| [102] | 1 | from asap._asap import sdtable
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| 2 | from numarray import ones
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| 3 | import sys
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| 4 |
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| 5 | class scantable(sdtable):
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| 6 | """
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| 7 | The ASAP container for scans
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| 8 | """
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| [113] | 9 |
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| [102] | 10 | def __init__(self, filename):
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| 11 | """
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| 12 | Create a scantable from a saved one or make a reference
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| 13 | Parameters:
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| 14 | filename: the name of an asap table on disk, or
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| 15 | [advanced] a refernce to an existing
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| 16 | scantable
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| 17 | """
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| [113] | 18 | self._vb = True
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| 19 | self._p = None
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| [102] | 20 | sdtable.__init__(self, filename)
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| 21 |
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| [116] | 22 | def save(self, name, format='ASAP'):
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| 23 | """
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| 24 | Store the scantable on disk. This can be a asap file or SDFITS/MS2.
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| 25 | Parameters:
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| 26 | name: the name of the outputfile
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| 27 | format: an optional file format. Default is ASAP.
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| 28 | Alllowed are 'ASAP', 'SDFITS' and 'MS2'
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| 29 | Example:
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| 30 | scan.save('myscan.asap')
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| 31 | scan.save('myscan.sdfits','SDFITS')
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| 32 | """
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| 33 | if format == 'ASAP':
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| 34 | self._save(name)
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| 35 | else:
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| 36 | from asap._asap import sdwriter as _sw
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| 37 | w = _sw()
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| 38 | if format == 'SDFITS':
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| 39 | w.write(self, name)
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| 40 | return
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| 41 |
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| [113] | 42 | def _verbose(self, *args):
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| 43 | """
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| 44 | Set the verbose level True or False, to indicate if output
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| 45 | should be printed as well as returned.
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| 46 | """
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| [126] | 47 | if len(args) == 0:
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| 48 | return self._vb
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| 49 | elif type(args[0]) is bool:
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| [113] | 50 | self._vb = args[0]
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| 51 | return
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| 52 |
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| [102] | 53 | def copy(self):
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| 54 | """
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| 55 | Return a copy of this scantable.
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| 56 | Parameters:
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| [113] | 57 | none
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| [102] | 58 | Example:
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| 59 | copiedscan = scan.copy()
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| 60 | """
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| [113] | 61 | sd = scantable(sdtable._copy(self))
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| 62 | return sd
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| 63 |
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| [102] | 64 | def get_scan(self, scanid=None):
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| 65 | """
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| 66 | Return a specific scan (by scanno) or collection of scans (by
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| 67 | source name) in a new scantable.
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| 68 | Parameters:
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| 69 | scanid: a scanno or a source name
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| 70 | Example:
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| [113] | 71 | scan.get_scan('323p459')
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| [102] | 72 | # gets all scans containing the source '323p459'
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| 73 | """
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| 74 | if scanid is None:
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| 75 | print "Please specify a scan no or name to retrieve from the scantable"
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| 76 | try:
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| 77 | if type(scanid) is str:
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| [113] | 78 | s = sdtable._getsource(self,scanid)
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| [102] | 79 | return scantable(s)
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| 80 | elif type(scanid) is int:
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| [113] | 81 | s = sdtable._getscan(self,scanid)
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| [102] | 82 | return scantable(s)
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| 83 | except RuntimeError:
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| 84 | print "Couldn't find any match."
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| 85 |
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| 86 | def __str__(self):
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| 87 | return sdtable.summary(self)
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| 88 |
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| 89 | def summary(self,filename=None):
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| 90 | """
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| 91 | Print a summary of the contents of this scantable.
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| 92 | Parameters:
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| 93 | filename: the name of a file to write the putput to
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| 94 | Default - no file output
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| 95 | """
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| 96 | info = sdtable.summary(self)
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| 97 | if filename is not None:
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| 98 | data = open(filename, 'w')
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| 99 | data.write(info)
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| 100 | data.close()
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| 101 | print info
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| 102 |
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| 103 | def set_selection(self, thebeam=0,theif=0,thepol=0):
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| 104 | """
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| 105 | Set the spectrum for individual operations.
