| 1 | from asap.scantable import scantable
|
|---|
| 2 | from asap import rcParams
|
|---|
| 3 | from asap import print_log
|
|---|
| 4 | from asap import selector
|
|---|
| 5 | from taskinit import *
|
|---|
| 6 |
|
|---|
| 7 | def average_time(*args, **kwargs):
|
|---|
| 8 | """
|
|---|
| 9 | Return the (time) average of a scan or list of scans. [in channels only]
|
|---|
| 10 | The cursor of the output scan is set to 0
|
|---|
| 11 | Parameters:
|
|---|
| 12 | one scan or comma separated scans or a list of scans
|
|---|
| 13 | mask: an optional mask (only used for 'var' and 'tsys' weighting)
|
|---|
| 14 | scanav: True averages each scan separately.
|
|---|
| 15 | False (default) averages all scans together,
|
|---|
| 16 | weight: Weighting scheme.
|
|---|
| 17 | 'none' (mean no weight)
|
|---|
| 18 | 'var' (1/var(spec) weighted)
|
|---|
| 19 | 'tsys' (1/Tsys**2 weighted)
|
|---|
| 20 | 'tint' (integration time weighted)
|
|---|
| 21 | 'tintsys' (Tint/Tsys**2)
|
|---|
| 22 | 'median' ( median averaging)
|
|---|
| 23 | align: align the spectra in velocity before averaging. It takes
|
|---|
| 24 | the time of the first spectrum in the first scantable
|
|---|
| 25 | as reference time.
|
|---|
| 26 | Example:
|
|---|
| 27 | # return a time averaged scan from scana and scanb
|
|---|
| 28 | # without using a mask
|
|---|
| 29 | scanav = average_time(scana,scanb)
|
|---|
| 30 | # or equivalent
|
|---|
| 31 | # scanav = average_time([scana, scanb])
|
|---|
| 32 | # return the (time) averaged scan, i.e. the average of
|
|---|
| 33 | # all correlator cycles
|
|---|
| 34 | scanav = average_time(scan, scanav=True)
|
|---|
| 35 | """
|
|---|
| 36 | scanav = False
|
|---|
| 37 | if kwargs.has_key('scanav'):
|
|---|
| 38 | scanav = kwargs.get('scanav')
|
|---|
| 39 | weight = 'tint'
|
|---|
| 40 | if kwargs.has_key('weight'):
|
|---|
| 41 | weight = kwargs.get('weight')
|
|---|
| 42 | mask = ()
|
|---|
| 43 | if kwargs.has_key('mask'):
|
|---|
| 44 | mask = kwargs.get('mask')
|
|---|
| 45 | align = False
|
|---|
| 46 | if kwargs.has_key('align'):
|
|---|
| 47 | align = kwargs.get('align')
|
|---|
| 48 | compel = False
|
|---|
| 49 | if kwargs.has_key('compel'):
|
|---|
| 50 | compel = kwargs.get('compel')
|
|---|
| 51 | varlist = vars()
|
|---|
| 52 | if isinstance(args[0],list):
|
|---|
| 53 | lst = args[0]
|
|---|
| 54 | elif isinstance(args[0],tuple):
|
|---|
| 55 | lst = list(args[0])
|
|---|
| 56 | else:
|
|---|
| 57 | lst = list(args)
|
|---|
| 58 |
|
|---|
| 59 | del varlist["kwargs"]
|
|---|
| 60 | varlist["args"] = "%d scantables" % len(lst)
|
|---|
| 61 | # need special formatting here for history...
