[1846] | 1 | """This module defines the scantable class."""
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| 2 |
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[1697] | 3 | import os
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[1948] | 4 | import numpy
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[1691] | 5 | try:
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| 6 | from functools import wraps as wraps_dec
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| 7 | except ImportError:
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| 8 | from asap.compatibility import wraps as wraps_dec
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| 9 |
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[1824] | 10 | from asap.env import is_casapy
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[876] | 11 | from asap._asap import Scantable
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[2004] | 12 | from asap._asap import filler, msfiller
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[1824] | 13 | from asap.parameters import rcParams
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[1862] | 14 | from asap.logging import asaplog, asaplog_post_dec
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[1824] | 15 | from asap.selector import selector
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| 16 | from asap.linecatalog import linecatalog
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[1600] | 17 | from asap.coordinate import coordinate
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[1859] | 18 | from asap.utils import _n_bools, mask_not, mask_and, mask_or, page
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[1907] | 19 | from asap.asapfitter import fitter
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[102] | 20 |
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[1689] | 21 |
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| 22 | def preserve_selection(func):
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[1691] | 23 | @wraps_dec(func)
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[1689] | 24 | def wrap(obj, *args, **kw):
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| 25 | basesel = obj.get_selection()
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[1857] | 26 | try:
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| 27 | val = func(obj, *args, **kw)
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| 28 | finally:
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| 29 | obj.set_selection(basesel)
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[1689] | 30 | return val
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| 31 | return wrap
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| 32 |
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[1846] | 33 | def is_scantable(filename):
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| 34 | """Is the given file a scantable?
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[1689] | 35 |
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[1846] | 36 | Parameters:
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| 37 |
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| 38 | filename: the name of the file/directory to test
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| 39 |
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| 40 | """
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[1883] | 41 | if ( os.path.isdir(filename)
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| 42 | and os.path.exists(filename+'/table.info')
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| 43 | and os.path.exists(filename+'/table.dat') ):
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| 44 | f=open(filename+'/table.info')
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| 45 | l=f.readline()
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| 46 | f.close()
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| 47 | #if ( l.find('Scantable') != -1 ):
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| 48 | if ( l.find('Measurement Set') == -1 ):
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| 49 | return True
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| 50 | else:
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| 51 | return False
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| 52 | else:
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| 53 | return False
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| 54 | ## return (os.path.isdir(filename)
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| 55 | ## and not os.path.exists(filename+'/table.f1')
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| 56 | ## and os.path.exists(filename+'/table.info'))
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[1697] | 57 |
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[1883] | 58 | def is_ms(filename):
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| 59 | """Is the given file a MeasurementSet?
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[1697] | 60 |
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[1883] | 61 | Parameters:
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| 62 |
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| 63 | filename: the name of the file/directory to test
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| 64 |
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| 65 | """
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| 66 | if ( os.path.isdir(filename)
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| 67 | and os.path.exists(filename+'/table.info')
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| 68 | and os.path.exists(filename+'/table.dat') ):
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| 69 | f=open(filename+'/table.info')
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| 70 | l=f.readline()
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| 71 | f.close()
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| 72 | if ( l.find('Measurement Set') != -1 ):
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| 73 | return True
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| 74 | else:
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| 75 | return False
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| 76 | else:
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| 77 | return False
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| 78 |
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[876] | 79 | class scantable(Scantable):
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[1846] | 80 | """\
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| 81 | The ASAP container for scans (single-dish data).
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[102] | 82 | """
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[1819] | 83 |
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[1862] | 84 | @asaplog_post_dec
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[1916] | 85 | #def __init__(self, filename, average=None, unit=None, getpt=None,
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| 86 | # antenna=None, parallactify=None):
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| 87 | def __init__(self, filename, average=None, unit=None, parallactify=None, **args):
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[1846] | 88 | """\
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[102] | 89 | Create a scantable from a saved one or make a reference
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[1846] | 90 |
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[102] | 91 | Parameters:
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[1846] | 92 |
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| 93 | filename: the name of an asap table on disk
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| 94 | or
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| 95 | the name of a rpfits/sdfits/ms file
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| 96 | (integrations within scans are auto averaged
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| 97 | and the whole file is read) or
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| 98 | [advanced] a reference to an existing scantable
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| 99 |
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| 100 | average: average all integrations withinb a scan on read.
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| 101 | The default (True) is taken from .asaprc.
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| 102 |
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[484] | 103 | unit: brightness unit; must be consistent with K or Jy.
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[1846] | 104 | Over-rides the default selected by the filler
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| 105 | (input rpfits/sdfits/ms) or replaces the value
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| 106 | in existing scantables
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| 107 |
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| 108 | getpt: for MeasurementSet input data only:
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| 109 | If True, all pointing data are filled.
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| 110 | The deafult is False, which makes time to load
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| 111 | the MS data faster in some cases.
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| 112 |
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[1920] | 113 | antenna: for MeasurementSet input data only:
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| 114 | Antenna selection. integer (id) or string (name or id).
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[1846] | 115 |
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| 116 | parallactify: Indicate that the data had been parallatified. Default
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| 117 | is taken from rc file.
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| 118 |
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[710] | 119 | """
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[976] | 120 | if average is None:
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[710] | 121 | average = rcParams['scantable.autoaverage']
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[1916] | 122 | #if getpt is None:
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| 123 | # getpt = True
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| 124 | #if antenna is not None:
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| 125 | # asaplog.push("Antenna selection currently unsupported."
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| 126 | # "Using ''")
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| 127 | # asaplog.post('WARN')
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| 128 | #if antenna is None:
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| 129 | # antenna = ''
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| 130 | #elif type(antenna) == int:
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| 131 | # antenna = '%s' % antenna
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| 132 | #elif type(antenna) == list:
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| 133 | # tmpstr = ''
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| 134 | # for i in range( len(antenna) ):
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| 135 | # if type(antenna[i]) == int:
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| 136 | # tmpstr = tmpstr + ('%s,'%(antenna[i]))
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| 137 | # elif type(antenna[i]) == str:
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| 138 | # tmpstr=tmpstr+antenna[i]+','
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| 139 | # else:
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| 140 | # raise TypeError('Bad antenna selection.')
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| 141 | # antenna = tmpstr.rstrip(',')
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[1593] | 142 | parallactify = parallactify or rcParams['scantable.parallactify']
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[1259] | 143 | varlist = vars()
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[876] | 144 | from asap._asap import stmath
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[1819] | 145 | self._math = stmath( rcParams['insitu'] )
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[876] | 146 | if isinstance(filename, Scantable):
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| 147 | Scantable.__init__(self, filename)
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[181] | 148 | else:
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[1697] | 149 | if isinstance(filename, str):
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[976] | 150 | filename = os.path.expandvars(filename)
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| 151 | filename = os.path.expanduser(filename)
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| 152 | if not os.path.exists(filename):
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| 153 | s = "File '%s' not found." % (filename)
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| 154 | raise IOError(s)
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[1697] | 155 | if is_scantable(filename):
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| 156 | ondisk = rcParams['scantable.storage'] == 'disk'
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| 157 | Scantable.__init__(self, filename, ondisk)
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| 158 | if unit is not None:
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| 159 | self.set_fluxunit(unit)
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[1819] | 160 | # do not reset to the default freqframe
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| 161 | #self.set_freqframe(rcParams['scantable.freqframe'])
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[1883] | 162 | #elif os.path.isdir(filename) \
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| 163 | # and not os.path.exists(filename+'/table.f1'):
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| 164 | elif is_ms(filename):
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[1916] | 165 | # Measurement Set
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| 166 | opts={'ms': {}}
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| 167 | mskeys=['getpt','antenna']
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| 168 | for key in mskeys:
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| 169 | if key in args.keys():
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| 170 | opts['ms'][key] = args[key]
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| 171 | #self._fill([filename], unit, average, getpt, antenna)
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| 172 | self._fill([filename], unit, average, opts)
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[1893] | 173 | elif os.path.isfile(filename):
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[1916] | 174 | #self._fill([filename], unit, average, getpt, antenna)
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| 175 | self._fill([filename], unit, average)
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[1883] | 176 | else:
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[1819] | 177 | msg = "The given file '%s'is not a valid " \
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| 178 | "asap table." % (filename)
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[1859] | 179 | raise IOError(msg)
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[1118] | 180 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \
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[976] | 181 | and isinstance(filename[-1], str):
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[1916] | 182 | #self._fill(filename, unit, average, getpt, antenna)
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| 183 | self._fill(filename, unit, average)
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[1586] | 184 | self.parallactify(parallactify)
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[1259] | 185 | self._add_history("scantable", varlist)
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[102] | 186 |
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[1862] | 187 | @asaplog_post_dec
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[876] | 188 | def save(self, name=None, format=None, overwrite=False):
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[1846] | 189 | """\
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[1280] | 190 | Store the scantable on disk. This can be an asap (aips++) Table,
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| 191 | SDFITS or MS2 format.
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[1846] | 192 |
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[116] | 193 | Parameters:
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[1846] | 194 |
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[1093] | 195 | name: the name of the outputfile. For format "ASCII"
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| 196 | this is the root file name (data in 'name'.txt
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[497] | 197 | and header in 'name'_header.txt)
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[1855] | 198 |
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[116] | 199 | format: an optional file format. Default is ASAP.
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[1855] | 200 | Allowed are:
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| 201 |
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| 202 | * 'ASAP' (save as ASAP [aips++] Table),
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| 203 | * 'SDFITS' (save as SDFITS file)
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| 204 | * 'ASCII' (saves as ascii text file)
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| 205 | * 'MS2' (saves as an casacore MeasurementSet V2)
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| 206 | * 'FITS' (save as image FITS - not readable by class)
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| 207 | * 'CLASS' (save as FITS readable by CLASS)
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| 208 |
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[411] | 209 | overwrite: If the file should be overwritten if it exists.
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[256] | 210 | The default False is to return with warning
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[411] | 211 | without writing the output. USE WITH CARE.
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[1855] | 212 |
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[1846] | 213 | Example::
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| 214 |
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[116] | 215 | scan.save('myscan.asap')
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[1118] | 216 | scan.save('myscan.sdfits', 'SDFITS')
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[1846] | 217 |
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[116] | 218 | """
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[411] | 219 | from os import path
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[1593] | 220 | format = format or rcParams['scantable.save']
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[256] | 221 | suffix = '.'+format.lower()
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[1118] | 222 | if name is None or name == "":
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[256] | 223 | name = 'scantable'+suffix
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[718] | 224 | msg = "No filename given. Using default name %s..." % name
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| 225 | asaplog.push(msg)
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[411] | 226 | name = path.expandvars(name)
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[256] | 227 | if path.isfile(name) or path.isdir(name):
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| 228 | if not overwrite:
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[718] | 229 | msg = "File %s exists." % name
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[1859] | 230 | raise IOError(msg)
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[451] | 231 | format2 = format.upper()
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| 232 | if format2 == 'ASAP':
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[116] | 233 | self._save(name)
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[2004] | 234 | ## elif format2 == 'MS2':
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| 235 | ## msopt = {'ms': {'overwrite': overwrite } }
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| 236 | ## from asap._asap import mswriter
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| 237 | ## writer = mswriter( self )
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| 238 | ## writer.write( name, msopt )
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[116] | 239 | else:
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[989] | 240 | from asap._asap import stwriter as stw
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[1118] | 241 | writer = stw(format2)
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| 242 | writer.write(self, name)
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[116] | 243 | return
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| 244 |
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[102] | 245 | def copy(self):
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[1846] | 246 | """Return a copy of this scantable.
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| 247 |
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| 248 | *Note*:
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| 249 |
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[1348] | 250 | This makes a full (deep) copy. scan2 = scan1 makes a reference.
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[1846] | 251 |
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| 252 | Example::
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| 253 |
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[102] | 254 | copiedscan = scan.copy()
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[1846] | 255 |
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[102] | 256 | """
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[876] | 257 | sd = scantable(Scantable._copy(self))
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[113] | 258 | return sd
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| 259 |
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[1093] | 260 | def drop_scan(self, scanid=None):
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[1846] | 261 | """\
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[1093] | 262 | Return a new scantable where the specified scan number(s) has(have)
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| 263 | been dropped.
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[1846] | 264 |
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[1093] | 265 | Parameters:
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[1846] | 266 |
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[1093] | 267 | scanid: a (list of) scan number(s)
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[1846] | 268 |
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[1093] | 269 | """
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| 270 | from asap import _is_sequence_or_number as _is_valid
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| 271 | from asap import _to_list
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| 272 | from asap import unique
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| 273 | if not _is_valid(scanid):
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[1859] | 274 | raise RuntimeError( 'Please specify a scanno to drop from the scantable' )
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| 275 | scanid = _to_list(scanid)
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| 276 | allscans = unique([ self.getscan(i) for i in range(self.nrow())])
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| 277 | for sid in scanid: allscans.remove(sid)
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| 278 | if len(allscans) == 0:
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| 279 | raise ValueError("Can't remove all scans")
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| 280 | sel = selector(scans=allscans)
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| 281 | return self._select_copy(sel)
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[1093] | 282 |
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[1594] | 283 | def _select_copy(self, selection):
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| 284 | orig = self.get_selection()
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| 285 | self.set_selection(orig+selection)
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| 286 | cp = self.copy()
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| 287 | self.set_selection(orig)
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| 288 | return cp
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| 289 |
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[102] | 290 | def get_scan(self, scanid=None):
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[1855] | 291 | """\
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[102] | 292 | Return a specific scan (by scanno) or collection of scans (by
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| 293 | source name) in a new scantable.
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[1846] | 294 |
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| 295 | *Note*:
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| 296 |
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[1348] | 297 | See scantable.drop_scan() for the inverse operation.
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[1846] | 298 |
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[102] | 299 | Parameters:
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[1846] | 300 |
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[513] | 301 | scanid: a (list of) scanno or a source name, unix-style
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| 302 | patterns are accepted for source name matching, e.g.
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| 303 | '*_R' gets all 'ref scans
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[1846] | 304 |
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| 305 | Example::
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| 306 |
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[513] | 307 | # get all scans containing the source '323p459'
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| 308 | newscan = scan.get_scan('323p459')
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| 309 | # get all 'off' scans
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| 310 | refscans = scan.get_scan('*_R')
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| 311 | # get a susbset of scans by scanno (as listed in scan.summary())
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[1118] | 312 | newscan = scan.get_scan([0, 2, 7, 10])
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[1846] | 313 |
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[102] | 314 | """
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| 315 | if scanid is None:
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[1859] | 316 | raise RuntimeError( 'Please specify a scan no or name to '
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| 317 | 'retrieve from the scantable' )
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[102] | 318 | try:
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[946] | 319 | bsel = self.get_selection()
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| 320 | sel = selector()
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[102] | 321 | if type(scanid) is str:
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[946] | 322 | sel.set_name(scanid)
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[1594] | 323 | return self._select_copy(sel)
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[102] | 324 | elif type(scanid) is int:
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[946] | 325 | sel.set_scans([scanid])
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[1594] | 326 | return self._select_copy(sel)
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[381] | 327 | elif type(scanid) is list:
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[946] | 328 | sel.set_scans(scanid)
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[1594] | 329 | return self._select_copy(sel)
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[381] | 330 | else:
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[718] | 331 | msg = "Illegal scanid type, use 'int' or 'list' if ints."
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[1859] | 332 | raise TypeError(msg)
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[102] | 333 | except RuntimeError:
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[1859] | 334 | raise
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[102] | 335 |
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| 336 | def __str__(self):
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[1118] | 337 | return Scantable._summary(self, True)
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[102] | 338 |
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[976] | 339 | def summary(self, filename=None):
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[1846] | 340 | """\
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[102] | 341 | Print a summary of the contents of this scantable.
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[1846] | 342 |
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[102] | 343 | Parameters:
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[1846] | 344 |
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[1931] | 345 | filename: the name of a file to write the putput to
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[102] | 346 | Default - no file output
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[1846] | 347 |
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[102] | 348 | """
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[976] | 349 | info = Scantable._summary(self, True)
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[102] | 350 | if filename is not None:
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[256] | 351 | if filename is "":
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| 352 | filename = 'scantable_summary.txt'
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[415] | 353 | from os.path import expandvars, isdir
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[411] | 354 | filename = expandvars(filename)
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[415] | 355 | if not isdir(filename):
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[413] | 356 | data = open(filename, 'w')
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| 357 | data.write(info)
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| 358 | data.close()
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| 359 | else:
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[718] | 360 | msg = "Illegal file name '%s'." % (filename)
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[1859] | 361 | raise IOError(msg)
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| 362 | return page(info)
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[710] | 363 |
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[1512] | 364 | def get_spectrum(self, rowno):
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[1471] | 365 | """Return the spectrum for the current row in the scantable as a list.
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[1846] | 366 |
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[1471] | 367 | Parameters:
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[1846] | 368 |
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[1573] | 369 | rowno: the row number to retrieve the spectrum from
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[1846] | 370 |
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[1471] | 371 | """
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| 372 | return self._getspectrum(rowno)
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[946] | 373 |
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[1471] | 374 | def get_mask(self, rowno):
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| 375 | """Return the mask for the current row in the scantable as a list.
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[1846] | 376 |
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[1471] | 377 | Parameters:
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[1846] | 378 |
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[1573] | 379 | rowno: the row number to retrieve the mask from
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[1846] | 380 |
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[1471] | 381 | """
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| 382 | return self._getmask(rowno)
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| 383 |
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| 384 | def set_spectrum(self, spec, rowno):
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[1938] | 385 | """Set the spectrum for the current row in the scantable.
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[1846] | 386 |
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[1471] | 387 | Parameters:
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[1846] | 388 |
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[1855] | 389 | spec: the new spectrum
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[1846] | 390 |
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[1855] | 391 | rowno: the row number to set the spectrum for
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| 392 |
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[1471] | 393 | """
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| 394 | assert(len(spec) == self.nchan())
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| 395 | return self._setspectrum(spec, rowno)
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| 396 |
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[1600] | 397 | def get_coordinate(self, rowno):
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| 398 | """Return the (spectral) coordinate for a a given 'rowno'.
