[876] | 1 | from asap._asap import Scantable
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[226] | 2 | from asap import rcParams
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[1118] | 3 | from asap import print_log
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| 4 | from asap import asaplog
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[946] | 5 | from asap import selector
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[1153] | 6 | from asap import linecatalog
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[1295] | 7 | from asap import _n_bools, mask_not, mask_and, mask_or
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[102] | 8 |
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[876] | 9 | class scantable(Scantable):
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[102] | 10 | """
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| 11 | The ASAP container for scans
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| 12 | """
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[710] | 13 |
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[1496] | 14 | def __init__(self, filename, average=None, unit=None, getpt=None):
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[102] | 15 | """
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| 16 | Create a scantable from a saved one or make a reference
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| 17 | Parameters:
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[181] | 18 | filename: the name of an asap table on disk
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| 19 | or
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| 20 | the name of a rpfits/sdfits/ms file
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| 21 | (integrations within scans are auto averaged
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| 22 | and the whole file is read)
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| 23 | or
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| 24 | [advanced] a reference to an existing
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[102] | 25 | scantable
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[484] | 26 | average: average all integrations withinb a scan on read.
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| 27 | The default (True) is taken from .asaprc.
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| 28 | unit: brightness unit; must be consistent with K or Jy.
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[340] | 29 | Over-rides the default selected by the reader
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| 30 | (input rpfits/sdfits/ms) or replaces the value
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| 31 | in existing scantables
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[1522] | 32 | getpt: for MeasurementSet input data only:
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| 33 | If True, all pointing data are filled.
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| 34 | The deafult is False, which makes time to load
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| 35 | the MS data faster in some cases.
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[710] | 36 | """
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[976] | 37 | if average is None:
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[710] | 38 | average = rcParams['scantable.autoaverage']
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[1496] | 39 | if getpt is None:
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| 40 | getpt = False
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[1259] | 41 | varlist = vars()
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[876] | 42 | from asap._asap import stmath
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| 43 | self._math = stmath()
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| 44 | if isinstance(filename, Scantable):
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| 45 | Scantable.__init__(self, filename)
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[181] | 46 | else:
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[1603] | 47 | if isinstance(filename, str):# or \
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| 48 | # (isinstance(filename, list) or isinstance(filename, tuple)) \
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| 49 | # and isinstance(filename[-1], str):
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[976] | 50 | import os.path
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| 51 | filename = os.path.expandvars(filename)
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| 52 | filename = os.path.expanduser(filename)
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| 53 | if not os.path.exists(filename):
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| 54 | s = "File '%s' not found." % (filename)
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[718] | 55 | if rcParams['verbose']:
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[976] | 56 | asaplog.push(s)
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| 57 | print asaplog.pop().strip()
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[718] | 58 | return
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[976] | 59 | raise IOError(s)
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[1115] | 60 | if os.path.isdir(filename) \
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[1118] | 61 | and not os.path.exists(filename+'/table.f1'):
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[976] | 62 | # crude check if asap table
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| 63 | if os.path.exists(filename+'/table.info'):
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[1118] | 64 | ondisk = rcParams['scantable.storage'] == 'disk'
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| 65 | Scantable.__init__(self, filename, ondisk)
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[976] | 66 | if unit is not None:
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| 67 | self.set_fluxunit(unit)
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[1496] | 68 | # do not reset to the default freqframe
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| 69 | #self.set_freqframe(rcParams['scantable.freqframe'])
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[718] | 70 | else:
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[1118] | 71 | msg = "The given file '%s'is not a valid " \
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| 72 | "asap table." % (filename)
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[976] | 73 | if rcParams['verbose']:
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| 74 | print msg
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| 75 | return
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| 76 | else:
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| 77 | raise IOError(msg)
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[226] | 78 | else:
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[1496] | 79 | self._fill([filename], unit, average, getpt)
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[1118] | 80 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \
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[976] | 81 | and isinstance(filename[-1], str):
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[1496] | 82 | self._fill(filename, unit, average, getpt)
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[1259] | 83 | self._add_history("scantable", varlist)
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[714] | 84 | print_log()
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[102] | 85 |
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[876] | 86 | def save(self, name=None, format=None, overwrite=False):
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[116] | 87 | """
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[1280] | 88 | Store the scantable on disk. This can be an asap (aips++) Table,
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| 89 | SDFITS or MS2 format.
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[116] | 90 | Parameters:
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[1093] | 91 | name: the name of the outputfile. For format "ASCII"
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| 92 | this is the root file name (data in 'name'.txt
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[497] | 93 | and header in 'name'_header.txt)
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[116] | 94 | format: an optional file format. Default is ASAP.
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[280] | 95 | Allowed are - 'ASAP' (save as ASAP [aips++] Table),
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[194] | 96 | 'SDFITS' (save as SDFITS file)
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[200] | 97 | 'ASCII' (saves as ascii text file)
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[226] | 98 | 'MS2' (saves as an aips++
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| 99 | MeasurementSet V2)
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[1603] | 100 | 'FITS' (save as image FITS - not
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| 101 | readable by class)
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| 102 | 'CLASS' (save as FITS readable by CLASS)
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[411] | 103 | overwrite: If the file should be overwritten if it exists.
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[256] | 104 | The default False is to return with warning
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[411] | 105 | without writing the output. USE WITH CARE.
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[116] | 106 | Example:
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| 107 | scan.save('myscan.asap')
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[1118] | 108 | scan.save('myscan.sdfits', 'SDFITS')
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[116] | 109 | """
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[411] | 110 | from os import path
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[226] | 111 | if format is None: format = rcParams['scantable.save']
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[256] | 112 | suffix = '.'+format.lower()
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[1118] | 113 | if name is None or name == "":
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[256] | 114 | name = 'scantable'+suffix
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[718] | 115 | msg = "No filename given. Using default name %s..." % name
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| 116 | asaplog.push(msg)
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[411] | 117 | name = path.expandvars(name)
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[256] | 118 | if path.isfile(name) or path.isdir(name):
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| 119 | if not overwrite:
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[718] | 120 | msg = "File %s exists." % name
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| 121 | if rcParams['verbose']:
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| 122 | print msg
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| 123 | return
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| 124 | else:
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| 125 | raise IOError(msg)
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[451] | 126 | format2 = format.upper()
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| 127 | if format2 == 'ASAP':
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[116] | 128 | self._save(name)
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| 129 | else:
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[989] | 130 | from asap._asap import stwriter as stw
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[1118] | 131 | writer = stw(format2)
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| 132 | writer.write(self, name)
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[718] | 133 | print_log()
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[116] | 134 | return
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| 135 |
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[102] | 136 | def copy(self):
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| 137 | """
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| 138 | Return a copy of this scantable.
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[1348] | 139 | Note:
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| 140 | This makes a full (deep) copy. scan2 = scan1 makes a reference.
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[102] | 141 | Parameters:
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[113] | 142 | none
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[102] | 143 | Example:
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| 144 | copiedscan = scan.copy()
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| 145 | """
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[876] | 146 | sd = scantable(Scantable._copy(self))
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[113] | 147 | return sd
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| 148 |
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[1093] | 149 | def drop_scan(self, scanid=None):
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| 150 | """
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| 151 | Return a new scantable where the specified scan number(s) has(have)
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| 152 | been dropped.
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| 153 | Parameters:
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| 154 | scanid: a (list of) scan number(s)
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| 155 | """
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| 156 | from asap import _is_sequence_or_number as _is_valid
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| 157 | from asap import _to_list
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| 158 | from asap import unique
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| 159 | if not _is_valid(scanid):
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| 160 | if rcParams['verbose']:
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| 161 | print "Please specify a scanno to drop from the scantable"
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| 162 | return
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| 163 | else:
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| 164 | raise RuntimeError("No scan given")
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| 165 | try:
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| 166 | scanid = _to_list(scanid)
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| 167 | allscans = unique([ self.getscan(i) for i in range(self.nrow())])
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| 168 | for sid in scanid: allscans.remove(sid)
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[1118] | 169 | if len(allscans) == 0:
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| 170 | raise ValueError("Can't remove all scans")
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[1093] | 171 | except ValueError:
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| 172 | if rcParams['verbose']:
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| 173 | print "Couldn't find any match."
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| 174 | return
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| 175 | else: raise
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| 176 | try:
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| 177 | bsel = self.get_selection()
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| 178 | sel = selector()
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| 179 | sel.set_scans(allscans)
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| 180 | self.set_selection(bsel+sel)
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| 181 | scopy = self._copy()
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| 182 | self.set_selection(bsel)
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| 183 | return scantable(scopy)
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| 184 | except RuntimeError:
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[1118] | 185 | if rcParams['verbose']:
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| 186 | print "Couldn't find any match."
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| 187 | else:
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| 188 | raise
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[1093] | 189 |
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| 190 |
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[102] | 191 | def get_scan(self, scanid=None):
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| 192 | """
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| 193 | Return a specific scan (by scanno) or collection of scans (by
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| 194 | source name) in a new scantable.
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[1348] | 195 | Note:
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| 196 | See scantable.drop_scan() for the inverse operation.
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[102] | 197 | Parameters:
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[513] | 198 | scanid: a (list of) scanno or a source name, unix-style
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| 199 | patterns are accepted for source name matching, e.g.
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| 200 | '*_R' gets all 'ref scans
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[102] | 201 | Example:
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[513] | 202 | # get all scans containing the source '323p459'
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| 203 | newscan = scan.get_scan('323p459')
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| 204 | # get all 'off' scans
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| 205 | refscans = scan.get_scan('*_R')
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| 206 | # get a susbset of scans by scanno (as listed in scan.summary())
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[1118] | 207 | newscan = scan.get_scan([0, 2, 7, 10])
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[102] | 208 | """
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| 209 | if scanid is None:
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[718] | 210 | if rcParams['verbose']:
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[1118] | 211 | print "Please specify a scan no or name to " \
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| 212 | "retrieve from the scantable"
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[718] | 213 | return
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| 214 | else:
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| 215 | raise RuntimeError("No scan given")
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| 216 |
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[102] | 217 | try:
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[946] | 218 | bsel = self.get_selection()
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| 219 | sel = selector()
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[102] | 220 | if type(scanid) is str:
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[946] | 221 | sel.set_name(scanid)
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| 222 | self.set_selection(bsel+sel)
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[876] | 223 | scopy = self._copy()
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[946] | 224 | self.set_selection(bsel)
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[876] | 225 | return scantable(scopy)
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[102] | 226 | elif type(scanid) is int:
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[946] | 227 | sel.set_scans([scanid])
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| 228 | self.set_selection(bsel+sel)
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[876] | 229 | scopy = self._copy()
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[946] | 230 | self.set_selection(bsel)
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[876] | 231 | return scantable(scopy)
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[381] | 232 | elif type(scanid) is list:
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[946] | 233 | sel.set_scans(scanid)
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| 234 | self.set_selection(sel)
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[876] | 235 | scopy = self._copy()
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[946] | 236 | self.set_selection(bsel)
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[876] | 237 | return scantable(scopy)
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[381] | 238 | else:
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[718] | 239 | msg = "Illegal scanid type, use 'int' or 'list' if ints."
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| 240 | if rcParams['verbose']:
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| 241 | print msg
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| 242 | else:
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| 243 | raise TypeError(msg)
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[102] | 244 | except RuntimeError:
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[718] | 245 | if rcParams['verbose']: print "Couldn't find any match."
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| 246 | else: raise
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[102] | 247 |
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| 248 | def __str__(self):
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[1118] | 249 | return Scantable._summary(self, True)
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[102] | 250 |
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[976] | 251 | def summary(self, filename=None):
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[102] | 252 | """
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| 253 | Print a summary of the contents of this scantable.
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| 254 | Parameters:
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| 255 | filename: the name of a file to write the putput to
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| 256 | Default - no file output
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[381] | 257 | verbose: print extra info such as the frequency table
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| 258 | The default (False) is taken from .asaprc
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[102] | 259 | """
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[976] | 260 | info = Scantable._summary(self, True)
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| 261 | #if verbose is None: verbose = rcParams['scantable.verbosesummary']
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[102] | 262 | if filename is not None:
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[256] | 263 | if filename is "":
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| 264 | filename = 'scantable_summary.txt'
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[415] | 265 | from os.path import expandvars, isdir
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[411] | 266 | filename = expandvars(filename)
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[415] | 267 | if not isdir(filename):
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[413] | 268 | data = open(filename, 'w')
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| 269 | data.write(info)
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| 270 | data.close()
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| 271 | else:
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[718] | 272 | msg = "Illegal file name '%s'." % (filename)
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| 273 | if rcParams['verbose']:
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| 274 | print msg
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| 275 | else:
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| 276 | raise IOError(msg)
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| 277 | if rcParams['verbose']:
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[794] | 278 | try:
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| 279 | from IPython.genutils import page as pager
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| 280 | except ImportError:
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| 281 | from pydoc import pager
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| 282 | pager(info)
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[718] | 283 | else:
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| 284 | return info
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[710] | 285 |
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[1603] | 286 | def get_spectrum(self, rowno):
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| 287 | """Return the spectrum for the current row in the scantable as a list.
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| 288 | Parameters:
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| 289 | rowno: the row number to retrieve the spectrum from
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| 290 | """
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| 291 | return self._getspectrum(rowno)
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[946] | 292 |
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[1603] | 293 | def get_mask(self, rowno):
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| 294 | """Return the mask for the current row in the scantable as a list.
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| 295 | Parameters:
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| 296 | rowno: the row number to retrieve the mask from
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| 297 | """
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| 298 | return self._getmask(rowno)
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| 299 |
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| 300 | def set_spectrum(self, spec, rowno):
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| 301 | """Return the spectrum for the current row in the scantable as a list.
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| 302 | Parameters:
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| 303 | spec: the spectrum
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| 304 | rowno: the row number to set the spectrum for
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| 305 | """
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| 306 | assert(len(spec) == self.nchan())
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| 307 | return self._setspectrum(spec, rowno)
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| 308 |
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[946] | 309 | def get_selection(self):
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| 310 | """
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[1005] | 311 | Get the selection object currently set on this scantable.
