| 1 | from asap._asap import sdtable
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| 2 | from asap import rcParams
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| 3 | from numarray import ones,zeros
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| 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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| 10 |
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| 11 | def __init__(self, filename, average=None, unit=None):
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| 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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| 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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| 22 | scantable
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| 23 | average: average all integrations withinb a scan on read.
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| 24 | The default (True) is taken from .asaprc.
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| 25 | unit: brightness unit; must be consistent with K or Jy.
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| 26 | Over-rides the default selected by the reader
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| 27 | (input rpfits/sdfits/ms) or replaces the value
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| 28 | in existing scantables
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| 29 | """
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| 30 | if average is None or type(average) is not bool:
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| 31 | average = rcParams['scantable.autoaverage']
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| 32 |
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| 33 | varlist = vars()
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| 34 | self._vb = rcParams['verbose']
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| 35 | self._p = None
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| 36 |
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| 37 | if isinstance(filename,sdtable):
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| 38 | sdtable.__init__(self, filename)
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| 39 | if unit is not None:
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| 40 | self.set_fluxunit(unit)
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| 41 | else:
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| 42 | import os.path
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| 43 | if not os.path.exists(filename):
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| 44 | print "File '%s' not found." % (filename)
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| 45 | return
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| 46 | filename = os.path.expandvars(filename)
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| 47 | if os.path.isdir(filename):
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| 48 | # crude check if asap table
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| 49 | if os.path.exists(filename+'/table.info'):
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| 50 | sdtable.__init__(self, filename)
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| 51 | if unit is not None:
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| 52 | self.set_fluxunit(unit)
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| 53 | else:
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| 54 | print "The given file '%s'is not a valid asap table." % (filename)
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| 55 | return
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| 56 | else:
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| 57 | from asap._asap import sdreader
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| 58 | ifSel = -1
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| 59 | beamSel = -1
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| 60 | r = sdreader(filename,ifSel,beamSel)
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| 61 | print 'Importing data...'
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| 62 | r._read([-1])
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| 63 | tbl = r._getdata()
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| 64 | if unit is not None:
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| 65 | tbl.set_fluxunit(unit)
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| 66 | if average:
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| 67 | from asap._asap import average as _av
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| 68 | print 'Auto averaging integrations...'
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| 69 | tbl2 = _av((tbl,),(),True,'none')
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| 70 | sdtable.__init__(self,tbl2)
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| 71 | del tbl2
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| 72 | else:
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| 73 | sdtable.__init__(self,tbl)
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| 74 | del r,tbl
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| 75 | self._add_history("scantable", varlist)
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| 76 |
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| 77 | def save(self, name=None, format=None, stokes=False, overwrite=False):
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| 78 | """
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| 79 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS,
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| 80 | Image FITS or MS2 format.
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| 81 | Parameters:
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| 82 | name: the name of the outputfile. For format="FITS" this
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| 83 | is the directory file name into which all the files
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| 84 | will be written (default is 'asap_FITS'). For format
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| 85 | "ASCII" this is the root file name (data in 'name'.txt
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| 86 | and header in 'name'_header.txt)
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| 87 | format: an optional file format. Default is ASAP.
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| 88 | Allowed are - 'ASAP' (save as ASAP [aips++] Table),
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| 89 | 'SDFITS' (save as SDFITS file)
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| 90 | 'FITS' (saves each row as a FITS Image)
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| 91 | 'ASCII' (saves as ascii text file)
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| 92 | 'MS2' (saves as an aips++
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| 93 | MeasurementSet V2)
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| 94 | stokes: Convert to Stokes parameters (only available
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| 95 | currently with FITS and ASCII formats.
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| 96 | Default is False.
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| 97 | overwrite: If the file should be overwritten if it exists.
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| 98 | The default False is to return with warning
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| 99 | without writing the output. USE WITH CARE.
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| 100 | Example:
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| 101 | scan.save('myscan.asap')
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| 102 | scan.save('myscan.sdfits','SDFITS')
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| 103 | """
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| 104 | from os import path
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| 105 | if format is None: format = rcParams['scantable.save']
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| 106 | suffix = '.'+format.lower()
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| 107 | if name is None or name =="":
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| 108 | name = 'scantable'+suffix
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| 109 | print "No filename given. Using default name %s..." % name
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| 110 | name = path.expandvars(name)
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| 111 | if path.isfile(name) or path.isdir(name):
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| 112 | if not overwrite:
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| 113 | print "File %s already exists." % name
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| 114 | return
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| 115 | format2 = format.upper()
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| 116 | if format2 == 'ASAP':
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| 117 | self._save(name)
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| 118 | else:
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| 119 | from asap._asap import sdwriter as _sw
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| 120 | w = _sw(format2)
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| 121 | w.write(self, name, stokes)
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| 122 | return
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| 123 |
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| 124 | def copy(self):
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| 125 | """
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| 126 | Return a copy of this scantable.
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| 127 | Parameters:
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| 128 | none
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| 129 | Example:
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| 130 | copiedscan = scan.copy()
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| 131 | """
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| 132 | sd = scantable(sdtable._copy(self))
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| 133 | return sd
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| 134 |
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| 135 | def get_scan(self, scanid=None):
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| 136 | """
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| 137 | Return a specific scan (by scanno) or collection of scans (by
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| 138 | source name) in a new scantable.
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| 139 | Parameters:
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| 140 | scanid: a (list of) scanno or a source name, unix-style
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| 141 | patterns are accepted for source name matching, e.g.
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| 142 | '*_R' gets all 'ref scans
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| 143 | Example:
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| 144 | # get all scans containing the source '323p459'
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| 145 | newscan = scan.get_scan('323p459')
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| 146 | # get all 'off' scans
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| 147 | refscans = scan.get_scan('*_R')
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| 148 | # get a susbset of scans by scanno (as listed in scan.summary())
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| 149 | newscan = scan.get_scan([0,2,7,10])
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| 150 | """
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| 151 | if scanid is None:
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| 152 | print "Please specify a scan no or name to retrieve from the scantable"
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| 153 | try:
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| 154 | if type(scanid) is str:
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| 155 | s = sdtable._getsource(self,scanid)
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| 156 | return scantable(s)
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| 157 | elif type(scanid) is int:
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| 158 | s = sdtable._getscan(self,[scanid])
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| 159 | return scantable(s)
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| 160 | elif type(scanid) is list:
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| 161 | s = sdtable._getscan(self,scanid)
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| 162 | return scantable(s)
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| 163 | else:
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| 164 | print "Illegal scanid type, use 'int' or 'list' if ints."
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| 165 | except RuntimeError:
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| 166 | print "Couldn't find any match."
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| 167 |
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| 168 | def __str__(self):
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| 169 | return sdtable._summary(self,True)
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| 170 |
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| 171 | def summary(self,filename=None, verbose=None):
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| 172 | """
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| 173 | Print a summary of the contents of this scantable.
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| 174 | Parameters:
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| 175 | filename: the name of a file to write the putput to
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| 176 | Default - no file output
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| 177 | verbose: print extra info such as the frequency table
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| 178 | The default (False) is taken from .asaprc
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| 179 | """
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| 180 | info = sdtable._summary(self, verbose)
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| 181 | if verbose is None: verbose = rcParams['scantable.verbosesummary']
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| 182 | if filename is not None:
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| 183 | if filename is "":
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| 184 | filename = 'scantable_summary.txt'
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| 185 | from os.path import expandvars, isdir
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| 186 | filename = expandvars(filename)
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| 187 | if not isdir(filename):
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| 188 | data = open(filename, 'w')
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| 189 | data.write(info)
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| 190 | data.close()
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| 191 | else:
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| 192 | print "Illegal file name '%s'." % (filename)
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| 193 | print info
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| 194 |
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| 195 | def set_cursor(self, thebeam=0,theif=0,thepol=0):
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| 196 | """
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| 197 | Set the spectrum for individual operations.
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| 198 | Parameters:
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| 199 | thebeam,theif,thepol: a number
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| 200 | Example:
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| 201 | scan.set_cursor(0,0,1)
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| 202 | pol1sig = scan.stats(all=False) # returns std dev for beam=0
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| 203 | # if=0, pol=1
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| 204 | """
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| 205 | varlist = vars()
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| 206 | self.setbeam(thebeam)
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| 207 | self.setpol(thepol)
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| 208 | self.setif(theif)
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| 209 | self._add_history("set_cursor",varlist)
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| 210 | return
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| 211 |
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| 212 | def get_cursor(self):
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| 213 | """
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| 214 | Return/print a the current 'cursor' into the Beam/IF/Pol cube.
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| 215 | Parameters:
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| 216 | none
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| 217 | Returns:
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| 218 | a list of values (currentBeam,currentIF,currentPol)
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| 219 | Example:
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| 220 | none
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| 221 | """
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| 222 | i = self.getbeam()
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| 223 | j = self.getif()
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| 224 | k = self.getpol()
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| 225 | if self._vb:
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| 226 | print "--------------------------------------------------"
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| 227 | print " Cursor position"
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| 228 | print "--------------------------------------------------"
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| 229 | out = 'Beam=%d IF=%d Pol=%d ' % (i,j,k)
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| 230 | print out
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| 231 | return i,j,k
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| 232 |
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| 233 | def stats(self, stat='stddev', mask=None, allaxes=None):
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| 234 | """
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| 235 | Determine the specified statistic of the current beam/if/pol
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| 236 | Takes a 'mask' as an optional parameter to specify which
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| 237 | channels should be excluded.
