[1846] | 1 | """This module defines the scantable class.""" |
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| 2 | |
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[1697] | 3 | import os |
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[1691] | 4 | try: |
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| 5 | from functools import wraps as wraps_dec |
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| 6 | except ImportError: |
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| 7 | from asap.compatibility import wraps as wraps_dec |
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| 8 | |
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[1824] | 9 | from asap.env import is_casapy |
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[876] | 10 | from asap._asap import Scantable |
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[1843] | 11 | from asap._asap import filler |
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[1824] | 12 | from asap.parameters import rcParams |
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[1862] | 13 | from asap.logging import asaplog, asaplog_post_dec |
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[1824] | 14 | from asap.selector import selector |
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| 15 | from asap.linecatalog import linecatalog |
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[1600] | 16 | from asap.coordinate import coordinate |
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[1859] | 17 | from asap.utils import _n_bools, mask_not, mask_and, mask_or, page |
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[102] | 18 | |
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[1689] | 19 | |
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| 20 | def preserve_selection(func): |
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[1691] | 21 | @wraps_dec(func) |
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[1689] | 22 | def wrap(obj, *args, **kw): |
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| 23 | basesel = obj.get_selection() |
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[1857] | 24 | try: |
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| 25 | val = func(obj, *args, **kw) |
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| 26 | finally: |
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| 27 | obj.set_selection(basesel) |
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[1689] | 28 | return val |
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| 29 | return wrap |
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| 30 | |
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[1846] | 31 | def is_scantable(filename): |
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| 32 | """Is the given file a scantable? |
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[1689] | 33 | |
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[1846] | 34 | Parameters: |
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| 35 | |
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| 36 | filename: the name of the file/directory to test |
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| 37 | |
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| 38 | """ |
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[1883] | 39 | if ( os.path.isdir(filename) |
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| 40 | and os.path.exists(filename+'/table.info') |
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| 41 | and os.path.exists(filename+'/table.dat') ): |
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| 42 | f=open(filename+'/table.info') |
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| 43 | l=f.readline() |
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| 44 | f.close() |
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| 45 | #if ( l.find('Scantable') != -1 ): |
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| 46 | if ( l.find('Measurement Set') == -1 ): |
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| 47 | return True |
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| 48 | else: |
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| 49 | return False |
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| 50 | else: |
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| 51 | return False |
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| 52 | ## return (os.path.isdir(filename) |
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| 53 | ## and not os.path.exists(filename+'/table.f1') |
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| 54 | ## and os.path.exists(filename+'/table.info')) |
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[1697] | 55 | |
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[1883] | 56 | def is_ms(filename): |
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| 57 | """Is the given file a MeasurementSet? |
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[1697] | 58 | |
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[1883] | 59 | Parameters: |
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| 60 | |
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| 61 | filename: the name of the file/directory to test |
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| 62 | |
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| 63 | """ |
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| 64 | if ( os.path.isdir(filename) |
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| 65 | and os.path.exists(filename+'/table.info') |
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| 66 | and os.path.exists(filename+'/table.dat') ): |
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| 67 | f=open(filename+'/table.info') |
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| 68 | l=f.readline() |
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| 69 | f.close() |
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| 70 | if ( l.find('Measurement Set') != -1 ): |
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| 71 | return True |
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| 72 | else: |
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| 73 | return False |
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| 74 | else: |
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| 75 | return False |
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| 76 | |
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[876] | 77 | class scantable(Scantable): |
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[1846] | 78 | """\ |
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| 79 | The ASAP container for scans (single-dish data). |
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[102] | 80 | """ |
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[1819] | 81 | |
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[1862] | 82 | @asaplog_post_dec |
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[1824] | 83 | def __init__(self, filename, average=None, unit=None, getpt=None, |
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| 84 | antenna=None, parallactify=None): |
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[1846] | 85 | """\ |
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[102] | 86 | Create a scantable from a saved one or make a reference |
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[1846] | 87 | |
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[102] | 88 | Parameters: |
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[1846] | 89 | |
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| 90 | filename: the name of an asap table on disk |
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| 91 | or |
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| 92 | the name of a rpfits/sdfits/ms file |
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| 93 | (integrations within scans are auto averaged |
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| 94 | and the whole file is read) or |
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| 95 | [advanced] a reference to an existing scantable |
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| 96 | |
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| 97 | average: average all integrations withinb a scan on read. |
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| 98 | The default (True) is taken from .asaprc. |
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| 99 | |
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[484] | 100 | unit: brightness unit; must be consistent with K or Jy. |
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[1846] | 101 | Over-rides the default selected by the filler |
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| 102 | (input rpfits/sdfits/ms) or replaces the value |
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| 103 | in existing scantables |
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| 104 | |
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| 105 | getpt: for MeasurementSet input data only: |
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| 106 | If True, all pointing data are filled. |
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| 107 | The deafult is False, which makes time to load |
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| 108 | the MS data faster in some cases. |
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| 109 | |
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| 110 | antenna: Antenna selection. integer (id) or string (name or id). |
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| 111 | |
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| 112 | parallactify: Indicate that the data had been parallatified. Default |
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| 113 | is taken from rc file. |
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| 114 | |
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[710] | 115 | """ |
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[976] | 116 | if average is None: |
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[710] | 117 | average = rcParams['scantable.autoaverage'] |
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[1819] | 118 | if getpt is None: |
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| 119 | getpt = True |
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[1843] | 120 | if antenna is not None: |
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| 121 | asaplog.push("Antenna selection currently unsupported." |
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[1883] | 122 | "Using ''") |
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[1861] | 123 | asaplog.post('WARN') |
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[1819] | 124 | if antenna is None: |
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| 125 | antenna = '' |
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| 126 | elif type(antenna) == int: |
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[1843] | 127 | antenna = '%s' % antenna |
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[1819] | 128 | elif type(antenna) == list: |
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| 129 | tmpstr = '' |
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| 130 | for i in range( len(antenna) ): |
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| 131 | if type(antenna[i]) == int: |
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| 132 | tmpstr = tmpstr + ('%s,'%(antenna[i])) |
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| 133 | elif type(antenna[i]) == str: |
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| 134 | tmpstr=tmpstr+antenna[i]+',' |
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| 135 | else: |
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[1859] | 136 | raise TypeError('Bad antenna selection.') |
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[1819] | 137 | antenna = tmpstr.rstrip(',') |
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[1593] | 138 | parallactify = parallactify or rcParams['scantable.parallactify'] |
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[1259] | 139 | varlist = vars() |
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[876] | 140 | from asap._asap import stmath |
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[1819] | 141 | self._math = stmath( rcParams['insitu'] ) |
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[876] | 142 | if isinstance(filename, Scantable): |
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| 143 | Scantable.__init__(self, filename) |
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[181] | 144 | else: |
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[1697] | 145 | if isinstance(filename, str): |
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[976] | 146 | filename = os.path.expandvars(filename) |
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| 147 | filename = os.path.expanduser(filename) |
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| 148 | if not os.path.exists(filename): |
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| 149 | s = "File '%s' not found." % (filename) |
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| 150 | raise IOError(s) |
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[1697] | 151 | if is_scantable(filename): |
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| 152 | ondisk = rcParams['scantable.storage'] == 'disk' |
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| 153 | Scantable.__init__(self, filename, ondisk) |
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| 154 | if unit is not None: |
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| 155 | self.set_fluxunit(unit) |
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[1819] | 156 | # do not reset to the default freqframe |
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| 157 | #self.set_freqframe(rcParams['scantable.freqframe']) |
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[1883] | 158 | #elif os.path.isdir(filename) \ |
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| 159 | # and not os.path.exists(filename+'/table.f1'): |
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| 160 | elif is_ms(filename): |
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| 161 | self._fill([filename], unit, average, getpt, antenna) |
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| 162 | else: |
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[1819] | 163 | msg = "The given file '%s'is not a valid " \ |
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| 164 | "asap table." % (filename) |
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[1859] | 165 | raise IOError(msg) |
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[1118] | 166 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
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[976] | 167 | and isinstance(filename[-1], str): |
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[1819] | 168 | self._fill(filename, unit, average, getpt, antenna) |
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[1586] | 169 | self.parallactify(parallactify) |
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[1259] | 170 | self._add_history("scantable", varlist) |
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[102] | 171 | |
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[1862] | 172 | @asaplog_post_dec |
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[876] | 173 | def save(self, name=None, format=None, overwrite=False): |
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[1846] | 174 | """\ |
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[1280] | 175 | Store the scantable on disk. This can be an asap (aips++) Table, |
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| 176 | SDFITS or MS2 format. |
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[1846] | 177 | |
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[116] | 178 | Parameters: |
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[1846] | 179 | |
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[1093] | 180 | name: the name of the outputfile. For format "ASCII" |
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| 181 | this is the root file name (data in 'name'.txt |