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| 312 | Parameters:
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| 313 | none
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| 314 | Example:
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| 315 | sel = scan.get_selection()
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| 316 | sel.set_ifs(0) # select IF 0
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| 317 | scan.set_selection(sel) # apply modified selection
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[946] | 318 | """
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| 319 | return selector(self._getselection())
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| 320 |
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[1005] | 321 | def set_selection(self, selection=selector()):
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[946] | 322 | """
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[1005] | 323 | Select a subset of the data. All following operations on this scantable
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| 324 | are only applied to thi selection.
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| 325 | Parameters:
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| 326 | selection: a selector object (default unset the selection)
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| 327 | Examples:
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| 328 | sel = selector() # create a selection object
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[1118] | 329 | self.set_scans([0, 3]) # select SCANNO 0 and 3
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[1005] | 330 | scan.set_selection(sel) # set the selection
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| 331 | scan.summary() # will only print summary of scanno 0 an 3
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| 332 | scan.set_selection() # unset the selection
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[946] | 333 | """
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| 334 | self._setselection(selection)
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| 335 |
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[1446] | 336 | def get_row(self, row=0, insitu=None):
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| 337 | """
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| 338 | Select a row in the scantable.
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| 339 | Return a scantable with single row.
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| 340 | Parameters:
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| 341 | row: row no of integration, default is 0.
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| 342 | insitu: if False a new scantable is returned.
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| 343 | Otherwise, the scaling is done in-situ
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| 344 | The default is taken from .asaprc (False)
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| 345 | """
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| 346 | if insitu is None: insitu = rcParams['insitu']
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| 347 | if not insitu:
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| 348 | workscan = self.copy()
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| 349 | else:
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| 350 | workscan = self
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| 351 | # Select a row
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| 352 | sel=selector()
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| 353 | sel.set_scans([workscan.getscan(row)])
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| 354 | sel.set_cycles([workscan.getcycle(row)])
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| 355 | sel.set_beams([workscan.getbeam(row)])
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| 356 | sel.set_ifs([workscan.getif(row)])
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| 357 | sel.set_polarisations([workscan.getpol(row)])
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| 358 | sel.set_name(workscan._getsourcename(row))
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| 359 | workscan.set_selection(sel)
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| 360 | if not workscan.nrow() == 1:
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| 361 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow())
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| 362 | raise RuntimeError(msg)
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| 363 | del sel
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| 364 | if insitu:
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| 365 | self._assign(workscan)
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| 366 | else:
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| 367 | return workscan
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| 368 |
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[876] | 369 | def stats(self, stat='stddev', mask=None):
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[102] | 370 | """
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[135] | 371 | Determine the specified statistic of the current beam/if/pol
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[102] | 372 | Takes a 'mask' as an optional parameter to specify which
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| 373 | channels should be excluded.
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| 374 | Parameters:
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[1517] | 375 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum',
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[1515] | 376 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median'
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[135] | 377 | mask: an optional mask specifying where the statistic
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[102] | 378 | should be determined.
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| 379 | Example:
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[113] | 380 | scan.set_unit('channel')
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[1118] | 381 | msk = scan.create_mask([100, 200], [500, 600])
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[135] | 382 | scan.stats(stat='mean', mask=m)
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[102] | 383 | """
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| 384 | if mask == None:
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[876] | 385 | mask = []
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[1118] | 386 | axes = ['Beam', 'IF', 'Pol', 'Time']
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[876] | 387 | if not self._check_ifs():
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[1118] | 388 | raise ValueError("Cannot apply mask as the IFs have different "
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| 389 | "number of channels. Please use setselection() "
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| 390 | "to select individual IFs")
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[1530] | 391 | rtnabc = False
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| 392 | if stat.lower().endswith('_abc'): rtnabc = True
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| 393 | getchan = False
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| 394 | if stat.lower().startswith('min') or stat.lower().startswith('max'):
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[1517] | 395 | chan = self._math._minmaxchan(self, mask, stat)
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| 396 | getchan = True
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[1515] | 397 | statvals = []
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[1530] | 398 | if not rtnabc: statvals = self._math._stats(self, mask, stat)
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| 399 |
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[876] | 400 | out = ''
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| 401 | axes = []
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| 402 | for i in range(self.nrow()):
|
---|
| 403 | axis = []
|
---|
| 404 | axis.append(self.getscan(i))
|
---|
| 405 | axis.append(self.getbeam(i))
|
---|
| 406 | axis.append(self.getif(i))
|
---|
| 407 | axis.append(self.getpol(i))
|
---|
| 408 | axis.append(self.getcycle(i))
|
---|
| 409 | axes.append(axis)
|
---|
| 410 | tm = self._gettime(i)
|
---|
| 411 | src = self._getsourcename(i)
|
---|
[1530] | 412 | refstr = ''
|
---|
| 413 | statunit= ''
|
---|
[1517] | 414 | if getchan:
|
---|
| 415 | qx, qy = self.chan2data(rowno=i, chan=chan[i])
|
---|
[1530] | 416 | if rtnabc:
|
---|
| 417 | statvals.append(qx['value'])
|
---|
| 418 | refstr = '(value: %3.3f' % (qy['value'])+' ['+qy['unit']+'])'
|
---|
| 419 | statunit= '['+qx['unit']+']'
|
---|
| 420 | else:
|
---|
| 421 | refstr = '(@ %3.3f' % (qx['value'])+' ['+qx['unit']+'])'
|
---|
| 422 | #statunit= ' ['+qy['unit']+']'
|
---|
[876] | 423 | out += 'Scan[%d] (%s) ' % (axis[0], src)
|
---|
| 424 | out += 'Time[%s]:\n' % (tm)
|
---|
| 425 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
|
---|
| 426 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
|
---|
| 427 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
|
---|
[1530] | 428 | out += '= %3.3f ' % (statvals[i]) +refstr+'\n'
|
---|
[876] | 429 | out += "--------------------------------------------------\n"
|
---|
[256] | 430 |
|
---|
[876] | 431 | if rcParams['verbose']:
|
---|
| 432 | print "--------------------------------------------------"
|
---|
[1530] | 433 | print " ", stat, statunit
|
---|
[876] | 434 | print "--------------------------------------------------"
|
---|
| 435 | print out
|
---|
[1295] | 436 | #else:
|
---|
| 437 | #retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'],
|
---|
| 438 | # 'axes' : axes,
|
---|
| 439 | # 'data': statvals}
|
---|
| 440 | return statvals
|
---|
[102] | 441 |
|
---|
[1517] | 442 | def chan2data(self, rowno=0, chan=0):
|
---|
[1515] | 443 | """
|
---|
[1517] | 444 | Returns channel/frequency/velocity and spectral value
|
---|
[1515] | 445 | at an arbitrary row and channel in the scantable.
|
---|
| 446 | Parameters:
|
---|
| 447 | rowno: a row number in the scantable. Default is the
|
---|
| 448 | first row, i.e. rowno=0
|
---|
[1517] | 449 | chan: a channel in the scantable. Default is the first
|
---|
[1515] | 450 | channel, i.e. pos=0
|
---|
| 451 | """
|
---|
[1517] | 452 | if isinstance(rowno, int) and isinstance(chan, int):
|
---|
[1530] | 453 | qx = {'unit': self.get_unit(),
|
---|
| 454 | 'value': self._getabcissa(rowno)[chan]}
|
---|
[1517] | 455 | qy = {'unit': self.get_fluxunit(),
|
---|
| 456 | 'value': self._getspectrum(rowno)[chan]}
|
---|
| 457 | return qx, qy
|
---|
[1515] | 458 |
|
---|
[1118] | 459 | def stddev(self, mask=None):
|
---|
[135] | 460 | """
|
---|
| 461 | Determine the standard deviation of the current beam/if/pol
|
---|
| 462 | Takes a 'mask' as an optional parameter to specify which
|
---|
| 463 | channels should be excluded.
|
---|
| 464 | Parameters:
|
---|
| 465 | mask: an optional mask specifying where the standard
|
---|
| 466 | deviation should be determined.
|
---|
| 467 |
|
---|
| 468 | Example:
|
---|
| 469 | scan.set_unit('channel')
|
---|
[1118] | 470 | msk = scan.create_mask([100, 200], [500, 600])
|
---|
[135] | 471 | scan.stddev(mask=m)
|
---|
| 472 | """
|
---|
[1118] | 473 | return self.stats(stat='stddev', mask=mask);
|
---|
[135] | 474 |
|
---|
[1003] | 475 |
|
---|
[1259] | 476 | def get_column_names(self):
|
---|
[1003] | 477 | """
|
---|
| 478 | Return a list of column names, which can be used for selection.
|
---|
| 479 | """
|
---|
[1259] | 480 | return list(Scantable.get_column_names(self))
|
---|
[1003] | 481 |
|
---|
[876] | 482 | def get_tsys(self):
|
---|
[113] | 483 | """
|
---|
| 484 | Return the System temperatures.
|
---|
| 485 | Returns:
|
---|
[876] | 486 | a list of Tsys values for the current selection
|
---|
[113] | 487 | """
|
---|
[256] | 488 |
|
---|
[876] | 489 | return self._row_callback(self._gettsys, "Tsys")
|
---|
[256] | 490 |
|
---|
[876] | 491 | def _row_callback(self, callback, label):
|
---|
| 492 | axes = []
|
---|
[1118] | 493 | axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno']
|
---|
[876] | 494 | out = ""
|
---|
[1118] | 495 | outvec = []
|
---|
[876] | 496 | for i in range(self.nrow()):
|
---|
| 497 | axis = []
|
---|
| 498 | axis.append(self.getscan(i))
|
---|
| 499 | axis.append(self.getbeam(i))
|
---|
| 500 | axis.append(self.getif(i))
|
---|
| 501 | axis.append(self.getpol(i))
|
---|
| 502 | axis.append(self.getcycle(i))
|
---|
| 503 | axes.append(axis)
|
---|
| 504 | tm = self._gettime(i)
|
---|
| 505 | src = self._getsourcename(i)
|
---|
| 506 | out += 'Scan[%d] (%s) ' % (axis[0], src)
|
---|
| 507 | out += 'Time[%s]:\n' % (tm)
|
---|
| 508 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1])
|
---|
| 509 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2])
|
---|
| 510 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3])
|
---|
| 511 | outvec.append(callback(i))
|
---|
| 512 | out += '= %3.3f\n' % (outvec[i])
|
---|
| 513 | out += "--------------------------------------------------\n"
|
---|
| 514 | if rcParams['verbose']:
|
---|
| 515 | print "--------------------------------------------------"
|
---|
| 516 | print " %s" % (label)
|
---|
| 517 | print "--------------------------------------------------"
|
---|
| 518 | print out
|
---|
[1175] | 519 | # disabled because the vector seems more useful
|
---|
| 520 | #retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec}
|
---|
| 521 | return outvec
|
---|
[256] | 522 |
|
---|
[1070] | 523 | def _get_column(self, callback, row=-1):
|
---|
| 524 | """
|
---|
| 525 | """
|
---|
| 526 | if row == -1:
|
---|
| 527 | return [callback(i) for i in range(self.nrow())]
|
---|
| 528 | else:
|
---|
| 529 | if 0 <= row < self.nrow():
|
---|
| 530 | return callback(row)
|
---|
[256] | 531 |
|
---|
[1070] | 532 |
|
---|
[1348] | 533 | def get_time(self, row=-1, asdatetime=False):
|
---|
[113] | 534 | """
|
---|
| 535 | Get a list of time stamps for the observations.
|
---|
[1348] | 536 | Return a datetime object for each integration time stamp in the scantable.
|
---|
[113] | 537 | Parameters:
|
---|
[1348] | 538 | row: row no of integration. Default -1 return all rows
|
---|
| 539 | asdatetime: return values as datetime objects rather than strings
|
---|
[113] | 540 | Example:
|
---|
| 541 | none
|
---|
| 542 | """
|
---|
[1175] | 543 | from time import strptime
|
---|
| 544 | from datetime import datetime
|
---|
[1457] | 545 | times = self._get_column(self._gettime, row)
|
---|
[1348] | 546 | if not asdatetime:
|
---|
[1603] | 547 | return times
|
---|
[1175] | 548 | format = "%Y/%m/%d/%H:%M:%S"
|
---|
| 549 | if isinstance(times, list):
|
---|
| 550 | return [datetime(*strptime(i, format)[:6]) for i in times]
|
---|
| 551 | else:
|
---|
| 552 | return datetime(*strptime(times, format)[:6])
|
---|
[102] | 553 |
|
---|
[1348] | 554 |
|
---|
| 555 | def get_inttime(self, row=-1):
|
---|
| 556 | """
|
---|
| 557 | Get a list of integration times for the observations.
|
---|
| 558 | Return a time in seconds for each integration in the scantable.
|
---|
| 559 | Parameters:
|
---|
| 560 | row: row no of integration. Default -1 return all rows.
|
---|
| 561 | Example:
|
---|
| 562 | none
|
---|
| 563 | """
|
---|
| 564 | return self._get_column(self._getinttime, row)
|
---|
| 565 |
|
---|
| 566 |
|
---|
[714] | 567 | def get_sourcename(self, row=-1):
|
---|
| 568 | """
|
---|
[794] | 569 | Get a list source names for the observations.
|
---|
[714] | 570 | Return a string for each integration in the scantable.
|
---|
| 571 | Parameters:
|
---|
[1348] | 572 | row: row no of integration. Default -1 return all rows.
|
---|
[714] | 573 | Example:
|
---|
| 574 | none
|
---|
| 575 | """
|
---|
[1070] | 576 | return self._get_column(self._getsourcename, row)
|
---|
[714] | 577 |
|
---|
[794] | 578 | def get_elevation(self, row=-1):
|
---|
| 579 | """
|
---|
| 580 | Get a list of elevations for the observations.
|
---|
| 581 | Return a float for each integration in the scantable.
