[102] | 1 | from asap._asap import sdtable
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[226] | 2 | from asap import rcParams
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[189] | 3 | from numarray import ones,zeros
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[102] | 4 | import sys
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| 5 |
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| 6 | class scantable(sdtable):
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| 7 | """
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| 8 | The ASAP container for scans
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| 9 | """
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[113] | 10 |
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[340] | 11 | def __init__(self, filename, unit=None):
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[102] | 12 | """
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| 13 | Create a scantable from a saved one or make a reference
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| 14 | Parameters:
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[181] | 15 | filename: the name of an asap table on disk
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| 16 | or
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| 17 | the name of a rpfits/sdfits/ms file
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| 18 | (integrations within scans are auto averaged
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| 19 | and the whole file is read)
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| 20 | or
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| 21 | [advanced] a reference to an existing
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[102] | 22 | scantable
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[340] | 23 | unit: brightness unit; must be consistent with K or Jy.
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| 24 | Over-rides the default selected by the reader
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| 25 | (input rpfits/sdfits/ms) or replaces the value
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| 26 | in existing scantables
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[102] | 27 | """
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[226] | 28 | self._vb = rcParams['verbose']
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[113] | 29 | self._p = None
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[181] | 30 | from os import stat as st
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| 31 | import stat
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| 32 | if isinstance(filename,sdtable):
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| 33 | sdtable.__init__(self, filename)
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[340] | 34 | if unit is not None:
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[346] | 35 | self.set_fluxunit(unit)
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[181] | 36 | else:
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[411] | 37 | import os.path
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| 38 | if not os.path.exists(filename):
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| 39 | print "File '%s' not found." % (filename)
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[226] | 40 | return
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[411] | 41 | filename = os.path.expandvars(filename)
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| 42 | if os.path.isdir(filename):
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[181] | 43 | # crude check if asap table
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[411] | 44 | if os.path.exists(filename+'/table.info'):
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[181] | 45 | sdtable.__init__(self, filename)
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[340] | 46 | if unit is not None:
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| 47 | self.set_fluxunit(unit)
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[181] | 48 | else:
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[411] | 49 | print "The given file '%s'is not a valid asap table." % (filename)
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[226] | 50 | return
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| 51 | else:
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| 52 | autoav = rcParams['scantable.autoaverage']
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| 53 |
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[181] | 54 | from asap._asap import sdreader
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[340] | 55 | ifSel = -1
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| 56 | beamSel = -1
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[345] | 57 | r = sdreader(filename,ifSel,beamSel)
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[181] | 58 | print 'Importing data...'
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[411] | 59 | r._read([-1])
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| 60 | tbl = r._getdata()
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[346] | 61 | if unit is not None:
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| 62 | tbl.set_fluxunit(unit)
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[226] | 63 | if autoav:
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| 64 | from asap._asap import average
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| 65 | tmp = tuple([tbl])
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| 66 | print 'Auto averaging integrations...'
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| 67 | tbl2 = average(tmp,(),True,'none')
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| 68 | sdtable.__init__(self,tbl2)
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| 69 | del r,tbl
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| 70 | else:
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| 71 | sdtable.__init__(self,tbl)
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[102] | 72 |
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[451] | 73 | def save(self, name=None, format=None, stokes=False, overwrite=False):
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[116] | 74 | """
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[280] | 75 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS,
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| 76 | Image FITS or MS2 format.
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[116] | 77 | Parameters:
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[196] | 78 | name: the name of the outputfile. For format="FITS" this
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[280] | 79 | is the directory file name into which all the files will
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| 80 | be written (default is 'asap_FITS')
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[116] | 81 | format: an optional file format. Default is ASAP.
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[280] | 82 | Allowed are - 'ASAP' (save as ASAP [aips++] Table),
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[194] | 83 | 'SDFITS' (save as SDFITS file)
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| 84 | 'FITS' (saves each row as a FITS Image)
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[200] | 85 | 'ASCII' (saves as ascii text file)
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[226] | 86 | 'MS2' (saves as an aips++
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| 87 | MeasurementSet V2)
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[445] | 88 | stokes: Convert to Stokes parameters (only available
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| 89 | currently with FITS and ASCII formats.
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[451] | 90 | Default is False.
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[411] | 91 | overwrite: If the file should be overwritten if it exists.
