| 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 | compel = False |
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| 48 | if kwargs.has_key('compel'): |
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| 49 | compel = kwargs.get('compel') |
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| 50 | varlist = vars() |
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| 51 | if isinstance(args[0],list): |
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| 52 | lst = args[0] |
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| 53 | elif isinstance(args[0],tuple): |
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| 54 | lst = list(args[0]) |
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| 55 | else: |
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| 56 | lst = list(args) |
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| 57 | |
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| 58 | del varlist["kwargs"] |
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| 59 | varlist["args"] = "%d scantables" % len(lst) |
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| 60 | # need special formatting here for history... |
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| 61 | |
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| 62 | from asap._asap import stmath |
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| 63 | stm = stmath() |
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| 64 | for s in lst: |
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| 65 | if not isinstance(s,scantable): |
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| 66 | msg = "Please give a list of scantables" |
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| 67 | if rcParams['verbose']: |
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| 68 | print msg |
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| 69 | return |
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| 70 | else: |
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| 71 | raise TypeError(msg) |
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| 72 | if scanav: scanav = "SCAN" |
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| 73 | else: scanav = "NONE" |
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| 74 | alignedlst = [] |
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| 75 | if align: |
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| 76 | refepoch = lst[0].get_time(0) |
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| 77 | for scan in lst: |
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| 78 | alignedlst.append(scan.freq_align(refepoch,insitu=False)) |
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| 79 | else: |
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| 80 | alignedlst = lst |
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| 81 | if weight.upper() == 'MEDIAN': |
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| 82 | # median doesn't support list of scantables - merge first |
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| 83 | merged = None |
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| 84 | if len(alignedlst) > 1: |
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| 85 | merged = merge(alignedlst) |
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| 86 | else: |
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| 87 | merged = alignedlst[0] |
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| 88 | s = scantable(stm._averagechannel(merged, 'MEDIAN', scanav)) |
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| 89 | del merged |
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| 90 | else: |
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| 91 | #s = scantable(stm._average(alignedlst, mask, weight.upper(), scanav)) |
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| 92 | s = scantable(stm._new_average(alignedlst, compel, mask, weight.upper(), scanav)) |
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| 93 | s._add_history("average_time",varlist) |
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| 94 | print_log() |
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| 95 | return s |
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| 96 | |
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| 97 | def quotient(source, reference, preserve=True): |
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| 98 | """ |
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| 99 | Return the quotient of a 'source' (signal) scan and a 'reference' scan. |
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| 100 | The reference can have just one scan, even if the signal has many. Otherwise |
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| 101 | they must have the same number of scans. |
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| 102 | The cursor of the output scan is set to 0 |
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| 103 | Parameters: |
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| 104 | source: the 'on' scan |
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| 105 | reference: the 'off' scan |
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| 106 | preserve: you can preserve (default) the continuum or |
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| 107 | remove it. The equations used are |
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| 108 | preserve: Output = Toff * (on/off) - Toff |
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| 109 | remove: Output = Toff * (on/off) - Ton |
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| 110 | """ |
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| 111 | varlist = vars() |
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| 112 | from asap._asap import stmath |
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| 113 | stm = stmath() |
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| 114 | stm._setinsitu(False) |
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| 115 | s = scantable(stm._quotient(source, reference, preserve)) |
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| 116 | s._add_history("quotient",varlist) |
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| 117 | print_log() |
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| 118 | return s |
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| 119 | |
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| 120 | def dototalpower(calon, caloff, tcalval=0.0): |
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| 121 | """ |
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| 122 | Do calibration for CAL on,off signals. |
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| 123 | Adopted from GBTIDL dototalpower |
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| 124 | Parameters: |
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| 125 | calon: the 'cal on' subintegration |
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| 126 | caloff: the 'cal off' subintegration |
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| 127 | tcalval: user supplied Tcal value |
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| 128 | """ |
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| 129 | varlist = vars() |
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| 130 | from asap._asap import stmath |
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| 131 | stm = stmath() |
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| 132 | stm._setinsitu(False) |
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| 133 | s = scantable(stm._dototalpower(calon, caloff, tcalval)) |
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| 134 | s._add_history("dototalpower",varlist) |
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| 135 | print_log() |
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| 136 | return s |
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| 137 | |
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| 138 | def dosigref(sig, ref, smooth, tsysval=0.0, tauval=0.0): |
