| 1 | from asap._asap import sdtable |
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| 2 | from asap import rcParams |
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| 3 | from numarray import ones,zeros |
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| 4 | import sys |
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| 5 | |
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| 6 | class scantable(sdtable): |
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| 7 | """ |
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| 8 | The ASAP container for scans |
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| 9 | """ |
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| 10 | |
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| 11 | def __init__(self, filename): |
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| 12 | """ |
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| 13 | Create a scantable from a saved one or make a reference |
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| 14 | Parameters: |
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| 15 | filename: the name of an asap table on disk |
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| 16 | or |
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| 17 | the name of a rpfits/sdfits/ms file |
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| 18 | (integrations within scans are auto averaged |
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| 19 | and the whole file is read) |
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| 20 | or |
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| 21 | [advanced] a reference to an existing |
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| 22 | scantable |
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| 23 | """ |
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| 24 | self._vb = rcParams['verbose'] |
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| 25 | self._p = None |
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| 26 | from os import stat as st |
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| 27 | import stat |
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| 28 | if isinstance(filename,sdtable): |
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| 29 | sdtable.__init__(self, filename) |
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| 30 | else: |
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| 31 | try: |
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| 32 | mode = st(filename)[stat.ST_MODE] |
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| 33 | except OSError: |
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| 34 | print "File not found" |
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| 35 | return |
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| 36 | if stat.S_ISDIR(mode): |
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| 37 | # crude check if asap table |
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| 38 | if stat.S_ISREG(st(filename+'/table.info')[stat.ST_MODE]): |
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| 39 | sdtable.__init__(self, filename) |
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| 40 | else: |
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| 41 | print 'The given file is not a valid asap table' |
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| 42 | return |
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| 43 | else: |
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| 44 | autoav = rcParams['scantable.autoaverage'] |
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| 45 | |
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| 46 | from asap._asap import sdreader |
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| 47 | r = sdreader(filename) |
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| 48 | print 'Importing data...' |
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| 49 | r.read([-1]) |
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| 50 | tbl = r.getdata() |
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| 51 | if autoav: |
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| 52 | from asap._asap import average |
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| 53 | tmp = tuple([tbl]) |
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| 54 | print 'Auto averaging integrations...' |
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| 55 | tbl2 = average(tmp,(),True,'none') |
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| 56 | sdtable.__init__(self,tbl2) |
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| 57 | del r,tbl |
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| 58 | else: |
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| 59 | sdtable.__init__(self,tbl) |
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| 60 | |
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| 61 | def save(self, name=None, format=None, overwrite=False): |
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| 62 | """ |
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| 63 | Store the scantable on disk. This can be a asap file or SDFITS/MS2. |
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| 64 | Parameters: |
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| 65 | name: the name of the outputfile. For format="FITS" this |
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| 66 | is the root file name (and can be empty). |
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| 67 | format: an optional file format. Default is ASAP. |
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| 68 | Allowed are - 'ASAP' (save as ASAP Table), |
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| 69 | 'SDFITS' (save as SDFITS file) |
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| 70 | 'FITS' (saves each row as a FITS Image) |
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| 71 | 'ASCII' (saves as ascii text file) |
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| 72 | 'MS2' (saves as an aips++ |
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| 73 | MeasurementSet V2) |
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| 74 | overwrite: if the file should be overwritten if it exists. |
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| 75 | The default False is to return with warning |
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| 76 | without writing the output |
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| 77 | Example: |
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| 78 | scan.save('myscan.asap') |
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| 79 | scan.save('myscan.sdfits','SDFITS') |
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| 80 | """ |
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| 81 | if format is None: format = rcParams['scantable.save'] |
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| 82 | suffix = '.'+format.lower() |
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| 83 | if name is None or name =="": |
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| 84 | name = 'scantable'+suffix |
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| 85 | from os import path |
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| 86 | if path.isfile(name) or path.isdir(name): |
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| 87 | if not overwrite: |
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| 88 | print "File %s already exists." % name |
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| 89 | return |
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| 90 | if format == 'ASAP': |
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| 91 | self._save(name) |
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| 92 | else: |
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| 93 | from asap._asap import sdwriter as _sw |
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| 94 | w = _sw(format) |
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| 95 | w.write(self, name) |
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| 96 | return |
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| 97 | |
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| 98 | def copy(self): |
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| 99 | """ |
