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