[102] | 1 | from asap._asap import sdtable |
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[226] | 2 | from asap import rcParams |
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[714] | 3 | from asap import print_log |
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[189] | 4 | from numarray import ones,zeros |
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[102] | 5 | import sys |
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| 6 | |
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| 7 | class scantable(sdtable): |
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| 8 | """ |
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| 9 | The ASAP container for scans |
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| 10 | """ |
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[710] | 11 | |
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[484] | 12 | def __init__(self, filename, average=None, unit=None): |
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[102] | 13 | """ |
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| 14 | Create a scantable from a saved one or make a reference |
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| 15 | Parameters: |
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[181] | 16 | filename: the name of an asap table on disk |
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| 17 | or |
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| 18 | the name of a rpfits/sdfits/ms file |
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| 19 | (integrations within scans are auto averaged |
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| 20 | and the whole file is read) |
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| 21 | or |
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| 22 | [advanced] a reference to an existing |
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[102] | 23 | scantable |
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[484] | 24 | average: average all integrations withinb a scan on read. |
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| 25 | The default (True) is taken from .asaprc. |
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| 26 | unit: brightness unit; must be consistent with K or Jy. |
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[340] | 27 | Over-rides the default selected by the reader |
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| 28 | (input rpfits/sdfits/ms) or replaces the value |
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| 29 | in existing scantables |
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[710] | 30 | """ |
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[489] | 31 | if average is None or type(average) is not bool: |
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[710] | 32 | average = rcParams['scantable.autoaverage'] |
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[489] | 33 | |
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[484] | 34 | varlist = vars() |
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[113] | 35 | self._p = None |
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[710] | 36 | from asap import asaplog |
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[181] | 37 | if isinstance(filename,sdtable): |
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[710] | 38 | sdtable.__init__(self, filename) |
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[340] | 39 | if unit is not None: |
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[710] | 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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[710] | 44 | s = "File '%s' not found." % (filename) |
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| 45 | if rcParams['verbose']: |
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| 46 | asaplog.push(s) |
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| 47 | print asaplog.pop().strip() |
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| 48 | return |
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| 49 | raise IOError(s) |
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[411] | 50 | filename = os.path.expandvars(filename) |
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| 51 | if os.path.isdir(filename): |
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[181] | 52 | # crude check if asap table |
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[411] | 53 | if os.path.exists(filename+'/table.info'): |
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[181] | 54 | sdtable.__init__(self, filename) |
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[340] | 55 | if unit is not None: |
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[710] | 56 | self.set_fluxunit(unit) |
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[181] | 57 | else: |
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[718] | 58 | msg = "The given file '%s'is not a valid asap table." % (filename) |
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| 59 | if rcParams['verbose']: |
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| 60 | print msg |
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| 61 | return |
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| 62 | else: |
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| 63 | raise IOError(msg) |
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[710] | 64 | else: |
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[181] | 65 | from asap._asap import sdreader |
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[340] | 66 | ifSel = -1 |
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| 67 | beamSel = -1 |
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[710] | 68 | r = sdreader() |
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| 69 | r._open(filename,ifSel,beamSel) |
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| 70 | asaplog.push('Importing data...') |
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[762] | 71 | print_log() |
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[411] | 72 | r._read([-1]) |
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| 73 | tbl = r._getdata() |
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[346] | 74 | if unit is not None: |
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| 75 | tbl.set_fluxunit(unit) |
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[489] | 76 | if average: |
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| 77 | from asap._asap import average as _av |
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[710] | 78 | asaplog.push('Auto averaging integrations...') |
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[762] | 79 | print_log() |
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[513] | 80 | tbl2 = _av((tbl,),(),True,'none') |
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[226] | 81 | sdtable.__init__(self,tbl2) |
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[513] | 82 | del tbl2 |
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[226] | 83 | else: |
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| 84 | sdtable.__init__(self,tbl) |
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[513] | 85 | del r,tbl |
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[484] | 86 | self._add_history("scantable", varlist) |
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[714] | 87 | print_log() |
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[102] | 88 | |
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[451] | 89 | def save(self, name=None, format=None, stokes=False, overwrite=False): |
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[116] | 90 | """ |
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[710] | 91 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, |
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[280] | 92 | Image FITS or MS2 format. |
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[116] | 93 | Parameters: |
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[196] | 94 | name: the name of the outputfile. For format="FITS" this |
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[489] | 95 | is the directory file name into which all the files |
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[497] | 96 | will be written (default is 'asap_FITS'). For format |
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| 97 | "ASCII" this is the root file name (data in 'name'.txt |
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| 98 | and header in 'name'_header.txt) |
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[116] | 99 | format: an optional file format. Default is ASAP. |
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[280] | 100 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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[194] | 101 | 'SDFITS' (save as SDFITS file) |
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[710] | 102 | 'FITS' (saves each row as a FITS Image) |
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[200] | 103 | 'ASCII' (saves as ascii text file) |
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[226] | 104 | 'MS2' (saves as an aips++ |
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| 105 | MeasurementSet V2) |
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[489] | 106 | stokes: Convert to Stokes parameters (only available |
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| 107 | currently with FITS and ASCII formats. |
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| 108 | Default is False. |
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[411] | 109 | overwrite: If the file should be overwritten if it exists. |
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[256] | 110 | The default False is to return with warning |
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[411] | 111 | without writing the output. USE WITH CARE. |
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[116] | 112 | Example: |
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| 113 | scan.save('myscan.asap') |
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| 114 | scan.save('myscan.sdfits','SDFITS') |
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| 115 | """ |
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[411] | 116 | from os import path |
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[226] | 117 | if format is None: format = rcParams['scantable.save'] |
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[256] | 118 | suffix = '.'+format.lower() |
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| 119 | if name is None or name =="": |
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| 120 | name = 'scantable'+suffix |
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[718] | 121 | from asap import asaplog |
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| 122 | msg = "No filename given. Using default name %s..." % name |
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| 123 | asaplog.push(msg) |
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[411] | 124 | name = path.expandvars(name) |
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[256] | 125 | if path.isfile(name) or path.isdir(name): |
