| 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 asap import asaplog
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| 5 | from asap import selector
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| 6 | from asap import linecatalog
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| 7 | from asap import _n_bools, mask_not, mask_and, mask_or
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| 8 |
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| 9 | class scantable(Scantable):
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| 10 | """
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| 11 | The ASAP container for scans
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| 12 | """
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| 13 |
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| 14 | def __init__(self, filename, average=None, unit=None, getpt=None):
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| 15 | """
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| 16 | Create a scantable from a saved one or make a reference
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| 17 | Parameters:
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| 18 | filename: the name of an asap table on disk
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| 19 | or
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| 20 | the name of a rpfits/sdfits/ms file
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| 21 | (integrations within scans are auto averaged
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| 22 | and the whole file is read)
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| 23 | or
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| 24 | [advanced] a reference to an existing
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| 25 | scantable
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| 26 | average: average all integrations withinb a scan on read.
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| 27 | The default (True) is taken from .asaprc.
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| 28 | unit: brightness unit; must be consistent with K or Jy.
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| 29 | Over-rides the default selected by the reader
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| 30 | (input rpfits/sdfits/ms) or replaces the value
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| 31 | in existing scantables
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| 32 | getpt: for MeasurementSet input data only:
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| 33 | If True, all pointing data are filled.
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| 34 | The deafult is False, which makes time to load
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| 35 | the MS data faster in some cases.
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| 36 | """
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| 37 | if average is None:
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| 38 | average = rcParams['scantable.autoaverage']
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| 39 | if getpt is None:
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| 40 | getpt = True
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| 41 | varlist = vars()
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| 42 | from asap._asap import stmath
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| 43 | self._math = stmath()
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| 44 | if isinstance(filename, Scantable):
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| 45 | Scantable.__init__(self, filename)
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| 46 | else:
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| 47 | if isinstance(filename, str):# or \
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| 48 | # (isinstance(filename, list) or isinstance(filename, tuple)) \
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| 49 | # and isinstance(filename[-1], str):
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| 50 | import os.path
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| 51 | filename = os.path.expandvars(filename)
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| 52 | filename = os.path.expanduser(filename)
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| 53 | if not os.path.exists(filename):
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| 54 | s = "File '%s' not found." % (filename)
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| 55 | if rcParams['verbose']:
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| 56 | asaplog.push(s)
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| 57 | #print asaplog.pop().strip()
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| 58 | print_log('ERROR')
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| 59 | return
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| 60 | raise IOError(s)
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| 61 | if os.path.isdir(filename) \
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| 62 | and not os.path.exists(filename+'/table.f1'):
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| 63 | # crude check if asap table
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| 64 | if os.path.exists(filename+'/table.info'):
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| 65 | ondisk = rcParams['scantable.storage'] == 'disk'
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| 66 | Scantable.__init__(self, filename, ondisk)
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| 67 | if unit is not None:
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| 68 | self.set_fluxunit(unit)
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| 69 | # do not reset to the default freqframe
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| 70 | #self.set_freqframe(rcParams['scantable.freqframe'])
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| 71 | else:
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| 72 | msg = "The given file '%s'is not a valid " \
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| 73 | "asap table." % (filename)
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| 74 | if rcParams['verbose']:
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| 75 | #print msg
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| 76 | asaplog.push( msg )
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| 77 | print_log( 'ERROR' )
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| 78 | return
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| 79 | else:
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| 80 | raise IOError(msg)
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| 81 | else:
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| 82 | self._fill([filename], unit, average, getpt)
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| 83 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \
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| 84 | and isinstance(filename[-1], str):
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| 85 | self._fill(filename, unit, average, getpt)
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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,
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| 92 | SDFITS or MS2 format.
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| 93 | Parameters:
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| 94 | name: the name of the outputfile. For format "ASCII"
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| 95 | this is the root file name (data in 'name'.txt
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| 96 | and header in 'name'_header.txt)
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| 97 | format: an optional file format. Default is ASAP.
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| 98 | Allowed are - 'ASAP' (save as ASAP [aips++] Table),
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| 99 | 'SDFITS' (save as SDFITS file)
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| 100 | 'ASCII' (saves as ascii text file)
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| 101 | 'MS2' (saves as an aips++
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| 102 | MeasurementSet V2)
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| 103 | 'FITS' (save as image FITS - not
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| 104 | readable by class)
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| 105 | 'CLASS' (save as FITS readable by CLASS)
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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 | msg = "No filename given. Using default name %s..." % name
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| 119 | asaplog.push(msg)
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| 120 | name = path.expandvars(name)
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| 121 | if path.isfile(name) or path.isdir(name):
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| 122 | if not overwrite:
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| 123 | msg = "File %s exists." % name
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| 124 | if rcParams['verbose']:
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| 125 | #print msg
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| 126 | asaplog.push( msg )
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| 127 | print_log( 'ERROR' )
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| 128 | return
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| 129 | else:
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| 130 | raise IOError(msg)
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| 131 | format2 = format.upper()
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| 132 | if format2 == 'ASAP':
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| 133 | self._save(name)
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| 134 | else:
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| 135 | from asap._asap import stwriter as stw
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| 136 | writer = stw(format2)
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| 137 | writer.write(self, name)
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| 138 | print_log()
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| 139 | return
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| 140 |
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| 141 | def copy(self):
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| 142 | """
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| 143 | Return a copy of this scantable.
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| 144 | Note:
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| 145 | This makes a full (deep) copy. scan2 = scan1 makes a reference.
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| 146 | Parameters:
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| 147 | none
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| 148 | Example:
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| 149 | copiedscan = scan.copy()
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| 150 | """
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| 151 | sd = scantable(Scantable._copy(self))
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| 152 | return sd
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| 153 |
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| 154 | def drop_scan(self, scanid=None):
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| 155 | """
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| 156 | Return a new scantable where the specified scan number(s) has(have)
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| 157 | been dropped.
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| 158 | Parameters:
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| 159 | scanid: a (list of) scan number(s)
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| 160 | """
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| 161 | from asap import _is_sequence_or_number as _is_valid
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| 162 | from asap import _to_list
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| 163 | from asap import unique
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| 164 | if not _is_valid(scanid):
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| 165 | if rcParams['verbose']:
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| 166 | #print "Please specify a scanno to drop from the scantable"
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| 167 | asaplog.push( 'Please specify a scanno to drop from the scantable' )
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| 168 | print_log( 'ERROR' )
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| 169 | return
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| 170 | else:
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| 171 | raise RuntimeError("No scan given")
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| 172 | try:
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| 173 | scanid = _to_list(scanid)
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| 174 | allscans = unique([ self.getscan(i) for i in range(self.nrow())])
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| 175 | for sid in scanid: allscans.remove(sid)
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| 176 | if len(allscans) == 0:
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| 177 | raise ValueError("Can't remove all scans")
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| 178 | except ValueError:
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| 179 | if rcParams['verbose']:
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| 180 | #print "Couldn't find any match."
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| 181 | print_log()
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| 182 | asaplog.push( "Couldn't find any match." )
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| 183 | print_log( 'ERROR' )
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| 184 | return
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| 185 | else: raise
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| 186 | try:
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| 187 | bsel = self.get_selection()
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| 188 | sel = selector()
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| 189 | sel.set_scans(allscans)
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| 190 | self.set_selection(bsel+sel)
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| 191 | scopy = self._copy()
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| 192 | self.set_selection(bsel)
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| 193 | return scantable(scopy)
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| 194 | except RuntimeError:
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| 195 | if rcParams['verbose']:
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| 196 | #print "Couldn't find any match."
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| 197 | print_log()
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| 198 | asaplog.push( "Couldn't find any match." )
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| 199 | print_log( 'ERROR' )
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| 200 | else:
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| 201 | raise
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| 202 |
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| 203 |
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| 204 | def get_scan(self, scanid=None):
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| 205 | """
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| 206 | Return a specific scan (by scanno) or collection of scans (by
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| 207 | source name) in a new scantable.
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| 208 | Note:
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| 209 | See scantable.drop_scan() for the inverse operation.
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| 210 | Parameters:
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| 211 | scanid: a (list of) scanno or a source name, unix-style
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| 212 | patterns are accepted for source name matching, e.g.
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| 213 | '*_R' gets all 'ref scans
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| 214 | Example:
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| 215 | # get all scans containing the source '323p459'
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| 216 | newscan = scan.get_scan('323p459')
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| 217 | # get all 'off' scans
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| 218 | refscans = scan.get_scan('*_R')
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| 219 | # get a susbset of scans by scanno (as listed in scan.summary())
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| 220 | newscan = scan.get_scan([0, 2, 7, 10])
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| 221 | """
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| 222 | if scanid is None:
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| 223 | if rcParams['verbose']:
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| 224 | #print "Please specify a scan no or name to " \
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| 225 | # "retrieve from the scantable"
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| 226 | asaplog.push( 'Please specify a scan no or name to retrieve from the scantable' )
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| 227 | print_log( 'ERROR' )
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| 228 | return
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| 229 | else:
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| 230 | raise RuntimeError("No scan given")
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| 231 |
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| 232 | try:
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| 233 | bsel = self.get_selection()
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| 234 | sel = selector()
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| 235 | if type(scanid) is str:
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| 236 | sel.set_name(scanid)
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| 237 | self.set_selection(bsel+sel)
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| 238 | scopy = self._copy()
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| 239 | self.set_selection(bsel)
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| 240 | return scantable(scopy)
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| 241 | elif type(scanid) is int:
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| 242 | sel.set_scans([scanid])
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| 243 | self.set_selection(bsel+sel)
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| 244 | scopy = self._copy()
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| 245 | self.set_selection(bsel)
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| 246 | return scantable(scopy)
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| 247 | elif type(scanid) is list:
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| 248 | sel.set_scans(scanid)
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| 249 | self.set_selection(sel)
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| 250 | scopy = self._copy()
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| 251 | self.set_selection(bsel)
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| 252 | return scantable(scopy)
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| 253 | else:
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| 254 | msg = "Illegal scanid type, use 'int' or 'list' if ints."
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| 255 | if rcParams['verbose']:
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| 256 | #print msg
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| 257 | asaplog.push( msg )
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| 258 | print_log( 'ERROR' )
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| 259 | else:
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| 260 | raise TypeError(msg)
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| 261 | except RuntimeError:
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| 262 | if rcParams['verbose']:
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| 263 | #print "Couldn't find any match."
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| 264 | print_log()
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| 265 | asaplog.push( "Couldn't find any match." )
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| 266 | print_log( 'ERROR' )
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| 267 | else: raise
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| 268 |
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| 269 | def __str__(self):
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| 270 | return Scantable._summary(self, True)
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| 271 |
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| 272 | def summary(self, filename=None):
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| 273 | """
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| 274 | Print a summary of the contents of this scantable.
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| 275 | Parameters:
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| 276 | filename: the name of a file to write the putput to
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| 277 | Default - no file output
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| 278 | verbose: print extra info such as the frequency table
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| 279 | The default (False) is taken from .asaprc
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| 280 | """
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| 281 | info = Scantable._summary(self, True)
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| 282 | #if verbose is None: verbose = rcParams['scantable.verbosesummary']
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| 283 | if filename is not None:
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| 284 | if filename is "":
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| 285 | filename = 'scantable_summary.txt'
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| 286 | from os.path import expandvars, isdir
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| 287 | filename = expandvars(filename)
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| 288 | if not isdir(filename):
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| 289 | data = open(filename, 'w')
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| 290 | data.write(info)
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| 291 | data.close()
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| 292 | else:
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| 293 | msg = "Illegal file name '%s'." % (filename)
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| 294 | if rcParams['verbose']:
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| 295 | #print msg
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| 296 | asaplog.push( msg )
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| 297 | print_log( 'ERROR' )
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| 298 | else:
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| 299 | raise IOError(msg)
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| 300 | if rcParams['verbose']:
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| 301 | try:
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| 302 | from IPython.genutils import page as pager
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| 303 | except ImportError:
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| 304 | from pydoc import pager
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| 305 | pager(info)
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| 306 | else:
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| 307 | return info
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| 308 |
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| 309 | def get_spectrum(self, rowno):
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| 310 | """Return the spectrum for the current row in the scantable as a list.
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| 311 | Parameters:
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| 312 | rowno: the row number to retrieve the spectrum from
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| 313 | """
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| 314 | return self._getspectrum(rowno)
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| 315 |
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| 316 | def get_mask(self, rowno):
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| 317 | """Return the mask for the current row in the scantable as a list.
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| 318 | Parameters:
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| 319 | rowno: the row number to retrieve the mask from
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| 320 | """
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| 321 | return self._getmask(rowno)
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| 322 |
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| 323 | def set_spectrum(self, spec, rowno):
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| 324 | """Return the spectrum for the current row in the scantable as a list.
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| 325 | Parameters:
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| 326 | spec: the spectrum
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| 327 | rowno: the row number to set the spectrum for
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| 328 | """
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| 329 | assert(len(spec) == self.nchan())
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| 330 | return self._setspectrum(spec, rowno)
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| 331 |
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| 332 | def get_selection(self):
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| 333 | """
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| 334 | Get the selection object currently set on this scantable.
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| 335 | Parameters:
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| 336 | none
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| 337 | Example:
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| 338 | sel = scan.get_selection()
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| 339 | sel.set_ifs(0) # select IF 0
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| 340 | scan.set_selection(sel) # apply modified selection
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| 341 | """
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| 342 | return selector(self._getselection())
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| 343 |
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| 344 | def set_selection(self, selection=selector()):
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| 345 | """
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| 346 | Select a subset of the data. All following operations on this scantable
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| 347 | are only applied to thi selection.
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| 348 | Parameters:
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| 349 | selection: a selector object (default unset the selection)
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| 350 | Examples:
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| 351 | sel = selector() # create a selection object
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| 352 | self.set_scans([0, 3]) # select SCANNO 0 and 3
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| 353 | scan.set_selection(sel) # set the selection
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| 354 | scan.summary() # will only print summary of scanno 0 an 3
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| 355 | scan.set_selection() # unset the selection
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| 356 | """
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| 357 | self._setselection(selection)
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| 358 |
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| 359 | def get_row(self, row=0, insitu=None):
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| 360 | """
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| 361 | Select a row in the scantable.
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| 362 | Return a scantable with single row.
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| 363 | Parameters:
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| 364 | row: row no of integration, default is 0.
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| 365 | insitu: if False a new scantable is returned.
