[876] | 1 | from asap._asap import Scantable |
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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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[876] | 7 | class scantable(Scantable): |
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[102] | 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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[876] | 35 | from asap._asap import stmath |
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| 36 | self._math = stmath() |
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[710] | 37 | from asap import asaplog |
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[876] | 38 | if isinstance(filename, Scantable): |
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| 39 | Scantable.__init__(self, filename) |
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[340] | 40 | if unit is not None: |
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[710] | 41 | self.set_fluxunit(unit) |
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[181] | 42 | else: |
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[411] | 43 | import os.path |
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| 44 | if not os.path.exists(filename): |
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[710] | 45 | s = "File '%s' not found." % (filename) |
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| 46 | if rcParams['verbose']: |
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| 47 | asaplog.push(s) |
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| 48 | print asaplog.pop().strip() |
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| 49 | return |
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| 50 | raise IOError(s) |
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[411] | 51 | filename = os.path.expandvars(filename) |
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| 52 | if os.path.isdir(filename): |
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[181] | 53 | # crude check if asap table |
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[411] | 54 | if os.path.exists(filename+'/table.info'): |
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[876] | 55 | Scantable.__init__(self, filename, "memory") |
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[340] | 56 | if unit is not None: |
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[710] | 57 | self.set_fluxunit(unit) |
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[181] | 58 | else: |
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[718] | 59 | msg = "The given file '%s'is not a valid asap table." % (filename) |
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| 60 | if rcParams['verbose']: |
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| 61 | print msg |
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| 62 | return |
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| 63 | else: |
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| 64 | raise IOError(msg) |
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[710] | 65 | else: |
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[876] | 66 | from asap._asap import stfiller |
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[340] | 67 | ifSel = -1 |
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| 68 | beamSel = -1 |
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[876] | 69 | r = stfiller() |
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[710] | 70 | r._open(filename,ifSel,beamSel) |
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| 71 | asaplog.push('Importing data...') |
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[762] | 72 | print_log() |
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[876] | 73 | r._read() |
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[411] | 74 | tbl = r._getdata() |
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[346] | 75 | if unit is not None: |
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| 76 | tbl.set_fluxunit(unit) |
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[489] | 77 | if average: |
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[710] | 78 | asaplog.push('Auto averaging integrations...') |
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[762] | 79 | print_log() |
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[876] | 80 | tbl2 = self._math._average((tbl,),(),'NONE','SCAN', False) |
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| 81 | Scantable.__init__(self,tbl2) |
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[513] | 82 | del tbl2 |
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[226] | 83 | else: |
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[876] | 84 | Scantable.__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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[876] | 89 | def save(self, name=None, format=None, 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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[411] | 106 | overwrite: If the file should be overwritten if it exists. |
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[256] | 107 | The default False is to return with warning |
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[411] | 108 | without writing the output. USE WITH CARE. |
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[116] | 109 | Example: |
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| 110 | scan.save('myscan.asap') |
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| 111 | scan.save('myscan.sdfits','SDFITS') |
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| 112 | """ |
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[411] | 113 | from os import path |
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[226] | 114 | if format is None: format = rcParams['scantable.save'] |
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[256] | 115 | suffix = '.'+format.lower() |
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| 116 | if name is None or name =="": |
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| 117 | name = 'scantable'+suffix |
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[718] | 118 | from asap import asaplog |
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| 119 | msg = "No filename given. Using default name %s..." % name |
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| 120 | asaplog.push(msg) |
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[411] | 121 | name = path.expandvars(name) |
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[256] | 122 | if path.isfile(name) or path.isdir(name): |
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| 123 | if not overwrite: |
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[718] | 124 | msg = "File %s exists." % name |
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| 125 | if rcParams['verbose']: |
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| 126 | print msg |
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| 127 | return |
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| 128 | else: |
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| 129 | raise IOError(msg) |
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[451] | 130 | format2 = format.upper() |
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| 131 | if format2 == 'ASAP': |
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[116] | 132 | self._save(name) |
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| 133 | else: |
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[876] | 134 | print "NYI" |
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| 135 | # from asap._asap import sdwriter as _sw |
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| 136 | # w = _sw(format2) |
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| 137 | # w.write(self, name, stokes) |
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[718] | 138 | |
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| 139 | print_log() |
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[116] | 140 | return |
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| 141 | |
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[102] | 142 | def copy(self): |
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| 143 | """ |
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| 144 | Return a copy of this scantable. |
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| 145 | Parameters: |
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[113] | 146 | none |
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[102] | 147 | Example: |
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| 148 | copiedscan = scan.copy() |
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| 149 | """ |
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[876] | 150 | sd = scantable(Scantable._copy(self)) |
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[113] | 151 | return sd |
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| 152 | |
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[102] | 153 | def get_scan(self, scanid=None): |
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| 154 | """ |
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| 155 | Return a specific scan (by scanno) or collection of scans (by |
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| 156 | source name) in a new scantable. |
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| 157 | Parameters: |
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[513] | 158 | scanid: a (list of) scanno or a source name, unix-style |
