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source: trunk/python/scantable.py@ 1494

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Last change on this file since 1494 was 1483, checked in by Malte Marquarding, 16 years ago
added flag_nans to help with possible non-flagged NaNs in the data
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 68.6 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:
[1435]	41	if isinstance(filename, str):# or \
	42	# (isinstance(filename, list) or isinstance(filename, tuple)) \
	43	# and isinstance(filename[-1], str):
[976]	44	import os.path
	45	filename = os.path.expandvars(filename)
	46	filename = os.path.expanduser(filename)
	47	if not os.path.exists(filename):
	48	s = "File '%s' not found." % (filename)
[718]	49	if rcParams['verbose']:
[976]	50	asaplog.push(s)
	51	print asaplog.pop().strip()
[718]	52	return
[976]	53	raise IOError(s)
[1115]	54	if os.path.isdir(filename) \
[1118]	55	and not os.path.exists(filename+'/table.f1'):
[976]	56	# crude check if asap table
	57	if os.path.exists(filename+'/table.info'):
[1118]	58	ondisk = rcParams['scantable.storage'] == 'disk'
	59	Scantable.__init__(self, filename, ondisk)
[976]	60	if unit is not None:
	61	self.set_fluxunit(unit)
	62	self.set_freqframe(rcParams['scantable.freqframe'])
[718]	63	else:
[1118]	64	msg = "The given file '%s'is not a valid " \
	65	"asap table." % (filename)
[976]	66	if rcParams['verbose']:
	67	print msg
	68	return
	69	else:
	70	raise IOError(msg)
[226]	71	else:
[1118]	72	self._fill([filename], unit, average)
	73	elif (isinstance(filename, list) or isinstance(filename, tuple)) \
[976]	74	and isinstance(filename[-1], str):
	75	self._fill(filename, unit, average)
[1259]	76	self._add_history("scantable", varlist)
[714]	77	print_log()
[102]	78
[876]	79	def save(self, name=None, format=None, overwrite=False):
[116]	80	"""
[1280]	81	Store the scantable on disk. This can be an asap (aips++) Table,
	82	SDFITS or MS2 format.
[116]	83	Parameters:
[1093]	84	name: the name of the outputfile. For format "ASCII"
	85	this is the root file name (data in 'name'.txt
[497]	86	and header in 'name'_header.txt)
[116]	87	format: an optional file format. Default is ASAP.
[280]	88	Allowed are - 'ASAP' (save as ASAP [aips++] Table),
[194]	89	'SDFITS' (save as SDFITS file)
[200]	90	'ASCII' (saves as ascii text file)
[226]	91	'MS2' (saves as an aips++
	92	MeasurementSet V2)
[1443]	93	'FITS' (save as image FITS - not
	94	readable by class)
	95	'CLASS' (save as FITS readable by CLASS)
[411]	96	overwrite: If the file should be overwritten if it exists.
[256]	97	The default False is to return with warning
[411]	98	without writing the output. USE WITH CARE.
[116]	99	Example:
	100	scan.save('myscan.asap')
[1118]	101	scan.save('myscan.sdfits', 'SDFITS')
[116]	102	"""
[411]	103	from os import path
[226]	104	if format is None: format = rcParams['scantable.save']
[256]	105	suffix = '.'+format.lower()
[1118]	106	if name is None or name == "":
[256]	107	name = 'scantable'+suffix
[718]	108	msg = "No filename given. Using default name %s..." % name
	109	asaplog.push(msg)
[411]	110	name = path.expandvars(name)
[256]	111	if path.isfile(name) or path.isdir(name):
	112	if not overwrite:
[718]	113	msg = "File %s exists." % name
	114	if rcParams['verbose']:
	115	print msg
	116	return
	117	else:
	118	raise IOError(msg)
[451]	119	format2 = format.upper()
	120	if format2 == 'ASAP':
[116]	121	self._save(name)
	122	else:
[989]	123	from asap._asap import stwriter as stw
[1118]	124	writer = stw(format2)
	125	writer.write(self, name)
[718]	126	print_log()
[116]	127	return
	128
[102]	129	def copy(self):
	130	"""
	131	Return a copy of this scantable.
[1348]	132	Note:
	133	This makes a full (deep) copy. scan2 = scan1 makes a reference.
[102]	134	Parameters:
[113]	135	none
[102]	136	Example:
	137	copiedscan = scan.copy()
	138	"""
[876]	139	sd = scantable(Scantable._copy(self))
[113]	140	return sd
	141
[1093]	142	def drop_scan(self, scanid=None):
	143	"""
	144	Return a new scantable where the specified scan number(s) has(have)
	145	been dropped.
	146	Parameters:
	147	scanid: a (list of) scan number(s)
	148	"""
	149	from asap import _is_sequence_or_number as _is_valid
	150	from asap import _to_list
	151	from asap import unique
	152	if not _is_valid(scanid):
	153	if rcParams['verbose']:
	154	print "Please specify a scanno to drop from the scantable"
	155	return
	156	else:
	157	raise RuntimeError("No scan given")
	158	try:
	159	scanid = _to_list(scanid)
	160	allscans = unique([ self.getscan(i) for i in range(self.nrow())])
	161	for sid in scanid: allscans.remove(sid)
[1118]	162	if len(allscans) == 0:
	163	raise ValueError("Can't remove all scans")
[1093]	164	except ValueError:
	165	if rcParams['verbose']:
	166	print "Couldn't find any match."
	167	return
	168	else: raise
	169	try:
	170	bsel = self.get_selection()
	171	sel = selector()
	172	sel.set_scans(allscans)
	173	self.set_selection(bsel+sel)
	174	scopy = self._copy()
	175	self.set_selection(bsel)
	176	return scantable(scopy)
	177	except RuntimeError:
[1118]	178	if rcParams['verbose']:
	179	print "Couldn't find any match."
	180	else:
	181	raise
[1093]	182
	183
[102]	184	def get_scan(self, scanid=None):
	185	"""
	186	Return a specific scan (by scanno) or collection of scans (by
	187	source name) in a new scantable.
[1348]	188	Note:
	189	See scantable.drop_scan() for the inverse operation.
[102]	190	Parameters:
[513]	191	scanid: a (list of) scanno or a source name, unix-style
	192	patterns are accepted for source name matching, e.g.
	193	'*_R' gets all 'ref scans
[102]	194	Example:
[513]	195	# get all scans containing the source '323p459'
	196	newscan = scan.get_scan('323p459')
	197	# get all 'off' scans
	198	refscans = scan.get_scan('*_R')
	199	# get a susbset of scans by scanno (as listed in scan.summary())
[1118]	200	newscan = scan.get_scan([0, 2, 7, 10])
[102]	201	"""
	202	if scanid is None:
[718]	203	if rcParams['verbose']:
[1118]	204	print "Please specify a scan no or name to " \
	205	"retrieve from the scantable"
[718]	206	return
	207	else:
	208	raise RuntimeError("No scan given")
	209
[102]	210	try:
[946]	211	bsel = self.get_selection()
	212	sel = selector()
[102]	213	if type(scanid) is str:
[946]	214	sel.set_name(scanid)
	215	self.set_selection(bsel+sel)
[876]	216	scopy = self._copy()
[946]	217	self.set_selection(bsel)
[876]	218	return scantable(scopy)
[102]	219	elif type(scanid) is int:
[946]	220	sel.set_scans([scanid])
	221	self.set_selection(bsel+sel)
[876]	222	scopy = self._copy()
[946]	223	self.set_selection(bsel)
[876]	224	return scantable(scopy)
[381]	225	elif type(scanid) is list:
[946]	226	sel.set_scans(scanid)
	227	self.set_selection(sel)
[876]	228	scopy = self._copy()
[946]	229	self.set_selection(bsel)
[876]	230	return scantable(scopy)
[381]	231	else:
[718]	232	msg = "Illegal scanid type, use 'int' or 'list' if ints."
	233	if rcParams['verbose']:
	234	print msg
	235	else:
	236	raise TypeError(msg)
[102]	237	except RuntimeError:
[718]	238	if rcParams['verbose']: print "Couldn't find any match."