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[256] | 92 | The default False is to return with warning
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[411] | 93 | without writing the output. USE WITH CARE.
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[116] | 94 | Example:
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| 95 | scan.save('myscan.asap')
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| 96 | scan.save('myscan.sdfits','SDFITS')
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| 97 | """
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[411] | 98 | from os import path
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[226] | 99 | if format is None: format = rcParams['scantable.save']
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[256] | 100 | suffix = '.'+format.lower()
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| 101 | if name is None or name =="":
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| 102 | name = 'scantable'+suffix
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[283] | 103 | print "No filename given. Using default name %s..." % name
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[411] | 104 | name = path.expandvars(name)
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[256] | 105 | if path.isfile(name) or path.isdir(name):
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| 106 | if not overwrite:
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| 107 | print "File %s already exists." % name
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| 108 | return
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[451] | 109 | format2 = format.upper()
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| 110 | if format2 == 'ASAP':
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[116] | 111 | self._save(name)
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| 112 | else:
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| 113 | from asap._asap import sdwriter as _sw
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[451] | 114 | w = _sw(format2)
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[445] | 115 | w.write(self, name, stokes)
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[116] | 116 | return
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| 117 |
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[102] | 118 | def copy(self):
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| 119 | """
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| 120 | Return a copy of this scantable.
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| 121 | Parameters:
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[113] | 122 | none
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[102] | 123 | Example:
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| 124 | copiedscan = scan.copy()
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| 125 | """
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[113] | 126 | sd = scantable(sdtable._copy(self))
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| 127 | return sd
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| 128 |
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[102] | 129 | def get_scan(self, scanid=None):
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| 130 | """
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| 131 | Return a specific scan (by scanno) or collection of scans (by
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| 132 | source name) in a new scantable.
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| 133 | Parameters:
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| 134 | scanid: a scanno or a source name
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| 135 | Example:
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[113] | 136 | scan.get_scan('323p459')
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[102] | 137 | # gets all scans containing the source '323p459'
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| 138 | """
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| 139 | if scanid is None:
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| 140 | print "Please specify a scan no or name to retrieve from the scantable"
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| 141 | try:
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| 142 | if type(scanid) is str:
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[113] | 143 | s = sdtable._getsource(self,scanid)
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[102] | 144 | return scantable(s)
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| 145 | elif type(scanid) is int:
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[381] | 146 | s = sdtable._getscan(self,[scanid])
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| 147 | return scantable(s)
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| 148 | elif type(scanid) is list:
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[113] | 149 | s = sdtable._getscan(self,scanid)
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[102] | 150 | return scantable(s)
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[381] | 151 | else:
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| 152 | print "Illegal scanid type, use 'int' or 'list' if ints."
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[102] | 153 | except RuntimeError:
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| 154 | print "Couldn't find any match."
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| 155 |
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| 156 | def __str__(self):
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[381] | 157 | return sdtable._summary(self,True)
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[102] | 158 |
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[381] | 159 | def summary(self,filename=None, verbose=None):
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[102] | 160 | """
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| 161 | Print a summary of the contents of this scantable.
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| 162 | Parameters:
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| 163 | filename: the name of a file to write the putput to
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| 164 | Default - no file output
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[381] | 165 | verbose: print extra info such as the frequency table
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| 166 | The default (False) is taken from .asaprc
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[102] | 167 | """
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[381] | 168 | info = sdtable._summary(self, verbose)
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| 169 | if verbose is None: verbose = rcParams['scantable.verbosesummary']
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[102] | 170 | if filename is not None:
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[256] | 171 | if filename is "":
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| 172 | filename = 'scantable_summary.txt'
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[415] | 173 | from os.path import expandvars, isdir
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[411] | 174 | filename = expandvars(filename)
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[415] | 175 | if not isdir(filename):
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[413] | 176 | data = open(filename, 'w')
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| 177 | data.write(info)
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| 178 | data.close()
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| 179 | else:
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| 180 | print "Illegal file name '%s'." % (filename)
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[102] | 181 | print info
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| 182 |
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[256] | 183 | def set_cursor(self, thebeam=0,theif=0,thepol=0):
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[102] | 184 | """
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| 185 | Set the spectrum for individual operations.
