[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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[1073] | 54 | Scantable.__init__(self, filename, rcParams['scantable.storage']=='disk') |
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[976] | 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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[989] | 117 | from asap._asap import stwriter as stw |
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| 118 | w = stw(format2) |
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| 119 | w.write(self, name) |
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[718] | 120 | print_log() |
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[116] | 121 | return |
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| 122 | |
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[102] | 123 | def copy(self): |
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| 124 | """ |
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| 125 | Return a copy of this scantable. |
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| 126 | Parameters: |
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[113] | 127 | none |
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[102] | 128 | Example: |
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| 129 | copiedscan = scan.copy() |
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| 130 | """ |
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[876] | 131 | sd = scantable(Scantable._copy(self)) |
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[113] | 132 | return sd |
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| 133 | |
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[102] | 134 | def get_scan(self, scanid=None): |
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| 135 | """ |
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| 136 | Return a specific scan (by scanno) or collection of scans (by |
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| 137 | source name) in a new scantable. |
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| 138 | Parameters: |
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[513] | 139 | scanid: a (list of) scanno or a source name, unix-style |
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| 140 | patterns are accepted for source name matching, e.g. |
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| 141 | '*_R' gets all 'ref scans |
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[102] | 142 | Example: |
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[513] | 143 | # get all scans containing the source '323p459' |
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| 144 | newscan = scan.get_scan('323p459') |
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| 145 | # get all 'off' scans |
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| 146 | refscans = scan.get_scan('*_R') |
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| 147 | # get a susbset of scans by scanno (as listed in scan.summary()) |
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| 148 | newscan = scan.get_scan([0,2,7,10]) |
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[102] | 149 | """ |
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| 150 | if scanid is None: |
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[718] | 151 | if rcParams['verbose']: |
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| 152 | print "Please specify a scan no or name to retrieve from the scantable" |
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| 153 | return |
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| 154 | else: |
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| 155 | raise RuntimeError("No scan given") |
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| 156 | |
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[102] | 157 | try: |
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[946] | 158 | bsel = self.get_selection() |
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| 159 | sel = selector() |
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[102] | 160 | if type(scanid) is str: |
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[946] | 161 | sel.set_name(scanid) |
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| 162 | self.set_selection(bsel+sel) |
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[876] | 163 | scopy = self._copy() |
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[946] | 164 | self.set_selection(bsel) |
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[876] | 165 | return scantable(scopy) |
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[102] | 166 | elif type(scanid) is int: |
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[946] | 167 | sel.set_scans([scanid]) |
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| 168 | self.set_selection(bsel+sel) |
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[876] | 169 | scopy = self._copy() |
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[946] | 170 | self.set_selection(bsel) |
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[876] | 171 | return scantable(scopy) |
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[381] | 172 | elif type(scanid) is list: |
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[946] | 173 | sel.set_scans(scanid) |
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| 174 | self.set_selection(sel) |
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[876] | 175 | scopy = self._copy() |
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[946] | 176 | self.set_selection(bsel) |
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[876] | 177 | return scantable(scopy) |
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[381] | 178 | else: |
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[718] | 179 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
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| 180 | if rcParams['verbose']: |
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| 181 | print msg |
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| 182 | else: |
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| 183 | raise TypeError(msg) |
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[102] | 184 | except RuntimeError: |
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[718] | 185 | if rcParams['verbose']: print "Couldn't find any match." |
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| 186 | else: raise |
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[102] | 187 | |
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| 188 | def __str__(self): |
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[876] | 189 | return Scantable._summary(self,True) |
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[102] | 190 | |
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[976] | 191 | def summary(self, filename=None): |
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[102] | 192 | """ |
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| 193 | Print a summary of the contents of this scantable. |
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| 194 | Parameters: |
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| 195 | filename: the name of a file to write the putput to |
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| 196 | Default - no file output |
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[381] | 197 | verbose: print extra info such as the frequency table |
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| 198 | The default (False) is taken from .asaprc |
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[102] | 199 | """ |
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[976] | 200 | info = Scantable._summary(self, True) |
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| 201 | #if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
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[102] | 202 | if filename is not None: |
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[256] | 203 | if filename is "": |
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| 204 | filename = 'scantable_summary.txt' |
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[415] | 205 | from os.path import expandvars, isdir |
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[411] | 206 | filename = expandvars(filename) |
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[415] | 207 | if not isdir(filename): |
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[413] | 208 | data = open(filename, 'w') |
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| 209 | data.write(info) |
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| 210 | data.close() |
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| 211 | else: |
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[718] | 212 | msg = "Illegal file name '%s'." % (filename) |
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| 213 | if rcParams['verbose']: |
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| 214 | print msg |
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| 215 | else: |
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| 216 | raise IOError(msg) |
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| 217 | if rcParams['verbose']: |
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[794] | 218 | try: |
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| 219 | from IPython.genutils import page as pager |
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| 220 | except ImportError: |
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| 221 | from pydoc import pager |
