[876] | 1 | from asap._asap import Scantable |
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[226] | 2 | from asap import rcParams |
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[1118] | 3 | from asap import print_log |
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| 4 | from asap import asaplog |
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[946] | 5 | from asap import selector |
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[1153] | 6 | from asap import linecatalog |
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[1295] | 7 | from asap import _n_bools, mask_not, mask_and, mask_or |
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[102] | 8 | |
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[876] | 9 | class scantable(Scantable): |
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[102] | 10 | """ |
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| 11 | The ASAP container for scans |
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| 12 | """ |
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[710] | 13 | |
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[1496] | 14 | def __init__(self, filename, average=None, unit=None, getpt=None): |
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[102] | 15 | """ |
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| 16 | Create a scantable from a saved one or make a reference |
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| 17 | Parameters: |
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[181] | 18 | filename: the name of an asap table on disk |
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| 19 | or |
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| 20 | the name of a rpfits/sdfits/ms file |
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| 21 | (integrations within scans are auto averaged |
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| 22 | and the whole file is read) |
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| 23 | or |
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| 24 | [advanced] a reference to an existing |
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[102] | 25 | scantable |
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[484] | 26 | average: average all integrations withinb a scan on read. |
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| 27 | The default (True) is taken from .asaprc. |
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| 28 | unit: brightness unit; must be consistent with K or Jy. |
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[340] | 29 | Over-rides the default selected by the reader |
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| 30 | (input rpfits/sdfits/ms) or replaces the value |
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| 31 | in existing scantables |
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[1522] | 32 | getpt: for MeasurementSet input data only: |
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| 33 | If True, all pointing data are filled. |
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| 34 | The deafult is False, which makes time to load |
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| 35 | the MS data faster in some cases. |
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[710] | 36 | """ |
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[976] | 37 | if average is None: |
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[710] | 38 | average = rcParams['scantable.autoaverage'] |
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[1496] | 39 | if getpt is None: |
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| 40 | getpt = False |
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[1259] | 41 | varlist = vars() |
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[876] | 42 | from asap._asap import stmath |
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| 43 | self._math = stmath() |
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| 44 | if isinstance(filename, Scantable): |
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| 45 | Scantable.__init__(self, filename) |
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[181] | 46 | else: |
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[1603] | 47 | if isinstance(filename, str):# or \ |
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| 48 | # (isinstance(filename, list) or isinstance(filename, tuple)) \ |
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| 49 | # and isinstance(filename[-1], str): |
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[976] | 50 | import os.path |
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| 51 | filename = os.path.expandvars(filename) |
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| 52 | filename = os.path.expanduser(filename) |
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| 53 | if not os.path.exists(filename): |
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| 54 | s = "File '%s' not found." % (filename) |
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[718] | 55 | if rcParams['verbose']: |
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[976] | 56 | asaplog.push(s) |
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[1612] | 57 | #print asaplog.pop().strip() |
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[1614] | 58 | print_log('ERROR') |
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[718] | 59 | return |
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[976] | 60 | raise IOError(s) |
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[1115] | 61 | if os.path.isdir(filename) \ |
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[1118] | 62 | and not os.path.exists(filename+'/table.f1'): |
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[976] | 63 | # crude check if asap table |
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| 64 | if os.path.exists(filename+'/table.info'): |
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[1118] | 65 | ondisk = rcParams['scantable.storage'] == 'disk' |
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| 66 | Scantable.__init__(self, filename, ondisk) |
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[976] | 67 | if unit is not None: |
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| 68 | self.set_fluxunit(unit) |
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[1496] | 69 | # do not reset to the default freqframe |
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| 70 | #self.set_freqframe(rcParams['scantable.freqframe']) |
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[718] | 71 | else: |
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[1118] | 72 | msg = "The given file '%s'is not a valid " \ |
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| 73 | "asap table." % (filename) |
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[976] | 74 | if rcParams['verbose']: |
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[1612] | 75 | #print msg |
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[1614] | 76 | asaplog.push( msg ) |
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| 77 | print_log( 'ERROR' ) |
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[976] | 78 | return |
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| 79 | else: |
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| 80 | raise IOError(msg) |
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[226] | 81 | else: |
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[1496] | 82 | self._fill([filename], unit, average, getpt) |
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[1118] | 83 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
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[976] | 84 | and isinstance(filename[-1], str): |
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[1496] | 85 | self._fill(filename, unit, average, getpt) |
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[1259] | 86 | self._add_history("scantable", varlist) |
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[714] | 87 | print_log() |
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[102] | 88 | |
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[876] | 89 | def save(self, name=None, format=None, overwrite=False): |
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[116] | 90 | """ |
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[1280] | 91 | Store the scantable on disk. This can be an asap (aips++) Table, |
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| 92 | SDFITS or MS2 format. |
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[116] | 93 | Parameters: |
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[1093] | 94 | name: the name of the outputfile. For format "ASCII" |
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| 95 | this is the root file name (data in 'name'.txt |
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[497] | 96 | and header in 'name'_header.txt) |
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[116] | 97 | format: an optional file format. Default is ASAP. |
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[280] | 98 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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[194] | 99 | 'SDFITS' (save as SDFITS file) |
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[200] | 100 | 'ASCII' (saves as ascii text file) |
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[226] | 101 | 'MS2' (saves as an aips++ |
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| 102 | MeasurementSet V2) |
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[1603] | 103 | 'FITS' (save as image FITS - not |
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| 104 | readable by class) |
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| 105 | 'CLASS' (save as FITS readable by CLASS) |
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[411] | 106 | overwrite: If the file should be overwritten if it exists. |
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[256] | 107 | The default False is to return with warning |
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[411] | 108 | without writing the output. USE WITH CARE. |
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[116] | 109 | Example: |
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| 110 | scan.save('myscan.asap') |
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[1118] | 111 | scan.save('myscan.sdfits', 'SDFITS') |
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[116] | 112 | """ |
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[411] | 113 | from os import path |
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[226] | 114 | if format is None: format = rcParams['scantable.save'] |
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[256] | 115 | suffix = '.'+format.lower() |
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[1118] | 116 | if name is None or name == "": |
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[256] | 117 | name = 'scantable'+suffix |
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[718] | 118 | msg = "No filename given. Using default name %s..." % name |
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| 119 | asaplog.push(msg) |
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[411] | 120 | name = path.expandvars(name) |
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[256] | 121 | if path.isfile(name) or path.isdir(name): |
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| 122 | if not overwrite: |
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[718] | 123 | msg = "File %s exists." % name |
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| 124 | if rcParams['verbose']: |
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[1612] | 125 | #print msg |
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[1614] | 126 | asaplog.push( msg ) |
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| 127 | print_log( 'ERROR' ) |
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[718] | 128 | return |
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| 129 | else: |
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| 130 | raise IOError(msg) |
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[451] | 131 | format2 = format.upper() |
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| 132 | if format2 == 'ASAP': |
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[116] | 133 | self._save(name) |
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| 134 | else: |
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[989] | 135 | from asap._asap import stwriter as stw |
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[1118] | 136 | writer = stw(format2) |
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| 137 | writer.write(self, name) |
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[718] | 138 | print_log() |
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[116] | 139 | return |
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| 140 | |
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[102] | 141 | def copy(self): |
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| 142 | """ |
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| 143 | Return a copy of this scantable. |
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[1348] | 144 | Note: |
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| 145 | This makes a full (deep) copy. scan2 = scan1 makes a reference. |
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[102] | 146 | Parameters: |
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[113] | 147 | none |
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[102] | 148 | Example: |
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| 149 | copiedscan = scan.copy() |
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| 150 | """ |
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[876] | 151 | sd = scantable(Scantable._copy(self)) |
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[113] | 152 | return sd |
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| 153 | |
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[1093] | 154 | def drop_scan(self, scanid=None): |
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| 155 | """ |
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| 156 | Return a new scantable where the specified scan number(s) has(have) |
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| 157 | been dropped. |
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| 158 | Parameters: |
