[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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| 13 | from asap.logging import asaplog, print_log, print_log_dec |
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| 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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[1824] | 17 | from asap.utils import _n_bools, mask_not, mask_and, mask_or |
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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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| 24 | val = func(obj, *args, **kw) |
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| 25 | obj.set_selection(basesel) |
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| 26 | return val |
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| 27 | return wrap |
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| 28 | |
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[1846] | 29 | def is_scantable(filename): |
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| 30 | """Is the given file a scantable? |
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[1689] | 31 | |
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[1846] | 32 | Parameters: |
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| 33 | |
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| 34 | filename: the name of the file/directory to test |
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| 35 | |
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| 36 | """ |
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[1697] | 37 | return (os.path.isdir(filename) |
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| 38 | and not os.path.exists(filename+'/table.f1') |
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| 39 | and os.path.exists(filename+'/table.info')) |
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| 40 | |
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| 41 | |
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[876] | 42 | class scantable(Scantable): |
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[1846] | 43 | """\ |
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| 44 | The ASAP container for scans (single-dish data). |
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[102] | 45 | """ |
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[1819] | 46 | |
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[1589] | 47 | @print_log_dec |
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[1824] | 48 | def __init__(self, filename, average=None, unit=None, getpt=None, |
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| 49 | antenna=None, parallactify=None): |
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[1846] | 50 | """\ |
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[102] | 51 | Create a scantable from a saved one or make a reference |
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[1846] | 52 | |
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[102] | 53 | Parameters: |
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[1846] | 54 | |
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| 55 | filename: the name of an asap table on disk |
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| 56 | or |
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| 57 | the name of a rpfits/sdfits/ms file |
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| 58 | (integrations within scans are auto averaged |
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| 59 | and the whole file is read) or |
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| 60 | [advanced] a reference to an existing scantable |
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| 61 | |
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| 62 | average: average all integrations withinb a scan on read. |
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| 63 | The default (True) is taken from .asaprc. |
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| 64 | |
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[484] | 65 | unit: brightness unit; must be consistent with K or Jy. |
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[1846] | 66 | Over-rides the default selected by the filler |
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| 67 | (input rpfits/sdfits/ms) or replaces the value |
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| 68 | in existing scantables |
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| 69 | |
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| 70 | getpt: for MeasurementSet input data only: |
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| 71 | If True, all pointing data are filled. |
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| 72 | The deafult is False, which makes time to load |
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| 73 | the MS data faster in some cases. |
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| 74 | |
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| 75 | antenna: Antenna selection. integer (id) or string (name or id). |
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| 76 | |
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| 77 | parallactify: Indicate that the data had been parallatified. Default |
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| 78 | is taken from rc file. |
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| 79 | |
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[710] | 80 | """ |
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[976] | 81 | if average is None: |
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[710] | 82 | average = rcParams['scantable.autoaverage'] |
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[1819] | 83 | if getpt is None: |
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| 84 | getpt = True |
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[1843] | 85 | if antenna is not None: |
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| 86 | asaplog.push("Antenna selection currently unsupported." |
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| 87 | "Using '0'") |
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| 88 | print_log('WARN') |
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[1819] | 89 | if antenna is None: |
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| 90 | antenna = '' |
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| 91 | elif type(antenna) == int: |
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[1843] | 92 | antenna = '%s' % antenna |
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[1819] | 93 | elif type(antenna) == list: |
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| 94 | tmpstr = '' |
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| 95 | for i in range( len(antenna) ): |
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| 96 | if type(antenna[i]) == int: |
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| 97 | tmpstr = tmpstr + ('%s,'%(antenna[i])) |
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| 98 | elif type(antenna[i]) == str: |
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| 99 | tmpstr=tmpstr+antenna[i]+',' |
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| 100 | else: |
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| 101 | asaplog.push('Bad antenna selection.') |
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| 102 | print_log('ERROR') |
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| 103 | return |
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| 104 | antenna = tmpstr.rstrip(',') |
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[1593] | 105 | parallactify = parallactify or rcParams['scantable.parallactify'] |
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[1259] | 106 | varlist = vars() |
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[876] | 107 | from asap._asap import stmath |
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[1819] | 108 | self._math = stmath( rcParams['insitu'] ) |
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[876] | 109 | if isinstance(filename, Scantable): |
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| 110 | Scantable.__init__(self, filename) |
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[181] | 111 | else: |
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[1697] | 112 | if isinstance(filename, str): |
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[976] | 113 | filename = os.path.expandvars(filename) |
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| 114 | filename = os.path.expanduser(filename) |
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| 115 | if not os.path.exists(filename): |
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| 116 | s = "File '%s' not found." % (filename) |
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[718] | 117 | if rcParams['verbose']: |
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[976] | 118 | asaplog.push(s) |
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[1819] | 119 | print_log('ERROR') |
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[718] | 120 | return |
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[976] | 121 | raise IOError(s) |
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[1697] | 122 | if is_scantable(filename): |
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| 123 | ondisk = rcParams['scantable.storage'] == 'disk' |
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| 124 | Scantable.__init__(self, filename, ondisk) |
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| 125 | if unit is not None: |
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| 126 | self.set_fluxunit(unit) |
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[1819] | 127 | # do not reset to the default freqframe |
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| 128 | #self.set_freqframe(rcParams['scantable.freqframe']) |
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| 129 | elif os.path.isdir(filename) \ |
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| 130 | and not os.path.exists(filename+'/table.f1'): |
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| 131 | msg = "The given file '%s'is not a valid " \ |
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| 132 | "asap table." % (filename) |
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| 133 | if rcParams['verbose']: |
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| 134 | #print msg |
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| 135 | asaplog.push( msg ) |
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| 136 | print_log( 'ERROR' ) |
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| 137 | return |
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| 138 | else: |
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| 139 | raise IOError(msg) |
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[226] | 140 | else: |
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[1819] | 141 | self._fill([filename], unit, average, getpt, antenna) |
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[1118] | 142 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
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[976] | 143 | and isinstance(filename[-1], str): |
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[1819] | 144 | self._fill(filename, unit, average, getpt, antenna) |
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[1586] | 145 | self.parallactify(parallactify) |
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[1259] | 146 | self._add_history("scantable", varlist) |
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[1819] | 147 | print_log() |
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[102] | 148 | |
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[1589] | 149 | @print_log_dec |
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[876] | 150 | def save(self, name=None, format=None, overwrite=False): |
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[1846] | 151 | """\ |
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[1280] | 152 | Store the scantable on disk. This can be an asap (aips++) Table, |
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| 153 | SDFITS or MS2 format. |
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[1846] | 154 | |
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[116] | 155 | Parameters: |
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[1846] | 156 | |
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[1093] | 157 | name: the name of the outputfile. For format "ASCII" |
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| 158 | this is the root file name (data in 'name'.txt |
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[497] | 159 | and header in 'name'_header.txt) |
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[116] | 160 | format: an optional file format. Default is ASAP. |
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[280] | 161 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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[194] | 162 | 'SDFITS' (save as SDFITS file) |
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[200] | 163 | 'ASCII' (saves as ascii text file) |
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[226] | 164 | 'MS2' (saves as an aips++ |
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| 165 | MeasurementSet V2) |
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[1573] | 166 | 'FITS' (save as image FITS - not |
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[1443] | 167 | readable by class) |
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| 168 | 'CLASS' (save as FITS readable by CLASS) |
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[411] | 169 | overwrite: If the file should be overwritten if it exists. |
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[256] | 170 | The default False is to return with warning |
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[411] | 171 | without writing the output. USE WITH CARE. |
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[1846] | 172 | Example:: |
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| 173 | |
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[116] | 174 | scan.save('myscan.asap') |
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[1118] | 175 | scan.save('myscan.sdfits', 'SDFITS') |
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[1846] | 176 | |
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[116] | 177 | """ |
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[411] | 178 | from os import path |
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[1593] | 179 | format = format or rcParams['scantable.save'] |
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[256] | 180 | suffix = '.'+format.lower() |
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[1118] | 181 | if name is None or name == "": |
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[256] | 182 | name = 'scantable'+suffix |
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[718] | 183 | msg = "No filename given. Using default name %s..." % name |
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| 184 | asaplog.push(msg) |
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[411] | 185 | name = path.expandvars(name) |
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[256] | 186 | if path.isfile(name) or path.isdir(name): |
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| 187 | if not overwrite: |
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[718] | 188 | msg = "File %s exists." % name |
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| 189 | if rcParams['verbose']: |
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[1819] | 190 | #print msg |
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| 191 | asaplog.push( msg ) |
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| 192 | print_log( 'ERROR' ) |
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[718] | 193 | return |
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| 194 | else: |
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| 195 | raise IOError(msg) |
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[451] | 196 | format2 = format.upper() |
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| 197 | if format2 == 'ASAP': |
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[116] | 198 | self._save(name) |
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| 199 | else: |
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[989] | 200 | from asap._asap import stwriter as stw |
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[1118] | 201 | writer = stw(format2) |
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| 202 | writer.write(self, name) |
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[1819] | 203 | print_log() |
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[116] | 204 | return |
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| 205 | |
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[102] | 206 | def copy(self): |
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[1846] | 207 | """Return a copy of this scantable. |
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| 208 | |
