[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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[484] | 11 | def __init__(self, filename, average=None, 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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[484] | 23 | average: average all integrations withinb a scan on read. |
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| 24 | The default (True) is taken from .asaprc. |
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| 25 | unit: brightness unit; must be consistent with K or Jy. |
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[340] | 26 | Over-rides the default selected by the reader |
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| 27 | (input rpfits/sdfits/ms) or replaces the value |
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| 28 | in existing scantables |
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[102] | 29 | """ |
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[484] | 30 | varlist = vars() |
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[226] | 31 | self._vb = rcParams['verbose'] |
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[113] | 32 | self._p = None |
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[484] | 33 | |
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| 34 | if average is None or type(average) is not bool: |
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| 35 | autoav = rcParams['scantable.autoaverage'] |
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| 36 | |
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[181] | 37 | if isinstance(filename,sdtable): |
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| 38 | sdtable.__init__(self, filename) |
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[340] | 39 | if unit is not None: |
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[346] | 40 | self.set_fluxunit(unit) |
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[181] | 41 | else: |
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[411] | 42 | import os.path |
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| 43 | if not os.path.exists(filename): |
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| 44 | print "File '%s' not found." % (filename) |
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[226] | 45 | return |
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[411] | 46 | filename = os.path.expandvars(filename) |
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| 47 | if os.path.isdir(filename): |
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[181] | 48 | # crude check if asap table |
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[411] | 49 | if os.path.exists(filename+'/table.info'): |
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[181] | 50 | sdtable.__init__(self, filename) |
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[340] | 51 | if unit is not None: |
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| 52 | self.set_fluxunit(unit) |
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[181] | 53 | else: |
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[411] | 54 | print "The given file '%s'is not a valid asap table." % (filename) |
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[226] | 55 | return |
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[484] | 56 | else: |
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[181] | 57 | from asap._asap import sdreader |
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[340] | 58 | ifSel = -1 |
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| 59 | beamSel = -1 |
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[345] | 60 | r = sdreader(filename,ifSel,beamSel) |
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[181] | 61 | print 'Importing data...' |
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[411] | 62 | r._read([-1]) |
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| 63 | tbl = r._getdata() |
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[346] | 64 | if unit is not None: |
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| 65 | tbl.set_fluxunit(unit) |
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[226] | 66 | if autoav: |
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| 67 | from asap._asap import average |
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| 68 | tmp = tuple([tbl]) |
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| 69 | print 'Auto averaging integrations...' |
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| 70 | tbl2 = average(tmp,(),True,'none') |
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| 71 | sdtable.__init__(self,tbl2) |
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| 72 | del r,tbl |
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| 73 | else: |
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| 74 | sdtable.__init__(self,tbl) |
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[484] | 75 | self._add_history("scantable", varlist) |
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[102] | 76 | |
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[451] | 77 | def save(self, name=None, format=None, stokes=False, overwrite=False): |
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[116] | 78 | """ |
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[280] | 79 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, |
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| 80 | Image FITS or MS2 format. |
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[116] | 81 | Parameters: |
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[196] | 82 | name: the name of the outputfile. For format="FITS" this |
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[280] | 83 | is the directory file name into which all the files will |
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| 84 | be written (default is 'asap_FITS') |
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[116] | 85 | format: an optional file format. Default is ASAP. |
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[280] | 86 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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[194] | 87 | 'SDFITS' (save as SDFITS file) |
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| 88 | 'FITS' (saves each row as a FITS Image) |
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[200] | 89 | 'ASCII' (saves as ascii text file) |
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[226] | 90 | 'MS2' (saves as an aips++ |
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| 91 | MeasurementSet V2) |
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[474] | 92 | stokes: Convert to Stokes parameters. Default is False. |
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[411] | 93 | overwrite: If the file should be overwritten if it exists. |
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[256] | 94 | The default False is to return with warning |