|
---|
| 582 | Parameters:
|
---|
[1348] | 583 | row: row no of integration. Default -1 return all rows.
|
---|
[794] | 584 | Example:
|
---|
| 585 | none
|
---|
| 586 | """
|
---|
[1070] | 587 | return self._get_column(self._getelevation, row)
|
---|
[794] | 588 |
|
---|
| 589 | def get_azimuth(self, row=-1):
|
---|
| 590 | """
|
---|
| 591 | Get a list of azimuths for the observations.
|
---|
| 592 | Return a float for each integration in the scantable.
|
---|
| 593 | Parameters:
|
---|
[1348] | 594 | row: row no of integration. Default -1 return all rows.
|
---|
[794] | 595 | Example:
|
---|
| 596 | none
|
---|
| 597 | """
|
---|
[1070] | 598 | return self._get_column(self._getazimuth, row)
|
---|
[794] | 599 |
|
---|
| 600 | def get_parangle(self, row=-1):
|
---|
| 601 | """
|
---|
| 602 | Get a list of parallactic angles for the observations.
|
---|
| 603 | Return a float for each integration in the scantable.
|
---|
| 604 | Parameters:
|
---|
[1348] | 605 | row: row no of integration. Default -1 return all rows.
|
---|
[794] | 606 | Example:
|
---|
| 607 | none
|
---|
| 608 | """
|
---|
[1070] | 609 | return self._get_column(self._getparangle, row)
|
---|
[794] | 610 |
|
---|
[1070] | 611 | def get_direction(self, row=-1):
|
---|
| 612 | """
|
---|
| 613 | Get a list of Positions on the sky (direction) for the observations.
|
---|
| 614 | Return a float for each integration in the scantable.
|
---|
| 615 | Parameters:
|
---|
| 616 | row: row no of integration. Default -1 return all rows
|
---|
| 617 | Example:
|
---|
| 618 | none
|
---|
| 619 | """
|
---|
| 620 | return self._get_column(self._getdirection, row)
|
---|
| 621 |
|
---|
[1389] | 622 | def get_directionval(self, row=-1):
|
---|
| 623 | """
|
---|
| 624 | Get a list of Positions on the sky (direction) for the observations.
|
---|
| 625 | Return a float for each integration in the scantable.
|
---|
| 626 | Parameters:
|
---|
| 627 | row: row no of integration. Default -1 return all rows
|
---|
| 628 | Example:
|
---|
| 629 | none
|
---|
| 630 | """
|
---|
| 631 | return self._get_column(self._getdirectionvec, row)
|
---|
| 632 |
|
---|
[102] | 633 | def set_unit(self, unit='channel'):
|
---|
| 634 | """
|
---|
| 635 | Set the unit for all following operations on this scantable
|
---|
| 636 | Parameters:
|
---|
| 637 | unit: optional unit, default is 'channel'
|
---|
[1118] | 638 | one of '*Hz', 'km/s', 'channel', ''
|
---|
[102] | 639 | """
|
---|
[484] | 640 | varlist = vars()
|
---|
[1118] | 641 | if unit in ['', 'pixel', 'channel']:
|
---|
[113] | 642 | unit = ''
|
---|
| 643 | inf = list(self._getcoordinfo())
|
---|
| 644 | inf[0] = unit
|
---|
| 645 | self._setcoordinfo(inf)
|
---|
[1118] | 646 | self._add_history("set_unit", varlist)
|
---|
[113] | 647 |
|
---|
[484] | 648 | def set_instrument(self, instr):
|
---|
[358] | 649 | """
|
---|
[1348] | 650 | Set the instrument for subsequent processing.
|
---|
[358] | 651 | Parameters:
|
---|
[710] | 652 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA',
|
---|
[407] | 653 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART'
|
---|
[358] | 654 | """
|
---|
| 655 | self._setInstrument(instr)
|
---|
[1118] | 656 | self._add_history("set_instument", vars())
|
---|
[718] | 657 | print_log()
|
---|
[358] | 658 |
|
---|
[1190] | 659 | def set_feedtype(self, feedtype):
|
---|
| 660 | """
|
---|
| 661 | Overwrite the feed type, which might not be set correctly.
|
---|
| 662 | Parameters:
|
---|
| 663 | feedtype: 'linear' or 'circular'
|
---|
| 664 | """
|
---|
| 665 | self._setfeedtype(feedtype)
|
---|
| 666 | self._add_history("set_feedtype", vars())
|
---|
| 667 | print_log()
|
---|
| 668 |
|
---|
[276] | 669 | def set_doppler(self, doppler='RADIO'):
|
---|
| 670 | """
|
---|
| 671 | Set the doppler for all following operations on this scantable.
|
---|
| 672 | Parameters:
|
---|
| 673 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
|
---|
| 674 | """
|
---|
[484] | 675 | varlist = vars()
|
---|
[276] | 676 | inf = list(self._getcoordinfo())
|
---|
| 677 | inf[2] = doppler
|
---|
| 678 | self._setcoordinfo(inf)
|
---|
[1118] | 679 | self._add_history("set_doppler", vars())
|
---|
[718] | 680 | print_log()
|
---|
[710] | 681 |
|
---|
[226] | 682 | def set_freqframe(self, frame=None):
|
---|
[113] | 683 | """
|
---|
| 684 | Set the frame type of the Spectral Axis.
|
---|
| 685 | Parameters:
|
---|
[591] | 686 | frame: an optional frame type, default 'LSRK'. Valid frames are:
|
---|
[1118] | 687 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY',
|
---|
| 688 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'
|
---|
[113] | 689 | Examples:
|
---|
| 690 | scan.set_freqframe('BARY')
|
---|
| 691 | """
|
---|
[484] | 692 | if frame is None: frame = rcParams['scantable.freqframe']
|
---|
| 693 | varlist = vars()
|
---|
[1118] | 694 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \
|
---|
| 695 | 'GEO', 'GALACTO', 'LGROUP', 'CMB']
|
---|
[591] | 696 |
|
---|
[989] | 697 | if frame in valid:
|
---|
[113] | 698 | inf = list(self._getcoordinfo())
|
---|
| 699 | inf[1] = frame
|
---|
| 700 | self._setcoordinfo(inf)
|
---|
[1118] | 701 | self._add_history("set_freqframe", varlist)
|
---|
[102] | 702 | else:
|
---|
[1118] | 703 | msg = "Please specify a valid freq type. Valid types are:\n", valid
|
---|
[718] | 704 | if rcParams['verbose']:
|
---|
| 705 | print msg
|
---|
| 706 | else:
|
---|
| 707 | raise TypeError(msg)
|
---|
| 708 | print_log()
|
---|
[710] | 709 |
|
---|
[989] | 710 | def set_dirframe(self, frame=""):
|
---|
| 711 | """
|
---|
| 712 | Set the frame type of the Direction on the sky.
|
---|
| 713 | Parameters:
|
---|
| 714 | frame: an optional frame type, default ''. Valid frames are:
|
---|
| 715 | 'J2000', 'B1950', 'GALACTIC'
|
---|
| 716 | Examples:
|
---|
| 717 | scan.set_dirframe('GALACTIC')
|
---|
| 718 | """
|
---|
| 719 | varlist = vars()
|
---|
| 720 | try:
|
---|
| 721 | Scantable.set_dirframe(self, frame)
|
---|
[1118] | 722 | except RuntimeError, msg:
|
---|
[989] | 723 | if rcParams['verbose']:
|
---|
| 724 | print msg
|
---|
| 725 | else:
|
---|
| 726 | raise
|
---|
[1118] | 727 | self._add_history("set_dirframe", varlist)
|
---|
[989] | 728 |
|
---|
[113] | 729 | def get_unit(self):
|
---|
| 730 | """
|
---|
| 731 | Get the default unit set in this scantable
|
---|
| 732 | Returns:
|
---|
| 733 | A unit string
|
---|
| 734 | """
|
---|
| 735 | inf = self._getcoordinfo()
|
---|
| 736 | unit = inf[0]
|
---|
| 737 | if unit == '': unit = 'channel'
|
---|
| 738 | return unit
|
---|
[102] | 739 |
|
---|
[158] | 740 | def get_abcissa(self, rowno=0):
|
---|
[102] | 741 | """
|
---|
[158] | 742 | Get the abcissa in the current coordinate setup for the currently
|
---|
[113] | 743 | selected Beam/IF/Pol
|
---|
| 744 | Parameters:
|
---|
[226] | 745 | rowno: an optional row number in the scantable. Default is the
|
---|
| 746 | first row, i.e. rowno=0
|
---|
[113] | 747 | Returns:
|
---|
[1348] | 748 | The abcissa values and the format string (as a dictionary)
|
---|
[113] | 749 | """
|
---|
[256] | 750 | abc = self._getabcissa(rowno)
|
---|
[710] | 751 | lbl = self._getabcissalabel(rowno)
|
---|
[718] | 752 | print_log()
|
---|
[158] | 753 | return abc, lbl
|
---|
[113] | 754 |
|
---|
[1401] | 755 | def flag(self, mask=None, unflag=False):
|
---|
[1001] | 756 | """
|
---|
| 757 | Flag the selected data using an optional channel mask.
|
---|
| 758 | Parameters:
|
---|
| 759 | mask: an optional channel mask, created with create_mask. Default
|
---|
| 760 | (no mask) is all channels.
|
---|
[1401] | 761 | unflag: if True, unflag the data
|
---|
[1001] | 762 | """
|
---|
| 763 | varlist = vars()
|
---|
[1118] | 764 | if mask is None:
|
---|
| 765 | mask = []
|
---|
[1001] | 766 | try:
|
---|
[1401] | 767 | self._flag(mask, unflag)
|
---|
[1118] | 768 | except RuntimeError, msg:
|
---|
[1001] | 769 | if rcParams['verbose']:
|
---|
| 770 | print msg
|
---|
| 771 | return
|
---|
| 772 | else: raise
|
---|
| 773 | self._add_history("flag", varlist)
|
---|
| 774 |
|
---|
[1203] | 775 | def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None):
|
---|
[1192] | 776 | """
|
---|
| 777 | Flag the data in 'lag' space by providing a frequency to remove.
|
---|
| 778 | Flagged data in the scantable gets set to 0.0 before the fft.
|
---|
| 779 | No taper is applied.
|
---|
| 780 | Parameters:
|
---|
[1348] | 781 | frequency: the frequency (really a period within the bandwidth)
|
---|
| 782 | to remove
|
---|
| 783 | width: the width of the frequency to remove, to remove a
|
---|
[1603] | 784 | range of frequencies around the centre.
|
---|
[1203] | 785 | unit: the frequency unit (default "GHz")
|
---|
| 786 | Notes:
|
---|
[1348] | 787 | It is recommended to flag edges of the band or strong
|
---|
| 788 | signals beforehand.
|
---|
[1192] | 789 | """
|
---|
| 790 | if insitu is None: insitu = rcParams['insitu']
|
---|
| 791 | self._math._setinsitu(insitu)
|
---|
| 792 | varlist = vars()
|
---|
[1370] | 793 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. }
|
---|
[1192] | 794 | if not base.has_key(unit):
|
---|
| 795 | raise ValueError("%s is not a valid unit." % unit)
|
---|
| 796 | try:
|
---|
[1200] | 797 | s = scantable(self._math._lag_flag(self, frequency*base[unit],
|
---|
| 798 | width*base[unit]))
|
---|
[1192] | 799 | except RuntimeError, msg:
|
---|
| 800 | if rcParams['verbose']:
|
---|
| 801 | print msg
|
---|
| 802 | return
|
---|
| 803 | else: raise
|
---|
| 804 | s._add_history("lag_flag", varlist)
|
---|
| 805 | print_log()
|
---|
| 806 | if insitu:
|
---|
| 807 | self._assign(s)
|
---|
| 808 | else:
|
---|
| 809 | return s
|
---|
[1001] | 810 |
|
---|
[1192] | 811 |
|
---|
[113] | 812 | def create_mask(self, *args, **kwargs):
|
---|
| 813 | """
|
---|
[1118] | 814 | Compute and return a mask based on [min, max] windows.
|
---|
[189] | 815 | The specified windows are to be INCLUDED, when the mask is
|
---|
[113] | 816 | applied.
|
---|
[102] | 817 | Parameters:
|
---|
[1118] | 818 | [min, max], [min2, max2], ...
|
---|
[1024] | 819 | Pairs of start/end points (inclusive)specifying the regions
|
---|
[102] | 820 | to be masked
|
---|
[189] | 821 | invert: optional argument. If specified as True,
|
---|
| 822 | return an inverted mask, i.e. the regions
|
---|
| 823 | specified are EXCLUDED
|
---|
[513] | 824 | row: create the mask using the specified row for
|
---|
| 825 | unit conversions, default is row=0
|
---|
| 826 | only necessary if frequency varies over rows.
|
---|
[102] | 827 | Example:
|
---|
[113] | 828 | scan.set_unit('channel')
|
---|
| 829 | a)
|
---|
[1118] | 830 | msk = scan.create_mask([400, 500], [800, 900])
|
---|
[189] | 831 | # masks everything outside 400 and 500
|
---|
[113] | 832 | # and 800 and 900 in the unit 'channel'
|
---|
| 833 |
|
---|
| 834 | b)
|
---|
[1118] | 835 | msk = scan.create_mask([400, 500], [800, 900], invert=True)
|
---|
[189] | 836 | # masks the regions between 400 and 500
|
---|
[113] | 837 | # and 800 and 900 in the unit 'channel'
|
---|
[1024] | 838 | c)
|
---|
| 839 | mask only channel 400
|
---|
[1118] | 840 | msk = scan.create_mask([400, 400])
|
---|
[102] | 841 | """
|
---|
[513] | 842 | row = 0
|
---|
| 843 | if kwargs.has_key("row"):
|
---|
| 844 | row = kwargs.get("row")
|
---|
| 845 | data = self._getabcissa(row)
|
---|
[113] | 846 | u = self._getcoordinfo()[0]
|
---|
[718] | 847 | if rcParams['verbose']:
|
---|
[113] | 848 | if u == "": u = "channel"
|
---|
[718] | 849 | msg = "The current mask window unit is %s" % u
|
---|
[1118] | 850 | i = self._check_ifs()
|
---|
| 851 | if not i:
|
---|
[876] | 852 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
---|
[718] | 853 | asaplog.push(msg)
|
---|
[102] | 854 | n = self.nchan()
|
---|
[1295] | 855 | msk = _n_bools(n, False)
|
---|
[710] | 856 | # test if args is a 'list' or a 'normal *args - UGLY!!!
