[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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[489] | 29 | """ |
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| 30 | if average is None or type(average) is not bool: |
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| 31 | average = rcParams['scantable.autoaverage'] |
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| 32 | |
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[484] | 33 | varlist = vars() |
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[226] | 34 | self._vb = rcParams['verbose'] |
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[113] | 35 | self._p = None |
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[484] | 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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[489] | 66 | if average: |
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| 67 | from asap._asap import average as _av |
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[226] | 68 | print 'Auto averaging integrations...' |
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[513] | 69 | tbl2 = _av((tbl,),(),True,'none') |
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[226] | 70 | sdtable.__init__(self,tbl2) |
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[513] | 71 | del tbl2 |
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[226] | 72 | else: |
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| 73 | sdtable.__init__(self,tbl) |
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[513] | 74 | del r,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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[489] | 83 | is the directory file name into which all the files |
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[497] | 84 | will be written (default is 'asap_FITS'). For format |
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| 85 | "ASCII" this is the root file name (data in 'name'.txt |
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| 86 | and header in 'name'_header.txt) |
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[116] | 87 | format: an optional file format. Default is ASAP. |
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[280] | 88 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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[194] | 89 | 'SDFITS' (save as SDFITS file) |
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| 90 | 'FITS' (saves each row as a FITS Image) |
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[200] | 91 | 'ASCII' (saves as ascii text file) |
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[226] | 92 | 'MS2' (saves as an aips++ |
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| 93 | MeasurementSet V2) |
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[489] | 94 | stokes: Convert to Stokes parameters (only available |
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| 95 | currently with FITS and ASCII formats. |
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| 96 | Default is False. |
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[411] | 97 | overwrite: If the file should be overwritten if it exists. |
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[256] | 98 | The default False is to return with warning |
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[411] | 99 | without writing the output. USE WITH CARE. |
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[116] | 100 | Example: |
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| 101 | scan.save('myscan.asap') |
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| 102 | scan.save('myscan.sdfits','SDFITS') |
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| 103 | """ |
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[411] | 104 | from os import path |
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[226] | 105 | if format is None: format = rcParams['scantable.save'] |
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[256] | 106 | suffix = '.'+format.lower() |
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| 107 | if name is None or name =="": |
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| 108 | name = 'scantable'+suffix |
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[283] | 109 | print "No filename given. Using default name %s..." % name |
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[411] | 110 | name = path.expandvars(name) |
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[256] | 111 | if path.isfile(name) or path.isdir(name): |
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| 112 | if not overwrite: |
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| 113 | print "File %s already exists." % name |
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| 114 | return |
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[451] | 115 | format2 = format.upper() |
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| 116 | if format2 == 'ASAP': |
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[116] | 117 | self._save(name) |
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| 118 | else: |
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| 119 | from asap._asap import sdwriter as _sw |
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[451] | 120 | w = _sw(format2) |
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[445] | 121 | w.write(self, name, stokes) |
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[116] | 122 | return |
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| 123 | |
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[102] | 124 | def copy(self): |
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| 125 | """ |
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| 126 | Return a copy of this scantable. |
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| 127 | Parameters: |
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[113] | 128 | none |
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[102] | 129 | Example: |
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| 130 | copiedscan = scan.copy() |
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| 131 | """ |
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[113] | 132 | sd = scantable(sdtable._copy(self)) |
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| 133 | return sd |
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| 134 | |
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[102] | 135 | def get_scan(self, scanid=None): |
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| 136 | """ |
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| 137 | Return a specific scan (by scanno) or collection of scans (by |
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| 138 | source name) in a new scantable. |
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| 139 | Parameters: |
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[513] | 140 | scanid: a (list of) scanno or a source name, unix-style |
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| 141 | patterns are accepted for source name matching, e.g. |
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| 142 | '*_R' gets all 'ref scans |
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[102] | 143 | Example: |
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[513] | 144 | # get all scans containing the source '323p459' |
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| 145 | newscan = scan.get_scan('323p459') |
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| 146 | # get all 'off' scans |
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| 147 | refscans = scan.get_scan('*_R') |
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| 148 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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| 149 | newscan = scan.get_scan([0,2,7,10]) |
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[102] | 150 | """ |
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| 151 | if scanid is None: |
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| 152 | print "Please specify a scan no or name to retrieve from the scantable" |
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| 153 | try: |
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| 154 | if type(scanid) is str: |
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[113] | 155 | s = sdtable._getsource(self,scanid) |
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[102] | 156 | return scantable(s) |
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| 157 | elif type(scanid) is int: |
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[381] | 158 | s = sdtable._getscan(self,[scanid]) |
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| 159 | return scantable(s) |
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| 160 | elif type(scanid) is list: |
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[113] | 161 | s = sdtable._getscan(self,scanid) |
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[102] | 162 | return scantable(s) |
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[381] | 163 | else: |
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| 164 | print "Illegal scanid type, use 'int' or 'list' if ints." |
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[102] | 165 | except RuntimeError: |
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| 166 | print "Couldn't find any match." |
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| 167 | |
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| 168 | def __str__(self): |
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[381] | 169 | return sdtable._summary(self,True) |