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[411] | 95 | without writing the output. USE WITH CARE. |
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[116] | 96 | Example: |
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| 97 | scan.save('myscan.asap') |
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| 98 | scan.save('myscan.sdfits','SDFITS') |
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| 99 | """ |
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[411] | 100 | from os import path |
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[226] | 101 | if format is None: format = rcParams['scantable.save'] |
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[256] | 102 | suffix = '.'+format.lower() |
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| 103 | if name is None or name =="": |
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| 104 | name = 'scantable'+suffix |
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[283] | 105 | print "No filename given. Using default name %s..." % name |
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[411] | 106 | name = path.expandvars(name) |
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[256] | 107 | if path.isfile(name) or path.isdir(name): |
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| 108 | if not overwrite: |
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| 109 | print "File %s already exists." % name |
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| 110 | return |
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[451] | 111 | format2 = format.upper() |
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| 112 | if format2 == 'ASAP': |
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[116] | 113 | self._save(name) |
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| 114 | else: |
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| 115 | from asap._asap import sdwriter as _sw |
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[451] | 116 | w = _sw(format2) |
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[445] | 117 | w.write(self, name, stokes) |
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[116] | 118 | return |
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| 119 | |
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[102] | 120 | def copy(self): |
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| 121 | """ |
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| 122 | Return a copy of this scantable. |
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| 123 | Parameters: |
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[113] | 124 | none |
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[102] | 125 | Example: |
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| 126 | copiedscan = scan.copy() |
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| 127 | """ |
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[113] | 128 | sd = scantable(sdtable._copy(self)) |
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| 129 | return sd |
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| 130 | |
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[102] | 131 | def get_scan(self, scanid=None): |
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| 132 | """ |
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| 133 | Return a specific scan (by scanno) or collection of scans (by |
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| 134 | source name) in a new scantable. |
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| 135 | Parameters: |
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| 136 | scanid: a scanno or a source name |
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| 137 | Example: |
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[113] | 138 | scan.get_scan('323p459') |
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[102] | 139 | # gets all scans containing the source '323p459' |
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| 140 | """ |
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| 141 | if scanid is None: |
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| 142 | print "Please specify a scan no or name to retrieve from the scantable" |
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| 143 | try: |
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| 144 | if type(scanid) is str: |
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[113] | 145 | s = sdtable._getsource(self,scanid) |
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[102] | 146 | return scantable(s) |
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| 147 | elif type(scanid) is int: |
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[381] | 148 | s = sdtable._getscan(self,[scanid]) |
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| 149 | return scantable(s) |
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| 150 | elif type(scanid) is list: |
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[113] | 151 | s = sdtable._getscan(self,scanid) |
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[102] | 152 | return scantable(s) |
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[381] | 153 | else: |
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| 154 | print "Illegal scanid type, use 'int' or 'list' if ints." |
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[102] | 155 | except RuntimeError: |
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| 156 | print "Couldn't find any match." |
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| 157 | |
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| 158 | def __str__(self): |
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[381] | 159 | return sdtable._summary(self,True) |
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[102] | 160 | |
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[381] | 161 | def summary(self,filename=None, verbose=None): |
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[102] | 162 | """ |
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| 163 | Print a summary of the contents of this scantable. |
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| 164 | Parameters: |
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| 165 | filename: the name of a file to write the putput to |
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| 166 | Default - no file output |
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[381] | 167 | verbose: print extra info such as the frequency table |
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| 168 | The default (False) is taken from .asaprc |
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[102] | 169 | """ |
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[381] | 170 | info = sdtable._summary(self, verbose) |