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| 238 | Parameters:
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| 239 | stat: 'min', 'max', 'sumsq', 'sum', 'mean'
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| 240 | 'var', 'stddev', 'avdev', 'rms', 'median'
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| 241 | mask: an optional mask specifying where the statistic
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| 242 | should be determined.
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| 243 | allaxes: if True apply to all spectra. Otherwise
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| 244 | apply only to the selected (beam/pol/if)spectra only.
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| 245 | The default is taken from .asaprc (True if none)
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| 246 | Example:
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| 247 | scan.set_unit('channel')
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| 248 | msk = scan.create_mask([100,200],[500,600])
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| 249 | scan.stats(stat='mean', mask=m)
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| 250 | """
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| 251 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 252 | from asap._asap import stats as _stats
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| 253 | from numarray import array,zeros,Float
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| 254 | if mask == None:
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| 255 | mask = ones(self.nchan())
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| 256 | axes = ['Beam','IF','Pol','Time']
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| 257 |
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| 258 | beamSel,IFSel,polSel = (self.getbeam(),self.getif(),self.getpol())
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| 259 | if allaxes:
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| 260 | n = self.nbeam()*self.nif()*self.npol()*self.nrow()
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| 261 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()]
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| 262 | arr = array(zeros(n),shape=shp,type=Float)
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| 263 |
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| 264 | for i in range(self.nbeam()):
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| 265 | self.setbeam(i)
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| 266 | for j in range(self.nif()):
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| 267 | self.setif(j)
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| 268 | for k in range(self.npol()):
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| 269 | self.setpol(k)
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| 270 | arr[i,j,k,:] = _stats(self,mask,stat,-1)
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| 271 | retval = {'axes': axes, 'data': arr, 'cursor':None}
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| 272 | tm = [self._gettime(val) for val in range(self.nrow())]
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| 273 | if self._vb:
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| 274 | self._print_values(retval,stat,tm)
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| 275 | self.setbeam(beamSel)
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| 276 | self.setif(IFSel)
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| 277 | self.setpol(polSel)
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| 278 | return retval
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| 279 |
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| 280 | else:
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| 281 | statval = _stats(self,mask,stat,-1)
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| 282 | out = ''
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| 283 | for l in range(self.nrow()):
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| 284 | tm = self._gettime(l)
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| 285 | out += 'Time[%s]:\n' % (tm)
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| 286 | if self.nbeam() > 1: out += ' Beam[%d] ' % (beamSel)
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| 287 | if self.nif() > 1: out += ' IF[%d] ' % (IFSel)
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| 288 | if self.npol() > 1: out += ' Pol[%d] ' % (polSel)
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| 289 | out += '= %3.3f\n' % (statval[l])
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| 290 | out += "--------------------------------------------------\n"
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| 291 |
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| 292 | if self._vb:
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| 293 | print "--------------------------------------------------"
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| 294 | print " ",stat
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| 295 | print "--------------------------------------------------"
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| 296 | print out
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| 297 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)}
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| 298 | return retval
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| 299 |
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| 300 | def stddev(self,mask=None, allaxes=None):
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| 301 | """
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| 302 | Determine the standard deviation of the current beam/if/pol
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| 303 | Takes a 'mask' as an optional parameter to specify which
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| 304 | channels should be excluded.
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| 305 | Parameters:
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| 306 | mask: an optional mask specifying where the standard
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| 307 | deviation should be determined.
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| 308 | allaxes: optional flag to show all or a cursor selected
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| 309 | spectrum of Beam/IF/Pol. Default is all or taken
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| 310 | from .asaprc
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| 311 |
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| 312 | Example:
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| 313 | scan.set_unit('channel')
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| 314 | msk = scan.create_mask([100,200],[500,600])
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| 315 | scan.stddev(mask=m)
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| 316 | """
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| 317 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 318 | return self.stats(stat='stddev',mask=mask, allaxes=allaxes);
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| 319 |
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| 320 | def get_tsys(self, allaxes=None):
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| 321 | """
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| 322 | Return the System temperatures.
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| 323 | Parameters:
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| 324 | allaxes: if True apply to all spectra. Otherwise
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| 325 | apply only to the selected (beam/pol/if)spectra only.
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| 326 | The default is taken from .asaprc (True if none)
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| 327 | Returns:
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| 328 | a list of Tsys values.
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| 329 | """
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| 330 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
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| 331 | from numarray import array,zeros,Float
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| 332 | axes = ['Beam','IF','Pol','Time']
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| 333 |
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| 334 | if allaxes:
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| 335 | n = self.nbeam()*self.nif()*self.npol()*self.nrow()
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| 336 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()]
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| 337 | arr = array(zeros(n),shape=shp,type=Float)
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| 338 |
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| 339 | for i in range(self.nbeam()):
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| 340 | self.setbeam(i)
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| 341 | for j in range(self.nif()):
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| 342 | self.setif(j)
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| 343 | for k in range(self.npol()):
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| 344 | self.setpol(k)
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| 345 | arr[i,j,k,:] = self._gettsys()
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| 346 | retval = {'axes': axes, 'data': arr, 'cursor':None}
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| 347 | tm = [self._gettime(val) for val in range(self.nrow())]
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| 348 | if self._vb:
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| 349 | self._print_values(retval,'Tsys',tm)
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| 350 | return retval
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| 351 |
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| 352 | else:
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| 353 | i,j,k = (self.getbeam(),self.getif(),self.getpol())
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| 354 | statval = self._gettsys()
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| 355 | out = ''
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| 356 | for l in range(self.nrow()):
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| 357 | tm = self._gettime(l)
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| 358 | out += 'Time[%s]:\n' % (tm)
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| 359 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i)
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| 360 | if self.nif() > 1: out += ' IF[%d] ' % (j)
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| 361 | if self.npol() > 1: out += ' Pol[%d] ' % (k)
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| 362 | out += '= %3.3f\n' % (statval[l])
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| 363 | out += "--------------------------------------------------\n"
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| 364 |
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| 365 | if self._vb:
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| 366 | print "--------------------------------------------------"
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| 367 | print " TSys"
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| 368 | print "--------------------------------------------------"
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| 369 | print out
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| 370 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)}
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| 371 | return retval
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| 372 |
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| 373 | def get_time(self, row=-1):
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| 374 | """
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| 375 | Get a list of time stamps for the observations.
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| 376 | Return a string for each integration in the scantable.
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| 377 | Parameters:
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| 378 | row: row no of integration. Default -1 return all rows
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| 379 | Example:
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| 380 | none
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| 381 | """
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| 382 | out = []
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| 383 | if row == -1:
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| 384 | for i in range(self.nrow()):
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| 385 | out.append(self._gettime(i))
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| 386 | return out
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| 387 | else:
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| 388 | if row < self.nrow():
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| 389 | return self._gettime(row)
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| 390 |
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| 391 | def set_unit(self, unit='channel'):
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| 392 | """
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| 393 | Set the unit for all following operations on this scantable
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| 394 | Parameters:
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| 395 | unit: optional unit, default is 'channel'
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| 396 | one of '*Hz','km/s','channel', ''
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| 397 | """
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| 398 | varlist = vars()
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| 399 | if unit in ['','pixel', 'channel']:
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| 400 | unit = ''
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| 401 | inf = list(self._getcoordinfo())
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| 402 | inf[0] = unit
|
|---|
| 403 | self._setcoordinfo(inf)
|
|---|
| 404 | if self._p: self.plot()
|
|---|
| 405 | self._add_history("set_unit",varlist)
|
|---|
| 406 |
|
|---|
| 407 | def set_instrument(self, instr):
|
|---|
| 408 | """
|
|---|
| 409 | Set the instrument for subsequent processing
|
|---|
| 410 | Parameters:
|
|---|
| 411 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
|
|---|
| 412 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
|
|---|
| 413 | """
|
|---|
| 414 | self._setInstrument(instr)
|
|---|
| 415 | self._add_history("set_instument",vars())
|
|---|
| 416 |
|
|---|
| 417 | def set_doppler(self, doppler='RADIO'):
|
|---|
| 418 | """
|
|---|
| 419 | Set the doppler for all following operations on this scantable.
|
|---|
| 420 | Parameters:
|
|---|
| 421 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
|
|---|
| 422 | """
|
|---|
| 423 | varlist = vars()
|
|---|
| 424 | inf = list(self._getcoordinfo())
|
|---|
| 425 | inf[2] = doppler
|
|---|
| 426 | self._setcoordinfo(inf)
|
|---|
| 427 | if self._p: self.plot()
|
|---|
| 428 | self._add_history("set_doppler",vars())
|
|---|
| 429 |
|
|---|
| 430 | def set_freqframe(self, frame=None):
|
|---|
| 431 | """
|
|---|
| 432 | Set the frame type of the Spectral Axis.
