Context Navigation

scantable.py@ 1600

Visit:

Last change on this file since 1600 was 1530, checked in by Kana Sugimoto, 16 years ago

New Development: No

JIRA Issue: Yes (CAS-1079)

Ready to Release: Yes

Interface Changes: Yes for scantable.stats()

What Interface Changed:
Return value is now a list of abcissa values
when stat='min_abc' and 'max_abc'.

Test Programs:

run scantable.stats() with the parameter stat='min_abc' or 'max_abc'.

Put in Release Notes: No

Module(s): sdstat

Description:

scantable.stats() are modified so that the tool returns abscissa
chan/freq/velocity of min or max when stat='min_abc' or 'max_abc',
respectively.
Minor changes in IPosition mathutil::minMaxPos() to accept both
min (max) and min_abc (max_abc) as a parameter.

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

File size: 74.3 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.
	347	Parameters:
[1517]	348	stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum',
[1515]	349	'mean', 'var', 'stddev', 'avdev', 'rms', 'median'
[135]	350	mask: an optional mask specifying where the statistic
[102]	351	should be determined.
	352	Example:
[113]	353	scan.set_unit('channel')
[1118]	354	msk = scan.create_mask([100, 200], [500, 600])
[135]	355	scan.stats(stat='mean', mask=m)
[102]	356	"""
	357	if mask == None:
[876]	358	mask = []
[1118]	359	axes = ['Beam', 'IF', 'Pol', 'Time']
[876]	360	if not self._check_ifs():
[1118]	361	raise ValueError("Cannot apply mask as the IFs have different "
	362	"number of channels. Please use setselection() "
	363	"to select individual IFs")
[1530]	364	rtnabc = False
	365	if stat.lower().endswith('_abc'): rtnabc = True
	366	getchan = False
	367	if stat.lower().startswith('min') or stat.lower().startswith('max'):
[1517]	368	chan = self._math._minmaxchan(self, mask, stat)
	369	getchan = True
[1515]	370	statvals = []
[1530]	371	if not rtnabc: statvals = self._math._stats(self, mask, stat)
	372
[876]	373	out = ''
	374	axes = []
	375	for i in range(self.nrow()):
	376	axis = []
	377	axis.append(self.getscan(i))
	378	axis.append(self.getbeam(i))
	379	axis.append(self.getif(i))
	380	axis.append(self.getpol(i))
	381	axis.append(self.getcycle(i))
	382	axes.append(axis)
	383	tm = self._gettime(i)
	384	src = self._getsourcename(i)
[1530]	385	refstr = ''
	386	statunit= ''
[1517]	387	if getchan:
	388	qx, qy = self.chan2data(rowno=i, chan=chan[i])
[1530]	389	if rtnabc:
	390	statvals.append(qx['value'])
	391	refstr = '(value: %3.3f' % (qy['value'])+' ['+qy['unit']+'])'
	392	statunit= '['+qx['unit']+']'
	393	else:
	394	refstr = '(@ %3.3f' % (qx['value'])+' ['+qx['unit']+'])'
	395	#statunit= ' ['+qy['unit']+']'
[876]	396	out += 'Scan[%d] (%s) ' % (axis[0], src)
	397	out += 'Time[%s]:\n' % (tm)
	398	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
	399	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
	400	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
[1530]	401	out += '= %3.3f ' % (statvals[i]) +refstr+'\n'
[876]	402	out += "--------------------------------------------------\n"
[256]	403
[876]	404	if rcParams['verbose']:
	405	print "--------------------------------------------------"
[1530]	406	print " ", stat, statunit
[876]	407	print "--------------------------------------------------"
	408	print out
[1295]	409	#else:
	410	#retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'],
	411	# 'axes' : axes,
	412	# 'data': statvals}
	413	return statvals
[102]	414
[1517]	415	def chan2data(self, rowno=0, chan=0):
[1515]	416	"""
[1517]	417	Returns channel/frequency/velocity and spectral value
[1515]	418	at an arbitrary row and channel in the scantable.
	419	Parameters:
	420	rowno: a row number in the scantable. Default is the
	421	first row, i.e. rowno=0
[1517]	422	chan: a channel in the scantable. Default is the first
[1515]	423	channel, i.e. pos=0
	424	"""
[1517]	425	if isinstance(rowno, int) and isinstance(chan, int):
[1530]	426	qx = {'unit': self.get_unit(),
	427	'value': self._getabcissa(rowno)[chan]}
[1517]	428	qy = {'unit': self.get_fluxunit(),
	429	'value': self._getspectrum(rowno)[chan]}
	430	return qx, qy
[1515]	431
[1118]	432	def stddev(self, mask=None):
[135]	433	"""
	434	Determine the standard deviation of the current beam/if/pol
	435	Takes a 'mask' as an optional parameter to specify which
	436	channels should be excluded.
	437	Parameters:
	438	mask: an optional mask specifying where the standard
	439	deviation should be determined.
	440
	441	Example:
	442	scan.set_unit('channel')
[1118]	443	msk = scan.create_mask([100, 200], [500, 600])
[135]	444	scan.stddev(mask=m)
	445	"""
[1118]	446	return self.stats(stat='stddev', mask=mask);
[135]	447
[1003]	448
[1259]	449	def get_column_names(self):
[1003]	450	"""
	451	Return a list of column names, which can be used for selection.
	452	"""
[1259]	453	return list(Scantable.get_column_names(self))
[1003]	454
[876]	455	def get_tsys(self):
[113]	456	"""
	457	Return the System temperatures.
	458	Returns:
[876]	459	a list of Tsys values for the current selection
[113]	460	"""
[256]	461
[876]	462	return self._row_callback(self._gettsys, "Tsys")
[256]	463
[876]	464	def _row_callback(self, callback, label):
	465	axes = []
[1118]	466	axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno']
[876]	467	out = ""
[1118]	468	outvec = []
[876]	469	for i in range(self.nrow()):
	470	axis = []
	471	axis.append(self.getscan(i))
	472	axis.append(self.getbeam(i))
	473	axis.append(self.getif(i))
	474	axis.append(self.getpol(i))
	475	axis.append(self.getcycle(i))
	476	axes.append(axis)
	477	tm = self._gettime(i)
	478	src = self._getsourcename(i)
	479	out += 'Scan[%d] (%s) ' % (axis[0], src)
	480	out += 'Time[%s]:\n' % (tm)
	481	if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
	482	if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
	483	if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
	484	outvec.append(callback(i))
	485	out += '= %3.3f\n' % (outvec[i])
	486	out += "--------------------------------------------------\n"
	487	if rcParams['verbose']:
	488	print "--------------------------------------------------"
	489	print " %s" % (label)
	490	print "--------------------------------------------------"
	491	print out
[1175]	492	# disabled because the vector seems more useful
	493	#retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
	494	return outvec
[256]	495
[1070]	496	def _get_column(self, callback, row=-1):
	497	"""
	498	"""
	499	if row == -1:
	500	return [callback(i) for i in range(self.nrow())]
	501	else:
	502	if 0 <= row < self.nrow():
	503	return callback(row)
[256]	504
[1070]	505
[1348]	506	def get_time(self, row=-1, asdatetime=False):
[113]	507	"""
	508	Get a list of time stamps for the observations.
[1348]	509	Return a datetime object for each integration time stamp in the scantable.
[113]	510	Parameters:
[1348]	511	row: row no of integration. Default -1 return all rows
	512	asdatetime: return values as datetime objects rather than strings
[113]	513	Example:
	514	none
	515	"""
[1175]	516	from time import strptime
	517	from datetime import datetime
[1457]	518	times = self._get_column(self._gettime, row)
[1348]	519	if not asdatetime:
[1457]	520	return times
[1175]	521	format = "%Y/%m/%d/%H:%M:%S"
	522	if isinstance(times, list):