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[1846] | 399 |
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| 400 | *Note*:
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| 401 |
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[1600] | 402 | * This coordinate is only valid until a scantable method modifies
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| 403 | the frequency axis.
|
---|
| 404 | * This coordinate does contain the original frequency set-up
|
---|
| 405 | NOT the new frame. The conversions however are done using the user
|
---|
| 406 | specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate,
|
---|
| 407 | use scantable.freq_align first. Without it there is no closure,
|
---|
[1846] | 408 | i.e.::
|
---|
[1600] | 409 |
|
---|
[1846] | 410 | c = myscan.get_coordinate(0)
|
---|
| 411 | c.to_frequency(c.get_reference_pixel()) != c.get_reference_value()
|
---|
| 412 |
|
---|
[1600] | 413 | Parameters:
|
---|
[1846] | 414 |
|
---|
[1600] | 415 | rowno: the row number for the spectral coordinate
|
---|
| 416 |
|
---|
| 417 | """
|
---|
| 418 | return coordinate(Scantable.get_coordinate(self, rowno))
|
---|
| 419 |
|
---|
[946] | 420 | def get_selection(self):
|
---|
[1846] | 421 | """\
|
---|
[1005] | 422 | Get the selection object currently set on this scantable.
|
---|
[1846] | 423 |
|
---|
| 424 | Example::
|
---|
| 425 |
|
---|
[1005] | 426 | sel = scan.get_selection()
|
---|
| 427 | sel.set_ifs(0) # select IF 0
|
---|
| 428 | scan.set_selection(sel) # apply modified selection
|
---|
[1846] | 429 |
|
---|
[946] | 430 | """
|
---|
| 431 | return selector(self._getselection())
|
---|
| 432 |
|
---|
[1576] | 433 | def set_selection(self, selection=None, **kw):
|
---|
[1846] | 434 | """\
|
---|
[1005] | 435 | Select a subset of the data. All following operations on this scantable
|
---|
| 436 | are only applied to thi selection.
|
---|
[1846] | 437 |
|
---|
[1005] | 438 | Parameters:
|
---|
[1697] | 439 |
|
---|
[1846] | 440 | selection: a selector object (default unset the selection), or
|
---|
| 441 | any combination of "pols", "ifs", "beams", "scans",
|
---|
| 442 | "cycles", "name", "query"
|
---|
[1697] | 443 |
|
---|
[1846] | 444 | Examples::
|
---|
[1697] | 445 |
|
---|
[1005] | 446 | sel = selector() # create a selection object
|
---|
[1118] | 447 | self.set_scans([0, 3]) # select SCANNO 0 and 3
|
---|
[1005] | 448 | scan.set_selection(sel) # set the selection
|
---|
| 449 | scan.summary() # will only print summary of scanno 0 an 3
|
---|
| 450 | scan.set_selection() # unset the selection
|
---|
[1697] | 451 | # or the equivalent
|
---|
| 452 | scan.set_selection(scans=[0,3])
|
---|
| 453 | scan.summary() # will only print summary of scanno 0 an 3
|
---|
| 454 | scan.set_selection() # unset the selection
|
---|
[1846] | 455 |
|
---|
[946] | 456 | """
|
---|
[1576] | 457 | if selection is None:
|
---|
| 458 | # reset
|
---|
| 459 | if len(kw) == 0:
|
---|
| 460 | selection = selector()
|
---|
| 461 | else:
|
---|
| 462 | # try keywords
|
---|
| 463 | for k in kw:
|
---|
| 464 | if k not in selector.fields:
|
---|
| 465 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields))
|
---|
| 466 | selection = selector(**kw)
|
---|
[946] | 467 | self._setselection(selection)
|
---|
| 468 |
|
---|
[1819] | 469 | def get_row(self, row=0, insitu=None):
|
---|
[1846] | 470 | """\
|
---|
[1819] | 471 | Select a row in the scantable.
|
---|
| 472 | Return a scantable with single row.
|
---|
[1846] | 473 |
|
---|
[1819] | 474 | Parameters:
|
---|
[1846] | 475 |
|
---|
| 476 | row: row no of integration, default is 0.
|
---|
| 477 | insitu: if False a new scantable is returned. Otherwise, the
|
---|
| 478 | scaling is done in-situ. The default is taken from .asaprc
|
---|
| 479 | (False)
|
---|
| 480 |
|
---|
[1819] | 481 | """
|
---|
| 482 | if insitu is None: insitu = rcParams['insitu']
|
---|
| 483 | if not insitu:
|
---|
| 484 | workscan = self.copy()
|
---|
| 485 | else:
|
---|
| 486 | workscan = self
|
---|
| 487 | # Select a row
|
---|
| 488 | sel=selector()
|
---|
[1992] | 489 | sel.set_rows([row])
|
---|
| 490 | #sel.set_scans([workscan.getscan(row)])
|
---|
| 491 | #sel.set_cycles([workscan.getcycle(row)])
|
---|
| 492 | #sel.set_beams([workscan.getbeam(row)])
|
---|
| 493 | #sel.set_ifs([workscan.getif(row)])
|
---|
| 494 | #sel.set_polarisations([workscan.getpol(row)])
|
---|
| 495 | #sel.set_name(workscan._getsourcename(row))
|
---|
[1819] | 496 | workscan.set_selection(sel)
|
---|
| 497 | if not workscan.nrow() == 1:
|
---|
| 498 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow())
|
---|
| 499 | raise RuntimeError(msg)
|
---|
| 500 | del sel
|
---|
| 501 | if insitu:
|
---|
| 502 | self._assign(workscan)
|
---|
| 503 | else:
|
---|
| 504 | return workscan
|
---|
| 505 |
|
---|
[1862] | 506 | @asaplog_post_dec
|
---|
[1907] | 507 | def stats(self, stat='stddev', mask=None, form='3.3f', row=None):
|
---|
[1846] | 508 | """\
|
---|
[135] | 509 | Determine the specified statistic of the current beam/if/pol
|
---|
[102] | 510 | Takes a 'mask' as an optional parameter to specify which
|
---|
| 511 | channels should be excluded.
|
---|
[1846] | 512 |
|
---|
[102] | 513 | Parameters:
|
---|
[1846] | 514 |
|
---|
[1819] | 515 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum',
|
---|
| 516 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median'
|
---|
[1855] | 517 |
|
---|
[135] | 518 | mask: an optional mask specifying where the statistic
|
---|
[102] | 519 | should be determined.
|
---|
[1855] | 520 |
|
---|
[1819] | 521 | form: format string to print statistic values
|
---|
[1846] | 522 |
|
---|
[1907] | 523 | row: row number of spectrum to process.
|
---|
| 524 | (default is None: for all rows)
|
---|
[1846] | 525 |
|
---|
[1907] | 526 | Example:
|
---|
[113] | 527 | scan.set_unit('channel')
|
---|
[1118] | 528 | msk = scan.create_mask([100, 200], [500, 600])
|
---|
[135] | 529 | scan.stats(stat='mean', mask=m)
|
---|
[1846] | 530 |
|
---|
[102] | 531 | """
|
---|
[1593] | 532 | mask = mask or []
|
---|
[876] | 533 | if not self._check_ifs():
|
---|
[1118] | 534 | raise ValueError("Cannot apply mask as the IFs have different "
|
---|
| 535 | "number of channels. Please use setselection() "
|
---|
| 536 | "to select individual IFs")
|
---|
[1819] | 537 | rtnabc = False
|
---|
| 538 | if stat.lower().endswith('_abc'): rtnabc = True
|
---|
| 539 | getchan = False
|
---|
| 540 | if stat.lower().startswith('min') or stat.lower().startswith('max'):
|
---|
| 541 | chan = self._math._minmaxchan(self, mask, stat)
|
---|
| 542 | getchan = True
|
---|
| 543 | statvals = []
|
---|
[1907] | 544 | if not rtnabc:
|
---|
| 545 | if row == None:
|
---|
| 546 | statvals = self._math._stats(self, mask, stat)
|
---|
| 547 | else:
|
---|
| 548 | statvals = self._math._statsrow(self, mask, stat, int(row))
|
---|
[256] | 549 |
|
---|
[1819] | 550 | #def cb(i):
|
---|
| 551 | # return statvals[i]
|
---|
[256] | 552 |
|
---|
[1819] | 553 | #return self._row_callback(cb, stat)
|
---|
[102] | 554 |
|
---|
[1819] | 555 | label=stat
|
---|
| 556 | #callback=cb
|
---|
| 557 | out = ""
|
---|
| 558 | #outvec = []
|
---|
| 559 | sep = '-'*50
|
---|
[1907] | 560 |
|
---|
| 561 | if row == None:
|
---|
| 562 | rows = xrange(self.nrow())
|
---|
| 563 | elif isinstance(row, int):
|
---|
| 564 | rows = [ row ]
|
---|
| 565 |
|
---|
| 566 | for i in rows:
|
---|
[1819] | 567 | refstr = ''
|
---|
| 568 | statunit= ''
|
---|
| 569 | if getchan:
|
---|
| 570 | qx, qy = self.chan2data(rowno=i, chan=chan[i])
|
---|
| 571 | if rtnabc:
|
---|
| 572 | statvals.append(qx['value'])
|
---|
| 573 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])'
|
---|
| 574 | statunit= '['+qx['unit']+']'
|
---|
| 575 | else:
|
---|
| 576 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])'
|
---|
| 577 |
|
---|
| 578 | tm = self._gettime(i)
|
---|
| 579 | src = self._getsourcename(i)
|
---|
| 580 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src)
|
---|
| 581 | out += 'Time[%s]:\n' % (tm)
|
---|
[1907] | 582 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (self.getbeam(i))
|
---|
| 583 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i))
|
---|
| 584 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i))
|
---|
[1819] | 585 | #outvec.append(callback(i))
|
---|
[1907] | 586 | if len(rows) > 1:
|
---|
| 587 | # out += ('= %'+form) % (outvec[i]) +' '+refstr+'\n'
|
---|
| 588 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n'
|
---|
| 589 | else:
|
---|
| 590 | # out += ('= %'+form) % (outvec[0]) +' '+refstr+'\n'
|
---|
| 591 | out += ('= %'+form) % (statvals[0]) +' '+refstr+'\n'
|
---|
[1819] | 592 | out += sep+"\n"
|
---|
| 593 |
|
---|
[1859] | 594 | import os
|
---|
| 595 | if os.environ.has_key( 'USER' ):
|
---|
| 596 | usr = os.environ['USER']
|
---|
| 597 | else:
|
---|
| 598 | import commands
|
---|
| 599 | usr = commands.getoutput( 'whoami' )
|
---|
| 600 | tmpfile = '/tmp/tmp_'+usr+'_casapy_asap_scantable_stats'
|
---|
| 601 | f = open(tmpfile,'w')
|
---|
| 602 | print >> f, sep
|
---|
| 603 | print >> f, ' %s %s' % (label, statunit)
|
---|
| 604 | print >> f, sep
|
---|
| 605 | print >> f, out
|
---|
| 606 | f.close()
|
---|
| 607 | f = open(tmpfile,'r')
|
---|
| 608 | x = f.readlines()
|
---|
| 609 | f.close()
|
---|
| 610 | asaplog.push(''.join(x), False)
|
---|
| 611 |
|
---|
[1819] | 612 | return statvals
|
---|
| 613 |
|
---|
| 614 | def chan2data(self, rowno=0, chan=0):
|
---|
[1846] | 615 | """\
|
---|
[1819] | 616 | Returns channel/frequency/velocity and spectral value
|
---|
| 617 | at an arbitrary row and channel in the scantable.
|
---|
[1846] | 618 |
|
---|
[1819] | 619 | Parameters:
|
---|
[1846] | 620 |
|
---|
[1819] | 621 | rowno: a row number in the scantable. Default is the
|
---|
| 622 | first row, i.e. rowno=0
|
---|
[1855] | 623 |
|
---|
[1819] | 624 | chan: a channel in the scantable. Default is the first
|
---|
| 625 | channel, i.e. pos=0
|
---|
[1846] | 626 |
|
---|
[1819] | 627 | """
|
---|
| 628 | if isinstance(rowno, int) and isinstance(chan, int):
|
---|
| 629 | qx = {'unit': self.get_unit(),
|
---|
| 630 | 'value': self._getabcissa(rowno)[chan]}
|
---|
| 631 | qy = {'unit': self.get_fluxunit(),
|
---|
| 632 | 'value': self._getspectrum(rowno)[chan]}
|
---|
| 633 | return qx, qy
|
---|
| 634 |
|
---|
[1118] | 635 | def stddev(self, mask=None):
|
---|
[1846] | 636 | """\
|
---|
[135] | 637 | Determine the standard deviation of the current beam/if/pol
|
---|
| 638 | Takes a 'mask' as an optional parameter to specify which
|
---|
| 639 | channels should be excluded.
|
---|
[1846] | 640 |
|
---|
[135] | 641 | Parameters:
|
---|
[1846] | 642 |
|
---|
[135] | 643 | mask: an optional mask specifying where the standard
|
---|
| 644 | deviation should be determined.
|
---|
| 645 |
|
---|
[1846] | 646 | Example::
|
---|
| 647 |
|
---|
[135] | 648 | scan.set_unit('channel')
|
---|
[1118] | 649 | msk = scan.create_mask([100, 200], [500, 600])
|
---|
[135] | 650 | scan.stddev(mask=m)
|
---|
[1846] | 651 |
|
---|
[135] | 652 | """
|
---|
[1118] | 653 | return self.stats(stat='stddev', mask=mask);
|
---|
[135] | 654 |
|
---|
[1003] | 655 |
|
---|
[1259] | 656 | def get_column_names(self):
|
---|
[1846] | 657 | """\
|
---|
[1003] | 658 | Return a list of column names, which can be used for selection.
|
---|
| 659 | """
|
---|
[1259] | 660 | return list(Scantable.get_column_names(self))
|
---|
[1003] | 661 |
|
---|
[1730] | 662 | def get_tsys(self, row=-1):
|
---|
[1846] | 663 | """\
|
---|
[113] | 664 | Return the System temperatures.
|
---|
[1846] | 665 |
|
---|
| 666 | Parameters:
|
---|
| 667 |
|
---|
| 668 | row: the rowno to get the information for. (default all rows)
|
---|
| 669 |
|
---|
[113] | 670 | Returns:
|
---|
[1846] | 671 |
|
---|
[876] | 672 | a list of Tsys values for the current selection
|
---|
[1846] | 673 |
|
---|
[113] | 674 | """
|
---|
[1730] | 675 | if row > -1:
|
---|
| 676 | return self._get_column(self._gettsys, row)
|
---|
[876] | 677 | return self._row_callback(self._gettsys, "Tsys")
|
---|
[256] | 678 |
|
---|
[1730] | 679 |
|
---|
| 680 | def get_weather(self, row=-1):
|
---|
[1846] | 681 | """\
|
---|
| 682 | Return the weather informations.
|
---|
| 683 |
|
---|
| 684 | Parameters:
|
---|
| 685 |
|
---|
| 686 | row: the rowno to get the information for. (default all rows)
|
---|
| 687 |
|
---|
| 688 | Returns:
|
---|
| 689 |
|
---|
| 690 | a dict or list of of dicts of values for the current selection
|
---|
| 691 |
|
---|
| 692 | """
|
---|
| 693 |
|
---|
[1730] | 694 | values = self._get_column(self._get_weather, row)
|
---|
| 695 | if row > -1:
|
---|
| 696 | return {'temperature': values[0],
|
---|
| 697 | 'pressure': values[1], 'humidity' : values[2],
|
---|
| 698 | 'windspeed' : values[3], 'windaz' : values[4]
|
---|
| 699 | }
|
---|
| 700 | else:
|
---|
| 701 | out = []
|
---|
| 702 | for r in values:
|
---|
| 703 |
|
---|
| 704 | out.append({'temperature': r[0],
|
---|
| 705 | 'pressure': r[1], 'humidity' : r[2],
|
---|
| 706 | 'windspeed' : r[3], 'windaz' : r[4]
|
---|
| 707 | })
|
---|
| 708 | return out
|
---|
| 709 |
|
---|
[876] | 710 | def _row_callback(self, callback, label):
|
---|
| 711 | out = ""
|
---|
[1118] | 712 | outvec = []
|
---|
[1590] | 713 | sep = '-'*50
|
---|
[876] | 714 | for i in range(self.nrow()):
|
---|
| 715 | tm = self._gettime(i)
|
---|
| 716 | src = self._getsourcename(i)
|
---|
[1590] | 717 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src)
|
---|
[876] | 718 | out += 'Time[%s]:\n' % (tm)
|
---|
[1590] | 719 | if self.nbeam(-1) > 1:
|
---|
| 720 | out += ' Beam[%d] ' % (self.getbeam(i))
|
---|
| 721 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i))
|
---|
| 722 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i))
|
---|
[876] | 723 | outvec.append(callback(i))
|
---|
| 724 | out += '= %3.3f\n' % (outvec[i])
|
---|
[1590] | 725 | out += sep+'\n'
|
---|
[1859] | 726 |
|
---|
| 727 | asaplog.push(sep)
|
---|
| 728 | asaplog.push(" %s" % (label))
|
---|
| 729 | asaplog.push(sep)
|
---|
| 730 | asaplog.push(out)
|
---|
[1861] | 731 | asaplog.post()
|
---|
[1175] | 732 | return outvec
|
---|
[256] | 733 |
|
---|
[1947] | 734 | def _get_column(self, callback, row=-1, *args):
|
---|
[1070] | 735 | """
|
---|
| 736 | """
|
---|
| 737 | if row == -1:
|
---|
[1947] | 738 | return [callback(i, *args) for i in range(self.nrow())]
|
---|
[1070] | 739 | else:
|
---|
[1819] | 740 | if 0 <= row < self.nrow():
|
---|
[1947] | 741 | return callback(row, *args)
|
---|
[256] | 742 |
|
---|
[1070] | 743 |
|
---|
[1948] | 744 | def get_time(self, row=-1, asdatetime=False, prec=-1):
|
---|
[1846] | 745 | """\
|
---|
[113] | 746 | Get a list of time stamps for the observations.
|
---|
[1938] | 747 | Return a datetime object or a string (default) for each
|
---|
| 748 | integration time stamp in the scantable.
|
---|
[1846] | 749 |
|
---|
[113] | 750 | Parameters:
|
---|
[1846] | 751 |
|
---|
[1348] | 752 | row: row no of integration. Default -1 return all rows
|
---|
[1855] | 753 |
|
---|
[1348] | 754 | asdatetime: return values as datetime objects rather than strings
|
---|
[1846] | 755 |
|
---|
[1948] | 756 | prec: number of digits shown. Default -1 to automatic calculation.
