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casa
$Rev:20696$
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casa
$Rev:20696$
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00001 # 00002 # This file was generated using xslt from its XML file 00003 # 00004 # Copyright 2008, Associated Universities Inc., Washington DC 00005 # 00006 import sys 00007 import os 00008 #from casac import * 00009 import casac 00010 import string 00011 import time 00012 import inspect 00013 import gc 00014 import numpy 00015 from odict import odict 00016 from taskmanager import tm 00017 from task_sdreduce import sdreduce 00018 class sdreduce_cli_: 00019 __name__ = "sdreduce" 00020 __async__ = {} 00021 rkey = None 00022 i_am_a_casapy_task = None 00023 # The existence of the i_am_a_casapy_task attribute allows help() 00024 # (and other) to treat casapy tasks as a special case. 00025 00026 def __init__(self) : 00027 self.__bases__ = (sdreduce_cli_,) 00028 self.__doc__ = self.__call__.__doc__ 00029 00030 self.parameters={'infile':None, 'antenna':None, 'fluxunit':None, 'telescopeparm':None, 'specunit':None, 'restfreq':None, 'frame':None, 'doppler':None, 'calmode':None, 'fraction':None, 'noff':None, 'width':None, 'elongated':None, 'markonly':None, 'plotpointings':None, 'scanlist':None, 'field':None, 'iflist':None, 'pollist':None, 'channelrange':None, 'average':None, 'scanaverage':None, 'timeaverage':None, 'tweight':None, 'averageall':None, 'polaverage':None, 'pweight':None, 'tau':None, 'kernel':None, 'kwidth':None, 'chanwidth':None, 'masklist':None, 'maskmode':None, 'thresh':None, 'avg_limit':None, 'edge':None, 'blfunc':None, 'order':None, 'npiece':None, 'applyfft':None, 'fftmethod':None, 'fftthresh':None, 'addwn':None, 'rejwn':None, 'clipthresh':None, 'clipniter':None, 'verifycal':None, 'verifysm':None, 'verifybl':None, 'verbosebl':None, 'bloutput':None, 'blformat':None, 'showprogress':None, 'minnrow':None, 'outfile':None, 'outform':None, 'overwrite':None, 'plotlevel':None, 'async':None} 00031 00032 00033 def result(self, key=None): 00034 #### here we will scan the task-ids in __async__ 00035 #### and add any that have completed... 00036 if key is not None and self.__async__.has_key(key) and self.__async__[key] is not None: 00037 ret = tm.retrieve(self.__async__[key]) 00038 if ret['state'] == "done" : 00039 self.__async__[key] = None 00040 elif ret['state'] == 'crashed' : 00041 self.__async__[key] = None 00042 return ret 00043 return None 00044 00045 00046 def __call__(self, infile=None, antenna=None, fluxunit=None, telescopeparm=None, specunit=None, restfreq=None, frame=None, doppler=None, calmode=None, fraction=None, noff=None, width=None, elongated=None, markonly=None, plotpointings=None, scanlist=None, field=None, iflist=None, pollist=None, channelrange=None, average=None, scanaverage=None, timeaverage=None, tweight=None, averageall=None, polaverage=None, pweight=None, tau=None, kernel=None, kwidth=None, chanwidth=None, masklist=None, maskmode=None, thresh=None, avg_limit=None, edge=None, blfunc=None, order=None, npiece=None, applyfft=None, fftmethod=None, fftthresh=None, addwn=None, rejwn=None, clipthresh=None, clipniter=None, verifycal=None, verifysm=None, verifybl=None, verbosebl=None, bloutput=None, blformat=None, showprogress=None, minnrow=None, outfile=None, outform=None, overwrite=None, plotlevel=None, async=None): 00047 00048 """ASAP SD task: do sdcal, sdsmooth, and sdbaseline in one task 00049 Keyword arguments: 00050 infile -- name of input SD dataset 00051 antenna -- antenna name or id (only effective for MS input). 00052 fluxunit -- units for line flux 00053 options: 'K','Jy','' 00054 default: '' (keep current fluxunit) 00055 WARNING: For GBT data, see description below. 00056 >>> fluxunit expandable parameter 00057 telescopeparm -- the telescope characteristics 00058 options: (str) name or (list) list of gain info 00059 default: '' (none set) 00060 example: if telescopeparm='', it tries to get the telescope 00061 name from the data. 00062 Full antenna parameters (diameter,ap.eff.) known 00063 to ASAP are 00064 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', 'DSS-43', 00065 'CEDUNA','HOBART'. For GBT, it fixes default fluxunit 00066 to 'K' first then convert to a new fluxunit. 00067 telescopeparm=[104.9,0.43] diameter(m), ap.eff. 00068 telescopeparm=[0.743] gain in Jy/K 00069 telescopeparm='FIX' to change default fluxunit 00070 see description below 00071 00072 specunit -- units for spectral axis 00073 options: (str) 'channel','km/s','GHz','MHz','kHz','Hz','' 00074 default: '' (=current) 00075 example: this will be the units for masklist 00076 >>> specunit expandable parameters 00077 restfreq -- rest frequency 00078 available type includes float, int, string, list of float, 00079 list of int, list of string, and list of dictionary. the 00080 default unit of restfreq in case of float, int, or string 00081 without unit is Hz. string input can be a value only 00082 (treated as Hz) or a value followed by unit for which 'GHz', 00083 'MHz','kHz',and 'Hz' are available. 00084 a list can be used to set different rest frequencies for 00085 each IF. the length of list input must be nIF. dictionary 00086 input should be a pair of molecule name and frequency with 00087 keys of 'name' and 'value', respectively. values in the 00088 dictionary input follows the same manner as for single 00089 float or string input. 