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| 139 | """ |
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| 140 | Calculate a quotient (sig-ref/ref * Tsys) |
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| 141 | Adopted from GBTIDL dosigref |
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| 142 | Parameters: |
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| 143 | sig: on source data |
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| 144 | ref: reference data |
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| 145 | smooth: width of box car smoothing for reference |
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| 146 | tsysval: user specified Tsys (scalar only) |
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| 147 | tauval: user specified Tau (required if tsysval is set) |
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| 148 | """ |
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| 149 | varlist = vars() |
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| 150 | from asap._asap import stmath |
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| 151 | stm = stmath() |
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| 152 | stm._setinsitu(False) |
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| 153 | s = scantable(stm._dosigref(sig, ref, smooth, tsysval, tauval)) |
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| 154 | s._add_history("dosigref",varlist) |
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| 155 | print_log() |
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| 156 | return s |
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| 157 | |
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| 158 | def calps(scantab, scannos, smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0): |
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| 159 | """ |
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| 160 | Calibrate GBT position switched data |
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| 161 | Adopted from GBTIDL getps |
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| 162 | Currently calps identify the scans as position switched data if they |
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| 163 | contain '_ps' in the source name. The data must contains 'CAL' signal |
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| 164 | on/off in each integration. To identify 'CAL' on state, the word, 'calon' |
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| 165 | need to be present in the source name field. |
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| 166 | (GBT MS data reading process to scantable automatically append these |
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| 167 | id names to the source names) |
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| 168 | |
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| 169 | Parameters: |
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| 170 | scantab: scantable |
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| 171 | scannos: list of scan numbers |
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| 172 | smooth: optional box smoothing order for the reference |
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| 173 | (default is 1 = no smoothing) |
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| 174 | tsysval: optional user specified Tsys (default is 0.0, |
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| 175 | use Tsys in the data) |
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| 176 | tauval: optional user specified Tau |
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| 177 | tcalval: optional user specified Tcal (default is 0.0, |
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| 178 | use Tcal value in the data) |
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| 179 | """ |
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| 180 | varlist = vars() |
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| 181 | # check for the appropriate data |
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| 182 | s = scantab.get_scan('*_ps*') |
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| 183 | if s is None: |
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| 184 | msg = "The input data appear to contain no position-switch mode data." |
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| 185 | if rcParams['verbose']: |
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| 186 | print msg |
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| 187 | return |
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| 188 | else: |
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| 189 | raise TypeError(msg) |
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| 190 | ssub = s.get_scan(scannos) |
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| 191 | if ssub is None: |
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| 192 | msg = "No data was found with given scan numbers!" |
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| 193 | if rcParams['verbose']: |
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| 194 | print msg |
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| 195 | return |
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| 196 | else: |
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| 197 | raise TypeError(msg) |
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| 198 | ssubon = ssub.get_scan('*calon') |
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| 199 | ssuboff = ssub.get_scan('*[^calon]') |
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| 200 | if ssubon.nrow() != ssuboff.nrow(): |
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| 201 | msg = "mismatch in numbers of CAL on/off scans. Cannot calibrate. Check the scan numbers." |
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| 202 | if rcParams['verbose']: |
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| 203 | print msg |
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| 204 | return |
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| 205 | else: |
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| 206 | raise TypeError(msg) |
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| 207 | cals = dototalpower(ssubon, ssuboff, tcalval) |
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| 208 | sig = cals.get_scan('*ps') |
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| 209 | ref = cals.get_scan('*psr') |
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| 210 | if sig.nscan() != ref.nscan(): |
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| 211 | msg = "mismatch in numbers of on/off scans. Cannot calibrate. Check the scan numbers." |
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| 212 | if rcParams['verbose']: |
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| 213 | print msg |
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| 214 | return |
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| 215 | else: |
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| 216 | raise TypeError(msg) |
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| 217 | |
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| 218 | #for user supplied Tsys |
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| 219 | if tsysval>0.0: |
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| 220 | if tauval<=0.0: |
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| 221 | msg = "Need to supply a valid tau to use the supplied Tsys" |
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| 222 | if rcParams['verbose']: |
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| 223 | print msg |
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| 224 | return |
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| 225 | else: |
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| 226 | raise TypeError(msg) |
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| 227 | else: |