	523	return [datetime(*strptime(i, format)[:6]) for i in times]
	524	else:
	525	return datetime(*strptime(times, format)[:6])
[102]	526
[1348]	527
	528	def get_inttime(self, row=-1):
	529	"""
	530	Get a list of integration times for the observations.
	531	Return a time in seconds for each integration in the scantable.
	532	Parameters:
	533	row: row no of integration. Default -1 return all rows.
	534	Example:
	535	none
	536	"""
	537	return self._get_column(self._getinttime, row)
	538
	539
[714]	540	def get_sourcename(self, row=-1):
	541	"""
[794]	542	Get a list source names for the observations.
[714]	543	Return a string for each integration in the scantable.
	544	Parameters:
[1348]	545	row: row no of integration. Default -1 return all rows.
[714]	546	Example:
	547	none
	548	"""
[1070]	549	return self._get_column(self._getsourcename, row)
[714]	550
[794]	551	def get_elevation(self, row=-1):
	552	"""
	553	Get a list of elevations for the observations.
	554	Return a float for each integration in the scantable.
	555	Parameters:
[1348]	556	row: row no of integration. Default -1 return all rows.
[794]	557	Example:
	558	none
	559	"""
[1070]	560	return self._get_column(self._getelevation, row)
[794]	561
	562	def get_azimuth(self, row=-1):
	563	"""
	564	Get a list of azimuths for the observations.
	565	Return a float for each integration in the scantable.
	566	Parameters:
[1348]	567	row: row no of integration. Default -1 return all rows.
[794]	568	Example:
	569	none
	570	"""
[1070]	571	return self._get_column(self._getazimuth, row)
[794]	572
	573	def get_parangle(self, row=-1):
	574	"""
	575	Get a list of parallactic angles for the observations.
	576	Return a float for each integration in the scantable.
	577	Parameters:
[1348]	578	row: row no of integration. Default -1 return all rows.
[794]	579	Example:
	580	none
	581	"""
[1070]	582	return self._get_column(self._getparangle, row)
[794]	583
[1070]	584	def get_direction(self, row=-1):
	585	"""
	586	Get a list of Positions on the sky (direction) for the observations.
	587	Return a float for each integration in the scantable.
	588	Parameters:
	589	row: row no of integration. Default -1 return all rows
	590	Example:
	591	none
	592	"""
	593	return self._get_column(self._getdirection, row)
	594
[1389]	595	def get_directionval(self, row=-1):
	596	"""
	597	Get a list of Positions on the sky (direction) for the observations.
	598	Return a float for each integration in the scantable.
	599	Parameters:
	600	row: row no of integration. Default -1 return all rows
	601	Example:
	602	none
	603	"""
	604	return self._get_column(self._getdirectionvec, row)
	605
[102]	606	def set_unit(self, unit='channel'):
	607	"""
	608	Set the unit for all following operations on this scantable
	609	Parameters:
	610	unit: optional unit, default is 'channel'
[1118]	611	one of '*Hz', 'km/s', 'channel', ''
[102]	612	"""
[484]	613	varlist = vars()
[1118]	614	if unit in ['', 'pixel', 'channel']:
[113]	615	unit = ''
	616	inf = list(self._getcoordinfo())
	617	inf[0] = unit
	618	self._setcoordinfo(inf)
[1118]	619	self._add_history("set_unit", varlist)
[113]	620
[484]	621	def set_instrument(self, instr):
[358]	622	"""
[1348]	623	Set the instrument for subsequent processing.
[358]	624	Parameters:
[710]	625	instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
[407]	626	'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
[358]	627	"""
	628	self._setInstrument(instr)
[1118]	629	self._add_history("set_instument", vars())
[718]	630	print_log()
[358]	631
[1190]	632	def set_feedtype(self, feedtype):
	633	"""
	634	Overwrite the feed type, which might not be set correctly.
	635	Parameters:
	636	feedtype: 'linear' or 'circular'
	637	"""
	638	self._setfeedtype(feedtype)
	639	self._add_history("set_feedtype", vars())
	640	print_log()
	641
[276]	642	def set_doppler(self, doppler='RADIO'):
	643	"""
	644	Set the doppler for all following operations on this scantable.
	645	Parameters:
	646	doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
	647	"""
[484]	648	varlist = vars()
[276]	649	inf = list(self._getcoordinfo())
	650	inf[2] = doppler
	651	self._setcoordinfo(inf)
[1118]	652	self._add_history("set_doppler", vars())
[718]	653	print_log()
[710]	654
[226]	655	def set_freqframe(self, frame=None):
[113]	656	"""
	657	Set the frame type of the Spectral Axis.
	658	Parameters:
[591]	659	frame: an optional frame type, default 'LSRK'. Valid frames are:
[1118]	660	'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY',
	661	'GEO', 'GALACTO', 'LGROUP', 'CMB'
[113]	662	Examples:
	663	scan.set_freqframe('BARY')
	664	"""
[484]	665	if frame is None: frame = rcParams['scantable.freqframe']
	666	varlist = vars()
[1118]	667	valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
	668	'GEO', 'GALACTO', 'LGROUP', 'CMB']
[591]	669
[989]	670	if frame in valid:
[113]	671	inf = list(self._getcoordinfo())
	672	inf[1] = frame
	673	self._setcoordinfo(inf)
[1118]	674	self._add_history("set_freqframe", varlist)
[102]	675	else:
[1118]	676	msg = "Please specify a valid freq type. Valid types are:\n", valid
[718]	677	if rcParams['verbose']:
	678	print msg
	679	else:
	680	raise TypeError(msg)
	681	print_log()
[710]	682
[989]	683	def set_dirframe(self, frame=""):
	684	"""
	685	Set the frame type of the Direction on the sky.
	686	Parameters:
	687	frame: an optional frame type, default ''. Valid frames are:
	688	'J2000', 'B1950', 'GALACTIC'
	689	Examples:
	690	scan.set_dirframe('GALACTIC')
	691	"""
	692	varlist = vars()
	693	try:
	694	Scantable.set_dirframe(self, frame)
[1118]	695	except RuntimeError, msg:
[989]	696	if rcParams['verbose']:
	697	print msg
	698	else:
	699	raise
[1118]	700	self._add_history("set_dirframe", varlist)
[989]	701
[113]	702	def get_unit(self):
	703	"""
	704	Get the default unit set in this scantable
	705	Returns:
	706	A unit string
	707	"""
	708	inf = self._getcoordinfo()
	709	unit = inf[0]
	710	if unit == '': unit = 'channel'
	711	return unit
[102]	712
[158]	713	def get_abcissa(self, rowno=0):
[102]	714	"""
[158]	715	Get the abcissa in the current coordinate setup for the currently
[113]	716	selected Beam/IF/Pol
	717	Parameters:
[226]	718	rowno: an optional row number in the scantable. Default is the
	719	first row, i.e. rowno=0
[113]	720	Returns:
[1348]	721	The abcissa values and the format string (as a dictionary)
[113]	722	"""
[256]	723	abc = self._getabcissa(rowno)
[710]	724	lbl = self._getabcissalabel(rowno)
[718]	725	print_log()
[158]	726	return abc, lbl
[113]	727
[1401]	728	def flag(self, mask=None, unflag=False):
[1001]	729	"""
	730	Flag the selected data using an optional channel mask.
	731	Parameters:
	732	mask: an optional channel mask, created with create_mask. Default
	733	(no mask) is all channels.
[1401]	734	unflag: if True, unflag the data
[1001]	735	"""
	736	varlist = vars()
[1118]	737	if mask is None:
	738	mask = []
[1001]	739	try:
[1401]	740	self._flag(mask, unflag)
[1118]	741	except RuntimeError, msg:
[1001]	742	if rcParams['verbose']:
	743	print msg
	744	return
	745	else: raise
	746	self._add_history("flag", varlist)
	747
[1203]	748	def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None):
[1192]	749	"""
	750	Flag the data in 'lag' space by providing a frequency to remove.