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| 126 | if not overwrite: |
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[718] | 127 | msg = "File %s exists." % name |
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| 128 | if rcParams['verbose']: |
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| 129 | print msg |
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| 130 | return |
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| 131 | else: |
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| 132 | raise IOError(msg) |
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[451] | 133 | format2 = format.upper() |
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| 134 | if format2 == 'ASAP': |
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[116] | 135 | self._save(name) |
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| 136 | else: |
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| 137 | from asap._asap import sdwriter as _sw |
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[451] | 138 | w = _sw(format2) |
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[445] | 139 | w.write(self, name, stokes) |
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[718] | 140 | |
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| 141 | print_log() |
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[116] | 142 | return |
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| 143 | |
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[102] | 144 | def copy(self): |
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| 145 | """ |
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| 146 | Return a copy of this scantable. |
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| 147 | Parameters: |
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[113] | 148 | none |
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[102] | 149 | Example: |
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| 150 | copiedscan = scan.copy() |
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| 151 | """ |
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[113] | 152 | sd = scantable(sdtable._copy(self)) |
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| 153 | return sd |
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| 154 | |
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[102] | 155 | def get_scan(self, scanid=None): |
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| 156 | """ |
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| 157 | Return a specific scan (by scanno) or collection of scans (by |
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| 158 | source name) in a new scantable. |
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| 159 | Parameters: |
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[513] | 160 | scanid: a (list of) scanno or a source name, unix-style |
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| 161 | patterns are accepted for source name matching, e.g. |
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| 162 | '*_R' gets all 'ref scans |
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[102] | 163 | Example: |
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[513] | 164 | # get all scans containing the source '323p459' |
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| 165 | newscan = scan.get_scan('323p459') |
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| 166 | # get all 'off' scans |
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| 167 | refscans = scan.get_scan('*_R') |
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| 168 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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| 169 | newscan = scan.get_scan([0,2,7,10]) |
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[102] | 170 | """ |
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| 171 | if scanid is None: |
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[718] | 172 | if rcParams['verbose']: |
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| 173 | print "Please specify a scan no or name to retrieve from the scantable" |
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| 174 | return |
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| 175 | else: |
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| 176 | raise RuntimeError("No scan given") |
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| 177 | |
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[102] | 178 | try: |
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| 179 | if type(scanid) is str: |
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[113] | 180 | s = sdtable._getsource(self,scanid) |
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[102] | 181 | return scantable(s) |
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| 182 | elif type(scanid) is int: |
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[381] | 183 | s = sdtable._getscan(self,[scanid]) |
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| 184 | return scantable(s) |
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| 185 | elif type(scanid) is list: |
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[113] | 186 | s = sdtable._getscan(self,scanid) |
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[102] | 187 | return scantable(s) |
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[381] | 188 | else: |
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[718] | 189 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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| 190 | if rcParams['verbose']: |
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| 191 | print msg |
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| 192 | else: |
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| 193 | raise TypeError(msg) |
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[102] | 194 | except RuntimeError: |
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[718] | 195 | if rcParams['verbose']: print "Couldn't find any match." |
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| 196 | else: raise |
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[102] | 197 | |
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| 198 | def __str__(self): |
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[381] | 199 | return sdtable._summary(self,True) |
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[102] | 200 | |
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[381] | 201 | def summary(self,filename=None, verbose=None): |
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[102] | 202 | """ |
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| 203 | Print a summary of the contents of this scantable. |
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| 204 | Parameters: |
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| 205 | filename: the name of a file to write the putput to |
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| 206 | Default - no file output |
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[381] | 207 | verbose: print extra info such as the frequency table |
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| 208 | The default (False) is taken from .asaprc |
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[102] | 209 | """ |
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[381] | 210 | info = sdtable._summary(self, verbose) |
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| 211 | if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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[102] | 212 | if filename is not None: |
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[256] | 213 | if filename is "": |
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| 214 | filename = 'scantable_summary.txt' |
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[415] | 215 | from os.path import expandvars, isdir |
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[411] | 216 | filename = expandvars(filename) |
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[415] | 217 | if not isdir(filename): |
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[413] | 218 | data = open(filename, 'w') |
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| 219 | data.write(info) |
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| 220 | data.close() |
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| 221 | else: |
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[718] | 222 | msg = "Illegal file name '%s'." % (filename) |
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| 223 | if rcParams['verbose']: |
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| 224 | print msg |
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| 225 | else: |
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| 226 | raise IOError(msg) |
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| 227 | if rcParams['verbose']: |
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[794] | 228 | try: |
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| 229 | from IPython.genutils import page as pager |
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| 230 | except ImportError: |
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| 231 | from pydoc import pager |
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| 232 | pager(info) |
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[718] | 233 | else: |
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| 234 | return info |
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[710] | 235 | |
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[553] | 236 | def set_cursor(self, beam=0, IF=0, pol=0): |
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[102] | 237 | """ |
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| 238 | Set the spectrum for individual operations. |
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| 239 | Parameters: |
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[553] | 240 | beam, IF, pol: a number |
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[102] | 241 | Example: |
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[256] | 242 | scan.set_cursor(0,0,1) |
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[135] | 243 | pol1sig = scan.stats(all=False) # returns std dev for beam=0 |
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[181] | 244 | # if=0, pol=1 |
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[102] | 245 | """ |
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[484] | 246 | varlist = vars() |
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[553] | 247 | self.setbeam(beam) |
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| 248 | self.setpol(pol) |
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| 249 | self.setif(IF) |
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[484] | 250 | self._add_history("set_cursor",varlist) |
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[102] | 251 | return |
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| 252 | |
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[256] | 253 | def get_cursor(self): |
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[113] | 254 | """ |
