[876] | 1 | from asap._asap import Scantable |
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[226] | 2 | from asap import rcParams |
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[976] | 3 | from asap import print_log, asaplog |
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[946] | 4 | from asap import selector |
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[189] | 5 | from numarray import ones,zeros |
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[102] | 6 | import sys |
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| 7 | |
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[876] | 8 | class scantable(Scantable): |
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[102] | 9 | """ |
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| 10 | The ASAP container for scans |
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| 11 | """ |
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[710] | 12 | |
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[484] | 13 | def __init__(self, filename, average=None, unit=None): |
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[102] | 14 | """ |
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| 15 | Create a scantable from a saved one or make a reference |
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| 16 | Parameters: |
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[181] | 17 | filename: the name of an asap table on disk |
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| 18 | or |
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| 19 | the name of a rpfits/sdfits/ms file |
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| 20 | (integrations within scans are auto averaged |
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| 21 | and the whole file is read) |
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| 22 | or |
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| 23 | [advanced] a reference to an existing |
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[102] | 24 | scantable |
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[484] | 25 | average: average all integrations withinb a scan on read. |
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| 26 | The default (True) is taken from .asaprc. |
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| 27 | unit: brightness unit; must be consistent with K or Jy. |
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[340] | 28 | Over-rides the default selected by the reader |
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| 29 | (input rpfits/sdfits/ms) or replaces the value |
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| 30 | in existing scantables |
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[710] | 31 | """ |
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[976] | 32 | if average is None: |
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[710] | 33 | average = rcParams['scantable.autoaverage'] |
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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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| 37 | if isinstance(filename, Scantable): |
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| 38 | Scantable.__init__(self, filename) |
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[181] | 39 | else: |
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[976] | 40 | if isinstance(filename,str): |
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| 41 | import os.path |
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| 42 | filename = os.path.expandvars(filename) |
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| 43 | filename = os.path.expanduser(filename) |
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| 44 | if not os.path.exists(filename): |
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| 45 | s = "File '%s' not found." % (filename) |
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[718] | 46 | if rcParams['verbose']: |
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[976] | 47 | asaplog.push(s) |
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| 48 | print asaplog.pop().strip() |
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[718] | 49 | return |
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[976] | 50 | raise IOError(s) |
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| 51 | if os.path.isdir(filename): |
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| 52 | # crude check if asap table |
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| 53 | if os.path.exists(filename+'/table.info'): |
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| 54 | Scantable.__init__(self, filename, "memory") |
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| 55 | if unit is not None: |
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| 56 | self.set_fluxunit(unit) |
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| 57 | self.set_freqframe(rcParams['scantable.freqframe']) |
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[718] | 58 | else: |
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[976] | 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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[226] | 65 | else: |
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[976] | 66 | self._fill([filename],unit, average) |
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| 67 | elif (isinstance(filename,list) or isinstance(filename,tuple)) \ |
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| 68 | and isinstance(filename[-1], str): |
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| 69 | self._fill(filename, unit, average) |
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[714] | 70 | print_log() |
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[102] | 71 | |
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[876] | 72 | def save(self, name=None, format=None, overwrite=False): |
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[116] | 73 | """ |
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[710] | 74 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, |
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[280] | 75 | Image FITS or MS2 format. |
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[116] | 76 | Parameters: |
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[196] | 77 | name: the name of the outputfile. For format="FITS" this |
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[489] | 78 | is the directory file name into which all the files |
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[497] | 79 | will be written (default is 'asap_FITS'). For format |
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| 80 | "ASCII" this is the root file name (data in 'name'.txt |
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| 81 | and header in 'name'_header.txt) |
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[116] | 82 | format: an optional file format. Default is ASAP. |
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[280] | 83 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
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[194] | 84 | 'SDFITS' (save as SDFITS file) |
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[710] | 85 | 'FITS' (saves each row as a FITS Image) |
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[200] | 86 | 'ASCII' (saves as ascii text file) |
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[226] | 87 | 'MS2' (saves as an aips++ |
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| 88 | MeasurementSet V2) |
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[411] | 89 | overwrite: If the file should be overwritten if it exists. |
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[256] | 90 | The default False is to return with warning |
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[411] | 91 | without writing the output. USE WITH CARE. |
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[116] | 92 | Example: |
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| 93 | scan.save('myscan.asap') |
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| 94 | scan.save('myscan.sdfits','SDFITS') |
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| 95 | """ |
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[411] | 96 | from os import path |
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[226] | 97 | if format is None: format = rcParams['scantable.save'] |
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[256] | 98 | suffix = '.'+format.lower() |
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| 99 | if name is None or name =="": |
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| 100 | name = 'scantable'+suffix |
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[718] | 101 | from asap import asaplog |
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| 102 | msg = "No filename given. Using default name %s..." % name |
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| 103 | asaplog.push(msg) |
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[411] | 104 | name = path.expandvars(name) |
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[256] | 105 | if path.isfile(name) or path.isdir(name): |
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| 106 | if not overwrite: |
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[718] | 107 | msg = "File %s exists." % name |
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| 108 | if rcParams['verbose']: |
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| 109 | print msg |
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| 110 | return |
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| 111 | else: |
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| 112 | raise IOError(msg) |
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[451] | 113 | format2 = format.upper() |
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| 114 | if format2 == 'ASAP': |
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[116] | 115 | self._save(name) |
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| 116 | else: |
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[876] | 117 | print "NYI" |
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| 118 | # from asap._asap import sdwriter as _sw |
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| 119 | # w = _sw(format2) |