|
|---|
| 62 |
|
|---|
| 63 | from asap._asap import stmath
|
|---|
| 64 | stm = stmath()
|
|---|
| 65 | for s in lst:
|
|---|
| 66 | if not isinstance(s,scantable):
|
|---|
| 67 | msg = "Please give a list of scantables"
|
|---|
| 68 | if rcParams['verbose']:
|
|---|
| 69 | #print msg
|
|---|
| 70 | casalog.post( msg, 'WARN' )
|
|---|
| 71 | return
|
|---|
| 72 | else:
|
|---|
| 73 | raise TypeError(msg)
|
|---|
| 74 | if scanav: scanav = "SCAN"
|
|---|
| 75 | else: scanav = "NONE"
|
|---|
| 76 | alignedlst = []
|
|---|
| 77 | if align:
|
|---|
| 78 | refepoch = lst[0].get_time(0)
|
|---|
| 79 | for scan in lst:
|
|---|
| 80 | alignedlst.append(scan.freq_align(refepoch,insitu=False))
|
|---|
| 81 | else:
|
|---|
| 82 | alignedlst = lst
|
|---|
| 83 | if weight.upper() == 'MEDIAN':
|
|---|
| 84 | # median doesn't support list of scantables - merge first
|
|---|
| 85 | merged = None
|
|---|
| 86 | if len(alignedlst) > 1:
|
|---|
| 87 | merged = merge(alignedlst)
|
|---|
| 88 | else:
|
|---|
| 89 | merged = alignedlst[0]
|
|---|
| 90 | s = scantable(stm._averagechannel(merged, 'MEDIAN', scanav))
|
|---|
| 91 | del merged
|
|---|
| 92 | else:
|
|---|
| 93 | #s = scantable(stm._average(alignedlst, mask, weight.upper(), scanav))
|
|---|
| 94 | s = scantable(stm._new_average(alignedlst, compel, mask, weight.upper(), scanav))
|
|---|
| 95 | s._add_history("average_time",varlist)
|
|---|
| 96 | print_log()
|
|---|
| 97 | return s
|
|---|
| 98 |
|
|---|
| 99 | def quotient(source, reference, preserve=True):
|
|---|
| 100 | """
|
|---|
| 101 | Return the quotient of a 'source' (signal) scan and a 'reference' scan.
|
|---|
| 102 | The reference can have just one scan, even if the signal has many. Otherwise
|
|---|
| 103 | they must have the same number of scans.
|
|---|
| 104 | The cursor of the output scan is set to 0
|
|---|
| 105 | Parameters:
|
|---|
| 106 | source: the 'on' scan
|
|---|
| 107 | reference: the 'off' scan
|
|---|
| 108 | preserve: you can preserve (default) the continuum or
|
|---|
| 109 | remove it. The equations used are
|
|---|
| 110 | preserve: Output = Toff * (on/off) - Toff
|
|---|
| 111 | remove: Output = Toff * (on/off) - Ton
|
|---|
| 112 | """
|
|---|
| 113 | varlist = vars()
|
|---|
| 114 | from asap._asap import stmath
|
|---|
| 115 | stm = stmath()
|
|---|
| 116 | stm._setinsitu(False)
|
|---|
| 117 | s = scantable(stm._quotient(source, reference, preserve))
|
|---|
| 118 | s._add_history("quotient",varlist)
|
|---|
| 119 | print_log()
|
|---|
| 120 | return s
|
|---|
| 121 |
|
|---|
| 122 | def dototalpower(calon, caloff, tcalval=0.0):
|
|---|
| 123 | """
|
|---|
| 124 | Do calibration for CAL on,off signals.