00090 example: 345.796 00091 '1420MHz' 00092 [345.8, 347.0, 356.7] 00093 ['345.8MHz', '347.0MHz', '356.7MHz'] 00094 [{'name':'CO','value':345}] 00095 frame -- frequency frame for spectral axis 00096 options: (str) 'LSRK','REST','TOPO','LSRD','BARY', 00097 'GEO','GALACTO','LGROUP','CMB' 00098 default: currently set frame in scantable 00099 WARNING: frame='REST' not yet implemented 00100 doppler -- doppler mode 00101 options: (str) 'RADIO','OPTICAL','Z','BETA','GAMMA' 00102 default: currently set doppler in scantable 00103 calmode -- calibration mode 00104 options: 'ps','nod','fs','fsotf','quotient','none' 00105 default: 'none' 00106 example: choose mode 'none' if you have 00107 already calibrated and want to 00108 try baselines or averaging 00109 >>> calmode expandable parameter 00110 fraction -- Edge marking parameter for 'otf' and 'otfraster'. 00111 specify a number of OFF scans as a fraction of 00112 total number of data points. 00113 default: '10%' 00114 options: '20%' in string style or float value less 00115 than 1.0 (e.g. 0.15). 00116 'auto' is available only for 'otfraster'. 00117 noff -- Edge marking parameter for 'otfraster'. 00118 It is used to specify a number of OFF scans near 00119 edge directly. Value of noff comes before setting 00120 by fraction. 00121 default: -1 (use fraction) 00122 options: any positive integer 00123 width -- Edge marking parameter for 'otf'. 00124 Pixel width with respect to a median spatial 00125 separation between neighboring two data in time. 00126 Default will be fine in most cases. 00127 default: 0.5 00128 options: float value 00129 elongated -- Edge marking parameter for 'otf'. 00130 Set True only if observed area is elongeted 00131 in one direction. 00132 default: False 00133 markonly -- Set True if you want to save data just after 00134 edge marking (i.e. uncalibrated data) to see 00135 how OFF scans are defined. 00136 default: False 00137 scanlist -- list of scan numbers to process 00138 default: [] (use all scans) 00139 example: [21,22,23,24] 00140 this selection is in addition to field, iflist, and pollist 00141 field -- selection string for selecting scans by name 00142 default: '' (no name selection) 00143 example: 'FLS3a*' 00144 this selection is in addition to scanlist, iflist, and pollist 00145 iflist -- list of IF id numbers to select 00146 default: [] (use all IFs) 00147 example: [15] 00148 this selection is in addition to scanlist, field, and pollist 00149 pollist -- list of polarization id numbers to select 00150 default: [] (use all polarizations) 00151 example: [1] 00152 this selection is in addition to scanlist, field, and iflist 00153 channelrange -- channel range selection 00154 default: [] (use all channel) 00155 example: [0,5000] 00156 Note that specified values are recognized as 'channel' 00157 regardless of the value of specunit 00158 average -- averaging on spectral data 00159 options: (bool) True,False 00160 default: False 00161 00162 >>>average expandable parameter 00163 scanaverage -- average integrations within scans 00164 options: (bool) True,False 00165 default: False 00166 example: if True, this happens in read-in 00167 For GBT, set False! 00168 timeaverage -- average times for multiple scan cycles 00169 options: (bool) True,False 00170 default: False 00171 example: if True, this happens after calibration 00172 tweight -- weighting for time average 00173 options: 'none' 00174 'var' (1/var(spec) weighted) 00175 'tsys' (1/Tsys**2 weighted) 00176 'tint' (integration time weighted) 00177 'tintsys' (Tint/Tsys**2) 00178 'median' ( median averaging) 00179 default: 'none' 00180 averageall -- average multi-resolution spectra 00181 spectra are averaged by referring 00182 their frequency coverage 00183 default: False 00184 polaverage -- average polarizations 00185 options: (bool) True,False 00186 default: False 00187 pweight -- weighting for polarization average 00188 options: 'none' 00189 'var' (1/var(spec) weighted) 00190 'tsys' (1/Tsys**2 weighted) 00191 00192 tau -- atmospheric optical depth 00193 default: 0.0 (no correction) 00194 kernel -- type of spectral smoothing 00195 options: 'none','hanning','gaussian','boxcar','regrid' 00196 default: 'none' (no smoothing) 00197 00198 >>>kernel expandable parameter 00199 kwidth -- width of spectral smoothing kernel 00200 options: (int) in channels 00201 default: 5 00202 example: 5 or 10 seem to be popular for boxcar 00203 ignored for hanning (fixed at 5 chans) 00204 (0 will turn off gaussian or boxcar) 00205 chanwidth -- channel width of regridded spectra 00206 default: '5' (in channels) 00207 example: '500MHz', '0.2km/s' 00208 masklist -- list or string of mask regions to INCLUDE in BASELINE fit 00209 a string masklist allows per IF selection of channels. 00210 default: [] (entire spectrum) 00211 example: [[1000,3000],[5000,7000]] 00212 '0:1000~3000;5000~7000, 1:200~350;450~600' 00213 when maskmode is 'auto' or 'interact', this mask 00214 will be applied first before fitting as base mask 00215 maskmode -- mode of setting additional channel masks for baselining 00216 options: (str) 'auto','list','interact' 00217 default: 'auto' 00218 example: maskmode='auto' runs linefinder to detect line regions 00219 to be excluded from fitting. this mode requires three 00220 expandable parameters: thresh, avg_limit, and edge. 00221 USE WITH CARE! May need to tweak the expandable parameters. 