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[102] | 170 | |
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[381] | 171 | def summary(self,filename=None, verbose=None): |
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[102] | 172 | """ |
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| 173 | Print a summary of the contents of this scantable. |
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| 174 | Parameters: |
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| 175 | filename: the name of a file to write the putput to |
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| 176 | Default - no file output |
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[381] | 177 | verbose: print extra info such as the frequency table |
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| 178 | The default (False) is taken from .asaprc |
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[102] | 179 | """ |
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[381] | 180 | info = sdtable._summary(self, verbose) |
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| 181 | if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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[102] | 182 | if filename is not None: |
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[256] | 183 | if filename is "": |
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| 184 | filename = 'scantable_summary.txt' |
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[415] | 185 | from os.path import expandvars, isdir |
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[411] | 186 | filename = expandvars(filename) |
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[415] | 187 | if not isdir(filename): |
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[413] | 188 | data = open(filename, 'w') |
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| 189 | data.write(info) |
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| 190 | data.close() |
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| 191 | else: |
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| 192 | print "Illegal file name '%s'." % (filename) |
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[102] | 193 | print info |
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[484] | 194 | |
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[553] | 195 | def set_cursor(self, beam=0, IF=0, pol=0): |
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[102] | 196 | """ |
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| 197 | Set the spectrum for individual operations. |
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| 198 | Parameters: |
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[553] | 199 | beam, IF, pol: a number |
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[102] | 200 | Example: |
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[256] | 201 | scan.set_cursor(0,0,1) |
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[135] | 202 | pol1sig = scan.stats(all=False) # returns std dev for beam=0 |
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[181] | 203 | # if=0, pol=1 |
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[102] | 204 | """ |
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[484] | 205 | varlist = vars() |
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[553] | 206 | self.setbeam(beam) |
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| 207 | self.setpol(pol) |
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| 208 | self.setif(IF) |
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[484] | 209 | self._add_history("set_cursor",varlist) |
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[102] | 210 | return |
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| 211 | |
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[256] | 212 | def get_cursor(self): |
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[113] | 213 | """ |
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| 214 | Return/print a the current 'cursor' into the Beam/IF/Pol cube. |
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| 215 | Parameters: |
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| 216 | none |
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| 217 | Returns: |
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| 218 | a list of values (currentBeam,currentIF,currentPol) |
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| 219 | Example: |
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| 220 | none |
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| 221 | """ |
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[102] | 222 | i = self.getbeam() |
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| 223 | j = self.getif() |
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| 224 | k = self.getpol() |
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[113] | 225 | if self._vb: |
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[181] | 226 | print "--------------------------------------------------" |
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[256] | 227 | print " Cursor position" |
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[181] | 228 | print "--------------------------------------------------" |
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[226] | 229 | out = 'Beam=%d IF=%d Pol=%d ' % (i,j,k) |
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[113] | 230 | print out |
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[102] | 231 | return i,j,k |
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| 232 | |
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[436] | 233 | def stats(self, stat='stddev', mask=None, allaxes=None): |
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[102] | 234 | """ |
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[135] | 235 | Determine the specified statistic of the current beam/if/pol |
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[102] | 236 | Takes a 'mask' as an optional parameter to specify which |
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| 237 | channels should be excluded. |
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| 238 | Parameters: |
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[135] | 239 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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| 240 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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| 241 | mask: an optional mask specifying where the statistic |
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[102] | 242 | should be determined. |
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[436] | 243 | allaxes: if True apply to all spectra. Otherwise |
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| 244 | apply only to the selected (beam/pol/if)spectra only. |
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| 245 | The default is taken from .asaprc (True if none) |
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[102] | 246 | Example: |
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[113] | 247 | scan.set_unit('channel') |
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[102] | 248 | msk = scan.create_mask([100,200],[500,600]) |
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[135] | 249 | scan.stats(stat='mean', mask=m) |
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[102] | 250 | """ |
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[436] | 251 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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[135] | 252 | from asap._asap import stats as _stats |
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[256] | 253 | from numarray import array,zeros,Float |
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[102] | 254 | if mask == None: |
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| 255 | mask = ones(self.nchan()) |
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[256] | 256 | axes = ['Beam','IF','Pol','Time'] |
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| 257 | |
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[436] | 258 | beamSel,IFSel,polSel = (self.getbeam(),self.getif(),self.getpol()) |
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| 259 | if allaxes: |
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[256] | 260 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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| 261 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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| 262 | arr = array(zeros(n),shape=shp,type=Float) |
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| 263 | |
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| 264 | for i in range(self.nbeam()): |
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| 265 | self.setbeam(i) |
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| 266 | for j in range(self.nif()): |
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| 267 | self.setif(j) |
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| 268 | for k in range(self.npol()): |
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| 269 | self.setpol(k) |
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| 270 | arr[i,j,k,:] = _stats(self,mask,stat,-1) |
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| 271 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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| 272 | tm = [self._gettime(val) for val in range(self.nrow())] |
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[181] | 273 | if self._vb: |