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| 222 | pager(info) |
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[718] | 223 | else: |
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| 224 | return info |
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[710] | 225 | |
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[946] | 226 | |
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| 227 | def get_selection(self): |
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| 228 | """ |
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[1005] | 229 | Get the selection object currently set on this scantable. |
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| 230 | Parameters: |
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| 231 | none |
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| 232 | Example: |
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| 233 | sel = scan.get_selection() |
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| 234 | sel.set_ifs(0) # select IF 0 |
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| 235 | scan.set_selection(sel) # apply modified selection |
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[946] | 236 | """ |
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| 237 | return selector(self._getselection()) |
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| 238 | |
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[1005] | 239 | def set_selection(self, selection=selector()): |
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[946] | 240 | """ |
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[1005] | 241 | Select a subset of the data. All following operations on this scantable |
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| 242 | are only applied to thi selection. |
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| 243 | Parameters: |
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| 244 | selection: a selector object (default unset the selection) |
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| 245 | Examples: |
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| 246 | sel = selector() # create a selection object |
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| 247 | self.set_scans([0,3]) # select SCANNO 0 and 3 |
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| 248 | scan.set_selection(sel) # set the selection |
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| 249 | scan.summary() # will only print summary of scanno 0 an 3 |
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| 250 | scan.set_selection() # unset the selection |
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[946] | 251 | """ |
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| 252 | self._setselection(selection) |
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| 253 | |
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[553] | 254 | def set_cursor(self, beam=0, IF=0, pol=0): |
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[1006] | 255 | print "DEPRECATED - use set_selection" |
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[102] | 256 | |
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[256] | 257 | def get_cursor(self): |
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[1006] | 258 | print "DEPRECATED - use get_selection" |
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[102] | 259 | |
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[876] | 260 | def stats(self, stat='stddev', mask=None): |
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[102] | 261 | """ |
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[135] | 262 | Determine the specified statistic of the current beam/if/pol |
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[102] | 263 | Takes a 'mask' as an optional parameter to specify which |
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| 264 | channels should be excluded. |
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| 265 | Parameters: |
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[135] | 266 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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| 267 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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| 268 | mask: an optional mask specifying where the statistic |
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[102] | 269 | should be determined. |
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| 270 | Example: |
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[113] | 271 | scan.set_unit('channel') |
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[102] | 272 | msk = scan.create_mask([100,200],[500,600]) |
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[135] | 273 | scan.stats(stat='mean', mask=m) |
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[102] | 274 | """ |
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[256] | 275 | from numarray import array,zeros,Float |
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[102] | 276 | if mask == None: |
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[876] | 277 | mask = [] |
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[256] | 278 | axes = ['Beam','IF','Pol','Time'] |
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[876] | 279 | if not self._check_ifs(): |
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| 280 | raise ValueError("Cannot apply mask as the IFs have different number of channels" |
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| 281 | "Please use setselection() to select individual IFs") |
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[256] | 282 | |
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[876] | 283 | statvals = self._math._stats(self, mask, stat) |
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| 284 | out = '' |
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| 285 | axes = [] |
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| 286 | for i in range(self.nrow()): |
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| 287 | axis = [] |
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| 288 | axis.append(self.getscan(i)) |
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| 289 | axis.append(self.getbeam(i)) |
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| 290 | axis.append(self.getif(i)) |
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| 291 | axis.append(self.getpol(i)) |
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| 292 | axis.append(self.getcycle(i)) |
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| 293 | axes.append(axis) |
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| 294 | tm = self._gettime(i) |
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| 295 | src = self._getsourcename(i) |
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| 296 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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| 297 | out += 'Time[%s]:\n' % (tm) |
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| 298 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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| 299 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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| 300 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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| 301 | out += '= %3.3f\n' % (statvals[i]) |
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| 302 | out += "--------------------------------------------------\n" |
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[256] | 303 | |
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[876] | 304 | if rcParams['verbose']: |
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| 305 | print "--------------------------------------------------" |
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| 306 | print " ",stat |
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| 307 | print "--------------------------------------------------" |
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| 308 | print out |
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| 309 | retval = { 'axesnames': ['scanno','beamno','ifno','polno','cycleno'], |
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| 310 | 'axes' : axes, |
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| 311 | 'data': statvals} |
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| 312 | return retval |
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[102] | 313 | |
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[876] | 314 | def stddev(self,mask=None): |
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[135] | 315 | """ |
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| 316 | Determine the standard deviation of the current beam/if/pol |
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| 317 | Takes a 'mask' as an optional parameter to specify which |
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| 318 | channels should be excluded. |
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| 319 | Parameters: |
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| 320 | mask: an optional mask specifying where the standard |
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| 321 | deviation should be determined. |
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| 322 | |
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| 323 | Example: |
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| 324 | scan.set_unit('channel') |
