| [101] | 1 | from scantable import scantable
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| [258] | 2 | from asap import rcParams
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| [101] | 3 |
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| [143] | 4 | def average_time(*args, **kwargs):
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| [101] | 5 | """
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| [113] | 6 | Return the (time) average of a scan or list of scans. [in channels only]
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| [305] | 7 | The cursor of the output scan is set to 0
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| [113] | 8 | Parameters:
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| 9 | one scan or comma separated scans
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| [143] | 10 | mask: an optional mask (only used for 'var' and 'tsys' weighting)
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| [424] | 11 | scanav: True (default) averages each scan separately
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| 12 | False averages all scans together,
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| [143] | 13 | weight: Weighting scheme. 'none' (default), 'var' (variance
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| 14 | weighted), 'tsys'
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| [113] | 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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| [129] | 18 | scanav = average_time(scana,scanb)
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| [113] | 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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| [143] | 22 |
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| [101] | 23 | """
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| [424] | 24 | scanAv = True
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| [143] | 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 | lst = tuple(args)
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| 34 | from asap._asap import average as _av
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| [113] | 35 | for s in lst:
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| [101] | 36 | if not isinstance(s,scantable):
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| 37 | print "Please give a list of scantables"
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| 38 | return
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| [143] | 39 | return scantable(_av(lst, mask, scanAv, weight))
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| [101] | 40 |
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| [245] | 41 | def quotient(source, reference, preserve=True):
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| [101] | 42 | """
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| [246] | 43 | Return the quotient of a 'source' (signal) scan and a 'reference' scan.
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| 44 | The reference can have just one row, even if the signal has many. Otherwise
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| 45 | they must have the same number of rows.
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| [305] | 46 | The cursor of the output scan is set to 0
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| [101] | 47 | Parameters:
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| 48 | source: the 'on' scan
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| 49 | reference: the 'off' scan
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| [245] | 50 | preserve: you can preserve (default) the continuum or
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| 51 | remove it. The equations used are
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| 52 | preserve - Output = Tref * (sig/ref) - Tref
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| 53 | remove - Output = Tref * (sig/ref) - Tsig
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| [101] | 54 | """
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| 55 | from asap._asap import quotient as _quot
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| [245] | 56 | return scantable(_quot(source, reference, preserve))
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| [101] | 57 |
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| [296] | 58 | def simple_math(left, right, op='add', tsys=True):
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| [242] | 59 | """
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| 60 | Apply simple mathematical binary operations to two
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| 61 | scan tables, returning the result in a new scan table.
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| 62 | The operation is applied to both the correlations and the TSys data
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| [305] | 63 | The cursor of the output scan is set to 0
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| [242] | 64 | Parameters:
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| 65 | left: the 'left' scan
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| 66 | right: the 'right' scan
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| 67 | op: the operation: 'add' (default), 'sub', 'mul', 'div'
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| [296] | 68 | tsys: if True (default) then apply the operation to Tsys
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| 69 | as well as the data
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| [242] | 70 | """
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| [258] | 71 | if not isinstance(left,scantable) and not isinstance(right,scantable):
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| 72 | print "Please provide two scantables as input"
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| 73 | return
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| [242] | 74 | from asap._asap import b_operate as _bop
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| [296] | 75 | return scantable(_bop(left, right, op, tsys))
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| [242] | 76 |
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| [296] | 77 | def scale(scan, factor, insitu=None, allaxes=None, tsys=True):
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| [101] | 78 | """
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| 79 | Return a scan where all spectra are scaled by the give 'factor'
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| 80 | Parameters:
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| 81 | scan: a scantable
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| [113] | 82 | factor: the scaling factor
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| [258] | 83 | insitu: if False a new scantable is returned.
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| [150] | 84 | Otherwise, the scaling is done in-situ
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| [258] | 85 | The default is taken from .asaprc (False)
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| 86 | allaxes: if True apply to all spectra. Otherwise
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| 87 | apply only to the selected (beam/pol/if)spectra only.