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[256] | 274 | self._print_values(retval,stat,tm) |
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[436] | 275 | self.setbeam(beamSel) |
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| 276 | self.setif(IFSel) |
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| 277 | self.setpol(polSel) |
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[256] | 278 | return retval |
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[102] | 279 | |
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| 280 | else: |
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[241] | 281 | statval = _stats(self,mask,stat,-1) |
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[181] | 282 | out = '' |
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| 283 | for l in range(self.nrow()): |
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| 284 | tm = self._gettime(l) |
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| 285 | out += 'Time[%s]:\n' % (tm) |
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[436] | 286 | if self.nbeam() > 1: out += ' Beam[%d] ' % (beamSel) |
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| 287 | if self.nif() > 1: out += ' IF[%d] ' % (IFSel) |
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| 288 | if self.npol() > 1: out += ' Pol[%d] ' % (polSel) |
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[181] | 289 | out += '= %3.3f\n' % (statval[l]) |
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| 290 | out += "--------------------------------------------------\n" |
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[226] | 291 | |
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[181] | 292 | if self._vb: |
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| 293 | print "--------------------------------------------------" |
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| 294 | print " ",stat |
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| 295 | print "--------------------------------------------------" |
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| 296 | print out |
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[256] | 297 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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| 298 | return retval |
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[102] | 299 | |
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[436] | 300 | def stddev(self,mask=None, allaxes=None): |
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[135] | 301 | """ |
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| 302 | Determine the standard deviation of the current beam/if/pol |
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| 303 | Takes a 'mask' as an optional parameter to specify which |
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| 304 | channels should be excluded. |
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| 305 | Parameters: |
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| 306 | mask: an optional mask specifying where the standard |
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| 307 | deviation should be determined. |
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[436] | 308 | allaxes: optional flag to show all or a cursor selected |
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[226] | 309 | spectrum of Beam/IF/Pol. Default is all or taken |
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| 310 | from .asaprc |
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[135] | 311 | |
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| 312 | Example: |
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| 313 | scan.set_unit('channel') |
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| 314 | msk = scan.create_mask([100,200],[500,600]) |
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| 315 | scan.stddev(mask=m) |
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| 316 | """ |
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[436] | 317 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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| 318 | return self.stats(stat='stddev',mask=mask, allaxes=allaxes); |
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[135] | 319 | |
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[436] | 320 | def get_tsys(self, allaxes=None): |
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[113] | 321 | """ |
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| 322 | Return the System temperatures. |
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| 323 | Parameters: |
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[436] | 324 | allaxes: if True apply to all spectra. Otherwise |
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| 325 | apply only to the selected (beam/pol/if)spectra only. |
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| 326 | The default is taken from .asaprc (True if none) |
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[113] | 327 | Returns: |
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| 328 | a list of Tsys values. |
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| 329 | """ |
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[436] | 330 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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[256] | 331 | from numarray import array,zeros,Float |
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| 332 | axes = ['Beam','IF','Pol','Time'] |
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| 333 | |
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[436] | 334 | if allaxes: |
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[256] | 335 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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| 336 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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| 337 | arr = array(zeros(n),shape=shp,type=Float) |
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| 338 | |
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| 339 | for i in range(self.nbeam()): |
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| 340 | self.setbeam(i) |
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| 341 | for j in range(self.nif()): |
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| 342 | self.setif(j) |
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| 343 | for k in range(self.npol()): |
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| 344 | self.setpol(k) |
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| 345 | arr[i,j,k,:] = self._gettsys() |
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| 346 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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| 347 | tm = [self._gettime(val) for val in range(self.nrow())] |
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[181] | 348 | if self._vb: |
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[256] | 349 | self._print_values(retval,'Tsys',tm) |
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| 350 | return retval |
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| 351 | |
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[102] | 352 | else: |
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[256] | 353 | i,j,k = (self.getbeam(),self.getif(),self.getpol()) |
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| 354 | statval = self._gettsys() |
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[181] | 355 | out = '' |
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| 356 | for l in range(self.nrow()): |
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| 357 | tm = self._gettime(l) |
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| 358 | out += 'Time[%s]:\n' % (tm) |
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| 359 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i) |
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| 360 | if self.nif() > 1: out += ' IF[%d] ' % (j) |
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| 361 | if self.npol() > 1: out += ' Pol[%d] ' % (k) |
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[256] | 362 | out += '= %3.3f\n' % (statval[l]) |
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| 363 | out += "--------------------------------------------------\n" |
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| 364 | |
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[181] | 365 | if self._vb: |
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| 366 | print "--------------------------------------------------" |
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[256] | 367 | print " TSys" |
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[181] | 368 | print "--------------------------------------------------" |
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| 369 | print out |
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[256] | 370 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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| 371 | return retval |
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[113] | 372 | |
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[407] | 373 | def get_time(self, row=-1): |
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[113] | 374 | """ |
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| 375 | Get a list of time stamps for the observations. |
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[181] | 376 | Return a string for each integration in the scantable. |
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[113] | 377 | Parameters: |
