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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 string 00010 import time 00011 import inspect 00012 import gc 00013 import numpy 00014 from odict import odict 00015 from task_sdfit import sdfit 00016 from task_sdfit import casalog 00017 00018 class sdfit_pg_: 00019 __name__ = "sdfit" 00020 00021 def __init__(self) : 00022 self.__bases__ = (sdfit_pg_,) 00023 self.__doc__ = self.__call__.__doc__ 00024 00025 00026 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, fitfunc=None, fitmode=None, maskline=None, invertmask=None, nfit=None, thresh=None, min_nchan=None, avg_limit=None, box_size=None, edge=None, outfile=None, overwrite=None, plotlevel=None, async=None): 00027 00028 """ASAP SD task: fit a spectral line 00029 Keyword arguments: 00030 infile -- name of input SD dataset 00031 default: none - must input file name 00032 example: 'mysd.asap' 00033 See sdcal for allowed formats. 00034 antenna -- antenna name or id (only effective for MS input). 00035 fluxunit -- units for line flux 00036 options: (str) 'K','Jy','' 00037 default: '' (keep current fluxunit) 00038 WARNING: For GBT data, see description below. 00039 >>> fluxunit expandable parameter 00040 telescopeparm -- the telescope characteristics 00041 options: (str) name or (list) list of gain info 00042 default: '' (none set) 00043 example: if telescopeparm='', it tries to get the telescope 00044 name from the data. 00045 Full antenna parameters (diameter,ap.eff.) known 00046 to ASAP are 00047 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', 'DSS-43', 00048 'CEDUNA','HOBART'. For GBT, it fixes default fluxunit 00049 to 'K' first then convert to a new fluxunit. 00050 telescopeparm=[104.9,0.43] diameter(m), ap.eff. 00051 telescopeparm=[0.743] gain in Jy/K 00052 telescopeparm='FIX' to change default fluxunit 00053 see description below 00054 00055 specunit -- units for spectral axis 00056 options: (str) 'channel','km/s','GHz','MHz','kHz','Hz','' 00057 default: '' (=current) 00058 example: this will be the units for maskline 00059 >>> specunit expandable parameters 00060 restfreq -- rest frequency 00061 available type includes float, int, string, list of float, 00062 list of int, list of string, and list of dictionary. the 00063 default unit of restfreq in case of float, int, or string 00064 without unit is Hz. string input can be a value only 00065 (treated as Hz) or a value followed by unit for which 'GHz', 00066 'MHz','kHz',and 'Hz' are available. 00067 a list can be used to set different rest frequencies for 00068 each IF. the length of list input must be nIF. dictionary 00069 input should be a pair of molecule name and frequency with 00070 keys of 'name' and 'value', respectively. values in the 00071 dictionary input follows the same manner as for single 00072 float or string input. 00073 example: 345.796 00074 '1420MHz' 00075 [345.8, 347.0, 356.7] 00076 ['345.8MHz', '347.0MHz', '356.7MHz'] 00077 [{'name':'CO','value':345}] 00078 frame -- frequency frame for spectral axis 00079 options: (str) 'LSRK','REST','TOPO','LSRD','BARY', 00080 'GEO','GALACTO','LGROUP','CMB' 00081 default: currently set frame in scantable 00082 WARNING: frame='REST' not yet implemented 00083 doppler -- doppler mode 00084 options: (str) 'RADIO','OPTICAL','Z','BETA','GAMMA' 00085 default: currently set doppler in scantable 00086 scanlist -- list of scan numbers to process 00087 default: [] (use all scans) 00088 example: [21,22,23,24] 00089 field -- selection string for