| 1 | from scantable import scantable
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| 2 | from asap import rcParams
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| 3 |
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| 4 | def average_time(*args, **kwargs):
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| 5 | """
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| 6 | Return the (time) average of a scan or list of scans. [in channels only]
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| 7 | The cursor of the output scan is set to 0
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| 8 | Parameters:
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| 9 | one scan or comma separated scans
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| 10 | mask: an optional mask (only used for 'var' and 'tsys' weighting)
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| 11 | scanav: True (default) averages each scan separately
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| 12 | False averages all scans together,
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| 13 | weight: Weighting scheme. 'none' (default), 'var' (variance
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| 14 | weighted), 'tsys'
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| 15 | Example:
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| 16 | # return a time averaged scan from scana and scanb
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| 17 | # without using a mask
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| 18 | scanav = average_time(scana,scanb)
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| 19 | # return the (time) averaged scan, i.e. the average of
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| 20 | # all correlator cycles
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| 21 | scanav = average_time(scan)
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| 22 |
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| 23 | """
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| 24 | scanAv = True
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| 25 | if kwargs.has_key('scanav'):
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| 26 | scanAv = kwargs.get('scanav')
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| 27 | weight = 'none'
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| 28 | if kwargs.has_key('weight'):
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| 29 | weight = kwargs.get('weight')
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| 30 | mask = ()
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| 31 | if kwargs.has_key('mask'):
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| 32 | mask = kwargs.get('mask')
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| 33 | varlist = vars()
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| 34 | lst = tuple(args)
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| 35 | del varlist["kwargs"]
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| 36 | varlist["args"] = "%d scantables" % len(lst)
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| 37 | # need special formatting her for history...
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| 38 |
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| 39 | from asap._asap import average as _av
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| 40 | for s in lst:
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| 41 | if not isinstance(s,scantable):
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| 42 | print "Please give a list of scantables"
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| 43 | return
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| 44 | s = scantable(_av(lst, mask, scanAv, weight))
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| 45 | s._add_history("average_time",varlist)
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| 46 | return s
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| 47 |
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| 48 | def quotient(source, reference, preserve=True):
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| 49 | """
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| 50 | Return the quotient of a 'source' (signal) scan and a 'reference' scan.
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| 51 | The reference can have just one row, even if the signal has many. Otherwise
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| 52 | they must have the same number of rows.
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| 53 | The cursor of the output scan is set to 0
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| 54 | Parameters:
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| 55 | source: the 'on' scan
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| 56 | reference: the 'off' scan
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| 57 | preserve: you can preserve (default) the continuum or
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| 58 | remove it. The equations used are
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| 59 | preserve - Output = Tref * (sig/ref) - Tref
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| 60 | remove - Output = Tref * (sig/ref) - Tsig
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| 61 | """
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| 62 | from asap._asap import quotient as _quot
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| 63 | return scantable(_quot(source, reference, preserve))
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| 64 |
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| 65 | def simple_math(left, right, op='add', tsys=True):
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| 66 | """
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| 67 | Apply simple mathematical binary operations to two
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| 68 | scan tables, returning the result in a new scan table.
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| 69 | The operation is applied to both the correlations and the TSys data
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| 70 | The cursor of the output scan is set to 0
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| 71 | Parameters:
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| 72 | left: the 'left' scan
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| 73 | right: the 'right' scan
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| 74 | op: the operation: 'add' (default), 'sub', 'mul', 'div'
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| 75 | tsys: if True (default) then apply the operation to Tsys
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| 76 | as well as the data
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| 77 | """
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| 78 | varlist = vars()
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| 79 | if not isinstance(left,scantable) and not isinstance(right,scantable):
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| 80 | print "Please provide two scantables as input"
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| 81 | return
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| 82 | from asap._asap import b_operate as _bop
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| 83 | s = scantable(_bop(left, right, op, tsys))
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| 84 | s._add_history("simple_math", varlist)
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| 85 | return s
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| 86 |
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| 87 | def scale(scan, factor, insitu=None, allaxes=None, tsys=True):
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| 88 | """
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| 89 | Return a scan where all spectra are scaled by the give 'factor'
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| 90 | Parameters:
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| 91 | scan: a scantable
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| 92 | factor: the scaling factor
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| 93 | insitu: if False a new scantable is returned.
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| 94 | Otherwise, the scaling is done in-situ
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| 95 | The default is taken from .asaprc (False)
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| 96 | allaxes: if True apply to all spectra. Otherwise
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| 97 | apply only to the selected (beam/pol/if)spectra only.