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[497] | 182 | and header in 'name'_header.txt) |
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[1855] | 183 | |
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[116] | 184 | format: an optional file format. Default is ASAP. |
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[1855] | 185 | Allowed are: |
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| 186 | |
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| 187 | * 'ASAP' (save as ASAP [aips++] Table), |
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| 188 | * 'SDFITS' (save as SDFITS file) |
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| 189 | * 'ASCII' (saves as ascii text file) |
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| 190 | * 'MS2' (saves as an casacore MeasurementSet V2) |
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| 191 | * 'FITS' (save as image FITS - not readable by class) |
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| 192 | * 'CLASS' (save as FITS readable by CLASS) |
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| 193 | |
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[411] | 194 | overwrite: If the file should be overwritten if it exists. |
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[256] | 195 | The default False is to return with warning |
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[411] | 196 | without writing the output. USE WITH CARE. |
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[1855] | 197 | |
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[1846] | 198 | Example:: |
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| 199 | |
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[116] | 200 | scan.save('myscan.asap') |
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[1118] | 201 | scan.save('myscan.sdfits', 'SDFITS') |
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[1846] | 202 | |
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[116] | 203 | """ |
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[411] | 204 | from os import path |
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[1593] | 205 | format = format or rcParams['scantable.save'] |
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[256] | 206 | suffix = '.'+format.lower() |
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[1118] | 207 | if name is None or name == "": |
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[256] | 208 | name = 'scantable'+suffix |
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[718] | 209 | msg = "No filename given. Using default name %s..." % name |
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| 210 | asaplog.push(msg) |
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[411] | 211 | name = path.expandvars(name) |
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[256] | 212 | if path.isfile(name) or path.isdir(name): |
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| 213 | if not overwrite: |
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[718] | 214 | msg = "File %s exists." % name |
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[1859] | 215 | raise IOError(msg) |
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[451] | 216 | format2 = format.upper() |
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| 217 | if format2 == 'ASAP': |
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[116] | 218 | self._save(name) |
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| 219 | else: |
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[989] | 220 | from asap._asap import stwriter as stw |
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[1118] | 221 | writer = stw(format2) |
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| 222 | writer.write(self, name) |
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[116] | 223 | return |
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| 224 | |
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[102] | 225 | def copy(self): |
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[1846] | 226 | """Return a copy of this scantable. |
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| 227 | |
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| 228 | *Note*: |
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| 229 | |
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[1348] | 230 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
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[1846] | 231 | |
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| 232 | Example:: |
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| 233 | |
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[102] | 234 | copiedscan = scan.copy() |
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[1846] | 235 | |
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[102] | 236 | """ |
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[876] | 237 | sd = scantable(Scantable._copy(self)) |
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[113] | 238 | return sd |
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| 239 | |
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[1093] | 240 | def drop_scan(self, scanid=None): |
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[1846] | 241 | """\ |
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[1093] | 242 | Return a new scantable where the specified scan number(s) has(have) |
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| 243 | been dropped. |
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[1846] | 244 | |
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[1093] | 245 | Parameters: |
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[1846] | 246 | |
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[1093] | 247 | scanid: a (list of) scan number(s) |
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[1846] | 248 | |
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[1093] | 249 | """ |
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| 250 | from asap import _is_sequence_or_number as _is_valid |
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| 251 | from asap import _to_list |
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| 252 | from asap import unique |
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| 253 | if not _is_valid(scanid): |
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[1859] | 254 | raise RuntimeError( 'Please specify a scanno to drop from the scantable' ) |
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| 255 | scanid = _to_list(scanid) |
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| 256 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
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| 257 | for sid in scanid: allscans.remove(sid) |
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| 258 | if len(allscans) == 0: |
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| 259 | raise ValueError("Can't remove all scans") |
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| 260 | sel = selector(scans=allscans) |
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| 261 | return self._select_copy(sel) |
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[1093] | 262 | |
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[1594] | 263 | def _select_copy(self, selection): |
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| 264 | orig = self.get_selection() |
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| 265 | self.set_selection(orig+selection) |
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| 266 | cp = self.copy() |
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| 267 | self.set_selection(orig) |
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| 268 | return cp |
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| 269 | |
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[102] | 270 | def get_scan(self, scanid=None): |
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[1855] | 271 | """\ |
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[102] | 272 | Return a specific scan (by scanno) or collection of scans (by |
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| 273 | source name) in a new scantable. |
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[1846] | 274 | |
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| 275 | *Note*: |
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| 276 | |
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[1348] | 277 | See scantable.drop_scan() for the inverse operation. |
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[1846] | 278 | |
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[102] | 279 | Parameters: |
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[1846] | 280 | |
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[513] | 281 | scanid: a (list of) scanno or a source name, unix-style |
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| 282 | patterns are accepted for source name matching, e.g. |
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| 283 | '*_R' gets all 'ref scans |
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[1846] | 284 | |
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| 285 | Example:: |
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| 286 | |
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[513] | 287 | # get all scans containing the source '323p459' |
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| 288 | newscan = scan.get_scan('323p459') |
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| 289 | # get all 'off' scans |
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| 290 | refscans = scan.get_scan('*_R') |
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| 291 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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[1118] | 292 | newscan = scan.get_scan([0, 2, 7, 10]) |
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[1846] | 293 | |
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[102] | 294 | """ |
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| 295 | if scanid is None: |
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[1859] | 296 | raise RuntimeError( 'Please specify a scan no or name to ' |
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| 297 | 'retrieve from the scantable' ) |
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[102] | 298 | try: |
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[946] | 299 | bsel = self.get_selection() |
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| 300 | sel = selector() |
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[102] | 301 | if type(scanid) is str: |
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[946] | 302 | sel.set_name(scanid) |
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[1594] | 303 | return self._select_copy(sel) |
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[102] | 304 | elif type(scanid) is int: |
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[946] | 305 | sel.set_scans([scanid]) |
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[1594] | 306 | return self._select_copy(sel) |
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[381] | 307 | elif type(scanid) is list: |
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[946] | 308 | sel.set_scans(scanid) |
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[1594] | 309 | return self._select_copy(sel) |
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[381] | 310 | else: |
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[718] | 311 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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[1859] | 312 | raise TypeError(msg) |
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[102] | 313 | except RuntimeError: |
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[1859] | 314 | raise |
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[102] | 315 | |
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| 316 | def __str__(self): |
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[1118] | 317 | return Scantable._summary(self, True) |
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[102] | 318 | |
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[976] | 319 | def summary(self, filename=None): |
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[1846] | 320 | """\ |
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[102] | 321 | Print a summary of the contents of this scantable. |
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[1846] | 322 | |
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[102] | 323 | Parameters: |
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[1846] | 324 | |
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[102] | 325 | filename: the name of a file to write the putput to |
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| 326 | Default - no file output |
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[1846] | 327 | |
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[102] | 328 | """ |
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[976] | 329 | info = Scantable._summary(self, True) |
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[102] | 330 | if filename is not None: |
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[256] | 331 | if filename is "": |
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| 332 | filename = 'scantable_summary.txt' |
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[415] | 333 | from os.path import expandvars, isdir |
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[411] | 334 | filename = expandvars(filename) |
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[415] | 335 | if not isdir(filename): |
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[413] | 336 | data = open(filename, 'w') |
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| 337 | data.write(info) |
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| 338 | data.close() |
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| 339 | else: |
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[718] | 340 | msg = "Illegal file name '%s'." % (filename) |
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[1859] | 341 | raise IOError(msg) |
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| 342 | return page(info) |
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[710] | 343 | |
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[1512] | 344 | def get_spectrum(self, rowno): |
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[1471] | 345 | """Return the spectrum for the current row in the scantable as a list. |
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[1846] | 346 | |
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[1471] | 347 | Parameters: |
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[1846] | 348 | |
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[1573] | 349 | rowno: the row number to retrieve the spectrum from |
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[1846] | 350 | |
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[1471] | 351 | """ |
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| 352 | return self._getspectrum(rowno) |
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[946] | 353 | |
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[1471] | 354 | def get_mask(self, rowno): |
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| 355 | """Return the mask for the current row in the scantable as a list. |
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[1846] | 356 | |
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[1471] | 357 | Parameters: |
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[1846] | 358 | |
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[1573] | 359 | rowno: the row number to retrieve the mask from |
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[1846] | 360 | |
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[1471] | 361 | """ |
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| 362 | return self._getmask(rowno) |
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| 363 | |
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| 364 | def set_spectrum(self, spec, rowno): |