selecting scans by name 00090 default: '' (no name selection) 00091 example: 'FLS3a*' 00092 this selection is in addition to scanlist and iflist 00093 iflist -- list of IF id numbers to select 00094 default: [] (use all IFs) 00095 example: [15] 00096 pollist -- list of polarization id numbers to select 00097 default: [] (use all polarizations) 00098 example: [1] 00099 fitfunc -- function for fitting 00100 options: (str) 'gauss','lorentz' 00101 default: 'gauss' 00102 fitmode -- mode for fitting 00103 options: (str) 'list','auto','interact' 00104 default: 'auto' 00105 example: 'list' will use maskline to define regions to 00106 fit for lines with nfit in each 00107 'auto' will use the linefinder to fit for lines 00108 using the following parameters 00109 'interact' allows adding and deleting mask 00110 regions by drawing rectangles on the plot 00111 with mouse. Draw a rectangle with LEFT-mouse 00112 to ADD the region to the mask and with RIGHT-mouse 00113 to DELETE the region. 00114 00115 >>> fitmode expandable parameters 00116 thresh -- S/N threshold for linefinder 00117 default: 5 00118 example: a single channel S/N ratio above which the channel is 00119 considered to be a detection 00120 min_nchan -- minimum number of consecutive channels for linefinder 00121 default: 3 00122 example: minimum number of consecutive channels required to pass threshold 00123 avg_limit -- channel averaging for broad lines 00124 default: 4 00125 example: a number of consecutive channels not greater than 00126 this parameter can be averaged to search for broad lines 00127 box_size -- running mean box size 00128 default: 0.2 00129 example: a running mean box size specified as a fraction 00130 of the total spectrum length 00131 edge -- channels to drop at beginning and end of spectrum 00132 default: 0 00133 example: [1000] drops 1000 channels at beginning AND end 00134 [1000,500] drops 1000 from beginning and 500 from end 00135 00136 Note: For bad baselines threshold should be increased, 00137 and avg_limit decreased (or even switched off completely by 00138 setting this parameter to 1) to avoid detecting baseline 00139 undulations instead of real lines. 00140 00141 maskline -- list of mask regions to INCLUDE in LINE fitting 00142 default: all 00143 example: maskline=[[3900,4300]] for a single region, or 00144 maskline=[[3900,4300],[5000,5400]] for two, etc. 00145 invertmask -- invert mask (EXCLUDE masklist instead) 00146 options: (bool) True, False 00147 default: False 00148 example: invertmask=True, then will make one region that is 00149 the exclusion of the maskline regions 00150 nfit -- list of number of gaussian/lorentzian lines to fit in in maskline region (ignored when fitmode='auto') 00151 default: 0 (no fitting) 00152 example: nfit=[1] for single line in single region, 00153 nfit=[2] for two lines in single region, 00154 nfit=[1,1] for single lines in each of two regions, etc. 00155 outfile -- name of output file for fit results 00156 default: no output fit file 00157 example: 'mysd.fit' 00158 overwrite -- overwrite the outfile if already exists 00159 options: (bool) True, False 00160 default: False 00161 plotlevel -- control for plotting of results 00162 options: (int) 0=none, 1=some, 2=more 00163 default: 0 (no plotting) 00164 example: plotlevel=1 plots fit 00165 plotlevel=2 plots fit and residual 00166 no hardcopy available for fitter 00167 WARNING: be careful plotting OTF data with lots of fields 00168 00169 ------------------------------------------------------------------- 00170 Returns a Python dictionary of line statistics 00171 keys: 'peak','cent','fwhm','nfit' 00172 example: each value is a list of lists with one list of 00173 2 entries [fitvalue,error] per component. 