[876] | 1 | from asap._asap import Scantable |
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[226] | 2 | from asap import rcParams |
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[1118] | 3 | from asap import print_log |
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| 4 | from asap import asaplog |
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[946] | 5 | from asap import selector |
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[1153] | 6 | from asap import linecatalog |
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[1295] | 7 | from asap import _n_bools, mask_not, mask_and, mask_or |
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[102] | 8 | |
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[876] | 9 | class scantable(Scantable): |
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[102] | 10 | """ |
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| 11 | The ASAP container for scans |
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| 12 | """ |
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[710] | 13 | |
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[484] | 14 | def __init__(self, filename, average=None, unit=None): |
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[102] | 15 | """ |
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| 16 | Create a scantable from a saved one or make a reference |
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| 17 | Parameters: |
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[181] | 18 | filename: the name of an asap table on disk |
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| 19 | or |
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| 20 | the name of a rpfits/sdfits/ms file |
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| 21 | (integrations within scans are auto averaged |
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| 22 | and the whole file is read) |
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| 23 | or |
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| 24 | [advanced] a reference to an existing |
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[102] | 25 | scantable |
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[484] | 26 | average: average all integrations withinb a scan on read. |
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| 27 | The default (True) is taken from .asaprc. |
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| 28 | unit: brightness unit; must be consistent with K or Jy. |
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[340] | 29 | Over-rides the default selected by the reader |
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| 30 | (input rpfits/sdfits/ms) or replaces the value |
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| 31 | in existing scantables |
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[710] | 32 | """ |
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[976] | 33 | if average is None: |
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[710] | 34 | average = rcParams['scantable.autoaverage'] |
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[1259] | 35 | varlist = vars() |
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[876] | 36 | from asap._asap import stmath |
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| 37 | self._math = stmath() |
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| 38 | if isinstance(filename, Scantable): |
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| 39 | Scantable.__init__(self, filename) |
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[181] | 40 | else: |
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[1435] | 41 | if isinstance(filename, str):# or \ |
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| 42 | # (isinstance(filename, list) or isinstance(filename, tuple)) \ |
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| 43 | # and isinstance(filename[-1], str): |
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[976] | 44 | import os.path |
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| 45 | filename = os.path.expandvars(filename) |
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| 46 | filename = os.path.expanduser(filename) |
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| 47 | if not os.path.exists(filename): |
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| 48 | s = "File '%s' not found." % (filename) |
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[718] | 49 | if rcParams['verbose']: |
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[976] | 50 | asaplog.push(s) |
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| 51 | print asaplog.pop().strip() |
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[718] | 52 | return |
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[976] | 53 | raise IOError(s) |
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[1115] | 54 | if os.path.isdir(filename) \ |
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[1118] | 55 | and not os.path.exists(filename+'/table.f1'): |
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[976] | 56 | # crude check if asap table |
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| 57 | if os.path.exists(filename+'/table.info'): |
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[1118] | 58 | ondisk = rcParams['scantable.storage'] == 'disk' |
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| 59 | Scantable.__init__(self, filename, ondisk) |
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[976] | 60 | if unit is not None: |
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| 61 | self.set_fluxunit(unit) |
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| 62 | self.set_freqframe(rcParams['scantable.freqframe']) |
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[718] | 63 | else: |
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[1118] | 64 | msg = "The given file '%s'is not a valid " \ |
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| 65 | "asap table." % (filename) |
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[976] | 66 | if rcParams['verbose']: |
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| 67 | print msg |
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| 68 | return |
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| 69 | else: |
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| 70 | raise IOError(msg) |
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[226] | 71 | else: |
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[1118] | 72 | self._fill([filename], unit, average) |
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| 73 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
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[976] | 74 | and isinstance(filename[-1], str): |
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| 75 | self._fill(filename, unit, average) |
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[1259] | 76 | self._add_history("scantable", varlist) |
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[714] | 77 | print_log() |
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[102] | 78 | |
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[876] | 79 | def save(self, name=None, format=None, overwrite=False): |
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[116] | 80 | """ |
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[1280] | 81 | Store the scantable on disk. This can be an asap (aips++) Table, |
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| 82 | SDFITS or MS2 format. |
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[116] | 83 | Parameters: |
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[1093] | 84 | name: the name of the outputfile. For format "ASCII" |
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| 85 | this is the root file name (data in 'name'.txt |
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[497] | 86 | and header in 'name'_header.txt) |
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[116] | 87 | format: an optional file format. Default is ASAP. |
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[280] | 88 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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[194] | 89 | 'SDFITS' (save as SDFITS file) |
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[200] | 90 | 'ASCII' (saves as ascii text file) |
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[226] | 91 | 'MS2' (saves as an aips++ |
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| 92 | MeasurementSet V2) |
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[1443] | 93 | 'FITS' (save as image FITS - not |
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| 94 | readable by class) |
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| 95 | 'CLASS' (save as FITS readable by CLASS) |
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[411] | 96 | overwrite: If the file should be overwritten if it exists. |
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[256] | 97 | The default False is to return with warning |
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[411] | 98 | without writing the output. USE WITH CARE. |
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[116] | 99 | Example: |
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| 100 | scan.save('myscan.asap') |
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[1118] | 101 | scan.save('myscan.sdfits', 'SDFITS') |
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[116] | 102 | """ |
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[411] | 103 | from os import path |
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[226] | 104 | if format is None: format = rcParams['scantable.save'] |
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[256] | 105 | suffix = '.'+format.lower() |
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[1118] | 106 | if name is None or name == "": |
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[256] | 107 | name = 'scantable'+suffix |
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[718] | 108 | msg = "No filename given. Using default name %s..." % name |
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| 109 | asaplog.push(msg) |
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[411] | 110 | name = path.expandvars(name) |
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[256] | 111 | if path.isfile(name) or path.isdir(name): |
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| 112 | if not overwrite: |
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[718] | 113 | msg = "File %s exists." % name |
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| 114 | if rcParams['verbose']: |
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| 115 | print msg |
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| 116 | return |
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| 117 | else: |
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| 118 | raise IOError(msg) |
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[451] | 119 | format2 = format.upper() |
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| 120 | if format2 == 'ASAP': |
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[116] | 121 | self._save(name) |
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| 122 | else: |
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[989] | 123 | from asap._asap import stwriter as stw |
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[1118] | 124 | writer = stw(format2) |
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| 125 | writer.write(self, name) |
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[718] | 126 | print_log() |
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[116] | 127 | return |
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| 128 | |
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[102] | 129 | def copy(self): |
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| 130 | """ |
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| 131 | Return a copy of this scantable. |
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[1348] | 132 | Note: |
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| 133 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