|
---|
| 857 |
|
---|
[1118] | 858 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \
|
---|
| 859 | and args or args[0]
|
---|
[710] | 860 | for window in ws:
|
---|
[102] | 861 | if (len(window) != 2 or window[0] > window[1] ):
|
---|
[1118] | 862 | raise TypeError("A window needs to be defined as [min, max]")
|
---|
[102] | 863 | for i in range(n):
|
---|
[1024] | 864 | if data[i] >= window[0] and data[i] <= window[1]:
|
---|
[1295] | 865 | msk[i] = True
|
---|
[113] | 866 | if kwargs.has_key('invert'):
|
---|
| 867 | if kwargs.get('invert'):
|
---|
[1295] | 868 | msk = mask_not(msk)
|
---|
[718] | 869 | print_log()
|
---|
[102] | 870 | return msk
|
---|
[710] | 871 |
|
---|
[1446] | 872 | def get_masklist(self, mask=None, row=0):
|
---|
[256] | 873 | """
|
---|
[1446] | 874 | Compute and return a list of mask windows, [min, max].
|
---|
| 875 | Parameters:
|
---|
| 876 | mask: channel mask, created with create_mask.
|
---|
| 877 | row: calcutate the masklist using the specified row
|
---|
| 878 | for unit conversions, default is row=0
|
---|
| 879 | only necessary if frequency varies over rows.
|
---|
| 880 | Returns:
|
---|
| 881 | [min, max], [min2, max2], ...
|
---|
| 882 | Pairs of start/end points (inclusive)specifying
|
---|
| 883 | the masked regions
|
---|
| 884 | """
|
---|
| 885 | if not (isinstance(mask,list) or isinstance(mask, tuple)):
|
---|
| 886 | raise TypeError("The mask should be list or tuple.")
|
---|
| 887 | if len(mask) < 2:
|
---|
| 888 | raise TypeError("The mask elements should be > 1")
|
---|
| 889 | if self.nchan() != len(mask):
|
---|
| 890 | msg = "Number of channels in scantable != number of mask elements"
|
---|
| 891 | raise TypeError(msg)
|
---|
| 892 | data = self._getabcissa(row)
|
---|
| 893 | u = self._getcoordinfo()[0]
|
---|
| 894 | if rcParams['verbose']:
|
---|
| 895 | if u == "": u = "channel"
|
---|
| 896 | msg = "The current mask window unit is %s" % u
|
---|
| 897 | i = self._check_ifs()
|
---|
| 898 | if not i:
|
---|
| 899 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i))
|
---|
| 900 | asaplog.push(msg)
|
---|
| 901 | masklist=[]
|
---|
| 902 | ist, ien = None, None
|
---|
| 903 | ist, ien=self.get_mask_indices(mask)
|
---|
| 904 | if ist is not None and ien is not None:
|
---|
| 905 | for i in xrange(len(ist)):
|
---|
| 906 | range=[data[ist[i]],data[ien[i]]]
|
---|
| 907 | range.sort()
|
---|
| 908 | masklist.append([range[0],range[1]])
|
---|
| 909 | return masklist
|
---|
| 910 |
|
---|
| 911 | def get_mask_indices(self, mask=None):
|
---|
| 912 | """
|
---|
| 913 | Compute and Return lists of mask start indices and mask end indices.
|
---|
| 914 | Parameters:
|
---|
| 915 | mask: channel mask, created with create_mask.
|
---|
| 916 | Returns:
|
---|
| 917 | List of mask start indices and that of mask end indices,
|
---|
| 918 | i.e., [istart1,istart2,....], [iend1,iend2,....].
|
---|
| 919 | """
|
---|
| 920 | if not (isinstance(mask,list) or isinstance(mask, tuple)):
|
---|
| 921 | raise TypeError("The mask should be list or tuple.")
|
---|
| 922 | if len(mask) < 2:
|
---|
| 923 | raise TypeError("The mask elements should be > 1")
|
---|
| 924 | istart=[]
|
---|
| 925 | iend=[]
|
---|
| 926 | if mask[0]: istart.append(0)
|
---|
| 927 | for i in range(len(mask)-1):
|
---|
| 928 | if not mask[i] and mask[i+1]:
|
---|
| 929 | istart.append(i+1)
|
---|
| 930 | elif mask[i] and not mask[i+1]:
|
---|
| 931 | iend.append(i)
|
---|
| 932 | if mask[len(mask)-1]: iend.append(len(mask)-1)
|
---|
| 933 | if len(istart) != len(iend):
|
---|
| 934 | raise RuntimeError("Numbers of mask start != mask end.")
|
---|
| 935 | for i in range(len(istart)):
|
---|
| 936 | if istart[i] > iend[i]:
|
---|
| 937 | raise RuntimeError("Mask start index > mask end index")
|
---|
| 938 | break
|
---|
| 939 | return istart,iend
|
---|
| 940 |
|
---|
| 941 | # def get_restfreqs(self):
|
---|
| 942 | # """
|
---|
| 943 | # Get the restfrequency(s) stored in this scantable.
|
---|
| 944 | # The return value(s) are always of unit 'Hz'
|
---|
| 945 | # Parameters:
|
---|
| 946 | # none
|
---|
| 947 | # Returns:
|
---|
| 948 | # a list of doubles
|
---|
| 949 | # """
|
---|
| 950 | # return list(self._getrestfreqs())
|
---|
| 951 |
|
---|
| 952 | def get_restfreqs(self, ids=None):
|
---|
| 953 | """
|
---|
[256] | 954 | Get the restfrequency(s) stored in this scantable.
|
---|
| 955 | The return value(s) are always of unit 'Hz'
|
---|
| 956 | Parameters:
|
---|
[1446] | 957 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to
|
---|
| 958 | be retrieved
|
---|
[256] | 959 | Returns:
|
---|
[1446] | 960 | dictionary containing ids and a list of doubles for each id
|
---|
[256] | 961 | """
|
---|
[1446] | 962 | if ids is None:
|
---|
| 963 | rfreqs={}
|
---|
| 964 | idlist = self.getmolnos()
|
---|
| 965 | for i in idlist:
|
---|
| 966 | rfreqs[i]=list(self._getrestfreqs(i))
|
---|
| 967 | return rfreqs
|
---|
| 968 | else:
|
---|
| 969 | if type(ids)==list or type(ids)==tuple:
|
---|
| 970 | rfreqs={}
|
---|
| 971 | for i in ids:
|
---|
| 972 | rfreqs[i]=list(self._getrestfreqs(i))
|
---|
| 973 | return rfreqs
|
---|
| 974 | else:
|
---|
| 975 | return list(self._getrestfreqs(ids))
|
---|
| 976 | #return list(self._getrestfreqs(ids))
|
---|
[102] | 977 |
|
---|
[931] | 978 | def set_restfreqs(self, freqs=None, unit='Hz'):
|
---|
| 979 | """
|
---|
[1446] | 980 | ********NEED TO BE UPDATED begin************
|
---|
[931] | 981 | Set or replace the restfrequency specified and
|
---|
| 982 | If the 'freqs' argument holds a scalar,
|
---|
| 983 | then that rest frequency will be applied to all the selected
|
---|
| 984 | data. If the 'freqs' argument holds
|
---|
| 985 | a vector, then it MUST be of equal or smaller length than
|
---|
| 986 | the number of IFs (and the available restfrequencies will be
|
---|
| 987 | replaced by this vector). In this case, *all* data have
|
---|
| 988 | the restfrequency set per IF according
|
---|
| 989 | to the corresponding value you give in the 'freqs' vector.
|
---|
[1118] | 990 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and
|
---|
[931] | 991 | IF 1 gets restfreq 2e9.
|
---|
[1446] | 992 | ********NEED TO BE UPDATED end************
|
---|
[1603] | 993 | You can also specify the frequencies via a linecatalog.
|
---|
[1153] | 994 |
|
---|
[931] | 995 | Parameters:
|
---|
| 996 | freqs: list of rest frequency values or string idenitfiers
|
---|
| 997 | unit: unit for rest frequency (default 'Hz')
|
---|
[402] | 998 |
|
---|
[931] | 999 | Example:
|
---|
[1446] | 1000 | # set the given restfrequency for the all currently selected IFs
|
---|
[931] | 1001 | scan.set_restfreqs(freqs=1.4e9)
|
---|
[1446] | 1002 | # set multiple restfrequencies to all the selected data
|
---|
| 1003 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9])
|
---|
| 1004 | # If the number of IFs in the data is >= 2 the IF0 gets the first
|
---|
| 1005 | # value IF1 the second... NOTE that freqs needs to be
|
---|
| 1006 | # specified in list of list (e.g. [[],[],...] ).
|
---|
| 1007 | scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]])
|
---|
[931] | 1008 | #set the given restfrequency for the whole table (by name)
|
---|
| 1009 | scan.set_restfreqs(freqs="OH1667")
|
---|
[391] | 1010 |
|
---|
[931] | 1011 | Note:
|
---|
| 1012 | To do more sophisticate Restfrequency setting, e.g. on a
|
---|
| 1013 | source and IF basis, use scantable.set_selection() before using
|
---|
| 1014 | this function.
|
---|
| 1015 | # provide your scantable is call scan
|
---|
| 1016 | selection = selector()
|
---|
| 1017 | selection.set_name("ORION*")
|
---|
| 1018 | selection.set_ifs([1])
|
---|
| 1019 | scan.set_selection(selection)
|
---|
| 1020 | scan.set_restfreqs(freqs=86.6e9)
|
---|
| 1021 |
|
---|
| 1022 | """
|
---|
| 1023 | varlist = vars()
|
---|
[1157] | 1024 | from asap import linecatalog
|
---|
| 1025 | # simple value
|
---|
[1118] | 1026 | if isinstance(freqs, int) or isinstance(freqs, float):
|
---|
[1446] | 1027 | # TT mod
|
---|
| 1028 | #self._setrestfreqs(freqs, "",unit)
|
---|
| 1029 | self._setrestfreqs([freqs], [""],unit)
|
---|
[1157] | 1030 | # list of values
|
---|
[1118] | 1031 | elif isinstance(freqs, list) or isinstance(freqs, tuple):
|
---|
[1157] | 1032 | # list values are scalars
|
---|
[1118] | 1033 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float):
|
---|
[1446] | 1034 | self._setrestfreqs(freqs, [""],unit)
|
---|
[1157] | 1035 | # list values are tuples, (value, name)
|
---|
| 1036 | elif isinstance(freqs[-1], dict):
|
---|
[1446] | 1037 | #sel = selector()
|
---|
| 1038 | #savesel = self._getselection()
|
---|
| 1039 | #iflist = self.getifnos()
|
---|
| 1040 | #for i in xrange(len(freqs)):
|
---|
| 1041 | # sel.set_ifs(iflist[i])
|
---|
| 1042 | # self._setselection(sel)
|
---|
| 1043 | # self._setrestfreqs(freqs[i], "",unit)
|
---|
| 1044 | #self._setselection(savesel)
|
---|
| 1045 | self._setrestfreqs(freqs["value"],
|
---|
| 1046 | freqs["name"], "MHz")
|
---|
| 1047 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple):
|
---|
[1157] | 1048 | sel = selector()
|
---|
| 1049 | savesel = self._getselection()
|
---|
[1322] | 1050 | iflist = self.getifnos()
|
---|
[1446] | 1051 | if len(freqs)>len(iflist):
|
---|
| 1052 | raise ValueError("number of elements in list of list exeeds the current IF selections")
|
---|
[1157] | 1053 | for i in xrange(len(freqs)):
|
---|
[1322] | 1054 | sel.set_ifs(iflist[i])
|
---|
[1259] | 1055 | self._setselection(sel)
|
---|
[1157] | 1056 | self._setrestfreqs(freqs[i]["value"],
|
---|
| 1057 | freqs[i]["name"], "MHz")
|
---|
| 1058 | self._setselection(savesel)
|
---|
| 1059 | # freqs are to be taken from a linecatalog
|
---|
[1153] | 1060 | elif isinstance(freqs, linecatalog):
|
---|
| 1061 | sel = selector()
|
---|
| 1062 | savesel = self._getselection()
|
---|
| 1063 | for i in xrange(freqs.nrow()):
|
---|
[1322] | 1064 | sel.set_ifs(iflist[i])
|
---|
[1153] | 1065 | self._setselection(sel)
|
---|
| 1066 | self._setrestfreqs(freqs.get_frequency(i),
|
---|
| 1067 | freqs.get_name(i), "MHz")
|
---|
| 1068 | # ensure that we are not iterating past nIF
|
---|
| 1069 | if i == self.nif()-1: break
|
---|
| 1070 | self._setselection(savesel)
|
---|
[931] | 1071 | else:
|
---|
| 1072 | return
|
---|
| 1073 | self._add_history("set_restfreqs", varlist)
|
---|
| 1074 |
|
---|
[1360] | 1075 | def shift_refpix(self, delta):
|
---|
| 1076 | """
|
---|
| 1077 | Shift the reference pixel of the Spectra Coordinate by an
|
---|
| 1078 | integer amount.
|
---|
| 1079 | Parameters:
|
---|
| 1080 | delta: the amount to shift by
|
---|
| 1081 | Note:
|
---|
| 1082 | Be careful using this with broadband data.
|
---|
| 1083 | """
|
---|
| 1084 | Scantable.shift(self, delta)
|
---|
[931] | 1085 |
|
---|
[1259] | 1086 | def history(self, filename=None):
|
---|
| 1087 | """
|
---|
| 1088 | Print the history. Optionally to a file.