|
|---|
| 125 | Adopted from GBTIDL dototalpower
|
|---|
| 126 | Parameters:
|
|---|
| 127 | calon: the 'cal on' subintegration
|
|---|
| 128 | caloff: the 'cal off' subintegration
|
|---|
| 129 | tcalval: user supplied Tcal value
|
|---|
| 130 | """
|
|---|
| 131 | varlist = vars()
|
|---|
| 132 | from asap._asap import stmath
|
|---|
| 133 | stm = stmath()
|
|---|
| 134 | stm._setinsitu(False)
|
|---|
| 135 | s = scantable(stm._dototalpower(calon, caloff, tcalval))
|
|---|
| 136 | s._add_history("dototalpower",varlist)
|
|---|
| 137 | print_log()
|
|---|
| 138 | return s
|
|---|
| 139 |
|
|---|
| 140 | def dosigref(sig, ref, smooth, tsysval=0.0, tauval=0.0):
|
|---|
| 141 | """
|
|---|
| 142 | Calculate a quotient (sig-ref/ref * Tsys)
|
|---|
| 143 | Adopted from GBTIDL dosigref
|
|---|
| 144 | Parameters:
|
|---|
| 145 | sig: on source data
|
|---|
| 146 | ref: reference data
|
|---|
| 147 | smooth: width of box car smoothing for reference
|
|---|
| 148 | tsysval: user specified Tsys (scalar only)
|
|---|
| 149 | tauval: user specified Tau (required if tsysval is set)
|
|---|
| 150 | """
|
|---|
| 151 | varlist = vars()
|
|---|
| 152 | from asap._asap import stmath
|
|---|
| 153 | stm = stmath()
|
|---|
| 154 | stm._setinsitu(False)
|
|---|
| 155 | s = scantable(stm._dosigref(sig, ref, smooth, tsysval, tauval))
|
|---|
| 156 | s._add_history("dosigref",varlist)
|
|---|
| 157 | print_log()
|
|---|
| 158 | return s
|
|---|
| 159 |
|
|---|
| 160 | def calps(scantab, scannos, smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0):
|
|---|
| 161 | """
|
|---|
| 162 | Calibrate GBT position switched data
|
|---|
| 163 | Adopted from GBTIDL getps
|
|---|
| 164 | Currently calps identify the scans as position switched data if they
|
|---|
| 165 | contain '_ps' in the source name. The data must contains 'CAL' signal
|
|---|
| 166 | on/off in each integration. To identify 'CAL' on state, the word, 'calon'
|
|---|
| 167 | need to be present in the source name field.
|
|---|
| 168 | (GBT MS data reading process to scantable automatically append these
|
|---|
| 169 | id names to the source names)
|
|---|
| 170 |
|
|---|
| 171 | Parameters:
|
|---|
| 172 | scantab: scantable
|
|---|
| 173 | scannos: list of scan numbers
|
|---|
| 174 | smooth: optional box smoothing order for the reference
|
|---|
| 175 | (default is 1 = no smoothing)
|
|---|
| 176 | tsysval: optional user specified Tsys (default is 0.0,
|
|---|
| 177 | use Tsys in the data)
|
|---|
| 178 | tauval: optional user specified Tau
|
|---|
| 179 | tcalval: optional user specified Tcal (default is 0.0,
|
|---|
| 180 | use Tcal value in the data)
|
|---|
| 181 | """
|
|---|
| 182 | varlist = vars()
|
|---|
| 183 | # check for the appropriate data
|
|---|
| 184 | s = scantab.get_scan('*_ps*')
|
|---|
| 185 | if s is None:
|
|---|
| 186 | msg = "The input data appear to contain no position-switch mode data."
|
|---|
| 187 | if rcParams['verbose']:
|
|---|
| 188 | #print msg
|
|---|
| 189 | casalog.post( msg, 'WARN' )
|
|---|
| 190 | return
|
|---|
| 191 | else:
|
|---|
| 192 | raise TypeError(msg)
|
|---|
| 193 | ssub = s.get_scan(scannos)
|
|---|
| 194 | if ssub is None:
|
|---|
| 195 | msg = "No data was found with given scan numbers!"
|
|---|
| 196 | if rcParams['verbose']:
|
|---|
| 197 | #print msg
|
|---|
| 198 | casalog.post( msg, 'WARN' )
|
|---|
| 199 | return
|
|---|
| 200 | else:
|
|---|
| 201 | raise TypeError(msg)
|
|---|
| 202 | ssubon = ssub.get_scan('*calon')
|
|---|
| 203 | ssuboff = ssub.get_scan('*[^calon]')
|
|---|
| 204 | if ssubon.nrow() != ssuboff.nrow():
|
|---|
| 205 | msg = "mismatch in numbers of CAL on/off scans. Cannot calibrate. Check the scan numbers."