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| 120 | # w.write(self, name, stokes) |
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[718] | 121 | |
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| 122 | print_log() |
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[116] | 123 | return |
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| 124 | |
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[102] | 125 | def copy(self): |
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| 126 | """ |
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| 127 | Return a copy of this scantable. |
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| 128 | Parameters: |
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[113] | 129 | none |
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[102] | 130 | Example: |
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| 131 | copiedscan = scan.copy() |
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| 132 | """ |
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[876] | 133 | sd = scantable(Scantable._copy(self)) |
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[113] | 134 | return sd |
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| 135 | |
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[102] | 136 | def get_scan(self, scanid=None): |
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| 137 | """ |
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| 138 | Return a specific scan (by scanno) or collection of scans (by |
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| 139 | source name) in a new scantable. |
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| 140 | Parameters: |
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[513] | 141 | scanid: a (list of) scanno or a source name, unix-style |
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| 142 | patterns are accepted for source name matching, e.g. |
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| 143 | '*_R' gets all 'ref scans |
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[102] | 144 | Example: |
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[513] | 145 | # get all scans containing the source '323p459' |
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| 146 | newscan = scan.get_scan('323p459') |
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| 147 | # get all 'off' scans |
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| 148 | refscans = scan.get_scan('*_R') |
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| 149 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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| 150 | newscan = scan.get_scan([0,2,7,10]) |
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[102] | 151 | """ |
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| 152 | if scanid is None: |
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[718] | 153 | if rcParams['verbose']: |
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| 154 | print "Please specify a scan no or name to retrieve from the scantable" |
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| 155 | return |
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| 156 | else: |
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| 157 | raise RuntimeError("No scan given") |
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| 158 | |
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[102] | 159 | try: |
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[946] | 160 | bsel = self.get_selection() |
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| 161 | sel = selector() |
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[102] | 162 | if type(scanid) is str: |
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[946] | 163 | sel.set_name(scanid) |
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| 164 | self.set_selection(bsel+sel) |
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[876] | 165 | scopy = self._copy() |
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[946] | 166 | self.set_selection(bsel) |
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[876] | 167 | return scantable(scopy) |
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[102] | 168 | elif type(scanid) is int: |
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[946] | 169 | sel.set_scans([scanid]) |
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| 170 | self.set_selection(bsel+sel) |
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[876] | 171 | scopy = self._copy() |
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[946] | 172 | self.set_selection(bsel) |
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[876] | 173 | return scantable(scopy) |
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[381] | 174 | elif type(scanid) is list: |
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[946] | 175 | sel.set_scans(scanid) |
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| 176 | self.set_selection(sel) |
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[876] | 177 | scopy = self._copy() |
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[946] | 178 | self.set_selection(bsel) |
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[876] | 179 | return scantable(scopy) |
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[381] | 180 | else: |
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[718] | 181 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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| 182 | if rcParams['verbose']: |
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| 183 | print msg |
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| 184 | else: |
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| 185 | raise TypeError(msg) |
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[102] | 186 | except RuntimeError: |
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[718] | 187 | if rcParams['verbose']: print "Couldn't find any match." |
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| 188 | else: raise |
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[102] | 189 | |
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| 190 | def __str__(self): |
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[876] | 191 | return Scantable._summary(self,True) |
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[102] | 192 | |
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[976] | 193 | def summary(self, filename=None): |
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[102] | 194 | """ |
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| 195 | Print a summary of the contents of this scantable. |
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| 196 | Parameters: |
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| 197 | filename: the name of a file to write the putput to |
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| 198 | Default - no file output |
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[381] | 199 | verbose: print extra info such as the frequency table |
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| 200 | The default (False) is taken from .asaprc |
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[102] | 201 | """ |
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[976] | 202 | info = Scantable._summary(self, True) |
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| 203 | #if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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[102] | 204 | if filename is not None: |
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[256] | 205 | if filename is "": |
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| 206 | filename = 'scantable_summary.txt' |
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[415] | 207 | from os.path import expandvars, isdir |
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[411] | 208 | filename = expandvars(filename) |
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[415] | 209 | if not isdir(filename): |
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[413] | 210 | data = open(filename, 'w') |
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| 211 | data.write(info) |
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| 212 | data.close() |
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| 213 | else: |
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[718] | 214 | msg = "Illegal file name '%s'." % (filename) |
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| 215 | if rcParams['verbose']: |
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| 216 | print msg |
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| 217 | else: |
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| 218 | raise IOError(msg) |
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| 219 | if rcParams['verbose']: |
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[794] | 220 | try: |
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| 221 | from IPython.genutils import page as pager |
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| 222 | except ImportError: |
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| 223 | from pydoc import pager |
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| 224 | pager(info) |
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[718] | 225 | else: |
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| 226 | return info |
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[710] | 227 | |
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[946] | 228 | |
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| 229 | def get_selection(self): |
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| 230 | """ |
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| 231 | """ |
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| 232 | return selector(self._getselection()) |
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| 233 | |
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| 234 | def set_selection(self, selection): |
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| 235 | """ |
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| 236 | """ |
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| 237 | self._setselection(selection) |
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| 238 | |