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| 366 | Otherwise, the scaling is done in-situ
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| 367 | The default is taken from .asaprc (False)
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| 368 | """
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| 369 | if insitu is None: insitu = rcParams['insitu']
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| 370 | if not insitu:
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| 371 | workscan = self.copy()
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| 372 | else:
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| 373 | workscan = self
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| 374 | # Select a row
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| 375 | sel=selector()
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| 376 | sel.set_scans([workscan.getscan(row)])
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| 377 | sel.set_cycles([workscan.getcycle(row)])
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| 378 | sel.set_beams([workscan.getbeam(row)])
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| 379 | sel.set_ifs([workscan.getif(row)])
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| 380 | sel.set_polarisations([workscan.getpol(row)])
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| 381 | sel.set_name(workscan._getsourcename(row))
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| 382 | workscan.set_selection(sel)
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| 383 | if not workscan.nrow() == 1:
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| 384 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow())
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| 385 | raise RuntimeError(msg)
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| 386 | del sel
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| 387 | if insitu:
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| 388 | self._assign(workscan)
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| 389 | else:
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| 390 | return workscan
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| 391 |
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| 392 | #def stats(self, stat='stddev', mask=None):
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| 393 | def stats(self, stat='stddev', mask=None, form='3.3f'):
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| 394 | """
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| 395 | Determine the specified statistic of the current beam/if/pol
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| 396 | Takes a 'mask' as an optional parameter to specify which
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| 397 | channels should be excluded.
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| 398 | Parameters:
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| 399 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum',
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| 400 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median'
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| 401 | mask: an optional mask specifying where the statistic
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| 402 | should be determined.
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| 403 | form: format string to print statistic values
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| 404 | Example:
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| 405 | scan.set_unit('channel')
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| 406 | msk = scan.create_mask([100, 200], [500, 600])
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| 407 | scan.stats(stat='mean', mask=m)
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| 408 | """
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| 409 | if mask == None:
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| 410 | mask = []
|
|---|
| 411 | axes = ['Beam', 'IF', 'Pol', 'Time']
|
|---|
| 412 | if not self._check_ifs():
|
|---|
| 413 | raise ValueError("Cannot apply mask as the IFs have different "
|
|---|
| 414 | "number of channels. Please use setselection() "
|
|---|
| 415 | "to select individual IFs")
|
|---|
| 416 | rtnabc = False
|
|---|
| 417 | if stat.lower().endswith('_abc'): rtnabc = True
|
|---|
| 418 | getchan = False
|
|---|
| 419 | if stat.lower().startswith('min') or stat.lower().startswith('max'):
|
|---|
| 420 | chan = self._math._minmaxchan(self, mask, stat)
|
|---|
| 421 | getchan = True
|
|---|
| 422 | statvals = []
|
|---|
| 423 | if not rtnabc: statvals = self._math._stats(self, mask, stat)
|
|---|
| 424 |
|
|---|
| 425 | out = ''
|
|---|
| 426 | axes = []
|
|---|
| 427 | for i in range(self.nrow()):
|
|---|
| 428 | axis = []
|
|---|
| 429 | axis.append(self.getscan(i))
|
|---|
| 430 | axis.append(self.getbeam(i))
|
|---|
| 431 | axis.append(self.getif(i))
|
|---|
| 432 | axis.append(self.getpol(i))
|
|---|
| 433 | axis.append(self.getcycle(i))
|
|---|
| 434 | axes.append(axis)
|
|---|
| 435 | tm = self._gettime(i)
|
|---|
| 436 | src = self._getsourcename(i)
|
|---|
| 437 | refstr = ''
|
|---|
| 438 | statunit= ''
|
|---|
| 439 | if getchan:
|
|---|
| 440 | qx, qy = self.chan2data(rowno=i, chan=chan[i])
|
|---|
| 441 | if rtnabc:
|
|---|
| 442 | statvals.append(qx['value'])
|
|---|
| 443 | #refstr = '(value: %3.3f' % (qy['value'])+' ['+qy['unit']+'])'
|
|---|
| 444 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])'
|
|---|
| 445 | statunit= '['+qx['unit']+']'
|
|---|
| 446 | else:
|
|---|
| 447 | #refstr = '(@ %3.3f' % (qx['value'])+' ['+qx['unit']+'])'
|
|---|
| 448 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])'
|
|---|
| 449 | #statunit= ' ['+qy['unit']+']'
|
|---|
| 450 | out += 'Scan[%d] (%s) ' % (axis[0], src)
|
|---|
| 451 | out += 'Time[%s]:\n' % (tm)
|
|---|
| 452 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
|
|---|
| 453 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
|
|---|
| 454 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
|
|---|
| 455 | #out += '= %3.3f ' % (statvals[i]) +refstr+'\n'
|
|---|
| 456 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n'
|
|---|
| 457 | out += "--------------------------------------------------\n"
|
|---|
| 458 |
|
|---|
| 459 | if rcParams['verbose']:
|
|---|
| 460 | import os
|
|---|
| 461 | if os.environ.has_key( 'USER' ):
|
|---|
| 462 | usr=os.environ['USER']
|
|---|
| 463 | else:
|
|---|
| 464 | import commands
|
|---|
| 465 | usr=commands.getoutput( 'whoami' )
|
|---|
| 466 | tmpfile='/tmp/tmp_'+usr+'_casapy_asap_scantable_stats'
|
|---|
| 467 | f=open(tmpfile,'w')
|
|---|
| 468 | print >> f, "--------------------------------------------------"
|
|---|
| 469 | print >> f, " ", stat, statunit
|
|---|
| 470 | print >> f, "--------------------------------------------------"
|
|---|
| 471 | print >> f, out
|
|---|
| 472 | f.close()
|
|---|
| 473 | f=open(tmpfile,'r')
|
|---|
| 474 | x=f.readlines()
|
|---|
| 475 | f.close()
|
|---|
| 476 | for xx in x:
|
|---|
| 477 | asaplog.push( xx, False )
|
|---|
| 478 | print_log()
|
|---|
| 479 | #else:
|
|---|
| 480 | #retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'],
|
|---|
| 481 | # 'axes' : axes,
|
|---|
| 482 | # 'data': statvals}
|
|---|
| 483 | return statvals
|
|---|
| 484 |
|
|---|
| 485 | def chan2data(self, rowno=0, chan=0):
|
|---|
| 486 | """
|
|---|
| 487 | Returns channel/frequency/velocity and spectral value
|
|---|
| 488 | at an arbitrary row and channel in the scantable.
|
|---|
| 489 | Parameters:
|
|---|
| 490 | rowno: a row number in the scantable. Default is the
|
|---|
| 491 | first row, i.e. rowno=0
|
|---|
| 492 | chan: a channel in the scantable. Default is the first
|
|---|
| 493 | channel, i.e. pos=0
|
|---|
| 494 | """
|
|---|
| 495 | if isinstance(rowno, int) and isinstance(chan, int):
|
|---|
| 496 | qx = {'unit': self.get_unit(),
|
|---|
| 497 | 'value': self._getabcissa(rowno)[chan]}
|
|---|
| 498 | qy = {'unit': self.get_fluxunit(),
|
|---|
| 499 | 'value': self._getspectrum(rowno)[chan]}
|
|---|
| 500 | return qx, qy
|
|---|
| 501 |
|
|---|
| 502 | def stddev(self, mask=None):
|
|---|
| 503 | """
|
|---|
| 504 | Determine the standard deviation of the current beam/if/pol
|
|---|
| 505 | Takes a 'mask' as an optional parameter to specify which
|
|---|
| 506 | channels should be excluded.
|
|---|
| 507 | Parameters:
|
|---|
| 508 | mask: an optional mask specifying where the standard
|
|---|
| 509 | deviation should be determined.
|
|---|
| 510 |
|
|---|
| 511 | Example:
|
|---|
| 512 | scan.set_unit('channel')
|
|---|
| 513 | msk = scan.create_mask([100, 200], [500, 600])
|
|---|
| 514 | scan.stddev(mask=m)
|
|---|
| 515 | """
|
|---|
| 516 | return self.stats(stat='stddev', mask=mask);
|
|---|
| 517 |
|
|---|
| 518 |
|
|---|
| 519 | def get_column_names(self):
|
|---|
| 520 | """
|
|---|
| 521 | Return a list of column names, which can be used for selection.
|
|---|
| 522 | """
|
|---|
| 523 | return list(Scantable.get_column_names(self))
|
|---|
| 524 |
|
|---|
| 525 | def get_tsys(self):
|
|---|
| 526 | """
|
|---|
| 527 | Return the System temperatures.
|
|---|
| 528 | Returns:
|
|---|
| 529 | a list of Tsys values for the current selection
|
|---|
| 530 | """
|
|---|
| 531 |
|
|---|
| 532 | return self._row_callback(self._gettsys, "Tsys")
|
|---|
| 533 |
|
|---|
| 534 | def _row_callback(self, callback, label):
|
|---|
| 535 | axes = []
|
|---|
| 536 | axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno']
|
|---|
| 537 | out = ""
|
|---|
| 538 | outvec = []
|
|---|
| 539 | for i in range(self.nrow()):
|
|---|
| 540 | axis = []
|
|---|
| 541 | axis.append(self.getscan(i))
|
|---|
| 542 | axis.append(self.getbeam(i))
|
|---|
| 543 | axis.append(self.getif(i))
|
|---|
| 544 | axis.append(self.getpol(i))
|
|---|
| 545 | axis.append(self.getcycle(i))
|
|---|
| 546 | axes.append(axis)
|
|---|
| 547 | tm = self._gettime(i)
|
|---|
| 548 | src = self._getsourcename(i)
|
|---|
| 549 | out += 'Scan[%d] (%s) ' % (axis[0], src)
|
|---|
| 550 | out += 'Time[%s]:\n' % (tm)
|
|---|
| 551 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
|
|---|
| 552 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
|
|---|
| 553 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
|
|---|
| 554 | outvec.append(callback(i))
|
|---|
| 555 | out += '= %3.3f\n' % (outvec[i])
|
|---|
| 556 | out += "--------------------------------------------------\n"
|
|---|
| 557 | if rcParams['verbose']:
|
|---|
| 558 | asaplog.push("--------------------------------------------------")
|
|---|
| 559 | asaplog.push(" %s" % (label))
|
|---|
| 560 | asaplog.push("--------------------------------------------------")
|
|---|
| 561 | asaplog.push(out)
|
|---|
| 562 | print_log()
|
|---|
| 563 | # disabled because the vector seems more useful
|
|---|
| 564 | #retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
|
|---|
| 565 | return outvec
|
|---|
| 566 |
|
|---|
| 567 | def _get_column(self, callback, row=-1):
|
|---|
| 568 | """
|
|---|
| 569 | """
|
|---|
| 570 | if row == -1:
|
|---|
| 571 | return [callback(i) for i in range(self.nrow())]
|
|---|
| 572 | else:
|
|---|
| 573 | if 0 <= row < self.nrow():
|
|---|
| 574 | return callback(row)
|
|---|
| 575 |
|
|---|
| 576 |
|
|---|
| 577 | def get_time(self, row=-1, asdatetime=False):
|
|---|
| 578 | """
|
|---|
| 579 | Get a list of time stamps for the observations.
|
|---|
| 580 | Return a datetime object for each integration time stamp in the scantable.
|
|---|
| 581 | Parameters:
|
|---|
| 582 | row: row no of integration. Default -1 return all rows
|
|---|
| 583 | asdatetime: return values as datetime objects rather than strings
|
|---|
| 584 | Example:
|
|---|
| 585 | none
|
|---|
| 586 | """
|
|---|
| 587 | from time import strptime
|
|---|
| 588 | from datetime import datetime
|
|---|
| 589 | times = self._get_column(self._gettime, row)
|
|---|
| 590 | if not asdatetime:
|
|---|
| 591 | return times
|
|---|
| 592 | format = "%Y/%m/%d/%H:%M:%S"
|
|---|
| 593 | if isinstance(times, list):
|
|---|
| 594 | return [datetime(*strptime(i, format)[:6]) for i in times]
|
|---|
| 595 | else:
|
|---|
| 596 | return datetime(*strptime(times, format)[:6])
|
|---|
| 597 |
|
|---|
| 598 |
|
|---|
| 599 | def get_inttime(self, row=-1):
|
|---|
| 600 | """
|
|---|
| 601 | Get a list of integration times for the observations.
|
|---|
| 602 | Return a time in seconds for each integration in the scantable.
|
|---|
| 603 | Parameters:
|
|---|
| 604 | row: row no of integration. Default -1 return all rows.
|
|---|
| 605 | Example:
|
|---|
| 606 | none
|
|---|
| 607 | """
|
|---|
| 608 | return self._get_column(self._getinttime, row)
|
|---|
| 609 |
|
|---|
| 610 |
|
|---|
| 611 | def get_sourcename(self, row=-1):
|
|---|
| 612 | """
|
|---|
| 613 | Get a list source names for the observations.
|
|---|
| 614 | Return a string for each integration in the scantable.
|
|---|
| 615 | Parameters:
|
|---|
| 616 | row: row no of integration. Default -1 return all rows.
|
|---|
| 617 | Example:
|
|---|
| 618 | none
|
|---|
| 619 | """
|
|---|
| 620 | return self._get_column(self._getsourcename, row)
|
|---|
| 621 |
|
|---|
| 622 | def get_elevation(self, row=-1):
|
|---|
| 623 | """
|
|---|
| 624 | Get a list of elevations for the observations.
|
|---|
| 625 | Return a float for each integration in the scantable.
|
|---|
| 626 | Parameters:
|
|---|
| 627 | row: row no of integration. Default -1 return all rows.
|
|---|
| 628 | Example:
|
|---|
| 629 | none
|
|---|
| 630 | """
|
|---|
| 631 | return self._get_column(self._getelevation, row)
|
|---|
| 632 |
|
|---|
| 633 | def get_azimuth(self, row=-1):
|
|---|
| 634 | """
|
|---|
| 635 | Get a list of azimuths for the observations.
|
|---|
| 636 | Return a float for each integration in the scantable.
|
|---|
| 637 | Parameters:
|
|---|
| 638 | row: row no of integration. Default -1 return all rows.
|
|---|
| 639 | Example:
|
|---|
| 640 | none
|
|---|
| 641 | """
|
|---|
| 642 | return self._get_column(self._getazimuth, row)
|
|---|
| 643 |
|
|---|
| 644 | def get_parangle(self, row=-1):
|
|---|
| 645 | """
|
|---|
| 646 | Get a list of parallactic angles for the observations.
|
|---|
| 647 | Return a float for each integration in the scantable.
|
|---|
| 648 | Parameters:
|
|---|
| 649 | row: row no of integration. Default -1 return all rows.
|
|---|
| 650 | Example:
|
|---|
| 651 | none
|
|---|
| 652 | """
|
|---|
| 653 | return self._get_column(self._getparangle, row)
|
|---|
| 654 |
|
|---|
| 655 | def get_direction(self, row=-1):
|
|---|
| 656 | """
|
|---|
| 657 | Get a list of Positions on the sky (direction) for the observations.
|
|---|
| 658 | Return a float for each integration in the scantable.