|
|---|
| 206 | if rcParams['verbose']:
|
|---|
| 207 | #print msg
|
|---|
| 208 | casalog.post( msg, 'WARN' )
|
|---|
| 209 | return
|
|---|
| 210 | else:
|
|---|
| 211 | raise TypeError(msg)
|
|---|
| 212 | cals = dototalpower(ssubon, ssuboff, tcalval)
|
|---|
| 213 | sig = cals.get_scan('*ps')
|
|---|
| 214 | ref = cals.get_scan('*psr')
|
|---|
| 215 | if sig.nscan() != ref.nscan():
|
|---|
| 216 | msg = "mismatch in numbers of on/off scans. Cannot calibrate. Check the scan numbers."
|
|---|
| 217 | if rcParams['verbose']:
|
|---|
| 218 | #print msg
|
|---|
| 219 | casalog.post( msg, 'WARN' )
|
|---|
| 220 | return
|
|---|
| 221 | else:
|
|---|
| 222 | raise TypeError(msg)
|
|---|
| 223 |
|
|---|
| 224 | #for user supplied Tsys
|
|---|
| 225 | if tsysval>0.0:
|
|---|
| 226 | if tauval<=0.0:
|
|---|
| 227 | msg = "Need to supply a valid tau to use the supplied Tsys"
|
|---|
| 228 | if rcParams['verbose']:
|
|---|
| 229 | #print msg
|
|---|
| 230 | casalog.post( msg, 'WARN' )
|
|---|
| 231 | return
|
|---|
| 232 | else:
|
|---|
| 233 | raise TypeError(msg)
|
|---|
| 234 | else:
|
|---|
| 235 | sig.recalc_azel()
|
|---|
| 236 | ref.recalc_azel()
|
|---|
| 237 | #msg = "Use of user specified Tsys is not fully implemented yet."
|
|---|
| 238 | #if rcParams['verbose']:
|
|---|
| 239 | # print msg
|
|---|
| 240 | # return
|
|---|
| 241 | #else:
|
|---|
| 242 | # raise TypeError(msg)
|
|---|
| 243 | # use get_elevation to get elevation and
|
|---|
| 244 | # calculate a scaling factor using the formula
|
|---|
| 245 | # -> tsys use to dosigref
|
|---|
| 246 |
|
|---|
| 247 | #ress = dosigref(sig, ref, smooth, tsysval)
|
|---|
| 248 | ress = dosigref(sig, ref, smooth, tsysval, tauval)
|
|---|
| 249 | ress._add_history("calps", varlist)
|
|---|
| 250 | print_log()
|
|---|
| 251 | return ress
|
|---|
| 252 |
|
|---|
| 253 | def calnod(scantab, scannos=[], smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0):
|
|---|
| 254 | """
|
|---|
| 255 | Do full (but a pair of scans at time) processing of GBT Nod data
|
|---|
| 256 | calibration.
|
|---|
| 257 | Adopted from GBTIDL's getnod
|
|---|
| 258 | Parameters:
|
|---|
| 259 | scantab: scantable
|
|---|
| 260 | scannos: a pair of scan numbers, or the first scan number of the pair
|
|---|
| 261 | smooth: box car smoothing order
|
|---|
| 262 | tsysval: optional user specified Tsys value
|
|---|
| 263 | tauval: optional user specified tau value (not implemented yet)
|
|---|
| 264 | tcalval: optional user specified Tcal value
|
|---|
| 265 | """
|
|---|
| 266 | varlist = vars()
|
|---|
| 267 | from asap._asap import stmath
|
|---|
| 268 | stm = stmath()
|
|---|
| 269 | stm._setinsitu(False)
|
|---|
| 270 |
|
|---|
| 271 | # check for the appropriate data
|
|---|
| 272 | s = scantab.get_scan('*_nod*')
|
|---|
| 273 | if s is None:
|
|---|
| 274 | msg = "The input data appear to contain no Nod observing mode data."
|
|---|
| 275 | if rcParams['verbose']:
|
|---|
| 276 | #print msg
|
|---|
| 277 | casalog.post( msg, 'WARN' )
|
|---|
| 278 | return
|
|---|
| 279 | else:
|
|---|
| 280 | raise TypeError(msg)
|
|---|
| 281 |
|
|---|
| 282 | # need check correspondance of each beam with sig-ref ...
