| 1 | from asap.scantable import scantable
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| 2 | from asap import rcParams
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| 3 | from asap import print_log
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| 4 | from asap import selector
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| 5 |
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| 6 | def average_time(*args, **kwargs):
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| 7 | """
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| 8 | Return the (time) average of a scan or list of scans. [in channels only]
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| 9 | The cursor of the output scan is set to 0
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| 10 | Parameters:
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| 11 | one scan or comma separated scans or a list of scans
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| 12 | mask: an optional mask (only used for 'var' and 'tsys' weighting)
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| 13 | scanav: True averages each scan separately.
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| 14 | False (default) averages all scans together,
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| 15 | weight: Weighting scheme.
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| 16 | 'none' (mean no weight)
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| 17 | 'var' (1/var(spec) weighted)
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| 18 | 'tsys' (1/Tsys**2 weighted)
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| 19 | 'tint' (integration time weighted)
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| 20 | 'tintsys' (Tint/Tsys**2)
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| 21 | 'median' ( median averaging)
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| 22 | align: align the spectra in velocity before averaging. It takes
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| 23 | the time of the first spectrum in the first scantable
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| 24 | as reference time.
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| 25 | Example:
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| 26 | # return a time averaged scan from scana and scanb
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| 27 | # without using a mask
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| 28 | scanav = average_time(scana,scanb)
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| 29 | # or equivalent
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| 30 | # scanav = average_time([scana, scanb])
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| 31 | # return the (time) averaged scan, i.e. the average of
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| 32 | # all correlator cycles
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| 33 | scanav = average_time(scan, scanav=True)
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| 34 | """
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| 35 | scanav = False
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| 36 | if kwargs.has_key('scanav'):
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| 37 | scanav = kwargs.get('scanav')
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| 38 | weight = 'tint'
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| 39 | if kwargs.has_key('weight'):
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| 40 | weight = kwargs.get('weight')
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| 41 | mask = ()
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| 42 | if kwargs.has_key('mask'):
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| 43 | mask = kwargs.get('mask')
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| 44 | align = False
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| 45 | if kwargs.has_key('align'):
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| 46 | align = kwargs.get('align')
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| 47 | varlist = vars()
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| 48 | if isinstance(args[0],list):
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| 49 | lst = args[0]
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| 50 | elif isinstance(args[0],tuple):
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| 51 | lst = list(args[0])
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| 52 | else:
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| 53 | lst = list(args)
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| 54 |
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| 55 | del varlist["kwargs"]
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| 56 | varlist["args"] = "%d scantables" % len(lst)
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| 57 | # need special formatting here for history...
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| 58 |
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| 59 | from asap._asap import stmath
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| 60 | stm = stmath()
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| 61 | for s in lst:
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| 62 | if not isinstance(s,scantable):
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| 63 | msg = "Please give a list of scantables"
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| 64 | if rcParams['verbose']:
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| 65 | print msg
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| 66 | return
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| 67 | else:
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| 68 | raise TypeError(msg)
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| 69 | if scanav: scanav = "SCAN"
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| 70 | else: scanav = "NONE"
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| 71 | alignedlst = []
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| 72 | if align:
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| 73 | refepoch = lst[0].get_time(0)
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| 74 | for scan in lst:
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| 75 | alignedlst.append(scan.freq_align(refepoch,insitu=False))
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| 76 | else:
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| 77 | alignedlst = lst
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| 78 | if weight.upper() == 'MEDIAN':
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| 79 | # median doesn't support list of scantables - merge first
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| 80 | merged = None
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| 81 | if len(alignedlst) > 1:
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| 82 | merged = merge(alignedlst)
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| 83 | else:
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| 84 | merged = alignedlst[0]
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| 85 | s = scantable(stm._averagechannel(merged, 'MEDIAN', scanav))
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| 86 | del merged
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| 87 | else:
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| 88 | s = scantable(stm._average(alignedlst, mask, weight.upper(), scanav))
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| 89 | s._add_history("average_time",varlist)
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| 90 | print_log()
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| 91 | return s
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| 92 |
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| 93 | def quotient(source, reference, preserve=True):
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| 94 | """
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| 95 | Return the quotient of a 'source' (signal) scan and a 'reference' scan.
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| 96 | The reference can have just one scan, even if the signal has many. Otherwise
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| 97 | they must have the same number of scans.