|
|---|
| 433 | Parameters:
|
|---|
| 434 | frame: an optional frame type, default 'LSRK'.
|
|---|
| 435 | Examples:
|
|---|
| 436 | scan.set_freqframe('BARY')
|
|---|
| 437 | """
|
|---|
| 438 | if frame is None: frame = rcParams['scantable.freqframe']
|
|---|
| 439 | varlist = vars()
|
|---|
| 440 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \
|
|---|
| 441 | 'GEO','GALACTO','LGROUP','CMB']
|
|---|
| 442 | if frame in valid:
|
|---|
| 443 | inf = list(self._getcoordinfo())
|
|---|
| 444 | inf[1] = frame
|
|---|
| 445 | self._setcoordinfo(inf)
|
|---|
| 446 | self._add_history("set_freqframe",varlist)
|
|---|
| 447 | else:
|
|---|
| 448 | print "Please specify a valid freq type. Valid types are:\n",valid
|
|---|
| 449 |
|
|---|
| 450 | def get_unit(self):
|
|---|
| 451 | """
|
|---|
| 452 | Get the default unit set in this scantable
|
|---|
| 453 | Parameters:
|
|---|
| 454 | Returns:
|
|---|
| 455 | A unit string
|
|---|
| 456 | """
|
|---|
| 457 | inf = self._getcoordinfo()
|
|---|
| 458 | unit = inf[0]
|
|---|
| 459 | if unit == '': unit = 'channel'
|
|---|
| 460 | return unit
|
|---|
| 461 |
|
|---|
| 462 | def get_abcissa(self, rowno=0):
|
|---|
| 463 | """
|
|---|
| 464 | Get the abcissa in the current coordinate setup for the currently
|
|---|
| 465 | selected Beam/IF/Pol
|
|---|
| 466 | Parameters:
|
|---|
| 467 | rowno: an optional row number in the scantable. Default is the
|
|---|
| 468 | first row, i.e. rowno=0
|
|---|
| 469 | Returns:
|
|---|
| 470 | The abcissa values and it's format string (as a dictionary)
|
|---|
| 471 | """
|
|---|
| 472 | abc = self._getabcissa(rowno)
|
|---|
| 473 | lbl = self._getabcissalabel(rowno)
|
|---|
| 474 | return abc, lbl
|
|---|
| 475 | #return {'abcissa':abc,'label':lbl}
|
|---|
| 476 |
|
|---|
| 477 | def create_mask(self, *args, **kwargs):
|
|---|
| 478 | """
|
|---|
| 479 | Compute and return a mask based on [min,max] windows.
|
|---|
| 480 | The specified windows are to be INCLUDED, when the mask is
|
|---|
| 481 | applied.
|
|---|
| 482 | Parameters:
|
|---|
| 483 | [min,max],[min2,max2],...
|
|---|
| 484 | Pairs of start/end points specifying the regions
|
|---|
| 485 | to be masked
|
|---|
| 486 | invert: optional argument. If specified as True,
|
|---|
| 487 | return an inverted mask, i.e. the regions
|
|---|
| 488 | specified are EXCLUDED
|
|---|
| 489 | row: create the mask using the specified row for
|
|---|
| 490 | unit conversions, default is row=0
|
|---|
| 491 | only necessary if frequency varies over rows.
|
|---|
| 492 | Example:
|
|---|
| 493 | scan.set_unit('channel')
|
|---|
| 494 |
|
|---|
| 495 | a)
|
|---|
| 496 | msk = scan.set_mask([400,500],[800,900])
|
|---|
| 497 | # masks everything outside 400 and 500
|
|---|
| 498 | # and 800 and 900 in the unit 'channel'
|
|---|
| 499 |
|
|---|
| 500 | b)
|
|---|
| 501 | msk = scan.set_mask([400,500],[800,900], invert=True)
|
|---|
| 502 | # masks the regions between 400 and 500
|
|---|
| 503 | # and 800 and 900 in the unit 'channel'
|
|---|
| 504 |
|
|---|
| 505 | """
|
|---|
| 506 | row = 0
|
|---|
| 507 | if kwargs.has_key("row"):
|
|---|
| 508 | row = kwargs.get("row")
|
|---|
| 509 | data = self._getabcissa(row)
|
|---|
| 510 | u = self._getcoordinfo()[0]
|
|---|
| 511 | if self._vb:
|
|---|
| 512 | if u == "": u = "channel"
|
|---|
| 513 | print "The current mask window unit is", u
|
|---|
| 514 | n = self.nchan()
|
|---|
| 515 | msk = zeros(n)
|
|---|
| 516 | for window in args:
|
|---|
| 517 | if (len(window) != 2 or window[0] > window[1] ):
|
|---|
| 518 | print "A window needs to be defined as [min,max]"
|
|---|
| 519 | return
|
|---|
| 520 | for i in range(n):
|
|---|
| 521 | if data[i] >= window[0] and data[i] < window[1]:
|
|---|
| 522 | msk[i] = 1
|
|---|
| 523 | if kwargs.has_key('invert'):
|
|---|
| 524 | if kwargs.get('invert'):
|
|---|
| 525 | from numarray import logical_not
|
|---|
| 526 | msk = logical_not(msk)
|
|---|
| 527 | return msk
|
|---|
| 528 |
|
|---|
| 529 | def get_restfreqs(self):
|
|---|
| 530 | """
|
|---|
| 531 | Get the restfrequency(s) stored in this scantable.
|
|---|
| 532 | The return value(s) are always of unit 'Hz'
|
|---|
| 533 | Parameters:
|
|---|
| 534 | none
|
|---|
| 535 | Returns:
|
|---|
| 536 | a list of doubles
|
|---|
| 537 | """
|
|---|
| 538 | return list(self._getrestfreqs())
|
|---|
| 539 |
|
|---|
| 540 | def lines(self):
|
|---|
| 541 | """
|
|---|
| 542 | Print the list of known spectral lines
|
|---|
| 543 | """
|
|---|
| 544 | sdtable._lines(self)
|
|---|
| 545 |
|
|---|
| 546 | def set_restfreqs(self, freqs=None, unit='Hz', lines=None, source=None,
|
|---|
| 547 | theif=None):
|
|---|
| 548 | """
|
|---|
| 549 | Select the restfrequency for the specified source and IF OR
|
|---|
| 550 | replace for all IFs. If the 'freqs' argument holds a scalar,
|
|---|
| 551 | then that rest frequency will be applied to the selected
|
|---|
| 552 | data (and added to the list of available rest frequencies).
|
|---|
| 553 | In this way, you can set a rest frequency for each
|
|---|
| 554 | source and IF combination. If the 'freqs' argument holds
|
|---|
| 555 | a vector, then it MUST be of length the number of IFs
|
|---|
| 556 | (and the available restfrequencies will be replaced by
|
|---|
| 557 | this vector). In this case, *all* data ('source' and
|
|---|
| 558 | 'theif' are ignored) have the restfrequency set per IF according
|
|---|
| 559 | to the corresponding value you give in the 'freqs' vector.
|
|---|
| 560 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and
|
|---|
| 561 | IF 1 gets restfreq 2e9.
|
|---|
| 562 |
|
|---|
| 563 | You can also specify the frequencies via known line names
|
|---|
| 564 | in the argument 'lines'. Use 'freqs' or 'lines'. 'freqs'
|
|---|
| 565 | takes precedence. See the list of known names via function
|
|---|
| 566 | scantable.lines()
|
|---|
| 567 | Parameters:
|
|---|
| 568 | freqs: list of rest frequencies
|
|---|
| 569 | unit: unit for rest frequency (default 'Hz')
|
|---|
| 570 | lines: list of known spectral lines names (alternative to freqs).
|
|---|
| 571 | See possible list via scantable.lines()
|
|---|
| 572 | source: Source name (blank means all)
|
|---|
| 573 | theif: IF (-1 means all)
|
|---|
| 574 | Example:
|
|---|
| 575 | scan.set_restfreqs(freqs=1.4e9, source='NGC253', theif=2)
|
|---|
| 576 | scan.set_restfreqs(freqs=[1.4e9,1.67e9])
|
|---|
| 577 | """
|
|---|
| 578 | varlist = vars()
|
|---|
| 579 | if source is None:
|
|---|
| 580 | source = ""
|
|---|
| 581 | if theif is None:
|
|---|
| 582 | theif = -1
|
|---|
| 583 | t = type(freqs)
|
|---|
| 584 | if t is int or t is float:
|
|---|
| 585 | freqs = [freqs]
|
|---|
| 586 | if freqs is None:
|
|---|
| 587 | freqs = []
|
|---|
| 588 | t = type(lines)
|
|---|
| 589 | if t is str:
|
|---|
| 590 | lines = [lines]
|
|---|
| 591 | if lines is None:
|
|---|
| 592 | lines = []
|
|---|
| 593 | sdtable._setrestfreqs(self, freqs, unit, lines, source, theif)
|
|---|
| 594 | self._add_history("set_restfreqs", varlist)
|
|---|
| 595 |
|
|---|
| 596 |
|
|---|
| 597 |
|
|---|
| 598 | def flag_spectrum(self, thebeam, theif, thepol):
|
|---|
| 599 | """
|
|---|
| 600 | This flags a selected spectrum in the scan 'for good'.