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| 159 | patterns are accepted for source name matching, e.g. |
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| 160 | '*_R' gets all 'ref scans |
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[102] | 161 | Example: |
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[513] | 162 | # get all scans containing the source '323p459' |
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| 163 | newscan = scan.get_scan('323p459') |
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| 164 | # get all 'off' scans |
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| 165 | refscans = scan.get_scan('*_R') |
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| 166 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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| 167 | newscan = scan.get_scan([0,2,7,10]) |
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[102] | 168 | """ |
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| 169 | if scanid is None: |
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[718] | 170 | if rcParams['verbose']: |
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| 171 | print "Please specify a scan no or name to retrieve from the scantable" |
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| 172 | return |
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| 173 | else: |
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| 174 | raise RuntimeError("No scan given") |
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| 175 | |
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[102] | 176 | try: |
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[876] | 177 | bsel = self._getselection() |
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| 178 | sel = asap._asap.Selector() |
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[102] | 179 | if type(scanid) is str: |
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[876] | 180 | sel._setname() |
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| 181 | self._setselection(sel) |
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| 182 | scopy = self._copy() |
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| 183 | self._setselection(bsel) |
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| 184 | return scantable(scopy) |
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[102] | 185 | elif type(scanid) is int: |
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[876] | 186 | sel._setscans([scanid]) |
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| 187 | self._setselection(sel) |
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| 188 | scopy = self._copy() |
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| 189 | self._setselection(bsel) |
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| 190 | return scantable(scopy) |
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[381] | 191 | elif type(scanid) is list: |
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[876] | 192 | sel._setscans(scanid) |
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| 193 | self._setselection(sel) |
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| 194 | scopy = self._copy() |
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| 195 | self._setselection(bsel) |
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| 196 | return scantable(scopy) |
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[381] | 197 | else: |
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[718] | 198 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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| 199 | if rcParams['verbose']: |
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| 200 | print msg |
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| 201 | else: |
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| 202 | raise TypeError(msg) |
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[102] | 203 | except RuntimeError: |
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[718] | 204 | if rcParams['verbose']: print "Couldn't find any match." |
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| 205 | else: raise |
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[102] | 206 | |
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| 207 | def __str__(self): |
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[876] | 208 | return Scantable._summary(self,True) |
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[102] | 209 | |
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[876] | 210 | def summary(self, filename=None, verbose=None): |
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[102] | 211 | """ |
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| 212 | Print a summary of the contents of this scantable. |
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| 213 | Parameters: |
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| 214 | filename: the name of a file to write the putput to |
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| 215 | Default - no file output |
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[381] | 216 | verbose: print extra info such as the frequency table |
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| 217 | The default (False) is taken from .asaprc |
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[102] | 218 | """ |
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[876] | 219 | info = Scantable._summary(self, verbose) |
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[381] | 220 | if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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[102] | 221 | if filename is not None: |
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[256] | 222 | if filename is "": |
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| 223 | filename = 'scantable_summary.txt' |
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[415] | 224 | from os.path import expandvars, isdir |
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[411] | 225 | filename = expandvars(filename) |
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[415] | 226 | if not isdir(filename): |
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[413] | 227 | data = open(filename, 'w') |
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| 228 | data.write(info) |
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| 229 | data.close() |
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| 230 | else: |
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[718] | 231 | msg = "Illegal file name '%s'." % (filename) |
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| 232 | if rcParams['verbose']: |
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| 233 | print msg |
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| 234 | else: |
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| 235 | raise IOError(msg) |
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| 236 | if rcParams['verbose']: |
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[794] | 237 | try: |
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| 238 | from IPython.genutils import page as pager |
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| 239 | except ImportError: |
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| 240 | from pydoc import pager |
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| 241 | pager(info) |
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[718] | 242 | else: |
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| 243 | return info |
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[710] | 244 | |
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[553] | 245 | def set_cursor(self, beam=0, IF=0, pol=0): |
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[102] | 246 | """ |
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| 247 | Set the spectrum for individual operations. |
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| 248 | Parameters: |
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[553] | 249 | beam, IF, pol: a number |
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[102] | 250 | Example: |
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[256] | 251 | scan.set_cursor(0,0,1) |
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[135] | 252 | pol1sig = scan.stats(all=False) # returns std dev for beam=0 |
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[181] | 253 | # if=0, pol=1 |
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[102] | 254 | """ |
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[876] | 255 | print "DEPRECATED" |
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[484] | 256 | varlist = vars() |
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[876] | 257 | sel = asap._asap.Selector() |
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| 258 | sel._setbeams([beam]) |
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| 259 | sel._setpols([pol]) |
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| 260 | sel._setifs([IF]) |
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| 261 | self._add_history("set_cursor", varlist) |
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[102] | 262 | return |
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| 263 | |
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[256] | 264 | def get_cursor(self): |
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[113] | 265 | """ |
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| 266 | Return/print a the current 'cursor' into the Beam/IF/Pol cube. |
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| 267 | Parameters: |
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| 268 | none |