|
---|
| 757 | Note this number is equals to the digits of MVTime,
|
---|
| 758 | i.e., 0<prec<3: dates with hh:: only,
|
---|
| 759 | <5: with hh:mm:, <7 or 0: with hh:mm:ss,
|
---|
[1947] | 760 | and 6> : with hh:mm:ss.tt... (prec-6 t's added)
|
---|
| 761 |
|
---|
[113] | 762 | """
|
---|
[1175] | 763 | from datetime import datetime
|
---|
[1948] | 764 | if prec < 0:
|
---|
| 765 | # automagically set necessary precision +1
|
---|
[1950] | 766 | prec = 7 - numpy.floor(numpy.log10(numpy.min(self.get_inttime(row))))
|
---|
[1948] | 767 | prec = max(6, int(prec))
|
---|
| 768 | else:
|
---|
| 769 | prec = max(0, prec)
|
---|
| 770 | if asdatetime:
|
---|
| 771 | #precision can be 1 millisecond at max
|
---|
| 772 | prec = min(12, prec)
|
---|
| 773 |
|
---|
[1947] | 774 | times = self._get_column(self._gettime, row, prec)
|
---|
[1348] | 775 | if not asdatetime:
|
---|
[1392] | 776 | return times
|
---|
[1947] | 777 | format = "%Y/%m/%d/%H:%M:%S.%f"
|
---|
| 778 | if prec < 7:
|
---|
| 779 | nsub = 1 + (((6-prec)/2) % 3)
|
---|
| 780 | substr = [".%f","%S","%M"]
|
---|
| 781 | for i in range(nsub):
|
---|
| 782 | format = format.replace(substr[i],"")
|
---|
[1175] | 783 | if isinstance(times, list):
|
---|
[1947] | 784 | return [datetime.strptime(i, format) for i in times]
|
---|
[1175] | 785 | else:
|
---|
[1947] | 786 | return datetime.strptime(times, format)
|
---|
[102] | 787 |
|
---|
[1348] | 788 |
|
---|
| 789 | def get_inttime(self, row=-1):
|
---|
[1846] | 790 | """\
|
---|
[1348] | 791 | Get a list of integration times for the observations.
|
---|
| 792 | Return a time in seconds for each integration in the scantable.
|
---|
[1846] | 793 |
|
---|
[1348] | 794 | Parameters:
|
---|
[1846] | 795 |
|
---|
[1348] | 796 | row: row no of integration. Default -1 return all rows.
|
---|
[1846] | 797 |
|
---|
[1348] | 798 | """
|
---|
[1573] | 799 | return self._get_column(self._getinttime, row)
|
---|
[1348] | 800 |
|
---|
[1573] | 801 |
|
---|
[714] | 802 | def get_sourcename(self, row=-1):
|
---|
[1846] | 803 | """\
|
---|
[794] | 804 | Get a list source names for the observations.
|
---|
[714] | 805 | Return a string for each integration in the scantable.
|
---|
| 806 | Parameters:
|
---|
[1846] | 807 |
|
---|
[1348] | 808 | row: row no of integration. Default -1 return all rows.
|
---|
[1846] | 809 |
|
---|
[714] | 810 | """
|
---|
[1070] | 811 | return self._get_column(self._getsourcename, row)
|
---|
[714] | 812 |
|
---|
[794] | 813 | def get_elevation(self, row=-1):
|
---|
[1846] | 814 | """\
|
---|
[794] | 815 | Get a list of elevations for the observations.
|
---|
| 816 | Return a float for each integration in the scantable.
|
---|
[1846] | 817 |
|
---|
[794] | 818 | Parameters:
|
---|
[1846] | 819 |
|
---|
[1348] | 820 | row: row no of integration. Default -1 return all rows.
|
---|
[1846] | 821 |
|
---|
[794] | 822 | """
|
---|
[1070] | 823 | return self._get_column(self._getelevation, row)
|
---|
[794] | 824 |
|
---|
| 825 | def get_azimuth(self, row=-1):
|
---|
[1846] | 826 | """\
|
---|
[794] | 827 | Get a list of azimuths for the observations.
|
---|
| 828 | Return a float for each integration in the scantable.
|
---|
[1846] | 829 |
|
---|
[794] | 830 | Parameters:
|
---|
[1348] | 831 | row: row no of integration. Default -1 return all rows.
|
---|
[1846] | 832 |
|
---|
[794] | 833 | """
|
---|
[1070] | 834 | return self._get_column(self._getazimuth, row)
|
---|
[794] | 835 |
|
---|
| 836 | def get_parangle(self, row=-1):
|
---|
[1846] | 837 | """\
|
---|
[794] | 838 | Get a list of parallactic angles for the observations.
|
---|
| 839 | Return a float for each integration in the scantable.
|
---|
[1846] | 840 |
|
---|
[794] | 841 | Parameters:
|
---|
[1846] | 842 |
|
---|
[1348] | 843 | row: row no of integration. Default -1 return all rows.
|
---|
[1846] | 844 |
|
---|
[794] | 845 | """
|
---|
[1070] | 846 | return self._get_column(self._getparangle, row)
|
---|
[794] | 847 |
|
---|
[1070] | 848 | def get_direction(self, row=-1):
|
---|
| 849 | """
|
---|
| 850 | Get a list of Positions on the sky (direction) for the observations.
|
---|
[1594] | 851 | Return a string for each integration in the scantable.
|
---|
[1855] | 852 |
|
---|
[1070] | 853 | Parameters:
|
---|
[1855] | 854 |
|
---|
[1070] | 855 | row: row no of integration. Default -1 return all rows
|
---|
[1855] | 856 |
|
---|
[1070] | 857 | """
|
---|
| 858 | return self._get_column(self._getdirection, row)
|
---|
| 859 |
|
---|
[1391] | 860 | def get_directionval(self, row=-1):
|
---|
[1846] | 861 | """\
|
---|
[1391] | 862 | Get a list of Positions on the sky (direction) for the observations.
|
---|
| 863 | Return a float for each integration in the scantable.
|
---|
[1846] | 864 |
|
---|
[1391] | 865 | Parameters:
|
---|
[1846] | 866 |
|
---|
[1391] | 867 | row: row no of integration. Default -1 return all rows
|
---|
[1846] | 868 |
|
---|
[1391] | 869 | """
|
---|
| 870 | return self._get_column(self._getdirectionvec, row)
|
---|
| 871 |
|
---|
[1862] | 872 | @asaplog_post_dec
|
---|
[102] | 873 | def set_unit(self, unit='channel'):
|
---|
[1846] | 874 | """\
|
---|
[102] | 875 | Set the unit for all following operations on this scantable
|
---|
[1846] | 876 |
|
---|
[102] | 877 | Parameters:
|
---|
[1846] | 878 |
|
---|
| 879 | unit: optional unit, default is 'channel'. Use one of '*Hz',
|
---|
| 880 | 'km/s', 'channel' or equivalent ''
|
---|
| 881 |
|
---|
[102] | 882 | """
|
---|
[484] | 883 | varlist = vars()
|
---|
[1118] | 884 | if unit in ['', 'pixel', 'channel']:
|
---|
[113] | 885 | unit = ''
|
---|
| 886 | inf = list(self._getcoordinfo())
|
---|
| 887 | inf[0] = unit
|
---|
| 888 | self._setcoordinfo(inf)
|
---|
[1118] | 889 | self._add_history("set_unit", varlist)
|
---|
[113] | 890 |
|
---|
[1862] | 891 | @asaplog_post_dec
|
---|
[484] | 892 | def set_instrument(self, instr):
|
---|
[1846] | 893 | """\
|
---|
[1348] | 894 | Set the instrument for subsequent processing.
|
---|
[1846] | 895 |
|
---|
[358] | 896 | Parameters:
|
---|
[1846] | 897 |
|
---|
[710] | 898 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
|
---|
[407] | 899 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
|
---|
[1846] | 900 |
|
---|
[358] | 901 | """
|
---|
| 902 | self._setInstrument(instr)
|
---|
[1118] | 903 | self._add_history("set_instument", vars())
|
---|
[358] | 904 |
|
---|
[1862] | 905 | @asaplog_post_dec
|
---|
[1190] | 906 | def set_feedtype(self, feedtype):
|
---|
[1846] | 907 | """\
|
---|
[1190] | 908 | Overwrite the feed type, which might not be set correctly.
|
---|
[1846] | 909 |
|
---|
[1190] | 910 | Parameters:
|
---|
[1846] | 911 |
|
---|
[1190] | 912 | feedtype: 'linear' or 'circular'
|
---|
[1846] | 913 |
|
---|
[1190] | 914 | """
|
---|
| 915 | self._setfeedtype(feedtype)
|
---|
| 916 | self._add_history("set_feedtype", vars())
|
---|
| 917 |
|
---|
[1862] | 918 | @asaplog_post_dec
|
---|
[276] | 919 | def set_doppler(self, doppler='RADIO'):
|
---|
[1846] | 920 | """\
|
---|
[276] | 921 | Set the doppler for all following operations on this scantable.
|
---|
[1846] | 922 |
|
---|
[276] | 923 | Parameters:
|
---|
[1846] | 924 |
|
---|
[276] | 925 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
|
---|
[1846] | 926 |
|
---|
[276] | 927 | """
|
---|
[484] | 928 | varlist = vars()
|
---|
[276] | 929 | inf = list(self._getcoordinfo())
|
---|
| 930 | inf[2] = doppler
|
---|
| 931 | self._setcoordinfo(inf)
|
---|
[1118] | 932 | self._add_history("set_doppler", vars())
|
---|
[710] | 933 |
|
---|
[1862] | 934 | @asaplog_post_dec
|
---|
[226] | 935 | def set_freqframe(self, frame=None):
|
---|
[1846] | 936 | """\
|
---|
[113] | 937 | Set the frame type of the Spectral Axis.
|
---|
[1846] | 938 |
|
---|
[113] | 939 | Parameters:
|
---|
[1846] | 940 |
|
---|
[591] | 941 | frame: an optional frame type, default 'LSRK'. Valid frames are:
|
---|
[1819] | 942 | 'TOPO', 'LSRD', 'LSRK', 'BARY',
|
---|
[1118] | 943 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'
|
---|
[1846] | 944 |
|
---|
| 945 | Example::
|
---|
| 946 |
|
---|
[113] | 947 | scan.set_freqframe('BARY')
|
---|
[1846] | 948 |
|
---|
[113] | 949 | """
|
---|
[1593] | 950 | frame = frame or rcParams['scantable.freqframe']
|
---|
[484] | 951 | varlist = vars()
|
---|
[1819] | 952 | # "REST" is not implemented in casacore
|
---|
| 953 | #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
|
---|
| 954 | # 'GEO', 'GALACTO', 'LGROUP', 'CMB']
|
---|
| 955 | valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \
|
---|
[1118] | 956 | 'GEO', 'GALACTO', 'LGROUP', 'CMB']
|
---|
[591] | 957 |
|
---|
[989] | 958 | if frame in valid:
|
---|
[113] | 959 | inf = list(self._getcoordinfo())
|
---|
| 960 | inf[1] = frame
|
---|
| 961 | self._setcoordinfo(inf)
|
---|
[1118] | 962 | self._add_history("set_freqframe", varlist)
|
---|
[102] | 963 | else:
|
---|
[1118] | 964 | msg = "Please specify a valid freq type. Valid types are:\n", valid
|
---|
[1859] | 965 | raise TypeError(msg)
|
---|
[710] | 966 |
|
---|
[1862] | 967 | @asaplog_post_dec
|
---|
[989] | 968 | def set_dirframe(self, frame=""):
|
---|
[1846] | 969 | """\
|
---|
[989] | 970 | Set the frame type of the Direction on the sky.
|
---|
[1846] | 971 |
|
---|
[989] | 972 | Parameters:
|
---|
[1846] | 973 |
|
---|
[989] | 974 | frame: an optional frame type, default ''. Valid frames are:
|
---|
| 975 | 'J2000', 'B1950', 'GALACTIC'
|
---|
[1846] | 976 |
|
---|
| 977 | Example:
|
---|
| 978 |
|
---|
[989] | 979 | scan.set_dirframe('GALACTIC')
|
---|
[1846] | 980 |
|
---|
[989] | 981 | """
|
---|
| 982 | varlist = vars()
|
---|
[1859] | 983 | Scantable.set_dirframe(self, frame)
|
---|
[1118] | 984 | self._add_history("set_dirframe", varlist)
|
---|
[989] | 985 |
|
---|
[113] | 986 | def get_unit(self):
|
---|
[1846] | 987 | """\
|
---|
[113] | 988 | Get the default unit set in this scantable
|
---|
[1846] | 989 |
|
---|
[113] | 990 | Returns:
|
---|
[1846] | 991 |
|
---|
[113] | 992 | A unit string
|
---|
[1846] | 993 |
|
---|
[113] | 994 | """
|
---|
| 995 | inf = self._getcoordinfo()
|
---|
| 996 | unit = inf[0]
|
---|
| 997 | if unit == '': unit = 'channel'
|
---|
| 998 | return unit
|
---|
[102] | 999 |
|
---|
[1862] | 1000 | @asaplog_post_dec
|
---|
[158] | 1001 | def get_abcissa(self, rowno=0):
|
---|
[1846] | 1002 | """\
|
---|
[158] | 1003 | Get the abcissa in the current coordinate setup for the currently
|
---|
[113] | 1004 | selected Beam/IF/Pol
|
---|
[1846] | 1005 |
|
---|
[113] | 1006 | Parameters:
|
---|
[1846] | 1007 |
|
---|
[226] | 1008 | rowno: an optional row number in the scantable. Default is the
|
---|
| 1009 | first row, i.e. rowno=0
|
---|
[1846] | 1010 |
|
---|
[113] | 1011 | Returns:
|
---|
[1846] | 1012 |
|
---|
[1348] | 1013 | The abcissa values and the format string (as a dictionary)
|
---|
[1846] | 1014 |
|
---|
[113] | 1015 | """
|
---|
[256] | 1016 | abc = self._getabcissa(rowno)
|
---|
[710] | 1017 | lbl = self._getabcissalabel(rowno)
|
---|
[158] | 1018 | return abc, lbl
|
---|
[113] | 1019 |
|
---|
[1862] | 1020 | @asaplog_post_dec
|
---|
[1994] | 1021 | def flag(self, row=-1, mask=None, unflag=False):
|
---|
[1846] | 1022 | """\
|
---|
[1001] | 1023 | Flag the selected data using an optional channel mask.
|
---|
[1846] | 1024 |
|
---|
[1001] | 1025 | Parameters:
|
---|
[1846] | 1026 |
|
---|
[1994] | 1027 | row: an optional row number in the scantable.
|
---|
| 1028 | Default -1 flags all rows
|
---|
| 1029 |
|
---|
[1001] | 1030 | mask: an optional channel mask, created with create_mask. Default
|
---|
| 1031 | (no mask) is all channels.
|
---|
[1855] | 1032 |
|
---|
[1819] | 1033 | unflag: if True, unflag the data
|
---|
[1846] | 1034 |
|
---|
[1001] | 1035 | """
|
---|
| 1036 | varlist = vars()
|
---|
[1593] | 1037 | mask = mask or []
|
---|
[1994] | 1038 | self._flag(row, mask, unflag)
|
---|
[1001] | 1039 | self._add_history("flag", varlist)
|
---|
| 1040 |
|
---|
[1862] | 1041 | @asaplog_post_dec
|
---|
[1819] | 1042 | def flag_row(self, rows=[], unflag=False):
|
---|
[1846] | 1043 | """\
|
---|
[1819] | 1044 | Flag the selected data in row-based manner.
|
---|
[1846] | 1045 |
|
---|
[1819] | 1046 | Parameters:
|
---|
[1846] | 1047 |
|
---|
[1843] | 1048 | rows: list of row numbers to be flagged. Default is no row
|
---|
| 1049 | (must be explicitly specified to execute row-based flagging).
|
---|
[1855] | 1050 |
|
---|
[1819] | 1051 | unflag: if True, unflag the data.
|
---|
[1846] | 1052 |
|
---|
[1819] | 1053 | """
|
---|
| 1054 | varlist = vars()
|
---|
[1859] | 1055 | self._flag_row(rows, unflag)
|
---|
[1819] | 1056 | self._add_history("flag_row", varlist)
|
---|
| 1057 |
|
---|
[1862] | 1058 | @asaplog_post_dec
|
---|
[1819] | 1059 | def clip(self, uthres=None, dthres=None, clipoutside=True, unflag=False):
|
---|
[1846] | 1060 | """\
|
---|
[1819] | 1061 | Flag the selected data outside a specified range (in channel-base)
|
---|
[1846] | 1062 |
|
---|
[1819] | 1063 | Parameters:
|
---|
[1846] | 1064 |
|
---|
[1819] | 1065 | uthres: upper threshold.
|
---|
[1855] | 1066 |
|
---|
[1819] | 1067 | dthres: lower threshold
|
---|
[1846] | 1068 |
|
---|
[1819] | 1069 | clipoutside: True for flagging data outside the range [dthres:uthres].
|
---|
[1928] | 1070 | False for flagging data inside the range.
|
---|
[1855] | 1071 |
|
---|
[1846] | 1072 | unflag: if True, unflag the data.
|
---|
| 1073 |
|
---|
[1819] | 1074 | """
|
---|
| 1075 | varlist = vars()
|
---|
[1859] | 1076 | self._clip(uthres, dthres, clipoutside, unflag)
|
---|
[1819] | 1077 | self._add_history("clip", varlist)
|
---|
| 1078 |
|
---|
[1862] | 1079 | @asaplog_post_dec
|
---|
[1584] | 1080 | def lag_flag(self, start, end, unit="MHz", insitu=None):
|
---|
[1846] | 1081 | """\
|
---|
[1192] | 1082 | Flag the data in 'lag' space by providing a frequency to remove.
|
---|
[1584] | 1083 | Flagged data in the scantable gets interpolated over the region.
|
---|
[1192] | 1084 | No taper is applied.
|
---|
[1846] | 1085 |
|
---|
[1192] | 1086 | Parameters:
|
---|
[1846] | 1087 |
|
---|
[1579] | 1088 | start: the start frequency (really a period within the
|
---|
| 1089 | bandwidth) or period to remove
|
---|
[1855] | 1090 |
|
---|
[1579] | 1091 | end: the end frequency or period to remove
|
---|
[1855] | 1092 |
|
---|
[1584] | 1093 | unit: the frequency unit (default "MHz") or "" for
|
---|
[1579] | 1094 | explicit lag channels
|
---|
[1846] | 1095 |
|
---|
| 1096 | *Notes*:
|
---|
| 1097 |
|
---|
[1579] | 1098 | It is recommended to flag edges of the band or strong
|
---|
[1348] | 1099 | signals beforehand.
|
---|
[1846] | 1100 |
|
---|
[1192] | 1101 | """
|
---|
| 1102 | if insitu is None: insitu = rcParams['insitu']
|
---|
| 1103 | self._math._setinsitu(insitu)
|
---|
| 1104 | varlist = vars()
|
---|
[1579] | 1105 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.}
|
---|
| 1106 | if not (unit == "" or base.has_key(unit)):
|
---|
[1192] | 1107 | raise ValueError("%s is not a valid unit." % unit)
|
---|
[1859] | 1108 | if unit == "":
|
---|
| 1109 | s = scantable(self._math._lag_flag(self, start, end, "lags"))
|
---|
| 1110 | else:
|
---|
| 1111 | s = scantable(self._math._lag_flag(self, start*base[unit],
|
---|
| 1112 | end*base[unit], "frequency"))
|
---|
[1192] | 1113 | s._add_history("lag_flag", varlist)
|
---|
| 1114 | if insitu:
|
---|
| 1115 | self._assign(s)
|
---|
| 1116 | else:
|
---|
| 1117 | return s
|
---|
[1001] | 1118 |
|
---|
[1862] | 1119 | @asaplog_post_dec
|
---|
[113] | 1120 | def create_mask(self, *args, **kwargs):
|
---|
[1846] | 1121 | """\
|
---|
[1118] | 1122 | Compute and return a mask based on [min, max] windows.