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| 159 | scanid: a (list of) scan number(s) |
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| 160 | """ |
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| 161 | from asap import _is_sequence_or_number as _is_valid |
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| 162 | from asap import _to_list |
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| 163 | from asap import unique |
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| 164 | if not _is_valid(scanid): |
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| 165 | if rcParams['verbose']: |
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[1612] | 166 | #print "Please specify a scanno to drop from the scantable" |
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[1614] | 167 | asaplog.push( 'Please specify a scanno to drop from the scantable' ) |
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| 168 | print_log( 'ERROR' ) |
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[1093] | 169 | return |
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| 170 | else: |
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| 171 | raise RuntimeError("No scan given") |
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| 172 | try: |
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| 173 | scanid = _to_list(scanid) |
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| 174 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
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| 175 | for sid in scanid: allscans.remove(sid) |
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[1118] | 176 | if len(allscans) == 0: |
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| 177 | raise ValueError("Can't remove all scans") |
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[1093] | 178 | except ValueError: |
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| 179 | if rcParams['verbose']: |
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[1612] | 180 | #print "Couldn't find any match." |
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[1614] | 181 | print_log() |
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| 182 | asaplog.push( "Couldn't find any match." ) |
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| 183 | print_log( 'ERROR' ) |
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[1093] | 184 | return |
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| 185 | else: raise |
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| 186 | try: |
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| 187 | bsel = self.get_selection() |
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| 188 | sel = selector() |
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| 189 | sel.set_scans(allscans) |
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| 190 | self.set_selection(bsel+sel) |
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| 191 | scopy = self._copy() |
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| 192 | self.set_selection(bsel) |
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| 193 | return scantable(scopy) |
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| 194 | except RuntimeError: |
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[1118] | 195 | if rcParams['verbose']: |
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[1612] | 196 | #print "Couldn't find any match." |
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[1614] | 197 | print_log() |
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| 198 | asaplog.push( "Couldn't find any match." ) |
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| 199 | print_log( 'ERROR' ) |
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[1118] | 200 | else: |
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| 201 | raise |
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[1093] | 202 | |
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| 203 | |
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[102] | 204 | def get_scan(self, scanid=None): |
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| 205 | """ |
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| 206 | Return a specific scan (by scanno) or collection of scans (by |
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| 207 | source name) in a new scantable. |
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[1348] | 208 | Note: |
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| 209 | See scantable.drop_scan() for the inverse operation. |
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[102] | 210 | Parameters: |
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[513] | 211 | scanid: a (list of) scanno or a source name, unix-style |
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| 212 | patterns are accepted for source name matching, e.g. |
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| 213 | '*_R' gets all 'ref scans |
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[102] | 214 | Example: |
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[513] | 215 | # get all scans containing the source '323p459' |
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| 216 | newscan = scan.get_scan('323p459') |
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| 217 | # get all 'off' scans |
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| 218 | refscans = scan.get_scan('*_R') |
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| 219 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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[1118] | 220 | newscan = scan.get_scan([0, 2, 7, 10]) |
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[102] | 221 | """ |
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| 222 | if scanid is None: |
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[718] | 223 | if rcParams['verbose']: |
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[1612] | 224 | #print "Please specify a scan no or name to " \ |
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| 225 | # "retrieve from the scantable" |
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[1614] | 226 | asaplog.push( 'Please specify a scan no or name to retrieve from the scantable' ) |
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| 227 | print_log( 'ERROR' ) |
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[718] | 228 | return |
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| 229 | else: |
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| 230 | raise RuntimeError("No scan given") |
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| 231 | |
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[102] | 232 | try: |
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[946] | 233 | bsel = self.get_selection() |
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| 234 | sel = selector() |
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[102] | 235 | if type(scanid) is str: |
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[946] | 236 | sel.set_name(scanid) |
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| 237 | self.set_selection(bsel+sel) |
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[876] | 238 | scopy = self._copy() |
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[946] | 239 | self.set_selection(bsel) |
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[876] | 240 | return scantable(scopy) |
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[102] | 241 | elif type(scanid) is int: |
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[946] | 242 | sel.set_scans([scanid]) |
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| 243 | self.set_selection(bsel+sel) |
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[876] | 244 | scopy = self._copy() |
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[946] | 245 | self.set_selection(bsel) |
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[876] | 246 | return scantable(scopy) |
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[381] | 247 | elif type(scanid) is list: |
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[946] | 248 | sel.set_scans(scanid) |
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| 249 | self.set_selection(sel) |
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[876] | 250 | scopy = self._copy() |
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[946] | 251 | self.set_selection(bsel) |
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[876] | 252 | return scantable(scopy) |
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[381] | 253 | else: |
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[718] | 254 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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| 255 | if rcParams['verbose']: |
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[1612] | 256 | #print msg |
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[1614] | 257 | asaplog.push( msg ) |
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| 258 | print_log( 'ERROR' ) |
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[718] | 259 | else: |
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| 260 | raise TypeError(msg) |
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[102] | 261 | except RuntimeError: |
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[1612] | 262 | if rcParams['verbose']: |
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| 263 | #print "Couldn't find any match." |
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[1614] | 264 | print_log() |
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| 265 | asaplog.push( "Couldn't find any match." ) |
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| 266 | print_log( 'ERROR' ) |
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[718] | 267 | else: raise |
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[102] | 268 | |
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| 269 | def __str__(self): |
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[1118] | 270 | return Scantable._summary(self, True) |
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[102] | 271 | |
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[976] | 272 | def summary(self, filename=None): |
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[102] | 273 | """ |
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| 274 | Print a summary of the contents of this scantable. |
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| 275 | Parameters: |
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| 276 | filename: the name of a file to write the putput to |
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| 277 | Default - no file output |
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[381] | 278 | verbose: print extra info such as the frequency table |
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| 279 | The default (False) is taken from .asaprc |
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[102] | 280 | """ |
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[976] | 281 | info = Scantable._summary(self, True) |
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| 282 | #if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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[102] | 283 | if filename is not None: |
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[256] | 284 | if filename is "": |
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| 285 | filename = 'scantable_summary.txt' |
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[415] | 286 | from os.path import expandvars, isdir |
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[411] | 287 | filename = expandvars(filename) |
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[415] | 288 | if not isdir(filename): |
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[413] | 289 | data = open(filename, 'w') |
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| 290 | data.write(info) |
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| 291 | data.close() |
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| 292 | else: |
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[718] | 293 | msg = "Illegal file name '%s'." % (filename) |
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| 294 | if rcParams['verbose']: |
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[1612] | 295 | #print msg |
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[1614] | 296 | asaplog.push( msg ) |
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| 297 | print_log( 'ERROR' ) |
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[718] | 298 | else: |
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| 299 | raise IOError(msg) |
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| 300 | if rcParams['verbose']: |
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[794] | 301 | try: |
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| 302 | from IPython.genutils import page as pager |
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| 303 | except ImportError: |
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| 304 | from pydoc import pager |
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| 305 | pager(info) |
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[718] | 306 | else: |
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| 307 | return info |
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[710] | 308 | |
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[1603] | 309 | def get_spectrum(self, rowno): |
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| 310 | """Return the spectrum for the current row in the scantable as a list. |
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| 311 | Parameters: |
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| 312 | rowno: the row number to retrieve the spectrum from |
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| 313 | """ |
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| 314 | return self._getspectrum(rowno) |
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[946] | 315 | |
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[1603] | 316 | def get_mask(self, rowno): |
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| 317 | """Return the mask for the current row in the scantable as a list. |
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| 318 | Parameters: |
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| 319 | rowno: the row number to retrieve the mask from |
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| 320 | """ |