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[553] | 239 | def set_cursor(self, beam=0, IF=0, pol=0): |
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[102] | 240 | """ |
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| 241 | Set the spectrum for individual operations. |
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| 242 | Parameters: |
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[553] | 243 | beam, IF, pol: a number |
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[102] | 244 | Example: |
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[256] | 245 | scan.set_cursor(0,0,1) |
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[135] | 246 | pol1sig = scan.stats(all=False) # returns std dev for beam=0 |
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[181] | 247 | # if=0, pol=1 |
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[102] | 248 | """ |
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[876] | 249 | print "DEPRECATED" |
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[484] | 250 | varlist = vars() |
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[876] | 251 | sel = asap._asap.Selector() |
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| 252 | sel._setbeams([beam]) |
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| 253 | sel._setpols([pol]) |
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| 254 | sel._setifs([IF]) |
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| 255 | self._add_history("set_cursor", varlist) |
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[102] | 256 | return |
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| 257 | |
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[256] | 258 | def get_cursor(self): |
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[113] | 259 | """ |
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| 260 | Return/print a the current 'cursor' into the Beam/IF/Pol cube. |
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| 261 | Parameters: |
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| 262 | none |
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| 263 | Returns: |
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| 264 | a list of values (currentBeam,currentIF,currentPol) |
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| 265 | Example: |
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| 266 | none |
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| 267 | """ |
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[876] | 268 | print "DEPRECATED" |
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| 269 | sel = self._getselection() |
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| 270 | i = sel.getbeams()[0] |
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| 271 | j = sel.getifs()[0] |
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| 272 | k = sel.getpols()[0] |
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[721] | 273 | from asap import asaplog |
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| 274 | out = "--------------------------------------------------\n" |
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| 275 | out += " Cursor position\n" |
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| 276 | out += "--------------------------------------------------\n" |
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| 277 | out += 'Beam=%d IF=%d Pol=%d ' % (i,j,k) |
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| 278 | asaplog.push(out) |
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| 279 | print_log() |
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| 280 | return i,j,k |
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[102] | 281 | |
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[876] | 282 | def stats(self, stat='stddev', mask=None): |
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[102] | 283 | """ |
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[135] | 284 | Determine the specified statistic of the current beam/if/pol |
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[102] | 285 | Takes a 'mask' as an optional parameter to specify which |
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| 286 | channels should be excluded. |
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| 287 | Parameters: |
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[135] | 288 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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| 289 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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| 290 | mask: an optional mask specifying where the statistic |
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[102] | 291 | should be determined. |
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| 292 | Example: |
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[113] | 293 | scan.set_unit('channel') |
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[102] | 294 | msk = scan.create_mask([100,200],[500,600]) |
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[135] | 295 | scan.stats(stat='mean', mask=m) |
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[102] | 296 | """ |
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[256] | 297 | from numarray import array,zeros,Float |
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[102] | 298 | if mask == None: |
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[876] | 299 | mask = [] |
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[256] | 300 | axes = ['Beam','IF','Pol','Time'] |
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[876] | 301 | if not self._check_ifs(): |
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| 302 | raise ValueError("Cannot apply mask as the IFs have different number of channels" |
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| 303 | "Please use setselection() to select individual IFs") |
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[256] | 304 | |
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[876] | 305 | statvals = self._math._stats(self, mask, stat) |
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| 306 | out = '' |
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| 307 | axes = [] |
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| 308 | for i in range(self.nrow()): |
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| 309 | axis = [] |
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| 310 | axis.append(self.getscan(i)) |
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| 311 | axis.append(self.getbeam(i)) |
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| 312 | axis.append(self.getif(i)) |
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| 313 | axis.append(self.getpol(i)) |
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| 314 | axis.append(self.getcycle(i)) |
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| 315 | axes.append(axis) |
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| 316 | tm = self._gettime(i) |
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| 317 | src = self._getsourcename(i) |
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| 318 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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| 319 | out += 'Time[%s]:\n' % (tm) |
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| 320 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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| 321 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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| 322 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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| 323 | out += '= %3.3f\n' % (statvals[i]) |
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| 324 | out += "--------------------------------------------------\n" |
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[256] | 325 | |
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[876] | 326 | if rcParams['verbose']: |
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| 327 | print "--------------------------------------------------" |
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| 328 | print " ",stat |
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| 329 | print "--------------------------------------------------" |
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| 330 | print out |
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| 331 | retval = { 'axesnames': ['scanno','beamno','ifno','polno','cycleno'], |
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| 332 | 'axes' : axes, |
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| 333 | 'data': statvals} |
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| 334 | return retval |
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[102] | 335 | |
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[876] | 336 | def stddev(self,mask=None): |
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[135] | 337 | """ |
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| 338 | Determine the standard deviation of the current beam/if/pol |
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| 339 | Takes a 'mask' as an optional parameter to specify which |
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| 340 | channels should be excluded. |
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| 341 | Parameters: |
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| 342 | mask: an optional mask specifying where the standard |
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| 343 | deviation should be determined. |
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| 344 | |
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| 345 | Example: |
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| 346 | scan.set_unit('channel') |
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| 347 | msk = scan.create_mask([100,200],[500,600]) |
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| 348 | scan.stddev(mask=m) |
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| 349 | """ |
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[876] | 350 | return self.stats(stat='stddev',mask=mask); |
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[135] | 351 | |