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| 98 | The cursor of the output scan is set to 0
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| 99 | Parameters:
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| 100 | source: the 'on' scan
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| 101 | reference: the 'off' scan
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| 102 | preserve: you can preserve (default) the continuum or
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| 103 | remove it. The equations used are
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| 104 | preserve: Output = Toff * (on/off) - Toff
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| 105 | remove: Output = Toff * (on/off) - Ton
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| 106 | """
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| 107 | varlist = vars()
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| 108 | from asap._asap import stmath
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| 109 | stm = stmath()
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| 110 | stm._setinsitu(False)
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| 111 | s = scantable(stm._quotient(source, reference, preserve))
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| 112 | s._add_history("quotient",varlist)
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| 113 | print_log()
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| 114 | return s
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| 115 |
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| 116 | def dototalpower(calon, caloff, tcalval=0.0):
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| 117 | """
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| 118 | Do calibration for CAL on,off signals.
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| 119 | Adopted from GBTIDL dototalpower
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| 120 | Parameters:
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| 121 | calon: the 'cal on' subintegration
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| 122 | caloff: the 'cal off' subintegration
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| 123 | tcalval: user supplied Tcal value
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| 124 | """
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| 125 | varlist = vars()
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| 126 | from asap._asap import stmath
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| 127 | stm = stmath()
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| 128 | stm._setinsitu(False)
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| 129 | s = scantable(stm._dototalpower(calon, caloff, tcalval))
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| 130 | s._add_history("dototalpower",varlist)
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| 131 | print_log()
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| 132 | return s
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| 133 |
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| 134 | def dosigref(sig, ref, smooth, tsysval=0.0, tauval=0.0):
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| 135 | """
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| 136 | Calculate a quotient (sig-ref/ref * Tsys)
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| 137 | Adopted from GBTIDL dosigref
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| 138 | Parameters:
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| 139 | sig: on source data
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| 140 | ref: reference data
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| 141 | smooth: width of box car smoothing for reference
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| 142 | tsysval: user specified Tsys (scalar only)
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| 143 | tauval: user specified Tau (required if tsysval is set)
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| 144 | """
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| 145 | varlist = vars()
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| 146 | from asap._asap import stmath
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| 147 | stm = stmath()
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| 148 | stm._setinsitu(False)
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| 149 | s = scantable(stm._dosigref(sig, ref, smooth, tsysval, tauval))
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| 150 | s._add_history("dosigref",varlist)
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| 151 | print_log()
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| 152 | return s
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| 153 |
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| 154 | def calps(scantab, scannos, smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0):
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| 155 | """
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| 156 | Calibrate GBT position switched data
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| 157 | Adopted from GBTIDL getps
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| 158 | Currently calps identify the scans as position switched data if they
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| 159 | contain '_ps' in the source name. The data must contains 'CAL' signal
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| 160 | on/off in each integration. To identify 'CAL' on state, the word, 'calon'
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| 161 | need to be present in the source name field.
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| 162 | (GBT MS data reading process to scantable automatically append these
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| 163 | id names to the source names)
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| 164 |
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| 165 | Parameters:
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| 166 | scantab: scantable
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| 167 | scannos: list of scan numbers
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| 168 | smooth: optional box smoothing order for the reference
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| 169 | (default is 1 = no smoothing)
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| 170 | tsysval: optional user specified Tsys (default is 0.0,
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| 171 | use Tsys in the data)
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| 172 | tauval: optional user specified Tau
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| 173 | tcalval: optional user specified Tcal (default is 0.0,
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| 174 | use Tcal value in the data)
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| 175 | """
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| 176 | varlist = vars()
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| 177 | # check for the appropriate data
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| 178 | s = scantab.get_scan('*_ps*')
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| 179 | if s is None:
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| 180 | msg = "The input data appear to contain no position-switch mode data."
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| 181 | if rcParams['verbose']:
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| 182 | print msg
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| 183 | return
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| 184 | else:
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| 185 | raise TypeError(msg)
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| 186 | ssub = s.get_scan(scannos)
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| 187 | if ssub is None:
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| 188 | msg = "No data was found with given scan numbers!"
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| 189 | if rcParams['verbose']:
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| 190 | print msg
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| 191 | return
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| 192 | else:
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| 193 | raise TypeError(msg)
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| 194 | ssubon = ssub.get_scan('*calon')
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| 195 | ssuboff = ssub.get_scan('*[^calon]')
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| 196 | if ssubon.nrow() != ssuboff.nrow():
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| 197 | msg = "mismatch in numbers of CAL on/off scans. Cannot calibrate. Check the scan numbers."