	239	else: raise
[102]	240
	241	def __str__(self):
[1118]	242	return Scantable._summary(self, True)
[102]	243
[976]	244	def summary(self, filename=None):
[102]	245	"""
	246	Print a summary of the contents of this scantable.
	247	Parameters:
	248	filename: the name of a file to write the putput to
	249	Default - no file output
[381]	250	verbose: print extra info such as the frequency table
	251	The default (False) is taken from .asaprc
[102]	252	"""
[976]	253	info = Scantable._summary(self, True)
	254	#if verbose is None: verbose = rcParams['scantable.verbosesummary']
[102]	255	if filename is not None:
[256]	256	if filename is "":
	257	filename = 'scantable_summary.txt'
[415]	258	from os.path import expandvars, isdir
[411]	259	filename = expandvars(filename)
[415]	260	if not isdir(filename):
[413]	261	data = open(filename, 'w')
	262	data.write(info)
	263	data.close()
	264	else:
[718]	265	msg = "Illegal file name '%s'." % (filename)
	266	if rcParams['verbose']:
	267	print msg
	268	else:
	269	raise IOError(msg)
	270	if rcParams['verbose']:
[794]	271	try:
	272	from IPython.genutils import page as pager
	273	except ImportError:
	274	from pydoc import pager
	275	pager(info)
[718]	276	else:
	277	return info
[710]	278
[1471]	279	def get_spectrum(self, rownow):
	280	"""Return the spectrum for the current row in the scantable as a list.
	281	Parameters:
	282	rowno: the row number to retrieve the spectrum from
	283	"""
	284	return self._getspectrum(rowno)
[946]	285
[1471]	286	def get_mask(self, rowno):
	287	"""Return the mask for the current row in the scantable as a list.
	288	Parameters:
	289	rowno: the row number to retrieve the mask from
	290	"""
	291	return self._getmask(rowno)
	292
	293	def set_spectrum(self, spec, rowno):
	294	"""Return the spectrum for the current row in the scantable as a list.
	295	Parameters:
	296	spec: the spectrum
	297	rowno: the row number to set the spectrum for
	298	"""
	299	assert(len(spec) == self.nchan())
	300	return self._setspectrum(spec, rowno)
	301
[946]	302	def get_selection(self):
	303	"""
[1005]	304	Get the selection object currently set on this scantable.
	305	Parameters:
	306	none
	307	Example:
	308	sel = scan.get_selection()
	309	sel.set_ifs(0) # select IF 0
	310	scan.set_selection(sel) # apply modified selection
[946]	311	"""
	312	return selector(self._getselection())
	313
[1005]	314	def set_selection(self, selection=selector()):
[946]	315	"""
[1005]	316	Select a subset of the data. All following operations on this scantable
	317	are only applied to thi selection.
	318	Parameters:
	319	selection: a selector object (default unset the selection)
	320	Examples:
	321	sel = selector() # create a selection object
[1118]	322	self.set_scans([0, 3]) # select SCANNO 0 and 3
[1005]	323	scan.set_selection(sel) # set the selection
	324	scan.summary() # will only print summary of scanno 0 an 3
	325	scan.set_selection() # unset the selection
[946]	326	"""
	327	self._setselection(selection)
	328
[876]	329	def stats(self, stat='stddev', mask=None):
[102]	330	"""
[135]	331	Determine the specified statistic of the current beam/if/pol
[102]	332	Takes a 'mask' as an optional parameter to specify which
	333	channels should be excluded.
	334	Parameters:
[135]	335	stat: 'min', 'max', 'sumsq', 'sum', 'mean'
	336	'var', 'stddev', 'avdev', 'rms', 'median'
	337	mask: an optional mask specifying where the statistic
[102]	338	should be determined.
	339	Example:
[113]	340	scan.set_unit('channel')
[1118]	341	msk = scan.create_mask([100, 200], [500, 600])
[135]	342	scan.stats(stat='mean', mask=m)
[102]	343	"""
	344	if mask == None:
[876]	345	mask = []
[1118]	346	axes = ['Beam', 'IF', 'Pol', 'Time']
[876]	347	if not self._check_ifs():
[1118]	348	raise ValueError("Cannot apply mask as the IFs have different "
	349	"number of channels. Please use setselection() "
	350	"to select individual IFs")
[256]	351
[876]	352	statvals = self._math._stats(self, mask, stat)
	353	out = ''
	354	axes = []
	355	for i in range(self.nrow()):
	356	axis = []
	357	axis.append(self.getscan(i))
	358	axis.append(self.getbeam(i))
	359	axis.append(self.getif(i))
	360	axis.append(self.getpol(i))
	361	axis.append(self.getcycle(i))
	362	axes.append(axis)
	363	tm = self._gettime(i)
	364	src = self._getsourcename(i)
	365	out += 'Scan[%d] (%s) ' % (axis[0], src)
	366	out += 'Time[%s]:\n' % (tm)
	367	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
	368	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
	369	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
	370	out += '= %3.3f\n' % (statvals[i])
	371	out += "--------------------------------------------------\n"
[256]	372
[876]	373	if rcParams['verbose']:
	374	print "--------------------------------------------------"
[1118]	375	print " ", stat
[876]	376	print "--------------------------------------------------"
	377	print out
[1295]	378	#else:
	379	#retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'],
	380	# 'axes' : axes,
	381	# 'data': statvals}
	382	return statvals
[102]	383
[1118]	384	def stddev(self, mask=None):
[135]	385	"""
	386	Determine the standard deviation of the current beam/if/pol
	387	Takes a 'mask' as an optional parameter to specify which
	388	channels should be excluded.
	389	Parameters:
	390	mask: an optional mask specifying where the standard
	391	deviation should be determined.
	392
	393	Example:
	394	scan.set_unit('channel')
[1118]	395	msk = scan.create_mask([100, 200], [500, 600])
[135]	396	scan.stddev(mask=m)
	397	"""
[1118]	398	return self.stats(stat='stddev', mask=mask);
[135]	399
[1003]	400
[1259]	401	def get_column_names(self):
[1003]	402	"""
	403	Return a list of column names, which can be used for selection.
	404	"""
[1259]	405	return list(Scantable.get_column_names(self))
[1003]	406
[876]	407	def get_tsys(self):
[113]	408	"""
	409	Return the System temperatures.
	410	Returns:
[876]	411	a list of Tsys values for the current selection
[113]	412	"""
[256]	413
[876]	414	return self._row_callback(self._gettsys, "Tsys")
[256]	415
[876]	416	def _row_callback(self, callback, label):
	417	axes = []
[1118]	418	axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno']
[876]	419	out = ""
[1118]	420	outvec = []
[876]	421	for i in range(self.nrow()):
	422	axis = []
	423	axis.append(self.getscan(i))
	424	axis.append(self.getbeam(i))
	425	axis.append(self.getif(i))
	426	axis.append(self.getpol(i))
	427	axis.append(self.getcycle(i))
	428	axes.append(axis)
	429	tm = self._gettime(i)
	430	src = self._getsourcename(i)
	431	out += 'Scan[%d] (%s) ' % (axis[0], src)
	432	out += 'Time[%s]:\n' % (tm)
	433	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
	434	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
	435	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
	436	outvec.append(callback(i))
	437	out += '= %3.3f\n' % (outvec[i])
	438	out += "--------------------------------------------------\n"
	439	if rcParams['verbose']:
	440	print "--------------------------------------------------"
	441	print " %s" % (label)
	442	print "--------------------------------------------------"
	443	print out
[1175]	444	# disabled because the vector seems more useful
	445	#retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
	446	return outvec
[256]	447
[1070]	448	def _get_column(self, callback, row=-1):
	449	"""
	450	"""
	451	if row == -1:
	452	return [callback(i) for i in range(self.nrow())]
	453	else:
	454	if 0 <= row < self.nrow():
	455	return callback(row)
[256]	456
[1070]	457
[1348]	458	def get_time(self, row=-1, asdatetime=False):
[113]	459	"""
	460	Get a list of time stamps for the observations.
[1348]	461	Return a datetime object for each integration time stamp in the scantable.
[113]	462	Parameters:
[1348]	463	row: row no of integration. Default -1 return all rows
	464	asdatetime: return values as datetime objects rather than strings
[113]	465	Example:
	466	none
	467	"""
[1175]	468	from time import strptime
	469	from datetime import datetime
[1392]	470	times = self._get_column(self._gettime, row)
[1348]	471	if not asdatetime:
[1392]	472	return times
[1175]	473	format = "%Y/%m/%d/%H:%M:%S"
	474	if isinstance(times, list):
	475	return [datetime(*strptime(i, format)[:6]) for i in times]
	476	else:
	477	return datetime(*strptime(times, format)[:6])
[102]	478
[1348]	479
	480	def get_inttime(self, row=-1):
	481	"""
	482	Get a list of integration times for the observations.
	483	Return a time in seconds for each integration in the scantable.
	484	Parameters:
	485	row: row no of integration. Default -1 return all rows.
	486	Example:
	487	none
	488	"""
	489	return self._get_column(self._getinttime, row)
	490
	491
[714]	492	def get_sourcename(self, row=-1):
	493	"""
[794]	494	Get a list source names for the observations.
[714]	495	Return a string for each integration in the scantable.
	496	Parameters:
[1348]	497	row: row no of integration. Default -1 return all rows.
