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