00222 maskmode='list' uses the given masklist only: 00223 no additional masks applied. 00224 maskmode='interact' allows users to manually modify the 00225 mask regions by dragging mouse on the spectrum plotter GUI. 00226 use LEFT or RIGHT button to add or delete regions, 00227 respectively. 00228 00229 >>> maskmode expandable parameters 00230 thresh -- S/N threshold for linefinder 00231 default: 5 00232 example: a single channel S/N ratio above which the channel is 00233 considered to be a detection 00234 avg_limit -- channel averaging for broad lines 00235 default: 4 00236 example: a number of consecutive channels not greater than 00237 this parameter can be averaged to search for broad lines 00238 edge -- channels to drop at beginning and end of spectrum 00239 default: 0 00240 example: [1000] drops 1000 channels at beginning AND end 00241 [1000,500] drops 1000 from beginning and 500 from end 00242 00243 Note: For bad baselines threshold should be increased, 00244 and avg_limit decreased (or even switched off completely by 00245 setting this parameter to 1) to avoid detecting baseline 00246 undulations instead of real lines. 00247 00248 blfunc -- baseline model function 00249 options: (str) 'none','poly','chebyshev','cspline','sinusoid' 00250 default: 'none' (no baselining) 00251 example: blfunc='poly' uses a single polynomial line of 00252 any order which should be given as an expandable 00253 parameter 'order' to fit baseline. 00254 blfunc='chebyshev' uses Chebyshev polynomials. 00255 blfunc='cspline' uses a cubic spline function, a piecewise 00256 cubic polynomial having C2-continuity (i.e., the second 00257 derivative is continuous at the joining points). 00258 blfunc='sinusoid' uses a combination of sinusoidal curves. 00259 >>> blfunc expandable parameters 00260 order -- order of baseline polynomial 00261 options: (int) (<0 turns off baseline fitting) 00262 default: 5 00263 example: typically in range 2-9 (higher values 00264 seem to be needed for GBT) 00265 npiece -- number of the element polynomials of cubic spline curve 00266 options: (int) (<0 turns off baseline fitting) 00267 default: 2 00268 applyfft -- automatically set wave numbers of sinusoidal functions 00269 for fitting by applying some method like FFT. 00270 options: (bool) True, False 00271 default: True 00272 fftmethod -- method to be used when applyfft=True. Now only 00273 'fft' is available and it is the default. 00274 fftthresh -- threshold to select wave numbers to be used for 00275 sinusoidal fitting. both (float) and (str) accepted. 00276 given a float value, the unit is set to sigma. 00277 for string values, allowed formats include: 00278 'xsigma' or 'x' (= x-sigma level. e.g., '3sigma'), or 00279 'topx' (= the x strongest ones, e.g. 'top5'). 00280 default is 3.0 (unit: sigma). 00281 addwn -- additional wave number(s) of sinusoids to be used 00282 for fitting. 00283 (list) and (int) are accepted to specify every 00284 wave numbers. also (str) can be used in case 00285 you need to specify wave numbers in a certain range, 00286 e.g., 'a-b' (= a, a+1, a+2, ..., b-1, b), 00287 '<a' (= 0,1,...,a-2,a-1), 00288 '>=a' (= a, a+1, ... up to the maximum wave 00289 number corresponding to the Nyquist 00290 frequency for the case of FFT). 00291 default: [] 00292 rejwn -- wave number(s) of sinusoid NOT to be used for fitting. 00293 can be set just as addwn but has higher priority: 00294 wave numbers which are specified both in addwn 00295 and rejwn will NOT be used. 00296 default: [] 00297 clipthresh -- clipping threshold for iterative fitting 00298 default: 3 00299 clipniter -- maximum iteration number 00300 default: 0 (no iteration, i.e., no clipping) 00301 00302 verifycal -- verify the results of calibration 00303 options: (bool) True,False 00304 default: False 00305 WARNING: Currently verifying parameters just asks whether you 00306 accept the displayed calibraion/fit and if not, 00307 continues without doing any calibraion/baseline fit. 00308 verifysm -- verify the results of smoothing 00309 options: (bool) True,False 00310 default: False 00311 Note: verification is not yet available for kernel='regrid' 00312 verifybl -- verify the results of baseline fitting 00313 options: (bool) True,False 00314 default: False 00315 NOTE: Currently available only when blfunc='poly' 00316 verbosebl -- output fitting results to logger 00317 default: True 00318 example: If False, the fitting results including coefficients, 00319 residual rms, etc., are not output to the CASA logger, 00320 while the processing speed gets faster 00321 bloutput -- output fitting results to a text file 00322 default: True 00323 example: If False, the fitting results including coefficients, 00324 residual rms, etc., are not output to a text file 00325 (<outfile>_blparam.txt), while the processing 00326 speed gets faster 00327 blformat -- format of the logger output and text file specified with bloutput 00328 options: '', 'csv' 00329 default: '' (same as in the past, easy to read but huge) 00330 showprogress -- show progress status for large data 00331 default: True 00332 minnrow -- minimum number of input spectra to show progress status 00333 default: 1000 00334 outfile -- Name of output file 00335 default: '' (<infile>_cal) 00336 outform -- format of output file 00337 options: 'ASCII','SDFITS','MS','ASAP' 00338 default: 'ASAP' 00339 example: the ASAP format is easiest for further sd 00340 processing; use MS for CASA imaging. 