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| 365 | """Return the spectrum for the current row in the scantable as a list. |
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[1846] | 366 | |
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[1471] | 367 | Parameters: |
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[1846] | 368 | |
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[1855] | 369 | spec: the new spectrum |
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[1846] | 370 | |
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[1855] | 371 | rowno: the row number to set the spectrum for |
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| 372 | |
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[1471] | 373 | """ |
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| 374 | assert(len(spec) == self.nchan()) |
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| 375 | return self._setspectrum(spec, rowno) |
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| 376 | |
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[1600] | 377 | def get_coordinate(self, rowno): |
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| 378 | """Return the (spectral) coordinate for a a given 'rowno'. |
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[1846] | 379 | |
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| 380 | *Note*: |
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| 381 | |
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[1600] | 382 | * This coordinate is only valid until a scantable method modifies |
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| 383 | the frequency axis. |
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| 384 | * This coordinate does contain the original frequency set-up |
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| 385 | NOT the new frame. The conversions however are done using the user |
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| 386 | specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate, |
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| 387 | use scantable.freq_align first. Without it there is no closure, |
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[1846] | 388 | i.e.:: |
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[1600] | 389 | |
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[1846] | 390 | c = myscan.get_coordinate(0) |
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| 391 | c.to_frequency(c.get_reference_pixel()) != c.get_reference_value() |
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| 392 | |
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[1600] | 393 | Parameters: |
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[1846] | 394 | |
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[1600] | 395 | rowno: the row number for the spectral coordinate |
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| 396 | |
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| 397 | """ |
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| 398 | return coordinate(Scantable.get_coordinate(self, rowno)) |
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| 399 | |
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[946] | 400 | def get_selection(self): |
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[1846] | 401 | """\ |
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[1005] | 402 | Get the selection object currently set on this scantable. |
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[1846] | 403 | |
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| 404 | Example:: |
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| 405 | |
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[1005] | 406 | sel = scan.get_selection() |
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| 407 | sel.set_ifs(0) # select IF 0 |
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| 408 | scan.set_selection(sel) # apply modified selection |
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[1846] | 409 | |
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[946] | 410 | """ |
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| 411 | return selector(self._getselection()) |
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| 412 | |
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[1576] | 413 | def set_selection(self, selection=None, **kw): |
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[1846] | 414 | """\ |
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[1005] | 415 | Select a subset of the data. All following operations on this scantable |
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| 416 | are only applied to thi selection. |
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[1846] | 417 | |
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[1005] | 418 | Parameters: |
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[1697] | 419 | |
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[1846] | 420 | selection: a selector object (default unset the selection), or |
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| 421 | any combination of "pols", "ifs", "beams", "scans", |
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| 422 | "cycles", "name", "query" |
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[1697] | 423 | |
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[1846] | 424 | Examples:: |
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[1697] | 425 | |
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[1005] | 426 | sel = selector() # create a selection object |
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[1118] | 427 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
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[1005] | 428 | scan.set_selection(sel) # set the selection |
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| 429 | scan.summary() # will only print summary of scanno 0 an 3 |
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| 430 | scan.set_selection() # unset the selection |
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[1697] | 431 | # or the equivalent |
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| 432 | scan.set_selection(scans=[0,3]) |
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| 433 | scan.summary() # will only print summary of scanno 0 an 3 |
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| 434 | scan.set_selection() # unset the selection |
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[1846] | 435 | |
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[946] | 436 | """ |
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[1576] | 437 | if selection is None: |
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| 438 | # reset |
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| 439 | if len(kw) == 0: |
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| 440 | selection = selector() |
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| 441 | else: |
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| 442 | # try keywords |
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| 443 | for k in kw: |
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| 444 | if k not in selector.fields: |
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| 445 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields)) |
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| 446 | selection = selector(**kw) |
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[946] | 447 | self._setselection(selection) |
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| 448 | |
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[1819] | 449 | def get_row(self, row=0, insitu=None): |
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[1846] | 450 | """\ |
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[1819] | 451 | Select a row in the scantable. |
---|
| 452 | Return a scantable with single row. |
---|
[1846] | 453 | |
---|
[1819] | 454 | Parameters: |
---|
[1846] | 455 | |
---|
| 456 | row: row no of integration, default is 0. |
---|
| 457 | insitu: if False a new scantable is returned. Otherwise, the |
---|
| 458 | scaling is done in-situ. The default is taken from .asaprc |
---|
| 459 | (False) |
---|
| 460 | |
---|
[1819] | 461 | """ |
---|
| 462 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 463 | if not insitu: |
---|
| 464 | workscan = self.copy() |
---|
| 465 | else: |
---|
| 466 | workscan = self |
---|
| 467 | # Select a row |
---|
| 468 | sel=selector() |
---|
| 469 | sel.set_scans([workscan.getscan(row)]) |
---|
| 470 | sel.set_cycles([workscan.getcycle(row)]) |
---|
| 471 | sel.set_beams([workscan.getbeam(row)]) |
---|
| 472 | sel.set_ifs([workscan.getif(row)]) |
---|
| 473 | sel.set_polarisations([workscan.getpol(row)]) |
---|
| 474 | sel.set_name(workscan._getsourcename(row)) |
---|
| 475 | workscan.set_selection(sel) |
---|
| 476 | if not workscan.nrow() == 1: |
---|
| 477 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow()) |
---|
| 478 | raise RuntimeError(msg) |
---|
| 479 | del sel |
---|
| 480 | if insitu: |
---|
| 481 | self._assign(workscan) |
---|
| 482 | else: |
---|
| 483 | return workscan |
---|
| 484 | |
---|
[1862] | 485 | @asaplog_post_dec |
---|
[1819] | 486 | def stats(self, stat='stddev', mask=None, form='3.3f'): |
---|
[1846] | 487 | """\ |
---|
[135] | 488 | Determine the specified statistic of the current beam/if/pol |
---|
[102] | 489 | Takes a 'mask' as an optional parameter to specify which |
---|
| 490 | channels should be excluded. |
---|
[1846] | 491 | |
---|
[102] | 492 | Parameters: |
---|
[1846] | 493 | |
---|
[1819] | 494 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum', |
---|
| 495 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
[1855] | 496 | |
---|
[135] | 497 | mask: an optional mask specifying where the statistic |
---|
[102] | 498 | should be determined. |
---|
[1855] | 499 | |
---|
[1819] | 500 | form: format string to print statistic values |
---|
[1846] | 501 | |
---|
| 502 | Example:: |
---|
| 503 | |
---|
[113] | 504 | scan.set_unit('channel') |
---|
[1118] | 505 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 506 | scan.stats(stat='mean', mask=m) |
---|
[1846] | 507 | |
---|
[102] | 508 | """ |
---|
[1593] | 509 | mask = mask or [] |
---|
[876] | 510 | if not self._check_ifs(): |
---|
[1118] | 511 | raise ValueError("Cannot apply mask as the IFs have different " |
---|
| 512 | "number of channels. Please use setselection() " |
---|
| 513 | "to select individual IFs") |
---|
[1819] | 514 | rtnabc = False |
---|
| 515 | if stat.lower().endswith('_abc'): rtnabc = True |
---|
| 516 | getchan = False |
---|
| 517 | if stat.lower().startswith('min') or stat.lower().startswith('max'): |
---|
| 518 | chan = self._math._minmaxchan(self, mask, stat) |
---|
| 519 | getchan = True |
---|
| 520 | statvals = [] |
---|
| 521 | if not rtnabc: statvals = self._math._stats(self, mask, stat) |
---|
[256] | 522 | |
---|
[1819] | 523 | #def cb(i): |
---|
| 524 | # return statvals[i] |
---|
[256] | 525 | |
---|
[1819] | 526 | #return self._row_callback(cb, stat) |
---|
[102] | 527 | |
---|
[1819] | 528 | label=stat |
---|
| 529 | #callback=cb |
---|
| 530 | out = "" |
---|
| 531 | #outvec = [] |
---|
| 532 | sep = '-'*50 |
---|
| 533 | for i in range(self.nrow()): |
---|
| 534 | refstr = '' |
---|
| 535 | statunit= '' |
---|
| 536 | if getchan: |
---|
| 537 | qx, qy = self.chan2data(rowno=i, chan=chan[i]) |
---|
| 538 | if rtnabc: |
---|
| 539 | statvals.append(qx['value']) |
---|
| 540 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])' |
---|
| 541 | statunit= '['+qx['unit']+']' |
---|
| 542 | else: |
---|
| 543 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])' |
---|
| 544 | |
---|
| 545 | tm = self._gettime(i) |
---|
| 546 | src = self._getsourcename(i) |
---|
| 547 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
| 548 | out += 'Time[%s]:\n' % (tm) |
---|
| 549 | if self.nbeam(-1) > 1: |
---|
| 550 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 551 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 552 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
| 553 | #outvec.append(callback(i)) |
---|
| 554 | #out += ('= %'+form) % (outvec[i]) +' '+refstr+'\n' |
---|
| 555 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n' |
---|
| 556 | out += sep+"\n" |
---|
| 557 | |
---|
[1859] | 558 | |
---|
| 559 | import os |
---|
| 560 | if os.environ.has_key( 'USER' ): |
---|
| 561 | usr = os.environ['USER'] |
---|
| 562 | else: |
---|
| 563 | import commands |
---|
| 564 | usr = commands.getoutput( 'whoami' ) |
---|
| 565 | tmpfile = '/tmp/tmp_'+usr+'_casapy_asap_scantable_stats' |
---|
| 566 | f = open(tmpfile,'w') |
---|
| 567 | print >> f, sep |
---|
| 568 | print >> f, ' %s %s' % (label, statunit) |
---|
| 569 | print >> f, sep |
---|
| 570 | print >> f, out |
---|
| 571 | f.close() |
---|
| 572 | f = open(tmpfile,'r') |
---|
| 573 | x = f.readlines() |
---|
| 574 | f.close() |
---|
| 575 | asaplog.push(''.join(x), False) |
---|
| 576 | |
---|
[1819] | 577 | return statvals |
---|
| 578 | |
---|
| 579 | def chan2data(self, rowno=0, chan=0): |
---|
[1846] | 580 | """\ |
---|
[1819] | 581 | Returns channel/frequency/velocity and spectral value |
---|
| 582 | at an arbitrary row and channel in the scantable. |
---|
[1846] | 583 | |
---|
[1819] | 584 | Parameters: |
---|
[1846] | 585 | |
---|
[1819] | 586 | rowno: a row number in the scantable. Default is the |
---|
| 587 | first row, i.e. rowno=0 |
---|
[1855] | 588 | |
---|
[1819] | 589 | chan: a channel in the scantable. Default is the first |
---|
| 590 | channel, i.e. pos=0 |
---|
[1846] | 591 | |
---|
[1819] | 592 | """ |
---|
| 593 | if isinstance(rowno, int) and isinstance(chan, int): |
---|
| 594 | qx = {'unit': self.get_unit(), |
---|
| 595 | 'value': self._getabcissa(rowno)[chan]} |
---|
| 596 | qy = {'unit': self.get_fluxunit(), |
---|
| 597 | 'value': self._getspectrum(rowno)[chan]} |
---|
| 598 | return qx, qy |
---|
| 599 | |
---|
[1118] | 600 | def stddev(self, mask=None): |
---|
[1846] | 601 | """\ |
---|
[135] | 602 | Determine the standard deviation of the current beam/if/pol |
---|
| 603 | Takes a 'mask' as an optional parameter to specify which |
---|
| 604 | channels should be excluded. |
---|
[1846] | 605 | |
---|
[135] | 606 | Parameters: |
---|
[1846] | 607 | |
---|
[135] | 608 | mask: an optional mask specifying where the standard |
---|
| 609 | deviation should be determined. |
---|
| 610 | |
---|
[1846] | 611 | Example:: |
---|
| 612 | |
---|
[135] | 613 | scan.set_unit('channel') |
---|
[1118] | 614 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 615 | scan.stddev(mask=m) |
---|
[1846] | 616 | |
---|
[135] | 617 | """ |
---|
[1118] | 618 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 619 | |
---|
[1003] | 620 | |
---|
[1259] | 621 | def get_column_names(self): |
---|
[1846] | 622 | """\ |
---|
[1003] | 623 | Return a list of column names, which can be used for selection. |
---|
| 624 | """ |
---|
[1259] | 625 | return list(Scantable.get_column_names(self)) |
---|
[1003] | 626 | |
---|
[1730] | 627 | def get_tsys(self, row=-1): |
---|
[1846] | 628 | """\ |
---|
[113] | 629 | Return the System temperatures. |
---|
[1846] | 630 | |
---|
| 631 | Parameters: |
---|
| 632 | |
---|
| 633 | row: the rowno to get the information for. (default all rows) |
---|
| 634 | |
---|
[113] | 635 | Returns: |
---|
[1846] | 636 | |
---|
[876] | 637 | a list of Tsys values for the current selection |
---|
[1846] | 638 | |
---|
[113] | 639 | """ |
---|
[1730] | 640 | if row > -1: |
---|
| 641 | return self._get_column(self._gettsys, row) |
---|
[876] | 642 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 643 | |
---|
[1730] | 644 | |
---|
| 645 | def get_weather(self, row=-1): |
---|
[1846] | 646 | """\ |
---|
| 647 | Return the weather informations. |
---|
| 648 | |
---|
| 649 | Parameters: |
---|
| 650 | |
---|
| 651 | row: the rowno to get the information for. (default all rows) |
---|
| 652 | |
---|
| 653 | Returns: |
---|
| 654 | |
---|
| 655 | a dict or list of of dicts of values for the current selection |
---|
| 656 | |
---|
| 657 | """ |
---|
| 658 | |
---|
[1730] | 659 | values = self._get_column(self._get_weather, row) |
---|
| 660 | if row > -1: |
---|
| 661 | return {'temperature': values[0], |
---|
| 662 | 'pressure': values[1], 'humidity' : values[2], |
---|