|
|---|
| 283 | # check for timestamps, scan numbers, subscan id (not available in
|
|---|
| 284 | # ASAP data format...). Assume 1st scan of the pair (beam 0 - sig
|
|---|
| 285 | # and beam 1 - ref...)
|
|---|
| 286 | # First scan number of paired scans or list of pairs of
|
|---|
| 287 | # scan numbers (has to have even number of pairs.)
|
|---|
| 288 |
|
|---|
| 289 | #data splitting
|
|---|
| 290 | scan1no = scan2no = 0
|
|---|
| 291 |
|
|---|
| 292 | if len(scannos)==1:
|
|---|
| 293 | scan1no = scannos[0]
|
|---|
| 294 | scan2no = scannos[0]+1
|
|---|
| 295 | pairScans = [scan1no, scan2no]
|
|---|
| 296 | else:
|
|---|
| 297 | #if len(scannos)>2:
|
|---|
| 298 | # msg = "calnod can only process a pair of nod scans at time."
|
|---|
| 299 | # if rcParams['verbose']:
|
|---|
| 300 | # print msg
|
|---|
| 301 | # return
|
|---|
| 302 | # else:
|
|---|
| 303 | # raise TypeError(msg)
|
|---|
| 304 | #
|
|---|
| 305 | #if len(scannos)==2:
|
|---|
| 306 | # scan1no = scannos[0]
|
|---|
| 307 | # scan2no = scannos[1]
|
|---|
| 308 | pairScans = list(scannos)
|
|---|
| 309 |
|
|---|
| 310 | if tsysval>0.0:
|
|---|
| 311 | if tauval<=0.0:
|
|---|
| 312 | msg = "Need to supply a valid tau to use the supplied Tsys"
|
|---|
| 313 | if rcParams['verbose']:
|
|---|
| 314 | #print msg
|
|---|
| 315 | casalog.post( msg, 'WARN' )
|
|---|
| 316 | return
|
|---|
| 317 | else:
|
|---|
| 318 | raise TypeError(msg)
|
|---|
| 319 | else:
|
|---|
| 320 | scantab.recalc_azel()
|
|---|
| 321 | resspec = scantable(stm._donod(scantab, pairScans, smooth, tsysval,tauval,tcalval))
|
|---|
| 322 | resspec._add_history("calnod",varlist)
|
|---|
| 323 | print_log()
|
|---|
| 324 | return resspec
|
|---|
| 325 |
|
|---|
| 326 | def calfs(scantab, scannos=[], smooth=1, tsysval=0.0, tauval=0.0, tcalval=0.0):
|
|---|
| 327 | """
|
|---|
| 328 | Calibrate GBT frequency switched data.
|
|---|
| 329 | Adopted from GBTIDL getfs.
|
|---|
| 330 | Currently calfs identify the scans as frequency switched data if they
|
|---|
| 331 | contain '_fs' in the source name. The data must contains 'CAL' signal
|
|---|
| 332 | on/off in each integration. To identify 'CAL' on state, the word, 'calon'
|
|---|
| 333 | need to be present in the source name field.
|
|---|
| 334 | (GBT MS data reading via scantable automatically append these
|
|---|
| 335 | id names to the source names)
|
|---|
| 336 |
|
|---|
| 337 | Parameters:
|
|---|
| 338 | scantab: scantable
|
|---|
| 339 | scannos: list of scan numbers
|
|---|
| 340 | smooth: optional box smoothing order for the reference
|
|---|
| 341 | (default is 1 = no smoothing)
|
|---|
| 342 | tsysval: optional user specified Tsys (default is 0.0,
|
|---|
| 343 | use Tsys in the data)
|
|---|
| 344 | tauval: optional user specified Tau
|
|---|
| 345 | """
|
|---|
| 346 | varlist = vars()
|
|---|
| 347 | from asap._asap import stmath
|
|---|
| 348 | stm = stmath()
|
|---|
| 349 | stm._setinsitu(False)
|
|---|
| 350 |
|
|---|
| 351 | # check = scantab.get_scan('*_fs*')
|
|---|
| 352 | # if check is None:
|
|---|
| 353 | # msg = "The input data appear to contain no Nod observing mode data."