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| 106 | Parameters:
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| 107 | thebeam,theif,thepol: a number
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| 108 | Example:
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| 109 | scan.set_selection(0,0,1)
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| [135] | 110 | pol1sig = scan.stats(all=False) # returns std dev for beam=0
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| [102] | 111 | # if=0, pol=1
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| 112 | """
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| 113 | self.setbeam(thebeam)
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| 114 | self.setpol(thepol)
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| 115 | self.setif(theif)
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| 116 | return
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| 117 |
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| 118 | def get_selection(self):
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| [113] | 119 | """
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| 120 | Return/print a the current 'cursor' into the Beam/IF/Pol cube.
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| 121 | Parameters:
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| 122 | none
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| 123 | Returns:
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| 124 | a list of values (currentBeam,currentIF,currentPol)
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| 125 | Example:
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| 126 | none
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| 127 | """
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| [102] | 128 | i = self.getbeam()
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| 129 | j = self.getif()
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| 130 | k = self.getpol()
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| [113] | 131 | if self._vb:
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| 132 | out = 'Beam=%d IF=%d Pol=%d '% (i,j,k)
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| 133 | print out
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| [102] | 134 | return i,j,k
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| 135 |
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| [135] | 136 | def stats(self, stat='stddev', mask=None, all=True):
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| [102] | 137 | """
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| [135] | 138 | Determine the specified statistic of the current beam/if/pol
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| [102] | 139 | Takes a 'mask' as an optional parameter to specify which
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| 140 | channels should be excluded.
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| 141 | Parameters:
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| [135] | 142 | stat: 'min', 'max', 'sumsq', 'sum', 'mean'
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| 143 | 'var', 'stddev', 'avdev', 'rms', 'median'
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| 144 | mask: an optional mask specifying where the statistic
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| [102] | 145 | should be determined.
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| [156] | 146 | all: optional flag to show all (default) or a selected
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| [102] | 147 | spectrum of Beam/IF/Pol
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| 148 |
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| 149 | Example:
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| [113] | 150 | scan.set_unit('channel')
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| [102] | 151 | msk = scan.create_mask([100,200],[500,600])
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| [135] | 152 | scan.stats(stat='mean', mask=m)
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| [102] | 153 | """
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| [135] | 154 | from asap._asap import stats as _stats
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| [102] | 155 | if mask == None:
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| 156 | mask = ones(self.nchan())
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| 157 | if all:
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| 158 | out = ''
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| 159 | tmp = []
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| 160 | for i in range(self.nbeam()):
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| 161 | self.setbeam(i)
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| 162 | for j in range(self.nif()):
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| 163 | self.setif(j)
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| 164 | for k in range(self.npol()):
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| 165 | self.setpol(k)
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| [135] | 166 | statVal = _stats(self,mask,stat)
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| 167 | tmp.append(statVal)
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| 168 | # out += 'Beam[%d], IF[%d], Pol[%d] = %3.3f\n' % (i,j,k,statVal)
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| 169 | # if self._vb:
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| 170 | # print out
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| [102] | 171 | return tmp
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| 172 |
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| 173 | else:
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| 174 | i = self.getbeam()
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| 175 | j = self.getif()
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| 176 | k = self.getpol()
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| [135] | 177 | statVal = _stats(self,mask,stat)
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| 178 | # out = 'Beam[%d], IF[%d], Pol[%d] = %3.3f' % (i,j,k,statVal)
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| 179 | # if self._vb:
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| 180 | # print out
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| 181 | return statVal
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| [102] | 182 |
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| [135] | 183 | def stddev(self,mask=None, all=True):
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| 184 | """
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| 185 | Determine the standard deviation of the current beam/if/pol
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| 186 | Takes a 'mask' as an optional parameter to specify which
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| 187 | channels should be excluded.
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| 188 | Parameters:
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| 189 | mask: an optional mask specifying where the standard
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| 190 | deviation should be determined.