|
---|
[1348] | 1089 | Parameters:
|
---|
| 1090 | filename: The name of the file to save the history to.
|
---|
[1259] | 1091 | """
|
---|
[484] | 1092 | hist = list(self._gethistory())
|
---|
[794] | 1093 | out = "-"*80
|
---|
[484] | 1094 | for h in hist:
|
---|
[489] | 1095 | if h.startswith("---"):
|
---|
[794] | 1096 | out += "\n"+h
|
---|
[489] | 1097 | else:
|
---|
| 1098 | items = h.split("##")
|
---|
| 1099 | date = items[0]
|
---|
| 1100 | func = items[1]
|
---|
| 1101 | items = items[2:]
|
---|
[794] | 1102 | out += "\n"+date+"\n"
|
---|
| 1103 | out += "Function: %s\n Parameters:" % (func)
|
---|
[489] | 1104 | for i in items:
|
---|
| 1105 | s = i.split("=")
|
---|
[1118] | 1106 | out += "\n %s = %s" % (s[0], s[1])
|
---|
[794] | 1107 | out += "\n"+"-"*80
|
---|
[1259] | 1108 | if filename is not None:
|
---|
| 1109 | if filename is "":
|
---|
| 1110 | filename = 'scantable_history.txt'
|
---|
| 1111 | import os
|
---|
| 1112 | filename = os.path.expandvars(os.path.expanduser(filename))
|
---|
| 1113 | if not os.path.isdir(filename):
|
---|
| 1114 | data = open(filename, 'w')
|
---|
| 1115 | data.write(out)
|
---|
| 1116 | data.close()
|
---|
| 1117 | else:
|
---|
| 1118 | msg = "Illegal file name '%s'." % (filename)
|
---|
| 1119 | if rcParams['verbose']:
|
---|
| 1120 | print msg
|
---|
| 1121 | else:
|
---|
| 1122 | raise IOError(msg)
|
---|
| 1123 | if rcParams['verbose']:
|
---|
| 1124 | try:
|
---|
| 1125 | from IPython.genutils import page as pager
|
---|
| 1126 | except ImportError:
|
---|
| 1127 | from pydoc import pager
|
---|
| 1128 | pager(out)
|
---|
| 1129 | else:
|
---|
| 1130 | return out
|
---|
[484] | 1131 | return
|
---|
[513] | 1132 | #
|
---|
| 1133 | # Maths business
|
---|
| 1134 | #
|
---|
| 1135 |
|
---|
[931] | 1136 | def average_time(self, mask=None, scanav=False, weight='tint', align=False):
|
---|
[513] | 1137 | """
|
---|
[1070] | 1138 | Return the (time) weighted average of a scan.
|
---|
[513] | 1139 | Note:
|
---|
[1070] | 1140 | in channels only - align if necessary
|
---|
[513] | 1141 | Parameters:
|
---|
| 1142 | mask: an optional mask (only used for 'var' and 'tsys'
|
---|
| 1143 | weighting)
|
---|
[558] | 1144 | scanav: True averages each scan separately
|
---|
| 1145 | False (default) averages all scans together,
|
---|
[1099] | 1146 | weight: Weighting scheme.
|
---|
| 1147 | 'none' (mean no weight)
|
---|
| 1148 | 'var' (1/var(spec) weighted)
|
---|
| 1149 | 'tsys' (1/Tsys**2 weighted)
|
---|
| 1150 | 'tint' (integration time weighted)
|
---|
| 1151 | 'tintsys' (Tint/Tsys**2)
|
---|
| 1152 | 'median' ( median averaging)
|
---|
[535] | 1153 | The default is 'tint'
|
---|
[931] | 1154 | align: align the spectra in velocity before averaging. It takes
|
---|
| 1155 | the time of the first spectrum as reference time.
|
---|
[513] | 1156 | Example:
|
---|
| 1157 | # time average the scantable without using a mask
|
---|
[710] | 1158 | newscan = scan.average_time()
|
---|
[513] | 1159 | """
|
---|
| 1160 | varlist = vars()
|
---|
[976] | 1161 | if weight is None: weight = 'TINT'
|
---|
[513] | 1162 | if mask is None: mask = ()
|
---|
[1099] | 1163 | if scanav: scanav = "SCAN"
|
---|
| 1164 | else: scanav = "NONE"
|
---|
[1118] | 1165 | scan = (self, )
|
---|
[989] | 1166 | try:
|
---|
[1118] | 1167 | if align:
|
---|
| 1168 | scan = (self.freq_align(insitu=False), )
|
---|
| 1169 | s = None
|
---|
| 1170 | if weight.upper() == 'MEDIAN':
|
---|
| 1171 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN',
|
---|
| 1172 | scanav))
|
---|
| 1173 | else:
|
---|
| 1174 | s = scantable(self._math._average(scan, mask, weight.upper(),
|
---|
| 1175 | scanav))
|
---|
| 1176 | except RuntimeError, msg:
|
---|
[989] | 1177 | if rcParams['verbose']:
|
---|
| 1178 | print msg
|
---|
| 1179 | return
|
---|
| 1180 | else: raise
|
---|
[1099] | 1181 | s._add_history("average_time", varlist)
|
---|
[718] | 1182 | print_log()
|
---|
[513] | 1183 | return s
|
---|
[710] | 1184 |
|
---|
[876] | 1185 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None):
|
---|
[513] | 1186 | """
|
---|
| 1187 | Return a scan where all spectra are converted to either
|
---|
| 1188 | Jansky or Kelvin depending upon the flux units of the scan table.
|
---|
| 1189 | By default the function tries to look the values up internally.
|
---|
| 1190 | If it can't find them (or if you want to over-ride), you must
|
---|
| 1191 | specify EITHER jyperk OR eta (and D which it will try to look up
|
---|
| 1192 | also if you don't set it). jyperk takes precedence if you set both.
|
---|
| 1193 | Parameters:
|
---|
| 1194 | jyperk: the Jy / K conversion factor
|
---|
| 1195 | eta: the aperture efficiency
|
---|
| 1196 | d: the geomtric diameter (metres)
|
---|
| 1197 | insitu: if False a new scantable is returned.
|
---|
| 1198 | Otherwise, the scaling is done in-situ
|
---|
| 1199 | The default is taken from .asaprc (False)
|
---|
| 1200 | """
|
---|
| 1201 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1202 | self._math._setinsitu(insitu)
|
---|
[513] | 1203 | varlist = vars()
|
---|
| 1204 | if jyperk is None: jyperk = -1.0
|
---|
| 1205 | if d is None: d = -1.0
|
---|
| 1206 | if eta is None: eta = -1.0
|
---|
[876] | 1207 | s = scantable(self._math._convertflux(self, d, eta, jyperk))
|
---|
| 1208 | s._add_history("convert_flux", varlist)
|
---|
| 1209 | print_log()
|
---|
| 1210 | if insitu: self._assign(s)
|
---|
| 1211 | else: return s
|
---|
[513] | 1212 |
|
---|
[876] | 1213 | def gain_el(self, poly=None, filename="", method="linear", insitu=None):
|
---|
[513] | 1214 | """
|
---|
| 1215 | Return a scan after applying a gain-elevation correction.
|
---|
| 1216 | The correction can be made via either a polynomial or a
|
---|
| 1217 | table-based interpolation (and extrapolation if necessary).
|
---|
| 1218 | You specify polynomial coefficients, an ascii table or neither.
|
---|
| 1219 | If you specify neither, then a polynomial correction will be made
|
---|
| 1220 | with built in coefficients known for certain telescopes (an error
|
---|
| 1221 | will occur if the instrument is not known).
|
---|
| 1222 | The data and Tsys are *divided* by the scaling factors.
|
---|
| 1223 | Parameters:
|
---|
| 1224 | poly: Polynomial coefficients (default None) to compute a
|
---|
| 1225 | gain-elevation correction as a function of
|
---|
| 1226 | elevation (in degrees).
|
---|
| 1227 | filename: The name of an ascii file holding correction factors.
|
---|
| 1228 | The first row of the ascii file must give the column
|
---|
| 1229 | names and these MUST include columns
|
---|
| 1230 | "ELEVATION" (degrees) and "FACTOR" (multiply data
|
---|
| 1231 | by this) somewhere.
|
---|
| 1232 | The second row must give the data type of the
|
---|
| 1233 | column. Use 'R' for Real and 'I' for Integer.
|
---|
| 1234 | An example file would be
|
---|
| 1235 | (actual factors are arbitrary) :
|
---|
| 1236 |
|
---|
| 1237 | TIME ELEVATION FACTOR
|
---|
| 1238 | R R R
|
---|
| 1239 | 0.1 0 0.8
|
---|
| 1240 | 0.2 20 0.85
|
---|
| 1241 | 0.3 40 0.9
|
---|
| 1242 | 0.4 60 0.85
|
---|
| 1243 | 0.5 80 0.8
|
---|
| 1244 | 0.6 90 0.75
|
---|
| 1245 | method: Interpolation method when correcting from a table.
|
---|
| 1246 | Values are "nearest", "linear" (default), "cubic"
|
---|
| 1247 | and "spline"
|
---|
| 1248 | insitu: if False a new scantable is returned.
|
---|
| 1249 | Otherwise, the scaling is done in-situ
|
---|
| 1250 | The default is taken from .asaprc (False)
|
---|
| 1251 | """
|
---|
| 1252 |
|
---|
| 1253 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1254 | self._math._setinsitu(insitu)
|
---|
[513] | 1255 | varlist = vars()
|
---|
| 1256 | if poly is None:
|
---|
[1118] | 1257 | poly = ()
|
---|
[513] | 1258 | from os.path import expandvars
|
---|
| 1259 | filename = expandvars(filename)
|
---|
[876] | 1260 | s = scantable(self._math._gainel(self, poly, filename, method))
|
---|
| 1261 | s._add_history("gain_el", varlist)
|
---|
| 1262 | print_log()
|
---|
| 1263 | if insitu: self._assign(s)
|
---|
| 1264 | else: return s
|
---|
[710] | 1265 |
|
---|
[931] | 1266 | def freq_align(self, reftime=None, method='cubic', insitu=None):
|
---|
[513] | 1267 | """
|
---|
| 1268 | Return a scan where all rows have been aligned in frequency/velocity.
|
---|
| 1269 | The alignment frequency frame (e.g. LSRK) is that set by function
|
---|
| 1270 | set_freqframe.
|
---|
| 1271 | Parameters:
|
---|
| 1272 | reftime: reference time to align at. By default, the time of
|
---|
| 1273 | the first row of data is used.
|
---|
| 1274 | method: Interpolation method for regridding the spectra.
|
---|
| 1275 | Choose from "nearest", "linear", "cubic" (default)
|
---|
| 1276 | and "spline"
|
---|
| 1277 | insitu: if False a new scantable is returned.
|
---|
| 1278 | Otherwise, the scaling is done in-situ
|
---|
| 1279 | The default is taken from .asaprc (False)
|
---|
| 1280 | """
|
---|
[931] | 1281 | if insitu is None: insitu = rcParams["insitu"]
|
---|
[876] | 1282 | self._math._setinsitu(insitu)
|
---|
[513] | 1283 | varlist = vars()
|
---|
[931] | 1284 | if reftime is None: reftime = ""
|
---|
| 1285 | s = scantable(self._math._freq_align(self, reftime, method))
|
---|
[876] | 1286 | s._add_history("freq_align", varlist)
|
---|
| 1287 | print_log()
|
---|
| 1288 | if insitu: self._assign(s)
|
---|
| 1289 | else: return s
|
---|
[513] | 1290 |
|
---|
[876] | 1291 | def opacity(self, tau, insitu=None):
|
---|
[513] | 1292 | """
|
---|
| 1293 | Apply an opacity correction. The data
|
---|
| 1294 | and Tsys are multiplied by the correction factor.
|
---|
| 1295 | Parameters:
|
---|
| 1296 | tau: Opacity from which the correction factor is
|
---|
| 1297 | exp(tau*ZD)
|
---|
| 1298 | where ZD is the zenith-distance
|
---|
| 1299 | insitu: if False a new scantable is returned.
|
---|
| 1300 | Otherwise, the scaling is done in-situ
|
---|
| 1301 | The default is taken from .asaprc (False)
|
---|
| 1302 | """
|
---|
| 1303 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1304 | self._math._setinsitu(insitu)
|
---|
[513] | 1305 | varlist = vars()
|
---|
[876] | 1306 | s = scantable(self._math._opacity(self, tau))
|
---|
| 1307 | s._add_history("opacity", varlist)
|
---|
| 1308 | print_log()
|
---|
| 1309 | if insitu: self._assign(s)
|
---|
| 1310 | else: return s
|
---|
[513] | 1311 |
|
---|
| 1312 | def bin(self, width=5, insitu=None):
|
---|
| 1313 | """
|
---|
| 1314 | Return a scan where all spectra have been binned up.
|
---|
[1348] | 1315 | Parameters:
|
---|
[513] | 1316 | width: The bin width (default=5) in pixels
|
---|
| 1317 | insitu: if False a new scantable is returned.
|
---|
| 1318 | Otherwise, the scaling is done in-situ
|
---|
| 1319 | The default is taken from .asaprc (False)
|
---|
| 1320 | """
|
---|
| 1321 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1322 | self._math._setinsitu(insitu)
|
---|
[513] | 1323 | varlist = vars()
|
---|
[876] | 1324 | s = scantable(self._math._bin(self, width))
|
---|
[1118] | 1325 | s._add_history("bin", varlist)
|
---|
[876] | 1326 | print_log()
|
---|
| 1327 | if insitu: self._assign(s)
|
---|
| 1328 | else: return s
|
---|
[513] | 1329 |
|
---|
[710] | 1330 |
|
---|
[513] | 1331 | def resample(self, width=5, method='cubic', insitu=None):
|
---|
| 1332 | """
|
---|
[1348] | 1333 | Return a scan where all spectra have been binned up.
|
---|
| 1334 |
|
---|
| 1335 | Parameters:
|
---|
[513] | 1336 | width: The bin width (default=5) in pixels
|
---|
| 1337 | method: Interpolation method when correcting from a table.
