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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_sdbaseline import sdbaseline 00018 class sdbaseline_cli_: 00019 __name__ = "sdbaseline" 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__ = (sdbaseline_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, 'scanlist':None, 'field':None, 'iflist':None, 'pollist':None, 'tau':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, 'verify':None, 'verbose':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, scanlist=None, field=None, iflist=None, pollist=None, tau=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, verify=None, verbose=None, bloutput=None, blformat=None, showprogress=None, minnrow=None, outfile=None, outform=None, overwrite=None, plotlevel=None, async=None): 00047 00048 """ASAP SD task: fit/subtract a spectral baseline 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 specunit -- units for spectral axis 00072 options: (str) 'channel','km/s','GHz','MHz','kHz','Hz','' 00073 default: '' (=current) 00074 example: this will be the units for masklist 00075 >>> specunit expandable parameters 00076 restfreq -- rest frequency 00077 available type includes float, int, string, list of float, 00078 list of int, list of string, and list of dictionary. the 00079 default unit of restfreq in case of float, int, or string 00080 without unit is Hz. string input can be a value only 00081 (treated as Hz) or a value followed by unit for which 'GHz', 00082 'MHz','kHz',and 'Hz' are available. 00083 a list can be used to set different rest frequencies for 00084 each IF. the length of list input must be nIF. dictionary 00085 input should be a pair of molecule name and frequency with 00086 keys of 'name' and 'value', respectively. values in the 00087 dictionary input follows the same manner as for single 00088 float or string input. 00089 example: 345.796 00090 '1420MHz' 00091 [345.8, 347.0, 356.7] 00092 ['345.8MHz', '347.0MHz', '356.7MHz'] 00093 [{'name':'CO','value':345}] 00094 frame -- frequency frame for spectral axis 00095 options: (str) 'LSRK','REST','TOPO','LSRD','BARY', 00096 'GEO','GALACTO','LGROUP','CMB' 00097 default: currently set frame in scantable 00098 WARNING: frame='REST' not yet implemented 00099 doppler -- doppler mode 00100 options: (str) 'RADIO','OPTICAL','Z','BETA','GAMMA' 00101 default: currently set doppler in scantable 00102 scanlist -- list of scan numbers to process 00103 default: [] (use all scans) 00104 example: [21,22,23,24] 00105 this selection is in addition to field, iflist, and pollist 00106 field -- selection string for selecting scans by name 00107 default: '' (no name selection) 00108 example: 'FLS3a*' 00109 this selection is in addition to scanlist, iflist, and pollist 00110 iflist -- list of IF id numbers to select 00111 default: [] (use all IFs) 00112 example: [15] 00113 this selection is in addition to scanlist, field, and pollist 00114 pollist -- list of polarization id numbers to select 00115 default: [] (use all polarizations) 00116 example: [1] 00117 this selection is in addition to scanlist, field, and iflist 00118 tau -- atmospheric optical depth 00119 default: 0.0 (no correction) 00120 masklist -- list or string of mask regions to INCLUDE in BASELINE fit 00121 a string masklist allows per IF selection of channels. 00122 default: [] (entire spectrum) 00123 example: [[1000,3000],[5000,7000]] 00124 '0:1000~3000;5000~7000, 1:200~350;450~600' 00125 when maskmode is 'auto' or 'interact', this mask 00126 will be applied first before fitting as base mask 00127 maskmode -- mode of setting additional channel masks 00128 options: (str) 'auto','list','interact' 00129 default: 'auto' 00130 example: maskmode='auto' runs linefinder to detect line regions 00131 to be excluded from fitting. this mode requires three 00132 expandable parameters: thresh, avg_limit, and edge. 00133 USE WITH CARE! May need to tweak the expandable parameters. 