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| 255 | Return/print a the current 'cursor' into the Beam/IF/Pol cube. |
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| 256 | Parameters: |
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| 257 | none |
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| 258 | Returns: |
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| 259 | a list of values (currentBeam,currentIF,currentPol) |
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| 260 | Example: |
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| 261 | none |
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| 262 | """ |
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[102] | 263 | i = self.getbeam() |
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| 264 | j = self.getif() |
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| 265 | k = self.getpol() |
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[721] | 266 | from asap import asaplog |
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| 267 | out = "--------------------------------------------------\n" |
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| 268 | out += " Cursor position\n" |
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| 269 | out += "--------------------------------------------------\n" |
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| 270 | out += 'Beam=%d IF=%d Pol=%d ' % (i,j,k) |
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| 271 | asaplog.push(out) |
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| 272 | print_log() |
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| 273 | return i,j,k |
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[102] | 274 | |
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[436] | 275 | def stats(self, stat='stddev', mask=None, allaxes=None): |
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[102] | 276 | """ |
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[135] | 277 | Determine the specified statistic of the current beam/if/pol |
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[102] | 278 | Takes a 'mask' as an optional parameter to specify which |
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| 279 | channels should be excluded. |
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| 280 | Parameters: |
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[135] | 281 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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| 282 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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| 283 | mask: an optional mask specifying where the statistic |
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[102] | 284 | should be determined. |
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[436] | 285 | allaxes: if True apply to all spectra. Otherwise |
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| 286 | apply only to the selected (beam/pol/if)spectra only. |
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| 287 | The default is taken from .asaprc (True if none) |
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[102] | 288 | Example: |
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[113] | 289 | scan.set_unit('channel') |
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[102] | 290 | msk = scan.create_mask([100,200],[500,600]) |
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[135] | 291 | scan.stats(stat='mean', mask=m) |
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[102] | 292 | """ |
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[436] | 293 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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[135] | 294 | from asap._asap import stats as _stats |
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[256] | 295 | from numarray import array,zeros,Float |
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[102] | 296 | if mask == None: |
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| 297 | mask = ones(self.nchan()) |
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[256] | 298 | axes = ['Beam','IF','Pol','Time'] |
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| 299 | |
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[436] | 300 | beamSel,IFSel,polSel = (self.getbeam(),self.getif(),self.getpol()) |
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| 301 | if allaxes: |
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[256] | 302 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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| 303 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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| 304 | arr = array(zeros(n),shape=shp,type=Float) |
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| 305 | |
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| 306 | for i in range(self.nbeam()): |
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| 307 | self.setbeam(i) |
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| 308 | for j in range(self.nif()): |
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| 309 | self.setif(j) |
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| 310 | for k in range(self.npol()): |
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| 311 | self.setpol(k) |
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| 312 | arr[i,j,k,:] = _stats(self,mask,stat,-1) |
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| 313 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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| 314 | tm = [self._gettime(val) for val in range(self.nrow())] |
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[718] | 315 | if rcParams['verbose']: |
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[256] | 316 | self._print_values(retval,stat,tm) |
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[436] | 317 | self.setbeam(beamSel) |
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| 318 | self.setif(IFSel) |
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| 319 | self.setpol(polSel) |
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[256] | 320 | return retval |
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[102] | 321 | |
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| 322 | else: |
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[241] | 323 | statval = _stats(self,mask,stat,-1) |
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[181] | 324 | out = '' |
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| 325 | for l in range(self.nrow()): |
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| 326 | tm = self._gettime(l) |
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| 327 | out += 'Time[%s]:\n' % (tm) |
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[436] | 328 | if self.nbeam() > 1: out += ' Beam[%d] ' % (beamSel) |
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| 329 | if self.nif() > 1: out += ' IF[%d] ' % (IFSel) |
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| 330 | if self.npol() > 1: out += ' Pol[%d] ' % (polSel) |
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[181] | 331 | out += '= %3.3f\n' % (statval[l]) |
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| 332 | out += "--------------------------------------------------\n" |
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[226] | 333 | |
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[718] | 334 | if rcParams['verbose']: |
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[181] | 335 | print "--------------------------------------------------" |
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| 336 | print " ",stat |
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| 337 | print "--------------------------------------------------" |
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| 338 | print out |
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[256] | 339 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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| 340 | return retval |
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[102] | 341 | |
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[436] | 342 | def stddev(self,mask=None, allaxes=None): |
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[135] | 343 | """ |
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| 344 | Determine the standard deviation of the current beam/if/pol |
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| 345 | Takes a 'mask' as an optional parameter to specify which |
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| 346 | channels should be excluded. |
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| 347 | Parameters: |
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| 348 | mask: an optional mask specifying where the standard |
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| 349 | deviation should be determined. |
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[436] | 350 | allaxes: optional flag to show all or a cursor selected |
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[226] | 351 | spectrum of Beam/IF/Pol. Default is all or taken |
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| 352 | from .asaprc |
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[135] | 353 | |
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| 354 | Example: |
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| 355 | scan.set_unit('channel') |
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| 356 | msk = scan.create_mask([100,200],[500,600]) |
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| 357 | scan.stddev(mask=m) |
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| 358 | """ |
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[436] | 359 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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| 360 | return self.stats(stat='stddev',mask=mask, allaxes=allaxes); |
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[135] | 361 | |
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[436] | 362 | def get_tsys(self, allaxes=None): |
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[113] | 363 | """ |
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| 364 | Return the System temperatures. |
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| 365 | Parameters: |
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[436] | 366 | allaxes: if True apply to all spectra. Otherwise |
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| 367 | apply only to the selected (beam/pol/if)spectra only. |
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| 368 | The default is taken from .asaprc (True if none) |
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[113] | 369 | Returns: |
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| 370 | a list of Tsys values. |
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| 371 | """ |
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[436] | 372 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
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[256] | 373 | from numarray import array,zeros,Float |
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| 374 | axes = ['Beam','IF','Pol','Time'] |