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| 100 | Return a copy of this scantable. |
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| 101 | Parameters: |
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| 102 | none |
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| 103 | Example: |
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| 104 | copiedscan = scan.copy() |
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| 105 | """ |
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| 106 | sd = scantable(sdtable._copy(self)) |
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| 107 | return sd |
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| 108 | |
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| 109 | def get_scan(self, scanid=None): |
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| 110 | """ |
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| 111 | Return a specific scan (by scanno) or collection of scans (by |
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| 112 | source name) in a new scantable. |
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| 113 | Parameters: |
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| 114 | scanid: a scanno or a source name |
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| 115 | Example: |
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| 116 | scan.get_scan('323p459') |
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| 117 | # gets all scans containing the source '323p459' |
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| 118 | """ |
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| 119 | if scanid is None: |
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| 120 | print "Please specify a scan no or name to retrieve from the scantable" |
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| 121 | try: |
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| 122 | if type(scanid) is str: |
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| 123 | s = sdtable._getsource(self,scanid) |
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| 124 | return scantable(s) |
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| 125 | elif type(scanid) is int: |
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| 126 | s = sdtable._getscan(self,scanid) |
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| 127 | return scantable(s) |
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| 128 | except RuntimeError: |
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| 129 | print "Couldn't find any match." |
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| 130 | |
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| 131 | def __str__(self): |
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| 132 | return sdtable._summary(self) |
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| 133 | |
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| 134 | def summary(self,filename=None): |
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| 135 | """ |
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| 136 | Print a summary of the contents of this scantable. |
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| 137 | Parameters: |
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| 138 | filename: the name of a file to write the putput to |
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| 139 | Default - no file output |
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| 140 | """ |
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| 141 | info = sdtable._summary(self) |
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| 142 | if filename is not None: |
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| 143 | if filename is "": |
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| 144 | filename = 'scantable_summary.txt' |
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| 145 | data = open(filename, 'w') |
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| 146 | data.write(info) |
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| 147 | data.close() |
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| 148 | print info |
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| 149 | |
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| 150 | def set_cursor(self, thebeam=0,theif=0,thepol=0): |
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| 151 | """ |
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| 152 | Set the spectrum for individual operations. |
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| 153 | Parameters: |
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| 154 | thebeam,theif,thepol: a number |
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| 155 | Example: |
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| 156 | scan.set_cursor(0,0,1) |
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| 157 | pol1sig = scan.stats(all=False) # returns std dev for beam=0 |
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| 158 | # if=0, pol=1 |
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| 159 | """ |
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| 160 | self.setbeam(thebeam) |
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| 161 | self.setpol(thepol) |
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| 162 | self.setif(theif) |
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| 163 | return |
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| 164 | |
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| 165 | def get_cursor(self): |
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| 166 | """ |
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| 167 | Return/print a the current 'cursor' into the Beam/IF/Pol cube. |
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| 168 | Parameters: |
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| 169 | none |
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| 170 | Returns: |
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| 171 | a list of values (currentBeam,currentIF,currentPol) |
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| 172 | Example: |
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| 173 | none |
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| 174 | """ |
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| 175 | i = self.getbeam() |
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| 176 | j = self.getif() |
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| 177 | k = self.getpol() |
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| 178 | if self._vb: |
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| 179 | print "--------------------------------------------------" |
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| 180 | print " Cursor position" |
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| 181 | print "--------------------------------------------------" |
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| 182 | out = 'Beam=%d IF=%d Pol=%d ' % (i,j,k) |
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| 183 | print out |
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| 184 | return i,j,k |
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| 185 | |
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| 186 | def stats(self, stat='stddev', mask=None, all=None): |
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| 187 | """ |
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| 188 | Determine the specified statistic of the current beam/if/pol |
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| 189 | Takes a 'mask' as an optional parameter to specify which |
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| 190 | channels should be excluded. |
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| 191 | Parameters: |
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| 192 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
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| 193 | 'var', 'stddev', 'avdev', 'rms', 'median' |
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| 194 | mask: an optional mask specifying where the statistic |
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| 195 | should be determined. |
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| 196 | all: if true show all (default or .asaprc) rather |