| 663 | 'windspeed' : values[3], 'windaz' : values[4] |
---|
| 664 | } |
---|
| 665 | else: |
---|
| 666 | out = [] |
---|
| 667 | for r in values: |
---|
| 668 | |
---|
| 669 | out.append({'temperature': r[0], |
---|
| 670 | 'pressure': r[1], 'humidity' : r[2], |
---|
| 671 | 'windspeed' : r[3], 'windaz' : r[4] |
---|
| 672 | }) |
---|
| 673 | return out |
---|
| 674 | |
---|
[876] | 675 | def _row_callback(self, callback, label): |
---|
| 676 | out = "" |
---|
[1118] | 677 | outvec = [] |
---|
[1590] | 678 | sep = '-'*50 |
---|
[876] | 679 | for i in range(self.nrow()): |
---|
| 680 | tm = self._gettime(i) |
---|
| 681 | src = self._getsourcename(i) |
---|
[1590] | 682 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
[876] | 683 | out += 'Time[%s]:\n' % (tm) |
---|
[1590] | 684 | if self.nbeam(-1) > 1: |
---|
| 685 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 686 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 687 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
[876] | 688 | outvec.append(callback(i)) |
---|
| 689 | out += '= %3.3f\n' % (outvec[i]) |
---|
[1590] | 690 | out += sep+'\n' |
---|
[1859] | 691 | |
---|
| 692 | asaplog.push(sep) |
---|
| 693 | asaplog.push(" %s" % (label)) |
---|
| 694 | asaplog.push(sep) |
---|
| 695 | asaplog.push(out) |
---|
[1861] | 696 | asaplog.post() |
---|
[1175] | 697 | return outvec |
---|
[256] | 698 | |
---|
[1070] | 699 | def _get_column(self, callback, row=-1): |
---|
| 700 | """ |
---|
| 701 | """ |
---|
| 702 | if row == -1: |
---|
| 703 | return [callback(i) for i in range(self.nrow())] |
---|
| 704 | else: |
---|
[1819] | 705 | if 0 <= row < self.nrow(): |
---|
[1070] | 706 | return callback(row) |
---|
[256] | 707 | |
---|
[1070] | 708 | |
---|
[1348] | 709 | def get_time(self, row=-1, asdatetime=False): |
---|
[1846] | 710 | """\ |
---|
[113] | 711 | Get a list of time stamps for the observations. |
---|
[1348] | 712 | Return a datetime object for each integration time stamp in the scantable. |
---|
[1846] | 713 | |
---|
[113] | 714 | Parameters: |
---|
[1846] | 715 | |
---|
[1348] | 716 | row: row no of integration. Default -1 return all rows |
---|
[1855] | 717 | |
---|
[1348] | 718 | asdatetime: return values as datetime objects rather than strings |
---|
[1846] | 719 | |
---|
[113] | 720 | """ |
---|
[1175] | 721 | from time import strptime |
---|
| 722 | from datetime import datetime |
---|
[1392] | 723 | times = self._get_column(self._gettime, row) |
---|
[1348] | 724 | if not asdatetime: |
---|
[1392] | 725 | return times |
---|
[1175] | 726 | format = "%Y/%m/%d/%H:%M:%S" |
---|
| 727 | if isinstance(times, list): |
---|
| 728 | return [datetime(*strptime(i, format)[:6]) for i in times] |
---|
| 729 | else: |
---|
| 730 | return datetime(*strptime(times, format)[:6]) |
---|
[102] | 731 | |
---|
[1348] | 732 | |
---|
| 733 | def get_inttime(self, row=-1): |
---|
[1846] | 734 | """\ |
---|
[1348] | 735 | Get a list of integration times for the observations. |
---|
| 736 | Return a time in seconds for each integration in the scantable. |
---|
[1846] | 737 | |
---|
[1348] | 738 | Parameters: |
---|
[1846] | 739 | |
---|
[1348] | 740 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 741 | |
---|
[1348] | 742 | """ |
---|
[1573] | 743 | return self._get_column(self._getinttime, row) |
---|
[1348] | 744 | |
---|
[1573] | 745 | |
---|
[714] | 746 | def get_sourcename(self, row=-1): |
---|
[1846] | 747 | """\ |
---|
[794] | 748 | Get a list source names for the observations. |
---|
[714] | 749 | Return a string for each integration in the scantable. |
---|
| 750 | Parameters: |
---|
[1846] | 751 | |
---|
[1348] | 752 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 753 | |
---|
[714] | 754 | """ |
---|
[1070] | 755 | return self._get_column(self._getsourcename, row) |
---|
[714] | 756 | |
---|
[794] | 757 | def get_elevation(self, row=-1): |
---|
[1846] | 758 | """\ |
---|
[794] | 759 | Get a list of elevations for the observations. |
---|
| 760 | Return a float for each integration in the scantable. |
---|
[1846] | 761 | |
---|
[794] | 762 | Parameters: |
---|
[1846] | 763 | |
---|
[1348] | 764 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 765 | |
---|
[794] | 766 | """ |
---|
[1070] | 767 | return self._get_column(self._getelevation, row) |
---|
[794] | 768 | |
---|
| 769 | def get_azimuth(self, row=-1): |
---|
[1846] | 770 | """\ |
---|
[794] | 771 | Get a list of azimuths for the observations. |
---|
| 772 | Return a float for each integration in the scantable. |
---|
[1846] | 773 | |
---|
[794] | 774 | Parameters: |
---|
[1348] | 775 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 776 | |
---|
[794] | 777 | """ |
---|
[1070] | 778 | return self._get_column(self._getazimuth, row) |
---|
[794] | 779 | |
---|
| 780 | def get_parangle(self, row=-1): |
---|
[1846] | 781 | """\ |
---|
[794] | 782 | Get a list of parallactic angles for the observations. |
---|
| 783 | Return a float for each integration in the scantable. |
---|
[1846] | 784 | |
---|
[794] | 785 | Parameters: |
---|
[1846] | 786 | |
---|
[1348] | 787 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 788 | |
---|
[794] | 789 | """ |
---|
[1070] | 790 | return self._get_column(self._getparangle, row) |
---|
[794] | 791 | |
---|
[1070] | 792 | def get_direction(self, row=-1): |
---|
| 793 | """ |
---|
| 794 | Get a list of Positions on the sky (direction) for the observations. |
---|
[1594] | 795 | Return a string for each integration in the scantable. |
---|
[1855] | 796 | |
---|
[1070] | 797 | Parameters: |
---|
[1855] | 798 | |
---|
[1070] | 799 | row: row no of integration. Default -1 return all rows |
---|
[1855] | 800 | |
---|
[1070] | 801 | """ |
---|
| 802 | return self._get_column(self._getdirection, row) |
---|
| 803 | |
---|
[1391] | 804 | def get_directionval(self, row=-1): |
---|
[1846] | 805 | """\ |
---|
[1391] | 806 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 807 | Return a float for each integration in the scantable. |
---|
[1846] | 808 | |
---|
[1391] | 809 | Parameters: |
---|
[1846] | 810 | |
---|
[1391] | 811 | row: row no of integration. Default -1 return all rows |
---|
[1846] | 812 | |
---|
[1391] | 813 | """ |
---|
| 814 | return self._get_column(self._getdirectionvec, row) |
---|
| 815 | |
---|
[1862] | 816 | @asaplog_post_dec |
---|
[102] | 817 | def set_unit(self, unit='channel'): |
---|
[1846] | 818 | """\ |
---|
[102] | 819 | Set the unit for all following operations on this scantable |
---|
[1846] | 820 | |
---|
[102] | 821 | Parameters: |
---|
[1846] | 822 | |
---|
| 823 | unit: optional unit, default is 'channel'. Use one of '*Hz', |
---|
| 824 | 'km/s', 'channel' or equivalent '' |
---|
| 825 | |
---|
[102] | 826 | """ |
---|
[484] | 827 | varlist = vars() |
---|
[1118] | 828 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 829 | unit = '' |
---|
| 830 | inf = list(self._getcoordinfo()) |
---|
| 831 | inf[0] = unit |
---|
| 832 | self._setcoordinfo(inf) |
---|
[1118] | 833 | self._add_history("set_unit", varlist) |
---|
[113] | 834 | |
---|
[1862] | 835 | @asaplog_post_dec |
---|
[484] | 836 | def set_instrument(self, instr): |
---|
[1846] | 837 | """\ |
---|
[1348] | 838 | Set the instrument for subsequent processing. |
---|
[1846] | 839 | |
---|
[358] | 840 | Parameters: |
---|
[1846] | 841 | |
---|
[710] | 842 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 843 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[1846] | 844 | |
---|
[358] | 845 | """ |
---|
| 846 | self._setInstrument(instr) |
---|
[1118] | 847 | self._add_history("set_instument", vars()) |
---|
[358] | 848 | |
---|
[1862] | 849 | @asaplog_post_dec |
---|
[1190] | 850 | def set_feedtype(self, feedtype): |
---|
[1846] | 851 | """\ |
---|
[1190] | 852 | Overwrite the feed type, which might not be set correctly. |
---|
[1846] | 853 | |
---|
[1190] | 854 | Parameters: |
---|
[1846] | 855 | |
---|
[1190] | 856 | feedtype: 'linear' or 'circular' |
---|
[1846] | 857 | |
---|
[1190] | 858 | """ |
---|
| 859 | self._setfeedtype(feedtype) |
---|
| 860 | self._add_history("set_feedtype", vars()) |
---|
| 861 | |
---|
[1862] | 862 | @asaplog_post_dec |
---|
[276] | 863 | def set_doppler(self, doppler='RADIO'): |
---|
[1846] | 864 | """\ |
---|
[276] | 865 | Set the doppler for all following operations on this scantable. |
---|
[1846] | 866 | |
---|
[276] | 867 | Parameters: |
---|
[1846] | 868 | |
---|
[276] | 869 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
[1846] | 870 | |
---|
[276] | 871 | """ |
---|
[484] | 872 | varlist = vars() |
---|
[276] | 873 | inf = list(self._getcoordinfo()) |
---|
| 874 | inf[2] = doppler |
---|
| 875 | self._setcoordinfo(inf) |
---|
[1118] | 876 | self._add_history("set_doppler", vars()) |
---|
[710] | 877 | |
---|
[1862] | 878 | @asaplog_post_dec |
---|
[226] | 879 | def set_freqframe(self, frame=None): |
---|
[1846] | 880 | """\ |
---|
[113] | 881 | Set the frame type of the Spectral Axis. |
---|
[1846] | 882 | |
---|
[113] | 883 | Parameters: |
---|
[1846] | 884 | |
---|
[591] | 885 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1819] | 886 | 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
[1118] | 887 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[1846] | 888 | |
---|
| 889 | Example:: |
---|
| 890 | |
---|
[113] | 891 | scan.set_freqframe('BARY') |
---|
[1846] | 892 | |
---|
[113] | 893 | """ |
---|
[1593] | 894 | frame = frame or rcParams['scantable.freqframe'] |
---|
[484] | 895 | varlist = vars() |
---|
[1819] | 896 | # "REST" is not implemented in casacore |
---|
| 897 | #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 898 | # 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
| 899 | valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
[1118] | 900 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 901 | |
---|
[989] | 902 | if frame in valid: |
---|
[113] | 903 | inf = list(self._getcoordinfo()) |
---|
| 904 | inf[1] = frame |
---|
| 905 | self._setcoordinfo(inf) |
---|
[1118] | 906 | self._add_history("set_freqframe", varlist) |
---|
[102] | 907 | else: |
---|
[1118] | 908 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[1859] | 909 | raise TypeError(msg) |
---|
[710] | 910 | |
---|
[1862] | 911 | @asaplog_post_dec |
---|
[989] | 912 | def set_dirframe(self, frame=""): |
---|
[1846] | 913 | """\ |
---|
[989] | 914 | Set the frame type of the Direction on the sky. |
---|
[1846] | 915 | |
---|
[989] | 916 | Parameters: |
---|
[1846] | 917 | |
---|
[989] | 918 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 919 | 'J2000', 'B1950', 'GALACTIC' |
---|
[1846] | 920 | |
---|
| 921 | Example: |
---|
| 922 | |
---|
[989] | 923 | scan.set_dirframe('GALACTIC') |
---|
[1846] | 924 | |
---|
[989] | 925 | """ |
---|
| 926 | varlist = vars() |
---|
[1859] | 927 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 928 | self._add_history("set_dirframe", varlist) |
---|
[989] | 929 | |
---|
[113] | 930 | def get_unit(self): |
---|
[1846] | 931 | """\ |
---|
[113] | 932 | Get the default unit set in this scantable |
---|
[1846] | 933 | |
---|
[113] | 934 | Returns: |
---|
[1846] | 935 | |
---|
[113] | 936 | A unit string |
---|
[1846] | 937 | |
---|
[113] | 938 | """ |
---|
| 939 | inf = self._getcoordinfo() |
---|
| 940 | unit = inf[0] |
---|
| 941 | if unit == '': unit = 'channel' |
---|
| 942 | return unit |
---|
[102] | 943 | |
---|
[1862] | 944 | @asaplog_post_dec |
---|
[158] | 945 | def get_abcissa(self, rowno=0): |
---|
[1846] | 946 | """\ |
---|
[158] | 947 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 948 | selected Beam/IF/Pol |
---|
[1846] | 949 | |
---|
[113] | 950 | Parameters: |
---|
[1846] | 951 | |
---|
[226] | 952 | rowno: an optional row number in the scantable. Default is the |
---|
| 953 | first row, i.e. rowno=0 |
---|
[1846] | 954 | |
---|
[113] | 955 | Returns: |
---|
[1846] | 956 | |
---|
[1348] | 957 | The abcissa values and the format string (as a dictionary) |
---|
[1846] | 958 | |
---|
[113] | 959 | """ |
---|
[256] | 960 | abc = self._getabcissa(rowno) |
---|
[710] | 961 | lbl = self._getabcissalabel(rowno) |
---|
[158] | 962 | return abc, lbl |
---|
[113] | 963 | |
---|
[1862] | 964 | @asaplog_post_dec |
---|
[1819] | 965 | def flag(self, mask=None, unflag=False): |
---|
[1846] | 966 | """\ |
---|
[1001] | 967 | Flag the selected data using an optional channel mask. |
---|
[1846] | 968 | |
---|
[1001] | 969 | Parameters: |
---|
[1846] | 970 | |
---|
[1001] | 971 | mask: an optional channel mask, created with create_mask. Default |
---|
| 972 | (no mask) is all channels. |
---|
[1855] | 973 | |
---|
[1819] | 974 | unflag: if True, unflag the data |
---|
[1846] | 975 | |
---|
[1001] | 976 | """ |
---|
| 977 | varlist = vars() |
---|
[1593] | 978 | mask = mask or [] |
---|
[1859] | 979 | self._flag(mask, unflag) |
---|
[1001] | 980 | self._add_history("flag", varlist) |
---|
| 981 | |
---|
[1862] | 982 | @asaplog_post_dec |
---|
[1819] | 983 | def flag_row(self, rows=[], unflag=False): |
---|
[1846] | 984 | """\ |
---|
[1819] | 985 | Flag the selected data in row-based manner. |
---|
[1846] | 986 | |
---|
[1819] | 987 | Parameters: |
---|
[1846] | 988 | |
---|
[1843] | 989 | rows: list of row numbers to be flagged. Default is no row |
---|
| 990 | (must be explicitly specified to execute row-based flagging). |
---|
[1855] | 991 | |
---|
[1819] | 992 | unflag: if True, unflag the data. |
---|
[1846] | 993 | |
---|
[1819] | 994 | """ |
---|
| 995 | varlist = vars() |
---|
[1859] | 996 | self._flag_row(rows, unflag) |
---|
[1819] | 997 | self._add_history("flag_row", varlist) |
---|
| 998 | |
---|
[1862] | 999 | @asaplog_post_dec |
---|
[1819] | 1000 | def clip(self, uthres=None, dthres=None, clipoutside=True, unflag=False): |
---|
[1846] | 1001 | """\ |
---|
[1819] | 1002 | Flag the selected data outside a specified range (in channel-base) |
---|
[1846] | 1003 | |
---|
[1819] | 1004 | Parameters: |
---|
[1846] | 1005 | |
---|
[1819] | 1006 | uthres: upper threshold. |
---|
[1855] | 1007 | |
---|
[1819] | 1008 | dthres: lower threshold |
---|
[1846] | 1009 | |
---|
[1819] | 1010 | clipoutside: True for flagging data outside the range [dthres:uthres]. |
---|
| 1011 | False for glagging data inside the range. |
---|
[1855] | 1012 | |
---|
[1846] | 1013 | unflag: if True, unflag the data. |
---|
| 1014 | |
---|
[1819] | 1015 | """ |
---|
| 1016 | varlist = vars() |
---|
[1859] | 1017 | self._clip(uthres, dthres, clipoutside, unflag) |
---|
[1819] | 1018 | self._add_history("clip", varlist) |
---|
| 1019 | |
---|
[1862] | 1020 | @asaplog_post_dec |
---|
[1584] | 1021 | def lag_flag(self, start, end, unit="MHz", insitu=None): |
---|
[1846] | 1022 | """\ |
---|
[1192] | 1023 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
[1584] | 1024 | Flagged data in the scantable gets interpolated over the region. |
---|
[1192] | 1025 | No taper is applied. |
---|
[1846] | 1026 | |
---|
[1192] | 1027 | Parameters: |
---|
[1846] | 1028 | |
---|
[1579] | 1029 | start: the start frequency (really a period within the |
---|
| 1030 | bandwidth) or period to remove |
---|
[1855] | 1031 | |
---|
[1579] | 1032 | end: the end frequency or period to remove |
---|
[1855] | 1033 | |
---|
[1584] | 1034 | unit: the frequency unit (default "MHz") or "" for |
---|
[1579] | 1035 | explicit lag channels |
---|
[1846] | 1036 | |
---|
| 1037 | *Notes*: |
---|
| 1038 | |
---|
[1579] | 1039 | It is recommended to flag edges of the band or strong |
---|
[1348] | 1040 | signals beforehand. |
---|
[1846] | 1041 | |
---|
[1192] | 1042 | """ |
---|
| 1043 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1044 | self._math._setinsitu(insitu) |
---|
| 1045 | varlist = vars() |
---|
[1579] | 1046 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.} |
---|
| 1047 | if not (unit == "" or base.has_key(unit)): |
---|
[1192] | 1048 | raise ValueError("%s is not a valid unit." % unit) |
---|
[1859] | 1049 | if unit == "": |
---|
| 1050 | s = scantable(self._math._lag_flag(self, start, end, "lags")) |
---|
| 1051 | else: |
---|
| 1052 | s = scantable(self._math._lag_flag(self, start*base[unit], |
---|
| 1053 | end*base[unit], "frequency")) |
---|
[1192] | 1054 | s._add_history("lag_flag", varlist) |
---|
| 1055 | if insitu: |
---|
| 1056 | self._assign(s) |
---|
| 1057 | else: |
---|
| 1058 | return s |
---|
[1001] | 1059 | |
---|
[1862] | 1060 | @asaplog_post_dec |
---|
[113] | 1061 | def create_mask(self, *args, **kwargs): |
---|
[1846] | 1062 | """\ |
---|