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[407] | 378 | row: row no of integration. Default -1 return all rows |
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[113] | 379 | Example: |
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| 380 | none |
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| 381 | """ |
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| 382 | out = [] |
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[407] | 383 | if row == -1: |
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| 384 | for i in range(self.nrow()): |
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| 385 | out.append(self._gettime(i)) |
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| 386 | return out |
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| 387 | else: |
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| 388 | if row < self.nrow(): |
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| 389 | return self._gettime(row) |
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[102] | 390 | |
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| 391 | def set_unit(self, unit='channel'): |
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| 392 | """ |
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| 393 | Set the unit for all following operations on this scantable |
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| 394 | Parameters: |
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| 395 | unit: optional unit, default is 'channel' |
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[113] | 396 | one of '*Hz','km/s','channel', '' |
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[102] | 397 | """ |
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[484] | 398 | varlist = vars() |
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[113] | 399 | if unit in ['','pixel', 'channel']: |
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| 400 | unit = '' |
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| 401 | inf = list(self._getcoordinfo()) |
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| 402 | inf[0] = unit |
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| 403 | self._setcoordinfo(inf) |
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| 404 | if self._p: self.plot() |
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[484] | 405 | self._add_history("set_unit",varlist) |
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[113] | 406 | |
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[484] | 407 | def set_instrument(self, instr): |
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[358] | 408 | """ |
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| 409 | Set the instrument for subsequent processing |
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| 410 | Parameters: |
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[407] | 411 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
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| 412 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
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[358] | 413 | """ |
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| 414 | self._setInstrument(instr) |
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[484] | 415 | self._add_history("set_instument",vars()) |
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[358] | 416 | |
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[276] | 417 | def set_doppler(self, doppler='RADIO'): |
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| 418 | """ |
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| 419 | Set the doppler for all following operations on this scantable. |
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| 420 | Parameters: |
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| 421 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
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| 422 | """ |
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[484] | 423 | varlist = vars() |
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[276] | 424 | inf = list(self._getcoordinfo()) |
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| 425 | inf[2] = doppler |
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| 426 | self._setcoordinfo(inf) |
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| 427 | if self._p: self.plot() |
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[484] | 428 | self._add_history("set_doppler",vars()) |
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[432] | 429 | |
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[226] | 430 | def set_freqframe(self, frame=None): |
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[113] | 431 | """ |
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| 432 | Set the frame type of the Spectral Axis. |
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| 433 | Parameters: |
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[589] | 434 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
| 435 | 'REST','TOPO','LSRD','LSRK','BARY', |
---|
| 436 | 'GEO','GALACTO','LGROUP','CMB' |
---|
[113] | 437 | Examples: |
---|
| 438 | scan.set_freqframe('BARY') |
---|
| 439 | """ |
---|
[484] | 440 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
| 441 | varlist = vars() |
---|
[113] | 442 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
---|
| 443 | 'GEO','GALACTO','LGROUP','CMB'] |
---|
[589] | 444 | |
---|
[113] | 445 | if frame in valid: |
---|
| 446 | inf = list(self._getcoordinfo()) |
---|
| 447 | inf[1] = frame |
---|
| 448 | self._setcoordinfo(inf) |
---|
[484] | 449 | self._add_history("set_freqframe",varlist) |
---|
[102] | 450 | else: |
---|
[113] | 451 | print "Please specify a valid freq type. Valid types are:\n",valid |
---|
| 452 | |
---|
| 453 | def get_unit(self): |
---|
| 454 | """ |
---|
| 455 | Get the default unit set in this scantable |
---|
| 456 | Parameters: |
---|
| 457 | Returns: |
---|
| 458 | A unit string |
---|
| 459 | """ |
---|
| 460 | inf = self._getcoordinfo() |
---|
| 461 | unit = inf[0] |
---|
| 462 | if unit == '': unit = 'channel' |
---|
| 463 | return unit |
---|
[102] | 464 | |
---|
[158] | 465 | def get_abcissa(self, rowno=0): |
---|
[102] | 466 | """ |
---|
[158] | 467 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 468 | selected Beam/IF/Pol |
---|
| 469 | Parameters: |
---|
[226] | 470 | rowno: an optional row number in the scantable. Default is the |
---|
| 471 | first row, i.e. rowno=0 |
---|
[113] | 472 | Returns: |
---|
[407] | 473 | The abcissa values and it's format string (as a dictionary) |
---|
[113] | 474 | """ |
---|
[256] | 475 | abc = self._getabcissa(rowno) |
---|
[407] | 476 | lbl = self._getabcissalabel(rowno) |
---|
[158] | 477 | return abc, lbl |
---|
[407] | 478 | #return {'abcissa':abc,'label':lbl} |
---|
[113] | 479 | |
---|
| 480 | def create_mask(self, *args, **kwargs): |
---|
| 481 | """ |
---|
[102] | 482 | Compute and return a mask based on [min,max] windows. |
---|
[189] | 483 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 484 | applied. |
---|
[102] | 485 | Parameters: |
---|
| 486 | [min,max],[min2,max2],... |
---|
| 487 | Pairs of start/end points specifying the regions |
---|
| 488 | to be masked |
---|
[189] | 489 | invert: optional argument. If specified as True, |
---|
| 490 | return an inverted mask, i.e. the regions |
---|
| 491 | specified are EXCLUDED |
---|
[513] | 492 | row: create the mask using the specified row for |
---|
| 493 | unit conversions, default is row=0 |
---|
| 494 | only necessary if frequency varies over rows. |
---|
[102] | 495 | Example: |
---|
[113] | 496 | scan.set_unit('channel') |
---|
| 497 | |
---|
| 498 | a) |
---|
[102] | 499 | msk = scan.set_mask([400,500],[800,900]) |
---|
[189] | 500 | # masks everything outside 400 and 500 |
---|
[113] | 501 | # and 800 and 900 in the unit 'channel' |
---|
| 502 | |
---|
| 503 | b) |
---|
| 504 | msk = scan.set_mask([400,500],[800,900], invert=True) |
---|
[189] | 505 | # masks the regions between 400 and 500 |
---|
[113] | 506 | # and 800 and 900 in the unit 'channel' |
---|
| 507 | |
---|
[102] | 508 | """ |
---|
[513] | 509 | row = 0 |
---|
| 510 | if kwargs.has_key("row"): |
---|
| 511 | row = kwargs.get("row") |
---|
| 512 | data = self._getabcissa(row) |
---|
[113] | 513 | u = self._getcoordinfo()[0] |
---|
| 514 | if self._vb: |
---|
| 515 | if u == "": u = "channel" |
---|
| 516 | print "The current mask window unit is", u |
---|
[102] | 517 | n = self.nchan() |
---|
[189] | 518 | msk = zeros(n) |
---|
[484] | 519 | for window in args: |
---|
[102] | 520 | if (len(window) != 2 or window[0] > window[1] ): |
---|
| 521 | print "A window needs to be defined as [min,max]" |
---|
| 522 | return |
---|
| 523 | for i in range(n): |
---|
[113] | 524 | if data[i] >= window[0] and data[i] < window[1]: |
---|
[189] | 525 | msk[i] = 1 |
---|
[113] | 526 | if kwargs.has_key('invert'): |
---|
| 527 | if kwargs.get('invert'): |
---|
| 528 | from numarray import logical_not |
---|
[513] | 529 | msk = logical_not(msk) |
---|
[102] | 530 | return msk |
---|
[113] | 531 | |
---|
[256] | 532 | def get_restfreqs(self): |
---|
| 533 | """ |
---|
| 534 | Get the restfrequency(s) stored in this scantable. |
---|
| 535 | The return value(s) are always of unit 'Hz' |
---|
| 536 | Parameters: |
---|
| 537 | none |
---|
| 538 | Returns: |
---|
| 539 | a list of doubles |
---|
| 540 | """ |
---|
| 541 | return list(self._getrestfreqs()) |
---|
[102] | 542 | |
---|
[402] | 543 | def lines(self): |
---|
[391] | 544 | """ |
---|
[402] | 545 | Print the list of known spectral lines |
---|
| 546 | """ |
---|
