| 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, print_log_dec
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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 | @print_log_dec
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| 14 | def __init__(self, filename, average=None, unit=None, parallactify=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 | parallactify: Indcicate that the data had been parallatified.
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| 33 | Default is taken form rc file.
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| 34 | """
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| 35 | if average is None:
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| 36 | average = rcParams['scantable.autoaverage']
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| 37 | parallactify = parallactify or rcParams['scantable.parallactify']
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| 38 | varlist = vars()
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| 39 | from asap._asap import stmath
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| 40 | self._math = stmath()
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| 41 | if isinstance(filename, Scantable):
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| 42 | Scantable.__init__(self, filename)
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| 43 | else:
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| 44 | if isinstance(filename, str):# or \
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| 45 | # (isinstance(filename, list) or isinstance(filename, tuple)) \
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| 46 | # and isinstance(filename[-1], str):
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| 47 | import os.path
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| 48 | filename = os.path.expandvars(filename)
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| 49 | filename = os.path.expanduser(filename)
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| 50 | if not os.path.exists(filename):
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| 51 | s = "File '%s' not found." % (filename)
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| 52 | if rcParams['verbose']:
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| 53 | asaplog.push(s)
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| 54 | #print asaplog.pop().strip()
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| 55 | return
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| 56 | raise IOError(s)
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| 57 | if os.path.isdir(filename) \
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| 58 | and not os.path.exists(filename+'/table.f1'):
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| 59 | # crude check if asap table
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| 60 | if os.path.exists(filename+'/table.info'):
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| 61 | ondisk = rcParams['scantable.storage'] == 'disk'
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| 62 | Scantable.__init__(self, filename, ondisk)
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| 63 | if unit is not None:
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| 64 | self.set_fluxunit(unit)
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| 65 | self.set_freqframe(rcParams['scantable.freqframe'])
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| 66 | else:
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| 67 | msg = "The given file '%s'is not a valid " \
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| 68 | "asap table." % (filename)
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| 69 | if rcParams['verbose']:
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| 70 | print msg
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| 71 | return
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| 72 | else:
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| 73 | raise IOError(msg)
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| 74 | else:
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| 75 | self._fill([filename], unit, average)
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| 76 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \
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| 77 | and isinstance(filename[-1], str):
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| 78 | self._fill(filename, unit, average)
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| 79 | self.parallactify(parallactify)
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| 80 | self._add_history("scantable", varlist)
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| 81 |
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| 82 | @print_log_dec
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| 83 | def save(self, name=None, format=None, overwrite=False):
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| 84 | """
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| 85 | Store the scantable on disk. This can be an asap (aips++) Table,
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| 86 | SDFITS or MS2 format.
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| 87 | Parameters:
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| 88 | name: the name of the outputfile. For format "ASCII"
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| 89 | this is the root file name (data in 'name'.txt
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| 90 | and header in 'name'_header.txt)
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| 91 | format: an optional file format. Default is ASAP.
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| 92 | Allowed are - 'ASAP' (save as ASAP [aips++] Table),
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| 93 | 'SDFITS' (save as SDFITS file)
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| 94 | 'ASCII' (saves as ascii text file)
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| 95 | 'MS2' (saves as an aips++
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| 96 | MeasurementSet V2)
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| 97 | 'FITS' (save as image FITS - not
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| 98 | readable by class)
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| 99 | 'CLASS' (save as FITS readable by CLASS)
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| 100 | overwrite: If the file should be overwritten if it exists.
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| 101 | The default False is to return with warning
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| 102 | without writing the output. USE WITH CARE.
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| 103 | Example:
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| 104 | scan.save('myscan.asap')
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| 105 | scan.save('myscan.sdfits', 'SDFITS')
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| 106 | """
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| 107 | from os import path
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| 108 | format = format or rcParams['scantable.save']
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| 109 | suffix = '.'+format.lower()
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| 110 | if name is None or name == "":
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| 111 | name = 'scantable'+suffix
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| 112 | msg = "No filename given. Using default name %s..." % name
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| 113 | asaplog.push(msg)
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| 114 | name = path.expandvars(name)
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| 115 | if path.isfile(name) or path.isdir(name):
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| 116 | if not overwrite:
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| 117 | msg = "File %s exists." % name
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| 118 | if rcParams['verbose']:
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| 119 | print msg
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| 120 | return
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| 121 | else:
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| 122 | raise IOError(msg)
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| 123 | format2 = format.upper()
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| 124 | if format2 == 'ASAP':
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| 125 | self._save(name)
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| 126 | else:
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| 127 | from asap._asap import stwriter as stw
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| 128 | writer = stw(format2)
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| 129 | writer.write(self, name)
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| 130 | return
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| 131 |
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| 132 | def copy(self):
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| 133 | """
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| 134 | Return a copy of this scantable.
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| 135 | Note:
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| 136 | This makes a full (deep) copy. scan2 = scan1 makes a reference.
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| 137 | Parameters:
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| 138 | none
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| 139 | Example:
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| 140 | copiedscan = scan.copy()
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| 141 | """
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| 142 | sd = scantable(Scantable._copy(self))
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| 143 | return sd
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| 144 |
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| 145 | def drop_scan(self, scanid=None):
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| 146 | """
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| 147 | Return a new scantable where the specified scan number(s) has(have)
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| 148 | been dropped.
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| 149 | Parameters:
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| 150 | scanid: a (list of) scan number(s)
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| 151 | """
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| 152 | from asap import _is_sequence_or_number as _is_valid
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| 153 | from asap import _to_list
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| 154 | from asap import unique
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| 155 | if not _is_valid(scanid):
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| 156 | if rcParams['verbose']:
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| 157 | print "Please specify a scanno to drop from the scantable"
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| 158 | return
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| 159 | else:
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| 160 | raise RuntimeError("No scan given")
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| 161 | try:
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| 162 | scanid = _to_list(scanid)
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| 163 | allscans = unique([ self.getscan(i) for i in range(self.nrow())])
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| 164 | for sid in scanid: allscans.remove(sid)
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| 165 | if len(allscans) == 0:
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| 166 | raise ValueError("Can't remove all scans")
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| 167 | except ValueError:
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| 168 | if rcParams['verbose']:
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| 169 | print "Couldn't find any match."
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| 170 | return
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| 171 | else: raise
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| 172 | try:
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| 173 | bsel = self.get_selection()
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| 174 | sel = selector(scans=allscans)
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| 175 | self.set_selection(bsel+sel)
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| 176 | scopy = self._copy()
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| 177 | self.set_selection(bsel)
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| 178 | return scantable(scopy)
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| 179 | except RuntimeError:
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| 180 | if rcParams['verbose']:
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| 181 | print "Couldn't find any match."
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| 182 | else:
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| 183 | raise
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| 184 |
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| 185 | def get_scan(self, scanid=None):
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| 186 | """
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| 187 | Return a specific scan (by scanno) or collection of scans (by
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| 188 | source name) in a new scantable.
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| 189 | Note:
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| 190 | See scantable.drop_scan() for the inverse operation.
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| 191 | Parameters:
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| 192 | scanid: a (list of) scanno or a source name, unix-style
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| 193 | patterns are accepted for source name matching, e.g.
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| 194 | '*_R' gets all 'ref scans
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| 195 | Example:
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| 196 | # get all scans containing the source '323p459'
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| 197 | newscan = scan.get_scan('323p459')
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| 198 | # get all 'off' scans
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| 199 | refscans = scan.get_scan('*_R')
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| 200 | # get a susbset of scans by scanno (as listed in scan.summary())
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| 201 | newscan = scan.get_scan([0, 2, 7, 10])
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| 202 | """
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| 203 | if scanid is None:
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| 204 | if rcParams['verbose']:
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| 205 | print "Please specify a scan no or name to " \
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| 206 | "retrieve from the scantable"
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| 207 | return
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| 208 | else:
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| 209 | raise RuntimeError("No scan given")
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| 210 |
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| 211 | try:
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| 212 | bsel = self.get_selection()
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| 213 | sel = selector()
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| 214 | if type(scanid) is str:
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| 215 | sel.set_name(scanid)
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| 216 | self.set_selection(bsel+sel)
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| 217 | scopy = self._copy()
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| 218 | self.set_selection(bsel)
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| 219 | return scantable(scopy)
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| 220 | elif type(scanid) is int:
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| 221 | sel.set_scans([scanid])
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| 222 | self.set_selection(bsel+sel)
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| 223 | scopy = self._copy()
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| 224 | self.set_selection(bsel)
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| 225 | return scantable(scopy)
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| 226 | elif type(scanid) is list:
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| 227 | sel.set_scans(scanid)
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| 228 | self.set_selection(sel)
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| 229 | scopy = self._copy()
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| 230 | self.set_selection(bsel)
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| 231 | return scantable(scopy)
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| 232 | else:
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| 233 | msg = "Illegal scanid type, use 'int' or 'list' if ints."
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| 234 | if rcParams['verbose']:
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| 235 | print msg
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| 236 | else:
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| 237 | raise TypeError(msg)
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| 238 | except RuntimeError:
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| 239 | if rcParams['verbose']: print "Couldn't find any match."
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| 240 | else: raise
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| 241 |
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| 242 | def __str__(self):
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| 243 | return Scantable._summary(self, True)
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| 244 |
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| 245 | def summary(self, filename=None):
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| 246 | """
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| 247 | Print a summary of the contents of this scantable.
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| 248 | Parameters:
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| 249 | filename: the name of a file to write the putput to
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| 250 | Default - no file output
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| 251 | verbose: print extra info such as the frequency table
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| 252 | The default (False) is taken from .asaprc
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| 253 | """
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| 254 | info = Scantable._summary(self, True)
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| 255 | if filename is not None:
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| 256 | if filename is "":
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| 257 | filename = 'scantable_summary.txt'
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| 258 | from os.path import expandvars, isdir
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| 259 | filename = expandvars(filename)
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| 260 | if not isdir(filename):
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| 261 | data = open(filename, 'w')
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| 262 | data.write(info)
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| 263 | data.close()
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| 264 | else:
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| 265 | msg = "Illegal file name '%s'." % (filename)
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| 266 | if rcParams['verbose']:
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| 267 | print msg
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| 268 | else:
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| 269 | raise IOError(msg)
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| 270 | if rcParams['verbose']:
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| 271 | try:
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| 272 | from IPython.genutils import page as pager
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| 273 | except ImportError:
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| 274 | from pydoc import pager
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| 275 | pager(info)
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| 276 | else:
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| 277 | return info
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| 278 |
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| 279 | def get_spectrum(self, rowno):
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| 280 | """Return the spectrum for the current row in the scantable as a list.
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| 281 | Parameters:
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| 282 | rowno: the row number to retrieve the spectrum from
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| 283 | """
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| 284 | return self._getspectrum(rowno)
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| 285 |
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| 286 | def get_mask(self, rowno):
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| 287 | """Return the mask for the current row in the scantable as a list.
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| 288 | Parameters:
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| 289 | rowno: the row number to retrieve the mask from
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| 290 | """
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| 291 | return self._getmask(rowno)
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| 292 |
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| 293 | def set_spectrum(self, spec, rowno):
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| 294 | """Return the spectrum for the current row in the scantable as a list.
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| 295 | Parameters:
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| 296 | spec: the spectrum
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| 297 | rowno: the row number to set the spectrum for
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| 298 | """
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| 299 | assert(len(spec) == self.nchan())
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| 300 | return self._setspectrum(spec, rowno)
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| 301 |
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| 302 | def get_selection(self):
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| 303 | """
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| 304 | Get the selection object currently set on this scantable.
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| 305 | Parameters:
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| 306 | none
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| 307 | Example:
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| 308 | sel = scan.get_selection()
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| 309 | sel.set_ifs(0) # select IF 0
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| 310 | scan.set_selection(sel) # apply modified selection
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| 311 | """
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| 312 | return selector(self._getselection())
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| 313 |
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| 314 | def set_selection(self, selection=None, **kw):
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| 315 | """
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| 316 | Select a subset of the data. All following operations on this scantable
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| 317 | are only applied to thi selection.