	751	Flagged data in the scantable gets set to 0.0 before the fft.
	752	No taper is applied.
	753	Parameters:
[1348]	754	frequency: the frequency (really a period within the bandwidth)
	755	to remove
	756	width: the width of the frequency to remove, to remove a
	757	range of frequencies aroung the centre.
[1203]	758	unit: the frequency unit (default "GHz")
	759	Notes:
[1348]	760	It is recommended to flag edges of the band or strong
	761	signals beforehand.
[1192]	762	"""
	763	if insitu is None: insitu = rcParams['insitu']
	764	self._math._setinsitu(insitu)
	765	varlist = vars()
[1370]	766	base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. }
[1192]	767	if not base.has_key(unit):
	768	raise ValueError("%s is not a valid unit." % unit)
	769	try:
[1200]	770	s = scantable(self._math._lag_flag(self, frequency*base[unit],
	771	width*base[unit]))
[1192]	772	except RuntimeError, msg:
	773	if rcParams['verbose']:
	774	print msg
	775	return
	776	else: raise
	777	s._add_history("lag_flag", varlist)
	778	print_log()
	779	if insitu:
	780	self._assign(s)
	781	else:
	782	return s
[1001]	783
[1192]	784
[113]	785	def create_mask(self, args, *kwargs):
	786	"""
[1118]	787	Compute and return a mask based on [min, max] windows.
[189]	788	The specified windows are to be INCLUDED, when the mask is
[113]	789	applied.
[102]	790	Parameters:
[1118]	791	[min, max], [min2, max2], ...
[1024]	792	Pairs of start/end points (inclusive)specifying the regions
[102]	793	to be masked
[189]	794	invert: optional argument. If specified as True,
	795	return an inverted mask, i.e. the regions
	796	specified are EXCLUDED
[513]	797	row: create the mask using the specified row for
	798	unit conversions, default is row=0
	799	only necessary if frequency varies over rows.
[102]	800	Example:
[113]	801	scan.set_unit('channel')
	802	a)
[1118]	803	msk = scan.create_mask([400, 500], [800, 900])
[189]	804	# masks everything outside 400 and 500
[113]	805	# and 800 and 900 in the unit 'channel'
	806
	807	b)
[1118]	808	msk = scan.create_mask([400, 500], [800, 900], invert=True)
[189]	809	# masks the regions between 400 and 500
[113]	810	# and 800 and 900 in the unit 'channel'
[1024]	811	c)
	812	mask only channel 400
[1118]	813	msk = scan.create_mask([400, 400])
[102]	814	"""
[513]	815	row = 0
	816	if kwargs.has_key("row"):
	817	row = kwargs.get("row")
	818	data = self._getabcissa(row)
[113]	819	u = self._getcoordinfo()[0]
[718]	820	if rcParams['verbose']:
[113]	821	if u == "": u = "channel"
[718]	822	msg = "The current mask window unit is %s" % u
[1118]	823	i = self._check_ifs()
	824	if not i:
[876]	825	msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
[718]	826	asaplog.push(msg)
[102]	827	n = self.nchan()
[1295]	828	msk = _n_bools(n, False)
[710]	829	# test if args is a 'list' or a 'normal *args - UGLY!!!
	830
[1118]	831	ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
	832	and args or args[0]
[710]	833	for window in ws:
[102]	834	if (len(window) != 2 or window[0] > window[1] ):
[1118]	835	raise TypeError("A window needs to be defined as [min, max]")
[102]	836	for i in range(n):
[1024]	837	if data[i] >= window[0] and data[i] <= window[1]:
[1295]	838	msk[i] = True
[113]	839	if kwargs.has_key('invert'):
	840	if kwargs.get('invert'):
[1295]	841	msk = mask_not(msk)
[718]	842	print_log()
[102]	843	return msk
[710]	844
[1446]	845	def get_masklist(self, mask=None, row=0):
[256]	846	"""
[1446]	847	Compute and return a list of mask windows, [min, max].
	848	Parameters:
	849	mask: channel mask, created with create_mask.
	850	row: calcutate the masklist using the specified row
	851	for unit conversions, default is row=0
	852	only necessary if frequency varies over rows.
	853	Returns:
	854	[min, max], [min2, max2], ...
	855	Pairs of start/end points (inclusive)specifying
	856	the masked regions
	857	"""
	858	if not (isinstance(mask,list) or isinstance(mask, tuple)):
	859	raise TypeError("The mask should be list or tuple.")
	860	if len(mask) < 2:
	861	raise TypeError("The mask elements should be > 1")
	862	if self.nchan() != len(mask):
	863	msg = "Number of channels in scantable != number of mask elements"
	864	raise TypeError(msg)
	865	data = self._getabcissa(row)
	866	u = self._getcoordinfo()[0]
	867	if rcParams['verbose']:
	868	if u == "": u = "channel"
	869	msg = "The current mask window unit is %s" % u
	870	i = self._check_ifs()
	871	if not i:
	872	msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
	873	asaplog.push(msg)
	874	masklist=[]
	875	ist, ien = None, None
	876	ist, ien=self.get_mask_indices(mask)
	877	if ist is not None and ien is not None:
	878	for i in xrange(len(ist)):
	879	range=[data[ist[i]],data[ien[i]]]
	880	range.sort()
	881	masklist.append([range[0],range[1]])
	882	return masklist
	883
	884	def get_mask_indices(self, mask=None):
	885	"""
	886	Compute and Return lists of mask start indices and mask end indices.
	887	Parameters:
	888	mask: channel mask, created with create_mask.
	889	Returns:
	890	List of mask start indices and that of mask end indices,
	891	i.e., [istart1,istart2,....], [iend1,iend2,....].
	892	"""
	893	if not (isinstance(mask,list) or isinstance(mask, tuple)):
	894	raise TypeError("The mask should be list or tuple.")
	895	if len(mask) < 2:
	896	raise TypeError("The mask elements should be > 1")
	897	istart=[]
	898	iend=[]
	899	if mask[0]: istart.append(0)
	900	for i in range(len(mask)-1):
	901	if not mask[i] and mask[i+1]:
	902	istart.append(i+1)
	903	elif mask[i] and not mask[i+1]:
	904	iend.append(i)
	905	if mask[len(mask)-1]: iend.append(len(mask)-1)
	906	if len(istart) != len(iend):
	907	raise RuntimeError("Numbers of mask start != mask end.")
	908	for i in range(len(istart)):
	909	if istart[i] > iend[i]:
	910	raise RuntimeError("Mask start index > mask end index")
	911	break
	912	return istart,iend
	913
	914	# def get_restfreqs(self):
	915	# """
	916	# Get the restfrequency(s) stored in this scantable.
	917	# The return value(s) are always of unit 'Hz'
	918	# Parameters:
	919	# none
	920	# Returns:
	921	# a list of doubles
	922	# """
	923	# return list(self._getrestfreqs())
	924
	925	def get_restfreqs(self, ids=None):
	926	"""
[256]	927	Get the restfrequency(s) stored in this scantable.
	928	The return value(s) are always of unit 'Hz'
	929	Parameters:
[1446]	930	ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to
	931	be retrieved
[256]	932	Returns:
[1446]	933	dictionary containing ids and a list of doubles for each id
[256]	934	"""
[1446]	935	if ids is None:
	936	rfreqs={}
	937	idlist = self.getmolnos()
	938	for i in idlist:
	939	rfreqs[i]=list(self._getrestfreqs(i))
	940	return rfreqs
	941	else:
	942	if type(ids)==list or type(ids)==tuple:
	943	rfreqs={}
	944	for i in ids:
	945	rfreqs[i]=list(self._getrestfreqs(i))
	946	return rfreqs
	947	else:
	948	return list(self._getrestfreqs(ids))
	949	#return list(self._getrestfreqs(ids))
[102]	950
[931]	951	def set_restfreqs(self, freqs=None, unit='Hz'):
	952	"""
[1446]	953	******NEED TO BE UPDATED begin**********
[931]	954	Set or replace the restfrequency specified and
	955	If the 'freqs' argument holds a scalar,
	956	then that rest frequency will be applied to all the selected
	957	data. If the 'freqs' argument holds
	958	a vector, then it MUST be of equal or smaller length than