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[876] | 352 | def get_tsys(self): |
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[113] | 353 | """ |
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| 354 | Return the System temperatures. |
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| 355 | Parameters: |
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[876] | 356 | |
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[113] | 357 | Returns: |
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[876] | 358 | a list of Tsys values for the current selection |
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[113] | 359 | """ |
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[256] | 360 | |
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[876] | 361 | return self._row_callback(self._gettsys, "Tsys") |
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[256] | 362 | |
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[876] | 363 | def _row_callback(self, callback, label): |
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| 364 | axes = [] |
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| 365 | axesnames = ['scanno','beamno','ifno','polno','cycleno'] |
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| 366 | out = "" |
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| 367 | outvec =[] |
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| 368 | for i in range(self.nrow()): |
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| 369 | axis = [] |
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| 370 | axis.append(self.getscan(i)) |
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| 371 | axis.append(self.getbeam(i)) |
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| 372 | axis.append(self.getif(i)) |
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| 373 | axis.append(self.getpol(i)) |
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| 374 | axis.append(self.getcycle(i)) |
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| 375 | axes.append(axis) |
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| 376 | tm = self._gettime(i) |
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| 377 | src = self._getsourcename(i) |
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| 378 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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| 379 | out += 'Time[%s]:\n' % (tm) |
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| 380 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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| 381 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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| 382 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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| 383 | outvec.append(callback(i)) |
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| 384 | out += '= %3.3f\n' % (outvec[i]) |
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| 385 | out += "--------------------------------------------------\n" |
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| 386 | if rcParams['verbose']: |
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| 387 | print "--------------------------------------------------" |
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| 388 | print " %s" % (label) |
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| 389 | print "--------------------------------------------------" |
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| 390 | print out |
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| 391 | retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec} |
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| 392 | return retval |
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[256] | 393 | |
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| 394 | |
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[407] | 395 | def get_time(self, row=-1): |
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[113] | 396 | """ |
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| 397 | Get a list of time stamps for the observations. |
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[181] | 398 | Return a string for each integration in the scantable. |
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[113] | 399 | Parameters: |
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[407] | 400 | row: row no of integration. Default -1 return all rows |
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[113] | 401 | Example: |
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| 402 | none |
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| 403 | """ |
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| 404 | out = [] |
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[407] | 405 | if row == -1: |
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| 406 | for i in range(self.nrow()): |
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| 407 | out.append(self._gettime(i)) |
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| 408 | return out |
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| 409 | else: |
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| 410 | if row < self.nrow(): |
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| 411 | return self._gettime(row) |
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[102] | 412 | |
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[714] | 413 | def get_sourcename(self, row=-1): |
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| 414 | """ |
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[794] | 415 | Get a list source names for the observations. |
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[714] | 416 | Return a string for each integration in the scantable. |
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| 417 | Parameters: |
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| 418 | row: row no of integration. Default -1 return all rows |
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| 419 | Example: |
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| 420 | none |
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| 421 | """ |
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| 422 | out = [] |
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| 423 | if row == -1: |
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| 424 | return [self._getsourcename(i) for i in range(self.nrow())] |
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| 425 | else: |
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| 426 | if 0 <= row < self.nrow(): |
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| 427 | return self._getsourcename(row) |
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| 428 | |
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[794] | 429 | def get_elevation(self, row=-1): |
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| 430 | """ |
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| 431 | Get a list of elevations for the observations. |
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| 432 | Return a float for each integration in the scantable. |
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| 433 | Parameters: |
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| 434 | row: row no of integration. Default -1 return all rows |
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| 435 | Example: |
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| 436 | none |
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| 437 | """ |
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| 438 | out = [] |
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| 439 | if row == -1: |
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| 440 | return [self._getelevation(i) for i in range(self.nrow())] |
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| 441 | else: |
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| 442 | if 0 <= row < self.nrow(): |
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| 443 | return self._getelevation(row) |
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| 444 | |
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| 445 | def get_azimuth(self, row=-1): |
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| 446 | """ |
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| 447 | Get a list of azimuths for the observations. |
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| 448 | Return a float for each integration in the scantable. |
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| 449 | Parameters: |
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| 450 | row: row no of integration. Default -1 return all rows |
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| 451 | Example: |
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| 452 | none |
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| 453 | """ |
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| 454 | out = [] |
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| 455 | if row == -1: |
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| 456 | return [self._getazimuth(i) for i in range(self.nrow())] |
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| 457 | else: |
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| 458 | if 0 <= row < self.nrow(): |
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| 459 | return self._getazimuth(row) |
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| 460 | |
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| 461 | def get_parangle(self, row=-1): |
---|
| 462 | """ |
---|
| 463 | Get a list of parallactic angles for the observations. |
---|
| 464 | Return a float for each integration in the scantable. |
---|
| 465 | Parameters: |
---|
| 466 | row: row no of integration. Default -1 return all rows |
---|
| 467 | Example: |
---|
| 468 | none |
---|
| 469 | """ |
---|
| 470 | out = [] |
---|
| 471 | if row == -1: |
---|
| 472 | return [self._getparangle(i) for i in range(self.nrow())] |
---|
| 473 | else: |
---|
| 474 | if 0 <= row < self.nrow(): |
---|
| 475 | return self._getparangle(row) |
---|
| 476 | |
---|
[102] | 477 | def set_unit(self, unit='channel'): |
---|
| 478 | """ |
---|
| 479 | Set the unit for all following operations on this scantable |
---|
| 480 | Parameters: |
---|
| 481 | unit: optional unit, default is 'channel' |