[1118] | 1063 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 1064 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 1065 | applied. |
---|
[1846] | 1066 | |
---|
[102] | 1067 | Parameters: |
---|
[1846] | 1068 | |
---|
[1118] | 1069 | [min, max], [min2, max2], ... |
---|
[1024] | 1070 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 1071 | to be masked |
---|
[1855] | 1072 | |
---|
[189] | 1073 | invert: optional argument. If specified as True, |
---|
| 1074 | return an inverted mask, i.e. the regions |
---|
| 1075 | specified are EXCLUDED |
---|
[1855] | 1076 | |
---|
[513] | 1077 | row: create the mask using the specified row for |
---|
| 1078 | unit conversions, default is row=0 |
---|
| 1079 | only necessary if frequency varies over rows. |
---|
[1846] | 1080 | |
---|
| 1081 | Examples:: |
---|
| 1082 | |
---|
[113] | 1083 | scan.set_unit('channel') |
---|
[1846] | 1084 | # a) |
---|
[1118] | 1085 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 1086 | # masks everything outside 400 and 500 |
---|
[113] | 1087 | # and 800 and 900 in the unit 'channel' |
---|
| 1088 | |
---|
[1846] | 1089 | # b) |
---|
[1118] | 1090 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 1091 | # masks the regions between 400 and 500 |
---|
[113] | 1092 | # and 800 and 900 in the unit 'channel' |
---|
[1846] | 1093 | |
---|
| 1094 | # c) |
---|
| 1095 | #mask only channel 400 |
---|
[1554] | 1096 | msk = scan.create_mask([400]) |
---|
[1846] | 1097 | |
---|
[102] | 1098 | """ |
---|
[1554] | 1099 | row = kwargs.get("row", 0) |
---|
[513] | 1100 | data = self._getabcissa(row) |
---|
[113] | 1101 | u = self._getcoordinfo()[0] |
---|
[1859] | 1102 | if u == "": |
---|
| 1103 | u = "channel" |
---|
| 1104 | msg = "The current mask window unit is %s" % u |
---|
| 1105 | i = self._check_ifs() |
---|
| 1106 | if not i: |
---|
| 1107 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 1108 | asaplog.push(msg) |
---|
[102] | 1109 | n = self.nchan() |
---|
[1295] | 1110 | msk = _n_bools(n, False) |
---|
[710] | 1111 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 1112 | |
---|
[1118] | 1113 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 1114 | and args or args[0] |
---|
[710] | 1115 | for window in ws: |
---|
[1554] | 1116 | if len(window) == 1: |
---|
| 1117 | window = [window[0], window[0]] |
---|
| 1118 | if len(window) == 0 or len(window) > 2: |
---|
| 1119 | raise ValueError("A window needs to be defined as [start(, end)]") |
---|
[1545] | 1120 | if window[0] > window[1]: |
---|
| 1121 | tmp = window[0] |
---|
| 1122 | window[0] = window[1] |
---|
| 1123 | window[1] = tmp |
---|
[102] | 1124 | for i in range(n): |
---|
[1024] | 1125 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 1126 | msk[i] = True |
---|
[113] | 1127 | if kwargs.has_key('invert'): |
---|
| 1128 | if kwargs.get('invert'): |
---|
[1295] | 1129 | msk = mask_not(msk) |
---|
[102] | 1130 | return msk |
---|
[710] | 1131 | |
---|
[1819] | 1132 | def get_masklist(self, mask=None, row=0): |
---|
[1846] | 1133 | """\ |
---|
[1819] | 1134 | Compute and return a list of mask windows, [min, max]. |
---|
[1846] | 1135 | |
---|
[1819] | 1136 | Parameters: |
---|
[1846] | 1137 | |
---|
[1819] | 1138 | mask: channel mask, created with create_mask. |
---|
[1855] | 1139 | |
---|
[1819] | 1140 | row: calcutate the masklist using the specified row |
---|
| 1141 | for unit conversions, default is row=0 |
---|
| 1142 | only necessary if frequency varies over rows. |
---|
[1846] | 1143 | |
---|
[1819] | 1144 | Returns: |
---|
[1846] | 1145 | |
---|
[1819] | 1146 | [min, max], [min2, max2], ... |
---|
| 1147 | Pairs of start/end points (inclusive)specifying |
---|
| 1148 | the masked regions |
---|
[1846] | 1149 | |
---|
[1819] | 1150 | """ |
---|
| 1151 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1152 | raise TypeError("The mask should be list or tuple.") |
---|
| 1153 | if len(mask) < 2: |
---|
| 1154 | raise TypeError("The mask elements should be > 1") |
---|
| 1155 | if self.nchan() != len(mask): |
---|
| 1156 | msg = "Number of channels in scantable != number of mask elements" |
---|
| 1157 | raise TypeError(msg) |
---|
| 1158 | data = self._getabcissa(row) |
---|
| 1159 | u = self._getcoordinfo()[0] |
---|
[1859] | 1160 | if u == "": |
---|
| 1161 | u = "channel" |
---|
| 1162 | msg = "The current mask window unit is %s" % u |
---|
| 1163 | i = self._check_ifs() |
---|
| 1164 | if not i: |
---|
| 1165 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 1166 | asaplog.push(msg) |
---|
[1819] | 1167 | masklist=[] |
---|
| 1168 | ist, ien = None, None |
---|
| 1169 | ist, ien=self.get_mask_indices(mask) |
---|
| 1170 | if ist is not None and ien is not None: |
---|
| 1171 | for i in xrange(len(ist)): |
---|
| 1172 | range=[data[ist[i]],data[ien[i]]] |
---|
| 1173 | range.sort() |
---|
| 1174 | masklist.append([range[0],range[1]]) |
---|
| 1175 | return masklist |
---|
| 1176 | |
---|
| 1177 | def get_mask_indices(self, mask=None): |
---|
[1846] | 1178 | """\ |
---|
[1819] | 1179 | Compute and Return lists of mask start indices and mask end indices. |
---|
[1855] | 1180 | |
---|
| 1181 | Parameters: |
---|
| 1182 | |
---|
[1819] | 1183 | mask: channel mask, created with create_mask. |
---|
[1846] | 1184 | |
---|
[1819] | 1185 | Returns: |
---|
[1846] | 1186 | |
---|
[1819] | 1187 | List of mask start indices and that of mask end indices, |
---|
| 1188 | i.e., [istart1,istart2,....], [iend1,iend2,....]. |
---|
[1846] | 1189 | |
---|
[1819] | 1190 | """ |
---|
| 1191 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1192 | raise TypeError("The mask should be list or tuple.") |
---|
| 1193 | if len(mask) < 2: |
---|
| 1194 | raise TypeError("The mask elements should be > 1") |
---|
| 1195 | istart=[] |
---|
| 1196 | iend=[] |
---|
| 1197 | if mask[0]: istart.append(0) |
---|
| 1198 | for i in range(len(mask)-1): |
---|
| 1199 | if not mask[i] and mask[i+1]: |
---|
| 1200 | istart.append(i+1) |
---|
| 1201 | elif mask[i] and not mask[i+1]: |
---|
| 1202 | iend.append(i) |
---|
| 1203 | if mask[len(mask)-1]: iend.append(len(mask)-1) |
---|
| 1204 | if len(istart) != len(iend): |
---|
| 1205 | raise RuntimeError("Numbers of mask start != mask end.") |
---|
| 1206 | for i in range(len(istart)): |
---|
| 1207 | if istart[i] > iend[i]: |
---|
| 1208 | raise RuntimeError("Mask start index > mask end index") |
---|
| 1209 | break |
---|
| 1210 | return istart,iend |
---|
| 1211 | |
---|
| 1212 | # def get_restfreqs(self): |
---|
| 1213 | # """ |
---|
| 1214 | # Get the restfrequency(s) stored in this scantable. |
---|
| 1215 | # The return value(s) are always of unit 'Hz' |
---|
| 1216 | # Parameters: |
---|
| 1217 | # none |
---|
| 1218 | # Returns: |
---|
| 1219 | # a list of doubles |
---|
| 1220 | # """ |
---|
| 1221 | # return list(self._getrestfreqs()) |
---|
| 1222 | |
---|
| 1223 | def get_restfreqs(self, ids=None): |
---|
[1846] | 1224 | """\ |
---|
[256] | 1225 | Get the restfrequency(s) stored in this scantable. |
---|
| 1226 | The return value(s) are always of unit 'Hz' |
---|
[1846] | 1227 | |
---|
[256] | 1228 | Parameters: |
---|
[1846] | 1229 | |
---|
[1819] | 1230 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to |
---|
| 1231 | be retrieved |
---|
[1846] | 1232 | |
---|
[256] | 1233 | Returns: |
---|
[1846] | 1234 | |
---|
[1819] | 1235 | dictionary containing ids and a list of doubles for each id |
---|
[1846] | 1236 | |
---|
[256] | 1237 | """ |
---|
[1819] | 1238 | if ids is None: |
---|
| 1239 | rfreqs={} |
---|
| 1240 | idlist = self.getmolnos() |
---|
| 1241 | for i in idlist: |
---|
| 1242 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1243 | return rfreqs |
---|
| 1244 | else: |
---|
| 1245 | if type(ids)==list or type(ids)==tuple: |
---|
| 1246 | rfreqs={} |
---|
| 1247 | for i in ids: |
---|
| 1248 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1249 | return rfreqs |
---|
| 1250 | else: |
---|
| 1251 | return list(self._getrestfreqs(ids)) |
---|
| 1252 | #return list(self._getrestfreqs(ids)) |
---|
[102] | 1253 | |
---|
[931] | 1254 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
[1846] | 1255 | """\ |
---|
[931] | 1256 | Set or replace the restfrequency specified and |
---|
| 1257 | If the 'freqs' argument holds a scalar, |
---|
| 1258 | then that rest frequency will be applied to all the selected |
---|
| 1259 | data. If the 'freqs' argument holds |
---|
| 1260 | a vector, then it MUST be of equal or smaller length than |
---|
| 1261 | the number of IFs (and the available restfrequencies will be |
---|
| 1262 | replaced by this vector). In this case, *all* data have |
---|
| 1263 | the restfrequency set per IF according |
---|
| 1264 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 1265 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 1266 | IF 1 gets restfreq 2e9. |
---|
[1846] | 1267 | |
---|
[1395] | 1268 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 1269 | |
---|
[931] | 1270 | Parameters: |
---|
[1846] | 1271 | |
---|
[931] | 1272 | freqs: list of rest frequency values or string idenitfiers |
---|
[1855] | 1273 | |
---|
[931] | 1274 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 1275 | |
---|
[1846] | 1276 | |
---|
| 1277 | Example:: |
---|
| 1278 | |
---|
[1819] | 1279 | # set the given restfrequency for the all currently selected IFs |
---|
[931] | 1280 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1845] | 1281 | # set restfrequencies for the n IFs (n > 1) in the order of the |
---|
| 1282 | # list, i.e |
---|
| 1283 | # IF0 -> 1.4e9, IF1 -> 1.41e9, IF3 -> 1.42e9 |
---|
| 1284 | # len(list_of_restfreqs) == nIF |
---|
| 1285 | # for nIF == 1 the following will set multiple restfrequency for |
---|
| 1286 | # that IF |
---|
[1819] | 1287 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9]) |
---|
[1845] | 1288 | # set multiple restfrequencies per IF. as a list of lists where |
---|
| 1289 | # the outer list has nIF elements, the inner s arbitrary |
---|
| 1290 | scan.set_restfreqs(freqs=[[1.4e9, 1.41e9], [1.67e9]]) |
---|
[391] | 1291 | |
---|
[1846] | 1292 | *Note*: |
---|
[1845] | 1293 | |
---|
[931] | 1294 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 1295 | source and IF basis, use scantable.set_selection() before using |
---|
[1846] | 1296 | this function:: |
---|
[931] | 1297 | |
---|
[1846] | 1298 | # provided your scantable is called scan |
---|
| 1299 | selection = selector() |
---|
| 1300 | selection.set_name("ORION*") |
---|
| 1301 | selection.set_ifs([1]) |
---|
| 1302 | scan.set_selection(selection) |
---|
| 1303 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 1304 | |
---|
[931] | 1305 | """ |
---|
| 1306 | varlist = vars() |
---|
[1157] | 1307 | from asap import linecatalog |
---|
| 1308 | # simple value |
---|
[1118] | 1309 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1845] | 1310 | self._setrestfreqs([freqs], [""], unit) |
---|
[1157] | 1311 | # list of values |
---|
[1118] | 1312 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 1313 | # list values are scalars |
---|
[1118] | 1314 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[1845] | 1315 | if len(freqs) == 1: |
---|
| 1316 | self._setrestfreqs(freqs, [""], unit) |
---|
| 1317 | else: |
---|
| 1318 | # allow the 'old' mode of setting mulitple IFs |
---|
| 1319 | sel = selector() |
---|
| 1320 | savesel = self._getselection() |
---|
| 1321 | iflist = self.getifnos() |
---|
| 1322 | if len(freqs)>len(iflist): |
---|
| 1323 | raise ValueError("number of elements in list of list " |
---|
| 1324 | "exeeds the current IF selections") |
---|
| 1325 | iflist = self.getifnos() |
---|
| 1326 | for i, fval in enumerate(freqs): |
---|
| 1327 | sel.set_ifs(iflist[i]) |
---|
| 1328 | self._setselection(sel) |
---|
| 1329 | self._setrestfreqs([fval], [""], unit) |
---|
| 1330 | self._setselection(savesel) |
---|
| 1331 | |
---|
| 1332 | # list values are dict, {'value'=, 'name'=) |
---|
[1157] | 1333 | elif isinstance(freqs[-1], dict): |
---|
[1845] | 1334 | values = [] |
---|
| 1335 | names = [] |
---|
| 1336 | for d in freqs: |
---|
| 1337 | values.append(d["value"]) |
---|
| 1338 | names.append(d["name"]) |
---|
| 1339 | self._setrestfreqs(values, names, unit) |
---|
[1819] | 1340 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple): |
---|
[1157] | 1341 | sel = selector() |
---|
| 1342 | savesel = self._getselection() |
---|
[1322] | 1343 | iflist = self.getifnos() |
---|
[1819] | 1344 | if len(freqs)>len(iflist): |
---|
[1845] | 1345 | raise ValueError("number of elements in list of list exeeds" |
---|
| 1346 | " the current IF selections") |
---|
| 1347 | for i, fval in enumerate(freqs): |
---|
[1322] | 1348 | sel.set_ifs(iflist[i]) |
---|
[1259] | 1349 | self._setselection(sel) |
---|
[1845] | 1350 | self._setrestfreqs(fval, [""], unit) |
---|
[1157] | 1351 | self._setselection(savesel) |
---|
| 1352 | # freqs are to be taken from a linecatalog |
---|
[1153] | 1353 | elif isinstance(freqs, linecatalog): |
---|
| 1354 | sel = selector() |
---|
| 1355 | savesel = self._getselection() |
---|
| 1356 | for i in xrange(freqs.nrow()): |
---|
[1322] | 1357 | sel.set_ifs(iflist[i]) |
---|
[1153] | 1358 | self._setselection(sel) |
---|
[1845] | 1359 | self._setrestfreqs([freqs.get_frequency(i)], |
---|
| 1360 | [freqs.get_name(i)], "MHz") |
---|
[1153] | 1361 | # ensure that we are not iterating past nIF |
---|
| 1362 | if i == self.nif()-1: break |
---|
| 1363 | self._setselection(savesel) |
---|
[931] | 1364 | else: |
---|
| 1365 | return |
---|
| 1366 | self._add_history("set_restfreqs", varlist) |
---|
| 1367 | |
---|
[1360] | 1368 | def shift_refpix(self, delta): |
---|
[1846] | 1369 | """\ |
---|
[1589] | 1370 | Shift the reference pixel of the Spectra Coordinate by an |
---|
| 1371 | integer amount. |
---|
[1846] | 1372 | |
---|
[1589] | 1373 | Parameters: |
---|
[1846] | 1374 | |
---|
[1589] | 1375 | delta: the amount to shift by |
---|
[1846] | 1376 | |
---|
| 1377 | *Note*: |
---|
| 1378 | |
---|
[1589] | 1379 | Be careful using this with broadband data. |
---|
[1846] | 1380 | |
---|
[1360] | 1381 | """ |
---|
[1731] | 1382 | Scantable.shift_refpix(self, delta) |
---|
[931] | 1383 | |
---|
[1862] | 1384 | @asaplog_post_dec |
---|
[1259] | 1385 | def history(self, filename=None): |
---|
[1846] | 1386 | """\ |
---|
[1259] | 1387 | Print the history. Optionally to a file. |
---|
[1846] | 1388 | |
---|
[1348] | 1389 | Parameters: |
---|
[1846] | 1390 | |
---|
[1348] | 1391 | filename: The name of the file to save the history to. |
---|
[1846] | 1392 | |
---|
[1259] | 1393 | """ |
---|
[484] | 1394 | hist = list(self._gethistory()) |
---|
[794] | 1395 | out = "-"*80 |
---|
[484] | 1396 | for h in hist: |
---|
[489] | 1397 | if h.startswith("---"): |
---|
[1857] | 1398 | out = "\n".join([out, h]) |
---|
[489] | 1399 | else: |
---|
| 1400 | items = h.split("##") |
---|
| 1401 | date = items[0] |
---|
| 1402 | func = items[1] |
---|
| 1403 | items = items[2:] |
---|
[794] | 1404 | out += "\n"+date+"\n" |
---|
| 1405 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 1406 | for i in items: |
---|
| 1407 | s = i.split("=") |
---|
[1118] | 1408 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[1857] | 1409 | out = "\n".join([out, "-"*80]) |
---|
[1259] | 1410 | if filename is not None: |
---|
| 1411 | if filename is "": |
---|
| 1412 | filename = 'scantable_history.txt' |
---|
| 1413 | import os |
---|
| 1414 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 1415 | if not os.path.isdir(filename): |
---|
| 1416 | data = open(filename, 'w') |
---|
| 1417 | data.write(out) |
---|
| 1418 | data.close() |
---|
| 1419 | else: |
---|
| 1420 | msg = "Illegal file name '%s'." % (filename) |
---|
[1859] | 1421 | raise IOError(msg) |
---|
| 1422 | return page(out) |
---|
[513] | 1423 | # |
---|
| 1424 | # Maths business |
---|
| 1425 | # |
---|
[1862] | 1426 | @asaplog_post_dec |
---|
[931] | 1427 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[1846] | 1428 | """\ |
---|
[1070] | 1429 | Return the (time) weighted average of a scan. |
---|
[1846] | 1430 | |
---|
| 1431 | *Note*: |
---|
| 1432 | |
---|
[1070] | 1433 | in channels only - align if necessary |
---|
[1846] | 1434 | |
---|
[513] | 1435 | Parameters: |
---|
[1846] | 1436 | |
---|
[513] | 1437 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 1438 | weighting) |
---|
[1855] | 1439 | |
---|
[558] | 1440 | scanav: True averages each scan separately |
---|
| 1441 | False (default) averages all scans together, |