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| 197 | that the cursor selected spectrum of Beam/IF/Pol |
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| 198 | |
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| 199 | Example: |
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| 200 | scan.set_unit('channel') |
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| 201 | msk = scan.create_mask([100,200],[500,600]) |
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| 202 | scan.stats(stat='mean', mask=m) |
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| 203 | """ |
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| 204 | if all is None: all = rcParams['scantable.allaxes'] |
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| 205 | from asap._asap import stats as _stats |
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| 206 | from numarray import array,zeros,Float |
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| 207 | if mask == None: |
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| 208 | mask = ones(self.nchan()) |
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| 209 | axes = ['Beam','IF','Pol','Time'] |
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| 210 | |
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| 211 | if all: |
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| 212 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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| 213 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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| 214 | arr = array(zeros(n),shape=shp,type=Float) |
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| 215 | |
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| 216 | for i in range(self.nbeam()): |
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| 217 | self.setbeam(i) |
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| 218 | for j in range(self.nif()): |
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| 219 | self.setif(j) |
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| 220 | for k in range(self.npol()): |
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| 221 | self.setpol(k) |
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| 222 | arr[i,j,k,:] = _stats(self,mask,stat,-1) |
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| 223 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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| 224 | tm = [self._gettime(val) for val in range(self.nrow())] |
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| 225 | if self._vb: |
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| 226 | self._print_values(retval,stat,tm) |
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| 227 | return retval |
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| 228 | |
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| 229 | else: |
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| 230 | i,j,k = (self.getbeam(),self.getif(),self.getpol()) |
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| 231 | statval = _stats(self,mask,stat,-1) |
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| 232 | out = '' |
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| 233 | for l in range(self.nrow()): |
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| 234 | tm = self._gettime(l) |
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| 235 | out += 'Time[%s]:\n' % (tm) |
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| 236 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i) |
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| 237 | if self.nif() > 1: out += ' IF[%d] ' % (j) |
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| 238 | if self.npol() > 1: out += ' Pol[%d] ' % (k) |
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| 239 | out += '= %3.3f\n' % (statval[l]) |
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| 240 | out += "--------------------------------------------------\n" |
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| 241 | |
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| 242 | if self._vb: |
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| 243 | print "--------------------------------------------------" |
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| 244 | print " ",stat |
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| 245 | print "--------------------------------------------------" |
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| 246 | print out |
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| 247 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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| 248 | return retval |
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| 249 | |
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| 250 | def stddev(self,mask=None, all=None): |
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| 251 | """ |
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| 252 | Determine the standard deviation of the current beam/if/pol |
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| 253 | Takes a 'mask' as an optional parameter to specify which |
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| 254 | channels should be excluded. |
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| 255 | Parameters: |
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| 256 | mask: an optional mask specifying where the standard |
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| 257 | deviation should be determined. |
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| 258 | all: optional flag to show all or a cursor selected |
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| 259 | spectrum of Beam/IF/Pol. Default is all or taken |
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| 260 | from .asaprc |
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| 261 | |
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| 262 | Example: |
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| 263 | scan.set_unit('channel') |
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| 264 | msk = scan.create_mask([100,200],[500,600]) |
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| 265 | scan.stddev(mask=m) |
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| 266 | """ |
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| 267 | if all is None: all = rcParams['scantable.allaxes'] |
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| 268 | return self.stats(stat='stddev',mask=mask, all=all); |
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| 269 | |
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| 270 | def get_tsys(self, all=None): |
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| 271 | """ |
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| 272 | Return the System temperatures. |
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| 273 | Parameters: |
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| 274 | all: optional parameter to get the Tsys values for all |
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| 275 | Beams/IFs/Pols (default) or just the one selected |
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| 276 | with scantable.set_cursor() |
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| 277 | [True or False] |
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| 278 | Returns: |
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| 279 | a list of Tsys values. |
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| 280 | """ |
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| 281 | if all is None: all = rcParams['scantable.allaxes'] |
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| 282 | from numarray import array,zeros,Float |
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| 283 | axes = ['Beam','IF','Pol','Time'] |
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| 284 | |
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| 285 | if all: |
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| 286 | n = self.nbeam()*self.nif()*self.npol()*self.nrow() |
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| 287 | shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()] |
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| 288 | arr = array(zeros(n),shape=shp,type=Float) |
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| 289 | |