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| 186 | Parameters:
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| 187 | thebeam,theif,thepol: a number
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| 188 | Example:
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[256] | 189 | scan.set_cursor(0,0,1)
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[135] | 190 | pol1sig = scan.stats(all=False) # returns std dev for beam=0
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[181] | 191 | # if=0, pol=1
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[102] | 192 | """
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| 193 | self.setbeam(thebeam)
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| 194 | self.setpol(thepol)
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| 195 | self.setif(theif)
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| 196 | return
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| 197 |
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[256] | 198 | def get_cursor(self):
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[113] | 199 | """
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| 200 | Return/print a the current 'cursor' into the Beam/IF/Pol cube.
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| 201 | Parameters:
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| 202 | none
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| 203 | Returns:
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| 204 | a list of values (currentBeam,currentIF,currentPol)
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| 205 | Example:
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| 206 | none
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| 207 | """
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[102] | 208 | i = self.getbeam()
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| 209 | j = self.getif()
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| 210 | k = self.getpol()
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[113] | 211 | if self._vb:
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[181] | 212 | print "--------------------------------------------------"
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[256] | 213 | print " Cursor position"
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[181] | 214 | print "--------------------------------------------------"
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[226] | 215 | out = 'Beam=%d IF=%d Pol=%d ' % (i,j,k)
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[113] | 216 | print out
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[102] | 217 | return i,j,k
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| 218 |
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[436] | 219 | def stats(self, stat='stddev', mask=None, allaxes=None):
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[102] | 220 | """
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[135] | 221 | Determine the specified statistic of the current beam/if/pol
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[102] | 222 | Takes a 'mask' as an optional parameter to specify which
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| 223 | channels should be excluded.
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| 224 | Parameters:
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[135] | 225 | stat: 'min', 'max', 'sumsq', 'sum', 'mean'
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| 226 | 'var', 'stddev', 'avdev', 'rms', 'median'
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| 227 | mask: an optional mask specifying where the statistic
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[102] | 228 | should be determined.
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[436] | 229 | allaxes: if True apply to all spectra. Otherwise
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| 230 | apply only to the selected (beam/pol/if)spectra only.
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| 231 | The default is taken from .asaprc (True if none)
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[102] | 232 | Example:
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[113] | 233 | scan.set_unit('channel')
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[102] | 234 | msk = scan.create_mask([100,200],[500,600])
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[135] | 235 | scan.stats(stat='mean', mask=m)
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[102] | 236 | """
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[436] | 237 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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[135] | 238 | from asap._asap import stats as _stats
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[256] | 239 | from numarray import array,zeros,Float
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[102] | 240 | if mask == None:
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| 241 | mask = ones(self.nchan())
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[256] | 242 | axes = ['Beam','IF','Pol','Time']
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| 243 |
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[436] | 244 | beamSel,IFSel,polSel = (self.getbeam(),self.getif(),self.getpol())
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| 245 | if allaxes:
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[256] | 246 | n = self.nbeam()*self.nif()*self.npol()*self.nrow()
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| 247 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()]
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| 248 | arr = array(zeros(n),shape=shp,type=Float)
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| 249 |
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| 250 | for i in range(self.nbeam()):
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| 251 | self.setbeam(i)
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| 252 | for j in range(self.nif()):
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| 253 | self.setif(j)
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| 254 | for k in range(self.npol()):
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| 255 | self.setpol(k)
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| 256 | arr[i,j,k,:] = _stats(self,mask,stat,-1)
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| 257 | retval = {'axes': axes, 'data': arr, 'cursor':None}
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| 258 | tm = [self._gettime(val) for val in range(self.nrow())]
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[181] | 259 | if self._vb:
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[256] | 260 | self._print_values(retval,stat,tm)
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[436] | 261 | self.setbeam(beamSel)
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| 262 | self.setif(IFSel)
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| 263 | self.setpol(polSel)
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[256] | 264 | return retval
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[102] | 265 |
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| 266 | else:
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[241] | 267 | statval = _stats(self,mask,stat,-1)
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[181] | 268 | out = ''
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| 269 | for l in range(self.nrow()):
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| 270 | tm = self._gettime(l)
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| 271 | out += 'Time[%s]:\n' % (tm)
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[436] | 272 | if self.nbeam() > 1: out += ' Beam[%d] ' % (beamSel)
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| 273 | if self.nif() > 1: out += ' IF[%d] ' % (IFSel)
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| 274 | if self.npol() > 1: out += ' Pol[%d] ' % (polSel)
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[181] | 275 | out += '= %3.3f\n' % (statval[l])
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| 276 | out += "--------------------------------------------------\n"
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[226] | 277 |
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[181] | 278 | if self._vb:
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| 279 | print "--------------------------------------------------"
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| 280 | print " ",stat
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| 281 | print "--------------------------------------------------"
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| 282 | print out
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[256] | 283 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)}
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| 284 | return retval
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[102] | 285 |
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[436] | 286 | def stddev(self,mask=None, allaxes=None):
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[135] | 287 | """
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| 288 | Determine the standard deviation of the current beam/if/pol
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| 289 | Takes a 'mask' as an optional parameter to specify which
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| 290 | channels should be excluded.