| 547 | sdtable._lines(self) |
---|
| 548 | |
---|
[484] | 549 | def set_restfreqs(self, freqs=None, unit='Hz', lines=None, source=None, |
---|
| 550 | theif=None): |
---|
[402] | 551 | """ |
---|
[393] | 552 | Select the restfrequency for the specified source and IF OR |
---|
| 553 | replace for all IFs. If the 'freqs' argument holds a scalar, |
---|
| 554 | then that rest frequency will be applied to the selected |
---|
| 555 | data (and added to the list of available rest frequencies). |
---|
| 556 | In this way, you can set a rest frequency for each |
---|
| 557 | source and IF combination. If the 'freqs' argument holds |
---|
| 558 | a vector, then it MUST be of length the number of IFs |
---|
| 559 | (and the available restfrequencies will be replaced by |
---|
| 560 | this vector). In this case, *all* data ('source' and |
---|
| 561 | 'theif' are ignored) have the restfrequency set per IF according |
---|
| 562 | to the corresponding value you give in the 'freqs' vector. |
---|
| 563 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
| 564 | IF 1 gets restfreq 2e9. |
---|
[402] | 565 | |
---|
| 566 | You can also specify the frequencies via known line names |
---|
| 567 | in the argument 'lines'. Use 'freqs' or 'lines'. 'freqs' |
---|
| 568 | takes precedence. See the list of known names via function |
---|
| 569 | scantable.lines() |
---|
[391] | 570 | Parameters: |
---|
[402] | 571 | freqs: list of rest frequencies |
---|
[393] | 572 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 573 | lines: list of known spectral lines names (alternative to freqs). |
---|
| 574 | See possible list via scantable.lines() |
---|
[391] | 575 | source: Source name (blank means all) |
---|
| 576 | theif: IF (-1 means all) |
---|
| 577 | Example: |
---|
[393] | 578 | scan.set_restfreqs(freqs=1.4e9, source='NGC253', theif=2) |
---|
| 579 | scan.set_restfreqs(freqs=[1.4e9,1.67e9]) |
---|
[391] | 580 | """ |
---|
[484] | 581 | varlist = vars() |
---|
[391] | 582 | if source is None: |
---|
| 583 | source = "" |
---|
| 584 | if theif is None: |
---|
| 585 | theif = -1 |
---|
[393] | 586 | t = type(freqs) |
---|
| 587 | if t is int or t is float: |
---|
| 588 | freqs = [freqs] |
---|
[402] | 589 | if freqs is None: |
---|
| 590 | freqs = [] |
---|
| 591 | t = type(lines) |
---|
| 592 | if t is str: |
---|
| 593 | lines = [lines] |
---|
| 594 | if lines is None: |
---|
| 595 | lines = [] |
---|
| 596 | sdtable._setrestfreqs(self, freqs, unit, lines, source, theif) |
---|
[484] | 597 | self._add_history("set_restfreqs", varlist) |
---|
| 598 | |
---|
[391] | 599 | |
---|
| 600 | |
---|
[102] | 601 | def flag_spectrum(self, thebeam, theif, thepol): |
---|
| 602 | """ |
---|
| 603 | This flags a selected spectrum in the scan 'for good'. |
---|
| 604 | USE WITH CARE - not reversible. |
---|
| 605 | Use masks for non-permanent exclusion of channels. |
---|
| 606 | Parameters: |
---|
| 607 | thebeam,theif,thepol: all have to be explicitly |
---|
| 608 | specified |
---|
| 609 | Example: |
---|
| 610 | scan.flag_spectrum(0,0,1) |
---|
| 611 | flags the spectrum for Beam=0, IF=0, Pol=1 |
---|
| 612 | """ |
---|
[407] | 613 | if (thebeam < self.nbeam() and |
---|
| 614 | theif < self.nif() and |
---|
| 615 | thepol < self.npol()): |
---|
| 616 | sdtable.setbeam(self, thebeam) |
---|
| 617 | sdtable.setif(self, theif) |
---|
| 618 | sdtable.setpol(self, thepol) |
---|
| 619 | sdtable._flag(self) |
---|
[484] | 620 | self._add_history("flag_spectrum", vars()) |
---|
[102] | 621 | else: |
---|
| 622 | print "Please specify a valid (Beam/IF/Pol)" |
---|
| 623 | return |
---|
[113] | 624 | |
---|
| 625 | def plot(self, what='spectrum',col='Pol', panel=None): |
---|
| 626 | """ |
---|
| 627 | Plot the spectra contained in the scan. Alternatively you can also |
---|
| 628 | Plot Tsys vs Time |
---|
| 629 | Parameters: |
---|
| 630 | what: a choice of 'spectrum' (default) or 'tsys' |
---|
[135] | 631 | col: which out of Beams/IFs/Pols should be colour stacked |
---|
[113] | 632 | panel: set up multiple panels, currently not working. |
---|
| 633 | """ |
---|
[283] | 634 | print "Warning! Not fully functional. Use plotter.plot() instead" |
---|
| 635 | |
---|
[113] | 636 | validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()} |
---|
[124] | 637 | |
---|
[113] | 638 | validyax = ['spectrum','tsys'] |
---|
[189] | 639 | from asap.asaplot import ASAPlot |
---|
[113] | 640 | if not self._p: |
---|
| 641 | self._p = ASAPlot() |
---|
[189] | 642 | #print "Plotting not enabled" |
---|
| 643 | #return |
---|
| 644 | if self._p.is_dead: |
---|
| 645 | del self._p |
---|
| 646 | self._p = ASAPlot() |
---|
[113] | 647 | npan = 1 |
---|
| 648 | x = None |
---|
| 649 | if what == 'tsys': |
---|
| 650 | n = self.nrow() |
---|
| 651 | if n < 2: |
---|
| 652 | print "Only one integration. Can't plot." |
---|
| 653 | return |
---|
[124] | 654 | self._p.hold() |
---|
| 655 | self._p.clear() |
---|
[113] | 656 | if panel == 'Time': |
---|
| 657 | npan = self.nrow() |
---|
[124] | 658 | self._p.set_panels(rows=npan) |
---|
[113] | 659 | xlab,ylab,tlab = None,None,None |
---|
[226] | 660 | self._vb = False |
---|
[256] | 661 | sel = self.get_cursor() |
---|
[113] | 662 | for i in range(npan): |
---|
[226] | 663 | if npan > 1: |
---|
| 664 | self._p.subplot(i) |
---|
[113] | 665 | for j in range(validcol[col]): |
---|
| 666 | x = None |
---|
| 667 | y = None |
---|
| 668 | m = None |
---|
| 669 | tlab = self._getsourcename(i) |
---|
[124] | 670 | import re |
---|
| 671 | tlab = re.sub('_S','',tlab) |
---|
[113] | 672 | if col == 'Beam': |
---|
| 673 | self.setbeam(j) |
---|
| 674 | elif col == 'IF': |
---|
| 675 | self.setif(j) |
---|
| 676 | elif col == 'Pol': |
---|
| 677 | self.setpol(j) |
---|
| 678 | if what == 'tsys': |
---|
| 679 | x = range(self.nrow()) |
---|
| 680 | xlab = 'Time [pixel]' |
---|
| 681 | m = list(ones(len(x))) |
---|
| 682 | y = [] |
---|
| 683 | ylab = r'$T_{sys}$' |
---|
| 684 | for k in range(len(x)): |
---|
| 685 | y.append(self._gettsys(k)) |
---|
| 686 | else: |
---|
[158] | 687 | x,xlab = self.get_abcissa(i) |
---|
[256] | 688 | y = self._getspectrum(i) |
---|
[113] | 689 | ylab = r'Flux' |
---|
[256] | 690 | m = self._getmask(i) |
---|
[113] | 691 | llab = col+' '+str(j) |
---|
| 692 | self._p.set_line(label=llab) |
---|
| 693 | self._p.plot(x,y,m) |
---|
[124] | 694 | self._p.set_axes('xlabel',xlab) |
---|
| 695 | self._p.set_axes('ylabel',ylab) |
---|
| 696 | self._p.set_axes('title',tlab) |
---|
[113] | 697 | self._p.release() |
---|
[256] | 698 | self.set_cursor(sel[0],sel[1],sel[2]) |
---|
[226] | 699 | self._vb = rcParams['verbose'] |
---|
[113] | 700 | return |
---|
[256] | 701 | |
---|
| 702 | print out |
---|
| 703 | |
---|
| 704 | def _print_values(self, dat, label='', timestamps=[]): |
---|
| 705 | d = dat['data'] |
---|
| 706 | a = dat['axes'] |
---|
| 707 | shp = d.getshape() |
---|
| 708 | out = '' |
---|
| 709 | for i in range(shp[3]): |
---|
| 710 | out += '%s [%s]:\n' % (a[3],timestamps[i]) |
---|
| 711 | t = d[:,:,:,i] |
---|
| 712 | for j in range(shp[0]): |
---|
| 713 | if shp[0] > 1: out += ' %s[%d] ' % (a[0],j) |
---|
| 714 | for k in range(shp[1]): |
---|
| 715 | if shp[1] > 1: out += ' %s[%d] ' % (a[1],k) |
---|
| 716 | for l in range(shp[2]): |
---|
| 717 | if shp[2] > 1: out += ' %s[%d] ' % (a[2],l) |
---|
| 718 | out += '= %3.3f\n' % (t[j,k,l]) |
---|
[484] | 719 | out += "-"*80 |
---|
| 720 | out += "\n" |
---|
| 721 | print "-"*80 |
---|
[256] | 722 | print " ", label |
---|
[484] | 723 | print "-"*80 |
---|
[256] | 724 | print out |
---|
[484] | 725 | |
---|
| 726 | def history(self): |
---|
| 727 | hist = list(self._gethistory()) |
---|
| 728 | print "-"*80 |
---|
| 729 | for h in hist: |
---|
[489] | 730 | if h.startswith("---"): |
---|
| 731 | print h |
---|
| 732 | else: |
---|
| 733 | items = h.split("##") |
---|
| 734 | date = items[0] |
---|
| 735 | func = items[1] |
---|
| 736 | items = items[2:] |
---|
| 737 | print date |
---|
| 738 | print "Function: %s\n Parameters:" % (func) |
---|
| 739 | for i in items: |
---|
| 740 | s = i.split("=") |
---|
| 741 | print " %s = %s" % (s[0],s[1]) |
---|
| 742 | print "-"*80 |
---|
[484] | 743 | return |
---|
| 744 | |
---|
[513] | 745 | # |
---|
| 746 | # Maths business |
---|
| 747 | # |
---|
| 748 | |
---|
[558] | 749 | def average_time(self, mask=None, scanav=False, weight='tint'): |
---|
[513] | 750 | """ |
---|
| 751 | Return the (time) average of a scan, or apply it 'insitu'. |
---|
| 752 | Note: |
---|
| 753 | in channels only |
---|
| 754 | The cursor of the output scan is set to 0. |
---|
| 755 | Parameters: |
---|
| 756 | one scan or comma separated scans |
---|
| 757 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 758 | weighting) |
---|
[558] | 759 | scanav: True averages each scan separately |
---|
| 760 | False (default) averages all scans together, |
---|
[524] | 761 | weight: Weighting scheme. 'none', 'var' (1/var(spec) |
---|
[535] | 762 | weighted), 'tsys' (1/Tsys**2 weighted), 'tint' |
---|
| 763 | (integration time weighted) or 'tintsys' (Tint/Tsys**2). |
---|
| 764 | The default is 'tint' |
---|
[513] | 765 | Example: |
---|
| 766 | # time average the scantable without using a mask |
---|
| 767 | newscan = scan.average_time() |
---|
| 768 | """ |
---|
| 769 | varlist = vars() |
---|
[524] | 770 | if weight is None: weight = 'tint' |
---|
[513] | 771 | if mask is None: mask = () |
---|
| 772 | from asap._asap import average as _av |
---|
| 773 | s = scantable(_av((self,), mask, scanav, weight)) |
---|
| 774 | s._add_history("average_time",varlist) |
---|
| 775 | return s |
---|
| 776 | |
---|
| 777 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None, |
---|
| 778 | allaxes=None): |
---|