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| 269 | Returns: |
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| 270 | a list of values (currentBeam,currentIF,currentPol) |
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| 271 | Example: |
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| 272 | none |
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| 273 | """ |
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[876] | 274 | print "DEPRECATED" |
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| 275 | sel = self._getselection() |
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| 276 | i = sel.getbeams()[0] |
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| 277 | j = sel.getifs()[0] |
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| 278 | k = sel.getpols()[0] |
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[721] | 279 | from asap import asaplog |
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| 280 | out = "--------------------------------------------------\n" |
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| 281 | out += " Cursor position\n" |
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| 282 | out += "--------------------------------------------------\n" |
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| 283 | out += 'Beam=%d IF=%d Pol=%d ' % (i,j,k) |
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| 284 | asaplog.push(out) |
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| 285 | print_log() |
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| 286 | return i,j,k |
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[102] | 287 | |
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[876] | 288 | def stats(self, stat='stddev', mask=None): |
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[102] | 289 | """ |
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[135] | 290 | Determine the specified statistic of the current beam/if/pol |
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[102] | 291 | Takes a 'mask' as an optional parameter to specify which |
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| 292 | channels should be excluded. |
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| 293 | Parameters: |
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[135] | 294 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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| 295 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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| 296 | mask: an optional mask specifying where the statistic |
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[102] | 297 | should be determined. |
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| 298 | Example: |
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[113] | 299 | scan.set_unit('channel') |
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[102] | 300 | msk = scan.create_mask([100,200],[500,600]) |
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[135] | 301 | scan.stats(stat='mean', mask=m) |
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[102] | 302 | """ |
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[256] | 303 | from numarray import array,zeros,Float |
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[102] | 304 | if mask == None: |
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[876] | 305 | mask = [] |
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[256] | 306 | axes = ['Beam','IF','Pol','Time'] |
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[876] | 307 | if not self._check_ifs(): |
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| 308 | raise ValueError("Cannot apply mask as the IFs have different number of channels" |
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| 309 | "Please use setselection() to select individual IFs") |
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[256] | 310 | |
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[876] | 311 | statvals = self._math._stats(self, mask, stat) |
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| 312 | out = '' |
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| 313 | axes = [] |
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| 314 | for i in range(self.nrow()): |
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| 315 | axis = [] |
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| 316 | axis.append(self.getscan(i)) |
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| 317 | axis.append(self.getbeam(i)) |
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| 318 | axis.append(self.getif(i)) |
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| 319 | axis.append(self.getpol(i)) |
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| 320 | axis.append(self.getcycle(i)) |
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| 321 | axes.append(axis) |
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| 322 | tm = self._gettime(i) |
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| 323 | src = self._getsourcename(i) |
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| 324 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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| 325 | out += 'Time[%s]:\n' % (tm) |
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| 326 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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| 327 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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| 328 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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| 329 | out += '= %3.3f\n' % (statvals[i]) |
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| 330 | out += "--------------------------------------------------\n" |
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[256] | 331 | |
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[876] | 332 | if rcParams['verbose']: |
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| 333 | print "--------------------------------------------------" |
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| 334 | print " ",stat |
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| 335 | print "--------------------------------------------------" |
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| 336 | print out |
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| 337 | retval = { 'axesnames': ['scanno','beamno','ifno','polno','cycleno'], |
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| 338 | 'axes' : axes, |
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| 339 | 'data': statvals} |
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| 340 | return retval |
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[102] | 341 | |
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[876] | 342 | def stddev(self,mask=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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| 350 | |
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| 351 | Example: |
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| 352 | scan.set_unit('channel') |
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| 353 | msk = scan.create_mask([100,200],[500,600]) |
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| 354 | scan.stddev(mask=m) |
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| 355 | """ |
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[876] | 356 | return self.stats(stat='stddev',mask=mask); |
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[135] | 357 | |
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[876] | 358 | def get_tsys(self): |
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[113] | 359 | """ |
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| 360 | Return the System temperatures. |
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| 361 | Parameters: |
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[876] | 362 | |
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[113] | 363 | Returns: |
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[876] | 364 | a list of Tsys values for the current selection |
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[113] | 365 | """ |
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[256] | 366 | |
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[876] | 367 | return self._row_callback(self._gettsys, "Tsys") |
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[256] | 368 | |
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[876] | 369 | def _row_callback(self, callback, label): |
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| 370 | axes = [] |
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| 371 | axesnames = ['scanno','beamno','ifno','polno','cycleno'] |
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| 372 | out = "" |
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| 373 | outvec =[] |
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| 374 | for i in range(self.nrow()): |
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| 375 | axis = [] |
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| 376 | axis.append(self.getscan(i)) |
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| 377 | axis.append(self.getbeam(i)) |
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| 378 | axis.append(self.getif(i)) |
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| 379 | axis.append(self.getpol(i)) |
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| 380 | axis.append(self.getcycle(i)) |
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| 381 | axes.append(axis) |
