| 1 | from asap._asap import Scantable
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| 2 | from asap import rcParams
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| 3 | from asap import print_log
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| 4 | from numarray import ones,zeros
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| 5 | import sys
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| 6 |
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| 7 | class scantable(Scantable):
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| 8 | """
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| 9 | The ASAP container for scans
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| 10 | """
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| 11 |
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| 12 | def __init__(self, filename, average=None, unit=None):
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| 13 | """
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| 14 | Create a scantable from a saved one or make a reference
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| 15 | Parameters:
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| 16 | filename: the name of an asap table on disk
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| 17 | or
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| 18 | the name of a rpfits/sdfits/ms file
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| 19 | (integrations within scans are auto averaged
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| 20 | and the whole file is read)
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| 21 | or
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| 22 | [advanced] a reference to an existing
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| 23 | scantable
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| 24 | average: average all integrations withinb a scan on read.
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| 25 | The default (True) is taken from .asaprc.
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| 26 | unit: brightness unit; must be consistent with K or Jy.
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| 27 | Over-rides the default selected by the reader
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| 28 | (input rpfits/sdfits/ms) or replaces the value
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| 29 | in existing scantables
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| 30 | """
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| 31 | if average is None or type(average) is not bool:
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| 32 | average = rcParams['scantable.autoaverage']
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| 33 |
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| 34 | varlist = vars()
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| 35 | from asap._asap import stmath
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| 36 | self._math = stmath()
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| 37 | from asap import asaplog
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| 38 | if isinstance(filename, Scantable):
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| 39 | Scantable.__init__(self, filename)
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| 40 | if unit is not None:
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| 41 | self.set_fluxunit(unit)
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| 42 | else:
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| 43 | import os.path
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| 44 | if not os.path.exists(filename):
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| 45 | s = "File '%s' not found." % (filename)
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| 46 | if rcParams['verbose']:
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| 47 | asaplog.push(s)
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| 48 | print asaplog.pop().strip()
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| 49 | return
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| 50 | raise IOError(s)
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| 51 | filename = os.path.expandvars(filename)
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| 52 | if os.path.isdir(filename):
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| 53 | # crude check if asap table
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| 54 | if os.path.exists(filename+'/table.info'):
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| 55 | Scantable.__init__(self, filename, "memory")
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| 56 | if unit is not None:
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| 57 | self.set_fluxunit(unit)
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| 58 | else:
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| 59 | msg = "The given file '%s'is not a valid asap table." % (filename)
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| 60 | if rcParams['verbose']:
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| 61 | print msg
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| 62 | return
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| 63 | else:
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| 64 | raise IOError(msg)
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| 65 | else:
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| 66 | from asap._asap import stfiller
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| 67 | ifSel = -1
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| 68 | beamSel = -1
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| 69 | r = stfiller()
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| 70 | r._open(filename,ifSel,beamSel)
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| 71 | asaplog.push('Importing data...')
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| 72 | print_log()
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| 73 | r._read()
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| 74 | tbl = r._getdata()
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| 75 | if unit is not None:
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| 76 | tbl.set_fluxunit(unit)
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| 77 | if average:
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| 78 | asaplog.push('Auto averaging integrations...')
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| 79 | print_log()
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| 80 | tbl2 = self._math._average((tbl,),(),'NONE','SCAN', False)
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| 81 | Scantable.__init__(self,tbl2)
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| 82 | del tbl2
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| 83 | else:
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| 84 | Scantable.__init__(self,tbl)
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| 85 | del r,tbl
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| 86 | self._add_history("scantable", varlist)
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| 87 | print_log()
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| 88 |
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| 89 | def save(self, name=None, format=None, overwrite=False):
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| 90 | """
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| 91 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS,
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| 92 | Image FITS or MS2 format.
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| 93 | Parameters:
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| 94 | name: the name of the outputfile. For format="FITS" this
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| 95 | is the directory file name into which all the files
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| 96 | will be written (default is 'asap_FITS'). For format
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| 97 | "ASCII" this is the root file name (data in 'name'.txt
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| 98 | and header in 'name'_header.txt)
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| 99 | format: an optional file format. Default is ASAP.
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| 100 | Allowed are - 'ASAP' (save as ASAP [aips++] Table),
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| 101 | 'SDFITS' (save as SDFITS file)
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| 102 | 'FITS' (saves each row as a FITS Image)
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| 103 | 'ASCII' (saves as ascii text file)
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| 104 | 'MS2' (saves as an aips++
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| 105 | MeasurementSet V2)
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| 106 | overwrite: If the file should be overwritten if it exists.
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| 107 | The default False is to return with warning
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| 108 | without writing the output. USE WITH CARE.
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| 109 | Example:
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| 110 | scan.save('myscan.asap')
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| 111 | scan.save('myscan.sdfits','SDFITS')
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| 112 | """
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| 113 | from os import path
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| 114 | if format is None: format = rcParams['scantable.save']
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| 115 | suffix = '.'+format.lower()
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| 116 | if name is None or name =="":
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| 117 | name = 'scantable'+suffix
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| 118 | from asap import asaplog
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| 119 | msg = "No filename given. Using default name %s..." % name
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| 120 | asaplog.push(msg)
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| 121 | name = path.expandvars(name)
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| 122 | if path.isfile(name) or path.isdir(name):
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| 123 | if not overwrite:
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| 124 | msg = "File %s exists." % name
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| 125 | if rcParams['verbose']:
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| 126 | print msg
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| 127 | return
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| 128 | else:
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| 129 | raise IOError(msg)
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| 130 | format2 = format.upper()
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| 131 | if format2 == 'ASAP':
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| 132 | self._save(name)
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| 133 | else:
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| 134 | print "NYI"
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| 135 | # from asap._asap import sdwriter as _sw
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| 136 | # w = _sw(format2)
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| 137 | # w.write(self, name, stokes)
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| 138 |
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| 139 | print_log()
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| 140 | return
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| 141 |
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| 142 | def copy(self):
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| 143 | """
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| 144 | Return a copy of this scantable.
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| 145 | Parameters:
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| 146 | none
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| 147 | Example:
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| 148 | copiedscan = scan.copy()
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| 149 | """
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| 150 | sd = scantable(Scantable._copy(self))
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| 151 | return sd
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| 152 |
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| 153 | def get_scan(self, scanid=None):
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| 154 | """
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| 155 | Return a specific scan (by scanno) or collection of scans (by
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| 156 | source name) in a new scantable.
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| 157 | Parameters:
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| 158 | scanid: a (list of) scanno or a source name, unix-style
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| 159 | patterns are accepted for source name matching, e.g.
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| 160 | '*_R' gets all 'ref scans
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| 161 | Example:
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| 162 | # get all scans containing the source '323p459'
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| 163 | newscan = scan.get_scan('323p459')
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| 164 | # get all 'off' scans
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| 165 | refscans = scan.get_scan('*_R')
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| 166 | # get a susbset of scans by scanno (as listed in scan.summary())
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| 167 | newscan = scan.get_scan([0,2,7,10])
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| 168 | """
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| 169 | if scanid is None:
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| 170 | if rcParams['verbose']:
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| 171 | print "Please specify a scan no or name to retrieve from the scantable"
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| 172 | return
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| 173 | else:
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| 174 | raise RuntimeError("No scan given")
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| 175 |
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| 176 | try:
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| 177 | bsel = self._getselection()
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| 178 | sel = asap._asap.Selector()
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| 179 | if type(scanid) is str:
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| 180 | sel._setname()
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| 181 | self._setselection(sel)
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| 182 | scopy = self._copy()
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| 183 | self._setselection(bsel)
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| 184 | return scantable(scopy)
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| 185 | elif type(scanid) is int:
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| 186 | sel._setscans([scanid])
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| 187 | self._setselection(sel)
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| 188 | scopy = self._copy()
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| 189 | self._setselection(bsel)
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| 190 | return scantable(scopy)
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| 191 | elif type(scanid) is list:
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| 192 | sel._setscans(scanid)
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| 193 | self._setselection(sel)
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| 194 | scopy = self._copy()
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| 195 | self._setselection(bsel)
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| 196 | return scantable(scopy)
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| 197 | else:
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| 198 | msg = "Illegal scanid type, use 'int' or 'list' if ints."
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| 199 | if rcParams['verbose']:
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| 200 | print msg
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| 201 | else:
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| 202 | raise TypeError(msg)
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| 203 | except RuntimeError:
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| 204 | if rcParams['verbose']: print "Couldn't find any match."
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| 205 | else: raise
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| 206 |
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| 207 | def __str__(self):
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| 208 | return Scantable._summary(self,True)
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| 209 |
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| 210 | def summary(self, filename=None, verbose=None):
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| 211 | """
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| 212 | Print a summary of the contents of this scantable.