00341 If ASCII, then will append some stuff to 00342 the outfile name 00343 overwrite -- overwrite the output file if already exists 00344 options: (bool) True,False 00345 default: False 00346 WARNING: if outform='ASCII', this parameter is ignored 00347 plotlevel -- control for plotting of results 00348 options: (int) 0=none, 1=some, 2=more, <0=hardcopy 00349 default: 0 (no plotting) 00350 example: plotlevel<0 as abs(plotlevel), e.g. 00351 -1 => hardcopy of final plot (will be named 00352 <outfile>_calspec.eps) 00353 WARNING: be careful plotting in fsotf mode! 00354 00355 00356 DESCRIPTION: 00357 00358 Task sdreduce performs data selection, calibration, and/or spectral 00359 baseline fitting for single-dish spectra. This task internally calls the 00360 tasks, sdcal, sdsmooth, and sdbaseline and it can be used to run all the 00361 three steps in one task execution. 00362 By setting calmode='none', one can run sdreduce on already calibrated data, 00363 for further selection, averaging and atmospheric optical depth correction. 00364 To save the output spectra in a certain range of channels, you set the 00365 range in channelrange. 00366 00367 If you give multiple IFs in iflist, then your scantable will have 00368 multiple IFs by default. Averaging of multi-resolution (multi-IFs) 00369 spectra can be achieved by setting a sub-parameter of average, 00370 averageall, to True. It handles multi-IFs by selecting overlaps in 00371 frequency coverages and assigning new IFs in the output spectra. 00372 00373 ASAP recognizes the data of the "AT" telescopes, but currently 00374 does not know about the GBT or any other telescope. This task 00375 does know about GBT. Telescope name is obtained from the data. 00376 If you wish to change the fluxunit (see below), by leaving 00377 the sub-parameter telescopeparm unset (telescopeparm=''), 00378 it will use internal telescope parameters for 00379 flux conversion for the data from AT telescopes and it will use an 00380 approximate aperture efficiency conversion for the GBT data. 00381 If you give telescopeparm a list, then if the list has a single float it 00382 is assumed to be the gain in Jy/K, if two or more elements they are assumed 00383 to be telescope diameter (m) and aperture efficiency 00384 respectively. 00385 00386 Note that sdreduce assumes that the fluxunit is set correctly in 00387 the data already. If not, then set telescopeparm='FIX' and it 00388 will set the default units to fluxunit without conversion. 00389 NOTE: If the data in infile is an ms from GBT and the default flux 00390 unit is missing and this task automatically fixes the default fluxunit 00391 to 'K' before the conversion. 00392 00393 WARNING for the GBT raw SDFITS format data as input: 00394 SDtasks are able to handle GBT raw SDFITS format data since the 00395 data filler is available. However, the functionality is not well 00396 tested yet, so that there may be unknown bugs. 00397 00398 00399 """ 00400 if not hasattr(self, "__globals__") or self.__globals__ == None : 00401 self.__globals__=sys._getframe(len(inspect.stack())-1).f_globals 00402 #casac = self.__globals__['casac'] 00403 casalog = self.__globals__['casalog'] 00404 #casalog = casac.casac.logsink() 00405 self.__globals__['__last_task'] = 'sdreduce' 00406 self.__globals__['taskname'] = 'sdreduce' 00407 ### 00408 self.__globals__['update_params'](func=self.__globals__['taskname'],printtext=False,ipython_globals=self.__globals__) 00409 ### 00410 ### 00411 #Handle globals or user over-ride of arguments 00412 # 00413 function_signature_defaults=dict(zip(self.__call__.func_code.co_varnames,self.__call__.func_defaults)) 00414 useLocalDefaults = False 00415 00416 for item in function_signature_defaults.iteritems(): 00417 key,val = item 00418 keyVal = eval(key) 00419 if (keyVal == None): 00420 #user hasn't set it - use global/default 00421 pass 00422 else: 00423 #user has set it - use over-ride 00424 if (key != 'self') : 00425 useLocalDefaults = True 00426 00427 myparams = {} 00428 if useLocalDefaults : 00429 for item in function_signature_defaults.iteritems(): 00430 key,val = item 00431 keyVal = eval(key) 00432 exec('myparams[key] = keyVal') 00433 self.parameters[key] = keyVal 00434 if (keyVal == None): 00435 exec('myparams[key] = '+ key + ' = self.itsdefault(key)') 00436 keyVal = eval(key) 00437 if(type(keyVal) == dict) : 00438 if len(keyVal) > 0 : 00439 exec('myparams[key] = ' + key + ' = keyVal[len(keyVal)-1][\'value\']') 00440 else : 00441 exec('myparams[key] = ' + key + ' = {}') 00442 00443 else : 00444 async = self.parameters['async'] 00445 myparams['infile'] = infile = self.parameters['infile'] 00446 myparams['antenna'] = antenna = self.parameters['antenna'] 00447 myparams['fluxunit'] = fluxunit = self.parameters['fluxunit'] 00448 myparams['telescopeparm'] = telescopeparm = self.parameters['telescopeparm'] 00449 myparams['specunit'] = specunit = self.parameters['specunit'] 00450 myparams['restfreq'] = restfreq = self.parameters['restfreq'] 00451 myparams['frame'] = frame = self.parameters['frame'] 00452 myparams['doppler'] = doppler = self.parameters['doppler'] 00453 myparams['calmode'] = calmode = self.parameters['calmode'] 00454 myparams['fraction'] = fraction = self.parameters['fraction'] 00455 myparams['noff'] = noff = self.parameters['noff'] 00456 myparams['width'] = width = self.parameters['width'] 00457 