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| 318 | Parameters:
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| 319 | selection: a selector object (default unset the selection)
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| 320 | Examples:
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| 321 | sel = selector() # create a selection object
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| 322 | self.set_scans([0, 3]) # select SCANNO 0 and 3
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| 323 | scan.set_selection(sel) # set the selection
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| 324 | scan.summary() # will only print summary of scanno 0 an 3
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| 325 | scan.set_selection() # unset the selection
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| 326 | """
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| 327 | if selection is None:
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| 328 | # reset
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| 329 | if len(kw) == 0:
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| 330 | selection = selector()
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| 331 | else:
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| 332 | # try keywords
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| 333 | for k in kw:
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| 334 | if k not in selector.fields:
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| 335 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields))
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| 336 | selection = selector(**kw)
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| 337 | self._setselection(selection)
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| 338 |
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| 339 | def stats(self, stat='stddev', mask=None):
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| 340 | """
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| 341 | Determine the specified statistic of the current beam/if/pol
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| 342 | Takes a 'mask' as an optional parameter to specify which
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| 343 | channels should be excluded.
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| 344 | Parameters:
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| 345 | stat: 'min', 'max', 'sumsq', 'sum', 'mean'
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| 346 | 'var', 'stddev', 'avdev', 'rms', 'median'
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| 347 | mask: an optional mask specifying where the statistic
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| 348 | should be determined.
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| 349 | Example:
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| 350 | scan.set_unit('channel')
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| 351 | msk = scan.create_mask([100, 200], [500, 600])
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| 352 | scan.stats(stat='mean', mask=m)
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| 353 | """
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| 354 | mask = mask or []
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| 355 | if not self._check_ifs():
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| 356 | raise ValueError("Cannot apply mask as the IFs have different "
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| 357 | "number of channels. Please use setselection() "
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| 358 | "to select individual IFs")
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| 359 |
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| 360 | statvals = self._math._stats(self, mask, stat)
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| 361 | def cb(i):
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| 362 | return statvals[i]
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| 363 |
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| 364 | return self._row_callback(cb, stat)
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| 365 |
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| 366 | def stddev(self, mask=None):
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| 367 | """
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| 368 | Determine the standard deviation of the current beam/if/pol
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| 369 | Takes a 'mask' as an optional parameter to specify which
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| 370 | channels should be excluded.
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| 371 | Parameters:
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| 372 | mask: an optional mask specifying where the standard
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| 373 | deviation should be determined.
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| 374 |
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| 375 | Example:
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| 376 | scan.set_unit('channel')
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| 377 | msk = scan.create_mask([100, 200], [500, 600])
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| 378 | scan.stddev(mask=m)
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| 379 | """
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| 380 | return self.stats(stat='stddev', mask=mask);
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| 381 |
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| 382 |
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| 383 | def get_column_names(self):
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| 384 | """
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| 385 | Return a list of column names, which can be used for selection.
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| 386 | """
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| 387 | return list(Scantable.get_column_names(self))
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| 388 |
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| 389 | def get_tsys(self):
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| 390 | """
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| 391 | Return the System temperatures.
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| 392 | Returns:
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| 393 | a list of Tsys values for the current selection
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| 394 | """
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| 395 |
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| 396 | return self._row_callback(self._gettsys, "Tsys")
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| 397 |
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| 398 | def _row_callback(self, callback, label):
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| 399 | out = ""
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| 400 | outvec = []
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| 401 | sep = '-'*50
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| 402 | for i in range(self.nrow()):
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| 403 | tm = self._gettime(i)
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| 404 | src = self._getsourcename(i)
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| 405 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src)
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| 406 | out += 'Time[%s]:\n' % (tm)
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| 407 | if self.nbeam(-1) > 1:
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| 408 | out += ' Beam[%d] ' % (self.getbeam(i))
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| 409 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i))
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| 410 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i))
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| 411 | outvec.append(callback(i))
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| 412 | out += '= %3.3f\n' % (outvec[i])
|
|---|
| 413 | out += sep+'\n'
|
|---|
| 414 | if rcParams['verbose']:
|
|---|
| 415 | print sep
|
|---|
| 416 | print " %s" % (label)
|
|---|
| 417 | print sep
|
|---|
| 418 | print out
|
|---|
| 419 | return outvec
|
|---|
| 420 |
|
|---|
| 421 | def _get_column(self, callback, row=-1):
|
|---|
| 422 | """
|
|---|
| 423 | """
|
|---|
| 424 | if row == -1:
|
|---|
| 425 | return [callback(i) for i in range(self.nrow())]
|
|---|
| 426 | else:
|
|---|
| 427 | if 0 <= row < self.nrow():
|
|---|
| 428 | return callback(row)
|
|---|
| 429 |
|
|---|
| 430 |
|
|---|
| 431 | def get_time(self, row=-1, asdatetime=False):
|
|---|
| 432 | """
|
|---|
| 433 | Get a list of time stamps for the observations.
|
|---|
| 434 | Return a datetime object for each integration time stamp in the scantable.
|
|---|
| 435 | Parameters:
|
|---|
| 436 | row: row no of integration. Default -1 return all rows
|
|---|
| 437 | asdatetime: return values as datetime objects rather than strings
|
|---|
| 438 | Example:
|
|---|
| 439 | none
|
|---|
| 440 | """
|
|---|
| 441 | from time import strptime
|
|---|
| 442 | from datetime import datetime
|
|---|
| 443 | times = self._get_column(self._gettime, row)
|
|---|
| 444 | if not asdatetime:
|
|---|
| 445 | return times
|
|---|
| 446 | format = "%Y/%m/%d/%H:%M:%S"
|
|---|
| 447 | if isinstance(times, list):
|
|---|
| 448 | return [datetime(*strptime(i, format)[:6]) for i in times]
|
|---|
| 449 | else:
|
|---|
| 450 | return datetime(*strptime(times, format)[:6])
|
|---|
| 451 |
|
|---|
| 452 |
|
|---|
| 453 | def get_inttime(self, row=-1):
|
|---|
| 454 | """
|
|---|
| 455 | Get a list of integration times for the observations.
|
|---|
| 456 | Return a time in seconds for each integration in the scantable.
|
|---|
| 457 | Parameters:
|
|---|
| 458 | row: row no of integration. Default -1 return all rows.
|
|---|
| 459 | Example:
|
|---|
| 460 | none
|
|---|
| 461 | """
|
|---|
| 462 | return self._get_column(self._getinttime, row)
|
|---|
| 463 |
|
|---|
| 464 |
|
|---|
| 465 | def get_sourcename(self, row=-1):
|
|---|
| 466 | """
|
|---|
| 467 | Get a list source names for the observations.
|
|---|
| 468 | Return a string for each integration in the scantable.
|
|---|
| 469 | Parameters:
|
|---|
| 470 | row: row no of integration. Default -1 return all rows.
|
|---|
| 471 | Example:
|
|---|
| 472 | none
|
|---|
| 473 | """
|
|---|
| 474 | return self._get_column(self._getsourcename, row)
|
|---|
| 475 |
|
|---|
| 476 | def get_elevation(self, row=-1):
|
|---|
| 477 | """
|
|---|
| 478 | Get a list of elevations for the observations.
|
|---|
| 479 | Return a float for each integration in the scantable.
|
|---|
| 480 | Parameters:
|
|---|
| 481 | row: row no of integration. Default -1 return all rows.
|
|---|
| 482 | Example:
|
|---|
| 483 | none
|
|---|
| 484 | """
|
|---|
| 485 | return self._get_column(self._getelevation, row)
|
|---|
| 486 |
|
|---|
| 487 | def get_azimuth(self, row=-1):
|
|---|
| 488 | """
|
|---|
| 489 | Get a list of azimuths for the observations.
|
|---|
| 490 | Return a float for each integration in the scantable.
|
|---|
| 491 | Parameters:
|
|---|
| 492 | row: row no of integration. Default -1 return all rows.
|
|---|
| 493 | Example:
|
|---|
| 494 | none
|
|---|
| 495 | """
|
|---|
| 496 | return self._get_column(self._getazimuth, row)
|
|---|
| 497 |
|
|---|
| 498 | def get_parangle(self, row=-1):
|
|---|
| 499 | """
|
|---|
| 500 | Get a list of parallactic angles for the observations.
|
|---|
| 501 | Return a float for each integration in the scantable.
|
|---|
| 502 | Parameters:
|
|---|
| 503 | row: row no of integration. Default -1 return all rows.
|
|---|
| 504 | Example:
|
|---|
| 505 | none
|
|---|
| 506 | """
|
|---|
| 507 | return self._get_column(self._getparangle, row)
|
|---|
| 508 |
|
|---|
| 509 | def get_direction(self, row=-1):
|
|---|
| 510 | """
|
|---|
| 511 | Get a list of Positions on the sky (direction) for the observations.
|
|---|
| 512 | Return a float for each integration in the scantable.
|
|---|
| 513 | Parameters:
|
|---|
| 514 | row: row no of integration. Default -1 return all rows
|
|---|
| 515 | Example:
|
|---|
| 516 | none
|
|---|
| 517 | """
|
|---|
| 518 | return self._get_column(self._getdirection, row)
|
|---|
| 519 |
|
|---|
| 520 | def get_directionval(self, row=-1):
|
|---|
| 521 | """
|
|---|
| 522 | Get a list of Positions on the sky (direction) for the observations.
|
|---|
| 523 | Return a float for each integration in the scantable.
|
|---|
| 524 | Parameters:
|
|---|
| 525 | row: row no of integration. Default -1 return all rows
|
|---|
| 526 | Example:
|
|---|
| 527 | none
|
|---|
| 528 | """
|
|---|
| 529 | return self._get_column(self._getdirectionvec, row)
|
|---|
| 530 |
|
|---|
| 531 |
|
|---|
| 532 | def set_unit(self, unit='channel'):
|
|---|
| 533 | """
|
|---|
| 534 | Set the unit for all following operations on this scantable
|
|---|
| 535 | Parameters:
|
|---|
| 536 | unit: optional unit, default is 'channel'
|
|---|
| 537 | one of '*Hz', 'km/s', 'channel', ''
|
|---|
| 538 | """
|
|---|
| 539 | varlist = vars()
|
|---|
| 540 | if unit in ['', 'pixel', 'channel']:
|
|---|
| 541 | unit = ''
|
|---|
| 542 | inf = list(self._getcoordinfo())
|
|---|
| 543 | inf[0] = unit
|
|---|
| 544 | self._setcoordinfo(inf)
|
|---|
| 545 | self._add_history("set_unit", varlist)
|
|---|
| 546 |
|
|---|
| 547 | @print_log_dec
|
|---|
| 548 | def set_instrument(self, instr):
|
|---|
| 549 | """
|
|---|
| 550 | Set the instrument for subsequent processing.
|
|---|
| 551 | Parameters:
|
|---|
| 552 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
|
|---|
| 553 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
|
|---|
| 554 | """
|
|---|
| 555 | self._setInstrument(instr)
|
|---|
| 556 | self._add_history("set_instument", vars())
|
|---|
| 557 |
|
|---|
| 558 | @print_log_dec
|
|---|
| 559 | def set_feedtype(self, feedtype):
|
|---|
| 560 | """
|
|---|
| 561 | Overwrite the feed type, which might not be set correctly.
|
|---|
| 562 | Parameters:
|
|---|
| 563 | feedtype: 'linear' or 'circular'
|
|---|
| 564 | """
|
|---|
| 565 | self._setfeedtype(feedtype)
|
|---|
| 566 | self._add_history("set_feedtype", vars())
|
|---|
| 567 |
|
|---|
| 568 | @print_log_dec
|
|---|
| 569 | def set_doppler(self, doppler='RADIO'):
|
|---|
| 570 | """
|
|---|
| 571 | Set the doppler for all following operations on this scantable.