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| 171 | if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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[102] | 172 | if filename is not None: |
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[256] | 173 | if filename is "": |
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| 174 | filename = 'scantable_summary.txt' |
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[415] | 175 | from os.path import expandvars, isdir |
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[411] | 176 | filename = expandvars(filename) |
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[415] | 177 | if not isdir(filename): |
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[413] | 178 | data = open(filename, 'w') |
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| 179 | data.write(info) |
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| 180 | data.close() |
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| 181 | else: |
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| 182 | print "Illegal file name '%s'." % (filename) |
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[102] | 183 | print info |
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[484] | 184 | |
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[256] | 185 | def set_cursor(self, thebeam=0,theif=0,thepol=0): |
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[102] | 186 | """ |
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| 187 | Set the spectrum for individual operations. |
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| 188 | Parameters: |
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| 189 | thebeam,theif,thepol: a number |
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| 190 | Example: |
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[256] | 191 | scan.set_cursor(0,0,1) |
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[135] | 192 | pol1sig = scan.stats(all=False) # returns std dev for beam=0 |
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[181] | 193 | # if=0, pol=1 |
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[102] | 194 | """ |
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[484] | 195 | varlist = vars() |
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[102] | 196 | self.setbeam(thebeam) |
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| 197 | self.setpol(thepol) |
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| 198 | self.setif(theif) |
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[484] | 199 | self._add_history("set_cursor",varlist) |
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[102] | 200 | return |
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| 201 | |
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[256] | 202 | def get_cursor(self): |
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[113] | 203 | """ |
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| 204 | Return/print a the current 'cursor' into the Beam/IF/Pol cube. |
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| 205 | Parameters: |
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| 206 | none |
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| 207 | Returns: |
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| 208 | a list of values (currentBeam,currentIF,currentPol) |
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| 209 | Example: |
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| 210 | none |
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| 211 | """ |
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[102] | 212 | i = self.getbeam() |
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| 213 | j = self.getif() |
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| 214 | k = self.getpol() |
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[113] | 215 | if self._vb: |
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[181] | 216 | print "--------------------------------------------------" |
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[256] | 217 | print " Cursor position" |
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[181] | 218 | print "--------------------------------------------------" |
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[226] | 219 | out = 'Beam=%d IF=%d Pol=%d ' % (i,j,k) |
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[113] | 220 | print out |
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[102] | 221 | return i,j,k |
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| 222 | |
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[436] | 223 | def stats(self, stat='stddev', mask=None, allaxes=None): |
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[102] | 224 | """ |
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[135] | 225 | Determine the specified statistic of the current beam/if/pol |
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[102] | 226 | Takes a 'mask' as an optional parameter to specify which |
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| 227 | channels should be excluded. |
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| 228 | Parameters: |
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[135] | 229 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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| 230 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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| 231 | mask: an optional mask specifying where the statistic |
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[102] | 232 | should be determined. |
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[436] | 233 | allaxes: if True apply to all spectra. Otherwise |
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| 234 | apply only to the selected (beam/pol/if)spectra only. |
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| 235 | The default is taken from .asaprc (True if none) |
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[102] | 236 | Example: |
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[113] | 237 | scan.set_unit('channel') |
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[102] | 238 | msk = scan.create_mask([100,200],[500,600]) |
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[135] | 239 | scan.stats(stat='mean', mask=m) |
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[102] | 240 | """ |
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[436] | 241 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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[135] | 242 | from asap._asap import stats as _stats |
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[256] | 243 | from numarray import array,zeros,Float |
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[102] | 244 | if mask == None: |
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| 245 | mask = ones(self.nchan()) |
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[256] | 246 | axes = ['Beam','IF','Pol','Time'] |