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[102] | 134 | Parameters: |
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[113] | 135 | none |
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[102] | 136 | Example: |
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| 137 | copiedscan = scan.copy() |
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| 138 | """ |
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[876] | 139 | sd = scantable(Scantable._copy(self)) |
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[113] | 140 | return sd |
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| 141 | |
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[1093] | 142 | def drop_scan(self, scanid=None): |
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| 143 | """ |
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| 144 | Return a new scantable where the specified scan number(s) has(have) |
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| 145 | been dropped. |
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| 146 | Parameters: |
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| 147 | scanid: a (list of) scan number(s) |
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| 148 | """ |
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| 149 | from asap import _is_sequence_or_number as _is_valid |
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| 150 | from asap import _to_list |
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| 151 | from asap import unique |
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| 152 | if not _is_valid(scanid): |
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| 153 | if rcParams['verbose']: |
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| 154 | print "Please specify a scanno to drop from the scantable" |
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| 155 | return |
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| 156 | else: |
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| 157 | raise RuntimeError("No scan given") |
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| 158 | try: |
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| 159 | scanid = _to_list(scanid) |
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| 160 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
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| 161 | for sid in scanid: allscans.remove(sid) |
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[1118] | 162 | if len(allscans) == 0: |
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| 163 | raise ValueError("Can't remove all scans") |
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[1093] | 164 | except ValueError: |
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| 165 | if rcParams['verbose']: |
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| 166 | print "Couldn't find any match." |
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| 167 | return |
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| 168 | else: raise |
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| 169 | try: |
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| 170 | bsel = self.get_selection() |
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| 171 | sel = selector() |
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| 172 | sel.set_scans(allscans) |
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| 173 | self.set_selection(bsel+sel) |
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| 174 | scopy = self._copy() |
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| 175 | self.set_selection(bsel) |
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| 176 | return scantable(scopy) |
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| 177 | except RuntimeError: |
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[1118] | 178 | if rcParams['verbose']: |
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| 179 | print "Couldn't find any match." |
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| 180 | else: |
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| 181 | raise |
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[1093] | 182 | |
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| 183 | |
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[102] | 184 | def get_scan(self, scanid=None): |
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| 185 | """ |
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| 186 | Return a specific scan (by scanno) or collection of scans (by |
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| 187 | source name) in a new scantable. |
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[1348] | 188 | Note: |
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| 189 | See scantable.drop_scan() for the inverse operation. |
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[102] | 190 | Parameters: |
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[513] | 191 | scanid: a (list of) scanno or a source name, unix-style |
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| 192 | patterns are accepted for source name matching, e.g. |
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| 193 | '*_R' gets all 'ref scans |
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[102] | 194 | Example: |
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[513] | 195 | # get all scans containing the source '323p459' |
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| 196 | newscan = scan.get_scan('323p459') |
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| 197 | # get all 'off' scans |
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| 198 | refscans = scan.get_scan('*_R') |
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| 199 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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[1118] | 200 | newscan = scan.get_scan([0, 2, 7, 10]) |
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[102] | 201 | """ |
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| 202 | if scanid is None: |
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[718] | 203 | if rcParams['verbose']: |
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[1118] | 204 | print "Please specify a scan no or name to " \ |
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| 205 | "retrieve from the scantable" |
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[718] | 206 | return |
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| 207 | else: |
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| 208 | raise RuntimeError("No scan given") |
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| 209 | |
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[102] | 210 | try: |
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[946] | 211 | bsel = self.get_selection() |
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| 212 | sel = selector() |
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[102] | 213 | if type(scanid) is str: |
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[946] | 214 | sel.set_name(scanid) |
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| 215 | self.set_selection(bsel+sel) |
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[876] | 216 | scopy = self._copy() |
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[946] | 217 | self.set_selection(bsel) |
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[876] | 218 | return scantable(scopy) |
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[102] | 219 | elif type(scanid) is int: |
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[946] | 220 | sel.set_scans([scanid]) |
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| 221 | self.set_selection(bsel+sel) |
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[876] | 222 | scopy = self._copy() |
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[946] | 223 | self.set_selection(bsel) |
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[876] | 224 | return scantable(scopy) |
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[381] | 225 | elif type(scanid) is list: |
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[946] | 226 | sel.set_scans(scanid) |
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| 227 | self.set_selection(sel) |
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[876] | 228 | scopy = self._copy() |
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[946] | 229 | self.set_selection(bsel) |
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[876] | 230 | return scantable(scopy) |
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[381] | 231 | else: |
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[718] | 232 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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| 233 | if rcParams['verbose']: |
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| 234 | print msg |
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| 235 | else: |
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| 236 | raise TypeError(msg) |
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[102] | 237 | except RuntimeError: |
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[718] | 238 | if rcParams['verbose']: print "Couldn't find any match." |
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| 239 | else: raise |
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[102] | 240 | |
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| 241 | def __str__(self): |
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[1118] | 242 | return Scantable._summary(self, True) |
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[102] | 243 | |
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[976] | 244 | def summary(self, filename=None): |
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[102] | 245 | """ |
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| 246 | Print a summary of the contents of this scantable. |
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| 247 | Parameters: |
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| 248 | filename: the name of a file to write the putput to |
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| 249 | Default - no file output |
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[381] | 250 | verbose: print extra info such as the frequency table |
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| 251 | The default (False) is taken from .asaprc |
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[102] | 252 | """ |
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[976] | 253 | info = Scantable._summary(self, True) |
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| 254 | #if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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[102] | 255 | if filename is not None: |
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[256] | 256 | if filename is "": |
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| 257 | filename = 'scantable_summary.txt' |
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[415] | 258 | from os.path import expandvars, isdir |
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[411] | 259 | filename = expandvars(filename) |
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[415] | 260 | if not isdir(filename): |
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[413] | 261 | data = open(filename, 'w') |
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| 262 | data.write(info) |
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| 263 | data.close() |
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| 264 | else: |
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[718] | 265 | msg = "Illegal file name '%s'." % (filename) |
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| 266 | if rcParams['verbose']: |
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| 267 | print msg |
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| 268 | else: |
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| 269 | raise IOError(msg) |
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| 270 | if rcParams['verbose']: |
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[794] | 271 | try: |
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| 272 | from IPython.genutils import page as pager |