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| 325 | msk = scan.create_mask([100,200],[500,600]) |
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| 326 | scan.stddev(mask=m) |
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| 327 | """ |
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[876] | 328 | return self.stats(stat='stddev',mask=mask); |
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[135] | 329 | |
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[1003] | 330 | |
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| 331 | def column_names(self): |
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| 332 | """ |
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| 333 | Return a list of column names, which can be used for selection. |
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| 334 | """ |
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| 335 | return list(Scantable.column_names(self)) |
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| 336 | |
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[876] | 337 | def get_tsys(self): |
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[113] | 338 | """ |
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| 339 | Return the System temperatures. |
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| 340 | Parameters: |
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[876] | 341 | |
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[113] | 342 | Returns: |
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[876] | 343 | a list of Tsys values for the current selection |
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[113] | 344 | """ |
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[256] | 345 | |
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[876] | 346 | return self._row_callback(self._gettsys, "Tsys") |
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[256] | 347 | |
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[876] | 348 | def _row_callback(self, callback, label): |
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| 349 | axes = [] |
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| 350 | axesnames = ['scanno','beamno','ifno','polno','cycleno'] |
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| 351 | out = "" |
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| 352 | outvec =[] |
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| 353 | for i in range(self.nrow()): |
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| 354 | axis = [] |
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| 355 | axis.append(self.getscan(i)) |
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| 356 | axis.append(self.getbeam(i)) |
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| 357 | axis.append(self.getif(i)) |
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| 358 | axis.append(self.getpol(i)) |
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| 359 | axis.append(self.getcycle(i)) |
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| 360 | axes.append(axis) |
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| 361 | tm = self._gettime(i) |
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| 362 | src = self._getsourcename(i) |
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| 363 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
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| 364 | out += 'Time[%s]:\n' % (tm) |
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| 365 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
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| 366 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
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| 367 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
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| 368 | outvec.append(callback(i)) |
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| 369 | out += '= %3.3f\n' % (outvec[i]) |
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| 370 | out += "--------------------------------------------------\n" |
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| 371 | if rcParams['verbose']: |
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| 372 | print "--------------------------------------------------" |
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| 373 | print " %s" % (label) |
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| 374 | print "--------------------------------------------------" |
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| 375 | print out |
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| 376 | retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec} |
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| 377 | return retval |
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[256] | 378 | |
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[1070] | 379 | def _get_column(self, callback, row=-1): |
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| 380 | """ |
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| 381 | """ |
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| 382 | if row == -1: |
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| 383 | return [callback(i) for i in range(self.nrow())] |
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| 384 | else: |
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| 385 | if 0 <= row < self.nrow(): |
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| 386 | return callback(row) |
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[256] | 387 | |
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[1070] | 388 | |
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[407] | 389 | def get_time(self, row=-1): |
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[113] | 390 | """ |
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| 391 | Get a list of time stamps for the observations. |
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[181] | 392 | Return a string for each integration in the scantable. |
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[113] | 393 | Parameters: |
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[407] | 394 | row: row no of integration. Default -1 return all rows |
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[113] | 395 | Example: |
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| 396 | none |
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| 397 | """ |
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[1070] | 398 | return self._get_column(self._gettime, row) |
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[102] | 399 | |
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[714] | 400 | def get_sourcename(self, row=-1): |
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| 401 | """ |
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[794] | 402 | Get a list source names for the observations. |
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[714] | 403 | Return a string for each integration in the scantable. |
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| 404 | Parameters: |
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| 405 | row: row no of integration. Default -1 return all rows |
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| 406 | Example: |
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| 407 | none |
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| 408 | """ |
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[1070] | 409 | return self._get_column(self._getsourcename, row) |
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[714] | 410 | |
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[794] | 411 | def get_elevation(self, row=-1): |
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| 412 | """ |
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| 413 | Get a list of elevations for the observations. |
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| 414 | Return a float for each integration in the scantable. |
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| 415 | Parameters: |
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| 416 | row: row no of integration. Default -1 return all rows |
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| 417 | Example: |
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| 418 | none |
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| 419 | """ |
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[1070] | 420 | return self._get_column(self._getelevation, row) |
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[794] | 421 | |
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| 422 | def get_azimuth(self, row=-1): |
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| 423 | """ |
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| 424 | Get a list of azimuths for the observations. |
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| 425 | Return a float for each integration in the scantable. |
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| 426 | Parameters: |
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| 427 | row: row no of integration. Default -1 return all rows |
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| 428 | Example: |
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| 429 | none |
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| 430 | """ |
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[1070] | 431 | return self._get_column(self._getazimuth, row) |
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[794] | 432 | |
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| 433 | def get_parangle(self, row=-1): |