|
---|
| 1338 | Values are "nearest", "linear", "cubic" (default)
|
---|
| 1339 | and "spline"
|
---|
| 1340 | insitu: if False a new scantable is returned.
|
---|
| 1341 | Otherwise, the scaling is done in-situ
|
---|
| 1342 | The default is taken from .asaprc (False)
|
---|
| 1343 | """
|
---|
| 1344 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1345 | self._math._setinsitu(insitu)
|
---|
[513] | 1346 | varlist = vars()
|
---|
[876] | 1347 | s = scantable(self._math._resample(self, method, width))
|
---|
[1118] | 1348 | s._add_history("resample", varlist)
|
---|
[876] | 1349 | print_log()
|
---|
| 1350 | if insitu: self._assign(s)
|
---|
| 1351 | else: return s
|
---|
[513] | 1352 |
|
---|
| 1353 |
|
---|
[946] | 1354 | def average_pol(self, mask=None, weight='none'):
|
---|
| 1355 | """
|
---|
| 1356 | Average the Polarisations together.
|
---|
| 1357 | Parameters:
|
---|
| 1358 | mask: An optional mask defining the region, where the
|
---|
| 1359 | averaging will be applied. The output will have all
|
---|
| 1360 | specified points masked.
|
---|
| 1361 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
---|
| 1362 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
---|
| 1363 | """
|
---|
| 1364 | varlist = vars()
|
---|
| 1365 | if mask is None:
|
---|
| 1366 | mask = ()
|
---|
[1010] | 1367 | s = scantable(self._math._averagepol(self, mask, weight.upper()))
|
---|
[1118] | 1368 | s._add_history("average_pol", varlist)
|
---|
[946] | 1369 | print_log()
|
---|
[992] | 1370 | return s
|
---|
[513] | 1371 |
|
---|
[1145] | 1372 | def average_beam(self, mask=None, weight='none'):
|
---|
| 1373 | """
|
---|
| 1374 | Average the Beams together.
|
---|
| 1375 | Parameters:
|
---|
| 1376 | mask: An optional mask defining the region, where the
|
---|
| 1377 | averaging will be applied. The output will have all
|
---|
| 1378 | specified points masked.
|
---|
| 1379 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec)
|
---|
| 1380 | weighted), or 'tsys' (1/Tsys**2 weighted)
|
---|
| 1381 | """
|
---|
| 1382 | varlist = vars()
|
---|
| 1383 | if mask is None:
|
---|
| 1384 | mask = ()
|
---|
| 1385 | s = scantable(self._math._averagebeams(self, mask, weight.upper()))
|
---|
| 1386 | s._add_history("average_beam", varlist)
|
---|
| 1387 | print_log()
|
---|
| 1388 | return s
|
---|
| 1389 |
|
---|
[992] | 1390 | def convert_pol(self, poltype=None):
|
---|
| 1391 | """
|
---|
| 1392 | Convert the data to a different polarisation type.
|
---|
| 1393 | Parameters:
|
---|
| 1394 | poltype: The new polarisation type. Valid types are:
|
---|
| 1395 | "linear", "stokes" and "circular"
|
---|
| 1396 | """
|
---|
| 1397 | varlist = vars()
|
---|
| 1398 | try:
|
---|
| 1399 | s = scantable(self._math._convertpol(self, poltype))
|
---|
[1118] | 1400 | except RuntimeError, msg:
|
---|
[992] | 1401 | if rcParams['verbose']:
|
---|
[1118] | 1402 | print msg
|
---|
| 1403 | return
|
---|
[992] | 1404 | else:
|
---|
| 1405 | raise
|
---|
[1118] | 1406 | s._add_history("convert_pol", varlist)
|
---|
[992] | 1407 | print_log()
|
---|
| 1408 | return s
|
---|
| 1409 |
|
---|
[876] | 1410 | def smooth(self, kernel="hanning", width=5.0, insitu=None):
|
---|
[513] | 1411 | """
|
---|
| 1412 | Smooth the spectrum by the specified kernel (conserving flux).
|
---|
| 1413 | Parameters:
|
---|
| 1414 | kernel: The type of smoothing kernel. Select from
|
---|
[1373] | 1415 | 'hanning' (default), 'gaussian', 'boxcar' and
|
---|
| 1416 | 'rmedian'
|
---|
[513] | 1417 | width: The width of the kernel in pixels. For hanning this is
|
---|
| 1418 | ignored otherwise it defauls to 5 pixels.
|
---|
| 1419 | For 'gaussian' it is the Full Width Half
|
---|
| 1420 | Maximum. For 'boxcar' it is the full width.
|
---|
[1373] | 1421 | For 'rmedian' it is the half width.
|
---|
[513] | 1422 | insitu: if False a new scantable is returned.
|
---|
| 1423 | Otherwise, the scaling is done in-situ
|
---|
| 1424 | The default is taken from .asaprc (False)
|
---|
| 1425 | Example:
|
---|
| 1426 | none
|
---|
| 1427 | """
|
---|
| 1428 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1429 | self._math._setinsitu(insitu)
|
---|
[513] | 1430 | varlist = vars()
|
---|
[1118] | 1431 | s = scantable(self._math._smooth(self, kernel.lower(), width))
|
---|
[876] | 1432 | s._add_history("smooth", varlist)
|
---|
| 1433 | print_log()
|
---|
| 1434 | if insitu: self._assign(s)
|
---|
| 1435 | else: return s
|
---|
[513] | 1436 |
|
---|
[876] | 1437 |
|
---|
[1389] | 1438 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None):
|
---|
[513] | 1439 | """
|
---|
| 1440 | Return a scan which has been baselined (all rows) by a polynomial.
|
---|
| 1441 | Parameters:
|
---|
[794] | 1442 | mask: an optional mask
|
---|
| 1443 | order: the order of the polynomial (default is 0)
|
---|
[1061] | 1444 | plot: plot the fit and the residual. In this each
|
---|
| 1445 | indivual fit has to be approved, by typing 'y'
|
---|
| 1446 | or 'n'
|
---|
[1389] | 1447 | uselin: use linear polynomial fit
|
---|
[794] | 1448 | insitu: if False a new scantable is returned.
|
---|
| 1449 | Otherwise, the scaling is done in-situ
|
---|
| 1450 | The default is taken from .asaprc (False)
|
---|
[513] | 1451 | Example:
|
---|
| 1452 | # return a scan baselined by a third order polynomial,
|
---|
| 1453 | # not using a mask
|
---|
| 1454 | bscan = scan.poly_baseline(order=3)
|
---|
[579] | 1455 | """
|
---|
[513] | 1456 | if insitu is None: insitu = rcParams['insitu']
|
---|
| 1457 | varlist = vars()
|
---|
| 1458 | if mask is None:
|
---|
[1295] | 1459 | mask = [True for i in xrange(self.nchan(-1))]
|
---|
[513] | 1460 | from asap.asapfitter import fitter
|
---|
[1217] | 1461 | try:
|
---|
| 1462 | f = fitter()
|
---|
| 1463 | f.set_scan(self, mask)
|
---|
[1389] | 1464 | if uselin:
|
---|
| 1465 | f.set_function(lpoly=order)
|
---|
| 1466 | else:
|
---|
| 1467 | f.set_function(poly=order)
|
---|
[1217] | 1468 | s = f.auto_fit(insitu, plot=plot)
|
---|
[1446] | 1469 | # Save parameters of baseline fits as a class attribute.
|
---|
| 1470 | # NOTICE: It does not reflect changes in scantable!
|
---|
| 1471 | self.blpars = f.blpars
|
---|
[1217] | 1472 | s._add_history("poly_baseline", varlist)
|
---|
| 1473 | print_log()
|
---|
| 1474 | if insitu: self._assign(s)
|
---|
| 1475 | else: return s
|
---|
| 1476 | except RuntimeError:
|
---|
| 1477 | msg = "The fit failed, possibly because it didn't converge."
|
---|
| 1478 | if rcParams['verbose']:
|
---|
| 1479 | print msg
|
---|
| 1480 | return
|
---|
| 1481 | else:
|
---|
| 1482 | raise RuntimeError(msg)
|
---|
[513] | 1483 |
|
---|
[1217] | 1484 |
|
---|
[1118] | 1485 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0,
|
---|
[1280] | 1486 | threshold=3, chan_avg_limit=1, plot=False,
|
---|
| 1487 | insitu=None):
|
---|
[880] | 1488 | """
|
---|
| 1489 | Return a scan which has been baselined (all rows) by a polynomial.
|
---|
| 1490 | Spectral lines are detected first using linefinder and masked out
|
---|
| 1491 | to avoid them affecting the baseline solution.
|
---|
| 1492 |
|
---|
| 1493 | Parameters:
|
---|
| 1494 | mask: an optional mask retreived from scantable
|
---|
| 1495 | edge: an optional number of channel to drop at
|
---|
| 1496 | the edge of spectrum. If only one value is
|
---|
| 1497 | specified, the same number will be dropped from
|
---|
| 1498 | both sides of the spectrum. Default is to keep
|
---|
[907] | 1499 | all channels. Nested tuples represent individual
|
---|
[976] | 1500 | edge selection for different IFs (a number of spectral
|
---|
| 1501 | channels can be different)
|
---|
[880] | 1502 | order: the order of the polynomial (default is 0)
|
---|
| 1503 | threshold: the threshold used by line finder. It is better to
|
---|
| 1504 | keep it large as only strong lines affect the
|
---|
| 1505 | baseline solution.
|
---|
[1280] | 1506 | chan_avg_limit:
|
---|
| 1507 | a maximum number of consequtive spectral channels to
|
---|
| 1508 | average during the search of weak and broad lines.
|
---|
| 1509 | The default is no averaging (and no search for weak
|
---|
| 1510 | lines). If such lines can affect the fitted baseline
|
---|
| 1511 | (e.g. a high order polynomial is fitted), increase this
|
---|
| 1512 | parameter (usually values up to 8 are reasonable). Most
|
---|
| 1513 | users of this method should find the default value
|
---|
| 1514 | sufficient.
|
---|
[1061] | 1515 | plot: plot the fit and the residual. In this each
|
---|
| 1516 | indivual fit has to be approved, by typing 'y'
|
---|
| 1517 | or 'n'
|
---|
[880] | 1518 | insitu: if False a new scantable is returned.
|
---|
| 1519 | Otherwise, the scaling is done in-situ
|
---|
| 1520 | The default is taken from .asaprc (False)
|
---|
| 1521 |
|
---|
| 1522 | Example:
|
---|
| 1523 | scan2=scan.auto_poly_baseline(order=7)
|
---|
| 1524 | """
|
---|
| 1525 | if insitu is None: insitu = rcParams['insitu']
|
---|
| 1526 | varlist = vars()
|
---|
| 1527 | from asap.asapfitter import fitter
|
---|
| 1528 | from asap.asaplinefind import linefinder
|
---|
| 1529 | from asap import _is_sequence_or_number as _is_valid
|
---|
| 1530 |
|
---|
[976] | 1531 | # check whether edge is set up for each IF individually
|
---|
[1118] | 1532 | individualedge = False;
|
---|
| 1533 | if len(edge) > 1:
|
---|
| 1534 | if isinstance(edge[0], list) or isinstance(edge[0], tuple):
|
---|
| 1535 | individualedge = True;
|
---|
[907] | 1536 |
|
---|
[1118] | 1537 | if not _is_valid(edge, int) and not individualedge:
|
---|
[909] | 1538 | raise ValueError, "Parameter 'edge' has to be an integer or a \
|
---|
[907] | 1539 | pair of integers specified as a tuple. Nested tuples are allowed \
|
---|
| 1540 | to make individual selection for different IFs."
|
---|
[919] | 1541 |
|
---|
[1118] | 1542 | curedge = (0, 0)
|
---|
| 1543 | if individualedge:
|
---|
| 1544 | for edgepar in edge:
|
---|
| 1545 | if not _is_valid(edgepar, int):
|
---|
| 1546 | raise ValueError, "Each element of the 'edge' tuple has \
|
---|
| 1547 | to be a pair of integers or an integer."
|
---|
[907] | 1548 | else:
|
---|
[1118] | 1549 | curedge = edge;
|
---|
[880] | 1550 |
|
---|
| 1551 | # setup fitter
|
---|
| 1552 | f = fitter()
|
---|
| 1553 | f.set_function(poly=order)
|
---|
| 1554 |
|
---|
| 1555 | # setup line finder
|
---|
[1118] | 1556 | fl = linefinder()
|
---|
[1268] | 1557 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit)
|
---|
[880] | 1558 |
|
---|
| 1559 | if not insitu:
|
---|
[1118] | 1560 | workscan = self.copy()
|
---|
[880] | 1561 | else:
|
---|
[1118] | 1562 | workscan = self
|
---|
[880] | 1563 |
|
---|
[907] | 1564 | fl.set_scan(workscan)
|
---|
| 1565 |
|
---|
[1118] | 1566 | rows = range(workscan.nrow())
|
---|
[1446] | 1567 | # Save parameters of baseline fits & masklists as a class attribute.
|
---|
| 1568 | # NOTICE: It does not reflect changes in scantable!