00134 maskmode='list' uses the given masklist only: no additional 00135 masks applied. 00136 maskmode='interact' allows users to manually modify the 00137 mask regions by dragging mouse on the spectrum plotter GUI. 00138 use LEFT or RIGHT button to add or delete regions, 00139 respectively. 00140 00141 >>> maskmode expandable parameters 00142 thresh -- S/N threshold for linefinder 00143 default: 5 00144 example: a single channel S/N ratio above which the channel is 00145 considered to be a detection 00146 avg_limit -- channel averaging for broad lines 00147 default: 4 00148 example: a number of consecutive channels not greater than 00149 this parameter can be averaged to search for broad lines 00150 edge -- channels to drop at beginning and end of spectrum 00151 default: 0 00152 example: [1000] drops 1000 channels at beginning AND end 00153 [1000,500] drops 1000 from beginning and 500 from end 00154 Note: For bad baselines threshold should be increased, 00155 and avg_limit decreased (or even switched off completely by 00156 setting this parameter to 1) to avoid detecting baseline 00157 undulations instead of real lines. 00158 blfunc -- baseline model function 00159 options: (str) 'poly','chebyshev','cspline','sinusoid' 00160 default: 'poly' 00161 example: blfunc='poly' uses a single polynomial line of 00162 any order which should be given as an expandable 00163 parameter 'order' to fit baseline. 00164 blfunc='chebyshev' uses Chebyshev polynomials. 00165 blfunc='cspline' uses a cubic spline function, a piecewise 00166 cubic polynomial having C2-continuity (i.e., the second 00167 derivative is continuous at the joining points). 00168 blfunc='sinusoid' uses a combination of sinusoidal curves. 00169 >>> blfunc expandable parameters 00170 order -- order of baseline polynomial 00171 options: (int) (<0 turns off baseline fitting) 00172 default: 5 00173 example: typically in range 2-9 (higher values 00174 seem to be needed for GBT) 00175 npiece -- number of the element polynomials of cubic spline curve 00176 options: (int) (<0 turns off baseline fitting) 00177 default: 2 00178 applyfft -- automatically set wave numbers of sinusoidal functions 00179 for fitting by applying some method like FFT. 00180 options: (bool) True, False 00181 default: True 00182 fftmethod -- method to be used when applyfft=True. Now only 00183 'fft' is available and it is the default. 00184 fftthresh -- threshold to select wave numbers to be used for 00185 sinusoidal fitting. both (float) and (str) accepted. 00186 given a float value, the unit is set to sigma. 00187 for string values, allowed formats include: 00188 'xsigma' or 'x' (= x-sigma level. e.g., '3sigma'), or 00189 'topx' (= the x strongest ones, e.g. 'top5'). 00190 default is 3.0 (unit: sigma). 00191 addwn -- additional wave number(s) of sinusoids to be used 00192 for fitting. 00193 (list) and (int) are accepted to specify every 00194 wave numbers. also (str) can be used in case 00195 you need to specify wave numbers in a certain range, 00196 e.g., 'a-b' (= a, a+1, a+2, ..., b-1, b), 00197 '<a' (= 0,1,...,a-2,a-1), 00198 '>=a' (= a, a+1, ... up to the maximum wave 00199 number corresponding to the Nyquist 00200 frequency for the case of FFT). 00201 default: [0] (i.e., constant is subtracted at least) 00202 rejwn -- wave number(s) of sinusoid NOT to be used for fitting. 