|
|---|
| 659 | Parameters:
|
|---|
| 660 | row: row no of integration. Default -1 return all rows
|
|---|
| 661 | Example:
|
|---|
| 662 | none
|
|---|
| 663 | """
|
|---|
| 664 | return self._get_column(self._getdirection, row)
|
|---|
| 665 |
|
|---|
| 666 | def get_directionval(self, row=-1):
|
|---|
| 667 | """
|
|---|
| 668 | Get a list of Positions on the sky (direction) for the observations.
|
|---|
| 669 | Return a float for each integration in the scantable.
|
|---|
| 670 | Parameters:
|
|---|
| 671 | row: row no of integration. Default -1 return all rows
|
|---|
| 672 | Example:
|
|---|
| 673 | none
|
|---|
| 674 | """
|
|---|
| 675 | return self._get_column(self._getdirectionvec, row)
|
|---|
| 676 |
|
|---|
| 677 | def set_unit(self, unit='channel'):
|
|---|
| 678 | """
|
|---|
| 679 | Set the unit for all following operations on this scantable
|
|---|
| 680 | Parameters:
|
|---|
| 681 | unit: optional unit, default is 'channel'
|
|---|
| 682 | one of '*Hz', 'km/s', 'channel', ''
|
|---|
| 683 | """
|
|---|
| 684 | varlist = vars()
|
|---|
| 685 | if unit in ['', 'pixel', 'channel']:
|
|---|
| 686 | unit = ''
|
|---|
| 687 | inf = list(self._getcoordinfo())
|
|---|
| 688 | inf[0] = unit
|
|---|
| 689 | self._setcoordinfo(inf)
|
|---|
| 690 | self._add_history("set_unit", varlist)
|
|---|
| 691 |
|
|---|
| 692 | def set_instrument(self, instr):
|
|---|
| 693 | """
|
|---|
| 694 | Set the instrument for subsequent processing.
|
|---|
| 695 | Parameters:
|
|---|
| 696 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
|
|---|
| 697 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
|
|---|
| 698 | """
|
|---|
| 699 | self._setInstrument(instr)
|
|---|
| 700 | self._add_history("set_instument", vars())
|
|---|
| 701 | print_log()
|
|---|
| 702 |
|
|---|
| 703 | def set_feedtype(self, feedtype):
|
|---|
| 704 | """
|
|---|
| 705 | Overwrite the feed type, which might not be set correctly.
|
|---|
| 706 | Parameters:
|
|---|
| 707 | feedtype: 'linear' or 'circular'
|
|---|
| 708 | """
|
|---|
| 709 | self._setfeedtype(feedtype)
|
|---|
| 710 | self._add_history("set_feedtype", vars())
|
|---|
| 711 | print_log()
|
|---|
| 712 |
|
|---|
| 713 | def set_doppler(self, doppler='RADIO'):
|
|---|
| 714 | """
|
|---|
| 715 | Set the doppler for all following operations on this scantable.
|
|---|
| 716 | Parameters:
|
|---|
| 717 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
|
|---|
| 718 | """
|
|---|
| 719 | varlist = vars()
|
|---|
| 720 | inf = list(self._getcoordinfo())
|
|---|
| 721 | inf[2] = doppler
|
|---|
| 722 | self._setcoordinfo(inf)
|
|---|
| 723 | self._add_history("set_doppler", vars())
|
|---|
| 724 | print_log()
|
|---|
| 725 |
|
|---|
| 726 | def set_freqframe(self, frame=None):
|
|---|
| 727 | """
|
|---|
| 728 | Set the frame type of the Spectral Axis.
|
|---|
| 729 | Parameters:
|
|---|
| 730 | frame: an optional frame type, default 'LSRK'. Valid frames are:
|
|---|
| 731 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY',
|
|---|
| 732 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'
|
|---|
| 733 | Examples:
|
|---|
| 734 | scan.set_freqframe('BARY')
|
|---|
| 735 | """
|
|---|
| 736 | if frame is None: frame = rcParams['scantable.freqframe']
|
|---|
| 737 | varlist = vars()
|
|---|
| 738 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
|
|---|
| 739 | 'GEO', 'GALACTO', 'LGROUP', 'CMB']
|
|---|
| 740 |
|
|---|
| 741 | if frame in valid:
|
|---|
| 742 | inf = list(self._getcoordinfo())
|
|---|
| 743 | inf[1] = frame
|
|---|
| 744 | self._setcoordinfo(inf)
|
|---|
| 745 | self._add_history("set_freqframe", varlist)
|
|---|
| 746 | else:
|
|---|
| 747 | msg = "Please specify a valid freq type. Valid types are:\n", valid
|
|---|
| 748 | if rcParams['verbose']:
|
|---|
| 749 | #print msg
|
|---|
| 750 | asaplog.push( msg )
|
|---|
| 751 | print_log( 'ERROR' )
|
|---|
| 752 | else:
|
|---|
| 753 | raise TypeError(msg)
|
|---|
| 754 | print_log()
|
|---|
| 755 |
|
|---|
| 756 | def set_dirframe(self, frame=""):
|
|---|
| 757 | """
|
|---|
| 758 | Set the frame type of the Direction on the sky.
|
|---|
| 759 | Parameters:
|
|---|
| 760 | frame: an optional frame type, default ''. Valid frames are:
|
|---|
| 761 | 'J2000', 'B1950', 'GALACTIC'
|
|---|
| 762 | Examples:
|
|---|
| 763 | scan.set_dirframe('GALACTIC')
|
|---|
| 764 | """
|
|---|
| 765 | varlist = vars()
|
|---|
| 766 | try:
|
|---|
| 767 | Scantable.set_dirframe(self, frame)
|
|---|
| 768 | except RuntimeError, msg:
|
|---|
| 769 | if rcParams['verbose']:
|
|---|
| 770 | #print msg
|
|---|
| 771 | print_log()
|
|---|
| 772 | asaplog.push( msg.message )
|
|---|
| 773 | print_log( 'ERROR' )
|
|---|
| 774 | else:
|
|---|
| 775 | raise
|
|---|
| 776 | self._add_history("set_dirframe", varlist)
|
|---|
| 777 |
|
|---|
| 778 | def get_unit(self):
|
|---|
| 779 | """
|
|---|
| 780 | Get the default unit set in this scantable
|
|---|
| 781 | Returns:
|
|---|
| 782 | A unit string
|
|---|
| 783 | """
|
|---|
| 784 | inf = self._getcoordinfo()
|
|---|
| 785 | unit = inf[0]
|
|---|
| 786 | if unit == '': unit = 'channel'
|
|---|
| 787 | return unit
|
|---|
| 788 |
|
|---|
| 789 | def get_abcissa(self, rowno=0):
|
|---|
| 790 | """
|
|---|
| 791 | Get the abcissa in the current coordinate setup for the currently
|
|---|
| 792 | selected Beam/IF/Pol
|
|---|
| 793 | Parameters:
|
|---|
| 794 | rowno: an optional row number in the scantable. Default is the
|
|---|
| 795 | first row, i.e. rowno=0
|
|---|
| 796 | Returns:
|
|---|
| 797 | The abcissa values and the format string (as a dictionary)
|
|---|
| 798 | """
|
|---|
| 799 | abc = self._getabcissa(rowno)
|
|---|
| 800 | lbl = self._getabcissalabel(rowno)
|
|---|
| 801 | print_log()
|
|---|
| 802 | return abc, lbl
|
|---|
| 803 |
|
|---|
| 804 | def flag(self, mask=None, unflag=False):
|
|---|
| 805 | """
|
|---|
| 806 | Flag the selected data using an optional channel mask.
|
|---|
| 807 | Parameters:
|
|---|
| 808 | mask: an optional channel mask, created with create_mask. Default
|
|---|
| 809 | (no mask) is all channels.
|
|---|
| 810 | unflag: if True, unflag the data
|
|---|
| 811 | """
|
|---|
| 812 | varlist = vars()
|
|---|
| 813 | if mask is None:
|
|---|
| 814 | mask = []
|
|---|
| 815 | try:
|
|---|
| 816 | self._flag(mask, unflag)
|
|---|
| 817 | except RuntimeError, msg:
|
|---|
| 818 | if rcParams['verbose']:
|
|---|
| 819 | #print msg
|
|---|
| 820 | print_log()
|
|---|
| 821 | asaplog.push( msg.message )
|
|---|
| 822 | print_log( 'ERROR' )
|
|---|
| 823 | return
|
|---|
| 824 | else: raise
|
|---|
| 825 | self._add_history("flag", varlist)
|
|---|
| 826 |
|
|---|
| 827 | def flag_row(self, rows=[], unflag=False):
|
|---|
| 828 | """
|
|---|
| 829 | Flag the selected data in row-based manner.
|
|---|
| 830 | Parameters:
|
|---|
| 831 | rows: list of row numbers to be flagged. Default is no row (must be explicitly specified to execute row-based flagging).
|
|---|
| 832 | unflag: if True, unflag the data.
|
|---|
| 833 | """
|
|---|
| 834 | varlist = vars()
|
|---|
| 835 | try:
|
|---|
| 836 | self._flag_row(rows, unflag)
|
|---|
| 837 | except RuntimeError, msg:
|
|---|
| 838 | if rcParams['verbose']:
|
|---|
| 839 | print_log()
|
|---|
| 840 | asaplog.push(msg.message)
|
|---|
| 841 | print_log('ERROR')
|
|---|
| 842 | return
|
|---|
| 843 | else: raise
|
|---|
| 844 | self._add_history("flag_row", varlist)
|
|---|
| 845 |
|
|---|
| 846 |
|
|---|
| 847 | def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None):
|
|---|
| 848 | """
|
|---|
| 849 | Flag the data in 'lag' space by providing a frequency to remove.
|
|---|
| 850 | Flagged data in the scantable gets set to 0.0 before the fft.
|
|---|
| 851 | No taper is applied.
|
|---|
| 852 | Parameters:
|
|---|
| 853 | frequency: the frequency (really a period within the bandwidth)
|
|---|
| 854 | to remove
|
|---|
| 855 | width: the width of the frequency to remove, to remove a
|
|---|
| 856 | range of frequencies around the centre.
|
|---|
| 857 | unit: the frequency unit (default "GHz")
|
|---|
| 858 | Notes:
|
|---|
| 859 | It is recommended to flag edges of the band or strong
|
|---|
| 860 | signals beforehand.
|
|---|
| 861 | """
|
|---|
| 862 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 863 | self._math._setinsitu(insitu)
|
|---|
| 864 | varlist = vars()
|
|---|
| 865 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. }
|
|---|
| 866 | if not base.has_key(unit):
|
|---|
| 867 | raise ValueError("%s is not a valid unit." % unit)
|
|---|
| 868 | try:
|
|---|
| 869 | s = scantable(self._math._lag_flag(self, frequency*base[unit],
|
|---|
| 870 | width*base[unit]))
|
|---|
| 871 | except RuntimeError, msg:
|
|---|
| 872 | if rcParams['verbose']:
|
|---|
| 873 | #print msg
|
|---|
| 874 | print_log()
|
|---|
| 875 | asaplog.push( msg.message )
|
|---|
| 876 | print_log( 'ERROR' )
|
|---|
| 877 | return
|
|---|
| 878 | else: raise
|
|---|
| 879 | s._add_history("lag_flag", varlist)
|
|---|
| 880 | print_log()
|
|---|
| 881 | if insitu:
|
|---|
| 882 | self._assign(s)
|
|---|
| 883 | else:
|
|---|
| 884 | return s
|
|---|
| 885 |
|
|---|
| 886 |
|
|---|
| 887 | def create_mask(self, *args, **kwargs):
|
|---|
| 888 | """
|
|---|
| 889 | Compute and return a mask based on [min, max] windows.
|
|---|
| 890 | The specified windows are to be INCLUDED, when the mask is
|
|---|
| 891 | applied.
|
|---|
| 892 | Parameters:
|
|---|
| 893 | [min, max], [min2, max2], ...
|
|---|
| 894 | Pairs of start/end points (inclusive)specifying the regions
|
|---|
| 895 | to be masked
|
|---|
| 896 | invert: optional argument. If specified as True,
|
|---|
| 897 | return an inverted mask, i.e. the regions
|
|---|
| 898 | specified are EXCLUDED
|
|---|
| 899 | row: create the mask using the specified row for
|
|---|
| 900 | unit conversions, default is row=0
|
|---|
| 901 | only necessary if frequency varies over rows.
|
|---|
| 902 | Example:
|
|---|
| 903 | scan.set_unit('channel')
|
|---|
| 904 | a)
|
|---|
| 905 | msk = scan.create_mask([400, 500], [800, 900])
|
|---|
| 906 | # masks everything outside 400 and 500
|
|---|
| 907 | # and 800 and 900 in the unit 'channel'
|
|---|
| 908 |
|
|---|
| 909 | b)
|
|---|
| 910 | msk = scan.create_mask([400, 500], [800, 900], invert=True)
|
|---|
| 911 | # masks the regions between 400 and 500
|
|---|
| 912 | # and 800 and 900 in the unit 'channel'
|
|---|
| 913 | c)
|
|---|
| 914 | mask only channel 400
|
|---|
| 915 | msk = scan.create_mask([400, 400])
|
|---|
| 916 | """
|
|---|
| 917 | row = 0
|
|---|
| 918 | if kwargs.has_key("row"):
|
|---|
| 919 | row = kwargs.get("row")
|
|---|
| 920 | data = self._getabcissa(row)
|
|---|
| 921 | u = self._getcoordinfo()[0]
|
|---|
| 922 | if rcParams['verbose']:
|
|---|
| 923 | if u == "": u = "channel"
|
|---|
| 924 | msg = "The current mask window unit is %s" % u
|
|---|
| 925 | i = self._check_ifs()
|
|---|
| 926 | if not i:
|
|---|
| 927 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
|---|
| 928 | asaplog.push(msg)
|
|---|
| 929 | n = self.nchan()
|
|---|
| 930 | msk = _n_bools(n, False)
|
|---|
| 931 | # test if args is a 'list' or a 'normal *args - UGLY!!!
|
|---|
| 932 |
|
|---|
| 933 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
|
|---|
| 934 | and args or args[0]
|
|---|
| 935 | for window in ws:
|
|---|
| 936 | if (len(window) != 2 or window[0] > window[1] ):
|
|---|
| 937 | raise TypeError("A window needs to be defined as [min, max]")
|
|---|
| 938 | for i in range(n):
|
|---|
| 939 | if data[i] >= window[0] and data[i] <= window[1]:
|
|---|
| 940 | msk[i] = True
|
|---|
| 941 | if kwargs.has_key('invert'):
|
|---|
| 942 | if kwargs.get('invert'):
|
|---|
| 943 | msk = mask_not(msk)
|
|---|
| 944 | print_log()
|
|---|
| 945 | return msk
|
|---|
| 946 |
|
|---|
| 947 | def get_masklist(self, mask=None, row=0):
|
|---|
| 948 | """
|
|---|
| 949 | Compute and return a list of mask windows, [min, max].
