[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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[1673] | 40 | getpt = True |
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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= '' |
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[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: |
---|
[1666] | 477 | asaplog.push( xx, False ) |
---|
[1614] | 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 | |
---|
[1655] | 827 | def flag_row(self, rows=[], unflag=False): |
---|
| 828 | """ |
---|
| 829 | Flag the selected data in row-based manner. |
---|
| 830 | Parameters: |
---|
| 831 | rows: list of row numbers to be flagged. Default is no row (must be explicitly specified to execute row-based flagging). |
---|
| 832 | unflag: if True, unflag the data. |
---|
| 833 | """ |
---|
| 834 | varlist = vars() |
---|
| 835 | try: |
---|
| 836 | self._flag_row(rows, unflag) |
---|
| 837 | except RuntimeError, msg: |
---|
| 838 | if rcParams['verbose']: |
---|
| 839 | print_log() |
---|
| 840 | asaplog.push(msg.message) |
---|
| 841 | print_log('ERROR') |
---|
| 842 | return |
---|
| 843 | else: raise |
---|
| 844 | self._add_history("flag_row", varlist) |
---|
| 845 | |
---|
| 846 | |
---|
[1203] | 847 | def lag_flag(self, frequency, width=0.0, unit="GHz", insitu=None): |
---|
[1192] | 848 | """ |
---|
| 849 | Flag the data in 'lag' space by providing a frequency to remove. |
---|
| 850 | Flagged data in the scantable gets set to 0.0 before the fft. |
---|
| 851 | No taper is applied. |
---|
| 852 | Parameters: |
---|
[1348] | 853 | frequency: the frequency (really a period within the bandwidth) |
---|
| 854 | to remove |
---|
| 855 | width: the width of the frequency to remove, to remove a |
---|
[1603] | 856 | range of frequencies around the centre. |
---|
[1203] | 857 | unit: the frequency unit (default "GHz") |
---|
| 858 | Notes: |
---|
[1348] | 859 | It is recommended to flag edges of the band or strong |
---|
| 860 | signals beforehand. |
---|
[1192] | 861 | """ |
---|
| 862 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 863 | self._math._setinsitu(insitu) |
---|
| 864 | varlist = vars() |
---|
[1370] | 865 | base = { "GHz": 1000000000., "MHz": 1000000., "kHz": 1000., "Hz": 1. } |
---|
[1192] | 866 | if not base.has_key(unit): |
---|
| 867 | raise ValueError("%s is not a valid unit." % unit) |
---|
| 868 | try: |
---|
[1200] | 869 | s = scantable(self._math._lag_flag(self, frequency*base[unit], |
---|
| 870 | width*base[unit])) |
---|
[1192] | 871 | except RuntimeError, msg: |
---|
| 872 | if rcParams['verbose']: |
---|
[1612] | 873 | #print msg |
---|
[1614] | 874 | print_log() |
---|
[1627] | 875 | asaplog.push( msg.message ) |
---|
[1614] | 876 | print_log( 'ERROR' ) |
---|
[1192] | 877 | return |
---|
| 878 | else: raise |
---|
| 879 | s._add_history("lag_flag", varlist) |
---|
| 880 | print_log() |
---|
| 881 | if insitu: |
---|
| 882 | self._assign(s) |
---|
| 883 | else: |
---|
| 884 | return s |
---|
[1001] | 885 | |
---|
[1192] | 886 | |
---|
[113] | 887 | def create_mask(self, *args, **kwargs): |
---|
| 888 | """ |
---|
[1118] | 889 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 890 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 891 | applied. |
---|
[102] | 892 | Parameters: |
---|
[1118] | 893 | [min, max], [min2, max2], ... |
---|
[1024] | 894 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 895 | to be masked |
---|
[189] | 896 | invert: optional argument. If specified as True, |
---|
| 897 | return an inverted mask, i.e. the regions |
---|
| 898 | specified are EXCLUDED |
---|
[513] | 899 | row: create the mask using the specified row for |
---|
| 900 | unit conversions, default is row=0 |
---|
| 901 | only necessary if frequency varies over rows. |
---|
[102] | 902 | Example: |
---|
[113] | 903 | scan.set_unit('channel') |
---|
| 904 | a) |
---|
[1118] | 905 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 906 | # masks everything outside 400 and 500 |
---|
[113] | 907 | # and 800 and 900 in the unit 'channel' |
---|
| 908 | |
---|
| 909 | b) |
---|
[1118] | 910 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 911 | # masks the regions between 400 and 500 |
---|
[113] | 912 | # and 800 and 900 in the unit 'channel' |
---|
[1024] | 913 | c) |
---|
| 914 | mask only channel 400 |
---|
[1118] | 915 | msk = scan.create_mask([400, 400]) |
---|
[102] | 916 | """ |
---|
[513] | 917 | row = 0 |
---|
| 918 | if kwargs.has_key("row"): |
---|
| 919 | row = kwargs.get("row") |
---|
| 920 | data = self._getabcissa(row) |
---|
[113] | 921 | u = self._getcoordinfo()[0] |
---|
[718] | 922 | if rcParams['verbose']: |
---|
[113] | 923 | if u == "": u = "channel" |
---|
[718] | 924 | msg = "The current mask window unit is %s" % u |
---|
[1118] | 925 | i = self._check_ifs() |
---|
| 926 | if not i: |
---|
[876] | 927 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 928 | asaplog.push(msg) |
---|
[102] | 929 | n = self.nchan() |
---|
[1295] | 930 | msk = _n_bools(n, False) |
---|
[710] | 931 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 932 | |
---|
[1118] | 933 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 934 | and args or args[0] |
---|
[710] | 935 | for window in ws: |
---|
[102] | 936 | if (len(window) != 2 or window[0] > window[1] ): |
---|
[1118] | 937 | raise TypeError("A window needs to be defined as [min, max]") |
---|
[102] | 938 | for i in range(n): |
---|
[1024] | 939 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[1295] | 940 | msk[i] = True |
---|
[113] | 941 | if kwargs.has_key('invert'): |
---|
| 942 | if kwargs.get('invert'): |
---|
[1295] | 943 | msk = mask_not(msk) |
---|
[718] | 944 | print_log() |
---|
[102] | 945 | return msk |
---|
[710] | 946 | |
---|
[1446] | 947 | def get_masklist(self, mask=None, row=0): |
---|
[256] | 948 | """ |
---|
[1446] | 949 | Compute and return a list of mask windows, [min, max]. |
---|
| 950 | Parameters: |
---|
| 951 | mask: channel mask, created with create_mask. |
---|
| 952 | row: calcutate the masklist using the specified row |
---|
| 953 | for unit conversions, default is row=0 |
---|
| 954 | only necessary if frequency varies over rows. |
---|
| 955 | Returns: |
---|
| 956 | [min, max], [min2, max2], ... |
---|
| 957 | Pairs of start/end points (inclusive)specifying |
---|
| 958 | the masked regions |
---|
| 959 | """ |
---|
| 960 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 961 | raise TypeError("The mask should be list or tuple.") |
---|
| 962 | if len(mask) < 2: |
---|
| 963 | raise TypeError("The mask elements should be > 1") |
---|
| 964 | if self.nchan() != len(mask): |
---|
| 965 | msg = "Number of channels in scantable != number of mask elements" |
---|
| 966 | raise TypeError(msg) |
---|
| 967 | data = self._getabcissa(row) |
---|
| 968 | u = self._getcoordinfo()[0] |
---|
| 969 | if rcParams['verbose']: |
---|
| 970 | if u == "": u = "channel" |
---|
| 971 | msg = "The current mask window unit is %s" % u |
---|
| 972 | i = self._check_ifs() |
---|
| 973 | if not i: |
---|
| 974 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
| 975 | asaplog.push(msg) |
---|
| 976 | masklist=[] |
---|
| 977 | ist, ien = None, None |
---|
| 978 | ist, ien=self.get_mask_indices(mask) |
---|
| 979 | if ist is not None and ien is not None: |
---|
| 980 | for i in xrange(len(ist)): |
---|
| 981 | range=[data[ist[i]],data[ien[i]]] |
---|
| 982 | range.sort() |
---|
| 983 | masklist.append([range[0],range[1]]) |
---|
| 984 | return masklist |
---|
| 985 | |
---|
| 986 | def get_mask_indices(self, mask=None): |
---|
| 987 | """ |
---|
| 988 | Compute and Return lists of mask start indices and mask end indices. |
---|
| 989 | Parameters: |
---|
| 990 | mask: channel mask, created with create_mask. |
---|
| 991 | Returns: |
---|
| 992 | List of mask start indices and that of mask end indices, |
---|
| 993 | i.e., [istart1,istart2,....], [iend1,iend2,....]. |