00203 can be set just as addwn but has higher priority: 00204 wave numbers which are specified both in addwn 00205 and rejwn will NOT be used. 00206 default: [] 00207 clipthresh -- clipping threshold for iterative fitting 00208 default: 3 00209 clipniter -- maximum iteration number 00210 default: 0 (no iteration, i.e., no clipping) 00211 verify -- verify the results of baseline fitting 00212 options: (bool) True,False 00213 default: False 00214 NOTE: Currently available only when blfunc='poly' 00215 WARNING: Currently this just asks whether you accept 00216 the displayed fit and if not, continues 00217 without doing any baseline fit. 00218 verbose -- output fitting results to logger 00219 default: True 00220 example: If False, the fitting results including coefficients, 00221 residual rms, etc., are not output to the CASA logger, 00222 while the processing speed gets faster 00223 bloutput -- output fitting results to a text file 00224 default: True 00225 example: If False, the fitting results including coefficients, 00226 residual rms, etc., are not output to a text file 00227 (<outfile>_blparam.txt), while the processing 00228 speed gets faster 00229 blformat -- format of the logger output and text file specified with bloutput 00230 options: '', 'csv' 00231 default: '' (same as in the past, easy to read but huge) 00232 showprogress -- show progress status for large data 00233 default: True 00234 minnrow -- minimum number of input spectra to show progress status 00235 default: 1000 00236 outfile -- Name of output file 00237 default: '' (<infile>_bs) 00238 outform -- format of output file 00239 options: 'ASCII','SDFITS','MS','ASAP' 00240 default: 'ASAP' 00241 example: the ASAP format is easiest for further sd 00242 processing; use MS for CASA imaging. 00243 If ASCII, then will append some stuff to 00244 the outfile name 00245 overwrite -- overwrite the output file if already exists 00246 options: (bool) True,False 00247 default: False 00248 WARNING: if outform='ASCII', this parameter is ignored 00249 plotlevel -- control for plotting of results 00250 options: (int) 0=none, 1=some, 2=more, <0=hardcopy 00251 default: 0 (no plotting) 00252 example: plotlevel<0 as abs(plotlevel), e.g. 00253 -1 => hardcopy of final plot (will be named 00254 <outfile>_bspec.eps) 00255 WARNING: be careful plotting in fsotf mode! 00256 00257 00258 00259 DESCRIPTION: 00260 00261 Task sdbaseline performs baseline fitting/removal for single-dish spectra. 00262 The fit parameters, terms and rms of base-line are saved to an ascii 00263 file, '<outfile>_blparam.txt'. 00264 00265 ASAP recognizes the data of the "AT" telescopes, but currently 00266 does not know about the GBT or any other telescope. This task 00267 does know about GBT. Telescope name is obtained from the data. 00268 If you wish to change the fluxunit (see below), and telescopeparm='', 00269 for the AT telescopes it will use internal telescope parameters for 00270 flux conversion. For GBT, it will use an approximate aperture 00271 efficiency conversion. If you give telescopeparm a list , 00272 then if the list has a single float it is assumed to 00273 be the gain in Jy/K, if two or more elements they are assumed 00274 to be telescope diameter (m) and aperture efficiency 00275 respectively. 00276 00277 Note that sdbaseline assumes that the fluxunit is set correctly in 00278 the data already. If not, then set telescopeparm='FIX' and it 00279 will set the default units to fluxunit without conversion. 00280 NOTE: If the data in infile is an ms from GBT and the default flux 00281 unit is missing and this task automatically fixes the default fluxunit 00282 to 'K' before the conversion. 