[714]	498	Example:
	499	none
	500	"""
[1070]	501	return self._get_column(self._getsourcename, row)
[714]	502
[794]	503	def get_elevation(self, row=-1):
	504	"""
	505	Get a list of elevations for the observations.
	506	Return a float for each integration in the scantable.
	507	Parameters:
[1348]	508	row: row no of integration. Default -1 return all rows.
[794]	509	Example:
	510	none
	511	"""
[1070]	512	return self._get_column(self._getelevation, row)
[794]	513
	514	def get_azimuth(self, row=-1):
	515	"""
	516	Get a list of azimuths for the observations.
	517	Return a float for each integration in the scantable.
	518	Parameters:
[1348]	519	row: row no of integration. Default -1 return all rows.
[794]	520	Example:
	521	none
	522	"""
[1070]	523	return self._get_column(self._getazimuth, row)
[794]	524
	525	def get_parangle(self, row=-1):
	526	"""
	527	Get a list of parallactic angles for the observations.
	528	Return a float for each integration in the scantable.
	529	Parameters:
[1348]	530	row: row no of integration. Default -1 return all rows.
[794]	531	Example:
	532	none
	533	"""
[1070]	534	return self._get_column(self._getparangle, row)
[794]	535
[1070]	536	def get_direction(self, row=-1):
	537	"""
	538	Get a list of Positions on the sky (direction) for the observations.
	539	Return a float for each integration in the scantable.
	540	Parameters:
	541	row: row no of integration. Default -1 return all rows
	542	Example:
	543	none
	544	"""
	545	return self._get_column(self._getdirection, row)
	546
[1391]	547	def get_directionval(self, row=-1):
	548	"""
	549	Get a list of Positions on the sky (direction) for the observations.
	550	Return a float for each integration in the scantable.
	551	Parameters:
	552	row: row no of integration. Default -1 return all rows
	553	Example:
	554	none
	555	"""
	556	return self._get_column(self._getdirectionvec, row)
	557
	558
[102]	559	def set_unit(self, unit='channel'):
	560	"""
	561	Set the unit for all following operations on this scantable
	562	Parameters:
	563	unit: optional unit, default is 'channel'
[1118]	564	one of '*Hz', 'km/s', 'channel', ''
[102]	565	"""
[484]	566	varlist = vars()
[1118]	567	if unit in ['', 'pixel', 'channel']:
[113]	568	unit = ''
	569	inf = list(self._getcoordinfo())
	570	inf[0] = unit
	571	self._setcoordinfo(inf)
[1118]	572	self._add_history("set_unit", varlist)
[113]	573
[484]	574	def set_instrument(self, instr):
[358]	575	"""
[1348]	576	Set the instrument for subsequent processing.
[358]	577	Parameters:
[710]	578	instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
[407]	579	'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
[358]	580	"""
	581	self._setInstrument(instr)
[1118]	582	self._add_history("set_instument", vars())
[718]	583	print_log()
[358]	584
[1190]	585	def set_feedtype(self, feedtype):
	586	"""
	587	Overwrite the feed type, which might not be set correctly.
	588	Parameters:
	589	feedtype: 'linear' or 'circular'
	590	"""
	591	self._setfeedtype(feedtype)
	592	self._add_history("set_feedtype", vars())
	593	print_log()
	594
[276]	595	def set_doppler(self, doppler='RADIO'):
	596	"""
	597	Set the doppler for all following operations on this scantable.
	598	Parameters:
	599	doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
	600	"""
[484]	601	varlist = vars()
[276]	602	inf = list(self._getcoordinfo())
	603	inf[2] = doppler
	604	self._setcoordinfo(inf)
[1118]	605	self._add_history("set_doppler", vars())
[718]	606	print_log()
[710]	607
[226]	608	def set_freqframe(self, frame=None):
[113]	609	"""
	610	Set the frame type of the Spectral Axis.
	611	Parameters:
[591]	612	frame: an optional frame type, default 'LSRK'. Valid frames are:
[1118]	613	'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY',
	614	'GEO', 'GALACTO', 'LGROUP', 'CMB'
[113]	615	Examples:
	616	scan.set_freqframe('BARY')
	617	"""
[484]	618	if frame is None: frame = rcParams['scantable.freqframe']
	619	varlist = vars()
[1118]	620	valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
	621	'GEO', 'GALACTO', 'LGROUP', 'CMB']
[591]	622
[989]	623	if frame in valid:
[113]	624	inf = list(self._getcoordinfo())
	625	inf[1] = frame
	626	self._setcoordinfo(inf)
[1118]	627	self._add_history("set_freqframe", varlist)
[102]	628	else:
[1118]	629	msg = "Please specify a valid freq type. Valid types are:\n", valid
[718]	630	if rcParams['verbose']:
	631	print msg
	632	else:
	633	raise TypeError(msg)
	634	print_log()
[710]	635
[989]	636	def set_dirframe(self, frame=""):
	637	"""
	638	Set the frame type of the Direction on the sky.
	639	Parameters:
	640	frame: an optional frame type, default ''. Valid frames are:
	641	'J2000', 'B1950', 'GALACTIC'
	642	Examples:
	643	scan.set_dirframe('GALACTIC')
	644	"""
	645	varlist = vars()
	646	try:
	647	Scantable.set_dirframe(self, frame)
[1118]	648	except RuntimeError, msg:
[989]	649	if rcParams['verbose']:
	650	print msg
	651	else:
	652	raise
[1118]	653	self._add_history("set_dirframe", varlist)
[989]	654
[113]	655	def get_unit(self):
	656	"""
	657	Get the default unit set in this scantable
	658	Returns:
	659	A unit string
	660	"""
	661	inf = self._getcoordinfo()
	662	unit = inf[0]
	663	if unit == '': unit = 'channel'
	664	return unit
[102]	665
[158]	666	def get_abcissa(self, rowno=0):
[102]	667	"""
[158]	668	Get the abcissa in the current coordinate setup for the currently
[113]	669	selected Beam/IF/Pol
	670	Parameters:
[226]	671	rowno: an optional row number in the scantable. Default is the
	672	first row, i.e. rowno=0
[113]	673	Returns:
[1348]	674	The abcissa values and the format string (as a dictionary)
[113]	675	"""
[256]	676	abc = self._getabcissa(rowno)
[710]	677	lbl = self._getabcissalabel(rowno)
[718]	678	print_log()
[158]	679	return abc, lbl
[113]	680
[1118]	681	def flag(self, mask=None):
[1001]	682	"""
	683	Flag the selected data using an optional channel mask.
	684	Parameters:
	685	mask: an optional channel mask, created with create_mask. Default
	686	(no mask) is all channels.
	687	"""
	688	varlist = vars()
[1118]	689	if mask is None:
	690	mask = []
[1001]	691	try:
	692	self._flag(mask)
[1118]	693	except RuntimeError, msg:
[1001]	694	if rcParams['verbose']:
	695	print msg
	696	return
	697	else: raise
	698	self._add_history("flag", varlist)
	699
[1203]	700	def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None):
[1192]	701	"""
	702	Flag the data in 'lag' space by providing a frequency to remove.
	703	Flagged data in the scantable gets set to 0.0 before the fft.
	704	No taper is applied.
	705	Parameters:
[1348]	706	frequency: the frequency (really a period within the bandwidth)
	707	to remove
	708	width: the width of the frequency to remove, to remove a
[1471]	709	range of frequencies around the centre.
[1203]	710	unit: the frequency unit (default "GHz")
	711	Notes:
[1348]	712	It is recommended to flag edges of the band or strong
	713	signals beforehand.
[1192]	714	"""
	715	if insitu is None: insitu = rcParams['insitu']
	716	self._math._setinsitu(insitu)
	717	varlist = vars()
[1370]	718	base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. }
[1192]	719	if not base.has_key(unit):
	720	raise ValueError("%s is not a valid unit." % unit)
	721	try:
[1200]	722	s = scantable(self._math._lag_flag(self, frequency*base[unit],
	723	width*base[unit]))
[1192]	724	except RuntimeError, msg:
	725	if rcParams['verbose']:
	726	print msg
	727	return
	728	else: raise
	729	s._add_history("lag_flag", varlist)
	730	print_log()
	731	if insitu:
	732	self._assign(s)
	733	else:
	734	return s
[1001]	735
[1192]	736
[113]	737	def create_mask(self, args, *kwargs):
	738	"""
[1118]	739	Compute and return a mask based on [min, max] windows.
[189]	740	The specified windows are to be INCLUDED, when the mask is
[113]	741	applied.
[102]	742	Parameters:
[1118]	743	[min, max], [min2, max2], ...
[1024]	744	Pairs of start/end points (inclusive)specifying the regions
[102]	745	to be masked
[189]	746	invert: optional argument. If specified as True,
	747	return an inverted mask, i.e. the regions
	748	specified are EXCLUDED
[513]	749	row: create the mask using the specified row for
	750	unit conversions, default is row=0
	751	only necessary if frequency varies over rows.