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| 375 | |
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[436] | 376 | if allaxes: |
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[256] | 377 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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| 378 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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| 379 | arr = array(zeros(n),shape=shp,type=Float) |
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| 380 | |
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| 381 | for i in range(self.nbeam()): |
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| 382 | self.setbeam(i) |
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| 383 | for j in range(self.nif()): |
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| 384 | self.setif(j) |
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| 385 | for k in range(self.npol()): |
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| 386 | self.setpol(k) |
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| 387 | arr[i,j,k,:] = self._gettsys() |
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| 388 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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| 389 | tm = [self._gettime(val) for val in range(self.nrow())] |
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[718] | 390 | if rcParams['verbose']: |
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[256] | 391 | self._print_values(retval,'Tsys',tm) |
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| 392 | return retval |
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| 393 | |
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[102] | 394 | else: |
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[256] | 395 | i,j,k = (self.getbeam(),self.getif(),self.getpol()) |
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| 396 | statval = self._gettsys() |
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[181] | 397 | out = '' |
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| 398 | for l in range(self.nrow()): |
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| 399 | tm = self._gettime(l) |
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| 400 | out += 'Time[%s]:\n' % (tm) |
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| 401 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i) |
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| 402 | if self.nif() > 1: out += ' IF[%d] ' % (j) |
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| 403 | if self.npol() > 1: out += ' Pol[%d] ' % (k) |
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[256] | 404 | out += '= %3.3f\n' % (statval[l]) |
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| 405 | out += "--------------------------------------------------\n" |
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| 406 | |
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[718] | 407 | if rcParams['verbose']: |
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[181] | 408 | print "--------------------------------------------------" |
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[256] | 409 | print " TSys" |
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[181] | 410 | print "--------------------------------------------------" |
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| 411 | print out |
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[256] | 412 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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| 413 | return retval |
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[710] | 414 | |
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[407] | 415 | def get_time(self, row=-1): |
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[113] | 416 | """ |
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| 417 | Get a list of time stamps for the observations. |
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[181] | 418 | Return a string for each integration in the scantable. |
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[113] | 419 | Parameters: |
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[407] | 420 | row: row no of integration. Default -1 return all rows |
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[113] | 421 | Example: |
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| 422 | none |
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| 423 | """ |
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| 424 | out = [] |
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[407] | 425 | if row == -1: |
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| 426 | for i in range(self.nrow()): |
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| 427 | out.append(self._gettime(i)) |
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| 428 | return out |
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| 429 | else: |
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| 430 | if row < self.nrow(): |
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| 431 | return self._gettime(row) |
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[102] | 432 | |
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[714] | 433 | def get_sourcename(self, row=-1): |
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| 434 | """ |
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[794] | 435 | Get a list source names for the observations. |
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[714] | 436 | Return a string for each integration in the scantable. |
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| 437 | Parameters: |
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| 438 | row: row no of integration. Default -1 return all rows |
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| 439 | Example: |
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| 440 | none |
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| 441 | """ |
---|
| 442 | out = [] |
---|
| 443 | if row == -1: |
---|
| 444 | return [self._getsourcename(i) for i in range(self.nrow())] |
---|
| 445 | else: |
---|
| 446 | if 0 <= row < self.nrow(): |
---|
| 447 | return self._getsourcename(row) |
---|
| 448 | |
---|
[794] | 449 | def get_elevation(self, row=-1): |
---|
| 450 | """ |
---|
| 451 | Get a list of elevations for the observations. |
---|
| 452 | Return a float for each integration in the scantable. |
---|
| 453 | Parameters: |
---|
| 454 | row: row no of integration. Default -1 return all rows |
---|
| 455 | Example: |
---|
| 456 | none |
---|
| 457 | """ |
---|
| 458 | out = [] |
---|
| 459 | if row == -1: |
---|
| 460 | return [self._getelevation(i) for i in range(self.nrow())] |
---|
| 461 | else: |
---|
| 462 | if 0 <= row < self.nrow(): |
---|
| 463 | return self._getelevation(row) |
---|
| 464 | |
---|
| 465 | def get_azimuth(self, row=-1): |
---|
| 466 | """ |
---|
| 467 | Get a list of azimuths for the observations. |
---|
| 468 | Return a float for each integration in the scantable. |
---|
| 469 | Parameters: |
---|
| 470 | row: row no of integration. Default -1 return all rows |
---|
| 471 | Example: |
---|
| 472 | none |
---|
| 473 | """ |
---|
| 474 | out = [] |
---|
| 475 | if row == -1: |
---|
| 476 | return [self._getazimuth(i) for i in range(self.nrow())] |
---|
| 477 | else: |
---|
| 478 | if 0 <= row < self.nrow(): |
---|
| 479 | return self._getazimuth(row) |
---|
| 480 | |
---|
| 481 | def get_parangle(self, row=-1): |
---|
| 482 | """ |
---|
| 483 | Get a list of parallactic angles for the observations. |
---|
| 484 | Return a float for each integration in the scantable. |
---|
| 485 | Parameters: |
---|
| 486 | row: row no of integration. Default -1 return all rows |
---|
| 487 | Example: |
---|
| 488 | none |
---|
| 489 | """ |
---|
| 490 | out = [] |
---|
| 491 | if row == -1: |
---|
| 492 | return [self._getparangle(i) for i in range(self.nrow())] |
---|
| 493 | else: |
---|
| 494 | if 0 <= row < self.nrow(): |
---|
| 495 | return self._getparangle(row) |
---|
| 496 | |
---|
[102] | 497 | def set_unit(self, unit='channel'): |
---|
| 498 | """ |
---|
| 499 | Set the unit for all following operations on this scantable |
---|
| 500 | Parameters: |
---|
| 501 | unit: optional unit, default is 'channel' |
---|
[113] | 502 | one of '*Hz','km/s','channel', '' |
---|
[102] | 503 | """ |
---|
[484] | 504 | varlist = vars() |
---|
[113] | 505 | if unit in ['','pixel', 'channel']: |
---|
| 506 | unit = '' |
---|
| 507 | inf = list(self._getcoordinfo()) |
---|
| 508 | inf[0] = unit |
---|
| 509 | self._setcoordinfo(inf) |
---|
| 510 | if self._p: self.plot() |
---|
[484] | 511 | self._add_history("set_unit",varlist) |
---|
[113] | 512 | |
---|
[484] | 513 | def set_instrument(self, instr): |
---|
[358] | 514 | """ |
---|
| 515 | Set the instrument for subsequent processing |
---|
| 516 | Parameters: |
---|
[710] | 517 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 518 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 519 | """ |
---|
| 520 | self._setInstrument(instr) |
---|
[484] | 521 | self._add_history("set_instument",vars()) |
---|
[718] | 522 | print_log() |
---|
[358] | 523 | |
---|
[276] | 524 | def set_doppler(self, doppler='RADIO'): |
---|
| 525 | """ |
---|
| 526 | Set the doppler for all following operations on this scantable. |
---|
| 527 | Parameters: |
---|
| 528 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 529 | """ |
---|
[484] | 530 | varlist = vars() |
---|
[276] | 531 | inf = list(self._getcoordinfo()) |
---|
| 532 | inf[2] = doppler |
---|
| 533 | self._setcoordinfo(inf) |
---|
| 534 | if self._p: self.plot() |
---|
[484] | 535 | self._add_history("set_doppler",vars()) |
---|
[718] | 536 | print_log() |
---|
[710] | 537 | |
---|
[226] | 538 | def set_freqframe(self, frame=None): |
---|
[113] | 539 | """ |
---|
| 540 | Set the frame type of the Spectral Axis. |
---|
| 541 | Parameters: |
---|
[591] | 542 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
| 543 | 'REST','TOPO','LSRD','LSRK','BARY', |
---|
| 544 | 'GEO','GALACTO','LGROUP','CMB' |
---|
[113] | 545 | Examples: |
---|
| 546 | scan.set_freqframe('BARY') |
---|
| 547 | """ |
---|
[484] | 548 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
| 549 | varlist = vars() |
---|
[113] | 550 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
---|
| 551 | 'GEO','GALACTO','LGROUP','CMB'] |
---|
[591] | 552 | |
---|
[113] | 553 | if frame in valid: |
---|
| 554 | inf = list(self._getcoordinfo()) |
---|
| 555 | inf[1] = frame |
---|
| 556 | self._setcoordinfo(inf) |
---|
[484] | 557 | self._add_history("set_freqframe",varlist) |
---|
[102] | 558 | else: |
---|
[718] | 559 | msg = "Please specify a valid freq type. Valid types are:\n",valid |
---|
| 560 | if rcParams['verbose']: |
---|
| 561 | print msg |
---|
| 562 | else: |
---|
| 563 | raise TypeError(msg) |
---|
| 564 | print_log() |
---|
[710] | 565 | |
---|
[113] | 566 | def get_unit(self): |
---|
| 567 | """ |
---|
| 568 | Get the default unit set in this scantable |
---|
| 569 | Parameters: |
---|
| 570 | Returns: |
---|
| 571 | A unit string |
---|
| 572 | """ |
---|
| 573 | inf = self._getcoordinfo() |
---|
| 574 | unit = inf[0] |
---|
| 575 | if unit == '': unit = 'channel' |