---|
| 994 | """ |
---|
| 995 | if not (isinstance(mask,list) or isinstance(mask, tuple)): |
---|
| 996 | raise TypeError("The mask should be list or tuple.") |
---|
| 997 | if len(mask) < 2: |
---|
| 998 | raise TypeError("The mask elements should be > 1") |
---|
| 999 | istart=[] |
---|
| 1000 | iend=[] |
---|
| 1001 | if mask[0]: istart.append(0) |
---|
| 1002 | for i in range(len(mask)-1): |
---|
| 1003 | if not mask[i] and mask[i+1]: |
---|
| 1004 | istart.append(i+1) |
---|
| 1005 | elif mask[i] and not mask[i+1]: |
---|
| 1006 | iend.append(i) |
---|
| 1007 | if mask[len(mask)-1]: iend.append(len(mask)-1) |
---|
| 1008 | if len(istart) != len(iend): |
---|
| 1009 | raise RuntimeError("Numbers of mask start != mask end.") |
---|
| 1010 | for i in range(len(istart)): |
---|
| 1011 | if istart[i] > iend[i]: |
---|
| 1012 | raise RuntimeError("Mask start index > mask end index") |
---|
| 1013 | break |
---|
| 1014 | return istart,iend |
---|
| 1015 | |
---|
| 1016 | # def get_restfreqs(self): |
---|
| 1017 | # """ |
---|
| 1018 | # Get the restfrequency(s) stored in this scantable. |
---|
| 1019 | # The return value(s) are always of unit 'Hz' |
---|
| 1020 | # Parameters: |
---|
| 1021 | # none |
---|
| 1022 | # Returns: |
---|
| 1023 | # a list of doubles |
---|
| 1024 | # """ |
---|
| 1025 | # return list(self._getrestfreqs()) |
---|
| 1026 | |
---|
| 1027 | def get_restfreqs(self, ids=None): |
---|
| 1028 | """ |
---|
[256] | 1029 | Get the restfrequency(s) stored in this scantable. |
---|
| 1030 | The return value(s) are always of unit 'Hz' |
---|
| 1031 | Parameters: |
---|
[1446] | 1032 | ids: (optional) a list of MOLECULE_ID for that restfrequency(s) to |
---|
| 1033 | be retrieved |
---|
[256] | 1034 | Returns: |
---|
[1446] | 1035 | dictionary containing ids and a list of doubles for each id |
---|
[256] | 1036 | """ |
---|
[1446] | 1037 | if ids is None: |
---|
| 1038 | rfreqs={} |
---|
| 1039 | idlist = self.getmolnos() |
---|
| 1040 | for i in idlist: |
---|
| 1041 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1042 | return rfreqs |
---|
| 1043 | else: |
---|
| 1044 | if type(ids)==list or type(ids)==tuple: |
---|
| 1045 | rfreqs={} |
---|
| 1046 | for i in ids: |
---|
| 1047 | rfreqs[i]=list(self._getrestfreqs(i)) |
---|
| 1048 | return rfreqs |
---|
| 1049 | else: |
---|
| 1050 | return list(self._getrestfreqs(ids)) |
---|
| 1051 | #return list(self._getrestfreqs(ids)) |
---|
[102] | 1052 | |
---|
[931] | 1053 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
| 1054 | """ |
---|
[1446] | 1055 | ********NEED TO BE UPDATED begin************ |
---|
[931] | 1056 | Set or replace the restfrequency specified and |
---|
| 1057 | If the 'freqs' argument holds a scalar, |
---|
| 1058 | then that rest frequency will be applied to all the selected |
---|
| 1059 | data. If the 'freqs' argument holds |
---|
| 1060 | a vector, then it MUST be of equal or smaller length than |
---|
| 1061 | the number of IFs (and the available restfrequencies will be |
---|
| 1062 | replaced by this vector). In this case, *all* data have |
---|
| 1063 | the restfrequency set per IF according |
---|
| 1064 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 1065 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 1066 | IF 1 gets restfreq 2e9. |
---|
[1446] | 1067 | ********NEED TO BE UPDATED end************ |
---|
[1603] | 1068 | You can also specify the frequencies via a linecatalog. |
---|
[1153] | 1069 | |
---|
[931] | 1070 | Parameters: |
---|
| 1071 | freqs: list of rest frequency values or string idenitfiers |
---|
| 1072 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 1073 | |
---|
[931] | 1074 | Example: |
---|
[1446] | 1075 | # set the given restfrequency for the all currently selected IFs |
---|
[931] | 1076 | scan.set_restfreqs(freqs=1.4e9) |
---|
[1446] | 1077 | # set multiple restfrequencies to all the selected data |
---|
| 1078 | scan.set_restfreqs(freqs=[1.4e9, 1.41e9, 1.42e9]) |
---|
| 1079 | # If the number of IFs in the data is >= 2 the IF0 gets the first |
---|
| 1080 | # value IF1 the second... NOTE that freqs needs to be |
---|
| 1081 | # specified in list of list (e.g. [[],[],...] ). |
---|
| 1082 | scan.set_restfreqs(freqs=[[1.4e9],[1.67e9]]) |
---|
[931] | 1083 | #set the given restfrequency for the whole table (by name) |
---|
| 1084 | scan.set_restfreqs(freqs="OH1667") |
---|
[391] | 1085 | |
---|
[931] | 1086 | Note: |
---|
| 1087 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 1088 | source and IF basis, use scantable.set_selection() before using |
---|
| 1089 | this function. |
---|
| 1090 | # provide your scantable is call scan |
---|
| 1091 | selection = selector() |
---|
| 1092 | selection.set_name("ORION*") |
---|
| 1093 | selection.set_ifs([1]) |
---|
| 1094 | scan.set_selection(selection) |
---|
| 1095 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 1096 | |
---|
| 1097 | """ |
---|
| 1098 | varlist = vars() |
---|
[1157] | 1099 | from asap import linecatalog |
---|
| 1100 | # simple value |
---|
[1118] | 1101 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1446] | 1102 | # TT mod |
---|
| 1103 | #self._setrestfreqs(freqs, "",unit) |
---|
| 1104 | self._setrestfreqs([freqs], [""],unit) |
---|
[1157] | 1105 | # list of values |
---|
[1118] | 1106 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 1107 | # list values are scalars |
---|
[1118] | 1108 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[1446] | 1109 | self._setrestfreqs(freqs, [""],unit) |
---|
[1157] | 1110 | # list values are tuples, (value, name) |
---|
| 1111 | elif isinstance(freqs[-1], dict): |
---|
[1446] | 1112 | #sel = selector() |
---|
| 1113 | #savesel = self._getselection() |
---|
| 1114 | #iflist = self.getifnos() |
---|
| 1115 | #for i in xrange(len(freqs)): |
---|
| 1116 | # sel.set_ifs(iflist[i]) |
---|
| 1117 | # self._setselection(sel) |
---|
| 1118 | # self._setrestfreqs(freqs[i], "",unit) |
---|
| 1119 | #self._setselection(savesel) |
---|
| 1120 | self._setrestfreqs(freqs["value"], |
---|
| 1121 | freqs["name"], "MHz") |
---|
| 1122 | elif isinstance(freqs[-1], list) or isinstance(freqs[-1], tuple): |
---|
[1157] | 1123 | sel = selector() |
---|
| 1124 | savesel = self._getselection() |
---|
[1322] | 1125 | iflist = self.getifnos() |
---|
[1446] | 1126 | if len(freqs)>len(iflist): |
---|
| 1127 | raise ValueError("number of elements in list of list exeeds the current IF selections") |
---|
[1157] | 1128 | for i in xrange(len(freqs)): |
---|
[1322] | 1129 | sel.set_ifs(iflist[i]) |
---|
[1259] | 1130 | self._setselection(sel) |
---|
[1157] | 1131 | self._setrestfreqs(freqs[i]["value"], |
---|
| 1132 | freqs[i]["name"], "MHz") |
---|
| 1133 | self._setselection(savesel) |
---|
| 1134 | # freqs are to be taken from a linecatalog |
---|
[1153] | 1135 | elif isinstance(freqs, linecatalog): |
---|
| 1136 | sel = selector() |
---|
| 1137 | savesel = self._getselection() |
---|
| 1138 | for i in xrange(freqs.nrow()): |
---|
[1322] | 1139 | sel.set_ifs(iflist[i]) |
---|
[1153] | 1140 | self._setselection(sel) |
---|
| 1141 | self._setrestfreqs(freqs.get_frequency(i), |
---|
| 1142 | freqs.get_name(i), "MHz") |
---|
| 1143 | # ensure that we are not iterating past nIF |
---|
| 1144 | if i == self.nif()-1: break |
---|
| 1145 | self._setselection(savesel) |
---|
[931] | 1146 | else: |
---|
| 1147 | return |
---|
| 1148 | self._add_history("set_restfreqs", varlist) |
---|
| 1149 | |
---|
[1360] | 1150 | def shift_refpix(self, delta): |
---|
| 1151 | """ |
---|
| 1152 | Shift the reference pixel of the Spectra Coordinate by an |
---|
| 1153 | integer amount. |
---|
| 1154 | Parameters: |
---|
| 1155 | delta: the amount to shift by |
---|
| 1156 | Note: |
---|
| 1157 | Be careful using this with broadband data. |
---|
| 1158 | """ |
---|
| 1159 | Scantable.shift(self, delta) |
---|
[931] | 1160 | |
---|
[1259] | 1161 | def history(self, filename=None): |
---|
| 1162 | """ |
---|