---|
[113] | 482 | one of '*Hz','km/s','channel', '' |
---|
[102] | 483 | """ |
---|
[484] | 484 | varlist = vars() |
---|
[113] | 485 | if unit in ['','pixel', 'channel']: |
---|
| 486 | unit = '' |
---|
| 487 | inf = list(self._getcoordinfo()) |
---|
| 488 | inf[0] = unit |
---|
| 489 | self._setcoordinfo(inf) |
---|
[484] | 490 | self._add_history("set_unit",varlist) |
---|
[113] | 491 | |
---|
[484] | 492 | def set_instrument(self, instr): |
---|
[358] | 493 | """ |
---|
| 494 | Set the instrument for subsequent processing |
---|
| 495 | Parameters: |
---|
[710] | 496 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 497 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 498 | """ |
---|
| 499 | self._setInstrument(instr) |
---|
[484] | 500 | self._add_history("set_instument",vars()) |
---|
[718] | 501 | print_log() |
---|
[358] | 502 | |
---|
[276] | 503 | def set_doppler(self, doppler='RADIO'): |
---|
| 504 | """ |
---|
| 505 | Set the doppler for all following operations on this scantable. |
---|
| 506 | Parameters: |
---|
| 507 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 508 | """ |
---|
[484] | 509 | varlist = vars() |
---|
[276] | 510 | inf = list(self._getcoordinfo()) |
---|
| 511 | inf[2] = doppler |
---|
| 512 | self._setcoordinfo(inf) |
---|
[484] | 513 | self._add_history("set_doppler",vars()) |
---|
[718] | 514 | print_log() |
---|
[710] | 515 | |
---|
[226] | 516 | def set_freqframe(self, frame=None): |
---|
[113] | 517 | """ |
---|
| 518 | Set the frame type of the Spectral Axis. |
---|
| 519 | Parameters: |
---|
[591] | 520 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
| 521 | 'REST','TOPO','LSRD','LSRK','BARY', |
---|
| 522 | 'GEO','GALACTO','LGROUP','CMB' |
---|
[113] | 523 | Examples: |
---|
| 524 | scan.set_freqframe('BARY') |
---|
| 525 | """ |
---|
[484] | 526 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
| 527 | varlist = vars() |
---|
[113] | 528 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
---|
| 529 | 'GEO','GALACTO','LGROUP','CMB'] |
---|
[591] | 530 | |
---|
[876] | 531 | if 1:#frame in valid: |
---|
[113] | 532 | inf = list(self._getcoordinfo()) |
---|
| 533 | inf[1] = frame |
---|
| 534 | self._setcoordinfo(inf) |
---|
[484] | 535 | self._add_history("set_freqframe",varlist) |
---|
[102] | 536 | else: |
---|
[718] | 537 | msg = "Please specify a valid freq type. Valid types are:\n",valid |
---|
| 538 | if rcParams['verbose']: |
---|
| 539 | print msg |
---|
| 540 | else: |
---|
| 541 | raise TypeError(msg) |
---|
| 542 | print_log() |
---|
[710] | 543 | |
---|
[113] | 544 | def get_unit(self): |
---|
| 545 | """ |
---|
| 546 | Get the default unit set in this scantable |
---|
| 547 | Parameters: |
---|
| 548 | Returns: |
---|
| 549 | A unit string |
---|
| 550 | """ |
---|
| 551 | inf = self._getcoordinfo() |
---|
| 552 | unit = inf[0] |
---|
| 553 | if unit == '': unit = 'channel' |
---|
| 554 | return unit |
---|
[102] | 555 | |
---|
[158] | 556 | def get_abcissa(self, rowno=0): |
---|
[102] | 557 | """ |
---|
[158] | 558 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 559 | selected Beam/IF/Pol |
---|
| 560 | Parameters: |
---|
[226] | 561 | rowno: an optional row number in the scantable. Default is the |
---|
| 562 | first row, i.e. rowno=0 |
---|
[113] | 563 | Returns: |
---|
[407] | 564 | The abcissa values and it's format string (as a dictionary) |
---|
[113] | 565 | """ |
---|
[256] | 566 | abc = self._getabcissa(rowno) |
---|
[710] | 567 | lbl = self._getabcissalabel(rowno) |
---|
[718] | 568 | print_log() |
---|
[158] | 569 | return abc, lbl |
---|
[113] | 570 | |
---|
| 571 | def create_mask(self, *args, **kwargs): |
---|
| 572 | """ |
---|
[102] | 573 | Compute and return a mask based on [min,max] windows. |
---|
[189] | 574 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 575 | applied. |
---|
[102] | 576 | Parameters: |
---|
| 577 | [min,max],[min2,max2],... |
---|
| 578 | Pairs of start/end points specifying the regions |
---|
| 579 | to be masked |
---|
[189] | 580 | invert: optional argument. If specified as True, |
---|
| 581 | return an inverted mask, i.e. the regions |
---|
| 582 | specified are EXCLUDED |
---|
[513] | 583 | row: create the mask using the specified row for |
---|
| 584 | unit conversions, default is row=0 |
---|
| 585 | only necessary if frequency varies over rows. |
---|
[102] | 586 | Example: |
---|
[113] | 587 | scan.set_unit('channel') |
---|
| 588 | |
---|
| 589 | a) |
---|
[102] | 590 | msk = scan.set_mask([400,500],[800,900]) |
---|
[189] | 591 | # masks everything outside 400 and 500 |
---|
[113] | 592 | # and 800 and 900 in the unit 'channel' |
---|
| 593 | |
---|
| 594 | b) |
---|
| 595 | msk = scan.set_mask([400,500],[800,900], invert=True) |
---|
[189] | 596 | # masks the regions between 400 and 500 |
---|
[113] | 597 | # and 800 and 900 in the unit 'channel' |
---|
[710] | 598 | |
---|
[102] | 599 | """ |
---|
[513] | 600 | row = 0 |
---|
| 601 | if kwargs.has_key("row"): |
---|
| 602 | row = kwargs.get("row") |
---|
| 603 | data = self._getabcissa(row) |
---|
[113] | 604 | u = self._getcoordinfo()[0] |
---|
[718] | 605 | if rcParams['verbose']: |
---|
[113] | 606 | if u == "": u = "channel" |
---|
[718] | 607 | from asap import asaplog |
---|
| 608 | msg = "The current mask window unit is %s" % u |
---|
[914] | 609 | if not self._check_ifs(): |
---|
[876] | 610 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 611 | asaplog.push(msg) |
---|
[102] | 612 | n = self.nchan() |
---|
[189] | 613 | msk = zeros(n) |
---|
[710] | 614 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 615 | |
---|
| 616 | ws = (isinstance(args[-1][-1],int) or isinstance(args[-1][-1],float)) and args or args[0] |
---|
| 617 | for window in ws: |
---|
[102] | 618 | if (len(window) != 2 or window[0] > window[1] ): |
---|
[718] | 619 | raise TypeError("A window needs to be defined as [min,max]") |
---|
[102] | 620 | for i in range(n): |
---|
[113] | 621 | if data[i] >= window[0] and data[i] < window[1]: |
---|
[189] | 622 | msk[i] = 1 |
---|
[113] | 623 | if kwargs.has_key('invert'): |
---|
| 624 | if kwargs.get('invert'): |
---|
| 625 | from numarray import logical_not |
---|
[710] | 626 | msk = logical_not(msk) |
---|
[718] | 627 | print_log() |
---|
[102] | 628 | return msk |
---|
[710] | 629 | |
---|
[256] | 630 | def get_restfreqs(self): |
---|
| 631 | """ |
---|
| 632 | Get the restfrequency(s) stored in this scantable. |
---|
| 633 | The return value(s) are always of unit 'Hz' |
---|
| 634 | Parameters: |
---|
| 635 | none |
---|
| 636 | Returns: |
---|
| 637 | a list of doubles |
---|
| 638 | """ |
---|
| 639 | return list(self._getrestfreqs()) |
---|
[102] | 640 | |
---|
[402] | 641 | |
---|
[931] | 642 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
| 643 | """ |
---|
| 644 | Set or replace the restfrequency specified and |
---|
| 645 | If the 'freqs' argument holds a scalar, |
---|
| 646 | then that rest frequency will be applied to all the selected |
---|
| 647 | data. If the 'freqs' argument holds |
---|
| 648 | a vector, then it MUST be of equal or smaller length than |
---|
| 649 | the number of IFs (and the available restfrequencies will be |
---|
| 650 | replaced by this vector). In this case, *all* data have |
---|
| 651 | the restfrequency set per IF according |
---|
| 652 | to the corresponding value you give in the 'freqs' vector. |
---|
| 653 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
| 654 | IF 1 gets restfreq 2e9. |
---|
| 655 | You can also specify the frequencies via known line names |
---|
| 656 | from the built-in Lovas table. |
---|
| 657 | Parameters: |
---|
| 658 | freqs: list of rest frequency values or string idenitfiers |
---|
| 659 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 660 | |
---|
[931] | 661 | Example: |
---|
| 662 | # set the given restfrequency for the whole table |
---|
| 663 | scan.set_restfreqs(freqs=1.4e9) |
---|
| 664 | # If thee number of IFs in the data is >= 2 the IF0 gets the first |
---|
| 665 | # value IF1 the second... |
---|
| 666 | scan.set_restfreqs(freqs=[1.4e9,1.67e9]) |
---|
| 667 | #set the given restfrequency for the whole table (by name) |
---|
| 668 | scan.set_restfreqs(freqs="OH1667") |
---|
[391] | 669 | |
---|
[931] | 670 | Note: |
---|
| 671 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 672 | source and IF basis, use scantable.set_selection() before using |
---|
| 673 | this function. |
---|
| 674 | # provide your scantable is call scan |
---|
| 675 | selection = selector() |
---|
| 676 | selection.set_name("ORION*") |
---|
| 677 | selection.set_ifs([1]) |
---|
| 678 | scan.set_selection(selection) |
---|
| 679 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 680 | |
---|
| 681 | """ |
---|
| 682 | varlist = vars() |
---|
| 683 | |
---|
| 684 | t = type(freqs) |
---|
| 685 | if isinstance(freqs, int) or isinstance(freqs,float): |
---|
| 686 | self._setrestfreqs(freqs, unit) |
---|
| 687 | elif isinstance(freqs, list) or isinstance(freqs,tuple): |
---|
| 688 | if isinstance(freqs[-1], int) or isinstance(freqs[-1],float): |
---|
| 689 | sel = selector() |
---|
| 690 | savesel = self._getselection() |
---|
| 691 | for i in xrange(len(freqs)): |
---|
[946] | 692 | sel.set_ifs([i]) |
---|
[931] | 693 | self._setselection(sel) |
---|
| 694 | self._setrestfreqs(freqs[i], unit) |
---|
| 695 | self._setselection(savesel) |
---|
| 696 | elif isinstance(freqs[-1], str): |
---|
| 697 | # not yet implemented |
---|
| 698 | pass |
---|
| 699 | else: |
---|
| 700 | return |
---|
| 701 | self._add_history("set_restfreqs", varlist) |
---|
| 702 | |
---|
| 703 | |
---|
| 704 | |
---|
[484] | 705 | def history(self): |
---|
| 706 | hist = list(self._gethistory()) |
---|
[794] | 707 | out = "-"*80 |
---|
[484] | 708 | for h in hist: |
---|
[489] | 709 | if h.startswith("---"): |
---|
[794] | 710 | out += "\n"+h |
---|
[489] | 711 | else: |
---|
| 712 | items = h.split("##") |
---|
| 713 | date = items[0] |
---|
| 714 | func = items[1] |
---|
| 715 | items = items[2:] |
---|
[794] | 716 | out += "\n"+date+"\n" |
---|
| 717 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 718 | for i in items: |
---|
| 719 | s = i.split("=") |
---|
[794] | 720 | out += "\n %s = %s" % (s[0],s[1]) |
---|
| 721 | out += "\n"+"-"*80 |
---|
| 722 | try: |
---|
| 723 | from IPython.genutils import page as pager |
---|
| 724 | except ImportError: |
---|
| 725 | from pydoc import pager |