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| [435] | 88 | The default is taken from .asaprc (True if none)
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| [296] | 89 | tsys: if True (default) then apply the operation to Tsys
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| 90 | as well as the data
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| [101] | 91 | """
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| [258] | 92 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 93 | if insitu is None: insitu = rcParams['insitu']
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| [141] | 94 | if not insitu:
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| 95 | from asap._asap import scale as _scale
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| [296] | 96 | return scantable(_scale(scan, factor, allaxes, tsys))
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| [141] | 97 | else:
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| 98 | from asap._asap import scale_insitu as _scale
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| [296] | 99 | _scale(scan, factor, allaxes, tsys)
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| [141] | 100 | return
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| 101 |
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| [101] | 102 |
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| [258] | 103 | def add(scan, offset, insitu=None, allaxes=None):
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| [113] | 104 | """
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| [150] | 105 | Return a scan where all spectra have the offset added
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| [113] | 106 | Parameters:
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| 107 | scan: a scantable
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| [150] | 108 | offset: the offset
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| [258] | 109 | insitu: if False a new scantable is returned.
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| 110 | Otherwise, the scaling is done in-situ
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| 111 | The default is taken from .asaprc (False)
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| 112 | allaxes: if True apply to all spectra. Otherwise
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| [150] | 113 | apply only to the selected (beam/pol/if)spectra only
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| [435] | 114 | The default is taken from .asaprc (True if none)
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| [113] | 115 | """
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| [258] | 116 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 117 | if insitu is None: insitu = rcParams['insitu']
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| [150] | 118 | if not insitu:
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| 119 | from asap._asap import add as _add
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| [258] | 120 | return scantable(_add(scan, offset, allaxes))
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| [150] | 121 | else:
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| 122 | from asap._asap import add_insitu as _add
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| [258] | 123 | _add(scan, offset, allaxes)
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| [150] | 124 | return
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| 125 |
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| [359] | 126 | def convert_flux(scan, jyperk=None, eta=None, d=None, insitu=None, allaxes=None):
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| [224] | 127 | """
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| 128 | Return a scan where all spectra are converted to either Jansky or Kelvin
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| [359] | 129 | depending upon the flux units of the scan table. By default the
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| 130 | function tries to look the values up internally. If it can't find
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| 131 | them (or if you want to over-ride), you must specify EITHER jyperk
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| 132 | OR eta (and D which it will try to look up also if you don't
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| 133 | set it). jyperk takes precedence if you set both.
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| [224] | 134 | Parameters:
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| 135 | scan: a scantable
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| [359] | 136 | jyperk: the Jy / K conversion factor
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| 137 | eta: the aperture efficiency
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| 138 | d: the geomtric diameter (metres)
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| [258] | 139 | insitu: if False a new scantable is returned.
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| 140 | Otherwise, the scaling is done in-situ
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| 141 | The default is taken from .asaprc (False)
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| 142 | allaxes: if True apply to all spectra. Otherwise
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| [224] | 143 | apply only to the selected (beam/pol/if)spectra only
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| [435] | 144 | The default is taken from .asaprc (True if none)
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| [224] | 145 | """
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| [258] | 146 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 147 | if insitu is None: insitu = rcParams['insitu']
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| [359] | 148 | if jyperk is None: jyperk = -1.0
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| 149 | if d is None: d = -1.0
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| 150 | if eta is None: eta = -1.0
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| [224] | 151 | if not insitu:
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| 152 | from asap._asap import convertflux as _convert
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| [359] | 153 | return scantable(_convert(scan, d, eta, jyperk, allaxes))
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| [224] | 154 | else:
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| 155 | from asap._asap import convertflux_insitu as _convert
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| [359] | 156 | _convert(scan, d, eta, jyperk, allaxes)
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| [224] | 157 | return
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| [229] | 158 |
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| [411] | 159 | def gain_el(scan, poly=None, filename="", method="linear",
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| 160 | insitu=None, allaxes=None):
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| [229] | 161 | """
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| [242] | 162 | Return a scan after applying a gain-elevation correction. The correction
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| 163 | can be made via either a polynomial or a table-based interpolation
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| 164 | (and extrapolation if necessary).