|
---|
| 1569 | if len(rows) > 0:
|
---|
| 1570 | self.blpars=[]
|
---|
| 1571 | self.masklists=[]
|
---|
[880] | 1572 | asaplog.push("Processing:")
|
---|
| 1573 | for r in rows:
|
---|
[1118] | 1574 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \
|
---|
| 1575 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \
|
---|
| 1576 | workscan.getpol(r), workscan.getcycle(r))
|
---|
[880] | 1577 | asaplog.push(msg, False)
|
---|
[907] | 1578 |
|
---|
[976] | 1579 | # figure out edge parameter
|
---|
[1118] | 1580 | if individualedge:
|
---|
| 1581 | if len(edge) >= workscan.getif(r):
|
---|
| 1582 | raise RuntimeError, "Number of edge elements appear to " \
|
---|
| 1583 | "be less than the number of IFs"
|
---|
| 1584 | curedge = edge[workscan.getif(r)]
|
---|
[919] | 1585 |
|
---|
[976] | 1586 | # setup line finder
|
---|
[1118] | 1587 | fl.find_lines(r, mask, curedge)
|
---|
[1446] | 1588 | outmask=fl.get_mask()
|
---|
[880] | 1589 | f.set_scan(workscan, fl.get_mask())
|
---|
| 1590 | f.x = workscan._getabcissa(r)
|
---|
| 1591 | f.y = workscan._getspectrum(r)
|
---|
| 1592 | f.data = None
|
---|
| 1593 | f.fit()
|
---|
[1446] | 1594 |
|
---|
| 1595 | # Show mask list
|
---|
| 1596 | masklist=workscan.get_masklist(fl.get_mask(),row=r)
|
---|
| 1597 | msg = "mask range: "+str(masklist)
|
---|
| 1598 | asaplog.push(msg, False)
|
---|
| 1599 |
|
---|
| 1600 | fpar = f.get_parameters()
|
---|
[1061] | 1601 | if plot:
|
---|
| 1602 | f.plot(residual=True)
|
---|
| 1603 | x = raw_input("Accept fit ( [y]/n ): ")
|
---|
| 1604 | if x.upper() == 'N':
|
---|
[1446] | 1605 | self.blpars.append(None)
|
---|
| 1606 | self.masklists.append(None)
|
---|
[1061] | 1607 | continue
|
---|
[880] | 1608 | workscan._setspectrum(f.fitter.getresidual(), r)
|
---|
[1446] | 1609 | self.blpars.append(fpar)
|
---|
| 1610 | self.masklists.append(masklist)
|
---|
[1061] | 1611 | if plot:
|
---|
| 1612 | f._p.unmap()
|
---|
| 1613 | f._p = None
|
---|
| 1614 | workscan._add_history("auto_poly_baseline", varlist)
|
---|
[880] | 1615 | if insitu:
|
---|
| 1616 | self._assign(workscan)
|
---|
| 1617 | else:
|
---|
| 1618 | return workscan
|
---|
| 1619 |
|
---|
[914] | 1620 | def rotate_linpolphase(self, angle):
|
---|
| 1621 | """
|
---|
| 1622 | Rotate the phase of the complex polarization O=Q+iU correlation.
|
---|
| 1623 | This is always done in situ in the raw data. So if you call this
|
---|
| 1624 | function more than once then each call rotates the phase further.
|
---|
| 1625 | Parameters:
|
---|
| 1626 | angle: The angle (degrees) to rotate (add) by.
|
---|
| 1627 | Examples:
|
---|
| 1628 | scan.rotate_linpolphase(2.3)
|
---|
| 1629 | """
|
---|
| 1630 | varlist = vars()
|
---|
[936] | 1631 | self._math._rotate_linpolphase(self, angle)
|
---|
[914] | 1632 | self._add_history("rotate_linpolphase", varlist)
|
---|
| 1633 | print_log()
|
---|
| 1634 | return
|
---|
[710] | 1635 |
|
---|
[513] | 1636 |
|
---|
[914] | 1637 | def rotate_xyphase(self, angle):
|
---|
| 1638 | """
|
---|
| 1639 | Rotate the phase of the XY correlation. This is always done in situ
|
---|
| 1640 | in the data. So if you call this function more than once
|
---|
| 1641 | then each call rotates the phase further.
|
---|
| 1642 | Parameters:
|
---|
| 1643 | angle: The angle (degrees) to rotate (add) by.
|
---|
| 1644 | Examples:
|
---|
| 1645 | scan.rotate_xyphase(2.3)
|
---|
| 1646 | """
|
---|
| 1647 | varlist = vars()
|
---|
[936] | 1648 | self._math._rotate_xyphase(self, angle)
|
---|
[914] | 1649 | self._add_history("rotate_xyphase", varlist)
|
---|
| 1650 | print_log()
|
---|
| 1651 | return
|
---|
| 1652 |
|
---|
| 1653 | def swap_linears(self):
|
---|
| 1654 | """
|
---|
[1348] | 1655 | Swap the linear polarisations XX and YY, or better the first two
|
---|
| 1656 | polarisations as this also works for ciculars.
|
---|
[914] | 1657 | """
|
---|
| 1658 | varlist = vars()
|
---|
[936] | 1659 | self._math._swap_linears(self)
|
---|
[914] | 1660 | self._add_history("swap_linears", varlist)
|
---|
| 1661 | print_log()
|
---|
| 1662 | return
|
---|
| 1663 |
|
---|
| 1664 | def invert_phase(self):
|
---|
| 1665 | """
|
---|
| 1666 | Invert the phase of the complex polarisation
|
---|
| 1667 | """
|
---|
| 1668 | varlist = vars()
|
---|
[936] | 1669 | self._math._invert_phase(self)
|
---|
[914] | 1670 | self._add_history("invert_phase", varlist)
|
---|
| 1671 | print_log()
|
---|
| 1672 | return
|
---|
| 1673 |
|
---|
[876] | 1674 | def add(self, offset, insitu=None):
|
---|
[513] | 1675 | """
|
---|
| 1676 | Return a scan where all spectra have the offset added
|
---|
| 1677 | Parameters:
|
---|
| 1678 | offset: the offset
|
---|
| 1679 | insitu: if False a new scantable is returned.
|
---|
| 1680 | Otherwise, the scaling is done in-situ
|
---|
| 1681 | The default is taken from .asaprc (False)
|
---|
| 1682 | """
|
---|
| 1683 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1684 | self._math._setinsitu(insitu)
|
---|
[513] | 1685 | varlist = vars()
|
---|
[876] | 1686 | s = scantable(self._math._unaryop(self, offset, "ADD", False))
|
---|
[1118] | 1687 | s._add_history("add", varlist)
|
---|
[876] | 1688 | print_log()
|
---|
| 1689 | if insitu:
|
---|
| 1690 | self._assign(s)
|
---|
| 1691 | else:
|
---|
[513] | 1692 | return s
|
---|
| 1693 |
|
---|
[1308] | 1694 | def scale(self, factor, tsys=True, insitu=None):
|
---|
[513] | 1695 | """
|
---|
| 1696 | Return a scan where all spectra are scaled by the give 'factor'
|
---|
| 1697 | Parameters:
|
---|
| 1698 | factor: the scaling factor
|
---|
| 1699 | insitu: if False a new scantable is returned.
|
---|
| 1700 | Otherwise, the scaling is done in-situ
|
---|
| 1701 | The default is taken from .asaprc (False)
|
---|
| 1702 | tsys: if True (default) then apply the operation to Tsys
|
---|
| 1703 | as well as the data
|
---|
| 1704 | """
|
---|
| 1705 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1706 | self._math._setinsitu(insitu)
|
---|
[513] | 1707 | varlist = vars()
|
---|
[876] | 1708 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys))
|
---|
[1118] | 1709 | s._add_history("scale", varlist)
|
---|
[876] | 1710 | print_log()
|
---|
| 1711 | if insitu:
|
---|
| 1712 | self._assign(s)
|
---|
| 1713 | else:
|
---|
[513] | 1714 | return s
|
---|
| 1715 |
|
---|
[1603] | 1716 | def set_sourcetype(self, match, matchtype="pattern",
|
---|
| 1717 | sourcetype="reference"):
|
---|
| 1718 | """
|
---|
| 1719 | Set the type of the source to be an source or reference scan
|
---|
| 1720 | using the provided pattern:
|
---|
| 1721 | Parameters:
|
---|
| 1722 | match: a Unix style pattern, regular expression or selector
|
---|
| 1723 | matchtype: 'pattern' (default) UNIX style pattern or
|
---|
| 1724 | 'regex' regular expression
|
---|
| 1725 | sourcetype: the type of the source to use (source/reference)
|
---|
| 1726 | """
|
---|
| 1727 | varlist = vars()
|
---|
| 1728 | basesel = self.get_selection()
|
---|
| 1729 | stype = -1
|
---|
| 1730 | if sourcetype.lower().startswith("r"):
|
---|
| 1731 | stype = 1
|
---|
| 1732 | elif sourcetype.lower().startswith("s"):
|
---|
| 1733 | stype = 0
|
---|
| 1734 | else:
|
---|
| 1735 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)")
|
---|
| 1736 | if matchtype.lower().startswith("p"):
|
---|
| 1737 | matchtype = "pattern"
|
---|
| 1738 | elif matchtype.lower().startswith("r"):
|
---|
| 1739 | matchtype = "regex"
|
---|
| 1740 | else:
|
---|
| 1741 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)")
|
---|
| 1742 | sel = selector()
|
---|
| 1743 | if isinstance(match, selector):
|
---|
| 1744 | sel = match
|
---|
| 1745 | else:
|
---|
| 1746 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match))
|
---|
| 1747 | self.set_selection(basesel+sel)
|
---|
| 1748 | self._setsourcetype(stype)
|
---|
| 1749 | self.set_selection(basesel)
|
---|
| 1750 | s._add_history("set_sourcetype", varlist)
|
---|
| 1751 |
|
---|
[1348] | 1752 | def auto_quotient(self, preserve=True, mode='paired'):
|
---|
[670] | 1753 | """
|
---|
| 1754 | This function allows to build quotients automatically.
|
---|
| 1755 | It assumes the observation to have the same numer of
|
---|
| 1756 | "ons" and "offs"
|
---|
| 1757 | Parameters:
|
---|
[710] | 1758 | preserve: you can preserve (default) the continuum or
|
---|
| 1759 | remove it. The equations used are
|
---|
[670] | 1760 | preserve: Output = Toff * (on/off) - Toff
|
---|
[1070] | 1761 | remove: Output = Toff * (on/off) - Ton
|
---|
[1348] | 1762 | mode: the on/off detection mode
|
---|
| 1763 | 'paired' (default)
|
---|
| 1764 | identifies 'off' scans by the
|
---|
| 1765 | trailing '_R' (Mopra/Parkes) or
|
---|
| 1766 | '_e'/'_w' (Tid) and matches
|
---|
| 1767 | on/off pairs from the observing pattern
|
---|
[1603] | 1768 | 'time'
|
---|
| 1769 | finds the closest off in time
|
---|
[1348] | 1770 |
|
---|
[670] | 1771 | """
|
---|
[1348] | 1772 | modes = ["time", "paired"]
|
---|
[670] | 1773 | if not mode in modes:
|
---|
[876] | 1774 | msg = "please provide valid mode. Valid modes are %s" % (modes)
|
---|
| 1775 | raise ValueError(msg)
|
---|
| 1776 | varlist = vars()
|
---|
[1348] | 1777 | s = None
|
---|
| 1778 | if mode.lower() == "paired":
|
---|
| 1779 | basesel = self.get_selection()
|
---|
[1356] | 1780 | sel = selector()+basesel
|
---|
| 1781 | sel.set_query("SRCTYPE==1")
|
---|
| 1782 | self.set_selection(sel)
|
---|
[1348] | 1783 | offs = self.copy()
|
---|
| 1784 | sel.set_query("SRCTYPE==0")
|
---|
[1356] | 1785 | self.set_selection(sel)
|
---|
[1348] | 1786 | ons = self.copy()
|
---|
| 1787 | s = scantable(self._math._quotient(ons, offs, preserve))
|
---|
| 1788 | self.set_selection(basesel)
|
---|
| 1789 | elif mode.lower() == "time":
|
---|
| 1790 | s = scantable(self._math._auto_quotient(self, mode, preserve))
|
---|
[1118] | 1791 | s._add_history("auto_quotient", varlist)
|
---|
[876] | 1792 | print_log()
|
---|
| 1793 | return s
|
---|
[710] | 1794 |
|
---|
[1145] | 1795 | def mx_quotient(self, mask = None, weight='median', preserve=True):
|
---|
[1141] | 1796 | """
|
---|
[1143] | 1797 | Form a quotient using "off" beams when observing in "MX" mode.
|
---|
| 1798 | Parameters:
|
---|
[1145] | 1799 | mask: an optional mask to be used when weight == 'stddev'
|
---|
[1143] | 1800 | weight: How to average the off beams. Default is 'median'.
|
---|
[1145] | 1801 | preserve: you can preserve (default) the continuum or
|
---|
| 1802 | remove it. The equations used are
|
---|
| 1803 | preserve: Output = Toff * (on/off) - Toff
|
---|
| 1804 | remove: Output = Toff * (on/off) - Ton
|
---|
[1217] | 1805 | """
|
---|
[1143] | 1806 | if mask is None: mask = ()
|
---|
[1141] | 1807 | varlist = vars()
|
---|
| 1808 | on = scantable(self._math._mx_extract(self, 'on'))
|
---|
[1143] | 1809 | preoff = scantable(self._math._mx_extract(self, 'off'))
|
---|
| 1810 | off = preoff.average_time(mask=mask, weight=weight, scanav=False)
|
---|
[1217] | 1811 | from asapmath import quotient
|
---|
[1145] | 1812 | q = quotient(on, off, preserve)
|
---|
[1143] | 1813 | q._add_history("mx_quotient", varlist)
|
---|
[1145] | 1814 | print_log()
|
---|
[1217] | 1815 | return q
|
---|
[513] | 1816 |
|
---|
[718] | 1817 | def freq_switch(self, insitu=None):
|
---|
| 1818 | """
|
---|
| 1819 | Apply frequency switching to the data.
|
---|
| 1820 | Parameters:
|
---|
| 1821 | insitu: if False a new scantable is returned.
|
---|
| 1822 | Otherwise, the swictching is done in-situ
|
---|
| 1823 | The default is taken from .asaprc (False)
|
---|
| 1824 | Example:
|
---|
| 1825 | none
|
---|
| 1826 | """
|
---|
| 1827 | if insitu is None: insitu = rcParams['insitu']
|
---|
[876] | 1828 | self._math._setinsitu(insitu)
|
---|
[718] | 1829 | varlist = vars()
|
---|
[876] | 1830 | s = scantable(self._math._freqswitch(self))
|
---|
[1118] | 1831 | s._add_history("freq_switch", varlist)
|
---|
[876] | 1832 | print_log()
|
---|
| 1833 | if insitu: self._assign(s)
|
---|
| 1834 | else: return s
|
---|
[718] | 1835 |
|
---|
[780] | 1836 | def recalc_azel(self):
|
---|
| 1837 | """
|
---|
| 1838 | Recalculate the azimuth and elevation for each position.