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| 98 | The default is taken from .asaprc (True if none)
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| 99 | tsys: if True (default) then apply the operation to Tsys
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| 100 | as well as the data
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| 101 | """
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| 102 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 103 | if insitu is None: insitu = rcParams['insitu']
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| 104 | varlist = vars()
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| 105 | if not insitu:
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| 106 | from asap._asap import scale as _scale
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| 107 | s = scantable(_scale(scan, factor, allaxes, tsys))
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| 108 | s._add_history("scale",varlist)
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| 109 | return s
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| 110 | else:
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| 111 | from asap._asap import scale_insitu as _scale
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| 112 | _scale(scan, factor, allaxes, tsys)
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| 113 | scan._add_history("scale",varlist)
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| 114 | return
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| 115 |
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| 116 | def add(scan, offset, insitu=None, allaxes=None):
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| 117 | """
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| 118 | Return a scan where all spectra have the offset added
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| 119 | Parameters:
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| 120 | scan: a scantable
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| 121 | offset: the offset
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| 122 | insitu: if False a new scantable is returned.
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| 123 | Otherwise, the scaling is done in-situ
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| 124 | The default is taken from .asaprc (False)
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| 125 | allaxes: if True apply to all spectra. Otherwise
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| 126 | apply only to the selected (beam/pol/if)spectra only
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| 127 | The default is taken from .asaprc (True if none)
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| 128 | """
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| 129 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 130 | if insitu is None: insitu = rcParams['insitu']
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| 131 | if not insitu:
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| 132 | from asap._asap import add as _add
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| 133 | return scantable(_add(scan, offset, allaxes))
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| 134 | else:
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| 135 | from asap._asap import add_insitu as _add
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| 136 | _add(scan, offset, allaxes)
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| 137 | return
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| 138 |
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| 139 | def convert_flux(scan, jyperk=None, eta=None, d=None, insitu=None,
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| 140 | allaxes=None):
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| 141 | """
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| 142 | Return a scan where all spectra are converted to either Jansky or Kelvin
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| 143 | depending upon the flux units of the scan table. By default the
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| 144 | function tries to look the values up internally. If it can't find
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| 145 | them (or if you want to over-ride), you must specify EITHER jyperk
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| 146 | OR eta (and D which it will try to look up also if you don't
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| 147 | set it). jyperk takes precedence if you set both.
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| 148 | Parameters:
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| 149 | scan: a scantable
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| 150 | jyperk: the Jy / K conversion factor
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| 151 | eta: the aperture efficiency
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| 152 | d: the geomtric diameter (metres)
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| 153 | insitu: if False a new scantable is returned.
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| 154 | Otherwise, the scaling is done in-situ
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| 155 | The default is taken from .asaprc (False)
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| 156 | allaxes: if True apply to all spectra. Otherwise
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| 157 | apply only to the selected (beam/pol/if)spectra only
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| 158 | The default is taken from .asaprc (True if none)
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| 159 | """
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| 160 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 161 | if insitu is None: insitu = rcParams['insitu']
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| 162 | varlist = vars()
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| 163 | if jyperk is None: jyperk = -1.0
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| 164 | if d is None: d = -1.0
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| 165 | if eta is None: eta = -1.0
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| 166 | if not insitu:
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| 167 | from asap._asap import convertflux as _convert
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| 168 | s = scantable(_convert(scan, d, eta, jyperk, allaxes))
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| 169 | s._add_history("convert_flux", varlist)
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| 170 | return s
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| 171 | else:
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| 172 | from asap._asap import convertflux_insitu as _convert
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| 173 | _convert(scan, d, eta, jyperk, allaxes)
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| 174 | scan._add_history("convert_flux", varlist)
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| 175 | return
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| 176 |
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| 177 | def gain_el(scan, poly=None, filename="", method="linear",
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| 178 | insitu=None, allaxes=None):
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| 179 | """
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| 180 | Return a scan after applying a gain-elevation correction. The correction
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| 181 | can be made via either a polynomial or a table-based interpolation
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| 182 | (and extrapolation if necessary).
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| 183 | You specify polynomial coefficients, an ascii table or neither.
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| 184 | If you specify neither, then a polynomial correction will be made
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| 185 | with built in coefficients known for certain telescopes (an error will
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| 186 | occur if the instrument is not known). The data and Tsys are *divided*
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| 187 | by the scaling factors.
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| 188 | Parameters:
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| 189 | scan: a scantable
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| 190 | poly: Polynomial coefficients (default None) to compute a
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| 191 | gain-elevation correction as a function of
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| 192 | elevation (in degrees).
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| 193 | filename: The name of an ascii file holding correction factors.
