]	1808	raise TypeError("Other input is not a scantable or float value")
[513]	1809	s._add_history("operator -", varlist)
[718]	1810	print_log()
[513]	1811	return s
[710]	1812
[513]	1813	def __mul__(self, other):
	1814	"""
	1815	implicit on all axes and on Tsys
	1816	"""
	1817	varlist = vars()
	1818	s = None
	1819	if isinstance(other, scantable):
[1308]	1820	s = scantable(self._math._binaryop(self, other, "MUL"))
[513]	1821	elif isinstance(other, float):
[876]	1822	s = scantable(self._math._unaryop(self, other, "MUL", False))
[513]	1823	else:
[718]	1824	raise TypeError("Other input is not a scantable or float value")
[513]	1825	s._add_history("operator *", varlist)
[718]	1826	print_log()
[513]	1827	return s
	1828
[710]	1829
[513]	1830	def __div__(self, other):
	1831	"""
	1832	implicit on all axes and on Tsys
	1833	"""
	1834	varlist = vars()
	1835	s = None
	1836	if isinstance(other, scantable):
[1308]	1837	s = scantable(self._math._binaryop(self, other, "DIV"))
[513]	1838	elif isinstance(other, float):
	1839	if other == 0.0:
[718]	1840	raise ZeroDivisionError("Dividing by zero is not recommended")
[876]	1841	s = scantable(self._math._unaryop(self, other, "DIV", False))
[513]	1842	else:
[718]	1843	raise TypeError("Other input is not a scantable or float value")
[513]	1844	s._add_history("operator /", varlist)
[718]	1845	print_log()
[513]	1846	return s
	1847
[530]	1848	def get_fit(self, row=0):
	1849	"""
	1850	Print or return the stored fits for a row in the scantable
	1851	Parameters:
	1852	row: the row which the fit has been applied to.
	1853	"""
	1854	if row > self.nrow():
	1855	return
[976]	1856	from asap.asapfit import asapfit
[530]	1857	fit = asapfit(self._getfit(row))
[718]	1858	if rcParams['verbose']:
[530]	1859	print fit
	1860	return
	1861	else:
	1862	return fit.as_dict()
	1863
[484]	1864	def _add_history(self, funcname, parameters):
	1865	# create date
	1866	sep = "##"
	1867	from datetime import datetime
	1868	dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
	1869	hist = dstr+sep
	1870	hist += funcname+sep#cdate+sep
	1871	if parameters.has_key('self'): del parameters['self']
[1118]	1872	for k, v in parameters.iteritems():
[484]	1873	if type(v) is dict:
[1118]	1874	for k2, v2 in v.iteritems():
[484]	1875	hist += k2
	1876	hist += "="
[1118]	1877	if isinstance(v2, scantable):
[484]	1878	hist += 'scantable'
	1879	elif k2 == 'mask':
[1118]	1880	if isinstance(v2, list) or isinstance(v2, tuple):
[513]	1881	hist += str(self._zip_mask(v2))
	1882	else:
	1883	hist += str(v2)
[484]	1884	else:
[513]	1885	hist += str(v2)
[484]	1886	else:
	1887	hist += k
	1888	hist += "="
[1118]	1889	if isinstance(v, scantable):
[484]	1890	hist += 'scantable'
	1891	elif k == 'mask':
[1118]	1892	if isinstance(v, list) or isinstance(v, tuple):
[513]	1893	hist += str(self._zip_mask(v))
	1894	else:
	1895	hist += str(v)
[484]	1896	else:
	1897	hist += str(v)
	1898	hist += sep
	1899	hist = hist[:-2] # remove trailing '##'
	1900	self._addhistory(hist)
	1901
[710]	1902
[484]	1903	def _zip_mask(self, mask):
	1904	mask = list(mask)
	1905	i = 0
	1906	segments = []
	1907	while mask[i:].count(1):
	1908	i += mask[i:].index(1)
	1909	if mask[i:].count(0):
	1910	j = i + mask[i:].index(0)
	1911	else:
[710]	1912	j = len(mask)
[1118]	1913	segments.append([i, j])
[710]	1914	i = j
[484]	1915	return segments
[714]	1916
[626]	1917	def _get_ordinate_label(self):
	1918	fu = "("+self.get_fluxunit()+")"
	1919	import re
	1920	lbl = "Intensity"
[1118]	1921	if re.match(".K.", fu):
[626]	1922	lbl = "Brightness Temperature "+ fu
[1118]	1923	elif re.match(".Jy.", fu):
[626]	1924	lbl = "Flux density "+ fu
	1925	return lbl
[710]	1926
[876]	1927	def _check_ifs(self):
	1928	nchans = [self.nchan(i) for i in range(self.nif(-1))]
[889]	1929	nchans = filter(lambda t: t > 0, nchans)
[876]	1930	return (sum(nchans)/len(nchans) == nchans[0])
[976]	1931
[1496]	1932	def _fill(self, names, unit, average, getpt):
[976]	1933	import os
	1934	from asap._asap import stfiller
	1935	first = True
	1936	fullnames = []
	1937	for name in names:
	1938	name = os.path.expandvars(name)
	1939	name = os.path.expanduser(name)
	1940	if not os.path.exists(name):
	1941	msg = "File '%s' does not exists" % (name)
	1942	if rcParams['verbose']:
	1943	asaplog.push(msg)
	1944	print asaplog.pop().strip()
	1945	return
	1946	raise IOError(msg)
	1947	fullnames.append(name)
	1948	if average:
	1949	asaplog.push('Auto averaging integrations')
[1079]	1950	stype = int(rcParams['scantable.storage'].lower() == 'disk')
[976]	1951	for name in fullnames:
[1073]	1952	tbl = Scantable(stype)
	1953	r = stfiller(tbl)
[976]	1954	msg = "Importing %s..." % (name)
[1118]	1955	asaplog.push(msg, False)
[976]	1956	print_log()
[1496]	1957	r._open(name, -1, -1, getpt)
[976]	1958	r._read()
[1073]	1959	#tbl = r._getdata()
[976]	1960	if average:
[1118]	1961	tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
[976]	1962	#tbl = tbl2
	1963	if not first:
	1964	tbl = self._math._merge([self, tbl])
	1965	#tbl = tbl2
	1966	Scantable.__init__(self, tbl)
	1967	r._close()
[1118]	1968	del r, tbl
[976]	1969	first = False
	1970	if unit is not None:
	1971	self.set_fluxunit(unit)
[1446]	1972	#self.set_freqframe(rcParams['scantable.freqframe'])
[976]	1973

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