|
|---|
| 950 | Parameters:
|
|---|
| 951 | mask: channel mask, created with create_mask.
|
|---|
| 952 | row: calcutate the masklist using the specified row
|
|---|
| 953 | for unit conversions, default is row=0
|
|---|
| 954 | only necessary if frequency varies over rows.
|
|---|
| 955 | Returns:
|
|---|
| 956 | [min, max], [min2, max2], ...
|
|---|
| 957 | Pairs of start/end points (inclusive)specifying
|
|---|
| 958 | the masked regions
|
|---|
| 959 | """
|
|---|
| 960 | if not (isinstance(mask,list) or isinstance(mask, tuple)):
|
|---|
| 961 | raise TypeError("The mask should be list or tuple.")
|
|---|
| 962 | if len(mask) < 2:
|
|---|
| 963 | raise TypeError("The mask elements should be > 1")
|
|---|
| 964 | if self.nchan() != len(mask):
|
|---|
| 965 | msg = "Number of channels in scantable != number of mask elements"
|
|---|
| 966 | raise TypeError(msg)
|
|---|
| 967 | data = self._getabcissa(row)
|
|---|
| 968 | u = self._getcoordinfo()[0]
|
|---|
| 969 | if rcParams['verbose']:
|
|---|
| 970 | if u == "": u = "channel"
|
|---|
| 971 | msg = "The current mask window unit is %s" % u
|
|---|
| 972 | i = self._check_ifs()
|
|---|
| 973 | if not i:
|
|---|
| 974 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
|---|
| 975 | asaplog.push(msg)
|
|---|
| 976 | masklist=[]
|
|---|
| 977 | ist, ien = None, None
|
|---|
| 978 | ist, ien=self.get_mask_indices(mask)
|
|---|
| 979 | if ist is not None and ien is not None:
|
|---|
| 980 | for i in xrange(len(ist)):
|
|---|
| 981 | range=[data[ist[i]],data[ien[i]]]
|
|---|
| 982 | range.sort()
|
|---|
| 983 | masklist.append([range[0],range[1]])
|
|---|
| 984 | return masklist
|
|---|
| 985 |
|
|---|
| 986 | def get_mask_indices(self, mask=None):
|
|---|
| 987 | """
|
|---|
| 988 | Compute and Return lists of mask start indices and mask end indices.
|
|---|
| 989 | Parameters:
|
|---|
| 990 | mask: channel mask, created with create_mask.
|
|---|
| 991 | Returns:
|
|---|
| 992 | List of mask start indices and that of mask end indices,
|
|---|
| 993 | i.e., [istart1,istart2,....], [iend1,iend2,....].
|
|---|
| 994 | """
|
|---|
| 995 | if not (isinstance(mask,list) or isinstance(mask, tuple)):
|
|---|
| 996 | raise TypeError("The mask should be list or tuple.")
|
|---|
| 997 | if len(mask) < 2:
|
|---|
| 998 | raise TypeError("The mask elements should be > 1")
|
|---|
| 999 | istart=[]
|
|---|
| 1000 | iend=[]
|
|---|
| 1001 | if mask[0]: istart.append(0)
|
|---|
| 1002 | for i in range(len(mask)-1):
|
|---|
| 1003 | if not mask[i] and mask[i+1]:
|
|---|
| 1004 | istart.append(i+1)
|
|---|
| 1005 | elif mask[i] and not mask[i+1]:
|
|---|
| 1006 | iend.append(i)
|
|---|
| 1007 | if mask[len(mask)-1]: iend.append(len(mask)-1)
|
|---|
| 1008 | if len(istart) != len(iend):
|
|---|
| 1009 | raise RuntimeError("Numbers of mask start != mask end.")
|
|---|
| 1010 | for i in range(len(istart)):
|
|---|
| 1011 | if istart[i] > iend[i]:
|
|---|
| 1012 | raise RuntimeError("Mask start index > mask end index")
|
|---|
| 1013 | break
|
|---|
| 1014 | return istart,iend
|
|---|
| 1015 |
|
|---|
| 1016 | # def get_restfreqs(self):
|
|---|
| 1017 | # """
|
|---|
| 1018 | # Get the restfrequency(s) stored in this scantable.
|
|---|
| 1019 | # The return value(s) are always of unit 'Hz'
|
|---|
| 1020 | # Parameters:
|
|---|
| 1021 | # none
|
|---|
| 1022 | # Returns:
|
|---|
| 1023 | # a list of doubles
|
|---|
| 1024 | # """
|
|---|
| 1025 | # return list(self._getrestfreqs())
|
|---|
| 1026 |
|
|---|
| 1027 | def get_restfreqs(self, ids=None):
|
|---|
| 1028 | """
|
|---|
| 1029 | Get the restfrequency(s) stored in this scantable.
|
|---|
| 1030 | The return value(s) are always of unit 'Hz'
|
|---|
| 1031 | Parameters:
|
|---|
| 1032 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to
|
|---|
| 1033 | be retrieved
|
|---|
| 1034 | Returns:
|
|---|
| 1035 | dictionary containing ids and a list of doubles for each id
|
|---|
| 1036 | """
|
|---|
| 1037 | if ids is None:
|
|---|
| 1038 | rfreqs={}
|
|---|
| 1039 | idlist = self.getmolnos()
|
|---|
| 1040 | for i in idlist:
|
|---|
| 1041 | rfreqs[i]=list(self._getrestfreqs(i))
|
|---|
| 1042 | return rfreqs
|
|---|
| 1043 | else:
|
|---|
| 1044 | if type(ids)==list or type(ids)==tuple:
|
|---|
| 1045 | rfreqs={}
|
|---|
| 1046 | for i in ids:
|
|---|
| 1047 | rfreqs[i]=list(self._getrestfreqs(i))
|
|---|
| 1048 | return rfreqs
|
|---|
| 1049 | else:
|
|---|
| 1050 | return list(self._getrestfreqs(ids))
|
|---|
| 1051 | #return list(self._getrestfreqs(ids))
|
|---|
| 1052 |
|
|---|
| 1053 | def set_restfreqs(self, freqs=None, unit='Hz'):
|
|---|
| 1054 | """
|
|---|
| 1055 | ********NEED TO BE UPDATED begin************
|
|---|
| 1056 | Set or replace the restfrequency specified and
|
|---|
| 1057 | If the 'freqs' argument holds a scalar,
|
|---|
| 1058 | then that rest frequency will be applied to all the selected
|
|---|
| 1059 | data. If the 'freqs' argument holds
|
|---|
| 1060 | a vector, then it MUST be of equal or smaller length than
|
|---|
| 1061 | the number of IFs (and the available restfrequencies will be
|
|---|
| 1062 | replaced by this vector). In this case, *all* data have
|
|---|
| 1063 | the restfrequency set per IF according
|
|---|
| 1064 | to the corresponding value you give in the 'freqs' vector.
|
|---|
| 1065 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
|
|---|
| 1066 | IF 1 gets restfreq 2e9.
|
|---|
| 1067 | ********NEED TO BE UPDATED end************
|
|---|
| 1068 | You can also specify the frequencies via a linecatalog.
|
|---|
| 1069 |
|
|---|
| 1070 | Parameters:
|
|---|
| 1071 | freqs: list of rest frequency values or string idenitfiers
|
|---|
| 1072 | unit: unit for rest frequency (default 'Hz')
|
|---|
| 1073 |
|
|---|
| 1074 | Example:
|
|---|
| 1075 | # set the given restfrequency for the all currently selected IFs
|
|---|
| 1076 | scan.set_restfreqs(freqs=1.4e9)
|
|---|
| 1077 | # set multiple restfrequencies to all the selected data
|
|---|
| 1078 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9])
|
|---|
| 1079 | # If the number of IFs in the data is >= 2 the IF0 gets the first
|
|---|
| 1080 | # value IF1 the second... NOTE that freqs needs to be
|
|---|
| 1081 | # specified in list of list (e.g. [[],[],...] ).
|
|---|
| 1082 | scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]])
|
|---|
| 1083 | #set the given restfrequency for the whole table (by name)
|
|---|
| 1084 | scan.set_restfreqs(freqs="OH1667")
|
|---|
| 1085 |
|
|---|
| 1086 | Note:
|
|---|
| 1087 | To do more sophisticate Restfrequency setting, e.g. on a
|
|---|
| 1088 | source and IF basis, use scantable.set_selection() before using
|
|---|
| 1089 | this function.
|
|---|
| 1090 | # provide your scantable is call scan
|
|---|
| 1091 | selection = selector()
|
|---|
| 1092 | selection.set_name("ORION*")
|
|---|
| 1093 | selection.set_ifs([1])
|
|---|
| 1094 | scan.set_selection(selection)
|
|---|
| 1095 | scan.set_restfreqs(freqs=86.6e9)
|
|---|
| 1096 |
|
|---|
| 1097 | """
|
|---|
| 1098 | varlist = vars()
|
|---|
| 1099 | from asap import linecatalog
|
|---|
| 1100 | # simple value
|
|---|
| 1101 | if isinstance(freqs, int) or isinstance(freqs, float):
|
|---|
| 1102 | # TT mod
|
|---|
| 1103 | #self._setrestfreqs(freqs, "",unit)
|
|---|
| 1104 | self._setrestfreqs([freqs], [""],unit)
|
|---|
| 1105 | # list of values
|
|---|
| 1106 | elif isinstance(freqs, list) or isinstance(freqs, tuple):
|
|---|
| 1107 | # list values are scalars
|
|---|
| 1108 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
|
|---|
| 1109 | self._setrestfreqs(freqs, [""],unit)
|
|---|
| 1110 | # list values are tuples, (value, name)
|
|---|
| 1111 | elif isinstance(freqs[-1], dict):
|
|---|
| 1112 | #sel = selector()
|
|---|
| 1113 | #savesel = self._getselection()
|
|---|
| 1114 | #iflist = self.getifnos()
|
|---|
| 1115 | #for i in xrange(len(freqs)):
|
|---|
| 1116 | # sel.set_ifs(iflist[i])
|
|---|
| 1117 | # self._setselection(sel)
|
|---|
| 1118 | # self._setrestfreqs(freqs[i], "",unit)
|
|---|
| 1119 | #self._setselection(savesel)
|
|---|
| 1120 | self._setrestfreqs(freqs["value"],
|
|---|
| 1121 | freqs["name"], "MHz")
|
|---|
| 1122 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple):
|
|---|
| 1123 | sel = selector()
|
|---|
| 1124 | savesel = self._getselection()
|
|---|
| 1125 | iflist = self.getifnos()
|
|---|
| 1126 | if len(freqs)>len(iflist):
|
|---|
| 1127 | raise ValueError("number of elements in list of list exeeds the current IF selections")
|
|---|
| 1128 | for i in xrange(len(freqs)):
|
|---|
| 1129 | sel.set_ifs(iflist[i])
|
|---|
| 1130 | self._setselection(sel)
|
|---|
| 1131 | self._setrestfreqs(freqs[i]["value"],
|
|---|
| 1132 | freqs[i]["name"], "MHz")
|
|---|
| 1133 | self._setselection(savesel)
|
|---|
| 1134 | # freqs are to be taken from a linecatalog
|
|---|
| 1135 | elif isinstance(freqs, linecatalog):
|
|---|
| 1136 | sel = selector()
|
|---|
| 1137 | savesel = self._getselection()
|
|---|
| 1138 | for i in xrange(freqs.nrow()):
|
|---|
| 1139 | sel.set_ifs(iflist[i])
|
|---|
| 1140 | self._setselection(sel)
|
|---|
| 1141 | self._setrestfreqs(freqs.get_frequency(i),
|
|---|
| 1142 | freqs.get_name(i), "MHz")
|
|---|
| 1143 | # ensure that we are not iterating past nIF
|
|---|
| 1144 | if i == self.nif()-1: break
|
|---|
| 1145 | self._setselection(savesel)
|
|---|
| 1146 | else:
|
|---|
| 1147 | return
|
|---|
| 1148 | self._add_history("set_restfreqs", varlist)
|
|---|
| 1149 |
|
|---|
| 1150 | def shift_refpix(self, delta):
|
|---|
| 1151 | """
|
|---|
| 1152 | Shift the reference pixel of the Spectra Coordinate by an
|
|---|
| 1153 | integer amount.
|
|---|
| 1154 | Parameters:
|
|---|
| 1155 | delta: the amount to shift by
|
|---|
| 1156 | Note:
|
|---|
| 1157 | Be careful using this with broadband data.
|
|---|
| 1158 | """
|
|---|
| 1159 | Scantable.shift(self, delta)
|
|---|
| 1160 |
|
|---|
| 1161 | def history(self, filename=None):
|
|---|
| 1162 | """
|
|---|
| 1163 | Print the history. Optionally to a file.
|
|---|
| 1164 | Parameters:
|
|---|
| 1165 | filename: The name of the file to save the history to.
|
|---|
| 1166 | """
|
|---|
| 1167 | hist = list(self._gethistory())
|
|---|
| 1168 | out = "-"*80
|
|---|
| 1169 | for h in hist:
|
|---|
| 1170 | if h.startswith("---"):
|
|---|
| 1171 | out += "\n"+h
|
|---|
| 1172 | else:
|
|---|
| 1173 | items = h.split("##")
|
|---|
| 1174 | date = items[0]
|
|---|
| 1175 | func = items[1]
|
|---|
| 1176 | items = items[2:]
|
|---|
| 1177 | out += "\n"+date+"\n"
|
|---|
| 1178 | out += "Function: %s\n Parameters:" % (func)
|
|---|
| 1179 | for i in items:
|
|---|
| 1180 | s = i.split("=")
|
|---|
| 1181 | out += "\n %s = %s" % (s[0], s[1])
|
|---|
| 1182 | out += "\n"+"-"*80
|
|---|
| 1183 | if filename is not None:
|
|---|
| 1184 | if filename is "":
|
|---|
| 1185 | filename = 'scantable_history.txt'
|
|---|
| 1186 | import os
|
|---|
| 1187 | filename = os.path.expandvars(os.path.expanduser(filename))
|
|---|
| 1188 | if not os.path.isdir(filename):
|
|---|
| 1189 | data = open(filename, 'w')
|
|---|
| 1190 | data.write(out)
|
|---|
| 1191 | data.close()
|
|---|
| 1192 | else:
|
|---|
| 1193 | msg = "Illegal file name '%s'." % (filename)
|
|---|
| 1194 | if rcParams['verbose']:
|
|---|
| 1195 | #print msg
|
|---|
| 1196 | asaplog.push( msg )
|
|---|
| 1197 | print_log( 'ERROR' )
|
|---|
| 1198 | else:
|
|---|
| 1199 | raise IOError(msg)
|
|---|
| 1200 | if rcParams['verbose']:
|
|---|
| 1201 | try:
|
|---|
| 1202 | from IPython.genutils import page as pager
|
|---|
| 1203 | except ImportError:
|
|---|
| 1204 | from pydoc import pager
|
|---|
| 1205 | pager(out)
|
|---|
| 1206 | else:
|
|---|
| 1207 | return out
|
|---|
| 1208 | return
|
|---|
| 1209 | #
|
|---|
| 1210 | # Maths business
|
|---|
| 1211 | #
|
|---|
| 1212 |
|
|---|
| 1213 | def average_time(self, mask=None, scanav=False, weight='tint', align=False):
|
|---|
| 1214 | """
|
|---|
| 1215 | Return the (time) weighted average of a scan.