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| 194 | The first row of the ascii file must give the column
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| 195 | names and these MUST include columns
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| 196 | "ELEVATION" (degrees) and "FACTOR" (multiply data by this)
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| 197 | somewhere.
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| 198 | The second row must give the data type of the column. Use
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| 199 | 'R' for Real and 'I' for Integer. An example file
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| 200 | would be (actual factors are arbitrary) :
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| 201 |
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| 202 | TIME ELEVATION FACTOR
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| 203 | R R R
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| 204 | 0.1 0 0.8
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| 205 | 0.2 20 0.85
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| 206 | 0.3 40 0.9
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| 207 | 0.4 60 0.85
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| 208 | 0.5 80 0.8
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| 209 | 0.6 90 0.75
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| 210 | method: Interpolation method when correcting from a table. Values
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| 211 | are "nearest", "linear" (default), "cubic" and "spline"
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| 212 | insitu: if False a new scantable is returned.
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| 213 | Otherwise, the scaling is done in-situ
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| 214 | The default is taken from .asaprc (False)
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| 215 | allaxes: if True apply to all spectra. Otherwise
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| 216 | apply only to the selected (beam/pol/if) spectra only
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| 217 | The default is taken from .asaprc (True if none)
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| 218 | """
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| 219 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 220 | if insitu is None: insitu = rcParams['insitu']
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| 221 | varlist = vars()
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| 222 | if poly is None:
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| 223 | poly = ()
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| 224 | from os.path import expandvars
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| 225 | filename = expandvars(filename)
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| 226 | if not insitu:
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| 227 | from asap._asap import gainel as _gainEl
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| 228 | s = scantable(_gainEl(scan, poly, filename, method, allaxes))
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| 229 | s._add_history("gain_el", varlist)
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| 230 | return s
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| 231 | else:
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| 232 | from asap._asap import gainel_insitu as _gainEl
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| 233 | _gainEl(scan, poly, filename, method, allaxes)
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| 234 | scan._add_history("gain_el", varlist)
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| 235 | return
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| 236 |
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| 237 | def freq_align(scan, reftime=None, method='cubic', perif=False, insitu=None):
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| 238 | """
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| 239 | Return a scan where all rows have been aligned in frequency/velocity.
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| 240 | The alignment frequency frame (e.g. LSRK) is that set by function
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| 241 | set_freqframe.
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| 242 | scan: a scantable
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| 243 | reftime: reference time to align at. By default, the time of
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| 244 | the first row of data is used.
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| 245 | method: Interpolation method for regridding the spectra. Choose
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| 246 | from "nearest", "linear", "cubic" (default) and "spline"
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| 247 | perif: Generate aligners per freqID (no doppler tracking) or
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| 248 | per IF (scan-based doppler tracking)
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| 249 | insitu: if False a new scantable is returned.
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| 250 | Otherwise, the scaling is done in-situ
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| 251 | The default is taken from .asaprc (False)
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| 252 | """
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| 253 | if insitu is None: insitu = rcParams['insitu']
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| 254 | varlist = vars()
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| 255 | if reftime is None: reftime = ''
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| 256 | perfreqid = not perif
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| 257 | if not insitu:
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| 258 | from asap._asap import freq_align as _align
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| 259 | s = scantable(_align(scan, reftime, method, perfreqid))
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| 260 | s._add_history("freq_align", varlist)
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| 261 | return s
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| 262 | else:
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| 263 | from asap._asap import freq_align_insitu as _align
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| 264 | _align(scan, reftime, method, perfreqid)
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| 265 | scan._add_history("freq_align", varlist)
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| 266 | return
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| 267 |
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| 268 | def opacity(scan, tau, insitu=None, allaxes=None):
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| 269 | """
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| 270 | Return a scan after applying an opacity correction. The data
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| 271 | and Tsys are multiplied by the correction factor.
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| 272 | Parameters:
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| 273 | scan: a scantable
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| 274 | tau: Opacity from which the correction factor is exp(tau*ZD)
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| 275 | where ZD is the zenith-distance
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| 276 | insitu: if False a new scantable is returned.