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| 291 | Parameters:
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| 292 | mask: an optional mask specifying where the standard
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| 293 | deviation should be determined.
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[436] | 294 | allaxes: optional flag to show all or a cursor selected
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[226] | 295 | spectrum of Beam/IF/Pol. Default is all or taken
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| 296 | from .asaprc
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[135] | 297 |
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| 298 | Example:
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| 299 | scan.set_unit('channel')
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| 300 | msk = scan.create_mask([100,200],[500,600])
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| 301 | scan.stddev(mask=m)
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| 302 | """
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[436] | 303 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 304 | return self.stats(stat='stddev',mask=mask, allaxes=allaxes);
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[135] | 305 |
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[436] | 306 | def get_tsys(self, allaxes=None):
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[113] | 307 | """
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| 308 | Return the System temperatures.
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| 309 | Parameters:
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[436] | 310 | allaxes: if True apply to all spectra. Otherwise
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| 311 | apply only to the selected (beam/pol/if)spectra only.
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| 312 | The default is taken from .asaprc (True if none)
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[113] | 313 | Returns:
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| 314 | a list of Tsys values.
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| 315 | """
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[436] | 316 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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[256] | 317 | from numarray import array,zeros,Float
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| 318 | axes = ['Beam','IF','Pol','Time']
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| 319 |
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[436] | 320 | if allaxes:
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[256] | 321 | n = self.nbeam()*self.nif()*self.npol()*self.nrow()
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| 322 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()]
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| 323 | arr = array(zeros(n),shape=shp,type=Float)
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| 324 |
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| 325 | for i in range(self.nbeam()):
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| 326 | self.setbeam(i)
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| 327 | for j in range(self.nif()):
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| 328 | self.setif(j)
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| 329 | for k in range(self.npol()):
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| 330 | self.setpol(k)
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| 331 | arr[i,j,k,:] = self._gettsys()
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| 332 | retval = {'axes': axes, 'data': arr, 'cursor':None}
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| 333 | tm = [self._gettime(val) for val in range(self.nrow())]
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[181] | 334 | if self._vb:
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[256] | 335 | self._print_values(retval,'Tsys',tm)
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| 336 | return retval
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| 337 |
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[102] | 338 | else:
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[256] | 339 | i,j,k = (self.getbeam(),self.getif(),self.getpol())
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| 340 | statval = self._gettsys()
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[181] | 341 | out = ''
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| 342 | for l in range(self.nrow()):
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| 343 | tm = self._gettime(l)
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| 344 | out += 'Time[%s]:\n' % (tm)
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| 345 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i)
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| 346 | if self.nif() > 1: out += ' IF[%d] ' % (j)
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| 347 | if self.npol() > 1: out += ' Pol[%d] ' % (k)
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[256] | 348 | out += '= %3.3f\n' % (statval[l])
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| 349 | out += "--------------------------------------------------\n"
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| 350 |
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[181] | 351 | if self._vb:
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| 352 | print "--------------------------------------------------"
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[256] | 353 | print " TSys"
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[181] | 354 | print "--------------------------------------------------"
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| 355 | print out
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[256] | 356 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)}
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| 357 | return retval
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[113] | 358 |
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[407] | 359 | def get_time(self, row=-1):
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[113] | 360 | """
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| 361 | Get a list of time stamps for the observations.
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[181] | 362 | Return a string for each integration in the scantable.