| 779 | """ |
---|
| 780 | Return a scan where all spectra are converted to either |
---|
| 781 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 782 | By default the function tries to look the values up internally. |
---|
| 783 | If it can't find them (or if you want to over-ride), you must |
---|
| 784 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 785 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 786 | Parameters: |
---|
| 787 | jyperk: the Jy / K conversion factor |
---|
| 788 | eta: the aperture efficiency |
---|
| 789 | d: the geomtric diameter (metres) |
---|
| 790 | insitu: if False a new scantable is returned. |
---|
| 791 | Otherwise, the scaling is done in-situ |
---|
| 792 | The default is taken from .asaprc (False) |
---|
| 793 | allaxes: if True apply to all spectra. Otherwise |
---|
| 794 | apply only to the selected (beam/pol/if)spectra only |
---|
| 795 | The default is taken from .asaprc (True if none) |
---|
| 796 | """ |
---|
| 797 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 798 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 799 | varlist = vars() |
---|
| 800 | if jyperk is None: jyperk = -1.0 |
---|
| 801 | if d is None: d = -1.0 |
---|
| 802 | if eta is None: eta = -1.0 |
---|
| 803 | if not insitu: |
---|
| 804 | from asap._asap import convertflux as _convert |
---|
| 805 | s = scantable(_convert(self, d, eta, jyperk, allaxes)) |
---|
| 806 | s._add_history("convert_flux", varlist) |
---|
| 807 | return s |
---|
| 808 | else: |
---|
| 809 | from asap._asap import convertflux_insitu as _convert |
---|
| 810 | _convert(self, d, eta, jyperk, allaxes) |
---|
| 811 | self._add_history("convert_flux", varlist) |
---|
| 812 | return |
---|
| 813 | |
---|
| 814 | def gain_el(self, poly=None, filename="", method="linear", |
---|
| 815 | insitu=None, allaxes=None): |
---|
| 816 | """ |
---|
| 817 | Return a scan after applying a gain-elevation correction. |
---|
| 818 | The correction can be made via either a polynomial or a |
---|
| 819 | table-based interpolation (and extrapolation if necessary). |
---|
| 820 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 821 | If you specify neither, then a polynomial correction will be made |
---|
| 822 | with built in coefficients known for certain telescopes (an error |
---|
| 823 | will occur if the instrument is not known). |
---|
| 824 | The data and Tsys are *divided* by the scaling factors. |
---|
| 825 | Parameters: |
---|
| 826 | poly: Polynomial coefficients (default None) to compute a |
---|
| 827 | gain-elevation correction as a function of |
---|
| 828 | elevation (in degrees). |
---|
| 829 | filename: The name of an ascii file holding correction factors. |
---|
| 830 | The first row of the ascii file must give the column |
---|
| 831 | names and these MUST include columns |
---|
| 832 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 833 | by this) somewhere. |
---|
| 834 | The second row must give the data type of the |
---|
| 835 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 836 | An example file would be |
---|
| 837 | (actual factors are arbitrary) : |
---|
| 838 | |
---|
| 839 | TIME ELEVATION FACTOR |
---|
| 840 | R R R |
---|
| 841 | 0.1 0 0.8 |
---|
| 842 | 0.2 20 0.85 |
---|
| 843 | 0.3 40 0.9 |
---|
| 844 | 0.4 60 0.85 |
---|
| 845 | 0.5 80 0.8 |
---|
| 846 | 0.6 90 0.75 |
---|
| 847 | method: Interpolation method when correcting from a table. |
---|
| 848 | Values are "nearest", "linear" (default), "cubic" |
---|
| 849 | and "spline" |
---|
| 850 | insitu: if False a new scantable is returned. |
---|
| 851 | Otherwise, the scaling is done in-situ |
---|
| 852 | The default is taken from .asaprc (False) |
---|
| 853 | allaxes: If True apply to all spectra. Otherwise |
---|
| 854 | apply only to the selected (beam/pol/if) spectra only |
---|
| 855 | The default is taken from .asaprc (True if none) |
---|
| 856 | """ |
---|
| 857 | |
---|
| 858 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 859 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 860 | varlist = vars() |
---|
| 861 | if poly is None: |
---|
| 862 | poly = () |
---|
| 863 | from os.path import expandvars |
---|
| 864 | filename = expandvars(filename) |
---|
| 865 | if not insitu: |
---|
| 866 | from asap._asap import gainel as _gainEl |
---|
| 867 | s = scantable(_gainEl(self, poly, filename, method, allaxes)) |
---|
| 868 | s._add_history("gain_el", varlist) |
---|
| 869 | return s |
---|
| 870 | else: |
---|
| 871 | from asap._asap import gainel_insitu as _gainEl |
---|
| 872 | _gainEl(self, poly, filename, method, allaxes) |
---|
| 873 | self._add_history("gain_el", varlist) |
---|
| 874 | return |
---|
| 875 | |
---|
| 876 | def freq_align(self, reftime=None, method='cubic', perif=False, |
---|
| 877 | insitu=None): |
---|
| 878 | """ |
---|
| 879 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 880 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 881 | set_freqframe. |
---|
| 882 | Parameters: |
---|
| 883 | reftime: reference time to align at. By default, the time of |
---|
| 884 | the first row of data is used. |
---|
| 885 | method: Interpolation method for regridding the spectra. |
---|
| 886 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 887 | and "spline" |
---|
| 888 | perif: Generate aligners per freqID (no doppler tracking) or |
---|
| 889 | per IF (scan-based doppler tracking) |
---|
| 890 | insitu: if False a new scantable is returned. |
---|
| 891 | Otherwise, the scaling is done in-situ |
---|
| 892 | The default is taken from .asaprc (False) |
---|
| 893 | """ |
---|
| 894 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 895 | varlist = vars() |
---|
| 896 | if reftime is None: reftime = '' |
---|
| 897 | perfreqid = not perif |
---|
| 898 | if not insitu: |
---|
| 899 | from asap._asap import freq_align as _align |
---|
| 900 | s = scantable(_align(self, reftime, method, perfreqid)) |
---|
| 901 | s._add_history("freq_align", varlist) |
---|
| 902 | return s |
---|
| 903 | else: |
---|
| 904 | from asap._asap import freq_align_insitu as _align |
---|
| 905 | _align(self, reftime, method, perfreqid) |
---|
| 906 | self._add_history("freq_align", varlist) |
---|
| 907 | return |
---|
| 908 | |
---|
| 909 | def opacity(self, tau, insitu=None, allaxes=None): |
---|
| 910 | """ |
---|
| 911 | Apply an opacity correction. The data |
---|
| 912 | and Tsys are multiplied by the correction factor. |
---|
| 913 | Parameters: |
---|
| 914 | tau: Opacity from which the correction factor is |
---|
| 915 | exp(tau*ZD) |
---|
| 916 | where ZD is the zenith-distance |
---|
| 917 | insitu: if False a new scantable is returned. |
---|
| 918 | Otherwise, the scaling is done in-situ |
---|
| 919 | The default is taken from .asaprc (False) |
---|
| 920 | allaxes: if True apply to all spectra. Otherwise |
---|
| 921 | apply only to the selected (beam/pol/if)spectra only |
---|
| 922 | The default is taken from .asaprc (True if none) |
---|
| 923 | """ |
---|
| 924 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 925 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 926 | varlist = vars() |
---|
| 927 | if not insitu: |
---|
| 928 | from asap._asap import opacity as _opacity |
---|
| 929 | s = scantable(_opacity(self, tau, allaxes)) |
---|
| 930 | s._add_history("opacity", varlist) |
---|
| 931 | return s |
---|
| 932 | else: |
---|
| 933 | from asap._asap import opacity_insitu as _opacity |
---|
| 934 | _opacity(self, tau, allaxes) |
---|
| 935 | self._add_history("opacity", varlist) |
---|
| 936 | return |
---|
| 937 | |
---|
| 938 | def bin(self, width=5, insitu=None): |
---|
| 939 | """ |
---|
| 940 | Return a scan where all spectra have been binned up. |
---|
| 941 | width: The bin width (default=5) in pixels |
---|
| 942 | insitu: if False a new scantable is returned. |
---|
| 943 | Otherwise, the scaling is done in-situ |
---|
| 944 | The default is taken from .asaprc (False) |
---|
| 945 | """ |
---|
| 946 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 947 | varlist = vars() |
---|
| 948 | if not insitu: |
---|
| 949 | from asap._asap import bin as _bin |
---|
| 950 | s = scantable(_bin(self, width)) |
---|
| 951 | s._add_history("bin",varlist) |
---|
| 952 | return s |
---|
| 953 | else: |
---|
| 954 | from asap._asap import bin_insitu as _bin |
---|
| 955 | _bin(self, width) |
---|
| 956 | self._add_history("bin",varlist) |
---|
| 957 | return |
---|
| 958 | |
---|
| 959 | |
---|
| 960 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 961 | """ |
---|
| 962 | Return a scan where all spectra have been binned up |
---|
| 963 | width: The bin width (default=5) in pixels |
---|
| 964 | method: Interpolation method when correcting from a table. |
---|
| 965 | Values are "nearest", "linear", "cubic" (default) |
---|
| 966 | and "spline" |
---|
| 967 | insitu: if False a new scantable is returned. |
---|
| 968 | Otherwise, the scaling is done in-situ |
---|
| 969 | The default is taken from .asaprc (False) |
---|
| 970 | """ |
---|
| 971 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 972 | varlist = vars() |
---|
| 973 | if not insitu: |
---|
| 974 | from asap._asap import resample as _resample |
---|
| 975 | s = scantable(_resample(self, method, width)) |
---|
| 976 | s._add_history("resample",varlist) |
---|
| 977 | return s |
---|
| 978 | else: |
---|
| 979 | from asap._asap import resample_insitu as _resample |
---|
| 980 | _resample(self, method, width) |
---|
| 981 | self._add_history("resample",varlist) |
---|
| 982 | return |
---|
| 983 | |
---|
| 984 | def average_pol(self, mask=None, weight='none', insitu=None): |
---|
| 985 | """ |
---|
| 986 | Average the Polarisations together. |
---|
| 987 | The polarisation cursor of the output scan is set to 0 |