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| 209 | *Note*: |
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| 210 | |
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[1348] | 211 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
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[1846] | 212 | |
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| 213 | Example:: |
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| 214 | |
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[102] | 215 | copiedscan = scan.copy() |
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[1846] | 216 | |
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[102] | 217 | """ |
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[876] | 218 | sd = scantable(Scantable._copy(self)) |
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[113] | 219 | return sd |
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| 220 | |
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[1093] | 221 | def drop_scan(self, scanid=None): |
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[1846] | 222 | """\ |
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[1093] | 223 | Return a new scantable where the specified scan number(s) has(have) |
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| 224 | been dropped. |
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[1846] | 225 | |
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[1093] | 226 | Parameters: |
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[1846] | 227 | |
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[1093] | 228 | scanid: a (list of) scan number(s) |
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[1846] | 229 | |
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[1093] | 230 | """ |
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| 231 | from asap import _is_sequence_or_number as _is_valid |
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| 232 | from asap import _to_list |
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| 233 | from asap import unique |
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| 234 | if not _is_valid(scanid): |
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| 235 | if rcParams['verbose']: |
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[1819] | 236 | #print "Please specify a scanno to drop from the scantable" |
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| 237 | asaplog.push( 'Please specify a scanno to drop from the scantable' ) |
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| 238 | print_log( 'ERROR' ) |
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[1093] | 239 | return |
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| 240 | else: |
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| 241 | raise RuntimeError("No scan given") |
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| 242 | try: |
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| 243 | scanid = _to_list(scanid) |
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| 244 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
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| 245 | for sid in scanid: allscans.remove(sid) |
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[1118] | 246 | if len(allscans) == 0: |
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| 247 | raise ValueError("Can't remove all scans") |
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[1093] | 248 | except ValueError: |
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| 249 | if rcParams['verbose']: |
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[1819] | 250 | #print "Couldn't find any match." |
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| 251 | print_log() |
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| 252 | asaplog.push( "Couldn't find any match." ) |
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| 253 | print_log( 'ERROR' ) |
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[1093] | 254 | return |
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| 255 | else: raise |
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| 256 | try: |
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[1593] | 257 | sel = selector(scans=allscans) |
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[1594] | 258 | return self._select_copy(sel) |
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[1093] | 259 | except RuntimeError: |
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[1118] | 260 | if rcParams['verbose']: |
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[1819] | 261 | #print "Couldn't find any match." |
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| 262 | print_log() |
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| 263 | asaplog.push( "Couldn't find any match." ) |
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| 264 | print_log( 'ERROR' ) |
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[1118] | 265 | else: |
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| 266 | raise |
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[1093] | 267 | |
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[1594] | 268 | def _select_copy(self, selection): |
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| 269 | orig = self.get_selection() |
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| 270 | self.set_selection(orig+selection) |
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| 271 | cp = self.copy() |
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| 272 | self.set_selection(orig) |
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| 273 | return cp |
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| 274 | |
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[102] | 275 | def get_scan(self, scanid=None): |
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| 276 | """ |
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| 277 | Return a specific scan (by scanno) or collection of scans (by |
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| 278 | source name) in a new scantable. |
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[1846] | 279 | |
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| 280 | *Note*: |
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| 281 | |
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[1348] | 282 | See scantable.drop_scan() for the inverse operation. |
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[1846] | 283 | |
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[102] | 284 | Parameters: |
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[1846] | 285 | |
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[513] | 286 | scanid: a (list of) scanno or a source name, unix-style |
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| 287 | patterns are accepted for source name matching, e.g. |
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| 288 | '*_R' gets all 'ref scans |
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[1846] | 289 | |
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| 290 | Example:: |
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| 291 | |
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[513] | 292 | # get all scans containing the source '323p459' |
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| 293 | newscan = scan.get_scan('323p459') |
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| 294 | # get all 'off' scans |
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| 295 | refscans = scan.get_scan('*_R') |
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| 296 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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[1118] | 297 | newscan = scan.get_scan([0, 2, 7, 10]) |
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[1846] | 298 | |
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[102] | 299 | """ |
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| 300 | if scanid is None: |
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[718] | 301 | if rcParams['verbose']: |
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[1819] | 302 | #print "Please specify a scan no or name to " \ |
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| 303 | # "retrieve from the scantable" |
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[1846] | 304 | asaplog.push( 'Please specify a scan no or name to retrieve' |
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| 305 | ' from the scantable' ) |
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[1819] | 306 | print_log( 'ERROR' ) |
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[718] | 307 | return |
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| 308 | else: |
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| 309 | raise RuntimeError("No scan given") |
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| 310 | |
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[102] | 311 | try: |
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[946] | 312 | bsel = self.get_selection() |
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| 313 | sel = selector() |
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[102] | 314 | if type(scanid) is str: |
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[946] | 315 | sel.set_name(scanid) |
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[1594] | 316 | return self._select_copy(sel) |
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[102] | 317 | elif type(scanid) is int: |
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[946] | 318 | sel.set_scans([scanid]) |
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[1594] | 319 | return self._select_copy(sel) |
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[381] | 320 | elif type(scanid) is list: |
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[946] | 321 | sel.set_scans(scanid) |
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[1594] | 322 | return self._select_copy(sel) |
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[381] | 323 | else: |
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[718] | 324 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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| 325 | if rcParams['verbose']: |
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[1819] | 326 | #print msg |
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| 327 | asaplog.push( msg ) |
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| 328 | print_log( 'ERROR' ) |
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[718] | 329 | else: |
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| 330 | raise TypeError(msg) |
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[102] | 331 | except RuntimeError: |
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[1819] | 332 | if rcParams['verbose']: |
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| 333 | #print "Couldn't find any match." |
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| 334 | print_log() |
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| 335 | asaplog.push( "Couldn't find any match." ) |
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| 336 | print_log( 'ERROR' ) |
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[718] | 337 | else: raise |
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[102] | 338 | |
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| 339 | def __str__(self): |
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[1118] | 340 | return Scantable._summary(self, True) |
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[102] | 341 | |
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[976] | 342 | def summary(self, filename=None): |
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[1846] | 343 | """\ |
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[102] | 344 | Print a summary of the contents of this scantable. |
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[1846] | 345 | |
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[102] | 346 | Parameters: |
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[1846] | 347 | |
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[102] | 348 | filename: the name of a file to write the putput to |
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| 349 | Default - no file output |
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[1846] | 350 | |
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[102] | 351 | """ |
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[976] | 352 | info = Scantable._summary(self, True) |
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[102] | 353 | if filename is not None: |
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[256] | 354 | if filename is "": |
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| 355 | filename = 'scantable_summary.txt' |
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[415] | 356 | from os.path import expandvars, isdir |
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[411] | 357 | filename = expandvars(filename) |
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[415] | 358 | if not isdir(filename): |
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[413] | 359 | data = open(filename, 'w') |
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| 360 | data.write(info) |
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| 361 | data.close() |
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| 362 | else: |
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[718] | 363 | msg = "Illegal file name '%s'." % (filename) |
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| 364 | if rcParams['verbose']: |
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[1819] | 365 | #print msg |
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| 366 | asaplog.push( msg ) |
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| 367 | print_log( 'ERROR' ) |
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[718] | 368 | else: |
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| 369 | raise IOError(msg) |
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| 370 | if rcParams['verbose']: |
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[794] | 371 | try: |
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| 372 | from IPython.genutils import page as pager |
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| 373 | except ImportError: |
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| 374 | from pydoc import pager |
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| 375 | pager(info) |
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[718] | 376 | else: |
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| 377 | return info |
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[710] | 378 | |
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[1512] | 379 | def get_spectrum(self, rowno): |
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[1471] | 380 | """Return the spectrum for the current row in the scantable as a list. |
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[1846] | 381 | |
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[1471] | 382 | Parameters: |
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[1846] | 383 | |
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[1573] | 384 | rowno: the row number to retrieve the spectrum from |
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[1846] | 385 | |
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[1471] | 386 | """ |
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| 387 | return self._getspectrum(rowno) |
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[946] | 388 | |
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[1471] | 389 | def get_mask(self, rowno): |
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| 390 | """Return the mask for the current row in the scantable as a list. |
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[1846] | 391 | |
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[1471] | 392 | Parameters: |
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[1846] | 393 | |
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[1573] | 394 | rowno: the row number to retrieve the mask from |
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[1846] | 395 | |
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[1471] | 396 | """ |
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| 397 | return self._getmask(rowno) |
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| 398 | |
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| 399 | def set_spectrum(self, spec, rowno): |
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| 400 | """Return the spectrum for the current row in the scantable as a list. |
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[1846] | 401 | |
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[1471] | 402 | Parameters: |
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[1846] | 403 | |
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[1471] | 404 | spec: the spectrum |
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[1573] | 405 | rowno: the row number to set the spectrum for |
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[1846] | 406 | |