myparams['elongated'] = elongated = self.parameters['elongated'] 00458 myparams['markonly'] = markonly = self.parameters['markonly'] 00459 myparams['plotpointings'] = plotpointings = self.parameters['plotpointings'] 00460 myparams['scanlist'] = scanlist = self.parameters['scanlist'] 00461 myparams['field'] = field = self.parameters['field'] 00462 myparams['iflist'] = iflist = self.parameters['iflist'] 00463 myparams['pollist'] = pollist = self.parameters['pollist'] 00464 myparams['channelrange'] = channelrange = self.parameters['channelrange'] 00465 myparams['average'] = average = self.parameters['average'] 00466 myparams['scanaverage'] = scanaverage = self.parameters['scanaverage'] 00467 myparams['timeaverage'] = timeaverage = self.parameters['timeaverage'] 00468 myparams['tweight'] = tweight = self.parameters['tweight'] 00469 myparams['averageall'] = averageall = self.parameters['averageall'] 00470 myparams['polaverage'] = polaverage = self.parameters['polaverage'] 00471 myparams['pweight'] = pweight = self.parameters['pweight'] 00472 myparams['tau'] = tau = self.parameters['tau'] 00473 myparams['kernel'] = kernel = self.parameters['kernel'] 00474 myparams['kwidth'] = kwidth = self.parameters['kwidth'] 00475 myparams['chanwidth'] = chanwidth = self.parameters['chanwidth'] 00476 myparams['masklist'] = masklist = self.parameters['masklist'] 00477 myparams['maskmode'] = maskmode = self.parameters['maskmode'] 00478 myparams['thresh'] = thresh = self.parameters['thresh'] 00479 myparams['avg_limit'] = avg_limit = self.parameters['avg_limit'] 00480 myparams['edge'] = edge = self.parameters['edge'] 00481 myparams['blfunc'] = blfunc = self.parameters['blfunc'] 00482 myparams['order'] = order = self.parameters['order'] 00483 myparams['npiece'] = npiece = self.parameters['npiece'] 00484 myparams['applyfft'] = applyfft = self.parameters['applyfft'] 00485 myparams['fftmethod'] = fftmethod = self.parameters['fftmethod'] 00486 myparams['fftthresh'] = fftthresh = self.parameters['fftthresh'] 00487 myparams['addwn'] = addwn = self.parameters['addwn'] 00488 myparams['rejwn'] = rejwn = self.parameters['rejwn'] 00489 myparams['clipthresh'] = clipthresh = self.parameters['clipthresh'] 00490 myparams['clipniter'] = clipniter = self.parameters['clipniter'] 00491 myparams['verifycal'] = verifycal = self.parameters['verifycal'] 00492 myparams['verifysm'] = verifysm = self.parameters['verifysm'] 00493 myparams['verifybl'] = verifybl = self.parameters['verifybl'] 00494 myparams['verbosebl'] = verbosebl = self.parameters['verbosebl'] 00495 myparams['bloutput'] = bloutput = self.parameters['bloutput'] 00496 myparams['blformat'] = blformat = self.parameters['blformat'] 00497 myparams['showprogress'] = showprogress = self.parameters['showprogress'] 00498 myparams['minnrow'] = minnrow = self.parameters['minnrow'] 00499 myparams['outfile'] = outfile = self.parameters['outfile'] 00500 myparams['outform'] = outform = self.parameters['outform'] 00501 myparams['overwrite'] = overwrite = self.parameters['overwrite'] 00502 myparams['plotlevel'] = plotlevel = self.parameters['plotlevel'] 00503 00504 if type(scanlist)==int: scanlist=[scanlist] 00505 if type(iflist)==int: iflist=[iflist] 00506 if type(pollist)==int: pollist=[pollist] 00507 if type(channelrange)==int: channelrange=[channelrange] 00508 if type(edge)==int: edge=[edge] 00509 00510 result = None 00511 00512 # 00513 # The following is work around to avoid a bug with current python translation 00514 # 00515 mytmp = {} 00516 00517 mytmp['infile'] = infile 00518 mytmp['antenna'] = antenna 00519 mytmp['fluxunit'] = fluxunit 00520 mytmp['telescopeparm'] = telescopeparm 00521 mytmp['specunit'] = specunit 00522 mytmp['restfreq'] = restfreq 00523 mytmp['frame'] = frame 00524 mytmp['doppler'] = doppler 00525 mytmp['calmode'] = calmode 00526 mytmp['fraction'] = fraction 00527 mytmp['noff'] = noff 00528 mytmp['width'] = width 00529 mytmp['elongated'] = elongated 00530 mytmp['markonly'] = markonly 00531 mytmp['plotpointings'] = plotpointings 00532 mytmp['scanlist'] = scanlist 00533 mytmp['field'] = field 00534 mytmp['iflist'] = iflist 00535 mytmp['pollist'] = pollist 00536 mytmp['channelrange'] = channelrange 00537 mytmp['average'] = average 00538 mytmp['scanaverage'] = scanaverage 00539 mytmp['timeaverage'] = timeaverage 00540 mytmp['tweight'] = tweight 00541 mytmp['averageall'] = averageall 00542 mytmp['polaverage'] = polaverage 00543 mytmp['pweight'] = pweight 00544 mytmp['tau'] = tau 00545 mytmp['kernel'] = kernel 00546 mytmp['kwidth'] = kwidth 00547 mytmp['chanwidth'] = chanwidth 00548 mytmp['masklist'] = masklist 00549 mytmp['maskmode'] = maskmode 00550 mytmp['thresh'] = thresh 00551 mytmp['avg_limit'] = avg_limit 00552 mytmp['edge'] = edge 00553 mytmp['blfunc'] = blfunc 00554 mytmp['order'] = order 00555 mytmp['npiece'] = npiece 00556 mytmp['applyfft'] = applyfft 00557 mytmp['fftmethod'] = fftmethod 00558 mytmp['fftthresh'] = fftthresh 00559 mytmp['addwn'] = addwn 00560 mytmp['rejwn'] = rejwn 00561 mytmp['clipthresh'] = clipthresh 00562 mytmp['clipniter'] = clipniter 00563 mytmp['verifycal'] = verifycal 00564 mytmp['verifysm'] = verifysm 00565 mytmp['verifybl'] = verifybl 00566 mytmp['verbosebl'] = verbosebl 00567 mytmp['bloutput'] = bloutput 00568 mytmp['blformat'] = blformat 00569 mytmp['showprogress'] = showprogress 00570 mytmp['minnrow'] = minnrow 00571 mytmp['outfile'] = outfile 00572 mytmp['outform'] = outform 00573 mytmp['overwrite'] = overwrite 00574 mytmp['plotlevel'] = plotlevel 00575 pathname='file:///'+os.environ.get('CASAPATH').split()[0]+'/share/xml/' 00576 trec = casac.casac.utils().torecord(pathname+'sdreduce.xml') 00577 00578 casalog.origin('sdreduce') 00579 try : 00580 #if not trec.has_key('sdreduce') or not casac.casac.utils().verify(mytmp, trec['sdreduce']) : 00581 #return False 00582 00583 casac.casac.utils().verify(mytmp, trec['sdreduce'], True) 00584 scriptstr=[''] 00585 saveinputs = self.