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| 273 | except ImportError: |
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| 274 | from pydoc import pager |
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| 275 | pager(info) |
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[718] | 276 | else: |
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| 277 | return info |
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[710] | 278 | |
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[946] | 279 | |
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| 280 | def get_selection(self): |
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| 281 | """ |
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[1005] | 282 | Get the selection object currently set on this scantable. |
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| 283 | Parameters: |
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| 284 | none |
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| 285 | Example: |
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| 286 | sel = scan.get_selection() |
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| 287 | sel.set_ifs(0) # select IF 0 |
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| 288 | scan.set_selection(sel) # apply modified selection |
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[946] | 289 | """ |
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| 290 | return selector(self._getselection()) |
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| 291 | |
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[1005] | 292 | def set_selection(self, selection=selector()): |
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[946] | 293 | """ |
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[1005] | 294 | Select a subset of the data. All following operations on this scantable |
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| 295 | are only applied to thi selection. |
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| 296 | Parameters: |
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| 297 | selection: a selector object (default unset the selection) |
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| 298 | Examples: |
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| 299 | sel = selector() # create a selection object |
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[1118] | 300 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
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[1005] | 301 | scan.set_selection(sel) # set the selection |
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| 302 | scan.summary() # will only print summary of scanno 0 an 3 |
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| 303 | scan.set_selection() # unset the selection |
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[946] | 304 | """ |
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| 305 | self._setselection(selection) |
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| 306 | |
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[876] | 307 | def stats(self, stat='stddev', mask=None): |
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[102] | 308 | """ |
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[135] | 309 | Determine the specified statistic of the current beam/if/pol |
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[102] | 310 | Takes a 'mask' as an optional parameter to specify which |
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| 311 | channels should be excluded. |
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| 312 | Parameters: |
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[135] | 313 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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| 314 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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| 315 | mask: an optional mask specifying where the statistic |
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[102] | 316 | should be determined. |
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| 317 | Example: |
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[113] | 318 | scan.set_unit('channel') |
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[1118] | 319 | msk = scan.create_mask([100, 200], [500, 600]) |
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[135] | 320 | scan.stats(stat='mean', mask=m) |
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[102] | 321 | """ |
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| 322 | if mask == None: |
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[876] | 323 | mask = [] |
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[1118] | 324 | axes = ['Beam', 'IF', 'Pol', 'Time'] |
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[876] | 325 | if not self._check_ifs(): |
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[1118] | 326 | raise ValueError("Cannot apply mask as the IFs have different " |
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| 327 | "number of channels. Please use setselection() " |
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| 328 | "to select individual IFs") |
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[256] | 329 | |
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[876] | 330 | statvals = self._math._stats(self, mask, stat) |
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| 331 | out = '' |
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| 332 | axes = [] |
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| 333 | for i in range(self.nrow()): |
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| 334 | axis = [] |
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| 335 | axis.append(self.getscan(i)) |
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| 336 | axis.append(self.getbeam(i)) |
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| 337 | axis.append(self.getif(i)) |
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| 338 | axis.append(self.getpol(i)) |
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| 339 | axis.append(self.getcycle(i)) |
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| 340 | axes.append(axis) |
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| 341 | tm = self._gettime(i) |
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| 342 | src = self._getsourcename(i) |
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| 343 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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| 344 | out += 'Time[%s]:\n' % (tm) |
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| 345 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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| 346 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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| 347 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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| 348 | out += '= %3.3f\n' % (statvals[i]) |
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| 349 | out += "--------------------------------------------------\n" |
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[256] | 350 | |
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[876] | 351 | if rcParams['verbose']: |
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| 352 | print "--------------------------------------------------" |
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[1118] | 353 | print " ", stat |
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[876] | 354 | print "--------------------------------------------------" |
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| 355 | print out |
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[1295] | 356 | #else: |
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| 357 | #retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'], |
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| 358 | # 'axes' : axes, |
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| 359 | # 'data': statvals} |
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| 360 | return statvals |
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[102] | 361 | |
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[1118] | 362 | def stddev(self, mask=None): |
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[135] | 363 | """ |
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| 364 | Determine the standard deviation of the current beam/if/pol |
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| 365 | Takes a 'mask' as an optional parameter to specify which |
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| 366 | channels should be excluded. |
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| 367 | Parameters: |
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| 368 | mask: an optional mask specifying where the standard |
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| 369 | deviation should be determined. |
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| 370 | |
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| 371 | Example: |
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| 372 | scan.set_unit('channel') |
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[1118] | 373 | msk = scan.create_mask([100, 200], [500, 600]) |
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[135] | 374 | scan.stddev(mask=m) |
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| 375 | """ |
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[1118] | 376 | return self.stats(stat='stddev', mask=mask); |
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[135] | 377 | |
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[1003] | 378 | |
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[1259] | 379 | def get_column_names(self): |
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[1003] | 380 | """ |
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| 381 | Return a list of column names, which can be used for selection. |
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| 382 | """ |
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[1259] | 383 | return list(Scantable.get_column_names(self)) |
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[1003] | 384 | |
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[876] | 385 | def get_tsys(self): |
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[113] | 386 | """ |
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| 387 | Return the System temperatures. |
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| 388 | Returns: |
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[876] | 389 | a list of Tsys values for the current selection |
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[113] | 390 | """ |
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[256] | 391 | |
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[876] | 392 | return self._row_callback(self._gettsys, "Tsys") |
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[256] | 393 | |
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[876] | 394 | def _row_callback(self, callback, label): |
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| 395 | axes = [] |
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[1118] | 396 | axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'] |
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[876] | 397 | out = "" |
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[1118] | 398 | outvec = [] |
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[876] | 399 | for i in range(self.nrow()): |
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| 400 | axis = [] |
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| 401 | axis.append(self.getscan(i)) |
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| 402 | axis.append(self.getbeam(i)) |
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| 403 | axis.append(self.getif(i)) |
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| 404 | axis.append(self.getpol(i)) |
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| 405 | axis.append(self.getcycle(i)) |
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| 406 | axes.append(axis) |
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| 407 | tm = self._gettime(i) |