00174 e.g. xstat['peak']=[[234.9, 4.8],[234.2, 5.3]] 00175 for 2 components. 00176 00177 00178 DESCRIPTION: 00179 00180 Task sdfit is a basic line-fitter for single-dish spectra. 00181 It assumes that the spectra have been calibrated in sdcal 00182 or sdreduce. 00183 00184 Furthermore, it assumes that any selection of scans, IFs, 00185 polarizations, and time and channel averaging/smoothing has 00186 also already been done (in other sd tasks) as there are no controls 00187 for these. Note that you can use sdsave to do selection, writing 00188 out a new scantable. 00189 00190 Note that multiple scans, IFs, and polarizations can in principle 00191 be handled, but we recommend that you use scanlist, field, iflist, 00192 and pollist to give a single selection for each fit. 00193 00194 Currently, you can choose Gaussian or Lorentzian profile as a 00195 fitting model. 00196 00197 For complicated spectra, sdfit does not do a good job of 00198 "auto-guessing" the starting model for the fit. We recommend 00199 you use sd.fitter in the toolkit which has more options, such 00200 as fixing components in the fit and supplying starting guesses 00201 by hand. 00202 00203 WARNING: sdfit will currently return the fit for the first 00204 row in the scantable. 00205 00206 ASAP recognizes the data of the "AT" telescopes, but currently 00207 does not know about the GBT or any other telescope. This task 00208 does know about GBT. Telescope name is obtained from the data. 00209 If you wish to change the fluxunit (see below), and telescopeparm='', 00210 for the AT telescopes it will use internal telescope parameters for 00211 flux conversion. For GBT, it will use an approximate aperture 00212 efficiency conversion. If you give telescopeparm a list, then 00213 if the list has a single float it is assumed to be the gain in Jy/K, 00214 if two or more elements they are assumed to be telescope diameter (m) 00215 and aperture efficiency respectively. 00216 00217 WARNING for the GBT raw SDFITS format data as input: 00218 SDtasks are able to handle GBT raw SDFITS format data since the 00219 data filler is available. However, the functionality is not well 00220 tested yet, so that there may be unknown bugs. 00221 00222 00223 """ 00224 a=inspect.stack() 00225 stacklevel=0 00226 for k in range(len(a)): 00227 if (string.find(a[k][1], 'ipython console') > 0) or (string.find(a[k][1], '<string>') >= 0): 00228 stacklevel=k 00229 break 00230 myf=sys._getframe(stacklevel).f_globals 00231 myf['__last_task'] = 'sdfit' 00232 myf['taskname'] = 'sdfit' 00233 ### 00234 myf['update_params'](func=myf['taskname'],printtext=False) 00235 ### 00236 ### 00237 #Handle globals or user over-ride of arguments 00238 # 00239 function_signature_defaults=dict(zip(self.__call__.func_code.co_varnames,self.