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[1471] | 407 | """ |
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| 408 | assert(len(spec) == self.nchan()) |
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| 409 | return self._setspectrum(spec, rowno) |
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| 410 | |
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[1600] | 411 | def get_coordinate(self, rowno): |
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| 412 | """Return the (spectral) coordinate for a a given 'rowno'. |
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[1846] | 413 | |
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| 414 | *Note*: |
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| 415 | |
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[1600] | 416 | * This coordinate is only valid until a scantable method modifies |
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| 417 | the frequency axis. |
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| 418 | * This coordinate does contain the original frequency set-up |
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| 419 | NOT the new frame. The conversions however are done using the user |
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| 420 | specified frame (e.g. LSRK/TOPO). To get the 'real' coordinate, |
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| 421 | use scantable.freq_align first. Without it there is no closure, |
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[1846] | 422 | i.e.:: |
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[1600] | 423 | |
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[1846] | 424 | c = myscan.get_coordinate(0) |
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| 425 | c.to_frequency(c.get_reference_pixel()) != c.get_reference_value() |
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| 426 | |
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[1600] | 427 | Parameters: |
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[1846] | 428 | |
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[1600] | 429 | rowno: the row number for the spectral coordinate |
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| 430 | |
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| 431 | """ |
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| 432 | return coordinate(Scantable.get_coordinate(self, rowno)) |
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| 433 | |
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[946] | 434 | def get_selection(self): |
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[1846] | 435 | """\ |
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[1005] | 436 | Get the selection object currently set on this scantable. |
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[1846] | 437 | |
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| 438 | Example:: |
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| 439 | |
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[1005] | 440 | sel = scan.get_selection() |
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| 441 | sel.set_ifs(0) # select IF 0 |
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| 442 | scan.set_selection(sel) # apply modified selection |
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[1846] | 443 | |
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[946] | 444 | """ |
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| 445 | return selector(self._getselection()) |
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| 446 | |
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[1576] | 447 | def set_selection(self, selection=None, **kw): |
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[1846] | 448 | """\ |
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[1005] | 449 | Select a subset of the data. All following operations on this scantable |
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| 450 | are only applied to thi selection. |
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[1846] | 451 | |
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[1005] | 452 | Parameters: |
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[1697] | 453 | |
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[1846] | 454 | selection: a selector object (default unset the selection), or |
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| 455 | any combination of "pols", "ifs", "beams", "scans", |
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| 456 | "cycles", "name", "query" |
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[1697] | 457 | |
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[1846] | 458 | Examples:: |
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[1697] | 459 | |
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[1005] | 460 | sel = selector() # create a selection object |
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[1118] | 461 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
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[1005] | 462 | scan.set_selection(sel) # set the selection |
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| 463 | scan.summary() # will only print summary of scanno 0 an 3 |
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| 464 | scan.set_selection() # unset the selection |
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[1697] | 465 | # or the equivalent |
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| 466 | scan.set_selection(scans=[0,3]) |
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| 467 | scan.summary() # will only print summary of scanno 0 an 3 |
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| 468 | scan.set_selection() # unset the selection |
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[1846] | 469 | |
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[946] | 470 | """ |
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[1576] | 471 | if selection is None: |
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| 472 | # reset |
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| 473 | if len(kw) == 0: |
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| 474 | selection = selector() |
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| 475 | else: |
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| 476 | # try keywords |
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| 477 | for k in kw: |
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| 478 | if k not in selector.fields: |
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| 479 | raise KeyError("Invalid selection key '%s', valid keys are %s" % (k, selector.fields)) |
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| 480 | selection = selector(**kw) |
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[946] | 481 | self._setselection(selection) |
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| 482 | |
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[1819] | 483 | def get_row(self, row=0, insitu=None): |
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[1846] | 484 | """\ |
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[1819] | 485 | Select a row in the scantable. |
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| 486 | Return a scantable with single row. |
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[1846] | 487 | |
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[1819] | 488 | Parameters: |
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[1846] | 489 | |
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| 490 | row: row no of integration, default is 0. |
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| 491 | insitu: if False a new scantable is returned. Otherwise, the |
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| 492 | scaling is done in-situ. The default is taken from .asaprc |
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| 493 | (False) |
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| 494 | |
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[1819] | 495 | """ |
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| 496 | if insitu is None: insitu = rcParams['insitu'] |
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| 497 | if not insitu: |
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| 498 | workscan = self.copy() |
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| 499 | else: |
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| 500 | workscan = self |
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| 501 | # Select a row |
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| 502 | sel=selector() |
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| 503 | sel.set_scans([workscan.getscan(row)]) |
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| 504 | sel.set_cycles([workscan.getcycle(row)]) |
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| 505 | sel.set_beams([workscan.getbeam(row)]) |
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| 506 | sel.set_ifs([workscan.getif(row)]) |
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| 507 | sel.set_polarisations([workscan.getpol(row)]) |
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| 508 | sel.set_name(workscan._getsourcename(row)) |
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| 509 | workscan.set_selection(sel) |
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| 510 | if not workscan.nrow() == 1: |
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| 511 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow()) |
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| 512 | raise RuntimeError(msg) |
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| 513 | del sel |
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| 514 | if insitu: |
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| 515 | self._assign(workscan) |
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| 516 | else: |
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| 517 | return workscan |
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| 518 | |
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| 519 | #def stats(self, stat='stddev', mask=None): |
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| 520 | def stats(self, stat='stddev', mask=None, form='3.3f'): |
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[1846] | 521 | """\ |
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[135] | 522 | Determine the specified statistic of the current beam/if/pol |
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[102] | 523 | Takes a 'mask' as an optional parameter to specify which |
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| 524 | channels should be excluded. |
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[1846] | 525 | |
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[102] | 526 | Parameters: |
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[1846] | 527 | |
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[1819] | 528 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum', |
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| 529 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median' |
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[135] | 530 | mask: an optional mask specifying where the statistic |
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[102] | 531 | should be determined. |
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[1819] | 532 | form: format string to print statistic values |
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[1846] | 533 | |
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| 534 | Example:: |
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| 535 | |
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[113] | 536 | scan.set_unit('channel') |
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[1118] | 537 | msk = scan.create_mask([100, 200], [500, 600]) |
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[135] | 538 | scan.stats(stat='mean', mask=m) |
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[1846] | 539 | |
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[102] | 540 | """ |
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[1593] | 541 | mask = mask or [] |
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[876] | 542 | if not self._check_ifs(): |
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[1118] | 543 | raise ValueError("Cannot apply mask as the IFs have different " |
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| 544 | "number of channels. Please use setselection() " |
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| 545 | "to select individual IFs") |
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[1819] | 546 | rtnabc = False |
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| 547 | if stat.lower().endswith('_abc'): rtnabc = True |
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| 548 | getchan = False |
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| 549 | if stat.lower().startswith('min') or stat.lower().startswith('max'): |
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| 550 | chan = self._math._minmaxchan(self, mask, stat) |
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| 551 | getchan = True |
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| 552 | statvals = [] |
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| 553 | if not rtnabc: statvals = self._math._stats(self, mask, stat) |
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[256] | 554 | |
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[1819] | 555 | #def cb(i): |
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| 556 | # return statvals[i] |
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[256] | 557 | |
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[1819] | 558 | #return self._row_callback(cb, stat) |
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[102] | 559 | |
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[1819] | 560 | label=stat |
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| 561 | #callback=cb |
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| 562 | out = "" |
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| 563 | #outvec = [] |
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| 564 | sep = '-'*50 |
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| 565 | for i in range(self.nrow()): |
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| 566 | refstr = '' |
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| 567 | statunit= '' |
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| 568 | if getchan: |
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| 569 | qx, qy = self.chan2data(rowno=i, chan=chan[i]) |
---|
| 570 | if rtnabc: |
---|
| 571 | statvals.append(qx['value']) |
---|
| 572 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])' |
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| 573 | statunit= '['+qx['unit']+']' |
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| 574 | else: |
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| 575 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])' |
---|
| 576 | |
---|
| 577 | tm = self._gettime(i) |
---|
| 578 | src = self._getsourcename(i) |
---|
| 579 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
| 580 | out += 'Time[%s]:\n' % (tm) |
---|
| 581 | if self.nbeam(-1) > 1: |
---|
| 582 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 583 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 584 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
| 585 | #outvec.append(callback(i)) |
---|
| 586 | #out += ('= %'+form) % (outvec[i]) +' '+refstr+'\n' |
---|
| 587 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n' |
---|
| 588 | out += sep+"\n" |
---|
| 589 | |
---|
| 590 | if rcParams['verbose']: |
---|
| 591 | import os |
---|
| 592 | if os.environ.has_key( 'USER' ): |
---|
| 593 | usr=os.environ['USER'] |
---|
| 594 | else: |
---|
| 595 | import commands |
---|
| 596 | usr=commands.getoutput( 'whoami' ) |
---|
| 597 | tmpfile='/tmp/tmp_'+usr+'_casapy_asap_scantable_stats' |
---|
| 598 | f=open(tmpfile,'w') |
---|
| 599 | print >> f, sep |
---|
| 600 | print >> f, ' %s %s' % (label, statunit) |
---|
| 601 | print >> f, sep |
---|
| 602 | print >> f, out |
---|
| 603 | f.close() |
---|
| 604 | f=open(tmpfile,'r') |
---|
| 605 | x=f.readlines() |
---|
| 606 | f.close() |
---|
| 607 | blanc='' |
---|
| 608 | asaplog.push(blanc.join(x), False) |
---|
| 609 | #for xx in x: |
---|
| 610 | # asaplog.push( xx, False ) |
---|
| 611 | print_log() |
---|
| 612 | return statvals |
---|
| 613 | |
---|
| 614 | def chan2data(self, rowno=0, chan=0): |
---|
[1846] | 615 | """\ |
---|
[1819] | 616 | Returns channel/frequency/velocity and spectral value |
---|
| 617 | at an arbitrary row and channel in the scantable. |
---|
[1846] | 618 | |
---|
[1819] | 619 | Parameters: |
---|
[1846] | 620 | |
---|
[1819] | 621 | rowno: a row number in the scantable. Default is the |
---|
| 622 | first row, i.e. rowno=0 |
---|
| 623 | chan: a channel in the scantable. Default is the first |
---|
| 624 | channel, i.e. pos=0 |
---|
[1846] | 625 | |
---|
[1819] | 626 | """ |
---|
| 627 | if isinstance(rowno, int) and isinstance(chan, int): |
---|
| 628 | qx = {'unit': self.get_unit(), |
---|