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| 213 | Parameters:
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| 214 | filename: the name of a file to write the putput to
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| 215 | Default - no file output
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| 216 | verbose: print extra info such as the frequency table
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| 217 | The default (False) is taken from .asaprc
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| 218 | """
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| 219 | info = Scantable._summary(self, verbose)
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| 220 | if verbose is None: verbose = rcParams['scantable.verbosesummary']
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| 221 | if filename is not None:
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| 222 | if filename is "":
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| 223 | filename = 'scantable_summary.txt'
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| 224 | from os.path import expandvars, isdir
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| 225 | filename = expandvars(filename)
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| 226 | if not isdir(filename):
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| 227 | data = open(filename, 'w')
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| 228 | data.write(info)
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| 229 | data.close()
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| 230 | else:
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| 231 | msg = "Illegal file name '%s'." % (filename)
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| 232 | if rcParams['verbose']:
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| 233 | print msg
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| 234 | else:
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| 235 | raise IOError(msg)
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| 236 | if rcParams['verbose']:
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| 237 | try:
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| 238 | from IPython.genutils import page as pager
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| 239 | except ImportError:
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| 240 | from pydoc import pager
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| 241 | pager(info)
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| 242 | else:
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| 243 | return info
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| 244 |
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| 245 | def set_cursor(self, beam=0, IF=0, pol=0):
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| 246 | """
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| 247 | Set the spectrum for individual operations.
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| 248 | Parameters:
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| 249 | beam, IF, pol: a number
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| 250 | Example:
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| 251 | scan.set_cursor(0,0,1)
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| 252 | pol1sig = scan.stats(all=False) # returns std dev for beam=0
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| 253 | # if=0, pol=1
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| 254 | """
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| 255 | print "DEPRECATED"
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| 256 | varlist = vars()
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| 257 | sel = asap._asap.Selector()
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| 258 | sel._setbeams([beam])
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| 259 | sel._setpols([pol])
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| 260 | sel._setifs([IF])
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| 261 | self._add_history("set_cursor", varlist)
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| 262 | return
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| 263 |
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| 264 | def get_cursor(self):
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| 265 | """
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| 266 | Return/print a the current 'cursor' into the Beam/IF/Pol cube.
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| 267 | Parameters:
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| 268 | none
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| 269 | Returns:
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| 270 | a list of values (currentBeam,currentIF,currentPol)
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| 271 | Example:
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| 272 | none
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| 273 | """
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| 274 | print "DEPRECATED"
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| 275 | sel = self._getselection()
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| 276 | i = sel.getbeams()[0]
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| 277 | j = sel.getifs()[0]
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| 278 | k = sel.getpols()[0]
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| 279 | from asap import asaplog
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| 280 | out = "--------------------------------------------------\n"
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| 281 | out += " Cursor position\n"
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| 282 | out += "--------------------------------------------------\n"
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| 283 | out += 'Beam=%d IF=%d Pol=%d ' % (i,j,k)
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| 284 | asaplog.push(out)
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| 285 | print_log()
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| 286 | return i,j,k
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| 287 |
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| 288 | def stats(self, stat='stddev', mask=None):
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| 289 | """
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| 290 | Determine the specified statistic of the current beam/if/pol
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| 291 | Takes a 'mask' as an optional parameter to specify which
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| 292 | channels should be excluded.
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| 293 | Parameters:
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| 294 | stat: 'min', 'max', 'sumsq', 'sum', 'mean'
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| 295 | 'var', 'stddev', 'avdev', 'rms', 'median'
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| 296 | mask: an optional mask specifying where the statistic
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| 297 | should be determined.
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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.stats(stat='mean', mask=m)
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| 302 | """
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| 303 | from numarray import array,zeros,Float
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| 304 | if mask == None:
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| 305 | mask = []
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| 306 | axes = ['Beam','IF','Pol','Time']
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| 307 | if not self._check_ifs():
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| 308 | raise ValueError("Cannot apply mask as the IFs have different number of channels"
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| 309 | "Please use setselection() to select individual IFs")
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| 310 |
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| 311 | statvals = self._math._stats(self, mask, stat)
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| 312 | out = ''
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| 313 | axes = []
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| 314 | for i in range(self.nrow()):
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| 315 | axis = []
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| 316 | axis.append(self.getscan(i))
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| 317 | axis.append(self.getbeam(i))
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| 318 | axis.append(self.getif(i))
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| 319 | axis.append(self.getpol(i))
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| 320 | axis.append(self.getcycle(i))
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| 321 | axes.append(axis)
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| 322 | tm = self._gettime(i)
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| 323 | src = self._getsourcename(i)
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| 324 | out += 'Scan[%d] (%s) ' % (axis[0], src)
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| 325 | out += 'Time[%s]:\n' % (tm)
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| 326 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
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| 327 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
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| 328 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
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| 329 | out += '= %3.3f\n' % (statvals[i])
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| 330 | out += "--------------------------------------------------\n"
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| 331 |
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| 332 | if rcParams['verbose']:
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| 333 | print "--------------------------------------------------"
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| 334 | print " ",stat
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| 335 | print "--------------------------------------------------"
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| 336 | print out
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| 337 | retval = { 'axesnames': ['scanno','beamno','ifno','polno','cycleno'],
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| 338 | 'axes' : axes,
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| 339 | 'data': statvals}
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| 340 | return retval
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| 341 |
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| 342 | def stddev(self,mask=None):
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| 343 | """
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| 344 | Determine the standard deviation of the current beam/if/pol
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| 345 | Takes a 'mask' as an optional parameter to specify which
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| 346 | channels should be excluded.
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| 347 | Parameters:
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| 348 | mask: an optional mask specifying where the standard
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| 349 | deviation should be determined.
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| 350 |
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| 351 | Example:
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| 352 | scan.set_unit('channel')
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| 353 | msk = scan.create_mask([100,200],[500,600])
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| 354 | scan.stddev(mask=m)
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| 355 | """
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| 356 | return self.stats(stat='stddev',mask=mask);
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| 357 |
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| 358 | def get_tsys(self):
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| 359 | """
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| 360 | Return the System temperatures.
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| 361 | Parameters:
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| 362 |
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| 363 | Returns:
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| 364 | a list of Tsys values for the current selection
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| 365 | """
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| 366 |
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| 367 | return self._row_callback(self._gettsys, "Tsys")
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| 368 |
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| 369 | def _row_callback(self, callback, label):
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| 370 | axes = []
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| 371 | axesnames = ['scanno','beamno','ifno','polno','cycleno']
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| 372 | out = ""
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| 373 | outvec =[]
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| 374 | for i in range(self.nrow()):
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| 375 | axis = []
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| 376 | axis.append(self.getscan(i))
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| 377 | axis.append(self.getbeam(i))
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| 378 | axis.append(self.getif(i))
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| 379 | axis.append(self.getpol(i))
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| 380 | axis.append(self.getcycle(i))
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| 381 | axes.append(axis)
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| 382 | tm = self._gettime(i)
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| 383 | src = self._getsourcename(i)
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| 384 | out += 'Scan[%d] (%s) ' % (axis[0], src)
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| 385 | out += 'Time[%s]:\n' % (tm)
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| 386 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
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| 387 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
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| 388 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
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| 389 | outvec.append(callback(i))
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| 390 | out += '= %3.3f\n' % (outvec[i])
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| 391 | out += "--------------------------------------------------\n"
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| 392 | if rcParams['verbose']:
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| 393 | print "--------------------------------------------------"
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| 394 | print " %s" % (label)
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| 395 | print "--------------------------------------------------"
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| 396 | print out
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| 397 | retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
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| 398 | return retval
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| 399 |
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| 400 |
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| 401 | def get_time(self, row=-1):
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| 402 | """
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| 403 | Get a list of time stamps for the observations.
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| 404 | Return a string for each integration in the scantable.