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| 382 | tm = self._gettime(i) |
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| 383 | src = self._getsourcename(i) |
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| 384 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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| 385 | out += 'Time[%s]:\n' % (tm) |
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| 386 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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| 387 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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| 388 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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| 389 | outvec.append(callback(i)) |
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| 390 | out += '= %3.3f\n' % (outvec[i]) |
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| 391 | out += "--------------------------------------------------\n" |
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| 392 | if rcParams['verbose']: |
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| 393 | print "--------------------------------------------------" |
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| 394 | print " %s" % (label) |
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| 395 | print "--------------------------------------------------" |
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| 396 | print out |
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| 397 | retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec} |
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| 398 | return retval |
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[256] | 399 | |
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| 400 | |
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[407] | 401 | def get_time(self, row=-1): |
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[113] | 402 | """ |
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| 403 | Get a list of time stamps for the observations. |
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[181] | 404 | Return a string for each integration in the scantable. |
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[113] | 405 | Parameters: |
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[407] | 406 | row: row no of integration. Default -1 return all rows |
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[113] | 407 | Example: |
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| 408 | none |
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| 409 | """ |
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| 410 | out = [] |
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[407] | 411 | if row == -1: |
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| 412 | for i in range(self.nrow()): |
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| 413 | out.append(self._gettime(i)) |
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| 414 | return out |
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| 415 | else: |
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| 416 | if row < self.nrow(): |
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| 417 | return self._gettime(row) |
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[102] | 418 | |
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[714] | 419 | def get_sourcename(self, row=-1): |
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| 420 | """ |
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[794] | 421 | Get a list source names for the observations. |
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[714] | 422 | Return a string for each integration in the scantable. |
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| 423 | Parameters: |
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| 424 | row: row no of integration. Default -1 return all rows |
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| 425 | Example: |
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| 426 | none |
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| 427 | """ |
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| 428 | out = [] |
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| 429 | if row == -1: |
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| 430 | return [self._getsourcename(i) for i in range(self.nrow())] |
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| 431 | else: |
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| 432 | if 0 <= row < self.nrow(): |
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| 433 | return self._getsourcename(row) |
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| 434 | |
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[794] | 435 | def get_elevation(self, row=-1): |
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| 436 | """ |
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| 437 | Get a list of elevations for the observations. |
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| 438 | Return a float for each integration in the scantable. |
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| 439 | Parameters: |
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| 440 | row: row no of integration. Default -1 return all rows |
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| 441 | Example: |
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| 442 | none |
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| 443 | """ |
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| 444 | out = [] |
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| 445 | if row == -1: |
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| 446 | return [self._getelevation(i) for i in range(self.nrow())] |
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| 447 | else: |
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| 448 | if 0 <= row < self.nrow(): |
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| 449 | return self._getelevation(row) |
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| 450 | |
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| 451 | def get_azimuth(self, row=-1): |
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| 452 | """ |
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| 453 | Get a list of azimuths for the observations. |
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| 454 | Return a float for each integration in the scantable. |
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| 455 | Parameters: |
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| 456 | row: row no of integration. Default -1 return all rows |
---|
| 457 | Example: |
---|
| 458 | none |
---|
| 459 | """ |
---|
| 460 | out = [] |
---|
| 461 | if row == -1: |
---|
| 462 | return [self._getazimuth(i) for i in range(self.nrow())] |
---|
| 463 | else: |
---|
| 464 | if 0 <= row < self.nrow(): |
---|
| 465 | return self._getazimuth(row) |
---|
| 466 | |
---|
| 467 | def get_parangle(self, row=-1): |
---|
| 468 | """ |
---|
| 469 | Get a list of parallactic angles for the observations. |
---|
| 470 | Return a float for each integration in the scantable. |
---|
| 471 | Parameters: |
---|
| 472 | row: row no of integration. Default -1 return all rows |
---|
| 473 | Example: |
---|
| 474 | none |
---|
| 475 | """ |
---|
| 476 | out = [] |
---|
| 477 | if row == -1: |
---|
| 478 | return [self._getparangle(i) for i in range(self.nrow())] |
---|
| 479 | else: |
---|
| 480 | if 0 <= row < self.nrow(): |
---|
| 481 | return self._getparangle(row) |
---|
| 482 | |
---|
[102] | 483 | def set_unit(self, unit='channel'): |
---|
| 484 | """ |
---|
| 485 | Set the unit for all following operations on this scantable |
---|
| 486 | Parameters: |
---|
| 487 | unit: optional unit, default is 'channel' |
---|
[113] | 488 | one of '*Hz','km/s','channel', '' |
---|
[102] | 489 | """ |
---|
[484] | 490 | varlist = vars() |
---|
[113] | 491 | if unit in ['','pixel', 'channel']: |
---|
| 492 | unit = '' |
---|
| 493 | inf = list(self._getcoordinfo()) |
---|
| 494 | inf[0] = unit |
---|
| 495 | self._setcoordinfo(inf) |
---|
[484] | 496 | self._add_history("set_unit",varlist) |
---|
[113] | 497 | |
---|
[484] | 498 | def set_instrument(self, instr): |
---|
[358] | 499 | """ |
---|
| 500 | Set the instrument for subsequent processing |
---|
| 501 | Parameters: |
---|
[710] | 502 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 503 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 504 | """ |
---|
| 505 | self._setInstrument(instr) |
---|
[484] | 506 | self._add_history("set_instument",vars()) |
---|
[718] | 507 | print_log() |
---|
[358] | 508 | |
---|
[276] | 509 | def set_doppler(self, doppler='RADIO'): |
---|
| 510 | """ |
---|
| 511 | Set the doppler for all following operations on this scantable. |
---|
| 512 | Parameters: |
---|
| 513 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 514 | """ |
---|
[484] | 515 | varlist = vars() |
---|
[276] | 516 | inf = list(self._getcoordinfo()) |
---|
| 517 | inf[2] = doppler |
---|
| 518 | self._setcoordinfo(inf) |
---|
[484] | 519 | self._add_history("set_doppler",vars()) |
---|
[718] | 520 | print_log() |
---|
[710] | 521 | |
---|
[226] | 522 | def set_freqframe(self, frame=None): |
---|
[113] | 523 | """ |
---|
| 524 | Set the frame type of the Spectral Axis. |
---|
| 525 | Parameters: |
---|
[591] | 526 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
| 527 | 'REST','TOPO','LSRD','LSRK','BARY', |
---|
| 528 | 'GEO','GALACTO','LGROUP','CMB' |
---|
[113] | 529 | Examples: |
---|
| 530 | scan.set_freqframe('BARY') |
---|
| 531 | """ |
---|
[484] | 532 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