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| 290 | for i in range(self.nbeam()): |
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| 291 | self.setbeam(i) |
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| 292 | for j in range(self.nif()): |
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| 293 | self.setif(j) |
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| 294 | for k in range(self.npol()): |
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| 295 | self.setpol(k) |
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| 296 | arr[i,j,k,:] = self._gettsys() |
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| 297 | retval = {'axes': axes, 'data': arr, 'cursor':None} |
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| 298 | tm = [self._gettime(val) for val in range(self.nrow())] |
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| 299 | if self._vb: |
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| 300 | self._print_values(retval,'Tsys',tm) |
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| 301 | return retval |
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| 302 | |
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| 303 | else: |
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| 304 | i,j,k = (self.getbeam(),self.getif(),self.getpol()) |
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| 305 | statval = self._gettsys() |
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| 306 | out = '' |
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| 307 | for l in range(self.nrow()): |
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| 308 | tm = self._gettime(l) |
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| 309 | out += 'Time[%s]:\n' % (tm) |
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| 310 | if self.nbeam() > 1: out += ' Beam[%d] ' % (i) |
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| 311 | if self.nif() > 1: out += ' IF[%d] ' % (j) |
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| 312 | if self.npol() > 1: out += ' Pol[%d] ' % (k) |
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| 313 | out += '= %3.3f\n' % (statval[l]) |
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| 314 | out += "--------------------------------------------------\n" |
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| 315 | |
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| 316 | if self._vb: |
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| 317 | print "--------------------------------------------------" |
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| 318 | print " TSys" |
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| 319 | print "--------------------------------------------------" |
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| 320 | print out |
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| 321 | retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)} |
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| 322 | return retval |
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| 323 | |
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| 324 | def get_time(self): |
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| 325 | """ |
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| 326 | Get a list of time stamps for the observations. |
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| 327 | Return a string for each integration in the scantable. |
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| 328 | Parameters: |
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| 329 | none |
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| 330 | Example: |
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| 331 | none |
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| 332 | """ |
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| 333 | out = [] |
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| 334 | for i in range(self.nrow()): |
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| 335 | out.append(self._gettime(i)) |
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| 336 | return out |
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| 337 | |
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| 338 | def set_unit(self, unit='channel'): |
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| 339 | """ |
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| 340 | Set the unit for all following operations on this scantable |
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| 341 | Parameters: |
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| 342 | unit: optional unit, default is 'channel' |
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| 343 | one of '*Hz','km/s','channel', '' |
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| 344 | """ |
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| 345 | |
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| 346 | if unit in ['','pixel', 'channel']: |
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| 347 | unit = '' |
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| 348 | inf = list(self._getcoordinfo()) |
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| 349 | inf[0] = unit |
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| 350 | self._setcoordinfo(inf) |
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| 351 | if self._p: self.plot() |
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| 352 | |
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| 353 | def set_freqframe(self, frame=None): |
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| 354 | """ |
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| 355 | Set the frame type of the Spectral Axis. |
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| 356 | Parameters: |
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| 357 | frame: an optional frame type, default 'LSRK'. |
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| 358 | Examples: |
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| 359 | scan.set_freqframe('BARY') |
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| 360 | """ |
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| 361 | if not frame: frame = rcParams['scantable.freqframe'] |
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| 362 | valid = ['REST','TOPO','LSRD','LSRK','BARY', \ |
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| 363 | 'GEO','GALACTO','LGROUP','CMB'] |
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| 364 | if frame in valid: |
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| 365 | inf = list(self._getcoordinfo()) |
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| 366 | inf[1] = frame |
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| 367 | self._setcoordinfo(inf) |
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| 368 | else: |
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| 369 | print "Please specify a valid freq type. Valid types are:\n",valid |
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| 370 | |
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| 371 | def get_unit(self): |
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| 372 | """ |
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| 373 | Get the default unit set in this scantable |
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| 374 | Parameters: |
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| 375 | Returns: |
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| 376 | A unit string |
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| 377 | """ |
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| 378 | inf = self._getcoordinfo() |
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| 379 | unit = inf[0] |
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| 380 | if unit == '': unit = 'channel' |
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| 381 | return unit |
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| 382 | |
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| 383 | def get_abcissa(self, rowno=0): |
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| 384 | """ |
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| 385 | Get the abcissa in the current coordinate setup for the currently |
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| 386 | selected Beam/IF/Pol |
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| 387 | Parameters: |