|
---|
[189] | 1123 | The specified windows are to be INCLUDED, when the mask is
|
---|
[113] | 1124 | applied.
|
---|
[1846] | 1125 |
|
---|
[102] | 1126 | Parameters:
|
---|
[1846] | 1127 |
|
---|
[1118] | 1128 | [min, max], [min2, max2], ...
|
---|
[1024] | 1129 | Pairs of start/end points (inclusive)specifying the regions
|
---|
[102] | 1130 | to be masked
|
---|
[1855] | 1131 |
|
---|
[189] | 1132 | invert: optional argument. If specified as True,
|
---|
| 1133 | return an inverted mask, i.e. the regions
|
---|
| 1134 | specified are EXCLUDED
|
---|
[1855] | 1135 |
|
---|
[513] | 1136 | row: create the mask using the specified row for
|
---|
| 1137 | unit conversions, default is row=0
|
---|
| 1138 | only necessary if frequency varies over rows.
|
---|
[1846] | 1139 |
|
---|
| 1140 | Examples::
|
---|
| 1141 |
|
---|
[113] | 1142 | scan.set_unit('channel')
|
---|
[1846] | 1143 | # a)
|
---|
[1118] | 1144 | msk = scan.create_mask([400, 500], [800, 900])
|
---|
[189] | 1145 | # masks everything outside 400 and 500
|
---|
[113] | 1146 | # and 800 and 900 in the unit 'channel'
|
---|
| 1147 |
|
---|
[1846] | 1148 | # b)
|
---|
[1118] | 1149 | msk = scan.create_mask([400, 500], [800, 900], invert=True)
|
---|
[189] | 1150 | # masks the regions between 400 and 500
|
---|
[113] | 1151 | # and 800 and 900 in the unit 'channel'
|
---|
[1846] | 1152 |
|
---|
| 1153 | # c)
|
---|
| 1154 | #mask only channel 400
|
---|
[1554] | 1155 | msk = scan.create_mask([400])
|
---|
[1846] | 1156 |
|
---|
[102] | 1157 | """
|
---|
[1554] | 1158 | row = kwargs.get("row", 0)
|
---|
[513] | 1159 | data = self._getabcissa(row)
|
---|
[113] | 1160 | u = self._getcoordinfo()[0]
|
---|
[1859] | 1161 | if u == "":
|
---|
| 1162 | u = "channel"
|
---|
| 1163 | msg = "The current mask window unit is %s" % u
|
---|
| 1164 | i = self._check_ifs()
|
---|
| 1165 | if not i:
|
---|
| 1166 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
---|
| 1167 | asaplog.push(msg)
|
---|
[102] | 1168 | n = self.nchan()
|
---|
[1295] | 1169 | msk = _n_bools(n, False)
|
---|
[710] | 1170 | # test if args is a 'list' or a 'normal *args - UGLY!!!
|
---|
| 1171 |
|
---|
[1118] | 1172 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
|
---|
| 1173 | and args or args[0]
|
---|
[710] | 1174 | for window in ws:
|
---|
[1554] | 1175 | if len(window) == 1:
|
---|
| 1176 | window = [window[0], window[0]]
|
---|
| 1177 | if len(window) == 0 or len(window) > 2:
|
---|
| 1178 | raise ValueError("A window needs to be defined as [start(, end)]")
|
---|
[1545] | 1179 | if window[0] > window[1]:
|
---|
| 1180 | tmp = window[0]
|
---|
| 1181 | window[0] = window[1]
|
---|
| 1182 | window[1] = tmp
|
---|
[102] | 1183 | for i in range(n):
|
---|
[1024] | 1184 | if data[i] >= window[0] and data[i] <= window[1]:
|
---|
[1295] | 1185 | msk[i] = True
|
---|
[113] | 1186 | if kwargs.has_key('invert'):
|
---|
| 1187 | if kwargs.get('invert'):
|
---|
[1295] | 1188 | msk = mask_not(msk)
|
---|
[102] | 1189 | return msk
|
---|
[710] | 1190 |
|
---|
[1931] | 1191 | def get_masklist(self, mask=None, row=0, silent=False):
|
---|
[1846] | 1192 | """\
|
---|
[1819] | 1193 | Compute and return a list of mask windows, [min, max].
|
---|
[1846] | 1194 |
|
---|
[1819] | 1195 | Parameters:
|
---|
[1846] | 1196 |
|
---|
[1819] | 1197 | mask: channel mask, created with create_mask.
|
---|
[1855] | 1198 |
|
---|
[1819] | 1199 | row: calcutate the masklist using the specified row
|
---|
| 1200 | for unit conversions, default is row=0
|
---|
| 1201 | only necessary if frequency varies over rows.
|
---|
[1846] | 1202 |
|
---|
[1819] | 1203 | Returns:
|
---|
[1846] | 1204 |
|
---|
[1819] | 1205 | [min, max], [min2, max2], ...
|
---|
| 1206 | Pairs of start/end points (inclusive)specifying
|
---|
| 1207 | the masked regions
|
---|
[1846] | 1208 |
|
---|
[1819] | 1209 | """
|
---|
| 1210 | if not (isinstance(mask,list) or isinstance(mask, tuple)):
|
---|
| 1211 | raise TypeError("The mask should be list or tuple.")
|
---|
| 1212 | if len(mask) < 2:
|
---|
| 1213 | raise TypeError("The mask elements should be > 1")
|
---|
| 1214 | if self.nchan() != len(mask):
|
---|
| 1215 | msg = "Number of channels in scantable != number of mask elements"
|
---|
| 1216 | raise TypeError(msg)
|
---|
| 1217 | data = self._getabcissa(row)
|
---|
| 1218 | u = self._getcoordinfo()[0]
|
---|
[1859] | 1219 | if u == "":
|
---|
| 1220 | u = "channel"
|
---|
| 1221 | msg = "The current mask window unit is %s" % u
|
---|
| 1222 | i = self._check_ifs()
|
---|
| 1223 | if not i:
|
---|
| 1224 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
---|
[1931] | 1225 | if not silent:
|
---|
| 1226 | asaplog.push(msg)
|
---|
[1819] | 1227 | masklist=[]
|
---|
| 1228 | ist, ien = None, None
|
---|
| 1229 | ist, ien=self.get_mask_indices(mask)
|
---|
| 1230 | if ist is not None and ien is not None:
|
---|
| 1231 | for i in xrange(len(ist)):
|
---|
| 1232 | range=[data[ist[i]],data[ien[i]]]
|
---|
| 1233 | range.sort()
|
---|
| 1234 | masklist.append([range[0],range[1]])
|
---|
| 1235 | return masklist
|
---|
| 1236 |
|
---|
| 1237 | def get_mask_indices(self, mask=None):
|
---|
[1846] | 1238 | """\
|
---|
[1819] | 1239 | Compute and Return lists of mask start indices and mask end indices.
|
---|
[1855] | 1240 |
|
---|
| 1241 | Parameters:
|
---|
| 1242 |
|
---|
[1819] | 1243 | mask: channel mask, created with create_mask.
|
---|
[1846] | 1244 |
|
---|
[1819] | 1245 | Returns:
|
---|
[1846] | 1246 |
|
---|
[1819] | 1247 | List of mask start indices and that of mask end indices,
|
---|
| 1248 | i.e., [istart1,istart2,....], [iend1,iend2,....].
|
---|
[1846] | 1249 |
|
---|
[1819] | 1250 | """
|
---|
| 1251 | if not (isinstance(mask,list) or isinstance(mask, tuple)):
|
---|
| 1252 | raise TypeError("The mask should be list or tuple.")
|
---|
| 1253 | if len(mask) < 2:
|
---|
| 1254 | raise TypeError("The mask elements should be > 1")
|
---|
| 1255 | istart=[]
|
---|
| 1256 | iend=[]
|
---|
| 1257 | if mask[0]: istart.append(0)
|
---|
| 1258 | for i in range(len(mask)-1):
|
---|
| 1259 | if not mask[i] and mask[i+1]:
|
---|
| 1260 | istart.append(i+1)
|
---|
| 1261 | elif mask[i] and not mask[i+1]:
|
---|
| 1262 | iend.append(i)
|
---|
| 1263 | if mask[len(mask)-1]: iend.append(len(mask)-1)
|
---|
| 1264 | if len(istart) != len(iend):
|
---|
| 1265 | raise RuntimeError("Numbers of mask start != mask end.")
|
---|
| 1266 | for i in range(len(istart)):
|
---|
| 1267 | if istart[i] > iend[i]:
|
---|
| 1268 | raise RuntimeError("Mask start index > mask end index")
|
---|
| 1269 | break
|
---|
| 1270 | return istart,iend
|
---|
| 1271 |
|
---|
| 1272 | # def get_restfreqs(self):
|
---|
| 1273 | # """
|
---|
| 1274 | # Get the restfrequency(s) stored in this scantable.
|
---|
| 1275 | # The return value(s) are always of unit 'Hz'
|
---|
| 1276 | # Parameters:
|
---|
| 1277 | # none
|
---|
| 1278 | # Returns:
|
---|
| 1279 | # a list of doubles
|
---|
| 1280 | # """
|
---|
| 1281 | # return list(self._getrestfreqs())
|
---|
| 1282 |
|
---|
| 1283 | def get_restfreqs(self, ids=None):
|
---|
[1846] | 1284 | """\
|
---|
[256] | 1285 | Get the restfrequency(s) stored in this scantable.
|
---|
| 1286 | The return value(s) are always of unit 'Hz'
|
---|
[1846] | 1287 |
|
---|
[256] | 1288 | Parameters:
|
---|
[1846] | 1289 |
|
---|
[1819] | 1290 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to
|
---|
| 1291 | be retrieved
|
---|
[1846] | 1292 |
|
---|
[256] | 1293 | Returns:
|
---|
[1846] | 1294 |
|
---|
[1819] | 1295 | dictionary containing ids and a list of doubles for each id
|
---|
[1846] | 1296 |
|
---|
[256] | 1297 | """
|
---|
[1819] | 1298 | if ids is None:
|
---|
| 1299 | rfreqs={}
|
---|
| 1300 | idlist = self.getmolnos()
|
---|
| 1301 | for i in idlist:
|
---|
| 1302 | rfreqs[i]=list(self._getrestfreqs(i))
|
---|
| 1303 | return rfreqs
|
---|
| 1304 | else:
|
---|
| 1305 | if type(ids)==list or type(ids)==tuple:
|
---|
| 1306 | rfreqs={}
|
---|
| 1307 | for i in ids:
|
---|
| 1308 | rfreqs[i]=list(self._getrestfreqs(i))
|
---|
| 1309 | return rfreqs
|
---|
| 1310 | else:
|
---|
| 1311 | return list(self._getrestfreqs(ids))
|
---|
| 1312 | #return list(self._getrestfreqs(ids))
|
---|
[102] | 1313 |
|
---|
[931] | 1314 | def set_restfreqs(self, freqs=None, unit='Hz'):
|
---|
[1846] | 1315 | """\
|
---|
[931] | 1316 | Set or replace the restfrequency specified and
|
---|
[1938] | 1317 | if the 'freqs' argument holds a scalar,
|
---|
[931] | 1318 | then that rest frequency will be applied to all the selected
|
---|
| 1319 | data. If the 'freqs' argument holds
|
---|
| 1320 | a vector, then it MUST be of equal or smaller length than
|
---|
| 1321 | the number of IFs (and the available restfrequencies will be
|
---|
| 1322 | replaced by this vector). In this case, *all* data have
|
---|
| 1323 | the restfrequency set per IF according
|
---|
| 1324 | to the corresponding value you give in the 'freqs' vector.
|
---|
[1118] | 1325 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
|
---|
[931] | 1326 | IF 1 gets restfreq 2e9.
|
---|
[1846] | 1327 |
|
---|
[1395] | 1328 | You can also specify the frequencies via a linecatalog.
|
---|
[1153] | 1329 |
|
---|
[931] | 1330 | Parameters:
|
---|
[1846] | 1331 |
|
---|
[931] | 1332 | freqs: list of rest frequency values or string idenitfiers
|
---|
[1855] | 1333 |
|
---|
[931] | 1334 | unit: unit for rest frequency (default 'Hz')
|
---|
[402] | 1335 |
|
---|
[1846] | 1336 |
|
---|
| 1337 | Example::
|
---|
| 1338 |
|
---|
[1819] | 1339 | # set the given restfrequency for the all currently selected IFs
|
---|
[931] | 1340 | scan.set_restfreqs(freqs=1.4e9)
|
---|
[1845] | 1341 | # set restfrequencies for the n IFs (n > 1) in the order of the
|
---|
| 1342 | # list, i.e
|
---|
| 1343 | # IF0 -> 1.4e9, IF1 -> 1.41e9, IF3 -> 1.42e9
|
---|
| 1344 | # len(list_of_restfreqs) == nIF
|
---|
| 1345 | # for nIF == 1 the following will set multiple restfrequency for
|
---|
| 1346 | # that IF
|
---|
[1819] | 1347 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9])
|
---|
[1845] | 1348 | # set multiple restfrequencies per IF. as a list of lists where
|
---|
| 1349 | # the outer list has nIF elements, the inner s arbitrary
|
---|
| 1350 | scan.set_restfreqs(freqs=[[1.4e9, 1.41e9], [1.67e9]])
|
---|
[391] | 1351 |
|
---|
[1846] | 1352 | *Note*:
|
---|
[1845] | 1353 |
|
---|
[931] | 1354 | To do more sophisticate Restfrequency setting, e.g. on a
|
---|
| 1355 | source and IF basis, use scantable.set_selection() before using
|
---|
[1846] | 1356 | this function::
|
---|
[931] | 1357 |
|
---|
[1846] | 1358 | # provided your scantable is called scan
|
---|
| 1359 | selection = selector()
|
---|
| 1360 | selection.set_name("ORION*")
|
---|
| 1361 | selection.set_ifs([1])
|
---|
| 1362 | scan.set_selection(selection)
|
---|
| 1363 | scan.set_restfreqs(freqs=86.6e9)
|
---|
| 1364 |
|
---|
[931] | 1365 | """
|
---|
| 1366 | varlist = vars()
|
---|
[1157] | 1367 | from asap import linecatalog
|
---|
| 1368 | # simple value
|
---|
[1118] | 1369 | if isinstance(freqs, int) or isinstance(freqs, float):
|
---|
[1845] | 1370 | self._setrestfreqs([freqs], [""], unit)
|
---|
[1157] | 1371 | # list of values
|
---|
[1118] | 1372 | elif isinstance(freqs, list) or isinstance(freqs, tuple):
|
---|
[1157] | 1373 | # list values are scalars
|
---|
[1118] | 1374 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
|
---|
[1845] | 1375 | if len(freqs) == 1:
|
---|
| 1376 | self._setrestfreqs(freqs, [""], unit)
|
---|
| 1377 | else:
|
---|
| 1378 | # allow the 'old' mode of setting mulitple IFs
|
---|
| 1379 | sel = selector()
|
---|
| 1380 | savesel = self._getselection()
|
---|
| 1381 | iflist = self.getifnos()
|
---|
| 1382 | if len(freqs)>len(iflist):
|
---|
| 1383 | raise ValueError("number of elements in list of list "
|
---|
| 1384 | "exeeds the current IF selections")
|
---|
| 1385 | iflist = self.getifnos()
|
---|
| 1386 | for i, fval in enumerate(freqs):
|
---|
| 1387 | sel.set_ifs(iflist[i])
|
---|
| 1388 | self._setselection(sel)
|
---|
| 1389 | self._setrestfreqs([fval], [""], unit)
|
---|
| 1390 | self._setselection(savesel)
|
---|
| 1391 |
|
---|
| 1392 | # list values are dict, {'value'=, 'name'=)
|
---|
[1157] | 1393 | elif isinstance(freqs[-1], dict):
|
---|
[1845] | 1394 | values = []
|
---|
| 1395 | names = []
|
---|
| 1396 | for d in freqs:
|
---|
| 1397 | values.append(d["value"])
|
---|
| 1398 | names.append(d["name"])
|
---|
| 1399 | self._setrestfreqs(values, names, unit)
|
---|
[1819] | 1400 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple):
|
---|
[1157] | 1401 | sel = selector()
|
---|
| 1402 | savesel = self._getselection()
|
---|
[1322] | 1403 | iflist = self.getifnos()
|
---|
[1819] | 1404 | if len(freqs)>len(iflist):
|
---|
[1845] | 1405 | raise ValueError("number of elements in list of list exeeds"
|
---|
| 1406 | " the current IF selections")
|
---|
| 1407 | for i, fval in enumerate(freqs):
|
---|
[1322] | 1408 | sel.set_ifs(iflist[i])
|
---|
[1259] | 1409 | self._setselection(sel)
|
---|
[1845] | 1410 | self._setrestfreqs(fval, [""], unit)
|
---|
[1157] | 1411 | self._setselection(savesel)
|
---|
| 1412 | # freqs are to be taken from a linecatalog
|
---|
[1153] | 1413 | elif isinstance(freqs, linecatalog):
|
---|
| 1414 | sel = selector()
|
---|
| 1415 | savesel = self._getselection()
|
---|
| 1416 | for i in xrange(freqs.nrow()):
|
---|
[1322] | 1417 | sel.set_ifs(iflist[i])
|
---|
[1153] | 1418 | self._setselection(sel)
|
---|
[1845] | 1419 | self._setrestfreqs([freqs.get_frequency(i)],
|
---|
| 1420 | [freqs.get_name(i)], "MHz")
|
---|
[1153] | 1421 | # ensure that we are not iterating past nIF
|
---|
| 1422 | if i == self.nif()-1: break
|
---|
| 1423 | self._setselection(savesel)
|
---|
[931] | 1424 | else:
|
---|
| 1425 | return
|
---|
| 1426 | self._add_history("set_restfreqs", varlist)
|
---|
| 1427 |
|
---|
[1360] | 1428 | def shift_refpix(self, delta):
|
---|
[1846] | 1429 | """\
|
---|
[1589] | 1430 | Shift the reference pixel of the Spectra Coordinate by an
|
---|
| 1431 | integer amount.
|
---|
[1846] | 1432 |
|
---|
[1589] | 1433 | Parameters:
|
---|
[1846] | 1434 |
|
---|
[1589] | 1435 | delta: the amount to shift by
|
---|
[1846] | 1436 |
|
---|
| 1437 | *Note*:
|
---|
| 1438 |
|
---|
[1589] | 1439 | Be careful using this with broadband data.