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[113] | 363 | Parameters:
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[407] | 364 | row: row no of integration. Default -1 return all rows
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[113] | 365 | Example:
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| 366 | none
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| 367 | """
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| 368 | out = []
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[407] | 369 | if row == -1:
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| 370 | for i in range(self.nrow()):
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| 371 | out.append(self._gettime(i))
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| 372 | return out
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| 373 | else:
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| 374 | if row < self.nrow():
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| 375 | return self._gettime(row)
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[102] | 376 |
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| 377 | def set_unit(self, unit='channel'):
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| 378 | """
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| 379 | Set the unit for all following operations on this scantable
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| 380 | Parameters:
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| 381 | unit: optional unit, default is 'channel'
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[113] | 382 | one of '*Hz','km/s','channel', ''
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[102] | 383 | """
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[113] | 384 |
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| 385 | if unit in ['','pixel', 'channel']:
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| 386 | unit = ''
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| 387 | inf = list(self._getcoordinfo())
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| 388 | inf[0] = unit
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| 389 | self._setcoordinfo(inf)
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| 390 | if self._p: self.plot()
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| 391 |
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[358] | 392 | def set_instrument (self, instr):
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| 393 | """
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| 394 | Set the instrument for subsequent processing
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| 395 | Parameters:
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[407] | 396 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
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| 397 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
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[358] | 398 | """
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| 399 | self._setInstrument(instr)
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| 400 |
|
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[276] | 401 | def set_doppler(self, doppler='RADIO'):
|
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| 402 | """
|
---|
| 403 | Set the doppler for all following operations on this scantable.
|
---|
| 404 | Parameters:
|
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| 405 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
|
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| 406 | """
|
---|
| 407 |
|
---|
| 408 | inf = list(self._getcoordinfo())
|
---|
| 409 | inf[2] = doppler
|
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| 410 | self._setcoordinfo(inf)
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| 411 | if self._p: self.plot()
|
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[432] | 412 |
|
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[226] | 413 | def set_freqframe(self, frame=None):
|
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[113] | 414 | """
|
---|
| 415 | Set the frame type of the Spectral Axis.
|
---|
| 416 | Parameters:
|
---|
| 417 | frame: an optional frame type, default 'LSRK'.
|
---|
| 418 | Examples:
|
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| 419 | scan.set_freqframe('BARY')
|
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| 420 | """
|
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[226] | 421 | if not frame: frame = rcParams['scantable.freqframe']
|
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[113] | 422 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \
|
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| 423 | 'GEO','GALACTO','LGROUP','CMB']
|
---|
| 424 | if frame in valid:
|
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| 425 | inf = list(self._getcoordinfo())
|
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| 426 | inf[1] = frame
|
---|
| 427 | self._setcoordinfo(inf)
|
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[102] | 428 | else:
|
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[113] | 429 | print "Please specify a valid freq type. Valid types are:\n",valid
|
---|
| 430 |
|
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| 431 | def get_unit(self):
|
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| 432 | """
|
---|
| 433 | Get the default unit set in this scantable
|
---|
| 434 | Parameters:
|
---|
| 435 | Returns:
|
---|
| 436 | A unit string
|
---|
| 437 | """
|
---|
| 438 | inf = self._getcoordinfo()
|
---|
| 439 | unit = inf[0]
|
---|
| 440 | if unit == '': unit = 'channel'
|
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| 441 | return unit
|
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[102] | 442 |
|
---|
[158] | 443 | def get_abcissa(self, rowno=0):
|
---|
[102] | 444 | """
|
---|
[158] | 445 | Get the abcissa in the current coordinate setup for the currently
|
---|
[113] | 446 | selected Beam/IF/Pol
|
---|
| 447 | Parameters:
|
---|
[226] | 448 | rowno: an optional row number in the scantable. Default is the
|
---|
| 449 | first row, i.e. rowno=0
|
---|
[113] | 450 | Returns:
|
---|
[407] | 451 | The abcissa values and it's format string (as a dictionary)
|
---|
[113] | 452 | """
|
---|
[256] | 453 | abc = self._getabcissa(rowno)
|
---|
[407] | 454 | lbl = self._getabcissalabel(rowno)
|
---|
[158] | 455 | return abc, lbl
|
---|
[407] | 456 | #return {'abcissa':abc,'label':lbl}
|
---|
[113] | 457 |
|
---|
| 458 | def create_mask(self, *args, **kwargs):
|
---|
| 459 | """
|
---|
[102] | 460 | Compute and return a mask based on [min,max] windows.
|
---|
[189] | 461 | The specified windows are to be INCLUDED, when the mask is
|
---|
[113] | 462 | applied.