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| 277 | Otherwise, the scaling is done in-situ
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| 278 | The default is taken from .asaprc (False)
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| 279 | allaxes: if True apply to all spectra. Otherwise
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| 280 | apply only to the selected (beam/pol/if)spectra only
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| 281 | The default is taken from .asaprc (True if none)
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| 282 | """
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| 283 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 284 | if insitu is None: insitu = rcParams['insitu']
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| 285 | varlist = vars()
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| 286 | if not insitu:
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| 287 | from asap._asap import opacity as _opacity
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| 288 | s = scantable(_opacity(scan, tau, allaxes))
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| 289 | s._add_history("opacity", varlist)
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| 290 | return s
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| 291 | else:
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| 292 | from asap._asap import opacity_insitu as _opacity
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| 293 | _opacity(scan, tau, allaxes)
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| 294 | scan._add_history("opacity", varlist)
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| 295 | return
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| 296 |
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| 297 | def bin(scan, width=5, insitu=None):
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| 298 | """
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| 299 | Return a scan where all spectra have been binned up
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| 300 | width: The bin width (default=5) in pixels
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| 301 | insitu: if False a new scantable is returned.
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| 302 | Otherwise, the scaling is done in-situ
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| 303 | The default is taken from .asaprc (False)
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| 304 | """
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| 305 | if insitu is None: insitu = rcParams['insitu']
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| 306 | varlist = vars()
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| 307 | if not insitu:
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| 308 | from asap._asap import bin as _bin
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| 309 | s = scantable(_bin(scan, width))
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| 310 | s._add_history("bin",varlist)
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| 311 | return s
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| 312 | else:
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| 313 | from asap._asap import bin_insitu as _bin
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| 314 | _bin(scan, width)
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| 315 | scan._add_history("bin",varlist)
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| 316 | return
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| 317 |
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| 318 | def resample(scan, width=5, method='cubic', insitu=None):
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| 319 | """
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| 320 | Return a scan where all spectra have been binned up
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| 321 | width: The bin width (default=5) in pixels
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| 322 | method: Interpolation method when correcting from a table. Values
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| 323 | are "nearest", "linear", "cubic" (default) and "spline"
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| 324 | insitu: if False a new scantable is returned.
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| 325 | Otherwise, the scaling is done in-situ
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| 326 | The default is taken from .asaprc (False)
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| 327 | """
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| 328 | if insitu is None: insitu = rcParams['insitu']
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| 329 | varlist = vars()
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| 330 | if not insitu:
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| 331 | from asap._asap import resample as _resample
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| 332 | s = scantable(_resample(scan, method, width))
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| 333 | s._add_history("resample",varlist)
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| 334 | return s
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| 335 | else:
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| 336 | from asap._asap import resample_insitu as _resample
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| 337 | _resample(scan, method, width)
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| 338 | scan._add_history("resample",varlist)
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| 339 | return
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| 340 |
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| 341 | def average_pol(scan, mask=None, weight='none', insitu=None):
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| 342 | """
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| 343 | Average the Polarisations together.
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| 344 | The polarisation cursor of the output scan is set to 0
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| 345 | Parameters:
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| 346 | scan: The scantable
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| 347 | mask: An optional mask defining the region, where the
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| 348 | averaging will be applied. The output will have all
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| 349 | specified points masked.
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| 350 | weight: Weighting scheme. 'none' (default), or 'var' (variance
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| 351 | weighted)
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| 352 | insitu: if False a new scantable is returned.
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| 353 | Otherwise, the scaling is done in-situ
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| 354 | The default is taken from .asaprc (False)
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| 355 | Example:
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| 356 | polav = average_pols(myscan)
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| 357 | """
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| 358 | if insitu is None: insitu = rcParams['insitu']
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| 359 | varlist = vars()
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| 360 |
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| 361 | if mask is None:
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| 362 | mask = ()
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| 363 | if not insitu:
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| 364 | from asap._asap import averagepol as _avpol
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| 365 | s = scantable(_avpol(scan, mask, weight))
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| 366 | s._add_history("average_pol",varlist)
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| 367 | return s
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| 368 | else:
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| 369 | from asap._asap import averagepol_insitu as _avpol
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| 370 | _avpol(scan, mask, weight)
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| 371 | scan._add_history("average_pol",varlist)
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| 372 | return
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| 373 |
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| 374 | def smooth(scan, kernel="hanning", width=5.0, insitu=None, allaxes=None):
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| 375 | """
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| 376 | Smooth the spectrum by the specified kernel (conserving flux).
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| 377 | Parameters:
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| 378 | scan: The input scan
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| 379 | kernel: The type of smoothing kernel. Select from
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| 380 | 'hanning' (default), 'gaussian' and 'boxcar'.
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| 381 | The first three characters are sufficient.
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| 382 | width: The width of the kernel in pixels. For hanning this is
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| 383 | ignored otherwise it defauls to 5 pixels.
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| 384 | For 'gaussian' it is the Full Width Half
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| 385 | Maximum. For 'boxcar' it is the full width.
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| 386 | insitu: if False a new scantable is returned.