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| 228 | sig.recalc_azel() |
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| 229 | ref.recalc_azel() |
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| 230 | #msg = "Use of user specified Tsys is not fully implemented yet." |
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| 231 | #if rcParams['verbose']: |
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| 232 | # print msg |
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| 233 | # return |
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| 234 | #else: |
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| 235 | # raise TypeError(msg) |
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| 236 | # use get_elevation to get elevation and |
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| 237 | # calculate a scaling factor using the formula |
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| 238 | # -> tsys use to dosigref |
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| 239 | |
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| 240 | #ress = dosigref(sig, ref, smooth, tsysval) |
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| 241 | ress = dosigref(sig, ref, smooth, tsysval, tauval) |
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| 242 | ress._add_history("calps", varlist) |
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| 243 | print_log() |
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| 244 | return ress |
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| 245 | |
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| 246 | def calnod(scantab, scannos=[], smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0): |
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| 247 | """ |
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| 248 | Do full (but a pair of scans at time) processing of GBT Nod data |
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| 249 | calibration. |
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| 250 | Adopted from GBTIDL's getnod |
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| 251 | Parameters: |
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| 252 | scantab: scantable |
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| 253 | scannos: a pair of scan numbers, or the first scan number of the pair |
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| 254 | smooth: box car smoothing order |
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| 255 | tsysval: optional user specified Tsys value |
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| 256 | tauval: optional user specified tau value (not implemented yet) |
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| 257 | tcalval: optional user specified Tcal value |
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| 258 | """ |
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| 259 | varlist = vars() |
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| 260 | from asap._asap import stmath |
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| 261 | stm = stmath() |
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| 262 | stm._setinsitu(False) |
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| 263 | |
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| 264 | # check for the appropriate data |
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| 265 | s = scantab.get_scan('*_nod*') |
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| 266 | if s is None: |
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| 267 | msg = "The input data appear to contain no Nod observing mode data." |
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| 268 | if rcParams['verbose']: |
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| 269 | print msg |
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| 270 | return |
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| 271 | else: |
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| 272 | raise TypeError(msg) |
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| 273 | |
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| 274 | # need check correspondance of each beam with sig-ref ... |
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| 275 | # check for timestamps, scan numbers, subscan id (not available in |
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| 276 | # ASAP data format...). Assume 1st scan of the pair (beam 0 - sig |
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| 277 | # and beam 1 - ref...) |
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| 278 | # First scan number of paired scans or list of pairs of |
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| 279 | # scan numbers (has to have even number of pairs.) |
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| 280 | |
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| 281 | #data splitting |
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| 282 | scan1no = scan2no = 0 |
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| 283 | |
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| 284 | if len(scannos)==1: |
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| 285 | scan1no = scannos[0] |
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| 286 | scan2no = scannos[0]+1 |
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| 287 | pairScans = [scan1no, scan2no] |
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| 288 | else: |
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| 289 | #if len(scannos)>2: |
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| 290 | # msg = "calnod can only process a pair of nod scans at time." |
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| 291 | # if rcParams['verbose']: |
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| 292 | # print msg |
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| 293 | # return |
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| 294 | # else: |
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| 295 | # raise TypeError(msg) |
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| 296 | # |
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| 297 | #if len(scannos)==2: |
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| 298 | # scan1no = scannos[0] |
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| 299 | # scan2no = scannos[1] |
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| 300 | pairScans = list(scannos) |
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| 301 | |
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| 302 | if tsysval>0.0: |
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| 303 | if tauval<=0.0: |
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| 304 | msg = "Need to supply a valid tau to use the supplied Tsys" |
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| 305 | if rcParams['verbose']: |
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| 306 | print msg |
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| 307 | return |
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| 308 | else: |
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| 309 | raise TypeError(msg) |
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| 310 | else: |
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| 311 | scantab.recalc_azel() |
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| 312 | resspec = scantable(stm._donod(scantab, pairScans, smooth, tsysval,tauval,tcalval)) |
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| 313 | resspec._add_history("calnod",varlist) |
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| 314 | print_log() |
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| 315 | return resspec |
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| 316 | |
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| 317 | def calfs(scantab, scannos=[], smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0): |
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| 318 | """ |