|
---|
[102] | 463 | Parameters:
|
---|
| 464 | [min,max],[min2,max2],...
|
---|
| 465 | Pairs of start/end points specifying the regions
|
---|
| 466 | to be masked
|
---|
[189] | 467 | invert: optional argument. If specified as True,
|
---|
| 468 | return an inverted mask, i.e. the regions
|
---|
| 469 | specified are EXCLUDED
|
---|
[102] | 470 | Example:
|
---|
[113] | 471 | scan.set_unit('channel')
|
---|
| 472 |
|
---|
| 473 | a)
|
---|
[102] | 474 | msk = scan.set_mask([400,500],[800,900])
|
---|
[189] | 475 | # masks everything outside 400 and 500
|
---|
[113] | 476 | # and 800 and 900 in the unit 'channel'
|
---|
| 477 |
|
---|
| 478 | b)
|
---|
| 479 | msk = scan.set_mask([400,500],[800,900], invert=True)
|
---|
[189] | 480 | # masks the regions between 400 and 500
|
---|
[113] | 481 | # and 800 and 900 in the unit 'channel'
|
---|
| 482 |
|
---|
[102] | 483 | """
|
---|
[113] | 484 | u = self._getcoordinfo()[0]
|
---|
| 485 | if self._vb:
|
---|
| 486 | if u == "": u = "channel"
|
---|
| 487 | print "The current mask window unit is", u
|
---|
[102] | 488 | n = self.nchan()
|
---|
[256] | 489 | data = self._getabcissa()
|
---|
[189] | 490 | msk = zeros(n)
|
---|
[102] | 491 | for window in args:
|
---|
| 492 | if (len(window) != 2 or window[0] > window[1] ):
|
---|
| 493 | print "A window needs to be defined as [min,max]"
|
---|
| 494 | return
|
---|
| 495 | for i in range(n):
|
---|
[113] | 496 | if data[i] >= window[0] and data[i] < window[1]:
|
---|
[189] | 497 | msk[i] = 1
|
---|
[113] | 498 | if kwargs.has_key('invert'):
|
---|
| 499 | if kwargs.get('invert'):
|
---|
| 500 | from numarray import logical_not
|
---|
| 501 | msk = logical_not(msk)
|
---|
[102] | 502 | return msk
|
---|
[113] | 503 |
|
---|
[256] | 504 | def get_restfreqs(self):
|
---|
| 505 | """
|
---|
| 506 | Get the restfrequency(s) stored in this scantable.
|
---|
| 507 | The return value(s) are always of unit 'Hz'
|
---|
| 508 | Parameters:
|
---|
| 509 | none
|
---|
| 510 | Returns:
|
---|
| 511 | a list of doubles
|
---|
| 512 | """
|
---|
| 513 | return list(self._getrestfreqs())
|
---|
[102] | 514 |
|
---|
[402] | 515 | def lines(self):
|
---|
[391] | 516 | """
|
---|
[402] | 517 | Print the list of known spectral lines
|
---|
| 518 | """
|
---|
| 519 | sdtable._lines(self)
|
---|
| 520 |
|
---|
| 521 | def set_restfreqs(self, freqs=None, unit='Hz', lines=None, source=None, theif=None):
|
---|
| 522 | """
|
---|
[393] | 523 | Select the restfrequency for the specified source and IF OR
|
---|
| 524 | replace for all IFs. If the 'freqs' argument holds a scalar,
|
---|
| 525 | then that rest frequency will be applied to the selected
|
---|
| 526 | data (and added to the list of available rest frequencies).
|
---|
| 527 | In this way, you can set a rest frequency for each
|
---|
| 528 | source and IF combination. If the 'freqs' argument holds
|
---|
| 529 | a vector, then it MUST be of length the number of IFs
|
---|
| 530 | (and the available restfrequencies will be replaced by
|
---|
| 531 | this vector). In this case, *all* data ('source' and
|
---|
| 532 | 'theif' are ignored) have the restfrequency set per IF according
|
---|
| 533 | to the corresponding value you give in the 'freqs' vector.
|
---|
| 534 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and
|
---|
| 535 | IF 1 gets restfreq 2e9.