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| 247 | |
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[436] | 248 | beamSel,IFSel,polSel = (self.getbeam(),self.getif(),self.getpol()) |
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| 249 | if allaxes: |
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[256] | 250 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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| 251 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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| 252 | arr = array(zeros(n),shape=shp,type=Float) |
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| 253 | |
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| 254 | for i in range(self.nbeam()): |
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| 255 | self.setbeam(i) |
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| 256 | for j in range(self.nif()): |
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| 257 | self.setif(j) |
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| 258 | for k in range(self.npol()): |
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| 259 | self.setpol(k) |
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| 260 | arr[i,j,k,:] = _stats(self,mask,stat,-1) |
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| 261 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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| 262 | tm = [self._gettime(val) for val in range(self.nrow())] |
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[181] | 263 | if self._vb: |
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[256] | 264 | self._print_values(retval,stat,tm) |
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[436] | 265 | self.setbeam(beamSel) |
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| 266 | self.setif(IFSel) |
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| 267 | self.setpol(polSel) |
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[256] | 268 | return retval |
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[102] | 269 | |
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| 270 | else: |
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[241] | 271 | statval = _stats(self,mask,stat,-1) |
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[181] | 272 | out = '' |
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| 273 | for l in range(self.nrow()): |
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| 274 | tm = self._gettime(l) |
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| 275 | out += 'Time[%s]:\n' % (tm) |
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[436] | 276 | if self.nbeam() > 1: out += ' Beam[%d] ' % (beamSel) |
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| 277 | if self.nif() > 1: out += ' IF[%d] ' % (IFSel) |
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| 278 | if self.npol() > 1: out += ' Pol[%d] ' % (polSel) |
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[181] | 279 | out += '= %3.3f\n' % (statval[l]) |
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| 280 | out += "--------------------------------------------------\n" |
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[226] | 281 | |
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[181] | 282 | if self._vb: |
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| 283 | print "--------------------------------------------------" |
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| 284 | print " ",stat |
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| 285 | print "--------------------------------------------------" |
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| 286 | print out |
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[256] | 287 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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| 288 | return retval |
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[102] | 289 | |
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[436] | 290 | def stddev(self,mask=None, allaxes=None): |
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[135] | 291 | """ |
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| 292 | Determine the standard deviation of the current beam/if/pol |
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| 293 | Takes a 'mask' as an optional parameter to specify which |
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| 294 | channels should be excluded. |
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| 295 | Parameters: |
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| 296 | mask: an optional mask specifying where the standard |
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| 297 | deviation should be determined. |
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[436] | 298 | allaxes: optional flag to show all or a cursor selected |
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[226] | 299 | spectrum of Beam/IF/Pol. Default is all or taken |
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| 300 | from .asaprc |
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[135] | 301 | |
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| 302 | Example: |
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| 303 | scan.set_unit('channel') |
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| 304 | msk = scan.create_mask([100,200],[500,600]) |
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| 305 | scan.stddev(mask=m) |
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| 306 | """ |
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[436] | 307 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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| 308 | return self.stats(stat='stddev',mask=mask, allaxes=allaxes); |
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[135] | 309 | |
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[436] | 310 | def get_tsys(self, allaxes=None): |
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[113] | 311 | """ |
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| 312 | Return the System temperatures. |
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| 313 | Parameters: |
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[436] | 314 | allaxes: if True apply to all spectra. Otherwise |
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| 315 | apply only to the selected (beam/pol/if)spectra only. |
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| 316 | The default is taken from .asaprc (True if none) |
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[113] | 317 | Returns: |
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| 318 | a list of Tsys values. |
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| 319 | """ |
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[436] | 320 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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[256] | 321 | from numarray import array,zeros,Float |