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| 321 | return self._getmask(rowno) |
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| 322 | |
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| 323 | def set_spectrum(self, spec, rowno): |
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| 324 | """Return the spectrum for the current row in the scantable as a list. |
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| 325 | Parameters: |
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| 326 | spec: the spectrum |
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| 327 | rowno: the row number to set the spectrum for |
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| 328 | """ |
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| 329 | assert(len(spec) == self.nchan()) |
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| 330 | return self._setspectrum(spec, rowno) |
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| 331 | |
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[946] | 332 | def get_selection(self): |
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| 333 | """ |
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[1005] | 334 | Get the selection object currently set on this scantable. |
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| 335 | Parameters: |
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| 336 | none |
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| 337 | Example: |
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| 338 | sel = scan.get_selection() |
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| 339 | sel.set_ifs(0) # select IF 0 |
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| 340 | scan.set_selection(sel) # apply modified selection |
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[946] | 341 | """ |
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| 342 | return selector(self._getselection()) |
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| 343 | |
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[1005] | 344 | def set_selection(self, selection=selector()): |
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[946] | 345 | """ |
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[1005] | 346 | Select a subset of the data. All following operations on this scantable |
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| 347 | are only applied to thi selection. |
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| 348 | Parameters: |
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| 349 | selection: a selector object (default unset the selection) |
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| 350 | Examples: |
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| 351 | sel = selector() # create a selection object |
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[1118] | 352 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
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[1005] | 353 | scan.set_selection(sel) # set the selection |
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| 354 | scan.summary() # will only print summary of scanno 0 an 3 |
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| 355 | scan.set_selection() # unset the selection |
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[946] | 356 | """ |
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| 357 | self._setselection(selection) |
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| 358 | |
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[1446] | 359 | def get_row(self, row=0, insitu=None): |
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| 360 | """ |
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| 361 | Select a row in the scantable. |
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| 362 | Return a scantable with single row. |
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| 363 | Parameters: |
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| 364 | row: row no of integration, default is 0. |
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| 365 | insitu: if False a new scantable is returned. |
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| 366 | Otherwise, the scaling is done in-situ |
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| 367 | The default is taken from .asaprc (False) |
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| 368 | """ |
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| 369 | if insitu is None: insitu = rcParams['insitu'] |
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| 370 | if not insitu: |
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| 371 | workscan = self.copy() |
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| 372 | else: |
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| 373 | workscan = self |
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| 374 | # Select a row |
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| 375 | sel=selector() |
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| 376 | sel.set_scans([workscan.getscan(row)]) |
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| 377 | sel.set_cycles([workscan.getcycle(row)]) |
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| 378 | sel.set_beams([workscan.getbeam(row)]) |
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| 379 | sel.set_ifs([workscan.getif(row)]) |
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| 380 | sel.set_polarisations([workscan.getpol(row)]) |
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| 381 | sel.set_name(workscan._getsourcename(row)) |
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| 382 | workscan.set_selection(sel) |
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| 383 | if not workscan.nrow() == 1: |
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| 384 | msg = "Cloud not identify single row. %d rows selected."%(workscan.nrow()) |
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| 385 | raise RuntimeError(msg) |
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| 386 | del sel |
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| 387 | if insitu: |
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| 388 | self._assign(workscan) |
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| 389 | else: |
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| 390 | return workscan |
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| 391 | |
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[1629] | 392 | #def stats(self, stat='stddev', mask=None): |
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| 393 | def stats(self, stat='stddev', mask=None, form='3.3f'): |
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[102] | 394 | """ |
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[135] | 395 | Determine the specified statistic of the current beam/if/pol |
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[102] | 396 | Takes a 'mask' as an optional parameter to specify which |
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| 397 | channels should be excluded. |
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| 398 | Parameters: |
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[1517] | 399 | stat: 'min', 'max', 'min_abc', 'max_abc', 'sumsq', 'sum', |
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[1515] | 400 | 'mean', 'var', 'stddev', 'avdev', 'rms', 'median' |
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[135] | 401 | mask: an optional mask specifying where the statistic |
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[102] | 402 | should be determined. |
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[1629] | 403 | form: format string to print statistic values |
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[102] | 404 | Example: |
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[113] | 405 | scan.set_unit('channel') |
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[1118] | 406 | msk = scan.create_mask([100, 200], [500, 600]) |
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[135] | 407 | scan.stats(stat='mean', mask=m) |
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[102] | 408 | """ |
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| 409 | if mask == None: |
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[876] | 410 | mask = [] |
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[1118] | 411 | axes = ['Beam', 'IF', 'Pol', 'Time'] |
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[876] | 412 | if not self._check_ifs(): |
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[1118] | 413 | raise ValueError("Cannot apply mask as the IFs have different " |
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| 414 | "number of channels. Please use setselection() " |
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| 415 | "to select individual IFs") |
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[1530] | 416 | rtnabc = False |
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| 417 | if stat.lower().endswith('_abc'): rtnabc = True |
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| 418 | getchan = False |
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| 419 | if stat.lower().startswith('min') or stat.lower().startswith('max'): |
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[1517] | 420 | chan = self._math._minmaxchan(self, mask, stat) |
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| 421 | getchan = True |
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[1515] | 422 | statvals = [] |
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[1530] | 423 | if not rtnabc: statvals = self._math._stats(self, mask, stat) |
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| 424 | |
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[876] | 425 | out = '' |
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| 426 | axes = [] |
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| 427 | for i in range(self.nrow()): |
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| 428 | axis = [] |
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| 429 | axis.append(self.getscan(i)) |
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| 430 | axis.append(self.getbeam(i)) |
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| 431 | axis.append(self.getif(i)) |
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| 432 | axis.append(self.getpol(i)) |
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| 433 | axis.append(self.getcycle(i)) |
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| 434 | axes.append(axis) |
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| 435 | tm = self._gettime(i) |
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| 436 | src = self._getsourcename(i) |
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[1530] | 437 | refstr = '' |
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| 438 | statunit= '' |
---|
[1517] | 439 | if getchan: |
---|
| 440 | qx, qy = self.chan2data(rowno=i, chan=chan[i]) |
---|
[1530] | 441 | if rtnabc: |
---|
| 442 | statvals.append(qx['value']) |
---|
[1629] | 443 | #refstr = '(value: %3.3f' % (qy['value'])+' ['+qy['unit']+'])' |
---|
| 444 | refstr = ('(value: %'+form) % (qy['value'])+' ['+qy['unit']+'])' |
---|
[1530] | 445 | statunit= '['+qx['unit']+']' |
---|
| 446 | else: |
---|
[1629] | 447 | #refstr = '(@ %3.3f' % (qx['value'])+' ['+qx['unit']+'])' |
---|
| 448 | refstr = ('(@ %'+form) % (qx['value'])+' ['+qx['unit']+'])' |
---|
[1530] | 449 | #statunit= ' ['+qy['unit']+']' |
---|
[876] | 450 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
---|
| 451 | out += 'Time[%s]:\n' % (tm) |
---|
| 452 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
---|
| 453 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
---|
| 454 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
---|
[1629] | 455 | #out += '= %3.3f ' % (statvals[i]) +refstr+'\n' |
---|
| 456 | out += ('= %'+form) % (statvals[i]) +' '+refstr+'\n' |
---|
[876] | 457 | out += "--------------------------------------------------\n" |
---|
[256] | 458 | |
---|
[876] | 459 | if rcParams['verbose']: |
---|
[1615] | 460 | import os |
---|
[1625] | 461 | if os.environ.has_key( 'USER' ): |
---|
| 462 | usr=os.environ['USER'] |
---|
| 463 | else: |
---|
| 464 | import commands |
---|
| 465 | usr=commands.getoutput( 'whoami' ) |
---|
[1613] | 466 | tmpfile='/tmp/tmp_'+usr+'_casapy_asap_scantable_stats' |
---|
[1612] | 467 | f=open(tmpfile,'w') |
---|
| 468 | print >> f, "--------------------------------------------------" |
---|
| 469 | print >> f, " ", stat, statunit |
---|
| 470 | print >> f, "--------------------------------------------------" |
---|
| 471 | print >> f, out |
---|
| 472 | f.close() |
---|
| 473 | f=open(tmpfile,'r') |
---|
| 474 | x=f.readlines() |
---|
| 475 | f.close() |
---|
| 476 | for xx in x: |
---|
[1614] | 477 | asaplog.push( xx ) |
---|
| 478 | print_log() |
---|
[1295] | 479 | #else: |
---|
| 480 | #retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'], |
---|
| 481 | # 'axes' : axes, |
---|
| 482 | # 'data': statvals} |
---|
| 483 | return statvals |
---|
[102] | 484 | |
---|
[1517] | 485 | def chan2data(self, rowno=0, chan=0): |
---|
[1515] | 486 | """ |
---|
[1517] | 487 | Returns channel/frequency/velocity and spectral value |
---|
[1515] | 488 | at an arbitrary row and channel in the scantable. |
---|
| 489 | Parameters: |
---|
| 490 | rowno: a row number in the scantable. Default is the |
---|
| 491 | first row, i.e. rowno=0 |
---|
[1517] | 492 | chan: a channel in the scantable. Default is the first |
---|
[1515] | 493 | channel, i.e. pos=0 |
---|
| 494 | """ |
---|
[1517] | 495 | if isinstance(rowno, int) and isinstance(chan, int): |
---|
[1530] | 496 | qx = {'unit': self.get_unit(), |
---|
| 497 | 'value': self._getabcissa(rowno)[chan]} |
---|
[1517] | 498 | qy = {'unit': self.get_fluxunit(), |
---|
| 499 | 'value': self._getspectrum(rowno)[chan]} |
---|
| 500 | return qx, qy |
---|
[1515] | 501 | |
---|
[1118] | 502 | def stddev(self, mask=None): |
---|
[135] | 503 | """ |
---|
| 504 | Determine the standard deviation of the current beam/if/pol |
---|
| 505 | Takes a 'mask' as an optional parameter to specify which |
---|
| 506 | channels should be excluded. |
---|
| 507 | Parameters: |
---|
| 508 | mask: an optional mask specifying where the standard |
---|
| 509 | deviation should be determined. |
---|
| 510 | |
---|
| 511 | Example: |
---|
| 512 | scan.set_unit('channel') |
---|
[1118] | 513 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 514 | scan.stddev(mask=m) |
---|
| 515 | """ |
---|