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| 408 | src = self._getsourcename(i) |
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| 409 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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| 410 | out += 'Time[%s]:\n' % (tm) |
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| 411 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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| 412 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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| 413 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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| 414 | outvec.append(callback(i)) |
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| 415 | out += '= %3.3f\n' % (outvec[i]) |
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| 416 | out += "--------------------------------------------------\n" |
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| 417 | if rcParams['verbose']: |
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| 418 | print "--------------------------------------------------" |
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| 419 | print " %s" % (label) |
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| 420 | print "--------------------------------------------------" |
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| 421 | print out |
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[1175] | 422 | # disabled because the vector seems more useful |
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| 423 | #retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec} |
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| 424 | return outvec |
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[256] | 425 | |
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[1070] | 426 | def _get_column(self, callback, row=-1): |
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| 427 | """ |
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| 428 | """ |
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| 429 | if row == -1: |
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| 430 | return [callback(i) for i in range(self.nrow())] |
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| 431 | else: |
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| 432 | if 0 <= row < self.nrow(): |
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| 433 | return callback(row) |
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[256] | 434 | |
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[1070] | 435 | |
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[1348] | 436 | def get_time(self, row=-1, asdatetime=False): |
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[113] | 437 | """ |
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| 438 | Get a list of time stamps for the observations. |
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[1348] | 439 | Return a datetime object for each integration time stamp in the scantable. |
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[113] | 440 | Parameters: |
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[1348] | 441 | row: row no of integration. Default -1 return all rows |
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| 442 | asdatetime: return values as datetime objects rather than strings |
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[113] | 443 | Example: |
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| 444 | none |
---|
| 445 | """ |
---|
[1175] | 446 | from time import strptime |
---|
| 447 | from datetime import datetime |
---|
[1392] | 448 | times = self._get_column(self._gettime, row) |
---|
[1348] | 449 | if not asdatetime: |
---|
[1392] | 450 | return times |
---|
[1175] | 451 | format = "%Y/%m/%d/%H:%M:%S" |
---|
| 452 | if isinstance(times, list): |
---|
| 453 | return [datetime(*strptime(i, format)[:6]) for i in times] |
---|
| 454 | else: |
---|
| 455 | return datetime(*strptime(times, format)[:6]) |
---|
[102] | 456 | |
---|
[1348] | 457 | |
---|
| 458 | def get_inttime(self, row=-1): |
---|
| 459 | """ |
---|
| 460 | Get a list of integration times for the observations. |
---|
| 461 | Return a time in seconds for each integration in the scantable. |
---|
| 462 | Parameters: |
---|
| 463 | row: row no of integration. Default -1 return all rows. |
---|
| 464 | Example: |
---|
| 465 | none |
---|
| 466 | """ |
---|
| 467 | return self._get_column(self._getinttime, row) |
---|
| 468 | |
---|
| 469 | |
---|
[714] | 470 | def get_sourcename(self, row=-1): |
---|
| 471 | """ |
---|
[794] | 472 | Get a list source names for the observations. |
---|
[714] | 473 | Return a string for each integration in the scantable. |
---|
| 474 | Parameters: |
---|
[1348] | 475 | row: row no of integration. Default -1 return all rows. |
---|
[714] | 476 | Example: |
---|
| 477 | none |
---|
| 478 | """ |
---|
[1070] | 479 | return self._get_column(self._getsourcename, row) |
---|
[714] | 480 | |
---|
[794] | 481 | def get_elevation(self, row=-1): |
---|
| 482 | """ |
---|
| 483 | Get a list of elevations for the observations. |
---|
| 484 | Return a float for each integration in the scantable. |
---|
| 485 | Parameters: |
---|
[1348] | 486 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 487 | Example: |
---|
| 488 | none |
---|
| 489 | """ |
---|
[1070] | 490 | return self._get_column(self._getelevation, row) |
---|
[794] | 491 | |
---|
| 492 | def get_azimuth(self, row=-1): |
---|
| 493 | """ |
---|
| 494 | Get a list of azimuths for the observations. |
---|
| 495 | Return a float for each integration in the scantable. |
---|
| 496 | Parameters: |
---|
[1348] | 497 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 498 | Example: |
---|
| 499 | none |
---|
| 500 | """ |
---|
[1070] | 501 | return self._get_column(self._getazimuth, row) |
---|
[794] | 502 | |
---|
| 503 | def get_parangle(self, row=-1): |
---|
| 504 | """ |
---|
| 505 | Get a list of parallactic angles for the observations. |
---|
| 506 | Return a float for each integration in the scantable. |
---|
| 507 | Parameters: |
---|
[1348] | 508 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 509 | Example: |
---|
| 510 | none |
---|
| 511 | """ |
---|
[1070] | 512 | return self._get_column(self._getparangle, row) |
---|
[794] | 513 | |
---|
[1070] | 514 | def get_direction(self, row=-1): |
---|
| 515 | """ |
---|
| 516 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 517 | Return a float for each integration in the scantable. |
---|
| 518 | Parameters: |
---|
| 519 | row: row no of integration. Default -1 return all rows |
---|
| 520 | Example: |
---|
| 521 | none |
---|
| 522 | """ |
---|
| 523 | return self._get_column(self._getdirection, row) |
---|
| 524 | |
---|
[1391] | 525 | def get_directionval(self, row=-1): |
---|
| 526 | """ |
---|
| 527 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 528 | Return a float for each integration in the scantable. |
---|
| 529 | Parameters: |
---|
| 530 | row: row no of integration. Default -1 return all rows |
---|
| 531 | Example: |
---|
| 532 | none |
---|
| 533 | """ |
---|
| 534 | return self._get_column(self._getdirectionvec, row) |
---|
| 535 | |
---|
| 536 | |
---|
[102] | 537 | def set_unit(self, unit='channel'): |
---|
| 538 | """ |
---|
| 539 | Set the unit for all following operations on this scantable |
---|
| 540 | Parameters: |
---|
| 541 | unit: optional unit, default is 'channel' |
---|
[1118] | 542 | one of '*Hz', 'km/s', 'channel', '' |
---|
[102] | 543 | """ |
---|
[484] | 544 | varlist = vars() |
---|
[1118] | 545 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 546 | unit = '' |
---|
| 547 | inf = list(self._getcoordinfo()) |
---|
| 548 | inf[0] = unit |
---|
| 549 | self._setcoordinfo(inf) |
---|
[1118] | 550 | self._add_history("set_unit", varlist) |
---|
[113] | 551 | |
---|
[484] | 552 | def set_instrument(self, instr): |
---|
[358] | 553 | """ |
---|
[1348] | 554 | Set the instrument for subsequent processing. |
---|
[358] | 555 | Parameters: |
---|
[710] | 556 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 557 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 558 | """ |
---|
| 559 | self._setInstrument(instr) |
---|
[1118] | 560 | self._add_history("set_instument", vars()) |
---|
[718] | 561 | print_log() |
---|
[358] | 562 | |
---|
[1190] | 563 | def set_feedtype(self, feedtype): |
---|
| 564 | """ |
---|
| 565 | Overwrite the feed type, which might not be set correctly. |
---|
| 566 | Parameters: |
---|
| 567 | feedtype: 'linear' or 'circular' |
---|
| 568 | """ |
---|
| 569 | self._setfeedtype(feedtype) |
---|
| 570 | self._add_history("set_feedtype", vars()) |
---|
| 571 | print_log() |
---|
| 572 | |
---|
[276] | 573 | def set_doppler(self, doppler='RADIO'): |
---|
| 574 | """ |
---|
| 575 | Set the doppler for all following operations on this scantable. |
---|
| 576 | Parameters: |
---|
| 577 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 578 | """ |
---|
[484] | 579 | varlist = vars() |
---|
[276] | 580 | inf = list(self._getcoordinfo()) |
---|
| 581 | inf[2] = doppler |
---|
| 582 | self._setcoordinfo(inf) |
---|
[1118] | 583 | self._add_history("set_doppler", vars()) |
---|
[718] | 584 | print_log() |
---|
[710] | 585 | |
---|
[226] | 586 | def set_freqframe(self, frame=None): |
---|
[113] | 587 | """ |
---|
| 588 | Set the frame type of the Spectral Axis. |
---|
| 589 | Parameters: |
---|
[591] | 590 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1118] | 591 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
| 592 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[113] | 593 | Examples: |
---|
| 594 | scan.set_freqframe('BARY') |
---|
| 595 | """ |
---|
[484] | 596 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
| 597 | varlist = vars() |
---|
[1118] | 598 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 599 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 600 | |
---|
[989] | 601 | if frame in valid: |
---|
[113] | 602 | inf = list(self._getcoordinfo()) |
---|
| 603 | inf[1] = frame |
---|
| 604 | self._setcoordinfo(inf) |
---|
[1118] | 605 | self._add_history("set_freqframe", varlist) |
---|
[102] | 606 | else: |
---|
[1118] | 607 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[718] | 608 | if rcParams['verbose']: |
---|
| 609 | print msg |
---|
| 610 | else: |
---|
| 611 | raise TypeError(msg) |
---|
| 612 | print_log() |
---|
[710] | 613 | |
---|
[989] | 614 | def set_dirframe(self, frame=""): |
---|
| 615 | """ |
---|
| 616 | Set the frame type of the Direction on the sky. |
---|
| 617 | Parameters: |
---|
| 618 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 619 | 'J2000', 'B1950', 'GALACTIC' |
---|
| 620 | Examples: |
---|
| 621 | scan.set_dirframe('GALACTIC') |
---|
| 622 | """ |
---|
| 623 | varlist = vars() |
---|
| 624 | try: |
---|
| 625 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 626 | except RuntimeError, msg: |
---|
[989] | 627 | if rcParams['verbose']: |
---|
| 628 | print msg |
---|
| 629 | else: |
---|
| 630 | raise |
---|
[1118] | 631 | self._add_history("set_dirframe", varlist) |
---|
[989] | 632 | |
---|
[113] | 633 | def get_unit(self): |
---|
| 634 | """ |
---|
| 635 | Get the default unit set in this scantable |
---|
| 636 | Returns: |
---|
| 637 | A unit string |
---|
| 638 | """ |
---|
| 639 | inf = self._getcoordinfo() |
---|
| 640 | unit = inf[0] |
---|
| 641 | if unit == '': unit = 'channel' |
---|
| 642 | return unit |
---|
[102] | 643 | |
---|
[158] | 644 | def get_abcissa(self, rowno=0): |
---|
[102] | 645 | """ |
---|
[158] | 646 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 647 | selected Beam/IF/Pol |
---|
| 648 | Parameters: |
---|
[226] | 649 | rowno: an optional row number in the scantable. Default is the |
---|
| 650 | first row, i.e. rowno=0 |
---|
[113] | 651 | Returns: |
---|
[1348] | 652 | The abcissa values and the format string (as a dictionary) |
---|
[113] | 653 | """ |
---|
[256] | 654 | abc = self._getabcissa(rowno) |
---|
[710] | 655 | lbl = self._getabcissalabel(rowno) |
---|
[718] | 656 | print_log() |
---|
[158] | 657 | return abc, lbl |
---|
[113] | 658 | |
---|
[1118] | 659 | def flag(self, mask=None): |
---|
[1001] | 660 | """ |
---|
| 661 | Flag the selected data using an optional channel mask. |