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| 322 | axes = ['Beam','IF','Pol','Time'] |
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| 323 | |
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[436] | 324 | if allaxes: |
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[256] | 325 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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| 326 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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| 327 | arr = array(zeros(n),shape=shp,type=Float) |
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| 328 | |
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| 329 | for i in range(self.nbeam()): |
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| 330 | self.setbeam(i) |
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| 331 | for j in range(self.nif()): |
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| 332 | self.setif(j) |
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| 333 | for k in range(self.npol()): |
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| 334 | self.setpol(k) |
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| 335 | arr[i,j,k,:] = self._gettsys() |
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| 336 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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| 337 | tm = [self._gettime(val) for val in range(self.nrow())] |
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[181] | 338 | if self._vb: |
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[256] | 339 | self._print_values(retval,'Tsys',tm) |
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| 340 | return retval |
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| 341 | |
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[102] | 342 | else: |
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[256] | 343 | i,j,k = (self.getbeam(),self.getif(),self.getpol()) |
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| 344 | statval = self._gettsys() |
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[181] | 345 | out = '' |
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| 346 | for l in range(self.nrow()): |
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| 347 | tm = self._gettime(l) |
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| 348 | out += 'Time[%s]:\n' % (tm) |
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| 349 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i) |
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| 350 | if self.nif() > 1: out += ' IF[%d] ' % (j) |
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| 351 | if self.npol() > 1: out += ' Pol[%d] ' % (k) |
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[256] | 352 | out += '= %3.3f\n' % (statval[l]) |
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| 353 | out += "--------------------------------------------------\n" |
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| 354 | |
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[181] | 355 | if self._vb: |
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| 356 | print "--------------------------------------------------" |
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[256] | 357 | print " TSys" |
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[181] | 358 | print "--------------------------------------------------" |
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| 359 | print out |
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[256] | 360 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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| 361 | return retval |
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[113] | 362 | |
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[407] | 363 | def get_time(self, row=-1): |
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[113] | 364 | """ |
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| 365 | Get a list of time stamps for the observations. |
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[181] | 366 | Return a string for each integration in the scantable. |
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[113] | 367 | Parameters: |
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[407] | 368 | row: row no of integration. Default -1 return all rows |
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[113] | 369 | Example: |
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| 370 | none |
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| 371 | """ |
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| 372 | out = [] |
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[407] | 373 | if row == -1: |
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| 374 | for i in range(self.nrow()): |
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| 375 | out.append(self._gettime(i)) |
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| 376 | return out |
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| 377 | else: |
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| 378 | if row < self.nrow(): |
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| 379 | return self._gettime(row) |
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[102] | 380 | |
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| 381 | def set_unit(self, unit='channel'): |
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| 382 | """ |
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| 383 | Set the unit for all following operations on this scantable |
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| 384 | Parameters: |
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| 385 | unit: optional unit, default is 'channel' |
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[113] | 386 | one of '*Hz','km/s','channel', '' |
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[102] | 387 | """ |
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[484] | 388 | varlist = vars() |
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[113] | 389 | if unit in ['','pixel', 'channel']: |
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| 390 | unit = '' |
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| 391 | inf = list(self._getcoordinfo()) |
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| 392 | inf[0] = unit |
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| 393 | self._setcoordinfo(inf) |
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| 394 | if self._p: self.plot() |
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[484] | 395 | self._add_history("set_unit",varlist) |
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[113] | 396 | |
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[484] | 397 | def set_instrument(self, instr): |
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[358] | 398 | """ |