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| 434 | """ |
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| 435 | Get a list of parallactic angles for the observations. |
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| 436 | Return a float for each integration in the scantable. |
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| 437 | Parameters: |
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| 438 | row: row no of integration. Default -1 return all rows |
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| 439 | Example: |
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| 440 | none |
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| 441 | """ |
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[1070] | 442 | return self._get_column(self._getparangle, row) |
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[794] | 443 | |
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[1070] | 444 | def get_direction(self, row=-1): |
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| 445 | """ |
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| 446 | Get a list of Positions on the sky (direction) for the observations. |
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| 447 | Return a float for each integration in the scantable. |
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| 448 | Parameters: |
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| 449 | row: row no of integration. Default -1 return all rows |
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| 450 | Example: |
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| 451 | none |
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| 452 | """ |
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| 453 | return self._get_column(self._getdirection, row) |
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| 454 | |
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[102] | 455 | def set_unit(self, unit='channel'): |
---|
| 456 | """ |
---|
| 457 | Set the unit for all following operations on this scantable |
---|
| 458 | Parameters: |
---|
| 459 | unit: optional unit, default is 'channel' |
---|
[113] | 460 | one of '*Hz','km/s','channel', '' |
---|
[102] | 461 | """ |
---|
[484] | 462 | varlist = vars() |
---|
[113] | 463 | if unit in ['','pixel', 'channel']: |
---|
| 464 | unit = '' |
---|
| 465 | inf = list(self._getcoordinfo()) |
---|
| 466 | inf[0] = unit |
---|
| 467 | self._setcoordinfo(inf) |
---|
[484] | 468 | self._add_history("set_unit",varlist) |
---|
[113] | 469 | |
---|
[484] | 470 | def set_instrument(self, instr): |
---|
[358] | 471 | """ |
---|
| 472 | Set the instrument for subsequent processing |
---|
| 473 | Parameters: |
---|
[710] | 474 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 475 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 476 | """ |
---|
| 477 | self._setInstrument(instr) |
---|
[484] | 478 | self._add_history("set_instument",vars()) |
---|
[718] | 479 | print_log() |
---|
[358] | 480 | |
---|
[276] | 481 | def set_doppler(self, doppler='RADIO'): |
---|
| 482 | """ |
---|
| 483 | Set the doppler for all following operations on this scantable. |
---|
| 484 | Parameters: |
---|
| 485 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 486 | """ |
---|
[484] | 487 | varlist = vars() |
---|
[276] | 488 | inf = list(self._getcoordinfo()) |
---|
| 489 | inf[2] = doppler |
---|
| 490 | self._setcoordinfo(inf) |
---|
[484] | 491 | self._add_history("set_doppler",vars()) |
---|
[718] | 492 | print_log() |
---|
[710] | 493 | |
---|
[226] | 494 | def set_freqframe(self, frame=None): |
---|
[113] | 495 | """ |
---|
| 496 | Set the frame type of the Spectral Axis. |
---|
| 497 | Parameters: |
---|
[591] | 498 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
| 499 | 'REST','TOPO','LSRD','LSRK','BARY', |
---|
| 500 | 'GEO','GALACTO','LGROUP','CMB' |
---|
[113] | 501 | Examples: |
---|
| 502 | scan.set_freqframe('BARY') |
---|
| 503 | """ |
---|
[484] | 504 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
| 505 | varlist = vars() |
---|
[113] | 506 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
---|
| 507 | 'GEO','GALACTO','LGROUP','CMB'] |
---|
[591] | 508 | |
---|
[989] | 509 | if frame in valid: |
---|
[113] | 510 | inf = list(self._getcoordinfo()) |
---|
| 511 | inf[1] = frame |
---|
| 512 | self._setcoordinfo(inf) |
---|
[484] | 513 | self._add_history("set_freqframe",varlist) |
---|
[102] | 514 | else: |
---|
[718] | 515 | msg = "Please specify a valid freq type. Valid types are:\n",valid |
---|
| 516 | if rcParams['verbose']: |
---|
| 517 | print msg |
---|
| 518 | else: |
---|
| 519 | raise TypeError(msg) |
---|
| 520 | print_log() |
---|
[710] | 521 | |
---|
[989] | 522 | def set_dirframe(self, frame=""): |
---|
| 523 | """ |
---|
| 524 | Set the frame type of the Direction on the sky. |
---|
| 525 | Parameters: |
---|
| 526 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 527 | 'J2000', 'B1950', 'GALACTIC' |
---|
| 528 | Examples: |
---|
| 529 | scan.set_dirframe('GALACTIC') |
---|
| 530 | """ |
---|
| 531 | varlist = vars() |
---|
| 532 | try: |
---|
| 533 | Scantable.set_dirframe(self, frame) |
---|
| 534 | except RuntimeError,msg: |
---|
| 535 | if rcParams['verbose']: |
---|
| 536 | print msg |
---|
| 537 | else: |
---|
| 538 | raise |
---|
| 539 | self._add_history("set_dirframe",varlist) |
---|
| 540 | |
---|
[113] | 541 | def get_unit(self): |
---|
| 542 | """ |
---|
| 543 | Get the default unit set in this scantable |
---|
| 544 | Parameters: |
---|
| 545 | Returns: |
---|
| 546 | A unit string |
---|
| 547 | """ |
---|
| 548 | inf = self._getcoordinfo() |
---|
| 549 | unit = inf[0] |
---|
| 550 | if unit == '': unit = 'channel' |
---|
| 551 | return unit |
---|
[102] | 552 | |
---|
[158] | 553 | def get_abcissa(self, rowno=0): |
---|
[102] | 554 | """ |
---|
[158] | 555 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 556 | selected Beam/IF/Pol |
---|
| 557 | Parameters: |
---|
[226] | 558 | rowno: an optional row number in the scantable. Default is the |
---|
| 559 | first row, i.e. rowno=0 |
---|
[113] | 560 | Returns: |
---|
[407] | 561 | The abcissa values and it's format string (as a dictionary) |
---|
[113] | 562 | """ |
---|
[256] | 563 | abc = self._getabcissa(rowno) |
---|
[710] | 564 | lbl = self._getabcissalabel(rowno) |
---|
[718] | 565 | print_log() |
---|
[158] | 566 | return abc, lbl |
---|
[113] | 567 | |
---|
[1001] | 568 | def flag(self, mask=[]): |
---|
| 569 | """ |
---|
| 570 | Flag the selected data using an optional channel mask. |
---|
| 571 | Parameters: |
---|
| 572 | mask: an optional channel mask, created with create_mask. Default |
---|
| 573 | (no mask) is all channels. |
---|
| 574 | """ |
---|
| 575 | varlist = vars() |
---|
| 576 | try: |
---|
| 577 | self._flag(mask) |
---|
| 578 | except RuntimeError,msg: |
---|
| 579 | if rcParams['verbose']: |
---|
| 580 | print msg |
---|
| 581 | return |
---|
| 582 | else: raise |
---|
| 583 | self._add_history("flag", varlist) |
---|
| 584 | |
---|
| 585 | |
---|
[113] | 586 | def create_mask(self, *args, **kwargs): |
---|
| 587 | """ |
---|
[102] | 588 | Compute and return a mask based on [min,max] windows. |
---|
[189] | 589 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 590 | applied. |
---|
[102] | 591 | Parameters: |
---|
| 592 | [min,max],[min2,max2],... |
---|
[1024] | 593 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 594 | to be masked |
---|
[189] | 595 | invert: optional argument. If specified as True, |
---|
| 596 | return an inverted mask, i.e. the regions |
---|
| 597 | specified are EXCLUDED |
---|
[513] | 598 | row: create the mask using the specified row for |
---|
| 599 | unit conversions, default is row=0 |
---|
| 600 | only necessary if frequency varies over rows. |
---|
[102] | 601 | Example: |
---|
[113] | 602 | scan.set_unit('channel') |
---|
| 603 | a) |
---|
[1024] | 604 | msk = scan.create_mask([400,500],[800,900]) |
---|
[189] | 605 | # masks everything outside 400 and 500 |
---|
[113] | 606 | # and 800 and 900 in the unit 'channel' |
---|
| 607 | |
---|
| 608 | b) |
---|
[1024] | 609 | msk = scan.create_mask([400,500],[800,900], invert=True) |
---|
[189] | 610 | # masks the regions between 400 and 500 |
---|
[113] | 611 | # and 800 and 900 in the unit 'channel' |
---|
[1024] | 612 | c) |
---|
| 613 | mask only channel 400 |
---|
| 614 | msk = scan.create_mask([400,400]) |
---|
[102] | 615 | """ |
---|
[513] | 616 | row = 0 |
---|
| 617 | if kwargs.has_key("row"): |
---|
| 618 | row = kwargs.get("row") |
---|
| 619 | data = self._getabcissa(row) |
---|
[113] | 620 | u = self._getcoordinfo()[0] |
---|
[718] | 621 | if rcParams['verbose']: |
---|
[113] | 622 | if u == "": u = "channel" |
---|
[718] | 623 | from asap import asaplog |
---|
| 624 | msg = "The current mask window unit is %s" % u |
---|
[914] | 625 | if not self._check_ifs(): |
---|
[876] | 626 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 627 | asaplog.push(msg) |
---|
[102] | 628 | n = self.nchan() |
---|
[189] | 629 | msk = zeros(n) |
---|
[710] | 630 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 631 | |
---|
| 632 | ws = (isinstance(args[-1][-1],int) or isinstance(args[-1][-1],float)) and args or args[0] |
---|
| 633 | for window in ws: |
---|
[102] | 634 | if (len(window) != 2 or window[0] > window[1] ): |
---|
[718] | 635 | raise TypeError("A window needs to be defined as [min,max]") |
---|
[102] | 636 | for i in range(n): |
---|
[1024] | 637 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[189] | 638 | msk[i] = 1 |
---|
[113] | 639 | if kwargs.has_key('invert'): |
---|
| 640 | if kwargs.get('invert'): |
---|