| 533 | varlist = vars() |
---|
[113] | 534 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
---|
| 535 | 'GEO','GALACTO','LGROUP','CMB'] |
---|
[591] | 536 | |
---|
[876] | 537 | if 1:#frame in valid: |
---|
[113] | 538 | inf = list(self._getcoordinfo()) |
---|
| 539 | inf[1] = frame |
---|
| 540 | self._setcoordinfo(inf) |
---|
[484] | 541 | self._add_history("set_freqframe",varlist) |
---|
[102] | 542 | else: |
---|
[718] | 543 | msg = "Please specify a valid freq type. Valid types are:\n",valid |
---|
| 544 | if rcParams['verbose']: |
---|
| 545 | print msg |
---|
| 546 | else: |
---|
| 547 | raise TypeError(msg) |
---|
| 548 | print_log() |
---|
[710] | 549 | |
---|
[113] | 550 | def get_unit(self): |
---|
| 551 | """ |
---|
| 552 | Get the default unit set in this scantable |
---|
| 553 | Parameters: |
---|
| 554 | Returns: |
---|
| 555 | A unit string |
---|
| 556 | """ |
---|
| 557 | inf = self._getcoordinfo() |
---|
| 558 | unit = inf[0] |
---|
| 559 | if unit == '': unit = 'channel' |
---|
| 560 | return unit |
---|
[102] | 561 | |
---|
[158] | 562 | def get_abcissa(self, rowno=0): |
---|
[102] | 563 | """ |
---|
[158] | 564 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 565 | selected Beam/IF/Pol |
---|
| 566 | Parameters: |
---|
[226] | 567 | rowno: an optional row number in the scantable. Default is the |
---|
| 568 | first row, i.e. rowno=0 |
---|
[113] | 569 | Returns: |
---|
[407] | 570 | The abcissa values and it's format string (as a dictionary) |
---|
[113] | 571 | """ |
---|
[256] | 572 | abc = self._getabcissa(rowno) |
---|
[710] | 573 | lbl = self._getabcissalabel(rowno) |
---|
[718] | 574 | print_log() |
---|
[158] | 575 | return abc, lbl |
---|
[113] | 576 | |
---|
| 577 | def create_mask(self, *args, **kwargs): |
---|
| 578 | """ |
---|
[102] | 579 | Compute and return a mask based on [min,max] windows. |
---|
[189] | 580 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 581 | applied. |
---|
[102] | 582 | Parameters: |
---|
| 583 | [min,max],[min2,max2],... |
---|
| 584 | Pairs of start/end points specifying the regions |
---|
| 585 | to be masked |
---|
[189] | 586 | invert: optional argument. If specified as True, |
---|
| 587 | return an inverted mask, i.e. the regions |
---|
| 588 | specified are EXCLUDED |
---|
[513] | 589 | row: create the mask using the specified row for |
---|
| 590 | unit conversions, default is row=0 |
---|
| 591 | only necessary if frequency varies over rows. |
---|
[102] | 592 | Example: |
---|
[113] | 593 | scan.set_unit('channel') |
---|
| 594 | |
---|
| 595 | a) |
---|
[102] | 596 | msk = scan.set_mask([400,500],[800,900]) |
---|
[189] | 597 | # masks everything outside 400 and 500 |
---|
[113] | 598 | # and 800 and 900 in the unit 'channel' |
---|
| 599 | |
---|
| 600 | b) |
---|
| 601 | msk = scan.set_mask([400,500],[800,900], invert=True) |
---|
[189] | 602 | # masks the regions between 400 and 500 |
---|
[113] | 603 | # and 800 and 900 in the unit 'channel' |
---|
[710] | 604 | |
---|
[102] | 605 | """ |
---|
[513] | 606 | row = 0 |
---|
| 607 | if kwargs.has_key("row"): |
---|
| 608 | row = kwargs.get("row") |
---|
| 609 | data = self._getabcissa(row) |
---|
[113] | 610 | u = self._getcoordinfo()[0] |
---|
[718] | 611 | if rcParams['verbose']: |
---|
[113] | 612 | if u == "": u = "channel" |
---|
[718] | 613 | from asap import asaplog |
---|
| 614 | msg = "The current mask window unit is %s" % u |
---|
[914] | 615 | if not self._check_ifs(): |
---|
[876] | 616 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 617 | asaplog.push(msg) |
---|
[102] | 618 | n = self.nchan() |
---|
[189] | 619 | msk = zeros(n) |
---|
[710] | 620 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 621 | |
---|
| 622 | ws = (isinstance(args[-1][-1],int) or isinstance(args[-1][-1],float)) and args or args[0] |
---|
| 623 | for window in ws: |
---|
[102] | 624 | if (len(window) != 2 or window[0] > window[1] ): |
---|
[718] | 625 | raise TypeError("A window needs to be defined as [min,max]") |
---|
[102] | 626 | for i in range(n): |
---|
[113] | 627 | if data[i] >= window[0] and data[i] < window[1]: |
---|
[189] | 628 | msk[i] = 1 |
---|
[113] | 629 | if kwargs.has_key('invert'): |
---|
| 630 | if kwargs.get('invert'): |
---|
| 631 | from numarray import logical_not |
---|
[710] | 632 | msk = logical_not(msk) |
---|
[718] | 633 | print_log() |
---|
[102] | 634 | return msk |
---|
[710] | 635 | |
---|
[256] | 636 | def get_restfreqs(self): |
---|
| 637 | """ |
---|
| 638 | Get the restfrequency(s) stored in this scantable. |
---|
| 639 | The return value(s) are always of unit 'Hz' |
---|
| 640 | Parameters: |
---|
| 641 | none |
---|
| 642 | Returns: |
---|
| 643 | a list of doubles |
---|
| 644 | """ |
---|
| 645 | return list(self._getrestfreqs()) |
---|
[102] | 646 | |
---|
[402] | 647 | |
---|
[931] | 648 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
| 649 | """ |
---|
| 650 | Set or replace the restfrequency specified and |
---|
| 651 | If the 'freqs' argument holds a scalar, |
---|
| 652 | then that rest frequency will be applied to all the selected |
---|
| 653 | data. If the 'freqs' argument holds |
---|
| 654 | a vector, then it MUST be of equal or smaller length than |
---|
| 655 | the number of IFs (and the available restfrequencies will be |
---|
| 656 | replaced by this vector). In this case, *all* data have |
---|
| 657 | the restfrequency set per IF according |
---|
| 658 | to the corresponding value you give in the 'freqs' vector. |
---|
| 659 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
| 660 | IF 1 gets restfreq 2e9. |
---|
| 661 | You can also specify the frequencies via known line names |
---|
| 662 | from the built-in Lovas table. |
---|
| 663 | Parameters: |
---|
| 664 | freqs: list of rest frequency values or string idenitfiers |
---|
| 665 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 666 | |
---|
[931] | 667 | Example: |
---|
| 668 | # set the given restfrequency for the whole table |
---|
| 669 | scan.set_restfreqs(freqs=1.4e9) |
---|
| 670 | # If thee number of IFs in the data is >= 2 the IF0 gets the first |
---|
| 671 | # value IF1 the second... |
---|
| 672 | scan.set_restfreqs(freqs=[1.4e9,1.67e9]) |
---|
| 673 | #set the given restfrequency for the whole table (by name) |
---|
| 674 | scan.set_restfreqs(freqs="OH1667") |
---|
[391] | 675 | |
---|
[931] | 676 | Note: |
---|
| 677 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 678 | source and IF basis, use scantable.set_selection() before using |
---|
| 679 | this function. |
---|
| 680 | # provide your scantable is call scan |
---|
| 681 | selection = selector() |
---|
| 682 | selection.set_name("ORION*") |
---|
| 683 | selection.set_ifs([1]) |
---|
| 684 | scan.set_selection(selection) |
---|
| 685 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 686 | |
---|
| 687 | """ |
---|
| 688 | varlist = vars() |
---|
| 689 | |
---|
| 690 | t = type(freqs) |
---|
| 691 | if isinstance(freqs, int) or isinstance(freqs,float): |
---|
| 692 | self._setrestfreqs(freqs, unit) |
---|
| 693 | elif isinstance(freqs, list) or isinstance(freqs,tuple): |
---|
| 694 | if isinstance(freqs[-1], int) or isinstance(freqs[-1],float): |
---|
| 695 | from asap._asap import selector |
---|
| 696 | sel = selector() |
---|
| 697 | savesel = self._getselection() |
---|
| 698 | for i in xrange(len(freqs)): |
---|
| 699 | sel._setifs([i]) |
---|
| 700 | self._setselection(sel) |
---|
| 701 | self._setrestfreqs(freqs[i], unit) |
---|
| 702 | self._setselection(savesel) |
---|
| 703 | elif isinstance(freqs[-1], str): |
---|
| 704 | # not yet implemented |
---|
| 705 | pass |
---|
| 706 | else: |
---|
| 707 | return |
---|
| 708 | self._add_history("set_restfreqs", varlist) |
---|
| 709 | |
---|
| 710 | |
---|
| 711 | |
---|
[484] | 712 | def history(self): |
---|
| 713 | hist = list(self._gethistory()) |
---|
[794] | 714 | out = "-"*80 |
---|
[484] | 715 | for h in hist: |
---|
[489] | 716 | if h.startswith("---"): |
---|
[794] | 717 | out += "\n"+h |
---|
[489] | 718 | else: |
---|
| 719 | items = h.split("##") |
---|
| 720 | date = items[0] |
---|
| 721 | func = items[1] |
---|
| 722 | items = items[2:] |
---|
[794] | 723 | out += "\n"+date+"\n" |
---|
| 724 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 725 | for i in items: |
---|
| 726 | s = i.split("=") |
---|
[794] | 727 | out += "\n %s = %s" % (s[0],s[1]) |
---|
| 728 | out += "\n"+"-"*80 |
---|
| 729 | try: |
---|
| 730 | from IPython.genutils import page as pager |
---|
| 731 | except ImportError: |
---|
| 732 | from pydoc import pager |
---|
| 733 | pager(out) |
---|
[484] | 734 | return |
---|
| 735 | |
---|
[513] | 736 | # |
---|
| 737 | # Maths business |
---|
| 738 | # |
---|
| 739 | |
---|
[931] | 740 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[513] | 741 | """ |
---|
| 742 | Return the (time) average of a scan, or apply it 'insitu'. |
---|
| 743 | Note: |
---|
| 744 | in channels only |
---|
| 745 | The cursor of the output scan is set to 0. |
---|
| 746 | Parameters: |
---|
| 747 | one scan or comma separated scans |
---|
| 748 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 749 | weighting) |
---|
[558] | 750 | scanav: True averages each scan separately |
---|
| 751 | False (default) averages all scans together, |
---|
[524] | 752 | weight: Weighting scheme. 'none', 'var' (1/var(spec) |
---|
[535] | 753 | weighted), 'tsys' (1/Tsys**2 weighted), 'tint' |
---|
| 754 | (integration time weighted) or 'tintsys' (Tint/Tsys**2). |
---|
| 755 | The default is 'tint' |
---|
[931] | 756 | align: align the spectra in velocity before averaging. It takes |
---|
| 757 | the time of the first spectrum as reference time. |
---|
[513] | 758 | Example: |
---|