__globals__['saveinputs'] 00586 saveinputs('sdreduce', 'sdreduce.last', myparams, self.__globals__,scriptstr=scriptstr) 00587 if async : 00588 count = 0 00589 keybase = time.strftime("%y%m%d.%H%M%S") 00590 key = keybase + "_" + str(count) 00591 while self.__async__.has_key(key) : 00592 count += 1 00593 key = keybase + "_" + str(count) 00594 result = tm.execute('sdreduce', infile, antenna, fluxunit, telescopeparm, specunit, restfreq, frame, doppler, calmode, fraction, noff, width, elongated, markonly, plotpointings, scanlist, field, iflist, pollist, channelrange, average, scanaverage, timeaverage, tweight, averageall, polaverage, pweight, tau, kernel, kwidth, chanwidth, masklist, maskmode, thresh, avg_limit, edge, blfunc, order, npiece, applyfft, fftmethod, fftthresh, addwn, rejwn, clipthresh, clipniter, verifycal, verifysm, verifybl, verbosebl, bloutput, blformat, showprogress, minnrow, outfile, outform, overwrite, plotlevel) 00595 print "Use: " 00596 print " tm.retrieve(return_value) # to retrieve the status" 00597 print 00598 self.rkey = key 00599 self.__async__[key] = result 00600 else : 00601 tname = 'sdreduce' 00602 spaces = ' '*(18-len(tname)) 00603 casalog.post('\n##########################################'+ 00604 '\n##### Begin Task: ' + tname + spaces + ' #####') 00605 casalog.post(scriptstr[1][1:]+'\n', 'INFO') 00606 result = sdreduce(infile, antenna, fluxunit, telescopeparm, specunit, restfreq, frame, doppler, calmode, fraction, noff, width, elongated, markonly, plotpointings, scanlist, field, iflist, pollist, channelrange, average, scanaverage, timeaverage, tweight, averageall, polaverage, pweight, tau, kernel, kwidth, chanwidth, masklist, maskmode, thresh, avg_limit, edge, blfunc, order, npiece, applyfft, fftmethod, fftthresh, addwn, rejwn, clipthresh, clipniter, verifycal, verifysm, verifybl, verbosebl, bloutput, blformat, showprogress, minnrow, outfile, outform, overwrite, plotlevel) 00607 casalog.post('##### End Task: ' + tname + ' ' + spaces + ' #####'+ 00608 '\n##########################################') 00609 00610 except Exception, instance: 00611 if(self.__globals__.has_key('__rethrow_casa_exceptions') and self.__globals__['__rethrow_casa_exceptions']) : 00612 raise 00613 else : 00614 #print '**** Error **** ',instance 00615 tname = 'sdreduce' 00616 casalog.post('An error occurred running task '+tname+'.', 'ERROR') 00617 pass 00618 00619 gc.collect() 00620 return result 00621 # 00622 # 00623 # 00624 def paramgui(self, useGlobals=True, ipython_globals=None): 00625 """ 00626 Opens a parameter GUI for this task. If useGlobals is true, then any relevant global parameter settings are used. 00627 """ 00628 import paramgui 00629 if not hasattr(self, "__globals__") or self.__globals__ == None : 00630 self.__globals__=sys._getframe(len(inspect.stack())-1).f_globals 00631 00632 if useGlobals: 00633 if ipython_globals == None: 00634 myf=self.__globals__ 00635 else: 00636 myf=ipython_globals 00637 00638 paramgui.setGlobals(myf) 00639 else: 00640 paramgui.setGlobals({}) 00641 00642 paramgui.runTask('sdreduce', myf['_ip']) 00643 paramgui.setGlobals({}) 00644 00645 # 00646 # 00647 # 00648 def defaults(self, param=None, ipython_globals=None, paramvalue=None, subparam=None): 00649 if not hasattr(self, "__globals__") or self.__globals__ == None : 00650 self.__globals__=sys._getframe(len(inspect.stack())-1).f_globals 00651 if ipython_globals == None: 00652 myf=self.__globals__ 00653 else: 00654 myf=ipython_globals 00655 00656 a = odict() 00657 a['infile'] = '' 00658 a['antenna'] = 0 00659 a['fluxunit'] = '' 00660 a['specunit'] = '' 00661 a['frame'] = '' 00662 a['doppler'] = '' 00663 a['calmode'] = 'none' 00664 a['scanlist'] = [] 00665 a['field'] = '' 00666 a['iflist'] = [] 00667 a['pollist'] = [] 00668 a['channelrange'] = [] 00669 a['average'] = False 00670 a['tau'] = 0.0 00671 a['kernel'] = 'none' 00672 a['masklist'] = [] 00673 a['maskmode'] = 'auto' 00674 a['blfunc'] = 'none' 00675 a['verifycal'] = False 00676 a['verifysm'] = False 00677 a['verifybl'] = False 00678 a['verbosebl'] = True 00679 a['bloutput'] = True 00680 a['blformat'] = '' 00681 a['showprogress'] = True 00682 a['outfile'] = '' 00683 a['outform'] = 'ASAP' 00684 a['overwrite'] = False 00685 a['plotlevel'] = 0 00686 00687 a['async']=False 00688 a['fluxunit'] = { 00689 0:{'value':''}, 00690 1:odict([{'value':'K'}, {'telescopeparm':""}]), 00691 2:odict([{'value':'k'}, {'telescopeparm':""}]), 00692 3:odict([{'value':'Jy'}, {'telescopeparm':""}]), 00693 4:odict([{'value':'jy'}, {'telescopeparm':""}])} 00694 a['specunit'] = { 00695 0:{'value':''}, 00696 1:{'value':'channel'}, 00697 2:{'value':'GHz'}, 00698 3:{'value':'MHz'}, 00699 4:{'value':'kHz'}, 00700 5:{'value':'Hz'}, 00701 6:odict([{'value':'km/s'}, {'restfreq':''}])} 00702 a['average'] = { 00703 0:{'value':False}, 00704 