| 641 | from numarray import logical_not |
---|
[710] | 642 | msk = logical_not(msk) |
---|
[718] | 643 | print_log() |
---|
[102] | 644 | return msk |
---|
[710] | 645 | |
---|
[256] | 646 | def get_restfreqs(self): |
---|
| 647 | """ |
---|
| 648 | Get the restfrequency(s) stored in this scantable. |
---|
| 649 | The return value(s) are always of unit 'Hz' |
---|
| 650 | Parameters: |
---|
| 651 | none |
---|
| 652 | Returns: |
---|
| 653 | a list of doubles |
---|
| 654 | """ |
---|
| 655 | return list(self._getrestfreqs()) |
---|
[102] | 656 | |
---|
[402] | 657 | |
---|
[931] | 658 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
| 659 | """ |
---|
| 660 | Set or replace the restfrequency specified and |
---|
| 661 | If the 'freqs' argument holds a scalar, |
---|
| 662 | then that rest frequency will be applied to all the selected |
---|
| 663 | data. If the 'freqs' argument holds |
---|
| 664 | a vector, then it MUST be of equal or smaller length than |
---|
| 665 | the number of IFs (and the available restfrequencies will be |
---|
| 666 | replaced by this vector). In this case, *all* data have |
---|
| 667 | the restfrequency set per IF according |
---|
| 668 | to the corresponding value you give in the 'freqs' vector. |
---|
| 669 | E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
| 670 | IF 1 gets restfreq 2e9. |
---|
| 671 | You can also specify the frequencies via known line names |
---|
| 672 | from the built-in Lovas table. |
---|
| 673 | Parameters: |
---|
| 674 | freqs: list of rest frequency values or string idenitfiers |
---|
| 675 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 676 | |
---|
[931] | 677 | Example: |
---|
| 678 | # set the given restfrequency for the whole table |
---|
| 679 | scan.set_restfreqs(freqs=1.4e9) |
---|
| 680 | # If thee number of IFs in the data is >= 2 the IF0 gets the first |
---|
| 681 | # value IF1 the second... |
---|
| 682 | scan.set_restfreqs(freqs=[1.4e9,1.67e9]) |
---|
| 683 | #set the given restfrequency for the whole table (by name) |
---|
| 684 | scan.set_restfreqs(freqs="OH1667") |
---|
[391] | 685 | |
---|
[931] | 686 | Note: |
---|
| 687 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 688 | source and IF basis, use scantable.set_selection() before using |
---|
| 689 | this function. |
---|
| 690 | # provide your scantable is call scan |
---|
| 691 | selection = selector() |
---|
| 692 | selection.set_name("ORION*") |
---|
| 693 | selection.set_ifs([1]) |
---|
| 694 | scan.set_selection(selection) |
---|
| 695 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 696 | |
---|
| 697 | """ |
---|
| 698 | varlist = vars() |
---|
| 699 | |
---|
| 700 | t = type(freqs) |
---|
| 701 | if isinstance(freqs, int) or isinstance(freqs,float): |
---|
| 702 | self._setrestfreqs(freqs, unit) |
---|
| 703 | elif isinstance(freqs, list) or isinstance(freqs,tuple): |
---|
| 704 | if isinstance(freqs[-1], int) or isinstance(freqs[-1],float): |
---|
| 705 | sel = selector() |
---|
| 706 | savesel = self._getselection() |
---|
| 707 | for i in xrange(len(freqs)): |
---|
[946] | 708 | sel.set_ifs([i]) |
---|
[931] | 709 | self._setselection(sel) |
---|
| 710 | self._setrestfreqs(freqs[i], unit) |
---|
| 711 | self._setselection(savesel) |
---|
| 712 | elif isinstance(freqs[-1], str): |
---|
| 713 | # not yet implemented |
---|
| 714 | pass |
---|
| 715 | else: |
---|
| 716 | return |
---|
| 717 | self._add_history("set_restfreqs", varlist) |
---|
| 718 | |
---|
| 719 | |
---|
| 720 | |
---|
[484] | 721 | def history(self): |
---|
| 722 | hist = list(self._gethistory()) |
---|
[794] | 723 | out = "-"*80 |
---|
[484] | 724 | for h in hist: |
---|
[489] | 725 | if h.startswith("---"): |
---|
[794] | 726 | out += "\n"+h |
---|
[489] | 727 | else: |
---|
| 728 | items = h.split("##") |
---|
| 729 | date = items[0] |
---|
| 730 | func = items[1] |
---|
| 731 | items = items[2:] |
---|
[794] | 732 | out += "\n"+date+"\n" |
---|
| 733 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 734 | for i in items: |
---|
| 735 | s = i.split("=") |
---|
[794] | 736 | out += "\n %s = %s" % (s[0],s[1]) |
---|
| 737 | out += "\n"+"-"*80 |
---|
| 738 | try: |
---|
| 739 | from IPython.genutils import page as pager |
---|
| 740 | except ImportError: |
---|
| 741 | from pydoc import pager |
---|
| 742 | pager(out) |
---|
[484] | 743 | return |
---|
| 744 | |
---|
[513] | 745 | # |
---|
| 746 | # Maths business |
---|
| 747 | # |
---|
| 748 | |
---|
[931] | 749 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[513] | 750 | """ |
---|
[1070] | 751 | Return the (time) weighted average of a scan. |
---|
[513] | 752 | Note: |
---|
[1070] | 753 | in channels only - align if necessary |
---|
[513] | 754 | Parameters: |
---|
| 755 | one scan or comma separated scans |
---|
| 756 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 757 | weighting) |
---|
[558] | 758 | scanav: True averages each scan separately |
---|
| 759 | False (default) averages all scans together, |
---|
[524] | 760 | weight: Weighting scheme. 'none', 'var' (1/var(spec) |
---|
[535] | 761 | weighted), 'tsys' (1/Tsys**2 weighted), 'tint' |
---|
| 762 | (integration time weighted) or 'tintsys' (Tint/Tsys**2). |
---|
| 763 | The default is 'tint' |
---|
[931] | 764 | align: align the spectra in velocity before averaging. It takes |
---|
| 765 | the time of the first spectrum as reference time. |
---|
[513] | 766 | Example: |
---|
| 767 | # time average the scantable without using a mask |
---|
[710] | 768 | newscan = scan.average_time() |
---|
[513] | 769 | """ |
---|
| 770 | varlist = vars() |
---|
[976] | 771 | if weight is None: weight = 'TINT' |
---|
[513] | 772 | if mask is None: mask = () |
---|
[876] | 773 | if scanav: |
---|
[981] | 774 | scanav = "SCAN" |
---|
[876] | 775 | else: |
---|
[981] | 776 | scanav = "NONE" |
---|
| 777 | scan = (self,) |
---|
[989] | 778 | try: |
---|
| 779 | if align: |
---|
| 780 | scan = (self.freq_align(insitu=False),) |
---|
| 781 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 782 | scanav)) |
---|
| 783 | except RuntimeError,msg: |
---|
| 784 | if rcParams['verbose']: |
---|
| 785 | print msg |
---|
| 786 | return |
---|
| 787 | else: raise |
---|
[513] | 788 | s._add_history("average_time",varlist) |
---|
[718] | 789 | print_log() |
---|
[513] | 790 | return s |
---|
[710] | 791 | |
---|
[1073] | 792 | def average_channel(self, mode="MEDIAN", scanav=False, align=False): |
---|
[1070] | 793 | """ |
---|
| 794 | Return the (median) average of a scan. |
---|
| 795 | Note: |
---|
| 796 | in channels only - align if necessary |
---|
[1073] | 797 | the median Tsys is computed. |
---|
[1070] | 798 | Parameters: |
---|
| 799 | one scan or comma separated scans |
---|
| 800 | mode: type of average, default "MEDIAN" |
---|
[1073] | 801 | scanav: True averages each scan separately |
---|
| 802 | False (default) averages all scans together, |
---|
[1070] | 803 | align: align the spectra in velocity before averaging. It takes |
---|
| 804 | the time of the first spectrum as reference time. |
---|
| 805 | Example: |
---|
[1073] | 806 | # median average the scan |
---|
[1070] | 807 | newscan = scan.average_channel() |
---|
| 808 | """ |
---|
| 809 | varlist = vars() |
---|
| 810 | if mode is None: mode = 'MEDIAN' |
---|
[1073] | 811 | scanav = "NONE" |
---|
| 812 | if scanav: scanav = "SCAN" |
---|
[1070] | 813 | scan = self |
---|
| 814 | try: |
---|
| 815 | if align: |
---|
| 816 | scan = self.freq_align(insitu=False) |
---|
[1073] | 817 | s = scantable(self._math._averagechannel(scan, mode, scanav)) |
---|
[1070] | 818 | except RuntimeError,msg: |
---|
| 819 | if rcParams['verbose']: |
---|
| 820 | print msg |
---|
| 821 | return |
---|
| 822 | else: raise |
---|
| 823 | s._add_history("average_channel",varlist) |
---|
| 824 | print_log() |
---|
| 825 | return s |
---|
| 826 | |
---|
[876] | 827 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[513] | 828 | """ |
---|
| 829 | Return a scan where all spectra are converted to either |
---|
| 830 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 831 | By default the function tries to look the values up internally. |
---|
| 832 | If it can't find them (or if you want to over-ride), you must |
---|
| 833 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 834 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 835 | Parameters: |
---|
| 836 | jyperk: the Jy / K conversion factor |
---|
| 837 | eta: the aperture efficiency |
---|
| 838 | d: the geomtric diameter (metres) |
---|
| 839 | insitu: if False a new scantable is returned. |
---|
| 840 | Otherwise, the scaling is done in-situ |
---|
| 841 | The default is taken from .asaprc (False) |
---|
| 842 | allaxes: if True apply to all spectra. Otherwise |
---|
| 843 | apply only to the selected (beam/pol/if)spectra only |
---|
| 844 | The default is taken from .asaprc (True if none) |
---|
| 845 | """ |
---|
| 846 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 847 | self._math._setinsitu(insitu) |
---|
[513] | 848 | varlist = vars() |
---|
| 849 | if jyperk is None: jyperk = -1.0 |
---|
| 850 | if d is None: d = -1.0 |
---|
| 851 | if eta is None: eta = -1.0 |
---|
[876] | 852 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 853 | s._add_history("convert_flux", varlist) |
---|
| 854 | print_log() |
---|
| 855 | if insitu: self._assign(s) |
---|
| 856 | else: return s |
---|
[513] | 857 | |
---|
[876] | 858 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[513] | 859 | """ |
---|
| 860 | Return a scan after applying a gain-elevation correction. |
---|
| 861 | The correction can be made via either a polynomial or a |
---|
| 862 | table-based interpolation (and extrapolation if necessary). |