|
|---|
| 601 | USE WITH CARE - not reversible.
|
|---|
| 602 | Use masks for non-permanent exclusion of channels.
|
|---|
| 603 | Parameters:
|
|---|
| 604 | thebeam,theif,thepol: all have to be explicitly
|
|---|
| 605 | specified
|
|---|
| 606 | Example:
|
|---|
| 607 | scan.flag_spectrum(0,0,1)
|
|---|
| 608 | flags the spectrum for Beam=0, IF=0, Pol=1
|
|---|
| 609 | """
|
|---|
| 610 | if (thebeam < self.nbeam() and
|
|---|
| 611 | theif < self.nif() and
|
|---|
| 612 | thepol < self.npol()):
|
|---|
| 613 | sdtable.setbeam(self, thebeam)
|
|---|
| 614 | sdtable.setif(self, theif)
|
|---|
| 615 | sdtable.setpol(self, thepol)
|
|---|
| 616 | sdtable._flag(self)
|
|---|
| 617 | self._add_history("flag_spectrum", vars())
|
|---|
| 618 | else:
|
|---|
| 619 | print "Please specify a valid (Beam/IF/Pol)"
|
|---|
| 620 | return
|
|---|
| 621 |
|
|---|
| 622 | def plot(self, what='spectrum',col='Pol', panel=None):
|
|---|
| 623 | """
|
|---|
| 624 | Plot the spectra contained in the scan. Alternatively you can also
|
|---|
| 625 | Plot Tsys vs Time
|
|---|
| 626 | Parameters:
|
|---|
| 627 | what: a choice of 'spectrum' (default) or 'tsys'
|
|---|
| 628 | col: which out of Beams/IFs/Pols should be colour stacked
|
|---|
| 629 | panel: set up multiple panels, currently not working.
|
|---|
| 630 | """
|
|---|
| 631 | print "Warning! Not fully functional. Use plotter.plot() instead"
|
|---|
| 632 |
|
|---|
| 633 | validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()}
|
|---|
| 634 |
|
|---|
| 635 | validyax = ['spectrum','tsys']
|
|---|
| 636 | from asap.asaplot import ASAPlot
|
|---|
| 637 | if not self._p:
|
|---|
| 638 | self._p = ASAPlot()
|
|---|
| 639 | #print "Plotting not enabled"
|
|---|
| 640 | #return
|
|---|
| 641 | if self._p.is_dead:
|
|---|
| 642 | del self._p
|
|---|
| 643 | self._p = ASAPlot()
|
|---|
| 644 | npan = 1
|
|---|
| 645 | x = None
|
|---|
| 646 | if what == 'tsys':
|
|---|
| 647 | n = self.nrow()
|
|---|
| 648 | if n < 2:
|
|---|
| 649 | print "Only one integration. Can't plot."
|
|---|
| 650 | return
|
|---|
| 651 | self._p.hold()
|
|---|
| 652 | self._p.clear()
|
|---|
| 653 | if panel == 'Time':
|
|---|
| 654 | npan = self.nrow()
|
|---|
| 655 | self._p.set_panels(rows=npan)
|
|---|
| 656 | xlab,ylab,tlab = None,None,None
|
|---|
| 657 | self._vb = False
|
|---|
| 658 | sel = self.get_cursor()
|
|---|
| 659 | for i in range(npan):
|
|---|
| 660 | if npan > 1:
|
|---|
| 661 | self._p.subplot(i)
|
|---|
| 662 | for j in range(validcol[col]):
|
|---|
| 663 | x = None
|
|---|
| 664 | y = None
|
|---|
| 665 | m = None
|
|---|
| 666 | tlab = self._getsourcename(i)
|
|---|
| 667 | import re
|
|---|
| 668 | tlab = re.sub('_S','',tlab)
|
|---|
| 669 | if col == 'Beam':
|
|---|
| 670 | self.setbeam(j)
|
|---|
| 671 | elif col == 'IF':
|
|---|
| 672 | self.setif(j)
|
|---|
| 673 | elif col == 'Pol':
|
|---|
| 674 | self.setpol(j)
|
|---|
| 675 | if what == 'tsys':
|
|---|
| 676 | x = range(self.nrow())
|
|---|
| 677 | xlab = 'Time [pixel]'
|
|---|
| 678 | m = list(ones(len(x)))
|
|---|
| 679 | y = []
|
|---|
| 680 | ylab = r'$T_{sys}$'
|
|---|
| 681 | for k in range(len(x)):
|
|---|
| 682 | y.append(self._gettsys(k))
|
|---|
| 683 | else:
|
|---|
| 684 | x,xlab = self.get_abcissa(i)
|
|---|
| 685 | y = self._getspectrum(i)
|
|---|
| 686 | ylab = r'Flux'
|
|---|
| 687 | m = self._getmask(i)
|
|---|
| 688 | llab = col+' '+str(j)
|
|---|
| 689 | self._p.set_line(label=llab)
|
|---|
| 690 | self._p.plot(x,y,m)
|
|---|
| 691 | self._p.set_axes('xlabel',xlab)
|
|---|
| 692 | self._p.set_axes('ylabel',ylab)
|
|---|
| 693 | self._p.set_axes('title',tlab)
|
|---|
| 694 | self._p.release()
|
|---|
| 695 | self.set_cursor(sel[0],sel[1],sel[2])
|
|---|
| 696 | self._vb = rcParams['verbose']
|
|---|
| 697 | return
|
|---|
| 698 |
|
|---|
| 699 | print out
|
|---|
| 700 |
|
|---|
| 701 | def _print_values(self, dat, label='', timestamps=[]):
|
|---|
| 702 | d = dat['data']
|
|---|
| 703 | a = dat['axes']
|
|---|
| 704 | shp = d.getshape()
|
|---|
| 705 | out = ''
|
|---|
| 706 | for i in range(shp[3]):
|
|---|
| 707 | out += '%s [%s]:\n' % (a[3],timestamps[i])
|
|---|
| 708 | t = d[:,:,:,i]
|
|---|
| 709 | for j in range(shp[0]):
|
|---|
| 710 | if shp[0] > 1: out += ' %s[%d] ' % (a[0],j)
|
|---|
| 711 | for k in range(shp[1]):
|
|---|
| 712 | if shp[1] > 1: out += ' %s[%d] ' % (a[1],k)
|
|---|
| 713 | for l in range(shp[2]):
|
|---|
| 714 | if shp[2] > 1: out += ' %s[%d] ' % (a[2],l)
|
|---|
| 715 | out += '= %3.3f\n' % (t[j,k,l])
|
|---|
| 716 | out += "-"*80
|
|---|
| 717 | out += "\n"
|
|---|
| 718 | print "-"*80
|
|---|
| 719 | print " ", label
|
|---|
| 720 | print "-"*80
|
|---|
| 721 | print out
|
|---|
| 722 |
|
|---|
| 723 | def history(self):
|
|---|
| 724 | hist = list(self._gethistory())
|
|---|
| 725 | print "-"*80
|
|---|
| 726 | for h in hist:
|
|---|
| 727 | if h.startswith("---"):
|
|---|
| 728 | print h
|
|---|
| 729 | else:
|
|---|
| 730 | items = h.split("##")
|
|---|
| 731 | date = items[0]
|
|---|
| 732 | func = items[1]
|
|---|
| 733 | items = items[2:]
|
|---|
| 734 | print date
|
|---|
| 735 | print "Function: %s\n Parameters:" % (func)
|
|---|
| 736 | for i in items:
|
|---|
| 737 | s = i.split("=")
|
|---|
| 738 | print " %s = %s" % (s[0],s[1])
|
|---|
| 739 | print "-"*80
|
|---|
| 740 | return
|
|---|
| 741 |
|
|---|
| 742 | #
|
|---|
| 743 | # Maths business
|
|---|
| 744 | #
|
|---|
| 745 |
|
|---|
| 746 | def average_time(self, mask=None, scanav=True, weight=None):
|
|---|
| 747 | """
|
|---|
| 748 | Return the (time) average of a scan, or apply it 'insitu'.
|
|---|
| 749 | Note:
|
|---|
| 750 | in channels only
|
|---|
| 751 | The cursor of the output scan is set to 0.
|
|---|
| 752 | Parameters:
|
|---|
| 753 | one scan or comma separated scans
|
|---|
| 754 | mask: an optional mask (only used for 'var' and 'tsys'
|
|---|
| 755 | weighting)
|
|---|
| 756 | scanav: True (default) averages each scan separately
|
|---|
| 757 | False averages all scans together,
|
|---|
| 758 | weight: Weighting scheme. 'none' (default), 'var' (variance
|
|---|
| 759 | weighted), 'tsys'
|
|---|
| 760 |
|
|---|
| 761 | Example:
|
|---|
| 762 | # time average the scantable without using a mask
|
|---|
| 763 | newscan = scan.average_time()
|
|---|
| 764 | """
|
|---|
| 765 | varlist = vars()
|
|---|
| 766 | if weight is None: weight = 'none'
|
|---|
| 767 | if mask is None: mask = ()
|
|---|
| 768 | from asap._asap import average as _av
|
|---|
| 769 | s = scantable(_av((self,), mask, scanav, weight))
|
|---|
| 770 | s._add_history("average_time",varlist)
|
|---|
| 771 | return s
|
|---|
| 772 |
|
|---|
| 773 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None,
|
|---|
| 774 | allaxes=None):
|
|---|
| 775 | """
|
|---|
| 776 | Return a scan where all spectra are converted to either
|
|---|
| 777 | Jansky or Kelvin depending upon the flux units of the scan table.