1:odict([{'value':True}, {'scanaverage':False}, {'timeaverage':False}, {'tweight':'none'}, {'averageall':False}, {'polaverage':False}, {'pweight':'none'}])} 00705 a['kernel'] = { 00706 0:{'value':'none'}, 00707 1:{'value':'hanning'}, 00708 2:odict([{'value':'gaussian'}, {'kwidth':5}]), 00709 3:odict([{'value':'boxcar'}, {'kwidth':5}]), 00710 4:odict([{'value':'regrid'}, {'chanwidth':'5'}])} 00711 a['maskmode'] = { 00712 0:odict([{'value':'auto'}, {'thresh':5.0}, {'avg_limit':4}, {'edge':[0]}]), 00713 1:{'value':'list'}, 00714 2:{'value':'interact'}} 00715 a['blfunc'] = { 00716 0:{'value':'none'}, 00717 1:odict([{'value':'poly'}, {'order':5}]), 00718 2:odict([{'value':'cspline'}, {'npiece':2}, {'clipthresh':3.0}, {'clipniter':0}]), 00719 3:odict([{'value':'sinusoid'}, {'applyfft':True}, {'fftmethod':'fft'}, {'fftthresh':3.0}, {'addwn':[]}, {'rejwn':[]}, {'clipthresh':3.0}, {'clipniter':0}])} 00720 a['showprogress'] = { 00721 0:odict([{'value':True}, {'minnrow':1000}])} 00722 a['calmode'] = { 00723 0:{'value':'none'}, 00724 1:{'value':'ps'}, 00725 2:{'value':'nod'}, 00726 3:{'value':'fs'}, 00727 4:{'value':'fsotf'}, 00728 5:{'value':'quotient'}, 00729 6:odict([{'value':'otf'}, {'fraction':'10%'}, {'width':0.5}, {'elongated':False}, {'markonly':False}, {'plotpointings':False}]), 00730 7:odict([{'value':'otfraster'}, {'fraction':'10%'}, {'noff':-1}, {'markonly':False}, {'plotpointings':False}])} 00731 00732 ### This function sets the default values but also will return the list of 00733 ### parameters or the default value of a given parameter 00734 if(param == None): 00735 myf['__set_default_parameters'](a) 00736 elif(param == 'paramkeys'): 00737 return a.keys() 00738 else: 00739 if(paramvalue==None and subparam==None): 00740 if(a.has_key(param)): 00741 return a[param] 00742 else: 00743 return self.itsdefault(param) 00744 else: 00745 retval=a[param] 00746 if(type(a[param])==dict): 00747 for k in range(len(a[param])): 00748 valornotval='value' 00749 if(a[param][k].has_key('notvalue')): 00750 valornotval='notvalue' 00751 if((a[param][k][valornotval])==paramvalue): 00752 retval=a[param][k].copy() 00753 retval.pop(valornotval) 00754 if(subparam != None): 00755 if(retval.has_key(subparam)): 00756 retval=retval[subparam] 00757 else: 00758 retval=self.itsdefault(subparam) 00759 else: 00760 retval=self.itsdefault(subparam) 00761 return retval 00762 00763 00764 # 00765 # 00766 def check_params(self, param=None, value=None, ipython_globals=None): 00767 if ipython_globals == None: 00768 myf=self.__globals__ 00769 else: 00770 myf=ipython_globals 00771 # print 'param:', param, 'value:', value 00772 try : 00773 if str(type(value)) != "<type 'instance'>" : 00774 value0 = value 00775 value = myf['cu'].expandparam(param, value) 00776 matchtype = False 00777 if(type(value) == numpy.ndarray): 00778 if(type(value) == type(value0)): 00779 myf[param] = value.tolist() 00780 else: 00781 #print 'value:', value, 'value0:', value0 00782 #print 'type(value):', type(value), 'type(value0):', type(value0) 00783 myf[param] = value0 00784 if type(value0) != list : 00785 matchtype = True 00786 else : 00787 myf[param] = value 00788 value = myf['cu'].verifyparam({param:value}) 00789 if matchtype: 00790 value = False 00791 except Exception, instance: 00792 #ignore the exception and just return it unchecked 00793 myf[param] = value 00794 return value 00795 # 00796 # 00797 def description(self, key='sdreduce', subkey=None): 00798 desc={'sdreduce': 'ASAP SD task: do sdcal, sdsmooth, and sdbaseline in one task', 00799 'infile': 'name of input SD dataset', 00800 'antenna': 'antenna name or id (only effective for MS input)', 00801 'fluxunit': 'units for line flux (K,Jy) (''=current)', 00802 'telescopeparm': 'param of telescope for flux conversion', 00803 'specunit': 'units for spectral axis (channel,km/s,GHz)', 00804 'restfreq': 'rest frequency (default unit: Hz)', 00805 'frame': 'frequency reference frame, e.g. LSRK (''=current)', 00806 'doppler': 'doppler convention, e.g. RADIO (''=current)', 00807 'calmode': 'SD calibration mode (ps,nod,otf,otfraster,fs,fsotf,none)', 00808 'fraction': 'fraction of the OFF data to mark', 00809 'noff': 'number of the OFF data to mark', 00810 'width': 'width of the pixel for edge detection', 00811 'elongated': 'whether observed area is elongated in one direction or not', 00812 'markonly': 'do calibration (False) or just mark OFF (True)', 00813 'plotpointings': 'plot pointing direction for ON and OFF', 00814 'scanlist': 'list of scans to use (e.g. [1,2,3,4])', 00815 'field': 'string for selection by source name', 00816 'iflist': 'list of IF ids to select (e.g. [0,1])', 00817 'pollist': 'list of polarization ids to select (e.g. [0,1])', 00818 'channelrange': 'channel range selection (e.g. [0,5000])', 00819 'average': 'data averaging (True,False) ', 00820 'scanaverage': 'average integs within scans (True,False) ', 00821 'timeaverage': 'average scans over time (True,False)', 00822 'tweight': 'weighting for time averaging', 00823 'averageall': 'set True only when averaging spectra with different spectral resolutions', 00824 'polaverage': 'average over polarizations (True,False)', 00825 'pweight': '', 00826 'tau': 'atmospheric optical depth for correction', 00827 'kernel': 'type of spectral smoothing', 00828 'kwidth': 'width of spectral kernel in channels', 00829 'chanwidth': 'width of regridded channels', 00830 'masklist': 'list or string of mask regions to INCLUDE in BASELINE fit', 00831 