__call__.func_defaults)) 00240 useLocalDefaults = False 00241 00242 for item in function_signature_defaults.iteritems(): 00243 key,val = item 00244 keyVal = eval(key) 00245 if (keyVal == None): 00246 #user hasn't set it - use global/default 00247 pass 00248 else: 00249 #user has set it - use over-ride 00250 if (key != 'self') : 00251 useLocalDefaults = True 00252 #myf[key]=keyVal 00253 00254 myparams = {} 00255 if useLocalDefaults : 00256 for item in function_signature_defaults.iteritems(): 00257 key,val = item 00258 keyVal = eval(key) 00259 exec('myparams[key] = keyVal') 00260 if (keyVal == None): 00261 exec('myparams[key] = '+ key + ' = self.itsdefault(key)') 00262 keyVal = eval(key) 00263 if(type(keyVal) == dict) : 00264 exec('myparams[key] = ' + key + ' = keyVal[len(keyVal)-1][\'value\']') 00265 00266 else : 00267 uselessvariable = None 00268 myparams['infile'] = infile = myf['infile'] 00269 myparams['antenna'] = antenna = myf['antenna'] 00270 myparams['fluxunit'] = fluxunit = myf['fluxunit'] 00271 myparams['telescopeparm'] = telescopeparm = myf['telescopeparm'] 00272 myparams['specunit'] = specunit = myf['specunit'] 00273 myparams['restfreq'] = restfreq = myf['restfreq'] 00274 myparams['frame'] = frame = myf['frame'] 00275 myparams['doppler'] = doppler = myf['doppler'] 00276 myparams['scanlist'] = scanlist = myf['scanlist'] 00277 myparams['field'] = field = myf['field'] 00278 myparams['iflist'] = iflist = myf['iflist'] 00279 myparams['pollist'] = pollist = myf['pollist'] 00280 myparams['fitfunc'] = fitfunc = myf['fitfunc'] 00281 myparams['fitmode'] = fitmode = myf['fitmode'] 00282 myparams['maskline'] = maskline = myf['maskline'] 00283 myparams['invertmask'] = invertmask = myf['invertmask'] 00284 myparams['nfit'] = nfit = myf['nfit'] 00285 myparams['thresh'] = thresh = myf['thresh'] 00286 myparams['min_nchan'] = min_nchan = myf['min_nchan'] 00287 myparams['avg_limit'] = avg_limit = myf['avg_limit'] 00288 myparams['box_size'] = box_size = myf['box_size'] 00289 myparams['edge'] = edge = myf['edge'] 00290 myparams['outfile'] = outfile = myf['outfile'] 00291 myparams['overwrite'] = overwrite = myf['overwrite'] 00292 myparams['plotlevel'] = plotlevel = myf['plotlevel'] 00293 00294 if type(scanlist)==int: scanlist=[scanlist] 00295 if type(iflist)==int: iflist=[iflist] 00296 if type(pollist)==int: pollist=[pollist] 00297 if type(nfit)==int: nfit=[nfit] 00298 if type(edge)==int: edge=[edge] 00299 00300 result = None 00301 00302 # 00303 # The following is work around to avoid a bug with current python translation 00304 # 00305 mytmp = {} 00306 00307 mytmp['infile'] = infile 00308 mytmp['antenna'] = antenna 00309 mytmp['fluxunit'] = fluxunit 00310 mytmp['telescopeparm'] = telescopeparm 00311 mytmp['specunit'] = specunit 00312 mytmp['restfreq'] = restfreq 00313 mytmp['frame'] = frame 00314 mytmp['doppler'] = doppler 00315 mytmp['scanlist'] = scanlist 00316 mytmp['field'] = field 00317 mytmp['iflist'] = iflist 00318 mytmp['pollist'] = pollist 00319 mytmp['fitfunc'] = fitfunc 00320 mytmp['fitmode'] = fitmode 00321 mytmp['maskline'] = maskline 00322 mytmp['invertmask'] = invertmask 00323 mytmp['nfit'] = nfit 00324 mytmp['thresh'] = thresh 00325 mytmp['min_nchan'] = min_nchan 00326 mytmp['avg_limit'] = avg_limit 00327 mytmp['box_size'] = box_size 00328 mytmp['edge'] = edge 00329 mytmp['outfile'] = outfile 00330 mytmp['overwrite'] = overwrite 00331 mytmp['plotlevel'] = plotlevel 00332 pathname='file:///'+os.environ.get('CASAPATH').split()[0]+'/share/xml/' 00333 trec = casac.utils().torecord(pathname+'sdfit.xml') 00334 00335 casalog.origin('sdfit') 00336 if not trec.has_key('sdfit') or not casac.utils().verify(mytmp, trec['sdfit']) : 00337 return False 00338 00339 00340 try : 00341 casalog.post('') 00342 casalog.post('##########################################') 00343 casalog.post('##### Begin Task: sdfit #####') 00344 casalog.post('') 00345 result = sdfit(infile, antenna, fluxunit, telescopeparm, specunit, restfreq, frame, doppler, scanlist, field, iflist, pollist, fitfunc, fitmode, maskline, invertmask, nfit, thresh, min_nchan, avg_limit, box_size, edge, outfile, overwrite, plotlevel) 