| 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, asaplog
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| 4 | from asap import selector
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| 5 | from numarray import ones,zeros
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| 6 | import sys
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| 7 |
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| 8 | class scantable(Scantable):
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| 9 | """
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| 10 | The ASAP container for scans
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| 11 | """
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| 12 |
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| 13 | def __init__(self, filename, average=None, unit=None):
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| 14 | """
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| 15 | Create a scantable from a saved one or make a reference
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| 16 | Parameters:
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| 17 | filename: the name of an asap table on disk
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| 18 | or
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| 19 | the name of a rpfits/sdfits/ms file
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| 20 | (integrations within scans are auto averaged
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| 21 | and the whole file is read)
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| 22 | or
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| 23 | [advanced] a reference to an existing
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| 24 | scantable
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| 25 | average: average all integrations withinb a scan on read.
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| 26 | The default (True) is taken from .asaprc.
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| 27 | unit: brightness unit; must be consistent with K or Jy.
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| 28 | Over-rides the default selected by the reader
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| 29 | (input rpfits/sdfits/ms) or replaces the value
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| 30 | in existing scantables
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| 31 | """
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| 32 | if average is None:
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| 33 | average = rcParams['scantable.autoaverage']
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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 | if isinstance(filename, Scantable):
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| 38 | Scantable.__init__(self, filename)
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| 39 | else:
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| 40 | if isinstance(filename,str):
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| 41 | import os.path
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| 42 | filename = os.path.expandvars(filename)
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| 43 | filename = os.path.expanduser(filename)
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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 | if os.path.isdir(filename):
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| 52 | # crude check if asap table
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| 53 | if os.path.exists(filename+'/table.info'):
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| 54 | Scantable.__init__(self, filename, "memory")
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| 55 | if unit is not None:
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| 56 | self.set_fluxunit(unit)
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| 57 | self.set_freqframe(rcParams['scantable.freqframe'])
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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 | self._fill([filename],unit, average)
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| 67 | elif (isinstance(filename,list) or isinstance(filename,tuple)) \
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| 68 | and isinstance(filename[-1], str):
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| 69 | self._fill(filename, unit, average)
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| 70 | print_log()
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| 71 |
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| 72 | def save(self, name=None, format=None, overwrite=False):
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| 73 | """
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| 74 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS,
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| 75 | Image FITS or MS2 format.
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| 76 | Parameters:
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| 77 | name: the name of the outputfile. For format="FITS" this
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| 78 | is the directory file name into which all the files
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| 79 | will be written (default is 'asap_FITS'). For format
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| 80 | "ASCII" this is the root file name (data in 'name'.txt
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| 81 | and header in 'name'_header.txt)
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| 82 | format: an optional file format. Default is ASAP.
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| 83 | Allowed are - 'ASAP' (save as ASAP [aips++] Table),
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| 84 | 'SDFITS' (save as SDFITS file)
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| 85 | 'FITS' (saves each row as a FITS Image)
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| 86 | 'ASCII' (saves as ascii text file)
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| 87 | 'MS2' (saves as an aips++
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| 88 | MeasurementSet V2)
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| 89 | overwrite: If the file should be overwritten if it exists.
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| 90 | The default False is to return with warning
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| 91 | without writing the output. USE WITH CARE.
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| 92 | Example:
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| 93 | scan.save('myscan.asap')
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| 94 | scan.save('myscan.sdfits','SDFITS')
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| 95 | """
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| 96 | from os import path
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| 97 | if format is None: format = rcParams['scantable.save']
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| 98 | suffix = '.'+format.lower()
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| 99 | if name is None or name =="":
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| 100 | name = 'scantable'+suffix
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| 101 | from asap import asaplog
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| 102 | msg = "No filename given. Using default name %s..." % name
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| 103 | asaplog.push(msg)
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| 104 | name = path.expandvars(name)
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| 105 | if path.isfile(name) or path.isdir(name):
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| 106 | if not overwrite:
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| 107 | msg = "File %s exists." % name
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| 108 | if rcParams['verbose']:
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| 109 | print msg
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| 110 | return
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| 111 | else:
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| 112 | raise IOError(msg)
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| 113 | format2 = format.upper()
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| 114 | if format2 == 'ASAP':
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| 115 | self._save(name)
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| 116 | else:
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| 117 | print "NYI"
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| 118 | # from asap._asap import sdwriter as _sw
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| 119 | # w = _sw(format2)
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| 120 | # w.write(self, name, stokes)
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| 121 |
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| 122 | print_log()
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| 123 | return
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| 124 |
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| 125 | def copy(self):
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| 126 | """
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| 127 | Return a copy of this scantable.
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| 128 | Parameters:
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| 129 | none
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| 130 | Example:
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| 131 | copiedscan = scan.copy()
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| 132 | """
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| 133 | sd = scantable(Scantable._copy(self))
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| 134 | return sd
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| 135 |
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| 136 | def get_scan(self, scanid=None):
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| 137 | """
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| 138 | Return a specific scan (by scanno) or collection of scans (by
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| 139 | source name) in a new scantable.
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| 140 | Parameters:
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| 141 | scanid: a (list of) scanno or a source name, unix-style
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| 142 | patterns are accepted for source name matching, e.g.
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| 143 | '*_R' gets all 'ref scans
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| 144 | Example:
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| 145 | # get all scans containing the source '323p459'
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| 146 | newscan = scan.get_scan('323p459')
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| 147 | # get all 'off' scans
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| 148 | refscans = scan.get_scan('*_R')
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| 149 | # get a susbset of scans by scanno (as listed in scan.summary())
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| 150 | newscan = scan.get_scan([0,2,7,10])
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| 151 | """
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| 152 | if scanid is None:
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| 153 | if rcParams['verbose']:
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| 154 | print "Please specify a scan no or name to retrieve from the scantable"
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| 155 | return
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| 156 | else:
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| 157 | raise RuntimeError("No scan given")
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| 158 |
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| 159 | try:
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| 160 | bsel = self.get_selection()
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| 161 | sel = selector()
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| 162 | if type(scanid) is str:
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| 163 | sel.set_name(scanid)
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| 164 | self.set_selection(bsel+sel)
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| 165 | scopy = self._copy()
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| 166 | self.set_selection(bsel)
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| 167 | return scantable(scopy)
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| 168 | elif type(scanid) is int:
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| 169 | sel.set_scans([scanid])
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| 170 | self.set_selection(bsel+sel)
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| 171 | scopy = self._copy()
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| 172 | self.set_selection(bsel)
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| 173 | return scantable(scopy)
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| 174 | elif type(scanid) is list:
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| 175 | sel.set_scans(scanid)
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| 176 | self.set_selection(sel)
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| 177 | scopy = self._copy()
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| 178 | self.set_selection(bsel)
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| 179 | return scantable(scopy)
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| 180 | else:
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| 181 | msg = "Illegal scanid type, use 'int' or 'list' if ints."
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| 182 | if rcParams['verbose']:
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| 183 | print msg
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| 184 | else:
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| 185 | raise TypeError(msg)
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| 186 | except RuntimeError:
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| 187 | if rcParams['verbose']: print "Couldn't find any match."
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| 188 | else: raise
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| 189 |
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| 190 | def __str__(self):
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| 191 | return Scantable._summary(self,True)
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| 192 |
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| 193 | def summary(self, filename=None):
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| 194 | """
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| 195 | Print a summary of the contents of this scantable.
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| 196 | Parameters:
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| 197 | filename: the name of a file to write the putput to
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| 198 | Default - no file output
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| 199 | verbose: print extra info such as the frequency table
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| 200 | The default (False) is taken from .asaprc
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| 201 | """
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| 202 | info = Scantable._summary(self, True)
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| 203 | #if verbose is None: verbose = rcParams['scantable.verbosesummary']
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| 204 | if filename is not None:
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| 205 | if filename is "":
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| 206 | filename = 'scantable_summary.txt'
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| 207 | from os.path import expandvars, isdir
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| 208 | filename = expandvars(filename)
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| 209 | if not isdir(filename):
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| 210 | data = open(filename, 'w')
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| 211 | data.write(info)
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| 212 | data.close()
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| 213 | else:
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| 214 | msg = "Illegal file name '%s'." % (filename)
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| 215 | if rcParams['verbose']:
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| 216 | print msg
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| 217 | else:
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| 218 | raise IOError(msg)
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| 219 | if rcParams['verbose']:
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| 220 | try:
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| 221 | from IPython.genutils import page as pager
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| 222 | except ImportError:
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| 223 | from pydoc import pager
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| 224 | pager(info)
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| 225 | else:
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| 226 | return info
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| 227 |
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| 228 |
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| 229 | def get_selection(self):
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| 230 | """
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| 231 | """
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| 232 | return selector(self._getselection())
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| 233 |
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| 234 | def set_selection(self, selection):
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| 235 | """
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| 236 | """
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| 237 | self._setselection(selection)
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| 238 |
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| 239 | def set_cursor(self, beam=0, IF=0, pol=0):
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| 240 | """
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| 241 | Set the spectrum for individual operations.