| 629 | 'value': self._getabcissa(rowno)[chan]} |
---|
| 630 | qy = {'unit': self.get_fluxunit(), |
---|
| 631 | 'value': self._getspectrum(rowno)[chan]} |
---|
| 632 | return qx, qy |
---|
| 633 | |
---|
[1118] | 634 | def stddev(self, mask=None): |
---|
[1846] | 635 | """\ |
---|
[135] | 636 | Determine the standard deviation of the current beam/if/pol |
---|
| 637 | Takes a 'mask' as an optional parameter to specify which |
---|
| 638 | channels should be excluded. |
---|
[1846] | 639 | |
---|
[135] | 640 | Parameters: |
---|
[1846] | 641 | |
---|
[135] | 642 | mask: an optional mask specifying where the standard |
---|
| 643 | deviation should be determined. |
---|
| 644 | |
---|
[1846] | 645 | Example:: |
---|
| 646 | |
---|
[135] | 647 | scan.set_unit('channel') |
---|
[1118] | 648 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 649 | scan.stddev(mask=m) |
---|
[1846] | 650 | |
---|
[135] | 651 | """ |
---|
[1118] | 652 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 653 | |
---|
[1003] | 654 | |
---|
[1259] | 655 | def get_column_names(self): |
---|
[1846] | 656 | """\ |
---|
[1003] | 657 | Return a list of column names, which can be used for selection. |
---|
| 658 | """ |
---|
[1259] | 659 | return list(Scantable.get_column_names(self)) |
---|
[1003] | 660 | |
---|
[1730] | 661 | def get_tsys(self, row=-1): |
---|
[1846] | 662 | """\ |
---|
[113] | 663 | Return the System temperatures. |
---|
[1846] | 664 | |
---|
| 665 | Parameters: |
---|
| 666 | |
---|
| 667 | row: the rowno to get the information for. (default all rows) |
---|
| 668 | |
---|
[113] | 669 | Returns: |
---|
[1846] | 670 | |
---|
[876] | 671 | a list of Tsys values for the current selection |
---|
[1846] | 672 | |
---|
[113] | 673 | """ |
---|
[1730] | 674 | if row > -1: |
---|
| 675 | return self._get_column(self._gettsys, row) |
---|
[876] | 676 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 677 | |
---|
[1730] | 678 | |
---|
| 679 | def get_weather(self, row=-1): |
---|
[1846] | 680 | """\ |
---|
| 681 | Return the weather informations. |
---|
| 682 | |
---|
| 683 | Parameters: |
---|
| 684 | |
---|
| 685 | row: the rowno to get the information for. (default all rows) |
---|
| 686 | |
---|
| 687 | Returns: |
---|
| 688 | |
---|
| 689 | a dict or list of of dicts of values for the current selection |
---|
| 690 | |
---|
| 691 | """ |
---|
| 692 | |
---|
[1730] | 693 | values = self._get_column(self._get_weather, row) |
---|
| 694 | if row > -1: |
---|
| 695 | return {'temperature': values[0], |
---|
| 696 | 'pressure': values[1], 'humidity' : values[2], |
---|
| 697 | 'windspeed' : values[3], 'windaz' : values[4] |
---|
| 698 | } |
---|
| 699 | else: |
---|
| 700 | out = [] |
---|
| 701 | for r in values: |
---|
| 702 | |
---|
| 703 | out.append({'temperature': r[0], |
---|
| 704 | 'pressure': r[1], 'humidity' : r[2], |
---|
| 705 | 'windspeed' : r[3], 'windaz' : r[4] |
---|
| 706 | }) |
---|
| 707 | return out |
---|
| 708 | |
---|
[876] | 709 | def _row_callback(self, callback, label): |
---|
| 710 | out = "" |
---|
[1118] | 711 | outvec = [] |
---|
[1590] | 712 | sep = '-'*50 |
---|
[876] | 713 | for i in range(self.nrow()): |
---|
| 714 | tm = self._gettime(i) |
---|
| 715 | src = self._getsourcename(i) |
---|
[1590] | 716 | out += 'Scan[%d] (%s) ' % (self.getscan(i), src) |
---|
[876] | 717 | out += 'Time[%s]:\n' % (tm) |
---|
[1590] | 718 | if self.nbeam(-1) > 1: |
---|
| 719 | out += ' Beam[%d] ' % (self.getbeam(i)) |
---|
| 720 | if self.nif(-1) > 1: out += ' IF[%d] ' % (self.getif(i)) |
---|
| 721 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (self.getpol(i)) |
---|
[876] | 722 | outvec.append(callback(i)) |
---|
| 723 | out += '= %3.3f\n' % (outvec[i]) |
---|
[1590] | 724 | out += sep+'\n' |
---|
[876] | 725 | if rcParams['verbose']: |
---|
[1819] | 726 | asaplog.push(sep) |
---|
| 727 | asaplog.push(" %s" % (label)) |
---|
| 728 | asaplog.push(sep) |
---|
| 729 | asaplog.push(out) |
---|
| 730 | print_log() |
---|
[1175] | 731 | return outvec |
---|
[256] | 732 | |
---|
[1070] | 733 | def _get_column(self, callback, row=-1): |
---|
| 734 | """ |
---|
| 735 | """ |
---|
| 736 | if row == -1: |
---|
| 737 | return [callback(i) for i in range(self.nrow())] |
---|
| 738 | else: |
---|
[1819] | 739 | if 0 <= row < self.nrow(): |
---|
[1070] | 740 | return callback(row) |
---|
[256] | 741 | |
---|
[1070] | 742 | |
---|
[1348] | 743 | def get_time(self, row=-1, asdatetime=False): |
---|
[1846] | 744 | """\ |
---|
[113] | 745 | Get a list of time stamps for the observations. |
---|
[1348] | 746 | Return a datetime object for each integration time stamp in the scantable. |
---|
[1846] | 747 | |
---|
[113] | 748 | Parameters: |
---|
[1846] | 749 | |
---|
[1348] | 750 | row: row no of integration. Default -1 return all rows |
---|
| 751 | asdatetime: return values as datetime objects rather than strings |
---|
[1846] | 752 | |
---|
[113] | 753 | """ |
---|
[1175] | 754 | from time import strptime |
---|
| 755 | from datetime import datetime |
---|
[1392] | 756 | times = self._get_column(self._gettime, row) |
---|
[1348] | 757 | if not asdatetime: |
---|
[1392] | 758 | return times |
---|
[1175] | 759 | format = "%Y/%m/%d/%H:%M:%S" |
---|
| 760 | if isinstance(times, list): |
---|
| 761 | return [datetime(*strptime(i, format)[:6]) for i in times] |
---|
| 762 | else: |
---|
| 763 | return datetime(*strptime(times, format)[:6]) |
---|
[102] | 764 | |
---|
[1348] | 765 | |
---|
| 766 | def get_inttime(self, row=-1): |
---|
[1846] | 767 | """\ |
---|
[1348] | 768 | Get a list of integration times for the observations. |
---|
| 769 | Return a time in seconds for each integration in the scantable. |
---|
[1846] | 770 | |
---|
[1348] | 771 | Parameters: |
---|
[1846] | 772 | |
---|
[1348] | 773 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 774 | |
---|
[1348] | 775 | """ |
---|
[1573] | 776 | return self._get_column(self._getinttime, row) |
---|
[1348] | 777 | |
---|
[1573] | 778 | |
---|
[714] | 779 | def get_sourcename(self, row=-1): |
---|
[1846] | 780 | """\ |
---|
[794] | 781 | Get a list source names for the observations. |
---|
[714] | 782 | Return a string for each integration in the scantable. |
---|
| 783 | Parameters: |
---|
[1846] | 784 | |
---|
[1348] | 785 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 786 | |
---|
[714] | 787 | """ |
---|
[1070] | 788 | return self._get_column(self._getsourcename, row) |
---|
[714] | 789 | |
---|
[794] | 790 | def get_elevation(self, row=-1): |
---|
[1846] | 791 | """\ |
---|
[794] | 792 | Get a list of elevations for the observations. |
---|
| 793 | Return a float for each integration in the scantable. |
---|
[1846] | 794 | |
---|
[794] | 795 | Parameters: |
---|
[1846] | 796 | |
---|
[1348] | 797 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 798 | |
---|
[794] | 799 | """ |
---|
[1070] | 800 | return self._get_column(self._getelevation, row) |
---|
[794] | 801 | |
---|
| 802 | def get_azimuth(self, row=-1): |
---|
[1846] | 803 | """\ |
---|
[794] | 804 | Get a list of azimuths for the observations. |
---|
| 805 | Return a float for each integration in the scantable. |
---|
[1846] | 806 | |
---|
[794] | 807 | Parameters: |
---|
[1348] | 808 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 809 | |
---|
[794] | 810 | """ |
---|
[1070] | 811 | return self._get_column(self._getazimuth, row) |
---|
[794] | 812 | |
---|
| 813 | def get_parangle(self, row=-1): |
---|
[1846] | 814 | """\ |
---|
[794] | 815 | Get a list of parallactic angles for the observations. |
---|
| 816 | Return a float for each integration in the scantable. |
---|
[1846] | 817 | |
---|
[794] | 818 | Parameters: |
---|
[1846] | 819 | |
---|
[1348] | 820 | row: row no of integration. Default -1 return all rows. |
---|
[1846] | 821 | |
---|
[794] | 822 | """ |
---|
[1070] | 823 | return self._get_column(self._getparangle, row) |
---|
[794] | 824 | |
---|
[1070] | 825 | def get_direction(self, row=-1): |
---|
| 826 | """ |
---|
| 827 | Get a list of Positions on the sky (direction) for the observations. |
---|
[1594] | 828 | Return a string for each integration in the scantable. |
---|
[1070] | 829 | Parameters: |
---|
| 830 | row: row no of integration. Default -1 return all rows |
---|
| 831 | Example: |
---|
| 832 | none |
---|
| 833 | """ |
---|
| 834 | return self._get_column(self._getdirection, row) |
---|
| 835 | |
---|
[1391] | 836 | def get_directionval(self, row=-1): |
---|
[1846] | 837 | """\ |
---|
[1391] | 838 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 839 | Return a float for each integration in the scantable. |
---|
[1846] | 840 | |
---|
[1391] | 841 | Parameters: |
---|
[1846] | 842 | |
---|
[1391] | 843 | row: row no of integration. Default -1 return all rows |
---|
[1846] | 844 | |
---|
[1391] | 845 | """ |
---|
| 846 | return self._get_column(self._getdirectionvec, row) |
---|
| 847 | |
---|
[1730] | 848 | @print_log_dec |
---|
[102] | 849 | def set_unit(self, unit='channel'): |
---|
[1846] | 850 | """\ |
---|
[102] | 851 | Set the unit for all following operations on this scantable |
---|
[1846] | 852 | |
---|
[102] | 853 | Parameters: |
---|
[1846] | 854 | |
---|
| 855 | unit: optional unit, default is 'channel'. Use one of '*Hz', |
---|
| 856 | 'km/s', 'channel' or equivalent '' |
---|
| 857 | |
---|
[102] | 858 | """ |
---|
[484] | 859 | varlist = vars() |
---|
[1118] | 860 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 861 | unit = '' |
---|
| 862 | inf = list(self._getcoordinfo()) |
---|
| 863 | inf[0] = unit |
---|
| 864 | self._setcoordinfo(inf) |
---|
[1118] | 865 | self._add_history("set_unit", varlist) |
---|
[113] | 866 | |
---|
[1589] | 867 | @print_log_dec |
---|
[484] | 868 | def set_instrument(self, instr): |
---|
[1846] | 869 | """\ |
---|
[1348] | 870 | Set the instrument for subsequent processing. |
---|
[1846] | 871 | |
---|
[358] | 872 | Parameters: |
---|
[1846] | 873 | |
---|
[710] | 874 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 875 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[1846] | 876 | |
---|
[358] | 877 | """ |
---|
| 878 | self._setInstrument(instr) |
---|
[1118] | 879 | self._add_history("set_instument", vars()) |
---|
[1819] | 880 | print_log() |
---|
[358] | 881 | |
---|
[1589] | 882 | @print_log_dec |
---|
[1190] | 883 | def set_feedtype(self, feedtype): |
---|
[1846] | 884 | """\ |
---|
[1190] | 885 | Overwrite the feed type, which might not be set correctly. |
---|
[1846] | 886 | |
---|
[1190] | 887 | Parameters: |
---|
[1846] | 888 | |
---|
[1190] | 889 | feedtype: 'linear' or 'circular' |
---|
[1846] | 890 | |
---|
[1190] | 891 | """ |
---|
| 892 | self._setfeedtype(feedtype) |
---|
| 893 | self._add_history("set_feedtype", vars()) |
---|
[1819] | 894 | print_log() |
---|
[1190] | 895 | |
---|
[1589] | 896 | @print_log_dec |
---|
[276] | 897 | def set_doppler(self, doppler='RADIO'): |
---|
[1846] | 898 | """\ |
---|
[276] | 899 | Set the doppler for all following operations on this scantable. |
---|
[1846] | 900 | |
---|
[276] | 901 | Parameters: |
---|
[1846] | 902 | |
---|
[276] | 903 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
[1846] | 904 | |
---|
[276] | 905 | """ |
---|
[484] | 906 | varlist = vars() |
---|
[276] | 907 | inf = list(self._getcoordinfo()) |
---|
| 908 | inf[2] = doppler |
---|
| 909 | self._setcoordinfo(inf) |
---|
[1118] | 910 | self._add_history("set_doppler", vars()) |
---|
[1819] | 911 | print_log() |
---|
[710] | 912 | |
---|
[1589] | 913 | @print_log_dec |
---|
[226] | 914 | def set_freqframe(self, frame=None): |
---|
[1846] | 915 | """\ |
---|
[113] | 916 | Set the frame type of the Spectral Axis. |
---|
[1846] | 917 | |
---|
[113] | 918 | Parameters: |
---|
[1846] | 919 | |
---|
[591] | 920 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1819] | 921 | 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
[1118] | 922 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[1846] | 923 | |
---|
| 924 | Example:: |
---|
| 925 | |
---|
[113] | 926 | scan.set_freqframe('BARY') |
---|
[1846] | 927 | |
---|
[113] | 928 | """ |
---|
[1593] | 929 | frame = frame or rcParams['scantable.freqframe'] |
---|
[484] | 930 | varlist = vars() |
---|
[1819] | 931 | # "REST" is not implemented in casacore |
---|
| 932 | #valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 933 | # 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
| 934 | valid = ['TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
[1118] | 935 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 936 | |
---|
[989] | 937 | if frame in valid: |
---|
[113] | 938 | inf = list(self._getcoordinfo()) |
---|
| 939 | inf[1] = frame |
---|
| 940 | self._setcoordinfo(inf) |
---|
[1118] | 941 | self._add_history("set_freqframe", varlist) |
---|
[102] | 942 | else: |
---|
[1118] | 943 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[718] | 944 | if rcParams['verbose']: |
---|
[1819] | 945 | #print msg |
---|
| 946 | asaplog.push( msg ) |
---|
| 947 | print_log( 'ERROR' ) |
---|
[718] | 948 | else: |
---|
| 949 | raise TypeError(msg) |
---|
[1819] | 950 | print_log() |
---|
[710] | 951 | |
---|
[989] | 952 | def set_dirframe(self, frame=""): |
---|
[1846] | 953 | """\ |
---|
[989] | 954 | Set the frame type of the Direction on the sky. |
---|
[1846] | 955 | |
---|
[989] | 956 | Parameters: |
---|
[1846] | 957 | |
---|
[989] | 958 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 959 | 'J2000', 'B1950', 'GALACTIC' |
---|
[1846] | 960 | |
---|
| 961 | Example: |
---|
| 962 | |
---|
[989] | 963 | scan.set_dirframe('GALACTIC') |
---|
[1846] | 964 | |
---|
[989] | 965 | """ |
---|
| 966 | varlist = vars() |
---|
| 967 | try: |
---|
| 968 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 969 | except RuntimeError, msg: |
---|
[989] | 970 | if rcParams['verbose']: |
---|
[1819] | 971 | #print msg |
---|
| 972 | print_log() |
---|
| 973 | asaplog.push( str(msg) ) |
---|
| 974 | print_log( 'ERROR' ) |
---|
[989] | 975 | else: |
---|
| 976 | raise |
---|
[1118] | 977 | self._add_history("set_dirframe", varlist) |
---|
[989] | 978 | |
---|
[113] | 979 | def get_unit(self): |
---|
[1846] | 980 | """\ |
---|
[113] | 981 | Get the default unit set in this scantable |
---|
[1846] | 982 | |
---|
[113] | 983 | Returns: |
---|
[1846] | 984 | |
---|
[113] | 985 | A unit string |
---|
[1846] | 986 | |
---|
[113] | 987 | """ |
---|
| 988 | inf = self._getcoordinfo() |
---|
| 989 | unit = inf[0] |
---|
| 990 | if unit == '': unit = 'channel' |
---|
| 991 | return unit |
---|
[102] | 992 | |
---|
[158] | 993 | def get_abcissa(self, rowno=0): |
---|
[1846] | 994 | """\ |
---|
[158] | 995 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 996 | selected Beam/IF/Pol |
---|
[1846] | 997 | |
---|
[113] | 998 | Parameters: |
---|
[1846] | 999 | |
---|
[226] | 1000 | rowno: an optional row number in the scantable. Default is the |
---|
| 1001 | first row, i.e. rowno=0 |
---|
[1846] | 1002 | |
---|
[113] | 1003 | Returns: |
---|
[1846] | 1004 | |
---|
[1348] | 1005 | The abcissa values and the format string (as a dictionary) |
---|
[1846] | 1006 | |
---|
[113] | 1007 | """ |
---|
[256] | 1008 | abc = self._getabcissa(rowno) |
---|
[710] | 1009 | lbl = self._getabcissalabel(rowno) |
---|
[1819] | 1010 | print_log() |
---|
[158] | 1011 | return abc, lbl |
---|
[113] | 1012 | |
---|
[1819] | 1013 | def flag(self, mask=None, unflag=False): |
---|
[1846] | 1014 | """\ |
---|
[1001] | 1015 | Flag the selected data using an optional channel mask. |
---|
[1846] | 1016 | |
---|
[1001] | 1017 | Parameters: |
---|
[1846] | 1018 | |
---|
[1001] | 1019 | mask: an optional channel mask, created with create_mask. Default |
---|
| 1020 | (no mask) is all channels. |
---|
[1819] | 1021 | unflag: if True, unflag the data |
---|
[1846] | 1022 | |
---|
[1001] | 1023 | """ |
---|
| 1024 | varlist = vars() |
---|
[1593] | 1025 | mask = mask or [] |
---|
[1001] | 1026 | try: |
---|
[1819] | 1027 | self._flag(mask, unflag) |
---|
[1118] | 1028 | except RuntimeError, msg: |
---|
[1001] | 1029 | if rcParams['verbose']: |
---|
[1819] | 1030 | #print msg |
---|
| 1031 | print_log() |
---|
| 1032 | asaplog.push( str(msg) ) |
---|
| 1033 | print_log( 'ERROR' ) |
---|
[1001] | 1034 | return |
---|
| 1035 | else: raise |
---|
| 1036 | self._add_history("flag", varlist) |
---|
| 1037 | |
---|
[1819] | 1038 | def flag_row(self, rows=[], unflag=False): |
---|
[1846] | 1039 | """\ |
---|
[1819] | 1040 | Flag the selected data in row-based manner. |
---|
[1846] | 1041 | |
---|
[1819] | 1042 | Parameters: |
---|
[1846] | 1043 | |
---|
[1843] | 1044 | rows: list of row numbers to be flagged. Default is no row |
---|
| 1045 | (must be explicitly specified to execute row-based flagging). |
---|
[1819] | 1046 | unflag: if True, unflag the data. |
---|
[1846] | 1047 | |
---|
[1819] | 1048 | """ |
---|
| 1049 | varlist = vars() |
---|
| 1050 | try: |
---|
| 1051 | self._flag_row(rows, unflag) |
---|
| 1052 | except RuntimeError, msg: |
---|
| 1053 | if rcParams['verbose']: |
---|
| 1054 | print_log() |
---|
| 1055 | asaplog.push( str(msg) ) |
---|
| 1056 | print_log('ERROR') |
---|
| 1057 | return |
---|
| 1058 | else: raise |
---|
| 1059 | self._add_history("flag_row", varlist) |
---|
| 1060 | |
---|
| 1061 | def clip(self, uthres=None, dthres=None, clipoutside=True, unflag=False): |
---|
[1846] | 1062 | """\ |
---|
[1819] | 1063 | Flag the selected data outside a specified range (in channel-base) |