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| 198 | if rcParams['verbose']:
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| 199 | print msg
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| 200 | return
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| 201 | else:
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| 202 | raise TypeError(msg)
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| 203 | cals = dototalpower(ssubon, ssuboff, tcalval)
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| 204 | sig = cals.get_scan('*ps')
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| 205 | ref = cals.get_scan('*psr')
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| 206 | if sig.nscan() != ref.nscan():
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| 207 | msg = "mismatch in numbers of on/off scans. Cannot calibrate. Check the scan numbers."
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| 208 | if rcParams['verbose']:
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| 209 | print msg
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| 210 | return
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| 211 | else:
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| 212 | raise TypeError(msg)
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| 213 |
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| 214 | #for user supplied Tsys
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| 215 | if tsysval>0.0:
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| 216 | if tauval<=0.0:
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| 217 | msg = "Need to supply a valid tau to use the supplied Tsys"
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| 218 | if rcParams['verbose']:
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| 219 | print msg
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| 220 | return
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| 221 | else:
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| 222 | raise TypeError(msg)
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| 223 | else:
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| 224 | sig.recalc_azel()
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| 225 | ref.recalc_azel()
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| 226 | #msg = "Use of user specified Tsys is not fully implemented yet."
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| 227 | #if rcParams['verbose']:
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| 228 | # print msg
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| 229 | # return
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| 230 | #else:
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| 231 | # raise TypeError(msg)
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| 232 | # use get_elevation to get elevation and
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| 233 | # calculate a scaling factor using the formula
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| 234 | # -> tsys use to dosigref
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| 235 |
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| 236 | #ress = dosigref(sig, ref, smooth, tsysval)
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| 237 | ress = dosigref(sig, ref, smooth, tsysval, tauval)
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| 238 | ress._add_history("calps", varlist)
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| 239 | print_log()
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| 240 | return ress
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| 241 |
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| 242 | def calnod(scantab, scannos=[], smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0):
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| 243 | """
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| 244 | Do full (but a pair of scans at time) processing of GBT Nod data
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| 245 | calibration.
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| 246 | Adopted from GBTIDL's getnod
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| 247 | Parameters:
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| 248 | scantab: scantable
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| 249 | scannos: a pair of scan numbers, or the first scan number of the pair
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| 250 | smooth: box car smoothing order
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| 251 | tsysval: optional user specified Tsys value
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| 252 | tauval: optional user specified tau value (not implemented yet)
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| 253 | tcalval: optional user specified Tcal value
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| 254 | """
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| 255 | varlist = vars()
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| 256 | from asap._asap import stmath
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| 257 | stm = stmath()
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| 258 | stm._setinsitu(False)
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| 259 |
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| 260 | # check for the appropriate data
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| 261 | s = scantab.get_scan('*_nod*')
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| 262 | if s is None:
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| 263 | msg = "The input data appear to contain no Nod observing mode data."
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| 264 | if rcParams['verbose']:
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| 265 | print msg
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| 266 | return
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| 267 | else:
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| 268 | raise TypeError(msg)
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| 269 |
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| 270 | # need check correspondance of each beam with sig-ref ...
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| 271 | # check for timestamps, scan numbers, subscan id (not available in
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| 272 | # ASAP data format...). Assume 1st scan of the pair (beam 0 - sig
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| 273 | # and beam 1 - ref...)
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| 274 | # First scan number of paired scans or list of pairs of
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| 275 | # scan numbers (has to have even number of pairs.)
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| 276 |
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| 277 | #data splitting
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| 278 | scan1no = scan2no = 0
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| 279 |
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| 280 | if len(scannos)==1:
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| 281 | scan1no = scannos[0]
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| 282 | scan2no = scannos[0]+1
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| 283 | pairScans = [scan1no, scan2no]
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| 284 | else:
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| 285 | #if len(scannos)>2:
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| 286 | # msg = "calnod can only process a pair of nod scans at time."