00283 00284 WARNING for the GBT raw SDFITS format data as input: 00285 SDtasks are able to handle GBT raw SDFITS format data since the 00286 data filler is available. However, the functionality is not well 00287 tested yet, so that there may be unknown bugs. 00288 00289 00290 """ 00291 if not hasattr(self, "__globals__") or self.__globals__ == None : 00292 self.__globals__=sys._getframe(len(inspect.stack())-1).f_globals 00293 #casac = self.__globals__['casac'] 00294 casalog = self.__globals__['casalog'] 00295 #casalog = casac.casac.logsink() 00296 self.__globals__['__last_task'] = 'sdbaseline' 00297 self.__globals__['taskname'] = 'sdbaseline' 00298 ### 00299 self.__globals__['update_params'](func=self.__globals__['taskname'],printtext=False,ipython_globals=self.__globals__) 00300 ### 00301 ### 00302 #Handle globals or user over-ride of arguments 00303 # 00304 function_signature_defaults=dict(zip(self.__call__.func_code.co_varnames,self.__call__.func_defaults)) 00305 useLocalDefaults = False 00306 00307 for item in function_signature_defaults.iteritems(): 00308 key,val = item 00309 keyVal = eval(key) 00310 if (keyVal == None): 00311 #user hasn't set it - use global/default 00312 pass 00313 else: 00314 #user has set it - use over-ride 00315 if (key != 'self') : 00316 useLocalDefaults = True 00317 00318 myparams = {} 00319 if useLocalDefaults : 00320 for item in function_signature_defaults.iteritems(): 00321 key,val = item 00322 keyVal = eval(key) 00323 exec('myparams[key] = keyVal') 00324 self.parameters[key] = keyVal 00325 if (keyVal == None): 00326 exec('myparams[key] = '+ key + ' = self.itsdefault(key)') 00327 keyVal = eval(key) 00328 if(type(keyVal) == dict) : 00329 if len(keyVal) > 0 : 00330 exec('myparams[key] = ' + key + ' = keyVal[len(keyVal)-1][\'value\']') 00331 else : 00332 exec('myparams[key] = ' + key + ' = {}') 00333 00334 else : 00335 async = self.parameters['async'] 00336 myparams['infile'] = infile = self.parameters['infile'] 00337 myparams['antenna'] = antenna = self.parameters['antenna'] 00338 myparams['fluxunit'] = fluxunit = self.parameters['fluxunit'] 00339 myparams['telescopeparm'] = telescopeparm = self.parameters['telescopeparm'] 00340 myparams['specunit'] = specunit = self.parameters['specunit'] 00341 myparams['restfreq'] = restfreq = self.parameters['restfreq'] 00342 myparams['frame'] = frame = self.parameters['frame'] 00343 myparams['doppler'] = doppler = self.parameters['doppler'] 00344 myparams['scanlist'] = scanlist = self.parameters['scanlist'] 00345 myparams['field'] = field = self.parameters['field'] 00346 myparams['iflist'] = iflist = self.parameters['iflist'] 00347 myparams['pollist'] = pollist = self.parameters['pollist'] 00348 myparams['tau'] = tau = self.parameters['tau'] 00349 myparams['masklist'] = masklist = self.parameters['masklist'] 00350 myparams['maskmode'] = maskmode = self.parameters['maskmode'] 00351 myparams['thresh'] = thresh = self.parameters['thresh'] 00352 myparams['avg_limit'] = avg_limit = self.parameters['avg_limit'] 00353 myparams['edge'] = edge = self.parameters['edge'] 00354 myparams['blfunc'] = blfunc = self.parameters['blfunc'] 00355 myparams['order'] = order = self.parameters['order'] 00356 myparams['npiece'] = npiece = self.parameters['npiece'] 00357 myparams['applyfft'] = applyfft = self.parameters['applyfft'] 00358 myparams['fftmethod'] = fftmethod = self.parameters['fftmethod'] 00359 myparams['fftthresh'] = fftthresh = self.parameters['fftthresh'] 00360 myparams['addwn'] = addwn = self.parameters['addwn'] 00361 myparams['rejwn'] = rejwn = self.parameters['rejwn'] 00362 myparams['clipthresh'] = clipthresh = self.parameters['clipthresh'] 