|
---|
[1846] | 1440 |
|
---|
[1360] | 1441 | """
|
---|
[1731] | 1442 | Scantable.shift_refpix(self, delta)
|
---|
[931] | 1443 |
|
---|
[1862] | 1444 | @asaplog_post_dec
|
---|
[1259] | 1445 | def history(self, filename=None):
|
---|
[1846] | 1446 | """\
|
---|
[1259] | 1447 | Print the history. Optionally to a file.
|
---|
[1846] | 1448 |
|
---|
[1348] | 1449 | Parameters:
|
---|
[1846] | 1450 |
|
---|
[1928] | 1451 | filename: The name of the file to save the history to.
|
---|
[1846] | 1452 |
|
---|
[1259] | 1453 | """
|
---|
[484] | 1454 | hist = list(self._gethistory())
|
---|
[794] | 1455 | out = "-"*80
|
---|
[484] | 1456 | for h in hist:
|
---|
[489] | 1457 | if h.startswith("---"):
|
---|
[1857] | 1458 | out = "\n".join([out, h])
|
---|
[489] | 1459 | else:
|
---|
| 1460 | items = h.split("##")
|
---|
| 1461 | date = items[0]
|
---|
| 1462 | func = items[1]
|
---|
| 1463 | items = items[2:]
|
---|
[794] | 1464 | out += "\n"+date+"\n"
|
---|
| 1465 | out += "Function: %s\n Parameters:" % (func)
|
---|
[489] | 1466 | for i in items:
|
---|
[1938] | 1467 | if i == '':
|
---|
| 1468 | continue
|
---|
[489] | 1469 | s = i.split("=")
|
---|
[1118] | 1470 | out += "\n %s = %s" % (s[0], s[1])
|
---|
[1857] | 1471 | out = "\n".join([out, "-"*80])
|
---|
[1259] | 1472 | if filename is not None:
|
---|
| 1473 | if filename is "":
|
---|
| 1474 | filename = 'scantable_history.txt'
|
---|
| 1475 | import os
|
---|
| 1476 | filename = os.path.expandvars(os.path.expanduser(filename))
|
---|
| 1477 | if not os.path.isdir(filename):
|
---|
| 1478 | data = open(filename, 'w')
|
---|
| 1479 | data.write(out)
|
---|
| 1480 | data.close()
|
---|
| 1481 | else:
|
---|
| 1482 | msg = "Illegal file name '%s'." % (filename)
|
---|
[1859] | 1483 | raise IOError(msg)
|
---|
| 1484 | return page(out)
|
---|
[513] | 1485 | #
|
---|
| 1486 | # Maths business
|
---|
| 1487 | #
|
---|
[1862] | 1488 | @asaplog_post_dec
|
---|
[931] | 1489 | def average_time(self, mask=None, scanav=False, weight='tint', align=False):
|
---|
[1846] | 1490 | """\
|
---|
[1070] | 1491 | Return the (time) weighted average of a scan.
|
---|
[1846] | 1492 |
|
---|
| 1493 | *Note*:
|
---|
| 1494 |
|
---|
[1070] | 1495 | in channels only - align if necessary
|
---|
[1846] | 1496 |
|
---|
[513] | 1497 | Parameters:
|
---|
[1846] | 1498 |
|
---|
[513] | 1499 | mask: an optional mask (only used for 'var' and 'tsys'
|
---|
| 1500 | weighting)
|
---|
[1855] | 1501 |
|
---|
[558] | 1502 | scanav: True averages each scan separately
|
---|
| 1503 | False (default) averages all scans together,
|
---|
[1855] | 1504 |
|
---|
[1099] | 1505 | weight: Weighting scheme.
|
---|
| 1506 | 'none' (mean no weight)
|
---|
| 1507 | 'var' (1/var(spec) weighted)
|
---|
| 1508 | 'tsys' (1/Tsys**2 weighted)
|
---|
| 1509 | 'tint' (integration time weighted)
|
---|
| 1510 | 'tintsys' (Tint/Tsys**2)
|
---|
| 1511 | 'median' ( median averaging)
|
---|
[535] | 1512 | The default is 'tint'
|
---|
[1855] | 1513 |
|
---|
[931] | 1514 | align: align the spectra in velocity before averaging. It takes
|
---|
| 1515 | the time of the first spectrum as reference time.
|
---|
[1846] | 1516 |
|
---|
| 1517 | Example::
|
---|
| 1518 |
|
---|
[513] | 1519 | # time average the scantable without using a mask
|
---|
[710] | 1520 | newscan = scan.average_time()
|
---|
[1846] | 1521 |
|
---|
[513] | 1522 | """
|
---|
| 1523 | varlist = vars()
|
---|
[1593] | 1524 | weight = weight or 'TINT'
|
---|
| 1525 | mask = mask or ()
|
---|
| 1526 | scanav = (scanav and 'SCAN') or 'NONE'
|
---|
[1118] | 1527 | scan = (self, )
|
---|
[1859] | 1528 |
|
---|
| 1529 | if align:
|
---|
| 1530 | scan = (self.freq_align(insitu=False), )
|
---|
| 1531 | s = None
|
---|
| 1532 | if weight.upper() == 'MEDIAN':
|
---|
| 1533 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
|
---|
| 1534 | scanav))
|
---|
| 1535 | else:
|
---|
| 1536 | s = scantable(self._math._average(scan, mask, weight.upper(),
|
---|
| 1537 | scanav))
|
---|
[1099] | 1538 | s._add_history("average_time", varlist)
|
---|
[513] | 1539 | return s
|
---|
[710] | 1540 |
|
---|
[1862] | 1541 | @asaplog_post_dec
|
---|
[876] | 1542 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
|
---|
[1846] | 1543 | """\
|
---|
[513] | 1544 | Return a scan where all spectra are converted to either
|
---|
| 1545 | Jansky or Kelvin depending upon the flux units of the scan table.
|
---|
| 1546 | By default the function tries to look the values up internally.
|
---|
| 1547 | If it can't find them (or if you want to over-ride), you must
|
---|
| 1548 | specify EITHER jyperk OR eta (and D which it will try to look up
|
---|
| 1549 | also if you don't set it). jyperk takes precedence if you set both.
|
---|
[1846] | 1550 |
|
---|
[513] | 1551 | Parameters:
|
---|
[1846] | 1552 |
|
---|
[513] | 1553 | jyperk: the Jy / K conversion factor
|
---|
[1855] | 1554 |
|
---|
[513] | 1555 | eta: the aperture efficiency
|
---|
[1855] | 1556 |
|
---|
[1928] | 1557 | d: the geometric diameter (metres)
|
---|
[1855] | 1558 |
|
---|
[513] | 1559 | insitu: if False a new scantable is returned.
|
---|
| 1560 | Otherwise, the scaling is done in-situ
|
---|
| 1561 | The default is taken from .asaprc (False)
|
---|
[1846] | 1562 |
|
---|
[513] | 1563 | """
|
---|
| 1564 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1565 | self._math._setinsitu(insitu)
|
---|
[513] | 1566 | varlist = vars()
|
---|
[1593] | 1567 | jyperk = jyperk or -1.0
|
---|
| 1568 | d = d or -1.0
|
---|
| 1569 | eta = eta or -1.0
|
---|
[876] | 1570 | s = scantable(self._math._convertflux(self, d, eta, jyperk))
|
---|
| 1571 | s._add_history("convert_flux", varlist)
|
---|
| 1572 | if insitu: self._assign(s)
|
---|
| 1573 | else: return s
|
---|
[513] | 1574 |
|
---|
[1862] | 1575 | @asaplog_post_dec
|
---|
[876] | 1576 | def gain_el(self, poly=None, filename="", method="linear", insitu=None):
|
---|
[1846] | 1577 | """\
|
---|
[513] | 1578 | Return a scan after applying a gain-elevation correction.
|
---|
| 1579 | The correction can be made via either a polynomial or a
|
---|
| 1580 | table-based interpolation (and extrapolation if necessary).
|
---|
| 1581 | You specify polynomial coefficients, an ascii table or neither.
|
---|
| 1582 | If you specify neither, then a polynomial correction will be made
|
---|
| 1583 | with built in coefficients known for certain telescopes (an error
|
---|
| 1584 | will occur if the instrument is not known).
|
---|
| 1585 | The data and Tsys are *divided* by the scaling factors.
|
---|
[1846] | 1586 |
|
---|
[513] | 1587 | Parameters:
|
---|
[1846] | 1588 |
|
---|
[513] | 1589 | poly: Polynomial coefficients (default None) to compute a
|
---|
| 1590 | gain-elevation correction as a function of
|
---|
| 1591 | elevation (in degrees).
|
---|
[1855] | 1592 |
|
---|
[513] | 1593 | filename: The name of an ascii file holding correction factors.
|
---|
| 1594 | The first row of the ascii file must give the column
|
---|
| 1595 | names and these MUST include columns
|
---|
| 1596 | "ELEVATION" (degrees) and "FACTOR" (multiply data
|
---|
| 1597 | by this) somewhere.
|
---|
| 1598 | The second row must give the data type of the
|
---|
| 1599 | column. Use 'R' for Real and 'I' for Integer.
|
---|
| 1600 | An example file would be
|
---|
| 1601 | (actual factors are arbitrary) :
|
---|
| 1602 |
|
---|
| 1603 | TIME ELEVATION FACTOR
|
---|
| 1604 | R R R
|
---|
| 1605 | 0.1 0 0.8
|
---|
| 1606 | 0.2 20 0.85
|
---|
| 1607 | 0.3 40 0.9
|
---|
| 1608 | 0.4 60 0.85
|
---|
| 1609 | 0.5 80 0.8
|
---|
| 1610 | 0.6 90 0.75
|
---|
[1855] | 1611 |
|
---|
[513] | 1612 | method: Interpolation method when correcting from a table.
|
---|
| 1613 | Values are "nearest", "linear" (default), "cubic"
|
---|
| 1614 | and "spline"
|
---|
[1855] | 1615 |
|
---|
[513] | 1616 | insitu: if False a new scantable is returned.
|
---|
| 1617 | Otherwise, the scaling is done in-situ
|
---|
| 1618 | The default is taken from .asaprc (False)
|
---|
[1846] | 1619 |
|
---|
[513] | 1620 | """
|
---|
| 1621 |
|
---|
| 1622 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1623 | self._math._setinsitu(insitu)
|
---|
[513] | 1624 | varlist = vars()
|
---|
[1593] | 1625 | poly = poly or ()
|
---|
[513] | 1626 | from os.path import expandvars
|
---|
| 1627 | filename = expandvars(filename)
|
---|
[876] | 1628 | s = scantable(self._math._gainel(self, poly, filename, method))
|
---|
| 1629 | s._add_history("gain_el", varlist)
|
---|
[1593] | 1630 | if insitu:
|
---|
| 1631 | self._assign(s)
|
---|
| 1632 | else:
|
---|
| 1633 | return s
|
---|
[710] | 1634 |
|
---|
[1862] | 1635 | @asaplog_post_dec
|
---|
[931] | 1636 | def freq_align(self, reftime=None, method='cubic', insitu=None):
|
---|
[1846] | 1637 | """\
|
---|
[513] | 1638 | Return a scan where all rows have been aligned in frequency/velocity.
|
---|
| 1639 | The alignment frequency frame (e.g. LSRK) is that set by function
|
---|
| 1640 | set_freqframe.
|
---|
[1846] | 1641 |
|
---|
[513] | 1642 | Parameters:
|
---|
[1855] | 1643 |
|
---|
[513] | 1644 | reftime: reference time to align at. By default, the time of
|
---|
| 1645 | the first row of data is used.
|
---|
[1855] | 1646 |
|
---|
[513] | 1647 | method: Interpolation method for regridding the spectra.
|
---|
| 1648 | Choose from "nearest", "linear", "cubic" (default)
|
---|
| 1649 | and "spline"
|
---|
[1855] | 1650 |
|
---|
[513] | 1651 | insitu: if False a new scantable is returned.
|
---|
| 1652 | Otherwise, the scaling is done in-situ
|
---|
| 1653 | The default is taken from .asaprc (False)
|
---|
[1846] | 1654 |
|
---|
[513] | 1655 | """
|
---|
[931] | 1656 | if insitu is None: insitu = rcParams["insitu"]
|
---|
[876] | 1657 | self._math._setinsitu(insitu)
|
---|
[513] | 1658 | varlist = vars()
|
---|
[1593] | 1659 | reftime = reftime or ""
|
---|
[931] | 1660 | s = scantable(self._math._freq_align(self, reftime, method))
|
---|
[876] | 1661 | s._add_history("freq_align", varlist)
|
---|
| 1662 | if insitu: self._assign(s)
|
---|
| 1663 | else: return s
|
---|
[513] | 1664 |
|
---|
[1862] | 1665 | @asaplog_post_dec
|
---|
[1725] | 1666 | def opacity(self, tau=None, insitu=None):
|
---|
[1846] | 1667 | """\
|
---|
[513] | 1668 | Apply an opacity correction. The data
|
---|
| 1669 | and Tsys are multiplied by the correction factor.
|
---|
[1846] | 1670 |
|
---|
[513] | 1671 | Parameters:
|
---|
[1855] | 1672 |
|
---|
[1689] | 1673 | tau: (list of) opacity from which the correction factor is
|
---|
[513] | 1674 | exp(tau*ZD)
|
---|
[1689] | 1675 | where ZD is the zenith-distance.
|
---|
| 1676 | If a list is provided, it has to be of length nIF,
|
---|
| 1677 | nIF*nPol or 1 and in order of IF/POL, e.g.
|
---|
| 1678 | [opif0pol0, opif0pol1, opif1pol0 ...]
|
---|
[1725] | 1679 | if tau is `None` the opacities are determined from a
|
---|
| 1680 | model.
|
---|
[1855] | 1681 |
|
---|
[513] | 1682 | insitu: if False a new scantable is returned.
|
---|
| 1683 | Otherwise, the scaling is done in-situ
|
---|
| 1684 | The default is taken from .asaprc (False)
|
---|
[1846] | 1685 |
|
---|
[513] | 1686 | """
|
---|
| 1687 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1688 | self._math._setinsitu(insitu)
|
---|
[513] | 1689 | varlist = vars()
|
---|
[1689] | 1690 | if not hasattr(tau, "__len__"):
|
---|
| 1691 | tau = [tau]
|
---|
[876] | 1692 | s = scantable(self._math._opacity(self, tau))
|
---|
| 1693 | s._add_history("opacity", varlist)
|
---|
| 1694 | if insitu: self._assign(s)
|
---|
| 1695 | else: return s
|
---|
[513] | 1696 |
|
---|
[1862] | 1697 | @asaplog_post_dec
|
---|
[513] | 1698 | def bin(self, width=5, insitu=None):
|
---|
[1846] | 1699 | """\
|
---|
[513] | 1700 | Return a scan where all spectra have been binned up.
|
---|
[1846] | 1701 |
|
---|
[1348] | 1702 | Parameters:
|
---|
[1846] | 1703 |
|
---|
[513] | 1704 | width: The bin width (default=5) in pixels
|
---|
[1855] | 1705 |
|
---|
[513] | 1706 | insitu: if False a new scantable is returned.
|
---|
| 1707 | Otherwise, the scaling is done in-situ
|
---|
| 1708 | The default is taken from .asaprc (False)
|
---|
[1846] | 1709 |
|
---|
[513] | 1710 | """
|
---|
| 1711 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1712 | self._math._setinsitu(insitu)
|
---|
[513] | 1713 | varlist = vars()
|
---|
[876] | 1714 | s = scantable(self._math._bin(self, width))
|
---|
[1118] | 1715 | s._add_history("bin", varlist)
|
---|
[1589] | 1716 | if insitu:
|
---|
| 1717 | self._assign(s)
|
---|
| 1718 | else:
|
---|
| 1719 | return s
|
---|
[513] | 1720 |
|
---|
[1862] | 1721 | @asaplog_post_dec
|
---|
[513] | 1722 | def resample(self, width=5, method='cubic', insitu=None):
|
---|
[1846] | 1723 | """\
|
---|
[1348] | 1724 | Return a scan where all spectra have been binned up.
|
---|
[1573] | 1725 |
|
---|
[1348] | 1726 | Parameters:
|
---|
[1846] | 1727 |
|
---|
[513] | 1728 | width: The bin width (default=5) in pixels
|
---|
[1855] | 1729 |
|
---|
[513] | 1730 | method: Interpolation method when correcting from a table.
|
---|
| 1731 | Values are "nearest", "linear", "cubic" (default)
|
---|
| 1732 | and "spline"
|
---|
[1855] | 1733 |
|
---|
[513] | 1734 | insitu: if False a new scantable is returned.
|
---|
| 1735 | Otherwise, the scaling is done in-situ
|
---|
| 1736 | The default is taken from .asaprc (False)
|
---|
[1846] | 1737 |
|
---|
[513] | 1738 | """
|
---|
| 1739 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1740 | self._math._setinsitu(insitu)
|
---|
[513] | 1741 | varlist = vars()
|
---|
[876] | 1742 | s = scantable(self._math._resample(self, method, width))
|
---|
[1118] | 1743 | s._add_history("resample", varlist)
|
---|
[876] | 1744 | if insitu: self._assign(s)
|
---|
| 1745 | else: return s
|
---|
[513] | 1746 |
|
---|
[1862] | 1747 | @asaplog_post_dec
|
---|
[946] | 1748 | def average_pol(self, mask=None, weight='none'):
|
---|
[1846] | 1749 | """\
|
---|
[946] | 1750 | Average the Polarisations together.
|
---|
[1846] | 1751 |
|
---|
[946] | 1752 | Parameters:
|
---|
[1846] | 1753 |
|
---|
[946] | 1754 | mask: An optional mask defining the region, where the
|
---|
| 1755 | averaging will be applied. The output will have all
|
---|
| 1756 | specified points masked.
|
---|
[1855] | 1757 |
|
---|
[946] | 1758 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
---|
| 1759 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
---|
[1846] | 1760 |
|
---|
[946] | 1761 | """
|
---|
| 1762 | varlist = vars()
|
---|
[1593] | 1763 | mask = mask or ()
|
---|
[1010] | 1764 | s = scantable(self._math._averagepol(self, mask, weight.upper()))
|
---|
[1118] | 1765 | s._add_history("average_pol", varlist)
|
---|
[992] | 1766 | return s
|
---|
[513] | 1767 |
|
---|
[1862] | 1768 | @asaplog_post_dec
|
---|
[1145] | 1769 | def average_beam(self, mask=None, weight='none'):
|
---|
[1846] | 1770 | """\
|
---|
[1145] | 1771 | Average the Beams together.
|
---|
[1846] | 1772 |
|
---|
[1145] | 1773 | Parameters:
|
---|
| 1774 | mask: An optional mask defining the region, where the
|
---|
| 1775 | averaging will be applied. The output will have all
|
---|
| 1776 | specified points masked.