---|
| 576 | return unit |
---|
[102] | 577 | |
---|
[158] | 578 | def get_abcissa(self, rowno=0): |
---|
[102] | 579 | """ |
---|
[158] | 580 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 581 | selected Beam/IF/Pol |
---|
| 582 | Parameters: |
---|
[226] | 583 | rowno: an optional row number in the scantable. Default is the |
---|
| 584 | first row, i.e. rowno=0 |
---|
[113] | 585 | Returns: |
---|
[407] | 586 | The abcissa values and it's format string (as a dictionary) |
---|
[113] | 587 | """ |
---|
[256] | 588 | abc = self._getabcissa(rowno) |
---|
[710] | 589 | lbl = self._getabcissalabel(rowno) |
---|
[718] | 590 | print_log() |
---|
[158] | 591 | return abc, lbl |
---|
[113] | 592 | |
---|
| 593 | def create_mask(self, *args, **kwargs): |
---|
| 594 | """ |
---|
[102] | 595 | Compute and return a mask based on [min,max] windows. |
---|
[189] | 596 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 597 | applied. |
---|
[102] | 598 | Parameters: |
---|
| 599 | [min,max],[min2,max2],... |
---|
| 600 | Pairs of start/end points specifying the regions |
---|
| 601 | to be masked |
---|
[189] | 602 | invert: optional argument. If specified as True, |
---|
| 603 | return an inverted mask, i.e. the regions |
---|
| 604 | specified are EXCLUDED |
---|
[513] | 605 | row: create the mask using the specified row for |
---|
| 606 | unit conversions, default is row=0 |
---|
| 607 | only necessary if frequency varies over rows. |
---|
[102] | 608 | Example: |
---|
[113] | 609 | scan.set_unit('channel') |
---|
| 610 | |
---|
| 611 | a) |
---|
[102] | 612 | msk = scan.set_mask([400,500],[800,900]) |
---|
[189] | 613 | # masks everything outside 400 and 500 |
---|
[113] | 614 | # and 800 and 900 in the unit 'channel' |
---|
| 615 | |
---|
| 616 | b) |
---|
| 617 | msk = scan.set_mask([400,500],[800,900], invert=True) |
---|
[189] | 618 | # masks the regions between 400 and 500 |
---|
[113] | 619 | # and 800 and 900 in the unit 'channel' |
---|
[710] | 620 | |
---|
[102] | 621 | """ |
---|
[513] | 622 | row = 0 |
---|
| 623 | if kwargs.has_key("row"): |
---|
| 624 | row = kwargs.get("row") |
---|
| 625 | data = self._getabcissa(row) |
---|
[113] | 626 | u = self._getcoordinfo()[0] |
---|
[718] | 627 | if rcParams['verbose']: |
---|
[113] | 628 | if u == "": u = "channel" |
---|
[718] | 629 | from asap import asaplog |
---|
| 630 | msg = "The current mask window unit is %s" % u |
---|
| 631 | asaplog.push(msg) |
---|
[102] | 632 | n = self.nchan() |
---|
[189] | 633 | msk = zeros(n) |
---|
[710] | 634 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 635 | |
---|
| 636 | ws = (isinstance(args[-1][-1],int) or isinstance(args[-1][-1],float)) and args or args[0] |
---|
| 637 | for window in ws: |
---|
[102] | 638 | if (len(window) != 2 or window[0] > window[1] ): |
---|
[718] | 639 | raise TypeError("A window needs to be defined as [min,max]") |
---|
[102] | 640 | for i in range(n): |
---|
[113] | 641 | if data[i] >= window[0] and data[i] < window[1]: |
---|
[189] | 642 | msk[i] = 1 |
---|
[113] | 643 | if kwargs.has_key('invert'): |
---|
| 644 | if kwargs.get('invert'): |
---|
| 645 | from numarray import logical_not |
---|
[710] | 646 | msk = logical_not(msk) |
---|
[718] | 647 | print_log() |
---|
[102] | 648 | return msk |
---|
[710] | 649 | |
---|
[256] | 650 | def get_restfreqs(self): |
---|
| 651 | """ |
---|
| 652 | Get the restfrequency(s) stored in this scantable. |
---|
| 653 | The return value(s) are always of unit 'Hz' |
---|
| 654 | Parameters: |
---|
| 655 | none |
---|
| 656 | Returns: |
---|
| 657 | a list of doubles |
---|
| 658 | """ |
---|
| 659 | return list(self._getrestfreqs()) |
---|
[102] | 660 | |
---|
[402] | 661 | def lines(self): |
---|
[391] | 662 | """ |
---|
[402] | 663 | Print the list of known spectral lines |
---|
| 664 | """ |
---|
[714] | 665 | l = sdtable._lines(self) |
---|
| 666 | if rcParams['verbose']: |
---|
| 667 | print l |
---|
| 668 | else: |
---|
| 669 | return l |
---|
[402] | 670 | |
---|
[484] | 671 | def set_restfreqs(self, freqs=None, unit='Hz', lines=None, source=None, |
---|
| 672 | theif=None): |
---|
[402] | 673 | """ |
---|
[393] | 674 | Select the restfrequency for the specified source and IF OR |
---|
| 675 | replace for all IFs. If the 'freqs' argument holds a scalar, |
---|
| 676 | then that rest frequency will be applied to the selected |
---|
| 677 | data (and added to the list of available rest frequencies). |
---|
| 678 | In this way, you can set a rest frequency for each |
---|
| 679 | source and IF combination. If the 'freqs' argument holds |
---|
| 680 | a vector, then it MUST be of length the number of IFs |
---|
| 681 | (and the available restfrequencies will be replaced by |
---|
[710] | 682 | this vector). In this case, *all* data ('source' and |
---|
| 683 | 'theif' are ignored) have the restfrequency set per IF according |
---|
| 684 | to the corresponding value you give in the 'freqs' vector. |
---|
| 685 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[393] | 686 | IF 1 gets restfreq 2e9. |
---|
[402] | 687 | |
---|
| 688 | You can also specify the frequencies via known line names |
---|
| 689 | in the argument 'lines'. Use 'freqs' or 'lines'. 'freqs' |
---|
| 690 | takes precedence. See the list of known names via function |
---|
| 691 | scantable.lines() |
---|
[391] | 692 | Parameters: |
---|
[402] | 693 | freqs: list of rest frequencies |
---|
[393] | 694 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 695 | lines: list of known spectral lines names (alternative to freqs). |
---|
| 696 | See possible list via scantable.lines() |
---|
[391] | 697 | source: Source name (blank means all) |
---|
| 698 | theif: IF (-1 means all) |
---|
| 699 | Example: |
---|
[393] | 700 | scan.set_restfreqs(freqs=1.4e9, source='NGC253', theif=2) |
---|
| 701 | scan.set_restfreqs(freqs=[1.4e9,1.67e9]) |
---|
[391] | 702 | """ |
---|
[484] | 703 | varlist = vars() |
---|
[391] | 704 | if source is None: |
---|
| 705 | source = "" |
---|
| 706 | if theif is None: |
---|
| 707 | theif = -1 |
---|
[393] | 708 | t = type(freqs) |
---|
| 709 | if t is int or t is float: |
---|
| 710 | freqs = [freqs] |
---|
[402] | 711 | if freqs is None: |
---|
| 712 | freqs = [] |
---|
| 713 | t = type(lines) |
---|
| 714 | if t is str: |
---|
| 715 | lines = [lines] |
---|
| 716 | if lines is None: |
---|
| 717 | lines = [] |
---|
| 718 | sdtable._setrestfreqs(self, freqs, unit, lines, source, theif) |
---|
[484] | 719 | self._add_history("set_restfreqs", varlist) |
---|
[391] | 720 | |
---|
| 721 | |
---|
[710] | 722 | |
---|
[102] | 723 | def flag_spectrum(self, thebeam, theif, thepol): |
---|
| 724 | """ |
---|
| 725 | This flags a selected spectrum in the scan 'for good'. |
---|
| 726 | USE WITH CARE - not reversible. |
---|
| 727 | Use masks for non-permanent exclusion of channels. |
---|
| 728 | Parameters: |
---|
| 729 | thebeam,theif,thepol: all have to be explicitly |
---|
| 730 | specified |
---|
| 731 | Example: |
---|
| 732 | scan.flag_spectrum(0,0,1) |
---|
| 733 | flags the spectrum for Beam=0, IF=0, Pol=1 |
---|
| 734 | """ |
---|
[407] | 735 | if (thebeam < self.nbeam() and |
---|
| 736 | theif < self.nif() and |
---|
| 737 | thepol < self.npol()): |
---|
| 738 | sdtable.setbeam(self, thebeam) |
---|
| 739 | sdtable.setif(self, theif) |
---|
| 740 | sdtable.setpol(self, thepol) |
---|
| 741 | sdtable._flag(self) |
---|
[484] | 742 | self._add_history("flag_spectrum", vars()) |
---|
[102] | 743 | else: |
---|
| 744 | print "Please specify a valid (Beam/IF/Pol)" |
---|
| 745 | return |
---|
[113] | 746 | |
---|
[256] | 747 | def _print_values(self, dat, label='', timestamps=[]): |
---|
| 748 | d = dat['data'] |
---|
| 749 | a = dat['axes'] |
---|
| 750 | shp = d.getshape() |
---|
| 751 | out = '' |
---|
| 752 | for i in range(shp[3]): |
---|
| 753 | out += '%s [%s]:\n' % (a[3],timestamps[i]) |
---|
| 754 | t = d[:,:,:,i] |
---|
| 755 | for j in range(shp[0]): |
---|
| 756 | if shp[0] > 1: out += ' %s[%d] ' % (a[0],j) |
---|
| 757 | for k in range(shp[1]): |
---|
| 758 | if shp[1] > 1: out += ' %s[%d] ' % (a[1],k) |
---|
| 759 | for l in range(shp[2]): |
---|
| 760 | if shp[2] > 1: out += ' %s[%d] ' % (a[2],l) |
---|
| 761 | out += '= %3.3f\n' % (t[j,k,l]) |
---|
[484] | 762 | out += "-"*80 |
---|
| 763 | out += "\n" |
---|
| 764 | print "-"*80 |
---|
[256] | 765 | print " ", label |
---|
[484] | 766 | print "-"*80 |
---|
[710] | 767 | print out |
---|
[484] | 768 | |
---|
| 769 | def history(self): |
---|
| 770 | hist = list(self._gethistory()) |
---|
[794] | 771 | out = "-"*80 |
---|
[484] | 772 | for h in hist: |
---|
[489] | 773 | if h.startswith("---"): |
---|
[794] | 774 | out += "\n"+h |
---|
[489] | 775 | else: |
---|
| 776 | items = h.split("##") |
---|
| 777 | date = items[0] |
---|
| 778 | func = items[1] |
---|
| 779 | items = items[2:] |
---|
[794] | 780 | out += "\n"+date+"\n" |
---|
| 781 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 782 | for i in items: |
---|
| 783 | s = i.split("=") |
---|
[794] | 784 | out += "\n %s = %s" % (s[0],s[1]) |
---|
| 785 | out += "\n"+"-"*80 |
---|
| 786 | try: |
---|
| 787 | from IPython.genutils import page as pager |
---|
| 788 | except ImportError: |
---|
| 789 | from pydoc import pager |
---|
| 790 | pager(out) |
---|
[484] | 791 | return |
---|
| 792 | |
---|
[513] | 793 | # |
---|
| 794 | # Maths business |
---|
| 795 | # |
---|
| 796 | |
---|
[558] | 797 | def average_time(self, mask=None, scanav=False, weight='tint'): |
---|
[513] | 798 | """ |
---|
| 799 | Return the (time) average of a scan, or apply it 'insitu'. |
---|
| 800 | Note: |
---|
| 801 | in channels only |
---|
| 802 | The cursor of the output scan is set to 0. |
---|
| 803 | Parameters: |
---|
| 804 | one scan or comma separated scans |
---|
| 805 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 806 | weighting) |
---|
[558] | 807 | scanav: True averages each scan separately |
---|
| 808 | False (default) averages all scans together, |
---|
[524] | 809 | weight: Weighting scheme. 'none', 'var' (1/var(spec) |
---|
[535] | 810 | weighted), 'tsys' (1/Tsys**2 weighted), 'tint' |
---|
| 811 | (integration time weighted) or 'tintsys' (Tint/Tsys**2). |
---|
| 812 | The default is 'tint' |
---|
[513] | 813 | Example: |
---|
| 814 | # time average the scantable without using a mask |
---|
[710] | 815 | newscan = scan.average_time() |
---|
[513] | 816 | """ |
---|
| 817 | varlist = vars() |
---|
[524] | 818 | if weight is None: weight = 'tint' |
---|
[513] | 819 | if mask is None: mask = () |
---|
[710] | 820 | from asap._asap import average as _av |
---|
[513] | 821 | s = scantable(_av((self,), mask, scanav, weight)) |
---|
| 822 | s._add_history("average_time",varlist) |
---|
[718] | 823 | print_log() |
---|
[513] | 824 | return s |
---|
[710] | 825 | |
---|
[513] | 826 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None, |
---|
| 827 | allaxes=None): |
---|
| 828 | """ |
---|
| 829 | Return a scan where all spectra are converted to either |
---|
| 830 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 831 | By default the function tries to look the values up internally. |
---|
| 832 | If it can't find them (or if you want to over-ride), you must |
---|
| 833 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 834 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 835 | Parameters: |