00363 myparams['clipniter'] = clipniter = self.parameters['clipniter'] 00364 myparams['verify'] = verify = self.parameters['verify'] 00365 myparams['verbose'] = verbose = self.parameters['verbose'] 00366 myparams['bloutput'] = bloutput = self.parameters['bloutput'] 00367 myparams['blformat'] = blformat = self.parameters['blformat'] 00368 myparams['showprogress'] = showprogress = self.parameters['showprogress'] 00369 myparams['minnrow'] = minnrow = self.parameters['minnrow'] 00370 myparams['outfile'] = outfile = self.parameters['outfile'] 00371 myparams['outform'] = outform = self.parameters['outform'] 00372 myparams['overwrite'] = overwrite = self.parameters['overwrite'] 00373 myparams['plotlevel'] = plotlevel = self.parameters['plotlevel'] 00374 00375 if type(scanlist)==int: scanlist=[scanlist] 00376 if type(iflist)==int: iflist=[iflist] 00377 if type(pollist)==int: pollist=[pollist] 00378 if type(edge)==int: edge=[edge] 00379 00380 result = None 00381 00382 # 00383 # The following is work around to avoid a bug with current python translation 00384 # 00385 mytmp = {} 00386 00387 mytmp['infile'] = infile 00388 mytmp['antenna'] = antenna 00389 mytmp['fluxunit'] = fluxunit 00390 mytmp['telescopeparm'] = telescopeparm 00391 mytmp['specunit'] = specunit 00392 mytmp['restfreq'] = restfreq 00393 mytmp['frame'] = frame 00394 mytmp['doppler'] = doppler 00395 mytmp['scanlist'] = scanlist 00396 mytmp['field'] = field 00397 mytmp['iflist'] = iflist 00398 mytmp['pollist'] = pollist 00399 mytmp['tau'] = tau 00400 mytmp['masklist'] = masklist 00401 mytmp['maskmode'] = maskmode 00402 mytmp['thresh'] = thresh 00403 mytmp['avg_limit'] = avg_limit 00404 mytmp['edge'] = edge 00405 mytmp['blfunc'] = blfunc 00406 mytmp['order'] = order 00407 mytmp['npiece'] = npiece 00408 mytmp['applyfft'] = applyfft 00409 mytmp['fftmethod'] = fftmethod 00410 mytmp['fftthresh'] = fftthresh 00411 mytmp['addwn'] = addwn 00412 mytmp['rejwn'] = rejwn 00413 mytmp['clipthresh'] = clipthresh 00414 mytmp['clipniter'] = clipniter 00415 mytmp['verify'] = verify 00416 mytmp['verbose'] = verbose 00417 mytmp['bloutput'] = bloutput 00418 mytmp['blformat'] = blformat 00419 mytmp['showprogress'] = showprogress 00420 mytmp['minnrow'] = minnrow 00421 mytmp['outfile'] = outfile 00422 mytmp['outform'] = outform 00423 mytmp['overwrite'] = overwrite 00424 mytmp['plotlevel'] = plotlevel 00425 pathname='file:///'+os.environ.get('CASAPATH').split()[0]+'/share/xml/' 00426 trec = casac.casac.utils().torecord(pathname+'sdbaseline.xml') 00427 00428 casalog.origin('sdbaseline') 00429 try : 00430 #if not trec.has_key('sdbaseline') or not casac.casac.utils().verify(mytmp, trec['sdbaseline']) : 00431 #return False 00432 00433 casac.casac.utils().verify(mytmp, trec['sdbaseline'], True) 00434 scriptstr=[''] 00435 saveinputs = self.__globals__['saveinputs'] 00436 saveinputs('sdbaseline', 'sdbaseline.last', myparams, self.__globals__,scriptstr=scriptstr) 00437 if async : 00438 count = 0 00439 keybase = time.strftime("%y%m%d.%H%M%S") 00440 key = keybase + "_" + str(count) 00441 while self.__async__.has_key(key) : 00442 count += 1 00443 key = keybase + "_" + str(count) 00444 result = tm.execute('sdbaseline', infile, antenna, fluxunit, telescopeparm, specunit, restfreq, frame, doppler, scanlist, field, iflist, pollist, tau, masklist, maskmode, thresh, avg_limit, edge, blfunc, order, npiece, applyfft, fftmethod, fftthresh, addwn, rejwn, clipthresh, clipniter, verify, verbose, bloutput, blformat, showprogress, minnrow, outfile, outform, overwrite, plotlevel) 00445 print "Use: " 00446 print " tm.retrieve(return_value) # to retrieve the status" 00447 print 00448 self.rkey = key 00449 self.