---|
| 726 | pager(out) |
---|
[484] | 727 | return |
---|
| 728 | |
---|
[513] | 729 | # |
---|
| 730 | # Maths business |
---|
| 731 | # |
---|
| 732 | |
---|
[931] | 733 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[513] | 734 | """ |
---|
| 735 | Return the (time) average of a scan, or apply it 'insitu'. |
---|
| 736 | Note: |
---|
| 737 | in channels only |
---|
| 738 | The cursor of the output scan is set to 0. |
---|
| 739 | Parameters: |
---|
| 740 | one scan or comma separated scans |
---|
| 741 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 742 | weighting) |
---|
[558] | 743 | scanav: True averages each scan separately |
---|
| 744 | False (default) averages all scans together, |
---|
[524] | 745 | weight: Weighting scheme. 'none', 'var' (1/var(spec) |
---|
[535] | 746 | weighted), 'tsys' (1/Tsys**2 weighted), 'tint' |
---|
| 747 | (integration time weighted) or 'tintsys' (Tint/Tsys**2). |
---|
| 748 | The default is 'tint' |
---|
[931] | 749 | align: align the spectra in velocity before averaging. It takes |
---|
| 750 | the time of the first spectrum as reference time. |
---|
[513] | 751 | Example: |
---|
| 752 | # time average the scantable without using a mask |
---|
[710] | 753 | newscan = scan.average_time() |
---|
[513] | 754 | """ |
---|
| 755 | varlist = vars() |
---|
[976] | 756 | if weight is None: weight = 'TINT' |
---|
[513] | 757 | if mask is None: mask = () |
---|
[876] | 758 | if scanav: |
---|
| 759 | scanav = "SCAN" |
---|
| 760 | else: |
---|
| 761 | scanav = "NONE" |
---|
[931] | 762 | s = scantable(self._math._average((self,), mask, weight.upper(), |
---|
| 763 | scanav, align)) |
---|
[513] | 764 | s._add_history("average_time",varlist) |
---|
[718] | 765 | print_log() |
---|
[513] | 766 | return s |
---|
[710] | 767 | |
---|
[876] | 768 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[513] | 769 | """ |
---|
| 770 | Return a scan where all spectra are converted to either |
---|
| 771 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 772 | By default the function tries to look the values up internally. |
---|
| 773 | If it can't find them (or if you want to over-ride), you must |
---|
| 774 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 775 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 776 | Parameters: |
---|
| 777 | jyperk: the Jy / K conversion factor |
---|
| 778 | eta: the aperture efficiency |
---|
| 779 | d: the geomtric diameter (metres) |
---|
| 780 | insitu: if False a new scantable is returned. |
---|
| 781 | Otherwise, the scaling is done in-situ |
---|
| 782 | The default is taken from .asaprc (False) |
---|
| 783 | allaxes: if True apply to all spectra. Otherwise |
---|
| 784 | apply only to the selected (beam/pol/if)spectra only |
---|
| 785 | The default is taken from .asaprc (True if none) |
---|
| 786 | """ |
---|
| 787 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 788 | self._math._setinsitu(insitu) |
---|
[513] | 789 | varlist = vars() |
---|
| 790 | if jyperk is None: jyperk = -1.0 |
---|
| 791 | if d is None: d = -1.0 |
---|
| 792 | if eta is None: eta = -1.0 |
---|
[876] | 793 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 794 | s._add_history("convert_flux", varlist) |
---|
| 795 | print_log() |
---|
| 796 | if insitu: self._assign(s) |
---|
| 797 | else: return s |
---|
[513] | 798 | |
---|
[876] | 799 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[513] | 800 | """ |
---|
| 801 | Return a scan after applying a gain-elevation correction. |
---|
| 802 | The correction can be made via either a polynomial or a |
---|
| 803 | table-based interpolation (and extrapolation if necessary). |
---|
| 804 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 805 | If you specify neither, then a polynomial correction will be made |
---|
| 806 | with built in coefficients known for certain telescopes (an error |
---|
| 807 | will occur if the instrument is not known). |
---|
| 808 | The data and Tsys are *divided* by the scaling factors. |
---|
| 809 | Parameters: |
---|
| 810 | poly: Polynomial coefficients (default None) to compute a |
---|
| 811 | gain-elevation correction as a function of |
---|
| 812 | elevation (in degrees). |
---|
| 813 | filename: The name of an ascii file holding correction factors. |
---|
| 814 | The first row of the ascii file must give the column |
---|
| 815 | names and these MUST include columns |
---|
| 816 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 817 | by this) somewhere. |
---|
| 818 | The second row must give the data type of the |
---|
| 819 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 820 | An example file would be |
---|
| 821 | (actual factors are arbitrary) : |
---|
| 822 | |
---|
| 823 | TIME ELEVATION FACTOR |
---|
| 824 | R R R |
---|
| 825 | 0.1 0 0.8 |
---|
| 826 | 0.2 20 0.85 |
---|
| 827 | 0.3 40 0.9 |
---|
| 828 | 0.4 60 0.85 |
---|
| 829 | 0.5 80 0.8 |
---|
| 830 | 0.6 90 0.75 |
---|
| 831 | method: Interpolation method when correcting from a table. |
---|
| 832 | Values are "nearest", "linear" (default), "cubic" |
---|
| 833 | and "spline" |
---|
| 834 | insitu: if False a new scantable is returned. |
---|
| 835 | Otherwise, the scaling is done in-situ |
---|
| 836 | The default is taken from .asaprc (False) |
---|
| 837 | """ |
---|
| 838 | |
---|
| 839 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 840 | self._math._setinsitu(insitu) |
---|
[513] | 841 | varlist = vars() |
---|
| 842 | if poly is None: |
---|
| 843 | poly = () |
---|
| 844 | from os.path import expandvars |
---|
| 845 | filename = expandvars(filename) |
---|
[876] | 846 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 847 | s._add_history("gain_el", varlist) |
---|
| 848 | print_log() |
---|
| 849 | if insitu: self._assign(s) |
---|
| 850 | else: return s |
---|
[710] | 851 | |
---|
[931] | 852 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[513] | 853 | """ |
---|
| 854 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 855 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 856 | set_freqframe. |
---|
| 857 | Parameters: |
---|
| 858 | reftime: reference time to align at. By default, the time of |
---|
| 859 | the first row of data is used. |
---|
| 860 | method: Interpolation method for regridding the spectra. |
---|
| 861 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 862 | and "spline" |
---|
| 863 | insitu: if False a new scantable is returned. |
---|
| 864 | Otherwise, the scaling is done in-situ |
---|
| 865 | The default is taken from .asaprc (False) |
---|
| 866 | """ |
---|
[931] | 867 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 868 | self._math._setinsitu(insitu) |
---|
[513] | 869 | varlist = vars() |
---|
[931] | 870 | if reftime is None: reftime = "" |
---|
| 871 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 872 | s._add_history("freq_align", varlist) |
---|
| 873 | print_log() |
---|
| 874 | if insitu: self._assign(s) |
---|
| 875 | else: return s |
---|
[513] | 876 | |
---|
[876] | 877 | def opacity(self, tau, insitu=None): |
---|
[513] | 878 | """ |
---|
| 879 | Apply an opacity correction. The data |
---|
| 880 | and Tsys are multiplied by the correction factor. |
---|
| 881 | Parameters: |
---|
| 882 | tau: Opacity from which the correction factor is |
---|
| 883 | exp(tau*ZD) |
---|
| 884 | where ZD is the zenith-distance |
---|
| 885 | insitu: if False a new scantable is returned. |
---|
| 886 | Otherwise, the scaling is done in-situ |
---|
| 887 | The default is taken from .asaprc (False) |
---|
| 888 | """ |
---|
| 889 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 890 | self._math._setinsitu(insitu) |
---|
[513] | 891 | varlist = vars() |
---|
[876] | 892 | s = scantable(self._math._opacity(self, tau)) |
---|
| 893 | s._add_history("opacity", varlist) |
---|
| 894 | print_log() |
---|
| 895 | if insitu: self._assign(s) |
---|
| 896 | else: return s |
---|
[513] | 897 | |
---|
| 898 | def bin(self, width=5, insitu=None): |
---|
| 899 | """ |
---|
| 900 | Return a scan where all spectra have been binned up. |
---|
| 901 | width: The bin width (default=5) in pixels |
---|
| 902 | insitu: if False a new scantable is returned. |
---|
| 903 | Otherwise, the scaling is done in-situ |
---|
| 904 | The default is taken from .asaprc (False) |
---|
| 905 | """ |
---|
| 906 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 907 | self._math._setinsitu(insitu) |
---|
[513] | 908 | varlist = vars() |
---|
[876] | 909 | s = scantable(self._math._bin(self, width)) |
---|
| 910 | s._add_history("bin",varlist) |
---|
| 911 | print_log() |
---|
| 912 | if insitu: self._assign(s) |
---|
| 913 | else: return s |
---|
[513] | 914 | |
---|
[710] | 915 | |
---|
[513] | 916 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 917 | """ |
---|
| 918 | Return a scan where all spectra have been binned up |
---|
| 919 | width: The bin width (default=5) in pixels |
---|
| 920 | method: Interpolation method when correcting from a table. |
---|
| 921 | Values are "nearest", "linear", "cubic" (default) |
---|
| 922 | and "spline" |
---|
| 923 | insitu: if False a new scantable is returned. |
---|
| 924 | Otherwise, the scaling is done in-situ |
---|
| 925 | The default is taken from .asaprc (False) |
---|
| 926 | """ |
---|
| 927 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 928 | self._math._setinsitu(insitu) |
---|
[513] | 929 | varlist = vars() |
---|
[876] | 930 | s = scantable(self._math._resample(self, method, width)) |
---|
| 931 | s._add_history("resample",varlist) |
---|
| 932 | print_log() |
---|
| 933 | if insitu: self._assign(s) |
---|
| 934 | else: return s |
---|
[513] | 935 | |
---|
| 936 | |
---|
[946] | 937 | def average_pol(self, mask=None, weight='none'): |
---|
| 938 | """ |
---|
| 939 | Average the Polarisations together. |
---|
| 940 | Parameters: |
---|
| 941 | mask: An optional mask defining the region, where the |
---|
| 942 | averaging will be applied. The output will have all |
---|
| 943 | specified points masked. |
---|
| 944 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 945 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 946 | """ |
---|
| 947 | varlist = vars() |
---|
| 948 | if mask is None: |
---|
| 949 | mask = () |
---|
| 950 | s = self._math._averagepol(self, mask, weight) |
---|
| 951 | s._add_history("average_pol",varlist) |
---|
| 952 | print_log() |
---|
| 953 | return scantable(s) |
---|
[513] | 954 | |
---|