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| 242 | Parameters:
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| 243 | beam, IF, pol: a number
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| 244 | Example:
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| 245 | scan.set_cursor(0,0,1)
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| 246 | pol1sig = scan.stats(all=False) # returns std dev for beam=0
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| 247 | # if=0, pol=1
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| 248 | """
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| 249 | print "DEPRECATED"
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| 250 | varlist = vars()
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| 251 | sel = asap._asap.Selector()
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| 252 | sel._setbeams([beam])
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| 253 | sel._setpols([pol])
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| 254 | sel._setifs([IF])
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| 255 | self._add_history("set_cursor", varlist)
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| 256 | return
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| 257 |
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| 258 | def get_cursor(self):
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| 259 | """
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| 260 | Return/print a the current 'cursor' into the Beam/IF/Pol cube.
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| 261 | Parameters:
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| 262 | none
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| 263 | Returns:
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| 264 | a list of values (currentBeam,currentIF,currentPol)
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| 265 | Example:
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| 266 | none
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| 267 | """
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| 268 | print "DEPRECATED"
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| 269 | sel = self._getselection()
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| 270 | i = sel.getbeams()[0]
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| 271 | j = sel.getifs()[0]
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| 272 | k = sel.getpols()[0]
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| 273 | from asap import asaplog
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| 274 | out = "--------------------------------------------------\n"
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| 275 | out += " Cursor position\n"
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| 276 | out += "--------------------------------------------------\n"
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| 277 | out += 'Beam=%d IF=%d Pol=%d ' % (i,j,k)
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| 278 | asaplog.push(out)
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| 279 | print_log()
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| 280 | return i,j,k
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| 281 |
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| 282 | def stats(self, stat='stddev', mask=None):
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| 283 | """
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| 284 | Determine the specified statistic of the current beam/if/pol
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| 285 | Takes a 'mask' as an optional parameter to specify which
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| 286 | channels should be excluded.
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| 287 | Parameters:
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| 288 | stat: 'min', 'max', 'sumsq', 'sum', 'mean'
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| 289 | 'var', 'stddev', 'avdev', 'rms', 'median'
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| 290 | mask: an optional mask specifying where the statistic
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| 291 | should be determined.
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| 292 | Example:
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| 293 | scan.set_unit('channel')
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| 294 | msk = scan.create_mask([100,200],[500,600])
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| 295 | scan.stats(stat='mean', mask=m)
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| 296 | """
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| 297 | from numarray import array,zeros,Float
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| 298 | if mask == None:
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| 299 | mask = []
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| 300 | axes = ['Beam','IF','Pol','Time']
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| 301 | if not self._check_ifs():
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| 302 | raise ValueError("Cannot apply mask as the IFs have different number of channels"
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| 303 | "Please use setselection() to select individual IFs")
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| 304 |
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| 305 | statvals = self._math._stats(self, mask, stat)
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| 306 | out = ''
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| 307 | axes = []
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| 308 | for i in range(self.nrow()):
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| 309 | axis = []
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| 310 | axis.append(self.getscan(i))
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| 311 | axis.append(self.getbeam(i))
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| 312 | axis.append(self.getif(i))
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| 313 | axis.append(self.getpol(i))
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| 314 | axis.append(self.getcycle(i))
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| 315 | axes.append(axis)
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| 316 | tm = self._gettime(i)
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| 317 | src = self._getsourcename(i)
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| 318 | out += 'Scan[%d] (%s) ' % (axis[0], src)
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| 319 | out += 'Time[%s]:\n' % (tm)
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| 320 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
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| 321 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
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| 322 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
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| 323 | out += '= %3.3f\n' % (statvals[i])
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| 324 | out += "--------------------------------------------------\n"
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| 325 |
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| 326 | if rcParams['verbose']:
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| 327 | print "--------------------------------------------------"
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| 328 | print " ",stat
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| 329 | print "--------------------------------------------------"
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| 330 | print out
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| 331 | retval = { 'axesnames': ['scanno','beamno','ifno','polno','cycleno'],
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| 332 | 'axes' : axes,
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| 333 | 'data': statvals}
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| 334 | return retval
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| 335 |
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| 336 | def stddev(self,mask=None):
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| 337 | """
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| 338 | Determine the standard deviation of the current beam/if/pol
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| 339 | Takes a 'mask' as an optional parameter to specify which
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| 340 | channels should be excluded.
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| 341 | Parameters:
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| 342 | mask: an optional mask specifying where the standard
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| 343 | deviation should be determined.
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| 344 |
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| 345 | Example:
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| 346 | scan.set_unit('channel')
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| 347 | msk = scan.create_mask([100,200],[500,600])
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| 348 | scan.stddev(mask=m)
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| 349 | """
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| 350 | return self.stats(stat='stddev',mask=mask);
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| 351 |
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| 352 | def get_tsys(self):
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| 353 | """
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| 354 | Return the System temperatures.
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| 355 | Parameters:
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| 356 |
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| 357 | Returns:
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| 358 | a list of Tsys values for the current selection
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| 359 | """
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| 360 |
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| 361 | return self._row_callback(self._gettsys, "Tsys")
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| 362 |
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| 363 | def _row_callback(self, callback, label):
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| 364 | axes = []
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| 365 | axesnames = ['scanno','beamno','ifno','polno','cycleno']
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| 366 | out = ""
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| 367 | outvec =[]
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| 368 | for i in range(self.nrow()):
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| 369 | axis = []
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| 370 | axis.append(self.getscan(i))
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| 371 | axis.append(self.getbeam(i))
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| 372 | axis.append(self.getif(i))
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| 373 | axis.append(self.getpol(i))
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| 374 | axis.append(self.getcycle(i))
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| 375 | axes.append(axis)
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| 376 | tm = self._gettime(i)
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| 377 | src = self._getsourcename(i)
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| 378 | out += 'Scan[%d] (%s) ' % (axis[0], src)
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| 379 | out += 'Time[%s]:\n' % (tm)
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| 380 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
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| 381 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
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| 382 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
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| 383 | outvec.append(callback(i))
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| 384 | out += '= %3.3f\n' % (outvec[i])
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| 385 | out += "--------------------------------------------------\n"
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| 386 | if rcParams['verbose']:
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| 387 | print "--------------------------------------------------"
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| 388 | print " %s" % (label)
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| 389 | print "--------------------------------------------------"
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| 390 | print out
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| 391 | retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
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| 392 | return retval
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| 393 |
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| 394 |
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| 395 | def get_time(self, row=-1):
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| 396 | """
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| 397 | Get a list of time stamps for the observations.
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| 398 | Return a string for each integration in the scantable.
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| 399 | Parameters:
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| 400 | row: row no of integration. Default -1 return all rows
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| 401 | Example:
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| 402 | none
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| 403 | """
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| 404 | out = []
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| 405 | if row == -1:
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| 406 | for i in range(self.nrow()):
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| 407 | out.append(self._gettime(i))
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| 408 | return out
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| 409 | else:
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| 410 | if row < self.nrow():
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| 411 | return self._gettime(row)
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| 412 |
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| 413 | def get_sourcename(self, row=-1):
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| 414 | """
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| 415 | Get a list source names for the observations.
|
|---|
| 416 | Return a string for each integration in the scantable.
|
|---|
| 417 | Parameters:
|
|---|
| 418 | row: row no of integration. Default -1 return all rows
|
|---|
| 419 | Example:
|
|---|
| 420 | none
|
|---|
| 421 | """
|
|---|
| 422 | out = []
|
|---|
| 423 | if row == -1:
|
|---|
| 424 | return [self._getsourcename(i) for i in range(self.nrow())]
|
|---|
| 425 | else:
|
|---|
| 426 | if 0 <= row < self.nrow():
|
|---|
| 427 | return self._getsourcename(row)
|
|---|
| 428 |
|
|---|
| 429 | def get_elevation(self, row=-1):
|
|---|
| 430 | """
|
|---|
| 431 | Get a list of elevations for the observations.
|
|---|
| 432 | Return a float for each integration in the scantable.
|
|---|
| 433 | Parameters:
|
|---|
| 434 | row: row no of integration. Default -1 return all rows
|
|---|
| 435 | Example:
|
|---|
| 436 | none
|
|---|
| 437 | """
|
|---|
| 438 | out = []
|
|---|
| 439 | if row == -1:
|
|---|
| 440 | return [self._getelevation(i) for i in range(self.nrow())]
|
|---|
| 441 | else:
|
|---|
| 442 | if 0 <= row < self.nrow():
|
|---|
| 443 | return self._getelevation(row)
|
|---|
| 444 |
|
|---|
| 445 | def get_azimuth(self, row=-1):
|
|---|
| 446 | """
|
|---|
| 447 | Get a list of azimuths for the observations.
|
|---|
| 448 | Return a float for each integration in the scantable.
|
|---|
| 449 | Parameters:
|
|---|
| 450 | row: row no of integration. Default -1 return all rows
|
|---|
| 451 | Example:
|
|---|
| 452 | none
|
|---|
| 453 | """
|
|---|
| 454 | out = []
|
|---|
| 455 | if row == -1:
|
|---|
| 456 | return [self._getazimuth(i) for i in range(self.nrow())]
|
|---|
| 457 | else:
|
|---|
| 458 | if 0 <= row < self.nrow():
|
|---|
| 459 | return self._getazimuth(row)
|
|---|
| 460 |
|
|---|
| 461 | def get_parangle(self, row=-1):
|
|---|
| 462 | """
|
|---|
| 463 | Get a list of parallactic angles for the observations.