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| 405 | Parameters:
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| 406 | row: row no of integration. Default -1 return all rows
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| 407 | Example:
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| 408 | none
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| 409 | """
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| 410 | out = []
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| 411 | if row == -1:
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| 412 | for i in range(self.nrow()):
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| 413 | out.append(self._gettime(i))
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| 414 | return out
|
|---|
| 415 | else:
|
|---|
| 416 | if row < self.nrow():
|
|---|
| 417 | return self._gettime(row)
|
|---|
| 418 |
|
|---|
| 419 | def get_sourcename(self, row=-1):
|
|---|
| 420 | """
|
|---|
| 421 | Get a list source names for the observations.
|
|---|
| 422 | Return a string for each integration in the scantable.
|
|---|
| 423 | Parameters:
|
|---|
| 424 | row: row no of integration. Default -1 return all rows
|
|---|
| 425 | Example:
|
|---|
| 426 | none
|
|---|
| 427 | """
|
|---|
| 428 | out = []
|
|---|
| 429 | if row == -1:
|
|---|
| 430 | return [self._getsourcename(i) for i in range(self.nrow())]
|
|---|
| 431 | else:
|
|---|
| 432 | if 0 <= row < self.nrow():
|
|---|
| 433 | return self._getsourcename(row)
|
|---|
| 434 |
|
|---|
| 435 | def get_elevation(self, row=-1):
|
|---|
| 436 | """
|
|---|
| 437 | Get a list of elevations for the observations.
|
|---|
| 438 | Return a float for each integration in the scantable.
|
|---|
| 439 | Parameters:
|
|---|
| 440 | row: row no of integration. Default -1 return all rows
|
|---|
| 441 | Example:
|
|---|
| 442 | none
|
|---|
| 443 | """
|
|---|
| 444 | out = []
|
|---|
| 445 | if row == -1:
|
|---|
| 446 | return [self._getelevation(i) for i in range(self.nrow())]
|
|---|
| 447 | else:
|
|---|
| 448 | if 0 <= row < self.nrow():
|
|---|
| 449 | return self._getelevation(row)
|
|---|
| 450 |
|
|---|
| 451 | def get_azimuth(self, row=-1):
|
|---|
| 452 | """
|
|---|
| 453 | Get a list of azimuths for the observations.
|
|---|
| 454 | Return a float for each integration in the scantable.
|
|---|
| 455 | Parameters:
|
|---|
| 456 | row: row no of integration. Default -1 return all rows
|
|---|
| 457 | Example:
|
|---|
| 458 | none
|
|---|
| 459 | """
|
|---|
| 460 | out = []
|
|---|
| 461 | if row == -1:
|
|---|
| 462 | return [self._getazimuth(i) for i in range(self.nrow())]
|
|---|
| 463 | else:
|
|---|
| 464 | if 0 <= row < self.nrow():
|
|---|
| 465 | return self._getazimuth(row)
|
|---|
| 466 |
|
|---|
| 467 | def get_parangle(self, row=-1):
|
|---|
| 468 | """
|
|---|
| 469 | Get a list of parallactic angles for the observations.
|
|---|
| 470 | Return a float for each integration in the scantable.
|
|---|
| 471 | Parameters:
|
|---|
| 472 | row: row no of integration. Default -1 return all rows
|
|---|
| 473 | Example:
|
|---|
| 474 | none
|
|---|
| 475 | """
|
|---|
| 476 | out = []
|
|---|
| 477 | if row == -1:
|
|---|
| 478 | return [self._getparangle(i) for i in range(self.nrow())]
|
|---|
| 479 | else:
|
|---|
| 480 | if 0 <= row < self.nrow():
|
|---|
| 481 | return self._getparangle(row)
|
|---|
| 482 |
|
|---|
| 483 | def set_unit(self, unit='channel'):
|
|---|
| 484 | """
|
|---|
| 485 | Set the unit for all following operations on this scantable
|
|---|
| 486 | Parameters:
|
|---|
| 487 | unit: optional unit, default is 'channel'
|
|---|
| 488 | one of '*Hz','km/s','channel', ''
|
|---|
| 489 | """
|
|---|
| 490 | varlist = vars()
|
|---|
| 491 | if unit in ['','pixel', 'channel']:
|
|---|
| 492 | unit = ''
|
|---|
| 493 | inf = list(self._getcoordinfo())
|
|---|
| 494 | inf[0] = unit
|
|---|
| 495 | self._setcoordinfo(inf)
|
|---|
| 496 | self._add_history("set_unit",varlist)
|
|---|
| 497 |
|
|---|
| 498 | def set_instrument(self, instr):
|
|---|
| 499 | """
|
|---|
| 500 | Set the instrument for subsequent processing
|
|---|
| 501 | Parameters:
|
|---|
| 502 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
|
|---|
| 503 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
|
|---|
| 504 | """
|
|---|
| 505 | self._setInstrument(instr)
|
|---|
| 506 | self._add_history("set_instument",vars())
|
|---|
| 507 | print_log()
|
|---|
| 508 |
|
|---|
| 509 | def set_doppler(self, doppler='RADIO'):
|
|---|
| 510 | """
|
|---|
| 511 | Set the doppler for all following operations on this scantable.
|
|---|
| 512 | Parameters:
|
|---|
| 513 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
|
|---|
| 514 | """
|
|---|
| 515 | varlist = vars()
|
|---|
| 516 | inf = list(self._getcoordinfo())
|
|---|
| 517 | inf[2] = doppler
|
|---|
| 518 | self._setcoordinfo(inf)
|
|---|
| 519 | self._add_history("set_doppler",vars())
|
|---|
| 520 | print_log()
|
|---|
| 521 |
|
|---|
| 522 | def set_freqframe(self, frame=None):
|
|---|
| 523 | """
|
|---|
| 524 | Set the frame type of the Spectral Axis.
|
|---|
| 525 | Parameters:
|
|---|
| 526 | frame: an optional frame type, default 'LSRK'. Valid frames are:
|
|---|
| 527 | 'REST','TOPO','LSRD','LSRK','BARY',
|
|---|
| 528 | 'GEO','GALACTO','LGROUP','CMB'
|
|---|
| 529 | Examples:
|
|---|
| 530 | scan.set_freqframe('BARY')
|
|---|
| 531 | """
|
|---|
| 532 | if frame is None: frame = rcParams['scantable.freqframe']
|
|---|
| 533 | varlist = vars()
|
|---|
| 534 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \
|
|---|
| 535 | 'GEO','GALACTO','LGROUP','CMB']
|
|---|
| 536 |
|
|---|
| 537 | if 1:#frame in valid:
|
|---|
| 538 | inf = list(self._getcoordinfo())
|
|---|
| 539 | inf[1] = frame
|
|---|
| 540 | self._setcoordinfo(inf)
|
|---|
| 541 | self._add_history("set_freqframe",varlist)
|
|---|
| 542 | else:
|
|---|
| 543 | msg = "Please specify a valid freq type. Valid types are:\n",valid
|
|---|
| 544 | if rcParams['verbose']:
|
|---|
| 545 | print msg
|
|---|
| 546 | else:
|
|---|
| 547 | raise TypeError(msg)
|
|---|
| 548 | print_log()
|
|---|
| 549 |
|
|---|
| 550 | def get_unit(self):
|
|---|
| 551 | """
|
|---|
| 552 | Get the default unit set in this scantable
|
|---|
| 553 | Parameters:
|
|---|
| 554 | Returns:
|
|---|
| 555 | A unit string
|
|---|
| 556 | """
|
|---|
| 557 | inf = self._getcoordinfo()
|
|---|
| 558 | unit = inf[0]
|
|---|
| 559 | if unit == '': unit = 'channel'
|
|---|
| 560 | return unit
|
|---|
| 561 |
|
|---|
| 562 | def get_abcissa(self, rowno=0):
|
|---|
| 563 | """
|
|---|
| 564 | Get the abcissa in the current coordinate setup for the currently
|
|---|
| 565 | selected Beam/IF/Pol
|
|---|
| 566 | Parameters:
|
|---|
| 567 | rowno: an optional row number in the scantable. Default is the
|
|---|
| 568 | first row, i.e. rowno=0
|
|---|
| 569 | Returns:
|
|---|
| 570 | The abcissa values and it's format string (as a dictionary)
|
|---|
| 571 | """
|
|---|
| 572 | abc = self._getabcissa(rowno)
|
|---|
| 573 | lbl = self._getabcissalabel(rowno)
|
|---|
| 574 | print_log()
|
|---|
| 575 | return abc, lbl
|
|---|
| 576 |
|
|---|
| 577 | def create_mask(self, *args, **kwargs):
|
|---|
| 578 | """
|
|---|
| 579 | Compute and return a mask based on [min,max] windows.
|
|---|
| 580 | The specified windows are to be INCLUDED, when the mask is
|
|---|
| 581 | applied.
|
|---|
| 582 | Parameters:
|
|---|
| 583 | [min,max],[min2,max2],...
|
|---|
| 584 | Pairs of start/end points specifying the regions
|
|---|
| 585 | to be masked
|
|---|
| 586 | invert: optional argument. If specified as True,
|
|---|
| 587 | return an inverted mask, i.e. the regions
|
|---|
| 588 | specified are EXCLUDED
|
|---|
| 589 | row: create the mask using the specified row for
|
|---|
| 590 | unit conversions, default is row=0
|
|---|
| 591 | only necessary if frequency varies over rows.