---|
| 836 | jyperk: the Jy / K conversion factor |
---|
| 837 | eta: the aperture efficiency |
---|
| 838 | d: the geomtric diameter (metres) |
---|
| 839 | insitu: if False a new scantable is returned. |
---|
| 840 | Otherwise, the scaling is done in-situ |
---|
| 841 | The default is taken from .asaprc (False) |
---|
| 842 | allaxes: if True apply to all spectra. Otherwise |
---|
| 843 | apply only to the selected (beam/pol/if)spectra only |
---|
| 844 | The default is taken from .asaprc (True if none) |
---|
| 845 | """ |
---|
| 846 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 847 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 848 | varlist = vars() |
---|
| 849 | if jyperk is None: jyperk = -1.0 |
---|
| 850 | if d is None: d = -1.0 |
---|
| 851 | if eta is None: eta = -1.0 |
---|
| 852 | if not insitu: |
---|
| 853 | from asap._asap import convertflux as _convert |
---|
| 854 | s = scantable(_convert(self, d, eta, jyperk, allaxes)) |
---|
| 855 | s._add_history("convert_flux", varlist) |
---|
[718] | 856 | print_log() |
---|
[513] | 857 | return s |
---|
| 858 | else: |
---|
| 859 | from asap._asap import convertflux_insitu as _convert |
---|
| 860 | _convert(self, d, eta, jyperk, allaxes) |
---|
| 861 | self._add_history("convert_flux", varlist) |
---|
[718] | 862 | print_log() |
---|
[513] | 863 | return |
---|
| 864 | |
---|
| 865 | def gain_el(self, poly=None, filename="", method="linear", |
---|
| 866 | insitu=None, allaxes=None): |
---|
| 867 | """ |
---|
| 868 | Return a scan after applying a gain-elevation correction. |
---|
| 869 | The correction can be made via either a polynomial or a |
---|
| 870 | table-based interpolation (and extrapolation if necessary). |
---|
| 871 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 872 | If you specify neither, then a polynomial correction will be made |
---|
| 873 | with built in coefficients known for certain telescopes (an error |
---|
| 874 | will occur if the instrument is not known). |
---|
| 875 | The data and Tsys are *divided* by the scaling factors. |
---|
| 876 | Parameters: |
---|
| 877 | poly: Polynomial coefficients (default None) to compute a |
---|
| 878 | gain-elevation correction as a function of |
---|
| 879 | elevation (in degrees). |
---|
| 880 | filename: The name of an ascii file holding correction factors. |
---|
| 881 | The first row of the ascii file must give the column |
---|
| 882 | names and these MUST include columns |
---|
| 883 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 884 | by this) somewhere. |
---|
| 885 | The second row must give the data type of the |
---|
| 886 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 887 | An example file would be |
---|
| 888 | (actual factors are arbitrary) : |
---|
| 889 | |
---|
| 890 | TIME ELEVATION FACTOR |
---|
| 891 | R R R |
---|
| 892 | 0.1 0 0.8 |
---|
| 893 | 0.2 20 0.85 |
---|
| 894 | 0.3 40 0.9 |
---|
| 895 | 0.4 60 0.85 |
---|
| 896 | 0.5 80 0.8 |
---|
| 897 | 0.6 90 0.75 |
---|
| 898 | method: Interpolation method when correcting from a table. |
---|
| 899 | Values are "nearest", "linear" (default), "cubic" |
---|
| 900 | and "spline" |
---|
| 901 | insitu: if False a new scantable is returned. |
---|
| 902 | Otherwise, the scaling is done in-situ |
---|
| 903 | The default is taken from .asaprc (False) |
---|
| 904 | allaxes: If True apply to all spectra. Otherwise |
---|
| 905 | apply only to the selected (beam/pol/if) spectra only |
---|
| 906 | The default is taken from .asaprc (True if none) |
---|
| 907 | """ |
---|
| 908 | |
---|
| 909 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 910 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 911 | varlist = vars() |
---|
| 912 | if poly is None: |
---|
| 913 | poly = () |
---|
| 914 | from os.path import expandvars |
---|
| 915 | filename = expandvars(filename) |
---|
| 916 | if not insitu: |
---|
| 917 | from asap._asap import gainel as _gainEl |
---|
| 918 | s = scantable(_gainEl(self, poly, filename, method, allaxes)) |
---|
| 919 | s._add_history("gain_el", varlist) |
---|
[718] | 920 | print_log() |
---|
[513] | 921 | return s |
---|
| 922 | else: |
---|
| 923 | from asap._asap import gainel_insitu as _gainEl |
---|
| 924 | _gainEl(self, poly, filename, method, allaxes) |
---|
| 925 | self._add_history("gain_el", varlist) |
---|
[718] | 926 | print_log() |
---|
[513] | 927 | return |
---|
[710] | 928 | |
---|
[513] | 929 | def freq_align(self, reftime=None, method='cubic', perif=False, |
---|
| 930 | insitu=None): |
---|
| 931 | """ |
---|
| 932 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 933 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 934 | set_freqframe. |
---|
| 935 | Parameters: |
---|
| 936 | reftime: reference time to align at. By default, the time of |
---|
| 937 | the first row of data is used. |
---|
| 938 | method: Interpolation method for regridding the spectra. |
---|
| 939 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 940 | and "spline" |
---|
| 941 | perif: Generate aligners per freqID (no doppler tracking) or |
---|
| 942 | per IF (scan-based doppler tracking) |
---|
| 943 | insitu: if False a new scantable is returned. |
---|
| 944 | Otherwise, the scaling is done in-situ |
---|
| 945 | The default is taken from .asaprc (False) |
---|
| 946 | """ |
---|
| 947 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 948 | varlist = vars() |
---|
| 949 | if reftime is None: reftime = '' |
---|
| 950 | perfreqid = not perif |
---|
| 951 | if not insitu: |
---|
| 952 | from asap._asap import freq_align as _align |
---|
| 953 | s = scantable(_align(self, reftime, method, perfreqid)) |
---|
| 954 | s._add_history("freq_align", varlist) |
---|
[718] | 955 | print_log() |
---|
[513] | 956 | return s |
---|
| 957 | else: |
---|
| 958 | from asap._asap import freq_align_insitu as _align |
---|
| 959 | _align(self, reftime, method, perfreqid) |
---|
| 960 | self._add_history("freq_align", varlist) |
---|
[718] | 961 | print_log() |
---|
[513] | 962 | return |
---|
| 963 | |
---|
| 964 | def opacity(self, tau, insitu=None, allaxes=None): |
---|
| 965 | """ |
---|
| 966 | Apply an opacity correction. The data |
---|
| 967 | and Tsys are multiplied by the correction factor. |
---|
| 968 | Parameters: |
---|
| 969 | tau: Opacity from which the correction factor is |
---|
| 970 | exp(tau*ZD) |
---|
| 971 | where ZD is the zenith-distance |
---|
| 972 | insitu: if False a new scantable is returned. |
---|
| 973 | Otherwise, the scaling is done in-situ |
---|
| 974 | The default is taken from .asaprc (False) |
---|
| 975 | allaxes: if True apply to all spectra. Otherwise |
---|
| 976 | apply only to the selected (beam/pol/if)spectra only |
---|
| 977 | The default is taken from .asaprc (True if none) |
---|
| 978 | """ |
---|
| 979 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 980 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 981 | varlist = vars() |
---|
| 982 | if not insitu: |
---|
| 983 | from asap._asap import opacity as _opacity |
---|
| 984 | s = scantable(_opacity(self, tau, allaxes)) |
---|
| 985 | s._add_history("opacity", varlist) |
---|
[718] | 986 | print_log() |
---|
[513] | 987 | return s |
---|
| 988 | else: |
---|
| 989 | from asap._asap import opacity_insitu as _opacity |
---|
| 990 | _opacity(self, tau, allaxes) |
---|
| 991 | self._add_history("opacity", varlist) |
---|
[718] | 992 | print_log() |
---|
[513] | 993 | return |
---|
| 994 | |
---|
| 995 | def bin(self, width=5, insitu=None): |
---|
| 996 | """ |
---|
| 997 | Return a scan where all spectra have been binned up. |
---|
| 998 | width: The bin width (default=5) in pixels |
---|
| 999 | insitu: if False a new scantable is returned. |
---|
| 1000 | Otherwise, the scaling is done in-situ |
---|
| 1001 | The default is taken from .asaprc (False) |
---|
| 1002 | """ |
---|
| 1003 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1004 | varlist = vars() |
---|
| 1005 | if not insitu: |
---|
| 1006 | from asap._asap import bin as _bin |
---|
| 1007 | s = scantable(_bin(self, width)) |
---|
| 1008 | s._add_history("bin",varlist) |
---|
[718] | 1009 | print_log() |
---|
[513] | 1010 | return s |
---|
| 1011 | else: |
---|
| 1012 | from asap._asap import bin_insitu as _bin |
---|
| 1013 | _bin(self, width) |
---|
| 1014 | self._add_history("bin",varlist) |
---|
[718] | 1015 | print_log() |
---|
[513] | 1016 | return |
---|
| 1017 | |
---|
[710] | 1018 | |
---|
[513] | 1019 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 1020 | """ |
---|
| 1021 | Return a scan where all spectra have been binned up |
---|
| 1022 | width: The bin width (default=5) in pixels |
---|
| 1023 | method: Interpolation method when correcting from a table. |
---|
| 1024 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1025 | and "spline" |
---|
| 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 | """ |
---|
| 1030 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1031 | varlist = vars() |
---|
| 1032 | if not insitu: |
---|
| 1033 | from asap._asap import resample as _resample |
---|
| 1034 | s = scantable(_resample(self, method, width)) |
---|
| 1035 | s._add_history("resample",varlist) |
---|
[718] | 1036 | print_log() |
---|
[513] | 1037 | return s |
---|
| 1038 | else: |
---|
| 1039 | from asap._asap import resample_insitu as _resample |
---|
| 1040 | _resample(self, method, width) |
---|
| 1041 | self._add_history("resample",varlist) |
---|
[718] | 1042 | print_log() |
---|
[513] | 1043 | return |
---|
| 1044 | |
---|
| 1045 | def average_pol(self, mask=None, weight='none', insitu=None): |
---|
| 1046 | """ |
---|
| 1047 | Average the Polarisations together. |
---|
| 1048 | The polarisation cursor of the output scan is set to 0 |
---|
| 1049 | Parameters: |
---|
| 1050 | mask: An optional mask defining the region, where the |
---|
| 1051 | averaging will be applied. The output will have all |
---|
| 1052 | specified points masked. |
---|
[532] | 1053 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1054 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
[513] | 1055 | insitu: if False a new scantable is returned. |
---|
| 1056 | Otherwise, the scaling is done in-situ |
---|
| 1057 | The default is taken from .asaprc (False) |
---|
| 1058 | """ |
---|
| 1059 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1060 | varlist = vars() |
---|
| 1061 | |
---|
| 1062 | if mask is None: |
---|
| 1063 | mask = () |
---|
| 1064 | if not insitu: |
---|
| 1065 | from asap._asap import averagepol as _avpol |
---|
| 1066 | s = scantable(_avpol(self, mask, weight)) |
---|
| 1067 | s._add_history("average_pol",varlist) |
---|
[718] | 1068 | print_log() |
---|
[513] | 1069 | return s |
---|
| 1070 | else: |
---|
| 1071 | from asap._asap import averagepol_insitu as _avpol |
---|
| 1072 | _avpol(self, mask, weight) |
---|
| 1073 | self._add_history("average_pol",varlist) |
---|
[718] | 1074 | print_log() |
---|
[513] | 1075 | return |
---|
| 1076 | |
---|
| 1077 | def smooth(self, kernel="hanning", width=5.0, insitu=None, allaxes=None): |
---|
| 1078 | """ |
---|
| 1079 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 1080 | Parameters: |
---|
| 1081 | scan: The input scan |
---|
| 1082 | kernel: The type of smoothing kernel. Select from |
---|
| 1083 | 'hanning' (default), 'gaussian' and 'boxcar'. |
---|