|
|---|
| 464 | Return a float for each integration in the scantable.
|
|---|
| 465 | Parameters:
|
|---|
| 466 | row: row no of integration. Default -1 return all rows
|
|---|
| 467 | Example:
|
|---|
| 468 | none
|
|---|
| 469 | """
|
|---|
| 470 | out = []
|
|---|
| 471 | if row == -1:
|
|---|
| 472 | return [self._getparangle(i) for i in range(self.nrow())]
|
|---|
| 473 | else:
|
|---|
| 474 | if 0 <= row < self.nrow():
|
|---|
| 475 | return self._getparangle(row)
|
|---|
| 476 |
|
|---|
| 477 | def set_unit(self, unit='channel'):
|
|---|
| 478 | """
|
|---|
| 479 | Set the unit for all following operations on this scantable
|
|---|
| 480 | Parameters:
|
|---|
| 481 | unit: optional unit, default is 'channel'
|
|---|
| 482 | one of '*Hz','km/s','channel', ''
|
|---|
| 483 | """
|
|---|
| 484 | varlist = vars()
|
|---|
| 485 | if unit in ['','pixel', 'channel']:
|
|---|
| 486 | unit = ''
|
|---|
| 487 | inf = list(self._getcoordinfo())
|
|---|
| 488 | inf[0] = unit
|
|---|
| 489 | self._setcoordinfo(inf)
|
|---|
| 490 | self._add_history("set_unit",varlist)
|
|---|
| 491 |
|
|---|
| 492 | def set_instrument(self, instr):
|
|---|
| 493 | """
|
|---|
| 494 | Set the instrument for subsequent processing
|
|---|
| 495 | Parameters:
|
|---|
| 496 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
|
|---|
| 497 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
|
|---|
| 498 | """
|
|---|
| 499 | self._setInstrument(instr)
|
|---|
| 500 | self._add_history("set_instument",vars())
|
|---|
| 501 | print_log()
|
|---|
| 502 |
|
|---|
| 503 | def set_doppler(self, doppler='RADIO'):
|
|---|
| 504 | """
|
|---|
| 505 | Set the doppler for all following operations on this scantable.
|
|---|
| 506 | Parameters:
|
|---|
| 507 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
|
|---|
| 508 | """
|
|---|
| 509 | varlist = vars()
|
|---|
| 510 | inf = list(self._getcoordinfo())
|
|---|
| 511 | inf[2] = doppler
|
|---|
| 512 | self._setcoordinfo(inf)
|
|---|
| 513 | self._add_history("set_doppler",vars())
|
|---|
| 514 | print_log()
|
|---|
| 515 |
|
|---|
| 516 | def set_freqframe(self, frame=None):
|
|---|
| 517 | """
|
|---|
| 518 | Set the frame type of the Spectral Axis.
|
|---|
| 519 | Parameters:
|
|---|
| 520 | frame: an optional frame type, default 'LSRK'. Valid frames are:
|
|---|
| 521 | 'REST','TOPO','LSRD','LSRK','BARY',
|
|---|
| 522 | 'GEO','GALACTO','LGROUP','CMB'
|
|---|
| 523 | Examples:
|
|---|
| 524 | scan.set_freqframe('BARY')
|
|---|
| 525 | """
|
|---|
| 526 | if frame is None: frame = rcParams['scantable.freqframe']
|
|---|
| 527 | varlist = vars()
|
|---|
| 528 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \
|
|---|
| 529 | 'GEO','GALACTO','LGROUP','CMB']
|
|---|
| 530 |
|
|---|
| 531 | if 1:#frame in valid:
|
|---|
| 532 | inf = list(self._getcoordinfo())
|
|---|
| 533 | inf[1] = frame
|
|---|
| 534 | self._setcoordinfo(inf)
|
|---|
| 535 | self._add_history("set_freqframe",varlist)
|
|---|
| 536 | else:
|
|---|
| 537 | msg = "Please specify a valid freq type. Valid types are:\n",valid
|
|---|
| 538 | if rcParams['verbose']:
|
|---|
| 539 | print msg
|
|---|
| 540 | else:
|
|---|
| 541 | raise TypeError(msg)
|
|---|
| 542 | print_log()
|
|---|
| 543 |
|
|---|
| 544 | def get_unit(self):
|
|---|
| 545 | """
|
|---|
| 546 | Get the default unit set in this scantable
|
|---|
| 547 | Parameters:
|
|---|
| 548 | Returns:
|
|---|
| 549 | A unit string
|
|---|
| 550 | """
|
|---|
| 551 | inf = self._getcoordinfo()
|
|---|
| 552 | unit = inf[0]
|
|---|
| 553 | if unit == '': unit = 'channel'
|
|---|
| 554 | return unit
|
|---|
| 555 |
|
|---|
| 556 | def get_abcissa(self, rowno=0):
|
|---|
| 557 | """
|
|---|
| 558 | Get the abcissa in the current coordinate setup for the currently
|
|---|
| 559 | selected Beam/IF/Pol
|
|---|
| 560 | Parameters:
|
|---|
| 561 | rowno: an optional row number in the scantable. Default is the
|
|---|
| 562 | first row, i.e. rowno=0
|
|---|
| 563 | Returns:
|
|---|
| 564 | The abcissa values and it's format string (as a dictionary)
|
|---|
| 565 | """
|
|---|
| 566 | abc = self._getabcissa(rowno)
|
|---|
| 567 | lbl = self._getabcissalabel(rowno)
|
|---|
| 568 | print_log()
|
|---|
| 569 | return abc, lbl
|
|---|
| 570 |
|
|---|
| 571 | def create_mask(self, *args, **kwargs):
|
|---|
| 572 | """
|
|---|
| 573 | Compute and return a mask based on [min,max] windows.
|
|---|
| 574 | The specified windows are to be INCLUDED, when the mask is
|
|---|
| 575 | applied.
|
|---|
| 576 | Parameters:
|
|---|
| 577 | [min,max],[min2,max2],...
|
|---|
| 578 | Pairs of start/end points specifying the regions
|
|---|
| 579 | to be masked
|
|---|
| 580 | invert: optional argument. If specified as True,
|
|---|
| 581 | return an inverted mask, i.e. the regions
|
|---|
| 582 | specified are EXCLUDED
|
|---|
| 583 | row: create the mask using the specified row for
|
|---|
| 584 | unit conversions, default is row=0
|
|---|
| 585 | only necessary if frequency varies over rows.
|
|---|
| 586 | Example:
|
|---|
| 587 | scan.set_unit('channel')
|
|---|
| 588 |
|
|---|
| 589 | a)
|
|---|
| 590 | msk = scan.set_mask([400,500],[800,900])
|
|---|
| 591 | # masks everything outside 400 and 500
|
|---|
| 592 | # and 800 and 900 in the unit 'channel'
|
|---|
| 593 |
|
|---|
| 594 | b)
|
|---|
| 595 | msk = scan.set_mask([400,500],[800,900], invert=True)
|
|---|
| 596 | # masks the regions between 400 and 500
|
|---|
| 597 | # and 800 and 900 in the unit 'channel'
|
|---|
| 598 |
|
|---|
| 599 | """
|
|---|
| 600 | row = 0
|
|---|
| 601 | if kwargs.has_key("row"):
|
|---|
| 602 | row = kwargs.get("row")
|
|---|
| 603 | data = self._getabcissa(row)
|
|---|
| 604 | u = self._getcoordinfo()[0]
|
|---|
| 605 | if rcParams['verbose']:
|
|---|
| 606 | if u == "": u = "channel"
|
|---|
| 607 | from asap import asaplog
|
|---|
| 608 | msg = "The current mask window unit is %s" % u
|
|---|
| 609 | if not self._check_ifs():
|
|---|
| 610 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
|---|
| 611 | asaplog.push(msg)
|
|---|
| 612 | n = self.nchan()
|
|---|
| 613 | msk = zeros(n)
|
|---|
| 614 | # test if args is a 'list' or a 'normal *args - UGLY!!!
|
|---|
| 615 |
|
|---|
| 616 | ws = (isinstance(args[-1][-1],int) or isinstance(args[-1][-1],float)) and args or args[0]
|
|---|
| 617 | for window in ws:
|
|---|
| 618 | if (len(window) != 2 or window[0] > window[1] ):
|
|---|
| 619 | raise TypeError("A window needs to be defined as [min,max]")
|
|---|
| 620 | for i in range(n):
|
|---|
| 621 | if data[i] >= window[0] and data[i] < window[1]:
|
|---|
| 622 | msk[i] = 1
|
|---|
| 623 | if kwargs.has_key('invert'):
|
|---|
| 624 | if kwargs.get('invert'):
|
|---|
| 625 | from numarray import logical_not
|
|---|
| 626 | msk = logical_not(msk)
|
|---|
| 627 | print_log()
|
|---|
| 628 | return msk
|
|---|
| 629 |
|
|---|
| 630 | def get_restfreqs(self):
|
|---|
| 631 | """
|
|---|
| 632 | Get the restfrequency(s) stored in this scantable.