|
---|
[402] | 536 |
|
---|
| 537 | You can also specify the frequencies via known line names
|
---|
| 538 | in the argument 'lines'. Use 'freqs' or 'lines'. 'freqs'
|
---|
| 539 | takes precedence. See the list of known names via function
|
---|
| 540 | scantable.lines()
|
---|
[391] | 541 | Parameters:
|
---|
[402] | 542 | freqs: list of rest frequencies
|
---|
[393] | 543 | unit: unit for rest frequency (default 'Hz')
|
---|
[402] | 544 | lines: list of known spectral lines names (alternative to freqs).
|
---|
| 545 | See possible list via scantable.lines()
|
---|
[391] | 546 | source: Source name (blank means all)
|
---|
| 547 | theif: IF (-1 means all)
|
---|
| 548 | Example:
|
---|
[393] | 549 | scan.set_restfreqs(freqs=1.4e9, source='NGC253', theif=2)
|
---|
| 550 | scan.set_restfreqs(freqs=[1.4e9,1.67e9])
|
---|
[391] | 551 | """
|
---|
| 552 | if source is None:
|
---|
| 553 | source = ""
|
---|
| 554 | if theif is None:
|
---|
| 555 | theif = -1
|
---|
[393] | 556 | t = type(freqs)
|
---|
| 557 | if t is int or t is float:
|
---|
| 558 | freqs = [freqs]
|
---|
[402] | 559 | if freqs is None:
|
---|
| 560 | freqs = []
|
---|
| 561 | t = type(lines)
|
---|
| 562 | if t is str:
|
---|
| 563 | lines = [lines]
|
---|
| 564 | if lines is None:
|
---|
| 565 | lines = []
|
---|
| 566 | sdtable._setrestfreqs(self, freqs, unit, lines, source, theif)
|
---|
[391] | 567 | return
|
---|
| 568 |
|
---|
| 569 |
|
---|
[102] | 570 | def flag_spectrum(self, thebeam, theif, thepol):
|
---|
| 571 | """
|
---|
| 572 | This flags a selected spectrum in the scan 'for good'.
|
---|
| 573 | USE WITH CARE - not reversible.
|
---|
| 574 | Use masks for non-permanent exclusion of channels.
|
---|
| 575 | Parameters:
|
---|
| 576 | thebeam,theif,thepol: all have to be explicitly
|
---|
| 577 | specified
|
---|
| 578 | Example:
|
---|
| 579 | scan.flag_spectrum(0,0,1)
|
---|
| 580 | flags the spectrum for Beam=0, IF=0, Pol=1
|
---|
| 581 | """
|
---|
[407] | 582 | if (thebeam < self.nbeam() and
|
---|
| 583 | theif < self.nif() and
|
---|
| 584 | thepol < self.npol()):
|
---|
| 585 | sdtable.setbeam(self, thebeam)
|
---|
| 586 | sdtable.setif(self, theif)
|
---|
| 587 | sdtable.setpol(self, thepol)
|
---|
| 588 | sdtable._flag(self)
|
---|
[102] | 589 | else:
|
---|
| 590 | print "Please specify a valid (Beam/IF/Pol)"
|
---|
| 591 | return
|
---|
[113] | 592 |
|
---|
| 593 | def plot(self, what='spectrum',col='Pol', panel=None):
|
---|
| 594 | """
|
---|
| 595 | Plot the spectra contained in the scan. Alternatively you can also
|
---|
| 596 | Plot Tsys vs Time
|
---|
| 597 | Parameters:
|
---|
| 598 | what: a choice of 'spectrum' (default) or 'tsys'
|
---|
[135] | 599 | col: which out of Beams/IFs/Pols should be colour stacked
|
---|
[113] | 600 | panel: set up multiple panels, currently not working.
|
---|
| 601 | """
|
---|
[283] | 602 | print "Warning! Not fully functional. Use plotter.plot() instead"
|
---|
| 603 |
|
---|
[113] | 604 | validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()}
|
---|
[124] | 605 |
|
---|
[113] | 606 | validyax = ['spectrum','tsys']
|
---|
[189] | 607 | from asap.asaplot import ASAPlot
|
---|
[113] | 608 | if not self._p:
|
---|
| 609 | self._p = ASAPlot()
|
---|
[189] | 610 | #print "Plotting not enabled"
|
---|
| 611 | #return
|
---|
| 612 | if self._p.is_dead:
|
---|
| 613 | del self._p
|
---|
| 614 | self._p = ASAPlot()
|
---|
[113] | 615 | npan = 1
|
---|
| 616 | x = None
|
---|
| 617 | if what == 'tsys':
|
---|
| 618 | n = self.nrow()
|
---|
| 619 | if n < 2:
|
---|
| 620 | print "Only one integration. Can't plot."