|
|---|
| 572 | Parameters:
|
|---|
| 573 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
|
|---|
| 574 | """
|
|---|
| 575 | varlist = vars()
|
|---|
| 576 | inf = list(self._getcoordinfo())
|
|---|
| 577 | inf[2] = doppler
|
|---|
| 578 | self._setcoordinfo(inf)
|
|---|
| 579 | self._add_history("set_doppler", vars())
|
|---|
| 580 |
|
|---|
| 581 | @print_log_dec
|
|---|
| 582 | def set_freqframe(self, frame=None):
|
|---|
| 583 | """
|
|---|
| 584 | Set the frame type of the Spectral Axis.
|
|---|
| 585 | Parameters:
|
|---|
| 586 | frame: an optional frame type, default 'LSRK'. Valid frames are:
|
|---|
| 587 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY',
|
|---|
| 588 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'
|
|---|
| 589 | Examples:
|
|---|
| 590 | scan.set_freqframe('BARY')
|
|---|
| 591 | """
|
|---|
| 592 | frame = frame or rcParams['scantable.freqframe']
|
|---|
| 593 | varlist = vars()
|
|---|
| 594 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
|
|---|
| 595 | 'GEO', 'GALACTO', 'LGROUP', 'CMB']
|
|---|
| 596 |
|
|---|
| 597 | if frame in valid:
|
|---|
| 598 | inf = list(self._getcoordinfo())
|
|---|
| 599 | inf[1] = frame
|
|---|
| 600 | self._setcoordinfo(inf)
|
|---|
| 601 | self._add_history("set_freqframe", varlist)
|
|---|
| 602 | else:
|
|---|
| 603 | msg = "Please specify a valid freq type. Valid types are:\n", valid
|
|---|
| 604 | if rcParams['verbose']:
|
|---|
| 605 | print msg
|
|---|
| 606 | else:
|
|---|
| 607 | raise TypeError(msg)
|
|---|
| 608 |
|
|---|
| 609 | def set_dirframe(self, frame=""):
|
|---|
| 610 | """
|
|---|
| 611 | Set the frame type of the Direction on the sky.
|
|---|
| 612 | Parameters:
|
|---|
| 613 | frame: an optional frame type, default ''. Valid frames are:
|
|---|
| 614 | 'J2000', 'B1950', 'GALACTIC'
|
|---|
| 615 | Examples:
|
|---|
| 616 | scan.set_dirframe('GALACTIC')
|
|---|
| 617 | """
|
|---|
| 618 | varlist = vars()
|
|---|
| 619 | try:
|
|---|
| 620 | Scantable.set_dirframe(self, frame)
|
|---|
| 621 | except RuntimeError, msg:
|
|---|
| 622 | if rcParams['verbose']:
|
|---|
| 623 | print msg
|
|---|
| 624 | else:
|
|---|
| 625 | raise
|
|---|
| 626 | self._add_history("set_dirframe", varlist)
|
|---|
| 627 |
|
|---|
| 628 | def get_unit(self):
|
|---|
| 629 | """
|
|---|
| 630 | Get the default unit set in this scantable
|
|---|
| 631 | Returns:
|
|---|
| 632 | A unit string
|
|---|
| 633 | """
|
|---|
| 634 | inf = self._getcoordinfo()
|
|---|
| 635 | unit = inf[0]
|
|---|
| 636 | if unit == '': unit = 'channel'
|
|---|
| 637 | return unit
|
|---|
| 638 |
|
|---|
| 639 | def get_abcissa(self, rowno=0):
|
|---|
| 640 | """
|
|---|
| 641 | Get the abcissa in the current coordinate setup for the currently
|
|---|
| 642 | selected Beam/IF/Pol
|
|---|
| 643 | Parameters:
|
|---|
| 644 | rowno: an optional row number in the scantable. Default is the
|
|---|
| 645 | first row, i.e. rowno=0
|
|---|
| 646 | Returns:
|
|---|
| 647 | The abcissa values and the format string (as a dictionary)
|
|---|
| 648 | """
|
|---|
| 649 | abc = self._getabcissa(rowno)
|
|---|
| 650 | lbl = self._getabcissalabel(rowno)
|
|---|
| 651 | return abc, lbl
|
|---|
| 652 |
|
|---|
| 653 | def flag(self, mask=None):
|
|---|
| 654 | """
|
|---|
| 655 | Flag the selected data using an optional channel mask.
|
|---|
| 656 | Parameters:
|
|---|
| 657 | mask: an optional channel mask, created with create_mask. Default
|
|---|
| 658 | (no mask) is all channels.
|
|---|
| 659 | """
|
|---|
| 660 | varlist = vars()
|
|---|
| 661 | mask = mask or []
|
|---|
| 662 | try:
|
|---|
| 663 | self._flag(mask)
|
|---|
| 664 | except RuntimeError, msg:
|
|---|
| 665 | if rcParams['verbose']:
|
|---|
| 666 | print msg
|
|---|
| 667 | return
|
|---|
| 668 | else: raise
|
|---|
| 669 | self._add_history("flag", varlist)
|
|---|
| 670 |
|
|---|
| 671 | @print_log_dec
|
|---|
| 672 | def lag_flag(self, start, end, unit="MHz", insitu=None):
|
|---|
| 673 | """
|
|---|
| 674 | Flag the data in 'lag' space by providing a frequency to remove.
|
|---|
| 675 | Flagged data in the scantable gets interpolated over the region.
|
|---|
| 676 | No taper is applied.
|
|---|
| 677 | Parameters:
|
|---|
| 678 | start: the start frequency (really a period within the
|
|---|
| 679 | bandwidth) or period to remove
|
|---|
| 680 | end: the end frequency or period to remove
|
|---|
| 681 | unit: the frequency unit (default "MHz") or "" for
|
|---|
| 682 | explicit lag channels
|
|---|
| 683 | Notes:
|
|---|
| 684 | It is recommended to flag edges of the band or strong
|
|---|
| 685 | signals beforehand.
|
|---|
| 686 | """
|
|---|
| 687 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 688 | self._math._setinsitu(insitu)
|
|---|
| 689 | varlist = vars()
|
|---|
| 690 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.}
|
|---|
| 691 | if not (unit == "" or base.has_key(unit)):
|
|---|
| 692 | raise ValueError("%s is not a valid unit." % unit)
|
|---|
| 693 | try:
|
|---|
| 694 | if unit == "":
|
|---|
| 695 | s = scantable(self._math._lag_flag(self, start, end, "lags"))
|
|---|
| 696 | else:
|
|---|
| 697 | s = scantable(self._math._lag_flag(self, start*base[unit],
|
|---|
| 698 | end*base[unit], "frequency"))
|
|---|
| 699 | except RuntimeError, msg:
|
|---|
| 700 | if rcParams['verbose']:
|
|---|
| 701 | print msg
|
|---|
| 702 | return
|
|---|
| 703 | else: raise
|
|---|
| 704 | s._add_history("lag_flag", varlist)
|
|---|
| 705 | if insitu:
|
|---|
| 706 | self._assign(s)
|
|---|
| 707 | else:
|
|---|
| 708 | return s
|
|---|
| 709 |
|
|---|
| 710 | @print_log_dec
|
|---|
| 711 | def create_mask(self, *args, **kwargs):
|
|---|
| 712 | """
|
|---|
| 713 | Compute and return a mask based on [min, max] windows.
|
|---|
| 714 | The specified windows are to be INCLUDED, when the mask is
|
|---|
| 715 | applied.
|
|---|
| 716 | Parameters:
|
|---|
| 717 | [min, max], [min2, max2], ...
|
|---|
| 718 | Pairs of start/end points (inclusive)specifying the regions
|
|---|
| 719 | to be masked
|
|---|
| 720 | invert: optional argument. If specified as True,
|
|---|
| 721 | return an inverted mask, i.e. the regions
|
|---|
| 722 | specified are EXCLUDED
|
|---|
| 723 | row: create the mask using the specified row for
|
|---|
| 724 | unit conversions, default is row=0
|
|---|
| 725 | only necessary if frequency varies over rows.
|
|---|
| 726 | Example:
|
|---|
| 727 | scan.set_unit('channel')
|
|---|
| 728 | a)
|
|---|
| 729 | msk = scan.create_mask([400, 500], [800, 900])
|
|---|
| 730 | # masks everything outside 400 and 500
|
|---|
| 731 | # and 800 and 900 in the unit 'channel'
|
|---|
| 732 |
|
|---|
| 733 | b)
|
|---|
| 734 | msk = scan.create_mask([400, 500], [800, 900], invert=True)
|
|---|
| 735 | # masks the regions between 400 and 500
|
|---|
| 736 | # and 800 and 900 in the unit 'channel'
|
|---|
| 737 | c)
|
|---|
| 738 | mask only channel 400
|
|---|
| 739 | msk = scan.create_mask([400])
|
|---|
| 740 | """
|
|---|
| 741 | row = kwargs.get("row", 0)
|
|---|
| 742 | data = self._getabcissa(row)
|
|---|
| 743 | u = self._getcoordinfo()[0]
|
|---|
| 744 | if rcParams['verbose']:
|
|---|
| 745 | if u == "": u = "channel"
|
|---|
| 746 | msg = "The current mask window unit is %s" % u
|
|---|
| 747 | i = self._check_ifs()
|
|---|
| 748 | if not i:
|
|---|
| 749 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
|---|
| 750 | asaplog.push(msg)
|
|---|
| 751 | n = self.nchan()
|
|---|
| 752 | msk = _n_bools(n, False)
|
|---|
| 753 | # test if args is a 'list' or a 'normal *args - UGLY!!!
|
|---|
| 754 |
|
|---|
| 755 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
|
|---|
| 756 | and args or args[0]
|
|---|
| 757 | for window in ws:
|
|---|
| 758 | if len(window) == 1:
|
|---|
| 759 | window = [window[0], window[0]]
|
|---|
| 760 | if len(window) == 0 or len(window) > 2:
|
|---|
| 761 | raise ValueError("A window needs to be defined as [start(, end)]")
|
|---|
| 762 | if window[0] > window[1]:
|
|---|
| 763 | tmp = window[0]
|
|---|
| 764 | window[0] = window[1]
|
|---|
| 765 | window[1] = tmp
|
|---|
| 766 | for i in range(n):
|
|---|
| 767 | if data[i] >= window[0] and data[i] <= window[1]:
|
|---|
| 768 | msk[i] = True
|
|---|
| 769 | if kwargs.has_key('invert'):
|
|---|
| 770 | if kwargs.get('invert'):
|
|---|
| 771 | msk = mask_not(msk)
|
|---|
| 772 | return msk
|
|---|
| 773 |
|
|---|
| 774 | def get_restfreqs(self):
|
|---|
| 775 | """
|
|---|
| 776 | Get the restfrequency(s) stored in this scantable.
|
|---|
| 777 | The return value(s) are always of unit 'Hz'
|
|---|
| 778 | Parameters:
|
|---|
| 779 | none
|
|---|
| 780 | Returns:
|
|---|
| 781 | a list of doubles
|
|---|
| 782 | """
|
|---|
| 783 | return list(self._getrestfreqs())
|
|---|
| 784 |
|
|---|
| 785 |
|
|---|
| 786 | def set_restfreqs(self, freqs=None, unit='Hz'):
|
|---|
| 787 | """
|
|---|
| 788 | Set or replace the restfrequency specified and
|
|---|
| 789 | If the 'freqs' argument holds a scalar,
|
|---|
| 790 | then that rest frequency will be applied to all the selected
|
|---|
| 791 | data. If the 'freqs' argument holds
|
|---|
| 792 | a vector, then it MUST be of equal or smaller length than
|
|---|
| 793 | the number of IFs (and the available restfrequencies will be
|
|---|
| 794 | replaced by this vector). In this case, *all* data have
|
|---|
| 795 | the restfrequency set per IF according
|
|---|
| 796 | to the corresponding value you give in the 'freqs' vector.