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| 399 | Set the instrument for subsequent processing |
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| 400 | Parameters: |
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[407] | 401 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
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| 402 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
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[358] | 403 | """ |
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| 404 | self._setInstrument(instr) |
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[484] | 405 | self._add_history("set_instument",vars()) |
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[358] | 406 | |
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[276] | 407 | def set_doppler(self, doppler='RADIO'): |
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| 408 | """ |
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| 409 | Set the doppler for all following operations on this scantable. |
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| 410 | Parameters: |
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| 411 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
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| 412 | """ |
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[484] | 413 | varlist = vars() |
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[276] | 414 | inf = list(self._getcoordinfo()) |
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| 415 | inf[2] = doppler |
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| 416 | self._setcoordinfo(inf) |
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| 417 | if self._p: self.plot() |
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[484] | 418 | self._add_history("set_doppler",vars()) |
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[432] | 419 | |
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[226] | 420 | def set_freqframe(self, frame=None): |
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[113] | 421 | """ |
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| 422 | Set the frame type of the Spectral Axis. |
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| 423 | Parameters: |
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| 424 | frame: an optional frame type, default 'LSRK'. |
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| 425 | Examples: |
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| 426 | scan.set_freqframe('BARY') |
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| 427 | """ |
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[484] | 428 | if frame is None: frame = rcParams['scantable.freqframe'] |
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| 429 | varlist = vars() |
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[113] | 430 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
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| 431 | 'GEO','GALACTO','LGROUP','CMB'] |
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| 432 | if frame in valid: |
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| 433 | inf = list(self._getcoordinfo()) |
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| 434 | inf[1] = frame |
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| 435 | self._setcoordinfo(inf) |
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[484] | 436 | self._add_history("set_freqframe",varlist) |
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[102] | 437 | else: |
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[113] | 438 | print "Please specify a valid freq type. Valid types are:\n",valid |
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| 439 | |
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| 440 | def get_unit(self): |
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| 441 | """ |
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| 442 | Get the default unit set in this scantable |
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| 443 | Parameters: |
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| 444 | Returns: |
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| 445 | A unit string |
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| 446 | """ |
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| 447 | inf = self._getcoordinfo() |
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| 448 | unit = inf[0] |
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| 449 | if unit == '': unit = 'channel' |
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| 450 | return unit |
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[102] | 451 | |
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[158] | 452 | def get_abcissa(self, rowno=0): |
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[102] | 453 | """ |
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[158] | 454 | Get the abcissa in the current coordinate setup for the currently |
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[113] | 455 | selected Beam/IF/Pol |
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| 456 | Parameters: |
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[226] | 457 | rowno: an optional row number in the scantable. Default is the |
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| 458 | first row, i.e. rowno=0 |
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[113] | 459 | Returns: |
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[407] | 460 | The abcissa values and it's format string (as a dictionary) |
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[113] | 461 | """ |
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[256] | 462 | abc = self._getabcissa(rowno) |
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[407] | 463 | lbl = self._getabcissalabel(rowno) |
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[158] | 464 | return abc, lbl |
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[407] | 465 | #return {'abcissa':abc,'label':lbl} |
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[113] | 466 | |
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| 467 | def create_mask(self, *args, **kwargs): |
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| 468 | """ |
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[102] | 469 | Compute and return a mask based on [min,max] windows. |
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[189] | 470 | The specified windows are to be INCLUDED, when the mask is |
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[113] | 471 | applied. |
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[102] | 472 | Parameters: |
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| 473 | [min,max],[min2,max2],... |
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| 474 | Pairs of start/end points specifying the regions |
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| 475 | to be masked |