|
|---|
| 633 | The return value(s) are always of unit 'Hz'
|
|---|
| 634 | Parameters:
|
|---|
| 635 | none
|
|---|
| 636 | Returns:
|
|---|
| 637 | a list of doubles
|
|---|
| 638 | """
|
|---|
| 639 | return list(self._getrestfreqs())
|
|---|
| 640 |
|
|---|
| 641 |
|
|---|
| 642 | def set_restfreqs(self, freqs=None, unit='Hz'):
|
|---|
| 643 | """
|
|---|
| 644 | Set or replace the restfrequency specified and
|
|---|
| 645 | If the 'freqs' argument holds a scalar,
|
|---|
| 646 | then that rest frequency will be applied to all the selected
|
|---|
| 647 | data. If the 'freqs' argument holds
|
|---|
| 648 | a vector, then it MUST be of equal or smaller length than
|
|---|
| 649 | the number of IFs (and the available restfrequencies will be
|
|---|
| 650 | replaced by this vector). In this case, *all* data have
|
|---|
| 651 | the restfrequency set per IF according
|
|---|
| 652 | to the corresponding value you give in the 'freqs' vector.
|
|---|
| 653 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and
|
|---|
| 654 | IF 1 gets restfreq 2e9.
|
|---|
| 655 | You can also specify the frequencies via known line names
|
|---|
| 656 | from the built-in Lovas table.
|
|---|
| 657 | Parameters:
|
|---|
| 658 | freqs: list of rest frequency values or string idenitfiers
|
|---|
| 659 | unit: unit for rest frequency (default 'Hz')
|
|---|
| 660 |
|
|---|
| 661 | Example:
|
|---|
| 662 | # set the given restfrequency for the whole table
|
|---|
| 663 | scan.set_restfreqs(freqs=1.4e9)
|
|---|
| 664 | # If thee number of IFs in the data is >= 2 the IF0 gets the first
|
|---|
| 665 | # value IF1 the second...
|
|---|
| 666 | scan.set_restfreqs(freqs=[1.4e9,1.67e9])
|
|---|
| 667 | #set the given restfrequency for the whole table (by name)
|
|---|
| 668 | scan.set_restfreqs(freqs="OH1667")
|
|---|
| 669 |
|
|---|
| 670 | Note:
|
|---|
| 671 | To do more sophisticate Restfrequency setting, e.g. on a
|
|---|
| 672 | source and IF basis, use scantable.set_selection() before using
|
|---|
| 673 | this function.
|
|---|
| 674 | # provide your scantable is call scan
|
|---|
| 675 | selection = selector()
|
|---|
| 676 | selection.set_name("ORION*")
|
|---|
| 677 | selection.set_ifs([1])
|
|---|
| 678 | scan.set_selection(selection)
|
|---|
| 679 | scan.set_restfreqs(freqs=86.6e9)
|
|---|
| 680 |
|
|---|
| 681 | """
|
|---|
| 682 | varlist = vars()
|
|---|
| 683 |
|
|---|
| 684 | t = type(freqs)
|
|---|
| 685 | if isinstance(freqs, int) or isinstance(freqs,float):
|
|---|
| 686 | self._setrestfreqs(freqs, unit)
|
|---|
| 687 | elif isinstance(freqs, list) or isinstance(freqs,tuple):
|
|---|
| 688 | if isinstance(freqs[-1], int) or isinstance(freqs[-1],float):
|
|---|
| 689 | sel = selector()
|
|---|
| 690 | savesel = self._getselection()
|
|---|
| 691 | for i in xrange(len(freqs)):
|
|---|
| 692 | sel.set_ifs([i])
|
|---|
| 693 | self._setselection(sel)
|
|---|
| 694 | self._setrestfreqs(freqs[i], unit)
|
|---|
| 695 | self._setselection(savesel)
|
|---|
| 696 | elif isinstance(freqs[-1], str):
|
|---|
| 697 | # not yet implemented
|
|---|
| 698 | pass
|
|---|
| 699 | else:
|
|---|
| 700 | return
|
|---|
| 701 | self._add_history("set_restfreqs", varlist)
|
|---|
| 702 |
|
|---|
| 703 |
|
|---|
| 704 |
|
|---|
| 705 | def history(self):
|
|---|
| 706 | hist = list(self._gethistory())
|
|---|
| 707 | out = "-"*80
|
|---|
| 708 | for h in hist:
|
|---|
| 709 | if h.startswith("---"):
|
|---|
| 710 | out += "\n"+h
|
|---|
| 711 | else:
|
|---|
| 712 | items = h.split("##")
|
|---|
| 713 | date = items[0]
|
|---|
| 714 | func = items[1]
|
|---|
| 715 | items = items[2:]
|
|---|
| 716 | out += "\n"+date+"\n"
|
|---|
| 717 | out += "Function: %s\n Parameters:" % (func)
|
|---|
| 718 | for i in items:
|
|---|
| 719 | s = i.split("=")
|
|---|
| 720 | out += "\n %s = %s" % (s[0],s[1])
|
|---|
| 721 | out += "\n"+"-"*80
|
|---|
| 722 | try:
|
|---|
| 723 | from IPython.genutils import page as pager
|
|---|
| 724 | except ImportError:
|
|---|
| 725 | from pydoc import pager
|
|---|
| 726 | pager(out)
|
|---|
| 727 | return
|
|---|
| 728 |
|
|---|
| 729 | #
|
|---|
| 730 | # Maths business
|
|---|
| 731 | #
|
|---|
| 732 |
|
|---|
| 733 | def average_time(self, mask=None, scanav=False, weight='tint', align=False):
|
|---|
| 734 | """
|
|---|
| 735 | Return the (time) average of a scan, or apply it 'insitu'.
|
|---|
| 736 | Note:
|
|---|
| 737 | in channels only
|
|---|
| 738 | The cursor of the output scan is set to 0.
|
|---|
| 739 | Parameters:
|
|---|
| 740 | one scan or comma separated scans
|
|---|
| 741 | mask: an optional mask (only used for 'var' and 'tsys'
|
|---|
| 742 | weighting)
|
|---|
| 743 | scanav: True averages each scan separately
|
|---|
| 744 | False (default) averages all scans together,
|
|---|
| 745 | weight: Weighting scheme. 'none', 'var' (1/var(spec)
|
|---|
| 746 | weighted), 'tsys' (1/Tsys**2 weighted), 'tint'
|
|---|
| 747 | (integration time weighted) or 'tintsys' (Tint/Tsys**2).
|
|---|
| 748 | The default is 'tint'
|
|---|
| 749 | align: align the spectra in velocity before averaging. It takes
|
|---|
| 750 | the time of the first spectrum as reference time.
|
|---|
| 751 | Example:
|
|---|
| 752 | # time average the scantable without using a mask
|
|---|
| 753 | newscan = scan.average_time()
|
|---|
| 754 | """
|
|---|
| 755 | varlist = vars()
|
|---|
| 756 | if weight is None: weight = 'TINT'
|
|---|
| 757 | if mask is None: mask = ()
|
|---|
| 758 | if scanav:
|
|---|
| 759 | scanav = "SCAN"
|
|---|
| 760 | else:
|
|---|
| 761 | scanav = "NONE"
|
|---|
| 762 | s = scantable(self._math._average((self,), mask, weight.upper(),
|
|---|
| 763 | scanav, align))
|
|---|
| 764 | s._add_history("average_time",varlist)
|
|---|
| 765 | print_log()
|
|---|
| 766 | return s
|
|---|
| 767 |
|
|---|
| 768 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
|
|---|
| 769 | """
|
|---|
| 770 | Return a scan where all spectra are converted to either
|
|---|
| 771 | Jansky or Kelvin depending upon the flux units of the scan table.
|
|---|
| 772 | By default the function tries to look the values up internally.
|
|---|
| 773 | If it can't find them (or if you want to over-ride), you must
|
|---|
| 774 | specify EITHER jyperk OR eta (and D which it will try to look up
|
|---|
| 775 | also if you don't set it). jyperk takes precedence if you set both.
|
|---|
| 776 | Parameters:
|
|---|
| 777 | jyperk: the Jy / K conversion factor
|
|---|
| 778 | eta: the aperture efficiency
|
|---|
| 779 | d: the geomtric diameter (metres)
|
|---|
| 780 | insitu: if False a new scantable is returned.