|
|---|
| 1216 | Note:
|
|---|
| 1217 | in channels only - align if necessary
|
|---|
| 1218 | Parameters:
|
|---|
| 1219 | mask: an optional mask (only used for 'var' and 'tsys'
|
|---|
| 1220 | weighting)
|
|---|
| 1221 | scanav: True averages each scan separately
|
|---|
| 1222 | False (default) averages all scans together,
|
|---|
| 1223 | weight: Weighting scheme.
|
|---|
| 1224 | 'none' (mean no weight)
|
|---|
| 1225 | 'var' (1/var(spec) weighted)
|
|---|
| 1226 | 'tsys' (1/Tsys**2 weighted)
|
|---|
| 1227 | 'tint' (integration time weighted)
|
|---|
| 1228 | 'tintsys' (Tint/Tsys**2)
|
|---|
| 1229 | 'median' ( median averaging)
|
|---|
| 1230 | The default is 'tint'
|
|---|
| 1231 | align: align the spectra in velocity before averaging. It takes
|
|---|
| 1232 | the time of the first spectrum as reference time.
|
|---|
| 1233 | Example:
|
|---|
| 1234 | # time average the scantable without using a mask
|
|---|
| 1235 | newscan = scan.average_time()
|
|---|
| 1236 | """
|
|---|
| 1237 | varlist = vars()
|
|---|
| 1238 | if weight is None: weight = 'TINT'
|
|---|
| 1239 | if mask is None: mask = ()
|
|---|
| 1240 | if scanav: scanav = "SCAN"
|
|---|
| 1241 | else: scanav = "NONE"
|
|---|
| 1242 | scan = (self, )
|
|---|
| 1243 | try:
|
|---|
| 1244 | if align:
|
|---|
| 1245 | scan = (self.freq_align(insitu=False), )
|
|---|
| 1246 | s = None
|
|---|
| 1247 | if weight.upper() == 'MEDIAN':
|
|---|
| 1248 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
|
|---|
| 1249 | scanav))
|
|---|
| 1250 | else:
|
|---|
| 1251 | s = scantable(self._math._average(scan, mask, weight.upper(),
|
|---|
| 1252 | scanav))
|
|---|
| 1253 | except RuntimeError, msg:
|
|---|
| 1254 | if rcParams['verbose']:
|
|---|
| 1255 | #print msg
|
|---|
| 1256 | print_log()
|
|---|
| 1257 | asaplog.push( msg.message )
|
|---|
| 1258 | print_log( 'ERROR' )
|
|---|
| 1259 | return
|
|---|
| 1260 | else: raise
|
|---|
| 1261 | s._add_history("average_time", varlist)
|
|---|
| 1262 | print_log()
|
|---|
| 1263 | return s
|
|---|
| 1264 |
|
|---|
| 1265 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
|
|---|
| 1266 | """
|
|---|
| 1267 | Return a scan where all spectra are converted to either
|
|---|
| 1268 | Jansky or Kelvin depending upon the flux units of the scan table.
|
|---|
| 1269 | By default the function tries to look the values up internally.
|
|---|
| 1270 | If it can't find them (or if you want to over-ride), you must
|
|---|
| 1271 | specify EITHER jyperk OR eta (and D which it will try to look up
|
|---|
| 1272 | also if you don't set it). jyperk takes precedence if you set both.
|
|---|
| 1273 | Parameters:
|
|---|
| 1274 | jyperk: the Jy / K conversion factor
|
|---|
| 1275 | eta: the aperture efficiency
|
|---|
| 1276 | d: the geomtric diameter (metres)
|
|---|
| 1277 | insitu: if False a new scantable is returned.
|
|---|
| 1278 | Otherwise, the scaling is done in-situ
|
|---|
| 1279 | The default is taken from .asaprc (False)
|
|---|
| 1280 | """
|
|---|
| 1281 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1282 | self._math._setinsitu(insitu)
|
|---|
| 1283 | varlist = vars()
|
|---|
| 1284 | if jyperk is None: jyperk = -1.0
|
|---|
| 1285 | if d is None: d = -1.0
|
|---|
| 1286 | if eta is None: eta = -1.0
|
|---|
| 1287 | s = scantable(self._math._convertflux(self, d, eta, jyperk))
|
|---|
| 1288 | s._add_history("convert_flux", varlist)
|
|---|
| 1289 | print_log()
|
|---|
| 1290 | if insitu: self._assign(s)
|
|---|
| 1291 | else: return s
|
|---|
| 1292 |
|
|---|
| 1293 | def gain_el(self, poly=None, filename="", method="linear", insitu=None):
|
|---|
| 1294 | """
|
|---|
| 1295 | Return a scan after applying a gain-elevation correction.
|
|---|
| 1296 | The correction can be made via either a polynomial or a
|
|---|
| 1297 | table-based interpolation (and extrapolation if necessary).
|
|---|
| 1298 | You specify polynomial coefficients, an ascii table or neither.
|
|---|
| 1299 | If you specify neither, then a polynomial correction will be made
|
|---|
| 1300 | with built in coefficients known for certain telescopes (an error
|
|---|
| 1301 | will occur if the instrument is not known).
|
|---|
| 1302 | The data and Tsys are *divided* by the scaling factors.
|
|---|
| 1303 | Parameters:
|
|---|
| 1304 | poly: Polynomial coefficients (default None) to compute a
|
|---|
| 1305 | gain-elevation correction as a function of
|
|---|
| 1306 | elevation (in degrees).
|
|---|
| 1307 | filename: The name of an ascii file holding correction factors.
|
|---|
| 1308 | The first row of the ascii file must give the column
|
|---|
| 1309 | names and these MUST include columns
|
|---|
| 1310 | "ELEVATION" (degrees) and "FACTOR" (multiply data
|
|---|
| 1311 | by this) somewhere.
|
|---|
| 1312 | The second row must give the data type of the
|
|---|
| 1313 | column. Use 'R' for Real and 'I' for Integer.
|
|---|
| 1314 | An example file would be
|
|---|
| 1315 | (actual factors are arbitrary) :
|
|---|
| 1316 |
|
|---|
| 1317 | TIME ELEVATION FACTOR
|
|---|
| 1318 | R R R
|
|---|
| 1319 | 0.1 0 0.8
|
|---|
| 1320 | 0.2 20 0.85
|
|---|
| 1321 | 0.3 40 0.9
|
|---|
| 1322 | 0.4 60 0.85
|
|---|
| 1323 | 0.5 80 0.8
|
|---|
| 1324 | 0.6 90 0.75
|
|---|
| 1325 | method: Interpolation method when correcting from a table.
|
|---|
| 1326 | Values are "nearest", "linear" (default), "cubic"
|
|---|
| 1327 | and "spline"
|
|---|
| 1328 | insitu: if False a new scantable is returned.
|
|---|
| 1329 | Otherwise, the scaling is done in-situ
|
|---|
| 1330 | The default is taken from .asaprc (False)
|
|---|
| 1331 | """
|
|---|
| 1332 |
|
|---|
| 1333 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1334 | self._math._setinsitu(insitu)
|
|---|
| 1335 | varlist = vars()
|
|---|
| 1336 | if poly is None:
|
|---|
| 1337 | poly = ()
|
|---|
| 1338 | from os.path import expandvars
|
|---|
| 1339 | filename = expandvars(filename)
|
|---|
| 1340 | s = scantable(self._math._gainel(self, poly, filename, method))
|
|---|
| 1341 | s._add_history("gain_el", varlist)
|
|---|
| 1342 | print_log()
|
|---|
| 1343 | if insitu: self._assign(s)
|
|---|
| 1344 | else: return s
|
|---|
| 1345 |
|
|---|
| 1346 | def freq_align(self, reftime=None, method='cubic', insitu=None):
|
|---|
| 1347 | """
|
|---|
| 1348 | Return a scan where all rows have been aligned in frequency/velocity.
|
|---|
| 1349 | The alignment frequency frame (e.g. LSRK) is that set by function
|
|---|
| 1350 | set_freqframe.
|
|---|
| 1351 | Parameters:
|
|---|
| 1352 | reftime: reference time to align at. By default, the time of
|
|---|
| 1353 | the first row of data is used.
|
|---|
| 1354 | method: Interpolation method for regridding the spectra.
|
|---|
| 1355 | Choose from "nearest", "linear", "cubic" (default)
|
|---|
| 1356 | and "spline"
|
|---|
| 1357 | insitu: if False a new scantable is returned.
|
|---|
| 1358 | Otherwise, the scaling is done in-situ
|
|---|
| 1359 | The default is taken from .asaprc (False)
|
|---|
| 1360 | """
|
|---|
| 1361 | if insitu is None: insitu = rcParams["insitu"]
|
|---|
| 1362 | self._math._setinsitu(insitu)
|
|---|
| 1363 | varlist = vars()
|
|---|
| 1364 | if reftime is None: reftime = ""
|
|---|
| 1365 | s = scantable(self._math._freq_align(self, reftime, method))
|
|---|
| 1366 | s._add_history("freq_align", varlist)
|
|---|
| 1367 | print_log()
|
|---|
| 1368 | if insitu: self._assign(s)
|
|---|
| 1369 | else: return s
|
|---|
| 1370 |
|
|---|
| 1371 | def opacity(self, tau, insitu=None):
|
|---|
| 1372 | """
|
|---|
| 1373 | Apply an opacity correction. The data
|
|---|
| 1374 | and Tsys are multiplied by the correction factor.
|
|---|
| 1375 | Parameters:
|
|---|
| 1376 | tau: Opacity from which the correction factor is
|
|---|
| 1377 | exp(tau*ZD)
|
|---|
| 1378 | where ZD is the zenith-distance
|
|---|
| 1379 | insitu: if False a new scantable is returned.
|
|---|
| 1380 | Otherwise, the scaling is done in-situ
|
|---|
| 1381 | The default is taken from .asaprc (False)
|
|---|
| 1382 | """
|
|---|
| 1383 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1384 | self._math._setinsitu(insitu)
|
|---|
| 1385 | varlist = vars()
|
|---|
| 1386 | s = scantable(self._math._opacity(self, tau))
|
|---|
| 1387 | s._add_history("opacity", varlist)
|
|---|
| 1388 | print_log()
|
|---|
| 1389 | if insitu: self._assign(s)
|
|---|
| 1390 | else: return s
|
|---|
| 1391 |
|
|---|
| 1392 | def bin(self, width=5, insitu=None):
|
|---|
| 1393 | """
|
|---|
| 1394 | Return a scan where all spectra have been binned up.
|
|---|
| 1395 | Parameters:
|
|---|
| 1396 | width: The bin width (default=5) in pixels
|
|---|
| 1397 | insitu: if False a new scantable is returned.
|
|---|
| 1398 | Otherwise, the scaling is done in-situ
|
|---|
| 1399 | The default is taken from .asaprc (False)
|
|---|
| 1400 | """
|
|---|
| 1401 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1402 | self._math._setinsitu(insitu)
|
|---|
| 1403 | varlist = vars()
|
|---|
| 1404 | s = scantable(self._math._bin(self, width))
|
|---|
| 1405 | s._add_history("bin", varlist)
|
|---|
| 1406 | print_log()
|
|---|
| 1407 | if insitu: self._assign(s)
|
|---|
| 1408 | else: return s
|
|---|
| 1409 |
|
|---|
| 1410 |
|
|---|
| 1411 | def resample(self, width=5, method='cubic', insitu=None):
|
|---|
| 1412 | """
|
|---|
| 1413 | Return a scan where all spectra have been binned up.
|
|---|
| 1414 |
|
|---|
| 1415 | Parameters:
|
|---|
| 1416 | width: The bin width (default=5) in pixels
|
|---|
| 1417 | method: Interpolation method when correcting from a table.
|
|---|
| 1418 | Values are "nearest", "linear", "cubic" (default)
|
|---|
| 1419 | and "spline"
|
|---|
| 1420 | insitu: if False a new scantable is returned.
|
|---|
| 1421 | Otherwise, the scaling is done in-situ
|
|---|
| 1422 | The default is taken from .asaprc (False)
|
|---|
| 1423 | """
|
|---|
| 1424 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1425 | self._math._setinsitu(insitu)
|
|---|
| 1426 | varlist = vars()
|
|---|
| 1427 | s = scantable(self._math._resample(self, method, width))
|
|---|
| 1428 | s._add_history("resample", varlist)
|
|---|
| 1429 | print_log()
|
|---|
| 1430 | if insitu: self._assign(s)
|
|---|
| 1431 | else: return s
|
|---|
| 1432 |
|
|---|
| 1433 |
|
|---|
| 1434 | def average_pol(self, mask=None, weight='none'):
|
|---|
| 1435 | """
|
|---|
| 1436 | Average the Polarisations together.
|
|---|
| 1437 | Parameters:
|
|---|
| 1438 | mask: An optional mask defining the region, where the
|
|---|
| 1439 | averaging will be applied. The output will have all
|
|---|
| 1440 | specified points masked.
|
|---|
| 1441 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
|---|
| 1442 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
|---|
| 1443 | """
|
|---|
| 1444 | varlist = vars()
|
|---|
| 1445 | if mask is None:
|
|---|
| 1446 | mask = ()
|
|---|
| 1447 | s = scantable(self._math._averagepol(self, mask, weight.upper()))
|
|---|
| 1448 | s._add_history("average_pol", varlist)
|
|---|
| 1449 | print_log()
|
|---|
| 1450 | return s
|
|---|
| 1451 |
|
|---|
| 1452 | def average_beam(self, mask=None, weight='none'):
|
|---|
| 1453 | """
|
|---|
| 1454 | Average the Beams together.
|
|---|
| 1455 | Parameters:
|
|---|
| 1456 | mask: An optional mask defining the region, where the
|
|---|
| 1457 | averaging will be applied. The output will have all
|
|---|
| 1458 | specified points masked.