|
|---|
| 778 | By default the function tries to look the values up internally.
|
|---|
| 779 | If it can't find them (or if you want to over-ride), you must
|
|---|
| 780 | specify EITHER jyperk OR eta (and D which it will try to look up
|
|---|
| 781 | also if you don't set it). jyperk takes precedence if you set both.
|
|---|
| 782 | Parameters:
|
|---|
| 783 | jyperk: the Jy / K conversion factor
|
|---|
| 784 | eta: the aperture efficiency
|
|---|
| 785 | d: the geomtric diameter (metres)
|
|---|
| 786 | insitu: if False a new scantable is returned.
|
|---|
| 787 | Otherwise, the scaling is done in-situ
|
|---|
| 788 | The default is taken from .asaprc (False)
|
|---|
| 789 | allaxes: if True apply to all spectra. Otherwise
|
|---|
| 790 | apply only to the selected (beam/pol/if)spectra only
|
|---|
| 791 | The default is taken from .asaprc (True if none)
|
|---|
| 792 | """
|
|---|
| 793 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
|
|---|
| 794 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 795 | varlist = vars()
|
|---|
| 796 | if jyperk is None: jyperk = -1.0
|
|---|
| 797 | if d is None: d = -1.0
|
|---|
| 798 | if eta is None: eta = -1.0
|
|---|
| 799 | if not insitu:
|
|---|
| 800 | from asap._asap import convertflux as _convert
|
|---|
| 801 | s = scantable(_convert(self, d, eta, jyperk, allaxes))
|
|---|
| 802 | s._add_history("convert_flux", varlist)
|
|---|
| 803 | return s
|
|---|
| 804 | else:
|
|---|
| 805 | from asap._asap import convertflux_insitu as _convert
|
|---|
| 806 | _convert(self, d, eta, jyperk, allaxes)
|
|---|
| 807 | self._add_history("convert_flux", varlist)
|
|---|
| 808 | return
|
|---|
| 809 |
|
|---|
| 810 | def gain_el(self, poly=None, filename="", method="linear",
|
|---|
| 811 | insitu=None, allaxes=None):
|
|---|
| 812 | """
|
|---|
| 813 | Return a scan after applying a gain-elevation correction.
|
|---|
| 814 | The correction can be made via either a polynomial or a
|
|---|
| 815 | table-based interpolation (and extrapolation if necessary).
|
|---|
| 816 | You specify polynomial coefficients, an ascii table or neither.
|
|---|
| 817 | If you specify neither, then a polynomial correction will be made
|
|---|
| 818 | with built in coefficients known for certain telescopes (an error
|
|---|
| 819 | will occur if the instrument is not known).
|
|---|
| 820 | The data and Tsys are *divided* by the scaling factors.
|
|---|
| 821 | Parameters:
|
|---|
| 822 | poly: Polynomial coefficients (default None) to compute a
|
|---|
| 823 | gain-elevation correction as a function of
|
|---|
| 824 | elevation (in degrees).
|
|---|
| 825 | filename: The name of an ascii file holding correction factors.
|
|---|
| 826 | The first row of the ascii file must give the column
|
|---|
| 827 | names and these MUST include columns
|
|---|
| 828 | "ELEVATION" (degrees) and "FACTOR" (multiply data
|
|---|
| 829 | by this) somewhere.
|
|---|
| 830 | The second row must give the data type of the
|
|---|
| 831 | column. Use 'R' for Real and 'I' for Integer.
|
|---|
| 832 | An example file would be
|
|---|
| 833 | (actual factors are arbitrary) :
|
|---|
| 834 |
|
|---|
| 835 | TIME ELEVATION FACTOR
|
|---|
| 836 | R R R
|
|---|
| 837 | 0.1 0 0.8
|
|---|
| 838 | 0.2 20 0.85
|
|---|
| 839 | 0.3 40 0.9
|
|---|
| 840 | 0.4 60 0.85
|
|---|
| 841 | 0.5 80 0.8
|
|---|
| 842 | 0.6 90 0.75
|
|---|
| 843 | method: Interpolation method when correcting from a table.
|
|---|
| 844 | Values are "nearest", "linear" (default), "cubic"
|
|---|
| 845 | and "spline"
|
|---|
| 846 | insitu: if False a new scantable is returned.
|
|---|
| 847 | Otherwise, the scaling is done in-situ
|
|---|
| 848 | The default is taken from .asaprc (False)
|
|---|
| 849 | allaxes: If True apply to all spectra. Otherwise
|
|---|
| 850 | apply only to the selected (beam/pol/if) spectra only
|
|---|
| 851 | The default is taken from .asaprc (True if none)
|
|---|
| 852 | """
|
|---|
| 853 |
|
|---|
| 854 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
|
|---|
| 855 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 856 | varlist = vars()
|
|---|
| 857 | if poly is None:
|
|---|
| 858 | poly = ()
|
|---|
| 859 | from os.path import expandvars
|
|---|
| 860 | filename = expandvars(filename)
|
|---|
| 861 | if not insitu:
|
|---|
| 862 | from asap._asap import gainel as _gainEl
|
|---|
| 863 | s = scantable(_gainEl(self, poly, filename, method, allaxes))
|
|---|
| 864 | s._add_history("gain_el", varlist)
|
|---|
| 865 | return s
|
|---|
| 866 | else:
|
|---|
| 867 | from asap._asap import gainel_insitu as _gainEl
|
|---|
| 868 | _gainEl(self, poly, filename, method, allaxes)
|
|---|
| 869 | self._add_history("gain_el", varlist)
|
|---|
| 870 | return
|
|---|
| 871 |
|
|---|
| 872 | def freq_align(self, reftime=None, method='cubic', perif=False,
|
|---|
| 873 | insitu=None):
|
|---|
| 874 | """
|
|---|
| 875 | Return a scan where all rows have been aligned in frequency/velocity.
|
|---|
| 876 | The alignment frequency frame (e.g. LSRK) is that set by function
|
|---|
| 877 | set_freqframe.
|
|---|
| 878 | Parameters:
|
|---|
| 879 | reftime: reference time to align at. By default, the time of
|
|---|
| 880 | the first row of data is used.
|
|---|
| 881 | method: Interpolation method for regridding the spectra.
|
|---|
| 882 | Choose from "nearest", "linear", "cubic" (default)
|
|---|
| 883 | and "spline"
|
|---|
| 884 | perif: Generate aligners per freqID (no doppler tracking) or
|
|---|
| 885 | per IF (scan-based doppler tracking)
|
|---|
| 886 | insitu: if False a new scantable is returned.
|
|---|
| 887 | Otherwise, the scaling is done in-situ
|
|---|
| 888 | The default is taken from .asaprc (False)
|
|---|
| 889 | """
|
|---|
| 890 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 891 | varlist = vars()
|
|---|
| 892 | if reftime is None: reftime = ''
|
|---|
| 893 | perfreqid = not perif
|
|---|
| 894 | if not insitu:
|
|---|
| 895 | from asap._asap import freq_align as _align
|
|---|
| 896 | s = scantable(_align(self, reftime, method, perfreqid))
|
|---|
| 897 | s._add_history("freq_align", varlist)
|
|---|
| 898 | return s
|
|---|
| 899 | else:
|
|---|
| 900 | from asap._asap import freq_align_insitu as _align
|
|---|
| 901 | _align(self, reftime, method, perfreqid)
|
|---|
| 902 | self._add_history("freq_align", varlist)
|
|---|
| 903 | return
|
|---|
| 904 |
|
|---|
| 905 | def opacity(self, tau, insitu=None, allaxes=None):
|
|---|
| 906 | """
|
|---|
| 907 | Apply an opacity correction. The data
|
|---|
| 908 | and Tsys are multiplied by the correction factor.
|
|---|
| 909 | Parameters:
|
|---|
| 910 | tau: Opacity from which the correction factor is
|
|---|
| 911 | exp(tau*ZD)
|
|---|
| 912 | where ZD is the zenith-distance
|
|---|
| 913 | insitu: if False a new scantable is returned.