---|
| 988 | Parameters: |
---|
| 989 | mask: An optional mask defining the region, where the |
---|
| 990 | averaging will be applied. The output will have all |
---|
| 991 | specified points masked. |
---|
[532] | 992 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 993 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[513] | 994 | insitu: if False a new scantable is returned. |
---|
| 995 | Otherwise, the scaling is done in-situ |
---|
| 996 | The default is taken from .asaprc (False) |
---|
| 997 | """ |
---|
| 998 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 999 | varlist = vars() |
---|
| 1000 | |
---|
| 1001 | if mask is None: |
---|
| 1002 | mask = () |
---|
| 1003 | if not insitu: |
---|
| 1004 | from asap._asap import averagepol as _avpol |
---|
| 1005 | s = scantable(_avpol(self, mask, weight)) |
---|
| 1006 | s._add_history("average_pol",varlist) |
---|
| 1007 | return s |
---|
| 1008 | else: |
---|
| 1009 | from asap._asap import averagepol_insitu as _avpol |
---|
| 1010 | _avpol(self, mask, weight) |
---|
| 1011 | self._add_history("average_pol",varlist) |
---|
| 1012 | return |
---|
| 1013 | |
---|
| 1014 | def smooth(self, kernel="hanning", width=5.0, insitu=None, allaxes=None): |
---|
| 1015 | """ |
---|
| 1016 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 1017 | Parameters: |
---|
| 1018 | scan: The input scan |
---|
| 1019 | kernel: The type of smoothing kernel. Select from |
---|
| 1020 | 'hanning' (default), 'gaussian' and 'boxcar'. |
---|
| 1021 | The first three characters are sufficient. |
---|
| 1022 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1023 | ignored otherwise it defauls to 5 pixels. |
---|
| 1024 | For 'gaussian' it is the Full Width Half |
---|
| 1025 | Maximum. For 'boxcar' it is the full width. |
---|
| 1026 | insitu: if False a new scantable is returned. |
---|
| 1027 | Otherwise, the scaling is done in-situ |
---|
| 1028 | The default is taken from .asaprc (False) |
---|
| 1029 | allaxes: If True (default) apply to all spectra. Otherwise |
---|
| 1030 | apply only to the selected (beam/pol/if)spectra only |
---|
| 1031 | The default is taken from .asaprc (True if none) |
---|
| 1032 | Example: |
---|
| 1033 | none |
---|
| 1034 | """ |
---|
| 1035 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 1036 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1037 | varlist = vars() |
---|
| 1038 | if not insitu: |
---|
| 1039 | from asap._asap import smooth as _smooth |
---|
| 1040 | s = scantable(_smooth(self,kernel,width,allaxes)) |
---|
| 1041 | s._add_history("smooth", varlist) |
---|
| 1042 | return s |
---|
| 1043 | else: |
---|
| 1044 | from asap._asap import smooth_insitu as _smooth |
---|
| 1045 | _smooth(self,kernel,width,allaxes) |
---|
| 1046 | self._add_history("smooth", varlist) |
---|
| 1047 | return |
---|
| 1048 | |
---|
| 1049 | def poly_baseline(self, mask=None, order=0, insitu=None): |
---|
| 1050 | """ |
---|
| 1051 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1052 | Parameters: |
---|
| 1053 | scan: a scantable |
---|
| 1054 | mask: an optional mask |
---|
| 1055 | order: the order of the polynomial (default is 0) |
---|
| 1056 | insitu: if False a new scantable is returned. |
---|
| 1057 | Otherwise, the scaling is done in-situ |
---|
| 1058 | The default is taken from .asaprc (False) |
---|
| 1059 | Example: |
---|
| 1060 | # return a scan baselined by a third order polynomial, |
---|
| 1061 | # not using a mask |
---|
| 1062 | bscan = scan.poly_baseline(order=3) |
---|
[577] | 1063 | """ |
---|
[513] | 1064 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1065 | varlist = vars() |
---|
| 1066 | if mask is None: |
---|
| 1067 | from numarray import ones |
---|
[623] | 1068 | mask = list(ones(self.nchan())) |
---|
[513] | 1069 | from asap.asapfitter import fitter |
---|
| 1070 | f = fitter() |
---|
| 1071 | f._verbose(True) |
---|
| 1072 | f.set_scan(self, mask) |
---|
| 1073 | f.set_function(poly=order) |
---|
| 1074 | sf = f.auto_fit(insitu) |
---|
| 1075 | if insitu: |
---|
| 1076 | self._add_history("poly_baseline", varlist) |
---|
| 1077 | return |
---|
| 1078 | else: |
---|
| 1079 | sf._add_history("poly_baseline", varlist) |
---|
| 1080 | return sf |
---|
| 1081 | |
---|
| 1082 | def auto_poly_baseline(self, mask=None, edge=(0,0), order=0, |
---|
| 1083 | threshold=3,insitu=None): |
---|
| 1084 | """ |
---|
| 1085 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1086 | Spectral lines are detected first using linefinder and masked out |
---|
| 1087 | to avoid them affecting the baseline solution. |
---|
| 1088 | |
---|
| 1089 | Parameters: |
---|
| 1090 | scan: a scantable |
---|
| 1091 | mask: an optional mask retreived from scantable |
---|
| 1092 | edge: an optional number of channel to drop at |
---|
| 1093 | the edge of spectrum. If only one value is |
---|
| 1094 | specified, the same number will be dropped from |
---|
| 1095 | both sides of the spectrum. Default is to keep |
---|
| 1096 | all channels |
---|
| 1097 | order: the order of the polynomial (default is 0) |
---|
| 1098 | threshold: the threshold used by line finder. It is better to |
---|
| 1099 | keep it large as only strong lines affect the |
---|
| 1100 | baseline solution. |
---|
| 1101 | insitu: if False a new scantable is returned. |
---|
| 1102 | Otherwise, the scaling is done in-situ |
---|
| 1103 | The default is taken from .asaprc (False) |
---|
| 1104 | |
---|
| 1105 | Example: |
---|
[516] | 1106 | scan2=scan.auto_poly_baseline(order=7) |
---|
[513] | 1107 | """ |
---|
| 1108 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1109 | varlist = vars() |
---|
| 1110 | from asap.asapfitter import fitter |
---|
| 1111 | from asap.asaplinefind import linefinder |
---|
| 1112 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1113 | |
---|
| 1114 | if not _is_valid(edge, int): |
---|
[516] | 1115 | raise RuntimeError, "Parameter 'edge' has to be an integer or a \ |
---|
| 1116 | pair of integers specified as a tuple" |
---|
[513] | 1117 | |
---|
| 1118 | # setup fitter |
---|
| 1119 | f = fitter() |
---|
| 1120 | f._verbose(True) |
---|
| 1121 | f.set_function(poly=order) |
---|
| 1122 | |
---|
| 1123 | # setup line finder |
---|
| 1124 | fl=linefinder() |
---|
| 1125 | fl.set_options(threshold=threshold) |
---|
| 1126 | |
---|
| 1127 | if not insitu: |
---|
| 1128 | workscan=self.copy() |
---|
| 1129 | else: |
---|
| 1130 | workscan=self |
---|
| 1131 | |
---|
| 1132 | vb=workscan._vb |
---|
| 1133 | # remember the verbose parameter and selection |
---|
| 1134 | workscan._vb=False |
---|
| 1135 | sel=workscan.get_cursor() |
---|
| 1136 | rows=range(workscan.nrow()) |
---|
| 1137 | for i in range(workscan.nbeam()): |
---|
| 1138 | workscan.setbeam(i) |
---|
| 1139 | for j in range(workscan.nif()): |
---|
| 1140 | workscan.setif(j) |
---|
| 1141 | for k in range(workscan.npol()): |
---|
| 1142 | workscan.setpol(k) |
---|
| 1143 | if f._vb: |
---|
| 1144 | print "Processing:" |
---|
| 1145 | print 'Beam[%d], IF[%d], Pol[%d]' % (i,j,k) |
---|
| 1146 | for iRow in rows: |
---|
| 1147 | fl.set_scan(workscan,mask,edge) |
---|
| 1148 | fl.find_lines(iRow) |
---|
| 1149 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1150 | f.x=workscan._getabcissa(iRow) |
---|
| 1151 | f.y=workscan._getspectrum(iRow) |
---|
| 1152 | f.data=None |
---|
| 1153 | f.fit() |
---|
| 1154 | x=f.get_parameters() |
---|
| 1155 | workscan._setspectrum(f.fitter.getresidual(),iRow) |
---|
| 1156 | workscan.set_cursor(sel[0],sel[1],sel[2]) |
---|
| 1157 | workscan._vb = vb |
---|
| 1158 | if not insitu: |
---|
| 1159 | return workscan |
---|
| 1160 | |
---|
| 1161 | def rotate_linpolphase(self, angle, allaxes=None): |
---|
| 1162 | """ |
---|
| 1163 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1164 | This is always done in situ in the raw data. So if you call this |
---|
| 1165 | function more than once then each call rotates the phase further. |
---|
| 1166 | Parameters: |
---|
| 1167 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1168 | allaxes: If True apply to all spectra. Otherwise |
---|
| 1169 | apply only to the selected (beam/pol/if)spectra only. |
---|
| 1170 | The default is taken from .asaprc (True if none) |
---|
| 1171 | Examples: |
---|
| 1172 | scan.rotate_linpolphase(2.3) |
---|
| 1173 | """ |
---|
| 1174 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 1175 | varlist = vars() |
---|
| 1176 | from asap._asap import _rotate_linpolphase as _rotate |
---|
| 1177 | _rotate(self, angle, allaxes) |
---|
| 1178 | self._add_history("rotate_linpolphase", varlist) |
---|
| 1179 | return |
---|
| 1180 | |
---|
| 1181 | |
---|
| 1182 | def rotate_xyphase(self, angle, allaxes=None): |
---|
| 1183 | """ |
---|
| 1184 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1185 | in the data. So if you call this function more than once |
---|
| 1186 | then each call rotates the phase further. |
---|
| 1187 | Parameters: |
---|
| 1188 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1189 | allaxes: If True apply to all spectra. Otherwise |
---|
| 1190 | apply only to the selected (beam/pol/if)spectra only. |
---|
| 1191 | The default is taken from .asaprc (True if none) |
---|
| 1192 | Examples: |
---|
| 1193 | scan.rotate_xyphase(2.3) |
---|
| 1194 | """ |
---|
| 1195 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 1196 | varlist = vars() |
---|
| 1197 | from asap._asap import rotate_xyphase as _rotate_xyphase |
---|
| 1198 | _rotate_xyphase(self, angle, allaxes) |
---|
| 1199 | self._add_history("rotate_xyphase", varlist) |
---|
| 1200 | return |
---|
| 1201 | |
---|
| 1202 | |
---|
| 1203 | def add(self, offset, insitu=None, allaxes=None): |
---|
| 1204 | """ |
---|