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| 319 | Calibrate GBT frequency switched data. |
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| 320 | Adopted from GBTIDL getfs. |
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| 321 | Currently calfs identify the scans as frequency switched data if they |
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| 322 | contain '_fs' in the source name. The data must contains 'CAL' signal |
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| 323 | on/off in each integration. To identify 'CAL' on state, the word, 'calon' |
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| 324 | need to be present in the source name field. |
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| 325 | (GBT MS data reading via scantable automatically append these |
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| 326 | id names to the source names) |
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| 327 | |
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| 328 | Parameters: |
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| 329 | scantab: scantable |
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| 330 | scannos: list of scan numbers |
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| 331 | smooth: optional box smoothing order for the reference |
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| 332 | (default is 1 = no smoothing) |
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| 333 | tsysval: optional user specified Tsys (default is 0.0, |
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| 334 | use Tsys in the data) |
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| 335 | tauval: optional user specified Tau |
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| 336 | """ |
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| 337 | varlist = vars() |
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| 338 | from asap._asap import stmath |
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| 339 | stm = stmath() |
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| 340 | stm._setinsitu(False) |
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| 341 | |
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| 342 | # check = scantab.get_scan('*_fs*') |
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| 343 | # if check is None: |
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| 344 | # msg = "The input data appear to contain no Nod observing mode data." |
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| 345 | # if rcParams['verbose']: |
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| 346 | # print msg |
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| 347 | # return |
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| 348 | # else: |
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| 349 | # raise TypeError(msg) |
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| 350 | s = scantab.get_scan(scannos) |
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| 351 | del scantab |
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| 352 | |
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| 353 | resspec = scantable(stm._dofs(s, scannos, smooth, tsysval,tauval,tcalval)) |
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| 354 | resspec._add_history("calfs",varlist) |
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| 355 | print_log() |
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| 356 | return resspec |
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| 357 | |
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| 358 | def simple_math(left, right, op='add', tsys=True): |
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| 359 | """ |
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| 360 | Apply simple mathematical binary operations to two |
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| 361 | scan tables, returning the result in a new scan table. |
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| 362 | The operation is applied to both the correlations and the TSys data |
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| 363 | The cursor of the output scan is set to 0 |
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| 364 | Parameters: |
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| 365 | left: the 'left' scan |
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| 366 | right: the 'right' scan |
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| 367 | op: the operation: 'add' (default), 'sub', 'mul', 'div' |
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| 368 | tsys: if True (default) then apply the operation to Tsys |
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| 369 | as well as the data |
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| 370 | """ |
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| 371 | print "simple_math is deprecated use +=/* instead." |
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| 372 | |
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| 373 | def merge(*args): |
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| 374 | """ |
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| 375 | Merge a list of scanatables, or comma-sperated scantables into one |
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| 376 | scnatble. |
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| 377 | Parameters: |
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| 378 | A list [scan1, scan2] or scan1, scan2. |
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| 379 | Example: |
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| 380 | myscans = [scan1, scan2] |
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| 381 | allscans = merge(myscans) |
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| 382 | # or equivalent |
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| 383 | sameallscans = merge(scan1, scan2) |
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| 384 | """ |
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| 385 | varlist = vars() |
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| 386 | if isinstance(args[0],list): |
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| 387 | lst = tuple(args[0]) |
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| 388 | elif isinstance(args[0],tuple): |
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| 389 | lst = args[0] |
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| 390 | else: |
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| 391 | lst = tuple(args) |
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| 392 | varlist["args"] = "%d scantables" % len(lst) |
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| 393 | # need special formatting her for history... |
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| 394 | from asap._asap import stmath |
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| 395 | stm = stmath() |
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| 396 | for s in lst: |
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| 397 | if not isinstance(s,scantable): |
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| 398 | msg = "Please give a list of scantables" |
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| 399 | if rcParams['verbose']: |
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| 400 | print msg |
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| 401 | return |
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| 402 | else: |
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| 403 | raise TypeError(msg) |
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| 404 | s = scantable(stm._merge(lst)) |
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| 405 | s._add_history("merge", varlist) |
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| 406 | print_log() |
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| 407 | return s |
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| 408 | |
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