|
|---|
| 797 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
|
|---|
| 798 | IF 1 gets restfreq 2e9.
|
|---|
| 799 | You can also specify the frequencies via a linecatalog.
|
|---|
| 800 |
|
|---|
| 801 | Parameters:
|
|---|
| 802 | freqs: list of rest frequency values or string idenitfiers
|
|---|
| 803 | unit: unit for rest frequency (default 'Hz')
|
|---|
| 804 |
|
|---|
| 805 | Example:
|
|---|
| 806 | # set the given restfrequency for the whole table
|
|---|
| 807 | scan.set_restfreqs(freqs=1.4e9)
|
|---|
| 808 | # If thee number of IFs in the data is >= 2 IF0 gets the first
|
|---|
| 809 | # value IF1 the second...
|
|---|
| 810 | scan.set_restfreqs(freqs=[1.4e9, 1.67e9])
|
|---|
| 811 | #set the given restfrequency for the whole table (by name)
|
|---|
| 812 | scan.set_restfreqs(freqs="OH1667")
|
|---|
| 813 |
|
|---|
| 814 | Note:
|
|---|
| 815 | To do more sophisticate Restfrequency setting, e.g. on a
|
|---|
| 816 | source and IF basis, use scantable.set_selection() before using
|
|---|
| 817 | this function.
|
|---|
| 818 | # provide your scantable is called scan
|
|---|
| 819 | selection = selector()
|
|---|
| 820 | selection.set_name("ORION*")
|
|---|
| 821 | selection.set_ifs([1])
|
|---|
| 822 | scan.set_selection(selection)
|
|---|
| 823 | scan.set_restfreqs(freqs=86.6e9)
|
|---|
| 824 |
|
|---|
| 825 | """
|
|---|
| 826 | varlist = vars()
|
|---|
| 827 | from asap import linecatalog
|
|---|
| 828 | # simple value
|
|---|
| 829 | if isinstance(freqs, int) or isinstance(freqs, float):
|
|---|
| 830 | self._setrestfreqs(freqs, "",unit)
|
|---|
| 831 | # list of values
|
|---|
| 832 | elif isinstance(freqs, list) or isinstance(freqs, tuple):
|
|---|
| 833 | # list values are scalars
|
|---|
| 834 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
|
|---|
| 835 | sel = selector()
|
|---|
| 836 | savesel = self._getselection()
|
|---|
| 837 | iflist = self.getifnos()
|
|---|
| 838 | for i in xrange(len(freqs)):
|
|---|
| 839 | sel.set_ifs(iflist[i])
|
|---|
| 840 | self._setselection(sel)
|
|---|
| 841 | self._setrestfreqs(freqs[i], "",unit)
|
|---|
| 842 | self._setselection(savesel)
|
|---|
| 843 | # list values are tuples, (value, name)
|
|---|
| 844 | elif isinstance(freqs[-1], dict):
|
|---|
| 845 | sel = selector()
|
|---|
| 846 | savesel = self._getselection()
|
|---|
| 847 | iflist = self.getifnos()
|
|---|
| 848 | for i in xrange(len(freqs)):
|
|---|
| 849 | sel.set_ifs(iflist[i])
|
|---|
| 850 | self._setselection(sel)
|
|---|
| 851 | self._setrestfreqs(freqs[i]["value"],
|
|---|
| 852 | freqs[i]["name"], "MHz")
|
|---|
| 853 | self._setselection(savesel)
|
|---|
| 854 | # freqs are to be taken from a linecatalog
|
|---|
| 855 | elif isinstance(freqs, linecatalog):
|
|---|
| 856 | sel = selector()
|
|---|
| 857 | savesel = self._getselection()
|
|---|
| 858 | iflist = self.getifnos()
|
|---|
| 859 | for i in xrange(freqs.nrow()):
|
|---|
| 860 | sel.set_ifs(iflist[i])
|
|---|
| 861 | self._setselection(sel)
|
|---|
| 862 | self._setrestfreqs(freqs.get_frequency(i),
|
|---|
| 863 | freqs.get_name(i), "MHz")
|
|---|
| 864 | # ensure that we are not iterating past nIF
|
|---|
| 865 | if i == self.nif()-1: break
|
|---|
| 866 | self._setselection(savesel)
|
|---|
| 867 | else:
|
|---|
| 868 | return
|
|---|
| 869 | self._add_history("set_restfreqs", varlist)
|
|---|
| 870 |
|
|---|
| 871 | def shift_refpix(self, delta):
|
|---|
| 872 | """
|
|---|
| 873 | Shift the reference pixel of the Spectra Coordinate by an
|
|---|
| 874 | integer amount.
|
|---|
| 875 | Parameters:
|
|---|
| 876 | delta: the amount to shift by
|
|---|
| 877 | Note:
|
|---|
| 878 | Be careful using this with broadband data.
|
|---|
| 879 | """
|
|---|
| 880 | Scantable.shift(self, delta)
|
|---|
| 881 |
|
|---|
| 882 | def history(self, filename=None):
|
|---|
| 883 | """
|
|---|
| 884 | Print the history. Optionally to a file.
|
|---|
| 885 | Parameters:
|
|---|
| 886 | filename: The name of the file to save the history to.
|
|---|
| 887 | """
|
|---|
| 888 | hist = list(self._gethistory())
|
|---|
| 889 | out = "-"*80
|
|---|
| 890 | for h in hist:
|
|---|
| 891 | if h.startswith("---"):
|
|---|
| 892 | out += "\n"+h
|
|---|
| 893 | else:
|
|---|
| 894 | items = h.split("##")
|
|---|
| 895 | date = items[0]
|
|---|
| 896 | func = items[1]
|
|---|
| 897 | items = items[2:]
|
|---|
| 898 | out += "\n"+date+"\n"
|
|---|
| 899 | out += "Function: %s\n Parameters:" % (func)
|
|---|
| 900 | for i in items:
|
|---|
| 901 | s = i.split("=")
|
|---|
| 902 | out += "\n %s = %s" % (s[0], s[1])
|
|---|
| 903 | out += "\n"+"-"*80
|
|---|
| 904 | if filename is not None:
|
|---|
| 905 | if filename is "":
|
|---|
| 906 | filename = 'scantable_history.txt'
|
|---|
| 907 | import os
|
|---|
| 908 | filename = os.path.expandvars(os.path.expanduser(filename))
|
|---|
| 909 | if not os.path.isdir(filename):
|
|---|
| 910 | data = open(filename, 'w')
|
|---|
| 911 | data.write(out)
|
|---|
| 912 | data.close()
|
|---|
| 913 | else:
|
|---|
| 914 | msg = "Illegal file name '%s'." % (filename)
|
|---|
| 915 | if rcParams['verbose']:
|
|---|
| 916 | print msg
|
|---|
| 917 | else:
|
|---|
| 918 | raise IOError(msg)
|
|---|
| 919 | if rcParams['verbose']:
|
|---|
| 920 | try:
|
|---|
| 921 | from IPython.genutils import page as pager
|
|---|
| 922 | except ImportError:
|
|---|
| 923 | from pydoc import pager
|
|---|
| 924 | pager(out)
|
|---|
| 925 | else:
|
|---|
| 926 | return out
|
|---|
| 927 | return
|
|---|
| 928 | #
|
|---|
| 929 | # Maths business
|
|---|
| 930 | #
|
|---|
| 931 | @print_log_dec
|
|---|
| 932 | def average_time(self, mask=None, scanav=False, weight='tint', align=False):
|
|---|
| 933 | """
|
|---|
| 934 | Return the (time) weighted average of a scan.
|
|---|
| 935 | Note:
|
|---|
| 936 | in channels only - align if necessary
|
|---|
| 937 | Parameters:
|
|---|
| 938 | mask: an optional mask (only used for 'var' and 'tsys'
|
|---|
| 939 | weighting)
|
|---|
| 940 | scanav: True averages each scan separately
|
|---|
| 941 | False (default) averages all scans together,
|
|---|
| 942 | weight: Weighting scheme.
|
|---|
| 943 | 'none' (mean no weight)
|
|---|
| 944 | 'var' (1/var(spec) weighted)
|
|---|
| 945 | 'tsys' (1/Tsys**2 weighted)
|
|---|
| 946 | 'tint' (integration time weighted)
|
|---|
| 947 | 'tintsys' (Tint/Tsys**2)
|
|---|
| 948 | 'median' ( median averaging)
|
|---|
| 949 | The default is 'tint'
|
|---|
| 950 | align: align the spectra in velocity before averaging. It takes
|
|---|
| 951 | the time of the first spectrum as reference time.
|
|---|
| 952 | Example:
|
|---|
| 953 | # time average the scantable without using a mask
|
|---|
| 954 | newscan = scan.average_time()
|
|---|
| 955 | """
|
|---|
| 956 | varlist = vars()
|
|---|
| 957 | weight = weight or 'TINT'
|
|---|
| 958 | mask = mask or ()
|
|---|
| 959 | scanav = (scanav and 'SCAN') or 'NONE'
|
|---|
| 960 | scan = (self, )
|
|---|
| 961 | try:
|
|---|
| 962 | if align:
|
|---|
| 963 | scan = (self.freq_align(insitu=False), )
|
|---|
| 964 | s = None
|
|---|
| 965 | if weight.upper() == 'MEDIAN':
|
|---|
| 966 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
|
|---|
| 967 | scanav))
|
|---|
| 968 | else:
|
|---|
| 969 | s = scantable(self._math._average(scan, mask, weight.upper(),
|
|---|
| 970 | scanav))
|
|---|
| 971 | except RuntimeError, msg:
|
|---|
| 972 | if rcParams['verbose']:
|
|---|
| 973 | print msg
|
|---|
| 974 | return
|
|---|
| 975 | else: raise
|
|---|
| 976 | s._add_history("average_time", varlist)
|
|---|
| 977 | return s
|
|---|
| 978 |
|
|---|
| 979 | @print_log_dec
|
|---|
| 980 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
|
|---|
| 981 | """
|
|---|
| 982 | Return a scan where all spectra are converted to either
|
|---|
| 983 | Jansky or Kelvin depending upon the flux units of the scan table.
|
|---|
| 984 | By default the function tries to look the values up internally.
|
|---|
| 985 | If it can't find them (or if you want to over-ride), you must
|
|---|
| 986 | specify EITHER jyperk OR eta (and D which it will try to look up
|
|---|
| 987 | also if you don't set it). jyperk takes precedence if you set both.
|
|---|
| 988 | Parameters:
|
|---|
| 989 | jyperk: the Jy / K conversion factor
|
|---|
| 990 | eta: the aperture efficiency
|
|---|
| 991 | d: the geomtric diameter (metres)
|
|---|
| 992 | insitu: if False a new scantable is returned.
|
|---|
| 993 | Otherwise, the scaling is done in-situ
|
|---|
| 994 | The default is taken from .asaprc (False)
|
|---|
| 995 | """
|
|---|
| 996 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 997 | self._math._setinsitu(insitu)
|
|---|
| 998 | varlist = vars()
|
|---|
| 999 | jyperk = jyperk or -1.0
|
|---|
| 1000 | d = d or -1.0
|
|---|
| 1001 | eta = eta or -1.0
|
|---|
| 1002 | s = scantable(self._math._convertflux(self, d, eta, jyperk))
|
|---|
| 1003 | s._add_history("convert_flux", varlist)
|
|---|
| 1004 | if insitu: self._assign(s)
|
|---|
| 1005 | else: return s
|
|---|
| 1006 |
|
|---|
| 1007 | @print_log_dec
|
|---|
| 1008 | def gain_el(self, poly=None, filename="", method="linear", insitu=None):
|
|---|
| 1009 | """
|
|---|
| 1010 | Return a scan after applying a gain-elevation correction.