|
|---|
| 1459 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
|---|
| 1460 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
|---|
| 1461 | """
|
|---|
| 1462 | varlist = vars()
|
|---|
| 1463 | if mask is None:
|
|---|
| 1464 | mask = ()
|
|---|
| 1465 | s = scantable(self._math._averagebeams(self, mask, weight.upper()))
|
|---|
| 1466 | s._add_history("average_beam", varlist)
|
|---|
| 1467 | print_log()
|
|---|
| 1468 | return s
|
|---|
| 1469 |
|
|---|
| 1470 | def convert_pol(self, poltype=None):
|
|---|
| 1471 | """
|
|---|
| 1472 | Convert the data to a different polarisation type.
|
|---|
| 1473 | Parameters:
|
|---|
| 1474 | poltype: The new polarisation type. Valid types are:
|
|---|
| 1475 | "linear", "stokes" and "circular"
|
|---|
| 1476 | """
|
|---|
| 1477 | varlist = vars()
|
|---|
| 1478 | try:
|
|---|
| 1479 | s = scantable(self._math._convertpol(self, poltype))
|
|---|
| 1480 | except RuntimeError, msg:
|
|---|
| 1481 | if rcParams['verbose']:
|
|---|
| 1482 | #print msg
|
|---|
| 1483 | print_log()
|
|---|
| 1484 | asaplog.push( msg.message )
|
|---|
| 1485 | print_log( 'ERROR' )
|
|---|
| 1486 | return
|
|---|
| 1487 | else:
|
|---|
| 1488 | raise
|
|---|
| 1489 | s._add_history("convert_pol", varlist)
|
|---|
| 1490 | print_log()
|
|---|
| 1491 | return s
|
|---|
| 1492 |
|
|---|
| 1493 | #def smooth(self, kernel="hanning", width=5.0, insitu=None):
|
|---|
| 1494 | def smooth(self, kernel="hanning", width=5.0, plot=False, insitu=None):
|
|---|
| 1495 | """
|
|---|
| 1496 | Smooth the spectrum by the specified kernel (conserving flux).
|
|---|
| 1497 | Parameters:
|
|---|
| 1498 | kernel: The type of smoothing kernel. Select from
|
|---|
| 1499 | 'hanning' (default), 'gaussian', 'boxcar' and
|
|---|
| 1500 | 'rmedian'
|
|---|
| 1501 | width: The width of the kernel in pixels. For hanning this is
|
|---|
| 1502 | ignored otherwise it defauls to 5 pixels.
|
|---|
| 1503 | For 'gaussian' it is the Full Width Half
|
|---|
| 1504 | Maximum. For 'boxcar' it is the full width.
|
|---|
| 1505 | For 'rmedian' it is the half width.
|
|---|
| 1506 | plot: plot the original and the smoothed spectra.
|
|---|
| 1507 | In this each indivual fit has to be approved, by
|
|---|
| 1508 | typing 'y' or 'n'
|
|---|
| 1509 | insitu: if False a new scantable is returned.
|
|---|
| 1510 | Otherwise, the scaling is done in-situ
|
|---|
| 1511 | The default is taken from .asaprc (False)
|
|---|
| 1512 | Example:
|
|---|
| 1513 | none
|
|---|
| 1514 | """
|
|---|
| 1515 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1516 | self._math._setinsitu(insitu)
|
|---|
| 1517 | varlist = vars()
|
|---|
| 1518 |
|
|---|
| 1519 | if plot: orgscan = self.copy()
|
|---|
| 1520 |
|
|---|
| 1521 | s = scantable(self._math._smooth(self, kernel.lower(), width))
|
|---|
| 1522 | s._add_history("smooth", varlist)
|
|---|
| 1523 |
|
|---|
| 1524 | if plot:
|
|---|
| 1525 | if rcParams['plotter.gui']:
|
|---|
| 1526 | from asap.asaplotgui import asaplotgui as asaplot
|
|---|
| 1527 | else:
|
|---|
| 1528 | from asap.asaplot import asaplot
|
|---|
| 1529 | self._p=asaplot()
|
|---|
| 1530 | self._p.set_panels()
|
|---|
| 1531 | ylab=s._get_ordinate_label()
|
|---|
| 1532 | #self._p.palette(0,["#777777","red"])
|
|---|
| 1533 | for r in xrange(s.nrow()):
|
|---|
| 1534 | xsm=s._getabcissa(r)
|
|---|
| 1535 | ysm=s._getspectrum(r)
|
|---|
| 1536 | xorg=orgscan._getabcissa(r)
|
|---|
| 1537 | yorg=orgscan._getspectrum(r)
|
|---|
| 1538 | self._p.clear()
|
|---|
| 1539 | self._p.hold()
|
|---|
| 1540 | self._p.set_axes('ylabel',ylab)
|
|---|
| 1541 | self._p.set_axes('xlabel',s._getabcissalabel(r))
|
|---|
| 1542 | self._p.set_axes('title',s._getsourcename(r))
|
|---|
| 1543 | self._p.set_line(label='Original',color="#777777")
|
|---|
| 1544 | self._p.plot(xorg,yorg)
|
|---|
| 1545 | self._p.set_line(label='Smoothed',color="red")
|
|---|
| 1546 | self._p.plot(xsm,ysm)
|
|---|
| 1547 | ### Ugly part for legend
|
|---|
| 1548 | for i in [0,1]:
|
|---|
| 1549 | self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]])
|
|---|
| 1550 | self._p.release()
|
|---|
| 1551 | ### Ugly part for legend
|
|---|
| 1552 | self._p.subplots[0]['lines']=[]
|
|---|
| 1553 | res = raw_input("Accept smoothing ([y]/n): ")
|
|---|
| 1554 | if res.upper() == 'N':
|
|---|
| 1555 | s._setspectrum(yorg, r)
|
|---|
| 1556 | self._p.unmap()
|
|---|
| 1557 | self._p = None
|
|---|
| 1558 | del orgscan
|
|---|
| 1559 |
|
|---|
| 1560 | print_log()
|
|---|
| 1561 | if insitu: self._assign(s)
|
|---|
| 1562 | else: return s
|
|---|
| 1563 |
|
|---|
| 1564 |
|
|---|
| 1565 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None):
|
|---|
| 1566 | """
|
|---|
| 1567 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 1568 | Parameters:
|
|---|
| 1569 | mask: an optional mask
|
|---|
| 1570 | order: the order of the polynomial (default is 0)
|
|---|
| 1571 | plot: plot the fit and the residual. In this each
|
|---|
| 1572 | indivual fit has to be approved, by typing 'y'
|
|---|
| 1573 | or 'n'
|
|---|
| 1574 | uselin: use linear polynomial fit
|
|---|
| 1575 | insitu: if False a new scantable is returned.
|
|---|
| 1576 | Otherwise, the scaling is done in-situ
|
|---|
| 1577 | The default is taken from .asaprc (False)
|
|---|
| 1578 | Example:
|
|---|
| 1579 | # return a scan baselined by a third order polynomial,
|
|---|
| 1580 | # not using a mask
|
|---|
| 1581 | bscan = scan.poly_baseline(order=3)
|
|---|
| 1582 | """
|
|---|
| 1583 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1584 | if not insitu:
|
|---|
| 1585 | workscan = self.copy()
|
|---|
| 1586 | else:
|
|---|
| 1587 | workscan = self
|
|---|
| 1588 | varlist = vars()
|
|---|
| 1589 | if mask is None:
|
|---|
| 1590 | mask = [True for i in xrange(self.nchan(-1))]
|
|---|
| 1591 |
|
|---|
| 1592 | from asap.asapfitter import fitter
|
|---|
| 1593 | try:
|
|---|
| 1594 | f = fitter()
|
|---|
| 1595 | if uselin:
|
|---|
| 1596 | f.set_function(lpoly=order)
|
|---|
| 1597 | else:
|
|---|
| 1598 | f.set_function(poly=order)
|
|---|
| 1599 |
|
|---|
| 1600 | rows = range(workscan.nrow())
|
|---|
| 1601 | if len(rows) > 0:
|
|---|
| 1602 | self.blpars = []
|
|---|
| 1603 |
|
|---|
| 1604 | for r in rows:
|
|---|
| 1605 | # take into account flagtra info (CAS-1434)
|
|---|
| 1606 | flagtra = workscan._getmask(r)
|
|---|
| 1607 | actualmask = mask[:]
|
|---|
| 1608 | if len(actualmask) == 0:
|
|---|
| 1609 | actualmask = list(flagtra[:])
|
|---|
| 1610 | else:
|
|---|
| 1611 | if len(actualmask) != len(flagtra):
|
|---|
| 1612 | raise RuntimeError, "Mask and flagtra have different length"
|
|---|
| 1613 | else:
|
|---|
| 1614 | for i in range(0, len(actualmask)):
|
|---|
| 1615 | actualmask[i] = actualmask[i] and flagtra[i]
|
|---|
| 1616 | f.set_scan(workscan, actualmask)
|
|---|
| 1617 | f.x = workscan._getabcissa(r)
|
|---|
| 1618 | f.y = workscan._getspectrum(r)
|
|---|
| 1619 | f.data = None
|
|---|
| 1620 | f.fit()
|
|---|
| 1621 | if plot:
|
|---|
| 1622 | f.plot(residual=True)
|
|---|
| 1623 | x = raw_input("Accept fit ( [y]/n ): ")
|
|---|
| 1624 | if x.upper() == 'N':
|
|---|
| 1625 | self.blpars.append(None)
|
|---|
| 1626 | continue
|
|---|
| 1627 | workscan._setspectrum(f.fitter.getresidual(), r)
|
|---|
| 1628 | self.blpars.append(f.get_parameters())
|
|---|
| 1629 |
|
|---|
| 1630 | if plot:
|
|---|
| 1631 | f._p.unmap()
|
|---|
| 1632 | f._p = None
|
|---|
| 1633 | workscan._add_history("poly_baseline", varlist)
|
|---|
| 1634 | print_log()
|
|---|
| 1635 | if insitu: self._assign(workscan)
|
|---|
| 1636 | else: return workscan
|
|---|
| 1637 | except RuntimeError:
|
|---|
| 1638 | msg = "The fit failed, possibly because it didn't converge."
|
|---|
| 1639 | if rcParams['verbose']:
|
|---|
| 1640 | #print msg
|
|---|
| 1641 | print_log()
|
|---|
| 1642 | asaplog.push( msg.message )
|
|---|
| 1643 | print_log( 'ERROR' )
|
|---|
| 1644 | return
|
|---|
| 1645 | else:
|
|---|
| 1646 | raise RuntimeError(msg)
|
|---|
| 1647 |
|
|---|
| 1648 |
|
|---|
| 1649 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0,
|
|---|
| 1650 | threshold=3, chan_avg_limit=1, plot=False,
|
|---|
| 1651 | insitu=None):
|
|---|
| 1652 | """
|
|---|
| 1653 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 1654 | Spectral lines are detected first using linefinder and masked out
|
|---|
| 1655 | to avoid them affecting the baseline solution.
|
|---|
| 1656 |
|
|---|
| 1657 | Parameters:
|
|---|
| 1658 | mask: an optional mask retreived from scantable
|
|---|
| 1659 | edge: an optional number of channel to drop at
|
|---|
| 1660 | the edge of spectrum. If only one value is
|
|---|
| 1661 | specified, the same number will be dropped from
|
|---|
| 1662 | both sides of the spectrum. Default is to keep
|
|---|
| 1663 | all channels. Nested tuples represent individual
|
|---|
| 1664 | edge selection for different IFs (a number of spectral
|
|---|
| 1665 | channels can be different)
|
|---|
| 1666 | order: the order of the polynomial (default is 0)
|
|---|
| 1667 | threshold: the threshold used by line finder. It is better to
|
|---|
| 1668 | keep it large as only strong lines affect the
|
|---|
| 1669 | baseline solution.
|
|---|
| 1670 | chan_avg_limit:
|
|---|
| 1671 | a maximum number of consequtive spectral channels to
|
|---|
| 1672 | average during the search of weak and broad lines.
|
|---|
| 1673 | The default is no averaging (and no search for weak
|
|---|
| 1674 | lines). If such lines can affect the fitted baseline
|
|---|
| 1675 | (e.g. a high order polynomial is fitted), increase this
|
|---|
| 1676 | parameter (usually values up to 8 are reasonable). Most
|
|---|
| 1677 | users of this method should find the default value
|
|---|
| 1678 | sufficient.
|
|---|
| 1679 | plot: plot the fit and the residual. In this each
|
|---|
| 1680 | indivual fit has to be approved, by typing 'y'
|
|---|
| 1681 | or 'n'
|
|---|
| 1682 | insitu: if False a new scantable is returned.
|
|---|
| 1683 | Otherwise, the scaling is done in-situ
|
|---|
| 1684 | The default is taken from .asaprc (False)
|
|---|
| 1685 |
|
|---|
| 1686 | Example:
|
|---|
| 1687 | scan2=scan.auto_poly_baseline(order=7)
|
|---|
| 1688 | """
|
|---|
| 1689 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1690 | varlist = vars()
|
|---|
| 1691 | from asap.asapfitter import fitter
|
|---|
| 1692 | from asap.asaplinefind import linefinder
|
|---|
| 1693 | from asap import _is_sequence_or_number as _is_valid
|
|---|
| 1694 |
|
|---|
| 1695 | # check whether edge is set up for each IF individually
|
|---|
| 1696 | individualedge = False;
|
|---|
| 1697 | if len(edge) > 1:
|
|---|
| 1698 | if isinstance(edge[0], list) or isinstance(edge[0], tuple):
|
|---|
| 1699 | individualedge = True;
|
|---|
| 1700 |
|
|---|
| 1701 | if not _is_valid(edge, int) and not individualedge:
|
|---|
| 1702 | raise ValueError, "Parameter 'edge' has to be an integer or a \
|
|---|
| 1703 | pair of integers specified as a tuple. Nested tuples are allowed \
|
|---|
| 1704 | to make individual selection for different IFs."
|
|---|
| 1705 |
|
|---|
| 1706 | curedge = (0, 0)
|
|---|
| 1707 | if individualedge:
|
|---|
| 1708 | for edgepar in edge:
|
|---|
| 1709 | if not _is_valid(edgepar, int):
|
|---|
| 1710 | raise ValueError, "Each element of the 'edge' tuple has \
|
|---|
| 1711 | to be a pair of integers or an integer."