---|
| 863 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 864 | If you specify neither, then a polynomial correction will be made |
---|
| 865 | with built in coefficients known for certain telescopes (an error |
---|
| 866 | will occur if the instrument is not known). |
---|
| 867 | The data and Tsys are *divided* by the scaling factors. |
---|
| 868 | Parameters: |
---|
| 869 | poly: Polynomial coefficients (default None) to compute a |
---|
| 870 | gain-elevation correction as a function of |
---|
| 871 | elevation (in degrees). |
---|
| 872 | filename: The name of an ascii file holding correction factors. |
---|
| 873 | The first row of the ascii file must give the column |
---|
| 874 | names and these MUST include columns |
---|
| 875 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 876 | by this) somewhere. |
---|
| 877 | The second row must give the data type of the |
---|
| 878 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 879 | An example file would be |
---|
| 880 | (actual factors are arbitrary) : |
---|
| 881 | |
---|
| 882 | TIME ELEVATION FACTOR |
---|
| 883 | R R R |
---|
| 884 | 0.1 0 0.8 |
---|
| 885 | 0.2 20 0.85 |
---|
| 886 | 0.3 40 0.9 |
---|
| 887 | 0.4 60 0.85 |
---|
| 888 | 0.5 80 0.8 |
---|
| 889 | 0.6 90 0.75 |
---|
| 890 | method: Interpolation method when correcting from a table. |
---|
| 891 | Values are "nearest", "linear" (default), "cubic" |
---|
| 892 | and "spline" |
---|
| 893 | insitu: if False a new scantable is returned. |
---|
| 894 | Otherwise, the scaling is done in-situ |
---|
| 895 | The default is taken from .asaprc (False) |
---|
| 896 | """ |
---|
| 897 | |
---|
| 898 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 899 | self._math._setinsitu(insitu) |
---|
[513] | 900 | varlist = vars() |
---|
| 901 | if poly is None: |
---|
| 902 | poly = () |
---|
| 903 | from os.path import expandvars |
---|
| 904 | filename = expandvars(filename) |
---|
[876] | 905 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 906 | s._add_history("gain_el", varlist) |
---|
| 907 | print_log() |
---|
| 908 | if insitu: self._assign(s) |
---|
| 909 | else: return s |
---|
[710] | 910 | |
---|
[931] | 911 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[513] | 912 | """ |
---|
| 913 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 914 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 915 | set_freqframe. |
---|
| 916 | Parameters: |
---|
| 917 | reftime: reference time to align at. By default, the time of |
---|
| 918 | the first row of data is used. |
---|
| 919 | method: Interpolation method for regridding the spectra. |
---|
| 920 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 921 | and "spline" |
---|
| 922 | insitu: if False a new scantable is returned. |
---|
| 923 | Otherwise, the scaling is done in-situ |
---|
| 924 | The default is taken from .asaprc (False) |
---|
| 925 | """ |
---|
[931] | 926 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 927 | self._math._setinsitu(insitu) |
---|
[513] | 928 | varlist = vars() |
---|
[931] | 929 | if reftime is None: reftime = "" |
---|
| 930 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 931 | s._add_history("freq_align", varlist) |
---|
| 932 | print_log() |
---|
| 933 | if insitu: self._assign(s) |
---|
| 934 | else: return s |
---|
[513] | 935 | |
---|
[876] | 936 | def opacity(self, tau, insitu=None): |
---|
[513] | 937 | """ |
---|
| 938 | Apply an opacity correction. The data |
---|
| 939 | and Tsys are multiplied by the correction factor. |
---|
| 940 | Parameters: |
---|
| 941 | tau: Opacity from which the correction factor is |
---|
| 942 | exp(tau*ZD) |
---|
| 943 | where ZD is the zenith-distance |
---|
| 944 | insitu: if False a new scantable is returned. |
---|
| 945 | Otherwise, the scaling is done in-situ |
---|
| 946 | The default is taken from .asaprc (False) |
---|
| 947 | """ |
---|
| 948 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 949 | self._math._setinsitu(insitu) |
---|
[513] | 950 | varlist = vars() |
---|
[876] | 951 | s = scantable(self._math._opacity(self, tau)) |
---|
| 952 | s._add_history("opacity", varlist) |
---|
| 953 | print_log() |
---|
| 954 | if insitu: self._assign(s) |
---|
| 955 | else: return s |
---|
[513] | 956 | |
---|
| 957 | def bin(self, width=5, insitu=None): |
---|
| 958 | """ |
---|
| 959 | Return a scan where all spectra have been binned up. |
---|
| 960 | width: The bin width (default=5) in pixels |
---|
| 961 | insitu: if False a new scantable is returned. |
---|
| 962 | Otherwise, the scaling is done in-situ |
---|
| 963 | The default is taken from .asaprc (False) |
---|
| 964 | """ |
---|
| 965 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 966 | self._math._setinsitu(insitu) |
---|
[513] | 967 | varlist = vars() |
---|
[876] | 968 | s = scantable(self._math._bin(self, width)) |
---|
| 969 | s._add_history("bin",varlist) |
---|
| 970 | print_log() |
---|
| 971 | if insitu: self._assign(s) |
---|
| 972 | else: return s |
---|
[513] | 973 | |
---|
[710] | 974 | |
---|
[513] | 975 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 976 | """ |
---|
| 977 | Return a scan where all spectra have been binned up |
---|
| 978 | width: The bin width (default=5) in pixels |
---|
| 979 | method: Interpolation method when correcting from a table. |
---|
| 980 | Values are "nearest", "linear", "cubic" (default) |
---|
| 981 | and "spline" |
---|
| 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 | """ |
---|
| 986 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 987 | self._math._setinsitu(insitu) |
---|
[513] | 988 | varlist = vars() |
---|
[876] | 989 | s = scantable(self._math._resample(self, method, width)) |
---|
| 990 | s._add_history("resample",varlist) |
---|
| 991 | print_log() |
---|
| 992 | if insitu: self._assign(s) |
---|
| 993 | else: return s |
---|
[513] | 994 | |
---|
| 995 | |
---|
[946] | 996 | def average_pol(self, mask=None, weight='none'): |
---|
| 997 | """ |
---|
| 998 | Average the Polarisations together. |
---|
| 999 | Parameters: |
---|
| 1000 | mask: An optional mask defining the region, where the |
---|
| 1001 | averaging will be applied. The output will have all |
---|
| 1002 | specified points masked. |
---|
| 1003 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1004 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1005 | """ |
---|
| 1006 | varlist = vars() |
---|
| 1007 | if mask is None: |
---|
| 1008 | mask = () |
---|
[1010] | 1009 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[946] | 1010 | s._add_history("average_pol",varlist) |
---|
| 1011 | print_log() |
---|
[992] | 1012 | return s |
---|
[513] | 1013 | |
---|
[992] | 1014 | def convert_pol(self, poltype=None): |
---|
| 1015 | """ |
---|
| 1016 | Convert the data to a different polarisation type. |
---|
| 1017 | Parameters: |
---|
| 1018 | poltype: The new polarisation type. Valid types are: |
---|
| 1019 | "linear", "stokes" and "circular" |
---|
| 1020 | """ |
---|
| 1021 | varlist = vars() |
---|
| 1022 | try: |
---|
| 1023 | s = scantable(self._math._convertpol(self, poltype)) |
---|
| 1024 | except RuntimeError,msg: |
---|
| 1025 | if rcParams['verbose']: |
---|
| 1026 | print msg |
---|
| 1027 | return |
---|
| 1028 | else: |
---|
| 1029 | raise |
---|
| 1030 | s._add_history("convert_pol",varlist) |
---|
| 1031 | print_log() |
---|
| 1032 | return s |
---|
| 1033 | |
---|
[876] | 1034 | def smooth(self, kernel="hanning", width=5.0, insitu=None): |
---|
[513] | 1035 | """ |
---|
| 1036 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 1037 | Parameters: |
---|
| 1038 | scan: The input scan |
---|
| 1039 | kernel: The type of smoothing kernel. Select from |
---|
| 1040 | 'hanning' (default), 'gaussian' and 'boxcar'. |
---|
| 1041 | The first three characters are sufficient. |
---|
| 1042 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1043 | ignored otherwise it defauls to 5 pixels. |
---|
| 1044 | For 'gaussian' it is the Full Width Half |
---|
| 1045 | Maximum. For 'boxcar' it is the full width. |
---|
| 1046 | insitu: if False a new scantable is returned. |
---|
| 1047 | Otherwise, the scaling is done in-situ |
---|
| 1048 | The default is taken from .asaprc (False) |
---|
| 1049 | Example: |
---|
| 1050 | none |
---|
| 1051 | """ |
---|
| 1052 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1053 | self._math._setinsitu(insitu) |
---|
[513] | 1054 | varlist = vars() |
---|
[1033] | 1055 | s = scantable(self._math._smooth(self,kernel.lower(),width)) |
---|
[876] | 1056 | s._add_history("smooth", varlist) |
---|
| 1057 | print_log() |
---|
| 1058 | if insitu: self._assign(s) |
---|
| 1059 | else: return s |
---|
[513] | 1060 | |
---|
[876] | 1061 | |
---|
[1061] | 1062 | def poly_baseline(self, mask=None, order=0, plot=False, insitu=None): |
---|
[513] | 1063 | """ |
---|
| 1064 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1065 | Parameters: |
---|
[794] | 1066 | scan: a scantable |
---|
| 1067 | mask: an optional mask |
---|
| 1068 | order: the order of the polynomial (default is 0) |
---|
[1061] | 1069 | plot: plot the fit and the residual. In this each |
---|
| 1070 | indivual fit has to be approved, by typing 'y' |
---|
| 1071 | or 'n' |
---|
[794] | 1072 | insitu: if False a new scantable is returned. |
---|
| 1073 | Otherwise, the scaling is done in-situ |
---|
| 1074 | The default is taken from .asaprc (False) |
---|
[513] | 1075 | Example: |
---|
| 1076 | # return a scan baselined by a third order polynomial, |
---|
| 1077 | # not using a mask |
---|
| 1078 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1079 | """ |
---|
[513] | 1080 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1081 | varlist = vars() |