---|
[1855] | 1442 | |
---|
[1099] | 1443 | weight: Weighting scheme. |
---|
| 1444 | 'none' (mean no weight) |
---|
| 1445 | 'var' (1/var(spec) weighted) |
---|
| 1446 | 'tsys' (1/Tsys**2 weighted) |
---|
| 1447 | 'tint' (integration time weighted) |
---|
| 1448 | 'tintsys' (Tint/Tsys**2) |
---|
| 1449 | 'median' ( median averaging) |
---|
[535] | 1450 | The default is 'tint' |
---|
[1855] | 1451 | |
---|
[931] | 1452 | align: align the spectra in velocity before averaging. It takes |
---|
| 1453 | the time of the first spectrum as reference time. |
---|
[1846] | 1454 | |
---|
| 1455 | Example:: |
---|
| 1456 | |
---|
[513] | 1457 | # time average the scantable without using a mask |
---|
[710] | 1458 | newscan = scan.average_time() |
---|
[1846] | 1459 | |
---|
[513] | 1460 | """ |
---|
| 1461 | varlist = vars() |
---|
[1593] | 1462 | weight = weight or 'TINT' |
---|
| 1463 | mask = mask or () |
---|
| 1464 | scanav = (scanav and 'SCAN') or 'NONE' |
---|
[1118] | 1465 | scan = (self, ) |
---|
[1859] | 1466 | |
---|
| 1467 | if align: |
---|
| 1468 | scan = (self.freq_align(insitu=False), ) |
---|
| 1469 | s = None |
---|
| 1470 | if weight.upper() == 'MEDIAN': |
---|
| 1471 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 1472 | scanav)) |
---|
| 1473 | else: |
---|
| 1474 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 1475 | scanav)) |
---|
[1099] | 1476 | s._add_history("average_time", varlist) |
---|
[513] | 1477 | return s |
---|
[710] | 1478 | |
---|
[1862] | 1479 | @asaplog_post_dec |
---|
[876] | 1480 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[1846] | 1481 | """\ |
---|
[513] | 1482 | Return a scan where all spectra are converted to either |
---|
| 1483 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 1484 | By default the function tries to look the values up internally. |
---|
| 1485 | If it can't find them (or if you want to over-ride), you must |
---|
| 1486 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 1487 | also if you don't set it). jyperk takes precedence if you set both. |
---|
[1846] | 1488 | |
---|
[513] | 1489 | Parameters: |
---|
[1846] | 1490 | |
---|
[513] | 1491 | jyperk: the Jy / K conversion factor |
---|
[1855] | 1492 | |
---|
[513] | 1493 | eta: the aperture efficiency |
---|
[1855] | 1494 | |
---|
[513] | 1495 | d: the geomtric diameter (metres) |
---|
[1855] | 1496 | |
---|
[513] | 1497 | insitu: if False a new scantable is returned. |
---|
| 1498 | Otherwise, the scaling is done in-situ |
---|
| 1499 | The default is taken from .asaprc (False) |
---|
[1846] | 1500 | |
---|
[513] | 1501 | """ |
---|
| 1502 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1503 | self._math._setinsitu(insitu) |
---|
[513] | 1504 | varlist = vars() |
---|
[1593] | 1505 | jyperk = jyperk or -1.0 |
---|
| 1506 | d = d or -1.0 |
---|
| 1507 | eta = eta or -1.0 |
---|
[876] | 1508 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 1509 | s._add_history("convert_flux", varlist) |
---|
| 1510 | if insitu: self._assign(s) |
---|
| 1511 | else: return s |
---|
[513] | 1512 | |
---|
[1862] | 1513 | @asaplog_post_dec |
---|
[876] | 1514 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[1846] | 1515 | """\ |
---|
[513] | 1516 | Return a scan after applying a gain-elevation correction. |
---|
| 1517 | The correction can be made via either a polynomial or a |
---|
| 1518 | table-based interpolation (and extrapolation if necessary). |
---|
| 1519 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 1520 | If you specify neither, then a polynomial correction will be made |
---|
| 1521 | with built in coefficients known for certain telescopes (an error |
---|
| 1522 | will occur if the instrument is not known). |
---|
| 1523 | The data and Tsys are *divided* by the scaling factors. |
---|
[1846] | 1524 | |
---|
[513] | 1525 | Parameters: |
---|
[1846] | 1526 | |
---|
[513] | 1527 | poly: Polynomial coefficients (default None) to compute a |
---|
| 1528 | gain-elevation correction as a function of |
---|
| 1529 | elevation (in degrees). |
---|
[1855] | 1530 | |
---|
[513] | 1531 | filename: The name of an ascii file holding correction factors. |
---|
| 1532 | The first row of the ascii file must give the column |
---|
| 1533 | names and these MUST include columns |
---|
| 1534 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 1535 | by this) somewhere. |
---|
| 1536 | The second row must give the data type of the |
---|
| 1537 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 1538 | An example file would be |
---|
| 1539 | (actual factors are arbitrary) : |
---|
| 1540 | |
---|
| 1541 | TIME ELEVATION FACTOR |
---|
| 1542 | R R R |
---|
| 1543 | 0.1 0 0.8 |
---|
| 1544 | 0.2 20 0.85 |
---|
| 1545 | 0.3 40 0.9 |
---|
| 1546 | 0.4 60 0.85 |
---|
| 1547 | 0.5 80 0.8 |
---|
| 1548 | 0.6 90 0.75 |
---|
[1855] | 1549 | |
---|
[513] | 1550 | method: Interpolation method when correcting from a table. |
---|
| 1551 | Values are "nearest", "linear" (default), "cubic" |
---|
| 1552 | and "spline" |
---|
[1855] | 1553 | |
---|
[513] | 1554 | insitu: if False a new scantable is returned. |
---|
| 1555 | Otherwise, the scaling is done in-situ |
---|
| 1556 | The default is taken from .asaprc (False) |
---|
[1846] | 1557 | |
---|
[513] | 1558 | """ |
---|
| 1559 | |
---|
| 1560 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1561 | self._math._setinsitu(insitu) |
---|
[513] | 1562 | varlist = vars() |
---|
[1593] | 1563 | poly = poly or () |
---|
[513] | 1564 | from os.path import expandvars |
---|
| 1565 | filename = expandvars(filename) |
---|
[876] | 1566 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 1567 | s._add_history("gain_el", varlist) |
---|
[1593] | 1568 | if insitu: |
---|
| 1569 | self._assign(s) |
---|
| 1570 | else: |
---|
| 1571 | return s |
---|
[710] | 1572 | |
---|
[1862] | 1573 | @asaplog_post_dec |
---|
[931] | 1574 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[1846] | 1575 | """\ |
---|
[513] | 1576 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 1577 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 1578 | set_freqframe. |
---|
[1846] | 1579 | |
---|
[513] | 1580 | Parameters: |
---|
[1855] | 1581 | |
---|
[513] | 1582 | reftime: reference time to align at. By default, the time of |
---|
| 1583 | the first row of data is used. |
---|
[1855] | 1584 | |
---|
[513] | 1585 | method: Interpolation method for regridding the spectra. |
---|
| 1586 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 1587 | and "spline" |
---|
[1855] | 1588 | |
---|
[513] | 1589 | insitu: if False a new scantable is returned. |
---|
| 1590 | Otherwise, the scaling is done in-situ |
---|
| 1591 | The default is taken from .asaprc (False) |
---|
[1846] | 1592 | |
---|
[513] | 1593 | """ |
---|
[931] | 1594 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 1595 | self._math._setinsitu(insitu) |
---|
[513] | 1596 | varlist = vars() |
---|
[1593] | 1597 | reftime = reftime or "" |
---|
[931] | 1598 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 1599 | s._add_history("freq_align", varlist) |
---|
| 1600 | if insitu: self._assign(s) |
---|
| 1601 | else: return s |
---|
[513] | 1602 | |
---|
[1862] | 1603 | @asaplog_post_dec |
---|
[1725] | 1604 | def opacity(self, tau=None, insitu=None): |
---|
[1846] | 1605 | """\ |
---|
[513] | 1606 | Apply an opacity correction. The data |
---|
| 1607 | and Tsys are multiplied by the correction factor. |
---|
[1846] | 1608 | |
---|
[513] | 1609 | Parameters: |
---|
[1855] | 1610 | |
---|
[1689] | 1611 | tau: (list of) opacity from which the correction factor is |
---|
[513] | 1612 | exp(tau*ZD) |
---|
[1689] | 1613 | where ZD is the zenith-distance. |
---|
| 1614 | If a list is provided, it has to be of length nIF, |
---|
| 1615 | nIF*nPol or 1 and in order of IF/POL, e.g. |
---|
| 1616 | [opif0pol0, opif0pol1, opif1pol0 ...] |
---|
[1725] | 1617 | if tau is `None` the opacities are determined from a |
---|
| 1618 | model. |
---|
[1855] | 1619 | |
---|
[513] | 1620 | insitu: if False a new scantable is returned. |
---|
| 1621 | Otherwise, the scaling is done in-situ |
---|
| 1622 | The default is taken from .asaprc (False) |
---|
[1846] | 1623 | |
---|
[513] | 1624 | """ |
---|
| 1625 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1626 | self._math._setinsitu(insitu) |
---|
[513] | 1627 | varlist = vars() |
---|
[1689] | 1628 | if not hasattr(tau, "__len__"): |
---|
| 1629 | tau = [tau] |
---|
[876] | 1630 | s = scantable(self._math._opacity(self, tau)) |
---|
| 1631 | s._add_history("opacity", varlist) |
---|
| 1632 | if insitu: self._assign(s) |
---|
| 1633 | else: return s |
---|
[513] | 1634 | |
---|
[1862] | 1635 | @asaplog_post_dec |
---|
[513] | 1636 | def bin(self, width=5, insitu=None): |
---|
[1846] | 1637 | """\ |
---|
[513] | 1638 | Return a scan where all spectra have been binned up. |
---|
[1846] | 1639 | |
---|
[1348] | 1640 | Parameters: |
---|
[1846] | 1641 | |
---|
[513] | 1642 | width: The bin width (default=5) in pixels |
---|
[1855] | 1643 | |
---|
[513] | 1644 | insitu: if False a new scantable is returned. |
---|
| 1645 | Otherwise, the scaling is done in-situ |
---|
| 1646 | The default is taken from .asaprc (False) |
---|
[1846] | 1647 | |
---|
[513] | 1648 | """ |
---|
| 1649 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1650 | self._math._setinsitu(insitu) |
---|
[513] | 1651 | varlist = vars() |
---|
[876] | 1652 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1653 | s._add_history("bin", varlist) |
---|
[1589] | 1654 | if insitu: |
---|
| 1655 | self._assign(s) |
---|
| 1656 | else: |
---|
| 1657 | return s |
---|
[513] | 1658 | |
---|
[1862] | 1659 | @asaplog_post_dec |
---|
[513] | 1660 | def resample(self, width=5, method='cubic', insitu=None): |
---|
[1846] | 1661 | """\ |
---|
[1348] | 1662 | Return a scan where all spectra have been binned up. |
---|
[1573] | 1663 | |
---|
[1348] | 1664 | Parameters: |
---|
[1846] | 1665 | |
---|
[513] | 1666 | width: The bin width (default=5) in pixels |
---|
[1855] | 1667 | |
---|
[513] | 1668 | method: Interpolation method when correcting from a table. |
---|
| 1669 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1670 | and "spline" |
---|
[1855] | 1671 | |
---|
[513] | 1672 | insitu: if False a new scantable is returned. |
---|
| 1673 | Otherwise, the scaling is done in-situ |
---|
| 1674 | The default is taken from .asaprc (False) |
---|
[1846] | 1675 | |
---|
[513] | 1676 | """ |
---|
| 1677 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1678 | self._math._setinsitu(insitu) |
---|
[513] | 1679 | varlist = vars() |
---|
[876] | 1680 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1681 | s._add_history("resample", varlist) |
---|
[876] | 1682 | if insitu: self._assign(s) |
---|
| 1683 | else: return s |
---|
[513] | 1684 | |
---|
[1862] | 1685 | @asaplog_post_dec |
---|
[946] | 1686 | def average_pol(self, mask=None, weight='none'): |
---|
[1846] | 1687 | """\ |
---|
[946] | 1688 | Average the Polarisations together. |
---|
[1846] | 1689 | |
---|
[946] | 1690 | Parameters: |
---|
[1846] | 1691 | |
---|
[946] | 1692 | mask: An optional mask defining the region, where the |
---|
| 1693 | averaging will be applied. The output will have all |
---|
| 1694 | specified points masked. |
---|
[1855] | 1695 | |
---|
[946] | 1696 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1697 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 1698 | |
---|
[946] | 1699 | """ |
---|
| 1700 | varlist = vars() |
---|
[1593] | 1701 | mask = mask or () |
---|
[1010] | 1702 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1703 | s._add_history("average_pol", varlist) |
---|
[992] | 1704 | return s |
---|
[513] | 1705 | |
---|
[1862] | 1706 | @asaplog_post_dec |
---|
[1145] | 1707 | def average_beam(self, mask=None, weight='none'): |
---|
[1846] | 1708 | """\ |
---|
[1145] | 1709 | Average the Beams together. |
---|
[1846] | 1710 | |
---|
[1145] | 1711 | Parameters: |
---|
| 1712 | mask: An optional mask defining the region, where the |
---|
| 1713 | averaging will be applied. The output will have all |
---|
| 1714 | specified points masked. |
---|
[1855] | 1715 | |
---|
[1145] | 1716 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1717 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 1718 | |
---|
[1145] | 1719 | """ |
---|
| 1720 | varlist = vars() |
---|
[1593] | 1721 | mask = mask or () |
---|
[1145] | 1722 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1723 | s._add_history("average_beam", varlist) |
---|
| 1724 | return s |
---|
| 1725 | |
---|
[1586] | 1726 | def parallactify(self, pflag): |
---|
[1846] | 1727 | """\ |
---|
[1843] | 1728 | Set a flag to indicate whether this data should be treated as having |
---|
[1617] | 1729 | been 'parallactified' (total phase == 0.0) |
---|
[1846] | 1730 | |
---|
[1617] | 1731 | Parameters: |
---|
[1855] | 1732 | |
---|
[1843] | 1733 | pflag: Bool indicating whether to turn this on (True) or |
---|
[1617] | 1734 | off (False) |
---|
[1846] | 1735 | |
---|
[1617] | 1736 | """ |
---|
[1586] | 1737 | varlist = vars() |
---|
| 1738 | self._parallactify(pflag) |
---|
| 1739 | self._add_history("parallactify", varlist) |
---|
| 1740 | |
---|
[1862] | 1741 | @asaplog_post_dec |
---|
[992] | 1742 | def convert_pol(self, poltype=None): |
---|
[1846] | 1743 | """\ |
---|
[992] | 1744 | Convert the data to a different polarisation type. |
---|
[1565] | 1745 | Note that you will need cross-polarisation terms for most conversions. |
---|
[1846] | 1746 | |
---|
[992] | 1747 | Parameters: |
---|
[1855] | 1748 | |
---|
[992] | 1749 | poltype: The new polarisation type. Valid types are: |
---|
[1565] | 1750 | "linear", "circular", "stokes" and "linpol" |
---|
[1846] | 1751 | |
---|
[992] | 1752 | """ |
---|
| 1753 | varlist = vars() |
---|
[1859] | 1754 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1755 | s._add_history("convert_pol", varlist) |
---|
[992] | 1756 | return s |
---|
| 1757 | |
---|
[1862] | 1758 | @asaplog_post_dec |
---|
[1819] | 1759 | def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, insitu=None): |
---|
[1846] | 1760 | """\ |
---|
[513] | 1761 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
[1846] | 1762 | |
---|
[513] | 1763 | Parameters: |
---|
[1846] | 1764 | |
---|
[513] | 1765 | kernel: The type of smoothing kernel. Select from |
---|
[1574] | 1766 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian' |
---|
| 1767 | or 'poly' |
---|
[1855] | 1768 | |
---|
[513] | 1769 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1770 | ignored otherwise it defauls to 5 pixels. |
---|
| 1771 | For 'gaussian' it is the Full Width Half |
---|
| 1772 | Maximum. For 'boxcar' it is the full width. |
---|
[1574] | 1773 | For 'rmedian' and 'poly' it is the half width. |
---|
[1855] | 1774 | |
---|
[1574] | 1775 | order: Optional parameter for 'poly' kernel (default is 2), to |
---|
| 1776 | specify the order of the polnomial. Ignored by all other |
---|
| 1777 | kernels. |
---|
[1855] | 1778 | |
---|
[1819] | 1779 | plot: plot the original and the smoothed spectra. |
---|
| 1780 | In this each indivual fit has to be approved, by |
---|
| 1781 | typing 'y' or 'n' |
---|
[1855] | 1782 | |
---|
[513] | 1783 | insitu: if False a new scantable is returned. |
---|
| 1784 | Otherwise, the scaling is done in-situ |
---|
| 1785 | The default is taken from .asaprc (False) |
---|
[1846] | 1786 | |
---|
[513] | 1787 | """ |
---|
| 1788 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1789 | self._math._setinsitu(insitu) |
---|
[513] | 1790 | varlist = vars() |
---|
[1819] | 1791 | |
---|
| 1792 | if plot: orgscan = self.copy() |
---|
| 1793 | |
---|
[1574] | 1794 | s = scantable(self._math._smooth(self, kernel.lower(), width, order)) |
---|
[876] | 1795 | s._add_history("smooth", varlist) |
---|
[1819] | 1796 | |
---|
| 1797 | if plot: |
---|
| 1798 | if rcParams['plotter.gui']: |
---|
| 1799 | from asap.asaplotgui import asaplotgui as asaplot |
---|
| 1800 | else: |
---|
| 1801 | from asap.asaplot import asaplot |
---|
| 1802 | self._p=asaplot() |
---|
| 1803 | self._p.set_panels() |
---|
| 1804 | ylab=s._get_ordinate_label() |
---|
| 1805 | #self._p.palette(0,["#777777","red"]) |
---|
| 1806 | for r in xrange(s.nrow()): |
---|
| 1807 | xsm=s._getabcissa(r) |
---|
| 1808 | ysm=s._getspectrum(r) |
---|
| 1809 | xorg=orgscan._getabcissa(r) |
---|
| 1810 | yorg=orgscan._getspectrum(r) |
---|
| 1811 | self._p.clear() |