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| 191 | all: optional flag to show all or a selected
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| 192 | spectrum of Beam/IF/Pol
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| 193 |
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| 194 | Example:
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| 195 | scan.set_unit('channel')
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| 196 | msk = scan.create_mask([100,200],[500,600])
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| 197 | scan.stddev(mask=m)
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| 198 | """
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| 199 | return self.stats(stat='stddev',mask=mask, all=all);
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| 200 |
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| [102] | 201 | def get_tsys(self, all=True):
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| [113] | 202 | """
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| 203 | Return the System temperatures.
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| 204 | Parameters:
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| 205 | all: optional parameter to get the Tsys values for all
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| 206 | Beams/IFs/Pols (default) or just the one selected
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| 207 | with scantable.set_selection()
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| 208 | [True or False]
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| 209 | Returns:
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| 210 | a list of Tsys values.
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| 211 | """
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| [102] | 212 | if all:
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| 213 | tmp = []
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| 214 | out = ''
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| 215 | for i in range(self.nbeam()):
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| 216 | self.setbeam(i)
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| 217 | for j in range(self.nif()):
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| 218 | self.setif(j)
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| 219 | for k in range(self.npol()):
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| 220 | self.setpol(k)
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| [113] | 221 | ts = self._gettsys()
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| [102] | 222 | tmp.append(ts)
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| [156] | 223 | # out += 'TSys: Beam[%d], IF[%d], Pol[%d] = %3.3f\n' % (i,j,k,ts)
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| 224 | # if self._vb:
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| 225 | # print out
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| [102] | 226 | return tmp
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| 227 | else:
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| 228 | i = self.getbeam()
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| 229 | j = self.getif()
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| 230 | k = self.getpol()
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| [113] | 231 | ts = self._gettsys()
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| [156] | 232 | # out = 'TSys: Beam[%d], IF[%d], Pol[%d] = %3.3f' % (i,j,k,ts)
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| 233 | # if self._vb:
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| 234 | # print out
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| [102] | 235 | return ts
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| [113] | 236 |
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| 237 | def get_time(self):
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| 238 | """
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| 239 | Get a list of time stamps for the observations.
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| 240 | Return a string for each intergration in the scantable.
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| 241 | Parameters:
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| 242 | none
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| 243 | Example:
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| 244 | none
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| 245 | """
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| 246 | out = []
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| 247 | for i in range(self.nrow()):
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| 248 | out.append(self._gettime(i))
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| 249 | return out
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| [102] | 250 |
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| 251 | def set_unit(self, unit='channel'):
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| 252 | """
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| 253 | Set the unit for all following operations on this scantable
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| 254 | Parameters:
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| 255 | unit: optional unit, default is 'channel'
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| [113] | 256 | one of '*Hz','km/s','channel', ''
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| [102] | 257 | """
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| [113] | 258 |
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| 259 | if unit in ['','pixel', 'channel']:
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| 260 | unit = ''
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| 261 | inf = list(self._getcoordinfo())
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| 262 | inf[0] = unit
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| 263 | self._setcoordinfo(inf)
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| 264 | if self._p: self.plot()
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| 265 |
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| 266 | def set_freqframe(self, frame='LSRK'):
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| 267 | """
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| 268 | Set the frame type of the Spectral Axis.
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| 269 | Parameters:
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| 270 | frame: an optional frame type, default 'LSRK'.
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| 271 | Examples:
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| 272 | scan.set_freqframe('BARY')
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| 273 | """
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| 274 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \
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| 275 | 'GEO','GALACTO','LGROUP','CMB']
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| 276 | if frame in valid:
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| 277 | inf = list(self._getcoordinfo())
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| 278 | inf[1] = frame
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| 279 | self._setcoordinfo(inf)
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| [102] | 280 | else:
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| [113] | 281 | print "Please specify a valid freq type. Valid types are:\n",valid
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| 282 |
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| 283 | def get_unit(self):
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| 284 | """
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| 285 | Get the default unit set in this scantable
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| 286 | Parameters:
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| 287 | Returns:
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| 288 | A unit string
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| 289 | """
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| 290 | inf = self._getcoordinfo()
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| 291 | unit = inf[0]
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| 292 | if unit == '': unit = 'channel'
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| 293 | return unit
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| [102] | 294 |
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| [158] | 295 | def get_abcissa(self, rowno=0):
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| [102] | 296 | """
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| [158] | 297 | Get the abcissa in the current coordinate setup for the currently
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| [113] | 298 | selected Beam/IF/Pol
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| 299 | Parameters:
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| 300 | none
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| 301 | Returns:
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| [158] | 302 | The abcissa values and it's format string.