| 1163 | Print the history. Optionally to a file. |
---|
[1348] | 1164 | Parameters: |
---|
| 1165 | filename: The name of the file to save the history to. |
---|
[1259] | 1166 | """ |
---|
[484] | 1167 | hist = list(self._gethistory()) |
---|
[794] | 1168 | out = "-"*80 |
---|
[484] | 1169 | for h in hist: |
---|
[489] | 1170 | if h.startswith("---"): |
---|
[794] | 1171 | out += "\n"+h |
---|
[489] | 1172 | else: |
---|
| 1173 | items = h.split("##") |
---|
| 1174 | date = items[0] |
---|
| 1175 | func = items[1] |
---|
| 1176 | items = items[2:] |
---|
[794] | 1177 | out += "\n"+date+"\n" |
---|
| 1178 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 1179 | for i in items: |
---|
| 1180 | s = i.split("=") |
---|
[1118] | 1181 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[794] | 1182 | out += "\n"+"-"*80 |
---|
[1259] | 1183 | if filename is not None: |
---|
| 1184 | if filename is "": |
---|
| 1185 | filename = 'scantable_history.txt' |
---|
| 1186 | import os |
---|
| 1187 | filename = os.path.expandvars(os.path.expanduser(filename)) |
---|
| 1188 | if not os.path.isdir(filename): |
---|
| 1189 | data = open(filename, 'w') |
---|
| 1190 | data.write(out) |
---|
| 1191 | data.close() |
---|
| 1192 | else: |
---|
| 1193 | msg = "Illegal file name '%s'." % (filename) |
---|
| 1194 | if rcParams['verbose']: |
---|
[1612] | 1195 | #print msg |
---|
[1614] | 1196 | asaplog.push( msg ) |
---|
| 1197 | print_log( 'ERROR' ) |
---|
[1259] | 1198 | else: |
---|
| 1199 | raise IOError(msg) |
---|
| 1200 | if rcParams['verbose']: |
---|
| 1201 | try: |
---|
| 1202 | from IPython.genutils import page as pager |
---|
| 1203 | except ImportError: |
---|
| 1204 | from pydoc import pager |
---|
| 1205 | pager(out) |
---|
| 1206 | else: |
---|
| 1207 | return out |
---|
[484] | 1208 | return |
---|
[513] | 1209 | # |
---|
| 1210 | # Maths business |
---|
| 1211 | # |
---|
| 1212 | |
---|
[931] | 1213 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[513] | 1214 | """ |
---|
[1070] | 1215 | Return the (time) weighted average of a scan. |
---|
[513] | 1216 | Note: |
---|
[1070] | 1217 | in channels only - align if necessary |
---|
[513] | 1218 | Parameters: |
---|
| 1219 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 1220 | weighting) |
---|
[558] | 1221 | scanav: True averages each scan separately |
---|
| 1222 | False (default) averages all scans together, |
---|
[1099] | 1223 | weight: Weighting scheme. |
---|
| 1224 | 'none' (mean no weight) |
---|
| 1225 | 'var' (1/var(spec) weighted) |
---|
| 1226 | 'tsys' (1/Tsys**2 weighted) |
---|
| 1227 | 'tint' (integration time weighted) |
---|
| 1228 | 'tintsys' (Tint/Tsys**2) |
---|
| 1229 | 'median' ( median averaging) |
---|
[535] | 1230 | The default is 'tint' |
---|
[931] | 1231 | align: align the spectra in velocity before averaging. It takes |
---|
| 1232 | the time of the first spectrum as reference time. |
---|
[513] | 1233 | Example: |
---|
| 1234 | # time average the scantable without using a mask |
---|
[710] | 1235 | newscan = scan.average_time() |
---|
[513] | 1236 | """ |
---|
| 1237 | varlist = vars() |
---|
[976] | 1238 | if weight is None: weight = 'TINT' |
---|
[513] | 1239 | if mask is None: mask = () |
---|
[1099] | 1240 | if scanav: scanav = "SCAN" |
---|
| 1241 | else: scanav = "NONE" |
---|
[1118] | 1242 | scan = (self, ) |
---|
[989] | 1243 | try: |
---|
[1118] | 1244 | if align: |
---|
| 1245 | scan = (self.freq_align(insitu=False), ) |
---|
| 1246 | s = None |
---|
| 1247 | if weight.upper() == 'MEDIAN': |
---|
| 1248 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 1249 | scanav)) |
---|
| 1250 | else: |
---|
| 1251 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 1252 | scanav)) |
---|
| 1253 | except RuntimeError, msg: |
---|
[989] | 1254 | if rcParams['verbose']: |
---|
[1612] | 1255 | #print msg |
---|
[1614] | 1256 | print_log() |
---|
[1627] | 1257 | asaplog.push( msg.message ) |
---|
[1614] | 1258 | print_log( 'ERROR' ) |
---|
[989] | 1259 | return |
---|
| 1260 | else: raise |
---|
[1099] | 1261 | s._add_history("average_time", varlist) |
---|
[718] | 1262 | print_log() |
---|
[513] | 1263 | return s |
---|
[710] | 1264 | |
---|
[876] | 1265 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[513] | 1266 | """ |
---|
| 1267 | Return a scan where all spectra are converted to either |
---|
| 1268 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 1269 | By default the function tries to look the values up internally. |
---|
| 1270 | If it can't find them (or if you want to over-ride), you must |
---|
| 1271 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 1272 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 1273 | Parameters: |
---|
| 1274 | jyperk: the Jy / K conversion factor |
---|
| 1275 | eta: the aperture efficiency |
---|
| 1276 | d: the geomtric diameter (metres) |
---|
| 1277 | insitu: if False a new scantable is returned. |
---|
| 1278 | Otherwise, the scaling is done in-situ |
---|
| 1279 | The default is taken from .asaprc (False) |
---|
| 1280 | """ |
---|
| 1281 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1282 | self._math._setinsitu(insitu) |
---|
[513] | 1283 | varlist = vars() |
---|
| 1284 | if jyperk is None: jyperk = -1.0 |
---|
| 1285 | if d is None: d = -1.0 |
---|
| 1286 | if eta is None: eta = -1.0 |
---|
[876] | 1287 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 1288 | s._add_history("convert_flux", varlist) |
---|
| 1289 | print_log() |
---|
| 1290 | if insitu: self._assign(s) |
---|
| 1291 | else: return s |
---|
[513] | 1292 | |
---|
[876] | 1293 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[513] | 1294 | """ |
---|
| 1295 | Return a scan after applying a gain-elevation correction. |
---|
| 1296 | The correction can be made via either a polynomial or a |
---|
| 1297 | table-based interpolation (and extrapolation if necessary). |
---|
| 1298 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 1299 | If you specify neither, then a polynomial correction will be made |
---|
| 1300 | with built in coefficients known for certain telescopes (an error |
---|
| 1301 | will occur if the instrument is not known). |
---|
| 1302 | The data and Tsys are *divided* by the scaling factors. |
---|
| 1303 | Parameters: |
---|
| 1304 | poly: Polynomial coefficients (default None) to compute a |
---|
| 1305 | gain-elevation correction as a function of |
---|
| 1306 | elevation (in degrees). |
---|
| 1307 | filename: The name of an ascii file holding correction factors. |
---|
| 1308 | The first row of the ascii file must give the column |
---|
| 1309 | names and these MUST include columns |
---|
| 1310 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 1311 | by this) somewhere. |
---|
| 1312 | The second row must give the data type of the |
---|
| 1313 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 1314 | An example file would be |
---|
| 1315 | (actual factors are arbitrary) : |
---|
| 1316 | |
---|
| 1317 | TIME ELEVATION FACTOR |
---|
| 1318 | R R R |
---|
| 1319 | 0.1 0 0.8 |
---|
| 1320 | 0.2 20 0.85 |
---|
| 1321 | 0.3 40 0.9 |
---|
| 1322 | 0.4 60 0.85 |
---|
| 1323 | 0.5 80 0.8 |
---|
| 1324 | 0.6 90 0.75 |
---|
| 1325 | method: Interpolation method when correcting from a table. |
---|
| 1326 | Values are "nearest", "linear" (default), "cubic" |
---|
| 1327 | and "spline" |
---|
| 1328 | insitu: if False a new scantable is returned. |
---|
| 1329 | Otherwise, the scaling is done in-situ |
---|
| 1330 | The default is taken from .asaprc (False) |
---|
| 1331 | """ |
---|
| 1332 | |
---|
| 1333 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1334 | self._math._setinsitu(insitu) |
---|
[513] | 1335 | varlist = vars() |
---|
| 1336 | if poly is None: |
---|
[1118] | 1337 | poly = () |
---|
[513] | 1338 | from os.path import expandvars |
---|
| 1339 | filename = expandvars(filename) |
---|
[876] | 1340 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 1341 | s._add_history("gain_el", varlist) |