| 759 | # time average the scantable without using a mask |
---|
[710] | 760 | newscan = scan.average_time() |
---|
[513] | 761 | """ |
---|
| 762 | varlist = vars() |
---|
[524] | 763 | if weight is None: weight = 'tint' |
---|
[513] | 764 | if mask is None: mask = () |
---|
[876] | 765 | if scanav: |
---|
| 766 | scanav = "SCAN" |
---|
| 767 | else: |
---|
| 768 | scanav = "NONE" |
---|
[931] | 769 | s = scantable(self._math._average((self,), mask, weight.upper(), |
---|
| 770 | scanav, align)) |
---|
[513] | 771 | s._add_history("average_time",varlist) |
---|
[718] | 772 | print_log() |
---|
[513] | 773 | return s |
---|
[710] | 774 | |
---|
[876] | 775 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[513] | 776 | """ |
---|
| 777 | Return a scan where all spectra are converted to either |
---|
| 778 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 779 | By default the function tries to look the values up internally. |
---|
| 780 | If it can't find them (or if you want to over-ride), you must |
---|
| 781 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 782 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 783 | Parameters: |
---|
| 784 | jyperk: the Jy / K conversion factor |
---|
| 785 | eta: the aperture efficiency |
---|
| 786 | d: the geomtric diameter (metres) |
---|
| 787 | insitu: if False a new scantable is returned. |
---|
| 788 | Otherwise, the scaling is done in-situ |
---|
| 789 | The default is taken from .asaprc (False) |
---|
| 790 | allaxes: if True apply to all spectra. Otherwise |
---|
| 791 | apply only to the selected (beam/pol/if)spectra only |
---|
| 792 | The default is taken from .asaprc (True if none) |
---|
| 793 | """ |
---|
| 794 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 795 | self._math._setinsitu(insitu) |
---|
[513] | 796 | varlist = vars() |
---|
| 797 | if jyperk is None: jyperk = -1.0 |
---|
| 798 | if d is None: d = -1.0 |
---|
| 799 | if eta is None: eta = -1.0 |
---|
[876] | 800 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 801 | s._add_history("convert_flux", varlist) |
---|
| 802 | print_log() |
---|
| 803 | if insitu: self._assign(s) |
---|
| 804 | else: return s |
---|
[513] | 805 | |
---|
[876] | 806 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[513] | 807 | """ |
---|
| 808 | Return a scan after applying a gain-elevation correction. |
---|
| 809 | The correction can be made via either a polynomial or a |
---|
| 810 | table-based interpolation (and extrapolation if necessary). |
---|
| 811 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 812 | If you specify neither, then a polynomial correction will be made |
---|
| 813 | with built in coefficients known for certain telescopes (an error |
---|
| 814 | will occur if the instrument is not known). |
---|
| 815 | The data and Tsys are *divided* by the scaling factors. |
---|
| 816 | Parameters: |
---|
| 817 | poly: Polynomial coefficients (default None) to compute a |
---|
| 818 | gain-elevation correction as a function of |
---|
| 819 | elevation (in degrees). |
---|
| 820 | filename: The name of an ascii file holding correction factors. |
---|
| 821 | The first row of the ascii file must give the column |
---|
| 822 | names and these MUST include columns |
---|
| 823 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 824 | by this) somewhere. |
---|
| 825 | The second row must give the data type of the |
---|
| 826 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 827 | An example file would be |
---|
| 828 | (actual factors are arbitrary) : |
---|
| 829 | |
---|
| 830 | TIME ELEVATION FACTOR |
---|
| 831 | R R R |
---|
| 832 | 0.1 0 0.8 |
---|
| 833 | 0.2 20 0.85 |
---|
| 834 | 0.3 40 0.9 |
---|
| 835 | 0.4 60 0.85 |
---|
| 836 | 0.5 80 0.8 |
---|
| 837 | 0.6 90 0.75 |
---|
| 838 | method: Interpolation method when correcting from a table. |
---|
| 839 | Values are "nearest", "linear" (default), "cubic" |
---|
| 840 | and "spline" |
---|
| 841 | insitu: if False a new scantable is returned. |
---|
| 842 | Otherwise, the scaling is done in-situ |
---|
| 843 | The default is taken from .asaprc (False) |
---|
| 844 | """ |
---|
| 845 | |
---|
| 846 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 847 | self._math._setinsitu(insitu) |
---|
[513] | 848 | varlist = vars() |
---|
| 849 | if poly is None: |
---|
| 850 | poly = () |
---|
| 851 | from os.path import expandvars |
---|
| 852 | filename = expandvars(filename) |
---|
[876] | 853 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 854 | s._add_history("gain_el", varlist) |
---|
| 855 | print_log() |
---|
| 856 | if insitu: self._assign(s) |
---|
| 857 | else: return s |
---|
[710] | 858 | |
---|
[931] | 859 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[513] | 860 | """ |
---|
| 861 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 862 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 863 | set_freqframe. |
---|
| 864 | Parameters: |
---|
| 865 | reftime: reference time to align at. By default, the time of |
---|
| 866 | the first row of data is used. |
---|
| 867 | method: Interpolation method for regridding the spectra. |
---|
| 868 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 869 | and "spline" |
---|
| 870 | insitu: if False a new scantable is returned. |
---|
| 871 | Otherwise, the scaling is done in-situ |
---|
| 872 | The default is taken from .asaprc (False) |
---|
| 873 | """ |
---|
[931] | 874 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 875 | self._math._setinsitu(insitu) |
---|
[513] | 876 | varlist = vars() |
---|
[931] | 877 | if reftime is None: reftime = "" |
---|
| 878 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 879 | s._add_history("freq_align", varlist) |
---|
| 880 | print_log() |
---|
| 881 | if insitu: self._assign(s) |
---|
| 882 | else: return s |
---|
[513] | 883 | |
---|
[876] | 884 | def opacity(self, tau, insitu=None): |
---|
[513] | 885 | """ |
---|
| 886 | Apply an opacity correction. The data |
---|
| 887 | and Tsys are multiplied by the correction factor. |
---|
| 888 | Parameters: |
---|
| 889 | tau: Opacity from which the correction factor is |
---|
| 890 | exp(tau*ZD) |
---|
| 891 | where ZD is the zenith-distance |
---|
| 892 | insitu: if False a new scantable is returned. |
---|
| 893 | Otherwise, the scaling is done in-situ |
---|
| 894 | The default is taken from .asaprc (False) |
---|
| 895 | """ |
---|
| 896 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 897 | self._math._setinsitu(insitu) |
---|
[513] | 898 | varlist = vars() |
---|
[876] | 899 | s = scantable(self._math._opacity(self, tau)) |
---|
| 900 | s._add_history("opacity", varlist) |
---|
| 901 | print_log() |
---|
| 902 | if insitu: self._assign(s) |
---|
| 903 | else: return s |
---|
[513] | 904 | |
---|
| 905 | def bin(self, width=5, insitu=None): |
---|
| 906 | """ |
---|
| 907 | Return a scan where all spectra have been binned up. |
---|
| 908 | width: The bin width (default=5) in pixels |
---|
| 909 | insitu: if False a new scantable is returned. |
---|
| 910 | Otherwise, the scaling is done in-situ |
---|
| 911 | The default is taken from .asaprc (False) |
---|
| 912 | """ |
---|
| 913 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 914 | self._math._setinsitu(insitu) |
---|
[513] | 915 | varlist = vars() |
---|
[876] | 916 | s = scantable(self._math._bin(self, width)) |
---|
| 917 | s._add_history("bin",varlist) |
---|
| 918 | print_log() |
---|
| 919 | if insitu: self._assign(s) |
---|
| 920 | else: return s |
---|
[513] | 921 | |
---|
[710] | 922 | |
---|
[513] | 923 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 924 | """ |
---|
| 925 | Return a scan where all spectra have been binned up |
---|
| 926 | width: The bin width (default=5) in pixels |
---|
| 927 | method: Interpolation method when correcting from a table. |
---|
| 928 | Values are "nearest", "linear", "cubic" (default) |
---|
| 929 | and "spline" |
---|
| 930 | insitu: if False a new scantable is returned. |
---|
| 931 | Otherwise, the scaling is done in-situ |
---|
| 932 | The default is taken from .asaprc (False) |
---|
| 933 | """ |
---|
| 934 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 935 | self._math._setinsitu(insitu) |
---|
[513] | 936 | varlist = vars() |
---|
[876] | 937 | s = scantable(self._math._resample(self, method, width)) |
---|
| 938 | s._add_history("resample",varlist) |
---|
| 939 | print_log() |
---|
| 940 | if insitu: self._assign(s) |
---|
| 941 | else: return s |
---|
[513] | 942 | |
---|
| 943 | |
---|
[876] | 944 | # def average_pol(self, mask=None, weight='none', insitu=None): |
---|
| 945 | # """ |
---|
| 946 | # Average the Polarisations together. |
---|
| 947 | # The polarisation cursor of the output scan is set to 0 |
---|
| 948 | # Parameters: |
---|
| 949 | # mask: An optional mask defining the region, where the |
---|
| 950 | # averaging will be applied. The output will have all |
---|
| 951 | # specified points masked. |
---|
| 952 | # weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 953 | # weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 954 | # insitu: if False a new scantable is returned. |
---|
| 955 | # Otherwise, the scaling is done in-situ |
---|
| 956 | # The default is taken from .asaprc (False) |
---|
| 957 | # """ |
---|
| 958 | # if insitu is None: insitu = rcParams['insitu'] |
---|
| 959 | # self._math._setinsitu(insitu) |
---|
| 960 | # varlist = vars() |
---|
| 961 | # |
---|
| 962 | # if mask is None: |
---|
| 963 | # mask = () |
---|
| 964 | # s = self._math._averagepol(self, mask, weight) |
---|
| 965 | # s._add_history("average_pol",varlist) |
---|
| 966 | # print_log() |
---|
| 967 | # if insitu: self._assign(s) |
---|
| 968 | # else: return scantable(s) |
---|