[1118] | 516 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 517 | |
---|
[1003] | 518 | |
---|
[1259] | 519 | def get_column_names(self): |
---|
[1003] | 520 | """ |
---|
| 521 | Return a list of column names, which can be used for selection. |
---|
| 522 | """ |
---|
[1259] | 523 | return list(Scantable.get_column_names(self)) |
---|
[1003] | 524 | |
---|
[876] | 525 | def get_tsys(self): |
---|
[113] | 526 | """ |
---|
| 527 | Return the System temperatures. |
---|
| 528 | Returns: |
---|
[876] | 529 | a list of Tsys values for the current selection |
---|
[113] | 530 | """ |
---|
[256] | 531 | |
---|
[876] | 532 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 533 | |
---|
[876] | 534 | def _row_callback(self, callback, label): |
---|
| 535 | axes = [] |
---|
[1118] | 536 | axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'] |
---|
[876] | 537 | out = "" |
---|
[1118] | 538 | outvec = [] |
---|
[876] | 539 | for i in range(self.nrow()): |
---|
| 540 | axis = [] |
---|
| 541 | axis.append(self.getscan(i)) |
---|
| 542 | axis.append(self.getbeam(i)) |
---|
| 543 | axis.append(self.getif(i)) |
---|
| 544 | axis.append(self.getpol(i)) |
---|
| 545 | axis.append(self.getcycle(i)) |
---|
| 546 | axes.append(axis) |
---|
| 547 | tm = self._gettime(i) |
---|
| 548 | src = self._getsourcename(i) |
---|
| 549 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
---|
| 550 | out += 'Time[%s]:\n' % (tm) |
---|
| 551 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
---|
| 552 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
---|
| 553 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
---|
| 554 | outvec.append(callback(i)) |
---|
| 555 | out += '= %3.3f\n' % (outvec[i]) |
---|
| 556 | out += "--------------------------------------------------\n" |
---|
| 557 | if rcParams['verbose']: |
---|
[1615] | 558 | asaplog.push("--------------------------------------------------") |
---|
| 559 | asaplog.push(" %s" % (label)) |
---|
| 560 | asaplog.push("--------------------------------------------------") |
---|
| 561 | asaplog.push(out) |
---|
[1614] | 562 | print_log() |
---|
[1175] | 563 | # disabled because the vector seems more useful |
---|
| 564 | #retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec} |
---|
| 565 | return outvec |
---|
[256] | 566 | |
---|
[1070] | 567 | def _get_column(self, callback, row=-1): |
---|
| 568 | """ |
---|
| 569 | """ |
---|
| 570 | if row == -1: |
---|
| 571 | return [callback(i) for i in range(self.nrow())] |
---|
| 572 | else: |
---|
| 573 | if 0 <= row < self.nrow(): |
---|
| 574 | return callback(row) |
---|
[256] | 575 | |
---|
[1070] | 576 | |
---|
[1348] | 577 | def get_time(self, row=-1, asdatetime=False): |
---|
[113] | 578 | """ |
---|
| 579 | Get a list of time stamps for the observations. |
---|
[1348] | 580 | Return a datetime object for each integration time stamp in the scantable. |
---|
[113] | 581 | Parameters: |
---|
[1348] | 582 | row: row no of integration. Default -1 return all rows |
---|
| 583 | asdatetime: return values as datetime objects rather than strings |
---|
[113] | 584 | Example: |
---|
| 585 | none |
---|
| 586 | """ |
---|
[1175] | 587 | from time import strptime |
---|
| 588 | from datetime import datetime |
---|
[1457] | 589 | times = self._get_column(self._gettime, row) |
---|
[1348] | 590 | if not asdatetime: |
---|
[1603] | 591 | return times |
---|
[1175] | 592 | format = "%Y/%m/%d/%H:%M:%S" |
---|
| 593 | if isinstance(times, list): |
---|
| 594 | return [datetime(*strptime(i, format)[:6]) for i in times] |
---|
| 595 | else: |
---|
| 596 | return datetime(*strptime(times, format)[:6]) |
---|
[102] | 597 | |
---|
[1348] | 598 | |
---|
| 599 | def get_inttime(self, row=-1): |
---|
| 600 | """ |
---|
| 601 | Get a list of integration times for the observations. |
---|
| 602 | Return a time in seconds for each integration in the scantable. |
---|
| 603 | Parameters: |
---|
| 604 | row: row no of integration. Default -1 return all rows. |
---|
| 605 | Example: |
---|
| 606 | none |
---|
| 607 | """ |
---|
| 608 | return self._get_column(self._getinttime, row) |
---|
| 609 | |
---|
| 610 | |
---|
[714] | 611 | def get_sourcename(self, row=-1): |
---|
| 612 | """ |
---|
[794] | 613 | Get a list source names for the observations. |
---|
[714] | 614 | Return a string for each integration in the scantable. |
---|
| 615 | Parameters: |
---|
[1348] | 616 | row: row no of integration. Default -1 return all rows. |
---|
[714] | 617 | Example: |
---|
| 618 | none |
---|
| 619 | """ |
---|
[1070] | 620 | return self._get_column(self._getsourcename, row) |
---|
[714] | 621 | |
---|
[794] | 622 | def get_elevation(self, row=-1): |
---|
| 623 | """ |
---|
| 624 | Get a list of elevations for the observations. |
---|
| 625 | Return a float for each integration in the scantable. |
---|
| 626 | Parameters: |
---|
[1348] | 627 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 628 | Example: |
---|
| 629 | none |
---|
| 630 | """ |
---|
[1070] | 631 | return self._get_column(self._getelevation, row) |
---|
[794] | 632 | |
---|
| 633 | def get_azimuth(self, row=-1): |
---|
| 634 | """ |
---|
| 635 | Get a list of azimuths for the observations. |
---|
| 636 | Return a float for each integration in the scantable. |
---|
| 637 | Parameters: |
---|
[1348] | 638 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 639 | Example: |
---|
| 640 | none |
---|
| 641 | """ |
---|
[1070] | 642 | return self._get_column(self._getazimuth, row) |
---|
[794] | 643 | |
---|
| 644 | def get_parangle(self, row=-1): |
---|
| 645 | """ |
---|
| 646 | Get a list of parallactic angles for the observations. |
---|
| 647 | Return a float for each integration in the scantable. |
---|
| 648 | Parameters: |
---|
[1348] | 649 | row: row no of integration. Default -1 return all rows. |
---|
[794] | 650 | Example: |
---|
| 651 | none |
---|
| 652 | """ |
---|
[1070] | 653 | return self._get_column(self._getparangle, row) |
---|
[794] | 654 | |
---|
[1070] | 655 | def get_direction(self, row=-1): |
---|
| 656 | """ |
---|
| 657 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 658 | Return a float for each integration in the scantable. |
---|
| 659 | Parameters: |
---|
| 660 | row: row no of integration. Default -1 return all rows |
---|
| 661 | Example: |
---|
| 662 | none |
---|
| 663 | """ |
---|
| 664 | return self._get_column(self._getdirection, row) |
---|
| 665 | |
---|
[1389] | 666 | def get_directionval(self, row=-1): |
---|
| 667 | """ |
---|
| 668 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 669 | Return a float for each integration in the scantable. |
---|
| 670 | Parameters: |
---|
| 671 | row: row no of integration. Default -1 return all rows |
---|
| 672 | Example: |
---|
| 673 | none |
---|
| 674 | """ |
---|
| 675 | return self._get_column(self._getdirectionvec, row) |
---|
| 676 | |
---|
[102] | 677 | def set_unit(self, unit='channel'): |
---|
| 678 | """ |
---|
| 679 | Set the unit for all following operations on this scantable |
---|
| 680 | Parameters: |
---|
| 681 | unit: optional unit, default is 'channel' |
---|
[1118] | 682 | one of '*Hz', 'km/s', 'channel', '' |
---|
[102] | 683 | """ |
---|
[484] | 684 | varlist = vars() |
---|
[1118] | 685 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 686 | unit = '' |
---|
| 687 | inf = list(self._getcoordinfo()) |
---|
| 688 | inf[0] = unit |
---|
| 689 | self._setcoordinfo(inf) |
---|
[1118] | 690 | self._add_history("set_unit", varlist) |
---|
[113] | 691 | |
---|
[484] | 692 | def set_instrument(self, instr): |
---|
[358] | 693 | """ |
---|
[1348] | 694 | Set the instrument for subsequent processing. |
---|
[358] | 695 | Parameters: |
---|
[710] | 696 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 697 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 698 | """ |
---|
| 699 | self._setInstrument(instr) |
---|
[1118] | 700 | self._add_history("set_instument", vars()) |
---|
[718] | 701 | print_log() |
---|
[358] | 702 | |
---|
[1190] | 703 | def set_feedtype(self, feedtype): |
---|
| 704 | """ |
---|
| 705 | Overwrite the feed type, which might not be set correctly. |
---|
| 706 | Parameters: |
---|
| 707 | feedtype: 'linear' or 'circular' |
---|
| 708 | """ |
---|
| 709 | self._setfeedtype(feedtype) |
---|
| 710 | self._add_history("set_feedtype", vars()) |
---|
| 711 | print_log() |
---|
| 712 | |
---|
[276] | 713 | def set_doppler(self, doppler='RADIO'): |
---|
| 714 | """ |
---|
| 715 | Set the doppler for all following operations on this scantable. |
---|
| 716 | Parameters: |
---|
| 717 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 718 | """ |
---|
[484] | 719 | varlist = vars() |
---|
[276] | 720 | inf = list(self._getcoordinfo()) |
---|
| 721 | inf[2] = doppler |
---|
| 722 | self._setcoordinfo(inf) |
---|
[1118] | 723 | self._add_history("set_doppler", vars()) |
---|
[718] | 724 | print_log() |
---|
[710] | 725 | |
---|
[226] | 726 | def set_freqframe(self, frame=None): |
---|
[113] | 727 | """ |
---|
| 728 | Set the frame type of the Spectral Axis. |
---|
| 729 | Parameters: |
---|
[591] | 730 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1118] | 731 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
| 732 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[113] | 733 | Examples: |
---|
| 734 | scan.set_freqframe('BARY') |
---|
| 735 | """ |
---|
[484] | 736 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
| 737 | varlist = vars() |
---|
[1118] | 738 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 739 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 740 | |
---|
[989] | 741 | if frame in valid: |
---|
[113] | 742 | inf = list(self._getcoordinfo()) |
---|
| 743 | inf[1] = frame |
---|
| 744 | self._setcoordinfo(inf) |
---|
[1118] | 745 | self._add_history("set_freqframe", varlist) |
---|
[102] | 746 | else: |
---|
[1118] | 747 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[718] | 748 | if rcParams['verbose']: |
---|
[1612] | 749 | #print msg |
---|
[1614] | 750 | asaplog.push( msg ) |
---|
| 751 | print_log( 'ERROR' ) |
---|
[718] | 752 | else: |
---|
| 753 | raise TypeError(msg) |
---|
| 754 | print_log() |
---|
[710] | 755 | |
---|
[989] | 756 | def set_dirframe(self, frame=""): |
---|
| 757 | """ |
---|
| 758 | Set the frame type of the Direction on the sky. |
---|
| 759 | Parameters: |
---|
| 760 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 761 | 'J2000', 'B1950', 'GALACTIC' |
---|
| 762 | Examples: |
---|
| 763 | scan.set_dirframe('GALACTIC') |
---|
| 764 | """ |
---|
| 765 | varlist = vars() |
---|
| 766 | try: |
---|
| 767 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 768 | except RuntimeError, msg: |
---|
[989] | 769 | if rcParams['verbose']: |
---|
[1612] | 770 | #print msg |
---|
[1614] | 771 | print_log() |
---|
[1627] | 772 | asaplog.push( msg.message ) |
---|
[1614] | 773 | print_log( 'ERROR' ) |
---|
[989] | 774 | else: |
---|
| 775 | raise |
---|
[1118] | 776 | self._add_history("set_dirframe", varlist) |
---|
[989] | 777 | |
---|
[113] | 778 | def get_unit(self): |
---|
| 779 | """ |
---|
| 780 | Get the default unit set in this scantable |
---|
| 781 | Returns: |
---|
| 782 | A unit string |
---|
| 783 | """ |
---|
| 784 | inf = self._getcoordinfo() |
---|
| 785 | unit = inf[0] |
---|
| 786 | if unit == '': unit = 'channel' |
---|
| 787 | return unit |
---|
[102] | 788 | |
---|
[158] | 789 | def get_abcissa(self, rowno=0): |
---|
[102] | 790 | """ |
---|
[158] | 791 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 792 | selected Beam/IF/Pol |
---|
| 793 | Parameters: |
---|
[226] | 794 | rowno: an optional row number in the scantable. Default is the |
---|
| 795 | first row, i.e. rowno=0 |
---|
[113] | 796 | Returns: |
---|
[1348] | 797 | The abcissa values and the format string (as a dictionary) |
---|
[113] | 798 | """ |
---|
[256] | 799 | abc = self._getabcissa(rowno) |
---|
[710] | 800 | lbl = self._getabcissalabel(rowno) |
---|
[718] | 801 | print_log() |
---|
[158] | 802 | return abc, lbl |
---|
[113] | 803 | |
---|
[1401] | 804 | def flag(self, mask=None, unflag=False): |
---|
[1001] | 805 | """ |
---|
| 806 | Flag the selected data using an optional channel mask. |
---|
| 807 | Parameters: |
---|
| 808 | mask: an optional channel mask, created with create_mask. Default |
---|
| 809 | (no mask) is all channels. |
---|
[1401] | 810 | unflag: if True, unflag the data |
---|
[1001] | 811 | """ |
---|
| 812 | varlist = vars() |
---|
[1118] | 813 | if mask is None: |
---|
| 814 | mask = [] |
---|
[1001] | 815 | try: |
---|
[1401] | 816 | self._flag(mask, unflag) |
---|
[1118] | 817 | except RuntimeError, msg: |
---|
[1001] | 818 | if rcParams['verbose']: |
---|
[1612] | 819 | #print msg |
---|
[1614] | 820 | print_log() |
---|
[1627] | 821 | asaplog.push( msg.message ) |
---|
[1614] | 822 | print_log( 'ERROR' ) |
---|
[1001] | 823 | return |
---|
| 824 | else: raise |
---|
| 825 | self._add_history("flag", varlist) |
---|
| 826 | |
---|
[1203] | 827 | def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None): |
---|
[1192] | 828 | """ |
---|
| 829 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
| 830 | Flagged data in the scantable gets set to 0.0 before the fft. |
---|
| 831 | No taper is applied. |
---|
| 832 | Parameters: |
---|
[1348] | 833 | frequency: the frequency (really a period within the bandwidth) |
---|
| 834 | to remove |
---|
| 835 | width: the width of the frequency to remove, to remove a |
---|
[1603] | 836 | range of frequencies around the centre. |
---|
[1203] | 837 | unit: the frequency unit (default "GHz") |
---|
| 838 | Notes: |
---|
[1348] | 839 | It is recommended to flag edges of the band or strong |
---|
| 840 | signals beforehand. |
---|
[1192] | 841 | """ |
---|
| 842 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 843 | self._math._setinsitu(insitu) |
---|
| 844 | varlist = vars() |
---|
[1370] | 845 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. } |
---|
[1192] | 846 | if not base.has_key(unit): |
---|
| 847 | raise ValueError("%s is not a valid unit." % unit) |
---|
| 848 | try: |
---|
[1200] | 849 | s = scantable(self._math._lag_flag(self, frequency*base[unit], |
---|
| 850 | width*base[unit])) |
---|
[1192] | 851 | except RuntimeError, msg: |
---|
| 852 | if rcParams['verbose']: |
---|
[1612] | 853 | #print msg |
---|
[1614] | 854 | print_log() |
---|
[1627] | 855 | asaplog.push( msg.message ) |
---|
[1614] | 856 | print_log( 'ERROR' ) |
---|
[1192] | 857 | return |
---|
| 858 | else: raise |
---|
| 859 | s._add_history("lag_flag", varlist) |
---|
| 860 | print_log() |
---|
| 861 | if insitu: |
---|
| 862 | self._assign(s) |
---|
| 863 | else: |
---|
| 864 | return s |
---|