| 1084 | The first three characters are sufficient. |
---|
| 1085 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1086 | ignored otherwise it defauls to 5 pixels. |
---|
| 1087 | For 'gaussian' it is the Full Width Half |
---|
| 1088 | Maximum. For 'boxcar' it is the full width. |
---|
| 1089 | insitu: if False a new scantable is returned. |
---|
| 1090 | Otherwise, the scaling is done in-situ |
---|
| 1091 | The default is taken from .asaprc (False) |
---|
| 1092 | allaxes: If True (default) apply to all spectra. Otherwise |
---|
| 1093 | apply only to the selected (beam/pol/if)spectra only |
---|
| 1094 | The default is taken from .asaprc (True if none) |
---|
| 1095 | Example: |
---|
| 1096 | none |
---|
| 1097 | """ |
---|
| 1098 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 1099 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1100 | varlist = vars() |
---|
| 1101 | if not insitu: |
---|
| 1102 | from asap._asap import smooth as _smooth |
---|
| 1103 | s = scantable(_smooth(self,kernel,width,allaxes)) |
---|
| 1104 | s._add_history("smooth", varlist) |
---|
[718] | 1105 | print_log() |
---|
[513] | 1106 | return s |
---|
| 1107 | else: |
---|
| 1108 | from asap._asap import smooth_insitu as _smooth |
---|
| 1109 | _smooth(self,kernel,width,allaxes) |
---|
| 1110 | self._add_history("smooth", varlist) |
---|
[718] | 1111 | print_log() |
---|
[513] | 1112 | return |
---|
| 1113 | |
---|
[794] | 1114 | def poly_baseline(self, mask=None, order=0, insitu=None, allaxes=None): |
---|
[513] | 1115 | """ |
---|
| 1116 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1117 | Parameters: |
---|
[794] | 1118 | scan: a scantable |
---|
| 1119 | mask: an optional mask |
---|
| 1120 | order: the order of the polynomial (default is 0) |
---|
| 1121 | insitu: if False a new scantable is returned. |
---|
| 1122 | Otherwise, the scaling is done in-situ |
---|
| 1123 | The default is taken from .asaprc (False) |
---|
| 1124 | allaxes: If True (default) apply to all spectra. Otherwise |
---|
| 1125 | apply only to the selected (beam/pol/if)spectra only |
---|
| 1126 | The default is taken from .asaprc (True if none) |
---|
[513] | 1127 | Example: |
---|
| 1128 | # return a scan baselined by a third order polynomial, |
---|
| 1129 | # not using a mask |
---|
| 1130 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1131 | """ |
---|
[794] | 1132 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
[513] | 1133 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1134 | varlist = vars() |
---|
| 1135 | if mask is None: |
---|
| 1136 | from numarray import ones |
---|
[626] | 1137 | mask = list(ones(self.nchan())) |
---|
[513] | 1138 | from asap.asapfitter import fitter |
---|
| 1139 | f = fitter() |
---|
| 1140 | f.set_scan(self, mask) |
---|
| 1141 | f.set_function(poly=order) |
---|
[794] | 1142 | sf = f.auto_fit(insitu,allaxes) |
---|
[513] | 1143 | if insitu: |
---|
| 1144 | self._add_history("poly_baseline", varlist) |
---|
[718] | 1145 | print_log() |
---|
[513] | 1146 | return |
---|
| 1147 | else: |
---|
| 1148 | sf._add_history("poly_baseline", varlist) |
---|
[718] | 1149 | print_log() |
---|
[513] | 1150 | return sf |
---|
| 1151 | |
---|
| 1152 | def auto_poly_baseline(self, mask=None, edge=(0,0), order=0, |
---|
| 1153 | threshold=3,insitu=None): |
---|
| 1154 | """ |
---|
| 1155 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1156 | Spectral lines are detected first using linefinder and masked out |
---|
| 1157 | to avoid them affecting the baseline solution. |
---|
| 1158 | |
---|
| 1159 | Parameters: |
---|
| 1160 | mask: an optional mask retreived from scantable |
---|
| 1161 | edge: an optional number of channel to drop at |
---|
| 1162 | the edge of spectrum. If only one value is |
---|
| 1163 | specified, the same number will be dropped from |
---|
| 1164 | both sides of the spectrum. Default is to keep |
---|
| 1165 | all channels |
---|
| 1166 | order: the order of the polynomial (default is 0) |
---|
| 1167 | threshold: the threshold used by line finder. It is better to |
---|
| 1168 | keep it large as only strong lines affect the |
---|
| 1169 | baseline solution. |
---|
| 1170 | insitu: if False a new scantable is returned. |
---|
| 1171 | Otherwise, the scaling is done in-situ |
---|
| 1172 | The default is taken from .asaprc (False) |
---|
| 1173 | |
---|
| 1174 | Example: |
---|
[516] | 1175 | scan2=scan.auto_poly_baseline(order=7) |
---|
[513] | 1176 | """ |
---|
| 1177 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1178 | varlist = vars() |
---|
| 1179 | from asap.asapfitter import fitter |
---|
| 1180 | from asap.asaplinefind import linefinder |
---|
| 1181 | from asap import _is_sequence_or_number as _is_valid |
---|
[710] | 1182 | |
---|
[513] | 1183 | if not _is_valid(edge, int): |
---|
[718] | 1184 | |
---|
[516] | 1185 | raise RuntimeError, "Parameter 'edge' has to be an integer or a \ |
---|
| 1186 | pair of integers specified as a tuple" |
---|
[710] | 1187 | |
---|
[513] | 1188 | # setup fitter |
---|
| 1189 | f = fitter() |
---|
| 1190 | f.set_function(poly=order) |
---|
| 1191 | |
---|
| 1192 | # setup line finder |
---|
| 1193 | fl=linefinder() |
---|
| 1194 | fl.set_options(threshold=threshold) |
---|
| 1195 | |
---|
| 1196 | if not insitu: |
---|
| 1197 | workscan=self.copy() |
---|
| 1198 | else: |
---|
| 1199 | workscan=self |
---|
| 1200 | |
---|
| 1201 | sel=workscan.get_cursor() |
---|
| 1202 | rows=range(workscan.nrow()) |
---|
[718] | 1203 | from asap import asaplog |
---|
[513] | 1204 | for i in range(workscan.nbeam()): |
---|
| 1205 | workscan.setbeam(i) |
---|
| 1206 | for j in range(workscan.nif()): |
---|
| 1207 | workscan.setif(j) |
---|
| 1208 | for k in range(workscan.npol()): |
---|
| 1209 | workscan.setpol(k) |
---|
[718] | 1210 | asaplog.push("Processing:") |
---|
| 1211 | msg = 'Beam[%d], IF[%d], Pol[%d]' % (i,j,k) |
---|
| 1212 | asaplog.push(msg) |
---|
[513] | 1213 | for iRow in rows: |
---|
| 1214 | fl.set_scan(workscan,mask,edge) |
---|
| 1215 | fl.find_lines(iRow) |
---|
| 1216 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1217 | f.x=workscan._getabcissa(iRow) |
---|
| 1218 | f.y=workscan._getspectrum(iRow) |
---|
| 1219 | f.data=None |
---|
| 1220 | f.fit() |
---|
| 1221 | x=f.get_parameters() |
---|
| 1222 | workscan._setspectrum(f.fitter.getresidual(),iRow) |
---|
| 1223 | workscan.set_cursor(sel[0],sel[1],sel[2]) |
---|
| 1224 | if not insitu: |
---|
[718] | 1225 | return workscan |
---|
[513] | 1226 | |
---|
| 1227 | def rotate_linpolphase(self, angle, allaxes=None): |
---|
| 1228 | """ |
---|
[710] | 1229 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1230 | This is always done in situ in the raw data. So if you call this |
---|
[513] | 1231 | function more than once then each call rotates the phase further. |
---|
| 1232 | Parameters: |
---|
| 1233 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1234 | allaxes: If True apply to all spectra. Otherwise |
---|
| 1235 | apply only to the selected (beam/pol/if)spectra only. |
---|
| 1236 | The default is taken from .asaprc (True if none) |
---|
| 1237 | Examples: |
---|
| 1238 | scan.rotate_linpolphase(2.3) |
---|
| 1239 | """ |
---|
| 1240 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 1241 | varlist = vars() |
---|
| 1242 | from asap._asap import _rotate_linpolphase as _rotate |
---|
| 1243 | _rotate(self, angle, allaxes) |
---|
| 1244 | self._add_history("rotate_linpolphase", varlist) |
---|
[718] | 1245 | print_log() |
---|
[513] | 1246 | return |
---|
| 1247 | |
---|
[710] | 1248 | |
---|
[513] | 1249 | def rotate_xyphase(self, angle, allaxes=None): |
---|
| 1250 | """ |
---|
| 1251 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1252 | in the data. So if you call this function more than once |
---|
| 1253 | then each call rotates the phase further. |
---|
| 1254 | Parameters: |
---|
| 1255 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1256 | allaxes: If True apply to all spectra. Otherwise |
---|
| 1257 | apply only to the selected (beam/pol/if)spectra only. |
---|
| 1258 | The default is taken from .asaprc (True if none) |
---|
| 1259 | Examples: |
---|
| 1260 | scan.rotate_xyphase(2.3) |
---|
| 1261 | """ |
---|
| 1262 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 1263 | varlist = vars() |
---|
[670] | 1264 | from asap._asap import _rotate_xyphase |
---|
[513] | 1265 | _rotate_xyphase(self, angle, allaxes) |
---|
| 1266 | self._add_history("rotate_xyphase", varlist) |
---|
[718] | 1267 | print_log() |
---|
[513] | 1268 | return |
---|
| 1269 | |
---|
| 1270 | |
---|
| 1271 | def add(self, offset, insitu=None, allaxes=None): |
---|
| 1272 | """ |
---|
| 1273 | Return a scan where all spectra have the offset added |
---|
| 1274 | Parameters: |
---|
| 1275 | offset: the offset |
---|
| 1276 | insitu: if False a new scantable is returned. |
---|
| 1277 | Otherwise, the scaling is done in-situ |
---|
| 1278 | The default is taken from .asaprc (False) |
---|
| 1279 | allaxes: if True apply to all spectra. Otherwise |
---|
| 1280 | apply only to the selected (beam/pol/if)spectra only |
---|
| 1281 | The default is taken from .asaprc (True if none) |
---|
| 1282 | """ |
---|
| 1283 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 1284 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1285 | varlist = vars() |
---|
| 1286 | if not insitu: |
---|
| 1287 | from asap._asap import add as _add |
---|
| 1288 | s = scantable(_add(self, offset, allaxes)) |
---|
| 1289 | s._add_history("add",varlist) |
---|
[718] | 1290 | print_log() |
---|
[513] | 1291 | return s |
---|
| 1292 | else: |
---|
| 1293 | from asap._asap import add_insitu as _add |
---|
| 1294 | _add(self, offset, allaxes) |
---|
| 1295 | self._add_history("add",varlist) |
---|
[718] | 1296 | print_log() |
---|
[513] | 1297 | return |
---|
| 1298 | |
---|
| 1299 | def scale(self, factor, insitu=None, allaxes=None, tsys=True): |
---|
| 1300 | """ |
---|
| 1301 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 1302 | Parameters: |
---|
| 1303 | factor: the scaling factor |
---|
| 1304 | insitu: if False a new scantable is returned. |
---|
| 1305 | Otherwise, the scaling is done in-situ |
---|
| 1306 | The default is taken from .asaprc (False) |
---|
| 1307 | allaxes: if True apply to all spectra. Otherwise |
---|
| 1308 | apply only to the selected (beam/pol/if)spectra only. |
---|
| 1309 | The default is taken from .asaprc (True if none) |
---|
| 1310 | tsys: if True (default) then apply the operation to Tsys |
---|
| 1311 | as well as the data |
---|
| 1312 | """ |
---|
| 1313 | if allaxes is None: allaxes = rcParams['scantable.allaxes'] |
---|
| 1314 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1315 | varlist = vars() |
---|
| 1316 | if not insitu: |
---|
| 1317 | from asap._asap import scale as _scale |
---|
| 1318 | s = scantable(_scale(self, factor, allaxes, tsys)) |
---|
| 1319 | s._add_history("scale",varlist) |
---|
[718] | 1320 | print_log() |
---|
[513] | 1321 | return s |
---|
| 1322 | else: |
---|
| 1323 | from asap._asap import scale_insitu as _scale |
---|
| 1324 | _scale(self, factor, allaxes, tsys) |
---|
| 1325 | self._add_history("scale",varlist) |
---|
[718] | 1326 | print_log() |
---|
[513] | 1327 | return |
---|
| 1328 | |
---|
[670] | 1329 | def auto_quotient(self, mode='suffix', preserve=True): |
---|