---|
| 1082 | if mask is None: |
---|
| 1083 | from numarray import ones |
---|
[876] | 1084 | mask = list(ones(self.nchan(-1))) |
---|
[513] | 1085 | from asap.asapfitter import fitter |
---|
| 1086 | f = fitter() |
---|
| 1087 | f.set_scan(self, mask) |
---|
| 1088 | f.set_function(poly=order) |
---|
[1061] | 1089 | s = f.auto_fit(insitu, plot=plot) |
---|
[876] | 1090 | s._add_history("poly_baseline", varlist) |
---|
[718] | 1091 | print_log() |
---|
[876] | 1092 | if insitu: self._assign(s) |
---|
| 1093 | else: return s |
---|
[513] | 1094 | |
---|
[931] | 1095 | def auto_poly_baseline(self, mask=[], edge=(0,0), order=0, |
---|
[1061] | 1096 | threshold=3, plot=False, insitu=None): |
---|
[880] | 1097 | """ |
---|
| 1098 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1099 | Spectral lines are detected first using linefinder and masked out |
---|
| 1100 | to avoid them affecting the baseline solution. |
---|
| 1101 | |
---|
| 1102 | Parameters: |
---|
| 1103 | mask: an optional mask retreived from scantable |
---|
| 1104 | edge: an optional number of channel to drop at |
---|
| 1105 | the edge of spectrum. If only one value is |
---|
| 1106 | specified, the same number will be dropped from |
---|
| 1107 | both sides of the spectrum. Default is to keep |
---|
[907] | 1108 | all channels. Nested tuples represent individual |
---|
[976] | 1109 | edge selection for different IFs (a number of spectral |
---|
| 1110 | channels can be different) |
---|
[880] | 1111 | order: the order of the polynomial (default is 0) |
---|
| 1112 | threshold: the threshold used by line finder. It is better to |
---|
| 1113 | keep it large as only strong lines affect the |
---|
| 1114 | baseline solution. |
---|
[1061] | 1115 | plot: plot the fit and the residual. In this each |
---|
| 1116 | indivual fit has to be approved, by typing 'y' |
---|
| 1117 | or 'n' |
---|
[880] | 1118 | insitu: if False a new scantable is returned. |
---|
| 1119 | Otherwise, the scaling is done in-situ |
---|
| 1120 | The default is taken from .asaprc (False) |
---|
| 1121 | |
---|
| 1122 | Example: |
---|
| 1123 | scan2=scan.auto_poly_baseline(order=7) |
---|
| 1124 | """ |
---|
| 1125 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1126 | varlist = vars() |
---|
| 1127 | from asap.asapfitter import fitter |
---|
| 1128 | from asap.asaplinefind import linefinder |
---|
| 1129 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1130 | |
---|
[976] | 1131 | # check whether edge is set up for each IF individually |
---|
| 1132 | individualEdge = False; |
---|
| 1133 | if len(edge)>1: |
---|
| 1134 | if isinstance(edge[0],list) or isinstance(edge[0],tuple): |
---|
| 1135 | individualEdge = True; |
---|
[907] | 1136 | |
---|
| 1137 | if not _is_valid(edge, int) and not individualEdge: |
---|
[909] | 1138 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1139 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1140 | to make individual selection for different IFs." |
---|
[919] | 1141 | |
---|
[976] | 1142 | curedge = (0,0) |
---|
| 1143 | if individualEdge: |
---|
| 1144 | for edge_par in edge: |
---|
| 1145 | if not _is_valid(edge,int): |
---|
| 1146 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
[907] | 1147 | to be a pair of integers or an integer." |
---|
| 1148 | else: |
---|
[976] | 1149 | curedge = edge; |
---|
[880] | 1150 | |
---|
| 1151 | # setup fitter |
---|
| 1152 | f = fitter() |
---|
| 1153 | f.set_function(poly=order) |
---|
| 1154 | |
---|
| 1155 | # setup line finder |
---|
| 1156 | fl=linefinder() |
---|
| 1157 | fl.set_options(threshold=threshold) |
---|
| 1158 | |
---|
| 1159 | if not insitu: |
---|
| 1160 | workscan=self.copy() |
---|
| 1161 | else: |
---|
| 1162 | workscan=self |
---|
| 1163 | |
---|
[907] | 1164 | fl.set_scan(workscan) |
---|
| 1165 | |
---|
[880] | 1166 | rows=range(workscan.nrow()) |
---|
| 1167 | from asap import asaplog |
---|
| 1168 | asaplog.push("Processing:") |
---|
| 1169 | for r in rows: |
---|
| 1170 | 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)) |
---|
| 1171 | asaplog.push(msg, False) |
---|
[907] | 1172 | |
---|
[976] | 1173 | # figure out edge parameter |
---|
| 1174 | if individualEdge: |
---|
| 1175 | if len(edge)>=workscan.getif(r): |
---|
| 1176 | raise RuntimeError, "Number of edge elements appear to be less than the number of IFs" |
---|
| 1177 | curedge = edge[workscan.getif(r)] |
---|
[919] | 1178 | |
---|
[976] | 1179 | # setup line finder |
---|
[907] | 1180 | fl.find_lines(r,mask,curedge) |
---|
[880] | 1181 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1182 | f.x = workscan._getabcissa(r) |
---|
| 1183 | f.y = workscan._getspectrum(r) |
---|
| 1184 | f.data = None |
---|
| 1185 | f.fit() |
---|
| 1186 | x = f.get_parameters() |
---|
[1061] | 1187 | if plot: |
---|
| 1188 | f.plot(residual=True) |
---|
| 1189 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1190 | if x.upper() == 'N': |
---|
| 1191 | continue |
---|
[880] | 1192 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1061] | 1193 | if plot: |
---|
| 1194 | f._p.unmap() |
---|
| 1195 | f._p = None |
---|
| 1196 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 1197 | if insitu: |
---|
| 1198 | self._assign(workscan) |
---|
| 1199 | else: |
---|
| 1200 | return workscan |
---|
| 1201 | |
---|
[914] | 1202 | def rotate_linpolphase(self, angle): |
---|
| 1203 | """ |
---|
| 1204 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1205 | This is always done in situ in the raw data. So if you call this |
---|
| 1206 | function more than once then each call rotates the phase further. |
---|
| 1207 | Parameters: |
---|
| 1208 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1209 | Examples: |
---|
| 1210 | scan.rotate_linpolphase(2.3) |
---|
| 1211 | """ |
---|
| 1212 | varlist = vars() |
---|
[936] | 1213 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 1214 | self._add_history("rotate_linpolphase", varlist) |
---|
| 1215 | print_log() |
---|
| 1216 | return |
---|
[710] | 1217 | |
---|
[513] | 1218 | |
---|
[914] | 1219 | def rotate_xyphase(self, angle): |
---|
| 1220 | """ |
---|
| 1221 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1222 | in the data. So if you call this function more than once |
---|
| 1223 | then each call rotates the phase further. |
---|
| 1224 | Parameters: |
---|
| 1225 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1226 | Examples: |
---|
| 1227 | scan.rotate_xyphase(2.3) |
---|
| 1228 | """ |
---|
| 1229 | varlist = vars() |
---|
[936] | 1230 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 1231 | self._add_history("rotate_xyphase", varlist) |
---|
| 1232 | print_log() |
---|
| 1233 | return |
---|
| 1234 | |
---|
| 1235 | def swap_linears(self): |
---|
| 1236 | """ |
---|
| 1237 | Swap the linear polarisations XX and YY |
---|
| 1238 | """ |
---|
| 1239 | varlist = vars() |
---|
[936] | 1240 | self._math._swap_linears(self) |
---|
[914] | 1241 | self._add_history("swap_linears", varlist) |
---|
| 1242 | print_log() |
---|
| 1243 | return |
---|
| 1244 | |
---|
| 1245 | def invert_phase(self): |
---|
| 1246 | """ |
---|
| 1247 | Invert the phase of the complex polarisation |
---|
| 1248 | """ |
---|
| 1249 | varlist = vars() |
---|
[936] | 1250 | self._math._invert_phase(self) |
---|
[914] | 1251 | self._add_history("invert_phase", varlist) |
---|
| 1252 | print_log() |
---|
| 1253 | return |
---|
| 1254 | |
---|
[876] | 1255 | def add(self, offset, insitu=None): |
---|
[513] | 1256 | """ |
---|
| 1257 | Return a scan where all spectra have the offset added |
---|
| 1258 | Parameters: |
---|
| 1259 | offset: the offset |
---|
| 1260 | insitu: if False a new scantable is returned. |
---|
| 1261 | Otherwise, the scaling is done in-situ |
---|
| 1262 | The default is taken from .asaprc (False) |
---|
| 1263 | """ |
---|
| 1264 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1265 | self._math._setinsitu(insitu) |
---|
[513] | 1266 | varlist = vars() |
---|
[876] | 1267 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
| 1268 | s._add_history("add",varlist) |
---|
| 1269 | print_log() |
---|
| 1270 | if insitu: |
---|
| 1271 | self._assign(s) |
---|
| 1272 | else: |
---|
[513] | 1273 | return s |
---|
| 1274 | |
---|
[876] | 1275 | def scale(self, factor, tsys=True, insitu=None,): |
---|
[513] | 1276 | """ |
---|
| 1277 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 1278 | Parameters: |
---|
| 1279 | factor: the scaling factor |
---|
| 1280 | insitu: if False a new scantable is returned. |
---|
| 1281 | Otherwise, the scaling is done in-situ |
---|
| 1282 | The default is taken from .asaprc (False) |
---|
| 1283 | tsys: if True (default) then apply the operation to Tsys |
---|
| 1284 | as well as the data |
---|
| 1285 | """ |
---|
| 1286 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1287 | self._math._setinsitu(insitu) |
---|
[513] | 1288 | varlist = vars() |
---|
[876] | 1289 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
| 1290 | s._add_history("scale",varlist) |
---|
| 1291 | print_log() |
---|
| 1292 | if insitu: |
---|
| 1293 | self._assign(s) |
---|
| 1294 | else: |
---|
[513] | 1295 | return s |
---|
| 1296 | |
---|
[876] | 1297 | def auto_quotient(self, mode='time', preserve=True): |
---|
[670] | 1298 | """ |
---|
| 1299 | This function allows to build quotients automatically. |
---|
| 1300 | It assumes the observation to have the same numer of |
---|
| 1301 | "ons" and "offs" |
---|
| 1302 | It will support "closest off in time" in the future |
---|
| 1303 | Parameters: |
---|
| 1304 | mode: the on/off detection mode; 'suffix' (default) |
---|
| 1305 | 'suffix' identifies 'off' scans by the |