00346 casalog.post('') 00347 casalog.post('##### End Task: sdfit #####') 00348 casalog.post('##########################################') 00349 00350 00351 # saveinputs for individule engine has no use 00352 # saveinputs should alos be removed from casa_in_py.py 00353 # 00354 # 00355 # saveinputs = myf['saveinputs'] 00356 # saveinputs('sdfit', 'sdfit.last', myparams) 00357 # 00358 # 00359 except Exception, instance: 00360 #print '**** Error **** ',instance 00361 pass 00362 00363 gc.collect() 00364 return result 00365 # 00366 # 00367 ## 00368 # def paramgui(self, useGlobals=True): 00369 # """ 00370 # Opens a parameter GUI for this task. If useGlobals is true, then any relevant global parameter settings are used. 00371 # """ 00372 # import paramgui 00373 # 00374 # a=inspect.stack() 00375 # stacklevel=0 00376 # for k in range(len(a)): 00377 # if (string.find(a[k][1], 'ipython console') > 0) or (string.find(a[k][1], '<string>') >= 0): 00378 # stacklevel=k 00379 # break 00380 # myf = sys._getframe(stacklevel).f_globals 00381 # 00382 # if useGlobals: 00383 # paramgui.setGlobals(myf) 00384 # else: 00385 # paramgui.setGlobals({}) 00386 # 00387 # paramgui.runTask('sdfit', myf['_ip']) 00388 # paramgui.setGlobals({}) 00389 # 00390 # 00391 # 00392 # 00393 def defaults(self, param=None): 00394 a=inspect.stack() 00395 stacklevel=0 00396 for k in range(len(a)): 00397 if (string.find(a[k][1], 'ipython console') > 0) or (string.find(a[k][1], '<string>') >= 0): 00398 stacklevel=k 00399 break 00400 myf=sys._getframe(stacklevel).f_globals 00401 a = odict() 00402 a['infile'] = '' 00403 a['antenna'] = 0 00404 a['fluxunit'] = '' 00405 a['specunit'] = '' 00406 a['frame'] = '' 00407 a['doppler'] = '' 00408 a['scanlist'] = [] 00409 a['field'] = '' 00410 a['iflist'] = [] 00411 a['pollist'] = [] 00412 a['fitfunc'] = 'gauss' 00413 a['fitmode'] = 'auto' 00414 a['maskline'] = [] 00415 a['invertmask'] = False 00416 a['nfit'] = [] 00417 a['outfile'] = '' 00418 a['overwrite'] = False 00419 a['plotlevel'] = 0 00420 00421 a['async']=False 00422 a['fluxunit'] = { 00423 0:{'value':''}, 00424 1:odict([{'value':'K'}, {'telescopeparm':''}]), 00425 2:odict([{'value':'k'}, {'telescopeparm':''}]), 00426 3:odict([{'value':'Jy'}, {'telescopeparm':''}]), 00427 4:odict([{'value':'jy'}, {'telescopeparm':''}])} 00428 a['specunit'] = { 00429 0:{'value':''}, 00430 1:{'value':'channel'}, 00431 2:{'value':'GHz'}, 00432 3:{'value':'MHz'}, 00433 4:{'value':'kHz'}, 00434 5:{'value':'Hz'}, 00435 6:odict([{'value':'km/s'}, {'restfreq':''}])} 00436 a['fitmode'] = { 00437 0:odict([{'value':'auto'}, {'thresh':5.0}, {'min_nchan':3}, {'avg_limit':4}, {'box_size':0.2}, {'edge':[0]}]), 00438 1:{'value':'list'}, 00439 2:{'value':'interact'}} 00440 00441 ### This function sets the default values but also will return the list of 00442 ### parameters or the default value of a given parameter 00443 if(param == None): 00444 myf['__set_default_parameters'](a) 00445 elif(param == 'paramkeys'): 00446 return a.keys() 00447 else: 00448 if(a.has_key(param)): 00449 #if(type(a[param]) == dict) : 00450 # return a[param][len(a[param])-1]['value'] 00451 #else : 00452 return a[param] 00453 00454 00455 # 00456 # 00457 def check_params(self, param=None, value=None): 00458 a=inspect.stack() 00459 stacklevel=0 00460 for k in range(len(a)): 00461 if (string.find(a[k][1], 'ipython console') > 0) or (string.find(a[k][1], '<string>') >= 