|
|---|
| 781 | Otherwise, the scaling is done in-situ
|
|---|
| 782 | The default is taken from .asaprc (False)
|
|---|
| 783 | allaxes: if True apply to all spectra. Otherwise
|
|---|
| 784 | apply only to the selected (beam/pol/if)spectra only
|
|---|
| 785 | The default is taken from .asaprc (True if none)
|
|---|
| 786 | """
|
|---|
| 787 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 788 | self._math._setinsitu(insitu)
|
|---|
| 789 | varlist = vars()
|
|---|
| 790 | if jyperk is None: jyperk = -1.0
|
|---|
| 791 | if d is None: d = -1.0
|
|---|
| 792 | if eta is None: eta = -1.0
|
|---|
| 793 | s = scantable(self._math._convertflux(self, d, eta, jyperk))
|
|---|
| 794 | s._add_history("convert_flux", varlist)
|
|---|
| 795 | print_log()
|
|---|
| 796 | if insitu: self._assign(s)
|
|---|
| 797 | else: return s
|
|---|
| 798 |
|
|---|
| 799 | def gain_el(self, poly=None, filename="", method="linear", insitu=None):
|
|---|
| 800 | """
|
|---|
| 801 | Return a scan after applying a gain-elevation correction.
|
|---|
| 802 | The correction can be made via either a polynomial or a
|
|---|
| 803 | table-based interpolation (and extrapolation if necessary).
|
|---|
| 804 | You specify polynomial coefficients, an ascii table or neither.
|
|---|
| 805 | If you specify neither, then a polynomial correction will be made
|
|---|
| 806 | with built in coefficients known for certain telescopes (an error
|
|---|
| 807 | will occur if the instrument is not known).
|
|---|
| 808 | The data and Tsys are *divided* by the scaling factors.
|
|---|
| 809 | Parameters:
|
|---|
| 810 | poly: Polynomial coefficients (default None) to compute a
|
|---|
| 811 | gain-elevation correction as a function of
|
|---|
| 812 | elevation (in degrees).
|
|---|
| 813 | filename: The name of an ascii file holding correction factors.
|
|---|
| 814 | The first row of the ascii file must give the column
|
|---|
| 815 | names and these MUST include columns
|
|---|
| 816 | "ELEVATION" (degrees) and "FACTOR" (multiply data
|
|---|
| 817 | by this) somewhere.
|
|---|
| 818 | The second row must give the data type of the
|
|---|
| 819 | column. Use 'R' for Real and 'I' for Integer.
|
|---|
| 820 | An example file would be
|
|---|
| 821 | (actual factors are arbitrary) :
|
|---|
| 822 |
|
|---|
| 823 | TIME ELEVATION FACTOR
|
|---|
| 824 | R R R
|
|---|
| 825 | 0.1 0 0.8
|
|---|
| 826 | 0.2 20 0.85
|
|---|
| 827 | 0.3 40 0.9
|
|---|
| 828 | 0.4 60 0.85
|
|---|
| 829 | 0.5 80 0.8
|
|---|
| 830 | 0.6 90 0.75
|
|---|
| 831 | method: Interpolation method when correcting from a table.
|
|---|
| 832 | Values are "nearest", "linear" (default), "cubic"
|
|---|
| 833 | and "spline"
|
|---|
| 834 | insitu: if False a new scantable is returned.
|
|---|
| 835 | Otherwise, the scaling is done in-situ
|
|---|
| 836 | The default is taken from .asaprc (False)
|
|---|
| 837 | """
|
|---|
| 838 |
|
|---|
| 839 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 840 | self._math._setinsitu(insitu)
|
|---|
| 841 | varlist = vars()
|
|---|
| 842 | if poly is None:
|
|---|
| 843 | poly = ()
|
|---|
| 844 | from os.path import expandvars
|
|---|
| 845 | filename = expandvars(filename)
|
|---|
| 846 | s = scantable(self._math._gainel(self, poly, filename, method))
|
|---|
| 847 | s._add_history("gain_el", varlist)
|
|---|
| 848 | print_log()
|
|---|
| 849 | if insitu: self._assign(s)
|
|---|
| 850 | else: return s
|
|---|
| 851 |
|
|---|
| 852 | def freq_align(self, reftime=None, method='cubic', insitu=None):
|
|---|
| 853 | """
|
|---|
| 854 | Return a scan where all rows have been aligned in frequency/velocity.
|
|---|
| 855 | The alignment frequency frame (e.g. LSRK) is that set by function
|
|---|
| 856 | set_freqframe.
|
|---|
| 857 | Parameters:
|
|---|
| 858 | reftime: reference time to align at. By default, the time of
|
|---|
| 859 | the first row of data is used.
|
|---|
| 860 | method: Interpolation method for regridding the spectra.
|
|---|
| 861 | Choose from "nearest", "linear", "cubic" (default)
|
|---|
| 862 | and "spline"
|
|---|
| 863 | insitu: if False a new scantable is returned.
|
|---|
| 864 | Otherwise, the scaling is done in-situ
|
|---|
| 865 | The default is taken from .asaprc (False)
|
|---|
| 866 | """
|
|---|
| 867 | if insitu is None: insitu = rcParams["insitu"]
|
|---|
| 868 | self._math._setinsitu(insitu)
|
|---|
| 869 | varlist = vars()
|
|---|
| 870 | if reftime is None: reftime = ""
|
|---|
| 871 | s = scantable(self._math._freq_align(self, reftime, method))
|
|---|
| 872 | s._add_history("freq_align", varlist)
|
|---|
| 873 | print_log()
|
|---|
| 874 | if insitu: self._assign(s)
|
|---|
| 875 | else: return s
|
|---|
| 876 |
|
|---|
| 877 | def opacity(self, tau, insitu=None):
|
|---|
| 878 | """
|
|---|
| 879 | Apply an opacity correction. The data
|
|---|
| 880 | and Tsys are multiplied by the correction factor.
|
|---|
| 881 | Parameters:
|
|---|
| 882 | tau: Opacity from which the correction factor is
|
|---|
| 883 | exp(tau*ZD)
|
|---|
| 884 | where ZD is the zenith-distance
|
|---|
| 885 | insitu: if False a new scantable is returned.
|
|---|
| 886 | Otherwise, the scaling is done in-situ
|
|---|
| 887 | The default is taken from .asaprc (False)
|
|---|
| 888 | """
|
|---|
| 889 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 890 | self._math._setinsitu(insitu)
|
|---|
| 891 | varlist = vars()
|
|---|
| 892 | s = scantable(self._math._opacity(self, tau))
|
|---|
| 893 | s._add_history("opacity", varlist)
|
|---|
| 894 | print_log()
|
|---|
| 895 | if insitu: self._assign(s)
|
|---|
| 896 | else: return s
|
|---|
| 897 |
|
|---|
| 898 | def bin(self, width=5, insitu=None):
|
|---|
| 899 | """
|
|---|
| 900 | Return a scan where all spectra have been binned up.
|
|---|
| 901 | width: The bin width (default=5) in pixels
|
|---|
| 902 | insitu: if False a new scantable is returned.
|
|---|
| 903 | Otherwise, the scaling is done in-situ
|
|---|
| 904 | The default is taken from .asaprc (False)
|
|---|
| 905 | """
|
|---|
| 906 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 907 | self._math._setinsitu(insitu)
|
|---|
| 908 | varlist = vars()
|
|---|
| 909 | s = scantable(self._math._bin(self, width))
|
|---|
| 910 | s._add_history("bin",varlist)
|
|---|
| 911 | print_log()
|
|---|
| 912 | if insitu: self._assign(s)
|
|---|
| 913 | else: return s
|
|---|
| 914 |
|
|---|
| 915 |
|
|---|
| 916 | def resample(self, width=5, method='cubic', insitu=None):
|
|---|
| 917 | """
|
|---|
| 918 | Return a scan where all spectra have been binned up
|
|---|
| 919 | width: The bin width (default=5) in pixels
|
|---|
| 920 | method: Interpolation method when correcting from a table.
|
|---|
| 921 | Values are "nearest", "linear", "cubic" (default)
|
|---|
| 922 | and "spline"
|
|---|
| 923 | insitu: if False a new scantable is returned.
|
|---|
| 924 | Otherwise, the scaling is done in-situ
|
|---|
| 925 | The default is taken from .asaprc (False)
|
|---|
| 926 | """
|
|---|
| 927 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 928 | self._math._setinsitu(insitu)
|
|---|
| 929 | varlist = vars()
|
|---|
| 930 | s = scantable(self._math._resample(self, method, width))
|
|---|
| 931 | s._add_history("resample",varlist)
|
|---|
| 932 | print_log()
|
|---|
| 933 | if insitu: self._assign(s)
|
|---|
| 934 | else: return s
|
|---|
| 935 |
|
|---|
| 936 |
|
|---|
| 937 | def average_pol(self, mask=None, weight='none'):
|
|---|
| 938 | """
|
|---|
| 939 | Average the Polarisations together.
|
|---|
| 940 | Parameters:
|
|---|
| 941 | mask: An optional mask defining the region, where the
|
|---|
| 942 | averaging will be applied. The output will have all
|
|---|
| 943 | specified points masked.
|
|---|
| 944 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
|---|
| 945 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
|---|
| 946 | """
|
|---|
| 947 | varlist = vars()
|
|---|
| 948 | if mask is None:
|
|---|
| 949 | mask = ()
|
|---|
| 950 | s = self._math._averagepol(self, mask, weight)
|
|---|
| 951 | s._add_history("average_pol",varlist)
|
|---|
| 952 | print_log()
|
|---|
| 953 | return scantable(s)
|
|---|
| 954 |
|
|---|
| 955 | def smooth(self, kernel="hanning", width=5.0, insitu=None):
|
|---|
| 956 | """
|
|---|
| 957 | Smooth the spectrum by the specified kernel (conserving flux).