---|
| 1812 | self._p.hold() |
---|
| 1813 | self._p.set_axes('ylabel',ylab) |
---|
| 1814 | self._p.set_axes('xlabel',s._getabcissalabel(r)) |
---|
| 1815 | self._p.set_axes('title',s._getsourcename(r)) |
---|
| 1816 | self._p.set_line(label='Original',color="#777777") |
---|
| 1817 | self._p.plot(xorg,yorg) |
---|
| 1818 | self._p.set_line(label='Smoothed',color="red") |
---|
| 1819 | self._p.plot(xsm,ysm) |
---|
| 1820 | ### Ugly part for legend |
---|
| 1821 | for i in [0,1]: |
---|
| 1822 | self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]]) |
---|
| 1823 | self._p.release() |
---|
| 1824 | ### Ugly part for legend |
---|
| 1825 | self._p.subplots[0]['lines']=[] |
---|
| 1826 | res = raw_input("Accept smoothing ([y]/n): ") |
---|
| 1827 | if res.upper() == 'N': |
---|
| 1828 | s._setspectrum(yorg, r) |
---|
| 1829 | self._p.unmap() |
---|
| 1830 | self._p = None |
---|
| 1831 | del orgscan |
---|
| 1832 | |
---|
[876] | 1833 | if insitu: self._assign(s) |
---|
| 1834 | else: return s |
---|
[513] | 1835 | |
---|
[1862] | 1836 | @asaplog_post_dec |
---|
[1617] | 1837 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, |
---|
| 1838 | insitu=None): |
---|
[1846] | 1839 | """\ |
---|
[513] | 1840 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
[1846] | 1841 | |
---|
[513] | 1842 | Parameters: |
---|
[1846] | 1843 | |
---|
[794] | 1844 | mask: an optional mask |
---|
[1855] | 1845 | |
---|
[794] | 1846 | order: the order of the polynomial (default is 0) |
---|
[1855] | 1847 | |
---|
[1061] | 1848 | plot: plot the fit and the residual. In this each |
---|
| 1849 | indivual fit has to be approved, by typing 'y' |
---|
| 1850 | or 'n' |
---|
[1855] | 1851 | |
---|
[1391] | 1852 | uselin: use linear polynomial fit |
---|
[1855] | 1853 | |
---|
[794] | 1854 | insitu: if False a new scantable is returned. |
---|
| 1855 | Otherwise, the scaling is done in-situ |
---|
| 1856 | The default is taken from .asaprc (False) |
---|
[1846] | 1857 | |
---|
| 1858 | Example:: |
---|
| 1859 | |
---|
[513] | 1860 | # return a scan baselined by a third order polynomial, |
---|
| 1861 | # not using a mask |
---|
| 1862 | bscan = scan.poly_baseline(order=3) |
---|
[1846] | 1863 | |
---|
[579] | 1864 | """ |
---|
[513] | 1865 | if insitu is None: insitu = rcParams['insitu'] |
---|
[1819] | 1866 | if not insitu: |
---|
| 1867 | workscan = self.copy() |
---|
| 1868 | else: |
---|
| 1869 | workscan = self |
---|
[513] | 1870 | varlist = vars() |
---|
| 1871 | if mask is None: |
---|
[1295] | 1872 | mask = [True for i in xrange(self.nchan(-1))] |
---|
[1819] | 1873 | |
---|
[513] | 1874 | from asap.asapfitter import fitter |
---|
[1217] | 1875 | try: |
---|
| 1876 | f = fitter() |
---|
[1391] | 1877 | if uselin: |
---|
| 1878 | f.set_function(lpoly=order) |
---|
| 1879 | else: |
---|
| 1880 | f.set_function(poly=order) |
---|
[1819] | 1881 | |
---|
| 1882 | rows = range(workscan.nrow()) |
---|
| 1883 | if len(rows) > 0: |
---|
| 1884 | self.blpars = [] |
---|
| 1885 | |
---|
| 1886 | for r in rows: |
---|
| 1887 | # take into account flagtra info (CAS-1434) |
---|
| 1888 | flagtra = workscan._getmask(r) |
---|
| 1889 | actualmask = mask[:] |
---|
| 1890 | if len(actualmask) == 0: |
---|
| 1891 | actualmask = list(flagtra[:]) |
---|
| 1892 | else: |
---|
| 1893 | if len(actualmask) != len(flagtra): |
---|
| 1894 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 1895 | else: |
---|
| 1896 | for i in range(0, len(actualmask)): |
---|
| 1897 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 1898 | f.set_scan(workscan, actualmask) |
---|
| 1899 | f.x = workscan._getabcissa(r) |
---|
| 1900 | f.y = workscan._getspectrum(r) |
---|
| 1901 | f.data = None |
---|
| 1902 | f.fit() |
---|
| 1903 | if plot: |
---|
| 1904 | f.plot(residual=True) |
---|
| 1905 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1906 | if x.upper() == 'N': |
---|
| 1907 | self.blpars.append(None) |
---|
| 1908 | continue |
---|
| 1909 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
| 1910 | self.blpars.append(f.get_parameters()) |
---|
| 1911 | |
---|
| 1912 | if plot: |
---|
| 1913 | f._p.unmap() |
---|
| 1914 | f._p = None |
---|
| 1915 | workscan._add_history("poly_baseline", varlist) |
---|
[1856] | 1916 | if insitu: |
---|
| 1917 | self._assign(workscan) |
---|
| 1918 | else: |
---|
| 1919 | return workscan |
---|
[1217] | 1920 | except RuntimeError: |
---|
| 1921 | msg = "The fit failed, possibly because it didn't converge." |
---|
[1859] | 1922 | raise RuntimeError(msg) |
---|
[513] | 1923 | |
---|
[1819] | 1924 | |
---|
[1118] | 1925 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
[1280] | 1926 | threshold=3, chan_avg_limit=1, plot=False, |
---|
| 1927 | insitu=None): |
---|
[1846] | 1928 | """\ |
---|
[880] | 1929 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1930 | Spectral lines are detected first using linefinder and masked out |
---|
| 1931 | to avoid them affecting the baseline solution. |
---|
| 1932 | |
---|
| 1933 | Parameters: |
---|
[1846] | 1934 | |
---|
[880] | 1935 | mask: an optional mask retreived from scantable |
---|
[1846] | 1936 | |
---|
| 1937 | edge: an optional number of channel to drop at the edge of |
---|
| 1938 | spectrum. If only one value is |
---|
[880] | 1939 | specified, the same number will be dropped from |
---|
| 1940 | both sides of the spectrum. Default is to keep |
---|
[907] | 1941 | all channels. Nested tuples represent individual |
---|
[976] | 1942 | edge selection for different IFs (a number of spectral |
---|
| 1943 | channels can be different) |
---|
[1846] | 1944 | |
---|
[880] | 1945 | order: the order of the polynomial (default is 0) |
---|
[1846] | 1946 | |
---|
[880] | 1947 | threshold: the threshold used by line finder. It is better to |
---|
| 1948 | keep it large as only strong lines affect the |
---|
| 1949 | baseline solution. |
---|
[1846] | 1950 | |
---|
[1280] | 1951 | chan_avg_limit: |
---|
| 1952 | a maximum number of consequtive spectral channels to |
---|
| 1953 | average during the search of weak and broad lines. |
---|
| 1954 | The default is no averaging (and no search for weak |
---|
| 1955 | lines). If such lines can affect the fitted baseline |
---|
| 1956 | (e.g. a high order polynomial is fitted), increase this |
---|
| 1957 | parameter (usually values up to 8 are reasonable). Most |
---|
| 1958 | users of this method should find the default value |
---|
| 1959 | sufficient. |
---|
[1846] | 1960 | |
---|
[1061] | 1961 | plot: plot the fit and the residual. In this each |
---|
| 1962 | indivual fit has to be approved, by typing 'y' |
---|
| 1963 | or 'n' |
---|
[1846] | 1964 | |
---|
[880] | 1965 | insitu: if False a new scantable is returned. |
---|
| 1966 | Otherwise, the scaling is done in-situ |
---|
| 1967 | The default is taken from .asaprc (False) |
---|
| 1968 | |
---|
[1846] | 1969 | |
---|
| 1970 | Example:: |
---|
| 1971 | |
---|
| 1972 | scan2 = scan.auto_poly_baseline(order=7, insitu=False) |
---|
| 1973 | |
---|
[880] | 1974 | """ |
---|
| 1975 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1976 | varlist = vars() |
---|
| 1977 | from asap.asapfitter import fitter |
---|
| 1978 | from asap.asaplinefind import linefinder |
---|
| 1979 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1980 | |
---|
[976] | 1981 | # check whether edge is set up for each IF individually |
---|
[1118] | 1982 | individualedge = False; |
---|
| 1983 | if len(edge) > 1: |
---|
| 1984 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 1985 | individualedge = True; |
---|
[907] | 1986 | |
---|
[1118] | 1987 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 1988 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1989 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1990 | to make individual selection for different IFs." |
---|
[919] | 1991 | |
---|
[1118] | 1992 | curedge = (0, 0) |
---|
| 1993 | if individualedge: |
---|
| 1994 | for edgepar in edge: |
---|
| 1995 | if not _is_valid(edgepar, int): |
---|
| 1996 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 1997 | to be a pair of integers or an integer." |
---|
[907] | 1998 | else: |
---|
[1118] | 1999 | curedge = edge; |
---|
[880] | 2000 | |
---|
| 2001 | # setup fitter |
---|
| 2002 | f = fitter() |
---|
| 2003 | f.set_function(poly=order) |
---|
| 2004 | |
---|
| 2005 | # setup line finder |
---|
[1118] | 2006 | fl = linefinder() |
---|
[1268] | 2007 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
[880] | 2008 | |
---|
| 2009 | if not insitu: |
---|
[1118] | 2010 | workscan = self.copy() |
---|
[880] | 2011 | else: |
---|
[1118] | 2012 | workscan = self |
---|
[880] | 2013 | |
---|
[907] | 2014 | fl.set_scan(workscan) |
---|
| 2015 | |
---|
[1118] | 2016 | rows = range(workscan.nrow()) |
---|
[1819] | 2017 | # Save parameters of baseline fits & masklists as a class attribute. |
---|
| 2018 | # NOTICE: It does not reflect changes in scantable! |
---|
| 2019 | if len(rows) > 0: |
---|
| 2020 | self.blpars=[] |
---|
| 2021 | self.masklists=[] |
---|
[880] | 2022 | asaplog.push("Processing:") |
---|
| 2023 | for r in rows: |
---|
[1118] | 2024 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 2025 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 2026 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 2027 | asaplog.push(msg, False) |
---|
[907] | 2028 | |
---|
[976] | 2029 | # figure out edge parameter |
---|
[1118] | 2030 | if individualedge: |
---|
| 2031 | if len(edge) >= workscan.getif(r): |
---|
| 2032 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 2033 | "be less than the number of IFs" |
---|
| 2034 | curedge = edge[workscan.getif(r)] |
---|
[919] | 2035 | |
---|
[1819] | 2036 | # take into account flagtra info (CAS-1434) |
---|
| 2037 | flagtra = workscan._getmask(r) |
---|
| 2038 | actualmask = mask[:] |
---|
| 2039 | if len(actualmask) == 0: |
---|
| 2040 | actualmask = list(flagtra[:]) |
---|
| 2041 | else: |
---|
| 2042 | if len(actualmask) != len(flagtra): |
---|
| 2043 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 2044 | else: |
---|
| 2045 | for i in range(0, len(actualmask)): |
---|
| 2046 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 2047 | |
---|
[976] | 2048 | # setup line finder |
---|
[1819] | 2049 | fl.find_lines(r, actualmask, curedge) |
---|
| 2050 | outmask=fl.get_mask() |
---|
| 2051 | f.set_scan(workscan, fl.get_mask()) |
---|
| 2052 | f.x = workscan._getabcissa(r) |
---|
| 2053 | f.y = workscan._getspectrum(r) |
---|
| 2054 | f.data = None |
---|
[880] | 2055 | f.fit() |
---|
[1819] | 2056 | |
---|
| 2057 | # Show mask list |
---|
| 2058 | masklist=workscan.get_masklist(fl.get_mask(),row=r) |
---|
| 2059 | msg = "mask range: "+str(masklist) |
---|
| 2060 | asaplog.push(msg, False) |
---|
| 2061 | |
---|
[1061] | 2062 | if plot: |
---|
| 2063 | f.plot(residual=True) |
---|
| 2064 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 2065 | if x.upper() == 'N': |
---|
[1819] | 2066 | self.blpars.append(None) |
---|
| 2067 | self.masklists.append(None) |
---|
[1061] | 2068 | continue |
---|
[1819] | 2069 | |
---|
[880] | 2070 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1819] | 2071 | self.blpars.append(f.get_parameters()) |
---|
| 2072 | self.masklists.append(masklist) |
---|
[1061] | 2073 | if plot: |
---|
| 2074 | f._p.unmap() |
---|
| 2075 | f._p = None |
---|
| 2076 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 2077 | if insitu: |
---|
| 2078 | self._assign(workscan) |
---|
| 2079 | else: |
---|
| 2080 | return workscan |
---|
| 2081 | |
---|
[1862] | 2082 | @asaplog_post_dec |
---|
[914] | 2083 | def rotate_linpolphase(self, angle): |
---|
[1846] | 2084 | """\ |
---|
[914] | 2085 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 2086 | This is always done in situ in the raw data. So if you call this |
---|
| 2087 | function more than once then each call rotates the phase further. |
---|
[1846] | 2088 | |
---|
[914] | 2089 | Parameters: |
---|
[1846] | 2090 | |
---|
[914] | 2091 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 2092 | |
---|
| 2093 | Example:: |
---|
| 2094 | |
---|
[914] | 2095 | scan.rotate_linpolphase(2.3) |
---|
[1846] | 2096 | |
---|
[914] | 2097 | """ |
---|
| 2098 | varlist = vars() |
---|
[936] | 2099 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 2100 | self._add_history("rotate_linpolphase", varlist) |
---|
| 2101 | return |
---|
[710] | 2102 | |
---|
[1862] | 2103 | @asaplog_post_dec |
---|
[914] | 2104 | def rotate_xyphase(self, angle): |
---|
[1846] | 2105 | """\ |
---|
[914] | 2106 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 2107 | in the data. So if you call this function more than once |
---|
| 2108 | then each call rotates the phase further. |
---|
[1846] | 2109 | |
---|
[914] | 2110 | Parameters: |
---|
[1846] | 2111 | |
---|
[914] | 2112 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 2113 | |
---|
| 2114 | Example:: |
---|
| 2115 | |
---|
[914] | 2116 | scan.rotate_xyphase(2.3) |
---|
[1846] | 2117 | |
---|
[914] | 2118 | """ |
---|
| 2119 | varlist = vars() |
---|
[936] | 2120 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 2121 | self._add_history("rotate_xyphase", varlist) |
---|
| 2122 | return |
---|
| 2123 | |
---|
[1862] | 2124 | @asaplog_post_dec |
---|
[914] | 2125 | def swap_linears(self): |
---|
[1846] | 2126 | """\ |
---|
[1573] | 2127 | Swap the linear polarisations XX and YY, or better the first two |
---|
[1348] | 2128 | polarisations as this also works for ciculars. |
---|
[914] | 2129 | """ |
---|
| 2130 | varlist = vars() |
---|
[936] | 2131 | self._math._swap_linears(self) |
---|
[914] | 2132 | self._add_history("swap_linears", varlist) |
---|
| 2133 | return |
---|
| 2134 | |
---|
[1862] | 2135 | @asaplog_post_dec |
---|
[914] | 2136 | def invert_phase(self): |
---|
[1846] | 2137 | """\ |
---|
[914] | 2138 | Invert the phase of the complex polarisation |
---|
| 2139 | """ |
---|
| 2140 | varlist = vars() |
---|
[936] | 2141 | self._math._invert_phase(self) |
---|
[914] | 2142 | self._add_history("invert_phase", varlist) |
---|
| 2143 | return |
---|
| 2144 | |
---|
[1862] | 2145 | @asaplog_post_dec |
---|
[876] | 2146 | def add(self, offset, insitu=None): |
---|
[1846] | 2147 | """\ |
---|
[513] | 2148 | Return a scan where all spectra have the offset added |
---|
[1846] | 2149 | |
---|
[513] | 2150 | Parameters: |
---|
[1846] | 2151 | |
---|
[513] | 2152 | offset: the offset |
---|
[1855] | 2153 | |
---|
[513] | 2154 | insitu: if False a new scantable is returned. |
---|
| 2155 | Otherwise, the scaling is done in-situ |
---|
| 2156 | The default is taken from .asaprc (False) |
---|
[1846] | 2157 | |
---|
[513] | 2158 | """ |
---|
| 2159 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2160 | self._math._setinsitu(insitu) |
---|
[513] | 2161 | varlist = vars() |
---|
[876] | 2162 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 2163 | s._add_history("add", varlist) |
---|
[876] | 2164 | if insitu: |
---|
| 2165 | self._assign(s) |
---|
| 2166 | else: |
---|
[513] | 2167 | return s |
---|
| 2168 | |
---|
[1862] | 2169 | @asaplog_post_dec |
---|
[1308] | 2170 | def scale(self, factor, tsys=True, insitu=None): |
---|
[1846] | 2171 | """\ |
---|
| 2172 | |
---|
[513] | 2173 | Return a scan where all spectra are scaled by the give 'factor' |
---|
[1846] | 2174 | |
---|
[513] | 2175 | Parameters: |
---|
[1846] | 2176 | |
---|
[1819] | 2177 | factor: the scaling factor (float or 1D float list) |
---|
[1855] | 2178 | |
---|
[513] | 2179 | insitu: if False a new scantable is returned. |
---|
| 2180 | Otherwise, the scaling is done in-situ |
---|
| 2181 | The default is taken from .asaprc (False) |
---|
[1855] | 2182 | |
---|
[513] | 2183 | tsys: if True (default) then apply the operation to Tsys |
---|
| 2184 | as well as the data |
---|
[1846] | 2185 | |
---|
[513] | 2186 | """ |
---|
| 2187 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2188 | self._math._setinsitu(insitu) |
---|
[513] | 2189 | varlist = vars() |
---|
[1819] | 2190 | s = None |
---|
| 2191 | import numpy |
---|
| 2192 | if isinstance(factor, list) or isinstance(factor, numpy.ndarray): |
---|
| 2193 | if isinstance(factor[0], list) or isinstance(factor[0], numpy.ndarray): |
---|
| 2194 | from asapmath import _array2dOp |
---|
| 2195 | s = _array2dOp( self.copy(), factor, "MUL", tsys ) |
---|
| 2196 | else: |
---|
| 2197 | s = scantable( self._math._arrayop( self.copy(), factor, "MUL", tsys ) ) |
---|