|
|---|
| 592 | Example:
|
|---|
| 593 | scan.set_unit('channel')
|
|---|
| 594 |
|
|---|
| 595 | a)
|
|---|
| 596 | msk = scan.set_mask([400,500],[800,900])
|
|---|
| 597 | # masks everything outside 400 and 500
|
|---|
| 598 | # and 800 and 900 in the unit 'channel'
|
|---|
| 599 |
|
|---|
| 600 | b)
|
|---|
| 601 | msk = scan.set_mask([400,500],[800,900], invert=True)
|
|---|
| 602 | # masks the regions between 400 and 500
|
|---|
| 603 | # and 800 and 900 in the unit 'channel'
|
|---|
| 604 |
|
|---|
| 605 | """
|
|---|
| 606 | row = 0
|
|---|
| 607 | if kwargs.has_key("row"):
|
|---|
| 608 | row = kwargs.get("row")
|
|---|
| 609 | data = self._getabcissa(row)
|
|---|
| 610 | u = self._getcoordinfo()[0]
|
|---|
| 611 | if rcParams['verbose']:
|
|---|
| 612 | if u == "": u = "channel"
|
|---|
| 613 | from asap import asaplog
|
|---|
| 614 | msg = "The current mask window unit is %s" % u
|
|---|
| 615 | if not _check_ifs():
|
|---|
| 616 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
|---|
| 617 | asaplog.push(msg)
|
|---|
| 618 | n = self.nchan()
|
|---|
| 619 | msk = zeros(n)
|
|---|
| 620 | # test if args is a 'list' or a 'normal *args - UGLY!!!
|
|---|
| 621 |
|
|---|
| 622 | ws = (isinstance(args[-1][-1],int) or isinstance(args[-1][-1],float)) and args or args[0]
|
|---|
| 623 | for window in ws:
|
|---|
| 624 | if (len(window) != 2 or window[0] > window[1] ):
|
|---|
| 625 | raise TypeError("A window needs to be defined as [min,max]")
|
|---|
| 626 | for i in range(n):
|
|---|
| 627 | if data[i] >= window[0] and data[i] < window[1]:
|
|---|
| 628 | msk[i] = 1
|
|---|
| 629 | if kwargs.has_key('invert'):
|
|---|
| 630 | if kwargs.get('invert'):
|
|---|
| 631 | from numarray import logical_not
|
|---|
| 632 | msk = logical_not(msk)
|
|---|
| 633 | print_log()
|
|---|
| 634 | return msk
|
|---|
| 635 |
|
|---|
| 636 | def get_restfreqs(self):
|
|---|
| 637 | """
|
|---|
| 638 | Get the restfrequency(s) stored in this scantable.
|
|---|
| 639 | The return value(s) are always of unit 'Hz'
|
|---|
| 640 | Parameters:
|
|---|
| 641 | none
|
|---|
| 642 | Returns:
|
|---|
| 643 | a list of doubles
|
|---|
| 644 | """
|
|---|
| 645 | return list(self._getrestfreqs())
|
|---|
| 646 |
|
|---|
| 647 |
|
|---|
| 648 | # def set_restfreqs(self, freqs=None, unit='Hz', lines=None, source=None,
|
|---|
| 649 | # theif=None):
|
|---|
| 650 | # """
|
|---|
| 651 | # Select the restfrequency for the specified source and IF OR
|
|---|
| 652 | # replace for all IFs. If the 'freqs' argument holds a scalar,
|
|---|
| 653 | # then that rest frequency will be applied to the selected
|
|---|
| 654 | # data (and added to the list of available rest frequencies).
|
|---|
| 655 | # In this way, you can set a rest frequency for each
|
|---|
| 656 | # source and IF combination. If the 'freqs' argument holds
|
|---|
| 657 | # a vector, then it MUST be of length the number of IFs
|
|---|
| 658 | # (and the available restfrequencies will be replaced by
|
|---|
| 659 | # this vector). In this case, *all* data ('source' and
|
|---|
| 660 | # 'theif' are ignored) have the restfrequency set per IF according
|
|---|
| 661 | # to the corresponding value you give in the 'freqs' vector.
|
|---|
| 662 | # E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and
|
|---|
| 663 | # IF 1 gets restfreq 2e9.
|
|---|
| 664 | #
|
|---|
| 665 | # You can also specify the frequencies via known line names
|
|---|
| 666 | # in the argument 'lines'. Use 'freqs' or 'lines'. 'freqs'
|
|---|
| 667 | # takes precedence. See the list of known names via function
|
|---|
| 668 | # scantable.lines()
|
|---|
| 669 | # Parameters:
|
|---|
| 670 | # freqs: list of rest frequencies
|
|---|
| 671 | # unit: unit for rest frequency (default 'Hz')
|
|---|
| 672 | # lines: list of known spectral lines names (alternative to freqs).
|
|---|
| 673 | # See possible list via scantable.lines()
|
|---|
| 674 | # source: Source name (blank means all)
|
|---|
| 675 | # theif: IF (-1 means all)
|
|---|
| 676 | # Example:
|
|---|
| 677 | # scan.set_restfreqs(freqs=1.4e9, source='NGC253', theif=2)
|
|---|
| 678 | # scan.set_restfreqs(freqs=[1.4e9,1.67e9])
|
|---|
| 679 | # """
|
|---|
| 680 | # varlist = vars()
|
|---|
| 681 | # if source is None:
|
|---|
| 682 | # source = ""
|
|---|
| 683 | # if theif is None:
|
|---|
| 684 | # theif = -1
|
|---|
| 685 | # t = type(freqs)
|
|---|
| 686 | # if t is int or t is float:
|
|---|
| 687 | # freqs = [freqs]
|
|---|
| 688 | # if freqs is None:
|
|---|
| 689 | # freqs = []
|
|---|
| 690 | # t = type(lines)
|
|---|
| 691 | # if t is str:
|
|---|
| 692 | # lines = [lines]
|
|---|
| 693 | # if lines is None:
|
|---|
| 694 | # lines = []
|
|---|
| 695 | # self._setrestfreqs(freqs, unit, lines, source, theif)
|
|---|
| 696 | # self._add_history("set_restfreqs", varlist)
|
|---|
| 697 | #
|
|---|
| 698 |
|
|---|
| 699 |
|
|---|
| 700 | def history(self):
|
|---|
| 701 | hist = list(self._gethistory())
|
|---|
| 702 | out = "-"*80
|
|---|
| 703 | for h in hist:
|
|---|
| 704 | if h.startswith("---"):
|
|---|
| 705 | out += "\n"+h
|
|---|
| 706 | else:
|
|---|
| 707 | items = h.split("##")
|
|---|
| 708 | date = items[0]
|
|---|
| 709 | func = items[1]
|
|---|
| 710 | items = items[2:]
|
|---|
| 711 | out += "\n"+date+"\n"
|
|---|
| 712 | out += "Function: %s\n Parameters:" % (func)
|
|---|
| 713 | for i in items:
|
|---|
| 714 | s = i.split("=")
|
|---|
| 715 | out += "\n %s = %s" % (s[0],s[1])
|
|---|
| 716 | out += "\n"+"-"*80
|
|---|
| 717 | try:
|
|---|
| 718 | from IPython.genutils import page as pager
|
|---|
| 719 | except ImportError:
|
|---|
| 720 | from pydoc import pager
|
|---|
| 721 | pager(out)
|
|---|
| 722 | return
|
|---|
| 723 |
|
|---|
| 724 | #
|
|---|
| 725 | # Maths business
|
|---|
| 726 | #
|
|---|
| 727 |
|
|---|
| 728 | def average_time(self, mask=None, scanav=False, weight='tint'):
|
|---|
| 729 | """
|
|---|
| 730 | Return the (time) average of a scan, or apply it 'insitu'.
|
|---|
| 731 | Note:
|
|---|
| 732 | in channels only
|
|---|
| 733 | The cursor of the output scan is set to 0.
|
|---|
| 734 | Parameters:
|
|---|
| 735 | one scan or comma separated scans
|
|---|
| 736 | mask: an optional mask (only used for 'var' and 'tsys'
|
|---|
| 737 | weighting)
|
|---|
| 738 | scanav: True averages each scan separately
|
|---|
| 739 | False (default) averages all scans together,
|
|---|
| 740 | weight: Weighting scheme. 'none', 'var' (1/var(spec)
|
|---|
| 741 | weighted), 'tsys' (1/Tsys**2 weighted), 'tint'
|
|---|
| 742 | (integration time weighted) or 'tintsys' (Tint/Tsys**2).
|
|---|
| 743 | The default is 'tint'
|
|---|
| 744 | Example:
|
|---|
| 745 | # time average the scantable without using a mask
|
|---|
| 746 | newscan = scan.average_time()
|
|---|
| 747 | """
|
|---|
| 748 | varlist = vars()
|
|---|
| 749 | if weight is None: weight = 'tint'
|
|---|
| 750 | if mask is None: mask = ()
|
|---|
| 751 | if scanav:
|
|---|
| 752 | scanav = "SCAN"
|
|---|
| 753 | else:
|
|---|
| 754 | scanav = "NONE"
|
|---|
| 755 | s = scantable(self._math._average((self,), mask, weight, scanav, False))
|
|---|
| 756 | s._add_history("average_time",varlist)
|
|---|
| 757 | print_log()
|
|---|
| 758 | return s
|
|---|
| 759 |
|
|---|
| 760 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
|
|---|
| 761 | """
|
|---|
| 762 | Return a scan where all spectra are converted to either
|
|---|
| 763 | Jansky or Kelvin depending upon the flux units of the scan table.