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[189] | 476 | invert: optional argument. If specified as True, |
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| 477 | return an inverted mask, i.e. the regions |
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| 478 | specified are EXCLUDED |
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[102] | 479 | Example: |
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[113] | 480 | scan.set_unit('channel') |
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| 481 | |
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| 482 | a) |
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[102] | 483 | msk = scan.set_mask([400,500],[800,900]) |
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[189] | 484 | # masks everything outside 400 and 500 |
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[113] | 485 | # and 800 and 900 in the unit 'channel' |
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| 486 | |
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| 487 | b) |
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| 488 | msk = scan.set_mask([400,500],[800,900], invert=True) |
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[189] | 489 | # masks the regions between 400 and 500 |
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[113] | 490 | # and 800 and 900 in the unit 'channel' |
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| 491 | |
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[102] | 492 | """ |
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[484] | 493 | varlist = vars() |
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[113] | 494 | u = self._getcoordinfo()[0] |
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| 495 | if self._vb: |
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| 496 | if u == "": u = "channel" |
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| 497 | print "The current mask window unit is", u |
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[102] | 498 | n = self.nchan() |
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[256] | 499 | data = self._getabcissa() |
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[189] | 500 | msk = zeros(n) |
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[484] | 501 | for window in args: |
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[102] | 502 | if (len(window) != 2 or window[0] > window[1] ): |
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| 503 | print "A window needs to be defined as [min,max]" |
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| 504 | return |
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| 505 | for i in range(n): |
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[113] | 506 | if data[i] >= window[0] and data[i] < window[1]: |
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[189] | 507 | msk[i] = 1 |
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[113] | 508 | if kwargs.has_key('invert'): |
---|
| 509 | if kwargs.get('invert'): |
---|
| 510 | from numarray import logical_not |
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| 511 | msk = logical_not(msk) |
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[484] | 512 | self._add_history("create_mask", varlist) |
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[102] | 513 | return msk |
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[113] | 514 | |
---|
[256] | 515 | def get_restfreqs(self): |
---|
| 516 | """ |
---|
| 517 | Get the restfrequency(s) stored in this scantable. |
---|
| 518 | The return value(s) are always of unit 'Hz' |
---|
| 519 | Parameters: |
---|
| 520 | none |
---|
| 521 | Returns: |
---|
| 522 | a list of doubles |
---|
| 523 | """ |
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| 524 | return list(self._getrestfreqs()) |
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[102] | 525 | |
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[402] | 526 | def lines(self): |
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[391] | 527 | """ |
---|
[402] | 528 | Print the list of known spectral lines |
---|
| 529 | """ |
---|
| 530 | sdtable._lines(self) |
---|
| 531 | |
---|
[484] | 532 | def set_restfreqs(self, freqs=None, unit='Hz', lines=None, source=None, |
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| 533 | theif=None): |
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[402] | 534 | """ |
---|
[393] | 535 | Select the restfrequency for the specified source and IF OR |
---|
| 536 | replace for all IFs. If the 'freqs' argument holds a scalar, |
---|
| 537 | then that rest frequency will be applied to the selected |
---|
| 538 | data (and added to the list of available rest frequencies). |
---|
| 539 | In this way, you can set a rest frequency for each |
---|
| 540 | source and IF combination. If the 'freqs' argument holds |
---|
| 541 | a vector, then it MUST be of length the number of IFs |
---|
| 542 | (and the available restfrequencies will be replaced by |
---|
| 543 | this vector). In this case, *all* data ('source' and |
---|
| 544 | 'theif' are ignored) have the restfrequency set per IF according |
---|
| 545 | to the corresponding value you give in the 'freqs' vector. |
---|
| 546 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
| 547 | IF 1 gets restfreq 2e9. |
---|
[402] | 548 | |
---|
| 549 | You can also specify the frequencies via known line names |
---|
| 550 | in the argument 'lines'. Use 'freqs' or 'lines'. 'freqs' |
---|
| 551 | takes precedence. See the list of known names via function |
---|
| 552 | scantable.lines() |
---|
[391] | 553 | Parameters: |
---|
[402] | 554 | freqs: list of rest frequencies |
---|
[393] | 555 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 556 | lines: list of known spectral lines names (alternative to freqs). |
---|
| 557 | See possible list via scantable.lines() |
---|
[391] | 558 | source: Source name (blank means all) |
---|
| 559 | theif: IF (-1 means all) |
---|
| 560 | Example: |
---|
[393] | 561 | scan.set_restfreqs(freqs=1.4e9, source='NGC253', theif=2) |
---|
| 562 | scan.set_restfreqs(freqs=[1.4e9,1.67e9]) |
---|
[391] | 563 | """ |
---|
[484] | 564 | varlist = vars() |
---|
[391] | 565 | if source is None: |
---|
| 566 | source = "" |
---|
| 567 | if theif is None: |
---|
| 568 | theif = -1 |
---|
[393] | 569 | t = type(freqs) |
---|
| 570 | if t is int or t is float: |
---|
| 571 | freqs = [freqs] |
---|
[402] | 572 | if freqs is None: |
---|
| 573 | freqs = [] |
---|
| 574 | t = type(lines) |
---|
| 575 | if t is str: |
---|
| 576 | lines = [lines] |
---|
| 577 | if lines is None: |
---|
| 578 | lines = [] |
---|
| 579 | sdtable._setrestfreqs(self, freqs, unit, lines, source, theif) |
---|
[484] | 580 | self._add_history("set_restfreqs", varlist) |
---|
| 581 | |
---|
[391] | 582 | |
---|
| 583 | |
---|
[102] | 584 | def flag_spectrum(self, thebeam, theif, thepol): |
---|
| 585 | """ |
---|