|
|---|
| 354 | # if rcParams['verbose']:
|
|---|
| 355 | # print msg
|
|---|
| 356 | # return
|
|---|
| 357 | # else:
|
|---|
| 358 | # raise TypeError(msg)
|
|---|
| 359 | s = scantab.get_scan(scannos)
|
|---|
| 360 | del scantab
|
|---|
| 361 |
|
|---|
| 362 | resspec = scantable(stm._dofs(s, scannos, smooth, tsysval,tauval,tcalval))
|
|---|
| 363 | resspec._add_history("calfs",varlist)
|
|---|
| 364 | print_log()
|
|---|
| 365 | return resspec
|
|---|
| 366 |
|
|---|
| 367 | def simple_math(left, right, op='add', tsys=True):
|
|---|
| 368 | """
|
|---|
| 369 | Apply simple mathematical binary operations to two
|
|---|
| 370 | scan tables, returning the result in a new scan table.
|
|---|
| 371 | The operation is applied to both the correlations and the TSys data
|
|---|
| 372 | The cursor of the output scan is set to 0
|
|---|
| 373 | Parameters:
|
|---|
| 374 | left: the 'left' scan
|
|---|
| 375 | right: the 'right' scan
|
|---|
| 376 | op: the operation: 'add' (default), 'sub', 'mul', 'div'
|
|---|
| 377 | tsys: if True (default) then apply the operation to Tsys
|
|---|
| 378 | as well as the data
|
|---|
| 379 | """
|
|---|
| 380 | #print "simple_math is deprecated use +=/* instead."
|
|---|
| 381 | casalog.post( "simple_math is deprecated use +=/* instead.", 'WARN' )
|
|---|
| 382 |
|
|---|
| 383 | def merge(*args):
|
|---|
| 384 | """
|
|---|
| 385 | Merge a list of scanatables, or comma-sperated scantables into one
|
|---|
| 386 | scnatble.
|
|---|
| 387 | Parameters:
|
|---|
| 388 | A list [scan1, scan2] or scan1, scan2.
|
|---|
| 389 | Example:
|
|---|
| 390 | myscans = [scan1, scan2]
|
|---|
| 391 | allscans = merge(myscans)
|
|---|
| 392 | # or equivalent
|
|---|
| 393 | sameallscans = merge(scan1, scan2)
|
|---|
| 394 | """
|
|---|
| 395 | varlist = vars()
|
|---|
| 396 | if isinstance(args[0],list):
|
|---|
| 397 | lst = tuple(args[0])
|
|---|
| 398 | elif isinstance(args[0],tuple):
|
|---|
| 399 | lst = args[0]
|
|---|
| 400 | else:
|
|---|
| 401 | lst = tuple(args)
|
|---|
| 402 | varlist["args"] = "%d scantables" % len(lst)
|
|---|
| 403 | # need special formatting her for history...
|
|---|
| 404 | from asap._asap import stmath
|
|---|
| 405 | stm = stmath()
|
|---|
| 406 | for s in lst:
|
|---|
| 407 | if not isinstance(s,scantable):
|
|---|
| 408 | msg = "Please give a list of scantables"
|
|---|
| 409 | if rcParams['verbose']:
|
|---|
| 410 | #print msg
|
|---|
| 411 | casalog.post( msg, 'WARN' )
|
|---|
| 412 | return
|
|---|
| 413 | else:
|
|---|
| 414 | raise TypeError(msg)
|
|---|
| 415 | s = scantable(stm._merge(lst))
|
|---|
| 416 | s._add_history("merge", varlist)
|
|---|
| 417 | print_log()
|
|---|
| 418 | return s
|
|---|
| 419 |
|
|---|