|
|---|
| 764 | By default the function tries to look the values up internally.
|
|---|
| 765 | If it can't find them (or if you want to over-ride), you must
|
|---|
| 766 | specify EITHER jyperk OR eta (and D which it will try to look up
|
|---|
| 767 | also if you don't set it). jyperk takes precedence if you set both.
|
|---|
| 768 | Parameters:
|
|---|
| 769 | jyperk: the Jy / K conversion factor
|
|---|
| 770 | eta: the aperture efficiency
|
|---|
| 771 | d: the geomtric diameter (metres)
|
|---|
| 772 | insitu: if False a new scantable is returned.
|
|---|
| 773 | Otherwise, the scaling is done in-situ
|
|---|
| 774 | The default is taken from .asaprc (False)
|
|---|
| 775 | allaxes: if True apply to all spectra. Otherwise
|
|---|
| 776 | apply only to the selected (beam/pol/if)spectra only
|
|---|
| 777 | The default is taken from .asaprc (True if none)
|
|---|
| 778 | """
|
|---|
| 779 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 780 | self._math._setinsitu(insitu)
|
|---|
| 781 | varlist = vars()
|
|---|
| 782 | if jyperk is None: jyperk = -1.0
|
|---|
| 783 | if d is None: d = -1.0
|
|---|
| 784 | if eta is None: eta = -1.0
|
|---|
| 785 | s = scantable(self._math._convertflux(self, d, eta, jyperk))
|
|---|
| 786 | s._add_history("convert_flux", varlist)
|
|---|
| 787 | print_log()
|
|---|
| 788 | if insitu: self._assign(s)
|
|---|
| 789 | else: return s
|
|---|
| 790 |
|
|---|
| 791 | def gain_el(self, poly=None, filename="", method="linear", insitu=None):
|
|---|
| 792 | """
|
|---|
| 793 | Return a scan after applying a gain-elevation correction.
|
|---|
| 794 | The correction can be made via either a polynomial or a
|
|---|
| 795 | table-based interpolation (and extrapolation if necessary).
|
|---|
| 796 | You specify polynomial coefficients, an ascii table or neither.
|
|---|
| 797 | If you specify neither, then a polynomial correction will be made
|
|---|
| 798 | with built in coefficients known for certain telescopes (an error
|
|---|
| 799 | will occur if the instrument is not known).
|
|---|
| 800 | The data and Tsys are *divided* by the scaling factors.
|
|---|
| 801 | Parameters:
|
|---|
| 802 | poly: Polynomial coefficients (default None) to compute a
|
|---|
| 803 | gain-elevation correction as a function of
|
|---|
| 804 | elevation (in degrees).
|
|---|
| 805 | filename: The name of an ascii file holding correction factors.
|
|---|
| 806 | The first row of the ascii file must give the column
|
|---|
| 807 | names and these MUST include columns
|
|---|
| 808 | "ELEVATION" (degrees) and "FACTOR" (multiply data
|
|---|
| 809 | by this) somewhere.
|
|---|
| 810 | The second row must give the data type of the
|
|---|
| 811 | column. Use 'R' for Real and 'I' for Integer.
|
|---|
| 812 | An example file would be
|
|---|
| 813 | (actual factors are arbitrary) :
|
|---|
| 814 |
|
|---|
| 815 | TIME ELEVATION FACTOR
|
|---|
| 816 | R R R
|
|---|
| 817 | 0.1 0 0.8
|
|---|
| 818 | 0.2 20 0.85
|
|---|
| 819 | 0.3 40 0.9
|
|---|
| 820 | 0.4 60 0.85
|
|---|
| 821 | 0.5 80 0.8
|
|---|
| 822 | 0.6 90 0.75
|
|---|
| 823 | method: Interpolation method when correcting from a table.
|
|---|
| 824 | Values are "nearest", "linear" (default), "cubic"
|
|---|
| 825 | and "spline"
|
|---|
| 826 | insitu: if False a new scantable is returned.
|
|---|
| 827 | Otherwise, the scaling is done in-situ
|
|---|
| 828 | The default is taken from .asaprc (False)
|
|---|
| 829 | """
|
|---|
| 830 |
|
|---|
| 831 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 832 | self._math._setinsitu(insitu)
|
|---|
| 833 | varlist = vars()
|
|---|
| 834 | if poly is None:
|
|---|
| 835 | poly = ()
|
|---|
| 836 | from os.path import expandvars
|
|---|
| 837 | filename = expandvars(filename)
|
|---|
| 838 | s = scantable(self._math._gainel(self, poly, filename, method))
|
|---|
| 839 | s._add_history("gain_el", varlist)
|
|---|
| 840 | print_log()
|
|---|
| 841 | if insitu: self._assign(s)
|
|---|
| 842 | else: return s
|
|---|
| 843 |
|
|---|
| 844 | def freq_align(self, reftime=None, method='cubic', perif=False,
|
|---|
| 845 | insitu=None):
|
|---|
| 846 | """
|
|---|
| 847 | Return a scan where all rows have been aligned in frequency/velocity.
|
|---|
| 848 | The alignment frequency frame (e.g. LSRK) is that set by function
|
|---|
| 849 | set_freqframe.
|
|---|
| 850 | Parameters:
|
|---|
| 851 | reftime: reference time to align at. By default, the time of
|
|---|
| 852 | the first row of data is used.
|
|---|
| 853 | method: Interpolation method for regridding the spectra.
|
|---|
| 854 | Choose from "nearest", "linear", "cubic" (default)
|
|---|
| 855 | and "spline"
|
|---|
| 856 | perif: Generate aligners per freqID (no doppler tracking) or
|
|---|
| 857 | per IF (scan-based doppler tracking)
|
|---|
| 858 | insitu: if False a new scantable is returned.
|
|---|
| 859 | Otherwise, the scaling is done in-situ
|
|---|
| 860 | The default is taken from .asaprc (False)
|
|---|
| 861 | """
|
|---|
| 862 | print "Not yet implemented"
|
|---|
| 863 | return
|
|---|
| 864 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 865 | self._math._setinsitu(insitu)
|
|---|
| 866 | varlist = vars()
|
|---|
| 867 | if reftime is None: reftime = ''
|
|---|
| 868 | perfreqid = not perif
|
|---|
| 869 | s = scantable(self._math._freqalign(self, reftime, method, perfreqid))
|
|---|
| 870 | s._add_history("freq_align", varlist)
|
|---|
| 871 | print_log()
|
|---|
| 872 | if insitu: self._assign(s)
|
|---|
| 873 | else: return s
|
|---|
| 874 |
|
|---|
| 875 | def opacity(self, tau, insitu=None):
|
|---|
| 876 | """
|
|---|
| 877 | Apply an opacity correction. The data
|
|---|
| 878 | and Tsys are multiplied by the correction factor.
|
|---|
| 879 | Parameters:
|
|---|
| 880 | tau: Opacity from which the correction factor is
|
|---|
| 881 | exp(tau*ZD)
|
|---|
| 882 | where ZD is the zenith-distance
|
|---|
| 883 | insitu: if False a new scantable is returned.
|
|---|
| 884 | Otherwise, the scaling is done in-situ
|
|---|
| 885 | The default is taken from .asaprc (False)
|
|---|
| 886 | """
|
|---|
| 887 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 888 | self._math._setinsitu(insitu)
|
|---|
| 889 | varlist = vars()
|
|---|
| 890 | s = scantable(self._math._opacity(self, tau))
|
|---|
| 891 | s._add_history("opacity", varlist)
|
|---|
| 892 | print_log()
|
|---|
| 893 | if insitu: self._assign(s)
|
|---|
| 894 | else: return s
|
|---|
| 895 |
|
|---|
| 896 | def bin(self, width=5, insitu=None):
|
|---|
| 897 | """
|
|---|
| 898 | Return a scan where all spectra have been binned up.
|
|---|
| 899 | width: The bin width (default=5) in pixels
|
|---|
| 900 | insitu: if False a new scantable is returned.
|
|---|
| 901 | Otherwise, the scaling is done in-situ
|
|---|
| 902 | The default is taken from .asaprc (False)
|
|---|
| 903 | """
|
|---|
| 904 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 905 | self._math._setinsitu(insitu)
|
|---|
| 906 | varlist = vars()
|
|---|
| 907 | s = scantable(self._math._bin(self, width))
|
|---|
| 908 | s._add_history("bin",varlist)
|
|---|
| 909 | print_log()
|
|---|
| 910 | if insitu: self._assign(s)
|
|---|
| 911 | else: return s
|
|---|
| 912 |
|
|---|
| 913 |
|
|---|
| 914 | def resample(self, width=5, method='cubic', insitu=None):
|
|---|
| 915 | """
|
|---|
| 916 | Return a scan where all spectra have been binned up
|
|---|
| 917 | width: The bin width (default=5) in pixels
|
|---|
| 918 | method: Interpolation method when correcting from a table.