|
|---|
| 958 | Parameters:
|
|---|
| 959 | scan: The input scan
|
|---|
| 960 | kernel: The type of smoothing kernel. Select from
|
|---|
| 961 | 'hanning' (default), 'gaussian' and 'boxcar'.
|
|---|
| 962 | The first three characters are sufficient.
|
|---|
| 963 | width: The width of the kernel in pixels. For hanning this is
|
|---|
| 964 | ignored otherwise it defauls to 5 pixels.
|
|---|
| 965 | For 'gaussian' it is the Full Width Half
|
|---|
| 966 | Maximum. For 'boxcar' it is the full width.
|
|---|
| 967 | insitu: if False a new scantable is returned.
|
|---|
| 968 | Otherwise, the scaling is done in-situ
|
|---|
| 969 | The default is taken from .asaprc (False)
|
|---|
| 970 | Example:
|
|---|
| 971 | none
|
|---|
| 972 | """
|
|---|
| 973 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 974 | self._math._setinsitu(insitu)
|
|---|
| 975 | varlist = vars()
|
|---|
| 976 | s = scantable(self._math._smooth(self,kernel,width))
|
|---|
| 977 | s._add_history("smooth", varlist)
|
|---|
| 978 | print_log()
|
|---|
| 979 | if insitu: self._assign(s)
|
|---|
| 980 | else: return s
|
|---|
| 981 |
|
|---|
| 982 |
|
|---|
| 983 | def poly_baseline(self, mask=None, order=0, insitu=None):
|
|---|
| 984 | """
|
|---|
| 985 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 986 | Parameters:
|
|---|
| 987 | scan: a scantable
|
|---|
| 988 | mask: an optional mask
|
|---|
| 989 | order: the order of the polynomial (default is 0)
|
|---|
| 990 | insitu: if False a new scantable is returned.
|
|---|
| 991 | Otherwise, the scaling is done in-situ
|
|---|
| 992 | The default is taken from .asaprc (False)
|
|---|
| 993 | allaxes: If True (default) apply to all spectra. Otherwise
|
|---|
| 994 | apply only to the selected (beam/pol/if)spectra only
|
|---|
| 995 | The default is taken from .asaprc (True if none)
|
|---|
| 996 | Example:
|
|---|
| 997 | # return a scan baselined by a third order polynomial,
|
|---|
| 998 | # not using a mask
|
|---|
| 999 | bscan = scan.poly_baseline(order=3)
|
|---|
| 1000 | """
|
|---|
| 1001 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1002 | varlist = vars()
|
|---|
| 1003 | if mask is None:
|
|---|
| 1004 | from numarray import ones
|
|---|
| 1005 | mask = list(ones(self.nchan(-1)))
|
|---|
| 1006 | from asap.asapfitter import fitter
|
|---|
| 1007 | f = fitter()
|
|---|
| 1008 | f.set_scan(self, mask)
|
|---|
| 1009 | f.set_function(poly=order)
|
|---|
| 1010 | s = f.auto_fit(insitu)
|
|---|
| 1011 | s._add_history("poly_baseline", varlist)
|
|---|
| 1012 | print_log()
|
|---|
| 1013 | if insitu: self._assign(s)
|
|---|
| 1014 | else: return s
|
|---|
| 1015 |
|
|---|
| 1016 | def auto_poly_baseline(self, mask=[], edge=(0,0), order=0,
|
|---|
| 1017 | threshold=3, insitu=None):
|
|---|
| 1018 | """
|
|---|
| 1019 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 1020 | Spectral lines are detected first using linefinder and masked out
|
|---|
| 1021 | to avoid them affecting the baseline solution.
|
|---|
| 1022 |
|
|---|
| 1023 | Parameters:
|
|---|
| 1024 | mask: an optional mask retreived from scantable
|
|---|
| 1025 | edge: an optional number of channel to drop at
|
|---|
| 1026 | the edge of spectrum. If only one value is
|
|---|
| 1027 | specified, the same number will be dropped from
|
|---|
| 1028 | both sides of the spectrum. Default is to keep
|
|---|
| 1029 | all channels. Nested tuples represent individual
|
|---|
| 1030 | edge selection for different IFs (a number of spectral
|
|---|
| 1031 | channels can be different)
|
|---|
| 1032 | order: the order of the polynomial (default is 0)
|
|---|
| 1033 | threshold: the threshold used by line finder. It is better to
|
|---|
| 1034 | keep it large as only strong lines affect the
|
|---|
| 1035 | baseline solution.
|
|---|
| 1036 | insitu: if False a new scantable is returned.
|
|---|
| 1037 | Otherwise, the scaling is done in-situ
|
|---|
| 1038 | The default is taken from .asaprc (False)
|
|---|
| 1039 |
|
|---|
| 1040 | Example:
|
|---|
| 1041 | scan2=scan.auto_poly_baseline(order=7)
|
|---|
| 1042 | """
|
|---|
| 1043 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1044 | varlist = vars()
|
|---|
| 1045 | from asap.asapfitter import fitter
|
|---|
| 1046 | from asap.asaplinefind import linefinder
|
|---|
| 1047 | from asap import _is_sequence_or_number as _is_valid
|
|---|
| 1048 |
|
|---|
| 1049 | # check whether edge is set up for each IF individually
|
|---|
| 1050 | individualEdge = False;
|
|---|
| 1051 | if len(edge)>1:
|
|---|
| 1052 | if isinstance(edge[0],list) or isinstance(edge[0],tuple):
|
|---|
| 1053 | individualEdge = True;
|
|---|
| 1054 |
|
|---|
| 1055 | if not _is_valid(edge, int) and not individualEdge:
|
|---|
| 1056 | raise ValueError, "Parameter 'edge' has to be an integer or a \
|
|---|
| 1057 | pair of integers specified as a tuple. Nested tuples are allowed \
|
|---|
| 1058 | to make individual selection for different IFs."
|
|---|
| 1059 |
|
|---|
| 1060 | curedge = (0,0)
|
|---|
| 1061 | if individualEdge:
|
|---|
| 1062 | for edge_par in edge:
|
|---|
| 1063 | if not _is_valid(edge,int):
|
|---|
| 1064 | raise ValueError, "Each element of the 'edge' tuple has \
|
|---|
| 1065 | to be a pair of integers or an integer."
|
|---|
| 1066 | else:
|
|---|
| 1067 | curedge = edge;
|
|---|
| 1068 |
|
|---|
| 1069 | # setup fitter
|
|---|
| 1070 | f = fitter()
|
|---|
| 1071 | f.set_function(poly=order)
|
|---|
| 1072 |
|
|---|
| 1073 | # setup line finder
|
|---|
| 1074 | fl=linefinder()
|
|---|
| 1075 | fl.set_options(threshold=threshold)
|
|---|
| 1076 |
|
|---|
| 1077 | if not insitu:
|
|---|
| 1078 | workscan=self.copy()
|
|---|
| 1079 | else:
|
|---|
| 1080 | workscan=self
|
|---|
| 1081 |
|
|---|
| 1082 | fl.set_scan(workscan)
|
|---|
| 1083 |
|
|---|
| 1084 | rows=range(workscan.nrow())
|
|---|
| 1085 | from asap import asaplog
|
|---|
| 1086 | asaplog.push("Processing:")
|
|---|
| 1087 | for r in rows:
|
|---|
| 1088 | 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))
|
|---|
| 1089 | asaplog.push(msg, False)
|
|---|
| 1090 |
|
|---|
| 1091 | # figure out edge parameter
|
|---|
| 1092 | if individualEdge:
|
|---|
| 1093 | if len(edge)>=workscan.getif(r):
|
|---|
| 1094 | raise RuntimeError, "Number of edge elements appear to be less than the number of IFs"
|
|---|
| 1095 | curedge = edge[workscan.getif(r)]
|
|---|
| 1096 |
|
|---|
| 1097 | # setup line finder
|
|---|
| 1098 | fl.find_lines(r,mask,curedge)
|
|---|
| 1099 | f.set_scan(workscan, fl.get_mask())
|
|---|
| 1100 | f.x = workscan._getabcissa(r)
|
|---|
| 1101 | f.y = workscan._getspectrum(r)
|
|---|
| 1102 | f.data = None
|
|---|
| 1103 | f.fit()
|
|---|
| 1104 | x = f.get_parameters()
|
|---|
| 1105 | workscan._setspectrum(f.fitter.getresidual(), r)
|
|---|
| 1106 | workscan._add_history("poly_baseline", varlist)
|
|---|
| 1107 | if insitu:
|
|---|
| 1108 | self._assign(workscan)
|
|---|
| 1109 | else:
|
|---|
| 1110 | return workscan
|
|---|
| 1111 |
|
|---|
| 1112 | def rotate_linpolphase(self, angle):
|
|---|
| 1113 | """
|
|---|
| 1114 | Rotate the phase of the complex polarization O=Q+iU correlation.