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| 388 | rowno: an optional row number in the scantable. Default is the |
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| 389 | first row, i.e. rowno=0 |
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| 390 | Returns: |
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| 391 | The abcissa values and it's format string. |
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| 392 | """ |
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| 393 | abc = self._getabcissa(rowno) |
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| 394 | lbl = self._getabcissalabel(rowno) |
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| 395 | return abc, lbl |
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| 396 | |
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| 397 | def create_mask(self, *args, **kwargs): |
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| 398 | """ |
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| 399 | Compute and return a mask based on [min,max] windows. |
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| 400 | The specified windows are to be INCLUDED, when the mask is |
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| 401 | applied. |
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| 402 | Parameters: |
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| 403 | [min,max],[min2,max2],... |
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| 404 | Pairs of start/end points specifying the regions |
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| 405 | to be masked |
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| 406 | invert: optional argument. If specified as True, |
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| 407 | return an inverted mask, i.e. the regions |
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| 408 | specified are EXCLUDED |
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| 409 | Example: |
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| 410 | scan.set_unit('channel') |
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| 411 | |
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| 412 | a) |
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| 413 | msk = scan.set_mask([400,500],[800,900]) |
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| 414 | # masks everything outside 400 and 500 |
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| 415 | # and 800 and 900 in the unit 'channel' |
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| 416 | |
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| 417 | b) |
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| 418 | msk = scan.set_mask([400,500],[800,900], invert=True) |
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| 419 | # masks the regions between 400 and 500 |
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| 420 | # and 800 and 900 in the unit 'channel' |
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| 421 | |
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| 422 | """ |
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| 423 | u = self._getcoordinfo()[0] |
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| 424 | if self._vb: |
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| 425 | if u == "": u = "channel" |
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| 426 | print "The current mask window unit is", u |
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| 427 | n = self.nchan() |
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| 428 | data = self._getabcissa() |
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| 429 | msk = zeros(n) |
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| 430 | for window in args: |
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| 431 | if (len(window) != 2 or window[0] > window[1] ): |
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| 432 | print "A window needs to be defined as [min,max]" |
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| 433 | return |
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| 434 | for i in range(n): |
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| 435 | if data[i] >= window[0] and data[i] < window[1]: |
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| 436 | msk[i] = 1 |
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| 437 | if kwargs.has_key('invert'): |
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| 438 | if kwargs.get('invert'): |
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| 439 | from numarray import logical_not |
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| 440 | msk = logical_not(msk) |
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| 441 | return msk |
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| 442 | |
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| 443 | def set_restfreqs(self, freqs, unit='Hz'): |
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| 444 | """ |
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| 445 | Set the restfrequency(s) for this scantable. |
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| 446 | Parameters: |
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| 447 | freqs: one or more frequencies |
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| 448 | unit: optional 'unit', default 'Hz' |
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| 449 | Example: |
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| 450 | scan.set_restfreqs([1000000000.0]) |
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| 451 | """ |
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| 452 | if type(freqs) is float or int: |
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| 453 | freqs = (freqs) |
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| 454 | sdtable._setrestfreqs(self,freqs, unit) |
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| 455 | return |
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| 456 | def get_restfreqs(self): |
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| 457 | """ |
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| 458 | Get the restfrequency(s) stored in this scantable. |
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| 459 | The return value(s) are always of unit 'Hz' |
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| 460 | Parameters: |
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| 461 | none |
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| 462 | Returns: |
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| 463 | a list of doubles |
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| 464 | """ |
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| 465 | return list(self._getrestfreqs()) |
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| 466 | |
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| 467 | def flag_spectrum(self, thebeam, theif, thepol): |
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| 468 | """ |
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| 469 | This flags a selected spectrum in the scan 'for good'. |
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| 470 | USE WITH CARE - not reversible. |
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| 471 | Use masks for non-permanent exclusion of channels. |
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| 472 | Parameters: |
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| 473 | thebeam,theif,thepol: all have to be explicitly |
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| 474 | specified |
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| 475 | Example: |
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| 476 | scan.flag_spectrum(0,0,1) |
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| 477 | flags the spectrum for Beam=0, IF=0, Pol=1 |
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| 478 | """ |
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| 479 | if (thebeam < self.nbeam() and theif < self.nif() and thepol < self.npol()): |
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| 480 | stable.setbeam(thebeam) |
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| 481 | stable.setif(theif) |
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| 482 | stable.setpol(thepol) |
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| 483 | stable._flag(self) |