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| [113] | 303 | """
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| [158] | 304 | abc = self.getabcissa(rowno)
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| 305 | lbl = self.getabcissalabel(rowno)
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| 306 | return abc, lbl
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| [113] | 307 |
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| 308 | def create_mask(self, *args, **kwargs):
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| 309 | """
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| [102] | 310 | Compute and return a mask based on [min,max] windows.
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| [113] | 311 | The specified windows are to be EXCLUDED, when the mask is
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| 312 | applied.
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| [102] | 313 | Parameters:
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| 314 | [min,max],[min2,max2],...
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| 315 | Pairs of start/end points specifying the regions
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| 316 | to be masked
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| [113] | 317 | invert: return an inverted mask, i.e. the regions
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| 318 | specified are not masked (INCLUDED)
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| [102] | 319 | Example:
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| [113] | 320 | scan.set_unit('channel')
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| 321 |
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| 322 | a)
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| [102] | 323 | msk = scan.set_mask([400,500],[800,900])
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| [113] | 324 | # masks the regions between 400 and 500
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| 325 | # and 800 and 900 in the unit 'channel'
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| 326 |
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| 327 | b)
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| 328 | msk = scan.set_mask([400,500],[800,900], invert=True)
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| 329 | # masks the regions outside 400 and 500
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| 330 | # and 800 and 900 in the unit 'channel'
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| 331 |
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| [102] | 332 | """
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| [113] | 333 | u = self._getcoordinfo()[0]
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| 334 | if self._vb:
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| 335 | if u == "": u = "channel"
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| 336 | print "The current mask window unit is", u
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| [102] | 337 | n = self.nchan()
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| [158] | 338 | data = self.getabcissa()
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| [102] | 339 | msk = ones(n)
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| 340 | for window in args:
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| 341 | if (len(window) != 2 or window[0] > window[1] ):
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| 342 | print "A window needs to be defined as [min,max]"
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| 343 | return
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| 344 | for i in range(n):
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| [113] | 345 | if data[i] >= window[0] and data[i] < window[1]:
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| [102] | 346 | msk[i] = 0
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| [113] | 347 | if kwargs.has_key('invert'):
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| 348 | if kwargs.get('invert'):
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| 349 | from numarray import logical_not
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| 350 | msk = logical_not(msk)
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| [102] | 351 | return msk
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| [113] | 352 |
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| 353 | def set_restfreqs(self, freqs, unit='Hz'):
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| [102] | 354 | """
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| 355 | Set the restfrequency(s) for this scantable.
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| 356 | Parameters:
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| 357 | freqs: one or more frequencies
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| 358 | unit: optional 'unit', default 'Hz'
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| 359 | Example:
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| [113] | 360 | scan.set_restfreqs([1000000000.0])
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| [102] | 361 | """
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| [113] | 362 | if type(freqs) is float or int:
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| 363 | freqs = (freqs)
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| 364 | sdtable._setrestfreqs(self,freqs, unit)
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| [102] | 365 | return
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| 366 |
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| 367 | def flag_spectrum(self, thebeam, theif, thepol):
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| 368 | """
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| 369 | This flags a selected spectrum in the scan 'for good'.
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| 370 | USE WITH CARE - not reversible.
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| 371 | Use masks for non-permanent exclusion of channels.