|
|---|
| 1115 | This is always done in situ in the raw data. So if you call this
|
|---|
| 1116 | function more than once then each call rotates the phase further.
|
|---|
| 1117 | Parameters:
|
|---|
| 1118 | angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1119 | Examples:
|
|---|
| 1120 | scan.rotate_linpolphase(2.3)
|
|---|
| 1121 | """
|
|---|
| 1122 | varlist = vars()
|
|---|
| 1123 | self._math._rotate_linpolphase(self, angle)
|
|---|
| 1124 | self._add_history("rotate_linpolphase", varlist)
|
|---|
| 1125 | print_log()
|
|---|
| 1126 | return
|
|---|
| 1127 |
|
|---|
| 1128 |
|
|---|
| 1129 | def rotate_xyphase(self, angle):
|
|---|
| 1130 | """
|
|---|
| 1131 | Rotate the phase of the XY correlation. This is always done in situ
|
|---|
| 1132 | in the data. So if you call this function more than once
|
|---|
| 1133 | then each call rotates the phase further.
|
|---|
| 1134 | Parameters:
|
|---|
| 1135 | angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1136 | Examples:
|
|---|
| 1137 | scan.rotate_xyphase(2.3)
|
|---|
| 1138 | """
|
|---|
| 1139 | varlist = vars()
|
|---|
| 1140 | self._math._rotate_xyphase(self, angle)
|
|---|
| 1141 | self._add_history("rotate_xyphase", varlist)
|
|---|
| 1142 | print_log()
|
|---|
| 1143 | return
|
|---|
| 1144 |
|
|---|
| 1145 | def swap_linears(self):
|
|---|
| 1146 | """
|
|---|
| 1147 | Swap the linear polarisations XX and YY
|
|---|
| 1148 | """
|
|---|
| 1149 | varlist = vars()
|
|---|
| 1150 | self._math._swap_linears(self)
|
|---|
| 1151 | self._add_history("swap_linears", varlist)
|
|---|
| 1152 | print_log()
|
|---|
| 1153 | return
|
|---|
| 1154 |
|
|---|
| 1155 | def invert_phase(self):
|
|---|
| 1156 | """
|
|---|
| 1157 | Invert the phase of the complex polarisation
|
|---|
| 1158 | """
|
|---|
| 1159 | varlist = vars()
|
|---|
| 1160 | self._math._invert_phase(self)
|
|---|
| 1161 | self._add_history("invert_phase", varlist)
|
|---|
| 1162 | print_log()
|
|---|
| 1163 | return
|
|---|
| 1164 |
|
|---|
| 1165 | def add(self, offset, insitu=None):
|
|---|
| 1166 | """
|
|---|
| 1167 | Return a scan where all spectra have the offset added
|
|---|
| 1168 | Parameters:
|
|---|
| 1169 | offset: the offset
|
|---|
| 1170 | insitu: if False a new scantable is returned.
|
|---|
| 1171 | Otherwise, the scaling is done in-situ
|
|---|
| 1172 | The default is taken from .asaprc (False)
|
|---|
| 1173 | """
|
|---|
| 1174 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1175 | self._math._setinsitu(insitu)
|
|---|
| 1176 | varlist = vars()
|
|---|
| 1177 | s = scantable(self._math._unaryop(self, offset, "ADD", False))
|
|---|
| 1178 | s._add_history("add",varlist)
|
|---|
| 1179 | print_log()
|
|---|
| 1180 | if insitu:
|
|---|
| 1181 | self._assign(s)
|
|---|
| 1182 | else:
|
|---|
| 1183 | return s
|
|---|
| 1184 |
|
|---|
| 1185 | def scale(self, factor, tsys=True, insitu=None,):
|
|---|
| 1186 | """
|
|---|
| 1187 | Return a scan where all spectra are scaled by the give 'factor'
|
|---|
| 1188 | Parameters:
|
|---|
| 1189 | factor: the scaling factor
|
|---|
| 1190 | insitu: if False a new scantable is returned.
|
|---|
| 1191 | Otherwise, the scaling is done in-situ
|
|---|
| 1192 | The default is taken from .asaprc (False)
|
|---|
| 1193 | tsys: if True (default) then apply the operation to Tsys
|
|---|
| 1194 | as well as the data
|
|---|
| 1195 | """
|
|---|
| 1196 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1197 | self._math._setinsitu(insitu)
|
|---|
| 1198 | varlist = vars()
|
|---|
| 1199 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
|
|---|
| 1200 | s._add_history("scale",varlist)
|
|---|
| 1201 | print_log()
|
|---|
| 1202 | if insitu:
|
|---|
| 1203 | self._assign(s)
|
|---|
| 1204 | else:
|
|---|
| 1205 | return s
|
|---|
| 1206 |
|
|---|
| 1207 | def auto_quotient(self, mode='time', preserve=True):
|
|---|
| 1208 | """
|
|---|
| 1209 | This function allows to build quotients automatically.
|
|---|
| 1210 | It assumes the observation to have the same numer of
|
|---|
| 1211 | "ons" and "offs"
|
|---|
| 1212 | It will support "closest off in time" in the future
|
|---|
| 1213 | Parameters:
|
|---|
| 1214 | mode: the on/off detection mode; 'suffix' (default)
|
|---|
| 1215 | 'suffix' identifies 'off' scans by the
|
|---|
| 1216 | trailing '_R' (Mopra/Parkes) or
|
|---|
| 1217 | '_e'/'_w' (Tid)
|
|---|
| 1218 | preserve: you can preserve (default) the continuum or
|
|---|
| 1219 | remove it. The equations used are
|
|---|
| 1220 | preserve: Output = Toff * (on/off) - Toff
|
|---|
| 1221 | remove: Output = Tref * (on/off) - Ton
|
|---|
| 1222 | """
|
|---|
| 1223 | modes = ["time"]
|
|---|
| 1224 | if not mode in modes:
|
|---|
| 1225 | msg = "please provide valid mode. Valid modes are %s" % (modes)
|
|---|
| 1226 | raise ValueError(msg)
|
|---|
| 1227 | varlist = vars()
|
|---|
| 1228 | s = scantable(self._math._quotient(self, mode, preserve))
|
|---|
| 1229 | s._add_history("auto_quotient",varlist)
|
|---|
| 1230 | print_log()
|
|---|
| 1231 | return s
|
|---|
| 1232 |
|
|---|
| 1233 |
|
|---|
| 1234 |
|
|---|
| 1235 |
|
|---|
| 1236 | def freq_switch(self, insitu=None):
|
|---|
| 1237 | """
|
|---|
| 1238 | Apply frequency switching to the data.
|
|---|
| 1239 | Parameters:
|
|---|
| 1240 | insitu: if False a new scantable is returned.
|
|---|
| 1241 | Otherwise, the swictching is done in-situ
|
|---|
| 1242 | The default is taken from .asaprc (False)
|
|---|
| 1243 | Example:
|
|---|
| 1244 | none
|
|---|
| 1245 | """
|
|---|
| 1246 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1247 | self._math._setinsitu(insitu)
|
|---|
| 1248 | varlist = vars()
|
|---|
| 1249 | s = scantable(self._math._freqswitch(self))
|
|---|
| 1250 | s._add_history("freq_switch",varlist)
|
|---|
| 1251 | print_log()
|
|---|
| 1252 | if insitu: self._assign(s)
|
|---|
| 1253 | else: return s
|
|---|
| 1254 |
|
|---|
| 1255 | def recalc_azel(self):
|
|---|
| 1256 | """
|
|---|
| 1257 | Recalculate the azimuth and elevation for each position.