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| 387 | Otherwise, the scaling is done in-situ
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| 388 | The default is taken from .asaprc (False)
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| 389 | allaxes: If True (default) apply to all spectra. Otherwise
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| 390 | apply only to the selected (beam/pol/if)spectra only
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| 391 | The default is taken from .asaprc (True if none)
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| 392 | Example:
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| 393 | none
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| 394 | """
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| 395 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 396 | if insitu is None: insitu = rcParams['insitu']
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| 397 | varlist = vars()
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| 398 | if not insitu:
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| 399 | from asap._asap import smooth as _smooth
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| 400 | s = scantable(_smooth(scan,kernel,width,allaxes))
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| 401 | s._add_history("smooth", varlist)
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| 402 | return s
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| 403 | else:
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| 404 | from asap._asap import smooth_insitu as _smooth
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| 405 | _smooth(scan,kernel,width,allaxes)
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| 406 | scan._add_history("smooth", varlist)
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| 407 | return
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| 408 |
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| 409 | def poly_baseline(scan, mask=None, order=0, insitu=None):
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| 410 | """
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| 411 | Return a scan which has been baselined (all rows) by a polynomial.
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| 412 | Parameters:
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| 413 | scan: a scantable
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| 414 | mask: an optional mask
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| 415 | order: the order of the polynomial (default is 0)
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| 416 | insitu: if False a new scantable is returned.
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| 417 | Otherwise, the scaling is done in-situ
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| 418 | The default is taken from .asaprc (False)
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| 419 | Example:
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| 420 | # return a scan baselined by a third order polynomial,
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| 421 | # not using a mask
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| 422 | bscan = poly_baseline(scan, order=3)
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| 423 | """
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| 424 | if insitu is None: insitu = rcParams['insitu']
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| 425 | varlist = vars()
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| 426 | from asap.asapfitter import fitter
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| 427 | if mask is None:
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| 428 | from numarray import ones
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| 429 | mask = tuple(ones(scan.nchan()))
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| 430 | f = fitter()
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| 431 | f._verbose(True)
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| 432 | f.set_scan(scan, mask)
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| 433 | f.set_function(poly=order)
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| 434 | sf = f.auto_fit(insitu)
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| 435 | sf._add_history("poly_baseline", varlist)
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| 436 | return sf
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| 437 |
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| 438 | def rotate_xyphase(scan, angle, allaxes=None):
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| 439 | """
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| 440 | Rotate the phase of the XY correlation. This is always done in situ
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| 441 | in the data. So if you call this function more than once
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| 442 | then each call rotates the phase further.
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| 443 | Parameters:
|
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| 444 | angle: The angle (degrees) to rotate (add) by.
|
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| 445 | allaxes: If True apply to all spectra. Otherwise
|
|---|
| 446 | apply only to the selected (beam/pol/if)spectra only.
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| 447 | The default is taken from .asaprc (True if none)
|
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| 448 | Examples:
|
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| 449 | rotate_xyphase(scan, 2.3)
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| 450 | """
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| 451 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
|
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| 452 | varlist = vars()
|
|---|
| 453 | from asap._asap import _rotate_xyphase as _rotate
|
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| 454 | _rotate(scan, angle, allaxes)
|
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| 455 | scan._add_history("rotate_xyphase", varlist)
|
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| 456 | return
|
|---|
| 457 |
|
|---|
| 458 | def rotate_linpolphase(scan, angle, allaxes=None):
|
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| 459 | """
|
|---|
| 460 | Rotate the phase of the complex polarization O=Q+iU correlation.
|
|---|
| 461 | This is always done in situ in the raw data. So if you call this
|
|---|
| 462 | function more than once then each call rotates the phase further.
|
|---|
| 463 | Parameters:
|
|---|
| 464 | angle: The angle (degrees) to rotate (add) by.
|
|---|
| 465 | allaxes: If True apply to all spectra. Otherwise
|
|---|
| 466 | apply only to the selected (beam/pol/if)spectra only.
|
|---|
| 467 | The default is taken from .asaprc (True if none)
|
|---|
| 468 | Examples:
|
|---|
| 469 | rotate_linpolphase(scan, 2.3)
|
|---|
| 470 | """
|
|---|
| 471 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
|
|---|
| 472 | varlist = vars()
|
|---|
| 473 | from asap._asap import _rotate_linpolphase as _rotate
|
|---|
| 474 | _rotate(scan, angle, allaxes)
|
|---|
| 475 | scan._add_history("rotate_linpolphase", varlist)
|
|---|
| 476 | return
|
|---|
| 477 |
|
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