---|
[1846] | 1064 | |
---|
[1819] | 1065 | Parameters: |
---|
[1846] | 1066 | |
---|
[1819] | 1067 | uthres: upper threshold. |
---|
| 1068 | dthres: lower threshold |
---|
[1846] | 1069 | |
---|
[1819] | 1070 | clipoutside: True for flagging data outside the range [dthres:uthres]. |
---|
| 1071 | False for glagging data inside the range. |
---|
[1846] | 1072 | unflag: if True, unflag the data. |
---|
| 1073 | |
---|
[1819] | 1074 | """ |
---|
| 1075 | varlist = vars() |
---|
| 1076 | try: |
---|
| 1077 | self._clip(uthres, dthres, clipoutside, unflag) |
---|
| 1078 | except RuntimeError, msg: |
---|
| 1079 | if rcParams['verbose']: |
---|
| 1080 | print_log() |
---|
| 1081 | asaplog.push(str(msg)) |
---|
| 1082 | print_log('ERROR') |
---|
| 1083 | return |
---|
| 1084 | else: raise |
---|
| 1085 | self._add_history("clip", varlist) |
---|
| 1086 | |
---|
[1589] | 1087 | @print_log_dec |
---|
[1584] | 1088 | def lag_flag(self, start, end, unit="MHz", insitu=None): |
---|
[1846] | 1089 | """\ |
---|
[1192] | 1090 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
[1584] | 1091 | Flagged data in the scantable gets interpolated over the region. |
---|
[1192] | 1092 | No taper is applied. |
---|
[1846] | 1093 | |
---|
[1192] | 1094 | Parameters: |
---|
[1846] | 1095 | |
---|
[1579] | 1096 | start: the start frequency (really a period within the |
---|
| 1097 | bandwidth) or period to remove |
---|
| 1098 | end: the end frequency or period to remove |
---|
[1584] | 1099 | unit: the frequency unit (default "MHz") or "" for |
---|
[1579] | 1100 | explicit lag channels |
---|
[1846] | 1101 | |
---|
| 1102 | *Notes*: |
---|
| 1103 | |
---|
[1579] | 1104 | It is recommended to flag edges of the band or strong |
---|
[1348] | 1105 | signals beforehand. |
---|
[1846] | 1106 | |
---|
[1192] | 1107 | """ |
---|
| 1108 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1109 | self._math._setinsitu(insitu) |
---|
| 1110 | varlist = vars() |
---|
[1579] | 1111 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1.} |
---|
| 1112 | if not (unit == "" or base.has_key(unit)): |
---|
[1192] | 1113 | raise ValueError("%s is not a valid unit." % unit) |
---|
| 1114 | try: |
---|
[1579] | 1115 | if unit == "": |
---|
| 1116 | s = scantable(self._math._lag_flag(self, start, end, "lags")) |
---|
| 1117 | else: |
---|
| 1118 | s = scantable(self._math._lag_flag(self, start*base[unit], |
---|
| 1119 | end*base[unit], "frequency")) |
---|
[1192] | 1120 | except RuntimeError, msg: |
---|
| 1121 | if rcParams['verbose']: |
---|
[1819] | 1122 | #print msg |
---|
| 1123 | print_log() |
---|
| 1124 | asaplog.push( str(msg) ) |
---|
| 1125 | print_log( 'ERROR' ) |
---|
[1192] | 1126 | return |
---|
| 1127 | else: raise |
---|
| 1128 | s._add_history("lag_flag", varlist) |
---|
[1819] | 1129 | print_log() |
---|
[1192] | 1130 | if insitu: |
---|
| 1131 | self._assign(s) |
---|
| 1132 | else: |
---|
| 1133 | return s |
---|
[1001] | 1134 | |
---|
[1589] | 1135 | @print_log_dec |
---|
[113] | 1136 | def create_mask(self, *args, **kwargs): |
---|
[1846] | 1137 | """\ |
---|
[1118] | 1138 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 1139 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 1140 | applied. |
---|
[1846] | 1141 | |
---|
[102] | 1142 | Parameters: |
---|
[1846] | 1143 | |
---|
[1118] | 1144 | [min, max], [min2, max2], ... |
---|
[1024] | 1145 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 1146 | to be masked |
---|
[189] | 1147 | invert: optional argument. If specified as True, |
---|
| 1148 | return an inverted mask, i.e. the regions |
---|
| 1149 | specified are EXCLUDED |
---|
[513] | 1150 | row: create the mask using the specified row for |
---|
| 1151 | unit conversions, default is row=0 |
---|
| 1152 | only necessary if frequency varies over rows. |
---|
[1846] | 1153 | |
---|
| 1154 | Examples:: |
---|
| 1155 | |
---|
[113] | 1156 | scan.set_unit('channel') |
---|
[1846] | 1157 | # a) |
---|
[1118] | 1158 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 1159 | # masks everything outside 400 and 500 |
---|
[113] | 1160 | # and 800 and 900 in the unit 'channel' |
---|
| 1161 | |
---|
[1846] | 1162 | # b) |
---|
[1118] | 1163 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 1164 | # masks the regions between 400 and 500 |
---|
[113] | 1165 | # and 800 and 900 in the unit 'channel' |
---|
[1846] | 1166 | |
---|
| 1167 | # c) |
---|
| 1168 | #mask only channel 400 |
---|
[1554] | 1169 | msk = scan.create_mask([400]) |
---|
[1846] | 1170 | |
---|
[102] | 1171 | """ |
---|
[1554] | 1172 | row = kwargs.get("row", 0) |
---|
[513] | 1173 | data = self._getabcissa(row) |
---|
[113] | 1174 | u = self._getcoordinfo()[0] |
---|
[718] | 1175 | if rcParams['verbose']: |
---|
[113] | 1176 | if u == "": u = "channel" |
---|
[718] | 1177 | msg = "The current mask window unit is %s" % u |
---|
[1118] | 1178 | i = self._check_ifs() |
---|
| 1179 | if not i: |
---|
[876] | 1180 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 1181 | asaplog.push(msg) |
---|
[102] | 1182 | n = self.nchan() |
---|
[1295] | 1183 | msk = _n_bools(n, False) |
---|
[710] | 1184 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 1185 | |
---|
[1118] | 1186 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 1187 | and args or args[0] |
---|
[710] | 1188 | for window in ws: |
---|
[1554] | 1189 | if len(window) == 1: |
---|
| 1190 | window = [window[0], window[0]] |
---|
| 1191 | if len(window) == 0 or len(window) > 2: |
---|
| 1192 | raise ValueError("A window needs to be defined as [start(, end)]") |
---|
[1545] | 1193 | if window[0] > window[1]: |
---|
| 1194 | tmp = window[0] |
---|
| 1195 | window[0] = window[1] |
---|
| 1196 | window[1] = tmp |
---|
[102] | 1197 | for i in range(n): |
---|
[1024] | 1198 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 1199 | msk[i] = True |
---|
[113] | 1200 | if kwargs.has_key('invert'): |
---|
| 1201 | if kwargs.get('invert'): |
---|
[1295] | 1202 | msk = mask_not(msk) |
---|
[1819] | 1203 | print_log() |
---|
[102] | 1204 | return msk |
---|
[710] | 1205 | |
---|
[1819] | 1206 | def get_masklist(self, mask=None, row=0): |
---|
[1846] | 1207 | """\ |
---|
[1819] | 1208 | Compute and return a list of mask windows, [min, max]. |
---|
[1846] | 1209 | |
---|
[1819] | 1210 | Parameters: |
---|
[1846] | 1211 | |
---|
[1819] | 1212 | mask: channel mask, created with create_mask. |
---|
| 1213 | row: calcutate the masklist using the specified row |
---|
| 1214 | for unit conversions, default is row=0 |
---|
| 1215 | only necessary if frequency varies over rows. |
---|
[1846] | 1216 | |
---|
[1819] | 1217 | Returns: |
---|
[1846] | 1218 | |
---|
[1819] | 1219 | [min, max], [min2, max2], ... |
---|
| 1220 | Pairs of start/end points (inclusive)specifying |
---|
| 1221 | the masked regions |
---|
[1846] | 1222 | |
---|
[1819] | 1223 | """ |
---|
| 1224 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1225 | raise TypeError("The mask should be list or tuple.") |
---|
| 1226 | if len(mask) < 2: |
---|
| 1227 | raise TypeError("The mask elements should be > 1") |
---|
| 1228 | if self.nchan() != len(mask): |
---|
| 1229 | msg = "Number of channels in scantable != number of mask elements" |
---|
| 1230 | raise TypeError(msg) |
---|
| 1231 | data = self._getabcissa(row) |
---|
| 1232 | u = self._getcoordinfo()[0] |
---|
| 1233 | if rcParams['verbose']: |
---|
| 1234 | if u == "": u = "channel" |
---|
| 1235 | msg = "The current mask window unit is %s" % u |
---|
| 1236 | i = self._check_ifs() |
---|
| 1237 | if not i: |
---|
| 1238 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 1239 | asaplog.push(msg) |
---|
| 1240 | masklist=[] |
---|
| 1241 | ist, ien = None, None |
---|
| 1242 | ist, ien=self.get_mask_indices(mask) |
---|
| 1243 | if ist is not None and ien is not None: |
---|
| 1244 | for i in xrange(len(ist)): |
---|
| 1245 | range=[data[ist[i]],data[ien[i]]] |
---|
| 1246 | range.sort() |
---|
| 1247 | masklist.append([range[0],range[1]]) |
---|
| 1248 | return masklist |
---|
| 1249 | |
---|
| 1250 | def get_mask_indices(self, mask=None): |
---|
[1846] | 1251 | """\ |
---|
[1819] | 1252 | Compute and Return lists of mask start indices and mask end indices. |
---|
| 1253 | Parameters: |
---|
| 1254 | mask: channel mask, created with create_mask. |
---|
[1846] | 1255 | |
---|
[1819] | 1256 | Returns: |
---|
[1846] | 1257 | |
---|
[1819] | 1258 | List of mask start indices and that of mask end indices, |
---|
| 1259 | i.e., [istart1,istart2,....], [iend1,iend2,....]. |
---|
[1846] | 1260 | |
---|
[1819] | 1261 | """ |
---|
| 1262 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 1263 | raise TypeError("The mask should be list or tuple.") |
---|
| 1264 | if len(mask) < 2: |
---|
| 1265 | raise TypeError("The mask elements should be > 1") |
---|
| 1266 | istart=[] |
---|
| 1267 | iend=[] |
---|
| 1268 | if mask[0]: istart.append(0) |
---|
| 1269 | for i in range(len(mask)-1): |
---|
| 1270 | if not mask[i] and mask[i+1]: |
---|
| 1271 | istart.append(i+1) |
---|
| 1272 | elif mask[i] and not mask[i+1]: |
---|
| 1273 | iend.append(i) |
---|
| 1274 | if mask[len(mask)-1]: iend.append(len(mask)-1) |
---|
| 1275 | if len(istart) != len(iend): |
---|
| 1276 | raise RuntimeError("Numbers of mask start != mask end.") |
---|
| 1277 | for i in range(len(istart)): |
---|
| 1278 | if istart[i] > iend[i]: |
---|
| 1279 | raise RuntimeError("Mask start index > mask end index") |
---|
| 1280 | break |
---|
| 1281 | return istart,iend |
---|
| 1282 | |
---|
| 1283 | # def get_restfreqs(self): |
---|
| 1284 | # """ |
---|
| 1285 | # Get the restfrequency(s) stored in this scantable. |
---|
| 1286 | # The return value(s) are always of unit 'Hz' |
---|
| 1287 | # Parameters: |
---|
| 1288 | # none |
---|
| 1289 | # Returns: |
---|
| 1290 | # a list of doubles |
---|
| 1291 | # """ |
---|
| 1292 | # return list(self._getrestfreqs()) |
---|
| 1293 | |
---|
| 1294 | def get_restfreqs(self, ids=None): |
---|
[1846] | 1295 | """\ |
---|
[256] | 1296 | Get the restfrequency(s) stored in this scantable. |
---|
| 1297 | The return value(s) are always of unit 'Hz' |
---|
[1846] | 1298 | |
---|
[256] | 1299 | Parameters: |
---|
[1846] | 1300 | |
---|
[1819] | 1301 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to |
---|
| 1302 | be retrieved |
---|
[1846] | 1303 | |
---|
[256] | 1304 | Returns: |
---|
[1846] | 1305 | |
---|
[1819] | 1306 | dictionary containing ids and a list of doubles for each id |
---|
[1846] | 1307 | |
---|
[256] | 1308 | """ |
---|
[1819] | 1309 | if ids is None: |
---|
| 1310 | rfreqs={} |
---|
| 1311 | idlist = self.getmolnos() |
---|
| 1312 | for i in idlist: |
---|
| 1313 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1314 | return rfreqs |
---|
| 1315 | else: |
---|
| 1316 | if type(ids)==list or type(ids)==tuple: |
---|
| 1317 | rfreqs={} |
---|
| 1318 | for i in ids: |
---|
| 1319 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1320 | return rfreqs |
---|
| 1321 | else: |
---|
| 1322 | return list(self._getrestfreqs(ids)) |
---|
| 1323 | #return list(self._getrestfreqs(ids)) |
---|
[102] | 1324 | |
---|
[931] | 1325 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
[1846] | 1326 | """\ |
---|
[931] | 1327 | Set or replace the restfrequency specified and |
---|
| 1328 | If the 'freqs' argument holds a scalar, |
---|
| 1329 | then that rest frequency will be applied to all the selected |
---|
| 1330 | data. If the 'freqs' argument holds |
---|
| 1331 | a vector, then it MUST be of equal or smaller length than |
---|
| 1332 | the number of IFs (and the available restfrequencies will be |
---|
| 1333 | replaced by this vector). In this case, *all* data have |
---|
| 1334 | the restfrequency set per IF according |
---|
| 1335 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 1336 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 1337 | IF 1 gets restfreq 2e9. |
---|
[1846] | 1338 | |
---|
[1395] | 1339 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 1340 | |
---|
[931] | 1341 | Parameters: |
---|
[1846] | 1342 | |
---|
[931] | 1343 | freqs: list of rest frequency values or string idenitfiers |
---|
| 1344 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 1345 | |
---|
[1846] | 1346 | |
---|
| 1347 | Example:: |
---|
| 1348 | |
---|
[1819] | 1349 | # set the given restfrequency for the all currently selected IFs |
---|
[931] | 1350 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1845] | 1351 | # set restfrequencies for the n IFs (n > 1) in the order of the |
---|
| 1352 | # list, i.e |
---|
| 1353 | # IF0 -> 1.4e9, IF1 -> 1.41e9, IF3 -> 1.42e9 |
---|
| 1354 | # len(list_of_restfreqs) == nIF |
---|
| 1355 | # for nIF == 1 the following will set multiple restfrequency for |
---|
| 1356 | # that IF |
---|
[1819] | 1357 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9]) |
---|
[1845] | 1358 | # set multiple restfrequencies per IF. as a list of lists where |
---|
| 1359 | # the outer list has nIF elements, the inner s arbitrary |
---|
| 1360 | scan.set_restfreqs(freqs=[[1.4e9, 1.41e9], [1.67e9]]) |
---|
[391] | 1361 | |
---|
[1846] | 1362 | *Note*: |
---|
[1845] | 1363 | |
---|
[931] | 1364 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 1365 | source and IF basis, use scantable.set_selection() before using |
---|
[1846] | 1366 | this function:: |
---|
[931] | 1367 | |
---|
[1846] | 1368 | # provided your scantable is called scan |
---|
| 1369 | selection = selector() |
---|
| 1370 | selection.set_name("ORION*") |
---|
| 1371 | selection.set_ifs([1]) |
---|
| 1372 | scan.set_selection(selection) |
---|
| 1373 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 1374 | |
---|
[931] | 1375 | """ |
---|
| 1376 | varlist = vars() |
---|
[1157] | 1377 | from asap import linecatalog |
---|
| 1378 | # simple value |
---|
[1118] | 1379 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1845] | 1380 | self._setrestfreqs([freqs], [""], unit) |
---|
[1157] | 1381 | # list of values |
---|
[1118] | 1382 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 1383 | # list values are scalars |
---|
[1118] | 1384 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[1845] | 1385 | if len(freqs) == 1: |
---|
| 1386 | self._setrestfreqs(freqs, [""], unit) |
---|
| 1387 | else: |
---|
| 1388 | # allow the 'old' mode of setting mulitple IFs |
---|
| 1389 | sel = selector() |
---|
| 1390 | savesel = self._getselection() |
---|
| 1391 | iflist = self.getifnos() |
---|
| 1392 | if len(freqs)>len(iflist): |
---|
| 1393 | raise ValueError("number of elements in list of list " |
---|
| 1394 | "exeeds the current IF selections") |
---|
| 1395 | iflist = self.getifnos() |
---|
| 1396 | for i, fval in enumerate(freqs): |
---|
| 1397 | sel.set_ifs(iflist[i]) |
---|
| 1398 | self._setselection(sel) |
---|
| 1399 | self._setrestfreqs([fval], [""], unit) |
---|
| 1400 | self._setselection(savesel) |
---|
| 1401 | |
---|
| 1402 | # list values are dict, {'value'=, 'name'=) |
---|
[1157] | 1403 | elif isinstance(freqs[-1], dict): |
---|
[1845] | 1404 | values = [] |
---|
| 1405 | names = [] |
---|
| 1406 | for d in freqs: |
---|
| 1407 | values.append(d["value"]) |
---|
| 1408 | names.append(d["name"]) |
---|
| 1409 | self._setrestfreqs(values, names, unit) |
---|
[1819] | 1410 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple): |
---|
[1157] | 1411 | sel = selector() |
---|
| 1412 | savesel = self._getselection() |
---|
[1322] | 1413 | iflist = self.getifnos() |
---|
[1819] | 1414 | if len(freqs)>len(iflist): |
---|
[1845] | 1415 | raise ValueError("number of elements in list of list exeeds" |
---|
| 1416 | " the current IF selections") |
---|
| 1417 | for i, fval in enumerate(freqs): |
---|
[1322] | 1418 | sel.set_ifs(iflist[i]) |
---|
[1259] | 1419 | self._setselection(sel) |
---|
[1845] | 1420 | self._setrestfreqs(fval, [""], unit) |
---|
[1157] | 1421 | self._setselection(savesel) |
---|
| 1422 | # freqs are to be taken from a linecatalog |
---|
[1153] | 1423 | elif isinstance(freqs, linecatalog): |
---|
| 1424 | sel = selector() |
---|
| 1425 | savesel = self._getselection() |
---|
| 1426 | for i in xrange(freqs.nrow()): |
---|
[1322] | 1427 | sel.set_ifs(iflist[i]) |
---|
[1153] | 1428 | self._setselection(sel) |
---|
[1845] | 1429 | self._setrestfreqs([freqs.get_frequency(i)], |
---|
| 1430 | [freqs.get_name(i)], "MHz") |
---|
[1153] | 1431 | # ensure that we are not iterating past nIF |
---|
| 1432 | if i == self.nif()-1: break |
---|
| 1433 | self._setselection(savesel) |
---|
[931] | 1434 | else: |
---|
| 1435 | return |
---|
| 1436 | self._add_history("set_restfreqs", varlist) |
---|
| 1437 | |
---|
[1360] | 1438 | def shift_refpix(self, delta): |
---|
[1846] | 1439 | """\ |
---|
[1589] | 1440 | Shift the reference pixel of the Spectra Coordinate by an |
---|
| 1441 | integer amount. |
---|
[1846] | 1442 | |
---|
[1589] | 1443 | Parameters: |
---|
[1846] | 1444 | |
---|
[1589] | 1445 | delta: the amount to shift by |
---|
[1846] | 1446 | |
---|
| 1447 | *Note*: |
---|
| 1448 | |
---|
[1589] | 1449 | Be careful using this with broadband data. |
---|
[1846] | 1450 | |
---|
[1360] | 1451 | """ |
---|
[1731] | 1452 | Scantable.shift_refpix(self, delta) |
---|
[931] | 1453 | |
---|
[1259] | 1454 | def history(self, filename=None): |
---|
[1846] | 1455 | """\ |
---|
[1259] | 1456 | Print the history. Optionally to a file. |
---|
[1846] | 1457 | |
---|
[1348] | 1458 | Parameters: |
---|
[1846] | 1459 | |
