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 |
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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() |
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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 |
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457 | |
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458 | def rotate_linpolphase(scan, angle, allaxes=None): |
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459 | """ |
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460 | Rotate the phase of the complex polarization O=Q+iU correlation. |
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461 | This is always done in situ in the raw data. So if you call this |
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462 | function more than once then each call rotates the phase further. |
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463 | Parameters: |
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464 | angle: The angle (degrees) to rotate (add) by. |
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465 | allaxes: If True apply to all spectra. Otherwise |
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466 | apply only to the selected (beam/pol/if)spectra only. |
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467 | The default is taken from .asaprc (True if none) |
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468 | Examples: |
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469 | rotate_linpolphase(scan, 2.3) |
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470 | """ |
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471 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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472 | varlist = vars() |
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473 | from asap._asap import _rotate_linpolphase as _rotate |
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474 | _rotate(scan, angle, allaxes) |
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475 | scan._add_history("rotate_linpolphase", varlist) |
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476 | return |
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477 | |
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