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| 287 | # if rcParams['verbose']:
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| 288 | # print msg
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| 289 | # return
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| 290 | # else:
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| 291 | # raise TypeError(msg)
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| 292 | #
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| 293 | #if len(scannos)==2:
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| 294 | # scan1no = scannos[0]
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| 295 | # scan2no = scannos[1]
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| 296 | pairScans = list(scannos)
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| 297 |
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| 298 | if tsysval>0.0:
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| 299 | if tauval<=0.0:
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| 300 | msg = "Need to supply a valid tau to use the supplied Tsys"
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| 301 | if rcParams['verbose']:
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| 302 | print msg
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| 303 | return
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| 304 | else:
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| 305 | raise TypeError(msg)
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| 306 | else:
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| 307 | scantab.recalc_azel()
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| 308 | resspec = scantable(stm._donod(scantab, pairScans, smooth, tsysval,tauval,tcalval))
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| 309 | resspec._add_history("calnod",varlist)
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| 310 | print_log()
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| 311 | return resspec
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| 312 |
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| 313 | def calfs(scantab, scannos=[], smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0):
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| 314 | """
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| 315 | Calibrate GBT frequency switched data.
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| 316 | Adopted from GBTIDL getfs.
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| 317 | Currently calfs identify the scans as frequency switched data if they
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| 318 | contain '_fs' in the source name. The data must contains 'CAL' signal
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| 319 | on/off in each integration. To identify 'CAL' on state, the word, 'calon'
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| 320 | need to be present in the source name field.
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| 321 | (GBT MS data reading via scantable automatically append these
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| 322 | id names to the source names)
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| 323 |
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| 324 | Parameters:
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| 325 | scantab: scantable
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| 326 | scannos: list of scan numbers
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| 327 | smooth: optional box smoothing order for the reference
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| 328 | (default is 1 = no smoothing)
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| 329 | tsysval: optional user specified Tsys (default is 0.0,
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| 330 | use Tsys in the data)
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| 331 | tauval: optional user specified Tau
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| 332 | """
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| 333 | varlist = vars()
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| 334 | from asap._asap import stmath
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| 335 | stm = stmath()
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| 336 | stm._setinsitu(False)
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| 337 |
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| 338 | # check = scantab.get_scan('*_fs*')
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| 339 | # if check is None:
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| 340 | # msg = "The input data appear to contain no Nod observing mode data."
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| 341 | # if rcParams['verbose']:
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| 342 | # print msg
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| 343 | # return
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| 344 | # else:
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| 345 | # raise TypeError(msg)
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| 346 | s = scantab.get_scan(scannos)
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| 347 | del scantab
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| 348 |
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| 349 | resspec = scantable(stm._dofs(s, scannos, smooth, tsysval,tauval,tcalval))
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| 350 | resspec._add_history("calfs",varlist)
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| 351 | print_log()
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| 352 | return resspec
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| 353 |
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| 354 | def simple_math(left, right, op='add', tsys=True):
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| 355 | """
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| 356 | Apply simple mathematical binary operations to two
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| 357 | scan tables, returning the result in a new scan table.
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| 358 | The operation is applied to both the correlations and the TSys data
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| 359 | The cursor of the output scan is set to 0
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| 360 | Parameters:
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| 361 | left: the 'left' scan
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| 362 | right: the 'right' scan
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| 363 | op: the operation: 'add' (default), 'sub', 'mul', 'div'
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| 364 | tsys: if True (default) then apply the operation to Tsys
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| 365 | as well as the data
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| 366 | """
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| 367 | print "simple_math is deprecated use +=/* instead."
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| 368 |
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| 369 | def merge(*args):
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| 370 | """
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| 371 | Merge a list of scanatables, or comma-sperated scantables into one
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| 372 | scnatble.
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| 373 | Parameters:
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| 374 | A list [scan1, scan2] or scan1, scan2.
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| 375 | Example:
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| 376 | myscans = [scan1, scan2]
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| 377 | allscans = merge(myscans)
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| 378 | # or equivalent
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| 379 | sameallscans = merge(scan1, scan2)
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| 380 | """
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| 381 | varlist = vars()
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| 382 | if isinstance(args[0],list):
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| 383 | lst = tuple(args[0])
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| 384 | elif isinstance(args[0],tuple):
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| 385 | lst = args[0]
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| 386 | else:
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| 387 | lst = tuple(args)
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| 388 | varlist["args"] = "%d scantables" % len(lst)
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| 389 | # need special formatting her for history...
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| 390 | from asap._asap import stmath
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| 391 | stm = stmath()
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| 392 | for s in lst:
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| 393 | if not isinstance(s,scantable):
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| 394 | msg = "Please give a list of scantables"
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| 395 | if rcParams['verbose']:
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| 396 | print msg
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| 397 | return
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| 398 | else:
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| 399 | raise TypeError(msg)
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| 400 | s = scantable(stm._merge(lst))
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| 401 | s._add_history("merge", varlist)
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| 402 | print_log()
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| 403 | return s
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| 404 |
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