[102]	752	Example:
[113]	753	scan.set_unit('channel')
	754	a)
[1118]	755	msk = scan.create_mask([400, 500], [800, 900])
[189]	756	# masks everything outside 400 and 500
[113]	757	# and 800 and 900 in the unit 'channel'
	758
	759	b)
[1118]	760	msk = scan.create_mask([400, 500], [800, 900], invert=True)
[189]	761	# masks the regions between 400 and 500
[113]	762	# and 800 and 900 in the unit 'channel'
[1024]	763	c)
	764	mask only channel 400
[1118]	765	msk = scan.create_mask([400, 400])
[102]	766	"""
[513]	767	row = 0
	768	if kwargs.has_key("row"):
	769	row = kwargs.get("row")
	770	data = self._getabcissa(row)
[113]	771	u = self._getcoordinfo()[0]
[718]	772	if rcParams['verbose']:
[113]	773	if u == "": u = "channel"
[718]	774	msg = "The current mask window unit is %s" % u
[1118]	775	i = self._check_ifs()
	776	if not i:
[876]	777	msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
[718]	778	asaplog.push(msg)
[102]	779	n = self.nchan()
[1295]	780	msk = _n_bools(n, False)
[710]	781	# test if args is a 'list' or a 'normal *args - UGLY!!!
	782
[1118]	783	ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
	784	and args or args[0]
[710]	785	for window in ws:
[102]	786	if (len(window) != 2 or window[0] > window[1] ):
[1118]	787	raise TypeError("A window needs to be defined as [min, max]")
[102]	788	for i in range(n):
[1024]	789	if data[i] >= window[0] and data[i] <= window[1]:
[1295]	790	msk[i] = True
[113]	791	if kwargs.has_key('invert'):
	792	if kwargs.get('invert'):
[1295]	793	msk = mask_not(msk)
[718]	794	print_log()
[102]	795	return msk
[710]	796
[256]	797	def get_restfreqs(self):
	798	"""
	799	Get the restfrequency(s) stored in this scantable.
	800	The return value(s) are always of unit 'Hz'
	801	Parameters:
	802	none
	803	Returns:
	804	a list of doubles
	805	"""
	806	return list(self._getrestfreqs())
[102]	807
[402]	808
[931]	809	def set_restfreqs(self, freqs=None, unit='Hz'):
	810	"""
	811	Set or replace the restfrequency specified and
	812	If the 'freqs' argument holds a scalar,
	813	then that rest frequency will be applied to all the selected
	814	data. If the 'freqs' argument holds
	815	a vector, then it MUST be of equal or smaller length than
	816	the number of IFs (and the available restfrequencies will be
	817	replaced by this vector). In this case, all data have
	818	the restfrequency set per IF according
	819	to the corresponding value you give in the 'freqs' vector.
[1118]	820	E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
[931]	821	IF 1 gets restfreq 2e9.
[1395]	822	You can also specify the frequencies via a linecatalog.
[1153]	823
[931]	824	Parameters:
	825	freqs: list of rest frequency values or string idenitfiers
	826	unit: unit for rest frequency (default 'Hz')
[402]	827
[931]	828	Example:
	829	# set the given restfrequency for the whole table
	830	scan.set_restfreqs(freqs=1.4e9)
[1348]	831	# If thee number of IFs in the data is >= 2 IF0 gets the first
[931]	832	# value IF1 the second...
[1118]	833	scan.set_restfreqs(freqs=[1.4e9, 1.67e9])
[931]	834	#set the given restfrequency for the whole table (by name)
	835	scan.set_restfreqs(freqs="OH1667")
[391]	836
[931]	837	Note:
	838	To do more sophisticate Restfrequency setting, e.g. on a
	839	source and IF basis, use scantable.set_selection() before using
	840	this function.
	841	# provide your scantable is call scan
	842	selection = selector()
	843	selection.set_name("ORION*")
	844	selection.set_ifs([1])
	845	scan.set_selection(selection)
	846	scan.set_restfreqs(freqs=86.6e9)
	847
	848	"""
	849	varlist = vars()
[1157]	850	from asap import linecatalog
	851	# simple value
[1118]	852	if isinstance(freqs, int) or isinstance(freqs, float):
[1153]	853	self._setrestfreqs(freqs, "",unit)
[1157]	854	# list of values
[1118]	855	elif isinstance(freqs, list) or isinstance(freqs, tuple):
[1157]	856	# list values are scalars
[1118]	857	if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
[931]	858	sel = selector()
	859	savesel = self._getselection()
[1322]	860	iflist = self.getifnos()
[931]	861	for i in xrange(len(freqs)):
[1322]	862	sel.set_ifs(iflist[i])
[931]	863	self._setselection(sel)
[1153]	864	self._setrestfreqs(freqs[i], "",unit)
[931]	865	self._setselection(savesel)
[1157]	866	# list values are tuples, (value, name)
	867	elif isinstance(freqs[-1], dict):
	868	sel = selector()
	869	savesel = self._getselection()
[1322]	870	iflist = self.getifnos()
[1157]	871	for i in xrange(len(freqs)):
[1322]	872	sel.set_ifs(iflist[i])
[1259]	873	self._setselection(sel)
[1157]	874	self._setrestfreqs(freqs[i]["value"],
	875	freqs[i]["name"], "MHz")
	876	self._setselection(savesel)
	877	# freqs are to be taken from a linecatalog
[1153]	878	elif isinstance(freqs, linecatalog):
	879	sel = selector()
	880	savesel = self._getselection()
[1322]	881	iflist = self.getifnos()
[1153]	882	for i in xrange(freqs.nrow()):
[1322]	883	sel.set_ifs(iflist[i])
[1153]	884	self._setselection(sel)
	885	self._setrestfreqs(freqs.get_frequency(i),
	886	freqs.get_name(i), "MHz")
	887	# ensure that we are not iterating past nIF
	888	if i == self.nif()-1: break
	889	self._setselection(savesel)
[931]	890	else:
	891	return
	892	self._add_history("set_restfreqs", varlist)
	893
[1360]	894	def shift_refpix(self, delta):
	895	"""
	896	Shift the reference pixel of the Spectra Coordinate by an
	897	integer amount.
	898	Parameters:
	899	delta: the amount to shift by
	900	Note:
	901	Be careful using this with broadband data.
	902	"""
	903	Scantable.shift(self, delta)
[931]	904
[1259]	905	def history(self, filename=None):
	906	"""
	907	Print the history. Optionally to a file.
[1348]	908	Parameters:
	909	filename: The name of the file to save the history to.
[1259]	910	"""
[484]	911	hist = list(self._gethistory())
[794]	912	out = "-"*80
[484]	913	for h in hist:
[489]	914	if h.startswith("---"):
[794]	915	out += "\n"+h
[489]	916	else:
	917	items = h.split("##")
	918	date = items[0]
	919	func = items[1]
	920	items = items[2:]
[794]	921	out += "\n"+date+"\n"
	922	out += "Function: %s\n Parameters:" % (func)
[489]	923	for i in items:
	924	s = i.split("=")
[1118]	925	out += "\n %s = %s" % (s[0], s[1])
[794]	926	out += "\n"+"-"*80
[1259]	927	if filename is not None:
	928	if filename is "":
	929	filename = 'scantable_history.txt'
	930	import os
	931	filename = os.path.expandvars(os.path.expanduser(filename))
	932	if not os.path.isdir(filename):
	933	data = open(filename, 'w')
	934	data.write(out)
	935	data.close()
	936	else:
	937	msg = "Illegal file name '%s'." % (filename)
	938	if rcParams['verbose']:
	939	print msg
	940	else:
	941	raise IOError(msg)
	942	if rcParams['verbose']:
	943	try:
	944	from IPython.genutils import page as pager
	945	except ImportError:
	946	from pydoc import pager
	947	pager(out)
	948	else:
	949	return out
[484]	950	return
[513]	951	#
	952	# Maths business
	953	#
	954
[931]	955	def average_time(self, mask=None, scanav=False, weight='tint', align=False):
[513]	956	"""
[1070]	957	Return the (time) weighted average of a scan.
[513]	958	Note:
[1070]	959	in channels only - align if necessary
[513]	960	Parameters:
	961	mask: an optional mask (only used for 'var' and 'tsys'
	962	weighting)
[558]	963	scanav: True averages each scan separately
	964	False (default) averages all scans together,
[1099]	965	weight: Weighting scheme.
	966	'none' (mean no weight)
	967	'var' (1/var(spec) weighted)
	968	'tsys' (1/Tsys**2 weighted)
	969	'tint' (integration time weighted)
	970	'tintsys' (Tint/Tsys**2)
	971	'median' ( median averaging)
[535]	972	The default is 'tint'
[931]	973	align: align the spectra in velocity before averaging. It takes
	974	the time of the first spectrum as reference time.