__async__[key] = result 00450 else : 00451 tname = 'sdbaseline' 00452 spaces = ' '*(18-len(tname)) 00453 casalog.post('\n##########################################'+ 00454 '\n##### Begin Task: ' + tname + spaces + ' #####') 00455 casalog.post(scriptstr[1][1:]+'\n', 'INFO') 00456 result = sdbaseline(infile, antenna, fluxunit, telescopeparm, specunit, restfreq, frame, doppler, scanlist, field, iflist, pollist, tau, masklist, maskmode, thresh, avg_limit, edge, blfunc, order, npiece, applyfft, fftmethod, fftthresh, addwn, rejwn, clipthresh, clipniter, verify, verbose, bloutput, blformat, showprogress, minnrow, outfile, outform, overwrite, plotlevel) 00457 casalog.post('##### End Task: ' + tname + ' ' + spaces + ' #####'+ 00458 '\n##########################################') 00459 00460 except Exception, instance: 00461 if(self.__globals__.has_key('__rethrow_casa_exceptions') and self.__globals__['__rethrow_casa_exceptions']) : 00462 raise 00463 else : 00464 #print '**** Error **** ',instance 00465 tname = 'sdbaseline' 00466 casalog.post('An error occurred running task '+tname+'.', 'ERROR') 00467 pass 00468 00469 gc.collect() 00470 return result 00471 # 00472 # 00473 # 00474 def paramgui(self, useGlobals=True, ipython_globals=None): 00475 """ 00476 Opens a parameter GUI for this task. If useGlobals is true, then any relevant global parameter settings are used. 00477 """ 00478 import paramgui 00479 if not hasattr(self, "__globals__") or self.__globals__ == None : 00480 self.__globals__=sys._getframe(len(inspect.stack())-1).f_globals 00481 00482 if useGlobals: 00483 if ipython_globals == None: 00484 myf=self.__globals__ 00485 else: 00486 myf=ipython_globals 00487 00488 paramgui.setGlobals(myf) 00489 else: 00490 paramgui.setGlobals({}) 00491 00492 paramgui.runTask('sdbaseline', myf['_ip']) 00493 paramgui.setGlobals({}) 00494 00495 # 00496 # 00497 # 00498 def defaults(self, param=None, ipython_globals=None, paramvalue=None, subparam=None): 00499 if not hasattr(self, "__globals__") or self.__globals__ == None : 00500 self.__globals__=sys._getframe(len(inspect.stack())-1).f_globals 00501 if ipython_globals == None: 00502 myf=self.__globals__ 00503 else: 00504 myf=ipython_globals 00505 00506 a = odict() 00507 a['infile'] = '' 00508 a['antenna'] = 0 00509 a['fluxunit'] = '' 00510 a['specunit'] = '' 00511 a['frame'] = '' 00512 a['doppler'] = '' 00513 a['scanlist'] = [] 00514 a['field'] = '' 00515 a['iflist'] = [] 00516 a['pollist'] = [] 00517 a['tau'] = 0.0 00518 a['masklist'] = [] 00519 a['maskmode'] = '' 00520 a['blfunc'] = 'poly' 00521 a['verify'] = False 00522 a['verbose'] = True 00523 a['bloutput'] = True 00524 a['blformat'] = '' 00525 a['showprogress'] = True 00526 a['outfile'] = '' 00527 a['outform'] = 'ASAP' 00528 a['overwrite'] = False 00529 a['plotlevel'] = 0 00530 00531 a['async']=False 00532 a['fluxunit'] = { 00533 0:{'value':''}, 00534 1:odict([{'value':'K'}, {'telescopeparm':''}]), 00535 2:odict([{'value':'k'}, {'telescopeparm':''}]), 00536 3:odict([{'value':'Jy'}, {'telescopeparm':''}]), 00537 4:odict([{'value':'jy'}, {'telescopeparm':''}])} 00538 a['specunit'] = { 00539 0:{'value':''}, 00540 1:{'value':'channel'}, 00541 2:{'value':'GHz'}, 00542 3:{'value':'MHz'}, 00543 4:{'value':'kHz'}, 00544 5:{'value':'Hz'}, 00545 6:odict([{'value':'km/s'}, {'restfreq':''}])} 00546 a['maskmode'] = { 00547 0:odict([{'value':'auto'}, {'thresh':5.0}, {'avg_limit':4}, {'edge':[0]}]), 00548 1:{'value':'list'}, 00549 2:{'value':'interact'}} 00550 a['blfunc'] = { 00551 0:odict([{'value':'poly'}, {'order':5}]), 00552 1:odict([{'value':'chebyshev'}, {'order':5}, {'clipthresh':3.0}, {'clipniter':0}]), 