[1001] | 865 | |
---|
[1192] | 866 | |
---|
[113] | 867 | def create_mask(self, *args, **kwargs): |
---|
| 868 | """ |
---|
[1118] | 869 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 870 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 871 | applied. |
---|
[102] | 872 | Parameters: |
---|
[1118] | 873 | [min, max], [min2, max2], ... |
---|
[1024] | 874 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 875 | to be masked |
---|
[189] | 876 | invert: optional argument. If specified as True, |
---|
| 877 | return an inverted mask, i.e. the regions |
---|
| 878 | specified are EXCLUDED |
---|
[513] | 879 | row: create the mask using the specified row for |
---|
| 880 | unit conversions, default is row=0 |
---|
| 881 | only necessary if frequency varies over rows. |
---|
[102] | 882 | Example: |
---|
[113] | 883 | scan.set_unit('channel') |
---|
| 884 | a) |
---|
[1118] | 885 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 886 | # masks everything outside 400 and 500 |
---|
[113] | 887 | # and 800 and 900 in the unit 'channel' |
---|
| 888 | |
---|
| 889 | b) |
---|
[1118] | 890 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 891 | # masks the regions between 400 and 500 |
---|
[113] | 892 | # and 800 and 900 in the unit 'channel' |
---|
[1024] | 893 | c) |
---|
| 894 | mask only channel 400 |
---|
[1118] | 895 | msk = scan.create_mask([400, 400]) |
---|
[102] | 896 | """ |
---|
[513] | 897 | row = 0 |
---|
| 898 | if kwargs.has_key("row"): |
---|
| 899 | row = kwargs.get("row") |
---|
| 900 | data = self._getabcissa(row) |
---|
[113] | 901 | u = self._getcoordinfo()[0] |
---|
[718] | 902 | if rcParams['verbose']: |
---|
[113] | 903 | if u == "": u = "channel" |
---|
[718] | 904 | msg = "The current mask window unit is %s" % u |
---|
[1118] | 905 | i = self._check_ifs() |
---|
| 906 | if not i: |
---|
[876] | 907 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 908 | asaplog.push(msg) |
---|
[102] | 909 | n = self.nchan() |
---|
[1295] | 910 | msk = _n_bools(n, False) |
---|
[710] | 911 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 912 | |
---|
[1118] | 913 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 914 | and args or args[0] |
---|
[710] | 915 | for window in ws: |
---|
[102] | 916 | if (len(window) != 2 or window[0] > window[1] ): |
---|
[1118] | 917 | raise TypeError("A window needs to be defined as [min, max]") |
---|
[102] | 918 | for i in range(n): |
---|
[1024] | 919 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 920 | msk[i] = True |
---|
[113] | 921 | if kwargs.has_key('invert'): |
---|
| 922 | if kwargs.get('invert'): |
---|
[1295] | 923 | msk = mask_not(msk) |
---|
[718] | 924 | print_log() |
---|
[102] | 925 | return msk |
---|
[710] | 926 | |
---|
[1446] | 927 | def get_masklist(self, mask=None, row=0): |
---|
[256] | 928 | """ |
---|
[1446] | 929 | Compute and return a list of mask windows, [min, max]. |
---|
| 930 | Parameters: |
---|
| 931 | mask: channel mask, created with create_mask. |
---|
| 932 | row: calcutate the masklist using the specified row |
---|
| 933 | for unit conversions, default is row=0 |
---|
| 934 | only necessary if frequency varies over rows. |
---|
| 935 | Returns: |
---|
| 936 | [min, max], [min2, max2], ... |
---|
| 937 | Pairs of start/end points (inclusive)specifying |
---|
| 938 | the masked regions |
---|
| 939 | """ |
---|
| 940 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 941 | raise TypeError("The mask should be list or tuple.") |
---|
| 942 | if len(mask) < 2: |
---|
| 943 | raise TypeError("The mask elements should be > 1") |
---|
| 944 | if self.nchan() != len(mask): |
---|
| 945 | msg = "Number of channels in scantable != number of mask elements" |
---|
| 946 | raise TypeError(msg) |
---|
| 947 | data = self._getabcissa(row) |
---|
| 948 | u = self._getcoordinfo()[0] |
---|
| 949 | if rcParams['verbose']: |
---|
| 950 | if u == "": u = "channel" |
---|
| 951 | msg = "The current mask window unit is %s" % u |
---|
| 952 | i = self._check_ifs() |
---|
| 953 | if not i: |
---|
| 954 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 955 | asaplog.push(msg) |
---|
| 956 | masklist=[] |
---|
| 957 | ist, ien = None, None |
---|
| 958 | ist, ien=self.get_mask_indices(mask) |
---|
| 959 | if ist is not None and ien is not None: |
---|
| 960 | for i in xrange(len(ist)): |
---|
| 961 | range=[data[ist[i]],data[ien[i]]] |
---|
| 962 | range.sort() |
---|
| 963 | masklist.append([range[0],range[1]]) |
---|
| 964 | return masklist |
---|
| 965 | |
---|
| 966 | def get_mask_indices(self, mask=None): |
---|
| 967 | """ |
---|
| 968 | Compute and Return lists of mask start indices and mask end indices. |
---|
| 969 | Parameters: |
---|
| 970 | mask: channel mask, created with create_mask. |
---|
| 971 | Returns: |
---|
| 972 | List of mask start indices and that of mask end indices, |
---|
| 973 | i.e., [istart1,istart2,....], [iend1,iend2,....]. |
---|
| 974 | """ |
---|
| 975 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 976 | raise TypeError("The mask should be list or tuple.") |
---|
| 977 | if len(mask) < 2: |
---|
| 978 | raise TypeError("The mask elements should be > 1") |
---|
| 979 | istart=[] |
---|
| 980 | iend=[] |
---|
| 981 | if mask[0]: istart.append(0) |
---|
| 982 | for i in range(len(mask)-1): |
---|
| 983 | if not mask[i] and mask[i+1]: |
---|
| 984 | istart.append(i+1) |
---|
| 985 | elif mask[i] and not mask[i+1]: |
---|
| 986 | iend.append(i) |
---|
| 987 | if mask[len(mask)-1]: iend.append(len(mask)-1) |
---|
| 988 | if len(istart) != len(iend): |
---|
| 989 | raise RuntimeError("Numbers of mask start != mask end.") |
---|
| 990 | for i in range(len(istart)): |
---|
| 991 | if istart[i] > iend[i]: |
---|
| 992 | raise RuntimeError("Mask start index > mask end index") |
---|
| 993 | break |
---|
| 994 | return istart,iend |
---|
| 995 | |
---|
| 996 | # def get_restfreqs(self): |
---|
| 997 | # """ |
---|
| 998 | # Get the restfrequency(s) stored in this scantable. |
---|
| 999 | # The return value(s) are always of unit 'Hz' |
---|
| 1000 | # Parameters: |
---|
| 1001 | # none |
---|
| 1002 | # Returns: |
---|
| 1003 | # a list of doubles |
---|
| 1004 | # """ |
---|
| 1005 | # return list(self._getrestfreqs()) |
---|
| 1006 | |
---|
| 1007 | def get_restfreqs(self, ids=None): |
---|
| 1008 | """ |
---|
[256] | 1009 | Get the restfrequency(s) stored in this scantable. |
---|
| 1010 | The return value(s) are always of unit 'Hz' |
---|
| 1011 | Parameters: |
---|
[1446] | 1012 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to |
---|
| 1013 | be retrieved |
---|
[256] | 1014 | Returns: |
---|
[1446] | 1015 | dictionary containing ids and a list of doubles for each id |
---|
[256] | 1016 | """ |
---|
[1446] | 1017 | if ids is None: |
---|
| 1018 | rfreqs={} |
---|
| 1019 | idlist = self.getmolnos() |
---|
| 1020 | for i in idlist: |
---|
| 1021 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1022 | return rfreqs |
---|
| 1023 | else: |
---|
| 1024 | if type(ids)==list or type(ids)==tuple: |
---|
| 1025 | rfreqs={} |
---|
| 1026 | for i in ids: |
---|
| 1027 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1028 | return rfreqs |
---|
| 1029 | else: |
---|
| 1030 | return list(self._getrestfreqs(ids)) |
---|
| 1031 | #return list(self._getrestfreqs(ids)) |
---|
[102] | 1032 | |
---|
[931] | 1033 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
| 1034 | """ |
---|
[1446] | 1035 | ********NEED TO BE UPDATED begin************ |
---|
[931] | 1036 | Set or replace the restfrequency specified and |
---|
| 1037 | If the 'freqs' argument holds a scalar, |
---|
| 1038 | then that rest frequency will be applied to all the selected |
---|
| 1039 | data. If the 'freqs' argument holds |
---|
| 1040 | a vector, then it MUST be of equal or smaller length than |
---|
| 1041 | the number of IFs (and the available restfrequencies will be |
---|
| 1042 | replaced by this vector). In this case, *all* data have |
---|
| 1043 | the restfrequency set per IF according |
---|
| 1044 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 1045 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 1046 | IF 1 gets restfreq 2e9. |
---|
[1446] | 1047 | ********NEED TO BE UPDATED end************ |
---|
[1603] | 1048 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 1049 | |
---|
[931] | 1050 | Parameters: |
---|
| 1051 | freqs: list of rest frequency values or string idenitfiers |
---|
| 1052 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 1053 | |
---|
[931] | 1054 | Example: |
---|
[1446] | 1055 | # set the given restfrequency for the all currently selected IFs |
---|
[931] | 1056 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1446] | 1057 | # set multiple restfrequencies to all the selected data |
---|
| 1058 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9]) |
---|
| 1059 | # If the number of IFs in the data is >= 2 the IF0 gets the first |
---|
| 1060 | # value IF1 the second... NOTE that freqs needs to be |
---|
| 1061 | # specified in list of list (e.g. [[],[],...] ). |
---|
| 1062 | scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]]) |
---|
[931] | 1063 | #set the given restfrequency for the whole table (by name) |
---|
| 1064 | scan.set_restfreqs(freqs="OH1667") |
---|
[391] | 1065 | |
---|
[931] | 1066 | Note: |
---|
| 1067 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 1068 | source and IF basis, use scantable.set_selection() before using |
---|
| 1069 | this function. |
---|
| 1070 | # provide your scantable is call scan |
---|
| 1071 | selection = selector() |
---|
| 1072 | selection.set_name("ORION*") |
---|
| 1073 | selection.set_ifs([1]) |
---|
| 1074 | scan.set_selection(selection) |
---|
| 1075 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 1076 | |
---|
| 1077 | """ |
---|
| 1078 | varlist = vars() |
---|
[1157] | 1079 | from asap import linecatalog |
---|
| 1080 | # simple value |
---|
[1118] | 1081 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1446] | 1082 | # TT mod |
---|
| 1083 | #self._setrestfreqs(freqs, "",unit) |
---|
| 1084 | self._setrestfreqs([freqs], [""],unit) |
---|
[1157] | 1085 | # list of values |
---|
[1118] | 1086 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 1087 | # list values are scalars |
---|
[1118] | 1088 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[1446] | 1089 | self._setrestfreqs(freqs, [""],unit) |
---|
[1157] | 1090 | # list values are tuples, (value, name) |
---|
| 1091 | elif isinstance(freqs[-1], dict): |
---|
[1446] | 1092 | #sel = selector() |
---|
| 1093 | #savesel = self._getselection() |
---|
| 1094 | #iflist = self.getifnos() |
---|
| 1095 | #for i in xrange(len(freqs)): |
---|
| 1096 | # sel.set_ifs(iflist[i]) |
---|
| 1097 | # self._setselection(sel) |
---|
| 1098 | # self._setrestfreqs(freqs[i], "",unit) |
---|
| 1099 | #self._setselection(savesel) |
---|
| 1100 | self._setrestfreqs(freqs["value"], |
---|
| 1101 | freqs["name"], "MHz") |
---|
| 1102 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple): |
---|
[1157] | 1103 | sel = selector() |
---|
| 1104 | savesel = self._getselection() |
---|
[1322] | 1105 | iflist = self.getifnos() |
---|
[1446] | 1106 | if len(freqs)>len(iflist): |
---|
| 1107 | raise ValueError("number of elements in list of list exeeds the current IF selections") |
---|
[1157] | 1108 | for i in xrange(len(freqs)): |
---|
[1322] | 1109 | sel.set_ifs(iflist[i]) |
---|
[1259] | 1110 | self._setselection(sel) |
---|
[1157] | 1111 | self._setrestfreqs(freqs[i]["value"], |
---|
| 1112 | freqs[i]["name"], "MHz") |
---|
| 1113 | self._setselection(savesel) |
---|
| 1114 | # freqs are to be taken from a linecatalog |
---|
[1153] | 1115 | elif isinstance(freqs, linecatalog): |
---|
| 1116 | sel = selector() |
---|
| 1117 | savesel = self._getselection() |
---|
| 1118 | for i in xrange(freqs.nrow()): |
---|
[1322] | 1119 | sel.set_ifs(iflist[i]) |
---|
[1153] | 1120 | self._setselection(sel) |
---|
| 1121 | self._setrestfreqs(freqs.get_frequency(i), |
---|
| 1122 | freqs.get_name(i), "MHz") |
---|
| 1123 | # ensure that we are not iterating past nIF |
---|
| 1124 | if i == self.nif()-1: break |
---|
| 1125 | self._setselection(savesel) |
---|
[931] | 1126 | else: |
---|
| 1127 | return |
---|
| 1128 | self._add_history("set_restfreqs", varlist) |
---|
| 1129 | |
---|
[1360] | 1130 | def shift_refpix(self, delta): |
---|
| 1131 | """ |
---|
| 1132 | Shift the reference pixel of the Spectra Coordinate by an |
---|
| 1133 | integer amount. |
---|
| 1134 | Parameters: |
---|
| 1135 | delta: the amount to shift by |
---|
| 1136 | Note: |
---|
| 1137 | Be careful using this with broadband data. |
---|
| 1138 | """ |
---|
| 1139 | Scantable.shift(self, delta) |
---|
[931] | 1140 | |
---|
[1259] | 1141 | def history(self, filename=None): |
---|
| 1142 | """ |
---|
| 1143 | Print the history. Optionally to a file. |
---|
[1348] | 1144 | Parameters: |
---|
| 1145 | filename: The name of the file to save the history to. |
---|
[1259] | 1146 | """ |
---|
[484] | 1147 | hist = list(self._gethistory()) |
---|
[794] | 1148 | out = "-"*80 |
---|
[484] | 1149 | for h in hist: |
---|
[489] | 1150 | if h.startswith("---"): |
---|
[794] | 1151 | out += "\n"+h |
---|
[489] | 1152 | else: |
---|
| 1153 | items = h.split("##") |
---|
| 1154 | date = items[0] |
---|
| 1155 | func = items[1] |
---|
| 1156 | items = items[2:] |
---|
[794] | 1157 | out += "\n"+date+"\n" |
---|
| 1158 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 1159 | for i in items: |
---|
| 1160 | s = i.split("=") |
---|
[1118] | 1161 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[794] | 1162 | out += "\n"+"-"*80 |
---|
[1259] | 1163 | if filename is not None: |
---|
| 1164 | if filename is "": |
---|
| 1165 | filename = 'scantable_history.txt' |
---|
| 1166 | import os |
---|
| 1167 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 1168 | if not os.path.isdir(filename): |
---|
| 1169 | data = open(filename, 'w') |
---|
| 1170 | data.write(out) |
---|
| 1171 | data.close() |
---|
| 1172 | else: |
---|
| 1173 | msg = "Illegal file name '%s'." % (filename) |
---|
| 1174 | if rcParams['verbose']: |
---|
[1612] | 1175 | #print msg |
---|
[1614] | 1176 | asaplog.push( msg ) |
---|
| 1177 | print_log( 'ERROR' ) |
---|
[1259] | 1178 | else: |
---|
| 1179 | raise IOError(msg) |
---|
| 1180 | if rcParams['verbose']: |
---|
| 1181 | try: |
---|
| 1182 | from IPython.genutils import page as pager |
---|
| 1183 | except ImportError: |
---|
| 1184 | from pydoc import pager |
---|
| 1185 | pager(out) |
---|
| 1186 | else: |
---|
| 1187 | return out |
---|
[484] | 1188 | return |
---|
[513] | 1189 | # |
---|
| 1190 | # Maths business |
---|
| 1191 | # |
---|