---|
| 662 | Parameters: |
---|
| 663 | mask: an optional channel mask, created with create_mask. Default |
---|
| 664 | (no mask) is all channels. |
---|
| 665 | """ |
---|
| 666 | varlist = vars() |
---|
[1118] | 667 | if mask is None: |
---|
| 668 | mask = [] |
---|
[1001] | 669 | try: |
---|
| 670 | self._flag(mask) |
---|
[1118] | 671 | except RuntimeError, msg: |
---|
[1001] | 672 | if rcParams['verbose']: |
---|
| 673 | print msg |
---|
| 674 | return |
---|
| 675 | else: raise |
---|
| 676 | self._add_history("flag", varlist) |
---|
| 677 | |
---|
[1203] | 678 | def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None): |
---|
[1192] | 679 | """ |
---|
| 680 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
| 681 | Flagged data in the scantable gets set to 0.0 before the fft. |
---|
| 682 | No taper is applied. |
---|
| 683 | Parameters: |
---|
[1348] | 684 | frequency: the frequency (really a period within the bandwidth) |
---|
| 685 | to remove |
---|
| 686 | width: the width of the frequency to remove, to remove a |
---|
| 687 | range of frequencies aroung the centre. |
---|
[1203] | 688 | unit: the frequency unit (default "GHz") |
---|
| 689 | Notes: |
---|
[1348] | 690 | It is recommended to flag edges of the band or strong |
---|
| 691 | signals beforehand. |
---|
[1192] | 692 | """ |
---|
| 693 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 694 | self._math._setinsitu(insitu) |
---|
| 695 | varlist = vars() |
---|
[1370] | 696 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. } |
---|
[1192] | 697 | if not base.has_key(unit): |
---|
| 698 | raise ValueError("%s is not a valid unit." % unit) |
---|
| 699 | try: |
---|
[1200] | 700 | s = scantable(self._math._lag_flag(self, frequency*base[unit], |
---|
| 701 | width*base[unit])) |
---|
[1192] | 702 | except RuntimeError, msg: |
---|
| 703 | if rcParams['verbose']: |
---|
| 704 | print msg |
---|
| 705 | return |
---|
| 706 | else: raise |
---|
| 707 | s._add_history("lag_flag", varlist) |
---|
| 708 | print_log() |
---|
| 709 | if insitu: |
---|
| 710 | self._assign(s) |
---|
| 711 | else: |
---|
| 712 | return s |
---|
[1001] | 713 | |
---|
[1192] | 714 | |
---|
[113] | 715 | def create_mask(self, *args, **kwargs): |
---|
| 716 | """ |
---|
[1118] | 717 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 718 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 719 | applied. |
---|
[102] | 720 | Parameters: |
---|
[1118] | 721 | [min, max], [min2, max2], ... |
---|
[1024] | 722 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 723 | to be masked |
---|
[189] | 724 | invert: optional argument. If specified as True, |
---|
| 725 | return an inverted mask, i.e. the regions |
---|
| 726 | specified are EXCLUDED |
---|
[513] | 727 | row: create the mask using the specified row for |
---|
| 728 | unit conversions, default is row=0 |
---|
| 729 | only necessary if frequency varies over rows. |
---|
[102] | 730 | Example: |
---|
[113] | 731 | scan.set_unit('channel') |
---|
| 732 | a) |
---|
[1118] | 733 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 734 | # masks everything outside 400 and 500 |
---|
[113] | 735 | # and 800 and 900 in the unit 'channel' |
---|
| 736 | |
---|
| 737 | b) |
---|
[1118] | 738 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 739 | # masks the regions between 400 and 500 |
---|
[113] | 740 | # and 800 and 900 in the unit 'channel' |
---|
[1024] | 741 | c) |
---|
| 742 | mask only channel 400 |
---|
[1118] | 743 | msk = scan.create_mask([400, 400]) |
---|
[102] | 744 | """ |
---|
[513] | 745 | row = 0 |
---|
| 746 | if kwargs.has_key("row"): |
---|
| 747 | row = kwargs.get("row") |
---|
| 748 | data = self._getabcissa(row) |
---|
[113] | 749 | u = self._getcoordinfo()[0] |
---|
[718] | 750 | if rcParams['verbose']: |
---|
[113] | 751 | if u == "": u = "channel" |
---|
[718] | 752 | msg = "The current mask window unit is %s" % u |
---|
[1118] | 753 | i = self._check_ifs() |
---|
| 754 | if not i: |
---|
[876] | 755 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 756 | asaplog.push(msg) |
---|
[102] | 757 | n = self.nchan() |
---|
[1295] | 758 | msk = _n_bools(n, False) |
---|
[710] | 759 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 760 | |
---|
[1118] | 761 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 762 | and args or args[0] |
---|
[710] | 763 | for window in ws: |
---|
[102] | 764 | if (len(window) != 2 or window[0] > window[1] ): |
---|
[1118] | 765 | raise TypeError("A window needs to be defined as [min, max]") |
---|
[102] | 766 | for i in range(n): |
---|
[1024] | 767 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 768 | msk[i] = True |
---|
[113] | 769 | if kwargs.has_key('invert'): |
---|
| 770 | if kwargs.get('invert'): |
---|
[1295] | 771 | msk = mask_not(msk) |
---|
[718] | 772 | print_log() |
---|
[102] | 773 | return msk |
---|
[710] | 774 | |
---|
[256] | 775 | def get_restfreqs(self): |
---|
| 776 | """ |
---|
| 777 | Get the restfrequency(s) stored in this scantable. |
---|
| 778 | The return value(s) are always of unit 'Hz' |
---|
| 779 | Parameters: |
---|
| 780 | none |
---|
| 781 | Returns: |
---|
| 782 | a list of doubles |
---|
| 783 | """ |
---|
| 784 | return list(self._getrestfreqs()) |
---|
[102] | 785 | |
---|
[402] | 786 | |
---|
[931] | 787 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
| 788 | """ |
---|
| 789 | Set or replace the restfrequency specified and |
---|
| 790 | If the 'freqs' argument holds a scalar, |
---|
| 791 | then that rest frequency will be applied to all the selected |
---|
| 792 | data. If the 'freqs' argument holds |
---|
| 793 | a vector, then it MUST be of equal or smaller length than |
---|
| 794 | the number of IFs (and the available restfrequencies will be |
---|
| 795 | replaced by this vector). In this case, *all* data have |
---|
| 796 | the restfrequency set per IF according |
---|
| 797 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 798 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 799 | IF 1 gets restfreq 2e9. |
---|
[1395] | 800 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 801 | |
---|
[931] | 802 | Parameters: |
---|
| 803 | freqs: list of rest frequency values or string idenitfiers |
---|
| 804 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 805 | |
---|
[931] | 806 | Example: |
---|
| 807 | # set the given restfrequency for the whole table |
---|
| 808 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1348] | 809 | # If thee number of IFs in the data is >= 2 IF0 gets the first |
---|
[931] | 810 | # value IF1 the second... |
---|
[1118] | 811 | scan.set_restfreqs(freqs=[1.4e9, 1.67e9]) |
---|
[931] | 812 | #set the given restfrequency for the whole table (by name) |
---|
| 813 | scan.set_restfreqs(freqs="OH1667") |
---|
[391] | 814 | |
---|
[931] | 815 | Note: |
---|
| 816 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 817 | source and IF basis, use scantable.set_selection() before using |
---|
| 818 | this function. |
---|
| 819 | # provide your scantable is call scan |
---|
| 820 | selection = selector() |
---|
| 821 | selection.set_name("ORION*") |
---|
| 822 | selection.set_ifs([1]) |
---|
| 823 | scan.set_selection(selection) |
---|
| 824 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 825 | |
---|
| 826 | """ |
---|
| 827 | varlist = vars() |
---|
[1157] | 828 | from asap import linecatalog |
---|
| 829 | # simple value |
---|
[1118] | 830 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1153] | 831 | self._setrestfreqs(freqs, "",unit) |
---|
[1157] | 832 | # list of values |
---|
[1118] | 833 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 834 | # list values are scalars |
---|
[1118] | 835 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[931] | 836 | sel = selector() |
---|
| 837 | savesel = self._getselection() |
---|
[1322] | 838 | iflist = self.getifnos() |
---|
[931] | 839 | for i in xrange(len(freqs)): |
---|
[1322] | 840 | sel.set_ifs(iflist[i]) |
---|
[931] | 841 | self._setselection(sel) |
---|
[1153] | 842 | self._setrestfreqs(freqs[i], "",unit) |
---|
[931] | 843 | self._setselection(savesel) |
---|
[1157] | 844 | # list values are tuples, (value, name) |
---|
| 845 | elif isinstance(freqs[-1], dict): |
---|
| 846 | sel = selector() |
---|
| 847 | savesel = self._getselection() |
---|
[1322] | 848 | iflist = self.getifnos() |
---|
[1157] | 849 | for i in xrange(len(freqs)): |
---|
[1322] | 850 | sel.set_ifs(iflist[i]) |
---|
[1259] | 851 | self._setselection(sel) |
---|
[1157] | 852 | self._setrestfreqs(freqs[i]["value"], |
---|
| 853 | freqs[i]["name"], "MHz") |
---|
| 854 | self._setselection(savesel) |
---|
| 855 | # freqs are to be taken from a linecatalog |
---|
[1153] | 856 | elif isinstance(freqs, linecatalog): |
---|
| 857 | sel = selector() |
---|
| 858 | savesel = self._getselection() |
---|
[1322] | 859 | iflist = self.getifnos() |
---|
[1153] | 860 | for i in xrange(freqs.nrow()): |
---|
[1322] | 861 | sel.set_ifs(iflist[i]) |
---|
[1153] | 862 | self._setselection(sel) |
---|
| 863 | self._setrestfreqs(freqs.get_frequency(i), |
---|
| 864 | freqs.get_name(i), "MHz") |
---|
| 865 | # ensure that we are not iterating past nIF |
---|
| 866 | if i == self.nif()-1: break |
---|
| 867 | self._setselection(savesel) |
---|
[931] | 868 | else: |
---|
| 869 | return |
---|
| 870 | self._add_history("set_restfreqs", varlist) |
---|
| 871 | |
---|
[1360] | 872 | def shift_refpix(self, delta): |
---|
| 873 | """ |
---|
| 874 | Shift the reference pixel of the Spectra Coordinate by an |
---|
| 875 | integer amount. |
---|
| 876 | Parameters: |
---|
| 877 | delta: the amount to shift by |
---|
| 878 | Note: |
---|
| 879 | Be careful using this with broadband data. |
---|
| 880 | """ |
---|
| 881 | Scantable.shift(self, delta) |
---|
[931] | 882 | |
---|
[1259] | 883 | def history(self, filename=None): |
---|
| 884 | """ |
---|
| 885 | Print the history. Optionally to a file. |
---|
[1348] | 886 | Parameters: |
---|
| 887 | filename: The name of the file to save the history to. |
---|
[1259] | 888 | """ |
---|
[484] | 889 | hist = list(self._gethistory()) |
---|
[794] | 890 | out = "-"*80 |
---|
[484] | 891 | for h in hist: |
---|
[489] | 892 | if h.startswith("---"): |
---|
[794] | 893 | out += "\n"+h |
---|
[489] | 894 | else: |
---|
| 895 | items = h.split("##") |
---|
| 896 | date = items[0] |
---|
| 897 | func = items[1] |
---|
| 898 | items = items[2:] |
---|
[794] | 899 | out += "\n"+date+"\n" |
---|
| 900 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 901 | for i in items: |
---|
| 902 | s = i.split("=") |
---|
[1118] | 903 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[794] | 904 | out += "\n"+"-"*80 |
---|
[1259] | 905 | if filename is not None: |
---|
| 906 | if filename is "": |
---|
| 907 | filename = 'scantable_history.txt' |
---|
| 908 | import os |
---|
| 909 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 910 | if not os.path.isdir(filename): |
---|
| 911 | data = open(filename, 'w') |
---|
| 912 | data.write(out) |
---|
| 913 | data.close() |
---|
| 914 | else: |
---|
| 915 | msg = "Illegal file name '%s'." % (filename) |
---|
| 916 | if rcParams['verbose']: |
---|
| 917 | print msg |
---|
| 918 | else: |
---|
| 919 | raise IOError(msg) |
---|
| 920 | if rcParams['verbose']: |
---|
| 921 | try: |
---|
| 922 | from IPython.genutils import page as pager |
---|
| 923 | except ImportError: |
---|
| 924 | from pydoc import pager |
---|
| 925 | pager(out) |
---|
| 926 | else: |
---|
| 927 | return out |
---|
[484] | 928 | return |
---|
[513] | 929 | # |
---|
| 930 | # Maths business |
---|
| 931 | # |
---|
| 932 | |
---|
[931] | 933 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[513] | 934 | """ |
---|
[1070] | 935 | Return the (time) weighted average of a scan. |
---|
[513] | 936 | Note: |
---|
[1070] | 937 | in channels only - align if necessary |
---|
[513] | 938 | Parameters: |
---|
| 939 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 940 | weighting) |
---|
[558] | 941 | scanav: True averages each scan separately |
---|
| 942 | False (default) averages all scans together, |
---|
[1099] | 943 | weight: Weighting scheme. |
---|
| 944 | 'none' (mean no weight) |
---|
| 945 | 'var' (1/var(spec) weighted) |
---|
| 946 | 'tsys' (1/Tsys**2 weighted) |
---|
| 947 | 'tint' (integration time weighted) |
---|
| 948 | 'tintsys' (Tint/Tsys**2) |
---|