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| 165 | You specify polynomial coefficients, an ascii table or neither.
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| 166 | If you specify neither, then a polynomial correction will be made
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| 167 | with built in coefficients known for certain telescopes (an error will
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| 168 | occur if the instrument is not known).
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| [229] | 169 | Parameters:
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| 170 | scan: a scantable
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| [258] | 171 | poly: Polynomial coefficients (default None) to compute a
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| 172 | gain-elevation correction as a function of
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| 173 | elevation (in degrees).
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| [242] | 174 | filename: The name of an ascii file holding correction factors.
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| 175 | The first row of the ascii file must give the column
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| 176 | names and these MUST include columns
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| [258] | 177 | "ELEVATION" (degrees) and "FACTOR" (multiply data by this)
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| 178 | somewhere.
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| 179 | The second row must give the data type of the column. Use
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| 180 | 'R' for Real and 'I' for Integer. An example file
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| 181 | would be:
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| [229] | 182 |
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| [242] | 183 | TIME ELEVATION FACTOR
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| 184 | R R R
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| 185 | 0.1 0 1.5
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| 186 | 0.2 20 1.4
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| 187 | 0.3 40 1.3
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| 188 | 0.4 60 1.2
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| 189 | 0.5 80 1.1
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| 190 | 0.6 90 1.0
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| 191 | method: Interpolation method when correcting from a table. Values
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| 192 | are "nearest", "linear" (default), "cubic" and "spline"
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| [258] | 193 | insitu: if False a new scantable is returned.
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| 194 | Otherwise, the scaling is done in-situ
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| 195 | The default is taken from .asaprc (False)
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| 196 | allaxes: if True apply to all spectra. Otherwise
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| 197 | apply only to the selected (beam/pol/if) spectra only
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| [435] | 198 | The default is taken from .asaprc (True if none)
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| [229] | 199 | """
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| [258] | 200 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| [242] | 201 | if poly is None:
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| 202 | poly = ()
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| [258] | 203 | if insitu is None: insitu = rcParams['insitu']
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| [411] | 204 | from os.path import expandvars
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| 205 | filename = expandvars(filename)
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| [229] | 206 | if not insitu:
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| 207 | from asap._asap import gainel as _gainEl
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| [258] | 208 | return scantable(_gainEl(scan, poly, filename, method, allaxes))
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| [229] | 209 | else:
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| 210 | from asap._asap import gainel_insitu as _gainEl
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| [258] | 211 | _gainEl(scan, poly, filename, method, allaxes)
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| [229] | 212 | return
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| [224] | 213 |
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| [399] | 214 | def freq_align(scan, reftime=None, method='cubic', perif=False, insitu=None):
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| [269] | 215 | """
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| [313] | 216 | Return a scan where all rows have been aligned in frequency. The
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| 217 | alignment frequency frame (e.g. LSRK) is that set by function
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| 218 | set_freqframe.
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| [269] | 219 | scan: a scantable
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| [273] | 220 | reftime: reference time to align at. By default, the time of
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| 221 | the first row of data is used.
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| [319] | 222 | method: Interpolation method for regridding the spectra. Choose
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| 223 | from "nearest", "linear", "cubic" (default) and "spline"
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| [399] | 224 | perif: Generate aligners per freqID (no doppler tracking) or
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| 225 | per IF (scan-based doppler tracking)
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| [269] | 226 | insitu: if False a new scantable is returned.