	959	the number of IFs (and the available restfrequencies will be
	960	replaced by this vector). In this case, all data have
	961	the restfrequency set per IF according
	962	to the corresponding value you give in the 'freqs' vector.
[1118]	963	E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
[931]	964	IF 1 gets restfreq 2e9.
[1446]	965	******NEED TO BE UPDATED end**********
[1153]	966	You can also specify the frequencies via a linecatalog/
	967
[931]	968	Parameters:
	969	freqs: list of rest frequency values or string idenitfiers
	970	unit: unit for rest frequency (default 'Hz')
[402]	971
[931]	972	Example:
[1446]	973	# set the given restfrequency for the all currently selected IFs
[931]	974	scan.set_restfreqs(freqs=1.4e9)
[1446]	975	# set multiple restfrequencies to all the selected data
	976	scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9])
	977	# If the number of IFs in the data is >= 2 the IF0 gets the first
	978	# value IF1 the second... NOTE that freqs needs to be
	979	# specified in list of list (e.g. [[],[],...] ).
	980	scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]])
[931]	981	#set the given restfrequency for the whole table (by name)
	982	scan.set_restfreqs(freqs="OH1667")
[391]	983
[931]	984	Note:
	985	To do more sophisticate Restfrequency setting, e.g. on a
	986	source and IF basis, use scantable.set_selection() before using
	987	this function.
	988	# provide your scantable is call scan
	989	selection = selector()
	990	selection.set_name("ORION*")
	991	selection.set_ifs([1])
	992	scan.set_selection(selection)
	993	scan.set_restfreqs(freqs=86.6e9)
	994
	995	"""
	996	varlist = vars()
[1157]	997	from asap import linecatalog
	998	# simple value
[1118]	999	if isinstance(freqs, int) or isinstance(freqs, float):
[1446]	1000	# TT mod
	1001	#self._setrestfreqs(freqs, "",unit)
	1002	self._setrestfreqs([freqs], [""],unit)
[1157]	1003	# list of values
[1118]	1004	elif isinstance(freqs, list) or isinstance(freqs, tuple):
[1157]	1005	# list values are scalars
[1118]	1006	if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
[1446]	1007	self._setrestfreqs(freqs, [""],unit)
[1157]	1008	# list values are tuples, (value, name)
	1009	elif isinstance(freqs[-1], dict):
[1446]	1010	#sel = selector()
	1011	#savesel = self._getselection()
	1012	#iflist = self.getifnos()
	1013	#for i in xrange(len(freqs)):
	1014	# sel.set_ifs(iflist[i])
	1015	# self._setselection(sel)
	1016	# self._setrestfreqs(freqs[i], "",unit)
	1017	#self._setselection(savesel)
	1018	self._setrestfreqs(freqs["value"],
	1019	freqs["name"], "MHz")
	1020	elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple):
[1157]	1021	sel = selector()
	1022	savesel = self._getselection()
[1322]	1023	iflist = self.getifnos()
[1446]	1024	if len(freqs)>len(iflist):
	1025	raise ValueError("number of elements in list of list exeeds the current IF selections")
[1157]	1026	for i in xrange(len(freqs)):
[1322]	1027	sel.set_ifs(iflist[i])
[1259]	1028	self._setselection(sel)
[1157]	1029	self._setrestfreqs(freqs[i]["value"],
	1030	freqs[i]["name"], "MHz")
	1031	self._setselection(savesel)
	1032	# freqs are to be taken from a linecatalog
[1153]	1033	elif isinstance(freqs, linecatalog):
	1034	sel = selector()
	1035	savesel = self._getselection()
	1036	for i in xrange(freqs.nrow()):
[1322]	1037	sel.set_ifs(iflist[i])
[1153]	1038	self._setselection(sel)
	1039	self._setrestfreqs(freqs.get_frequency(i),
	1040	freqs.get_name(i), "MHz")
	1041	# ensure that we are not iterating past nIF
	1042	if i == self.nif()-1: break
	1043	self._setselection(savesel)
[931]	1044	else:
	1045	return
	1046	self._add_history("set_restfreqs", varlist)
	1047
[1360]	1048	def shift_refpix(self, delta):
	1049	"""
	1050	Shift the reference pixel of the Spectra Coordinate by an
	1051	integer amount.
	1052	Parameters:
	1053	delta: the amount to shift by
	1054	Note:
	1055	Be careful using this with broadband data.
	1056	"""
	1057	Scantable.shift(self, delta)
[931]	1058
[1259]	1059	def history(self, filename=None):
	1060	"""
	1061	Print the history. Optionally to a file.
[1348]	1062	Parameters:
	1063	filename: The name of the file to save the history to.
[1259]	1064	"""
[484]	1065	hist = list(self._gethistory())
[794]	1066	out = "-"*80
[484]	1067	for h in hist:
[489]	1068	if h.startswith("---"):
[794]	1069	out += "\n"+h
[489]	1070	else:
	1071	items = h.split("##")
	1072	date = items[0]
	1073	func = items[1]
	1074	items = items[2:]
[794]	1075	out += "\n"+date+"\n"
	1076	out += "Function: %s\n Parameters:" % (func)
[489]	1077	for i in items:
	1078	s = i.split("=")
[1118]	1079	out += "\n %s = %s" % (s[0], s[1])
[794]	1080	out += "\n"+"-"*80
[1259]	1081	if filename is not None:
	1082	if filename is "":
	1083	filename = 'scantable_history.txt'
	1084	import os
	1085	filename = os.path.expandvars(os.path.expanduser(filename))
	1086	if not os.path.isdir(filename):
	1087	data = open(filename, 'w')
	1088	data.write(out)
	1089	data.close()
	1090	else:
	1091	msg = "Illegal file name '%s'." % (filename)
	1092	if rcParams['verbose']:
	1093	print msg
	1094	else:
	1095	raise IOError(msg)
	1096	if rcParams['verbose']:
	1097	try:
	1098	from IPython.genutils import page as pager
	1099	except ImportError:
	1100	from pydoc import pager
	1101	pager(out)
	1102	else:
	1103	return out
[484]	1104	return
[513]	1105	#
	1106	# Maths business
	1107	#
	1108
[931]	1109	def average_time(self, mask=None, scanav=False, weight='tint', align=False):
[513]	1110	"""
[1070]	1111	Return the (time) weighted average of a scan.
[513]	1112	Note:
[1070]	1113	in channels only - align if necessary
[513]	1114	Parameters:
	1115	mask: an optional mask (only used for 'var' and 'tsys'
	1116	weighting)
[558]	1117	scanav: True averages each scan separately
	1118	False (default) averages all scans together,
[1099]	1119	weight: Weighting scheme.
	1120	'none' (mean no weight)
	1121	'var' (1/var(spec) weighted)
	1122	'tsys' (1/Tsys**2 weighted)
	1123	'tint' (integration time weighted)
	1124	'tintsys' (Tint/Tsys**2)
	1125	'median' ( median averaging)
[535]	1126	The default is 'tint'
[931]	1127	align: align the spectra in velocity before averaging. It takes
	1128	the time of the first spectrum as reference time.
[513]	1129	Example:
	1130	# time average the scantable without using a mask
[710]	1131	newscan = scan.average_time()
[513]	1132	"""
	1133	varlist = vars()
[976]	1134	if weight is None: weight = 'TINT'
[513]	1135	if mask is None: mask = ()
[1099]	1136	if scanav: scanav = "SCAN"
	1137	else: scanav = "NONE"
[1118]	1138	scan = (self, )
[989]	1139	try:
[1118]	1140	if align:
	1141	scan = (self.freq_align(insitu=False), )
	1142	s = None
	1143	if weight.upper() == 'MEDIAN':
	1144	s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
	1145	scanav))
	1146	else:
	1147	s = scantable(self._math._average(scan, mask, weight.upper(),
	1148	scanav))
	1149	except RuntimeError, msg:
[989]	1150	if rcParams['verbose']:
	1151	print msg
	1152	return
	1153	else: raise
[1099]	1154	s._add_history("average_time", varlist)
[718]	1155	print_log()
[513]	1156	return s
[710]	1157
[876]	1158	def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
[513]	1159	"""
	1160	Return a scan where all spectra are converted to either
	1161	Jansky or Kelvin depending upon the flux units of the scan table.