| 949 | 'median' ( median averaging) |
---|
[535] | 950 | The default is 'tint' |
---|
[931] | 951 | align: align the spectra in velocity before averaging. It takes |
---|
| 952 | the time of the first spectrum as reference time. |
---|
[513] | 953 | Example: |
---|
| 954 | # time average the scantable without using a mask |
---|
[710] | 955 | newscan = scan.average_time() |
---|
[513] | 956 | """ |
---|
| 957 | varlist = vars() |
---|
[976] | 958 | if weight is None: weight = 'TINT' |
---|
[513] | 959 | if mask is None: mask = () |
---|
[1099] | 960 | if scanav: scanav = "SCAN" |
---|
| 961 | else: scanav = "NONE" |
---|
[1118] | 962 | scan = (self, ) |
---|
[989] | 963 | try: |
---|
[1118] | 964 | if align: |
---|
| 965 | scan = (self.freq_align(insitu=False), ) |
---|
| 966 | s = None |
---|
| 967 | if weight.upper() == 'MEDIAN': |
---|
| 968 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 969 | scanav)) |
---|
| 970 | else: |
---|
| 971 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 972 | scanav)) |
---|
| 973 | except RuntimeError, msg: |
---|
[989] | 974 | if rcParams['verbose']: |
---|
| 975 | print msg |
---|
| 976 | return |
---|
| 977 | else: raise |
---|
[1099] | 978 | s._add_history("average_time", varlist) |
---|
[718] | 979 | print_log() |
---|
[513] | 980 | return s |
---|
[710] | 981 | |
---|
[876] | 982 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[513] | 983 | """ |
---|
| 984 | Return a scan where all spectra are converted to either |
---|
| 985 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 986 | By default the function tries to look the values up internally. |
---|
| 987 | If it can't find them (or if you want to over-ride), you must |
---|
| 988 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 989 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 990 | Parameters: |
---|
| 991 | jyperk: the Jy / K conversion factor |
---|
| 992 | eta: the aperture efficiency |
---|
| 993 | d: the geomtric diameter (metres) |
---|
| 994 | insitu: if False a new scantable is returned. |
---|
| 995 | Otherwise, the scaling is done in-situ |
---|
| 996 | The default is taken from .asaprc (False) |
---|
| 997 | """ |
---|
| 998 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 999 | self._math._setinsitu(insitu) |
---|
[513] | 1000 | varlist = vars() |
---|
| 1001 | if jyperk is None: jyperk = -1.0 |
---|
| 1002 | if d is None: d = -1.0 |
---|
| 1003 | if eta is None: eta = -1.0 |
---|
[876] | 1004 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 1005 | s._add_history("convert_flux", varlist) |
---|
| 1006 | print_log() |
---|
| 1007 | if insitu: self._assign(s) |
---|
| 1008 | else: return s |
---|
[513] | 1009 | |
---|
[876] | 1010 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[513] | 1011 | """ |
---|
| 1012 | Return a scan after applying a gain-elevation correction. |
---|
| 1013 | The correction can be made via either a polynomial or a |
---|
| 1014 | table-based interpolation (and extrapolation if necessary). |
---|
| 1015 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 1016 | If you specify neither, then a polynomial correction will be made |
---|
| 1017 | with built in coefficients known for certain telescopes (an error |
---|
| 1018 | will occur if the instrument is not known). |
---|
| 1019 | The data and Tsys are *divided* by the scaling factors. |
---|
| 1020 | Parameters: |
---|
| 1021 | poly: Polynomial coefficients (default None) to compute a |
---|
| 1022 | gain-elevation correction as a function of |
---|
| 1023 | elevation (in degrees). |
---|
| 1024 | filename: The name of an ascii file holding correction factors. |
---|
| 1025 | The first row of the ascii file must give the column |
---|
| 1026 | names and these MUST include columns |
---|
| 1027 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 1028 | by this) somewhere. |
---|
| 1029 | The second row must give the data type of the |
---|
| 1030 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 1031 | An example file would be |
---|
| 1032 | (actual factors are arbitrary) : |
---|
| 1033 | |
---|
| 1034 | TIME ELEVATION FACTOR |
---|
| 1035 | R R R |
---|
| 1036 | 0.1 0 0.8 |
---|
| 1037 | 0.2 20 0.85 |
---|
| 1038 | 0.3 40 0.9 |
---|
| 1039 | 0.4 60 0.85 |
---|
| 1040 | 0.5 80 0.8 |
---|
| 1041 | 0.6 90 0.75 |
---|
| 1042 | method: Interpolation method when correcting from a table. |
---|
| 1043 | Values are "nearest", "linear" (default), "cubic" |
---|
| 1044 | and "spline" |
---|
| 1045 | insitu: if False a new scantable is returned. |
---|
| 1046 | Otherwise, the scaling is done in-situ |
---|
| 1047 | The default is taken from .asaprc (False) |
---|
| 1048 | """ |
---|
| 1049 | |
---|
| 1050 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1051 | self._math._setinsitu(insitu) |
---|
[513] | 1052 | varlist = vars() |
---|
| 1053 | if poly is None: |
---|
[1118] | 1054 | poly = () |
---|
[513] | 1055 | from os.path import expandvars |
---|
| 1056 | filename = expandvars(filename) |
---|
[876] | 1057 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 1058 | s._add_history("gain_el", varlist) |
---|
| 1059 | print_log() |
---|
| 1060 | if insitu: self._assign(s) |
---|
| 1061 | else: return s |
---|
[710] | 1062 | |
---|
[931] | 1063 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[513] | 1064 | """ |
---|
| 1065 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 1066 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 1067 | set_freqframe. |
---|
| 1068 | Parameters: |
---|
| 1069 | reftime: reference time to align at. By default, the time of |
---|
| 1070 | the first row of data is used. |
---|
| 1071 | method: Interpolation method for regridding the spectra. |
---|
| 1072 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 1073 | and "spline" |
---|
| 1074 | insitu: if False a new scantable is returned. |
---|
| 1075 | Otherwise, the scaling is done in-situ |
---|
| 1076 | The default is taken from .asaprc (False) |
---|
| 1077 | """ |
---|
[931] | 1078 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 1079 | self._math._setinsitu(insitu) |
---|
[513] | 1080 | varlist = vars() |
---|
[931] | 1081 | if reftime is None: reftime = "" |
---|
| 1082 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 1083 | s._add_history("freq_align", varlist) |
---|
| 1084 | print_log() |
---|
| 1085 | if insitu: self._assign(s) |
---|
| 1086 | else: return s |
---|
[513] | 1087 | |
---|
[876] | 1088 | def opacity(self, tau, insitu=None): |
---|
[513] | 1089 | """ |
---|
| 1090 | Apply an opacity correction. The data |
---|
| 1091 | and Tsys are multiplied by the correction factor. |
---|
| 1092 | Parameters: |
---|
| 1093 | tau: Opacity from which the correction factor is |
---|
| 1094 | exp(tau*ZD) |
---|
| 1095 | where ZD is the zenith-distance |
---|
| 1096 | insitu: if False a new scantable is returned. |
---|
| 1097 | Otherwise, the scaling is done in-situ |
---|
| 1098 | The default is taken from .asaprc (False) |
---|
| 1099 | """ |
---|
| 1100 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1101 | self._math._setinsitu(insitu) |
---|
[513] | 1102 | varlist = vars() |
---|
[876] | 1103 | s = scantable(self._math._opacity(self, tau)) |
---|
| 1104 | s._add_history("opacity", varlist) |
---|
| 1105 | print_log() |
---|
| 1106 | if insitu: self._assign(s) |
---|
| 1107 | else: return s |
---|
[513] | 1108 | |
---|
| 1109 | def bin(self, width=5, insitu=None): |
---|
| 1110 | """ |
---|
| 1111 | Return a scan where all spectra have been binned up. |
---|
[1348] | 1112 | Parameters: |
---|
[513] | 1113 | width: The bin width (default=5) in pixels |
---|
| 1114 | insitu: if False a new scantable is returned. |
---|
| 1115 | Otherwise, the scaling is done in-situ |
---|
| 1116 | The default is taken from .asaprc (False) |
---|
| 1117 | """ |
---|
| 1118 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1119 | self._math._setinsitu(insitu) |
---|
[513] | 1120 | varlist = vars() |
---|
[876] | 1121 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1122 | s._add_history("bin", varlist) |
---|
[876] | 1123 | print_log() |
---|
| 1124 | if insitu: self._assign(s) |
---|
| 1125 | else: return s |
---|
[513] | 1126 | |
---|
[710] | 1127 | |
---|
[513] | 1128 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 1129 | """ |
---|
[1348] | 1130 | Return a scan where all spectra have been binned up. |
---|
| 1131 | |
---|
| 1132 | Parameters: |
---|
[513] | 1133 | width: The bin width (default=5) in pixels |
---|
| 1134 | method: Interpolation method when correcting from a table. |
---|
| 1135 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1136 | and "spline" |
---|
| 1137 | insitu: if False a new scantable is returned. |
---|
| 1138 | Otherwise, the scaling is done in-situ |
---|
| 1139 | The default is taken from .asaprc (False) |
---|
| 1140 | """ |
---|
| 1141 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1142 | self._math._setinsitu(insitu) |
---|
[513] | 1143 | varlist = vars() |
---|
[876] | 1144 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1145 | s._add_history("resample", varlist) |
---|
[876] | 1146 | print_log() |
---|
| 1147 | if insitu: self._assign(s) |
---|
| 1148 | else: return s |
---|
[513] | 1149 | |
---|
| 1150 | |
---|
[946] | 1151 | def average_pol(self, mask=None, weight='none'): |
---|
| 1152 | """ |
---|
| 1153 | Average the Polarisations together. |
---|
| 1154 | Parameters: |
---|
| 1155 | mask: An optional mask defining the region, where the |
---|
| 1156 | averaging will be applied. The output will have all |
---|
| 1157 | specified points masked. |
---|
| 1158 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1159 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1160 | """ |
---|
| 1161 | varlist = vars() |
---|
| 1162 | if mask is None: |
---|
| 1163 | mask = () |
---|
[1010] | 1164 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1165 | s._add_history("average_pol", varlist) |
---|
[946] | 1166 | print_log() |
---|
[992] | 1167 | return s |
---|
[513] | 1168 | |
---|
[1145] | 1169 | def average_beam(self, mask=None, weight='none'): |
---|
| 1170 | """ |
---|
| 1171 | Average the Beams together. |
---|
| 1172 | Parameters: |
---|
| 1173 | mask: An optional mask defining the region, where the |
---|
| 1174 | averaging will be applied. The output will have all |
---|
| 1175 | specified points masked. |
---|
| 1176 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1177 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1178 | """ |
---|
| 1179 | varlist = vars() |
---|
| 1180 | if mask is None: |
---|
| 1181 | mask = () |
---|
| 1182 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1183 | s._add_history("average_beam", varlist) |
---|
| 1184 | print_log() |
---|
| 1185 | return s |
---|
| 1186 | |
---|
[992] | 1187 | def convert_pol(self, poltype=None): |
---|
| 1188 | """ |
---|
| 1189 | Convert the data to a different polarisation type. |
---|
| 1190 | Parameters: |
---|
| 1191 | poltype: The new polarisation type. Valid types are: |
---|
| 1192 | "linear", "stokes" and "circular" |
---|
| 1193 | """ |
---|
| 1194 | varlist = vars() |
---|
| 1195 | try: |
---|
| 1196 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1197 | except RuntimeError, msg: |
---|
[992] | 1198 | if rcParams['verbose']: |
---|
[1118] | 1199 | print msg |
---|
| 1200 | return |
---|
[992] | 1201 | else: |
---|
| 1202 | raise |
---|
[1118] | 1203 | s._add_history("convert_pol", varlist) |
---|
[992] | 1204 | print_log() |
---|
| 1205 | return s |
---|
| 1206 | |
---|
[876] | 1207 | def smooth(self, kernel="hanning", width=5.0, insitu=None): |
---|
[513] | 1208 | """ |
---|
| 1209 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 1210 | Parameters: |
---|
| 1211 | kernel: The type of smoothing kernel. Select from |
---|
[1373] | 1212 | 'hanning' (default), 'gaussian', 'boxcar' and |
---|
| 1213 | 'rmedian' |
---|
[513] | 1214 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1215 | ignored otherwise it defauls to 5 pixels. |
---|
| 1216 | For 'gaussian' it is the Full Width Half |
---|
| 1217 | Maximum. For 'boxcar' it is the full width. |
---|
[1373] | 1218 | For 'rmedian' it is the half width. |
---|
[513] | 1219 | insitu: if False a new scantable is returned. |
---|
| 1220 | Otherwise, the scaling is done in-situ |
---|
| 1221 | The default is taken from .asaprc (False) |
---|
| 1222 | Example: |
---|