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| 227 | Otherwise, the scaling is done in-situ
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| 228 | The default is taken from .asaprc (False)
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| 229 | """
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| [273] | 230 | if reftime is None: reftime = ''
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| [269] | 231 | if insitu is None: insitu = rcParams['insitu']
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| [399] | 232 | perfreqid = not perif
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| [269] | 233 | if not insitu:
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| [313] | 234 | from asap._asap import freq_align as _align
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| [399] | 235 | return scantable(_align(scan, reftime, method, perfreqid))
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| [269] | 236 | else:
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| [313] | 237 | from asap._asap import freq_align_insitu as _align
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| [399] | 238 | _align(scan, reftime, method, perfreqid)
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| [269] | 239 | return
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| 240 |
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| [258] | 241 | def opacity(scan, tau, insitu=None, allaxes=None):
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| [242] | 242 | """
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| 243 | Return a scan after applying an opacity correction.
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| 244 | Parameters:
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| 245 | scan: a scantable
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| 246 | tau: Opacity from which the correction factor is exp(tau*ZD)
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| 247 | where ZD is the zenith-distance
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| [258] | 248 | insitu: if False a new scantable is returned.
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| 249 | Otherwise, the scaling is done in-situ
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| 250 | The default is taken from .asaprc (False)
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| 251 | allaxes: if True apply to all spectra. Otherwise
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| [242] | 252 | apply only to the selected (beam/pol/if)spectra only
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| [435] | 253 | The default is taken from .asaprc (True if none)
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| [242] | 254 | """
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| [258] | 255 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 256 | if insitu is None: insitu = rcParams['insitu']
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| [242] | 257 | if not insitu:
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| 258 | from asap._asap import opacity as _opacity
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| [258] | 259 | return scantable(_opacity(scan, tau, allaxes))
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| [242] | 260 | else:
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| 261 | from asap._asap import opacity_insitu as _opacity
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| [258] | 262 | _opacity(scan, tau, allaxes)
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| [242] | 263 | return
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| 264 |
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| [258] | 265 | def bin(scan, width=5, insitu=None):
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| [101] | 266 | """
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| [167] | 267 | Return a scan where all spectra have been binned up
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| [172] | 268 | width: The bin width (default=5) in pixels
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| [258] | 269 | insitu: if False a new scantable is returned.
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| 270 | Otherwise, the scaling is done in-situ
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| 271 | The default is taken from .asaprc (False)
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| [101] | 272 | """
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| [258] | 273 | if insitu is None: insitu = rcParams['insitu']
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| [167] | 274 | if not insitu:
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| 275 | from asap._asap import bin as _bin
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| 276 | return scantable(_bin(scan, width))
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| 277 | else:
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| 278 | from asap._asap import bin_insitu as _bin
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| 279 | _bin(scan, width)
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| 280 | return
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| [113] | 281 |
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| [301] | 282 | def resample(scan, width=5, method='cubic', insitu=None):
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| 283 | """
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| 284 | Return a scan where all spectra have been binned up
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| 285 | width: The bin width (default=5) in pixels
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| 286 | method: Interpolation method when correcting from a table. Values
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| 287 | are "nearest", "linear", "cubic" (default) and "spline"
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| 288 | insitu: if False a new scantable is returned.
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| 289 | Otherwise, the scaling is done in-situ
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| 290 | The default is taken from .asaprc (False)
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| 291 | """
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| 292 | if insitu is None: insitu = rcParams['insitu']
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| 293 | if not insitu:
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| 294 | from asap._asap import resample as _resample
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| 295 | return scantable(_resample(scan, method, width))
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| 296 | else:
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| 297 | from asap._asap import resample_insitu as _resample
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| 298 | _resample(scan, method, width)
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| 299 | return
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| 300 |
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| [316] | 301 | def average_pol(scan, mask=None, weight='none', insitu=None):
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| [113] | 302 | """
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| 303 | Average the Polarisations together.
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| [305] | 304 | The polarisation cursor of the output scan is set to 0
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| [113] | 305 | Parameters:
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| [172] | 306 | scan: The scantable
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| 307 | mask: An optional mask defining the region, where the
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| 308 | averaging will be applied. The output will have all
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| 309 | specified points masked.