| 1192 | |
---|
[931] | 1193 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[513] | 1194 | """ |
---|
[1070] | 1195 | Return the (time) weighted average of a scan. |
---|
[513] | 1196 | Note: |
---|
[1070] | 1197 | in channels only - align if necessary |
---|
[513] | 1198 | Parameters: |
---|
| 1199 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 1200 | weighting) |
---|
[558] | 1201 | scanav: True averages each scan separately |
---|
| 1202 | False (default) averages all scans together, |
---|
[1099] | 1203 | weight: Weighting scheme. |
---|
| 1204 | 'none' (mean no weight) |
---|
| 1205 | 'var' (1/var(spec) weighted) |
---|
| 1206 | 'tsys' (1/Tsys**2 weighted) |
---|
| 1207 | 'tint' (integration time weighted) |
---|
| 1208 | 'tintsys' (Tint/Tsys**2) |
---|
| 1209 | 'median' ( median averaging) |
---|
[535] | 1210 | The default is 'tint' |
---|
[931] | 1211 | align: align the spectra in velocity before averaging. It takes |
---|
| 1212 | the time of the first spectrum as reference time. |
---|
[513] | 1213 | Example: |
---|
| 1214 | # time average the scantable without using a mask |
---|
[710] | 1215 | newscan = scan.average_time() |
---|
[513] | 1216 | """ |
---|
| 1217 | varlist = vars() |
---|
[976] | 1218 | if weight is None: weight = 'TINT' |
---|
[513] | 1219 | if mask is None: mask = () |
---|
[1099] | 1220 | if scanav: scanav = "SCAN" |
---|
| 1221 | else: scanav = "NONE" |
---|
[1118] | 1222 | scan = (self, ) |
---|
[989] | 1223 | try: |
---|
[1118] | 1224 | if align: |
---|
| 1225 | scan = (self.freq_align(insitu=False), ) |
---|
| 1226 | s = None |
---|
| 1227 | if weight.upper() == 'MEDIAN': |
---|
| 1228 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 1229 | scanav)) |
---|
| 1230 | else: |
---|
| 1231 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 1232 | scanav)) |
---|
| 1233 | except RuntimeError, msg: |
---|
[989] | 1234 | if rcParams['verbose']: |
---|
[1612] | 1235 | #print msg |
---|
[1614] | 1236 | print_log() |
---|
[1627] | 1237 | asaplog.push( msg.message ) |
---|
[1614] | 1238 | print_log( 'ERROR' ) |
---|
[989] | 1239 | return |
---|
| 1240 | else: raise |
---|
[1099] | 1241 | s._add_history("average_time", varlist) |
---|
[718] | 1242 | print_log() |
---|
[513] | 1243 | return s |
---|
[710] | 1244 | |
---|
[876] | 1245 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[513] | 1246 | """ |
---|
| 1247 | Return a scan where all spectra are converted to either |
---|
| 1248 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 1249 | By default the function tries to look the values up internally. |
---|
| 1250 | If it can't find them (or if you want to over-ride), you must |
---|
| 1251 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 1252 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 1253 | Parameters: |
---|
| 1254 | jyperk: the Jy / K conversion factor |
---|
| 1255 | eta: the aperture efficiency |
---|
| 1256 | d: the geomtric diameter (metres) |
---|
| 1257 | insitu: if False a new scantable is returned. |
---|
| 1258 | Otherwise, the scaling is done in-situ |
---|
| 1259 | The default is taken from .asaprc (False) |
---|
| 1260 | """ |
---|
| 1261 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1262 | self._math._setinsitu(insitu) |
---|
[513] | 1263 | varlist = vars() |
---|
| 1264 | if jyperk is None: jyperk = -1.0 |
---|
| 1265 | if d is None: d = -1.0 |
---|
| 1266 | if eta is None: eta = -1.0 |
---|
[876] | 1267 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 1268 | s._add_history("convert_flux", varlist) |
---|
| 1269 | print_log() |
---|
| 1270 | if insitu: self._assign(s) |
---|
| 1271 | else: return s |
---|
[513] | 1272 | |
---|
[876] | 1273 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[513] | 1274 | """ |
---|
| 1275 | Return a scan after applying a gain-elevation correction. |
---|
| 1276 | The correction can be made via either a polynomial or a |
---|
| 1277 | table-based interpolation (and extrapolation if necessary). |
---|
| 1278 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 1279 | If you specify neither, then a polynomial correction will be made |
---|
| 1280 | with built in coefficients known for certain telescopes (an error |
---|
| 1281 | will occur if the instrument is not known). |
---|
| 1282 | The data and Tsys are *divided* by the scaling factors. |
---|
| 1283 | Parameters: |
---|
| 1284 | poly: Polynomial coefficients (default None) to compute a |
---|
| 1285 | gain-elevation correction as a function of |
---|
| 1286 | elevation (in degrees). |
---|
| 1287 | filename: The name of an ascii file holding correction factors. |
---|
| 1288 | The first row of the ascii file must give the column |
---|
| 1289 | names and these MUST include columns |
---|
| 1290 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 1291 | by this) somewhere. |
---|
| 1292 | The second row must give the data type of the |
---|
| 1293 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 1294 | An example file would be |
---|
| 1295 | (actual factors are arbitrary) : |
---|
| 1296 | |
---|
| 1297 | TIME ELEVATION FACTOR |
---|
| 1298 | R R R |
---|
| 1299 | 0.1 0 0.8 |
---|
| 1300 | 0.2 20 0.85 |
---|
| 1301 | 0.3 40 0.9 |
---|
| 1302 | 0.4 60 0.85 |
---|
| 1303 | 0.5 80 0.8 |
---|
| 1304 | 0.6 90 0.75 |
---|
| 1305 | method: Interpolation method when correcting from a table. |
---|
| 1306 | Values are "nearest", "linear" (default), "cubic" |
---|
| 1307 | and "spline" |
---|
| 1308 | insitu: if False a new scantable is returned. |
---|
| 1309 | Otherwise, the scaling is done in-situ |
---|
| 1310 | The default is taken from .asaprc (False) |
---|
| 1311 | """ |
---|
| 1312 | |
---|
| 1313 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1314 | self._math._setinsitu(insitu) |
---|
[513] | 1315 | varlist = vars() |
---|
| 1316 | if poly is None: |
---|
[1118] | 1317 | poly = () |
---|
[513] | 1318 | from os.path import expandvars |
---|
| 1319 | filename = expandvars(filename) |
---|
[876] | 1320 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 1321 | s._add_history("gain_el", varlist) |
---|
| 1322 | print_log() |
---|
| 1323 | if insitu: self._assign(s) |
---|
| 1324 | else: return s |
---|
[710] | 1325 | |
---|
[931] | 1326 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[513] | 1327 | """ |
---|
| 1328 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 1329 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 1330 | set_freqframe. |
---|
| 1331 | Parameters: |
---|
| 1332 | reftime: reference time to align at. By default, the time of |
---|
| 1333 | the first row of data is used. |
---|
| 1334 | method: Interpolation method for regridding the spectra. |
---|
| 1335 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 1336 | and "spline" |
---|
| 1337 | insitu: if False a new scantable is returned. |
---|
| 1338 | Otherwise, the scaling is done in-situ |
---|
| 1339 | The default is taken from .asaprc (False) |
---|
| 1340 | """ |
---|
[931] | 1341 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 1342 | self._math._setinsitu(insitu) |
---|
[513] | 1343 | varlist = vars() |
---|
[931] | 1344 | if reftime is None: reftime = "" |
---|
| 1345 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 1346 | s._add_history("freq_align", varlist) |
---|
| 1347 | print_log() |
---|
| 1348 | if insitu: self._assign(s) |
---|
| 1349 | else: return s |
---|
[513] | 1350 | |
---|
[876] | 1351 | def opacity(self, tau, insitu=None): |
---|
[513] | 1352 | """ |
---|
| 1353 | Apply an opacity correction. The data |
---|
| 1354 | and Tsys are multiplied by the correction factor. |
---|
| 1355 | Parameters: |
---|
| 1356 | tau: Opacity from which the correction factor is |
---|
| 1357 | exp(tau*ZD) |
---|
| 1358 | where ZD is the zenith-distance |
---|
| 1359 | insitu: if False a new scantable is returned. |
---|
| 1360 | Otherwise, the scaling is done in-situ |
---|
| 1361 | The default is taken from .asaprc (False) |
---|
| 1362 | """ |
---|
| 1363 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1364 | self._math._setinsitu(insitu) |
---|
[513] | 1365 | varlist = vars() |
---|
[876] | 1366 | s = scantable(self._math._opacity(self, tau)) |
---|
| 1367 | s._add_history("opacity", varlist) |
---|
| 1368 | print_log() |
---|
| 1369 | if insitu: self._assign(s) |
---|
| 1370 | else: return s |
---|
[513] | 1371 | |
---|
| 1372 | def bin(self, width=5, insitu=None): |
---|
| 1373 | """ |
---|
| 1374 | Return a scan where all spectra have been binned up. |
---|
[1348] | 1375 | Parameters: |
---|
[513] | 1376 | width: The bin width (default=5) in pixels |
---|
| 1377 | insitu: if False a new scantable is returned. |
---|
| 1378 | Otherwise, the scaling is done in-situ |
---|
| 1379 | The default is taken from .asaprc (False) |
---|
| 1380 | """ |
---|
| 1381 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1382 | self._math._setinsitu(insitu) |
---|
[513] | 1383 | varlist = vars() |
---|
[876] | 1384 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1385 | s._add_history("bin", varlist) |
---|
[876] | 1386 | print_log() |
---|
| 1387 | if insitu: self._assign(s) |
---|
| 1388 | else: return s |
---|
[513] | 1389 | |
---|
[710] | 1390 | |
---|
[513] | 1391 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 1392 | """ |
---|
[1348] | 1393 | Return a scan where all spectra have been binned up. |
---|
| 1394 | |
---|
| 1395 | Parameters: |
---|
[513] | 1396 | width: The bin width (default=5) in pixels |
---|
| 1397 | method: Interpolation method when correcting from a table. |
---|
| 1398 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1399 | and "spline" |
---|
| 1400 | insitu: if False a new scantable is returned. |
---|
| 1401 | Otherwise, the scaling is done in-situ |
---|
| 1402 | The default is taken from .asaprc (False) |
---|
| 1403 | """ |
---|
| 1404 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1405 | self._math._setinsitu(insitu) |
---|
[513] | 1406 | varlist = vars() |
---|
[876] | 1407 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1408 | s._add_history("resample", varlist) |
---|
[876] | 1409 | print_log() |
---|
| 1410 | if insitu: self._assign(s) |
---|
| 1411 | else: return s |
---|
[513] | 1412 | |
---|
| 1413 | |
---|
[946] | 1414 | def average_pol(self, mask=None, weight='none'): |
---|
| 1415 | """ |
---|
| 1416 | Average the Polarisations together. |
---|
| 1417 | Parameters: |
---|
| 1418 | mask: An optional mask defining the region, where the |
---|
| 1419 | averaging will be applied. The output will have all |
---|
| 1420 | specified points masked. |
---|
| 1421 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1422 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1423 | """ |
---|
| 1424 | varlist = vars() |
---|
| 1425 | if mask is None: |
---|
| 1426 | mask = () |
---|
[1010] | 1427 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1428 | s._add_history("average_pol", varlist) |
---|
[946] | 1429 | print_log() |
---|
[992] | 1430 | return s |
---|
[513] | 1431 | |
---|
[1145] | 1432 | def average_beam(self, mask=None, weight='none'): |
---|
| 1433 | """ |
---|
| 1434 | Average the Beams together. |
---|
| 1435 | Parameters: |
---|
| 1436 | mask: An optional mask defining the region, where the |
---|
| 1437 | averaging will be applied. The output will have all |
---|
| 1438 | specified points masked. |
---|
| 1439 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1440 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1441 | """ |
---|
| 1442 | varlist = vars() |
---|
| 1443 | if mask is None: |
---|
| 1444 | mask = () |
---|
| 1445 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1446 | s._add_history("average_beam", varlist) |
---|
| 1447 | print_log() |
---|
| 1448 | return s |
---|
| 1449 | |
---|
[992] | 1450 | def convert_pol(self, poltype=None): |
---|
| 1451 | """ |
---|
| 1452 | Convert the data to a different polarisation type. |
---|
| 1453 | Parameters: |
---|
| 1454 | poltype: The new polarisation type. Valid types are: |
---|
| 1455 | "linear", "stokes" and "circular" |
---|
| 1456 | """ |
---|
| 1457 | varlist = vars() |
---|
| 1458 | try: |
---|
| 1459 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1460 | except RuntimeError, msg: |
---|
[992] | 1461 | if rcParams['verbose']: |
---|
[1612] | 1462 | #print msg |
---|
[1614] | 1463 | print_log() |
---|
[1627] | 1464 | asaplog.push( msg.message ) |
---|
[1614] | 1465 | print_log( 'ERROR' ) |
---|
[1118] | 1466 | return |
---|
[992] | 1467 | else: |
---|
| 1468 | raise |
---|
[1118] | 1469 | s._add_history("convert_pol", varlist) |
---|
[992] | 1470 | print_log() |
---|
| 1471 | return s |
---|
| 1472 | |
---|
[876] | 1473 | def smooth(self, kernel="hanning", width=5.0, insitu=None): |
---|
[513] | 1474 | """ |
---|
| 1475 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 1476 | Parameters: |
---|
| 1477 | kernel: The type of smoothing kernel. Select from |
---|
[1373] | 1478 | 'hanning' (default), 'gaussian', 'boxcar' and |
---|
| 1479 | 'rmedian' |
---|
[513] | 1480 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1481 | ignored otherwise it defauls to 5 pixels. |
---|
| 1482 | For 'gaussian' it is the Full Width Half |
---|
| 1483 | Maximum. For 'boxcar' it is the full width. |
---|
[1373] | 1484 | For 'rmedian' it is the half width. |
---|
[513] | 1485 | insitu: if False a new scantable is returned. |
---|
| 1486 | Otherwise, the scaling is done in-situ |
---|
| 1487 | The default is taken from .asaprc (False) |
---|
| 1488 | Example: |
---|
| 1489 | none |
---|
| 1490 | """ |
---|
| 1491 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1492 | self._math._setinsitu(insitu) |
---|
[513] | 1493 | varlist = vars() |
---|
[1118] | 1494 | s = scantable(self._math._smooth(self, kernel.lower(), width)) |
---|
[876] | 1495 | s._add_history("smooth", varlist) |
---|
| 1496 | print_log() |
---|
| 1497 | if insitu: self._assign(s) |
---|
| 1498 | else: return s |
---|
[513] | 1499 | |
---|
[876] | 1500 | |
---|
[1389] | 1501 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None): |
---|
[513] | 1502 | """ |
---|
| 1503 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1504 | Parameters: |
---|
[794] | 1505 | mask: an optional mask |
---|
| 1506 | order: the order of the polynomial (default is 0) |
---|
[1061] | 1507 | plot: plot the fit and the residual. In this each |
---|
| 1508 | indivual fit has to be approved, by typing 'y' |
---|
| 1509 | or 'n' |
---|
[1389] | 1510 | uselin: use linear polynomial fit |
---|
[794] | 1511 | insitu: if False a new scantable is returned. |
---|
| 1512 | Otherwise, the scaling is done in-situ |
---|
| 1513 | The default is taken from .asaprc (False) |
---|
[513] | 1514 | Example: |