| 1223 | none |
---|
| 1224 | """ |
---|
| 1225 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1226 | self._math._setinsitu(insitu) |
---|
[513] | 1227 | varlist = vars() |
---|
[1118] | 1228 | s = scantable(self._math._smooth(self, kernel.lower(), width)) |
---|
[876] | 1229 | s._add_history("smooth", varlist) |
---|
| 1230 | print_log() |
---|
| 1231 | if insitu: self._assign(s) |
---|
| 1232 | else: return s |
---|
[513] | 1233 | |
---|
[876] | 1234 | |
---|
[1391] | 1235 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None): |
---|
[513] | 1236 | """ |
---|
| 1237 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1238 | Parameters: |
---|
[794] | 1239 | mask: an optional mask |
---|
| 1240 | order: the order of the polynomial (default is 0) |
---|
[1061] | 1241 | plot: plot the fit and the residual. In this each |
---|
| 1242 | indivual fit has to be approved, by typing 'y' |
---|
| 1243 | or 'n' |
---|
[1391] | 1244 | uselin: use linear polynomial fit |
---|
[794] | 1245 | insitu: if False a new scantable is returned. |
---|
| 1246 | Otherwise, the scaling is done in-situ |
---|
| 1247 | The default is taken from .asaprc (False) |
---|
[513] | 1248 | Example: |
---|
| 1249 | # return a scan baselined by a third order polynomial, |
---|
| 1250 | # not using a mask |
---|
| 1251 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1252 | """ |
---|
[513] | 1253 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1254 | varlist = vars() |
---|
| 1255 | if mask is None: |
---|
[1295] | 1256 | mask = [True for i in xrange(self.nchan(-1))] |
---|
[513] | 1257 | from asap.asapfitter import fitter |
---|
[1217] | 1258 | try: |
---|
| 1259 | f = fitter() |
---|
| 1260 | f.set_scan(self, mask) |
---|
[1391] | 1261 | #f.set_function(poly=order) |
---|
| 1262 | if uselin: |
---|
| 1263 | f.set_function(lpoly=order) |
---|
| 1264 | else: |
---|
| 1265 | f.set_function(poly=order) |
---|
[1217] | 1266 | s = f.auto_fit(insitu, plot=plot) |
---|
| 1267 | s._add_history("poly_baseline", varlist) |
---|
| 1268 | print_log() |
---|
| 1269 | if insitu: self._assign(s) |
---|
| 1270 | else: return s |
---|
| 1271 | except RuntimeError: |
---|
| 1272 | msg = "The fit failed, possibly because it didn't converge." |
---|
| 1273 | if rcParams['verbose']: |
---|
| 1274 | print msg |
---|
| 1275 | return |
---|
| 1276 | else: |
---|
| 1277 | raise RuntimeError(msg) |
---|
[513] | 1278 | |
---|
[1217] | 1279 | |
---|
[1118] | 1280 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
[1280] | 1281 | threshold=3, chan_avg_limit=1, plot=False, |
---|
| 1282 | insitu=None): |
---|
[880] | 1283 | """ |
---|
| 1284 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1285 | Spectral lines are detected first using linefinder and masked out |
---|
| 1286 | to avoid them affecting the baseline solution. |
---|
| 1287 | |
---|
| 1288 | Parameters: |
---|
| 1289 | mask: an optional mask retreived from scantable |
---|
| 1290 | edge: an optional number of channel to drop at |
---|
| 1291 | the edge of spectrum. If only one value is |
---|
| 1292 | specified, the same number will be dropped from |
---|
| 1293 | both sides of the spectrum. Default is to keep |
---|
[907] | 1294 | all channels. Nested tuples represent individual |
---|
[976] | 1295 | edge selection for different IFs (a number of spectral |
---|
| 1296 | channels can be different) |
---|
[880] | 1297 | order: the order of the polynomial (default is 0) |
---|
| 1298 | threshold: the threshold used by line finder. It is better to |
---|
| 1299 | keep it large as only strong lines affect the |
---|
| 1300 | baseline solution. |
---|
[1280] | 1301 | chan_avg_limit: |
---|
| 1302 | a maximum number of consequtive spectral channels to |
---|
| 1303 | average during the search of weak and broad lines. |
---|
| 1304 | The default is no averaging (and no search for weak |
---|
| 1305 | lines). If such lines can affect the fitted baseline |
---|
| 1306 | (e.g. a high order polynomial is fitted), increase this |
---|
| 1307 | parameter (usually values up to 8 are reasonable). Most |
---|
| 1308 | users of this method should find the default value |
---|
| 1309 | sufficient. |
---|
[1061] | 1310 | plot: plot the fit and the residual. In this each |
---|
| 1311 | indivual fit has to be approved, by typing 'y' |
---|
| 1312 | or 'n' |
---|
[880] | 1313 | insitu: if False a new scantable is returned. |
---|
| 1314 | Otherwise, the scaling is done in-situ |
---|
| 1315 | The default is taken from .asaprc (False) |
---|
| 1316 | |
---|
| 1317 | Example: |
---|
| 1318 | scan2=scan.auto_poly_baseline(order=7) |
---|
| 1319 | """ |
---|
| 1320 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1321 | varlist = vars() |
---|
| 1322 | from asap.asapfitter import fitter |
---|
| 1323 | from asap.asaplinefind import linefinder |
---|
| 1324 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1325 | |
---|
[976] | 1326 | # check whether edge is set up for each IF individually |
---|
[1118] | 1327 | individualedge = False; |
---|
| 1328 | if len(edge) > 1: |
---|
| 1329 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 1330 | individualedge = True; |
---|
[907] | 1331 | |
---|
[1118] | 1332 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 1333 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1334 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1335 | to make individual selection for different IFs." |
---|
[919] | 1336 | |
---|
[1118] | 1337 | curedge = (0, 0) |
---|
| 1338 | if individualedge: |
---|
| 1339 | for edgepar in edge: |
---|
| 1340 | if not _is_valid(edgepar, int): |
---|
| 1341 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 1342 | to be a pair of integers or an integer." |
---|
[907] | 1343 | else: |
---|
[1118] | 1344 | curedge = edge; |
---|
[880] | 1345 | |
---|
| 1346 | # setup fitter |
---|
| 1347 | f = fitter() |
---|
| 1348 | f.set_function(poly=order) |
---|
| 1349 | |
---|
| 1350 | # setup line finder |
---|
[1118] | 1351 | fl = linefinder() |
---|
[1268] | 1352 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
[880] | 1353 | |
---|
| 1354 | if not insitu: |
---|
[1118] | 1355 | workscan = self.copy() |
---|
[880] | 1356 | else: |
---|
[1118] | 1357 | workscan = self |
---|
[880] | 1358 | |
---|
[907] | 1359 | fl.set_scan(workscan) |
---|
| 1360 | |
---|
[1118] | 1361 | rows = range(workscan.nrow()) |
---|
[880] | 1362 | asaplog.push("Processing:") |
---|
| 1363 | for r in rows: |
---|
[1118] | 1364 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 1365 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 1366 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 1367 | asaplog.push(msg, False) |
---|
[907] | 1368 | |
---|
[976] | 1369 | # figure out edge parameter |
---|
[1118] | 1370 | if individualedge: |
---|
| 1371 | if len(edge) >= workscan.getif(r): |
---|
| 1372 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 1373 | "be less than the number of IFs" |
---|
| 1374 | curedge = edge[workscan.getif(r)] |
---|
[919] | 1375 | |
---|
[976] | 1376 | # setup line finder |
---|
[1118] | 1377 | fl.find_lines(r, mask, curedge) |
---|
[880] | 1378 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1379 | f.x = workscan._getabcissa(r) |
---|
| 1380 | f.y = workscan._getspectrum(r) |
---|
| 1381 | f.data = None |
---|
| 1382 | f.fit() |
---|
| 1383 | x = f.get_parameters() |
---|
[1061] | 1384 | if plot: |
---|
| 1385 | f.plot(residual=True) |
---|
| 1386 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1387 | if x.upper() == 'N': |
---|
| 1388 | continue |
---|
[880] | 1389 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1061] | 1390 | if plot: |
---|
| 1391 | f._p.unmap() |
---|
| 1392 | f._p = None |
---|
| 1393 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 1394 | if insitu: |
---|
| 1395 | self._assign(workscan) |
---|
| 1396 | else: |
---|
| 1397 | return workscan |
---|
| 1398 | |
---|
[914] | 1399 | def rotate_linpolphase(self, angle): |
---|
| 1400 | """ |
---|
| 1401 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1402 | This is always done in situ in the raw data. So if you call this |
---|
| 1403 | function more than once then each call rotates the phase further. |
---|
| 1404 | Parameters: |
---|
| 1405 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1406 | Examples: |
---|
| 1407 | scan.rotate_linpolphase(2.3) |
---|
| 1408 | """ |
---|
| 1409 | varlist = vars() |
---|
[936] | 1410 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 1411 | self._add_history("rotate_linpolphase", varlist) |
---|
| 1412 | print_log() |
---|
| 1413 | return |
---|
[710] | 1414 | |
---|
[513] | 1415 | |
---|
[914] | 1416 | def rotate_xyphase(self, angle): |
---|
| 1417 | """ |
---|
| 1418 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1419 | in the data. So if you call this function more than once |
---|
| 1420 | then each call rotates the phase further. |
---|
| 1421 | Parameters: |
---|
| 1422 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1423 | Examples: |
---|
| 1424 | scan.rotate_xyphase(2.3) |
---|
| 1425 | """ |
---|
| 1426 | varlist = vars() |
---|
[936] | 1427 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 1428 | self._add_history("rotate_xyphase", varlist) |
---|
| 1429 | print_log() |
---|
| 1430 | return |
---|
| 1431 | |
---|
| 1432 | def swap_linears(self): |
---|
| 1433 | """ |
---|
[1348] | 1434 | Swap the linear polarisations XX and YY, or better the first two |
---|
| 1435 | polarisations as this also works for ciculars. |
---|
[914] | 1436 | """ |
---|
| 1437 | varlist = vars() |
---|
[936] | 1438 | self._math._swap_linears(self) |
---|
[914] | 1439 | self._add_history("swap_linears", varlist) |
---|
| 1440 | print_log() |
---|
| 1441 | return |
---|
| 1442 | |
---|
| 1443 | def invert_phase(self): |
---|
| 1444 | """ |
---|
| 1445 | Invert the phase of the complex polarisation |
---|
| 1446 | """ |
---|
| 1447 | varlist = vars() |
---|
[936] | 1448 | self._math._invert_phase(self) |
---|
[914] | 1449 | self._add_history("invert_phase", varlist) |
---|
| 1450 | print_log() |
---|
| 1451 | return |
---|
| 1452 | |
---|
[876] | 1453 | def add(self, offset, insitu=None): |
---|
[513] | 1454 | """ |
---|
| 1455 | Return a scan where all spectra have the offset added |
---|
| 1456 | Parameters: |
---|
| 1457 | offset: the offset |
---|
| 1458 | insitu: if False a new scantable is returned. |
---|
| 1459 | Otherwise, the scaling is done in-situ |
---|
| 1460 | The default is taken from .asaprc (False) |
---|
| 1461 | """ |
---|
| 1462 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1463 | self._math._setinsitu(insitu) |
---|
[513] | 1464 | varlist = vars() |
---|
[876] | 1465 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 1466 | s._add_history("add", varlist) |
---|
[876] | 1467 | print_log() |
---|
| 1468 | if insitu: |
---|
| 1469 | self._assign(s) |
---|
| 1470 | else: |
---|
[513] | 1471 | return s |
---|
| 1472 | |
---|
[1308] | 1473 | def scale(self, factor, tsys=True, insitu=None): |
---|
[513] | 1474 | """ |
---|
| 1475 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 1476 | Parameters: |
---|
| 1477 | factor: the scaling factor |
---|
| 1478 | insitu: if False a new scantable is returned. |
---|
| 1479 | Otherwise, the scaling is done in-situ |
---|
| 1480 | The default is taken from .asaprc (False) |
---|
| 1481 | tsys: if True (default) then apply the operation to Tsys |
---|
| 1482 | as well as the data |
---|
| 1483 | """ |
---|
| 1484 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1485 | self._math._setinsitu(insitu) |
---|
[513] | 1486 | varlist = vars() |
---|
[876] | 1487 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
[1118] | 1488 | s._add_history("scale", varlist) |
---|
[876] | 1489 | print_log() |
---|
| 1490 | if insitu: |
---|
| 1491 | self._assign(s) |
---|
| 1492 | else: |
---|
[513] | 1493 | return s |
---|
| 1494 | |
---|
[1348] | 1495 | def auto_quotient(self, preserve=True, mode='paired'): |
---|
[670] | 1496 | """ |
---|
| 1497 | This function allows to build quotients automatically. |
---|
| 1498 | It assumes the observation to have the same numer of |
---|
| 1499 | "ons" and "offs" |
---|
| 1500 | Parameters: |
---|
[710] | 1501 | preserve: you can preserve (default) the continuum or |
---|
| 1502 | remove it. The equations used are |
---|
[670] | 1503 | preserve: Output = Toff * (on/off) - Toff |
---|