|
|---|
| 919 | Values are "nearest", "linear", "cubic" (default)
|
|---|
| 920 | and "spline"
|
|---|
| 921 | insitu: if False a new scantable is returned.
|
|---|
| 922 | Otherwise, the scaling is done in-situ
|
|---|
| 923 | The default is taken from .asaprc (False)
|
|---|
| 924 | """
|
|---|
| 925 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 926 | self._math._setinsitu(insitu)
|
|---|
| 927 | varlist = vars()
|
|---|
| 928 | s = scantable(self._math._resample(self, method, width))
|
|---|
| 929 | s._add_history("resample",varlist)
|
|---|
| 930 | print_log()
|
|---|
| 931 | if insitu: self._assign(s)
|
|---|
| 932 | else: return s
|
|---|
| 933 |
|
|---|
| 934 |
|
|---|
| 935 | # def average_pol(self, mask=None, weight='none', insitu=None):
|
|---|
| 936 | # """
|
|---|
| 937 | # Average the Polarisations together.
|
|---|
| 938 | # The polarisation cursor of the output scan is set to 0
|
|---|
| 939 | # Parameters:
|
|---|
| 940 | # mask: An optional mask defining the region, where the
|
|---|
| 941 | # averaging will be applied. The output will have all
|
|---|
| 942 | # specified points masked.
|
|---|
| 943 | # weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
|---|
| 944 | # weighted), or 'tsys' (1/Tsys**2 weighted)
|
|---|
| 945 | # insitu: if False a new scantable is returned.
|
|---|
| 946 | # Otherwise, the scaling is done in-situ
|
|---|
| 947 | # The default is taken from .asaprc (False)
|
|---|
| 948 | # """
|
|---|
| 949 | # if insitu is None: insitu = rcParams['insitu']
|
|---|
| 950 | # self._math._setinsitu(insitu)
|
|---|
| 951 | # varlist = vars()
|
|---|
| 952 | #
|
|---|
| 953 | # if mask is None:
|
|---|
| 954 | # mask = ()
|
|---|
| 955 | # s = self._math._averagepol(self, mask, weight)
|
|---|
| 956 | # s._add_history("average_pol",varlist)
|
|---|
| 957 | # print_log()
|
|---|
| 958 | # if insitu: self._assign(s)
|
|---|
| 959 | # else: return scantable(s)
|
|---|
| 960 |
|
|---|
| 961 | def smooth(self, kernel="hanning", width=5.0, insitu=None):
|
|---|
| 962 | """
|
|---|
| 963 | Smooth the spectrum by the specified kernel (conserving flux).
|
|---|
| 964 | Parameters:
|
|---|
| 965 | scan: The input scan
|
|---|
| 966 | kernel: The type of smoothing kernel. Select from
|
|---|
| 967 | 'hanning' (default), 'gaussian' and 'boxcar'.
|
|---|
| 968 | The first three characters are sufficient.
|
|---|
| 969 | width: The width of the kernel in pixels. For hanning this is
|
|---|
| 970 | ignored otherwise it defauls to 5 pixels.
|
|---|
| 971 | For 'gaussian' it is the Full Width Half
|
|---|
| 972 | Maximum. For 'boxcar' it is the full width.
|
|---|
| 973 | insitu: if False a new scantable is returned.
|
|---|
| 974 | Otherwise, the scaling is done in-situ
|
|---|
| 975 | The default is taken from .asaprc (False)
|
|---|
| 976 | Example:
|
|---|
| 977 | none
|
|---|
| 978 | """
|
|---|
| 979 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 980 | self._math._setinsitu(insitu)
|
|---|
| 981 | varlist = vars()
|
|---|
| 982 | s = scantable(self._math._smooth(self,kernel,width))
|
|---|
| 983 | s._add_history("smooth", varlist)
|
|---|
| 984 | print_log()
|
|---|
| 985 | if insitu: self._assign(s)
|
|---|
| 986 | else: return s
|
|---|
| 987 |
|
|---|
| 988 |
|
|---|
| 989 | def poly_baseline(self, mask=None, order=0, insitu=None):
|
|---|
| 990 | """
|
|---|
| 991 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 992 | Parameters:
|
|---|
| 993 | scan: a scantable
|
|---|
| 994 | mask: an optional mask
|
|---|
| 995 | order: the order of the polynomial (default is 0)
|
|---|
| 996 | insitu: if False a new scantable is returned.
|
|---|
| 997 | Otherwise, the scaling is done in-situ
|
|---|
| 998 | The default is taken from .asaprc (False)
|
|---|
| 999 | allaxes: If True (default) apply to all spectra. Otherwise
|
|---|
| 1000 | apply only to the selected (beam/pol/if)spectra only
|
|---|
| 1001 | The default is taken from .asaprc (True if none)
|
|---|
| 1002 | Example:
|
|---|
| 1003 | # return a scan baselined by a third order polynomial,
|
|---|
| 1004 | # not using a mask
|
|---|
| 1005 | bscan = scan.poly_baseline(order=3)
|
|---|
| 1006 | """
|
|---|
| 1007 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1008 | varlist = vars()
|
|---|
| 1009 | if mask is None:
|
|---|
| 1010 | from numarray import ones
|
|---|
| 1011 | mask = list(ones(self.nchan(-1)))
|
|---|
| 1012 | from asap.asapfitter import fitter
|
|---|
| 1013 | f = fitter()
|
|---|
| 1014 | f.set_scan(self, mask)
|
|---|
| 1015 | f.set_function(poly=order)
|
|---|
| 1016 | s = f.auto_fit(insitu)
|
|---|
| 1017 | s._add_history("poly_baseline", varlist)
|
|---|
| 1018 | print_log()
|
|---|
| 1019 | if insitu: self._assign(s)
|
|---|
| 1020 | else: return s
|
|---|
| 1021 |
|
|---|
| 1022 | def auto_poly_baseline(self, mask=None, edge=(0,0), order=0,
|
|---|
| 1023 | threshold=3, insitu=None):
|
|---|
| 1024 | """
|
|---|
| 1025 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 1026 | Spectral lines are detected first using linefinder and masked out
|
|---|
| 1027 | to avoid them affecting the baseline solution.
|
|---|
| 1028 |
|
|---|
| 1029 | Parameters:
|
|---|
| 1030 | mask: an optional mask retreived from scantable
|
|---|
| 1031 | edge: an optional number of channel to drop at
|
|---|
| 1032 | the edge of spectrum. If only one value is
|
|---|
| 1033 | specified, the same number will be dropped from
|
|---|
| 1034 | both sides of the spectrum. Default is to keep
|
|---|
| 1035 | all channels. Nested tuples represent individual
|
|---|
| 1036 | edge selection for different IFs (a number of spectral
|
|---|
| 1037 | channels can be different)
|
|---|
| 1038 | order: the order of the polynomial (default is 0)
|
|---|
| 1039 | threshold: the threshold used by line finder. It is better to
|
|---|
| 1040 | keep it large as only strong lines affect the
|
|---|
| 1041 | baseline solution.
|
|---|
| 1042 | insitu: if False a new scantable is returned.
|
|---|
| 1043 | Otherwise, the scaling is done in-situ
|
|---|
| 1044 | The default is taken from .asaprc (False)
|
|---|
| 1045 |
|
|---|
| 1046 | Example:
|
|---|
| 1047 | scan2=scan.auto_poly_baseline(order=7)
|
|---|
| 1048 | """
|
|---|
| 1049 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1050 | varlist = vars()
|
|---|
| 1051 | from asap.asapfitter import fitter
|
|---|
| 1052 | from asap.asaplinefind import linefinder
|
|---|
| 1053 | from asap import _is_sequence_or_number as _is_valid
|
|---|
| 1054 |
|
|---|
| 1055 | # check whether edge is set up for each IF individually
|
|---|
| 1056 | individualEdge = False;
|
|---|
| 1057 | if len(edge)>1:
|
|---|
| 1058 | if isinstance(edge[0],list) or isinstance(edge[0],tuple):
|
|---|
| 1059 | individualEdge = True;
|
|---|
| 1060 |
|
|---|
| 1061 | if not _is_valid(edge, int) and not individualEdge:
|
|---|
| 1062 | raise RuntimeError, "Parameter 'edge' has to be an integer or a \
|
|---|
| 1063 | pair of integers specified as a tuple. Nested tuples are allowed \
|
|---|
| 1064 | to make individual selection for different IFs."
|
|---|
| 1065 |
|
|---|
| 1066 | curedge = (0,0)
|
|---|
| 1067 | if individualEdge:
|
|---|
| 1068 | for edge_par in edge:
|
|---|
| 1069 | if not _is_valid(edge,int):
|
|---|
| 1070 | raise RuntimeError, "Each element of the 'edge' tuple has \
|
|---|
| 1071 | to be a pair of integers or an integer."