|
---|
| 1839 | Parameters:
|
---|
| 1840 | none
|
---|
| 1841 | Example:
|
---|
| 1842 | """
|
---|
| 1843 | varlist = vars()
|
---|
[876] | 1844 | self._recalcazel()
|
---|
[780] | 1845 | self._add_history("recalc_azel", varlist)
|
---|
| 1846 | print_log()
|
---|
| 1847 | return
|
---|
| 1848 |
|
---|
[513] | 1849 | def __add__(self, other):
|
---|
| 1850 | varlist = vars()
|
---|
| 1851 | s = None
|
---|
| 1852 | if isinstance(other, scantable):
|
---|
[1308] | 1853 | s = scantable(self._math._binaryop(self, other, "ADD"))
|
---|
[513] | 1854 | elif isinstance(other, float):
|
---|
[876] | 1855 | s = scantable(self._math._unaryop(self, other, "ADD", False))
|
---|
[513] | 1856 | else:
|
---|
[718] | 1857 | raise TypeError("Other input is not a scantable or float value")
|
---|
[513] | 1858 | s._add_history("operator +", varlist)
|
---|
[718] | 1859 | print_log()
|
---|
[513] | 1860 | return s
|
---|
| 1861 |
|
---|
| 1862 | def __sub__(self, other):
|
---|
| 1863 | """
|
---|
| 1864 | implicit on all axes and on Tsys
|
---|
| 1865 | """
|
---|
| 1866 | varlist = vars()
|
---|
| 1867 | s = None
|
---|
| 1868 | if isinstance(other, scantable):
|
---|
[1308] | 1869 | s = scantable(self._math._binaryop(self, other, "SUB"))
|
---|
[513] | 1870 | elif isinstance(other, float):
|
---|
[876] | 1871 | s = scantable(self._math._unaryop(self, other, "SUB", False))
|
---|
[513] | 1872 | else:
|
---|
[718] | 1873 | raise TypeError("Other input is not a scantable or float value")
|
---|
[513] | 1874 | s._add_history("operator -", varlist)
|
---|
[718] | 1875 | print_log()
|
---|
[513] | 1876 | return s
|
---|
[710] | 1877 |
|
---|
[513] | 1878 | def __mul__(self, other):
|
---|
| 1879 | """
|
---|
| 1880 | implicit on all axes and on Tsys
|
---|
| 1881 | """
|
---|
| 1882 | varlist = vars()
|
---|
| 1883 | s = None
|
---|
| 1884 | if isinstance(other, scantable):
|
---|
[1308] | 1885 | s = scantable(self._math._binaryop(self, other, "MUL"))
|
---|
[513] | 1886 | elif isinstance(other, float):
|
---|
[876] | 1887 | s = scantable(self._math._unaryop(self, other, "MUL", False))
|
---|
[513] | 1888 | else:
|
---|
[718] | 1889 | raise TypeError("Other input is not a scantable or float value")
|
---|
[513] | 1890 | s._add_history("operator *", varlist)
|
---|
[718] | 1891 | print_log()
|
---|
[513] | 1892 | return s
|
---|
| 1893 |
|
---|
[710] | 1894 |
|
---|
[513] | 1895 | def __div__(self, other):
|
---|
| 1896 | """
|
---|
| 1897 | implicit on all axes and on Tsys
|
---|
| 1898 | """
|
---|
| 1899 | varlist = vars()
|
---|
| 1900 | s = None
|
---|
| 1901 | if isinstance(other, scantable):
|
---|
[1308] | 1902 | s = scantable(self._math._binaryop(self, other, "DIV"))
|
---|
[513] | 1903 | elif isinstance(other, float):
|
---|
| 1904 | if other == 0.0:
|
---|
[718] | 1905 | raise ZeroDivisionError("Dividing by zero is not recommended")
|
---|
[876] | 1906 | s = scantable(self._math._unaryop(self, other, "DIV", False))
|
---|
[513] | 1907 | else:
|
---|
[718] | 1908 | raise TypeError("Other input is not a scantable or float value")
|
---|
[513] | 1909 | s._add_history("operator /", varlist)
|
---|
[718] | 1910 | print_log()
|
---|
[513] | 1911 | return s
|
---|
| 1912 |
|
---|
[530] | 1913 | def get_fit(self, row=0):
|
---|
| 1914 | """
|
---|
| 1915 | Print or return the stored fits for a row in the scantable
|
---|
| 1916 | Parameters:
|
---|
| 1917 | row: the row which the fit has been applied to.
|
---|
| 1918 | """
|
---|
| 1919 | if row > self.nrow():
|
---|
| 1920 | return
|
---|
[976] | 1921 | from asap.asapfit import asapfit
|
---|
[530] | 1922 | fit = asapfit(self._getfit(row))
|
---|
[718] | 1923 | if rcParams['verbose']:
|
---|
[530] | 1924 | print fit
|
---|
| 1925 | return
|
---|
| 1926 | else:
|
---|
| 1927 | return fit.as_dict()
|
---|
| 1928 |
|
---|
[1603] | 1929 | def flag_nans(self):
|
---|
| 1930 | """
|
---|
| 1931 | Utility function to flag NaN values in the scantable.
|
---|
| 1932 | """
|
---|
| 1933 | import numpy
|
---|
| 1934 | basesel = self.get_selection()
|
---|
| 1935 | for i in range(self.nrow()):
|
---|
| 1936 | sel = selector()+basesel
|
---|
| 1937 | sel.set_scans(self.getscan(i))
|
---|
| 1938 | sel.set_beams(self.getbeam(i))
|
---|
| 1939 | sel.set_ifs(self.getif(i))
|
---|
| 1940 | sel.set_polarisations(self.getpol(i))
|
---|
| 1941 | self.set_selection(sel)
|
---|
| 1942 | nans = numpy.isnan(self._getspectrum(0))
|
---|
| 1943 | if numpy.any(nans):
|
---|
| 1944 | bnans = [ bool(v) for v in nans]
|
---|
| 1945 | self.flag(bnans)
|
---|
| 1946 | self.set_selection(basesel)
|
---|
| 1947 |
|
---|
| 1948 |
|
---|
[484] | 1949 | def _add_history(self, funcname, parameters):
|
---|
[1603] | 1950 | if not rcParams['scantable.history']:
|
---|
| 1951 | return
|
---|
[484] | 1952 | # create date
|
---|
| 1953 | sep = "##"
|
---|
| 1954 | from datetime import datetime
|
---|
| 1955 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S')
|
---|
| 1956 | hist = dstr+sep
|
---|
| 1957 | hist += funcname+sep#cdate+sep
|
---|
| 1958 | if parameters.has_key('self'): del parameters['self']
|
---|
[1118] | 1959 | for k, v in parameters.iteritems():
|
---|
[484] | 1960 | if type(v) is dict:
|
---|
[1118] | 1961 | for k2, v2 in v.iteritems():
|
---|
[484] | 1962 | hist += k2
|
---|
| 1963 | hist += "="
|
---|
[1118] | 1964 | if isinstance(v2, scantable):
|
---|
[484] | 1965 | hist += 'scantable'
|
---|
| 1966 | elif k2 == 'mask':
|
---|
[1118] | 1967 | if isinstance(v2, list) or isinstance(v2, tuple):
|
---|
[513] | 1968 | hist += str(self._zip_mask(v2))
|
---|
| 1969 | else:
|
---|
| 1970 | hist += str(v2)
|
---|
[484] | 1971 | else:
|
---|
[513] | 1972 | hist += str(v2)
|
---|
[484] | 1973 | else:
|
---|
| 1974 | hist += k
|
---|
| 1975 | hist += "="
|
---|
[1118] | 1976 | if isinstance(v, scantable):
|
---|
[484] | 1977 | hist += 'scantable'
|
---|
| 1978 | elif k == 'mask':
|
---|
[1118] | 1979 | if isinstance(v, list) or isinstance(v, tuple):
|
---|
[513] | 1980 | hist += str(self._zip_mask(v))
|
---|
| 1981 | else:
|
---|
| 1982 | hist += str(v)
|
---|
[484] | 1983 | else:
|
---|
| 1984 | hist += str(v)
|
---|
| 1985 | hist += sep
|
---|
| 1986 | hist = hist[:-2] # remove trailing '##'
|
---|
| 1987 | self._addhistory(hist)
|
---|
| 1988 |
|
---|
[710] | 1989 |
|
---|
[484] | 1990 | def _zip_mask(self, mask):
|
---|
| 1991 | mask = list(mask)
|
---|
| 1992 | i = 0
|
---|
| 1993 | segments = []
|
---|
| 1994 | while mask[i:].count(1):
|
---|
| 1995 | i += mask[i:].index(1)
|
---|
| 1996 | if mask[i:].count(0):
|
---|
| 1997 | j = i + mask[i:].index(0)
|
---|
| 1998 | else:
|
---|
[710] | 1999 | j = len(mask)
|
---|
[1118] | 2000 | segments.append([i, j])
|
---|
[710] | 2001 | i = j
|
---|
[484] | 2002 | return segments
|
---|
[714] | 2003 |
|
---|
[626] | 2004 | def _get_ordinate_label(self):
|
---|
| 2005 | fu = "("+self.get_fluxunit()+")"
|
---|
| 2006 | import re
|
---|
| 2007 | lbl = "Intensity"
|
---|
[1118] | 2008 | if re.match(".K.", fu):
|
---|
[626] | 2009 | lbl = "Brightness Temperature "+ fu
|
---|
[1118] | 2010 | elif re.match(".Jy.", fu):
|
---|
[626] | 2011 | lbl = "Flux density "+ fu
|
---|
| 2012 | return lbl
|
---|
[710] | 2013 |
|
---|
[876] | 2014 | def _check_ifs(self):
|
---|
| 2015 | nchans = [self.nchan(i) for i in range(self.nif(-1))]
|
---|
[889] | 2016 | nchans = filter(lambda t: t > 0, nchans)
|
---|
[876] | 2017 | return (sum(nchans)/len(nchans) == nchans[0])
|
---|
[976] | 2018 |
|
---|
[1496] | 2019 | def _fill(self, names, unit, average, getpt):
|
---|
[976] | 2020 | import os
|
---|
| 2021 | from asap._asap import stfiller
|
---|
| 2022 | first = True
|
---|
| 2023 | fullnames = []
|
---|
| 2024 | for name in names:
|
---|
| 2025 | name = os.path.expandvars(name)
|
---|
| 2026 | name = os.path.expanduser(name)
|
---|
| 2027 | if not os.path.exists(name):
|
---|
| 2028 | msg = "File '%s' does not exists" % (name)
|
---|
| 2029 | if rcParams['verbose']:
|
---|
| 2030 | asaplog.push(msg)
|
---|
| 2031 | print asaplog.pop().strip()
|
---|
| 2032 | return
|
---|
| 2033 | raise IOError(msg)
|
---|
| 2034 | fullnames.append(name)
|
---|
| 2035 | if average:
|
---|
| 2036 | asaplog.push('Auto averaging integrations')
|
---|
[1079] | 2037 | stype = int(rcParams['scantable.storage'].lower() == 'disk')
|
---|
[976] | 2038 | for name in fullnames:
|
---|
[1073] | 2039 | tbl = Scantable(stype)
|
---|
| 2040 | r = stfiller(tbl)
|
---|
[1603] | 2041 | rx = rcParams['scantable.reference']
|
---|
| 2042 | r._setreferenceexpr(rx)
|
---|
[976] | 2043 | msg = "Importing %s..." % (name)
|
---|
[1118] | 2044 | asaplog.push(msg, False)
|
---|
[976] | 2045 | print_log()
|
---|
[1496] | 2046 | r._open(name, -1, -1, getpt)
|
---|
[976] | 2047 | r._read()
|
---|
| 2048 | if average:
|
---|
[1118] | 2049 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN')
|
---|
[976] | 2050 | if not first:
|
---|
| 2051 | tbl = self._math._merge([self, tbl])
|
---|
| 2052 | Scantable.__init__(self, tbl)
|
---|
| 2053 | r._close()
|
---|
[1118] | 2054 | del r, tbl
|
---|
[976] | 2055 | first = False
|
---|
| 2056 | if unit is not None:
|
---|
| 2057 | self.set_fluxunit(unit)
|
---|
[1446] | 2058 | #self.set_freqframe(rcParams['scantable.freqframe'])
|
---|
[976] | 2059 |
|
---|
[1603] | 2060 | def __getitem__(self, key):
|
---|
| 2061 | if key < 0:
|
---|
| 2062 | key += self.nrow()
|
---|
| 2063 | if key >= self.nrow():
|
---|
| 2064 | raise IndexError("Row index out of range.")
|
---|
| 2065 | return self._getspectrum(key)
|
---|
| 2066 |
|
---|
| 2067 | def __setitem__(self, key, value):
|
---|
| 2068 | if key < 0:
|
---|
| 2069 | key += self.nrow()
|
---|
| 2070 | if key >= self.nrow():
|
---|
| 2071 | raise IndexError("Row index out of range.")
|
---|
| 2072 | if not hasattr(value, "__len__") or \
|
---|
| 2073 | len(value) > self.nchan(self.getif(key)):
|
---|
| 2074 | raise ValueError("Spectrum length doesn't match.")
|
---|
| 2075 | return self._setspectrum(value, key)
|
---|
| 2076 |
|
---|
| 2077 | def __len__(self):
|
---|
| 2078 | return self.nrow()
|
---|
| 2079 |
|
---|
| 2080 | def __iter__(self):
|
---|
| 2081 | for i in range(len(self)):
|
---|
| 2082 | yield self[i]
|
---|