[1070] | 1504 | remove: Output = Toff * (on/off) - Ton |
---|
[1348] | 1505 | mode: the on/off detection mode |
---|
| 1506 | 'paired' (default) |
---|
| 1507 | identifies 'off' scans by the |
---|
| 1508 | trailing '_R' (Mopra/Parkes) or |
---|
| 1509 | '_e'/'_w' (Tid) and matches |
---|
| 1510 | on/off pairs from the observing pattern |
---|
| 1511 | 'time' |
---|
| 1512 | finds the closest off in time |
---|
| 1513 | |
---|
[670] | 1514 | """ |
---|
[1348] | 1515 | modes = ["time", "paired"] |
---|
[670] | 1516 | if not mode in modes: |
---|
[876] | 1517 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 1518 | raise ValueError(msg) |
---|
| 1519 | varlist = vars() |
---|
[1348] | 1520 | s = None |
---|
| 1521 | if mode.lower() == "paired": |
---|
| 1522 | basesel = self.get_selection() |
---|
[1356] | 1523 | sel = selector()+basesel |
---|
| 1524 | sel.set_query("SRCTYPE==1") |
---|
| 1525 | self.set_selection(sel) |
---|
[1348] | 1526 | offs = self.copy() |
---|
| 1527 | sel.set_query("SRCTYPE==0") |
---|
[1356] | 1528 | self.set_selection(sel) |
---|
[1348] | 1529 | ons = self.copy() |
---|
| 1530 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 1531 | self.set_selection(basesel) |
---|
| 1532 | elif mode.lower() == "time": |
---|
| 1533 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 1534 | s._add_history("auto_quotient", varlist) |
---|
[876] | 1535 | print_log() |
---|
| 1536 | return s |
---|
[710] | 1537 | |
---|
[1145] | 1538 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1141] | 1539 | """ |
---|
[1143] | 1540 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
| 1541 | Parameters: |
---|
[1145] | 1542 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1143] | 1543 | weight: How to average the off beams. Default is 'median'. |
---|
[1145] | 1544 | preserve: you can preserve (default) the continuum or |
---|
| 1545 | remove it. The equations used are |
---|
| 1546 | preserve: Output = Toff * (on/off) - Toff |
---|
| 1547 | remove: Output = Toff * (on/off) - Ton |
---|
[1217] | 1548 | """ |
---|
[1143] | 1549 | if mask is None: mask = () |
---|
[1141] | 1550 | varlist = vars() |
---|
| 1551 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 1552 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 1553 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 1554 | from asapmath import quotient |
---|
[1145] | 1555 | q = quotient(on, off, preserve) |
---|
[1143] | 1556 | q._add_history("mx_quotient", varlist) |
---|
[1145] | 1557 | print_log() |
---|
[1217] | 1558 | return q |
---|
[513] | 1559 | |
---|
[718] | 1560 | def freq_switch(self, insitu=None): |
---|
| 1561 | """ |
---|
| 1562 | Apply frequency switching to the data. |
---|
| 1563 | Parameters: |
---|
| 1564 | insitu: if False a new scantable is returned. |
---|
| 1565 | Otherwise, the swictching is done in-situ |
---|
| 1566 | The default is taken from .asaprc (False) |
---|
| 1567 | Example: |
---|
| 1568 | none |
---|
| 1569 | """ |
---|
| 1570 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1571 | self._math._setinsitu(insitu) |
---|
[718] | 1572 | varlist = vars() |
---|
[876] | 1573 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 1574 | s._add_history("freq_switch", varlist) |
---|
[876] | 1575 | print_log() |
---|
| 1576 | if insitu: self._assign(s) |
---|
| 1577 | else: return s |
---|
[718] | 1578 | |
---|
[780] | 1579 | def recalc_azel(self): |
---|
| 1580 | """ |
---|
| 1581 | Recalculate the azimuth and elevation for each position. |
---|
| 1582 | Parameters: |
---|
| 1583 | none |
---|
| 1584 | Example: |
---|
| 1585 | """ |
---|
| 1586 | varlist = vars() |
---|
[876] | 1587 | self._recalcazel() |
---|
[780] | 1588 | self._add_history("recalc_azel", varlist) |
---|
| 1589 | print_log() |
---|
| 1590 | return |
---|
| 1591 | |
---|
[513] | 1592 | def __add__(self, other): |
---|
| 1593 | varlist = vars() |
---|
| 1594 | s = None |
---|
| 1595 | if isinstance(other, scantable): |
---|
[1308] | 1596 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
[513] | 1597 | elif isinstance(other, float): |
---|
[876] | 1598 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 1599 | else: |
---|
[718] | 1600 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1601 | s._add_history("operator +", varlist) |
---|
[718] | 1602 | print_log() |
---|
[513] | 1603 | return s |
---|
| 1604 | |
---|
| 1605 | def __sub__(self, other): |
---|
| 1606 | """ |
---|
| 1607 | implicit on all axes and on Tsys |
---|
| 1608 | """ |
---|
| 1609 | varlist = vars() |
---|
| 1610 | s = None |
---|
| 1611 | if isinstance(other, scantable): |
---|
[1308] | 1612 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
[513] | 1613 | elif isinstance(other, float): |
---|
[876] | 1614 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 1615 | else: |
---|
[718] | 1616 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1617 | s._add_history("operator -", varlist) |
---|
[718] | 1618 | print_log() |
---|
[513] | 1619 | return s |
---|
[710] | 1620 | |
---|
[513] | 1621 | def __mul__(self, other): |
---|
| 1622 | """ |
---|
| 1623 | implicit on all axes and on Tsys |
---|
| 1624 | """ |
---|
| 1625 | varlist = vars() |
---|
| 1626 | s = None |
---|
| 1627 | if isinstance(other, scantable): |
---|
[1308] | 1628 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
[513] | 1629 | elif isinstance(other, float): |
---|
[876] | 1630 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 1631 | else: |
---|
[718] | 1632 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1633 | s._add_history("operator *", varlist) |
---|
[718] | 1634 | print_log() |
---|
[513] | 1635 | return s |
---|
| 1636 | |
---|
[710] | 1637 | |
---|
[513] | 1638 | def __div__(self, other): |
---|
| 1639 | """ |
---|
| 1640 | implicit on all axes and on Tsys |
---|
| 1641 | """ |
---|
| 1642 | varlist = vars() |
---|
| 1643 | s = None |
---|
| 1644 | if isinstance(other, scantable): |
---|
[1308] | 1645 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
[513] | 1646 | elif isinstance(other, float): |
---|
| 1647 | if other == 0.0: |
---|
[718] | 1648 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 1649 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 1650 | else: |
---|
[718] | 1651 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1652 | s._add_history("operator /", varlist) |
---|
[718] | 1653 | print_log() |
---|
[513] | 1654 | return s |
---|
| 1655 | |
---|
[530] | 1656 | def get_fit(self, row=0): |
---|
| 1657 | """ |
---|
| 1658 | Print or return the stored fits for a row in the scantable |
---|
| 1659 | Parameters: |
---|
| 1660 | row: the row which the fit has been applied to. |
---|
| 1661 | """ |
---|
| 1662 | if row > self.nrow(): |
---|
| 1663 | return |
---|
[976] | 1664 | from asap.asapfit import asapfit |
---|
[530] | 1665 | fit = asapfit(self._getfit(row)) |
---|
[718] | 1666 | if rcParams['verbose']: |
---|
[530] | 1667 | print fit |
---|
| 1668 | return |
---|
| 1669 | else: |
---|
| 1670 | return fit.as_dict() |
---|
| 1671 | |
---|
[484] | 1672 | def _add_history(self, funcname, parameters): |
---|
[1435] | 1673 | if not rcParams['scantable.history']: |
---|
| 1674 | return |
---|
[484] | 1675 | # create date |
---|
| 1676 | sep = "##" |
---|
| 1677 | from datetime import datetime |
---|
| 1678 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 1679 | hist = dstr+sep |
---|
| 1680 | hist += funcname+sep#cdate+sep |
---|
| 1681 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 1682 | for k, v in parameters.iteritems(): |
---|
[484] | 1683 | if type(v) is dict: |
---|
[1118] | 1684 | for k2, v2 in v.iteritems(): |
---|
[484] | 1685 | hist += k2 |
---|
| 1686 | hist += "=" |
---|
[1118] | 1687 | if isinstance(v2, scantable): |
---|
[484] | 1688 | hist += 'scantable' |
---|
| 1689 | elif k2 == 'mask': |
---|
[1118] | 1690 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 1691 | hist += str(self._zip_mask(v2)) |
---|
| 1692 | else: |
---|
| 1693 | hist += str(v2) |
---|
[484] | 1694 | else: |
---|
[513] | 1695 | hist += str(v2) |
---|
[484] | 1696 | else: |
---|
| 1697 | hist += k |
---|
| 1698 | hist += "=" |
---|
[1118] | 1699 | if isinstance(v, scantable): |
---|
[484] | 1700 | hist += 'scantable' |
---|
| 1701 | elif k == 'mask': |
---|
[1118] | 1702 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 1703 | hist += str(self._zip_mask(v)) |
---|
| 1704 | else: |
---|
| 1705 | hist += str(v) |
---|
[484] | 1706 | else: |
---|
| 1707 | hist += str(v) |
---|
| 1708 | hist += sep |
---|
| 1709 | hist = hist[:-2] # remove trailing '##' |
---|
| 1710 | self._addhistory(hist) |
---|
| 1711 | |
---|
[710] | 1712 | |
---|
[484] | 1713 | def _zip_mask(self, mask): |
---|
| 1714 | mask = list(mask) |
---|
| 1715 | i = 0 |
---|
| 1716 | segments = [] |
---|
| 1717 | while mask[i:].count(1): |
---|
| 1718 | i += mask[i:].index(1) |
---|
| 1719 | if mask[i:].count(0): |
---|
| 1720 | j = i + mask[i:].index(0) |
---|
| 1721 | else: |
---|
[710] | 1722 | j = len(mask) |
---|
[1118] | 1723 | segments.append([i, j]) |
---|
[710] | 1724 | i = j |
---|
[484] | 1725 | return segments |
---|
[714] | 1726 | |
---|
[626] | 1727 | def _get_ordinate_label(self): |
---|
| 1728 | fu = "("+self.get_fluxunit()+")" |
---|
| 1729 | import re |
---|
| 1730 | lbl = "Intensity" |
---|
[1118] | 1731 | if re.match(".K.", fu): |
---|
[626] | 1732 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 1733 | elif re.match(".Jy.", fu): |
---|
[626] | 1734 | lbl = "Flux density "+ fu |
---|
| 1735 | return lbl |
---|
[710] | 1736 | |
---|
[876] | 1737 | def _check_ifs(self): |
---|
| 1738 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 1739 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 1740 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 1741 | |
---|
| 1742 | def _fill(self, names, unit, average): |
---|
| 1743 | import os |
---|
| 1744 | from asap._asap import stfiller |
---|
| 1745 | first = True |
---|
| 1746 | fullnames = [] |
---|
| 1747 | for name in names: |
---|
| 1748 | name = os.path.expandvars(name) |
---|
| 1749 | name = os.path.expanduser(name) |
---|
| 1750 | if not os.path.exists(name): |
---|
| 1751 | msg = "File '%s' does not exists" % (name) |
---|
| 1752 | if rcParams['verbose']: |
---|
| 1753 | asaplog.push(msg) |
---|
| 1754 | print asaplog.pop().strip() |
---|
| 1755 | return |
---|
| 1756 | raise IOError(msg) |
---|
| 1757 | fullnames.append(name) |
---|
| 1758 | if average: |
---|
| 1759 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 1760 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 1761 | for name in fullnames: |
---|
[1073] | 1762 | tbl = Scantable(stype) |
---|
| 1763 | r = stfiller(tbl) |
---|
[976] | 1764 | msg = "Importing %s..." % (name) |
---|
[1118] | 1765 | asaplog.push(msg, False) |
---|
[976] | 1766 | print_log() |
---|
[1118] | 1767 | r._open(name, -1, -1) |
---|
[976] | 1768 | r._read() |
---|
[1073] | 1769 | #tbl = r._getdata() |
---|
[976] | 1770 | if average: |
---|
[1118] | 1771 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 1772 | #tbl = tbl2 |
---|
| 1773 | if not first: |
---|
| 1774 | tbl = self._math._merge([self, tbl]) |
---|
| 1775 | #tbl = tbl2 |
---|
| 1776 | Scantable.__init__(self, tbl) |
---|
| 1777 | r._close() |
---|
[1118] | 1778 | del r, tbl |
---|
[976] | 1779 | first = False |
---|
| 1780 | if unit is not None: |
---|
| 1781 | self.set_fluxunit(unit) |
---|
| 1782 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
| 1783 | |
---|
[1402] | 1784 | def __getitem__(self, key): |
---|
| 1785 | if key < 0: |
---|
| 1786 | key += self.nrow() |
---|
| 1787 | if key >= self.nrow(): |
---|
| 1788 | raise IndexError("Row index out of range.") |
---|
| 1789 | return self._getspectrum(key) |
---|
| 1790 | |
---|
| 1791 | def __setitem__(self, key, value): |
---|
| 1792 | if key < 0: |
---|
| 1793 | key += self.nrow() |
---|
| 1794 | if key >= self.nrow(): |
---|
| 1795 | raise IndexError("Row index out of range.") |
---|
| 1796 | if not hasattr(value, "__len__") or \ |
---|
| 1797 | len(value) > self.nchan(self.getif(key)): |
---|
| 1798 | raise ValueError("Spectrum length doesn't match.") |
---|
| 1799 | return self._setspectrum(value, key) |
---|
| 1800 | |
---|
| 1801 | def __len__(self): |
---|
| 1802 | return self.nrow() |
---|
| 1803 | |
---|
| 1804 | def __iter__(self): |
---|
| 1805 | for i in range(len(self)): |
---|
| 1806 | yield self[i] |
---|