|
|---|
| 1011 | The correction can be made via either a polynomial or a
|
|---|
| 1012 | table-based interpolation (and extrapolation if necessary).
|
|---|
| 1013 | You specify polynomial coefficients, an ascii table or neither.
|
|---|
| 1014 | If you specify neither, then a polynomial correction will be made
|
|---|
| 1015 | with built in coefficients known for certain telescopes (an error
|
|---|
| 1016 | will occur if the instrument is not known).
|
|---|
| 1017 | The data and Tsys are *divided* by the scaling factors.
|
|---|
| 1018 | Parameters:
|
|---|
| 1019 | poly: Polynomial coefficients (default None) to compute a
|
|---|
| 1020 | gain-elevation correction as a function of
|
|---|
| 1021 | elevation (in degrees).
|
|---|
| 1022 | filename: The name of an ascii file holding correction factors.
|
|---|
| 1023 | The first row of the ascii file must give the column
|
|---|
| 1024 | names and these MUST include columns
|
|---|
| 1025 | "ELEVATION" (degrees) and "FACTOR" (multiply data
|
|---|
| 1026 | by this) somewhere.
|
|---|
| 1027 | The second row must give the data type of the
|
|---|
| 1028 | column. Use 'R' for Real and 'I' for Integer.
|
|---|
| 1029 | An example file would be
|
|---|
| 1030 | (actual factors are arbitrary) :
|
|---|
| 1031 |
|
|---|
| 1032 | TIME ELEVATION FACTOR
|
|---|
| 1033 | R R R
|
|---|
| 1034 | 0.1 0 0.8
|
|---|
| 1035 | 0.2 20 0.85
|
|---|
| 1036 | 0.3 40 0.9
|
|---|
| 1037 | 0.4 60 0.85
|
|---|
| 1038 | 0.5 80 0.8
|
|---|
| 1039 | 0.6 90 0.75
|
|---|
| 1040 | method: Interpolation method when correcting from a table.
|
|---|
| 1041 | Values are "nearest", "linear" (default), "cubic"
|
|---|
| 1042 | and "spline"
|
|---|
| 1043 | insitu: if False a new scantable is returned.
|
|---|
| 1044 | Otherwise, the scaling is done in-situ
|
|---|
| 1045 | The default is taken from .asaprc (False)
|
|---|
| 1046 | """
|
|---|
| 1047 |
|
|---|
| 1048 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1049 | self._math._setinsitu(insitu)
|
|---|
| 1050 | varlist = vars()
|
|---|
| 1051 | poly = poly or ()
|
|---|
| 1052 | from os.path import expandvars
|
|---|
| 1053 | filename = expandvars(filename)
|
|---|
| 1054 | s = scantable(self._math._gainel(self, poly, filename, method))
|
|---|
| 1055 | s._add_history("gain_el", varlist)
|
|---|
| 1056 | if insitu:
|
|---|
| 1057 | self._assign(s)
|
|---|
| 1058 | else:
|
|---|
| 1059 | return s
|
|---|
| 1060 |
|
|---|
| 1061 | @print_log_dec
|
|---|
| 1062 | def freq_align(self, reftime=None, method='cubic', insitu=None):
|
|---|
| 1063 | """
|
|---|
| 1064 | Return a scan where all rows have been aligned in frequency/velocity.
|
|---|
| 1065 | The alignment frequency frame (e.g. LSRK) is that set by function
|
|---|
| 1066 | set_freqframe.
|
|---|
| 1067 | Parameters:
|
|---|
| 1068 | reftime: reference time to align at. By default, the time of
|
|---|
| 1069 | the first row of data is used.
|
|---|
| 1070 | method: Interpolation method for regridding the spectra.
|
|---|
| 1071 | Choose from "nearest", "linear", "cubic" (default)
|
|---|
| 1072 | and "spline"
|
|---|
| 1073 | insitu: if False a new scantable is returned.
|
|---|
| 1074 | Otherwise, the scaling is done in-situ
|
|---|
| 1075 | The default is taken from .asaprc (False)
|
|---|
| 1076 | """
|
|---|
| 1077 | if insitu is None: insitu = rcParams["insitu"]
|
|---|
| 1078 | self._math._setinsitu(insitu)
|
|---|
| 1079 | varlist = vars()
|
|---|
| 1080 | reftime = reftime or ""
|
|---|
| 1081 | s = scantable(self._math._freq_align(self, reftime, method))
|
|---|
| 1082 | s._add_history("freq_align", varlist)
|
|---|
| 1083 | if insitu: self._assign(s)
|
|---|
| 1084 | else: return s
|
|---|
| 1085 |
|
|---|
| 1086 | @print_log_dec
|
|---|
| 1087 | def opacity(self, tau, insitu=None):
|
|---|
| 1088 | """
|
|---|
| 1089 | Apply an opacity correction. The data
|
|---|
| 1090 | and Tsys are multiplied by the correction factor.
|
|---|
| 1091 | Parameters:
|
|---|
| 1092 | tau: Opacity from which the correction factor is
|
|---|
| 1093 | exp(tau*ZD)
|
|---|
| 1094 | where ZD is the zenith-distance
|
|---|
| 1095 | insitu: if False a new scantable is returned.
|
|---|
| 1096 | Otherwise, the scaling is done in-situ
|
|---|
| 1097 | The default is taken from .asaprc (False)
|
|---|
| 1098 | """
|
|---|
| 1099 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1100 | self._math._setinsitu(insitu)
|
|---|
| 1101 | varlist = vars()
|
|---|
| 1102 | s = scantable(self._math._opacity(self, tau))
|
|---|
| 1103 | s._add_history("opacity", varlist)
|
|---|
| 1104 | if insitu: self._assign(s)
|
|---|
| 1105 | else: return s
|
|---|
| 1106 |
|
|---|
| 1107 | @print_log_dec
|
|---|
| 1108 | def bin(self, width=5, insitu=None):
|
|---|
| 1109 | """
|
|---|
| 1110 | Return a scan where all spectra have been binned up.
|
|---|
| 1111 | Parameters:
|
|---|
| 1112 | width: The bin width (default=5) in pixels
|
|---|
| 1113 | insitu: if False a new scantable is returned.
|
|---|
| 1114 | Otherwise, the scaling is done in-situ
|
|---|
| 1115 | The default is taken from .asaprc (False)
|
|---|
| 1116 | """
|
|---|
| 1117 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1118 | self._math._setinsitu(insitu)
|
|---|
| 1119 | varlist = vars()
|
|---|
| 1120 | s = scantable(self._math._bin(self, width))
|
|---|
| 1121 | s._add_history("bin", varlist)
|
|---|
| 1122 | if insitu:
|
|---|
| 1123 | self._assign(s)
|
|---|
| 1124 | else:
|
|---|
| 1125 | return s
|
|---|
| 1126 |
|
|---|
| 1127 | @print_log_dec
|
|---|
| 1128 | def resample(self, width=5, method='cubic', insitu=None):
|
|---|
| 1129 | """
|
|---|
| 1130 | Return a scan where all spectra have been binned up.
|
|---|
| 1131 |
|
|---|
| 1132 | Parameters:
|
|---|
| 1133 | width: The bin width (default=5) in pixels
|
|---|
| 1134 | method: Interpolation method when correcting from a table.
|
|---|
| 1135 | Values are "nearest", "linear", "cubic" (default)
|
|---|
| 1136 | and "spline"
|
|---|
| 1137 | insitu: if False a new scantable is returned.
|
|---|
| 1138 | Otherwise, the scaling is done in-situ
|
|---|
| 1139 | The default is taken from .asaprc (False)
|
|---|
| 1140 | """
|
|---|
| 1141 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1142 | self._math._setinsitu(insitu)
|
|---|
| 1143 | varlist = vars()
|
|---|
| 1144 | s = scantable(self._math._resample(self, method, width))
|
|---|
| 1145 | s._add_history("resample", varlist)
|
|---|
| 1146 | if insitu: self._assign(s)
|
|---|
| 1147 | else: return s
|
|---|
| 1148 |
|
|---|
| 1149 | @print_log_dec
|
|---|
| 1150 | def average_pol(self, mask=None, weight='none'):
|
|---|
| 1151 | """
|
|---|
| 1152 | Average the Polarisations together.
|
|---|
| 1153 | Parameters:
|
|---|
| 1154 | mask: An optional mask defining the region, where the
|
|---|
| 1155 | averaging will be applied. The output will have all
|
|---|
| 1156 | specified points masked.
|
|---|
| 1157 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
|---|
| 1158 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
|---|
| 1159 | """
|
|---|
| 1160 | varlist = vars()
|
|---|
| 1161 | mask = mask or ()
|
|---|
| 1162 | s = scantable(self._math._averagepol(self, mask, weight.upper()))
|
|---|
| 1163 | s._add_history("average_pol", varlist)
|
|---|
| 1164 | return s
|
|---|
| 1165 |
|
|---|
| 1166 | @print_log_dec
|
|---|
| 1167 | def average_beam(self, mask=None, weight='none'):
|
|---|
| 1168 | """
|
|---|
| 1169 | Average the Beams together.
|
|---|
| 1170 | Parameters:
|
|---|
| 1171 | mask: An optional mask defining the region, where the
|
|---|
| 1172 | averaging will be applied. The output will have all
|
|---|
| 1173 | specified points masked.
|
|---|
| 1174 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
|---|
| 1175 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
|---|
| 1176 | """
|
|---|
| 1177 | varlist = vars()
|
|---|
| 1178 | mask = mask or ()
|
|---|
| 1179 | s = scantable(self._math._averagebeams(self, mask, weight.upper()))
|
|---|
| 1180 | s._add_history("average_beam", varlist)
|
|---|
| 1181 | return s
|
|---|
| 1182 |
|
|---|
| 1183 | def parallactify(self, pflag):
|
|---|
| 1184 | varlist = vars()
|
|---|
| 1185 | self._parallactify(pflag)
|
|---|
| 1186 | self._add_history("parallactify", varlist)
|
|---|
| 1187 |
|
|---|
| 1188 | @print_log_dec
|
|---|
| 1189 | def convert_pol(self, poltype=None):
|
|---|
| 1190 | """
|
|---|
| 1191 | Convert the data to a different polarisation type.
|
|---|
| 1192 | Note that you will need cross-polarisation terms for most conversions.
|
|---|
| 1193 | Parameters:
|
|---|
| 1194 | poltype: The new polarisation type. Valid types are:
|
|---|
| 1195 | "linear", "circular", "stokes" and "linpol"
|
|---|
| 1196 | """
|
|---|
| 1197 | varlist = vars()
|
|---|
| 1198 | try:
|
|---|
| 1199 | s = scantable(self._math._convertpol(self, poltype))
|
|---|
| 1200 | except RuntimeError, msg:
|
|---|
| 1201 | if rcParams['verbose']:
|
|---|
| 1202 | print msg
|
|---|
| 1203 | return
|
|---|
| 1204 | else:
|
|---|
| 1205 | raise
|
|---|
| 1206 | s._add_history("convert_pol", varlist)
|
|---|
| 1207 | return s
|
|---|
| 1208 |
|
|---|
| 1209 | @print_log_dec
|
|---|
| 1210 | def smooth(self, kernel="hanning", width=5.0, order=2, insitu=None):
|
|---|
| 1211 | """
|
|---|
| 1212 | Smooth the spectrum by the specified kernel (conserving flux).
|
|---|
| 1213 | Parameters:
|
|---|
| 1214 | kernel: The type of smoothing kernel. Select from
|
|---|
| 1215 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian'
|
|---|
| 1216 | or 'poly'
|
|---|
| 1217 | width: The width of the kernel in pixels. For hanning this is
|
|---|
| 1218 | ignored otherwise it defauls to 5 pixels.
|
|---|
| 1219 | For 'gaussian' it is the Full Width Half
|
|---|
| 1220 | Maximum. For 'boxcar' it is the full width.