|
---|
| 621 | return
|
---|
[124] | 622 | self._p.hold()
|
---|
| 623 | self._p.clear()
|
---|
[113] | 624 | if panel == 'Time':
|
---|
| 625 | npan = self.nrow()
|
---|
[124] | 626 | self._p.set_panels(rows=npan)
|
---|
[113] | 627 | xlab,ylab,tlab = None,None,None
|
---|
[226] | 628 | self._vb = False
|
---|
[256] | 629 | sel = self.get_cursor()
|
---|
[113] | 630 | for i in range(npan):
|
---|
[226] | 631 | if npan > 1:
|
---|
| 632 | self._p.subplot(i)
|
---|
[113] | 633 | for j in range(validcol[col]):
|
---|
| 634 | x = None
|
---|
| 635 | y = None
|
---|
| 636 | m = None
|
---|
| 637 | tlab = self._getsourcename(i)
|
---|
[124] | 638 | import re
|
---|
| 639 | tlab = re.sub('_S','',tlab)
|
---|
[113] | 640 | if col == 'Beam':
|
---|
| 641 | self.setbeam(j)
|
---|
| 642 | elif col == 'IF':
|
---|
| 643 | self.setif(j)
|
---|
| 644 | elif col == 'Pol':
|
---|
| 645 | self.setpol(j)
|
---|
| 646 | if what == 'tsys':
|
---|
| 647 | x = range(self.nrow())
|
---|
| 648 | xlab = 'Time [pixel]'
|
---|
| 649 | m = list(ones(len(x)))
|
---|
| 650 | y = []
|
---|
| 651 | ylab = r'$T_{sys}$'
|
---|
| 652 | for k in range(len(x)):
|
---|
| 653 | y.append(self._gettsys(k))
|
---|
| 654 | else:
|
---|
[158] | 655 | x,xlab = self.get_abcissa(i)
|
---|
[256] | 656 | y = self._getspectrum(i)
|
---|
[113] | 657 | ylab = r'Flux'
|
---|
[256] | 658 | m = self._getmask(i)
|
---|
[113] | 659 | llab = col+' '+str(j)
|
---|
| 660 | self._p.set_line(label=llab)
|
---|
| 661 | self._p.plot(x,y,m)
|
---|
[124] | 662 | self._p.set_axes('xlabel',xlab)
|
---|
| 663 | self._p.set_axes('ylabel',ylab)
|
---|
| 664 | self._p.set_axes('title',tlab)
|
---|
[113] | 665 | self._p.release()
|
---|
[256] | 666 | self.set_cursor(sel[0],sel[1],sel[2])
|
---|
[226] | 667 | self._vb = rcParams['verbose']
|
---|
[113] | 668 | return
|
---|
[256] | 669 |
|
---|
| 670 | print out
|
---|
| 671 |
|
---|
| 672 | def _print_values(self, dat, label='', timestamps=[]):
|
---|
| 673 | d = dat['data']
|
---|
| 674 | a = dat['axes']
|
---|
| 675 | shp = d.getshape()
|
---|
| 676 | out = ''
|
---|
| 677 | for i in range(shp[3]):
|
---|
| 678 | out += '%s [%s]:\n' % (a[3],timestamps[i])
|
---|
| 679 | t = d[:,:,:,i]
|
---|
| 680 | for j in range(shp[0]):
|
---|
| 681 | if shp[0] > 1: out += ' %s[%d] ' % (a[0],j)
|
---|
| 682 | for k in range(shp[1]):
|
---|
| 683 | if shp[1] > 1: out += ' %s[%d] ' % (a[1],k)
|
---|
| 684 | for l in range(shp[2]):
|
---|
| 685 | if shp[2] > 1: out += ' %s[%d] ' % (a[2],l)
|
---|
| 686 | out += '= %3.3f\n' % (t[j,k,l])
|
---|
| 687 | out += "--------------------------------------------------\n"
|
---|
| 688 | print "--------------------------------------------------"
|
---|
| 689 | print " ", label
|
---|
| 690 | print "--------------------------------------------------"
|
---|
| 691 | print out
|
---|