0): 00462 stacklevel=k 00463 break 00464 myf=sys._getframe(stacklevel).f_globals 00465 00466 # print 'param:', param, 'value:', value 00467 try : 00468 if str(type(value)) != "<type 'instance'>" : 00469 value0 = value 00470 value = myf['cu'].expandparam(param, value) 00471 matchtype = False 00472 if(type(value) == numpy.ndarray): 00473 if(type(value) == type(value0)): 00474 myf[param] = value.tolist() 00475 else: 00476 #print 'value:', value, 'value0:', value0 00477 #print 'type(value):', type(value), 'type(value0):', type(value0) 00478 myf[param] = value0 00479 if type(value0) != list : 00480 matchtype = True 00481 else : 00482 myf[param] = value 00483 value = myf['cu'].verifyparam({param:value}) 00484 if matchtype: 00485 value = False 00486 except Exception, instance: 00487 #ignore the exception and just return it unchecked 00488 myf[param] = value 00489 return value 00490 00491 # 00492 # 00493 def description(self, key='sdfit', subkey=None): 00494 desc={'sdfit': 'ASAP SD task: fit a spectral line', 00495 'infile': 'name of input SD dataset', 00496 'antenna': 'antenna name or id (only effective for MS input)', 00497 'fluxunit': 'units for line flux (K,Jy) (''=current)', 00498 'telescopeparm': 'param of telescope for flux conversion', 00499 'specunit': 'units for spectral axis (channel,km/s,GHz)', 00500 'restfreq': 'rest frequency (default unit: Hz)', 00501 'frame': 'frequency reference frame, e.g. LSRK (''=current)', 00502 'doppler': 'doppler convention, e.g. RADIO (''=current)', 00503 'scanlist': 'list of scans to use (e.g. [1,2,3,4])', 00504 'field': 'string for selection by source name', 00505 'iflist': 'list of IF ids to select (e.g. [0,1])', 00506 'pollist': 'list of polarization ids to select (e.g. [1])', 00507 'fitfunc': 'function for fitting', 00508 'fitmode': 'mode for fitting', 00509 'maskline': 'list of mask regions to INCLUDE in LINE fitting', 00510 'invertmask': 'invert mask (EXCLUDE masklist instead)', 00511 'nfit': 'list of number of gaussian/lorentzian lines to fit in in maskline region (ignored when fitmode="auto")', 00512 'thresh': 'S/N threshold for linefinder', 00513 'min_nchan': 'minimum number of consecutive channels for linefinder', 00514 'avg_limit': 'channel averaging for broad lines', 00515 'box_size': 'running mean box size', 00516 'edge': 'channels to drop at beginning and end of spectrum', 00517 'outfile': 'name of output file for fit results', 00518 'overwrite': 'overwrite the outfile if already exists', 00519 'plotlevel': 'control for plotting of results', 00520 00521 'async': 'If true the taskname must be started using sdfit(...)' 00522 } 00523 00524 # 00525 # Set subfields defaults if needed 00526 # 00527 00528 if(desc.has_key(key)) : 00529 return desc[key] 00530 00531 def itsdefault(self, paramname) : 00532 a = {} 00533 a['infile'] = '' 00534 a['antenna'] = 0 00535 a['fluxunit'] = '' 00536 a['telescopeparm'] = '' 00537 a['specunit'] = '' 00538 a['restfreq'] = '' 00539 a['frame'] = '' 00540 a['doppler'] = '' 00541 a['scanlist'] = [] 00542 a['field'] = '' 00543 a['iflist'] = [] 00544 a['pollist'] = [] 00545 a['fitfunc'] = 'gauss' 00546 a['fitmode'] = 'auto' 00547 a['maskline'] = [] 00548 a['invertmask'] = False 00549 a['nfit'] = [] 00550 a['thresh'] = 5.0 00551 a['min_nchan'] = 3 00552 a['avg_limit'] = 4 00553 a['box_size'] = 0.2 00554 a['edge'] = [0] 00555 a['outfile'] = '' 00556 a['overwrite'] = False 00557 a['plotlevel'] = 0 00558 00559 if a.has_key(paramname) : 00560 return a[paramname] 00561 sdfit_pg = sdfit_pg_()
1.8.0