[876] | 955 | def smooth(self, kernel="hanning", width=5.0, insitu=None): |
---|
[513] | 956 | """ |
---|
| 957 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 958 | Parameters: |
---|
| 959 | scan: The input scan |
---|
| 960 | kernel: The type of smoothing kernel. Select from |
---|
| 961 | 'hanning' (default), 'gaussian' and 'boxcar'. |
---|
| 962 | The first three characters are sufficient. |
---|
| 963 | width: The width of the kernel in pixels. For hanning this is |
---|
| 964 | ignored otherwise it defauls to 5 pixels. |
---|
| 965 | For 'gaussian' it is the Full Width Half |
---|
| 966 | Maximum. For 'boxcar' it is the full width. |
---|
| 967 | insitu: if False a new scantable is returned. |
---|
| 968 | Otherwise, the scaling is done in-situ |
---|
| 969 | The default is taken from .asaprc (False) |
---|
| 970 | Example: |
---|
| 971 | none |
---|
| 972 | """ |
---|
| 973 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 974 | self._math._setinsitu(insitu) |
---|
[513] | 975 | varlist = vars() |
---|
[876] | 976 | s = scantable(self._math._smooth(self,kernel,width)) |
---|
| 977 | s._add_history("smooth", varlist) |
---|
| 978 | print_log() |
---|
| 979 | if insitu: self._assign(s) |
---|
| 980 | else: return s |
---|
[513] | 981 | |
---|
[876] | 982 | |
---|
| 983 | def poly_baseline(self, mask=None, order=0, insitu=None): |
---|
[513] | 984 | """ |
---|
| 985 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 986 | Parameters: |
---|
[794] | 987 | scan: a scantable |
---|
| 988 | mask: an optional mask |
---|
| 989 | order: the order of the polynomial (default is 0) |
---|
| 990 | insitu: if False a new scantable is returned. |
---|
| 991 | Otherwise, the scaling is done in-situ |
---|
| 992 | The default is taken from .asaprc (False) |
---|
| 993 | allaxes: If True (default) apply to all spectra. Otherwise |
---|
| 994 | apply only to the selected (beam/pol/if)spectra only |
---|
| 995 | The default is taken from .asaprc (True if none) |
---|
[513] | 996 | Example: |
---|
| 997 | # return a scan baselined by a third order polynomial, |
---|
| 998 | # not using a mask |
---|
| 999 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1000 | """ |
---|
[513] | 1001 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1002 | varlist = vars() |
---|
| 1003 | if mask is None: |
---|
| 1004 | from numarray import ones |
---|
[876] | 1005 | mask = list(ones(self.nchan(-1))) |
---|
[513] | 1006 | from asap.asapfitter import fitter |
---|
| 1007 | f = fitter() |
---|
| 1008 | f.set_scan(self, mask) |
---|
| 1009 | f.set_function(poly=order) |
---|
[876] | 1010 | s = f.auto_fit(insitu) |
---|
| 1011 | s._add_history("poly_baseline", varlist) |
---|
[718] | 1012 | print_log() |
---|
[876] | 1013 | if insitu: self._assign(s) |
---|
| 1014 | else: return s |
---|
[513] | 1015 | |
---|
[931] | 1016 | def auto_poly_baseline(self, mask=[], edge=(0,0), order=0, |
---|
[880] | 1017 | threshold=3, insitu=None): |
---|
| 1018 | """ |
---|
| 1019 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1020 | Spectral lines are detected first using linefinder and masked out |
---|
| 1021 | to avoid them affecting the baseline solution. |
---|
| 1022 | |
---|
| 1023 | Parameters: |
---|
| 1024 | mask: an optional mask retreived from scantable |
---|
| 1025 | edge: an optional number of channel to drop at |
---|
| 1026 | the edge of spectrum. If only one value is |
---|
| 1027 | specified, the same number will be dropped from |
---|
| 1028 | both sides of the spectrum. Default is to keep |
---|
[907] | 1029 | all channels. Nested tuples represent individual |
---|
[976] | 1030 | edge selection for different IFs (a number of spectral |
---|
| 1031 | channels can be different) |
---|
[880] | 1032 | order: the order of the polynomial (default is 0) |
---|
| 1033 | threshold: the threshold used by line finder. It is better to |
---|
| 1034 | keep it large as only strong lines affect the |
---|
| 1035 | baseline solution. |
---|
| 1036 | insitu: if False a new scantable is returned. |
---|
| 1037 | Otherwise, the scaling is done in-situ |
---|
| 1038 | The default is taken from .asaprc (False) |
---|
| 1039 | |
---|
| 1040 | Example: |
---|
| 1041 | scan2=scan.auto_poly_baseline(order=7) |
---|
| 1042 | """ |
---|
| 1043 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1044 | varlist = vars() |
---|
| 1045 | from asap.asapfitter import fitter |
---|
| 1046 | from asap.asaplinefind import linefinder |
---|
| 1047 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1048 | |
---|
[976] | 1049 | # check whether edge is set up for each IF individually |
---|
| 1050 | individualEdge = False; |
---|
| 1051 | if len(edge)>1: |
---|
| 1052 | if isinstance(edge[0],list) or isinstance(edge[0],tuple): |
---|
| 1053 | individualEdge = True; |
---|
[907] | 1054 | |
---|
| 1055 | if not _is_valid(edge, int) and not individualEdge: |
---|
[909] | 1056 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1057 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1058 | to make individual selection for different IFs." |
---|
[919] | 1059 | |
---|
[976] | 1060 | curedge = (0,0) |
---|
| 1061 | if individualEdge: |
---|
| 1062 | for edge_par in edge: |
---|
| 1063 | if not _is_valid(edge,int): |
---|
| 1064 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
[907] | 1065 | to be a pair of integers or an integer." |
---|
| 1066 | else: |
---|
[976] | 1067 | curedge = edge; |
---|
[880] | 1068 | |
---|
| 1069 | # setup fitter |
---|
| 1070 | f = fitter() |
---|
| 1071 | f.set_function(poly=order) |
---|
| 1072 | |
---|
| 1073 | # setup line finder |
---|
| 1074 | fl=linefinder() |
---|
| 1075 | fl.set_options(threshold=threshold) |
---|
| 1076 | |
---|
| 1077 | if not insitu: |
---|
| 1078 | workscan=self.copy() |
---|
| 1079 | else: |
---|
| 1080 | workscan=self |
---|
| 1081 | |
---|
[907] | 1082 | fl.set_scan(workscan) |
---|
| 1083 | |
---|
[880] | 1084 | rows=range(workscan.nrow()) |
---|
| 1085 | from asap import asaplog |
---|
| 1086 | asaplog.push("Processing:") |
---|
| 1087 | for r in rows: |
---|
| 1088 | 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)) |
---|
| 1089 | asaplog.push(msg, False) |
---|
[907] | 1090 | |
---|
[976] | 1091 | # figure out edge parameter |
---|
| 1092 | if individualEdge: |
---|
| 1093 | if len(edge)>=workscan.getif(r): |
---|
| 1094 | raise RuntimeError, "Number of edge elements appear to be less than the number of IFs" |
---|
| 1095 | curedge = edge[workscan.getif(r)] |
---|
[919] | 1096 | |
---|
[976] | 1097 | # setup line finder |
---|
[907] | 1098 | fl.find_lines(r,mask,curedge) |
---|
[880] | 1099 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1100 | f.x = workscan._getabcissa(r) |
---|
| 1101 | f.y = workscan._getspectrum(r) |
---|
| 1102 | f.data = None |
---|
| 1103 | f.fit() |
---|
| 1104 | x = f.get_parameters() |
---|
| 1105 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
| 1106 | workscan._add_history("poly_baseline", varlist) |
---|
| 1107 | if insitu: |
---|
| 1108 | self._assign(workscan) |
---|
| 1109 | else: |
---|
| 1110 | return workscan |
---|
| 1111 | |
---|
[914] | 1112 | def rotate_linpolphase(self, angle): |
---|
| 1113 | """ |
---|
| 1114 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1115 | This is always done in situ in the raw data. So if you call this |
---|
| 1116 | function more than once then each call rotates the phase further. |
---|
| 1117 | Parameters: |
---|
| 1118 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1119 | Examples: |
---|
| 1120 | scan.rotate_linpolphase(2.3) |
---|
| 1121 | """ |
---|
| 1122 | varlist = vars() |
---|
[936] | 1123 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 1124 | self._add_history("rotate_linpolphase", varlist) |
---|
| 1125 | print_log() |
---|
| 1126 | return |
---|
[710] | 1127 | |
---|
[513] | 1128 | |
---|
[914] | 1129 | def rotate_xyphase(self, angle): |
---|
| 1130 | """ |
---|
| 1131 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1132 | in the data. So if you call this function more than once |
---|
| 1133 | then each call rotates the phase further. |
---|
| 1134 | Parameters: |
---|
| 1135 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1136 | Examples: |
---|
| 1137 | scan.rotate_xyphase(2.3) |
---|
| 1138 | """ |
---|
| 1139 | varlist = vars() |
---|
[936] | 1140 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 1141 | self._add_history("rotate_xyphase", varlist) |
---|
| 1142 | print_log() |
---|
| 1143 | return |
---|
| 1144 | |
---|
| 1145 | def swap_linears(self): |
---|
| 1146 | """ |
---|
| 1147 | Swap the linear polarisations XX and YY |
---|
| 1148 | """ |
---|
| 1149 | varlist = vars() |
---|
[936] | 1150 | self._math._swap_linears(self) |
---|
[914] | 1151 | self._add_history("swap_linears", varlist) |
---|
| 1152 | print_log() |
---|
| 1153 | return |
---|
| 1154 | |
---|
| 1155 | def invert_phase(self): |
---|
| 1156 | """ |
---|
| 1157 | Invert the phase of the complex polarisation |
---|
| 1158 | """ |
---|
| 1159 | varlist = vars() |
---|
[936] | 1160 | self._math._invert_phase(self) |
---|
[914] | 1161 | self._add_history("invert_phase", varlist) |
---|
| 1162 | print_log() |
---|
| 1163 | return |
---|
| 1164 | |
---|
[876] | 1165 | def add(self, offset, insitu=None): |
---|
[513] | 1166 | """ |
---|
| 1167 | Return a scan where all spectra have the offset added |
---|
| 1168 | Parameters: |
---|
| 1169 | offset: the offset |
---|
| 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 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1175 | self._math._setinsitu(insitu) |
---|
[513] | 1176 | varlist = vars() |
---|
[876] | 1177 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
| 1178 | s._add_history("add",varlist) |
---|
| 1179 | print_log() |
---|
| 1180 | if insitu: |
---|
| 1181 | self._assign(s) |
---|
| 1182 | else: |
---|
[513] | 1183 | return s |
---|
| 1184 | |
---|
[876] | 1185 | def scale(self, factor, tsys=True, insitu=None,): |
---|
[513] | 1186 | """ |
---|
| 1187 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 1188 | Parameters: |
---|
| 1189 | factor: the scaling factor |
---|
| 1190 | insitu: if False a new scantable is returned. |
---|
| 1191 | Otherwise, the scaling is done in-situ |
---|
| 1192 | The default is taken from .asaprc (False) |
---|
| 1193 | tsys: if True (default) then apply the operation to Tsys |
---|
| 1194 | as well as the data |
---|
| 1195 | """ |
---|