---|
| 1515 | # return a scan baselined by a third order polynomial, |
---|
| 1516 | # not using a mask |
---|
| 1517 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1518 | """ |
---|
[513] | 1519 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1520 | varlist = vars() |
---|
| 1521 | if mask is None: |
---|
[1295] | 1522 | mask = [True for i in xrange(self.nchan(-1))] |
---|
[1637] | 1523 | |
---|
[513] | 1524 | from asap.asapfitter import fitter |
---|
[1217] | 1525 | try: |
---|
| 1526 | f = fitter() |
---|
[1389] | 1527 | if uselin: |
---|
| 1528 | f.set_function(lpoly=order) |
---|
| 1529 | else: |
---|
| 1530 | f.set_function(poly=order) |
---|
[1637] | 1531 | |
---|
| 1532 | rows = range(self.nrow()) |
---|
| 1533 | if len(rows) > 0: |
---|
| 1534 | self.blpars = [] |
---|
| 1535 | |
---|
| 1536 | for r in rows: |
---|
| 1537 | # take into account flagtra info (CAS-1434) |
---|
| 1538 | flagtra = self._getmask(r) |
---|
| 1539 | actualmask = mask[:] |
---|
| 1540 | if len(actualmask) == 0: |
---|
| 1541 | actualmask = list(flagtra[:]) |
---|
| 1542 | else: |
---|
| 1543 | if len(actualmask) != len(flagtra): |
---|
| 1544 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 1545 | else: |
---|
| 1546 | for i in range(0, len(actualmask)): |
---|
| 1547 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 1548 | f.set_scan(self, actualmask) |
---|
| 1549 | f.x = self._getabcissa(r) |
---|
| 1550 | f.y = self._getspectrum(r) |
---|
| 1551 | f.data = None |
---|
| 1552 | f.fit() |
---|
| 1553 | fpar = f.get_parameters() |
---|
| 1554 | self.blpars.append(fpar) |
---|
| 1555 | |
---|
| 1556 | #f.set_scan(self, mask) |
---|
| 1557 | #s = f.auto_fit(insitu, plot=plot) |
---|
| 1558 | ## Save parameters of baseline fits as a class attribute. |
---|
| 1559 | ## NOTICE: It does not reflect changes in scantable! |
---|
| 1560 | #self.blpars = f.blpars |
---|
[1217] | 1561 | s._add_history("poly_baseline", varlist) |
---|
| 1562 | print_log() |
---|
| 1563 | if insitu: self._assign(s) |
---|
| 1564 | else: return s |
---|
| 1565 | except RuntimeError: |
---|
| 1566 | msg = "The fit failed, possibly because it didn't converge." |
---|
| 1567 | if rcParams['verbose']: |
---|
[1612] | 1568 | #print msg |
---|
[1614] | 1569 | print_log() |
---|
[1627] | 1570 | asaplog.push( msg.message ) |
---|
[1614] | 1571 | print_log( 'ERROR' ) |
---|
[1217] | 1572 | return |
---|
| 1573 | else: |
---|
| 1574 | raise RuntimeError(msg) |
---|
[513] | 1575 | |
---|
[1217] | 1576 | |
---|
[1118] | 1577 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
[1280] | 1578 | threshold=3, chan_avg_limit=1, plot=False, |
---|
| 1579 | insitu=None): |
---|
[880] | 1580 | """ |
---|
| 1581 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1582 | Spectral lines are detected first using linefinder and masked out |
---|
| 1583 | to avoid them affecting the baseline solution. |
---|
| 1584 | |
---|
| 1585 | Parameters: |
---|
| 1586 | mask: an optional mask retreived from scantable |
---|
| 1587 | edge: an optional number of channel to drop at |
---|
| 1588 | the edge of spectrum. If only one value is |
---|
| 1589 | specified, the same number will be dropped from |
---|
| 1590 | both sides of the spectrum. Default is to keep |
---|
[907] | 1591 | all channels. Nested tuples represent individual |
---|
[976] | 1592 | edge selection for different IFs (a number of spectral |
---|
| 1593 | channels can be different) |
---|
[880] | 1594 | order: the order of the polynomial (default is 0) |
---|
| 1595 | threshold: the threshold used by line finder. It is better to |
---|
| 1596 | keep it large as only strong lines affect the |
---|
| 1597 | baseline solution. |
---|
[1280] | 1598 | chan_avg_limit: |
---|
| 1599 | a maximum number of consequtive spectral channels to |
---|
| 1600 | average during the search of weak and broad lines. |
---|
| 1601 | The default is no averaging (and no search for weak |
---|
| 1602 | lines). If such lines can affect the fitted baseline |
---|
| 1603 | (e.g. a high order polynomial is fitted), increase this |
---|
| 1604 | parameter (usually values up to 8 are reasonable). Most |
---|
| 1605 | users of this method should find the default value |
---|
| 1606 | sufficient. |
---|
[1061] | 1607 | plot: plot the fit and the residual. In this each |
---|
| 1608 | indivual fit has to be approved, by typing 'y' |
---|
| 1609 | or 'n' |
---|
[880] | 1610 | insitu: if False a new scantable is returned. |
---|
| 1611 | Otherwise, the scaling is done in-situ |
---|
| 1612 | The default is taken from .asaprc (False) |
---|
| 1613 | |
---|
| 1614 | Example: |
---|
| 1615 | scan2=scan.auto_poly_baseline(order=7) |
---|
| 1616 | """ |
---|
| 1617 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1618 | varlist = vars() |
---|
| 1619 | from asap.asapfitter import fitter |
---|
| 1620 | from asap.asaplinefind import linefinder |
---|
| 1621 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1622 | |
---|
[976] | 1623 | # check whether edge is set up for each IF individually |
---|
[1118] | 1624 | individualedge = False; |
---|
| 1625 | if len(edge) > 1: |
---|
| 1626 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 1627 | individualedge = True; |
---|
[907] | 1628 | |
---|
[1118] | 1629 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 1630 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1631 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1632 | to make individual selection for different IFs." |
---|
[919] | 1633 | |
---|
[1118] | 1634 | curedge = (0, 0) |
---|
| 1635 | if individualedge: |
---|
| 1636 | for edgepar in edge: |
---|
| 1637 | if not _is_valid(edgepar, int): |
---|
| 1638 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 1639 | to be a pair of integers or an integer." |
---|
[907] | 1640 | else: |
---|
[1118] | 1641 | curedge = edge; |
---|
[880] | 1642 | |
---|
| 1643 | # setup fitter |
---|
| 1644 | f = fitter() |
---|
| 1645 | f.set_function(poly=order) |
---|
| 1646 | |
---|
| 1647 | # setup line finder |
---|
[1118] | 1648 | fl = linefinder() |
---|
[1268] | 1649 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
[880] | 1650 | |
---|
| 1651 | if not insitu: |
---|
[1118] | 1652 | workscan = self.copy() |
---|
[880] | 1653 | else: |
---|
[1118] | 1654 | workscan = self |
---|
[880] | 1655 | |
---|
[907] | 1656 | fl.set_scan(workscan) |
---|
| 1657 | |
---|
[1118] | 1658 | rows = range(workscan.nrow()) |
---|
[1446] | 1659 | # Save parameters of baseline fits & masklists as a class attribute. |
---|
| 1660 | # NOTICE: It does not reflect changes in scantable! |
---|
| 1661 | if len(rows) > 0: |
---|
| 1662 | self.blpars=[] |
---|
| 1663 | self.masklists=[] |
---|
[880] | 1664 | asaplog.push("Processing:") |
---|
| 1665 | for r in rows: |
---|
[1118] | 1666 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 1667 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 1668 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 1669 | asaplog.push(msg, False) |
---|
[907] | 1670 | |
---|
[976] | 1671 | # figure out edge parameter |
---|
[1118] | 1672 | if individualedge: |
---|
| 1673 | if len(edge) >= workscan.getif(r): |
---|
| 1674 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 1675 | "be less than the number of IFs" |
---|
| 1676 | curedge = edge[workscan.getif(r)] |
---|
[919] | 1677 | |
---|
[1637] | 1678 | # take into account flagtra info (CAS-1434) |
---|
| 1679 | flagtra = workscan._getmask(r) |
---|
| 1680 | actualmask = mask[:] |
---|
| 1681 | if len(actualmask) == 0: |
---|
| 1682 | actualmask = list(flagtra[:]) |
---|
| 1683 | else: |
---|
| 1684 | if len(actualmask) != len(flagtra): |
---|
| 1685 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 1686 | else: |
---|
| 1687 | for i in range(0, len(actualmask)): |
---|
| 1688 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 1689 | |
---|
[976] | 1690 | # setup line finder |
---|
[1637] | 1691 | fl.find_lines(r, actualmask, curedge) |
---|
[1446] | 1692 | outmask=fl.get_mask() |
---|
[880] | 1693 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1694 | f.x = workscan._getabcissa(r) |
---|
| 1695 | f.y = workscan._getspectrum(r) |
---|
| 1696 | f.data = None |
---|
| 1697 | f.fit() |
---|
[1446] | 1698 | |
---|
| 1699 | # Show mask list |
---|
| 1700 | masklist=workscan.get_masklist(fl.get_mask(),row=r) |
---|
| 1701 | msg = "mask range: "+str(masklist) |
---|
| 1702 | asaplog.push(msg, False) |
---|
| 1703 | |
---|
| 1704 | fpar = f.get_parameters() |
---|
[1061] | 1705 | if plot: |
---|
| 1706 | f.plot(residual=True) |
---|
| 1707 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1708 | if x.upper() == 'N': |
---|
[1446] | 1709 | self.blpars.append(None) |
---|
| 1710 | self.masklists.append(None) |
---|
[1061] | 1711 | continue |
---|
[880] | 1712 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1446] | 1713 | self.blpars.append(fpar) |
---|
| 1714 | self.masklists.append(masklist) |
---|
[1061] | 1715 | if plot: |
---|
| 1716 | f._p.unmap() |
---|
| 1717 | f._p = None |
---|
| 1718 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 1719 | if insitu: |
---|
| 1720 | self._assign(workscan) |
---|
| 1721 | else: |
---|
| 1722 | return workscan |
---|
| 1723 | |
---|
[914] | 1724 | def rotate_linpolphase(self, angle): |
---|
| 1725 | """ |
---|
| 1726 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1727 | This is always done in situ in the raw data. So if you call this |
---|
| 1728 | function more than once then each call rotates the phase further. |
---|
| 1729 | Parameters: |
---|
| 1730 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1731 | Examples: |
---|
| 1732 | scan.rotate_linpolphase(2.3) |
---|
| 1733 | """ |
---|
| 1734 | varlist = vars() |
---|
[936] | 1735 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 1736 | self._add_history("rotate_linpolphase", varlist) |
---|
| 1737 | print_log() |
---|
| 1738 | return |
---|
[710] | 1739 | |
---|
[513] | 1740 | |
---|
[914] | 1741 | def rotate_xyphase(self, angle): |
---|
| 1742 | """ |
---|
| 1743 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1744 | in the data. So if you call this function more than once |
---|
| 1745 | then each call rotates the phase further. |
---|
| 1746 | Parameters: |
---|
| 1747 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1748 | Examples: |
---|
| 1749 | scan.rotate_xyphase(2.3) |
---|
| 1750 | """ |
---|
| 1751 | varlist = vars() |
---|
[936] | 1752 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 1753 | self._add_history("rotate_xyphase", varlist) |
---|
| 1754 | print_log() |
---|
| 1755 | return |
---|
| 1756 | |
---|
| 1757 | def swap_linears(self): |
---|
| 1758 | """ |
---|
[1348] | 1759 | Swap the linear polarisations XX and YY, or better the first two |
---|
| 1760 | polarisations as this also works for ciculars. |
---|
[914] | 1761 | """ |
---|
| 1762 | varlist = vars() |
---|
[936] | 1763 | self._math._swap_linears(self) |
---|
[914] | 1764 | self._add_history("swap_linears", varlist) |
---|
| 1765 | print_log() |
---|
| 1766 | return |
---|
| 1767 | |
---|
| 1768 | def invert_phase(self): |
---|
| 1769 | """ |
---|
| 1770 | Invert the phase of the complex polarisation |
---|
| 1771 | """ |
---|
| 1772 | varlist = vars() |
---|
[936] | 1773 | self._math._invert_phase(self) |
---|
[914] | 1774 | self._add_history("invert_phase", varlist) |
---|
| 1775 | print_log() |
---|
| 1776 | return |
---|
| 1777 | |
---|
[876] | 1778 | def add(self, offset, insitu=None): |
---|
[513] | 1779 | """ |
---|
| 1780 | Return a scan where all spectra have the offset added |
---|
| 1781 | Parameters: |
---|
| 1782 | offset: the offset |
---|
| 1783 | insitu: if False a new scantable is returned. |
---|
| 1784 | Otherwise, the scaling is done in-situ |
---|
| 1785 | The default is taken from .asaprc (False) |
---|
| 1786 | """ |
---|
| 1787 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1788 | self._math._setinsitu(insitu) |
---|
[513] | 1789 | varlist = vars() |
---|
[876] | 1790 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 1791 | s._add_history("add", varlist) |
---|
[876] | 1792 | print_log() |
---|
| 1793 | if insitu: |
---|
| 1794 | self._assign(s) |
---|
| 1795 | else: |
---|
[513] | 1796 | return s |
---|
| 1797 | |
---|
[1308] | 1798 | def scale(self, factor, tsys=True, insitu=None): |
---|
[513] | 1799 | """ |
---|
| 1800 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 1801 | Parameters: |
---|
| 1802 | factor: the scaling factor |
---|
| 1803 | insitu: if False a new scantable is returned. |
---|
| 1804 | Otherwise, the scaling is done in-situ |
---|
| 1805 | The default is taken from .asaprc (False) |
---|
| 1806 | tsys: if True (default) then apply the operation to Tsys |
---|
| 1807 | as well as the data |
---|
| 1808 | """ |
---|
| 1809 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1810 | self._math._setinsitu(insitu) |
---|
[513] | 1811 | varlist = vars() |
---|
[876] | 1812 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
[1118] | 1813 | s._add_history("scale", varlist) |
---|
[876] | 1814 | print_log() |
---|
| 1815 | if insitu: |
---|
| 1816 | self._assign(s) |
---|
| 1817 | else: |
---|
[513] | 1818 | return s |
---|
| 1819 | |
---|
[1603] | 1820 | def set_sourcetype(self, match, matchtype="pattern", |
---|
| 1821 | sourcetype="reference"): |
---|
| 1822 | """ |
---|
| 1823 | Set the type of the source to be an source or reference scan |
---|
| 1824 | using the provided pattern: |
---|
| 1825 | Parameters: |
---|
| 1826 | match: a Unix style pattern, regular expression or selector |
---|
| 1827 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
| 1828 | 'regex' regular expression |
---|
| 1829 | sourcetype: the type of the source to use (source/reference) |
---|
| 1830 | """ |
---|
| 1831 | varlist = vars() |
---|
| 1832 | basesel = self.get_selection() |
---|
| 1833 | stype = -1 |
---|
| 1834 | if sourcetype.lower().startswith("r"): |
---|
| 1835 | stype = 1 |
---|
| 1836 | elif sourcetype.lower().startswith("s"): |
---|
| 1837 | stype = 0 |
---|
| 1838 | else: |
---|
| 1839 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)") |
---|
| 1840 | if matchtype.lower().startswith("p"): |
---|
| 1841 | matchtype = "pattern" |
---|
| 1842 | elif matchtype.lower().startswith("r"): |
---|
| 1843 | matchtype = "regex" |
---|
| 1844 | else: |
---|
| 1845 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
| 1846 | sel = selector() |
---|
| 1847 | if isinstance(match, selector): |
---|
| 1848 | sel = match |
---|
| 1849 | else: |
---|
| 1850 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match)) |
---|
| 1851 | self.set_selection(basesel+sel) |
---|
| 1852 | self._setsourcetype(stype) |