| 2198 | else: |
---|
| 2199 | s = scantable(self._math._unaryop(self.copy(), factor, "MUL", tsys)) |
---|
[1118] | 2200 | s._add_history("scale", varlist) |
---|
[876] | 2201 | if insitu: |
---|
| 2202 | self._assign(s) |
---|
| 2203 | else: |
---|
[513] | 2204 | return s |
---|
| 2205 | |
---|
[1504] | 2206 | def set_sourcetype(self, match, matchtype="pattern", |
---|
| 2207 | sourcetype="reference"): |
---|
[1846] | 2208 | """\ |
---|
[1502] | 2209 | Set the type of the source to be an source or reference scan |
---|
[1846] | 2210 | using the provided pattern. |
---|
| 2211 | |
---|
[1502] | 2212 | Parameters: |
---|
[1846] | 2213 | |
---|
[1504] | 2214 | match: a Unix style pattern, regular expression or selector |
---|
[1855] | 2215 | |
---|
[1504] | 2216 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
| 2217 | 'regex' regular expression |
---|
[1855] | 2218 | |
---|
[1502] | 2219 | sourcetype: the type of the source to use (source/reference) |
---|
[1846] | 2220 | |
---|
[1502] | 2221 | """ |
---|
| 2222 | varlist = vars() |
---|
| 2223 | basesel = self.get_selection() |
---|
| 2224 | stype = -1 |
---|
| 2225 | if sourcetype.lower().startswith("r"): |
---|
| 2226 | stype = 1 |
---|
| 2227 | elif sourcetype.lower().startswith("s"): |
---|
| 2228 | stype = 0 |
---|
[1504] | 2229 | else: |
---|
[1502] | 2230 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)") |
---|
[1504] | 2231 | if matchtype.lower().startswith("p"): |
---|
| 2232 | matchtype = "pattern" |
---|
| 2233 | elif matchtype.lower().startswith("r"): |
---|
| 2234 | matchtype = "regex" |
---|
| 2235 | else: |
---|
| 2236 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
[1502] | 2237 | sel = selector() |
---|
| 2238 | if isinstance(match, selector): |
---|
| 2239 | sel = match |
---|
| 2240 | else: |
---|
[1504] | 2241 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match)) |
---|
[1502] | 2242 | self.set_selection(basesel+sel) |
---|
| 2243 | self._setsourcetype(stype) |
---|
| 2244 | self.set_selection(basesel) |
---|
[1573] | 2245 | self._add_history("set_sourcetype", varlist) |
---|
[1502] | 2246 | |
---|
[1862] | 2247 | @asaplog_post_dec |
---|
[1857] | 2248 | @preserve_selection |
---|
[1819] | 2249 | def auto_quotient(self, preserve=True, mode='paired', verify=False): |
---|
[1846] | 2250 | """\ |
---|
[670] | 2251 | This function allows to build quotients automatically. |
---|
[1819] | 2252 | It assumes the observation to have the same number of |
---|
[670] | 2253 | "ons" and "offs" |
---|
[1846] | 2254 | |
---|
[670] | 2255 | Parameters: |
---|
[1846] | 2256 | |
---|
[710] | 2257 | preserve: you can preserve (default) the continuum or |
---|
| 2258 | remove it. The equations used are |
---|
[1857] | 2259 | |
---|
[670] | 2260 | preserve: Output = Toff * (on/off) - Toff |
---|
[1857] | 2261 | |
---|
[1070] | 2262 | remove: Output = Toff * (on/off) - Ton |
---|
[1855] | 2263 | |
---|
[1573] | 2264 | mode: the on/off detection mode |
---|
[1348] | 2265 | 'paired' (default) |
---|
| 2266 | identifies 'off' scans by the |
---|
| 2267 | trailing '_R' (Mopra/Parkes) or |
---|
| 2268 | '_e'/'_w' (Tid) and matches |
---|
| 2269 | on/off pairs from the observing pattern |
---|
[1502] | 2270 | 'time' |
---|
| 2271 | finds the closest off in time |
---|
[1348] | 2272 | |
---|
[1857] | 2273 | .. todo:: verify argument is not implemented |
---|
| 2274 | |
---|
[670] | 2275 | """ |
---|
[1857] | 2276 | varlist = vars() |
---|
[1348] | 2277 | modes = ["time", "paired"] |
---|
[670] | 2278 | if not mode in modes: |
---|
[876] | 2279 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 2280 | raise ValueError(msg) |
---|
[1348] | 2281 | s = None |
---|
| 2282 | if mode.lower() == "paired": |
---|
[1857] | 2283 | sel = self.get_selection() |
---|
[1875] | 2284 | sel.set_query("SRCTYPE==psoff") |
---|
[1356] | 2285 | self.set_selection(sel) |
---|
[1348] | 2286 | offs = self.copy() |
---|
[1875] | 2287 | sel.set_query("SRCTYPE==pson") |
---|
[1356] | 2288 | self.set_selection(sel) |
---|
[1348] | 2289 | ons = self.copy() |
---|
| 2290 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 2291 | elif mode.lower() == "time": |
---|
| 2292 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 2293 | s._add_history("auto_quotient", varlist) |
---|
[876] | 2294 | return s |
---|
[710] | 2295 | |
---|
[1862] | 2296 | @asaplog_post_dec |
---|
[1145] | 2297 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1846] | 2298 | """\ |
---|
[1143] | 2299 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
[1846] | 2300 | |
---|
[1143] | 2301 | Parameters: |
---|
[1846] | 2302 | |
---|
[1145] | 2303 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1855] | 2304 | |
---|
[1143] | 2305 | weight: How to average the off beams. Default is 'median'. |
---|
[1855] | 2306 | |
---|
[1145] | 2307 | preserve: you can preserve (default) the continuum or |
---|
[1855] | 2308 | remove it. The equations used are: |
---|
[1846] | 2309 | |
---|
[1855] | 2310 | preserve: Output = Toff * (on/off) - Toff |
---|
| 2311 | |
---|
| 2312 | remove: Output = Toff * (on/off) - Ton |
---|
| 2313 | |
---|
[1217] | 2314 | """ |
---|
[1593] | 2315 | mask = mask or () |
---|
[1141] | 2316 | varlist = vars() |
---|
| 2317 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 2318 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 2319 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 2320 | from asapmath import quotient |
---|
[1145] | 2321 | q = quotient(on, off, preserve) |
---|
[1143] | 2322 | q._add_history("mx_quotient", varlist) |
---|
[1217] | 2323 | return q |
---|
[513] | 2324 | |
---|
[1862] | 2325 | @asaplog_post_dec |
---|
[718] | 2326 | def freq_switch(self, insitu=None): |
---|
[1846] | 2327 | """\ |
---|
[718] | 2328 | Apply frequency switching to the data. |
---|
[1846] | 2329 | |
---|
[718] | 2330 | Parameters: |
---|
[1846] | 2331 | |
---|
[718] | 2332 | insitu: if False a new scantable is returned. |
---|
| 2333 | Otherwise, the swictching is done in-situ |
---|
| 2334 | The default is taken from .asaprc (False) |
---|
[1846] | 2335 | |
---|
[718] | 2336 | """ |
---|
| 2337 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2338 | self._math._setinsitu(insitu) |
---|
[718] | 2339 | varlist = vars() |
---|
[876] | 2340 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 2341 | s._add_history("freq_switch", varlist) |
---|
[1856] | 2342 | if insitu: |
---|
| 2343 | self._assign(s) |
---|
| 2344 | else: |
---|
| 2345 | return s |
---|
[718] | 2346 | |
---|
[1862] | 2347 | @asaplog_post_dec |
---|
[780] | 2348 | def recalc_azel(self): |
---|
[1846] | 2349 | """Recalculate the azimuth and elevation for each position.""" |
---|
[780] | 2350 | varlist = vars() |
---|
[876] | 2351 | self._recalcazel() |
---|
[780] | 2352 | self._add_history("recalc_azel", varlist) |
---|
| 2353 | return |
---|
| 2354 | |
---|
[1862] | 2355 | @asaplog_post_dec |
---|
[513] | 2356 | def __add__(self, other): |
---|
| 2357 | varlist = vars() |
---|
| 2358 | s = None |
---|
| 2359 | if isinstance(other, scantable): |
---|
[1573] | 2360 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
[513] | 2361 | elif isinstance(other, float): |
---|
[876] | 2362 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 2363 | else: |
---|
[718] | 2364 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2365 | s._add_history("operator +", varlist) |
---|
| 2366 | return s |
---|
| 2367 | |
---|
[1862] | 2368 | @asaplog_post_dec |
---|
[513] | 2369 | def __sub__(self, other): |
---|
| 2370 | """ |
---|
| 2371 | implicit on all axes and on Tsys |
---|
| 2372 | """ |
---|
| 2373 | varlist = vars() |
---|
| 2374 | s = None |
---|
| 2375 | if isinstance(other, scantable): |
---|
[1588] | 2376 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
[513] | 2377 | elif isinstance(other, float): |
---|
[876] | 2378 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 2379 | else: |
---|
[718] | 2380 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2381 | s._add_history("operator -", varlist) |
---|
| 2382 | return s |
---|
[710] | 2383 | |
---|
[1862] | 2384 | @asaplog_post_dec |
---|
[513] | 2385 | def __mul__(self, other): |
---|
| 2386 | """ |
---|
| 2387 | implicit on all axes and on Tsys |
---|
| 2388 | """ |
---|
| 2389 | varlist = vars() |
---|
| 2390 | s = None |
---|
| 2391 | if isinstance(other, scantable): |
---|
[1588] | 2392 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
[513] | 2393 | elif isinstance(other, float): |
---|
[876] | 2394 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 2395 | else: |
---|
[718] | 2396 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2397 | s._add_history("operator *", varlist) |
---|
| 2398 | return s |
---|
| 2399 | |
---|
[710] | 2400 | |
---|
[1862] | 2401 | @asaplog_post_dec |
---|
[513] | 2402 | def __div__(self, other): |
---|
| 2403 | """ |
---|
| 2404 | implicit on all axes and on Tsys |
---|
| 2405 | """ |
---|
| 2406 | varlist = vars() |
---|
| 2407 | s = None |
---|
| 2408 | if isinstance(other, scantable): |
---|
[1589] | 2409 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
[513] | 2410 | elif isinstance(other, float): |
---|
| 2411 | if other == 0.0: |
---|
[718] | 2412 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 2413 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 2414 | else: |
---|
[718] | 2415 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2416 | s._add_history("operator /", varlist) |
---|
| 2417 | return s |
---|
| 2418 | |
---|
[1862] | 2419 | @asaplog_post_dec |
---|
[530] | 2420 | def get_fit(self, row=0): |
---|
[1846] | 2421 | """\ |
---|
[530] | 2422 | Print or return the stored fits for a row in the scantable |
---|
[1846] | 2423 | |
---|
[530] | 2424 | Parameters: |
---|
[1846] | 2425 | |
---|
[530] | 2426 | row: the row which the fit has been applied to. |
---|
[1846] | 2427 | |
---|
[530] | 2428 | """ |
---|
| 2429 | if row > self.nrow(): |
---|
| 2430 | return |
---|
[976] | 2431 | from asap.asapfit import asapfit |
---|
[530] | 2432 | fit = asapfit(self._getfit(row)) |
---|
[1859] | 2433 | asaplog.push( '%s' %(fit) ) |
---|
| 2434 | return fit.as_dict() |
---|
[530] | 2435 | |
---|
[1483] | 2436 | def flag_nans(self): |
---|
[1846] | 2437 | """\ |
---|
[1483] | 2438 | Utility function to flag NaN values in the scantable. |
---|
| 2439 | """ |
---|
| 2440 | import numpy |
---|
| 2441 | basesel = self.get_selection() |
---|
| 2442 | for i in range(self.nrow()): |
---|
[1589] | 2443 | sel = self.get_row_selector(i) |
---|
| 2444 | self.set_selection(basesel+sel) |
---|
[1483] | 2445 | nans = numpy.isnan(self._getspectrum(0)) |
---|
| 2446 | if numpy.any(nans): |
---|
| 2447 | bnans = [ bool(v) for v in nans] |
---|
| 2448 | self.flag(bnans) |
---|
| 2449 | self.set_selection(basesel) |
---|
| 2450 | |
---|
[1588] | 2451 | def get_row_selector(self, rowno): |
---|
| 2452 | return selector(beams=self.getbeam(rowno), |
---|
| 2453 | ifs=self.getif(rowno), |
---|
| 2454 | pols=self.getpol(rowno), |
---|
| 2455 | scans=self.getscan(rowno), |
---|
| 2456 | cycles=self.getcycle(rowno)) |
---|
[1573] | 2457 | |
---|
[484] | 2458 | def _add_history(self, funcname, parameters): |
---|
[1435] | 2459 | if not rcParams['scantable.history']: |
---|
| 2460 | return |
---|
[484] | 2461 | # create date |
---|
| 2462 | sep = "##" |
---|
| 2463 | from datetime import datetime |
---|
| 2464 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 2465 | hist = dstr+sep |
---|
| 2466 | hist += funcname+sep#cdate+sep |
---|
| 2467 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 2468 | for k, v in parameters.iteritems(): |
---|
[484] | 2469 | if type(v) is dict: |
---|
[1118] | 2470 | for k2, v2 in v.iteritems(): |
---|
[484] | 2471 | hist += k2 |
---|
| 2472 | hist += "=" |
---|
[1118] | 2473 | if isinstance(v2, scantable): |
---|
[484] | 2474 | hist += 'scantable' |
---|
| 2475 | elif k2 == 'mask': |
---|
[1118] | 2476 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 2477 | hist += str(self._zip_mask(v2)) |
---|
| 2478 | else: |
---|
| 2479 | hist += str(v2) |
---|
[484] | 2480 | else: |
---|
[513] | 2481 | hist += str(v2) |
---|
[484] | 2482 | else: |
---|
| 2483 | hist += k |
---|
| 2484 | hist += "=" |
---|
[1118] | 2485 | if isinstance(v, scantable): |
---|
[484] | 2486 | hist += 'scantable' |
---|
| 2487 | elif k == 'mask': |
---|
[1118] | 2488 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 2489 | hist += str(self._zip_mask(v)) |
---|
| 2490 | else: |
---|
| 2491 | hist += str(v) |
---|
[484] | 2492 | else: |
---|
| 2493 | hist += str(v) |
---|
| 2494 | hist += sep |
---|
| 2495 | hist = hist[:-2] # remove trailing '##' |
---|
| 2496 | self._addhistory(hist) |
---|
| 2497 | |
---|
[710] | 2498 | |
---|
[484] | 2499 | def _zip_mask(self, mask): |
---|
| 2500 | mask = list(mask) |
---|
| 2501 | i = 0 |
---|
| 2502 | segments = [] |
---|
| 2503 | while mask[i:].count(1): |
---|
| 2504 | i += mask[i:].index(1) |
---|
| 2505 | if mask[i:].count(0): |
---|
| 2506 | j = i + mask[i:].index(0) |
---|
| 2507 | else: |
---|
[710] | 2508 | j = len(mask) |
---|
[1118] | 2509 | segments.append([i, j]) |
---|
[710] | 2510 | i = j |
---|
[484] | 2511 | return segments |
---|
[714] | 2512 | |
---|
[626] | 2513 | def _get_ordinate_label(self): |
---|
| 2514 | fu = "("+self.get_fluxunit()+")" |
---|
| 2515 | import re |
---|
| 2516 | lbl = "Intensity" |
---|
[1118] | 2517 | if re.match(".K.", fu): |
---|
[626] | 2518 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 2519 | elif re.match(".Jy.", fu): |
---|
[626] | 2520 | lbl = "Flux density "+ fu |
---|
| 2521 | return lbl |
---|
[710] | 2522 | |
---|
[876] | 2523 | def _check_ifs(self): |
---|
| 2524 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 2525 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 2526 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 2527 | |
---|
[1862] | 2528 | @asaplog_post_dec |
---|
[1819] | 2529 | def _fill(self, names, unit, average, getpt, antenna): |
---|
[976] | 2530 | first = True |
---|
| 2531 | fullnames = [] |
---|
| 2532 | for name in names: |
---|
| 2533 | name = os.path.expandvars(name) |
---|
| 2534 | name = os.path.expanduser(name) |
---|
| 2535 | if not os.path.exists(name): |
---|
| 2536 | msg = "File '%s' does not exists" % (name) |
---|
| 2537 | raise IOError(msg) |
---|
| 2538 | fullnames.append(name) |
---|
| 2539 | if average: |
---|
| 2540 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 2541 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 2542 | for name in fullnames: |
---|
[1073] | 2543 | tbl = Scantable(stype) |
---|
[1843] | 2544 | r = filler(tbl) |
---|
[1504] | 2545 | rx = rcParams['scantable.reference'] |
---|
[1843] | 2546 | r.setreferenceexpr(rx) |
---|
[976] | 2547 | msg = "Importing %s..." % (name) |
---|
[1118] | 2548 | asaplog.push(msg, False) |
---|
[1843] | 2549 | r.open(name)# antenna, -1, -1, getpt) |
---|
| 2550 | r.fill() |
---|
[976] | 2551 | if average: |
---|
[1118] | 2552 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 2553 | if not first: |
---|
| 2554 | tbl = self._math._merge([self, tbl]) |
---|
| 2555 | Scantable.__init__(self, tbl) |
---|
[1843] | 2556 | r.close() |
---|
[1118] | 2557 | del r, tbl |
---|
[976] | 2558 | first = False |
---|
[1861] | 2559 | #flush log |
---|
| 2560 | asaplog.post() |
---|
[976] | 2561 | if unit is not None: |
---|
| 2562 | self.set_fluxunit(unit) |
---|
[1824] | 2563 | if not is_casapy(): |
---|
| 2564 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[976] | 2565 | |
---|
[1402] | 2566 | def __getitem__(self, key): |
---|
| 2567 | if key < 0: |
---|
| 2568 | key += self.nrow() |
---|
| 2569 | if key >= self.nrow(): |
---|
| 2570 | raise IndexError("Row index out of range.") |
---|
| 2571 | return self._getspectrum(key) |
---|
| 2572 | |
---|
| 2573 | def __setitem__(self, key, value): |
---|
| 2574 | if key < 0: |
---|
| 2575 | key += self.nrow() |
---|
| 2576 | if key >= self.nrow(): |
---|
| 2577 | raise IndexError("Row index out of range.") |
---|
| 2578 | if not hasattr(value, "__len__") or \ |
---|
| 2579 | len(value) > self.nchan(self.getif(key)): |
---|
| 2580 | raise ValueError("Spectrum length doesn't match.") |
---|
| 2581 | return self._setspectrum(value, key) |
---|
| 2582 | |
---|
| 2583 | def __len__(self): |
---|
| 2584 | return self.nrow() |
---|
| 2585 | |
---|
| 2586 | def __iter__(self): |
---|
| 2587 | for i in range(len(self)): |
---|
| 2588 | yield self[i] |
---|