	1162	By default the function tries to look the values up internally.
	1163	If it can't find them (or if you want to over-ride), you must
	1164	specify EITHER jyperk OR eta (and D which it will try to look up
	1165	also if you don't set it). jyperk takes precedence if you set both.
	1166	Parameters:
	1167	jyperk: the Jy / K conversion factor
	1168	eta: the aperture efficiency
	1169	d: the geomtric diameter (metres)
	1170	insitu: if False a new scantable is returned.
	1171	Otherwise, the scaling is done in-situ
	1172	The default is taken from .asaprc (False)
	1173	"""
	1174	if insitu is None: insitu = rcParams['insitu']
[876]	1175	self._math._setinsitu(insitu)
[513]	1176	varlist = vars()
	1177	if jyperk is None: jyperk = -1.0
	1178	if d is None: d = -1.0
	1179	if eta is None: eta = -1.0
[876]	1180	s = scantable(self._math._convertflux(self, d, eta, jyperk))
	1181	s._add_history("convert_flux", varlist)
	1182	print_log()
	1183	if insitu: self._assign(s)
	1184	else: return s
[513]	1185
[876]	1186	def gain_el(self, poly=None, filename="", method="linear", insitu=None):
[513]	1187	"""
	1188	Return a scan after applying a gain-elevation correction.
	1189	The correction can be made via either a polynomial or a
	1190	table-based interpolation (and extrapolation if necessary).
	1191	You specify polynomial coefficients, an ascii table or neither.
	1192	If you specify neither, then a polynomial correction will be made
	1193	with built in coefficients known for certain telescopes (an error
	1194	will occur if the instrument is not known).
	1195	The data and Tsys are divided by the scaling factors.
	1196	Parameters:
	1197	poly: Polynomial coefficients (default None) to compute a
	1198	gain-elevation correction as a function of
	1199	elevation (in degrees).
	1200	filename: The name of an ascii file holding correction factors.
	1201	The first row of the ascii file must give the column
	1202	names and these MUST include columns
	1203	"ELEVATION" (degrees) and "FACTOR" (multiply data
	1204	by this) somewhere.
	1205	The second row must give the data type of the
	1206	column. Use 'R' for Real and 'I' for Integer.
	1207	An example file would be
	1208	(actual factors are arbitrary) :
	1209
	1210	TIME ELEVATION FACTOR
	1211	R R R
	1212	0.1 0 0.8
	1213	0.2 20 0.85
	1214	0.3 40 0.9
	1215	0.4 60 0.85
	1216	0.5 80 0.8
	1217	0.6 90 0.75
	1218	method: Interpolation method when correcting from a table.
	1219	Values are "nearest", "linear" (default), "cubic"
	1220	and "spline"
	1221	insitu: if False a new scantable is returned.
	1222	Otherwise, the scaling is done in-situ
	1223	The default is taken from .asaprc (False)
	1224	"""
	1225
	1226	if insitu is None: insitu = rcParams['insitu']
[876]	1227	self._math._setinsitu(insitu)
[513]	1228	varlist = vars()
	1229	if poly is None:
[1118]	1230	poly = ()
[513]	1231	from os.path import expandvars
	1232	filename = expandvars(filename)
[876]	1233	s = scantable(self._math._gainel(self, poly, filename, method))
	1234	s._add_history("gain_el", varlist)
	1235	print_log()
	1236	if insitu: self._assign(s)
	1237	else: return s
[710]	1238
[931]	1239	def freq_align(self, reftime=None, method='cubic', insitu=None):
[513]	1240	"""
	1241	Return a scan where all rows have been aligned in frequency/velocity.
	1242	The alignment frequency frame (e.g. LSRK) is that set by function
	1243	set_freqframe.
	1244	Parameters:
	1245	reftime: reference time to align at. By default, the time of
	1246	the first row of data is used.
	1247	method: Interpolation method for regridding the spectra.
	1248	Choose from "nearest", "linear", "cubic" (default)
	1249	and "spline"
	1250	insitu: if False a new scantable is returned.
	1251	Otherwise, the scaling is done in-situ
	1252	The default is taken from .asaprc (False)
	1253	"""
[931]	1254	if insitu is None: insitu = rcParams["insitu"]
[876]	1255	self._math._setinsitu(insitu)
[513]	1256	varlist = vars()
[931]	1257	if reftime is None: reftime = ""
	1258	s = scantable(self._math._freq_align(self, reftime, method))
[876]	1259	s._add_history("freq_align", varlist)
	1260	print_log()
	1261	if insitu: self._assign(s)
	1262	else: return s
[513]	1263
[876]	1264	def opacity(self, tau, insitu=None):
[513]	1265	"""
	1266	Apply an opacity correction. The data
	1267	and Tsys are multiplied by the correction factor.
	1268	Parameters:
	1269	tau: Opacity from which the correction factor is
	1270	exp(tau*ZD)
	1271	where ZD is the zenith-distance
	1272	insitu: if False a new scantable is returned.
	1273	Otherwise, the scaling is done in-situ
	1274	The default is taken from .asaprc (False)
	1275	"""
	1276	if insitu is None: insitu = rcParams['insitu']
[876]	1277	self._math._setinsitu(insitu)
[513]	1278	varlist = vars()
[876]	1279	s = scantable(self._math._opacity(self, tau))
	1280	s._add_history("opacity", varlist)
	1281	print_log()
	1282	if insitu: self._assign(s)
	1283	else: return s
[513]	1284
	1285	def bin(self, width=5, insitu=None):
	1286	"""
	1287	Return a scan where all spectra have been binned up.
[1348]	1288	Parameters:
[513]	1289	width: The bin width (default=5) in pixels
	1290	insitu: if False a new scantable is returned.
	1291	Otherwise, the scaling is done in-situ
	1292	The default is taken from .asaprc (False)
	1293	"""
	1294	if insitu is None: insitu = rcParams['insitu']
[876]	1295	self._math._setinsitu(insitu)
[513]	1296	varlist = vars()
[876]	1297	s = scantable(self._math._bin(self, width))
[1118]	1298	s._add_history("bin", varlist)
[876]	1299	print_log()
	1300	if insitu: self._assign(s)
	1301	else: return s
[513]	1302
[710]	1303
[513]	1304	def resample(self, width=5, method='cubic', insitu=None):
	1305	"""
[1348]	1306	Return a scan where all spectra have been binned up.
	1307
	1308	Parameters:
[513]	1309	width: The bin width (default=5) in pixels
	1310	method: Interpolation method when correcting from a table.
	1311	Values are "nearest", "linear", "cubic" (default)
	1312	and "spline"
	1313	insitu: if False a new scantable is returned.
	1314	Otherwise, the scaling is done in-situ
	1315	The default is taken from .asaprc (False)
	1316	"""
	1317	if insitu is None: insitu = rcParams['insitu']
[876]	1318	self._math._setinsitu(insitu)
[513]	1319	varlist = vars()
[876]	1320	s = scantable(self._math._resample(self, method, width))
[1118]	1321	s._add_history("resample", varlist)
[876]	1322	print_log()
	1323	if insitu: self._assign(s)
	1324	else: return s
[513]	1325
	1326
[946]	1327	def average_pol(self, mask=None, weight='none'):
	1328	"""
	1329	Average the Polarisations together.
	1330	Parameters:
	1331	mask: An optional mask defining the region, where the
	1332	averaging will be applied. The output will have all
	1333	specified points masked.
	1334	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
	1335	weighted), or 'tsys' (1/Tsys**2 weighted)
	1336	"""
	1337	varlist = vars()
	1338	if mask is None:
	1339	mask = ()
[1010]	1340	s = scantable(self._math._averagepol(self, mask, weight.upper()))
[1118]	1341	s._add_history("average_pol", varlist)
[946]	1342	print_log()
[992]	1343	return s
[513]	1344
[1145]	1345	def average_beam(self, mask=None, weight='none'):
	1346	"""
	1347	Average the Beams together.
	1348	Parameters:
	1349	mask: An optional mask defining the region, where the