|
|---|
| 1221 | For 'rmedian' and 'poly' it is the half width.
|
|---|
| 1222 | order: Optional parameter for 'poly' kernel (default is 2), to
|
|---|
| 1223 | specify the order of the polnomial. Ignored by all other
|
|---|
| 1224 | kernels.
|
|---|
| 1225 | insitu: if False a new scantable is returned.
|
|---|
| 1226 | Otherwise, the scaling is done in-situ
|
|---|
| 1227 | The default is taken from .asaprc (False)
|
|---|
| 1228 | Example:
|
|---|
| 1229 | none
|
|---|
| 1230 | """
|
|---|
| 1231 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1232 | self._math._setinsitu(insitu)
|
|---|
| 1233 | varlist = vars()
|
|---|
| 1234 | s = scantable(self._math._smooth(self, kernel.lower(), width, order))
|
|---|
| 1235 | s._add_history("smooth", varlist)
|
|---|
| 1236 | if insitu: self._assign(s)
|
|---|
| 1237 | else: return s
|
|---|
| 1238 |
|
|---|
| 1239 | @print_log_dec
|
|---|
| 1240 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None):
|
|---|
| 1241 | """
|
|---|
| 1242 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 1243 | Parameters:
|
|---|
| 1244 | mask: an optional mask
|
|---|
| 1245 | order: the order of the polynomial (default is 0)
|
|---|
| 1246 | plot: plot the fit and the residual. In this each
|
|---|
| 1247 | indivual fit has to be approved, by typing 'y'
|
|---|
| 1248 | or 'n'
|
|---|
| 1249 | uselin: use linear polynomial fit
|
|---|
| 1250 | insitu: if False a new scantable is returned.
|
|---|
| 1251 | Otherwise, the scaling is done in-situ
|
|---|
| 1252 | The default is taken from .asaprc (False)
|
|---|
| 1253 | Example:
|
|---|
| 1254 | # return a scan baselined by a third order polynomial,
|
|---|
| 1255 | # not using a mask
|
|---|
| 1256 | bscan = scan.poly_baseline(order=3)
|
|---|
| 1257 | """
|
|---|
| 1258 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1259 | varlist = vars()
|
|---|
| 1260 | if mask is None:
|
|---|
| 1261 | mask = [True for i in xrange(self.nchan(-1))]
|
|---|
| 1262 | from asap.asapfitter import fitter
|
|---|
| 1263 | try:
|
|---|
| 1264 | f = fitter()
|
|---|
| 1265 | f.set_scan(self, mask)
|
|---|
| 1266 | #f.set_function(poly=order)
|
|---|
| 1267 | if uselin:
|
|---|
| 1268 | f.set_function(lpoly=order)
|
|---|
| 1269 | else:
|
|---|
| 1270 | f.set_function(poly=order)
|
|---|
| 1271 | s = f.auto_fit(insitu, plot=plot)
|
|---|
| 1272 | s._add_history("poly_baseline", varlist)
|
|---|
| 1273 | if insitu: self._assign(s)
|
|---|
| 1274 | else: return s
|
|---|
| 1275 | except RuntimeError:
|
|---|
| 1276 | msg = "The fit failed, possibly because it didn't converge."
|
|---|
| 1277 | if rcParams['verbose']:
|
|---|
| 1278 | print msg
|
|---|
| 1279 | return
|
|---|
| 1280 | else:
|
|---|
| 1281 | raise RuntimeError(msg)
|
|---|
| 1282 |
|
|---|
| 1283 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0,
|
|---|
| 1284 | threshold=3, chan_avg_limit=1, plot=False,
|
|---|
| 1285 | insitu=None):
|
|---|
| 1286 | """
|
|---|
| 1287 | Return a scan which has been baselined (all rows) by a polynomial.
|
|---|
| 1288 | Spectral lines are detected first using linefinder and masked out
|
|---|
| 1289 | to avoid them affecting the baseline solution.
|
|---|
| 1290 |
|
|---|
| 1291 | Parameters:
|
|---|
| 1292 | mask: an optional mask retreived from scantable
|
|---|
| 1293 | edge: an optional number of channel to drop at
|
|---|
| 1294 | the edge of spectrum. If only one value is
|
|---|
| 1295 | specified, the same number will be dropped from
|
|---|
| 1296 | both sides of the spectrum. Default is to keep
|
|---|
| 1297 | all channels. Nested tuples represent individual
|
|---|
| 1298 | edge selection for different IFs (a number of spectral
|
|---|
| 1299 | channels can be different)
|
|---|
| 1300 | order: the order of the polynomial (default is 0)
|
|---|
| 1301 | threshold: the threshold used by line finder. It is better to
|
|---|
| 1302 | keep it large as only strong lines affect the
|
|---|
| 1303 | baseline solution.
|
|---|
| 1304 | chan_avg_limit:
|
|---|
| 1305 | a maximum number of consequtive spectral channels to
|
|---|
| 1306 | average during the search of weak and broad lines.
|
|---|
| 1307 | The default is no averaging (and no search for weak
|
|---|
| 1308 | lines). If such lines can affect the fitted baseline
|
|---|
| 1309 | (e.g. a high order polynomial is fitted), increase this
|
|---|
| 1310 | parameter (usually values up to 8 are reasonable). Most
|
|---|
| 1311 | users of this method should find the default value
|
|---|
| 1312 | sufficient.
|
|---|
| 1313 | plot: plot the fit and the residual. In this each
|
|---|
| 1314 | indivual fit has to be approved, by typing 'y'
|
|---|
| 1315 | or 'n'
|
|---|
| 1316 | insitu: if False a new scantable is returned.
|
|---|
| 1317 | Otherwise, the scaling is done in-situ
|
|---|
| 1318 | The default is taken from .asaprc (False)
|
|---|
| 1319 |
|
|---|
| 1320 | Example:
|
|---|
| 1321 | scan2=scan.auto_poly_baseline(order=7)
|
|---|
| 1322 | """
|
|---|
| 1323 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1324 | varlist = vars()
|
|---|
| 1325 | from asap.asapfitter import fitter
|
|---|
| 1326 | from asap.asaplinefind import linefinder
|
|---|
| 1327 | from asap import _is_sequence_or_number as _is_valid
|
|---|
| 1328 |
|
|---|
| 1329 | # check whether edge is set up for each IF individually
|
|---|
| 1330 | individualedge = False;
|
|---|
| 1331 | if len(edge) > 1:
|
|---|
| 1332 | if isinstance(edge[0], list) or isinstance(edge[0], tuple):
|
|---|
| 1333 | individualedge = True;
|
|---|
| 1334 |
|
|---|
| 1335 | if not _is_valid(edge, int) and not individualedge:
|
|---|
| 1336 | raise ValueError, "Parameter 'edge' has to be an integer or a \
|
|---|
| 1337 | pair of integers specified as a tuple. Nested tuples are allowed \
|
|---|
| 1338 | to make individual selection for different IFs."
|
|---|
| 1339 |
|
|---|
| 1340 | curedge = (0, 0)
|
|---|
| 1341 | if individualedge:
|
|---|
| 1342 | for edgepar in edge:
|
|---|
| 1343 | if not _is_valid(edgepar, int):
|
|---|
| 1344 | raise ValueError, "Each element of the 'edge' tuple has \
|
|---|
| 1345 | to be a pair of integers or an integer."
|
|---|
| 1346 | else:
|
|---|
| 1347 | curedge = edge;
|
|---|
| 1348 |
|
|---|
| 1349 | # setup fitter
|
|---|
| 1350 | f = fitter()
|
|---|
| 1351 | f.set_function(poly=order)
|
|---|
| 1352 |
|
|---|
| 1353 | # setup line finder
|
|---|
| 1354 | fl = linefinder()
|
|---|
| 1355 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
|
|---|
| 1356 |
|
|---|
| 1357 | if not insitu:
|
|---|
| 1358 | workscan = self.copy()
|
|---|
| 1359 | else:
|
|---|
| 1360 | workscan = self
|
|---|
| 1361 |
|
|---|
| 1362 | fl.set_scan(workscan)
|
|---|
| 1363 |
|
|---|
| 1364 | rows = range(workscan.nrow())
|
|---|
| 1365 | asaplog.push("Processing:")
|
|---|
| 1366 | for r in rows:
|
|---|
| 1367 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
|
|---|
| 1368 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
|
|---|
| 1369 | workscan.getpol(r), workscan.getcycle(r))
|
|---|
| 1370 | asaplog.push(msg, False)
|
|---|
| 1371 |
|
|---|
| 1372 | # figure out edge parameter
|
|---|
| 1373 | if individualedge:
|
|---|
| 1374 | if len(edge) >= workscan.getif(r):
|
|---|
| 1375 | raise RuntimeError, "Number of edge elements appear to " \
|
|---|
| 1376 | "be less than the number of IFs"
|
|---|
| 1377 | curedge = edge[workscan.getif(r)]
|
|---|
| 1378 |
|
|---|
| 1379 | # setup line finder
|
|---|
| 1380 | fl.find_lines(r, mask, curedge)
|
|---|
| 1381 | f.set_data(workscan._getabcissa(r), workscan._getspectrum(r),
|
|---|
| 1382 | mask_and(workscan._getmask(r), fl.get_mask()))
|
|---|
| 1383 | f.fit()
|
|---|
| 1384 | x = f.get_parameters()
|
|---|
| 1385 | if plot:
|
|---|
| 1386 | f.plot(residual=True)
|
|---|
| 1387 | x = raw_input("Accept fit ( [y]/n ): ")
|
|---|
| 1388 | if x.upper() == 'N':
|
|---|
| 1389 | continue
|
|---|
| 1390 | workscan._setspectrum(f.fitter.getresidual(), r)
|
|---|
| 1391 | if plot:
|
|---|
| 1392 | f._p.unmap()
|
|---|
| 1393 | f._p = None
|
|---|
| 1394 | workscan._add_history("auto_poly_baseline", varlist)
|
|---|
| 1395 | if insitu:
|
|---|
| 1396 | self._assign(workscan)
|
|---|
| 1397 | else:
|
|---|
| 1398 | return workscan
|
|---|
| 1399 |
|
|---|
| 1400 | @print_log_dec
|
|---|
| 1401 | def rotate_linpolphase(self, angle):
|
|---|
| 1402 | """
|
|---|
| 1403 | Rotate the phase of the complex polarization O=Q+iU correlation.
|
|---|
| 1404 | This is always done in situ in the raw data. So if you call this
|
|---|
| 1405 | function more than once then each call rotates the phase further.
|
|---|
| 1406 | Parameters:
|
|---|
| 1407 | angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1408 | Examples:
|
|---|
| 1409 | scan.rotate_linpolphase(2.3)
|
|---|
| 1410 | """
|
|---|
| 1411 | varlist = vars()
|
|---|
| 1412 | self._math._rotate_linpolphase(self, angle)
|
|---|
| 1413 | self._add_history("rotate_linpolphase", varlist)
|
|---|
| 1414 | return
|
|---|
| 1415 |
|
|---|
| 1416 | @print_log_dec
|
|---|
| 1417 | def rotate_xyphase(self, angle):
|
|---|
| 1418 | """
|
|---|
| 1419 | Rotate the phase of the XY correlation. This is always done in situ
|
|---|
| 1420 | in the data. So if you call this function more than once
|
|---|
| 1421 | then each call rotates the phase further.
|
|---|
| 1422 | Parameters:
|
|---|
| 1423 | angle: The angle (degrees) to rotate (add) by.
|
|---|
| 1424 | Examples:
|
|---|
| 1425 | scan.rotate_xyphase(2.3)
|
|---|
| 1426 | """
|
|---|
| 1427 | varlist = vars()
|
|---|
| 1428 | self._math._rotate_xyphase(self, angle)
|
|---|
| 1429 | self._add_history("rotate_xyphase", varlist)
|
|---|
| 1430 | return
|
|---|
| 1431 |
|
|---|
| 1432 | @print_log_dec
|
|---|
| 1433 | def swap_linears(self):
|
|---|
| 1434 | """
|
|---|
| 1435 | Swap the linear polarisations XX and YY, or better the first two
|
|---|
| 1436 | polarisations as this also works for ciculars.