---|
| 1342 | print_log() |
---|
| 1343 | if insitu: self._assign(s) |
---|
| 1344 | else: return s |
---|
[710] | 1345 | |
---|
[931] | 1346 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[513] | 1347 | """ |
---|
| 1348 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 1349 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 1350 | set_freqframe. |
---|
| 1351 | Parameters: |
---|
| 1352 | reftime: reference time to align at. By default, the time of |
---|
| 1353 | the first row of data is used. |
---|
| 1354 | method: Interpolation method for regridding the spectra. |
---|
| 1355 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 1356 | and "spline" |
---|
| 1357 | insitu: if False a new scantable is returned. |
---|
| 1358 | Otherwise, the scaling is done in-situ |
---|
| 1359 | The default is taken from .asaprc (False) |
---|
| 1360 | """ |
---|
[931] | 1361 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 1362 | self._math._setinsitu(insitu) |
---|
[513] | 1363 | varlist = vars() |
---|
[931] | 1364 | if reftime is None: reftime = "" |
---|
| 1365 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 1366 | s._add_history("freq_align", varlist) |
---|
| 1367 | print_log() |
---|
| 1368 | if insitu: self._assign(s) |
---|
| 1369 | else: return s |
---|
[513] | 1370 | |
---|
[876] | 1371 | def opacity(self, tau, insitu=None): |
---|
[513] | 1372 | """ |
---|
| 1373 | Apply an opacity correction. The data |
---|
| 1374 | and Tsys are multiplied by the correction factor. |
---|
| 1375 | Parameters: |
---|
| 1376 | tau: Opacity from which the correction factor is |
---|
| 1377 | exp(tau*ZD) |
---|
| 1378 | where ZD is the zenith-distance |
---|
| 1379 | insitu: if False a new scantable is returned. |
---|
| 1380 | Otherwise, the scaling is done in-situ |
---|
| 1381 | The default is taken from .asaprc (False) |
---|
| 1382 | """ |
---|
| 1383 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1384 | self._math._setinsitu(insitu) |
---|
[513] | 1385 | varlist = vars() |
---|
[876] | 1386 | s = scantable(self._math._opacity(self, tau)) |
---|
| 1387 | s._add_history("opacity", varlist) |
---|
| 1388 | print_log() |
---|
| 1389 | if insitu: self._assign(s) |
---|
| 1390 | else: return s |
---|
[513] | 1391 | |
---|
| 1392 | def bin(self, width=5, insitu=None): |
---|
| 1393 | """ |
---|
| 1394 | Return a scan where all spectra have been binned up. |
---|
[1348] | 1395 | Parameters: |
---|
[513] | 1396 | width: The bin width (default=5) in pixels |
---|
| 1397 | insitu: if False a new scantable is returned. |
---|
| 1398 | Otherwise, the scaling is done in-situ |
---|
| 1399 | The default is taken from .asaprc (False) |
---|
| 1400 | """ |
---|
| 1401 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1402 | self._math._setinsitu(insitu) |
---|
[513] | 1403 | varlist = vars() |
---|
[876] | 1404 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1405 | s._add_history("bin", varlist) |
---|
[876] | 1406 | print_log() |
---|
| 1407 | if insitu: self._assign(s) |
---|
| 1408 | else: return s |
---|
[513] | 1409 | |
---|
[710] | 1410 | |
---|
[513] | 1411 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 1412 | """ |
---|
[1348] | 1413 | Return a scan where all spectra have been binned up. |
---|
| 1414 | |
---|
| 1415 | Parameters: |
---|
[513] | 1416 | width: The bin width (default=5) in pixels |
---|
| 1417 | method: Interpolation method when correcting from a table. |
---|
| 1418 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1419 | and "spline" |
---|
| 1420 | insitu: if False a new scantable is returned. |
---|
| 1421 | Otherwise, the scaling is done in-situ |
---|
| 1422 | The default is taken from .asaprc (False) |
---|
| 1423 | """ |
---|
| 1424 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1425 | self._math._setinsitu(insitu) |
---|
[513] | 1426 | varlist = vars() |
---|
[876] | 1427 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1428 | s._add_history("resample", varlist) |
---|
[876] | 1429 | print_log() |
---|
| 1430 | if insitu: self._assign(s) |
---|
| 1431 | else: return s |
---|
[513] | 1432 | |
---|
| 1433 | |
---|
[946] | 1434 | def average_pol(self, mask=None, weight='none'): |
---|
| 1435 | """ |
---|
| 1436 | Average the Polarisations together. |
---|
| 1437 | Parameters: |
---|
| 1438 | mask: An optional mask defining the region, where the |
---|
| 1439 | averaging will be applied. The output will have all |
---|
| 1440 | specified points masked. |
---|
| 1441 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1442 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1443 | """ |
---|
| 1444 | varlist = vars() |
---|
| 1445 | if mask is None: |
---|
| 1446 | mask = () |
---|
[1010] | 1447 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1448 | s._add_history("average_pol", varlist) |
---|
[946] | 1449 | print_log() |
---|
[992] | 1450 | return s |
---|
[513] | 1451 | |
---|
[1145] | 1452 | def average_beam(self, mask=None, weight='none'): |
---|
| 1453 | """ |
---|
| 1454 | Average the Beams together. |
---|
| 1455 | Parameters: |
---|
| 1456 | mask: An optional mask defining the region, where the |
---|
| 1457 | averaging will be applied. The output will have all |
---|
| 1458 | specified points masked. |
---|
| 1459 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1460 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1461 | """ |
---|
| 1462 | varlist = vars() |
---|
| 1463 | if mask is None: |
---|
| 1464 | mask = () |
---|
| 1465 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1466 | s._add_history("average_beam", varlist) |
---|
| 1467 | print_log() |
---|
| 1468 | return s |
---|
| 1469 | |
---|
[992] | 1470 | def convert_pol(self, poltype=None): |
---|
| 1471 | """ |
---|
| 1472 | Convert the data to a different polarisation type. |
---|
| 1473 | Parameters: |
---|
| 1474 | poltype: The new polarisation type. Valid types are: |
---|
| 1475 | "linear", "stokes" and "circular" |
---|
| 1476 | """ |
---|
| 1477 | varlist = vars() |
---|
| 1478 | try: |
---|
| 1479 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1480 | except RuntimeError, msg: |
---|
[992] | 1481 | if rcParams['verbose']: |
---|
[1612] | 1482 | #print msg |
---|
[1614] | 1483 | print_log() |
---|
[1627] | 1484 | asaplog.push( msg.message ) |
---|
[1614] | 1485 | print_log( 'ERROR' ) |
---|
[1118] | 1486 | return |
---|
[992] | 1487 | else: |
---|
| 1488 | raise |
---|
[1118] | 1489 | s._add_history("convert_pol", varlist) |
---|
[992] | 1490 | print_log() |
---|
| 1491 | return s |
---|
| 1492 | |
---|
[1653] | 1493 | #def smooth(self, kernel="hanning", width=5.0, insitu=None): |
---|
| 1494 | def smooth(self, kernel="hanning", width=5.0, plot=False, insitu=None): |
---|
[513] | 1495 | """ |
---|
| 1496 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 1497 | Parameters: |
---|
| 1498 | kernel: The type of smoothing kernel. Select from |
---|
[1373] | 1499 | 'hanning' (default), 'gaussian', 'boxcar' and |
---|
| 1500 | 'rmedian' |
---|
[513] | 1501 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1502 | ignored otherwise it defauls to 5 pixels. |
---|
| 1503 | For 'gaussian' it is the Full Width Half |
---|
| 1504 | Maximum. For 'boxcar' it is the full width. |
---|
[1373] | 1505 | For 'rmedian' it is the half width. |
---|
[1653] | 1506 | plot: plot the original and the smoothed spectra. |
---|
| 1507 | In this each indivual fit has to be approved, by |
---|
| 1508 | typing 'y' or 'n' |
---|
[513] | 1509 | insitu: if False a new scantable is returned. |
---|
| 1510 | Otherwise, the scaling is done in-situ |
---|
| 1511 | The default is taken from .asaprc (False) |
---|
| 1512 | Example: |
---|
| 1513 | none |
---|
| 1514 | """ |
---|
| 1515 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1516 | self._math._setinsitu(insitu) |
---|
[513] | 1517 | varlist = vars() |
---|
[1653] | 1518 | |
---|
| 1519 | if plot: orgscan = self.copy() |
---|
| 1520 | |
---|
[1118] | 1521 | s = scantable(self._math._smooth(self, kernel.lower(), width)) |
---|
[876] | 1522 | s._add_history("smooth", varlist) |
---|
[1653] | 1523 | |
---|
| 1524 | if plot: |
---|
| 1525 | if rcParams['plotter.gui']: |
---|
| 1526 | from asap.asaplotgui import asaplotgui as asaplot |
---|
| 1527 | else: |
---|
| 1528 | from asap.asaplot import asaplot |
---|
| 1529 | self._p=asaplot() |
---|
| 1530 | self._p.set_panels() |
---|
| 1531 | ylab=s._get_ordinate_label() |
---|
| 1532 | #self._p.palette(0,["#777777","red"]) |
---|
| 1533 | for r in xrange(s.nrow()): |
---|
| 1534 | xsm=s._getabcissa(r) |
---|
| 1535 | ysm=s._getspectrum(r) |
---|
| 1536 | xorg=orgscan._getabcissa(r) |
---|
| 1537 | yorg=orgscan._getspectrum(r) |
---|
| 1538 | self._p.clear() |
---|
| 1539 | self._p.hold() |
---|
| 1540 | self._p.set_axes('ylabel',ylab) |
---|
| 1541 | self._p.set_axes('xlabel',s._getabcissalabel(r)) |
---|
| 1542 | self._p.set_axes('title',s._getsourcename(r)) |
---|
| 1543 | self._p.set_line(label='Original',color="#777777") |
---|
| 1544 | self._p.plot(xorg,yorg) |
---|
| 1545 | self._p.set_line(label='Smoothed',color="red") |
---|
| 1546 | self._p.plot(xsm,ysm) |
---|
| 1547 | ### Ugly part for legend |
---|
| 1548 | for i in [0,1]: |
---|
| 1549 | self._p.subplots[0]['lines'].append([self._p.subplots[0]['axes'].lines[i]]) |
---|
| 1550 | self._p.release() |
---|
| 1551 | ### Ugly part for legend |
---|
| 1552 | self._p.subplots[0]['lines']=[] |
---|
| 1553 | res = raw_input("Accept smoothing ([y]/n): ") |
---|
| 1554 | if res.upper() == 'N': |
---|
| 1555 | s._setspectrum(yorg, r) |
---|
| 1556 | self._p.unmap() |
---|
| 1557 | self._p = None |
---|
| 1558 | del orgscan |
---|
| 1559 | |
---|
[876] | 1560 | print_log() |
---|
| 1561 | if insitu: self._assign(s) |
---|
| 1562 | else: return s |
---|
[513] | 1563 | |
---|
[876] | 1564 | |
---|
[1389] | 1565 | def poly_baseline(self, mask=None, order=0, plot=False, uselin=False, insitu=None): |
---|
[513] | 1566 | """ |
---|
| 1567 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1568 | Parameters: |
---|
[794] | 1569 | mask: an optional mask |
---|
| 1570 | order: the order of the polynomial (default is 0) |
---|
[1061] | 1571 | plot: plot the fit and the residual. In this each |
---|
| 1572 | indivual fit has to be approved, by typing 'y' |
---|
| 1573 | or 'n' |
---|
[1389] | 1574 | uselin: use linear polynomial fit |
---|
[794] | 1575 | insitu: if False a new scantable is returned. |
---|
| 1576 | Otherwise, the scaling is done in-situ |
---|
| 1577 | The default is taken from .asaprc (False) |
---|
[513] | 1578 | Example: |
---|
| 1579 | # return a scan baselined by a third order polynomial, |
---|
| 1580 | # not using a mask |
---|
| 1581 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1582 | """ |
---|
[513] | 1583 | if insitu is None: insitu = rcParams['insitu'] |
---|
[1649] | 1584 | if not insitu: |
---|
| 1585 | workscan = self.copy() |
---|
| 1586 | else: |
---|
| 1587 | workscan = self |
---|
[513] | 1588 | varlist = vars() |
---|
| 1589 | if mask is None: |
---|
[1295] | 1590 | mask = [True for i in xrange(self.nchan(-1))] |
---|
[1637] | 1591 | |
---|
[513] | 1592 | from asap.asapfitter import fitter |
---|
[1217] | 1593 | try: |
---|
| 1594 | f = fitter() |
---|
[1389] | 1595 | if uselin: |
---|
| 1596 | f.set_function(lpoly=order) |
---|
| 1597 | else: |
---|
| 1598 | f.set_function(poly=order) |
---|
[1637] | 1599 | |
---|
[1655] | 1600 | rows = range(workscan.nrow()) |
---|
[1637] | 1601 | if len(rows) > 0: |
---|
| 1602 | self.blpars = [] |
---|
| 1603 | |
---|
| 1604 | for r in rows: |
---|
| 1605 | # take into account flagtra info (CAS-1434) |
---|
[1655] | 1606 | flagtra = workscan._getmask(r) |
---|
[1637] | 1607 | actualmask = mask[:] |
---|
| 1608 | if len(actualmask) == 0: |
---|
| 1609 | actualmask = list(flagtra[:]) |
---|
| 1610 | else: |
---|
| 1611 | if len(actualmask) != len(flagtra): |
---|
| 1612 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 1613 | else: |
---|
| 1614 | for i in range(0, len(actualmask)): |
---|
| 1615 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
[1655] | 1616 | f.set_scan(workscan, actualmask) |
---|
| 1617 | f.x = workscan._getabcissa(r) |
---|
| 1618 | f.y = workscan._getspectrum(r) |
---|
[1637] | 1619 | f.data = None |
---|
| 1620 | f.fit() |
---|
[1653] | 1621 | if plot: |
---|
| 1622 | f.plot(residual=True) |
---|
| 1623 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1624 | if x.upper() == 'N': |
---|
| 1625 | self.blpars.append(None) |
---|
| 1626 | continue |
---|
[1649] | 1627 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1655] | 1628 | self.blpars.append(f.get_parameters()) |
---|
| 1629 | |
---|
[1653] | 1630 | if plot: |
---|
| 1631 | f._p.unmap() |
---|
| 1632 | f._p = None |
---|
[1649] | 1633 | workscan._add_history("poly_baseline", varlist) |
---|
[1217] | 1634 | print_log() |
---|
[1649] | 1635 | if insitu: self._assign(workscan) |
---|
| 1636 | else: return workscan |
---|
[1217] | 1637 | except RuntimeError: |
---|
| 1638 | msg = "The fit failed, possibly because it didn't converge." |
---|
| 1639 | if rcParams['verbose']: |
---|
[1612] | 1640 | #print msg |
---|
[1614] | 1641 | print_log() |
---|
[1627] | 1642 | asaplog.push( msg.message ) |
---|
[1614] | 1643 | print_log( 'ERROR' ) |
---|
[1217] | 1644 | return |
---|
| 1645 | else: |
---|
| 1646 | raise RuntimeError(msg) |
---|
[513] | 1647 | |
---|
[1217] | 1648 | |
---|
[1118] | 1649 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
[1280] | 1650 | threshold=3, chan_avg_limit=1, plot=False, |
---|
| 1651 | insitu=None): |
---|
[880] | 1652 | """ |
---|
| 1653 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1654 | Spectral lines are detected first using linefinder and masked out |
---|
| 1655 | to avoid them affecting the baseline solution. |
---|
| 1656 | |
---|
| 1657 | Parameters: |
---|
| 1658 | mask: an optional mask retreived from scantable |
---|
| 1659 | edge: an optional number of channel to drop at |
---|
| 1660 | the edge of spectrum. If only one value is |
---|
| 1661 | specified, the same number will be dropped from |
---|
| 1662 | both sides of the spectrum. Default is to keep |
---|
[907] | 1663 | all channels. Nested tuples represent individual |
---|
[976] | 1664 | edge selection for different IFs (a number of spectral |
---|
| 1665 | channels can be different) |
---|
[880] | 1666 | order: the order of the polynomial (default is 0) |
---|
| 1667 | threshold: the threshold used by line finder. It is better to |
---|
| 1668 | keep it large as only strong lines affect the |
---|
| 1669 | baseline solution. |
---|
[1280] | 1670 | chan_avg_limit: |
---|
| 1671 | a maximum number of consequtive spectral channels to |
---|
| 1672 | average during the search of weak and broad lines. |
---|
| 1673 | The default is no averaging (and no search for weak |
---|
| 1674 | lines). If such lines can affect the fitted baseline |
---|
| 1675 | (e.g. a high order polynomial is fitted), increase this |
---|
| 1676 | parameter (usually values up to 8 are reasonable). Most |
---|
| 1677 | users of this method should find the default value |
---|
| 1678 | sufficient. |
---|
[1061] | 1679 | plot: plot the fit and the residual. In this each |
---|
| 1680 | indivual fit has to be approved, by typing 'y' |
---|
| 1681 | or 'n' |
---|
[880] | 1682 | insitu: if False a new scantable is returned. |
---|
| 1683 | Otherwise, the scaling is done in-situ |
---|
| 1684 | The default is taken from .asaprc (False) |
---|
| 1685 | |
---|
| 1686 | Example: |
---|
| 1687 | scan2=scan.auto_poly_baseline(order=7) |
---|
| 1688 | """ |
---|
| 1689 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1690 | varlist = vars() |
---|
| 1691 | from asap.asapfitter import fitter |
---|
| 1692 | from asap.asaplinefind import linefinder |
---|
| 1693 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1694 | |
---|
[976] | 1695 | # check whether edge is set up for each IF individually |
---|
[1118] | 1696 | individualedge = False; |
---|
| 1697 | if len(edge) > 1: |
---|
| 1698 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 1699 | individualedge = True; |
---|
[907] | 1700 | |
---|
[1118] | 1701 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 1702 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1703 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1704 | to make individual selection for different IFs." |
---|
[919] | 1705 | |
---|
[1118] | 1706 | curedge = (0, 0) |
---|
| 1707 | if individualedge: |
---|
| 1708 | for edgepar in edge: |
---|
| 1709 | if not _is_valid(edgepar, int): |
---|
| 1710 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 1711 | to be a pair of integers or an integer." |
---|
[907] | 1712 | else: |
---|
[1118] | 1713 | curedge = edge; |
---|
[880] | 1714 | |
---|
| 1715 | # setup fitter |
---|
| 1716 | f = fitter() |
---|
| 1717 | f.set_function(poly=order) |
---|
| 1718 | |
---|
| 1719 | # setup line finder |
---|
[1118] | 1720 | fl = linefinder() |
---|
[1268] | 1721 | fl.set_options(threshold=threshold,avg_limit=chan_avg_limit) |
---|
[880] | 1722 | |
---|
| 1723 | if not insitu: |
---|
[1118] | 1724 | workscan = self.copy() |
---|
[880] | 1725 | else: |
---|
[1118] | 1726 | workscan = self |
---|
[880] | 1727 | |
---|
[907] | 1728 | fl.set_scan(workscan) |
---|
| 1729 | |
---|
[1118] | 1730 | rows = range(workscan.nrow()) |
---|
[1446] | 1731 | # Save parameters of baseline fits & masklists as a class attribute. |
---|
| 1732 | # NOTICE: It does not reflect changes in scantable! |
---|
| 1733 | if len(rows) > 0: |
---|
| 1734 | self.blpars=[] |
---|
| 1735 | self.masklists=[] |
---|
[880] | 1736 | asaplog.push("Processing:") |
---|
| 1737 | for r in rows: |
---|
[1118] | 1738 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 1739 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 1740 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 1741 | asaplog.push(msg, False) |
---|
[907] | 1742 | |
---|
[976] | 1743 | # figure out edge parameter |
---|
[1118] | 1744 | if individualedge: |
---|
| 1745 | if len(edge) >= workscan.getif(r): |
---|
| 1746 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 1747 | "be less than the number of IFs" |
---|
| 1748 | curedge = edge[workscan.getif(r)] |
---|
[919] | 1749 | |
---|
[1637] | 1750 | # take into account flagtra info (CAS-1434) |
---|
| 1751 | flagtra = workscan._getmask(r) |
---|
| 1752 | actualmask = mask[:] |
---|
| 1753 | if len(actualmask) == 0: |
---|
| 1754 | actualmask = list(flagtra[:]) |
---|
| 1755 | else: |
---|
| 1756 | if len(actualmask) != len(flagtra): |
---|
| 1757 | raise RuntimeError, "Mask and flagtra have different length" |
---|
| 1758 | else: |
---|
| 1759 | for i in range(0, len(actualmask)): |
---|
| 1760 | actualmask[i] = actualmask[i] and flagtra[i] |
---|
| 1761 | |
---|
[976] | 1762 | # setup line finder |
---|
[1637] | 1763 | fl.find_lines(r, actualmask, curedge) |
---|
[1446] | 1764 | outmask=fl.get_mask() |
---|
[880] | 1765 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1766 | f.x = workscan._getabcissa(r) |
---|
| 1767 | f.y = workscan._getspectrum(r) |
---|
| 1768 | f.data = None |
---|
| 1769 | f.fit() |
---|
[1446] | 1770 | |
---|
| 1771 | # Show mask list |
---|
| 1772 | masklist=workscan.get_masklist(fl.get_mask(),row=r) |
---|
| 1773 | msg = "mask range: "+str(masklist) |
---|
| 1774 | asaplog.push(msg, False) |
---|
| 1775 | |
---|
[1061] | 1776 | if plot: |
---|
| 1777 | f.plot(residual=True) |
---|
| 1778 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1779 | if x.upper() == 'N': |
---|
[1446] | 1780 | self.blpars.append(None) |
---|
| 1781 | self.masklists.append(None) |
---|
[1061] | 1782 | continue |
---|
[1655] | 1783 | |
---|
[880] | 1784 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1655] | 1785 | self.blpars.append(f.get_parameters()) |
---|
[1446] | 1786 | self.masklists.append(masklist) |
---|
[1061] | 1787 | if plot: |
---|
| 1788 | f._p.unmap() |
---|
| 1789 | f._p = None |
---|
| 1790 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 1791 | if insitu: |
---|
| 1792 | self._assign(workscan) |
---|
| 1793 | else: |
---|
| 1794 | return workscan |
---|
| 1795 | |
---|
[914] | 1796 | def rotate_linpolphase(self, angle): |
---|
| 1797 | """ |
---|
| 1798 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1799 | This is always done in situ in the raw data. So if you call this |
---|
| 1800 | function more than once then each call rotates the phase further. |
---|
| 1801 | Parameters: |
---|
| 1802 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1803 | Examples: |
---|
| 1804 | scan.rotate_linpolphase(2.3) |
---|
| 1805 | """ |
---|
| 1806 | varlist = vars() |
---|
[936] | 1807 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 1808 | self._add_history("rotate_linpolphase", varlist) |
---|
| 1809 | print_log() |
---|
| 1810 | return |
---|
[710] | 1811 | |
---|
[513] | 1812 | |
---|
[914] | 1813 | def rotate_xyphase(self, angle): |
---|
| 1814 | """ |
---|
| 1815 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1816 | in the data. So if you call this function more than once |
---|
| 1817 | then each call rotates the phase further. |
---|
| 1818 | Parameters: |
---|
| 1819 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1820 | Examples: |
---|
| 1821 | scan.rotate_xyphase(2.3) |
---|
| 1822 | """ |
---|
| 1823 | varlist = vars() |
---|
[936] | 1824 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 1825 | self._add_history("rotate_xyphase", varlist) |
---|
| 1826 | print_log() |
---|
| 1827 | return |
---|
| 1828 | |
---|
| 1829 | def swap_linears(self): |
---|
| 1830 | """ |
---|
[1348] | 1831 | Swap the linear polarisations XX and YY, or better the first two |
---|
| 1832 | polarisations as this also works for ciculars. |
---|
[914] | 1833 | """ |
---|
| 1834 | varlist = vars() |
---|
[936] | 1835 | self._math._swap_linears(self) |
---|
[914] | 1836 | self._add_history("swap_linears", varlist) |
---|
| 1837 | print_log() |
---|
| 1838 | return |
---|
| 1839 | |
---|
| 1840 | def invert_phase(self): |
---|
| 1841 | """ |
---|
| 1842 | Invert the phase of the complex polarisation |
---|
| 1843 | """ |
---|
| 1844 | varlist = vars() |
---|
[936] | 1845 | self._math._invert_phase(self) |
---|
[914] | 1846 | self._add_history("invert_phase", varlist) |
---|
| 1847 | print_log() |
---|
| 1848 | return |
---|
| 1849 | |
---|
[876] | 1850 | def add(self, offset, insitu=None): |
---|
[513] | 1851 | """ |
---|
| 1852 | Return a scan where all spectra have the offset added |
---|
| 1853 | Parameters: |
---|
| 1854 | offset: the offset |
---|
| 1855 | insitu: if False a new scantable is returned. |
---|
| 1856 | Otherwise, the scaling is done in-situ |
---|
| 1857 | The default is taken from .asaprc (False) |
---|
| 1858 | """ |
---|
| 1859 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1860 | self._math._setinsitu(insitu) |
---|
[513] | 1861 | varlist = vars() |
---|
[876] | 1862 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 1863 | s._add_history("add", varlist) |
---|
[876] | 1864 | print_log() |
---|
| 1865 | if insitu: |
---|
| 1866 | self._assign(s) |
---|
| 1867 | else: |
---|
[513] | 1868 | return s |
---|
| 1869 | |
---|
[1308] | 1870 | def scale(self, factor, tsys=True, insitu=None): |
---|
[513] | 1871 | """ |
---|
| 1872 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 1873 | Parameters: |
---|
| 1874 | factor: the scaling factor |
---|
| 1875 | insitu: if False a new scantable is returned. |
---|
| 1876 | Otherwise, the scaling is done in-situ |
---|
| 1877 | The default is taken from .asaprc (False) |
---|
| 1878 | tsys: if True (default) then apply the operation to Tsys |
---|
| 1879 | as well as the data |
---|
| 1880 | """ |
---|
| 1881 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1882 | self._math._setinsitu(insitu) |
---|
[513] | 1883 | varlist = vars() |
---|
[876] | 1884 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
[1118] | 1885 | s._add_history("scale", varlist) |
---|
[876] | 1886 | print_log() |
---|
| 1887 | if insitu: |
---|
| 1888 | self._assign(s) |
---|
| 1889 | else: |
---|
[513] | 1890 | return s |
---|
| 1891 | |
---|
[1603] | 1892 | def set_sourcetype(self, match, matchtype="pattern", |
---|
| 1893 | sourcetype="reference"): |
---|
| 1894 | """ |
---|
| 1895 | Set the type of the source to be an source or reference scan |
---|
| 1896 | using the provided pattern: |
---|
| 1897 | Parameters: |
---|
| 1898 | match: a Unix style pattern, regular expression or selector |
---|
| 1899 | matchtype: 'pattern' (default) UNIX style pattern or |
---|
| 1900 | 'regex' regular expression |
---|
| 1901 | sourcetype: the type of the source to use (source/reference) |
---|
| 1902 | """ |
---|
| 1903 | varlist = vars() |
---|
| 1904 | basesel = self.get_selection() |
---|
| 1905 | stype = -1 |
---|
| 1906 | if sourcetype.lower().startswith("r"): |
---|
| 1907 | stype = 1 |
---|
| 1908 | elif sourcetype.lower().startswith("s"): |
---|
| 1909 | stype = 0 |
---|
| 1910 | else: |
---|
| 1911 | raise ValueError("Illegal sourcetype use s(ource) or r(eference)") |
---|
| 1912 | if matchtype.lower().startswith("p"): |
---|
| 1913 | matchtype = "pattern" |
---|
| 1914 | elif matchtype.lower().startswith("r"): |
---|
| 1915 | matchtype = "regex" |
---|
| 1916 | else: |
---|
| 1917 | raise ValueError("Illegal matchtype, use p(attern) or r(egex)") |
---|
| 1918 | sel = selector() |
---|
| 1919 | if isinstance(match, selector): |
---|
| 1920 | sel = match |
---|
| 1921 | else: |
---|
| 1922 | sel.set_query("SRCNAME == %s('%s')" % (matchtype, match)) |
---|
| 1923 | self.set_selection(basesel+sel) |
---|
| 1924 | self._setsourcetype(stype) |
---|
| 1925 | self.set_selection(basesel) |
---|
| 1926 | s._add_history("set_sourcetype", varlist) |
---|
| 1927 | |
---|
[1631] | 1928 | def auto_quotient(self, preserve=True, mode='paired', verify=False): |
---|
[670] | 1929 | """ |
---|
| 1930 | This function allows to build quotients automatically. |
---|
[1631] | 1931 | It assumes the observation to have the same number of |
---|
[670] | 1932 | "ons" and "offs" |
---|
| 1933 | Parameters: |
---|
[710] | 1934 | preserve: you can preserve (default) the continuum or |
---|
| 1935 | remove it. The equations used are |
---|
[670] | 1936 | preserve: Output = Toff * (on/off) - Toff |
---|
[1070] | 1937 | remove: Output = Toff * (on/off) - Ton |
---|
[1348] | 1938 | mode: the on/off detection mode |
---|
| 1939 | 'paired' (default) |
---|
| 1940 | identifies 'off' scans by the |
---|
| 1941 | trailing '_R' (Mopra/Parkes) or |
---|
| 1942 | '_e'/'_w' (Tid) and matches |
---|
| 1943 | on/off pairs from the observing pattern |
---|
[1603] | 1944 | 'time' |
---|
| 1945 | finds the closest off in time |
---|
[1348] | 1946 | |
---|
[670] | 1947 | """ |
---|
[1348] | 1948 | modes = ["time", "paired"] |
---|
[670] | 1949 | if not mode in modes: |
---|
[876] | 1950 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 1951 | raise ValueError(msg) |
---|
| 1952 | varlist = vars() |
---|
[1348] | 1953 | s = None |
---|
| 1954 | if mode.lower() == "paired": |
---|
| 1955 | basesel = self.get_selection() |
---|
[1356] | 1956 | sel = selector()+basesel |
---|
| 1957 | sel.set_query("SRCTYPE==1") |
---|
| 1958 | self.set_selection(sel) |
---|
[1348] | 1959 | offs = self.copy() |
---|
| 1960 | sel.set_query("SRCTYPE==0") |
---|
[1356] | 1961 | self.set_selection(sel) |
---|
[1348] | 1962 | ons = self.copy() |
---|
| 1963 | s = scantable(self._math._quotient(ons, offs, preserve)) |
---|
| 1964 | self.set_selection(basesel) |
---|
| 1965 | elif mode.lower() == "time": |
---|
| 1966 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 1967 | s._add_history("auto_quotient", varlist) |
---|
[876] | 1968 | print_log() |
---|
| 1969 | return s |
---|
[710] | 1970 | |
---|
[1145] | 1971 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1141] | 1972 | """ |
---|
[1143] | 1973 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
| 1974 | Parameters: |
---|
[1145] | 1975 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1143] | 1976 | weight: How to average the off beams. Default is 'median'. |
---|
[1145] | 1977 | preserve: you can preserve (default) the continuum or |
---|
| 1978 | remove it. The equations used are |
---|
| 1979 | preserve: Output = Toff * (on/off) - Toff |
---|
| 1980 | remove: Output = Toff * (on/off) - Ton |
---|
[1217] | 1981 | """ |
---|
[1143] | 1982 | if mask is None: mask = () |
---|
[1141] | 1983 | varlist = vars() |
---|
| 1984 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 1985 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 1986 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1217] | 1987 | from asapmath import quotient |
---|
[1145] | 1988 | q = quotient(on, off, preserve) |
---|
[1143] | 1989 | q._add_history("mx_quotient", varlist) |
---|
[1145] | 1990 | print_log() |
---|
[1217] | 1991 | return q |
---|
[513] | 1992 | |
---|
[718] | 1993 | def freq_switch(self, insitu=None): |
---|
| 1994 | """ |
---|
| 1995 | Apply frequency switching to the data. |
---|
| 1996 | Parameters: |
---|
| 1997 | insitu: if False a new scantable is returned. |
---|
| 1998 | Otherwise, the swictching is done in-situ |
---|
| 1999 | The default is taken from .asaprc (False) |
---|
| 2000 | Example: |
---|
| 2001 | none |
---|
| 2002 | """ |
---|
| 2003 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 2004 | self._math._setinsitu(insitu) |
---|
[718] | 2005 | varlist = vars() |
---|
[876] | 2006 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 2007 | s._add_history("freq_switch", varlist) |
---|
[876] | 2008 | print_log() |
---|
| 2009 | if insitu: self._assign(s) |
---|
| 2010 | else: return s |
---|
[718] | 2011 | |
---|
[780] | 2012 | def recalc_azel(self): |
---|
| 2013 | """ |
---|
| 2014 | Recalculate the azimuth and elevation for each position. |
---|
| 2015 | Parameters: |
---|
| 2016 | none |
---|
| 2017 | Example: |
---|
| 2018 | """ |
---|
| 2019 | varlist = vars() |
---|
[876] | 2020 | self._recalcazel() |
---|
[780] | 2021 | self._add_history("recalc_azel", varlist) |
---|
| 2022 | print_log() |
---|
| 2023 | return |
---|
| 2024 | |
---|
[513] | 2025 | def __add__(self, other): |
---|
| 2026 | varlist = vars() |
---|
| 2027 | s = None |
---|
| 2028 | if isinstance(other, scantable): |
---|
[1308] | 2029 | s = scantable(self._math._binaryop(self, other, "ADD")) |
---|
[513] | 2030 | elif isinstance(other, float): |
---|
[876] | 2031 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 2032 | else: |
---|
[718] | 2033 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2034 | s._add_history("operator +", varlist) |
---|
[718] | 2035 | print_log() |
---|
[513] | 2036 | return s |
---|
| 2037 | |
---|
| 2038 | def __sub__(self, other): |
---|
| 2039 | """ |
---|
| 2040 | implicit on all axes and on Tsys |
---|
| 2041 | """ |
---|
| 2042 | varlist = vars() |
---|
| 2043 | s = None |
---|
| 2044 | if isinstance(other, scantable): |
---|
[1308] | 2045 | s = scantable(self._math._binaryop(self, other, "SUB")) |
---|
[513] | 2046 | elif isinstance(other, float): |
---|
[876] | 2047 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 2048 | else: |
---|
[718] | 2049 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2050 | s._add_history("operator -", varlist) |
---|
[718] | 2051 | print_log() |
---|
[513] | 2052 | return s |
---|
[710] | 2053 | |
---|
[513] | 2054 | def __mul__(self, other): |
---|
| 2055 | """ |
---|
| 2056 | implicit on all axes and on Tsys |
---|
| 2057 | """ |
---|
| 2058 | varlist = vars() |
---|
| 2059 | s = None |
---|
| 2060 | if isinstance(other, scantable): |
---|
[1308] | 2061 | s = scantable(self._math._binaryop(self, other, "MUL")) |
---|
[513] | 2062 | elif isinstance(other, float): |
---|
[876] | 2063 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 2064 | else: |
---|
[718] | 2065 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2066 | s._add_history("operator *", varlist) |
---|
[718] | 2067 | print_log() |
---|
[513] | 2068 | return s |
---|
| 2069 | |
---|
[710] | 2070 | |
---|
[513] | 2071 | def __div__(self, other): |
---|
| 2072 | """ |
---|
| 2073 | implicit on all axes and on Tsys |
---|
| 2074 | """ |
---|
| 2075 | varlist = vars() |
---|
| 2076 | s = None |
---|
| 2077 | if isinstance(other, scantable): |
---|
[1308] | 2078 | s = scantable(self._math._binaryop(self, other, "DIV")) |
---|
[513] | 2079 | elif isinstance(other, float): |
---|
| 2080 | if other == 0.0: |
---|
[718] | 2081 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 2082 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 2083 | else: |
---|
[718] | 2084 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 2085 | s._add_history("operator /", varlist) |
---|
[718] | 2086 | print_log() |
---|
[513] | 2087 | return s |
---|
| 2088 | |
---|
[530] | 2089 | def get_fit(self, row=0): |
---|
| 2090 | """ |
---|
| 2091 | Print or return the stored fits for a row in the scantable |
---|
| 2092 | Parameters: |
---|
| 2093 | row: the row which the fit has been applied to. |
---|
| 2094 | """ |
---|
| 2095 | if row > self.nrow(): |
---|
| 2096 | return |
---|
[976] | 2097 | from asap.asapfit import asapfit |
---|
[530] | 2098 | fit = asapfit(self._getfit(row)) |
---|
[718] | 2099 | if rcParams['verbose']: |
---|
[1612] | 2100 | #print fit |
---|
[1614] | 2101 | asaplog.push( '%s' %(fit) ) |
---|
| 2102 | print_log() |
---|
[530] | 2103 | return |
---|
| 2104 | else: |
---|
| 2105 | return fit.as_dict() |
---|
| 2106 | |
---|
[1603] | 2107 | def flag_nans(self): |
---|
| 2108 | """ |
---|
| 2109 | Utility function to flag NaN values in the scantable. |
---|
| 2110 | """ |
---|
| 2111 | import numpy |
---|
| 2112 | basesel = self.get_selection() |
---|
| 2113 | for i in range(self.nrow()): |
---|
| 2114 | sel = selector()+basesel |
---|
| 2115 | sel.set_scans(self.getscan(i)) |
---|
| 2116 | sel.set_beams(self.getbeam(i)) |
---|
| 2117 | sel.set_ifs(self.getif(i)) |
---|
| 2118 | sel.set_polarisations(self.getpol(i)) |
---|
| 2119 | self.set_selection(sel) |
---|
| 2120 | nans = numpy.isnan(self._getspectrum(0)) |
---|
| 2121 | if numpy.any(nans): |
---|
| 2122 | bnans = [ bool(v) for v in nans] |
---|
| 2123 | self.flag(bnans) |
---|
| 2124 | self.set_selection(basesel) |
---|
| 2125 | |
---|
| 2126 | |
---|
[484] | 2127 | def _add_history(self, funcname, parameters): |
---|
[1603] | 2128 | if not rcParams['scantable.history']: |
---|
| 2129 | return |
---|
[484] | 2130 | # create date |
---|
| 2131 | sep = "##" |
---|
| 2132 | from datetime import datetime |
---|
| 2133 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 2134 | hist = dstr+sep |
---|
| 2135 | hist += funcname+sep#cdate+sep |
---|
| 2136 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 2137 | for k, v in parameters.iteritems(): |
---|
[484] | 2138 | if type(v) is dict: |
---|
[1118] | 2139 | for k2, v2 in v.iteritems(): |
---|
[484] | 2140 | hist += k2 |
---|
| 2141 | hist += "=" |
---|
[1118] | 2142 | if isinstance(v2, scantable): |
---|
[484] | 2143 | hist += 'scantable' |
---|
| 2144 | elif k2 == 'mask': |
---|
[1118] | 2145 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 2146 | hist += str(self._zip_mask(v2)) |
---|
| 2147 | else: |
---|
| 2148 | hist += str(v2) |
---|
[484] | 2149 | else: |
---|
[513] | 2150 | hist += str(v2) |
---|
[484] | 2151 | else: |
---|
| 2152 | hist += k |
---|
| 2153 | hist += "=" |
---|
[1118] | 2154 | if isinstance(v, scantable): |
---|
[484] | 2155 | hist += 'scantable' |
---|
| 2156 | elif k == 'mask': |
---|
[1118] | 2157 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 2158 | hist += str(self._zip_mask(v)) |
---|
| 2159 | else: |
---|
| 2160 | hist += str(v) |
---|
[484] | 2161 | else: |
---|
| 2162 | hist += str(v) |
---|
| 2163 | hist += sep |
---|
| 2164 | hist = hist[:-2] # remove trailing '##' |
---|
| 2165 | self._addhistory(hist) |
---|
| 2166 | |
---|
[710] | 2167 | |
---|
[484] | 2168 | def _zip_mask(self, mask): |
---|
| 2169 | mask = list(mask) |
---|
| 2170 | i = 0 |
---|
| 2171 | segments = [] |
---|
| 2172 | while mask[i:].count(1): |
---|
| 2173 | i += mask[i:].index(1) |
---|
| 2174 | if mask[i:].count(0): |
---|
| 2175 | j = i + mask[i:].index(0) |
---|
| 2176 | else: |
---|
[710] | 2177 | j = len(mask) |
---|
[1118] | 2178 | segments.append([i, j]) |
---|
[710] | 2179 | i = j |
---|
[484] | 2180 | return segments |
---|
[714] | 2181 | |
---|
[626] | 2182 | def _get_ordinate_label(self): |
---|
| 2183 | fu = "("+self.get_fluxunit()+")" |
---|
| 2184 | import re |
---|
| 2185 | lbl = "Intensity" |
---|
[1118] | 2186 | if re.match(".K.", fu): |
---|
[626] | 2187 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 2188 | elif re.match(".Jy.", fu): |
---|
[626] | 2189 | lbl = "Flux density "+ fu |
---|
| 2190 | return lbl |
---|
[710] | 2191 | |
---|
[876] | 2192 | def _check_ifs(self): |
---|
| 2193 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 2194 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 2195 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 2196 | |
---|
[1496] | 2197 | def _fill(self, names, unit, average, getpt): |
---|
[976] | 2198 | import os |
---|
| 2199 | from asap._asap import stfiller |
---|
| 2200 | first = True |
---|
| 2201 | fullnames = [] |
---|
| 2202 | for name in names: |
---|
| 2203 | name = os.path.expandvars(name) |
---|
| 2204 | name = os.path.expanduser(name) |
---|
| 2205 | if not os.path.exists(name): |
---|
| 2206 | msg = "File '%s' does not exists" % (name) |
---|
| 2207 | if rcParams['verbose']: |
---|
| 2208 | asaplog.push(msg) |
---|
[1612] | 2209 | #print asaplog.pop().strip() |
---|
[1614] | 2210 | print_log( 'ERROR' ) |
---|
[976] | 2211 | return |
---|
| 2212 | raise IOError(msg) |
---|
| 2213 | fullnames.append(name) |
---|
| 2214 | if average: |
---|
| 2215 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 2216 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 2217 | for name in fullnames: |
---|
[1073] | 2218 | tbl = Scantable(stype) |
---|
| 2219 | r = stfiller(tbl) |
---|
[1603] | 2220 | rx = rcParams['scantable.reference'] |
---|
| 2221 | r._setreferenceexpr(rx) |
---|
[976] | 2222 | msg = "Importing %s..." % (name) |
---|
[1118] | 2223 | asaplog.push(msg, False) |
---|
[976] | 2224 | print_log() |
---|
[1496] | 2225 | r._open(name, -1, -1, getpt) |
---|
[976] | 2226 | r._read() |
---|
| 2227 | if average: |
---|
[1118] | 2228 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 2229 | if not first: |
---|
| 2230 | tbl = self._math._merge([self, tbl]) |
---|
| 2231 | Scantable.__init__(self, tbl) |
---|
| 2232 | r._close() |
---|
[1118] | 2233 | del r, tbl |
---|
[976] | 2234 | first = False |
---|
| 2235 | if unit is not None: |
---|
| 2236 | self.set_fluxunit(unit) |
---|
[1446] | 2237 | #self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[976] | 2238 | |
---|
[1603] | 2239 | def __getitem__(self, key): |
---|
| 2240 | if key < 0: |
---|
| 2241 | key += self.nrow() |
---|
| 2242 | if key >= self.nrow(): |
---|
| 2243 | raise IndexError("Row index out of range.") |
---|
| 2244 | return self._getspectrum(key) |
---|
| 2245 | |
---|
| 2246 | def __setitem__(self, key, value): |
---|
| 2247 | if key < 0: |
---|
| 2248 | key += self.nrow() |
---|
| 2249 | if key >= self.nrow(): |
---|
| 2250 | raise IndexError("Row index out of range.") |
---|
| 2251 | if not hasattr(value, "__len__") or \ |
---|
| 2252 | len(value) > self.nchan(self.getif(key)): |
---|
| 2253 | raise ValueError("Spectrum length doesn't match.") |
---|
| 2254 | return self._setspectrum(value, key) |
---|
| 2255 | |
---|
| 2256 | def __len__(self): |
---|
| 2257 | return self.nrow() |
---|
| 2258 | |
---|
| 2259 | def __iter__(self): |
---|
| 2260 | for i in range(len(self)): |
---|
| 2261 | yield self[i] |
---|