|
|---|
| 1712 | else:
|
|---|
| 1713 | curedge = edge;
|
|---|
| 1714 |
|
|---|
| 1715 | # setup fitter
|
|---|
| 1716 | f = fitter()
|
|---|
| 1717 | f.set_function(poly=order)
|
|---|
| 1718 |
|
|---|
| 1719 | # setup line finder
|
|---|
| 1720 | fl = linefinder()
|
|---|
| 1721 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
|
|---|
| 1722 |
|
|---|
| 1723 | if not insitu:
|
|---|
| 1724 | workscan = self.copy()
|
|---|
| 1725 | else:
|
|---|
| 1726 | workscan = self
|
|---|
| 1727 |
|
|---|
| 1728 | fl.set_scan(workscan)
|
|---|
| 1729 |
|
|---|
| 1730 | rows = range(workscan.nrow())
|
|---|
| 1731 | # Save parameters of baseline fits & masklists as a class attribute.
|
|---|
| 1732 | # NOTICE: It does not reflect changes in scantable!
|
|---|
| 1733 | if len(rows) > 0:
|
|---|
| 1734 | self.blpars=[]
|
|---|
| 1735 | self.masklists=[]
|
|---|
| 1736 | asaplog.push("Processing:")
|
|---|
| 1737 | for r in rows:
|
|---|
| 1738 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
|
|---|
| 1739 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
|
|---|
| 1740 | workscan.getpol(r), workscan.getcycle(r))
|
|---|
| 1741 | asaplog.push(msg, False)
|
|---|
| 1742 |
|
|---|
| 1743 | # figure out edge parameter
|
|---|
| 1744 | if individualedge:
|
|---|
| 1745 | if len(edge) >= workscan.getif(r):
|
|---|
| 1746 | raise RuntimeError, "Number of edge elements appear to " \
|
|---|
| 1747 | "be less than the number of IFs"
|
|---|
| 1748 | curedge = edge[workscan.getif(r)]
|
|---|
| 1749 |
|
|---|
| 1750 | # take into account flagtra info (CAS-1434)
|
|---|
| 1751 | flagtra = workscan._getmask(r)
|
|---|
| 1752 | actualmask = mask[:]
|
|---|
| 1753 | if len(actualmask) == 0:
|
|---|
| 1754 | actualmask = list(flagtra[:])
|
|---|
| 1755 | else:
|
|---|
| 1756 | if len(actualmask) != len(flagtra):
|
|---|
| 1757 | raise RuntimeError, "Mask and flagtra have different length"
|
|---|
| 1758 | else:
|
|---|
| 1759 | for i in range(0, len(actualmask)):
|
|---|
| 1760 | actualmask[i] = actualmask[i] and flagtra[i]
|
|---|
| 1761 |
|
|---|
| 1762 | # setup line finder
|
|---|
| 1763 | fl.find_lines(r, actualmask, curedge)
|
|---|
| 1764 | outmask=fl.get_mask()
|
|---|
| 1765 | f.set_scan(workscan, fl.get_mask())
|
|---|
| 1766 | f.x = workscan._getabcissa(r)
|
|---|
| 1767 | f.y = workscan._getspectrum(r)
|
|---|
| 1768 | f.data = None
|
|---|
| 1769 | f.fit()
|
|---|
| 1770 |
|
|---|
| 1771 | # Show mask list
|
|---|
| 1772 | masklist=workscan.get_masklist(fl.get_mask(),row=r)
|
|---|
| 1773 | msg = "mask range: "+str(masklist)
|
|---|
| 1774 | asaplog.push(msg, False)
|
|---|
| 1775 |
|
|---|
| 1776 | if plot:
|
|---|
| 1777 | f.plot(residual=True)
|
|---|
| 1778 | x = raw_input("Accept fit ( [y]/n ): ")
|
|---|
| 1779 | if x.upper() == 'N':
|
|---|
| 1780 | self.blpars.append(None)
|
|---|
| 1781 | self.masklists.append(None)
|
|---|
| 1782 | continue
|
|---|
| 1783 |
|
|---|
| 1784 | workscan._setspectrum(f.fitter.getresidual(), r)
|
|---|
| 1785 | self.blpars.append(f.get_parameters())
|
|---|
| 1786 | self.masklists.append(masklist)
|
|---|
| 1787 | if plot:
|
|---|
| 1788 | f._p.unmap()
|
|---|
| 1789 | f._p = None
|
|---|
| 1790 | workscan._add_history("auto_poly_baseline", varlist)
|
|---|
| 1791 | if insitu:
|
|---|
| 1792 | self._assign(workscan)
|
|---|
| 1793 | else:
|
|---|
| 1794 | return workscan
|
|---|
| 1795 |
|
|---|
| 1796 | def rotate_linpolphase(self, angle):
|
|---|
| 1797 | """
|
|---|
| 1798 | Rotate the phase of the complex polarization O=Q+iU correlation.
|
|---|
| 1799 | This is always done in situ in the raw data. So if you call this
|
|---|
| 1800 | function more than once then each call rotates the phase further.
|
|---|
| 1801 | Parameters:
|
|---|
| 1802 | angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1803 | Examples:
|
|---|
| 1804 | scan.rotate_linpolphase(2.3)
|
|---|
| 1805 | """
|
|---|
| 1806 | varlist = vars()
|
|---|
| 1807 | self._math._rotate_linpolphase(self, angle)
|
|---|
| 1808 | self._add_history("rotate_linpolphase", varlist)
|
|---|
| 1809 | print_log()
|
|---|
| 1810 | return
|
|---|
| 1811 |
|
|---|
| 1812 |
|
|---|
| 1813 | def rotate_xyphase(self, angle):
|
|---|
| 1814 | """
|
|---|
| 1815 | Rotate the phase of the XY correlation. This is always done in situ
|
|---|
| 1816 | in the data. So if you call this function more than once
|
|---|
| 1817 | then each call rotates the phase further.
|
|---|
| 1818 | Parameters:
|
|---|
| 1819 | angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1820 | Examples:
|
|---|
| 1821 | scan.rotate_xyphase(2.3)
|
|---|
| 1822 | """
|
|---|
| 1823 | varlist = vars()
|
|---|
| 1824 | self._math._rotate_xyphase(self, angle)
|
|---|
| 1825 | self._add_history("rotate_xyphase", varlist)
|
|---|
| 1826 | print_log()
|
|---|
| 1827 | return
|
|---|
| 1828 |
|
|---|
| 1829 | def swap_linears(self):
|
|---|
| 1830 | """
|
|---|
| 1831 | Swap the linear polarisations XX and YY, or better the first two
|
|---|
| 1832 | polarisations as this also works for ciculars.
|
|---|
| 1833 | """
|
|---|
| 1834 | varlist = vars()
|
|---|
| 1835 | self._math._swap_linears(self)
|
|---|
| 1836 | self._add_history("swap_linears", varlist)
|
|---|
| 1837 | print_log()
|
|---|
| 1838 | return
|
|---|
| 1839 |
|
|---|
| 1840 | def invert_phase(self):
|
|---|
| 1841 | """
|
|---|
| 1842 | Invert the phase of the complex polarisation
|
|---|
| 1843 | """
|
|---|
| 1844 | varlist = vars()
|
|---|
| 1845 | self._math._invert_phase(self)
|
|---|
| 1846 | self._add_history("invert_phase", varlist)
|
|---|
| 1847 | print_log()
|
|---|
| 1848 | return
|
|---|
| 1849 |
|
|---|
| 1850 | def add(self, offset, insitu=None):
|
|---|
| 1851 | """
|
|---|
| 1852 | Return a scan where all spectra have the offset added
|
|---|
| 1853 | Parameters:
|
|---|
| 1854 | offset: the offset
|
|---|
| 1855 | insitu: if False a new scantable is returned.
|
|---|
| 1856 | Otherwise, the scaling is done in-situ
|
|---|
| 1857 | The default is taken from .asaprc (False)
|
|---|
| 1858 | """
|
|---|
| 1859 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1860 | self._math._setinsitu(insitu)
|
|---|
| 1861 | varlist = vars()
|
|---|
| 1862 | s = scantable(self._math._unaryop(self, offset, "ADD", False))
|
|---|
| 1863 | s._add_history("add", varlist)
|
|---|
| 1864 | print_log()
|
|---|
| 1865 | if insitu:
|
|---|
| 1866 | self._assign(s)
|
|---|
| 1867 | else:
|
|---|
| 1868 | return s
|
|---|
| 1869 |
|
|---|
| 1870 | def scale(self, factor, tsys=True, insitu=None):
|
|---|
| 1871 | """
|
|---|
| 1872 | Return a scan where all spectra are scaled by the give 'factor'
|
|---|
| 1873 | Parameters:
|
|---|
| 1874 | factor: the scaling factor
|
|---|
| 1875 | insitu: if False a new scantable is returned.
|
|---|
| 1876 | Otherwise, the scaling is done in-situ
|
|---|
| 1877 | The default is taken from .asaprc (False)
|
|---|
| 1878 | tsys: if True (default) then apply the operation to Tsys
|
|---|
| 1879 | as well as the data
|
|---|
| 1880 | """
|
|---|
| 1881 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1882 | self._math._setinsitu(insitu)
|
|---|
| 1883 | varlist = vars()
|
|---|
| 1884 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
|
|---|
| 1885 | s._add_history("scale", varlist)
|
|---|
| 1886 | print_log()
|
|---|
| 1887 | if insitu:
|
|---|
| 1888 | self._assign(s)
|
|---|
| 1889 | else:
|
|---|
| 1890 | return s
|
|---|
| 1891 |
|
|---|
| 1892 | def set_sourcetype(self, match, matchtype="pattern",
|
|---|
| 1893 | sourcetype="reference"):
|
|---|
| 1894 | """
|
|---|
| 1895 | Set the type of the source to be an source or reference scan
|
|---|
| 1896 | using the provided pattern:
|
|---|
| 1897 | Parameters:
|
|---|
| 1898 | match: a Unix style pattern, regular expression or selector
|
|---|
| 1899 | matchtype: 'pattern' (default) UNIX style pattern or
|
|---|
| 1900 | 'regex' regular expression
|
|---|
| 1901 | sourcetype: the type of the source to use (source/reference)
|
|---|
| 1902 | """
|
|---|
| 1903 | varlist = vars()
|
|---|
| 1904 | basesel = self.get_selection()
|
|---|
| 1905 | stype = -1
|
|---|
| 1906 | if sourcetype.lower().startswith("r"):
|
|---|
| 1907 | stype = 1
|
|---|
| 1908 | elif sourcetype.lower().startswith("s"):
|
|---|
| 1909 | stype = 0
|
|---|
| 1910 | else:
|
|---|
| 1911 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)")
|
|---|
| 1912 | if matchtype.lower().startswith("p"):
|
|---|
| 1913 | matchtype = "pattern"
|
|---|
| 1914 | elif matchtype.lower().startswith("r"):
|
|---|
| 1915 | matchtype = "regex"
|
|---|
| 1916 | else:
|
|---|
| 1917 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)")
|
|---|
| 1918 | sel = selector()
|
|---|
| 1919 | if isinstance(match, selector):
|
|---|
| 1920 | sel = match
|
|---|
| 1921 | else:
|
|---|
| 1922 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match))
|
|---|
| 1923 | self.set_selection(basesel+sel)
|
|---|
| 1924 | self._setsourcetype(stype)
|
|---|
| 1925 | self.set_selection(basesel)
|
|---|
| 1926 | s._add_history("set_sourcetype", varlist)
|
|---|
| 1927 |
|
|---|
| 1928 | def auto_quotient(self, preserve=True, mode='paired', verify=False):
|
|---|
| 1929 | """
|
|---|
| 1930 | This function allows to build quotients automatically.
|
|---|
| 1931 | It assumes the observation to have the same number of
|
|---|
| 1932 | "ons" and "offs"
|
|---|
| 1933 | Parameters:
|
|---|
| 1934 | preserve: you can preserve (default) the continuum or
|
|---|
| 1935 | remove it. The equations used are
|
|---|
| 1936 | preserve: Output = Toff * (on/off) - Toff
|
|---|
| 1937 | remove: Output = Toff * (on/off) - Ton
|
|---|
| 1938 | mode: the on/off detection mode
|
|---|
| 1939 | 'paired' (default)
|
|---|
| 1940 | identifies 'off' scans by the
|
|---|
| 1941 | trailing '_R' (Mopra/Parkes) or
|
|---|
| 1942 | '_e'/'_w' (Tid) and matches
|
|---|
| 1943 | on/off pairs from the observing pattern
|
|---|
| 1944 | 'time'
|
|---|
| 1945 | finds the closest off in time
|
|---|
| 1946 |
|
|---|
| 1947 | """
|
|---|
| 1948 | modes = ["time", "paired"]
|
|---|
| 1949 | if not mode in modes:
|
|---|
| 1950 | msg = "please provide valid mode. Valid modes are %s" % (modes)
|
|---|
| 1951 | raise ValueError(msg)
|
|---|
| 1952 | varlist = vars()
|
|---|
| 1953 | s = None
|
|---|
| 1954 | if mode.lower() == "paired":
|
|---|
| 1955 | basesel = self.get_selection()
|
|---|
| 1956 | sel = selector()+basesel
|
|---|
| 1957 | sel.set_query("SRCTYPE==1")
|
|---|
| 1958 | self.set_selection(sel)
|
|---|
| 1959 | offs = self.copy()
|
|---|
| 1960 | sel.set_query("SRCTYPE==0")
|
|---|
| 1961 | self.set_selection(sel)
|
|---|
| 1962 | ons = self.copy()
|
|---|
| 1963 | s = scantable(self._math._quotient(ons, offs, preserve))
|
|---|
| 1964 | self.set_selection(basesel)
|
|---|
| 1965 | elif mode.lower() == "time":
|
|---|
| 1966 | s = scantable(self._math._auto_quotient(self, mode, preserve))
|
|---|
| 1967 | s._add_history("auto_quotient", varlist)
|
|---|
| 1968 | print_log()
|
|---|
| 1969 | return s
|
|---|
| 1970 |
|
|---|
| 1971 | def mx_quotient(self, mask = None, weight='median', preserve=True):
|
|---|
| 1972 | """
|
|---|
| 1973 | Form a quotient using "off" beams when observing in "MX" mode.
|
|---|
| 1974 | Parameters:
|
|---|
| 1975 | mask: an optional mask to be used when weight == 'stddev'
|
|---|
| 1976 | weight: How to average the off beams. Default is 'median'.
|
|---|
| 1977 | preserve: you can preserve (default) the continuum or
|
|---|
| 1978 | remove it. The equations used are
|
|---|
| 1979 | preserve: Output = Toff * (on/off) - Toff
|
|---|
| 1980 | remove: Output = Toff * (on/off) - Ton
|
|---|
| 1981 | """
|
|---|
| 1982 | if mask is None: mask = ()
|
|---|
| 1983 | varlist = vars()
|
|---|
| 1984 | on = scantable(self._math._mx_extract(self, 'on'))
|
|---|
| 1985 | preoff = scantable(self._math._mx_extract(self, 'off'))
|
|---|
| 1986 | off = preoff.average_time(mask=mask, weight=weight, scanav=False)
|
|---|
| 1987 | from asapmath import quotient
|
|---|
| 1988 | q = quotient(on, off, preserve)
|
|---|
| 1989 | q._add_history("mx_quotient", varlist)
|
|---|
| 1990 | print_log()
|
|---|
| 1991 | return q
|
|---|
| 1992 |
|
|---|
| 1993 | def freq_switch(self, insitu=None):
|
|---|
| 1994 | """
|
|---|
| 1995 | Apply frequency switching to the data.