[513] | 969 | |
---|
[876] | 970 | def smooth(self, kernel="hanning", width=5.0, insitu=None): |
---|
[513] | 971 | """ |
---|
| 972 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 973 | Parameters: |
---|
| 974 | scan: The input scan |
---|
| 975 | kernel: The type of smoothing kernel. Select from |
---|
| 976 | 'hanning' (default), 'gaussian' and 'boxcar'. |
---|
| 977 | The first three characters are sufficient. |
---|
| 978 | width: The width of the kernel in pixels. For hanning this is |
---|
| 979 | ignored otherwise it defauls to 5 pixels. |
---|
| 980 | For 'gaussian' it is the Full Width Half |
---|
| 981 | Maximum. For 'boxcar' it is the full width. |
---|
| 982 | insitu: if False a new scantable is returned. |
---|
| 983 | Otherwise, the scaling is done in-situ |
---|
| 984 | The default is taken from .asaprc (False) |
---|
| 985 | Example: |
---|
| 986 | none |
---|
| 987 | """ |
---|
| 988 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 989 | self._math._setinsitu(insitu) |
---|
[513] | 990 | varlist = vars() |
---|
[876] | 991 | s = scantable(self._math._smooth(self,kernel,width)) |
---|
| 992 | s._add_history("smooth", varlist) |
---|
| 993 | print_log() |
---|
| 994 | if insitu: self._assign(s) |
---|
| 995 | else: return s |
---|
[513] | 996 | |
---|
[876] | 997 | |
---|
| 998 | def poly_baseline(self, mask=None, order=0, insitu=None): |
---|
[513] | 999 | """ |
---|
| 1000 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1001 | Parameters: |
---|
[794] | 1002 | scan: a scantable |
---|
| 1003 | mask: an optional mask |
---|
| 1004 | order: the order of the polynomial (default is 0) |
---|
| 1005 | insitu: if False a new scantable is returned. |
---|
| 1006 | Otherwise, the scaling is done in-situ |
---|
| 1007 | The default is taken from .asaprc (False) |
---|
| 1008 | allaxes: If True (default) apply to all spectra. Otherwise |
---|
| 1009 | apply only to the selected (beam/pol/if)spectra only |
---|
| 1010 | The default is taken from .asaprc (True if none) |
---|
[513] | 1011 | Example: |
---|
| 1012 | # return a scan baselined by a third order polynomial, |
---|
| 1013 | # not using a mask |
---|
| 1014 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1015 | """ |
---|
[513] | 1016 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1017 | varlist = vars() |
---|
| 1018 | if mask is None: |
---|
| 1019 | from numarray import ones |
---|
[876] | 1020 | mask = list(ones(self.nchan(-1))) |
---|
[513] | 1021 | from asap.asapfitter import fitter |
---|
| 1022 | f = fitter() |
---|
| 1023 | f.set_scan(self, mask) |
---|
| 1024 | f.set_function(poly=order) |
---|
[876] | 1025 | s = f.auto_fit(insitu) |
---|
| 1026 | s._add_history("poly_baseline", varlist) |
---|
[718] | 1027 | print_log() |
---|
[876] | 1028 | if insitu: self._assign(s) |
---|
| 1029 | else: return s |
---|
[513] | 1030 | |
---|
[931] | 1031 | def auto_poly_baseline(self, mask=[], edge=(0,0), order=0, |
---|
[880] | 1032 | threshold=3, insitu=None): |
---|
| 1033 | """ |
---|
| 1034 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1035 | Spectral lines are detected first using linefinder and masked out |
---|
| 1036 | to avoid them affecting the baseline solution. |
---|
| 1037 | |
---|
| 1038 | Parameters: |
---|
| 1039 | mask: an optional mask retreived from scantable |
---|
| 1040 | edge: an optional number of channel to drop at |
---|
| 1041 | the edge of spectrum. If only one value is |
---|
| 1042 | specified, the same number will be dropped from |
---|
| 1043 | both sides of the spectrum. Default is to keep |
---|
[907] | 1044 | all channels. Nested tuples represent individual |
---|
| 1045 | edge selection for different IFs (a number of spectral |
---|
| 1046 | channels can be different) |
---|
[880] | 1047 | order: the order of the polynomial (default is 0) |
---|
| 1048 | threshold: the threshold used by line finder. It is better to |
---|
| 1049 | keep it large as only strong lines affect the |
---|
| 1050 | baseline solution. |
---|
| 1051 | insitu: if False a new scantable is returned. |
---|
| 1052 | Otherwise, the scaling is done in-situ |
---|
| 1053 | The default is taken from .asaprc (False) |
---|
| 1054 | |
---|
| 1055 | Example: |
---|
| 1056 | scan2=scan.auto_poly_baseline(order=7) |
---|
| 1057 | """ |
---|
| 1058 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1059 | varlist = vars() |
---|
| 1060 | from asap.asapfitter import fitter |
---|
| 1061 | from asap.asaplinefind import linefinder |
---|
| 1062 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1063 | |
---|
[907] | 1064 | # check whether edge is set up for each IF individually |
---|
| 1065 | individualEdge = False; |
---|
| 1066 | if len(edge)>1: |
---|
| 1067 | if isinstance(edge[0],list) or isinstance(edge[0],tuple): |
---|
[919] | 1068 | individualEdge = True; |
---|
[907] | 1069 | |
---|
| 1070 | if not _is_valid(edge, int) and not individualEdge: |
---|
[909] | 1071 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1072 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1073 | to make individual selection for different IFs." |
---|
[919] | 1074 | |
---|
[907] | 1075 | curedge = (0,0) |
---|
| 1076 | if individualEdge: |
---|
| 1077 | for edge_par in edge: |
---|
| 1078 | if not _is_valid(edge,int): |
---|
[909] | 1079 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
[907] | 1080 | to be a pair of integers or an integer." |
---|
| 1081 | else: |
---|
| 1082 | curedge = edge; |
---|
[880] | 1083 | |
---|
| 1084 | # setup fitter |
---|
| 1085 | f = fitter() |
---|
| 1086 | f.set_function(poly=order) |
---|
| 1087 | |
---|
| 1088 | # setup line finder |
---|
| 1089 | fl=linefinder() |
---|
| 1090 | fl.set_options(threshold=threshold) |
---|
| 1091 | |
---|
| 1092 | if not insitu: |
---|
| 1093 | workscan=self.copy() |
---|
| 1094 | else: |
---|
| 1095 | workscan=self |
---|
| 1096 | |
---|
[907] | 1097 | fl.set_scan(workscan) |
---|
| 1098 | |
---|
[880] | 1099 | rows=range(workscan.nrow()) |
---|
| 1100 | from asap import asaplog |
---|
| 1101 | asaplog.push("Processing:") |
---|
| 1102 | for r in rows: |
---|
| 1103 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % (workscan.getscan(r),workscan.getbeam(r),workscan.getif(r),workscan.getpol(r), workscan.getcycle(r)) |
---|
| 1104 | asaplog.push(msg, False) |
---|
[907] | 1105 | |
---|
| 1106 | # figure out edge parameter |
---|
| 1107 | if individualEdge: |
---|
| 1108 | if len(edge)>=workscan.getif(r): |
---|
| 1109 | raise RuntimeError, "Number of edge elements appear to be less than the number of IFs" |
---|
| 1110 | curedge = edge[workscan.getif(r)] |
---|
[919] | 1111 | |
---|
[907] | 1112 | # setup line finder |
---|
| 1113 | fl.find_lines(r,mask,curedge) |
---|
[880] | 1114 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1115 | f.x = workscan._getabcissa(r) |
---|
| 1116 | f.y = workscan._getspectrum(r) |
---|
| 1117 | f.data = None |
---|
| 1118 | f.fit() |
---|
| 1119 | x = f.get_parameters() |
---|
| 1120 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
| 1121 | workscan._add_history("poly_baseline", varlist) |
---|
| 1122 | if insitu: |
---|
| 1123 | self._assign(workscan) |
---|
| 1124 | else: |
---|
| 1125 | return workscan |
---|
| 1126 | |
---|
[914] | 1127 | def rotate_linpolphase(self, angle): |
---|
| 1128 | """ |
---|
| 1129 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1130 | This is always done in situ in the raw data. So if you call this |
---|
| 1131 | function more than once then each call rotates the phase further. |
---|
| 1132 | Parameters: |
---|
| 1133 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1134 | Examples: |
---|
| 1135 | scan.rotate_linpolphase(2.3) |
---|
| 1136 | """ |
---|
| 1137 | varlist = vars() |
---|
[936] | 1138 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 1139 | self._add_history("rotate_linpolphase", varlist) |
---|
| 1140 | print_log() |
---|
| 1141 | return |
---|
[710] | 1142 | |
---|
[513] | 1143 | |
---|
[914] | 1144 | def rotate_xyphase(self, angle): |
---|
| 1145 | """ |
---|
| 1146 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1147 | in the data. So if you call this function more than once |
---|
| 1148 | then each call rotates the phase further. |
---|
| 1149 | Parameters: |
---|
| 1150 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1151 | Examples: |
---|
| 1152 | scan.rotate_xyphase(2.3) |
---|
| 1153 | """ |
---|
| 1154 | varlist = vars() |
---|
[936] | 1155 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 1156 | self._add_history("rotate_xyphase", varlist) |
---|
| 1157 | print_log() |
---|
| 1158 | return |
---|
| 1159 | |
---|
| 1160 | def swap_linears(self): |
---|
| 1161 | """ |
---|
| 1162 | Swap the linear polarisations XX and YY |
---|
| 1163 | """ |
---|
| 1164 | varlist = vars() |
---|
[936] | 1165 | self._math._swap_linears(self) |
---|
[914] | 1166 | self._add_history("swap_linears", varlist) |
---|
| 1167 | print_log() |
---|
| 1168 | return |
---|
| 1169 | |
---|
| 1170 | def invert_phase(self): |
---|
| 1171 | """ |
---|
| 1172 | Invert the phase of the complex polarisation |
---|
| 1173 | """ |
---|
| 1174 | varlist = vars() |
---|
[936] | 1175 | self._math._invert_phase(self) |
---|
[914] | 1176 | self._add_history("invert_phase", varlist) |
---|
| 1177 | print_log() |
---|
| 1178 | return |
---|
| 1179 | |
---|
[876] | 1180 | def add(self, offset, insitu=None): |
---|
[513] | 1181 | """ |
---|
| 1182 | Return a scan where all spectra have the offset added |
---|
| 1183 | Parameters: |
---|
| 1184 | offset: the offset |
---|
| 1185 | insitu: if False a new scantable is returned. |
---|
| 1186 | Otherwise, the scaling is done in-situ |
---|
| 1187 | The default is taken from .asaprc (False) |
---|
| 1188 | """ |