[513]	975	Example:
	976	# time average the scantable without using a mask
[710]	977	newscan = scan.average_time()
[513]	978	"""
	979	varlist = vars()
[976]	980	if weight is None: weight = 'TINT'
[513]	981	if mask is None: mask = ()
[1099]	982	if scanav: scanav = "SCAN"
	983	else: scanav = "NONE"
[1118]	984	scan = (self, )
[989]	985	try:
[1118]	986	if align:
	987	scan = (self.freq_align(insitu=False), )
	988	s = None
	989	if weight.upper() == 'MEDIAN':
	990	s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
	991	scanav))
	992	else:
	993	s = scantable(self._math._average(scan, mask, weight.upper(),
	994	scanav))
	995	except RuntimeError, msg:
[989]	996	if rcParams['verbose']:
	997	print msg
	998	return
	999	else: raise
[1099]	1000	s._add_history("average_time", varlist)
[718]	1001	print_log()
[513]	1002	return s
[710]	1003
[876]	1004	def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
[513]	1005	"""
	1006	Return a scan where all spectra are converted to either
	1007	Jansky or Kelvin depending upon the flux units of the scan table.
	1008	By default the function tries to look the values up internally.
	1009	If it can't find them (or if you want to over-ride), you must
	1010	specify EITHER jyperk OR eta (and D which it will try to look up
	1011	also if you don't set it). jyperk takes precedence if you set both.
	1012	Parameters:
	1013	jyperk: the Jy / K conversion factor
	1014	eta: the aperture efficiency
	1015	d: the geomtric diameter (metres)
	1016	insitu: if False a new scantable is returned.
	1017	Otherwise, the scaling is done in-situ
	1018	The default is taken from .asaprc (False)
	1019	"""
	1020	if insitu is None: insitu = rcParams['insitu']
[876]	1021	self._math._setinsitu(insitu)
[513]	1022	varlist = vars()
	1023	if jyperk is None: jyperk = -1.0
	1024	if d is None: d = -1.0
	1025	if eta is None: eta = -1.0
[876]	1026	s = scantable(self._math._convertflux(self, d, eta, jyperk))
	1027	s._add_history("convert_flux", varlist)
	1028	print_log()
	1029	if insitu: self._assign(s)
	1030	else: return s
[513]	1031
[876]	1032	def gain_el(self, poly=None, filename="", method="linear", insitu=None):
[513]	1033	"""
	1034	Return a scan after applying a gain-elevation correction.
	1035	The correction can be made via either a polynomial or a
	1036	table-based interpolation (and extrapolation if necessary).
	1037	You specify polynomial coefficients, an ascii table or neither.
	1038	If you specify neither, then a polynomial correction will be made
	1039	with built in coefficients known for certain telescopes (an error
	1040	will occur if the instrument is not known).
	1041	The data and Tsys are divided by the scaling factors.
	1042	Parameters:
	1043	poly: Polynomial coefficients (default None) to compute a
	1044	gain-elevation correction as a function of
	1045	elevation (in degrees).
	1046	filename: The name of an ascii file holding correction factors.
	1047	The first row of the ascii file must give the column
	1048	names and these MUST include columns
	1049	"ELEVATION" (degrees) and "FACTOR" (multiply data
	1050	by this) somewhere.
	1051	The second row must give the data type of the
	1052	column. Use 'R' for Real and 'I' for Integer.
	1053	An example file would be
	1054	(actual factors are arbitrary) :
	1055
	1056	TIME ELEVATION FACTOR
	1057	R R R
	1058	0.1 0 0.8
	1059	0.2 20 0.85
	1060	0.3 40 0.9
	1061	0.4 60 0.85
	1062	0.5 80 0.8
	1063	0.6 90 0.75
	1064	method: Interpolation method when correcting from a table.
	1065	Values are "nearest", "linear" (default), "cubic"
	1066	and "spline"
	1067	insitu: if False a new scantable is returned.
	1068	Otherwise, the scaling is done in-situ
	1069	The default is taken from .asaprc (False)
	1070	"""
	1071
	1072	if insitu is None: insitu = rcParams['insitu']
[876]	1073	self._math._setinsitu(insitu)
[513]	1074	varlist = vars()
	1075	if poly is None:
[1118]	1076	poly = ()
[513]	1077	from os.path import expandvars
	1078	filename = expandvars(filename)
[876]	1079	s = scantable(self._math._gainel(self, poly, filename, method))
	1080	s._add_history("gain_el", varlist)
	1081	print_log()
	1082	if insitu: self._assign(s)
	1083	else: return s
[710]	1084
[931]	1085	def freq_align(self, reftime=None, method='cubic', insitu=None):
[513]	1086	"""
	1087	Return a scan where all rows have been aligned in frequency/velocity.
	1088	The alignment frequency frame (e.g. LSRK) is that set by function
	1089	set_freqframe.
	1090	Parameters:
	1091	reftime: reference time to align at. By default, the time of
	1092	the first row of data is used.
	1093	method: Interpolation method for regridding the spectra.
	1094	Choose from "nearest", "linear", "cubic" (default)
	1095	and "spline"
	1096	insitu: if False a new scantable is returned.
	1097	Otherwise, the scaling is done in-situ
	1098	The default is taken from .asaprc (False)
	1099	"""
[931]	1100	if insitu is None: insitu = rcParams["insitu"]
[876]	1101	self._math._setinsitu(insitu)
[513]	1102	varlist = vars()
[931]	1103	if reftime is None: reftime = ""
	1104	s = scantable(self._math._freq_align(self, reftime, method))
[876]	1105	s._add_history("freq_align", varlist)
	1106	print_log()
	1107	if insitu: self._assign(s)
	1108	else: return s
[513]	1109
[876]	1110	def opacity(self, tau, insitu=None):
[513]	1111	"""
	1112	Apply an opacity correction. The data
	1113	and Tsys are multiplied by the correction factor.
	1114	Parameters:
	1115	tau: Opacity from which the correction factor is
	1116	exp(tau*ZD)
	1117	where ZD is the zenith-distance
	1118	insitu: if False a new scantable is returned.
	1119	Otherwise, the scaling is done in-situ
	1120	The default is taken from .asaprc (False)
	1121	"""
	1122	if insitu is None: insitu = rcParams['insitu']
[876]	1123	self._math._setinsitu(insitu)
[513]	1124	varlist = vars()
[876]	1125	s = scantable(self._math._opacity(self, tau))
	1126	s._add_history("opacity", varlist)
	1127	print_log()
	1128	if insitu: self._assign(s)
	1129	else: return s
[513]	1130
	1131	def bin(self, width=5, insitu=None):
	1132	"""
	1133	Return a scan where all spectra have been binned up.
[1348]	1134	Parameters:
[513]	1135	width: The bin width (default=5) in pixels
	1136	insitu: if False a new scantable is returned.
	1137	Otherwise, the scaling is done in-situ
	1138	The default is taken from .asaprc (False)
	1139	"""
	1140	if insitu is None: insitu = rcParams['insitu']
[876]	1141	self._math._setinsitu(insitu)
[513]	1142	varlist = vars()
[876]	1143	s = scantable(self._math._bin(self, width))
[1118]	1144	s._add_history("bin", varlist)
[876]	1145	print_log()
	1146	if insitu: self._assign(s)
	1147	else: return s
[513]	1148
[710]	1149
[513]	1150	def resample(self, width=5, method='cubic', insitu=None):
	1151	"""
[1348]	1152	Return a scan where all spectra have been binned up.
	1153
	1154	Parameters:
[513]	1155	width: The bin width (default=5) in pixels
	1156	method: Interpolation method when correcting from a table.
	1157	Values are "nearest", "linear", "cubic" (default)
	1158	and "spline"
	1159	insitu: if False a new scantable is returned.
	1160	Otherwise, the scaling is done in-situ
	1161	The default is taken from .asaprc (False)
	1162	"""
	1163	if insitu is None: insitu = rcParams['insitu']
[876]	1164	self._math._setinsitu(insitu)
[513]	1165	varlist = vars()
[876]	1166	s = scantable(self._math._resample(self, method, width))
[1118]	1167	s._add_history("resample", varlist)
[876]	1168	print_log()
	1169	if insitu: self._assign(s)
	1170	else: return s
[513]	1171
	1172
[946]	1173	def average_pol(self, mask=None, weight='none'):
	1174	"""
	1175	Average the Polarisations together.
	1176	Parameters:
	1177	mask: An optional mask defining the region, where the
	1178	averaging will be applied. The output will have all
	1179	specified points masked.