|
|---|
| 1996 | Parameters:
|
|---|
| 1997 | insitu: if False a new scantable is returned.
|
|---|
| 1998 | Otherwise, the swictching is done in-situ
|
|---|
| 1999 | The default is taken from .asaprc (False)
|
|---|
| 2000 | Example:
|
|---|
| 2001 | none
|
|---|
| 2002 | """
|
|---|
| 2003 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 2004 | self._math._setinsitu(insitu)
|
|---|
| 2005 | varlist = vars()
|
|---|
| 2006 | s = scantable(self._math._freqswitch(self))
|
|---|
| 2007 | s._add_history("freq_switch", varlist)
|
|---|
| 2008 | print_log()
|
|---|
| 2009 | if insitu: self._assign(s)
|
|---|
| 2010 | else: return s
|
|---|
| 2011 |
|
|---|
| 2012 | def recalc_azel(self):
|
|---|
| 2013 | """
|
|---|
| 2014 | Recalculate the azimuth and elevation for each position.
|
|---|
| 2015 | Parameters:
|
|---|
| 2016 | none
|
|---|
| 2017 | Example:
|
|---|
| 2018 | """
|
|---|
| 2019 | varlist = vars()
|
|---|
| 2020 | self._recalcazel()
|
|---|
| 2021 | self._add_history("recalc_azel", varlist)
|
|---|
| 2022 | print_log()
|
|---|
| 2023 | return
|
|---|
| 2024 |
|
|---|
| 2025 | def __add__(self, other):
|
|---|
| 2026 | varlist = vars()
|
|---|
| 2027 | s = None
|
|---|
| 2028 | if isinstance(other, scantable):
|
|---|
| 2029 | s = scantable(self._math._binaryop(self, other, "ADD"))
|
|---|
| 2030 | elif isinstance(other, float):
|
|---|
| 2031 | s = scantable(self._math._unaryop(self, other, "ADD", False))
|
|---|
| 2032 | else:
|
|---|
| 2033 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 2034 | s._add_history("operator +", varlist)
|
|---|
| 2035 | print_log()
|
|---|
| 2036 | return s
|
|---|
| 2037 |
|
|---|
| 2038 | def __sub__(self, other):
|
|---|
| 2039 | """
|
|---|
| 2040 | implicit on all axes and on Tsys
|
|---|
| 2041 | """
|
|---|
| 2042 | varlist = vars()
|
|---|
| 2043 | s = None
|
|---|
| 2044 | if isinstance(other, scantable):
|
|---|
| 2045 | s = scantable(self._math._binaryop(self, other, "SUB"))
|
|---|
| 2046 | elif isinstance(other, float):
|
|---|
| 2047 | s = scantable(self._math._unaryop(self, other, "SUB", False))
|
|---|
| 2048 | else:
|
|---|
| 2049 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 2050 | s._add_history("operator -", varlist)
|
|---|
| 2051 | print_log()
|
|---|
| 2052 | return s
|
|---|
| 2053 |
|
|---|
| 2054 | def __mul__(self, other):
|
|---|
| 2055 | """
|
|---|
| 2056 | implicit on all axes and on Tsys
|
|---|
| 2057 | """
|
|---|
| 2058 | varlist = vars()
|
|---|
| 2059 | s = None
|
|---|
| 2060 | if isinstance(other, scantable):
|
|---|
| 2061 | s = scantable(self._math._binaryop(self, other, "MUL"))
|
|---|
| 2062 | elif isinstance(other, float):
|
|---|
| 2063 | s = scantable(self._math._unaryop(self, other, "MUL", False))
|
|---|
| 2064 | else:
|
|---|
| 2065 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 2066 | s._add_history("operator *", varlist)
|
|---|
| 2067 | print_log()
|
|---|
| 2068 | return s
|
|---|
| 2069 |
|
|---|
| 2070 |
|
|---|
| 2071 | def __div__(self, other):
|
|---|
| 2072 | """
|
|---|
| 2073 | implicit on all axes and on Tsys
|
|---|
| 2074 | """
|
|---|
| 2075 | varlist = vars()
|
|---|
| 2076 | s = None
|
|---|
| 2077 | if isinstance(other, scantable):
|
|---|
| 2078 | s = scantable(self._math._binaryop(self, other, "DIV"))
|
|---|
| 2079 | elif isinstance(other, float):
|
|---|
| 2080 | if other == 0.0:
|
|---|
| 2081 | raise ZeroDivisionError("Dividing by zero is not recommended")
|
|---|
| 2082 | s = scantable(self._math._unaryop(self, other, "DIV", False))
|
|---|
| 2083 | else:
|
|---|
| 2084 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 2085 | s._add_history("operator /", varlist)
|
|---|
| 2086 | print_log()
|
|---|
| 2087 | return s
|
|---|
| 2088 |
|
|---|
| 2089 | def get_fit(self, row=0):
|
|---|
| 2090 | """
|
|---|
| 2091 | Print or return the stored fits for a row in the scantable
|
|---|
| 2092 | Parameters:
|
|---|
| 2093 | row: the row which the fit has been applied to.
|
|---|
| 2094 | """
|
|---|
| 2095 | if row > self.nrow():
|
|---|
| 2096 | return
|
|---|
| 2097 | from asap.asapfit import asapfit
|
|---|
| 2098 | fit = asapfit(self._getfit(row))
|
|---|
| 2099 | if rcParams['verbose']:
|
|---|
| 2100 | #print fit
|
|---|
| 2101 | asaplog.push( '%s' %(fit) )
|
|---|
| 2102 | print_log()
|
|---|
| 2103 | return
|
|---|
| 2104 | else:
|
|---|
| 2105 | return fit.as_dict()
|
|---|
| 2106 |
|
|---|
| 2107 | def flag_nans(self):
|
|---|
| 2108 | """
|
|---|
| 2109 | Utility function to flag NaN values in the scantable.
|
|---|
| 2110 | """
|
|---|
| 2111 | import numpy
|
|---|
| 2112 | basesel = self.get_selection()
|
|---|
| 2113 | for i in range(self.nrow()):
|
|---|
| 2114 | sel = selector()+basesel
|
|---|
| 2115 | sel.set_scans(self.getscan(i))
|
|---|
| 2116 | sel.set_beams(self.getbeam(i))
|
|---|
| 2117 | sel.set_ifs(self.getif(i))
|
|---|
| 2118 | sel.set_polarisations(self.getpol(i))
|
|---|
| 2119 | self.set_selection(sel)
|
|---|
| 2120 | nans = numpy.isnan(self._getspectrum(0))
|
|---|
| 2121 | if numpy.any(nans):
|
|---|
| 2122 | bnans = [ bool(v) for v in nans]
|
|---|
| 2123 | self.flag(bnans)
|
|---|
| 2124 | self.set_selection(basesel)
|
|---|
| 2125 |
|
|---|
| 2126 |
|
|---|
| 2127 | def _add_history(self, funcname, parameters):
|
|---|
| 2128 | if not rcParams['scantable.history']:
|
|---|
| 2129 | return
|
|---|
| 2130 | # create date
|
|---|
| 2131 | sep = "##"
|
|---|
| 2132 | from datetime import datetime
|
|---|
| 2133 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
|
|---|
| 2134 | hist = dstr+sep
|
|---|
| 2135 | hist += funcname+sep#cdate+sep
|
|---|
| 2136 | if parameters.has_key('self'): del parameters['self']
|
|---|
| 2137 | for k, v in parameters.iteritems():
|
|---|
| 2138 | if type(v) is dict:
|
|---|
| 2139 | for k2, v2 in v.iteritems():
|
|---|
| 2140 | hist += k2
|
|---|
| 2141 | hist += "="
|
|---|
| 2142 | if isinstance(v2, scantable):
|
|---|
| 2143 | hist += 'scantable'
|
|---|
| 2144 | elif k2 == 'mask':
|
|---|
| 2145 | if isinstance(v2, list) or isinstance(v2, tuple):
|
|---|
| 2146 | hist += str(self._zip_mask(v2))
|
|---|
| 2147 | else:
|
|---|
| 2148 | hist += str(v2)
|
|---|
| 2149 | else:
|
|---|
| 2150 | hist += str(v2)
|
|---|
| 2151 | else:
|
|---|
| 2152 | hist += k
|
|---|
| 2153 | hist += "="
|
|---|
| 2154 | if isinstance(v, scantable):
|
|---|
| 2155 | hist += 'scantable'
|
|---|
| 2156 | elif k == 'mask':
|
|---|
| 2157 | if isinstance(v, list) or isinstance(v, tuple):
|
|---|
| 2158 | hist += str(self._zip_mask(v))
|
|---|
| 2159 | else:
|
|---|
| 2160 | hist += str(v)
|
|---|
| 2161 | else:
|
|---|
| 2162 | hist += str(v)
|
|---|
| 2163 | hist += sep
|
|---|
| 2164 | hist = hist[:-2] # remove trailing '##'
|
|---|
| 2165 | self._addhistory(hist)
|
|---|
| 2166 |
|
|---|
| 2167 |
|
|---|
| 2168 | def _zip_mask(self, mask):
|
|---|
| 2169 | mask = list(mask)
|
|---|
| 2170 | i = 0
|
|---|
| 2171 | segments = []
|
|---|
| 2172 | while mask[i:].count(1):
|
|---|
| 2173 | i += mask[i:].index(1)
|
|---|
| 2174 | if mask[i:].count(0):
|
|---|
| 2175 | j = i + mask[i:].index(0)
|
|---|
| 2176 | else:
|
|---|
| 2177 | j = len(mask)
|
|---|
| 2178 | segments.append([i, j])
|
|---|
| 2179 | i = j
|
|---|
| 2180 | return segments
|
|---|
| 2181 |
|
|---|
| 2182 | def _get_ordinate_label(self):
|
|---|
| 2183 | fu = "("+self.get_fluxunit()+")"
|
|---|
| 2184 | import re
|
|---|
| 2185 | lbl = "Intensity"
|
|---|
| 2186 | if re.match(".K.", fu):
|
|---|
| 2187 | lbl = "Brightness Temperature "+ fu
|
|---|
| 2188 | elif re.match(".Jy.", fu):
|
|---|
| 2189 | lbl = "Flux density "+ fu
|
|---|
| 2190 | return lbl
|
|---|
| 2191 |
|
|---|
| 2192 | def _check_ifs(self):
|
|---|
| 2193 | nchans = [self.nchan(i) for i in range(self.nif(-1))]
|
|---|
| 2194 | nchans = filter(lambda t: t > 0, nchans)
|
|---|
| 2195 | return (sum(nchans)/len(nchans) == nchans[0])
|
|---|
| 2196 |
|
|---|
| 2197 | def _fill(self, names, unit, average, getpt):
|
|---|
| 2198 | import os
|
|---|
| 2199 | from asap._asap import stfiller
|
|---|
| 2200 | first = True
|
|---|
| 2201 | fullnames = []
|
|---|
| 2202 | for name in names:
|
|---|
| 2203 | name = os.path.expandvars(name)
|
|---|
| 2204 | name = os.path.expanduser(name)
|
|---|
| 2205 | if not os.path.exists(name):
|
|---|
| 2206 | msg = "File '%s' does not exists" % (name)
|
|---|
| 2207 | if rcParams['verbose']:
|
|---|
| 2208 | asaplog.push(msg)
|
|---|
| 2209 | #print asaplog.pop().strip()
|
|---|
| 2210 | print_log( 'ERROR' )
|
|---|
| 2211 | return
|
|---|
| 2212 | raise IOError(msg)
|
|---|
| 2213 | fullnames.append(name)
|
|---|
| 2214 | if average:
|
|---|
| 2215 | asaplog.push('Auto averaging integrations')
|
|---|
| 2216 | stype = int(rcParams['scantable.storage'].lower() == 'disk')
|
|---|
| 2217 | for name in fullnames:
|
|---|
| 2218 | tbl = Scantable(stype)
|
|---|
| 2219 | r = stfiller(tbl)
|
|---|
| 2220 | rx = rcParams['scantable.reference']
|
|---|
| 2221 | r._setreferenceexpr(rx)
|
|---|
| 2222 | msg = "Importing %s..." % (name)
|
|---|
| 2223 | asaplog.push(msg, False)
|
|---|
| 2224 | print_log()
|
|---|
| 2225 | r._open(name, -1, -1, getpt)
|
|---|
| 2226 | r._read()
|
|---|
| 2227 | if average:
|
|---|
| 2228 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
|
|---|
| 2229 | if not first:
|
|---|
| 2230 | tbl = self._math._merge([self, tbl])
|
|---|
| 2231 | Scantable.__init__(self, tbl)
|
|---|
| 2232 | r._close()
|
|---|
| 2233 | del r, tbl
|
|---|
| 2234 | first = False
|
|---|
| 2235 | if unit is not None:
|
|---|
| 2236 | self.set_fluxunit(unit)
|
|---|
| 2237 | #self.set_freqframe(rcParams['scantable.freqframe'])
|
|---|
| 2238 |
|
|---|
| 2239 | def __getitem__(self, key):
|
|---|
| 2240 | if key < 0:
|
|---|
| 2241 | key += self.nrow()
|
|---|
| 2242 | if key >= self.nrow():
|
|---|
| 2243 | raise IndexError("Row index out of range.")
|
|---|
| 2244 | return self._getspectrum(key)
|
|---|
| 2245 |
|
|---|
| 2246 | def __setitem__(self, key, value):
|
|---|
| 2247 | if key < 0:
|
|---|
| 2248 | key += self.nrow()
|
|---|
| 2249 | if key >= self.nrow():
|
|---|
| 2250 | raise IndexError("Row index out of range.")
|
|---|
| 2251 | if not hasattr(value, "__len__") or \
|
|---|
| 2252 | len(value) > self.nchan(self.getif(key)):
|
|---|
| 2253 | raise ValueError("Spectrum length doesn't match.")
|
|---|
| 2254 | return self._setspectrum(value, key)
|
|---|
| 2255 |
|
|---|
| 2256 | def __len__(self):
|
|---|
| 2257 | return self.nrow()
|
|---|
| 2258 |
|
|---|
| 2259 | def __iter__(self):
|
|---|
| 2260 | for i in range(len(self)):
|
|---|
| 2261 | yield self[i]
|
|---|