| 586 | This flags a selected spectrum in the scan 'for good'. |
---|
| 587 | USE WITH CARE - not reversible. |
---|
| 588 | Use masks for non-permanent exclusion of channels. |
---|
| 589 | Parameters: |
---|
| 590 | thebeam,theif,thepol: all have to be explicitly |
---|
| 591 | specified |
---|
| 592 | Example: |
---|
| 593 | scan.flag_spectrum(0,0,1) |
---|
| 594 | flags the spectrum for Beam=0, IF=0, Pol=1 |
---|
| 595 | """ |
---|
[407] | 596 | if (thebeam < self.nbeam() and |
---|
| 597 | theif < self.nif() and |
---|
| 598 | thepol < self.npol()): |
---|
| 599 | sdtable.setbeam(self, thebeam) |
---|
| 600 | sdtable.setif(self, theif) |
---|
| 601 | sdtable.setpol(self, thepol) |
---|
| 602 | sdtable._flag(self) |
---|
[484] | 603 | self._add_history("flag_spectrum", vars()) |
---|
[102] | 604 | else: |
---|
| 605 | print "Please specify a valid (Beam/IF/Pol)" |
---|
| 606 | return |
---|
[113] | 607 | |
---|
| 608 | def plot(self, what='spectrum',col='Pol', panel=None): |
---|
| 609 | """ |
---|
| 610 | Plot the spectra contained in the scan. Alternatively you can also |
---|
| 611 | Plot Tsys vs Time |
---|
| 612 | Parameters: |
---|
| 613 | what: a choice of 'spectrum' (default) or 'tsys' |
---|
[135] | 614 | col: which out of Beams/IFs/Pols should be colour stacked |
---|
[113] | 615 | panel: set up multiple panels, currently not working. |
---|
| 616 | """ |
---|
[283] | 617 | print "Warning! Not fully functional. Use plotter.plot() instead" |
---|
| 618 | |
---|
[113] | 619 | validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()} |
---|
[124] | 620 | |
---|
[113] | 621 | validyax = ['spectrum','tsys'] |
---|
[189] | 622 | from asap.asaplot import ASAPlot |
---|
[113] | 623 | if not self._p: |
---|
| 624 | self._p = ASAPlot() |
---|
[189] | 625 | #print "Plotting not enabled" |
---|
| 626 | #return |
---|
| 627 | if self._p.is_dead: |
---|
| 628 | del self._p |
---|
| 629 | self._p = ASAPlot() |
---|
[113] | 630 | npan = 1 |
---|
| 631 | x = None |
---|
| 632 | if what == 'tsys': |
---|
| 633 | n = self.nrow() |
---|
| 634 | if n < 2: |
---|
| 635 | print "Only one integration. Can't plot." |
---|
| 636 | return |
---|
[124] | 637 | self._p.hold() |
---|
| 638 | self._p.clear() |
---|
[113] | 639 | if panel == 'Time': |
---|
| 640 | npan = self.nrow() |
---|
[124] | 641 | self._p.set_panels(rows=npan) |
---|
[113] | 642 | xlab,ylab,tlab = None,None,None |
---|
[226] | 643 | self._vb = False |
---|
[256] | 644 | sel = self.get_cursor() |
---|
[113] | 645 | for i in range(npan): |
---|
[226] | 646 | if npan > 1: |
---|
| 647 | self._p.subplot(i) |
---|
[113] | 648 | for j in range(validcol[col]): |
---|
| 649 | x = None |
---|
| 650 | y = None |
---|
| 651 | m = None |
---|
| 652 | tlab = self._getsourcename(i) |
---|
[124] | 653 | import re |
---|
| 654 | tlab = re.sub('_S','',tlab) |
---|
[113] | 655 | if col == 'Beam': |
---|
| 656 | self.setbeam(j) |
---|
| 657 | elif col == 'IF': |
---|
| 658 | self.setif(j) |
---|
| 659 | elif col == 'Pol': |
---|
| 660 | self.setpol(j) |
---|
| 661 | if what == 'tsys': |
---|
| 662 | x = range(self.nrow()) |
---|
| 663 | xlab = 'Time [pixel]' |
---|
| 664 | m = list(ones(len(x))) |
---|
| 665 | y = [] |
---|
| 666 | ylab = r'$T_{sys}$' |
---|
| 667 | for k in range(len(x)): |
---|
| 668 | y.append(self._gettsys(k)) |
---|
| 669 | else: |
---|
[158] | 670 | x,xlab = self.get_abcissa(i) |
---|
[256] | 671 | y = self._getspectrum(i) |
---|
[113] | 672 | ylab = r'Flux' |
---|
[256] | 673 | m = self._getmask(i) |
---|
[113] | 674 | llab = col+' '+str(j) |
---|
| 675 | self._p.set_line(label=llab) |
---|
| 676 | self._p.plot(x,y,m) |
---|
[124] | 677 | self._p.set_axes('xlabel',xlab) |
---|
| 678 | self._p.set_axes('ylabel',ylab) |
---|
| 679 | self._p.set_axes('title',tlab) |
---|
[113] | 680 | self._p.release() |
---|
[256] | 681 | self.set_cursor(sel[0],sel[1],sel[2]) |
---|
[226] | 682 | self._vb = rcParams['verbose'] |
---|
[113] | 683 | return |
---|
[256] | 684 | |
---|
| 685 | print out |
---|
| 686 | |
---|
| 687 | def _print_values(self, dat, label='', timestamps=[]): |
---|
| 688 | d = dat['data'] |
---|
| 689 | a = dat['axes'] |
---|
| 690 | shp = d.getshape() |
---|
| 691 | out = '' |
---|
| 692 | for i in range(shp[3]): |
---|
| 693 | out += '%s [%s]:\n' % (a[3],timestamps[i]) |
---|
| 694 | t = d[:,:,:,i] |
---|
| 695 | for j in range(shp[0]): |
---|
| 696 | if shp[0] > 1: out += ' %s[%d] ' % (a[0],j) |
---|
| 697 | for k in range(shp[1]): |
---|
| 698 | if shp[1] > 1: out += ' %s[%d] ' % (a[1],k) |
---|
| 699 | for l in range(shp[2]): |
---|
| 700 | if shp[2] > 1: out += ' %s[%d] ' % (a[2],l) |
---|
| 701 | out += '= %3.3f\n' % (t[j,k,l]) |
---|
[484] | 702 | out += "-"*80 |
---|
| 703 | out += "\n" |
---|
| 704 | print "-"*80 |
---|
[256] | 705 | print " ", label |
---|
[484] | 706 | print "-"*80 |
---|
[256] | 707 | print out |
---|
[484] | 708 | |
---|
| 709 | def history(self): |
---|
| 710 | hist = list(self._gethistory()) |
---|
| 711 | print "-"*80 |
---|
| 712 | for h in hist: |
---|
| 713 | items = h.split("##") |
---|
| 714 | date = items[0] |
---|
| 715 | func = items[1] |
---|
| 716 | items = items[2:] |
---|
| 717 | print date |
---|
| 718 | print "Function: %s\n Parameters:" % (func) |
---|
| 719 | for i in items: |
---|
| 720 | s = i.split("=") |
---|
| 721 | print " %s: %s" % (s[0],s[1]) |
---|
| 722 | print "-"*80 |
---|
| 723 | return |
---|
| 724 | |
---|
| 725 | def _add_history(self, funcname, parameters): |
---|
| 726 | # create date |
---|
| 727 | sep = "##" |
---|
| 728 | from datetime import datetime |
---|
| 729 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 730 | hist = dstr+sep |
---|
| 731 | hist += funcname+sep#cdate+sep |
---|
| 732 | if parameters.has_key('self'): del parameters['self'] |
---|
| 733 | for k,v in parameters.iteritems(): |
---|
| 734 | if type(v) is dict: |
---|
| 735 | for k2,v2 in v.iteritems(): |
---|
| 736 | hist += k2 |
---|
| 737 | hist += "=" |
---|
| 738 | if isinstance(v2,scantable): |
---|
| 739 | hist += 'scantable' |
---|
| 740 | elif k2 == 'mask': |
---|
| 741 | hist += str(self._zip_mask(v2)) |
---|
| 742 | else: |
---|
| 743 | hist += str(v2) |
---|
| 744 | else: |
---|
| 745 | hist += k |
---|
| 746 | hist += "=" |
---|
| 747 | if isinstance(v,scantable): |
---|
| 748 | hist += 'scantable' |
---|
| 749 | elif k == 'mask': |
---|
| 750 | hist += str(self._zip_mask(v)) |
---|
| 751 | else: |
---|
| 752 | hist += str(v) |
---|
| 753 | hist += sep |
---|
| 754 | hist = hist[:-2] # remove trailing '##' |
---|
| 755 | self._addhistory(hist) |
---|
| 756 | |
---|
| 757 | |
---|
| 758 | def _zip_mask(self, mask): |
---|
| 759 | mask = list(mask) |
---|
| 760 | i = 0 |
---|
| 761 | segments = [] |
---|
| 762 | while mask[i:].count(1): |
---|
| 763 | i += mask[i:].index(1) |
---|
| 764 | if mask[i:].count(0): |
---|
| 765 | j = i + mask[i:].index(0) |
---|
| 766 | else: |
---|
| 767 | j = len(mask) |
---|
| 768 | segments.append([i,j]) |
---|
| 769 | i = j |
---|
| 770 | return segments |
---|