| 1196 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1197 | self._math._setinsitu(insitu) |
---|
[513] | 1198 | varlist = vars() |
---|
[876] | 1199 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
| 1200 | s._add_history("scale",varlist) |
---|
| 1201 | print_log() |
---|
| 1202 | if insitu: |
---|
| 1203 | self._assign(s) |
---|
| 1204 | else: |
---|
[513] | 1205 | return s |
---|
| 1206 | |
---|
[876] | 1207 | def auto_quotient(self, mode='time', preserve=True): |
---|
[670] | 1208 | """ |
---|
| 1209 | This function allows to build quotients automatically. |
---|
| 1210 | It assumes the observation to have the same numer of |
---|
| 1211 | "ons" and "offs" |
---|
| 1212 | It will support "closest off in time" in the future |
---|
| 1213 | Parameters: |
---|
| 1214 | mode: the on/off detection mode; 'suffix' (default) |
---|
| 1215 | 'suffix' identifies 'off' scans by the |
---|
| 1216 | trailing '_R' (Mopra/Parkes) or |
---|
| 1217 | '_e'/'_w' (Tid) |
---|
[710] | 1218 | preserve: you can preserve (default) the continuum or |
---|
| 1219 | remove it. The equations used are |
---|
[670] | 1220 | preserve: Output = Toff * (on/off) - Toff |
---|
| 1221 | remove: Output = Tref * (on/off) - Ton |
---|
| 1222 | """ |
---|
[876] | 1223 | modes = ["time"] |
---|
[670] | 1224 | if not mode in modes: |
---|
[876] | 1225 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 1226 | raise ValueError(msg) |
---|
| 1227 | varlist = vars() |
---|
| 1228 | s = scantable(self._math._quotient(self, mode, preserve)) |
---|
| 1229 | s._add_history("auto_quotient",varlist) |
---|
| 1230 | print_log() |
---|
| 1231 | return s |
---|
[710] | 1232 | |
---|
[513] | 1233 | |
---|
[876] | 1234 | |
---|
| 1235 | |
---|
[718] | 1236 | def freq_switch(self, insitu=None): |
---|
| 1237 | """ |
---|
| 1238 | Apply frequency switching to the data. |
---|
| 1239 | Parameters: |
---|
| 1240 | insitu: if False a new scantable is returned. |
---|
| 1241 | Otherwise, the swictching is done in-situ |
---|
| 1242 | The default is taken from .asaprc (False) |
---|
| 1243 | Example: |
---|
| 1244 | none |
---|
| 1245 | """ |
---|
| 1246 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1247 | self._math._setinsitu(insitu) |
---|
[718] | 1248 | varlist = vars() |
---|
[876] | 1249 | s = scantable(self._math._freqswitch(self)) |
---|
| 1250 | s._add_history("freq_switch",varlist) |
---|
| 1251 | print_log() |
---|
| 1252 | if insitu: self._assign(s) |
---|
| 1253 | else: return s |
---|
[718] | 1254 | |
---|
[780] | 1255 | def recalc_azel(self): |
---|
| 1256 | """ |
---|
| 1257 | Recalculate the azimuth and elevation for each position. |
---|
| 1258 | Parameters: |
---|
| 1259 | none |
---|
| 1260 | Example: |
---|
| 1261 | """ |
---|
| 1262 | varlist = vars() |
---|
[876] | 1263 | self._recalcazel() |
---|
[780] | 1264 | self._add_history("recalc_azel", varlist) |
---|
| 1265 | print_log() |
---|
| 1266 | return |
---|
| 1267 | |
---|
[513] | 1268 | def __add__(self, other): |
---|
| 1269 | varlist = vars() |
---|
| 1270 | s = None |
---|
| 1271 | if isinstance(other, scantable): |
---|
[876] | 1272 | print "scantable + scantable NYI" |
---|
| 1273 | return |
---|
[513] | 1274 | elif isinstance(other, float): |
---|
[876] | 1275 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 1276 | else: |
---|
[718] | 1277 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1278 | s._add_history("operator +", varlist) |
---|
[718] | 1279 | print_log() |
---|
[513] | 1280 | return s |
---|
| 1281 | |
---|
| 1282 | def __sub__(self, other): |
---|
| 1283 | """ |
---|
| 1284 | implicit on all axes and on Tsys |
---|
| 1285 | """ |
---|
| 1286 | varlist = vars() |
---|
| 1287 | s = None |
---|
| 1288 | if isinstance(other, scantable): |
---|
[876] | 1289 | print "scantable - scantable NYI" |
---|
| 1290 | return |
---|
[513] | 1291 | elif isinstance(other, float): |
---|
[876] | 1292 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 1293 | else: |
---|
[718] | 1294 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1295 | s._add_history("operator -", varlist) |
---|
[718] | 1296 | print_log() |
---|
[513] | 1297 | return s |
---|
[710] | 1298 | |
---|
[513] | 1299 | def __mul__(self, other): |
---|
| 1300 | """ |
---|
| 1301 | implicit on all axes and on Tsys |
---|
| 1302 | """ |
---|
| 1303 | varlist = vars() |
---|
| 1304 | s = None |
---|
| 1305 | if isinstance(other, scantable): |
---|
[876] | 1306 | print "scantable * scantable NYI" |
---|
| 1307 | return |
---|
[513] | 1308 | elif isinstance(other, float): |
---|
[876] | 1309 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 1310 | else: |
---|
[718] | 1311 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1312 | s._add_history("operator *", varlist) |
---|
[718] | 1313 | print_log() |
---|
[513] | 1314 | return s |
---|
| 1315 | |
---|
[710] | 1316 | |
---|
[513] | 1317 | def __div__(self, other): |
---|
| 1318 | """ |
---|
| 1319 | implicit on all axes and on Tsys |
---|
| 1320 | """ |
---|
| 1321 | varlist = vars() |
---|
| 1322 | s = None |
---|
| 1323 | if isinstance(other, scantable): |
---|
[876] | 1324 | print "scantable / scantable NYI" |
---|
| 1325 | return |
---|
[513] | 1326 | elif isinstance(other, float): |
---|
| 1327 | if other == 0.0: |
---|
[718] | 1328 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 1329 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 1330 | else: |
---|
[718] | 1331 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1332 | s._add_history("operator /", varlist) |
---|
[718] | 1333 | print_log() |
---|
[513] | 1334 | return s |
---|
| 1335 | |
---|
[530] | 1336 | def get_fit(self, row=0): |
---|
| 1337 | """ |
---|
| 1338 | Print or return the stored fits for a row in the scantable |
---|
| 1339 | Parameters: |
---|
| 1340 | row: the row which the fit has been applied to. |
---|
| 1341 | """ |
---|
| 1342 | if row > self.nrow(): |
---|
| 1343 | return |
---|
[976] | 1344 | from asap.asapfit import asapfit |
---|
[530] | 1345 | fit = asapfit(self._getfit(row)) |
---|
[718] | 1346 | if rcParams['verbose']: |
---|
[530] | 1347 | print fit |
---|
| 1348 | return |
---|
| 1349 | else: |
---|
| 1350 | return fit.as_dict() |
---|
| 1351 | |
---|
[484] | 1352 | def _add_history(self, funcname, parameters): |
---|
| 1353 | # create date |
---|
| 1354 | sep = "##" |
---|
| 1355 | from datetime import datetime |
---|
| 1356 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 1357 | hist = dstr+sep |
---|
| 1358 | hist += funcname+sep#cdate+sep |
---|
| 1359 | if parameters.has_key('self'): del parameters['self'] |
---|
| 1360 | for k,v in parameters.iteritems(): |
---|
| 1361 | if type(v) is dict: |
---|
| 1362 | for k2,v2 in v.iteritems(): |
---|
| 1363 | hist += k2 |
---|
| 1364 | hist += "=" |
---|
| 1365 | if isinstance(v2,scantable): |
---|
| 1366 | hist += 'scantable' |
---|
| 1367 | elif k2 == 'mask': |
---|
[513] | 1368 | if isinstance(v2,list) or isinstance(v2,tuple): |
---|
| 1369 | hist += str(self._zip_mask(v2)) |
---|
| 1370 | else: |
---|
| 1371 | hist += str(v2) |
---|
[484] | 1372 | else: |
---|
[513] | 1373 | hist += str(v2) |
---|
[484] | 1374 | else: |
---|
| 1375 | hist += k |
---|
| 1376 | hist += "=" |
---|
| 1377 | if isinstance(v,scantable): |
---|
| 1378 | hist += 'scantable' |
---|
| 1379 | elif k == 'mask': |
---|
[513] | 1380 | if isinstance(v,list) or isinstance(v,tuple): |
---|
| 1381 | hist += str(self._zip_mask(v)) |
---|
| 1382 | else: |
---|
| 1383 | hist += str(v) |
---|
[484] | 1384 | else: |
---|
| 1385 | hist += str(v) |
---|
| 1386 | hist += sep |
---|
| 1387 | hist = hist[:-2] # remove trailing '##' |
---|
| 1388 | self._addhistory(hist) |
---|
| 1389 | |
---|
[710] | 1390 | |
---|
[484] | 1391 | def _zip_mask(self, mask): |
---|
| 1392 | mask = list(mask) |
---|
| 1393 | i = 0 |
---|
| 1394 | segments = [] |
---|
| 1395 | while mask[i:].count(1): |
---|
| 1396 | i += mask[i:].index(1) |
---|
| 1397 | if mask[i:].count(0): |
---|
| 1398 | j = i + mask[i:].index(0) |
---|
| 1399 | else: |
---|
[710] | 1400 | j = len(mask) |
---|
[484] | 1401 | segments.append([i,j]) |
---|
[710] | 1402 | i = j |
---|
[484] | 1403 | return segments |
---|
[714] | 1404 | |
---|
[626] | 1405 | def _get_ordinate_label(self): |
---|
| 1406 | fu = "("+self.get_fluxunit()+")" |
---|
| 1407 | import re |
---|
| 1408 | lbl = "Intensity" |
---|
| 1409 | if re.match(".K.",fu): |
---|
| 1410 | lbl = "Brightness Temperature "+ fu |
---|
| 1411 | elif re.match(".Jy.",fu): |
---|
| 1412 | lbl = "Flux density "+ fu |
---|
| 1413 | return lbl |
---|
[710] | 1414 | |
---|
[876] | 1415 | def _check_ifs(self): |
---|
| 1416 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 1417 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 1418 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 1419 | |
---|
| 1420 | def _fill(self, names, unit, average): |
---|
| 1421 | import os |
---|
| 1422 | varlist = vars() |
---|
| 1423 | from asap._asap import stfiller |
---|
| 1424 | first = True |
---|
| 1425 | fullnames = [] |
---|
| 1426 | for name in names: |
---|
| 1427 | name = os.path.expandvars(name) |
---|
| 1428 | name = os.path.expanduser(name) |
---|
| 1429 | if not os.path.exists(name): |
---|
| 1430 | msg = "File '%s' does not exists" % (name) |
---|
| 1431 | if rcParams['verbose']: |
---|
| 1432 | asaplog.push(msg) |
---|
| 1433 | print asaplog.pop().strip() |
---|
| 1434 | return |
---|
| 1435 | raise IOError(msg) |
---|
| 1436 | fullnames.append(name) |
---|
| 1437 | if average: |
---|
| 1438 | asaplog.push('Auto averaging integrations') |
---|
| 1439 | for name in fullnames: |
---|
| 1440 | r = stfiller() |
---|
| 1441 | msg = "Importing %s..." % (name) |
---|
| 1442 | asaplog.push(msg,False) |
---|
| 1443 | print_log() |
---|
| 1444 | r._open(name,-1,-1) |
---|
| 1445 | r._read() |
---|
| 1446 | tbl = r._getdata() |
---|
| 1447 | if average: |
---|
| 1448 | tbl = self._math._average((tbl,),(),'NONE','SCAN', False) |
---|
| 1449 | #tbl = tbl2 |
---|
| 1450 | if not first: |
---|
| 1451 | tbl = self._math._merge([self, tbl]) |
---|
| 1452 | #tbl = tbl2 |
---|
| 1453 | Scantable.__init__(self, tbl) |
---|
| 1454 | r._close() |
---|
| 1455 | del r,tbl |
---|
| 1456 | first = False |
---|
| 1457 | if unit is not None: |
---|
| 1458 | self.set_fluxunit(unit) |
---|
| 1459 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
| 1460 | #self._add_history("scantable", varlist) |
---|
| 1461 | |
---|