	1350	averaging will be applied. The output will have all
	1351	specified points masked.
	1352	weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
	1353	weighted), or 'tsys' (1/Tsys**2 weighted)
	1354	"""
	1355	varlist = vars()
	1356	if mask is None:
	1357	mask = ()
	1358	s = scantable(self._math._averagebeams(self, mask, weight.upper()))
	1359	s._add_history("average_beam", varlist)
	1360	print_log()
	1361	return s
	1362
[992]	1363	def convert_pol(self, poltype=None):
	1364	"""
	1365	Convert the data to a different polarisation type.
	1366	Parameters:
	1367	poltype: The new polarisation type. Valid types are:
	1368	"linear", "stokes" and "circular"
	1369	"""
	1370	varlist = vars()
	1371	try:
	1372	s = scantable(self._math._convertpol(self, poltype))
[1118]	1373	except RuntimeError, msg:
[992]	1374	if rcParams['verbose']:
[1118]	1375	print msg
	1376	return
[992]	1377	else:
	1378	raise
[1118]	1379	s._add_history("convert_pol", varlist)
[992]	1380	print_log()
	1381	return s
	1382
[876]	1383	def smooth(self, kernel="hanning", width=5.0, insitu=None):
[513]	1384	"""
	1385	Smooth the spectrum by the specified kernel (conserving flux).
	1386	Parameters:
	1387	kernel: The type of smoothing kernel. Select from
[1373]	1388	'hanning' (default), 'gaussian', 'boxcar' and
	1389	'rmedian'
[513]	1390	width: The width of the kernel in pixels. For hanning this is
	1391	ignored otherwise it defauls to 5 pixels.
	1392	For 'gaussian' it is the Full Width Half
	1393	Maximum. For 'boxcar' it is the full width.
[1373]	1394	For 'rmedian' it is the half width.
[513]	1395	insitu: if False a new scantable is returned.
	1396	Otherwise, the scaling is done in-situ
	1397	The default is taken from .asaprc (False)
	1398	Example:
	1399	none
	1400	"""
	1401	if insitu is None: insitu = rcParams['insitu']
[876]	1402	self._math._setinsitu(insitu)
[513]	1403	varlist = vars()
[1118]	1404	s = scantable(self._math._smooth(self, kernel.lower(), width))
[876]	1405	s._add_history("smooth", varlist)
	1406	print_log()
	1407	if insitu: self._assign(s)
	1408	else: return s
[513]	1409
[876]	1410
[1389]	1411	def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None):
[513]	1412	"""
	1413	Return a scan which has been baselined (all rows) by a polynomial.
	1414	Parameters:
[794]	1415	mask: an optional mask
	1416	order: the order of the polynomial (default is 0)
[1061]	1417	plot: plot the fit and the residual. In this each
	1418	indivual fit has to be approved, by typing 'y'
	1419	or 'n'
[1389]	1420	uselin: use linear polynomial fit
[794]	1421	insitu: if False a new scantable is returned.
	1422	Otherwise, the scaling is done in-situ
	1423	The default is taken from .asaprc (False)
[513]	1424	Example:
	1425	# return a scan baselined by a third order polynomial,
	1426	# not using a mask
	1427	bscan = scan.poly_baseline(order=3)
[579]	1428	"""
[513]	1429	if insitu is None: insitu = rcParams['insitu']
	1430	varlist = vars()
	1431	if mask is None:
[1295]	1432	mask = [True for i in xrange(self.nchan(-1))]
[513]	1433	from asap.asapfitter import fitter
[1217]	1434	try:
	1435	f = fitter()
	1436	f.set_scan(self, mask)
[1389]	1437	if uselin:
	1438	f.set_function(lpoly=order)
	1439	else:
	1440	f.set_function(poly=order)
[1217]	1441	s = f.auto_fit(insitu, plot=plot)
[1446]	1442	# Save parameters of baseline fits as a class attribute.
	1443	# NOTICE: It does not reflect changes in scantable!
	1444	self.blpars = f.blpars
[1217]	1445	s._add_history("poly_baseline", varlist)
	1446	print_log()
	1447	if insitu: self._assign(s)
	1448	else: return s
	1449	except RuntimeError:
	1450	msg = "The fit failed, possibly because it didn't converge."
	1451	if rcParams['verbose']:
	1452	print msg
	1453	return
	1454	else:
	1455	raise RuntimeError(msg)
[513]	1456
[1217]	1457
[1118]	1458	def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0,
[1280]	1459	threshold=3, chan_avg_limit=1, plot=False,
	1460	insitu=None):
[880]	1461	"""
	1462	Return a scan which has been baselined (all rows) by a polynomial.
	1463	Spectral lines are detected first using linefinder and masked out
	1464	to avoid them affecting the baseline solution.
	1465
	1466	Parameters:
	1467	mask: an optional mask retreived from scantable
	1468	edge: an optional number of channel to drop at
	1469	the edge of spectrum. If only one value is
	1470	specified, the same number will be dropped from
	1471	both sides of the spectrum. Default is to keep
[907]	1472	all channels. Nested tuples represent individual
[976]	1473	edge selection for different IFs (a number of spectral
	1474	channels can be different)
[880]	1475	order: the order of the polynomial (default is 0)
	1476	threshold: the threshold used by line finder. It is better to
	1477	keep it large as only strong lines affect the
	1478	baseline solution.
[1280]	1479	chan_avg_limit:
	1480	a maximum number of consequtive spectral channels to
	1481	average during the search of weak and broad lines.
	1482	The default is no averaging (and no search for weak
	1483	lines). If such lines can affect the fitted baseline
	1484	(e.g. a high order polynomial is fitted), increase this
	1485	parameter (usually values up to 8 are reasonable). Most
	1486	users of this method should find the default value
	1487	sufficient.
[1061]	1488	plot: plot the fit and the residual. In this each
	1489	indivual fit has to be approved, by typing 'y'
	1490	or 'n'
[880]	1491	insitu: if False a new scantable is returned.
	1492	Otherwise, the scaling is done in-situ
	1493	The default is taken from .asaprc (False)
	1494
	1495	Example:
	1496	scan2=scan.auto_poly_baseline(order=7)
	1497	"""
	1498	if insitu is None: insitu = rcParams['insitu']
	1499	varlist = vars()
	1500	from asap.asapfitter import fitter
	1501	from asap.asaplinefind import linefinder
	1502	from asap import _is_sequence_or_number as _is_valid
	1503
[976]	1504	# check whether edge is set up for each IF individually
[1118]	1505	individualedge = False;
	1506	if len(edge) > 1:
	1507	if isinstance(edge[0], list) or isinstance(edge[0], tuple):
	1508	individualedge = True;
[907]	1509
[1118]	1510	if not _is_valid(edge, int) and not individualedge:
[909]	1511	raise ValueError, "Parameter 'edge' has to be an integer or a \
[907]	1512	pair of integers specified as a tuple. Nested tuples are allowed \
	1513	to make individual selection for different IFs."
[919]	1514
[1118]	1515	curedge = (0, 0)
	1516	if individualedge:
	1517	for edgepar in edge:
	1518	if not _is_valid(edgepar, int):
	1519	raise ValueError, "Each element of the 'edge' tuple has \
	1520	to be a pair of integers or an integer."
[907]	1521	else:
[1118]	1522	curedge = edge;
[880]	1523
	1524	# setup fitter
	1525	f = fitter()
	1526	f.set_function(poly=order)
	1527
	1528	# setup line finder
[1118]	1529	fl = linefinder()
[1268]	1530	fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
[880]	1531
	1532	if not insitu:
[1118]	1533	workscan = self.copy()
[880]	1534	else:
[1118]	1535	workscan = self
[880]	1536
[907]	1537	fl.set_scan(workscan)
	1538
[1118]	1539	rows = range(workscan.nrow())
[1446]	1540	# Save parameters of baseline fits & masklists as a class attribute.
	1541	# NOTICE: It does not reflect changes in scantable!
	1542	if len(rows) > 0:
	1543	self.blpars=[]