|
|---|
| 914 | Otherwise, the scaling is done in-situ
|
|---|
| 915 | The default is taken from .asaprc (False)
|
|---|
| 916 | allaxes: if True apply to all spectra. Otherwise
|
|---|
| 917 | apply only to the selected (beam/pol/if)spectra only
|
|---|
| 918 | The default is taken from .asaprc (True if none)
|
|---|
| 919 | """
|
|---|
| 920 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
|
|---|
| 921 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 922 | varlist = vars()
|
|---|
| 923 | if not insitu:
|
|---|
| 924 | from asap._asap import opacity as _opacity
|
|---|
| 925 | s = scantable(_opacity(self, tau, allaxes))
|
|---|
| 926 | s._add_history("opacity", varlist)
|
|---|
| 927 | return s
|
|---|
| 928 | else:
|
|---|
| 929 | from asap._asap import opacity_insitu as _opacity
|
|---|
| 930 | _opacity(self, tau, allaxes)
|
|---|
| 931 | self._add_history("opacity", varlist)
|
|---|
| 932 | return
|
|---|
| 933 |
|
|---|
| 934 | def bin(self, width=5, insitu=None):
|
|---|
| 935 | """
|
|---|
| 936 | Return a scan where all spectra have been binned up.
|
|---|
| 937 | width: The bin width (default=5) in pixels
|
|---|
| 938 | insitu: if False a new scantable is returned.
|
|---|
| 939 | Otherwise, the scaling is done in-situ
|
|---|
| 940 | The default is taken from .asaprc (False)
|
|---|
| 941 | """
|
|---|
| 942 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 943 | varlist = vars()
|
|---|
| 944 | if not insitu:
|
|---|
| 945 | from asap._asap import bin as _bin
|
|---|
| 946 | s = scantable(_bin(self, width))
|
|---|
| 947 | s._add_history("bin",varlist)
|
|---|
| 948 | return s
|
|---|
| 949 | else:
|
|---|
| 950 | from asap._asap import bin_insitu as _bin
|
|---|
| 951 | _bin(self, width)
|
|---|
| 952 | self._add_history("bin",varlist)
|
|---|
| 953 | return
|
|---|
| 954 |
|
|---|
| 955 |
|
|---|
| 956 | def resample(self, width=5, method='cubic', insitu=None):
|
|---|
| 957 | """
|
|---|
| 958 | Return a scan where all spectra have been binned up
|
|---|
| 959 | width: The bin width (default=5) in pixels
|
|---|
| 960 | method: Interpolation method when correcting from a table.
|
|---|
| 961 | Values are "nearest", "linear", "cubic" (default)
|
|---|
| 962 | and "spline"
|
|---|
| 963 | insitu: if False a new scantable is returned.
|
|---|
| 964 | Otherwise, the scaling is done in-situ
|
|---|
| 965 | The default is taken from .asaprc (False)
|
|---|
| 966 | """
|
|---|
| 967 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 968 | varlist = vars()
|
|---|
| 969 | if not insitu:
|
|---|
| 970 | from asap._asap import resample as _resample
|
|---|
| 971 | s = scantable(_resample(self, method, width))
|
|---|
| 972 | s._add_history("resample",varlist)
|
|---|
| 973 | return s
|
|---|
| 974 | else:
|
|---|
| 975 | from asap._asap import resample_insitu as _resample
|
|---|
| 976 | _resample(self, method, width)
|
|---|
| 977 | self._add_history("resample",varlist)
|
|---|
| 978 | return
|
|---|
| 979 |
|
|---|
| 980 | def average_pol(self, mask=None, weight='none', insitu=None):
|
|---|
| 981 | """
|
|---|
| 982 | Average the Polarisations together.
|
|---|
| 983 | The polarisation cursor of the output scan is set to 0
|
|---|
| 984 | Parameters:
|
|---|
| 985 | scan: The scantable
|
|---|
| 986 | mask: An optional mask defining the region, where the
|
|---|
| 987 | averaging will be applied. The output will have all
|
|---|
| 988 | specified points masked.
|
|---|
| 989 | weight: Weighting scheme. 'none' (default), or
|
|---|
| 990 | 'var' (variance weighted)
|
|---|
| 991 | insitu: if False a new scantable is returned.
|
|---|
| 992 | Otherwise, the scaling is done in-situ
|
|---|
| 993 | The default is taken from .asaprc (False)
|
|---|
| 994 | Example:
|
|---|
| 995 | polav = average_pols(myscan)
|
|---|
| 996 | """
|
|---|
| 997 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 998 | varlist = vars()
|
|---|
| 999 |
|
|---|
| 1000 | if mask is None:
|
|---|
| 1001 | mask = ()
|
|---|
| 1002 | if not insitu:
|
|---|
| 1003 | from asap._asap import averagepol as _avpol
|
|---|
| 1004 | s = scantable(_avpol(self, mask, weight))
|
|---|
| 1005 | s._add_history("average_pol",varlist)
|
|---|
| 1006 | return s
|
|---|
| 1007 | else:
|
|---|
| 1008 | from asap._asap import averagepol_insitu as _avpol
|
|---|
| 1009 | _avpol(self, mask, weight)
|
|---|
| 1010 | self._add_history("average_pol",varlist)
|
|---|
| 1011 | return
|
|---|
| 1012 |
|
|---|
| 1013 | def smooth(self, kernel="hanning", width=5.0, insitu=None, allaxes=None):
|
|---|
| 1014 | """
|
|---|
| 1015 | Smooth the spectrum by the specified kernel (conserving flux).
|
|---|
| 1016 | Parameters:
|
|---|
| 1017 | scan: The input scan
|
|---|
| 1018 | kernel: The type of smoothing kernel. Select from
|
|---|
| 1019 | 'hanning' (default), 'gaussian' and 'boxcar'.
|
|---|
| 1020 | The first three characters are sufficient.
|
|---|
| 1021 | width: The width of the kernel in pixels. For hanning this is
|
|---|
| 1022 | ignored otherwise it defauls to 5 pixels.
|
|---|
| 1023 | For 'gaussian' it is the Full Width Half
|
|---|
| 1024 | Maximum. For 'boxcar' it is the full width.
|
|---|
| 1025 | insitu: if False a new scantable is returned.
|
|---|
| 1026 | Otherwise, the scaling is done in-situ
|
|---|
| 1027 | The default is taken from .asaprc (False)
|
|---|
| 1028 | allaxes: If True (default) apply to all spectra. Otherwise
|
|---|
| 1029 | apply only to the selected (beam/pol/if)spectra only
|
|---|
| 1030 | The default is taken from .asaprc (True if none)
|
|---|
| 1031 | Example:
|
|---|
| 1032 | none
|
|---|
| 1033 | """
|
|---|
| 1034 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
|
|---|
| 1035 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1036 | varlist = vars()
|
|---|
| 1037 | if not insitu:
|
|---|
| 1038 | from asap._asap import smooth as _smooth
|
|---|
| 1039 | s = scantable(_smooth(self,kernel,width,allaxes))
|
|---|
| 1040 | s._add_history("smooth", varlist)
|
|---|
| 1041 | return s
|
|---|
| 1042 | else:
|
|---|
| 1043 | from asap._asap import smooth_insitu as _smooth
|
|---|
| 1044 | _smooth(self,kernel,width,allaxes)
|
|---|
| 1045 | self._add_history("smooth", varlist)
|
|---|
| 1046 | return
|
|---|
| 1047 |
|
|---|
| 1048 | def poly_baseline(self, mask=None, order=0, insitu=None):
|
|---|
| 1049 | """
|
|---|
| 1050 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 1051 | Parameters:
|
|---|
| 1052 | scan: a scantable
|
|---|
| 1053 | mask: an optional mask
|
|---|
| 1054 | order: the order of the polynomial (default is 0)
|
|---|
| 1055 | insitu: if False a new scantable is returned.
|
|---|
| 1056 | Otherwise, the scaling is done in-situ
|
|---|
| 1057 | The default is taken from .asaprc (False)
|
|---|
| 1058 | Example:
|
|---|
| 1059 | # return a scan baselined by a third order polynomial,
|
|---|
| 1060 | # not using a mask
|
|---|
| 1061 | bscan = scan.poly_baseline(order=3)
|
|---|
| 1062 | """
|
|---|
| 1063 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1064 | varlist = vars()
|
|---|
| 1065 | if mask is None:
|
|---|
| 1066 | from numarray import ones
|
|---|
| 1067 | mask = list(ones(scan.nchan()))
|
|---|
| 1068 | from asap.asapfitter import fitter
|
|---|
| 1069 | f = fitter()
|
|---|
| 1070 | f._verbose(True)
|
|---|
| 1071 | f.set_scan(self, mask)
|
|---|
| 1072 | f.set_function(poly=order)
|
|---|
| 1073 | sf = f.auto_fit(insitu)
|
|---|
| 1074 | if insitu:
|
|---|
| 1075 | self._add_history("poly_baseline", varlist)
|
|---|
| 1076 | return
|
|---|
| 1077 | else:
|
|---|
| 1078 | sf._add_history("poly_baseline", varlist)
|
|---|
| 1079 | return sf
|
|---|
| 1080 |
|
|---|
| 1081 | def auto_poly_baseline(self, mask=None, edge=(0,0), order=0,
|
|---|
| 1082 | threshold=3,insitu=None):
|
|---|
| 1083 | """
|
|---|
| 1084 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 1085 | Spectral lines are detected first using linefinder and masked out
|
|---|
| 1086 | to avoid them affecting the baseline solution.