00553 2:odict([{'value':'cspline'}, {'npiece':2}, {'clipthresh':3.0}, {'clipniter':0}]), 00554 3:odict([{'value':'sinusoid'}, {'applyfft':True}, {'fftmethod':'fft'}, {'fftthresh':3.0}, {'addwn':[0]}, {'rejwn':[]}, {'clipthresh':3.0}, {'clipniter':0}])} 00555 a['showprogress'] = { 00556 0:odict([{'value':True}, {'minnrow':1000}])} 00557 00558 ### This function sets the default values but also will return the list of 00559 ### parameters or the default value of a given parameter 00560 if(param == None): 00561 myf['__set_default_parameters'](a) 00562 elif(param == 'paramkeys'): 00563 return a.keys() 00564 else: 00565 if(paramvalue==None and subparam==None): 00566 if(a.has_key(param)): 00567 return a[param] 00568 else: 00569 return self.itsdefault(param) 00570 else: 00571 retval=a[param] 00572 if(type(a[param])==dict): 00573 for k in range(len(a[param])): 00574 valornotval='value' 00575 if(a[param][k].has_key('notvalue')): 00576 valornotval='notvalue' 00577 if((a[param][k][valornotval])==paramvalue): 00578 retval=a[param][k].copy() 00579 retval.pop(valornotval) 00580 if(subparam != None): 00581 if(retval.has_key(subparam)): 00582 retval=retval[subparam] 00583 else: 00584 retval=self.itsdefault(subparam) 00585 else: 00586 retval=self.itsdefault(subparam) 00587 return retval 00588 00589 00590 # 00591 # 00592 def check_params(self, param=None, value=None, ipython_globals=None): 00593 if ipython_globals == None: 00594 myf=self.__globals__ 00595 else: 00596 myf=ipython_globals 00597 # print 'param:', param, 'value:', value 00598 try : 00599 if str(type(value)) != "<type 'instance'>" : 00600 value0 = value 00601 value = myf['cu'].expandparam(param, value) 00602 matchtype = False 00603 if(type(value) == numpy.ndarray): 00604 if(type(value) == type(value0)): 00605 myf[param] = value.tolist() 00606 else: 00607 #print 'value:', value, 'value0:', value0 00608 #print 'type(value):', type(value), 'type(value0):', type(value0) 00609 myf[param] = value0 00610 if type(value0) != list : 00611 matchtype = True 00612 else : 00613 myf[param] = value 00614 value = myf['cu'].verifyparam({param:value}) 00615 if matchtype: 00616 value = False 00617 except Exception, instance: 00618 #ignore the exception and just return it unchecked 00619 myf[param] = value 00620 return value 00621 # 00622 # 00623 def description(self, key='sdbaseline', subkey=None): 00624 desc={'sdbaseline': 'ASAP SD task: fit/subtract a spectral baseline ', 00625 'infile': 'name of input SD dataset', 00626 'antenna': 'antenna name or id (only effective for MS input)', 00627 'fluxunit': 'units for line flux (K,Jy) (''=current)', 00628 'telescopeparm': 'param of telescope for flux conversion', 00629 'specunit': 'units for spectral axis (channel,km/s,GHz)', 00630 'restfreq': 'rest frequency (default unit: Hz)', 00631 'frame': 'frequency reference frame, e.g. LSRK (''=current)', 00632 'doppler': 'doppler convention, e.g. RADIO (''=current)', 00633 'scanlist': 'list of scans to use (e.g. [1,2,3,4])', 00634 'field': 'string for selection by source name', 00635 'iflist': 'list of IF ids to select (e.g. [0,1])', 00636 'pollist': 'list of polarization ids to select (e.g. [0,1])', 00637 'tau': 'atmospheric optical depth for correction', 00638 'masklist': 'list or string of mask regions to INCLUDE in BASELINE fit', 00639 'maskmode': 'mode of setting additional channel masks', 00640 'thresh': 'S/N threshold for linefinder', 00641 'avg_limit': 'channel averaging for broad lines', 00642 'edge': 'channels to drop at beginning and end of spectrum', 00643 'blfunc': 'baseline model function', 00644 'order': 'order of baseline polynomial', 00645 'npiece': 'number