	1544	self.masklists=[]
[880]	1545	asaplog.push("Processing:")
	1546	for r in rows:
[1118]	1547	msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
	1548	(workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
	1549	workscan.getpol(r), workscan.getcycle(r))
[880]	1550	asaplog.push(msg, False)
[907]	1551
[976]	1552	# figure out edge parameter
[1118]	1553	if individualedge:
	1554	if len(edge) >= workscan.getif(r):
	1555	raise RuntimeError, "Number of edge elements appear to " \
	1556	"be less than the number of IFs"
	1557	curedge = edge[workscan.getif(r)]
[919]	1558
[976]	1559	# setup line finder
[1118]	1560	fl.find_lines(r, mask, curedge)
[1446]	1561	outmask=fl.get_mask()
[880]	1562	f.set_scan(workscan, fl.get_mask())
	1563	f.x = workscan._getabcissa(r)
	1564	f.y = workscan._getspectrum(r)
	1565	f.data = None
	1566	f.fit()
[1446]	1567
	1568	# Show mask list
	1569	masklist=workscan.get_masklist(fl.get_mask(),row=r)
	1570	msg = "mask range: "+str(masklist)
	1571	asaplog.push(msg, False)
	1572
	1573	fpar = f.get_parameters()
[1061]	1574	if plot:
	1575	f.plot(residual=True)
	1576	x = raw_input("Accept fit ( [y]/n ): ")
	1577	if x.upper() == 'N':
[1446]	1578	self.blpars.append(None)
	1579	self.masklists.append(None)
[1061]	1580	continue
[880]	1581	workscan._setspectrum(f.fitter.getresidual(), r)
[1446]	1582	self.blpars.append(fpar)
	1583	self.masklists.append(masklist)
[1061]	1584	if plot:
	1585	f._p.unmap()
	1586	f._p = None
	1587	workscan._add_history("auto_poly_baseline", varlist)
[880]	1588	if insitu:
	1589	self._assign(workscan)
	1590	else:
	1591	return workscan
	1592
[914]	1593	def rotate_linpolphase(self, angle):
	1594	"""
	1595	Rotate the phase of the complex polarization O=Q+iU correlation.
	1596	This is always done in situ in the raw data. So if you call this
	1597	function more than once then each call rotates the phase further.
	1598	Parameters:
	1599	angle: The angle (degrees) to rotate (add) by.
	1600	Examples:
	1601	scan.rotate_linpolphase(2.3)
	1602	"""
	1603	varlist = vars()
[936]	1604	self._math._rotate_linpolphase(self, angle)
[914]	1605	self._add_history("rotate_linpolphase", varlist)
	1606	print_log()
	1607	return
[710]	1608
[513]	1609
[914]	1610	def rotate_xyphase(self, angle):
	1611	"""
	1612	Rotate the phase of the XY correlation. This is always done in situ
	1613	in the data. So if you call this function more than once
	1614	then each call rotates the phase further.
	1615	Parameters:
	1616	angle: The angle (degrees) to rotate (add) by.
	1617	Examples:
	1618	scan.rotate_xyphase(2.3)
	1619	"""
	1620	varlist = vars()
[936]	1621	self._math._rotate_xyphase(self, angle)
[914]	1622	self._add_history("rotate_xyphase", varlist)
	1623	print_log()
	1624	return
	1625
	1626	def swap_linears(self):
	1627	"""
[1348]	1628	Swap the linear polarisations XX and YY, or better the first two
	1629	polarisations as this also works for ciculars.
[914]	1630	"""
	1631	varlist = vars()
[936]	1632	self._math._swap_linears(self)
[914]	1633	self._add_history("swap_linears", varlist)
	1634	print_log()
	1635	return
	1636
	1637	def invert_phase(self):
	1638	"""
	1639	Invert the phase of the complex polarisation
	1640	"""
	1641	varlist = vars()
[936]	1642	self._math._invert_phase(self)
[914]	1643	self._add_history("invert_phase", varlist)
	1644	print_log()
	1645	return
	1646
[876]	1647	def add(self, offset, insitu=None):
[513]	1648	"""
	1649	Return a scan where all spectra have the offset added
	1650	Parameters:
	1651	offset: the offset
	1652	insitu: if False a new scantable is returned.
	1653	Otherwise, the scaling is done in-situ
	1654	The default is taken from .asaprc (False)
	1655	"""
	1656	if insitu is None: insitu = rcParams['insitu']
[876]	1657	self._math._setinsitu(insitu)
[513]	1658	varlist = vars()
[876]	1659	s = scantable(self._math._unaryop(self, offset, "ADD", False))
[1118]	1660	s._add_history("add", varlist)
[876]	1661	print_log()
	1662	if insitu:
	1663	self._assign(s)
	1664	else:
[513]	1665	return s
	1666
[1308]	1667	def scale(self, factor, tsys=True, insitu=None):
[513]	1668	"""
	1669	Return a scan where all spectra are scaled by the give 'factor'
	1670	Parameters:
	1671	factor: the scaling factor
	1672	insitu: if False a new scantable is returned.
	1673	Otherwise, the scaling is done in-situ
	1674	The default is taken from .asaprc (False)
	1675	tsys: if True (default) then apply the operation to Tsys
	1676	as well as the data
	1677	"""
	1678	if insitu is None: insitu = rcParams['insitu']
[876]	1679	self._math._setinsitu(insitu)
[513]	1680	varlist = vars()
[876]	1681	s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
[1118]	1682	s._add_history("scale", varlist)
[876]	1683	print_log()
	1684	if insitu:
	1685	self._assign(s)
	1686	else:
[513]	1687	return s
	1688
[1348]	1689	def auto_quotient(self, preserve=True, mode='paired'):
[670]	1690	"""
	1691	This function allows to build quotients automatically.
	1692	It assumes the observation to have the same numer of
	1693	"ons" and "offs"
	1694	Parameters:
[710]	1695	preserve: you can preserve (default) the continuum or
	1696	remove it. The equations used are
[670]	1697	preserve: Output = Toff * (on/off) - Toff
[1070]	1698	remove: Output = Toff * (on/off) - Ton
[1348]	1699	mode: the on/off detection mode
	1700	'paired' (default)
	1701	identifies 'off' scans by the
	1702	trailing '_R' (Mopra/Parkes) or
	1703	'_e'/'_w' (Tid) and matches
	1704	on/off pairs from the observing pattern
	1705	'time'
	1706	finds the closest off in time
	1707
[670]	1708	"""
[1348]	1709	modes = ["time", "paired"]
[670]	1710	if not mode in modes:
[876]	1711	msg = "please provide valid mode. Valid modes are %s" % (modes)
	1712	raise ValueError(msg)
	1713	varlist = vars()
[1348]	1714	s = None
	1715	if mode.lower() == "paired":
	1716	basesel = self.get_selection()
[1356]	1717	sel = selector()+basesel
	1718	sel.set_query("SRCTYPE==1")
	1719	self.set_selection(sel)
[1348]	1720	offs = self.copy()
	1721	sel.set_query("SRCTYPE==0")
[1356]	1722	self.set_selection(sel)
[1348]	1723	ons = self.copy()
	1724	s = scantable(self._math._quotient(ons, offs, preserve))
	1725	self.set_selection(basesel)
	1726	elif mode.lower() == "time":
	1727	s = scantable(self._math._auto_quotient(self, mode, preserve))
[1118]	1728	s._add_history("auto_quotient", varlist)
[876]	1729	print_log()
	1730	return s
[710]	1731
[1145]	1732	def mx_quotient(self, mask = None, weight='median', preserve=True):
[1141]	1733	"""
[1143]	1734	Form a quotient using "off" beams when observing in "MX" mode.
	1735	Parameters:
[1145]	1736	mask: an optional mask to be used when weight == 'stddev'
[1143]	1737	weight: How to average the off beams. Default is 'median'.
[1145]	1738	preserve: you can preserve (default) the continuum or
	1739	remove it. The equations used are
	1740	preserve: Output = Toff * (on/off) - Toff
	1741	remove: Output = Toff * (on/off) - Ton
[1217]	1742	"""
[1143]	1743	if mask is None: mask = ()
[1141]	1744	varlist = vars()
	1745	on = scantable(self._math._mx_extract(self, 'on'))
[1143]	1746	preoff = scantable(self._math._mx_extract(self, 'off'))
	1747	off = preoff.average_time(mask=mask, weight=weight, scanav=False)
[1217]	1748	from asapmath import quotient
[1145]	1749	q = quotient(on, off, preserve)