|
|---|
| 1072 | else:
|
|---|
| 1073 | curedge = edge;
|
|---|
| 1074 |
|
|---|
| 1075 | # setup fitter
|
|---|
| 1076 | f = fitter()
|
|---|
| 1077 | f.set_function(poly=order)
|
|---|
| 1078 |
|
|---|
| 1079 | # setup line finder
|
|---|
| 1080 | fl=linefinder()
|
|---|
| 1081 | fl.set_options(threshold=threshold)
|
|---|
| 1082 |
|
|---|
| 1083 | if not insitu:
|
|---|
| 1084 | workscan=self.copy()
|
|---|
| 1085 | else:
|
|---|
| 1086 | workscan=self
|
|---|
| 1087 |
|
|---|
| 1088 | fl.set_scan(workscan)
|
|---|
| 1089 |
|
|---|
| 1090 | rows=range(workscan.nrow())
|
|---|
| 1091 | from asap import asaplog
|
|---|
| 1092 | asaplog.push("Processing:")
|
|---|
| 1093 | for r in rows:
|
|---|
| 1094 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (workscan.getscan(r),workscan.getbeam(r),workscan.getif(r),workscan.getpol(r), workscan.getcycle(r))
|
|---|
| 1095 | asaplog.push(msg, False)
|
|---|
| 1096 |
|
|---|
| 1097 | # figure out edge parameter
|
|---|
| 1098 | if individualEdge:
|
|---|
| 1099 | if len(edge)>=workscan.getif(r):
|
|---|
| 1100 | raise RuntimeError, "Number of edge elements appear to be less than the number of IFs"
|
|---|
| 1101 | curedge = edge[workscan.getif(r)]
|
|---|
| 1102 |
|
|---|
| 1103 | # setup line finder
|
|---|
| 1104 | fl.find_lines(r,mask,curedge)
|
|---|
| 1105 | f.set_scan(workscan, fl.get_mask())
|
|---|
| 1106 | f.x = workscan._getabcissa(r)
|
|---|
| 1107 | f.y = workscan._getspectrum(r)
|
|---|
| 1108 | f.data = None
|
|---|
| 1109 | f.fit()
|
|---|
| 1110 | x = f.get_parameters()
|
|---|
| 1111 | workscan._setspectrum(f.fitter.getresidual(), r)
|
|---|
| 1112 | workscan._add_history("poly_baseline", varlist)
|
|---|
| 1113 | if insitu:
|
|---|
| 1114 | self._assign(workscan)
|
|---|
| 1115 | else:
|
|---|
| 1116 | return workscan
|
|---|
| 1117 |
|
|---|
| 1118 | # def rotate_linpolphase(self, angle):
|
|---|
| 1119 | # """
|
|---|
| 1120 | # Rotate the phase of the complex polarization O=Q+iU correlation.
|
|---|
| 1121 | # This is always done in situ in the raw data. So if you call this
|
|---|
| 1122 | # function more than once then each call rotates the phase further.
|
|---|
| 1123 | # Parameters:
|
|---|
| 1124 | # angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1125 | # Examples:
|
|---|
| 1126 | # scan.rotate_linpolphase(2.3)
|
|---|
| 1127 | # """
|
|---|
| 1128 | # varlist = vars()
|
|---|
| 1129 | # from asap._asap import _rotate_linpolphase as _rotate
|
|---|
| 1130 | # _rotate(self, angle, allaxes)
|
|---|
| 1131 | # self._add_history("rotate_linpolphase", varlist)
|
|---|
| 1132 | # print_log()
|
|---|
| 1133 | # return
|
|---|
| 1134 | #
|
|---|
| 1135 | #
|
|---|
| 1136 | # def rotate_xyphase(self, angle):
|
|---|
| 1137 | # """
|
|---|
| 1138 | # Rotate the phase of the XY correlation. This is always done in situ
|
|---|
| 1139 | # in the data. So if you call this function more than once
|
|---|
| 1140 | # then each call rotates the phase further.
|
|---|
| 1141 | # Parameters:
|
|---|
| 1142 | # angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1143 | # Examples:
|
|---|
| 1144 | # scan.rotate_xyphase(2.3)
|
|---|
| 1145 | # """
|
|---|
| 1146 | # varlist = vars()
|
|---|
| 1147 | # from asap._asap import _rotate_xyphase
|
|---|
| 1148 | # _rotate_xyphase(self, angle, allaxes)
|
|---|
| 1149 | # self._add_history("rotate_xyphase", varlist)
|
|---|
| 1150 | # print_log()
|
|---|
| 1151 | # return
|
|---|
| 1152 |
|
|---|
| 1153 |
|
|---|
| 1154 | def add(self, offset, insitu=None):
|
|---|
| 1155 | """
|
|---|
| 1156 | Return a scan where all spectra have the offset added
|
|---|
| 1157 | Parameters:
|
|---|
| 1158 | offset: the offset
|
|---|
| 1159 | insitu: if False a new scantable is returned.
|
|---|
| 1160 | Otherwise, the scaling is done in-situ
|
|---|
| 1161 | The default is taken from .asaprc (False)
|
|---|
| 1162 | """
|
|---|
| 1163 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1164 | self._math._setinsitu(insitu)
|
|---|
| 1165 | varlist = vars()
|
|---|
| 1166 | s = scantable(self._math._unaryop(self, offset, "ADD", False))
|
|---|
| 1167 | s._add_history("add",varlist)
|
|---|
| 1168 | print_log()
|
|---|
| 1169 | if insitu:
|
|---|
| 1170 | self._assign(s)
|
|---|
| 1171 | else:
|
|---|
| 1172 | return s
|
|---|
| 1173 |
|
|---|
| 1174 | def scale(self, factor, tsys=True, insitu=None,):
|
|---|
| 1175 | """
|
|---|
| 1176 | Return a scan where all spectra are scaled by the give 'factor'
|
|---|
| 1177 | Parameters:
|
|---|
| 1178 | factor: the scaling factor
|
|---|
| 1179 | insitu: if False a new scantable is returned.
|
|---|
| 1180 | Otherwise, the scaling is done in-situ
|
|---|
| 1181 | The default is taken from .asaprc (False)
|
|---|
| 1182 | tsys: if True (default) then apply the operation to Tsys
|
|---|
| 1183 | as well as the data
|
|---|
| 1184 | """
|
|---|
| 1185 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1186 | self._math._setinsitu(insitu)
|
|---|
| 1187 | varlist = vars()
|
|---|
| 1188 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
|
|---|
| 1189 | s._add_history("scale",varlist)
|
|---|
| 1190 | print_log()
|
|---|
| 1191 | if insitu:
|
|---|
| 1192 | self._assign(s)
|
|---|
| 1193 | else:
|
|---|
| 1194 | return s
|
|---|
| 1195 |
|
|---|
| 1196 | def auto_quotient(self, mode='time', preserve=True):
|
|---|
| 1197 | """
|
|---|
| 1198 | This function allows to build quotients automatically.
|
|---|
| 1199 | It assumes the observation to have the same numer of
|
|---|
| 1200 | "ons" and "offs"
|
|---|
| 1201 | It will support "closest off in time" in the future
|
|---|
| 1202 | Parameters:
|
|---|
| 1203 | mode: the on/off detection mode; 'suffix' (default)
|
|---|
| 1204 | 'suffix' identifies 'off' scans by the
|
|---|
| 1205 | trailing '_R' (Mopra/Parkes) or
|
|---|
| 1206 | '_e'/'_w' (Tid)
|
|---|
| 1207 | preserve: you can preserve (default) the continuum or
|
|---|
| 1208 | remove it. The equations used are
|
|---|
| 1209 | preserve: Output = Toff * (on/off) - Toff
|
|---|
| 1210 | remove: Output = Tref * (on/off) - Ton
|
|---|
| 1211 | """
|
|---|
| 1212 | modes = ["time"]
|
|---|
| 1213 | if not mode in modes:
|
|---|
| 1214 | msg = "please provide valid mode. Valid modes are %s" % (modes)
|
|---|
| 1215 | raise ValueError(msg)
|
|---|
| 1216 | varlist = vars()
|
|---|
| 1217 | s = scantable(self._math._quotient(self, mode, preserve))
|
|---|
| 1218 | s._add_history("auto_quotient",varlist)
|
|---|
| 1219 | print_log()
|
|---|
| 1220 | return s
|
|---|
| 1221 |
|
|---|
| 1222 |
|
|---|
| 1223 |
|
|---|
| 1224 |
|
|---|
| 1225 | def freq_switch(self, insitu=None):
|
|---|
| 1226 | """
|
|---|
| 1227 | Apply frequency switching to the data.
|
|---|
| 1228 | Parameters:
|
|---|
| 1229 | insitu: if False a new scantable is returned.