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| [316] | 310 | weight: Weighting scheme. 'none' (default), or 'var' (variance
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| 311 | weighted)
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| [258] | 312 | insitu: if False a new scantable is returned.
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| 313 | Otherwise, the scaling is done in-situ
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| 314 | The default is taken from .asaprc (False)
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| [113] | 315 | Example:
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| 316 | polav = average_pols(myscan)
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| 317 | """
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| 318 | if mask is None:
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| [166] | 319 | mask = ()
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| [258] | 320 | if insitu is None: insitu = rcParams['insitu']
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| [166] | 321 | if not insitu:
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| 322 | from asap._asap import averagepol as _avpol
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| [316] | 323 | return scantable(_avpol(scan, mask, weight))
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| [166] | 324 | else:
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| 325 | from asap._asap import averagepol_insitu as _avpol
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| [316] | 326 | _avpol(scan, mask, weight)
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| [166] | 327 | return
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| [113] | 328 |
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| [258] | 329 | def smooth(scan, kernel="hanning", width=5.0, insitu=None, allaxes=None):
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| [113] | 330 | """
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| [180] | 331 | Smooth the spectrum by the specified kernel (conserving flux).
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| [113] | 332 | Parameters:
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| [172] | 333 | scan: The input scan
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| [180] | 334 | kernel: The type of smoothing kernel. Select from
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| 335 | 'hanning' (default), 'gaussian' and 'boxcar'.
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| 336 | The first three characters are sufficient.
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| 337 | width: The width of the kernel in pixels. For hanning this is
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| 338 | ignored otherwise it defauls to 5 pixels.
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| 339 | For 'gaussian' it is the Full Width Half
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| 340 | Maximum. For 'boxcar' it is the full width.
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| [258] | 341 | insitu: if False a new scantable is returned.
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| [172] | 342 | Otherwise, the scaling is done in-situ
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| [258] | 343 | The default is taken from .asaprc (False)
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| 344 | allaxes: If True (default) apply to all spectra. Otherwise
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| [180] | 345 | apply only to the selected (beam/pol/if)spectra only
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| [435] | 346 | The default is taken from .asaprc (True if none)
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| [113] | 347 | Example:
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| 348 | none
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| 349 | """
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| [258] | 350 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 351 | if insitu is None: insitu = rcParams['insitu']
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| [172] | 352 | if not insitu:
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| [180] | 353 | from asap._asap import smooth as _smooth
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| [258] | 354 | return scantable(_smooth(scan,kernel,width,allaxes))
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| [172] | 355 | else:
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| [180] | 356 | from asap._asap import smooth_insitu as _smooth
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| [258] | 357 | _smooth(scan,kernel,width,allaxes)
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| [172] | 358 | return
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| [113] | 359 |
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| [258] | 360 | def poly_baseline(scan, mask=None, order=0, insitu=None):
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| [113] | 361 | """
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| [160] | 362 | Return a scan which has been baselined (all rows) by a polynomial.
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| [113] | 363 | Parameters:
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| 364 | scan: a scantable
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| 365 | mask: an optional mask
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| 366 | order: the order of the polynomial (default is 0)
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| [258] | 367 | insitu: if False a new scantable is returned.
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| 368 | Otherwise, the scaling is done in-situ
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| 369 | The default is taken from .asaprc (False)
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| [113] | 370 | Example:
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| 371 | # return a scan baselined by a third order polynomial,
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| 372 | # not using a mask
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| 373 | bscan = poly_baseline(scan, order=3)
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| 374 | """
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| 375 | from asap.asapfitter import fitter
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| 376 | if mask is None:
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| 377 | from numarray import ones
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| 378 | mask = tuple(ones(scan.nchan()))
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| 379 | f = fitter()
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| 380 | f._verbose(True)
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| 381 | f.set_scan(scan, mask)
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| 382 | f.set_function(poly=order)
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| [258] | 383 | sf = f.auto_fit(insitu)
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| [113] | 384 | return sf
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