|
---|
[1855] | 1777 |
|
---|
[1145] | 1778 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
---|
| 1779 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
---|
[1846] | 1780 |
|
---|
[1145] | 1781 | """
|
---|
| 1782 | varlist = vars()
|
---|
[1593] | 1783 | mask = mask or ()
|
---|
[1145] | 1784 | s = scantable(self._math._averagebeams(self, mask, weight.upper()))
|
---|
| 1785 | s._add_history("average_beam", varlist)
|
---|
| 1786 | return s
|
---|
| 1787 |
|
---|
[1586] | 1788 | def parallactify(self, pflag):
|
---|
[1846] | 1789 | """\
|
---|
[1843] | 1790 | Set a flag to indicate whether this data should be treated as having
|
---|
[1617] | 1791 | been 'parallactified' (total phase == 0.0)
|
---|
[1846] | 1792 |
|
---|
[1617] | 1793 | Parameters:
|
---|
[1855] | 1794 |
|
---|
[1843] | 1795 | pflag: Bool indicating whether to turn this on (True) or
|
---|
[1617] | 1796 | off (False)
|
---|
[1846] | 1797 |
|
---|
[1617] | 1798 | """
|
---|
[1586] | 1799 | varlist = vars()
|
---|
| 1800 | self._parallactify(pflag)
|
---|
| 1801 | self._add_history("parallactify", varlist)
|
---|
| 1802 |
|
---|
[1862] | 1803 | @asaplog_post_dec
|
---|
[992] | 1804 | def convert_pol(self, poltype=None):
|
---|
[1846] | 1805 | """\
|
---|
[992] | 1806 | Convert the data to a different polarisation type.
|
---|
[1565] | 1807 | Note that you will need cross-polarisation terms for most conversions.
|
---|
[1846] | 1808 |
|
---|
[992] | 1809 | Parameters:
|
---|
[1855] | 1810 |
|
---|
[992] | 1811 | poltype: The new polarisation type. Valid types are:
|
---|
[1565] | 1812 | "linear", "circular", "stokes" and "linpol"
|
---|
[1846] | 1813 |
|
---|
[992] | 1814 | """
|
---|
| 1815 | varlist = vars()
|
---|
[1859] | 1816 | s = scantable(self._math._convertpol(self, poltype))
|
---|
[1118] | 1817 | s._add_history("convert_pol", varlist)
|
---|
[992] | 1818 | return s
|
---|
| 1819 |
|
---|
[1862] | 1820 | @asaplog_post_dec
|
---|
[1819] | 1821 | def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, insitu=None):
|
---|
[1846] | 1822 | """\
|
---|
[513] | 1823 | Smooth the spectrum by the specified kernel (conserving flux).
|
---|
[1846] | 1824 |
|
---|
[513] | 1825 | Parameters:
|
---|
[1846] | 1826 |
|
---|
[513] | 1827 | kernel: The type of smoothing kernel. Select from
|
---|
[1574] | 1828 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian'
|
---|
| 1829 | or 'poly'
|
---|
[1855] | 1830 |
|
---|
[513] | 1831 | width: The width of the kernel in pixels. For hanning this is
|
---|
| 1832 | ignored otherwise it defauls to 5 pixels.
|
---|
| 1833 | For 'gaussian' it is the Full Width Half
|
---|
| 1834 | Maximum. For 'boxcar' it is the full width.
|
---|
[1574] | 1835 | For 'rmedian' and 'poly' it is the half width.
|
---|
[1855] | 1836 |
|
---|
[1574] | 1837 | order: Optional parameter for 'poly' kernel (default is 2), to
|
---|
| 1838 | specify the order of the polnomial. Ignored by all other
|
---|
| 1839 | kernels.
|
---|
[1855] | 1840 |
|
---|
[1819] | 1841 | plot: plot the original and the smoothed spectra.
|
---|
| 1842 | In this each indivual fit has to be approved, by
|
---|
| 1843 | typing 'y' or 'n'
|
---|
[1855] | 1844 |
|
---|
[513] | 1845 | insitu: if False a new scantable is returned.
|
---|
| 1846 | Otherwise, the scaling is done in-situ
|
---|
| 1847 | The default is taken from .asaprc (False)
|
---|
[1846] | 1848 |
|
---|
[513] | 1849 | """
|
---|
| 1850 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1851 | self._math._setinsitu(insitu)
|
---|
[513] | 1852 | varlist = vars()
|
---|
[1819] | 1853 |
|
---|
| 1854 | if plot: orgscan = self.copy()
|
---|
| 1855 |
|
---|
[1574] | 1856 | s = scantable(self._math._smooth(self, kernel.lower(), width, order))
|
---|
[876] | 1857 | s._add_history("smooth", varlist)
|
---|
[1819] | 1858 |
|
---|
| 1859 | if plot:
|
---|
| 1860 | if rcParams['plotter.gui']:
|
---|
| 1861 | from asap.asaplotgui import asaplotgui as asaplot
|
---|
| 1862 | else:
|
---|
| 1863 | from asap.asaplot import asaplot
|
---|
| 1864 | self._p=asaplot()
|
---|
| 1865 | self._p.set_panels()
|
---|
| 1866 | ylab=s._get_ordinate_label()
|
---|
| 1867 | #self._p.palette(0,["#777777","red"])
|
---|
| 1868 | for r in xrange(s.nrow()):
|
---|
| 1869 | xsm=s._getabcissa(r)
|
---|
| 1870 | ysm=s._getspectrum(r)
|
---|
| 1871 | xorg=orgscan._getabcissa(r)
|
---|
| 1872 | yorg=orgscan._getspectrum(r)
|
---|
| 1873 | self._p.clear()
|
---|
| 1874 | self._p.hold()
|
---|
| 1875 | self._p.set_axes('ylabel',ylab)
|
---|
| 1876 | self._p.set_axes('xlabel',s._getabcissalabel(r))
|
---|
| 1877 | self._p.set_axes('title',s._getsourcename(r))
|
---|
| 1878 | self._p.set_line(label='Original',color="#777777")
|
---|
| 1879 | self._p.plot(xorg,yorg)
|
---|
| 1880 | self._p.set_line(label='Smoothed',color="red")
|
---|
| 1881 | self._p.plot(xsm,ysm)
|
---|
| 1882 | ### Ugly part for legend
|
---|
| 1883 | for i in [0,1]:
|
---|
| 1884 | self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]])
|
---|
| 1885 | self._p.release()
|
---|
| 1886 | ### Ugly part for legend
|
---|
| 1887 | self._p.subplots[0]['lines']=[]
|
---|
| 1888 | res = raw_input("Accept smoothing ([y]/n): ")
|
---|
| 1889 | if res.upper() == 'N':
|
---|
| 1890 | s._setspectrum(yorg, r)
|
---|
| 1891 | self._p.unmap()
|
---|
| 1892 | self._p = None
|
---|
| 1893 | del orgscan
|
---|
| 1894 |
|
---|
[876] | 1895 | if insitu: self._assign(s)
|
---|
| 1896 | else: return s
|
---|
[513] | 1897 |
|
---|
[1862] | 1898 | @asaplog_post_dec
|
---|
[1907] | 1899 | def old_poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None, rows=None):
|
---|
[1846] | 1900 | """\
|
---|
[513] | 1901 | Return a scan which has been baselined (all rows) by a polynomial.
|
---|
[1907] | 1902 |
|
---|
[513] | 1903 | Parameters:
|
---|
[1846] | 1904 |
|
---|
[794] | 1905 | mask: an optional mask
|
---|
[1855] | 1906 |
|
---|
[794] | 1907 | order: the order of the polynomial (default is 0)
|
---|
[1855] | 1908 |
|
---|
[1061] | 1909 | plot: plot the fit and the residual. In this each
|
---|
| 1910 | indivual fit has to be approved, by typing 'y'
|
---|
| 1911 | or 'n'
|
---|
[1855] | 1912 |
|
---|
[1391] | 1913 | uselin: use linear polynomial fit
|
---|
[1855] | 1914 |
|
---|
[794] | 1915 | insitu: if False a new scantable is returned.
|
---|
| 1916 | Otherwise, the scaling is done in-situ
|
---|
| 1917 | The default is taken from .asaprc (False)
|
---|
[1846] | 1918 |
|
---|
[1907] | 1919 | rows: row numbers of spectra to be processed.
|
---|
| 1920 | (default is None: for all rows)
|
---|
| 1921 |
|
---|
| 1922 | Example:
|
---|
[513] | 1923 | # return a scan baselined by a third order polynomial,
|
---|
| 1924 | # not using a mask
|
---|
| 1925 | bscan = scan.poly_baseline(order=3)
|
---|
[1846] | 1926 |
|
---|
[579] | 1927 | """
|
---|
[513] | 1928 | if insitu is None: insitu = rcParams['insitu']
|
---|
[1819] | 1929 | if not insitu:
|
---|
| 1930 | workscan = self.copy()
|
---|
| 1931 | else:
|
---|
| 1932 | workscan = self
|
---|
[513] | 1933 | varlist = vars()
|
---|
| 1934 | if mask is None:
|
---|
[1907] | 1935 | mask = [True for i in xrange(self.nchan())]
|
---|
[1819] | 1936 |
|
---|
[1217] | 1937 | try:
|
---|
| 1938 | f = fitter()
|
---|
[1391] | 1939 | if uselin:
|
---|
| 1940 | f.set_function(lpoly=order)
|
---|
| 1941 | else:
|
---|
| 1942 | f.set_function(poly=order)
|
---|
[1819] | 1943 |
|
---|
[1907] | 1944 | if rows == None:
|
---|
| 1945 | rows = xrange(workscan.nrow())
|
---|
| 1946 | elif isinstance(rows, int):
|
---|
| 1947 | rows = [ rows ]
|
---|
| 1948 |
|
---|
[1819] | 1949 | if len(rows) > 0:
|
---|
| 1950 | self.blpars = []
|
---|
[1907] | 1951 | self.masklists = []
|
---|
| 1952 | self.actualmask = []
|
---|
| 1953 |
|
---|
[1819] | 1954 | for r in rows:
|
---|
| 1955 | f.x = workscan._getabcissa(r)
|
---|
| 1956 | f.y = workscan._getspectrum(r)
|
---|
[1907] | 1957 | f.mask = mask_and(mask, workscan._getmask(r)) # (CAS-1434)
|
---|
[1819] | 1958 | f.data = None
|
---|
| 1959 | f.fit()
|
---|
| 1960 | if plot:
|
---|
| 1961 | f.plot(residual=True)
|
---|
| 1962 | x = raw_input("Accept fit ( [y]/n ): ")
|
---|
| 1963 | if x.upper() == 'N':
|
---|
| 1964 | self.blpars.append(None)
|
---|
[1907] | 1965 | self.masklists.append(None)
|
---|
| 1966 | self.actualmask.append(None)
|
---|
[1819] | 1967 | continue
|
---|
| 1968 | workscan._setspectrum(f.fitter.getresidual(), r)
|
---|
| 1969 | self.blpars.append(f.get_parameters())
|
---|
[1931] | 1970 | self.masklists.append(workscan.get_masklist(f.mask, row=r, silent=True))
|
---|
[1907] | 1971 | self.actualmask.append(f.mask)
|
---|
[1819] | 1972 |
|
---|
| 1973 | if plot:
|
---|
| 1974 | f._p.unmap()
|
---|
| 1975 | f._p = None
|
---|
| 1976 | workscan._add_history("poly_baseline", varlist)
|
---|
[1856] | 1977 | if insitu:
|
---|
| 1978 | self._assign(workscan)
|
---|
| 1979 | else:
|
---|
| 1980 | return workscan
|
---|
[1217] | 1981 | except RuntimeError:
|
---|
| 1982 | msg = "The fit failed, possibly because it didn't converge."
|
---|
[1859] | 1983 | raise RuntimeError(msg)
|
---|
[513] | 1984 |
|
---|
[1931] | 1985 | @asaplog_post_dec
|
---|
[1907] | 1986 | def poly_baseline(self, mask=None, order=0, plot=False, batch=False, insitu=None, rows=None):
|
---|
| 1987 | """\
|
---|
| 1988 | Return a scan which has been baselined (all rows) by a polynomial.
|
---|
| 1989 | Parameters:
|
---|
| 1990 | mask: an optional mask
|
---|
| 1991 | order: the order of the polynomial (default is 0)
|
---|
| 1992 | plot: plot the fit and the residual. In this each
|
---|
| 1993 | indivual fit has to be approved, by typing 'y'
|
---|
| 1994 | or 'n'. Ignored if batch = True.
|
---|
| 1995 | batch: if True a faster algorithm is used and logs
|
---|
| 1996 | including the fit results are not output
|
---|
| 1997 | (default is False)
|
---|
| 1998 | insitu: if False a new scantable is returned.
|
---|
| 1999 | Otherwise, the scaling is done in-situ
|
---|
| 2000 | The default is taken from .asaprc (False)
|
---|
[1931] | 2001 | rows: row numbers of spectra to be baselined.
|
---|
[1907] | 2002 | (default is None: for all rows)
|
---|
| 2003 | Example:
|
---|
| 2004 | # return a scan baselined by a third order polynomial,
|
---|
| 2005 | # not using a mask
|
---|
| 2006 | bscan = scan.poly_baseline(order=3)
|
---|
| 2007 | """
|
---|
[1931] | 2008 |
|
---|
| 2009 | varlist = vars()
|
---|
| 2010 |
|
---|
[1907] | 2011 | if insitu is None: insitu = rcParams["insitu"]
|
---|
| 2012 | if insitu:
|
---|
| 2013 | workscan = self
|
---|
| 2014 | else:
|
---|
| 2015 | workscan = self.copy()
|
---|
| 2016 |
|
---|
| 2017 | nchan = workscan.nchan()
|
---|
| 2018 |
|
---|
| 2019 | if mask is None:
|
---|
| 2020 | mask = [True for i in xrange(nchan)]
|
---|
| 2021 |
|
---|
| 2022 | try:
|
---|
| 2023 | if rows == None:
|
---|
| 2024 | rows = xrange(workscan.nrow())
|
---|
| 2025 | elif isinstance(rows, int):
|
---|
| 2026 | rows = [ rows ]
|
---|
| 2027 |
|
---|
| 2028 | if len(rows) > 0:
|
---|
[1931] | 2029 | workscan.blpars = []
|
---|
| 2030 | workscan.masklists = []
|
---|
| 2031 | workscan.actualmask = []
|
---|
[1907] | 2032 |
|
---|
| 2033 | if batch:
|
---|
[1931] | 2034 | workscan._poly_baseline_batch(mask, order)
|
---|
[1907] | 2035 | elif plot:
|
---|
| 2036 | f = fitter()
|
---|
| 2037 | f.set_function(lpoly=order)
|
---|
| 2038 | for r in rows:
|
---|
| 2039 | f.x = workscan._getabcissa(r)
|
---|
| 2040 | f.y = workscan._getspectrum(r)
|
---|
| 2041 | f.mask = mask_and(mask, workscan._getmask(r)) # (CAS-1434)
|
---|
| 2042 | f.data = None
|
---|
| 2043 | f.fit()
|
---|
| 2044 |
|
---|
| 2045 | f.plot(residual=True)
|
---|
| 2046 | accept_fit = raw_input("Accept fit ( [y]/n ): ")
|
---|
| 2047 | if accept_fit.upper() == "N":
|
---|
| 2048 | self.blpars.append(None)
|
---|
| 2049 | self.masklists.append(None)
|
---|
| 2050 | self.actualmask.append(None)
|
---|
| 2051 | continue
|
---|
| 2052 | workscan._setspectrum(f.fitter.getresidual(), r)
|
---|
[1931] | 2053 | workscan.blpars.append(f.get_parameters())
|
---|
| 2054 | workscan.masklists.append(workscan.get_masklist(f.mask, row=r))
|
---|
| 2055 | workscan.actualmask.append(f.mask)
|
---|
[1907] | 2056 |
|
---|
| 2057 | f._p.unmap()
|
---|
| 2058 | f._p = None
|
---|
| 2059 | else:
|
---|
| 2060 | for r in rows:
|
---|
[1931] | 2061 | fitparams = workscan._poly_baseline(mask, order, r)
|
---|
| 2062 | params = fitparams.getparameters()
|
---|
| 2063 | fmtd = ", ".join(["p%d = %3.6f" % (i, v) for i, v in enumerate(params)])
|
---|
| 2064 | errors = fitparams.geterrors()
|
---|
| 2065 | fmask = mask_and(mask, workscan._getmask(r))
|
---|
| 2066 |
|
---|
| 2067 | workscan.blpars.append({"params":params,
|
---|
| 2068 | "fixed": fitparams.getfixedparameters(),
|
---|
| 2069 | "formatted":fmtd, "errors":errors})
|
---|
| 2070 | workscan.masklists.append(workscan.get_masklist(fmask, r, silent=True))
|
---|
| 2071 | workscan.actualmask.append(fmask)
|
---|
[1907] | 2072 |
|
---|
[1931] | 2073 | asaplog.push(fmtd)
|
---|
[1907] | 2074 |
|
---|
| 2075 | workscan._add_history("poly_baseline", varlist)
|
---|
| 2076 |
|
---|
| 2077 | if insitu:
|
---|
| 2078 | self._assign(workscan)
|
---|
| 2079 | else:
|
---|
| 2080 | return workscan
|
---|
| 2081 |
|
---|
[1919] | 2082 | except RuntimeError, e:
|
---|
[1907] | 2083 | msg = "The fit failed, possibly because it didn't converge."
|
---|
| 2084 | if rcParams["verbose"]:
|
---|
[1919] | 2085 | asaplog.push(str(e))
|
---|
[1907] | 2086 | asaplog.push(str(msg))
|
---|
| 2087 | return
|
---|
| 2088 | else:
|
---|
[1919] | 2089 | raise RuntimeError(str(e)+'\n'+msg)
|
---|
[1907] | 2090 |
|
---|
| 2091 |
|
---|
| 2092 | def auto_poly_baseline(self, mask=None, edge=(0, 0), order=0,
|
---|
[1280] | 2093 | threshold=3, chan_avg_limit=1, plot=False,
|
---|
[1907] | 2094 | insitu=None, rows=None):
|
---|
[1846] | 2095 | """\
|
---|
[1931] | 2096 | Return a scan which has been baselined (all rows) by a polynomial.
|
---|
[880] | 2097 | Spectral lines are detected first using linefinder and masked out
|
---|
| 2098 | to avoid them affecting the baseline solution.