---|
[1348] | 1460 | filename: The name of the file to save the history to. |
---|
[1846] | 1461 | |
---|
[1259] | 1462 | """ |
---|
[484] | 1463 | hist = list(self._gethistory()) |
---|
[794] | 1464 | out = "-"*80 |
---|
[484] | 1465 | for h in hist: |
---|
[489] | 1466 | if h.startswith("---"): |
---|
[794] | 1467 | out += "\n"+h |
---|
[489] | 1468 | else: |
---|
| 1469 | items = h.split("##") |
---|
| 1470 | date = items[0] |
---|
| 1471 | func = items[1] |
---|
| 1472 | items = items[2:] |
---|
[794] | 1473 | out += "\n"+date+"\n" |
---|
| 1474 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 1475 | for i in items: |
---|
| 1476 | s = i.split("=") |
---|
[1118] | 1477 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[794] | 1478 | out += "\n"+"-"*80 |
---|
[1259] | 1479 | if filename is not None: |
---|
| 1480 | if filename is "": |
---|
| 1481 | filename = 'scantable_history.txt' |
---|
| 1482 | import os |
---|
| 1483 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 1484 | if not os.path.isdir(filename): |
---|
| 1485 | data = open(filename, 'w') |
---|
| 1486 | data.write(out) |
---|
| 1487 | data.close() |
---|
| 1488 | else: |
---|
| 1489 | msg = "Illegal file name '%s'." % (filename) |
---|
| 1490 | if rcParams['verbose']: |
---|
[1819] | 1491 | #print msg |
---|
| 1492 | asaplog.push( msg ) |
---|
| 1493 | print_log( 'ERROR' ) |
---|
[1259] | 1494 | else: |
---|
| 1495 | raise IOError(msg) |
---|
| 1496 | if rcParams['verbose']: |
---|
| 1497 | try: |
---|
| 1498 | from IPython.genutils import page as pager |
---|
| 1499 | except ImportError: |
---|
| 1500 | from pydoc import pager |
---|
| 1501 | pager(out) |
---|
| 1502 | else: |
---|
| 1503 | return out |
---|
[484] | 1504 | return |
---|
[513] | 1505 | # |
---|
| 1506 | # Maths business |
---|
| 1507 | # |
---|
[1589] | 1508 | @print_log_dec |
---|
[931] | 1509 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[1846] | 1510 | """\ |
---|
[1070] | 1511 | Return the (time) weighted average of a scan. |
---|
[1846] | 1512 | |
---|
| 1513 | *Note*: |
---|
| 1514 | |
---|
[1070] | 1515 | in channels only - align if necessary |
---|
[1846] | 1516 | |
---|
[513] | 1517 | Parameters: |
---|
[1846] | 1518 | |
---|
[513] | 1519 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 1520 | weighting) |
---|
[558] | 1521 | scanav: True averages each scan separately |
---|
| 1522 | False (default) averages all scans together, |
---|
[1099] | 1523 | weight: Weighting scheme. |
---|
| 1524 | 'none' (mean no weight) |
---|
| 1525 | 'var' (1/var(spec) weighted) |
---|
| 1526 | 'tsys' (1/Tsys**2 weighted) |
---|
| 1527 | 'tint' (integration time weighted) |
---|
| 1528 | 'tintsys' (Tint/Tsys**2) |
---|
| 1529 | 'median' ( median averaging) |
---|
[535] | 1530 | The default is 'tint' |
---|
[931] | 1531 | align: align the spectra in velocity before averaging. It takes |
---|
| 1532 | the time of the first spectrum as reference time. |
---|
[1846] | 1533 | |
---|
| 1534 | Example:: |
---|
| 1535 | |
---|
[513] | 1536 | # time average the scantable without using a mask |
---|
[710] | 1537 | newscan = scan.average_time() |
---|
[1846] | 1538 | |
---|
[513] | 1539 | """ |
---|
| 1540 | varlist = vars() |
---|
[1593] | 1541 | weight = weight or 'TINT' |
---|
| 1542 | mask = mask or () |
---|
| 1543 | scanav = (scanav and 'SCAN') or 'NONE' |
---|
[1118] | 1544 | scan = (self, ) |
---|
[989] | 1545 | try: |
---|
[1118] | 1546 | if align: |
---|
| 1547 | scan = (self.freq_align(insitu=False), ) |
---|
| 1548 | s = None |
---|
| 1549 | if weight.upper() == 'MEDIAN': |
---|
| 1550 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 1551 | scanav)) |
---|
| 1552 | else: |
---|
| 1553 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 1554 | scanav)) |
---|
| 1555 | except RuntimeError, msg: |
---|
[989] | 1556 | if rcParams['verbose']: |
---|
[1819] | 1557 | #print msg |
---|
| 1558 | print_log() |
---|
| 1559 | asaplog.push( str(msg) ) |
---|
| 1560 | print_log( 'ERROR' ) |
---|
[989] | 1561 | return |
---|
| 1562 | else: raise |
---|
[1099] | 1563 | s._add_history("average_time", varlist) |
---|
[1819] | 1564 | print_log() |
---|
[513] | 1565 | return s |
---|
[710] | 1566 | |
---|
[1589] | 1567 | @print_log_dec |
---|
[876] | 1568 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[1846] | 1569 | """\ |
---|
[513] | 1570 | Return a scan where all spectra are converted to either |
---|
| 1571 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 1572 | By default the function tries to look the values up internally. |
---|
| 1573 | If it can't find them (or if you want to over-ride), you must |
---|
| 1574 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 1575 | also if you don't set it). jyperk takes precedence if you set both. |
---|
[1846] | 1576 | |
---|
[513] | 1577 | Parameters: |
---|
[1846] | 1578 | |
---|
[513] | 1579 | jyperk: the Jy / K conversion factor |
---|
| 1580 | eta: the aperture efficiency |
---|
| 1581 | d: the geomtric diameter (metres) |
---|
| 1582 | insitu: if False a new scantable is returned. |
---|
| 1583 | Otherwise, the scaling is done in-situ |
---|
| 1584 | The default is taken from .asaprc (False) |
---|
[1846] | 1585 | |
---|
[513] | 1586 | """ |
---|
| 1587 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1588 | self._math._setinsitu(insitu) |
---|
[513] | 1589 | varlist = vars() |
---|
[1593] | 1590 | jyperk = jyperk or -1.0 |
---|
| 1591 | d = d or -1.0 |
---|
| 1592 | eta = eta or -1.0 |
---|
[876] | 1593 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 1594 | s._add_history("convert_flux", varlist) |
---|
[1819] | 1595 | print_log() |
---|
[876] | 1596 | if insitu: self._assign(s) |
---|
| 1597 | else: return s |
---|
[513] | 1598 | |
---|
[1589] | 1599 | @print_log_dec |
---|
[876] | 1600 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[1846] | 1601 | """\ |
---|
[513] | 1602 | Return a scan after applying a gain-elevation correction. |
---|
| 1603 | The correction can be made via either a polynomial or a |
---|
| 1604 | table-based interpolation (and extrapolation if necessary). |
---|
| 1605 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 1606 | If you specify neither, then a polynomial correction will be made |
---|
| 1607 | with built in coefficients known for certain telescopes (an error |
---|
| 1608 | will occur if the instrument is not known). |
---|
| 1609 | The data and Tsys are *divided* by the scaling factors. |
---|
[1846] | 1610 | |
---|
[513] | 1611 | Parameters: |
---|
[1846] | 1612 | |
---|
[513] | 1613 | poly: Polynomial coefficients (default None) to compute a |
---|
| 1614 | gain-elevation correction as a function of |
---|
| 1615 | elevation (in degrees). |
---|
| 1616 | filename: The name of an ascii file holding correction factors. |
---|
| 1617 | The first row of the ascii file must give the column |
---|
| 1618 | names and these MUST include columns |
---|
| 1619 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 1620 | by this) somewhere. |
---|
| 1621 | The second row must give the data type of the |
---|
| 1622 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 1623 | An example file would be |
---|
| 1624 | (actual factors are arbitrary) : |
---|
| 1625 | |
---|
| 1626 | TIME ELEVATION FACTOR |
---|
| 1627 | R R R |
---|
| 1628 | 0.1 0 0.8 |
---|
| 1629 | 0.2 20 0.85 |
---|
| 1630 | 0.3 40 0.9 |
---|
| 1631 | 0.4 60 0.85 |
---|
| 1632 | 0.5 80 0.8 |
---|
| 1633 | 0.6 90 0.75 |
---|
| 1634 | method: Interpolation method when correcting from a table. |
---|
| 1635 | Values are "nearest", "linear" (default), "cubic" |
---|
| 1636 | and "spline" |
---|
| 1637 | insitu: if False a new scantable is returned. |
---|
| 1638 | Otherwise, the scaling is done in-situ |
---|
| 1639 | The default is taken from .asaprc (False) |
---|
[1846] | 1640 | |
---|
[513] | 1641 | """ |
---|
| 1642 | |
---|
| 1643 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1644 | self._math._setinsitu(insitu) |
---|
[513] | 1645 | varlist = vars() |
---|
[1593] | 1646 | poly = poly or () |
---|
[513] | 1647 | from os.path import expandvars |
---|
| 1648 | filename = expandvars(filename) |
---|
[876] | 1649 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 1650 | s._add_history("gain_el", varlist) |
---|
[1819] | 1651 | print_log() |
---|
[1593] | 1652 | if insitu: |
---|
| 1653 | self._assign(s) |
---|
| 1654 | else: |
---|
| 1655 | return s |
---|
[710] | 1656 | |
---|
[1589] | 1657 | @print_log_dec |
---|
[931] | 1658 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[1846] | 1659 | """\ |
---|
[513] | 1660 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 1661 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 1662 | set_freqframe. |
---|
[1846] | 1663 | |
---|
[513] | 1664 | Parameters: |
---|
| 1665 | reftime: reference time to align at. By default, the time of |
---|
| 1666 | the first row of data is used. |
---|
| 1667 | method: Interpolation method for regridding the spectra. |
---|
| 1668 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 1669 | and "spline" |
---|
| 1670 | insitu: if False a new scantable is returned. |
---|
| 1671 | Otherwise, the scaling is done in-situ |
---|
| 1672 | The default is taken from .asaprc (False) |
---|
[1846] | 1673 | |
---|
[513] | 1674 | """ |
---|
[931] | 1675 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 1676 | self._math._setinsitu(insitu) |
---|
[513] | 1677 | varlist = vars() |
---|
[1593] | 1678 | reftime = reftime or "" |
---|
[931] | 1679 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 1680 | s._add_history("freq_align", varlist) |
---|
[1819] | 1681 | print_log() |
---|
[876] | 1682 | if insitu: self._assign(s) |
---|
| 1683 | else: return s |
---|
[513] | 1684 | |
---|
[1589] | 1685 | @print_log_dec |
---|
[1725] | 1686 | def opacity(self, tau=None, insitu=None): |
---|
[1846] | 1687 | """\ |
---|
[513] | 1688 | Apply an opacity correction. The data |
---|
| 1689 | and Tsys are multiplied by the correction factor. |
---|
[1846] | 1690 | |
---|
[513] | 1691 | Parameters: |
---|
[1689] | 1692 | tau: (list of) opacity from which the correction factor is |
---|
[513] | 1693 | exp(tau*ZD) |
---|
[1689] | 1694 | where ZD is the zenith-distance. |
---|
| 1695 | If a list is provided, it has to be of length nIF, |
---|
| 1696 | nIF*nPol or 1 and in order of IF/POL, e.g. |
---|
| 1697 | [opif0pol0, opif0pol1, opif1pol0 ...] |
---|
[1725] | 1698 | if tau is `None` the opacities are determined from a |
---|
| 1699 | model. |
---|
[513] | 1700 | insitu: if False a new scantable is returned. |
---|
| 1701 | Otherwise, the scaling is done in-situ |
---|
| 1702 | The default is taken from .asaprc (False) |
---|
[1846] | 1703 | |
---|
[513] | 1704 | """ |
---|
| 1705 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1706 | self._math._setinsitu(insitu) |
---|
[513] | 1707 | varlist = vars() |
---|
[1689] | 1708 | if not hasattr(tau, "__len__"): |
---|
| 1709 | tau = [tau] |
---|
[876] | 1710 | s = scantable(self._math._opacity(self, tau)) |
---|
| 1711 | s._add_history("opacity", varlist) |
---|
[1819] | 1712 | print_log() |
---|
[876] | 1713 | if insitu: self._assign(s) |
---|
| 1714 | else: return s |
---|
[513] | 1715 | |
---|
[1589] | 1716 | @print_log_dec |
---|
[513] | 1717 | def bin(self, width=5, insitu=None): |
---|
[1846] | 1718 | """\ |
---|
[513] | 1719 | Return a scan where all spectra have been binned up. |
---|
[1846] | 1720 | |
---|
[1348] | 1721 | Parameters: |
---|
[1846] | 1722 | |
---|
[513] | 1723 | width: The bin width (default=5) in pixels |
---|
| 1724 | insitu: if False a new scantable is returned. |
---|
| 1725 | Otherwise, the scaling is done in-situ |
---|
| 1726 | The default is taken from .asaprc (False) |
---|
[1846] | 1727 | |
---|
[513] | 1728 | """ |
---|
| 1729 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1730 | self._math._setinsitu(insitu) |
---|
[513] | 1731 | varlist = vars() |
---|
[876] | 1732 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1733 | s._add_history("bin", varlist) |
---|
[1819] | 1734 | print_log() |
---|
[1589] | 1735 | if insitu: |
---|
| 1736 | self._assign(s) |
---|
| 1737 | else: |
---|
| 1738 | return s |
---|
[513] | 1739 | |
---|
[1589] | 1740 | @print_log_dec |
---|
[513] | 1741 | def resample(self, width=5, method='cubic', insitu=None): |
---|
[1846] | 1742 | """\ |
---|
[1348] | 1743 | Return a scan where all spectra have been binned up. |
---|
[1573] | 1744 | |
---|
[1348] | 1745 | Parameters: |
---|
[1846] | 1746 | |
---|
[513] | 1747 | width: The bin width (default=5) in pixels |
---|
| 1748 | method: Interpolation method when correcting from a table. |
---|
| 1749 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1750 | and "spline" |
---|
| 1751 | insitu: if False a new scantable is returned. |
---|
| 1752 | Otherwise, the scaling is done in-situ |
---|
| 1753 | The default is taken from .asaprc (False) |
---|
[1846] | 1754 | |
---|
[513] | 1755 | """ |
---|
| 1756 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1757 | self._math._setinsitu(insitu) |
---|
[513] | 1758 | varlist = vars() |
---|
[876] | 1759 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1760 | s._add_history("resample", varlist) |
---|
[1819] | 1761 | print_log() |
---|
[876] | 1762 | if insitu: self._assign(s) |
---|
| 1763 | else: return s |
---|
[513] | 1764 | |
---|
[1589] | 1765 | @print_log_dec |
---|
[946] | 1766 | def average_pol(self, mask=None, weight='none'): |
---|
[1846] | 1767 | """\ |
---|
[946] | 1768 | Average the Polarisations together. |
---|
[1846] | 1769 | |
---|
[946] | 1770 | Parameters: |
---|
[1846] | 1771 | |
---|
[946] | 1772 | mask: An optional mask defining the region, where the |
---|
| 1773 | averaging will be applied. The output will have all |
---|
| 1774 | specified points masked. |
---|
| 1775 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1776 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 1777 | |
---|
[946] | 1778 | """ |
---|
| 1779 | varlist = vars() |
---|
[1593] | 1780 | mask = mask or () |
---|
[1010] | 1781 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1782 | s._add_history("average_pol", varlist) |
---|
[1819] | 1783 | print_log() |
---|
[992] | 1784 | return s |
---|
[513] | 1785 | |
---|
[1589] | 1786 | @print_log_dec |
---|
[1145] | 1787 | def average_beam(self, mask=None, weight='none'): |
---|
[1846] | 1788 | """\ |
---|
[1145] | 1789 | Average the Beams together. |
---|
[1846] | 1790 | |
---|
[1145] | 1791 | Parameters: |
---|
| 1792 | mask: An optional mask defining the region, where the |
---|
| 1793 | averaging will be applied. The output will have all |
---|
| 1794 | specified points masked. |
---|
| 1795 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1796 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[1846] | 1797 | |
---|
[1145] | 1798 | """ |
---|
| 1799 | varlist = vars() |
---|
[1593] | 1800 | mask = mask or () |
---|
[1145] | 1801 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1802 | s._add_history("average_beam", varlist) |
---|
[1819] | 1803 | print_log() |
---|
[1145] | 1804 | return s |
---|
| 1805 | |
---|
[1586] | 1806 | def parallactify(self, pflag): |
---|
[1846] | 1807 | """\ |
---|
[1843] | 1808 | Set a flag to indicate whether this data should be treated as having |
---|
[1617] | 1809 | been 'parallactified' (total phase == 0.0) |
---|
[1846] | 1810 | |
---|
[1617] | 1811 | Parameters: |
---|
[1843] | 1812 | pflag: Bool indicating whether to turn this on (True) or |
---|
[1617] | 1813 | off (False) |
---|
[1846] | 1814 | |
---|
[1617] | 1815 | """ |
---|
[1586] | 1816 | varlist = vars() |
---|
| 1817 | self._parallactify(pflag) |
---|
| 1818 | self._add_history("parallactify", varlist) |
---|
| 1819 | |
---|
[1589] | 1820 | @print_log_dec |
---|
[992] | 1821 | def convert_pol(self, poltype=None): |
---|
[1846] | 1822 | """\ |
---|
[992] | 1823 | Convert the data to a different polarisation type. |
---|
[1565] | 1824 | Note that you will need cross-polarisation terms for most conversions. |
---|
[1846] | 1825 | |
---|
[992] | 1826 | Parameters: |
---|
| 1827 | poltype: The new polarisation type. Valid types are: |
---|
[1565] | 1828 | "linear", "circular", "stokes" and "linpol" |
---|
[1846] | 1829 | |
---|
[992] | 1830 | """ |
---|
| 1831 | varlist = vars() |
---|
| 1832 | try: |
---|
| 1833 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1834 | except RuntimeError, msg: |
---|
[992] | 1835 | if rcParams['verbose']: |
---|
[1819] | 1836 | #print msg |
---|
| 1837 | print_log() |
---|
| 1838 | asaplog.push( str(msg) ) |
---|
| 1839 | print_log( 'ERROR' ) |
---|
[1118] | 1840 | return |
---|
[992] | 1841 | else: |
---|
| 1842 | raise |
---|
[1118] | 1843 | s._add_history("convert_pol", varlist) |
---|
[1819] | 1844 | print_log() |
---|
[992] | 1845 | return s |
---|
| 1846 | |
---|
[1589] | 1847 | @print_log_dec |
---|
[1819] | 1848 | def smooth(self, kernel="hanning", width=5.0, order=2, plot=False, insitu=None): |
---|
[1846] | 1849 | """\ |
---|
[513] | 1850 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
[1846] | 1851 | |
---|
[513] | 1852 | Parameters: |
---|
[1846] | 1853 | |
---|
[513] | 1854 | kernel: The type of smoothing kernel. Select from |
---|
[1574] | 1855 | 'hanning' (default), 'gaussian', 'boxcar', 'rmedian' |
---|
| 1856 | or 'poly' |
---|
[513] | 1857 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1858 | ignored otherwise it defauls to 5 pixels. |
---|