	1180	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
	1181	weighted), or 'tsys' (1/Tsys**2 weighted)
	1182	"""
	1183	varlist = vars()
	1184	if mask is None:
	1185	mask = ()
[1010]	1186	s = scantable(self._math._averagepol(self, mask, weight.upper()))
[1118]	1187	s._add_history("average_pol", varlist)
[946]	1188	print_log()
[992]	1189	return s
[513]	1190
[1145]	1191	def average_beam(self, mask=None, weight='none'):
	1192	"""
	1193	Average the Beams together.
	1194	Parameters:
	1195	mask: An optional mask defining the region, where the
	1196	averaging will be applied. The output will have all
	1197	specified points masked.
	1198	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
	1199	weighted), or 'tsys' (1/Tsys**2 weighted)
	1200	"""
	1201	varlist = vars()
	1202	if mask is None:
	1203	mask = ()
	1204	s = scantable(self._math._averagebeams(self, mask, weight.upper()))
	1205	s._add_history("average_beam", varlist)
	1206	print_log()
	1207	return s
	1208
[992]	1209	def convert_pol(self, poltype=None):
	1210	"""
	1211	Convert the data to a different polarisation type.
	1212	Parameters:
	1213	poltype: The new polarisation type. Valid types are:
	1214	"linear", "stokes" and "circular"
	1215	"""
	1216	varlist = vars()
	1217	try:
	1218	s = scantable(self._math._convertpol(self, poltype))
[1118]	1219	except RuntimeError, msg:
[992]	1220	if rcParams['verbose']:
[1118]	1221	print msg
	1222	return
[992]	1223	else:
	1224	raise
[1118]	1225	s._add_history("convert_pol", varlist)
[992]	1226	print_log()
	1227	return s
	1228
[876]	1229	def smooth(self, kernel="hanning", width=5.0, insitu=None):
[513]	1230	"""
	1231	Smooth the spectrum by the specified kernel (conserving flux).
	1232	Parameters:
	1233	kernel: The type of smoothing kernel. Select from
[1373]	1234	'hanning' (default), 'gaussian', 'boxcar' and
	1235	'rmedian'
[513]	1236	width: The width of the kernel in pixels. For hanning this is
	1237	ignored otherwise it defauls to 5 pixels.
	1238	For 'gaussian' it is the Full Width Half
	1239	Maximum. For 'boxcar' it is the full width.
[1373]	1240	For 'rmedian' it is the half width.
[513]	1241	insitu: if False a new scantable is returned.
	1242	Otherwise, the scaling is done in-situ
	1243	The default is taken from .asaprc (False)
	1244	Example:
	1245	none
	1246	"""
	1247	if insitu is None: insitu = rcParams['insitu']
[876]	1248	self._math._setinsitu(insitu)
[513]	1249	varlist = vars()
[1118]	1250	s = scantable(self._math._smooth(self, kernel.lower(), width))
[876]	1251	s._add_history("smooth", varlist)
	1252	print_log()
	1253	if insitu: self._assign(s)
	1254	else: return s
[513]	1255
[876]	1256
[1391]	1257	def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None):
[513]	1258	"""
	1259	Return a scan which has been baselined (all rows) by a polynomial.
	1260	Parameters:
[794]	1261	mask: an optional mask
	1262	order: the order of the polynomial (default is 0)
[1061]	1263	plot: plot the fit and the residual. In this each
	1264	indivual fit has to be approved, by typing 'y'
	1265	or 'n'
[1391]	1266	uselin: use linear polynomial fit
[794]	1267	insitu: if False a new scantable is returned.
	1268	Otherwise, the scaling is done in-situ
	1269	The default is taken from .asaprc (False)
[513]	1270	Example:
	1271	# return a scan baselined by a third order polynomial,
	1272	# not using a mask
	1273	bscan = scan.poly_baseline(order=3)
[579]	1274	"""
[513]	1275	if insitu is None: insitu = rcParams['insitu']
	1276	varlist = vars()
	1277	if mask is None:
[1295]	1278	mask = [True for i in xrange(self.nchan(-1))]
[513]	1279	from asap.asapfitter import fitter
[1217]	1280	try:
	1281	f = fitter()
	1282	f.set_scan(self, mask)
[1391]	1283	#f.set_function(poly=order)
	1284	if uselin:
	1285	f.set_function(lpoly=order)
	1286	else:
	1287	f.set_function(poly=order)
[1217]	1288	s = f.auto_fit(insitu, plot=plot)
	1289	s._add_history("poly_baseline", varlist)
	1290	print_log()
	1291	if insitu: self._assign(s)
	1292	else: return s
	1293	except RuntimeError:
	1294	msg = "The fit failed, possibly because it didn't converge."
	1295	if rcParams['verbose']:
	1296	print msg
	1297	return
	1298	else:
	1299	raise RuntimeError(msg)
[513]	1300
[1217]	1301
[1118]	1302	def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0,
[1280]	1303	threshold=3, chan_avg_limit=1, plot=False,
	1304	insitu=None):
[880]	1305	"""
	1306	Return a scan which has been baselined (all rows) by a polynomial.
	1307	Spectral lines are detected first using linefinder and masked out
	1308	to avoid them affecting the baseline solution.
	1309
	1310	Parameters:
	1311	mask: an optional mask retreived from scantable
	1312	edge: an optional number of channel to drop at
	1313	the edge of spectrum. If only one value is
	1314	specified, the same number will be dropped from
	1315	both sides of the spectrum. Default is to keep
[907]	1316	all channels. Nested tuples represent individual
[976]	1317	edge selection for different IFs (a number of spectral
	1318	channels can be different)
[880]	1319	order: the order of the polynomial (default is 0)
	1320	threshold: the threshold used by line finder. It is better to
	1321	keep it large as only strong lines affect the
	1322	baseline solution.
[1280]	1323	chan_avg_limit:
	1324	a maximum number of consequtive spectral channels to
	1325	average during the search of weak and broad lines.
	1326	The default is no averaging (and no search for weak
	1327	lines). If such lines can affect the fitted baseline
	1328	(e.g. a high order polynomial is fitted), increase this
	1329	parameter (usually values up to 8 are reasonable). Most
	1330	users of this method should find the default value
	1331	sufficient.
[1061]	1332	plot: plot the fit and the residual. In this each
	1333	indivual fit has to be approved, by typing 'y'
	1334	or 'n'
[880]	1335	insitu: if False a new scantable is returned.
	1336	Otherwise, the scaling is done in-situ
	1337	The default is taken from .asaprc (False)
	1338
	1339	Example:
	1340	scan2=scan.auto_poly_baseline(order=7)
	1341	"""
	1342	if insitu is None: insitu = rcParams['insitu']
	1343	varlist = vars()
	1344	from asap.asapfitter import fitter
	1345	from asap.asaplinefind import linefinder
	1346	from asap import _is_sequence_or_number as _is_valid
	1347
[976]	1348	# check whether edge is set up for each IF individually
[1118]	1349	individualedge = False;
	1350	if len(edge) > 1:
	1351	if isinstance(edge[0], list) or isinstance(edge[0], tuple):
	1352	individualedge = True;
[907]	1353
[1118]	1354	if not _is_valid(edge, int) and not individualedge:
[909]	1355	raise ValueError, "Parameter 'edge' has to be an integer or a \
[907]	1356	pair of integers specified as a tuple. Nested tuples are allowed \
	1357	to make individual selection for different IFs."
[919]	1358
[1118]	1359	curedge = (0, 0)
	1360	if individualedge:
	1361	for edgepar in edge:
	1362	if not _is_valid(edgepar, int):
	1363	raise ValueError, "Each element of the 'edge' tuple has \
	1364	to be a pair of integers or an integer."
[907]	1365	else:
[1118]	1366	curedge = edge;
[880]	1367
	1368	# setup fitter
	1369	f = fitter()
	1370	f.set_function(poly=order)
	1371
	1372	# setup line finder
[1118]	1373	fl = linefinder()
[1268]	1374	fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
[880]	1375
	1376	if not insitu:
[1118]	1377	workscan = self.copy()
[880]	1378	else:
[1118]	1379	workscan = self
[880]	1380
[907]	1381	fl.set_scan(workscan)
	1382
[1118]	1383	rows = range(workscan.nrow())
[880]	1384	asaplog.push("Processing:")
	1385	for r in rows:
[1118]	1386	msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
	1387	(workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
	1388	workscan.getpol(r), workscan.getcycle(r))
[880]	1389	asaplog.push(msg, False)
[907]	1390
[976]	1391	# figure out edge parameter
[1118]	1392	if individualedge:
	1393	if len(edge) >= workscan.getif(r):
	1394	raise RuntimeError, "Number of edge elements appear to " \
	1395	"be less than the number of IFs"
	1396	curedge = edge[workscan.getif(r)]
[919]	1397
[976]	1398	# setup line finder
[1118]	1399	fl.find_lines(r, mask, curedge)
[880]	1400	f.set_scan(workscan, fl.get_mask())
	1401	f.x = workscan._getabcissa(r)
	1402	f.y = workscan._getspectrum(r)
	1403	f.data = None
	1404	f.fit()
	1405	x = f.get_parameters()
[1061]	1406	if plot:
	1407	f.plot(residual=True)
	1408	x = raw_input("Accept fit ( [y]/n ): ")
	1409	if x.upper() == 'N':
	1410	continue
[880]	1411	workscan._setspectrum(f.fitter.getresidual(), r)
[1061]	1412	if plot:
	1413	f._p.unmap()
	1414	f._p = None
	1415	workscan._add_history("auto_poly_baseline", varlist)
[880]	1416	if insitu:
	1417	self._assign(workscan)
	1418	else:
	1419	return workscan
	1420
[914]	1421	def rotate_linpolphase(self, angle):
	1422	"""
	1423	Rotate the phase of the complex polarization O=Q+iU correlation.
	1424	This is always done in situ in the raw data. So if you call this
	1425	function more than once then each call rotates the phase further.