---|
| 1189 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1190 | self._math._setinsitu(insitu) |
---|
[513] | 1191 | varlist = vars() |
---|
[876] | 1192 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
| 1193 | s._add_history("add",varlist) |
---|
| 1194 | print_log() |
---|
| 1195 | if insitu: |
---|
| 1196 | self._assign(s) |
---|
| 1197 | else: |
---|
[513] | 1198 | return s |
---|
| 1199 | |
---|
[876] | 1200 | def scale(self, factor, tsys=True, insitu=None,): |
---|
[513] | 1201 | """ |
---|
| 1202 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 1203 | Parameters: |
---|
| 1204 | factor: the scaling factor |
---|
| 1205 | insitu: if False a new scantable is returned. |
---|
| 1206 | Otherwise, the scaling is done in-situ |
---|
| 1207 | The default is taken from .asaprc (False) |
---|
| 1208 | tsys: if True (default) then apply the operation to Tsys |
---|
| 1209 | as well as the data |
---|
| 1210 | """ |
---|
| 1211 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1212 | self._math._setinsitu(insitu) |
---|
[513] | 1213 | varlist = vars() |
---|
[876] | 1214 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
| 1215 | s._add_history("scale",varlist) |
---|
| 1216 | print_log() |
---|
| 1217 | if insitu: |
---|
| 1218 | self._assign(s) |
---|
| 1219 | else: |
---|
[513] | 1220 | return s |
---|
| 1221 | |
---|
[876] | 1222 | def auto_quotient(self, mode='time', preserve=True): |
---|
[670] | 1223 | """ |
---|
| 1224 | This function allows to build quotients automatically. |
---|
| 1225 | It assumes the observation to have the same numer of |
---|
| 1226 | "ons" and "offs" |
---|
| 1227 | It will support "closest off in time" in the future |
---|
| 1228 | Parameters: |
---|
| 1229 | mode: the on/off detection mode; 'suffix' (default) |
---|
| 1230 | 'suffix' identifies 'off' scans by the |
---|
| 1231 | trailing '_R' (Mopra/Parkes) or |
---|
| 1232 | '_e'/'_w' (Tid) |
---|
[710] | 1233 | preserve: you can preserve (default) the continuum or |
---|
| 1234 | remove it. The equations used are |
---|
[670] | 1235 | preserve: Output = Toff * (on/off) - Toff |
---|
| 1236 | remove: Output = Tref * (on/off) - Ton |
---|
| 1237 | """ |
---|
[876] | 1238 | modes = ["time"] |
---|
[670] | 1239 | if not mode in modes: |
---|
[876] | 1240 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 1241 | raise ValueError(msg) |
---|
| 1242 | varlist = vars() |
---|
| 1243 | s = scantable(self._math._quotient(self, mode, preserve)) |
---|
| 1244 | s._add_history("auto_quotient",varlist) |
---|
| 1245 | print_log() |
---|
| 1246 | return s |
---|
[710] | 1247 | |
---|
[513] | 1248 | |
---|
[876] | 1249 | |
---|
| 1250 | |
---|
[718] | 1251 | def freq_switch(self, insitu=None): |
---|
| 1252 | """ |
---|
| 1253 | Apply frequency switching to the data. |
---|
| 1254 | Parameters: |
---|
| 1255 | insitu: if False a new scantable is returned. |
---|
| 1256 | Otherwise, the swictching is done in-situ |
---|
| 1257 | The default is taken from .asaprc (False) |
---|
| 1258 | Example: |
---|
| 1259 | none |
---|
| 1260 | """ |
---|
| 1261 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1262 | self._math._setinsitu(insitu) |
---|
[718] | 1263 | varlist = vars() |
---|
[876] | 1264 | s = scantable(self._math._freqswitch(self)) |
---|
| 1265 | s._add_history("freq_switch",varlist) |
---|
| 1266 | print_log() |
---|
| 1267 | if insitu: self._assign(s) |
---|
| 1268 | else: return s |
---|
[718] | 1269 | |
---|
[780] | 1270 | def recalc_azel(self): |
---|
| 1271 | """ |
---|
| 1272 | Recalculate the azimuth and elevation for each position. |
---|
| 1273 | Parameters: |
---|
| 1274 | none |
---|
| 1275 | Example: |
---|
| 1276 | """ |
---|
| 1277 | varlist = vars() |
---|
[876] | 1278 | self._recalcazel() |
---|
[780] | 1279 | self._add_history("recalc_azel", varlist) |
---|
| 1280 | print_log() |
---|
| 1281 | return |
---|
| 1282 | |
---|
[513] | 1283 | def __add__(self, other): |
---|
| 1284 | varlist = vars() |
---|
| 1285 | s = None |
---|
| 1286 | if isinstance(other, scantable): |
---|
[876] | 1287 | print "scantable + scantable NYI" |
---|
| 1288 | return |
---|
[513] | 1289 | elif isinstance(other, float): |
---|
[876] | 1290 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 1291 | else: |
---|
[718] | 1292 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1293 | s._add_history("operator +", varlist) |
---|
[718] | 1294 | print_log() |
---|
[513] | 1295 | return s |
---|
| 1296 | |
---|
| 1297 | def __sub__(self, other): |
---|
| 1298 | """ |
---|
| 1299 | implicit on all axes and on Tsys |
---|
| 1300 | """ |
---|
| 1301 | varlist = vars() |
---|
| 1302 | s = None |
---|
| 1303 | if isinstance(other, scantable): |
---|
[876] | 1304 | print "scantable - scantable NYI" |
---|
| 1305 | return |
---|
[513] | 1306 | elif isinstance(other, float): |
---|
[876] | 1307 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 1308 | else: |
---|
[718] | 1309 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1310 | s._add_history("operator -", varlist) |
---|
[718] | 1311 | print_log() |
---|
[513] | 1312 | return s |
---|
[710] | 1313 | |
---|
[513] | 1314 | def __mul__(self, other): |
---|
| 1315 | """ |
---|
| 1316 | implicit on all axes and on Tsys |
---|
| 1317 | """ |
---|
| 1318 | varlist = vars() |
---|
| 1319 | s = None |
---|
| 1320 | if isinstance(other, scantable): |
---|
[876] | 1321 | print "scantable * scantable NYI" |
---|
| 1322 | return |
---|
[513] | 1323 | elif isinstance(other, float): |
---|
[876] | 1324 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 1325 | else: |
---|
[718] | 1326 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1327 | s._add_history("operator *", varlist) |
---|
[718] | 1328 | print_log() |
---|
[513] | 1329 | return s |
---|
| 1330 | |
---|
[710] | 1331 | |
---|
[513] | 1332 | def __div__(self, other): |
---|
| 1333 | """ |
---|
| 1334 | implicit on all axes and on Tsys |
---|
| 1335 | """ |
---|
| 1336 | varlist = vars() |
---|
| 1337 | s = None |
---|
| 1338 | if isinstance(other, scantable): |
---|
[876] | 1339 | print "scantable / scantable NYI" |
---|
| 1340 | return |
---|
[513] | 1341 | elif isinstance(other, float): |
---|
| 1342 | if other == 0.0: |
---|
[718] | 1343 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 1344 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 1345 | else: |
---|
[718] | 1346 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1347 | s._add_history("operator /", varlist) |
---|
[718] | 1348 | print_log() |
---|
[513] | 1349 | return s |
---|
| 1350 | |
---|
[530] | 1351 | def get_fit(self, row=0): |
---|
| 1352 | """ |
---|
| 1353 | Print or return the stored fits for a row in the scantable |
---|
| 1354 | Parameters: |
---|
| 1355 | row: the row which the fit has been applied to. |
---|
| 1356 | """ |
---|
| 1357 | if row > self.nrow(): |
---|
| 1358 | return |
---|
| 1359 | from asap import asapfit |
---|
| 1360 | fit = asapfit(self._getfit(row)) |
---|
[718] | 1361 | if rcParams['verbose']: |
---|
[530] | 1362 | print fit |
---|
| 1363 | return |
---|
| 1364 | else: |
---|
| 1365 | return fit.as_dict() |
---|
| 1366 | |
---|
[484] | 1367 | def _add_history(self, funcname, parameters): |
---|
| 1368 | # create date |
---|
| 1369 | sep = "##" |
---|
| 1370 | from datetime import datetime |
---|
| 1371 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 1372 | hist = dstr+sep |
---|
| 1373 | hist += funcname+sep#cdate+sep |
---|
| 1374 | if parameters.has_key('self'): del parameters['self'] |
---|
| 1375 | for k,v in parameters.iteritems(): |
---|
| 1376 | if type(v) is dict: |
---|
| 1377 | for k2,v2 in v.iteritems(): |
---|
| 1378 | hist += k2 |
---|
| 1379 | hist += "=" |
---|
| 1380 | if isinstance(v2,scantable): |
---|
| 1381 | hist += 'scantable' |
---|
| 1382 | elif k2 == 'mask': |
---|
[513] | 1383 | if isinstance(v2,list) or isinstance(v2,tuple): |
---|
| 1384 | hist += str(self._zip_mask(v2)) |
---|
| 1385 | else: |
---|
| 1386 | hist += str(v2) |
---|
[484] | 1387 | else: |
---|
[513] | 1388 | hist += str(v2) |
---|
[484] | 1389 | else: |
---|
| 1390 | hist += k |
---|
| 1391 | hist += "=" |
---|
| 1392 | if isinstance(v,scantable): |
---|
| 1393 | hist += 'scantable' |
---|
| 1394 | elif k == 'mask': |
---|
[513] | 1395 | if isinstance(v,list) or isinstance(v,tuple): |
---|
| 1396 | hist += str(self._zip_mask(v)) |
---|
| 1397 | else: |
---|
| 1398 | hist += str(v) |
---|
[484] | 1399 | else: |
---|
| 1400 | hist += str(v) |
---|
| 1401 | hist += sep |
---|
| 1402 | hist = hist[:-2] # remove trailing '##' |
---|
| 1403 | self._addhistory(hist) |
---|
| 1404 | |
---|
[710] | 1405 | |
---|
[484] | 1406 | def _zip_mask(self, mask): |
---|
| 1407 | mask = list(mask) |
---|
| 1408 | i = 0 |
---|
| 1409 | segments = [] |
---|
| 1410 | while mask[i:].count(1): |
---|
| 1411 | i += mask[i:].index(1) |
---|
| 1412 | if mask[i:].count(0): |
---|
| 1413 | j = i + mask[i:].index(0) |
---|
| 1414 | else: |
---|
[710] | 1415 | j = len(mask) |
---|
[484] | 1416 | segments.append([i,j]) |
---|
[710] | 1417 | i = j |
---|
[484] | 1418 | return segments |
---|
[714] | 1419 | |
---|
[626] | 1420 | def _get_ordinate_label(self): |
---|
| 1421 | fu = "("+self.get_fluxunit()+")" |
---|
| 1422 | import re |
---|
| 1423 | lbl = "Intensity" |
---|
| 1424 | if re.match(".K.",fu): |
---|
| 1425 | lbl = "Brightness Temperature "+ fu |
---|
| 1426 | elif re.match(".Jy.",fu): |
---|
| 1427 | lbl = "Flux density "+ fu |
---|
| 1428 | return lbl |
---|
[710] | 1429 | |
---|
[876] | 1430 | def _check_ifs(self): |
---|
| 1431 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 1432 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 1433 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|