|
---|
| 2099 |
|
---|
| 2100 | Parameters:
|
---|
[1846] | 2101 |
|
---|
[880] | 2102 | mask: an optional mask retreived from scantable
|
---|
[1846] | 2103 |
|
---|
| 2104 | edge: an optional number of channel to drop at the edge of
|
---|
| 2105 | spectrum. If only one value is
|
---|
[880] | 2106 | specified, the same number will be dropped from
|
---|
| 2107 | both sides of the spectrum. Default is to keep
|
---|
[907] | 2108 | all channels. Nested tuples represent individual
|
---|
[976] | 2109 | edge selection for different IFs (a number of spectral
|
---|
| 2110 | channels can be different)
|
---|
[1846] | 2111 |
|
---|
[880] | 2112 | order: the order of the polynomial (default is 0)
|
---|
[1846] | 2113 |
|
---|
[880] | 2114 | threshold: the threshold used by line finder. It is better to
|
---|
| 2115 | keep it large as only strong lines affect the
|
---|
| 2116 | baseline solution.
|
---|
[1846] | 2117 |
|
---|
[1280] | 2118 | chan_avg_limit:
|
---|
| 2119 | a maximum number of consequtive spectral channels to
|
---|
| 2120 | average during the search of weak and broad lines.
|
---|
| 2121 | The default is no averaging (and no search for weak
|
---|
| 2122 | lines). If such lines can affect the fitted baseline
|
---|
| 2123 | (e.g. a high order polynomial is fitted), increase this
|
---|
| 2124 | parameter (usually values up to 8 are reasonable). Most
|
---|
| 2125 | users of this method should find the default value
|
---|
| 2126 | sufficient.
|
---|
[1846] | 2127 |
|
---|
[1061] | 2128 | plot: plot the fit and the residual. In this each
|
---|
| 2129 | indivual fit has to be approved, by typing 'y'
|
---|
| 2130 | or 'n'
|
---|
[1846] | 2131 |
|
---|
[880] | 2132 | insitu: if False a new scantable is returned.
|
---|
| 2133 | Otherwise, the scaling is done in-situ
|
---|
| 2134 | The default is taken from .asaprc (False)
|
---|
[1907] | 2135 | rows: row numbers of spectra to be processed.
|
---|
| 2136 | (default is None: for all rows)
|
---|
[880] | 2137 |
|
---|
[1846] | 2138 |
|
---|
| 2139 | Example::
|
---|
| 2140 |
|
---|
| 2141 | scan2 = scan.auto_poly_baseline(order=7, insitu=False)
|
---|
| 2142 |
|
---|
[880] | 2143 | """
|
---|
| 2144 | if insitu is None: insitu = rcParams['insitu']
|
---|
| 2145 | varlist = vars()
|
---|
| 2146 | from asap.asaplinefind import linefinder
|
---|
| 2147 | from asap import _is_sequence_or_number as _is_valid
|
---|
| 2148 |
|
---|
[976] | 2149 | # check whether edge is set up for each IF individually
|
---|
[1118] | 2150 | individualedge = False;
|
---|
| 2151 | if len(edge) > 1:
|
---|
| 2152 | if isinstance(edge[0], list) or isinstance(edge[0], tuple):
|
---|
| 2153 | individualedge = True;
|
---|
[907] | 2154 |
|
---|
[1118] | 2155 | if not _is_valid(edge, int) and not individualedge:
|
---|
[909] | 2156 | raise ValueError, "Parameter 'edge' has to be an integer or a \
|
---|
[907] | 2157 | pair of integers specified as a tuple. Nested tuples are allowed \
|
---|
| 2158 | to make individual selection for different IFs."
|
---|
[919] | 2159 |
|
---|
[1118] | 2160 | curedge = (0, 0)
|
---|
| 2161 | if individualedge:
|
---|
| 2162 | for edgepar in edge:
|
---|
| 2163 | if not _is_valid(edgepar, int):
|
---|
| 2164 | raise ValueError, "Each element of the 'edge' tuple has \
|
---|
| 2165 | to be a pair of integers or an integer."
|
---|
[907] | 2166 | else:
|
---|
[1118] | 2167 | curedge = edge;
|
---|
[880] | 2168 |
|
---|
[1907] | 2169 | if not insitu:
|
---|
| 2170 | workscan = self.copy()
|
---|
| 2171 | else:
|
---|
| 2172 | workscan = self
|
---|
| 2173 |
|
---|
[880] | 2174 | # setup fitter
|
---|
| 2175 | f = fitter()
|
---|
[1907] | 2176 | f.set_function(lpoly=order)
|
---|
[880] | 2177 |
|
---|
| 2178 | # setup line finder
|
---|
[1118] | 2179 | fl = linefinder()
|
---|
[1268] | 2180 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
|
---|
[880] | 2181 |
|
---|
[907] | 2182 | fl.set_scan(workscan)
|
---|
| 2183 |
|
---|
[1907] | 2184 | if mask is None:
|
---|
| 2185 | mask = _n_bools(workscan.nchan(), True)
|
---|
| 2186 |
|
---|
| 2187 | if rows is None:
|
---|
| 2188 | rows = xrange(workscan.nrow())
|
---|
| 2189 | elif isinstance(rows, int):
|
---|
| 2190 | rows = [ rows ]
|
---|
| 2191 |
|
---|
[1819] | 2192 | # Save parameters of baseline fits & masklists as a class attribute.
|
---|
| 2193 | # NOTICE: It does not reflect changes in scantable!
|
---|
| 2194 | if len(rows) > 0:
|
---|
| 2195 | self.blpars=[]
|
---|
| 2196 | self.masklists=[]
|
---|
[1907] | 2197 | self.actualmask=[]
|
---|
[880] | 2198 | asaplog.push("Processing:")
|
---|
| 2199 | for r in rows:
|
---|
[1118] | 2200 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
|
---|
| 2201 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
|
---|
| 2202 | workscan.getpol(r), workscan.getcycle(r))
|
---|
[880] | 2203 | asaplog.push(msg, False)
|
---|
[907] | 2204 |
|
---|
[976] | 2205 | # figure out edge parameter
|
---|
[1118] | 2206 | if individualedge:
|
---|
| 2207 | if len(edge) >= workscan.getif(r):
|
---|
| 2208 | raise RuntimeError, "Number of edge elements appear to " \
|
---|
| 2209 | "be less than the number of IFs"
|
---|
| 2210 | curedge = edge[workscan.getif(r)]
|
---|
[919] | 2211 |
|
---|
[1907] | 2212 | actualmask = mask_and(mask, workscan._getmask(r)) # (CAS-1434)
|
---|
[1819] | 2213 |
|
---|
[976] | 2214 | # setup line finder
|
---|
[1819] | 2215 | fl.find_lines(r, actualmask, curedge)
|
---|
[1907] | 2216 |
|
---|
[1819] | 2217 | f.x = workscan._getabcissa(r)
|
---|
| 2218 | f.y = workscan._getspectrum(r)
|
---|
[1907] | 2219 | f.mask = fl.get_mask()
|
---|
[1819] | 2220 | f.data = None
|
---|
[880] | 2221 | f.fit()
|
---|
[1819] | 2222 |
|
---|
| 2223 | # Show mask list
|
---|
[1931] | 2224 | masklist=workscan.get_masklist(f.mask, row=r, silent=True)
|
---|
[1819] | 2225 | msg = "mask range: "+str(masklist)
|
---|
| 2226 | asaplog.push(msg, False)
|
---|
| 2227 |
|
---|
[1061] | 2228 | if plot:
|
---|
| 2229 | f.plot(residual=True)
|
---|
| 2230 | x = raw_input("Accept fit ( [y]/n ): ")
|
---|
| 2231 | if x.upper() == 'N':
|
---|
[1819] | 2232 | self.blpars.append(None)
|
---|
| 2233 | self.masklists.append(None)
|
---|
[1907] | 2234 | self.actualmask.append(None)
|
---|
[1061] | 2235 | continue
|
---|
[1819] | 2236 |
|
---|
[880] | 2237 | workscan._setspectrum(f.fitter.getresidual(), r)
|
---|
[1819] | 2238 | self.blpars.append(f.get_parameters())
|
---|
| 2239 | self.masklists.append(masklist)
|
---|
[1907] | 2240 | self.actualmask.append(f.mask)
|
---|
[1061] | 2241 | if plot:
|
---|
| 2242 | f._p.unmap()
|
---|
| 2243 | f._p = None
|
---|
| 2244 | workscan._add_history("auto_poly_baseline", varlist)
|
---|
[880] | 2245 | if insitu:
|
---|
| 2246 | self._assign(workscan)
|
---|
| 2247 | else:
|
---|
| 2248 | return workscan
|
---|
| 2249 |
|
---|
[1862] | 2250 | @asaplog_post_dec
|
---|
[914] | 2251 | def rotate_linpolphase(self, angle):
|
---|
[1846] | 2252 | """\
|
---|
[914] | 2253 | Rotate the phase of the complex polarization O=Q+iU correlation.
|
---|
| 2254 | This is always done in situ in the raw data. So if you call this
|
---|
| 2255 | function more than once then each call rotates the phase further.
|
---|
[1846] | 2256 |
|
---|
[914] | 2257 | Parameters:
|
---|
[1846] | 2258 |
|
---|
[914] | 2259 | angle: The angle (degrees) to rotate (add) by.
|
---|
[1846] | 2260 |
|
---|
| 2261 | Example::
|
---|
| 2262 |
|
---|
[914] | 2263 | scan.rotate_linpolphase(2.3)
|
---|
[1846] | 2264 |
|
---|
[914] | 2265 | """
|
---|
| 2266 | varlist = vars()
|
---|
[936] | 2267 | self._math._rotate_linpolphase(self, angle)
|
---|
[914] | 2268 | self._add_history("rotate_linpolphase", varlist)
|
---|
| 2269 | return
|
---|
[710] | 2270 |
|
---|
[1862] | 2271 | @asaplog_post_dec
|
---|
[914] | 2272 | def rotate_xyphase(self, angle):
|
---|
[1846] | 2273 | """\
|
---|
[914] | 2274 | Rotate the phase of the XY correlation. This is always done in situ
|
---|
| 2275 | in the data. So if you call this function more than once
|
---|
| 2276 | then each call rotates the phase further.
|
---|
[1846] | 2277 |
|
---|
[914] | 2278 | Parameters:
|
---|
[1846] | 2279 |
|
---|
[914] | 2280 | angle: The angle (degrees) to rotate (add) by.
|
---|
[1846] | 2281 |
|
---|
| 2282 | Example::
|
---|
| 2283 |
|
---|
[914] | 2284 | scan.rotate_xyphase(2.3)
|
---|
[1846] | 2285 |
|
---|
[914] | 2286 | """
|
---|
| 2287 | varlist = vars()
|
---|
[936] | 2288 | self._math._rotate_xyphase(self, angle)
|
---|
[914] | 2289 | self._add_history("rotate_xyphase", varlist)
|
---|
| 2290 | return
|
---|
| 2291 |
|
---|
[1862] | 2292 | @asaplog_post_dec
|
---|
[914] | 2293 | def swap_linears(self):
|
---|
[1846] | 2294 | """\
|
---|
[1573] | 2295 | Swap the linear polarisations XX and YY, or better the first two
|
---|
[1348] | 2296 | polarisations as this also works for ciculars.
|
---|
[914] | 2297 | """
|
---|
| 2298 | varlist = vars()
|
---|
[936] | 2299 | self._math._swap_linears(self)
|
---|
[914] | 2300 | self._add_history("swap_linears", varlist)
|
---|
| 2301 | return
|
---|
| 2302 |
|
---|
[1862] | 2303 | @asaplog_post_dec
|
---|
[914] | 2304 | def invert_phase(self):
|
---|
[1846] | 2305 | """\
|
---|
[914] | 2306 | Invert the phase of the complex polarisation
|
---|
| 2307 | """
|
---|
| 2308 | varlist = vars()
|
---|
[936] | 2309 | self._math._invert_phase(self)
|
---|
[914] | 2310 | self._add_history("invert_phase", varlist)
|
---|
| 2311 | return
|
---|
| 2312 |
|
---|
[1862] | 2313 | @asaplog_post_dec
|
---|
[876] | 2314 | def add(self, offset, insitu=None):
|
---|
[1846] | 2315 | """\
|
---|
[513] | 2316 | Return a scan where all spectra have the offset added
|
---|
[1846] | 2317 |
|
---|
[513] | 2318 | Parameters:
|
---|
[1846] | 2319 |
|
---|
[513] | 2320 | offset: the offset
|
---|
[1855] | 2321 |
|
---|
[513] | 2322 | insitu: if False a new scantable is returned.
|
---|
| 2323 | Otherwise, the scaling is done in-situ
|
---|
| 2324 | The default is taken from .asaprc (False)
|
---|
[1846] | 2325 |
|
---|
[513] | 2326 | """
|
---|
| 2327 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 2328 | self._math._setinsitu(insitu)
|
---|
[513] | 2329 | varlist = vars()
|
---|
[876] | 2330 | s = scantable(self._math._unaryop(self, offset, "ADD", False))
|
---|
[1118] | 2331 | s._add_history("add", varlist)
|
---|
[876] | 2332 | if insitu:
|
---|
| 2333 | self._assign(s)
|
---|
| 2334 | else:
|
---|
[513] | 2335 | return s
|
---|
| 2336 |
|
---|
[1862] | 2337 | @asaplog_post_dec
|
---|
[1308] | 2338 | def scale(self, factor, tsys=True, insitu=None):
|
---|
[1846] | 2339 | """\
|
---|
| 2340 |
|
---|
[1938] | 2341 | Return a scan where all spectra are scaled by the given 'factor'
|
---|
[1846] | 2342 |
|
---|
[513] | 2343 | Parameters:
|
---|
[1846] | 2344 |
|
---|
[1819] | 2345 | factor: the scaling factor (float or 1D float list)
|
---|
[1855] | 2346 |
|
---|
[513] | 2347 | insitu: if False a new scantable is returned.
|
---|
| 2348 | Otherwise, the scaling is done in-situ
|
---|
| 2349 | The default is taken from .asaprc (False)
|
---|
[1855] | 2350 |
|
---|
[513] | 2351 | tsys: if True (default) then apply the operation to Tsys
|
---|
| 2352 | as well as the data
|
---|
[1846] | 2353 |
|
---|
[513] | 2354 | """
|
---|
| 2355 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 2356 | self._math._setinsitu(insitu)
|
---|
[513] | 2357 | varlist = vars()
|
---|
[1819] | 2358 | s = None
|
---|
| 2359 | import numpy
|
---|
| 2360 | if isinstance(factor, list) or isinstance(factor, numpy.ndarray):
|
---|
| 2361 | if isinstance(factor[0], list) or isinstance(factor[0], numpy.ndarray):
|
---|
| 2362 | from asapmath import _array2dOp
|
---|
| 2363 | s = _array2dOp( self.copy(), factor, "MUL", tsys )
|
---|
| 2364 | else:
|
---|
| 2365 | s = scantable( self._math._arrayop( self.copy(), factor, "MUL", tsys ) )
|
---|
| 2366 | else:
|
---|
| 2367 | s = scantable(self._math._unaryop(self.copy(), factor, "MUL", tsys))
|
---|
[1118] | 2368 | s._add_history("scale", varlist)
|
---|
[876] | 2369 | if insitu:
|
---|
| 2370 | self._assign(s)
|
---|
| 2371 | else:
|
---|
[513] | 2372 | return s
|
---|
| 2373 |
|
---|
[1504] | 2374 | def set_sourcetype(self, match, matchtype="pattern",
|
---|
| 2375 | sourcetype="reference"):
|
---|
[1846] | 2376 | """\
|
---|
[1502] | 2377 | Set the type of the source to be an source or reference scan
|
---|
[1846] | 2378 | using the provided pattern.
|
---|
| 2379 |
|
---|
[1502] | 2380 | Parameters:
|
---|
[1846] | 2381 |
|
---|
[1504] | 2382 | match: a Unix style pattern, regular expression or selector
|
---|
[1855] | 2383 |
|
---|
[1504] | 2384 | matchtype: 'pattern' (default) UNIX style pattern or
|
---|
| 2385 | 'regex' regular expression
|
---|
[1855] | 2386 |
|
---|
[1502] | 2387 | sourcetype: the type of the source to use (source/reference)
|
---|
[1846] | 2388 |
|
---|
[1502] | 2389 | """
|
---|
| 2390 | varlist = vars()
|
---|
| 2391 | basesel = self.get_selection()
|
---|
| 2392 | stype = -1
|
---|
| 2393 | if sourcetype.lower().startswith("r"):
|
---|
| 2394 | stype = 1
|
---|
| 2395 | elif sourcetype.lower().startswith("s"):
|
---|
| 2396 | stype = 0
|
---|
[1504] | 2397 | else:
|
---|
[1502] | 2398 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)")
|
---|
[1504] | 2399 | if matchtype.lower().startswith("p"):
|
---|
| 2400 | matchtype = "pattern"
|
---|
| 2401 | elif matchtype.lower().startswith("r"):
|
---|
| 2402 | matchtype = "regex"
|
---|
| 2403 | else:
|
---|
| 2404 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)")
|
---|
[1502] | 2405 | sel = selector()
|
---|
| 2406 | if isinstance(match, selector):
|
---|
| 2407 | sel = match
|
---|
| 2408 | else:
|
---|
[1504] | 2409 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match))
|
---|
[1502] | 2410 | self.set_selection(basesel+sel)
|
---|
| 2411 | self._setsourcetype(stype)
|
---|
| 2412 | self.set_selection(basesel)
|
---|
[1573] | 2413 | self._add_history("set_sourcetype", varlist)
|
---|
[1502] | 2414 |
|
---|
[1862] | 2415 | @asaplog_post_dec
|
---|
[1857] | 2416 | @preserve_selection
|
---|
[1819] | 2417 | def auto_quotient(self, preserve=True, mode='paired', verify=False):
|
---|
[1846] | 2418 | """\
|
---|
[670] | 2419 | This function allows to build quotients automatically.