| 1205 | Return a scan where all spectra have the offset added |
---|
| 1206 | Parameters: |
---|
| 1207 | offset: the offset |
---|
| 1208 | insitu: if False a new scantable is returned. |
---|
| 1209 | Otherwise, the scaling is done in-situ |
---|
| 1210 | The default is taken from .asaprc (False) |
---|
| 1211 | allaxes: if True apply to all spectra. Otherwise |
---|
| 1212 | apply only to the selected (beam/pol/if)spectra only |
---|
| 1213 | The default is taken from .asaprc (True if none) |
---|
| 1214 | """ |
---|
| 1215 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 1216 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1217 | varlist = vars() |
---|
| 1218 | if not insitu: |
---|
| 1219 | from asap._asap import add as _add |
---|
| 1220 | s = scantable(_add(self, offset, allaxes)) |
---|
| 1221 | s._add_history("add",varlist) |
---|
| 1222 | return s |
---|
| 1223 | else: |
---|
| 1224 | from asap._asap import add_insitu as _add |
---|
| 1225 | _add(self, offset, allaxes) |
---|
| 1226 | self._add_history("add",varlist) |
---|
| 1227 | return |
---|
| 1228 | |
---|
| 1229 | def scale(self, factor, insitu=None, allaxes=None, tsys=True): |
---|
| 1230 | """ |
---|
| 1231 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 1232 | Parameters: |
---|
| 1233 | factor: the scaling factor |
---|
| 1234 | insitu: if False a new scantable is returned. |
---|
| 1235 | Otherwise, the scaling is done in-situ |
---|
| 1236 | The default is taken from .asaprc (False) |
---|
| 1237 | allaxes: if True apply to all spectra. Otherwise |
---|
| 1238 | apply only to the selected (beam/pol/if)spectra only. |
---|
| 1239 | The default is taken from .asaprc (True if none) |
---|
| 1240 | tsys: if True (default) then apply the operation to Tsys |
---|
| 1241 | as well as the data |
---|
| 1242 | """ |
---|
| 1243 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 1244 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1245 | varlist = vars() |
---|
| 1246 | if not insitu: |
---|
| 1247 | from asap._asap import scale as _scale |
---|
| 1248 | s = scantable(_scale(self, factor, allaxes, tsys)) |
---|
| 1249 | s._add_history("scale",varlist) |
---|
| 1250 | return s |
---|
| 1251 | else: |
---|
| 1252 | from asap._asap import scale_insitu as _scale |
---|
| 1253 | _scale(self, factor, allaxes, tsys) |
---|
| 1254 | self._add_history("scale",varlist) |
---|
| 1255 | return |
---|
| 1256 | |
---|
| 1257 | |
---|
| 1258 | def quotient(self, other, isreference=True, preserve=True): |
---|
| 1259 | """ |
---|
[580] | 1260 | Return the quotient of a 'source' (on) scan and a 'reference' (off) |
---|
| 1261 | scan. |
---|
[513] | 1262 | The reference can have just one row, even if the signal has many. |
---|
| 1263 | Otherwise they must have the same number of rows. |
---|
| 1264 | The cursor of the output scan is set to 0 |
---|
| 1265 | Parameters: |
---|
[580] | 1266 | other: the 'other' scan |
---|
[513] | 1267 | isreference: if the 'other' scan is the reference (default) |
---|
| 1268 | or source |
---|
| 1269 | preserve: you can preserve (default) the continuum or |
---|
| 1270 | remove it. The equations used are |
---|
[580] | 1271 | preserve: Output = Toff * (on/off) - Toff |
---|
| 1272 | remove: Output = Tref * (on/off) - Ton |
---|
[513] | 1273 | Example: |
---|
| 1274 | # src is a scantable for an 'on' scan, ref for an 'off' scantable |
---|
| 1275 | q1 = src.quotient(ref) |
---|
| 1276 | q2 = ref.quotient(src, isreference=False) |
---|
| 1277 | # gives the same result |
---|
| 1278 | """ |
---|
| 1279 | from asap._asap import quotient as _quot |
---|
| 1280 | if isreference: |
---|
| 1281 | return scantable(_quot(self, other, preserve)) |
---|
| 1282 | else: |
---|
| 1283 | return scantable(_quot(other, self, preserve)) |
---|
| 1284 | |
---|
| 1285 | def __add__(self, other): |
---|
| 1286 | varlist = vars() |
---|
| 1287 | s = None |
---|
| 1288 | if isinstance(other, scantable): |
---|
| 1289 | from asap._asap import b_operate as _bop |
---|
| 1290 | s = scantable(_bop(self, other, 'add', True)) |
---|
| 1291 | elif isinstance(other, float): |
---|
| 1292 | from asap._asap import add as _add |
---|
| 1293 | s = scantable(_add(self, other, True)) |
---|
| 1294 | else: |
---|
| 1295 | print "Other input is not a scantable or float value" |
---|
| 1296 | return |
---|
| 1297 | s._add_history("operator +", varlist) |
---|
| 1298 | return s |
---|
| 1299 | |
---|
| 1300 | |
---|
| 1301 | def __sub__(self, other): |
---|
| 1302 | """ |
---|
| 1303 | implicit on all axes and on Tsys |
---|
| 1304 | """ |
---|
| 1305 | varlist = vars() |
---|
| 1306 | s = None |
---|
| 1307 | if isinstance(other, scantable): |
---|
| 1308 | from asap._asap import b_operate as _bop |
---|
| 1309 | s = scantable(_bop(self, other, 'sub', True)) |
---|
| 1310 | elif isinstance(other, float): |
---|
| 1311 | from asap._asap import add as _add |
---|
| 1312 | s = scantable(_add(self, -other, True)) |
---|
| 1313 | else: |
---|
| 1314 | print "Other input is not a scantable or float value" |
---|
| 1315 | return |
---|
| 1316 | s._add_history("operator -", varlist) |
---|
| 1317 | return s |
---|
| 1318 | |
---|
| 1319 | def __mul__(self, other): |
---|
| 1320 | """ |
---|
| 1321 | implicit on all axes and on Tsys |
---|
| 1322 | """ |
---|
| 1323 | varlist = vars() |
---|
| 1324 | s = None |
---|
| 1325 | if isinstance(other, scantable): |
---|
| 1326 | from asap._asap import b_operate as _bop |
---|
| 1327 | s = scantable(_bop(self, other, 'mul', True)) |
---|
| 1328 | elif isinstance(other, float): |
---|
| 1329 | if other == 0.0: |
---|
| 1330 | print "Multiplying by zero is not recommended." |
---|
| 1331 | return |
---|
| 1332 | from asap._asap import scale as _sca |
---|
| 1333 | s = scantable(_sca(self, other, True)) |
---|
| 1334 | else: |
---|
| 1335 | print "Other input is not a scantable or float value" |
---|
| 1336 | return |
---|
| 1337 | s._add_history("operator *", varlist) |
---|
| 1338 | return s |
---|
| 1339 | |
---|
| 1340 | |
---|
| 1341 | def __div__(self, other): |
---|
| 1342 | """ |
---|
| 1343 | implicit on all axes and on Tsys |
---|
| 1344 | """ |
---|
| 1345 | varlist = vars() |
---|
| 1346 | s = None |
---|
| 1347 | if isinstance(other, scantable): |
---|
| 1348 | from asap._asap import b_operate as _bop |
---|
| 1349 | s = scantable(_bop(self, other, 'div', True)) |
---|
| 1350 | elif isinstance(other, float): |
---|
| 1351 | if other == 0.0: |
---|
| 1352 | print "Dividing by zero is not recommended" |
---|
| 1353 | return |
---|
| 1354 | from asap._asap import scale as _sca |
---|
| 1355 | s = scantable(_sca(self, 1.0/other, True)) |
---|
| 1356 | else: |
---|
| 1357 | print "Other input is not a scantable or float value" |
---|
| 1358 | return |
---|
| 1359 | s._add_history("operator /", varlist) |
---|
| 1360 | return s |
---|
| 1361 | |
---|
[530] | 1362 | def get_fit(self, row=0): |
---|
| 1363 | """ |
---|
| 1364 | Print or return the stored fits for a row in the scantable |
---|
| 1365 | Parameters: |
---|
| 1366 | row: the row which the fit has been applied to. |
---|
| 1367 | """ |
---|
| 1368 | if row > self.nrow(): |
---|
| 1369 | return |
---|
| 1370 | from asap import asapfit |
---|
| 1371 | fit = asapfit(self._getfit(row)) |
---|
| 1372 | if self._vb: |
---|
| 1373 | print fit |
---|
| 1374 | return |
---|
| 1375 | else: |
---|
| 1376 | return fit.as_dict() |
---|
| 1377 | |
---|
[484] | 1378 | def _add_history(self, funcname, parameters): |
---|
| 1379 | # create date |
---|
| 1380 | sep = "##" |
---|
| 1381 | from datetime import datetime |
---|
| 1382 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 1383 | hist = dstr+sep |
---|
| 1384 | hist += funcname+sep#cdate+sep |
---|
| 1385 | if parameters.has_key('self'): del parameters['self'] |
---|
| 1386 | for k,v in parameters.iteritems(): |
---|
| 1387 | if type(v) is dict: |
---|
| 1388 | for k2,v2 in v.iteritems(): |
---|
| 1389 | hist += k2 |
---|
| 1390 | hist += "=" |
---|
| 1391 | if isinstance(v2,scantable): |
---|
| 1392 | hist += 'scantable' |
---|
| 1393 | elif k2 == 'mask': |
---|
[513] | 1394 | if isinstance(v2,list) or isinstance(v2,tuple): |
---|
| 1395 | hist += str(self._zip_mask(v2)) |
---|
| 1396 | else: |
---|
| 1397 | hist += str(v2) |
---|
[484] | 1398 | else: |
---|
[513] | 1399 | hist += str(v2) |
---|
[484] | 1400 | else: |
---|
| 1401 | hist += k |
---|
| 1402 | hist += "=" |
---|
| 1403 | if isinstance(v,scantable): |
---|
| 1404 | hist += 'scantable' |
---|
| 1405 | elif k == 'mask': |
---|
[513] | 1406 | if isinstance(v,list) or isinstance(v,tuple): |
---|
| 1407 | hist += str(self._zip_mask(v)) |
---|
| 1408 | else: |
---|
| 1409 | hist += str(v) |
---|
[484] | 1410 | else: |
---|
| 1411 | hist += str(v) |
---|
| 1412 | hist += sep |
---|
| 1413 | hist = hist[:-2] # remove trailing '##' |
---|
| 1414 | self._addhistory(hist) |
---|
| 1415 | |
---|
| 1416 | |
---|
| 1417 | def _zip_mask(self, mask): |
---|
| 1418 | mask = list(mask) |
---|
| 1419 | i = 0 |
---|
| 1420 | segments = [] |
---|
| 1421 | while mask[i:].count(1): |
---|
| 1422 | i += mask[i:].index(1) |
---|
| 1423 | if mask[i:].count(0): |
---|
| 1424 | j = i + mask[i:].index(0) |
---|
| 1425 | else: |
---|
| 1426 | j = len(mask) |
---|
| 1427 | segments.append([i,j]) |
---|
[513] | 1428 | i = j |
---|
[484] | 1429 | return segments |
---|
[623] | 1430 | def _get_ordinate_label(self): |
---|
| 1431 | fu = "("+self.get_fluxunit()+")" |
---|
| 1432 | import re |
---|
| 1433 | lbl = "Intensity" |
---|
| 1434 | if re.match(".K.",fu): |
---|
| 1435 | lbl = "Brightness Temperature "+ fu |
---|
| 1436 | elif re.match(".Jy.",fu): |
---|
| 1437 | lbl = "Flux density "+ fu |
---|
| 1438 | return lbl |
---|
| 1439 | |
---|