| 1859 | For 'gaussian' it is the Full Width Half |
---|
| 1860 | Maximum. For 'boxcar' it is the full width. |
---|
[1574] | 1861 | For 'rmedian' and 'poly' it is the half width. |
---|
| 1862 | order: Optional parameter for 'poly' kernel (default is 2), to |
---|
| 1863 | specify the order of the polnomial. Ignored by all other |
---|
| 1864 | kernels. |
---|
[1819] | 1865 | plot: plot the original and the smoothed spectra. |
---|
| 1866 | In this each indivual fit has to be approved, by |
---|
| 1867 | typing 'y' or 'n' |
---|
[513] | 1868 | insitu: if False a new scantable is returned. |
---|
| 1869 | Otherwise, the scaling is done in-situ |
---|
| 1870 | The default is taken from .asaprc (False) |
---|
[1846] | 1871 | |
---|
[513] | 1872 | """ |
---|
| 1873 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1874 | self._math._setinsitu(insitu) |
---|
[513] | 1875 | varlist = vars() |
---|
[1819] | 1876 | |
---|
| 1877 | if plot: orgscan = self.copy() |
---|
| 1878 | |
---|
[1574] | 1879 | s = scantable(self._math._smooth(self, kernel.lower(), width, order)) |
---|
[876] | 1880 | s._add_history("smooth", varlist) |
---|
[1819] | 1881 | |
---|
| 1882 | if plot: |
---|
| 1883 | if rcParams['plotter.gui']: |
---|
| 1884 | from asap.asaplotgui import asaplotgui as asaplot |
---|
| 1885 | else: |
---|
| 1886 | from asap.asaplot import asaplot |
---|
| 1887 | self._p=asaplot() |
---|
| 1888 | self._p.set_panels() |
---|
| 1889 | ylab=s._get_ordinate_label() |
---|
| 1890 | #self._p.palette(0,["#777777","red"]) |
---|
| 1891 | for r in xrange(s.nrow()): |
---|
| 1892 | xsm=s._getabcissa(r) |
---|
| 1893 | ysm=s._getspectrum(r) |
---|
| 1894 | xorg=orgscan._getabcissa(r) |
---|
| 1895 | yorg=orgscan._getspectrum(r) |
---|
| 1896 | self._p.clear() |
---|
| 1897 | self._p.hold() |
---|
| 1898 | self._p.set_axes('ylabel',ylab) |
---|
| 1899 | self._p.set_axes('xlabel',s._getabcissalabel(r)) |
---|
| 1900 | self._p.set_axes('title',s._getsourcename(r)) |
---|
| 1901 | self._p.set_line(label='Original',color="#777777") |
---|
| 1902 | self._p.plot(xorg,yorg) |
---|
| 1903 | self._p.set_line(label='Smoothed',color="red") |
---|
| 1904 | self._p.plot(xsm,ysm) |
---|
| 1905 | ### Ugly part for legend |
---|
| 1906 | for i in [0,1]: |
---|
| 1907 | self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]]) |
---|
| 1908 | self._p.release() |
---|
| 1909 | ### Ugly part for legend |
---|
| 1910 | self._p.subplots[0]['lines']=[] |
---|
| 1911 | res = raw_input("Accept smoothing ([y]/n): ") |
---|
| 1912 | if res.upper() == 'N': |
---|
| 1913 | s._setspectrum(yorg, r) |
---|
| 1914 | self._p.unmap() |
---|
| 1915 | self._p = None |
---|
| 1916 | del orgscan |
---|
| 1917 | |
---|
| 1918 | print_log() |
---|
[876] | 1919 | if insitu: self._assign(s) |
---|
| 1920 | else: return s |
---|
[513] | 1921 | |
---|
[1589] | 1922 | @print_log_dec |
---|
[1617] | 1923 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, |
---|
| 1924 | insitu=None): |
---|
[1846] | 1925 | """\ |
---|
[513] | 1926 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
[1846] | 1927 | |
---|
[513] | 1928 | Parameters: |
---|
[1846] | 1929 | |
---|
[794] | 1930 | mask: an optional mask |
---|
| 1931 | order: the order of the polynomial (default is 0) |
---|
[1061] | 1932 | plot: plot the fit and the residual. In this each |
---|
| 1933 | indivual fit has to be approved, by typing 'y' |
---|
| 1934 | or 'n' |
---|
[1391] | 1935 | uselin: use linear polynomial fit |
---|
[794] | 1936 | insitu: if False a new scantable is returned. |
---|
| 1937 | Otherwise, the scaling is done in-situ |
---|
| 1938 | The default is taken from .asaprc (False) |
---|
[1846] | 1939 | |
---|
| 1940 | Example:: |
---|
| 1941 | |
---|
[513] | 1942 | # return a scan baselined by a third order polynomial, |
---|
| 1943 | # not using a mask |
---|
| 1944 | bscan = scan.poly_baseline(order=3) |
---|
[1846] | 1945 | |
---|
[579] | 1946 | """ |
---|
[513] | 1947 | if insitu is None: insitu = rcParams['insitu'] |
---|
[1819] | 1948 | if not insitu: |
---|
| 1949 | workscan = self.copy() |
---|
| 1950 | else: |
---|
| 1951 | workscan = self |
---|
[513] | 1952 | varlist = vars() |
---|
| 1953 | if mask is None: |
---|
[1295] | 1954 | mask = [True for i in xrange(self.nchan(-1))] |
---|
[1819] | 1955 | |
---|
[513] | 1956 | from asap.asapfitter import fitter |
---|
[1217] | 1957 | try: |
---|
| 1958 | f = fitter() |
---|
[1391] | 1959 | if uselin: |
---|
| 1960 | f.set_function(lpoly=order) |
---|
| 1961 | else: |
---|
| 1962 | f.set_function(poly=order) |
---|
[1819] | 1963 | |
---|
| 1964 | rows = range(workscan.nrow()) |
---|
| 1965 | if len(rows) > 0: |
---|
| 1966 | self.blpars = [] |
---|
| 1967 | |
---|
| 1968 | for r in rows: |
---|
| 1969 | # take into account flagtra info (CAS-1434) |
---|
| 1970 | flagtra = workscan._getmask(r) |
---|
| 1971 | actualmask = mask[:] |
---|
| 1972 | if len(actualmask) == 0: |
---|
| 1973 | actualmask = list(flagtra[:]) |
---|
| 1974 | else: |
---|
| 1975 | if len(actualmask) != len(flagtra): |
---|
| 1976 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 1977 | else: |
---|
| 1978 | for i in range(0, len(actualmask)): |
---|
| 1979 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 1980 | f.set_scan(workscan, actualmask) |
---|
| 1981 | f.x = workscan._getabcissa(r) |
---|
| 1982 | f.y = workscan._getspectrum(r) |
---|
| 1983 | f.data = None |
---|
| 1984 | f.fit() |
---|
| 1985 | if plot: |
---|
| 1986 | f.plot(residual=True) |
---|
| 1987 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1988 | if x.upper() == 'N': |
---|
| 1989 | self.blpars.append(None) |
---|
| 1990 | continue |
---|
| 1991 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
| 1992 | self.blpars.append(f.get_parameters()) |
---|
| 1993 | |
---|
| 1994 | if plot: |
---|
| 1995 | f._p.unmap() |
---|
| 1996 | f._p = None |
---|
| 1997 | workscan._add_history("poly_baseline", varlist) |
---|
| 1998 | print_log() |
---|
| 1999 | if insitu: self._assign(workscan) |
---|
| 2000 | else: return workscan |
---|
[1217] | 2001 | except RuntimeError: |
---|
| 2002 | msg = "The fit failed, possibly because it didn't converge." |
---|
| 2003 | if rcParams['verbose']: |
---|
[1819] | 2004 | #print msg |
---|
| 2005 | print_log() |
---|
| 2006 | asaplog.push( str(msg) ) |
---|
| 2007 | print_log( 'ERROR' ) |
---|
[1217] | 2008 | return |
---|
| 2009 | else: |
---|
| 2010 | raise RuntimeError(msg) |
---|
[513] | 2011 | |
---|
[1819] | 2012 | |
---|
[1118] | 2013 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
[1280] | 2014 | threshold=3, chan_avg_limit=1, plot=False, |
---|
| 2015 | insitu=None): |
---|
[1846] | 2016 | """\ |
---|
[880] | 2017 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 2018 | Spectral lines are detected first using linefinder and masked out |
---|
| 2019 | to avoid them affecting the baseline solution. |
---|
| 2020 | |
---|
| 2021 | Parameters: |
---|
[1846] | 2022 | |
---|
[880] | 2023 | mask: an optional mask retreived from scantable |
---|
[1846] | 2024 | |
---|
| 2025 | edge: an optional number of channel to drop at the edge of |
---|
| 2026 | spectrum. If only one value is |
---|
[880] | 2027 | specified, the same number will be dropped from |
---|
| 2028 | both sides of the spectrum. Default is to keep |
---|
[907] | 2029 | all channels. Nested tuples represent individual |
---|
[976] | 2030 | edge selection for different IFs (a number of spectral |
---|
| 2031 | channels can be different) |
---|
[1846] | 2032 | |
---|
[880] | 2033 | order: the order of the polynomial (default is 0) |
---|
[1846] | 2034 | |
---|
[880] | 2035 | threshold: the threshold used by line finder. It is better to |
---|
| 2036 | keep it large as only strong lines affect the |
---|
| 2037 | baseline solution. |
---|
[1846] | 2038 | |
---|
[1280] | 2039 | chan_avg_limit: |
---|
| 2040 | a maximum number of consequtive spectral channels to |
---|
| 2041 | average during the search of weak and broad lines. |
---|
| 2042 | The default is no averaging (and no search for weak |
---|
| 2043 | lines). If such lines can affect the fitted baseline |
---|
| 2044 | (e.g. a high order polynomial is fitted), increase this |
---|
| 2045 | parameter (usually values up to 8 are reasonable). Most |
---|
| 2046 | users of this method should find the default value |
---|
| 2047 | sufficient. |
---|
[1846] | 2048 | |
---|
[1061] | 2049 | plot: plot the fit and the residual. In this each |
---|
| 2050 | indivual fit has to be approved, by typing 'y' |
---|
| 2051 | or 'n' |
---|
[1846] | 2052 | |
---|
[880] | 2053 | insitu: if False a new scantable is returned. |
---|
| 2054 | Otherwise, the scaling is done in-situ |
---|
| 2055 | The default is taken from .asaprc (False) |
---|
| 2056 | |
---|
[1846] | 2057 | |
---|
| 2058 | Example:: |
---|
| 2059 | |
---|
| 2060 | scan2 = scan.auto_poly_baseline(order=7, insitu=False) |
---|
| 2061 | |
---|
[880] | 2062 | """ |
---|
| 2063 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 2064 | varlist = vars() |
---|
| 2065 | from asap.asapfitter import fitter |
---|
| 2066 | from asap.asaplinefind import linefinder |
---|
| 2067 | from asap import _is_sequence_or_number as _is_valid |
---|
| 2068 | |
---|
[976] | 2069 | # check whether edge is set up for each IF individually |
---|
[1118] | 2070 | individualedge = False; |
---|
| 2071 | if len(edge) > 1: |
---|
| 2072 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 2073 | individualedge = True; |
---|
[907] | 2074 | |
---|
[1118] | 2075 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 2076 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 2077 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 2078 | to make individual selection for different IFs." |
---|
[919] | 2079 | |
---|
[1118] | 2080 | curedge = (0, 0) |
---|
| 2081 | if individualedge: |
---|
| 2082 | for edgepar in edge: |
---|
| 2083 | if not _is_valid(edgepar, int): |
---|
| 2084 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 2085 | to be a pair of integers or an integer." |
---|
[907] | 2086 | else: |
---|
[1118] | 2087 | curedge = edge; |
---|
[880] | 2088 | |
---|
| 2089 | # setup fitter |
---|
| 2090 | f = fitter() |
---|
| 2091 | f.set_function(poly=order) |
---|
| 2092 | |
---|
| 2093 | # setup line finder |
---|
[1118] | 2094 | fl = linefinder() |
---|
[1268] | 2095 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
[880] | 2096 | |
---|
| 2097 | if not insitu: |
---|
[1118] | 2098 | workscan = self.copy() |
---|
[880] | 2099 | else: |
---|
[1118] | 2100 | workscan = self |
---|
[880] | 2101 | |
---|
[907] | 2102 | fl.set_scan(workscan) |
---|
| 2103 | |
---|
[1118] | 2104 | rows = range(workscan.nrow()) |
---|
[1819] | 2105 | # Save parameters of baseline fits & masklists as a class attribute. |
---|
| 2106 | # NOTICE: It does not reflect changes in scantable! |
---|
| 2107 | if len(rows) > 0: |
---|
| 2108 | self.blpars=[] |
---|
| 2109 | self.masklists=[] |
---|
[880] | 2110 | asaplog.push("Processing:") |
---|
| 2111 | for r in rows: |
---|
[1118] | 2112 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 2113 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 2114 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 2115 | asaplog.push(msg, False) |
---|
[907] | 2116 | |
---|
[976] | 2117 | # figure out edge parameter |
---|
[1118] | 2118 | if individualedge: |
---|
| 2119 | if len(edge) >= workscan.getif(r): |
---|
| 2120 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 2121 | "be less than the number of IFs" |
---|
| 2122 | curedge = edge[workscan.getif(r)] |
---|
[919] | 2123 | |
---|
[1819] | 2124 | # take into account flagtra info (CAS-1434) |
---|
| 2125 | flagtra = workscan._getmask(r) |
---|
| 2126 | actualmask = mask[:] |
---|
| 2127 | if len(actualmask) == 0: |
---|
| 2128 | actualmask = list(flagtra[:]) |
---|
| 2129 | else: |
---|
| 2130 | if len(actualmask) != len(flagtra): |
---|
| 2131 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 2132 | else: |
---|
| 2133 | for i in range(0, len(actualmask)): |
---|
| 2134 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 2135 | |
---|
[976] | 2136 | # setup line finder |
---|
[1819] | 2137 | fl.find_lines(r, actualmask, curedge) |
---|
| 2138 | outmask=fl.get_mask() |
---|
| 2139 | f.set_scan(workscan, fl.get_mask()) |
---|
| 2140 | f.x = workscan._getabcissa(r) |
---|
| 2141 | f.y = workscan._getspectrum(r) |
---|
| 2142 | f.data = None |
---|
[880] | 2143 | f.fit() |
---|
[1819] | 2144 | |
---|
| 2145 | # Show mask list |
---|
| 2146 | masklist=workscan.get_masklist(fl.get_mask(),row=r) |
---|
| 2147 | msg = "mask range: "+str(masklist) |
---|
| 2148 | asaplog.push(msg, False) |
---|
| 2149 | |
---|
[1061] | 2150 | if plot: |
---|
| 2151 | f.plot(residual=True) |
---|
| 2152 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 2153 | if x.upper() == 'N': |
---|
[1819] | 2154 | self.blpars.append(None) |
---|
| 2155 | self.masklists.append(None) |
---|
[1061] | 2156 | continue |
---|
[1819] | 2157 | |
---|
[880] | 2158 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1819] | 2159 | self.blpars.append(f.get_parameters()) |
---|
| 2160 | self.masklists.append(masklist) |
---|
[1061] | 2161 | if plot: |
---|
| 2162 | f._p.unmap() |
---|
| 2163 | f._p = None |
---|
| 2164 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 2165 | if insitu: |
---|
| 2166 | self._assign(workscan) |
---|
| 2167 | else: |
---|
| 2168 | return workscan |
---|
| 2169 | |
---|
[1589] | 2170 | @print_log_dec |
---|
[914] | 2171 | def rotate_linpolphase(self, angle): |
---|
[1846] | 2172 | """\ |
---|
[914] | 2173 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 2174 | This is always done in situ in the raw data. So if you call this |
---|
| 2175 | function more than once then each call rotates the phase further. |
---|
[1846] | 2176 | |
---|
[914] | 2177 | Parameters: |
---|
[1846] | 2178 | |
---|
[914] | 2179 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 2180 | |
---|
| 2181 | Example:: |
---|
| 2182 | |
---|
[914] | 2183 | scan.rotate_linpolphase(2.3) |
---|
[1846] | 2184 | |
---|
[914] | 2185 | """ |
---|
| 2186 | varlist = vars() |
---|
[936] | 2187 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 2188 | self._add_history("rotate_linpolphase", varlist) |
---|
[1819] | 2189 | print_log() |
---|
[914] | 2190 | return |
---|
[710] | 2191 | |
---|
[1589] | 2192 | @print_log_dec |
---|
[914] | 2193 | def rotate_xyphase(self, angle): |
---|
[1846] | 2194 | """\ |
---|
[914] | 2195 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 2196 | in the data. So if you call this function more than once |
---|
| 2197 | then each call rotates the phase further. |
---|
[1846] | 2198 | |
---|
[914] | 2199 | Parameters: |
---|
[1846] | 2200 | |
---|
[914] | 2201 | angle: The angle (degrees) to rotate (add) by. |
---|
[1846] | 2202 | |
---|
| 2203 | Example:: |
---|
| 2204 | |
---|
[914] | 2205 | scan.rotate_xyphase(2.3) |
---|
[1846] | 2206 | |
---|
[914] | 2207 | """ |
---|
| 2208 | varlist = vars() |
---|
[936] | 2209 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 2210 | self._add_history("rotate_xyphase", varlist) |
---|
[1819] | 2211 | print_log() |
---|
[914] | 2212 | return |
---|
| 2213 | |
---|
[1589] | 2214 | @print_log_dec |
---|
[914] | 2215 | def swap_linears(self): |
---|
[1846] | 2216 | """\ |
---|
[1573] | 2217 | Swap the linear polarisations XX and YY, or better the first two |
---|
[1348] | 2218 | polarisations as this also works for ciculars. |
---|
[914] | 2219 | """ |
---|
| 2220 | varlist = vars() |
---|
[936] | 2221 | self._math._swap_linears(self) |
---|
[914] | 2222 | self._add_history("swap_linears", varlist) |
---|
[1819] | 2223 | print_log() |
---|
[914] | 2224 | return |
---|
| 2225 | |
---|
[1589] | 2226 | @print_log_dec |
---|
[914] | 2227 | def invert_phase(self): |
---|
[1846] | 2228 | """\ |
---|
[914] | 2229 | Invert the phase of the complex polarisation |
---|
| 2230 | """ |
---|
| 2231 | varlist = vars() |
---|
[936] | 2232 | self._math._invert_phase(self) |
---|
[914] | 2233 | self._add_history("invert_phase", varlist) |
---|
| 2234 | return |
---|
| 2235 | |
---|
[1589] | 2236 | @print_log_dec |
---|
[876] | 2237 | def add(self, offset, insitu=None): |
---|
[1846] | 2238 | """\ |
---|
[513] | 2239 | Return a scan where all spectra have the offset added |
---|
[1846] | 2240 | |
---|
[513] | 2241 | Parameters: |
---|
[1846] | 2242 | |
---|
[513] | 2243 | offset: the offset |
---|
| 2244 | insitu: if False a new scantable is returned. |
---|
| 2245 | Otherwise, the scaling is done in-situ |
---|
| 2246 | The default is taken from .asaprc (False) |
---|
[1846] | 2247 | |
---|
[513] | 2248 | """ |
---|
| 2249 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2250 | self._math._setinsitu(insitu) |
---|
[513] | 2251 | varlist = vars() |
---|
[876] | 2252 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 2253 | s._add_history("add", varlist) |
---|
[876] | 2254 | if insitu: |
---|
| 2255 | self._assign(s) |
---|
| 2256 | else: |
---|
[513] | 2257 | return s |
---|
| 2258 | |
---|
[1589] | 2259 | @print_log_dec |
---|
[1308] | 2260 | def scale(self, factor, tsys=True, insitu=None): |
---|
[1846] | 2261 | """\ |
---|
| 2262 | |
---|
[513] | 2263 | Return a scan where all spectra are scaled by the give 'factor' |
---|
[1846] | 2264 | |
---|
[513] | 2265 | Parameters: |
---|
[1846] | 2266 | |
---|
[1819] | 2267 | factor: the scaling factor (float or 1D float list) |