---|
| 1853 | self.set_selection(basesel) |
---|
| 1854 | s._add_history("set_sourcetype", varlist) |
---|
| 1855 | |
---|
[1631] | 1856 | def auto_quotient(self, preserve=True, mode='paired', verify=False): |
---|
[670] | 1857 | """ |
---|
| 1858 | This function allows to build quotients automatically. |
---|
[1631] | 1859 | It assumes the observation to have the same number of |
---|
[670] | 1860 | "ons" and "offs" |
---|
| 1861 | Parameters: |
---|
[710] | 1862 | preserve: you can preserve (default) the continuum or |
---|
| 1863 | remove it. The equations used are |
---|
[670] | 1864 | preserve: Output = Toff * (on/off) - Toff |
---|
[1070] | 1865 | remove: Output = Toff * (on/off) - Ton |
---|
[1348] | 1866 | mode: the on/off detection mode |
---|
| 1867 | 'paired' (default) |
---|
| 1868 | identifies 'off' scans by the |
---|
| 1869 | trailing '_R' (Mopra/Parkes) or |
---|
| 1870 | '_e'/'_w' (Tid) and matches |
---|
| 1871 | on/off pairs from the observing pattern |
---|
[1603] | 1872 | 'time' |
---|
| 1873 | finds the closest off in time |
---|
[1348] | 1874 | |
---|
[670] | 1875 | """ |
---|
[1348] | 1876 | modes = ["time", "paired"] |
---|
[670] | 1877 | if not mode in modes: |
---|
[876] | 1878 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 1879 | raise ValueError(msg) |
---|
| 1880 | varlist = vars() |
---|
[1348] | 1881 | s = None |
---|
| 1882 | if mode.lower() == "paired": |
---|
| 1883 | basesel = self.get_selection() |
---|
[1356] | 1884 | sel = selector()+basesel |
---|
| 1885 | sel.set_query("SRCTYPE==1") |
---|
| 1886 | self.set_selection(sel) |
---|
[1348] | 1887 | offs = self.copy() |
---|
| 1888 | sel.set_query("SRCTYPE==0") |
---|
[1356] | 1889 | self.set_selection(sel) |
---|
[1348] | 1890 | ons = self.copy() |
---|
| 1891 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 1892 | self.set_selection(basesel) |
---|
| 1893 | elif mode.lower() == "time": |
---|
| 1894 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 1895 | s._add_history("auto_quotient", varlist) |
---|
[876] | 1896 | print_log() |
---|
| 1897 | return s |
---|
[710] | 1898 | |
---|
[1145] | 1899 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1141] | 1900 | """ |
---|
[1143] | 1901 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
| 1902 | Parameters: |
---|
[1145] | 1903 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1143] | 1904 | weight: How to average the off beams. Default is 'median'. |
---|
[1145] | 1905 | preserve: you can preserve (default) the continuum or |
---|
| 1906 | remove it. The equations used are |
---|
| 1907 | preserve: Output = Toff * (on/off) - Toff |
---|
| 1908 | remove: Output = Toff * (on/off) - Ton |
---|
[1217] | 1909 | """ |
---|
[1143] | 1910 | if mask is None: mask = () |
---|
[1141] | 1911 | varlist = vars() |
---|
| 1912 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 1913 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 1914 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 1915 | from asapmath import quotient |
---|
[1145] | 1916 | q = quotient(on, off, preserve) |
---|
[1143] | 1917 | q._add_history("mx_quotient", varlist) |
---|
[1145] | 1918 | print_log() |
---|
[1217] | 1919 | return q |
---|
[513] | 1920 | |
---|
[718] | 1921 | def freq_switch(self, insitu=None): |
---|
| 1922 | """ |
---|
| 1923 | Apply frequency switching to the data. |
---|
| 1924 | Parameters: |
---|
| 1925 | insitu: if False a new scantable is returned. |
---|
| 1926 | Otherwise, the swictching is done in-situ |
---|
| 1927 | The default is taken from .asaprc (False) |
---|
| 1928 | Example: |
---|
| 1929 | none |
---|
| 1930 | """ |
---|
| 1931 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1932 | self._math._setinsitu(insitu) |
---|
[718] | 1933 | varlist = vars() |
---|
[876] | 1934 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 1935 | s._add_history("freq_switch", varlist) |
---|
[876] | 1936 | print_log() |
---|
| 1937 | if insitu: self._assign(s) |
---|
| 1938 | else: return s |
---|
[718] | 1939 | |
---|
[780] | 1940 | def recalc_azel(self): |
---|
| 1941 | """ |
---|
| 1942 | Recalculate the azimuth and elevation for each position. |
---|
| 1943 | Parameters: |
---|
| 1944 | none |
---|
| 1945 | Example: |
---|
| 1946 | """ |
---|
| 1947 | varlist = vars() |
---|
[876] | 1948 | self._recalcazel() |
---|
[780] | 1949 | self._add_history("recalc_azel", varlist) |
---|
| 1950 | print_log() |
---|
| 1951 | return |
---|
| 1952 | |
---|
[513] | 1953 | def __add__(self, other): |
---|
| 1954 | varlist = vars() |
---|
| 1955 | s = None |
---|
| 1956 | if isinstance(other, scantable): |
---|
[1308] | 1957 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
[513] | 1958 | elif isinstance(other, float): |
---|
[876] | 1959 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 1960 | else: |
---|
[718] | 1961 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1962 | s._add_history("operator +", varlist) |
---|
[718] | 1963 | print_log() |
---|
[513] | 1964 | return s |
---|
| 1965 | |
---|
| 1966 | def __sub__(self, other): |
---|
| 1967 | """ |
---|
| 1968 | implicit on all axes and on Tsys |
---|
| 1969 | """ |
---|
| 1970 | varlist = vars() |
---|
| 1971 | s = None |
---|
| 1972 | if isinstance(other, scantable): |
---|
[1308] | 1973 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
[513] | 1974 | elif isinstance(other, float): |
---|
[876] | 1975 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 1976 | else: |
---|
[718] | 1977 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1978 | s._add_history("operator -", varlist) |
---|
[718] | 1979 | print_log() |
---|
[513] | 1980 | return s |
---|
[710] | 1981 | |
---|
[513] | 1982 | def __mul__(self, other): |
---|
| 1983 | """ |
---|
| 1984 | implicit on all axes and on Tsys |
---|
| 1985 | """ |
---|
| 1986 | varlist = vars() |
---|
| 1987 | s = None |
---|
| 1988 | if isinstance(other, scantable): |
---|
[1308] | 1989 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
[513] | 1990 | elif isinstance(other, float): |
---|
[876] | 1991 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 1992 | else: |
---|
[718] | 1993 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1994 | s._add_history("operator *", varlist) |
---|
[718] | 1995 | print_log() |
---|
[513] | 1996 | return s |
---|
| 1997 | |
---|
[710] | 1998 | |
---|
[513] | 1999 | def __div__(self, other): |
---|
| 2000 | """ |
---|
| 2001 | implicit on all axes and on Tsys |
---|
| 2002 | """ |
---|
| 2003 | varlist = vars() |
---|
| 2004 | s = None |
---|
| 2005 | if isinstance(other, scantable): |
---|
[1308] | 2006 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
[513] | 2007 | elif isinstance(other, float): |
---|
| 2008 | if other == 0.0: |
---|
[718] | 2009 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 2010 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 2011 | else: |
---|
[718] | 2012 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2013 | s._add_history("operator /", varlist) |
---|
[718] | 2014 | print_log() |
---|
[513] | 2015 | return s |
---|
| 2016 | |
---|
[530] | 2017 | def get_fit(self, row=0): |
---|
| 2018 | """ |
---|
| 2019 | Print or return the stored fits for a row in the scantable |
---|
| 2020 | Parameters: |
---|
| 2021 | row: the row which the fit has been applied to. |
---|
| 2022 | """ |
---|
| 2023 | if row > self.nrow(): |
---|
| 2024 | return |
---|
[976] | 2025 | from asap.asapfit import asapfit |
---|
[530] | 2026 | fit = asapfit(self._getfit(row)) |
---|
[718] | 2027 | if rcParams['verbose']: |
---|
[1612] | 2028 | #print fit |
---|
[1614] | 2029 | asaplog.push( '%s' %(fit) ) |
---|
| 2030 | print_log() |
---|
[530] | 2031 | return |
---|
| 2032 | else: |
---|
| 2033 | return fit.as_dict() |
---|
| 2034 | |
---|
[1603] | 2035 | def flag_nans(self): |
---|
| 2036 | """ |
---|
| 2037 | Utility function to flag NaN values in the scantable. |
---|
| 2038 | """ |
---|
| 2039 | import numpy |
---|
| 2040 | basesel = self.get_selection() |
---|
| 2041 | for i in range(self.nrow()): |
---|
| 2042 | sel = selector()+basesel |
---|
| 2043 | sel.set_scans(self.getscan(i)) |
---|
| 2044 | sel.set_beams(self.getbeam(i)) |
---|
| 2045 | sel.set_ifs(self.getif(i)) |
---|
| 2046 | sel.set_polarisations(self.getpol(i)) |
---|
| 2047 | self.set_selection(sel) |
---|
| 2048 | nans = numpy.isnan(self._getspectrum(0)) |
---|
| 2049 | if numpy.any(nans): |
---|
| 2050 | bnans = [ bool(v) for v in nans] |
---|
| 2051 | self.flag(bnans) |
---|
| 2052 | self.set_selection(basesel) |
---|
| 2053 | |
---|
| 2054 | |
---|
[484] | 2055 | def _add_history(self, funcname, parameters): |
---|
[1603] | 2056 | if not rcParams['scantable.history']: |
---|
| 2057 | return |
---|
[484] | 2058 | # create date |
---|
| 2059 | sep = "##" |
---|
| 2060 | from datetime import datetime |
---|
| 2061 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 2062 | hist = dstr+sep |
---|
| 2063 | hist += funcname+sep#cdate+sep |
---|
| 2064 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 2065 | for k, v in parameters.iteritems(): |
---|
[484] | 2066 | if type(v) is dict: |
---|
[1118] | 2067 | for k2, v2 in v.iteritems(): |
---|
[484] | 2068 | hist += k2 |
---|
| 2069 | hist += "=" |
---|
[1118] | 2070 | if isinstance(v2, scantable): |
---|
[484] | 2071 | hist += 'scantable' |
---|
| 2072 | elif k2 == 'mask': |
---|
[1118] | 2073 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 2074 | hist += str(self._zip_mask(v2)) |
---|
| 2075 | else: |
---|
| 2076 | hist += str(v2) |
---|
[484] | 2077 | else: |
---|
[513] | 2078 | hist += str(v2) |
---|
[484] | 2079 | else: |
---|
| 2080 | hist += k |
---|
| 2081 | hist += "=" |
---|
[1118] | 2082 | if isinstance(v, scantable): |
---|
[484] | 2083 | hist += 'scantable' |
---|
| 2084 | elif k == 'mask': |
---|
[1118] | 2085 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 2086 | hist += str(self._zip_mask(v)) |
---|
| 2087 | else: |
---|
| 2088 | hist += str(v) |
---|
[484] | 2089 | else: |
---|
| 2090 | hist += str(v) |
---|
| 2091 | hist += sep |
---|
| 2092 | hist = hist[:-2] # remove trailing '##' |
---|
| 2093 | self._addhistory(hist) |
---|
| 2094 | |
---|
[710] | 2095 | |
---|
[484] | 2096 | def _zip_mask(self, mask): |
---|
| 2097 | mask = list(mask) |
---|
| 2098 | i = 0 |
---|
| 2099 | segments = [] |
---|
| 2100 | while mask[i:].count(1): |
---|
| 2101 | i += mask[i:].index(1) |
---|
| 2102 | if mask[i:].count(0): |
---|
| 2103 | j = i + mask[i:].index(0) |
---|
| 2104 | else: |
---|
[710] | 2105 | j = len(mask) |
---|
[1118] | 2106 | segments.append([i, j]) |
---|
[710] | 2107 | i = j |
---|
[484] | 2108 | return segments |
---|
[714] | 2109 | |
---|
[626] | 2110 | def _get_ordinate_label(self): |
---|
| 2111 | fu = "("+self.get_fluxunit()+")" |
---|
| 2112 | import re |
---|
| 2113 | lbl = "Intensity" |
---|
[1118] | 2114 | if re.match(".K.", fu): |
---|
[626] | 2115 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 2116 | elif re.match(".Jy.", fu): |
---|
[626] | 2117 | lbl = "Flux density "+ fu |
---|
| 2118 | return lbl |
---|
[710] | 2119 | |
---|
[876] | 2120 | def _check_ifs(self): |
---|
| 2121 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 2122 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 2123 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 2124 | |
---|
[1496] | 2125 | def _fill(self, names, unit, average, getpt): |
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[976] | 2126 | import os |
---|
| 2127 | from asap._asap import stfiller |
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| 2128 | first = True |
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| 2129 | fullnames = [] |
---|
| 2130 | for name in names: |
---|
| 2131 | name = os.path.expandvars(name) |
---|
| 2132 | name = os.path.expanduser(name) |
---|
| 2133 | if not os.path.exists(name): |
---|
| 2134 | msg = "File '%s' does not exists" % (name) |
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| 2135 | if rcParams['verbose']: |
---|
| 2136 | asaplog.push(msg) |
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[1612] | 2137 | #print asaplog.pop().strip() |
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[1614] | 2138 | print_log( 'ERROR' ) |
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[976] | 2139 | return |
---|
| 2140 | raise IOError(msg) |
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| 2141 | fullnames.append(name) |
---|
| 2142 | if average: |
---|
| 2143 | asaplog.push('Auto averaging integrations') |
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[1079] | 2144 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
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[976] | 2145 | for name in fullnames: |
---|
[1073] | 2146 | tbl = Scantable(stype) |
---|
| 2147 | r = stfiller(tbl) |
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[1603] | 2148 | rx = rcParams['scantable.reference'] |
---|
| 2149 | r._setreferenceexpr(rx) |
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[976] | 2150 | msg = "Importing %s..." % (name) |
---|
[1118] | 2151 | asaplog.push(msg, False) |
---|
[976] | 2152 | print_log() |
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[1496] | 2153 | r._open(name, -1, -1, getpt) |
---|
[976] | 2154 | r._read() |
---|
| 2155 | if average: |
---|
[1118] | 2156 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 2157 | if not first: |
---|
| 2158 | tbl = self._math._merge([self, tbl]) |
---|
| 2159 | Scantable.__init__(self, tbl) |
---|
| 2160 | r._close() |
---|
[1118] | 2161 | del r, tbl |
---|
[976] | 2162 | first = False |
---|
| 2163 | if unit is not None: |
---|
| 2164 | self.set_fluxunit(unit) |
---|
[1446] | 2165 | #self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[976] | 2166 | |
---|
[1603] | 2167 | def __getitem__(self, key): |
---|
| 2168 | if key < 0: |
---|
| 2169 | key += self.nrow() |
---|
| 2170 | if key >= self.nrow(): |
---|
| 2171 | raise IndexError("Row index out of range.") |
---|
| 2172 | return self._getspectrum(key) |
---|
| 2173 | |
---|
| 2174 | def __setitem__(self, key, value): |
---|
| 2175 | if key < 0: |
---|
| 2176 | key += self.nrow() |
---|
| 2177 | if key >= self.nrow(): |
---|
| 2178 | raise IndexError("Row index out of range.") |
---|
| 2179 | if not hasattr(value, "__len__") or \ |
---|
| 2180 | len(value) > self.nchan(self.getif(key)): |
---|
| 2181 | raise ValueError("Spectrum length doesn't match.") |
---|
| 2182 | return self._setspectrum(value, key) |
---|
| 2183 | |
---|
| 2184 | def __len__(self): |
---|
| 2185 | return self.nrow() |
---|
| 2186 | |
---|
| 2187 | def __iter__(self): |
---|
| 2188 | for i in range(len(self)): |
---|
| 2189 | yield self[i] |
---|