	1426	Parameters:
	1427	angle: The angle (degrees) to rotate (add) by.
	1428	Examples:
	1429	scan.rotate_linpolphase(2.3)
	1430	"""
	1431	varlist = vars()
[936]	1432	self._math._rotate_linpolphase(self, angle)
[914]	1433	self._add_history("rotate_linpolphase", varlist)
	1434	print_log()
	1435	return
[710]	1436
[513]	1437
[914]	1438	def rotate_xyphase(self, angle):
	1439	"""
	1440	Rotate the phase of the XY correlation. This is always done in situ
	1441	in the data. So if you call this function more than once
	1442	then each call rotates the phase further.
	1443	Parameters:
	1444	angle: The angle (degrees) to rotate (add) by.
	1445	Examples:
	1446	scan.rotate_xyphase(2.3)
	1447	"""
	1448	varlist = vars()
[936]	1449	self._math._rotate_xyphase(self, angle)
[914]	1450	self._add_history("rotate_xyphase", varlist)
	1451	print_log()
	1452	return
	1453
	1454	def swap_linears(self):
	1455	"""
[1348]	1456	Swap the linear polarisations XX and YY, or better the first two
	1457	polarisations as this also works for ciculars.
[914]	1458	"""
	1459	varlist = vars()
[936]	1460	self._math._swap_linears(self)
[914]	1461	self._add_history("swap_linears", varlist)
	1462	print_log()
	1463	return
	1464
	1465	def invert_phase(self):
	1466	"""
	1467	Invert the phase of the complex polarisation
	1468	"""
	1469	varlist = vars()
[936]	1470	self._math._invert_phase(self)
[914]	1471	self._add_history("invert_phase", varlist)
	1472	print_log()
	1473	return
	1474
[876]	1475	def add(self, offset, insitu=None):
[513]	1476	"""
	1477	Return a scan where all spectra have the offset added
	1478	Parameters:
	1479	offset: the offset
	1480	insitu: if False a new scantable is returned.
	1481	Otherwise, the scaling is done in-situ
	1482	The default is taken from .asaprc (False)
	1483	"""
	1484	if insitu is None: insitu = rcParams['insitu']
[876]	1485	self._math._setinsitu(insitu)
[513]	1486	varlist = vars()
[876]	1487	s = scantable(self._math._unaryop(self, offset, "ADD", False))
[1118]	1488	s._add_history("add", varlist)
[876]	1489	print_log()
	1490	if insitu:
	1491	self._assign(s)
	1492	else:
[513]	1493	return s
	1494
[1308]	1495	def scale(self, factor, tsys=True, insitu=None):
[513]	1496	"""
	1497	Return a scan where all spectra are scaled by the give 'factor'
	1498	Parameters:
	1499	factor: the scaling factor
	1500	insitu: if False a new scantable is returned.
	1501	Otherwise, the scaling is done in-situ
	1502	The default is taken from .asaprc (False)
	1503	tsys: if True (default) then apply the operation to Tsys
	1504	as well as the data
	1505	"""
	1506	if insitu is None: insitu = rcParams['insitu']
[876]	1507	self._math._setinsitu(insitu)
[513]	1508	varlist = vars()
[876]	1509	s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
[1118]	1510	s._add_history("scale", varlist)
[876]	1511	print_log()
	1512	if insitu:
	1513	self._assign(s)
	1514	else:
[513]	1515	return s
	1516
[1348]	1517	def auto_quotient(self, preserve=True, mode='paired'):
[670]	1518	"""
	1519	This function allows to build quotients automatically.
	1520	It assumes the observation to have the same numer of
	1521	"ons" and "offs"
	1522	Parameters:
[710]	1523	preserve: you can preserve (default) the continuum or
	1524	remove it. The equations used are
[670]	1525	preserve: Output = Toff * (on/off) - Toff
[1070]	1526	remove: Output = Toff * (on/off) - Ton
[1348]	1527	mode: the on/off detection mode
	1528	'paired' (default)
	1529	identifies 'off' scans by the
	1530	trailing '_R' (Mopra/Parkes) or
	1531	'_e'/'_w' (Tid) and matches
	1532	on/off pairs from the observing pattern
	1533	'time'
	1534	finds the closest off in time
	1535
[670]	1536	"""
[1348]	1537	modes = ["time", "paired"]
[670]	1538	if not mode in modes:
[876]	1539	msg = "please provide valid mode. Valid modes are %s" % (modes)
	1540	raise ValueError(msg)
	1541	varlist = vars()
[1348]	1542	s = None
	1543	if mode.lower() == "paired":
	1544	basesel = self.get_selection()
[1356]	1545	sel = selector()+basesel
	1546	sel.set_query("SRCTYPE==1")
	1547	self.set_selection(sel)
[1348]	1548	offs = self.copy()
	1549	sel.set_query("SRCTYPE==0")
[1356]	1550	self.set_selection(sel)
[1348]	1551	ons = self.copy()
	1552	s = scantable(self._math._quotient(ons, offs, preserve))
	1553	self.set_selection(basesel)
	1554	elif mode.lower() == "time":
	1555	s = scantable(self._math._auto_quotient(self, mode, preserve))
[1118]	1556	s._add_history("auto_quotient", varlist)
[876]	1557	print_log()
	1558	return s
[710]	1559
[1145]	1560	def mx_quotient(self, mask = None, weight='median', preserve=True):
[1141]	1561	"""
[1143]	1562	Form a quotient using "off" beams when observing in "MX" mode.
	1563	Parameters:
[1145]	1564	mask: an optional mask to be used when weight == 'stddev'
[1143]	1565	weight: How to average the off beams. Default is 'median'.
[1145]	1566	preserve: you can preserve (default) the continuum or
	1567	remove it. The equations used are
	1568	preserve: Output = Toff * (on/off) - Toff
	1569	remove: Output = Toff * (on/off) - Ton
[1217]	1570	"""
[1143]	1571	if mask is None: mask = ()
[1141]	1572	varlist = vars()
	1573	on = scantable(self._math._mx_extract(self, 'on'))
[1143]	1574	preoff = scantable(self._math._mx_extract(self, 'off'))
	1575	off = preoff.average_time(mask=mask, weight=weight, scanav=False)
[1217]	1576	from asapmath import quotient
[1145]	1577	q = quotient(on, off, preserve)
[1143]	1578	q._add_history("mx_quotient", varlist)
[1145]	1579	print_log()
[1217]	1580	return q
[513]	1581
[718]	1582	def freq_switch(self, insitu=None):
	1583	"""
	1584	Apply frequency switching to the data.
	1585	Parameters:
	1586	insitu: if False a new scantable is returned.