---|
| 1306 | trailing '_R' (Mopra/Parkes) or |
---|
| 1307 | '_e'/'_w' (Tid) |
---|
[710] | 1308 | preserve: you can preserve (default) the continuum or |
---|
| 1309 | remove it. The equations used are |
---|
[670] | 1310 | preserve: Output = Toff * (on/off) - Toff |
---|
[1070] | 1311 | remove: Output = Toff * (on/off) - Ton |
---|
[670] | 1312 | """ |
---|
[876] | 1313 | modes = ["time"] |
---|
[670] | 1314 | if not mode in modes: |
---|
[876] | 1315 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 1316 | raise ValueError(msg) |
---|
| 1317 | varlist = vars() |
---|
[1070] | 1318 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[876] | 1319 | s._add_history("auto_quotient",varlist) |
---|
| 1320 | print_log() |
---|
| 1321 | return s |
---|
[710] | 1322 | |
---|
[513] | 1323 | |
---|
[876] | 1324 | |
---|
| 1325 | |
---|
[718] | 1326 | def freq_switch(self, insitu=None): |
---|
| 1327 | """ |
---|
| 1328 | Apply frequency switching to the data. |
---|
| 1329 | Parameters: |
---|
| 1330 | insitu: if False a new scantable is returned. |
---|
| 1331 | Otherwise, the swictching is done in-situ |
---|
| 1332 | The default is taken from .asaprc (False) |
---|
| 1333 | Example: |
---|
| 1334 | none |
---|
| 1335 | """ |
---|
| 1336 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1337 | self._math._setinsitu(insitu) |
---|
[718] | 1338 | varlist = vars() |
---|
[876] | 1339 | s = scantable(self._math._freqswitch(self)) |
---|
| 1340 | s._add_history("freq_switch",varlist) |
---|
| 1341 | print_log() |
---|
| 1342 | if insitu: self._assign(s) |
---|
| 1343 | else: return s |
---|
[718] | 1344 | |
---|
[780] | 1345 | def recalc_azel(self): |
---|
| 1346 | """ |
---|
| 1347 | Recalculate the azimuth and elevation for each position. |
---|
| 1348 | Parameters: |
---|
| 1349 | none |
---|
| 1350 | Example: |
---|
| 1351 | """ |
---|
| 1352 | varlist = vars() |
---|
[876] | 1353 | self._recalcazel() |
---|
[780] | 1354 | self._add_history("recalc_azel", varlist) |
---|
| 1355 | print_log() |
---|
| 1356 | return |
---|
| 1357 | |
---|
[513] | 1358 | def __add__(self, other): |
---|
| 1359 | varlist = vars() |
---|
| 1360 | s = None |
---|
| 1361 | if isinstance(other, scantable): |
---|
[876] | 1362 | print "scantable + scantable NYI" |
---|
| 1363 | return |
---|
[513] | 1364 | elif isinstance(other, float): |
---|
[876] | 1365 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 1366 | else: |
---|
[718] | 1367 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1368 | s._add_history("operator +", varlist) |
---|
[718] | 1369 | print_log() |
---|
[513] | 1370 | return s |
---|
| 1371 | |
---|
| 1372 | def __sub__(self, other): |
---|
| 1373 | """ |
---|
| 1374 | implicit on all axes and on Tsys |
---|
| 1375 | """ |
---|
| 1376 | varlist = vars() |
---|
| 1377 | s = None |
---|
| 1378 | if isinstance(other, scantable): |
---|
[876] | 1379 | print "scantable - scantable NYI" |
---|
| 1380 | return |
---|
[513] | 1381 | elif isinstance(other, float): |
---|
[876] | 1382 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 1383 | else: |
---|
[718] | 1384 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1385 | s._add_history("operator -", varlist) |
---|
[718] | 1386 | print_log() |
---|
[513] | 1387 | return s |
---|
[710] | 1388 | |
---|
[513] | 1389 | def __mul__(self, other): |
---|
| 1390 | """ |
---|
| 1391 | implicit on all axes and on Tsys |
---|
| 1392 | """ |
---|
| 1393 | varlist = vars() |
---|
| 1394 | s = None |
---|
| 1395 | if isinstance(other, scantable): |
---|
[876] | 1396 | print "scantable * scantable NYI" |
---|
| 1397 | return |
---|
[513] | 1398 | elif isinstance(other, float): |
---|
[876] | 1399 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 1400 | else: |
---|
[718] | 1401 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1402 | s._add_history("operator *", varlist) |
---|
[718] | 1403 | print_log() |
---|
[513] | 1404 | return s |
---|
| 1405 | |
---|
[710] | 1406 | |
---|
[513] | 1407 | def __div__(self, other): |
---|
| 1408 | """ |
---|
| 1409 | implicit on all axes and on Tsys |
---|
| 1410 | """ |
---|
| 1411 | varlist = vars() |
---|
| 1412 | s = None |
---|
| 1413 | if isinstance(other, scantable): |
---|
[876] | 1414 | print "scantable / scantable NYI" |
---|
| 1415 | return |
---|
[513] | 1416 | elif isinstance(other, float): |
---|
| 1417 | if other == 0.0: |
---|
[718] | 1418 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 1419 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 1420 | else: |
---|
[718] | 1421 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1422 | s._add_history("operator /", varlist) |
---|
[718] | 1423 | print_log() |
---|
[513] | 1424 | return s |
---|
| 1425 | |
---|
[530] | 1426 | def get_fit(self, row=0): |
---|
| 1427 | """ |
---|
| 1428 | Print or return the stored fits for a row in the scantable |
---|
| 1429 | Parameters: |
---|
| 1430 | row: the row which the fit has been applied to. |
---|
| 1431 | """ |
---|
| 1432 | if row > self.nrow(): |
---|
| 1433 | return |
---|
[976] | 1434 | from asap.asapfit import asapfit |
---|
[530] | 1435 | fit = asapfit(self._getfit(row)) |
---|
[718] | 1436 | if rcParams['verbose']: |
---|
[530] | 1437 | print fit |
---|
| 1438 | return |
---|
| 1439 | else: |
---|
| 1440 | return fit.as_dict() |
---|
| 1441 | |
---|
[484] | 1442 | def _add_history(self, funcname, parameters): |
---|
| 1443 | # create date |
---|
| 1444 | sep = "##" |
---|
| 1445 | from datetime import datetime |
---|
| 1446 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 1447 | hist = dstr+sep |
---|
| 1448 | hist += funcname+sep#cdate+sep |
---|
| 1449 | if parameters.has_key('self'): del parameters['self'] |
---|
| 1450 | for k,v in parameters.iteritems(): |
---|
| 1451 | if type(v) is dict: |
---|
| 1452 | for k2,v2 in v.iteritems(): |
---|
| 1453 | hist += k2 |
---|
| 1454 | hist += "=" |
---|
| 1455 | if isinstance(v2,scantable): |
---|
| 1456 | hist += 'scantable' |
---|
| 1457 | elif k2 == 'mask': |
---|
[513] | 1458 | if isinstance(v2,list) or isinstance(v2,tuple): |
---|
| 1459 | hist += str(self._zip_mask(v2)) |
---|
| 1460 | else: |
---|
| 1461 | hist += str(v2) |
---|
[484] | 1462 | else: |
---|
[513] | 1463 | hist += str(v2) |
---|
[484] | 1464 | else: |
---|
| 1465 | hist += k |
---|
| 1466 | hist += "=" |
---|
| 1467 | if isinstance(v,scantable): |
---|
| 1468 | hist += 'scantable' |
---|
| 1469 | elif k == 'mask': |
---|
[513] | 1470 | if isinstance(v,list) or isinstance(v,tuple): |
---|
| 1471 | hist += str(self._zip_mask(v)) |
---|
| 1472 | else: |
---|
| 1473 | hist += str(v) |
---|
[484] | 1474 | else: |
---|
| 1475 | hist += str(v) |
---|
| 1476 | hist += sep |
---|
| 1477 | hist = hist[:-2] # remove trailing '##' |
---|
| 1478 | self._addhistory(hist) |
---|
| 1479 | |
---|
[710] | 1480 | |
---|
[484] | 1481 | def _zip_mask(self, mask): |
---|
| 1482 | mask = list(mask) |
---|
| 1483 | i = 0 |
---|
| 1484 | segments = [] |
---|
| 1485 | while mask[i:].count(1): |
---|
| 1486 | i += mask[i:].index(1) |
---|
| 1487 | if mask[i:].count(0): |
---|
| 1488 | j = i + mask[i:].index(0) |
---|
| 1489 | else: |
---|
[710] | 1490 | j = len(mask) |
---|
[484] | 1491 | segments.append([i,j]) |
---|
[710] | 1492 | i = j |
---|
[484] | 1493 | return segments |
---|
[714] | 1494 | |
---|
[626] | 1495 | def _get_ordinate_label(self): |
---|
| 1496 | fu = "("+self.get_fluxunit()+")" |
---|
| 1497 | import re |
---|
| 1498 | lbl = "Intensity" |
---|
| 1499 | if re.match(".K.",fu): |
---|
| 1500 | lbl = "Brightness Temperature "+ fu |
---|
| 1501 | elif re.match(".Jy.",fu): |
---|
| 1502 | lbl = "Flux density "+ fu |
---|
| 1503 | return lbl |
---|
[710] | 1504 | |
---|
[876] | 1505 | def _check_ifs(self): |
---|
| 1506 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 1507 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 1508 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 1509 | |
---|
| 1510 | def _fill(self, names, unit, average): |
---|
| 1511 | import os |
---|
| 1512 | varlist = vars() |
---|
| 1513 | from asap._asap import stfiller |
---|
| 1514 | first = True |
---|
| 1515 | fullnames = [] |
---|
| 1516 | for name in names: |
---|
| 1517 | name = os.path.expandvars(name) |
---|
| 1518 | name = os.path.expanduser(name) |
---|
| 1519 | if not os.path.exists(name): |
---|
| 1520 | msg = "File '%s' does not exists" % (name) |
---|
| 1521 | if rcParams['verbose']: |
---|
| 1522 | asaplog.push(msg) |
---|
| 1523 | print asaplog.pop().strip() |
---|
| 1524 | return |
---|
| 1525 | raise IOError(msg) |
---|
| 1526 | fullnames.append(name) |
---|
| 1527 | if average: |
---|
| 1528 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 1529 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 1530 | for name in fullnames: |
---|
[1073] | 1531 | tbl = Scantable(stype) |
---|
| 1532 | r = stfiller(tbl) |
---|
[976] | 1533 | msg = "Importing %s..." % (name) |
---|
| 1534 | asaplog.push(msg,False) |
---|
| 1535 | print_log() |
---|
| 1536 | r._open(name,-1,-1) |
---|
| 1537 | r._read() |
---|
[1073] | 1538 | #tbl = r._getdata() |
---|
[976] | 1539 | if average: |
---|
[981] | 1540 | tbl = self._math._average((tbl,),(),'NONE','SCAN') |
---|
[976] | 1541 | #tbl = tbl2 |
---|
| 1542 | if not first: |
---|
| 1543 | tbl = self._math._merge([self, tbl]) |
---|
| 1544 | #tbl = tbl2 |
---|
| 1545 | Scantable.__init__(self, tbl) |
---|
| 1546 | r._close() |
---|
| 1547 | del r,tbl |
---|
| 1548 | first = False |
---|
| 1549 | if unit is not None: |
---|
| 1550 | self.set_fluxunit(unit) |
---|
| 1551 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
| 1552 | #self._add_history("scantable", varlist) |
---|
| 1553 | |
---|