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| 372 | Parameters:
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| 373 | thebeam,theif,thepol: all have to be explicitly
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| 374 | specified
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| 375 | Example:
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| 376 | scan.flag_spectrum(0,0,1)
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| 377 | flags the spectrum for Beam=0, IF=0, Pol=1
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| 378 | """
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| 379 | if (thebeam < self.nbeam() and theif < self.nif() and thepol < self.npol()):
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| 380 | stable.setbeam(thebeam)
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| 381 | stable.setif(theif)
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| 382 | stable.setpol(thepol)
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| 383 | stable._flag(self)
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| 384 | else:
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| 385 | print "Please specify a valid (Beam/IF/Pol)"
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| 386 | return
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| [113] | 387 |
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| 388 | def plot(self, what='spectrum',col='Pol', panel=None):
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| 389 | """
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| 390 | Plot the spectra contained in the scan. Alternatively you can also
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| 391 | Plot Tsys vs Time
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| 392 | Parameters:
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| 393 | what: a choice of 'spectrum' (default) or 'tsys'
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| [135] | 394 | col: which out of Beams/IFs/Pols should be colour stacked
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| [113] | 395 | panel: set up multiple panels, currently not working.
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| 396 | """
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| 397 | validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()}
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| [124] | 398 |
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| [113] | 399 | validyax = ['spectrum','tsys']
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| 400 | if not self._p:
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| 401 | from asap.asaplot import ASAPlot
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| 402 | self._p = ASAPlot()
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| 403 | # print "Plotting not enabled"
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| 404 | # return
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| 405 | npan = 1
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| 406 | x = None
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| 407 | if what == 'tsys':
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| 408 | n = self.nrow()
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| 409 | if n < 2:
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| 410 | print "Only one integration. Can't plot."
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| 411 | return
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| [124] | 412 | self._p.hold()
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| 413 | self._p.clear()
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| [113] | 414 | if panel == 'Time':
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| 415 | npan = self.nrow()
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| [124] | 416 | self._p.set_panels(rows=npan)
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| [113] | 417 | xlab,ylab,tlab = None,None,None
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| [124] | 418 | vb = self._verbose()
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| [113] | 419 | self._verbose(False)
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| 420 | sel = self.get_selection()
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|---|
| 421 | for i in range(npan):
|
|---|
| [124] | 422 | self._p.subplot(i)
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|---|
| [113] | 423 | for j in range(validcol[col]):
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|---|
| 424 | x = None
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|---|
| 425 | y = None
|
|---|
| 426 | m = None
|
|---|
| 427 | tlab = self._getsourcename(i)
|
|---|
| [124] | 428 | import re
|
|---|
| 429 | tlab = re.sub('_S','',tlab)
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|---|
| [113] | 430 | if col == 'Beam':
|
|---|
| 431 | self.setbeam(j)
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|---|
| 432 | elif col == 'IF':
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|---|
| 433 | self.setif(j)
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|---|
| 434 | elif col == 'Pol':
|
|---|
| 435 | self.setpol(j)
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|---|
| 436 | if what == 'tsys':
|
|---|
| 437 | x = range(self.nrow())
|
|---|
| 438 | xlab = 'Time [pixel]'
|
|---|
| 439 | m = list(ones(len(x)))
|
|---|
| 440 | y = []
|
|---|
| 441 | ylab = r'$T_{sys}$'
|
|---|
| 442 | for k in range(len(x)):
|
|---|
| 443 | y.append(self._gettsys(k))
|
|---|
| 444 | else:
|
|---|
| [158] | 445 | x,xlab = self.get_abcissa(i)
|
|---|
| [113] | 446 | y = self.getspectrum(i)
|
|---|
| 447 | ylab = r'Flux'
|
|---|
| 448 | m = self.getmask(i)
|
|---|
| 449 | llab = col+' '+str(j)
|
|---|
| 450 | self._p.set_line(label=llab)
|
|---|
| 451 | self._p.plot(x,y,m)
|
|---|
| [124] | 452 | self._p.set_axes('xlabel',xlab)
|
|---|
| 453 | self._p.set_axes('ylabel',ylab)
|
|---|
| 454 | self._p.set_axes('title',tlab)
|
|---|
| [113] | 455 | self._p.release()
|
|---|
| 456 | self.set_selection(sel[0],sel[1],sel[2])
|
|---|
| 457 | self._verbose(vb)
|
|---|
| 458 | return
|
|---|