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| 484 | else: |
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| 485 | print "Please specify a valid (Beam/IF/Pol)" |
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| 486 | return |
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| 487 | |
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| 488 | def plot(self, what='spectrum',col='Pol', panel=None): |
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| 489 | """ |
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| 490 | Plot the spectra contained in the scan. Alternatively you can also |
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| 491 | Plot Tsys vs Time |
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| 492 | Parameters: |
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| 493 | what: a choice of 'spectrum' (default) or 'tsys' |
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| 494 | col: which out of Beams/IFs/Pols should be colour stacked |
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| 495 | panel: set up multiple panels, currently not working. |
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| 496 | """ |
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| 497 | validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()} |
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| 498 | |
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| 499 | validyax = ['spectrum','tsys'] |
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| 500 | from asap.asaplot import ASAPlot |
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| 501 | if not self._p: |
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| 502 | self._p = ASAPlot() |
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| 503 | #print "Plotting not enabled" |
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| 504 | #return |
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| 505 | if self._p.is_dead: |
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| 506 | del self._p |
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| 507 | self._p = ASAPlot() |
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| 508 | npan = 1 |
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| 509 | x = None |
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| 510 | if what == 'tsys': |
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| 511 | n = self.nrow() |
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| 512 | if n < 2: |
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| 513 | print "Only one integration. Can't plot." |
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| 514 | return |
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| 515 | self._p.hold() |
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| 516 | self._p.clear() |
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| 517 | if panel == 'Time': |
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| 518 | npan = self.nrow() |
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| 519 | self._p.set_panels(rows=npan) |
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| 520 | xlab,ylab,tlab = None,None,None |
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| 521 | self._vb = False |
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| 522 | sel = self.get_cursor() |
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| 523 | for i in range(npan): |
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| 524 | if npan > 1: |
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| 525 | self._p.subplot(i) |
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| 526 | for j in range(validcol[col]): |
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| 527 | x = None |
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| 528 | y = None |
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| 529 | m = None |
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| 530 | tlab = self._getsourcename(i) |
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| 531 | import re |
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| 532 | tlab = re.sub('_S','',tlab) |
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| 533 | if col == 'Beam': |
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| 534 | self.setbeam(j) |
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| 535 | elif col == 'IF': |
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| 536 | self.setif(j) |
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| 537 | elif col == 'Pol': |
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| 538 | self.setpol(j) |
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| 539 | if what == 'tsys': |
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| 540 | x = range(self.nrow()) |
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| 541 | xlab = 'Time [pixel]' |
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| 542 | m = list(ones(len(x))) |
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| 543 | y = [] |
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| 544 | ylab = r'$T_{sys}$' |
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| 545 | for k in range(len(x)): |
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| 546 | y.append(self._gettsys(k)) |
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| 547 | else: |
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| 548 | x,xlab = self.get_abcissa(i) |
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| 549 | y = self._getspectrum(i) |
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| 550 | ylab = r'Flux' |
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| 551 | m = self._getmask(i) |
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| 552 | llab = col+' '+str(j) |
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| 553 | self._p.set_line(label=llab) |
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| 554 | self._p.plot(x,y,m) |
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| 555 | self._p.set_axes('xlabel',xlab) |
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| 556 | self._p.set_axes('ylabel',ylab) |
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| 557 | self._p.set_axes('title',tlab) |
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| 558 | self._p.release() |
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| 559 | self.set_cursor(sel[0],sel[1],sel[2]) |
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| 560 | self._vb = rcParams['verbose'] |
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| 561 | return |
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| 562 | |
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| 563 | print out |
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| 564 | |
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| 565 | def _print_values(self, dat, label='', timestamps=[]): |
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| 566 | d = dat['data'] |
|---|
| 567 | a = dat['axes'] |
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| 568 | shp = d.getshape() |
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| 569 | out = '' |
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| 570 | for i in range(shp[3]): |
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| 571 | out += '%s [%s]:\n' % (a[3],timestamps[i]) |
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| 572 | t = d[:,:,:,i] |
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| 573 | for j in range(shp[0]): |
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| 574 | if shp[0] > 1: out += ' %s[%d] ' % (a[0],j) |
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| 575 | for k in range(shp[1]): |
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| 576 | if shp[1] > 1: out += ' %s[%d] ' % (a[1],k) |
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| 577 | for l in range(shp[2]): |
|---|
| 578 | if shp[2] > 1: out += ' %s[%d] ' % (a[2],l) |
|---|
| 579 | out += '= %3.3f\n' % (t[j,k,l]) |
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| 580 | out += "--------------------------------------------------\n" |
|---|
| 581 | print "--------------------------------------------------" |
|---|
| 582 | print " ", label |
|---|
| 583 | print "--------------------------------------------------" |
|---|
| 584 | print out |
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