---|
[513] | 2268 | insitu: if False a new scantable is returned. |
---|
| 2269 | Otherwise, the scaling is done in-situ |
---|
| 2270 | The default is taken from .asaprc (False) |
---|
| 2271 | tsys: if True (default) then apply the operation to Tsys |
---|
| 2272 | as well as the data |
---|
[1846] | 2273 | |
---|
[513] | 2274 | """ |
---|
| 2275 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2276 | self._math._setinsitu(insitu) |
---|
[513] | 2277 | varlist = vars() |
---|
[1819] | 2278 | s = None |
---|
| 2279 | import numpy |
---|
| 2280 | if isinstance(factor, list) or isinstance(factor, numpy.ndarray): |
---|
| 2281 | if isinstance(factor[0], list) or isinstance(factor[0], numpy.ndarray): |
---|
| 2282 | from asapmath import _array2dOp |
---|
| 2283 | s = _array2dOp( self.copy(), factor, "MUL", tsys ) |
---|
| 2284 | else: |
---|
| 2285 | s = scantable( self._math._arrayop( self.copy(), factor, "MUL", tsys ) ) |
---|
| 2286 | else: |
---|
| 2287 | s = scantable(self._math._unaryop(self.copy(), factor, "MUL", tsys)) |
---|
[1118] | 2288 | s._add_history("scale", varlist) |
---|
[1819] | 2289 | print_log() |
---|
[876] | 2290 | if insitu: |
---|
| 2291 | self._assign(s) |
---|
| 2292 | else: |
---|
[513] | 2293 | return s |
---|
| 2294 | |
---|
[1504] | 2295 | def set_sourcetype(self, match, matchtype="pattern", |
---|
| 2296 | sourcetype="reference"): |
---|
[1846] | 2297 | """\ |
---|
[1502] | 2298 | Set the type of the source to be an source or reference scan |
---|
[1846] | 2299 | using the provided pattern. |
---|
| 2300 | |
---|
[1502] | 2301 | Parameters: |
---|
[1846] | 2302 | |
---|
[1504] | 2303 | match: a Unix style pattern, regular expression or selector |
---|
| 2304 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
| 2305 | 'regex' regular expression |
---|
[1502] | 2306 | sourcetype: the type of the source to use (source/reference) |
---|
[1846] | 2307 | |
---|
[1502] | 2308 | """ |
---|
| 2309 | varlist = vars() |
---|
| 2310 | basesel = self.get_selection() |
---|
| 2311 | stype = -1 |
---|
| 2312 | if sourcetype.lower().startswith("r"): |
---|
| 2313 | stype = 1 |
---|
| 2314 | elif sourcetype.lower().startswith("s"): |
---|
| 2315 | stype = 0 |
---|
[1504] | 2316 | else: |
---|
[1502] | 2317 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)") |
---|
[1504] | 2318 | if matchtype.lower().startswith("p"): |
---|
| 2319 | matchtype = "pattern" |
---|
| 2320 | elif matchtype.lower().startswith("r"): |
---|
| 2321 | matchtype = "regex" |
---|
| 2322 | else: |
---|
| 2323 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
[1502] | 2324 | sel = selector() |
---|
| 2325 | if isinstance(match, selector): |
---|
| 2326 | sel = match |
---|
| 2327 | else: |
---|
[1504] | 2328 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match)) |
---|
[1502] | 2329 | self.set_selection(basesel+sel) |
---|
| 2330 | self._setsourcetype(stype) |
---|
| 2331 | self.set_selection(basesel) |
---|
[1573] | 2332 | self._add_history("set_sourcetype", varlist) |
---|
[1502] | 2333 | |
---|
[1589] | 2334 | @print_log_dec |
---|
[1819] | 2335 | def auto_quotient(self, preserve=True, mode='paired', verify=False): |
---|
[1846] | 2336 | """\ |
---|
[670] | 2337 | This function allows to build quotients automatically. |
---|
[1819] | 2338 | It assumes the observation to have the same number of |
---|
[670] | 2339 | "ons" and "offs" |
---|
[1846] | 2340 | |
---|
[670] | 2341 | Parameters: |
---|
[1846] | 2342 | |
---|
[710] | 2343 | preserve: you can preserve (default) the continuum or |
---|
| 2344 | remove it. The equations used are |
---|
[670] | 2345 | preserve: Output = Toff * (on/off) - Toff |
---|
[1070] | 2346 | remove: Output = Toff * (on/off) - Ton |
---|
[1573] | 2347 | mode: the on/off detection mode |
---|
[1348] | 2348 | 'paired' (default) |
---|
| 2349 | identifies 'off' scans by the |
---|
| 2350 | trailing '_R' (Mopra/Parkes) or |
---|
| 2351 | '_e'/'_w' (Tid) and matches |
---|
| 2352 | on/off pairs from the observing pattern |
---|
[1502] | 2353 | 'time' |
---|
| 2354 | finds the closest off in time |
---|
[1348] | 2355 | |
---|
[670] | 2356 | """ |
---|
[1348] | 2357 | modes = ["time", "paired"] |
---|
[670] | 2358 | if not mode in modes: |
---|
[876] | 2359 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 2360 | raise ValueError(msg) |
---|
| 2361 | varlist = vars() |
---|
[1348] | 2362 | s = None |
---|
| 2363 | if mode.lower() == "paired": |
---|
| 2364 | basesel = self.get_selection() |
---|
[1356] | 2365 | sel = selector()+basesel |
---|
| 2366 | sel.set_query("SRCTYPE==1") |
---|
| 2367 | self.set_selection(sel) |
---|
[1348] | 2368 | offs = self.copy() |
---|
| 2369 | sel.set_query("SRCTYPE==0") |
---|
[1356] | 2370 | self.set_selection(sel) |
---|
[1348] | 2371 | ons = self.copy() |
---|
| 2372 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 2373 | self.set_selection(basesel) |
---|
| 2374 | elif mode.lower() == "time": |
---|
| 2375 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 2376 | s._add_history("auto_quotient", varlist) |
---|
[1819] | 2377 | print_log() |
---|
[876] | 2378 | return s |
---|
[710] | 2379 | |
---|
[1589] | 2380 | @print_log_dec |
---|
[1145] | 2381 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1846] | 2382 | """\ |
---|
[1143] | 2383 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
[1846] | 2384 | |
---|
[1143] | 2385 | Parameters: |
---|
[1846] | 2386 | |
---|
[1145] | 2387 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1143] | 2388 | weight: How to average the off beams. Default is 'median'. |
---|
[1145] | 2389 | preserve: you can preserve (default) the continuum or |
---|
| 2390 | remove it. The equations used are |
---|
| 2391 | preserve: Output = Toff * (on/off) - Toff |
---|
| 2392 | remove: Output = Toff * (on/off) - Ton |
---|
[1846] | 2393 | |
---|
[1217] | 2394 | """ |
---|
[1593] | 2395 | mask = mask or () |
---|
[1141] | 2396 | varlist = vars() |
---|
| 2397 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 2398 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 2399 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 2400 | from asapmath import quotient |
---|
[1145] | 2401 | q = quotient(on, off, preserve) |
---|
[1143] | 2402 | q._add_history("mx_quotient", varlist) |
---|
[1819] | 2403 | print_log() |
---|
[1217] | 2404 | return q |
---|
[513] | 2405 | |
---|
[1589] | 2406 | @print_log_dec |
---|
[718] | 2407 | def freq_switch(self, insitu=None): |
---|
[1846] | 2408 | """\ |
---|
[718] | 2409 | Apply frequency switching to the data. |
---|
[1846] | 2410 | |
---|
[718] | 2411 | Parameters: |
---|
[1846] | 2412 | |
---|
[718] | 2413 | insitu: if False a new scantable is returned. |
---|
| 2414 | Otherwise, the swictching is done in-situ |
---|
| 2415 | The default is taken from .asaprc (False) |
---|
[1846] | 2416 | |
---|
[718] | 2417 | """ |
---|
| 2418 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2419 | self._math._setinsitu(insitu) |
---|
[718] | 2420 | varlist = vars() |
---|
[876] | 2421 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 2422 | s._add_history("freq_switch", varlist) |
---|
[1819] | 2423 | print_log() |
---|
[876] | 2424 | if insitu: self._assign(s) |
---|
| 2425 | else: return s |
---|
[718] | 2426 | |
---|
[1589] | 2427 | @print_log_dec |
---|
[780] | 2428 | def recalc_azel(self): |
---|
[1846] | 2429 | """Recalculate the azimuth and elevation for each position.""" |
---|
[780] | 2430 | varlist = vars() |
---|
[876] | 2431 | self._recalcazel() |
---|
[780] | 2432 | self._add_history("recalc_azel", varlist) |
---|
[1819] | 2433 | print_log() |
---|
[780] | 2434 | return |
---|
| 2435 | |
---|
[1589] | 2436 | @print_log_dec |
---|
[513] | 2437 | def __add__(self, other): |
---|
| 2438 | varlist = vars() |
---|
| 2439 | s = None |
---|
| 2440 | if isinstance(other, scantable): |
---|
[1573] | 2441 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
[513] | 2442 | elif isinstance(other, float): |
---|
[876] | 2443 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 2444 | else: |
---|
[718] | 2445 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2446 | s._add_history("operator +", varlist) |
---|
| 2447 | return s |
---|
| 2448 | |
---|
[1589] | 2449 | @print_log_dec |
---|
[513] | 2450 | def __sub__(self, other): |
---|
| 2451 | """ |
---|
| 2452 | implicit on all axes and on Tsys |
---|
| 2453 | """ |
---|
| 2454 | varlist = vars() |
---|
| 2455 | s = None |
---|
| 2456 | if isinstance(other, scantable): |
---|
[1588] | 2457 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
[513] | 2458 | elif isinstance(other, float): |
---|
[876] | 2459 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 2460 | else: |
---|
[718] | 2461 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2462 | s._add_history("operator -", varlist) |
---|
| 2463 | return s |
---|
[710] | 2464 | |
---|
[1589] | 2465 | @print_log_dec |
---|
[513] | 2466 | def __mul__(self, other): |
---|
| 2467 | """ |
---|
| 2468 | implicit on all axes and on Tsys |
---|
| 2469 | """ |
---|
| 2470 | varlist = vars() |
---|
| 2471 | s = None |
---|
| 2472 | if isinstance(other, scantable): |
---|
[1588] | 2473 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
[513] | 2474 | elif isinstance(other, float): |
---|
[876] | 2475 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 2476 | else: |
---|
[718] | 2477 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2478 | s._add_history("operator *", varlist) |
---|
| 2479 | return s |
---|
| 2480 | |
---|
[710] | 2481 | |
---|
[1589] | 2482 | @print_log_dec |
---|
[513] | 2483 | def __div__(self, other): |
---|
| 2484 | """ |
---|
| 2485 | implicit on all axes and on Tsys |
---|
| 2486 | """ |
---|
| 2487 | varlist = vars() |
---|
| 2488 | s = None |
---|
| 2489 | if isinstance(other, scantable): |
---|
[1589] | 2490 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
[513] | 2491 | elif isinstance(other, float): |
---|
| 2492 | if other == 0.0: |
---|
[718] | 2493 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 2494 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 2495 | else: |
---|
[718] | 2496 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2497 | s._add_history("operator /", varlist) |
---|
| 2498 | return s |
---|
| 2499 | |
---|
[530] | 2500 | def get_fit(self, row=0): |
---|
[1846] | 2501 | """\ |
---|
[530] | 2502 | Print or return the stored fits for a row in the scantable |
---|
[1846] | 2503 | |
---|
[530] | 2504 | Parameters: |
---|
[1846] | 2505 | |
---|
[530] | 2506 | row: the row which the fit has been applied to. |
---|
[1846] | 2507 | |
---|
[530] | 2508 | """ |
---|
| 2509 | if row > self.nrow(): |
---|
| 2510 | return |
---|
[976] | 2511 | from asap.asapfit import asapfit |
---|
[530] | 2512 | fit = asapfit(self._getfit(row)) |
---|
[718] | 2513 | if rcParams['verbose']: |
---|
[1819] | 2514 | #print fit |
---|
| 2515 | asaplog.push( '%s' %(fit) ) |
---|
| 2516 | print_log() |
---|
[530] | 2517 | return |
---|
| 2518 | else: |
---|
| 2519 | return fit.as_dict() |
---|
| 2520 | |
---|
[1483] | 2521 | def flag_nans(self): |
---|
[1846] | 2522 | """\ |
---|
[1483] | 2523 | Utility function to flag NaN values in the scantable. |
---|
| 2524 | """ |
---|
| 2525 | import numpy |
---|
| 2526 | basesel = self.get_selection() |
---|
| 2527 | for i in range(self.nrow()): |
---|
[1589] | 2528 | sel = self.get_row_selector(i) |
---|
| 2529 | self.set_selection(basesel+sel) |
---|
[1483] | 2530 | nans = numpy.isnan(self._getspectrum(0)) |
---|
| 2531 | if numpy.any(nans): |
---|
| 2532 | bnans = [ bool(v) for v in nans] |
---|
| 2533 | self.flag(bnans) |
---|
| 2534 | self.set_selection(basesel) |
---|
| 2535 | |
---|
[1588] | 2536 | def get_row_selector(self, rowno): |
---|
| 2537 | return selector(beams=self.getbeam(rowno), |
---|
| 2538 | ifs=self.getif(rowno), |
---|
| 2539 | pols=self.getpol(rowno), |
---|
| 2540 | scans=self.getscan(rowno), |
---|
| 2541 | cycles=self.getcycle(rowno)) |
---|
[1573] | 2542 | |
---|
[484] | 2543 | def _add_history(self, funcname, parameters): |
---|
[1435] | 2544 | if not rcParams['scantable.history']: |
---|
| 2545 | return |
---|
[484] | 2546 | # create date |
---|
| 2547 | sep = "##" |
---|
| 2548 | from datetime import datetime |
---|
| 2549 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 2550 | hist = dstr+sep |
---|
| 2551 | hist += funcname+sep#cdate+sep |
---|
| 2552 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 2553 | for k, v in parameters.iteritems(): |
---|
[484] | 2554 | if type(v) is dict: |
---|
[1118] | 2555 | for k2, v2 in v.iteritems(): |
---|
[484] | 2556 | hist += k2 |
---|
| 2557 | hist += "=" |
---|
[1118] | 2558 | if isinstance(v2, scantable): |
---|
[484] | 2559 | hist += 'scantable' |
---|
| 2560 | elif k2 == 'mask': |
---|
[1118] | 2561 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 2562 | hist += str(self._zip_mask(v2)) |
---|
| 2563 | else: |
---|
| 2564 | hist += str(v2) |
---|
[484] | 2565 | else: |
---|
[513] | 2566 | hist += str(v2) |
---|
[484] | 2567 | else: |
---|
| 2568 | hist += k |
---|
| 2569 | hist += "=" |
---|
[1118] | 2570 | if isinstance(v, scantable): |
---|
[484] | 2571 | hist += 'scantable' |
---|
| 2572 | elif k == 'mask': |
---|
[1118] | 2573 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 2574 | hist += str(self._zip_mask(v)) |
---|
| 2575 | else: |
---|
| 2576 | hist += str(v) |
---|
[484] | 2577 | else: |
---|
| 2578 | hist += str(v) |
---|
| 2579 | hist += sep |
---|
| 2580 | hist = hist[:-2] # remove trailing '##' |
---|
| 2581 | self._addhistory(hist) |
---|
| 2582 | |
---|
[710] | 2583 | |
---|
[484] | 2584 | def _zip_mask(self, mask): |
---|
| 2585 | mask = list(mask) |
---|
| 2586 | i = 0 |
---|
| 2587 | segments = [] |
---|
| 2588 | while mask[i:].count(1): |
---|
| 2589 | i += mask[i:].index(1) |
---|
| 2590 | if mask[i:].count(0): |
---|
| 2591 | j = i + mask[i:].index(0) |
---|
| 2592 | else: |
---|
[710] | 2593 | j = len(mask) |
---|
[1118] | 2594 | segments.append([i, j]) |
---|
[710] | 2595 | i = j |
---|
[484] | 2596 | return segments |
---|
[714] | 2597 | |
---|
[626] | 2598 | def _get_ordinate_label(self): |
---|
| 2599 | fu = "("+self.get_fluxunit()+")" |
---|
| 2600 | import re |
---|
| 2601 | lbl = "Intensity" |
---|
[1118] | 2602 | if re.match(".K.", fu): |
---|
[626] | 2603 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 2604 | elif re.match(".Jy.", fu): |
---|
[626] | 2605 | lbl = "Flux density "+ fu |
---|
| 2606 | return lbl |
---|
[710] | 2607 | |
---|
[876] | 2608 | def _check_ifs(self): |
---|
| 2609 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 2610 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 2611 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 2612 | |
---|
[1819] | 2613 | def _fill(self, names, unit, average, getpt, antenna): |
---|
[976] | 2614 | first = True |
---|
| 2615 | fullnames = [] |
---|
| 2616 | for name in names: |
---|
| 2617 | name = os.path.expandvars(name) |
---|
| 2618 | name = os.path.expanduser(name) |
---|
| 2619 | if not os.path.exists(name): |
---|
| 2620 | msg = "File '%s' does not exists" % (name) |
---|
| 2621 | if rcParams['verbose']: |
---|
| 2622 | asaplog.push(msg) |
---|
[1819] | 2623 | print_log( 'ERROR' ) |
---|
[976] | 2624 | return |
---|
| 2625 | raise IOError(msg) |
---|
| 2626 | fullnames.append(name) |
---|
| 2627 | if average: |
---|
| 2628 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 2629 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 2630 | for name in fullnames: |
---|
[1073] | 2631 | tbl = Scantable(stype) |
---|
[1843] | 2632 | r = filler(tbl) |
---|
[1504] | 2633 | rx = rcParams['scantable.reference'] |
---|
[1843] | 2634 | r.setreferenceexpr(rx) |
---|
[976] | 2635 | msg = "Importing %s..." % (name) |
---|
[1118] | 2636 | asaplog.push(msg, False) |
---|
[976] | 2637 | print_log() |
---|
[1843] | 2638 | r.open(name)# antenna, -1, -1, getpt) |
---|
| 2639 | r.fill() |
---|
[976] | 2640 | if average: |
---|
[1118] | 2641 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 2642 | if not first: |
---|
| 2643 | tbl = self._math._merge([self, tbl]) |
---|
| 2644 | Scantable.__init__(self, tbl) |
---|
[1843] | 2645 | r.close() |
---|
[1118] | 2646 | del r, tbl |
---|
[976] | 2647 | first = False |
---|
| 2648 | if unit is not None: |
---|
| 2649 | self.set_fluxunit(unit) |
---|
[1824] | 2650 | if not is_casapy(): |
---|
| 2651 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[976] | 2652 | |
---|
[1402] | 2653 | def __getitem__(self, key): |
---|
| 2654 | if key < 0: |
---|
| 2655 | key += self.nrow() |
---|
| 2656 | if key >= self.nrow(): |
---|
| 2657 | raise IndexError("Row index out of range.") |
---|
| 2658 | return self._getspectrum(key) |
---|
| 2659 | |
---|
| 2660 | def __setitem__(self, key, value): |
---|
| 2661 | if key < 0: |
---|
| 2662 | key += self.nrow() |
---|
| 2663 | if key >= self.nrow(): |
---|
| 2664 | raise IndexError("Row index out of range.") |
---|
| 2665 | if not hasattr(value, "__len__") or \ |
---|
| 2666 | len(value) > self.nchan(self.getif(key)): |
---|
| 2667 | raise ValueError("Spectrum length doesn't match.") |
---|
| 2668 | return self._setspectrum(value, key) |
---|
| 2669 | |
---|
| 2670 | def __len__(self): |
---|
| 2671 | return self.nrow() |
---|
| 2672 | |
---|
| 2673 | def __iter__(self): |
---|
| 2674 | for i in range(len(self)): |
---|
| 2675 | yield self[i] |
---|