|
|---|
| 1437 | """
|
|---|
| 1438 | varlist = vars()
|
|---|
| 1439 | self._math._swap_linears(self)
|
|---|
| 1440 | self._add_history("swap_linears", varlist)
|
|---|
| 1441 | return
|
|---|
| 1442 |
|
|---|
| 1443 | @print_log_dec
|
|---|
| 1444 | def invert_phase(self):
|
|---|
| 1445 | """
|
|---|
| 1446 | Invert the phase of the complex polarisation
|
|---|
| 1447 | """
|
|---|
| 1448 | varlist = vars()
|
|---|
| 1449 | self._math._invert_phase(self)
|
|---|
| 1450 | self._add_history("invert_phase", varlist)
|
|---|
| 1451 | return
|
|---|
| 1452 |
|
|---|
| 1453 | @print_log_dec
|
|---|
| 1454 | def add(self, offset, insitu=None):
|
|---|
| 1455 | """
|
|---|
| 1456 | Return a scan where all spectra have the offset added
|
|---|
| 1457 | Parameters:
|
|---|
| 1458 | offset: the offset
|
|---|
| 1459 | insitu: if False a new scantable is returned.
|
|---|
| 1460 | Otherwise, the scaling is done in-situ
|
|---|
| 1461 | The default is taken from .asaprc (False)
|
|---|
| 1462 | """
|
|---|
| 1463 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1464 | self._math._setinsitu(insitu)
|
|---|
| 1465 | varlist = vars()
|
|---|
| 1466 | s = scantable(self._math._unaryop(self, offset, "ADD", False))
|
|---|
| 1467 | s._add_history("add", varlist)
|
|---|
| 1468 | if insitu:
|
|---|
| 1469 | self._assign(s)
|
|---|
| 1470 | else:
|
|---|
| 1471 | return s
|
|---|
| 1472 |
|
|---|
| 1473 | @print_log_dec
|
|---|
| 1474 | def scale(self, factor, tsys=True, insitu=None):
|
|---|
| 1475 | """
|
|---|
| 1476 | Return a scan where all spectra are scaled by the give 'factor'
|
|---|
| 1477 | Parameters:
|
|---|
| 1478 | factor: the scaling factor
|
|---|
| 1479 | insitu: if False a new scantable is returned.
|
|---|
| 1480 | Otherwise, the scaling is done in-situ
|
|---|
| 1481 | The default is taken from .asaprc (False)
|
|---|
| 1482 | tsys: if True (default) then apply the operation to Tsys
|
|---|
| 1483 | as well as the data
|
|---|
| 1484 | """
|
|---|
| 1485 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1486 | self._math._setinsitu(insitu)
|
|---|
| 1487 | varlist = vars()
|
|---|
| 1488 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
|
|---|
| 1489 | s._add_history("scale", varlist)
|
|---|
| 1490 | if insitu:
|
|---|
| 1491 | self._assign(s)
|
|---|
| 1492 | else:
|
|---|
| 1493 | return s
|
|---|
| 1494 |
|
|---|
| 1495 | def set_sourcetype(self, match, matchtype="pattern",
|
|---|
| 1496 | sourcetype="reference"):
|
|---|
| 1497 | """
|
|---|
| 1498 | Set the type of the source to be an source or reference scan
|
|---|
| 1499 | using the provided pattern:
|
|---|
| 1500 | Parameters:
|
|---|
| 1501 | match: a Unix style pattern, regular expression or selector
|
|---|
| 1502 | matchtype: 'pattern' (default) UNIX style pattern or
|
|---|
| 1503 | 'regex' regular expression
|
|---|
| 1504 | sourcetype: the type of the source to use (source/reference)
|
|---|
| 1505 | """
|
|---|
| 1506 | varlist = vars()
|
|---|
| 1507 | basesel = self.get_selection()
|
|---|
| 1508 | stype = -1
|
|---|
| 1509 | if sourcetype.lower().startswith("r"):
|
|---|
| 1510 | stype = 1
|
|---|
| 1511 | elif sourcetype.lower().startswith("s"):
|
|---|
| 1512 | stype = 0
|
|---|
| 1513 | else:
|
|---|
| 1514 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)")
|
|---|
| 1515 | if matchtype.lower().startswith("p"):
|
|---|
| 1516 | matchtype = "pattern"
|
|---|
| 1517 | elif matchtype.lower().startswith("r"):
|
|---|
| 1518 | matchtype = "regex"
|
|---|
| 1519 | else:
|
|---|
| 1520 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)")
|
|---|
| 1521 | sel = selector()
|
|---|
| 1522 | if isinstance(match, selector):
|
|---|
| 1523 | sel = match
|
|---|
| 1524 | else:
|
|---|
| 1525 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match))
|
|---|
| 1526 | self.set_selection(basesel+sel)
|
|---|
| 1527 | self._setsourcetype(stype)
|
|---|
| 1528 | self.set_selection(basesel)
|
|---|
| 1529 | self._add_history("set_sourcetype", varlist)
|
|---|
| 1530 |
|
|---|
| 1531 | @print_log_dec
|
|---|
| 1532 | def auto_quotient(self, preserve=True, mode='paired'):
|
|---|
| 1533 | """
|
|---|
| 1534 | This function allows to build quotients automatically.
|
|---|
| 1535 | It assumes the observation to have the same numer of
|
|---|
| 1536 | "ons" and "offs"
|
|---|
| 1537 | Parameters:
|
|---|
| 1538 | preserve: you can preserve (default) the continuum or
|
|---|
| 1539 | remove it. The equations used are
|
|---|
| 1540 | preserve: Output = Toff * (on/off) - Toff
|
|---|
| 1541 | remove: Output = Toff * (on/off) - Ton
|
|---|
| 1542 | mode: the on/off detection mode
|
|---|
| 1543 | 'paired' (default)
|
|---|
| 1544 | identifies 'off' scans by the
|
|---|
| 1545 | trailing '_R' (Mopra/Parkes) or
|
|---|
| 1546 | '_e'/'_w' (Tid) and matches
|
|---|
| 1547 | on/off pairs from the observing pattern
|
|---|
| 1548 | 'time'
|
|---|
| 1549 | finds the closest off in time
|
|---|
| 1550 |
|
|---|
| 1551 | """
|
|---|
| 1552 | modes = ["time", "paired"]
|
|---|
| 1553 | if not mode in modes:
|
|---|
| 1554 | msg = "please provide valid mode. Valid modes are %s" % (modes)
|
|---|
| 1555 | raise ValueError(msg)
|
|---|
| 1556 | varlist = vars()
|
|---|
| 1557 | s = None
|
|---|
| 1558 | if mode.lower() == "paired":
|
|---|
| 1559 | basesel = self.get_selection()
|
|---|
| 1560 | sel = selector()+basesel
|
|---|
| 1561 | sel.set_query("SRCTYPE==1")
|
|---|
| 1562 | self.set_selection(sel)
|
|---|
| 1563 | offs = self.copy()
|
|---|
| 1564 | sel.set_query("SRCTYPE==0")
|
|---|
| 1565 | self.set_selection(sel)
|
|---|
| 1566 | ons = self.copy()
|
|---|
| 1567 | s = scantable(self._math._quotient(ons, offs, preserve))
|
|---|
| 1568 | self.set_selection(basesel)
|
|---|
| 1569 | elif mode.lower() == "time":
|
|---|
| 1570 | s = scantable(self._math._auto_quotient(self, mode, preserve))
|
|---|
| 1571 | s._add_history("auto_quotient", varlist)
|
|---|
| 1572 | return s
|
|---|
| 1573 |
|
|---|
| 1574 | @print_log_dec
|
|---|
| 1575 | def mx_quotient(self, mask = None, weight='median', preserve=True):
|
|---|
| 1576 | """
|
|---|
| 1577 | Form a quotient using "off" beams when observing in "MX" mode.
|
|---|
| 1578 | Parameters:
|
|---|
| 1579 | mask: an optional mask to be used when weight == 'stddev'
|
|---|
| 1580 | weight: How to average the off beams. Default is 'median'.
|
|---|
| 1581 | preserve: you can preserve (default) the continuum or
|
|---|
| 1582 | remove it. The equations used are
|
|---|
| 1583 | preserve: Output = Toff * (on/off) - Toff
|
|---|
| 1584 | remove: Output = Toff * (on/off) - Ton
|
|---|
| 1585 | """
|
|---|
| 1586 | mask = mask or ()
|
|---|
| 1587 | varlist = vars()
|
|---|
| 1588 | on = scantable(self._math._mx_extract(self, 'on'))
|
|---|
| 1589 | preoff = scantable(self._math._mx_extract(self, 'off'))
|
|---|
| 1590 | off = preoff.average_time(mask=mask, weight=weight, scanav=False)
|
|---|
| 1591 | from asapmath import quotient
|
|---|
| 1592 | q = quotient(on, off, preserve)
|
|---|
| 1593 | q._add_history("mx_quotient", varlist)
|
|---|
| 1594 | return q
|
|---|
| 1595 |
|
|---|
| 1596 | @print_log_dec
|
|---|
| 1597 | def freq_switch(self, insitu=None):
|
|---|
| 1598 | """
|
|---|
| 1599 | Apply frequency switching to the data.
|
|---|
| 1600 | Parameters:
|
|---|
| 1601 | insitu: if False a new scantable is returned.
|
|---|
| 1602 | Otherwise, the swictching is done in-situ
|
|---|
| 1603 | The default is taken from .asaprc (False)
|
|---|
| 1604 | Example:
|
|---|
| 1605 | none
|
|---|
| 1606 | """
|
|---|
| 1607 | if insitu is None: insitu = rcParams['insitu']
|
|---|
| 1608 | self._math._setinsitu(insitu)
|
|---|
| 1609 | varlist = vars()
|
|---|
| 1610 | s = scantable(self._math._freqswitch(self))
|
|---|
| 1611 | s._add_history("freq_switch", varlist)
|
|---|
| 1612 | if insitu: self._assign(s)
|
|---|
| 1613 | else: return s
|
|---|
| 1614 |
|
|---|
| 1615 | @print_log_dec
|
|---|
| 1616 | def recalc_azel(self):
|
|---|
| 1617 | """
|
|---|
| 1618 | Recalculate the azimuth and elevation for each position.