| 1330 | """ |
---|
| 1331 | This function allows to build quotients automatically. |
---|
| 1332 | It assumes the observation to have the same numer of |
---|
| 1333 | "ons" and "offs" |
---|
| 1334 | It will support "closest off in time" in the future |
---|
| 1335 | Parameters: |
---|
| 1336 | mode: the on/off detection mode; 'suffix' (default) |
---|
| 1337 | 'suffix' identifies 'off' scans by the |
---|
| 1338 | trailing '_R' (Mopra/Parkes) or |
---|
| 1339 | '_e'/'_w' (Tid) |
---|
[710] | 1340 | preserve: you can preserve (default) the continuum or |
---|
| 1341 | remove it. The equations used are |
---|
[670] | 1342 | preserve: Output = Toff * (on/off) - Toff |
---|
| 1343 | remove: Output = Tref * (on/off) - Ton |
---|
| 1344 | """ |
---|
| 1345 | modes = ["suffix","time"] |
---|
| 1346 | if not mode in modes: |
---|
| 1347 | print "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 1348 | return None |
---|
| 1349 | from asap._asap import quotient as _quot |
---|
| 1350 | if mode == "suffix": |
---|
| 1351 | srcs = self.get_scan("*[^_ewR]") |
---|
| 1352 | refs = self.get_scan("*[_ewR]") |
---|
[710] | 1353 | if isinstance(srcs,scantable) and isinstance(refs,scantable): |
---|
[794] | 1354 | from asap import asaplog |
---|
[710] | 1355 | ns,nr = srcs.nrow(),refs.nrow() |
---|
[794] | 1356 | msg = "Found %i Off and %i On scans" % (ns,nr) |
---|
| 1357 | asaplog.push(msg) |
---|
[710] | 1358 | if nr > ns: |
---|
[794] | 1359 | asaplog("Found more Off integrations than On scans - dropping excess Offs.") |
---|
[710] | 1360 | refs = refs.get_scan(range(ns)) |
---|
[718] | 1361 | print_log() |
---|
[710] | 1362 | return scantable(_quot(srcs,refs, preserve)) |
---|
| 1363 | else: |
---|
[718] | 1364 | msg = "Couldn't find any on/off pairs" |
---|
| 1365 | if rcParams['verbose']: |
---|
| 1366 | print msg |
---|
| 1367 | return |
---|
| 1368 | else: |
---|
| 1369 | raise RuntimeError() |
---|
[670] | 1370 | else: |
---|
[718] | 1371 | if rcParams['verbose']: print "not yet implemented" |
---|
[670] | 1372 | return None |
---|
[710] | 1373 | |
---|
[513] | 1374 | def quotient(self, other, isreference=True, preserve=True): |
---|
| 1375 | """ |
---|
[582] | 1376 | Return the quotient of a 'source' (on) scan and a 'reference' (off) |
---|
| 1377 | scan. |
---|
[513] | 1378 | The reference can have just one row, even if the signal has many. |
---|
| 1379 | Otherwise they must have the same number of rows. |
---|
| 1380 | The cursor of the output scan is set to 0 |
---|
| 1381 | Parameters: |
---|
[582] | 1382 | other: the 'other' scan |
---|
[513] | 1383 | isreference: if the 'other' scan is the reference (default) |
---|
| 1384 | or source |
---|
[710] | 1385 | preserve: you can preserve (default) the continuum or |
---|
| 1386 | remove it. The equations used are |
---|
[582] | 1387 | preserve: Output = Toff * (on/off) - Toff |
---|
| 1388 | remove: Output = Tref * (on/off) - Ton |
---|
[513] | 1389 | Example: |
---|
| 1390 | # src is a scantable for an 'on' scan, ref for an 'off' scantable |
---|
| 1391 | q1 = src.quotient(ref) |
---|
| 1392 | q2 = ref.quotient(src, isreference=False) |
---|
| 1393 | # gives the same result |
---|
| 1394 | """ |
---|
| 1395 | from asap._asap import quotient as _quot |
---|
[718] | 1396 | try: |
---|
| 1397 | s = None |
---|
| 1398 | if isreference: |
---|
| 1399 | s = scantable(_quot(self, other, preserve)) |
---|
| 1400 | else: |
---|
| 1401 | s = scantable(_quot(other, self, preserve)) |
---|
| 1402 | print_log() |
---|
| 1403 | return s |
---|
| 1404 | except RuntimeError,e: |
---|
| 1405 | if rcParams['verbose']: |
---|
| 1406 | print e |
---|
| 1407 | return |
---|
| 1408 | else: raise |
---|
[513] | 1409 | |
---|
[718] | 1410 | def freq_switch(self, insitu=None): |
---|
| 1411 | """ |
---|
| 1412 | Apply frequency switching to the data. |
---|
| 1413 | Parameters: |
---|
| 1414 | insitu: if False a new scantable is returned. |
---|
| 1415 | Otherwise, the swictching is done in-situ |
---|
| 1416 | The default is taken from .asaprc (False) |
---|
| 1417 | Example: |
---|
| 1418 | none |
---|
| 1419 | """ |
---|
| 1420 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1421 | varlist = vars() |
---|
| 1422 | try: |
---|
| 1423 | if insitu: |
---|
| 1424 | from asap._asap import _frequency_switch_insitu |
---|
| 1425 | _frequency_switch_insitu(self) |
---|
| 1426 | self._add_history("freq_switch", varlist) |
---|
| 1427 | print_log() |
---|
| 1428 | return |
---|
| 1429 | else: |
---|
| 1430 | from asap._asap import _frequency_switch |
---|
| 1431 | sf = scantable(_frequency_switch(self)) |
---|
| 1432 | sf._add_history("freq_switch", varlist) |
---|
| 1433 | print_log() |
---|
| 1434 | return sf |
---|
| 1435 | except RuntimeError,e: |
---|
| 1436 | if rcParams['verbose']: print e |
---|
| 1437 | else: raise |
---|
| 1438 | |
---|
[780] | 1439 | def recalc_azel(self): |
---|
| 1440 | """ |
---|
| 1441 | Recalculate the azimuth and elevation for each position. |
---|
| 1442 | Parameters: |
---|
| 1443 | none |
---|
| 1444 | Example: |
---|
| 1445 | """ |
---|
| 1446 | varlist = vars() |
---|
| 1447 | self._recalc_azel() |
---|
| 1448 | self._add_history("recalc_azel", varlist) |
---|
| 1449 | print_log() |
---|
| 1450 | return |
---|
| 1451 | |
---|
[513] | 1452 | def __add__(self, other): |
---|
| 1453 | varlist = vars() |
---|
| 1454 | s = None |
---|
| 1455 | if isinstance(other, scantable): |
---|
[710] | 1456 | from asap._asap import b_operate as _bop |
---|
[513] | 1457 | s = scantable(_bop(self, other, 'add', True)) |
---|
| 1458 | elif isinstance(other, float): |
---|
| 1459 | from asap._asap import add as _add |
---|
| 1460 | s = scantable(_add(self, other, True)) |
---|
| 1461 | else: |
---|
[718] | 1462 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1463 | s._add_history("operator +", varlist) |
---|
[718] | 1464 | print_log() |
---|
[513] | 1465 | return s |
---|
| 1466 | |
---|
| 1467 | def __sub__(self, other): |
---|
| 1468 | """ |
---|
| 1469 | implicit on all axes and on Tsys |
---|
| 1470 | """ |
---|
| 1471 | varlist = vars() |
---|
| 1472 | s = None |
---|
| 1473 | if isinstance(other, scantable): |
---|
[710] | 1474 | from asap._asap import b_operate as _bop |
---|
[513] | 1475 | s = scantable(_bop(self, other, 'sub', True)) |
---|
| 1476 | elif isinstance(other, float): |
---|
| 1477 | from asap._asap import add as _add |
---|
| 1478 | s = scantable(_add(self, -other, True)) |
---|
| 1479 | else: |
---|
[718] | 1480 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1481 | s._add_history("operator -", varlist) |
---|
[718] | 1482 | print_log() |
---|
[513] | 1483 | return s |
---|
[710] | 1484 | |
---|
[513] | 1485 | def __mul__(self, other): |
---|
| 1486 | """ |
---|
| 1487 | implicit on all axes and on Tsys |
---|
| 1488 | """ |
---|
| 1489 | varlist = vars() |
---|
| 1490 | s = None |
---|
| 1491 | if isinstance(other, scantable): |
---|
[710] | 1492 | from asap._asap import b_operate as _bop |
---|
[513] | 1493 | s = scantable(_bop(self, other, 'mul', True)) |
---|
| 1494 | elif isinstance(other, float): |
---|
| 1495 | if other == 0.0: |
---|
[718] | 1496 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[513] | 1497 | from asap._asap import scale as _sca |
---|
| 1498 | s = scantable(_sca(self, other, True)) |
---|
| 1499 | else: |
---|
[718] | 1500 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1501 | s._add_history("operator *", varlist) |
---|
[718] | 1502 | print_log() |
---|
[513] | 1503 | return s |
---|
| 1504 | |
---|
[710] | 1505 | |
---|
[513] | 1506 | def __div__(self, other): |
---|
| 1507 | """ |
---|
| 1508 | implicit on all axes and on Tsys |
---|
| 1509 | """ |
---|
| 1510 | varlist = vars() |
---|
| 1511 | s = None |
---|
| 1512 | if isinstance(other, scantable): |
---|
[710] | 1513 | from asap._asap import b_operate as _bop |
---|
[513] | 1514 | s = scantable(_bop(self, other, 'div', True)) |
---|
| 1515 | elif isinstance(other, float): |
---|
| 1516 | if other == 0.0: |
---|
[718] | 1517 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[513] | 1518 | from asap._asap import scale as _sca |
---|
| 1519 | s = scantable(_sca(self, 1.0/other, True)) |
---|
| 1520 | else: |
---|
[718] | 1521 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1522 | s._add_history("operator /", varlist) |
---|
[718] | 1523 | print_log() |
---|
[513] | 1524 | return s |
---|
| 1525 | |
---|
[530] | 1526 | def get_fit(self, row=0): |
---|
| 1527 | """ |
---|
| 1528 | Print or return the stored fits for a row in the scantable |
---|
| 1529 | Parameters: |
---|
| 1530 | row: the row which the fit has been applied to. |
---|
| 1531 | """ |
---|
| 1532 | if row > self.nrow(): |
---|
| 1533 | return |
---|
| 1534 | from asap import asapfit |
---|
| 1535 | fit = asapfit(self._getfit(row)) |
---|
[718] | 1536 | if rcParams['verbose']: |
---|
[530] | 1537 | print fit |
---|
| 1538 | return |
---|
| 1539 | else: |
---|
| 1540 | return fit.as_dict() |
---|
| 1541 | |
---|
[484] | 1542 | def _add_history(self, funcname, parameters): |
---|
| 1543 | # create date |
---|
| 1544 | sep = "##" |
---|
| 1545 | from datetime import datetime |
---|
| 1546 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 1547 | hist = dstr+sep |
---|
| 1548 | hist += funcname+sep#cdate+sep |
---|
| 1549 | if parameters.has_key('self'): del parameters['self'] |
---|
| 1550 | for k,v in parameters.iteritems(): |
---|
| 1551 | if type(v) is dict: |
---|
| 1552 | for k2,v2 in v.iteritems(): |
---|
| 1553 | hist += k2 |
---|
| 1554 | hist += "=" |
---|
| 1555 | if isinstance(v2,scantable): |
---|
| 1556 | hist += 'scantable' |
---|
| 1557 | elif k2 == 'mask': |
---|
[513] | 1558 | if isinstance(v2,list) or isinstance(v2,tuple): |
---|
| 1559 | hist += str(self._zip_mask(v2)) |
---|
| 1560 | else: |
---|
| 1561 | hist += str(v2) |
---|
[484] | 1562 | else: |
---|
[513] | 1563 | hist += str(v2) |
---|
[484] | 1564 | else: |
---|
| 1565 | hist += k |
---|
| 1566 | hist += "=" |
---|
| 1567 | if isinstance(v,scantable): |
---|
| 1568 | hist += 'scantable' |
---|
| 1569 | elif k == 'mask': |
---|
[513] | 1570 | if isinstance(v,list) or isinstance(v,tuple): |
---|
| 1571 | hist += str(self._zip_mask(v)) |
---|
| 1572 | else: |
---|
| 1573 | hist += str(v) |
---|
[484] | 1574 | else: |
---|
| 1575 | hist += str(v) |
---|
| 1576 | hist += sep |
---|
| 1577 | hist = hist[:-2] # remove trailing '##' |
---|
| 1578 | self._addhistory(hist) |
---|
| 1579 | |
---|
[710] | 1580 | |
---|
[484] | 1581 | def _zip_mask(self, mask): |
---|
| 1582 | mask = list(mask) |
---|
| 1583 | i = 0 |
---|
| 1584 | segments = [] |
---|
| 1585 | while mask[i:].count(1): |
---|
| 1586 | i += mask[i:].index(1) |
---|
| 1587 | if mask[i:].count(0): |
---|
| 1588 | j = i + mask[i:].index(0) |
---|
| 1589 | else: |
---|
[710] | 1590 | j = len(mask) |
---|
[484] | 1591 | segments.append([i,j]) |
---|
[710] | 1592 | i = j |
---|
[484] | 1593 | return segments |
---|
[714] | 1594 | |
---|
[626] | 1595 | def _get_ordinate_label(self): |
---|
| 1596 | fu = "("+self.get_fluxunit()+")" |
---|
| 1597 | import re |
---|
| 1598 | lbl = "Intensity" |
---|
| 1599 | if re.match(".K.",fu): |
---|
| 1600 | lbl = "Brightness Temperature "+ fu |
---|
| 1601 | elif re.match(".Jy.",fu): |
---|
| 1602 | lbl = "Flux density "+ fu |
---|
| 1603 | return lbl |
---|
[710] | 1604 | |
---|