|
|---|
| 1087 |
|
|---|
| 1088 | Parameters:
|
|---|
| 1089 | scan: a scantable
|
|---|
| 1090 | mask: an optional mask retreived from scantable
|
|---|
| 1091 | edge: an optional number of channel to drop at
|
|---|
| 1092 | the edge of spectrum. If only one value is
|
|---|
| 1093 | specified, the same number will be dropped from
|
|---|
| 1094 | both sides of the spectrum. Default is to keep
|
|---|
| 1095 | all channels
|
|---|
| 1096 | order: the order of the polynomial (default is 0)
|
|---|
| 1097 | threshold: the threshold used by line finder. It is better to
|
|---|
| 1098 | keep it large as only strong lines affect the
|
|---|
| 1099 | baseline solution.
|
|---|
| 1100 | insitu: if False a new scantable is returned.
|
|---|
| 1101 | Otherwise, the scaling is done in-situ
|
|---|
| 1102 | The default is taken from .asaprc (False)
|
|---|
| 1103 |
|
|---|
| 1104 | Example:
|
|---|
| 1105 | sc2=auto_poly_baseline(order=7)
|
|---|
| 1106 | """
|
|---|
| 1107 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1108 | varlist = vars()
|
|---|
| 1109 | from asap.asapfitter import fitter
|
|---|
| 1110 | from asap.asaplinefind import linefinder
|
|---|
| 1111 | from asap import _is_sequence_or_number as _is_valid
|
|---|
| 1112 |
|
|---|
| 1113 | if not _is_valid(edge, int):
|
|---|
| 1114 | print "Parameter 'edge' as to be an integer or a pair of integers"
|
|---|
| 1115 | return
|
|---|
| 1116 |
|
|---|
| 1117 | # setup fitter
|
|---|
| 1118 | f = fitter()
|
|---|
| 1119 | f._verbose(True)
|
|---|
| 1120 | f.set_function(poly=order)
|
|---|
| 1121 |
|
|---|
| 1122 | # setup line finder
|
|---|
| 1123 | fl=linefinder()
|
|---|
| 1124 | fl.set_options(threshold=threshold)
|
|---|
| 1125 |
|
|---|
| 1126 | if not insitu:
|
|---|
| 1127 | workscan=self.copy()
|
|---|
| 1128 | else:
|
|---|
| 1129 | workscan=self
|
|---|
| 1130 |
|
|---|
| 1131 | vb=workscan._vb
|
|---|
| 1132 | # remember the verbose parameter and selection
|
|---|
| 1133 | workscan._vb=False
|
|---|
| 1134 | sel=workscan.get_cursor()
|
|---|
| 1135 | rows=range(workscan.nrow())
|
|---|
| 1136 | for i in range(workscan.nbeam()):
|
|---|
| 1137 | workscan.setbeam(i)
|
|---|
| 1138 | for j in range(workscan.nif()):
|
|---|
| 1139 | workscan.setif(j)
|
|---|
| 1140 | for k in range(workscan.npol()):
|
|---|
| 1141 | workscan.setpol(k)
|
|---|
| 1142 | if f._vb:
|
|---|
| 1143 | print "Processing:"
|
|---|
| 1144 | print 'Beam[%d], IF[%d], Pol[%d]' % (i,j,k)
|
|---|
| 1145 | for iRow in rows:
|
|---|
| 1146 | fl.set_scan(workscan,mask,edge)
|
|---|
| 1147 | fl.find_lines(iRow)
|
|---|
| 1148 | f.set_scan(workscan, fl.get_mask())
|
|---|
| 1149 | f.x=workscan._getabcissa(iRow)
|
|---|
| 1150 | f.y=workscan._getspectrum(iRow)
|
|---|
| 1151 | f.data=None
|
|---|
| 1152 | f.fit()
|
|---|
| 1153 | x=f.get_parameters()
|
|---|
| 1154 | workscan._setspectrum(f.fitter.getresidual(),iRow)
|
|---|
| 1155 | workscan.set_cursor(sel[0],sel[1],sel[2])
|
|---|
| 1156 | workscan._vb = vb
|
|---|
| 1157 | if not insitu:
|
|---|
| 1158 | return workscan
|
|---|
| 1159 |
|
|---|
| 1160 | def rotate_linpolphase(self, angle, allaxes=None):
|
|---|
| 1161 | """
|
|---|
| 1162 | Rotate the phase of the complex polarization O=Q+iU correlation.
|
|---|
| 1163 | This is always done in situ in the raw data. So if you call this
|
|---|
| 1164 | function more than once then each call rotates the phase further.
|
|---|
| 1165 | Parameters:
|
|---|
| 1166 | angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1167 | allaxes: If True apply to all spectra. Otherwise
|
|---|
| 1168 | apply only to the selected (beam/pol/if)spectra only.
|
|---|
| 1169 | The default is taken from .asaprc (True if none)
|
|---|
| 1170 | Examples:
|
|---|
| 1171 | scan.rotate_linpolphase(2.3)
|
|---|
| 1172 | """
|
|---|
| 1173 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
|
|---|
| 1174 | varlist = vars()
|
|---|
| 1175 | from asap._asap import _rotate_linpolphase as _rotate
|
|---|
| 1176 | _rotate(self, angle, allaxes)
|
|---|
| 1177 | self._add_history("rotate_linpolphase", varlist)
|
|---|
| 1178 | return
|
|---|
| 1179 |
|
|---|
| 1180 |
|
|---|
| 1181 | def rotate_xyphase(self, angle, allaxes=None):
|
|---|
| 1182 | """
|
|---|
| 1183 | Rotate the phase of the XY correlation. This is always done in situ
|
|---|
| 1184 | in the data. So if you call this function more than once
|
|---|
| 1185 | then each call rotates the phase further.
|
|---|
| 1186 | Parameters:
|
|---|
| 1187 | angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1188 | allaxes: If True apply to all spectra. Otherwise
|
|---|
| 1189 | apply only to the selected (beam/pol/if)spectra only.
|
|---|
| 1190 | The default is taken from .asaprc (True if none)
|
|---|
| 1191 | Examples:
|
|---|
| 1192 | scan.rotate_xyphase(2.3)
|
|---|
| 1193 | """
|
|---|
| 1194 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
|
|---|
| 1195 | varlist = vars()
|
|---|
| 1196 | from asap._asap import rotate_xyphase as _rotate_xyphase
|
|---|
| 1197 | _rotate_xyphase(self, angle, allaxes)
|
|---|
| 1198 | self._add_history("rotate_xyphase", varlist)
|
|---|
| 1199 | return
|
|---|
| 1200 |
|
|---|
| 1201 |
|
|---|
| 1202 | def add(self, offset, insitu=None, allaxes=None):
|
|---|
| 1203 | """
|
|---|
| 1204 | Return a scan where all spectra have the offset added
|
|---|
| 1205 | Parameters:
|
|---|
| 1206 | offset: the offset
|
|---|
| 1207 | insitu: if False a new scantable is returned.
|
|---|
| 1208 | Otherwise, the scaling is done in-situ
|
|---|
| 1209 | The default is taken from .asaprc (False)
|
|---|
| 1210 | allaxes: if True apply to all spectra. Otherwise
|
|---|
| 1211 | apply only to the selected (beam/pol/if)spectra only
|
|---|
| 1212 | The default is taken from .asaprc (True if none)
|
|---|
| 1213 | """
|
|---|
| 1214 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
|
|---|
| 1215 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1216 | varlist = vars()
|
|---|
| 1217 | if not insitu:
|
|---|
| 1218 | from asap._asap import add as _add
|
|---|
| 1219 | s = scantable(_add(self, offset, allaxes))
|
|---|
| 1220 | s._add_history("add",varlist)
|
|---|
| 1221 | return s
|
|---|
| 1222 | else:
|
|---|
| 1223 | from asap._asap import add_insitu as _add
|
|---|
| 1224 | _add(self, offset, allaxes)
|
|---|
| 1225 | self._add_history("add",varlist)
|
|---|
| 1226 | return
|
|---|
| 1227 |
|
|---|
| 1228 | def scale(self, factor, insitu=None, allaxes=None, tsys=True):
|
|---|
| 1229 | """
|
|---|
| 1230 | Return a scan where all spectra are scaled by the give 'factor'
|
|---|
| 1231 | Parameters:
|
|---|
| 1232 | factor: the scaling factor
|
|---|
| 1233 | insitu: if False a new scantable is returned.
|
|---|
| 1234 | Otherwise, the scaling is done in-situ
|
|---|
| 1235 | The default is taken from .asaprc (False)
|
|---|
| 1236 | allaxes: if True apply to all spectra. Otherwise
|
|---|
| 1237 | apply only to the selected (beam/pol/if)spectra only.