'maskmode': 'mode of setting additional channel masks for baselining', 00832 'thresh': 'S/N threshold for linefinder', 00833 'avg_limit': 'channel averaging for broad lines', 00834 'edge': 'channels to drop at beginning and end of spectrum', 00835 'blfunc': 'baseline model function', 00836 'order': 'order of baseline polynomial', 00837 'npiece': 'number of element polynomials of spline', 00838 'applyfft': 'automatically set wave numbers of sinusoids', 00839 'fftmethod': 'method for automatically set wave numbers of sinusoids', 00840 'fftthresh': 'threshold to select wave numbers of sinusoids', 00841 'addwn': 'additional wave numbers to use', 00842 'rejwn': 'wave numbers NOT to use', 00843 'clipthresh': 'clipping threshold for iterative fitting', 00844 'clipniter': 'maximum iteration number', 00845 'verifycal': 'verify the results of calibration', 00846 'verifysm': 'verify the results of smoothing [not available for kernel="regrid"]', 00847 'verifybl': 'verify the results of baseline fitting (only for blfunc="poly")', 00848 'verbosebl': 'output fitting results to logger', 00849 'bloutput': 'output fitting results to a text file', 00850 'blformat': 'format of the text file specified with bloutput', 00851 'showprogress': 'show progress status for large data', 00852 'minnrow': 'minimum number of input spectra to show progress status', 00853 'outfile': 'output file name', 00854 'outform': 'output file format (ASCII,MS,SDFITS,ASAP)', 00855 'overwrite': 'overwrite the output file if already exists', 00856 'plotlevel': 'plot results (0=none,1+=some,<0=hardcopy)', 00857 00858 'async': 'If true the taskname must be started using sdreduce(...)' 00859 } 00860 00861 # 00862 # Set subfields defaults if needed 00863 # 00864 00865 if(desc.has_key(key)) : 00866 return desc[key] 00867 00868 def itsdefault(self, paramname) : 00869 a = {} 00870 a['infile'] = '' 00871 a['antenna'] = 0 00872 a['fluxunit'] = '' 00873 a['telescopeparm'] = '' 00874 a['specunit'] = '' 00875 a['restfreq'] = '' 00876 a['frame'] = '' 00877 a['doppler'] = '' 00878 a['calmode'] = 'none' 00879 a['fraction'] = '10%' 00880 a['noff'] = -1 00881 a['width'] = 0.5 00882 a['elongated'] = False 00883 a['markonly'] = False 00884 a['plotpointings'] = False 00885 a['scanlist'] = [] 00886 a['field'] = '' 00887 a['iflist'] = [] 00888 a['pollist'] = [] 00889 a['channelrange'] = [] 00890 a['average'] = False 00891 a['scanaverage'] = False 00892 a['timeaverage'] = False 00893 a['tweight'] = 'none' 00894 a['averageall'] = False 00895 a['polaverage'] = False 00896 a['pweight'] = 'none' 00897 a['tau'] = 0.0 00898 a['kernel'] = 'none' 00899 a['kwidth'] = 5 00900 a['chanwidth'] = '5' 00901 a['masklist'] = [] 00902 a['maskmode'] = 'auto' 00903 a['thresh'] = 5.0 00904 a['avg_limit'] = 4 00905 a['edge'] = [0] 00906 a['blfunc'] = 'none' 00907 a['order'] = 5 00908 a['npiece'] = 2 00909 a['applyfft'] = True 00910 a['fftmethod'] = 'fft' 00911 a['fftthresh'] = 3.0 00912 a['addwn'] = [] 00913 a['rejwn'] = [] 00914 a['clipthresh'] = 3.0 00915 a['clipniter'] = 0 00916 a['verifycal'] = False 00917 a['verifysm'] = False 00918 a['verifybl'] = False 00919 a['verbosebl'] = True 00920 a['bloutput'] = True 00921 a['blformat'] = '' 00922 a['showprogress'] = True 00923 a['minnrow'] = 1000 00924 a['outfile'] = '' 00925 a['outform'] = 'ASAP' 00926 a['overwrite'] = False 00927 a['plotlevel'] = 0 00928 00929 #a = sys._getframe(len(inspect.stack())-1).f_globals 00930 00931 if self.parameters['fluxunit'] == 'K': 00932 a['telescopeparm'] = "" 00933 00934 if self.parameters['fluxunit'] == 'k': 00935 a['telescopeparm'] = "" 00936 00937 if self.parameters['fluxunit'] == 'Jy': 00938 a['telescopeparm'] = "" 00939 00940 if self.parameters['fluxunit'] == 'jy': 00941 a['telescopeparm'] = "" 00942 00943 if self.parameters['specunit'] == 'km/s': 00944 a['restfreq'] = '' 00945 00946 if self.parameters['average'] == True: 00947 a['scanaverage'] = False 00948 a['timeaverage'] = False 00949 a['tweight'] = 'none' 00950 a['averageall'] = False 00951 a['polaverage'] = False 00952 a['pweight'] = 'none' 00953 00954 if self.parameters['kernel'] == 'gaussian': 00955 a['kwidth'] = 5 00956 00957 if self.parameters['kernel'] == 'boxcar': 00958 a['kwidth'] = 5 00959 00960 if self.parameters['kernel'] == 'regrid': 00961 a['chanwidth'] = '5' 00962 00963 if self.parameters['maskmode'] == 'auto': 00964 a['thresh'] = 5.0 00965 a['avg_limit'] = 4 00966 a['edge'] = [0] 00967 00968 if self.parameters['blfunc'] == 'poly': 00969 a['order'] = 5 00970 00971 if self.parameters['blfunc'] == 'cspline': 00972 a['npiece'] = 2 00973 a['clipthresh'] = 3.0 00974 a['clipniter'] = 0 00975 00976 if self.parameters['blfunc'] == 'sinusoid': 00977 a['applyfft'] = True 00978 a['fftmethod'] = 'fft' 00979 a['fftthresh'] = 3.0 00980 a['addwn'] = [] 00981 a['rejwn'] = [] 00982 a['clipthresh'] = 3.0 00983 a['clipniter'] = 0 00984 00985 if self.parameters['showprogress'] == True: 00986 a['minnrow'] = 1000 00987 00988 if self.parameters['calmode'] == 'otf': 00989 a['fraction'] = '10%' 00990 a['width'] = 0.5 00991 a['elongated'] = False 00992 a['markonly'] = False 00993 a['plotpointings'] = False 00994 00995 if self.parameters['calmode'] == 'otfraster': 00996 a['fraction'] = '10%' 00997 a['noff'] = -1 00998 a['markonly'] = False 00999 a['plotpointings'] = False 01000 01001 if a.has_key(paramname) : 01002 return a[paramname] 01003 sdreduce_cli = sdreduce_cli_()
1.8.0