	1587	Otherwise, the swictching is done in-situ
	1588	The default is taken from .asaprc (False)
	1589	Example:
	1590	none
	1591	"""
	1592	if insitu is None: insitu = rcParams['insitu']
[876]	1593	self._math._setinsitu(insitu)
[718]	1594	varlist = vars()
[876]	1595	s = scantable(self._math._freqswitch(self))
[1118]	1596	s._add_history("freq_switch", varlist)
[876]	1597	print_log()
	1598	if insitu: self._assign(s)
	1599	else: return s
[718]	1600
[780]	1601	def recalc_azel(self):
	1602	"""
	1603	Recalculate the azimuth and elevation for each position.
	1604	Parameters:
	1605	none
	1606	Example:
	1607	"""
	1608	varlist = vars()
[876]	1609	self._recalcazel()
[780]	1610	self._add_history("recalc_azel", varlist)
	1611	print_log()
	1612	return
	1613
[513]	1614	def __add__(self, other):
	1615	varlist = vars()
	1616	s = None
	1617	if isinstance(other, scantable):
[1308]	1618	s = scantable(self._math._binaryop(self, other, "ADD"))
[513]	1619	elif isinstance(other, float):
[876]	1620	s = scantable(self._math._unaryop(self, other, "ADD", False))
[513]	1621	else:
[718]	1622	raise TypeError("Other input is not a scantable or float value")
[513]	1623	s._add_history("operator +", varlist)
[718]	1624	print_log()
[513]	1625	return s
	1626
	1627	def __sub__(self, other):
	1628	"""
	1629	implicit on all axes and on Tsys
	1630	"""
	1631	varlist = vars()
	1632	s = None
	1633	if isinstance(other, scantable):
[1308]	1634	s = scantable(self._math._binaryop(self, other, "SUB"))
[513]	1635	elif isinstance(other, float):
[876]	1636	s = scantable(self._math._unaryop(self, other, "SUB", False))
[513]	1637	else:
[718]	1638	raise TypeError("Other input is not a scantable or float value")
[513]	1639	s._add_history("operator -", varlist)
[718]	1640	print_log()
[513]	1641	return s
[710]	1642
[513]	1643	def __mul__(self, other):
	1644	"""
	1645	implicit on all axes and on Tsys
	1646	"""
	1647	varlist = vars()
	1648	s = None
	1649	if isinstance(other, scantable):
[1308]	1650	s = scantable(self._math._binaryop(self, other, "MUL"))
[513]	1651	elif isinstance(other, float):
[876]	1652	s = scantable(self._math._unaryop(self, other, "MUL", False))
[513]	1653	else:
[718]	1654	raise TypeError("Other input is not a scantable or float value")
[513]	1655	s._add_history("operator *", varlist)
[718]	1656	print_log()
[513]	1657	return s
	1658
[710]	1659
[513]	1660	def __div__(self, other):
	1661	"""
	1662	implicit on all axes and on Tsys
	1663	"""
	1664	varlist = vars()
	1665	s = None
	1666	if isinstance(other, scantable):
[1308]	1667	s = scantable(self._math._binaryop(self, other, "DIV"))
[513]	1668	elif isinstance(other, float):
	1669	if other == 0.0:
[718]	1670	raise ZeroDivisionError("Dividing by zero is not recommended")
[876]	1671	s = scantable(self._math._unaryop(self, other, "DIV", False))
[513]	1672	else:
[718]	1673	raise TypeError("Other input is not a scantable or float value")
[513]	1674	s._add_history("operator /", varlist)
[718]	1675	print_log()
[513]	1676	return s
	1677
[530]	1678	def get_fit(self, row=0):
	1679	"""
	1680	Print or return the stored fits for a row in the scantable
	1681	Parameters:
	1682	row: the row which the fit has been applied to.
	1683	"""
	1684	if row > self.nrow():
	1685	return
[976]	1686	from asap.asapfit import asapfit
[530]	1687	fit = asapfit(self._getfit(row))
[718]	1688	if rcParams['verbose']:
[530]	1689	print fit
	1690	return
	1691	else:
	1692	return fit.as_dict()
	1693
[1483]	1694	def flag_nans(self):
	1695	"""
	1696	Utility function to flag NaN values in the scantable.
	1697	"""
	1698	import numpy
	1699	basesel = self.get_selection()
	1700	for i in range(self.nrow()):
	1701	sel = selector()+basesel
	1702	sel.set_scans(self.getscan(i))
	1703	sel.set_beams(self.getbeam(i))
	1704	sel.set_ifs(self.getif(i))
	1705	sel.set_polarisations(self.getpol(i))
	1706	self.set_selection(sel)
	1707	nans = numpy.isnan(self._getspectrum(0))
	1708	if numpy.any(nans):
	1709	bnans = [ bool(v) for v in nans]
	1710	self.flag(bnans)
	1711	self.set_selection(basesel)
	1712
	1713
[484]	1714	def _add_history(self, funcname, parameters):
[1435]	1715	if not rcParams['scantable.history']:
	1716	return
[484]	1717	# create date
	1718	sep = "##"
	1719	from datetime import datetime
	1720	dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
	1721	hist = dstr+sep
	1722	hist += funcname+sep#cdate+sep
	1723	if parameters.has_key('self'): del parameters['self']
[1118]	1724	for k, v in parameters.iteritems():
[484]	1725	if type(v) is dict:
[1118]	1726	for k2, v2 in v.iteritems():
[484]	1727	hist += k2
	1728	hist += "="
[1118]	1729	if isinstance(v2, scantable):
[484]	1730	hist += 'scantable'
	1731	elif k2 == 'mask':
[1118]	1732	if isinstance(v2, list) or isinstance(v2, tuple):
[513]	1733	hist += str(self._zip_mask(v2))
	1734	else:
	1735	hist += str(v2)
[484]	1736	else:
[513]	1737	hist += str(v2)
[484]	1738	else:
	1739	hist += k
	1740	hist += "="
[1118]	1741	if isinstance(v, scantable):
[484]	1742	hist += 'scantable'
	1743	elif k == 'mask':
[1118]	1744	if isinstance(v, list) or isinstance(v, tuple):
[513]	1745	hist += str(self._zip_mask(v))
	1746	else:
	1747	hist += str(v)
[484]	1748	else:
	1749	hist += str(v)
	1750	hist += sep
	1751	hist = hist[:-2] # remove trailing '##'
	1752	self._addhistory(hist)
	1753
[710]	1754
[484]	1755	def _zip_mask(self, mask):
	1756	mask = list(mask)
	1757	i = 0
	1758	segments = []
	1759	while mask[i:].count(1):
	1760	i += mask[i:].index(1)
	1761	if mask[i:].count(0):
	1762	j = i + mask[i:].index(0)
	1763	else:
[710]	1764	j = len(mask)
[1118]	1765	segments.append([i, j])
[710]	1766	i = j
[484]	1767	return segments
[714]	1768
[626]	1769	def _get_ordinate_label(self):
	1770	fu = "("+self.get_fluxunit()+")"
	1771	import re
	1772	lbl = "Intensity"
[1118]	1773	if re.match(".K.", fu):
[626]	1774	lbl = "Brightness Temperature "+ fu
[1118]	1775	elif re.match(".Jy.", fu):
[626]	1776	lbl = "Flux density "+ fu
	1777	return lbl
[710]	1778
[876]	1779	def _check_ifs(self):
	1780	nchans = [self.nchan(i) for i in range(self.nif(-1))]
[889]	1781	nchans = filter(lambda t: t > 0, nchans)
[876]	1782	return (sum(nchans)/len(nchans) == nchans[0])
[976]	1783
	1784	def _fill(self, names, unit, average):
	1785	import os
	1786	from asap._asap import stfiller
	1787	first = True
	1788	fullnames = []
	1789	for name in names:
	1790	name = os.path.expandvars(name)
	1791	name = os.path.expanduser(name)
	1792	if not os.path.exists(name):
	1793	msg = "File '%s' does not exists" % (name)
	1794	if rcParams['verbose']:
	1795	asaplog.push(msg)
	1796	print asaplog.pop().strip()
	1797	return
	1798	raise IOError(msg)
	1799	fullnames.append(name)
	1800	if average:
	1801	asaplog.push('Auto averaging integrations')
[1079]	1802	stype = int(rcParams['scantable.storage'].lower() == 'disk')
[976]	1803	for name in fullnames:
[1073]	1804	tbl = Scantable(stype)
	1805	r = stfiller(tbl)
[976]	1806	msg = "Importing %s..." % (name)
[1118]	1807	asaplog.push(msg, False)
[976]	1808	print_log()
[1118]	1809	r._open(name, -1, -1)
[976]	1810	r._read()
[1073]	1811	#tbl = r._getdata()
[976]	1812	if average:
[1118]	1813	tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
[976]	1814	#tbl = tbl2
	1815	if not first:
	1816	tbl = self._math._merge([self, tbl])
	1817	#tbl = tbl2
	1818	Scantable.__init__(self, tbl)
	1819	r._close()
[1118]	1820	del r, tbl
[976]	1821	first = False
	1822	if unit is not None:
	1823	self.set_fluxunit(unit)
	1824	self.set_freqframe(rcParams['scantable.freqframe'])
	1825
[1402]	1826	def __getitem__(self, key):
	1827	if key < 0:
	1828	key += self.nrow()
	1829	if key >= self.nrow():
	1830	raise IndexError("Row index out of range.")
	1831	return self._getspectrum(key)
	1832
	1833	def __setitem__(self, key, value):
	1834	if key < 0:
	1835	key += self.nrow()
	1836	if key >= self.nrow():
	1837	raise IndexError("Row index out of range.")
	1838	if not hasattr(value, "__len__") or \
	1839	len(value) > self.nchan(self.getif(key)):
	1840	raise ValueError("Spectrum length doesn't match.")
	1841	return self._setspectrum(value, key)
	1842
	1843	def __len__(self):
	1844	return self.nrow()
	1845
	1846	def __iter__(self):
	1847	for i in range(len(self)):
	1848	yield self[i]

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