|
|---|
| 1238 | The default is taken from .asaprc (True if none)
|
|---|
| 1239 | tsys: if True (default) then apply the operation to Tsys
|
|---|
| 1240 | as well as the data
|
|---|
| 1241 | """
|
|---|
| 1242 | if allaxes is None: allaxes = rcParams['scantable.allaxes']
|
|---|
| 1243 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1244 | varlist = vars()
|
|---|
| 1245 | if not insitu:
|
|---|
| 1246 | from asap._asap import scale as _scale
|
|---|
| 1247 | s = scantable(_scale(self, factor, allaxes, tsys))
|
|---|
| 1248 | s._add_history("scale",varlist)
|
|---|
| 1249 | return s
|
|---|
| 1250 | else:
|
|---|
| 1251 | from asap._asap import scale_insitu as _scale
|
|---|
| 1252 | _scale(self, factor, allaxes, tsys)
|
|---|
| 1253 | self._add_history("scale",varlist)
|
|---|
| 1254 | return
|
|---|
| 1255 |
|
|---|
| 1256 |
|
|---|
| 1257 | def quotient(self, other, isreference=True, preserve=True):
|
|---|
| 1258 | """
|
|---|
| 1259 | Return the quotient of a 'source' (signal) scan and a 'reference' scan.
|
|---|
| 1260 | The reference can have just one row, even if the signal has many.
|
|---|
| 1261 | Otherwise they must have the same number of rows.
|
|---|
| 1262 | The cursor of the output scan is set to 0
|
|---|
| 1263 | Parameters:
|
|---|
| 1264 | source: the 'other' scan
|
|---|
| 1265 | isreference: if the 'other' scan is the reference (default)
|
|---|
| 1266 | or source
|
|---|
| 1267 | preserve: you can preserve (default) the continuum or
|
|---|
| 1268 | remove it. The equations used are
|
|---|
| 1269 | preserve - Output = Tref * (sig/ref) - Tref
|
|---|
| 1270 | remove - Output = Tref * (sig/ref) - Tsig
|
|---|
| 1271 | Example:
|
|---|
| 1272 | # src is a scantable for an 'on' scan, ref for an 'off' scantable
|
|---|
| 1273 | q1 = src.quotient(ref)
|
|---|
| 1274 | q2 = ref.quotient(src, isreference=False)
|
|---|
| 1275 | # gives the same result
|
|---|
| 1276 | """
|
|---|
| 1277 | from asap._asap import quotient as _quot
|
|---|
| 1278 | if isreference:
|
|---|
| 1279 | return scantable(_quot(self, other, preserve))
|
|---|
| 1280 | else:
|
|---|
| 1281 | return scantable(_quot(other, self, preserve))
|
|---|
| 1282 |
|
|---|
| 1283 | def __add__(self, other):
|
|---|
| 1284 | varlist = vars()
|
|---|
| 1285 | s = None
|
|---|
| 1286 | if isinstance(other, scantable):
|
|---|
| 1287 | from asap._asap import b_operate as _bop
|
|---|
| 1288 | s = scantable(_bop(self, other, 'add', True))
|
|---|
| 1289 | elif isinstance(other, float):
|
|---|
| 1290 | from asap._asap import add as _add
|
|---|
| 1291 | s = scantable(_add(self, other, True))
|
|---|
| 1292 | else:
|
|---|
| 1293 | print "Other input is not a scantable or float value"
|
|---|
| 1294 | return
|
|---|
| 1295 | s._add_history("operator +", varlist)
|
|---|
| 1296 | return s
|
|---|
| 1297 |
|
|---|
| 1298 |
|
|---|
| 1299 | def __sub__(self, other):
|
|---|
| 1300 | """
|
|---|
| 1301 | implicit on all axes and on Tsys
|
|---|
| 1302 | """
|
|---|
| 1303 | varlist = vars()
|
|---|
| 1304 | s = None
|
|---|
| 1305 | if isinstance(other, scantable):
|
|---|
| 1306 | from asap._asap import b_operate as _bop
|
|---|
| 1307 | s = scantable(_bop(self, other, 'sub', True))
|
|---|
| 1308 | elif isinstance(other, float):
|
|---|
| 1309 | from asap._asap import add as _add
|
|---|
| 1310 | s = scantable(_add(self, -other, True))
|
|---|
| 1311 | else:
|
|---|
| 1312 | print "Other input is not a scantable or float value"
|
|---|
| 1313 | return
|
|---|
| 1314 | s._add_history("operator -", varlist)
|
|---|
| 1315 | return s
|
|---|
| 1316 |
|
|---|
| 1317 | def __mul__(self, other):
|
|---|
| 1318 | """
|
|---|
| 1319 | implicit on all axes and on Tsys
|
|---|
| 1320 | """
|
|---|
| 1321 | varlist = vars()
|
|---|
| 1322 | s = None
|
|---|
| 1323 | if isinstance(other, scantable):
|
|---|
| 1324 | from asap._asap import b_operate as _bop
|
|---|
| 1325 | s = scantable(_bop(self, other, 'mul', True))
|
|---|
| 1326 | elif isinstance(other, float):
|
|---|
| 1327 | if other == 0.0:
|
|---|
| 1328 | print "Multiplying by zero is not recommended."
|
|---|
| 1329 | return
|
|---|
| 1330 | from asap._asap import scale as _sca
|
|---|
| 1331 | s = scantable(_sca(self, other, True))
|
|---|
| 1332 | else:
|
|---|
| 1333 | print "Other input is not a scantable or float value"
|
|---|
| 1334 | return
|
|---|
| 1335 | s._add_history("operator *", varlist)
|
|---|
| 1336 | return s
|
|---|
| 1337 |
|
|---|
| 1338 |
|
|---|
| 1339 | def __div__(self, other):
|
|---|
| 1340 | """
|
|---|
| 1341 | implicit on all axes and on Tsys
|
|---|
| 1342 | """
|
|---|
| 1343 | varlist = vars()
|
|---|
| 1344 | s = None
|
|---|
| 1345 | if isinstance(other, scantable):
|
|---|
| 1346 | from asap._asap import b_operate as _bop
|
|---|
| 1347 | s = scantable(_bop(self, other, 'div', True))
|
|---|
| 1348 | elif isinstance(other, float):
|
|---|
| 1349 | if other == 0.0:
|
|---|
| 1350 | print "Dividing by zero is not recommended"
|
|---|
| 1351 | return
|
|---|
| 1352 | from asap._asap import scale as _sca
|
|---|
| 1353 | s = scantable(_sca(self, 1.0/other, True))
|
|---|
| 1354 | else:
|
|---|
| 1355 | print "Other input is not a scantable or float value"
|
|---|
| 1356 | return
|
|---|
| 1357 | s._add_history("operator /", varlist)
|
|---|
| 1358 | return s
|
|---|
| 1359 |
|
|---|
| 1360 | def _add_history(self, funcname, parameters):
|
|---|
| 1361 | # create date
|
|---|
| 1362 | sep = "##"
|
|---|
| 1363 | from datetime import datetime
|
|---|
| 1364 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
|
|---|
| 1365 | hist = dstr+sep
|
|---|
| 1366 | hist += funcname+sep#cdate+sep
|
|---|
| 1367 | if parameters.has_key('self'): del parameters['self']
|
|---|
| 1368 | for k,v in parameters.iteritems():
|
|---|
| 1369 | if type(v) is dict:
|
|---|
| 1370 | for k2,v2 in v.iteritems():
|
|---|
| 1371 | hist += k2
|
|---|
| 1372 | hist += "="
|
|---|
| 1373 | if isinstance(v2,scantable):
|
|---|
| 1374 | hist += 'scantable'
|
|---|
| 1375 | elif k2 == 'mask':
|
|---|
| 1376 | if isinstance(v2,list) or isinstance(v2,tuple):
|
|---|
| 1377 | hist += str(self._zip_mask(v2))
|
|---|
| 1378 | else:
|
|---|
| 1379 | hist += str(v2)
|
|---|
| 1380 | else:
|
|---|
| 1381 | hist += str(v2)
|
|---|
| 1382 | else:
|
|---|
| 1383 | hist += k
|
|---|
| 1384 | hist += "="
|
|---|
| 1385 | if isinstance(v,scantable):
|
|---|
| 1386 | hist += 'scantable'
|
|---|
| 1387 | elif k == 'mask':
|
|---|
| 1388 | if isinstance(v,list) or isinstance(v,tuple):
|
|---|
| 1389 | hist += str(self._zip_mask(v))
|
|---|
| 1390 | else:
|
|---|
| 1391 | hist += str(v)
|
|---|
| 1392 | else:
|
|---|
| 1393 | hist += str(v)
|
|---|
| 1394 | hist += sep
|
|---|
| 1395 | hist = hist[:-2] # remove trailing '##'
|
|---|
| 1396 | self._addhistory(hist)
|
|---|
| 1397 |
|
|---|
| 1398 |
|
|---|
| 1399 | def _zip_mask(self, mask):
|
|---|
| 1400 | mask = list(mask)
|
|---|
| 1401 | i = 0
|
|---|
| 1402 | segments = []
|
|---|
| 1403 | while mask[i:].count(1):
|
|---|
| 1404 | i += mask[i:].index(1)
|
|---|
| 1405 | if mask[i:].count(0):
|
|---|
| 1406 | j = i + mask[i:].index(0)
|
|---|
| 1407 | else:
|
|---|
| 1408 | j = len(mask)
|
|---|
| 1409 | segments.append([i,j])
|
|---|
| 1410 | i = j
|
|---|
| 1411 | return segments
|
|---|