|
|---|
| 1619 | Parameters:
|
|---|
| 1620 | none
|
|---|
| 1621 | Example:
|
|---|
| 1622 | """
|
|---|
| 1623 | varlist = vars()
|
|---|
| 1624 | self._recalcazel()
|
|---|
| 1625 | self._add_history("recalc_azel", varlist)
|
|---|
| 1626 | return
|
|---|
| 1627 |
|
|---|
| 1628 | @print_log_dec
|
|---|
| 1629 | def __add__(self, other):
|
|---|
| 1630 | varlist = vars()
|
|---|
| 1631 | s = None
|
|---|
| 1632 | if isinstance(other, scantable):
|
|---|
| 1633 | s = scantable(self._math._binaryop(self, other, "ADD"))
|
|---|
| 1634 | elif isinstance(other, float):
|
|---|
| 1635 | s = scantable(self._math._unaryop(self, other, "ADD", False))
|
|---|
| 1636 | else:
|
|---|
| 1637 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1638 | s._add_history("operator +", varlist)
|
|---|
| 1639 | return s
|
|---|
| 1640 |
|
|---|
| 1641 | @print_log_dec
|
|---|
| 1642 | def __sub__(self, other):
|
|---|
| 1643 | """
|
|---|
| 1644 | implicit on all axes and on Tsys
|
|---|
| 1645 | """
|
|---|
| 1646 | varlist = vars()
|
|---|
| 1647 | s = None
|
|---|
| 1648 | if isinstance(other, scantable):
|
|---|
| 1649 | s = scantable(self._math._binaryop(self, other, "SUB"))
|
|---|
| 1650 | elif isinstance(other, float):
|
|---|
| 1651 | s = scantable(self._math._unaryop(self, other, "SUB", False))
|
|---|
| 1652 | else:
|
|---|
| 1653 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1654 | s._add_history("operator -", varlist)
|
|---|
| 1655 | return s
|
|---|
| 1656 |
|
|---|
| 1657 | @print_log_dec
|
|---|
| 1658 | def __mul__(self, other):
|
|---|
| 1659 | """
|
|---|
| 1660 | implicit on all axes and on Tsys
|
|---|
| 1661 | """
|
|---|
| 1662 | varlist = vars()
|
|---|
| 1663 | s = None
|
|---|
| 1664 | if isinstance(other, scantable):
|
|---|
| 1665 | s = scantable(self._math._binaryop(self, other, "MUL"))
|
|---|
| 1666 | elif isinstance(other, float):
|
|---|
| 1667 | s = scantable(self._math._unaryop(self, other, "MUL", False))
|
|---|
| 1668 | else:
|
|---|
| 1669 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1670 | s._add_history("operator *", varlist)
|
|---|
| 1671 | return s
|
|---|
| 1672 |
|
|---|
| 1673 |
|
|---|
| 1674 | @print_log_dec
|
|---|
| 1675 | def __div__(self, other):
|
|---|
| 1676 | """
|
|---|
| 1677 | implicit on all axes and on Tsys
|
|---|
| 1678 | """
|
|---|
| 1679 | varlist = vars()
|
|---|
| 1680 | s = None
|
|---|
| 1681 | if isinstance(other, scantable):
|
|---|
| 1682 | s = scantable(self._math._binaryop(self, other, "DIV"))
|
|---|
| 1683 | elif isinstance(other, float):
|
|---|
| 1684 | if other == 0.0:
|
|---|
| 1685 | raise ZeroDivisionError("Dividing by zero is not recommended")
|
|---|
| 1686 | s = scantable(self._math._unaryop(self, other, "DIV", False))
|
|---|
| 1687 | else:
|
|---|
| 1688 | raise TypeError("Other input is not a scantable or float value")
|
|---|
| 1689 | s._add_history("operator /", varlist)
|
|---|
| 1690 | return s
|
|---|
| 1691 |
|
|---|
| 1692 | def get_fit(self, row=0):
|
|---|
| 1693 | """
|
|---|
| 1694 | Print or return the stored fits for a row in the scantable
|
|---|
| 1695 | Parameters:
|
|---|
| 1696 | row: the row which the fit has been applied to.
|
|---|
| 1697 | """
|
|---|
| 1698 | if row > self.nrow():
|
|---|
| 1699 | return
|
|---|
| 1700 | from asap.asapfit import asapfit
|
|---|
| 1701 | fit = asapfit(self._getfit(row))
|
|---|
| 1702 | if rcParams['verbose']:
|
|---|
| 1703 | print fit
|
|---|
| 1704 | return
|
|---|
| 1705 | else:
|
|---|
| 1706 | return fit.as_dict()
|
|---|
| 1707 |
|
|---|
| 1708 | def flag_nans(self):
|
|---|
| 1709 | """
|
|---|
| 1710 | Utility function to flag NaN values in the scantable.
|
|---|
| 1711 | """
|
|---|
| 1712 | import numpy
|
|---|
| 1713 | basesel = self.get_selection()
|
|---|
| 1714 | for i in range(self.nrow()):
|
|---|
| 1715 | sel = self.get_row_selector(i)
|
|---|
| 1716 | self.set_selection(basesel+sel)
|
|---|
| 1717 | nans = numpy.isnan(self._getspectrum(0))
|
|---|
| 1718 | if numpy.any(nans):
|
|---|
| 1719 | bnans = [ bool(v) for v in nans]
|
|---|
| 1720 | self.flag(bnans)
|
|---|
| 1721 | self.set_selection(basesel)
|
|---|
| 1722 |
|
|---|
| 1723 | def get_row_selector(self, rowno):
|
|---|
| 1724 | return selector(beams=self.getbeam(rowno),
|
|---|
| 1725 | ifs=self.getif(rowno),
|
|---|
| 1726 | pols=self.getpol(rowno),
|
|---|
| 1727 | scans=self.getscan(rowno),
|
|---|
| 1728 | cycles=self.getcycle(rowno))
|
|---|
| 1729 |
|
|---|
| 1730 | def _add_history(self, funcname, parameters):
|
|---|
| 1731 | if not rcParams['scantable.history']:
|
|---|
| 1732 | return
|
|---|
| 1733 | # create date
|
|---|
| 1734 | sep = "##"
|
|---|
| 1735 | from datetime import datetime
|
|---|
| 1736 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
|
|---|
| 1737 | hist = dstr+sep
|
|---|
| 1738 | hist += funcname+sep#cdate+sep
|
|---|
| 1739 | if parameters.has_key('self'): del parameters['self']
|
|---|
| 1740 | for k, v in parameters.iteritems():
|
|---|
| 1741 | if type(v) is dict:
|
|---|
| 1742 | for k2, v2 in v.iteritems():
|
|---|
| 1743 | hist += k2
|
|---|
| 1744 | hist += "="
|
|---|
| 1745 | if isinstance(v2, scantable):
|
|---|
| 1746 | hist += 'scantable'
|
|---|
| 1747 | elif k2 == 'mask':
|
|---|
| 1748 | if isinstance(v2, list) or isinstance(v2, tuple):
|
|---|
| 1749 | hist += str(self._zip_mask(v2))
|
|---|
| 1750 | else:
|
|---|
| 1751 | hist += str(v2)
|
|---|
| 1752 | else:
|
|---|
| 1753 | hist += str(v2)
|
|---|
| 1754 | else:
|
|---|
| 1755 | hist += k
|
|---|
| 1756 | hist += "="
|
|---|
| 1757 | if isinstance(v, scantable):
|
|---|
| 1758 | hist += 'scantable'
|
|---|
| 1759 | elif k == 'mask':
|
|---|
| 1760 | if isinstance(v, list) or isinstance(v, tuple):
|
|---|
| 1761 | hist += str(self._zip_mask(v))
|
|---|
| 1762 | else:
|
|---|
| 1763 | hist += str(v)
|
|---|
| 1764 | else:
|
|---|
| 1765 | hist += str(v)
|
|---|
| 1766 | hist += sep
|
|---|
| 1767 | hist = hist[:-2] # remove trailing '##'
|
|---|
| 1768 | self._addhistory(hist)
|
|---|
| 1769 |
|
|---|
| 1770 |
|
|---|
| 1771 | def _zip_mask(self, mask):
|
|---|
| 1772 | mask = list(mask)
|
|---|
| 1773 | i = 0
|
|---|
| 1774 | segments = []
|
|---|
| 1775 | while mask[i:].count(1):
|
|---|
| 1776 | i += mask[i:].index(1)
|
|---|
| 1777 | if mask[i:].count(0):
|
|---|
| 1778 | j = i + mask[i:].index(0)
|
|---|
| 1779 | else:
|
|---|
| 1780 | j = len(mask)
|
|---|
| 1781 | segments.append([i, j])
|
|---|
| 1782 | i = j
|
|---|
| 1783 | return segments
|
|---|
| 1784 |
|
|---|
| 1785 | def _get_ordinate_label(self):
|
|---|
| 1786 | fu = "("+self.get_fluxunit()+")"
|
|---|
| 1787 | import re
|
|---|
| 1788 | lbl = "Intensity"
|
|---|
| 1789 | if re.match(".K.", fu):
|
|---|
| 1790 | lbl = "Brightness Temperature "+ fu
|
|---|
| 1791 | elif re.match(".Jy.", fu):
|
|---|
| 1792 | lbl = "Flux density "+ fu
|
|---|
| 1793 | return lbl
|
|---|
| 1794 |
|
|---|
| 1795 | def _check_ifs(self):
|
|---|
| 1796 | nchans = [self.nchan(i) for i in range(self.nif(-1))]
|
|---|
| 1797 | nchans = filter(lambda t: t > 0, nchans)
|
|---|
| 1798 | return (sum(nchans)/len(nchans) == nchans[0])
|
|---|
| 1799 |
|
|---|
| 1800 | def _fill(self, names, unit, average):
|
|---|
| 1801 | import os
|
|---|
| 1802 | from asap._asap import stfiller
|
|---|
| 1803 | first = True
|
|---|
| 1804 | fullnames = []
|
|---|
| 1805 | for name in names:
|
|---|
| 1806 | name = os.path.expandvars(name)
|
|---|
| 1807 | name = os.path.expanduser(name)
|
|---|
| 1808 | if not os.path.exists(name):
|
|---|
| 1809 | msg = "File '%s' does not exists" % (name)
|
|---|
| 1810 | if rcParams['verbose']:
|
|---|
| 1811 | asaplog.push(msg)
|
|---|
| 1812 | print asaplog.pop().strip()
|
|---|
| 1813 | return
|
|---|
| 1814 | raise IOError(msg)
|
|---|
| 1815 | fullnames.append(name)
|
|---|
| 1816 | if average:
|
|---|
| 1817 | asaplog.push('Auto averaging integrations')
|
|---|
| 1818 | stype = int(rcParams['scantable.storage'].lower() == 'disk')
|
|---|
| 1819 | for name in fullnames:
|
|---|
| 1820 | tbl = Scantable(stype)
|
|---|
| 1821 | r = stfiller(tbl)
|
|---|
| 1822 | rx = rcParams['scantable.reference']
|
|---|
| 1823 | r._setreferenceexpr(rx)
|
|---|
| 1824 | msg = "Importing %s..." % (name)
|
|---|
| 1825 | asaplog.push(msg, False)
|
|---|
| 1826 | print_log()
|
|---|
| 1827 | r._open(name, -1, -1)
|
|---|
| 1828 | r._read()
|
|---|
| 1829 | if average:
|
|---|
| 1830 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
|
|---|
| 1831 | if not first:
|
|---|
| 1832 | tbl = self._math._merge([self, tbl])
|
|---|
| 1833 | Scantable.__init__(self, tbl)
|
|---|
| 1834 | r._close()
|
|---|
| 1835 | del r, tbl
|
|---|
| 1836 | first = False
|
|---|
| 1837 | if unit is not None:
|
|---|
| 1838 | self.set_fluxunit(unit)
|
|---|
| 1839 | self.set_freqframe(rcParams['scantable.freqframe'])
|
|---|
| 1840 |
|
|---|
| 1841 | def __getitem__(self, key):
|
|---|
| 1842 | if key < 0:
|
|---|
| 1843 | key += self.nrow()
|
|---|
| 1844 | if key >= self.nrow():
|
|---|
| 1845 | raise IndexError("Row index out of range.")
|
|---|
| 1846 | return self._getspectrum(key)
|
|---|
| 1847 |
|
|---|
| 1848 | def __setitem__(self, key, value):
|
|---|
| 1849 | if key < 0:
|
|---|
| 1850 | key += self.nrow()
|
|---|
| 1851 | if key >= self.nrow():
|
|---|
| 1852 | raise IndexError("Row index out of range.")
|
|---|
| 1853 | if not hasattr(value, "__len__") or \
|
|---|
| 1854 | len(value) > self.nchan(self.getif(key)):
|
|---|
| 1855 | raise ValueError("Spectrum length doesn't match.")
|
|---|
| 1856 | return self._setspectrum(value, key)
|
|---|
| 1857 |
|
|---|
| 1858 | def __len__(self):
|
|---|
| 1859 | return self.nrow()
|
|---|
| 1860 |
|
|---|
| 1861 | def __iter__(self):
|
|---|
| 1862 | for i in range(len(self)):
|
|---|
| 1863 | yield self[i]
|
|---|