[1143]	1750	q._add_history("mx_quotient", varlist)
[1145]	1751	print_log()
[1217]	1752	return q
[513]	1753
[718]	1754	def freq_switch(self, insitu=None):
	1755	"""
	1756	Apply frequency switching to the data.
	1757	Parameters:
	1758	insitu: if False a new scantable is returned.
	1759	Otherwise, the swictching is done in-situ
	1760	The default is taken from .asaprc (False)
	1761	Example:
	1762	none
	1763	"""
	1764	if insitu is None: insitu = rcParams['insitu']
[876]	1765	self._math._setinsitu(insitu)
[718]	1766	varlist = vars()
[876]	1767	s = scantable(self._math._freqswitch(self))
[1118]	1768	s._add_history("freq_switch", varlist)
[876]	1769	print_log()
	1770	if insitu: self._assign(s)
	1771	else: return s
[718]	1772
[780]	1773	def recalc_azel(self):
	1774	"""
	1775	Recalculate the azimuth and elevation for each position.
	1776	Parameters:
	1777	none
	1778	Example:
	1779	"""
	1780	varlist = vars()
[876]	1781	self._recalcazel()
[780]	1782	self._add_history("recalc_azel", varlist)
	1783	print_log()
	1784	return
	1785
[513]	1786	def __add__(self, other):
	1787	varlist = vars()
	1788	s = None
	1789	if isinstance(other, scantable):
[1308]	1790	s = scantable(self._math._binaryop(self, other, "ADD"))
[513]	1791	elif isinstance(other, float):
[876]	1792	s = scantable(self._math._unaryop(self, other, "ADD", False))
[513]	1793	else:
[718]	1794	raise TypeError("Other input is not a scantable or float value")
[513]	1795	s._add_history("operator +", varlist)
[718]	1796	print_log()
[513]	1797	return s
	1798
	1799	def __sub__(self, other):
	1800	"""
	1801	implicit on all axes and on Tsys
	1802	"""
	1803	varlist = vars()
	1804	s = None
	1805	if isinstance(other, scantable):
[1308]	1806	s = scantable(self._math._binaryop(self, other, "SUB"))
[513]	1807	elif isinstance(other, float):
[876]	1808	s = scantable(self._math._unaryop(self, other, "SUB", False))
[513]	1809	else:
[718]	1810	raise TypeError("Other input is not a scantable or float value")
[513]	1811	s._add_history("operator -", varlist)
[718]	1812	print_log()
[513]	1813	return s
[710]	1814
[513]	1815	def __mul__(self, other):
	1816	"""
	1817	implicit on all axes and on Tsys
	1818	"""
	1819	varlist = vars()
	1820	s = None
	1821	if isinstance(other, scantable):
[1308]	1822	s = scantable(self._math._binaryop(self, other, "MUL"))
[513]	1823	elif isinstance(other, float):
[876]	1824	s = scantable(self._math._unaryop(self, other, "MUL", False))
[513]	1825	else:
[718]	1826	raise TypeError("Other input is not a scantable or float value")
[513]	1827	s._add_history("operator *", varlist)
[718]	1828	print_log()
[513]	1829	return s
	1830
[710]	1831
[513]	1832	def __div__(self, other):
	1833	"""
	1834	implicit on all axes and on Tsys
	1835	"""
	1836	varlist = vars()
	1837	s = None
	1838	if isinstance(other, scantable):
[1308]	1839	s = scantable(self._math._binaryop(self, other, "DIV"))
[513]	1840	elif isinstance(other, float):
	1841	if other == 0.0:
[718]	1842	raise ZeroDivisionError("Dividing by zero is not recommended")
[876]	1843	s = scantable(self._math._unaryop(self, other, "DIV", False))
[513]	1844	else:
[718]	1845	raise TypeError("Other input is not a scantable or float value")
[513]	1846	s._add_history("operator /", varlist)
[718]	1847	print_log()
[513]	1848	return s
	1849
[530]	1850	def get_fit(self, row=0):
	1851	"""
	1852	Print or return the stored fits for a row in the scantable
	1853	Parameters:
	1854	row: the row which the fit has been applied to.
	1855	"""
	1856	if row > self.nrow():
	1857	return
[976]	1858	from asap.asapfit import asapfit
[530]	1859	fit = asapfit(self._getfit(row))
[718]	1860	if rcParams['verbose']:
[530]	1861	print fit
	1862	return
	1863	else:
	1864	return fit.as_dict()
	1865
[484]	1866	def _add_history(self, funcname, parameters):
	1867	# create date
	1868	sep = "##"
	1869	from datetime import datetime
	1870	dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
	1871	hist = dstr+sep
	1872	hist += funcname+sep#cdate+sep
	1873	if parameters.has_key('self'): del parameters['self']
[1118]	1874	for k, v in parameters.iteritems():
[484]	1875	if type(v) is dict:
[1118]	1876	for k2, v2 in v.iteritems():
[484]	1877	hist += k2
	1878	hist += "="
[1118]	1879	if isinstance(v2, scantable):
[484]	1880	hist += 'scantable'
	1881	elif k2 == 'mask':
[1118]	1882	if isinstance(v2, list) or isinstance(v2, tuple):
[513]	1883	hist += str(self._zip_mask(v2))
	1884	else:
	1885	hist += str(v2)
[484]	1886	else:
[513]	1887	hist += str(v2)
[484]	1888	else:
	1889	hist += k
	1890	hist += "="
[1118]	1891	if isinstance(v, scantable):
[484]	1892	hist += 'scantable'
	1893	elif k == 'mask':
[1118]	1894	if isinstance(v, list) or isinstance(v, tuple):
[513]	1895	hist += str(self._zip_mask(v))
	1896	else:
	1897	hist += str(v)
[484]	1898	else:
	1899	hist += str(v)
	1900	hist += sep
	1901	hist = hist[:-2] # remove trailing '##'
	1902	self._addhistory(hist)
	1903
[710]	1904
[484]	1905	def _zip_mask(self, mask):
	1906	mask = list(mask)
	1907	i = 0
	1908	segments = []
	1909	while mask[i:].count(1):
	1910	i += mask[i:].index(1)
	1911	if mask[i:].count(0):
	1912	j = i + mask[i:].index(0)
	1913	else:
[710]	1914	j = len(mask)
[1118]	1915	segments.append([i, j])
[710]	1916	i = j
[484]	1917	return segments
[714]	1918
[626]	1919	def _get_ordinate_label(self):
	1920	fu = "("+self.get_fluxunit()+")"
	1921	import re
	1922	lbl = "Intensity"
[1118]	1923	if re.match(".K.", fu):
[626]	1924	lbl = "Brightness Temperature "+ fu
[1118]	1925	elif re.match(".Jy.", fu):
[626]	1926	lbl = "Flux density "+ fu
	1927	return lbl
[710]	1928
[876]	1929	def _check_ifs(self):
	1930	nchans = [self.nchan(i) for i in range(self.nif(-1))]
[889]	1931	nchans = filter(lambda t: t > 0, nchans)
[876]	1932	return (sum(nchans)/len(nchans) == nchans[0])
[976]	1933
[1496]	1934	def _fill(self, names, unit, average, getpt):
[976]	1935	import os
	1936	from asap._asap import stfiller
	1937	first = True
	1938	fullnames = []
	1939	for name in names:
	1940	name = os.path.expandvars(name)
	1941	name = os.path.expanduser(name)
	1942	if not os.path.exists(name):
	1943	msg = "File '%s' does not exists" % (name)
	1944	if rcParams['verbose']:
	1945	asaplog.push(msg)
	1946	print asaplog.pop().strip()
	1947	return
	1948	raise IOError(msg)
	1949	fullnames.append(name)
	1950	if average:
	1951	asaplog.push('Auto averaging integrations')
[1079]	1952	stype = int(rcParams['scantable.storage'].lower() == 'disk')
[976]	1953	for name in fullnames:
[1073]	1954	tbl = Scantable(stype)
	1955	r = stfiller(tbl)
[976]	1956	msg = "Importing %s..." % (name)
[1118]	1957	asaplog.push(msg, False)
[976]	1958	print_log()
[1496]	1959	r._open(name, -1, -1, getpt)
[976]	1960	r._read()
[1073]	1961	#tbl = r._getdata()
[976]	1962	if average:
[1118]	1963	tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
[976]	1964	#tbl = tbl2
	1965	if not first:
	1966	tbl = self._math._merge([self, tbl])
	1967	#tbl = tbl2
	1968	Scantable.__init__(self, tbl)
	1969	r._close()
[1118]	1970	del r, tbl
[976]	1971	first = False
	1972	if unit is not None:
	1973	self.set_fluxunit(unit)
[1446]	1974	#self.set_freqframe(rcParams['scantable.freqframe'])
[976]	1975

Note: See TracBrowser for help on using the repository browser.

Context Navigation

source: branches/alma/python/scantable.py@ 1600

Download in other formats: