[102] | 1 | from asap._asap import sdtable |
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[226] | 2 | from asap import rcParams |
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[189] | 3 | from numarray import ones,zeros |
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[102] | 4 | import sys |
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| 5 | |
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| 6 | class scantable(sdtable): |
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| 7 | """ |
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| 8 | The ASAP container for scans |
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| 9 | """ |
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[113] | 10 | |
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[340] | 11 | def __init__(self, filename, unit=None): |
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[102] | 12 | """ |
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| 13 | Create a scantable from a saved one or make a reference |
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| 14 | Parameters: |
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[181] | 15 | filename: the name of an asap table on disk |
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| 16 | or |
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| 17 | the name of a rpfits/sdfits/ms file |
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| 18 | (integrations within scans are auto averaged |
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| 19 | and the whole file is read) |
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| 20 | or |
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| 21 | [advanced] a reference to an existing |
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[102] | 22 | scantable |
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[340] | 23 | unit: brightness unit; must be consistent with K or Jy. |
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| 24 | Over-rides the default selected by the reader |
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| 25 | (input rpfits/sdfits/ms) or replaces the value |
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| 26 | in existing scantables |
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[102] | 27 | """ |
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[226] | 28 | self._vb = rcParams['verbose'] |
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[113] | 29 | self._p = None |
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[181] | 30 | from os import stat as st |
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| 31 | import stat |
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| 32 | if isinstance(filename,sdtable): |
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| 33 | sdtable.__init__(self, filename) |
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[340] | 34 | if unit is not None: |
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[346] | 35 | self.set_fluxunit(unit) |
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[181] | 36 | else: |
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[411] | 37 | import os.path |
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| 38 | if not os.path.exists(filename): |
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| 39 | print "File '%s' not found." % (filename) |
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[226] | 40 | return |
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[411] | 41 | filename = os.path.expandvars(filename) |
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| 42 | if os.path.isdir(filename): |
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[181] | 43 | # crude check if asap table |
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[411] | 44 | if os.path.exists(filename+'/table.info'): |
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[181] | 45 | sdtable.__init__(self, filename) |
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[340] | 46 | if unit is not None: |
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| 47 | self.set_fluxunit(unit) |
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[181] | 48 | else: |
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[411] | 49 | print "The given file '%s'is not a valid asap table." % (filename) |
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[226] | 50 | return |
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| 51 | else: |
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| 52 | autoav = rcParams['scantable.autoaverage'] |
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| 53 | |
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[181] | 54 | from asap._asap import sdreader |
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[340] | 55 | ifSel = -1 |
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| 56 | beamSel = -1 |
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[345] | 57 | r = sdreader(filename,ifSel,beamSel) |
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[181] | 58 | print 'Importing data...' |
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[411] | 59 | r._read([-1]) |
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| 60 | tbl = r._getdata() |
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[346] | 61 | if unit is not None: |
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| 62 | tbl.set_fluxunit(unit) |
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[226] | 63 | if autoav: |
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| 64 | from asap._asap import average |
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| 65 | tmp = tuple([tbl]) |
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| 66 | print 'Auto averaging integrations...' |
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| 67 | tbl2 = average(tmp,(),True,'none') |
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| 68 | sdtable.__init__(self,tbl2) |
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| 69 | del r,tbl |
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| 70 | else: |
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| 71 | sdtable.__init__(self,tbl) |
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[102] | 72 | |
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[445] | 73 | def save(self, name=None, format=None, stokes=True, overwrite=False): |
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[116] | 74 | """ |
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[280] | 75 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, |
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| 76 | Image FITS or MS2 format. |
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[116] | 77 | Parameters: |
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[196] | 78 | name: the name of the outputfile. For format="FITS" this |
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[280] | 79 | is the directory file name into which all the files will |
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| 80 | be written (default is 'asap_FITS') |
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[116] | 81 | format: an optional file format. Default is ASAP. |
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[280] | 82 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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[194] | 83 | 'SDFITS' (save as SDFITS file) |
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| 84 | 'FITS' (saves each row as a FITS Image) |
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[200] | 85 | 'ASCII' (saves as ascii text file) |
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[226] | 86 | 'MS2' (saves as an aips++ |
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| 87 | MeasurementSet V2) |
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[445] | 88 | stokes: Convert to Stokes parameters (only available |
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| 89 | currently with FITS and ASCII formats. |
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[411] | 90 | overwrite: If the file should be overwritten if it exists. |
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[256] | 91 | The default False is to return with warning |
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[411] | 92 | without writing the output. USE WITH CARE. |
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[116] | 93 | Example: |
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| 94 | scan.save('myscan.asap') |
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| 95 | scan.save('myscan.sdfits','SDFITS') |
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| 96 | """ |
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[411] | 97 | from os import path |
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[226] | 98 | if format is None: format = rcParams['scantable.save'] |
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[256] | 99 | suffix = '.'+format.lower() |
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| 100 | if name is None or name =="": |
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| 101 | name = 'scantable'+suffix |
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[283] | 102 | print "No filename given. Using default name %s..." % name |
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[411] | 103 | name = path.expandvars(name) |
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[256] | 104 | if path.isfile(name) or path.isdir(name): |
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| 105 | if not overwrite: |
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| 106 | print "File %s already exists." % name |
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| 107 | return |
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[116] | 108 | if format == 'ASAP': |
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| 109 | self._save(name) |
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| 110 | else: |
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| 111 | from asap._asap import sdwriter as _sw |
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[194] | 112 | w = _sw(format) |
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[445] | 113 | w.write(self, name, stokes) |
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[116] | 114 | return |
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| 115 | |
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[102] | 116 | def copy(self): |
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| 117 | """ |
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| 118 | Return a copy of this scantable. |
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| 119 | Parameters: |
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[113] | 120 | none |
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[102] | 121 | Example: |
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| 122 | copiedscan = scan.copy() |
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| 123 | """ |
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[113] | 124 | sd = scantable(sdtable._copy(self)) |
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| 125 | return sd |
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| 126 | |
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[102] | 127 | def get_scan(self, scanid=None): |
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| 128 | """ |
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| 129 | Return a specific scan (by scanno) or collection of scans (by |
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| 130 | source name) in a new scantable. |
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| 131 | Parameters: |
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| 132 | scanid: a scanno or a source name |
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| 133 | Example: |
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[113] | 134 | scan.get_scan('323p459') |
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[102] | 135 | # gets all scans containing the source '323p459' |
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| 136 | """ |
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| 137 | if scanid is None: |
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| 138 | print "Please specify a scan no or name to retrieve from the scantable" |
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| 139 | try: |
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| 140 | if type(scanid) is str: |
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[113] | 141 | s = sdtable._getsource(self,scanid) |
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[102] | 142 | return scantable(s) |
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| 143 | elif type(scanid) is int: |
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[381] | 144 | s = sdtable._getscan(self,[scanid]) |
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| 145 | return scantable(s) |
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| 146 | elif type(scanid) is list: |
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[113] | 147 | s = sdtable._getscan(self,scanid) |
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[102] | 148 | return scantable(s) |
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[381] | 149 | else: |
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| 150 | print "Illegal scanid type, use 'int' or 'list' if ints." |
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[102] | 151 | except RuntimeError: |
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| 152 | print "Couldn't find any match." |
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| 153 | |
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| 154 | def __str__(self): |
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[381] | 155 | return sdtable._summary(self,True) |
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[102] | 156 | |
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[381] | 157 | def summary(self,filename=None, verbose=None): |
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[102] | 158 | """ |
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| 159 | Print a summary of the contents of this scantable. |
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| 160 | Parameters: |
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| 161 | filename: the name of a file to write the putput to |
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| 162 | Default - no file output |
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[381] | 163 | verbose: print extra info such as the frequency table |
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| 164 | The default (False) is taken from .asaprc |
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[102] | 165 | """ |
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[381] | 166 | info = sdtable._summary(self, verbose) |
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| 167 | if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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[102] | 168 | if filename is not None: |
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[256] | 169 | if filename is "": |
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| 170 | filename = 'scantable_summary.txt' |
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[415] | 171 | from os.path import expandvars, isdir |
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[411] | 172 | filename = expandvars(filename) |
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[415] | 173 | if not isdir(filename): |
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[413] | 174 | data = open(filename, 'w') |
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| 175 | data.write(info) |
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| 176 | data.close() |
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| 177 | else: |
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| 178 | print "Illegal file name '%s'." % (filename) |
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[102] | 179 | print info |
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| 180 | |
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[256] | 181 | def set_cursor(self, thebeam=0,theif=0,thepol=0): |
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[102] | 182 | """ |
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| 183 | Set the spectrum for individual operations. |
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| 184 | Parameters: |
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| 185 | thebeam,theif,thepol: a number |
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| 186 | Example: |
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[256] | 187 | scan.set_cursor(0,0,1) |
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[135] | 188 | pol1sig = scan.stats(all=False) # returns std dev for beam=0 |
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[181] | 189 | # if=0, pol=1 |
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[102] | 190 | """ |
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| 191 | self.setbeam(thebeam) |
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| 192 | self.setpol(thepol) |
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| 193 | self.setif(theif) |
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| 194 | return |
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| 195 | |
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[256] | 196 | def get_cursor(self): |
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[113] | 197 | """ |
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| 198 | Return/print a the current 'cursor' into the Beam/IF/Pol cube. |
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| 199 | Parameters: |
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| 200 | none |
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| 201 | Returns: |
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| 202 | a list of values (currentBeam,currentIF,currentPol) |
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| 203 | Example: |
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| 204 | none |
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| 205 | """ |
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[102] | 206 | i = self.getbeam() |
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| 207 | j = self.getif() |
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| 208 | k = self.getpol() |
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[113] | 209 | if self._vb: |
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[181] | 210 | print "--------------------------------------------------" |
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[256] | 211 | print " Cursor position" |
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[181] | 212 | print "--------------------------------------------------" |
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[226] | 213 | out = 'Beam=%d IF=%d Pol=%d ' % (i,j,k) |
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[113] | 214 | print out |
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[102] | 215 | return i,j,k |
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| 216 | |
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[436] | 217 | def stats(self, stat='stddev', mask=None, allaxes=None): |
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[102] | 218 | """ |
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[135] | 219 | Determine the specified statistic of the current beam/if/pol |
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[102] | 220 | Takes a 'mask' as an optional parameter to specify which |
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| 221 | channels should be excluded. |
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| 222 | Parameters: |
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[135] | 223 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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| 224 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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| 225 | mask: an optional mask specifying where the statistic |
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[102] | 226 | should be determined. |
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[436] | 227 | allaxes: if True apply to all spectra. Otherwise |
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| 228 | apply only to the selected (beam/pol/if)spectra only. |
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| 229 | The default is taken from .asaprc (True if none) |
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[102] | 230 | Example: |
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[113] | 231 | scan.set_unit('channel') |
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[102] | 232 | msk = scan.create_mask([100,200],[500,600]) |
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[135] | 233 | scan.stats(stat='mean', mask=m) |
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[102] | 234 | """ |
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[436] | 235 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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[135] | 236 | from asap._asap import stats as _stats |
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[256] | 237 | from numarray import array,zeros,Float |
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[102] | 238 | if mask == None: |
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| 239 | mask = ones(self.nchan()) |
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[256] | 240 | axes = ['Beam','IF','Pol','Time'] |
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| 241 | |
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[436] | 242 | beamSel,IFSel,polSel = (self.getbeam(),self.getif(),self.getpol()) |
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| 243 | if allaxes: |
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[256] | 244 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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| 245 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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| 246 | arr = array(zeros(n),shape=shp,type=Float) |
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| 247 | |
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| 248 | for i in range(self.nbeam()): |
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| 249 | self.setbeam(i) |
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| 250 | for j in range(self.nif()): |
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| 251 | self.setif(j) |
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| 252 | for k in range(self.npol()): |
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| 253 | self.setpol(k) |
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| 254 | arr[i,j,k,:] = _stats(self,mask,stat,-1) |
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| 255 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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| 256 | tm = [self._gettime(val) for val in range(self.nrow())] |
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[181] | 257 | if self._vb: |
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[256] | 258 | self._print_values(retval,stat,tm) |
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[436] | 259 | self.setbeam(beamSel) |
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| 260 | self.setif(IFSel) |
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| 261 | self.setpol(polSel) |
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[256] | 262 | return retval |
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[102] | 263 | |
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| 264 | else: |
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[241] | 265 | statval = _stats(self,mask,stat,-1) |
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[181] | 266 | out = '' |
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| 267 | for l in range(self.nrow()): |
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| 268 | tm = self._gettime(l) |
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| 269 | out += 'Time[%s]:\n' % (tm) |
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[436] | 270 | if self.nbeam() > 1: out += ' Beam[%d] ' % (beamSel) |
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| 271 | if self.nif() > 1: out += ' IF[%d] ' % (IFSel) |
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| 272 | if self.npol() > 1: out += ' Pol[%d] ' % (polSel) |
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[181] | 273 | out += '= %3.3f\n' % (statval[l]) |
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| 274 | out += "--------------------------------------------------\n" |
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[226] | 275 | |
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[181] | 276 | if self._vb: |
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| 277 | print "--------------------------------------------------" |
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| 278 | print " ",stat |
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| 279 | print "--------------------------------------------------" |
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| 280 | print out |
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[256] | 281 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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| 282 | return retval |
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[102] | 283 | |
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[436] | 284 | def stddev(self,mask=None, allaxes=None): |
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[135] | 285 | """ |
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| 286 | Determine the standard deviation of the current beam/if/pol |
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| 287 | Takes a 'mask' as an optional parameter to specify which |
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| 288 | channels should be excluded. |
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| 289 | Parameters: |
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| 290 | mask: an optional mask specifying where the standard |
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| 291 | deviation should be determined. |
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[436] | 292 | allaxes: optional flag to show all or a cursor selected |
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[226] | 293 | spectrum of Beam/IF/Pol. Default is all or taken |
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| 294 | from .asaprc |
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[135] | 295 | |
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| 296 | Example: |
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| 297 | scan.set_unit('channel') |
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| 298 | msk = scan.create_mask([100,200],[500,600]) |
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| 299 | scan.stddev(mask=m) |
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| 300 | """ |
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[436] | 301 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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| 302 | return self.stats(stat='stddev',mask=mask, allaxes=allaxes); |
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[135] | 303 | |
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[436] | 304 | def get_tsys(self, allaxes=None): |
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[113] | 305 | """ |
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| 306 | Return the System temperatures. |
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| 307 | Parameters: |
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[436] | 308 | allaxes: if True apply to all spectra. Otherwise |
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| 309 | apply only to the selected (beam/pol/if)spectra only. |
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| 310 | The default is taken from .asaprc (True if none) |
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[113] | 311 | Returns: |
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| 312 | a list of Tsys values. |
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| 313 | """ |
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[436] | 314 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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[256] | 315 | from numarray import array,zeros,Float |
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| 316 | axes = ['Beam','IF','Pol','Time'] |
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| 317 | |
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[436] | 318 | if allaxes: |
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[256] | 319 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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| 320 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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| 321 | arr = array(zeros(n),shape=shp,type=Float) |
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| 322 | |
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| 323 | for i in range(self.nbeam()): |
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| 324 | self.setbeam(i) |
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| 325 | for j in range(self.nif()): |
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| 326 | self.setif(j) |
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| 327 | for k in range(self.npol()): |
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| 328 | self.setpol(k) |
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| 329 | arr[i,j,k,:] = self._gettsys() |
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| 330 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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| 331 | tm = [self._gettime(val) for val in range(self.nrow())] |
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[181] | 332 | if self._vb: |
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[256] | 333 | self._print_values(retval,'Tsys',tm) |
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| 334 | return retval |
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| 335 | |
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[102] | 336 | else: |
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[256] | 337 | i,j,k = (self.getbeam(),self.getif(),self.getpol()) |
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| 338 | statval = self._gettsys() |
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[181] | 339 | out = '' |
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| 340 | for l in range(self.nrow()): |
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| 341 | tm = self._gettime(l) |
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| 342 | out += 'Time[%s]:\n' % (tm) |
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| 343 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i) |
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| 344 | if self.nif() > 1: out += ' IF[%d] ' % (j) |
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| 345 | if self.npol() > 1: out += ' Pol[%d] ' % (k) |
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[256] | 346 | out += '= %3.3f\n' % (statval[l]) |
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| 347 | out += "--------------------------------------------------\n" |
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| 348 | |
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[181] | 349 | if self._vb: |
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| 350 | print "--------------------------------------------------" |
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[256] | 351 | print " TSys" |
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[181] | 352 | print "--------------------------------------------------" |
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| 353 | print out |
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[256] | 354 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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| 355 | return retval |
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[113] | 356 | |
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[407] | 357 | def get_time(self, row=-1): |
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[113] | 358 | """ |
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| 359 | Get a list of time stamps for the observations. |
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[181] | 360 | Return a string for each integration in the scantable. |
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[113] | 361 | Parameters: |
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[407] | 362 | row: row no of integration. Default -1 return all rows |
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[113] | 363 | Example: |
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| 364 | none |
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| 365 | """ |
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| 366 | out = [] |
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[407] | 367 | if row == -1: |
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| 368 | for i in range(self.nrow()): |
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| 369 | out.append(self._gettime(i)) |
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| 370 | return out |
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| 371 | else: |
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| 372 | if row < self.nrow(): |
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| 373 | return self._gettime(row) |
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[102] | 374 | |
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| 375 | def set_unit(self, unit='channel'): |
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| 376 | """ |
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| 377 | Set the unit for all following operations on this scantable |
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| 378 | Parameters: |
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| 379 | unit: optional unit, default is 'channel' |
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[113] | 380 | one of '*Hz','km/s','channel', '' |
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[102] | 381 | """ |
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[113] | 382 | |
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| 383 | if unit in ['','pixel', 'channel']: |
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| 384 | unit = '' |
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| 385 | inf = list(self._getcoordinfo()) |
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| 386 | inf[0] = unit |
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| 387 | self._setcoordinfo(inf) |
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| 388 | if self._p: self.plot() |
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| 389 | |
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[358] | 390 | def set_instrument (self, instr): |
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| 391 | """ |
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| 392 | Set the instrument for subsequent processing |
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| 393 | Parameters: |
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[407] | 394 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
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| 395 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
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[358] | 396 | """ |
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| 397 | self._setInstrument(instr) |
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| 398 | |
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[276] | 399 | def set_doppler(self, doppler='RADIO'): |
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| 400 | """ |
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| 401 | Set the doppler for all following operations on this scantable. |
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| 402 | Parameters: |
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| 403 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
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| 404 | """ |
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| 405 | |
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| 406 | inf = list(self._getcoordinfo()) |
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| 407 | inf[2] = doppler |
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| 408 | self._setcoordinfo(inf) |
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| 409 | if self._p: self.plot() |
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[432] | 410 | |
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[226] | 411 | def set_freqframe(self, frame=None): |
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[113] | 412 | """ |
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| 413 | Set the frame type of the Spectral Axis. |
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| 414 | Parameters: |
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| 415 | frame: an optional frame type, default 'LSRK'. |
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| 416 | Examples: |
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| 417 | scan.set_freqframe('BARY') |
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| 418 | """ |
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[226] | 419 | if not frame: frame = rcParams['scantable.freqframe'] |
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[113] | 420 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
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| 421 | 'GEO','GALACTO','LGROUP','CMB'] |
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| 422 | if frame in valid: |
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| 423 | inf = list(self._getcoordinfo()) |
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| 424 | inf[1] = frame |
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| 425 | self._setcoordinfo(inf) |
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[102] | 426 | else: |
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[113] | 427 | print "Please specify a valid freq type. Valid types are:\n",valid |
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| 428 | |
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| 429 | def get_unit(self): |
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| 430 | """ |
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| 431 | Get the default unit set in this scantable |
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| 432 | Parameters: |
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| 433 | Returns: |
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| 434 | A unit string |
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| 435 | """ |
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| 436 | inf = self._getcoordinfo() |
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| 437 | unit = inf[0] |
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| 438 | if unit == '': unit = 'channel' |
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| 439 | return unit |
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[102] | 440 | |
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[158] | 441 | def get_abcissa(self, rowno=0): |
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[102] | 442 | """ |
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[158] | 443 | Get the abcissa in the current coordinate setup for the currently |
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[113] | 444 | selected Beam/IF/Pol |
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| 445 | Parameters: |
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[226] | 446 | rowno: an optional row number in the scantable. Default is the |
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| 447 | first row, i.e. rowno=0 |
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[113] | 448 | Returns: |
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[407] | 449 | The abcissa values and it's format string (as a dictionary) |
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[113] | 450 | """ |
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[256] | 451 | abc = self._getabcissa(rowno) |
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[407] | 452 | lbl = self._getabcissalabel(rowno) |
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[158] | 453 | return abc, lbl |
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[407] | 454 | #return {'abcissa':abc,'label':lbl} |
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[113] | 455 | |
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| 456 | def create_mask(self, *args, **kwargs): |
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| 457 | """ |
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[102] | 458 | Compute and return a mask based on [min,max] windows. |
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[189] | 459 | The specified windows are to be INCLUDED, when the mask is |
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[113] | 460 | applied. |
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[102] | 461 | Parameters: |
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| 462 | [min,max],[min2,max2],... |
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| 463 | Pairs of start/end points specifying the regions |
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| 464 | to be masked |
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[189] | 465 | invert: optional argument. If specified as True, |
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| 466 | return an inverted mask, i.e. the regions |
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| 467 | specified are EXCLUDED |
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[102] | 468 | Example: |
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[113] | 469 | scan.set_unit('channel') |
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| 470 | |
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| 471 | a) |
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[102] | 472 | msk = scan.set_mask([400,500],[800,900]) |
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[189] | 473 | # masks everything outside 400 and 500 |
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[113] | 474 | # and 800 and 900 in the unit 'channel' |
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| 475 | |
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| 476 | b) |
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| 477 | msk = scan.set_mask([400,500],[800,900], invert=True) |
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[189] | 478 | # masks the regions between 400 and 500 |
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[113] | 479 | # and 800 and 900 in the unit 'channel' |
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| 480 | |
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[102] | 481 | """ |
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[113] | 482 | u = self._getcoordinfo()[0] |
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| 483 | if self._vb: |
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| 484 | if u == "": u = "channel" |
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| 485 | print "The current mask window unit is", u |
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[102] | 486 | n = self.nchan() |
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[256] | 487 | data = self._getabcissa() |
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[189] | 488 | msk = zeros(n) |
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[102] | 489 | for window in args: |
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| 490 | if (len(window) != 2 or window[0] > window[1] ): |
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| 491 | print "A window needs to be defined as [min,max]" |
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| 492 | return |
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| 493 | for i in range(n): |
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[113] | 494 | if data[i] >= window[0] and data[i] < window[1]: |
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[189] | 495 | msk[i] = 1 |
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[113] | 496 | if kwargs.has_key('invert'): |
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| 497 | if kwargs.get('invert'): |
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| 498 | from numarray import logical_not |
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| 499 | msk = logical_not(msk) |
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[102] | 500 | return msk |
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[113] | 501 | |
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[256] | 502 | def get_restfreqs(self): |
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| 503 | """ |
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| 504 | Get the restfrequency(s) stored in this scantable. |
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| 505 | The return value(s) are always of unit 'Hz' |
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| 506 | Parameters: |
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| 507 | none |
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| 508 | Returns: |
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| 509 | a list of doubles |
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| 510 | """ |
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| 511 | return list(self._getrestfreqs()) |
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[102] | 512 | |
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[402] | 513 | def lines(self): |
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[391] | 514 | """ |
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[402] | 515 | Print the list of known spectral lines |
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| 516 | """ |
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| 517 | sdtable._lines(self) |
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| 518 | |
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| 519 | def set_restfreqs(self, freqs=None, unit='Hz', lines=None, source=None, theif=None): |
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| 520 | """ |
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[393] | 521 | Select the restfrequency for the specified source and IF OR |
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| 522 | replace for all IFs. If the 'freqs' argument holds a scalar, |
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| 523 | then that rest frequency will be applied to the selected |
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| 524 | data (and added to the list of available rest frequencies). |
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| 525 | In this way, you can set a rest frequency for each |
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| 526 | source and IF combination. If the 'freqs' argument holds |
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| 527 | a vector, then it MUST be of length the number of IFs |
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| 528 | (and the available restfrequencies will be replaced by |
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| 529 | this vector). In this case, *all* data ('source' and |
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| 530 | 'theif' are ignored) have the restfrequency set per IF according |
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| 531 | to the corresponding value you give in the 'freqs' vector. |
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| 532 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and |
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| 533 | IF 1 gets restfreq 2e9. |
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[402] | 534 | |
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| 535 | You can also specify the frequencies via known line names |
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| 536 | in the argument 'lines'. Use 'freqs' or 'lines'. 'freqs' |
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| 537 | takes precedence. See the list of known names via function |
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| 538 | scantable.lines() |
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[391] | 539 | Parameters: |
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[402] | 540 | freqs: list of rest frequencies |
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[393] | 541 | unit: unit for rest frequency (default 'Hz') |
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[402] | 542 | lines: list of known spectral lines names (alternative to freqs). |
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| 543 | See possible list via scantable.lines() |
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[391] | 544 | source: Source name (blank means all) |
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| 545 | theif: IF (-1 means all) |
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| 546 | Example: |
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[393] | 547 | scan.set_restfreqs(freqs=1.4e9, source='NGC253', theif=2) |
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| 548 | scan.set_restfreqs(freqs=[1.4e9,1.67e9]) |
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[391] | 549 | """ |
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| 550 | if source is None: |
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| 551 | source = "" |
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| 552 | if theif is None: |
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| 553 | theif = -1 |
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[393] | 554 | t = type(freqs) |
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| 555 | if t is int or t is float: |
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| 556 | freqs = [freqs] |
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[402] | 557 | if freqs is None: |
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| 558 | freqs = [] |
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| 559 | t = type(lines) |
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| 560 | if t is str: |
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| 561 | lines = [lines] |
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| 562 | if lines is None: |
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| 563 | lines = [] |
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| 564 | sdtable._setrestfreqs(self, freqs, unit, lines, source, theif) |
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[391] | 565 | return |
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| 566 | |
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| 567 | |
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[102] | 568 | def flag_spectrum(self, thebeam, theif, thepol): |
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| 569 | """ |
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| 570 | This flags a selected spectrum in the scan 'for good'. |
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| 571 | USE WITH CARE - not reversible. |
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| 572 | Use masks for non-permanent exclusion of channels. |
---|
| 573 | Parameters: |
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| 574 | thebeam,theif,thepol: all have to be explicitly |
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| 575 | specified |
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| 576 | Example: |
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| 577 | scan.flag_spectrum(0,0,1) |
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| 578 | flags the spectrum for Beam=0, IF=0, Pol=1 |
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| 579 | """ |
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[407] | 580 | if (thebeam < self.nbeam() and |
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| 581 | theif < self.nif() and |
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| 582 | thepol < self.npol()): |
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| 583 | sdtable.setbeam(self, thebeam) |
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| 584 | sdtable.setif(self, theif) |
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| 585 | sdtable.setpol(self, thepol) |
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| 586 | sdtable._flag(self) |
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[102] | 587 | else: |
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| 588 | print "Please specify a valid (Beam/IF/Pol)" |
---|
| 589 | return |
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[113] | 590 | |
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[436] | 591 | def rotate_xyphase (self, angle, allaxes=None): |
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[432] | 592 | """ |
---|
| 593 | Rotate the phase of the XY correlation. This is done in situ |
---|
| 594 | in the data. So if you call this function more than once |
---|
| 595 | then each call rotates the phase further. |
---|
| 596 | Parameters: |
---|
| 597 | angle: The angle (degrees) to rotate (add) by. |
---|
[436] | 598 | allaxes: If True apply to all spectra. Otherwise |
---|
| 599 | apply only to the selected (beam/pol/if)spectra only. |
---|
| 600 | The default is taken from .asaprc (True if none) |
---|
[432] | 601 | Examples: |
---|
| 602 | scan.rotate_xyphase(2.3) |
---|
| 603 | """ |
---|
[436] | 604 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 605 | sdtable._rotate_xyphase(self, angle, allaxes) |
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[432] | 606 | |
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[113] | 607 | def plot(self, what='spectrum',col='Pol', panel=None): |
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| 608 | """ |
---|
| 609 | Plot the spectra contained in the scan. Alternatively you can also |
---|
| 610 | Plot Tsys vs Time |
---|
| 611 | Parameters: |
---|
| 612 | what: a choice of 'spectrum' (default) or 'tsys' |
---|
[135] | 613 | col: which out of Beams/IFs/Pols should be colour stacked |
---|
[113] | 614 | panel: set up multiple panels, currently not working. |
---|
| 615 | """ |
---|
[283] | 616 | print "Warning! Not fully functional. Use plotter.plot() instead" |
---|
| 617 | |
---|
[113] | 618 | validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()} |
---|
[124] | 619 | |
---|
[113] | 620 | validyax = ['spectrum','tsys'] |
---|
[189] | 621 | from asap.asaplot import ASAPlot |
---|
[113] | 622 | if not self._p: |
---|
| 623 | self._p = ASAPlot() |
---|
[189] | 624 | #print "Plotting not enabled" |
---|
| 625 | #return |
---|
| 626 | if self._p.is_dead: |
---|
| 627 | del self._p |
---|
| 628 | self._p = ASAPlot() |
---|
[113] | 629 | npan = 1 |
---|
| 630 | x = None |
---|
| 631 | if what == 'tsys': |
---|
| 632 | n = self.nrow() |
---|
| 633 | if n < 2: |
---|
| 634 | print "Only one integration. Can't plot." |
---|
| 635 | return |
---|
[124] | 636 | self._p.hold() |
---|
| 637 | self._p.clear() |
---|
[113] | 638 | if panel == 'Time': |
---|
| 639 | npan = self.nrow() |
---|
[124] | 640 | self._p.set_panels(rows=npan) |
---|
[113] | 641 | xlab,ylab,tlab = None,None,None |
---|
[226] | 642 | self._vb = False |
---|
[256] | 643 | sel = self.get_cursor() |
---|
[113] | 644 | for i in range(npan): |
---|
[226] | 645 | if npan > 1: |
---|
| 646 | self._p.subplot(i) |
---|
[113] | 647 | for j in range(validcol[col]): |
---|
| 648 | x = None |
---|
| 649 | y = None |
---|
| 650 | m = None |
---|
| 651 | tlab = self._getsourcename(i) |
---|
[124] | 652 | import re |
---|
| 653 | tlab = re.sub('_S','',tlab) |
---|
[113] | 654 | if col == 'Beam': |
---|
| 655 | self.setbeam(j) |
---|
| 656 | elif col == 'IF': |
---|
| 657 | self.setif(j) |
---|
| 658 | elif col == 'Pol': |
---|
| 659 | self.setpol(j) |
---|
| 660 | if what == 'tsys': |
---|
| 661 | x = range(self.nrow()) |
---|
| 662 | xlab = 'Time [pixel]' |
---|
| 663 | m = list(ones(len(x))) |
---|
| 664 | y = [] |
---|
| 665 | ylab = r'$T_{sys}$' |
---|
| 666 | for k in range(len(x)): |
---|
| 667 | y.append(self._gettsys(k)) |
---|
| 668 | else: |
---|
[158] | 669 | x,xlab = self.get_abcissa(i) |
---|
[256] | 670 | y = self._getspectrum(i) |
---|
[113] | 671 | ylab = r'Flux' |
---|
[256] | 672 | m = self._getmask(i) |
---|
[113] | 673 | llab = col+' '+str(j) |
---|
| 674 | self._p.set_line(label=llab) |
---|
| 675 | self._p.plot(x,y,m) |
---|
[124] | 676 | self._p.set_axes('xlabel',xlab) |
---|
| 677 | self._p.set_axes('ylabel',ylab) |
---|
| 678 | self._p.set_axes('title',tlab) |
---|
[113] | 679 | self._p.release() |
---|
[256] | 680 | self.set_cursor(sel[0],sel[1],sel[2]) |
---|
[226] | 681 | self._vb = rcParams['verbose'] |
---|
[113] | 682 | return |
---|
[256] | 683 | |
---|
| 684 | print out |
---|
| 685 | |
---|
| 686 | def _print_values(self, dat, label='', timestamps=[]): |
---|
| 687 | d = dat['data'] |
---|
| 688 | a = dat['axes'] |
---|
| 689 | shp = d.getshape() |
---|
| 690 | out = '' |
---|
| 691 | for i in range(shp[3]): |
---|
| 692 | out += '%s [%s]:\n' % (a[3],timestamps[i]) |
---|
| 693 | t = d[:,:,:,i] |
---|
| 694 | for j in range(shp[0]): |
---|
| 695 | if shp[0] > 1: out += ' %s[%d] ' % (a[0],j) |
---|
| 696 | for k in range(shp[1]): |
---|
| 697 | if shp[1] > 1: out += ' %s[%d] ' % (a[1],k) |
---|
| 698 | for l in range(shp[2]): |
---|
| 699 | if shp[2] > 1: out += ' %s[%d] ' % (a[2],l) |
---|
| 700 | out += '= %3.3f\n' % (t[j,k,l]) |
---|
| 701 | out += "--------------------------------------------------\n" |
---|
| 702 | print "--------------------------------------------------" |
---|
| 703 | print " ", label |
---|
| 704 | print "--------------------------------------------------" |
---|
| 705 | print out |
---|