|
|---|
| 1230 | Otherwise, the swictching is done in-situ
|
|---|
| 1231 | The default is taken from .asaprc (False)
|
|---|
| 1232 | Example:
|
|---|
| 1233 | none
|
|---|
| 1234 | """
|
|---|
| 1235 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1236 | self._math._setinsitu(insitu)
|
|---|
| 1237 | varlist = vars()
|
|---|
| 1238 | s = scantable(self._math._freqswitch(self))
|
|---|
| 1239 | s._add_history("freq_switch",varlist)
|
|---|
| 1240 | print_log()
|
|---|
| 1241 | if insitu: self._assign(s)
|
|---|
| 1242 | else: return s
|
|---|
| 1243 |
|
|---|
| 1244 | def recalc_azel(self):
|
|---|
| 1245 | """
|
|---|
| 1246 | Recalculate the azimuth and elevation for each position.
|
|---|
| 1247 | Parameters:
|
|---|
| 1248 | none
|
|---|
| 1249 | Example:
|
|---|
| 1250 | """
|
|---|
| 1251 | varlist = vars()
|
|---|
| 1252 | self._recalcazel()
|
|---|
| 1253 | self._add_history("recalc_azel", varlist)
|
|---|
| 1254 | print_log()
|
|---|
| 1255 | return
|
|---|
| 1256 |
|
|---|
| 1257 | def __add__(self, other):
|
|---|
| 1258 | varlist = vars()
|
|---|
| 1259 | s = None
|
|---|
| 1260 | if isinstance(other, scantable):
|
|---|
| 1261 | print "scantable + scantable NYI"
|
|---|
| 1262 | return
|
|---|
| 1263 | elif isinstance(other, float):
|
|---|
| 1264 | s = scantable(self._math._unaryop(self, other, "ADD", False))
|
|---|
| 1265 | else:
|
|---|
| 1266 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1267 | s._add_history("operator +", varlist)
|
|---|
| 1268 | print_log()
|
|---|
| 1269 | return s
|
|---|
| 1270 |
|
|---|
| 1271 | def __sub__(self, other):
|
|---|
| 1272 | """
|
|---|
| 1273 | implicit on all axes and on Tsys
|
|---|
| 1274 | """
|
|---|
| 1275 | varlist = vars()
|
|---|
| 1276 | s = None
|
|---|
| 1277 | if isinstance(other, scantable):
|
|---|
| 1278 | print "scantable - scantable NYI"
|
|---|
| 1279 | return
|
|---|
| 1280 | elif isinstance(other, float):
|
|---|
| 1281 | s = scantable(self._math._unaryop(self, other, "SUB", False))
|
|---|
| 1282 | else:
|
|---|
| 1283 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1284 | s._add_history("operator -", varlist)
|
|---|
| 1285 | print_log()
|
|---|
| 1286 | return s
|
|---|
| 1287 |
|
|---|
| 1288 | def __mul__(self, other):
|
|---|
| 1289 | """
|
|---|
| 1290 | implicit on all axes and on Tsys
|
|---|
| 1291 | """
|
|---|
| 1292 | varlist = vars()
|
|---|
| 1293 | s = None
|
|---|
| 1294 | if isinstance(other, scantable):
|
|---|
| 1295 | print "scantable * scantable NYI"
|
|---|
| 1296 | return
|
|---|
| 1297 | elif isinstance(other, float):
|
|---|
| 1298 | s = scantable(self._math._unaryop(self, other, "MUL", False))
|
|---|
| 1299 | else:
|
|---|
| 1300 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1301 | s._add_history("operator *", varlist)
|
|---|
| 1302 | print_log()
|
|---|
| 1303 | return s
|
|---|
| 1304 |
|
|---|
| 1305 |
|
|---|
| 1306 | def __div__(self, other):
|
|---|
| 1307 | """
|
|---|
| 1308 | implicit on all axes and on Tsys
|
|---|
| 1309 | """
|
|---|
| 1310 | varlist = vars()
|
|---|
| 1311 | s = None
|
|---|
| 1312 | if isinstance(other, scantable):
|
|---|
| 1313 | print "scantable / scantable NYI"
|
|---|
| 1314 | return
|
|---|
| 1315 | elif isinstance(other, float):
|
|---|
| 1316 | if other == 0.0:
|
|---|
| 1317 | raise ZeroDivisionError("Dividing by zero is not recommended")
|
|---|
| 1318 | s = scantable(self._math._unaryop(self, other, "DIV", False))
|
|---|
| 1319 | else:
|
|---|
| 1320 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1321 | s._add_history("operator /", varlist)
|
|---|
| 1322 | print_log()
|
|---|
| 1323 | return s
|
|---|
| 1324 |
|
|---|
| 1325 | def get_fit(self, row=0):
|
|---|
| 1326 | """
|
|---|
| 1327 | Print or return the stored fits for a row in the scantable
|
|---|
| 1328 | Parameters:
|
|---|
| 1329 | row: the row which the fit has been applied to.
|
|---|
| 1330 | """
|
|---|
| 1331 | if row > self.nrow():
|
|---|
| 1332 | return
|
|---|
| 1333 | from asap import asapfit
|
|---|
| 1334 | fit = asapfit(self._getfit(row))
|
|---|
| 1335 | if rcParams['verbose']:
|
|---|
| 1336 | print fit
|
|---|
| 1337 | return
|
|---|
| 1338 | else:
|
|---|
| 1339 | return fit.as_dict()
|
|---|
| 1340 |
|
|---|
| 1341 | def _add_history(self, funcname, parameters):
|
|---|
| 1342 | # create date
|
|---|
| 1343 | sep = "##"
|
|---|
| 1344 | from datetime import datetime
|
|---|
| 1345 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
|
|---|
| 1346 | hist = dstr+sep
|
|---|
| 1347 | hist += funcname+sep#cdate+sep
|
|---|
| 1348 | if parameters.has_key('self'): del parameters['self']
|
|---|
| 1349 | for k,v in parameters.iteritems():
|
|---|
| 1350 | if type(v) is dict:
|
|---|
| 1351 | for k2,v2 in v.iteritems():
|
|---|
| 1352 | hist += k2
|
|---|
| 1353 | hist += "="
|
|---|
| 1354 | if isinstance(v2,scantable):
|
|---|
| 1355 | hist += 'scantable'
|
|---|
| 1356 | elif k2 == 'mask':
|
|---|
| 1357 | if isinstance(v2,list) or isinstance(v2,tuple):
|
|---|
| 1358 | hist += str(self._zip_mask(v2))
|
|---|
| 1359 | else:
|
|---|
| 1360 | hist += str(v2)
|
|---|
| 1361 | else:
|
|---|
| 1362 | hist += str(v2)
|
|---|
| 1363 | else:
|
|---|
| 1364 | hist += k
|
|---|
| 1365 | hist += "="
|
|---|
| 1366 | if isinstance(v,scantable):
|
|---|
| 1367 | hist += 'scantable'
|
|---|
| 1368 | elif k == 'mask':
|
|---|
| 1369 | if isinstance(v,list) or isinstance(v,tuple):
|
|---|
| 1370 | hist += str(self._zip_mask(v))
|
|---|
| 1371 | else:
|
|---|
| 1372 | hist += str(v)
|
|---|
| 1373 | else:
|
|---|
| 1374 | hist += str(v)
|
|---|
| 1375 | hist += sep
|
|---|
| 1376 | hist = hist[:-2] # remove trailing '##'
|
|---|
| 1377 | self._addhistory(hist)
|
|---|
| 1378 |
|
|---|
| 1379 |
|
|---|
| 1380 | def _zip_mask(self, mask):
|
|---|
| 1381 | mask = list(mask)
|
|---|
| 1382 | i = 0
|
|---|
| 1383 | segments = []
|
|---|
| 1384 | while mask[i:].count(1):
|
|---|
| 1385 | i += mask[i:].index(1)
|
|---|
| 1386 | if mask[i:].count(0):
|
|---|
| 1387 | j = i + mask[i:].index(0)
|
|---|
| 1388 | else:
|
|---|
| 1389 | j = len(mask)
|
|---|
| 1390 | segments.append([i,j])
|
|---|
| 1391 | i = j
|
|---|
| 1392 | return segments
|
|---|
| 1393 |
|
|---|
| 1394 | def _get_ordinate_label(self):
|
|---|
| 1395 | fu = "("+self.get_fluxunit()+")"
|
|---|
| 1396 | import re
|
|---|
| 1397 | lbl = "Intensity"
|
|---|
| 1398 | if re.match(".K.",fu):
|
|---|
| 1399 | lbl = "Brightness Temperature "+ fu
|
|---|
| 1400 | elif re.match(".Jy.",fu):
|
|---|
| 1401 | lbl = "Flux density "+ fu
|
|---|
| 1402 | return lbl
|
|---|
| 1403 |
|
|---|
| 1404 | def _check_ifs(self):
|
|---|
| 1405 | nchans = [self.nchan(i) for i in range(self.nif(-1))]
|
|---|
| 1406 | nchans = filter(lambda t: t > 0, nchans)
|
|---|
| 1407 | return (sum(nchans)/len(nchans) == nchans[0])
|
|---|