|
---|
[1819] | 2420 | It assumes the observation to have the same number of
|
---|
[670] | 2421 | "ons" and "offs"
|
---|
[1846] | 2422 |
|
---|
[670] | 2423 | Parameters:
|
---|
[1846] | 2424 |
|
---|
[710] | 2425 | preserve: you can preserve (default) the continuum or
|
---|
| 2426 | remove it. The equations used are
|
---|
[1857] | 2427 |
|
---|
[670] | 2428 | preserve: Output = Toff * (on/off) - Toff
|
---|
[1857] | 2429 |
|
---|
[1070] | 2430 | remove: Output = Toff * (on/off) - Ton
|
---|
[1855] | 2431 |
|
---|
[1573] | 2432 | mode: the on/off detection mode
|
---|
[1348] | 2433 | 'paired' (default)
|
---|
| 2434 | identifies 'off' scans by the
|
---|
| 2435 | trailing '_R' (Mopra/Parkes) or
|
---|
| 2436 | '_e'/'_w' (Tid) and matches
|
---|
| 2437 | on/off pairs from the observing pattern
|
---|
[1502] | 2438 | 'time'
|
---|
| 2439 | finds the closest off in time
|
---|
[1348] | 2440 |
|
---|
[1857] | 2441 | .. todo:: verify argument is not implemented
|
---|
| 2442 |
|
---|
[670] | 2443 | """
|
---|
[1857] | 2444 | varlist = vars()
|
---|
[1348] | 2445 | modes = ["time", "paired"]
|
---|
[670] | 2446 | if not mode in modes:
|
---|
[876] | 2447 | msg = "please provide valid mode. Valid modes are %s" % (modes)
|
---|
| 2448 | raise ValueError(msg)
|
---|
[1348] | 2449 | s = None
|
---|
| 2450 | if mode.lower() == "paired":
|
---|
[1857] | 2451 | sel = self.get_selection()
|
---|
[1875] | 2452 | sel.set_query("SRCTYPE==psoff")
|
---|
[1356] | 2453 | self.set_selection(sel)
|
---|
[1348] | 2454 | offs = self.copy()
|
---|
[1875] | 2455 | sel.set_query("SRCTYPE==pson")
|
---|
[1356] | 2456 | self.set_selection(sel)
|
---|
[1348] | 2457 | ons = self.copy()
|
---|
| 2458 | s = scantable(self._math._quotient(ons, offs, preserve))
|
---|
| 2459 | elif mode.lower() == "time":
|
---|
| 2460 | s = scantable(self._math._auto_quotient(self, mode, preserve))
|
---|
[1118] | 2461 | s._add_history("auto_quotient", varlist)
|
---|
[876] | 2462 | return s
|
---|
[710] | 2463 |
|
---|
[1862] | 2464 | @asaplog_post_dec
|
---|
[1145] | 2465 | def mx_quotient(self, mask = None, weight='median', preserve=True):
|
---|
[1846] | 2466 | """\
|
---|
[1143] | 2467 | Form a quotient using "off" beams when observing in "MX" mode.
|
---|
[1846] | 2468 |
|
---|
[1143] | 2469 | Parameters:
|
---|
[1846] | 2470 |
|
---|
[1145] | 2471 | mask: an optional mask to be used when weight == 'stddev'
|
---|
[1855] | 2472 |
|
---|
[1143] | 2473 | weight: How to average the off beams. Default is 'median'.
|
---|
[1855] | 2474 |
|
---|
[1145] | 2475 | preserve: you can preserve (default) the continuum or
|
---|
[1855] | 2476 | remove it. The equations used are:
|
---|
[1846] | 2477 |
|
---|
[1855] | 2478 | preserve: Output = Toff * (on/off) - Toff
|
---|
| 2479 |
|
---|
| 2480 | remove: Output = Toff * (on/off) - Ton
|
---|
| 2481 |
|
---|
[1217] | 2482 | """
|
---|
[1593] | 2483 | mask = mask or ()
|
---|
[1141] | 2484 | varlist = vars()
|
---|
| 2485 | on = scantable(self._math._mx_extract(self, 'on'))
|
---|
[1143] | 2486 | preoff = scantable(self._math._mx_extract(self, 'off'))
|
---|
| 2487 | off = preoff.average_time(mask=mask, weight=weight, scanav=False)
|
---|
[1217] | 2488 | from asapmath import quotient
|
---|
[1145] | 2489 | q = quotient(on, off, preserve)
|
---|
[1143] | 2490 | q._add_history("mx_quotient", varlist)
|
---|
[1217] | 2491 | return q
|
---|
[513] | 2492 |
|
---|
[1862] | 2493 | @asaplog_post_dec
|
---|
[718] | 2494 | def freq_switch(self, insitu=None):
|
---|
[1846] | 2495 | """\
|
---|
[718] | 2496 | Apply frequency switching to the data.
|
---|
[1846] | 2497 |
|
---|
[718] | 2498 | Parameters:
|
---|
[1846] | 2499 |
|
---|
[718] | 2500 | insitu: if False a new scantable is returned.
|
---|
| 2501 | Otherwise, the swictching is done in-situ
|
---|
| 2502 | The default is taken from .asaprc (False)
|
---|
[1846] | 2503 |
|
---|
[718] | 2504 | """
|
---|
| 2505 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 2506 | self._math._setinsitu(insitu)
|
---|
[718] | 2507 | varlist = vars()
|
---|
[876] | 2508 | s = scantable(self._math._freqswitch(self))
|
---|
[1118] | 2509 | s._add_history("freq_switch", varlist)
|
---|
[1856] | 2510 | if insitu:
|
---|
| 2511 | self._assign(s)
|
---|
| 2512 | else:
|
---|
| 2513 | return s
|
---|
[718] | 2514 |
|
---|
[1862] | 2515 | @asaplog_post_dec
|
---|
[780] | 2516 | def recalc_azel(self):
|
---|
[1846] | 2517 | """Recalculate the azimuth and elevation for each position."""
|
---|
[780] | 2518 | varlist = vars()
|
---|
[876] | 2519 | self._recalcazel()
|
---|
[780] | 2520 | self._add_history("recalc_azel", varlist)
|
---|
| 2521 | return
|
---|
| 2522 |
|
---|
[1862] | 2523 | @asaplog_post_dec
|
---|
[513] | 2524 | def __add__(self, other):
|
---|
| 2525 | varlist = vars()
|
---|
| 2526 | s = None
|
---|
| 2527 | if isinstance(other, scantable):
|
---|
[1573] | 2528 | s = scantable(self._math._binaryop(self, other, "ADD"))
|
---|
[513] | 2529 | elif isinstance(other, float):
|
---|
[876] | 2530 | s = scantable(self._math._unaryop(self, other, "ADD", False))
|
---|
[513] | 2531 | else:
|
---|
[718] | 2532 | raise TypeError("Other input is not a scantable or float value")
|
---|
[513] | 2533 | s._add_history("operator +", varlist)
|
---|
| 2534 | return s
|
---|
| 2535 |
|
---|
[1862] | 2536 | @asaplog_post_dec
|
---|
[513] | 2537 | def __sub__(self, other):
|
---|
| 2538 | """
|
---|
| 2539 | implicit on all axes and on Tsys
|
---|
| 2540 | """
|
---|
| 2541 | varlist = vars()
|
---|
| 2542 | s = None
|
---|
| 2543 | if isinstance(other, scantable):
|
---|
[1588] | 2544 | s = scantable(self._math._binaryop(self, other, "SUB"))
|
---|
[513] | 2545 | elif isinstance(other, float):
|
---|
[876] | 2546 | s = scantable(self._math._unaryop(self, other, "SUB", False))
|
---|
[513] | 2547 | else:
|
---|
[718] | 2548 | raise TypeError("Other input is not a scantable or float value")
|
---|
[513] | 2549 | s._add_history("operator -", varlist)
|
---|
| 2550 | return s
|
---|
[710] | 2551 |
|
---|
[1862] | 2552 | @asaplog_post_dec
|
---|
[513] | 2553 | def __mul__(self, other):
|
---|
| 2554 | """
|
---|
| 2555 | implicit on all axes and on Tsys
|
---|
| 2556 | """
|
---|
| 2557 | varlist = vars()
|
---|
| 2558 | s = None
|
---|
| 2559 | if isinstance(other, scantable):
|
---|
[1588] | 2560 | s = scantable(self._math._binaryop(self, other, "MUL"))
|
---|
[513] | 2561 | elif isinstance(other, float):
|
---|
[876] | 2562 | s = scantable(self._math._unaryop(self, other, "MUL", False))
|
---|
[513] | 2563 | else:
|
---|
[718] | 2564 | raise TypeError("Other input is not a scantable or float value")
|
---|
[513] | 2565 | s._add_history("operator *", varlist)
|
---|
| 2566 | return s
|
---|
| 2567 |
|
---|
[710] | 2568 |
|
---|
[1862] | 2569 | @asaplog_post_dec
|
---|
[513] | 2570 | def __div__(self, other):
|
---|
| 2571 | """
|
---|
| 2572 | implicit on all axes and on Tsys
|
---|
| 2573 | """
|
---|
| 2574 | varlist = vars()
|
---|
| 2575 | s = None
|
---|
| 2576 | if isinstance(other, scantable):
|
---|
[1589] | 2577 | s = scantable(self._math._binaryop(self, other, "DIV"))
|
---|
[513] | 2578 | elif isinstance(other, float):
|
---|
| 2579 | if other == 0.0:
|
---|
[718] | 2580 | raise ZeroDivisionError("Dividing by zero is not recommended")
|
---|
[876] | 2581 | s = scantable(self._math._unaryop(self, other, "DIV", False))
|
---|
[513] | 2582 | else:
|
---|
[718] | 2583 | raise TypeError("Other input is not a scantable or float value")
|
---|
[513] | 2584 | s._add_history("operator /", varlist)
|
---|
| 2585 | return s
|
---|
| 2586 |
|
---|
[1862] | 2587 | @asaplog_post_dec
|
---|
[530] | 2588 | def get_fit(self, row=0):
|
---|
[1846] | 2589 | """\
|
---|
[530] | 2590 | Print or return the stored fits for a row in the scantable
|
---|
[1846] | 2591 |
|
---|
[530] | 2592 | Parameters:
|
---|
[1846] | 2593 |
|
---|
[530] | 2594 | row: the row which the fit has been applied to.
|
---|
[1846] | 2595 |
|
---|
[530] | 2596 | """
|
---|
| 2597 | if row > self.nrow():
|
---|
| 2598 | return
|
---|
[976] | 2599 | from asap.asapfit import asapfit
|
---|
[530] | 2600 | fit = asapfit(self._getfit(row))
|
---|
[1859] | 2601 | asaplog.push( '%s' %(fit) )
|
---|
| 2602 | return fit.as_dict()
|
---|
[530] | 2603 |
|
---|
[1483] | 2604 | def flag_nans(self):
|
---|
[1846] | 2605 | """\
|
---|
[1483] | 2606 | Utility function to flag NaN values in the scantable.
|
---|
| 2607 | """
|
---|
| 2608 | import numpy
|
---|
| 2609 | basesel = self.get_selection()
|
---|
| 2610 | for i in range(self.nrow()):
|
---|
[1589] | 2611 | sel = self.get_row_selector(i)
|
---|
| 2612 | self.set_selection(basesel+sel)
|
---|
[1483] | 2613 | nans = numpy.isnan(self._getspectrum(0))
|
---|
| 2614 | if numpy.any(nans):
|
---|
| 2615 | bnans = [ bool(v) for v in nans]
|
---|
| 2616 | self.flag(bnans)
|
---|
| 2617 | self.set_selection(basesel)
|
---|
| 2618 |
|
---|
[1588] | 2619 | def get_row_selector(self, rowno):
|
---|
[1992] | 2620 | #return selector(beams=self.getbeam(rowno),
|
---|
| 2621 | # ifs=self.getif(rowno),
|
---|
| 2622 | # pols=self.getpol(rowno),
|
---|
| 2623 | # scans=self.getscan(rowno),
|
---|
| 2624 | # cycles=self.getcycle(rowno))
|
---|
| 2625 | return selector(rows=[rowno])
|
---|
[1573] | 2626 |
|
---|
[484] | 2627 | def _add_history(self, funcname, parameters):
|
---|
[1435] | 2628 | if not rcParams['scantable.history']:
|
---|
| 2629 | return
|
---|
[484] | 2630 | # create date
|
---|
| 2631 | sep = "##"
|
---|
| 2632 | from datetime import datetime
|
---|
| 2633 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
|
---|
| 2634 | hist = dstr+sep
|
---|
| 2635 | hist += funcname+sep#cdate+sep
|
---|
| 2636 | if parameters.has_key('self'): del parameters['self']
|
---|
[1118] | 2637 | for k, v in parameters.iteritems():
|
---|
[484] | 2638 | if type(v) is dict:
|
---|
[1118] | 2639 | for k2, v2 in v.iteritems():
|
---|
[484] | 2640 | hist += k2
|
---|
| 2641 | hist += "="
|
---|
[1118] | 2642 | if isinstance(v2, scantable):
|
---|
[484] | 2643 | hist += 'scantable'
|
---|
| 2644 | elif k2 == 'mask':
|
---|
[1118] | 2645 | if isinstance(v2, list) or isinstance(v2, tuple):
|
---|
[513] | 2646 | hist += str(self._zip_mask(v2))
|
---|
| 2647 | else:
|
---|
| 2648 | hist += str(v2)
|
---|
[484] | 2649 | else:
|
---|
[513] | 2650 | hist += str(v2)
|
---|
[484] | 2651 | else:
|
---|
| 2652 | hist += k
|
---|
| 2653 | hist += "="
|
---|
[1118] | 2654 | if isinstance(v, scantable):
|
---|
[484] | 2655 | hist += 'scantable'
|
---|
| 2656 | elif k == 'mask':
|
---|
[1118] | 2657 | if isinstance(v, list) or isinstance(v, tuple):
|
---|
[513] | 2658 | hist += str(self._zip_mask(v))
|
---|
| 2659 | else:
|
---|
| 2660 | hist += str(v)
|
---|
[484] | 2661 | else:
|
---|
| 2662 | hist += str(v)
|
---|
| 2663 | hist += sep
|
---|
| 2664 | hist = hist[:-2] # remove trailing '##'
|
---|
| 2665 | self._addhistory(hist)
|
---|
| 2666 |
|
---|
[710] | 2667 |
|
---|
[484] | 2668 | def _zip_mask(self, mask):
|
---|
| 2669 | mask = list(mask)
|
---|
| 2670 | i = 0
|
---|
| 2671 | segments = []
|
---|
| 2672 | while mask[i:].count(1):
|
---|
| 2673 | i += mask[i:].index(1)
|
---|
| 2674 | if mask[i:].count(0):
|
---|
| 2675 | j = i + mask[i:].index(0)
|
---|
| 2676 | else:
|
---|
[710] | 2677 | j = len(mask)
|
---|
[1118] | 2678 | segments.append([i, j])
|
---|
[710] | 2679 | i = j
|
---|
[484] | 2680 | return segments
|
---|
[714] | 2681 |
|
---|
[626] | 2682 | def _get_ordinate_label(self):
|
---|
| 2683 | fu = "("+self.get_fluxunit()+")"
|
---|
| 2684 | import re
|
---|
| 2685 | lbl = "Intensity"
|
---|
[1118] | 2686 | if re.match(".K.", fu):
|
---|
[626] | 2687 | lbl = "Brightness Temperature "+ fu
|
---|
[1118] | 2688 | elif re.match(".Jy.", fu):
|
---|
[626] | 2689 | lbl = "Flux density "+ fu
|
---|
| 2690 | return lbl
|
---|
[710] | 2691 |
|
---|
[876] | 2692 | def _check_ifs(self):
|
---|
[1986] | 2693 | #nchans = [self.nchan(i) for i in range(self.nif(-1))]
|
---|
| 2694 | nchans = [self.nchan(i) for i in self.getifnos()]
|
---|
[2004] | 2695 | nchans = filter(lambda t: t > 0, nchans)
|
---|
[876] | 2696 | return (sum(nchans)/len(nchans) == nchans[0])
|
---|
[976] | 2697 |
|
---|
[1862] | 2698 | @asaplog_post_dec
|
---|
[1916] | 2699 | #def _fill(self, names, unit, average, getpt, antenna):
|
---|
| 2700 | def _fill(self, names, unit, average, opts={}):
|
---|
[976] | 2701 | first = True
|
---|
| 2702 | fullnames = []
|
---|
| 2703 | for name in names:
|
---|
| 2704 | name = os.path.expandvars(name)
|
---|
| 2705 | name = os.path.expanduser(name)
|
---|
| 2706 | if not os.path.exists(name):
|
---|
| 2707 | msg = "File '%s' does not exists" % (name)
|
---|
| 2708 | raise IOError(msg)
|
---|
| 2709 | fullnames.append(name)
|
---|
| 2710 | if average:
|
---|
| 2711 | asaplog.push('Auto averaging integrations')
|
---|
[1079] | 2712 | stype = int(rcParams['scantable.storage'].lower() == 'disk')
|
---|
[976] | 2713 | for name in fullnames:
|
---|
[1073] | 2714 | tbl = Scantable(stype)
|
---|
[2004] | 2715 | if is_ms( name ):
|
---|
| 2716 | r = msfiller( tbl )
|
---|
| 2717 | else:
|
---|
| 2718 | r = filler( tbl )
|
---|
| 2719 | rx = rcParams['scantable.reference']
|
---|
| 2720 | r.setreferenceexpr(rx)
|
---|
| 2721 | #r = filler(tbl)
|
---|
| 2722 | #rx = rcParams['scantable.reference']
|
---|
| 2723 | #r.setreferenceexpr(rx)
|
---|
[976] | 2724 | msg = "Importing %s..." % (name)
|
---|
[1118] | 2725 | asaplog.push(msg, False)
|
---|
[1916] | 2726 | #opts = {'ms': {'antenna' : antenna, 'getpt': getpt} }
|
---|
[1904] | 2727 | r.open(name, opts)# antenna, -1, -1, getpt)
|
---|
[1843] | 2728 | r.fill()
|
---|
[976] | 2729 | if average:
|
---|
[1118] | 2730 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
|
---|
[976] | 2731 | if not first:
|
---|
| 2732 | tbl = self._math._merge([self, tbl])
|
---|
| 2733 | Scantable.__init__(self, tbl)
|
---|
[1843] | 2734 | r.close()
|
---|
[1118] | 2735 | del r, tbl
|
---|
[976] | 2736 | first = False
|
---|
[1861] | 2737 | #flush log
|
---|
| 2738 | asaplog.post()
|
---|
[976] | 2739 | if unit is not None:
|
---|
| 2740 | self.set_fluxunit(unit)
|
---|
[1824] | 2741 | if not is_casapy():
|
---|
| 2742 | self.set_freqframe(rcParams['scantable.freqframe'])
|
---|
[976] | 2743 |
|
---|
[1402] | 2744 | def __getitem__(self, key):
|
---|
| 2745 | if key < 0:
|
---|
| 2746 | key += self.nrow()
|
---|
| 2747 | if key >= self.nrow():
|
---|
| 2748 | raise IndexError("Row index out of range.")
|
---|
| 2749 | return self._getspectrum(key)
|
---|
| 2750 |
|
---|
| 2751 | def __setitem__(self, key, value):
|
---|
| 2752 | if key < 0:
|
---|
| 2753 | key += self.nrow()
|
---|
| 2754 | if key >= self.nrow():
|
---|
| 2755 | raise IndexError("Row index out of range.")
|
---|
| 2756 | if not hasattr(value, "__len__") or \
|
---|
| 2757 | len(value) > self.nchan(self.getif(key)):
|
---|
| 2758 | raise ValueError("Spectrum length doesn't match.")
|
---|
| 2759 | return self._setspectrum(value, key)
|
---|
| 2760 |
|
---|
| 2761 | def __len__(self):
|
---|
| 2762 | return self.nrow()
|
---|
| 2763 |
|
---|
| 2764 | def __iter__(self):
|
---|
| 2765 | for i in range(len(self)):
|
---|
| 2766 | yield self[i]
|
---|