|
|---|
| 1258 | Parameters:
|
|---|
| 1259 | none
|
|---|
| 1260 | Example:
|
|---|
| 1261 | """
|
|---|
| 1262 | varlist = vars()
|
|---|
| 1263 | self._recalcazel()
|
|---|
| 1264 | self._add_history("recalc_azel", varlist)
|
|---|
| 1265 | print_log()
|
|---|
| 1266 | return
|
|---|
| 1267 |
|
|---|
| 1268 | def __add__(self, other):
|
|---|
| 1269 | varlist = vars()
|
|---|
| 1270 | s = None
|
|---|
| 1271 | if isinstance(other, scantable):
|
|---|
| 1272 | print "scantable + scantable NYI"
|
|---|
| 1273 | return
|
|---|
| 1274 | elif isinstance(other, float):
|
|---|
| 1275 | s = scantable(self._math._unaryop(self, other, "ADD", False))
|
|---|
| 1276 | else:
|
|---|
| 1277 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1278 | s._add_history("operator +", varlist)
|
|---|
| 1279 | print_log()
|
|---|
| 1280 | return s
|
|---|
| 1281 |
|
|---|
| 1282 | def __sub__(self, other):
|
|---|
| 1283 | """
|
|---|
| 1284 | implicit on all axes and on Tsys
|
|---|
| 1285 | """
|
|---|
| 1286 | varlist = vars()
|
|---|
| 1287 | s = None
|
|---|
| 1288 | if isinstance(other, scantable):
|
|---|
| 1289 | print "scantable - scantable NYI"
|
|---|
| 1290 | return
|
|---|
| 1291 | elif isinstance(other, float):
|
|---|
| 1292 | s = scantable(self._math._unaryop(self, other, "SUB", False))
|
|---|
| 1293 | else:
|
|---|
| 1294 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1295 | s._add_history("operator -", varlist)
|
|---|
| 1296 | print_log()
|
|---|
| 1297 | return s
|
|---|
| 1298 |
|
|---|
| 1299 | def __mul__(self, other):
|
|---|
| 1300 | """
|
|---|
| 1301 | implicit on all axes and on Tsys
|
|---|
| 1302 | """
|
|---|
| 1303 | varlist = vars()
|
|---|
| 1304 | s = None
|
|---|
| 1305 | if isinstance(other, scantable):
|
|---|
| 1306 | print "scantable * scantable NYI"
|
|---|
| 1307 | return
|
|---|
| 1308 | elif isinstance(other, float):
|
|---|
| 1309 | s = scantable(self._math._unaryop(self, other, "MUL", False))
|
|---|
| 1310 | else:
|
|---|
| 1311 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1312 | s._add_history("operator *", varlist)
|
|---|
| 1313 | print_log()
|
|---|
| 1314 | return s
|
|---|
| 1315 |
|
|---|
| 1316 |
|
|---|
| 1317 | def __div__(self, other):
|
|---|
| 1318 | """
|
|---|
| 1319 | implicit on all axes and on Tsys
|
|---|
| 1320 | """
|
|---|
| 1321 | varlist = vars()
|
|---|
| 1322 | s = None
|
|---|
| 1323 | if isinstance(other, scantable):
|
|---|
| 1324 | print "scantable / scantable NYI"
|
|---|
| 1325 | return
|
|---|
| 1326 | elif isinstance(other, float):
|
|---|
| 1327 | if other == 0.0:
|
|---|
| 1328 | raise ZeroDivisionError("Dividing by zero is not recommended")
|
|---|
| 1329 | s = scantable(self._math._unaryop(self, other, "DIV", False))
|
|---|
| 1330 | else:
|
|---|
| 1331 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1332 | s._add_history("operator /", varlist)
|
|---|
| 1333 | print_log()
|
|---|
| 1334 | return s
|
|---|
| 1335 |
|
|---|
| 1336 | def get_fit(self, row=0):
|
|---|
| 1337 | """
|
|---|
| 1338 | Print or return the stored fits for a row in the scantable
|
|---|
| 1339 | Parameters:
|
|---|
| 1340 | row: the row which the fit has been applied to.
|
|---|
| 1341 | """
|
|---|
| 1342 | if row > self.nrow():
|
|---|
| 1343 | return
|
|---|
| 1344 | from asap.asapfit import asapfit
|
|---|
| 1345 | fit = asapfit(self._getfit(row))
|
|---|
| 1346 | if rcParams['verbose']:
|
|---|
| 1347 | print fit
|
|---|
| 1348 | return
|
|---|
| 1349 | else:
|
|---|
| 1350 | return fit.as_dict()
|
|---|
| 1351 |
|
|---|
| 1352 | def _add_history(self, funcname, parameters):
|
|---|
| 1353 | # create date
|
|---|
| 1354 | sep = "##"
|
|---|
| 1355 | from datetime import datetime
|
|---|
| 1356 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
|
|---|
| 1357 | hist = dstr+sep
|
|---|
| 1358 | hist += funcname+sep#cdate+sep
|
|---|
| 1359 | if parameters.has_key('self'): del parameters['self']
|
|---|
| 1360 | for k,v in parameters.iteritems():
|
|---|
| 1361 | if type(v) is dict:
|
|---|
| 1362 | for k2,v2 in v.iteritems():
|
|---|
| 1363 | hist += k2
|
|---|
| 1364 | hist += "="
|
|---|
| 1365 | if isinstance(v2,scantable):
|
|---|
| 1366 | hist += 'scantable'
|
|---|
| 1367 | elif k2 == 'mask':
|
|---|
| 1368 | if isinstance(v2,list) or isinstance(v2,tuple):
|
|---|
| 1369 | hist += str(self._zip_mask(v2))
|
|---|
| 1370 | else:
|
|---|
| 1371 | hist += str(v2)
|
|---|
| 1372 | else:
|
|---|
| 1373 | hist += str(v2)
|
|---|
| 1374 | else:
|
|---|
| 1375 | hist += k
|
|---|
| 1376 | hist += "="
|
|---|
| 1377 | if isinstance(v,scantable):
|
|---|
| 1378 | hist += 'scantable'
|
|---|
| 1379 | elif k == 'mask':
|
|---|
| 1380 | if isinstance(v,list) or isinstance(v,tuple):
|
|---|
| 1381 | hist += str(self._zip_mask(v))
|
|---|
| 1382 | else:
|
|---|
| 1383 | hist += str(v)
|
|---|
| 1384 | else:
|
|---|
| 1385 | hist += str(v)
|
|---|
| 1386 | hist += sep
|
|---|
| 1387 | hist = hist[:-2] # remove trailing '##'
|
|---|
| 1388 | self._addhistory(hist)
|
|---|
| 1389 |
|
|---|
| 1390 |
|
|---|
| 1391 | def _zip_mask(self, mask):
|
|---|
| 1392 | mask = list(mask)
|
|---|
| 1393 | i = 0
|
|---|
| 1394 | segments = []
|
|---|
| 1395 | while mask[i:].count(1):
|
|---|
| 1396 | i += mask[i:].index(1)
|
|---|
| 1397 | if mask[i:].count(0):
|
|---|
| 1398 | j = i + mask[i:].index(0)
|
|---|
| 1399 | else:
|
|---|
| 1400 | j = len(mask)
|
|---|
| 1401 | segments.append([i,j])
|
|---|
| 1402 | i = j
|
|---|
| 1403 | return segments
|
|---|
| 1404 |
|
|---|
| 1405 | def _get_ordinate_label(self):
|
|---|
| 1406 | fu = "("+self.get_fluxunit()+")"
|
|---|
| 1407 | import re
|
|---|
| 1408 | lbl = "Intensity"
|
|---|
| 1409 | if re.match(".K.",fu):
|
|---|
| 1410 | lbl = "Brightness Temperature "+ fu
|
|---|
| 1411 | elif re.match(".Jy.",fu):
|
|---|
| 1412 | lbl = "Flux density "+ fu
|
|---|
| 1413 | return lbl
|
|---|
| 1414 |
|
|---|
| 1415 | def _check_ifs(self):
|
|---|
| 1416 | nchans = [self.nchan(i) for i in range(self.nif(-1))]
|
|---|
| 1417 | nchans = filter(lambda t: t > 0, nchans)
|
|---|
| 1418 | return (sum(nchans)/len(nchans) == nchans[0])
|
|---|
| 1419 |
|
|---|
| 1420 | def _fill(self, names, unit, average):
|
|---|
| 1421 | import os
|
|---|
| 1422 | varlist = vars()
|
|---|
| 1423 | from asap._asap import stfiller
|
|---|
| 1424 | first = True
|
|---|
| 1425 | fullnames = []
|
|---|
| 1426 | for name in names:
|
|---|
| 1427 | name = os.path.expandvars(name)
|
|---|
| 1428 | name = os.path.expanduser(name)
|
|---|
| 1429 | if not os.path.exists(name):
|
|---|
| 1430 | msg = "File '%s' does not exists" % (name)
|
|---|
| 1431 | if rcParams['verbose']:
|
|---|
| 1432 | asaplog.push(msg)
|
|---|
| 1433 | print asaplog.pop().strip()
|
|---|
| 1434 | return
|
|---|
| 1435 | raise IOError(msg)
|
|---|
| 1436 | fullnames.append(name)
|
|---|
| 1437 | if average:
|
|---|
| 1438 | asaplog.push('Auto averaging integrations')
|
|---|
| 1439 | for name in fullnames:
|
|---|
| 1440 | r = stfiller()
|
|---|
| 1441 | msg = "Importing %s..." % (name)
|
|---|
| 1442 | asaplog.push(msg,False)
|
|---|
| 1443 | print_log()
|
|---|
| 1444 | r._open(name,-1,-1)
|
|---|
| 1445 | r._read()
|
|---|
| 1446 | tbl = r._getdata()
|
|---|
| 1447 | if average:
|
|---|
| 1448 | tbl = self._math._average((tbl,),(),'NONE','SCAN', False)
|
|---|
| 1449 | #tbl = tbl2
|
|---|
| 1450 | if not first:
|
|---|
| 1451 | tbl = self._math._merge([self, tbl])
|
|---|
| 1452 | #tbl = tbl2
|
|---|
| 1453 | Scantable.__init__(self, tbl)
|
|---|
| 1454 | r._close()
|
|---|
| 1455 | del r,tbl
|
|---|
| 1456 | first = False
|
|---|
| 1457 | if unit is not None:
|
|---|
| 1458 | self.set_fluxunit(unit)
|
|---|
| 1459 | self.set_freqframe(rcParams['scantable.freqframe'])
|
|---|
| 1460 | #self._add_history("scantable", varlist)
|
|---|
| 1461 |
|
|---|