of element polynomials of spline', 00646 'applyfft': 'automatically set wave numbers of sinusoids', 00647 'fftmethod': 'method for automatically set wave numbers of sinusoids', 00648 'fftthresh': 'threshold to select wave numbers of sinusoids', 00649 'addwn': 'additional wave numbers to use', 00650 'rejwn': 'wave numbers NOT to use', 00651 'clipthresh': 'clipping threshold for iterative fitting', 00652 'clipniter': 'maximum iteration number', 00653 'verify': 'verify the results of baseline fitting (only for blfunc="poly")', 00654 'verbose': 'output fitting results to logger', 00655 'bloutput': 'output fitting results to a text file', 00656 'blformat': 'format of the text file specified with bloutput', 00657 'showprogress': 'show progress status for large data', 00658 'minnrow': 'minimum number of input spectra to show progress status', 00659 'outfile': 'output file name', 00660 'outform': 'output file format (ASCII,MS,SDFITS,ASAP)', 00661 'overwrite': 'overwrite the output file if already exists', 00662 'plotlevel': 'plot results (0=none,1+=some,<0=hardcopy)', 00663 00664 'async': 'If true the taskname must be started using sdbaseline(...)' 00665 } 00666 00667 # 00668 # Set subfields defaults if needed 00669 # 00670 00671 if(desc.has_key(key)) : 00672 return desc[key] 00673 00674 def itsdefault(self, paramname) : 00675 a = {} 00676 a['infile'] = '' 00677 a['antenna'] = 0 00678 a['fluxunit'] = '' 00679 a['telescopeparm'] = '' 00680 a['specunit'] = '' 00681 a['restfreq'] = '' 00682 a['frame'] = '' 00683 a['doppler'] = '' 00684 a['scanlist'] = [] 00685 a['field'] = '' 00686 a['iflist'] = [] 00687 a['pollist'] = [] 00688 a['tau'] = 0.0 00689 a['masklist'] = [] 00690 a['maskmode'] = '' 00691 a['thresh'] = 5.0 00692 a['avg_limit'] = 4 00693 a['edge'] = [0] 00694 a['blfunc'] = 'poly' 00695 a['order'] = 5 00696 a['npiece'] = 2 00697 a['applyfft'] = True 00698 a['fftmethod'] = 'fft' 00699 a['fftthresh'] = 3.0 00700 a['addwn'] = [0] 00701 a['rejwn'] = [] 00702 a['clipthresh'] = 3.0 00703 a['clipniter'] = 0 00704 a['verify'] = False 00705 a['verbose'] = True 00706 a['bloutput'] = True 00707 a['blformat'] = '' 00708 a['showprogress'] = True 00709 a['minnrow'] = 1000 00710 a['outfile'] = '' 00711 a['outform'] = 'ASAP' 00712 a['overwrite'] = False 00713 a['plotlevel'] = 0 00714 00715 #a = sys._getframe(len(inspect.stack())-1).f_globals 00716 00717 if self.parameters['fluxunit'] == 'K': 00718 a['telescopeparm'] = '' 00719 00720 if self.parameters['fluxunit'] == 'k': 00721 a['telescopeparm'] = '' 00722 00723 if self.parameters['fluxunit'] == 'Jy': 00724 a['telescopeparm'] = '' 00725 00726 if self.parameters['fluxunit'] == 'jy': 00727 a['telescopeparm'] = '' 00728 00729 if self.parameters['specunit'] == 'km/s': 00730 a['restfreq'] = '' 00731 00732 if self.parameters['maskmode'] == 'auto': 00733 a['thresh'] = 5.0 00734 a['avg_limit'] = 4 00735 a['edge'] = [0] 00736 00737 if self.parameters['blfunc'] == 'poly': 00738 a['order'] = 5 00739 00740 if self.parameters['blfunc'] == 'chebyshev': 00741 a['order'] = 5 00742 a['clipthresh'] = 3.0 00743 a['clipniter'] = 0 00744 00745 if self.parameters['blfunc'] == 'cspline': 00746 a['npiece'] = 2 00747 a['clipthresh'] = 3.0 00748 a['clipniter'] = 0 00749 00750 if self.parameters['blfunc'] == 'sinusoid': 00751 a['applyfft'] = True 00752 a['fftmethod'] = 'fft' 00753 a['fftthresh'] = 3.0 00754 a['addwn'] = [0] 00755 a['rejwn'] = [] 00756 a['clipthresh'] = 3.0 00757 a['clipniter'] = 0 00758 00759 if self.parameters['showprogress'] == True: 00760 a['minnrow'] = 1000 00761 00762 if a.has_key(paramname) : 00763 return a[paramname] 00764 sdbaseline_cli = sdbaseline_cli_()
1.8.0
